Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004243.1 Hibiscus syriacus cultivar Beakdansim tig00009302_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: 96313
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1527 original size:22 final size:22
Alignment explanation
Indices: 1492--1535 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1482 TAATTATTCA
1492 ATTTTAAATATA-TTCAAGTTAT
1 ATTTTAAATATATTTCAA-TTAT
* *
1514 ATTTTAATTTTATTTCAATTAT
1 ATTTTAAATATATTTCAATTAT
1536 TTATCATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (22 bp):
ATTTTAAATATATTTCAATTAT
Found at i:11381 original size:24 final size:23
Alignment explanation
Indices: 11339--11386 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
11329 TCGAGGTAGA
11339 TTTATTCATTTAAGAGCTTAAGGG
1 TTTATTCATTTAAGAGCTT-AGGG
*
11363 TTTATTCATTCT-AGGGCTTAGGG
1 TTTATTCATT-TAAGAGCTTAGGG
11386 T
1 T
11387 ATTTTGAGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 16 0.73
25 1 0.05
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.44
Consensus pattern (23 bp):
TTTATTCATTTAAGAGCTTAGGG
Found at i:12293 original size:19 final size:21
Alignment explanation
Indices: 12269--12316 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
12259 ATATACGTTT
12269 TATGAACAGT-AA-AATACGG
1 TATGAACAGTGAATAATACGG
**
12288 TATGAACAGTGAATAATATTG
1 TATGAACAGTGAATAATACGG
12309 TATGAACA
1 TATGAACA
12317 ATAATGAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 10 0.40
20 2 0.08
21 13 0.52
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.27
Consensus pattern (21 bp):
TATGAACAGTGAATAATACGG
Found at i:12398 original size:24 final size:23
Alignment explanation
Indices: 12379--12422 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
12369 ATTGCTTGAG
12379 GGGAACCGATTCCCCCTGCTACA
1 GGGAACCGATTCCCCCTGCTACA
*
12402 GGGTACCGATT--CCCTGCTACA
1 GGGAACCGATTCCCCCTGCTACA
12423 ATACTTTCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 10 0.50
23 10 0.50
ACGTcount: A:0.20, C:0.36, G:0.23, T:0.20
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTGCTACA
Found at i:14280 original size:37 final size:37
Alignment explanation
Indices: 14234--14304 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
14224 GACTTTTTGG
*
14234 TCAAGGTCAAC-GATCAAAGTCAAAGTCAACGGGTAGT
1 TCAAAGTCAACGGATC-AAGTCAAAGTCAACGGGTAGT
* * *
14271 TCAAAGTCAACGGTTCAGGTCAAGGTCAACGGGT
1 TCAAAGTCAACGGATCAAGTCAAAGTCAACGGGT
14305 CAGACCTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 26 0.90
38 3 0.10
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.20
Consensus pattern (37 bp):
TCAAAGTCAACGGATCAAGTCAAAGTCAACGGGTAGT
Found at i:14298 original size:19 final size:19
Alignment explanation
Indices: 14252--14307 Score: 78
Period size: 19 Copynumber: 3.0 Consensus size: 19
14242 AACGATCAAA
14252 GTCAAAGTCAACGGGT-AG
1 GTCAAAGTCAACGGGTCAG
* *
14270 TTCAAAGTCAACGGTTCAG
1 GTCAAAGTCAACGGGTCAG
*
14289 GTCAAGGTCAACGGGTCAG
1 GTCAAAGTCAACGGGTCAG
14308 ACCTTTCAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 14 0.44
19 18 0.56
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (19 bp):
GTCAAAGTCAACGGGTCAG
Found at i:14934 original size:31 final size:32
Alignment explanation
Indices: 14883--14957 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 32
14873 AGGATAATTT
* *
14883 TTTTTGGGA-TTTCTCAAGTTGGGTATTTCGA
1 TTTTGGGGATTTTCACAAGTTGGGTATTTCGA
* * *
14914 -TTTGGGGATTTTCACAAGTTGGTTGTTTTGA
1 TTTTGGGGATTTTCACAAGTTGGGTATTTCGA
14945 TTTTGGGGATTTT
1 TTTTGGGGATTTT
14958 GGATATATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 7 0.19
31 18 0.49
32 12 0.32
ACGTcount: A:0.15, C:0.07, G:0.28, T:0.51
Consensus pattern (32 bp):
TTTTGGGGATTTTCACAAGTTGGGTATTTCGA
Found at i:15586 original size:15 final size:15
Alignment explanation
Indices: 15566--15597 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
15556 AATCAATGTT
15566 TACAAAGTTTATGGA
1 TACAAAGTTTATGGA
15581 TACAAAGTTTATGGA
1 TACAAAGTTTATGGA
15596 TA
1 TA
15598 ATGATGAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (15 bp):
TACAAAGTTTATGGA
Found at i:16758 original size:17 final size:17
Alignment explanation
Indices: 16736--16769 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
16726 CATACTTTTT
16736 TTTTAAATATTT-AATAA
1 TTTTAAAT-TTTCAATAA
16753 TTTTAAATTTTCAATAA
1 TTTTAAATTTTCAATAA
16770 GACGAATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTAAATTTTCAATAA
Found at i:17651 original size:14 final size:15
Alignment explanation
Indices: 17632--17669 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
17622 TGAATGTTAT
17632 TATAATATTATG-AA
1 TATAATATTATGTAA
17646 TATAATGATTATGTAA
1 TATAAT-ATTATGTAA
17662 TAATAATA
1 T-ATAATA
17670 ATTACGAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.29
15 6 0.29
16 4 0.19
17 5 0.24
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (15 bp):
TATAATATTATGTAA
Found at i:17687 original size:3 final size:3
Alignment explanation
Indices: 17681--17722 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
17671 TTACGAACAA
17681 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
17723 GTAGCAGACG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:21074 original size:33 final size:33
Alignment explanation
Indices: 21032--21099 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
21022 ATAAAATGGC
21032 ATCATATAATCGAAGGATCATTTTATAACTTTA
1 ATCATATAATCGAAGGATCATTTTATAACTTTA
21065 ATCATATAATCGAAGGATCATTTTATAACTTTA
1 ATCATATAATCGAAGGATCATTTTATAACTTTA
21098 AT
1 AT
21100 AGTTGAGGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (33 bp):
ATCATATAATCGAAGGATCATTTTATAACTTTA
Found at i:32924 original size:15 final size:15
Alignment explanation
Indices: 32901--32930 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
32891 CATGATTTAT
*
32901 TATGTTGGTACAACA
1 TATGGTGGTACAACA
32916 TATGGTGGTACAACA
1 TATGGTGGTACAACA
32931 ATCTCTTGGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.30
Consensus pattern (15 bp):
TATGGTGGTACAACA
Found at i:34224 original size:30 final size:30
Alignment explanation
Indices: 34188--34257 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
34178 TTCAAATGTA
* *
34188 ACAAATTAGTCACTAACATTTTTATTTATT
1 ACAAATTAATCACTAACATTTTAATTTATT
34218 ACAAATTAATCACTAACATTTTAATTTATT
1 ACAAATTAATCACTAACATTTTAATTTATT
*
34248 ATAAATTAAT
1 ACAAATTAAT
34258 ATAATATTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.43, C:0.11, G:0.01, T:0.44
Consensus pattern (30 bp):
ACAAATTAATCACTAACATTTTAATTTATT
Found at i:36573 original size:16 final size:16
Alignment explanation
Indices: 36552--36585 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
36542 ACATGACAAT
36552 TCACATGTATTATATG
1 TCACATGTATTATATG
36568 TCACATGTATTATATG
1 TCACATGTATTATATG
36584 TC
1 TC
36586 CTGTAATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (16 bp):
TCACATGTATTATATG
Found at i:52172 original size:32 final size:32
Alignment explanation
Indices: 52108--52172 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
52098 GGGAGGAAAG
*
52108 TATAATTAACCATAAAAAATAAGGGGGCAAAA
1 TATAATTAACCATAAAAAATAAGAGGGCAAAA
* * *
52140 TATAATTAACCATAGAAAATGAGAGGGTAAAA
1 TATAATTAACCATAAAAAATAAGAGGGCAAAA
52172 T
1 T
52173 TAAAATAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.54, C:0.08, G:0.17, T:0.22
Consensus pattern (32 bp):
TATAATTAACCATAAAAAATAAGAGGGCAAAA
Found at i:53839 original size:22 final size:22
Alignment explanation
Indices: 53814--53857 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
53804 TAAACATGCA
*
53814 TAAATTCAAAACCAAGCGATTT
1 TAAATCCAAAACCAAGCGATTT
53836 TAAATCCAAAACCAAGCGATTT
1 TAAATCCAAAACCAAGCGATTT
53858 CAGTAGCTAA
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:0.45, C:0.20, G:0.09, T:0.25
Consensus pattern (22 bp):
TAAATCCAAAACCAAGCGATTT
Found at i:54883 original size:11 final size:11
Alignment explanation
Indices: 54862--54921 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 11
54852 GCTAAAAAAT
54862 AAAAAAT-ATA
1 AAAAAATAATA
54872 AAAAAATAATA
1 AAAAAATAATA
*
54883 ATAATAATGAA-A
1 A-AAAAAT-AATA
54895 GAAATAAATAATA
1 -AAA-AAATAATA
*
54908 AAATAATAATA
1 AAAAAATAATA
54919 AAA
1 AAA
54922 GGTTAAATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
10 7 0.17
11 14 0.34
12 13 0.32
13 7 0.17
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (11 bp):
AAAAAATAATA
Found at i:54886 original size:23 final size:22
Alignment explanation
Indices: 54857--54961 Score: 63
Period size: 23 Copynumber: 4.6 Consensus size: 22
54847 AAAATGCTAA
54857 AAAATAAAAAATATAAAAAAAT
1 AAAATAAAAAATATAAAAAAAT
* * *
54879 AATAAT-AATAAT-GAAAGAAAT
1 AA-AATAAAAAATATAAAAAAAT
*
54900 -AAATAATAAAATAATAATAAAAGGTT
1 AAAATAA-AAAAT-ATAA-AAAA--AT
* * *
54926 AAATTAAAAAATATTTAAAAAGT
1 AAAATAAAAAATA-TAAAAAAAT
54949 AAAATAAAAAATA
1 AAAATAAAAAATA
54962 AAGATAAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 19
0.67 0.12 0.21
Matches are distributed among these distances:
19 3 0.05
20 2 0.03
21 11 0.18
22 7 0.11
23 18 0.29
24 3 0.05
25 5 0.08
26 8 0.13
27 5 0.08
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (22 bp):
AAAATAAAAAATATAAAAAAAT
Found at i:54914 original size:8 final size:8
Alignment explanation
Indices: 54857--54916 Score: 52
Period size: 8 Copynumber: 7.2 Consensus size: 8
54847 AAAATGCTAA
*
54857 AAAATAAA
1 AAAATAAT
*
54865 AAATATAAA
1 AAA-ATAAT
54874 AAAATAAT
1 AAAATAAT
54882 AATAATAAT
1 AA-AATAAT
54891 GAAAGA-AAT
1 -AAA-ATAAT
54900 -AAATAAT
1 AAAATAAT
54907 AAAATAAT
1 AAAATAAT
54915 AA
1 AA
54917 TAAAAGGTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
6 1 0.02
7 5 0.11
8 18 0.40
9 18 0.40
10 3 0.07
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (8 bp):
AAAATAAT
Found at i:54968 original size:13 final size:12
Alignment explanation
Indices: 54854--54970 Score: 55
Period size: 12 Copynumber: 9.4 Consensus size: 12
54844 AACAAAATGC
54854 TAAAAAATAAAA
1 TAAAAAATAAAA
54866 -AATATAAA-AAAA
1 TAA-A-AAATAAAA
*
54878 T-AATAATAATAA
1 TAAAAAATAA-AA
54890 TGAAAGAAAT-AAA
1 T-AAA-AAATAAAA
54903 TAATAAAATAATAA
1 TAA-AAAATAA-AA
** *
54917 TAAAAGGTTAAAT
1 TAAAA-AATAAAA
**
54930 TAAAAAAT-ATT
1 TAAAAAATAAAA
*
54941 TAAAAAGTAAAA
1 TAAAAAATAAAA
54953 TAAAAAATAAAGA
1 TAAAAAATAAA-A
54966 TAAAA
1 TAAAA
54971 TTTAGGATCA
Statistics
Matches: 79, Mismatches: 12, Indels: 27
0.67 0.10 0.23
Matches are distributed among these distances:
10 2 0.03
11 14 0.18
12 27 0.34
13 22 0.28
14 11 0.14
15 3 0.04
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (12 bp):
TAAAAAATAAAA
Found at i:56194 original size:16 final size:15
Alignment explanation
Indices: 56153--56194 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
56143 CTGCAACAAA
56153 ATAA-AAATAAAAAT
1 ATAATAAATAAAAAT
* *
56167 AAAATAAGTAAAATAT
1 ATAATAAATAAAA-AT
56183 ATAATAAATAAA
1 ATAATAAATAAA
56195 TAACAAAAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 3 0.14
15 7 0.32
16 12 0.55
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (15 bp):
ATAATAAATAAAAAT
Found at i:56293 original size:36 final size:37
Alignment explanation
Indices: 56223--56318 Score: 131
Period size: 36 Copynumber: 2.6 Consensus size: 37
56213 TAAATAAATA
* *
56223 AAAAACATTTCCAAAAATCTATATAATATATTTTTTT
1 AAAAACATTTCCAAAATTATATATAATATATTTTTTT
* * * *
56260 AAAAATATTT-TAAAATTATATATTATATGTTTTTTT
1 AAAAACATTTCCAAAATTATATATAATATATTTTTTT
56296 AAAAACATTTCCAAAATTATATA
1 AAAAACATTTCCAAAATTATATA
56319 GTTTTTTAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
36 30 0.60
37 20 0.40
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (37 bp):
AAAAACATTTCCAAAATTATATATAATATATTTTTTT
Found at i:56537 original size:36 final size:36
Alignment explanation
Indices: 56428--56683 Score: 193
Period size: 36 Copynumber: 7.2 Consensus size: 36
56418 TTTAAAAAAC
*
56428 TATATATATTTTCAAAAT-GTTTAAAAACTATATAA
1 TATATATATTTTCAAAATACTTTAAAAACTATATAA
* * * *
56463 TATATAT-TTTTTAAAAAACAAGTTTTAAAAAATTATATAG
1 TATATATATTTTCAAAATAC----TTT-AAAAACTATATAA
*
56503 TATATTTATTTTCAAAATACTTTAAAAACTATATAA
1 TATATATATTTTCAAAATACTTTAAAAACTATATAA
56539 TATATATATTTTC-AAA-AC--T----A-TATAT--
1 TATATATATTTTCAAAATACTTTAAAAACTATATAA
*
56564 TATATTTATTTTCAAAATACTTTAAAAACTATATAA
1 TATATATATTTTCAAAATACTTTAAAAACTATATAA
* * *
56600 TATATAAATATTTCAAACATGA-TTTCAAAACTATATAT
1 TATATATAT-TTTCAAA-AT-ACTTTAAAAACTATATAA
* *
56638 TATATATAGGTTTTAAAAATA-TTTTAAAACTATA-ATA
1 TATATATA--TTTTCAAAATACTTTAAAAACTATATA-A
56675 TATATATAT
1 TATATATAT
56684 CTATATAAGT
Statistics
Matches: 177, Mismatches: 20, Indels: 48
0.72 0.08 0.20
Matches are distributed among these distances:
25 12 0.07
26 3 0.02
27 7 0.04
28 1 0.01
29 1 0.01
32 1 0.01
33 1 0.01
34 15 0.08
35 11 0.06
36 31 0.18
37 31 0.18
38 25 0.14
39 10 0.06
40 18 0.10
41 10 0.06
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (36 bp):
TATATATATTTTCAAAATACTTTAAAAACTATATAA
Found at i:56561 original size:25 final size:25
Alignment explanation
Indices: 56527--56580 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
56517 AAATACTTTA
56527 AAAACTATATAATATATATATTTTC
1 AAAACTATATAATATATATATTTTC
* *
56552 AAAACTATATATTATATTTATTTTC
1 AAAACTATATAATATATATATTTTC
56577 AAAA
1 AAAA
56581 TACTTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (25 bp):
AAAACTATATAATATATATATTTTC
Found at i:56591 original size:61 final size:62
Alignment explanation
Indices: 56491--56616 Score: 218
Period size: 61 Copynumber: 2.0 Consensus size: 62
56481 CAAGTTTTAA
* *
56491 AAAATTATATAGTATATTTATTTTCAAAATACTTTAAAAACTATATAATATATATAT-TTTC
1 AAAACTATATAGTATATTTATTTTCAAAATACTTTAAAAACTATATAATATATAAATATTTC
*
56552 AAAACTATATATTATATTTATTTTCAAAATACTTTAAAAACTATATAATATATAAATATTTC
1 AAAACTATATAGTATATTTATTTTCAAAATACTTTAAAAACTATATAATATATAAATATTTC
56614 AAA
1 AAA
56617 CATGATTTCA
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
61 54 0.89
62 7 0.11
ACGTcount: A:0.48, C:0.07, G:0.01, T:0.44
Consensus pattern (62 bp):
AAAACTATATAGTATATTTATTTTCAAAATACTTTAAAAACTATATAATATATAAATATTTC
Found at i:56637 original size:137 final size:133
Alignment explanation
Indices: 56428--56683 Score: 302
Period size: 136 Copynumber: 1.9 Consensus size: 133
56418 TTTAAAAAAC
* * * *
56428 TATATATATTTTCAAAATGTTTAAAAACTATATAATATATATTTTTTAAAAAACAAGTTTTAAAA
1 TATATATATTTTCAAAATCTTTAAAAACTATATAATATATAATATTT-AAAAACAAGATTTAAAA
* *
56493 AATTATATAGTATATTTA-TTTTCAAAATACTTTAAAAACTAT-ATAATATATATATTTTCAAAA
65 AATTATAT--TATATATAGTTTTAAAAATA-TTTAAAAACTATAAT-ATATATATATTTTCAAAA
56556 CTATATAT
126 CTATATAT
* * * *
56564 TATATTTATTTTCAAAATACTTTAAAAACTATATAATATATAAATATTT-CAAACATGATTTCAA
1 TATATATATTTTCAAAAT-CTTTAAAAACTATATAATATAT-AATATTTAAAAACAAGATTTAAA
* *
56628 AACTATATATTATATATAGGTTTTAAAAATATTTTAAAACTATAATATATATATAT
64 AAAT-TATATTATATATA-GTTTTAAAAATATTTAAAAACTATAATATATATATAT
56684 CTATATAAGT
Statistics
Matches: 102, Mismatches: 12, Indels: 12
0.81 0.10 0.10
Matches are distributed among these distances:
135 7 0.07
136 52 0.51
137 38 0.37
138 5 0.05
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (133 bp):
TATATATATTTTCAAAATCTTTAAAAACTATATAATATATAATATTTAAAAACAAGATTTAAAAA
ATTATATTATATATAGTTTTAAAAATATTTAAAAACTATAATATATATATATTTTCAAAACTATA
TAT
Found at i:56679 original size:37 final size:35
Alignment explanation
Indices: 56544--56683 Score: 138
Period size: 38 Copynumber: 3.8 Consensus size: 35
56534 TATAATATAT
* *
56544 ATATTTTCAAAACTATATATTATATTTATTTTCAAA
1 ATATTTT-AAAACTATATATTATATATATTTTAAAA
* * * *
56580 ATACTTTAAAAACTATATAATATATAAATATTTCAAAC
1 ATA-TTTTAAAACTATAT-AT-TATATATATTTTAAAA
*
56618 ATGATTTCAAAACTATATATTATATATAGGTTTTAAAA
1 AT-ATTTTAAAACTATATATTATATATA--TTTTAAAA
56656 ATATTTTAAAACTATA-ATATATATATAT
1 ATATTTTAAAACTATATAT-TATATATAT
56684 CTATATAAGT
Statistics
Matches: 86, Mismatches: 11, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
35 1 0.01
36 22 0.26
37 28 0.33
38 34 0.40
39 1 0.01
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (35 bp):
ATATTTTAAAACTATATATTATATATATTTTAAAA
Found at i:57438 original size:84 final size:81
Alignment explanation
Indices: 57294--57761 Score: 492
Period size: 84 Copynumber: 5.7 Consensus size: 81
57284 TTGAATATAA
* * * *
57294 TCGAACTCGGAGGTC-TTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
1 TCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCC
*
57358 TTGGAGCTGAGCGGAG
66 TTGGAGCTGAGCGTAG
* * * * *
57374 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTCCTAGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTCTTTTGG---CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGT
* * * *
57439 GCCCTCGAAGCTGAGTGTAA
63 G-CCTTGGAGCTGAGCGTAG
** * *
57459 TCGAACTCGGGGGTC-TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
1 TCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCC
57523 TTGGAGCTGAGCGTAG
66 TTGGAGCTGAGCGTAG
* * * *
57539 TCGAACTCGAAGGTCTTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTCTTTTGG---CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGT
* * * *
57604 GCCCTCGAAGCTGAGTGTAA
63 G-CCTTGGAGCTGAGCGTAG
** * * *
57624 TCGAACTCGGGGGTC-TTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCC
1 TCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCC
*
57688 TTGGAGCTGAACGTAG
66 TTGGAGCTGAGCGTAG
* * * * * *
57704 TCGAACTCGAAGGTCTTGGTGGCAGATAGCCCTTCTGGCCTTGAGCTAAGCTGCAAAT
1 TCGAACTCGAAGGTCTT-TTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAAT
57762 AGTTTGTTTA
Statistics
Matches: 315, Mismatches: 61, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
80 67 0.21
81 80 0.25
82 34 0.11
84 81 0.26
85 53 0.17
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (81 bp):
TCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCC
TTGGAGCTGAGCGTAG
Found at i:57476 original size:165 final size:165
Alignment explanation
Indices: 57291--57720 Score: 797
Period size: 165 Copynumber: 2.6 Consensus size: 165
57281 AAGTTGAATA
* *
57291 TAATCGAACTCGGAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
*
57356 CCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTCCTAGCCTTGAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTCCTAGCCTTGAG
57421 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
131 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
57456 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* *
57521 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTTACAGATAACCCTTCTAGCCTTGAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTCCTAGCCTTGAG
57586 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
131 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
*
57621 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG
1 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
*
57686 CCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTT
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
57721 GGTGGCAGAT
Statistics
Matches: 258, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
165 258 1.00
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (165 bp):
TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTCCTAGCCTTGAG
TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
Found at i:61104 original size:19 final size:19
Alignment explanation
Indices: 61080--61125 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
61070 AGTTAATGTG
* *
61080 AATGCAGAGAAAATAATAA
1 AATGCAAAGAAAATAAAAA
61099 AATGCAAAGAAAATAAAAA
1 AATGCAAAGAAAATAAAAA
61118 AATGCAAA
1 AATGCAAA
61126 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (19 bp):
AATGCAAAGAAAATAAAAA
Found at i:62879 original size:16 final size:17
Alignment explanation
Indices: 62860--62926 Score: 59
Period size: 16 Copynumber: 3.9 Consensus size: 17
62850 AACAAAATGC
62860 TAAAAAATAA-AAAATA
1 TAAAAAATAATAAAATA
62876 TAAAAAATAATAATAATAA
1 TAAAAAATAATAA-AAT-A
*
62895 TGAAAGAAATAA-ATAATA
1 T-AAA-AAATAATAAAATA
*
62913 -AAATAATAATAAAA
1 TAAAAAATAATAAAA
62927 GGTTAAATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
15 5 0.12
16 16 0.38
17 2 0.05
18 4 0.10
19 5 0.12
20 4 0.10
21 6 0.14
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (17 bp):
TAAAAAATAATAAAATA
Found at i:64199 original size:26 final size:25
Alignment explanation
Indices: 64160--64231 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 25
64150 CTGCAACAAA
64160 ATAAAAATAAAAATAAAATAA-GTAAAAT
1 ATAAAAAT--AAATAAAA-AAGGT-AAAT
64188 ATAAAAATAAATAACAAAAGGTAAAT
1 ATAAAAATAAATAA-AAAAGGTAAAT
64214 A-AATAAATAAATAAAAAA
1 ATAA-AAATAAATAAAAAA
64232 CATTTCCAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
25 6 0.15
26 23 0.56
27 4 0.10
28 8 0.20
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.19
Consensus pattern (25 bp):
ATAAAAATAAATAAAAAAGGTAAAT
Found at i:64287 original size:36 final size:36
Alignment explanation
Indices: 64240--64560 Score: 121
Period size: 36 Copynumber: 8.8 Consensus size: 36
64230 AACATTTCCA
64240 AAAATCTATATAATATATATTTTTTTAAAAATATTTT
1 AAAAT-TATATAATATATATTTTTTTAAAAATATTTT
* * *
64277 AAAATTATATATTATATGTTTTTTTAAAAACA-TTT
1 AAAATTATATAATATATATTTTTTTAAAAATATTTT
** * * *
64312 CCAA--A-AT--TATATAGTTTTTTAAAATGTTTTTTT
1 AAAATTATATAATATATATTTTTTTAAAA--ATATTTT
** * *
64345 AAAATTATAT-AT-TATAAGTTTTT-GAAATGATTTA
1 AAAATTATATAATATATATTTTTTTAAAAAT-ATTTT
* *
64379 AAAACTATATAATATATATATGTTCTTCAAAAAATATTTTTTTT
1 AAAATTATATAATATATAT-T-TT-TT-TAAAAATA----TTTT
* * * * *
64423 AAAA--A-AAAACTATATA-TATTTTCAAAATGTTTA
1 AAAATTATATAA-TATATATTTTTTTAAAAATATTTT
* * *
64456 AAAACTATATAATATATATTTTTTAAAAAACAAGTTTT
1 AAAATTATATAATATATATTTTTTTAAAAA-TA-TTTT
* * * *
64494 AAAAAATTATATAGTATAT-TTATTTTCAAAATACTTTA
1 --AAAATTATATAATATATATTTTTTTAAAAATA-TTTT
* * *
64532 AAAACTATATAATATATATATTTTCAAAA
1 AAAATTATATAATATATATTTTTTTAAAA
64561 CTATATATTA
Statistics
Matches: 204, Mismatches: 51, Indels: 58
0.65 0.16 0.19
Matches are distributed among these distances:
30 15 0.07
32 2 0.01
33 14 0.07
34 12 0.06
35 17 0.08
36 65 0.32
37 18 0.09
38 11 0.05
39 12 0.06
40 17 0.08
41 7 0.03
42 7 0.03
44 7 0.03
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (36 bp):
AAAATTATATAATATATATTTTTTTAAAAATATTTT
Found at i:64300 original size:37 final size:36
Alignment explanation
Indices: 64227--64324 Score: 126
Period size: 36 Copynumber: 2.6 Consensus size: 36
64217 TAAATAAATA
64227 AAAAACATTTCCAAAAATCTATATAATATATATTTTTTT
1 AAAAACATTTCC-AAAAT-TATATAATATAT-TTTTTTT
* * *
64266 AAAAATATTT-TAAAATTATATATTATATGTTTTTTT
1 AAAAACATTTCCAAAATTATATAATATAT-TTTTTTT
64302 AAAAACATTTCCAAAATTATATA
1 AAAAACATTTCCAAAATTATATA
64325 GTTTTTTAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
36 27 0.52
37 16 0.31
39 9 0.17
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (36 bp):
AAAAACATTTCCAAAATTATATAATATATTTTTTTT
Found at i:64523 original size:75 final size:72
Alignment explanation
Indices: 64369--64560 Score: 206
Period size: 76 Copynumber: 2.5 Consensus size: 72
64359 TAAGTTTTTG
* **
64369 AAATGATTTAAAAACTATATAATATATATATGTTCTTCAAAAAATATTTTTTTTAAAAAAAAACT
1 AAATG-TTTAAAAACTATATAATATATAT-T-TT-TT-AAAAAACA-TAGTTTTAAAAAAAAACT
64434 ATATATATTTTCA
60 ATATATATTTTCA
*
64447 AAATGTTTAAAAACTATATAATATATATTTTTTAAAAAACA-AGTTTTAAAAAATTATATAGTAT
1 AAATGTTTAAAAACTATATAATATATATTTTTTAAAAAACATAGTTTTAAAAAA--A-A-ACTAT
*
64511 ATTTATTTTCA
62 ATATATTTTCA
* * *
64522 AAATACTTTAAAAACTATATAATATATATATTTTCAAAA
1 AAAT-GTTTAAAAACTATATAATATATATTTTTTAAAAA
64561 CTATATATTA
Statistics
Matches: 101, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
71 10 0.10
73 8 0.08
74 3 0.03
75 20 0.20
76 32 0.32
77 23 0.23
78 5 0.05
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (72 bp):
AAATGTTTAAAAACTATATAATATATATTTTTTAAAAAACATAGTTTTAAAAAAAAACTATATAT
ATTTTCA
Found at i:64566 original size:25 final size:25
Alignment explanation
Indices: 64532--64585 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
64522 AAATACTTTA
64532 AAAACTATATAATATATATATTTTC
1 AAAACTATATAATATATATATTTTC
* *
64557 AAAACTATATATTATATTTATTTTC
1 AAAACTATATAATATATATATTTTC
64582 AAAA
1 AAAA
64586 TACTTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (25 bp):
AAAACTATATAATATATATATTTTC
Found at i:64596 original size:61 final size:62
Alignment explanation
Indices: 64496--64621 Score: 218
Period size: 61 Copynumber: 2.0 Consensus size: 62
64486 CAAGTTTTAA
* *
64496 AAAATTATATAGTATATTTATTTTCAAAATACTTTAAAAACTATATAATATATATAT-TTTC
1 AAAACTATATAGTATATTTATTTTCAAAATACTTTAAAAACTATATAATATATAAATATTTC
*
64557 AAAACTATATATTATATTTATTTTCAAAATACTTTAAAAACTATATAATATATAAATATTTC
1 AAAACTATATAGTATATTTATTTTCAAAATACTTTAAAAACTATATAATATATAAATATTTC
64619 AAA
1 AAA
64622 CATGATTTCA
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
61 54 0.89
62 7 0.11
ACGTcount: A:0.48, C:0.07, G:0.01, T:0.44
Consensus pattern (62 bp):
AAAACTATATAGTATATTTATTTTCAAAATACTTTAAAAACTATATAATATATAAATATTTC
Found at i:64635 original size:38 final size:36
Alignment explanation
Indices: 64553--64687 Score: 130
Period size: 38 Copynumber: 3.6 Consensus size: 36
64543 ATATATATAT
**
64553 TTTCAAAACTATATATTATATTTATTTTCAAAATAC
1 TTTCAAAACTATATATTATATAAATTTTCAAAATAC
* *
64589 TTTAAAAACTATATAATATATAAATATTTCAAACATGA-
1 TTTCAAAACTATATATTATATAAAT-TTTCAAA-AT-AC
* *
64627 TTTCAAAACTATATATTATATATAGGTTTTAAAAATA-
1 TTTCAAAACTATATATTATATA-A-ATTTTCAAAATAC
*
64664 TTTTAAAACTATAATATATATATA
1 TTTCAAAACTAT-ATAT-TATATA
64688 TCTATATATA
Statistics
Matches: 83, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
36 21 0.25
37 19 0.23
38 28 0.34
39 14 0.17
40 1 0.01
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.43
Consensus pattern (36 bp):
TTTCAAAACTATATATTATATAAATTTTCAAAATAC
Found at i:64642 original size:137 final size:133
Alignment explanation
Indices: 64433--64688 Score: 302
Period size: 136 Copynumber: 1.9 Consensus size: 133
64423 AAAAAAAAAC
* * * *
64433 TATATATATTTTCAAAATGTTTAAAAACTATATAATATATATTTTTTAAAAAACAAGTTTTAAAA
1 TATATATATTTTCAAAATCTTTAAAAACTATATAATATATAATATTT-AAAAACAAGATTTAAAA
* *
64498 AATTATATAGTATATTTA-TTTTCAAAATACTTTAAAAACTAT-ATAATATATATATTTTCAAAA
65 AATTATAT--TATATATAGTTTTAAAAATA-TTTAAAAACTATAAT-ATATATATATTTTCAAAA
64561 CTATATAT
126 CTATATAT
* * * *
64569 TATATTTATTTTCAAAATACTTTAAAAACTATATAATATATAAATATTT-CAAACATGATTTCAA
1 TATATATATTTTCAAAAT-CTTTAAAAACTATATAATATAT-AATATTTAAAAACAAGATTTAAA
* *
64633 AACTATATATTATATATAGGTTTTAAAAATATTTTAAAACTATAATATATATATAT
64 AAAT-TATATTATATATA-GTTTTAAAAATATTTAAAAACTATAATATATATATAT
64689 CTATATATAA
Statistics
Matches: 102, Mismatches: 12, Indels: 12
0.81 0.10 0.10
Matches are distributed among these distances:
135 7 0.07
136 52 0.51
137 38 0.37
138 5 0.05
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (133 bp):
TATATATATTTTCAAAATCTTTAAAAACTATATAATATATAATATTTAAAAACAAGATTTAAAAA
ATTATATTATATATAGTTTTAAAAATATTTAAAAACTATAATATATATATATTTTCAAAACTATA
TAT
Found at i:67945 original size:23 final size:24
Alignment explanation
Indices: 67908--67953 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
67898 AAAGAGGGAC
*
67908 ATTTTTTGATATATTCTTTATTTT
1 ATTTTTTAATATATTCTTTATTTT
*
67932 ATTTTTTAAT-TATTTTTTATTT
1 ATTTTTTAATATATTCTTTATTT
67954 ATTCAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (24 bp):
ATTTTTTAATATATTCTTTATTTT
Found at i:69836 original size:59 final size:58
Alignment explanation
Indices: 69761--69873 Score: 181
Period size: 59 Copynumber: 1.9 Consensus size: 58
69751 TTAATATCCA
* *
69761 TCCGTTCAAAATTAACACGTTTAATAACTAAACTATCTGTTTTGATACGCTTTACCCC
1 TCCGTTAAAAATTAACACGTTTAATAACTAAACTATCCGTTTTGATACGCTTTACCCC
* *
69819 TCCGTTAAAAACTTAACACGTTTAGTAACTAAACTATCCGTTTTGATATGCTTTA
1 TCCGTTAAAAA-TTAACACGTTTAATAACTAAACTATCCGTTTTGATACGCTTTA
69874 GTATCTAAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
58 10 0.20
59 40 0.80
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (58 bp):
TCCGTTAAAAATTAACACGTTTAATAACTAAACTATCCGTTTTGATACGCTTTACCCC
Found at i:74515 original size:31 final size:31
Alignment explanation
Indices: 74477--74569 Score: 143
Period size: 31 Copynumber: 3.0 Consensus size: 31
74467 TGACTTTCAA
74477 TTACTATTCGGACTTTGAAACAACGCTACGC
1 TTACTATTCGGACTTTGAAACAACGCTACGC
74508 TTACTATTCGGACTTTGAAACAACGCTACG-
1 TTACTATTCGGACTTTGAAACAACGCTACGC
* * *
74538 TGGACTATTCGGACTTGGAAATAACGCTACGC
1 T-TACTATTCGGACTTTGAAACAACGCTACGC
74570 GGATCACCCA
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
30 1 0.02
31 56 0.98
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (31 bp):
TTACTATTCGGACTTTGAAACAACGCTACGC
Found at i:76463 original size:24 final size:24
Alignment explanation
Indices: 76431--76485 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
76421 TCAACTCAGT
**
76431 CTGCCTTCGGTGCCGGGAGCACCC
1 CTGCCTTCGGTGCCGCAAGCACCC
76455 CTGCCTTCGGTGCCGCAAGCACCC
1 CTGCCTTCGGTGCCGCAAGCACCC
76479 CTGCCTT
1 CTGCCTT
76486 TGGTTCTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.09, C:0.44, G:0.27, T:0.20
Consensus pattern (24 bp):
CTGCCTTCGGTGCCGCAAGCACCC
Found at i:76556 original size:24 final size:24
Alignment explanation
Indices: 76524--76584 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
76514 AGCACTGGAA
* *
76524 CTGCATTTGGAGGATC-AAGCACAC
1 CTGCTTTTGGAGCATCTAA-CACAC
*
76548 CTGCTTTTGGCA-CATCTAACACTC
1 CTGCTTTTGG-AGCATCTAACACAC
76572 CTGCTTTTGGAGC
1 CTGCTTTTGGAGC
76585 CTCAGCTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 1 0.03
24 27 0.87
25 3 0.10
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (24 bp):
CTGCTTTTGGAGCATCTAACACAC
Found at i:80229 original size:36 final size:36
Alignment explanation
Indices: 80182--80254 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
80172 TTGCAAAAAA
80182 ATAATCATACTCTCATTGGTTAGATACTATAACCCG
1 ATAATCATACTCTCATTGGTTAGATACTATAACCCG
80218 ATAATCATACTCTCATTGGTTAGATACTATAACCCG
1 ATAATCATACTCTCATTGGTTAGATACTATAACCCG
80254 A
1 A
80255 CACTAACCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.33
Consensus pattern (36 bp):
ATAATCATACTCTCATTGGTTAGATACTATAACCCG
Found at i:94865 original size:2 final size:2
Alignment explanation
Indices: 94858--94895 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
94848 TTACATTTGT
94858 TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
94896 CATTTTTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Done.