Multiple sequence alignment - TraesCS6B01G289800

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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 TraesCS6B01G289800 chr6B 100.000 2561 0 0 1 2561 521468840 521471400 0.000000e+00 4730.0
1 TraesCS6B01G289800 chr6B 96.774 93 3 0 802 894 514685866 514685958 3.410000e-34 156.0
2 TraesCS6B01G289800 chr6B 98.305 59 1 0 835 893 18455289 18455231 1.250000e-18 104.0
3 TraesCS6B01G289800 chr6D 95.517 1093 43 3 902 1992 345315701 345316789 0.000000e+00 1742.0
4 TraesCS6B01G289800 chr6D 88.453 433 47 3 2130 2561 451113411 451112981 1.050000e-143 520.0
5 TraesCS6B01G289800 chr6A 93.508 1109 53 7 907 2006 485880946 485882044 0.000000e+00 1631.0
6 TraesCS6B01G289800 chr2B 99.138 812 5 2 1 810 236475938 236475127 0.000000e+00 1459.0
7 TraesCS6B01G289800 chr2B 99.014 811 5 3 1 808 533952616 533953426 0.000000e+00 1450.0
8 TraesCS6B01G289800 chr2B 88.532 436 45 4 2130 2561 105902867 105903301 8.120000e-145 523.0
9 TraesCS6B01G289800 chr2B 79.348 92 19 0 802 893 176698759 176698668 5.910000e-07 65.8
10 TraesCS6B01G289800 chr4B 99.135 809 5 2 1 808 261935574 261936381 0.000000e+00 1454.0
11 TraesCS6B01G289800 chr4B 98.893 813 6 3 1 810 202196022 202195210 0.000000e+00 1448.0
12 TraesCS6B01G289800 chr4B 98.893 813 6 3 1 810 202768721 202767909 0.000000e+00 1448.0
13 TraesCS6B01G289800 chr4B 98.894 814 4 5 1 810 218515171 218515983 0.000000e+00 1448.0
14 TraesCS6B01G289800 chr4B 98.893 813 6 3 1 810 218737231 218736419 0.000000e+00 1448.0
15 TraesCS6B01G289800 chr4B 98.893 813 6 3 1 810 297523802 297524614 0.000000e+00 1448.0
16 TraesCS6B01G289800 chr4A 99.016 813 5 3 1 810 475447128 475447940 0.000000e+00 1454.0
17 TraesCS6B01G289800 chr4A 96.875 96 3 0 802 897 734451183 734451088 7.330000e-36 161.0
18 TraesCS6B01G289800 chr7D 87.991 433 50 2 2130 2561 431374316 431373885 6.320000e-141 510.0
19 TraesCS6B01G289800 chr3D 88.290 427 46 4 2130 2553 279192662 279193087 2.270000e-140 508.0
20 TraesCS6B01G289800 chr2D 87.788 434 50 3 2130 2561 303629982 303629550 2.940000e-139 505.0
21 TraesCS6B01G289800 chr2D 88.152 422 48 2 2139 2560 587272418 587271999 3.800000e-138 501.0
22 TraesCS6B01G289800 chr4D 87.760 433 49 4 2130 2561 501042142 501041713 1.060000e-138 503.0
23 TraesCS6B01G289800 chr1D 87.760 433 50 3 2130 2561 42975548 42975978 1.060000e-138 503.0
24 TraesCS6B01G289800 chr1D 87.385 436 53 2 2128 2561 493865911 493866346 1.370000e-137 499.0
25 TraesCS6B01G289800 chr1D 91.045 67 6 0 830 896 416222003 416222069 9.760000e-15 91.6
26 TraesCS6B01G289800 chr1B 96.875 96 2 1 802 897 60378229 60378135 2.640000e-35 159.0
27 TraesCS6B01G289800 chr1B 95.604 91 4 0 802 892 63912216 63912306 2.050000e-31 147.0
28 TraesCS6B01G289800 chr7B 95.652 92 4 0 802 893 684720175 684720266 5.710000e-32 148.0
29 TraesCS6B01G289800 chr3B 90.000 60 5 1 834 893 561566937 561566879 2.730000e-10 76.8


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 TraesCS6B01G289800 chr6B 521468840 521471400 2560 False 4730 4730 100.000 1 2561 1 chr6B.!!$F2 2560
1 TraesCS6B01G289800 chr6D 345315701 345316789 1088 False 1742 1742 95.517 902 1992 1 chr6D.!!$F1 1090
2 TraesCS6B01G289800 chr6A 485880946 485882044 1098 False 1631 1631 93.508 907 2006 1 chr6A.!!$F1 1099
3 TraesCS6B01G289800 chr2B 236475127 236475938 811 True 1459 1459 99.138 1 810 1 chr2B.!!$R2 809
4 TraesCS6B01G289800 chr2B 533952616 533953426 810 False 1450 1450 99.014 1 808 1 chr2B.!!$F2 807
5 TraesCS6B01G289800 chr4B 261935574 261936381 807 False 1454 1454 99.135 1 808 1 chr4B.!!$F2 807
6 TraesCS6B01G289800 chr4B 202195210 202196022 812 True 1448 1448 98.893 1 810 1 chr4B.!!$R1 809
7 TraesCS6B01G289800 chr4B 202767909 202768721 812 True 1448 1448 98.893 1 810 1 chr4B.!!$R2 809
8 TraesCS6B01G289800 chr4B 218515171 218515983 812 False 1448 1448 98.894 1 810 1 chr4B.!!$F1 809
9 TraesCS6B01G289800 chr4B 218736419 218737231 812 True 1448 1448 98.893 1 810 1 chr4B.!!$R3 809
10 TraesCS6B01G289800 chr4B 297523802 297524614 812 False 1448 1448 98.893 1 810 1 chr4B.!!$F3 809
11 TraesCS6B01G289800 chr4A 475447128 475447940 812 False 1454 1454 99.016 1 810 1 chr4A.!!$F1 809


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
812 816 0.179032 TCCTGACAACGTGGCATGTT 60.179 50.0 19.04 19.04 33.12 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2411 2426 0.034059 GTCGGGCATGGTAGAGGATG 59.966 60.0 0.0 0.0 0.0 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.