Multiple sequence alignment - TraesCS4D01G147000

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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 TraesCS4D01G147000 chr4D 100.000 3840 0 0 650 4489 137768159 137764320 0.000000e+00 7092
1 TraesCS4D01G147000 chr4D 100.000 284 0 0 1 284 137768808 137768525 4.320000e-145 525
2 TraesCS4D01G147000 chr4D 100.000 64 0 0 4807 4870 137764002 137763939 8.560000e-23 119
3 TraesCS4D01G147000 chr4A 96.388 3821 91 16 676 4476 423894626 423890833 0.000000e+00 6248
4 TraesCS4D01G147000 chr4A 92.050 239 9 6 1 233 423895316 423895082 1.310000e-85 327
5 TraesCS4D01G147000 chr4B 95.536 3853 142 15 650 4489 230011762 230007927 0.000000e+00 6135
6 TraesCS4D01G147000 chr4B 94.774 287 6 6 1 279 230012366 230012081 5.790000e-119 438


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 TraesCS4D01G147000 chr4D 137763939 137768808 4869 True 2578.666667 7092 100.000 1 4870 3 chr4D.!!$R1 4869
1 TraesCS4D01G147000 chr4A 423890833 423895316 4483 True 3287.500000 6248 94.219 1 4476 2 chr4A.!!$R1 4475
2 TraesCS4D01G147000 chr4B 230007927 230012366 4439 True 3286.500000 6135 95.155 1 4489 2 chr4B.!!$R1 4488

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
737 758 0.035725 TCTCCTCGTTAGCTCGTGGA 60.036 55.000 15.31 15.31 46.36 4.02 F
2550 2572 2.017049 GGAGCATAACTGTTCGGCATT 58.983 47.619 15.68 0.13 33.72 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2734 2760 2.037251 TCGGATATTGAACAGCTAGCCC 59.963 50.0 12.13 0.0 0.0 5.19 R
4458 4502 0.108615 AGTTCAAGATGAGGACGGCG 60.109 55.0 4.80 4.8 0.0 6.46 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
117 125 1.451067 ACGACACTAGAACGAGAGGG 58.549 55.000 0.00 0.00 0.00 4.30
118 126 1.002888 ACGACACTAGAACGAGAGGGA 59.997 52.381 0.00 0.00 0.00 4.20
119 127 1.666700 CGACACTAGAACGAGAGGGAG 59.333 57.143 0.00 0.00 0.00 4.30
123 131 4.150359 ACACTAGAACGAGAGGGAGAAAA 58.850 43.478 0.00 0.00 0.00 2.29
124 132 4.773149 ACACTAGAACGAGAGGGAGAAAAT 59.227 41.667 0.00 0.00 0.00 1.82
127 135 7.039223 ACACTAGAACGAGAGGGAGAAAATAAA 60.039 37.037 0.00 0.00 0.00 1.40
283 291 3.349006 CGCACAGCCACACCACTC 61.349 66.667 0.00 0.00 0.00 3.51
728 749 1.134189 TGGCTCGATCTCTCCTCGTTA 60.134 52.381 0.00 0.00 37.40 3.18
737 758 0.035725 TCTCCTCGTTAGCTCGTGGA 60.036 55.000 15.31 15.31 46.36 4.02
1113 1134 4.786425 AGGCCAAAGAGTTATCCATTCTC 58.214 43.478 5.01 0.00 0.00 2.87
1149 1170 4.344104 TCATTCTTCTCATGTTTTCCCCC 58.656 43.478 0.00 0.00 0.00 5.40
1251 1272 6.942576 GGTCAACAAGCCCATAATATGACTAT 59.057 38.462 1.10 0.00 36.91 2.12
1335 1356 8.719648 GTTGTAATTTTGCCATTGAATTGATCA 58.280 29.630 0.00 0.00 35.85 2.92
1352 1373 9.590451 GAATTGATCAATTTCTTGGCTGATTAA 57.410 29.630 29.44 0.00 40.77 1.40
1390 1411 7.822658 AGGGAATTGATTTTTCAATGCATTTG 58.177 30.769 9.83 5.89 39.92 2.32
1584 1606 5.593909 TGTTTTCAGATATGGGGTGCTAATG 59.406 40.000 0.00 0.00 0.00 1.90
1756 1778 7.335924 TCTGTTTACCTGCTGAACCAATTATAC 59.664 37.037 0.00 0.00 0.00 1.47
2025 2047 3.622166 TCAAGAGAGCAGCATGATTGA 57.378 42.857 0.00 0.00 39.69 2.57
2038 2060 8.133627 AGCAGCATGATTGAAGAAATGTATAAC 58.866 33.333 0.00 0.00 39.69 1.89
2187 2209 2.691526 TCGGTATCTAATGCTCGTTGGT 59.308 45.455 0.00 0.00 0.00 3.67
2299 2321 2.744202 ACCAATTCACTTAAGCAGCTCG 59.256 45.455 1.29 0.00 0.00 5.03
2540 2562 5.954150 ACCATGAAAATTGAGGAGCATAACT 59.046 36.000 0.00 0.00 0.00 2.24
2544 2566 6.913170 TGAAAATTGAGGAGCATAACTGTTC 58.087 36.000 0.00 0.00 32.27 3.18
2550 2572 2.017049 GGAGCATAACTGTTCGGCATT 58.983 47.619 15.68 0.13 33.72 3.56
2734 2760 1.530720 TGCACACTGTTCAGCATAACG 59.469 47.619 0.00 0.00 31.76 3.18
2894 2920 4.695455 TGCTGCTCAGGTAATAGTTTTCAC 59.305 41.667 0.00 0.00 0.00 3.18
3041 3067 3.542676 TCGTGGTTCCACAGCGGT 61.543 61.111 19.90 0.00 36.82 5.68
3634 3678 5.513094 GCCATCTGCCCAAGTGAGTAATATA 60.513 44.000 0.00 0.00 0.00 0.86
3732 3776 1.393883 GACGAACGAGCATTTCTTCCC 59.606 52.381 0.14 0.00 0.00 3.97
3750 3794 3.750371 TCCCAATATCCGCGAAATGATT 58.250 40.909 8.23 0.00 0.00 2.57
3751 3795 3.501828 TCCCAATATCCGCGAAATGATTG 59.498 43.478 8.23 9.68 0.00 2.67
3873 3917 2.021355 GCAGCAGCAACTCTGATAGT 57.979 50.000 0.00 0.00 45.72 2.12
4129 4173 9.613428 TTAACTCTAATGTAAACTATGCTGCAT 57.387 29.630 20.18 20.18 0.00 3.96
4403 4447 1.153353 GTCGACCGGCTGAAATTTCA 58.847 50.000 19.45 19.45 35.57 2.69
4431 4475 1.709147 CCTGCCAGACGTGCATAAGC 61.709 60.000 0.00 0.00 38.22 3.09
4478 4522 1.363744 GCCGTCCTCATCTTGAACTG 58.636 55.000 0.00 0.00 0.00 3.16
4481 4525 2.613977 CCGTCCTCATCTTGAACTGCTT 60.614 50.000 0.00 0.00 0.00 3.91
4482 4526 3.070018 CGTCCTCATCTTGAACTGCTTT 58.930 45.455 0.00 0.00 0.00 3.51
4826 4870 3.699894 CCTCCTCGCTGCCACACT 61.700 66.667 0.00 0.00 0.00 3.55
4827 4871 2.345244 CTCCTCGCTGCCACACTT 59.655 61.111 0.00 0.00 0.00 3.16
4828 4872 1.739562 CTCCTCGCTGCCACACTTC 60.740 63.158 0.00 0.00 0.00 3.01
4829 4873 2.743928 CCTCGCTGCCACACTTCC 60.744 66.667 0.00 0.00 0.00 3.46
4830 4874 3.114616 CTCGCTGCCACACTTCCG 61.115 66.667 0.00 0.00 0.00 4.30
4831 4875 4.680237 TCGCTGCCACACTTCCGG 62.680 66.667 0.00 0.00 0.00 5.14
4837 4881 4.003788 CCACACTTCCGGGCTCGT 62.004 66.667 4.71 0.00 33.95 4.18
4838 4882 2.738521 CACACTTCCGGGCTCGTG 60.739 66.667 4.71 6.70 33.95 4.35
4839 4883 4.681978 ACACTTCCGGGCTCGTGC 62.682 66.667 4.71 0.00 38.76 5.34
4849 4893 4.427661 GCTCGTGCGCTCCTCACT 62.428 66.667 9.73 0.00 32.54 3.41
4850 4894 2.505777 CTCGTGCGCTCCTCACTG 60.506 66.667 9.73 0.00 32.54 3.66
4851 4895 4.724602 TCGTGCGCTCCTCACTGC 62.725 66.667 9.73 0.00 32.54 4.40
4854 4898 3.619767 TGCGCTCCTCACTGCACT 61.620 61.111 9.73 0.00 31.31 4.40
4855 4899 2.358003 GCGCTCCTCACTGCACTT 60.358 61.111 0.00 0.00 0.00 3.16
4856 4900 1.963338 GCGCTCCTCACTGCACTTT 60.963 57.895 0.00 0.00 0.00 2.66
4857 4901 0.670546 GCGCTCCTCACTGCACTTTA 60.671 55.000 0.00 0.00 0.00 1.85
4858 4902 1.354040 CGCTCCTCACTGCACTTTAG 58.646 55.000 0.00 0.00 0.00 1.85
4859 4903 1.731720 GCTCCTCACTGCACTTTAGG 58.268 55.000 0.00 0.00 0.00 2.69
4860 4904 1.731720 CTCCTCACTGCACTTTAGGC 58.268 55.000 0.00 0.00 0.00 3.93
4861 4905 0.324943 TCCTCACTGCACTTTAGGCC 59.675 55.000 0.00 0.00 0.00 5.19
4862 4906 0.678048 CCTCACTGCACTTTAGGCCC 60.678 60.000 0.00 0.00 0.00 5.80
4863 4907 0.678048 CTCACTGCACTTTAGGCCCC 60.678 60.000 0.00 0.00 0.00 5.80
4864 4908 2.040544 CACTGCACTTTAGGCCCCG 61.041 63.158 0.00 0.00 0.00 5.73
4865 4909 2.221299 ACTGCACTTTAGGCCCCGA 61.221 57.895 0.00 0.00 0.00 5.14
4866 4910 1.745489 CTGCACTTTAGGCCCCGAC 60.745 63.158 0.00 0.00 0.00 4.79
4867 4911 2.818274 GCACTTTAGGCCCCGACG 60.818 66.667 0.00 0.00 0.00 5.12
4868 4912 2.660802 CACTTTAGGCCCCGACGT 59.339 61.111 0.00 0.00 0.00 4.34
4869 4913 1.740296 CACTTTAGGCCCCGACGTG 60.740 63.158 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.526846 TGAAATGTTCCATTTCTTTTGTGCC 59.473 36.000 22.95 3.09 38.47 5.01
75 83 7.067737 TCGTTCACACCTTCATGTATCTATACA 59.932 37.037 5.33 5.33 46.21 2.29
152 160 6.019881 CAGTTGGAAATGTTTTTCGTTTCTCC 60.020 38.462 10.80 0.00 45.87 3.71
728 749 2.499214 GAGGTGATCTCCACGAGCT 58.501 57.895 15.93 0.00 46.62 4.09
737 758 0.329596 GGCCAAACAGGAGGTGATCT 59.670 55.000 0.00 0.00 41.22 2.75
1113 1134 7.592051 TGAGAAGAATGAGATCGATATCACAG 58.408 38.462 23.97 0.00 36.36 3.66
1149 1170 2.811873 GCATATGGTAGGCCTTCCACTG 60.812 54.545 31.35 28.40 36.50 3.66
1390 1411 5.638596 ACGGGTAAATTTCAGAATTGGTC 57.361 39.130 0.00 0.00 35.69 4.02
1584 1606 7.656137 TGATTTAACTCTGCCGTCCTAAATATC 59.344 37.037 0.00 0.00 0.00 1.63
2038 2060 6.727824 ACATAGTGAGAAATTTCGTTGGAG 57.272 37.500 12.42 4.62 0.00 3.86
2299 2321 8.020861 TCAATCAATAAAGCAGCAAATTTGTC 57.979 30.769 19.03 11.45 0.00 3.18
2734 2760 2.037251 TCGGATATTGAACAGCTAGCCC 59.963 50.000 12.13 0.00 0.00 5.19
2795 2821 2.168521 ACAGGGTACAACATGAGATCGG 59.831 50.000 0.00 0.00 0.00 4.18
2894 2920 6.340522 ACCAAAAGTTCTGAATTTGTGAAGG 58.659 36.000 15.14 8.27 33.31 3.46
3634 3678 6.519679 TCAAGATTTTTGCTATGCATGAGT 57.480 33.333 10.16 0.00 38.76 3.41
3732 3776 4.847633 ACACAATCATTTCGCGGATATTG 58.152 39.130 6.13 10.89 0.00 1.90
3777 3821 4.759183 AGACCAGATCAAAAGCTGAAGAAC 59.241 41.667 0.00 0.00 41.56 3.01
3870 3914 1.129251 CGTGGTCGAACGAAGCTACTA 59.871 52.381 3.56 0.00 46.49 1.82
3873 3917 4.853507 CGTGGTCGAACGAAGCTA 57.146 55.556 3.56 0.00 46.49 3.32
3891 3935 2.125673 GCTGATGTACGGCGGTGT 60.126 61.111 13.24 0.00 41.21 4.16
4129 4173 3.950395 CCCAACCTTTTTCATGGCAAAAA 59.050 39.130 0.00 5.29 34.72 1.94
4395 4439 1.136774 GGCGACCGGCTGAAATTTC 59.863 57.895 11.41 11.41 42.94 2.17
4458 4502 0.108615 AGTTCAAGATGAGGACGGCG 60.109 55.000 4.80 4.80 0.00 6.46
4809 4853 3.245668 AAGTGTGGCAGCGAGGAGG 62.246 63.158 0.00 0.00 0.00 4.30
4810 4854 1.739562 GAAGTGTGGCAGCGAGGAG 60.740 63.158 0.00 0.00 0.00 3.69
4811 4855 2.343758 GAAGTGTGGCAGCGAGGA 59.656 61.111 0.00 0.00 0.00 3.71
4812 4856 2.743928 GGAAGTGTGGCAGCGAGG 60.744 66.667 0.00 0.00 0.00 4.63
4813 4857 3.114616 CGGAAGTGTGGCAGCGAG 61.115 66.667 0.00 0.00 0.00 5.03
4814 4858 4.680237 CCGGAAGTGTGGCAGCGA 62.680 66.667 0.00 0.00 0.00 4.93
4820 4864 4.003788 ACGAGCCCGGAAGTGTGG 62.004 66.667 0.73 0.00 40.78 4.17
4821 4865 2.738521 CACGAGCCCGGAAGTGTG 60.739 66.667 0.73 2.32 40.78 3.82
4822 4866 4.681978 GCACGAGCCCGGAAGTGT 62.682 66.667 0.73 0.00 40.78 3.55
4832 4876 4.427661 AGTGAGGAGCGCACGAGC 62.428 66.667 11.47 0.00 39.08 5.03
4833 4877 2.505777 CAGTGAGGAGCGCACGAG 60.506 66.667 11.47 0.00 39.08 4.18
4834 4878 4.724602 GCAGTGAGGAGCGCACGA 62.725 66.667 11.47 0.00 39.08 4.35
4836 4880 3.418068 GTGCAGTGAGGAGCGCAC 61.418 66.667 11.47 1.97 46.85 5.34
4837 4881 2.665008 AAAGTGCAGTGAGGAGCGCA 62.665 55.000 11.47 0.00 43.35 6.09
4838 4882 0.670546 TAAAGTGCAGTGAGGAGCGC 60.671 55.000 0.00 0.00 41.35 5.92
4839 4883 1.354040 CTAAAGTGCAGTGAGGAGCG 58.646 55.000 0.00 0.00 0.00 5.03
4840 4884 1.731720 CCTAAAGTGCAGTGAGGAGC 58.268 55.000 14.99 0.00 0.00 4.70
4841 4885 1.677217 GGCCTAAAGTGCAGTGAGGAG 60.677 57.143 21.69 6.21 0.00 3.69
4842 4886 0.324943 GGCCTAAAGTGCAGTGAGGA 59.675 55.000 21.69 0.00 0.00 3.71
4843 4887 0.678048 GGGCCTAAAGTGCAGTGAGG 60.678 60.000 15.57 15.57 0.00 3.86
4844 4888 0.678048 GGGGCCTAAAGTGCAGTGAG 60.678 60.000 0.84 0.00 0.00 3.51
4845 4889 1.378762 GGGGCCTAAAGTGCAGTGA 59.621 57.895 0.84 0.00 0.00 3.41
4846 4890 2.040544 CGGGGCCTAAAGTGCAGTG 61.041 63.158 0.84 0.00 0.00 3.66
4847 4891 2.221299 TCGGGGCCTAAAGTGCAGT 61.221 57.895 0.84 0.00 0.00 4.40
4848 4892 1.745489 GTCGGGGCCTAAAGTGCAG 60.745 63.158 0.84 0.00 0.00 4.41
4849 4893 2.349755 GTCGGGGCCTAAAGTGCA 59.650 61.111 0.84 0.00 0.00 4.57
4850 4894 2.818274 CGTCGGGGCCTAAAGTGC 60.818 66.667 0.84 0.00 0.00 4.40
4851 4895 1.740296 CACGTCGGGGCCTAAAGTG 60.740 63.158 0.84 6.92 0.00 3.16
4852 4896 2.660802 CACGTCGGGGCCTAAAGT 59.339 61.111 0.84 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.