Multiple sequence alignment - TraesCS6B01G044900

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 TraesCS6B01G044900 chr6B 100.000 2425 0 0 482 2906 26794566 26792142 0.000000e+00 4479.0
1 TraesCS6B01G044900 chr6B 87.245 1419 138 20 976 2356 26389184 26390597 0.000000e+00 1578.0
2 TraesCS6B01G044900 chr6B 95.158 475 20 2 2338 2809 26390784 26391258 0.000000e+00 747.0
3 TraesCS6B01G044900 chr6B 100.000 100 0 0 1 100 26795047 26794948 4.950000e-43 185.0
4 TraesCS6B01G044900 chr6D 87.446 1386 125 24 1021 2364 15344815 15343437 0.000000e+00 1550.0
5 TraesCS6B01G044900 chr6D 83.014 1460 208 22 959 2388 14503317 14504766 0.000000e+00 1286.0
6 TraesCS6B01G044900 chr6D 81.624 1453 209 25 962 2365 14422037 14423480 0.000000e+00 1151.0
7 TraesCS6B01G044900 chr6D 81.499 1454 213 22 961 2388 14727358 14725935 0.000000e+00 1144.0
8 TraesCS6B01G044900 chr6D 81.406 1124 159 18 1286 2388 14442271 14443365 0.000000e+00 872.0
9 TraesCS6B01G044900 chr6D 81.454 949 127 19 1484 2391 15352522 15351582 0.000000e+00 732.0
10 TraesCS6B01G044900 chr6D 80.104 960 151 13 1466 2388 14435570 14436526 0.000000e+00 678.0
11 TraesCS6B01G044900 chr6D 82.496 657 83 12 1759 2390 15349400 15348751 5.470000e-152 547.0
12 TraesCS6B01G044900 chr6D 87.449 494 36 18 2422 2906 14938721 14938245 1.970000e-151 545.0
13 TraesCS6B01G044900 chr6D 82.574 505 57 17 2426 2906 15347862 15347365 1.610000e-112 416.0
14 TraesCS6B01G044900 chr6D 80.174 575 71 18 1853 2390 14441405 14441973 9.760000e-105 390.0
15 TraesCS6B01G044900 chr6D 91.667 84 7 0 2681 2764 14505302 14505385 1.830000e-22 117.0
16 TraesCS6B01G044900 chr6D 86.813 91 12 0 2674 2764 14437100 14437190 5.120000e-18 102.0
17 TraesCS6B01G044900 chr6A 82.947 1466 187 27 969 2390 15694583 15696029 0.000000e+00 1264.0
18 TraesCS6B01G044900 chr6A 81.289 1427 201 26 982 2388 15700725 15702105 0.000000e+00 1096.0
19 TraesCS6B01G044900 chr6A 79.820 1447 225 40 971 2360 15684828 15686264 0.000000e+00 992.0
20 TraesCS6B01G044900 chr6A 82.218 1136 173 16 1079 2191 15914065 15912936 0.000000e+00 952.0
21 TraesCS6B01G044900 chr6A 75.889 506 67 22 2417 2897 15712956 15713431 1.060000e-49 207.0
22 TraesCS6B01G044900 chr6A 87.912 91 11 0 2674 2764 15702679 15702769 1.100000e-19 108.0
23 TraesCS6B01G044900 chr6A 93.220 59 4 0 686 744 530114427 530114485 1.430000e-13 87.9
24 TraesCS6B01G044900 chr1B 80.588 1463 228 28 976 2390 48062374 48060920 0.000000e+00 1077.0
25 TraesCS6B01G044900 chr1B 80.760 816 115 17 1612 2390 48163118 48162308 1.490000e-167 599.0
26 TraesCS6B01G044900 chr1B 86.765 68 7 2 678 744 629177578 629177644 1.120000e-09 75.0
27 TraesCS6B01G044900 chrUn 96.296 108 4 0 1971 2078 23843020 23843127 8.280000e-41 178.0
28 TraesCS6B01G044900 chrUn 96.296 108 4 0 1971 2078 275137799 275137906 8.280000e-41 178.0
29 TraesCS6B01G044900 chrUn 96.296 108 4 0 1971 2078 289112916 289112809 8.280000e-41 178.0
30 TraesCS6B01G044900 chrUn 96.296 108 4 0 1971 2078 466550867 466550760 8.280000e-41 178.0
31 TraesCS6B01G044900 chr1A 96.296 108 4 0 1971 2078 20589468 20589361 8.280000e-41 178.0
32 TraesCS6B01G044900 chr3D 85.897 78 8 2 682 757 42694024 42693948 2.400000e-11 80.5
33 TraesCS6B01G044900 chr1D 87.879 66 8 0 681 746 464729542 464729477 8.630000e-11 78.7
34 TraesCS6B01G044900 chr2A 87.500 64 8 0 681 744 373201937 373202000 1.120000e-09 75.0
35 TraesCS6B01G044900 chr7D 85.938 64 9 0 681 744 206212054 206212117 5.200000e-08 69.4
36 TraesCS6B01G044900 chr7A 87.719 57 4 3 687 742 29653917 29653971 2.420000e-06 63.9
37 TraesCS6B01G044900 chr4B 85.484 62 3 4 712 769 663409877 663409936 3.130000e-05 60.2
38 TraesCS6B01G044900 chr4B 85.484 62 3 4 712 769 663411902 663411961 3.130000e-05 60.2
39 TraesCS6B01G044900 chr4B 85.484 62 3 4 712 769 663413137 663413196 3.130000e-05 60.2
40 TraesCS6B01G044900 chr4B 85.484 62 3 4 712 769 663415615 663415674 3.130000e-05 60.2
41 TraesCS6B01G044900 chr2D 100.000 28 0 0 679 706 29847326 29847353 5.000000e-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 TraesCS6B01G044900 chr6B 26792142 26795047 2905 True 2332.00 4479 100.0000 1 2906 2 chr6B.!!$R1 2905
1 TraesCS6B01G044900 chr6B 26389184 26391258 2074 False 1162.50 1578 91.2015 976 2809 2 chr6B.!!$F1 1833
2 TraesCS6B01G044900 chr6D 14422037 14423480 1443 False 1151.00 1151 81.6240 962 2365 1 chr6D.!!$F1 1403
3 TraesCS6B01G044900 chr6D 14725935 14727358 1423 True 1144.00 1144 81.4990 961 2388 1 chr6D.!!$R1 1427
4 TraesCS6B01G044900 chr6D 15343437 15352522 9085 True 811.25 1550 83.4925 1021 2906 4 chr6D.!!$R3 1885
5 TraesCS6B01G044900 chr6D 14503317 14505385 2068 False 701.50 1286 87.3405 959 2764 2 chr6D.!!$F4 1805
6 TraesCS6B01G044900 chr6D 14441405 14443365 1960 False 631.00 872 80.7900 1286 2390 2 chr6D.!!$F3 1104
7 TraesCS6B01G044900 chr6D 14435570 14437190 1620 False 390.00 678 83.4585 1466 2764 2 chr6D.!!$F2 1298
8 TraesCS6B01G044900 chr6A 15694583 15696029 1446 False 1264.00 1264 82.9470 969 2390 1 chr6A.!!$F2 1421
9 TraesCS6B01G044900 chr6A 15684828 15686264 1436 False 992.00 992 79.8200 971 2360 1 chr6A.!!$F1 1389
10 TraesCS6B01G044900 chr6A 15912936 15914065 1129 True 952.00 952 82.2180 1079 2191 1 chr6A.!!$R1 1112
11 TraesCS6B01G044900 chr6A 15700725 15702769 2044 False 602.00 1096 84.6005 982 2764 2 chr6A.!!$F5 1782
12 TraesCS6B01G044900 chr1B 48060920 48062374 1454 True 1077.00 1077 80.5880 976 2390 1 chr1B.!!$R1 1414
13 TraesCS6B01G044900 chr1B 48162308 48163118 810 True 599.00 599 80.7600 1612 2390 1 chr1B.!!$R2 778


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
874 875 0.034477 ACCAAATTAGAGCCCACCCG 60.034 55.0 0.0 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2841 11684 0.179009 AGGCTTCAGTGCAGCAGAAA 60.179 50.0 16.69 0.0 39.21 2.52 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.