Multiple sequence alignment - TraesCS1D01G281000

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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 TraesCS1D01G281000 chr1D 100.000 5194 0 0 1 5194 379452155 379457348 0.000000e+00 9592.0
1 TraesCS1D01G281000 chr1D 89.326 178 13 4 4198 4371 324412389 324412214 8.760000e-53 219.0
2 TraesCS1D01G281000 chr1D 97.959 49 1 0 4589 4637 115574106 115574058 9.270000e-13 86.1
3 TraesCS1D01G281000 chr1A 94.443 3455 117 34 796 4197 480546484 480549916 0.000000e+00 5247.0
4 TraesCS1D01G281000 chr1A 91.367 417 33 3 4734 5149 511219648 511219234 7.550000e-158 568.0
5 TraesCS1D01G281000 chr1A 90.574 244 19 2 4355 4594 480549915 480550158 2.330000e-83 320.0
6 TraesCS1D01G281000 chr1A 100.000 33 0 0 5146 5178 480550317 480550349 1.560000e-05 62.1
7 TraesCS1D01G281000 chr1B 90.840 1976 94 36 800 2732 508540866 508542797 0.000000e+00 2566.0
8 TraesCS1D01G281000 chr1B 96.655 867 25 4 3331 4197 508543585 508544447 0.000000e+00 1437.0
9 TraesCS1D01G281000 chr1B 92.203 590 25 8 2749 3332 508542947 508543521 0.000000e+00 815.0
10 TraesCS1D01G281000 chr1B 94.256 383 18 2 4355 4733 508544446 508544828 2.700000e-162 582.0
11 TraesCS1D01G281000 chr1B 91.071 168 11 3 4194 4358 314565535 314565701 1.880000e-54 224.0
12 TraesCS1D01G281000 chr1B 89.326 178 13 4 4198 4371 436689151 436688976 8.760000e-53 219.0
13 TraesCS1D01G281000 chr1B 96.078 51 1 1 5145 5194 508544819 508544869 1.200000e-11 82.4
14 TraesCS1D01G281000 chr7A 94.981 797 36 4 1 795 20655785 20654991 0.000000e+00 1247.0
15 TraesCS1D01G281000 chr7A 94.643 56 2 1 4591 4646 561581039 561580985 9.270000e-13 86.1
16 TraesCS1D01G281000 chr7D 94.836 794 37 4 1 792 32697831 32698622 0.000000e+00 1236.0
17 TraesCS1D01G281000 chr7D 91.990 412 30 3 4734 5145 89076138 89075730 4.510000e-160 575.0
18 TraesCS1D01G281000 chr7B 94.836 794 37 4 1 791 674964571 674965363 0.000000e+00 1236.0
19 TraesCS1D01G281000 chr2B 94.830 793 38 3 1 791 694247624 694246833 0.000000e+00 1234.0
20 TraesCS1D01G281000 chr2B 92.718 412 21 6 4734 5145 391525938 391525536 2.080000e-163 586.0
21 TraesCS1D01G281000 chr2B 91.807 415 30 3 4734 5146 785279438 785279026 4.510000e-160 575.0
22 TraesCS1D01G281000 chr2B 91.566 166 10 2 4195 4356 578597700 578597865 5.230000e-55 226.0
23 TraesCS1D01G281000 chr3B 94.584 794 39 4 1 791 744908679 744909471 0.000000e+00 1225.0
24 TraesCS1D01G281000 chr3B 94.458 794 36 6 1 791 804746747 804745959 0.000000e+00 1216.0
25 TraesCS1D01G281000 chr3B 94.081 794 43 4 6 797 631665159 631664368 0.000000e+00 1203.0
26 TraesCS1D01G281000 chr3B 90.951 431 28 10 4726 5152 521474899 521475322 2.100000e-158 569.0
27 TraesCS1D01G281000 chr6B 94.332 794 42 3 1 792 665693912 665694704 0.000000e+00 1214.0
28 TraesCS1D01G281000 chr6B 85.915 71 7 1 4593 4660 237701955 237701885 7.210000e-09 73.1
29 TraesCS1D01G281000 chr4B 93.992 799 44 4 1 797 570126233 570125437 0.000000e+00 1206.0
30 TraesCS1D01G281000 chr4D 93.947 413 23 2 4734 5146 334160740 334160330 1.590000e-174 623.0
31 TraesCS1D01G281000 chr4A 92.961 412 21 7 4734 5145 738099138 738098735 1.250000e-165 593.0
32 TraesCS1D01G281000 chr5A 92.574 404 27 2 4743 5146 600045474 600045074 1.250000e-160 577.0
33 TraesCS1D01G281000 chr5B 91.827 416 27 6 4734 5145 608557272 608556860 1.620000e-159 573.0
34 TraesCS1D01G281000 chr2A 92.593 162 10 1 4198 4357 696850717 696850878 1.120000e-56 231.0
35 TraesCS1D01G281000 chr2A 91.617 167 10 2 4194 4356 70985750 70985584 1.460000e-55 228.0
36 TraesCS1D01G281000 chr2A 94.444 54 2 1 4591 4644 159097068 159097016 1.200000e-11 82.4
37 TraesCS1D01G281000 chr3D 92.121 165 9 3 4197 4357 577155173 577155009 4.050000e-56 230.0
38 TraesCS1D01G281000 chrUn 92.025 163 10 2 4197 4356 178663685 178663523 5.230000e-55 226.0
39 TraesCS1D01G281000 chrUn 92.025 163 10 2 4197 4356 178723572 178723410 5.230000e-55 226.0
40 TraesCS1D01G281000 chrUn 98.000 50 1 0 4589 4638 42338338 42338387 2.580000e-13 87.9
41 TraesCS1D01G281000 chrUn 98.000 50 1 0 4589 4638 42530611 42530562 2.580000e-13 87.9
42 TraesCS1D01G281000 chrUn 98.000 50 1 0 4589 4638 474064264 474064215 2.580000e-13 87.9
43 TraesCS1D01G281000 chr3A 94.545 55 2 1 4591 4645 616476018 616476071 3.330000e-12 84.2


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 TraesCS1D01G281000 chr1D 379452155 379457348 5193 False 9592.000000 9592 100.000000 1 5194 1 chr1D.!!$F1 5193
1 TraesCS1D01G281000 chr1A 480546484 480550349 3865 False 1876.366667 5247 95.005667 796 5178 3 chr1A.!!$F1 4382
2 TraesCS1D01G281000 chr1B 508540866 508544869 4003 False 1096.480000 2566 94.006400 800 5194 5 chr1B.!!$F2 4394
3 TraesCS1D01G281000 chr7A 20654991 20655785 794 True 1247.000000 1247 94.981000 1 795 1 chr7A.!!$R1 794
4 TraesCS1D01G281000 chr7D 32697831 32698622 791 False 1236.000000 1236 94.836000 1 792 1 chr7D.!!$F1 791
5 TraesCS1D01G281000 chr7B 674964571 674965363 792 False 1236.000000 1236 94.836000 1 791 1 chr7B.!!$F1 790
6 TraesCS1D01G281000 chr2B 694246833 694247624 791 True 1234.000000 1234 94.830000 1 791 1 chr2B.!!$R2 790
7 TraesCS1D01G281000 chr3B 744908679 744909471 792 False 1225.000000 1225 94.584000 1 791 1 chr3B.!!$F2 790
8 TraesCS1D01G281000 chr3B 804745959 804746747 788 True 1216.000000 1216 94.458000 1 791 1 chr3B.!!$R2 790
9 TraesCS1D01G281000 chr3B 631664368 631665159 791 True 1203.000000 1203 94.081000 6 797 1 chr3B.!!$R1 791
10 TraesCS1D01G281000 chr6B 665693912 665694704 792 False 1214.000000 1214 94.332000 1 792 1 chr6B.!!$F1 791
11 TraesCS1D01G281000 chr4B 570125437 570126233 796 True 1206.000000 1206 93.992000 1 797 1 chr4B.!!$R1 796


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
924 934 1.457346 CAGCCACATGAGGGTTTCTC 58.543 55.000 11.46 0.00 42.74 2.87 F
1535 1568 1.062810 AGGGAGCCCTCTAGGTAACAG 60.063 57.143 1.14 0.00 44.43 3.16 F
1767 1802 0.035458 AGTTCGAAAGGGCCTGAGTG 59.965 55.000 6.92 0.00 0.00 3.51 F
1777 1812 0.108424 GGCCTGAGTGTAGCTGTGAG 60.108 60.000 0.00 0.00 0.00 3.51 F
3419 3709 0.237498 GTCCGTGTTTTGGCTAGCAC 59.763 55.000 18.24 6.51 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 1802 1.066573 ACATCACAGGCTCACAGCTAC 60.067 52.381 0.00 0.00 41.99 3.58 R
3508 3798 0.447801 CCCAGCGAAGAAATTCCACG 59.552 55.000 5.37 5.37 0.00 4.94 R
3544 3834 0.677731 ACCAAGATGATGCACCACCG 60.678 55.000 0.00 0.00 0.00 4.94 R
3720 4010 4.464008 GGGAATTGAGGATATGCAGTTCA 58.536 43.478 0.00 0.00 33.86 3.18 R
4724 5071 0.325296 AATCCGCCTCCACCACTCTA 60.325 55.000 0.00 0.00 0.00 2.43 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.