Multiple sequence alignment - TraesCS4A01G319300

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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 TraesCS4A01G319300 chr4A 100.000 5396 0 0 1 5396 608272046 608266651 0.000000e+00 9965.0
1 TraesCS4A01G319300 chr4A 86.221 3527 457 17 966 4476 608481514 608478001 0.000000e+00 3794.0
2 TraesCS4A01G319300 chr4A 82.531 3658 585 40 781 4406 608234851 608231216 0.000000e+00 3166.0
3 TraesCS4A01G319300 chr4A 78.519 270 29 12 5017 5264 608477445 608477183 3.370000e-32 150.0
4 TraesCS4A01G319300 chr5D 92.591 5156 269 50 314 5394 564226130 564231247 0.000000e+00 7300.0
5 TraesCS4A01G319300 chr5D 85.071 3731 505 43 782 4480 563979879 563976169 0.000000e+00 3757.0
6 TraesCS4A01G319300 chr5D 92.697 178 12 1 5185 5362 564290661 564290837 6.940000e-64 255.0
7 TraesCS4A01G319300 chr5D 90.196 153 13 1 783 935 564226475 564226625 1.190000e-46 198.0
8 TraesCS4A01G319300 chr5D 90.698 129 10 2 10 137 564225963 564226090 2.580000e-38 171.0
9 TraesCS4A01G319300 chr5D 88.489 139 12 2 649 786 564226639 564226774 1.200000e-36 165.0
10 TraesCS4A01G319300 chr5B 96.527 4376 87 25 845 5182 706710109 706714457 0.000000e+00 7179.0
11 TraesCS4A01G319300 chr5B 85.292 3624 476 42 889 4480 706389074 706385476 0.000000e+00 3687.0
12 TraesCS4A01G319300 chr5B 84.655 3682 506 43 875 4526 706453385 706457037 0.000000e+00 3615.0
13 TraesCS4A01G319300 chr5B 84.816 3609 503 31 875 4459 705984575 705980988 0.000000e+00 3587.0
14 TraesCS4A01G319300 chr5B 94.796 269 10 1 5130 5394 706714444 706714712 3.010000e-112 416.0
15 TraesCS4A01G319300 chr5B 76.374 673 67 39 4759 5394 706457341 706457958 1.480000e-70 278.0
16 TraesCS4A01G319300 chr5B 88.525 122 9 3 4586 4702 706457137 706457258 5.630000e-30 143.0
17 TraesCS4A01G319300 chr5B 94.872 39 2 0 5030 5068 480026671 480026633 1.620000e-05 62.1
18 TraesCS4A01G319300 chr3B 83.512 3645 546 40 859 4467 8039806 8043431 0.000000e+00 3350.0


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 TraesCS4A01G319300 chr4A 608266651 608272046 5395 True 9965.000000 9965 100.000000 1 5396 1 chr4A.!!$R2 5395
1 TraesCS4A01G319300 chr4A 608231216 608234851 3635 True 3166.000000 3166 82.531000 781 4406 1 chr4A.!!$R1 3625
2 TraesCS4A01G319300 chr4A 608477183 608481514 4331 True 1972.000000 3794 82.370000 966 5264 2 chr4A.!!$R3 4298
3 TraesCS4A01G319300 chr5D 563976169 563979879 3710 True 3757.000000 3757 85.071000 782 4480 1 chr5D.!!$R1 3698
4 TraesCS4A01G319300 chr5D 564225963 564231247 5284 False 3735.500000 7300 91.644500 10 5394 2 chr5D.!!$F2 5384
5 TraesCS4A01G319300 chr5B 706710109 706714712 4603 False 3797.500000 7179 95.661500 845 5394 2 chr5B.!!$F2 4549
6 TraesCS4A01G319300 chr5B 706385476 706389074 3598 True 3687.000000 3687 85.292000 889 4480 1 chr5B.!!$R3 3591
7 TraesCS4A01G319300 chr5B 705980988 705984575 3587 True 3587.000000 3587 84.816000 875 4459 1 chr5B.!!$R2 3584
8 TraesCS4A01G319300 chr5B 706453385 706457958 4573 False 1345.333333 3615 83.184667 875 5394 3 chr5B.!!$F1 4519
9 TraesCS4A01G319300 chr3B 8039806 8043431 3625 False 3350.000000 3350 83.512000 859 4467 1 chr3B.!!$F1 3608

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
292 300 0.109597 ATTTCTTTTCAGGCGCGCTG 60.110 50.0 32.29 25.15 0.00 5.18 F
896 946 0.179062 GCCGGATTGAGCTCATCAGT 60.179 55.0 19.04 4.12 39.68 3.41 F
1374 1443 2.092968 TGTACCTGATGAGGGCATGAAC 60.093 50.0 2.36 0.00 44.84 3.18 F
2586 2677 0.871722 TGGCGATTGGTGTTTCTTCG 59.128 50.0 0.00 0.00 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 1644 0.540923 GCTCAGAGCCAGATGAACCT 59.459 55.000 11.84 0.00 34.48 3.50 R
2439 2530 0.175760 TAGTGCCACCAGATTCGCTC 59.824 55.000 0.00 0.00 0.00 5.03 R
3313 3406 1.004394 GCTAGGTAAAGTTGTGGCCCT 59.996 52.381 0.00 0.00 0.00 5.19 R
4545 4684 2.893637 ACAATGTGTATCACCGAGCTC 58.106 47.619 2.73 2.73 32.73 4.09 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
39 40 8.801882 TCCCTAATTTTTATAGACACCACAAG 57.198 34.615 0.00 0.00 0.00 3.16
46 47 8.740123 TTTTTATAGACACCACAAGAACAAGA 57.260 30.769 0.00 0.00 0.00 3.02
64 65 9.143631 AGAACAAGAAATTTTGCACATAATAGC 57.856 29.630 0.00 0.00 0.00 2.97
113 114 4.890158 TGAACACAATCCTAGAGCTTCA 57.110 40.909 0.00 0.00 0.00 3.02
115 116 3.618690 ACACAATCCTAGAGCTTCACC 57.381 47.619 0.00 0.00 0.00 4.02
122 124 2.758979 TCCTAGAGCTTCACCGGTAAAG 59.241 50.000 13.63 13.63 0.00 1.85
148 156 9.399403 GAATTTTAGCTTTATACTTAGCATGCC 57.601 33.333 15.66 0.00 39.85 4.40
152 160 5.066593 AGCTTTATACTTAGCATGCCCTTC 58.933 41.667 15.66 0.00 39.85 3.46
154 162 5.532779 GCTTTATACTTAGCATGCCCTTCTT 59.467 40.000 15.66 0.00 37.35 2.52
169 177 3.304829 CCTTCTTGGGAAAACAAAGGGA 58.695 45.455 0.00 0.00 28.93 4.20
170 178 3.321968 CCTTCTTGGGAAAACAAAGGGAG 59.678 47.826 0.00 0.00 28.93 4.30
171 179 3.963476 TCTTGGGAAAACAAAGGGAGA 57.037 42.857 0.00 0.00 0.00 3.71
172 180 3.832527 TCTTGGGAAAACAAAGGGAGAG 58.167 45.455 0.00 0.00 0.00 3.20
173 181 3.461831 TCTTGGGAAAACAAAGGGAGAGA 59.538 43.478 0.00 0.00 0.00 3.10
174 182 4.106341 TCTTGGGAAAACAAAGGGAGAGAT 59.894 41.667 0.00 0.00 0.00 2.75
175 183 5.312178 TCTTGGGAAAACAAAGGGAGAGATA 59.688 40.000 0.00 0.00 0.00 1.98
176 184 5.592587 TGGGAAAACAAAGGGAGAGATAA 57.407 39.130 0.00 0.00 0.00 1.75
177 185 5.321927 TGGGAAAACAAAGGGAGAGATAAC 58.678 41.667 0.00 0.00 0.00 1.89
178 186 4.705507 GGGAAAACAAAGGGAGAGATAACC 59.294 45.833 0.00 0.00 0.00 2.85
179 187 5.321927 GGAAAACAAAGGGAGAGATAACCA 58.678 41.667 0.00 0.00 0.00 3.67
180 188 5.773176 GGAAAACAAAGGGAGAGATAACCAA 59.227 40.000 0.00 0.00 0.00 3.67
181 189 6.071896 GGAAAACAAAGGGAGAGATAACCAAG 60.072 42.308 0.00 0.00 0.00 3.61
182 190 4.576330 ACAAAGGGAGAGATAACCAAGG 57.424 45.455 0.00 0.00 0.00 3.61
183 191 3.916989 ACAAAGGGAGAGATAACCAAGGT 59.083 43.478 0.00 0.00 0.00 3.50
184 192 5.098663 ACAAAGGGAGAGATAACCAAGGTA 58.901 41.667 0.00 0.00 0.00 3.08
185 193 5.731678 ACAAAGGGAGAGATAACCAAGGTAT 59.268 40.000 0.00 0.00 0.00 2.73
186 194 5.896073 AAGGGAGAGATAACCAAGGTATG 57.104 43.478 0.00 0.00 0.00 2.39
187 195 3.648545 AGGGAGAGATAACCAAGGTATGC 59.351 47.826 0.00 0.00 0.00 3.14
188 196 3.391296 GGGAGAGATAACCAAGGTATGCA 59.609 47.826 0.00 0.00 0.00 3.96
189 197 4.503991 GGGAGAGATAACCAAGGTATGCAG 60.504 50.000 0.00 0.00 0.00 4.41
190 198 4.345257 GGAGAGATAACCAAGGTATGCAGA 59.655 45.833 0.00 0.00 0.00 4.26
191 199 5.283457 AGAGATAACCAAGGTATGCAGAC 57.717 43.478 1.94 1.94 0.00 3.51
192 200 4.965532 AGAGATAACCAAGGTATGCAGACT 59.034 41.667 11.87 0.00 0.00 3.24
193 201 6.136857 AGAGATAACCAAGGTATGCAGACTA 58.863 40.000 11.87 0.00 0.00 2.59
194 202 6.266558 AGAGATAACCAAGGTATGCAGACTAG 59.733 42.308 11.87 1.63 0.00 2.57
195 203 2.990066 ACCAAGGTATGCAGACTAGC 57.010 50.000 11.87 0.00 0.00 3.42
202 210 4.701663 TGCAGACTAGCAAGTGCC 57.298 55.556 0.00 0.00 42.46 5.01
203 211 2.061220 TGCAGACTAGCAAGTGCCT 58.939 52.632 0.00 0.00 42.46 4.75
204 212 1.266178 TGCAGACTAGCAAGTGCCTA 58.734 50.000 0.00 0.00 42.46 3.93
205 213 1.833630 TGCAGACTAGCAAGTGCCTAT 59.166 47.619 0.00 0.00 42.46 2.57
206 214 2.208431 GCAGACTAGCAAGTGCCTATG 58.792 52.381 0.00 0.00 43.38 2.23
207 215 2.159043 GCAGACTAGCAAGTGCCTATGA 60.159 50.000 0.00 0.00 43.38 2.15
208 216 3.452474 CAGACTAGCAAGTGCCTATGAC 58.548 50.000 0.00 0.00 43.38 3.06
209 217 3.131933 CAGACTAGCAAGTGCCTATGACT 59.868 47.826 0.00 0.00 43.38 3.41
210 218 4.339530 CAGACTAGCAAGTGCCTATGACTA 59.660 45.833 0.00 0.00 43.38 2.59
211 219 4.956700 AGACTAGCAAGTGCCTATGACTAA 59.043 41.667 0.00 0.00 43.38 2.24
212 220 5.422331 AGACTAGCAAGTGCCTATGACTAAA 59.578 40.000 0.00 0.00 43.38 1.85
213 221 6.098982 AGACTAGCAAGTGCCTATGACTAAAT 59.901 38.462 0.00 0.00 43.38 1.40
214 222 6.653989 ACTAGCAAGTGCCTATGACTAAATT 58.346 36.000 0.00 0.00 43.38 1.82
215 223 6.763610 ACTAGCAAGTGCCTATGACTAAATTC 59.236 38.462 0.00 0.00 43.38 2.17
216 224 4.884164 AGCAAGTGCCTATGACTAAATTCC 59.116 41.667 0.00 0.00 43.38 3.01
217 225 4.260784 GCAAGTGCCTATGACTAAATTCCG 60.261 45.833 0.00 0.00 34.31 4.30
218 226 4.073293 AGTGCCTATGACTAAATTCCGG 57.927 45.455 0.00 0.00 0.00 5.14
219 227 3.709653 AGTGCCTATGACTAAATTCCGGA 59.290 43.478 0.00 0.00 0.00 5.14
220 228 3.808174 GTGCCTATGACTAAATTCCGGAC 59.192 47.826 1.83 0.00 0.00 4.79
221 229 3.181458 TGCCTATGACTAAATTCCGGACC 60.181 47.826 1.83 0.00 0.00 4.46
222 230 3.181458 GCCTATGACTAAATTCCGGACCA 60.181 47.826 1.83 0.00 0.00 4.02
223 231 4.505039 GCCTATGACTAAATTCCGGACCAT 60.505 45.833 1.83 0.00 0.00 3.55
224 232 5.238583 CCTATGACTAAATTCCGGACCATC 58.761 45.833 1.83 0.00 0.00 3.51
225 233 5.012148 CCTATGACTAAATTCCGGACCATCT 59.988 44.000 1.83 0.00 0.00 2.90
226 234 6.210784 CCTATGACTAAATTCCGGACCATCTA 59.789 42.308 1.83 0.00 0.00 1.98
227 235 5.531122 TGACTAAATTCCGGACCATCTAG 57.469 43.478 1.83 0.00 0.00 2.43
228 236 4.960469 TGACTAAATTCCGGACCATCTAGT 59.040 41.667 1.83 2.18 0.00 2.57
229 237 6.131264 TGACTAAATTCCGGACCATCTAGTA 58.869 40.000 1.83 0.00 0.00 1.82
230 238 6.781014 TGACTAAATTCCGGACCATCTAGTAT 59.219 38.462 1.83 0.00 0.00 2.12
231 239 7.289317 TGACTAAATTCCGGACCATCTAGTATT 59.711 37.037 1.83 0.00 0.00 1.89
232 240 8.030913 ACTAAATTCCGGACCATCTAGTATTT 57.969 34.615 1.83 6.93 0.00 1.40
233 241 8.491958 ACTAAATTCCGGACCATCTAGTATTTT 58.508 33.333 1.83 0.00 0.00 1.82
234 242 9.991906 CTAAATTCCGGACCATCTAGTATTTTA 57.008 33.333 1.83 0.00 0.00 1.52
236 244 8.904099 AATTCCGGACCATCTAGTATTTTAAG 57.096 34.615 1.83 0.00 0.00 1.85
237 245 7.427989 TTCCGGACCATCTAGTATTTTAAGT 57.572 36.000 1.83 0.00 0.00 2.24
238 246 8.537728 TTCCGGACCATCTAGTATTTTAAGTA 57.462 34.615 1.83 0.00 0.00 2.24
239 247 8.716674 TCCGGACCATCTAGTATTTTAAGTAT 57.283 34.615 0.00 0.00 0.00 2.12
240 248 9.151177 TCCGGACCATCTAGTATTTTAAGTATT 57.849 33.333 0.00 0.00 0.00 1.89
241 249 9.774413 CCGGACCATCTAGTATTTTAAGTATTT 57.226 33.333 0.00 0.00 0.00 1.40
264 272 8.911918 TTTTAACAAGACTATACAGAAGCCAA 57.088 30.769 0.00 0.00 0.00 4.52
265 273 9.515226 TTTTAACAAGACTATACAGAAGCCAAT 57.485 29.630 0.00 0.00 0.00 3.16
266 274 9.515226 TTTAACAAGACTATACAGAAGCCAATT 57.485 29.630 0.00 0.00 0.00 2.32
267 275 9.515226 TTAACAAGACTATACAGAAGCCAATTT 57.485 29.630 0.00 0.00 0.00 1.82
268 276 8.409358 AACAAGACTATACAGAAGCCAATTTT 57.591 30.769 0.00 0.00 0.00 1.82
269 277 8.409358 ACAAGACTATACAGAAGCCAATTTTT 57.591 30.769 0.00 0.00 0.00 1.94
270 278 9.515226 ACAAGACTATACAGAAGCCAATTTTTA 57.485 29.630 0.00 0.00 0.00 1.52
271 279 9.774742 CAAGACTATACAGAAGCCAATTTTTAC 57.225 33.333 0.00 0.00 0.00 2.01
272 280 9.515226 AAGACTATACAGAAGCCAATTTTTACA 57.485 29.630 0.00 0.00 0.00 2.41
273 281 9.515226 AGACTATACAGAAGCCAATTTTTACAA 57.485 29.630 0.00 0.00 0.00 2.41
279 287 8.962884 ACAGAAGCCAATTTTTACAATTTCTT 57.037 26.923 0.00 0.00 0.00 2.52
280 288 9.394767 ACAGAAGCCAATTTTTACAATTTCTTT 57.605 25.926 0.00 0.00 0.00 2.52
285 293 8.839343 AGCCAATTTTTACAATTTCTTTTCAGG 58.161 29.630 0.00 0.00 0.00 3.86
286 294 7.591057 GCCAATTTTTACAATTTCTTTTCAGGC 59.409 33.333 0.00 0.00 0.00 4.85
287 295 7.798052 CCAATTTTTACAATTTCTTTTCAGGCG 59.202 33.333 0.00 0.00 0.00 5.52
288 296 5.898630 TTTTACAATTTCTTTTCAGGCGC 57.101 34.783 0.00 0.00 0.00 6.53
289 297 2.050477 ACAATTTCTTTTCAGGCGCG 57.950 45.000 0.00 0.00 0.00 6.86
290 298 0.710017 CAATTTCTTTTCAGGCGCGC 59.290 50.000 25.94 25.94 0.00 6.86
291 299 0.598065 AATTTCTTTTCAGGCGCGCT 59.402 45.000 32.29 14.46 0.00 5.92
292 300 0.109597 ATTTCTTTTCAGGCGCGCTG 60.110 50.000 32.29 25.15 0.00 5.18
293 301 2.128853 TTTCTTTTCAGGCGCGCTGG 62.129 55.000 32.29 22.67 0.00 4.85
294 302 4.107051 CTTTTCAGGCGCGCTGGG 62.107 66.667 32.29 20.02 0.00 4.45
295 303 4.634703 TTTTCAGGCGCGCTGGGA 62.635 61.111 32.29 22.02 0.00 4.37
299 307 4.451150 CAGGCGCGCTGGGACTAA 62.451 66.667 32.29 0.00 29.95 2.24
300 308 3.702048 AGGCGCGCTGGGACTAAA 61.702 61.111 32.29 0.00 29.95 1.85
301 309 3.195698 GGCGCGCTGGGACTAAAG 61.196 66.667 32.29 0.00 0.00 1.85
302 310 2.434359 GCGCGCTGGGACTAAAGT 60.434 61.111 26.67 0.00 0.00 2.66
303 311 2.033194 GCGCGCTGGGACTAAAGTT 61.033 57.895 26.67 0.00 0.00 2.66
304 312 1.574702 GCGCGCTGGGACTAAAGTTT 61.575 55.000 26.67 0.00 0.00 2.66
305 313 1.717194 CGCGCTGGGACTAAAGTTTA 58.283 50.000 5.56 0.00 0.00 2.01
306 314 1.392510 CGCGCTGGGACTAAAGTTTAC 59.607 52.381 5.56 0.00 0.00 2.01
307 315 2.696506 GCGCTGGGACTAAAGTTTACT 58.303 47.619 0.00 0.00 0.00 2.24
308 316 2.671888 GCGCTGGGACTAAAGTTTACTC 59.328 50.000 0.00 0.00 0.00 2.59
309 317 3.863400 GCGCTGGGACTAAAGTTTACTCA 60.863 47.826 0.00 0.00 0.00 3.41
310 318 4.312443 CGCTGGGACTAAAGTTTACTCAA 58.688 43.478 0.00 0.00 0.00 3.02
311 319 4.389077 CGCTGGGACTAAAGTTTACTCAAG 59.611 45.833 0.00 0.00 0.00 3.02
312 320 5.548406 GCTGGGACTAAAGTTTACTCAAGA 58.452 41.667 0.00 0.00 0.00 3.02
328 336 0.250338 AAGAACAGGGGAACTCGTGC 60.250 55.000 0.00 0.00 0.00 5.34
329 337 1.070786 GAACAGGGGAACTCGTGCA 59.929 57.895 0.00 0.00 0.00 4.57
337 345 2.354805 GGGGAACTCGTGCATAGAAACT 60.355 50.000 6.07 0.00 0.00 2.66
338 346 2.930682 GGGAACTCGTGCATAGAAACTC 59.069 50.000 6.07 0.00 0.00 3.01
339 347 2.930682 GGAACTCGTGCATAGAAACTCC 59.069 50.000 6.07 4.28 0.00 3.85
352 360 2.893489 AGAAACTCCTTGGCAATGTTCC 59.107 45.455 0.00 0.00 0.00 3.62
354 362 2.683211 ACTCCTTGGCAATGTTCCTT 57.317 45.000 0.00 0.00 0.00 3.36
356 364 2.629617 ACTCCTTGGCAATGTTCCTTTG 59.370 45.455 0.00 0.00 0.00 2.77
377 385 3.194062 GGGTGTTGTTTGTTGACATTGG 58.806 45.455 0.00 0.00 0.00 3.16
384 392 7.491048 GTGTTGTTTGTTGACATTGGTTAGATT 59.509 33.333 0.00 0.00 0.00 2.40
407 415 6.484818 TGTAAATAGGTCACCGCTAAAAAC 57.515 37.500 0.00 0.00 0.00 2.43
419 429 5.517411 CACCGCTAAAAACTATATCGTGTCA 59.483 40.000 0.00 0.00 0.00 3.58
472 483 9.856162 AGTTGGTTACTTTCTTAGGTGATTAAA 57.144 29.630 0.00 0.00 31.29 1.52
506 517 8.263854 AGAATATATATTGAAGGGGGTATCCG 57.736 38.462 12.74 0.00 36.01 4.18
508 519 5.952347 ATATATTGAAGGGGGTATCCGAC 57.048 43.478 0.00 0.00 36.01 4.79
510 521 1.492764 TTGAAGGGGGTATCCGACTC 58.507 55.000 0.00 0.00 36.01 3.36
517 528 1.893801 GGGGTATCCGACTCGATCAAT 59.106 52.381 0.00 0.00 0.00 2.57
528 539 4.259970 CGACTCGATCAATGACCACATTTC 60.260 45.833 0.00 0.00 43.17 2.17
531 542 4.578871 TCGATCAATGACCACATTTCTGT 58.421 39.130 0.00 0.00 43.17 3.41
546 557 5.071250 ACATTTCTGTACAGGTGACCAACTA 59.929 40.000 22.48 0.00 32.49 2.24
553 564 2.224305 ACAGGTGACCAACTAGCTTGTC 60.224 50.000 3.63 0.00 0.00 3.18
565 576 5.449107 ACTAGCTTGTCGACTTACTGAAA 57.551 39.130 17.92 0.00 0.00 2.69
566 577 5.839621 ACTAGCTTGTCGACTTACTGAAAA 58.160 37.500 17.92 0.00 0.00 2.29
567 578 6.278363 ACTAGCTTGTCGACTTACTGAAAAA 58.722 36.000 17.92 0.00 0.00 1.94
569 580 8.086522 ACTAGCTTGTCGACTTACTGAAAAATA 58.913 33.333 17.92 0.00 0.00 1.40
588 599 4.989279 ATATTTGGCTGTGACAATCACC 57.011 40.909 6.51 0.00 46.40 4.02
601 612 6.072008 TGTGACAATCACCATTCATTTGTAGG 60.072 38.462 6.51 0.00 46.40 3.18
617 628 9.547753 TCATTTGTAGGACTAAAAGAGCATATC 57.452 33.333 0.00 0.00 0.00 1.63
619 630 9.771534 ATTTGTAGGACTAAAAGAGCATATCTC 57.228 33.333 0.00 0.00 37.23 2.75
636 647 6.519043 GCATATCTCTGGTACTGCCTATGAAA 60.519 42.308 0.00 0.00 38.35 2.69
652 663 9.532494 TGCCTATGAAACCTGCATATATAAATT 57.468 29.630 0.00 0.00 0.00 1.82
653 664 9.793252 GCCTATGAAACCTGCATATATAAATTG 57.207 33.333 0.00 0.00 0.00 2.32
662 673 9.404848 ACCTGCATATATAAATTGATCTCATGG 57.595 33.333 0.00 0.00 0.00 3.66
664 675 7.922837 TGCATATATAAATTGATCTCATGGCG 58.077 34.615 0.00 0.00 0.00 5.69
707 742 8.107095 ACCTTTCAGCATTAAGTAATCCTTACA 58.893 33.333 0.39 0.00 38.60 2.41
708 743 8.616076 CCTTTCAGCATTAAGTAATCCTTACAG 58.384 37.037 0.39 0.00 38.60 2.74
709 744 9.167311 CTTTCAGCATTAAGTAATCCTTACAGT 57.833 33.333 0.39 0.00 38.60 3.55
713 748 9.250624 CAGCATTAAGTAATCCTTACAGTAGTC 57.749 37.037 0.39 0.00 38.60 2.59
725 760 6.210185 TCCTTACAGTAGTCAAGTAAAGACCC 59.790 42.308 0.00 0.00 36.68 4.46
740 775 2.839228 AGACCCCTTGCTAGATTGAGT 58.161 47.619 0.00 0.00 0.00 3.41
750 785 6.373774 CCTTGCTAGATTGAGTTCATCAGTTT 59.626 38.462 0.00 0.00 39.68 2.66
759 794 6.951256 TGAGTTCATCAGTTTATCTGTTCG 57.049 37.500 0.00 0.00 43.97 3.95
779 814 8.937634 TGTTCGTCTTTTCCTTTATATAGGAC 57.062 34.615 11.11 0.65 43.91 3.85
791 826 8.573885 TCCTTTATATAGGACACAACTCATACG 58.426 37.037 7.77 0.00 39.40 3.06
832 871 1.960689 GGCAAAGTGCTTGAAAGGGTA 59.039 47.619 0.00 0.00 44.28 3.69
880 928 5.049405 ACAGTCAAGTAAAAATCTCTTGCCG 60.049 40.000 0.00 0.00 38.56 5.69
896 946 0.179062 GCCGGATTGAGCTCATCAGT 60.179 55.000 19.04 4.12 39.68 3.41
971 1036 3.612860 CAGACTAACCGACATGCTAACAC 59.387 47.826 0.00 0.00 0.00 3.32
991 1059 7.886629 AACACATTCTATCATTATTGCAGGT 57.113 32.000 0.00 0.00 0.00 4.00
1211 1280 7.265673 CAGCTTATTACCAGCACTAGTCTTAA 58.734 38.462 0.00 0.00 39.99 1.85
1299 1368 3.945285 GTCAAGACACAGTCCTTGGAAAA 59.055 43.478 10.72 0.00 32.18 2.29
1374 1443 2.092968 TGTACCTGATGAGGGCATGAAC 60.093 50.000 2.36 0.00 44.84 3.18
1445 1514 3.672808 ACACATTTCTGGAGCTCTTGAG 58.327 45.455 14.64 7.59 0.00 3.02
1558 1636 8.275015 TGAAGTTCTAGAGTTGATACTGAGAG 57.725 38.462 4.17 0.00 33.84 3.20
1584 1662 4.478206 TTTAGGTTCATCTGGCTCTGAG 57.522 45.455 0.00 0.00 0.00 3.35
1794 1872 3.007506 TGAAAAGGACGTTGCAGGAGATA 59.992 43.478 0.00 0.00 0.00 1.98
1843 1921 4.794278 TCTTTTGACCGTGCTGATAGTA 57.206 40.909 0.00 0.00 0.00 1.82
2439 2530 6.744537 GGATTTCTCACGATTTCATTGAACAG 59.255 38.462 0.00 0.00 0.00 3.16
2586 2677 0.871722 TGGCGATTGGTGTTTCTTCG 59.128 50.000 0.00 0.00 0.00 3.79
2962 3053 5.817816 GGATATACCCGCAATTCTATTCCTG 59.182 44.000 0.00 0.00 0.00 3.86
3313 3406 3.701542 AGAGCTCATGATCGAAGGTTACA 59.298 43.478 17.77 0.00 33.18 2.41
4099 4195 6.653320 GTGGTTTGGACAACTAATATCTGTCA 59.347 38.462 4.05 0.00 41.03 3.58
4545 4684 6.207417 ACAGAACCACAAATGTTAGAATCTGG 59.793 38.462 16.12 0.00 0.00 3.86
4634 4807 8.417106 TGGAAGTATTAGAAACATTGTGCAAAA 58.583 29.630 0.00 0.00 0.00 2.44
4649 4823 4.141981 TGTGCAAAATGTTGATTGGTCTGT 60.142 37.500 0.00 0.00 36.83 3.41
4667 4841 4.078537 TCTGTTGGTTTGTATGGATGGTG 58.921 43.478 0.00 0.00 0.00 4.17
4673 4847 6.259346 TGGTTTGTATGGATGGTGATGATA 57.741 37.500 0.00 0.00 0.00 2.15
4747 4981 5.163322 TGTGGGCTGAATTGATTTGTTTTCT 60.163 36.000 0.00 0.00 0.00 2.52
4941 5267 2.054021 TGATGTGGAACCCTTGTCAGA 58.946 47.619 0.00 0.00 34.36 3.27
4942 5268 2.038952 TGATGTGGAACCCTTGTCAGAG 59.961 50.000 0.00 0.00 34.36 3.35
5069 5408 4.282496 CACCCAGGATAGTCAGTAGTTCT 58.718 47.826 0.00 0.00 0.00 3.01
5114 5453 1.746220 CAAGGAGTAGGAGACTGACGG 59.254 57.143 0.00 0.00 43.88 4.79
5394 5818 6.459923 AGAAGGGAATTCTAGTATTGCGATC 58.540 40.000 5.23 7.86 46.75 3.69
5395 5819 5.808366 AGGGAATTCTAGTATTGCGATCA 57.192 39.130 5.23 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 9.965824 CTTGTTCTTGTGGTGTCTATAAAAATT 57.034 29.630 0.00 0.00 0.00 1.82
24 25 8.918202 ATTTCTTGTTCTTGTGGTGTCTATAA 57.082 30.769 0.00 0.00 0.00 0.98
29 30 6.455513 GCAAAATTTCTTGTTCTTGTGGTGTC 60.456 38.462 0.00 0.00 0.00 3.67
33 34 5.350914 TGTGCAAAATTTCTTGTTCTTGTGG 59.649 36.000 0.00 0.00 0.00 4.17
39 40 9.143631 AGCTATTATGTGCAAAATTTCTTGTTC 57.856 29.630 0.00 0.00 0.00 3.18
95 96 2.093973 CGGTGAAGCTCTAGGATTGTGT 60.094 50.000 0.00 0.00 0.00 3.72
113 114 9.676861 AGTATAAAGCTAAAATTCTTTACCGGT 57.323 29.630 13.98 13.98 37.53 5.28
122 124 9.399403 GGCATGCTAAGTATAAAGCTAAAATTC 57.601 33.333 18.92 0.00 39.53 2.17
148 156 3.304829 TCCCTTTGTTTTCCCAAGAAGG 58.695 45.455 0.00 0.00 32.35 3.46
152 160 3.832527 TCTCTCCCTTTGTTTTCCCAAG 58.167 45.455 0.00 0.00 0.00 3.61
154 162 5.321927 GTTATCTCTCCCTTTGTTTTCCCA 58.678 41.667 0.00 0.00 0.00 4.37
157 165 6.071896 CCTTGGTTATCTCTCCCTTTGTTTTC 60.072 42.308 0.00 0.00 0.00 2.29
158 166 5.775195 CCTTGGTTATCTCTCCCTTTGTTTT 59.225 40.000 0.00 0.00 0.00 2.43
163 171 5.398012 GCATACCTTGGTTATCTCTCCCTTT 60.398 44.000 0.00 0.00 0.00 3.11
165 173 3.648545 GCATACCTTGGTTATCTCTCCCT 59.351 47.826 0.00 0.00 0.00 4.20
166 174 3.391296 TGCATACCTTGGTTATCTCTCCC 59.609 47.826 0.00 0.00 0.00 4.30
167 175 4.345257 TCTGCATACCTTGGTTATCTCTCC 59.655 45.833 0.00 0.00 0.00 3.71
169 177 4.965532 AGTCTGCATACCTTGGTTATCTCT 59.034 41.667 0.00 0.00 0.00 3.10
170 178 5.283457 AGTCTGCATACCTTGGTTATCTC 57.717 43.478 0.00 0.00 0.00 2.75
171 179 5.221541 GCTAGTCTGCATACCTTGGTTATCT 60.222 44.000 0.00 0.00 0.00 1.98
172 180 4.991687 GCTAGTCTGCATACCTTGGTTATC 59.008 45.833 0.00 0.00 0.00 1.75
173 181 4.408921 TGCTAGTCTGCATACCTTGGTTAT 59.591 41.667 0.00 0.00 38.12 1.89
174 182 3.772572 TGCTAGTCTGCATACCTTGGTTA 59.227 43.478 0.00 0.00 38.12 2.85
175 183 2.571653 TGCTAGTCTGCATACCTTGGTT 59.428 45.455 0.00 0.00 38.12 3.67
176 184 2.187958 TGCTAGTCTGCATACCTTGGT 58.812 47.619 0.00 0.00 38.12 3.67
177 185 2.988010 TGCTAGTCTGCATACCTTGG 57.012 50.000 0.00 0.00 38.12 3.61
178 186 3.620374 CACTTGCTAGTCTGCATACCTTG 59.380 47.826 0.00 0.00 42.96 3.61
179 187 3.866651 CACTTGCTAGTCTGCATACCTT 58.133 45.455 0.00 0.00 42.96 3.50
180 188 2.419297 GCACTTGCTAGTCTGCATACCT 60.419 50.000 0.00 0.00 42.96 3.08
181 189 1.936547 GCACTTGCTAGTCTGCATACC 59.063 52.381 0.00 0.00 42.96 2.73
182 190 1.936547 GGCACTTGCTAGTCTGCATAC 59.063 52.381 11.64 0.00 42.96 2.39
183 191 1.833630 AGGCACTTGCTAGTCTGCATA 59.166 47.619 11.64 0.00 42.96 3.14
184 192 0.617413 AGGCACTTGCTAGTCTGCAT 59.383 50.000 11.64 3.16 42.96 3.96
185 193 1.266178 TAGGCACTTGCTAGTCTGCA 58.734 50.000 11.64 0.00 41.75 4.41
186 194 2.159043 TCATAGGCACTTGCTAGTCTGC 60.159 50.000 0.00 0.00 41.75 4.26
187 195 3.131933 AGTCATAGGCACTTGCTAGTCTG 59.868 47.826 0.00 0.00 41.75 3.51
188 196 3.370104 AGTCATAGGCACTTGCTAGTCT 58.630 45.455 0.00 0.00 41.75 3.24
189 197 3.810310 AGTCATAGGCACTTGCTAGTC 57.190 47.619 0.00 0.00 41.75 2.59
190 198 5.677319 TTTAGTCATAGGCACTTGCTAGT 57.323 39.130 0.38 0.00 41.75 2.57
191 199 6.203723 GGAATTTAGTCATAGGCACTTGCTAG 59.796 42.308 0.38 0.00 41.75 3.42
192 200 6.055588 GGAATTTAGTCATAGGCACTTGCTA 58.944 40.000 0.38 0.00 41.75 3.49
193 201 4.884164 GGAATTTAGTCATAGGCACTTGCT 59.116 41.667 0.38 0.00 41.75 3.91
194 202 4.260784 CGGAATTTAGTCATAGGCACTTGC 60.261 45.833 0.00 0.00 41.75 4.01
195 203 4.273480 CCGGAATTTAGTCATAGGCACTTG 59.727 45.833 0.00 0.00 41.75 3.16
196 204 4.163458 TCCGGAATTTAGTCATAGGCACTT 59.837 41.667 0.00 0.00 41.75 3.16
197 205 3.709653 TCCGGAATTTAGTCATAGGCACT 59.290 43.478 0.00 0.00 46.37 4.40
198 206 3.808174 GTCCGGAATTTAGTCATAGGCAC 59.192 47.826 5.23 0.00 0.00 5.01
199 207 3.181458 GGTCCGGAATTTAGTCATAGGCA 60.181 47.826 5.23 0.00 0.00 4.75
200 208 3.181458 TGGTCCGGAATTTAGTCATAGGC 60.181 47.826 5.23 0.00 0.00 3.93
201 209 4.682778 TGGTCCGGAATTTAGTCATAGG 57.317 45.455 5.23 0.00 0.00 2.57
202 210 6.102897 AGATGGTCCGGAATTTAGTCATAG 57.897 41.667 5.23 0.00 0.00 2.23
203 211 6.781014 ACTAGATGGTCCGGAATTTAGTCATA 59.219 38.462 5.23 0.00 0.00 2.15
204 212 5.602978 ACTAGATGGTCCGGAATTTAGTCAT 59.397 40.000 5.23 1.63 0.00 3.06
205 213 4.960469 ACTAGATGGTCCGGAATTTAGTCA 59.040 41.667 5.23 0.00 0.00 3.41
206 214 5.532664 ACTAGATGGTCCGGAATTTAGTC 57.467 43.478 5.23 0.00 0.00 2.59
207 215 7.613551 AATACTAGATGGTCCGGAATTTAGT 57.386 36.000 18.36 18.36 31.04 2.24
208 216 8.904099 AAAATACTAGATGGTCCGGAATTTAG 57.096 34.615 5.23 8.93 0.00 1.85
210 218 9.338622 CTTAAAATACTAGATGGTCCGGAATTT 57.661 33.333 5.23 2.00 0.00 1.82
211 219 8.491958 ACTTAAAATACTAGATGGTCCGGAATT 58.508 33.333 5.23 0.00 0.00 2.17
212 220 8.030913 ACTTAAAATACTAGATGGTCCGGAAT 57.969 34.615 5.23 0.00 0.00 3.01
213 221 7.427989 ACTTAAAATACTAGATGGTCCGGAA 57.572 36.000 5.23 0.00 0.00 4.30
214 222 8.716674 ATACTTAAAATACTAGATGGTCCGGA 57.283 34.615 0.00 0.00 0.00 5.14
215 223 9.774413 AAATACTTAAAATACTAGATGGTCCGG 57.226 33.333 0.00 0.00 0.00 5.14
238 246 9.515226 TTGGCTTCTGTATAGTCTTGTTAAAAT 57.485 29.630 0.00 0.00 0.00 1.82
239 247 8.911918 TTGGCTTCTGTATAGTCTTGTTAAAA 57.088 30.769 0.00 0.00 0.00 1.52
240 248 9.515226 AATTGGCTTCTGTATAGTCTTGTTAAA 57.485 29.630 0.00 0.00 0.00 1.52
241 249 9.515226 AAATTGGCTTCTGTATAGTCTTGTTAA 57.485 29.630 0.00 0.00 0.00 2.01
242 250 9.515226 AAAATTGGCTTCTGTATAGTCTTGTTA 57.485 29.630 0.00 0.00 0.00 2.41
243 251 8.409358 AAAATTGGCTTCTGTATAGTCTTGTT 57.591 30.769 0.00 0.00 0.00 2.83
244 252 8.409358 AAAAATTGGCTTCTGTATAGTCTTGT 57.591 30.769 0.00 0.00 0.00 3.16
245 253 9.774742 GTAAAAATTGGCTTCTGTATAGTCTTG 57.225 33.333 0.00 0.00 0.00 3.02
246 254 9.515226 TGTAAAAATTGGCTTCTGTATAGTCTT 57.485 29.630 0.00 0.00 0.00 3.01
247 255 9.515226 TTGTAAAAATTGGCTTCTGTATAGTCT 57.485 29.630 0.00 0.00 0.00 3.24
254 262 8.962884 AAGAAATTGTAAAAATTGGCTTCTGT 57.037 26.923 0.00 0.00 0.00 3.41
259 267 8.839343 CCTGAAAAGAAATTGTAAAAATTGGCT 58.161 29.630 0.00 0.00 0.00 4.75
260 268 7.591057 GCCTGAAAAGAAATTGTAAAAATTGGC 59.409 33.333 0.00 0.00 0.00 4.52
261 269 7.798052 CGCCTGAAAAGAAATTGTAAAAATTGG 59.202 33.333 0.00 0.00 0.00 3.16
262 270 7.321034 GCGCCTGAAAAGAAATTGTAAAAATTG 59.679 33.333 0.00 0.00 0.00 2.32
263 271 7.351981 GCGCCTGAAAAGAAATTGTAAAAATT 58.648 30.769 0.00 0.00 0.00 1.82
264 272 6.346518 CGCGCCTGAAAAGAAATTGTAAAAAT 60.347 34.615 0.00 0.00 0.00 1.82
265 273 5.051374 CGCGCCTGAAAAGAAATTGTAAAAA 60.051 36.000 0.00 0.00 0.00 1.94
266 274 4.442733 CGCGCCTGAAAAGAAATTGTAAAA 59.557 37.500 0.00 0.00 0.00 1.52
267 275 3.978217 CGCGCCTGAAAAGAAATTGTAAA 59.022 39.130 0.00 0.00 0.00 2.01
268 276 3.560503 CGCGCCTGAAAAGAAATTGTAA 58.439 40.909 0.00 0.00 0.00 2.41
269 277 2.667171 GCGCGCCTGAAAAGAAATTGTA 60.667 45.455 23.24 0.00 0.00 2.41
270 278 1.930371 GCGCGCCTGAAAAGAAATTGT 60.930 47.619 23.24 0.00 0.00 2.71
271 279 0.710017 GCGCGCCTGAAAAGAAATTG 59.290 50.000 23.24 0.00 0.00 2.32
272 280 0.598065 AGCGCGCCTGAAAAGAAATT 59.402 45.000 30.33 0.00 0.00 1.82
273 281 0.109597 CAGCGCGCCTGAAAAGAAAT 60.110 50.000 30.33 0.13 44.64 2.17
274 282 1.282570 CAGCGCGCCTGAAAAGAAA 59.717 52.632 30.33 0.00 44.64 2.52
275 283 2.616330 CCAGCGCGCCTGAAAAGAA 61.616 57.895 30.33 0.00 44.64 2.52
276 284 3.049674 CCAGCGCGCCTGAAAAGA 61.050 61.111 30.33 0.00 44.64 2.52
277 285 4.107051 CCCAGCGCGCCTGAAAAG 62.107 66.667 30.33 11.74 44.64 2.27
278 286 4.634703 TCCCAGCGCGCCTGAAAA 62.635 61.111 30.33 5.87 44.64 2.29
282 290 3.950794 TTTAGTCCCAGCGCGCCTG 62.951 63.158 30.33 23.73 41.41 4.85
283 291 3.665675 CTTTAGTCCCAGCGCGCCT 62.666 63.158 30.33 19.75 0.00 5.52
284 292 3.195698 CTTTAGTCCCAGCGCGCC 61.196 66.667 30.33 12.43 0.00 6.53
285 293 1.574702 AAACTTTAGTCCCAGCGCGC 61.575 55.000 26.66 26.66 0.00 6.86
286 294 1.392510 GTAAACTTTAGTCCCAGCGCG 59.607 52.381 0.00 0.00 0.00 6.86
287 295 2.671888 GAGTAAACTTTAGTCCCAGCGC 59.328 50.000 0.00 0.00 0.00 5.92
288 296 3.921677 TGAGTAAACTTTAGTCCCAGCG 58.078 45.455 12.10 0.00 0.00 5.18
289 297 5.548406 TCTTGAGTAAACTTTAGTCCCAGC 58.452 41.667 12.10 0.00 0.00 4.85
290 298 6.990349 TGTTCTTGAGTAAACTTTAGTCCCAG 59.010 38.462 12.10 9.00 0.00 4.45
291 299 6.891388 TGTTCTTGAGTAAACTTTAGTCCCA 58.109 36.000 12.10 1.40 0.00 4.37
292 300 6.427242 CCTGTTCTTGAGTAAACTTTAGTCCC 59.573 42.308 12.10 0.00 0.00 4.46
293 301 6.427242 CCCTGTTCTTGAGTAAACTTTAGTCC 59.573 42.308 12.10 0.42 0.00 3.85
294 302 6.427242 CCCCTGTTCTTGAGTAAACTTTAGTC 59.573 42.308 8.83 8.83 0.00 2.59
295 303 6.100714 TCCCCTGTTCTTGAGTAAACTTTAGT 59.899 38.462 0.00 0.00 0.00 2.24
296 304 6.531021 TCCCCTGTTCTTGAGTAAACTTTAG 58.469 40.000 0.00 0.00 0.00 1.85
297 305 6.503560 TCCCCTGTTCTTGAGTAAACTTTA 57.496 37.500 0.00 0.00 0.00 1.85
298 306 5.382664 TCCCCTGTTCTTGAGTAAACTTT 57.617 39.130 0.00 0.00 0.00 2.66
299 307 5.104067 AGTTCCCCTGTTCTTGAGTAAACTT 60.104 40.000 0.00 0.00 0.00 2.66
300 308 4.412528 AGTTCCCCTGTTCTTGAGTAAACT 59.587 41.667 0.00 0.00 0.00 2.66
301 309 4.715713 AGTTCCCCTGTTCTTGAGTAAAC 58.284 43.478 0.00 0.00 0.00 2.01
302 310 4.502604 CGAGTTCCCCTGTTCTTGAGTAAA 60.503 45.833 0.00 0.00 0.00 2.01
303 311 3.006537 CGAGTTCCCCTGTTCTTGAGTAA 59.993 47.826 0.00 0.00 0.00 2.24
304 312 2.561419 CGAGTTCCCCTGTTCTTGAGTA 59.439 50.000 0.00 0.00 0.00 2.59
305 313 1.344763 CGAGTTCCCCTGTTCTTGAGT 59.655 52.381 0.00 0.00 0.00 3.41
306 314 1.344763 ACGAGTTCCCCTGTTCTTGAG 59.655 52.381 0.00 0.00 0.00 3.02
307 315 1.070134 CACGAGTTCCCCTGTTCTTGA 59.930 52.381 0.00 0.00 0.00 3.02
308 316 1.512926 CACGAGTTCCCCTGTTCTTG 58.487 55.000 0.00 0.00 0.00 3.02
309 317 0.250338 GCACGAGTTCCCCTGTTCTT 60.250 55.000 0.00 0.00 0.00 2.52
310 318 1.371558 GCACGAGTTCCCCTGTTCT 59.628 57.895 0.00 0.00 0.00 3.01
311 319 0.321653 ATGCACGAGTTCCCCTGTTC 60.322 55.000 0.00 0.00 0.00 3.18
312 320 0.981183 TATGCACGAGTTCCCCTGTT 59.019 50.000 0.00 0.00 0.00 3.16
328 336 5.393461 GGAACATTGCCAAGGAGTTTCTATG 60.393 44.000 0.00 0.00 0.00 2.23
329 337 4.706962 GGAACATTGCCAAGGAGTTTCTAT 59.293 41.667 0.00 0.00 0.00 1.98
337 345 1.969923 CCAAAGGAACATTGCCAAGGA 59.030 47.619 0.00 0.00 35.51 3.36
338 346 1.002315 CCCAAAGGAACATTGCCAAGG 59.998 52.381 0.00 0.00 35.51 3.61
339 347 1.693606 ACCCAAAGGAACATTGCCAAG 59.306 47.619 0.00 0.00 35.51 3.61
352 360 3.919216 TGTCAACAAACAACACCCAAAG 58.081 40.909 0.00 0.00 0.00 2.77
354 362 4.248859 CAATGTCAACAAACAACACCCAA 58.751 39.130 0.00 0.00 31.81 4.12
356 364 3.194062 CCAATGTCAACAAACAACACCC 58.806 45.455 0.00 0.00 31.81 4.61
377 385 6.047231 AGCGGTGACCTATTTACAATCTAAC 58.953 40.000 0.00 0.00 0.00 2.34
384 392 6.232692 AGTTTTTAGCGGTGACCTATTTACA 58.767 36.000 0.00 0.00 0.00 2.41
407 415 7.421599 ACTCTGAAGAACATGACACGATATAG 58.578 38.462 0.00 0.00 0.00 1.31
440 450 6.066032 CCTAAGAAAGTAACCAACTCCCAAA 58.934 40.000 0.00 0.00 37.50 3.28
441 451 5.133153 ACCTAAGAAAGTAACCAACTCCCAA 59.867 40.000 0.00 0.00 37.50 4.12
443 453 5.001874 CACCTAAGAAAGTAACCAACTCCC 58.998 45.833 0.00 0.00 37.50 4.30
446 456 9.856162 TTTAATCACCTAAGAAAGTAACCAACT 57.144 29.630 0.00 0.00 41.49 3.16
485 496 6.748969 AGTCGGATACCCCCTTCAATATATA 58.251 40.000 0.00 0.00 0.00 0.86
493 504 0.466922 TCGAGTCGGATACCCCCTTC 60.467 60.000 13.54 0.00 0.00 3.46
497 508 1.325355 TTGATCGAGTCGGATACCCC 58.675 55.000 13.54 0.00 0.00 4.95
498 509 2.557056 TCATTGATCGAGTCGGATACCC 59.443 50.000 13.54 0.00 0.00 3.69
506 517 4.872691 AGAAATGTGGTCATTGATCGAGTC 59.127 41.667 0.00 0.00 42.60 3.36
508 519 4.633126 ACAGAAATGTGGTCATTGATCGAG 59.367 41.667 0.00 0.00 42.60 4.04
510 521 4.952262 ACAGAAATGTGGTCATTGATCG 57.048 40.909 0.00 0.00 42.60 3.69
517 528 3.389656 TCACCTGTACAGAAATGTGGTCA 59.610 43.478 24.68 5.30 0.00 4.02
528 539 2.563179 AGCTAGTTGGTCACCTGTACAG 59.437 50.000 16.34 16.34 0.00 2.74
531 542 2.969950 ACAAGCTAGTTGGTCACCTGTA 59.030 45.455 0.00 0.00 40.90 2.74
546 557 7.907214 ATATTTTTCAGTAAGTCGACAAGCT 57.093 32.000 19.50 9.06 0.00 3.74
553 564 7.271223 CACAGCCAAATATTTTTCAGTAAGTCG 59.729 37.037 0.00 0.00 0.00 4.18
588 599 8.044060 TGCTCTTTTAGTCCTACAAATGAATG 57.956 34.615 0.00 0.00 0.00 2.67
617 628 3.452627 AGGTTTCATAGGCAGTACCAGAG 59.547 47.826 0.00 0.00 43.14 3.35
619 630 3.535561 CAGGTTTCATAGGCAGTACCAG 58.464 50.000 0.00 0.00 43.14 4.00
636 647 9.404848 CCATGAGATCAATTTATATATGCAGGT 57.595 33.333 0.00 0.00 0.00 4.00
652 663 0.538584 AGCACTTCGCCATGAGATCA 59.461 50.000 0.00 0.00 44.04 2.92
653 664 1.329906 CAAGCACTTCGCCATGAGATC 59.670 52.381 0.00 0.00 44.04 2.75
654 665 1.065926 TCAAGCACTTCGCCATGAGAT 60.066 47.619 0.00 0.00 44.04 2.75
655 666 0.321346 TCAAGCACTTCGCCATGAGA 59.679 50.000 0.00 0.00 44.04 3.27
656 667 1.159285 TTCAAGCACTTCGCCATGAG 58.841 50.000 0.00 0.00 44.04 2.90
657 668 1.536766 CTTTCAAGCACTTCGCCATGA 59.463 47.619 0.00 0.00 44.04 3.07
658 669 1.401931 CCTTTCAAGCACTTCGCCATG 60.402 52.381 0.00 0.00 44.04 3.66
659 670 0.883833 CCTTTCAAGCACTTCGCCAT 59.116 50.000 0.00 0.00 44.04 4.40
660 671 1.172180 CCCTTTCAAGCACTTCGCCA 61.172 55.000 0.00 0.00 44.04 5.69
661 672 1.172812 ACCCTTTCAAGCACTTCGCC 61.173 55.000 0.00 0.00 44.04 5.54
662 673 1.197036 GTACCCTTTCAAGCACTTCGC 59.803 52.381 0.00 0.00 42.91 4.70
664 675 3.141767 AGGTACCCTTTCAAGCACTTC 57.858 47.619 8.74 0.00 0.00 3.01
707 742 4.262938 GCAAGGGGTCTTTACTTGACTACT 60.263 45.833 7.73 0.00 43.13 2.57
708 743 4.001652 GCAAGGGGTCTTTACTTGACTAC 58.998 47.826 7.73 0.00 43.13 2.73
709 744 3.908103 AGCAAGGGGTCTTTACTTGACTA 59.092 43.478 7.73 0.00 43.13 2.59
713 748 4.553330 TCTAGCAAGGGGTCTTTACTTG 57.447 45.455 0.00 0.00 43.28 3.16
723 758 3.634397 TGAACTCAATCTAGCAAGGGG 57.366 47.619 0.00 0.00 0.00 4.79
725 760 5.426504 ACTGATGAACTCAATCTAGCAAGG 58.573 41.667 0.00 0.00 32.14 3.61
869 916 1.211457 AGCTCAATCCGGCAAGAGATT 59.789 47.619 17.47 0.03 32.95 2.40
880 928 6.541641 ACAGATAAAACTGATGAGCTCAATCC 59.458 38.462 22.50 13.33 40.63 3.01
958 1023 6.775939 ATGATAGAATGTGTTAGCATGTCG 57.224 37.500 0.00 0.00 0.00 4.35
971 1036 9.806203 TTTGAAACCTGCAATAATGATAGAATG 57.194 29.630 0.00 0.00 0.00 2.67
991 1059 4.461431 AGCTGCAGACATCATGATTTGAAA 59.539 37.500 20.43 0.00 38.03 2.69
1026 1095 2.977914 GCTGATGAGAAACTACCAGCA 58.022 47.619 0.00 0.00 44.40 4.41
1033 1102 5.426504 CTGGATAACTGCTGATGAGAAACT 58.573 41.667 0.00 0.00 0.00 2.66
1160 1229 2.108362 CGACCTCGGTTATGGCCC 59.892 66.667 0.00 0.00 35.37 5.80
1211 1280 1.351350 GGAGGTTCCTTAGCCACTTGT 59.649 52.381 0.00 0.00 32.53 3.16
1286 1355 1.946768 TCTTGCGTTTTCCAAGGACTG 59.053 47.619 0.00 0.00 40.00 3.51
1374 1443 3.441222 TCTGCACAACATATTCAAGCCTG 59.559 43.478 0.00 0.00 0.00 4.85
1445 1514 3.827008 TGGATGATGAACTACTCTGCC 57.173 47.619 0.00 0.00 0.00 4.85
1478 1553 2.838637 AGAAGTAGTCTCTCCCCCAG 57.161 55.000 0.00 0.00 0.00 4.45
1558 1636 6.823689 TCAGAGCCAGATGAACCTAAAATAAC 59.176 38.462 0.00 0.00 0.00 1.89
1566 1644 0.540923 GCTCAGAGCCAGATGAACCT 59.459 55.000 11.84 0.00 34.48 3.50
1584 1662 1.607628 CTTATGCTGCTGGATTCTGGC 59.392 52.381 2.35 0.00 0.00 4.85
1794 1872 6.855763 TCATTTCCTTTTATGGAGCACAAT 57.144 33.333 0.00 0.00 37.43 2.71
1806 1884 7.599998 CGGTCAAAAGATGAATCATTTCCTTTT 59.400 33.333 12.52 12.52 40.50 2.27
1843 1921 9.725019 TTGAATATTGTTGACAACTGTCTCTAT 57.275 29.630 18.73 8.73 44.99 1.98
2143 2234 7.887996 TTTTTGCTATTTGCTCACCAATTAG 57.112 32.000 0.00 0.00 43.37 1.73
2439 2530 0.175760 TAGTGCCACCAGATTCGCTC 59.824 55.000 0.00 0.00 0.00 5.03
2586 2677 8.017946 GTCTCTTTGTGGAGAAAACATTCATAC 58.982 37.037 0.00 0.00 42.95 2.39
3200 3293 2.034685 GCTTCAAGGTGTTTCTTCCCAC 59.965 50.000 0.00 0.00 0.00 4.61
3313 3406 1.004394 GCTAGGTAAAGTTGTGGCCCT 59.996 52.381 0.00 0.00 0.00 5.19
4033 4129 3.872459 ATGAAGGGCCTCCAGATAAAG 57.128 47.619 6.46 0.00 34.83 1.85
4506 4619 5.119694 GTGGTTCTGTAATGGATCCTCTTC 58.880 45.833 14.23 2.17 0.00 2.87
4545 4684 2.893637 ACAATGTGTATCACCGAGCTC 58.106 47.619 2.73 2.73 32.73 4.09
4634 4807 4.405358 ACAAACCAACAGACCAATCAACAT 59.595 37.500 0.00 0.00 0.00 2.71
4649 4823 4.928263 TCATCACCATCCATACAAACCAA 58.072 39.130 0.00 0.00 0.00 3.67
4717 4951 5.486735 AATCAATTCAGCCCACAATTTCA 57.513 34.783 0.00 0.00 0.00 2.69
4941 5267 1.986882 CAACCTTGCTTCCCAGAACT 58.013 50.000 0.00 0.00 0.00 3.01
5069 5408 0.987294 CCTGAGCTTCCCTTCCTCAA 59.013 55.000 0.00 0.00 35.41 3.02


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

AutoCloner maintained by Alex Coulton.