Multiple sequence alignment - TraesCS2B01G335200

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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 TraesCS2B01G335200 chr2B 100.000 5994 0 0 1 5994 478891717 478897710 0.000000e+00 11069.0
1 TraesCS2B01G335200 chr2B 95.238 231 8 3 74 302 237318334 237318563 4.420000e-96 363.0
2 TraesCS2B01G335200 chr2D 92.208 3465 142 51 317 3722 404404264 404400869 0.000000e+00 4785.0
3 TraesCS2B01G335200 chr2D 89.846 1300 68 28 4485 5758 404399413 404398152 0.000000e+00 1611.0
4 TraesCS2B01G335200 chr2D 93.575 607 38 1 3871 4477 404400622 404400017 0.000000e+00 904.0
5 TraesCS2B01G335200 chr2D 87.383 214 13 8 5781 5994 404398100 404397901 3.610000e-57 233.0
6 TraesCS2B01G335200 chr2D 98.182 55 1 0 3746 3800 404400870 404400816 4.940000e-16 97.1
7 TraesCS2B01G335200 chr2A 91.069 3359 178 49 505 3800 542663737 542660438 0.000000e+00 4429.0
8 TraesCS2B01G335200 chr2A 90.949 1149 72 19 4480 5618 542659165 542658039 0.000000e+00 1517.0
9 TraesCS2B01G335200 chr2A 95.222 607 28 1 3871 4477 542660309 542659704 0.000000e+00 959.0
10 TraesCS2B01G335200 chr2A 82.081 173 10 2 308 479 542663946 542663794 1.750000e-25 128.0
11 TraesCS2B01G335200 chr7B 96.364 220 8 0 75 294 44809706 44809487 4.420000e-96 363.0
12 TraesCS2B01G335200 chr4A 95.495 222 10 0 75 296 675226330 675226109 7.390000e-94 355.0
13 TraesCS2B01G335200 chr4A 92.857 84 6 0 1 84 694884856 694884939 8.160000e-24 122.0
14 TraesCS2B01G335200 chr1B 95.111 225 11 0 75 299 283290447 283290223 7.390000e-94 355.0
15 TraesCS2B01G335200 chr1B 95.495 222 10 0 75 296 596317653 596317874 7.390000e-94 355.0
16 TraesCS2B01G335200 chr1B 93.991 233 13 1 75 307 615614813 615614582 9.560000e-93 351.0
17 TraesCS2B01G335200 chr1B 88.087 277 33 0 20 296 570480224 570479948 4.480000e-86 329.0
18 TraesCS2B01G335200 chr6B 94.397 232 10 3 75 306 279087202 279087430 2.660000e-93 353.0
19 TraesCS2B01G335200 chr5B 94.737 228 11 1 75 302 648994943 648995169 2.660000e-93 353.0
20 TraesCS2B01G335200 chr6A 94.253 87 4 1 1 87 57708353 57708268 1.360000e-26 132.0
21 TraesCS2B01G335200 chr6A 96.203 79 3 0 1 79 603303971 603303893 4.880000e-26 130.0
22 TraesCS2B01G335200 chr4D 95.181 83 4 0 4 86 4098711 4098629 1.360000e-26 132.0
23 TraesCS2B01G335200 chr3B 97.403 77 2 0 1 77 564250122 564250198 1.360000e-26 132.0
24 TraesCS2B01G335200 chr3B 97.403 77 2 0 1 77 786512737 786512813 1.360000e-26 132.0
25 TraesCS2B01G335200 chr3D 95.000 80 4 0 1 80 554686242 554686321 6.310000e-25 126.0
26 TraesCS2B01G335200 chr4B 85.577 104 15 0 6 109 551080521 551080624 6.350000e-20 110.0


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 TraesCS2B01G335200 chr2B 478891717 478897710 5993 False 11069.00 11069 100.00000 1 5994 1 chr2B.!!$F2 5993
1 TraesCS2B01G335200 chr2D 404397901 404404264 6363 True 1526.02 4785 92.23880 317 5994 5 chr2D.!!$R1 5677
2 TraesCS2B01G335200 chr2A 542658039 542663946 5907 True 1758.25 4429 89.83025 308 5618 4 chr2A.!!$R1 5310


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
174 175 0.029834 GCATTGGGAAGCGCTATGTG 59.970 55.0 12.05 5.56 33.74 3.21 F
293 294 0.043334 ACTCCCACTATGACCAGCCT 59.957 55.0 0.00 0.00 0.00 4.58 F
1295 1376 0.172127 GCGATCTGCTGTGACTCTGA 59.828 55.0 0.00 0.00 41.73 3.27 F
2412 2535 0.040157 CGAGTGTTCACCGTTCGGTA 60.040 55.0 16.51 0.00 36.64 4.02 F
3273 3413 0.899717 TTTGGGATGCCTTGACTGCC 60.900 55.0 4.35 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1316 1397 0.166814 GTCGAACATCTGCAACCAGC 59.833 55.0 0.00 0.00 45.96 4.85 R
1820 1933 1.645034 AAACGATGATCAGCCGACAG 58.355 50.0 22.04 4.55 0.00 3.51 R
2554 2678 0.993509 TCTAAGGGGGCCAATCTGGG 60.994 60.0 4.39 0.00 38.19 4.45 R
3312 3452 0.171679 CAATTTGATCCGCTGCAGCA 59.828 50.0 36.03 20.16 42.21 4.41 R
5188 6069 0.108945 AGAGGTAGCCGTTAACACGC 60.109 55.0 6.39 6.49 45.72 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.