Multiple sequence alignment - TraesCS5D01G229000

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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 TraesCS5D01G229000 chr5D 100.000 2892 0 0 1 2892 336240763 336237872 0.000000e+00 5341
1 TraesCS5D01G229000 chr5D 95.608 1890 56 11 1 1885 336337642 336339509 0.000000e+00 3005
2 TraesCS5D01G229000 chr5D 88.078 1644 111 39 295 1905 336314279 336315870 0.000000e+00 1871
3 TraesCS5D01G229000 chr5D 84.597 1636 139 61 310 1888 336382022 336380443 0.000000e+00 1520
4 TraesCS5D01G229000 chr5D 81.557 938 92 36 295 1200 336258529 336257641 0.000000e+00 699
5 TraesCS5D01G229000 chr5D 94.801 327 13 3 1580 1905 336257245 336256922 9.250000e-140 507
6 TraesCS5D01G229000 chr5B 89.667 1771 84 40 211 1905 394581881 394580134 0.000000e+00 2165
7 TraesCS5D01G229000 chr5B 88.091 1629 127 37 312 1905 394628742 394627146 0.000000e+00 1871
8 TraesCS5D01G229000 chr5B 90.674 1083 77 13 829 1905 394572568 394571504 0.000000e+00 1419
9 TraesCS5D01G229000 chr5B 87.090 914 75 23 1999 2892 394570472 394569582 0.000000e+00 994
10 TraesCS5D01G229000 chr5B 81.507 292 34 10 295 569 394573026 394572738 3.750000e-54 222
11 TraesCS5D01G229000 chr5B 88.000 150 12 5 623 768 394572738 394572591 3.830000e-39 172
12 TraesCS5D01G229000 chr5B 93.043 115 5 2 1898 2009 394571443 394571329 6.410000e-37 165
13 TraesCS5D01G229000 chr5B 82.249 169 25 4 9 175 208700696 208700861 1.080000e-29 141
14 TraesCS5D01G229000 chr5A 90.453 1613 85 33 321 1885 437400668 437399077 0.000000e+00 2061
15 TraesCS5D01G229000 chr5A 88.020 1636 106 44 295 1901 437393835 437392261 0.000000e+00 1853
16 TraesCS5D01G229000 chr5A 85.688 1607 98 56 321 1901 437413291 437411791 0.000000e+00 1572
17 TraesCS5D01G229000 chr5A 84.221 1014 50 34 1903 2892 437392189 437391262 0.000000e+00 885
18 TraesCS5D01G229000 chr5A 81.181 271 27 10 9 279 437408411 437408165 2.270000e-46 196
19 TraesCS5D01G229000 chr4B 81.548 168 29 2 4 170 163799250 163799416 1.400000e-28 137
20 TraesCS5D01G229000 chr4B 81.548 168 29 2 4 170 163799713 163799879 1.400000e-28 137
21 TraesCS5D01G229000 chr2D 85.484 124 17 1 14 137 486961286 486961408 8.410000e-26 128
22 TraesCS5D01G229000 chr2D 79.866 149 28 2 21 168 33326544 33326397 1.100000e-19 108
23 TraesCS5D01G229000 chr7D 79.878 164 31 2 6 168 115139817 115139655 5.060000e-23 119
24 TraesCS5D01G229000 chr7B 80.000 165 25 6 11 171 558915615 558915455 6.550000e-22 115
25 TraesCS5D01G229000 chr4A 79.874 159 28 4 13 170 429237142 429237297 2.360000e-21 113


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 TraesCS5D01G229000 chr5D 336237872 336240763 2891 True 5341.0 5341 100.0000 1 2892 1 chr5D.!!$R1 2891
1 TraesCS5D01G229000 chr5D 336337642 336339509 1867 False 3005.0 3005 95.6080 1 1885 1 chr5D.!!$F2 1884
2 TraesCS5D01G229000 chr5D 336314279 336315870 1591 False 1871.0 1871 88.0780 295 1905 1 chr5D.!!$F1 1610
3 TraesCS5D01G229000 chr5D 336380443 336382022 1579 True 1520.0 1520 84.5970 310 1888 1 chr5D.!!$R2 1578
4 TraesCS5D01G229000 chr5D 336256922 336258529 1607 True 603.0 699 88.1790 295 1905 2 chr5D.!!$R3 1610
5 TraesCS5D01G229000 chr5B 394580134 394581881 1747 True 2165.0 2165 89.6670 211 1905 1 chr5B.!!$R1 1694
6 TraesCS5D01G229000 chr5B 394627146 394628742 1596 True 1871.0 1871 88.0910 312 1905 1 chr5B.!!$R2 1593
7 TraesCS5D01G229000 chr5B 394569582 394573026 3444 True 594.4 1419 88.0628 295 2892 5 chr5B.!!$R3 2597
8 TraesCS5D01G229000 chr5A 437399077 437400668 1591 True 2061.0 2061 90.4530 321 1885 1 chr5A.!!$R1 1564
9 TraesCS5D01G229000 chr5A 437391262 437393835 2573 True 1369.0 1853 86.1205 295 2892 2 chr5A.!!$R2 2597
10 TraesCS5D01G229000 chr5A 437408165 437413291 5126 True 884.0 1572 83.4345 9 1901 2 chr5A.!!$R3 1892


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
52 53 1.073897 GCTGGATATGAGGGGTGCC 59.926 63.158 0.0 0.0 0.0 5.01 F
1000 1240 1.412710 GGTAGTCCGCCATGAAGATCA 59.587 52.381 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 2064 1.087202 AGCGAACGACAACTGCAACA 61.087 50.0 0.0 0.0 0.00 3.33 R
2220 3474 0.610232 AAGCAGCCTTTTCAGCGGAT 60.610 50.0 0.0 0.0 34.64 4.18 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
43 44 4.813161 CGCTCCATATTTAGGCTGGATATG 59.187 45.833 17.93 17.93 38.36 1.78
48 49 5.398353 CCATATTTAGGCTGGATATGAGGGG 60.398 48.000 22.87 10.36 36.37 4.79
52 53 1.073897 GCTGGATATGAGGGGTGCC 59.926 63.158 0.00 0.00 0.00 5.01
162 163 4.208686 GGGCGTCCGGCTGTAGAG 62.209 72.222 13.05 0.00 42.94 2.43
191 192 7.497579 TCTTACCATGCGAATACAAATATGTGT 59.502 33.333 3.51 3.51 40.84 3.72
250 251 8.167985 CACAAACAAATTTCTGAATTTTGACGT 58.832 29.630 29.68 22.37 42.14 4.34
1000 1240 1.412710 GGTAGTCCGCCATGAAGATCA 59.587 52.381 0.00 0.00 0.00 2.92
1219 1474 1.725557 CGACCTGGACGACATCGGAT 61.726 60.000 13.19 0.00 44.95 4.18
1773 2064 3.118884 GGATCTGATTTGCCAGTTTGCAT 60.119 43.478 0.00 0.00 41.70 3.96
1794 2085 1.771073 TTGCAGTTGTCGTTCGCTGG 61.771 55.000 0.00 0.00 0.00 4.85
2011 3250 1.012486 GTCGTTAACAGGCAGGGACG 61.012 60.000 6.39 0.00 0.00 4.79
2028 3267 3.057526 GGGACGGAAAAATTCAAGGACAG 60.058 47.826 0.00 0.00 0.00 3.51
2029 3268 3.568430 GGACGGAAAAATTCAAGGACAGT 59.432 43.478 0.00 0.00 0.00 3.55
2047 3286 1.609210 TCAGACCGGATGCTGACCA 60.609 57.895 9.46 0.00 36.31 4.02
2048 3287 1.448540 CAGACCGGATGCTGACCAC 60.449 63.158 9.46 0.00 34.06 4.16
2123 3371 6.473455 GCTGTTTATTTTAGTGTGATGATGCC 59.527 38.462 0.00 0.00 0.00 4.40
2155 3403 6.725834 AGACCATGAAATTATGTCCAACCTTT 59.274 34.615 0.00 0.00 0.00 3.11
2158 3406 7.877612 ACCATGAAATTATGTCCAACCTTTTTC 59.122 33.333 0.00 0.00 0.00 2.29
2159 3407 7.877097 CCATGAAATTATGTCCAACCTTTTTCA 59.123 33.333 0.00 0.00 36.58 2.69
2160 3408 9.439500 CATGAAATTATGTCCAACCTTTTTCAT 57.561 29.630 0.00 0.00 40.99 2.57
2294 3548 2.536761 TAACAGGGTCCAAAGTGACG 57.463 50.000 0.00 0.00 36.07 4.35
2305 3560 2.520979 CAAAGTGACGGCGTTTTTCAA 58.479 42.857 16.19 0.00 0.00 2.69
2310 3565 3.185797 AGTGACGGCGTTTTTCAAGATAC 59.814 43.478 16.19 0.00 0.00 2.24
2313 3568 4.141855 ACGGCGTTTTTCAAGATACTTG 57.858 40.909 6.77 5.29 0.00 3.16
2362 3617 7.492020 TGGCAATTGTAAGAATATCATTGCAAC 59.508 33.333 0.00 1.81 43.25 4.17
2538 3793 9.280174 TGAAATACTACCAAGGTCTAAAACAAG 57.720 33.333 0.00 0.00 0.00 3.16
2622 3879 3.010027 TCCATCAGCCACCTTACAATTGA 59.990 43.478 13.59 0.00 0.00 2.57
2625 3882 4.032960 TCAGCCACCTTACAATTGATGT 57.967 40.909 13.59 0.37 46.36 3.06
2651 3908 0.173708 CTCCTCTAGCCGTGTTGACC 59.826 60.000 0.00 0.00 0.00 4.02
2660 3917 3.047280 GTGTTGACCGCGGCATCA 61.047 61.111 28.58 24.00 0.00 3.07
2688 3945 3.366883 GCTAGCCGATCTAACTCATGAGG 60.367 52.174 26.08 9.26 0.00 3.86
2711 3970 4.816925 GGATTACATGTCTTCCTTAGGCAC 59.183 45.833 16.21 0.00 42.29 5.01
2712 3971 4.901197 TTACATGTCTTCCTTAGGCACA 57.099 40.909 0.00 0.00 42.29 4.57
2759 4032 6.800890 ACCTAGGGAAAGAACACCATAATTT 58.199 36.000 14.81 0.00 0.00 1.82
2824 6501 0.981183 TGTTTATGACCTCCACGCCT 59.019 50.000 0.00 0.00 0.00 5.52
2863 6540 1.645710 AGTTCTGGATCCCGAGTTGT 58.354 50.000 9.90 0.00 0.00 3.32
2864 6541 1.276421 AGTTCTGGATCCCGAGTTGTG 59.724 52.381 9.90 0.00 0.00 3.33
2865 6542 1.275291 GTTCTGGATCCCGAGTTGTGA 59.725 52.381 9.90 0.00 0.00 3.58
2883 6560 4.201657 TGTGATGCTAGAATTGGACCATG 58.798 43.478 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 4.083862 GTCTGACCGGCACCCCTC 62.084 72.222 0.00 0.00 0.00 4.30
85 86 0.031994 ACCTGTCACAAAAATGCGCC 59.968 50.000 4.18 0.00 0.00 6.53
162 163 2.833794 TGTATTCGCATGGTAAGAGCC 58.166 47.619 0.00 0.00 0.00 4.70
191 192 1.598601 TCGCGCACGTATATCAGTACA 59.401 47.619 8.75 0.00 41.18 2.90
484 541 3.748568 GTCAAAGAGCCGTTCAAGATCTT 59.251 43.478 0.88 0.88 0.00 2.40
1000 1240 1.600076 GCTGATCATCGGCTGCCAT 60.600 57.895 20.29 8.57 45.06 4.40
1773 2064 1.087202 AGCGAACGACAACTGCAACA 61.087 50.000 0.00 0.00 0.00 3.33
1781 2072 1.375396 CATCCCCAGCGAACGACAA 60.375 57.895 0.00 0.00 0.00 3.18
1794 2085 1.457346 CAGTTGCCTCTTCACATCCC 58.543 55.000 0.00 0.00 0.00 3.85
1901 2193 6.610075 ACCAAGCTTTGTTCAATCCAATAT 57.390 33.333 0.00 0.00 0.00 1.28
1928 2290 3.628942 TGCATGGTTCTGCACATAATCTC 59.371 43.478 0.00 0.00 46.76 2.75
1978 2344 7.512297 CCTGTTAACGACAACATTTTACGTAT 58.488 34.615 0.00 0.00 37.75 3.06
1979 2345 6.563753 GCCTGTTAACGACAACATTTTACGTA 60.564 38.462 0.26 0.00 37.75 3.57
1980 2346 5.740406 CCTGTTAACGACAACATTTTACGT 58.260 37.500 0.26 0.00 37.75 3.57
1981 2347 4.609708 GCCTGTTAACGACAACATTTTACG 59.390 41.667 0.26 0.00 37.75 3.18
1982 2348 5.512473 TGCCTGTTAACGACAACATTTTAC 58.488 37.500 0.26 0.00 37.75 2.01
2011 3250 5.278512 GGTCTGACTGTCCTTGAATTTTTCC 60.279 44.000 7.85 0.00 0.00 3.13
2029 3268 1.609210 TGGTCAGCATCCGGTCTGA 60.609 57.895 15.97 15.97 37.03 3.27
2047 3286 4.572007 GGGATTCCCAAAATAGGAACCAGT 60.572 45.833 17.36 0.00 45.93 4.00
2048 3287 3.960755 GGGATTCCCAAAATAGGAACCAG 59.039 47.826 17.36 0.00 45.93 4.00
2116 3360 3.134623 TCATGGTCTTACTTCGGCATCAT 59.865 43.478 0.00 0.00 0.00 2.45
2117 3361 2.499693 TCATGGTCTTACTTCGGCATCA 59.500 45.455 0.00 0.00 0.00 3.07
2123 3371 7.279981 TGGACATAATTTCATGGTCTTACTTCG 59.720 37.037 0.00 0.00 0.00 3.79
2155 3403 9.428097 CATAATCCAGACTCGATCATAATGAAA 57.572 33.333 0.00 0.00 0.00 2.69
2158 3406 7.490725 GGTCATAATCCAGACTCGATCATAATG 59.509 40.741 0.00 0.00 35.18 1.90
2159 3407 7.398618 AGGTCATAATCCAGACTCGATCATAAT 59.601 37.037 0.00 0.00 35.18 1.28
2160 3408 6.721668 AGGTCATAATCCAGACTCGATCATAA 59.278 38.462 0.00 0.00 35.18 1.90
2193 3447 1.141657 AGACAAGCAGCCTTTGACAGA 59.858 47.619 1.51 0.00 0.00 3.41
2196 3450 3.443099 AAAAGACAAGCAGCCTTTGAC 57.557 42.857 1.51 0.00 31.30 3.18
2220 3474 0.610232 AAGCAGCCTTTTCAGCGGAT 60.610 50.000 0.00 0.00 34.64 4.18
2226 3480 3.004734 GCAGAAAGTAAGCAGCCTTTTCA 59.995 43.478 9.73 0.00 31.30 2.69
2227 3481 3.004734 TGCAGAAAGTAAGCAGCCTTTTC 59.995 43.478 0.00 0.00 33.75 2.29
2228 3482 2.958355 TGCAGAAAGTAAGCAGCCTTTT 59.042 40.909 0.00 0.00 33.75 2.27
2229 3483 2.586425 TGCAGAAAGTAAGCAGCCTTT 58.414 42.857 0.00 0.00 33.75 3.11
2294 3548 4.909880 GTCACAAGTATCTTGAAAAACGCC 59.090 41.667 15.04 0.00 0.00 5.68
2556 3811 6.694447 AGTAATAAAGCGACCTGAGTTTGTA 58.306 36.000 0.00 0.00 0.00 2.41
2557 3812 5.548406 AGTAATAAAGCGACCTGAGTTTGT 58.452 37.500 0.00 0.00 0.00 2.83
2563 3818 7.330208 GTCTTGTAAAGTAATAAAGCGACCTGA 59.670 37.037 0.00 0.00 46.34 3.86
2565 3820 7.156673 TGTCTTGTAAAGTAATAAAGCGACCT 58.843 34.615 0.00 0.00 46.34 3.85
2622 3879 1.395826 GCTAGAGGAGCCACCGACAT 61.396 60.000 0.00 0.00 46.41 3.06
2688 3945 4.816925 GTGCCTAAGGAAGACATGTAATCC 59.183 45.833 17.70 17.70 0.00 3.01
2711 3970 7.402640 GTTATACTTCGGCTTCTTTCATTCTG 58.597 38.462 0.00 0.00 0.00 3.02
2712 3971 6.539103 GGTTATACTTCGGCTTCTTTCATTCT 59.461 38.462 0.00 0.00 0.00 2.40
2759 4032 3.278574 AGAAACGGCTGCTATTTATGCA 58.721 40.909 0.00 0.00 38.81 3.96
2824 6501 3.138283 ACTTGGTGGTGGAAGAATCAGAA 59.862 43.478 0.00 0.00 0.00 3.02
2863 6540 4.164796 AGACATGGTCCAATTCTAGCATCA 59.835 41.667 0.00 0.00 31.74 3.07
2864 6541 4.712476 AGACATGGTCCAATTCTAGCATC 58.288 43.478 0.00 0.00 31.74 3.91
2865 6542 4.785346 AGACATGGTCCAATTCTAGCAT 57.215 40.909 0.00 0.00 34.29 3.79



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

AutoCloner maintained by Alex Coulton.