Multiple sequence alignment - TraesCS2B01G213900

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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 TraesCS2B01G213900 chr2B 100.000 3176 0 0 1 3176 198635356 198638531 0.000000e+00 5866
1 TraesCS2B01G213900 chr2B 95.506 178 7 1 201 377 521848967 521849144 1.860000e-72 283
2 TraesCS2B01G213900 chr2D 90.126 2846 162 56 390 3176 139530054 139527269 0.000000e+00 3589
3 TraesCS2B01G213900 chr2D 89.437 142 8 4 40 174 139530191 139530050 4.210000e-39 172
4 TraesCS2B01G213900 chr2A 92.809 2058 89 26 413 2436 161328073 161330105 0.000000e+00 2926
5 TraesCS2B01G213900 chr2A 85.525 753 54 26 2450 3176 161330154 161330877 0.000000e+00 736
6 TraesCS2B01G213900 chr2A 93.431 137 7 2 40 174 161327941 161328077 5.370000e-48 202
7 TraesCS2B01G213900 chr3B 87.839 1143 76 20 1060 2177 402914850 402913746 0.000000e+00 1282
8 TraesCS2B01G213900 chr6B 84.538 692 48 25 1513 2180 492508887 492508231 5.780000e-177 630
9 TraesCS2B01G213900 chr6B 90.787 445 39 2 1059 1501 492521739 492521295 7.590000e-166 593
10 TraesCS2B01G213900 chr6B 89.888 89 9 0 204 292 44846334 44846246 7.200000e-22 115
11 TraesCS2B01G213900 chr7D 88.544 419 45 2 1202 1619 150762101 150762517 3.660000e-139 505
12 TraesCS2B01G213900 chr7B 84.687 431 61 3 1202 1629 112646887 112647315 2.930000e-115 425
13 TraesCS2B01G213900 chr1B 82.775 418 56 10 1202 1619 48272067 48272468 3.010000e-95 359
14 TraesCS2B01G213900 chr3A 94.505 182 8 2 201 380 683547568 683547749 2.410000e-71 279
15 TraesCS2B01G213900 chrUn 93.370 181 10 2 201 380 68464612 68464433 1.880000e-67 267


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 TraesCS2B01G213900 chr2B 198635356 198638531 3175 False 5866.0 5866 100.000000 1 3176 1 chr2B.!!$F1 3175
1 TraesCS2B01G213900 chr2D 139527269 139530191 2922 True 1880.5 3589 89.781500 40 3176 2 chr2D.!!$R1 3136
2 TraesCS2B01G213900 chr2A 161327941 161330877 2936 False 1288.0 2926 90.588333 40 3176 3 chr2A.!!$F1 3136
3 TraesCS2B01G213900 chr3B 402913746 402914850 1104 True 1282.0 1282 87.839000 1060 2177 1 chr3B.!!$R1 1117
4 TraesCS2B01G213900 chr6B 492508231 492508887 656 True 630.0 630 84.538000 1513 2180 1 chr6B.!!$R2 667

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
865 885 0.031585 TATTTCATCCGCTCGTCCCG 59.968 55.0 0.0 0.0 0.0 5.14 F
922 946 0.622665 CCTTCTTCCATCCCACAGCT 59.377 55.0 0.0 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 2066 0.167470 CTGCGGATTCTGCTTGTGTG 59.833 55.0 17.96 0.0 0.00 3.82 R
2249 2302 0.472925 GCCAAGGGGAAAGGGGAAAA 60.473 55.0 0.00 0.0 35.59 2.29 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
36 37 3.722147 ACGCAGTAGAAGCCAATATCTG 58.278 45.455 0.00 0.00 41.94 2.90
37 38 2.478134 CGCAGTAGAAGCCAATATCTGC 59.522 50.000 0.00 0.00 41.89 4.26
38 39 3.470709 GCAGTAGAAGCCAATATCTGCA 58.529 45.455 8.95 0.00 43.83 4.41
44 45 0.467384 AGCCAATATCTGCAGACGCT 59.533 50.000 20.97 17.04 39.64 5.07
97 98 2.625790 CCAAAACCGTCAAAATCAGGGA 59.374 45.455 0.00 0.00 0.00 4.20
99 100 4.048504 CAAAACCGTCAAAATCAGGGAAC 58.951 43.478 0.00 0.00 0.00 3.62
100 101 2.951229 ACCGTCAAAATCAGGGAACT 57.049 45.000 0.00 0.00 46.44 3.01
190 198 4.279043 GGGCAAACCACCGTGCAC 62.279 66.667 6.82 6.82 42.74 4.57
191 199 4.279043 GGCAAACCACCGTGCACC 62.279 66.667 12.15 0.00 42.74 5.01
192 200 3.522731 GCAAACCACCGTGCACCA 61.523 61.111 12.15 0.00 40.58 4.17
193 201 2.855514 GCAAACCACCGTGCACCAT 61.856 57.895 12.15 0.00 40.58 3.55
194 202 1.007502 CAAACCACCGTGCACCATG 60.008 57.895 12.15 9.64 0.00 3.66
195 203 2.855514 AAACCACCGTGCACCATGC 61.856 57.895 12.15 0.00 45.29 4.06
196 204 3.790416 AACCACCGTGCACCATGCT 62.790 57.895 12.15 0.00 45.31 3.79
197 205 3.434319 CCACCGTGCACCATGCTC 61.434 66.667 12.15 0.00 45.31 4.26
198 206 2.669229 CACCGTGCACCATGCTCA 60.669 61.111 12.15 0.00 45.31 4.26
199 207 2.669569 ACCGTGCACCATGCTCAC 60.670 61.111 12.15 0.00 45.31 3.51
202 210 3.171987 GTGCACCATGCTCACGAG 58.828 61.111 5.22 0.00 45.31 4.18
203 211 1.669115 GTGCACCATGCTCACGAGT 60.669 57.895 5.22 0.00 45.31 4.18
204 212 0.389817 GTGCACCATGCTCACGAGTA 60.390 55.000 5.22 0.00 45.31 2.59
205 213 0.320050 TGCACCATGCTCACGAGTAA 59.680 50.000 2.02 0.00 45.31 2.24
206 214 1.066215 TGCACCATGCTCACGAGTAAT 60.066 47.619 2.02 0.00 45.31 1.89
207 215 1.328680 GCACCATGCTCACGAGTAATG 59.671 52.381 0.00 1.24 40.96 1.90
208 216 1.328680 CACCATGCTCACGAGTAATGC 59.671 52.381 0.00 0.00 0.00 3.56
209 217 1.208052 ACCATGCTCACGAGTAATGCT 59.792 47.619 0.00 0.00 0.00 3.79
210 218 2.430694 ACCATGCTCACGAGTAATGCTA 59.569 45.455 0.00 0.00 0.00 3.49
211 219 3.055591 CCATGCTCACGAGTAATGCTAG 58.944 50.000 0.00 0.00 0.00 3.42
212 220 3.243535 CCATGCTCACGAGTAATGCTAGA 60.244 47.826 0.00 0.00 0.00 2.43
213 221 3.699779 TGCTCACGAGTAATGCTAGAG 57.300 47.619 0.00 0.00 0.00 2.43
214 222 2.223595 TGCTCACGAGTAATGCTAGAGC 60.224 50.000 11.05 11.05 42.27 4.09
215 223 2.034053 GCTCACGAGTAATGCTAGAGCT 59.966 50.000 10.81 0.00 40.50 4.09
216 224 3.251245 GCTCACGAGTAATGCTAGAGCTA 59.749 47.826 10.81 0.00 40.50 3.32
217 225 4.778904 CTCACGAGTAATGCTAGAGCTAC 58.221 47.826 2.72 0.00 42.66 3.58
218 226 4.196971 TCACGAGTAATGCTAGAGCTACA 58.803 43.478 2.72 0.00 42.66 2.74
219 227 4.273724 TCACGAGTAATGCTAGAGCTACAG 59.726 45.833 2.72 0.00 42.66 2.74
220 228 4.273724 CACGAGTAATGCTAGAGCTACAGA 59.726 45.833 2.72 0.00 42.66 3.41
221 229 4.273969 ACGAGTAATGCTAGAGCTACAGAC 59.726 45.833 2.72 0.00 42.66 3.51
222 230 4.513692 CGAGTAATGCTAGAGCTACAGACT 59.486 45.833 2.72 0.00 42.66 3.24
223 231 5.008217 CGAGTAATGCTAGAGCTACAGACTT 59.992 44.000 2.72 0.00 42.66 3.01
224 232 6.142818 AGTAATGCTAGAGCTACAGACTTG 57.857 41.667 2.72 0.00 42.66 3.16
225 233 5.654650 AGTAATGCTAGAGCTACAGACTTGT 59.345 40.000 2.72 0.00 42.66 3.16
226 234 5.413309 AATGCTAGAGCTACAGACTTGTT 57.587 39.130 2.72 0.00 42.66 2.83
227 235 4.873746 TGCTAGAGCTACAGACTTGTTT 57.126 40.909 2.72 0.00 42.66 2.83
228 236 5.215252 TGCTAGAGCTACAGACTTGTTTT 57.785 39.130 2.72 0.00 42.66 2.43
229 237 6.340962 TGCTAGAGCTACAGACTTGTTTTA 57.659 37.500 2.72 0.00 42.66 1.52
230 238 6.157211 TGCTAGAGCTACAGACTTGTTTTAC 58.843 40.000 2.72 0.00 42.66 2.01
231 239 6.157211 GCTAGAGCTACAGACTTGTTTTACA 58.843 40.000 0.00 0.00 38.76 2.41
232 240 6.309251 GCTAGAGCTACAGACTTGTTTTACAG 59.691 42.308 0.00 0.00 38.76 2.74
233 241 5.542779 AGAGCTACAGACTTGTTTTACAGG 58.457 41.667 0.00 0.00 38.76 4.00
234 242 5.304614 AGAGCTACAGACTTGTTTTACAGGA 59.695 40.000 0.00 0.00 38.76 3.86
235 243 6.014156 AGAGCTACAGACTTGTTTTACAGGAT 60.014 38.462 0.00 0.00 38.76 3.24
236 244 6.534634 AGCTACAGACTTGTTTTACAGGATT 58.465 36.000 0.00 0.00 38.76 3.01
237 245 6.998673 AGCTACAGACTTGTTTTACAGGATTT 59.001 34.615 0.00 0.00 38.76 2.17
238 246 8.154856 AGCTACAGACTTGTTTTACAGGATTTA 58.845 33.333 0.00 0.00 38.76 1.40
239 247 8.947115 GCTACAGACTTGTTTTACAGGATTTAT 58.053 33.333 0.00 0.00 38.76 1.40
242 250 9.131791 ACAGACTTGTTTTACAGGATTTATTGT 57.868 29.630 0.00 0.00 32.28 2.71
247 255 9.840427 CTTGTTTTACAGGATTTATTGTACAGG 57.160 33.333 0.00 0.00 30.03 4.00
248 256 7.822658 TGTTTTACAGGATTTATTGTACAGGC 58.177 34.615 0.00 0.00 30.03 4.85
249 257 7.668052 TGTTTTACAGGATTTATTGTACAGGCT 59.332 33.333 0.00 0.00 30.03 4.58
250 258 7.624360 TTTACAGGATTTATTGTACAGGCTG 57.376 36.000 14.16 14.16 30.03 4.85
251 259 5.435686 ACAGGATTTATTGTACAGGCTGA 57.564 39.130 23.66 1.56 0.00 4.26
252 260 6.006275 ACAGGATTTATTGTACAGGCTGAT 57.994 37.500 23.66 6.58 0.00 2.90
253 261 5.824624 ACAGGATTTATTGTACAGGCTGATG 59.175 40.000 23.66 0.00 0.00 3.07
254 262 5.824624 CAGGATTTATTGTACAGGCTGATGT 59.175 40.000 23.66 1.62 37.19 3.06
255 263 5.824624 AGGATTTATTGTACAGGCTGATGTG 59.175 40.000 23.66 0.00 34.56 3.21
256 264 5.009010 GGATTTATTGTACAGGCTGATGTGG 59.991 44.000 23.66 0.00 34.56 4.17
257 265 4.835284 TTATTGTACAGGCTGATGTGGA 57.165 40.909 23.66 2.02 34.56 4.02
258 266 2.768253 TTGTACAGGCTGATGTGGAG 57.232 50.000 23.66 0.00 34.56 3.86
259 267 0.250234 TGTACAGGCTGATGTGGAGC 59.750 55.000 23.66 2.39 34.56 4.70
260 268 0.250234 GTACAGGCTGATGTGGAGCA 59.750 55.000 23.66 0.00 38.27 4.26
261 269 0.983467 TACAGGCTGATGTGGAGCAA 59.017 50.000 23.66 0.00 38.27 3.91
262 270 0.111061 ACAGGCTGATGTGGAGCAAA 59.889 50.000 23.66 0.00 38.27 3.68
263 271 0.524862 CAGGCTGATGTGGAGCAAAC 59.475 55.000 9.42 0.00 38.27 2.93
264 272 0.403271 AGGCTGATGTGGAGCAAACT 59.597 50.000 0.00 0.00 38.27 2.66
265 273 0.524862 GGCTGATGTGGAGCAAACTG 59.475 55.000 0.00 0.00 38.27 3.16
266 274 1.527034 GCTGATGTGGAGCAAACTGA 58.473 50.000 0.00 0.00 36.40 3.41
267 275 2.089980 GCTGATGTGGAGCAAACTGAT 58.910 47.619 0.00 0.00 36.40 2.90
268 276 2.490903 GCTGATGTGGAGCAAACTGATT 59.509 45.455 0.00 0.00 36.40 2.57
269 277 3.672511 GCTGATGTGGAGCAAACTGATTG 60.673 47.826 0.00 0.00 42.21 2.67
270 278 2.821378 TGATGTGGAGCAAACTGATTGG 59.179 45.455 0.00 0.00 39.54 3.16
282 290 7.812309 GCAAACTGATTGGTTTAGGATTAAC 57.188 36.000 0.00 0.00 39.54 2.01
283 291 7.375053 GCAAACTGATTGGTTTAGGATTAACA 58.625 34.615 0.00 0.00 39.54 2.41
284 292 7.542130 GCAAACTGATTGGTTTAGGATTAACAG 59.458 37.037 0.00 0.00 39.54 3.16
285 293 6.759497 ACTGATTGGTTTAGGATTAACAGC 57.241 37.500 0.00 0.00 0.00 4.40
286 294 5.652452 ACTGATTGGTTTAGGATTAACAGCC 59.348 40.000 0.00 0.00 0.00 4.85
287 295 4.638421 TGATTGGTTTAGGATTAACAGCCG 59.362 41.667 0.00 0.00 0.00 5.52
288 296 2.993937 TGGTTTAGGATTAACAGCCGG 58.006 47.619 0.00 0.00 0.00 6.13
289 297 1.674441 GGTTTAGGATTAACAGCCGGC 59.326 52.381 21.89 21.89 0.00 6.13
290 298 1.674441 GTTTAGGATTAACAGCCGGCC 59.326 52.381 26.15 5.24 0.00 6.13
291 299 0.181824 TTAGGATTAACAGCCGGCCC 59.818 55.000 26.15 15.73 0.00 5.80
292 300 1.702022 TAGGATTAACAGCCGGCCCC 61.702 60.000 26.15 12.85 0.00 5.80
293 301 2.518587 GATTAACAGCCGGCCCCC 60.519 66.667 26.15 1.43 0.00 5.40
294 302 3.343326 ATTAACAGCCGGCCCCCA 61.343 61.111 26.15 3.71 0.00 4.96
295 303 3.655350 ATTAACAGCCGGCCCCCAC 62.655 63.158 26.15 0.00 0.00 4.61
305 313 3.683518 GCCCCCACCCCCTGAAAT 61.684 66.667 0.00 0.00 0.00 2.17
306 314 3.200565 CCCCCACCCCCTGAAATT 58.799 61.111 0.00 0.00 0.00 1.82
307 315 1.881057 GCCCCCACCCCCTGAAATTA 61.881 60.000 0.00 0.00 0.00 1.40
308 316 0.261696 CCCCCACCCCCTGAAATTAG 59.738 60.000 0.00 0.00 0.00 1.73
309 317 0.261696 CCCCACCCCCTGAAATTAGG 59.738 60.000 0.00 0.00 37.59 2.69
327 335 2.973052 GGGGGCGAGCGAATTAGC 60.973 66.667 1.81 1.81 37.41 3.09
328 336 2.203015 GGGGCGAGCGAATTAGCA 60.203 61.111 13.26 0.00 40.15 3.49
329 337 1.817941 GGGGCGAGCGAATTAGCAA 60.818 57.895 13.26 0.00 40.15 3.91
330 338 1.643832 GGGCGAGCGAATTAGCAAG 59.356 57.895 13.26 7.06 40.15 4.01
331 339 0.810031 GGGCGAGCGAATTAGCAAGA 60.810 55.000 13.26 0.00 40.15 3.02
332 340 0.579156 GGCGAGCGAATTAGCAAGAG 59.421 55.000 13.26 2.35 40.15 2.85
333 341 0.579156 GCGAGCGAATTAGCAAGAGG 59.421 55.000 13.26 0.00 40.15 3.69
334 342 1.212616 CGAGCGAATTAGCAAGAGGG 58.787 55.000 13.26 0.00 40.15 4.30
335 343 1.587547 GAGCGAATTAGCAAGAGGGG 58.412 55.000 13.26 0.00 40.15 4.79
336 344 0.181350 AGCGAATTAGCAAGAGGGGG 59.819 55.000 13.26 0.00 40.15 5.40
337 345 0.107165 GCGAATTAGCAAGAGGGGGT 60.107 55.000 5.59 0.00 37.05 4.95
338 346 1.954927 CGAATTAGCAAGAGGGGGTC 58.045 55.000 0.00 0.00 0.00 4.46
339 347 1.475213 CGAATTAGCAAGAGGGGGTCC 60.475 57.143 0.00 0.00 0.00 4.46
340 348 0.546598 AATTAGCAAGAGGGGGTCCG 59.453 55.000 0.00 0.00 38.33 4.79
341 349 0.620700 ATTAGCAAGAGGGGGTCCGT 60.621 55.000 0.00 0.00 38.33 4.69
342 350 0.041535 TTAGCAAGAGGGGGTCCGTA 59.958 55.000 0.00 0.00 38.33 4.02
343 351 0.041535 TAGCAAGAGGGGGTCCGTAA 59.958 55.000 0.00 0.00 38.33 3.18
344 352 1.221021 GCAAGAGGGGGTCCGTAAG 59.779 63.158 0.00 0.00 38.33 2.34
345 353 1.262640 GCAAGAGGGGGTCCGTAAGA 61.263 60.000 0.00 0.00 43.02 2.10
346 354 0.535797 CAAGAGGGGGTCCGTAAGAC 59.464 60.000 0.00 0.00 45.51 3.01
352 360 2.261215 GGGTCCGTAAGACACTCGT 58.739 57.895 0.00 0.00 46.23 4.18
353 361 1.453155 GGGTCCGTAAGACACTCGTA 58.547 55.000 0.00 0.00 46.23 3.43
354 362 1.812571 GGGTCCGTAAGACACTCGTAA 59.187 52.381 0.00 0.00 46.23 3.18
355 363 2.228822 GGGTCCGTAAGACACTCGTAAA 59.771 50.000 0.00 0.00 46.23 2.01
356 364 3.671702 GGGTCCGTAAGACACTCGTAAAG 60.672 52.174 0.00 0.00 46.23 1.85
357 365 2.913590 GTCCGTAAGACACTCGTAAAGC 59.086 50.000 0.00 0.00 45.55 3.51
358 366 2.095059 TCCGTAAGACACTCGTAAAGCC 60.095 50.000 0.00 0.00 43.02 4.35
359 367 2.257034 CGTAAGACACTCGTAAAGCCC 58.743 52.381 0.00 0.00 43.02 5.19
360 368 2.614779 GTAAGACACTCGTAAAGCCCC 58.385 52.381 0.00 0.00 0.00 5.80
361 369 0.323957 AAGACACTCGTAAAGCCCCC 59.676 55.000 0.00 0.00 0.00 5.40
362 370 1.447314 GACACTCGTAAAGCCCCCG 60.447 63.158 0.00 0.00 0.00 5.73
363 371 2.163601 GACACTCGTAAAGCCCCCGT 62.164 60.000 0.00 0.00 0.00 5.28
364 372 0.899717 ACACTCGTAAAGCCCCCGTA 60.900 55.000 0.00 0.00 0.00 4.02
365 373 0.459063 CACTCGTAAAGCCCCCGTAC 60.459 60.000 0.00 0.00 0.00 3.67
366 374 1.226773 CTCGTAAAGCCCCCGTACG 60.227 63.158 8.69 8.69 41.46 3.67
367 375 1.937546 CTCGTAAAGCCCCCGTACGT 61.938 60.000 15.21 0.00 41.02 3.57
368 376 1.517039 CGTAAAGCCCCCGTACGTC 60.517 63.158 15.21 0.32 36.68 4.34
369 377 1.893062 GTAAAGCCCCCGTACGTCT 59.107 57.895 15.21 2.77 0.00 4.18
370 378 1.102978 GTAAAGCCCCCGTACGTCTA 58.897 55.000 15.21 0.00 0.00 2.59
371 379 1.066152 GTAAAGCCCCCGTACGTCTAG 59.934 57.143 15.21 0.00 0.00 2.43
372 380 1.325476 AAAGCCCCCGTACGTCTAGG 61.325 60.000 15.21 7.92 0.00 3.02
373 381 2.124151 GCCCCCGTACGTCTAGGA 60.124 66.667 15.21 0.00 0.00 2.94
374 382 1.530183 GCCCCCGTACGTCTAGGAT 60.530 63.158 15.21 0.00 0.00 3.24
375 383 1.111715 GCCCCCGTACGTCTAGGATT 61.112 60.000 15.21 0.00 0.00 3.01
376 384 1.819305 GCCCCCGTACGTCTAGGATTA 60.819 57.143 15.21 0.00 0.00 1.75
377 385 2.800250 CCCCCGTACGTCTAGGATTAT 58.200 52.381 15.21 0.00 0.00 1.28
378 386 2.751806 CCCCCGTACGTCTAGGATTATC 59.248 54.545 15.21 0.00 0.00 1.75
379 387 2.417933 CCCCGTACGTCTAGGATTATCG 59.582 54.545 15.21 0.00 0.00 2.92
380 388 2.159599 CCCGTACGTCTAGGATTATCGC 60.160 54.545 15.21 0.00 0.00 4.58
381 389 2.159599 CCGTACGTCTAGGATTATCGCC 60.160 54.545 15.21 0.00 0.00 5.54
382 390 2.481568 CGTACGTCTAGGATTATCGCCA 59.518 50.000 7.22 0.00 0.00 5.69
383 391 3.126514 CGTACGTCTAGGATTATCGCCAT 59.873 47.826 7.22 0.00 0.00 4.40
384 392 3.577649 ACGTCTAGGATTATCGCCATG 57.422 47.619 0.00 0.00 0.00 3.66
385 393 2.263077 CGTCTAGGATTATCGCCATGC 58.737 52.381 0.00 0.00 0.00 4.06
386 394 2.094494 CGTCTAGGATTATCGCCATGCT 60.094 50.000 0.00 0.00 0.00 3.79
387 395 3.516615 GTCTAGGATTATCGCCATGCTC 58.483 50.000 0.00 0.00 0.00 4.26
388 396 3.056536 GTCTAGGATTATCGCCATGCTCA 60.057 47.826 0.00 0.00 0.00 4.26
790 806 6.031964 TGGAAGGGCCATTGGTTATTAATA 57.968 37.500 7.73 0.00 43.33 0.98
792 808 7.770662 TGGAAGGGCCATTGGTTATTAATATA 58.229 34.615 7.73 0.00 43.33 0.86
793 809 7.893302 TGGAAGGGCCATTGGTTATTAATATAG 59.107 37.037 7.73 0.00 43.33 1.31
794 810 7.342026 GGAAGGGCCATTGGTTATTAATATAGG 59.658 40.741 7.73 0.00 36.34 2.57
796 812 7.643123 AGGGCCATTGGTTATTAATATAGGAG 58.357 38.462 6.18 0.00 0.00 3.69
863 883 1.527311 GCTTATTTCATCCGCTCGTCC 59.473 52.381 0.00 0.00 0.00 4.79
864 884 2.135933 CTTATTTCATCCGCTCGTCCC 58.864 52.381 0.00 0.00 0.00 4.46
865 885 0.031585 TATTTCATCCGCTCGTCCCG 59.968 55.000 0.00 0.00 0.00 5.14
866 886 1.956629 ATTTCATCCGCTCGTCCCGT 61.957 55.000 0.00 0.00 0.00 5.28
867 887 2.552585 TTTCATCCGCTCGTCCCGTC 62.553 60.000 0.00 0.00 0.00 4.79
868 888 4.907034 CATCCGCTCGTCCCGTCG 62.907 72.222 0.00 0.00 0.00 5.12
881 901 4.790962 CGTCGTCTCCTCCCCGGA 62.791 72.222 0.73 0.00 40.30 5.14
906 926 1.613437 CAACGCACCCAATTCTTCCTT 59.387 47.619 0.00 0.00 0.00 3.36
917 941 4.570505 CCAATTCTTCCTTCTTCCATCCCA 60.571 45.833 0.00 0.00 0.00 4.37
922 946 0.622665 CCTTCTTCCATCCCACAGCT 59.377 55.000 0.00 0.00 0.00 4.24
923 947 1.407989 CCTTCTTCCATCCCACAGCTC 60.408 57.143 0.00 0.00 0.00 4.09
924 948 1.558756 CTTCTTCCATCCCACAGCTCT 59.441 52.381 0.00 0.00 0.00 4.09
1764 1794 2.202623 GCCTACGTGCTCCACTCG 60.203 66.667 0.00 0.00 40.98 4.18
1959 1989 4.517934 CCTCCCCTCGTCGCCCTA 62.518 72.222 0.00 0.00 0.00 3.53
1977 2009 2.658321 TATCCCAGTCCTCCTCCGCC 62.658 65.000 0.00 0.00 0.00 6.13
2010 2042 2.579410 AAACCAAGGTACCAATCGCT 57.421 45.000 15.94 0.00 0.00 4.93
2031 2063 1.002430 AGCTCCTCATCGAAGCACAAA 59.998 47.619 8.64 0.00 38.51 2.83
2032 2064 1.806542 GCTCCTCATCGAAGCACAAAA 59.193 47.619 1.19 0.00 36.06 2.44
2033 2065 2.421424 GCTCCTCATCGAAGCACAAAAT 59.579 45.455 1.19 0.00 36.06 1.82
2034 2066 3.486542 GCTCCTCATCGAAGCACAAAATC 60.487 47.826 1.19 0.00 36.06 2.17
2035 2067 3.673902 TCCTCATCGAAGCACAAAATCA 58.326 40.909 0.00 0.00 0.00 2.57
2041 2087 3.951306 TCGAAGCACAAAATCACACAAG 58.049 40.909 0.00 0.00 0.00 3.16
2180 2233 1.815003 TTGCGGCGGAGTGATGATG 60.815 57.895 9.78 0.00 0.00 3.07
2181 2234 2.106938 GCGGCGGAGTGATGATGA 59.893 61.111 9.78 0.00 0.00 2.92
2182 2235 1.301244 GCGGCGGAGTGATGATGAT 60.301 57.895 9.78 0.00 0.00 2.45
2183 2236 0.038251 GCGGCGGAGTGATGATGATA 60.038 55.000 9.78 0.00 0.00 2.15
2184 2237 1.702886 CGGCGGAGTGATGATGATAC 58.297 55.000 0.00 0.00 0.00 2.24
2185 2238 1.670087 CGGCGGAGTGATGATGATACC 60.670 57.143 0.00 0.00 0.00 2.73
2187 2240 1.620819 GCGGAGTGATGATGATACCCT 59.379 52.381 0.00 0.00 0.00 4.34
2188 2241 2.037772 GCGGAGTGATGATGATACCCTT 59.962 50.000 0.00 0.00 0.00 3.95
2189 2242 3.657634 CGGAGTGATGATGATACCCTTG 58.342 50.000 0.00 0.00 0.00 3.61
2190 2243 3.321968 CGGAGTGATGATGATACCCTTGA 59.678 47.826 0.00 0.00 0.00 3.02
2191 2244 4.560311 CGGAGTGATGATGATACCCTTGAG 60.560 50.000 0.00 0.00 0.00 3.02
2192 2245 4.314121 GAGTGATGATGATACCCTTGAGC 58.686 47.826 0.00 0.00 0.00 4.26
2193 2246 3.972638 AGTGATGATGATACCCTTGAGCT 59.027 43.478 0.00 0.00 0.00 4.09
2194 2247 4.063689 GTGATGATGATACCCTTGAGCTG 58.936 47.826 0.00 0.00 0.00 4.24
2195 2248 3.072038 TGATGATGATACCCTTGAGCTGG 59.928 47.826 0.00 0.00 0.00 4.85
2196 2249 2.763039 TGATGATACCCTTGAGCTGGA 58.237 47.619 0.00 0.00 0.00 3.86
2264 2317 0.830444 GCGTTTTTCCCCTTTCCCCT 60.830 55.000 0.00 0.00 0.00 4.79
2292 2345 4.828925 GAGACGAGCTGGGCTGGC 62.829 72.222 9.65 0.00 39.88 4.85
2395 2456 1.485397 CTCAAGCGAGATGATGACGG 58.515 55.000 0.00 0.00 42.34 4.79
2431 2492 3.589288 AGCCAAGTCTCCCTGTAAATTCT 59.411 43.478 0.00 0.00 0.00 2.40
2436 2497 6.717084 CCAAGTCTCCCTGTAAATTCTTTCTT 59.283 38.462 0.00 0.00 0.00 2.52
2438 2499 7.323052 AGTCTCCCTGTAAATTCTTTCTTCT 57.677 36.000 0.00 0.00 0.00 2.85
2439 2500 7.750655 AGTCTCCCTGTAAATTCTTTCTTCTT 58.249 34.615 0.00 0.00 0.00 2.52
2443 2504 6.715264 TCCCTGTAAATTCTTTCTTCTTCACC 59.285 38.462 0.00 0.00 0.00 4.02
2447 2543 9.455847 CTGTAAATTCTTTCTTCTTCACCTTTG 57.544 33.333 0.00 0.00 0.00 2.77
2448 2544 8.966868 TGTAAATTCTTTCTTCTTCACCTTTGT 58.033 29.630 0.00 0.00 0.00 2.83
2455 2551 8.674607 TCTTTCTTCTTCACCTTTGTTTTCTAC 58.325 33.333 0.00 0.00 0.00 2.59
2462 2558 7.660208 TCTTCACCTTTGTTTTCTACTACCATC 59.340 37.037 0.00 0.00 0.00 3.51
2479 2575 0.249398 ATCTTGGTTCGTTCCTCGGG 59.751 55.000 1.16 0.00 40.32 5.14
2480 2576 2.031465 TTGGTTCGTTCCTCGGGC 59.969 61.111 1.16 0.00 40.32 6.13
2481 2577 2.450479 CTTGGTTCGTTCCTCGGGCT 62.450 60.000 0.00 0.00 40.32 5.19
2612 2724 7.108847 AGAAAGATATTGTGTTCTCTGGAAGG 58.891 38.462 0.00 0.00 31.46 3.46
2689 2806 3.067106 ACATTCAGGTTCTAGCGTTGTG 58.933 45.455 0.00 0.00 0.00 3.33
2690 2807 2.163818 TTCAGGTTCTAGCGTTGTGG 57.836 50.000 0.00 0.00 0.00 4.17
2722 2842 0.824109 TATCTCAGGTTCCTGCGGTG 59.176 55.000 13.44 4.80 34.33 4.94
2808 2935 0.383949 TTTTGCTGGTTCAACCGAGC 59.616 50.000 18.85 18.85 42.58 5.03
2835 2962 1.539827 GGTCGGAATTTTCTGGTGGTG 59.460 52.381 0.00 0.00 34.32 4.17
2937 3074 4.506255 CAGGACGGAATGGCCCCC 62.506 72.222 0.00 0.00 0.00 5.40
2940 3077 2.278738 GACGGAATGGCCCCCAAT 59.721 61.111 0.00 0.00 36.95 3.16
2951 3088 1.101635 GCCCCCAATCGGTAAAGCTC 61.102 60.000 0.00 0.00 0.00 4.09
2965 3108 1.086634 AAGCTCAAAGATCTCGCGCC 61.087 55.000 0.00 0.00 0.00 6.53
3005 3148 3.035363 TGATTATTCGTCCCCTGTAGCA 58.965 45.455 0.00 0.00 0.00 3.49
3011 3154 1.695242 TCGTCCCCTGTAGCAGAAAAA 59.305 47.619 0.00 0.00 32.44 1.94
3064 3207 4.413565 TAGTTTTCGGGCCCGGGC 62.414 66.667 42.36 38.57 40.25 6.13
3106 3261 4.489771 GCCCATCCTCCCACACGG 62.490 72.222 0.00 0.00 0.00 4.94
3111 3266 1.305802 ATCCTCCCACACGGCTGTA 60.306 57.895 0.00 0.00 0.00 2.74
3112 3267 0.691078 ATCCTCCCACACGGCTGTAT 60.691 55.000 0.00 0.00 0.00 2.29
3113 3268 1.153369 CCTCCCACACGGCTGTATG 60.153 63.158 0.00 0.00 0.00 2.39
3114 3269 1.596934 CTCCCACACGGCTGTATGT 59.403 57.895 2.74 0.00 0.00 2.29
3115 3270 0.821517 CTCCCACACGGCTGTATGTA 59.178 55.000 2.74 0.00 0.00 2.29
3120 3275 3.120792 CCACACGGCTGTATGTATGTAC 58.879 50.000 2.74 0.00 0.00 2.90
3128 3283 4.511826 GGCTGTATGTATGTACCTTCAAGC 59.488 45.833 0.00 0.00 0.00 4.01
3131 3286 6.453926 TGTATGTATGTACCTTCAAGCGTA 57.546 37.500 0.00 0.00 0.00 4.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.110226 GCTTCTACTGCGTCATACGAC 58.890 52.381 3.22 0.00 46.05 4.34
8 9 1.065102 GGCTTCTACTGCGTCATACGA 59.935 52.381 3.22 0.00 46.05 3.43
9 10 1.202256 TGGCTTCTACTGCGTCATACG 60.202 52.381 0.00 0.00 45.88 3.06
10 11 2.579207 TGGCTTCTACTGCGTCATAC 57.421 50.000 0.00 0.00 0.00 2.39
11 12 3.819564 ATTGGCTTCTACTGCGTCATA 57.180 42.857 0.00 0.00 0.00 2.15
12 13 2.698855 ATTGGCTTCTACTGCGTCAT 57.301 45.000 0.00 0.00 0.00 3.06
13 14 3.384789 AGATATTGGCTTCTACTGCGTCA 59.615 43.478 0.00 0.00 0.00 4.35
14 15 3.738282 CAGATATTGGCTTCTACTGCGTC 59.262 47.826 0.00 0.00 0.00 5.19
15 16 3.722147 CAGATATTGGCTTCTACTGCGT 58.278 45.455 0.00 0.00 0.00 5.24
16 17 2.478134 GCAGATATTGGCTTCTACTGCG 59.522 50.000 0.00 0.00 39.42 5.18
17 18 3.470709 TGCAGATATTGGCTTCTACTGC 58.529 45.455 0.00 0.00 45.92 4.40
18 19 4.749099 GTCTGCAGATATTGGCTTCTACTG 59.251 45.833 21.47 0.00 0.00 2.74
19 20 4.500545 CGTCTGCAGATATTGGCTTCTACT 60.501 45.833 21.47 0.00 0.00 2.57
20 21 3.738282 CGTCTGCAGATATTGGCTTCTAC 59.262 47.826 21.47 1.24 0.00 2.59
21 22 3.800261 GCGTCTGCAGATATTGGCTTCTA 60.800 47.826 21.47 0.00 42.15 2.10
22 23 2.831333 CGTCTGCAGATATTGGCTTCT 58.169 47.619 21.47 0.00 0.00 2.85
23 24 1.262683 GCGTCTGCAGATATTGGCTTC 59.737 52.381 21.47 2.18 42.15 3.86
24 25 1.134280 AGCGTCTGCAGATATTGGCTT 60.134 47.619 21.47 6.32 46.23 4.35
25 26 0.467384 AGCGTCTGCAGATATTGGCT 59.533 50.000 21.47 19.07 46.23 4.75
26 27 0.585357 CAGCGTCTGCAGATATTGGC 59.415 55.000 21.47 17.24 46.23 4.52
37 38 1.372087 GAGGGAAATGGCAGCGTCTG 61.372 60.000 0.00 2.92 34.12 3.51
38 39 1.078143 GAGGGAAATGGCAGCGTCT 60.078 57.895 0.00 0.00 0.00 4.18
44 45 2.238521 GTGAAAGTGAGGGAAATGGCA 58.761 47.619 0.00 0.00 0.00 4.92
51 52 1.000607 CTTCGTCGTGAAAGTGAGGGA 60.001 52.381 0.00 0.00 35.79 4.20
97 98 4.280019 GTGCCCCGTTCCCCAGTT 62.280 66.667 0.00 0.00 0.00 3.16
173 181 4.279043 GTGCACGGTGGTTTGCCC 62.279 66.667 10.60 0.00 38.00 5.36
174 182 4.279043 GGTGCACGGTGGTTTGCC 62.279 66.667 11.45 0.00 38.00 4.52
175 183 2.855514 ATGGTGCACGGTGGTTTGC 61.856 57.895 11.45 0.00 39.33 3.68
176 184 1.007502 CATGGTGCACGGTGGTTTG 60.008 57.895 11.45 0.00 0.00 2.93
177 185 2.855514 GCATGGTGCACGGTGGTTT 61.856 57.895 11.45 0.00 44.26 3.27
178 186 3.294493 GCATGGTGCACGGTGGTT 61.294 61.111 11.45 0.00 44.26 3.67
187 195 1.328680 CATTACTCGTGAGCATGGTGC 59.671 52.381 0.00 0.00 45.46 5.01
188 196 1.328680 GCATTACTCGTGAGCATGGTG 59.671 52.381 0.00 0.00 0.00 4.17
189 197 1.208052 AGCATTACTCGTGAGCATGGT 59.792 47.619 0.00 0.00 31.88 3.55
190 198 1.945387 AGCATTACTCGTGAGCATGG 58.055 50.000 10.19 0.00 0.00 3.66
191 199 3.969899 TCTAGCATTACTCGTGAGCATG 58.030 45.455 0.00 1.49 0.00 4.06
192 200 3.551863 GCTCTAGCATTACTCGTGAGCAT 60.552 47.826 0.00 0.00 41.76 3.79
193 201 2.223595 GCTCTAGCATTACTCGTGAGCA 60.224 50.000 0.00 0.00 41.76 4.26
194 202 2.034053 AGCTCTAGCATTACTCGTGAGC 59.966 50.000 4.54 0.00 45.16 4.26
195 203 3.980646 AGCTCTAGCATTACTCGTGAG 57.019 47.619 4.54 0.00 45.16 3.51
196 204 4.196971 TGTAGCTCTAGCATTACTCGTGA 58.803 43.478 4.54 0.00 45.16 4.35
197 205 4.273724 TCTGTAGCTCTAGCATTACTCGTG 59.726 45.833 4.54 0.00 45.16 4.35
198 206 4.273969 GTCTGTAGCTCTAGCATTACTCGT 59.726 45.833 4.54 0.00 45.16 4.18
199 207 4.513692 AGTCTGTAGCTCTAGCATTACTCG 59.486 45.833 4.54 0.00 45.16 4.18
200 208 6.183360 ACAAGTCTGTAGCTCTAGCATTACTC 60.183 42.308 4.54 0.00 45.16 2.59
201 209 5.654650 ACAAGTCTGTAGCTCTAGCATTACT 59.345 40.000 4.54 0.00 45.16 2.24
202 210 5.897050 ACAAGTCTGTAGCTCTAGCATTAC 58.103 41.667 4.54 0.00 45.16 1.89
203 211 6.531503 AACAAGTCTGTAGCTCTAGCATTA 57.468 37.500 4.54 0.00 38.05 1.90
204 212 5.413309 AACAAGTCTGTAGCTCTAGCATT 57.587 39.130 4.54 0.00 38.05 3.56
205 213 5.413309 AAACAAGTCTGTAGCTCTAGCAT 57.587 39.130 4.54 0.00 38.05 3.79
206 214 4.873746 AAACAAGTCTGTAGCTCTAGCA 57.126 40.909 4.54 0.00 38.05 3.49
207 215 6.157211 TGTAAAACAAGTCTGTAGCTCTAGC 58.843 40.000 0.00 0.00 36.53 3.42
208 216 6.809196 CCTGTAAAACAAGTCTGTAGCTCTAG 59.191 42.308 0.00 0.00 33.45 2.43
209 217 6.492429 TCCTGTAAAACAAGTCTGTAGCTCTA 59.508 38.462 0.00 0.00 33.45 2.43
210 218 5.304614 TCCTGTAAAACAAGTCTGTAGCTCT 59.695 40.000 0.00 0.00 33.45 4.09
211 219 5.539048 TCCTGTAAAACAAGTCTGTAGCTC 58.461 41.667 0.00 0.00 33.45 4.09
212 220 5.546621 TCCTGTAAAACAAGTCTGTAGCT 57.453 39.130 0.00 0.00 33.45 3.32
213 221 6.803154 AATCCTGTAAAACAAGTCTGTAGC 57.197 37.500 0.00 0.00 33.45 3.58
216 224 9.131791 ACAATAAATCCTGTAAAACAAGTCTGT 57.868 29.630 0.00 0.00 37.39 3.41
221 229 9.840427 CCTGTACAATAAATCCTGTAAAACAAG 57.160 33.333 0.00 0.00 30.11 3.16
222 230 8.301002 GCCTGTACAATAAATCCTGTAAAACAA 58.699 33.333 0.00 0.00 30.11 2.83
223 231 7.668052 AGCCTGTACAATAAATCCTGTAAAACA 59.332 33.333 0.00 0.00 30.11 2.83
224 232 7.968405 CAGCCTGTACAATAAATCCTGTAAAAC 59.032 37.037 0.00 0.00 30.11 2.43
225 233 7.885922 TCAGCCTGTACAATAAATCCTGTAAAA 59.114 33.333 0.00 0.00 30.11 1.52
226 234 7.398829 TCAGCCTGTACAATAAATCCTGTAAA 58.601 34.615 0.00 0.00 30.11 2.01
227 235 6.953101 TCAGCCTGTACAATAAATCCTGTAA 58.047 36.000 0.00 0.00 30.11 2.41
228 236 6.553953 TCAGCCTGTACAATAAATCCTGTA 57.446 37.500 0.00 0.00 0.00 2.74
229 237 5.435686 TCAGCCTGTACAATAAATCCTGT 57.564 39.130 0.00 0.00 0.00 4.00
230 238 5.824624 ACATCAGCCTGTACAATAAATCCTG 59.175 40.000 0.00 0.00 0.00 3.86
231 239 5.824624 CACATCAGCCTGTACAATAAATCCT 59.175 40.000 0.00 0.00 0.00 3.24
232 240 5.009010 CCACATCAGCCTGTACAATAAATCC 59.991 44.000 0.00 0.00 0.00 3.01
233 241 5.822519 TCCACATCAGCCTGTACAATAAATC 59.177 40.000 0.00 0.00 0.00 2.17
234 242 5.754782 TCCACATCAGCCTGTACAATAAAT 58.245 37.500 0.00 0.00 0.00 1.40
235 243 5.172687 TCCACATCAGCCTGTACAATAAA 57.827 39.130 0.00 0.00 0.00 1.40
236 244 4.769688 CTCCACATCAGCCTGTACAATAA 58.230 43.478 0.00 0.00 0.00 1.40
237 245 3.432186 GCTCCACATCAGCCTGTACAATA 60.432 47.826 0.00 0.00 0.00 1.90
238 246 2.681976 GCTCCACATCAGCCTGTACAAT 60.682 50.000 0.00 0.00 0.00 2.71
239 247 1.339055 GCTCCACATCAGCCTGTACAA 60.339 52.381 0.00 0.00 0.00 2.41
240 248 0.250234 GCTCCACATCAGCCTGTACA 59.750 55.000 0.00 0.00 0.00 2.90
241 249 0.250234 TGCTCCACATCAGCCTGTAC 59.750 55.000 0.00 0.00 35.89 2.90
242 250 0.983467 TTGCTCCACATCAGCCTGTA 59.017 50.000 0.00 0.00 35.89 2.74
243 251 0.111061 TTTGCTCCACATCAGCCTGT 59.889 50.000 0.00 0.00 35.89 4.00
244 252 0.524862 GTTTGCTCCACATCAGCCTG 59.475 55.000 0.00 0.00 35.89 4.85
245 253 0.403271 AGTTTGCTCCACATCAGCCT 59.597 50.000 0.00 0.00 35.89 4.58
246 254 0.524862 CAGTTTGCTCCACATCAGCC 59.475 55.000 0.00 0.00 35.89 4.85
247 255 1.527034 TCAGTTTGCTCCACATCAGC 58.473 50.000 0.00 0.00 37.40 4.26
248 256 3.119602 CCAATCAGTTTGCTCCACATCAG 60.120 47.826 0.00 0.00 33.73 2.90
249 257 2.821378 CCAATCAGTTTGCTCCACATCA 59.179 45.455 0.00 0.00 33.73 3.07
250 258 2.821969 ACCAATCAGTTTGCTCCACATC 59.178 45.455 0.00 0.00 33.73 3.06
251 259 2.880443 ACCAATCAGTTTGCTCCACAT 58.120 42.857 0.00 0.00 33.73 3.21
252 260 2.363306 ACCAATCAGTTTGCTCCACA 57.637 45.000 0.00 0.00 33.73 4.17
253 261 3.733443 AAACCAATCAGTTTGCTCCAC 57.267 42.857 0.00 0.00 38.51 4.02
254 262 3.826157 CCTAAACCAATCAGTTTGCTCCA 59.174 43.478 0.09 0.00 40.15 3.86
255 263 4.079253 TCCTAAACCAATCAGTTTGCTCC 58.921 43.478 0.09 0.00 40.15 4.70
256 264 5.904362 ATCCTAAACCAATCAGTTTGCTC 57.096 39.130 0.09 0.00 40.15 4.26
257 265 7.232534 TGTTAATCCTAAACCAATCAGTTTGCT 59.767 33.333 0.09 0.00 40.15 3.91
258 266 7.375053 TGTTAATCCTAAACCAATCAGTTTGC 58.625 34.615 0.09 0.00 40.15 3.68
259 267 7.542130 GCTGTTAATCCTAAACCAATCAGTTTG 59.458 37.037 0.09 0.00 40.15 2.93
260 268 7.309805 GGCTGTTAATCCTAAACCAATCAGTTT 60.310 37.037 0.00 0.00 42.47 2.66
261 269 6.152831 GGCTGTTAATCCTAAACCAATCAGTT 59.847 38.462 0.00 0.00 0.00 3.16
262 270 5.652452 GGCTGTTAATCCTAAACCAATCAGT 59.348 40.000 0.00 0.00 0.00 3.41
263 271 5.220854 CGGCTGTTAATCCTAAACCAATCAG 60.221 44.000 0.00 0.00 0.00 2.90
264 272 4.638421 CGGCTGTTAATCCTAAACCAATCA 59.362 41.667 0.00 0.00 0.00 2.57
265 273 4.036380 CCGGCTGTTAATCCTAAACCAATC 59.964 45.833 0.00 0.00 0.00 2.67
266 274 3.951680 CCGGCTGTTAATCCTAAACCAAT 59.048 43.478 0.00 0.00 0.00 3.16
267 275 3.349022 CCGGCTGTTAATCCTAAACCAA 58.651 45.455 0.00 0.00 0.00 3.67
268 276 2.942306 GCCGGCTGTTAATCCTAAACCA 60.942 50.000 22.15 0.00 0.00 3.67
269 277 1.674441 GCCGGCTGTTAATCCTAAACC 59.326 52.381 22.15 0.00 0.00 3.27
270 278 1.674441 GGCCGGCTGTTAATCCTAAAC 59.326 52.381 28.56 0.00 0.00 2.01
271 279 1.409101 GGGCCGGCTGTTAATCCTAAA 60.409 52.381 28.56 0.00 0.00 1.85
272 280 0.181824 GGGCCGGCTGTTAATCCTAA 59.818 55.000 28.56 0.00 0.00 2.69
273 281 1.702022 GGGGCCGGCTGTTAATCCTA 61.702 60.000 28.56 0.00 0.00 2.94
274 282 2.595655 GGGCCGGCTGTTAATCCT 59.404 61.111 28.56 0.00 0.00 3.24
275 283 2.518587 GGGGCCGGCTGTTAATCC 60.519 66.667 28.56 16.97 0.00 3.01
276 284 2.518587 GGGGGCCGGCTGTTAATC 60.519 66.667 28.56 7.30 0.00 1.75
277 285 3.343326 TGGGGGCCGGCTGTTAAT 61.343 61.111 28.56 0.00 0.00 1.40
278 286 4.354162 GTGGGGGCCGGCTGTTAA 62.354 66.667 28.56 5.79 0.00 2.01
288 296 1.881057 TAATTTCAGGGGGTGGGGGC 61.881 60.000 0.00 0.00 0.00 5.80
289 297 0.261696 CTAATTTCAGGGGGTGGGGG 59.738 60.000 0.00 0.00 0.00 5.40
290 298 0.261696 CCTAATTTCAGGGGGTGGGG 59.738 60.000 0.00 0.00 31.47 4.96
291 299 3.924576 CCTAATTTCAGGGGGTGGG 57.075 57.895 0.00 0.00 31.47 4.61
310 318 2.973052 GCTAATTCGCTCGCCCCC 60.973 66.667 0.00 0.00 0.00 5.40
311 319 1.776034 CTTGCTAATTCGCTCGCCCC 61.776 60.000 3.41 0.00 0.00 5.80
312 320 0.810031 TCTTGCTAATTCGCTCGCCC 60.810 55.000 3.41 0.00 0.00 6.13
313 321 0.579156 CTCTTGCTAATTCGCTCGCC 59.421 55.000 3.41 0.00 0.00 5.54
314 322 0.579156 CCTCTTGCTAATTCGCTCGC 59.421 55.000 3.41 0.00 0.00 5.03
315 323 1.212616 CCCTCTTGCTAATTCGCTCG 58.787 55.000 3.41 0.00 0.00 5.03
316 324 1.587547 CCCCTCTTGCTAATTCGCTC 58.412 55.000 3.41 0.00 0.00 5.03
317 325 0.181350 CCCCCTCTTGCTAATTCGCT 59.819 55.000 3.41 0.00 0.00 4.93
318 326 0.107165 ACCCCCTCTTGCTAATTCGC 60.107 55.000 0.00 0.00 0.00 4.70
319 327 1.475213 GGACCCCCTCTTGCTAATTCG 60.475 57.143 0.00 0.00 0.00 3.34
320 328 1.475213 CGGACCCCCTCTTGCTAATTC 60.475 57.143 0.00 0.00 0.00 2.17
321 329 0.546598 CGGACCCCCTCTTGCTAATT 59.453 55.000 0.00 0.00 0.00 1.40
322 330 0.620700 ACGGACCCCCTCTTGCTAAT 60.621 55.000 0.00 0.00 0.00 1.73
323 331 0.041535 TACGGACCCCCTCTTGCTAA 59.958 55.000 0.00 0.00 0.00 3.09
324 332 0.041535 TTACGGACCCCCTCTTGCTA 59.958 55.000 0.00 0.00 0.00 3.49
325 333 1.229400 TTACGGACCCCCTCTTGCT 60.229 57.895 0.00 0.00 0.00 3.91
326 334 1.221021 CTTACGGACCCCCTCTTGC 59.779 63.158 0.00 0.00 0.00 4.01
327 335 0.535797 GTCTTACGGACCCCCTCTTG 59.464 60.000 0.00 0.00 38.93 3.02
328 336 0.115745 TGTCTTACGGACCCCCTCTT 59.884 55.000 0.00 0.00 43.89 2.85
329 337 0.614134 GTGTCTTACGGACCCCCTCT 60.614 60.000 0.00 0.00 43.89 3.69
330 338 0.614134 AGTGTCTTACGGACCCCCTC 60.614 60.000 0.00 0.00 43.89 4.30
331 339 0.614134 GAGTGTCTTACGGACCCCCT 60.614 60.000 0.00 0.00 43.89 4.79
332 340 1.895966 GAGTGTCTTACGGACCCCC 59.104 63.158 0.00 0.00 43.89 5.40
333 341 1.246737 ACGAGTGTCTTACGGACCCC 61.247 60.000 0.00 0.00 43.89 4.95
334 342 1.453155 TACGAGTGTCTTACGGACCC 58.547 55.000 0.00 0.00 43.89 4.46
335 343 3.496155 CTTTACGAGTGTCTTACGGACC 58.504 50.000 0.00 0.00 43.89 4.46
336 344 2.913590 GCTTTACGAGTGTCTTACGGAC 59.086 50.000 0.00 0.00 44.70 4.79
337 345 2.095059 GGCTTTACGAGTGTCTTACGGA 60.095 50.000 0.00 0.00 0.00 4.69
338 346 2.257034 GGCTTTACGAGTGTCTTACGG 58.743 52.381 0.00 0.00 0.00 4.02
339 347 2.257034 GGGCTTTACGAGTGTCTTACG 58.743 52.381 0.00 0.00 0.00 3.18
340 348 2.614779 GGGGCTTTACGAGTGTCTTAC 58.385 52.381 0.00 0.00 0.00 2.34
341 349 1.551883 GGGGGCTTTACGAGTGTCTTA 59.448 52.381 0.00 0.00 0.00 2.10
342 350 0.323957 GGGGGCTTTACGAGTGTCTT 59.676 55.000 0.00 0.00 0.00 3.01
343 351 1.885163 CGGGGGCTTTACGAGTGTCT 61.885 60.000 0.00 0.00 0.00 3.41
344 352 1.447314 CGGGGGCTTTACGAGTGTC 60.447 63.158 0.00 0.00 0.00 3.67
345 353 0.899717 TACGGGGGCTTTACGAGTGT 60.900 55.000 0.00 0.00 0.00 3.55
346 354 0.459063 GTACGGGGGCTTTACGAGTG 60.459 60.000 0.00 0.00 0.00 3.51
347 355 1.893062 GTACGGGGGCTTTACGAGT 59.107 57.895 0.00 0.00 0.00 4.18
348 356 1.226773 CGTACGGGGGCTTTACGAG 60.227 63.158 7.57 0.00 40.84 4.18
349 357 1.933115 GACGTACGGGGGCTTTACGA 61.933 60.000 21.06 0.00 40.84 3.43
350 358 1.517039 GACGTACGGGGGCTTTACG 60.517 63.158 21.06 0.00 43.34 3.18
351 359 1.066152 CTAGACGTACGGGGGCTTTAC 59.934 57.143 21.06 0.00 0.00 2.01
352 360 1.392589 CTAGACGTACGGGGGCTTTA 58.607 55.000 21.06 0.00 0.00 1.85
353 361 1.325476 CCTAGACGTACGGGGGCTTT 61.325 60.000 21.06 0.00 0.00 3.51
354 362 1.755783 CCTAGACGTACGGGGGCTT 60.756 63.158 21.06 0.00 0.00 4.35
355 363 2.004408 ATCCTAGACGTACGGGGGCT 62.004 60.000 21.06 12.98 0.00 5.19
356 364 1.111715 AATCCTAGACGTACGGGGGC 61.112 60.000 21.06 5.92 0.00 5.80
357 365 2.276732 TAATCCTAGACGTACGGGGG 57.723 55.000 21.06 14.73 0.00 5.40
358 366 2.417933 CGATAATCCTAGACGTACGGGG 59.582 54.545 21.06 15.07 0.00 5.73
359 367 2.159599 GCGATAATCCTAGACGTACGGG 60.160 54.545 21.06 11.08 0.00 5.28
360 368 2.159599 GGCGATAATCCTAGACGTACGG 60.160 54.545 21.06 0.68 0.00 4.02
361 369 2.481568 TGGCGATAATCCTAGACGTACG 59.518 50.000 15.01 15.01 0.00 3.67
362 370 4.413087 CATGGCGATAATCCTAGACGTAC 58.587 47.826 0.00 0.00 0.00 3.67
363 371 3.119602 GCATGGCGATAATCCTAGACGTA 60.120 47.826 0.00 0.00 0.00 3.57
364 372 2.352814 GCATGGCGATAATCCTAGACGT 60.353 50.000 0.00 0.00 0.00 4.34
365 373 2.094494 AGCATGGCGATAATCCTAGACG 60.094 50.000 0.00 0.00 0.00 4.18
366 374 3.056536 TGAGCATGGCGATAATCCTAGAC 60.057 47.826 0.00 0.00 0.00 2.59
367 375 3.056536 GTGAGCATGGCGATAATCCTAGA 60.057 47.826 0.00 0.00 0.00 2.43
368 376 3.257393 GTGAGCATGGCGATAATCCTAG 58.743 50.000 0.00 0.00 0.00 3.02
369 377 2.028112 GGTGAGCATGGCGATAATCCTA 60.028 50.000 0.00 0.00 0.00 2.94
370 378 1.271054 GGTGAGCATGGCGATAATCCT 60.271 52.381 0.00 0.00 0.00 3.24
371 379 1.160137 GGTGAGCATGGCGATAATCC 58.840 55.000 0.00 0.00 0.00 3.01
372 380 0.792640 CGGTGAGCATGGCGATAATC 59.207 55.000 0.00 0.00 0.00 1.75
373 381 2.918571 CGGTGAGCATGGCGATAAT 58.081 52.632 0.00 0.00 0.00 1.28
374 382 4.436515 CGGTGAGCATGGCGATAA 57.563 55.556 0.00 0.00 0.00 1.75
516 532 4.459331 GACGGCCGCGTACGTACA 62.459 66.667 28.58 0.00 44.24 2.90
572 588 2.125793 GGGACGAACCGGTAGCAC 60.126 66.667 8.00 0.00 40.11 4.40
652 668 0.165079 GTACGTGACAAATGGCGTGG 59.835 55.000 0.00 0.00 38.10 4.94
654 670 0.034337 AGGTACGTGACAAATGGCGT 59.966 50.000 0.00 0.00 40.76 5.68
657 673 2.158841 CGGAAAGGTACGTGACAAATGG 59.841 50.000 0.00 0.00 0.00 3.16
662 678 0.040157 CGTCGGAAAGGTACGTGACA 60.040 55.000 0.00 0.00 32.16 3.58
695 711 2.285368 TGGAATCAGACGGCCCCT 60.285 61.111 0.00 0.00 0.00 4.79
800 820 7.588488 GGCTGCTTAAATTAATCGCGTTAATTA 59.412 33.333 25.44 14.16 46.93 1.40
806 826 2.032924 GGGCTGCTTAAATTAATCGCGT 59.967 45.455 5.77 0.00 0.00 6.01
864 884 4.790962 TCCGGGGAGGAGACGACG 62.791 72.222 0.00 0.00 45.98 5.12
880 900 0.596341 AATTGGGTGCGTTGCGTTTC 60.596 50.000 0.00 0.00 0.00 2.78
881 901 0.596341 GAATTGGGTGCGTTGCGTTT 60.596 50.000 0.00 0.00 0.00 3.60
906 926 1.198713 GAGAGCTGTGGGATGGAAGA 58.801 55.000 0.00 0.00 0.00 2.87
917 941 1.212935 GAGAGAGAGAGGGAGAGCTGT 59.787 57.143 0.00 0.00 0.00 4.40
922 946 2.039418 CGAGAGAGAGAGAGAGGGAGA 58.961 57.143 0.00 0.00 0.00 3.71
923 947 1.541233 GCGAGAGAGAGAGAGAGGGAG 60.541 61.905 0.00 0.00 0.00 4.30
924 948 0.468226 GCGAGAGAGAGAGAGAGGGA 59.532 60.000 0.00 0.00 0.00 4.20
1563 1593 2.731571 GGACACCAGCAGCGGGATA 61.732 63.158 19.66 0.00 0.00 2.59
1564 1594 4.101448 GGACACCAGCAGCGGGAT 62.101 66.667 19.66 5.67 0.00 3.85
1959 1989 2.444895 GCGGAGGAGGACTGGGAT 60.445 66.667 0.00 0.00 0.00 3.85
1989 2021 2.817844 AGCGATTGGTACCTTGGTTTTC 59.182 45.455 14.36 0.00 0.00 2.29
2010 2042 1.474330 TGTGCTTCGATGAGGAGCTA 58.526 50.000 7.50 0.00 0.00 3.32
2031 2063 1.470098 GCGGATTCTGCTTGTGTGATT 59.530 47.619 10.31 0.00 0.00 2.57
2032 2064 1.089920 GCGGATTCTGCTTGTGTGAT 58.910 50.000 10.31 0.00 0.00 3.06
2033 2065 0.250252 TGCGGATTCTGCTTGTGTGA 60.250 50.000 17.96 0.00 0.00 3.58
2034 2066 0.167470 CTGCGGATTCTGCTTGTGTG 59.833 55.000 17.96 0.00 0.00 3.82
2035 2067 1.580845 GCTGCGGATTCTGCTTGTGT 61.581 55.000 17.96 0.00 0.00 3.72
2041 2087 2.817423 CGGAAGCTGCGGATTCTGC 61.817 63.158 22.00 10.66 37.41 4.26
2180 2233 1.559682 TGGTTCCAGCTCAAGGGTATC 59.440 52.381 0.00 0.00 0.00 2.24
2181 2234 1.668826 TGGTTCCAGCTCAAGGGTAT 58.331 50.000 0.00 0.00 0.00 2.73
2182 2235 1.440618 TTGGTTCCAGCTCAAGGGTA 58.559 50.000 0.00 0.00 0.00 3.69
2183 2236 0.779997 ATTGGTTCCAGCTCAAGGGT 59.220 50.000 0.00 0.00 0.00 4.34
2184 2237 1.821136 GAATTGGTTCCAGCTCAAGGG 59.179 52.381 0.00 0.00 0.00 3.95
2245 2298 0.830444 AGGGGAAAGGGGAAAAACGC 60.830 55.000 0.00 0.00 0.00 4.84
2246 2299 1.343142 CAAGGGGAAAGGGGAAAAACG 59.657 52.381 0.00 0.00 0.00 3.60
2247 2300 1.697432 CCAAGGGGAAAGGGGAAAAAC 59.303 52.381 0.00 0.00 35.59 2.43
2248 2301 2.042842 GCCAAGGGGAAAGGGGAAAAA 61.043 52.381 0.00 0.00 35.59 1.94
2249 2302 0.472925 GCCAAGGGGAAAGGGGAAAA 60.473 55.000 0.00 0.00 35.59 2.29
2264 2317 3.040414 CTCGTCTCGCTCTCGCCAA 62.040 63.158 0.00 0.00 35.26 4.52
2416 2477 7.661847 GTGAAGAAGAAAGAATTTACAGGGAGA 59.338 37.037 0.00 0.00 39.27 3.71
2431 2492 8.575649 AGTAGAAAACAAAGGTGAAGAAGAAA 57.424 30.769 0.00 0.00 0.00 2.52
2436 2497 6.891388 TGGTAGTAGAAAACAAAGGTGAAGA 58.109 36.000 0.00 0.00 0.00 2.87
2438 2499 7.514721 AGATGGTAGTAGAAAACAAAGGTGAA 58.485 34.615 0.00 0.00 0.00 3.18
2439 2500 7.074653 AGATGGTAGTAGAAAACAAAGGTGA 57.925 36.000 0.00 0.00 0.00 4.02
2462 2558 2.033194 GCCCGAGGAACGAACCAAG 61.033 63.158 0.00 0.00 45.77 3.61
2480 2576 2.415090 CGAATTTGGCTTGCTTCCTCAG 60.415 50.000 0.00 0.00 0.00 3.35
2481 2577 1.541147 CGAATTTGGCTTGCTTCCTCA 59.459 47.619 0.00 0.00 0.00 3.86
2689 2806 5.024785 CCTGAGATAGGTTTGGAGTAACC 57.975 47.826 0.00 0.00 46.45 2.85
2753 2880 4.167359 TCACTCGCTCGCTCGCTC 62.167 66.667 0.00 0.00 0.00 5.03
2754 2881 4.468615 GTCACTCGCTCGCTCGCT 62.469 66.667 0.00 0.00 0.00 4.93
2755 2882 3.955234 AAGTCACTCGCTCGCTCGC 62.955 63.158 0.00 0.00 0.00 5.03
2756 2883 2.148982 CAAGTCACTCGCTCGCTCG 61.149 63.158 0.00 0.00 0.00 5.03
2889 3020 2.978010 ACAAACGGCGGCAGAAGG 60.978 61.111 13.24 0.00 0.00 3.46
2900 3031 1.398390 GCATCTTCTAGGCCACAAACG 59.602 52.381 5.01 0.00 0.00 3.60
2937 3074 5.276584 CGAGATCTTTGAGCTTTACCGATTG 60.277 44.000 0.00 0.00 0.00 2.67
2938 3075 4.806247 CGAGATCTTTGAGCTTTACCGATT 59.194 41.667 0.00 0.00 0.00 3.34
2940 3077 3.770666 CGAGATCTTTGAGCTTTACCGA 58.229 45.455 0.00 0.00 0.00 4.69
2951 3088 3.929948 GCGGGCGCGAGATCTTTG 61.930 66.667 28.66 0.00 0.00 2.77
3005 3148 2.291741 CCAAAGAGCAGCGTCTTTTTCT 59.708 45.455 13.92 0.00 42.93 2.52
3011 3154 1.670406 CAGCCAAAGAGCAGCGTCT 60.670 57.895 0.00 0.00 34.23 4.18
3070 3213 3.531207 CGAGCTCCATGCCTCGGA 61.531 66.667 8.47 0.00 44.23 4.55
3071 3214 3.842923 ACGAGCTCCATGCCTCGG 61.843 66.667 23.30 11.82 42.34 4.63
3106 3261 4.209288 CGCTTGAAGGTACATACATACAGC 59.791 45.833 0.00 0.00 0.00 4.40
3111 3266 4.647853 TCCTACGCTTGAAGGTACATACAT 59.352 41.667 0.00 0.00 34.30 2.29
3112 3267 4.018490 TCCTACGCTTGAAGGTACATACA 58.982 43.478 0.00 0.00 34.30 2.29
3113 3268 4.644103 TCCTACGCTTGAAGGTACATAC 57.356 45.455 0.00 0.00 34.30 2.39
3114 3269 5.413499 GTTTCCTACGCTTGAAGGTACATA 58.587 41.667 0.00 0.00 34.30 2.29
3115 3270 4.251268 GTTTCCTACGCTTGAAGGTACAT 58.749 43.478 0.00 0.00 34.30 2.29
3131 3286 0.532862 CGCCATGCTATCCGTTTCCT 60.533 55.000 0.00 0.00 0.00 3.36
3143 3298 2.916502 TATGACGTGTCCCGCCATGC 62.917 60.000 0.00 0.00 40.08 4.06
3144 3299 1.142965 TATGACGTGTCCCGCCATG 59.857 57.895 0.00 0.00 40.08 3.66
3145 3300 1.143183 GTATGACGTGTCCCGCCAT 59.857 57.895 0.00 0.00 42.57 4.40
3146 3301 2.574929 GTATGACGTGTCCCGCCA 59.425 61.111 0.00 0.00 41.42 5.69
3147 3302 2.581409 CGTATGACGTGTCCCGCC 60.581 66.667 0.00 0.00 41.42 6.13


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

AutoCloner maintained by Alex Coulton.