Multiple sequence alignment - TraesCS4D01G044100

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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 TraesCS4D01G044100 chr4D 100.000 2162 0 0 1 2162 19928063 19930224 0 3993
1 TraesCS4D01G044100 chr5D 97.550 2163 52 1 1 2162 503217706 503219868 0 3699
2 TraesCS4D01G044100 chr5D 97.087 2163 62 1 1 2162 503278738 503276576 0 3644
3 TraesCS4D01G044100 chr5D 96.902 2163 66 1 1 2162 6188428 6190590 0 3622
4 TraesCS4D01G044100 chr3B 97.550 2163 52 1 1 2162 201526512 201528674 0 3699
5 TraesCS4D01G044100 chr1A 97.457 2163 54 1 1 2162 554511736 554513898 0 3688
6 TraesCS4D01G044100 chr6D 97.319 2163 57 1 1 2162 168254414 168256576 0 3672
7 TraesCS4D01G044100 chr3D 97.180 2163 57 3 1 2162 589280054 589277895 0 3653
8 TraesCS4D01G044100 chrUn 96.995 2163 63 2 1 2162 216519114 216516953 0 3633
9 TraesCS4D01G044100 chr3A 96.949 2163 64 2 1 2162 672910519 672908358 0 3627


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 TraesCS4D01G044100 chr4D 19928063 19930224 2161 False 3993 3993 100.000 1 2162 1 chr4D.!!$F1 2161
1 TraesCS4D01G044100 chr5D 503217706 503219868 2162 False 3699 3699 97.550 1 2162 1 chr5D.!!$F2 2161
2 TraesCS4D01G044100 chr5D 503276576 503278738 2162 True 3644 3644 97.087 1 2162 1 chr5D.!!$R1 2161
3 TraesCS4D01G044100 chr5D 6188428 6190590 2162 False 3622 3622 96.902 1 2162 1 chr5D.!!$F1 2161
4 TraesCS4D01G044100 chr3B 201526512 201528674 2162 False 3699 3699 97.550 1 2162 1 chr3B.!!$F1 2161
5 TraesCS4D01G044100 chr1A 554511736 554513898 2162 False 3688 3688 97.457 1 2162 1 chr1A.!!$F1 2161
6 TraesCS4D01G044100 chr6D 168254414 168256576 2162 False 3672 3672 97.319 1 2162 1 chr6D.!!$F1 2161
7 TraesCS4D01G044100 chr3D 589277895 589280054 2159 True 3653 3653 97.180 1 2162 1 chr3D.!!$R1 2161
8 TraesCS4D01G044100 chrUn 216516953 216519114 2161 True 3633 3633 96.995 1 2162 1 chrUn.!!$R1 2161
9 TraesCS4D01G044100 chr3A 672908358 672910519 2161 True 3627 3627 96.949 1 2162 1 chr3A.!!$R1 2161

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
272 273 1.959042 AATCTGCCGAATCGCTCATT 58.041 45.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 1661 1.533129 GGCTTAATGGTTAAAGCGCCG 60.533 52.381 2.29 0.0 28.48 6.46 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
193 194 8.097662 TGTATATGACGATCTCTAGACAGATGT 58.902 37.037 0.00 0.00 32.94 3.06
272 273 1.959042 AATCTGCCGAATCGCTCATT 58.041 45.000 0.00 0.00 0.00 2.57
301 302 5.718801 TCTTCTACATCCTAGGTCTCTGT 57.281 43.478 9.08 10.77 0.00 3.41
417 418 2.783510 GAGACATCCCTATTTTCCCCCA 59.216 50.000 0.00 0.00 0.00 4.96
434 435 2.174854 CCCCAGGGGTCTTAATTACCAG 59.825 54.545 18.09 0.00 38.25 4.00
1061 1063 5.221224 GCCGTCCATGGATCAAATTATTTCA 60.221 40.000 19.62 0.00 0.00 2.69
1157 1159 9.616156 TTTTGCCGTATTATTAAGTATTCTCCA 57.384 29.630 0.00 0.00 0.00 3.86
1199 1201 3.326880 AGAAGTGGAACAGAATAACCCGT 59.673 43.478 0.00 0.00 41.80 5.28
1222 1224 6.036735 CGTTTGAAGGGTAATGATCATACGTT 59.963 38.462 9.04 10.09 40.17 3.99
1323 1325 5.008712 CACCTTAACACCAAAGAAGAGTTCC 59.991 44.000 0.00 0.00 0.00 3.62
1496 1498 8.973378 CCAGTATCGATAAGAATTTGAGTTCTC 58.027 37.037 6.72 0.00 37.46 2.87
1522 1524 9.650371 CATTGTTCTTATGTTATGGTACGAATG 57.350 33.333 0.00 0.00 0.00 2.67
1659 1661 6.475402 CCCGCAAATTTACCAATTATGAGTTC 59.525 38.462 0.00 0.00 31.89 3.01
1675 1677 2.674357 GAGTTCGGCGCTTTAACCATTA 59.326 45.455 7.64 0.00 0.00 1.90
1709 1711 5.303333 TGCTTAACAGGGATCATCGTACATA 59.697 40.000 0.00 0.00 0.00 2.29
1824 1826 1.407258 CACCTCTCTGGATCCTCGAAC 59.593 57.143 14.23 0.00 39.71 3.95
1834 1836 4.026744 TGGATCCTCGAACTGAAAGAGAT 58.973 43.478 14.23 0.00 37.43 2.75
1844 1846 6.378564 TCGAACTGAAAGAGATATTGAGAGGT 59.621 38.462 0.00 0.00 37.43 3.85
2073 2075 8.367911 ACGTATATTCCTTGCTCATTATCAGAA 58.632 33.333 0.00 0.00 0.00 3.02
2153 2155 6.428083 GAAAACCCTTTTCATTCCCCTTAA 57.572 37.500 3.13 0.00 46.34 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
272 273 9.303116 GAGACCTAGGATGTAGAAGATCATAAA 57.697 37.037 17.98 0.0 0.00 1.40
301 302 2.236146 ACATAAGCCAGATGACGGAACA 59.764 45.455 0.00 0.0 0.00 3.18
363 364 6.269077 ACCCATAATATGTGGAAGTATCGACA 59.731 38.462 12.60 0.0 46.37 4.35
417 418 3.190439 AGCACTGGTAATTAAGACCCCT 58.810 45.455 6.83 0.0 35.99 4.79
434 435 3.917988 AGGCAAATTGAAAGCTAAGCAC 58.082 40.909 0.00 0.0 0.00 4.40
484 485 4.444876 CCTTGTTTCAAAGAGAGGAGGACA 60.445 45.833 0.00 0.0 0.00 4.02
602 603 1.317613 AACGGCAGCAAGTGATTGAA 58.682 45.000 0.00 0.0 0.00 2.69
726 727 9.126151 TGAGTGTGGTTTGAACTATTGATTTAA 57.874 29.630 0.00 0.0 0.00 1.52
746 747 3.421844 GAAATGCCCTACCTTTGAGTGT 58.578 45.455 0.00 0.0 0.00 3.55
1061 1063 5.336102 ACAGGAAAGTGAAATCCAATCCAT 58.664 37.500 0.00 0.0 38.23 3.41
1173 1175 6.342111 GGGTTATTCTGTTCCACTTCTAGAG 58.658 44.000 0.00 0.0 0.00 2.43
1199 1201 7.392113 ACAAACGTATGATCATTACCCTTCAAA 59.608 33.333 14.65 0.0 0.00 2.69
1222 1224 3.369175 TGGGCCATACAATGCATTACAA 58.631 40.909 12.53 0.6 0.00 2.41
1265 1267 2.304761 AGCCATCGACTACCTGGAAAAA 59.695 45.455 6.18 0.0 31.38 1.94
1323 1325 5.649782 AGACAGAAATAAAGCATTGGGTG 57.350 39.130 0.00 0.0 0.00 4.61
1428 1430 6.265422 GGGAAAGTCGATTTATGGATGGATTT 59.735 38.462 0.00 0.0 0.00 2.17
1430 1432 5.073691 AGGGAAAGTCGATTTATGGATGGAT 59.926 40.000 0.00 0.0 0.00 3.41
1496 1498 9.650371 CATTCGTACCATAACATAAGAACAATG 57.350 33.333 0.00 0.0 0.00 2.82
1522 1524 7.874016 TCCATACATAACGAATTGGTATGGTAC 59.126 37.037 21.76 0.0 45.91 3.34
1659 1661 1.533129 GGCTTAATGGTTAAAGCGCCG 60.533 52.381 2.29 0.0 28.48 6.46
1824 1826 9.695526 CTTGATACCTCTCAATATCTCTTTCAG 57.304 37.037 0.00 0.0 34.76 3.02
1915 1917 7.961326 ACCAAGGTCATTCTTTGCTAAATAT 57.039 32.000 0.00 0.0 32.75 1.28
2073 2075 6.326323 ACACAAGGTTTGGGAATAAGTGATTT 59.674 34.615 0.00 0.0 37.55 2.17


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

AutoCloner maintained by Alex Coulton.