Multiple sequence alignment - TraesCS3A01G469900

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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 TraesCS3A01G469900 chr3A 100.000 2603 0 0 1 2603 702150595 702147993 0.000000e+00 4807
1 TraesCS3A01G469900 chr3A 98.050 1333 22 4 1274 2603 702115597 702114266 0.000000e+00 2314
2 TraesCS3A01G469900 chr3A 88.317 1883 153 34 744 2603 702380829 702378991 0.000000e+00 2196
3 TraesCS3A01G469900 chr3A 87.211 1900 162 34 744 2603 702329526 702327668 0.000000e+00 2087
4 TraesCS3A01G469900 chr3A 97.625 800 19 0 434 1233 702116389 702115590 0.000000e+00 1373
5 TraesCS3A01G469900 chr3A 93.824 842 42 6 744 1582 702383496 702382662 0.000000e+00 1258
6 TraesCS3A01G469900 chr3A 93.824 842 42 6 744 1582 702401124 702400290 0.000000e+00 1258
7 TraesCS3A01G469900 chr3A 80.798 526 79 18 1428 1947 702059356 702058847 2.430000e-105 392
8 TraesCS3A01G469900 chr3A 92.157 102 1 4 511 605 702322766 702322665 1.260000e-28 137
9 TraesCS3A01G469900 chr3A 97.674 43 1 0 102 144 702329795 702329753 9.990000e-10 75
10 TraesCS3A01G469900 chr3D 95.108 2167 72 23 450 2603 566889894 566892039 0.000000e+00 3384
11 TraesCS3A01G469900 chr3D 96.537 231 7 1 1 231 566889483 566889712 5.260000e-102 381
12 TraesCS3A01G469900 chrUn 93.432 2162 112 17 453 2596 268821498 268819349 0.000000e+00 3179
13 TraesCS3A01G469900 chrUn 93.432 2162 112 17 453 2596 268830193 268832342 0.000000e+00 3179
14 TraesCS3A01G469900 chrUn 87.513 1898 152 40 730 2603 312095585 312097421 0.000000e+00 2113
15 TraesCS3A01G469900 chrUn 93.724 239 7 4 1 233 268821893 268821657 4.120000e-93 351
16 TraesCS3A01G469900 chrUn 93.724 239 7 4 1 233 268829798 268830034 4.120000e-93 351
17 TraesCS3A01G469900 chr7B 85.876 177 23 2 252 427 687184949 687185124 1.230000e-43 187
18 TraesCS3A01G469900 chr4A 86.310 168 21 2 262 428 698655788 698655954 5.720000e-42 182
19 TraesCS3A01G469900 chr7D 84.348 115 16 1 317 431 594850622 594850734 7.610000e-21 111


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 TraesCS3A01G469900 chr3A 702147993 702150595 2602 True 4807.0 4807 100.0000 1 2603 1 chr3A.!!$R2 2602
1 TraesCS3A01G469900 chr3A 702114266 702116389 2123 True 1843.5 2314 97.8375 434 2603 2 chr3A.!!$R5 2169
2 TraesCS3A01G469900 chr3A 702378991 702383496 4505 True 1727.0 2196 91.0705 744 2603 2 chr3A.!!$R7 1859
3 TraesCS3A01G469900 chr3A 702400290 702401124 834 True 1258.0 1258 93.8240 744 1582 1 chr3A.!!$R4 838
4 TraesCS3A01G469900 chr3A 702327668 702329795 2127 True 1081.0 2087 92.4425 102 2603 2 chr3A.!!$R6 2501
5 TraesCS3A01G469900 chr3A 702058847 702059356 509 True 392.0 392 80.7980 1428 1947 1 chr3A.!!$R1 519
6 TraesCS3A01G469900 chr3D 566889483 566892039 2556 False 1882.5 3384 95.8225 1 2603 2 chr3D.!!$F1 2602
7 TraesCS3A01G469900 chrUn 312095585 312097421 1836 False 2113.0 2113 87.5130 730 2603 1 chrUn.!!$F1 1873
8 TraesCS3A01G469900 chrUn 268819349 268821893 2544 True 1765.0 3179 93.5780 1 2596 2 chrUn.!!$R1 2595
9 TraesCS3A01G469900 chrUn 268829798 268832342 2544 False 1765.0 3179 93.5780 1 2596 2 chrUn.!!$F2 2595

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
354 360 0.036306 GGTTCCACCAGATGAACGGT 59.964 55.0 0.00 0.00 41.36 4.83 F
357 363 1.348064 TCCACCAGATGAACGGTTCT 58.652 50.0 20.53 7.38 31.41 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1180 3920 2.792878 ACCACTACTAGAACTCACGCT 58.207 47.619 0.0 0.0 0.0 5.07 R
2180 4943 7.775053 AAAAGAAAATTAGACCATGCACCTA 57.225 32.000 0.0 0.0 0.0 3.08 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
209 215 3.930229 CACGTGGTTTTGGATCGATCTTA 59.070 43.478 23.96 11.52 0.00 2.10
233 239 4.708421 CCATCCCACTTGAACTTGATCATT 59.292 41.667 0.00 0.00 0.00 2.57
235 241 6.377996 CCATCCCACTTGAACTTGATCATTTA 59.622 38.462 0.00 0.00 0.00 1.40
236 242 7.069085 CCATCCCACTTGAACTTGATCATTTAT 59.931 37.037 0.00 0.00 0.00 1.40
238 244 8.421249 TCCCACTTGAACTTGATCATTTATTT 57.579 30.769 0.00 0.00 0.00 1.40
239 245 8.869109 TCCCACTTGAACTTGATCATTTATTTT 58.131 29.630 0.00 0.00 0.00 1.82
291 297 6.974932 TTCTGTTGAAGAGATAGACATTGC 57.025 37.500 0.00 0.00 35.91 3.56
292 298 6.291648 TCTGTTGAAGAGATAGACATTGCT 57.708 37.500 0.00 0.00 0.00 3.91
293 299 6.705302 TCTGTTGAAGAGATAGACATTGCTT 58.295 36.000 0.00 0.00 0.00 3.91
294 300 7.164122 TCTGTTGAAGAGATAGACATTGCTTT 58.836 34.615 0.00 0.00 0.00 3.51
296 302 8.846943 TGTTGAAGAGATAGACATTGCTTTAA 57.153 30.769 0.00 0.00 0.00 1.52
303 309 7.657761 AGAGATAGACATTGCTTTAATTACGGG 59.342 37.037 0.00 0.00 0.00 5.28
304 310 7.506114 AGATAGACATTGCTTTAATTACGGGA 58.494 34.615 0.00 0.00 0.00 5.14
305 311 7.657761 AGATAGACATTGCTTTAATTACGGGAG 59.342 37.037 0.00 0.00 0.00 4.30
306 312 4.881850 AGACATTGCTTTAATTACGGGAGG 59.118 41.667 0.00 0.00 0.00 4.30
307 313 4.850680 ACATTGCTTTAATTACGGGAGGA 58.149 39.130 0.00 0.00 0.00 3.71
308 314 4.638865 ACATTGCTTTAATTACGGGAGGAC 59.361 41.667 0.00 0.00 0.00 3.85
309 315 3.985019 TGCTTTAATTACGGGAGGACA 57.015 42.857 0.00 0.00 0.00 4.02
310 316 4.497291 TGCTTTAATTACGGGAGGACAT 57.503 40.909 0.00 0.00 0.00 3.06
312 318 4.196971 GCTTTAATTACGGGAGGACATGT 58.803 43.478 0.00 0.00 0.00 3.21
314 320 5.423704 TTTAATTACGGGAGGACATGTCA 57.576 39.130 26.47 4.44 0.00 3.58
315 321 3.543680 AATTACGGGAGGACATGTCAG 57.456 47.619 26.47 13.91 0.00 3.51
316 322 2.225382 TTACGGGAGGACATGTCAGA 57.775 50.000 26.47 1.29 0.00 3.27
317 323 2.454336 TACGGGAGGACATGTCAGAT 57.546 50.000 26.47 12.26 0.00 2.90
318 324 1.115467 ACGGGAGGACATGTCAGATC 58.885 55.000 26.47 19.27 0.00 2.75
319 325 1.342474 ACGGGAGGACATGTCAGATCT 60.342 52.381 26.47 14.45 0.00 2.75
320 326 2.091830 ACGGGAGGACATGTCAGATCTA 60.092 50.000 26.47 0.00 0.00 1.98
322 328 3.300388 GGGAGGACATGTCAGATCTACA 58.700 50.000 26.47 1.13 0.00 2.74
323 329 3.068873 GGGAGGACATGTCAGATCTACAC 59.931 52.174 26.47 6.52 0.00 2.90
324 330 3.068873 GGAGGACATGTCAGATCTACACC 59.931 52.174 26.47 11.60 0.00 4.16
325 331 2.690497 AGGACATGTCAGATCTACACCG 59.310 50.000 26.47 0.00 0.00 4.94
327 333 3.630769 GGACATGTCAGATCTACACCGTA 59.369 47.826 26.47 0.00 0.00 4.02
328 334 4.097437 GGACATGTCAGATCTACACCGTAA 59.903 45.833 26.47 0.00 0.00 3.18
329 335 5.221263 GGACATGTCAGATCTACACCGTAAT 60.221 44.000 26.47 0.00 0.00 1.89
330 336 6.016527 GGACATGTCAGATCTACACCGTAATA 60.017 42.308 26.47 0.00 0.00 0.98
332 338 7.201145 ACATGTCAGATCTACACCGTAATAAC 58.799 38.462 0.00 0.00 0.00 1.89
333 339 7.068348 ACATGTCAGATCTACACCGTAATAACT 59.932 37.037 0.00 0.00 0.00 2.24
334 340 7.024340 TGTCAGATCTACACCGTAATAACTC 57.976 40.000 0.00 0.00 0.00 3.01
343 349 2.543641 CCGTAATAACTCGGTTCCACC 58.456 52.381 0.00 0.00 41.58 4.61
345 351 3.184541 CGTAATAACTCGGTTCCACCAG 58.815 50.000 0.00 0.00 38.47 4.00
346 352 3.119388 CGTAATAACTCGGTTCCACCAGA 60.119 47.826 0.00 0.00 38.47 3.86
347 353 4.441079 CGTAATAACTCGGTTCCACCAGAT 60.441 45.833 0.00 0.00 38.47 2.90
348 354 3.543680 ATAACTCGGTTCCACCAGATG 57.456 47.619 0.00 0.00 38.47 2.90
349 355 1.348064 AACTCGGTTCCACCAGATGA 58.652 50.000 0.00 0.00 38.47 2.92
350 356 1.348064 ACTCGGTTCCACCAGATGAA 58.652 50.000 0.00 0.00 38.47 2.57
351 357 1.002087 ACTCGGTTCCACCAGATGAAC 59.998 52.381 0.00 0.00 38.47 3.18
352 358 0.037697 TCGGTTCCACCAGATGAACG 60.038 55.000 0.00 0.00 41.36 3.95
353 359 1.019278 CGGTTCCACCAGATGAACGG 61.019 60.000 0.00 0.00 41.36 4.44
354 360 0.036306 GGTTCCACCAGATGAACGGT 59.964 55.000 0.00 0.00 41.36 4.83
355 361 1.544759 GGTTCCACCAGATGAACGGTT 60.545 52.381 0.00 0.00 41.36 4.44
357 363 1.348064 TCCACCAGATGAACGGTTCT 58.652 50.000 20.53 7.38 31.41 3.01
359 365 2.901192 TCCACCAGATGAACGGTTCTTA 59.099 45.455 20.53 3.01 31.41 2.10
360 366 3.325425 TCCACCAGATGAACGGTTCTTAA 59.675 43.478 20.53 2.29 31.41 1.85
363 369 5.183140 CCACCAGATGAACGGTTCTTAATTT 59.817 40.000 20.53 0.36 31.41 1.82
393 438 8.810652 TTAACACAATAATTTCTGGAAAGTGC 57.189 30.769 6.33 0.00 33.32 4.40
394 439 5.783111 ACACAATAATTTCTGGAAAGTGCC 58.217 37.500 6.33 0.00 33.32 5.01
395 440 5.539955 ACACAATAATTTCTGGAAAGTGCCT 59.460 36.000 6.33 0.00 33.32 4.75
396 441 6.719370 ACACAATAATTTCTGGAAAGTGCCTA 59.281 34.615 6.33 0.00 33.32 3.93
397 442 7.232534 ACACAATAATTTCTGGAAAGTGCCTAA 59.767 33.333 6.33 0.00 33.32 2.69
398 443 8.253113 CACAATAATTTCTGGAAAGTGCCTAAT 58.747 33.333 6.33 0.00 33.32 1.73
399 444 8.815912 ACAATAATTTCTGGAAAGTGCCTAATT 58.184 29.630 6.33 0.00 33.32 1.40
402 447 9.700831 ATAATTTCTGGAAAGTGCCTAATTAGT 57.299 29.630 11.50 0.00 33.32 2.24
404 449 9.700831 AATTTCTGGAAAGTGCCTAATTAGTAT 57.299 29.630 11.50 0.00 33.32 2.12
406 451 9.832445 TTTCTGGAAAGTGCCTAATTAGTATAG 57.168 33.333 11.50 0.00 0.00 1.31
407 452 7.963532 TCTGGAAAGTGCCTAATTAGTATAGG 58.036 38.462 11.50 0.00 42.41 2.57
408 453 7.567622 TCTGGAAAGTGCCTAATTAGTATAGGT 59.432 37.037 11.50 0.00 41.70 3.08
409 454 8.786710 TGGAAAGTGCCTAATTAGTATAGGTA 57.213 34.615 11.50 0.00 41.70 3.08
410 455 9.388672 TGGAAAGTGCCTAATTAGTATAGGTAT 57.611 33.333 11.50 0.00 41.70 2.73
728 779 3.683847 GCCTGGAGCTAGATGTGTTCATT 60.684 47.826 0.00 0.00 38.99 2.57
913 3652 2.364579 CCCCCAACATGCATGGCT 60.365 61.111 29.41 14.20 36.58 4.75
1230 3970 2.203938 GGTGGAGGTGGAGGTGGA 60.204 66.667 0.00 0.00 0.00 4.02
1231 3971 2.294078 GGTGGAGGTGGAGGTGGAG 61.294 68.421 0.00 0.00 0.00 3.86
1232 3972 2.122729 TGGAGGTGGAGGTGGAGG 59.877 66.667 0.00 0.00 0.00 4.30
1233 3973 2.122954 GGAGGTGGAGGTGGAGGT 59.877 66.667 0.00 0.00 0.00 3.85
1234 3974 2.294078 GGAGGTGGAGGTGGAGGTG 61.294 68.421 0.00 0.00 0.00 4.00
1235 3975 2.203998 AGGTGGAGGTGGAGGTGG 60.204 66.667 0.00 0.00 0.00 4.61
2180 4943 0.762418 TGAAGTCACGAATGGTGGGT 59.238 50.000 0.00 0.00 46.96 4.51
2333 5100 8.449251 AATTGTTATTCCAATGTTGTGCTTTT 57.551 26.923 0.00 0.00 35.30 2.27
2336 5111 8.948631 TGTTATTCCAATGTTGTGCTTTTAAA 57.051 26.923 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 3.543680 ACCGTGATACATAGCTGCTTT 57.456 42.857 7.79 0.00 0.00 3.51
129 130 4.766891 CCATATTATTTGATGCCCGGACTT 59.233 41.667 0.73 0.00 0.00 3.01
209 215 3.074390 TGATCAAGTTCAAGTGGGATGGT 59.926 43.478 0.00 0.00 0.00 3.55
265 271 9.102757 GCAATGTCTATCTCTTCAACAGAATAA 57.897 33.333 0.00 0.00 0.00 1.40
266 272 8.481314 AGCAATGTCTATCTCTTCAACAGAATA 58.519 33.333 0.00 0.00 0.00 1.75
267 273 7.337167 AGCAATGTCTATCTCTTCAACAGAAT 58.663 34.615 0.00 0.00 0.00 2.40
268 274 6.705302 AGCAATGTCTATCTCTTCAACAGAA 58.295 36.000 0.00 0.00 0.00 3.02
269 275 6.291648 AGCAATGTCTATCTCTTCAACAGA 57.708 37.500 0.00 0.00 0.00 3.41
270 276 6.981762 AAGCAATGTCTATCTCTTCAACAG 57.018 37.500 0.00 0.00 0.00 3.16
271 277 8.846943 TTAAAGCAATGTCTATCTCTTCAACA 57.153 30.769 0.00 0.00 0.00 3.33
276 282 9.046296 CCGTAATTAAAGCAATGTCTATCTCTT 57.954 33.333 0.00 0.00 0.00 2.85
277 283 7.657761 CCCGTAATTAAAGCAATGTCTATCTCT 59.342 37.037 0.00 0.00 0.00 3.10
278 284 7.656137 TCCCGTAATTAAAGCAATGTCTATCTC 59.344 37.037 0.00 0.00 0.00 2.75
279 285 7.506114 TCCCGTAATTAAAGCAATGTCTATCT 58.494 34.615 0.00 0.00 0.00 1.98
280 286 7.095187 CCTCCCGTAATTAAAGCAATGTCTATC 60.095 40.741 0.00 0.00 0.00 2.08
281 287 6.710744 CCTCCCGTAATTAAAGCAATGTCTAT 59.289 38.462 0.00 0.00 0.00 1.98
282 288 6.053005 CCTCCCGTAATTAAAGCAATGTCTA 58.947 40.000 0.00 0.00 0.00 2.59
283 289 4.881850 CCTCCCGTAATTAAAGCAATGTCT 59.118 41.667 0.00 0.00 0.00 3.41
284 290 4.879545 TCCTCCCGTAATTAAAGCAATGTC 59.120 41.667 0.00 0.00 0.00 3.06
289 295 3.985019 TGTCCTCCCGTAATTAAAGCA 57.015 42.857 0.00 0.00 0.00 3.91
291 297 5.424757 TGACATGTCCTCCCGTAATTAAAG 58.575 41.667 22.85 0.00 0.00 1.85
292 298 5.188163 TCTGACATGTCCTCCCGTAATTAAA 59.812 40.000 22.85 0.00 0.00 1.52
293 299 4.712829 TCTGACATGTCCTCCCGTAATTAA 59.287 41.667 22.85 0.00 0.00 1.40
294 300 4.283337 TCTGACATGTCCTCCCGTAATTA 58.717 43.478 22.85 0.00 0.00 1.40
296 302 2.747177 TCTGACATGTCCTCCCGTAAT 58.253 47.619 22.85 0.00 0.00 1.89
298 304 2.091830 AGATCTGACATGTCCTCCCGTA 60.092 50.000 22.85 1.47 0.00 4.02
299 305 1.115467 GATCTGACATGTCCTCCCGT 58.885 55.000 22.85 3.43 0.00 5.28
300 306 1.407936 AGATCTGACATGTCCTCCCG 58.592 55.000 22.85 6.62 0.00 5.14
301 307 3.068873 GTGTAGATCTGACATGTCCTCCC 59.931 52.174 22.85 9.86 0.00 4.30
303 309 3.243234 CGGTGTAGATCTGACATGTCCTC 60.243 52.174 22.85 15.85 0.00 3.71
304 310 2.690497 CGGTGTAGATCTGACATGTCCT 59.310 50.000 22.85 14.41 0.00 3.85
305 311 2.427453 ACGGTGTAGATCTGACATGTCC 59.573 50.000 22.85 7.53 0.00 4.02
306 312 3.784701 ACGGTGTAGATCTGACATGTC 57.215 47.619 19.27 19.27 0.00 3.06
307 313 5.854010 ATTACGGTGTAGATCTGACATGT 57.146 39.130 5.18 0.00 0.00 3.21
308 314 7.426410 AGTTATTACGGTGTAGATCTGACATG 58.574 38.462 5.18 5.92 0.00 3.21
309 315 7.520131 CGAGTTATTACGGTGTAGATCTGACAT 60.520 40.741 5.18 0.00 0.00 3.06
310 316 6.238293 CGAGTTATTACGGTGTAGATCTGACA 60.238 42.308 5.18 3.31 0.00 3.58
312 318 5.237996 CCGAGTTATTACGGTGTAGATCTGA 59.762 44.000 5.18 0.00 43.53 3.27
314 320 5.686159 CCGAGTTATTACGGTGTAGATCT 57.314 43.478 0.00 0.00 43.53 2.75
336 342 1.804748 GAACCGTTCATCTGGTGGAAC 59.195 52.381 6.38 0.00 38.82 3.62
337 343 1.697432 AGAACCGTTCATCTGGTGGAA 59.303 47.619 13.69 0.00 38.82 3.53
338 344 1.348064 AGAACCGTTCATCTGGTGGA 58.652 50.000 13.69 0.00 38.82 4.02
339 345 2.185004 AAGAACCGTTCATCTGGTGG 57.815 50.000 13.69 0.00 38.82 4.61
340 346 5.880054 AATTAAGAACCGTTCATCTGGTG 57.120 39.130 13.69 0.00 38.82 4.17
373 418 7.775053 TTAGGCACTTTCCAGAAATTATTGT 57.225 32.000 0.00 0.00 41.75 2.71
376 421 9.700831 ACTAATTAGGCACTTTCCAGAAATTAT 57.299 29.630 16.73 0.00 41.75 1.28
378 423 9.700831 ATACTAATTAGGCACTTTCCAGAAATT 57.299 29.630 16.73 0.00 41.75 1.82
380 425 9.832445 CTATACTAATTAGGCACTTTCCAGAAA 57.168 33.333 16.73 0.00 41.75 2.52
381 426 8.429641 CCTATACTAATTAGGCACTTTCCAGAA 58.570 37.037 16.73 0.00 41.75 3.02
382 427 7.567622 ACCTATACTAATTAGGCACTTTCCAGA 59.432 37.037 16.73 0.00 41.75 3.86
383 428 7.736893 ACCTATACTAATTAGGCACTTTCCAG 58.263 38.462 16.73 1.42 41.75 3.86
384 429 7.685849 ACCTATACTAATTAGGCACTTTCCA 57.314 36.000 16.73 0.00 41.75 3.53
431 476 9.810870 TGCATGCATCTATCTATCTATCTATCT 57.189 33.333 18.46 0.00 0.00 1.98
913 3652 6.508030 TGGATATTTATAGTGGTGCTTCCA 57.492 37.500 0.00 0.00 45.01 3.53
1180 3920 2.792878 ACCACTACTAGAACTCACGCT 58.207 47.619 0.00 0.00 0.00 5.07
2180 4943 7.775053 AAAAGAAAATTAGACCATGCACCTA 57.225 32.000 0.00 0.00 0.00 3.08
2242 5006 7.824779 AGCTAACTTTCTAATCTAACAAGTGGG 59.175 37.037 0.00 0.00 0.00 4.61
2448 5235 2.525055 CACAACTGTCAAAAACCGTGG 58.475 47.619 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.