Multiple sequence alignment - TraesCS3A01G481100

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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 TraesCS3A01G481100 chr3A 100.000 2185 0 0 1 2185 712308948 712311132 0.000000e+00 4036.0
1 TraesCS3A01G481100 chr3A 96.347 219 8 0 1230 1448 412693765 412693547 5.730000e-96 361.0
2 TraesCS3A01G481100 chr3A 95.000 220 11 0 1229 1448 684741811 684741592 1.610000e-91 346.0
3 TraesCS3A01G481100 chr3A 85.156 128 19 0 1633 1760 714629034 714629161 4.890000e-27 132.0
4 TraesCS3A01G481100 chr3A 87.129 101 9 3 1985 2082 727378211 727378310 6.380000e-21 111.0
5 TraesCS3A01G481100 chr3D 88.121 1187 96 21 57 1231 577153033 577151880 0.000000e+00 1369.0
6 TraesCS3A01G481100 chr3D 94.149 188 10 1 1447 1633 577151879 577151692 3.550000e-73 285.0
7 TraesCS3A01G481100 chr3B 89.861 1006 85 14 57 1052 766832586 766831588 0.000000e+00 1277.0
8 TraesCS3A01G481100 chr3B 86.719 768 65 22 57 810 768513251 768513995 0.000000e+00 819.0
9 TraesCS3A01G481100 chr3B 90.355 197 9 6 1447 1633 766831450 766831254 1.300000e-62 250.0
10 TraesCS3A01G481100 chr5D 91.971 274 15 4 922 1188 512411144 512411417 5.690000e-101 377.0
11 TraesCS3A01G481100 chr5D 91.971 274 15 4 922 1188 512418081 512418354 5.690000e-101 377.0
12 TraesCS3A01G481100 chr5D 91.941 273 15 4 922 1187 503292829 503293101 2.050000e-100 375.0
13 TraesCS3A01G481100 chr5D 91.513 271 15 5 925 1188 6175955 6175686 1.230000e-97 366.0
14 TraesCS3A01G481100 chr2D 91.971 274 15 4 922 1188 638425463 638425736 5.690000e-101 377.0
15 TraesCS3A01G481100 chr2D 78.109 201 31 10 323 513 640025656 640025853 4.930000e-22 115.0
16 TraesCS3A01G481100 chr1B 91.209 273 18 3 922 1188 633708651 633708923 1.230000e-97 366.0
17 TraesCS3A01G481100 chr1D 91.481 270 16 4 926 1188 254435995 254436264 4.430000e-97 364.0
18 TraesCS3A01G481100 chr1D 92.308 91 5 2 1985 2073 473673000 473673090 6.330000e-26 128.0
19 TraesCS3A01G481100 chr5A 90.647 278 19 4 917 1187 657452548 657452825 1.590000e-96 363.0
20 TraesCS3A01G481100 chr4A 94.783 230 12 0 1220 1449 572504790 572504561 2.060000e-95 359.0
21 TraesCS3A01G481100 chr4A 95.434 219 10 0 1230 1448 640236064 640235846 1.240000e-92 350.0
22 TraesCS3A01G481100 chr7A 95.516 223 8 1 1228 1448 50272272 50272050 2.670000e-94 355.0
23 TraesCS3A01G481100 chr7A 95.023 221 11 0 1229 1449 401405380 401405160 4.460000e-92 348.0
24 TraesCS3A01G481100 chr7A 94.196 224 12 1 1225 1448 641431636 641431414 7.470000e-90 340.0
25 TraesCS3A01G481100 chr6A 95.000 220 11 0 1229 1448 606612050 606611831 1.610000e-91 346.0
26 TraesCS3A01G481100 chr6A 84.138 145 22 1 1623 1766 586991194 586991050 2.920000e-29 139.0
27 TraesCS3A01G481100 chr6A 82.836 134 23 0 1633 1766 50190770 50190637 1.060000e-23 121.0
28 TraesCS3A01G481100 chr2A 94.570 221 12 0 1230 1450 417360448 417360228 2.080000e-90 342.0
29 TraesCS3A01G481100 chr2A 93.421 76 5 0 1985 2060 3261960 3261885 1.770000e-21 113.0
30 TraesCS3A01G481100 chr7B 96.059 203 7 1 1726 1928 60457608 60457407 1.620000e-86 329.0
31 TraesCS3A01G481100 chr7B 96.923 65 2 0 1960 2024 60457407 60457343 2.290000e-20 110.0
32 TraesCS3A01G481100 chr7B 93.548 62 4 0 2027 2088 60457318 60457257 2.310000e-15 93.5
33 TraesCS3A01G481100 chr7B 93.220 59 4 0 1632 1690 741954889 741954947 1.070000e-13 87.9
34 TraesCS3A01G481100 chr7B 93.220 59 4 0 1632 1690 741957905 741957963 1.070000e-13 87.9
35 TraesCS3A01G481100 chr7B 90.769 65 6 0 1632 1696 742899482 742899418 1.070000e-13 87.9
36 TraesCS3A01G481100 chr7B 90.769 65 6 0 1632 1696 742902756 742902692 1.070000e-13 87.9
37 TraesCS3A01G481100 chr4D 83.704 135 22 0 1632 1766 312585740 312585606 6.330000e-26 128.0
38 TraesCS3A01G481100 chr4D 92.308 65 5 0 1985 2049 469583074 469583010 2.310000e-15 93.5
39 TraesCS3A01G481100 chr7D 91.209 91 6 2 1985 2073 529483689 529483599 2.950000e-24 122.0
40 TraesCS3A01G481100 chr6B 90.000 90 7 2 1985 2072 7787 7876 4.930000e-22 115.0
41 TraesCS3A01G481100 chr5B 85.849 106 13 2 1985 2088 687395519 687395414 6.380000e-21 111.0
42 TraesCS3A01G481100 chrUn 93.220 59 4 0 1632 1690 344285179 344285237 1.070000e-13 87.9


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 TraesCS3A01G481100 chr3A 712308948 712311132 2184 False 4036.0 4036 100.000 1 2185 1 chr3A.!!$F1 2184
1 TraesCS3A01G481100 chr3D 577151692 577153033 1341 True 827.0 1369 91.135 57 1633 2 chr3D.!!$R1 1576
2 TraesCS3A01G481100 chr3B 768513251 768513995 744 False 819.0 819 86.719 57 810 1 chr3B.!!$F1 753
3 TraesCS3A01G481100 chr3B 766831254 766832586 1332 True 763.5 1277 90.108 57 1633 2 chr3B.!!$R1 1576


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
55 56 0.449388 GATTAGTGGTGTGCTGCTGC 59.551 55.0 8.89 8.89 40.2 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1261 1292 0.035439 ATTGACAACCTAGGGGCACG 60.035 55.0 14.81 0.0 35.63 5.34 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.