Multiple sequence alignment - TraesCS4D01G149500

Loading Multiple Alignment...

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 TraesCS4D01G149500 chr4D 100.000 2473 0 0 1 2473 155649659 155647187 0.000000e+00 4567
1 TraesCS4D01G149500 chr4D 97.974 543 11 0 1913 2455 291982604 291983146 0.000000e+00 942
2 TraesCS4D01G149500 chr4D 97.790 543 12 0 1913 2455 208108568 208108026 0.000000e+00 937
3 TraesCS4D01G149500 chr4D 97.606 543 13 0 1913 2455 248874525 248873983 0.000000e+00 931
4 TraesCS4D01G149500 chr4D 97.606 543 11 2 1913 2455 263747951 263747411 0.000000e+00 929
5 TraesCS4D01G149500 chr7D 95.558 1891 75 6 5 1894 585451691 585453573 0.000000e+00 3018
6 TraesCS4D01G149500 chr7D 97.455 550 13 1 1913 2462 447830048 447830596 0.000000e+00 937
7 TraesCS4D01G149500 chr7D 97.610 544 12 1 1913 2455 600000671 600000128 0.000000e+00 931
8 TraesCS4D01G149500 chr7D 90.909 143 8 4 1783 1921 550273965 550274106 1.170000e-43 187
9 TraesCS4D01G149500 chr3D 95.486 1883 67 9 1 1879 524198505 524200373 0.000000e+00 2990
10 TraesCS4D01G149500 chr3D 94.944 1879 76 8 3 1879 7112523 7114384 0.000000e+00 2926
11 TraesCS4D01G149500 chr3D 97.790 543 12 0 1913 2455 326136651 326136109 0.000000e+00 937
12 TraesCS4D01G149500 chr3D 91.447 152 7 6 1783 1929 8302876 8302726 1.160000e-48 204
13 TraesCS4D01G149500 chr3D 93.233 133 7 2 1783 1914 64839524 64839393 6.980000e-46 195
14 TraesCS4D01G149500 chr3D 92.593 135 6 3 1783 1914 578864921 578865054 9.030000e-45 191
15 TraesCS4D01G149500 chr6D 95.392 1888 63 10 1 1879 31859061 31860933 0.000000e+00 2983
16 TraesCS4D01G149500 chr6D 97.426 544 13 1 1913 2455 173999049 173999592 0.000000e+00 926
17 TraesCS4D01G149500 chr6D 93.284 134 7 2 1783 1914 441744263 441744130 1.940000e-46 196
18 TraesCS4D01G149500 chr5D 95.380 1883 65 11 1 1879 365120437 365118573 0.000000e+00 2976
19 TraesCS4D01G149500 chr5D 93.284 134 6 3 1783 1914 304882491 304882359 6.980000e-46 195
20 TraesCS4D01G149500 chr2D 95.372 1880 72 6 1 1879 588796856 588794991 0.000000e+00 2976
21 TraesCS4D01G149500 chr2D 95.266 1880 74 8 1 1879 476878771 476880636 0.000000e+00 2964
22 TraesCS4D01G149500 chr2D 93.233 133 8 1 1783 1914 620173173 620173041 6.980000e-46 195
23 TraesCS4D01G149500 chr1D 95.375 1881 70 9 1 1879 471280902 471282767 0.000000e+00 2976
24 TraesCS4D01G149500 chr1D 95.058 1882 74 11 1 1879 395974540 395976405 0.000000e+00 2942
25 TraesCS4D01G149500 chr1D 97.422 543 14 0 1913 2455 67054954 67055496 0.000000e+00 926
26 TraesCS4D01G149500 chr1B 91.367 139 8 4 1780 1915 334448660 334448523 1.170000e-43 187


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 TraesCS4D01G149500 chr4D 155647187 155649659 2472 True 4567 4567 100.000 1 2473 1 chr4D.!!$R1 2472
1 TraesCS4D01G149500 chr4D 291982604 291983146 542 False 942 942 97.974 1913 2455 1 chr4D.!!$F1 542
2 TraesCS4D01G149500 chr4D 208108026 208108568 542 True 937 937 97.790 1913 2455 1 chr4D.!!$R2 542
3 TraesCS4D01G149500 chr4D 248873983 248874525 542 True 931 931 97.606 1913 2455 1 chr4D.!!$R3 542
4 TraesCS4D01G149500 chr4D 263747411 263747951 540 True 929 929 97.606 1913 2455 1 chr4D.!!$R4 542
5 TraesCS4D01G149500 chr7D 585451691 585453573 1882 False 3018 3018 95.558 5 1894 1 chr7D.!!$F3 1889
6 TraesCS4D01G149500 chr7D 447830048 447830596 548 False 937 937 97.455 1913 2462 1 chr7D.!!$F1 549
7 TraesCS4D01G149500 chr7D 600000128 600000671 543 True 931 931 97.610 1913 2455 1 chr7D.!!$R1 542
8 TraesCS4D01G149500 chr3D 524198505 524200373 1868 False 2990 2990 95.486 1 1879 1 chr3D.!!$F2 1878
9 TraesCS4D01G149500 chr3D 7112523 7114384 1861 False 2926 2926 94.944 3 1879 1 chr3D.!!$F1 1876
10 TraesCS4D01G149500 chr3D 326136109 326136651 542 True 937 937 97.790 1913 2455 1 chr3D.!!$R3 542
11 TraesCS4D01G149500 chr6D 31859061 31860933 1872 False 2983 2983 95.392 1 1879 1 chr6D.!!$F1 1878
12 TraesCS4D01G149500 chr6D 173999049 173999592 543 False 926 926 97.426 1913 2455 1 chr6D.!!$F2 542
13 TraesCS4D01G149500 chr5D 365118573 365120437 1864 True 2976 2976 95.380 1 1879 1 chr5D.!!$R2 1878
14 TraesCS4D01G149500 chr2D 588794991 588796856 1865 True 2976 2976 95.372 1 1879 1 chr2D.!!$R1 1878
15 TraesCS4D01G149500 chr2D 476878771 476880636 1865 False 2964 2964 95.266 1 1879 1 chr2D.!!$F1 1878
16 TraesCS4D01G149500 chr1D 471280902 471282767 1865 False 2976 2976 95.375 1 1879 1 chr1D.!!$F3 1878
17 TraesCS4D01G149500 chr1D 395974540 395976405 1865 False 2942 2942 95.058 1 1879 1 chr1D.!!$F2 1878
18 TraesCS4D01G149500 chr1D 67054954 67055496 542 False 926 926 97.422 1913 2455 1 chr1D.!!$F1 542

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
471 472 0.106335 CGCCATGATCTCCTCTTGCT 59.894 55.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2168 2182 1.064783 GGCGCCAGAAATAGCTTGC 59.935 57.895 24.8 0.0 0.0 4.01 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
57 58 4.087892 AGCCGCGTTGCTCCAGAT 62.088 61.111 4.92 0.00 36.75 2.90
155 156 1.377463 CCTCACTCCTCCTCGACGT 60.377 63.158 0.00 0.00 0.00 4.34
295 296 1.607756 AGCTTGTCGAGGAGCTCCA 60.608 57.895 33.90 11.69 45.68 3.86
337 338 1.413767 CGCCAACGAGATCAAGTCCG 61.414 60.000 0.00 0.00 43.93 4.79
368 369 1.226575 CGATGTCGCTGCCGTCTTA 60.227 57.895 0.00 0.00 35.54 2.10
411 412 3.517140 GCCATTTGATCCGCGCCA 61.517 61.111 0.00 0.00 0.00 5.69
431 432 1.604378 CCCGAGCTCCCATGTCTTT 59.396 57.895 8.47 0.00 0.00 2.52
471 472 0.106335 CGCCATGATCTCCTCTTGCT 59.894 55.000 0.00 0.00 0.00 3.91
588 589 2.284039 TCGGATTGACCCCGTGGA 60.284 61.111 0.00 0.00 46.53 4.02
639 640 2.665000 CCTGCCGCTCTTCTTCCA 59.335 61.111 0.00 0.00 0.00 3.53
784 785 4.476410 CGCGCCACACTCTCGCTA 62.476 66.667 0.00 0.00 45.87 4.26
824 825 2.822399 CGGCCTATCCCTTCGCTT 59.178 61.111 0.00 0.00 0.00 4.68
964 965 2.546494 GCGTGTTGCTTCCTGCTGT 61.546 57.895 0.00 0.00 43.37 4.40
1015 1016 4.082523 CCATGCCCTCGACACCGT 62.083 66.667 0.00 0.00 37.05 4.83
1789 1801 6.936279 TGGTTGTAATAAAGAGTGGAGAGAG 58.064 40.000 0.00 0.00 0.00 3.20
1791 1803 7.093727 TGGTTGTAATAAAGAGTGGAGAGAGAG 60.094 40.741 0.00 0.00 0.00 3.20
1793 1805 8.524487 GTTGTAATAAAGAGTGGAGAGAGAGAA 58.476 37.037 0.00 0.00 0.00 2.87
1854 1867 2.716424 TGGTGGGAGGAGAGACAAAAAT 59.284 45.455 0.00 0.00 0.00 1.82
1895 1908 1.630148 GGAGACGATTCACCAACTCG 58.370 55.000 0.00 0.00 38.34 4.18
1899 1912 2.519377 ACGATTCACCAACTCGTCAA 57.481 45.000 0.00 0.00 41.42 3.18
1900 1913 2.828877 ACGATTCACCAACTCGTCAAA 58.171 42.857 0.00 0.00 41.42 2.69
1901 1914 3.399330 ACGATTCACCAACTCGTCAAAT 58.601 40.909 0.00 0.00 41.42 2.32
1902 1915 4.562082 ACGATTCACCAACTCGTCAAATA 58.438 39.130 0.00 0.00 41.42 1.40
1903 1916 4.625742 ACGATTCACCAACTCGTCAAATAG 59.374 41.667 0.00 0.00 41.42 1.73
1904 1917 4.032900 CGATTCACCAACTCGTCAAATAGG 59.967 45.833 0.00 0.00 0.00 2.57
1905 1918 4.610605 TTCACCAACTCGTCAAATAGGA 57.389 40.909 0.00 0.00 0.00 2.94
1906 1919 4.188247 TCACCAACTCGTCAAATAGGAG 57.812 45.455 0.00 0.00 44.15 3.69
2015 2028 4.433615 GGACGTGATGCCTATATACATGG 58.566 47.826 0.00 0.00 0.00 3.66
2168 2182 8.607441 TTTCCATCATATTAATCTTCCGACAG 57.393 34.615 0.00 0.00 0.00 3.51
2311 2327 0.609151 TTGACAACCCCTTATCGCGA 59.391 50.000 13.09 13.09 0.00 5.87
2319 2335 0.813610 CCCTTATCGCGATGGTTGCA 60.814 55.000 31.05 7.44 0.00 4.08
2455 2471 3.508845 TCCTCTTCAAGGGAAAACCAG 57.491 47.619 0.00 0.00 46.23 4.00
2457 2473 3.977999 TCCTCTTCAAGGGAAAACCAGTA 59.022 43.478 0.00 0.00 46.23 2.74
2458 2474 4.041691 TCCTCTTCAAGGGAAAACCAGTAG 59.958 45.833 0.00 0.00 46.23 2.57
2459 2475 3.751518 TCTTCAAGGGAAAACCAGTAGC 58.248 45.455 0.00 0.00 43.89 3.58
2460 2476 3.137544 TCTTCAAGGGAAAACCAGTAGCA 59.862 43.478 0.00 0.00 43.89 3.49
2461 2477 3.140325 TCAAGGGAAAACCAGTAGCAG 57.860 47.619 0.00 0.00 43.89 4.24
2462 2478 2.162681 CAAGGGAAAACCAGTAGCAGG 58.837 52.381 0.00 0.00 43.89 4.85
2463 2479 1.742308 AGGGAAAACCAGTAGCAGGA 58.258 50.000 0.00 0.00 43.89 3.86
2464 2480 2.062636 AGGGAAAACCAGTAGCAGGAA 58.937 47.619 0.00 0.00 43.89 3.36
2465 2481 2.160205 GGGAAAACCAGTAGCAGGAAC 58.840 52.381 0.00 0.00 39.85 3.62
2466 2482 2.160205 GGAAAACCAGTAGCAGGAACC 58.840 52.381 0.00 0.00 0.00 3.62
2467 2483 2.488347 GGAAAACCAGTAGCAGGAACCA 60.488 50.000 0.00 0.00 0.00 3.67
2468 2484 2.271944 AAACCAGTAGCAGGAACCAC 57.728 50.000 0.00 0.00 0.00 4.16
2469 2485 0.400594 AACCAGTAGCAGGAACCACC 59.599 55.000 0.00 0.00 39.35 4.61
2470 2486 1.079127 CCAGTAGCAGGAACCACCG 60.079 63.158 0.00 0.00 44.74 4.94
2471 2487 1.741770 CAGTAGCAGGAACCACCGC 60.742 63.158 0.00 0.00 44.74 5.68
2472 2488 2.214216 AGTAGCAGGAACCACCGCA 61.214 57.895 0.00 0.00 44.74 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
155 156 0.999712 GAAGTGGATTTGGGAGGGGA 59.000 55.000 0.00 0.00 0.00 4.81
203 204 1.733399 GGCGTCTGACTTCGTCCAC 60.733 63.158 6.21 0.00 0.00 4.02
295 296 0.319297 ACGAAGTAGCGAAGGCGTTT 60.319 50.000 0.00 0.00 46.35 3.60
353 354 1.211969 GAGTAAGACGGCAGCGACA 59.788 57.895 0.00 0.00 0.00 4.35
368 369 2.520968 GGTGGCCCAAGGTTGAGT 59.479 61.111 0.00 0.00 0.00 3.41
397 398 2.828549 GGGTGGCGCGGATCAAAT 60.829 61.111 8.83 0.00 0.00 2.32
411 412 3.083997 GACATGGGAGCTCGGGGT 61.084 66.667 7.83 3.06 0.00 4.95
431 432 2.366301 TCAATGGCGCCCTAGGGA 60.366 61.111 33.21 11.15 37.50 4.20
471 472 1.427753 GAGAGGGGAAACAGGGGAAAA 59.572 52.381 0.00 0.00 0.00 2.29
588 589 1.526917 GCATAGGAGCGGGCATGTT 60.527 57.895 0.00 0.00 0.00 2.71
722 723 4.935495 CAGTGGTGCGGTGGCTGT 62.935 66.667 0.00 0.00 40.82 4.40
808 809 1.894282 GCAAGCGAAGGGATAGGCC 60.894 63.158 0.00 0.00 0.00 5.19
849 850 2.203056 CATGATTGGAGGCGGCGA 60.203 61.111 12.98 0.00 0.00 5.54
943 944 2.546494 GCAGGAAGCAACACGCAGT 61.546 57.895 0.00 0.00 46.13 4.40
964 965 4.730081 CGGTAGAGCAGCGCATAA 57.270 55.556 11.47 0.00 41.87 1.90
1015 1016 2.024868 CCGCCACATTTGTCGACGA 61.025 57.895 11.62 6.16 0.00 4.20
1019 1020 2.398554 CCCTCCGCCACATTTGTCG 61.399 63.158 0.00 0.00 0.00 4.35
1326 1333 9.176460 CAATAAAACCCCATTTGCATAGAAATT 57.824 29.630 0.00 0.00 0.00 1.82
1575 1587 9.487790 GATTCCTTTTATTGGTTCAATTTGTCA 57.512 29.630 0.00 0.00 35.54 3.58
1681 1693 9.942850 ATCGATTCCTTTTATTGGTTCAATTTT 57.057 25.926 0.00 0.00 35.54 1.82
1789 1801 6.344702 CGCGGTTTATTTTCACTGTTTTTCTC 60.345 38.462 0.00 0.00 0.00 2.87
1791 1803 5.331980 CCGCGGTTTATTTTCACTGTTTTTC 60.332 40.000 19.50 0.00 0.00 2.29
1793 1805 4.045783 CCGCGGTTTATTTTCACTGTTTT 58.954 39.130 19.50 0.00 0.00 2.43
1825 1837 4.354943 CCTCCCACCACCCCCTCT 62.355 72.222 0.00 0.00 0.00 3.69
1854 1867 3.667430 CGCGGTTTATTTTCGCTGGTTTA 60.667 43.478 0.00 0.00 46.23 2.01
1905 1918 8.497730 CCAGCATGCATCTAGAGTATCTCTACT 61.498 44.444 21.98 0.00 39.48 2.57
1906 1919 6.404623 CCAGCATGCATCTAGAGTATCTCTAC 60.405 46.154 21.98 0.00 39.48 2.59
1907 1920 5.651576 CCAGCATGCATCTAGAGTATCTCTA 59.348 44.000 21.98 6.37 39.48 2.43
1908 1921 4.463539 CCAGCATGCATCTAGAGTATCTCT 59.536 45.833 21.98 4.69 39.48 3.10
1909 1922 4.462132 TCCAGCATGCATCTAGAGTATCTC 59.538 45.833 21.98 0.00 39.48 2.75
1910 1923 4.414677 TCCAGCATGCATCTAGAGTATCT 58.585 43.478 21.98 0.00 42.72 1.98
1911 1924 4.797800 TCCAGCATGCATCTAGAGTATC 57.202 45.455 21.98 0.00 31.97 2.24
2168 2182 1.064783 GGCGCCAGAAATAGCTTGC 59.935 57.895 24.80 0.00 0.00 4.01
2311 2327 6.997476 ACAAACAAATAAATCCTTGCAACCAT 59.003 30.769 0.00 0.00 0.00 3.55
2319 2335 7.151976 GCACCTACACAAACAAATAAATCCTT 58.848 34.615 0.00 0.00 0.00 3.36
2455 2471 2.345991 TGCGGTGGTTCCTGCTAC 59.654 61.111 0.00 0.00 36.93 3.58


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

AutoCloner maintained by Alex Coulton.