Multiple sequence alignment - TraesCS5B01G155000

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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 TraesCS5B01G155000 chr5B 100.000 3868 0 0 991 4858 285507174 285503307 0.000000e+00 7143
1 TraesCS5B01G155000 chr5B 100.000 514 0 0 1 514 285508164 285507651 0.000000e+00 950
2 TraesCS5B01G155000 chr5B 94.872 117 6 0 18 134 401702364 401702480 2.990000e-42 183
3 TraesCS5B01G155000 chr5D 95.253 3918 104 26 991 4858 253186028 253182143 0.000000e+00 6130
4 TraesCS5B01G155000 chr5D 99.020 102 0 1 414 514 253186231 253186130 1.070000e-41 182
5 TraesCS5B01G155000 chr5A 93.747 3934 129 36 991 4858 335680397 335676515 0.000000e+00 5794
6 TraesCS5B01G155000 chr5A 88.024 167 13 2 355 514 335680665 335680499 1.780000e-44 191
7 TraesCS5B01G155000 chr5A 85.965 171 17 4 149 313 29430178 29430009 5.000000e-40 176
8 TraesCS5B01G155000 chr5A 83.696 184 22 5 137 314 162168855 162169036 3.010000e-37 167
9 TraesCS5B01G155000 chr1B 95.726 117 4 1 18 134 264634808 264634923 2.310000e-43 187
10 TraesCS5B01G155000 chr2D 93.600 125 6 2 18 142 406118233 406118355 8.300000e-43 185
11 TraesCS5B01G155000 chr2D 84.066 182 21 5 138 313 306707318 306707497 8.360000e-38 169
12 TraesCS5B01G155000 chr2B 93.600 125 6 2 18 142 631625280 631625158 8.300000e-43 185
13 TraesCS5B01G155000 chr6D 94.915 118 5 1 17 134 362703624 362703740 2.990000e-42 183
14 TraesCS5B01G155000 chr6D 84.615 182 19 7 137 313 138191385 138191208 6.460000e-39 172
15 TraesCS5B01G155000 chr4A 94.915 118 5 1 17 134 539085409 539085293 2.990000e-42 183
16 TraesCS5B01G155000 chr3B 94.915 118 4 2 18 134 79328589 79328473 2.990000e-42 183
17 TraesCS5B01G155000 chr6B 94.872 117 5 1 18 134 185071447 185071332 1.070000e-41 182
18 TraesCS5B01G155000 chr4B 94.872 117 5 1 18 134 471975509 471975624 1.070000e-41 182
19 TraesCS5B01G155000 chr4B 84.656 189 22 4 132 313 514565513 514565325 1.070000e-41 182
20 TraesCS5B01G155000 chr2A 85.227 176 16 8 147 313 417090157 417089983 6.460000e-39 172
21 TraesCS5B01G155000 chr2A 85.380 171 19 4 147 312 471196962 471197131 6.460000e-39 172
22 TraesCS5B01G155000 chr1D 84.239 184 21 4 137 314 57064511 57064692 6.460000e-39 172
23 TraesCS5B01G155000 chr7A 83.243 185 26 3 138 317 467645087 467644903 1.080000e-36 165


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 TraesCS5B01G155000 chr5B 285503307 285508164 4857 True 4046.5 7143 100.0000 1 4858 2 chr5B.!!$R1 4857
1 TraesCS5B01G155000 chr5D 253182143 253186231 4088 True 3156.0 6130 97.1365 414 4858 2 chr5D.!!$R1 4444
2 TraesCS5B01G155000 chr5A 335676515 335680665 4150 True 2992.5 5794 90.8855 355 4858 2 chr5A.!!$R2 4503

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
188 189 0.041238 TCCGGAGTCTCATCCCAACT 59.959 55.0 0.0 0.0 35.82 3.16 F
1938 1957 0.312102 GAGCAAGTGTGTTTGAGGCC 59.688 55.0 0.0 0.0 0.00 5.19 F
2025 2044 0.521291 GCAATGACCGTGCTAAGCAA 59.479 50.0 0.0 0.0 41.47 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2025 2044 0.952497 CTGACGGTGAAGCATGCAGT 60.952 55.000 21.98 7.09 0.00 4.40 R
2829 2857 1.985614 CATGGGACCACTCTCAGCA 59.014 57.895 0.00 0.00 0.00 4.41 R
3904 3967 2.294195 TGGATACAGAAATCCCAGGGGA 60.294 50.000 10.00 10.00 46.55 4.81 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 6.395780 TTGTATAACCCTTCCAATCCTCAA 57.604 37.500 0.00 0.00 0.00 3.02
24 25 6.001449 TGTATAACCCTTCCAATCCTCAAG 57.999 41.667 0.00 0.00 0.00 3.02
25 26 5.491078 TGTATAACCCTTCCAATCCTCAAGT 59.509 40.000 0.00 0.00 0.00 3.16
26 27 6.674861 TGTATAACCCTTCCAATCCTCAAGTA 59.325 38.462 0.00 0.00 0.00 2.24
27 28 4.576330 AACCCTTCCAATCCTCAAGTAG 57.424 45.455 0.00 0.00 0.00 2.57
29 30 2.846827 CCCTTCCAATCCTCAAGTAGGT 59.153 50.000 0.00 0.00 46.62 3.08
30 31 4.037927 CCCTTCCAATCCTCAAGTAGGTA 58.962 47.826 0.00 0.00 46.62 3.08
31 32 4.473559 CCCTTCCAATCCTCAAGTAGGTAA 59.526 45.833 0.00 0.00 46.62 2.85
32 33 5.045140 CCCTTCCAATCCTCAAGTAGGTAAA 60.045 44.000 0.00 0.00 46.62 2.01
33 34 6.353951 CCCTTCCAATCCTCAAGTAGGTAAAT 60.354 42.308 0.00 0.00 46.62 1.40
34 35 6.543831 CCTTCCAATCCTCAAGTAGGTAAATG 59.456 42.308 0.00 0.00 46.62 2.32
35 36 6.884472 TCCAATCCTCAAGTAGGTAAATGA 57.116 37.500 0.00 0.00 46.62 2.57
36 37 7.451731 TCCAATCCTCAAGTAGGTAAATGAT 57.548 36.000 0.00 0.00 46.62 2.45
37 38 8.561536 TCCAATCCTCAAGTAGGTAAATGATA 57.438 34.615 0.00 0.00 46.62 2.15
38 39 8.998814 TCCAATCCTCAAGTAGGTAAATGATAA 58.001 33.333 0.00 0.00 46.62 1.75
39 40 9.627123 CCAATCCTCAAGTAGGTAAATGATAAA 57.373 33.333 0.00 0.00 46.62 1.40
126 127 7.692460 ATTAAGACATGAGTGATTCAAAGCA 57.308 32.000 0.00 0.00 39.77 3.91
127 128 7.509141 TTAAGACATGAGTGATTCAAAGCAA 57.491 32.000 0.00 0.00 39.77 3.91
128 129 6.585695 AAGACATGAGTGATTCAAAGCAAT 57.414 33.333 0.00 0.00 39.77 3.56
129 130 7.692460 AAGACATGAGTGATTCAAAGCAATA 57.308 32.000 0.00 0.00 39.77 1.90
130 131 7.317842 AGACATGAGTGATTCAAAGCAATAG 57.682 36.000 0.00 0.00 39.77 1.73
131 132 6.883217 AGACATGAGTGATTCAAAGCAATAGT 59.117 34.615 0.00 0.00 39.77 2.12
132 133 7.065563 AGACATGAGTGATTCAAAGCAATAGTC 59.934 37.037 0.00 0.00 39.77 2.59
133 134 6.883217 ACATGAGTGATTCAAAGCAATAGTCT 59.117 34.615 0.00 0.00 39.77 3.24
134 135 6.974932 TGAGTGATTCAAAGCAATAGTCTC 57.025 37.500 0.00 0.00 31.34 3.36
135 136 6.466812 TGAGTGATTCAAAGCAATAGTCTCA 58.533 36.000 0.00 0.00 31.34 3.27
136 137 6.369890 TGAGTGATTCAAAGCAATAGTCTCAC 59.630 38.462 0.00 0.00 31.34 3.51
137 138 6.471146 AGTGATTCAAAGCAATAGTCTCACT 58.529 36.000 0.00 0.00 36.81 3.41
138 139 6.593382 AGTGATTCAAAGCAATAGTCTCACTC 59.407 38.462 0.00 0.00 36.94 3.51
139 140 6.593382 GTGATTCAAAGCAATAGTCTCACTCT 59.407 38.462 0.00 0.00 0.00 3.24
140 141 7.118971 GTGATTCAAAGCAATAGTCTCACTCTT 59.881 37.037 0.00 0.00 0.00 2.85
141 142 7.663081 TGATTCAAAGCAATAGTCTCACTCTTT 59.337 33.333 0.00 0.00 0.00 2.52
142 143 6.791887 TCAAAGCAATAGTCTCACTCTTTG 57.208 37.500 0.00 0.00 37.52 2.77
143 144 6.291377 TCAAAGCAATAGTCTCACTCTTTGT 58.709 36.000 12.01 0.00 37.48 2.83
144 145 6.425114 TCAAAGCAATAGTCTCACTCTTTGTC 59.575 38.462 12.01 2.89 37.48 3.18
145 146 4.826556 AGCAATAGTCTCACTCTTTGTCC 58.173 43.478 0.00 0.00 0.00 4.02
146 147 3.935828 GCAATAGTCTCACTCTTTGTCCC 59.064 47.826 0.00 0.00 0.00 4.46
147 148 4.323104 GCAATAGTCTCACTCTTTGTCCCT 60.323 45.833 0.00 0.00 0.00 4.20
148 149 5.799213 CAATAGTCTCACTCTTTGTCCCTT 58.201 41.667 0.00 0.00 0.00 3.95
149 150 6.234177 CAATAGTCTCACTCTTTGTCCCTTT 58.766 40.000 0.00 0.00 0.00 3.11
150 151 4.779993 AGTCTCACTCTTTGTCCCTTTT 57.220 40.909 0.00 0.00 0.00 2.27
151 152 5.117406 AGTCTCACTCTTTGTCCCTTTTT 57.883 39.130 0.00 0.00 0.00 1.94
183 184 2.762535 TTTTGTCCGGAGTCTCATCC 57.237 50.000 3.06 0.00 35.88 3.51
184 185 0.902531 TTTGTCCGGAGTCTCATCCC 59.097 55.000 3.06 0.00 35.82 3.85
185 186 0.252057 TTGTCCGGAGTCTCATCCCA 60.252 55.000 3.06 0.00 35.82 4.37
186 187 0.252057 TGTCCGGAGTCTCATCCCAA 60.252 55.000 3.06 0.00 35.82 4.12
187 188 0.175989 GTCCGGAGTCTCATCCCAAC 59.824 60.000 3.06 0.00 35.82 3.77
188 189 0.041238 TCCGGAGTCTCATCCCAACT 59.959 55.000 0.00 0.00 35.82 3.16
189 190 0.905357 CCGGAGTCTCATCCCAACTT 59.095 55.000 0.00 0.00 35.82 2.66
190 191 1.406069 CCGGAGTCTCATCCCAACTTG 60.406 57.143 0.00 0.00 35.82 3.16
191 192 1.276421 CGGAGTCTCATCCCAACTTGT 59.724 52.381 1.47 0.00 35.82 3.16
192 193 2.496070 CGGAGTCTCATCCCAACTTGTA 59.504 50.000 1.47 0.00 35.82 2.41
193 194 3.429547 CGGAGTCTCATCCCAACTTGTAG 60.430 52.174 1.47 0.00 35.82 2.74
194 195 3.118592 GGAGTCTCATCCCAACTTGTAGG 60.119 52.174 1.47 0.00 32.79 3.18
195 196 2.840651 AGTCTCATCCCAACTTGTAGGG 59.159 50.000 0.00 0.00 46.90 3.53
196 197 2.092914 GTCTCATCCCAACTTGTAGGGG 60.093 54.545 0.00 0.00 45.51 4.79
202 203 3.669939 CCCAACTTGTAGGGGAATGAT 57.330 47.619 4.90 0.00 45.08 2.45
203 204 4.788925 CCCAACTTGTAGGGGAATGATA 57.211 45.455 4.90 0.00 45.08 2.15
204 205 4.718961 CCCAACTTGTAGGGGAATGATAG 58.281 47.826 4.90 0.00 45.08 2.08
205 206 4.166144 CCCAACTTGTAGGGGAATGATAGT 59.834 45.833 4.90 0.00 45.08 2.12
206 207 5.340027 CCCAACTTGTAGGGGAATGATAGTT 60.340 44.000 4.90 0.00 45.08 2.24
207 208 6.187682 CCAACTTGTAGGGGAATGATAGTTT 58.812 40.000 0.00 0.00 0.00 2.66
208 209 6.318900 CCAACTTGTAGGGGAATGATAGTTTC 59.681 42.308 0.00 0.00 0.00 2.78
209 210 6.002653 ACTTGTAGGGGAATGATAGTTTCC 57.997 41.667 0.00 0.00 41.64 3.13
210 211 5.491078 ACTTGTAGGGGAATGATAGTTTCCA 59.509 40.000 4.96 0.00 43.72 3.53
211 212 6.160459 ACTTGTAGGGGAATGATAGTTTCCAT 59.840 38.462 4.96 0.00 43.72 3.41
212 213 6.187727 TGTAGGGGAATGATAGTTTCCATC 57.812 41.667 4.96 0.00 43.72 3.51
213 214 5.669904 TGTAGGGGAATGATAGTTTCCATCA 59.330 40.000 4.96 0.00 43.72 3.07
214 215 5.937492 AGGGGAATGATAGTTTCCATCAT 57.063 39.130 4.96 0.00 43.72 2.45
215 216 5.885465 AGGGGAATGATAGTTTCCATCATC 58.115 41.667 4.96 0.00 43.72 2.92
216 217 5.012893 GGGGAATGATAGTTTCCATCATCC 58.987 45.833 4.96 2.99 43.72 3.51
217 218 5.222213 GGGGAATGATAGTTTCCATCATCCT 60.222 44.000 4.96 0.00 43.72 3.24
218 219 6.310149 GGGAATGATAGTTTCCATCATCCTT 58.690 40.000 4.96 0.00 43.72 3.36
219 220 6.779539 GGGAATGATAGTTTCCATCATCCTTT 59.220 38.462 4.96 0.00 43.72 3.11
220 221 7.040132 GGGAATGATAGTTTCCATCATCCTTTC 60.040 40.741 4.96 0.00 43.72 2.62
221 222 7.503566 GGAATGATAGTTTCCATCATCCTTTCA 59.496 37.037 0.00 0.00 41.24 2.69
222 223 9.075678 GAATGATAGTTTCCATCATCCTTTCAT 57.924 33.333 0.00 0.00 41.24 2.57
223 224 8.632906 ATGATAGTTTCCATCATCCTTTCATC 57.367 34.615 0.00 0.00 38.47 2.92
224 225 7.576403 TGATAGTTTCCATCATCCTTTCATCA 58.424 34.615 0.00 0.00 0.00 3.07
225 226 7.500227 TGATAGTTTCCATCATCCTTTCATCAC 59.500 37.037 0.00 0.00 0.00 3.06
226 227 5.824421 AGTTTCCATCATCCTTTCATCACT 58.176 37.500 0.00 0.00 0.00 3.41
227 228 5.651139 AGTTTCCATCATCCTTTCATCACTG 59.349 40.000 0.00 0.00 0.00 3.66
228 229 4.160642 TCCATCATCCTTTCATCACTGG 57.839 45.455 0.00 0.00 0.00 4.00
229 230 3.524789 TCCATCATCCTTTCATCACTGGT 59.475 43.478 0.00 0.00 0.00 4.00
230 231 4.721274 TCCATCATCCTTTCATCACTGGTA 59.279 41.667 0.00 0.00 0.00 3.25
231 232 5.370584 TCCATCATCCTTTCATCACTGGTAT 59.629 40.000 0.00 0.00 0.00 2.73
232 233 6.558394 TCCATCATCCTTTCATCACTGGTATA 59.442 38.462 0.00 0.00 0.00 1.47
233 234 7.072328 TCCATCATCCTTTCATCACTGGTATAA 59.928 37.037 0.00 0.00 0.00 0.98
234 235 7.886970 CCATCATCCTTTCATCACTGGTATAAT 59.113 37.037 0.00 0.00 0.00 1.28
235 236 9.948964 CATCATCCTTTCATCACTGGTATAATA 57.051 33.333 0.00 0.00 0.00 0.98
275 276 8.738199 TCACACTTCTATTTACTTACAACTCG 57.262 34.615 0.00 0.00 0.00 4.18
276 277 8.570488 TCACACTTCTATTTACTTACAACTCGA 58.430 33.333 0.00 0.00 0.00 4.04
277 278 9.355215 CACACTTCTATTTACTTACAACTCGAT 57.645 33.333 0.00 0.00 0.00 3.59
308 309 9.376075 AGAACAAAGTATGTCTCTACATGAATG 57.624 33.333 0.00 0.00 45.99 2.67
309 310 7.545362 ACAAAGTATGTCTCTACATGAATGC 57.455 36.000 0.00 0.00 45.99 3.56
310 311 6.540189 ACAAAGTATGTCTCTACATGAATGCC 59.460 38.462 0.00 0.00 45.99 4.40
311 312 6.491714 AAGTATGTCTCTACATGAATGCCT 57.508 37.500 0.00 0.00 45.99 4.75
312 313 6.095432 AGTATGTCTCTACATGAATGCCTC 57.905 41.667 0.00 0.00 45.99 4.70
313 314 5.837979 AGTATGTCTCTACATGAATGCCTCT 59.162 40.000 0.00 0.00 45.99 3.69
314 315 7.007116 AGTATGTCTCTACATGAATGCCTCTA 58.993 38.462 0.00 0.00 45.99 2.43
315 316 5.781210 TGTCTCTACATGAATGCCTCTAG 57.219 43.478 0.00 0.00 0.00 2.43
316 317 4.038522 TGTCTCTACATGAATGCCTCTAGC 59.961 45.833 0.00 0.00 44.14 3.42
317 318 3.576118 TCTCTACATGAATGCCTCTAGCC 59.424 47.826 0.00 0.00 42.71 3.93
318 319 3.308401 TCTACATGAATGCCTCTAGCCA 58.692 45.455 0.00 0.00 42.71 4.75
319 320 3.906218 TCTACATGAATGCCTCTAGCCAT 59.094 43.478 0.00 0.00 42.71 4.40
320 321 2.860009 ACATGAATGCCTCTAGCCATG 58.140 47.619 0.00 0.00 41.65 3.66
321 322 2.440627 ACATGAATGCCTCTAGCCATGA 59.559 45.455 0.00 0.00 39.61 3.07
322 323 3.117776 ACATGAATGCCTCTAGCCATGAA 60.118 43.478 0.00 0.00 39.61 2.57
323 324 3.204306 TGAATGCCTCTAGCCATGAAG 57.796 47.619 0.00 0.00 42.71 3.02
324 325 1.878734 GAATGCCTCTAGCCATGAAGC 59.121 52.381 0.00 0.00 42.71 3.86
325 326 0.841961 ATGCCTCTAGCCATGAAGCA 59.158 50.000 0.00 0.00 42.71 3.91
326 327 0.841961 TGCCTCTAGCCATGAAGCAT 59.158 50.000 0.00 0.00 42.71 3.79
327 328 1.202734 TGCCTCTAGCCATGAAGCATC 60.203 52.381 0.00 0.00 42.71 3.91
328 329 1.072015 GCCTCTAGCCATGAAGCATCT 59.928 52.381 0.00 0.00 34.35 2.90
329 330 2.486907 GCCTCTAGCCATGAAGCATCTT 60.487 50.000 0.00 0.00 34.35 2.40
330 331 3.401182 CCTCTAGCCATGAAGCATCTTC 58.599 50.000 0.00 0.00 34.23 2.87
331 332 3.058450 CTCTAGCCATGAAGCATCTTCG 58.942 50.000 0.00 0.00 34.23 3.79
332 333 2.695147 TCTAGCCATGAAGCATCTTCGA 59.305 45.455 0.00 0.00 34.23 3.71
333 334 2.408271 AGCCATGAAGCATCTTCGAA 57.592 45.000 0.00 0.00 34.23 3.71
334 335 2.928334 AGCCATGAAGCATCTTCGAAT 58.072 42.857 0.00 0.00 34.23 3.34
335 336 3.285484 AGCCATGAAGCATCTTCGAATT 58.715 40.909 0.00 0.00 34.23 2.17
336 337 3.698040 AGCCATGAAGCATCTTCGAATTT 59.302 39.130 0.00 0.00 34.23 1.82
337 338 4.159135 AGCCATGAAGCATCTTCGAATTTT 59.841 37.500 0.00 0.00 34.23 1.82
338 339 4.866486 GCCATGAAGCATCTTCGAATTTTT 59.134 37.500 0.00 0.00 0.00 1.94
370 371 7.758980 TGGTGAATCAAATAATGTCAAAATCCG 59.241 33.333 0.00 0.00 0.00 4.18
372 373 8.586273 GTGAATCAAATAATGTCAAAATCCGTG 58.414 33.333 0.00 0.00 0.00 4.94
374 375 9.781834 GAATCAAATAATGTCAAAATCCGTGTA 57.218 29.630 0.00 0.00 0.00 2.90
384 385 6.053005 GTCAAAATCCGTGTATATCCCTTCA 58.947 40.000 0.00 0.00 0.00 3.02
395 396 6.712547 GTGTATATCCCTTCAAATCCTCTTGG 59.287 42.308 0.00 0.00 0.00 3.61
1155 1163 0.832559 GGCTAGGGCGGATCTACCTT 60.833 60.000 8.33 2.32 39.81 3.50
1165 1173 2.550606 CGGATCTACCTTTCCTCTCTCG 59.449 54.545 0.00 0.00 36.31 4.04
1175 1183 4.263209 CTCTCTCGCGCGCATCCT 62.263 66.667 32.61 0.00 0.00 3.24
1218 1227 3.691342 CCGCGACCTCCTTCACCA 61.691 66.667 8.23 0.00 0.00 4.17
1247 1256 7.455008 TCTTCTACATCTTGTCTCTTTTACCCT 59.545 37.037 0.00 0.00 0.00 4.34
1280 1289 3.747976 GCGCGCAAATGACCCCTT 61.748 61.111 29.10 0.00 0.00 3.95
1347 1356 4.383774 TCACTACGCGTTTCAAATTCTG 57.616 40.909 20.78 0.00 0.00 3.02
1410 1423 1.071605 GTGCTACTGCTCCGTTTCTG 58.928 55.000 0.00 0.00 40.48 3.02
1450 1463 2.613595 CCAAACAGCAATATAGCTCGCA 59.386 45.455 0.00 0.00 44.54 5.10
1466 1479 4.764823 AGCTCGCATAACTATAGCTTCTCT 59.235 41.667 0.00 0.00 40.52 3.10
1593 1606 5.327091 CATTAAGCATCAACGGTTTCTCTG 58.673 41.667 0.00 0.00 0.00 3.35
1719 1734 2.297701 TGTTGGGTGAAGAACAGAAGC 58.702 47.619 0.00 0.00 0.00 3.86
1727 1742 2.355756 TGAAGAACAGAAGCTGTGTTGC 59.644 45.455 17.23 10.08 44.62 4.17
1770 1789 9.692749 CTAGGCTATGTTCGATAAAATCTACAA 57.307 33.333 0.00 0.00 0.00 2.41
1772 1791 8.204836 AGGCTATGTTCGATAAAATCTACAACT 58.795 33.333 0.00 0.00 0.00 3.16
1810 1829 4.497291 TTAAACCTAGGCCATGTTCGAT 57.503 40.909 9.30 0.00 0.00 3.59
1817 1836 2.301346 AGGCCATGTTCGATGAAATCC 58.699 47.619 5.01 0.00 41.39 3.01
1938 1957 0.312102 GAGCAAGTGTGTTTGAGGCC 59.688 55.000 0.00 0.00 0.00 5.19
2025 2044 0.521291 GCAATGACCGTGCTAAGCAA 59.479 50.000 0.00 0.00 41.47 3.91
2069 2088 4.314740 TGTGCTTTCAACAAATGGTACC 57.685 40.909 4.43 4.43 0.00 3.34
2076 2095 6.151144 GCTTTCAACAAATGGTACCTAGTGAT 59.849 38.462 14.36 0.00 0.00 3.06
2083 2102 4.873746 ATGGTACCTAGTGATTGGATCG 57.126 45.455 14.36 0.00 0.00 3.69
2090 2109 5.855045 ACCTAGTGATTGGATCGATAAACC 58.145 41.667 0.00 0.00 0.00 3.27
2203 2222 6.529463 TCGACACTGTATTGCATGATAATG 57.471 37.500 0.00 0.00 0.00 1.90
2204 2223 6.048509 TCGACACTGTATTGCATGATAATGT 58.951 36.000 0.00 0.00 0.00 2.71
2247 2267 6.753107 TTGGCAGATTTTAGCTTAGTAACC 57.247 37.500 0.00 0.00 0.00 2.85
2385 2412 3.198635 AGTCTTTAGCTGCCATGCTTCTA 59.801 43.478 0.00 0.00 43.74 2.10
2391 2418 1.947678 GCTGCCATGCTTCTACACTGT 60.948 52.381 0.00 0.00 0.00 3.55
2411 2438 6.634436 CACTGTTGTTAACTGAAAGAAGCATC 59.366 38.462 7.22 0.00 37.43 3.91
2430 2457 6.722972 GCATCTGTAAAATGCAACTTATCG 57.277 37.500 0.00 0.00 46.93 2.92
2431 2458 5.172053 GCATCTGTAAAATGCAACTTATCGC 59.828 40.000 0.00 0.00 46.93 4.58
2432 2459 5.871465 TCTGTAAAATGCAACTTATCGCA 57.129 34.783 0.00 0.00 43.45 5.10
2443 2470 7.275697 TGCAACTTATCGCATTTGTAAAATG 57.724 32.000 8.09 8.09 31.95 2.32
2444 2471 6.177822 GCAACTTATCGCATTTGTAAAATGC 58.822 36.000 21.98 21.98 46.97 3.56
2480 2507 3.745975 TGTTTATGTTGCTTCCAGTCTCG 59.254 43.478 0.00 0.00 0.00 4.04
2829 2857 1.229464 AGCTGAAGGGAGCAGGAGT 60.229 57.895 0.00 0.00 41.83 3.85
2941 2969 4.021544 TGGGCCTGTGTTAATTTGATGAAC 60.022 41.667 4.53 0.00 0.00 3.18
3020 3048 8.409358 AAGCATGTCTAACCATAAGAAAAAGT 57.591 30.769 0.00 0.00 0.00 2.66
3077 3106 7.806690 TGTAAACAAGTCTTATGATGCTCAAC 58.193 34.615 0.00 0.00 0.00 3.18
3078 3107 5.536554 AACAAGTCTTATGATGCTCAACG 57.463 39.130 0.00 0.00 0.00 4.10
3079 3108 3.935203 ACAAGTCTTATGATGCTCAACGG 59.065 43.478 0.00 0.00 0.00 4.44
3093 3148 4.165779 GCTCAACGGAAATGTATTTGGTG 58.834 43.478 0.00 0.00 0.00 4.17
3111 3166 4.096681 TGGTGTGGATCTCAGTGTAGAAT 58.903 43.478 0.00 0.00 0.00 2.40
3276 3331 3.118261 TGGCTGGTAGGAGAATGATCAAC 60.118 47.826 0.00 0.00 0.00 3.18
3400 3457 5.067273 CACTTAACCTACCAATGTTCCACA 58.933 41.667 0.00 0.00 0.00 4.17
3749 3806 2.039084 ACCTGACAACATCTTGGAGGTC 59.961 50.000 2.11 0.00 38.88 3.85
3756 3813 1.625818 ACATCTTGGAGGTCAGGACAC 59.374 52.381 1.41 0.00 34.20 3.67
3763 3820 3.724478 TGGAGGTCAGGACACTTATCAT 58.276 45.455 1.41 0.00 0.00 2.45
3904 3967 0.179076 GCTGTTGGCTTGCTTGGTTT 60.179 50.000 0.00 0.00 38.06 3.27
4031 4108 9.823647 CTAGACCTATTCATTGTAATCTTGTGT 57.176 33.333 0.00 0.00 0.00 3.72
4076 4153 7.951530 AAATTGATTTGATTCAACGAGCTTT 57.048 28.000 0.00 0.00 38.37 3.51
4431 4509 6.073222 CCACATGTAAACAAGTCTTCAGGTAC 60.073 42.308 0.00 0.00 0.00 3.34
4523 4601 7.450124 TTCACACCTTAAACACAAACACTAA 57.550 32.000 0.00 0.00 0.00 2.24
4560 4638 9.850198 TGGTATGTACCCCAAAAATTATACTAC 57.150 33.333 6.74 0.00 45.87 2.73
4758 4839 1.145738 ACCAGAAGTCAGGCCATTTGT 59.854 47.619 5.01 0.00 0.00 2.83
4767 4848 1.274167 CAGGCCATTTGTGATGCTTGT 59.726 47.619 5.01 0.00 0.00 3.16
4781 4862 4.099881 TGATGCTTGTTTGCTTCTCCTTTT 59.900 37.500 0.00 0.00 37.79 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.011981 ACTTGAGGATTGGAAGGGTTATACAA 60.012 38.462 0.00 0.00 0.00 2.41
1 2 5.491078 ACTTGAGGATTGGAAGGGTTATACA 59.509 40.000 0.00 0.00 0.00 2.29
2 3 6.002653 ACTTGAGGATTGGAAGGGTTATAC 57.997 41.667 0.00 0.00 0.00 1.47
3 4 7.374975 CTACTTGAGGATTGGAAGGGTTATA 57.625 40.000 0.00 0.00 0.00 0.98
5 6 5.693769 CTACTTGAGGATTGGAAGGGTTA 57.306 43.478 0.00 0.00 0.00 2.85
6 7 4.576330 CTACTTGAGGATTGGAAGGGTT 57.424 45.455 0.00 0.00 0.00 4.11
100 101 9.399797 TGCTTTGAATCACTCATGTCTTAATAT 57.600 29.630 0.00 0.00 32.78 1.28
101 102 8.791327 TGCTTTGAATCACTCATGTCTTAATA 57.209 30.769 0.00 0.00 32.78 0.98
102 103 7.692460 TGCTTTGAATCACTCATGTCTTAAT 57.308 32.000 0.00 0.00 32.78 1.40
103 104 7.509141 TTGCTTTGAATCACTCATGTCTTAA 57.491 32.000 0.00 0.00 32.78 1.85
104 105 7.692460 ATTGCTTTGAATCACTCATGTCTTA 57.308 32.000 0.00 0.00 32.78 2.10
105 106 6.585695 ATTGCTTTGAATCACTCATGTCTT 57.414 33.333 0.00 0.00 32.78 3.01
106 107 6.883217 ACTATTGCTTTGAATCACTCATGTCT 59.117 34.615 0.00 0.00 32.78 3.41
107 108 7.065563 AGACTATTGCTTTGAATCACTCATGTC 59.934 37.037 0.00 0.00 32.78 3.06
108 109 6.883217 AGACTATTGCTTTGAATCACTCATGT 59.117 34.615 0.00 0.00 32.78 3.21
109 110 7.065443 TGAGACTATTGCTTTGAATCACTCATG 59.935 37.037 0.00 0.00 32.78 3.07
110 111 7.065563 GTGAGACTATTGCTTTGAATCACTCAT 59.934 37.037 0.00 0.00 32.78 2.90
111 112 6.369890 GTGAGACTATTGCTTTGAATCACTCA 59.630 38.462 0.00 0.00 33.49 3.41
112 113 6.593382 AGTGAGACTATTGCTTTGAATCACTC 59.407 38.462 0.00 0.00 40.46 3.51
113 114 6.471146 AGTGAGACTATTGCTTTGAATCACT 58.529 36.000 0.00 0.00 39.86 3.41
114 115 6.593382 AGAGTGAGACTATTGCTTTGAATCAC 59.407 38.462 0.00 0.00 35.83 3.06
115 116 6.705302 AGAGTGAGACTATTGCTTTGAATCA 58.295 36.000 0.00 0.00 0.00 2.57
116 117 7.608308 AAGAGTGAGACTATTGCTTTGAATC 57.392 36.000 0.00 0.00 27.09 2.52
117 118 7.446625 ACAAAGAGTGAGACTATTGCTTTGAAT 59.553 33.333 19.07 3.97 37.98 2.57
118 119 6.767902 ACAAAGAGTGAGACTATTGCTTTGAA 59.232 34.615 19.07 0.00 37.98 2.69
119 120 6.291377 ACAAAGAGTGAGACTATTGCTTTGA 58.709 36.000 19.07 0.00 37.98 2.69
120 121 6.348050 GGACAAAGAGTGAGACTATTGCTTTG 60.348 42.308 0.00 0.00 39.85 2.77
121 122 5.703130 GGACAAAGAGTGAGACTATTGCTTT 59.297 40.000 0.00 0.00 29.00 3.51
122 123 5.241662 GGACAAAGAGTGAGACTATTGCTT 58.758 41.667 0.00 0.00 29.00 3.91
123 124 4.323104 GGGACAAAGAGTGAGACTATTGCT 60.323 45.833 0.00 0.00 29.00 3.91
124 125 3.935828 GGGACAAAGAGTGAGACTATTGC 59.064 47.826 0.00 0.00 29.00 3.56
125 126 5.413309 AGGGACAAAGAGTGAGACTATTG 57.587 43.478 0.00 0.00 29.00 1.90
126 127 6.441088 AAAGGGACAAAGAGTGAGACTATT 57.559 37.500 0.00 0.00 29.75 1.73
127 128 6.441088 AAAAGGGACAAAGAGTGAGACTAT 57.559 37.500 0.00 0.00 0.00 2.12
128 129 5.888982 AAAAGGGACAAAGAGTGAGACTA 57.111 39.130 0.00 0.00 0.00 2.59
129 130 4.779993 AAAAGGGACAAAGAGTGAGACT 57.220 40.909 0.00 0.00 0.00 3.24
163 164 2.290071 GGGATGAGACTCCGGACAAAAA 60.290 50.000 0.00 0.00 36.05 1.94
164 165 1.278127 GGGATGAGACTCCGGACAAAA 59.722 52.381 0.00 0.00 36.05 2.44
165 166 0.902531 GGGATGAGACTCCGGACAAA 59.097 55.000 0.00 0.00 36.05 2.83
166 167 0.252057 TGGGATGAGACTCCGGACAA 60.252 55.000 0.00 0.00 36.05 3.18
167 168 0.252057 TTGGGATGAGACTCCGGACA 60.252 55.000 0.00 0.00 36.05 4.02
168 169 0.175989 GTTGGGATGAGACTCCGGAC 59.824 60.000 0.00 0.00 36.05 4.79
169 170 0.041238 AGTTGGGATGAGACTCCGGA 59.959 55.000 2.93 2.93 36.05 5.14
170 171 0.905357 AAGTTGGGATGAGACTCCGG 59.095 55.000 0.00 0.00 36.05 5.14
171 172 1.276421 ACAAGTTGGGATGAGACTCCG 59.724 52.381 7.96 0.00 36.05 4.63
172 173 3.118592 CCTACAAGTTGGGATGAGACTCC 60.119 52.174 7.96 0.00 34.31 3.85
173 174 3.118592 CCCTACAAGTTGGGATGAGACTC 60.119 52.174 13.54 0.00 46.62 3.36
174 175 2.840651 CCCTACAAGTTGGGATGAGACT 59.159 50.000 13.54 0.00 46.62 3.24
175 176 2.092914 CCCCTACAAGTTGGGATGAGAC 60.093 54.545 19.32 0.00 46.62 3.36
176 177 2.196595 CCCCTACAAGTTGGGATGAGA 58.803 52.381 19.32 0.00 46.62 3.27
177 178 2.196595 TCCCCTACAAGTTGGGATGAG 58.803 52.381 19.32 4.68 46.62 2.90
178 179 2.352561 TCCCCTACAAGTTGGGATGA 57.647 50.000 19.32 7.72 46.62 2.92
181 182 2.638325 TCATTCCCCTACAAGTTGGGA 58.362 47.619 19.32 12.52 46.62 4.37
182 183 3.669939 ATCATTCCCCTACAAGTTGGG 57.330 47.619 12.08 12.08 43.89 4.12
183 184 5.373812 ACTATCATTCCCCTACAAGTTGG 57.626 43.478 7.96 0.00 0.00 3.77
184 185 6.318900 GGAAACTATCATTCCCCTACAAGTTG 59.681 42.308 0.00 0.00 40.41 3.16
185 186 6.011981 TGGAAACTATCATTCCCCTACAAGTT 60.012 38.462 3.06 0.00 44.72 2.66
186 187 5.491078 TGGAAACTATCATTCCCCTACAAGT 59.509 40.000 3.06 0.00 44.72 3.16
187 188 6.001449 TGGAAACTATCATTCCCCTACAAG 57.999 41.667 3.06 0.00 44.72 3.16
188 189 6.159575 TGATGGAAACTATCATTCCCCTACAA 59.840 38.462 3.06 0.00 44.72 2.41
189 190 5.669904 TGATGGAAACTATCATTCCCCTACA 59.330 40.000 3.06 0.00 44.72 2.74
190 191 6.187727 TGATGGAAACTATCATTCCCCTAC 57.812 41.667 3.06 0.00 44.72 3.18
191 192 6.012508 GGATGATGGAAACTATCATTCCCCTA 60.013 42.308 10.82 0.00 44.72 3.53
192 193 5.222213 GGATGATGGAAACTATCATTCCCCT 60.222 44.000 10.82 0.00 44.72 4.79
193 194 5.012893 GGATGATGGAAACTATCATTCCCC 58.987 45.833 10.82 5.66 44.72 4.81
194 195 5.885465 AGGATGATGGAAACTATCATTCCC 58.115 41.667 10.82 8.91 44.72 3.97
195 196 7.503566 TGAAAGGATGATGGAAACTATCATTCC 59.496 37.037 10.82 12.15 43.37 3.01
196 197 8.455903 TGAAAGGATGATGGAAACTATCATTC 57.544 34.615 10.82 9.33 43.37 2.67
197 198 9.075678 GATGAAAGGATGATGGAAACTATCATT 57.924 33.333 10.82 0.00 43.37 2.57
198 199 8.222637 TGATGAAAGGATGATGGAAACTATCAT 58.777 33.333 9.63 9.63 45.35 2.45
199 200 7.500227 GTGATGAAAGGATGATGGAAACTATCA 59.500 37.037 0.00 0.00 38.76 2.15
200 201 7.718753 AGTGATGAAAGGATGATGGAAACTATC 59.281 37.037 0.00 0.00 0.00 2.08
201 202 7.501559 CAGTGATGAAAGGATGATGGAAACTAT 59.498 37.037 0.00 0.00 0.00 2.12
202 203 6.825213 CAGTGATGAAAGGATGATGGAAACTA 59.175 38.462 0.00 0.00 0.00 2.24
203 204 5.651139 CAGTGATGAAAGGATGATGGAAACT 59.349 40.000 0.00 0.00 0.00 2.66
204 205 5.163581 CCAGTGATGAAAGGATGATGGAAAC 60.164 44.000 0.00 0.00 0.00 2.78
205 206 4.951715 CCAGTGATGAAAGGATGATGGAAA 59.048 41.667 0.00 0.00 0.00 3.13
206 207 4.018141 ACCAGTGATGAAAGGATGATGGAA 60.018 41.667 0.00 0.00 0.00 3.53
207 208 3.524789 ACCAGTGATGAAAGGATGATGGA 59.475 43.478 0.00 0.00 0.00 3.41
208 209 3.894759 ACCAGTGATGAAAGGATGATGG 58.105 45.455 0.00 0.00 0.00 3.51
209 210 8.859236 ATTATACCAGTGATGAAAGGATGATG 57.141 34.615 0.00 0.00 0.00 3.07
249 250 9.355215 CGAGTTGTAAGTAAATAGAAGTGTGAT 57.645 33.333 0.00 0.00 0.00 3.06
250 251 8.570488 TCGAGTTGTAAGTAAATAGAAGTGTGA 58.430 33.333 0.00 0.00 0.00 3.58
251 252 8.738199 TCGAGTTGTAAGTAAATAGAAGTGTG 57.262 34.615 0.00 0.00 0.00 3.82
282 283 9.376075 CATTCATGTAGAGACATACTTTGTTCT 57.624 33.333 0.00 0.00 44.82 3.01
283 284 8.119226 GCATTCATGTAGAGACATACTTTGTTC 58.881 37.037 0.00 0.00 44.82 3.18
284 285 7.066284 GGCATTCATGTAGAGACATACTTTGTT 59.934 37.037 0.00 0.00 44.82 2.83
285 286 6.540189 GGCATTCATGTAGAGACATACTTTGT 59.460 38.462 0.00 0.00 44.82 2.83
286 287 6.765036 AGGCATTCATGTAGAGACATACTTTG 59.235 38.462 0.00 0.00 44.82 2.77
287 288 6.893583 AGGCATTCATGTAGAGACATACTTT 58.106 36.000 0.00 0.00 44.82 2.66
288 289 6.326064 AGAGGCATTCATGTAGAGACATACTT 59.674 38.462 0.00 0.00 44.82 2.24
289 290 5.837979 AGAGGCATTCATGTAGAGACATACT 59.162 40.000 0.00 0.00 44.82 2.12
290 291 6.095432 AGAGGCATTCATGTAGAGACATAC 57.905 41.667 0.00 0.00 44.82 2.39
291 292 6.071672 GCTAGAGGCATTCATGTAGAGACATA 60.072 42.308 0.00 0.00 41.66 2.29
292 293 5.279406 GCTAGAGGCATTCATGTAGAGACAT 60.279 44.000 0.00 0.00 43.12 3.06
293 294 4.038522 GCTAGAGGCATTCATGTAGAGACA 59.961 45.833 0.00 0.00 41.35 3.41
294 295 4.555262 GCTAGAGGCATTCATGTAGAGAC 58.445 47.826 0.00 0.00 41.35 3.36
295 296 3.576118 GGCTAGAGGCATTCATGTAGAGA 59.424 47.826 0.00 0.00 44.01 3.10
296 297 3.323115 TGGCTAGAGGCATTCATGTAGAG 59.677 47.826 0.93 0.00 46.12 2.43
297 298 3.308401 TGGCTAGAGGCATTCATGTAGA 58.692 45.455 0.93 0.00 46.12 2.59
298 299 3.758755 TGGCTAGAGGCATTCATGTAG 57.241 47.619 0.93 0.00 46.12 2.74
308 309 1.072015 AGATGCTTCATGGCTAGAGGC 59.928 52.381 2.07 6.85 38.44 4.70
309 310 3.401182 GAAGATGCTTCATGGCTAGAGG 58.599 50.000 2.07 0.00 0.00 3.69
310 311 3.058450 CGAAGATGCTTCATGGCTAGAG 58.942 50.000 7.81 0.00 0.00 2.43
311 312 2.695147 TCGAAGATGCTTCATGGCTAGA 59.305 45.455 7.81 0.00 0.00 2.43
312 313 3.103447 TCGAAGATGCTTCATGGCTAG 57.897 47.619 7.81 0.00 0.00 3.42
313 314 3.541996 TTCGAAGATGCTTCATGGCTA 57.458 42.857 7.81 0.00 35.04 3.93
314 315 2.408271 TTCGAAGATGCTTCATGGCT 57.592 45.000 7.81 0.00 35.04 4.75
315 316 3.705043 AATTCGAAGATGCTTCATGGC 57.295 42.857 3.35 0.00 35.04 4.40
339 340 9.993454 TTTGACATTATTTGATTCACCAAATGA 57.007 25.926 15.60 4.67 43.99 2.57
343 344 9.434420 GGATTTTGACATTATTTGATTCACCAA 57.566 29.630 0.00 0.00 0.00 3.67
344 345 7.758980 CGGATTTTGACATTATTTGATTCACCA 59.241 33.333 0.00 0.00 0.00 4.17
345 346 7.759433 ACGGATTTTGACATTATTTGATTCACC 59.241 33.333 0.00 0.00 0.00 4.02
346 347 8.586273 CACGGATTTTGACATTATTTGATTCAC 58.414 33.333 0.00 0.00 0.00 3.18
347 348 8.303156 ACACGGATTTTGACATTATTTGATTCA 58.697 29.630 0.00 0.00 0.00 2.57
348 349 8.687824 ACACGGATTTTGACATTATTTGATTC 57.312 30.769 0.00 0.00 0.00 2.52
354 355 9.010029 GGGATATACACGGATTTTGACATTATT 57.990 33.333 0.00 0.00 0.00 1.40
355 356 8.383175 AGGGATATACACGGATTTTGACATTAT 58.617 33.333 0.00 0.00 0.00 1.28
356 357 7.741785 AGGGATATACACGGATTTTGACATTA 58.258 34.615 0.00 0.00 0.00 1.90
357 358 6.601332 AGGGATATACACGGATTTTGACATT 58.399 36.000 0.00 0.00 0.00 2.71
358 359 6.187727 AGGGATATACACGGATTTTGACAT 57.812 37.500 0.00 0.00 0.00 3.06
359 360 5.623956 AGGGATATACACGGATTTTGACA 57.376 39.130 0.00 0.00 0.00 3.58
360 361 6.053005 TGAAGGGATATACACGGATTTTGAC 58.947 40.000 0.00 0.00 0.00 3.18
361 362 6.241882 TGAAGGGATATACACGGATTTTGA 57.758 37.500 0.00 0.00 0.00 2.69
362 363 6.935741 TTGAAGGGATATACACGGATTTTG 57.064 37.500 0.00 0.00 0.00 2.44
370 371 6.712547 CCAAGAGGATTTGAAGGGATATACAC 59.287 42.308 0.00 0.00 36.89 2.90
372 373 6.044404 TCCCAAGAGGATTTGAAGGGATATAC 59.956 42.308 0.00 0.00 40.93 1.47
374 375 4.984268 TCCCAAGAGGATTTGAAGGGATAT 59.016 41.667 0.00 0.00 40.93 1.63
375 376 4.379875 TCCCAAGAGGATTTGAAGGGATA 58.620 43.478 0.00 0.00 40.93 2.59
377 378 2.578021 CTCCCAAGAGGATTTGAAGGGA 59.422 50.000 0.00 0.00 46.33 4.20
395 396 0.968393 TTTTACAATGCGGCCCCTCC 60.968 55.000 0.00 0.00 0.00 4.30
407 408 3.124466 CGAGATGCACGGATGTTTTACAA 59.876 43.478 0.00 0.00 0.00 2.41
410 411 3.186909 CTCGAGATGCACGGATGTTTTA 58.813 45.455 6.58 0.00 0.00 1.52
1155 1163 3.758088 GATGCGCGCGAGAGAGGAA 62.758 63.158 37.18 5.35 0.00 3.36
1175 1183 2.571653 ACGAAATGTGGAGATCCTGGAA 59.428 45.455 0.00 0.00 36.82 3.53
1209 1218 6.627087 AGATGTAGAAGATTTGGTGAAGGA 57.373 37.500 0.00 0.00 0.00 3.36
1243 1252 2.827921 GCATTTCAGTTCCAATGAGGGT 59.172 45.455 0.00 0.00 38.24 4.34
1247 1256 1.135717 CGCGCATTTCAGTTCCAATGA 60.136 47.619 8.75 0.00 32.91 2.57
1280 1289 5.258051 AGGGTCAAAACTTTCTACACACAA 58.742 37.500 0.00 0.00 0.00 3.33
1347 1356 6.042143 CCCAAACTATCAAATGGTTACATGC 58.958 40.000 0.00 0.00 37.40 4.06
1466 1479 9.719355 TTCTGCAAGATAATGTAGTTGAAACTA 57.281 29.630 0.00 0.00 46.36 2.24
1719 1734 3.820467 TGGATAAGGAAACAGCAACACAG 59.180 43.478 0.00 0.00 0.00 3.66
1727 1742 4.080299 AGCCTAGGTTGGATAAGGAAACAG 60.080 45.833 11.31 0.00 0.00 3.16
1770 1789 8.329502 AGGTTTAATAGACAAGGAAGCAATAGT 58.670 33.333 0.00 0.00 0.00 2.12
1772 1791 9.832445 CTAGGTTTAATAGACAAGGAAGCAATA 57.168 33.333 0.00 0.00 0.00 1.90
1784 1803 5.465724 CGAACATGGCCTAGGTTTAATAGAC 59.534 44.000 11.31 0.00 32.65 2.59
1810 1829 2.631160 ACGGAAGTGTGTGGATTTCA 57.369 45.000 0.00 0.00 46.97 2.69
1938 1957 2.099921 CACACGGTCCTCCTCTTCTATG 59.900 54.545 0.00 0.00 0.00 2.23
2010 2029 1.227999 GCAGTTGCTTAGCACGGTCA 61.228 55.000 6.34 0.00 38.71 4.02
2025 2044 0.952497 CTGACGGTGAAGCATGCAGT 60.952 55.000 21.98 7.09 0.00 4.40
2069 2088 5.529791 ACGGTTTATCGATCCAATCACTAG 58.470 41.667 0.00 0.00 0.00 2.57
2076 2095 3.448301 ACAGGTACGGTTTATCGATCCAA 59.552 43.478 0.00 0.00 27.95 3.53
2083 2102 2.702261 TGGCAACAGGTACGGTTTATC 58.298 47.619 0.00 0.00 46.05 1.75
2385 2412 5.414454 TGCTTCTTTCAGTTAACAACAGTGT 59.586 36.000 8.61 0.00 40.75 3.55
2391 2418 6.942532 ACAGATGCTTCTTTCAGTTAACAA 57.057 33.333 8.61 0.00 0.00 2.83
2444 2471 8.497554 AGCAACATAAACAAATGCAATAAGTTG 58.502 29.630 0.00 0.00 39.42 3.16
2445 2472 8.606040 AGCAACATAAACAAATGCAATAAGTT 57.394 26.923 0.00 0.00 39.42 2.66
2446 2473 8.606040 AAGCAACATAAACAAATGCAATAAGT 57.394 26.923 0.00 0.00 39.42 2.24
2447 2474 8.170553 GGAAGCAACATAAACAAATGCAATAAG 58.829 33.333 0.00 0.00 39.42 1.73
2480 2507 6.381481 TCAACATTGAAGGCATATGTGATC 57.619 37.500 4.29 1.14 33.10 2.92
2829 2857 1.985614 CATGGGACCACTCTCAGCA 59.014 57.895 0.00 0.00 0.00 4.41
2941 2969 7.754924 ACAAATACTAAATCAAGAAATGTGCCG 59.245 33.333 0.00 0.00 0.00 5.69
2996 3024 8.409358 AACTTTTTCTTATGGTTAGACATGCT 57.591 30.769 0.00 0.00 32.39 3.79
3006 3034 8.422577 AGCCTCATAAAACTTTTTCTTATGGT 57.577 30.769 0.00 0.00 34.95 3.55
3020 3048 3.245443 TGCCCTTACCAAGCCTCATAAAA 60.245 43.478 0.00 0.00 0.00 1.52
3077 3106 4.640201 AGATCCACACCAAATACATTTCCG 59.360 41.667 0.00 0.00 0.00 4.30
3078 3107 5.652014 TGAGATCCACACCAAATACATTTCC 59.348 40.000 0.00 0.00 0.00 3.13
3079 3108 6.375455 ACTGAGATCCACACCAAATACATTTC 59.625 38.462 0.00 0.00 0.00 2.17
3093 3148 8.547967 TTTGTAAATTCTACACTGAGATCCAC 57.452 34.615 0.00 0.00 0.00 4.02
3177 3232 4.640201 GCACTGATGGCAGATAAAGGTTTA 59.360 41.667 0.00 0.00 45.17 2.01
3226 3281 7.307989 CCTCGTTTGAGACAAATTCTACACAAT 60.308 37.037 0.00 0.00 45.57 2.71
3276 3331 2.486472 ATGTTGGCTCAGGTTCAGAG 57.514 50.000 0.00 0.00 36.21 3.35
3400 3457 7.172361 ACAAACCGCTGCAACAAAATTATAAAT 59.828 29.630 0.00 0.00 0.00 1.40
3749 3806 6.372659 AGCAAACAACTATGATAAGTGTCCTG 59.627 38.462 0.00 0.00 0.00 3.86
3756 3813 9.341899 GGTACAAAAGCAAACAACTATGATAAG 57.658 33.333 0.00 0.00 0.00 1.73
3763 3820 5.889289 AGGAAGGTACAAAAGCAAACAACTA 59.111 36.000 0.00 0.00 0.00 2.24
3805 3862 9.772605 TGCAAGGATATAAATTATCATCCCAAT 57.227 29.630 13.18 3.97 38.16 3.16
3904 3967 2.294195 TGGATACAGAAATCCCAGGGGA 60.294 50.000 10.00 10.00 46.55 4.81
4431 4509 4.669206 AGAGCTACATCATCAACTCCTG 57.331 45.455 0.00 0.00 0.00 3.86
4471 4549 5.477510 AGAACTGCATTCAACAAACACAAA 58.522 33.333 10.26 0.00 40.09 2.83
4560 4638 3.115554 CCTTGTGTTTTTCTTTCAGGCG 58.884 45.455 0.00 0.00 0.00 5.52
4758 4839 2.867624 AGGAGAAGCAAACAAGCATCA 58.132 42.857 0.00 0.00 34.86 3.07
4767 4848 2.665165 TCAGCCAAAAGGAGAAGCAAA 58.335 42.857 0.00 0.00 0.00 3.68
4795 4876 7.067615 TGCAAGTTACCTACATCTGTTTGAAAA 59.932 33.333 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.