Multiple sequence alignment - TraesCS3D01G453100

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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 TraesCS3D01G453100 chr3D 100.000 4934 0 0 1 4934 560316969 560321902 0.000000e+00 9112.0
1 TraesCS3D01G453100 chr3A 92.268 3272 165 34 894 4119 628697949 628701178 0.000000e+00 4560.0
2 TraesCS3D01G453100 chr3A 92.611 3221 149 39 948 4119 629054177 629050997 0.000000e+00 4547.0
3 TraesCS3D01G453100 chr3A 95.433 416 18 1 3705 4119 629048352 629047937 0.000000e+00 662.0
4 TraesCS3D01G453100 chr3A 88.814 295 22 7 434 722 628697460 628697749 7.860000e-93 351.0
5 TraesCS3D01G453100 chr3A 83.575 207 13 5 163 369 628695353 628695538 1.830000e-39 174.0
6 TraesCS3D01G453100 chr3A 87.413 143 3 5 434 576 629054310 629054183 3.080000e-32 150.0
7 TraesCS3D01G453100 chr3A 100.000 44 0 0 379 422 628697348 628697391 1.140000e-11 82.4
8 TraesCS3D01G453100 chr3B 91.363 2941 130 43 1234 4119 746877983 746875112 0.000000e+00 3910.0
9 TraesCS3D01G453100 chr3B 88.936 2594 137 50 615 3109 744577548 744580090 0.000000e+00 3062.0
10 TraesCS3D01G453100 chr3B 91.929 1016 49 14 3118 4119 744579831 744580827 0.000000e+00 1391.0
11 TraesCS3D01G453100 chr3B 86.177 586 33 17 615 1167 746879520 746878950 1.530000e-164 590.0
12 TraesCS3D01G453100 chr5A 81.450 593 50 26 4269 4825 709755020 709755588 9.810000e-117 431.0
13 TraesCS3D01G453100 chr4D 76.391 809 140 29 4171 4934 452793279 452794081 5.990000e-104 388.0
14 TraesCS3D01G453100 chrUn 81.621 506 44 23 4169 4633 162972851 162972354 1.680000e-99 374.0
15 TraesCS3D01G453100 chrUn 81.621 506 44 23 4169 4633 163013070 163012573 1.680000e-99 374.0
16 TraesCS3D01G453100 chrUn 81.621 506 44 23 4169 4633 402046632 402047129 1.680000e-99 374.0
17 TraesCS3D01G453100 chrUn 81.423 506 45 23 4169 4633 162945294 162944797 7.800000e-98 368.0
18 TraesCS3D01G453100 chrUn 81.713 432 33 22 4242 4633 163033169 163032744 7.970000e-83 318.0
19 TraesCS3D01G453100 chrUn 85.714 140 16 2 4169 4307 430926517 430926653 1.430000e-30 145.0
20 TraesCS3D01G453100 chrUn 79.724 217 21 9 4169 4369 309716762 309716553 8.620000e-28 135.0
21 TraesCS3D01G453100 chr7D 79.912 453 89 2 4465 4916 2859039 2859490 1.020000e-86 331.0
22 TraesCS3D01G453100 chr7D 74.531 852 153 38 4107 4898 635506169 635507016 3.710000e-81 313.0
23 TraesCS3D01G453100 chr5D 93.617 94 6 0 4273 4366 40958430 40958337 1.850000e-29 141.0
24 TraesCS3D01G453100 chr2B 79.724 217 21 9 4169 4369 41094003 41093794 8.620000e-28 135.0
25 TraesCS3D01G453100 chr7A 91.489 47 4 0 2484 2530 11033034 11033080 1.150000e-06 65.8
26 TraesCS3D01G453100 chr6D 100.000 29 0 0 56 84 82965178 82965150 2.000000e-03 54.7
27 TraesCS3D01G453100 chr6D 100.000 28 0 0 56 83 82969763 82969736 9.000000e-03 52.8


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 TraesCS3D01G453100 chr3D 560316969 560321902 4933 False 9112.000000 9112 100.00000 1 4934 1 chr3D.!!$F1 4933
1 TraesCS3D01G453100 chr3A 629047937 629054310 6373 True 1786.333333 4547 91.81900 434 4119 3 chr3A.!!$R1 3685
2 TraesCS3D01G453100 chr3A 628695353 628701178 5825 False 1291.850000 4560 91.16425 163 4119 4 chr3A.!!$F1 3956
3 TraesCS3D01G453100 chr3B 746875112 746879520 4408 True 2250.000000 3910 88.77000 615 4119 2 chr3B.!!$R1 3504
4 TraesCS3D01G453100 chr3B 744577548 744580827 3279 False 2226.500000 3062 90.43250 615 4119 2 chr3B.!!$F1 3504
5 TraesCS3D01G453100 chr5A 709755020 709755588 568 False 431.000000 431 81.45000 4269 4825 1 chr5A.!!$F1 556
6 TraesCS3D01G453100 chr4D 452793279 452794081 802 False 388.000000 388 76.39100 4171 4934 1 chr4D.!!$F1 763
7 TraesCS3D01G453100 chr7D 635506169 635507016 847 False 313.000000 313 74.53100 4107 4898 1 chr7D.!!$F2 791


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
144 145 0.447801 ATCGCTGCCAATTCGTGTTC 59.552 50.0 0.00 0.00 0.00 3.18 F
537 2395 0.617820 CCTCCTCTCCCCGGAAAAGA 60.618 60.0 0.73 1.09 0.00 2.52 F
1493 4436 0.251354 TTCAGGTCTCAGGAGCATGC 59.749 55.0 10.51 10.51 41.89 4.06 F
1710 4653 0.178068 ACACGTATCCTCATGTGGGC 59.822 55.0 13.71 4.35 39.33 5.36 F
2167 5142 0.732880 CTACGCCAGAAGACACGTGG 60.733 60.0 21.57 0.31 39.43 4.94 F
2837 5825 0.951040 GTGGTCAGCTGTACCTGCAC 60.951 60.0 25.75 16.85 37.91 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1125 3087 0.609131 AACGAGCCCCCATTGACAAG 60.609 55.000 0.00 0.00 0.00 3.16 R
1695 4638 1.071471 CCCGCCCACATGAGGATAC 59.929 63.158 11.19 0.00 0.00 2.24 R
2570 5551 0.603569 ACACGAAGCACTCCAGGTAG 59.396 55.000 0.00 0.00 0.00 3.18 R
3378 6382 1.065926 CAGCCATAGCAGTGACCTTCA 60.066 52.381 0.00 0.00 43.56 3.02 R
3493 6497 2.256117 TCCATAGTCTCTGCGATCGA 57.744 50.000 21.57 3.01 0.00 3.59 R
4370 10456 0.035458 AAAGGAGAAGGCACTGACGG 59.965 55.000 0.00 0.00 40.86 4.79 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.