Multiple sequence alignment - TraesCS4B01G158900

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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 TraesCS4B01G158900 chr4B 100.000 2189 0 0 1 2189 308679727 308677539 0 4043
1 TraesCS4B01G158900 chr2D 97.258 2188 54 6 3 2189 638424548 638426730 0 3703
2 TraesCS4B01G158900 chr5D 96.986 2190 59 7 3 2189 503291914 503294099 0 3672
3 TraesCS4B01G158900 chr5D 96.300 2189 58 9 3 2189 6176873 6174706 0 3572
4 TraesCS4B01G158900 chr5D 97.682 1855 38 5 3 1855 512410228 512412079 0 3182
5 TraesCS4B01G158900 chr5D 97.682 1855 37 6 3 1855 512417165 512419015 0 3182
6 TraesCS4B01G158900 chr5D 92.418 488 34 3 1702 2189 12935856 12936340 0 693
7 TraesCS4B01G158900 chr1D 96.758 2190 61 8 3 2189 254435077 254437259 0 3642
8 TraesCS4B01G158900 chr1D 95.477 2189 84 10 3 2189 51871894 51869719 0 3480
9 TraesCS4B01G158900 chr4D 93.656 2191 120 10 3 2189 207068182 207066007 0 3258
10 TraesCS4B01G158900 chr1B 96.930 1889 51 6 303 2189 633708037 633709920 0 3160


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 TraesCS4B01G158900 chr4B 308677539 308679727 2188 True 4043 4043 100.000 1 2189 1 chr4B.!!$R1 2188
1 TraesCS4B01G158900 chr2D 638424548 638426730 2182 False 3703 3703 97.258 3 2189 1 chr2D.!!$F1 2186
2 TraesCS4B01G158900 chr5D 503291914 503294099 2185 False 3672 3672 96.986 3 2189 1 chr5D.!!$F2 2186
3 TraesCS4B01G158900 chr5D 6174706 6176873 2167 True 3572 3572 96.300 3 2189 1 chr5D.!!$R1 2186
4 TraesCS4B01G158900 chr5D 512410228 512412079 1851 False 3182 3182 97.682 3 1855 1 chr5D.!!$F3 1852
5 TraesCS4B01G158900 chr5D 512417165 512419015 1850 False 3182 3182 97.682 3 1855 1 chr5D.!!$F4 1852
6 TraesCS4B01G158900 chr1D 254435077 254437259 2182 False 3642 3642 96.758 3 2189 1 chr1D.!!$F1 2186
7 TraesCS4B01G158900 chr1D 51869719 51871894 2175 True 3480 3480 95.477 3 2189 1 chr1D.!!$R1 2186
8 TraesCS4B01G158900 chr4D 207066007 207068182 2175 True 3258 3258 93.656 3 2189 1 chr4D.!!$R1 2186
9 TraesCS4B01G158900 chr1B 633708037 633709920 1883 False 3160 3160 96.930 303 2189 1 chr1B.!!$F1 1886


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
644 648 0.179116 CACTCAGCCATCTCTCCACG 60.179 60.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1653 1664 0.251742 TGGGATGCAAAGGAAGGGTG 60.252 55.0 0.0 0.0 0.0 4.61 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
49 50 2.488836 GGGAGGTTATCTTTGGAGGGA 58.511 52.381 0.00 0.00 0.00 4.20
208 209 5.652452 GCTCCTTTAGGCTCTTTAAATTCCA 59.348 40.000 0.00 0.00 34.44 3.53
598 602 7.396418 ACCCTCGATAGTTCCTAGAACTATAG 58.604 42.308 23.26 22.46 41.91 1.31
644 648 0.179116 CACTCAGCCATCTCTCCACG 60.179 60.000 0.00 0.00 0.00 4.94
784 789 6.707608 ACTGTATACACGGATACAAGATACGA 59.292 38.462 0.08 0.00 40.81 3.43
796 801 7.916450 GGATACAAGATACGATATACCTGCTTC 59.084 40.741 0.00 0.00 0.00 3.86
924 930 6.464530 AACCCCTCCTACTTCTTGTATTTT 57.535 37.500 0.00 0.00 0.00 1.82
987 994 4.192429 ACTTTATTTGATGGTGGCTTGC 57.808 40.909 0.00 0.00 0.00 4.01
1006 1013 6.293845 GGCTTGCAGGATTAGAAATATGACTG 60.294 42.308 0.00 0.00 0.00 3.51
1304 1312 2.262572 ATTTGCGTTCCGAATTGCTC 57.737 45.000 9.04 0.00 0.00 4.26
1308 1316 1.787847 CGTTCCGAATTGCTCGCTT 59.212 52.632 0.00 0.00 46.71 4.68
1447 1457 0.178984 TCGACCCAGGCGGATATACA 60.179 55.000 0.00 0.00 34.64 2.29
1519 1529 1.202545 GCCAAGGAGAAGATACGGGTC 60.203 57.143 0.00 0.00 0.00 4.46
1528 1538 0.105862 AGATACGGGTCCGATTCCCA 60.106 55.000 16.90 0.00 44.81 4.37
1653 1664 4.080687 AGTGCCGTATCCCTTACTATCTC 58.919 47.826 0.00 0.00 0.00 2.75
1673 1684 0.712380 ACCCTTCCTTTGCATCCCAT 59.288 50.000 0.00 0.00 0.00 4.00
1712 1724 2.168521 CCGGAGGCAGAAATAGAACTCA 59.831 50.000 0.00 0.00 46.14 3.41
1765 1778 1.555477 GACAAACAACGGGCAAACTG 58.445 50.000 0.00 0.00 0.00 3.16
1791 1805 3.805360 AAAGGGAAGGGAGAGGTAGAT 57.195 47.619 0.00 0.00 0.00 1.98
1848 1862 2.360475 AGAAGCCTTGCGCCTTCC 60.360 61.111 17.15 0.00 38.78 3.46
1917 1931 2.488347 GGGCCGGGAGCTAATGAATAAA 60.488 50.000 2.18 0.00 43.05 1.40
1948 1962 5.497285 TGGATATGCCCCTCTACCATATA 57.503 43.478 0.00 0.00 33.57 0.86
2019 2033 0.682852 ATCGAACCCGTGACCTCAAA 59.317 50.000 0.00 0.00 37.05 2.69
2062 2076 1.603236 AACTGCTCTCCTCCGCTCTG 61.603 60.000 0.00 0.00 0.00 3.35
2179 2208 2.125832 GGAATCGAACCCGCGTCA 60.126 61.111 4.92 0.00 35.37 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.131791 GTTGGGGAACACATTAGATATTTACAT 57.868 33.333 0.00 0.00 0.00 2.29
1 2 8.333235 AGTTGGGGAACACATTAGATATTTACA 58.667 33.333 0.00 0.00 0.00 2.41
151 152 2.890808 TCTGCTGAGTGTCGTTCTTT 57.109 45.000 0.00 0.00 0.00 2.52
208 209 2.792947 CGGTAGCTACGCCACCCAT 61.793 63.158 17.48 0.00 0.00 4.00
334 335 0.397941 AAACCTACTGCAGCAGCTCA 59.602 50.000 23.05 7.04 42.74 4.26
347 348 5.353123 CGATCGATTCCCTTTTCAAAACCTA 59.647 40.000 10.26 0.00 0.00 3.08
644 648 7.742767 TGTAGGAGTAAAATAAGGATTAGGCC 58.257 38.462 0.00 0.00 31.76 5.19
781 786 8.421784 TCTTTATTTCAGAAGCAGGTATATCGT 58.578 33.333 0.00 0.00 0.00 3.73
924 930 8.759782 TCCCTCACTTAACCAAAATTGTAAAAA 58.240 29.630 0.00 0.00 0.00 1.94
981 988 5.767168 AGTCATATTTCTAATCCTGCAAGCC 59.233 40.000 0.00 0.00 0.00 4.35
987 994 7.798596 AGCAACAGTCATATTTCTAATCCTG 57.201 36.000 0.00 0.00 0.00 3.86
1006 1013 6.421405 CAAAAACAGCTAATTGGAAAGCAAC 58.579 36.000 1.03 0.00 41.32 4.17
1124 1131 6.910191 AGTCCAATCCATAATGATGTACCAA 58.090 36.000 0.00 0.00 0.00 3.67
1304 1312 9.994432 ATTTCATAATACTGAAAGAGAAAAGCG 57.006 29.630 5.60 0.00 45.50 4.68
1447 1457 8.066595 CGCTCGCTACGGTATATATTTTATAGT 58.933 37.037 0.00 0.00 0.00 2.12
1528 1538 3.675619 AATTAAGCGGGCGAGCGGT 62.676 57.895 0.00 0.00 43.00 5.68
1653 1664 0.251742 TGGGATGCAAAGGAAGGGTG 60.252 55.000 0.00 0.00 0.00 4.61
1765 1778 4.737578 ACCTCTCCCTTCCCTTTAAAAAC 58.262 43.478 0.00 0.00 0.00 2.43
1791 1805 8.950208 AAATAAAAATGAAACGAAAGGGACAA 57.050 26.923 0.00 0.00 0.00 3.18
1872 1886 5.743636 AGAGGGCAAAATTGAGCAATTTA 57.256 34.783 18.37 0.00 46.76 1.40
1917 1931 2.477245 GGGGCATATCCAACCCTTTTT 58.523 47.619 0.00 0.00 43.68 1.94
1932 1946 6.417503 TTCTCTATATATGGTAGAGGGGCA 57.582 41.667 19.03 5.29 43.38 5.36
2019 2033 1.479709 AGCTCACGAGGCTCATAACT 58.520 50.000 15.95 1.79 34.70 2.24



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

AutoCloner maintained by Alex Coulton.