Multiple sequence alignment - TraesCS3B01G169400

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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 TraesCS3B01G169400 chr3B 100.000 2309 0 0 1 2309 169633418 169631110 0 4265
1 TraesCS3B01G169400 chr3D 95.437 2323 62 13 1 2309 116047224 116044932 0 3663
2 TraesCS3B01G169400 chr3A 85.214 1427 107 54 526 1901 112962358 112960985 0 1371
3 TraesCS3B01G169400 chr3A 97.108 415 11 1 1896 2309 112960324 112959910 0 699


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 TraesCS3B01G169400 chr3B 169631110 169633418 2308 True 4265 4265 100.000 1 2309 1 chr3B.!!$R1 2308
1 TraesCS3B01G169400 chr3D 116044932 116047224 2292 True 3663 3663 95.437 1 2309 1 chr3D.!!$R1 2308
2 TraesCS3B01G169400 chr3A 112959910 112962358 2448 True 1035 1371 91.161 526 2309 2 chr3A.!!$R1 1783

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
992 1049 0.895559 CAGTCCAAAGCAGTTCCCCC 60.896 60.0 0.0 0.0 0.0 5.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2125 2859 3.434309 AGCAAGAACAATACCATGGCTT 58.566 40.909 13.04 2.53 0.0 4.35 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
176 184 7.430441 ACAACAATACCACAAATACAAAGGTC 58.570 34.615 0.00 0.00 33.91 3.85
284 292 7.013178 CCTTGGCAACCATTTTATTTCTTTTGT 59.987 33.333 0.00 0.00 31.53 2.83
489 497 8.964420 TTTCGTTCATGATTACTTTCATTTCC 57.036 30.769 0.00 0.00 34.09 3.13
547 556 7.560991 TGGTGGCATACATGATCTTCTTAAAAT 59.439 33.333 0.00 0.00 0.00 1.82
588 597 9.624697 TTCATACATGCACAAATAACTCTTTTC 57.375 29.630 0.00 0.00 0.00 2.29
838 848 0.960364 CTGTTAATGGGCCGTGTGCT 60.960 55.000 0.00 0.00 40.92 4.40
908 921 2.241941 TGTCATGGCCCATGTCTGTATT 59.758 45.455 22.70 0.00 41.98 1.89
953 1000 4.742440 GCCCGAAAAGGAAACCAAGAAAAT 60.742 41.667 0.00 0.00 45.00 1.82
992 1049 0.895559 CAGTCCAAAGCAGTTCCCCC 60.896 60.000 0.00 0.00 0.00 5.40
1032 1089 2.430367 GAAGCCTCCACCACGGTT 59.570 61.111 0.00 0.00 35.57 4.44
1085 1142 1.592131 CGCATCCTGCTCTCTCTGC 60.592 63.158 0.00 0.00 42.25 4.26
1113 1170 9.764363 TTACATTCCTGTACTCATATGCTTTAG 57.236 33.333 0.00 0.00 37.58 1.85
1427 1489 9.176460 TGTATAATGTGTTGTGATGACATGAAT 57.824 29.630 0.00 0.00 30.69 2.57
1440 1502 3.389002 TGACATGAATCGATGACCATCCT 59.611 43.478 0.00 0.00 34.40 3.24
1561 1624 5.109210 AGTCGTGAGATTGCGATGATTTAA 58.891 37.500 0.00 0.00 45.19 1.52
1669 1732 7.017452 ACCATAGGTAGTTTACTGGTAAAACCA 59.983 37.037 20.14 0.00 39.33 3.67
1802 1870 4.021981 GCTTAGGATCAACTTTTGCCAAGT 60.022 41.667 0.00 0.00 0.00 3.16
1803 1871 5.183140 GCTTAGGATCAACTTTTGCCAAGTA 59.817 40.000 0.00 0.00 0.00 2.24
1804 1872 6.569179 TTAGGATCAACTTTTGCCAAGTAC 57.431 37.500 0.00 0.00 0.00 2.73
1971 2705 5.048083 TGCAGCAACTAGGGTGAATTTAAAG 60.048 40.000 0.00 0.00 38.52 1.85
2138 2872 3.243636 GCATTCCAGAAGCCATGGTATTG 60.244 47.826 14.67 7.11 39.01 1.90
2186 2920 2.290641 ACCACGGCAGATTTGATGGTAA 60.291 45.455 5.72 0.00 35.83 2.85
2258 2993 4.225042 TGAGTAGGTGATATGTTGGCAGTT 59.775 41.667 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.123273 AGCCCTGCTATTTCCCTAAAGA 58.877 45.455 0.00 0.00 36.99 2.52
140 148 8.608844 TTGTGGTATTGTTGTTTTTGTTTCTT 57.391 26.923 0.00 0.00 0.00 2.52
176 184 1.871676 CAATGCCTCCAGATGATCACG 59.128 52.381 0.00 0.00 0.00 4.35
575 584 6.710295 GGCCCATTTGTTGAAAAGAGTTATTT 59.290 34.615 0.00 0.00 0.00 1.40
588 597 5.771153 ATTTGAAAAAGGCCCATTTGTTG 57.229 34.783 8.01 0.00 0.00 3.33
838 848 5.165961 ACTTCTAAATGAGCTGGCAACTA 57.834 39.130 0.00 0.00 37.61 2.24
908 921 3.773860 ATGTTGTTGTTTCTGTGCGAA 57.226 38.095 0.00 0.00 0.00 4.70
923 970 3.366985 GGTTTCCTTTTCGGGCTATGTTG 60.367 47.826 0.00 0.00 0.00 3.33
924 971 2.823747 GGTTTCCTTTTCGGGCTATGTT 59.176 45.455 0.00 0.00 0.00 2.71
925 972 2.224917 TGGTTTCCTTTTCGGGCTATGT 60.225 45.455 0.00 0.00 0.00 2.29
953 1000 1.073284 GGGCTATGATTTCCGGGCTTA 59.927 52.381 0.00 0.00 0.00 3.09
1032 1089 1.924731 TGAAGGAGAAGAAGCGGAGA 58.075 50.000 0.00 0.00 0.00 3.71
1085 1142 8.668510 AAGCATATGAGTACAGGAATGTAAAG 57.331 34.615 6.97 0.00 0.00 1.85
1124 1181 1.805945 GCGGTGACAGAGGCGTTAG 60.806 63.158 0.00 0.00 0.00 2.34
1251 1308 2.048597 TCGGCTGCTACCAACACG 60.049 61.111 0.00 0.00 0.00 4.49
1536 1599 1.745653 TCATCGCAATCTCACGACTCT 59.254 47.619 0.00 0.00 41.76 3.24
1669 1732 2.836981 ACTAGGAGAATGCTGCAACTCT 59.163 45.455 26.59 21.68 37.36 3.24
1771 1834 7.415541 GCAAAAGTTGATCCTAAGCATCACATA 60.416 37.037 0.00 0.00 29.70 2.29
1803 1871 9.401058 GAATCCCTAATTGCATATGCTTATAGT 57.599 33.333 27.13 12.23 42.66 2.12
1804 1872 9.624373 AGAATCCCTAATTGCATATGCTTATAG 57.376 33.333 27.13 22.21 42.66 1.31
1971 2705 8.117370 GCTATAAAGAAGAGTTTTTCCATCGAC 58.883 37.037 0.00 0.00 0.00 4.20
2121 2855 3.624777 AGAACAATACCATGGCTTCTGG 58.375 45.455 13.04 0.00 39.80 3.86
2125 2859 3.434309 AGCAAGAACAATACCATGGCTT 58.566 40.909 13.04 2.53 0.00 4.35
2138 2872 7.536622 CACTGAAATCACATAGAAAGCAAGAAC 59.463 37.037 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.