Multiple sequence alignment - TraesCS1A01G212600

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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 TraesCS1A01G212600 chr1A 100.000 3703 0 0 1 3703 375466613 375470315 0.000000e+00 6839.0
1 TraesCS1A01G212600 chr1A 85.588 340 40 4 2365 2704 375112664 375112334 7.610000e-92 348.0
2 TraesCS1A01G212600 chr1A 92.982 171 11 1 1 170 476908458 476908288 7.940000e-62 248.0
3 TraesCS1A01G212600 chr1A 80.178 338 58 4 2369 2706 374689986 374689658 1.030000e-60 244.0
4 TraesCS1A01G212600 chr1A 84.043 188 28 2 1679 1865 375113130 375112944 2.940000e-41 180.0
5 TraesCS1A01G212600 chr1A 88.136 59 6 1 1152 1210 374959678 374959621 6.640000e-08 69.4
6 TraesCS1A01G212600 chr1D 93.456 1467 52 18 865 2310 300858278 300859721 0.000000e+00 2137.0
7 TraesCS1A01G212600 chr1D 95.718 794 17 6 2312 3093 300859778 300860566 0.000000e+00 1262.0
8 TraesCS1A01G212600 chr1D 91.971 411 23 8 185 593 300857880 300858282 5.370000e-158 568.0
9 TraesCS1A01G212600 chr1D 91.206 398 22 10 3316 3703 300860815 300861209 2.530000e-146 529.0
10 TraesCS1A01G212600 chr1D 86.176 340 38 4 2365 2704 300718368 300718038 3.520000e-95 359.0
11 TraesCS1A01G212600 chr1D 80.952 336 55 4 2368 2703 300326114 300325788 1.320000e-64 257.0
12 TraesCS1A01G212600 chr1D 85.549 173 18 7 2 170 270036674 270036843 1.370000e-39 174.0
13 TraesCS1A01G212600 chr1D 83.598 189 28 3 1679 1865 300718826 300718639 1.370000e-39 174.0
14 TraesCS1A01G212600 chr1D 85.465 172 19 6 2 170 431797783 431797951 1.370000e-39 174.0
15 TraesCS1A01G212600 chr1B 91.450 1462 60 31 868 2312 406035689 406037102 0.000000e+00 1947.0
16 TraesCS1A01G212600 chr1B 88.000 1400 57 46 2355 3687 406037229 406038584 0.000000e+00 1552.0
17 TraesCS1A01G212600 chr1B 93.187 411 21 4 187 593 406035274 406035681 6.850000e-167 597.0
18 TraesCS1A01G212600 chr1B 97.857 280 6 0 589 868 373149760 373149481 5.560000e-133 484.0
19 TraesCS1A01G212600 chr1B 85.000 340 42 4 2365 2704 405905528 405905198 1.650000e-88 337.0
20 TraesCS1A01G212600 chr1B 79.651 344 59 6 2368 2710 405525353 405525020 1.720000e-58 237.0
21 TraesCS1A01G212600 chr1B 83.511 188 29 2 1679 1865 405905985 405905799 1.370000e-39 174.0
22 TraesCS1A01G212600 chr1B 87.931 58 7 0 1153 1210 405673617 405673560 6.640000e-08 69.4
23 TraesCS1A01G212600 chr1B 100.000 28 0 0 3676 3703 406038584 406038611 7.000000e-03 52.8
24 TraesCS1A01G212600 chr7A 98.246 285 5 0 586 870 460109694 460109410 1.990000e-137 499.0
25 TraesCS1A01G212600 chr2A 97.872 282 6 0 589 870 773800680 773800399 4.300000e-134 488.0
26 TraesCS1A01G212600 chr2A 86.782 174 21 2 2 173 650492320 650492493 3.770000e-45 193.0
27 TraesCS1A01G212600 chr7B 97.857 280 6 0 589 868 388157173 388157452 5.560000e-133 484.0
28 TraesCS1A01G212600 chr7B 97.213 287 6 2 584 869 503365307 503365592 5.560000e-133 484.0
29 TraesCS1A01G212600 chr7B 87.135 171 20 2 3 172 87120734 87120903 3.770000e-45 193.0
30 TraesCS1A01G212600 chr6B 97.857 280 6 0 589 868 680300796 680301075 5.560000e-133 484.0
31 TraesCS1A01G212600 chr2B 97.857 280 6 0 589 868 81318791 81319070 5.560000e-133 484.0
32 TraesCS1A01G212600 chr4B 96.552 290 8 2 579 868 396520527 396520240 2.590000e-131 479.0
33 TraesCS1A01G212600 chr4B 88.563 341 34 3 2365 2701 659329679 659329340 3.440000e-110 409.0
34 TraesCS1A01G212600 chr4B 87.027 185 24 0 1682 1866 659330285 659330101 3.750000e-50 209.0
35 TraesCS1A01G212600 chr3B 95.932 295 9 3 593 886 696324536 696324244 3.350000e-130 475.0
36 TraesCS1A01G212600 chr3B 86.250 160 20 2 1707 1865 766631768 766631926 4.920000e-39 172.0
37 TraesCS1A01G212600 chr5A 87.966 349 36 5 2359 2701 694760245 694760593 1.240000e-109 407.0
38 TraesCS1A01G212600 chr5A 86.458 192 26 0 1682 1873 694759648 694759839 1.040000e-50 211.0
39 TraesCS1A01G212600 chr5A 74.438 356 65 12 2365 2695 693673783 693673429 3.000000e-26 130.0
40 TraesCS1A01G212600 chr5A 98.000 50 1 0 3360 3409 37403663 37403712 1.830000e-13 87.9
41 TraesCS1A01G212600 chr4D 86.559 372 35 10 2355 2712 508501893 508502263 2.680000e-106 396.0
42 TraesCS1A01G212600 chr6D 93.529 170 10 1 1 169 84476331 84476162 6.140000e-63 252.0
43 TraesCS1A01G212600 chr7D 88.235 170 17 3 3 170 577854130 577853962 2.260000e-47 200.0
44 TraesCS1A01G212600 chr7D 84.884 172 21 3 2 172 158993234 158993401 6.360000e-38 169.0
45 TraesCS1A01G212600 chr3A 85.119 168 24 1 2 168 595281722 595281889 1.770000e-38 171.0
46 TraesCS1A01G212600 chr6A 86.842 152 18 2 1707 1857 399722494 399722644 6.360000e-38 169.0


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 TraesCS1A01G212600 chr1A 375466613 375470315 3702 False 6839.0 6839 100.00000 1 3703 1 chr1A.!!$F1 3702
1 TraesCS1A01G212600 chr1A 375112334 375113130 796 True 264.0 348 84.81550 1679 2704 2 chr1A.!!$R4 1025
2 TraesCS1A01G212600 chr1D 300857880 300861209 3329 False 1124.0 2137 93.08775 185 3703 4 chr1D.!!$F3 3518
3 TraesCS1A01G212600 chr1D 300718038 300718826 788 True 266.5 359 84.88700 1679 2704 2 chr1D.!!$R2 1025
4 TraesCS1A01G212600 chr1B 406035274 406038611 3337 False 1037.2 1947 93.15925 187 3703 4 chr1B.!!$F1 3516
5 TraesCS1A01G212600 chr1B 405905198 405905985 787 True 255.5 337 84.25550 1679 2704 2 chr1B.!!$R4 1025
6 TraesCS1A01G212600 chr4B 659329340 659330285 945 True 309.0 409 87.79500 1682 2701 2 chr4B.!!$R2 1019
7 TraesCS1A01G212600 chr5A 694759648 694760593 945 False 309.0 407 87.21200 1682 2701 2 chr5A.!!$F2 1019


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
600 610 0.037326 CTCGTTGCTTAGGCTGGTCA 60.037 55.0 0.00 0.0 39.59 4.02 F
610 620 0.043334 AGGCTGGTCATAGTGGGAGT 59.957 55.0 0.00 0.0 0.00 3.85 F
1676 1713 0.161024 CGAAGCTGACGTTTCGTTCC 59.839 55.0 11.05 0.0 45.15 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1542 1576 0.530650 AGCGACTCAACACACACAGG 60.531 55.0 0.00 0.0 0.0 4.00 R
1983 2022 0.604511 ACTTTTAACTGCCCGGACGG 60.605 55.0 0.73 0.0 0.0 4.79 R
3247 3793 0.105964 GGCGCCAACTTTTTCCCTTT 59.894 50.0 24.80 0.0 0.0 3.11 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)



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AutoCloner maintained by Alex Coulton.