Multiple sequence alignment - TraesCS1A01G445200

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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 TraesCS1A01G445200 chr1A 100.000 2470 0 0 1 2470 592924123 592926592 0.000000e+00 4562.0
1 TraesCS1A01G445200 chr1A 85.413 1138 102 40 786 1868 592994122 592995250 0.000000e+00 1123.0
2 TraesCS1A01G445200 chr1A 80.863 742 76 36 933 1622 592100244 592099517 7.830000e-145 523.0
3 TraesCS1A01G445200 chr1A 81.371 569 54 34 1 548 592992956 592993493 1.370000e-112 416.0
4 TraesCS1A01G445200 chr1D 95.668 2493 60 18 8 2470 494305880 494308354 0.000000e+00 3962.0
5 TraesCS1A01G445200 chr1D 84.441 1234 121 44 854 2028 494349617 494350838 0.000000e+00 1149.0
6 TraesCS1A01G445200 chr1D 81.055 739 76 32 933 1622 493782611 493781888 4.680000e-147 531.0
7 TraesCS1A01G445200 chr1D 87.597 387 34 10 2085 2470 494350851 494351224 1.050000e-118 436.0
8 TraesCS1A01G445200 chrUn 91.539 1832 73 25 641 2436 290639177 290637392 0.000000e+00 2449.0
9 TraesCS1A01G445200 chrUn 91.539 1832 73 25 641 2436 290644902 290643117 0.000000e+00 2449.0
10 TraesCS1A01G445200 chrUn 91.539 1832 73 25 641 2436 320337287 320339072 0.000000e+00 2449.0
11 TraesCS1A01G445200 chrUn 92.202 654 35 10 1 652 290639865 290639226 0.000000e+00 911.0
12 TraesCS1A01G445200 chrUn 92.202 654 35 10 1 652 290645590 290644951 0.000000e+00 911.0
13 TraesCS1A01G445200 chrUn 92.202 654 35 10 1 652 320336599 320337238 0.000000e+00 911.0
14 TraesCS1A01G445200 chr1B 84.752 1292 129 37 794 2028 687531275 687532555 0.000000e+00 1232.0
15 TraesCS1A01G445200 chr1B 81.101 672 83 21 834 1461 686854002 686853331 4.740000e-137 497.0
16 TraesCS1A01G445200 chr1B 81.900 558 61 14 932 1463 687423108 687423651 3.770000e-118 435.0
17 TraesCS1A01G445200 chr1B 87.404 389 33 9 2085 2470 687532568 687532943 1.360000e-117 433.0
18 TraesCS1A01G445200 chr1B 79.507 527 47 37 32 541 687530145 687530627 3.960000e-83 318.0
19 TraesCS1A01G445200 chr1B 88.608 79 9 0 2338 2416 687533087 687533165 2.020000e-16 97.1


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 TraesCS1A01G445200 chr1A 592924123 592926592 2469 False 4562.000 4562 100.00000 1 2470 1 chr1A.!!$F1 2469
1 TraesCS1A01G445200 chr1A 592992956 592995250 2294 False 769.500 1123 83.39200 1 1868 2 chr1A.!!$F2 1867
2 TraesCS1A01G445200 chr1A 592099517 592100244 727 True 523.000 523 80.86300 933 1622 1 chr1A.!!$R1 689
3 TraesCS1A01G445200 chr1D 494305880 494308354 2474 False 3962.000 3962 95.66800 8 2470 1 chr1D.!!$F1 2462
4 TraesCS1A01G445200 chr1D 494349617 494351224 1607 False 792.500 1149 86.01900 854 2470 2 chr1D.!!$F2 1616
5 TraesCS1A01G445200 chr1D 493781888 493782611 723 True 531.000 531 81.05500 933 1622 1 chr1D.!!$R1 689
6 TraesCS1A01G445200 chrUn 290637392 290645590 8198 True 1680.000 2449 91.87050 1 2436 4 chrUn.!!$R1 2435
7 TraesCS1A01G445200 chrUn 320336599 320339072 2473 False 1680.000 2449 91.87050 1 2436 2 chrUn.!!$F1 2435
8 TraesCS1A01G445200 chr1B 687530145 687533165 3020 False 520.025 1232 85.06775 32 2470 4 chr1B.!!$F2 2438
9 TraesCS1A01G445200 chr1B 686853331 686854002 671 True 497.000 497 81.10100 834 1461 1 chr1B.!!$R1 627
10 TraesCS1A01G445200 chr1B 687423108 687423651 543 False 435.000 435 81.90000 932 1463 1 chr1B.!!$F1 531

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
296 334 0.110823 CGTGCTGTTTTCGGTGCTAC 60.111 55.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2004 8442 1.001641 AGCTTGTGGTGGAGGATGC 60.002 57.895 0.0 0.0 0.0 3.91 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
27 28 6.084738 AGCTAGATACATCCTCCACCATAAA 58.915 40.000 0.00 0.00 0.00 1.40
29 30 6.651225 GCTAGATACATCCTCCACCATAAAAC 59.349 42.308 0.00 0.00 0.00 2.43
30 31 6.831664 AGATACATCCTCCACCATAAAACT 57.168 37.500 0.00 0.00 0.00 2.66
45 50 7.606456 CACCATAAAACTAGCTCTAAGGTTCAA 59.394 37.037 0.00 0.00 0.00 2.69
75 81 2.443255 TCCTTCCTCTGTTTCTGCCTTT 59.557 45.455 0.00 0.00 0.00 3.11
91 101 5.598005 TCTGCCTTTTTCATTTTTCTCTGGA 59.402 36.000 0.00 0.00 0.00 3.86
92 102 6.268387 TCTGCCTTTTTCATTTTTCTCTGGAT 59.732 34.615 0.00 0.00 0.00 3.41
93 103 6.829849 TGCCTTTTTCATTTTTCTCTGGATT 58.170 32.000 0.00 0.00 0.00 3.01
94 104 6.707161 TGCCTTTTTCATTTTTCTCTGGATTG 59.293 34.615 0.00 0.00 0.00 2.67
126 136 1.692148 TACTAGTTGCATGCGCGCAC 61.692 55.000 39.05 25.56 42.87 5.34
254 280 3.345414 TGCATCCATTTTTGCCATTTCC 58.655 40.909 0.00 0.00 38.08 3.13
263 289 3.834489 TTTGCCATTTCCTTTCTTGCA 57.166 38.095 0.00 0.00 0.00 4.08
269 295 4.628766 GCCATTTCCTTTCTTGCATTCTTC 59.371 41.667 0.00 0.00 0.00 2.87
295 333 0.249531 TCGTGCTGTTTTCGGTGCTA 60.250 50.000 0.00 0.00 0.00 3.49
296 334 0.110823 CGTGCTGTTTTCGGTGCTAC 60.111 55.000 0.00 0.00 0.00 3.58
297 335 0.110823 GTGCTGTTTTCGGTGCTACG 60.111 55.000 0.00 0.00 0.00 3.51
298 336 0.531090 TGCTGTTTTCGGTGCTACGT 60.531 50.000 0.00 0.00 34.94 3.57
429 472 8.011844 AGCTATGTTCTTTTGTTCCTTTTCTT 57.988 30.769 0.00 0.00 0.00 2.52
619 741 2.224744 TGGTTGTTAGCAGAAGCCATGA 60.225 45.455 0.00 0.00 43.56 3.07
1039 1616 4.647853 AGGCATTGCTTGTTGATGATATGT 59.352 37.500 8.82 0.00 0.00 2.29
1094 1674 2.625737 CAAGTTCCACTGCGAGATCAT 58.374 47.619 0.00 0.00 0.00 2.45
1285 1907 9.008965 ACACAATATTTCTTGTACATGTGCTTA 57.991 29.630 17.54 2.68 40.29 3.09
1565 7963 8.586744 TGTCCGCACTATATTATAATTGTGGTA 58.413 33.333 19.69 11.86 36.28 3.25
1695 8115 6.147864 TCCTGTTAATTTATGCTTCATGGC 57.852 37.500 0.00 0.00 0.00 4.40
1697 8117 5.221028 CCTGTTAATTTATGCTTCATGGCGA 60.221 40.000 0.00 0.00 34.52 5.54
1716 8136 1.449601 GGGACACGTGCCTGTATGG 60.450 63.158 17.22 0.00 38.15 2.74
1830 8255 3.431766 CGTATAAAGCTAACCAGTGGCCT 60.432 47.826 9.78 0.00 0.00 5.19
1840 8265 1.064463 ACCAGTGGCCTCATGTAATGG 60.064 52.381 9.78 3.50 46.73 3.16
2004 8442 2.491022 AACCCGAGCTAGCTAGGCG 61.491 63.158 32.15 26.54 37.48 5.52
2028 8466 1.902508 CCTCCACCACAAGCTCTAAGA 59.097 52.381 0.00 0.00 0.00 2.10
2221 8662 2.346803 TCGTTAGCTCAGTTTGATGGC 58.653 47.619 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 5.491323 AGCTTTGAACCTTAGAGCTAGTT 57.509 39.130 0.00 0.00 41.54 2.24
29 30 6.096282 AGAGTAGCTTTGAACCTTAGAGCTAG 59.904 42.308 0.00 0.00 44.06 3.42
30 31 5.952947 AGAGTAGCTTTGAACCTTAGAGCTA 59.047 40.000 0.00 0.00 43.02 3.32
45 50 3.466395 ACAGAGGAAGGAGAGTAGCTT 57.534 47.619 0.00 0.00 0.00 3.74
75 81 5.804944 TGGCAATCCAGAGAAAAATGAAA 57.195 34.783 0.00 0.00 37.47 2.69
91 101 5.301835 ACTAGTAGAAGATGCATGGCAAT 57.698 39.130 2.46 0.00 43.62 3.56
92 102 4.760530 ACTAGTAGAAGATGCATGGCAA 57.239 40.909 2.46 0.00 43.62 4.52
93 103 4.445453 CAACTAGTAGAAGATGCATGGCA 58.555 43.478 2.46 0.00 44.86 4.92
94 104 3.249559 GCAACTAGTAGAAGATGCATGGC 59.750 47.826 2.46 0.00 42.86 4.40
126 136 5.333952 GCCTCTAGCAAATCTTGATCAATCG 60.334 44.000 8.96 0.00 42.97 3.34
254 280 5.386729 CGAAAAAGCGAAGAATGCAAGAAAG 60.387 40.000 0.00 0.00 33.85 2.62
263 289 2.290641 ACAGCACGAAAAAGCGAAGAAT 59.709 40.909 0.00 0.00 35.48 2.40
269 295 1.184908 CGAAAACAGCACGAAAAAGCG 59.815 47.619 0.00 0.00 35.48 4.68
295 333 4.640789 TTTCTTTTTGCCACATGTACGT 57.359 36.364 0.00 0.00 0.00 3.57
296 334 4.800993 TGTTTTCTTTTTGCCACATGTACG 59.199 37.500 0.00 0.00 0.00 3.67
297 335 6.292811 CCATGTTTTCTTTTTGCCACATGTAC 60.293 38.462 0.00 0.00 39.83 2.90
298 336 5.757320 CCATGTTTTCTTTTTGCCACATGTA 59.243 36.000 0.00 0.00 39.83 2.29
429 472 9.554395 GATACTTTGGAAAAGGAAAATGGAAAA 57.446 29.630 4.86 0.00 0.00 2.29
619 741 7.940688 TCTGCAACATCATGTTAGATCCATATT 59.059 33.333 1.72 0.00 38.77 1.28
652 775 6.603201 GGATGGATAATTTCTCCACACAGAAA 59.397 38.462 10.66 0.00 45.27 2.52
1039 1616 1.601903 GACAACCATGCGTTCAACTGA 59.398 47.619 0.00 0.00 29.93 3.41
1094 1674 0.695924 TTTCCCATTCTTCGCCAGGA 59.304 50.000 0.00 0.00 0.00 3.86
1285 1907 2.450476 GGATCTTCACAATGGCCTGTT 58.550 47.619 3.32 0.00 0.00 3.16
1695 8115 1.945354 ATACAGGCACGTGTCCCTCG 61.945 60.000 18.18 12.11 31.46 4.63
1697 8117 1.596934 CATACAGGCACGTGTCCCT 59.403 57.895 18.18 12.94 31.46 4.20
1830 8255 8.729756 CATGTTTACAGAAAGACCATTACATGA 58.270 33.333 0.00 0.00 40.74 3.07
2004 8442 1.001641 AGCTTGTGGTGGAGGATGC 60.002 57.895 0.00 0.00 0.00 3.91
2028 8466 3.771216 AGAGCCTTCACCAACAATGAAT 58.229 40.909 0.00 0.00 35.57 2.57
2221 8662 6.705381 TGAAAATAAATTGACCCAGCAAACTG 59.295 34.615 0.00 0.00 44.05 3.16
2262 8703 5.589050 AGAAACTCGGGCCTTTATTGATTAC 59.411 40.000 0.84 0.00 0.00 1.89
2359 8800 0.688487 CGGGGTAAAGTGAGGACCAA 59.312 55.000 0.00 0.00 34.73 3.67


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

AutoCloner maintained by Alex Coulton.