Multiple sequence alignment - TraesCS2D01G281400

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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 TraesCS2D01G281400 chr2D 100.000 2549 0 0 1 2549 354391814 354389266 0.000000e+00 4708.0
1 TraesCS2D01G281400 chr2A 91.657 2637 64 39 2 2547 473644997 473642426 0.000000e+00 3507.0
2 TraesCS2D01G281400 chr2B 91.651 2587 74 29 61 2549 421259879 421257337 0.000000e+00 3450.0
3 TraesCS2D01G281400 chr2B 97.436 39 1 0 2 40 421259915 421259877 1.640000e-07 67.6
4 TraesCS2D01G281400 chr7B 97.143 35 1 0 1141 1175 19677321 19677287 2.740000e-05 60.2


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 TraesCS2D01G281400 chr2D 354389266 354391814 2548 True 4708.0 4708 100.0000 1 2549 1 chr2D.!!$R1 2548
1 TraesCS2D01G281400 chr2A 473642426 473644997 2571 True 3507.0 3507 91.6570 2 2547 1 chr2A.!!$R1 2545
2 TraesCS2D01G281400 chr2B 421257337 421259915 2578 True 1758.8 3450 94.5435 2 2549 2 chr2B.!!$R1 2547

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
303 314 0.732538 GCGCCCCATGAAAGAAAACG 60.733 55.0 0.0 0.0 0.0 3.6 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 2190 0.755686 CATCTAGGAGTGGCAGTCCC 59.244 60.0 32.68 17.79 38.51 4.46 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
44 45 8.100508 AGCTAGTTGATCTTTTTAAAGGTGAC 57.899 34.615 2.63 0.00 36.67 3.67
275 286 3.199880 CCTACCATAAAGGCCTCACAG 57.800 52.381 5.23 0.00 43.14 3.66
276 287 2.158755 CCTACCATAAAGGCCTCACAGG 60.159 54.545 5.23 9.37 43.14 4.00
303 314 0.732538 GCGCCCCATGAAAGAAAACG 60.733 55.000 0.00 0.00 0.00 3.60
475 502 0.758685 CCTTGAGGCCACCAAACCAA 60.759 55.000 5.01 0.00 0.00 3.67
564 608 3.681473 GGGCAAACCGGAAGAAGG 58.319 61.111 9.46 0.00 36.48 3.46
731 800 2.101209 CTCGTGGCACGGACAAACAC 62.101 60.000 36.30 0.00 42.81 3.32
771 841 2.906897 CACAAAGCCACACCGCCT 60.907 61.111 0.00 0.00 0.00 5.52
772 842 1.599518 CACAAAGCCACACCGCCTA 60.600 57.895 0.00 0.00 0.00 3.93
773 843 1.599797 ACAAAGCCACACCGCCTAC 60.600 57.895 0.00 0.00 0.00 3.18
853 923 3.692745 CTTGCTTTCGCTCGCTCGC 62.693 63.158 0.00 0.00 36.97 5.03
954 1024 1.824230 ACAAGCCAAAGCACAACAAGA 59.176 42.857 0.00 0.00 43.56 3.02
1582 1700 0.319383 CGGAGATCGATGCTTCCTGG 60.319 60.000 0.54 0.00 42.43 4.45
1676 1822 5.598416 TGAGACGATAATCATCTGGTTGT 57.402 39.130 0.00 0.00 0.00 3.32
1677 1823 5.351458 TGAGACGATAATCATCTGGTTGTG 58.649 41.667 0.00 0.00 0.00 3.33
1678 1824 4.697514 AGACGATAATCATCTGGTTGTGG 58.302 43.478 0.00 0.00 0.00 4.17
1679 1825 4.162320 AGACGATAATCATCTGGTTGTGGT 59.838 41.667 0.00 0.00 0.00 4.16
1680 1826 4.843728 ACGATAATCATCTGGTTGTGGTT 58.156 39.130 0.00 0.00 0.00 3.67
1681 1827 4.635765 ACGATAATCATCTGGTTGTGGTTG 59.364 41.667 0.00 0.00 0.00 3.77
1809 1957 6.633856 CAGGCTGCCTTAATAAAGAAACAAT 58.366 36.000 20.79 0.00 34.37 2.71
1955 2109 1.005037 TGTTGAGCTAGTGCGGTGG 60.005 57.895 0.00 0.00 45.42 4.61
1965 2119 3.310307 TGCGGTGGCAGCAGTAGA 61.310 61.111 17.80 0.00 46.21 2.59
2012 2166 5.107133 CCATCAAGTTTGGATGATTTCAGC 58.893 41.667 4.07 0.00 43.80 4.26
2013 2167 5.105473 CCATCAAGTTTGGATGATTTCAGCT 60.105 40.000 4.07 0.00 43.80 4.24
2021 2175 5.698741 TGGATGATTTCAGCTCTCCTTTA 57.301 39.130 0.00 0.00 31.98 1.85
2036 2190 1.884579 CCTTTAGCCATGCATGCTAGG 59.115 52.381 21.69 20.36 41.94 3.02
2127 2287 1.572085 CTGCAAACTGGTCTCAGGCG 61.572 60.000 0.00 0.00 44.99 5.52
2139 2299 3.267483 GTCTCAGGCGCCTTAAATTGTA 58.733 45.455 30.60 5.53 0.00 2.41
2268 2428 0.318955 ATGTCAGCAAAACGCAAGCC 60.319 50.000 0.00 0.00 46.13 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.545113 GCTACAAGACAACAGGACGTCA 60.545 50.000 18.91 0.00 34.48 4.35
44 45 4.655762 TGTCTTATTGACTCCATCCTCG 57.344 45.455 0.00 0.00 45.54 4.63
278 289 4.776322 TTCATGGGGCGCGTCCAG 62.776 66.667 33.48 20.58 37.75 3.86
303 314 1.330306 GACGTGCATGCACATGTTTC 58.670 50.000 40.95 26.64 46.47 2.78
366 377 2.669364 CTGCTTTTGTTCCACATGCTC 58.331 47.619 0.00 0.00 0.00 4.26
564 608 3.120338 TCGTGGACGCAATTCAGATTTTC 60.120 43.478 0.00 0.00 39.60 2.29
853 923 5.154932 GTGTTTATACATCCTCCGATCGAG 58.845 45.833 18.66 11.81 36.50 4.04
954 1024 3.011257 GGTATATCTCCCTCTCCTGCTCT 59.989 52.174 0.00 0.00 0.00 4.09
979 1057 0.827368 GAAGATCGAGGCCAAGGAGT 59.173 55.000 5.01 0.00 0.00 3.85
982 1060 0.471617 ATGGAAGATCGAGGCCAAGG 59.528 55.000 5.01 0.00 33.51 3.61
1179 1263 3.072468 TTCGCCGGTGGAGTAGGG 61.072 66.667 16.49 0.00 0.00 3.53
1182 1266 2.672651 TCGTTCGCCGGTGGAGTA 60.673 61.111 16.49 0.00 37.11 2.59
1282 1375 2.049156 CGTCTGCTGCTTCACGGA 60.049 61.111 0.00 0.00 0.00 4.69
1716 1862 4.022242 AGCATGTACACCCGATGTATAGAC 60.022 45.833 0.00 0.00 45.59 2.59
1788 1934 6.630071 TCCATTGTTTCTTTATTAAGGCAGC 58.370 36.000 0.00 0.00 32.02 5.25
1955 2109 2.732412 TTGTCAGACTCTACTGCTGC 57.268 50.000 1.31 0.00 37.75 5.25
1979 2133 7.510001 TCATCCAAACTTGATGGCCAATATTAT 59.490 33.333 10.96 0.00 37.88 1.28
2012 2166 1.607628 GCATGCATGGCTAAAGGAGAG 59.392 52.381 27.34 0.00 0.00 3.20
2013 2167 1.213678 AGCATGCATGGCTAAAGGAGA 59.786 47.619 27.34 0.00 40.47 3.71
2021 2175 2.080536 TCCCCTAGCATGCATGGCT 61.081 57.895 27.34 24.08 45.18 4.75
2036 2190 0.755686 CATCTAGGAGTGGCAGTCCC 59.244 60.000 32.68 17.79 38.51 4.46
2127 2287 2.161609 AGCGCAGTGTACAATTTAAGGC 59.838 45.455 11.47 0.00 0.00 4.35
2139 2299 0.875908 CCATATACGCAGCGCAGTGT 60.876 55.000 22.63 22.63 36.08 3.55
2327 2502 3.935203 CTCCTGCAAACGTGTATCTGATT 59.065 43.478 0.00 0.00 0.00 2.57
2338 2514 3.423154 GGTCGCCTCCTGCAAACG 61.423 66.667 0.00 0.00 41.33 3.60


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

AutoCloner maintained by Alex Coulton.