Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008647.1 Hibiscus syriacus cultivar Beakdansim tig00111634_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1422586
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:291149 original size:15 final size:15
Alignment explanation
Indices: 291129--291159 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
291119 ATTCTTGATT
*
291129 TTTTTCTTCCTTTTC
1 TTTTTCTTCCTCTTC
291144 TTTTTCTTCCTCTTC
1 TTTTTCTTCCTCTTC
291159 T
1 T
291160 GCGTCAACCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTCTTCCTCTTC
Found at i:301652 original size:21 final size:22
Alignment explanation
Indices: 301628--301669 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
301618 AGGAATATTC
301628 AATTTTA-TTAGAGGGAAGTTA
1 AATTTTATTTAGAGGGAAGTTA
*
301649 AATTTTATTTGGAGGGAAGTT
1 AATTTTATTTAGAGGGAAGTT
301670 GAAAAATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.40
Consensus pattern (22 bp):
AATTTTATTTAGAGGGAAGTTA
Found at i:301874 original size:21 final size:21
Alignment explanation
Indices: 301850--301895 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
301840 AAAAAATGTC
*
301850 TTTTAATATATATTAAATAAT
1 TTTTAATATATATTAAAGAAT
*
301871 TTTTAATATATTTTAAAGAAT
1 TTTTAATATATATTAAAGAAT
301892 TTTT
1 TTTT
301896 TGGGATTGCA
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:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTTAATATATATTAAAGAAT
Found at i:311844 original size:5 final size:5
Alignment explanation
Indices: 311818--311858 Score: 57
Period size: 5 Copynumber: 8.0 Consensus size: 5
311808 AGATAAAGAC
311818 AAATA ATAATA AAA-A TAAATA AAATA AAATA AAATA AAATA
1 AAATA A-AATA AAATA -AAATA AAATA AAATA AAATA AAATA
311859 GTCATTTGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 1 0.03
5 26 0.79
6 6 0.18
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
AAATA
Found at i:311845 original size:15 final size:15
Alignment explanation
Indices: 311803--311858 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
311793 GACTGTTTGA
* * *
311803 AAATAAGATAAAGAC
1 AAATAAAATAAAAAT
311818 AAATAATAATAAAAAT
1 AAATAA-AATAAAAAT
311834 AAATAAAAT-AAAAT
1 AAATAAAATAAAAAT
311848 AAAATAAAATA
1 -AAATAAAATA
311859 GTCATTTGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 5 0.14
15 18 0.51
16 12 0.34
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (15 bp):
AAATAAAATAAAAAT
Found at i:312727 original size:17 final size:16
Alignment explanation
Indices: 312707--312740 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
312697 AAGATATAAT
312707 ATAATATAATATTTAAA
1 ATAATATAATA-TTAAA
*
312724 ATAATATATTATTAAA
1 ATAATATAATATTAAA
312740 A
1 A
312741 CATGAGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATAATATAATATTAAA
Found at i:315410 original size:36 final size:36
Alignment explanation
Indices: 315363--315439 Score: 154
Period size: 36 Copynumber: 2.1 Consensus size: 36
315353 TGCAATCGTG
315363 TTTATAAGTTTACAAAGAATCAAGCCTATGGTTGGT
1 TTTATAAGTTTACAAAGAATCAAGCCTATGGTTGGT
315399 TTTATAAGTTTACAAAGAATCAAGCCTATGGTTGGT
1 TTTATAAGTTTACAAAGAATCAAGCCTATGGTTGGT
315435 TTTAT
1 TTTAT
315440 CCTTTGACAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.39
Consensus pattern (36 bp):
TTTATAAGTTTACAAAGAATCAAGCCTATGGTTGGT
Found at i:325182 original size:2 final size:2
Alignment explanation
Indices: 325175--325227 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
325165 AAACAAAACC
325175 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
325216 AT AT AT AT AT AT
1 AT AT AT AT AT AT
325228 TCTCAATCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:326912 original size:16 final size:16
Alignment explanation
Indices: 326891--326946 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
326881 AATTATATTT
326891 GAACCGAAAGCAACCC
1 GAACCGAAAGCAACCC
326907 GAACCG-AAGTCAA-CC
1 GAACCGAAAG-CAACCC
* *
326922 GAACTGAAAGCAACTC
1 GAACCGAAAGCAACCC
*
326938 GAACTGAAA
1 GAACCGAAA
326947 ATAACCTGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
15 13 0.37
16 22 0.63
ACGTcount: A:0.45, C:0.29, G:0.20, T:0.07
Consensus pattern (16 bp):
GAACCGAAAGCAACCC
Found at i:327985 original size:25 final size:24
Alignment explanation
Indices: 327957--328031 Score: 61
Period size: 26 Copynumber: 3.2 Consensus size: 24
327947 AGTTGACACG
327957 AAAATCTAAAGGTTTGACCCGAACC
1 AAAATCTAAAGG-TTGACCCGAACC
* *
327982 AAAATC-AACCTGAATTGACCC--A--
1 AAAATCTAA--AG-GTTGACCCGAACC
328004 AAAATCTAAAGGTTGACCCGAACC
1 AAAATCTAAAGGTTGACCCGAACC
328028 AAAA
1 AAAA
328032 CAAACAGACC
Statistics
Matches: 38, Mismatches: 4, Indels: 17
0.64 0.07 0.29
Matches are distributed among these distances:
20 7 0.18
21 1 0.03
22 7 0.18
23 2 0.05
24 7 0.18
25 6 0.16
26 8 0.21
ACGTcount: A:0.45, C:0.24, G:0.13, T:0.17
Consensus pattern (24 bp):
AAAATCTAAAGGTTGACCCGAACC
Found at i:328008 original size:47 final size:46
Alignment explanation
Indices: 327936--328031 Score: 147
Period size: 47 Copynumber: 2.1 Consensus size: 46
327926 AAACAAATTG
* * *
327936 AAATCAACTTGAGTTGACACGAAAATCTAAAGGTTTGACCCGAACCA
1 AAATCAACCTGAATTGACACAAAAATCTAAAGG-TTGACCCGAACCA
*
327983 AAATCAACCTGAATTGACCCAAAAATCTAAAGGTTGACCCGAACCA
1 AAATCAACCTGAATTGACACAAAAATCTAAAGGTTGACCCGAACCA
328029 AAA
1 AAA
328032 CAAACAGACC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
46 16 0.36
47 29 0.64
ACGTcount: A:0.44, C:0.23, G:0.15, T:0.19
Consensus pattern (46 bp):
AAATCAACCTGAATTGACACAAAAATCTAAAGGTTGACCCGAACCA
Found at i:331943 original size:13 final size:13
Alignment explanation
Indices: 331910--331949 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
331900 CCGGTCAACA
331910 GTCAACGGGTCGG
1 GTCAACGGGTCGG
331923 GT---CGGGTCGG
1 GTCAACGGGTCGG
331933 GTCAACGGGTCGG
1 GTCAACGGGTCGG
331946 GTCA
1 GTCA
331950 GGTGAACGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
10 10 0.42
13 14 0.58
ACGTcount: A:0.12, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GTCAACGGGTCGG
Found at i:331943 original size:18 final size:18
Alignment explanation
Indices: 331920--331988 Score: 102
Period size: 18 Copynumber: 3.8 Consensus size: 18
331910 GTCAACGGGT
*
331920 CGGGTCGGGTCGGGTCAA
1 CGGGTCGGGTCGGGTGAA
*
331938 CGGGTCGGGTCAGGTGAA
1 CGGGTCGGGTCGGGTGAA
331956 CGGGTCGGGTCGGGTGAA
1 CGGGTCGGGTCGGGTGAA
* *
331974 CGGGACGGGACGGGT
1 CGGGTCGGGTCGGGT
331989 TATAACCGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.13, C:0.19, G:0.54, T:0.14
Consensus pattern (18 bp):
CGGGTCGGGTCGGGTGAA
Found at i:336720 original size:18 final size:18
Alignment explanation
Indices: 336697--336731 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
336687 GTCAACGGTC
336697 AACGGGTCGGGTCAGGTG
1 AACGGGTCGGGTCAGGTG
336715 AACGGGTCGGGTCAGGT
1 AACGGGTCGGGTCAGGT
336732 TGTAACCGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.49, T:0.17
Consensus pattern (18 bp):
AACGGGTCGGGTCAGGTG
Found at i:337955 original size:34 final size:35
Alignment explanation
Indices: 337917--337998 Score: 121
Period size: 34 Copynumber: 2.4 Consensus size: 35
337907 ATTACATTTT
* *
337917 AAACCCCAAATTCCAAAATACTTCAATTGCAT-TC
1 AAACCCCAAATTCCAAAATACTTCAATTACATGCC
*
337951 AAACCTCAAATTCCAAAATACTTCAATTACATGCC
1 AAACCCCAAATTCCAAAATACTTCAATTACATGCC
*
337986 CAACCCCAAATTC
1 AAACCCCAAATTC
337999 ATAATCCATT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 30 0.71
35 12 0.29
ACGTcount: A:0.41, C:0.32, G:0.02, T:0.24
Consensus pattern (35 bp):
AAACCCCAAATTCCAAAATACTTCAATTACATGCC
Found at i:338990 original size:35 final size:35
Alignment explanation
Indices: 338951--339027 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 35
338941 GGGATTGGGC
*
338951 ATGTAATTGAAGTATTTT-AGAATTTGAGGTTTAGA
1 ATGTAATTGAAGTATTTTGA-AATTTGAGGTTTAAA
* *
338986 ATGTAAATGAAGTATTTTGAAATTTGTGGTTTAAA
1 ATGTAATTGAAGTATTTTGAAATTTGAGGTTTAAA
339021 ATGTAAT
1 ATGTAAT
339028 CGTTGATTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
35 36 0.97
36 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (35 bp):
ATGTAATTGAAGTATTTTGAAATTTGAGGTTTAAA
Found at i:340302 original size:2 final size:2
Alignment explanation
Indices: 340259--340291 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
340249 GAAAAAAGTC
340259 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
340292 TTTCAAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:344065 original size:24 final size:24
Alignment explanation
Indices: 344013--344066 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
344003 AGGTATGATT
344013 TTAAAAAAATTGAAAGTTTAAGCA
1 TTAAAAAAATTGAAAGTTTAAGCA
* *
344037 CTAAAAAAATTGATAA-TTTAAGTA
1 TTAAAAAAATTGA-AAGTTTAAGCA
344061 TTAAAA
1 TTAAAA
344067 GTGTAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.56, C:0.04, G:0.09, T:0.31
Consensus pattern (24 bp):
TTAAAAAAATTGAAAGTTTAAGCA
Found at i:344353 original size:15 final size:15
Alignment explanation
Indices: 344324--344369 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
344314 ACGATTGTTT
344324 TAAATATTTTAAAAA
1 TAAATATTTTAAAAA
344339 TAAA-ATTTTATAAAA
1 TAAATATTTTA-AAAA
* *
344354 TATATATTTCAAAAA
1 TAAATATTTTAAAAA
344369 T
1 T
344370 TCTTGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 6 0.22
15 16 0.59
16 5 0.19
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAATATTTTAAAAA
Found at i:344947 original size:21 final size:20
Alignment explanation
Indices: 344923--344986 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 20
344913 TATTTATTAA
*
344923 TTTATTTTAATTTTTTAATTT
1 TTTATTTT-ATTTTTTAATAT
* *
344944 TTTAATTTA-TTTTAAATAT
1 TTTATTTTATTTTTTAATAT
344963 TTT-TTTTATTTCTTTAATAAT
1 TTTATTTTATTT-TTTAAT-AT
344984 TTT
1 TTT
344987 GTTCGATTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 4 0.11
19 13 0.37
20 6 0.17
21 12 0.34
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTATTTTATTTTTTAATAT
Found at i:344948 original size:26 final size:25
Alignment explanation
Indices: 344909--345062 Score: 107
Period size: 26 Copynumber: 5.8 Consensus size: 25
344899 TAGGTAGTAA
344909 TTTTTATTTATTAATTTATTTTAAT
1 TTTTTATTTATTAATTTATTTTAAT
*
344934 TTTTTAATTTTTTAATTTATTTTAAAT
1 TTTTT-ATTTATTAATTTATTTT-AAT
** *
344961 ATTTTT-TTTATTTCTTTA--ATAAT
1 -TTTTTATTTATTAATTTATTTTAAT
* *
344984 TTTGTTCGATTTATTTATTTATTTCAAAT
1 TTT-TT--ATTTATTAATTTATTT-TAAT
* *
345013 TTATTTATTTATTTATTTATTCATTCAT
1 TT-TTTATTTATTAATTTATT--TTAAT
*
345041 TTATTTATTTATTCATTTATTT
1 TT-TTTATTTATTAATTTATTT
345063 GTTTGTTTGT
Statistics
Matches: 105, Mismatches: 11, Indels: 25
0.74 0.08 0.18
Matches are distributed among these distances:
22 3 0.03
23 5 0.05
24 1 0.01
25 5 0.05
26 37 0.35
27 18 0.17
28 27 0.26
29 8 0.08
30 1 0.01
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (25 bp):
TTTTTATTTATTAATTTATTTTAAT
Found at i:344958 original size:10 final size:8
Alignment explanation
Indices: 344909--344951 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
344899 TAGGTAGTAA
344909 TTTTT-AT
1 TTTTTAAT
*
344916 TTATTAATT
1 TTTTTAA-T
344925 TATTTTAAT
1 T-TTTTAAT
344934 TTTTTAAT
1 TTTTTAAT
344942 TTTTTAAT
1 TTTTTAAT
344950 TT
1 TT
344952 ATTTTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
7 4 0.13
8 18 0.58
9 4 0.13
10 5 0.16
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTAAT
Found at i:344958 original size:18 final size:17
Alignment explanation
Indices: 344908--344954 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
344898 TTAGGTAGTA
*
344908 ATTTTTATTTATTAATTT
1 ATTTTAATTTATTAA-TT
*
344926 ATTTTAATTTTTTAATT
1 ATTTTAATTTATTAATT
344943 -TTTTAATTTATT
1 ATTTTAATTTATT
344955 TTAAATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 11 0.42
17 2 0.08
18 13 0.50
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTAATTTATTAATT
Found at i:345116 original size:4 final size:4
Alignment explanation
Indices: 344992--345102 Score: 109
Period size: 4 Copynumber: 27.2 Consensus size: 4
344982 ATTTTGTTCG
* *
344992 ATTT ATTT ATTT ATTT CAAATTT ATTT ATTT ATTT ATTT ATTC ATTC ATTT
1 ATTT ATTT ATTT ATTT ---ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
* * * *
345043 ATTT ATTT ATTC ATTT ATTT GTTT GTTT GTTT -TTT GATTT ATTT A-TT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT -ATTT ATTT ATTT
*
345090 ATTT ATTT GTTT A
1 ATTT ATTT ATTT A
345103 ATTCGAATTT
Statistics
Matches: 94, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
3 6 0.06
4 81 0.86
5 3 0.03
7 4 0.04
ACGTcount: A:0.23, C:0.04, G:0.05, T:0.69
Consensus pattern (4 bp):
ATTT
Found at i:346128 original size:30 final size:30
Alignment explanation
Indices: 346087--346144 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
346077 CCACTATATG
*
346087 CACTGAGTGTCCTTACACACTACAGTGCTA
1 CACTAAGTGTCCTTACACACTACAGTGCTA
*
346117 CACTAAGTGTCCTTACACACTATAGTGC
1 CACTAAGTGTCCTTACACACTACAGTGC
346145 CAATACACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.28
Consensus pattern (30 bp):
CACTAAGTGTCCTTACACACTACAGTGCTA
Found at i:346138 original size:17 final size:18
Alignment explanation
Indices: 346092--346143 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
346082 ATATGCACTG
346092 AGTGTCCTTACACACTAC
1 AGTGTCCTTACACACTAC
346110 AGTG--C-T--ACACTA-
1 AGTGTCCTTACACACTAC
*
346122 AGTGTCCTTACACACTAT
1 AGTGTCCTTACACACTAC
346140 AGTG
1 AGTG
346144 CCAATACACA
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
12 4 0.14
13 6 0.21
14 1 0.04
15 2 0.07
16 1 0.04
17 6 0.21
18 8 0.29
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (18 bp):
AGTGTCCTTACACACTAC
Found at i:346194 original size:58 final size:58
Alignment explanation
Indices: 346117--346258 Score: 234
Period size: 56 Copynumber: 2.5 Consensus size: 58
346107 TACAGTGCTA
*
346117 CACTAAGTGTCCTTACACACTATAGTGCCAATACACATAAGGTAGTGCCCACCATATG
1 CACTTAGTGTCCTTACACACTATAGTGCCAATACACATAAGGTAGTGCCCACCATATG
* * *
346175 CACTTAGTCTCCTTACACAC--TAGTGCTAATACACATAAGGTCGTGCCCACCATATG
1 CACTTAGTGTCCTTACACACTATAGTGCCAATACACATAAGGTAGTGCCCACCATATG
346231 CACTTAGTGTCCTTACACACTATAGTGC
1 CACTTAGTGTCCTTACACACTATAGTGC
346259 TGCACAAGTG
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
56 53 0.69
58 24 0.31
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (58 bp):
CACTTAGTGTCCTTACACACTATAGTGCCAATACACATAAGGTAGTGCCCACCATATG
Found at i:353634 original size:20 final size:21
Alignment explanation
Indices: 353590--353634 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
353580 GTTTGTTTTC
* *
353590 ATTTTTCAATTTTGAAACATC
1 ATTTTTCAATTTTGAAAAATA
*
353611 ATTTTTCTATTTT-AAAAATA
1 ATTTTTCAATTTTGAAAAATA
353631 ATTT
1 ATTT
353635 CTCATAATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTTTTCAATTTTGAAAAATA
Found at i:356034 original size:22 final size:22
Alignment explanation
Indices: 356006--356047 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
355996 CTGAAATAGC
356006 ATTCATGATAAACATCATATCT
1 ATTCATGATAAACATCATATCT
356028 ATTCATGATAAACATCATAT
1 ATTCATGATAAACATCATAT
356048 ATAATAACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
ATTCATGATAAACATCATATCT
Found at i:361454 original size:21 final size:22
Alignment explanation
Indices: 361421--361461 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
361411 TTAGGACTGG
*
361421 GAGTATCGGTAC-TCCTTTAAT
1 GAGTATCGATACTTCCTTTAAT
*
361442 GAGTATCTATACTTCCTTTA
1 GAGTATCGATACTTCCTTTA
361462 TAATTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (22 bp):
GAGTATCGATACTTCCTTTAAT
Found at i:364289 original size:20 final size:20
Alignment explanation
Indices: 364264--364301 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
364254 GGCCGTTTCT
364264 AGCCGTTGACGATAATTTGG
1 AGCCGTTGACGATAATTTGG
**
364284 AGCCGTTGGGGATAATTT
1 AGCCGTTGACGATAATTT
364302 TTTTGCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.13, G:0.32, T:0.32
Consensus pattern (20 bp):
AGCCGTTGACGATAATTTGG
Found at i:364364 original size:21 final size:22
Alignment explanation
Indices: 364331--364371 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
364321 TCAGGACAGG
364331 GAGTATCGATAC-TCCTTTAAT
1 GAGTATCGATACTTCCTTTAAT
* *
364352 GAGTGTCGGTACTTCCTTTA
1 GAGTATCGATACTTCCTTTA
364372 TAAATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.39
Consensus pattern (22 bp):
GAGTATCGATACTTCCTTTAAT
Found at i:365565 original size:12 final size:12
Alignment explanation
Indices: 365548--365574 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
365538 CATAGTGCTT
365548 CTAATAAATATA
1 CTAATAAATATA
365560 CTAATAAATATA
1 CTAATAAATATA
365572 CTA
1 CTA
365575 CATGTGCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (12 bp):
CTAATAAATATA
Found at i:367886 original size:31 final size:30
Alignment explanation
Indices: 367848--367971 Score: 101
Period size: 31 Copynumber: 4.1 Consensus size: 30
367838 TATAGTTTAT
* * *
367848 TAGTTTATAATAACTACATAGATTACACATA
1 TAGTTTATAATAACTA-ATAGTTTAAATATA
*
367879 TAGTTTATACAT-A-T-ATAGTTTATATATA
1 TAGTTTATA-ATAACTAATAGTTTAAATATA
* *
367907 TAGTTTATAATAACCATATATTTTAAATATA
1 TAGTTTATAATAACTA-ATAGTTTAAATATA
* * *
367938 TAATTTATAATAACTATATAATTTATATTATA
1 TAGTTTATAATAACTA-ATAGTTTA-AATATA
367970 TA
1 TA
367972 TATAGTTTAT
Statistics
Matches: 77, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
27 2 0.03
28 21 0.27
30 1 0.01
31 44 0.57
32 9 0.12
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.45
Consensus pattern (30 bp):
TAGTTTATAATAACTAATAGTTTAAATATA
Found at i:367890 original size:13 final size:13
Alignment explanation
Indices: 367874--367915 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
367864 CATAGATTAC
367874 ACATATAGTTTAT
1 ACATATAGTTTAT
367887 ACATATATAGTTTAT
1 AC--ATATAGTTTAT
*
367902 ATATATAGTTTAT
1 ACATATAGTTTAT
367915 A
1 A
367916 ATAACCATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 14 0.54
15 12 0.46
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (13 bp):
ACATATAGTTTAT
Found at i:367894 original size:15 final size:15
Alignment explanation
Indices: 367871--367915 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
367861 CTACATAGAT
*
367871 TACACATATAGTTTA
1 TACATATATAGTTTA
367886 TACATATATAGTTTA
1 TACATATATAGTTTA
367901 T--ATATATAGTTTA
1 TACATATATAGTTTA
367914 TA
1 TA
367916 ATAACCATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 13 0.46
15 15 0.54
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (15 bp):
TACATATATAGTTTA
Found at i:367944 original size:13 final size:14
Alignment explanation
Indices: 367876--367949 Score: 53
Period size: 15 Copynumber: 5.1 Consensus size: 14
367866 TAGATTACAC
*
367876 ATATAGTTTATACAT
1 ATATAATTTATA-AT
*
367891 ATATAGTTTAT-AT
1 ATATAATTTATAAT
*
367904 ATATAGTTTATAAT
1 ATATAATTTATAAT
*
367918 AACCATATATTT-TAAAT
1 -A-TATA-ATTTAT-AAT
367935 ATATAATTTATAAT
1 ATATAATTTATAAT
367949 A
1 A
367950 ACTATATAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
13 13 0.26
14 10 0.20
15 16 0.32
16 5 0.10
17 6 0.12
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (14 bp):
ATATAATTTATAAT
Found at i:367980 original size:18 final size:17
Alignment explanation
Indices: 367902--367981 Score: 69
Period size: 18 Copynumber: 4.8 Consensus size: 17
367892 TATAGTTTAT
*
367902 ATATATAGTTTATAATA
1 ATATATAATTTATAATA
*
367919 ACCATAT-ATTT-T-A-A
1 A-TATATAATTTATAATA
367933 ATATATAATTTATAATA
1 ATATATAATTTATAATA
*
367950 ACTATATAATTTATATTA
1 A-TATATAATTTATAATA
*
367968 TATATATAGTTTAT
1 -ATATATAATTTAT
367982 GCATAGTGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
13 4 0.08
14 6 0.12
15 2 0.04
16 2 0.04
17 6 0.12
18 30 0.59
19 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.49
Consensus pattern (17 bp):
ATATATAATTTATAATA
Found at i:368032 original size:2 final size:2
Alignment explanation
Indices: 368025--368123 Score: 168
Period size: 2 Copynumber: 51.0 Consensus size: 2
368015 ATTTATAGTT
368025 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
368067 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
368108 TA TA GA T- TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA
368124 CAACATATAT
Statistics
Matches: 92, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
1 3 0.03
2 89 0.97
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:368157 original size:34 final size:34
Alignment explanation
Indices: 368027--368189 Score: 126
Period size: 34 Copynumber: 4.8 Consensus size: 34
368017 TTATAGTTTA
* *
368027 TATATATATATAT-ATATATA-TATA-TATATA-
1 TATATATATATATAATATAGATTATATTATAAAC
* *
368057 TATATATATATATATATATATATATATATATATATA-
1 TATATATATATATA-ATATAGAT-TATAT-TATAAAC
368093 TATATATATATATAATATAGATTATATTATACAAC
1 TATATATATATATAATATAGATTATATTATA-AAC
* *
368128 -ATATATACTATATTA-ATAGTTTA-ATTTATAAAC
1 TATATATA-TATATAATATAGATTATA-TTATAAAC
* *
368161 TATATATAGTTTATACATATAGTTTATAT
1 TATATATA-TATATA-ATATAGATTATAT
368190 ACATAGTTTA
Statistics
Matches: 112, Mismatches: 7, Indels: 22
0.79 0.05 0.16
Matches are distributed among these distances:
30 13 0.12
32 7 0.06
33 8 0.07
34 40 0.36
35 14 0.12
36 29 0.26
37 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (34 bp):
TATATATATATATAATATAGATTATATTATAAAC
Found at i:368182 original size:13 final size:13
Alignment explanation
Indices: 368161--368275 Score: 99
Period size: 13 Copynumber: 8.5 Consensus size: 13
368151 ATTTATAAAC
368161 TATATATAGTTTA
1 TATATATAGTTTA
*
368174 TACATATAGTTTA
1 TATATATAGTTTA
*
368187 TATACATAGTTTA
1 TATATATAGTTTA
*
368200 TATATACT--TCATA
1 TATATA-TAGT-TTA
* *
368213 TAAACATAGTTTA
1 TATATATAGTTTA
368226 TATATATAGCTTATAA
1 TATATATAG-TT-T-A
368242 TAATTATATAGTTTA
1 T-A-TATATAGTTTA
*
368257 TATATATAATTTA
1 TATATATAGTTTA
368270 TATATA
1 TATATA
368276 AACTTATATT
Statistics
Matches: 82, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
12 2 0.02
13 59 0.72
14 5 0.06
15 3 0.04
16 3 0.04
17 3 0.04
18 7 0.09
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (13 bp):
TATATATAGTTTA
Found at i:368313 original size:19 final size:19
Alignment explanation
Indices: 368259--368313 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
368249 ATAGTTTATA
368259 TATATAATTTATATATAAACT
1 TATAT-ATTTA-ATATAAACT
368280 TATATTATATTAATATAAA-T
1 TATA-TAT-TTAATATAAACT
368300 TATATACTTTAATA
1 TATATA-TTTAATA
368314 CTTTATATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
19 8 0.26
20 6 0.19
21 13 0.42
22 4 0.13
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (19 bp):
TATATATTTAATATAAACT
Found at i:368484 original size:21 final size:21
Alignment explanation
Indices: 368455--368507 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
368445 ACATAAATCT
* *
368455 TATATATTATATA-TTTATATA
1 TATAAATTACATAGTTTAT-TA
368476 TATAAATTACATAGTTTATTA
1 TATAAATTACATAGTTTATTA
*
368497 -ATAAACTACAT
1 TATAAATTACAT
368508 GTAAACTACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.36
21 13 0.46
22 5 0.18
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (21 bp):
TATAAATTACATAGTTTATTA
Found at i:368514 original size:11 final size:11
Alignment explanation
Indices: 368497--368532 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
368487 TAGTTTATTA
368497 ATAAACTACAT
1 ATAAACTACAT
*
368508 GTAAACTACAT
1 ATAAACTACAT
*
368519 ATAAACTATAT
1 ATAAACTACAT
368530 ATA
1 ATA
368533 TTATATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.31
Consensus pattern (11 bp):
ATAAACTACAT
Found at i:368595 original size:20 final size:19
Alignment explanation
Indices: 368570--368616 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
368560 ATAATATATA
368570 TATATATAGTT-TATATAAAC
1 TATATATA-TTAT-TATAAAC
368590 TATATA-ATTATTATAAAC
1 TATATATATTATTATAAAC
368608 TATATATAT
1 TATATATAT
368617 GTAATCTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 15 0.60
19 4 0.16
20 6 0.24
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (19 bp):
TATATATATTATTATAAAC
Found at i:368595 original size:74 final size:75
Alignment explanation
Indices: 368517--368669 Score: 170
Period size: 74 Copynumber: 2.1 Consensus size: 75
368507 TGTAAACTAC
* * * ** *
368517 ATATAAACTA-TATATATTATATATTTGTCTTTATATACTTTATATAAT-ATA-TATATATATAG
1 ATATAAACTATTATAAACTATATATATGT-AATATATACTTTATA-AATAATAGTATATATATAA
368579 TTTATATAAACT
64 TTTATATAAACT
* * * *
368591 ATAT-AATTATTATAAACTATATATATGTAATCTATAGTTTATAAATAATAGTTTATATATAATT
1 ATATAAACTATTATAAACTATATATATGTAATATATACTTTATAAATAATAGTATATATATAATT
368655 TATATAAACT
66 TATATAAACT
368665 ATATA
1 ATATA
368670 TATAACCTAT
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
72 3 0.05
73 18 0.28
74 44 0.68
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (75 bp):
ATATAAACTATTATAAACTATATATATGTAATATATACTTTATAAATAATAGTATATATATAATT
TATATAAACT
Found at i:368643 original size:14 final size:14
Alignment explanation
Indices: 368624--368653 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
368614 TATGTAATCT
368624 ATAGTTTATAAATA
1 ATAGTTTATAAATA
*
368638 ATAGTTTATATATA
1 ATAGTTTATAAATA
368652 AT
1 AT
368654 TTATATAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (14 bp):
ATAGTTTATAAATA
Found at i:368658 original size:54 final size:55
Alignment explanation
Indices: 368590--368704 Score: 162
Period size: 54 Copynumber: 2.1 Consensus size: 55
368580 TTATATAAAC
* * * *
368590 TATATAATTAT-TATAAACTATATATATGTAATCTATAGTTTATAAATAATAGTTTA
1 TATATAATTATATATAAACTATATATA--TAACCTATAGTCTATAAACAATAGTTAA
368646 TATATAATT-TATATAAACTATATATATAACCTATAGTCTATAAACAATAGTTAA
1 TATATAATTATATATAAACTATATATATAACCTATAGTCTATAAACAATAGTTAA
368700 TATAT
1 TATAT
368705 GTAACCTATA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
54 29 0.54
55 1 0.02
56 24 0.44
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.43
Consensus pattern (55 bp):
TATATAATTATATATAAACTATATATATAACCTATAGTCTATAAACAATAGTTAA
Found at i:368781 original size:20 final size:20
Alignment explanation
Indices: 368758--368827 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
368748 TACAATACAT
*
368758 ATATGTATAAACTATGTATA
1 ATATATATAAACTATGTATA
*
368778 ATATATATAAACTATATAT-
1 ATATATATAAACTATGTATA
*
368797 ATATATATAACCTATAGTATA
1 ATATATATAAACTAT-GTATA
*
368818 TGTATATATA
1 -ATATATATA
368828 CAATCTATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 14 0.33
20 20 0.48
22 8 0.19
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (20 bp):
ATATATATAAACTATGTATA
Found at i:368835 original size:24 final size:23
Alignment explanation
Indices: 368790--368844 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
368780 ATATATAAAC
* *
368790 TATATATATATATATAACCTATAG
1 TATATGTATATATACAACCTAT-G
* *
368814 TATATGTATATATACAATCTATT
1 TATATGTATATATACAACCTATG
368837 TATATGTA
1 TATATGTA
368845 AACTATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 8 0.30
24 19 0.70
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (23 bp):
TATATGTATATATACAACCTATG
Found at i:368990 original size:21 final size:21
Alignment explanation
Indices: 368961--369006 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
368951 TAGTGTATTA
* *
368961 TATAGTTTATAACCTATAGTT
1 TATAATTTATAAACTATAGTT
368982 TATAATTTATAAACTATAGTT
1 TATAATTTATAAACTATAGTT
369003 TATA
1 TATA
369007 TTAATGTTAA
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:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (21 bp):
TATAATTTATAAACTATAGTT
Found at i:369064 original size:36 final size:37
Alignment explanation
Indices: 369024--369115 Score: 125
Period size: 36 Copynumber: 2.5 Consensus size: 37
369014 TAATTATCTT
*
369024 AACTATAATTTATATTAATA-CAGTATATAGTTTATA
1 AACTATAATTTATATTAATAGCAGTAGATAGTTTATA
* *
369060 AACTATAATTTGTATTAA-AGTAGTAGATAGTTTATA
1 AACTATAATTTATATTAATAGCAGTAGATAGTTTATA
* *
369096 AACTATAGTTTACATTAATA
1 AACTATAATTTATATTAATA
369116 TTAACATATT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
35 1 0.02
36 46 0.96
37 1 0.02
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.42
Consensus pattern (37 bp):
AACTATAATTTATATTAATAGCAGTAGATAGTTTATA
Found at i:369161 original size:18 final size:15
Alignment explanation
Indices: 369121--369164 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 15
369111 TAATATTAAC
369121 ATATTAATTATAGTTT
1 ATATTAA-TATAGTTT
369137 ATATTAATATAGTATAT
1 ATATTAATATAGT-T-T
369154 AGTATTAATAT
1 A-TATTAATAT
369165 TAATTATAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.24
16 8 0.32
17 2 0.08
18 9 0.36
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (15 bp):
ATATTAATATAGTTT
Found at i:369164 original size:24 final size:24
Alignment explanation
Indices: 369109--369179 Score: 83
Period size: 24 Copynumber: 2.9 Consensus size: 24
369099 TATAGTTTAC
* *
369109 ATTAATATTAACATATTAATTATAGT
1 ATTAATATTAATATAGT-A-TATAGT
369135 -TT-ATATTAATATAGTATATAGT
1 ATTAATATTAATATAGTATATAGT
369157 ATTAATATTAATTATAGTATATA
1 ATTAATATTAA-TATAGTATATA
369180 AACCATATAC
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
22 6 0.15
23 3 0.08
24 18 0.45
25 13 0.32
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (24 bp):
ATTAATATTAATATAGTATATAGT
Found at i:369172 original size:18 final size:18
Alignment explanation
Indices: 369138--369176 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
369128 TTATAGTTTA
*
369138 TATTAATATAGTATATAG
1 TATTAATATAATATATAG
369156 TATTAATATTAAT-TATAG
1 TATTAATA-TAATATATAG
369174 TAT
1 TAT
369177 ATAAACCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (18 bp):
TATTAATATAATATATAG
Found at i:369251 original size:14 final size:14
Alignment explanation
Indices: 369234--369290 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
369224 AAACCATACT
369234 ATATAATTTATAAA
1 ATATAATTTATAAA
* *
369248 ATATAGTTTATATTA
1 ATATAATTTATA-AA
369263 ATATTAATTTTATAAA
1 ATA-TAA-TTTATAAA
* *
369279 CTATATTTTATA
1 ATATAATTTATA
369291 TTAATAGTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
14 17 0.50
15 6 0.18
16 5 0.15
17 6 0.18
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (14 bp):
ATATAATTTATAAA
Found at i:369278 original size:31 final size:31
Alignment explanation
Indices: 369240--369302 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
369230 TACTATATAA
*
369240 TTTATAAAATATAGTTTATATTAATATTAAT
1 TTTATAAAATATAGTTTATATTAATAGTAAT
* *
369271 TTTATAAACTATATTTTATATTAATAGTAAT
1 TTTATAAAATATAGTTTATATTAATAGTAAT
369302 T
1 T
369303 ACAAATTCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (31 bp):
TTTATAAAATATAGTTTATATTAATAGTAAT
Found at i:369394 original size:29 final size:29
Alignment explanation
Indices: 369351--369417 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
369341 TTAACATTAA
* *
369351 TTATATTAATGTTAATTAT-AATCTATAAT
1 TTATATTAATATTAATTATAAAT-GATAAT
*
369380 TTATATTAATATTAATTATAAATGATAGT
1 TTATATTAATATTAATTATAAATGATAAT
369409 TTATATTAA
1 TTATATTAA
369418 CTCTATTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 31 0.91
30 3 0.09
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (29 bp):
TTATATTAATATTAATTATAAATGATAAT
Found at i:369954 original size:99 final size:102
Alignment explanation
Indices: 369755--369947 Score: 225
Period size: 99 Copynumber: 1.9 Consensus size: 102
369745 CTTTGAAAAA
* *
369755 AAAAACCTTCATTTGATCTTCAAAAACACCAAATCCTAAACATTTTTCTATTTTTTTCAATCAAA
1 AAAAACCTTCATTTGATCTTCAAAAACACCAAAACCCAAACA-TTTTCTATTTTTTT-AATCAAA
*
369820 CACACAAAATTTCTTAACTTGTTCATCCGAGTTCATACC
64 CACACAAAATTTCTTAACCTGTTCATCCGAGTTCATACC
* * * *
369859 AAAAACC-TCCTTTGATCTTCATAAACACCAAAACCCATACGA-TTTC-GTTTTTTT-ATCAAAC
1 AAAAACCTTCATTTGATCTTCAAAAACACCAAAACCCAAAC-ATTTTCTATTTTTTTAATCAAAC
* **
369920 ACCCAAAATTT-TCTCCCCTGTTCATCCG
65 ACACAAAATTTCT-TAACCTGTTCATCCG
369948 TATTCATCCT
Statistics
Matches: 77, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
98 1 0.01
99 29 0.38
101 7 0.09
102 4 0.05
103 28 0.36
104 8 0.10
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (102 bp):
AAAAACCTTCATTTGATCTTCAAAAACACCAAAACCCAAACATTTTCTATTTTTTTAATCAAACA
CACAAAATTTCTTAACCTGTTCATCCGAGTTCATACC
Found at i:370189 original size:6 final size:6
Alignment explanation
Indices: 370178--370235 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
370168 CATCTTCTAT
* * * * *
370178 AACCCG AACCCG AACCCA AACCTG AACCCG AACCCA AACCTG AACTCG
1 AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG
*
370226 AACCCA AACC
1 AACCCG AACC
370236 TGAATCCAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.40, C:0.45, G:0.10, T:0.05
Consensus pattern (6 bp):
AACCCG
Found at i:370199 original size:12 final size:12
Alignment explanation
Indices: 370178--370245 Score: 55
Period size: 12 Copynumber: 5.7 Consensus size: 12
370168 CATCTTCTAT
*
370178 AACCCGAACCCG
1 AACCCAAACCCG
*
370190 AACCCAAACCTG
1 AACCCAAACCCG
* *
370202 AACCCGAACCCA
1 AACCCAAACCCG
** *
370214 AACCTGAACTCG
1 AACCCAAACCCG
*
370226 AACCCAAACCTG
1 AACCCAAACCCG
*
370238 AATCCAAA
1 AACCCAAA
370246 GCAAACCCAA
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.41, C:0.41, G:0.10, T:0.07
Consensus pattern (12 bp):
AACCCAAACCCG
Found at i:370204 original size:18 final size:18
Alignment explanation
Indices: 370178--370239 Score: 106
Period size: 18 Copynumber: 3.4 Consensus size: 18
370168 CATCTTCTAT
*
370178 AACCCGAACCCGAACCCA
1 AACCTGAACCCGAACCCA
370196 AACCTGAACCCGAACCCA
1 AACCTGAACCCGAACCCA
*
370214 AACCTGAACTCGAACCCA
1 AACCTGAACCCGAACCCA
370232 AACCTGAA
1 AACCTGAA
370240 TCCAAAGCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.40, C:0.42, G:0.11, T:0.06
Consensus pattern (18 bp):
AACCTGAACCCGAACCCA
Found at i:374939 original size:15 final size:15
Alignment explanation
Indices: 374914--374955 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
374904 ACCGTCACTC
374914 AAATACCCTAA-ATCTA
1 AAAT-CCCTAATATC-A
*
374930 AAATCCCTAATATCC
1 AAATCCCTAATATCA
374945 AAATCCCTAAT
1 AAATCCCTAAT
374956 TCCTAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATCCCTAATATCA
Found at i:376542 original size:14 final size:14
Alignment explanation
Indices: 376523--376550 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
376513 CCATTCAACA
376523 TTTCAACTTTCATT
1 TTTCAACTTTCATT
376537 TTTCAACTTTCATT
1 TTTCAACTTTCATT
376551 ACATTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTCAACTTTCATT
Found at i:385904 original size:230 final size:232
Alignment explanation
Indices: 385501--385962 Score: 910
Period size: 230 Copynumber: 2.0 Consensus size: 232
385491 ACGTCGTTTA
385501 AGTCGTCGGTTGGAGCAAGGTGGGGTCACAAAGGCTTGGTGGCAGGCGTTGGGGTCAGTTTTAAG
1 AGTCGTCGGTTGGAGCAAGGTGGGGTCACAAAGGCTTGGTGGCAGGCGTTGGGGTCAGTTTTAAG
385566 CCTCTCAACTTGGTGAAGAGAAAGAACAAGAGAGGGAGATAACGGAGAGTTTTTGTAATATCCCA
66 CCTCTCAACTTGGTGAAGAGAAAGAACAAGAGAGGGAGATAACGGAGAGTTTTTGTAATATCCCA
385631 AAATAGGGTTGATGACTAAAATGTAAATTTTAAAAACTTTGTGATTAATTTTGAAACAAGTTAAA
131 AAATAGGGTTGATGACTAAAATGTAAATTTTAAAAACTTTGTGATTAATTTTGAAACAAGTTAAA
385696 ATTTCAGGGACTTAATTAGAGAATTTTG-T-TTGGAT
196 ATTTCAGGGACTTAATTAGAGAATTTTGATGTTGGAT
385731 AGTCGTCGGTTGGAGCAAGGTGGGGTCACAAAGGCTTGGTGGCAGGCGTTGGGGTCAGTTTTAAG
1 AGTCGTCGGTTGGAGCAAGGTGGGGTCACAAAGGCTTGGTGGCAGGCGTTGGGGTCAGTTTTAAG
385796 CCTCTCAACTTGGTGAAGAGAAAGAACAAGAGAGGGAGATAACGGAGAGTTTTTGTAATATCCCA
66 CCTCTCAACTTGGTGAAGAGAAAGAACAAGAGAGGGAGATAACGGAGAGTTTTTGTAATATCCCA
385861 AAATAGGGTTGATGACTAAAATGTAAATTTTAAAAACTTTGTGATTAATTTTGAAACAAGTTAAA
131 AAATAGGGTTGATGACTAAAATGTAAATTTTAAAAACTTTGTGATTAATTTTGAAACAAGTTAAA
385926 ATTTCAGGGACTTAATTAGAGAATTTTGATGTTGGAT
196 ATTTCAGGGACTTAATTAGAGAATTTTGATGTTGGAT
385963 TGATTAGCAA
Statistics
Matches: 230, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
230 223 0.97
231 1 0.00
232 6 0.03
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.29
Consensus pattern (232 bp):
AGTCGTCGGTTGGAGCAAGGTGGGGTCACAAAGGCTTGGTGGCAGGCGTTGGGGTCAGTTTTAAG
CCTCTCAACTTGGTGAAGAGAAAGAACAAGAGAGGGAGATAACGGAGAGTTTTTGTAATATCCCA
AAATAGGGTTGATGACTAAAATGTAAATTTTAAAAACTTTGTGATTAATTTTGAAACAAGTTAAA
ATTTCAGGGACTTAATTAGAGAATTTTGATGTTGGAT
Found at i:388703 original size:18 final size:18
Alignment explanation
Indices: 388680--388732 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
388670 CCACTATGAA
388680 ATGTCCCGAAGGACCACT
1 ATGTCCCGAAGGACCACT
*
388698 ATGTCCCGAATGACCACT
1 ATGTCCCGAAGGACCACT
*
388716 ATGTCCCGCAGGACCAC
1 ATGTCCCGAAGGACCAC
388733 GTAGAACCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.26, C:0.36, G:0.21, T:0.17
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACT
Found at i:389121 original size:19 final size:18
Alignment explanation
Indices: 389087--389140 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
389077 ACTCATTTAC
* *
389087 ATCATATATCATATACCA
1 ATCATATAACACATACCA
389105 ATACATATAACACATA-CA
1 AT-CATATAACACATACCA
389123 ATCATATCAACACATACC
1 ATCATAT-AACACATACC
389141 TATATTCATG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 5 0.16
18 14 0.45
19 12 0.39
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (18 bp):
ATCATATAACACATACCA
Found at i:392825 original size:41 final size:41
Alignment explanation
Indices: 392780--392877 Score: 151
Period size: 41 Copynumber: 2.4 Consensus size: 41
392770 CATATGAATT
* *
392780 TGTCCTGAATGACCACTATGAAATGTCTCGAAGGATCACAA
1 TGTCCTGAATGACCACTATGAAATGTCCCGAAGGACCACAA
*
392821 TGTCCTGAATGACCACTATGAAATGTCCCGAAGGACCACTA
1 TGTCCTGAATGACCACTATGAAATGTCCCGAAGGACCACAA
* *
392862 TGTCCCGAAGGACCAC
1 TGTCCTGAATGACCAC
392878 GTAGAACCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (41 bp):
TGTCCTGAATGACCACTATGAAATGTCCCGAAGGACCACAA
Found at i:392857 original size:23 final size:23
Alignment explanation
Indices: 392780--392863 Score: 79
Period size: 23 Copynumber: 3.9 Consensus size: 23
392770 CATATGAATT
* *
392780 TGTCCTGAATGACCACTATGAAA
1 TGTCCCGAAGGACCACTATGAAA
* *
392803 TGTCTCGAAGGATCAC-----AA
1 TGTCCCGAAGGACCACTATGAAA
* *
392821 TGTCCTGAATGACCACTATGAAA
1 TGTCCCGAAGGACCACTATGAAA
392844 TGTCCCGAAGGACCACTATG
1 TGTCCCGAAGGACCACTATG
392864 TCCCGAAGGA
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
18 14 0.30
23 32 0.70
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (23 bp):
TGTCCCGAAGGACCACTATGAAA
Found at i:392866 original size:18 final size:18
Alignment explanation
Indices: 392843--392877 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
392833 CCACTATGAA
392843 ATGTCCCGAAGGACCACT
1 ATGTCCCGAAGGACCACT
392861 ATGTCCCGAAGGACCAC
1 ATGTCCCGAAGGACCAC
392878 GTAGAACCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACT
Found at i:393257 original size:19 final size:17
Alignment explanation
Indices: 393231--393281 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
393221 ACTCATTTAT
* *
393231 ATCATATATCATATACCA
1 ATCATATAACACATA-CA
393249 ATACATATAACACATACA
1 AT-CATATAACACATACA
393267 ATCATATAAACACAT
1 ATCATAT-AACACAT
393282 GCCTATATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 5 0.17
18 13 0.45
19 11 0.38
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (17 bp):
ATCATATAACACATACA
Found at i:394119 original size:17 final size:16
Alignment explanation
Indices: 394097--394130 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
394087 TAAAAACAGT
394097 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
394114 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
394130 A
1 A
394131 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:394650 original size:24 final size:24
Alignment explanation
Indices: 394606--394655 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
394596 ATAAAGAACC
*
394606 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
394630 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
394654 AA
1 AA
394656 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:404355 original size:17 final size:16
Alignment explanation
Indices: 404333--404366 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
404323 TAAAAACAGT
404333 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
404350 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
404366 A
1 A
404367 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:404885 original size:24 final size:24
Alignment explanation
Indices: 404841--404890 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
404831 ATAAAGAACC
*
404841 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
404865 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
404889 AA
1 AA
404891 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:410719 original size:47 final size:47
Alignment explanation
Indices: 410661--410750 Score: 117
Period size: 47 Copynumber: 1.9 Consensus size: 47
410651 AAAAATCAAT
* *
410661 CGATCTGATATTGACCCGAAACGAAAACCAACCGATCCGATATGAAC
1 CGATCTAATATTAACCCGAAACGAAAACCAACCGATCCGATATGAAC
** * * *
410708 CGATCTAATATTAACCCGACCCGAAATCTAACTGATCCGATAT
1 CGATCTAATATTAACCCGAAACGAAAACCAACCGATCCGATAT
410751 TAACTTGATC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
47 36 1.00
ACGTcount: A:0.37, C:0.28, G:0.14, T:0.21
Consensus pattern (47 bp):
CGATCTAATATTAACCCGAAACGAAAACCAACCGATCCGATATGAAC
Found at i:411809 original size:96 final size:96
Alignment explanation
Indices: 411662--411855 Score: 388
Period size: 96 Copynumber: 2.0 Consensus size: 96
411652 CCCTATTTGG
411662 TTAAGTATAAAAATGATTTTCGATTATAGGTACTGCTTATTAAGTCTATAGACTATTAAAAGTAA
1 TTAAGTATAAAAATGATTTTCGATTATAGGTACTGCTTATTAAGTCTATAGACTATTAAAAGTAA
411727 TAAAATGGTTCTCCGATTTATAGAAGGTTGC
66 TAAAATGGTTCTCCGATTTATAGAAGGTTGC
411758 TTAAGTATAAAAATGATTTTCGATTATAGGTACTGCTTATTAAGTCTATAGACTATTAAAAGTAA
1 TTAAGTATAAAAATGATTTTCGATTATAGGTACTGCTTATTAAGTCTATAGACTATTAAAAGTAA
411823 TAAAATGGTTCTCCGATTTATAGAAGGTTGC
66 TAAAATGGTTCTCCGATTTATAGAAGGTTGC
411854 TT
1 TT
411856 TGTTAAGTCC
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.38
Consensus pattern (96 bp):
TTAAGTATAAAAATGATTTTCGATTATAGGTACTGCTTATTAAGTCTATAGACTATTAAAAGTAA
TAAAATGGTTCTCCGATTTATAGAAGGTTGC
Found at i:412589 original size:23 final size:23
Alignment explanation
Indices: 412554--412612 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
412544 ATCAAGTATA
*
412554 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
412577 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
412600 ATAATAAAATAGG
1 ATAATATAATAGG
412613 CATTTAACCG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.34
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:413000 original size:199 final size:199
Alignment explanation
Indices: 412660--413182 Score: 671
Period size: 199 Copynumber: 2.6 Consensus size: 199
412650 TAGGTAGCGC
* * * * * * *
412660 TTATATTGACTTATTTTCTCATAAAACCGCTATATTTATACCGGTAATATTGCAAATTTACCTAT
1 TTATATTGACATATTTTCTAATTAAACCGATATATTTATATCGGTTATATTGTAAATTTACCTAT
* *
412725 TACATTGTAATTATCGGTTTCGATATTTTTGGGATCGATACAATTT-TAAATGTATCGACACTTT
66 TACATTATAATTATCGGTTTCGAT-TTTTTGGGATCGATA-ATTTTATAAATGTATCGACACTTT
* * * **
412789 ATGCGTGCACCTC-GTTTGGCATTCATTCTGGACAAAATGTATCAACACAAAT-TTAAGAAGTGT
129 ATGCGTGCACCTCAGTTGGGCATTCATTCTAGACAAAAAGTATCAACACAAATCCCAA-AAGTGT
412852 AGATACA
193 AGATACA
*
412859 TTATATTGACCGT-TTTTCTAATTAAACCGATATATTTATATCGGTTATATTGTAAATTTACCTA
1 TTATATTGA-CATATTTTCTAATTAAACCGATATATTTATATCGGTTATATTGTAAATTTACCTA
*
412923 TTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATATTTTTATAAATGTATCGACACTTT
65 TTACATTATAATTATCGGTTTCGAT-TTTTTGGGATCGATAATTTTATAAATGTATCGACACTTT
* * *
412988 ATGCGTGCACCTCAGTTGGGCATTCATTCTAGACAAAAAGTATCGACACAAATCCCAAATGTGTC
129 ATGCGTGCACCTCAGTTGGGCATTCATTCTAGACAAAAAGTATCAACACAAATCCCAAAAGTGTA
413053 GATACA
194 GATACA
* * * * * * * *
413059 TTATGTTGACATGTTTTCGAATT-GACAGGTATATTTATATCGGTTACATTGTTAATTTACCTAT
1 TTATATTGACATATTTTCTAATTAAACCGATATATTTATATCGGTTATATTGTAAATTTACCTAT
* * * *
413123 TACATTATAATTATTGGTTTCGATTTTTAGGG-TTGATACTTTTATAAAATGTATCGACAC
66 TACATTATAATTATCGGTTTCGATTTTTTGGGATCGATAATTTTAT-AAATGTATCGACAC
413183 ACATGTTTAC
Statistics
Matches: 287, Mismatches: 31, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
197 11 0.04
198 24 0.08
199 185 0.64
200 65 0.23
201 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (199 bp):
TTATATTGACATATTTTCTAATTAAACCGATATATTTATATCGGTTATATTGTAAATTTACCTAT
TACATTATAATTATCGGTTTCGATTTTTTGGGATCGATAATTTTATAAATGTATCGACACTTTAT
GCGTGCACCTCAGTTGGGCATTCATTCTAGACAAAAAGTATCAACACAAATCCCAAAAGTGTAGA
TACA
Found at i:417517 original size:21 final size:21
Alignment explanation
Indices: 417475--417517 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
417465 TTTCTGGGTT
* * *
417475 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
417496 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
417517 A
1 A
417518 CGAATATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:417566 original size:20 final size:20
Alignment explanation
Indices: 417538--417578 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
417528 TTCCAGAATG
*
417538 CTAGAGGGGAATCGATACCC
1 CTAGAGGGGAACCGATACCC
*
417558 CTAGGGGGGAACCGATACCC
1 CTAGAGGGGAACCGATACCC
417578 C
1 C
417579 CTCATCGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.32, T:0.12
Consensus pattern (20 bp):
CTAGAGGGGAACCGATACCC
Found at i:417577 original size:66 final size:68
Alignment explanation
Indices: 417497--417647 Score: 225
Period size: 67 Copynumber: 2.2 Consensus size: 68
417487 ACCCATTCAA
* *
417497 GGGGAACCGATACCCCCTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGATACCCCTA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
417561 -GG
66 GGG
* * * *
417563 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
417628 GGG
66 GGG
*
417631 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
417648 ATGAGAAAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
66 27 0.36
67 31 0.41
68 18 0.24
ACGTcount: A:0.27, C:0.28, G:0.26, T:0.19
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GGG
Found at i:417983 original size:29 final size:29
Alignment explanation
Indices: 417949--418019 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
417939 CATATTATGA
* *
417949 TACATGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
417978 TACATGACATGAATTCATATGATATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
418007 TGCATGACATGAA
1 TACATGACATGAA
418020 ATATGCAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (29 bp):
TACATGACATGAATTCATATGAAATGTAT
Found at i:418077 original size:30 final size:30
Alignment explanation
Indices: 418035--418111 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
418025 CAGAAAAGTT
* *
418035 ATATGAGCTATGTGATAAAGGTATGTAAATG
1 ATATGA-CTATGTGATAAAGGTATGGAAATA
418066 ATATGACTATGTGATAAAGGTATGGAAATA
1 ATATGACTATGTGATAAAGGTATGGAAATA
*
418096 ATATGACTACGTGATA
1 ATATGACTATGTGATA
418112 TGAACTACGG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 37 0.86
31 6 0.14
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.31
Consensus pattern (30 bp):
ATATGACTATGTGATAAAGGTATGGAAATA
Found at i:418348 original size:22 final size:22
Alignment explanation
Indices: 418322--418363 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
418312 ATCATTATAT
418322 GGCACCACGGTGCAATTCTATG
1 GGCACCACGGTGCAATTCTATG
**
418344 GGCACTTCGGTGCAATTCTA
1 GGCACCACGGTGCAATTCTA
418364 CGGGGCACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (22 bp):
GGCACCACGGTGCAATTCTATG
Found at i:418373 original size:23 final size:22
Alignment explanation
Indices: 418329--418380 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 22
418319 TATGGCACCA
*
418329 CGGTGCAATTCTATGGGCACTT
1 CGGTGCAATTCTAGGGGCACTT
418351 CGGTGCAATTCTACGGGGCACTT
1 CGGTGCAATTCTA-GGGGCACTT
418374 CGGTGCA
1 CGGTGCA
418381 TTTATACGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.17, C:0.25, G:0.31, T:0.27
Consensus pattern (22 bp):
CGGTGCAATTCTAGGGGCACTT
Found at i:418388 original size:23 final size:23
Alignment explanation
Indices: 418329--418388 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
418319 TATGGCACCA
* *
418329 CGGTGCAATTCTA-TGGGCACTT
1 CGGTGCAATTATACGGGGCACTT
*
418351 CGGTGCAATTCTACGGGGCACTT
1 CGGTGCAATTATACGGGGCACTT
*
418374 CGGTGCATTTATACG
1 CGGTGCAATTATACG
418389 AGCTGTGGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 13 0.38
23 21 0.62
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.30
Consensus pattern (23 bp):
CGGTGCAATTATACGGGGCACTT
Found at i:424462 original size:21 final size:21
Alignment explanation
Indices: 424420--424462 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
424410 TTTCTGGGTT
* * *
424420 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
424441 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
424462 A
1 A
424463 CGAATATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:424523 original size:20 final size:20
Alignment explanation
Indices: 424483--424522 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
424473 TTCCAGAATG
*
424483 CTAGAGGGGAATCGATACCC
1 CTAGAGGGGAACCGATACCC
424503 CTAG-GGGGAACCGATACCC
1 CTAGAGGGGAACCGATACCC
424522 C
1 C
424523 CCTCATCGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.28, C:0.30, G:0.30, T:0.12
Consensus pattern (20 bp):
CTAGAGGGGAACCGATACCC
Found at i:424544 original size:67 final size:67
Alignment explanation
Indices: 424442--424591 Score: 205
Period size: 67 Copynumber: 2.3 Consensus size: 67
424432 ACCCATTCAA
* *
424442 GGGGAACCGATA-CCCCCTCAACGAATATGATTTCCAGAATGCTAGAGGGGAATCGATACCCCTA
1 GGGGAACCGATACCCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
424506 -G
66 GG
* * * * *
424507 GGGGAACCGATACCCCCCTCATCGTATATGAAATTCCATATTGCTTGAGGGGAATCGATACCCCC
1 GGGGAACCGATACCCCCCTCAACGAATATG-AATTCCAGAATGCTAGAGGGGAATCGATACCCCC
424572 AGG
65 AGG
*
424575 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
424592 ATGAGAAAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
65 12 0.16
66 15 0.20
67 30 0.41
68 17 0.23
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.19
Consensus pattern (67 bp):
GGGGAACCGATACCCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GG
Found at i:424580 original size:20 final size:20
Alignment explanation
Indices: 424555--424592 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
424545 TATTGCTTGA
*
424555 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
424575 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
424593 TGAGAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:424927 original size:29 final size:29
Alignment explanation
Indices: 424893--424964 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
424883 CATATTATGA
* *
424893 TACATGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
424922 TACATGACATGAATTCATATGATATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
424951 TGCATGACATGAAT
1 TACATGACATGAAT
424965 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATGAAATGTAT
Found at i:425020 original size:30 final size:30
Alignment explanation
Indices: 424978--425054 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
424968 CAGAAAAGTT
* *
424978 ATATGAGCTATGTGATAAAGGTATGTAAATG
1 ATATGA-CTATGTGATAAAGGTATGGAAATA
425009 ATATGACTATGTGATAAAGGTATGGAAATA
1 ATATGACTATGTGATAAAGGTATGGAAATA
*
425039 ATATGACTACGTGATA
1 ATATGACTATGTGATA
425055 TGAACTACGG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 37 0.86
31 6 0.14
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.31
Consensus pattern (30 bp):
ATATGACTATGTGATAAAGGTATGGAAATA
Found at i:425331 original size:23 final size:23
Alignment explanation
Indices: 425265--425323 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
425255 ATCATTATAT
*
425265 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
425287 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
425310 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
425324 TTTATACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:428783 original size:201 final size:199
Alignment explanation
Indices: 428333--428981 Score: 809
Period size: 200 Copynumber: 3.2 Consensus size: 199
428323 TTCTAAATTT
* * * * **
428333 GTGTCGATACATTGTGTAGACCTATTTTCTCATAAAACCGGTAGATTTCTACCAGTTACATTGTT
1 GTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATATTTATACTAGTTACATTGCA
* * * * * *
428398 AATTTACCTATTACATTGTAATTATTGGTTTCAATGTTTTTGGGATTGATACAATTT-TAAATGT
66 AAATTACCTATTACATTATAATTATGGGTTTCAATGTTTTTGAGATCGATACATTTTATAAATGT
* * * * *
428462 ATCGACACTTTATGTGTGCGCCTTGTTTGTCATTCATTCTGGACAAAAAGTATCGACACAAAATA
131 ATCGACACTTTATGCGTGCACC-TATTTGACATTCATTCTGGACAAAAAGTATCGACAC-AAATT
*
428527 AAAAAA
194 TAAAAA
* * * * * *
428533 GTGTCGATACAATATGTAGACCTATTTTCTCATAAAATCTGTGTATTTATACTGGTTACCTTGCA
1 GTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATATTTATACTAGTTACATTGCA
* * * *
428598 AAATTATCTATTACATTATAATTATGGGTTTCAATATTTTTGAGATCGATACTTTTTATAAATAT
66 AAATTACCTATTACATTATAATTATGGGTTTCAATGTTTTTGAGATCGATACATTTTATAAATGT
* *
428663 ATCGACCCTTTATGCGTGCACCTCATTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATT
131 ATCGACACTTTATGCGTGCACCT-ATTT-GACATTCATTCTGGACAAAAAGTATCGACACAAATT
428728 TAAAAA
194 TAAAAA
* * * * * *
428734 GTGTCGATATATTATGTTGACATGTTTTCTAATTAAACCGGTATATTTATA-TCAGTTACATTGC
1 GTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATATTTATACT-AGTTACATTGC
* *
428798 AAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTT-AGGATCGATACGTTTTATAAAT
65 AAAATTACCTATTACATTATAATTATGGGTTTCAATGTTTTTGA-GATCGATACATTTTATAAAT
* *
428862 GTATCGACACTTTATGCGTGCACCTAGTTTGACATTCATTCTAGACAAAATGTATCGACACAAAT
129 GTATCGACACTTTATGCGTGCACCTA-TTTGACATTCATTCTGGACAAAAAGTATCGACACAAAT
*
428927 TTAAAAT
193 TTAAAAA
* * **
428934 GTGTTGATACATTATGTAGACCTATTTTCTCATTAAACATGTATATTT
1 GTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATATTT
428982 TACCTATTAC
Statistics
Matches: 384, Mismatches: 59, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
200 183 0.48
201 171 0.45
202 30 0.08
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (199 bp):
GTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATATTTATACTAGTTACATTGCA
AAATTACCTATTACATTATAATTATGGGTTTCAATGTTTTTGAGATCGATACATTTTATAAATGT
ATCGACACTTTATGCGTGCACCTATTTGACATTCATTCTGGACAAAAAGTATCGACACAAATTTA
AAAA
Found at i:429102 original size:179 final size:178
Alignment explanation
Indices: 428802--429340 Score: 807
Period size: 179 Copynumber: 3.0 Consensus size: 178
428792 CATTGCAAAA
* * * * **
428802 TTACCTATTACATTATAATTATGGGTTTCGATGTTTTTAGGATCGATACGTT-TTATAAATGTAT
1 TTACCTATTACTTTATAATAATCGGTTTCGATGTTTTGA-GATCGATAC-TTACAATAAATGTAT
* ** * ** * * *
428866 CGACACTTTATGCGTGCACCTAGTTTGACATTCATTCTAGACAAAATGTATCGACACAAATTTA-
64 CGACACTTTATGCCTGCATTTCGTTTGGTATTCATTCTGGAGAAAAAGTATCGACAC-AATTTAT
** * *
428930 AAATGTGTTGATACATTATGTAGACCTATTTTCTCATTAAACATGTATATT
128 AAAAATATCGATACATTATGTAGACCTATTTTCTCATTAAACATGTATATT
428981 TTACCTATTACTTTATAATAATCGGTTTCGATGTTTTGAGAATCGATACTTACAATAAATGTATC
1 TTACCTATTACTTTATAATAATCGGTTTCGATGTTTTGAG-ATCGATACTTACAATAAATGTATC
429046 GACACTTTATGCCTGCATTTCGTTTGGTATTCATTCTGGAGAAAAAGTATCGACACAATTTATAA
65 GACACTTTATGCCTGCATTTCGTTTGGTATTCATTCTGGAGAAAAAGTATCGACACAATTTATAA
429111 AAATATCGATACATTATGTAGACCTATTTTCTCATTAAACATGTATATT
130 AAATATCGATACATTATGTAGACCTATTTTCTCATTAAACATGTATATT
429160 TTACCTATTACTTTATAATAATCGGTTTCGATGTTTTGATGATCGATACTTACAATAAATGTATC
1 TTACCTATTACTTTATAATAATCGGTTTCGATGTTTTGA-GATCGATACTTACAATAAATGTATC
429225 GACACTTTATGCCTGCATTTCGTTTGGTATTCATTCTGGAGAAAAAGTATCGACACAATTTATAA
65 GACACTTTATGCCTGCATTTCGTTTGGTATTCATTCTGGAGAAAAAGTATCGACACAATTTATAA
*
429290 AAATATCGATACATTATGTTGACCTATTTTCTCA-TAAA-ATCGGTATATT
130 AAATATCGATACATTATGTAGACCTATTTTCTCATTAAACAT--GTATATT
429339 TT
1 TT
429341 TATCGGTTAC
Statistics
Matches: 334, Mismatches: 20, Indels: 12
0.91 0.05 0.03
Matches are distributed among these distances:
177 2 0.01
178 13 0.04
179 318 0.95
180 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (178 bp):
TTACCTATTACTTTATAATAATCGGTTTCGATGTTTTGAGATCGATACTTACAATAAATGTATCG
ACACTTTATGCCTGCATTTCGTTTGGTATTCATTCTGGAGAAAAAGTATCGACACAATTTATAAA
AATATCGATACATTATGTAGACCTATTTTCTCATTAAACATGTATATT
Found at i:429771 original size:117 final size:118
Alignment explanation
Indices: 429557--429784 Score: 354
Period size: 117 Copynumber: 1.9 Consensus size: 118
429547 AAGAAACATG
* *
429557 TACAACAATCTATTGCTATATTTTCTCATCTTATACATAATTACTCCGACTATGTATAAGAAACA
1 TACAACAATCTATTGCTATATTTTCTCATCTCATACATAATTACTCCAACTATGTATAAGAAACA
* *
429622 TGTAGAACACCCTATTGCTAACTTTTCTCATCTCACACATAATTACATTTAGA
66 TGTACAACAACCTATTGCTAACTTTTCTCATCTCACACATAATTACATTTAGA
* *
429675 TACAATAATCTATTGCTA-ACTTTTCTCATCTCATACATAATTACAT-CAAC-ATGTATAATAAA
1 TACAACAATCTATTGCTATA-TTTTCTCATCTCATACATAATTAC-TCCAACTATGTATAAGAAA
*
429737 CATGTACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTAC
64 CATGTACAACAACCTATTGCTAACTTTTCTCATCTCACACATAATTAC
429785 TCCGACTATG
Statistics
Matches: 101, Mismatches: 7, Indels: 5
0.89 0.06 0.04
Matches are distributed among these distances:
117 57 0.56
118 43 0.43
119 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.36
Consensus pattern (118 bp):
TACAACAATCTATTGCTATATTTTCTCATCTCATACATAATTACTCCAACTATGTATAAGAAACA
TGTACAACAACCTATTGCTAACTTTTCTCATCTCACACATAATTACATTTAGA
Found at i:429781 original size:66 final size:68
Alignment explanation
Indices: 429675--429853 Score: 265
Period size: 67 Copynumber: 2.7 Consensus size: 68
429665 TACATTTAGA
* *
429675 TACAATAATCTATTGCTAACTTTTCTCATCTCATACATAATTACAT-CAAC-ATGTATAATAAAC
1 TACAATAACCTATTGCTAACTTTTCTCATCTCATACATAATTACATCCAACTATGTATAAGAAAC
429738 ATG
66 ATG
* * *
429741 TACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTAC-TCCGACTATGTATAAGAAAT
1 TACAATAACCTATTGCTAACTTTTCTCATCTCATACATAATTACATCCAACTATGTATAAGAAAC
429805 ATG
66 ATG
* * *
429808 TAGAATACCCTATTGCTAACTTTTCTCATCTCACACATAATTACAT
1 TACAATAACCTATTGCTAACTTTTCTCATCTCATACATAATTACAT
429854 TCAGATCAAA
Statistics
Matches: 101, Mismatches: 9, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
65 1 0.01
66 45 0.45
67 54 0.53
68 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (68 bp):
TACAATAACCTATTGCTAACTTTTCTCATCTCATACATAATTACATCCAACTATGTATAAGAAAC
ATG
Found at i:429871 original size:117 final size:117
Alignment explanation
Indices: 429741--430086 Score: 518
Period size: 117 Copynumber: 3.0 Consensus size: 117
429731 AATAAACATG
* * *
429741 TACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTAC-TCCGACTATGTATAAGAAAT
1 TACAAAAATCTATTGCTAACTTTTCTCATCTCATACATAATTACAT-C-ACTATGTATAAGAAAC
* * *
429805 ATGTAGAATACCCTATTGCTAACTTTTCTCATCTCACACATAATTACATTCAGA
64 ATGTACAATAACCTATTGCTAACTTTTCTCATCTCATACATAATTACATTCAGA
* * *
429859 T-CAAAAATCTATTGCTGACTTTTCTCATATCATACATAATTACATCAATATGTATAAGAAACAT
1 TACAAAAATCTATTGCTAACTTTTCTCATCTCATACATAATTACATCACTATGTATAAGAAACAT
*
429923 GTACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTACATTCAGA
66 GTACAATAACCTATTGCTAACTTTTCTCATCTCATACATAATTACATTCAGA
* * *
429975 TACAACAATCTATTGTTAACTTTTCTCATCTCTTACATAATTACATCAAC-ATGTATAAGAAACA
1 TACAAAAATCTATTGCTAACTTTTCTCATCTCATACATAATTACATC-ACTATGTATAAGAAACA
*
430039 TGTACAATAACATATTGCTAACTTTTCTCATCTCATACATAATTACAT
65 TGTACAATAACCTATTGCTAACTTTTCTCATCTCATACATAATTACAT
430087 CAACATGTAT
Statistics
Matches: 207, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
116 65 0.31
117 139 0.67
118 3 0.01
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.36
Consensus pattern (117 bp):
TACAAAAATCTATTGCTAACTTTTCTCATCTCATACATAATTACATCACTATGTATAAGAAACAT
GTACAATAACCTATTGCTAACTTTTCTCATCTCATACATAATTACATTCAGA
Found at i:429955 original size:183 final size:184
Alignment explanation
Indices: 429544--429967 Score: 735
Period size: 184 Copynumber: 2.3 Consensus size: 184
429534 CATACCTAAA
* *
429544 TATAAGAAACATGTACAACAATCTATTGCTATA-TTTTCTCATCTTATACATAATTACTCCGACT
1 TATAAGAAACATGTACAACAACCTATTGCTA-ACTTTTCTCATCTCATACATAATTACTCCGACT
*
429608 ATGTATAAGAAACATGTAGAACACCCTATTGCTAACTTTTCTCATCTCACACATAATTACATTTA
65 ATGTATAAGAAACATGTAGAACACCCTATTGCTAACTTTTCTCATCTCACACATAATTACATTCA
* *
429673 GATACAATAATCTATTGCTAACTTTTCTCATCTCATACATAATTACATCAACATG
130 GATACAAAAATCTATTGCTAACTTTTCTCATATCATACATAATTACATCAACATG
*
429728 TATAATAAACATGTACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTACTCCGACTA
1 TATAAGAAACATGTACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTACTCCGACTA
* *
429793 TGTATAAGAAATATGTAGAATACCCTATTGCTAACTTTTCTCATCTCACACATAATTACATTCAG
66 TGTATAAGAAACATGTAGAACACCCTATTGCTAACTTTTCTCATCTCACACATAATTACATTCAG
* *
429858 AT-CAAAAATCTATTGCTGACTTTTCTCATATCATACATAATTACATCAATATG
131 ATACAAAAATCTATTGCTAACTTTTCTCATATCATACATAATTACATCAACATG
429911 TATAAGAAACATGTACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTAC
1 TATAAGAAACATGTACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTAC
429968 ATTCAGATAC
Statistics
Matches: 228, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
183 104 0.46
184 124 0.54
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.35
Consensus pattern (184 bp):
TATAAGAAACATGTACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTACTCCGACTA
TGTATAAGAAACATGTAGAACACCCTATTGCTAACTTTTCTCATCTCACACATAATTACATTCAG
ATACAAAAATCTATTGCTAACTTTTCTCATATCATACATAATTACATCAACATG
Found at i:430000 original size:51 final size:51
Alignment explanation
Indices: 429924--430020 Score: 167
Period size: 51 Copynumber: 1.9 Consensus size: 51
429914 AAGAAACATG
429924 TACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTACATTCAGA
1 TACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTACATTCAGA
* * *
429975 TACAACAATCTATTGTTAACTTTTCTCATCTCTTACATAATTACAT
1 TACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTACAT
430021 CAACATGTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (51 bp):
TACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTACATTCAGA
Found at i:430081 original size:66 final size:66
Alignment explanation
Indices: 429975--430152 Score: 277
Period size: 66 Copynumber: 2.7 Consensus size: 66
429965 TACATTCAGA
* *
429975 TACAACAATC-TATTGTTAACTTTTCTCATCTCTTACATAATTACATCAACATGTATAAGAAACA
1 TACAACAA-CATATTGCTAACTTTTCTCATCTCATACATAATTACATCAACATGTATAAGAAACA
430039 TG
65 TG
*
430041 TACAATAACATATTGCTAACTTTTCTCATCTCATACATAATTACATCAACATGTATAAGAAACAT
1 TACAACAACATATTGCTAACTTTTCTCATCTCATACATAATTACATCAACATGTATAAGAAACAT
430106 G
66 G
* * * *
430107 TACAACAACATATTACTAACTTTTCTTACCTCAAACATAATTACAT
1 TACAACAACATATTGCTAACTTTTCTCATCTCATACATAATTACAT
430153 TTAGATACAA
Statistics
Matches: 103, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
65 1 0.01
66 102 0.99
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (66 bp):
TACAACAACATATTGCTAACTTTTCTCATCTCATACATAATTACATCAACATGTATAAGAAACAT
G
Found at i:431011 original size:18 final size:18
Alignment explanation
Indices: 430988--431027 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
430978 TTCCTCCTCA
*
430988 CTTCCTTCATCTTTTCTT
1 CTTCCTCCATCTTTTCTT
431006 CTTCCTCCATCTTTTCTT
1 CTTCCTCCATCTTTTCTT
431024 CTTC
1 CTTC
431028 ATATTTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.57
Consensus pattern (18 bp):
CTTCCTCCATCTTTTCTT
Found at i:433814 original size:20 final size:20
Alignment explanation
Indices: 433786--433834 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
433776 GCTTTATCGG
*
433786 TTTTTTCATTTGGAGACCGA
1 TTTTGTCATTTGGAGACCGA
*
433806 TTTTGTCATTTGGAGACCGG
1 TTTTGTCATTTGGAGACCGA
433826 TTTTGTCAT
1 TTTTGTCAT
433835 ATTTTTACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.16, C:0.14, G:0.22, T:0.47
Consensus pattern (20 bp):
TTTTGTCATTTGGAGACCGA
Found at i:433997 original size:69 final size:70
Alignment explanation
Indices: 433875--434026 Score: 252
Period size: 69 Copynumber: 2.2 Consensus size: 70
433865 TACATTTTTA
* * * *
433875 TAAAGTATCGACACTTTATAGGCGTTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTTGATACT
1 TAAAGTATCGACACTTTATAGGCGCTATGACTACTTCTCTTTTAAATTCCAAAAGTGTCGATACT
433940 TATAT
66 TATAT
*
433945 TAAAGTATCGACACTTTATA-GCGCTATGACTACTTCTCTTTTAAATTCCAAAAGTGTCGATATT
1 TAAAGTATCGACACTTTATAGGCGCTATGACTACTTCTCTTTTAAATTCCAAAAGTGTCGATACT
434009 TATAT
66 TATAT
434014 TAAAGTATCGACA
1 TAAAGTATCGACA
434027 TTTTCAACAT
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
69 57 0.74
70 20 0.26
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (70 bp):
TAAAGTATCGACACTTTATAGGCGCTATGACTACTTCTCTTTTAAATTCCAAAAGTGTCGATACT
TATAT
Found at i:434257 original size:182 final size:181
Alignment explanation
Indices: 433945--434855 Score: 1280
Period size: 182 Copynumber: 5.0 Consensus size: 181
433935 ATACTTATAT
* * * *
433945 TAAAGTATCGACACTTTATA-GCGCTATGACTACTTCTCTTTTAAATTCCAAAAGTGTCGATATT
1 TAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCATAAGTGTCGATACT
* * *
434009 TATATTAAAGTATCGACATTTTCAACATATCTGGTAGCGTTTTACCGGTTTTGTCATTTGGAGAC
66 TATATTAAAGTATCGACACTTTCAACATATCTGGTAGCGTTTTACC-GTTTTTTCATTTAGAGAC
* *
434074 CGGTTTTGTCATATTATTACCTGTTATATTGTTATGGATCGATACATTTTTA
130 CGGTTTTGTCATATTTTTACCTGTTATATTATTATGGATCGATACATTTTTA
* *
434126 TAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTAAAATGT-CATAAGTGTCAATAC
1 TAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAAT-TCCATAAGTGTCGATAC
434190 TTATATTAAAGTATCGACACTTTCAACATATCTGGTAGCGTTTTACCAGTTTTTTCATTTAGAGA
65 TTATATTAAAGTATCGACACTTTCAACATATCTGGTAGCGTTTTACC-GTTTTTTCATTTAGAGA
* * *
434255 CCGGTTTTGTCATATTTTTACATATTATATTGTTATGGATCGATACATTTTTA
129 CCGGTTTTGTCATATTTTTACCTGTTATATTATTATGGATCGATACATTTTTA
*
434308 TAAAGTATCGACACTTTATAGGCGCTATTATTGCTTCTCTTTTAAATTCCATAAGTGTCGATACT
1 TAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCATAAGTGTCGATACT
* * * * * * *
434373 TATACTAAAGTATCGACATTTTCAACATATCCGGTAGCCTTTTATCGGTTTTGTCATTTGGAGAC
66 TATATTAAAGTATCGACACTTTCAACATATCTGGTAGCGTTTTA-CCGTTTTTTCATTTAGAGAC
434438 CGGTTTTGTCATATTTTTACCTGTTATATTATTATGGATCGATACATTTTTA
130 CGGTTTTGTCATATTTTTACCTGTTATATTATTATGGATCGATACATTTTTA
* * * *
434490 TAAAGTATCGACATTTTATAGGCGTTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATAGT
1 TAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCATAAGTGTCGATACT
* * **
434555 TATATTAAAGTATCGAAACTTTCAACATAT-TCGGTAGCGCTTTACCGTTTTTGTCATTTCCAGA
66 TATATTAAAGTATCGACACTTTCAACATATCT-GGTAGCGTTTTACCGTTTTT-TCATTTAGAGA
* *
434619 TCGGTTTTATCATATTTTTACCTGTTATATTATTATGGATCGATACATTTTTA
129 CCGGTTTTGTCATATTTTTACCTGTTATATTATTATGGATCGATACATTTTTA
*
434672 TAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCTA-ATAGTGTCGATAC
1 TAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCATA-AGTGTCGATAC
* * * * * *
434736 TTAT-TTCAATGGAATCGATACTTTAAACATAT-TGGGTAGCGCTTTACCGTTTTTGTCA-TAAT
65 TTATATT-AA-AGTATCGACACTTTCAACATATCT-GGTAGCGTTTTACCGTTTTT-TCATTTA-
* *
434798 GAAACCGG-TTTGATCATATTTTTACCTGTTATACTATTATGGATCGATACATTTTTA
125 GAGACCGGTTTTG-TCATATTTTTACCTGTTATATTATTATGGATCGATACATTTTTA
434855 T
1 T
434856 TTGTATCGAT
Statistics
Matches: 660, Mismatches: 59, Indels: 20
0.89 0.08 0.03
Matches are distributed among these distances:
181 30 0.05
182 536 0.81
183 94 0.14
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.42
Consensus pattern (181 bp):
TAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCATAAGTGTCGATACT
TATATTAAAGTATCGACACTTTCAACATATCTGGTAGCGTTTTACCGTTTTTTCATTTAGAGACC
GGTTTTGTCATATTTTTACCTGTTATATTATTATGGATCGATACATTTTTA
Found at i:437247 original size:34 final size:35
Alignment explanation
Indices: 437179--437281 Score: 129
Period size: 34 Copynumber: 3.0 Consensus size: 35
437169 AAACTTGCAA
* *
437179 CAAAAT-CATCAATTACATTCTAAACCCCAAATTC
1 CAAAATACTTCAATTACATACTAAACCCCAAATTC
* *
437213 CAAAATACTTCAATTACATACTAAA-CTCATATTC
1 CAAAATACTTCAATTACATACTAAACCCCAAATTC
* **
437247 CAAAATACTTCAATTACATGCCCAACCCCAAATTC
1 CAAAATACTTCAATTACATACTAAACCCCAAATTC
437282 ATAATCCATT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
34 35 0.60
35 23 0.40
ACGTcount: A:0.43, C:0.29, G:0.01, T:0.27
Consensus pattern (35 bp):
CAAAATACTTCAATTACATACTAAACCCCAAATTC
Found at i:437941 original size:148 final size:148
Alignment explanation
Indices: 437762--438048 Score: 520
Period size: 148 Copynumber: 1.9 Consensus size: 148
437752 AAAACATTTT
* * ***
437762 ATTAGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACAGAAACTTGGAA
1 ATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAAA
437827 ATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAACTA
66 ATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAACTA
437892 TTTTATAAACTGAACTGA
131 TTTTATAAACTGAACTGA
437910 ATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAAA
1 ATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAAA
*
437975 ATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGGAAAAATTTCGAGTCAACTA
66 ATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAACTA
438040 TTTTATAAA
131 TTTTATAAA
438049 TTAAATTGAG
Statistics
Matches: 133, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
148 133 1.00
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.36
Consensus pattern (148 bp):
ATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAAA
ATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAACTA
TTTTATAAACTGAACTGA
Found at i:438261 original size:35 final size:35
Alignment explanation
Indices: 438222--438298 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
438212 ATTGGACATT
* *
438222 TAATTGAAGTATTTTGGAATTTGGGGTTTAGAATA
1 TAATTGAAGCATTTTGGAATTTGGGGTTTAAAATA
* * *
438257 TAATTAAAGCATTTTGGATTTTGGGGTTTAAAATG
1 TAATTGAAGCATTTTGGAATTTGGGGTTTAAAATA
438292 TAATTGA
1 TAATTGA
438299 TGATTGTGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.32, C:0.01, G:0.23, T:0.43
Consensus pattern (35 bp):
TAATTGAAGCATTTTGGAATTTGGGGTTTAAAATA
Found at i:439498 original size:32 final size:32
Alignment explanation
Indices: 439430--439531 Score: 79
Period size: 32 Copynumber: 3.3 Consensus size: 32
439420 TTTAATAGTT
* * * * *
439430 ATTATATTTTATATTAATATAAT-TATATAAA
1 ATTATTTTTTTTATTAAAATAATATTTATATA
439461 TATTATTTTTTTTATTAAAATAATATTTATATA
1 -ATTATTTTTTTTATTAAAATAATATTTATATA
* * * *
439494 ATTA--TTATTTATTTAAAT-TTATTAAT-TA
1 ATTATTTTTTTTATTAAAATAATATTTATATA
439522 ATTATTTTTT
1 ATTATTTTTT
439532 GTGCTATTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
28 6 0.11
29 6 0.11
30 15 0.26
32 24 0.42
33 6 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
ATTATTTTTTTTATTAAAATAATATTTATATA
Found at i:441363 original size:21 final size:21
Alignment explanation
Indices: 441311--441350 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
441301 ATCTCCACAG
*
441311 GGTTACATTCCTAGCCCGCCA
1 GGTTACATACCTAGCCCGCCA
441332 GGTTACATACCTAGCCCGC
1 GGTTACATACCTAGCCCGC
441351 ATGGTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.38, G:0.20, T:0.23
Consensus pattern (21 bp):
GGTTACATACCTAGCCCGCCA
Found at i:448379 original size:37 final size:38
Alignment explanation
Indices: 448295--448383 Score: 137
Period size: 38 Copynumber: 2.4 Consensus size: 38
448285 CCTAAACCCG
* *
448295 AACCCGACCTGACCTGACTCGAATATCACACTTAAAAA
1 AACCCGACCCGACCTGACCCGAATATCACACTTAAAAA
448333 AACCCGACCCGA-CTCGACCCGAATATCACACTT-AAAA
1 AACCCGACCCGACCT-GACCCGAATATCACACTTAAAAA
448370 AACCCGACCCGACC
1 AACCCGACCCGACC
448384 CGAACAAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
37 18 0.38
38 29 0.62
ACGTcount: A:0.37, C:0.38, G:0.11, T:0.13
Consensus pattern (38 bp):
AACCCGACCCGACCTGACCCGAATATCACACTTAAAAA
Found at i:448812 original size:262 final size:259
Alignment explanation
Indices: 448247--448856 Score: 929
Period size: 262 Copynumber: 2.3 Consensus size: 259
448237 TATAATTTAA
* * *
448247 AATTATATATTTTTTCGGGTTGGTCTGGTTTTTTTCACCCTAAACCCGAACCCGACCTGACCTGA
1 AATTATATATATTTTCGGGTTGGTCTGATTTTTTTCACCCTAAACCCGAACCCGACCTGACCCGA
* * * *
448312 CTCGAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCGA
66 CCCGAATAACACACTTAAAAAAACACGACCCGACTCGACCCGAATATCACACTTAAAAAACCAGA
* * *
448377 CCCGACCCGAACAAAATAAAGTTTCATCTGACCCGAATATATGAATTAGAAATTCGACCCGACCC
131 CCCGACCCGAACAAAATAAAGTTTCATCCGACCCGAATATATGAATTAGAAATCCAACCCGACCC
* *
448442 GACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCTACCCGACCCG
196 AACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCG
* ** *
448506 AATTATAGATATTTTCGGGCCGGTCTGATTTTTTTCACCCTAAACCCGAACCCGACCCGACCCGA
1 AATTATATATATTTTCGGGTTGGTCTGATTTTTTTCACCCTAAACCCGAACCCGACCTGACCCGA
* *
448571 CCCGAATAACACACTTAAAAAAACATGACCCGACTCGACCCGAATATTACACTTAAAAAACCAGA
66 CCCGAATAACACACTTAAAAAAACACGACCCGACTCGACCCGAATATCACACTTAAAAAACCAGA
* *
448636 -CTGACCTGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCAACCC
131 CCCGACCCGAACAAAATAAAGTTTCAT-----CCGACCCGAATATATGAATTAGAAATCCAACCC
*
448700 GACCTAACCCGAAATAATAAAAAA-TATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGA
191 GACCCAACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGA
*
448764 CCTG
256 CCCG
* *
448768 AATTATATATATTTTCGGGTTGGTCCGATTTTTTTCACCCTAAACCCGAACCCGACCTGACTCGA
1 AATTATATATATTTTCGGGTTGGTCTGATTTTTTTCACCCTAAACCCGAACCCGACCTGACCCGA
448833 CCCGAATATA-ACACTTAAAAAAAC
66 CCCGAATA-ACACACTTAAAAAAAC
448857 CCAATCCGAC
Statistics
Matches: 317, Mismatches: 28, Indels: 9
0.90 0.08 0.03
Matches are distributed among these distances:
258 24 0.08
259 117 0.37
262 123 0.39
263 53 0.17
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.25
Consensus pattern (259 bp):
AATTATATATATTTTCGGGTTGGTCTGATTTTTTTCACCCTAAACCCGAACCCGACCTGACCCGA
CCCGAATAACACACTTAAAAAAACACGACCCGACTCGACCCGAATATCACACTTAAAAAACCAGA
CCCGACCCGAACAAAATAAAGTTTCATCCGACCCGAATATATGAATTAGAAATCCAACCCGACCC
AACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCG
Found at i:449594 original size:22 final size:21
Alignment explanation
Indices: 449562--449610 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
449552 CTTGCGATTT
*
449562 TAAAAAATATATTTAAATATA
1 TAAAAAATATATTTAAAAATA
449583 TAAAAAATTATATTTAAAAATA
1 TAAAAAA-TATATTTAAAAATA
*
449605 CAAAAA
1 TAAAAA
449611 TTTTAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAAAATATATTTAAAAATA
Found at i:451055 original size:66 final size:66
Alignment explanation
Indices: 450962--451086 Score: 178
Period size: 66 Copynumber: 1.9 Consensus size: 66
450952 CGGGAACTCG
* * *
450962 AACGAGTCGACTGCTACCGAGGGACGTGGGAAAGAAACTGCACCCACCAACCCGAAGAAGAGCAC
1 AACGAGTCGACTACTACCGAGGAACGTGGGAAAGAAACTGCACCCACCAACCAGAAGAAGAGCAC
451027 C
66 C
* * * **
451028 AACGAGTCGACTATTACTGAGGAACGTGGGAGAGAAGTTGCACCCACCAACCAGAAGAA
1 AACGAGTCGACTACTACCGAGGAACGTGGGAAAGAAACTGCACCCACCAACCAGAAGAA
451087 AAAAAGGGAC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 51 1.00
ACGTcount: A:0.36, C:0.26, G:0.27, T:0.10
Consensus pattern (66 bp):
AACGAGTCGACTACTACCGAGGAACGTGGGAAAGAAACTGCACCCACCAACCAGAAGAAGAGCAC
C
Found at i:464115 original size:35 final size:35
Alignment explanation
Indices: 464068--464159 Score: 114
Period size: 35 Copynumber: 2.6 Consensus size: 35
464058 GTATATTTTC
* *
464068 AATGTGATTGCACTTTGTGTGTATATT-CTAATTCT
1 AATGTGATTGCACTTTGTGTGCATATTAC-AATTAT
* *
464103 GATGTGATTGCACTTAGTGTGCATATTACAATTAT
1 AATGTGATTGCACTTTGTGTGCATATTACAATTAT
* *
464138 AATGTGATAGCACTGTGTGTGC
1 AATGTGATTGCACTTTGTGTGC
464160 TCATTTATGA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 47 0.98
36 1 0.02
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.41
Consensus pattern (35 bp):
AATGTGATTGCACTTTGTGTGCATATTACAATTAT
Found at i:469895 original size:15 final size:15
Alignment explanation
Indices: 469851--469897 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 15
469841 ATGTGCATAA
469851 TCATAAAATAAAAAT
1 TCATAAAATAAAAAT
469866 TCAACTATAAA-AAAAAT
1 TC-A-TA-AAATAAAAAT
469883 TCATAAAATAAAAAT
1 TCATAAAATAAAAAT
469898 ACCATAGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 3 0.11
15 10 0.36
16 2 0.07
17 10 0.36
18 3 0.11
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.26
Consensus pattern (15 bp):
TCATAAAATAAAAAT
Found at i:478343 original size:2 final size:2
Alignment explanation
Indices: 478338--478363 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
478328 AAATATATGT
478338 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
478364 ATTTAGGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:480310 original size:19 final size:21
Alignment explanation
Indices: 480269--480314 Score: 69
Period size: 19 Copynumber: 2.3 Consensus size: 21
480259 TTGTTGTAAA
*
480269 TATTTATTTCACATTTTTGTT
1 TATTTATTTCACATTTGTGTT
480290 TATTTATTTC-CA-TTGTGTT
1 TATTTATTTCACATTTGTGTT
480309 TATTTA
1 TATTTA
480315 AATATTATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 12 0.50
20 2 0.08
21 10 0.42
ACGTcount: A:0.20, C:0.09, G:0.07, T:0.65
Consensus pattern (21 bp):
TATTTATTTCACATTTGTGTT
Found at i:482571 original size:21 final size:21
Alignment explanation
Indices: 482529--482571 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
482519 CATTTTTGCA
* *
482529 TTTGCATTTGCATCTTTACAT
1 TTTGCATATGCATCTTCACAT
482550 TTTGCATATGCAT-TTCATCAT
1 TTTGCATATGCATCTTCA-CAT
482571 T
1 T
482572 CATACAAACG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.21, C:0.19, G:0.09, T:0.51
Consensus pattern (21 bp):
TTTGCATATGCATCTTCACAT
Done.