Multiple sequence alignment - TraesCS7D01G305400

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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 TraesCS7D01G305400 chr7D 100.000 4126 0 0 1 4126 386843614 386847739 0.000000e+00 7620.0
1 TraesCS7D01G305400 chr7D 74.008 731 169 16 106 825 490443608 490444328 1.130000e-70 278.0
2 TraesCS7D01G305400 chr7B 89.160 3238 189 67 923 4124 382130443 382133554 0.000000e+00 3886.0
3 TraesCS7D01G305400 chr7B 96.970 33 1 0 3452 3484 730395439 730395407 5.760000e-04 56.5
4 TraesCS7D01G305400 chr7A 92.756 2333 111 26 839 3133 436881173 436883485 0.000000e+00 3319.0
5 TraesCS7D01G305400 chr7A 91.194 670 42 9 3281 3946 436883571 436884227 0.000000e+00 894.0
6 TraesCS7D01G305400 chr7A 91.083 157 0 4 3970 4126 436884219 436884361 2.520000e-47 200.0
7 TraesCS7D01G305400 chr1A 81.795 769 135 5 1 766 520175890 520175124 1.250000e-179 640.0
8 TraesCS7D01G305400 chr3D 83.578 682 108 4 6 685 554147277 554146598 1.620000e-178 636.0
9 TraesCS7D01G305400 chr3D 94.444 36 2 0 727 762 403675284 403675319 5.760000e-04 56.5
10 TraesCS7D01G305400 chr1D 84.683 568 85 2 1 566 423828118 423827551 2.150000e-157 566.0
11 TraesCS7D01G305400 chr4A 71.510 702 174 15 8 703 26424138 26423457 9.180000e-37 165.0
12 TraesCS7D01G305400 chr2D 71.408 703 173 25 6 694 252616084 252616772 4.270000e-35 159.0
13 TraesCS7D01G305400 chr3A 72.995 374 80 19 222 584 36555384 36555021 1.210000e-20 111.0
14 TraesCS7D01G305400 chr3A 94.444 36 2 0 727 762 525627500 525627535 5.760000e-04 56.5
15 TraesCS7D01G305400 chr3A 100.000 28 0 0 3454 3481 431818513 431818540 7.000000e-03 52.8
16 TraesCS7D01G305400 chr6D 74.057 212 55 0 29 240 246935293 246935504 2.040000e-13 87.9
17 TraesCS7D01G305400 chr6D 73.659 205 54 0 36 240 246932033 246932237 3.420000e-11 80.5
18 TraesCS7D01G305400 chr6D 83.582 67 11 0 29 95 246935944 246935878 3.440000e-06 63.9
19 TraesCS7D01G305400 chr5D 73.364 214 52 5 29 240 305725426 305725216 1.590000e-09 75.0
20 TraesCS7D01G305400 chr6A 93.478 46 1 2 415 459 611322443 611322399 2.660000e-07 67.6
21 TraesCS7D01G305400 chr3B 94.872 39 2 0 728 766 457204878 457204840 1.240000e-05 62.1
22 TraesCS7D01G305400 chr4D 100.000 31 0 0 3454 3484 113929715 113929685 1.600000e-04 58.4
23 TraesCS7D01G305400 chr1B 100.000 29 0 0 3454 3482 173123443 173123471 2.000000e-03 54.7


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 TraesCS7D01G305400 chr7D 386843614 386847739 4125 False 7620 7620 100.000000 1 4126 1 chr7D.!!$F1 4125
1 TraesCS7D01G305400 chr7D 490443608 490444328 720 False 278 278 74.008000 106 825 1 chr7D.!!$F2 719
2 TraesCS7D01G305400 chr7B 382130443 382133554 3111 False 3886 3886 89.160000 923 4124 1 chr7B.!!$F1 3201
3 TraesCS7D01G305400 chr7A 436881173 436884361 3188 False 1471 3319 91.677667 839 4126 3 chr7A.!!$F1 3287
4 TraesCS7D01G305400 chr1A 520175124 520175890 766 True 640 640 81.795000 1 766 1 chr1A.!!$R1 765
5 TraesCS7D01G305400 chr3D 554146598 554147277 679 True 636 636 83.578000 6 685 1 chr3D.!!$R1 679
6 TraesCS7D01G305400 chr1D 423827551 423828118 567 True 566 566 84.683000 1 566 1 chr1D.!!$R1 565


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
790 792 0.378257 CACAGTGACACGCTTTGCTT 59.622 50.000 0.0 0.0 0.0 3.91 F
917 919 1.029947 CCCAGCCCACATAAACGGTC 61.030 60.000 0.0 0.0 0.0 4.79 F
1682 1725 1.546773 GGGCATGTTGTGTTAGGTCCA 60.547 52.381 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2119 2168 0.458669 GAGCATCAAACTGCATGGGG 59.541 55.000 0.0 0.0 44.77 4.96 R
2120 2169 1.471119 AGAGCATCAAACTGCATGGG 58.529 50.000 0.0 0.0 44.77 4.00 R
3361 3429 1.672356 ATGTCTCCGCCAACACAGC 60.672 57.895 0.0 0.0 0.00 4.40 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.