Multiple sequence alignment - TraesCS1A01G267400

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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 TraesCS1A01G267400 chr1A 100.000 2548 0 0 1 2548 462528961 462531508 0.000000e+00 4706
1 TraesCS1A01G267400 chr1A 95.775 1728 67 6 565 2289 71245446 71243722 0.000000e+00 2782
2 TraesCS1A01G267400 chr1A 95.804 572 24 0 1 572 533484410 533484981 0.000000e+00 924
3 TraesCS1A01G267400 chr1A 99.286 280 2 0 2269 2548 531498278 531497999 8.130000e-140 507
4 TraesCS1A01G267400 chr2A 96.386 1937 66 3 573 2505 613866458 613868394 0.000000e+00 3186
5 TraesCS1A01G267400 chr2A 95.629 572 25 0 1 572 46247293 46246722 0.000000e+00 918
6 TraesCS1A01G267400 chr3A 96.404 1724 59 3 568 2289 735555336 735557058 0.000000e+00 2837
7 TraesCS1A01G267400 chr3A 95.785 1732 66 7 563 2289 617401012 617402741 0.000000e+00 2787
8 TraesCS1A01G267400 chr6A 96.107 1721 63 3 573 2289 617222869 617221149 0.000000e+00 2804
9 TraesCS1A01G267400 chr6A 95.879 1723 68 3 569 2289 616131292 616133013 0.000000e+00 2785
10 TraesCS1A01G267400 chr6A 96.329 572 21 0 1 572 103045773 103046344 0.000000e+00 941
11 TraesCS1A01G267400 chr6A 98.929 280 3 0 2269 2548 203519194 203518915 3.780000e-138 501
12 TraesCS1A01G267400 chr6A 98.929 280 2 1 2269 2548 61538570 61538292 1.360000e-137 499
13 TraesCS1A01G267400 chr6B 95.882 1724 67 3 569 2289 660437747 660436025 0.000000e+00 2787
14 TraesCS1A01G267400 chr2B 95.821 1723 68 3 570 2289 781094238 781095959 0.000000e+00 2780
15 TraesCS1A01G267400 chr2B 95.819 1722 68 3 571 2289 776222960 776224680 0.000000e+00 2778
16 TraesCS1A01G267400 chr3B 90.184 2007 139 22 572 2548 440311329 440313307 0.000000e+00 2562
17 TraesCS1A01G267400 chr1D 96.329 572 21 0 1 572 248164474 248163903 0.000000e+00 941
18 TraesCS1A01G267400 chr7A 96.154 572 22 0 1 572 228536881 228536310 0.000000e+00 935
19 TraesCS1A01G267400 chr7A 98.929 280 3 0 2269 2548 36947898 36948177 3.780000e-138 501
20 TraesCS1A01G267400 chr7A 98.929 280 3 0 2269 2548 689994639 689994360 3.780000e-138 501
21 TraesCS1A01G267400 chr4D 95.812 573 22 2 1 572 85298431 85297860 0.000000e+00 924
22 TraesCS1A01G267400 chr4A 95.629 572 24 1 1 572 25335365 25335935 0.000000e+00 917
23 TraesCS1A01G267400 chr4A 95.455 572 26 0 1 572 153280898 153280327 0.000000e+00 913
24 TraesCS1A01G267400 chr4A 95.455 572 26 0 1 572 349568780 349568209 0.000000e+00 913
25 TraesCS1A01G267400 chr5D 93.501 477 25 5 2075 2548 473076925 473077398 0.000000e+00 704
26 TraesCS1A01G267400 chrUn 98.571 280 4 0 2269 2548 353552083 353551804 1.760000e-136 496


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 TraesCS1A01G267400 chr1A 462528961 462531508 2547 False 4706 4706 100.000 1 2548 1 chr1A.!!$F1 2547
1 TraesCS1A01G267400 chr1A 71243722 71245446 1724 True 2782 2782 95.775 565 2289 1 chr1A.!!$R1 1724
2 TraesCS1A01G267400 chr1A 533484410 533484981 571 False 924 924 95.804 1 572 1 chr1A.!!$F2 571
3 TraesCS1A01G267400 chr2A 613866458 613868394 1936 False 3186 3186 96.386 573 2505 1 chr2A.!!$F1 1932
4 TraesCS1A01G267400 chr2A 46246722 46247293 571 True 918 918 95.629 1 572 1 chr2A.!!$R1 571
5 TraesCS1A01G267400 chr3A 735555336 735557058 1722 False 2837 2837 96.404 568 2289 1 chr3A.!!$F2 1721
6 TraesCS1A01G267400 chr3A 617401012 617402741 1729 False 2787 2787 95.785 563 2289 1 chr3A.!!$F1 1726
7 TraesCS1A01G267400 chr6A 617221149 617222869 1720 True 2804 2804 96.107 573 2289 1 chr6A.!!$R3 1716
8 TraesCS1A01G267400 chr6A 616131292 616133013 1721 False 2785 2785 95.879 569 2289 1 chr6A.!!$F2 1720
9 TraesCS1A01G267400 chr6A 103045773 103046344 571 False 941 941 96.329 1 572 1 chr6A.!!$F1 571
10 TraesCS1A01G267400 chr6B 660436025 660437747 1722 True 2787 2787 95.882 569 2289 1 chr6B.!!$R1 1720
11 TraesCS1A01G267400 chr2B 781094238 781095959 1721 False 2780 2780 95.821 570 2289 1 chr2B.!!$F2 1719
12 TraesCS1A01G267400 chr2B 776222960 776224680 1720 False 2778 2778 95.819 571 2289 1 chr2B.!!$F1 1718
13 TraesCS1A01G267400 chr3B 440311329 440313307 1978 False 2562 2562 90.184 572 2548 1 chr3B.!!$F1 1976
14 TraesCS1A01G267400 chr1D 248163903 248164474 571 True 941 941 96.329 1 572 1 chr1D.!!$R1 571
15 TraesCS1A01G267400 chr7A 228536310 228536881 571 True 935 935 96.154 1 572 1 chr7A.!!$R1 571
16 TraesCS1A01G267400 chr4D 85297860 85298431 571 True 924 924 95.812 1 572 1 chr4D.!!$R1 571
17 TraesCS1A01G267400 chr4A 25335365 25335935 570 False 917 917 95.629 1 572 1 chr4A.!!$F1 571
18 TraesCS1A01G267400 chr4A 153280327 153280898 571 True 913 913 95.455 1 572 1 chr4A.!!$R1 571
19 TraesCS1A01G267400 chr4A 349568209 349568780 571 True 913 913 95.455 1 572 1 chr4A.!!$R2 571

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
601 602 0.110486 TCCTTTTGCCCTCAGTGGTC 59.89 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2185 2218 1.957877 ACCATAAACACCACAAACCCG 59.042 47.619 0.0 0.0 0.0 5.28 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
86 87 3.197333 TGGATCCGATAACCCGTTAACAA 59.803 43.478 7.39 0.00 0.00 2.83
163 164 2.126307 CAGCTCGTCAGTGGGTCG 60.126 66.667 0.00 0.00 0.00 4.79
316 317 4.662278 GAATATAGCCCATTTACAGCCCA 58.338 43.478 0.00 0.00 0.00 5.36
325 326 3.627237 CCATTTACAGCCCACTAACCCAT 60.627 47.826 0.00 0.00 0.00 4.00
327 328 1.959710 TACAGCCCACTAACCCATGA 58.040 50.000 0.00 0.00 0.00 3.07
601 602 0.110486 TCCTTTTGCCCTCAGTGGTC 59.890 55.000 0.00 0.00 0.00 4.02
612 613 2.834549 CCTCAGTGGTCTCCATGTACTT 59.165 50.000 0.00 0.00 35.28 2.24
659 660 1.351017 CTCAGTTTTGCCCCTAGTCCA 59.649 52.381 0.00 0.00 0.00 4.02
667 668 2.735772 CCCCTAGTCCATGCGCACT 61.736 63.158 14.90 8.07 0.00 4.40
737 738 1.785353 GCCCTTACAGGTGGGACCAA 61.785 60.000 1.75 0.00 46.15 3.67
938 943 2.203437 TAGCTATGGAGGGCGCGA 60.203 61.111 12.10 0.00 0.00 5.87
1016 1021 2.169352 GCTCCATGTCTTCCTCAAGCTA 59.831 50.000 0.00 0.00 0.00 3.32
1023 1028 2.564553 CTTCCTCAAGCTACCGCGCT 62.565 60.000 5.56 0.00 43.31 5.92
1073 1078 2.941453 GACATGCCTGTCTTCGTCTA 57.059 50.000 14.17 0.00 46.84 2.59
1210 1216 0.250234 TGGTCGGGATCTTTGAGCAG 59.750 55.000 9.21 0.00 35.42 4.24
1246 1252 1.470098 GGTGTTCATGCAGGTGACATC 59.530 52.381 11.97 8.75 0.00 3.06
1271 1277 3.513912 TCTTTCTTTGGGTCGATGCTCTA 59.486 43.478 0.00 0.00 0.00 2.43
1311 1317 3.884693 TGAACTGCAAGAAGAGCATGAAA 59.115 39.130 0.00 0.00 41.82 2.69
1806 1817 1.486726 GTGCAGGCTAGACTAATGGGT 59.513 52.381 0.00 0.00 0.00 4.51
1864 1877 8.280497 TCTCTTGCGTATTTTTCTGTTTTCTAC 58.720 33.333 0.00 0.00 0.00 2.59
1927 1940 9.476202 ACTTTTTGTGGAAGCTAATTGAATTAC 57.524 29.630 0.00 0.00 0.00 1.89
1985 2017 6.616947 TGAAGCTGTTAATTAACCCAATTCG 58.383 36.000 22.47 6.37 37.93 3.34
2007 2039 7.780008 TCGAATACACCGTGATTTAAATCAT 57.220 32.000 28.66 17.29 46.17 2.45
2077 2109 3.261580 GCCAGGTGCCAAAATAAATGAC 58.738 45.455 0.00 0.00 0.00 3.06
2085 2117 7.174772 AGGTGCCAAAATAAATGACCATTTTTC 59.825 33.333 12.51 0.00 40.99 2.29
2202 2235 0.594110 CGCGGGTTTGTGGTGTTTAT 59.406 50.000 0.00 0.00 0.00 1.40
2205 2238 1.957877 CGGGTTTGTGGTGTTTATGGT 59.042 47.619 0.00 0.00 0.00 3.55
2273 2306 7.473593 GGTAGGGAAGGAAGGTATACATAGTA 58.526 42.308 5.01 0.00 0.00 1.82
2466 2500 8.891671 AAATTTGCATGTTAGTTCATGACTTT 57.108 26.923 10.28 0.00 45.41 2.66
2533 2569 7.359595 TCATTAATGAAAACCACAAGTTCTCG 58.640 34.615 15.82 0.00 37.88 4.04
2537 2573 3.375922 TGAAAACCACAAGTTCTCGAACC 59.624 43.478 6.20 0.00 42.06 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 0.411848 AATTTCCCATTGGTCGGGGT 59.588 50.000 1.20 0.00 44.62 4.95
110 111 5.010933 TCCGGCCAATAAGAATTTTACACA 58.989 37.500 2.24 0.00 0.00 3.72
163 164 3.551046 CGATGTATCATAGGCGCCTATCC 60.551 52.174 39.90 27.64 37.16 2.59
265 266 2.159382 CGTTAACAGGCTTTCCATGGT 58.841 47.619 12.58 0.00 33.74 3.55
316 317 2.420967 GCGTAATGGGTCATGGGTTAGT 60.421 50.000 0.00 0.00 0.00 2.24
325 326 1.053424 GGATAGGGCGTAATGGGTCA 58.947 55.000 0.00 0.00 0.00 4.02
327 328 0.470456 TCGGATAGGGCGTAATGGGT 60.470 55.000 0.00 0.00 0.00 4.51
601 602 4.589908 AGGGCAAAACTAAGTACATGGAG 58.410 43.478 0.00 0.00 0.00 3.86
612 613 1.277842 TCGCATCTGAGGGCAAAACTA 59.722 47.619 5.18 0.00 0.00 2.24
659 660 1.738099 GGAACGAGTCAGTGCGCAT 60.738 57.895 15.91 0.00 0.00 4.73
667 668 2.610479 GCAGAGTTCATGGAACGAGTCA 60.610 50.000 3.69 0.00 45.96 3.41
754 755 3.608073 GCATGCAACGGTCTGAATAAAAC 59.392 43.478 14.21 0.00 0.00 2.43
938 943 1.913762 ACTGCTAGCTTCCCACCGT 60.914 57.895 17.23 0.00 0.00 4.83
1087 1092 4.143333 CCTCCGATCAACGCCCGT 62.143 66.667 0.00 0.00 41.07 5.28
1210 1216 2.306847 ACACCAAACAGATCAACCCAC 58.693 47.619 0.00 0.00 0.00 4.61
1246 1252 2.162408 GCATCGACCCAAAGAAAGAAGG 59.838 50.000 0.00 0.00 0.00 3.46
1271 1277 4.019501 AGTTCATTCATCAGAGTCTTGGCT 60.020 41.667 0.00 0.00 0.00 4.75
1311 1317 4.582760 CAGCATGCGCAACCATTT 57.417 50.000 17.11 0.00 42.27 2.32
1360 1366 1.207791 GCCCTCCATCTCTTCTTCCA 58.792 55.000 0.00 0.00 0.00 3.53
1806 1817 2.378038 GGCCTAATTGGATGCAGTTGA 58.622 47.619 5.19 0.00 38.35 3.18
1927 1940 2.017049 CCTAATTGTTTGGCTCCGGAG 58.983 52.381 27.83 27.83 0.00 4.63
1977 2009 2.623535 TCACGGTGTATTCGAATTGGG 58.376 47.619 17.19 3.20 0.00 4.12
2007 2039 7.377398 CACATTTTCCATGACATTTTGGTCTA 58.623 34.615 0.00 0.00 38.61 2.59
2077 2109 6.171921 TCAATGTAATGCCCTTGAAAAATGG 58.828 36.000 0.00 0.00 0.00 3.16
2085 2117 6.222389 TGTTTTTCTCAATGTAATGCCCTTG 58.778 36.000 0.00 0.00 0.00 3.61
2159 2192 2.203182 TGGGTTCGAGTCCCCAGT 59.797 61.111 20.23 0.00 46.06 4.00
2185 2218 1.957877 ACCATAAACACCACAAACCCG 59.042 47.619 0.00 0.00 0.00 5.28
2202 2235 2.666862 CGGTTACCAGCGCAACCA 60.667 61.111 22.63 0.00 43.70 3.67
2273 2306 2.020720 TGTGCAAACATTCACGGTCTT 58.979 42.857 0.00 0.00 36.06 3.01


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

AutoCloner maintained by Alex Coulton.