Multiple sequence alignment - TraesCS3A01G459400

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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 TraesCS3A01G459400 chr3A 100.000 1764 0 0 669 2432 696051398 696049635 0.000000e+00 3258.0
1 TraesCS3A01G459400 chr3A 98.131 1766 24 5 669 2432 628713479 628711721 0.000000e+00 3070.0
2 TraesCS3A01G459400 chr3A 87.831 756 86 2 669 1418 696060261 696059506 0.000000e+00 881.0
3 TraesCS3A01G459400 chr3A 85.980 699 94 4 676 1372 695878805 695878109 0.000000e+00 745.0
4 TraesCS3A01G459400 chr3A 82.542 716 111 9 727 1441 628658045 628657343 3.440000e-173 617.0
5 TraesCS3A01G459400 chr3A 100.000 249 0 0 1 249 696052066 696051818 6.130000e-126 460.0
6 TraesCS3A01G459400 chr3A 93.846 195 4 1 4 198 628713650 628713464 1.100000e-73 287.0
7 TraesCS3A01G459400 chr3B 92.514 1563 99 9 669 2213 743542466 743540904 0.000000e+00 2222.0
8 TraesCS3A01G459400 chr3B 80.889 1193 153 34 669 1805 743123700 743122527 0.000000e+00 870.0
9 TraesCS3A01G459400 chr3B 84.674 783 107 6 669 1441 742668880 742668101 0.000000e+00 769.0
10 TraesCS3A01G459400 chr3B 85.035 715 100 6 728 1441 742513231 742512523 0.000000e+00 721.0
11 TraesCS3A01G459400 chr3B 84.916 179 8 3 2 169 743544264 743544094 1.930000e-36 163.0
12 TraesCS3A01G459400 chr3B 95.349 43 2 0 2213 2255 743521553 743521511 4.340000e-08 69.4
13 TraesCS3A01G459400 chr3B 96.875 32 1 0 2390 2421 25037431 25037462 1.000000e-03 54.7
14 TraesCS3A01G459400 chr3B 96.875 32 1 0 2390 2421 510195789 510195820 1.000000e-03 54.7
15 TraesCS3A01G459400 chr3D 94.645 803 27 3 1454 2255 559775949 559775162 0.000000e+00 1230.0
16 TraesCS3A01G459400 chr3D 95.000 740 37 0 669 1408 559776684 559775945 0.000000e+00 1162.0
17 TraesCS3A01G459400 chr3D 85.667 907 99 14 669 1544 559793759 559792853 0.000000e+00 926.0
18 TraesCS3A01G459400 chr3D 82.880 368 31 15 1455 1805 559611568 559611216 3.930000e-78 302.0
19 TraesCS3A01G459400 chr3D 91.160 181 11 5 2255 2432 327459929 327460107 8.690000e-60 241.0
20 TraesCS3A01G459400 chr3D 92.958 71 3 1 133 203 559776738 559776670 4.280000e-18 102.0
21 TraesCS3A01G459400 chr7A 90.608 181 13 3 2253 2432 718240894 718240717 1.120000e-58 237.0
22 TraesCS3A01G459400 chr4B 90.055 181 13 4 2254 2431 227208933 227208755 1.880000e-56 230.0
23 TraesCS3A01G459400 chr6B 96.875 32 1 0 2390 2421 282444360 282444329 1.000000e-03 54.7
24 TraesCS3A01G459400 chr5B 96.875 32 1 0 2390 2421 675066978 675066947 1.000000e-03 54.7


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 TraesCS3A01G459400 chr3A 696049635 696052066 2431 True 1859.000000 3258 100.0000 1 2432 2 chr3A.!!$R5 2431
1 TraesCS3A01G459400 chr3A 628711721 628713650 1929 True 1678.500000 3070 95.9885 4 2432 2 chr3A.!!$R4 2428
2 TraesCS3A01G459400 chr3A 696059506 696060261 755 True 881.000000 881 87.8310 669 1418 1 chr3A.!!$R3 749
3 TraesCS3A01G459400 chr3A 695878109 695878805 696 True 745.000000 745 85.9800 676 1372 1 chr3A.!!$R2 696
4 TraesCS3A01G459400 chr3A 628657343 628658045 702 True 617.000000 617 82.5420 727 1441 1 chr3A.!!$R1 714
5 TraesCS3A01G459400 chr3B 743540904 743544264 3360 True 1192.500000 2222 88.7150 2 2213 2 chr3B.!!$R5 2211
6 TraesCS3A01G459400 chr3B 743122527 743123700 1173 True 870.000000 870 80.8890 669 1805 1 chr3B.!!$R3 1136
7 TraesCS3A01G459400 chr3B 742668101 742668880 779 True 769.000000 769 84.6740 669 1441 1 chr3B.!!$R2 772
8 TraesCS3A01G459400 chr3B 742512523 742513231 708 True 721.000000 721 85.0350 728 1441 1 chr3B.!!$R1 713
9 TraesCS3A01G459400 chr3D 559792853 559793759 906 True 926.000000 926 85.6670 669 1544 1 chr3D.!!$R2 875
10 TraesCS3A01G459400 chr3D 559775162 559776738 1576 True 831.333333 1230 94.2010 133 2255 3 chr3D.!!$R3 2122

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
241 1807 0.478507 GAGAGAGAGGGAGAGGGAGG 59.521 65.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1853 3514 0.669318 CAGGGTGTGTGCGTATCGTT 60.669 55.0 0.0 0.0 0.0 3.85 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
53 54 5.507482 CGTCATACATATCTCTTCCAACGGT 60.507 44.000 0.0 0.0 0.0 4.83
54 55 5.921408 GTCATACATATCTCTTCCAACGGTC 59.079 44.000 0.0 0.0 0.0 4.79
55 56 5.596772 TCATACATATCTCTTCCAACGGTCA 59.403 40.000 0.0 0.0 0.0 4.02
56 57 4.124851 ACATATCTCTTCCAACGGTCAC 57.875 45.455 0.0 0.0 0.0 3.67
57 58 3.513912 ACATATCTCTTCCAACGGTCACA 59.486 43.478 0.0 0.0 0.0 3.58
58 59 2.751166 ATCTCTTCCAACGGTCACAG 57.249 50.000 0.0 0.0 0.0 3.66
59 60 1.699730 TCTCTTCCAACGGTCACAGA 58.300 50.000 0.0 0.0 0.0 3.41
60 61 1.340248 TCTCTTCCAACGGTCACAGAC 59.660 52.381 0.0 0.0 0.0 3.51
182 194 1.135333 GCGTTCCTTGGAGAGACTAGG 59.865 57.143 0.0 0.0 0.0 3.02
195 230 2.372172 GAGACTAGGGGAGAGAGAGAGG 59.628 59.091 0.0 0.0 0.0 3.69
209 244 2.370189 GAGAGAGGGAGAGAGAGAGAGG 59.630 59.091 0.0 0.0 0.0 3.69
222 257 3.312890 AGAGAGAGGGAGAGAGAGAGAG 58.687 54.545 0.0 0.0 0.0 3.20
224 259 3.312890 AGAGAGGGAGAGAGAGAGAGAG 58.687 54.545 0.0 0.0 0.0 3.20
225 260 3.051803 AGAGAGGGAGAGAGAGAGAGAGA 60.052 52.174 0.0 0.0 0.0 3.10
227 262 3.051803 AGAGGGAGAGAGAGAGAGAGAGA 60.052 52.174 0.0 0.0 0.0 3.10
234 269 3.312890 AGAGAGAGAGAGAGAGAGGGAG 58.687 54.545 0.0 0.0 0.0 4.30
235 270 3.051803 AGAGAGAGAGAGAGAGAGGGAGA 60.052 52.174 0.0 0.0 0.0 3.71
241 1807 0.478507 GAGAGAGAGGGAGAGGGAGG 59.521 65.000 0.0 0.0 0.0 4.30
242 1808 0.998945 AGAGAGAGGGAGAGGGAGGG 60.999 65.000 0.0 0.0 0.0 4.30
243 1809 0.996762 GAGAGAGGGAGAGGGAGGGA 60.997 65.000 0.0 0.0 0.0 4.20
244 1810 0.998945 AGAGAGGGAGAGGGAGGGAG 60.999 65.000 0.0 0.0 0.0 4.30
245 1811 0.996762 GAGAGGGAGAGGGAGGGAGA 60.997 65.000 0.0 0.0 0.0 3.71
246 1812 0.998945 AGAGGGAGAGGGAGGGAGAG 60.999 65.000 0.0 0.0 0.0 3.20
247 1813 0.996762 GAGGGAGAGGGAGGGAGAGA 60.997 65.000 0.0 0.0 0.0 3.10
248 1814 0.998945 AGGGAGAGGGAGGGAGAGAG 60.999 65.000 0.0 0.0 0.0 3.20
1083 2663 2.172505 TGATCACCCGCAAATGGACTAT 59.827 45.455 0.0 0.0 0.0 2.12
1165 2751 1.669115 CTCCACTTGCCGTCACTGG 60.669 63.158 0.0 0.0 0.0 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.036875 ACTTTCCCTTTCGCTCCCTG 59.963 55.000 0.00 0.0 0.00 4.45
1 2 0.325272 GACTTTCCCTTTCGCTCCCT 59.675 55.000 0.00 0.0 0.00 4.20
2 3 0.325272 AGACTTTCCCTTTCGCTCCC 59.675 55.000 0.00 0.0 0.00 4.30
53 54 2.826337 ACTGCCTGTGAGTCTGTGA 58.174 52.632 0.00 0.0 0.00 3.58
85 86 2.776536 CTGAGGGTCTCCATCTGGAAAT 59.223 50.000 0.00 0.0 44.91 2.17
182 194 1.421646 CTCTCTCCCTCTCTCTCTCCC 59.578 61.905 0.00 0.0 0.00 4.30
195 230 2.370189 CTCTCTCCCTCTCTCTCTCTCC 59.630 59.091 0.00 0.0 0.00 3.71
209 244 3.323403 CCTCTCTCTCTCTCTCTCTCTCC 59.677 56.522 0.00 0.0 0.00 3.71
222 257 0.478507 CCTCCCTCTCCCTCTCTCTC 59.521 65.000 0.00 0.0 0.00 3.20
224 259 0.996762 TCCCTCCCTCTCCCTCTCTC 60.997 65.000 0.00 0.0 0.00 3.20
225 260 0.998945 CTCCCTCCCTCTCCCTCTCT 60.999 65.000 0.00 0.0 0.00 3.10
227 262 0.998945 CTCTCCCTCCCTCTCCCTCT 60.999 65.000 0.00 0.0 0.00 3.69
825 2400 2.586635 GACACAACCACGTCGCCA 60.587 61.111 0.00 0.0 0.00 5.69
1165 2751 3.068873 TGGCTGAAAACCAAACATACCAC 59.931 43.478 0.00 0.0 33.12 4.16
1853 3514 0.669318 CAGGGTGTGTGCGTATCGTT 60.669 55.000 0.00 0.0 0.00 3.85
2182 3844 0.992695 ACCAAACCTAGGGAAGAGCC 59.007 55.000 14.81 0.0 0.00 4.70


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

AutoCloner maintained by Alex Coulton.