Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005845.1 Hibiscus syriacus cultivar Beakdansim tig00013716_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: 110891
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:8319 original size:21 final size:21
Alignment explanation
Indices: 8293--8334 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
8283 GGTTTATTTT
*
8293 TAAACTTTATTTTAATTATCG
1 TAAACTTTATTTCAATTATCG
*
8314 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
8335 AACTTGAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:8386 original size:33 final size:33
Alignment explanation
Indices: 8329--8431 Score: 147
Period size: 33 Copynumber: 3.2 Consensus size: 33
8319 TTTGTTTCAA
8329 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
*
8361 TTATCGAACTTGGAAATTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
** * *
8394 TTATTAAACTTGGAAGTATTTAAGTATTTCAA-
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
8426 TTATCG
1 TTATCG
8432 TAAATTTTGT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
32 15 0.24
33 47 0.76
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.46
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:12200 original size:13 final size:13
Alignment explanation
Indices: 12182--12208 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12172 CATAGTTGAA
12182 CAGTCTTCATATG
1 CAGTCTTCATATG
12195 CAGTCTTCATATG
1 CAGTCTTCATATG
12208 C
1 C
12209 GCGTCTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:26897 original size:51 final size:50
Alignment explanation
Indices: 26819--27203 Score: 276
Period size: 51 Copynumber: 7.2 Consensus size: 50
26809 AACCCTGAAG
* * *
26819 ATAGGGAGCGGACACATTTTATGAAGA-TCGAGTCTATTACTCTCTGAAGGA
1 ATAGAGAGCGGACACGTTTT-TAAAGATTCGAGTCTA-TACTCTCTGAAGGA
*
26870 ATAGAGAGCGGACACGTTTGTTAAAGATT-GAGTCCTATACTCTCTGAAAGA
1 ATAGAGAGCGGACACGTTT-TTAAAGATTCGAGT-CTATACTCTCTGAAGGA
* * *
26921 ATAGAGAGCGGGC-CTGTTTATTGAAGATTTTCCGAGTTCTATACTCTCTGAAGAA
1 ATAGAGAGCGGACAC-GTTT-TTAAAGA--TT-CGAG-TCTATACTCTCTGAAGGA
* * *
26976 ATAGAGAGCGGACCCGTTTTATAGAAGATTGTTCAAGTCTTAATACTCTCTGAATGA
1 ATAGAGAGCGGACACGTTTT-TA-AAGA---TTCGAGTC-T-ATACTCTCTGAAGGA
* *
27033 ATAGAGAGCAGACACGTTTATTGAAGA-TCGAGTCTTATACTCTCTGAAGGA
1 ATAGAGAGCGGACACGTTT-TTAAAGATTCGAGTC-TATACTCTCTGAAGGA
* * * *
27084 ATAGAGAGCGGACCCGTTTGTTGAAGATTATTTGAGTCTCATACTCTCTGAATGA
1 ATAGAGAGCGGACACGTTT-TT-AA-A-GATTCGAGTCT-ATACTCTCTGAAGGA
* * *
27139 ATAGAGAGCAGACACATTTTATGAAGAATTGTTCGAGTCTTATACT-TCCTGAAGGA
1 ATAGAGAGCGGACACGTTTT-TAAAG-A---TTCGAGTC-TATACTCT-CTGAAGGA
*
27195 ATAGGGAGC
1 ATAGAGAGC
27204 AGACTCGTCA
Statistics
Matches: 271, Mismatches: 35, Indels: 51
0.76 0.10 0.14
Matches are distributed among these distances:
50 1 0.00
51 94 0.35
52 14 0.05
53 5 0.02
54 5 0.02
55 75 0.28
56 41 0.15
57 35 0.13
58 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.30
Consensus pattern (50 bp):
ATAGAGAGCGGACACGTTTTTAAAGATTCGAGTCTATACTCTCTGAAGGA
Found at i:26979 original size:55 final size:51
Alignment explanation
Indices: 26846--27225 Score: 301
Period size: 55 Copynumber: 7.0 Consensus size: 51
26836 TTTATGAAGA
* *
26846 TCGAGTCTATTACTCTCTGAAGGAATAGAGAGCGGACACGTTTGTTAAAGA--T
1 TCGAGTCTA-TACTCTCTGAA-GAATAGAGAGCGGAC-CGTTTATTGAAGATTT
*
26898 T-GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGGCCTGTTTATTGAAGATTT
1 TCGAGT-CTATACTCTCTG-AAGAATAGAGAGCGGACC-GTTTATTGAAGATTT
*
26951 TCCGAGTTCTATACTCTCTGAAGAAATAGAGAGCGGACCCGTTTTATAGAAGATTGT
1 T-CGAG-TCTATACTCTCTGAAG-AATAGAGAGCGGA-CCG-TTTATTGAAGATT-T
* *
27008 TCAAGTCTTAATACTCTCTGAATGAATAGAGAGCAGACACGTTTATTGAAGA---
1 TCGAGTC-T-ATACTCTCTGAA-GAATAGAGAGCGGAC-CGTTTATTGAAGATTT
*
27060 TCGAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTAT
1 TCGAGTC-TATACTCTCTGAA-GAATAGAGAGCGGA-CCGTTTATTGAAGATT-T
* * *
27115 TTGAGTCTCATACTCTCTGAATGAATAGAGAGCAGACACATTT-TATGAAGAATTGT
1 TCGAGTCT-ATACTCTCTGAA-GAATAGAGAGCGGAC-CGTTTAT-TGAAG-ATT-T
* * *
27171 TCGAGTCTTATACT-TCCTGAAGGAATAGGGAGCAGACTCG-TCATTTGAAGATTT
1 TCGAGTC-TATACTCT-CTGAA-GAATAGAGAGCGGAC-CGTTTA-TTGAAGATTT
27225 T
1 T
27226 TCAAGTCTTA
Statistics
Matches: 276, Mismatches: 23, Indels: 56
0.78 0.06 0.16
Matches are distributed among these distances:
50 1 0.00
51 74 0.27
52 15 0.05
53 2 0.01
54 8 0.03
55 75 0.27
56 70 0.25
57 30 0.11
58 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.31
Consensus pattern (51 bp):
TCGAGTCTATACTCTCTGAAGAATAGAGAGCGGACCGTTTATTGAAGATTT
Found at i:27130 original size:163 final size:162
Alignment explanation
Indices: 26856--27207 Score: 471
Period size: 163 Copynumber: 2.2 Consensus size: 162
26846 TCGAGTCTAT
* * *
26856 TACTCTCTGAAGGAATAGAGAGCGGACACGTTTGTTAAAGATTGAGTCCTATACTCTCTGAAAGA
1 TACTCTCTGAAGGAATAGAGAGCAGACACGTTTATTAAAGATCGAGTCCTATACTCTCTGAAAGA
* *
26921 ATAGAGAGCGGGCCTGTTTATTGAAGATTTTCCGAGTTCTATACTCTCTGAA-GAAATAGAGAGC
66 ATAGAGAGCGGACCCGTTTATTGAAGATTTTCCGAGTTCTATACTCTCTGAATG-AATAGAGAGC
* * *
26985 GGACCCGTTTTATAGAAG-ATTGTTCAAGTCTTAA
130 AGACACATTTTAT-GAAGAATTGTTCAAGTCTT-A
* * * *
27019 TACTCTCTGAATGAATAGAGAGCAGACACGTTTATTGAAGATCGAGTCTTATACTCTCTGAAGGA
1 TACTCTCTGAAGGAATAGAGAGCAGACACGTTTATTAAAGATCGAGTCCTATACTCTCTGAAAGA
* *
27084 ATAGAGAGCGGACCCGTTTGTTGAAGATTATT-TGAG-TCTCATACTCTCTGAATGAATAGAGAG
66 ATAGAGAGCGGACCCGTTTATTGAAGATT-TTCCGAGTTCT-ATACTCTCTGAATGAATAGAGAG
*
27147 CAGACACATTTTATGAAGAATTGTTCGAGTCTTA
129 CAGACACATTTTATGAAGAATTGTTCAAGTCTTA
*
27181 TACT-TCCTGAAGGAATAGGGAGCAGAC
1 TACTCT-CTGAAGGAATAGAGAGCAGAC
27208 TCGTCATTTG
Statistics
Matches: 167, Mismatches: 17, Indels: 11
0.86 0.09 0.06
Matches are distributed among these distances:
161 1 0.01
162 31 0.19
163 132 0.79
164 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (162 bp):
TACTCTCTGAAGGAATAGAGAGCAGACACGTTTATTAAAGATCGAGTCCTATACTCTCTGAAAGA
ATAGAGAGCGGACCCGTTTATTGAAGATTTTCCGAGTTCTATACTCTCTGAATGAATAGAGAGCA
GACACATTTTATGAAGAATTGTTCAAGTCTTA
Found at i:38354 original size:21 final size:21
Alignment explanation
Indices: 38302--38355 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
38292 CGGTAAAACG
* * *
38302 CTACTTAAAATGTTATTTTTT
1 CTACCTAAAATGTTAATTTTA
*
38323 CTATC-AGAAATGTTAATTTTA
1 CTACCTA-AAATGTTAATTTTA
38344 CTACCTAAAATG
1 CTACCTAAAATG
38356 AATATTTCCG
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.44
Consensus pattern (21 bp):
CTACCTAAAATGTTAATTTTA
Found at i:38470 original size:47 final size:47
Alignment explanation
Indices: 38364--38453 Score: 137
Period size: 47 Copynumber: 1.9 Consensus size: 47
38354 TGAATATTTC
* * *
38364 CGATATTAACATTTCTGGTAGAAAAAAGTAAAATTTTAGGTAGCAGT
1 CGATAATAATATTTCCGGTAGAAAAAAGTAAAATTTTAGGTAGCAGT
*
38411 CGATAATAATATTTCCGGTAGAAAAAA-TAACATTTTAGGTAGC
1 CGATAATAATATTTCCGGTAGAAAAAAGTAAAATTTTAGGTAGC
38454 GCTCTACTAG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 15 0.38
47 24 0.62
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (47 bp):
CGATAATAATATTTCCGGTAGAAAAAAGTAAAATTTTAGGTAGCAGT
Found at i:39667 original size:20 final size:20
Alignment explanation
Indices: 39642--39712 Score: 133
Period size: 20 Copynumber: 3.5 Consensus size: 20
39632 TGGGAAAATT
39642 GCAATGCGATACTGACTATC
1 GCAATGCGATACTGACTATC
39662 GCAATGCGATACTGACTATC
1 GCAATGCGATACTGACTATC
*
39682 GCAATGCGATACTTACTATC
1 GCAATGCGATACTGACTATC
39702 GCAATGCGATA
1 GCAATGCGATA
39713 ATACAAAATC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (20 bp):
GCAATGCGATACTGACTATC
Found at i:40301 original size:20 final size:19
Alignment explanation
Indices: 40198--40323 Score: 145
Period size: 19 Copynumber: 6.8 Consensus size: 19
40188 CAAAATCACA
40198 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
40217 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
40236 TTGCGATTTTTATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
40255 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
**
40269 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
* *
40289 TTGCGATTCTCATTATCTCG
1 TTGCGATTTTCATT-TCGCG
40309 TTGCGATTTTCATTT
1 TTGCGATTTTCATTT
40324 TAACCAAAAG
Statistics
Matches: 91, Mismatches: 9, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
14 10 0.11
16 2 0.02
17 2 0.02
19 45 0.49
20 31 0.34
21 1 0.01
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:42190 original size:93 final size:89
Alignment explanation
Indices: 42009--42191 Score: 269
Period size: 93 Copynumber: 2.0 Consensus size: 89
41999 TAGATTGCTT
42009 AGTAAATTTATTCGGTTGCTGCCAAAACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
1 AGTAAATTTATTCGGTTGCTGCCAAAACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
*
42074 GTCTTTTGTTTTGTCTTTGGTTGA
66 GTCTTTTGTTTTATCTTTGGTTGA
** * *
42098 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACATTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAAAACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
42163 ATTTGTC-TTTGTTTTATCTTTTGGTTGA
62 ATTTGTCTTTTGTTTTATC-TTTGGTTGA
42191 A
1 A
42192 AGTTTGAAAT
Statistics
Matches: 84, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
89 34 0.40
91 3 0.04
92 12 0.14
93 35 0.42
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (89 bp):
AGTAAATTTATTCGGTTGCTGCCAAAACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
GTCTTTTGTTTTATCTTTGGTTGA
Found at i:42489 original size:42 final size:42
Alignment explanation
Indices: 42413--42492 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
42403 GACTCGCCTG
* * *
42413 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * *
42455 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
42493 ATTGTCATCG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.21, C:0.39, G:0.17, T:0.23
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:43908 original size:14 final size:14
Alignment explanation
Indices: 43889--43924 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
43879 ATTGTTTAAT
43889 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
43903 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
43917 TGATTTGT
1 TGATTTGT
43925 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:44055 original size:19 final size:19
Alignment explanation
Indices: 44031--44077 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
44021 AAAAAGTACT
*
44031 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
44050 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
44069 ATCGCAACG
1 ATCGCAACG
44078 AGAGAATCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:44148 original size:33 final size:32
Alignment explanation
Indices: 44106--44233 Score: 186
Period size: 33 Copynumber: 3.9 Consensus size: 32
44096 ATTAAATTCG
44106 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
44139 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
44172 CGTTGCGATTTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGA-TTTTCATTTCGCATTGCGATTC-CT
44206 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
44234 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
32 3 0.03
33 54 0.63
34 26 0.30
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:44198 original size:67 final size:66
Alignment explanation
Indices: 44099--44232 Score: 241
Period size: 67 Copynumber: 2.0 Consensus size: 66
44089 ACGCGAAATT
*
44099 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
44164 G
66 G
*
44165 AAATTAGCGTTGCGATTTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTG
1 AAATTAGCGTTGCGA-TTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTG
44230 CG
65 CG
44232 A
1 A
44233 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
66 14 0.22
67 51 0.78
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:45312 original size:20 final size:20
Alignment explanation
Indices: 45289--45333 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
45279 AATGAAAATA
45289 GCAACACGAAAATGACTATC
1 GCAACACGAAAATGACTATC
* **
45309 GCAACGCGAATTTGACTATC
1 GCAACACGAAAATGACTATC
45329 GCAAC
1 GCAAC
45334 GAGAGAATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
GCAACACGAAAATGACTATC
Found at i:45857 original size:20 final size:20
Alignment explanation
Indices: 45806--45911 Score: 88
Period size: 20 Copynumber: 5.2 Consensus size: 20
45796 GATTATGTAT
*
45806 TATCGCGTTGCAAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
45826 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
45846 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* * *
45867 TATCGCATTGCGATAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *
45887 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
45907 TATCG
1 TATCG
45912 TATTGCGATT
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
19 3 0.04
20 54 0.76
21 12 0.17
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:45892 original size:61 final size:61
Alignment explanation
Indices: 45786--45923 Score: 170
Period size: 61 Copynumber: 2.3 Consensus size: 61
45776 CGCTTTGAAA
* * * * *
45786 ATCGCATTGCGATTATGTATTATCGCGTTGCAAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGTATTGCGATTTTGTATTATCGCATTGCAAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
45847 ATC-TCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGT-ATTGCGATTTTGTATTATCGCATTGCAAAAGTAAGAATCGCATTGCGAAAGTCAGT
45908 ATCGTATTGCGATTTT
1 ATCGTATTGCGATTTT
45924 CCCAATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
61 63 0.98
62 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.36
Consensus pattern (61 bp):
ATCGTATTGCGATTTTGTATTATCGCATTGCAAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:45916 original size:20 final size:20
Alignment explanation
Indices: 45867--45920 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
45857 GATTTTGTAT
45867 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
45887 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
*
45907 TATCGTATTGCGAT
1 TATCGCATTGCGAT
45921 TTTCCCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:47672 original size:36 final size:35
Alignment explanation
Indices: 47623--47693 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 35
47613 AAAATGCAAA
** * *
47623 TGGGTACCTATACCCCTTCAAAGGGTATCCATACCC
1 TGGGTACAAATACCCCTGC-AAGGGTATCAATACCC
*
47659 TGGGTACAAATACCCCTGCATGGGTATCAATACCC
1 TGGGTACAAATACCCCTGCAAGGGTATCAATACCC
47694 CTATGATTAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
35 14 0.47
36 16 0.53
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (35 bp):
TGGGTACAAATACCCCTGCAAGGGTATCAATACCC
Found at i:47841 original size:21 final size:22
Alignment explanation
Indices: 47812--47852 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
47802 GAATTTAACA
47812 AAGGTAGTACCGATACCCCTTG
1 AAGGTAGTACCGATACCCCTTG
*
47834 AAGG-AGTACTGATACCCCT
1 AAGGTAGTACCGATACCCCT
47853 GTTATGGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (22 bp):
AAGGTAGTACCGATACCCCTTG
Found at i:50427 original size:57 final size:57
Alignment explanation
Indices: 50318--50427 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 57
50308 TTTAATGAAC
* * * * * **
50318 ATGATATCTCTCTAACAATTGATATCAACTTTTCAAATAATTTGATTTTAAATGCAA
1 ATGATATATCTCTAACAATTGATATCAAATTTTAAAAAAAATTGATCCTAAATGCAA
50375 ATGATATATCTCTAACAATTGATATCAAAATTTTAAAAAAAATTGA-CCTAAAT
1 ATGATATATCTCTAACAATTGATATC-AAATTTTAAAAAAAATTGATCCTAAAT
50428 TTAAATGTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
57 30 0.67
58 15 0.33
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (57 bp):
ATGATATATCTCTAACAATTGATATCAAATTTTAAAAAAAATTGATCCTAAATGCAA
Found at i:50886 original size:18 final size:19
Alignment explanation
Indices: 50858--50919 Score: 90
Period size: 18 Copynumber: 3.2 Consensus size: 19
50848 TTTTCATATA
50858 TTTTCTAACAATTGGTATC
1 TTTTCTAACAATTGGTATC
50877 TTTT-TAACAATTGGTATCC
1 TTTTCTAACAATTGGTAT-C
*
50896 TTTTGTAATCAATTGGTATC
1 TTTTCTAA-CAATTGGTATC
50916 TTTT
1 TTTT
50920 TCATTAAACA
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.32
19 9 0.22
20 8 0.20
21 10 0.25
ACGTcount: A:0.24, C:0.13, G:0.11, T:0.52
Consensus pattern (19 bp):
TTTTCTAACAATTGGTATC
Found at i:51190 original size:20 final size:20
Alignment explanation
Indices: 51165--51202 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
51155 TATCCATACT
*
51165 CTGGGTACCGATACCCCTGC
1 CTGGGTACCAATACCCCTGC
*
51185 CTGGGTATCAATACCCCT
1 CTGGGTACCAATACCCCT
51203 ATGACTGCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.37, G:0.21, T:0.24
Consensus pattern (20 bp):
CTGGGTACCAATACCCCTGC
Found at i:57151 original size:17 final size:18
Alignment explanation
Indices: 57125--57163 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
57115 ATAGAATGAT
57125 AAATTATAAAT-TATTATA
1 AAATTATAAATATATTA-A
57143 AAATT-TAAATATATTAA
1 AAATTATAAATATATTAA
57160 AAAT
1 AAAT
57164 ATATTATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATTATAAATATATTAA
Found at i:60195 original size:9 final size:9
Alignment explanation
Indices: 60165--60232 Score: 73
Period size: 9 Copynumber: 7.6 Consensus size: 9
60155 GAGAAGAAGC
60165 GGAAGAGGA
1 GGAAGAGGA
* * *
60174 AGACGATGA
1 GGAAGAGGA
60183 GGAAGAGGA
1 GGAAGAGGA
60192 GGAAGAGGA
1 GGAAGAGGA
*
60201 GGAGGAGGA
1 GGAAGAGGA
*
60210 GGAGGAGGA
1 GGAAGAGGA
*
60219 GGAGGAGGA
1 GGAAGAGGA
*
60228 AGAAG
1 GGAAG
60233 GGCGGAAGGA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.41, C:0.01, G:0.56, T:0.01
Consensus pattern (9 bp):
GGAAGAGGA
Found at i:60202 original size:3 final size:3
Alignment explanation
Indices: 60181--60227 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
60171 GGAAGACGAT
* *
60181 GAG GAA GAG GAG GAA GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
60228 AGAAGGGCGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:60202 original size:12 final size:12
Alignment explanation
Indices: 60187--60245 Score: 66
Period size: 12 Copynumber: 4.9 Consensus size: 12
60177 CGATGAGGAA
60187 GAGGAGGAAGAG
1 GAGGAGGAAGAG
*
60199 GAGGAGGAGGAG
1 GAGGAGGAAGAG
*
60211 GAGGAGGAGGAG
1 GAGGAGGAAGAG
*
60223 GAGGAAGAAG-G
1 GAGGAGGAAGAG
*
60234 GCGGAAGGAAGA
1 GAGG-AGGAAGA
60246 CAATGAATTG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
11 4 0.10
12 36 0.90
ACGTcount: A:0.39, C:0.02, G:0.59, T:0.00
Consensus pattern (12 bp):
GAGGAGGAAGAG
Found at i:76768 original size:25 final size:26
Alignment explanation
Indices: 76709--76769 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
76699 AAAGAGAGAG
*
76709 AAAATAAATAAATAACAATAAAATGTT
1 AAAATAAA-AAATAACAATAAAATATT
*
76736 AAGA-AAAAAAT-ACAAATAAAA-ATT
1 AAAATAAAAAATAAC-AATAAAATATT
76760 AAAATAAAAA
1 AAAATAAAAA
76770 GGAAAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 7 0.24
25 16 0.55
26 3 0.10
27 3 0.10
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (26 bp):
AAAATAAAAAATAACAATAAAATATT
Found at i:81078 original size:30 final size:30
Alignment explanation
Indices: 81019--81144 Score: 209
Period size: 30 Copynumber: 4.2 Consensus size: 30
81009 CCCGAAGGAC
* *
81019 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
81048 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
81078 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
81108 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
81138 CTGTCCA
1 CTATCCA
81145 TATGTTCCTT
Statistics
Matches: 93, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 19 0.20
30 74 0.80
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:81225 original size:32 final size:31
Alignment explanation
Indices: 81136--81231 Score: 97
Period size: 32 Copynumber: 3.0 Consensus size: 31
81126 GATCCTCGGT
* *
81136 AACTGTCCATATGTTCCTTAGAACATAAGT-A
1 AACTGTCCATAT-TTCCGTAGAACATAGGTAA
* * *
81167 TACTGTCCATATGTCTCG-AAAGACATAGGTAA
1 AACTGTCCATATTTC-CGTAGA-ACATAGGTAA
81199 AACTGTCCATATATTCCGTAGAACATAGGTAA
1 AACTGTCCATAT-TTCCGTAGAACATAGGTAA
81231 A
1 A
81232 CCCTCGACTC
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
30 4 0.08
31 19 0.37
32 25 0.48
33 4 0.08
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (31 bp):
AACTGTCCATATTTCCGTAGAACATAGGTAA
Found at i:82094 original size:21 final size:21
Alignment explanation
Indices: 82064--82108 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
82054 ATTCTGTCGT
* *
82064 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
82085 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
82106 TTG
1 TTG
82109 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:85898 original size:30 final size:30
Alignment explanation
Indices: 85864--85934 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
85854 TTATATGAGT
* * * *
85864 TATGTGGTAAATGTATGGAAATGATATGTC
1 TATGTGATAAAGGTATGAAAATAATATGTC
*
85894 TATGTGATAAAGGTATGAAAATAATATTTC
1 TATGTGATAAAGGTATGAAAATAATATGTC
*
85924 TACGTGATAAA
1 TATGTGATAAA
85935 AATTATGTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.35
Consensus pattern (30 bp):
TATGTGATAAAGGTATGAAAATAATATGTC
Found at i:86176 original size:23 final size:23
Alignment explanation
Indices: 86143--86210 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
86133 ATTATTATAT
86143 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
86166 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
86189 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
86211 AGCTGTGGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:87935 original size:32 final size:32
Alignment explanation
Indices: 87887--87950 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
87877 GAAAGAATTA
*
87887 AAAAACTTATTCTAAATTATTTATATTTGATT
1 AAAAACTTACTCTAAATTATTTATATTTGATT
* *
87919 AAAATCTTACTCTAAATTGTTTATATTTGATT
1 AAAAACTTACTCTAAATTATTTATATTTGATT
87951 TTTTTATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.50
Consensus pattern (32 bp):
AAAAACTTACTCTAAATTATTTATATTTGATT
Found at i:97430 original size:20 final size:21
Alignment explanation
Indices: 97394--97433 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
97384 ATATTAGATC
*
97394 AATCATTTTTTGAATCGAGTT
1 AATCAGTTTTTGAATCGAGTT
97415 AATCAGTTTTTG-ATCGAGT
1 AATCAGTTTTTGAATCGAGT
97434 CAATATCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (21 bp):
AATCAGTTTTTGAATCGAGTT
Found at i:100324 original size:86 final size:86
Alignment explanation
Indices: 100179--100374 Score: 331
Period size: 86 Copynumber: 2.3 Consensus size: 86
100169 CACCTCACAA
*
100179 ACAAACGAAAGTGGATATTTTCTAATAAATTTCATGATTTTTTTAGTATGTATTATTTAAGATCA
1 ACAAACGAAAGTGGATATTTTCTAATAAATTTCATGATTTTTTTAGTATGCATTATTTAAGATCA
*
100244 GAAAATTTTCTTTTAAATAAT
66 GAAAATTTTATTTTAAATAAT
* *
100265 ACAAACGAAAGTGGATATTTTCTGATAAATTTCATGA-TTTTTTAGTATGCCTTATTTTAAGATC
1 ACAAACGAAAGTGGATATTTTCTAATAAATTTCATGATTTTTTTAGTATGCATTA-TTTAAGATC
*
100329 AGAAAATTTTATTTTCAATAAT
65 AGAAAATTTTATTTTAAATAAT
100351 ACAAACGAAAGTGGATATTTTCTA
1 ACAAACGAAAGTGGATATTTTCTA
100375 CCATCCGACA
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
85 15 0.15
86 88 0.85
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.42
Consensus pattern (86 bp):
ACAAACGAAAGTGGATATTTTCTAATAAATTTCATGATTTTTTTAGTATGCATTATTTAAGATCA
GAAAATTTTATTTTAAATAAT
Found at i:101389 original size:21 final size:21
Alignment explanation
Indices: 101363--101459 Score: 142
Period size: 21 Copynumber: 4.7 Consensus size: 21
101353 GCGAATAAGT
101363 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
101384 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
101405 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
101425 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
101446 AAATCGCAATGCGA
1 AAATCGCAACGCGA
101460 TACTGACTAT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
20 16 0.24
21 50 0.76
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.15
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:101473 original size:20 final size:20
Alignment explanation
Indices: 101448--101541 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
101438 AATTGGGAAA
*
101448 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
101468 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* * *
101489 ATCGTAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
101509 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
101529 TTCGCAACGCGAT
1 ATCGCAACGCGAT
101542 TTACATAGCG
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:101490 original size:41 final size:41
Alignment explanation
Indices: 101445--101522 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
101435 GCGAATTGGG
* * *
101445 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* * *
101486 AAAATCGTAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
101523 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:101492 original size:62 final size:61
Alignment explanation
Indices: 101346--101486 Score: 207
Period size: 62 Copynumber: 2.3 Consensus size: 61
101336 TTTTCCCAAT
*
101346 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCGCAACGCGAACT-GGAAAA
* **
101408 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCGCAATGCGATACT-GACTA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCGCAACGCGA-ACTGGAAAA
101469 TCGCAATGCG-ATAA-TAAA
1 TCGCAATGCGAATAAGTAAA
101487 AAATCGTAAC
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
59 4 0.05
60 4 0.05
61 13 0.18
62 51 0.69
63 2 0.03
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.18
Consensus pattern (61 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCGCAACGCGAACTGGAAAA
Found at i:102109 original size:19 final size:19
Alignment explanation
Indices: 102037--102103 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
102027 TTCGAGAATG
*
102037 AAAATCGCAATGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
102057 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
102076 AAAATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
102095 AAAATCGCA
1 AAAATCGCA
102104 TTGCGATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 32 0.76
20 10 0.24
ACGTcount: A:0.49, C:0.21, G:0.16, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:102121 original size:19 final size:19
Alignment explanation
Indices: 102099--102244 Score: 105
Period size: 19 Copynumber: 8.1 Consensus size: 19
102089 GAAATAAAAA
*
102099 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
102118 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
*
102137 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
102153 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
102170 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
102184 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
102203 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
102223 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
102243 TC
1 TC
102245 AACCAAAAGA
Statistics
Matches: 100, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
14 20 0.20
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 40 0.40
20 31 0.31
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:102214 original size:34 final size:33
Alignment explanation
Indices: 102134--102219 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
102124 TGCGATTTTT
* *
102134 ATTTCGCGTTGCGATTGTCTGGTCGCGATAGTC
1 ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
*
102167 ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTC
1 ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
102200 ATTTCCGCGTTGCGATTCTC
1 ATTT-CGCGTTGCGATTCTC
102220 ATTATCTCGT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 34 0.69
34 15 0.31
ACGTcount: A:0.12, C:0.24, G:0.26, T:0.38
Consensus pattern (33 bp):
ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
Found at i:102221 original size:20 final size:20
Alignment explanation
Indices: 102187--102244 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
102177 GCGATTCTCT
**
102187 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
102207 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
102227 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
102245 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:104292 original size:41 final size:41
Alignment explanation
Indices: 104233--104354 Score: 120
Period size: 41 Copynumber: 3.0 Consensus size: 41
104223 AGCCGACTCG
* * *
104233 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGC
* * *
104274 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGC
* ** * *
104315 CACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 C-CTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
104355 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
41 36 0.55
42 26 0.39
43 4 0.06
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (41 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGC
Found at i:104312 original size:21 final size:21
Alignment explanation
Indices: 104288--104354 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
104278 TCATTCCTCG
104288 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
104309 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
104330 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
104351 AGAG
1 AGAG
104355 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:105713 original size:14 final size:14
Alignment explanation
Indices: 105694--105743 Score: 91
Period size: 14 Copynumber: 3.6 Consensus size: 14
105684 ATTGTTTAAT
105694 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
105708 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
105722 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
105736 TGATTTGT
1 TGATTTGT
105744 TTAATTGATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:105968 original size:33 final size:32
Alignment explanation
Indices: 105926--106048 Score: 167
Period size: 33 Copynumber: 3.8 Consensus size: 32
105916 ATTAAATTCG
105926 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
105959 CGTTGCGATTTTCATTTCGCATTGCAAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGC--GATTCCT
*
105992 CGTTGCGATTTTCATTTCGCATTACGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
106025 CGTTGCGATTTTCATTTCGCATTG
1 CGTTGCGATTTTCATTTCGCATTG
106049 TGATAGTAAT
Statistics
Matches: 78, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
31 3 0.04
33 72 0.92
35 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:106020 original size:66 final size:66
Alignment explanation
Indices: 105919--106048 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 66
105909 ACGCGAAATT
* *
105919 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTACGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
105984 A
66 A
*
105985 AAATTAGCGTTGCGATTTTCATTTCGCATTACGATTCTCTCGTTGCGATTTTCATTTCGCATTG
1 AAATTAGCGTTGCGATTTTCATTTCGCATTACGATTCCCTCGTTGCGATTTTCATTTCGCATTG
106049 TGATAGTAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTACGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
A
Found at i:108334 original size:12 final size:12
Alignment explanation
Indices: 108317--108341 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
108307 TCTTCGAGGA
108317 CTTTTTCTTCTT
1 CTTTTTCTTCTT
108329 CTTTTTCTTCTT
1 CTTTTTCTTCTT
108341 C
1 C
108342 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:108548 original size:24 final size:24
Alignment explanation
Indices: 108514--108567 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
108504 CTGAAACATC
* *
108514 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
108538 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
108562 ATCAAA
1 ATCAAA
108568 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:109641 original size:20 final size:20
Alignment explanation
Indices: 109616--109672 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 20
109606 ATTCATTTGA
*
109616 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
109636 CTATCGCAACGCG-AAATGG
1 CTATCGCAACGAGAAAATGG
*
109655 TTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
109673 CGCAATGCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:109764 original size:19 final size:19
Alignment explanation
Indices: 109740--109776 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
109730 GCATTGCGAT
109740 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
109759 TTTCGCATTGCGATTTTC
1 TTTCGCATTGCGATTTTC
109777 TCGTTGCGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.14, C:0.22, G:0.16, T:0.49
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:109766 original size:33 final size:32
Alignment explanation
Indices: 109722--109786 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
109712 ATTTTCACGA
109722 TTTCATTCGCATTGCGATTTTCGCATTGCGAT
1 TTTCATTCGCATTGCGATTTTCGCATTGCGAT
* *
109754 TTTCATTTCGCATTGCGATTTTCTCGTTGCGAT
1 TTTCA-TTCGCATTGCGATTTTCGCATTGCGAT
109787 AGCCATTTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 5 0.17
33 25 0.83
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (32 bp):
TTTCATTCGCATTGCGATTTTCGCATTGCGAT
Found at i:109776 original size:14 final size:14
Alignment explanation
Indices: 109727--109757 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
109717 CACGATTTCA
109727 TTCGCATTGCGATT
1 TTCGCATTGCGATT
109741 TTCGCATTGCGATT
1 TTCGCATTGCGATT
109755 TTC
1 TTC
109758 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (14 bp):
TTCGCATTGCGATT
Found at i:109794 original size:33 final size:33
Alignment explanation
Indices: 109727--109803 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
109717 CACGATTTCA
***
109727 TTCGCATTGCGATTTTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCGCATTGCGATAGCCAT
* *
109760 TTCGCATTGCGATTTTCTCGTTGCGATAGCCAT
1 TTCGCATTGCGATTTTCGCATTGCGATAGCCAT
109793 TTCG--TTGCGAT
1 TTCGCATTGCGAT
109804 AGTCTGTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 7 0.18
33 32 0.82
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.43
Consensus pattern (33 bp):
TTCGCATTGCGATTTTCGCATTGCGATAGCCAT
Done.