Multiple sequence alignment - TraesCS5D01G063300

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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 TraesCS5D01G063300 chr5D 100.000 2297 0 0 1 2297 58914288 58911992 0 4242
1 TraesCS5D01G063300 chrUn 96.953 2297 69 1 1 2297 261514798 261512503 0 3853
2 TraesCS5D01G063300 chrUn 96.909 2297 68 2 1 2297 45099060 45101353 0 3845
3 TraesCS5D01G063300 chr5B 96.909 2297 68 2 1 2297 130613169 130615462 0 3845
4 TraesCS5D01G063300 chr5B 96.648 2297 74 2 1 2297 130608145 130610438 0 3812
5 TraesCS5D01G063300 chr5B 96.607 2299 75 2 1 2297 130570491 130568194 0 3810
6 TraesCS5D01G063300 chr2D 96.868 2299 69 2 1 2297 644701528 644703825 0 3843
7 TraesCS5D01G063300 chr3A 96.778 2297 72 2 1 2297 66032046 66029752 0 3831
8 TraesCS5D01G063300 chr2B 96.561 2297 76 3 1 2297 112867381 112869674 0 3801
9 TraesCS5D01G063300 chr2A 96.212 2297 85 2 1 2297 735225205 735222911 0 3759


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 TraesCS5D01G063300 chr5D 58911992 58914288 2296 True 4242.0 4242 100.0000 1 2297 1 chr5D.!!$R1 2296
1 TraesCS5D01G063300 chrUn 261512503 261514798 2295 True 3853.0 3853 96.9530 1 2297 1 chrUn.!!$R1 2296
2 TraesCS5D01G063300 chrUn 45099060 45101353 2293 False 3845.0 3845 96.9090 1 2297 1 chrUn.!!$F1 2296
3 TraesCS5D01G063300 chr5B 130608145 130615462 7317 False 3828.5 3845 96.7785 1 2297 2 chr5B.!!$F1 2296
4 TraesCS5D01G063300 chr5B 130568194 130570491 2297 True 3810.0 3810 96.6070 1 2297 1 chr5B.!!$R1 2296
5 TraesCS5D01G063300 chr2D 644701528 644703825 2297 False 3843.0 3843 96.8680 1 2297 1 chr2D.!!$F1 2296
6 TraesCS5D01G063300 chr3A 66029752 66032046 2294 True 3831.0 3831 96.7780 1 2297 1 chr3A.!!$R1 2296
7 TraesCS5D01G063300 chr2B 112867381 112869674 2293 False 3801.0 3801 96.5610 1 2297 1 chr2B.!!$F1 2296
8 TraesCS5D01G063300 chr2A 735222911 735225205 2294 True 3759.0 3759 96.2120 1 2297 1 chr2A.!!$R1 2296

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
883 5910 0.685097 AACCTTGCTTCTACTCGCCA 59.315 50.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1906 6933 0.45339 GCAGCGAATCTCCCCTTTTG 59.547 55.0 0.0 0.0 0.0 2.44 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
190 191 1.879430 GCCGGCTAATCGTACGCAA 60.879 57.895 22.15 0.00 0.00 4.85
205 206 0.962356 CGCAACAGGAGCAAGGGAAT 60.962 55.000 0.00 0.00 0.00 3.01
232 233 0.807496 GTTCAGGAAGGCACATGAGC 59.193 55.000 6.57 6.57 32.42 4.26
233 234 0.694771 TTCAGGAAGGCACATGAGCT 59.305 50.000 14.91 0.00 32.42 4.09
238 239 1.661341 GAAGGCACATGAGCTCGAAT 58.339 50.000 14.91 0.00 34.17 3.34
258 259 5.107337 CGAATGCTATTATGAATGTGCGACT 60.107 40.000 0.00 0.00 0.00 4.18
271 272 2.619646 TGTGCGACTGACACTACACTAA 59.380 45.455 0.00 0.00 38.86 2.24
320 321 1.108776 CGGTCGGTCCTAGAAATGGA 58.891 55.000 0.00 0.00 0.00 3.41
328 329 2.092699 GTCCTAGAAATGGAGGCAGCTT 60.093 50.000 0.00 0.00 33.78 3.74
329 330 3.134804 GTCCTAGAAATGGAGGCAGCTTA 59.865 47.826 0.00 0.00 33.78 3.09
330 331 3.976654 TCCTAGAAATGGAGGCAGCTTAT 59.023 43.478 0.00 0.00 0.00 1.73
345 346 4.678309 GCAGCTTATGAGGAGTTAACGACT 60.678 45.833 0.00 2.30 42.70 4.18
438 5465 4.019321 CACAATTCTTCTTGGAGGAGGGTA 60.019 45.833 0.00 0.00 0.00 3.69
485 5512 3.073209 TGCCATAATATACTCCCGCCAAA 59.927 43.478 0.00 0.00 0.00 3.28
524 5551 5.657474 ACCGAAGTTGAACATACATACGAT 58.343 37.500 0.00 0.00 0.00 3.73
536 5563 6.458210 ACATACATACGATGATCTTCATGCA 58.542 36.000 9.10 0.00 37.20 3.96
672 5699 3.395941 AGGGGACATGATCAATAGAACCC 59.604 47.826 0.00 7.44 34.66 4.11
673 5700 3.138283 GGGGACATGATCAATAGAACCCA 59.862 47.826 21.08 0.00 36.85 4.51
736 5763 2.426522 TCTGAAAAGGTTCGCTCATGG 58.573 47.619 0.00 0.00 36.46 3.66
876 5903 7.828508 TCGGTATCTAATAACCTTGCTTCTA 57.171 36.000 0.00 0.00 33.34 2.10
883 5910 0.685097 AACCTTGCTTCTACTCGCCA 59.315 50.000 0.00 0.00 0.00 5.69
907 5934 2.158943 GGCGCACCTCTCCTAACTATTT 60.159 50.000 10.83 0.00 0.00 1.40
985 6012 9.485206 GCCAAATCCTTCTATTATTAAGTACGA 57.515 33.333 0.00 0.00 0.00 3.43
1170 6197 5.503662 TTTATGTGATCGCAGCATCAAAT 57.496 34.783 15.24 12.47 35.30 2.32
1225 6252 7.646922 GCTCAAAATATTTGATCTTAGGTGCAG 59.353 37.037 0.39 0.00 0.00 4.41
1237 6264 4.703703 GTGCAGTTCCCTCTGGAC 57.296 61.111 3.01 3.01 45.94 4.02
1383 6410 1.689273 GGCCGTGTCTTGATCTCCTAT 59.311 52.381 0.00 0.00 0.00 2.57
1384 6411 2.891580 GGCCGTGTCTTGATCTCCTATA 59.108 50.000 0.00 0.00 0.00 1.31
1408 6435 4.379603 CGCGAAAGATAAGATACGGGAGAT 60.380 45.833 0.00 0.00 36.20 2.75
1454 6481 1.831736 CCCTTGGTCTAGTTCCACGAT 59.168 52.381 12.12 0.00 34.45 3.73
1485 6512 2.669434 GCGTGGCGTAAAGTGAAGATTA 59.331 45.455 0.00 0.00 0.00 1.75
1619 6646 0.389391 CCCAGTGTCACACGTTCTCT 59.611 55.000 1.22 0.00 39.64 3.10
1692 6719 1.821061 CGGAGCCGAGCCAGGAATAT 61.821 60.000 2.00 0.00 42.83 1.28
1703 6730 2.550208 GCCAGGAATATCCGTTAGTGGG 60.550 54.545 0.00 0.00 42.75 4.61
1880 6907 3.068560 CCCCGTCGAAAGAATTAACACA 58.931 45.455 0.00 0.00 45.01 3.72
1931 6958 1.687123 GGGGAGATTCGCTGCTTACTA 59.313 52.381 0.00 0.00 34.97 1.82
1933 6960 2.546162 GGGAGATTCGCTGCTTACTACC 60.546 54.545 0.00 0.00 34.97 3.18
2020 7047 6.366061 CCGATCGCATAAAAAGTCATGAGATA 59.634 38.462 10.32 0.00 40.39 1.98
2082 7109 8.608844 AAAAAGTCAATATCTCGTTCTCTTGT 57.391 30.769 0.00 0.00 0.00 3.16
2084 7111 8.608844 AAAGTCAATATCTCGTTCTCTTGTTT 57.391 30.769 0.00 0.00 0.00 2.83
2170 7197 5.710099 AGGATTCTGCTTTTCGATTAAACCA 59.290 36.000 0.00 0.00 0.00 3.67
2232 7259 5.699458 CCTTAAGAACGGTCAAAGCTAGAAA 59.301 40.000 1.87 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 3.764160 CTCCTCCGCATCCCAAGCC 62.764 68.421 0.00 0.00 0.00 4.35
139 140 0.043637 AAGGATTAGGACGTCCCCCA 59.956 55.000 30.82 15.46 35.00 4.96
190 191 3.987594 GGAATTCCCTTGCTCCTGT 57.012 52.632 14.03 0.00 0.00 4.00
232 233 5.119125 TCGCACATTCATAATAGCATTCGAG 59.881 40.000 0.00 0.00 0.00 4.04
233 234 4.987912 TCGCACATTCATAATAGCATTCGA 59.012 37.500 0.00 0.00 0.00 3.71
238 239 4.507756 GTCAGTCGCACATTCATAATAGCA 59.492 41.667 0.00 0.00 0.00 3.49
281 282 3.807538 GCCTCACCTGCATGCACG 61.808 66.667 18.46 15.99 0.00 5.34
320 321 3.430929 CGTTAACTCCTCATAAGCTGCCT 60.431 47.826 3.71 0.00 0.00 4.75
328 329 3.376234 CGTCCAGTCGTTAACTCCTCATA 59.624 47.826 3.71 0.00 35.45 2.15
329 330 2.163815 CGTCCAGTCGTTAACTCCTCAT 59.836 50.000 3.71 0.00 35.45 2.90
330 331 1.538512 CGTCCAGTCGTTAACTCCTCA 59.461 52.381 3.71 0.00 35.45 3.86
345 346 1.005037 CTAGGTTGCAGCACGTCCA 60.005 57.895 2.05 0.00 0.00 4.02
509 5536 7.116805 GCATGAAGATCATCGTATGTATGTTCA 59.883 37.037 0.00 14.08 34.28 3.18
536 5563 2.821437 TCTTTCCTCTCGTCCCTTCAT 58.179 47.619 0.00 0.00 0.00 2.57
547 5574 1.555533 CTACCGCCCTTTCTTTCCTCT 59.444 52.381 0.00 0.00 0.00 3.69
736 5763 4.768968 TCACTAAGTGGTTAGTACCTCCAC 59.231 45.833 18.16 18.16 46.01 4.02
883 5910 1.609501 TTAGGAGAGGTGCGCCAGT 60.610 57.895 20.59 4.28 39.21 4.00
985 6012 3.695830 ACACATCGAAATGGTACCAGT 57.304 42.857 21.41 15.91 37.19 4.00
1170 6197 5.860611 TCCGTGGAAAATTCAGACTTTCTA 58.139 37.500 4.78 0.00 33.06 2.10
1237 6264 3.854286 GTCGCACCCGAACAATAATAG 57.146 47.619 0.00 0.00 46.34 1.73
1366 6393 3.556513 GCGTATAGGAGATCAAGACACG 58.443 50.000 0.00 0.00 0.00 4.49
1373 6400 6.653740 TCTTATCTTTCGCGTATAGGAGATCA 59.346 38.462 5.77 0.00 0.00 2.92
1383 6410 3.814842 TCCCGTATCTTATCTTTCGCGTA 59.185 43.478 5.77 0.00 0.00 4.42
1384 6411 2.620115 TCCCGTATCTTATCTTTCGCGT 59.380 45.455 5.77 0.00 0.00 6.01
1408 6435 0.651124 ACCCATACCATAGGACCCCA 59.349 55.000 0.00 0.00 0.00 4.96
1485 6512 1.700186 GGATTTCGCTCTATTCCCCCT 59.300 52.381 0.00 0.00 0.00 4.79
1619 6646 0.635009 ACTGGATCCCTTCGGACCTA 59.365 55.000 9.90 0.00 42.48 3.08
1692 6719 1.259840 GGTAGGTGCCCACTAACGGA 61.260 60.000 0.00 0.00 0.00 4.69
1703 6730 0.872388 CGGTGAAAAGTGGTAGGTGC 59.128 55.000 0.00 0.00 0.00 5.01
1745 6772 8.749354 GGACCCTGTGAACATATTTTCTTAATT 58.251 33.333 3.41 0.00 0.00 1.40
1769 6796 3.024547 CCTATGACCGAGTCTTTCTGGA 58.975 50.000 5.77 0.00 33.15 3.86
1880 6907 2.524148 GCTGGTGGCCCTTTTGGT 60.524 61.111 0.00 0.00 38.10 3.67
1906 6933 0.453390 GCAGCGAATCTCCCCTTTTG 59.547 55.000 0.00 0.00 0.00 2.44
1919 6946 1.509463 CGTGGGTAGTAAGCAGCGA 59.491 57.895 0.00 0.00 0.00 4.93
1948 6975 1.470979 CGGACGACTTGACCATAAGGG 60.471 57.143 0.00 0.00 44.81 3.95
2061 7088 7.378966 TGAAACAAGAGAACGAGATATTGACT 58.621 34.615 0.00 0.00 0.00 3.41
2082 7109 1.507140 AGGACGCCCCATCTATGAAA 58.493 50.000 0.00 0.00 37.41 2.69
2084 7111 2.457598 GATAGGACGCCCCATCTATGA 58.542 52.381 0.00 0.00 37.41 2.15
2170 7197 1.944024 TGAATCGCCGACTTGTGTTTT 59.056 42.857 0.00 0.00 0.00 2.43
2216 7243 7.108841 TGATATAGTTTCTAGCTTTGACCGT 57.891 36.000 0.00 0.00 0.00 4.83
2232 7259 4.584743 TCGTTCCAGCAGTCATGATATAGT 59.415 41.667 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.