Multiple sequence alignment - TraesCS5D01G285300

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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 TraesCS5D01G285300 chr5D 100.000 2270 0 0 1 2270 385979533 385977264 0.000000e+00 4193
1 TraesCS5D01G285300 chr5D 87.287 1290 71 38 347 1588 386036513 386035269 0.000000e+00 1387
2 TraesCS5D01G285300 chr5D 86.707 662 33 27 687 1320 386067700 386067066 0.000000e+00 684
3 TraesCS5D01G285300 chr5D 80.667 750 92 29 1406 2124 386057293 386056566 1.190000e-147 532
4 TraesCS5D01G285300 chr5D 84.335 549 59 12 1575 2103 386035243 386034702 1.560000e-141 512
5 TraesCS5D01G285300 chr5D 90.047 211 14 3 1 206 386036726 386036518 1.340000e-67 267
6 TraesCS5D01G285300 chr5D 90.244 205 18 1 1 205 386100367 386100569 1.340000e-67 267
7 TraesCS5D01G285300 chr5D 86.056 251 25 6 342 587 386100565 386100810 6.220000e-66 261
8 TraesCS5D01G285300 chr5D 85.222 203 16 5 3 205 386061023 386060835 1.780000e-46 196
9 TraesCS5D01G285300 chr5A 85.027 1683 117 57 342 1933 487919318 487917680 0.000000e+00 1587
10 TraesCS5D01G285300 chr5A 84.589 1181 62 45 570 1687 487925343 487924220 0.000000e+00 1062
11 TraesCS5D01G285300 chr5A 83.461 786 69 25 1395 2127 487947575 487946798 0.000000e+00 675
12 TraesCS5D01G285300 chr5A 87.544 562 37 17 852 1404 487985040 487984503 8.910000e-174 619
13 TraesCS5D01G285300 chr5A 93.261 371 16 4 984 1354 487948986 487948625 2.570000e-149 538
14 TraesCS5D01G285300 chr5A 80.671 745 89 24 1403 2124 487984152 487983440 5.550000e-146 527
15 TraesCS5D01G285300 chr5A 83.978 543 56 20 1403 1928 487940195 487939667 2.030000e-135 492
16 TraesCS5D01G285300 chr5A 88.114 387 27 8 590 959 487941239 487940855 2.070000e-120 442
17 TraesCS5D01G285300 chr5A 86.047 344 32 11 1938 2270 487917466 487917128 2.770000e-94 355
18 TraesCS5D01G285300 chr5A 81.862 419 56 13 1697 2101 487924126 487923714 3.610000e-88 335
19 TraesCS5D01G285300 chr5A 91.707 205 15 1 1 205 488016586 488016788 1.330000e-72 283
20 TraesCS5D01G285300 chr5A 89.091 220 18 3 342 559 487943180 487942965 3.720000e-68 268
21 TraesCS5D01G285300 chr5A 88.942 208 12 5 342 549 487949979 487949783 1.740000e-61 246
22 TraesCS5D01G285300 chr5A 87.745 204 19 4 3 205 487926688 487926490 1.360000e-57 233
23 TraesCS5D01G285300 chr5A 86.458 192 12 4 14 205 487943353 487943176 4.950000e-47 198
24 TraesCS5D01G285300 chr5A 80.000 285 24 17 687 938 488009185 488008901 1.790000e-41 180
25 TraesCS5D01G285300 chr5A 84.699 183 20 5 23 205 487950149 487949975 2.320000e-40 176
26 TraesCS5D01G285300 chr5A 84.153 183 22 6 1923 2101 487939241 487939062 1.080000e-38 171
27 TraesCS5D01G285300 chr5B 85.971 1333 110 33 852 2127 463918826 463917514 0.000000e+00 1354
28 TraesCS5D01G285300 chr5B 85.634 891 82 22 1405 2270 463911922 463911053 0.000000e+00 894
29 TraesCS5D01G285300 chr5B 84.058 966 52 49 417 1354 463912936 463912045 0.000000e+00 837
30 TraesCS5D01G285300 chr5B 86.446 664 36 19 687 1325 463945395 463944761 0.000000e+00 678
31 TraesCS5D01G285300 chr5B 84.311 682 75 19 1467 2127 463937376 463936706 2.460000e-179 638
32 TraesCS5D01G285300 chr5B 85.658 509 21 16 852 1348 463937845 463937377 2.620000e-134 488
33 TraesCS5D01G285300 chr5B 89.268 205 19 2 1 205 463969948 463970149 1.040000e-63 254
34 TraesCS5D01G285300 chr5B 88.000 200 15 4 13 205 463920885 463920688 6.310000e-56 228
35 TraesCS5D01G285300 chr5B 79.339 242 42 5 2004 2242 86241265 86241029 1.800000e-36 163
36 TraesCS5D01G285300 chr5B 87.500 88 11 0 345 432 463920689 463920602 3.990000e-18 102
37 TraesCS5D01G285300 chr1B 97.945 146 3 0 203 348 681005476 681005331 1.040000e-63 254
38 TraesCS5D01G285300 chr7B 97.279 147 4 0 199 345 109595844 109595698 1.350000e-62 250
39 TraesCS5D01G285300 chr7B 97.842 139 3 0 204 342 379776327 379776465 8.100000e-60 241
40 TraesCS5D01G285300 chr6B 97.902 143 3 0 203 345 9917290 9917148 4.840000e-62 248
41 TraesCS5D01G285300 chr1D 95.105 143 7 0 206 348 294221483 294221341 2.270000e-55 226
42 TraesCS5D01G285300 chr3B 95.070 142 7 0 209 350 828079975 828079834 8.160000e-55 224
43 TraesCS5D01G285300 chr3A 93.836 146 9 0 203 348 34528516 34528661 1.060000e-53 220
44 TraesCS5D01G285300 chr2B 94.406 143 8 0 203 345 135790588 135790446 1.060000e-53 220
45 TraesCS5D01G285300 chr2B 78.543 247 46 6 2003 2245 653613031 653612788 3.020000e-34 156
46 TraesCS5D01G285300 chr1A 92.763 152 11 0 198 349 256710596 256710747 1.060000e-53 220
47 TraesCS5D01G285300 chr4D 80.162 247 42 6 2004 2245 145579767 145579523 6.440000e-41 178
48 TraesCS5D01G285300 chr7D 79.528 254 39 10 2004 2245 143995736 143995484 3.880000e-38 169
49 TraesCS5D01G285300 chr7A 78.947 228 34 12 2015 2234 532735661 532735440 2.350000e-30 143
50 TraesCS5D01G285300 chr7A 77.686 242 47 5 2006 2242 699735887 699736126 8.450000e-30 141


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 TraesCS5D01G285300 chr5D 385977264 385979533 2269 True 4193.000000 4193 100.000000 1 2270 1 chr5D.!!$R1 2269
1 TraesCS5D01G285300 chr5D 386034702 386036726 2024 True 722.000000 1387 87.223000 1 2103 3 chr5D.!!$R3 2102
2 TraesCS5D01G285300 chr5D 386067066 386067700 634 True 684.000000 684 86.707000 687 1320 1 chr5D.!!$R2 633
3 TraesCS5D01G285300 chr5D 386056566 386061023 4457 True 364.000000 532 82.944500 3 2124 2 chr5D.!!$R4 2121
4 TraesCS5D01G285300 chr5A 487917128 487919318 2190 True 971.000000 1587 85.537000 342 2270 2 chr5A.!!$R2 1928
5 TraesCS5D01G285300 chr5A 487983440 487985040 1600 True 573.000000 619 84.107500 852 2124 2 chr5A.!!$R5 1272
6 TraesCS5D01G285300 chr5A 487923714 487926688 2974 True 543.333333 1062 84.732000 3 2101 3 chr5A.!!$R3 2098
7 TraesCS5D01G285300 chr5A 487939062 487950149 11087 True 356.222222 675 86.906333 14 2127 9 chr5A.!!$R4 2113
8 TraesCS5D01G285300 chr5B 463911053 463912936 1883 True 865.500000 894 84.846000 417 2270 2 chr5B.!!$R3 1853
9 TraesCS5D01G285300 chr5B 463944761 463945395 634 True 678.000000 678 86.446000 687 1325 1 chr5B.!!$R2 638
10 TraesCS5D01G285300 chr5B 463936706 463937845 1139 True 563.000000 638 84.984500 852 2127 2 chr5B.!!$R5 1275
11 TraesCS5D01G285300 chr5B 463917514 463920885 3371 True 561.333333 1354 87.157000 13 2127 3 chr5B.!!$R4 2114

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
218 234 0.032017 ATCTAGGGCCTGTTCGGAGT 60.032 55.0 18.53 0.0 33.16 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1288 6108 1.967779 CAAGGATCCGGTTGGGTTTTT 59.032 47.619 5.98 0.0 37.0 1.94 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
34 35 4.347453 CCAGGCACCAACTTGCGC 62.347 66.667 0.00 0.00 44.00 6.09
52 53 3.140814 GGTTGGAATCCAGGCGGC 61.141 66.667 0.86 0.00 33.81 6.53
84 90 4.574013 CAGTTCAGCCAGGATTCAGAATAC 59.426 45.833 0.00 0.00 0.00 1.89
87 93 4.774124 TCAGCCAGGATTCAGAATACTTG 58.226 43.478 4.97 3.60 26.27 3.16
139 155 1.199615 TCCTGATGTGCCGTGGATTA 58.800 50.000 0.00 0.00 0.00 1.75
141 157 2.172505 TCCTGATGTGCCGTGGATTATT 59.827 45.455 0.00 0.00 0.00 1.40
142 158 2.549754 CCTGATGTGCCGTGGATTATTC 59.450 50.000 0.00 0.00 0.00 1.75
143 159 3.470709 CTGATGTGCCGTGGATTATTCT 58.529 45.455 0.00 0.00 0.00 2.40
144 160 4.503123 CCTGATGTGCCGTGGATTATTCTA 60.503 45.833 0.00 0.00 0.00 2.10
145 161 5.227569 TGATGTGCCGTGGATTATTCTAT 57.772 39.130 0.00 0.00 0.00 1.98
146 162 6.353404 TGATGTGCCGTGGATTATTCTATA 57.647 37.500 0.00 0.00 0.00 1.31
206 222 5.369699 AGCTAGCCTATCTCTCTATCTAGGG 59.630 48.000 12.13 0.00 32.91 3.53
207 223 4.519906 AGCCTATCTCTCTATCTAGGGC 57.480 50.000 0.00 0.00 37.57 5.19
208 224 3.204382 AGCCTATCTCTCTATCTAGGGCC 59.796 52.174 0.00 0.00 37.98 5.80
209 225 3.204382 GCCTATCTCTCTATCTAGGGCCT 59.796 52.174 12.58 12.58 32.91 5.19
210 226 4.792068 CCTATCTCTCTATCTAGGGCCTG 58.208 52.174 18.53 6.47 0.00 4.85
211 227 4.229582 CCTATCTCTCTATCTAGGGCCTGT 59.770 50.000 18.53 4.61 0.00 4.00
212 228 4.757997 ATCTCTCTATCTAGGGCCTGTT 57.242 45.455 18.53 2.87 0.00 3.16
213 229 4.107127 TCTCTCTATCTAGGGCCTGTTC 57.893 50.000 18.53 0.00 0.00 3.18
214 230 2.817258 CTCTCTATCTAGGGCCTGTTCG 59.183 54.545 18.53 1.71 0.00 3.95
215 231 1.889829 CTCTATCTAGGGCCTGTTCGG 59.110 57.143 18.53 3.76 0.00 4.30
216 232 1.497716 TCTATCTAGGGCCTGTTCGGA 59.502 52.381 18.53 6.28 33.16 4.55
217 233 1.889829 CTATCTAGGGCCTGTTCGGAG 59.110 57.143 18.53 4.03 33.16 4.63
218 234 0.032017 ATCTAGGGCCTGTTCGGAGT 60.032 55.000 18.53 0.00 33.16 3.85
219 235 0.683504 TCTAGGGCCTGTTCGGAGTC 60.684 60.000 18.53 0.00 33.16 3.36
220 236 0.684805 CTAGGGCCTGTTCGGAGTCT 60.685 60.000 18.53 0.00 33.16 3.24
221 237 0.683504 TAGGGCCTGTTCGGAGTCTC 60.684 60.000 18.53 0.00 33.16 3.36
222 238 2.182030 GGCCTGTTCGGAGTCTCG 59.818 66.667 0.00 0.00 33.16 4.04
223 239 2.507324 GCCTGTTCGGAGTCTCGC 60.507 66.667 0.00 0.00 33.16 5.03
224 240 2.182030 CCTGTTCGGAGTCTCGCC 59.818 66.667 0.00 0.00 33.16 5.54
226 242 4.415332 TGTTCGGAGTCTCGCCGC 62.415 66.667 7.02 0.00 45.89 6.53
227 243 4.117661 GTTCGGAGTCTCGCCGCT 62.118 66.667 7.02 0.00 45.89 5.52
228 244 3.812019 TTCGGAGTCTCGCCGCTC 61.812 66.667 7.02 0.00 45.89 5.03
243 259 4.838486 CTCCGCACGACTCCGCTC 62.838 72.222 0.00 0.00 39.95 5.03
267 283 3.121030 CGGCCCGAGCTTCTGTTG 61.121 66.667 0.00 0.00 39.73 3.33
268 284 2.347490 GGCCCGAGCTTCTGTTGA 59.653 61.111 0.00 0.00 39.73 3.18
269 285 1.302511 GGCCCGAGCTTCTGTTGAA 60.303 57.895 0.00 0.00 39.73 2.69
270 286 0.889186 GGCCCGAGCTTCTGTTGAAA 60.889 55.000 0.00 0.00 39.73 2.69
271 287 0.951558 GCCCGAGCTTCTGTTGAAAA 59.048 50.000 0.00 0.00 35.50 2.29
272 288 1.541588 GCCCGAGCTTCTGTTGAAAAT 59.458 47.619 0.00 0.00 35.50 1.82
273 289 2.747446 GCCCGAGCTTCTGTTGAAAATA 59.253 45.455 0.00 0.00 35.50 1.40
274 290 3.426292 GCCCGAGCTTCTGTTGAAAATAC 60.426 47.826 0.00 0.00 35.50 1.89
275 291 3.181520 CCCGAGCTTCTGTTGAAAATACG 60.182 47.826 0.00 0.00 0.00 3.06
276 292 3.181520 CCGAGCTTCTGTTGAAAATACGG 60.182 47.826 0.00 0.00 32.97 4.02
277 293 3.678072 CGAGCTTCTGTTGAAAATACGGA 59.322 43.478 0.00 0.00 0.00 4.69
278 294 4.201628 CGAGCTTCTGTTGAAAATACGGAG 60.202 45.833 0.00 0.00 32.80 4.63
280 296 4.452455 AGCTTCTGTTGAAAATACGGAGTG 59.548 41.667 0.00 0.00 45.73 3.51
281 297 4.378459 GCTTCTGTTGAAAATACGGAGTGG 60.378 45.833 0.00 0.00 45.73 4.00
282 298 4.610605 TCTGTTGAAAATACGGAGTGGA 57.389 40.909 0.00 0.00 45.73 4.02
283 299 4.566004 TCTGTTGAAAATACGGAGTGGAG 58.434 43.478 0.00 0.00 45.73 3.86
284 300 4.282449 TCTGTTGAAAATACGGAGTGGAGA 59.718 41.667 0.00 0.00 45.73 3.71
285 301 4.963373 TGTTGAAAATACGGAGTGGAGAA 58.037 39.130 0.00 0.00 45.73 2.87
286 302 5.369833 TGTTGAAAATACGGAGTGGAGAAA 58.630 37.500 0.00 0.00 45.73 2.52
287 303 5.468746 TGTTGAAAATACGGAGTGGAGAAAG 59.531 40.000 0.00 0.00 45.73 2.62
288 304 5.477607 TGAAAATACGGAGTGGAGAAAGA 57.522 39.130 0.00 0.00 45.73 2.52
289 305 5.479306 TGAAAATACGGAGTGGAGAAAGAG 58.521 41.667 0.00 0.00 45.73 2.85
290 306 5.245301 TGAAAATACGGAGTGGAGAAAGAGA 59.755 40.000 0.00 0.00 45.73 3.10
291 307 5.941555 AAATACGGAGTGGAGAAAGAGAT 57.058 39.130 0.00 0.00 45.73 2.75
292 308 4.927978 ATACGGAGTGGAGAAAGAGATG 57.072 45.455 0.00 0.00 45.73 2.90
293 309 1.205893 ACGGAGTGGAGAAAGAGATGC 59.794 52.381 0.00 0.00 42.51 3.91
294 310 1.480137 CGGAGTGGAGAAAGAGATGCT 59.520 52.381 0.00 0.00 0.00 3.79
295 311 2.481104 CGGAGTGGAGAAAGAGATGCTC 60.481 54.545 0.00 0.00 0.00 4.26
296 312 2.158971 GGAGTGGAGAAAGAGATGCTCC 60.159 54.545 0.00 0.00 46.60 4.70
300 316 3.363341 GGAGAAAGAGATGCTCCGTAG 57.637 52.381 0.00 0.00 38.88 3.51
301 317 2.952978 GGAGAAAGAGATGCTCCGTAGA 59.047 50.000 0.00 0.00 38.88 2.59
302 318 3.572255 GGAGAAAGAGATGCTCCGTAGAT 59.428 47.826 0.00 0.00 38.88 1.98
303 319 4.038642 GGAGAAAGAGATGCTCCGTAGATT 59.961 45.833 0.00 0.00 38.88 2.40
304 320 5.195001 AGAAAGAGATGCTCCGTAGATTC 57.805 43.478 0.00 0.00 0.00 2.52
305 321 4.892934 AGAAAGAGATGCTCCGTAGATTCT 59.107 41.667 0.00 0.00 0.00 2.40
306 322 5.362430 AGAAAGAGATGCTCCGTAGATTCTT 59.638 40.000 0.00 0.00 0.00 2.52
307 323 4.582701 AGAGATGCTCCGTAGATTCTTG 57.417 45.455 0.00 0.00 0.00 3.02
308 324 3.957497 AGAGATGCTCCGTAGATTCTTGT 59.043 43.478 0.00 0.00 0.00 3.16
309 325 5.133941 AGAGATGCTCCGTAGATTCTTGTA 58.866 41.667 0.00 0.00 0.00 2.41
310 326 5.772672 AGAGATGCTCCGTAGATTCTTGTAT 59.227 40.000 0.00 0.00 0.00 2.29
311 327 6.266558 AGAGATGCTCCGTAGATTCTTGTATT 59.733 38.462 0.00 0.00 0.00 1.89
312 328 6.821388 AGATGCTCCGTAGATTCTTGTATTT 58.179 36.000 0.00 0.00 0.00 1.40
313 329 6.926272 AGATGCTCCGTAGATTCTTGTATTTC 59.074 38.462 0.00 0.00 0.00 2.17
314 330 6.222038 TGCTCCGTAGATTCTTGTATTTCT 57.778 37.500 0.00 0.00 0.00 2.52
315 331 6.640518 TGCTCCGTAGATTCTTGTATTTCTT 58.359 36.000 0.00 0.00 0.00 2.52
316 332 6.535150 TGCTCCGTAGATTCTTGTATTTCTTG 59.465 38.462 0.00 0.00 0.00 3.02
317 333 6.018669 GCTCCGTAGATTCTTGTATTTCTTGG 60.019 42.308 0.00 0.00 0.00 3.61
318 334 7.177832 TCCGTAGATTCTTGTATTTCTTGGA 57.822 36.000 0.00 0.00 0.00 3.53
319 335 7.265673 TCCGTAGATTCTTGTATTTCTTGGAG 58.734 38.462 0.00 0.00 0.00 3.86
320 336 6.018669 CCGTAGATTCTTGTATTTCTTGGAGC 60.019 42.308 0.00 0.00 0.00 4.70
321 337 6.291849 CGTAGATTCTTGTATTTCTTGGAGCG 60.292 42.308 0.00 0.00 0.00 5.03
322 338 4.878397 AGATTCTTGTATTTCTTGGAGCGG 59.122 41.667 0.00 0.00 0.00 5.52
323 339 3.695830 TCTTGTATTTCTTGGAGCGGT 57.304 42.857 0.00 0.00 0.00 5.68
324 340 3.334691 TCTTGTATTTCTTGGAGCGGTG 58.665 45.455 0.00 0.00 0.00 4.94
325 341 2.107950 TGTATTTCTTGGAGCGGTGG 57.892 50.000 0.00 0.00 0.00 4.61
326 342 1.626321 TGTATTTCTTGGAGCGGTGGA 59.374 47.619 0.00 0.00 0.00 4.02
327 343 2.238646 TGTATTTCTTGGAGCGGTGGAT 59.761 45.455 0.00 0.00 0.00 3.41
328 344 2.514458 ATTTCTTGGAGCGGTGGATT 57.486 45.000 0.00 0.00 0.00 3.01
329 345 1.533625 TTTCTTGGAGCGGTGGATTG 58.466 50.000 0.00 0.00 0.00 2.67
330 346 0.690192 TTCTTGGAGCGGTGGATTGA 59.310 50.000 0.00 0.00 0.00 2.57
331 347 0.036388 TCTTGGAGCGGTGGATTGAC 60.036 55.000 0.00 0.00 0.00 3.18
332 348 1.361668 CTTGGAGCGGTGGATTGACG 61.362 60.000 0.00 0.00 0.00 4.35
333 349 1.822114 TTGGAGCGGTGGATTGACGA 61.822 55.000 0.00 0.00 0.00 4.20
334 350 1.079405 GGAGCGGTGGATTGACGAA 60.079 57.895 0.00 0.00 0.00 3.85
335 351 1.359459 GGAGCGGTGGATTGACGAAC 61.359 60.000 0.00 0.00 0.00 3.95
336 352 0.669318 GAGCGGTGGATTGACGAACA 60.669 55.000 0.00 0.00 0.00 3.18
337 353 0.670546 AGCGGTGGATTGACGAACAG 60.671 55.000 0.00 0.00 0.00 3.16
338 354 1.635663 GCGGTGGATTGACGAACAGG 61.636 60.000 0.00 0.00 0.00 4.00
339 355 1.635663 CGGTGGATTGACGAACAGGC 61.636 60.000 0.00 0.00 0.00 4.85
340 356 1.305930 GGTGGATTGACGAACAGGCC 61.306 60.000 0.00 0.00 0.00 5.19
401 417 2.682856 GGAAGGCGAATTTCTGCATGTA 59.317 45.455 12.79 0.00 0.00 2.29
471 1819 4.694339 TCACGTCGATCAGATAGAGAAGA 58.306 43.478 0.00 0.00 0.00 2.87
476 4158 4.059511 TCGATCAGATAGAGAAGACCGAC 58.940 47.826 0.00 0.00 0.00 4.79
583 5250 6.183360 GCTAGGTCTTCGACTTTTGAATCTTC 60.183 42.308 0.00 0.00 32.47 2.87
587 5254 5.402867 GTCTTCGACTTTTGAATCTTCTCGT 59.597 40.000 0.00 0.00 0.00 4.18
614 5296 2.182537 GCGAAATGCAAGGCAGGG 59.817 61.111 0.00 0.00 43.65 4.45
977 5791 8.350238 GGTTTCCGAGAAACATACTATAGTTC 57.650 38.462 22.50 1.92 32.04 3.01
978 5792 7.437565 GGTTTCCGAGAAACATACTATAGTTCC 59.562 40.741 22.50 5.50 32.04 3.62
979 5793 6.309712 TCCGAGAAACATACTATAGTTCCG 57.690 41.667 11.40 7.78 0.00 4.30
980 5794 6.057533 TCCGAGAAACATACTATAGTTCCGA 58.942 40.000 11.40 0.00 0.00 4.55
981 5795 6.543465 TCCGAGAAACATACTATAGTTCCGAA 59.457 38.462 11.40 0.00 0.00 4.30
982 5796 6.636044 CCGAGAAACATACTATAGTTCCGAAC 59.364 42.308 11.40 2.81 0.00 3.95
1288 6108 6.065976 ACTGATTCATCAATCAAGGTACCA 57.934 37.500 15.94 0.00 46.35 3.25
1355 6192 4.333926 GTGTGAAATATCAGCAGGTCCTTC 59.666 45.833 0.00 0.00 35.88 3.46
1583 8188 6.483405 AAGCTTCTGAATTCTGAAGATCCTT 58.517 36.000 38.52 30.97 45.38 3.36
1594 8236 5.072741 TCTGAAGATCCTTCAAAAACAGGG 58.927 41.667 10.19 0.00 0.00 4.45
1624 8268 7.561722 TCTGTTGATTATCTAGTCCTTAGCTGT 59.438 37.037 0.00 0.00 0.00 4.40
1643 8287 4.673580 GCTGTGACCATGTTATTGAAGCAG 60.674 45.833 0.00 0.00 0.00 4.24
1648 8296 3.131577 ACCATGTTATTGAAGCAGGCATG 59.868 43.478 0.00 0.00 33.98 4.06
1660 8313 5.239963 TGAAGCAGGCATGATTATGTATGTG 59.760 40.000 0.12 0.00 34.53 3.21
1768 8520 4.363138 TCGCAGACTCTAGCATGTATTTG 58.637 43.478 0.00 0.00 0.00 2.32
1882 8647 7.195374 ACTTGTGCTTGGTAGAATATTCCTA 57.805 36.000 11.92 1.77 0.00 2.94
1919 8690 9.294030 CTTCAAGATTTGGATGTTTACATTAGC 57.706 33.333 0.00 0.00 36.57 3.09
1920 8691 8.579850 TCAAGATTTGGATGTTTACATTAGCT 57.420 30.769 0.00 0.00 36.57 3.32
1921 8692 9.679661 TCAAGATTTGGATGTTTACATTAGCTA 57.320 29.630 0.00 0.00 36.57 3.32
1979 8968 4.013728 GAGGGAGTAGATGCGAGTATGAT 58.986 47.826 0.00 0.00 0.00 2.45
2011 9000 6.183360 GCATCTGATAACTTGTGTACTCCCTA 60.183 42.308 0.00 0.00 0.00 3.53
2085 9076 9.674068 AAAAGTTTGGCCAAGTTTATAGAAAAA 57.326 25.926 19.48 0.00 37.07 1.94
2171 16088 8.126074 TGGTAATGATTTTGTATTGCATACGTC 58.874 33.333 0.00 0.00 38.59 4.34
2231 16148 8.965986 AAAGTTTGACTTCTCACAAAACTAAC 57.034 30.769 0.00 0.00 37.47 2.34
2242 16159 7.450074 TCTCACAAAACTAACATGTGGAGTAT 58.550 34.615 12.72 4.48 43.53 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.481441 TGGTGCCTGGAATCTGATAGT 58.519 47.619 0.00 0.00 0.00 2.12
9 10 1.637553 AGTTGGTGCCTGGAATCTGAT 59.362 47.619 0.00 0.00 0.00 2.90
34 35 2.824041 CCGCCTGGATTCCAACCG 60.824 66.667 6.88 11.51 37.49 4.44
36 37 3.140814 GGCCGCCTGGATTCCAAC 61.141 66.667 6.88 1.17 37.49 3.77
52 53 2.158986 CCTGGCTGAACTGATGTAGAGG 60.159 54.545 0.00 0.00 0.00 3.69
84 90 1.172175 GGCTGAGGAAAAGGAGCAAG 58.828 55.000 0.00 0.00 32.83 4.01
87 93 1.620822 TTTGGCTGAGGAAAAGGAGC 58.379 50.000 0.00 0.00 0.00 4.70
139 155 4.201930 GGAACGATCGAGCCGATATAGAAT 60.202 45.833 24.34 0.00 47.00 2.40
141 157 2.676839 GGAACGATCGAGCCGATATAGA 59.323 50.000 24.34 0.00 47.00 1.98
142 158 2.678836 AGGAACGATCGAGCCGATATAG 59.321 50.000 24.34 7.51 47.00 1.31
143 159 2.708051 AGGAACGATCGAGCCGATATA 58.292 47.619 24.34 0.00 47.00 0.86
144 160 1.535833 AGGAACGATCGAGCCGATAT 58.464 50.000 24.34 3.56 47.00 1.63
145 161 2.174363 TAGGAACGATCGAGCCGATA 57.826 50.000 24.34 8.70 47.00 2.92
206 222 2.507324 GCGAGACTCCGAACAGGC 60.507 66.667 0.00 0.00 40.77 4.85
207 223 2.182030 GGCGAGACTCCGAACAGG 59.818 66.667 0.00 0.00 42.97 4.00
226 242 4.838486 GAGCGGAGTCGTGCGGAG 62.838 72.222 0.90 0.00 38.11 4.63
250 266 3.121030 CAACAGAAGCTCGGGCCG 61.121 66.667 22.51 22.51 39.73 6.13
251 267 0.889186 TTTCAACAGAAGCTCGGGCC 60.889 55.000 2.00 0.00 39.73 5.80
252 268 0.951558 TTTTCAACAGAAGCTCGGGC 59.048 50.000 0.00 0.00 39.06 6.13
253 269 3.181520 CGTATTTTCAACAGAAGCTCGGG 60.182 47.826 0.00 0.00 0.00 5.14
254 270 3.181520 CCGTATTTTCAACAGAAGCTCGG 60.182 47.826 0.00 0.00 0.00 4.63
255 271 3.678072 TCCGTATTTTCAACAGAAGCTCG 59.322 43.478 0.00 0.00 0.00 5.03
256 272 4.691216 ACTCCGTATTTTCAACAGAAGCTC 59.309 41.667 0.00 0.00 0.00 4.09
257 273 4.452455 CACTCCGTATTTTCAACAGAAGCT 59.548 41.667 0.00 0.00 0.00 3.74
258 274 4.378459 CCACTCCGTATTTTCAACAGAAGC 60.378 45.833 0.00 0.00 0.00 3.86
259 275 4.994852 TCCACTCCGTATTTTCAACAGAAG 59.005 41.667 0.00 0.00 0.00 2.85
260 276 4.963373 TCCACTCCGTATTTTCAACAGAA 58.037 39.130 0.00 0.00 0.00 3.02
261 277 4.282449 TCTCCACTCCGTATTTTCAACAGA 59.718 41.667 0.00 0.00 0.00 3.41
262 278 4.566004 TCTCCACTCCGTATTTTCAACAG 58.434 43.478 0.00 0.00 0.00 3.16
263 279 4.610605 TCTCCACTCCGTATTTTCAACA 57.389 40.909 0.00 0.00 0.00 3.33
264 280 5.699458 TCTTTCTCCACTCCGTATTTTCAAC 59.301 40.000 0.00 0.00 0.00 3.18
265 281 5.860611 TCTTTCTCCACTCCGTATTTTCAA 58.139 37.500 0.00 0.00 0.00 2.69
266 282 5.245301 TCTCTTTCTCCACTCCGTATTTTCA 59.755 40.000 0.00 0.00 0.00 2.69
267 283 5.721232 TCTCTTTCTCCACTCCGTATTTTC 58.279 41.667 0.00 0.00 0.00 2.29
268 284 5.740290 TCTCTTTCTCCACTCCGTATTTT 57.260 39.130 0.00 0.00 0.00 1.82
269 285 5.665459 CATCTCTTTCTCCACTCCGTATTT 58.335 41.667 0.00 0.00 0.00 1.40
270 286 4.442192 GCATCTCTTTCTCCACTCCGTATT 60.442 45.833 0.00 0.00 0.00 1.89
271 287 3.068873 GCATCTCTTTCTCCACTCCGTAT 59.931 47.826 0.00 0.00 0.00 3.06
272 288 2.427453 GCATCTCTTTCTCCACTCCGTA 59.573 50.000 0.00 0.00 0.00 4.02
273 289 1.205893 GCATCTCTTTCTCCACTCCGT 59.794 52.381 0.00 0.00 0.00 4.69
274 290 1.480137 AGCATCTCTTTCTCCACTCCG 59.520 52.381 0.00 0.00 0.00 4.63
275 291 2.158971 GGAGCATCTCTTTCTCCACTCC 60.159 54.545 2.88 0.00 44.38 3.85
276 292 2.481104 CGGAGCATCTCTTTCTCCACTC 60.481 54.545 8.08 0.00 45.04 3.51
277 293 1.480137 CGGAGCATCTCTTTCTCCACT 59.520 52.381 8.08 0.00 45.04 4.00
278 294 1.205893 ACGGAGCATCTCTTTCTCCAC 59.794 52.381 8.08 0.00 45.04 4.02
279 295 1.561643 ACGGAGCATCTCTTTCTCCA 58.438 50.000 8.08 0.00 45.04 3.86
280 296 2.952978 TCTACGGAGCATCTCTTTCTCC 59.047 50.000 0.00 0.00 42.19 3.71
281 297 4.846779 ATCTACGGAGCATCTCTTTCTC 57.153 45.455 0.00 0.00 33.73 2.87
282 298 4.892934 AGAATCTACGGAGCATCTCTTTCT 59.107 41.667 0.00 0.00 33.73 2.52
283 299 5.195001 AGAATCTACGGAGCATCTCTTTC 57.805 43.478 0.00 0.00 33.73 2.62
284 300 5.105146 ACAAGAATCTACGGAGCATCTCTTT 60.105 40.000 2.91 0.00 33.73 2.52
285 301 4.404073 ACAAGAATCTACGGAGCATCTCTT 59.596 41.667 2.91 0.00 33.73 2.85
286 302 3.957497 ACAAGAATCTACGGAGCATCTCT 59.043 43.478 2.91 0.00 33.73 3.10
287 303 4.314740 ACAAGAATCTACGGAGCATCTC 57.685 45.455 2.91 0.00 33.73 2.75
288 304 6.412362 AATACAAGAATCTACGGAGCATCT 57.588 37.500 0.00 0.00 33.73 2.90
289 305 6.926272 AGAAATACAAGAATCTACGGAGCATC 59.074 38.462 0.00 0.00 0.00 3.91
290 306 6.821388 AGAAATACAAGAATCTACGGAGCAT 58.179 36.000 0.00 0.00 0.00 3.79
291 307 6.222038 AGAAATACAAGAATCTACGGAGCA 57.778 37.500 0.00 0.00 0.00 4.26
292 308 6.018669 CCAAGAAATACAAGAATCTACGGAGC 60.019 42.308 0.00 0.00 0.00 4.70
293 309 7.265673 TCCAAGAAATACAAGAATCTACGGAG 58.734 38.462 0.00 0.00 0.00 4.63
294 310 7.177832 TCCAAGAAATACAAGAATCTACGGA 57.822 36.000 0.00 0.00 0.00 4.69
295 311 6.018669 GCTCCAAGAAATACAAGAATCTACGG 60.019 42.308 0.00 0.00 0.00 4.02
296 312 6.291849 CGCTCCAAGAAATACAAGAATCTACG 60.292 42.308 0.00 0.00 0.00 3.51
297 313 6.018669 CCGCTCCAAGAAATACAAGAATCTAC 60.019 42.308 0.00 0.00 0.00 2.59
298 314 6.049149 CCGCTCCAAGAAATACAAGAATCTA 58.951 40.000 0.00 0.00 0.00 1.98
299 315 4.878397 CCGCTCCAAGAAATACAAGAATCT 59.122 41.667 0.00 0.00 0.00 2.40
300 316 4.636206 ACCGCTCCAAGAAATACAAGAATC 59.364 41.667 0.00 0.00 0.00 2.52
301 317 4.396166 CACCGCTCCAAGAAATACAAGAAT 59.604 41.667 0.00 0.00 0.00 2.40
302 318 3.751175 CACCGCTCCAAGAAATACAAGAA 59.249 43.478 0.00 0.00 0.00 2.52
303 319 3.334691 CACCGCTCCAAGAAATACAAGA 58.665 45.455 0.00 0.00 0.00 3.02
304 320 2.420022 CCACCGCTCCAAGAAATACAAG 59.580 50.000 0.00 0.00 0.00 3.16
305 321 2.039216 TCCACCGCTCCAAGAAATACAA 59.961 45.455 0.00 0.00 0.00 2.41
306 322 1.626321 TCCACCGCTCCAAGAAATACA 59.374 47.619 0.00 0.00 0.00 2.29
307 323 2.396590 TCCACCGCTCCAAGAAATAC 57.603 50.000 0.00 0.00 0.00 1.89
308 324 3.054728 TCAATCCACCGCTCCAAGAAATA 60.055 43.478 0.00 0.00 0.00 1.40
309 325 2.094675 CAATCCACCGCTCCAAGAAAT 58.905 47.619 0.00 0.00 0.00 2.17
310 326 1.073125 TCAATCCACCGCTCCAAGAAA 59.927 47.619 0.00 0.00 0.00 2.52
311 327 0.690192 TCAATCCACCGCTCCAAGAA 59.310 50.000 0.00 0.00 0.00 2.52
312 328 0.036388 GTCAATCCACCGCTCCAAGA 60.036 55.000 0.00 0.00 0.00 3.02
313 329 1.361668 CGTCAATCCACCGCTCCAAG 61.362 60.000 0.00 0.00 0.00 3.61
314 330 1.375396 CGTCAATCCACCGCTCCAA 60.375 57.895 0.00 0.00 0.00 3.53
315 331 1.822114 TTCGTCAATCCACCGCTCCA 61.822 55.000 0.00 0.00 0.00 3.86
316 332 1.079405 TTCGTCAATCCACCGCTCC 60.079 57.895 0.00 0.00 0.00 4.70
317 333 0.669318 TGTTCGTCAATCCACCGCTC 60.669 55.000 0.00 0.00 0.00 5.03
318 334 0.670546 CTGTTCGTCAATCCACCGCT 60.671 55.000 0.00 0.00 0.00 5.52
319 335 1.635663 CCTGTTCGTCAATCCACCGC 61.636 60.000 0.00 0.00 0.00 5.68
320 336 1.635663 GCCTGTTCGTCAATCCACCG 61.636 60.000 0.00 0.00 0.00 4.94
321 337 1.305930 GGCCTGTTCGTCAATCCACC 61.306 60.000 0.00 0.00 0.00 4.61
322 338 0.321653 AGGCCTGTTCGTCAATCCAC 60.322 55.000 3.11 0.00 0.00 4.02
323 339 0.036388 GAGGCCTGTTCGTCAATCCA 60.036 55.000 12.00 0.00 0.00 3.41
324 340 0.250513 AGAGGCCTGTTCGTCAATCC 59.749 55.000 12.00 0.00 0.00 3.01
325 341 2.166664 ACTAGAGGCCTGTTCGTCAATC 59.833 50.000 12.00 0.00 0.00 2.67
326 342 2.180276 ACTAGAGGCCTGTTCGTCAAT 58.820 47.619 12.00 0.00 0.00 2.57
327 343 1.629043 ACTAGAGGCCTGTTCGTCAA 58.371 50.000 12.00 0.00 0.00 3.18
328 344 2.502142 TACTAGAGGCCTGTTCGTCA 57.498 50.000 12.00 0.00 0.00 4.35
329 345 3.215975 AGATACTAGAGGCCTGTTCGTC 58.784 50.000 12.00 2.88 0.00 4.20
330 346 3.215975 GAGATACTAGAGGCCTGTTCGT 58.784 50.000 12.00 10.06 0.00 3.85
331 347 2.224549 CGAGATACTAGAGGCCTGTTCG 59.775 54.545 12.00 7.64 0.00 3.95
332 348 2.030628 GCGAGATACTAGAGGCCTGTTC 60.031 54.545 12.00 0.00 0.00 3.18
333 349 1.957877 GCGAGATACTAGAGGCCTGTT 59.042 52.381 12.00 0.00 0.00 3.16
334 350 1.144093 AGCGAGATACTAGAGGCCTGT 59.856 52.381 12.00 9.69 0.00 4.00
335 351 1.810151 GAGCGAGATACTAGAGGCCTG 59.190 57.143 12.00 0.00 0.00 4.85
336 352 1.609580 CGAGCGAGATACTAGAGGCCT 60.610 57.143 3.86 3.86 0.00 5.19
337 353 0.800012 CGAGCGAGATACTAGAGGCC 59.200 60.000 0.00 0.00 0.00 5.19
338 354 1.798283 TCGAGCGAGATACTAGAGGC 58.202 55.000 0.00 0.00 0.00 4.70
339 355 2.933906 GGATCGAGCGAGATACTAGAGG 59.066 54.545 0.00 0.00 0.00 3.69
340 356 3.591023 TGGATCGAGCGAGATACTAGAG 58.409 50.000 0.00 0.00 32.71 2.43
372 388 1.305930 AATTCGCCTTCCTTGTCGGC 61.306 55.000 0.00 0.00 40.40 5.54
381 397 2.927553 ACATGCAGAAATTCGCCTTC 57.072 45.000 0.00 0.00 0.00 3.46
433 1781 9.076643 GATCGACGTGATAAGCATATGCTCATC 62.077 44.444 27.62 27.62 44.17 2.92
471 1819 1.449726 TACGTCTGCACACTGTCGGT 61.450 55.000 0.00 0.00 32.32 4.69
476 4158 1.409412 GTGACTACGTCTGCACACTG 58.591 55.000 0.00 0.00 33.15 3.66
538 4224 1.982395 TCTCCGGCCACTGTACCAG 60.982 63.158 2.24 0.00 37.52 4.00
583 5250 3.654912 GCATTTCGCGATCATTTTACGAG 59.345 43.478 10.88 0.00 33.84 4.18
587 5254 4.350346 CCTTGCATTTCGCGATCATTTTA 58.650 39.130 10.88 0.00 46.97 1.52
614 5296 1.464997 CAGCAAAGAGTTTCTACGGGC 59.535 52.381 0.00 0.00 0.00 6.13
618 5300 4.820284 ACTTGCAGCAAAGAGTTTCTAC 57.180 40.909 9.65 0.00 0.00 2.59
619 5301 4.881273 TGAACTTGCAGCAAAGAGTTTCTA 59.119 37.500 9.65 0.00 32.85 2.10
620 5302 3.696051 TGAACTTGCAGCAAAGAGTTTCT 59.304 39.130 9.65 0.00 32.85 2.52
621 5303 4.032703 TGAACTTGCAGCAAAGAGTTTC 57.967 40.909 9.65 7.53 32.85 2.78
622 5304 4.158394 TCTTGAACTTGCAGCAAAGAGTTT 59.842 37.500 9.65 0.00 32.85 2.66
970 5784 4.209538 TGGATCGGAAGTTCGGAACTATA 58.790 43.478 22.67 9.71 41.91 1.31
972 5786 2.426024 CTGGATCGGAAGTTCGGAACTA 59.574 50.000 22.67 8.55 41.91 2.24
973 5787 1.204941 CTGGATCGGAAGTTCGGAACT 59.795 52.381 17.38 17.38 45.46 3.01
974 5788 1.067071 ACTGGATCGGAAGTTCGGAAC 60.067 52.381 16.07 12.91 29.49 3.62
975 5789 1.263356 ACTGGATCGGAAGTTCGGAA 58.737 50.000 16.07 0.90 29.49 4.30
976 5790 1.067142 CAACTGGATCGGAAGTTCGGA 60.067 52.381 14.68 14.68 34.41 4.55
977 5791 1.359848 CAACTGGATCGGAAGTTCGG 58.640 55.000 4.11 4.11 34.41 4.30
978 5792 1.067142 TCCAACTGGATCGGAAGTTCG 60.067 52.381 0.00 0.20 39.78 3.95
979 5793 2.233922 TCTCCAACTGGATCGGAAGTTC 59.766 50.000 0.00 0.00 44.46 3.01
980 5794 2.257207 TCTCCAACTGGATCGGAAGTT 58.743 47.619 0.00 2.23 44.46 2.66
981 5795 1.938585 TCTCCAACTGGATCGGAAGT 58.061 50.000 0.00 0.00 44.46 3.01
982 5796 2.169352 ACATCTCCAACTGGATCGGAAG 59.831 50.000 0.00 0.00 44.46 3.46
1258 6075 6.152323 CCTTGATTGATGAATCAGTTCCAAGT 59.848 38.462 7.66 0.00 46.83 3.16
1288 6108 1.967779 CAAGGATCCGGTTGGGTTTTT 59.032 47.619 5.98 0.00 37.00 1.94
1355 6192 5.048154 TGAGAAGTGACTGAGTTGAGATCTG 60.048 44.000 0.00 0.00 0.00 2.90
1607 8249 5.125367 TGGTCACAGCTAAGGACTAGATA 57.875 43.478 0.00 0.00 0.00 1.98
1624 8268 2.754552 GCCTGCTTCAATAACATGGTCA 59.245 45.455 0.00 0.00 0.00 4.02
1643 8287 6.779115 TCGTTACACATACATAATCATGCC 57.221 37.500 0.00 0.00 35.39 4.40
1660 8313 5.178809 ACCAAGTGCTAACAATCTTCGTTAC 59.821 40.000 0.00 0.00 0.00 2.50
1692 8368 9.542462 ACCTAATATTATGTACACACACATGTC 57.458 33.333 0.00 0.00 39.46 3.06
1768 8520 9.257651 GGGATTAGTAATACTGTACACAATGAC 57.742 37.037 2.68 0.00 0.00 3.06
1789 8541 8.929487 TGTTTACTTCAAAACTTATTGGGGATT 58.071 29.630 1.67 0.00 39.57 3.01
1921 8692 9.807921 AGGGATCGATAATGGTAAATTGTAAAT 57.192 29.630 0.00 0.00 0.00 1.40
1959 8940 4.792521 AATCATACTCGCATCTACTCCC 57.207 45.455 0.00 0.00 0.00 4.30
1979 8968 6.179756 ACACAAGTTATCAGATGCCACATAA 58.820 36.000 0.00 0.00 0.00 1.90
2231 16148 7.571983 GCATCTTCGGAAAATATACTCCACATG 60.572 40.741 0.00 0.00 0.00 3.21
2242 16159 5.739752 CAGTCATGCATCTTCGGAAAATA 57.260 39.130 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.