Multiple sequence alignment - TraesCS5A01G100800

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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 TraesCS5A01G100800 chr5A 100.000 2548 0 0 1 2548 145866026 145863479 0.000000e+00 4706
1 TraesCS5A01G100800 chr5A 96.853 572 18 0 1 572 606998407 606998978 0.000000e+00 957
2 TraesCS5A01G100800 chr1A 95.670 1986 74 8 572 2548 71245440 71243458 0.000000e+00 3181
3 TraesCS5A01G100800 chr1A 95.367 1964 57 5 616 2548 531499961 531498001 0.000000e+00 3092
4 TraesCS5A01G100800 chr1A 93.962 2004 85 7 576 2548 581942310 581944308 0.000000e+00 2998
5 TraesCS5A01G100800 chr1A 94.024 2008 63 8 570 2545 38372361 38374343 0.000000e+00 2990
6 TraesCS5A01G100800 chr1A 96.678 572 19 0 1 572 393369629 393369058 0.000000e+00 952
7 TraesCS5A01G100800 chr1A 86.691 278 7 1 2301 2548 462531229 462531506 5.370000e-72 281
8 TraesCS5A01G100800 chr6A 96.928 1888 54 4 572 2456 617222870 617220984 0.000000e+00 3162
9 TraesCS5A01G100800 chr6A 94.480 2011 73 12 573 2548 200078199 200080206 0.000000e+00 3064
10 TraesCS5A01G100800 chr6A 94.188 2013 65 7 572 2548 203520913 203518917 0.000000e+00 3022
11 TraesCS5A01G100800 chr6A 93.719 2022 83 8 570 2548 484400736 484402756 0.000000e+00 2990
12 TraesCS5A01G100800 chr6A 92.591 2038 76 26 576 2548 61540321 61538294 0.000000e+00 2857
13 TraesCS5A01G100800 chr6A 96.853 572 18 0 1 572 409260047 409260618 0.000000e+00 957
14 TraesCS5A01G100800 chr6A 96.678 572 19 0 1 572 595547541 595548112 0.000000e+00 952
15 TraesCS5A01G100800 chr6B 96.873 1887 56 3 572 2456 660437744 660435859 0.000000e+00 3155
16 TraesCS5A01G100800 chr6B 96.566 1893 62 3 566 2456 585915581 585917472 0.000000e+00 3133
17 TraesCS5A01G100800 chr3A 96.778 1893 55 5 567 2456 617401017 617402906 0.000000e+00 3153
18 TraesCS5A01G100800 chr3A 96.817 1885 58 2 573 2456 735555341 735557224 0.000000e+00 3147
19 TraesCS5A01G100800 chr3A 96.668 1891 61 2 567 2456 54951912 54953801 0.000000e+00 3142
20 TraesCS5A01G100800 chr2B 96.819 1886 57 3 573 2456 776222962 776224846 0.000000e+00 3147
21 TraesCS5A01G100800 chr4A 96.714 1887 59 3 573 2456 36562913 36564799 0.000000e+00 3138
22 TraesCS5A01G100800 chr7A 96.616 1891 60 4 570 2456 701581937 701583827 0.000000e+00 3134
23 TraesCS5A01G100800 chr7A 94.784 2013 67 8 571 2548 689996371 689994362 0.000000e+00 3101
24 TraesCS5A01G100800 chr7A 93.577 2024 79 10 573 2548 49208210 49210230 0.000000e+00 2970
25 TraesCS5A01G100800 chr7A 94.580 1679 58 4 901 2548 14472736 14471060 0.000000e+00 2566
26 TraesCS5A01G100800 chr7A 93.494 1706 68 18 878 2548 36946478 36948175 0.000000e+00 2495
27 TraesCS5A01G100800 chr7A 96.853 572 18 0 1 572 96596970 96596399 0.000000e+00 957
28 TraesCS5A01G100800 chr7A 96.853 572 18 0 1 572 291745126 291744555 0.000000e+00 957
29 TraesCS5A01G100800 chr7A 96.853 572 18 0 1 572 566362507 566361936 0.000000e+00 957
30 TraesCS5A01G100800 chr5D 93.787 2012 85 19 571 2548 336262622 336264627 0.000000e+00 2987
31 TraesCS5A01G100800 chr5D 93.085 2010 96 17 576 2548 520497536 520495533 0.000000e+00 2902
32 TraesCS5A01G100800 chr5D 92.143 2011 100 25 573 2548 213959303 213961290 0.000000e+00 2785
33 TraesCS5A01G100800 chr5D 93.124 1716 77 22 868 2548 324809588 324811297 0.000000e+00 2477
34 TraesCS5A01G100800 chr5D 93.040 1681 75 18 901 2548 336348071 336346400 0.000000e+00 2418
35 TraesCS5A01G100800 chr5D 81.362 279 18 12 2301 2548 114518022 114518297 2.000000e-46 196
36 TraesCS5A01G100800 chr2A 93.849 2016 60 14 566 2548 744582023 744584007 0.000000e+00 2977
37 TraesCS5A01G100800 chr7D 93.376 2008 87 14 576 2548 574727115 574725119 0.000000e+00 2929
38 TraesCS5A01G100800 chrUn 93.261 2018 84 19 576 2548 93726507 93724497 0.000000e+00 2926
39 TraesCS5A01G100800 chrUn 94.418 1666 79 9 895 2548 368600946 368602609 0.000000e+00 2549
40 TraesCS5A01G100800 chrUn 96.418 1396 47 3 1062 2456 88420799 88422192 0.000000e+00 2298
41 TraesCS5A01G100800 chrUn 96.174 1307 45 3 1154 2456 368111971 368113276 0.000000e+00 2132
42 TraesCS5A01G100800 chrUn 94.458 1191 35 2 1388 2548 353552995 353551806 0.000000e+00 1805
43 TraesCS5A01G100800 chrUn 96.853 572 18 0 1 572 356588265 356588836 0.000000e+00 957
44 TraesCS5A01G100800 chrUn 96.678 572 19 0 1 572 356586110 356586681 0.000000e+00 952
45 TraesCS5A01G100800 chrUn 86.949 613 40 17 1971 2548 37354555 37353948 0.000000e+00 652
46 TraesCS5A01G100800 chrUn 86.949 613 40 17 1971 2548 287430082 287429475 0.000000e+00 652
47 TraesCS5A01G100800 chrUn 84.638 690 45 27 1915 2548 60559861 60560545 4.630000e-177 630
48 TraesCS5A01G100800 chrUn 81.022 274 26 13 2301 2548 43409528 43409801 7.190000e-46 195
49 TraesCS5A01G100800 chrUn 80.882 272 27 13 2301 2548 20575002 20575272 9.300000e-45 191
50 TraesCS5A01G100800 chr6D 93.198 2014 91 26 572 2548 109963211 109965215 0.000000e+00 2918
51 TraesCS5A01G100800 chr6D 92.929 1994 93 21 592 2548 52521727 52519745 0.000000e+00 2857
52 TraesCS5A01G100800 chr6D 90.505 990 58 13 1587 2548 429625585 429626566 0.000000e+00 1275
53 TraesCS5A01G100800 chr4D 88.380 611 33 12 1971 2548 496431952 496431347 0.000000e+00 701
54 TraesCS5A01G100800 chr1D 81.206 282 19 6 2301 2548 435235553 435235272 2.000000e-46 196
55 TraesCS5A01G100800 chr1D 81.139 281 20 7 2301 2548 25466010 25466290 7.190000e-46 195


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 TraesCS5A01G100800 chr5A 145863479 145866026 2547 True 4706.0 4706 100.0000 1 2548 1 chr5A.!!$R1 2547
1 TraesCS5A01G100800 chr5A 606998407 606998978 571 False 957.0 957 96.8530 1 572 1 chr5A.!!$F1 571
2 TraesCS5A01G100800 chr1A 71243458 71245440 1982 True 3181.0 3181 95.6700 572 2548 1 chr1A.!!$R1 1976
3 TraesCS5A01G100800 chr1A 531498001 531499961 1960 True 3092.0 3092 95.3670 616 2548 1 chr1A.!!$R3 1932
4 TraesCS5A01G100800 chr1A 581942310 581944308 1998 False 2998.0 2998 93.9620 576 2548 1 chr1A.!!$F3 1972
5 TraesCS5A01G100800 chr1A 38372361 38374343 1982 False 2990.0 2990 94.0240 570 2545 1 chr1A.!!$F1 1975
6 TraesCS5A01G100800 chr1A 393369058 393369629 571 True 952.0 952 96.6780 1 572 1 chr1A.!!$R2 571
7 TraesCS5A01G100800 chr6A 617220984 617222870 1886 True 3162.0 3162 96.9280 572 2456 1 chr6A.!!$R3 1884
8 TraesCS5A01G100800 chr6A 200078199 200080206 2007 False 3064.0 3064 94.4800 573 2548 1 chr6A.!!$F1 1975
9 TraesCS5A01G100800 chr6A 203518917 203520913 1996 True 3022.0 3022 94.1880 572 2548 1 chr6A.!!$R2 1976
10 TraesCS5A01G100800 chr6A 484400736 484402756 2020 False 2990.0 2990 93.7190 570 2548 1 chr6A.!!$F3 1978
11 TraesCS5A01G100800 chr6A 61538294 61540321 2027 True 2857.0 2857 92.5910 576 2548 1 chr6A.!!$R1 1972
12 TraesCS5A01G100800 chr6A 409260047 409260618 571 False 957.0 957 96.8530 1 572 1 chr6A.!!$F2 571
13 TraesCS5A01G100800 chr6A 595547541 595548112 571 False 952.0 952 96.6780 1 572 1 chr6A.!!$F4 571
14 TraesCS5A01G100800 chr6B 660435859 660437744 1885 True 3155.0 3155 96.8730 572 2456 1 chr6B.!!$R1 1884
15 TraesCS5A01G100800 chr6B 585915581 585917472 1891 False 3133.0 3133 96.5660 566 2456 1 chr6B.!!$F1 1890
16 TraesCS5A01G100800 chr3A 617401017 617402906 1889 False 3153.0 3153 96.7780 567 2456 1 chr3A.!!$F2 1889
17 TraesCS5A01G100800 chr3A 735555341 735557224 1883 False 3147.0 3147 96.8170 573 2456 1 chr3A.!!$F3 1883
18 TraesCS5A01G100800 chr3A 54951912 54953801 1889 False 3142.0 3142 96.6680 567 2456 1 chr3A.!!$F1 1889
19 TraesCS5A01G100800 chr2B 776222962 776224846 1884 False 3147.0 3147 96.8190 573 2456 1 chr2B.!!$F1 1883
20 TraesCS5A01G100800 chr4A 36562913 36564799 1886 False 3138.0 3138 96.7140 573 2456 1 chr4A.!!$F1 1883
21 TraesCS5A01G100800 chr7A 701581937 701583827 1890 False 3134.0 3134 96.6160 570 2456 1 chr7A.!!$F3 1886
22 TraesCS5A01G100800 chr7A 689994362 689996371 2009 True 3101.0 3101 94.7840 571 2548 1 chr7A.!!$R5 1977
23 TraesCS5A01G100800 chr7A 49208210 49210230 2020 False 2970.0 2970 93.5770 573 2548 1 chr7A.!!$F2 1975
24 TraesCS5A01G100800 chr7A 14471060 14472736 1676 True 2566.0 2566 94.5800 901 2548 1 chr7A.!!$R1 1647
25 TraesCS5A01G100800 chr7A 36946478 36948175 1697 False 2495.0 2495 93.4940 878 2548 1 chr7A.!!$F1 1670
26 TraesCS5A01G100800 chr7A 96596399 96596970 571 True 957.0 957 96.8530 1 572 1 chr7A.!!$R2 571
27 TraesCS5A01G100800 chr7A 291744555 291745126 571 True 957.0 957 96.8530 1 572 1 chr7A.!!$R3 571
28 TraesCS5A01G100800 chr7A 566361936 566362507 571 True 957.0 957 96.8530 1 572 1 chr7A.!!$R4 571
29 TraesCS5A01G100800 chr5D 336262622 336264627 2005 False 2987.0 2987 93.7870 571 2548 1 chr5D.!!$F4 1977
30 TraesCS5A01G100800 chr5D 520495533 520497536 2003 True 2902.0 2902 93.0850 576 2548 1 chr5D.!!$R2 1972
31 TraesCS5A01G100800 chr5D 213959303 213961290 1987 False 2785.0 2785 92.1430 573 2548 1 chr5D.!!$F2 1975
32 TraesCS5A01G100800 chr5D 324809588 324811297 1709 False 2477.0 2477 93.1240 868 2548 1 chr5D.!!$F3 1680
33 TraesCS5A01G100800 chr5D 336346400 336348071 1671 True 2418.0 2418 93.0400 901 2548 1 chr5D.!!$R1 1647
34 TraesCS5A01G100800 chr2A 744582023 744584007 1984 False 2977.0 2977 93.8490 566 2548 1 chr2A.!!$F1 1982
35 TraesCS5A01G100800 chr7D 574725119 574727115 1996 True 2929.0 2929 93.3760 576 2548 1 chr7D.!!$R1 1972
36 TraesCS5A01G100800 chrUn 93724497 93726507 2010 True 2926.0 2926 93.2610 576 2548 1 chrUn.!!$R2 1972
37 TraesCS5A01G100800 chrUn 368600946 368602609 1663 False 2549.0 2549 94.4180 895 2548 1 chrUn.!!$F6 1653
38 TraesCS5A01G100800 chrUn 88420799 88422192 1393 False 2298.0 2298 96.4180 1062 2456 1 chrUn.!!$F4 1394
39 TraesCS5A01G100800 chrUn 368111971 368113276 1305 False 2132.0 2132 96.1740 1154 2456 1 chrUn.!!$F5 1302
40 TraesCS5A01G100800 chrUn 353551806 353552995 1189 True 1805.0 1805 94.4580 1388 2548 1 chrUn.!!$R4 1160
41 TraesCS5A01G100800 chrUn 356586110 356588836 2726 False 954.5 957 96.7655 1 572 2 chrUn.!!$F7 571
42 TraesCS5A01G100800 chrUn 37353948 37354555 607 True 652.0 652 86.9490 1971 2548 1 chrUn.!!$R1 577
43 TraesCS5A01G100800 chrUn 287429475 287430082 607 True 652.0 652 86.9490 1971 2548 1 chrUn.!!$R3 577
44 TraesCS5A01G100800 chrUn 60559861 60560545 684 False 630.0 630 84.6380 1915 2548 1 chrUn.!!$F3 633
45 TraesCS5A01G100800 chr6D 109963211 109965215 2004 False 2918.0 2918 93.1980 572 2548 1 chr6D.!!$F1 1976
46 TraesCS5A01G100800 chr6D 52519745 52521727 1982 True 2857.0 2857 92.9290 592 2548 1 chr6D.!!$R1 1956
47 TraesCS5A01G100800 chr6D 429625585 429626566 981 False 1275.0 1275 90.5050 1587 2548 1 chr6D.!!$F2 961
48 TraesCS5A01G100800 chr4D 496431347 496431952 605 True 701.0 701 88.3800 1971 2548 1 chr4D.!!$R1 577

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
961 3170 0.545309 TGGGAAGCTAGCAGTGGAGT 60.545 55.0 18.83 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2001 4284 6.930164 TCCATGACATTTTGGTCTTTGATTTG 59.07 34.615 0.0 0.0 38.61 2.32 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
77 78 7.139287 AGAGAGGAAGTTGATGATGATGATT 57.861 36.000 0.00 0.00 0.00 2.57
216 2372 4.471904 TGAACTATGAAGAAGCGATGGT 57.528 40.909 0.00 0.00 0.00 3.55
444 2600 4.407296 AGGGGTTGACTATGATGAGACTTC 59.593 45.833 0.00 0.00 0.00 3.01
491 2647 4.509970 CCGTCCGAATCATGTTAGCAATTA 59.490 41.667 0.00 0.00 0.00 1.40
614 2770 2.969262 TCAGTGGTGTCCATGTACTCAA 59.031 45.455 0.00 0.00 35.28 3.02
659 2815 1.351017 CTCAGTTTTGCCCCTAGTCCA 59.649 52.381 0.00 0.00 0.00 4.02
711 2867 1.343465 TCTCCGTCAGGTCAACCTTTC 59.657 52.381 0.00 0.00 46.09 2.62
792 2948 4.643387 GCGTGGCTTGTGGGACCT 62.643 66.667 0.00 0.00 0.00 3.85
850 3006 2.295253 GCTATATAAGCGGGCGACAT 57.705 50.000 0.00 0.00 42.53 3.06
933 3142 1.153269 GGAAGCTAGCTGTGGAGGC 60.153 63.158 20.16 2.06 0.00 4.70
961 3170 0.545309 TGGGAAGCTAGCAGTGGAGT 60.545 55.000 18.83 0.00 0.00 3.85
963 3172 0.610687 GGAAGCTAGCAGTGGAGTGT 59.389 55.000 18.83 0.00 0.00 3.55
1080 3319 0.934496 CTGTCTTTGTTTGTCCGCGA 59.066 50.000 8.23 0.00 0.00 5.87
1219 3462 3.119352 GGATCTTTGAGCAATGGGTTGAC 60.119 47.826 0.00 0.00 37.53 3.18
1537 3781 7.598493 ACTGGTTGTAATGTTGAAAATGTATGC 59.402 33.333 0.00 0.00 0.00 3.14
1720 3978 8.552865 CAGAAACTTTTGATCAATGAAATGCAA 58.447 29.630 9.40 0.00 0.00 4.08
1727 3985 6.432607 TGATCAATGAAATGCAACTCTCTC 57.567 37.500 0.00 0.00 0.00 3.20
2001 4284 6.189677 TCCAATTCAAATACACCGTGATTC 57.810 37.500 5.28 0.00 0.00 2.52
2199 4487 4.622456 CGCGTGGGTTTGTGGTGC 62.622 66.667 0.00 0.00 0.00 5.01
2270 4560 3.645212 GGGTAGGGAAGGAAGGTATACAC 59.355 52.174 5.01 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 8.097038 AGTAGCAACTTGATCTGAAGTTTCATA 58.903 33.333 8.13 1.33 42.33 2.15
128 2284 2.425592 CCACTCTGGTGCGGAACA 59.574 61.111 0.00 0.00 41.75 3.18
444 2600 2.202756 GCTTCGCTACGGGTGAGG 60.203 66.667 0.00 0.00 35.73 3.86
467 2623 0.582005 GCTAACATGATTCGGACGGC 59.418 55.000 0.00 0.00 0.00 5.68
491 2647 7.930325 CCATATCTCATAATCATAGAATGCGGT 59.070 37.037 0.00 0.00 0.00 5.68
574 2730 6.324770 CCACTGAGGGCAAAAGGATAATTAAT 59.675 38.462 0.00 0.00 0.00 1.40
614 2770 1.838112 TTCGCATCTGAGGGCAAAAT 58.162 45.000 5.18 0.00 0.00 1.82
659 2815 2.809601 GAACGAGTCGGTGCGCAT 60.810 61.111 15.91 0.00 0.00 4.73
792 2948 1.250840 TGCTCAACGGCTCTCTGCTA 61.251 55.000 0.00 0.00 42.39 3.49
1219 3462 1.000060 CCTGCATGAACACCAAACAGG 60.000 52.381 0.00 0.00 42.07 4.00
1420 3664 4.152580 GCTTCCTAACCTTCTTCTTCAACG 59.847 45.833 0.00 0.00 0.00 4.10
1537 3781 5.857471 TTCCTCCATAATTCATGCCTTTG 57.143 39.130 0.00 0.00 32.84 2.77
1720 3978 2.178580 CAGAAAGGCAGAGGAGAGAGT 58.821 52.381 0.00 0.00 0.00 3.24
1727 3985 2.276732 TTTGGACAGAAAGGCAGAGG 57.723 50.000 0.00 0.00 0.00 3.69
2001 4284 6.930164 TCCATGACATTTTGGTCTTTGATTTG 59.070 34.615 0.00 0.00 38.61 2.32


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

AutoCloner maintained by Alex Coulton.