Multiple sequence alignment - TraesCS1A01G410300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G410300 chr1A 100.000 3536 0 0 1 3536 571652043 571655578 0.000000e+00 6530
1 TraesCS1A01G410300 chr1A 84.746 118 15 3 3320 3435 571654941 571655057 8.020000e-22 115
2 TraesCS1A01G410300 chr1A 84.746 118 15 3 2899 3015 571655362 571655477 8.020000e-22 115
3 TraesCS1A01G410300 chr1B 94.018 2725 118 16 843 3536 661895295 661898005 0.000000e+00 4087
4 TraesCS1A01G410300 chr1B 87.500 120 12 2 3318 3435 661897354 661897472 6.160000e-28 135
5 TraesCS1A01G410300 chr1B 85.593 118 15 2 2899 3015 661897777 661897893 4.790000e-24 122
6 TraesCS1A01G410300 chr1B 91.011 89 7 1 57 144 249754528 249754440 6.200000e-23 119
7 TraesCS1A01G410300 chr1B 89.247 93 9 1 53 144 34898558 34898650 8.020000e-22 115
8 TraesCS1A01G410300 chr1D 96.105 1746 50 8 1144 2871 475816452 475818197 0.000000e+00 2832
9 TraesCS1A01G410300 chr1D 90.000 460 32 9 2899 3349 475818470 475818924 1.830000e-162 582
10 TraesCS1A01G410300 chr1D 88.703 478 37 13 312 781 475815223 475815691 5.120000e-158 568
11 TraesCS1A01G410300 chr1D 91.389 360 19 5 775 1130 475815714 475816065 1.910000e-132 483
12 TraesCS1A01G410300 chr1D 93.836 146 6 2 3394 3536 475818926 475819071 2.140000e-52 217
13 TraesCS1A01G410300 chr1D 81.746 252 43 3 2645 2894 475818606 475818856 1.290000e-49 207
14 TraesCS1A01G410300 chr7A 91.579 95 7 1 51 144 675081235 675081329 2.860000e-26 130
15 TraesCS1A01G410300 chr5D 91.398 93 7 1 52 143 458636345 458636253 3.710000e-25 126
16 TraesCS1A01G410300 chr2B 92.593 81 5 1 65 144 615255077 615255157 8.020000e-22 115
17 TraesCS1A01G410300 chr4A 89.888 89 7 2 57 144 368834117 368834030 2.880000e-21 113
18 TraesCS1A01G410300 chr4A 88.043 92 10 1 54 144 577368220 577368311 1.340000e-19 108
19 TraesCS1A01G410300 chr4A 87.778 90 8 3 57 144 577368313 577368225 6.240000e-18 102
20 TraesCS1A01G410300 chr6B 89.412 85 8 1 57 140 25916930 25916846 4.830000e-19 106


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G410300 chr1A 571652043 571655578 3535 False 2253.333333 6530 89.830667 1 3536 3 chr1A.!!$F1 3535
1 TraesCS1A01G410300 chr1B 661895295 661898005 2710 False 1448.000000 4087 89.037000 843 3536 3 chr1B.!!$F2 2693
2 TraesCS1A01G410300 chr1D 475815223 475819071 3848 False 814.833333 2832 90.296500 312 3536 6 chr1D.!!$F1 3224

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
342 343 0.249120 TATGGCCCGCGGATATTCAG 59.751 55.0 30.73 9.14 0.0 3.02 F
347 348 0.319900 CCCGCGGATATTCAGGTGAG 60.320 60.0 30.73 0.00 0.0 3.51 F
806 842 0.396974 AGCTGGCCTCCTGACTAGAG 60.397 60.0 3.32 0.00 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1753 2169 0.107410 AGCGGCCGGTCAATTATCAA 60.107 50.0 26.97 0.0 0.0 2.57 R
1983 2399 1.195115 CCTCCCGGAAATGAGTCAGA 58.805 55.0 0.73 0.0 0.0 3.27 R
2620 3051 0.036732 CTAGCCAACAACCCAGCAGA 59.963 55.0 0.00 0.0 0.0 4.26 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.418913 CACGCGACCGCCATGAAA 61.419 61.111 15.93 0.00 38.22 2.69
24 25 3.419759 ACGCGACCGCCATGAAAC 61.420 61.111 15.93 0.00 38.22 2.78
25 26 3.418913 CGCGACCGCCATGAAACA 61.419 61.111 0.00 0.00 37.98 2.83
26 27 2.950673 GCGACCGCCATGAAACAA 59.049 55.556 2.55 0.00 34.56 2.83
27 28 1.506262 GCGACCGCCATGAAACAAT 59.494 52.632 2.55 0.00 34.56 2.71
28 29 0.798009 GCGACCGCCATGAAACAATG 60.798 55.000 2.55 0.00 34.56 2.82
29 30 0.521291 CGACCGCCATGAAACAATGT 59.479 50.000 0.00 0.00 0.00 2.71
30 31 1.068610 CGACCGCCATGAAACAATGTT 60.069 47.619 0.00 0.00 0.00 2.71
31 32 2.595386 GACCGCCATGAAACAATGTTC 58.405 47.619 0.00 0.00 0.00 3.18
32 33 1.272212 ACCGCCATGAAACAATGTTCC 59.728 47.619 0.00 0.00 0.00 3.62
33 34 1.271934 CCGCCATGAAACAATGTTCCA 59.728 47.619 0.00 0.00 0.00 3.53
34 35 2.094078 CCGCCATGAAACAATGTTCCAT 60.094 45.455 0.00 0.00 0.00 3.41
35 36 2.924926 CGCCATGAAACAATGTTCCATG 59.075 45.455 16.84 16.84 0.00 3.66
36 37 2.674357 GCCATGAAACAATGTTCCATGC 59.326 45.455 18.10 10.83 0.00 4.06
37 38 2.924926 CCATGAAACAATGTTCCATGCG 59.075 45.455 18.10 9.04 0.00 4.73
38 39 2.063156 TGAAACAATGTTCCATGCGC 57.937 45.000 0.00 0.00 0.00 6.09
39 40 1.612950 TGAAACAATGTTCCATGCGCT 59.387 42.857 9.73 0.00 0.00 5.92
40 41 2.816672 TGAAACAATGTTCCATGCGCTA 59.183 40.909 9.73 0.00 0.00 4.26
41 42 3.254411 TGAAACAATGTTCCATGCGCTAA 59.746 39.130 9.73 0.00 0.00 3.09
42 43 4.082300 TGAAACAATGTTCCATGCGCTAAT 60.082 37.500 9.73 0.00 0.00 1.73
43 44 3.425577 ACAATGTTCCATGCGCTAATG 57.574 42.857 9.73 4.62 0.00 1.90
44 45 2.121786 CAATGTTCCATGCGCTAATGC 58.878 47.619 9.73 0.00 0.00 3.56
45 46 0.670162 ATGTTCCATGCGCTAATGCC 59.330 50.000 9.73 0.00 35.36 4.40
46 47 0.394216 TGTTCCATGCGCTAATGCCT 60.394 50.000 9.73 0.00 35.36 4.75
47 48 1.134250 TGTTCCATGCGCTAATGCCTA 60.134 47.619 9.73 0.00 35.36 3.93
48 49 1.946768 GTTCCATGCGCTAATGCCTAA 59.053 47.619 9.73 0.00 35.36 2.69
49 50 2.554032 GTTCCATGCGCTAATGCCTAAT 59.446 45.455 9.73 0.00 35.36 1.73
50 51 2.862541 TCCATGCGCTAATGCCTAATT 58.137 42.857 9.73 0.00 35.36 1.40
51 52 2.813754 TCCATGCGCTAATGCCTAATTC 59.186 45.455 9.73 0.00 35.36 2.17
52 53 2.553602 CCATGCGCTAATGCCTAATTCA 59.446 45.455 9.73 0.00 35.36 2.57
53 54 3.192001 CCATGCGCTAATGCCTAATTCAT 59.808 43.478 9.73 0.00 35.36 2.57
54 55 4.395854 CCATGCGCTAATGCCTAATTCATA 59.604 41.667 9.73 0.00 35.36 2.15
55 56 5.066893 CCATGCGCTAATGCCTAATTCATAT 59.933 40.000 9.73 0.00 35.36 1.78
56 57 6.405065 CCATGCGCTAATGCCTAATTCATATT 60.405 38.462 9.73 0.00 35.36 1.28
57 58 6.182039 TGCGCTAATGCCTAATTCATATTC 57.818 37.500 9.73 0.00 35.36 1.75
58 59 5.123820 TGCGCTAATGCCTAATTCATATTCC 59.876 40.000 9.73 0.00 35.36 3.01
59 60 5.449177 GCGCTAATGCCTAATTCATATTCCC 60.449 44.000 0.00 0.00 35.36 3.97
60 61 5.882557 CGCTAATGCCTAATTCATATTCCCT 59.117 40.000 0.00 0.00 35.36 4.20
61 62 6.037610 CGCTAATGCCTAATTCATATTCCCTC 59.962 42.308 0.00 0.00 35.36 4.30
62 63 7.115414 GCTAATGCCTAATTCATATTCCCTCT 58.885 38.462 0.00 0.00 0.00 3.69
63 64 7.066766 GCTAATGCCTAATTCATATTCCCTCTG 59.933 40.741 0.00 0.00 0.00 3.35
64 65 5.912149 TGCCTAATTCATATTCCCTCTGT 57.088 39.130 0.00 0.00 0.00 3.41
65 66 6.266131 TGCCTAATTCATATTCCCTCTGTT 57.734 37.500 0.00 0.00 0.00 3.16
66 67 6.299141 TGCCTAATTCATATTCCCTCTGTTC 58.701 40.000 0.00 0.00 0.00 3.18
67 68 5.707764 GCCTAATTCATATTCCCTCTGTTCC 59.292 44.000 0.00 0.00 0.00 3.62
68 69 6.691491 GCCTAATTCATATTCCCTCTGTTCCA 60.691 42.308 0.00 0.00 0.00 3.53
69 70 7.290061 CCTAATTCATATTCCCTCTGTTCCAA 58.710 38.462 0.00 0.00 0.00 3.53
70 71 7.779798 CCTAATTCATATTCCCTCTGTTCCAAA 59.220 37.037 0.00 0.00 0.00 3.28
71 72 9.189156 CTAATTCATATTCCCTCTGTTCCAAAA 57.811 33.333 0.00 0.00 0.00 2.44
72 73 8.613922 AATTCATATTCCCTCTGTTCCAAAAT 57.386 30.769 0.00 0.00 0.00 1.82
73 74 9.713684 AATTCATATTCCCTCTGTTCCAAAATA 57.286 29.630 0.00 0.00 0.00 1.40
74 75 8.752005 TTCATATTCCCTCTGTTCCAAAATAG 57.248 34.615 0.00 0.00 0.00 1.73
75 76 8.101309 TCATATTCCCTCTGTTCCAAAATAGA 57.899 34.615 0.00 0.00 32.42 1.98
76 77 8.727149 TCATATTCCCTCTGTTCCAAAATAGAT 58.273 33.333 0.00 0.00 32.88 1.98
77 78 8.790718 CATATTCCCTCTGTTCCAAAATAGATG 58.209 37.037 0.00 0.00 32.88 2.90
78 79 6.387192 TTCCCTCTGTTCCAAAATAGATGA 57.613 37.500 0.00 0.00 32.88 2.92
79 80 6.581388 TCCCTCTGTTCCAAAATAGATGAT 57.419 37.500 0.00 0.00 32.88 2.45
80 81 6.595682 TCCCTCTGTTCCAAAATAGATGATC 58.404 40.000 0.00 0.00 32.88 2.92
81 82 5.767168 CCCTCTGTTCCAAAATAGATGATCC 59.233 44.000 0.00 0.00 32.88 3.36
82 83 6.359804 CCTCTGTTCCAAAATAGATGATCCA 58.640 40.000 0.00 0.00 32.88 3.41
83 84 6.830324 CCTCTGTTCCAAAATAGATGATCCAA 59.170 38.462 0.00 0.00 32.88 3.53
84 85 7.504911 CCTCTGTTCCAAAATAGATGATCCAAT 59.495 37.037 0.00 0.00 32.88 3.16
85 86 8.827832 TCTGTTCCAAAATAGATGATCCAATT 57.172 30.769 0.00 0.00 28.72 2.32
86 87 9.258629 TCTGTTCCAAAATAGATGATCCAATTT 57.741 29.630 0.00 0.00 28.72 1.82
87 88 9.880157 CTGTTCCAAAATAGATGATCCAATTTT 57.120 29.630 9.17 9.17 33.07 1.82
136 137 7.111247 ACAAAATTGAGTCATCTGTTTTGGA 57.889 32.000 23.00 0.00 40.63 3.53
137 138 7.555087 ACAAAATTGAGTCATCTGTTTTGGAA 58.445 30.769 23.00 0.00 40.63 3.53
138 139 7.492344 ACAAAATTGAGTCATCTGTTTTGGAAC 59.508 33.333 23.00 0.00 40.63 3.62
139 140 4.811555 TTGAGTCATCTGTTTTGGAACG 57.188 40.909 0.00 0.00 38.65 3.95
140 141 3.138304 TGAGTCATCTGTTTTGGAACGG 58.862 45.455 0.00 0.00 42.39 4.44
144 145 3.015516 TCTGTTTTGGAACGGAGGC 57.984 52.632 0.00 0.00 44.24 4.70
145 146 0.472471 TCTGTTTTGGAACGGAGGCT 59.528 50.000 0.00 0.00 44.24 4.58
146 147 1.133915 TCTGTTTTGGAACGGAGGCTT 60.134 47.619 0.00 0.00 44.24 4.35
147 148 2.105134 TCTGTTTTGGAACGGAGGCTTA 59.895 45.455 0.00 0.00 44.24 3.09
148 149 2.882137 CTGTTTTGGAACGGAGGCTTAA 59.118 45.455 0.00 0.00 43.47 1.85
149 150 3.492337 TGTTTTGGAACGGAGGCTTAAT 58.508 40.909 0.00 0.00 38.65 1.40
150 151 4.653868 TGTTTTGGAACGGAGGCTTAATA 58.346 39.130 0.00 0.00 38.65 0.98
151 152 5.071370 TGTTTTGGAACGGAGGCTTAATAA 58.929 37.500 0.00 0.00 38.65 1.40
152 153 5.535406 TGTTTTGGAACGGAGGCTTAATAAA 59.465 36.000 0.00 0.00 38.65 1.40
153 154 5.632244 TTTGGAACGGAGGCTTAATAAAC 57.368 39.130 0.00 0.00 0.00 2.01
154 155 4.563140 TGGAACGGAGGCTTAATAAACT 57.437 40.909 0.00 0.00 0.00 2.66
155 156 5.680594 TGGAACGGAGGCTTAATAAACTA 57.319 39.130 0.00 0.00 0.00 2.24
156 157 6.052405 TGGAACGGAGGCTTAATAAACTAA 57.948 37.500 0.00 0.00 0.00 2.24
157 158 6.474630 TGGAACGGAGGCTTAATAAACTAAA 58.525 36.000 0.00 0.00 0.00 1.85
158 159 7.114095 TGGAACGGAGGCTTAATAAACTAAAT 58.886 34.615 0.00 0.00 0.00 1.40
159 160 8.266473 TGGAACGGAGGCTTAATAAACTAAATA 58.734 33.333 0.00 0.00 0.00 1.40
160 161 8.771766 GGAACGGAGGCTTAATAAACTAAATAG 58.228 37.037 0.00 0.00 0.00 1.73
161 162 7.725818 ACGGAGGCTTAATAAACTAAATAGC 57.274 36.000 0.00 0.00 0.00 2.97
162 163 7.277396 ACGGAGGCTTAATAAACTAAATAGCA 58.723 34.615 0.00 0.00 0.00 3.49
163 164 7.937394 ACGGAGGCTTAATAAACTAAATAGCAT 59.063 33.333 0.00 0.00 0.00 3.79
164 165 8.230486 CGGAGGCTTAATAAACTAAATAGCATG 58.770 37.037 0.00 0.00 0.00 4.06
165 166 9.067986 GGAGGCTTAATAAACTAAATAGCATGT 57.932 33.333 0.00 0.00 0.00 3.21
168 169 9.807386 GGCTTAATAAACTAAATAGCATGTACG 57.193 33.333 0.00 0.00 0.00 3.67
174 175 7.916914 AAACTAAATAGCATGTACGTTTCCT 57.083 32.000 0.00 0.00 0.00 3.36
175 176 7.535489 AACTAAATAGCATGTACGTTTCCTC 57.465 36.000 0.00 0.00 0.00 3.71
176 177 6.875076 ACTAAATAGCATGTACGTTTCCTCT 58.125 36.000 0.00 0.00 0.00 3.69
177 178 7.328737 ACTAAATAGCATGTACGTTTCCTCTT 58.671 34.615 0.00 0.00 0.00 2.85
178 179 7.822822 ACTAAATAGCATGTACGTTTCCTCTTT 59.177 33.333 0.00 0.00 0.00 2.52
179 180 6.422776 AATAGCATGTACGTTTCCTCTTTG 57.577 37.500 0.00 0.00 0.00 2.77
180 181 4.002906 AGCATGTACGTTTCCTCTTTGA 57.997 40.909 0.00 0.00 0.00 2.69
181 182 4.579869 AGCATGTACGTTTCCTCTTTGAT 58.420 39.130 0.00 0.00 0.00 2.57
182 183 4.393062 AGCATGTACGTTTCCTCTTTGATG 59.607 41.667 0.00 0.00 0.00 3.07
183 184 4.154195 GCATGTACGTTTCCTCTTTGATGT 59.846 41.667 0.00 0.00 0.00 3.06
184 185 5.671329 GCATGTACGTTTCCTCTTTGATGTC 60.671 44.000 0.00 0.00 0.00 3.06
185 186 5.209818 TGTACGTTTCCTCTTTGATGTCT 57.790 39.130 0.00 0.00 0.00 3.41
186 187 6.335471 TGTACGTTTCCTCTTTGATGTCTA 57.665 37.500 0.00 0.00 0.00 2.59
187 188 6.931838 TGTACGTTTCCTCTTTGATGTCTAT 58.068 36.000 0.00 0.00 0.00 1.98
188 189 7.033791 TGTACGTTTCCTCTTTGATGTCTATC 58.966 38.462 0.00 0.00 0.00 2.08
189 190 5.103000 ACGTTTCCTCTTTGATGTCTATCG 58.897 41.667 0.00 0.00 36.04 2.92
190 191 5.105877 ACGTTTCCTCTTTGATGTCTATCGA 60.106 40.000 0.00 0.00 36.04 3.59
191 192 5.457148 CGTTTCCTCTTTGATGTCTATCGAG 59.543 44.000 0.00 0.00 36.04 4.04
192 193 5.521906 TTCCTCTTTGATGTCTATCGAGG 57.478 43.478 0.00 0.00 38.65 4.63
193 194 4.793201 TCCTCTTTGATGTCTATCGAGGA 58.207 43.478 0.00 0.00 41.34 3.71
194 195 5.201243 TCCTCTTTGATGTCTATCGAGGAA 58.799 41.667 0.00 0.00 40.99 3.36
195 196 5.300539 TCCTCTTTGATGTCTATCGAGGAAG 59.699 44.000 0.00 0.00 40.99 3.46
196 197 5.300539 CCTCTTTGATGTCTATCGAGGAAGA 59.699 44.000 0.00 0.00 39.17 2.87
197 198 6.183360 CCTCTTTGATGTCTATCGAGGAAGAA 60.183 42.308 0.00 0.00 39.17 2.52
198 199 6.565234 TCTTTGATGTCTATCGAGGAAGAAC 58.435 40.000 0.00 0.00 36.04 3.01
199 200 5.914898 TTGATGTCTATCGAGGAAGAACA 57.085 39.130 0.00 0.00 36.04 3.18
200 201 6.471233 TTGATGTCTATCGAGGAAGAACAT 57.529 37.500 0.00 1.48 36.04 2.71
201 202 5.836347 TGATGTCTATCGAGGAAGAACATG 58.164 41.667 0.00 0.00 36.04 3.21
202 203 5.360999 TGATGTCTATCGAGGAAGAACATGT 59.639 40.000 0.00 0.00 36.04 3.21
203 204 6.546034 TGATGTCTATCGAGGAAGAACATGTA 59.454 38.462 0.00 0.00 36.04 2.29
204 205 6.961360 TGTCTATCGAGGAAGAACATGTAT 57.039 37.500 0.00 0.00 0.00 2.29
205 206 7.348080 TGTCTATCGAGGAAGAACATGTATT 57.652 36.000 0.00 0.00 0.00 1.89
206 207 7.426410 TGTCTATCGAGGAAGAACATGTATTC 58.574 38.462 12.98 12.98 0.00 1.75
207 208 7.285629 TGTCTATCGAGGAAGAACATGTATTCT 59.714 37.037 18.21 8.55 40.78 2.40
208 209 7.806014 GTCTATCGAGGAAGAACATGTATTCTC 59.194 40.741 18.21 11.91 37.99 2.87
209 210 5.914898 TCGAGGAAGAACATGTATTCTCA 57.085 39.130 18.21 4.25 37.99 3.27
210 211 6.471233 TCGAGGAAGAACATGTATTCTCAT 57.529 37.500 18.21 8.87 37.99 2.90
222 223 7.572523 CATGTATTCTCATGTACCATTTGGT 57.427 36.000 7.51 7.51 42.44 3.67
223 224 7.420002 CATGTATTCTCATGTACCATTTGGTG 58.580 38.462 12.54 0.00 42.07 4.17
224 225 7.282901 CATGTATTCTCATGTACCATTTGGTGA 59.717 37.037 12.54 0.38 42.07 4.02
241 242 2.154462 GTGATGTTCACAGAAGGTGGG 58.846 52.381 2.85 0.00 46.22 4.61
242 243 2.487265 GTGATGTTCACAGAAGGTGGGT 60.487 50.000 2.85 0.00 46.22 4.51
243 244 3.998604 GTGATGTTCACAGAAGGTGGGTT 60.999 47.826 2.85 0.00 46.22 4.11
244 245 5.467670 GTGATGTTCACAGAAGGTGGGTTT 61.468 45.833 2.85 0.00 46.22 3.27
245 246 6.899496 GTGATGTTCACAGAAGGTGGGTTTT 61.899 44.000 2.85 0.00 46.22 2.43
246 247 8.822318 GTGATGTTCACAGAAGGTGGGTTTTG 62.822 46.154 2.85 0.00 46.22 2.44
248 249 2.869233 CACAGAAGGTGGGTTTTGTG 57.131 50.000 0.00 0.00 44.04 3.33
249 250 1.111277 ACAGAAGGTGGGTTTTGTGC 58.889 50.000 0.00 0.00 0.00 4.57
250 251 1.341976 ACAGAAGGTGGGTTTTGTGCT 60.342 47.619 0.00 0.00 0.00 4.40
251 252 1.338020 CAGAAGGTGGGTTTTGTGCTC 59.662 52.381 0.00 0.00 0.00 4.26
252 253 1.215423 AGAAGGTGGGTTTTGTGCTCT 59.785 47.619 0.00 0.00 0.00 4.09
253 254 1.338020 GAAGGTGGGTTTTGTGCTCTG 59.662 52.381 0.00 0.00 0.00 3.35
254 255 0.468029 AGGTGGGTTTTGTGCTCTGG 60.468 55.000 0.00 0.00 0.00 3.86
255 256 1.463553 GGTGGGTTTTGTGCTCTGGG 61.464 60.000 0.00 0.00 0.00 4.45
256 257 0.467290 GTGGGTTTTGTGCTCTGGGA 60.467 55.000 0.00 0.00 0.00 4.37
257 258 0.260230 TGGGTTTTGTGCTCTGGGAA 59.740 50.000 0.00 0.00 0.00 3.97
258 259 0.961753 GGGTTTTGTGCTCTGGGAAG 59.038 55.000 0.00 0.00 0.00 3.46
259 260 1.692411 GGTTTTGTGCTCTGGGAAGT 58.308 50.000 0.00 0.00 0.00 3.01
260 261 2.488347 GGGTTTTGTGCTCTGGGAAGTA 60.488 50.000 0.00 0.00 0.00 2.24
261 262 2.814336 GGTTTTGTGCTCTGGGAAGTAG 59.186 50.000 0.00 0.00 0.00 2.57
262 263 3.496160 GGTTTTGTGCTCTGGGAAGTAGA 60.496 47.826 0.00 0.00 0.00 2.59
263 264 4.327680 GTTTTGTGCTCTGGGAAGTAGAT 58.672 43.478 0.00 0.00 0.00 1.98
264 265 4.640771 TTTGTGCTCTGGGAAGTAGATT 57.359 40.909 0.00 0.00 0.00 2.40
265 266 3.895232 TGTGCTCTGGGAAGTAGATTC 57.105 47.619 0.00 0.00 37.17 2.52
266 267 3.173151 TGTGCTCTGGGAAGTAGATTCA 58.827 45.455 0.00 0.00 39.91 2.57
267 268 3.776969 TGTGCTCTGGGAAGTAGATTCAT 59.223 43.478 0.00 0.00 39.91 2.57
268 269 4.125703 GTGCTCTGGGAAGTAGATTCATG 58.874 47.826 0.00 0.00 39.91 3.07
269 270 3.137533 GCTCTGGGAAGTAGATTCATGC 58.862 50.000 0.00 0.00 39.91 4.06
270 271 3.181456 GCTCTGGGAAGTAGATTCATGCT 60.181 47.826 0.00 0.00 39.91 3.79
271 272 4.630111 CTCTGGGAAGTAGATTCATGCTC 58.370 47.826 0.00 0.00 39.91 4.26
272 273 3.389329 TCTGGGAAGTAGATTCATGCTCC 59.611 47.826 0.00 0.00 39.91 4.70
273 274 2.439507 TGGGAAGTAGATTCATGCTCCC 59.560 50.000 0.00 0.00 39.91 4.30
274 275 2.708325 GGGAAGTAGATTCATGCTCCCT 59.292 50.000 0.00 0.00 39.91 4.20
275 276 3.137360 GGGAAGTAGATTCATGCTCCCTT 59.863 47.826 0.00 0.00 39.91 3.95
276 277 4.385754 GGGAAGTAGATTCATGCTCCCTTT 60.386 45.833 0.00 0.00 39.91 3.11
277 278 5.163195 GGGAAGTAGATTCATGCTCCCTTTA 60.163 44.000 0.00 0.00 39.91 1.85
278 279 6.466470 GGGAAGTAGATTCATGCTCCCTTTAT 60.466 42.308 0.00 0.00 39.91 1.40
279 280 7.001073 GGAAGTAGATTCATGCTCCCTTTATT 58.999 38.462 0.00 0.00 39.91 1.40
280 281 7.503902 GGAAGTAGATTCATGCTCCCTTTATTT 59.496 37.037 0.00 0.00 39.91 1.40
281 282 8.829373 AAGTAGATTCATGCTCCCTTTATTTT 57.171 30.769 0.00 0.00 0.00 1.82
282 283 9.920946 AAGTAGATTCATGCTCCCTTTATTTTA 57.079 29.630 0.00 0.00 0.00 1.52
283 284 9.566432 AGTAGATTCATGCTCCCTTTATTTTAG 57.434 33.333 0.00 0.00 0.00 1.85
284 285 9.561069 GTAGATTCATGCTCCCTTTATTTTAGA 57.439 33.333 0.00 0.00 0.00 2.10
286 287 9.479549 AGATTCATGCTCCCTTTATTTTAGAAA 57.520 29.630 0.00 0.00 0.00 2.52
342 343 0.249120 TATGGCCCGCGGATATTCAG 59.751 55.000 30.73 9.14 0.00 3.02
347 348 0.319900 CCCGCGGATATTCAGGTGAG 60.320 60.000 30.73 0.00 0.00 3.51
362 363 4.019411 TCAGGTGAGCCATGAGATTGTAAA 60.019 41.667 0.00 0.00 37.19 2.01
363 364 4.701651 CAGGTGAGCCATGAGATTGTAAAA 59.298 41.667 0.00 0.00 37.19 1.52
371 372 6.875195 AGCCATGAGATTGTAAAATTTTGTGG 59.125 34.615 13.76 8.18 0.00 4.17
372 373 6.873076 GCCATGAGATTGTAAAATTTTGTGGA 59.127 34.615 13.76 0.00 0.00 4.02
379 380 8.558700 AGATTGTAAAATTTTGTGGACAAATGC 58.441 29.630 16.75 11.27 44.30 3.56
382 383 8.273780 TGTAAAATTTTGTGGACAAATGCTTT 57.726 26.923 13.76 8.24 44.30 3.51
386 387 7.571080 AATTTTGTGGACAAATGCTTTCATT 57.429 28.000 5.80 0.00 44.30 2.57
401 402 0.825425 TCATTTGCGGCTTGGGTGAA 60.825 50.000 0.00 0.00 0.00 3.18
477 479 7.440523 TTGGTTTGTTATTTTTGCACAACTT 57.559 28.000 0.00 0.00 30.12 2.66
490 492 4.440880 TGCACAACTTGGAAAAAGAATGG 58.559 39.130 0.00 0.00 0.00 3.16
491 493 3.809279 GCACAACTTGGAAAAAGAATGGG 59.191 43.478 0.00 0.00 0.00 4.00
492 494 4.683129 GCACAACTTGGAAAAAGAATGGGT 60.683 41.667 0.00 0.00 0.00 4.51
596 600 4.065088 TCTGAGCACACTTGATGGTTTAC 58.935 43.478 0.00 0.00 0.00 2.01
597 601 3.146066 TGAGCACACTTGATGGTTTACC 58.854 45.455 0.00 0.00 0.00 2.85
609 613 3.248495 TGGTTTACCGATATTCGCACA 57.752 42.857 0.00 0.00 38.82 4.57
707 711 9.177608 TGGGAAATGAAGAAATGTTCATAGTAG 57.822 33.333 6.26 0.00 44.72 2.57
720 724 5.729229 TGTTCATAGTAGGAATGGGAAGGAA 59.271 40.000 0.00 0.00 0.00 3.36
721 725 5.888982 TCATAGTAGGAATGGGAAGGAAC 57.111 43.478 0.00 0.00 0.00 3.62
746 752 7.658575 ACAGCAGCATTTTCATTCAAATAACTT 59.341 29.630 0.00 0.00 0.00 2.66
774 780 4.944317 GGCTGCCTTCTGTATTTTCTACTT 59.056 41.667 12.43 0.00 0.00 2.24
797 833 2.200373 TTTAACTTGAGCTGGCCTCC 57.800 50.000 3.32 0.00 39.98 4.30
798 834 1.362224 TTAACTTGAGCTGGCCTCCT 58.638 50.000 3.32 0.00 39.98 3.69
799 835 0.615331 TAACTTGAGCTGGCCTCCTG 59.385 55.000 3.32 0.00 39.98 3.86
801 837 1.078567 CTTGAGCTGGCCTCCTGAC 60.079 63.158 3.32 0.00 39.98 3.51
802 838 1.537397 TTGAGCTGGCCTCCTGACT 60.537 57.895 3.32 0.00 39.98 3.41
806 842 0.396974 AGCTGGCCTCCTGACTAGAG 60.397 60.000 3.32 0.00 0.00 2.43
836 873 1.561076 AGTGAACAGCCCATCAGCATA 59.439 47.619 0.00 0.00 34.23 3.14
867 904 3.683937 CCCAACAAAGCCAGGCCG 61.684 66.667 8.22 0.00 0.00 6.13
869 906 2.629656 CCAACAAAGCCAGGCCGAG 61.630 63.158 8.22 0.00 0.00 4.63
882 919 4.559063 CCGAGAGCCCAGCCCATG 62.559 72.222 0.00 0.00 0.00 3.66
885 922 3.412624 GAGAGCCCAGCCCATGACC 62.413 68.421 0.00 0.00 0.00 4.02
891 928 3.341629 CAGCCCATGACCCCACCT 61.342 66.667 0.00 0.00 0.00 4.00
892 929 3.017581 AGCCCATGACCCCACCTC 61.018 66.667 0.00 0.00 0.00 3.85
893 930 3.338250 GCCCATGACCCCACCTCA 61.338 66.667 0.00 0.00 0.00 3.86
902 939 3.616219 TGACCCCACCTCAAAAATATCG 58.384 45.455 0.00 0.00 0.00 2.92
959 996 1.214673 GGTTTATCCCCACCCTCTTCC 59.785 57.143 0.00 0.00 0.00 3.46
960 997 2.206223 GTTTATCCCCACCCTCTTCCT 58.794 52.381 0.00 0.00 0.00 3.36
961 998 2.581246 GTTTATCCCCACCCTCTTCCTT 59.419 50.000 0.00 0.00 0.00 3.36
962 999 2.191981 TATCCCCACCCTCTTCCTTC 57.808 55.000 0.00 0.00 0.00 3.46
1753 2169 1.051556 GGAGGCCGAGGAGAGGAATT 61.052 60.000 0.00 0.00 0.00 2.17
1755 2171 0.543749 AGGCCGAGGAGAGGAATTTG 59.456 55.000 0.00 0.00 0.00 2.32
1758 2174 2.368875 GGCCGAGGAGAGGAATTTGATA 59.631 50.000 0.00 0.00 0.00 2.15
1761 2177 5.066593 GCCGAGGAGAGGAATTTGATAATT 58.933 41.667 0.00 0.00 36.68 1.40
1785 2201 2.030562 CCGCTCAGGTTCAACCGT 59.969 61.111 0.00 0.00 44.90 4.83
1869 2285 4.954933 ATGCCGTACATTTCGCCT 57.045 50.000 0.00 0.00 34.40 5.52
1983 2399 3.049674 CGCACGCTGGTTGACCAT 61.050 61.111 2.85 0.00 46.46 3.55
2268 2684 3.251004 CGCAAGGGTATAATGAAGGAAGC 59.749 47.826 0.00 0.00 0.00 3.86
2301 2717 5.869344 AGATGACGAAGACGATGATTTTTCA 59.131 36.000 0.00 0.00 42.66 2.69
2444 2860 0.318762 AGTCCACAAGAAGTCGAGGC 59.681 55.000 0.00 0.00 0.00 4.70
2451 2867 1.946768 CAAGAAGTCGAGGCACCAAAA 59.053 47.619 0.00 0.00 0.00 2.44
2452 2868 1.884235 AGAAGTCGAGGCACCAAAAG 58.116 50.000 0.00 0.00 0.00 2.27
2464 2880 3.989817 GGCACCAAAAGCAAAGAGTAATG 59.010 43.478 0.00 0.00 0.00 1.90
2467 2883 4.682860 CACCAAAAGCAAAGAGTAATGCAG 59.317 41.667 0.00 0.00 44.95 4.41
2548 2964 5.410355 ACGGTGGTAAACTGAGCTATTTA 57.590 39.130 0.00 0.00 38.65 1.40
2549 2965 5.797051 ACGGTGGTAAACTGAGCTATTTAA 58.203 37.500 0.00 0.00 38.65 1.52
2620 3051 5.821470 CCTATCTGATGTCTTTTGATGTGCT 59.179 40.000 0.00 0.00 0.00 4.40
2857 3291 6.539826 TGATTGATCATACCTTGTGATGTGTC 59.460 38.462 0.00 0.00 36.49 3.67
2873 3307 3.138304 TGTGTCGATCTGTTTTCAAGGG 58.862 45.455 0.00 0.00 0.00 3.95
2896 3575 3.550437 AAGTGTGAGCTGTCAAGAGTT 57.450 42.857 0.00 0.00 33.27 3.01
2897 3576 3.104843 AGTGTGAGCTGTCAAGAGTTC 57.895 47.619 0.00 0.00 33.27 3.01
3004 3683 1.664321 CTGATTGCAAGGCCCTCTGC 61.664 60.000 13.76 13.76 40.16 4.26
3064 3743 6.037062 CACCGAGCACATCATTAGAATAACAA 59.963 38.462 0.00 0.00 0.00 2.83
3088 3767 2.032799 TCACATTTTGAACGACCTGCAC 59.967 45.455 0.00 0.00 0.00 4.57
3126 3805 3.321111 GTCTTCAGTACAGTCCTCCAACA 59.679 47.826 0.00 0.00 0.00 3.33
3131 3810 6.428083 TCAGTACAGTCCTCCAACAAATAA 57.572 37.500 0.00 0.00 0.00 1.40
3210 3894 5.336372 GGCTGCAAATGTACCACTATTGAAA 60.336 40.000 0.50 0.00 0.00 2.69
3225 3909 7.036829 CACTATTGAAATTTGGATGCATGACA 58.963 34.615 2.46 0.00 0.00 3.58
3249 3933 5.877012 AGATCATACCTTGTGACATGTTGAC 59.123 40.000 0.00 0.49 0.00 3.18
3277 3965 6.839124 ATGCAAGGACTATCAATTGTCAAA 57.161 33.333 5.13 0.00 34.85 2.69
3466 4165 3.666638 CGCATGAGTAGCAGATAGAGTCG 60.667 52.174 0.00 0.00 0.00 4.18
3472 4172 7.569639 TGAGTAGCAGATAGAGTCGTATTTT 57.430 36.000 0.00 0.00 0.00 1.82
3519 4220 0.250467 TTCTTCAGCACAGCACTCCC 60.250 55.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.418913 TTTCATGGCGGTCGCGTG 61.419 61.111 5.77 10.46 43.06 5.34
7 8 3.419759 GTTTCATGGCGGTCGCGT 61.420 61.111 5.77 0.00 43.06 6.01
8 9 2.252127 ATTGTTTCATGGCGGTCGCG 62.252 55.000 0.00 0.00 43.06 5.87
9 10 0.798009 CATTGTTTCATGGCGGTCGC 60.798 55.000 6.83 6.83 41.06 5.19
10 11 0.521291 ACATTGTTTCATGGCGGTCG 59.479 50.000 0.00 0.00 0.00 4.79
11 12 2.595386 GAACATTGTTTCATGGCGGTC 58.405 47.619 3.08 0.00 0.00 4.79
12 13 1.272212 GGAACATTGTTTCATGGCGGT 59.728 47.619 3.08 0.00 0.00 5.68
13 14 1.271934 TGGAACATTGTTTCATGGCGG 59.728 47.619 6.41 0.00 0.00 6.13
14 15 2.721274 TGGAACATTGTTTCATGGCG 57.279 45.000 6.41 0.00 0.00 5.69
22 23 6.983776 GGCATTAGCGCATGGAACATTGTT 62.984 45.833 11.47 0.63 43.42 2.83
23 24 5.587553 GGCATTAGCGCATGGAACATTGT 62.588 47.826 11.47 0.00 43.42 2.71
24 25 3.113547 GGCATTAGCGCATGGAACATTG 61.114 50.000 11.47 0.00 43.42 2.82
25 26 1.067516 GGCATTAGCGCATGGAACATT 59.932 47.619 11.47 0.00 43.42 2.71
26 27 0.670162 GGCATTAGCGCATGGAACAT 59.330 50.000 11.47 0.00 43.42 2.71
27 28 0.394216 AGGCATTAGCGCATGGAACA 60.394 50.000 11.47 0.00 43.53 3.18
28 29 1.593196 TAGGCATTAGCGCATGGAAC 58.407 50.000 11.47 0.00 43.41 3.62
29 30 2.340210 TTAGGCATTAGCGCATGGAA 57.660 45.000 11.47 0.00 43.41 3.53
30 31 2.566833 ATTAGGCATTAGCGCATGGA 57.433 45.000 11.47 0.00 43.41 3.41
31 32 2.553602 TGAATTAGGCATTAGCGCATGG 59.446 45.455 11.47 0.00 43.41 3.66
32 33 3.902261 TGAATTAGGCATTAGCGCATG 57.098 42.857 11.47 6.78 43.41 4.06
33 34 6.183360 GGAATATGAATTAGGCATTAGCGCAT 60.183 38.462 11.47 0.00 43.41 4.73
34 35 5.123820 GGAATATGAATTAGGCATTAGCGCA 59.876 40.000 11.47 0.00 43.41 6.09
35 36 5.449177 GGGAATATGAATTAGGCATTAGCGC 60.449 44.000 0.00 0.00 43.41 5.92
36 37 5.882557 AGGGAATATGAATTAGGCATTAGCG 59.117 40.000 0.00 0.00 43.41 4.26
37 38 7.066766 CAGAGGGAATATGAATTAGGCATTAGC 59.933 40.741 0.00 0.00 41.10 3.09
38 39 8.105829 ACAGAGGGAATATGAATTAGGCATTAG 58.894 37.037 0.00 0.00 0.00 1.73
39 40 7.988937 ACAGAGGGAATATGAATTAGGCATTA 58.011 34.615 0.00 0.00 0.00 1.90
40 41 6.856757 ACAGAGGGAATATGAATTAGGCATT 58.143 36.000 0.00 0.00 0.00 3.56
41 42 6.460103 ACAGAGGGAATATGAATTAGGCAT 57.540 37.500 0.00 0.00 0.00 4.40
42 43 5.912149 ACAGAGGGAATATGAATTAGGCA 57.088 39.130 0.00 0.00 0.00 4.75
43 44 5.707764 GGAACAGAGGGAATATGAATTAGGC 59.292 44.000 0.00 0.00 0.00 3.93
44 45 6.841601 TGGAACAGAGGGAATATGAATTAGG 58.158 40.000 0.00 0.00 0.00 2.69
45 46 8.752005 TTTGGAACAGAGGGAATATGAATTAG 57.248 34.615 0.00 0.00 42.39 1.73
46 47 9.713684 ATTTTGGAACAGAGGGAATATGAATTA 57.286 29.630 0.00 0.00 42.39 1.40
47 48 8.613922 ATTTTGGAACAGAGGGAATATGAATT 57.386 30.769 0.00 0.00 42.39 2.17
48 49 9.359653 CTATTTTGGAACAGAGGGAATATGAAT 57.640 33.333 0.00 0.00 42.39 2.57
49 50 8.556589 TCTATTTTGGAACAGAGGGAATATGAA 58.443 33.333 0.00 0.00 42.39 2.57
50 51 8.101309 TCTATTTTGGAACAGAGGGAATATGA 57.899 34.615 0.00 0.00 42.39 2.15
51 52 8.790718 CATCTATTTTGGAACAGAGGGAATATG 58.209 37.037 0.00 0.00 42.39 1.78
52 53 8.727149 TCATCTATTTTGGAACAGAGGGAATAT 58.273 33.333 0.00 0.00 42.39 1.28
53 54 8.101309 TCATCTATTTTGGAACAGAGGGAATA 57.899 34.615 0.00 0.00 42.39 1.75
54 55 6.973642 TCATCTATTTTGGAACAGAGGGAAT 58.026 36.000 0.00 0.00 42.39 3.01
55 56 6.387192 TCATCTATTTTGGAACAGAGGGAA 57.613 37.500 0.00 0.00 42.39 3.97
56 57 6.409695 GGATCATCTATTTTGGAACAGAGGGA 60.410 42.308 0.00 0.00 42.39 4.20
57 58 5.767168 GGATCATCTATTTTGGAACAGAGGG 59.233 44.000 0.00 0.00 42.39 4.30
58 59 6.359804 TGGATCATCTATTTTGGAACAGAGG 58.640 40.000 0.00 0.00 42.39 3.69
59 60 7.870509 TTGGATCATCTATTTTGGAACAGAG 57.129 36.000 0.00 0.00 42.39 3.35
60 61 8.827832 AATTGGATCATCTATTTTGGAACAGA 57.172 30.769 0.00 0.00 42.39 3.41
61 62 9.880157 AAAATTGGATCATCTATTTTGGAACAG 57.120 29.630 9.05 0.00 42.39 3.16
110 111 8.859090 TCCAAAACAGATGACTCAATTTTGTAT 58.141 29.630 14.10 0.00 37.08 2.29
111 112 8.231692 TCCAAAACAGATGACTCAATTTTGTA 57.768 30.769 14.10 3.44 37.08 2.41
112 113 7.111247 TCCAAAACAGATGACTCAATTTTGT 57.889 32.000 14.10 3.18 37.08 2.83
113 114 7.306167 CGTTCCAAAACAGATGACTCAATTTTG 60.306 37.037 10.99 10.99 37.76 2.44
114 115 6.697019 CGTTCCAAAACAGATGACTCAATTTT 59.303 34.615 0.00 0.00 34.93 1.82
115 116 6.208644 CGTTCCAAAACAGATGACTCAATTT 58.791 36.000 0.00 0.00 34.93 1.82
116 117 5.278463 CCGTTCCAAAACAGATGACTCAATT 60.278 40.000 0.00 0.00 34.93 2.32
117 118 4.216257 CCGTTCCAAAACAGATGACTCAAT 59.784 41.667 0.00 0.00 34.93 2.57
118 119 3.563808 CCGTTCCAAAACAGATGACTCAA 59.436 43.478 0.00 0.00 34.93 3.02
119 120 3.138304 CCGTTCCAAAACAGATGACTCA 58.862 45.455 0.00 0.00 34.93 3.41
120 121 3.399330 TCCGTTCCAAAACAGATGACTC 58.601 45.455 0.00 0.00 34.93 3.36
121 122 3.403038 CTCCGTTCCAAAACAGATGACT 58.597 45.455 0.00 0.00 34.93 3.41
122 123 2.484264 CCTCCGTTCCAAAACAGATGAC 59.516 50.000 0.00 0.00 34.93 3.06
123 124 2.778299 CCTCCGTTCCAAAACAGATGA 58.222 47.619 0.00 0.00 34.93 2.92
124 125 1.200020 GCCTCCGTTCCAAAACAGATG 59.800 52.381 0.00 0.00 34.93 2.90
125 126 1.073923 AGCCTCCGTTCCAAAACAGAT 59.926 47.619 0.00 0.00 34.93 2.90
126 127 0.472471 AGCCTCCGTTCCAAAACAGA 59.528 50.000 0.00 0.00 34.93 3.41
127 128 1.318576 AAGCCTCCGTTCCAAAACAG 58.681 50.000 0.00 0.00 34.93 3.16
128 129 2.642154 TAAGCCTCCGTTCCAAAACA 57.358 45.000 0.00 0.00 34.93 2.83
129 130 5.632244 TTATTAAGCCTCCGTTCCAAAAC 57.368 39.130 0.00 0.00 0.00 2.43
130 131 5.771165 AGTTTATTAAGCCTCCGTTCCAAAA 59.229 36.000 0.00 0.00 0.00 2.44
131 132 5.318630 AGTTTATTAAGCCTCCGTTCCAAA 58.681 37.500 0.00 0.00 0.00 3.28
132 133 4.913784 AGTTTATTAAGCCTCCGTTCCAA 58.086 39.130 0.00 0.00 0.00 3.53
133 134 4.563140 AGTTTATTAAGCCTCCGTTCCA 57.437 40.909 0.00 0.00 0.00 3.53
134 135 6.990341 TTTAGTTTATTAAGCCTCCGTTCC 57.010 37.500 0.00 0.00 0.00 3.62
135 136 8.281194 GCTATTTAGTTTATTAAGCCTCCGTTC 58.719 37.037 0.00 0.00 0.00 3.95
136 137 7.771826 TGCTATTTAGTTTATTAAGCCTCCGTT 59.228 33.333 0.00 0.00 0.00 4.44
137 138 7.277396 TGCTATTTAGTTTATTAAGCCTCCGT 58.723 34.615 0.00 0.00 0.00 4.69
138 139 7.724305 TGCTATTTAGTTTATTAAGCCTCCG 57.276 36.000 0.00 0.00 0.00 4.63
139 140 9.067986 ACATGCTATTTAGTTTATTAAGCCTCC 57.932 33.333 0.00 0.00 0.00 4.30
142 143 9.807386 CGTACATGCTATTTAGTTTATTAAGCC 57.193 33.333 0.00 0.00 0.00 4.35
148 149 9.609346 AGGAAACGTACATGCTATTTAGTTTAT 57.391 29.630 0.00 0.00 31.76 1.40
149 150 9.090692 GAGGAAACGTACATGCTATTTAGTTTA 57.909 33.333 0.00 0.00 31.76 2.01
150 151 7.822822 AGAGGAAACGTACATGCTATTTAGTTT 59.177 33.333 0.00 0.00 33.90 2.66
151 152 7.328737 AGAGGAAACGTACATGCTATTTAGTT 58.671 34.615 0.00 0.00 0.00 2.24
152 153 6.875076 AGAGGAAACGTACATGCTATTTAGT 58.125 36.000 0.00 0.00 0.00 2.24
153 154 7.772332 AAGAGGAAACGTACATGCTATTTAG 57.228 36.000 0.00 0.00 0.00 1.85
154 155 7.820386 TCAAAGAGGAAACGTACATGCTATTTA 59.180 33.333 8.80 0.00 29.21 1.40
155 156 6.653320 TCAAAGAGGAAACGTACATGCTATTT 59.347 34.615 0.00 0.00 30.10 1.40
156 157 6.170506 TCAAAGAGGAAACGTACATGCTATT 58.829 36.000 0.00 0.00 0.00 1.73
157 158 5.730550 TCAAAGAGGAAACGTACATGCTAT 58.269 37.500 0.00 0.00 0.00 2.97
158 159 5.142061 TCAAAGAGGAAACGTACATGCTA 57.858 39.130 0.00 0.00 0.00 3.49
159 160 4.002906 TCAAAGAGGAAACGTACATGCT 57.997 40.909 0.00 0.00 0.00 3.79
160 161 4.154195 ACATCAAAGAGGAAACGTACATGC 59.846 41.667 0.00 0.00 0.00 4.06
161 162 5.639506 AGACATCAAAGAGGAAACGTACATG 59.360 40.000 0.00 0.00 0.00 3.21
162 163 5.794894 AGACATCAAAGAGGAAACGTACAT 58.205 37.500 0.00 0.00 0.00 2.29
163 164 5.209818 AGACATCAAAGAGGAAACGTACA 57.790 39.130 0.00 0.00 0.00 2.90
164 165 6.196724 CGATAGACATCAAAGAGGAAACGTAC 59.803 42.308 0.00 0.00 39.76 3.67
165 166 6.094464 TCGATAGACATCAAAGAGGAAACGTA 59.906 38.462 0.00 0.00 42.67 3.57
166 167 5.103000 CGATAGACATCAAAGAGGAAACGT 58.897 41.667 0.00 0.00 39.76 3.99
167 168 5.340803 TCGATAGACATCAAAGAGGAAACG 58.659 41.667 0.00 0.00 42.67 3.60
168 169 5.751028 CCTCGATAGACATCAAAGAGGAAAC 59.249 44.000 2.69 0.00 44.68 2.78
169 170 5.656859 TCCTCGATAGACATCAAAGAGGAAA 59.343 40.000 8.63 0.00 46.57 3.13
170 171 5.201243 TCCTCGATAGACATCAAAGAGGAA 58.799 41.667 8.63 0.00 46.57 3.36
172 173 5.300539 TCTTCCTCGATAGACATCAAAGAGG 59.699 44.000 2.44 2.44 42.67 3.69
173 174 6.384258 TCTTCCTCGATAGACATCAAAGAG 57.616 41.667 0.00 0.00 42.67 2.85
174 175 6.152831 TGTTCTTCCTCGATAGACATCAAAGA 59.847 38.462 0.00 0.00 42.67 2.52
175 176 6.333416 TGTTCTTCCTCGATAGACATCAAAG 58.667 40.000 0.00 0.00 42.67 2.77
176 177 6.280855 TGTTCTTCCTCGATAGACATCAAA 57.719 37.500 0.00 0.00 42.67 2.69
177 178 5.914898 TGTTCTTCCTCGATAGACATCAA 57.085 39.130 0.00 0.00 42.67 2.57
178 179 5.360999 ACATGTTCTTCCTCGATAGACATCA 59.639 40.000 0.00 0.00 42.67 3.07
179 180 5.837437 ACATGTTCTTCCTCGATAGACATC 58.163 41.667 0.00 0.00 42.67 3.06
180 181 5.860941 ACATGTTCTTCCTCGATAGACAT 57.139 39.130 0.00 0.00 42.67 3.06
181 182 6.961360 ATACATGTTCTTCCTCGATAGACA 57.039 37.500 2.30 0.00 42.67 3.41
182 183 7.653647 AGAATACATGTTCTTCCTCGATAGAC 58.346 38.462 2.30 0.00 36.01 2.59
183 184 7.502561 TGAGAATACATGTTCTTCCTCGATAGA 59.497 37.037 2.30 0.00 39.91 1.98
184 185 7.652727 TGAGAATACATGTTCTTCCTCGATAG 58.347 38.462 2.30 0.00 38.51 2.08
185 186 7.582667 TGAGAATACATGTTCTTCCTCGATA 57.417 36.000 2.30 0.00 38.51 2.92
186 187 6.471233 TGAGAATACATGTTCTTCCTCGAT 57.529 37.500 2.30 0.00 38.51 3.59
187 188 5.914898 TGAGAATACATGTTCTTCCTCGA 57.085 39.130 2.30 0.00 38.51 4.04
188 189 6.522233 CATGAGAATACATGTTCTTCCTCG 57.478 41.667 2.30 0.00 41.59 4.63
214 215 4.321452 CCTTCTGTGAACATCACCAAATGG 60.321 45.833 7.94 0.00 46.40 3.16
215 216 4.279169 ACCTTCTGTGAACATCACCAAATG 59.721 41.667 7.94 3.00 46.40 2.32
216 217 4.473444 ACCTTCTGTGAACATCACCAAAT 58.527 39.130 7.94 0.00 46.40 2.32
217 218 3.897239 ACCTTCTGTGAACATCACCAAA 58.103 40.909 7.94 2.23 46.40 3.28
218 219 3.576078 ACCTTCTGTGAACATCACCAA 57.424 42.857 7.94 1.02 46.40 3.67
229 230 1.202405 GCACAAAACCCACCTTCTGTG 60.202 52.381 0.00 0.00 45.01 3.66
230 231 1.111277 GCACAAAACCCACCTTCTGT 58.889 50.000 0.00 0.00 0.00 3.41
231 232 1.338020 GAGCACAAAACCCACCTTCTG 59.662 52.381 0.00 0.00 0.00 3.02
232 233 1.215423 AGAGCACAAAACCCACCTTCT 59.785 47.619 0.00 0.00 0.00 2.85
233 234 1.338020 CAGAGCACAAAACCCACCTTC 59.662 52.381 0.00 0.00 0.00 3.46
234 235 1.402787 CAGAGCACAAAACCCACCTT 58.597 50.000 0.00 0.00 0.00 3.50
235 236 0.468029 CCAGAGCACAAAACCCACCT 60.468 55.000 0.00 0.00 0.00 4.00
236 237 1.463553 CCCAGAGCACAAAACCCACC 61.464 60.000 0.00 0.00 0.00 4.61
237 238 0.467290 TCCCAGAGCACAAAACCCAC 60.467 55.000 0.00 0.00 0.00 4.61
238 239 0.260230 TTCCCAGAGCACAAAACCCA 59.740 50.000 0.00 0.00 0.00 4.51
239 240 0.961753 CTTCCCAGAGCACAAAACCC 59.038 55.000 0.00 0.00 0.00 4.11
240 241 1.692411 ACTTCCCAGAGCACAAAACC 58.308 50.000 0.00 0.00 0.00 3.27
241 242 3.740115 TCTACTTCCCAGAGCACAAAAC 58.260 45.455 0.00 0.00 0.00 2.43
242 243 4.640771 ATCTACTTCCCAGAGCACAAAA 57.359 40.909 0.00 0.00 0.00 2.44
243 244 4.041567 TGAATCTACTTCCCAGAGCACAAA 59.958 41.667 0.00 0.00 32.49 2.83
244 245 3.582647 TGAATCTACTTCCCAGAGCACAA 59.417 43.478 0.00 0.00 32.49 3.33
245 246 3.173151 TGAATCTACTTCCCAGAGCACA 58.827 45.455 0.00 0.00 32.49 4.57
246 247 3.895232 TGAATCTACTTCCCAGAGCAC 57.105 47.619 0.00 0.00 32.49 4.40
247 248 3.432749 GCATGAATCTACTTCCCAGAGCA 60.433 47.826 0.00 0.00 32.49 4.26
248 249 3.137533 GCATGAATCTACTTCCCAGAGC 58.862 50.000 0.00 0.00 32.49 4.09
249 250 4.502950 GGAGCATGAATCTACTTCCCAGAG 60.503 50.000 0.00 0.00 32.49 3.35
250 251 3.389329 GGAGCATGAATCTACTTCCCAGA 59.611 47.826 0.00 0.00 32.49 3.86
251 252 3.495806 GGGAGCATGAATCTACTTCCCAG 60.496 52.174 0.00 0.00 35.13 4.45
252 253 2.439507 GGGAGCATGAATCTACTTCCCA 59.560 50.000 0.00 0.00 35.13 4.37
253 254 2.708325 AGGGAGCATGAATCTACTTCCC 59.292 50.000 0.00 0.00 32.49 3.97
254 255 4.429854 AAGGGAGCATGAATCTACTTCC 57.570 45.455 0.00 0.00 32.49 3.46
255 256 8.457238 AAATAAAGGGAGCATGAATCTACTTC 57.543 34.615 0.00 0.00 0.00 3.01
256 257 8.829373 AAAATAAAGGGAGCATGAATCTACTT 57.171 30.769 0.00 0.55 0.00 2.24
257 258 9.566432 CTAAAATAAAGGGAGCATGAATCTACT 57.434 33.333 0.00 0.00 0.00 2.57
258 259 9.561069 TCTAAAATAAAGGGAGCATGAATCTAC 57.439 33.333 0.00 0.00 0.00 2.59
260 261 9.479549 TTTCTAAAATAAAGGGAGCATGAATCT 57.520 29.630 0.00 0.00 0.00 2.40
331 332 0.106708 TGGCTCACCTGAATATCCGC 59.893 55.000 0.00 0.00 36.63 5.54
332 333 2.037641 TCATGGCTCACCTGAATATCCG 59.962 50.000 0.00 0.00 36.63 4.18
334 335 4.613925 TCTCATGGCTCACCTGAATATC 57.386 45.455 0.00 0.00 36.63 1.63
342 343 5.841957 ATTTTACAATCTCATGGCTCACC 57.158 39.130 0.00 0.00 0.00 4.02
347 348 6.873076 TCCACAAAATTTTACAATCTCATGGC 59.127 34.615 2.44 0.00 0.00 4.40
378 379 1.015607 CCCAAGCCGCAAATGAAAGC 61.016 55.000 0.00 0.00 0.00 3.51
379 380 0.318120 ACCCAAGCCGCAAATGAAAG 59.682 50.000 0.00 0.00 0.00 2.62
382 383 0.825425 TTCACCCAAGCCGCAAATGA 60.825 50.000 0.00 0.00 0.00 2.57
386 387 2.202866 TTTTTCACCCAAGCCGCAA 58.797 47.368 0.00 0.00 0.00 4.85
451 452 8.049655 AGTTGTGCAAAAATAACAAACCAAAT 57.950 26.923 0.00 0.00 0.00 2.32
453 454 7.301054 CAAGTTGTGCAAAAATAACAAACCAA 58.699 30.769 0.00 0.00 0.00 3.67
596 600 2.225068 AGGAAGTGTGCGAATATCGG 57.775 50.000 1.64 0.00 40.84 4.18
597 601 5.907197 ATTTAGGAAGTGTGCGAATATCG 57.093 39.130 0.00 0.00 43.89 2.92
681 685 9.177608 CTACTATGAACATTTCTTCATTTCCCA 57.822 33.333 0.01 0.00 40.60 4.37
698 702 5.729229 TGTTCCTTCCCATTCCTACTATGAA 59.271 40.000 0.00 0.00 0.00 2.57
703 707 2.239907 GCTGTTCCTTCCCATTCCTACT 59.760 50.000 0.00 0.00 0.00 2.57
707 711 1.467920 CTGCTGTTCCTTCCCATTCC 58.532 55.000 0.00 0.00 0.00 3.01
720 724 7.156673 AGTTATTTGAATGAAAATGCTGCTGT 58.843 30.769 0.00 0.00 32.16 4.40
721 725 7.591006 AGTTATTTGAATGAAAATGCTGCTG 57.409 32.000 0.00 0.00 32.16 4.41
781 817 1.130054 TCAGGAGGCCAGCTCAAGTT 61.130 55.000 5.01 0.00 0.00 2.66
796 832 1.698506 ATCCGCTTCCTCTAGTCAGG 58.301 55.000 0.00 0.00 34.40 3.86
797 833 3.252215 CACTATCCGCTTCCTCTAGTCAG 59.748 52.174 0.00 0.00 0.00 3.51
798 834 3.118000 TCACTATCCGCTTCCTCTAGTCA 60.118 47.826 0.00 0.00 0.00 3.41
799 835 3.478509 TCACTATCCGCTTCCTCTAGTC 58.521 50.000 0.00 0.00 0.00 2.59
801 837 3.632604 TGTTCACTATCCGCTTCCTCTAG 59.367 47.826 0.00 0.00 0.00 2.43
802 838 3.628008 TGTTCACTATCCGCTTCCTCTA 58.372 45.455 0.00 0.00 0.00 2.43
806 842 1.291132 GCTGTTCACTATCCGCTTCC 58.709 55.000 0.00 0.00 0.00 3.46
811 848 1.138859 TGATGGGCTGTTCACTATCCG 59.861 52.381 0.00 0.00 0.00 4.18
867 904 2.191641 GTCATGGGCTGGGCTCTC 59.808 66.667 0.00 0.00 0.00 3.20
869 906 4.512914 GGGTCATGGGCTGGGCTC 62.513 72.222 0.00 0.00 0.00 4.70
882 919 2.357952 GCGATATTTTTGAGGTGGGGTC 59.642 50.000 0.00 0.00 0.00 4.46
885 922 1.681264 GGGCGATATTTTTGAGGTGGG 59.319 52.381 0.00 0.00 0.00 4.61
888 925 4.583073 GGTTATGGGCGATATTTTTGAGGT 59.417 41.667 0.00 0.00 0.00 3.85
891 928 3.892588 GGGGTTATGGGCGATATTTTTGA 59.107 43.478 0.00 0.00 0.00 2.69
892 929 3.006430 GGGGGTTATGGGCGATATTTTTG 59.994 47.826 0.00 0.00 0.00 2.44
893 930 3.236047 GGGGGTTATGGGCGATATTTTT 58.764 45.455 0.00 0.00 0.00 1.94
982 1019 1.135431 CATTTTTGCGGCTCGGATGAA 60.135 47.619 0.00 0.00 0.00 2.57
986 1023 1.302913 TCCATTTTTGCGGCTCGGA 60.303 52.632 0.00 0.00 0.00 4.55
1753 2169 0.107410 AGCGGCCGGTCAATTATCAA 60.107 50.000 26.97 0.00 0.00 2.57
1755 2171 2.235546 GAGCGGCCGGTCAATTATC 58.764 57.895 43.37 21.74 41.72 1.75
1785 2201 2.115910 CCCTTGGGCAGCTTCACA 59.884 61.111 0.00 0.00 0.00 3.58
1869 2285 1.443194 GTGCGAGAAGTCGGCGTAA 60.443 57.895 6.85 0.00 46.91 3.18
1983 2399 1.195115 CCTCCCGGAAATGAGTCAGA 58.805 55.000 0.73 0.00 0.00 3.27
2268 2684 2.854777 GTCTTCGTCATCTTCCATGTCG 59.145 50.000 0.00 0.00 33.25 4.35
2301 2717 4.017222 TCCCCAATCAAATCTTCCATGTCT 60.017 41.667 0.00 0.00 0.00 3.41
2444 2860 4.619973 TGCATTACTCTTTGCTTTTGGTG 58.380 39.130 0.00 0.00 39.60 4.17
2451 2867 2.205022 TGGCTGCATTACTCTTTGCT 57.795 45.000 0.50 0.00 39.60 3.91
2452 2868 3.119388 TCATTGGCTGCATTACTCTTTGC 60.119 43.478 0.50 0.00 39.33 3.68
2597 3013 6.762187 AGAGCACATCAAAAGACATCAGATAG 59.238 38.462 0.00 0.00 0.00 2.08
2620 3051 0.036732 CTAGCCAACAACCCAGCAGA 59.963 55.000 0.00 0.00 0.00 4.26
2675 3109 8.620416 GTTATCATGCAGGTTGTTCACAATATA 58.380 33.333 0.00 0.00 38.24 0.86
2857 3291 4.003648 ACTTAGCCCTTGAAAACAGATCG 58.996 43.478 0.00 0.00 0.00 3.69
2873 3307 2.992543 CTCTTGACAGCTCACACTTAGC 59.007 50.000 0.00 0.00 40.40 3.09
2896 3575 3.243359 AGCCATTTTTCACAAGAGGGA 57.757 42.857 0.00 0.00 0.00 4.20
2897 3576 4.060205 CAAAGCCATTTTTCACAAGAGGG 58.940 43.478 0.00 0.00 0.00 4.30
3004 3683 2.927871 GCCAGCTGTGCACATAAAAAGG 60.928 50.000 22.00 16.54 0.00 3.11
3035 3714 5.728637 TCTAATGATGTGCTCGGTGATAT 57.271 39.130 0.00 0.00 0.00 1.63
3064 3743 4.699735 TGCAGGTCGTTCAAAATGTGATAT 59.300 37.500 0.00 0.00 35.70 1.63
3088 3767 6.618770 CTGAAGACAGTGTTAGTGTTATCG 57.381 41.667 0.00 0.00 39.11 2.92
3210 3894 5.475909 GGTATGATCTGTCATGCATCCAAAT 59.524 40.000 0.00 0.00 45.80 2.32
3225 3909 5.877012 GTCAACATGTCACAAGGTATGATCT 59.123 40.000 0.00 0.00 0.00 2.75
3249 3933 5.294306 ACAATTGATAGTCCTTGCATACGTG 59.706 40.000 13.59 0.00 0.00 4.49
3322 4010 7.080724 TGAACAACAAAGCCATTTTTCAAAAC 58.919 30.769 0.00 0.00 0.00 2.43
3466 4165 9.013490 GTGTGATCATGCTGATTGTTAAAATAC 57.987 33.333 0.00 0.00 37.20 1.89
3472 4172 7.920160 TTTAGTGTGATCATGCTGATTGTTA 57.080 32.000 0.00 0.00 37.20 2.41


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.