Multiple sequence alignment - TraesCS2A01G342600

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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 TraesCS2A01G342600 chr2A 100.000 2890 0 0 1 2890 579617954 579615065 0.000000e+00 5337
1 TraesCS2A01G342600 chr2D 95.413 2507 68 23 7 2499 412282747 412280274 0.000000e+00 3949
2 TraesCS2A01G342600 chr2D 90.909 275 16 4 2616 2890 412279422 412279157 7.610000e-96 361
3 TraesCS2A01G342600 chr2B 96.390 1773 37 11 617 2381 485871936 485870183 0.000000e+00 2894
4 TraesCS2A01G342600 chr2B 91.626 406 19 4 2378 2774 485869902 485869503 5.440000e-152 547
5 TraesCS2A01G342600 chr2B 84.337 332 32 11 37 356 485888927 485888604 1.010000e-79 307


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 TraesCS2A01G342600 chr2A 579615065 579617954 2889 True 5337.0 5337 100.000 1 2890 1 chr2A.!!$R1 2889
1 TraesCS2A01G342600 chr2D 412279157 412282747 3590 True 2155.0 3949 93.161 7 2890 2 chr2D.!!$R1 2883
2 TraesCS2A01G342600 chr2B 485869503 485871936 2433 True 1720.5 2894 94.008 617 2774 2 chr2B.!!$R2 2157

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
597 600 0.037697 TCCAAAGGTGACCGTCATCG 60.038 55.0 4.13 0.0 31.44 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1997 2006 1.597663 CCAAAGAAGTCACGGACACAC 59.402 52.381 6.78 0.0 34.6 3.82 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
46 47 3.493272 CTCTATCGACTGACACACACAC 58.507 50.000 0.00 0.00 0.00 3.82
47 48 2.882137 TCTATCGACTGACACACACACA 59.118 45.455 0.00 0.00 0.00 3.72
58 59 5.704888 TGACACACACACAAAAACCTAAAG 58.295 37.500 0.00 0.00 0.00 1.85
63 64 5.654650 ACACACACAAAAACCTAAAGGATCA 59.345 36.000 2.23 0.00 38.94 2.92
76 77 8.950007 ACCTAAAGGATCACTCCAAAATTTAA 57.050 30.769 2.23 0.00 44.79 1.52
82 83 7.661040 AGGATCACTCCAAAATTTAAACTGTG 58.339 34.615 0.00 0.00 44.79 3.66
83 84 7.287696 AGGATCACTCCAAAATTTAAACTGTGT 59.712 33.333 0.00 0.00 44.79 3.72
102 103 9.783256 AACTGTGTAAAAACTATCAACACTTTC 57.217 29.630 5.61 0.00 40.78 2.62
226 227 9.066892 TCTGCACAAAACTGAAATTTACTCTAT 57.933 29.630 0.00 0.00 0.00 1.98
248 249 9.695526 TCTATATCAAATTGTATGCATTTTGCC 57.304 29.630 19.93 0.00 44.23 4.52
281 282 3.118847 GGTTAGCTAGGCGTAAGGTCTTT 60.119 47.826 0.00 0.00 38.28 2.52
286 287 3.428045 GCTAGGCGTAAGGTCTTTCGTTA 60.428 47.826 10.46 4.66 36.08 3.18
290 291 4.815846 AGGCGTAAGGTCTTTCGTTAAAAA 59.184 37.500 10.46 0.00 36.08 1.94
291 292 4.905866 GGCGTAAGGTCTTTCGTTAAAAAC 59.094 41.667 10.46 0.00 36.08 2.43
294 295 6.139638 GCGTAAGGTCTTTCGTTAAAAACAAG 59.860 38.462 10.46 0.00 36.08 3.16
295 296 7.401080 CGTAAGGTCTTTCGTTAAAAACAAGA 58.599 34.615 2.34 0.00 0.00 3.02
297 298 6.373186 AGGTCTTTCGTTAAAAACAAGAGG 57.627 37.500 0.00 0.00 27.95 3.69
451 452 3.023119 TGTGTTGAAGATGCCACTGTTT 58.977 40.909 0.00 0.00 0.00 2.83
453 454 4.081752 TGTGTTGAAGATGCCACTGTTTTT 60.082 37.500 0.00 0.00 0.00 1.94
491 492 1.445410 TCGGTTCGCACGATGAAGG 60.445 57.895 0.00 0.00 35.12 3.46
499 500 4.794248 TCGCACGATGAAGGATATTTTG 57.206 40.909 0.00 0.00 0.00 2.44
537 540 5.023533 ACCATATTGCGTTCTATGTGTCT 57.976 39.130 0.00 0.00 0.00 3.41
539 542 6.578944 ACCATATTGCGTTCTATGTGTCTAA 58.421 36.000 0.00 0.00 0.00 2.10
564 567 4.981806 AAAGTTGCATTATATGTGCGGT 57.018 36.364 9.47 0.00 45.37 5.68
572 575 6.402222 TGCATTATATGTGCGGTATGTCATA 58.598 36.000 9.47 0.00 45.37 2.15
597 600 0.037697 TCCAAAGGTGACCGTCATCG 60.038 55.000 4.13 0.00 31.44 3.84
602 605 2.380410 GGTGACCGTCATCGTGTGC 61.380 63.158 4.13 0.00 35.01 4.57
603 606 2.430075 TGACCGTCATCGTGTGCG 60.430 61.111 0.00 0.00 39.92 5.34
612 615 3.912157 TCGTGTGCGAAACGACTC 58.088 55.556 4.45 0.00 44.58 3.36
613 616 1.659335 TCGTGTGCGAAACGACTCC 60.659 57.895 4.45 0.00 44.58 3.85
614 617 1.660575 CGTGTGCGAAACGACTCCT 60.661 57.895 0.00 0.00 43.68 3.69
615 618 1.213094 CGTGTGCGAAACGACTCCTT 61.213 55.000 0.00 0.00 43.68 3.36
635 638 0.309612 GGCAATTATAACGCCCGTGG 59.690 55.000 14.33 0.00 40.07 4.94
647 650 1.004560 CCCGTGGATGGATGGATCG 60.005 63.158 0.00 0.00 0.00 3.69
666 669 6.098266 TGGATCGGATCTTCTTTCACTATTCA 59.902 38.462 16.96 0.00 0.00 2.57
721 724 1.947678 GCAGTCCCCACAGATCACAAG 60.948 57.143 0.00 0.00 0.00 3.16
836 840 0.178828 TACCACCCCAGGATTTCCCA 60.179 55.000 0.00 0.00 37.41 4.37
857 861 3.281240 CACATCTTGTGGCTGCCC 58.719 61.111 17.53 8.23 44.27 5.36
934 938 1.006102 CGCTCCAACAGACGTCCTT 60.006 57.895 13.01 0.52 0.00 3.36
1238 1242 3.935203 TCGTAAGTCTTCCTCGTTCGTAT 59.065 43.478 0.00 0.00 39.48 3.06
1240 1244 4.494764 CGTAAGTCTTCCTCGTTCGTATTG 59.505 45.833 0.00 0.00 0.00 1.90
1259 1263 0.089186 GTTTCTCTTCGTTCGTCGCG 59.911 55.000 0.00 0.00 39.67 5.87
1283 1287 2.404215 CATTAATCCCACTCTACGCGG 58.596 52.381 12.47 0.00 0.00 6.46
1997 2006 3.692576 GAAGAAGCAGCAGCAATGTATG 58.307 45.455 3.17 0.00 45.49 2.39
2021 2030 1.345415 GTCCGTGACTTCTTTGGGGTA 59.655 52.381 0.00 0.00 0.00 3.69
2058 2067 6.155565 TCGAATGGGGAATCAAGTACTCTTTA 59.844 38.462 0.00 0.00 0.00 1.85
2162 2176 6.285990 TCACCTACCAAGTCTTTTAGAACAC 58.714 40.000 1.03 0.00 0.00 3.32
2167 2181 4.576463 ACCAAGTCTTTTAGAACACTGCTG 59.424 41.667 0.00 0.00 0.00 4.41
2192 2206 6.303370 GCATATTTAAACAACCCGCAAAAAG 58.697 36.000 0.00 0.00 0.00 2.27
2195 2209 6.597262 ATTTAAACAACCCGCAAAAAGAAG 57.403 33.333 0.00 0.00 0.00 2.85
2196 2210 3.878160 AAACAACCCGCAAAAAGAAGA 57.122 38.095 0.00 0.00 0.00 2.87
2197 2211 3.878160 AACAACCCGCAAAAAGAAGAA 57.122 38.095 0.00 0.00 0.00 2.52
2198 2212 3.878160 ACAACCCGCAAAAAGAAGAAA 57.122 38.095 0.00 0.00 0.00 2.52
2199 2213 4.195225 ACAACCCGCAAAAAGAAGAAAA 57.805 36.364 0.00 0.00 0.00 2.29
2242 2256 3.247648 GCACGAAAACTAGCAAAGTCTGA 59.752 43.478 0.00 0.00 37.50 3.27
2333 2347 2.023673 CAGGTGTTGGCTCTGAAAACA 58.976 47.619 0.00 0.00 0.00 2.83
2334 2348 2.624838 CAGGTGTTGGCTCTGAAAACAT 59.375 45.455 4.26 0.00 36.31 2.71
2335 2349 3.820467 CAGGTGTTGGCTCTGAAAACATA 59.180 43.478 4.26 0.00 36.31 2.29
2342 2356 9.503427 GTGTTGGCTCTGAAAACATATTATAAC 57.497 33.333 4.26 0.00 36.31 1.89
2366 2380 7.796054 ACACAGAATATATTAACAGGAGCACT 58.204 34.615 0.00 0.00 0.00 4.40
2367 2381 8.924303 ACACAGAATATATTAACAGGAGCACTA 58.076 33.333 0.00 0.00 0.00 2.74
2368 2382 9.935241 CACAGAATATATTAACAGGAGCACTAT 57.065 33.333 0.00 0.00 0.00 2.12
2542 2849 0.878416 GCACCCAGCGACATTGTTAA 59.122 50.000 0.00 0.00 0.00 2.01
2546 2853 2.290641 ACCCAGCGACATTGTTAATCCA 60.291 45.455 0.00 0.00 0.00 3.41
2564 2872 4.993705 TCCAAAAACAGTATCCTCTGGT 57.006 40.909 0.00 0.00 39.48 4.00
2567 2875 4.455877 CCAAAAACAGTATCCTCTGGTGTC 59.544 45.833 0.00 0.00 39.48 3.67
2614 2922 3.131252 AGGTTGGTATAAGGGCAGGATT 58.869 45.455 0.00 0.00 0.00 3.01
2784 3818 6.322456 TGATTAGTGTTCTAGATGGACCTGAG 59.678 42.308 0.00 0.00 0.00 3.35
2785 3819 3.370104 AGTGTTCTAGATGGACCTGAGG 58.630 50.000 0.00 0.00 0.00 3.86
2786 3820 2.432510 GTGTTCTAGATGGACCTGAGGG 59.567 54.545 2.38 0.00 38.88 4.30
2787 3821 2.314852 TGTTCTAGATGGACCTGAGGGA 59.685 50.000 2.38 0.00 36.25 4.20
2788 3822 2.696187 GTTCTAGATGGACCTGAGGGAC 59.304 54.545 2.38 0.00 36.25 4.46
2789 3823 1.218196 TCTAGATGGACCTGAGGGACC 59.782 57.143 2.38 6.75 45.48 4.46
2790 3824 1.219213 CTAGATGGACCTGAGGGACCT 59.781 57.143 15.69 0.00 45.48 3.85
2791 3825 0.326048 AGATGGACCTGAGGGACCTG 60.326 60.000 15.69 0.00 45.48 4.00
2792 3826 0.325671 GATGGACCTGAGGGACCTGA 60.326 60.000 15.69 0.00 45.48 3.86
2798 3832 2.039624 TGAGGGACCTGAGGGCTC 59.960 66.667 3.37 0.00 35.63 4.70
2819 3853 7.309928 GGGCTCTGGACTATTATAAGGAGTTAC 60.310 44.444 4.72 3.13 0.00 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.211515 CAAGCTGCTAGTTCTTTTTGTCATT 58.788 36.000 0.90 0.00 0.00 2.57
1 2 5.766222 CAAGCTGCTAGTTCTTTTTGTCAT 58.234 37.500 0.90 0.00 0.00 3.06
2 3 4.498009 GCAAGCTGCTAGTTCTTTTTGTCA 60.498 41.667 0.90 0.00 40.96 3.58
3 4 3.977579 GCAAGCTGCTAGTTCTTTTTGTC 59.022 43.478 0.90 0.00 40.96 3.18
4 5 3.969899 GCAAGCTGCTAGTTCTTTTTGT 58.030 40.909 0.90 0.00 40.96 2.83
46 47 6.648879 TTGGAGTGATCCTTTAGGTTTTTG 57.351 37.500 0.00 0.00 36.34 2.44
47 48 7.669089 TTTTGGAGTGATCCTTTAGGTTTTT 57.331 32.000 0.00 0.00 36.34 1.94
58 59 7.433680 ACACAGTTTAAATTTTGGAGTGATCC 58.566 34.615 13.67 0.00 0.00 3.36
76 77 9.783256 GAAAGTGTTGATAGTTTTTACACAGTT 57.217 29.630 0.00 0.00 41.07 3.16
96 97 9.330063 TCTAGATTGCCATATTTAGTGAAAGTG 57.670 33.333 0.00 0.00 0.00 3.16
132 133 7.227910 TCTGTTTTGACCTTTTAACGCTAGAAT 59.772 33.333 0.00 0.00 0.00 2.40
226 227 6.887013 AGGGCAAAATGCATACAATTTGATA 58.113 32.000 20.55 0.00 45.58 2.15
248 249 6.053650 ACGCCTAGCTAACCTTTTATTTAGG 58.946 40.000 0.00 0.00 38.79 2.69
281 282 9.863845 ATTTCTTTTTCCTCTTGTTTTTAACGA 57.136 25.926 0.00 0.00 0.00 3.85
286 287 7.280876 GCTGGATTTCTTTTTCCTCTTGTTTTT 59.719 33.333 0.00 0.00 32.95 1.94
290 291 4.895297 TGCTGGATTTCTTTTTCCTCTTGT 59.105 37.500 0.00 0.00 32.95 3.16
291 292 5.458041 TGCTGGATTTCTTTTTCCTCTTG 57.542 39.130 0.00 0.00 32.95 3.02
294 295 5.397142 ACATGCTGGATTTCTTTTTCCTC 57.603 39.130 0.00 0.00 32.95 3.71
295 296 5.813513 AACATGCTGGATTTCTTTTTCCT 57.186 34.783 0.00 0.00 32.95 3.36
297 298 8.437742 CAACATAACATGCTGGATTTCTTTTTC 58.562 33.333 0.00 0.00 0.00 2.29
309 310 2.427812 TGCCATCCAACATAACATGCTG 59.572 45.455 0.00 0.00 0.00 4.41
335 336 3.003689 GCTTAACACAAGCTCACACATGT 59.996 43.478 0.00 0.00 40.01 3.21
410 411 3.904339 ACACCAGAGTTCAAGTCCTATGT 59.096 43.478 0.00 0.00 0.00 2.29
451 452 8.798402 ACCGATCTGTGGTTAAATGATTAAAAA 58.202 29.630 0.00 0.00 35.82 1.94
453 454 7.931578 ACCGATCTGTGGTTAAATGATTAAA 57.068 32.000 0.00 0.00 35.82 1.52
499 500 8.656849 CGCAATATGGTACTATTTTCTACCATC 58.343 37.037 11.71 0.00 46.57 3.51
511 512 7.013942 AGACACATAGAACGCAATATGGTACTA 59.986 37.037 0.00 0.00 34.36 1.82
564 567 5.665360 TCACCTTTGGAGATGGTATGACATA 59.335 40.000 0.00 0.00 34.23 2.29
572 575 0.324943 CGGTCACCTTTGGAGATGGT 59.675 55.000 0.00 0.00 36.28 3.55
597 600 0.232303 CAAGGAGTCGTTTCGCACAC 59.768 55.000 0.00 0.00 0.00 3.82
602 605 1.156736 ATTGCCAAGGAGTCGTTTCG 58.843 50.000 0.00 0.00 0.00 3.46
603 606 4.965119 ATAATTGCCAAGGAGTCGTTTC 57.035 40.909 0.00 0.00 0.00 2.78
604 607 5.163794 CGTTATAATTGCCAAGGAGTCGTTT 60.164 40.000 0.00 0.00 0.00 3.60
605 608 4.331717 CGTTATAATTGCCAAGGAGTCGTT 59.668 41.667 0.00 0.00 0.00 3.85
606 609 3.869246 CGTTATAATTGCCAAGGAGTCGT 59.131 43.478 0.00 0.00 0.00 4.34
607 610 3.303132 GCGTTATAATTGCCAAGGAGTCG 60.303 47.826 2.18 0.00 0.00 4.18
608 611 4.210832 GCGTTATAATTGCCAAGGAGTC 57.789 45.455 2.18 0.00 0.00 3.36
635 638 4.550076 AAGAAGATCCGATCCATCCATC 57.450 45.455 4.67 0.00 0.00 3.51
647 650 5.292101 CGTGGTGAATAGTGAAAGAAGATCC 59.708 44.000 0.00 0.00 0.00 3.36
666 669 0.034767 TGTCGTAGGATCTCCGTGGT 60.035 55.000 0.00 0.00 42.08 4.16
721 724 0.106318 ATCCTGGGCTTTGATGCTCC 60.106 55.000 0.00 0.00 31.16 4.70
1238 1242 1.519758 GCGACGAACGAAGAGAAACAA 59.480 47.619 0.00 0.00 45.77 2.83
1240 1244 0.089186 CGCGACGAACGAAGAGAAAC 59.911 55.000 0.00 0.00 45.77 2.78
1259 1263 2.802816 CGTAGAGTGGGATTAATGCAGC 59.197 50.000 9.34 0.99 0.00 5.25
1299 1303 1.085091 GTCTCAGAGTTGCTGCCATG 58.915 55.000 0.00 0.00 44.52 3.66
1300 1304 0.982704 AGTCTCAGAGTTGCTGCCAT 59.017 50.000 0.00 0.00 44.52 4.40
1301 1305 0.319728 GAGTCTCAGAGTTGCTGCCA 59.680 55.000 0.00 0.00 44.52 4.92
1302 1306 0.319728 TGAGTCTCAGAGTTGCTGCC 59.680 55.000 0.00 0.00 44.52 4.85
1448 1452 1.769098 CGATGAAGATGCCCAGCACG 61.769 60.000 0.00 0.00 43.04 5.34
1823 1827 2.522836 AGTAGAAGATGAGCATGGCG 57.477 50.000 0.00 0.00 0.00 5.69
1997 2006 1.597663 CCAAAGAAGTCACGGACACAC 59.402 52.381 6.78 0.00 34.60 3.82
2021 2030 3.008594 TCCCCATTCGATTTACACACACT 59.991 43.478 0.00 0.00 0.00 3.55
2162 2176 4.432712 GGGTTGTTTAAATATGCCAGCAG 58.567 43.478 0.00 0.00 0.00 4.24
2167 2181 3.512033 TGCGGGTTGTTTAAATATGCC 57.488 42.857 0.00 0.00 0.00 4.40
2197 2211 5.467735 GCTTCCTTCAACTGATGCAATTTTT 59.532 36.000 0.00 0.00 33.30 1.94
2198 2212 4.992951 GCTTCCTTCAACTGATGCAATTTT 59.007 37.500 0.00 0.00 33.30 1.82
2199 2213 4.039488 TGCTTCCTTCAACTGATGCAATTT 59.961 37.500 0.00 0.00 38.31 1.82
2342 2356 9.935241 ATAGTGCTCCTGTTAATATATTCTGTG 57.065 33.333 0.00 0.00 0.00 3.66
2366 2380 4.844085 TCCTCTGTTTCAGGTTCAGGAATA 59.156 41.667 3.51 0.00 30.98 1.75
2367 2381 3.652869 TCCTCTGTTTCAGGTTCAGGAAT 59.347 43.478 3.51 0.00 30.98 3.01
2368 2382 3.045634 TCCTCTGTTTCAGGTTCAGGAA 58.954 45.455 3.51 0.00 30.98 3.36
2370 2384 3.492102 TTCCTCTGTTTCAGGTTCAGG 57.508 47.619 0.00 0.00 32.20 3.86
2372 2386 6.490040 CCTAATTTTCCTCTGTTTCAGGTTCA 59.510 38.462 0.00 0.00 32.20 3.18
2373 2387 6.715264 TCCTAATTTTCCTCTGTTTCAGGTTC 59.285 38.462 0.00 0.00 32.20 3.62
2374 2388 6.610830 TCCTAATTTTCCTCTGTTTCAGGTT 58.389 36.000 0.00 0.00 32.20 3.50
2564 2872 7.817440 AGAGGGTATTAGATTCAGTCTAGACA 58.183 38.462 24.44 4.70 40.42 3.41
2567 2875 9.137459 TCAAAGAGGGTATTAGATTCAGTCTAG 57.863 37.037 0.00 0.00 40.42 2.43
2637 3671 7.560368 AGTCTCCTATTTACTCCAAATGTCTG 58.440 38.462 0.00 0.00 37.42 3.51
2665 3699 0.688087 CCCTAGACCTTTCTCCCGCT 60.688 60.000 0.00 0.00 32.75 5.52
2668 3702 3.512496 CCTATCCCTAGACCTTTCTCCC 58.488 54.545 0.00 0.00 32.75 4.30
2784 3818 3.086600 CCAGAGCCCTCAGGTCCC 61.087 72.222 0.00 0.00 44.46 4.46
2785 3819 2.039624 TCCAGAGCCCTCAGGTCC 59.960 66.667 6.62 0.00 44.46 4.46
2786 3820 0.033011 TAGTCCAGAGCCCTCAGGTC 60.033 60.000 6.62 2.00 43.67 3.85
2787 3821 0.639392 ATAGTCCAGAGCCCTCAGGT 59.361 55.000 6.62 0.00 37.50 4.00
2788 3822 1.799933 AATAGTCCAGAGCCCTCAGG 58.200 55.000 0.63 0.63 37.58 3.86
2789 3823 5.186797 CCTTATAATAGTCCAGAGCCCTCAG 59.813 48.000 0.00 0.00 0.00 3.35
2790 3824 5.087323 CCTTATAATAGTCCAGAGCCCTCA 58.913 45.833 0.00 0.00 0.00 3.86
2791 3825 5.334421 TCCTTATAATAGTCCAGAGCCCTC 58.666 45.833 0.00 0.00 0.00 4.30
2792 3826 5.162815 ACTCCTTATAATAGTCCAGAGCCCT 60.163 44.000 0.00 0.00 0.00 5.19
2863 3897 6.478344 CAGAAATTTTCTCGTCCTCTCCATAG 59.522 42.308 8.71 0.00 38.11 2.23
2865 3899 5.181748 CAGAAATTTTCTCGTCCTCTCCAT 58.818 41.667 8.71 0.00 38.11 3.41


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

AutoCloner maintained by Alex Coulton.