Multiple sequence alignment - TraesCS4D01G152200

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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 TraesCS4D01G152200 chr4D 100.000 3063 0 0 467 3529 180194385 180191323 0.000000e+00 5657.0
1 TraesCS4D01G152200 chr4D 100.000 40 0 0 1 40 180194851 180194812 1.360000e-09 75.0
2 TraesCS4D01G152200 chrUn 97.554 3066 47 11 467 3529 56132558 56129518 0.000000e+00 5221.0
3 TraesCS4D01G152200 chrUn 100.000 29 0 0 12 40 56132673 56132645 2.000000e-03 54.7
4 TraesCS4D01G152200 chr4A 96.395 3079 76 7 467 3528 296906211 296903151 0.000000e+00 5038.0
5 TraesCS4D01G152200 chr7B 100.000 28 0 0 873 900 231094248 231094221 6.000000e-03 52.8


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 TraesCS4D01G152200 chr4D 180191323 180194851 3528 True 2866.00 5657 100.000 1 3529 2 chr4D.!!$R1 3528
1 TraesCS4D01G152200 chrUn 56129518 56132673 3155 True 2637.85 5221 98.777 12 3529 2 chrUn.!!$R1 3517
2 TraesCS4D01G152200 chr4A 296903151 296906211 3060 True 5038.00 5038 96.395 467 3528 1 chr4A.!!$R1 3061


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
944 945 1.132588 GTCGGCGTAAGATCTGATGC 58.867 55.0 15.21 15.21 43.02 3.91 F
1736 1737 0.465097 CTCCTGCTGGCGGAATCAAT 60.465 55.0 4.42 0.00 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2331 2332 2.092968 TGCTTGACTGGTTGAGTGAAGT 60.093 45.455 0.00 0.0 45.12 3.01 R
2804 2821 3.423749 TCATGGACATGCAAATGTGACT 58.576 40.909 7.41 0.0 38.65 3.41 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
656 657 1.358830 CCATGCCTCCCCCAAGATCT 61.359 60.000 0.00 0.00 0.00 2.75
816 817 3.134127 GGGCATTCCTGGTGCGTC 61.134 66.667 3.53 0.00 43.40 5.19
944 945 1.132588 GTCGGCGTAAGATCTGATGC 58.867 55.000 15.21 15.21 43.02 3.91
1077 1078 2.806237 CGCCTCCGGGAGTACTTC 59.194 66.667 22.07 0.00 33.58 3.01
1161 1162 0.872388 GCTTCGGGTTCATCGTGTTT 59.128 50.000 0.00 0.00 0.00 2.83
1267 1268 4.937201 ACGCTAGGTTCATGATGATGTA 57.063 40.909 0.00 0.00 0.00 2.29
1736 1737 0.465097 CTCCTGCTGGCGGAATCAAT 60.465 55.000 4.42 0.00 0.00 2.57
1752 1753 8.128582 GCGGAATCAATTATGTTATGAACAGAA 58.871 33.333 2.24 2.24 45.43 3.02
1952 1953 2.155155 CGGTAGCTCGAACTTCAACAAC 59.845 50.000 0.00 0.00 0.00 3.32
2044 2045 2.607187 CTATGGTGGAGTCAACGACAC 58.393 52.381 0.00 0.00 34.60 3.67
2331 2332 1.138859 CTGGATCAGGTGGCGTCAATA 59.861 52.381 0.00 0.00 0.00 1.90
2543 2544 5.513267 GGGGCATTAACAGATAGAGGTTAGG 60.513 48.000 0.00 0.00 31.71 2.69
2630 2631 5.070180 AGTTCATGTACTAGCAGCATCAGAT 59.930 40.000 2.74 0.00 0.00 2.90
2644 2645 5.296283 CAGCATCAGATAAAGACCCTCAAAG 59.704 44.000 0.00 0.00 0.00 2.77
2804 2821 9.147732 CTCCCAGGATAATGCATATATGTAGTA 57.852 37.037 12.34 12.34 0.00 1.82
2912 2930 7.658167 TGAACTAAAAAGATGTCGTTACCATCA 59.342 33.333 0.00 0.00 40.93 3.07
2971 2989 7.444183 TCCCAATCGTTACATTAGGATGATTTC 59.556 37.037 0.00 0.00 36.73 2.17
3171 3189 8.408043 AGATTCATTTTGAACATGAACCTACA 57.592 30.769 8.73 0.00 42.17 2.74
3255 3273 7.049799 TGCCTTCTTTTTATTTGTGCTACTT 57.950 32.000 0.00 0.00 0.00 2.24
3336 3354 6.618287 TTTGTCATCTGTGAACTTAACCTG 57.382 37.500 0.00 0.00 35.80 4.00
3361 3379 9.752961 TGCATCTCAAATTATTTAATCCACATG 57.247 29.630 0.00 0.00 0.00 3.21
3413 3432 5.303589 CCATGAGCCCATATGAAAGAATTGT 59.696 40.000 3.65 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.701098 GTGCATTTATTCCATGATGAATATGTT 57.299 29.630 0.00 0.0 37.14 2.71
2 3 8.862085 TGTGCATTTATTCCATGATGAATATGT 58.138 29.630 0.00 0.0 37.14 2.29
3 4 9.869757 ATGTGCATTTATTCCATGATGAATATG 57.130 29.630 0.00 0.0 37.14 1.78
656 657 1.682344 TCTCGAGCTGGCTGCCTAA 60.682 57.895 21.03 0.0 44.23 2.69
708 709 2.093973 GGAGAGAGAGCGGTGAATTCAA 60.094 50.000 10.35 0.0 0.00 2.69
886 887 0.247301 CGGATCAAGAAAACGAGCGC 60.247 55.000 0.00 0.0 0.00 5.92
887 888 1.346365 TCGGATCAAGAAAACGAGCG 58.654 50.000 0.00 0.0 0.00 5.03
888 889 2.030946 CCATCGGATCAAGAAAACGAGC 59.969 50.000 0.00 0.0 36.97 5.03
944 945 1.331756 ACACAAAGACAGCAGCTTTCG 59.668 47.619 2.83 0.0 33.56 3.46
1077 1078 1.664321 CCACCTCCCCGTACTTCTCG 61.664 65.000 0.00 0.0 0.00 4.04
1267 1268 7.013823 AGCAATATAACAGCATGGATCTAGT 57.986 36.000 0.00 0.0 43.62 2.57
1736 1737 9.461312 AAGCTATTGGTTCTGTTCATAACATAA 57.539 29.630 0.00 0.0 41.26 1.90
1752 1753 7.885399 GGTATATCCATTGAGAAAGCTATTGGT 59.115 37.037 0.00 0.0 35.97 3.67
2044 2045 3.134458 GAGTTGAACACTGACCCAGAAG 58.866 50.000 0.00 0.0 35.01 2.85
2331 2332 2.092968 TGCTTGACTGGTTGAGTGAAGT 60.093 45.455 0.00 0.0 45.12 3.01
2543 2544 8.793592 ACAAGGGTAATACAATGAAGAAAAGAC 58.206 33.333 0.00 0.0 0.00 3.01
2563 2564 9.573133 CAAACTATATAAAGAAAAGCACAAGGG 57.427 33.333 0.00 0.0 0.00 3.95
2630 2631 5.382664 AGTTCCAACTTTGAGGGTCTTTA 57.617 39.130 0.00 0.0 35.21 1.85
2804 2821 3.423749 TCATGGACATGCAAATGTGACT 58.576 40.909 7.41 0.0 38.65 3.41
3255 3273 7.062749 AGGACAAGACAGTATTACAGTTCAA 57.937 36.000 0.00 0.0 0.00 2.69
3336 3354 9.199982 CCATGTGGATTAAATAATTTGAGATGC 57.800 33.333 0.00 0.0 37.39 3.91
3361 3379 4.713946 TGGATGACCAGCGTTTCC 57.286 55.556 0.00 0.0 41.77 3.13
3413 3432 9.602568 TTTCGTATAAGTAAATATGAGGTGCAA 57.397 29.630 0.00 0.0 30.89 4.08



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

AutoCloner maintained by Alex Coulton.