Multiple sequence alignment - TraesCS2B01G303000

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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 TraesCS2B01G303000 chr2B 100.000 2672 0 0 1 2672 429179274 429176603 0.000000e+00 4935
1 TraesCS2B01G303000 chr1B 97.832 2675 53 3 1 2672 256213743 256211071 0.000000e+00 4614
2 TraesCS2B01G303000 chr1B 78.674 347 70 3 2300 2644 670967797 670968141 7.440000e-56 228
3 TraesCS2B01G303000 chr1B 82.162 185 31 2 2382 2565 50810787 50810604 9.900000e-35 158
4 TraesCS2B01G303000 chr6D 97.291 2252 57 2 76 2324 235785679 235783429 0.000000e+00 3818
5 TraesCS2B01G303000 chr6D 96.581 351 9 1 2322 2672 235780969 235780622 1.780000e-161 579
6 TraesCS2B01G303000 chr6D 96.721 61 2 0 1 61 235785740 235785800 4.710000e-18 102
7 TraesCS2B01G303000 chr4B 98.693 153 2 0 2520 2672 479405123 479404971 3.390000e-69 272
8 TraesCS2B01G303000 chr4B 76.127 377 84 6 2192 2565 393411489 393411116 2.710000e-45 193
9 TraesCS2B01G303000 chr1A 75.877 456 104 5 2192 2644 521911740 521911288 7.440000e-56 228
10 TraesCS2B01G303000 chr3D 78.626 262 52 4 2306 2565 284927963 284927704 1.270000e-38 171
11 TraesCS2B01G303000 chr1D 75.399 313 75 2 2192 2503 259668200 259668511 1.660000e-32 150
12 TraesCS2B01G303000 chr7B 78.390 236 46 5 2300 2532 439628315 439628548 5.960000e-32 148


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 TraesCS2B01G303000 chr2B 429176603 429179274 2671 True 4935.0 4935 100.000 1 2672 1 chr2B.!!$R1 2671
1 TraesCS2B01G303000 chr1B 256211071 256213743 2672 True 4614.0 4614 97.832 1 2672 1 chr1B.!!$R2 2671
2 TraesCS2B01G303000 chr6D 235780622 235785679 5057 True 2198.5 3818 96.936 76 2672 2 chr6D.!!$R1 2596

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
278 279 0.610785 AATTGCCGGAACCCGTTCAT 60.611 50.000 5.05 0.0 46.80 2.57 F
661 662 1.133668 AGGTTGCTTCTGCTCAGGTTT 60.134 47.619 0.00 0.0 40.48 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1100 1101 0.178992 CTGGGACCCAAAGCAAGACA 60.179 55.0 15.87 0.0 30.8 3.41 R
2211 2218 0.251165 GGTTGCTTCTAGTTGGGCCA 60.251 55.0 0.00 0.0 0.0 5.36 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
278 279 0.610785 AATTGCCGGAACCCGTTCAT 60.611 50.000 5.05 0.00 46.80 2.57
382 383 3.387962 TCTTCATTAGATGGCCAGACCT 58.612 45.455 13.05 10.93 40.22 3.85
467 468 1.961180 GATGACCGTGACCAGGAGGG 61.961 65.000 0.00 0.00 44.81 4.30
661 662 1.133668 AGGTTGCTTCTGCTCAGGTTT 60.134 47.619 0.00 0.00 40.48 3.27
782 783 2.448542 GCCCCTAGCATCCCCTCA 60.449 66.667 0.00 0.00 42.97 3.86
988 989 3.772025 CCCTGTGACTTCTCCAACTAGAT 59.228 47.826 0.00 0.00 0.00 1.98
1037 1038 2.754658 CTGCCCGACGTCTACCCT 60.755 66.667 14.70 0.00 0.00 4.34
1100 1101 1.064389 GCCTATTGCCAGGAGAAAGGT 60.064 52.381 0.00 0.00 38.00 3.50
1152 1153 1.473257 GCCATCATCAACTACGAGCCA 60.473 52.381 0.00 0.00 0.00 4.75
1432 1433 1.088910 GCTTGCTGAGAGGCTGCTAC 61.089 60.000 0.00 0.00 41.53 3.58
1506 1507 6.753279 CCATCAGCAAATTCGTGTCATTATTT 59.247 34.615 0.00 0.00 0.00 1.40
2211 2218 9.804758 GTTATGTTCAAGCTAACTACAGTCTAT 57.195 33.333 1.29 0.00 0.00 1.98
2567 5036 1.227380 CTGATCACTGCCCGCTACC 60.227 63.158 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.451783 GTGTAGGGCTTGAATTGGCG 59.548 55.000 0.00 0.00 0.00 5.69
27 28 2.590092 GCGGGATGTGTAGGGCTT 59.410 61.111 0.00 0.00 0.00 4.35
278 279 2.875485 GCCGACAGCGTAGACAGA 59.125 61.111 0.00 0.00 35.23 3.41
382 383 2.626780 CCTGTCTGACGCGAGGACA 61.627 63.158 15.93 20.90 38.16 4.02
661 662 3.315949 ACCGCACGAAAGCCCCTA 61.316 61.111 0.00 0.00 0.00 3.53
770 771 1.271840 GGTGGTGTGAGGGGATGCTA 61.272 60.000 0.00 0.00 0.00 3.49
782 783 4.382040 CGATAATGTCTTCTGAGGTGGTGT 60.382 45.833 0.00 0.00 0.00 4.16
910 911 1.898154 GTGATACAGGCGGAGGTGT 59.102 57.895 0.00 0.00 0.00 4.16
912 913 1.255667 AACGTGATACAGGCGGAGGT 61.256 55.000 0.00 0.00 0.00 3.85
988 989 4.528206 AGAGTTGGGCATCACGATGATATA 59.472 41.667 11.21 0.00 41.20 0.86
1037 1038 1.011968 CGTCCGCGGAACAAAGATCA 61.012 55.000 32.93 0.00 0.00 2.92
1100 1101 0.178992 CTGGGACCCAAAGCAAGACA 60.179 55.000 15.87 0.00 30.80 3.41
1152 1153 4.664267 TCAGGGGAGGCTGTGGCT 62.664 66.667 0.00 0.00 42.48 4.75
1375 1376 1.219124 GCATCTTCTCCCGCAGACA 59.781 57.895 0.00 0.00 0.00 3.41
1432 1433 0.586319 ACAATGCCAAGACGTTGACG 59.414 50.000 1.41 1.41 46.33 4.35
1506 1507 1.133181 TGTCTGGCAACCTCCCATGA 61.133 55.000 0.00 0.00 0.00 3.07
2211 2218 0.251165 GGTTGCTTCTAGTTGGGCCA 60.251 55.000 0.00 0.00 0.00 5.36
2567 5036 0.609662 CCCTTTGTCATTGGCAAGGG 59.390 55.000 21.70 21.70 41.13 3.95


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

AutoCloner maintained by Alex Coulton.