Multiple sequence alignment - TraesCS6D01G271200

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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 TraesCS6D01G271200 chr6D 100.000 3179 0 0 1 3179 380504482 380501304 0.000000e+00 5871
1 TraesCS6D01G271200 chrUn 97.422 3181 79 3 1 3179 81311287 81314466 0.000000e+00 5417
2 TraesCS6D01G271200 chr7D 92.505 2962 215 7 221 3179 614795704 614798661 0.000000e+00 4233
3 TraesCS6D01G271200 chr5D 96.259 2352 86 2 830 3179 533247377 533249728 0.000000e+00 3855
4 TraesCS6D01G271200 chr5D 96.420 2151 67 5 1032 3179 311467713 311469856 0.000000e+00 3537
5 TraesCS6D01G271200 chr4A 88.344 3097 348 12 90 3179 688501519 688504609 0.000000e+00 3707
6 TraesCS6D01G271200 chr7A 87.262 2944 364 11 3 2944 641424862 641421928 0.000000e+00 3349
7 TraesCS6D01G271200 chr7A 81.642 3203 537 40 1 3179 12220074 12223249 0.000000e+00 2610
8 TraesCS6D01G271200 chr7A 77.078 2574 508 61 664 3179 14049337 14046788 0.000000e+00 1410
9 TraesCS6D01G271200 chr7A 76.734 447 89 14 1 435 679794219 679794662 5.300000e-58 235
10 TraesCS6D01G271200 chr7A 78.320 369 71 8 3 367 14050014 14049651 2.470000e-56 230
11 TraesCS6D01G271200 chr6A 87.615 2495 288 15 697 3179 91337318 91334833 0.000000e+00 2876
12 TraesCS6D01G271200 chr3A 82.887 3208 495 41 2 3179 12639417 12642600 0.000000e+00 2833
13 TraesCS6D01G271200 chr2D 90.178 2138 202 6 1 2136 563782911 563780780 0.000000e+00 2778
14 TraesCS6D01G271200 chr2A 81.855 3213 515 36 1 3179 669501229 669504407 0.000000e+00 2641
15 TraesCS6D01G271200 chr2A 76.248 3246 665 79 1 3179 186398744 186395538 0.000000e+00 1626


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 TraesCS6D01G271200 chr6D 380501304 380504482 3178 True 5871 5871 100.000 1 3179 1 chr6D.!!$R1 3178
1 TraesCS6D01G271200 chrUn 81311287 81314466 3179 False 5417 5417 97.422 1 3179 1 chrUn.!!$F1 3178
2 TraesCS6D01G271200 chr7D 614795704 614798661 2957 False 4233 4233 92.505 221 3179 1 chr7D.!!$F1 2958
3 TraesCS6D01G271200 chr5D 533247377 533249728 2351 False 3855 3855 96.259 830 3179 1 chr5D.!!$F2 2349
4 TraesCS6D01G271200 chr5D 311467713 311469856 2143 False 3537 3537 96.420 1032 3179 1 chr5D.!!$F1 2147
5 TraesCS6D01G271200 chr4A 688501519 688504609 3090 False 3707 3707 88.344 90 3179 1 chr4A.!!$F1 3089
6 TraesCS6D01G271200 chr7A 641421928 641424862 2934 True 3349 3349 87.262 3 2944 1 chr7A.!!$R1 2941
7 TraesCS6D01G271200 chr7A 12220074 12223249 3175 False 2610 2610 81.642 1 3179 1 chr7A.!!$F1 3178
8 TraesCS6D01G271200 chr7A 14046788 14050014 3226 True 820 1410 77.699 3 3179 2 chr7A.!!$R2 3176
9 TraesCS6D01G271200 chr6A 91334833 91337318 2485 True 2876 2876 87.615 697 3179 1 chr6A.!!$R1 2482
10 TraesCS6D01G271200 chr3A 12639417 12642600 3183 False 2833 2833 82.887 2 3179 1 chr3A.!!$F1 3177
11 TraesCS6D01G271200 chr2D 563780780 563782911 2131 True 2778 2778 90.178 1 2136 1 chr2D.!!$R1 2135
12 TraesCS6D01G271200 chr2A 669501229 669504407 3178 False 2641 2641 81.855 1 3179 1 chr2A.!!$F1 3178
13 TraesCS6D01G271200 chr2A 186395538 186398744 3206 True 1626 1626 76.248 1 3179 1 chr2A.!!$R1 3178

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
387 415 1.043673 GGGTGGATCTACTGCCTCGT 61.044 60.000 9.27 0.0 0.0 4.18 F
941 973 1.205893 GTTTGATCCTCCTCTGACGCT 59.794 52.381 0.00 0.0 0.0 5.07 F
1023 1058 1.507141 CGGACAAGAATATGCCGCCC 61.507 60.000 0.00 0.0 34.8 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1426 1477 0.603569 TCTCCGCAGTTCCTGAAGTC 59.396 55.000 0.00 0.00 32.44 3.01 R
2153 2220 1.202903 GGAGAGATGCATGCCTCCAAT 60.203 52.381 26.62 10.85 43.47 3.16 R
2417 2485 2.099141 TTTCCTCATCAGGTTCAGCG 57.901 50.000 0.00 0.00 41.28 5.18 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
70 71 1.891919 GTGCGTGCAGGAGTGGAAA 60.892 57.895 11.29 0.00 0.00 3.13
134 135 4.864334 CTGCGGCCATGAGGGTCC 62.864 72.222 2.24 0.00 38.37 4.46
363 364 1.141019 GCGCCTGAGGATCGTTACA 59.859 57.895 0.65 0.00 38.61 2.41
387 415 1.043673 GGGTGGATCTACTGCCTCGT 61.044 60.000 9.27 0.00 0.00 4.18
465 493 3.008049 ACCATTCGAGAGCTAACAAAGGT 59.992 43.478 0.00 0.00 39.11 3.50
935 967 1.908483 GCCCGTTTGATCCTCCTCT 59.092 57.895 0.00 0.00 0.00 3.69
941 973 1.205893 GTTTGATCCTCCTCTGACGCT 59.794 52.381 0.00 0.00 0.00 5.07
991 1023 1.683011 CGGGATCCAAGTCCTTTGCAT 60.683 52.381 15.23 0.00 38.38 3.96
997 1029 5.163301 GGATCCAAGTCCTTTGCATAGACTA 60.163 44.000 6.95 0.98 39.92 2.59
1023 1058 1.507141 CGGACAAGAATATGCCGCCC 61.507 60.000 0.00 0.00 34.80 6.13
1286 1337 4.940046 CCAGAAGAAAGCTTGCTTCATCTA 59.060 41.667 37.40 0.00 42.21 1.98
1318 1369 4.771577 AGGGTCACAATGTCAATAATTGCA 59.228 37.500 0.00 0.00 38.36 4.08
1340 1391 3.197790 CTGGGCGCAACCTCATCG 61.198 66.667 10.83 0.00 39.10 3.84
1396 1447 2.430694 CTGGGGTTCTATCACATCGACA 59.569 50.000 0.00 0.00 0.00 4.35
1426 1477 2.029918 GGTAAAGAAGCAAGTTGGCTGG 60.030 50.000 4.75 0.00 45.07 4.85
1812 1863 6.903516 TGTAGATTGGAATGGTCTGATGAAT 58.096 36.000 0.00 0.00 0.00 2.57
1873 1924 2.505819 GACCCAGCTAAGATCCCTTTCA 59.494 50.000 0.00 0.00 33.94 2.69
2013 2067 6.718912 TGGATGATGACAACAAGGTATTTGAA 59.281 34.615 0.00 0.00 39.21 2.69
2019 2073 5.997746 TGACAACAAGGTATTTGAAGAGGAG 59.002 40.000 0.00 0.00 39.21 3.69
2020 2074 5.316987 ACAACAAGGTATTTGAAGAGGAGG 58.683 41.667 0.00 0.00 39.21 4.30
2021 2075 5.073144 ACAACAAGGTATTTGAAGAGGAGGA 59.927 40.000 0.00 0.00 39.21 3.71
2153 2220 2.196742 ACATTCCATCCCCTGCTCTA 57.803 50.000 0.00 0.00 0.00 2.43
2180 2247 1.810794 GCATGCATCTCTCCTGTGAGG 60.811 57.143 14.21 0.00 39.23 3.86
2203 2270 6.069731 AGGGCTGATAAGAAGACTGAAGAAAT 60.070 38.462 0.00 0.00 0.00 2.17
2335 2402 3.077359 GTGGTGAAGCTGCTATCACTTT 58.923 45.455 27.67 6.27 44.20 2.66
2417 2485 6.341316 TGCTTCTAATACTGACAGTGAATCC 58.659 40.000 18.58 7.53 0.00 3.01
2941 3021 1.942776 TCTGGGAATGCTGTGAGAGA 58.057 50.000 0.00 0.00 0.00 3.10
3164 3247 3.862877 TGATTGGCATATGCTACCTGT 57.137 42.857 26.12 7.32 41.70 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 135 1.471676 CCTTCTTCGTTGGATCTCGGG 60.472 57.143 0.00 0.00 0.00 5.14
309 310 2.111878 GGATGCACTCCCATCGGG 59.888 66.667 0.00 0.00 46.11 5.14
363 364 0.983378 GCAGTAGATCCACCCCACCT 60.983 60.000 0.00 0.00 0.00 4.00
935 967 1.205417 TGATGATCTTGAGCAGCGTCA 59.795 47.619 0.00 0.00 0.00 4.35
941 973 1.767088 CCTCCCTGATGATCTTGAGCA 59.233 52.381 0.00 0.00 0.00 4.26
991 1023 3.562182 TCTTGTCCGCCATGATAGTCTA 58.438 45.455 0.00 0.00 0.00 2.59
997 1029 2.816087 GCATATTCTTGTCCGCCATGAT 59.184 45.455 0.00 0.00 0.00 2.45
1286 1337 2.312741 ACATTGTGACCCTCCAATCCAT 59.687 45.455 0.00 0.00 0.00 3.41
1340 1391 2.294512 CTCCCAAAGAAAGTGGCAACTC 59.705 50.000 0.00 0.00 34.77 3.01
1396 1447 2.054799 TGCTTCTTTACCCACAGGAGT 58.945 47.619 0.00 0.00 36.73 3.85
1409 1460 1.133668 AGTCCAGCCAACTTGCTTCTT 60.134 47.619 0.00 0.00 40.32 2.52
1426 1477 0.603569 TCTCCGCAGTTCCTGAAGTC 59.396 55.000 0.00 0.00 32.44 3.01
1812 1863 5.273208 ACCCTCACTTTCTCATAGAAGCTA 58.727 41.667 0.00 0.00 35.37 3.32
1873 1924 8.899887 TTTTTCCTCATCTCCATAATCCTTTT 57.100 30.769 0.00 0.00 0.00 2.27
1914 1965 5.017490 TGGTCAAAACCTTCCACAGTAAAA 58.983 37.500 0.00 0.00 46.60 1.52
2013 2067 6.126911 GGATGTCTTTATTCAGTTCCTCCTCT 60.127 42.308 0.00 0.00 0.00 3.69
2019 2073 5.745227 TCCAGGATGTCTTTATTCAGTTCC 58.255 41.667 0.00 0.00 0.00 3.62
2020 2074 7.050377 TCATCCAGGATGTCTTTATTCAGTTC 58.950 38.462 26.14 0.00 40.55 3.01
2021 2075 6.962182 TCATCCAGGATGTCTTTATTCAGTT 58.038 36.000 26.14 0.00 40.55 3.16
2153 2220 1.202903 GGAGAGATGCATGCCTCCAAT 60.203 52.381 26.62 10.85 43.47 3.16
2180 2247 8.608317 GTTATTTCTTCAGTCTTCTTATCAGCC 58.392 37.037 0.00 0.00 0.00 4.85
2335 2402 2.727123 TTTTTGAGCAGACACTGGGA 57.273 45.000 0.00 0.00 31.21 4.37
2417 2485 2.099141 TTTCCTCATCAGGTTCAGCG 57.901 50.000 0.00 0.00 41.28 5.18
2941 3021 5.940470 GGATGTGTCAGACTAAAAAGTCCAT 59.060 40.000 1.31 0.00 39.50 3.41


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

AutoCloner maintained by Alex Coulton.