Multiple sequence alignment - TraesCS6D01G109400

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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 TraesCS6D01G109400 chr6D 100.000 2576 0 0 1 2576 75012646 75010071 0.000000e+00 4758.0
1 TraesCS6D01G109400 chr6B 97.214 2584 52 9 8 2576 148693038 148690460 0.000000e+00 4355.0
2 TraesCS6D01G109400 chr6A 95.196 1915 74 12 1 1909 91294197 91292295 0.000000e+00 3011.0
3 TraesCS6D01G109400 chr6A 97.917 432 9 0 1906 2337 91292242 91291811 0.000000e+00 749.0
4 TraesCS6D01G109400 chr6A 99.592 245 1 0 2332 2576 91291460 91291216 5.060000e-122 448.0
5 TraesCS6D01G109400 chr6A 97.727 44 1 0 1934 1977 91292299 91292256 2.750000e-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 TraesCS6D01G109400 chr6D 75010071 75012646 2575 True 4758.0 4758 100.000 1 2576 1 chr6D.!!$R1 2575
1 TraesCS6D01G109400 chr6B 148690460 148693038 2578 True 4355.0 4355 97.214 8 2576 1 chr6B.!!$R1 2568
2 TraesCS6D01G109400 chr6A 91291216 91294197 2981 True 1071.2 3011 97.608 1 2576 4 chr6A.!!$R1 2575

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
256 262 1.072159 GAAGGCAGTCTGGCAGTGT 59.928 57.895 26.56 9.96 46.46 3.55 F
1154 1160 2.954316 GGGTTTTAATCCCAAAGCACG 58.046 47.619 6.24 0.00 44.05 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1157 1163 0.674534 ATCTCCGACGGTTATCTGGC 59.325 55.0 14.79 0.0 0.0 4.85 R
2008 2073 3.002791 CCGGGCTAGCATGTAACATATG 58.997 50.0 18.24 0.0 0.0 1.78 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
127 128 4.669206 TTGTTGTGCAGTGGATTCATTT 57.331 36.364 0.00 0.00 0.00 2.32
137 138 3.025978 GTGGATTCATTTGCATCAGGGA 58.974 45.455 0.00 0.00 0.00 4.20
148 149 3.889815 TGCATCAGGGAGAAGTATTTGG 58.110 45.455 0.00 0.00 0.00 3.28
256 262 1.072159 GAAGGCAGTCTGGCAGTGT 59.928 57.895 26.56 9.96 46.46 3.55
335 341 8.773404 TTTCTTTGAGTGTATTTAGCTCTACC 57.227 34.615 0.00 0.00 0.00 3.18
653 659 6.510879 AAGTTGACATATGACGACTACTCA 57.489 37.500 22.92 6.43 34.26 3.41
1090 1096 7.451877 TGTTATTACCCAAGGAGTTATGCAAAA 59.548 33.333 0.00 0.00 0.00 2.44
1154 1160 2.954316 GGGTTTTAATCCCAAAGCACG 58.046 47.619 6.24 0.00 44.05 5.34
1157 1163 3.313690 GTTTTAATCCCAAAGCACGTGG 58.686 45.455 18.88 0.00 35.77 4.94
1312 1318 0.245539 CGAAGCTCTACGGTTTCCCA 59.754 55.000 0.00 0.00 32.54 4.37
1351 1357 9.174166 GGTTACTAAATATCTTGGCAAAGAAGA 57.826 33.333 7.83 0.00 45.44 2.87
1447 1456 3.499918 AGGCAGAGAAAAGTTCAATGACG 59.500 43.478 0.00 0.00 32.50 4.35
2008 2073 5.109903 ACGTTGCATAACTTGGAGATAGAC 58.890 41.667 0.00 0.00 34.60 2.59
2163 2228 8.837099 ATTGTTCCAAATAATATTCCTGGTGA 57.163 30.769 0.00 0.00 0.00 4.02
2236 2301 5.153950 ACCCTCGAAATGCTAGGAATATC 57.846 43.478 0.00 0.00 31.16 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 5.105752 TCCACTGCACAACAAATTTACAAC 58.894 37.500 0.00 0.0 0.00 3.32
127 128 3.889815 CCAAATACTTCTCCCTGATGCA 58.110 45.455 0.00 0.0 0.00 3.96
137 138 5.221641 TGACACTGTACTGCCAAATACTTCT 60.222 40.000 0.00 0.0 0.00 2.85
148 149 3.795561 GTCACATTGACACTGTACTGC 57.204 47.619 0.00 0.0 46.22 4.40
172 173 4.716784 AGATATGGCTCTGAACTTGGTGTA 59.283 41.667 0.00 0.0 0.00 2.90
335 341 5.368989 AGAAAACTTTGACTACCTCCACAG 58.631 41.667 0.00 0.0 0.00 3.66
467 473 6.314896 GCAACTAGCAACAAGATCACTTAGAT 59.685 38.462 0.00 0.0 44.79 1.98
653 659 2.042162 AGCCTCTCATCCACCAAATGTT 59.958 45.455 0.00 0.0 0.00 2.71
1090 1096 3.265737 TGTGCCATTATGAGTGTACCCTT 59.734 43.478 0.00 0.0 0.00 3.95
1154 1160 1.520787 CCGACGGTTATCTGGCCAC 60.521 63.158 0.00 0.0 0.00 5.01
1157 1163 0.674534 ATCTCCGACGGTTATCTGGC 59.325 55.000 14.79 0.0 0.00 4.85
1189 1195 2.789409 AAGAGCACCTGGTAATGTCC 57.211 50.000 0.00 0.0 0.00 4.02
1312 1318 8.788325 ATATTTAGTAACCACTTTTCGAGCTT 57.212 30.769 0.00 0.0 36.14 3.74
1351 1357 0.991920 ACCGGGACTGACATTTCCAT 59.008 50.000 6.32 0.0 33.01 3.41
1487 1496 9.967451 TTCCTAACTTGGAACATACATCATTAA 57.033 29.630 0.00 0.0 40.80 1.40
2008 2073 3.002791 CCGGGCTAGCATGTAACATATG 58.997 50.000 18.24 0.0 0.00 1.78
2163 2228 4.881273 TCGCATATTGCAGACTAACCAAAT 59.119 37.500 0.00 0.0 45.36 2.32
2236 2301 6.601741 TTAAAACAAGAAAGCAGCCATTTG 57.398 33.333 0.00 0.0 0.00 2.32


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

AutoCloner maintained by Alex Coulton.