Multiple sequence alignment - TraesCS2A01G367500

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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 TraesCS2A01G367500 chr2A 100.000 2711 0 0 1 2711 611303673 611306383 0.000000e+00 5007
1 TraesCS2A01G367500 chr2D 94.581 2676 83 20 1 2635 469991432 469994086 0.000000e+00 4082
2 TraesCS2A01G367500 chr2D 93.750 80 2 2 2632 2711 469994125 469994201 1.710000e-22 117
3 TraesCS2A01G367500 chr2B 95.579 1832 65 10 1 1825 548624835 548626657 0.000000e+00 2920
4 TraesCS2A01G367500 chr2B 90.264 832 35 13 1826 2635 548626815 548627622 0.000000e+00 1046
5 TraesCS2A01G367500 chr2B 97.531 81 1 1 2632 2711 548627661 548627741 1.310000e-28 137
6 TraesCS2A01G367500 chr1A 87.755 1715 195 11 1 1710 8332792 8334496 0.000000e+00 1989
7 TraesCS2A01G367500 chr1A 85.383 1724 231 14 1 1720 8159024 8157318 0.000000e+00 1768
8 TraesCS2A01G367500 chr1D 87.101 1721 208 9 1 1718 6914004 6915713 0.000000e+00 1936
9 TraesCS2A01G367500 chr1D 84.202 1880 249 29 1 1859 6720759 6718907 0.000000e+00 1783
10 TraesCS2A01G367500 chr1B 86.361 1723 222 10 1 1716 10006655 10004939 0.000000e+00 1868
11 TraesCS2A01G367500 chr1B 86.361 1723 209 20 1 1715 8819080 8817376 0.000000e+00 1857
12 TraesCS2A01G367500 chr4B 85.127 1728 232 12 1 1718 36635023 36633311 0.000000e+00 1744


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 TraesCS2A01G367500 chr2A 611303673 611306383 2710 False 5007.000000 5007 100.0000 1 2711 1 chr2A.!!$F1 2710
1 TraesCS2A01G367500 chr2D 469991432 469994201 2769 False 2099.500000 4082 94.1655 1 2711 2 chr2D.!!$F1 2710
2 TraesCS2A01G367500 chr2B 548624835 548627741 2906 False 1367.666667 2920 94.4580 1 2711 3 chr2B.!!$F1 2710
3 TraesCS2A01G367500 chr1A 8332792 8334496 1704 False 1989.000000 1989 87.7550 1 1710 1 chr1A.!!$F1 1709
4 TraesCS2A01G367500 chr1A 8157318 8159024 1706 True 1768.000000 1768 85.3830 1 1720 1 chr1A.!!$R1 1719
5 TraesCS2A01G367500 chr1D 6914004 6915713 1709 False 1936.000000 1936 87.1010 1 1718 1 chr1D.!!$F1 1717
6 TraesCS2A01G367500 chr1D 6718907 6720759 1852 True 1783.000000 1783 84.2020 1 1859 1 chr1D.!!$R1 1858
7 TraesCS2A01G367500 chr1B 10004939 10006655 1716 True 1868.000000 1868 86.3610 1 1716 1 chr1B.!!$R2 1715
8 TraesCS2A01G367500 chr1B 8817376 8819080 1704 True 1857.000000 1857 86.3610 1 1715 1 chr1B.!!$R1 1714
9 TraesCS2A01G367500 chr4B 36633311 36635023 1712 True 1744.000000 1744 85.1270 1 1718 1 chr4B.!!$R1 1717

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
382 392 1.20229 CCACAAATCATAGCCGTTGCC 60.202 52.381 0.0 0.0 38.69 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 1823 0.108615 CAGACGATTTGGAGACCGCT 60.109 55.0 0.0 0.0 0.0 5.52 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
140 141 1.811266 CCTGACGATCCCTGCAACG 60.811 63.158 0.00 0.0 0.00 4.10
169 170 1.880027 GCCTGTGGACCTTTTACAGTG 59.120 52.381 8.45 0.0 40.04 3.66
382 392 1.202290 CCACAAATCATAGCCGTTGCC 60.202 52.381 0.00 0.0 38.69 4.52
698 712 7.093509 ACAGATTTAAGTGGTGTGGTTTTCTTT 60.094 33.333 0.00 0.0 0.00 2.52
702 716 4.918810 AGTGGTGTGGTTTTCTTTCATC 57.081 40.909 0.00 0.0 0.00 2.92
787 801 5.919141 TCGTGCTACTAAAAACTTCTCTGAC 59.081 40.000 0.00 0.0 0.00 3.51
820 834 5.163077 TGGTGGAGGTTTTGGTTCTGTATAA 60.163 40.000 0.00 0.0 0.00 0.98
822 836 6.072119 GGTGGAGGTTTTGGTTCTGTATAAAG 60.072 42.308 0.00 0.0 0.00 1.85
1189 1207 4.331992 CAGAGAACATACTTGTGGATGCAG 59.668 45.833 0.00 0.0 35.83 4.41
1359 1377 0.179084 GCTTCGGCATGGTACTGCTA 60.179 55.000 7.01 0.0 41.95 3.49
1406 1424 3.118775 TCCTCACCGGAAATATCACACAG 60.119 47.826 9.46 0.0 39.40 3.66
1498 1519 4.527038 ACGAGGGAGATGTGAAGAGTTTAA 59.473 41.667 0.00 0.0 0.00 1.52
1785 1823 4.443034 GGAATAAAAGAAGGAGGCGAGCTA 60.443 45.833 0.00 0.0 0.00 3.32
2051 2267 2.818751 AGTTTTCACAACCACCAGGA 57.181 45.000 0.00 0.0 38.69 3.86
2052 2268 3.094484 AGTTTTCACAACCACCAGGAA 57.906 42.857 0.00 0.0 38.69 3.36
2093 2309 9.036980 TCTTCTTAGACAACTTATAAAGGCTCT 57.963 33.333 0.00 0.0 0.00 4.09
2116 2332 2.603021 TCTCCAGAACAGAAGCACTCT 58.397 47.619 0.00 0.0 33.23 3.24
2126 2342 7.550551 CAGAACAGAAGCACTCTCCAATATTAA 59.449 37.037 0.00 0.0 29.07 1.40
2268 2493 1.938577 CTCATCTGAACATTGCCTCCG 59.061 52.381 0.00 0.0 0.00 4.63
2345 2574 0.106918 TCGGGTGCAAAACTGAACCT 60.107 50.000 2.31 0.0 37.64 3.50
2436 2666 1.307355 TGATGTTGCAGCCGTCCATG 61.307 55.000 0.00 0.0 0.00 3.66
2597 2827 2.238521 TGGAAAATGCCAGAACCTCAC 58.761 47.619 0.00 0.0 33.10 3.51
2607 2837 3.463944 CCAGAACCTCACACGTTTAGTT 58.536 45.455 0.00 0.0 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
382 392 1.690283 CGCATTCGCTCTGAGTGGTG 61.690 60.000 17.44 16.28 35.03 4.17
698 712 6.829849 TGCCTTGATTGTCATAGTATGATGA 58.170 36.000 15.77 8.23 42.04 2.92
702 716 5.819379 ACACTGCCTTGATTGTCATAGTATG 59.181 40.000 3.55 3.55 0.00 2.39
787 801 0.468029 AACCTCCACCACCAAGCTTG 60.468 55.000 19.93 19.93 0.00 4.01
820 834 2.414612 TGAGTCACTTAACACCCCCTT 58.585 47.619 0.00 0.00 0.00 3.95
822 836 2.943036 TTGAGTCACTTAACACCCCC 57.057 50.000 0.00 0.00 0.00 5.40
1189 1207 3.188460 TCTGCGACTTTAGGAACAAATGC 59.812 43.478 0.00 0.00 0.00 3.56
1392 1410 4.507710 TCTCAGTGCTGTGTGATATTTCC 58.492 43.478 0.00 0.00 0.00 3.13
1406 1424 1.964891 TTGCTGCTGCTCTCAGTGC 60.965 57.895 17.00 0.00 42.29 4.40
1498 1519 4.098349 GTCACCATGCAATTGTGTATCCAT 59.902 41.667 7.40 0.00 40.56 3.41
1785 1823 0.108615 CAGACGATTTGGAGACCGCT 60.109 55.000 0.00 0.00 0.00 5.52
1837 2032 2.900122 TTTCGCTACAATGCTTGCTC 57.100 45.000 0.00 0.00 0.00 4.26
2157 2373 7.284489 ACTTTCTACATTTTGTCTGCCTTGTTA 59.716 33.333 0.00 0.00 0.00 2.41
2212 2428 3.162666 AGGGTTAAGTGAGTCGTCATCA 58.837 45.455 0.00 0.00 34.36 3.07
2268 2493 0.402121 AGTTCAGGGGCTTGGTTCTC 59.598 55.000 0.00 0.00 0.00 2.87
2337 2566 2.158871 TCCGTACTTTTGCAGGTTCAGT 60.159 45.455 0.00 0.00 0.00 3.41
2345 2574 2.224670 ACCAGGATTCCGTACTTTTGCA 60.225 45.455 0.00 0.00 0.00 4.08
2436 2666 4.165779 CCTACATTGGCAAATCGTTCAAC 58.834 43.478 3.01 0.00 0.00 3.18
2597 2827 4.846137 GCACAGCTTCAATAACTAAACGTG 59.154 41.667 0.00 0.00 0.00 4.49
2607 2837 6.430925 AGACATACTTTTGCACAGCTTCAATA 59.569 34.615 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.