Multiple sequence alignment - TraesCS5B01G258500

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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 TraesCS5B01G258500 chr5B 100.000 2672 0 0 1 2672 440562810 440560139 0.000000e+00 4935.0
1 TraesCS5B01G258500 chr5B 99.775 2672 6 0 1 2672 440552001 440549330 0.000000e+00 4902.0
2 TraesCS5B01G258500 chr5B 79.717 424 59 14 1192 1594 441407943 441408360 5.630000e-72 281.0
3 TraesCS5B01G258500 chr5B 78.824 425 73 10 1892 2313 304333323 304332913 1.220000e-68 270.0
4 TraesCS5B01G258500 chr5B 77.386 482 63 26 676 1127 441407317 441407782 7.390000e-61 244.0
5 TraesCS5B01G258500 chr5D 95.652 1196 26 6 7 1182 371283795 371282606 0.000000e+00 1897.0
6 TraesCS5B01G258500 chr5D 95.624 1074 40 3 1602 2672 371281096 371280027 0.000000e+00 1716.0
7 TraesCS5B01G258500 chr5D 92.342 666 43 5 1856 2516 371016905 371017567 0.000000e+00 941.0
8 TraesCS5B01G258500 chr5D 90.332 693 33 14 1195 1869 371015087 371015763 0.000000e+00 878.0
9 TraesCS5B01G258500 chr5D 86.496 822 41 21 414 1179 371014151 371014958 0.000000e+00 839.0
10 TraesCS5B01G258500 chr5D 83.478 460 70 6 1870 2326 125962251 125961795 8.840000e-115 424.0
11 TraesCS5B01G258500 chr5D 96.721 122 4 0 2551 2672 371017568 371017689 1.250000e-48 204.0
12 TraesCS5B01G258500 chr5D 87.619 105 10 3 1078 1179 371011183 371011287 4.670000e-23 119.0
13 TraesCS5B01G258500 chrUn 100.000 797 0 0 1876 2672 340767284 340768080 0.000000e+00 1472.0
14 TraesCS5B01G258500 chr5A 85.047 642 55 19 570 1182 474144776 474144147 1.360000e-172 616.0
15 TraesCS5B01G258500 chr5A 85.047 642 55 19 570 1182 474256324 474256953 1.360000e-172 616.0
16 TraesCS5B01G258500 chr5A 84.424 642 59 14 570 1182 473982456 473983085 6.370000e-166 593.0
17 TraesCS5B01G258500 chr5A 91.214 387 33 1 25 411 474145450 474145065 2.360000e-145 525.0
18 TraesCS5B01G258500 chr5A 91.214 387 33 1 25 411 474255650 474256035 2.360000e-145 525.0
19 TraesCS5B01G258500 chr5A 90.956 387 34 1 25 411 473981781 473982166 1.100000e-143 520.0
20 TraesCS5B01G258500 chr5A 84.914 232 9 9 1254 1467 474287466 474287689 7.490000e-51 211.0
21 TraesCS5B01G258500 chr5A 84.483 232 10 9 1254 1467 474021917 474022140 3.490000e-49 206.0
22 TraesCS5B01G258500 chr5A 84.483 232 10 9 1254 1467 474155291 474155514 3.490000e-49 206.0
23 TraesCS5B01G258500 chr6D 83.656 465 60 9 1866 2326 67870855 67871307 8.840000e-115 424.0
24 TraesCS5B01G258500 chr6D 80.477 461 81 6 1872 2326 417460613 417460156 7.080000e-91 344.0
25 TraesCS5B01G258500 chr7B 83.405 464 63 9 1873 2326 680352682 680353141 4.110000e-113 418.0
26 TraesCS5B01G258500 chr2D 82.432 296 46 6 1892 2182 134462507 134462213 1.230000e-63 254.0
27 TraesCS5B01G258500 chr6B 84.962 133 17 2 2196 2326 628901348 628901479 6.000000e-27 132.0
28 TraesCS5B01G258500 chr1A 74.783 345 53 22 622 937 483648860 483648521 1.000000e-24 124.0
29 TraesCS5B01G258500 chr1B 79.870 154 27 4 784 937 514605394 514605245 2.810000e-20 110.0
30 TraesCS5B01G258500 chr2B 82.857 105 9 3 1354 1449 228911704 228911600 4.740000e-13 86.1
31 TraesCS5B01G258500 chr1D 100.000 28 0 0 1357 1384 383722504 383722477 5.000000e-03 52.8


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 TraesCS5B01G258500 chr5B 440560139 440562810 2671 True 4935.0 4935 100.0000 1 2672 1 chr5B.!!$R3 2671
1 TraesCS5B01G258500 chr5B 440549330 440552001 2671 True 4902.0 4902 99.7750 1 2672 1 chr5B.!!$R2 2671
2 TraesCS5B01G258500 chr5B 441407317 441408360 1043 False 262.5 281 78.5515 676 1594 2 chr5B.!!$F1 918
3 TraesCS5B01G258500 chr5D 371280027 371283795 3768 True 1806.5 1897 95.6380 7 2672 2 chr5D.!!$R2 2665
4 TraesCS5B01G258500 chr5D 371011183 371017689 6506 False 596.2 941 90.7020 414 2672 5 chr5D.!!$F1 2258
5 TraesCS5B01G258500 chrUn 340767284 340768080 796 False 1472.0 1472 100.0000 1876 2672 1 chrUn.!!$F1 796
6 TraesCS5B01G258500 chr5A 474144147 474145450 1303 True 570.5 616 88.1305 25 1182 2 chr5A.!!$R1 1157
7 TraesCS5B01G258500 chr5A 474255650 474256953 1303 False 570.5 616 88.1305 25 1182 2 chr5A.!!$F5 1157
8 TraesCS5B01G258500 chr5A 473981781 473983085 1304 False 556.5 593 87.6900 25 1182 2 chr5A.!!$F4 1157

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
360 361 0.107703 ATGATGTCGCCATTGACGGT 60.108 50.0 0.0 0.0 41.87 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1874 6908 4.372656 ACTAGGAGCTCGAATGTAATTGC 58.627 43.478 7.83 0.0 36.07 3.56 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
334 335 1.476891 TCGTCAACATAGAGGCTCACC 59.523 52.381 18.26 0.00 0.00 4.02
337 338 0.537188 CAACATAGAGGCTCACCCGT 59.463 55.000 18.26 5.19 39.21 5.28
338 339 1.754803 CAACATAGAGGCTCACCCGTA 59.245 52.381 18.26 0.00 39.21 4.02
339 340 2.154567 ACATAGAGGCTCACCCGTAA 57.845 50.000 18.26 0.00 39.21 3.18
340 341 2.679082 ACATAGAGGCTCACCCGTAAT 58.321 47.619 18.26 0.00 39.21 1.89
341 342 3.840991 ACATAGAGGCTCACCCGTAATA 58.159 45.455 18.26 0.00 39.21 0.98
342 343 4.417437 ACATAGAGGCTCACCCGTAATAT 58.583 43.478 18.26 0.00 39.21 1.28
345 346 3.511477 AGAGGCTCACCCGTAATATGAT 58.489 45.455 18.26 0.00 39.21 2.45
347 348 2.972713 AGGCTCACCCGTAATATGATGT 59.027 45.455 0.00 0.00 39.21 3.06
349 350 2.987149 GCTCACCCGTAATATGATGTCG 59.013 50.000 0.00 0.00 0.00 4.35
350 351 2.987149 CTCACCCGTAATATGATGTCGC 59.013 50.000 0.00 0.00 0.00 5.19
352 353 1.689813 ACCCGTAATATGATGTCGCCA 59.310 47.619 0.00 0.00 0.00 5.69
353 354 2.301870 ACCCGTAATATGATGTCGCCAT 59.698 45.455 0.00 0.00 0.00 4.40
354 355 3.244422 ACCCGTAATATGATGTCGCCATT 60.244 43.478 0.00 0.00 0.00 3.16
355 356 3.125146 CCCGTAATATGATGTCGCCATTG 59.875 47.826 0.00 0.00 0.00 2.82
358 359 4.432892 CGTAATATGATGTCGCCATTGACG 60.433 45.833 0.00 0.00 41.87 4.35
360 361 0.107703 ATGATGTCGCCATTGACGGT 60.108 50.000 0.00 0.00 41.87 4.83
362 363 1.003839 ATGTCGCCATTGACGGTGT 60.004 52.632 0.00 0.00 41.87 4.16
365 366 3.487202 CGCCATTGACGGTGTCGG 61.487 66.667 0.00 0.00 41.39 4.79
366 367 3.799755 GCCATTGACGGTGTCGGC 61.800 66.667 0.00 0.00 46.45 5.54
396 397 2.822255 GCCGTTGCCGCCTGAATA 60.822 61.111 0.00 0.00 0.00 1.75
397 398 2.403378 GCCGTTGCCGCCTGAATAA 61.403 57.895 0.00 0.00 0.00 1.40
398 399 1.724582 GCCGTTGCCGCCTGAATAAT 61.725 55.000 0.00 0.00 0.00 1.28
400 401 0.732571 CGTTGCCGCCTGAATAATGT 59.267 50.000 0.00 0.00 0.00 2.71
401 402 1.531677 CGTTGCCGCCTGAATAATGTG 60.532 52.381 0.00 0.00 0.00 3.21
402 403 1.742831 GTTGCCGCCTGAATAATGTGA 59.257 47.619 0.00 0.00 0.00 3.58
403 404 2.346766 TGCCGCCTGAATAATGTGAT 57.653 45.000 0.00 0.00 0.00 3.06
404 405 1.948834 TGCCGCCTGAATAATGTGATG 59.051 47.619 0.00 0.00 0.00 3.07
406 407 1.948834 CCGCCTGAATAATGTGATGCA 59.051 47.619 0.00 0.00 0.00 3.96
408 409 2.603892 CGCCTGAATAATGTGATGCAGC 60.604 50.000 0.00 0.00 31.75 5.25
409 410 2.359848 GCCTGAATAATGTGATGCAGCA 59.640 45.455 0.00 0.00 31.75 4.41
410 411 3.550233 GCCTGAATAATGTGATGCAGCAG 60.550 47.826 4.06 0.00 31.75 4.24
847 3512 2.604174 CGCTCGCGGGAACAACTTT 61.604 57.895 12.03 0.00 35.56 2.66
1874 6908 9.586435 GTTTTGATTGTCATTAGATAAAAGGGG 57.414 33.333 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
345 346 1.666553 GACACCGTCAATGGCGACA 60.667 57.895 9.51 0.00 37.33 4.35
349 350 3.799755 GCCGACACCGTCAATGGC 61.800 66.667 0.00 0.00 31.73 4.40
350 351 2.358125 TGCCGACACCGTCAATGG 60.358 61.111 0.00 0.00 32.09 3.16
352 353 2.742372 GCTGCCGACACCGTCAAT 60.742 61.111 0.00 0.00 32.09 2.57
353 354 4.228567 TGCTGCCGACACCGTCAA 62.229 61.111 0.00 0.00 32.09 3.18
354 355 4.662961 CTGCTGCCGACACCGTCA 62.663 66.667 0.00 0.00 32.09 4.35
382 383 1.742831 TCACATTATTCAGGCGGCAAC 59.257 47.619 13.08 0.00 0.00 4.17
383 384 2.121291 TCACATTATTCAGGCGGCAA 57.879 45.000 13.08 0.00 0.00 4.52
384 385 1.948834 CATCACATTATTCAGGCGGCA 59.051 47.619 13.08 0.00 0.00 5.69
386 387 1.948834 TGCATCACATTATTCAGGCGG 59.051 47.619 0.00 0.00 0.00 6.13
387 388 2.603892 GCTGCATCACATTATTCAGGCG 60.604 50.000 0.00 0.00 0.00 5.52
388 389 2.359848 TGCTGCATCACATTATTCAGGC 59.640 45.455 0.00 0.00 0.00 4.85
389 390 3.550233 GCTGCTGCATCACATTATTCAGG 60.550 47.826 11.11 0.00 39.41 3.86
392 393 3.703286 TGCTGCTGCATCACATTATTC 57.297 42.857 14.93 0.00 45.31 1.75
406 407 2.678934 CAATGGGGTGCTGCTGCT 60.679 61.111 17.00 0.00 40.48 4.24
413 414 1.194218 ATACCAAAGCAATGGGGTGC 58.806 50.000 11.91 0.00 45.18 5.01
415 416 1.554617 GCAATACCAAAGCAATGGGGT 59.445 47.619 11.91 2.29 45.18 4.95
416 417 1.554160 TGCAATACCAAAGCAATGGGG 59.446 47.619 11.91 0.00 45.18 4.96
417 418 2.028294 TGTGCAATACCAAAGCAATGGG 60.028 45.455 11.91 0.00 45.18 4.00
1874 6908 4.372656 ACTAGGAGCTCGAATGTAATTGC 58.627 43.478 7.83 0.00 36.07 3.56


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

AutoCloner maintained by Alex Coulton.