Multiple sequence alignment - TraesCS6D01G231300

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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 TraesCS6D01G231300 chr6D 100.000 3179 0 0 1 3179 324782145 324785323 0.000000e+00 5871.0
1 TraesCS6D01G231300 chr6D 76.303 1228 205 51 994 2184 324599424 324598246 7.650000e-161 577.0
2 TraesCS6D01G231300 chr6D 95.364 151 7 0 2680 2830 253748542 253748692 1.140000e-59 241.0
3 TraesCS6D01G231300 chr6D 94.805 154 8 0 2677 2830 266773284 266773131 1.140000e-59 241.0
4 TraesCS6D01G231300 chr6D 95.364 151 7 0 2680 2830 296863425 296863575 1.140000e-59 241.0
5 TraesCS6D01G231300 chr6A 92.228 2123 84 32 438 2525 462225307 462227383 0.000000e+00 2931.0
6 TraesCS6D01G231300 chr6A 87.611 339 36 3 1852 2184 461986876 461986538 3.850000e-104 388.0
7 TraesCS6D01G231300 chr6A 87.761 335 31 6 2849 3179 462227371 462227699 1.790000e-102 383.0
8 TraesCS6D01G231300 chr6A 74.427 786 130 41 994 1750 461987718 461986975 4.040000e-69 272.0
9 TraesCS6D01G231300 chr6A 87.719 57 7 0 79 135 462225254 462225310 2.050000e-07 67.6
10 TraesCS6D01G231300 chr6B 93.522 1976 77 22 570 2518 498544484 498542533 0.000000e+00 2892.0
11 TraesCS6D01G231300 chr6B 87.786 524 40 9 1 503 498552512 498551992 2.730000e-165 592.0
12 TraesCS6D01G231300 chr6B 89.877 326 22 8 2854 3179 498542538 498542224 2.950000e-110 409.0
13 TraesCS6D01G231300 chr6B 87.463 335 36 2 1853 2181 498852564 498852898 6.430000e-102 381.0
14 TraesCS6D01G231300 chr6B 87.568 185 23 0 2643 2827 630530183 630530367 6.910000e-52 215.0
15 TraesCS6D01G231300 chr6B 74.268 478 78 26 994 1460 498851680 498852123 3.280000e-35 159.0
16 TraesCS6D01G231300 chr6B 85.030 167 9 5 2526 2681 264059475 264059314 4.250000e-34 156.0
17 TraesCS6D01G231300 chr3D 89.435 1505 111 18 865 2350 580521643 580523118 0.000000e+00 1855.0
18 TraesCS6D01G231300 chr3D 81.447 318 29 12 2868 3179 580523310 580523603 1.910000e-57 233.0
19 TraesCS6D01G231300 chr3D 83.832 167 24 3 527 693 580520686 580520849 4.250000e-34 156.0
20 TraesCS6D01G231300 chr3D 84.431 167 10 5 2526 2681 453280587 453280426 1.980000e-32 150.0
21 TraesCS6D01G231300 chr3D 92.063 63 4 1 757 818 580521171 580521233 1.570000e-13 87.9
22 TraesCS6D01G231300 chr3A 89.112 1497 116 16 865 2342 715973647 715975115 0.000000e+00 1818.0
23 TraesCS6D01G231300 chr3A 81.562 320 29 14 2868 3179 715975331 715975628 1.470000e-58 237.0
24 TraesCS6D01G231300 chr3A 84.024 169 13 9 2524 2681 654404196 654404031 1.980000e-32 150.0
25 TraesCS6D01G231300 chr3B 88.654 1516 116 27 865 2350 775735414 775736903 0.000000e+00 1796.0
26 TraesCS6D01G231300 chr3B 81.588 277 23 10 2908 3178 775737106 775737360 1.490000e-48 204.0
27 TraesCS6D01G231300 chr3B 84.431 167 10 5 2526 2681 424849783 424849622 1.980000e-32 150.0
28 TraesCS6D01G231300 chr3B 84.431 167 10 5 2526 2681 666176113 666175952 1.980000e-32 150.0
29 TraesCS6D01G231300 chr3B 90.385 52 4 1 768 818 775735015 775735066 2.050000e-07 67.6
30 TraesCS6D01G231300 chr7D 96.026 151 6 0 2680 2830 163563479 163563629 2.450000e-61 246.0
31 TraesCS6D01G231300 chr4B 94.771 153 8 0 2678 2830 338425781 338425933 4.100000e-59 239.0
32 TraesCS6D01G231300 chr7B 94.737 152 8 0 2679 2830 460329556 460329707 1.470000e-58 237.0
33 TraesCS6D01G231300 chr2B 80.707 311 41 16 2522 2828 9033273 9033568 1.150000e-54 224.0
34 TraesCS6D01G231300 chr2B 84.431 167 12 6 2526 2681 778699922 778699759 5.490000e-33 152.0
35 TraesCS6D01G231300 chr5A 82.879 257 32 5 2580 2830 706668928 706668678 1.480000e-53 220.0
36 TraesCS6D01G231300 chr2D 85.455 165 10 9 2529 2681 609579806 609579644 3.280000e-35 159.0
37 TraesCS6D01G231300 chr1B 84.431 167 10 6 2526 2681 239055659 239055820 1.980000e-32 150.0


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 TraesCS6D01G231300 chr6D 324782145 324785323 3178 False 5871.000 5871 100.000000 1 3179 1 chr6D.!!$F3 3178
1 TraesCS6D01G231300 chr6D 324598246 324599424 1178 True 577.000 577 76.303000 994 2184 1 chr6D.!!$R2 1190
2 TraesCS6D01G231300 chr6A 462225254 462227699 2445 False 1127.200 2931 89.236000 79 3179 3 chr6A.!!$F1 3100
3 TraesCS6D01G231300 chr6A 461986538 461987718 1180 True 330.000 388 81.019000 994 2184 2 chr6A.!!$R1 1190
4 TraesCS6D01G231300 chr6B 498542224 498544484 2260 True 1650.500 2892 91.699500 570 3179 2 chr6B.!!$R3 2609
5 TraesCS6D01G231300 chr6B 498551992 498552512 520 True 592.000 592 87.786000 1 503 1 chr6B.!!$R2 502
6 TraesCS6D01G231300 chr6B 498851680 498852898 1218 False 270.000 381 80.865500 994 2181 2 chr6B.!!$F2 1187
7 TraesCS6D01G231300 chr3D 580520686 580523603 2917 False 582.975 1855 86.694250 527 3179 4 chr3D.!!$F1 2652
8 TraesCS6D01G231300 chr3A 715973647 715975628 1981 False 1027.500 1818 85.337000 865 3179 2 chr3A.!!$F1 2314
9 TraesCS6D01G231300 chr3B 775735015 775737360 2345 False 689.200 1796 86.875667 768 3178 3 chr3B.!!$F1 2410


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
942 1608 0.032678 GCTTATCTAGCTCGCAGCCA 59.967 55.0 0.0 0.0 46.77 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2628 3470 0.175302 CCACAAACAAGGCAGCAACA 59.825 50.0 0.0 0.0 0.0 3.33 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.