Multiple sequence alignment - TraesCS3D01G292200

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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 TraesCS3D01G292200 chr3D 100.000 2466 0 0 1 2466 402462548 402465013 0.000000e+00 4554.0
1 TraesCS3D01G292200 chr3D 81.919 271 36 10 326 583 19531230 19531500 1.490000e-52 217.0
2 TraesCS3D01G292200 chr3D 78.523 149 27 5 95 240 140782364 140782218 2.610000e-15 93.5
3 TraesCS3D01G292200 chr3A 95.995 1723 49 9 753 2466 523315570 523317281 0.000000e+00 2782.0
4 TraesCS3D01G292200 chr3A 86.990 515 46 12 1 510 523309661 523310159 5.960000e-156 560.0
5 TraesCS3D01G292200 chr3A 86.861 274 15 10 509 767 523315343 523315610 1.120000e-73 287.0
6 TraesCS3D01G292200 chr3A 79.195 149 26 5 95 240 158593918 158593772 5.610000e-17 99.0
7 TraesCS3D01G292200 chr3B 95.872 1720 41 11 753 2466 527899628 527901323 0.000000e+00 2756.0
8 TraesCS3D01G292200 chr3B 88.317 796 48 27 1 767 527898891 527899670 0.000000e+00 913.0
9 TraesCS3D01G292200 chr2A 86.923 260 24 10 326 578 520623295 520623551 1.440000e-72 283.0
10 TraesCS3D01G292200 chr6D 83.562 292 35 11 301 582 470606767 470606479 6.760000e-66 261.0
11 TraesCS3D01G292200 chr6D 85.200 250 24 9 350 592 459756625 459756868 6.810000e-61 244.0
12 TraesCS3D01G292200 chr6B 84.962 266 31 9 322 582 720556759 720557020 6.760000e-66 261.0
13 TraesCS3D01G292200 chr1D 83.908 261 32 8 329 586 341371534 341371281 8.810000e-60 241.0
14 TraesCS3D01G292200 chr1D 83.026 271 34 10 328 592 299564442 299564178 4.100000e-58 235.0
15 TraesCS3D01G292200 chr1D 82.270 282 30 15 327 600 341371283 341371552 2.470000e-55 226.0
16 TraesCS3D01G292200 chr1D 79.866 149 24 6 94 238 415213045 415213191 1.210000e-18 104.0
17 TraesCS3D01G292200 chr1A 85.714 56 8 0 161 216 579546795 579546740 2.650000e-05 60.2


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 TraesCS3D01G292200 chr3D 402462548 402465013 2465 False 4554.0 4554 100.0000 1 2466 1 chr3D.!!$F2 2465
1 TraesCS3D01G292200 chr3A 523315343 523317281 1938 False 1534.5 2782 91.4280 509 2466 2 chr3A.!!$F2 1957
2 TraesCS3D01G292200 chr3B 527898891 527901323 2432 False 1834.5 2756 92.0945 1 2466 2 chr3B.!!$F1 2465

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
501 508 0.941542 TTTTTCTCACGCCTTCCACG 59.058 50.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2073 2131 0.17668 TGTTGCCGTGCACCATTTTT 59.823 45.0 12.15 0.0 38.71 1.94 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
106 109 5.323371 TGCCCATAGCTTTATTCAAACAC 57.677 39.130 0.00 0.00 44.23 3.32
109 112 5.730568 GCCCATAGCTTTATTCAAACACGAG 60.731 44.000 0.00 0.00 38.99 4.18
116 119 8.492673 AGCTTTATTCAAACACGAGATCATTA 57.507 30.769 0.00 0.00 0.00 1.90
284 288 1.002544 AGTACCCTTGTGAGCTTGAGC 59.997 52.381 0.00 0.00 42.49 4.26
286 290 2.037136 CCCTTGTGAGCTTGAGCCG 61.037 63.158 0.00 0.00 43.38 5.52
298 302 2.079158 CTTGAGCCGAAATGAGCTTGA 58.921 47.619 0.00 0.00 40.11 3.02
386 392 7.397892 TGACAAATGTTCTAAGTGTTTGGAA 57.602 32.000 0.00 0.00 34.87 3.53
405 412 9.657419 GTTTGGAAATTTTTATCATGGATCACT 57.343 29.630 0.00 0.00 0.00 3.41
410 417 9.573133 GAAATTTTTATCATGGATCACTTTCGT 57.427 29.630 0.00 0.00 0.00 3.85
479 486 6.183360 CGAAAGTAGCATTTTTGGAGCATCTA 60.183 38.462 0.00 0.00 33.73 1.98
501 508 0.941542 TTTTTCTCACGCCTTCCACG 59.058 50.000 0.00 0.00 0.00 4.94
653 672 5.294552 GCAATTAGACCAGAATAGCGAAACT 59.705 40.000 0.00 0.00 0.00 2.66
673 692 2.400399 TGCTACTTCGGTTCTCAAACG 58.600 47.619 0.00 0.00 36.16 3.60
701 720 6.993786 AAAAAGAGAGAGCCTTAACTATGC 57.006 37.500 0.00 0.00 0.00 3.14
761 792 7.784633 TTTTTCTTTGAGCAAATGGGTTAAG 57.215 32.000 0.00 0.00 0.00 1.85
762 793 4.519540 TCTTTGAGCAAATGGGTTAAGC 57.480 40.909 0.00 0.00 0.00 3.09
763 794 3.894427 TCTTTGAGCAAATGGGTTAAGCA 59.106 39.130 7.03 0.00 0.00 3.91
764 795 3.940209 TTGAGCAAATGGGTTAAGCAG 57.060 42.857 7.03 0.00 0.00 4.24
765 796 1.545582 TGAGCAAATGGGTTAAGCAGC 59.454 47.619 7.03 2.55 0.00 5.25
766 797 1.821136 GAGCAAATGGGTTAAGCAGCT 59.179 47.619 7.03 7.17 0.00 4.24
767 798 2.232208 GAGCAAATGGGTTAAGCAGCTT 59.768 45.455 13.46 13.46 0.00 3.74
768 799 2.634453 AGCAAATGGGTTAAGCAGCTTT 59.366 40.909 14.29 0.00 0.00 3.51
769 800 3.071457 AGCAAATGGGTTAAGCAGCTTTT 59.929 39.130 14.29 0.00 0.00 2.27
770 801 4.283212 AGCAAATGGGTTAAGCAGCTTTTA 59.717 37.500 14.29 0.00 0.00 1.52
771 802 5.046376 AGCAAATGGGTTAAGCAGCTTTTAT 60.046 36.000 14.29 0.00 0.00 1.40
772 803 5.643348 GCAAATGGGTTAAGCAGCTTTTATT 59.357 36.000 14.29 4.82 0.00 1.40
773 804 6.149308 GCAAATGGGTTAAGCAGCTTTTATTT 59.851 34.615 14.29 10.14 0.00 1.40
774 805 7.308529 GCAAATGGGTTAAGCAGCTTTTATTTT 60.309 33.333 14.29 4.12 0.00 1.82
775 806 8.567104 CAAATGGGTTAAGCAGCTTTTATTTTT 58.433 29.630 14.29 4.64 0.00 1.94
890 922 1.745653 GGTCAATAAGGTGAAGCTGCC 59.254 52.381 0.00 0.00 0.00 4.85
892 924 1.003118 TCAATAAGGTGAAGCTGCCGT 59.997 47.619 0.00 0.00 0.00 5.68
897 929 2.358003 GTGAAGCTGCCGTGCTCT 60.358 61.111 0.00 0.00 43.24 4.09
898 930 2.047844 TGAAGCTGCCGTGCTCTC 60.048 61.111 0.00 0.00 43.24 3.20
899 931 2.817396 GAAGCTGCCGTGCTCTCC 60.817 66.667 0.00 0.00 43.24 3.71
900 932 3.596066 GAAGCTGCCGTGCTCTCCA 62.596 63.158 0.00 0.00 43.24 3.86
901 933 2.866085 GAAGCTGCCGTGCTCTCCAT 62.866 60.000 0.00 0.00 43.24 3.41
902 934 2.437359 GCTGCCGTGCTCTCCATT 60.437 61.111 0.00 0.00 0.00 3.16
903 935 2.467826 GCTGCCGTGCTCTCCATTC 61.468 63.158 0.00 0.00 0.00 2.67
952 989 1.702957 AGCAGTGTAGGGTTTTAGCCA 59.297 47.619 0.00 0.00 38.48 4.75
1202 1239 2.053627 GCATTCGTTTTGCCACTTGAG 58.946 47.619 0.00 0.00 33.95 3.02
1214 1251 2.297033 GCCACTTGAGCTGGATGAAAAA 59.703 45.455 0.00 0.00 0.00 1.94
1249 1286 0.613572 TCGGCATCTGTAGGTCACCA 60.614 55.000 0.00 0.00 0.00 4.17
1363 1400 2.041153 CACTGGGTTTGGTTGGCTC 58.959 57.895 0.00 0.00 0.00 4.70
1475 1520 5.236478 TGTTGAGCAGACTAGTTTTAGTTGC 59.764 40.000 0.00 1.46 40.21 4.17
1521 1566 1.354506 GGCTGATCACAAGCGCATC 59.645 57.895 11.47 3.59 0.00 3.91
1900 1945 4.227197 TCAAGCCCCAAAAGGTGAATAAA 58.773 39.130 0.00 0.00 0.00 1.40
1901 1946 4.039852 TCAAGCCCCAAAAGGTGAATAAAC 59.960 41.667 0.00 0.00 0.00 2.01
1902 1947 2.903784 AGCCCCAAAAGGTGAATAAACC 59.096 45.455 0.00 0.00 40.85 3.27
2073 2131 3.883830 AAGTGTGTTGCCATCACAAAA 57.116 38.095 10.03 0.00 45.36 2.44
2105 2164 2.670905 ACGGCAACAAAAGCTTCAAAAC 59.329 40.909 0.00 0.00 0.00 2.43
2130 2189 8.630037 ACACCTTTTGGCTATTATTATAGTTGC 58.370 33.333 1.02 0.00 45.59 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 9.628746 GTATTACTTTTTCCCGCAAAAATAAGA 57.371 29.630 4.31 2.33 42.02 2.10
85 88 4.095782 TCGTGTTTGAATAAAGCTATGGGC 59.904 41.667 0.00 0.00 42.19 5.36
92 95 8.175069 TGTAATGATCTCGTGTTTGAATAAAGC 58.825 33.333 0.00 0.00 0.00 3.51
106 109 5.448225 AGCATTGCACTTTGTAATGATCTCG 60.448 40.000 17.82 0.00 43.59 4.04
109 112 6.183360 CCAAAGCATTGCACTTTGTAATGATC 60.183 38.462 20.56 4.48 45.59 2.92
192 196 5.776173 ATCACGAGGAAGGTGTATCTAAG 57.224 43.478 0.00 0.00 36.76 2.18
249 253 5.789643 AGGGTACTTTCACGTGTAAAGTA 57.210 39.130 29.21 29.21 43.54 2.24
256 260 2.800544 CTCACAAGGGTACTTTCACGTG 59.199 50.000 9.94 9.94 33.81 4.49
284 288 4.424061 TGTTCATTCAAGCTCATTTCGG 57.576 40.909 0.00 0.00 0.00 4.30
349 355 7.607250 AGAACATTTGTCAAAGTTTACCACAA 58.393 30.769 4.03 3.84 0.00 3.33
359 365 7.973388 TCCAAACACTTAGAACATTTGTCAAAG 59.027 33.333 4.03 0.00 0.00 2.77
405 412 1.380524 TTTTCACGCCTTCCACGAAA 58.619 45.000 0.00 0.00 0.00 3.46
429 436 7.321746 CGAAAACATTTTGGAGCATTGATTTTG 59.678 33.333 0.00 0.00 0.00 2.44
430 437 7.226325 TCGAAAACATTTTGGAGCATTGATTTT 59.774 29.630 0.00 0.00 32.36 1.82
431 438 6.705381 TCGAAAACATTTTGGAGCATTGATTT 59.295 30.769 0.00 0.00 32.36 2.17
432 439 6.222389 TCGAAAACATTTTGGAGCATTGATT 58.778 32.000 0.00 0.00 32.36 2.57
437 444 5.600696 ACTTTCGAAAACATTTTGGAGCAT 58.399 33.333 12.41 0.00 36.49 3.79
445 452 8.334632 CCAAAAATGCTACTTTCGAAAACATTT 58.665 29.630 22.26 22.26 37.73 2.32
486 493 0.389817 CATTCGTGGAAGGCGTGAGA 60.390 55.000 0.00 0.00 0.00 3.27
487 494 0.670546 ACATTCGTGGAAGGCGTGAG 60.671 55.000 0.00 0.00 0.00 3.51
586 595 2.800881 TCGCACGAGCTCATATGAAT 57.199 45.000 15.40 0.00 39.10 2.57
592 611 0.312416 GGAGTATCGCACGAGCTCAT 59.688 55.000 15.40 0.00 39.10 2.90
653 672 2.223876 ACGTTTGAGAACCGAAGTAGCA 60.224 45.455 0.00 0.00 31.93 3.49
681 700 5.948742 AAGCATAGTTAAGGCTCTCTCTT 57.051 39.130 0.00 0.00 36.76 2.85
742 773 4.240096 CTGCTTAACCCATTTGCTCAAAG 58.760 43.478 1.43 0.00 33.32 2.77
743 774 3.554752 GCTGCTTAACCCATTTGCTCAAA 60.555 43.478 0.00 0.00 34.46 2.69
744 775 2.029110 GCTGCTTAACCCATTTGCTCAA 60.029 45.455 0.00 0.00 0.00 3.02
745 776 1.545582 GCTGCTTAACCCATTTGCTCA 59.454 47.619 0.00 0.00 0.00 4.26
746 777 1.821136 AGCTGCTTAACCCATTTGCTC 59.179 47.619 0.00 0.00 0.00 4.26
747 778 1.928868 AGCTGCTTAACCCATTTGCT 58.071 45.000 0.00 0.00 0.00 3.91
748 779 2.749280 AAGCTGCTTAACCCATTTGC 57.251 45.000 14.24 0.00 0.00 3.68
749 780 7.671495 AAATAAAAGCTGCTTAACCCATTTG 57.329 32.000 16.31 0.00 0.00 2.32
750 781 8.690203 AAAAATAAAAGCTGCTTAACCCATTT 57.310 26.923 16.31 12.78 0.00 2.32
772 803 6.082707 TGCTTAACCCATTTACCCCTAAAAA 58.917 36.000 0.00 0.00 0.00 1.94
773 804 5.652324 TGCTTAACCCATTTACCCCTAAAA 58.348 37.500 0.00 0.00 0.00 1.52
774 805 5.265989 CTGCTTAACCCATTTACCCCTAAA 58.734 41.667 0.00 0.00 0.00 1.85
775 806 4.862371 CTGCTTAACCCATTTACCCCTAA 58.138 43.478 0.00 0.00 0.00 2.69
776 807 3.372241 GCTGCTTAACCCATTTACCCCTA 60.372 47.826 0.00 0.00 0.00 3.53
777 808 2.623239 GCTGCTTAACCCATTTACCCCT 60.623 50.000 0.00 0.00 0.00 4.79
778 809 1.754803 GCTGCTTAACCCATTTACCCC 59.245 52.381 0.00 0.00 0.00 4.95
779 810 2.427095 CAGCTGCTTAACCCATTTACCC 59.573 50.000 0.00 0.00 0.00 3.69
780 811 3.089284 ACAGCTGCTTAACCCATTTACC 58.911 45.455 15.27 0.00 0.00 2.85
781 812 3.756434 TCACAGCTGCTTAACCCATTTAC 59.244 43.478 15.27 0.00 0.00 2.01
782 813 4.027674 TCACAGCTGCTTAACCCATTTA 57.972 40.909 15.27 0.00 0.00 1.40
890 922 0.804989 GTTTGGGAATGGAGAGCACG 59.195 55.000 0.00 0.00 0.00 5.34
892 924 0.960364 GCGTTTGGGAATGGAGAGCA 60.960 55.000 0.00 0.00 0.00 4.26
897 929 3.059386 GCGGCGTTTGGGAATGGA 61.059 61.111 9.37 0.00 0.00 3.41
898 930 4.128388 GGCGGCGTTTGGGAATGG 62.128 66.667 9.37 0.00 0.00 3.16
899 931 4.474846 CGGCGGCGTTTGGGAATG 62.475 66.667 24.74 0.00 0.00 2.67
952 989 1.381872 CAGTGGGAGGGGAGACGAT 60.382 63.158 0.00 0.00 0.00 3.73
1049 1086 4.507916 CCCCGCGGAGAGAGGAGA 62.508 72.222 30.73 0.00 43.02 3.71
1202 1239 3.996363 GGACACCAAATTTTTCATCCAGC 59.004 43.478 0.00 0.00 0.00 4.85
1214 1251 1.272212 GCCGAAACATGGACACCAAAT 59.728 47.619 0.00 0.00 36.95 2.32
1249 1286 1.554160 CAGAAGCTGGTCATCTCCACT 59.446 52.381 0.00 0.00 33.55 4.00
1363 1400 6.742109 AGAAATGTGAAAATCACCTTCTGTG 58.258 36.000 17.30 0.00 46.40 3.66
1475 1520 2.634600 ACTCTACTCTGCAGTCCGTAG 58.365 52.381 22.75 22.75 33.62 3.51
1521 1566 1.751351 TGATCTAACCCGCAGAGACTG 59.249 52.381 0.00 0.00 34.12 3.51
1812 1857 8.739972 GTGGAAGTATAAGATTGGTTTGAACAT 58.260 33.333 0.00 0.00 0.00 2.71
1817 1862 7.122650 ACCATGTGGAAGTATAAGATTGGTTTG 59.877 37.037 5.96 0.00 38.94 2.93
2073 2131 0.176680 TGTTGCCGTGCACCATTTTT 59.823 45.000 12.15 0.00 38.71 1.94
2105 2164 8.082242 GGCAACTATAATAATAGCCAAAAGGTG 58.918 37.037 0.00 0.00 39.01 4.00
2130 2189 2.702592 TGGTATAGCCAAAAGGTCGG 57.297 50.000 0.00 0.00 45.94 4.79
2411 2470 9.003658 AGGAGAATTTATGAAACACACTACAAG 57.996 33.333 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.