Multiple sequence alignment - TraesCS6D01G370500

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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 TraesCS6D01G370500 chr6D 100.000 3224 0 0 1 3224 456494411 456497634 0 5954
1 TraesCS6D01G370500 chr6A 92.886 3261 168 37 1 3224 603202145 603205378 0 4678
2 TraesCS6D01G370500 chr6B 92.613 3276 156 39 1 3224 694162397 694165638 0 4630


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 TraesCS6D01G370500 chr6D 456494411 456497634 3223 False 5954 5954 100.000 1 3224 1 chr6D.!!$F1 3223
1 TraesCS6D01G370500 chr6A 603202145 603205378 3233 False 4678 4678 92.886 1 3224 1 chr6A.!!$F1 3223
2 TraesCS6D01G370500 chr6B 694162397 694165638 3241 False 4630 4630 92.613 1 3224 1 chr6B.!!$F1 3223

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
900 928 0.311790 GGGCTGAATGTGTGTGTGTG 59.688 55.0 0.0 0.0 0.0 3.82 F
901 929 1.308047 GGCTGAATGTGTGTGTGTGA 58.692 50.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1989 2039 1.365633 GGGCAGCTGGTAGATCTCG 59.634 63.158 17.12 0.0 0.0 4.04 R
2589 2651 1.748493 AGTTGCAAGCCTTTCGAAACA 59.252 42.857 6.47 0.0 0.0 2.83 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 2.485795 GCGCAAGGTTGGGACAACA 61.486 57.895 0.30 0.00 43.04 3.33
98 99 2.124695 GTTGATGGAGCCGGGGAC 60.125 66.667 2.18 0.00 0.00 4.46
120 121 6.105397 ACTTAACCACCTCGACATTTTCTA 57.895 37.500 0.00 0.00 0.00 2.10
150 151 0.684153 CTCCCGGTTGCCAAATCCAT 60.684 55.000 0.00 0.00 0.00 3.41
220 221 2.700783 ATGTGGCACCTCCAGATGA 58.299 52.632 16.26 0.00 46.10 2.92
236 237 1.061131 GATGACGCCACTTTCGACATG 59.939 52.381 5.27 0.00 40.93 3.21
284 288 3.318017 GACTTGCGCTCTGTTTCTAAGA 58.682 45.455 9.73 0.00 0.00 2.10
289 293 3.181475 TGCGCTCTGTTTCTAAGATAGGG 60.181 47.826 9.73 0.00 0.00 3.53
300 304 3.711190 TCTAAGATAGGGCATGTGCAAGA 59.289 43.478 7.36 0.00 44.36 3.02
486 490 3.301794 TCGCAGGGGTACAAGTATAGA 57.698 47.619 0.00 0.00 0.00 1.98
488 492 3.382546 TCGCAGGGGTACAAGTATAGAAC 59.617 47.826 0.00 0.00 0.00 3.01
500 504 6.775088 ACAAGTATAGAACATGTTGAATGCG 58.225 36.000 17.58 4.03 36.66 4.73
501 505 6.371548 ACAAGTATAGAACATGTTGAATGCGT 59.628 34.615 17.58 7.96 36.66 5.24
651 660 4.143263 GCAAAGACGAAAAATGCCATGAAG 60.143 41.667 0.00 0.00 0.00 3.02
790 806 8.192068 TCGTGACCAGTTAATATATGTTGTTG 57.808 34.615 0.00 0.00 0.00 3.33
900 928 0.311790 GGGCTGAATGTGTGTGTGTG 59.688 55.000 0.00 0.00 0.00 3.82
901 929 1.308047 GGCTGAATGTGTGTGTGTGA 58.692 50.000 0.00 0.00 0.00 3.58
952 980 3.797353 CCATCGTCCCACCCCCAG 61.797 72.222 0.00 0.00 0.00 4.45
2009 2059 2.280457 GATCTACCAGCTGCCCGC 60.280 66.667 8.66 0.00 39.57 6.13
2165 2215 2.183555 GGCATTGCCTTCTGCTGC 59.816 61.111 20.66 0.00 46.69 5.25
2190 2240 0.177373 CTGCTGCTGCTGATGGTAGA 59.823 55.000 17.00 0.00 40.01 2.59
2315 2365 4.886579 AGGATGAAACAAAATGGCAGAAC 58.113 39.130 0.00 0.00 0.00 3.01
2402 2452 5.607119 AAGACCGATACATTGACAACAAC 57.393 39.130 0.00 0.00 38.90 3.32
2527 2589 2.577449 TGATAATCGCAGCTTGTCGA 57.423 45.000 5.16 5.16 39.17 4.20
2721 2786 4.851639 ATCAAAAGACTGCTGGGTAGAT 57.148 40.909 0.00 0.00 0.00 1.98
2903 2968 4.459390 TCAACATCCCAGCATCAAAATG 57.541 40.909 0.00 0.00 35.87 2.32
2906 2971 5.011840 TCAACATCCCAGCATCAAAATGAAA 59.988 36.000 0.00 0.00 34.61 2.69
2956 3021 6.270815 TCTAATCATACAGAAACCAGCGTAC 58.729 40.000 0.00 0.00 0.00 3.67
3087 3154 6.419484 AATCATCATAGTCCATCGGTGTAA 57.581 37.500 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.478471 CCACCATCAACTGTTGTCCCA 60.478 52.381 19.12 1.39 0.00 4.37
70 71 2.538437 CTCCATCAACTCAAGAGCTCG 58.462 52.381 8.37 0.00 0.00 5.03
98 99 7.438459 CCTATAGAAAATGTCGAGGTGGTTAAG 59.562 40.741 0.00 0.00 0.00 1.85
120 121 2.283966 CCGGGAGATCGGGCCTAT 60.284 66.667 0.84 0.00 45.78 2.57
141 142 0.757935 CCCCAGGCTCATGGATTTGG 60.758 60.000 1.65 0.00 43.57 3.28
220 221 0.949105 GTCCATGTCGAAAGTGGCGT 60.949 55.000 7.02 0.00 33.01 5.68
236 237 7.704472 CACACTATACTCTGAAAGATCAAGTCC 59.296 40.741 0.00 0.00 45.62 3.85
284 288 0.464373 CCGTCTTGCACATGCCCTAT 60.464 55.000 0.49 0.00 41.18 2.57
289 293 5.005779 GCTATATATACCGTCTTGCACATGC 59.994 44.000 0.00 0.00 42.50 4.06
300 304 4.529897 TGGTCGATGGCTATATATACCGT 58.470 43.478 0.00 6.03 0.00 4.83
486 490 9.585099 AATATTAAATGACGCATTCAACATGTT 57.415 25.926 4.92 4.92 37.92 2.71
816 832 7.121315 CCCAAGAACTAGGGTTTCTAATTTCTG 59.879 40.741 0.00 0.00 40.34 3.02
900 928 0.804989 CCATCTCACGTTGGGCTTTC 59.195 55.000 0.00 0.00 0.00 2.62
901 929 0.110486 ACCATCTCACGTTGGGCTTT 59.890 50.000 8.78 0.00 37.32 3.51
1989 2039 1.365633 GGGCAGCTGGTAGATCTCG 59.634 63.158 17.12 0.00 0.00 4.04
2212 2262 5.045578 ACACTCTGTAATCCTAGCCAACAAT 60.046 40.000 0.00 0.00 0.00 2.71
2315 2365 6.205464 ACATGAAACTCTTGGTCACAGTAATG 59.795 38.462 0.00 0.00 0.00 1.90
2402 2452 6.166982 AGAAGGTTCTTGAATCTTCCTTACG 58.833 40.000 24.44 0.00 37.05 3.18
2589 2651 1.748493 AGTTGCAAGCCTTTCGAAACA 59.252 42.857 6.47 0.00 0.00 2.83
2617 2679 7.719193 CCTTGGTTCCAAAACTTCCATTTTATT 59.281 33.333 5.76 0.00 35.61 1.40
2634 2697 3.077359 CACAGTGAGAATCCTTGGTTCC 58.923 50.000 0.00 0.00 0.00 3.62
2701 2766 3.327757 ACATCTACCCAGCAGTCTTTTGA 59.672 43.478 0.00 0.00 0.00 2.69
2956 3021 7.275183 TCCAGAGTAAGGTACATCATTTCATG 58.725 38.462 0.00 0.00 0.00 3.07
3057 3124 5.120363 CGATGGACTATGATGATTTGCTCAG 59.880 44.000 0.00 0.00 37.28 3.35
3107 3174 3.844577 CAAGAATGCAGGGTGAGAAAG 57.155 47.619 0.00 0.00 0.00 2.62


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

AutoCloner maintained by Alex Coulton.