Multiple sequence alignment - TraesCS7B01G274800

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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 TraesCS7B01G274800 chr7B 100.000 2627 0 0 1 2627 504201955 504199329 0.000000e+00 4852.0
1 TraesCS7B01G274800 chr7B 95.900 439 13 4 1896 2330 439310366 439310803 0.000000e+00 706.0
2 TraesCS7B01G274800 chr3A 97.221 2663 38 3 1 2627 506481559 506478897 0.000000e+00 4475.0
3 TraesCS7B01G274800 chr4A 96.598 2675 43 3 1 2627 645411591 645408917 0.000000e+00 4392.0
4 TraesCS7B01G274800 chr4A 96.909 744 10 2 1896 2627 683249429 683248687 0.000000e+00 1234.0
5 TraesCS7B01G274800 chrUn 98.984 984 10 0 877 1860 409399671 409398688 0.000000e+00 1762.0
6 TraesCS7B01G274800 chrUn 98.882 984 11 0 877 1860 406745206 406746189 0.000000e+00 1757.0
7 TraesCS7B01G274800 chrUn 98.679 984 13 0 877 1860 352840579 352841562 0.000000e+00 1746.0
8 TraesCS7B01G274800 chrUn 96.429 56 2 0 1854 1909 352841528 352841583 2.780000e-15 93.5
9 TraesCS7B01G274800 chrUn 96.429 56 2 0 1854 1909 406746155 406746210 2.780000e-15 93.5
10 TraesCS7B01G274800 chrUn 96.429 56 2 0 1854 1909 409398722 409398667 2.780000e-15 93.5
11 TraesCS7B01G274800 chr3B 98.984 984 10 0 877 1860 546821322 546820339 0.000000e+00 1762.0
12 TraesCS7B01G274800 chr3B 97.427 894 11 1 1 882 546831314 546830421 0.000000e+00 1513.0
13 TraesCS7B01G274800 chr1B 98.984 984 10 0 877 1860 167928860 167927877 0.000000e+00 1762.0
14 TraesCS7B01G274800 chr1B 97.204 894 13 1 1 882 167930059 167929166 0.000000e+00 1502.0
15 TraesCS7B01G274800 chr1B 95.767 756 8 2 1896 2627 167927513 167926758 0.000000e+00 1197.0
16 TraesCS7B01G274800 chr1B 92.574 404 20 6 2230 2627 573881195 573881594 2.930000e-159 571.0
17 TraesCS7B01G274800 chr1B 92.327 404 21 6 2230 2627 12511377 12511776 1.360000e-157 566.0
18 TraesCS7B01G274800 chr5A 98.882 984 11 0 877 1860 346307563 346308546 0.000000e+00 1757.0
19 TraesCS7B01G274800 chr5A 94.670 394 12 7 2237 2627 346309413 346309800 1.040000e-168 603.0
20 TraesCS7B01G274800 chr4B 98.879 981 11 0 877 1857 139743890 139744870 0.000000e+00 1751.0
21 TraesCS7B01G274800 chr4B 97.315 894 12 1 1 882 139742691 139743584 0.000000e+00 1507.0
22 TraesCS7B01G274800 chr4B 88.018 868 83 16 1 855 416152713 416151854 0.000000e+00 1007.0
23 TraesCS7B01G274800 chr5B 98.418 948 15 0 877 1824 383535818 383534871 0.000000e+00 1668.0
24 TraesCS7B01G274800 chr5B 96.980 894 15 1 1 882 514841238 514842131 0.000000e+00 1491.0
25 TraesCS7B01G274800 chr5B 95.467 750 15 7 1896 2627 56908906 56909654 0.000000e+00 1179.0
26 TraesCS7B01G274800 chr5B 95.050 404 11 3 2230 2627 383534226 383533826 6.170000e-176 627.0
27 TraesCS7B01G274800 chr1A 97.427 894 11 1 1 882 63763633 63762740 0.000000e+00 1513.0
28 TraesCS7B01G274800 chr1A 96.505 744 12 3 1896 2627 63760440 63759699 0.000000e+00 1218.0
29 TraesCS7B01G274800 chr1A 95.635 756 8 4 1896 2627 320477151 320476397 0.000000e+00 1190.0
30 TraesCS7B01G274800 chr1A 96.429 56 2 0 1854 1909 63760838 63760783 2.780000e-15 93.5
31 TraesCS7B01G274800 chr1A 96.429 56 2 0 1854 1909 63761485 63761430 2.780000e-15 93.5
32 TraesCS7B01G274800 chr1A 96.429 56 2 0 1854 1909 320477549 320477494 2.780000e-15 93.5
33 TraesCS7B01G274800 chr2B 97.315 894 11 2 1 882 652849751 652848859 0.000000e+00 1506.0
34 TraesCS7B01G274800 chr2B 95.635 756 8 3 1896 2627 652847236 652846482 0.000000e+00 1190.0
35 TraesCS7B01G274800 chr2B 92.822 404 20 5 2230 2627 679638026 679638426 6.300000e-161 577.0
36 TraesCS7B01G274800 chr2A 96.756 894 17 1 1 882 672536919 672537812 0.000000e+00 1480.0
37 TraesCS7B01G274800 chr2A 85.906 745 55 30 1912 2627 154842932 154843655 0.000000e+00 749.0
38 TraesCS7B01G274800 chr2A 94.614 427 10 2 1896 2310 672539267 672539692 0.000000e+00 649.0
39 TraesCS7B01G274800 chr6A 93.228 886 52 5 1 882 105157780 105156899 0.000000e+00 1297.0
40 TraesCS7B01G274800 chr7D 90.068 886 71 11 1 880 290912523 290911649 0.000000e+00 1133.0
41 TraesCS7B01G274800 chr6B 95.931 467 6 2 1 455 13819728 13820193 0.000000e+00 745.0


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 TraesCS7B01G274800 chr7B 504199329 504201955 2626 True 4852.00 4852 100.000000 1 2627 1 chr7B.!!$R1 2626
1 TraesCS7B01G274800 chr3A 506478897 506481559 2662 True 4475.00 4475 97.221000 1 2627 1 chr3A.!!$R1 2626
2 TraesCS7B01G274800 chr4A 645408917 645411591 2674 True 4392.00 4392 96.598000 1 2627 1 chr4A.!!$R1 2626
3 TraesCS7B01G274800 chr4A 683248687 683249429 742 True 1234.00 1234 96.909000 1896 2627 1 chr4A.!!$R2 731
4 TraesCS7B01G274800 chrUn 409398667 409399671 1004 True 927.75 1762 97.706500 877 1909 2 chrUn.!!$R1 1032
5 TraesCS7B01G274800 chrUn 406745206 406746210 1004 False 925.25 1757 97.655500 877 1909 2 chrUn.!!$F2 1032
6 TraesCS7B01G274800 chrUn 352840579 352841583 1004 False 919.75 1746 97.554000 877 1909 2 chrUn.!!$F1 1032
7 TraesCS7B01G274800 chr3B 546820339 546821322 983 True 1762.00 1762 98.984000 877 1860 1 chr3B.!!$R1 983
8 TraesCS7B01G274800 chr3B 546830421 546831314 893 True 1513.00 1513 97.427000 1 882 1 chr3B.!!$R2 881
9 TraesCS7B01G274800 chr1B 167926758 167930059 3301 True 1487.00 1762 97.318333 1 2627 3 chr1B.!!$R1 2626
10 TraesCS7B01G274800 chr5A 346307563 346309800 2237 False 1180.00 1757 96.776000 877 2627 2 chr5A.!!$F1 1750
11 TraesCS7B01G274800 chr4B 139742691 139744870 2179 False 1629.00 1751 98.097000 1 1857 2 chr4B.!!$F1 1856
12 TraesCS7B01G274800 chr4B 416151854 416152713 859 True 1007.00 1007 88.018000 1 855 1 chr4B.!!$R1 854
13 TraesCS7B01G274800 chr5B 514841238 514842131 893 False 1491.00 1491 96.980000 1 882 1 chr5B.!!$F2 881
14 TraesCS7B01G274800 chr5B 56908906 56909654 748 False 1179.00 1179 95.467000 1896 2627 1 chr5B.!!$F1 731
15 TraesCS7B01G274800 chr5B 383533826 383535818 1992 True 1147.50 1668 96.734000 877 2627 2 chr5B.!!$R1 1750
16 TraesCS7B01G274800 chr1A 63759699 63763633 3934 True 729.50 1513 96.697500 1 2627 4 chr1A.!!$R1 2626
17 TraesCS7B01G274800 chr1A 320476397 320477549 1152 True 641.75 1190 96.032000 1854 2627 2 chr1A.!!$R2 773
18 TraesCS7B01G274800 chr2B 652846482 652849751 3269 True 1348.00 1506 96.475000 1 2627 2 chr2B.!!$R1 2626
19 TraesCS7B01G274800 chr2A 672536919 672539692 2773 False 1064.50 1480 95.685000 1 2310 2 chr2A.!!$F2 2309
20 TraesCS7B01G274800 chr2A 154842932 154843655 723 False 749.00 749 85.906000 1912 2627 1 chr2A.!!$F1 715
21 TraesCS7B01G274800 chr6A 105156899 105157780 881 True 1297.00 1297 93.228000 1 882 1 chr6A.!!$R1 881
22 TraesCS7B01G274800 chr7D 290911649 290912523 874 True 1133.00 1133 90.068000 1 880 1 chr7D.!!$R1 879

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
985 1317 3.576078 TTGTTCAGTGGGTTGATGAGT 57.424 42.857 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2540 4167 1.270839 GGTACACAAGCTGCCTCAAGA 60.271 52.381 0.0 0.0 0.0 3.02 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
804 825 6.377146 TGTCATACTGTAGTGCTCATTGTAGA 59.623 38.462 0.00 0.00 0.00 2.59
866 887 5.752036 AATATAGGCTCAAGCATGCTCTA 57.248 39.130 22.93 17.37 44.36 2.43
985 1317 3.576078 TTGTTCAGTGGGTTGATGAGT 57.424 42.857 0.00 0.00 0.00 3.41
1143 1475 7.334858 TGGATGCACAATATGACAAGTTAGTA 58.665 34.615 0.00 0.00 0.00 1.82
1201 1533 6.833933 GGATAGGGTTGTGGATTTCAGTTATT 59.166 38.462 0.00 0.00 0.00 1.40
1503 1835 1.571955 TCCAGGTTGCTGATCTGCTA 58.428 50.000 23.02 14.48 0.00 3.49
1576 1908 1.481363 CTGAGCTCATGAAGGCAGAGA 59.519 52.381 18.63 0.00 0.00 3.10
1825 2157 4.397420 TGTGCATTTGAACTCCACTATGT 58.603 39.130 0.00 0.00 0.00 2.29
1826 2158 5.555966 TGTGCATTTGAACTCCACTATGTA 58.444 37.500 0.00 0.00 0.00 2.29
1827 2159 6.000840 TGTGCATTTGAACTCCACTATGTAA 58.999 36.000 0.00 0.00 0.00 2.41
1828 2160 6.658816 TGTGCATTTGAACTCCACTATGTAAT 59.341 34.615 0.00 0.00 0.00 1.89
1829 2161 6.968904 GTGCATTTGAACTCCACTATGTAATG 59.031 38.462 0.00 0.00 0.00 1.90
1830 2162 6.658816 TGCATTTGAACTCCACTATGTAATGT 59.341 34.615 0.00 0.00 0.00 2.71
1831 2163 6.968904 GCATTTGAACTCCACTATGTAATGTG 59.031 38.462 0.00 0.00 0.00 3.21
1832 2164 7.148255 GCATTTGAACTCCACTATGTAATGTGA 60.148 37.037 0.00 0.00 36.38 3.58
1833 2165 8.729756 CATTTGAACTCCACTATGTAATGTGAA 58.270 33.333 0.00 0.00 36.38 3.18
1834 2166 7.667043 TTGAACTCCACTATGTAATGTGAAC 57.333 36.000 0.00 0.00 36.38 3.18
1835 2167 6.764379 TGAACTCCACTATGTAATGTGAACA 58.236 36.000 0.00 0.00 36.38 3.18
1836 2168 7.220740 TGAACTCCACTATGTAATGTGAACAA 58.779 34.615 0.00 0.00 36.38 2.83
1837 2169 7.882791 TGAACTCCACTATGTAATGTGAACAAT 59.117 33.333 0.00 0.00 36.38 2.71
1838 2170 7.615582 ACTCCACTATGTAATGTGAACAATG 57.384 36.000 0.00 0.00 36.38 2.82
1839 2171 6.599244 ACTCCACTATGTAATGTGAACAATGG 59.401 38.462 0.00 0.00 36.38 3.16
1840 2172 6.480763 TCCACTATGTAATGTGAACAATGGT 58.519 36.000 0.00 0.00 36.38 3.55
1841 2173 6.945435 TCCACTATGTAATGTGAACAATGGTT 59.055 34.615 0.00 0.00 40.76 3.67
1842 2174 7.028962 CCACTATGTAATGTGAACAATGGTTG 58.971 38.462 0.00 0.00 37.36 3.77
1844 2176 7.538334 CACTATGTAATGTGAACAATGGTTGTG 59.462 37.037 0.00 0.00 44.59 3.33
1845 2177 5.843673 TGTAATGTGAACAATGGTTGTGT 57.156 34.783 0.00 0.00 44.59 3.72
1846 2178 6.944234 TGTAATGTGAACAATGGTTGTGTA 57.056 33.333 0.00 0.00 44.59 2.90
1847 2179 7.517614 TGTAATGTGAACAATGGTTGTGTAT 57.482 32.000 0.00 0.00 44.59 2.29
1848 2180 7.946207 TGTAATGTGAACAATGGTTGTGTATT 58.054 30.769 0.00 0.00 44.59 1.89
1849 2181 8.079203 TGTAATGTGAACAATGGTTGTGTATTC 58.921 33.333 0.00 0.00 44.59 1.75
1850 2182 5.446143 TGTGAACAATGGTTGTGTATTCC 57.554 39.130 0.00 0.00 44.59 3.01
1851 2183 5.136828 TGTGAACAATGGTTGTGTATTCCT 58.863 37.500 0.00 0.00 44.59 3.36
1852 2184 6.299922 TGTGAACAATGGTTGTGTATTCCTA 58.700 36.000 0.00 0.00 44.59 2.94
1964 3439 7.259882 CAAGCTTGCATAATCAATAACTCCAA 58.740 34.615 14.65 0.00 0.00 3.53
2024 3499 4.099881 AGTTGCATCCACATCAACAAAAGT 59.900 37.500 7.03 0.00 41.67 2.66
2127 3643 2.868964 TGCATAGAAGTACCTCCCCT 57.131 50.000 0.00 0.00 0.00 4.79
2158 3674 0.616111 CTACCACCAGCACCTCTCCT 60.616 60.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 133 3.362399 CTCGTCCCAGTCAGCGCAT 62.362 63.158 11.47 0.00 0.00 4.73
133 134 4.056125 CTCGTCCCAGTCAGCGCA 62.056 66.667 11.47 0.00 0.00 6.09
866 887 4.580167 ACAGTTAGTTCATGTGCACACAAT 59.420 37.500 24.37 11.10 45.41 2.71
985 1317 1.143329 TCCATTGTTGGGGGCCACTA 61.143 55.000 7.61 0.00 43.81 2.74
1105 1437 7.748691 ATTGTGCATCCAGCTTTTTATTTTT 57.251 28.000 0.00 0.00 45.94 1.94
1113 1445 4.018490 TGTCATATTGTGCATCCAGCTTT 58.982 39.130 0.00 0.00 45.94 3.51
1143 1475 4.341806 TCCACAAGTTGATGCACATCTTTT 59.658 37.500 10.54 1.68 36.69 2.27
1503 1835 9.143155 TCTTCTTTATGGTTTTCCTTAAGCTTT 57.857 29.630 3.20 0.00 39.59 3.51
1576 1908 5.490159 CTTGATCTTCTCCTTCAGCTTCTT 58.510 41.667 0.00 0.00 0.00 2.52
1736 2068 4.067896 ACATAAACAGCCAGAGTTCACAG 58.932 43.478 0.00 0.00 0.00 3.66
1825 2157 7.450014 AGGAATACACAACCATTGTTCACATTA 59.550 33.333 0.00 0.00 43.23 1.90
1826 2158 6.267471 AGGAATACACAACCATTGTTCACATT 59.733 34.615 0.00 0.00 43.23 2.71
1827 2159 5.774690 AGGAATACACAACCATTGTTCACAT 59.225 36.000 0.00 0.00 43.23 3.21
1828 2160 5.136828 AGGAATACACAACCATTGTTCACA 58.863 37.500 0.00 0.00 43.23 3.58
1829 2161 5.705609 AGGAATACACAACCATTGTTCAC 57.294 39.130 0.00 0.00 43.23 3.18
1830 2162 9.693739 ATTATAGGAATACACAACCATTGTTCA 57.306 29.630 0.00 0.00 43.23 3.18
1831 2163 9.950680 CATTATAGGAATACACAACCATTGTTC 57.049 33.333 0.00 0.00 43.23 3.18
1832 2164 9.474313 ACATTATAGGAATACACAACCATTGTT 57.526 29.630 0.00 0.00 43.23 2.83
1833 2165 8.902806 CACATTATAGGAATACACAACCATTGT 58.097 33.333 0.00 0.00 46.75 2.71
1834 2166 9.119418 TCACATTATAGGAATACACAACCATTG 57.881 33.333 0.00 0.00 0.00 2.82
1835 2167 9.693739 TTCACATTATAGGAATACACAACCATT 57.306 29.630 0.00 0.00 0.00 3.16
1836 2168 9.120538 GTTCACATTATAGGAATACACAACCAT 57.879 33.333 0.00 0.00 0.00 3.55
1837 2169 8.103935 TGTTCACATTATAGGAATACACAACCA 58.896 33.333 0.00 0.00 0.00 3.67
1838 2170 8.500753 TGTTCACATTATAGGAATACACAACC 57.499 34.615 0.00 0.00 0.00 3.77
1841 2173 9.119418 CCATTGTTCACATTATAGGAATACACA 57.881 33.333 0.00 0.00 0.00 3.72
1842 2174 9.120538 ACCATTGTTCACATTATAGGAATACAC 57.879 33.333 0.00 0.00 0.00 2.90
1843 2175 9.693739 AACCATTGTTCACATTATAGGAATACA 57.306 29.630 0.00 0.00 0.00 2.29
1844 2176 9.950680 CAACCATTGTTCACATTATAGGAATAC 57.049 33.333 0.00 0.00 30.42 1.89
1845 2177 9.693739 ACAACCATTGTTCACATTATAGGAATA 57.306 29.630 0.00 0.00 42.22 1.75
1846 2178 8.469200 CACAACCATTGTTCACATTATAGGAAT 58.531 33.333 0.00 0.00 43.23 3.01
1847 2179 7.450014 ACACAACCATTGTTCACATTATAGGAA 59.550 33.333 0.00 0.00 43.23 3.36
1848 2180 6.945435 ACACAACCATTGTTCACATTATAGGA 59.055 34.615 0.00 0.00 43.23 2.94
1849 2181 7.156876 ACACAACCATTGTTCACATTATAGG 57.843 36.000 0.00 0.00 43.23 2.57
1852 2184 8.250332 GGAATACACAACCATTGTTCACATTAT 58.750 33.333 0.00 0.00 43.23 1.28
1964 3439 6.521427 GCCTGGAATGGACTATCTTGATATGT 60.521 42.308 0.00 0.00 0.00 2.29
2127 3643 3.895656 GCTGGTGGTAGACATACTGGATA 59.104 47.826 0.00 0.00 32.12 2.59
2158 3674 1.833630 CTCCCTCCACATCTGTTGCTA 59.166 52.381 0.00 0.00 0.00 3.49
2288 3816 3.715097 GCTGGGAGAGGTGCTGCT 61.715 66.667 0.00 0.00 34.97 4.24
2540 4167 1.270839 GGTACACAAGCTGCCTCAAGA 60.271 52.381 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.