Multiple sequence alignment - TraesCS3B01G356300

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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 TraesCS3B01G356300 chr3B 100.000 1354 0 0 968 2321 566605818 566604465 0.000000e+00 2501
1 TraesCS3B01G356300 chr3B 100.000 677 0 0 1 677 566606785 566606109 0.000000e+00 1251
2 TraesCS3B01G356300 chr3D 93.239 710 36 9 968 1668 433542037 433541331 0.000000e+00 1035
3 TraesCS3B01G356300 chr3D 94.143 683 22 7 1 677 433542724 433542054 0.000000e+00 1024
4 TraesCS3B01G356300 chr3D 90.192 469 35 4 1707 2169 433541345 433540882 3.300000e-168 601
5 TraesCS3B01G356300 chr3D 88.796 357 13 6 1969 2321 433538417 433538084 1.660000e-111 412
6 TraesCS3B01G356300 chr3A 93.050 705 37 7 968 1668 572107359 572106663 0.000000e+00 1020
7 TraesCS3B01G356300 chr3A 91.266 687 27 17 1 677 572108045 572107382 0.000000e+00 905
8 TraesCS3B01G356300 chr3A 92.557 618 36 6 1707 2321 572106677 572106067 0.000000e+00 878
9 TraesCS3B01G356300 chr3A 88.550 262 22 4 3 264 572111181 572110928 6.230000e-81 311


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 TraesCS3B01G356300 chr3B 566604465 566606785 2320 True 1876.0 2501 100.00000 1 2321 2 chr3B.!!$R1 2320
1 TraesCS3B01G356300 chr3D 433538084 433542724 4640 True 768.0 1035 91.59250 1 2321 4 chr3D.!!$R1 2320
2 TraesCS3B01G356300 chr3A 572106067 572111181 5114 True 778.5 1020 91.35575 1 2321 4 chr3A.!!$R1 2320

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
556 3702 0.325296 TCAACCTCCGGCCTCTATGT 60.325 55.0 0.0 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1743 4905 0.71167 GAACGCGCGTCATTCTTACA 59.288 50.0 37.77 0.0 0.0 2.41 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
23 3161 1.134220 TGCTCGAGTTCTTGGGTGTTT 60.134 47.619 15.13 0.00 0.00 2.83
37 3175 1.817609 GTGTTTTTCACGACAACCCG 58.182 50.000 0.00 0.00 37.31 5.28
53 3191 1.425031 CCGACACCGAACATGCATG 59.575 57.895 25.09 25.09 38.22 4.06
147 3285 1.337823 GGGTGACACGTAGCATCAACT 60.338 52.381 0.00 0.00 33.48 3.16
148 3286 1.993370 GGTGACACGTAGCATCAACTC 59.007 52.381 0.00 0.00 30.70 3.01
149 3287 1.993370 GTGACACGTAGCATCAACTCC 59.007 52.381 0.00 0.00 0.00 3.85
150 3288 1.067142 TGACACGTAGCATCAACTCCC 60.067 52.381 0.00 0.00 0.00 4.30
151 3289 0.973632 ACACGTAGCATCAACTCCCA 59.026 50.000 0.00 0.00 0.00 4.37
152 3290 1.555075 ACACGTAGCATCAACTCCCAT 59.445 47.619 0.00 0.00 0.00 4.00
153 3291 1.935873 CACGTAGCATCAACTCCCATG 59.064 52.381 0.00 0.00 0.00 3.66
456 3600 3.268103 TTGGGGAGAAAGCCGCCTC 62.268 63.158 0.00 0.00 39.94 4.70
546 3692 2.264794 CGTCCCCTTCAACCTCCG 59.735 66.667 0.00 0.00 0.00 4.63
556 3702 0.325296 TCAACCTCCGGCCTCTATGT 60.325 55.000 0.00 0.00 0.00 2.29
557 3703 1.063492 TCAACCTCCGGCCTCTATGTA 60.063 52.381 0.00 0.00 0.00 2.29
650 3802 1.825474 CCGGACCTAGCTCAAGAAGAA 59.175 52.381 0.00 0.00 0.00 2.52
1122 4274 2.920912 AAGACGGAGCGGGTGGAA 60.921 61.111 0.00 0.00 0.00 3.53
1159 4311 1.159664 AAGAGGCAGGTCCAGGAGT 59.840 57.895 0.00 0.00 37.29 3.85
1198 4350 2.529389 ACGGCAAGGGGAAGAGGT 60.529 61.111 0.00 0.00 0.00 3.85
1206 4358 2.416432 GGGGAAGAGGTCGACGGAG 61.416 68.421 9.92 0.00 0.00 4.63
1329 4481 0.827368 AGGAGCCTTGACTTCGATCC 59.173 55.000 0.00 0.00 0.00 3.36
1371 4523 6.391227 TCTCTTGATTCTGATGTGCGTATA 57.609 37.500 0.00 0.00 0.00 1.47
1402 4554 1.482593 GCTGTATGTAGGAGTGCAGGT 59.517 52.381 0.00 0.00 0.00 4.00
1412 4564 5.959594 TGTAGGAGTGCAGGTATAGGTTTTA 59.040 40.000 0.00 0.00 0.00 1.52
1565 4721 4.320348 CGGACCTCTCGAGTATTTGGATAC 60.320 50.000 13.13 6.01 38.73 2.24
1662 4824 1.873591 ACACTTCACACTTCCGATTGC 59.126 47.619 0.00 0.00 0.00 3.56
1663 4825 1.197721 CACTTCACACTTCCGATTGCC 59.802 52.381 0.00 0.00 0.00 4.52
1664 4826 1.072331 ACTTCACACTTCCGATTGCCT 59.928 47.619 0.00 0.00 0.00 4.75
1665 4827 2.154462 CTTCACACTTCCGATTGCCTT 58.846 47.619 0.00 0.00 0.00 4.35
1666 4828 2.270352 TCACACTTCCGATTGCCTTT 57.730 45.000 0.00 0.00 0.00 3.11
1667 4829 2.582052 TCACACTTCCGATTGCCTTTT 58.418 42.857 0.00 0.00 0.00 2.27
1668 4830 2.955660 TCACACTTCCGATTGCCTTTTT 59.044 40.909 0.00 0.00 0.00 1.94
1691 4853 3.399440 TTTTGCAAATTCCGATTGGCT 57.601 38.095 13.65 0.00 41.84 4.75
1692 4854 3.399440 TTTGCAAATTCCGATTGGCTT 57.601 38.095 8.05 0.00 41.84 4.35
1693 4855 3.399440 TTGCAAATTCCGATTGGCTTT 57.601 38.095 0.00 0.00 41.84 3.51
1694 4856 3.399440 TGCAAATTCCGATTGGCTTTT 57.601 38.095 0.00 0.00 41.84 2.27
1695 4857 3.737850 TGCAAATTCCGATTGGCTTTTT 58.262 36.364 0.00 0.00 41.84 1.94
1696 4858 3.745458 TGCAAATTCCGATTGGCTTTTTC 59.255 39.130 0.00 0.00 41.84 2.29
1697 4859 3.996363 GCAAATTCCGATTGGCTTTTTCT 59.004 39.130 0.00 0.00 38.85 2.52
1698 4860 4.452114 GCAAATTCCGATTGGCTTTTTCTT 59.548 37.500 0.00 0.00 38.85 2.52
1699 4861 5.049474 GCAAATTCCGATTGGCTTTTTCTTT 60.049 36.000 0.00 0.00 38.85 2.52
1700 4862 6.513230 GCAAATTCCGATTGGCTTTTTCTTTT 60.513 34.615 0.00 0.00 38.85 2.27
1701 4863 6.544038 AATTCCGATTGGCTTTTTCTTTTG 57.456 33.333 0.00 0.00 34.14 2.44
1702 4864 3.389221 TCCGATTGGCTTTTTCTTTTGC 58.611 40.909 0.00 0.00 34.14 3.68
1703 4865 3.129871 CCGATTGGCTTTTTCTTTTGCA 58.870 40.909 0.00 0.00 0.00 4.08
1704 4866 3.559242 CCGATTGGCTTTTTCTTTTGCAA 59.441 39.130 0.00 0.00 0.00 4.08
1705 4867 4.034975 CCGATTGGCTTTTTCTTTTGCAAA 59.965 37.500 8.05 8.05 0.00 3.68
1706 4868 5.277925 CCGATTGGCTTTTTCTTTTGCAAAT 60.278 36.000 13.65 0.00 32.41 2.32
1707 4869 6.200808 CGATTGGCTTTTTCTTTTGCAAATT 58.799 32.000 13.65 0.00 30.17 1.82
1708 4870 6.357766 CGATTGGCTTTTTCTTTTGCAAATTC 59.642 34.615 13.65 0.00 30.17 2.17
1709 4871 6.756299 TTGGCTTTTTCTTTTGCAAATTCT 57.244 29.167 13.65 0.00 0.00 2.40
1710 4872 6.121613 TGGCTTTTTCTTTTGCAAATTCTG 57.878 33.333 13.65 4.37 0.00 3.02
1711 4873 5.879223 TGGCTTTTTCTTTTGCAAATTCTGA 59.121 32.000 13.65 6.65 0.00 3.27
1712 4874 6.543100 TGGCTTTTTCTTTTGCAAATTCTGAT 59.457 30.769 13.65 0.00 0.00 2.90
1713 4875 7.067251 TGGCTTTTTCTTTTGCAAATTCTGATT 59.933 29.630 13.65 0.00 0.00 2.57
1714 4876 7.377662 GGCTTTTTCTTTTGCAAATTCTGATTG 59.622 33.333 13.65 2.19 0.00 2.67
1715 4877 7.911727 GCTTTTTCTTTTGCAAATTCTGATTGT 59.088 29.630 13.65 0.00 0.00 2.71
1718 4880 8.721019 TTTCTTTTGCAAATTCTGATTGTCTT 57.279 26.923 13.65 0.00 0.00 3.01
1725 4887 8.394971 TGCAAATTCTGATTGTCTTTTCTAGA 57.605 30.769 0.00 0.00 0.00 2.43
1726 4888 8.849168 TGCAAATTCTGATTGTCTTTTCTAGAA 58.151 29.630 0.00 0.00 33.81 2.10
1819 4982 1.272490 GCGCTATATGCTCACCCACTA 59.728 52.381 0.00 0.00 40.11 2.74
1820 4983 2.093973 GCGCTATATGCTCACCCACTAT 60.094 50.000 0.00 0.00 40.11 2.12
1821 4984 3.617531 GCGCTATATGCTCACCCACTATT 60.618 47.826 0.00 0.00 40.11 1.73
1822 4985 4.381612 GCGCTATATGCTCACCCACTATTA 60.382 45.833 0.00 0.00 40.11 0.98
1823 4986 5.682471 GCGCTATATGCTCACCCACTATTAT 60.682 44.000 0.00 0.00 40.11 1.28
1853 5016 2.094182 CCCTCTAAGCGCAGTCAAACTA 60.094 50.000 11.47 0.00 0.00 2.24
1855 5018 3.368236 CCTCTAAGCGCAGTCAAACTAAC 59.632 47.826 11.47 0.00 0.00 2.34
1891 5054 6.849588 TTACATTACTAGCATCGACGACTA 57.150 37.500 0.00 0.00 0.00 2.59
1939 5102 6.098838 CAGTCTATGGGCTATGCCTATCAATA 59.901 42.308 10.63 0.00 46.95 1.90
1942 5105 7.659390 GTCTATGGGCTATGCCTATCAATAATC 59.341 40.741 10.63 0.00 46.95 1.75
2224 8061 2.936032 GTCCCTGCCTCCCACCTT 60.936 66.667 0.00 0.00 0.00 3.50
2227 8064 3.732849 CCTGCCTCCCACCTTCCC 61.733 72.222 0.00 0.00 0.00 3.97
2316 8153 4.760047 GCGGCGGCCTTCTTCTCA 62.760 66.667 18.34 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 3161 0.810823 GGTGTCGGGTTGTCGTGAAA 60.811 55.000 0.00 0.00 0.00 2.69
37 3175 1.137404 GGCATGCATGTTCGGTGTC 59.863 57.895 26.79 8.22 0.00 3.67
139 3277 0.034186 TGGGACATGGGAGTTGATGC 60.034 55.000 0.00 0.00 0.00 3.91
153 3291 2.125269 CAACGACCGGGATGGGAC 60.125 66.667 6.32 0.00 44.64 4.46
556 3702 8.333186 CCGCGCGATACAGCTTATATATATATA 58.667 37.037 34.63 8.16 34.40 0.86
557 3703 7.187480 CCGCGCGATACAGCTTATATATATAT 58.813 38.462 34.63 10.10 34.40 0.86
650 3802 1.694133 GCCTGGATGCTAGCTCTGGT 61.694 60.000 17.23 0.00 0.00 4.00
991 4143 2.991713 AGCAGTTCCCCATGGATGATAT 59.008 45.455 15.22 0.00 41.40 1.63
992 4144 2.421725 AGCAGTTCCCCATGGATGATA 58.578 47.619 15.22 0.00 41.40 2.15
993 4145 1.229131 AGCAGTTCCCCATGGATGAT 58.771 50.000 15.22 0.00 41.40 2.45
1092 4244 1.209383 CGTCTTCTCGTTCTCGCCA 59.791 57.895 0.00 0.00 36.96 5.69
1122 4274 2.030027 TGGTCACCCTGATCTTCACT 57.970 50.000 0.00 0.00 0.00 3.41
1198 4350 1.602605 TCAGCACCTTCTCCGTCGA 60.603 57.895 0.00 0.00 0.00 4.20
1206 4358 0.532573 TCAGATCCGTCAGCACCTTC 59.467 55.000 0.00 0.00 0.00 3.46
1335 4487 3.928858 AATCAAGAGATCGGTGGAACAGC 60.929 47.826 0.00 0.00 43.36 4.40
1371 4523 9.015367 CACTCCTACATACAGCAACTATATACT 57.985 37.037 0.00 0.00 0.00 2.12
1412 4564 6.484288 ACATCTCCTGATAGAATCTCGATCT 58.516 40.000 0.00 0.00 31.07 2.75
1427 4580 6.516739 TTTCTGTAGTCTGTACATCTCCTG 57.483 41.667 0.00 0.00 0.00 3.86
1589 4745 6.184580 TCTGCTTTCAGTTTACGTTTGAAA 57.815 33.333 0.00 5.29 41.10 2.69
1643 4805 1.197721 GGCAATCGGAAGTGTGAAGTG 59.802 52.381 0.00 0.00 0.00 3.16
1670 4832 3.737850 AGCCAATCGGAATTTGCAAAAA 58.262 36.364 17.19 0.00 36.29 1.94
1671 4833 3.399440 AGCCAATCGGAATTTGCAAAA 57.601 38.095 17.19 0.00 36.29 2.44
1672 4834 3.399440 AAGCCAATCGGAATTTGCAAA 57.601 38.095 15.44 15.44 36.29 3.68
1673 4835 3.399440 AAAGCCAATCGGAATTTGCAA 57.601 38.095 0.00 0.00 36.29 4.08
1674 4836 3.399440 AAAAGCCAATCGGAATTTGCA 57.601 38.095 0.00 0.00 36.29 4.08
1675 4837 3.996363 AGAAAAAGCCAATCGGAATTTGC 59.004 39.130 0.00 0.00 34.54 3.68
1676 4838 6.544038 AAAGAAAAAGCCAATCGGAATTTG 57.456 33.333 0.00 0.00 0.00 2.32
1677 4839 6.513230 GCAAAAGAAAAAGCCAATCGGAATTT 60.513 34.615 0.00 0.00 0.00 1.82
1678 4840 5.049474 GCAAAAGAAAAAGCCAATCGGAATT 60.049 36.000 0.00 0.00 0.00 2.17
1679 4841 4.452114 GCAAAAGAAAAAGCCAATCGGAAT 59.548 37.500 0.00 0.00 0.00 3.01
1680 4842 3.807071 GCAAAAGAAAAAGCCAATCGGAA 59.193 39.130 0.00 0.00 0.00 4.30
1681 4843 3.181471 TGCAAAAGAAAAAGCCAATCGGA 60.181 39.130 0.00 0.00 0.00 4.55
1682 4844 3.129871 TGCAAAAGAAAAAGCCAATCGG 58.870 40.909 0.00 0.00 0.00 4.18
1683 4845 4.792528 TTGCAAAAGAAAAAGCCAATCG 57.207 36.364 0.00 0.00 0.00 3.34
1684 4846 7.377662 CAGAATTTGCAAAAGAAAAAGCCAATC 59.622 33.333 17.19 0.00 0.00 2.67
1685 4847 7.067251 TCAGAATTTGCAAAAGAAAAAGCCAAT 59.933 29.630 17.19 0.00 0.00 3.16
1686 4848 6.373774 TCAGAATTTGCAAAAGAAAAAGCCAA 59.626 30.769 17.19 0.00 0.00 4.52
1687 4849 5.879223 TCAGAATTTGCAAAAGAAAAAGCCA 59.121 32.000 17.19 0.00 0.00 4.75
1688 4850 6.362210 TCAGAATTTGCAAAAGAAAAAGCC 57.638 33.333 17.19 0.00 0.00 4.35
1689 4851 7.911727 ACAATCAGAATTTGCAAAAGAAAAAGC 59.088 29.630 17.19 0.02 0.00 3.51
1690 4852 9.429600 GACAATCAGAATTTGCAAAAGAAAAAG 57.570 29.630 17.19 5.97 0.00 2.27
1691 4853 9.165035 AGACAATCAGAATTTGCAAAAGAAAAA 57.835 25.926 17.19 1.07 0.00 1.94
1692 4854 8.721019 AGACAATCAGAATTTGCAAAAGAAAA 57.279 26.923 17.19 2.72 0.00 2.29
1693 4855 8.721019 AAGACAATCAGAATTTGCAAAAGAAA 57.279 26.923 17.19 1.61 0.00 2.52
1694 4856 8.721019 AAAGACAATCAGAATTTGCAAAAGAA 57.279 26.923 17.19 0.87 0.00 2.52
1695 4857 8.721019 AAAAGACAATCAGAATTTGCAAAAGA 57.279 26.923 17.19 12.03 0.00 2.52
1696 4858 8.823818 AGAAAAGACAATCAGAATTTGCAAAAG 58.176 29.630 17.19 6.94 0.00 2.27
1697 4859 8.721019 AGAAAAGACAATCAGAATTTGCAAAA 57.279 26.923 17.19 0.00 0.00 2.44
1698 4860 9.467258 CTAGAAAAGACAATCAGAATTTGCAAA 57.533 29.630 15.44 15.44 0.00 3.68
1699 4861 8.849168 TCTAGAAAAGACAATCAGAATTTGCAA 58.151 29.630 0.00 0.00 0.00 4.08
1700 4862 8.394971 TCTAGAAAAGACAATCAGAATTTGCA 57.605 30.769 0.00 0.00 0.00 4.08
1701 4863 9.683069 TTTCTAGAAAAGACAATCAGAATTTGC 57.317 29.630 15.57 0.00 32.51 3.68
1740 4902 0.713883 CGCGCGTCATTCTTACACTT 59.286 50.000 24.19 0.00 0.00 3.16
1743 4905 0.711670 GAACGCGCGTCATTCTTACA 59.288 50.000 37.77 0.00 0.00 2.41
1744 4906 0.711670 TGAACGCGCGTCATTCTTAC 59.288 50.000 37.77 18.51 0.00 2.34
1745 4907 0.711670 GTGAACGCGCGTCATTCTTA 59.288 50.000 37.77 14.46 0.00 2.10
1746 4908 1.218875 TGTGAACGCGCGTCATTCTT 61.219 50.000 37.77 20.33 0.00 2.52
1748 4910 1.225475 CTGTGAACGCGCGTCATTC 60.225 57.895 37.77 29.19 0.00 2.67
1750 4912 1.014044 AATCTGTGAACGCGCGTCAT 61.014 50.000 37.77 22.99 0.00 3.06
1819 4982 5.638234 GCGCTTAGAGGGACGAAAATATAAT 59.362 40.000 0.00 0.00 0.00 1.28
1820 4983 4.986659 GCGCTTAGAGGGACGAAAATATAA 59.013 41.667 0.00 0.00 0.00 0.98
1821 4984 4.038282 TGCGCTTAGAGGGACGAAAATATA 59.962 41.667 9.73 0.00 0.00 0.86
1822 4985 3.181469 TGCGCTTAGAGGGACGAAAATAT 60.181 43.478 9.73 0.00 0.00 1.28
1823 4986 2.166870 TGCGCTTAGAGGGACGAAAATA 59.833 45.455 9.73 0.00 0.00 1.40
1853 5016 2.455674 TGTAATCGCAGCTGTCAGTT 57.544 45.000 16.64 8.13 0.00 3.16
1855 5018 4.115516 AGTAATGTAATCGCAGCTGTCAG 58.884 43.478 16.64 7.59 0.00 3.51
1891 5054 6.910191 TGGACCAATTCAGTGTGGAATATAT 58.090 36.000 5.31 0.00 36.51 0.86
2059 7892 5.070001 TGCTGCTTTTCTGTAAATACCTGT 58.930 37.500 0.00 0.00 0.00 4.00
2062 7895 5.768317 TGTTGCTGCTTTTCTGTAAATACC 58.232 37.500 0.00 0.00 0.00 2.73
2234 8071 1.687493 GGAGAGGAGAGTGGTGGGG 60.687 68.421 0.00 0.00 0.00 4.96
2235 8072 2.055042 CGGAGAGGAGAGTGGTGGG 61.055 68.421 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.