Multiple sequence alignment - TraesCS6D01G285300

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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 TraesCS6D01G285300 chr6D 100.000 2408 0 0 1 2408 393298428 393300835 0.000000e+00 4447
1 TraesCS6D01G285300 chr6B 95.182 1785 48 14 1 1765 587797865 587799631 0.000000e+00 2785
2 TraesCS6D01G285300 chr6B 95.954 346 10 2 2066 2408 587799827 587800171 2.090000e-155 558
3 TraesCS6D01G285300 chr6B 99.512 205 1 0 1827 2031 587799622 587799826 8.130000e-100 374
4 TraesCS6D01G285300 chr6A 93.989 1780 55 18 1 1747 539864670 539866430 0.000000e+00 2647
5 TraesCS6D01G285300 chr6A 93.155 599 13 9 1822 2408 539866723 539867305 0.000000e+00 854
6 TraesCS6D01G285300 chr7D 88.535 157 18 0 1247 1403 139829120 139829276 8.790000e-45 191
7 TraesCS6D01G285300 chr7B 88.535 157 18 0 1247 1403 104757901 104758057 8.790000e-45 191


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 TraesCS6D01G285300 chr6D 393298428 393300835 2407 False 4447.0 4447 100.000000 1 2408 1 chr6D.!!$F1 2407
1 TraesCS6D01G285300 chr6B 587797865 587800171 2306 False 1239.0 2785 96.882667 1 2408 3 chr6B.!!$F1 2407
2 TraesCS6D01G285300 chr6A 539864670 539867305 2635 False 1750.5 2647 93.572000 1 2408 2 chr6A.!!$F1 2407

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
367 387 0.375454 TCACAACCTCAAACGCAACG 59.625 50.0 0.0 0.0 0.0 4.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1805 1846 0.178891 AAGAGGGGAAGAGGCAGACA 60.179 55.0 0.0 0.0 0.0 3.41 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
33 34 3.594134 GCTGATTAGAGAGTTGCTGTGT 58.406 45.455 0.00 0.00 0.00 3.72
175 191 4.282873 GTGTTCTTTCTCCGAAAAGCTTG 58.717 43.478 0.00 0.00 36.41 4.01
213 229 3.589988 ACTCTCAATTTGCACTACTCGG 58.410 45.455 0.00 0.00 0.00 4.63
238 254 2.408835 GGCAATGCCGACGATTGG 59.591 61.111 9.14 0.00 39.62 3.16
367 387 0.375454 TCACAACCTCAAACGCAACG 59.625 50.000 0.00 0.00 0.00 4.10
575 595 4.489771 CCGATGACAGTGGGGCCC 62.490 72.222 18.17 18.17 0.00 5.80
736 757 0.618981 GTTCCCCAATCCGTTCTCCT 59.381 55.000 0.00 0.00 0.00 3.69
897 918 2.221055 CACCTTTTGAGCGTACACACTC 59.779 50.000 0.00 0.00 0.00 3.51
901 922 1.237533 TTGAGCGTACACACTCCGTA 58.762 50.000 5.40 0.00 31.65 4.02
955 980 2.022240 GCTCCGGCACTAGCTAGCTT 62.022 60.000 24.88 1.98 41.70 3.74
1156 1196 3.605013 TGCACACGCACATTACTCT 57.395 47.368 0.00 0.00 45.36 3.24
1414 1455 1.009900 CTCCGCTCGTGATCGTACC 60.010 63.158 0.00 0.00 38.33 3.34
1469 1510 1.312371 GCCAGGACAATTAAGCGGCA 61.312 55.000 1.45 0.00 37.98 5.69
1488 1529 4.899239 CGGCGCCATGGGTCTCTC 62.899 72.222 28.98 0.00 0.00 3.20
1489 1530 4.554036 GGCGCCATGGGTCTCTCC 62.554 72.222 24.80 0.00 0.00 3.71
1490 1531 4.899239 GCGCCATGGGTCTCTCCG 62.899 72.222 15.13 7.62 37.00 4.63
1756 1797 0.675837 TTCGATCGTCTCCTCCGTGT 60.676 55.000 15.94 0.00 0.00 4.49
1757 1798 1.062685 CGATCGTCTCCTCCGTGTG 59.937 63.158 7.03 0.00 0.00 3.82
1758 1799 1.226717 GATCGTCTCCTCCGTGTGC 60.227 63.158 0.00 0.00 0.00 4.57
1759 1800 1.658686 GATCGTCTCCTCCGTGTGCT 61.659 60.000 0.00 0.00 0.00 4.40
1760 1801 1.251527 ATCGTCTCCTCCGTGTGCTT 61.252 55.000 0.00 0.00 0.00 3.91
1761 1802 1.444553 CGTCTCCTCCGTGTGCTTC 60.445 63.158 0.00 0.00 0.00 3.86
1762 1803 1.079750 GTCTCCTCCGTGTGCTTCC 60.080 63.158 0.00 0.00 0.00 3.46
1763 1804 2.266055 CTCCTCCGTGTGCTTCCC 59.734 66.667 0.00 0.00 0.00 3.97
1764 1805 2.203788 TCCTCCGTGTGCTTCCCT 60.204 61.111 0.00 0.00 0.00 4.20
1765 1806 2.232298 CTCCTCCGTGTGCTTCCCTC 62.232 65.000 0.00 0.00 0.00 4.30
1766 1807 2.125912 CTCCGTGTGCTTCCCTCG 60.126 66.667 0.00 0.00 0.00 4.63
1767 1808 4.373116 TCCGTGTGCTTCCCTCGC 62.373 66.667 0.00 0.00 0.00 5.03
1768 1809 4.379243 CCGTGTGCTTCCCTCGCT 62.379 66.667 0.00 0.00 0.00 4.93
1769 1810 2.571757 CGTGTGCTTCCCTCGCTA 59.428 61.111 0.00 0.00 0.00 4.26
1770 1811 1.517257 CGTGTGCTTCCCTCGCTAG 60.517 63.158 0.00 0.00 0.00 3.42
1771 1812 1.811679 GTGTGCTTCCCTCGCTAGC 60.812 63.158 4.06 4.06 35.50 3.42
1772 1813 1.984570 TGTGCTTCCCTCGCTAGCT 60.985 57.895 13.93 0.00 35.93 3.32
1773 1814 1.227118 GTGCTTCCCTCGCTAGCTC 60.227 63.158 13.93 0.00 35.93 4.09
1774 1815 2.026879 GCTTCCCTCGCTAGCTCG 59.973 66.667 13.93 3.06 32.26 5.03
1775 1816 2.725008 CTTCCCTCGCTAGCTCGG 59.275 66.667 13.93 12.31 0.00 4.63
1776 1817 1.824329 CTTCCCTCGCTAGCTCGGA 60.824 63.158 13.93 11.37 0.00 4.55
1777 1818 1.791103 CTTCCCTCGCTAGCTCGGAG 61.791 65.000 13.93 11.80 0.00 4.63
1778 1819 3.972276 CCCTCGCTAGCTCGGAGC 61.972 72.222 22.13 22.13 42.84 4.70
1790 1831 1.134175 GCTCGGAGCTGGATAGATAGC 59.866 57.143 22.32 0.00 38.45 2.97
1795 1836 2.246091 AGCTGGATAGATAGCTCCCC 57.754 55.000 0.00 0.00 46.76 4.81
1796 1837 1.199615 GCTGGATAGATAGCTCCCCC 58.800 60.000 0.00 0.00 36.99 5.40
1810 1851 3.077556 CCCCCGTCCTCCTGTCTG 61.078 72.222 0.00 0.00 0.00 3.51
1811 1852 3.775654 CCCCGTCCTCCTGTCTGC 61.776 72.222 0.00 0.00 0.00 4.26
1812 1853 3.775654 CCCGTCCTCCTGTCTGCC 61.776 72.222 0.00 0.00 0.00 4.85
1813 1854 2.681778 CCGTCCTCCTGTCTGCCT 60.682 66.667 0.00 0.00 0.00 4.75
1814 1855 2.716017 CCGTCCTCCTGTCTGCCTC 61.716 68.421 0.00 0.00 0.00 4.70
1815 1856 1.680651 CGTCCTCCTGTCTGCCTCT 60.681 63.158 0.00 0.00 0.00 3.69
1816 1857 1.254284 CGTCCTCCTGTCTGCCTCTT 61.254 60.000 0.00 0.00 0.00 2.85
1817 1858 0.534873 GTCCTCCTGTCTGCCTCTTC 59.465 60.000 0.00 0.00 0.00 2.87
1818 1859 0.616111 TCCTCCTGTCTGCCTCTTCC 60.616 60.000 0.00 0.00 0.00 3.46
1819 1860 1.621672 CCTCCTGTCTGCCTCTTCCC 61.622 65.000 0.00 0.00 0.00 3.97
1820 1861 1.613630 TCCTGTCTGCCTCTTCCCC 60.614 63.158 0.00 0.00 0.00 4.81
1825 2084 0.988063 GTCTGCCTCTTCCCCTCTTT 59.012 55.000 0.00 0.00 0.00 2.52
2042 2307 7.862512 AATACTAGACTGGAGTGTACTGTAC 57.137 40.000 10.98 10.98 0.00 2.90
2043 2308 5.502089 ACTAGACTGGAGTGTACTGTACT 57.498 43.478 17.98 1.08 0.00 2.73
2044 2309 5.247084 ACTAGACTGGAGTGTACTGTACTG 58.753 45.833 17.98 0.00 0.00 2.74
2045 2310 4.101645 AGACTGGAGTGTACTGTACTGT 57.898 45.455 17.98 10.46 0.00 3.55
2046 2311 5.238624 AGACTGGAGTGTACTGTACTGTA 57.761 43.478 17.98 8.40 0.00 2.74
2047 2312 5.002516 AGACTGGAGTGTACTGTACTGTAC 58.997 45.833 27.19 27.19 42.10 2.90
2048 2313 4.077822 ACTGGAGTGTACTGTACTGTACC 58.922 47.826 29.33 22.58 41.34 3.34
2049 2314 3.076621 TGGAGTGTACTGTACTGTACCG 58.923 50.000 29.33 11.20 41.34 4.02
2050 2315 3.077359 GGAGTGTACTGTACTGTACCGT 58.923 50.000 29.33 20.59 41.34 4.83
2051 2316 4.253685 GGAGTGTACTGTACTGTACCGTA 58.746 47.826 29.33 15.42 41.34 4.02
2052 2317 4.093556 GGAGTGTACTGTACTGTACCGTAC 59.906 50.000 29.89 29.89 44.51 3.67
2053 2318 4.899502 AGTGTACTGTACTGTACCGTACT 58.100 43.478 32.96 24.33 44.53 2.73
2054 2319 4.692625 AGTGTACTGTACTGTACCGTACTG 59.307 45.833 32.96 23.52 44.53 2.74
2055 2320 4.452455 GTGTACTGTACTGTACCGTACTGT 59.548 45.833 32.96 29.16 46.89 3.55
2058 2323 4.392940 ACTGTACTGTACCGTACTGTTCT 58.607 43.478 24.49 10.47 44.71 3.01
2106 2374 1.741327 ATGATGCCGGGCTTTCATGC 61.741 55.000 26.52 9.51 33.44 4.06
2119 2387 3.441572 GCTTTCATGCTTGCTTCCTCTAA 59.558 43.478 0.00 0.00 0.00 2.10
2207 2479 8.664798 TCATCAGGTTAAAAACACGATGATTAG 58.335 33.333 14.41 1.58 41.57 1.73
2270 2544 1.238439 GACATGTATGGAATGGCCCG 58.762 55.000 0.00 0.00 34.97 6.13
2321 2595 0.881796 TGCTACGACCAGTGACTCTG 59.118 55.000 0.00 0.00 43.27 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
175 191 7.672983 TTGAGAGTTTTGATCATGGAGTAAC 57.327 36.000 0.00 0.00 0.00 2.50
232 248 1.134946 GAATCAAACCCCTGCCAATCG 59.865 52.381 0.00 0.00 0.00 3.34
238 254 0.608035 TGGACGAATCAAACCCCTGC 60.608 55.000 0.00 0.00 0.00 4.85
367 387 5.007136 GTCCAGGAAATCGACAAGATCATTC 59.993 44.000 0.00 0.00 38.98 2.67
489 509 3.983420 CCACCCACCACTGGCCAT 61.983 66.667 5.51 0.00 36.00 4.40
575 595 4.247380 GATGAGCCAGGCCTCCCG 62.247 72.222 8.22 0.00 35.76 5.14
578 598 1.153208 CACTGATGAGCCAGGCCTC 60.153 63.158 8.22 5.87 38.44 4.70
584 604 2.101415 CCGTCTAATCACTGATGAGCCA 59.899 50.000 0.00 0.00 38.57 4.75
736 757 3.374984 GGGAGAGGGTGTCTTTATAGGGA 60.375 52.174 0.00 0.00 34.71 4.20
1156 1196 0.106868 TAGCTAGCTGGCGAGTGGTA 60.107 55.000 27.68 0.00 37.29 3.25
1566 1607 4.042684 AGAAAGGGAGCAGAAAAGAGACAT 59.957 41.667 0.00 0.00 0.00 3.06
1567 1608 3.392616 AGAAAGGGAGCAGAAAAGAGACA 59.607 43.478 0.00 0.00 0.00 3.41
1625 1666 2.255316 GAGTGAAGCTTAGAGACACGC 58.745 52.381 0.00 0.66 36.71 5.34
1737 1778 0.675837 ACACGGAGGAGACGATCGAA 60.676 55.000 24.34 0.00 34.93 3.71
1756 1797 2.775856 CGAGCTAGCGAGGGAAGCA 61.776 63.158 9.55 0.00 38.75 3.91
1757 1798 2.026879 CGAGCTAGCGAGGGAAGC 59.973 66.667 9.55 0.00 36.48 3.86
1758 1799 1.791103 CTCCGAGCTAGCGAGGGAAG 61.791 65.000 24.58 15.25 0.00 3.46
1759 1800 1.824329 CTCCGAGCTAGCGAGGGAA 60.824 63.158 24.58 10.79 0.00 3.97
1760 1801 2.203224 CTCCGAGCTAGCGAGGGA 60.203 66.667 24.58 21.79 0.00 4.20
1761 1802 3.972276 GCTCCGAGCTAGCGAGGG 61.972 72.222 24.58 19.33 38.45 4.30
1770 1811 1.134175 GCTATCTATCCAGCTCCGAGC 59.866 57.143 12.80 12.80 42.84 5.03
1771 1812 2.722094 AGCTATCTATCCAGCTCCGAG 58.278 52.381 0.00 0.00 44.83 4.63
1772 1813 2.889170 AGCTATCTATCCAGCTCCGA 57.111 50.000 0.00 0.00 44.83 4.55
1777 1818 1.199615 GGGGGAGCTATCTATCCAGC 58.800 60.000 0.00 0.00 37.33 4.85
1793 1834 3.077556 CAGACAGGAGGACGGGGG 61.078 72.222 0.00 0.00 0.00 5.40
1794 1835 3.775654 GCAGACAGGAGGACGGGG 61.776 72.222 0.00 0.00 0.00 5.73
1795 1836 3.775654 GGCAGACAGGAGGACGGG 61.776 72.222 0.00 0.00 0.00 5.28
1796 1837 2.681778 AGGCAGACAGGAGGACGG 60.682 66.667 0.00 0.00 0.00 4.79
1797 1838 1.254284 AAGAGGCAGACAGGAGGACG 61.254 60.000 0.00 0.00 0.00 4.79
1798 1839 0.534873 GAAGAGGCAGACAGGAGGAC 59.465 60.000 0.00 0.00 0.00 3.85
1799 1840 0.616111 GGAAGAGGCAGACAGGAGGA 60.616 60.000 0.00 0.00 0.00 3.71
1800 1841 1.621672 GGGAAGAGGCAGACAGGAGG 61.622 65.000 0.00 0.00 0.00 4.30
1801 1842 1.621672 GGGGAAGAGGCAGACAGGAG 61.622 65.000 0.00 0.00 0.00 3.69
1802 1843 1.613630 GGGGAAGAGGCAGACAGGA 60.614 63.158 0.00 0.00 0.00 3.86
1803 1844 1.614824 AGGGGAAGAGGCAGACAGG 60.615 63.158 0.00 0.00 0.00 4.00
1804 1845 0.617249 AGAGGGGAAGAGGCAGACAG 60.617 60.000 0.00 0.00 0.00 3.51
1805 1846 0.178891 AAGAGGGGAAGAGGCAGACA 60.179 55.000 0.00 0.00 0.00 3.41
1806 1847 0.988063 AAAGAGGGGAAGAGGCAGAC 59.012 55.000 0.00 0.00 0.00 3.51
1807 1848 1.352352 CAAAAGAGGGGAAGAGGCAGA 59.648 52.381 0.00 0.00 0.00 4.26
1808 1849 1.074566 ACAAAAGAGGGGAAGAGGCAG 59.925 52.381 0.00 0.00 0.00 4.85
1809 1850 1.149101 ACAAAAGAGGGGAAGAGGCA 58.851 50.000 0.00 0.00 0.00 4.75
1810 1851 1.889170 CAACAAAAGAGGGGAAGAGGC 59.111 52.381 0.00 0.00 0.00 4.70
1811 1852 3.149981 GACAACAAAAGAGGGGAAGAGG 58.850 50.000 0.00 0.00 0.00 3.69
1812 1853 3.149981 GGACAACAAAAGAGGGGAAGAG 58.850 50.000 0.00 0.00 0.00 2.85
1813 1854 2.158519 GGGACAACAAAAGAGGGGAAGA 60.159 50.000 0.00 0.00 0.00 2.87
1814 1855 2.158460 AGGGACAACAAAAGAGGGGAAG 60.158 50.000 0.00 0.00 0.00 3.46
1815 1856 1.856920 AGGGACAACAAAAGAGGGGAA 59.143 47.619 0.00 0.00 0.00 3.97
1816 1857 1.529744 AGGGACAACAAAAGAGGGGA 58.470 50.000 0.00 0.00 0.00 4.81
1817 1858 2.381752 AAGGGACAACAAAAGAGGGG 57.618 50.000 0.00 0.00 0.00 4.79
1818 1859 3.566351 AGAAAGGGACAACAAAAGAGGG 58.434 45.455 0.00 0.00 0.00 4.30
1819 1860 4.644685 TCAAGAAAGGGACAACAAAAGAGG 59.355 41.667 0.00 0.00 0.00 3.69
1820 1861 5.835113 TCAAGAAAGGGACAACAAAAGAG 57.165 39.130 0.00 0.00 0.00 2.85
1825 2084 6.187727 AGTAGATCAAGAAAGGGACAACAA 57.812 37.500 0.00 0.00 0.00 2.83
2106 2374 2.172293 AGAGGGCATTAGAGGAAGCAAG 59.828 50.000 0.00 0.00 0.00 4.01
2119 2387 4.841617 TCGAGGGCGAGAGGGCAT 62.842 66.667 0.00 0.00 42.51 4.40
2270 2544 4.645921 GCCACCGCAACCACAAGC 62.646 66.667 0.00 0.00 34.03 4.01
2321 2595 1.495951 CCGTTTCCGTAGCACAAGC 59.504 57.895 0.00 0.00 42.56 4.01


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

AutoCloner maintained by Alex Coulton.