Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006034.1 Hibiscus syriacus cultivar Beakdansim tig00014242_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: 79880
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2924 original size:23 final size:24
Alignment explanation
Indices: 2875--2929 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
2865 ATAGCTGTGA
*
2875 TTTTTCTTAGCTACTGCAGTTTGT
1 TTTTTCATAGCTACTGCAGTTTGT
*
2899 TTTTTCATAGCTACTGCAGTTTTT
1 TTTTTCATAGCTACTGCAGTTTGT
2923 TTTTTCA
1 TTTTTCA
2930 AGTTGCCATA
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:0.15, C:0.16, G:0.13, T:0.56
Consensus pattern (24 bp):
TTTTTCATAGCTACTGCAGTTTGT
Found at i:4827 original size:16 final size:17
Alignment explanation
Indices: 4806--4838 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
4796 CATTATATTT
4806 AATTTTAATTT-TTATA
1 AATTTTAATTTATTATA
4822 AATTTTAATTTATTATA
1 AATTTTAATTTATTATA
4839 GATCTGCCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTTTAATTTATTATA
Found at i:4883 original size:43 final size:41
Alignment explanation
Indices: 4835--5118 Score: 282
Period size: 43 Copynumber: 6.7 Consensus size: 41
4825 TTTAATTTAT
* * *
4835 TATAGATCTGCCCTTTTGTGGCTTTTGATATAAAAAACGCCGC
1 TATAGATCTGACCTTTTGCGGCGTTTG-T-TAAAAAACGCCGC
* * **
4878 TATAGATCTGTCCTTTTGCGGCGTTTGATCTAAAACGCCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGTTAAAAAACGCCGC
* * *
4919 TATAGATATTGACCTTTTGCGACGTTTGTTCCAAAAAACGACGC
1 TATAGAT-CTGACCTTTTGCGGCGTTTGTT--AAAAAACGCCGC
* * * *
4963 TATAGA-CTGACATTTTACTGCGTTTGTTCCAAAAACGCCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGTT-AAAAAACGCCGC
* * *
5004 TATAGGTCTGACCTTTTGCGGCTTTTGTATCCAAAAACGCCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGT-T-AAAAAACGCCGC
* *
5047 TATATATCTGACCTTTTGCGGCGTTTGTTACAAAAACACCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGTTA-AAAAACGCCGC
* *
5089 TATAGATATCGACATTTTGCGGCGTTTGTT
1 TATAGATCT-GACCTTTTGCGGCGTTTGTT
5119 CCAAAAAAAC
Statistics
Matches: 201, Mismatches: 33, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
41 34 0.17
42 70 0.35
43 82 0.41
44 15 0.07
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.34
Consensus pattern (41 bp):
TATAGATCTGACCTTTTGCGGCGTTTGTTAAAAAACGCCGC
Found at i:4998 original size:85 final size:85
Alignment explanation
Indices: 4866--5153 Score: 339
Period size: 85 Copynumber: 3.4 Consensus size: 85
4856 CTTTTGATAT
* * *
4866 AAAAAACGCCGCTATAGATCTGTCCTTTTGCGGCGTTTGATCTAAAACGCCGCTATAGATATTGA
1 AAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCAAAAACGCCGCTATAGATATTGA
*
4931 CCTTTTGCGACGTTTGTTCC
66 CCTTTTGCGGCGTTTGTTCC
* * * * * *
4951 AAAAAACGACGCTATAGA-CTGACATTTTACTGCGTTTGTTCCAAAAACGCCGCTATAGGT-CTG
1 AAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTT-CAAAAACGCCGCTATAGATATTG
*
5014 ACCTTTTGCGGCTTTTGTATCC
65 ACCTTTTGCGGCGTTTGT-TCC
* * *
5036 -AAAAACGCCGCTATATATCTGACCTTTTGCGGCGTTTGTTACAAAAACACCGCTATAGATATCG
1 AAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTT-CAAAAACGCCGCTATAGATATTG
*
5100 ACATTTTGCGGCGTTTGTTCC
65 ACCTTTTGCGGCGTTTGTTCC
* * * *
5121 AAAAAAACACCACGATAGATCATGACCTATTGC
1 -AAAAAACGCCGCTATAGATC-TGACCTTTTGC
5154 AGTGTTTTCT
Statistics
Matches: 168, Mismatches: 28, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
84 50 0.30
85 76 0.45
86 17 0.10
87 15 0.09
88 10 0.06
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (85 bp):
AAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCAAAAACGCCGCTATAGATATTGA
CCTTTTGCGGCGTTTGTTCC
Found at i:5124 original size:43 final size:42
Alignment explanation
Indices: 4867--5125 Score: 306
Period size: 42 Copynumber: 6.1 Consensus size: 42
4857 TTTTGATATA
* * *
4867 AAAAACGCCGCTATAGATCTGTCCTTTTGCGGCGTTTGAT-C
1 AAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCC
* *
4908 TAAAACGCCGCTATAGATATTGACCTTTTGCGACGTTTGTTCC
1 AAAAACGCCGCTATAGATA-TGACCTTTTGCGGCGTTTGTTCC
* * * * *
4951 AAAAAACGACGCTATAGA-CTGACATTTTACTGCGTTTGTTCC
1 -AAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCC
* * *
4993 AAAAACGCCGCTATAGGTCTGACCTTTTGCGGCTTTTGTATCC
1 AAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGT-TCC
* * *
5036 AAAAACGCCGCTATATATCTGACCTTTTGCGGCGTTTGTTAC
1 AAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCC
* *
5078 AAAAACACCGCTATAGATATCGACATTTTGCGGCGTTTGTTCC
1 AAAAACGCCGCTATAGATAT-GACCTTTTGCGGCGTTTGTTCC
5121 AAAAA
1 AAAAA
5126 AACACCACGA
Statistics
Matches: 185, Mismatches: 27, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
41 32 0.17
42 73 0.39
43 65 0.35
44 15 0.08
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (42 bp):
AAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCC
Found at i:5678 original size:15 final size:16
Alignment explanation
Indices: 5654--5688 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
5644 ATTTTATAAA
*
5654 AATATATTATTATTTT
1 AATATATTATTATTAT
5670 AATAT-TTATTATTAT
1 AATATATTATTATTAT
5685 AATA
1 AATA
5689 ATAATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATATATTATTATTAT
Found at i:5690 original size:18 final size:18
Alignment explanation
Indices: 5639--5696 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
5629 GGATTAATTT
*
5639 TATTTATT-TTATAAAAA
1 TATTTATTATTATAATAA
5656 TATATTATTATT-T--TAA
1 TAT-TTATTATTATAATAA
5672 TATTTATTATTATAATAA
1 TATTTATTATTATAATAA
5690 TAATTTA
1 T-ATTTA
5697 ATTAAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
15 8 0.24
16 6 0.18
17 3 0.09
18 10 0.29
19 7 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTATTATTATAATAA
Found at i:7976 original size:19 final size:18
Alignment explanation
Indices: 7943--7979 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
7933 TTAATTCATT
*
7943 TTTATTTCGTATTGATTA
1 TTTATATCGTATTGATTA
7961 TTTATATCGATATTGATTA
1 TTTATATCG-TATTGATTA
7980 ACCCTATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (18 bp):
TTTATATCGTATTGATTA
Found at i:23381 original size:19 final size:21
Alignment explanation
Indices: 23339--23383 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
23329 ATCACAATTG
23339 AATTTGCCACGACATTTCATTC
1 AATTTGCCACGACA-TTCATTC
23361 AATTTGCCACGACA-T-ATTC
1 AATTTGCCACGACATTCATTC
23380 AATT
1 AATT
23384 GCAACCACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.35
20 1 0.04
22 14 0.61
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (21 bp):
AATTTGCCACGACATTCATTC
Found at i:24435 original size:35 final size:29
Alignment explanation
Indices: 24349--24440 Score: 175
Period size: 29 Copynumber: 3.1 Consensus size: 29
24339 TGGATTCTAA
24349 CATAAAAATAAAAAAATGTTGCATTTGCAC
1 CATAAAAAT-AAAAAATGTTGCATTTGCAC
24379 CATAAAAATAAAAAATGTTGCATTTGCAC
1 CATAAAAATAAAAAATGTTGCATTTGCAC
24408 CATAAAAATAAAAAATGTTGCATTTGCAC
1 CATAAAAATAAAAAATGTTGCATTTGCAC
24437 CATA
1 CATA
24441 TTTTCCATGC
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 53 0.85
30 9 0.15
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.27
Consensus pattern (29 bp):
CATAAAAATAAAAAATGTTGCATTTGCAC
Found at i:36788 original size:2 final size:2
Alignment explanation
Indices: 36783--36824 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
36773 ATTAGCAGTT
36783 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
36825 ATGATTAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39115 original size:3 final size:3
Alignment explanation
Indices: 39107--39154 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
39097 TCTAAGATAT
* *
39107 ATA ATA ATA ATA ATA ATA TTA TTAA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA
39153 AT
1 AT
39155 TGTTTTCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 40 0.95
4 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:39623 original size:19 final size:18
Alignment explanation
Indices: 39590--39629 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
39580 TTCATAATTT
*
39590 AATTTGTATTGTGAATAG
1 AATTTGTAATGTGAATAG
39608 AATTTGATAATGTGAATAG
1 AATTTG-TAATGTGAATAG
39627 AAT
1 AAT
39630 AAGTTGATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (18 bp):
AATTTGTAATGTGAATAG
Found at i:39647 original size:22 final size:21
Alignment explanation
Indices: 39622--39662 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
39612 TGATAATGTG
*
39622 AATAGAATAAGTTGATGTTATA
1 AATAAAATAAGTTG-TGTTATA
39644 AATAAAATAAGTTGTGTTA
1 AATAAAATAAGTTGTGTTA
39663 GAAGGGTTAT
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:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (21 bp):
AATAAAATAAGTTGTGTTATA
Found at i:44374 original size:26 final size:26
Alignment explanation
Indices: 44321--44376 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
44311 CAAATTTCTT
* * * * *
44321 AAAAATATTTAAAAATTTATATTTTA
1 AAAAATATTAAAAAAATTAAACTATA
44347 AAAAATATTAAAAAAATTAAACTATA
1 AAAAATATTAAAAAAATTAAACTATA
44373 AAAA
1 AAAA
44377 CTAACATCAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (26 bp):
AAAAATATTAAAAAAATTAAACTATA
Found at i:46148 original size:16 final size:17
Alignment explanation
Indices: 46124--46165 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
46114 ACTTCCCAAC
46124 TTTTATTTTATTA-GTG
1 TTTTATTTTATTATGTG
* *
46140 TTTTGTTTTTTTATGTG
1 TTTTATTTTATTATGTG
46157 -TTTATTTTA
1 TTTTATTTTA
46166 GGTATAGTGC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.14, C:0.00, G:0.12, T:0.74
Consensus pattern (17 bp):
TTTTATTTTATTATGTG
Found at i:47307 original size:3 final size:3
Alignment explanation
Indices: 47299--47355 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
47289 AAAATCTTTC
47299 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
47347 AAT AAT AAT
1 AAT AAT AAT
47356 CAACAGAAAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:48801 original size:23 final size:22
Alignment explanation
Indices: 48773--48826 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 22
48763 ATCCCGATTT
* * *
48773 TATTATTTTATTATTATAATAA
1 TATTATTTTATTACTAAAAAAA
48795 TAATTATTATTATTACTAAAAAAA
1 T-ATTATT-TTATTACTAAAAAAA
48819 TATTATTT
1 TATTATTT
48827 ACAAACAGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 2 0.07
23 12 0.44
24 13 0.48
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTATTTTATTACTAAAAAAA
Found at i:48806 original size:21 final size:20
Alignment explanation
Indices: 48780--48825 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
48770 TTTTATTATT
*
48780 TTATTATTA-TAATAATAATTA
1 TTATTATTACTAA-AA-AAATA
48801 TTATTATTACTAAAAAAATA
1 TTATTATTACTAAAAAAATA
48821 TTATT
1 TTATT
48826 TACAAACAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 9 0.39
21 11 0.48
22 3 0.13
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATTATTACTAAAAAAATA
Found at i:49244 original size:24 final size:24
Alignment explanation
Indices: 49209--49279 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 24
49199 TGCAAAGAAA
* *
49209 AAAAAAGGAGGAGACAGAGAGTAG
1 AAAAAAGAAGGAGACAGAGAGCAG
49233 AAAAAAGAA-G-GACAGAGAGCAG
1 AAAAAAGAAGGAGACAGAGAGCAG
* *
49255 AAAAACGGAGAGGAGACGGAGAGCA
1 AAAAA-AGA-AGGAGACAGAGAGCA
49280 ACCCAAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 16 0.41
23 3 0.08
24 9 0.23
25 1 0.03
26 10 0.26
ACGTcount: A:0.54, C:0.08, G:0.37, T:0.01
Consensus pattern (24 bp):
AAAAAAGAAGGAGACAGAGAGCAG
Found at i:49898 original size:15 final size:15
Alignment explanation
Indices: 49880--49910 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
49870 TTTAGTCCTT
49880 TATATTAAATAAATA
1 TATATTAAATAAATA
*
49895 TATATTAGATAAATA
1 TATATTAAATAAATA
49910 T
1 T
49911 CGTATTTAGT
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:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
TATATTAAATAAATA
Found at i:50138 original size:26 final size:26
Alignment explanation
Indices: 50083--50150 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 26
50073 ATTGCAATTT
*
50083 TATT-TTATTATTATATATTTAAATTA
1 TATTATTATTATTAT-TATTTAAATCA
*
50109 -ATTATTATTATTATTATTTTAATCA
1 TATTATTATTATTATTATTTAAATCA
*
50134 TATTAATATATATTATT
1 TATTATTAT-TATTATT
50151 TGATTAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
25 12 0.33
26 17 0.47
27 7 0.19
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (26 bp):
TATTATTATTATTATTATTTAAATCA
Found at i:50256 original size:150 final size:148
Alignment explanation
Indices: 50147--50434 Score: 345
Period size: 149 Copynumber: 1.9 Consensus size: 148
50137 TAATATATAT
* *
50147 TATTTGATTAAT-TTTATA-A-AAATTTTATAATAATATTTATTTATTTTTTTATATCAAA-GAA
1 TATTTGATTAATGTTTATAGATAAATGTT-T--TAATATTTATTTATTTTTTAATATCAAAGGAA
* * *
50208 AGGGGCAGTCTTAAAGCAACTAGATGTCTGTTTTCTGATATTTTTAAATAAATAAATATTTTAAT
63 A-GAGCAGTCTTAAAGCAACTAGAAG-CTCTTTTCTGATATTTTTAAATAAATAAATATTTTAAT
*
50273 TTTATAAATTGTATATATTAATC
126 TTTATAAATTGAATATATTAATC
** * *
50296 TATTTTTTTATTGTTTCTAGATAAATGTTTTAATATTTATTTATTTTTTAATATCAAAGGAAAGA
1 TATTTGATTAATGTTTATAGATAAATGTTTTAATATTTATTTATTTTTTAATATCAAAGGAAAGA
* * * * *
50361 GCTGTCTTAAAGCACCTAGAAGCTCTTTTCTGATATTTCTAAATAAATAAAAATCTT-ATTTATA
66 GCAGTCTTAAAGCAACTAGAAGCTCTTTTCTGATATTTTTAAATAAATAAATATTTTAATTT-TA
50425 TAAATT-AATA
130 TAAATTGAATA
50435 AATTTACTTA
Statistics
Matches: 119, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
147 7 0.06
148 39 0.33
149 56 0.47
150 9 0.08
151 2 0.02
152 6 0.05
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (148 bp):
TATTTGATTAATGTTTATAGATAAATGTTTTAATATTTATTTATTTTTTAATATCAAAGGAAAGA
GCAGTCTTAAAGCAACTAGAAGCTCTTTTCTGATATTTTTAAATAAATAAATATTTTAATTTTAT
AAATTGAATATATTAATC
Found at i:52575 original size:22 final size:22
Alignment explanation
Indices: 52523--52579 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
52513 GTTACATTCA
* *
52523 CATATTTACATTTGCATTTTTT
1 CATATTTACATTTGCATATTTC
**
52545 TGTATTTACATTTGCATATTTC
1 CATATTTACATTTGCATATTTC
*
52567 CATAATTACATTT
1 CATATTTACATTT
52580 TATTTCAAAC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.26, C:0.14, G:0.05, T:0.54
Consensus pattern (22 bp):
CATATTTACATTTGCATATTTC
Found at i:56967 original size:114 final size:114
Alignment explanation
Indices: 56634--56954 Score: 563
Period size: 114 Copynumber: 2.8 Consensus size: 114
56624 CATGTTCTCG
* *
56634 TAGTAGAAATAA-AGAGCCCCAATAGCATATTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 TAGTAGAAATAAGA-AGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
56698 TGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATTTGCTCA
65 TGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATTTGCTCA
56748 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
56813 GGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATTTGCTCA
66 GGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATTTGCTCA
* *
56862 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
* * *
56927 GGTAGGAACCCCAGAGCCAATCATTGGA
66 GGTATGAACCCCAAAACCAATCATTGGA
56955 ATAGGAAGAT
Statistics
Matches: 199, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
114 198 0.99
115 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31
Consensus pattern (114 bp):
TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
GGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATTTGCTCA
Found at i:59410 original size:22 final size:22
Alignment explanation
Indices: 59385--59460 Score: 107
Period size: 22 Copynumber: 3.5 Consensus size: 22
59375 TCTACACTTC
59385 TCAAAGATGATAGATTCTCTCT
1 TCAAAGATGATAGATTCTCTCT
* * *
59407 TCAAAGCTGATAAACTCTCTCT
1 TCAAAGATGATAGATTCTCTCT
* *
59429 TTAAAGATGATAGATTCTCTTT
1 TCAAAGATGATAGATTCTCTCT
59451 TCAAAGATGA
1 TCAAAGATGA
59461 AAGCTTTATT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (22 bp):
TCAAAGATGATAGATTCTCTCT
Found at i:60277 original size:165 final size:165
Alignment explanation
Indices: 59964--60290 Score: 530
Period size: 165 Copynumber: 2.0 Consensus size: 165
59954 CACAAGAATG
*
59964 AGCATTATCTTGAGATTGAGGCATGTTACCCAATCAACATGTTATTTTGAAAAATAATGAGAAAG
1 AGCATTATCTTGAGATTGAGGCATGTTACCCAATCAACATGTTATTTTGAAAAATAATGAGAAAA
* ** *
60029 TGATTTCCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACAATT
66 CGATTTCCATAGTTTCTCATTCAATCTTTACTAAAATGAAATTGTTGAAAAGTAAGAAAACAATT
* * *
60094 TCCTTAGTTTTTTTACTTAGTAAACTATTTCCAAC
131 TCCATAGTTATCTTACTTAGTAAACTATTTCCAAC
*
60129 AGCATTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTTGAAAAATAATGAGAAAA
1 AGCATTATCTTGAGATTGAGGCATGTTACCCAATCAACATGTTATTTTGAAAAATAATGAGAAAA
* *
60194 CGATTTTCATAGTTTCTCATTCAATCTTTACTGAAAATGAAATTGTTGAAAAGTAAGAAAACGAT
66 CGATTTCCATAGTTTCTCATTCAATCTTTACT-AAAATGAAATTGTTGAAAAGTAAGAAAACAAT
*
60259 TTCCATAG-TATCTTACTTAGTAAATTATTTCC
130 TTCCATAGTTATCTTACTTAGTAAACTATTTCC
60291 CACATCCATA
Statistics
Matches: 149, Mismatches: 12, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
165 111 0.74
166 38 0.26
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (165 bp):
AGCATTATCTTGAGATTGAGGCATGTTACCCAATCAACATGTTATTTTGAAAAATAATGAGAAAA
CGATTTCCATAGTTTCTCATTCAATCTTTACTAAAATGAAATTGTTGAAAAGTAAGAAAACAATT
TCCATAGTTATCTTACTTAGTAAACTATTTCCAAC
Found at i:60372 original size:36 final size:36
Alignment explanation
Indices: 60332--60450 Score: 130
Period size: 36 Copynumber: 3.3 Consensus size: 36
60322 TTTAAATAGC
60332 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
* * * ** ** **
60368 AATTTGTCTCGCTCGAGACAGTTTCACTCGAAACAGA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACA-A
*
60405 ACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
*
60441 AATTTGTCTC
1 AATTTATCTC
60451 GCTCGAGACA
Statistics
Matches: 61, Mismatches: 21, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
36 35 0.57
37 26 0.43
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (36 bp):
AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
Found at i:60453 original size:73 final size:73
Alignment explanation
Indices: 60334--60478 Score: 281
Period size: 73 Copynumber: 2.0 Consensus size: 73
60324 TAAATAGCAA
*
60334 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTCGAGACAGTTTCACTCGA
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTCGAGACAGTCTCACTCGA
60399 AACAGAAC
66 AACAGAAC
60407 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTCGAGACAGTCTCACTCGA
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTCGAGACAGTCTCACTCGA
60472 AACAGAA
66 AACAGAA
60479 ATTTCCATCA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (73 bp):
TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTCGAGACAGTCTCACTCGA
AACAGAAC
Found at i:60475 original size:36 final size:37
Alignment explanation
Indices: 60362--60482 Score: 129
Period size: 37 Copynumber: 3.3 Consensus size: 37
60352 GTTTTTCTTA
60362 AAACA-AAATTTGTCTCGCTCGAGACAGTTTCACTCG
1 AAACAGAAATTTGTCTCGCTCGAGACAGTTTCACTCG
* * * * ** ** **
60398 AAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTA
1 AAACAGAAATTTGTCTCGCTCGAGACAGTTTCACTCG
*
60435 AAACA-AAATTTGTCTCGCTCGAGACAGTCTCACTCG
1 AAACAGAAATTTGTCTCGCTCGAGACAGTTTCACTCG
60471 AAACAGAAATTT
1 AAACAGAAATTT
60483 CCATCACCTG
Statistics
Matches: 62, Mismatches: 21, Indels: 3
0.72 0.24 0.03
Matches are distributed among these distances:
36 30 0.48
37 32 0.52
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (37 bp):
AAACAGAAATTTGTCTCGCTCGAGACAGTTTCACTCG
Found at i:60646 original size:114 final size:114
Alignment explanation
Indices: 60484--60791 Score: 535
Period size: 114 Copynumber: 2.7 Consensus size: 114
60474 CAGAAATTTC
* * *
60484 CATCACCTGATGGATCAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTAAAGAAGGA
1 CATCACTTGATGGATCAGCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
60549 AGAAGAAATTCATAATGAGAAGAATTTGTTCCAACCTTTTGCTCGAATT
66 AGAACAAATTCATAATGAGAAGAATTTGTTCCAACCTTTTGCTCGAATT
* *
60598 CATTACTTGATGGATCAGCATTTCCAGGTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGA
1 CATCACTTGATGGATCAGCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
60663 AGAATAAATTCATAATGAGAAGAATTTGTTCCAACCTTTTGCTCGAATT
66 AGAACAAATTCATAATGAGAAGAATTTGTTCCAACCTTTTGCTCGAATT
*
60712 CATCACTTGATGGATCAGTATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAGCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
60777 ATAACAAATTCATAA
66 AGAACAAATTCATAA
60792 GAGTTCATAA
Statistics
Matches: 183, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 183 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.28
Consensus pattern (114 bp):
CATCACTTGATGGATCAGCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAACAAATTCATAATGAGAAGAATTTGTTCCAACCTTTTGCTCGAATT
Found at i:60800 original size:50 final size:50
Alignment explanation
Indices: 60741--60841 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
60731 ATTTCCAGGT
60741 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAACAAATTCATA
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAACAAATTCATA
*
60791 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAATTCATA
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAACAAATTCATA
60841 A
1 A
60842 TGAGAAGAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.22
Consensus pattern (50 bp):
AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAACAAATTCATA
Found at i:60902 original size:164 final size:164
Alignment explanation
Indices: 60627--60955 Score: 518
Period size: 164 Copynumber: 2.0 Consensus size: 164
60617 ATTTCCAGGT
* *
60627 AGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAATAAATTCATAATGAGAAGAATTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
* * *
60692 TCCAACCTTTTGCTCGAATTCATCACTTGATGGATCAGTATTTCCAG-GTAGAGTTCATAATGAG
66 TCCAACCTTTTGCTCGAATTCATCACTCGATGGATCACTATTTCCAGAG-AAAGTTCATAATGAG
* *
60756 AAGAACTCATCTGAAGAAGGAATAACAAATTCATA
130 AAGAACTCATCTGAAGAAAGAAGAACAAATTCATA
*
60791 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAATTCATAATGAGAAGAATTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
* *
60856 TCCAACCTTTTGTTTGAATTCATCACTCGATGGATCAACT-TTTCCAGAGAAAGTTCATAATGAG
66 TCCAACCTTTTGCTCGAATTCATCACTCGATGGATC-ACTATTTCCAGAGAAAGTTCATAATGAG
* *
60920 AAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATA
130 AAGAACTCATCTGAAGAAAGAAGAACAAATTCATA
60955 A
1 A
60956 TGAGAAGAGC
Statistics
Matches: 151, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
164 148 0.98
165 3 0.02
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27
Consensus pattern (164 bp):
AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
TCCAACCTTTTGCTCGAATTCATCACTCGATGGATCACTATTTCCAGAGAAAGTTCATAATGAGA
AGAACTCATCTGAAGAAAGAAGAACAAATTCATA
Found at i:61029 original size:124 final size:123
Alignment explanation
Indices: 60889--61224 Score: 557
Period size: 122 Copynumber: 2.7 Consensus size: 123
60879 CACTCGATGG
60889 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AAGAAGAAGAAGTTCAT
* *
60954 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAAC
65 AATGAGAAGAACTTGTTCAACCTTTTGCATAACTCTATCACAAAAGGAGATAGATCAAC
* * *
61013 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
*
61078 ATGAGAAGAACTTGTTCAACC-TTTGCATGACTCTATCACAAAAGGAGATAGATCAAC
66 ATGAGAAGAACTTGTTCAACCTTTTGCATAACTCTATCACAAAAGGAGATAGATCAAC
* * * *
61135 ATCAACATTTCTAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGACGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
*
61200 ATGAGAAGAACTTGTTCAAACTTTT
66 ATGAGAAGAACTTGTTCAACCTTTT
61225 TGCTAGATTA
Statistics
Matches: 198, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
122 113 0.57
123 39 0.20
124 46 0.23
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (123 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGCATAACTCTATCACAAAAGGAGATAGATCAAC
Found at i:61480 original size:19 final size:21
Alignment explanation
Indices: 61437--61481 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
61427 TTTTATTATT
61437 TTATTATTATAATAATAATTA
1 TTATTATTATAATAATAATTA
61458 TTATTATTACTAA-AA-AA-TA
1 TTATTATTA-TAATAATAATTA
61477 TTATT
1 TTATT
61482 TACAAACAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.30
20 2 0.09
21 11 0.48
22 3 0.13
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TTATTATTATAATAATAATTA
Found at i:61902 original size:22 final size:23
Alignment explanation
Indices: 61866--61935 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
61856 GCAAAGAAAA
* *
61866 AAAAAAGAGGAGACAGAGAGTAG
1 AAAAAAGAAGAGACAGAGAGCAG
61889 AAAAAAGAAG-GACAGAGAGCAG
1 AAAAAAGAAGAGACAGAGAGCAG
*
61911 AAAAATAGAGAAGAGACGGAGAGCA
1 -AAAA-A-AGAAGAGACAGAGAGCA
61936 ACCCAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
22 11 0.28
23 13 0.32
24 1 0.03
25 5 0.12
26 10 0.25
ACGTcount: A:0.57, C:0.07, G:0.33, T:0.03
Consensus pattern (23 bp):
AAAAAAGAAGAGACAGAGAGCAG
Found at i:61925 original size:20 final size:20
Alignment explanation
Indices: 61875--61926 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
61865 AAAAAAAGAG
*
61875 GAGACAGAGAGTAGAAAAAA
1 GAGACAGAGAGCAGAAAAAA
61895 GAAGGACAGAGAGCAGAAAAATA
1 G-A-GACAGAGAGCAGAAAAA-A
61918 GAGA-AGAGA
1 GAGACAGAGA
61927 CGGAGAGCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 6 0.21
21 3 0.11
22 17 0.61
23 2 0.07
ACGTcount: A:0.58, C:0.06, G:0.33, T:0.04
Consensus pattern (20 bp):
GAGACAGAGAGCAGAAAAAA
Found at i:62945 original size:146 final size:147
Alignment explanation
Indices: 62773--63061 Score: 381
Period size: 147 Copynumber: 2.0 Consensus size: 147
62763 TATTTTAATC
*
62773 ATATTAATATATATTTGATTAATTTTATAAAAAT-TTTATAATATTTATTTA-TTTTT-ATATCA
1 ATATTAATATATATTTGATTAATTTTAGAAAAATGTTT-TAATATTTATTTATTTTTTAATATCA
* * * * *
62835 AA-GAAAGGGGCAGTCTTAAAGCAACTAGATGTCTGTTTTCTGATATTTTTAAATAAATAAATAT
65 AATGAAA-GAGCAGTCTTAAAGCAACTAGAAG-CTCTTTTCTGATATTTCTAAATAAATAAAAAT
*
62899 TTTACTTT-TATAAATTGTAT
128 CTTA-TTTATATAAATTGTAT
* * * * *
62919 ATATTAATCTATTTTTTATTATTTTTAGATAAATGTTTTAATATTTATTTATTTTTTAATATCAA
1 ATATTAATATATATTTGATTAATTTTAGAAAAATGTTTTAATATTTATTTATTTTTTAATATCAA
* *
62984 ATGAAAGAGCTGTCTTAAAGCACCTAGAAGCTCTTTTCTGATATTTCTAAATAAATAAAAATCTT
66 ATGAAAGAGCAGTCTTAAAGCAACTAGAAGCTCTTTTCTGATATTTCTAAATAAATAAAAATCTT
63049 ATTTATATAAATT
131 ATTTATATAAATT
63062 AATAAATTTA
Statistics
Matches: 124, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
146 44 0.35
147 48 0.39
148 28 0.23
149 4 0.03
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (147 bp):
ATATTAATATATATTTGATTAATTTTAGAAAAATGTTTTAATATTTATTTATTTTTTAATATCAA
ATGAAAGAGCAGTCTTAAAGCAACTAGAAGCTCTTTTCTGATATTTCTAAATAAATAAAAATCTT
ATTTATATAAATTGTAT
Found at i:66404 original size:95 final size:95
Alignment explanation
Indices: 66222--66405 Score: 223
Period size: 95 Copynumber: 1.9 Consensus size: 95
66212 TCTTCTTCTA
* * *
66222 TGATGTAATTGAGCAAAAAGTTGAACAAATTCTTCTTCTTTTTCATATGAGTTCTTCTCATTATG
1 TGATGTAATTGAGCAAAAAGTTGAACAAATTCTTCTTCTTCTTCAGATGAGTTATTCTCATTATG
** *
66287 AACTTTCTCTGGCAACGCTGATCCATCGGG
66 AACTTTCTCTGAAAACACTGATCCATCGGG
*
66317 TGATG-AATTTGAGC-AAAAGATTGAACAAGTTCTTC-TCATTCTTCAGATGAGTTATTCTCATT
1 TGATGTAA-TTGAGCAAAAAG-TTGAACAAATTCTTCTTC-TTCTTCAGATGAGTTATTCTCATT
* *
66379 ATGAA-TTTCCTCTGAAAATATTGATCC
63 ATGAACTTT-CTCTGAAAACACTGATCC
66406 TCAAATAAGG
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
94 12 0.16
95 64 0.84
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (95 bp):
TGATGTAATTGAGCAAAAAGTTGAACAAATTCTTCTTCTTCTTCAGATGAGTTATTCTCATTATG
AACTTTCTCTGAAAACACTGATCCATCGGG
Found at i:66815 original size:113 final size:113
Alignment explanation
Indices: 66575--67698 Score: 1712
Period size: 113 Copynumber: 10.0 Consensus size: 113
66565 TAGAGTTATG
** *
66575 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
** * * * * *
66639 TTATGAAC-ACTTCTGGCAACA-CTGATCCATCGGGTGATGAATTTGAG
66 TTATGAACTTTTTCTGG-AAAAGCTGATCCATCAGATGATGGATTTGAA
* * * *
66686 CAAAAGATTGAACAAGTTCTTCGCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
**** * * * * * *
66751 TTATGAACTCGACCTGGCAATGTTGATTCATC-GAATGAT-GAATTCAA
66 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAG-ATGATGGATTTGAA
* * * *
66798 GCGAAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCT
1 -C-AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
** * * ** *
66862 CATTATGAAC-ACTTCTGG-AAAGATTGATCC-TCAAATGATATATTTGAG
64 CATTATGAACTTTTTCTGGAAAAG-CTGATCCATCAGATGATGGATTTGAA
*
66910 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
66975 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAG
66 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAA
* *
67023 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTTTTCTTA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
67088 TTATGAACTTTTTCTGGAAAAGCTGATCTATCAGATGATGGATTTGAA
66 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAA
67136 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
67201 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAA
66 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAA
*
67249 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
67314 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAA
66 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAA
*
67362 CAAAAGGTTGAACAAATTCTTCTTATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
67427 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAA
66 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAA
67475 CAAAAGGTTGAACAAATTC-T-TCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
67538 TTATGAACTTTTTTTGGAAAAGTTGATCCATCAGTTGATGGATTTGAA
66 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAA
67586 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
67651 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAGGTGATGGATTTGAA
66 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAA
67699 TCTTTGCTAA
Statistics
Matches: 937, Mismatches: 61, Indels: 28
0.91 0.06 0.03
Matches are distributed among these distances:
110 4 0.00
111 217 0.23
112 65 0.07
113 647 0.69
114 4 0.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAA
Found at i:66912 original size:224 final size:226
Alignment explanation
Indices: 66575--67698 Score: 1685
Period size: 224 Copynumber: 5.0 Consensus size: 226
66565 TAGAGTTATG
** *
66575 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
** * * * * * * *
66639 TTATGAAC-ACTTCTGGCAACA-CTGATCCATCGGGTGATGAATTTGAGCAAAAGATTGAACAAG
66 TTATGAACTTTTTCTGG-AAAAGCTGATCCATCAGATGATGGATTTGAACAAAAGGTTGAACAAA
* * ****
66702 TTCTTCGCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTG
130 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTG
* * * * *
66767 GCAATGTTGATTCATC-GAATGAT-GAATTCAA
195 GAAAAGCTGATCCATCAG-ATGATGGAATTGAA
* * * *
66798 GCGAAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCT
1 -C-AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
** * * ** *
66862 CATTATGAAC-ACTTCTGG-AAAGATTGATCC-TCAAATGATATATTTGAGCAAAAGGTTGAACA
64 CATTATGAACTTTTTCTGGAAAAG-CTGATCCATCAGATGATGGATTTGAACAAAAGGTTGAACA
*
66924 AATTCTTCTCATTATGAATTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTC
128 AATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTC
* *
66989 TGGAAAAGCTGATCCATCAGATGATGGATTTGAG
193 TGGAAAAGCTGATCCATCAGATGATGGAATTGAA
* *
67023 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTTTTCTTA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
67088 TTATGAACTTTTTCTGGAAAAGCTGATCTATCAGATGATGGATTTGAACAAAAGGTTGAACAAAT
66 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAACAAAAGGTTGAACAAAT
67153 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
131 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
*
67218 AAAAGCTGATCCATCAGATGATGGATTTGAA
196 AAAAGCTGATCCATCAGATGATGGAATTGAA
*
67249 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
67314 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAACAAAAGGTTGAACAAAT
66 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAACAAAAGGTTGAACAAAT
*
67379 TCTTCTTATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
131 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
*
67444 AAAAGCTGATCCATCAGATGATGGATTTGAA
196 AAAAGCTGATCCATCAGATGATGGAATTGAA
67475 CAAAAGGTTGAACAAATTC-T-TCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
67538 TTATGAACTTTTTTTGGAAAAGTTGATCCATCAGTTGATGGATTTGAACAAAAGGTTGAACAAAT
66 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAACAAAAGGTTGAACAAAT
67603 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
131 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
* *
67668 AAAAGCTGATCCATCAGGTGATGGATTTGAA
196 AAAAGCTGATCCATCAGATGATGGAATTGAA
67699 TCTTTGCTAA
Statistics
Matches: 839, Mismatches: 51, Indels: 20
0.92 0.06 0.02
Matches are distributed among these distances:
223 6 0.01
224 396 0.47
225 66 0.08
226 371 0.44
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (226 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAACAAAAGGTTGAACAAAT
TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG
AAAAGCTGATCCATCAGATGATGGAATTGAA
Found at i:67301 original size:563 final size:561
Alignment explanation
Indices: 66455--67698 Score: 1729
Period size: 563 Copynumber: 2.2 Consensus size: 561
66445 GAATCAATGC
* *
66455 AAGGTTGAACAAGTTCTTCTCATTATGAATTTTCTT-TTCC-TCTTCAGATAAGTTCTTCTCATT
1 AAGGTTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * *
66518 ATGAACTTTCTCTGGAAAAGTTGGTGTTGATCTATCTCCTTCTG-TGATAGAGTTATG--CAAAA
65 ATGAACTTTTTCTGGAAAA------GCTG----A--TCCATCAGATGATGGA-TT-TGAACAAAA
*
66580 GGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGA
116 GGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGA
* * * * *
66645 ACACTTCTGGCAACACTGATCCATCGGGTGATGAATTTGAGCAAAAGATTGAACAAGTTCTTCGC
181 ACACTTCTGGCAAAACTGATCCATCAGATGATGAATTTGAACAAAAGATTGAACAAATTCTTCGC
* * *
66710 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGTT
246 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGAAAAGCT
* *
66775 GATTCATC-GAATGAT-GAATTCAAGCGAAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTT
311 GATCCATCAG-ATGATGGAATTCAA-C-AAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTT
*
66837 CTTCATTCTTCAGATGAGTTCTTCTCATTATGAAC-ACTTCTGG-AAAGATTGATCC-TCAAATG
373 CTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTACTTCTGGAAAAG-CTGATCCATCAAATG
* * *
66899 ATATATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTTTTCCTTCTTCAGATG
437 ATAGATTTGAACAAAAGGTTGAACAAATTC-T-TCATTATGAATTTCTTCTTCCTTCTTCAGATG
*
66964 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGCAA
500 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAACAA
* *
67026 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTTTTCTTATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* *
67091 TGAACTTTTTCTGGAAAAGCTGATCTATCAGATGATGGATTTGAACAAAAGGTTGAACAAATTCT
66 TGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAACAAAAGGTTGAACAAACTCT
* **
67156 TCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGG-AA
131 TCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAAC-ACTTCTGGCAA
* * * *
67220 AAGCTGATCCATCAGATGATGGATTTGAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTC
194 AA-CTGATCCATCAGATGATGAATTTGAACAAAAGATTGAACAAATTCTTCGCATTATGAACTTC
* ****
67285 TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGAT
258 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGAAAAGCTGATCCATCAGAT
* * * *
67350 GATGGATTTGAACAAAAGGTTGAACAAATTCTTCTTATTATGAATTTCTTCTTCCTTCTTCAGAT
323 GATGGAATTCAACAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCATTCTTCAGAT
** * *
67415 GAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAACAAAA
388 GAGTTCTTCTCATTATGAACTACTTCTGGAAAAGCTGATCCATCAAATGATAGATTTGAACAAAA
67480 GGTTGAACAAATTCTTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
453 GGTTGAACAAATTCTTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
67545 CTTTTTTTGGAAAAGTTGATCCATCAGTTGATGGATTTGAACAA
518 CTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAACAA
67589 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
67654 TGAACTTTTTCTGGAAAAGCTGATCCATCAGGTGATGGATTTGAA
66 TGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAA
67699 TCTTTGCTAA
Statistics
Matches: 605, Mismatches: 54, Indels: 36
0.87 0.08 0.05
Matches are distributed among these distances:
559 2 0.00
560 7 0.01
561 44 0.07
562 39 0.06
563 377 0.62
564 20 0.03
565 37 0.06
566 3 0.00
570 6 0.01
571 32 0.05
572 38 0.06
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (561 bp):
AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAACAAAAGGTTGAACAAACTCT
TCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGCAAAA
CTGATCCATCAGATGATGAATTTGAACAAAAGATTGAACAAATTCTTCGCATTATGAACTTCTTC
TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGAAAAGCTGATCCATCAGATGAT
GGAATTCAACAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCATTCTTCAGATGAG
TTCTTCTCATTATGAACTACTTCTGGAAAAGCTGATCCATCAAATGATAGATTTGAACAAAAGGT
TGAACAAATTCTTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
TTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAACAA
Found at i:68120 original size:22 final size:22
Alignment explanation
Indices: 68095--68155 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
68085 TCTGATAAAG
68095 CTTTCATCTTTGAAAAGAGAAT
1 CTTTCATCTTTGAAAAGAGAAT
* *
68117 CTTTCATCTTTAAAAAGGGAAT
1 CTTTCATCTTTGAAAAGAGAAT
*
68139 CTATCATCTTTGAAAAG
1 CTTTCATCTTTGAAAAG
68156 TGTAGATGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (22 bp):
CTTTCATCTTTGAAAAGAGAAT
Found at i:76213 original size:14 final size:14
Alignment explanation
Indices: 76167--76218 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
76157 TTGTGCAATA
* *
76167 CAAATGCAAAGATG
1 CAAATGTAAAAATG
*
76181 CCAAATGT-AATATG
1 -CAAATGTAAAAATG
76195 CAAATGTAAAAATG
1 CAAATGTAAAAATG
*
76209 TAAATGTAAA
1 CAAATGTAAA
76219 TTATTTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 7 0.22
14 19 0.59
15 6 0.19
ACGTcount: A:0.52, C:0.10, G:0.15, T:0.23
Consensus pattern (14 bp):
CAAATGTAAAAATG
Done.