Multiple sequence alignment - TraesCS5D01G085700

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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 TraesCS5D01G085700 chr5D 100.000 2951 0 0 1 2951 90925830 90922880 0.000000e+00 5450
1 TraesCS5D01G085700 chr5B 96.386 2961 90 12 1 2951 96140474 96137521 0.000000e+00 4859
2 TraesCS5D01G085700 chr5A 95.907 2956 95 13 1 2951 84389675 84386741 0.000000e+00 4765
3 TraesCS5D01G085700 chr5A 89.103 156 15 2 4 157 1773592 1773437 3.000000e-45 193
4 TraesCS5D01G085700 chr2D 90.625 160 13 2 1 158 641491157 641491316 8.290000e-51 211
5 TraesCS5D01G085700 chr7D 88.304 171 16 4 1 167 7568278 7568448 4.990000e-48 202
6 TraesCS5D01G085700 chr4D 89.308 159 16 1 1 158 12696047 12695889 6.450000e-47 198
7 TraesCS5D01G085700 chr3B 89.241 158 15 2 1 156 23954306 23954463 2.320000e-46 196
8 TraesCS5D01G085700 chr7B 88.820 161 15 3 1 158 104298487 104298327 8.350000e-46 195
9 TraesCS5D01G085700 chr1D 88.272 162 15 4 1 158 463333295 463333456 1.080000e-44 191
10 TraesCS5D01G085700 chr2A 88.125 160 17 2 1 158 55953181 55953340 3.880000e-44 189


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 TraesCS5D01G085700 chr5D 90922880 90925830 2950 True 5450 5450 100.000 1 2951 1 chr5D.!!$R1 2950
1 TraesCS5D01G085700 chr5B 96137521 96140474 2953 True 4859 4859 96.386 1 2951 1 chr5B.!!$R1 2950
2 TraesCS5D01G085700 chr5A 84386741 84389675 2934 True 4765 4765 95.907 1 2951 1 chr5A.!!$R2 2950

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
986 993 0.618458 TCTGCGGGCCTTCTACATTT 59.382 50.0 0.84 0.0 0.0 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2767 2775 0.528017 TGCACGGCAAACAGAAAACA 59.472 45.0 0.0 0.0 34.76 2.83 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
18 19 3.728373 GGGAGGGGCAATGACGGT 61.728 66.667 0.00 0.00 0.00 4.83
108 110 9.646336 ATTTATATTATTTCTCGTGTTCGTTGC 57.354 29.630 0.00 0.00 38.33 4.17
112 114 1.647346 TTCTCGTGTTCGTTGCACTT 58.353 45.000 0.00 0.00 38.33 3.16
195 197 3.106242 GGTGACCAACCCAAACAATTC 57.894 47.619 0.00 0.00 44.02 2.17
327 332 2.410469 GCAGCACAATCATCCGCC 59.590 61.111 0.00 0.00 0.00 6.13
463 469 4.442401 GGGAAAAATATCTCCCCGGTTA 57.558 45.455 0.00 0.00 45.03 2.85
670 677 4.764679 TGTGAAATTCGAGGTGGATTTG 57.235 40.909 0.00 0.00 0.00 2.32
695 702 1.514087 GTCTGCGATTCCCCGTACA 59.486 57.895 0.00 0.00 0.00 2.90
826 833 5.048434 GCAAACTTCTGTGCTAATCCTTTCT 60.048 40.000 0.00 0.00 37.78 2.52
855 862 1.138859 TCTGATTACGCAGATGGGTGG 59.861 52.381 12.32 0.00 39.84 4.61
949 956 1.750780 GGCAGCTAGGGTTTGCTCC 60.751 63.158 0.00 0.00 37.44 4.70
969 976 1.760086 CCAGAGCCCCATCGTCTCT 60.760 63.158 0.00 0.00 37.66 3.10
979 986 3.082579 ATCGTCTCTGCGGGCCTTC 62.083 63.158 0.84 0.00 0.00 3.46
986 993 0.618458 TCTGCGGGCCTTCTACATTT 59.382 50.000 0.84 0.00 0.00 2.32
990 997 1.821216 CGGGCCTTCTACATTTGTGT 58.179 50.000 0.84 0.00 0.00 3.72
991 998 1.468520 CGGGCCTTCTACATTTGTGTG 59.531 52.381 0.84 0.00 0.00 3.82
1404 1411 0.178915 TCGGAAAGTCCCCTCTTGGA 60.179 55.000 0.00 0.00 35.39 3.53
1557 1564 7.328249 CAGAATTCTCAGCCTTCGATATCTTAC 59.672 40.741 4.57 0.00 0.00 2.34
1562 1569 3.325135 CAGCCTTCGATATCTTACCCCTT 59.675 47.826 0.34 0.00 0.00 3.95
2102 2109 2.369394 CATAGGGCTGAGGGTGTTTTC 58.631 52.381 0.00 0.00 0.00 2.29
2210 2217 5.221244 GCCAATACACCTTCACTTTGTTTCT 60.221 40.000 0.00 0.00 0.00 2.52
2322 2329 1.136113 GCTTCGCTCTGCTGAAGAAAC 60.136 52.381 19.66 5.05 39.52 2.78
2417 2424 3.684908 TGCTAGCTGCCAAGTTGATTTA 58.315 40.909 17.23 0.00 42.00 1.40
2534 2541 0.972983 GTGCAGACTAGGAGCCCTCA 60.973 60.000 0.00 0.00 34.61 3.86
2651 2658 1.401199 GGAGTAGCTACAGTGTCCGAC 59.599 57.143 25.28 0.00 0.00 4.79
2666 2673 3.706373 GACGGGCTGCTCCTCCAA 61.706 66.667 0.00 0.00 34.39 3.53
2690 2697 2.619074 GCAGTTTGGGCTTCTATCCACT 60.619 50.000 0.00 0.00 32.00 4.00
2711 2718 1.398390 GGCATTCGACGATTTTGCTCT 59.602 47.619 20.32 0.00 33.86 4.09
2716 2723 0.371645 CGACGATTTTGCTCTGAGCC 59.628 55.000 25.61 9.71 41.51 4.70
2767 2775 4.697352 GTCTGCCTATTTGTGTGTTCATCT 59.303 41.667 0.00 0.00 0.00 2.90
2782 2790 3.624326 TCATCTGTTTTCTGTTTGCCG 57.376 42.857 0.00 0.00 0.00 5.69
2867 2877 7.748677 TCTTCAATCCCTGATATAATGCTTCA 58.251 34.615 0.00 0.00 32.78 3.02
2922 2933 1.571457 TGTTCCCTTTGGTTCTTCCCA 59.429 47.619 0.00 0.00 34.77 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.080501 CACTGAAGCGAGCCGAAGA 60.081 57.895 0.00 0.00 0.00 2.87
153 155 8.147058 TCACCACATGTGTTGCTTATAATTTTT 58.853 29.630 23.79 0.00 45.61 1.94
154 156 7.598493 GTCACCACATGTGTTGCTTATAATTTT 59.402 33.333 23.79 0.00 45.61 1.82
155 157 7.090173 GTCACCACATGTGTTGCTTATAATTT 58.910 34.615 23.79 0.00 45.61 1.82
216 220 3.251245 ACACGTGCCGAAATAAAATGTCA 59.749 39.130 17.22 0.00 0.00 3.58
220 224 3.365565 GGTCACACGTGCCGAAATAAAAT 60.366 43.478 17.22 0.00 0.00 1.82
327 332 2.049627 GCTGATAGGTGGGCCCTGAG 62.050 65.000 25.70 6.72 45.81 3.35
341 346 1.344953 TGGGCTAATGTCCCGCTGAT 61.345 55.000 0.00 0.00 46.92 2.90
530 536 4.143333 AGGCCGAATCCACGACCG 62.143 66.667 0.00 0.00 40.51 4.79
670 677 2.174319 GGAATCGCAGACCCGAAGC 61.174 63.158 0.00 0.00 42.51 3.86
695 702 6.018832 CCAAAACAATGTTTTCGAGCAAATCT 60.019 34.615 19.89 0.00 0.00 2.40
734 741 2.260434 GGACGCACGGACAGCTTA 59.740 61.111 0.00 0.00 0.00 3.09
821 828 6.533012 TGCGTAATCAGATCAAGAAGAGAAAG 59.467 38.462 0.00 0.00 0.00 2.62
826 833 5.582689 TCTGCGTAATCAGATCAAGAAGA 57.417 39.130 0.00 0.00 38.11 2.87
949 956 1.743321 GAGACGATGGGGCTCTGGAG 61.743 65.000 0.00 0.00 0.00 3.86
969 976 0.037590 ACAAATGTAGAAGGCCCGCA 59.962 50.000 0.00 0.00 0.00 5.69
979 986 5.702865 CATCTTGGAACCACACAAATGTAG 58.297 41.667 0.00 0.00 36.72 2.74
986 993 1.608055 CTGCATCTTGGAACCACACA 58.392 50.000 0.00 0.00 0.00 3.72
990 997 0.112995 AAGGCTGCATCTTGGAACCA 59.887 50.000 0.50 0.00 0.00 3.67
991 998 0.813821 GAAGGCTGCATCTTGGAACC 59.186 55.000 0.50 0.00 0.00 3.62
1557 1564 9.401058 CCATTATTATAGCAAATCTCTAAGGGG 57.599 37.037 0.00 0.00 0.00 4.79
2102 2109 5.405935 TCCATGATGTATCATCCTAACCG 57.594 43.478 4.43 0.00 45.23 4.44
2178 2185 4.278419 GTGAAGGTGTATTGGCAGAAACTT 59.722 41.667 0.00 0.00 0.00 2.66
2210 2217 3.475575 TGTAAACAATCTGTGAGCAGCA 58.524 40.909 0.00 0.00 42.29 4.41
2234 2241 3.446161 CGGAACCTGGTTATCAGTACAGA 59.554 47.826 12.96 0.00 41.83 3.41
2322 2329 6.991938 TGAAAGAAAATAGGGGTGAACAATG 58.008 36.000 0.00 0.00 0.00 2.82
2438 2445 7.255942 CCAAAATTCAGATACCTGTGGAAACTT 60.256 37.037 0.00 0.00 41.16 2.66
2534 2541 4.261280 CGTAAACCCTTTCCAAATCGTTGT 60.261 41.667 0.00 0.00 32.40 3.32
2651 2658 3.710722 ACTTGGAGGAGCAGCCCG 61.711 66.667 0.00 0.00 37.37 6.13
2660 2667 1.809567 GCCCAAACTGCACTTGGAGG 61.810 60.000 20.01 8.77 45.31 4.30
2666 2673 2.619074 GGATAGAAGCCCAAACTGCACT 60.619 50.000 0.00 0.00 0.00 4.40
2690 2697 1.130373 GAGCAAAATCGTCGAATGCCA 59.870 47.619 20.56 0.00 37.73 4.92
2716 2723 2.438975 ATCACACATGGCAGGCGG 60.439 61.111 0.00 0.00 0.00 6.13
2767 2775 0.528017 TGCACGGCAAACAGAAAACA 59.472 45.000 0.00 0.00 34.76 2.83
2782 2790 0.889186 AGACACAACGGGGAATGCAC 60.889 55.000 0.00 0.00 0.00 4.57
2867 2877 5.234466 AGGAGCAGAAAGAATACACAAGT 57.766 39.130 0.00 0.00 0.00 3.16
2922 2933 5.047802 CAGGCCAGTTATTCAAACATCAGTT 60.048 40.000 5.01 0.00 40.40 3.16


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

AutoCloner maintained by Alex Coulton.