Multiple sequence alignment - TraesCS3A01G430800

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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 TraesCS3A01G430800 chr3A 100.000 2318 0 0 1 2318 672904196 672901879 0 4281
1 TraesCS3A01G430800 chr3A 98.146 2319 40 3 1 2318 66011805 66009489 0 4041
2 TraesCS3A01G430800 chr5D 98.361 2319 36 2 1 2318 503224035 503226352 0 4071
3 TraesCS3A01G430800 chr5D 98.017 2320 43 3 1 2318 503272510 503270192 0 4026
4 TraesCS3A01G430800 chr5D 97.717 2322 47 5 1 2318 503234350 503236669 0 3989
5 TraesCS3A01G430800 chrUn 97.671 2319 50 3 1 2318 216512789 216510474 0 3980


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 TraesCS3A01G430800 chr3A 672901879 672904196 2317 True 4281 4281 100.000 1 2318 1 chr3A.!!$R2 2317
1 TraesCS3A01G430800 chr3A 66009489 66011805 2316 True 4041 4041 98.146 1 2318 1 chr3A.!!$R1 2317
2 TraesCS3A01G430800 chr5D 503224035 503226352 2317 False 4071 4071 98.361 1 2318 1 chr5D.!!$F1 2317
3 TraesCS3A01G430800 chr5D 503270192 503272510 2318 True 4026 4026 98.017 1 2318 1 chr5D.!!$R1 2317
4 TraesCS3A01G430800 chr5D 503234350 503236669 2319 False 3989 3989 97.717 1 2318 1 chr5D.!!$F2 2317
5 TraesCS3A01G430800 chrUn 216510474 216512789 2315 True 3980 3980 97.671 1 2318 1 chrUn.!!$R1 2317

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
998 1001 0.392706 TGAGTCGCTTCCTTTCTGCA 59.607 50.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2060 2065 1.482593 CGAGGAACCCTAGATGCTGTT 59.517 52.381 0.0 0.0 31.76 3.16 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
43 46 5.280882 CCCAGATGAACCATATAGCCAAGAT 60.281 44.000 0.00 0.00 0.00 2.40
231 234 7.184022 ACATAAAAACATTCCCCCTAGAGTAGT 59.816 37.037 0.00 0.00 0.00 2.73
440 443 7.350467 GGCCGTTATGCTTATTACTAAACTTC 58.650 38.462 0.00 0.00 0.00 3.01
575 578 6.040729 TCCATTGAAGAGAAGCAAATGAAACA 59.959 34.615 0.00 0.00 0.00 2.83
809 812 8.090831 CGAGAGGGATTAGTTGATCATGATTTA 58.909 37.037 10.14 0.00 0.00 1.40
896 899 4.805719 TGATTCTTTTCCGATCGAGATGTG 59.194 41.667 18.66 0.00 0.00 3.21
906 909 1.616159 TCGAGATGTGCGGATCCATA 58.384 50.000 13.41 0.00 0.00 2.74
910 913 3.119495 CGAGATGTGCGGATCCATATGTA 60.119 47.826 13.41 0.00 0.00 2.29
994 997 4.509600 CCATTCTATGAGTCGCTTCCTTTC 59.490 45.833 0.00 0.00 0.00 2.62
998 1001 0.392706 TGAGTCGCTTCCTTTCTGCA 59.607 50.000 0.00 0.00 0.00 4.41
1270 1274 6.626302 TCTTTTGTTGAATCTTTTTCACGGT 58.374 32.000 0.00 0.00 0.00 4.83
1277 1281 6.160664 TGAATCTTTTTCACGGTTCGATAC 57.839 37.500 0.00 0.00 0.00 2.24
1736 1740 6.321181 AGTGTAATGGAAAAAGAAGTGCTTCA 59.679 34.615 13.58 0.00 41.84 3.02
1817 1822 1.764134 TGACACGGACAAAGTAAGGGT 59.236 47.619 0.00 0.00 0.00 4.34
1936 1941 2.812011 CCAGTCCCCTTACGAAACTTTG 59.188 50.000 0.00 0.00 0.00 2.77
2060 2065 4.213270 CCTTGTTGACGATTCTTTACTGCA 59.787 41.667 0.00 0.00 0.00 4.41
2089 2094 3.964688 TCTAGGGTTCCTCGAATAATGCA 59.035 43.478 0.00 0.00 34.61 3.96
2123 2128 3.686405 CGGGTAAATCCTTAACCCTTCCC 60.686 52.174 8.08 0.00 41.31 3.97
2184 2189 4.941873 GGCCAATACCAGGTATATAAGCAC 59.058 45.833 12.88 4.76 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 46 6.823689 GCTCTTCTATTCTGGTTCATGGTTTA 59.176 38.462 0.00 0.00 0.00 2.01
440 443 7.609532 ACCTTGGTTCTATTTCATCTCTTCAAG 59.390 37.037 0.00 0.00 0.00 3.02
477 480 6.491403 TCTGATGATCGATTCAACCTCTGATA 59.509 38.462 0.00 0.00 38.03 2.15
575 578 8.116753 CGATTCTACGAGCATTTTTATGAAAGT 58.883 33.333 0.00 0.00 35.09 2.66
628 631 7.443575 GGATGCAGTTACTAATTCATGATCTGT 59.556 37.037 0.00 0.00 0.00 3.41
716 719 6.944862 AGCATGGAATAAGGTTTGATCCTATC 59.055 38.462 0.00 0.00 36.74 2.08
809 812 9.725019 ACAAAAAGGAAAAGAAAGAGAAAACAT 57.275 25.926 0.00 0.00 0.00 2.71
925 928 7.660617 TGCACATTTTTGTTAATCCATGAACAT 59.339 29.630 0.00 0.00 35.57 2.71
941 944 5.636543 GCAAATAGAGCTCTTGCACATTTTT 59.363 36.000 26.64 10.99 43.89 1.94
998 1001 2.084930 GGGAGTGGGGGTGCCATAT 61.085 63.158 0.00 0.00 0.00 1.78
1206 1210 5.752892 TTGGTTTTACGTCAAGCAATACA 57.247 34.783 16.82 0.93 36.85 2.29
1245 1249 7.264947 ACCGTGAAAAAGATTCAACAAAAGAT 58.735 30.769 0.00 0.00 0.00 2.40
1270 1274 7.857734 TTGGCTTATCAAATTCTGTATCGAA 57.142 32.000 0.00 0.00 0.00 3.71
1736 1740 5.066505 GGTCCGAGTCAAATAGCAATGATTT 59.933 40.000 0.00 0.00 0.00 2.17
2060 2065 1.482593 CGAGGAACCCTAGATGCTGTT 59.517 52.381 0.00 0.00 31.76 3.16
2089 2094 4.658901 AGGATTTACCCGGTGTGAGATATT 59.341 41.667 0.00 0.00 40.05 1.28
2123 2128 9.968870 GAACATTCTGTAGTATTAGTAAGAGGG 57.031 37.037 0.00 0.00 0.00 4.30
2184 2189 7.066284 ACGATTAACCTCTGGATTTGAAATCAG 59.934 37.037 18.55 13.46 0.00 2.90


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

AutoCloner maintained by Alex Coulton.