Multiple sequence alignment - TraesCS3B01G228600

Loading Multiple Alignment...

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 TraesCS3B01G228600 chr3B 100.000 2846 0 0 1 2846 331024554 331027399 0.000000e+00 5256
1 TraesCS3B01G228600 chr3B 89.247 2855 268 26 1 2837 81049904 81052737 0.000000e+00 3535
2 TraesCS3B01G228600 chr3B 88.603 2834 294 22 24 2846 533671852 533669037 0.000000e+00 3417
3 TraesCS3B01G228600 chr7B 95.118 2847 137 2 1 2846 456121709 456124554 0.000000e+00 4486
4 TraesCS3B01G228600 chr7B 94.316 2850 148 11 1 2846 638612047 638609208 0.000000e+00 4353
5 TraesCS3B01G228600 chr1B 91.877 2856 184 35 27 2846 367657961 367660804 0.000000e+00 3945
6 TraesCS3B01G228600 chr1B 89.061 2843 283 21 21 2846 200994831 200997662 0.000000e+00 3502
7 TraesCS3B01G228600 chr4B 91.753 2801 192 31 74 2846 451467171 451469960 0.000000e+00 3856
8 TraesCS3B01G228600 chr2B 89.972 2862 218 53 19 2834 724014609 724011771 0.000000e+00 3631
9 TraesCS3B01G228600 chr2B 88.772 285 22 8 2551 2833 545609926 545609650 9.770000e-90 340
10 TraesCS3B01G228600 chr2B 85.950 242 25 7 2605 2846 465449102 465448870 1.690000e-62 250
11 TraesCS3B01G228600 chr1D 88.571 2835 287 28 29 2846 246372768 246375582 0.000000e+00 3406


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 TraesCS3B01G228600 chr3B 331024554 331027399 2845 False 5256 5256 100.000 1 2846 1 chr3B.!!$F2 2845
1 TraesCS3B01G228600 chr3B 81049904 81052737 2833 False 3535 3535 89.247 1 2837 1 chr3B.!!$F1 2836
2 TraesCS3B01G228600 chr3B 533669037 533671852 2815 True 3417 3417 88.603 24 2846 1 chr3B.!!$R1 2822
3 TraesCS3B01G228600 chr7B 456121709 456124554 2845 False 4486 4486 95.118 1 2846 1 chr7B.!!$F1 2845
4 TraesCS3B01G228600 chr7B 638609208 638612047 2839 True 4353 4353 94.316 1 2846 1 chr7B.!!$R1 2845
5 TraesCS3B01G228600 chr1B 367657961 367660804 2843 False 3945 3945 91.877 27 2846 1 chr1B.!!$F2 2819
6 TraesCS3B01G228600 chr1B 200994831 200997662 2831 False 3502 3502 89.061 21 2846 1 chr1B.!!$F1 2825
7 TraesCS3B01G228600 chr4B 451467171 451469960 2789 False 3856 3856 91.753 74 2846 1 chr4B.!!$F1 2772
8 TraesCS3B01G228600 chr2B 724011771 724014609 2838 True 3631 3631 89.972 19 2834 1 chr2B.!!$R3 2815
9 TraesCS3B01G228600 chr1D 246372768 246375582 2814 False 3406 3406 88.571 29 2846 1 chr1D.!!$F1 2817

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
188 198 1.068610 CGATCATTTTGGCACCGTTGT 60.069 47.619 0.00 0.00 0.00 3.32 F
724 735 2.079925 GCAACAACCCTGAGATCTCAC 58.920 52.381 21.67 4.94 35.46 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1139 1150 0.817654 CTCAGCTGGATGTGACGGTA 59.182 55.000 15.13 0.0 0.00 4.02 R
2297 2322 4.384098 CCATAGTGGTTAGGTGATTGCTCA 60.384 45.833 0.00 0.0 31.35 4.26 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)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 128 1.755977 CGCCTAGTCCCTGAGGAGAAT 60.756 57.143 0.00 0.00 45.21 2.40
147 155 3.998341 GACACTCGCAGTTTGGGTATAAA 59.002 43.478 0.00 0.00 0.00 1.40
181 191 5.290493 ACCTACTATCGATCATTTTGGCA 57.710 39.130 0.00 0.00 0.00 4.92
188 198 1.068610 CGATCATTTTGGCACCGTTGT 60.069 47.619 0.00 0.00 0.00 3.32
189 199 2.606795 CGATCATTTTGGCACCGTTGTT 60.607 45.455 0.00 0.00 0.00 2.83
240 250 7.735326 AGGCTATAGACTAGGTTTTTCTTCA 57.265 36.000 6.23 0.00 0.00 3.02
307 317 6.889722 CCTAACCCTTGTTCCAGATTATTTCA 59.110 38.462 0.00 0.00 35.87 2.69
360 371 3.173953 ACCATCTTCTTGGAAATGGCA 57.826 42.857 14.89 0.00 41.99 4.92
362 373 4.098894 ACCATCTTCTTGGAAATGGCATT 58.901 39.130 6.96 6.96 41.99 3.56
366 377 6.460676 CCATCTTCTTGGAAATGGCATTCTAC 60.461 42.308 14.04 7.43 39.25 2.59
468 479 4.686091 CGATTAGATGATTTAGCTCGGCAA 59.314 41.667 0.00 0.00 0.00 4.52
495 506 5.250774 AGAAGTAGTTTTTGAGGATAGGCCA 59.749 40.000 5.01 0.00 40.02 5.36
500 511 5.147767 AGTTTTTGAGGATAGGCCAAGTTT 58.852 37.500 5.01 0.00 40.02 2.66
601 612 3.054875 TGAATGTCAGCATGGCTACTCTT 60.055 43.478 0.00 0.00 44.57 2.85
609 620 2.168521 GCATGGCTACTCTTACACTCCA 59.831 50.000 0.00 0.00 0.00 3.86
611 622 2.457598 TGGCTACTCTTACACTCCAGG 58.542 52.381 0.00 0.00 0.00 4.45
724 735 2.079925 GCAACAACCCTGAGATCTCAC 58.920 52.381 21.67 4.94 35.46 3.51
780 791 3.135530 GGTATGAAGAGGAGAGCCACAAT 59.864 47.826 0.00 0.00 36.29 2.71
1067 1078 6.226787 AGAAGATTGAGAAGAACATCAACGT 58.773 36.000 0.00 0.00 38.19 3.99
1139 1150 5.195940 CCTTGATACATGTGAGGTTCCAAT 58.804 41.667 9.11 0.00 0.00 3.16
1162 1173 0.801251 GTCACATCCAGCTGAGCAAC 59.199 55.000 17.39 1.72 0.00 4.17
1189 1200 4.651778 CGAGAGTCCAGAGGAAGAGATAT 58.348 47.826 0.00 0.00 31.38 1.63
2292 2317 3.896648 ATTTGTGCTAAGTGTGTTCCG 57.103 42.857 0.00 0.00 0.00 4.30
2297 2322 2.806244 GTGCTAAGTGTGTTCCGATTGT 59.194 45.455 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 128 0.319211 CCCAAACTGCGAGTGTCGTA 60.319 55.000 0.00 0.0 42.81 3.43
147 155 3.703052 CGATAGTAGGTACAGTGGGGTTT 59.297 47.826 0.00 0.0 0.00 3.27
181 191 0.675522 CGCTAATCCCCAACAACGGT 60.676 55.000 0.00 0.0 0.00 4.83
188 198 1.143183 GCTCGACGCTAATCCCCAA 59.857 57.895 0.00 0.0 35.14 4.12
189 199 2.812499 GCTCGACGCTAATCCCCA 59.188 61.111 0.00 0.0 35.14 4.96
307 317 8.278729 TGCAAAATGGAAAAGAAAACAAAGAT 57.721 26.923 0.00 0.0 0.00 2.40
350 361 4.842531 TCTGAGTAGAATGCCATTTCCA 57.157 40.909 0.00 0.0 0.00 3.53
354 365 6.183810 TGATGATCTGAGTAGAATGCCATT 57.816 37.500 0.00 0.0 36.32 3.16
360 371 7.549842 GCATAAGCATGATGATCTGAGTAGAAT 59.450 37.037 0.00 0.0 41.58 2.40
362 373 6.396450 GCATAAGCATGATGATCTGAGTAGA 58.604 40.000 0.00 0.0 41.58 2.59
366 377 4.243270 TCGCATAAGCATGATGATCTGAG 58.757 43.478 0.00 0.0 42.27 3.35
468 479 6.631962 CCTATCCTCAAAAACTACTTCTCGT 58.368 40.000 0.00 0.0 0.00 4.18
495 506 9.413734 CCTCTGGAATAAGGATCATAAAAACTT 57.586 33.333 0.00 0.0 34.35 2.66
500 511 5.372363 TGGCCTCTGGAATAAGGATCATAAA 59.628 40.000 3.32 0.0 34.35 1.40
590 601 3.034635 CCTGGAGTGTAAGAGTAGCCAT 58.965 50.000 0.00 0.0 0.00 4.40
601 612 2.303175 GCCAAAACAACCTGGAGTGTA 58.697 47.619 0.00 0.0 34.35 2.90
609 620 1.708341 AGCTCATGCCAAAACAACCT 58.292 45.000 0.00 0.0 40.80 3.50
611 622 2.053627 CGAAGCTCATGCCAAAACAAC 58.946 47.619 0.00 0.0 40.80 3.32
724 735 6.202762 TGCATATGATTACTAGAAGCAAACGG 59.797 38.462 6.97 0.0 0.00 4.44
780 791 6.472016 TGAATAAGACTGTTGTGGAGCATAA 58.528 36.000 0.00 0.0 0.00 1.90
871 882 4.156922 CACTTGTGTTGAAGGTGTTGGTTA 59.843 41.667 0.00 0.0 0.00 2.85
917 928 1.363744 AAGTGCGAGCTTGTCTATGC 58.636 50.000 2.14 0.0 0.00 3.14
1067 1078 4.695455 GCTGTGAAGAAATAGTACTGCCAA 59.305 41.667 5.39 0.0 32.34 4.52
1139 1150 0.817654 CTCAGCTGGATGTGACGGTA 59.182 55.000 15.13 0.0 0.00 4.02
1162 1173 1.974265 TCCTCTGGACTCTCGCTATG 58.026 55.000 0.00 0.0 0.00 2.23
1189 1200 6.599638 TCGACTACATCTTCTTCAATCTGAGA 59.400 38.462 0.00 0.0 0.00 3.27
2297 2322 4.384098 CCATAGTGGTTAGGTGATTGCTCA 60.384 45.833 0.00 0.0 31.35 4.26


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.