Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008999.1 Hibiscus syriacus cultivar Beakdansim tig00112380_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: 605736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:534864 original size:9 final size:9
Alignment explanation
Indices: 534850--534880 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
534840 ACAACGGTTC
534850 CCGGTTGAA
1 CCGGTTGAA
534859 CCGGTTGAA
1 CCGGTTGAA
534868 CCGGTTGAA
1 CCGGTTGAA
534877 CCGG
1 CCGG
534881 CCTGTCCGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.19, C:0.26, G:0.35, T:0.19
Consensus pattern (9 bp):
CCGGTTGAA
Found at i:537163 original size:19 final size:19
Alignment explanation
Indices: 537141--537180 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
537131 ATTCTTTCAC
537141 TTCAATATTATTTTCGAGT
1 TTCAATATTATTTTCGAGT
537160 TTCAATATTATTTTCGAGT
1 TTCAATATTATTTTCGAGT
537179 TT
1 TT
537181 GAGTTGAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (19 bp):
TTCAATATTATTTTCGAGT
Found at i:539774 original size:102 final size:102
Alignment explanation
Indices: 539596--539880 Score: 338
Period size: 102 Copynumber: 2.8 Consensus size: 102
539586 TCATGAATAT
** * * * * * *
539596 ATTAAGTGTTAATTTCATTGGTGTAAGTCTATGTTAAGTTTCACCATTGGTATTAAGTGTTTATA
1 ATTAAGTGTTAATTTCACCGATGTAAGTCTATGTTAACTTTCACCACTGGAATTAAGTGTTAATT
* * * *
539661 TCAAC-AATGTAAGTCTATGTTAACTTCCAGCATTGAA
66 TC-ACTGATGTAAGTCTATGTTAACTTCCACCACTAAA
* * *
539698 ATTAAGTGTTAATATCACCGTTGTAAGTCTATGTTAACTTTCACCACTGGAATTAACTGTTAATT
1 ATTAAGTGTTAATTTCACCGATGTAAGTCTATGTTAACTTTCACCACTGGAATTAAGTGTTAATT
* * *
539763 TCACTGGTGTAAGTCTGTGTTAACTTCCACCGCTAAA
66 TCACTGATGTAAGTCTATGTTAACTTCCACCACTAAA
* * * **
539800 ATTAAGTGTTAATTTCCCCGATGTAAGTCTGTGTTAACTTCCACTGCTGGAATTAAGTGTTAATT
1 ATTAAGTGTTAATTTCACCGATGTAAGTCTATGTTAACTTTCACCACTGGAATTAAGTGTTAATT
*
539865 TCACTGAAGTAAGTCT
66 TCACTGATGTAAGTCT
539881 GTTATGAGGT
Statistics
Matches: 155, Mismatches: 27, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
101 2 0.01
102 153 0.99
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (102 bp):
ATTAAGTGTTAATTTCACCGATGTAAGTCTATGTTAACTTTCACCACTGGAATTAAGTGTTAATT
TCACTGATGTAAGTCTATGTTAACTTCCACCACTAAA
Found at i:539783 original size:25 final size:25
Alignment explanation
Indices: 539755--539882 Score: 76
Period size: 25 Copynumber: 5.0 Consensus size: 25
539745 TGGAATTAAC
*
539755 TGTTAATTTCACTGGTGTAAGTCTG
1 TGTTAATTTCACTGATGTAAGTCTG
* * * ** * **
539780 TGTTAACTTCCACCGCTAAAATTAAG
1 TGTTAA-TTTCACTGATGTAAGTCTG
* *
539806 TGTTAATTTCCCCGATGTAAGTCTG
1 TGTTAATTTCACTGATGTAAGTCTG
* * * * **
539831 TGTTAACTTCCACTGCTGGAATTAAG
1 TGTTAA-TTTCACTGATGTAAGTCTG
*
539857 TGTTAATTTCACTGAAGTAAGTCTG
1 TGTTAATTTCACTGATGTAAGTCTG
539882 T
1 T
539883 TATGAGGTAA
Statistics
Matches: 70, Mismatches: 31, Indels: 4
0.67 0.30 0.04
Matches are distributed among these distances:
25 36 0.51
26 34 0.49
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (25 bp):
TGTTAATTTCACTGATGTAAGTCTG
Found at i:539816 original size:26 final size:26
Alignment explanation
Indices: 539779--539862 Score: 80
Period size: 26 Copynumber: 3.3 Consensus size: 26
539769 GTGTAAGTCT
*
539779 GTGTTAACTTCCACCGCTAAAATTAA
1 GTGTTAACTTCCACCGCTGAAATTAA
* * * * **
539805 GTGTTAATTTCC-CCGATGTAAGTCT
1 GTGTTAACTTCCACCGCTGAAATTAA
* *
539830 GTGTTAACTTCCACTGCTGGAATTAA
1 GTGTTAACTTCCACCGCTGAAATTAA
539856 GTGTTAA
1 GTGTTAA
539863 TTTCACTGAA
Statistics
Matches: 43, Mismatches: 14, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
25 18 0.42
26 25 0.58
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (26 bp):
GTGTTAACTTCCACCGCTGAAATTAA
Found at i:539864 original size:51 final size:51
Alignment explanation
Indices: 539596--539882 Score: 277
Period size: 51 Copynumber: 5.6 Consensus size: 51
539586 TCATGAATAT
** * * * * ** **
539596 ATTAAGTGTTAATTTCATTGGTGTAAGTCTATGTTAAGTTTCACCATTGGT
1 ATTAAGTGTTAATTTCACCGATGTAAGTCTGTGTTAACTTCCACCGCTGAA
* * * * * * **
539647 ATTAAGTGTTTATATCAACAATGTAAGTCTATGTTAACTTCCAGCATTGAA
1 ATTAAGTGTTAATTTCACCGATGTAAGTCTGTGTTAACTTCCACCGCTGAA
* * * * * *
539698 ATTAAGTGTTAATATCACCGTTGTAAGTCTATGTTAACTTTCACCACTGGA
1 ATTAAGTGTTAATTTCACCGATGTAAGTCTGTGTTAACTTCCACCGCTGAA
* * * *
539749 ATTAACTGTTAATTTCACTGGTGTAAGTCTGTGTTAACTTCCACCGCTAAA
1 ATTAAGTGTTAATTTCACCGATGTAAGTCTGTGTTAACTTCCACCGCTGAA
* * *
539800 ATTAAGTGTTAATTTCCCCGATGTAAGTCTGTGTTAACTTCCACTGCTGGA
1 ATTAAGTGTTAATTTCACCGATGTAAGTCTGTGTTAACTTCCACCGCTGAA
* *
539851 ATTAAGTGTTAATTTCACTGAAGTAAGTCTGT
1 ATTAAGTGTTAATTTCACCGATGTAAGTCTGT
539883 TATGAGGTAA
Statistics
Matches: 198, Mismatches: 38, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 198 1.00
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (51 bp):
ATTAAGTGTTAATTTCACCGATGTAAGTCTGTGTTAACTTCCACCGCTGAA
Found at i:539877 original size:153 final size:152
Alignment explanation
Indices: 539596--539880 Score: 347
Period size: 153 Copynumber: 1.9 Consensus size: 152
539586 TCATGAATAT
* * * * * *** *
539596 ATTAAGTGTTAATTTCATTGGTGTAAGTCTATGTTAAGTTTCACCATTGGTATTAAGTGTTTATA
1 ATTAACTGTTAATTTCACTGGTGTAAGTCTATGTTAACTTCCACCACTAAAATTAAGTGTTAATA
**
539661 TCAACAATGTAAGTCTATGTTAACTTCCAGCATTGAAATTAAGTGTTAATATCACCGTTGTAAGT
66 TCAACAATGTAAGTCTATGTTAACTTCCAGCA-TGAAATTAAGTGTTAATATCACCGAAGTAAGT
539726 CTATGTTAACTTTCACCACTGGA
130 CTATGTTAACTTTCACCACTGGA
* * *
539749 ATTAACTGTTAATTTCACTGGTGTAAGTCTGTGTTAACTTCCACCGCTAAAATTAAGTGTTAATT
1 ATTAACTGTTAATTTCACTGGTGTAAGTCTATGTTAACTTCCACCACTAAAATTAAGTGTTAATA
** * * * * *
539814 TCCCCGATGTAAGTCTGTGTTAACTTCCACTGC-TGGAATTAAGTGTTAATTTCACTGAAGTAAG
66 TCAACAATGTAAGTCTATGTTAACTTCCA--GCATGAAATTAAGTGTTAATATCACCGAAGTAAG
539878 TCT
129 TCT
539881 GTTATGAGGT
Statistics
Matches: 109, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
153 107 0.98
155 2 0.02
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (152 bp):
ATTAACTGTTAATTTCACTGGTGTAAGTCTATGTTAACTTCCACCACTAAAATTAAGTGTTAATA
TCAACAATGTAAGTCTATGTTAACTTCCAGCATGAAATTAAGTGTTAATATCACCGAAGTAAGTC
TATGTTAACTTTCACCACTGGA
Found at i:539916 original size:51 final size:51
Alignment explanation
Indices: 539847--540171 Score: 248
Period size: 51 Copynumber: 6.4 Consensus size: 51
539837 CTTCCACTGC
* * * *
539847 TGGAATTA-AGTGTT-AATTTCACTGAAGTAAGTCTGTTATGAGGTAAATAT
1 TGGAATTATA-TGTTAAATTTGACTGATGTAAGTCTGTTATGAGTTCAATAT
* * * *
539897 TGGAATTATATGTTAAATTTGACTGGTGTAAGTTTGTTGTGAGCTCAATAT
1 TGGAATTATATGTTAAATTTGACTGATGTAAGTCTGTTATGAGTTCAATAT
* * * * * *
539948 TGAAATGATGTGCTAAATTTGACT-AGTGTAAGTCTGCTATGAGTTCAATGT
1 TGGAATTATATGTTAAATTTGACTGA-TGTAAGTCTGTTATGAGTTCAATAT
* * * * * *
539999 TTGAATTATGTGTTAAATTTTAC-GGTGTAAGTCTATTATGAGTTCAATGT
1 TGGAATTATATGTTAAATTTGACTGATGTAAGTCTGTTATGAGTTCAATAT
* * * * * *
540049 TGGAATTATGT-TCTAAATTTGACTCATGTAAATCTATTATGATTTAAATAT
1 TGGAATTATATGT-TAAATTTGACTGATGTAAGTCTGTTATGAGTTCAATAT
* * * * * * * *
540100 TGGGATTATGA-GTTAAATTTGGCTGGTGTAAATATGTTATAAGCTCAGTGAT
1 TGGAATTAT-ATGTTAAATTTGACTGATGTAAGTCTGTTATGAGTTCAAT-AT
*
540152 TTGAATTATATGTTAAATTT
1 TGGAATTATATGTTAAATTT
540172 CATCGGTATA
Statistics
Matches: 218, Mismatches: 47, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
49 1 0.00
50 54 0.25
51 144 0.66
52 19 0.09
ACGTcount: A:0.31, C:0.06, G:0.21, T:0.42
Consensus pattern (51 bp):
TGGAATTATATGTTAAATTTGACTGATGTAAGTCTGTTATGAGTTCAATAT
Found at i:540090 original size:101 final size:102
Alignment explanation
Indices: 539883--540130 Score: 284
Period size: 101 Copynumber: 2.4 Consensus size: 102
539873 GTAAGTCTGT
* * * * *
539883 TATGAGGTAAATATTGGAATTATATGTTAAATTTGACTGGTGTAAGTTTGTTGTGAGCTCAATAT
1 TATGAGTTAAATATTGGAATTATGTGTTAAATTTGACTGGTGTAAGTCTATTATGAGCTCAATAT
* *
539948 TGAAATGATGTGCTAAATTTGACTAGTGTAAGTCTGC
66 TGAAATGATGTGCTAAATTTGACTAGTGTAAATCTAC
* * * * * *
539985 TATGAGTTCAATGTTTGAATTATGTGTTAAATTTTAC-GGTGTAAGTCTATTATGAGTTCAATGT
1 TATGAGTTAAATATTGGAATTATGTGTTAAATTTGACTGGTGTAAGTCTATTATGAGCTCAATAT
* * * *
540049 TGGAATTATGTTCTAAATTTGACTCA-TGTAAATCTAT
66 TGAAATGATGTGCTAAATTTGACT-AGTGTAAATCTAC
* * * *
540086 TATGATTTAAATATTGGGATTATGAGTTAAATTTGGCTGGTGTAA
1 TATGAGTTAAATATTGGAATTATGTGTTAAATTTGACTGGTGTAA
540131 ATATGTTATA
Statistics
Matches: 119, Mismatches: 25, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
101 80 0.67
102 39 0.33
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.42
Consensus pattern (102 bp):
TATGAGTTAAATATTGGAATTATGTGTTAAATTTGACTGGTGTAAGTCTATTATGAGCTCAATAT
TGAAATGATGTGCTAAATTTGACTAGTGTAAATCTAC
Found at i:540109 original size:20 final size:19
Alignment explanation
Indices: 540084--540121 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
540074 ATGTAAATCT
*
540084 ATTATGATTTAAATATTGGG
1 ATTATGAGTTAAAT-TTGGG
540104 ATTATGAGTTAAATTTGG
1 ATTATGAGTTAAATTTGG
540122 CTGGTGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (19 bp):
ATTATGAGTTAAATTTGGG
Found at i:541030 original size:2 final size:2
Alignment explanation
Indices: 540987--541071 Score: 86
Period size: 2 Copynumber: 43.0 Consensus size: 2
540977 ACCTAAAATA
* * * *
540987 AT AT AT -T AT AT -T AT GAA AT AT ACT AT GT AT AA AT AA AT AT AT
1 AT AT AT AT AT AT AT AT -AT AT AT A-T AT AT AT AT AT AT AT AT AT
*
541029 AT AT AT A- AT AT AT AT AT AT AG AT AT 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
541070 AT
1 AT
541072 GTCACACCCC
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
1 3 0.04
2 62 0.91
3 3 0.04
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:544024 original size:22 final size:21
Alignment explanation
Indices: 543999--544039 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
543989 TATAAAAAAT
543999 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAAT-TTTTTGG
*
544021 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
544040 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:550877 original size:38 final size:38
Alignment explanation
Indices: 550835--550919 Score: 97
Period size: 36 Copynumber: 2.3 Consensus size: 38
550825 ACCCTTTCAT
*
550835 TAAATATTTTAT-ATTTTTAA-TTTTGTAAAAAAATTATA
1 TAAATATTTTATGA-ATTTAATTTTTGTAAAAAAA-TATA
* *
550873 TAAATA--TTATGAATTTAATTTTTTTTAAAAAATATA
1 TAAATATTTTATGAATTTAATTTTTGTAAAAAAATATA
550909 TAAATATTTTA
1 TAAATATTTTA
550920 CAATTTGTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
36 19 0.47
37 12 0.30
38 9 0.22
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (38 bp):
TAAATATTTTATGAATTTAATTTTTGTAAAAAAATATA
Found at i:551351 original size:15 final size:15
Alignment explanation
Indices: 551333--551397 Score: 66
Period size: 15 Copynumber: 4.5 Consensus size: 15
551323 GTTAAATTCT
551333 AATTATTTAAATAAA
1 AATTATTTAAATAAA
*
551348 AATTATTTATATAAA
1 AATTATTTAAATAAA
*
551363 AATTCA--TCAAT-AA
1 AATT-ATTTAAATAAA
*
551376 TA-TATTTAAATAAA
1 AATTATTTAAATAAA
551390 AATTATTT
1 AATTATTT
551398 TTATAAAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
11 1 0.03
12 1 0.03
13 7 0.18
14 6 0.15
15 23 0.59
16 1 0.03
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTATTTAAATAAA
Found at i:551601 original size:21 final size:21
Alignment explanation
Indices: 551571--551625 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
551561 ATTATTACTA
*
551571 TCGCAATGCGATTTT-CCAATT
1 TCGCATTGCGATTTTCCCAA-T
*
551592 TCGCGTTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
551613 TCGCATTGCGATT
1 TCGCATTGCGATT
551626 CGCAATGCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 26 0.87
22 4 0.13
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:551670 original size:20 final size:20
Alignment explanation
Indices: 551647--551778 Score: 90
Period size: 20 Copynumber: 6.5 Consensus size: 20
551637 TTTGAAAATT
551647 GCAATGCGATACTGACTATC
1 GCAATGCGATACTGACTATC
* * *
551667 GCAACGCGATAAT-ACAAAATC
1 GCAATGCGATACTGAC--TATC
*
551688 GCAATGCGATACTGACTTTC
1 GCAATGCGATACTGACTATC
* * *
551708 GCAACGCGATACTTACTTTC
1 GCAATGCGATACTGACTATC
* *
551728 GCAACT-AGATACTGACTTTC
1 GCAA-TGCGATACTGACTATC
* * *
551748 GCAACGAGATAAT-ACATAATC
1 GCAATGCGATACTGAC-T-ATC
551769 GCAATGCGAT
1 GCAATGCGAT
551779 TTTCAAAGCG
Statistics
Matches: 88, Mismatches: 17, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
19 4 0.05
20 58 0.66
21 24 0.27
22 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (20 bp):
GCAATGCGATACTGACTATC
Found at i:551692 original size:41 final size:41
Alignment explanation
Indices: 551641--551778 Score: 165
Period size: 41 Copynumber: 3.4 Consensus size: 41
551631 TGCGAATTTG
* *
551641 AAAATTGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTTTCGCAACGCGATAATAC
*
551682 AAAATCGCAATGCGATACTGACTTTCGCAACGCGATACTTAC
1 AAAATCGCAATGCGATACTGACTTTCGCAACGCGATA-ATAC
** * *
551724 --TTTCGCAACT-AGATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAA-TGCGATACTGACTTTCGCAACGCGATAATAC
*
551763 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
551779 TTTCAAAGCG
Statistics
Matches: 81, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
39 3 0.04
40 30 0.37
41 45 0.56
42 3 0.04
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (41 bp):
AAAATCGCAATGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:552142 original size:27 final size:27
Alignment explanation
Indices: 552112--552167 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
552102 AGGTTTTTCA
552112 TATTGAAATTGATGATAAGTTTACTGG
1 TATTGAAATTGATGATAAGTTTACTGG
552139 TATTGAAATTGATGATAAGTTTACTGG
1 TATTGAAATTGATGATAAGTTTACTGG
552166 TA
1 TA
552168 ATTTCAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (27 bp):
TATTGAAATTGATGATAAGTTTACTGG
Found at i:552317 original size:20 final size:20
Alignment explanation
Indices: 552294--552336 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
552284 GATAATCAAA
552294 TTCGCGTTGCGATTGTCATT
1 TTCGCGTTGCGATTGTCATT
* *
552314 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTGTCATT
552334 TTC
1 TTC
552337 AGAAACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.09, C:0.19, G:0.21, T:0.51
Consensus pattern (20 bp):
TTCGCGTTGCGATTGTCATT
Found at i:552527 original size:25 final size:24
Alignment explanation
Indices: 552473--552527 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
552463 TGTTTATTGT
* *
552473 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
552497 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
552523 TGTTT
1 TGTTT
552528 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:553655 original size:18 final size:18
Alignment explanation
Indices: 553634--553681 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
553624 TCCACTTCGG
553634 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
* *
553652 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
553670 GAGCCATCACCT
1 GAGCCATCACCT
553682 AATCGACCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.44, G:0.12, T:0.17
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:554270 original size:19 final size:20
Alignment explanation
Indices: 554216--554261 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
554206 TAGTTTACTT
* *
554216 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
554236 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
554256 TCGCAA
1 TCGCAA
554262 TGTGAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:554293 original size:14 final size:14
Alignment explanation
Indices: 554274--554329 Score: 51
Period size: 14 Copynumber: 3.6 Consensus size: 14
554264 TGAAATGAAA
554274 ATCGCAACGACAAG
1 ATCGCAACGACAAG
554288 ATCGCAATGCGA-AATG
1 ATCGCAA--CGACAA-G
554304 AAAATCGCAACGACAAG
1 ---ATCGCAACGACAAG
554321 ATCGCAACG
1 ATCGCAACG
554330 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
14 16 0.46
15 2 0.06
16 4 0.11
17 4 0.11
18 2 0.06
19 7 0.20
ACGTcount: A:0.43, C:0.25, G:0.21, T:0.11
Consensus pattern (14 bp):
ATCGCAACGACAAG
Found at i:554302 original size:33 final size:33
Alignment explanation
Indices: 554255--554346 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
554245 GGAAATGGCT
*
554255 ATCGCAATGTGAAATGAAAATCGCAACGACAAG
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAG
554288 ATCGCAATGCGAAATGAAAATCGCAACGACAAG
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAG
*
554321 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
554347 TGCGATTTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAG
Found at i:554312 original size:19 final size:19
Alignment explanation
Indices: 554255--554351 Score: 74
Period size: 19 Copynumber: 5.6 Consensus size: 19
554245 GGAAATGGCT
*
554255 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
554274 ATCGCAA--CGACAA-G---
1 ATCGCAATGCGA-AATGAAA
554288 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
554307 ATCGCAA--CGACAA-G---
1 ATCGCAATGCGA-AATGAAA
*
554321 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
554340 ATCGCAATGCGA
1 ATCGCAATGCGA
554352 TTTATGTTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 28
0.67 0.02 0.30
Matches are distributed among these distances:
14 14 0.23
15 4 0.06
16 8 0.13
17 7 0.11
18 4 0.06
19 25 0.40
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:554440 original size:20 final size:20
Alignment explanation
Indices: 554417--554454 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
554407 CGATGGTCAT
554417 TTTCGCGTTGCGAAAGTATG
1 TTTCGCGTTGCGAAAGTATG
*
554437 TTTCGTGTTGCGAAAGTA
1 TTTCGCGTTGCGAAAGTA
554455 AACTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.13, G:0.29, T:0.37
Consensus pattern (20 bp):
TTTCGCGTTGCGAAAGTATG
Found at i:554841 original size:42 final size:41
Alignment explanation
Indices: 554794--554872 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 41
554784 GACTCACCTG
*
554794 TCATCCCTCAAGAGTC-CACTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCTC-C-CCAACCGTTCAAGAGGCCCCTA
*
554836 TCATCCCTCAAGAGTCTCCCCCACCGTTCAAGAGGCC
1 TCATCCCTCAAGAGTCTCCCCAACCGTTCAAGAGGCC
554873 ACTGTCATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
41 16 0.47
42 17 0.50
43 1 0.03
ACGTcount: A:0.24, C:0.41, G:0.15, T:0.20
Consensus pattern (41 bp):
TCATCCCTCAAGAGTCTCCCCAACCGTTCAAGAGGCCCCTA
Found at i:556470 original size:14 final size:14
Alignment explanation
Indices: 556451--556503 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 14
556441 GAAACTGACT
*
556451 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
556465 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
556484 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
556498 ATCGCA
1 ATCGCA
556504 GTGCGATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:556551 original size:20 final size:20
Alignment explanation
Indices: 556535--556623 Score: 169
Period size: 20 Copynumber: 4.5 Consensus size: 20
556525 GCGATTTTTT
556535 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
556555 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
556575 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGTCATTTTCG
556595 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
556615 CGTTGCGAT
1 CGTTGCGAT
556624 TTCCCCGTTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:556559 original size:34 final size:37
Alignment explanation
Indices: 556516--556623 Score: 132
Period size: 40 Copynumber: 2.8 Consensus size: 37
556506 GCGATTTTCA
*
556516 TTTCGCGTTGCGAT-T-TTTT-CGTTGCGATAGTCAT
1 TTTCGCGTTGCGATATATTTTCCGTTGCGATAGCCAT
556550 TTTCGCGTTGCGATAGTCATTTTCGCGTTGCGATAGCCAT
1 TTTCGCGTTGCGATA-T-ATTTTC-CGTTGCGATAGCCAT
556590 TTTCGCGTTGCGATAGTCATTTTCGCGTTGCGAT
1 TTTCGCGTTGCGATA-T-ATTTTC-CGTTGCGAT
556624 TTCCCCGTTG
Statistics
Matches: 67, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
34 14 0.21
36 1 0.01
38 4 0.06
40 48 0.72
ACGTcount: A:0.13, C:0.20, G:0.25, T:0.42
Consensus pattern (37 bp):
TTTCGCGTTGCGATATATTTTCCGTTGCGATAGCCAT
Found at i:556991 original size:20 final size:20
Alignment explanation
Indices: 556970--557048 Score: 140
Period size: 20 Copynumber: 4.0 Consensus size: 20
556960 TGTATTATCT
* *
556970 CGTTGCGATAGTCAGAATCT
1 CGTTGCGAAAGTCAGAATCG
556990 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
557010 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
557030 CGTTGCGAAAGTCAGAATC
1 CGTTGCGAAAGTCAGAATC
557049 ACGATTTTTG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:557770 original size:24 final size:24
Alignment explanation
Indices: 557732--557778 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
557722 GTATTCGAAA
* *
557732 TTTGATCTTGTTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
*
557756 TTTGATATTGGTCAATACTCGGA
1 TTTGATATTGGTCAATACCCGGA
557779 TTTTAATGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:557977 original size:12 final size:12
Alignment explanation
Indices: 557960--557984 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
557950 ATATAATCCT
557960 GAAGAAGAAAAA
1 GAAGAAGAAAAA
557972 GAAGAAGAAAAA
1 GAAGAAGAAAAA
557984 G
1 G
557985 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:560299 original size:20 final size:20
Alignment explanation
Indices: 560232--560304 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
560222 GACATTCATT
560232 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACACGGAAA
**
560252 TGACGT-TCGCAATCATC-TTAA
1 TGAC-TATCGCAA-CA-CGGAAA
* *
560273 TGTCTATCGCAACGCGGAAA
1 TGACTATCGCAACACGGAAA
560293 TGACTATCGCAA
1 TGACTATCGCAA
560305 TGCGAAATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
19 1 0.02
20 25 0.61
21 14 0.34
22 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (20 bp):
TGACTATCGCAACACGGAAA
Found at i:560320 original size:19 final size:19
Alignment explanation
Indices: 560278--560427 Score: 87
Period size: 19 Copynumber: 8.6 Consensus size: 19
560268 CTTAATGTCT
* **
560278 ATCGCAACGCGGAAATGACT
1 ATCGCAATGC-GAAATGAAA
*
560298 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
560317 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
560331 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
560350 ATCACAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
560364 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
560383 ATCGCAAT--G--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
560397 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
560416 ATCGCAACGCGA
1 ATCGCAATGCGA
560428 TTTTAGTTTC
Statistics
Matches: 98, Mismatches: 17, Indels: 31
0.67 0.12 0.21
Matches are distributed among these distances:
14 27 0.28
15 3 0.03
16 5 0.05
17 5 0.05
18 3 0.03
19 46 0.47
20 9 0.09
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:560340 original size:33 final size:33
Alignment explanation
Indices: 560298--560424 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
560288 GGAAATGACT
*
560298 ATCGCAATGCGAAATAAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
560331 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
560364 ATCGCAATGCGAAATGAAAATCGCAATGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
560397 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
560425 CGATTTTAGT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:560446 original size:19 final size:19
Alignment explanation
Indices: 560424--560477 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
560414 AAATCGCAAC
560424 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
560443 GCGATTTT-G--T--CGTT
1 GCGATTTTAGTTTCGCGTT
560457 GCGATTTTCA-TTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
560476 GC
1 GC
560478 AATTCTCTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
14 12 0.41
16 1 0.03
17 1 0.03
18 1 0.03
19 14 0.48
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.46
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:560471 original size:33 final size:33
Alignment explanation
Indices: 560424--560513 Score: 128
Period size: 33 Copynumber: 2.7 Consensus size: 33
560414 AAATCGCAAC
* *
560424 GCGATTTT-AGTTTCGCGTTGCGATTTTGTCGTT
1 GCGATTTTCA-TTTCGCGTTGCGATTCTCTCGTT
*
560457 GCGATTTTCATTTCGCGTTGCAATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
560490 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
560514 AGTCATTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
33 50 0.98
34 1 0.02
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:560512 original size:19 final size:18
Alignment explanation
Indices: 560455--560513 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
560445 GATTTTGTCG
560455 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
* *
560473 GTTGC-A-ATTC-TCTCG-
1 -TTGCGATTTTCATTTCGC
560488 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
560506 ATTGCGAT
1 -TTGCGAT
560514 AGTCATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 4 0.13
15 1 0.03
16 7 0.23
17 7 0.23
18 1 0.03
19 11 0.35
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (18 bp):
TTGCGATTTTCATTTCGC
Found at i:560639 original size:14 final size:14
Alignment explanation
Indices: 560620--560656 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
560610 CATCAATTAA
560620 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
560634 ACAAATCATCTTTT
1 ACAAATCAACTTTT
560648 ACAAATCAA
1 ACAAATCAA
560657 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:562090 original size:42 final size:41
Alignment explanation
Indices: 562005--562127 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
561995 GTGAATCGGG
* * * *
562005 CTCTTGAATGGTGGGA-GGGACCTCTTCCACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
562047 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
562089 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
562128 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.22, C:0.20, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:562242 original size:20 final size:20
Alignment explanation
Indices: 562214--562430 Score: 109
Period size: 20 Copynumber: 10.7 Consensus size: 20
562204 CGATAGTCAG
*
562214 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
562234 ATTAGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
* * *
562254 AATTCGCATTACAATTTACTT
1 -ATTCGCATTGCGATTTACGT
* * *
562275 AATCGCGTTGCAATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
562295 ATTCGCATTGCGAATTATGAA
1 ATTCGCATTGCGATTTACG-T
* ** *
562316 AATCGCAACGCGA-ATACGT
1 ATTCGCATTGCGATTTACGT
* *
562335 AAATCGCATTGCGATTT-TGT
1 -ATTCGCATTGCGATTTACGT
* *
562355 ATTATCGCGTTGCGATAGT-CAGT
1 A-T-TCGCATTGCGAT-TTAC-GT
* **
562378 A-TCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
562398 ATTCGCATTGCGATTTACTT
1 ATTCGCATTGCGATTTACGT
562418 ATTCGCATTGCGA
1 ATTCGCATTGCGA
562431 ATTGGGAAAA
Statistics
Matches: 146, Mismatches: 40, Indels: 22
0.70 0.19 0.11
Matches are distributed among these distances:
19 1 0.01
20 91 0.62
21 50 0.34
22 1 0.01
23 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:562321 original size:21 final size:21
Alignment explanation
Indices: 562297--562472 Score: 62
Period size: 21 Copynumber: 8.5 Consensus size: 21
562287 ATTTACGTAT
562297 TCGCATTGCGAATTATGAAAA
1 TCGCATTGCGAATTATGAAAA
** * *
562318 TCGCAACGCGAA-TACGTAAA
1 TCGCATTGCGAATTATGAAAA
* **
562338 TCGCATTGCG-ATTTTGTATTA
1 TCGCATTGCGAATTATG-AAAA
* * **
562359 TCGCGTTGCG-A-TAGTCAGTA
1 TCGCATTGCGAATTA-TGAAAA
* * *
562379 TCGCATTGCG-ATTTTCCAAAT
1 TCGCATTGCGAATTAT-GAAAA
* * *
562400 TCGCATTGCGATTTACT--TAT
1 TCGCATTGCGAATTA-TGAAAA
**
562420 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATTATGAAAA
* *
562441 TCGCAATGCGAAATT-GGAAAA
1 TCGCATTGCG-AATTATGAAAA
562462 TCGCATTGCGA
1 TCGCATTGCGA
562473 TAGTAATAAT
Statistics
Matches: 115, Mismatches: 30, Indels: 21
0.69 0.18 0.13
Matches are distributed among these distances:
19 1 0.01
20 47 0.41
21 60 0.52
22 6 0.05
23 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.31
Consensus pattern (21 bp):
TCGCATTGCGAATTATGAAAA
Found at i:562698 original size:21 final size:21
Alignment explanation
Indices: 562656--562695 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
562646 ATTCATCGAT
*
562656 AATATATTATTTTATTATTTA
1 AATATATTATTGTATTATTTA
562677 AATATATTA-TGTATTATTT
1 AATATATTATTGTATTATTT
562696 TAATTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
AATATATTATTGTATTATTTA
Found at i:562711 original size:28 final size:28
Alignment explanation
Indices: 562660--562713 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
562650 ATCGATAATA
*
562660 TATTATTTTATTATTTAAATATATTATG
1 TATTATTTTAATATTTAAATATATTATG
*
562688 TATTATTTTAAT-TTTAATTAATATTA
1 TATTATTTTAATATTTAAAT-ATATTA
562714 AATTTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (28 bp):
TATTATTTTAATATTTAAATATATTATG
Found at i:566274 original size:22 final size:22
Alignment explanation
Indices: 566216--566276 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
566206 ATTACATAAT
*
566216 CTTTCAAAATTATATATATACA
1 CTTTCAAAACTATATATATACA
566238 CTTTCAAAACTATAT-TATACA
1 CTTTCAAAACTATATATATACA
*
566259 CATTTTAAAAGC-ATATAT
1 C-TTTCAAAA-CTATATAT
566277 GTTAATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 7 0.21
22 25 0.74
23 2 0.06
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.39
Consensus pattern (22 bp):
CTTTCAAAACTATATATATACA
Found at i:584505 original size:23 final size:21
Alignment explanation
Indices: 584479--584537 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
584469 TTCCCCTGTG
584479 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCC-TC-AA
*
584502 GGGGGAATCGGTT-CCCTCAG
1 GGGGGAATCGGTTCCCCTCAA
*
584522 GGGGGAATCGATTCCC
1 GGGGGAATCGGTTCCC
584538 TCTGCACCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.39
21 4 0.12
22 3 0.09
23 13 0.39
ACGTcount: A:0.19, C:0.25, G:0.36, T:0.20
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCCTCAA
Found at i:584539 original size:20 final size:21
Alignment explanation
Indices: 584455--584537 Score: 87
Period size: 21 Copynumber: 3.9 Consensus size: 21
584445 AGCAGAACCC
*
584455 CAGGGGGGTATCGATTCCCCT
1 CAGGGGGGAATCGATTCCCCT
** *
584476 GTGGGGGGAATCGGTTCCCCTT
1 CAGGGGGGAATCGATTCCCC-T
* *
584498 CAAAGGGGGAATCGGTT-CCCT
1 C-AGGGGGGAATCGATTCCCCT
584519 CAGGGGGGAATCGATTCCC
1 CAGGGGGGAATCGATTCCC
584538 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
20 13 0.26
21 20 0.40
22 4 0.08
23 13 0.26
ACGTcount: A:0.17, C:0.25, G:0.36, T:0.22
Consensus pattern (21 bp):
CAGGGGGGAATCGATTCCCCT
Found at i:588376 original size:22 final size:21
Alignment explanation
Indices: 588334--588373 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
588324 GAGTTTGTTT
*
588334 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
588355 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
588374 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:596497 original size:15 final size:15
Alignment explanation
Indices: 596459--596488 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
596449 TAGTAATTGT
596459 ATTGTATATCATATA
1 ATTGTATATCATATA
596474 ATTGTATATCATATA
1 ATTGTATATCATATA
596489 GTTTCATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (15 bp):
ATTGTATATCATATA
Done.