Multiple sequence alignment - TraesCS2B01G331000

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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 TraesCS2B01G331000 chr2B 100.000 2162 0 0 1 2162 474907938 474910099 0 3993
1 TraesCS2B01G331000 chr3B 98.293 2167 32 2 1 2162 201526508 201528674 0 3792
2 TraesCS2B01G331000 chr1A 98.293 2167 32 2 1 2162 554511732 554513898 0 3792
3 TraesCS2B01G331000 chr5D 98.154 2167 35 2 1 2162 503217702 503219868 0 3775
4 TraesCS2B01G331000 chr5D 97.970 2167 39 2 1 2162 503278742 503276576 0 3753
5 TraesCS2B01G331000 chr5D 97.693 2167 45 2 1 2162 6188424 6190590 0 3720
6 TraesCS2B01G331000 chr6D 98.062 2167 37 2 1 2162 168254410 168256576 0 3764
7 TraesCS2B01G331000 chr3D 97.923 2167 37 4 1 2162 589280058 589277895 0 3746
8 TraesCS2B01G331000 chr3A 97.600 2167 46 3 1 2162 672910523 672908358 0 3709


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 TraesCS2B01G331000 chr2B 474907938 474910099 2161 False 3993 3993 100.000 1 2162 1 chr2B.!!$F1 2161
1 TraesCS2B01G331000 chr3B 201526508 201528674 2166 False 3792 3792 98.293 1 2162 1 chr3B.!!$F1 2161
2 TraesCS2B01G331000 chr1A 554511732 554513898 2166 False 3792 3792 98.293 1 2162 1 chr1A.!!$F1 2161
3 TraesCS2B01G331000 chr5D 503217702 503219868 2166 False 3775 3775 98.154 1 2162 1 chr5D.!!$F2 2161
4 TraesCS2B01G331000 chr5D 503276576 503278742 2166 True 3753 3753 97.970 1 2162 1 chr5D.!!$R1 2161
5 TraesCS2B01G331000 chr5D 6188424 6190590 2166 False 3720 3720 97.693 1 2162 1 chr5D.!!$F1 2161
6 TraesCS2B01G331000 chr6D 168254410 168256576 2166 False 3764 3764 98.062 1 2162 1 chr6D.!!$F1 2161
7 TraesCS2B01G331000 chr3D 589277895 589280058 2163 True 3746 3746 97.923 1 2162 1 chr3D.!!$R1 2161
8 TraesCS2B01G331000 chr3A 672908358 672910523 2165 True 3709 3709 97.600 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
863 867 1.573108 TCTCTTCTCACCATCCCCAC 58.427 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1829 1837 4.87658 TCTTGATCCCTCTCAATCTCTCA 58.123 43.478 0.0 0.0 34.76 3.27 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
74 75 4.344359 TTCTATGTTATGCATGGCCGTA 57.656 40.909 10.16 2.00 38.47 4.02
268 270 3.635591 AGGAATCCAAATCTGCCGAATT 58.364 40.909 0.61 0.00 0.00 2.17
399 401 6.982160 TCCACATATTATGGGTAACGTAGT 57.018 37.500 8.48 0.00 39.60 2.73
439 441 2.158856 CCGGGGGTCTTAATTACCACTC 60.159 54.545 8.78 0.00 40.51 3.51
620 622 3.813443 ACTGAACTCAATCACTTGCTGT 58.187 40.909 0.00 0.00 32.11 4.40
683 685 6.725364 AGGTAGTCAAATTGGATCAGTGATT 58.275 36.000 7.16 0.00 0.00 2.57
863 867 1.573108 TCTCTTCTCACCATCCCCAC 58.427 55.000 0.00 0.00 0.00 4.61
1199 1207 5.952347 AGAAGTGGAATAGAATAACCCGT 57.048 39.130 0.00 0.00 0.00 5.28
1240 1248 4.765273 ACGTCTGTAATGCATTGTATGGA 58.235 39.130 22.27 9.66 34.26 3.41
1250 1258 5.372343 TGCATTGTATGGACCAGAATAGT 57.628 39.130 0.00 0.00 0.00 2.12
1361 1369 5.677319 TCTGTCTTAGTGAATCCCGATTT 57.323 39.130 0.00 0.00 0.00 2.17
1788 1796 3.744238 TCCGAGATGGCAAATATTCGA 57.256 42.857 0.00 0.00 37.80 3.71
1812 1820 5.983540 AGATGACTATGAAAACACCTCTCC 58.016 41.667 0.00 0.00 0.00 3.71
1813 1821 5.485353 AGATGACTATGAAAACACCTCTCCA 59.515 40.000 0.00 0.00 0.00 3.86
1823 1831 1.216678 ACACCTCTCCAGATCCTCGAT 59.783 52.381 0.00 0.00 0.00 3.59
1829 1837 4.040217 CCTCTCCAGATCCTCGATTTGAAT 59.960 45.833 0.00 0.00 0.00 2.57
2109 2117 2.233305 ACCTCGTGTGGGACTAATCT 57.767 50.000 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 2.404559 TCAACCGATATGCCCTTAGGT 58.595 47.619 0.00 0.00 34.57 3.08
160 162 9.733556 AGAGATCGTCATATACATCTAGAAAGT 57.266 33.333 0.00 1.14 30.75 2.66
399 401 2.976882 CGGGGGAAAATAGGGATGTCTA 59.023 50.000 0.00 0.00 0.00 2.59
439 441 4.460382 TCAGAGGCAAATTGAAAGCTAAGG 59.540 41.667 0.00 0.00 0.00 2.69
683 685 6.695292 GTTTACGACGAAACCTAGAAATCA 57.305 37.500 0.00 0.00 33.93 2.57
863 867 6.667007 TGCATACATTTGTCTCATACACTG 57.333 37.500 0.00 0.00 38.00 3.66
1199 1207 6.761242 CAGACGTATGATCATTACCCTTCAAA 59.239 38.462 14.65 0.00 0.00 2.69
1250 1258 6.958767 CCTGGAAAAGGTAGAAGAATAGGAA 58.041 40.000 0.00 0.00 41.74 3.36
1788 1796 6.013379 TGGAGAGGTGTTTTCATAGTCATCTT 60.013 38.462 0.00 0.00 0.00 2.40
1812 1820 5.840715 TCTCTCATTCAAATCGAGGATCTG 58.159 41.667 0.00 0.00 0.00 2.90
1813 1821 6.669125 ATCTCTCATTCAAATCGAGGATCT 57.331 37.500 0.00 0.00 0.00 2.75
1823 1831 6.157471 TGATCCCTCTCAATCTCTCATTCAAA 59.843 38.462 0.00 0.00 0.00 2.69
1829 1837 4.876580 TCTTGATCCCTCTCAATCTCTCA 58.123 43.478 0.00 0.00 34.76 3.27
2109 2117 9.487790 GTTTTCCATGAGATGGTAAATGAAAAA 57.512 29.630 9.71 2.71 46.61 1.94


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

AutoCloner maintained by Alex Coulton.