Multiple sequence alignment - TraesCS4A01G424100

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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 TraesCS4A01G424100 chr4A 100.000 2270 0 0 1 2270 694694585 694696854 0.000000e+00 4193.0
1 TraesCS4A01G424100 chr4A 97.215 1580 20 2 691 2270 694709374 694710929 0.000000e+00 2652.0
2 TraesCS4A01G424100 chr4A 96.728 1589 19 3 691 2270 694676616 694678180 0.000000e+00 2615.0
3 TraesCS4A01G424100 chr4A 98.340 783 12 1 1 783 694708576 694709357 0.000000e+00 1373.0
4 TraesCS4A01G424100 chr4A 86.588 932 72 15 554 1464 694438903 694439802 0.000000e+00 979.0
5 TraesCS4A01G424100 chr4A 90.566 265 18 1 525 789 694676348 694676605 6.000000e-91 344.0
6 TraesCS4A01G424100 chr4A 91.667 60 5 0 2160 2219 594275994 594276053 1.440000e-12 84.2
7 TraesCS4A01G424100 chr1B 96.374 524 19 0 1 524 327846256 327845733 0.000000e+00 863.0
8 TraesCS4A01G424100 chr5B 95.825 527 21 1 1 526 491080164 491080690 0.000000e+00 850.0
9 TraesCS4A01G424100 chr5B 93.346 526 35 0 1 526 568826095 568826620 0.000000e+00 778.0
10 TraesCS4A01G424100 chr2B 95.256 527 25 0 1 527 677867197 677866671 0.000000e+00 835.0
11 TraesCS4A01G424100 chr2B 100.000 51 0 0 1809 1859 535809362 535809412 6.680000e-16 95.3
12 TraesCS4A01G424100 chr3A 94.095 525 31 0 1 525 657465318 657464794 0.000000e+00 798.0
13 TraesCS4A01G424100 chr3D 93.143 525 36 0 1 525 160129925 160129401 0.000000e+00 771.0
14 TraesCS4A01G424100 chr3D 97.826 46 1 0 1821 1866 428552472 428552427 1.870000e-11 80.5
15 TraesCS4A01G424100 chr7B 92.966 526 37 0 1 526 89886237 89885712 0.000000e+00 767.0
16 TraesCS4A01G424100 chr5A 92.571 525 39 0 2 526 18064224 18064748 0.000000e+00 754.0
17 TraesCS4A01G424100 chr2A 81.450 469 65 15 860 1321 749626651 749626198 4.610000e-97 364.0
18 TraesCS4A01G424100 chr2D 80.879 455 65 14 885 1337 618693852 618693418 2.790000e-89 339.0
19 TraesCS4A01G424100 chr2D 81.992 261 22 10 594 846 618694782 618694539 4.950000e-47 198.0
20 TraesCS4A01G424100 chr2D 90.370 135 3 1 1809 1933 463581481 463581615 3.880000e-38 169.0
21 TraesCS4A01G424100 chr2D 88.889 135 5 1 1809 1933 644565824 644565958 8.390000e-35 158.0
22 TraesCS4A01G424100 chr7D 91.111 135 2 1 1809 1933 442990375 442990509 8.330000e-40 174.0
23 TraesCS4A01G424100 chr7D 89.630 135 4 1 1809 1933 69904868 69904734 1.800000e-36 163.0
24 TraesCS4A01G424100 chr3B 88.000 150 8 2 1810 1950 673836692 673836544 3.880000e-38 169.0
25 TraesCS4A01G424100 chr5D 89.630 135 4 1 1809 1933 295827923 295828057 1.800000e-36 163.0
26 TraesCS4A01G424100 chr1D 82.036 167 24 5 2088 2253 206801102 206800941 1.090000e-28 137.0
27 TraesCS4A01G424100 chr4B 79.762 168 30 3 2091 2257 25052771 25052607 3.960000e-23 119.0
28 TraesCS4A01G424100 chr7A 91.071 56 4 1 1553 1608 545930937 545930991 8.700000e-10 75.0


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 TraesCS4A01G424100 chr4A 694694585 694696854 2269 False 4193.0 4193 100.0000 1 2270 1 chr4A.!!$F3 2269
1 TraesCS4A01G424100 chr4A 694708576 694710929 2353 False 2012.5 2652 97.7775 1 2270 2 chr4A.!!$F5 2269
2 TraesCS4A01G424100 chr4A 694676348 694678180 1832 False 1479.5 2615 93.6470 525 2270 2 chr4A.!!$F4 1745
3 TraesCS4A01G424100 chr4A 694438903 694439802 899 False 979.0 979 86.5880 554 1464 1 chr4A.!!$F2 910
4 TraesCS4A01G424100 chr1B 327845733 327846256 523 True 863.0 863 96.3740 1 524 1 chr1B.!!$R1 523
5 TraesCS4A01G424100 chr5B 491080164 491080690 526 False 850.0 850 95.8250 1 526 1 chr5B.!!$F1 525
6 TraesCS4A01G424100 chr5B 568826095 568826620 525 False 778.0 778 93.3460 1 526 1 chr5B.!!$F2 525
7 TraesCS4A01G424100 chr2B 677866671 677867197 526 True 835.0 835 95.2560 1 527 1 chr2B.!!$R1 526
8 TraesCS4A01G424100 chr3A 657464794 657465318 524 True 798.0 798 94.0950 1 525 1 chr3A.!!$R1 524
9 TraesCS4A01G424100 chr3D 160129401 160129925 524 True 771.0 771 93.1430 1 525 1 chr3D.!!$R1 524
10 TraesCS4A01G424100 chr7B 89885712 89886237 525 True 767.0 767 92.9660 1 526 1 chr7B.!!$R1 525
11 TraesCS4A01G424100 chr5A 18064224 18064748 524 False 754.0 754 92.5710 2 526 1 chr5A.!!$F1 524
12 TraesCS4A01G424100 chr2D 618693418 618694782 1364 True 268.5 339 81.4355 594 1337 2 chr2D.!!$R1 743

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
179 180 2.669569 AAGCGGAACTGCATGCGT 60.670 55.556 14.09 11.19 36.44 5.24 F
401 402 3.192001 AGCACATCAGTTGGCTTTGTATG 59.808 43.478 0.00 0.00 30.55 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1084 1975 2.090400 CCGTCTATGATGGCTGGATG 57.910 55.000 0.00 0.0 31.58 3.51 R
1743 2634 2.567615 ACTAGAAAGCCTTGACACGGAT 59.432 45.455 1.33 0.0 0.00 4.18 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
179 180 2.669569 AAGCGGAACTGCATGCGT 60.670 55.556 14.09 11.19 36.44 5.24
401 402 3.192001 AGCACATCAGTTGGCTTTGTATG 59.808 43.478 0.00 0.00 30.55 2.39
773 993 7.148205 GGGATTGCCGTAAATCTTAGTGTAAAA 60.148 37.037 7.11 0.00 36.87 1.52
774 994 8.238631 GGATTGCCGTAAATCTTAGTGTAAAAA 58.761 33.333 7.11 0.00 36.87 1.94
775 995 9.783256 GATTGCCGTAAATCTTAGTGTAAAAAT 57.217 29.630 1.18 0.00 34.35 1.82
776 996 8.958175 TTGCCGTAAATCTTAGTGTAAAAATG 57.042 30.769 0.00 0.00 0.00 2.32
777 997 7.531716 TGCCGTAAATCTTAGTGTAAAAATGG 58.468 34.615 0.00 0.00 0.00 3.16
778 998 7.175293 TGCCGTAAATCTTAGTGTAAAAATGGT 59.825 33.333 0.00 0.00 0.00 3.55
779 999 8.667463 GCCGTAAATCTTAGTGTAAAAATGGTA 58.333 33.333 0.00 0.00 0.00 3.25
780 1000 9.977762 CCGTAAATCTTAGTGTAAAAATGGTAC 57.022 33.333 0.00 0.00 0.00 3.34
781 1001 9.679596 CGTAAATCTTAGTGTAAAAATGGTACG 57.320 33.333 0.00 0.00 0.00 3.67
782 1002 9.977762 GTAAATCTTAGTGTAAAAATGGTACGG 57.022 33.333 0.00 0.00 0.00 4.02
783 1003 8.625786 AAATCTTAGTGTAAAAATGGTACGGT 57.374 30.769 0.00 0.00 0.00 4.83
784 1004 7.605410 ATCTTAGTGTAAAAATGGTACGGTG 57.395 36.000 0.00 0.00 0.00 4.94
785 1005 6.523840 TCTTAGTGTAAAAATGGTACGGTGT 58.476 36.000 0.00 0.00 0.00 4.16
786 1006 6.991531 TCTTAGTGTAAAAATGGTACGGTGTT 59.008 34.615 0.00 0.00 0.00 3.32
787 1007 7.498570 TCTTAGTGTAAAAATGGTACGGTGTTT 59.501 33.333 0.00 0.00 0.00 2.83
788 1008 8.668510 TTAGTGTAAAAATGGTACGGTGTTTA 57.331 30.769 0.00 0.00 0.00 2.01
789 1009 7.565323 AGTGTAAAAATGGTACGGTGTTTAA 57.435 32.000 0.00 0.00 0.00 1.52
790 1010 8.168790 AGTGTAAAAATGGTACGGTGTTTAAT 57.831 30.769 0.00 0.00 0.00 1.40
791 1011 8.631797 AGTGTAAAAATGGTACGGTGTTTAATT 58.368 29.630 0.00 0.00 0.00 1.40
792 1012 9.890352 GTGTAAAAATGGTACGGTGTTTAATTA 57.110 29.630 0.00 0.00 0.00 1.40
866 1122 4.788679 TGACCAGAGACGATATACTTCCA 58.211 43.478 0.00 0.00 0.00 3.53
1084 1975 0.389037 GCAGTTGCTTAAGGCTTGCC 60.389 55.000 10.69 2.97 42.39 4.52
1654 2545 5.470437 TGTGCAATTAACGTAATCCTTGTCA 59.530 36.000 0.00 0.00 0.00 3.58
1669 2560 2.815211 TCAATCCTGAGCGCACGC 60.815 61.111 11.47 6.99 42.33 5.34
1743 2634 1.468506 TACGCCAGTGCTCTTCCACA 61.469 55.000 0.00 0.00 38.18 4.17
2095 2995 7.810766 TGAAACTTGTTTCTTGACATTGTTC 57.189 32.000 21.81 0.00 31.18 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
250 251 1.601759 AGTCAATGCTGCCAACGCT 60.602 52.632 0.00 0.00 35.36 5.07
401 402 3.119708 ACAGTAGTGAATTCCGTACGACC 60.120 47.826 18.76 1.24 0.00 4.79
775 995 8.189460 GCCATTAATTAATTAAACACCGTACCA 58.811 33.333 21.33 0.00 36.02 3.25
776 996 8.407832 AGCCATTAATTAATTAAACACCGTACC 58.592 33.333 21.33 6.13 36.02 3.34
777 997 9.228636 CAGCCATTAATTAATTAAACACCGTAC 57.771 33.333 21.33 8.18 36.02 3.67
778 998 7.916450 GCAGCCATTAATTAATTAAACACCGTA 59.084 33.333 21.33 0.38 36.02 4.02
779 999 6.754675 GCAGCCATTAATTAATTAAACACCGT 59.245 34.615 21.33 4.58 36.02 4.83
780 1000 6.075099 CGCAGCCATTAATTAATTAAACACCG 60.075 38.462 21.33 15.36 36.02 4.94
781 1001 6.754675 ACGCAGCCATTAATTAATTAAACACC 59.245 34.615 21.33 11.80 36.02 4.16
782 1002 7.749539 ACGCAGCCATTAATTAATTAAACAC 57.250 32.000 21.33 14.10 36.02 3.32
783 1003 8.679100 ACTACGCAGCCATTAATTAATTAAACA 58.321 29.630 21.33 3.05 36.02 2.83
789 1009 9.893305 GAAATTACTACGCAGCCATTAATTAAT 57.107 29.630 4.81 4.81 0.00 1.40
790 1010 8.894731 TGAAATTACTACGCAGCCATTAATTAA 58.105 29.630 0.00 0.00 0.00 1.40
791 1011 8.439993 TGAAATTACTACGCAGCCATTAATTA 57.560 30.769 0.00 0.00 0.00 1.40
792 1012 7.328277 TGAAATTACTACGCAGCCATTAATT 57.672 32.000 0.00 0.00 0.00 1.40
793 1013 6.017109 CCTGAAATTACTACGCAGCCATTAAT 60.017 38.462 0.00 0.00 0.00 1.40
794 1014 5.295787 CCTGAAATTACTACGCAGCCATTAA 59.704 40.000 0.00 0.00 0.00 1.40
795 1015 4.814234 CCTGAAATTACTACGCAGCCATTA 59.186 41.667 0.00 0.00 0.00 1.90
866 1122 1.073199 CAGGACCGGGCAGTTTTCT 59.927 57.895 11.00 0.00 0.00 2.52
1084 1975 2.090400 CCGTCTATGATGGCTGGATG 57.910 55.000 0.00 0.00 31.58 3.51
1654 2545 3.899981 TTGGCGTGCGCTCAGGATT 62.900 57.895 16.21 0.00 41.60 3.01
1682 2573 3.127895 CCAACACGTTCCACTCAGAAAAA 59.872 43.478 0.00 0.00 0.00 1.94
1743 2634 2.567615 ACTAGAAAGCCTTGACACGGAT 59.432 45.455 1.33 0.00 0.00 4.18
2012 2912 2.618442 TCTGAACACAGTGTGCATGA 57.382 45.000 23.21 11.47 34.92 3.07
2095 2995 7.966204 TCTGAGAAGAAAAACAACCTTAAAACG 59.034 33.333 0.00 0.00 0.00 3.60


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

AutoCloner maintained by Alex Coulton.