Multiple sequence alignment - TraesCS2B01G215300

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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 TraesCS2B01G215300 chr2B 100.000 2981 0 0 1 2981 200574807 200571827 0.000000e+00 5505
1 TraesCS2B01G215300 chr2A 92.364 2855 107 37 3 2773 158451413 158454240 0.000000e+00 3962
2 TraesCS2B01G215300 chr2A 83.000 200 7 11 2782 2981 158454369 158454541 3.980000e-34 156
3 TraesCS2B01G215300 chr2D 96.095 2100 47 14 375 2452 142668846 142666760 0.000000e+00 3391
4 TraesCS2B01G215300 chr2D 87.523 553 42 19 2441 2977 142666738 142666197 5.460000e-172 614
5 TraesCS2B01G215300 chr2D 94.262 366 16 2 3 363 142669420 142669055 3.360000e-154 555


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 TraesCS2B01G215300 chr2B 200571827 200574807 2980 True 5505 5505 100.000000 1 2981 1 chr2B.!!$R1 2980
1 TraesCS2B01G215300 chr2A 158451413 158454541 3128 False 2059 3962 87.682000 3 2981 2 chr2A.!!$F1 2978
2 TraesCS2B01G215300 chr2D 142666197 142669420 3223 True 1520 3391 92.626667 3 2977 3 chr2D.!!$R1 2974

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
461 675 0.108992 TAGCGCGAAACATCGACCTT 60.109 50.0 12.1 0.0 34.64 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 2240 0.234625 TTAGTTTCGCACGCTGCTTG 59.765 50.0 1.22 1.22 42.25 4.01 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
53 54 1.226859 ATCGGACGTACGCATGGTG 60.227 57.895 17.29 0.00 0.00 4.17
115 119 2.475487 GCTAAGAGTGTTTCGTCACCAC 59.525 50.000 0.00 0.00 38.91 4.16
149 153 6.326583 TCTTTGGACGATAGGGTTAGATCATT 59.673 38.462 0.00 0.00 43.77 2.57
150 154 6.494666 TTGGACGATAGGGTTAGATCATTT 57.505 37.500 0.00 0.00 43.77 2.32
151 155 6.097915 TGGACGATAGGGTTAGATCATTTC 57.902 41.667 0.00 0.00 43.77 2.17
269 273 3.894427 TGGTTGTTGGTGAGCAATGTTAT 59.106 39.130 0.00 0.00 0.00 1.89
303 315 5.649831 CGTCTACCATACCTAATACCCCTAC 59.350 48.000 0.00 0.00 0.00 3.18
313 325 6.939622 ACCTAATACCCCTACGCATTTATAC 58.060 40.000 0.00 0.00 0.00 1.47
317 329 4.332428 ACCCCTACGCATTTATACAGAC 57.668 45.455 0.00 0.00 0.00 3.51
361 373 9.458727 AGCCATTATCTCAAAGGAACATATATG 57.541 33.333 11.29 11.29 0.00 1.78
362 374 9.236006 GCCATTATCTCAAAGGAACATATATGT 57.764 33.333 12.75 12.75 44.20 2.29
436 650 1.901464 GGGACGGGAAAGCAAGCAA 60.901 57.895 0.00 0.00 0.00 3.91
446 660 2.927553 AAGCAAGCAATTCCTTAGCG 57.072 45.000 0.00 0.00 0.00 4.26
458 672 0.297820 CCTTAGCGCGAAACATCGAC 59.702 55.000 12.10 0.00 34.64 4.20
461 675 0.108992 TAGCGCGAAACATCGACCTT 60.109 50.000 12.10 0.00 34.64 3.50
501 715 0.895559 GAAGGGCTTTGTGGTGGAGG 60.896 60.000 0.00 0.00 0.00 4.30
503 717 1.303643 GGGCTTTGTGGTGGAGGAG 60.304 63.158 0.00 0.00 0.00 3.69
527 741 2.437716 CCGGTTGGCGGCTAATGT 60.438 61.111 11.43 0.00 0.00 2.71
779 1009 0.987294 CCACTGGAATCCACAGTCCT 59.013 55.000 0.00 0.00 45.50 3.85
988 1218 1.068287 GTCAGCAGACTTCGACTCGC 61.068 60.000 1.35 0.00 41.64 5.03
989 1219 1.081175 CAGCAGACTTCGACTCGCA 60.081 57.895 0.00 0.00 0.00 5.10
1347 1583 3.340953 ATGCATGCCGTTTGCGTCC 62.341 57.895 16.68 0.00 45.60 4.79
1350 1586 2.746277 ATGCCGTTTGCGTCCCTC 60.746 61.111 0.00 0.00 45.60 4.30
1394 1630 1.601663 CGGGAATCTGACGATGCTCTC 60.602 57.143 0.00 0.00 0.00 3.20
1834 2079 0.179097 GAAGATCGAGTGGGAGTGCC 60.179 60.000 0.00 0.00 0.00 5.01
1995 2240 1.677217 GCATGAGACACTCAAGACCCC 60.677 57.143 0.00 0.00 44.04 4.95
2207 2452 5.708230 AGGGAAAAATATGACGTGTGCTTTA 59.292 36.000 0.00 0.00 0.00 1.85
2210 2455 6.741358 GGAAAAATATGACGTGTGCTTTAGTC 59.259 38.462 0.00 0.00 0.00 2.59
2227 2472 0.588252 GTCAATTGCACGTCTGCTGT 59.412 50.000 0.00 0.00 44.57 4.40
2239 2484 2.799562 CGTCTGCTGTTGTGTTCTGAGA 60.800 50.000 0.00 0.00 0.00 3.27
2349 2595 0.457443 CTGGCAGCAGTCACGATCTA 59.543 55.000 0.00 0.00 0.00 1.98
2390 2636 9.031360 CGTGCACTAAGTTGACAAATATAGTAT 57.969 33.333 16.19 0.00 0.00 2.12
2446 2750 6.509418 TTTACAGGCAAGGCTAATAACAAG 57.491 37.500 0.00 0.00 0.00 3.16
2468 2772 3.843868 GCATTTTGATGAGATGAGCGACG 60.844 47.826 0.00 0.00 0.00 5.12
2672 2977 3.470709 CTTCCACTTGAAGTTCTCTGCA 58.529 45.455 4.17 0.00 44.59 4.41
2694 2999 1.337074 ACGTTTTGGGCTGCATGATTG 60.337 47.619 0.50 0.00 0.00 2.67
2835 3263 8.514594 TGAATGAAAAGACGATCTATTTTTGCT 58.485 29.630 0.00 0.00 0.00 3.91
2855 3283 3.242316 GCTATTTCGAAGCAGGGTAAACG 60.242 47.826 2.70 0.00 39.83 3.60
2869 3329 8.480501 AGCAGGGTAAACGAACTATAATTAAGA 58.519 33.333 0.00 0.00 0.00 2.10
2878 3338 9.583765 AACGAACTATAATTAAGAACTCAGACC 57.416 33.333 0.00 0.00 0.00 3.85
2879 3339 8.196103 ACGAACTATAATTAAGAACTCAGACCC 58.804 37.037 0.00 0.00 0.00 4.46
2880 3340 8.414778 CGAACTATAATTAAGAACTCAGACCCT 58.585 37.037 0.00 0.00 0.00 4.34
2881 3341 9.535878 GAACTATAATTAAGAACTCAGACCCTG 57.464 37.037 0.00 0.00 0.00 4.45
2882 3342 8.611051 ACTATAATTAAGAACTCAGACCCTGT 57.389 34.615 0.00 0.00 32.61 4.00
2883 3343 8.697292 ACTATAATTAAGAACTCAGACCCTGTC 58.303 37.037 0.00 0.00 32.61 3.51
2884 3344 4.828072 ATTAAGAACTCAGACCCTGTCC 57.172 45.455 0.00 0.00 32.18 4.02
2885 3345 2.103153 AAGAACTCAGACCCTGTCCA 57.897 50.000 0.00 0.00 32.18 4.02
2886 3346 2.103153 AGAACTCAGACCCTGTCCAA 57.897 50.000 0.00 0.00 32.18 3.53
2887 3347 1.694696 AGAACTCAGACCCTGTCCAAC 59.305 52.381 0.00 0.00 32.18 3.77
2888 3348 0.765510 AACTCAGACCCTGTCCAACC 59.234 55.000 0.00 0.00 32.18 3.77
2889 3349 0.104934 ACTCAGACCCTGTCCAACCT 60.105 55.000 0.00 0.00 32.18 3.50
2890 3350 1.149288 ACTCAGACCCTGTCCAACCTA 59.851 52.381 0.00 0.00 32.18 3.08
2891 3351 2.225650 ACTCAGACCCTGTCCAACCTAT 60.226 50.000 0.00 0.00 32.18 2.57
2892 3352 2.169352 CTCAGACCCTGTCCAACCTATG 59.831 54.545 0.00 0.00 32.18 2.23
2893 3353 1.909302 CAGACCCTGTCCAACCTATGT 59.091 52.381 0.00 0.00 32.18 2.29
2894 3354 1.909302 AGACCCTGTCCAACCTATGTG 59.091 52.381 0.00 0.00 32.18 3.21
2895 3355 0.328258 ACCCTGTCCAACCTATGTGC 59.672 55.000 0.00 0.00 0.00 4.57
2896 3356 0.327924 CCCTGTCCAACCTATGTGCA 59.672 55.000 0.00 0.00 0.00 4.57
2897 3357 1.679944 CCCTGTCCAACCTATGTGCAG 60.680 57.143 0.00 0.00 0.00 4.41
2898 3358 1.679944 CCTGTCCAACCTATGTGCAGG 60.680 57.143 0.00 0.00 40.35 4.85
2899 3359 1.278985 CTGTCCAACCTATGTGCAGGA 59.721 52.381 0.00 0.00 39.18 3.86
2900 3360 1.278985 TGTCCAACCTATGTGCAGGAG 59.721 52.381 0.00 0.00 39.18 3.69
2901 3361 1.279271 GTCCAACCTATGTGCAGGAGT 59.721 52.381 0.00 0.00 39.18 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.084287 TCCTAGCGAAACTCTAGTCCAAA 58.916 43.478 0.00 0.00 33.43 3.28
1 2 3.693807 TCCTAGCGAAACTCTAGTCCAA 58.306 45.455 0.00 0.00 33.43 3.53
15 16 1.872679 GCTCGTCCGTTTCCTAGCG 60.873 63.158 0.00 0.00 0.00 4.26
115 119 5.066505 CCCTATCGTCCAAAGAAATCAAAGG 59.933 44.000 0.00 0.00 0.00 3.11
149 153 7.148705 CGTACAAATTTGTGAGAGTAATCCGAA 60.149 37.037 29.72 5.43 42.31 4.30
150 154 6.309494 CGTACAAATTTGTGAGAGTAATCCGA 59.691 38.462 29.72 5.85 42.31 4.55
151 155 6.090358 ACGTACAAATTTGTGAGAGTAATCCG 59.910 38.462 29.72 17.34 42.31 4.18
303 315 5.354234 ACTTTTCCCAGTCTGTATAAATGCG 59.646 40.000 0.00 0.00 0.00 4.73
363 375 7.438160 GTACTTATGTACATGCTTATGCACAGA 59.562 37.037 18.81 0.00 44.24 3.41
364 376 7.567571 GTACTTATGTACATGCTTATGCACAG 58.432 38.462 18.81 4.56 44.24 3.66
400 614 2.162681 CCCCTGTTTCATCCTGTTGTC 58.837 52.381 0.00 0.00 0.00 3.18
413 627 2.002018 TTGCTTTCCCGTCCCCTGTT 62.002 55.000 0.00 0.00 0.00 3.16
436 650 1.593006 CGATGTTTCGCGCTAAGGAAT 59.407 47.619 5.56 0.00 38.75 3.01
446 660 3.949313 GACAAGGTCGATGTTTCGC 57.051 52.632 0.00 0.00 45.10 4.70
776 1006 1.557269 GCTGCTTTGGAGGGAGAGGA 61.557 60.000 0.00 0.00 0.00 3.71
779 1009 2.665000 CGCTGCTTTGGAGGGAGA 59.335 61.111 0.00 0.00 0.00 3.71
1419 1655 1.098712 CGTCCCTCTCCTCCTCTTCG 61.099 65.000 0.00 0.00 0.00 3.79
1422 1658 1.610873 GACGTCCCTCTCCTCCTCT 59.389 63.158 3.51 0.00 0.00 3.69
1995 2240 0.234625 TTAGTTTCGCACGCTGCTTG 59.765 50.000 1.22 1.22 42.25 4.01
2227 2472 5.244851 AGAAGCTCACTATCTCAGAACACAA 59.755 40.000 0.00 0.00 0.00 3.33
2239 2484 4.017808 ACGGAGTACAAGAAGCTCACTAT 58.982 43.478 0.00 0.00 41.94 2.12
2349 2595 1.898574 CACGCAAAGAAGGCCAGGT 60.899 57.895 5.01 0.00 0.00 4.00
2390 2636 6.530120 TCACACAGAATTTCTTGGCTACTAA 58.470 36.000 0.00 0.00 0.00 2.24
2446 2750 3.615614 GTCGCTCATCTCATCAAAATGC 58.384 45.455 0.00 0.00 32.58 3.56
2468 2772 1.678360 CACGCATTGCAACTGAACTC 58.322 50.000 0.00 0.00 0.00 3.01
2502 2806 5.627182 ATGAGCTAGAACATGTCTCCATT 57.373 39.130 0.00 0.00 37.84 3.16
2571 2875 9.358872 GAGATTTTCATAAGATGTTGTTTTCCC 57.641 33.333 0.00 0.00 0.00 3.97
2672 2977 1.832883 TCATGCAGCCCAAAACGTAT 58.167 45.000 0.00 0.00 0.00 3.06
2714 3019 4.999950 CAGGATGGATTGGCTGTTATACTC 59.000 45.833 0.00 0.00 0.00 2.59
2724 3030 5.221244 GGTTGTATTTACAGGATGGATTGGC 60.221 44.000 0.00 0.00 43.62 4.52
2792 3220 4.450757 TCATTCATGGAACTAACACACACG 59.549 41.667 0.00 0.00 0.00 4.49
2793 3221 5.940192 TCATTCATGGAACTAACACACAC 57.060 39.130 0.00 0.00 0.00 3.82
2794 3222 6.951062 TTTCATTCATGGAACTAACACACA 57.049 33.333 0.00 0.00 0.00 3.72
2795 3223 7.591426 GTCTTTTCATTCATGGAACTAACACAC 59.409 37.037 0.00 0.00 0.00 3.82
2835 3263 4.191033 TCGTTTACCCTGCTTCGAAATA 57.809 40.909 0.00 0.00 0.00 1.40
2855 3283 9.535878 CAGGGTCTGAGTTCTTAATTATAGTTC 57.464 37.037 0.00 0.00 32.44 3.01
2869 3329 0.765510 GGTTGGACAGGGTCTGAGTT 59.234 55.000 1.59 0.00 35.18 3.01
2871 3331 1.938585 TAGGTTGGACAGGGTCTGAG 58.061 55.000 1.59 0.00 35.18 3.35
2872 3332 2.187958 CATAGGTTGGACAGGGTCTGA 58.812 52.381 1.59 0.00 35.18 3.27
2873 3333 1.909302 ACATAGGTTGGACAGGGTCTG 59.091 52.381 0.00 0.00 37.52 3.51
2874 3334 1.909302 CACATAGGTTGGACAGGGTCT 59.091 52.381 0.00 0.00 32.47 3.85
2875 3335 1.679032 GCACATAGGTTGGACAGGGTC 60.679 57.143 0.00 0.00 0.00 4.46
2876 3336 0.328258 GCACATAGGTTGGACAGGGT 59.672 55.000 0.00 0.00 0.00 4.34
2877 3337 0.327924 TGCACATAGGTTGGACAGGG 59.672 55.000 0.00 0.00 0.00 4.45
2878 3338 1.679944 CCTGCACATAGGTTGGACAGG 60.680 57.143 0.00 0.00 42.56 4.00
2879 3339 1.278985 TCCTGCACATAGGTTGGACAG 59.721 52.381 0.00 0.00 38.99 3.51
2880 3340 1.278985 CTCCTGCACATAGGTTGGACA 59.721 52.381 0.00 0.00 38.99 4.02
2881 3341 1.279271 ACTCCTGCACATAGGTTGGAC 59.721 52.381 0.00 0.00 38.99 4.02
2882 3342 1.656587 ACTCCTGCACATAGGTTGGA 58.343 50.000 0.00 0.00 38.99 3.53
2883 3343 3.270877 GTTACTCCTGCACATAGGTTGG 58.729 50.000 0.00 0.00 38.99 3.77
2884 3344 3.937814 TGTTACTCCTGCACATAGGTTG 58.062 45.455 0.00 0.00 38.99 3.77
2885 3345 4.019321 ACATGTTACTCCTGCACATAGGTT 60.019 41.667 0.00 0.00 38.99 3.50
2886 3346 3.519510 ACATGTTACTCCTGCACATAGGT 59.480 43.478 0.00 0.00 38.99 3.08
2887 3347 4.142609 ACATGTTACTCCTGCACATAGG 57.857 45.455 0.00 0.00 39.29 2.57
2888 3348 7.792374 ATTTACATGTTACTCCTGCACATAG 57.208 36.000 2.30 0.00 29.78 2.23
2889 3349 9.845740 AATATTTACATGTTACTCCTGCACATA 57.154 29.630 2.30 0.00 29.78 2.29
2890 3350 8.752005 AATATTTACATGTTACTCCTGCACAT 57.248 30.769 2.30 0.00 0.00 3.21
2891 3351 8.574251 AAATATTTACATGTTACTCCTGCACA 57.426 30.769 2.30 0.00 0.00 4.57
2893 3353 9.899661 ACTAAATATTTACATGTTACTCCTGCA 57.100 29.630 2.30 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.