Multiple sequence alignment - TraesCS7D01G043500

Loading Multiple Alignment...

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 TraesCS7D01G043500 chr7D 100.000 2795 0 0 1 2795 22510756 22507962 0.000000e+00 5162.0
1 TraesCS7D01G043500 chr7D 90.111 991 56 16 760 1726 22270429 22269457 0.000000e+00 1249.0
2 TraesCS7D01G043500 chr7D 88.170 989 81 19 760 1726 22523176 22522202 0.000000e+00 1146.0
3 TraesCS7D01G043500 chr7D 86.559 558 41 9 1722 2248 22522247 22521693 4.010000e-163 584.0
4 TraesCS7D01G043500 chr7D 78.404 727 85 32 59 748 22271591 22270900 9.320000e-110 407.0
5 TraesCS7D01G043500 chr7D 81.230 309 24 10 1663 1945 22269557 22269257 4.690000e-53 219.0
6 TraesCS7D01G043500 chr7D 93.651 63 4 0 1 63 213380299 213380237 8.240000e-16 95.3
7 TraesCS7D01G043500 chr7A 89.474 1520 90 29 761 2260 22916649 22915180 0.000000e+00 1857.0
8 TraesCS7D01G043500 chr7A 89.836 974 51 12 760 1726 22898543 22897611 0.000000e+00 1206.0
9 TraesCS7D01G043500 chr7A 78.175 559 71 25 1718 2237 22897660 22897114 2.700000e-80 309.0
10 TraesCS7D01G043500 chr7A 92.157 51 3 1 1676 1726 22915727 22915678 1.390000e-08 71.3
11 TraesCS7D01G043500 chr4A 87.583 1208 67 25 547 1726 705055531 705054379 0.000000e+00 1323.0
12 TraesCS7D01G043500 chr4A 87.604 1202 65 23 547 1726 704808258 704807119 0.000000e+00 1317.0
13 TraesCS7D01G043500 chr4A 86.996 992 82 22 760 1726 705170665 705169696 0.000000e+00 1074.0
14 TraesCS7D01G043500 chr4A 84.021 388 49 7 1718 2102 705169745 705169368 7.360000e-96 361.0
15 TraesCS7D01G043500 chr4A 88.318 214 17 5 1736 1945 704807150 704806941 1.660000e-62 250.0
16 TraesCS7D01G043500 chr4A 89.630 135 14 0 1968 2102 705054046 705053912 3.700000e-39 172.0
17 TraesCS7D01G043500 chr4A 92.857 70 4 1 2726 2795 705052768 705052700 1.770000e-17 100.0
18 TraesCS7D01G043500 chr4A 91.429 70 5 1 2726 2795 705168189 705168121 8.240000e-16 95.3
19 TraesCS7D01G043500 chr4A 85.915 71 9 1 2182 2252 704806163 704806094 1.070000e-09 75.0
20 TraesCS7D01G043500 chr4A 82.609 92 9 7 2050 2139 704806443 704806357 1.070000e-09 75.0
21 TraesCS7D01G043500 chr5B 90.060 503 39 2 966 1466 469337832 469338325 2.350000e-180 641.0
22 TraesCS7D01G043500 chr5B 96.429 56 2 0 1 56 122835851 122835906 2.960000e-15 93.5
23 TraesCS7D01G043500 chr5B 93.548 62 4 0 1 62 551541220 551541281 2.960000e-15 93.5
24 TraesCS7D01G043500 chr6B 87.665 227 19 4 1099 1325 138522219 138522436 3.570000e-64 255.0
25 TraesCS7D01G043500 chr6B 81.124 249 22 15 1718 1945 138522478 138522722 2.860000e-40 176.0
26 TraesCS7D01G043500 chr6B 88.000 75 6 3 5 78 405863411 405863339 4.960000e-13 86.1
27 TraesCS7D01G043500 chr5D 80.498 241 38 8 196 432 315683896 315684131 2.860000e-40 176.0
28 TraesCS7D01G043500 chr1D 75.595 336 57 15 121 438 487885274 487884946 2.900000e-30 143.0
29 TraesCS7D01G043500 chr7B 76.604 265 47 12 197 456 734690917 734690663 6.280000e-27 132.0
30 TraesCS7D01G043500 chr1A 98.361 61 1 0 1473 1533 27383214 27383154 1.060000e-19 108.0
31 TraesCS7D01G043500 chr1A 96.721 61 2 0 1473 1533 442726932 442726872 4.930000e-18 102.0
32 TraesCS7D01G043500 chr4B 77.841 176 30 7 196 368 568713653 568713484 1.770000e-17 100.0
33 TraesCS7D01G043500 chr4D 96.552 58 2 0 1 58 182067030 182067087 2.290000e-16 97.1
34 TraesCS7D01G043500 chr4D 93.548 62 4 0 1 62 404108688 404108749 2.960000e-15 93.5
35 TraesCS7D01G043500 chr3A 95.082 61 3 0 1 61 641872893 641872953 2.290000e-16 97.1
36 TraesCS7D01G043500 chr3A 95.082 61 2 1 1 61 108026725 108026666 8.240000e-16 95.3
37 TraesCS7D01G043500 chr1B 93.846 65 3 1 1 64 146571502 146571438 2.290000e-16 97.1


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 TraesCS7D01G043500 chr7D 22507962 22510756 2794 True 5162.000000 5162 100.000000 1 2795 1 chr7D.!!$R1 2794
1 TraesCS7D01G043500 chr7D 22521693 22523176 1483 True 865.000000 1146 87.364500 760 2248 2 chr7D.!!$R4 1488
2 TraesCS7D01G043500 chr7D 22269257 22271591 2334 True 625.000000 1249 83.248333 59 1945 3 chr7D.!!$R3 1886
3 TraesCS7D01G043500 chr7A 22915180 22916649 1469 True 964.150000 1857 90.815500 761 2260 2 chr7A.!!$R2 1499
4 TraesCS7D01G043500 chr7A 22897114 22898543 1429 True 757.500000 1206 84.005500 760 2237 2 chr7A.!!$R1 1477
5 TraesCS7D01G043500 chr4A 705052700 705055531 2831 True 531.666667 1323 90.023333 547 2795 3 chr4A.!!$R2 2248
6 TraesCS7D01G043500 chr4A 705168121 705170665 2544 True 510.100000 1074 87.482000 760 2795 3 chr4A.!!$R3 2035
7 TraesCS7D01G043500 chr4A 704806094 704808258 2164 True 429.250000 1317 86.111500 547 2252 4 chr4A.!!$R1 1705
8 TraesCS7D01G043500 chr6B 138522219 138522722 503 False 215.500000 255 84.394500 1099 1945 2 chr6B.!!$F1 846


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
441 459 0.175989 TCATATGCCCGTGCGTGTAA 59.824 50.0 0.0 0.0 41.78 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2331 4371 0.036765 TTGTCCGGATCCACGAAAGG 60.037 55.0 7.81 3.47 35.47 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)



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

AutoCloner maintained by Alex Coulton.