Multiple sequence alignment - TraesCS5D01G032400

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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 TraesCS5D01G032400 chr5D 100.000 2635 0 0 756 3390 29628242 29630876 0.000000e+00 4867
1 TraesCS5D01G032400 chr5D 95.521 1987 63 15 756 2734 339382204 339384172 0.000000e+00 3153
2 TraesCS5D01G032400 chr5D 98.930 654 7 0 2737 3390 309390016 309390669 0.000000e+00 1170
3 TraesCS5D01G032400 chr5D 98.930 654 7 0 2737 3390 525198886 525198233 0.000000e+00 1170
4 TraesCS5D01G032400 chr5D 100.000 455 0 0 1 455 29627487 29627941 0.000000e+00 841
5 TraesCS5D01G032400 chr5D 96.681 452 12 3 1 449 339381524 339381975 0.000000e+00 749
6 TraesCS5D01G032400 chr7D 95.829 1990 59 10 756 2732 594650678 594652656 0.000000e+00 3193
7 TraesCS5D01G032400 chr7D 96.950 459 9 5 1 455 594650201 594650658 0.000000e+00 765
8 TraesCS5D01G032400 chr4D 95.685 1993 67 7 756 2734 332129465 332131452 0.000000e+00 3186
9 TraesCS5D01G032400 chr4D 98.930 654 7 0 2737 3390 216554218 216554871 0.000000e+00 1170
10 TraesCS5D01G032400 chr4D 98.930 654 7 0 2737 3390 375096897 375096244 0.000000e+00 1170
11 TraesCS5D01G032400 chr4D 95.852 458 16 2 1 455 332128988 332129445 0.000000e+00 737
12 TraesCS5D01G032400 chr2D 95.953 1952 72 3 790 2734 147701329 147703280 0.000000e+00 3160
13 TraesCS5D01G032400 chr2D 90.613 1257 83 12 836 2065 233888319 233889567 0.000000e+00 1635
14 TraesCS5D01G032400 chr2D 95.861 459 15 4 1 455 147700457 147700915 0.000000e+00 739
15 TraesCS5D01G032400 chr2D 95.175 456 14 6 1 448 92456673 92457128 0.000000e+00 713
16 TraesCS5D01G032400 chr6D 94.677 2010 79 7 756 2737 73254669 73252660 0.000000e+00 3094
17 TraesCS5D01G032400 chr6D 98.930 654 7 0 2737 3390 158101320 158101973 0.000000e+00 1170
18 TraesCS5D01G032400 chr6D 98.930 654 7 0 2737 3390 346262080 346261427 0.000000e+00 1170
19 TraesCS5D01G032400 chr6D 94.027 452 19 2 5 455 73255133 73254689 0.000000e+00 678
20 TraesCS5D01G032400 chr3D 95.552 1259 48 5 756 2008 231534028 231532772 0.000000e+00 2008
21 TraesCS5D01G032400 chr3D 98.930 654 7 0 2737 3390 275898824 275898171 0.000000e+00 1170
22 TraesCS5D01G032400 chr3D 98.930 654 7 0 2737 3390 321907341 321906688 0.000000e+00 1170
23 TraesCS5D01G032400 chr3D 95.690 696 21 2 2051 2737 231532772 231532077 0.000000e+00 1110
24 TraesCS5D01G032400 chr3D 96.499 457 13 3 1 455 231534503 231534048 0.000000e+00 752
25 TraesCS5D01G032400 chr1B 91.327 1153 64 13 895 2021 151150013 151148871 0.000000e+00 1543
26 TraesCS5D01G032400 chr4A 90.381 1102 78 12 836 1913 322881875 322882972 0.000000e+00 1423
27 TraesCS5D01G032400 chr4A 93.576 467 24 3 2274 2734 322883206 322883672 0.000000e+00 691
28 TraesCS5D01G032400 chr1D 99.083 654 6 0 2737 3390 275453074 275452421 0.000000e+00 1175
29 TraesCS5D01G032400 chr1D 91.339 127 11 0 2611 2737 386165921 386165795 1.250000e-39 174
30 TraesCS5D01G032400 chr1A 92.810 459 28 4 1 455 522944600 522945057 0.000000e+00 660
31 TraesCS5D01G032400 chr6A 92.779 457 22 10 1 448 104438685 104438231 0.000000e+00 651
32 TraesCS5D01G032400 chr6B 90.505 495 34 6 1771 2255 651365030 651364539 2.850000e-180 641
33 TraesCS5D01G032400 chr2B 90.323 496 36 4 1771 2255 306849224 306848730 1.030000e-179 640
34 TraesCS5D01G032400 chr2B 93.532 402 20 3 2338 2734 306848658 306848258 8.100000e-166 593
35 TraesCS5D01G032400 chr2B 87.712 236 10 3 2274 2492 149997365 149997132 1.210000e-64 257
36 TraesCS5D01G032400 chr7A 89.751 361 13 4 2274 2613 689072387 689072744 1.120000e-119 440
37 TraesCS5D01G032400 chr7A 95.370 108 0 1 756 858 25226162 25226055 2.090000e-37 167
38 TraesCS5D01G032400 chr5A 92.793 111 2 2 756 860 539826819 539826709 4.530000e-34 156
39 TraesCS5D01G032400 chr5A 89.815 108 6 3 756 858 374025599 374025492 2.120000e-27 134


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 TraesCS5D01G032400 chr5D 29627487 29630876 3389 False 2854.0 4867 100.000000 1 3390 2 chr5D.!!$F2 3389
1 TraesCS5D01G032400 chr5D 339381524 339384172 2648 False 1951.0 3153 96.101000 1 2734 2 chr5D.!!$F3 2733
2 TraesCS5D01G032400 chr5D 309390016 309390669 653 False 1170.0 1170 98.930000 2737 3390 1 chr5D.!!$F1 653
3 TraesCS5D01G032400 chr5D 525198233 525198886 653 True 1170.0 1170 98.930000 2737 3390 1 chr5D.!!$R1 653
4 TraesCS5D01G032400 chr7D 594650201 594652656 2455 False 1979.0 3193 96.389500 1 2732 2 chr7D.!!$F1 2731
5 TraesCS5D01G032400 chr4D 332128988 332131452 2464 False 1961.5 3186 95.768500 1 2734 2 chr4D.!!$F2 2733
6 TraesCS5D01G032400 chr4D 216554218 216554871 653 False 1170.0 1170 98.930000 2737 3390 1 chr4D.!!$F1 653
7 TraesCS5D01G032400 chr4D 375096244 375096897 653 True 1170.0 1170 98.930000 2737 3390 1 chr4D.!!$R1 653
8 TraesCS5D01G032400 chr2D 147700457 147703280 2823 False 1949.5 3160 95.907000 1 2734 2 chr2D.!!$F3 2733
9 TraesCS5D01G032400 chr2D 233888319 233889567 1248 False 1635.0 1635 90.613000 836 2065 1 chr2D.!!$F2 1229
10 TraesCS5D01G032400 chr6D 73252660 73255133 2473 True 1886.0 3094 94.352000 5 2737 2 chr6D.!!$R2 2732
11 TraesCS5D01G032400 chr6D 158101320 158101973 653 False 1170.0 1170 98.930000 2737 3390 1 chr6D.!!$F1 653
12 TraesCS5D01G032400 chr6D 346261427 346262080 653 True 1170.0 1170 98.930000 2737 3390 1 chr6D.!!$R1 653
13 TraesCS5D01G032400 chr3D 231532077 231534503 2426 True 1290.0 2008 95.913667 1 2737 3 chr3D.!!$R3 2736
14 TraesCS5D01G032400 chr3D 275898171 275898824 653 True 1170.0 1170 98.930000 2737 3390 1 chr3D.!!$R1 653
15 TraesCS5D01G032400 chr3D 321906688 321907341 653 True 1170.0 1170 98.930000 2737 3390 1 chr3D.!!$R2 653
16 TraesCS5D01G032400 chr1B 151148871 151150013 1142 True 1543.0 1543 91.327000 895 2021 1 chr1B.!!$R1 1126
17 TraesCS5D01G032400 chr4A 322881875 322883672 1797 False 1057.0 1423 91.978500 836 2734 2 chr4A.!!$F1 1898
18 TraesCS5D01G032400 chr1D 275452421 275453074 653 True 1175.0 1175 99.083000 2737 3390 1 chr1D.!!$R1 653
19 TraesCS5D01G032400 chr2B 306848258 306849224 966 True 616.5 640 91.927500 1771 2734 2 chr2B.!!$R2 963

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
279 283 2.311688 AATCACCGTCGGATGCTCCC 62.312 60.0 20.51 0.0 31.13 4.30 F
1114 1462 0.902516 AGCCTCCTGAAGACGAAGCT 60.903 55.0 0.00 0.0 0.00 3.74 F
2146 2521 0.036105 ACAGGATGCTGCGATCAACA 60.036 50.0 14.95 0.0 42.53 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2146 2521 0.550914 TGGGTCTTGTTGTTCAGGCT 59.449 50.000 0.00 0.0 0.00 4.58 R
2206 2581 2.135139 CTACGTGCACAAGAGCTTGAA 58.865 47.619 18.64 0.0 42.93 2.69 R
3224 3668 0.106268 TTGCCAAGTTGCCTTCTCCA 60.106 50.000 0.00 0.0 0.00 3.86 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
279 283 2.311688 AATCACCGTCGGATGCTCCC 62.312 60.000 20.51 0.0 31.13 4.30
320 324 2.529136 CCTCTCACCCACCCACCA 60.529 66.667 0.00 0.0 0.00 4.17
1010 1355 1.078848 CTCCTTCCCCACTGCTTCG 60.079 63.158 0.00 0.0 0.00 3.79
1011 1356 1.535444 TCCTTCCCCACTGCTTCGA 60.535 57.895 0.00 0.0 0.00 3.71
1107 1455 1.270907 GGTGAAGAGCCTCCTGAAGA 58.729 55.000 0.00 0.0 0.00 2.87
1114 1462 0.902516 AGCCTCCTGAAGACGAAGCT 60.903 55.000 0.00 0.0 0.00 3.74
1369 1717 1.137513 GTATACTTCGCGCCATGGAC 58.862 55.000 18.40 5.4 0.00 4.02
1424 1772 1.171308 CTGGTGATGCTTGTTCCTGG 58.829 55.000 0.00 0.0 0.00 4.45
1666 2014 7.112452 ACTTTAGTCAAATGTGCTTCCTTTT 57.888 32.000 0.00 0.0 0.00 2.27
1808 2171 1.281925 AATGGCCCGTCCTTCTGGAT 61.282 55.000 0.00 0.0 45.29 3.41
1868 2239 2.368548 TCTGACTACCTGCTTGCTCAAA 59.631 45.455 0.00 0.0 0.00 2.69
1930 2301 8.153550 CCATTCTTACTTTCTGGCATCTAGTAT 58.846 37.037 0.00 0.0 0.00 2.12
2146 2521 0.036105 ACAGGATGCTGCGATCAACA 60.036 50.000 14.95 0.0 42.53 3.33
2206 2581 1.005289 ATGTGGGGCAGGAGGATCT 59.995 57.895 0.00 0.0 33.73 2.75
2285 2710 1.165270 ATACCAGTGCTTTCGTTGCC 58.835 50.000 0.00 0.0 0.00 4.52
2348 2773 4.552883 TTCCATCCCATCTAGTAGGTGA 57.447 45.455 12.24 0.0 0.00 4.02
2734 3178 1.375908 CTAGGCTGGCGCAGTTTGA 60.376 57.895 10.83 0.0 38.10 2.69
2739 3183 1.283793 CTGGCGCAGTTTGACTTGG 59.716 57.895 10.83 0.0 0.00 3.61
2841 3285 6.822442 TCTACATGGTTAGTCTCAACACAAA 58.178 36.000 0.00 0.0 0.00 2.83
2940 3384 1.426423 CATGGATGAATCGCGAGGAG 58.574 55.000 16.66 0.0 0.00 3.69
3224 3668 6.864685 CACAAGCATCATCATTAACAACAAGT 59.135 34.615 0.00 0.0 0.00 3.16
3374 3818 4.020751 AGTCTAGCATGAGCAACTTCAAGA 60.021 41.667 0.00 0.0 45.49 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
344 352 1.528292 GAGAGAGGAGTGGTGTGCGT 61.528 60.000 0.00 0.00 0.00 5.24
384 392 2.363147 GGGAGAGGGTGAGAGCGT 60.363 66.667 0.00 0.00 0.00 5.07
1010 1355 1.660917 GTGGGATCGATCGGAGGTC 59.339 63.158 18.81 8.51 0.00 3.85
1011 1356 1.833049 GGTGGGATCGATCGGAGGT 60.833 63.158 18.81 0.00 0.00 3.85
1107 1455 4.758692 CTGTGGTGTCAGCTTCGT 57.241 55.556 3.30 0.00 0.00 3.85
1114 1462 2.592574 GCTGCTGCTGTGGTGTCA 60.593 61.111 8.53 0.00 36.03 3.58
1325 1673 3.463585 TAGGTACCTTGGCGGCGG 61.464 66.667 22.11 2.39 35.61 6.13
1357 1705 3.673956 AAATCGGTCCATGGCGCGA 62.674 57.895 12.10 13.13 0.00 5.87
1358 1706 3.202001 AAATCGGTCCATGGCGCG 61.202 61.111 6.96 0.00 0.00 6.86
1369 1717 6.391227 AATCAGTAAATTAGCCCAAATCGG 57.609 37.500 0.00 0.00 0.00 4.18
1666 2014 1.476085 CCAAGGTGCACAGTTGTTCAA 59.524 47.619 20.43 0.00 0.00 2.69
1808 2171 7.038048 CAGAACAGATTCAGACTAACTGCATA 58.962 38.462 0.00 0.00 45.38 3.14
1868 2239 4.338012 TGAATGTTCTCAAGTGCCATGAT 58.662 39.130 0.00 0.00 0.00 2.45
1914 2285 6.403049 TCGTTCAAATACTAGATGCCAGAAA 58.597 36.000 0.00 0.00 0.00 2.52
1930 2301 2.143122 GCCACTGTGAGATCGTTCAAA 58.857 47.619 9.86 0.00 0.00 2.69
2146 2521 0.550914 TGGGTCTTGTTGTTCAGGCT 59.449 50.000 0.00 0.00 0.00 4.58
2206 2581 2.135139 CTACGTGCACAAGAGCTTGAA 58.865 47.619 18.64 0.00 42.93 2.69
2285 2710 3.312146 TGTGGAGCATGCGTGTATTATTG 59.688 43.478 13.01 0.00 0.00 1.90
2348 2773 9.853555 TTATTTTATTTGTTTGCATCGAGTCAT 57.146 25.926 0.00 0.00 0.00 3.06
2550 2978 2.331194 GCTACAAGCAAGCAAACATGG 58.669 47.619 0.00 0.00 41.89 3.66
2734 3178 4.810345 TGAAGGGAAATTTACACCCAAGT 58.190 39.130 14.23 1.40 45.43 3.16
2739 3183 5.946377 AGAGTCATGAAGGGAAATTTACACC 59.054 40.000 2.10 0.43 0.00 4.16
2841 3285 7.255312 CGATGAAGCTTATACTTCCTCTAGTGT 60.255 40.741 0.00 0.00 44.50 3.55
2940 3384 5.695851 AATGCTATATTGCCTTGTGCTAC 57.304 39.130 6.69 0.00 42.00 3.58
3224 3668 0.106268 TTGCCAAGTTGCCTTCTCCA 60.106 50.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.