Multiple sequence alignment - TraesCS5D01G095000

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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 TraesCS5D01G095000 chr5D 100.000 2687 0 0 1 2687 104448061 104445375 0.000000e+00 4963.0
1 TraesCS5D01G095000 chr5D 92.767 871 49 8 894 1758 104398467 104397605 0.000000e+00 1247.0
2 TraesCS5D01G095000 chr5B 95.654 2715 62 19 1 2687 113824450 113821764 0.000000e+00 4309.0
3 TraesCS5D01G095000 chr5B 92.227 952 53 12 894 1837 113805884 113804946 0.000000e+00 1328.0
4 TraesCS5D01G095000 chr5A 92.952 1206 55 16 606 1794 106856230 106855038 0.000000e+00 1729.0
5 TraesCS5D01G095000 chr5A 92.857 728 44 5 894 1616 93188350 93189074 0.000000e+00 1050.0
6 TraesCS5D01G095000 chr5A 92.617 596 32 9 1 590 106856805 106856216 0.000000e+00 846.0
7 TraesCS5D01G095000 chr5A 83.963 767 76 10 1937 2687 93066210 93066945 0.000000e+00 691.0
8 TraesCS5D01G095000 chr5A 87.931 232 16 8 1609 1837 93189768 93189990 2.050000e-66 263.0
9 TraesCS5D01G095000 chr5A 90.728 151 8 4 1791 1941 106854900 106854756 2.110000e-46 196.0
10 TraesCS5D01G095000 chr2B 81.132 265 34 12 323 572 632562584 632562847 5.870000e-47 198.0
11 TraesCS5D01G095000 chr2B 81.373 102 14 5 606 705 157263938 157263840 7.980000e-11 78.7
12 TraesCS5D01G095000 chr1B 80.970 268 32 11 323 572 375862143 375862409 7.590000e-46 195.0
13 TraesCS5D01G095000 chr1B 80.669 269 31 12 323 572 198593020 198592754 3.530000e-44 189.0
14 TraesCS5D01G095000 chr1B 82.400 125 16 4 29 148 513973251 513973128 1.320000e-18 104.0
15 TraesCS5D01G095000 chr1B 92.188 64 4 1 2143 2206 12983696 12983758 3.680000e-14 89.8
16 TraesCS5D01G095000 chr3B 82.533 229 30 7 352 572 706780657 706780883 2.730000e-45 193.0
17 TraesCS5D01G095000 chr3B 83.838 99 12 3 2110 2205 603605900 603605997 1.020000e-14 91.6
18 TraesCS5D01G095000 chr3B 93.103 58 4 0 2144 2201 847256 847313 4.770000e-13 86.1
19 TraesCS5D01G095000 chr7A 79.791 287 38 9 323 590 675405311 675405596 9.820000e-45 191.0
20 TraesCS5D01G095000 chr7A 97.436 39 0 1 323 360 229206346 229206308 6.210000e-07 65.8
21 TraesCS5D01G095000 chr7B 79.359 281 40 13 327 590 54317492 54317771 5.910000e-42 182.0
22 TraesCS5D01G095000 chr7D 81.148 244 29 12 321 549 128346481 128346240 2.130000e-41 180.0
23 TraesCS5D01G095000 chr7D 79.565 230 37 8 352 572 204095933 204095705 3.580000e-34 156.0
24 TraesCS5D01G095000 chr7D 85.938 64 9 0 606 669 634434338 634434275 4.800000e-08 69.4
25 TraesCS5D01G095000 chr6D 81.385 231 30 11 352 572 94596607 94596834 2.750000e-40 176.0
26 TraesCS5D01G095000 chr2D 80.258 233 35 6 369 590 556713893 556713661 5.950000e-37 165.0
27 TraesCS5D01G095000 chr6A 75.636 275 46 18 328 582 601139670 601139397 1.690000e-22 117.0
28 TraesCS5D01G095000 chr6A 94.828 58 2 1 2143 2200 497792475 497792531 3.680000e-14 89.8
29 TraesCS5D01G095000 chr6A 94.737 57 1 2 2144 2200 99971813 99971867 1.330000e-13 87.9
30 TraesCS5D01G095000 chr6A 80.208 96 15 4 606 700 480304319 480304227 4.800000e-08 69.4
31 TraesCS5D01G095000 chr6A 92.857 42 1 2 606 645 176295503 176295544 2.890000e-05 60.2
32 TraesCS5D01G095000 chr3D 85.981 107 12 3 29 132 425145855 425145749 7.860000e-21 111.0
33 TraesCS5D01G095000 chr3D 78.049 123 19 7 608 727 3840357 3840240 1.330000e-08 71.3
34 TraesCS5D01G095000 chr3A 83.200 125 16 4 29 148 563400498 563400622 2.830000e-20 110.0
35 TraesCS5D01G095000 chr1D 96.552 58 2 0 2144 2201 206961794 206961851 2.200000e-16 97.1
36 TraesCS5D01G095000 chr2A 90.909 55 4 1 2144 2197 1549055 1549001 3.710000e-09 73.1
37 TraesCS5D01G095000 chr2A 79.817 109 13 9 607 711 103236598 103236495 1.330000e-08 71.3


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 TraesCS5D01G095000 chr5D 104445375 104448061 2686 True 4963.000000 4963 100.000 1 2687 1 chr5D.!!$R2 2686
1 TraesCS5D01G095000 chr5D 104397605 104398467 862 True 1247.000000 1247 92.767 894 1758 1 chr5D.!!$R1 864
2 TraesCS5D01G095000 chr5B 113821764 113824450 2686 True 4309.000000 4309 95.654 1 2687 1 chr5B.!!$R2 2686
3 TraesCS5D01G095000 chr5B 113804946 113805884 938 True 1328.000000 1328 92.227 894 1837 1 chr5B.!!$R1 943
4 TraesCS5D01G095000 chr5A 106854756 106856805 2049 True 923.666667 1729 92.099 1 1941 3 chr5A.!!$R1 1940
5 TraesCS5D01G095000 chr5A 93066210 93066945 735 False 691.000000 691 83.963 1937 2687 1 chr5A.!!$F1 750
6 TraesCS5D01G095000 chr5A 93188350 93189990 1640 False 656.500000 1050 90.394 894 1837 2 chr5A.!!$F2 943

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
822 864 3.365767 GCTGCTGCTTTCTCTCGAAAAAT 60.366 43.478 8.53 0.0 38.58 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2028 2925 0.03496 AGCTAGCTCTCAGTGGACGA 60.035 55.0 12.68 0.0 0.0 4.2 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
202 203 5.581085 CCCAATTTTCTAGGAGTTGTAGACG 59.419 44.000 0.00 0.00 0.00 4.18
531 541 6.016555 ACATAAGTTGGGCTTTAGATTTGGT 58.983 36.000 0.00 0.00 38.57 3.67
822 864 3.365767 GCTGCTGCTTTCTCTCGAAAAAT 60.366 43.478 8.53 0.00 38.58 1.82
846 888 6.211515 TGCAAAAGCAAAAGCAAAAGAAAAA 58.788 28.000 0.00 0.00 33.48 1.94
847 889 6.362820 TGCAAAAGCAAAAGCAAAAGAAAAAG 59.637 30.769 0.00 0.00 33.48 2.27
848 890 6.668090 GCAAAAGCAAAAGCAAAAGAAAAAGC 60.668 34.615 0.00 0.00 0.00 3.51
849 891 5.625921 AAGCAAAAGCAAAAGAAAAAGCA 57.374 30.435 0.00 0.00 0.00 3.91
850 892 5.625921 AGCAAAAGCAAAAGAAAAAGCAA 57.374 30.435 0.00 0.00 0.00 3.91
851 893 6.011476 AGCAAAAGCAAAAGAAAAAGCAAA 57.989 29.167 0.00 0.00 0.00 3.68
852 894 6.445475 AGCAAAAGCAAAAGAAAAAGCAAAA 58.555 28.000 0.00 0.00 0.00 2.44
853 895 6.583427 AGCAAAAGCAAAAGAAAAAGCAAAAG 59.417 30.769 0.00 0.00 0.00 2.27
854 896 6.581919 GCAAAAGCAAAAGAAAAAGCAAAAGA 59.418 30.769 0.00 0.00 0.00 2.52
855 897 7.114670 GCAAAAGCAAAAGAAAAAGCAAAAGAA 59.885 29.630 0.00 0.00 0.00 2.52
856 898 8.966194 CAAAAGCAAAAGAAAAAGCAAAAGAAA 58.034 25.926 0.00 0.00 0.00 2.52
857 899 9.526713 AAAAGCAAAAGAAAAAGCAAAAGAAAA 57.473 22.222 0.00 0.00 0.00 2.29
2012 2904 6.261603 TCTTCTTCTTTATGTGCTATGCCATG 59.738 38.462 0.00 0.00 0.00 3.66
2028 2925 3.327757 TGCCATGAGTCAGGTTAAGTCTT 59.672 43.478 3.80 0.00 0.00 3.01
2033 2930 3.255149 TGAGTCAGGTTAAGTCTTCGTCC 59.745 47.826 0.00 0.00 0.00 4.79
2095 2992 9.162764 ACATTATTAGTCATTGTACTTGACACC 57.837 33.333 22.90 5.36 44.73 4.16
2222 3120 8.628882 AAAACAAAAACTCACTTTAATCCTCG 57.371 30.769 0.00 0.00 0.00 4.63
2397 3306 6.120507 AGCATTTTGTAGTCCTCTCTTTCT 57.879 37.500 0.00 0.00 0.00 2.52
2409 3318 4.122776 CCTCTCTTTCTCTCTCTCTCTCG 58.877 52.174 0.00 0.00 0.00 4.04
2441 3368 5.089970 TCTCTCTCTCTCTCTCTCAGTTG 57.910 47.826 0.00 0.00 0.00 3.16
2489 3416 3.033764 GGCAACGTCGACGAGCAA 61.034 61.111 38.58 0.00 42.28 3.91
2512 3439 0.807667 CTGGCGAGGAAGATCCGTTG 60.808 60.000 0.00 0.00 42.75 4.10
2576 3503 2.743718 CTGCAGGGACCGACACTT 59.256 61.111 5.57 0.00 0.00 3.16
2587 3514 0.388134 CCGACACTTAGGTCACCACG 60.388 60.000 0.00 0.00 37.66 4.94
2627 3554 1.226746 GCAATACGGTACATGCTCCC 58.773 55.000 16.34 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 203 3.097342 TGTTCCCAGGACTAGACCTAC 57.903 52.381 13.62 8.91 38.32 3.18
427 431 9.628746 TTGATTTGAACATTTGTGACATGATAG 57.371 29.630 0.00 0.00 0.00 2.08
531 541 6.734502 ATTTGGCATCAATGTGATAATGGA 57.265 33.333 0.00 0.00 34.28 3.41
646 656 9.264719 TCTATATCACATTGACACATCATCAAC 57.735 33.333 0.00 0.00 38.84 3.18
846 888 4.100035 AGCCAGCTAACTTTTTCTTTTGCT 59.900 37.500 0.00 0.00 34.69 3.91
847 889 4.209911 CAGCCAGCTAACTTTTTCTTTTGC 59.790 41.667 0.00 0.00 0.00 3.68
848 890 4.209911 GCAGCCAGCTAACTTTTTCTTTTG 59.790 41.667 0.00 0.00 41.15 2.44
849 891 4.371786 GCAGCCAGCTAACTTTTTCTTTT 58.628 39.130 0.00 0.00 41.15 2.27
850 892 3.982475 GCAGCCAGCTAACTTTTTCTTT 58.018 40.909 0.00 0.00 41.15 2.52
851 893 3.650070 GCAGCCAGCTAACTTTTTCTT 57.350 42.857 0.00 0.00 41.15 2.52
1500 1547 1.796459 CAACGGTTCTTGAAGTACCCG 59.204 52.381 14.27 14.53 32.68 5.28
2012 2904 3.255149 TGGACGAAGACTTAACCTGACTC 59.745 47.826 0.00 0.00 0.00 3.36
2028 2925 0.034960 AGCTAGCTCTCAGTGGACGA 60.035 55.000 12.68 0.00 0.00 4.20
2033 2930 2.374184 AGGTGTAGCTAGCTCTCAGTG 58.626 52.381 23.26 0.00 0.00 3.66
2072 2969 9.562408 TTTGGTGTCAAGTACAATGACTAATAA 57.438 29.630 23.82 14.74 45.81 1.40
2095 2992 7.371159 GGGAAAGGAGAATAAAGTGAGTTTTG 58.629 38.462 0.00 0.00 0.00 2.44
2202 3100 7.115947 CGAGTACGAGGATTAAAGTGAGTTTTT 59.884 37.037 0.00 0.00 42.66 1.94
2216 3114 1.625616 CGTTTTGCGAGTACGAGGAT 58.374 50.000 5.07 0.00 44.77 3.24
2219 3117 4.999550 GCGTTTTGCGAGTACGAG 57.000 55.556 13.13 0.00 44.77 4.18
2249 3147 0.804933 GGACCAATCGCCGAGTACAC 60.805 60.000 0.00 0.00 0.00 2.90
2394 3303 2.766263 AGAGAGCGAGAGAGAGAGAGAA 59.234 50.000 0.00 0.00 0.00 2.87
2397 3306 2.362397 GAGAGAGAGCGAGAGAGAGAGA 59.638 54.545 0.00 0.00 0.00 3.10
2409 3318 3.640967 AGAGAGAGAGAGAGAGAGAGAGC 59.359 52.174 0.00 0.00 0.00 4.09
2489 3416 1.404843 GGATCTTCCTCGCCAGTAGT 58.595 55.000 0.00 0.00 32.53 2.73
2512 3439 0.528684 CCTCGCTCGTCATTCCCTTC 60.529 60.000 0.00 0.00 0.00 3.46
2576 3503 2.363975 GCCCATCCGTGGTGACCTA 61.364 63.158 2.11 0.00 44.48 3.08
2627 3554 3.119173 GCATGAGAGATAAGGGAGGATCG 60.119 52.174 0.00 0.00 34.37 3.69


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

AutoCloner maintained by Alex Coulton.