Multiple sequence alignment - TraesCS7D01G327400

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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 TraesCS7D01G327400 chr7D 100.000 2615 0 0 1 2615 418388387 418391001 0.000000e+00 4830.0
1 TraesCS7D01G327400 chr7D 93.361 1943 85 17 1 1909 418897891 418899823 0.000000e+00 2833.0
2 TraesCS7D01G327400 chr7D 89.813 697 54 8 957 1642 418050787 418051477 0.000000e+00 878.0
3 TraesCS7D01G327400 chr7D 85.732 827 77 20 844 1645 449507894 449508704 0.000000e+00 835.0
4 TraesCS7D01G327400 chr7D 88.551 690 54 7 957 1642 417925794 417926462 0.000000e+00 813.0
5 TraesCS7D01G327400 chr7D 89.645 647 44 11 807 1431 418596656 418597301 0.000000e+00 802.0
6 TraesCS7D01G327400 chr7D 85.524 677 95 3 1942 2615 19202498 19201822 0.000000e+00 704.0
7 TraesCS7D01G327400 chr7D 94.472 398 14 3 1427 1820 418611444 418611837 8.000000e-170 606.0
8 TraesCS7D01G327400 chr7D 96.970 66 2 0 1805 1870 418611855 418611920 7.650000e-21 111.0
9 TraesCS7D01G327400 chr7D 97.368 38 1 0 1872 1909 418611937 418611974 6.040000e-07 65.8
10 TraesCS7D01G327400 chr7B 93.810 1147 49 9 780 1909 434357712 434358853 0.000000e+00 1705.0
11 TraesCS7D01G327400 chr7B 90.509 864 61 9 812 1657 433865820 433866680 0.000000e+00 1122.0
12 TraesCS7D01G327400 chr7B 87.646 939 77 16 884 1801 212781780 212780860 0.000000e+00 1055.0
13 TraesCS7D01G327400 chr7B 90.949 685 46 9 818 1487 434160210 434160893 0.000000e+00 907.0
14 TraesCS7D01G327400 chr7B 92.308 247 10 4 1667 1909 434166414 434166655 2.490000e-90 342.0
15 TraesCS7D01G327400 chr7A 90.360 861 56 7 807 1642 483485310 483486168 0.000000e+00 1105.0
16 TraesCS7D01G327400 chr7A 88.746 702 72 3 576 1272 483652556 483653255 0.000000e+00 852.0
17 TraesCS7D01G327400 chr7A 90.698 430 27 10 807 1224 483756945 483757373 6.320000e-156 560.0
18 TraesCS7D01G327400 chr7A 79.551 401 54 22 1489 1876 514707118 514706733 7.180000e-66 261.0
19 TraesCS7D01G327400 chr7A 83.243 185 13 12 1688 1870 483486384 483486552 1.250000e-33 154.0
20 TraesCS7D01G327400 chr7A 91.525 59 5 0 1818 1876 483942678 483942736 6.000000e-12 82.4
21 TraesCS7D01G327400 chr4B 89.853 680 65 3 1940 2615 132342865 132342186 0.000000e+00 870.0
22 TraesCS7D01G327400 chr1B 89.004 673 71 2 1946 2615 95363265 95362593 0.000000e+00 830.0
23 TraesCS7D01G327400 chr1B 84.536 679 96 5 1941 2613 541015438 541014763 0.000000e+00 664.0
24 TraesCS7D01G327400 chr5D 88.496 678 75 2 1941 2615 246281657 246280980 0.000000e+00 817.0
25 TraesCS7D01G327400 chr5D 84.077 672 103 3 1945 2613 196404976 196404306 0.000000e+00 645.0
26 TraesCS7D01G327400 chr5D 76.221 307 47 20 215 519 227168160 227167878 3.510000e-29 139.0
27 TraesCS7D01G327400 chr6D 87.704 675 79 3 1941 2612 34517006 34516333 0.000000e+00 784.0
28 TraesCS7D01G327400 chr6D 91.250 80 6 1 429 507 20780165 20780244 9.900000e-20 108.0
29 TraesCS7D01G327400 chr2D 87.593 669 80 2 1941 2606 414992217 414992885 0.000000e+00 773.0
30 TraesCS7D01G327400 chr2D 82.166 157 17 8 432 582 641195386 641195537 9.830000e-25 124.0
31 TraesCS7D01G327400 chr2B 83.308 653 101 6 1966 2615 360051341 360051988 1.730000e-166 595.0


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 TraesCS7D01G327400 chr7D 418388387 418391001 2614 False 4830.000000 4830 100.0000 1 2615 1 chr7D.!!$F3 2614
1 TraesCS7D01G327400 chr7D 418897891 418899823 1932 False 2833.000000 2833 93.3610 1 1909 1 chr7D.!!$F5 1908
2 TraesCS7D01G327400 chr7D 418050787 418051477 690 False 878.000000 878 89.8130 957 1642 1 chr7D.!!$F2 685
3 TraesCS7D01G327400 chr7D 449507894 449508704 810 False 835.000000 835 85.7320 844 1645 1 chr7D.!!$F6 801
4 TraesCS7D01G327400 chr7D 417925794 417926462 668 False 813.000000 813 88.5510 957 1642 1 chr7D.!!$F1 685
5 TraesCS7D01G327400 chr7D 418596656 418597301 645 False 802.000000 802 89.6450 807 1431 1 chr7D.!!$F4 624
6 TraesCS7D01G327400 chr7D 19201822 19202498 676 True 704.000000 704 85.5240 1942 2615 1 chr7D.!!$R1 673
7 TraesCS7D01G327400 chr7D 418611444 418611974 530 False 260.933333 606 96.2700 1427 1909 3 chr7D.!!$F7 482
8 TraesCS7D01G327400 chr7B 434357712 434358853 1141 False 1705.000000 1705 93.8100 780 1909 1 chr7B.!!$F4 1129
9 TraesCS7D01G327400 chr7B 433865820 433866680 860 False 1122.000000 1122 90.5090 812 1657 1 chr7B.!!$F1 845
10 TraesCS7D01G327400 chr7B 212780860 212781780 920 True 1055.000000 1055 87.6460 884 1801 1 chr7B.!!$R1 917
11 TraesCS7D01G327400 chr7B 434160210 434160893 683 False 907.000000 907 90.9490 818 1487 1 chr7B.!!$F2 669
12 TraesCS7D01G327400 chr7A 483652556 483653255 699 False 852.000000 852 88.7460 576 1272 1 chr7A.!!$F1 696
13 TraesCS7D01G327400 chr7A 483485310 483486552 1242 False 629.500000 1105 86.8015 807 1870 2 chr7A.!!$F4 1063
14 TraesCS7D01G327400 chr4B 132342186 132342865 679 True 870.000000 870 89.8530 1940 2615 1 chr4B.!!$R1 675
15 TraesCS7D01G327400 chr1B 95362593 95363265 672 True 830.000000 830 89.0040 1946 2615 1 chr1B.!!$R1 669
16 TraesCS7D01G327400 chr1B 541014763 541015438 675 True 664.000000 664 84.5360 1941 2613 1 chr1B.!!$R2 672
17 TraesCS7D01G327400 chr5D 246280980 246281657 677 True 817.000000 817 88.4960 1941 2615 1 chr5D.!!$R3 674
18 TraesCS7D01G327400 chr5D 196404306 196404976 670 True 645.000000 645 84.0770 1945 2613 1 chr5D.!!$R1 668
19 TraesCS7D01G327400 chr6D 34516333 34517006 673 True 784.000000 784 87.7040 1941 2612 1 chr6D.!!$R1 671
20 TraesCS7D01G327400 chr2D 414992217 414992885 668 False 773.000000 773 87.5930 1941 2606 1 chr2D.!!$F1 665
21 TraesCS7D01G327400 chr2B 360051341 360051988 647 False 595.000000 595 83.3080 1966 2615 1 chr2B.!!$F1 649

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
682 690 0.925466 AAATATGTACGGACGCACGC 59.075 50.0 0.0 0.0 37.37 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1937 2273 0.24445 ATCATGGCCACGCTTTTGTG 59.756 50.0 8.16 0.0 39.6 3.33 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 4.997905 TCAAGAGCATCGTCTTTTGAAG 57.002 40.909 5.92 0.00 42.67 3.02
48 49 6.262049 TCGTCTTTTGAAGAATGGATGAACAA 59.738 34.615 0.00 0.00 39.67 2.83
88 89 9.862585 GGTGAACAAAATTTCAATTTGATGTAC 57.137 29.630 0.00 0.00 39.56 2.90
462 470 2.034436 AGGTTCGGGGAAGGTTCTAA 57.966 50.000 0.00 0.00 0.00 2.10
587 595 2.158310 CCAAATAGGAATTCCCCTCCCC 60.158 54.545 21.22 0.00 41.22 4.81
612 620 4.504112 TTCCGGTTTGCGGGAAAT 57.496 50.000 0.00 0.00 46.63 2.17
620 628 2.162809 GGTTTGCGGGAAATATGACGTT 59.837 45.455 0.00 0.00 0.00 3.99
652 660 7.277205 GCTGAACAGATCGATATAAAACTTCG 58.723 38.462 0.00 0.00 0.00 3.79
682 690 0.925466 AAATATGTACGGACGCACGC 59.075 50.000 0.00 0.00 37.37 5.34
714 722 2.654877 GGCGGTTTGAGAGTCGGA 59.345 61.111 0.00 0.00 0.00 4.55
823 831 4.710375 TGTAAGACACTAGAATCTGACCCC 59.290 45.833 0.00 0.00 0.00 4.95
826 834 2.832129 GACACTAGAATCTGACCCCACA 59.168 50.000 0.00 0.00 0.00 4.17
846 854 5.288804 CACAAAAGGACGTGGAAATCAAAT 58.711 37.500 0.00 0.00 0.00 2.32
847 855 5.402270 CACAAAAGGACGTGGAAATCAAATC 59.598 40.000 0.00 0.00 0.00 2.17
902 923 1.450669 GGAATTGGACGCCGCCTAA 60.451 57.895 0.00 0.00 0.00 2.69
1118 1165 2.437343 GCTTCGTCAGGTTCGAGCG 61.437 63.158 0.00 0.00 38.52 5.03
1349 1414 1.529438 GTTTGAGATCAACAACGGCGA 59.471 47.619 16.62 0.00 35.28 5.54
1351 1416 0.032815 TGAGATCAACAACGGCGACA 59.967 50.000 16.62 0.00 0.00 4.35
1352 1417 1.144969 GAGATCAACAACGGCGACAA 58.855 50.000 16.62 0.00 0.00 3.18
1734 2006 6.101332 AGTAATAGATTGTCGCCGTGTTTAA 58.899 36.000 0.00 0.00 0.00 1.52
1745 2017 2.855187 GCCGTGTTTAATGTTTGTCGCA 60.855 45.455 0.00 0.00 0.00 5.10
1870 2191 6.455360 AACATAACTCGATTTGATGCCATT 57.545 33.333 0.00 0.00 0.00 3.16
1909 2245 5.450550 GGCAAGCAAACTTAACTCTTGAGTT 60.451 40.000 18.32 18.32 40.69 3.01
1910 2246 6.036470 GCAAGCAAACTTAACTCTTGAGTTT 58.964 36.000 19.28 6.11 46.41 2.66
1916 2252 5.175090 ACTTAACTCTTGAGTTTGCTTGC 57.825 39.130 19.28 0.00 33.59 4.01
1917 2253 4.036852 ACTTAACTCTTGAGTTTGCTTGCC 59.963 41.667 19.28 0.00 33.59 4.52
1918 2254 0.947244 ACTCTTGAGTTTGCTTGCCG 59.053 50.000 0.00 0.00 0.00 5.69
1919 2255 1.229428 CTCTTGAGTTTGCTTGCCGA 58.771 50.000 0.00 0.00 0.00 5.54
1920 2256 1.196354 CTCTTGAGTTTGCTTGCCGAG 59.804 52.381 0.00 0.00 0.00 4.63
1981 2318 2.183300 GACGTGATGGCGGTGCTA 59.817 61.111 0.00 0.00 35.98 3.49
2106 2445 1.485019 CCCCATCAGCCTCCCATAGTA 60.485 57.143 0.00 0.00 0.00 1.82
2282 2621 0.550914 AGGCCAGTGTGTTCCTCAAA 59.449 50.000 5.01 0.00 0.00 2.69
2315 2654 3.073274 AGGGCTTTTGACTCGCTTAAT 57.927 42.857 0.00 0.00 0.00 1.40
2327 2666 4.813027 ACTCGCTTAATTGGTCGTTTCTA 58.187 39.130 0.00 0.00 0.00 2.10
2365 2704 5.353394 AGCAAAGGATTCGGTCATAAGTA 57.647 39.130 0.00 0.00 0.00 2.24
2434 2773 0.321034 GTCAACGGGGTTCCTGGTAC 60.321 60.000 0.00 0.00 33.40 3.34
2510 2849 3.007940 TCTTTGTGATCTCCATGGACGTT 59.992 43.478 11.44 2.46 0.00 3.99
2571 2910 3.423539 TTAGCAGTTTCACTGGCATCT 57.576 42.857 6.05 0.00 46.01 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.870826 TCAAAAGACGATGCTCTTGAATAAAA 58.129 30.769 0.00 0.00 30.54 1.52
12 13 5.702670 TCTTCAAAAGACGATGCTCTTGAAT 59.297 36.000 0.00 0.00 33.62 2.57
25 26 8.822652 AATTGTTCATCCATTCTTCAAAAGAC 57.177 30.769 0.00 0.00 37.23 3.01
35 36 8.853469 TTTTTGCAAAAATTGTTCATCCATTC 57.147 26.923 28.85 0.00 33.29 2.67
392 400 6.609616 TCTTTTGGGTGTTTCTTCCTTGTTAT 59.390 34.615 0.00 0.00 0.00 1.89
443 451 2.034436 TTAGAACCTTCCCCGAACCT 57.966 50.000 0.00 0.00 0.00 3.50
462 470 3.181459 CCAATCCGGTTTTGGAAAGGTTT 60.181 43.478 25.46 0.00 45.35 3.27
472 480 2.233676 GGCTTTCATCCAATCCGGTTTT 59.766 45.455 0.00 0.00 35.57 2.43
587 595 1.065031 CGCAAACCGGAAGCAAATCG 61.065 55.000 9.46 0.00 0.00 3.34
612 620 1.018910 TCAGCGATCCGAACGTCATA 58.981 50.000 0.00 0.00 0.00 2.15
620 628 0.029433 CGATCTGTTCAGCGATCCGA 59.971 55.000 0.00 0.00 34.04 4.55
652 660 6.128902 CGTCCGTACATATTTTTAGATCCAGC 60.129 42.308 0.00 0.00 0.00 4.85
682 690 2.969827 GCCCCCAATCGTTTGTGG 59.030 61.111 5.55 3.34 30.78 4.17
714 722 4.039603 ACTAGTACTAGGGTTCCAACGT 57.960 45.455 29.05 6.58 37.49 3.99
813 821 2.814097 CGTCCTTTTGTGGGGTCAGATT 60.814 50.000 0.00 0.00 0.00 2.40
823 831 3.980646 TGATTTCCACGTCCTTTTGTG 57.019 42.857 0.00 0.00 35.87 3.33
826 834 4.320935 CGGATTTGATTTCCACGTCCTTTT 60.321 41.667 0.00 0.00 32.45 2.27
841 849 1.006825 CACGTGCGACTCGGATTTGA 61.007 55.000 0.82 0.00 0.00 2.69
842 850 1.416049 CACGTGCGACTCGGATTTG 59.584 57.895 0.82 0.00 0.00 2.32
1072 1119 4.016706 CTCGCCGTTCCCTGGGTT 62.017 66.667 13.56 0.00 0.00 4.11
1077 1124 4.379243 CACAGCTCGCCGTTCCCT 62.379 66.667 0.00 0.00 0.00 4.20
1349 1414 4.681978 GGACGCGCTCCACCTTGT 62.682 66.667 18.80 0.75 39.21 3.16
1383 1451 1.420430 TGGGAAAGTTCACGAGGAGT 58.580 50.000 0.00 0.00 31.75 3.85
1394 1462 0.552848 ATGCGGATCCATGGGAAAGT 59.447 50.000 13.02 0.00 34.34 2.66
1482 1550 3.303135 AGCTCCTTGACGCCACGA 61.303 61.111 0.00 0.00 0.00 4.35
1659 1926 7.602644 TCGTAACAGCTAATCATTCAAGAGTTT 59.397 33.333 0.00 0.00 0.00 2.66
1788 2060 3.833545 TGACTCGTTAGCTTCAGTCTC 57.166 47.619 0.00 0.00 36.91 3.36
1825 2131 1.888512 CATGGTGTGAAAGGTTGAGGG 59.111 52.381 0.00 0.00 0.00 4.30
1870 2191 7.444792 AGTTTGCTTGCCAATATTGATCAAAAA 59.555 29.630 17.23 13.63 32.49 1.94
1928 2264 4.404654 GCTTTTGTGCCCGCTCCG 62.405 66.667 0.00 0.00 0.00 4.63
1929 2265 4.404654 CGCTTTTGTGCCCGCTCC 62.405 66.667 0.00 0.00 0.00 4.70
1930 2266 3.660111 ACGCTTTTGTGCCCGCTC 61.660 61.111 0.00 0.00 0.00 5.03
1931 2267 3.964875 CACGCTTTTGTGCCCGCT 61.965 61.111 0.00 0.00 32.31 5.52
1932 2268 4.999939 CCACGCTTTTGTGCCCGC 63.000 66.667 0.00 0.00 38.55 6.13
1933 2269 4.999939 GCCACGCTTTTGTGCCCG 63.000 66.667 0.00 0.00 38.55 6.13
1934 2270 4.662961 GGCCACGCTTTTGTGCCC 62.663 66.667 0.00 0.00 38.55 5.36
1935 2271 3.225069 ATGGCCACGCTTTTGTGCC 62.225 57.895 8.16 0.00 38.55 5.01
1936 2272 2.023223 CATGGCCACGCTTTTGTGC 61.023 57.895 8.16 0.00 38.55 4.57
1937 2273 0.244450 ATCATGGCCACGCTTTTGTG 59.756 50.000 8.16 0.00 39.60 3.33
1938 2274 0.527565 GATCATGGCCACGCTTTTGT 59.472 50.000 8.16 0.00 0.00 2.83
1939 2275 0.527113 TGATCATGGCCACGCTTTTG 59.473 50.000 8.16 0.07 0.00 2.44
1981 2318 4.504858 CATCTCCCACGTAAAGCTTTAGT 58.495 43.478 19.16 15.28 0.00 2.24
2282 2621 6.049790 GTCAAAAGCCCTAGAAATATCGAGT 58.950 40.000 0.00 0.00 0.00 4.18
2315 2654 3.256383 TCACCTCGAATAGAAACGACCAA 59.744 43.478 0.00 0.00 34.82 3.67
2327 2666 1.489481 TGCTCCTCATCACCTCGAAT 58.511 50.000 0.00 0.00 0.00 3.34
2365 2704 5.046014 AGCAGAATCAAGATCCAAGTACACT 60.046 40.000 0.00 0.00 0.00 3.55
2434 2773 1.667724 CCTTAGCGTGGATGAAGCTTG 59.332 52.381 2.10 0.00 40.27 4.01
2510 2849 4.738839 GCCTTGATCATGATTCTCGACAGA 60.739 45.833 10.14 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.