Multiple sequence alignment - TraesCS1D01G148200

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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 TraesCS1D01G148200 chr1D 100.000 6025 0 0 1 6025 204056893 204050869 0.000000e+00 11127.0
1 TraesCS1D01G148200 chr1A 99.119 5561 45 4 15 5573 259074871 259069313 0.000000e+00 9995.0
2 TraesCS1D01G148200 chr1A 99.338 453 3 0 5573 6025 259069197 259068745 0.000000e+00 821.0
3 TraesCS1D01G148200 chr1B 96.711 5595 126 20 1 5572 299659163 299653604 0.000000e+00 9260.0
4 TraesCS1D01G148200 chr1B 97.561 164 4 0 5569 5732 299653497 299653334 1.280000e-71 281.0
5 TraesCS1D01G148200 chr1B 93.478 184 11 1 5756 5939 299653241 299653059 7.690000e-69 272.0
6 TraesCS1D01G148200 chr1B 95.745 94 1 1 5932 6025 299653037 299652947 1.350000e-31 148.0
7 TraesCS1D01G148200 chr5A 77.372 1233 258 16 2395 3615 671444511 671445734 0.000000e+00 712.0
8 TraesCS1D01G148200 chr5A 96.774 31 1 0 1977 2007 455457887 455457857 1.100000e-02 52.8
9 TraesCS1D01G148200 chr4D 77.317 1230 264 11 2395 3615 490129122 490130345 0.000000e+00 712.0
10 TraesCS1D01G148200 chr4B 76.929 1231 267 13 2395 3615 629948887 629950110 0.000000e+00 684.0


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 TraesCS1D01G148200 chr1D 204050869 204056893 6024 True 11127.00 11127 100.00000 1 6025 1 chr1D.!!$R1 6024
1 TraesCS1D01G148200 chr1A 259068745 259074871 6126 True 5408.00 9995 99.22850 15 6025 2 chr1A.!!$R1 6010
2 TraesCS1D01G148200 chr1B 299652947 299659163 6216 True 2490.25 9260 95.87375 1 6025 4 chr1B.!!$R1 6024
3 TraesCS1D01G148200 chr5A 671444511 671445734 1223 False 712.00 712 77.37200 2395 3615 1 chr5A.!!$F1 1220
4 TraesCS1D01G148200 chr4D 490129122 490130345 1223 False 712.00 712 77.31700 2395 3615 1 chr4D.!!$F1 1220
5 TraesCS1D01G148200 chr4B 629948887 629950110 1223 False 684.00 684 76.92900 2395 3615 1 chr4B.!!$F1 1220

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
832 851 0.744874 TGCTGTAGTGGAGTATCGCC 59.255 55.000 0.00 0.00 34.37 5.54 F
1601 1620 1.923227 GCCAAGCTACCTGTTTCCGC 61.923 60.000 0.00 0.00 0.00 5.54 F
2075 2099 1.333258 GAAGCAGCACTTCGTGTGTTC 60.333 52.381 11.50 5.43 45.16 3.18 F
4986 5013 1.263356 ATGTTTCCAAGCTGCTGCAT 58.737 45.000 18.42 2.35 42.74 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 2099 5.568685 ACGAAGATATGTCTATCCCATCG 57.431 43.478 7.25 7.25 39.21 3.84 R
4351 4378 9.343103 AGATAATATTTCGACAGTATAGTTGCG 57.657 33.333 0.00 0.00 0.00 4.85 R
4642 4669 6.817765 TCTTATAGTGCAAAAACCTGAAGG 57.182 37.500 0.00 0.00 42.17 3.46 R
5876 6091 3.062122 CGGAGCAGGTTAAGGGTTTTA 57.938 47.619 0.00 0.00 0.00 1.52 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
122 135 2.092375 AGATTCCCGTTTCCTGGATTCC 60.092 50.000 0.00 0.00 33.49 3.01
193 206 2.552268 GCGCAAAACCGTCGCTTA 59.448 55.556 0.30 0.00 44.79 3.09
488 501 3.244318 GGTTTTTCTAGACCTGACGGGAA 60.244 47.826 7.51 0.00 38.76 3.97
514 527 2.002127 CGAGCTCCGAATCTTGCAC 58.998 57.895 8.47 0.00 41.76 4.57
832 851 0.744874 TGCTGTAGTGGAGTATCGCC 59.255 55.000 0.00 0.00 34.37 5.54
1585 1604 9.817809 TTAGTTGTAAAATTTTAACATGTGCCA 57.182 25.926 12.14 1.48 0.00 4.92
1601 1620 1.923227 GCCAAGCTACCTGTTTCCGC 61.923 60.000 0.00 0.00 0.00 5.54
2075 2099 1.333258 GAAGCAGCACTTCGTGTGTTC 60.333 52.381 11.50 5.43 45.16 3.18
4986 5013 1.263356 ATGTTTCCAAGCTGCTGCAT 58.737 45.000 18.42 2.35 42.74 3.96
5091 5118 9.921637 TTCTTTCAAATTTGTTTCACTTACACT 57.078 25.926 17.47 0.00 0.00 3.55
5148 5175 8.310382 ACCTACATGATTGAGAGATAATAGCAC 58.690 37.037 0.00 0.00 0.00 4.40
5437 5464 8.710239 TCAAGTACAGTATAATATTCCAGGCAA 58.290 33.333 0.00 0.00 0.00 4.52
5560 5588 1.202989 TGGATACTGGTGGCAAGCAAA 60.203 47.619 0.00 0.00 32.31 3.68
5876 6091 9.739276 TGATCACTTAATAGGAACACTGATTTT 57.261 29.630 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 135 0.727398 GAAAATGGACGAAGGCTCCG 59.273 55.000 0.00 0.00 0.00 4.63
488 501 1.608717 ATTCGGAGCTCGCAACCTCT 61.609 55.000 7.83 0.00 39.05 3.69
514 527 2.555199 CTAGCGAATTCCCCAACTGAG 58.445 52.381 0.00 0.00 0.00 3.35
772 791 3.055385 CGAAACTGAACTGGGGGATAAGA 60.055 47.826 0.00 0.00 0.00 2.10
832 851 1.016130 AGCAACGGAAGCACATCTCG 61.016 55.000 0.00 0.00 0.00 4.04
1585 1604 0.034337 TTCGCGGAAACAGGTAGCTT 59.966 50.000 6.13 0.00 0.00 3.74
1601 1620 9.716507 ATGAATATTTCCATTCGTTTAACTTCG 57.283 29.630 0.00 0.00 37.68 3.79
2075 2099 5.568685 ACGAAGATATGTCTATCCCATCG 57.431 43.478 7.25 7.25 39.21 3.84
4351 4378 9.343103 AGATAATATTTCGACAGTATAGTTGCG 57.657 33.333 0.00 0.00 0.00 4.85
4642 4669 6.817765 TCTTATAGTGCAAAAACCTGAAGG 57.182 37.500 0.00 0.00 42.17 3.46
4986 5013 2.951642 CAGGTGCTGTTTCCTCAAGAAA 59.048 45.455 0.00 0.00 42.28 2.52
5091 5118 8.593679 TCTGGAACTTTGTAATCTACTTCATCA 58.406 33.333 0.00 0.00 0.00 3.07
5148 5175 2.037121 AGAAAAAGGAAACATTGCCCGG 59.963 45.455 0.00 0.00 0.00 5.73
5216 5243 0.532115 ATTGGGAAGAACGGCATTGC 59.468 50.000 0.00 0.00 0.00 3.56
5437 5464 9.574516 ACTTAGACTCTTGGAAATTTTATGTGT 57.425 29.630 0.00 0.00 0.00 3.72
5876 6091 3.062122 CGGAGCAGGTTAAGGGTTTTA 57.938 47.619 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.