Multiple sequence alignment - TraesCS1B01G163900

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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 TraesCS1B01G163900 chr1B 100.000 3723 0 0 1 3723 286158672 286154950 0.000000e+00 6876
1 TraesCS1B01G163900 chr1B 96.164 2320 86 3 1 2317 338939591 338941910 0.000000e+00 3788
2 TraesCS1B01G163900 chr1B 95.776 2320 94 4 1 2317 135080133 135082451 0.000000e+00 3738
3 TraesCS1B01G163900 chr1B 95.206 897 35 4 2829 3718 342739569 342740464 0.000000e+00 1411
4 TraesCS1B01G163900 chr6B 96.726 2321 71 5 1 2317 394539960 394537641 0.000000e+00 3860
5 TraesCS1B01G163900 chr6B 95.603 2320 98 4 1 2317 264848878 264851196 0.000000e+00 3716
6 TraesCS1B01G163900 chr6B 95.095 897 42 2 2822 3717 533757024 533757919 0.000000e+00 1411
7 TraesCS1B01G163900 chr5B 96.552 2320 77 3 1 2317 127838684 127836365 0.000000e+00 3838
8 TraesCS1B01G163900 chr5B 95.740 892 37 1 2829 3719 274522619 274523510 0.000000e+00 1435
9 TraesCS1B01G163900 chr7B 96.424 2321 78 5 1 2317 716815493 716813174 0.000000e+00 3821
10 TraesCS1B01G163900 chr7B 95.302 894 36 3 2830 3718 133837611 133838503 0.000000e+00 1413
11 TraesCS1B01G163900 chr7B 95.078 894 40 3 2829 3718 219672845 219671952 0.000000e+00 1404
12 TraesCS1B01G163900 chr7B 97.287 516 10 2 2318 2829 716766869 716767384 0.000000e+00 872
13 TraesCS1B01G163900 chr7B 97.099 517 10 3 2318 2829 716813249 716812733 0.000000e+00 867
14 TraesCS1B01G163900 chr3B 96.250 2320 84 3 1 2317 483357566 483355247 0.000000e+00 3799
15 TraesCS1B01G163900 chr3B 95.095 897 41 2 2829 3723 804289357 804290252 0.000000e+00 1410
16 TraesCS1B01G163900 chr3B 96.705 516 13 2 2318 2829 201479422 201478907 0.000000e+00 856
17 TraesCS1B01G163900 chr3A 96.033 2319 90 2 1 2317 51918942 51921260 0.000000e+00 3771
18 TraesCS1B01G163900 chr3A 96.705 516 13 2 2318 2829 105549942 105550457 0.000000e+00 856
19 TraesCS1B01G163900 chr2D 95.472 2319 95 5 1 2317 521302189 521299879 0.000000e+00 3692
20 TraesCS1B01G163900 chr2D 96.169 522 14 4 2318 2834 521299953 521299433 0.000000e+00 848
21 TraesCS1B01G163900 chr4B 95.843 890 29 2 2830 3718 272111583 272110701 0.000000e+00 1432
22 TraesCS1B01G163900 chrUn 95.633 893 36 2 2829 3718 186225865 186226757 0.000000e+00 1430
23 TraesCS1B01G163900 chrUn 95.526 894 36 2 2829 3718 85584171 85583278 0.000000e+00 1426
24 TraesCS1B01G163900 chr1D 97.093 516 11 2 2318 2829 351090289 351090804 0.000000e+00 867
25 TraesCS1B01G163900 chr1D 96.699 515 13 2 2319 2829 254466420 254465906 0.000000e+00 854
26 TraesCS1B01G163900 chr1A 96.705 516 13 2 2318 2829 554489042 554488527 0.000000e+00 856
27 TraesCS1B01G163900 chr5D 96.512 516 14 2 2318 2829 503346447 503345932 0.000000e+00 850
28 TraesCS1B01G163900 chr7A 97.849 93 2 0 2225 2317 242862463 242862371 1.070000e-35 161


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 TraesCS1B01G163900 chr1B 286154950 286158672 3722 True 6876 6876 100.0000 1 3723 1 chr1B.!!$R1 3722
1 TraesCS1B01G163900 chr1B 338939591 338941910 2319 False 3788 3788 96.1640 1 2317 1 chr1B.!!$F2 2316
2 TraesCS1B01G163900 chr1B 135080133 135082451 2318 False 3738 3738 95.7760 1 2317 1 chr1B.!!$F1 2316
3 TraesCS1B01G163900 chr1B 342739569 342740464 895 False 1411 1411 95.2060 2829 3718 1 chr1B.!!$F3 889
4 TraesCS1B01G163900 chr6B 394537641 394539960 2319 True 3860 3860 96.7260 1 2317 1 chr6B.!!$R1 2316
5 TraesCS1B01G163900 chr6B 264848878 264851196 2318 False 3716 3716 95.6030 1 2317 1 chr6B.!!$F1 2316
6 TraesCS1B01G163900 chr6B 533757024 533757919 895 False 1411 1411 95.0950 2822 3717 1 chr6B.!!$F2 895
7 TraesCS1B01G163900 chr5B 127836365 127838684 2319 True 3838 3838 96.5520 1 2317 1 chr5B.!!$R1 2316
8 TraesCS1B01G163900 chr5B 274522619 274523510 891 False 1435 1435 95.7400 2829 3719 1 chr5B.!!$F1 890
9 TraesCS1B01G163900 chr7B 716812733 716815493 2760 True 2344 3821 96.7615 1 2829 2 chr7B.!!$R2 2828
10 TraesCS1B01G163900 chr7B 133837611 133838503 892 False 1413 1413 95.3020 2830 3718 1 chr7B.!!$F1 888
11 TraesCS1B01G163900 chr7B 219671952 219672845 893 True 1404 1404 95.0780 2829 3718 1 chr7B.!!$R1 889
12 TraesCS1B01G163900 chr7B 716766869 716767384 515 False 872 872 97.2870 2318 2829 1 chr7B.!!$F2 511
13 TraesCS1B01G163900 chr3B 483355247 483357566 2319 True 3799 3799 96.2500 1 2317 1 chr3B.!!$R2 2316
14 TraesCS1B01G163900 chr3B 804289357 804290252 895 False 1410 1410 95.0950 2829 3723 1 chr3B.!!$F1 894
15 TraesCS1B01G163900 chr3B 201478907 201479422 515 True 856 856 96.7050 2318 2829 1 chr3B.!!$R1 511
16 TraesCS1B01G163900 chr3A 51918942 51921260 2318 False 3771 3771 96.0330 1 2317 1 chr3A.!!$F1 2316
17 TraesCS1B01G163900 chr3A 105549942 105550457 515 False 856 856 96.7050 2318 2829 1 chr3A.!!$F2 511
18 TraesCS1B01G163900 chr2D 521299433 521302189 2756 True 2270 3692 95.8205 1 2834 2 chr2D.!!$R1 2833
19 TraesCS1B01G163900 chr4B 272110701 272111583 882 True 1432 1432 95.8430 2830 3718 1 chr4B.!!$R1 888
20 TraesCS1B01G163900 chrUn 186225865 186226757 892 False 1430 1430 95.6330 2829 3718 1 chrUn.!!$F1 889
21 TraesCS1B01G163900 chrUn 85583278 85584171 893 True 1426 1426 95.5260 2829 3718 1 chrUn.!!$R1 889
22 TraesCS1B01G163900 chr1D 351090289 351090804 515 False 867 867 97.0930 2318 2829 1 chr1D.!!$F1 511
23 TraesCS1B01G163900 chr1D 254465906 254466420 514 True 854 854 96.6990 2319 2829 1 chr1D.!!$R1 510
24 TraesCS1B01G163900 chr1A 554488527 554489042 515 True 856 856 96.7050 2318 2829 1 chr1A.!!$R1 511
25 TraesCS1B01G163900 chr5D 503345932 503346447 515 True 850 850 96.5120 2318 2829 1 chr5D.!!$R1 511

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
787 790 1.603172 GCATCGATACGAGGAAGGTGG 60.603 57.143 9.81 0.0 40.15 4.61 F
1941 1946 0.173708 AGGCAGCGAGTTAGTAGCAC 59.826 55.000 0.00 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2150 2156 0.394352 AAACATGATCCCAGGCGGAC 60.394 55.000 0.0 0.0 46.09 4.79 R
2787 2798 1.076024 ACAACGAGTAGTGGGGTCCTA 59.924 52.381 0.0 0.0 0.00 2.94 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
47 48 8.145122 GTGAAATAATTGTTTTGGGTCACCTTA 58.855 33.333 1.43 0.00 37.76 2.69
68 69 7.937394 ACCTTAGCTTTTGTGTTCAGTAGTTAT 59.063 33.333 0.00 0.00 0.00 1.89
80 81 7.881751 GTGTTCAGTAGTTATTAGGGGAAGTTT 59.118 37.037 0.00 0.00 0.00 2.66
116 117 4.528596 TCTCTCTTCCCTGTAGAAAACCAG 59.471 45.833 0.00 0.00 0.00 4.00
184 186 5.725362 AGCAAATATCGGATAGCCTAACTC 58.275 41.667 3.81 0.00 0.00 3.01
362 365 2.655090 TGGGCTCTGATTCACACAAA 57.345 45.000 0.00 0.00 0.00 2.83
403 406 4.226620 GTGGGTCACCCTTTTCCTCTATAA 59.773 45.833 16.04 0.00 45.70 0.98
411 414 8.390921 TCACCCTTTTCCTCTATAAATCTGTTT 58.609 33.333 0.00 0.00 0.00 2.83
442 445 3.243334 GGGCTTGCTATTCTCTGCAATTC 60.243 47.826 0.00 0.00 46.20 2.17
508 511 9.762933 CATCCAAACTTTCTTATTTCTTTCCAA 57.237 29.630 0.00 0.00 0.00 3.53
563 566 3.135348 AGAGCTGATGTATGGCTAAGCAA 59.865 43.478 0.00 0.00 36.37 3.91
657 660 3.449746 ACCCATTAACAAGCAAGGCTA 57.550 42.857 0.00 0.00 38.25 3.93
669 672 2.436173 AGCAAGGCTATAGTGAACCTCC 59.564 50.000 0.84 0.00 36.99 4.30
732 735 5.191722 AGTTGGGTGATCCATTAAGCTAAGA 59.808 40.000 0.00 0.00 46.52 2.10
787 790 1.603172 GCATCGATACGAGGAAGGTGG 60.603 57.143 9.81 0.00 40.15 4.61
845 848 5.467035 TTTCCTTTGGATTGTGGAATGAC 57.533 39.130 0.00 0.00 38.24 3.06
879 883 7.542477 CCTAATAGTAGTGATTTAGTGCGATGG 59.458 40.741 0.00 0.00 0.00 3.51
913 917 3.519579 GCGGGAGACTTTCTAAGGTTAC 58.480 50.000 0.00 0.00 0.00 2.50
951 955 2.478200 CGACTTTCTTAGACTCGGCTCC 60.478 54.545 0.00 0.00 0.00 4.70
1183 1187 0.598065 CGAAGGAGCAACCCCTTTTG 59.402 55.000 0.00 0.00 43.59 2.44
1314 1319 6.942532 TTGCTATTCTTTTCCTAATCGCAT 57.057 33.333 0.00 0.00 34.83 4.73
1406 1411 6.256053 CCCATTTATAGGACAAGGCCATAAT 58.744 40.000 5.01 0.00 0.00 1.28
1483 1488 3.181465 GCTATGCTAGGCTCTACAACCAA 60.181 47.826 0.00 0.00 0.00 3.67
1605 1610 4.558095 GCGGATTTCTAATAGTCGGTGCTA 60.558 45.833 0.00 0.00 0.00 3.49
1608 1613 6.072838 CGGATTTCTAATAGTCGGTGCTACTA 60.073 42.308 0.00 0.00 34.11 1.82
1615 1620 2.443416 AGTCGGTGCTACTACACATGA 58.557 47.619 0.00 0.00 42.55 3.07
1616 1621 3.024547 AGTCGGTGCTACTACACATGAT 58.975 45.455 0.00 0.00 42.55 2.45
1617 1622 4.204799 AGTCGGTGCTACTACACATGATA 58.795 43.478 0.00 0.00 42.55 2.15
1646 1651 9.712305 ATTTTTATGGTAAGAGACTATGATCCG 57.288 33.333 0.00 0.00 30.70 4.18
1654 1659 5.554437 AGAGACTATGATCCGACTACTCA 57.446 43.478 0.00 0.00 0.00 3.41
1926 1931 0.905809 TAGCTTAACGTGGGGAGGCA 60.906 55.000 0.00 0.00 0.00 4.75
1941 1946 0.173708 AGGCAGCGAGTTAGTAGCAC 59.826 55.000 0.00 0.00 0.00 4.40
1948 1953 2.681848 GCGAGTTAGTAGCACTAGGTGA 59.318 50.000 1.57 0.00 35.23 4.02
2150 2156 1.826385 GAGGGGGAACATGTCAAGTG 58.174 55.000 0.00 0.00 0.00 3.16
2254 2260 1.408266 GCAGTCGGATGTTTGGGGTAT 60.408 52.381 0.00 0.00 0.00 2.73
2271 2277 5.222048 TGGGGTATTATAAGTGATCAAGGGC 60.222 44.000 0.00 0.00 0.00 5.19
2368 2374 4.657039 GGTGGTAACTCATATTACAGGGGA 59.343 45.833 0.00 0.00 36.87 4.81
2530 2541 9.476202 GCCTTCAGTTTAATGTTTTTATTCAGT 57.524 29.630 0.00 0.00 0.00 3.41
2562 2573 7.099120 GGTTATTGGCAAGAACTCATTGAATT 58.901 34.615 29.91 1.95 33.32 2.17
2700 2711 4.574674 TGACATGGGCATTCTTCTTAGT 57.425 40.909 0.00 0.00 0.00 2.24
2843 2854 3.296854 TGCTACCTGATACGTCTCCAAT 58.703 45.455 0.00 0.00 0.00 3.16
2988 2999 8.032451 CCAGTTTCTGTTTTCTCCTTGTTTTTA 58.968 33.333 0.00 0.00 0.00 1.52
2995 3006 9.971744 CTGTTTTCTCCTTGTTTTTATGTTTTG 57.028 29.630 0.00 0.00 0.00 2.44
3028 3039 5.835280 GGATACCAAATGGAGTCCAATTGAT 59.165 40.000 32.77 23.41 44.56 2.57
3362 3383 0.769776 ATCTCGGAGGGGCCATCATT 60.770 55.000 21.12 0.00 35.94 2.57
3475 3497 1.146566 GCCATCAGGAGGGGAATCATT 59.853 52.381 1.81 0.00 36.89 2.57
3542 3564 2.207229 CGGTCCACTCTCCCACACA 61.207 63.158 0.00 0.00 0.00 3.72
3615 3637 5.300034 TCCAATGATGTGTTGCCATCTTATC 59.700 40.000 0.00 0.00 41.47 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 7.390718 CCCTAATAACTACTGAACACAAAAGCT 59.609 37.037 0.00 0.00 0.00 3.74
80 81 0.261991 AGAGAGATACCAAGCCGGGA 59.738 55.000 2.18 0.00 40.22 5.14
116 117 5.181433 GTGAAAATAAGGAGGGACTTGTGAC 59.819 44.000 0.00 0.00 41.55 3.67
168 170 4.667519 AAAACGAGTTAGGCTATCCGAT 57.332 40.909 14.59 3.63 37.47 4.18
231 234 6.008331 GGTTCCCTAGGTACATTCTGTTTTT 58.992 40.000 8.29 0.00 0.00 1.94
362 365 2.040544 CATCGCAAGGGCTTTCCGT 61.041 57.895 0.00 0.00 41.52 4.69
403 406 2.179427 GCCCCCTTTGCTAAACAGATT 58.821 47.619 0.00 0.00 0.00 2.40
411 414 0.926293 ATAGCAAGCCCCCTTTGCTA 59.074 50.000 18.49 18.49 39.57 3.49
508 511 7.931948 ACTATACGCATTCTACCTATGCTTTTT 59.068 33.333 0.00 0.00 44.78 1.94
515 518 8.591114 ACCATTACTATACGCATTCTACCTAT 57.409 34.615 0.00 0.00 0.00 2.57
625 628 6.294731 GCTTGTTAATGGGTTTCTGACTTCAT 60.295 38.462 0.00 0.00 0.00 2.57
669 672 6.894150 GTGCATTCCACAATCCCTTAAGGAG 61.894 48.000 23.74 12.87 45.80 3.69
732 735 6.166982 GTCACTAGGTTGTTCATAGCTCTTT 58.833 40.000 0.00 0.00 34.24 2.52
787 790 9.781834 CTATGAAGGAAATCGTATCTGATCTAC 57.218 37.037 0.00 0.00 0.00 2.59
830 833 3.561960 CCTTCCTGTCATTCCACAATCCA 60.562 47.826 0.00 0.00 0.00 3.41
845 848 6.426646 AATCACTACTATTAGGCCTTCCTG 57.573 41.667 12.58 1.80 44.08 3.86
895 899 7.902387 ATTTTCGTAACCTTAGAAAGTCTCC 57.098 36.000 0.00 0.00 35.62 3.71
913 917 5.479716 AAGTCGCCCTGTTATTATTTTCG 57.520 39.130 0.00 0.00 0.00 3.46
951 955 7.295952 ACGAACTTAATCAAAGAGTGCTATG 57.704 36.000 0.00 0.00 38.67 2.23
1183 1187 5.061684 GCGTATTTGGACCAATTTAAAGTGC 59.938 40.000 7.99 0.73 0.00 4.40
1242 1247 0.617820 AGCCAGAGACCACCGGTTAT 60.618 55.000 2.97 0.00 35.25 1.89
1314 1319 6.240147 CCCCAATTGGTCCTATACATATGACA 60.240 42.308 22.91 0.00 31.92 3.58
1406 1411 8.385898 ACGTTGTTAAGATTTCATAAAGACCA 57.614 30.769 0.00 0.00 0.00 4.02
1683 1688 1.765161 ATGATTGCATCGCGGTGTCG 61.765 55.000 22.24 0.00 39.81 4.35
1880 1885 1.102809 TTGTTGCACCAGGAGCTGTG 61.103 55.000 10.54 0.00 0.00 3.66
1926 1931 2.683867 CACCTAGTGCTACTAACTCGCT 59.316 50.000 0.00 0.00 29.00 4.93
1941 1946 3.904136 CAAAGCCACTTTGTCACCTAG 57.096 47.619 11.09 0.00 43.85 3.02
2008 2014 5.709631 ACAGTCACATGTATGGTAAATGCAA 59.290 36.000 0.00 0.00 0.00 4.08
2077 2083 6.710744 ACCTAGATTTGCTTTATTGGGTATCG 59.289 38.462 0.00 0.00 0.00 2.92
2150 2156 0.394352 AAACATGATCCCAGGCGGAC 60.394 55.000 0.00 0.00 46.09 4.79
2193 2199 6.375736 TGGAAAATGACTACCGAAATTGCATA 59.624 34.615 0.00 0.00 0.00 3.14
2254 2260 6.157994 AGTTACCAGCCCTTGATCACTTATAA 59.842 38.462 0.00 0.00 0.00 0.98
2271 2277 4.905456 TCCCCCTGTAATATGAGTTACCAG 59.095 45.833 0.00 0.00 34.43 4.00
2368 2374 5.343307 AATGGAACTCTGTGCAAAGTTTT 57.657 34.783 3.21 0.00 35.90 2.43
2530 2541 1.228583 TTGCCAATAACCACGGCCA 60.229 52.632 2.24 0.00 45.63 5.36
2562 2573 8.756927 TGAATTTGTTATGAGCCCAAATGATAA 58.243 29.630 0.00 0.00 38.44 1.75
2700 2711 7.445121 CCACTATCCTACTGCAATAATTCTCA 58.555 38.462 0.00 0.00 0.00 3.27
2787 2798 1.076024 ACAACGAGTAGTGGGGTCCTA 59.924 52.381 0.00 0.00 0.00 2.94
2988 2999 8.485578 TTTGGTATCCCTTTTCTACAAAACAT 57.514 30.769 0.00 0.00 0.00 2.71
2995 3006 6.424032 ACTCCATTTGGTATCCCTTTTCTAC 58.576 40.000 0.00 0.00 36.34 2.59
3028 3039 7.174599 CCATAAAAATCCTCAAAAATTGGCACA 59.825 33.333 0.00 0.00 0.00 4.57
3475 3497 3.982372 GAAGACGATCACCGCGGCA 62.982 63.158 28.58 13.44 43.32 5.69
3542 3564 2.463752 TCAAGTAGGGATTACAGCGGT 58.536 47.619 0.00 0.00 34.56 5.68
3615 3637 9.814899 AGACAGAAGATATCTACTCAAAACATG 57.185 33.333 5.46 0.00 36.32 3.21
3649 3671 7.957002 ACTCGTACCAATCTAGATCATCAATT 58.043 34.615 5.51 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.