Multiple sequence alignment - TraesCS6A01G269300

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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 TraesCS6A01G269300 chr6A 100.000 2126 0 0 1 2126 495683945 495686070 0.000000e+00 3927.0
1 TraesCS6A01G269300 chr6A 95.775 71 1 2 1806 1874 495685716 495685786 1.720000e-21 113.0
2 TraesCS6A01G269300 chr6A 95.775 71 1 2 1772 1842 495685750 495685818 1.720000e-21 113.0
3 TraesCS6A01G269300 chr6B 92.291 1881 87 20 2 1842 532336668 532338530 0.000000e+00 2617.0
4 TraesCS6A01G269300 chr6B 95.963 322 7 3 1806 2126 532338461 532338777 3.130000e-143 518.0
5 TraesCS6A01G269300 chr6B 97.368 38 0 1 1772 1809 532338494 532338530 1.760000e-06 63.9
6 TraesCS6A01G269300 chr6D 91.234 1369 71 17 1 1364 347689293 347687969 0.000000e+00 1818.0
7 TraesCS6A01G269300 chr6D 95.297 404 13 3 1444 1842 347687968 347687566 8.270000e-179 636.0
8 TraesCS6A01G269300 chr6D 97.516 322 6 2 1806 2126 347687635 347687315 1.110000e-152 549.0


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 TraesCS6A01G269300 chr6A 495683945 495686070 2125 False 1384.333333 3927 97.183333 1 2126 3 chr6A.!!$F1 2125
1 TraesCS6A01G269300 chr6B 532336668 532338777 2109 False 1066.300000 2617 95.207333 2 2126 3 chr6B.!!$F1 2124
2 TraesCS6A01G269300 chr6D 347687315 347689293 1978 True 1001.000000 1818 94.682333 1 2126 3 chr6D.!!$R1 2125


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
262 272 0.03759 ATGCAGGCGTTTTCCCACTA 59.962 50.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1562 1608 1.942776 TGAGCCTTGACCTCAGATGA 58.057 50.0 0.0 0.0 34.59 2.92 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
35 36 4.725790 AGCTTATTTTCAGGATTGTGCC 57.274 40.909 0.00 0.00 0.00 5.01
72 74 7.927629 TCTGTTTGGATTTTTCATCTTCCTTTG 59.072 33.333 0.00 0.00 0.00 2.77
203 213 3.880047 ATTGTGATTGAGGTGGCAATG 57.120 42.857 0.00 0.00 38.53 2.82
233 243 6.259829 AGTTTGAGAGAGAAGCTCAGAAAAAC 59.740 38.462 0.00 0.00 46.45 2.43
253 263 0.609131 AAGGTAGCAATGCAGGCGTT 60.609 50.000 8.35 2.09 36.08 4.84
260 270 0.667184 CAATGCAGGCGTTTTCCCAC 60.667 55.000 0.00 0.00 0.00 4.61
262 272 0.037590 ATGCAGGCGTTTTCCCACTA 59.962 50.000 0.00 0.00 0.00 2.74
263 273 0.179015 TGCAGGCGTTTTCCCACTAA 60.179 50.000 0.00 0.00 0.00 2.24
272 282 3.824443 CGTTTTCCCACTAATTCCAACCT 59.176 43.478 0.00 0.00 0.00 3.50
337 347 6.631636 GGATTTTGCTACGATAAATCCGTTTC 59.368 38.462 9.34 0.00 44.15 2.78
368 378 8.567948 AGTAATGGGATAGCAACATTATTTTCG 58.432 33.333 9.57 0.00 38.76 3.46
371 381 7.581213 TGGGATAGCAACATTATTTTCGAAT 57.419 32.000 0.00 0.00 0.00 3.34
374 384 9.313118 GGGATAGCAACATTATTTTCGAATTTT 57.687 29.630 0.00 0.00 0.00 1.82
388 398 7.531280 TTTCGAATTTTGATGTTTCAAGCAA 57.469 28.000 0.00 0.00 42.60 3.91
399 409 3.682858 TGTTTCAAGCAACGGTATAGCTC 59.317 43.478 0.00 0.00 37.70 4.09
408 418 1.607628 ACGGTATAGCTCGATCACCAC 59.392 52.381 0.00 0.00 0.00 4.16
467 477 7.227049 TGAATAGCATCATTGATAGTACCGA 57.773 36.000 0.00 0.00 0.00 4.69
468 478 7.840931 TGAATAGCATCATTGATAGTACCGAT 58.159 34.615 0.00 0.00 0.00 4.18
469 479 8.966868 TGAATAGCATCATTGATAGTACCGATA 58.033 33.333 0.00 0.00 0.00 2.92
470 480 9.239002 GAATAGCATCATTGATAGTACCGATAC 57.761 37.037 0.00 0.00 0.00 2.24
471 481 6.842437 AGCATCATTGATAGTACCGATACT 57.158 37.500 0.00 0.00 44.22 2.12
634 644 2.605837 TTGGTTCTAGCAACACGTGA 57.394 45.000 25.01 0.00 29.68 4.35
639 649 2.730672 CTAGCAACACGTGAGCCGC 61.731 63.158 25.01 17.56 41.42 6.53
649 659 3.625764 ACACGTGAGCCGCAAATTATTAT 59.374 39.130 25.01 0.00 41.42 1.28
698 708 1.276138 TGCTGTGTACAGACCTCCATG 59.724 52.381 15.78 0.00 46.59 3.66
774 784 6.563753 CGGAAATGTTGCTAAATTTGTGTTGG 60.564 38.462 0.73 0.00 0.00 3.77
796 806 5.419155 TGGTTTCTGATAGAGATCGTCAGTT 59.581 40.000 15.25 0.00 40.13 3.16
837 847 2.665649 AATGGTTCTACGTCGCATCA 57.334 45.000 0.00 0.00 0.00 3.07
851 861 2.106418 CGCATCAATGTTCATGCTTCG 58.894 47.619 0.33 0.00 42.84 3.79
943 979 7.552330 TCGACCACATCATTCTGATTCAAATAA 59.448 33.333 0.00 0.00 34.28 1.40
1246 1286 7.724061 TCCTTTCTTTTGTTCTATTGGCTAAGT 59.276 33.333 0.00 0.00 0.00 2.24
1265 1305 9.860898 GGCTAAGTTTTTATCATCTCATTTTGT 57.139 29.630 0.00 0.00 0.00 2.83
1422 1462 7.446931 TCAAACTGTTCTTTCCTGCATGTATTA 59.553 33.333 0.00 0.00 0.00 0.98
1562 1608 4.403432 AGTTGCCATTTGCTTGCTGTATAT 59.597 37.500 0.00 0.00 42.00 0.86
1659 1705 3.383761 CAAATCCAAGACAGCACAAACC 58.616 45.455 0.00 0.00 0.00 3.27
1701 1747 6.823182 TCAATTGACGGATCATACATCTGTTT 59.177 34.615 3.38 0.00 37.73 2.83
1787 1833 7.432869 TGTTGATTTTTCTTGATACCTGGTTG 58.567 34.615 3.84 0.00 0.00 3.77
1788 1834 7.069331 TGTTGATTTTTCTTGATACCTGGTTGT 59.931 33.333 3.84 0.00 0.00 3.32
1789 1835 7.214467 TGATTTTTCTTGATACCTGGTTGTC 57.786 36.000 3.84 4.77 0.00 3.18
1790 1836 6.208599 TGATTTTTCTTGATACCTGGTTGTCC 59.791 38.462 3.84 0.00 0.00 4.02
1791 1837 3.713826 TTCTTGATACCTGGTTGTCCC 57.286 47.619 3.84 0.00 0.00 4.46
1792 1838 2.626785 TCTTGATACCTGGTTGTCCCA 58.373 47.619 3.84 0.00 42.51 4.37
1793 1839 2.983192 TCTTGATACCTGGTTGTCCCAA 59.017 45.455 3.84 2.17 44.65 4.12
1794 1840 3.396276 TCTTGATACCTGGTTGTCCCAAA 59.604 43.478 3.84 0.00 44.65 3.28
1795 1841 3.433306 TGATACCTGGTTGTCCCAAAG 57.567 47.619 3.84 0.00 44.65 2.77
1796 1842 2.041081 TGATACCTGGTTGTCCCAAAGG 59.959 50.000 3.84 0.00 44.65 3.11
1797 1843 1.822425 TACCTGGTTGTCCCAAAGGA 58.178 50.000 3.84 0.00 44.65 3.36
1798 1844 0.930726 ACCTGGTTGTCCCAAAGGAA 59.069 50.000 0.00 0.00 46.38 3.36
1799 1845 1.289530 ACCTGGTTGTCCCAAAGGAAA 59.710 47.619 0.00 0.00 46.38 3.13
1800 1846 2.292587 ACCTGGTTGTCCCAAAGGAAAA 60.293 45.455 0.00 0.00 46.38 2.29
1801 1847 2.769095 CCTGGTTGTCCCAAAGGAAAAA 59.231 45.455 0.00 0.00 46.38 1.94
1802 1848 3.181466 CCTGGTTGTCCCAAAGGAAAAAG 60.181 47.826 0.00 0.00 46.38 2.27
1803 1849 2.769095 TGGTTGTCCCAAAGGAAAAAGG 59.231 45.455 0.00 0.00 46.38 3.11
1804 1850 2.484770 GGTTGTCCCAAAGGAAAAAGGC 60.485 50.000 0.00 0.00 46.38 4.35
1805 1851 2.434336 GTTGTCCCAAAGGAAAAAGGCT 59.566 45.455 0.00 0.00 46.38 4.58
1806 1852 2.758130 TGTCCCAAAGGAAAAAGGCTT 58.242 42.857 0.00 0.00 46.38 4.35
1807 1853 2.698274 TGTCCCAAAGGAAAAAGGCTTC 59.302 45.455 0.00 0.00 46.38 3.86
1808 1854 2.965831 GTCCCAAAGGAAAAAGGCTTCT 59.034 45.455 0.00 0.00 46.38 2.85
1809 1855 3.388024 GTCCCAAAGGAAAAAGGCTTCTT 59.612 43.478 0.00 0.00 46.38 2.52
1810 1856 3.387699 TCCCAAAGGAAAAAGGCTTCTTG 59.612 43.478 0.00 0.00 40.08 3.02
1811 1857 3.387699 CCCAAAGGAAAAAGGCTTCTTGA 59.612 43.478 0.00 0.00 33.47 3.02
1812 1858 4.040829 CCCAAAGGAAAAAGGCTTCTTGAT 59.959 41.667 0.00 0.00 33.47 2.57
1813 1859 5.245977 CCCAAAGGAAAAAGGCTTCTTGATA 59.754 40.000 0.00 0.00 33.47 2.15
1814 1860 6.159293 CCAAAGGAAAAAGGCTTCTTGATAC 58.841 40.000 0.00 0.00 0.00 2.24
1815 1861 5.984695 AAGGAAAAAGGCTTCTTGATACC 57.015 39.130 0.00 0.00 0.00 2.73
1816 1862 5.262455 AGGAAAAAGGCTTCTTGATACCT 57.738 39.130 0.00 0.00 0.00 3.08
1817 1863 5.012893 AGGAAAAAGGCTTCTTGATACCTG 58.987 41.667 0.00 0.00 31.32 4.00
1818 1864 4.158579 GGAAAAAGGCTTCTTGATACCTGG 59.841 45.833 0.00 0.00 31.32 4.45
1819 1865 4.388577 AAAAGGCTTCTTGATACCTGGT 57.611 40.909 4.05 4.05 31.32 4.00
1820 1866 4.388577 AAAGGCTTCTTGATACCTGGTT 57.611 40.909 3.84 0.00 31.32 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.185315 CCCGGCACAATCCTGAAAAT 58.815 50.000 0.00 0.00 0.00 1.82
31 32 1.244019 ACAGAAAAGCATCCCGGCAC 61.244 55.000 0.00 0.00 35.83 5.01
35 36 1.885887 TCCAAACAGAAAAGCATCCCG 59.114 47.619 0.00 0.00 0.00 5.14
72 74 4.327087 CGCAAAAATCTAAATCAGCCAACC 59.673 41.667 0.00 0.00 0.00 3.77
112 120 0.958876 AAGGCGCCTTTTAACGGGAG 60.959 55.000 35.84 0.00 31.29 4.30
166 176 4.983538 TCACAATTTACATTGCAAGCACAG 59.016 37.500 4.94 0.00 43.39 3.66
203 213 3.663025 AGCTTCTCTCTCAAACTTCTGC 58.337 45.455 0.00 0.00 0.00 4.26
233 243 1.308069 ACGCCTGCATTGCTACCTTG 61.308 55.000 10.49 0.00 0.00 3.61
253 263 4.508405 CCTCAGGTTGGAATTAGTGGGAAA 60.508 45.833 0.00 0.00 0.00 3.13
260 270 2.691409 TCGCCTCAGGTTGGAATTAG 57.309 50.000 0.00 0.00 0.00 1.73
262 272 3.864789 ATATCGCCTCAGGTTGGAATT 57.135 42.857 0.00 0.00 0.00 2.17
263 273 3.864789 AATATCGCCTCAGGTTGGAAT 57.135 42.857 0.00 0.00 0.00 3.01
272 282 3.118920 TCCGAACTCAAAATATCGCCTCA 60.119 43.478 0.00 0.00 34.13 3.86
330 340 1.339631 CCCATTACTGGCTGAAACGGA 60.340 52.381 0.00 0.00 41.64 4.69
337 347 2.880890 GTTGCTATCCCATTACTGGCTG 59.119 50.000 0.00 0.00 41.64 4.85
368 378 5.234116 ACCGTTGCTTGAAACATCAAAATTC 59.766 36.000 0.00 0.00 0.00 2.17
371 381 4.116747 ACCGTTGCTTGAAACATCAAAA 57.883 36.364 0.00 0.00 0.00 2.44
374 384 4.094294 GCTATACCGTTGCTTGAAACATCA 59.906 41.667 0.00 0.00 0.00 3.07
388 398 1.607628 GTGGTGATCGAGCTATACCGT 59.392 52.381 0.90 0.00 34.16 4.83
399 409 0.374758 CTCAATTGGCGTGGTGATCG 59.625 55.000 5.42 0.00 0.00 3.69
461 471 4.201783 GGACATTGCAAACAGTATCGGTAC 60.202 45.833 1.71 0.00 0.00 3.34
462 472 3.936453 GGACATTGCAAACAGTATCGGTA 59.064 43.478 1.71 0.00 0.00 4.02
464 474 2.746904 TGGACATTGCAAACAGTATCGG 59.253 45.455 1.71 0.00 0.00 4.18
465 475 3.728864 GCTGGACATTGCAAACAGTATCG 60.729 47.826 18.61 6.62 0.00 2.92
466 476 3.441572 AGCTGGACATTGCAAACAGTATC 59.558 43.478 18.61 9.29 0.00 2.24
467 477 3.424703 AGCTGGACATTGCAAACAGTAT 58.575 40.909 18.61 9.85 0.00 2.12
468 478 2.813754 GAGCTGGACATTGCAAACAGTA 59.186 45.455 18.61 2.14 0.00 2.74
469 479 1.610522 GAGCTGGACATTGCAAACAGT 59.389 47.619 18.61 12.07 0.00 3.55
470 480 1.068055 GGAGCTGGACATTGCAAACAG 60.068 52.381 1.71 10.97 0.00 3.16
471 481 0.961019 GGAGCTGGACATTGCAAACA 59.039 50.000 1.71 0.00 0.00 2.83
590 600 8.755696 ACATTAATGCACAAAACGAAACATAT 57.244 26.923 15.48 0.00 0.00 1.78
599 609 6.843069 AGAACCAACATTAATGCACAAAAC 57.157 33.333 15.48 2.76 0.00 2.43
634 644 6.952773 TTAAGTGGATAATAATTTGCGGCT 57.047 33.333 0.00 0.00 0.00 5.52
674 684 3.181445 TGGAGGTCTGTACACAGCAAAAT 60.181 43.478 4.43 0.00 43.46 1.82
726 736 9.681062 TCCGAATCTAGTTTAAAGAATCCATTT 57.319 29.630 0.00 0.00 0.00 2.32
734 744 8.234546 GCAACATTTCCGAATCTAGTTTAAAGA 58.765 33.333 0.00 0.00 0.00 2.52
749 759 6.354080 CAACACAAATTTAGCAACATTTCCG 58.646 36.000 0.00 0.00 0.00 4.30
774 784 6.470877 GTCAACTGACGATCTCTATCAGAAAC 59.529 42.308 15.79 9.15 42.07 2.78
796 806 9.161629 CCATTTGGATTATATATAACGCAGTCA 57.838 33.333 7.34 0.00 37.19 3.41
828 838 1.459756 GCATGAACATTGATGCGACG 58.540 50.000 0.00 0.00 37.99 5.12
837 847 4.218200 TCATTTCCACGAAGCATGAACATT 59.782 37.500 0.00 0.00 0.00 2.71
851 861 5.928264 CCAAAGGAACAAGAATCATTTCCAC 59.072 40.000 9.31 0.00 40.13 4.02
943 979 2.029649 GCTGGTGCAATCTGACACAATT 60.030 45.455 0.00 0.00 38.57 2.32
974 1014 5.473504 TCTTTGATGAACACTTTAAGCTCCC 59.526 40.000 0.00 0.00 0.00 4.30
1275 1315 3.133691 TGGAGATGATGCGCTGATAAAC 58.866 45.455 9.73 0.00 0.00 2.01
1422 1462 6.403866 TGGTTGATTTAGTTTTCACATGCT 57.596 33.333 0.00 0.00 0.00 3.79
1562 1608 1.942776 TGAGCCTTGACCTCAGATGA 58.057 50.000 0.00 0.00 34.59 2.92
1701 1747 3.934457 TCTTGTCTATCAGTTCGCACA 57.066 42.857 0.00 0.00 0.00 4.57
1787 1833 2.965831 AGAAGCCTTTTTCCTTTGGGAC 59.034 45.455 0.00 0.00 42.05 4.46
1788 1834 3.328535 AGAAGCCTTTTTCCTTTGGGA 57.671 42.857 0.00 0.00 40.36 4.37
1789 1835 3.387699 TCAAGAAGCCTTTTTCCTTTGGG 59.612 43.478 0.00 0.00 0.00 4.12
1790 1836 4.670896 TCAAGAAGCCTTTTTCCTTTGG 57.329 40.909 0.00 0.00 0.00 3.28
1791 1837 6.015095 AGGTATCAAGAAGCCTTTTTCCTTTG 60.015 38.462 0.00 0.00 0.00 2.77
1792 1838 6.015095 CAGGTATCAAGAAGCCTTTTTCCTTT 60.015 38.462 0.00 0.00 0.00 3.11
1793 1839 5.478332 CAGGTATCAAGAAGCCTTTTTCCTT 59.522 40.000 0.00 0.00 0.00 3.36
1794 1840 5.012893 CAGGTATCAAGAAGCCTTTTTCCT 58.987 41.667 0.00 0.00 0.00 3.36
1795 1841 4.158579 CCAGGTATCAAGAAGCCTTTTTCC 59.841 45.833 0.00 0.00 0.00 3.13
1796 1842 4.767409 ACCAGGTATCAAGAAGCCTTTTTC 59.233 41.667 0.00 0.00 0.00 2.29
1797 1843 4.740902 ACCAGGTATCAAGAAGCCTTTTT 58.259 39.130 0.00 0.00 0.00 1.94
1798 1844 4.388577 ACCAGGTATCAAGAAGCCTTTT 57.611 40.909 0.00 0.00 0.00 2.27
1799 1845 4.082125 CAACCAGGTATCAAGAAGCCTTT 58.918 43.478 0.00 0.00 0.00 3.11
1800 1846 3.074538 ACAACCAGGTATCAAGAAGCCTT 59.925 43.478 0.00 0.00 0.00 4.35
1801 1847 2.644798 ACAACCAGGTATCAAGAAGCCT 59.355 45.455 0.00 0.00 0.00 4.58
1802 1848 3.010420 GACAACCAGGTATCAAGAAGCC 58.990 50.000 0.00 0.00 0.00 4.35
1803 1849 3.010420 GGACAACCAGGTATCAAGAAGC 58.990 50.000 0.00 0.00 35.97 3.86
1804 1850 3.009033 TGGGACAACCAGGTATCAAGAAG 59.991 47.826 0.00 0.00 46.80 2.85
1805 1851 2.983192 TGGGACAACCAGGTATCAAGAA 59.017 45.455 0.00 0.00 46.80 2.52
1806 1852 2.626785 TGGGACAACCAGGTATCAAGA 58.373 47.619 0.00 0.00 46.80 3.02
1820 1866 2.091333 AGAAGCCTTTTCCTTTGGGACA 60.091 45.455 0.00 0.00 42.05 4.02
1927 1974 4.678256 ACAACTGTTATCCAGAGGAGAGA 58.322 43.478 0.00 0.00 44.49 3.10



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

AutoCloner maintained by Alex Coulton.