Multiple sequence alignment - TraesCS2D01G466200

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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 TraesCS2D01G466200 chr2D 100.000 3020 0 0 1 3020 571925620 571928639 0.000000e+00 5578.0
1 TraesCS2D01G466200 chr2B 88.728 1171 52 22 962 2102 683820151 683821271 0.000000e+00 1358.0
2 TraesCS2D01G466200 chr2B 88.462 130 4 2 571 689 683819848 683819977 2.430000e-31 147.0
3 TraesCS2D01G466200 chr2B 95.652 69 2 1 565 632 683819764 683819832 3.180000e-20 110.0
4 TraesCS2D01G466200 chr2B 96.875 64 2 0 2 65 683780175 683780238 1.140000e-19 108.0
5 TraesCS2D01G466200 chr2B 93.750 64 4 0 2 65 683782544 683782607 2.480000e-16 97.1
6 TraesCS2D01G466200 chr2B 100.000 38 0 0 164 201 226468789 226468826 1.500000e-08 71.3
7 TraesCS2D01G466200 chr2A 91.730 653 37 6 62 707 710387842 710388484 0.000000e+00 891.0
8 TraesCS2D01G466200 chr2A 87.249 698 42 20 1392 2052 710388642 710389329 0.000000e+00 752.0
9 TraesCS2D01G466200 chr2A 90.339 383 35 2 2638 3020 710391692 710392072 4.490000e-138 501.0
10 TraesCS2D01G466200 chr2A 90.458 262 22 2 705 963 2486517 2486256 2.880000e-90 342.0
11 TraesCS2D01G466200 chr2A 86.283 226 20 3 2417 2642 710389599 710389813 5.030000e-58 235.0
12 TraesCS2D01G466200 chr2A 78.229 271 47 7 1076 1346 710388572 710388830 2.410000e-36 163.0
13 TraesCS2D01G466200 chr2A 93.519 108 1 3 958 1061 710388478 710388583 4.030000e-34 156.0
14 TraesCS2D01G466200 chr2A 98.462 65 1 0 1 65 710387717 710387781 6.840000e-22 115.0
15 TraesCS2D01G466200 chr2A 93.671 79 1 2 2070 2148 710389515 710389589 6.840000e-22 115.0
16 TraesCS2D01G466200 chr3D 90.074 272 19 6 703 967 42096394 42096124 2.230000e-91 346.0
17 TraesCS2D01G466200 chr3D 90.421 261 21 4 706 963 295392199 295392458 1.040000e-89 340.0
18 TraesCS2D01G466200 chr4D 90.189 265 24 2 705 967 354048751 354049015 8.020000e-91 344.0
19 TraesCS2D01G466200 chr6D 90.458 262 21 3 705 963 26353979 26354239 2.880000e-90 342.0
20 TraesCS2D01G466200 chr6D 89.455 275 24 4 705 975 388990882 388990609 2.880000e-90 342.0
21 TraesCS2D01G466200 chr7A 90.458 262 20 5 705 963 730580095 730579836 1.040000e-89 340.0
22 TraesCS2D01G466200 chr5A 89.630 270 23 4 705 970 419685933 419686201 3.730000e-89 339.0
23 TraesCS2D01G466200 chr4A 89.630 270 23 4 702 968 159363723 159363456 3.730000e-89 339.0
24 TraesCS2D01G466200 chr5B 80.128 312 47 10 2348 2653 523362846 523363148 5.070000e-53 219.0
25 TraesCS2D01G466200 chr5B 88.889 126 14 0 2438 2563 469294942 469294817 4.030000e-34 156.0
26 TraesCS2D01G466200 chr7D 89.796 98 8 2 2435 2531 101555786 101555690 1.140000e-24 124.0
27 TraesCS2D01G466200 chr3A 84.706 85 9 3 2458 2542 28863541 28863461 6.940000e-12 82.4
28 TraesCS2D01G466200 chr6A 100.000 28 0 0 2491 2518 457358049 457358022 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 TraesCS2D01G466200 chr2D 571925620 571928639 3019 False 5578.000000 5578 100.000000 1 3020 1 chr2D.!!$F1 3019
1 TraesCS2D01G466200 chr2B 683819764 683821271 1507 False 538.333333 1358 90.947333 565 2102 3 chr2B.!!$F3 1537
2 TraesCS2D01G466200 chr2A 710387717 710392072 4355 False 366.000000 891 89.935250 1 3020 8 chr2A.!!$F1 3019


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
99 164 0.543277 ATGCTTTCTCGGCTCCATGA 59.457 50.0 0.0 0.0 0.0 3.07 F
1070 1283 0.340208 TTTCTCTCTCCCTCCCTCCC 59.660 60.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1939 2214 0.172127 TCACACGCAAGCAAGCAAAA 59.828 45.0 1.32 0.0 45.62 2.44 R
2296 2741 0.034059 CATACCCGGGCTCATCTGTC 59.966 60.0 24.08 0.0 0.00 3.51 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.