Multiple sequence alignment - TraesCS5D01G460000

Loading Multiple Alignment...

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 TraesCS5D01G460000 chr5D 100.000 2548 0 0 1 2548 503742775 503740228 0.000000e+00 4706.0
1 TraesCS5D01G460000 chr5D 83.891 807 106 9 854 1647 503808370 503807575 0.000000e+00 749.0
2 TraesCS5D01G460000 chr5D 81.522 736 116 11 947 1671 503883064 503882338 2.820000e-164 588.0
3 TraesCS5D01G460000 chr5D 87.755 294 31 4 1 290 126275684 126275392 3.140000e-89 339.0
4 TraesCS5D01G460000 chr5D 87.838 74 9 0 1261 1334 503878053 503877980 1.260000e-13 87.9
5 TraesCS5D01G460000 chr5B 98.032 2236 14 8 1 2228 632232223 632230010 0.000000e+00 3858.0
6 TraesCS5D01G460000 chr5B 98.457 324 4 1 2226 2548 632229907 632229584 1.020000e-158 569.0
7 TraesCS5D01G460000 chr5B 84.049 163 18 6 287 444 251628413 251628254 1.580000e-32 150.0
8 TraesCS5D01G460000 chr5A 86.525 1128 73 28 904 2015 631674703 631673639 0.000000e+00 1168.0
9 TraesCS5D01G460000 chr5A 79.189 913 136 31 854 1742 631706629 631705747 3.650000e-163 584.0
10 TraesCS5D01G460000 chr5A 82.987 529 85 5 1111 1636 632159066 632158540 8.250000e-130 473.0
11 TraesCS5D01G460000 chr5A 79.470 151 24 6 1191 1338 632004627 632004481 1.610000e-17 100.0
12 TraesCS5D01G460000 chr2D 88.966 290 30 2 1 289 388512463 388512751 8.670000e-95 357.0
13 TraesCS5D01G460000 chr2D 87.075 294 32 4 1 290 239965001 239965292 6.800000e-86 327.0
14 TraesCS5D01G460000 chr6B 87.415 294 31 4 1 290 35947383 35947674 1.460000e-87 333.0
15 TraesCS5D01G460000 chr4A 88.214 280 31 2 13 290 321432189 321431910 1.460000e-87 333.0
16 TraesCS5D01G460000 chr7A 87.372 293 31 4 1 290 722608779 722608490 5.250000e-87 331.0
17 TraesCS5D01G460000 chr7A 83.240 179 21 5 287 459 83996500 83996325 3.390000e-34 156.0
18 TraesCS5D01G460000 chr1B 87.415 294 29 6 1 290 217297686 217297397 5.250000e-87 331.0
19 TraesCS5D01G460000 chr7B 86.869 297 31 6 1 293 221522666 221522958 2.440000e-85 326.0
20 TraesCS5D01G460000 chr7B 84.706 170 16 7 308 471 464635234 464635069 7.300000e-36 161.0
21 TraesCS5D01G460000 chr6A 84.574 188 20 5 287 467 539713440 539713255 7.240000e-41 178.0
22 TraesCS5D01G460000 chr4B 85.714 161 14 5 308 462 372722493 372722336 7.300000e-36 161.0
23 TraesCS5D01G460000 chr4B 85.714 161 14 5 308 462 372780286 372780129 7.300000e-36 161.0
24 TraesCS5D01G460000 chr7D 81.188 202 25 9 309 502 82305407 82305211 1.580000e-32 150.0
25 TraesCS5D01G460000 chr3D 82.682 179 18 8 287 457 287286857 287287030 2.040000e-31 147.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G460000 chr5D 503740228 503742775 2547 True 4706.0 4706 100.0000 1 2548 1 chr5D.!!$R2 2547
1 TraesCS5D01G460000 chr5D 503807575 503808370 795 True 749.0 749 83.8910 854 1647 1 chr5D.!!$R3 793
2 TraesCS5D01G460000 chr5D 503882338 503883064 726 True 588.0 588 81.5220 947 1671 1 chr5D.!!$R5 724
3 TraesCS5D01G460000 chr5B 632229584 632232223 2639 True 2213.5 3858 98.2445 1 2548 2 chr5B.!!$R2 2547
4 TraesCS5D01G460000 chr5A 631673639 631674703 1064 True 1168.0 1168 86.5250 904 2015 1 chr5A.!!$R1 1111
5 TraesCS5D01G460000 chr5A 631705747 631706629 882 True 584.0 584 79.1890 854 1742 1 chr5A.!!$R2 888
6 TraesCS5D01G460000 chr5A 632158540 632159066 526 True 473.0 473 82.9870 1111 1636 1 chr5A.!!$R4 525

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
600 606 0.034337 CGTGGAGAGGGTTTTTCGGA 59.966 55.0 0.0 0.0 0.0 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2292 2461 2.544267 GTGAATGCTACTCCGGCAATAC 59.456 50.0 0.0 0.0 43.14 1.89 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
223 224 3.315749 AGGTAAAGAGATCGCCTACTTCG 59.684 47.826 0.00 0.00 0.00 3.79
412 418 3.726291 TTGCCAAAACTTGCCTAGAAC 57.274 42.857 0.00 0.00 0.00 3.01
440 446 9.693739 AAAATTGGGAAAAGGTCAAGTTTTTAT 57.306 25.926 0.00 0.00 35.93 1.40
462 468 2.124411 TGCCAAGTAGTCTAATCCCCC 58.876 52.381 0.00 0.00 0.00 5.40
463 469 2.124411 GCCAAGTAGTCTAATCCCCCA 58.876 52.381 0.00 0.00 0.00 4.96
464 470 2.158798 GCCAAGTAGTCTAATCCCCCAC 60.159 54.545 0.00 0.00 0.00 4.61
465 471 2.438392 CCAAGTAGTCTAATCCCCCACC 59.562 54.545 0.00 0.00 0.00 4.61
466 472 2.438392 CAAGTAGTCTAATCCCCCACCC 59.562 54.545 0.00 0.00 0.00 4.61
467 473 1.061579 AGTAGTCTAATCCCCCACCCC 60.062 57.143 0.00 0.00 0.00 4.95
468 474 0.269782 TAGTCTAATCCCCCACCCCC 59.730 60.000 0.00 0.00 0.00 5.40
495 501 1.906574 CCCCTACTAGACCAACTTGCA 59.093 52.381 0.00 0.00 0.00 4.08
593 599 1.878656 CGCTTCTCGTGGAGAGGGTT 61.879 60.000 6.85 0.00 46.82 4.11
600 606 0.034337 CGTGGAGAGGGTTTTTCGGA 59.966 55.000 0.00 0.00 0.00 4.55
603 609 1.071699 TGGAGAGGGTTTTTCGGACAG 59.928 52.381 0.00 0.00 0.00 3.51
691 697 3.259832 CGGTTTGTGGAAAAACGGG 57.740 52.632 0.44 0.00 40.29 5.28
802 808 7.613551 AAATTACATCCTAACTACCCGATCT 57.386 36.000 0.00 0.00 0.00 2.75
831 837 2.703536 TGCAGACAGTTTAAGGGTCAGA 59.296 45.455 0.00 0.00 34.04 3.27
1724 1786 6.036517 TGCGCAGTACTAGTACTACTTAGTTC 59.963 42.308 30.34 15.49 43.98 3.01
2090 2154 2.420628 TGAACCAAAGCATGAAAGCG 57.579 45.000 0.00 0.00 40.15 4.68
2205 2269 3.611113 CGAGTTCGGTTCAATGTATTCGT 59.389 43.478 0.00 0.00 35.37 3.85
2228 2292 4.567959 TGTTGATCTCAGCATTCACATACG 59.432 41.667 0.00 0.00 32.11 3.06
2292 2461 6.007936 TCCAAGAAACAAACATTCATACGG 57.992 37.500 0.00 0.00 0.00 4.02
2480 2650 1.830477 GCAAAGGATTTATGCCCACCA 59.170 47.619 0.00 0.00 35.03 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
223 224 3.935828 GCCTCACTCAGGTAAATCTTCAC 59.064 47.826 0.00 0.0 45.61 3.18
412 418 8.731275 AAAACTTGACCTTTTCCCAATTTTAG 57.269 30.769 0.00 0.0 0.00 1.85
440 446 3.053917 GGGGGATTAGACTACTTGGCAAA 60.054 47.826 0.00 0.0 0.00 3.68
488 494 4.024048 CGTCACTTTGTAGGATTGCAAGTT 60.024 41.667 4.94 0.0 30.44 2.66
495 501 1.722011 CGGCGTCACTTTGTAGGATT 58.278 50.000 0.00 0.0 0.00 3.01
593 599 3.131400 CCAAAAACCCTTCTGTCCGAAAA 59.869 43.478 0.00 0.0 0.00 2.29
600 606 1.691163 CCCACCCAAAAACCCTTCTGT 60.691 52.381 0.00 0.0 0.00 3.41
603 609 1.045407 GTCCCACCCAAAAACCCTTC 58.955 55.000 0.00 0.0 0.00 3.46
802 808 6.115446 CCCTTAAACTGTCTGCAATCATCTA 58.885 40.000 0.00 0.0 0.00 1.98
831 837 4.032960 TGGTGACCATTAAGTGCATCTT 57.967 40.909 0.00 0.0 39.89 2.40
2090 2154 6.060028 TGTTAGCATGAACAAGAACAGTTC 57.940 37.500 5.00 5.0 44.26 3.01
2205 2269 4.567959 CGTATGTGAATGCTGAGATCAACA 59.432 41.667 0.00 0.0 0.00 3.33
2258 2427 4.364415 TGTTTCTTGGAACAGAAAACGG 57.636 40.909 0.00 0.0 43.07 4.44
2292 2461 2.544267 GTGAATGCTACTCCGGCAATAC 59.456 50.000 0.00 0.0 43.14 1.89


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

AutoCloner maintained by Alex Coulton.