Multiple sequence alignment - TraesCS2A01G048200

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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 TraesCS2A01G048200 chr2A 100.000 2240 0 0 1 2240 18633361 18635600 0.000000e+00 4137
1 TraesCS2A01G048200 chr2A 85.307 667 67 19 1597 2240 18585373 18586031 0.000000e+00 660
2 TraesCS2A01G048200 chr2A 93.703 397 21 2 922 1314 18584510 18584906 1.920000e-165 592
3 TraesCS2A01G048200 chr2A 93.966 116 6 1 1367 1481 18585124 18585239 8.220000e-40 174
4 TraesCS2A01G048200 chr2D 95.630 1350 26 4 922 2240 17310612 17311959 0.000000e+00 2135
5 TraesCS2A01G048200 chr2D 93.320 1003 35 7 1269 2240 17167897 17168898 0.000000e+00 1452
6 TraesCS2A01G048200 chr2D 90.155 965 44 26 1 921 17164116 17165073 0.000000e+00 1208
7 TraesCS2A01G048200 chr2D 90.482 872 52 17 1 862 17309088 17309938 0.000000e+00 1122
8 TraesCS2A01G048200 chr2D 98.421 190 3 0 924 1113 17165704 17165893 3.560000e-88 335
9 TraesCS2A01G048200 chr2D 97.143 105 3 0 1167 1271 17165886 17165990 6.360000e-41 178
10 TraesCS2A01G048200 chr2D 89.147 129 10 3 794 921 17309836 17309961 8.280000e-35 158
11 TraesCS2A01G048200 chr2B 94.832 1161 48 5 922 2072 28907219 28908377 0.000000e+00 1801
12 TraesCS2A01G048200 chr2B 88.036 1329 110 30 929 2240 29993487 29992191 0.000000e+00 1528
13 TraesCS2A01G048200 chr2B 83.189 809 78 36 1473 2240 29045210 29046001 0.000000e+00 688
14 TraesCS2A01G048200 chr2B 91.832 404 27 6 922 1322 29044542 29044942 1.940000e-155 558
15 TraesCS2A01G048200 chr2B 81.498 454 70 7 102 545 29994817 29994368 5.880000e-96 361
16 TraesCS2A01G048200 chr2B 90.588 255 17 3 433 681 28906084 28906337 4.610000e-87 331
17 TraesCS2A01G048200 chr2B 87.671 219 13 10 1265 1481 29044977 29045183 2.220000e-60 243
18 TraesCS2A01G048200 chr2B 92.857 168 8 1 2073 2240 28920456 28920619 7.990000e-60 241


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 TraesCS2A01G048200 chr2A 18633361 18635600 2239 False 4137.000000 4137 100.00000 1 2240 1 chr2A.!!$F1 2239
1 TraesCS2A01G048200 chr2A 18584510 18586031 1521 False 475.333333 660 90.99200 922 2240 3 chr2A.!!$F2 1318
2 TraesCS2A01G048200 chr2D 17309088 17311959 2871 False 1138.333333 2135 91.75300 1 2240 3 chr2D.!!$F2 2239
3 TraesCS2A01G048200 chr2D 17164116 17168898 4782 False 793.250000 1452 94.75975 1 2240 4 chr2D.!!$F1 2239
4 TraesCS2A01G048200 chr2B 28906084 28908377 2293 False 1066.000000 1801 92.71000 433 2072 2 chr2B.!!$F2 1639
5 TraesCS2A01G048200 chr2B 29992191 29994817 2626 True 944.500000 1528 84.76700 102 2240 2 chr2B.!!$R1 2138
6 TraesCS2A01G048200 chr2B 29044542 29046001 1459 False 496.333333 688 87.56400 922 2240 3 chr2B.!!$F3 1318

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
622 642 1.281419 TCCCTCCGTTTATTCCAGCA 58.719 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
1894 4861 0.899019 GAGGAGAGAGGACGGCTTTT 59.101 55.0 0.0 0.0 0.0 2.27 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
183 190 2.204090 AAGGGGATGGGACCGTGT 60.204 61.111 0.00 0.00 0.00 4.49
369 381 3.375922 TGAAAAACGGTCAGGAAACTCAC 59.624 43.478 0.00 0.00 40.21 3.51
447 461 1.398692 AGCTTTCCAAAACCGCTTCA 58.601 45.000 0.00 0.00 0.00 3.02
505 523 3.057245 CAGAGGTGAGATCGTTCTGTCAA 60.057 47.826 0.00 0.00 30.30 3.18
609 629 4.884164 CCATAAAGATGACAAGTTCCCTCC 59.116 45.833 0.00 0.00 34.73 4.30
622 642 1.281419 TCCCTCCGTTTATTCCAGCA 58.719 50.000 0.00 0.00 0.00 4.41
772 890 7.565323 TTTGTTTTCAAAATCTGGGGAAATG 57.435 32.000 0.00 0.00 45.30 2.32
773 891 6.245890 TGTTTTCAAAATCTGGGGAAATGT 57.754 33.333 0.00 0.00 0.00 2.71
774 892 6.657875 TGTTTTCAAAATCTGGGGAAATGTT 58.342 32.000 0.00 0.00 0.00 2.71
775 893 7.115414 TGTTTTCAAAATCTGGGGAAATGTTT 58.885 30.769 0.00 0.00 0.00 2.83
776 894 7.613411 TGTTTTCAAAATCTGGGGAAATGTTTT 59.387 29.630 0.00 0.00 0.00 2.43
777 895 7.565323 TTTCAAAATCTGGGGAAATGTTTTG 57.435 32.000 0.00 0.00 37.69 2.44
778 896 6.491714 TCAAAATCTGGGGAAATGTTTTGA 57.508 33.333 6.91 6.91 40.90 2.69
779 897 6.893583 TCAAAATCTGGGGAAATGTTTTGAA 58.106 32.000 8.19 0.00 40.49 2.69
780 898 7.516452 TCAAAATCTGGGGAAATGTTTTGAAT 58.484 30.769 8.19 0.00 40.49 2.57
781 899 7.997803 TCAAAATCTGGGGAAATGTTTTGAATT 59.002 29.630 8.19 0.00 40.49 2.17
782 900 9.282569 CAAAATCTGGGGAAATGTTTTGAATTA 57.717 29.630 0.00 0.00 38.26 1.40
783 901 9.859152 AAAATCTGGGGAAATGTTTTGAATTAA 57.141 25.926 0.00 0.00 0.00 1.40
784 902 8.846943 AATCTGGGGAAATGTTTTGAATTAAC 57.153 30.769 0.00 0.00 0.00 2.01
785 903 7.366847 TCTGGGGAAATGTTTTGAATTAACA 57.633 32.000 0.00 0.00 39.58 2.41
786 904 7.796054 TCTGGGGAAATGTTTTGAATTAACAA 58.204 30.769 0.00 0.00 38.82 2.83
787 905 8.435982 TCTGGGGAAATGTTTTGAATTAACAAT 58.564 29.630 0.00 0.00 38.82 2.71
788 906 8.986929 TGGGGAAATGTTTTGAATTAACAATT 57.013 26.923 0.00 0.00 38.82 2.32
789 907 9.413734 TGGGGAAATGTTTTGAATTAACAATTT 57.586 25.926 0.00 0.22 38.82 1.82
862 994 8.821147 TCAAATTCATGGATTGTCTTTCAAAG 57.179 30.769 0.00 0.00 39.62 2.77
978 1796 3.375299 CCAGCAAGCCATAACACTTCTAC 59.625 47.826 0.00 0.00 0.00 2.59
1039 1857 1.473258 TGTCCTTGCCATGGTAATGC 58.527 50.000 16.19 9.48 31.93 3.56
1130 1948 4.755507 GACGGGAGAGGGGACGGT 62.756 72.222 0.00 0.00 0.00 4.83
1379 4273 7.881232 TGTGCTACCTATATGTAAATTAAGGGC 59.119 37.037 0.00 0.00 0.00 5.19
1518 4452 8.142994 TGAATCAGTCCGAAATATTAGCTTTC 57.857 34.615 0.00 0.00 0.00 2.62
1628 4590 9.358406 TGAAGTTGATATTGCTATGGATTCATT 57.642 29.630 0.00 0.00 34.96 2.57
1894 4861 6.983474 TCAGCGAATATTTCACTTTGATGA 57.017 33.333 0.00 0.00 30.75 2.92
1932 4901 2.739913 CTCAAAGGGCATGCATTGTTTG 59.260 45.455 21.36 20.08 0.00 2.93
1962 4960 5.006261 GCTGAAACCACACCAATTTGTTTAC 59.994 40.000 0.00 0.00 29.89 2.01
2125 5170 8.553459 ACATAAATAGCTTCATAAAGGATCGG 57.447 34.615 0.00 0.00 32.79 4.18
2130 5175 5.296151 AGCTTCATAAAGGATCGGAATGA 57.704 39.130 0.00 0.00 32.79 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 59 7.543359 TCTTGTTCCATCATTTCATTCCTTT 57.457 32.000 0.00 0.00 0.00 3.11
64 67 7.038048 GGGAAAGAATCTTGTTCCATCATTTC 58.962 38.462 13.85 0.00 42.26 2.17
505 523 2.058675 GGCTATGCCTCACCCGTAT 58.941 57.895 0.73 0.00 46.69 3.06
545 563 2.736995 GCGTGTGCTGCTTACGGA 60.737 61.111 23.04 0.00 38.20 4.69
609 629 3.127030 GGGAGAACTTGCTGGAATAAACG 59.873 47.826 0.00 0.00 0.00 3.60
744 862 9.859152 TTTCCCCAGATTTTGAAAACAAATATT 57.141 25.926 0.00 0.00 0.00 1.28
746 864 9.282569 CATTTCCCCAGATTTTGAAAACAAATA 57.717 29.630 0.00 0.00 31.20 1.40
747 865 7.779326 ACATTTCCCCAGATTTTGAAAACAAAT 59.221 29.630 0.00 0.00 31.20 2.32
748 866 7.115414 ACATTTCCCCAGATTTTGAAAACAAA 58.885 30.769 0.00 0.00 31.20 2.83
749 867 6.657875 ACATTTCCCCAGATTTTGAAAACAA 58.342 32.000 0.00 0.00 31.20 2.83
750 868 6.245890 ACATTTCCCCAGATTTTGAAAACA 57.754 33.333 0.00 0.00 31.20 2.83
751 869 7.566760 AAACATTTCCCCAGATTTTGAAAAC 57.433 32.000 0.00 0.00 31.20 2.43
752 870 7.831193 TCAAAACATTTCCCCAGATTTTGAAAA 59.169 29.630 7.32 0.00 40.93 2.29
753 871 7.341805 TCAAAACATTTCCCCAGATTTTGAAA 58.658 30.769 7.32 0.00 40.93 2.69
754 872 6.893583 TCAAAACATTTCCCCAGATTTTGAA 58.106 32.000 7.32 0.00 40.93 2.69
755 873 6.491714 TCAAAACATTTCCCCAGATTTTGA 57.508 33.333 5.98 5.98 41.36 2.69
756 874 7.748691 ATTCAAAACATTTCCCCAGATTTTG 57.251 32.000 0.00 0.00 38.03 2.44
757 875 9.859152 TTAATTCAAAACATTTCCCCAGATTTT 57.141 25.926 0.00 0.00 0.00 1.82
758 876 9.283768 GTTAATTCAAAACATTTCCCCAGATTT 57.716 29.630 0.00 0.00 0.00 2.17
759 877 8.435982 TGTTAATTCAAAACATTTCCCCAGATT 58.564 29.630 0.00 0.00 32.07 2.40
760 878 7.972301 TGTTAATTCAAAACATTTCCCCAGAT 58.028 30.769 0.00 0.00 32.07 2.90
761 879 7.366847 TGTTAATTCAAAACATTTCCCCAGA 57.633 32.000 0.00 0.00 32.07 3.86
762 880 8.620116 ATTGTTAATTCAAAACATTTCCCCAG 57.380 30.769 0.00 0.00 36.75 4.45
763 881 8.986929 AATTGTTAATTCAAAACATTTCCCCA 57.013 26.923 0.00 0.00 36.75 4.96
1130 1948 1.134848 TCGCATGGTGATTGTCGATCA 60.135 47.619 0.00 0.00 42.42 2.92
1211 2029 0.028637 GGCTTCTTCGCTAGCAATGC 59.971 55.000 16.45 10.02 39.15 3.56
1463 4359 4.888239 TGGTAGTACTCAAGAGCTCATACC 59.112 45.833 17.77 13.55 0.00 2.73
1549 4489 3.983044 AAGGATTCACTGTGTACCTCC 57.017 47.619 17.53 14.05 0.00 4.30
1894 4861 0.899019 GAGGAGAGAGGACGGCTTTT 59.101 55.000 0.00 0.00 0.00 2.27
1932 4901 2.294074 TGGTGTGGTTTCAGCTTACAC 58.706 47.619 0.00 0.00 40.53 2.90
1962 4960 7.420184 CAAATTGGTTTGGTTTTAGCTTAGG 57.580 36.000 0.00 0.00 40.78 2.69
2032 5046 8.905702 CAAGTGATTTATGTAAAGTGCTTTCAC 58.094 33.333 0.00 1.57 43.44 3.18
2125 5170 8.988934 TGTACACTAATGACTTGAAACTCATTC 58.011 33.333 0.00 0.00 38.01 2.67


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

AutoCloner maintained by Alex Coulton.