Multiple sequence alignment - TraesCS3A01G368100

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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 TraesCS3A01G368100 chr3A 100.000 2749 0 0 1 2749 617062319 617059571 0.000000e+00 5077
1 TraesCS3A01G368100 chr3D 94.156 2738 79 34 1 2713 474616658 474613977 0.000000e+00 4095
2 TraesCS3A01G368100 chr3B 93.181 2493 84 35 1 2472 631038556 631036129 0.000000e+00 3583
3 TraesCS3A01G368100 chr3B 97.535 284 4 3 2465 2747 631034949 631034668 1.480000e-132 483
4 TraesCS3A01G368100 chr1A 78.771 179 34 4 1039 1215 33398703 33398527 1.730000e-22 117
5 TraesCS3A01G368100 chr2D 78.378 185 35 4 1035 1215 590146420 590146603 6.220000e-22 115
6 TraesCS3A01G368100 chr1D 78.212 179 35 4 1039 1215 35060885 35060709 8.050000e-21 111
7 TraesCS3A01G368100 chr2B 77.838 185 36 4 1035 1215 714777656 714777839 2.890000e-20 110
8 TraesCS3A01G368100 chr5D 78.107 169 35 2 1048 1215 254023410 254023577 3.740000e-19 106
9 TraesCS3A01G368100 chr5A 78.107 169 35 2 1048 1215 336950101 336950268 3.740000e-19 106
10 TraesCS3A01G368100 chr5B 77.515 169 36 2 1048 1215 288892876 288892709 1.740000e-17 100


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 TraesCS3A01G368100 chr3A 617059571 617062319 2748 True 5077 5077 100.000 1 2749 1 chr3A.!!$R1 2748
1 TraesCS3A01G368100 chr3D 474613977 474616658 2681 True 4095 4095 94.156 1 2713 1 chr3D.!!$R1 2712
2 TraesCS3A01G368100 chr3B 631034668 631038556 3888 True 2033 3583 95.358 1 2747 2 chr3B.!!$R1 2746

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
120 121 0.031178 CTTGTCTTGTTGGCAGGTGC 59.969 55.0 0.0 0.0 41.14 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1907 1934 0.179134 GTCGTGCCTCTTGCGTCTAT 60.179 55.0 0.0 0.0 45.6 1.98 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
34 35 5.557576 TTTCCATCCTCTGATCCAGTATG 57.442 43.478 0.00 0.00 32.61 2.39
110 111 3.056250 AGCATCGATCTGTCTTGTCTTGT 60.056 43.478 0.00 0.00 0.00 3.16
120 121 0.031178 CTTGTCTTGTTGGCAGGTGC 59.969 55.000 0.00 0.00 41.14 5.01
192 193 5.118203 CGTTTAACTTGTTCGTAAGCTAGCT 59.882 40.000 12.68 12.68 37.18 3.32
193 194 6.306356 CGTTTAACTTGTTCGTAAGCTAGCTA 59.694 38.462 19.70 0.00 37.18 3.32
194 195 7.461156 CGTTTAACTTGTTCGTAAGCTAGCTAG 60.461 40.741 19.70 16.84 37.18 3.42
291 292 4.561735 TCAATGAACGAACTCCAAAACC 57.438 40.909 0.00 0.00 0.00 3.27
345 349 2.420466 GTACGATTCCCCTCGGCC 59.580 66.667 0.00 0.00 42.88 6.13
575 579 0.246086 AGGCGAGCTATGCTATCAGC 59.754 55.000 9.99 0.00 39.88 4.26
676 683 1.365368 CGCGCACTGAGAGAGAGAGA 61.365 60.000 8.75 0.00 0.00 3.10
874 883 1.042559 AGCACAACAAAGTGGGGGTG 61.043 55.000 0.00 0.00 39.87 4.61
889 898 3.243724 GGGGGTGAGATAGTAGAGCATT 58.756 50.000 0.00 0.00 0.00 3.56
896 905 7.044798 GGTGAGATAGTAGAGCATTTTGAAGT 58.955 38.462 0.00 0.00 0.00 3.01
897 906 7.550906 GGTGAGATAGTAGAGCATTTTGAAGTT 59.449 37.037 0.00 0.00 0.00 2.66
898 907 9.587772 GTGAGATAGTAGAGCATTTTGAAGTTA 57.412 33.333 0.00 0.00 0.00 2.24
899 908 9.809096 TGAGATAGTAGAGCATTTTGAAGTTAG 57.191 33.333 0.00 0.00 0.00 2.34
997 1013 4.941263 CAGATAGCTAGCTAGAGGTAGTGG 59.059 50.000 27.42 7.58 45.22 4.00
1290 1306 4.070552 GAAGAGACCGGCCGTGCT 62.071 66.667 26.12 20.49 0.00 4.40
1332 1348 3.695606 GACCTCGTGCTCCAGCCA 61.696 66.667 0.00 0.00 41.18 4.75
1347 1363 4.379243 CCACCCGAGAGCAAGCGT 62.379 66.667 0.00 0.00 0.00 5.07
1399 1415 5.050769 CGGATCATGACATGTAAGTTAGCAC 60.051 44.000 14.98 0.00 0.00 4.40
1414 1436 1.885850 GCACCCACGTCGTTGTTCT 60.886 57.895 0.00 0.00 0.00 3.01
1634 1661 4.373116 GCGGACAGGTTCAGCCGA 62.373 66.667 0.00 0.00 46.29 5.54
1804 1831 2.632512 TGCTTGTATCACCTGTCAGTCA 59.367 45.455 0.00 0.00 0.00 3.41
1805 1832 3.257393 GCTTGTATCACCTGTCAGTCAG 58.743 50.000 0.00 0.00 43.27 3.51
1806 1833 3.306364 GCTTGTATCACCTGTCAGTCAGT 60.306 47.826 0.00 0.00 42.19 3.41
1807 1834 4.489810 CTTGTATCACCTGTCAGTCAGTC 58.510 47.826 0.00 0.00 42.19 3.51
1826 1853 2.766263 GTCTACCTGACCATGGATGTCA 59.234 50.000 21.47 11.21 39.69 3.58
1847 1874 1.328680 CACACGCATCATTGCCTAGTC 59.671 52.381 0.00 0.00 46.57 2.59
1848 1875 0.940126 CACGCATCATTGCCTAGTCC 59.060 55.000 0.00 0.00 46.57 3.85
1849 1876 0.833287 ACGCATCATTGCCTAGTCCT 59.167 50.000 0.00 0.00 46.57 3.85
1850 1877 1.202580 ACGCATCATTGCCTAGTCCTC 60.203 52.381 0.00 0.00 46.57 3.71
1851 1878 1.506493 GCATCATTGCCTAGTCCTCG 58.494 55.000 0.00 0.00 43.38 4.63
1852 1879 1.069204 GCATCATTGCCTAGTCCTCGA 59.931 52.381 0.00 0.00 43.38 4.04
1853 1880 2.289320 GCATCATTGCCTAGTCCTCGAT 60.289 50.000 0.00 0.00 43.38 3.59
1854 1881 3.805108 GCATCATTGCCTAGTCCTCGATT 60.805 47.826 0.00 0.00 43.38 3.34
1855 1882 3.735237 TCATTGCCTAGTCCTCGATTC 57.265 47.619 0.00 0.00 0.00 2.52
1856 1883 3.300388 TCATTGCCTAGTCCTCGATTCT 58.700 45.455 0.00 0.00 0.00 2.40
1857 1884 3.068732 TCATTGCCTAGTCCTCGATTCTG 59.931 47.826 0.00 0.00 0.00 3.02
1858 1885 1.403814 TGCCTAGTCCTCGATTCTGG 58.596 55.000 0.00 0.00 0.00 3.86
1859 1886 0.032815 GCCTAGTCCTCGATTCTGGC 59.967 60.000 0.00 0.00 0.00 4.85
1860 1887 1.698506 CCTAGTCCTCGATTCTGGCT 58.301 55.000 0.00 0.00 0.00 4.75
1861 1888 2.865079 CCTAGTCCTCGATTCTGGCTA 58.135 52.381 0.00 0.00 0.00 3.93
1862 1889 2.554893 CCTAGTCCTCGATTCTGGCTAC 59.445 54.545 0.00 0.00 0.00 3.58
1863 1890 2.445682 AGTCCTCGATTCTGGCTACT 57.554 50.000 0.00 0.00 0.00 2.57
1867 1894 3.075148 TCCTCGATTCTGGCTACTATCG 58.925 50.000 0.00 0.00 40.76 2.92
1898 1925 1.607628 CTGTACGAGAAGGGATACGGG 59.392 57.143 0.00 0.00 37.60 5.28
1907 1934 1.502690 AGGGATACGGGCATGTGTTA 58.497 50.000 0.00 0.00 37.60 2.41
2044 2074 6.659824 TGTACTGTTTCTTTTCTTCCTCCTT 58.340 36.000 0.00 0.00 0.00 3.36
2045 2075 6.766467 TGTACTGTTTCTTTTCTTCCTCCTTC 59.234 38.462 0.00 0.00 0.00 3.46
2082 2112 8.774586 GTTGCATGGTCTACTATAATTAACCTG 58.225 37.037 0.00 2.03 0.00 4.00
2086 2116 6.823497 TGGTCTACTATAATTAACCTGTGGC 58.177 40.000 3.96 0.00 0.00 5.01
2108 2138 5.333645 GGCTGAAAACTGATGCTATATGACG 60.334 44.000 0.00 0.00 0.00 4.35
2109 2139 5.235186 GCTGAAAACTGATGCTATATGACGT 59.765 40.000 0.00 0.00 0.00 4.34
2110 2140 6.420903 GCTGAAAACTGATGCTATATGACGTA 59.579 38.462 0.00 0.00 0.00 3.57
2225 2257 1.473258 ACAAACTTGGCTGCAACTCA 58.527 45.000 0.50 0.00 0.00 3.41
2226 2258 1.824230 ACAAACTTGGCTGCAACTCAA 59.176 42.857 0.50 0.00 0.00 3.02
2252 2284 1.774894 AAGGCGTTAGGTGGGAAGCA 61.775 55.000 0.00 0.00 0.00 3.91
2291 2326 6.912082 TGATTTGACACAGTACATGGAATTG 58.088 36.000 0.00 0.00 0.00 2.32
2336 2371 8.696374 CATATATAATCCCCACCTAGTGTGTAG 58.304 40.741 9.57 2.64 43.85 2.74
2338 2373 1.933021 TCCCCACCTAGTGTGTAGTG 58.067 55.000 9.57 0.36 43.85 2.74
2339 2374 1.148446 TCCCCACCTAGTGTGTAGTGT 59.852 52.381 9.57 0.00 43.85 3.55
2340 2375 1.275291 CCCCACCTAGTGTGTAGTGTG 59.725 57.143 9.57 0.00 43.85 3.82
2612 3841 1.569493 GCACACTCGACGCACAAAT 59.431 52.632 0.00 0.00 0.00 2.32
2741 3971 5.172687 TGTTCCCACAGTATATGAGCAAA 57.827 39.130 0.00 0.00 0.00 3.68
2742 3972 5.754782 TGTTCCCACAGTATATGAGCAAAT 58.245 37.500 0.00 0.00 0.00 2.32
2743 3973 5.589855 TGTTCCCACAGTATATGAGCAAATG 59.410 40.000 0.00 0.00 0.00 2.32
2744 3974 5.628797 TCCCACAGTATATGAGCAAATGA 57.371 39.130 0.00 0.00 0.00 2.57
2745 3975 5.614308 TCCCACAGTATATGAGCAAATGAG 58.386 41.667 0.00 0.00 0.00 2.90
2746 3976 4.214971 CCCACAGTATATGAGCAAATGAGC 59.785 45.833 0.00 0.00 0.00 4.26
2748 3978 5.530171 CCACAGTATATGAGCAAATGAGCTT 59.470 40.000 0.00 0.00 46.75 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 3.639538 TCGCTCGCTCCATTATCTTAAC 58.360 45.455 0.00 0.00 0.00 2.01
192 193 3.430374 GGCGTGGATTTCTTGACTAGCTA 60.430 47.826 0.00 0.00 0.00 3.32
193 194 2.622436 GCGTGGATTTCTTGACTAGCT 58.378 47.619 0.00 0.00 0.00 3.32
194 195 1.666189 GGCGTGGATTTCTTGACTAGC 59.334 52.381 0.00 0.00 0.00 3.42
195 196 3.252974 AGGCGTGGATTTCTTGACTAG 57.747 47.619 0.00 0.00 0.00 2.57
198 199 1.468914 GGAAGGCGTGGATTTCTTGAC 59.531 52.381 0.00 0.00 0.00 3.18
291 292 0.448990 CGTGGTGCATGGACAATCTG 59.551 55.000 19.67 0.00 0.00 2.90
345 349 1.081376 GGGTCGTGACTCGTGACTG 60.081 63.158 0.00 0.00 40.80 3.51
575 579 1.956477 ACTGCTTGCAAAACCCTACTG 59.044 47.619 0.00 0.00 0.00 2.74
889 898 8.147058 GCTGGATGATCTATCTCTAACTTCAAA 58.853 37.037 0.00 0.00 36.03 2.69
896 905 5.331906 AGCAGCTGGATGATCTATCTCTAA 58.668 41.667 17.12 0.00 36.03 2.10
897 906 4.933134 AGCAGCTGGATGATCTATCTCTA 58.067 43.478 17.12 0.00 36.03 2.43
898 907 3.765511 GAGCAGCTGGATGATCTATCTCT 59.234 47.826 17.12 0.00 36.03 3.10
899 908 3.427909 CGAGCAGCTGGATGATCTATCTC 60.428 52.174 17.12 8.11 33.43 2.75
930 946 1.151777 CGATCACCACGGTGTATGCC 61.152 60.000 15.65 2.07 45.55 4.40
932 948 1.556564 GTCGATCACCACGGTGTATG 58.443 55.000 15.65 5.41 45.55 2.39
997 1013 3.885521 GCTCAGCGCCTCCATTGC 61.886 66.667 2.29 0.00 0.00 3.56
1332 1348 3.288308 CTCACGCTTGCTCTCGGGT 62.288 63.158 0.00 0.00 0.00 5.28
1399 1415 0.780002 CGTAAGAACAACGACGTGGG 59.220 55.000 7.41 2.79 42.90 4.61
1414 1436 4.060205 GGAACAAACCAAGCTCTACGTAA 58.940 43.478 0.00 0.00 0.00 3.18
1804 1831 3.034635 GACATCCATGGTCAGGTAGACT 58.965 50.000 12.58 0.00 46.72 3.24
1805 1832 2.766263 TGACATCCATGGTCAGGTAGAC 59.234 50.000 12.58 0.00 46.83 2.59
1806 1833 2.766263 GTGACATCCATGGTCAGGTAGA 59.234 50.000 12.58 0.00 45.21 2.59
1807 1834 2.501316 TGTGACATCCATGGTCAGGTAG 59.499 50.000 12.58 0.00 45.21 3.18
1847 1874 2.162608 CCGATAGTAGCCAGAATCGAGG 59.837 54.545 9.81 0.00 42.88 4.63
1848 1875 2.414824 GCCGATAGTAGCCAGAATCGAG 60.415 54.545 9.81 3.30 42.88 4.04
1849 1876 1.540267 GCCGATAGTAGCCAGAATCGA 59.460 52.381 9.81 0.00 42.88 3.59
1850 1877 1.269723 TGCCGATAGTAGCCAGAATCG 59.730 52.381 0.00 0.00 40.60 3.34
1851 1878 3.056536 TGATGCCGATAGTAGCCAGAATC 60.057 47.826 0.00 0.00 0.00 2.52
1852 1879 2.899900 TGATGCCGATAGTAGCCAGAAT 59.100 45.455 0.00 0.00 0.00 2.40
1853 1880 2.316108 TGATGCCGATAGTAGCCAGAA 58.684 47.619 0.00 0.00 0.00 3.02
1854 1881 1.995376 TGATGCCGATAGTAGCCAGA 58.005 50.000 0.00 0.00 0.00 3.86
1855 1882 2.820059 TTGATGCCGATAGTAGCCAG 57.180 50.000 0.00 0.00 0.00 4.85
1856 1883 3.466836 CTTTTGATGCCGATAGTAGCCA 58.533 45.455 0.00 0.00 0.00 4.75
1857 1884 2.224314 GCTTTTGATGCCGATAGTAGCC 59.776 50.000 0.00 0.00 0.00 3.93
1858 1885 3.059325 CAGCTTTTGATGCCGATAGTAGC 60.059 47.826 0.00 0.00 0.00 3.58
1859 1886 4.122776 ACAGCTTTTGATGCCGATAGTAG 58.877 43.478 0.00 0.00 39.89 2.57
1860 1887 4.137116 ACAGCTTTTGATGCCGATAGTA 57.863 40.909 0.00 0.00 39.89 1.82
1861 1888 2.991250 ACAGCTTTTGATGCCGATAGT 58.009 42.857 0.00 0.00 39.89 2.12
1862 1889 3.060272 CGTACAGCTTTTGATGCCGATAG 60.060 47.826 0.00 0.00 39.89 2.08
1863 1890 2.863740 CGTACAGCTTTTGATGCCGATA 59.136 45.455 0.00 0.00 39.89 2.92
1867 1894 2.346803 TCTCGTACAGCTTTTGATGCC 58.653 47.619 0.00 0.00 39.89 4.40
1898 1925 3.246226 CCTCTTGCGTCTATAACACATGC 59.754 47.826 0.00 0.00 0.00 4.06
1907 1934 0.179134 GTCGTGCCTCTTGCGTCTAT 60.179 55.000 0.00 0.00 45.60 1.98
1945 1972 2.755686 TGATCCTCTCAGATTCTGCCA 58.244 47.619 8.89 0.00 0.00 4.92
1990 2017 5.588648 TGATGAAATATCAACGGAAAGGGAC 59.411 40.000 0.00 0.00 39.49 4.46
2027 2055 5.386060 GGAAGGAAGGAGGAAGAAAAGAAA 58.614 41.667 0.00 0.00 0.00 2.52
2082 2112 5.528690 TCATATAGCATCAGTTTTCAGCCAC 59.471 40.000 0.00 0.00 0.00 5.01
2086 2116 6.834959 ACGTCATATAGCATCAGTTTTCAG 57.165 37.500 0.00 0.00 0.00 3.02
2147 2177 1.203313 TCTCCTAGGGCAAGACCTTGT 60.203 52.381 9.46 0.00 42.09 3.16
2206 2238 1.473258 TGAGTTGCAGCCAAGTTTGT 58.527 45.000 0.00 0.00 34.81 2.83
2207 2239 2.582728 TTGAGTTGCAGCCAAGTTTG 57.417 45.000 0.00 0.00 34.81 2.93
2208 2240 3.608316 TTTTGAGTTGCAGCCAAGTTT 57.392 38.095 0.00 0.00 34.81 2.66
2225 2257 2.621526 CCACCTAACGCCTTGAGTTTTT 59.378 45.455 0.00 0.00 33.42 1.94
2226 2258 2.227194 CCACCTAACGCCTTGAGTTTT 58.773 47.619 0.00 0.00 33.42 2.43
2252 2284 5.706833 TGTCAAATCATGTGTTCATACTGCT 59.293 36.000 0.00 0.00 32.47 4.24
2291 2326 3.604875 TGTAGGAAGGACGACATTTCC 57.395 47.619 10.76 10.76 40.52 3.13
2336 2371 3.503748 ACAGTCTAACGGGTAGTACACAC 59.496 47.826 2.92 0.00 0.00 3.82
2338 2373 3.181516 CGACAGTCTAACGGGTAGTACAC 60.182 52.174 2.06 0.00 0.00 2.90
2339 2374 3.002791 CGACAGTCTAACGGGTAGTACA 58.997 50.000 2.06 0.00 0.00 2.90
2340 2375 3.003480 ACGACAGTCTAACGGGTAGTAC 58.997 50.000 0.00 0.00 0.00 2.73
2612 3841 2.229543 GCAATTGAATCTCTGCCACACA 59.770 45.455 10.34 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.