Multiple sequence alignment - TraesCS1B01G199500

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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 TraesCS1B01G199500 chr1B 100.000 2510 0 0 1 2510 357469190 357471699 0.000000e+00 4636
1 TraesCS1B01G199500 chr1B 95.188 478 22 1 2034 2510 532660623 532660146 0.000000e+00 754
2 TraesCS1B01G199500 chr1B 94.526 475 22 2 2038 2510 370035758 370036230 0.000000e+00 730
3 TraesCS1B01G199500 chr1A 93.916 1545 53 18 470 2004 327272395 327270882 0.000000e+00 2294
4 TraesCS1B01G199500 chr1D 93.371 1433 51 14 584 2004 255427843 255426443 0.000000e+00 2080
5 TraesCS1B01G199500 chr1D 90.517 116 9 2 471 585 255436266 255436152 4.320000e-33 152
6 TraesCS1B01G199500 chr7B 96.406 473 17 0 1 473 626045684 626045212 0.000000e+00 780
7 TraesCS1B01G199500 chr7B 94.926 473 21 3 2038 2510 712768171 712768640 0.000000e+00 737
8 TraesCS1B01G199500 chr7B 94.292 473 25 1 2038 2510 685999869 686000339 0.000000e+00 723
9 TraesCS1B01G199500 chr2A 95.137 473 23 0 1 473 585191637 585191165 0.000000e+00 747
10 TraesCS1B01G199500 chr2A 93.658 473 30 0 1 473 595236869 595236397 0.000000e+00 708
11 TraesCS1B01G199500 chr5B 94.781 479 20 3 2034 2510 694236788 694236313 0.000000e+00 741
12 TraesCS1B01G199500 chr5B 94.480 471 25 1 2040 2510 326508932 326509401 0.000000e+00 725
13 TraesCS1B01G199500 chr2D 94.926 473 24 0 1 473 100427034 100426562 0.000000e+00 741
14 TraesCS1B01G199500 chr6B 95.117 471 20 2 2040 2510 182449992 182450459 0.000000e+00 739
15 TraesCS1B01G199500 chr6B 94.715 473 22 2 2038 2510 659251370 659251839 0.000000e+00 732
16 TraesCS1B01G199500 chr2B 94.503 473 22 2 2040 2510 585193424 585192954 0.000000e+00 726
17 TraesCS1B01G199500 chr5A 92.812 473 34 0 1 473 698753397 698752925 0.000000e+00 686
18 TraesCS1B01G199500 chr7A 86.596 470 63 0 4 473 271639725 271639256 1.030000e-143 520
19 TraesCS1B01G199500 chr7D 86.170 470 65 0 1 470 140815260 140815729 2.230000e-140 508
20 TraesCS1B01G199500 chr3D 86.170 470 65 0 4 473 432509480 432509011 2.230000e-140 508
21 TraesCS1B01G199500 chr4D 85.957 470 66 0 1 470 494282601 494283070 1.040000e-138 503


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 TraesCS1B01G199500 chr1B 357469190 357471699 2509 False 4636 4636 100.000 1 2510 1 chr1B.!!$F1 2509
1 TraesCS1B01G199500 chr1A 327270882 327272395 1513 True 2294 2294 93.916 470 2004 1 chr1A.!!$R1 1534
2 TraesCS1B01G199500 chr1D 255426443 255427843 1400 True 2080 2080 93.371 584 2004 1 chr1D.!!$R1 1420


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
203 204 0.03213 GTGTGTCGGAGAAGTGCTCA 59.968 55.0 0.0 0.0 45.81 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 2096 0.042621 CGCGCGGCAAACAAATTTTT 60.043 45.0 24.84 0.0 0.0 1.94 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.