Multiple sequence alignment - TraesCS5B01G318200

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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 TraesCS5B01G318200 chr5B 100.000 3631 0 0 1 3631 502375251 502378881 0.000000e+00 6706
1 TraesCS5B01G318200 chr5B 90.143 1684 129 13 961 2640 502264783 502266433 0.000000e+00 2156
2 TraesCS5B01G318200 chr5B 84.956 1602 197 28 1022 2614 503077800 503079366 0.000000e+00 1583
3 TraesCS5B01G318200 chr5B 97.081 925 22 4 2710 3631 492772807 492773729 0.000000e+00 1554
4 TraesCS5B01G318200 chr5B 87.516 761 79 11 1022 1777 503083057 503083806 0.000000e+00 865
5 TraesCS5B01G318200 chr5B 96.860 414 10 3 27 439 144584814 144585225 0.000000e+00 689
6 TraesCS5B01G318200 chr5B 94.937 316 13 3 469 781 478915712 478916027 3.260000e-135 492
7 TraesCS5B01G318200 chr5D 96.486 1878 36 8 778 2637 415767959 415769824 0.000000e+00 3075
8 TraesCS5B01G318200 chr5D 86.571 1668 188 22 964 2619 468340437 468342080 0.000000e+00 1807
9 TraesCS5B01G318200 chr5D 85.402 1603 195 26 1022 2619 416172967 416174535 0.000000e+00 1628
10 TraesCS5B01G318200 chr5D 91.327 980 71 9 965 1939 415746180 415747150 0.000000e+00 1327
11 TraesCS5B01G318200 chr5D 86.739 920 100 12 990 1895 416199515 416200426 0.000000e+00 1003
12 TraesCS5B01G318200 chr5D 91.486 646 55 0 1995 2640 415747178 415747823 0.000000e+00 889
13 TraesCS5B01G318200 chr5A 95.154 1692 58 13 986 2668 528490112 528488436 0.000000e+00 2649
14 TraesCS5B01G318200 chr5A 85.012 1608 197 29 1022 2614 528890799 528892377 0.000000e+00 1594
15 TraesCS5B01G318200 chr5A 91.753 97 3 2 853 944 528490221 528490125 2.940000e-26 130
16 TraesCS5B01G318200 chr4B 96.757 925 25 4 2710 3631 42528466 42527544 0.000000e+00 1537
17 TraesCS5B01G318200 chr4B 96.287 781 27 2 1 780 394374641 394375420 0.000000e+00 1280
18 TraesCS5B01G318200 chr4B 96.135 414 14 2 27 439 28687392 28687804 0.000000e+00 675
19 TraesCS5B01G318200 chr7B 96.332 927 27 4 2710 3631 6428688 6429612 0.000000e+00 1517
20 TraesCS5B01G318200 chr7B 96.350 411 12 3 30 439 93963040 93962632 0.000000e+00 673
21 TraesCS5B01G318200 chr7B 94.620 316 14 3 469 781 28891313 28891628 1.520000e-133 486
22 TraesCS5B01G318200 chr6A 95.983 921 31 5 2715 3631 76961023 76961941 0.000000e+00 1491
23 TraesCS5B01G318200 chr1B 95.802 929 27 8 2708 3631 667646971 667647892 0.000000e+00 1489
24 TraesCS5B01G318200 chr1B 95.685 927 32 6 2709 3631 8945200 8944278 0.000000e+00 1483
25 TraesCS5B01G318200 chr6B 95.484 930 31 7 2706 3631 11577090 11576168 0.000000e+00 1474
26 TraesCS5B01G318200 chr6B 90.880 943 58 16 2709 3631 6884686 6885620 0.000000e+00 1240
27 TraesCS5B01G318200 chr4A 97.692 780 16 2 1 779 615020311 615019533 0.000000e+00 1339
28 TraesCS5B01G318200 chr4A 95.894 341 11 3 100 439 598576019 598576357 1.910000e-152 549
29 TraesCS5B01G318200 chr4A 96.463 311 11 0 469 779 739616181 739615871 6.950000e-142 514
30 TraesCS5B01G318200 chr2A 97.692 780 17 1 1 779 683144946 683144167 0.000000e+00 1339
31 TraesCS5B01G318200 chr2A 96.517 402 11 3 39 439 19046673 19046274 0.000000e+00 662
32 TraesCS5B01G318200 chr2A 95.385 390 14 4 52 439 16712926 16712539 5.150000e-173 617
33 TraesCS5B01G318200 chr3D 91.130 947 55 12 2708 3631 565799811 565800751 0.000000e+00 1256
34 TraesCS5B01G318200 chr7A 95.479 752 29 4 30 779 21020916 21020168 0.000000e+00 1195
35 TraesCS5B01G318200 chr3B 96.610 413 12 2 27 439 183199014 183199424 0.000000e+00 684
36 TraesCS5B01G318200 chr3B 94.921 315 13 3 469 780 833066 833380 1.170000e-134 490
37 TraesCS5B01G318200 chr3B 94.603 315 13 4 469 780 833561 833874 5.450000e-133 484
38 TraesCS5B01G318200 chr2B 96.341 410 14 1 30 439 224841977 224841569 0.000000e+00 673
39 TraesCS5B01G318200 chrUn 95.511 401 17 1 39 439 208399880 208399481 1.100000e-179 640
40 TraesCS5B01G318200 chr7D 82.937 252 29 4 1117 1354 160568746 160568997 7.900000e-52 215


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 TraesCS5B01G318200 chr5B 502375251 502378881 3630 False 6706.0 6706 100.0000 1 3631 1 chr5B.!!$F5 3630
1 TraesCS5B01G318200 chr5B 502264783 502266433 1650 False 2156.0 2156 90.1430 961 2640 1 chr5B.!!$F4 1679
2 TraesCS5B01G318200 chr5B 492772807 492773729 922 False 1554.0 1554 97.0810 2710 3631 1 chr5B.!!$F3 921
3 TraesCS5B01G318200 chr5B 503077800 503083806 6006 False 1224.0 1583 86.2360 1022 2614 2 chr5B.!!$F6 1592
4 TraesCS5B01G318200 chr5D 415767959 415769824 1865 False 3075.0 3075 96.4860 778 2637 1 chr5D.!!$F1 1859
5 TraesCS5B01G318200 chr5D 468340437 468342080 1643 False 1807.0 1807 86.5710 964 2619 1 chr5D.!!$F4 1655
6 TraesCS5B01G318200 chr5D 416172967 416174535 1568 False 1628.0 1628 85.4020 1022 2619 1 chr5D.!!$F2 1597
7 TraesCS5B01G318200 chr5D 415746180 415747823 1643 False 1108.0 1327 91.4065 965 2640 2 chr5D.!!$F5 1675
8 TraesCS5B01G318200 chr5D 416199515 416200426 911 False 1003.0 1003 86.7390 990 1895 1 chr5D.!!$F3 905
9 TraesCS5B01G318200 chr5A 528890799 528892377 1578 False 1594.0 1594 85.0120 1022 2614 1 chr5A.!!$F1 1592
10 TraesCS5B01G318200 chr5A 528488436 528490221 1785 True 1389.5 2649 93.4535 853 2668 2 chr5A.!!$R1 1815
11 TraesCS5B01G318200 chr4B 42527544 42528466 922 True 1537.0 1537 96.7570 2710 3631 1 chr4B.!!$R1 921
12 TraesCS5B01G318200 chr4B 394374641 394375420 779 False 1280.0 1280 96.2870 1 780 1 chr4B.!!$F2 779
13 TraesCS5B01G318200 chr7B 6428688 6429612 924 False 1517.0 1517 96.3320 2710 3631 1 chr7B.!!$F1 921
14 TraesCS5B01G318200 chr6A 76961023 76961941 918 False 1491.0 1491 95.9830 2715 3631 1 chr6A.!!$F1 916
15 TraesCS5B01G318200 chr1B 667646971 667647892 921 False 1489.0 1489 95.8020 2708 3631 1 chr1B.!!$F1 923
16 TraesCS5B01G318200 chr1B 8944278 8945200 922 True 1483.0 1483 95.6850 2709 3631 1 chr1B.!!$R1 922
17 TraesCS5B01G318200 chr6B 11576168 11577090 922 True 1474.0 1474 95.4840 2706 3631 1 chr6B.!!$R1 925
18 TraesCS5B01G318200 chr6B 6884686 6885620 934 False 1240.0 1240 90.8800 2709 3631 1 chr6B.!!$F1 922
19 TraesCS5B01G318200 chr4A 615019533 615020311 778 True 1339.0 1339 97.6920 1 779 1 chr4A.!!$R1 778
20 TraesCS5B01G318200 chr2A 683144167 683144946 779 True 1339.0 1339 97.6920 1 779 1 chr2A.!!$R3 778
21 TraesCS5B01G318200 chr3D 565799811 565800751 940 False 1256.0 1256 91.1300 2708 3631 1 chr3D.!!$F1 923
22 TraesCS5B01G318200 chr7A 21020168 21020916 748 True 1195.0 1195 95.4790 30 779 1 chr7A.!!$R1 749
23 TraesCS5B01G318200 chr3B 833066 833874 808 False 487.0 490 94.7620 469 780 2 chr3B.!!$F2 311

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
759 766 1.033746 CCGGCGGAGACTACCAACTA 61.034 60.0 24.41 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2675 2876 0.03563 GTGCAAGGAGCCACTCTCAT 60.036 55.0 0.0 0.0 43.7 2.9 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
176 177 1.073373 TTTTTCCATCGTGCGGGGA 59.927 52.632 2.70 2.7 0.00 4.81
233 234 4.400961 GGCAGAGCAACGAGGGCT 62.401 66.667 0.00 0.0 46.07 5.19
454 456 4.591321 TTTTATGAATGAGAGCAGGGGT 57.409 40.909 0.00 0.0 0.00 4.95
481 483 8.801299 TGATTTGTTTCCTTAAAGTATGATGCA 58.199 29.630 0.00 0.0 0.00 3.96
759 766 1.033746 CCGGCGGAGACTACCAACTA 61.034 60.000 24.41 0.0 0.00 2.24
790 797 5.008331 AGAAGTAGAGATACGTGGTGTCAA 58.992 41.667 0.00 0.0 0.00 3.18
809 816 6.363357 GTGTCAAATGAATGAAGCCAAACTAC 59.637 38.462 0.00 0.0 0.00 2.73
815 822 2.507407 TGAAGCCAAACTACATCCCC 57.493 50.000 0.00 0.0 0.00 4.81
1020 1047 2.360350 TCTCCGTACGCCGTCCTT 60.360 61.111 10.49 0.0 33.66 3.36
1054 1090 2.202756 CCTTCTGCTACGCCGTCC 60.203 66.667 0.00 0.0 0.00 4.79
2675 2876 9.871238 ACTATTAGAAATAAAAGAGCGACTGAA 57.129 29.630 0.00 0.0 0.00 3.02
2679 2880 7.301068 AGAAATAAAAGAGCGACTGAATGAG 57.699 36.000 0.00 0.0 0.00 2.90
2680 2881 7.099764 AGAAATAAAAGAGCGACTGAATGAGA 58.900 34.615 0.00 0.0 0.00 3.27
2681 2882 6.900568 AATAAAAGAGCGACTGAATGAGAG 57.099 37.500 0.00 0.0 0.00 3.20
2682 2883 3.951775 AAAGAGCGACTGAATGAGAGT 57.048 42.857 0.00 0.0 0.00 3.24
2683 2884 2.937469 AGAGCGACTGAATGAGAGTG 57.063 50.000 0.00 0.0 0.00 3.51
2684 2885 1.476085 AGAGCGACTGAATGAGAGTGG 59.524 52.381 0.00 0.0 0.00 4.00
2685 2886 0.108424 AGCGACTGAATGAGAGTGGC 60.108 55.000 0.00 0.0 43.36 5.01
2686 2887 0.108424 GCGACTGAATGAGAGTGGCT 60.108 55.000 0.00 0.0 40.78 4.75
2687 2888 1.919918 CGACTGAATGAGAGTGGCTC 58.080 55.000 0.00 0.0 44.21 4.70
2688 2889 1.470632 CGACTGAATGAGAGTGGCTCC 60.471 57.143 0.00 0.0 43.26 4.70
2689 2890 1.830477 GACTGAATGAGAGTGGCTCCT 59.170 52.381 0.00 0.0 43.26 3.69
2692 2893 1.339438 TGAATGAGAGTGGCTCCTTGC 60.339 52.381 0.00 0.0 43.26 4.01
2694 2895 0.035630 ATGAGAGTGGCTCCTTGCAC 60.036 55.000 0.00 0.0 43.26 4.57
2696 2897 0.036022 GAGAGTGGCTCCTTGCACTT 59.964 55.000 0.00 0.0 45.15 3.16
2697 2898 0.250640 AGAGTGGCTCCTTGCACTTG 60.251 55.000 0.00 0.0 45.15 3.16
2698 2899 0.536006 GAGTGGCTCCTTGCACTTGT 60.536 55.000 0.00 0.0 45.15 3.16
2699 2900 0.536006 AGTGGCTCCTTGCACTTGTC 60.536 55.000 0.00 0.0 45.15 3.18
2703 2904 1.408702 GGCTCCTTGCACTTGTCAAAA 59.591 47.619 0.00 0.0 45.15 2.44
2704 2905 2.159114 GGCTCCTTGCACTTGTCAAAAA 60.159 45.455 0.00 0.0 45.15 1.94
3230 6333 2.151202 TCTCGCGGATTGAAGCTTTTT 58.849 42.857 6.13 0.0 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
176 177 0.328258 CTCGTTTGACCTCCCCCAAT 59.672 55.000 0.00 0.0 0.00 3.16
233 234 0.750546 CGTCCCGTCTCCCTACATCA 60.751 60.000 0.00 0.0 0.00 3.07
454 456 9.638239 GCATCATACTTTAAGGAAACAAATCAA 57.362 29.630 0.00 0.0 0.00 2.57
593 595 3.065648 ACTTTCCAAACGTACACGCAATT 59.934 39.130 0.85 0.0 44.43 2.32
759 766 6.487331 CCACGTATCTCTACTTCTAATGGAGT 59.513 42.308 0.00 0.0 0.00 3.85
790 797 5.127682 GGGATGTAGTTTGGCTTCATTCATT 59.872 40.000 0.00 0.0 35.71 2.57
815 822 6.814506 AAGAAAAGTGATGTCATTCCTGAG 57.185 37.500 0.00 0.0 30.18 3.35
1644 1689 4.796231 CCGGGGAGCACGTCTTCG 62.796 72.222 0.00 0.0 43.34 3.79
1962 2047 7.256012 CCAGAGTAGAGAAAAGAGTACCAAAGT 60.256 40.741 0.00 0.0 0.00 2.66
1963 2048 7.093992 CCAGAGTAGAGAAAAGAGTACCAAAG 58.906 42.308 0.00 0.0 0.00 2.77
2258 2435 1.395826 GGATCTCGTAGCCCTGCACT 61.396 60.000 0.00 0.0 0.00 4.40
2668 2869 1.470632 GGAGCCACTCTCATTCAGTCG 60.471 57.143 0.00 0.0 43.70 4.18
2670 2871 1.949799 AGGAGCCACTCTCATTCAGT 58.050 50.000 0.00 0.0 43.70 3.41
2671 2872 2.630158 CAAGGAGCCACTCTCATTCAG 58.370 52.381 0.00 0.0 43.24 3.02
2674 2875 0.694771 TGCAAGGAGCCACTCTCATT 59.305 50.000 0.00 0.0 45.69 2.57
2675 2876 0.035630 GTGCAAGGAGCCACTCTCAT 60.036 55.000 0.00 0.0 43.70 2.90
2676 2877 1.123861 AGTGCAAGGAGCCACTCTCA 61.124 55.000 0.00 0.0 43.70 3.27
2677 2878 0.036022 AAGTGCAAGGAGCCACTCTC 59.964 55.000 0.00 0.0 44.83 3.20
2679 2880 0.536006 ACAAGTGCAAGGAGCCACTC 60.536 55.000 0.00 0.0 44.83 3.51
2680 2881 0.536006 GACAAGTGCAAGGAGCCACT 60.536 55.000 0.00 0.0 44.83 4.00
2681 2882 0.819259 TGACAAGTGCAAGGAGCCAC 60.819 55.000 0.00 0.0 44.83 5.01
2682 2883 0.106769 TTGACAAGTGCAAGGAGCCA 60.107 50.000 0.00 0.0 44.83 4.75
2683 2884 1.032014 TTTGACAAGTGCAAGGAGCC 58.968 50.000 0.00 0.0 44.83 4.70
2684 2885 2.869233 TTTTGACAAGTGCAAGGAGC 57.131 45.000 0.00 0.0 45.96 4.70
2704 2905 0.240945 CGCAGATCGTTGCCCTTTTT 59.759 50.000 1.66 0.0 41.01 1.94
2997 3641 2.685999 GGGGGCTTTCTGCTGGAT 59.314 61.111 0.00 0.0 42.39 3.41


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

AutoCloner maintained by Alex Coulton.