Multiple sequence alignment - TraesCS3A01G497600

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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 TraesCS3A01G497600 chr3A 100.000 3104 0 0 1 3104 723662831 723659728 0.000000e+00 5733
1 TraesCS3A01G497600 chr3A 87.099 1589 163 24 1419 2976 724022968 724021391 0.000000e+00 1760
2 TraesCS3A01G497600 chr3A 89.492 295 28 3 764 1055 724023573 724023279 1.360000e-98 370
3 TraesCS3A01G497600 chr3D 96.276 3115 79 13 1 3104 592607019 592610107 0.000000e+00 5075
4 TraesCS3A01G497600 chr3D 86.522 1610 175 24 1413 2989 592576741 592578341 0.000000e+00 1733
5 TraesCS3A01G497600 chr3D 89.962 528 46 7 753 1274 592575667 592576193 0.000000e+00 675
6 TraesCS3A01G497600 chr3B 95.228 2389 88 10 1 2384 794545498 794543131 0.000000e+00 3757
7 TraesCS3A01G497600 chr3B 86.147 1617 184 29 1350 2934 794840188 794838580 0.000000e+00 1709
8 TraesCS3A01G497600 chr3B 88.208 1289 125 14 1419 2689 794593079 794591800 0.000000e+00 1513
9 TraesCS3A01G497600 chr3B 92.963 739 33 4 2373 3104 794541617 794540891 0.000000e+00 1059
10 TraesCS3A01G497600 chr3B 83.775 906 109 25 421 1297 794841070 794840174 0.000000e+00 824
11 TraesCS3A01G497600 chr3B 89.088 559 53 8 747 1297 794593698 794593140 0.000000e+00 688


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 TraesCS3A01G497600 chr3A 723659728 723662831 3103 True 5733.0 5733 100.0000 1 3104 1 chr3A.!!$R1 3103
1 TraesCS3A01G497600 chr3A 724021391 724023573 2182 True 1065.0 1760 88.2955 764 2976 2 chr3A.!!$R2 2212
2 TraesCS3A01G497600 chr3D 592607019 592610107 3088 False 5075.0 5075 96.2760 1 3104 1 chr3D.!!$F1 3103
3 TraesCS3A01G497600 chr3D 592575667 592578341 2674 False 1204.0 1733 88.2420 753 2989 2 chr3D.!!$F2 2236
4 TraesCS3A01G497600 chr3B 794540891 794545498 4607 True 2408.0 3757 94.0955 1 3104 2 chr3B.!!$R1 3103
5 TraesCS3A01G497600 chr3B 794838580 794841070 2490 True 1266.5 1709 84.9610 421 2934 2 chr3B.!!$R3 2513
6 TraesCS3A01G497600 chr3B 794591800 794593698 1898 True 1100.5 1513 88.6480 747 2689 2 chr3B.!!$R2 1942

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
112 113 0.322816 TTGGCTTGCCCTCTGATGTC 60.323 55.0 9.35 0.0 0.00 3.06 F
202 203 0.467804 AAAAATGTTTGGCGGGCAGT 59.532 45.0 3.91 0.0 0.00 4.40 F
1171 1226 1.413382 GCATAGACTGCGAGGAATCG 58.587 55.0 0.00 0.0 41.97 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1702 2239 1.154035 GCAAAAGCGGAATGGGTCG 60.154 57.895 0.00 0.0 0.0 4.79 R
1717 2254 1.165907 CGTTGCAACCCAGAGAGCAA 61.166 55.000 23.42 0.0 43.9 3.91 R
3052 5166 0.254178 TGAAAGAGAGGCCTCCATGC 59.746 55.000 29.54 14.6 40.3 4.06 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
112 113 0.322816 TTGGCTTGCCCTCTGATGTC 60.323 55.000 9.35 0.00 0.00 3.06
129 130 4.274214 TGATGTCGGAAGATCAATCAATGC 59.726 41.667 0.00 0.00 45.19 3.56
152 153 5.179182 GCTGCTTTTAGCTATCTCAAGGATC 59.821 44.000 0.00 0.00 42.97 3.36
170 171 3.006430 GGATCGGGTGTGGAAAAATGTTT 59.994 43.478 0.00 0.00 0.00 2.83
202 203 0.467804 AAAAATGTTTGGCGGGCAGT 59.532 45.000 3.91 0.00 0.00 4.40
209 210 1.531739 TTTGGCGGGCAGTGGAAATC 61.532 55.000 3.91 0.00 0.00 2.17
386 388 9.848710 TGTAATCCCGTTATAATGGAATAAACA 57.151 29.630 23.06 14.02 37.24 2.83
566 571 4.214310 TGTGGGCCATATAATTTCCAGTG 58.786 43.478 10.70 0.00 0.00 3.66
923 978 3.055891 CAGTTTCATCCCCACAAATTCCC 60.056 47.826 0.00 0.00 0.00 3.97
1028 1083 4.625742 ACATAGTAGTACAAGTGCAAAGCG 59.374 41.667 2.52 0.00 0.00 4.68
1171 1226 1.413382 GCATAGACTGCGAGGAATCG 58.587 55.000 0.00 0.00 41.97 3.34
1179 1234 2.279517 CGAGGAATCGAAGGGCGG 60.280 66.667 0.00 0.00 41.33 6.13
1717 2254 0.323629 TTCTCGACCCATTCCGCTTT 59.676 50.000 0.00 0.00 0.00 3.51
1796 2334 7.619964 ACCCCGTGTTATTAGTTCATTTAAG 57.380 36.000 0.00 0.00 0.00 1.85
1800 2338 9.165035 CCCGTGTTATTAGTTCATTTAAGGTTA 57.835 33.333 0.00 0.00 0.00 2.85
2609 4699 7.535258 CACTTATAACTTGAATGTTGTCTGCAC 59.465 37.037 0.00 0.00 0.00 4.57
2693 4787 1.798813 CTGTAGCCACCAAAGTCGAAC 59.201 52.381 0.00 0.00 0.00 3.95
2772 4870 2.952978 CCTCGTCACTACTTAGCTGGAT 59.047 50.000 0.00 0.00 0.00 3.41
2851 4949 2.551032 CTGTTTCACTTGCAGCAGATGA 59.449 45.455 6.58 6.58 0.00 2.92
3023 5137 6.540189 GGAAGAGAACACATGCACTATATTGT 59.460 38.462 0.00 0.00 0.00 2.71
3052 5166 1.593196 ACCAAGTCATCACACCAACG 58.407 50.000 0.00 0.00 0.00 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.203040 CCCCAGAACATCTCCTACCAAAT 59.797 47.826 0.00 0.0 0.00 2.32
112 113 2.617308 AGCAGCATTGATTGATCTTCCG 59.383 45.455 0.00 0.0 0.00 4.30
129 130 5.404968 CGATCCTTGAGATAGCTAAAAGCAG 59.595 44.000 0.00 0.0 38.53 4.24
152 153 3.305744 CCCTAAACATTTTTCCACACCCG 60.306 47.826 0.00 0.0 0.00 5.28
170 171 3.756082 ACATTTTTCCATCCAGCCCTA 57.244 42.857 0.00 0.0 0.00 3.53
202 203 3.071892 ACGAACTACCAACCAGATTTCCA 59.928 43.478 0.00 0.0 0.00 3.53
209 210 4.393990 GGGAATAAACGAACTACCAACCAG 59.606 45.833 0.00 0.0 0.00 4.00
343 345 2.191128 ACACAATCCAGAGGCAAGAC 57.809 50.000 0.00 0.0 0.00 3.01
597 607 6.743575 AGCCAACACATAATTAGTTCTGTC 57.256 37.500 0.00 0.0 0.00 3.51
599 609 6.324819 CCAAGCCAACACATAATTAGTTCTG 58.675 40.000 0.00 0.0 0.00 3.02
909 964 0.563173 TGTTGGGGAATTTGTGGGGA 59.437 50.000 0.00 0.0 0.00 4.81
923 978 0.595588 TGGCGCACATAGTTTGTTGG 59.404 50.000 10.83 0.0 36.00 3.77
1028 1083 3.308530 CCTTCATGGCGAAAACAAAGAC 58.691 45.455 0.00 0.0 31.71 3.01
1179 1234 4.752224 CGAACGACAATAATAGCAGAAGC 58.248 43.478 0.00 0.0 42.56 3.86
1702 2239 1.154035 GCAAAAGCGGAATGGGTCG 60.154 57.895 0.00 0.0 0.00 4.79
1717 2254 1.165907 CGTTGCAACCCAGAGAGCAA 61.166 55.000 23.42 0.0 43.90 3.91
2299 2853 1.337260 CCCATCACCTCTGCTATACGC 60.337 57.143 0.00 0.0 39.77 4.42
2484 4571 6.250951 CGTCTTTGTAGTTCTATTCTTCCGAC 59.749 42.308 0.00 0.0 0.00 4.79
2486 4573 5.515626 CCGTCTTTGTAGTTCTATTCTTCCG 59.484 44.000 0.00 0.0 0.00 4.30
2627 4717 4.698304 CCGAAAAGCTTTATTCCACCTGTA 59.302 41.667 13.10 0.0 0.00 2.74
2772 4870 4.202388 GGGGTATTCGGAATTTACTAGGCA 60.202 45.833 8.76 0.0 0.00 4.75
2851 4949 1.064825 ATCGACCTGTCCCCTTTTGT 58.935 50.000 0.00 0.0 0.00 2.83
3023 5137 5.049954 GTGTGATGACTTGGTAAGCGTTTAA 60.050 40.000 0.00 0.0 0.00 1.52
3052 5166 0.254178 TGAAAGAGAGGCCTCCATGC 59.746 55.000 29.54 14.6 40.30 4.06


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

AutoCloner maintained by Alex Coulton.