Multiple sequence alignment - TraesCS3D01G224400

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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 TraesCS3D01G224400 chr3D 100.000 2984 0 0 579 3562 305745125 305748108 0.000000e+00 5511
1 TraesCS3D01G224400 chr3D 100.000 202 0 0 1 202 305744547 305744748 1.210000e-99 374
2 TraesCS3D01G224400 chr3B 91.167 1585 99 20 1991 3562 416033067 416031511 0.000000e+00 2113
3 TraesCS3D01G224400 chr3B 93.137 1326 47 18 579 1895 416034358 416033068 0.000000e+00 1905
4 TraesCS3D01G224400 chr3B 94.059 101 6 0 1889 1989 373126012 373126112 1.710000e-33 154
5 TraesCS3D01G224400 chr3A 90.971 1329 78 20 579 1894 423706910 423708209 0.000000e+00 1751
6 TraesCS3D01G224400 chr3A 92.265 1254 57 15 2317 3562 423709077 423710298 0.000000e+00 1742
7 TraesCS3D01G224400 chr3A 95.161 310 15 0 2012 2321 423708466 423708775 1.150000e-134 490
8 TraesCS3D01G224400 chr6D 94.175 103 6 0 1894 1996 112829016 112828914 1.320000e-34 158
9 TraesCS3D01G224400 chr2A 93.396 106 6 1 1890 1994 268936706 268936601 4.760000e-34 156
10 TraesCS3D01G224400 chr2D 93.269 104 7 0 1893 1996 211559255 211559152 1.710000e-33 154
11 TraesCS3D01G224400 chr6A 91.818 110 7 2 1890 1997 70841113 70841222 6.160000e-33 152
12 TraesCS3D01G224400 chr6A 94.000 100 5 1 1894 1992 23355174 23355075 2.220000e-32 150
13 TraesCS3D01G224400 chr5A 91.743 109 7 2 1886 1993 354522194 354522301 2.220000e-32 150
14 TraesCS3D01G224400 chr1D 92.381 105 8 0 1885 1989 240128270 240128166 2.220000e-32 150
15 TraesCS3D01G224400 chr7D 90.351 114 9 1 1876 1989 617181776 617181665 7.970000e-32 148


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 TraesCS3D01G224400 chr3D 305744547 305748108 3561 False 2942.500000 5511 100.000 1 3562 2 chr3D.!!$F1 3561
1 TraesCS3D01G224400 chr3B 416031511 416034358 2847 True 2009.000000 2113 92.152 579 3562 2 chr3B.!!$R1 2983
2 TraesCS3D01G224400 chr3A 423706910 423710298 3388 False 1327.666667 1751 92.799 579 3562 3 chr3A.!!$F1 2983


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
94 95 0.036765 CCATCTCCCGTTCCGTTCAA 60.037 55.0 0.0 0.0 0.00 2.69 F
1032 1038 0.034670 GATCAGCCTGCCTTGAGGTT 60.035 55.0 0.0 0.0 35.29 3.50 F
1486 1518 0.037326 GTCATCACCTGGAACGAGCA 60.037 55.0 0.0 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1979 2017 0.598562 CGTATGATCCACTCCCTCCG 59.401 60.0 0.00 0.0 0.00 4.63 R
2510 3099 0.250081 GTCCATCGATCCAGGCCTTC 60.250 60.0 0.00 0.0 0.00 3.46 R
2934 3527 1.100463 TGTGCGGCACAACATTCTGT 61.100 50.0 31.72 0.0 41.69 3.41 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)



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AutoCloner maintained by Alex Coulton.