Multiple sequence alignment - TraesCS6D01G301600

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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 TraesCS6D01G301600 chr6D 100.000 3267 0 0 1 3267 411365372 411362106 0 6034
1 TraesCS6D01G301600 chr2D 97.032 3268 94 3 1 3267 536061444 536058179 0 5494
2 TraesCS6D01G301600 chr2D 96.787 3268 102 3 1 3267 534899897 534896632 0 5450
3 TraesCS6D01G301600 chr5D 97.032 3268 89 5 1 3267 539389230 539385970 0 5491
4 TraesCS6D01G301600 chr7D 96.879 3268 98 4 1 3267 518129537 518132801 0 5467
5 TraesCS6D01G301600 chr7D 96.511 3267 109 4 1 3267 610300223 610303484 0 5397
6 TraesCS6D01G301600 chr3D 96.847 3267 99 3 1 3267 335959059 335955797 0 5459
7 TraesCS6D01G301600 chr1D 96.670 3273 99 6 1 3267 366430891 366427623 0 5432
8 TraesCS6D01G301600 chr1D 96.638 3272 102 5 1 3267 466162874 466166142 0 5426
9 TraesCS6D01G301600 chr2A 95.044 3269 155 6 1 3267 307022426 307019163 0 5132


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 TraesCS6D01G301600 chr6D 411362106 411365372 3266 True 6034 6034 100.000 1 3267 1 chr6D.!!$R1 3266
1 TraesCS6D01G301600 chr2D 536058179 536061444 3265 True 5494 5494 97.032 1 3267 1 chr2D.!!$R2 3266
2 TraesCS6D01G301600 chr2D 534896632 534899897 3265 True 5450 5450 96.787 1 3267 1 chr2D.!!$R1 3266
3 TraesCS6D01G301600 chr5D 539385970 539389230 3260 True 5491 5491 97.032 1 3267 1 chr5D.!!$R1 3266
4 TraesCS6D01G301600 chr7D 518129537 518132801 3264 False 5467 5467 96.879 1 3267 1 chr7D.!!$F1 3266
5 TraesCS6D01G301600 chr7D 610300223 610303484 3261 False 5397 5397 96.511 1 3267 1 chr7D.!!$F2 3266
6 TraesCS6D01G301600 chr3D 335955797 335959059 3262 True 5459 5459 96.847 1 3267 1 chr3D.!!$R1 3266
7 TraesCS6D01G301600 chr1D 366427623 366430891 3268 True 5432 5432 96.670 1 3267 1 chr1D.!!$R1 3266
8 TraesCS6D01G301600 chr1D 466162874 466166142 3268 False 5426 5426 96.638 1 3267 1 chr1D.!!$F1 3266
9 TraesCS6D01G301600 chr2A 307019163 307022426 3263 True 5132 5132 95.044 1 3267 1 chr2A.!!$R1 3266

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
317 323 1.321474 ACCGTCTGTAACCTTCGACA 58.679 50.000 0.0 0.0 0.0 4.35 F
837 845 1.534476 TTCCGCCCTCACTACCACA 60.534 57.895 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 1894 1.290955 CCGGCGAAGGTGTAGAACA 59.709 57.895 9.3 0.0 0.0 3.18 R
2582 2596 0.324285 CTGCCACTCCTCAAGAAGCT 59.676 55.000 0.0 0.0 0.0 3.74 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
249 255 5.673337 TGTTTCGAGATTTTTCTGTGGAG 57.327 39.130 0.00 0.00 0.00 3.86
317 323 1.321474 ACCGTCTGTAACCTTCGACA 58.679 50.000 0.00 0.00 0.00 4.35
385 392 9.929180 TTTGTTCGCTATAGCATCTTAATAGAT 57.071 29.630 23.99 0.00 41.89 1.98
811 819 3.030308 CGCACAGCAACGACGAGT 61.030 61.111 0.00 0.00 0.00 4.18
837 845 1.534476 TTCCGCCCTCACTACCACA 60.534 57.895 0.00 0.00 0.00 4.17
873 881 3.319198 GCCTCCTCCACGACCCAA 61.319 66.667 0.00 0.00 0.00 4.12
896 904 3.522483 TGGCACAAAAGGGCAACTA 57.478 47.368 0.00 0.00 37.93 2.24
1068 1076 2.750637 AGCACCGAGGTCGACGAT 60.751 61.111 9.92 0.00 43.02 3.73
1490 1498 8.295288 CAGCAGAATAGATTTTGAACTTGACTT 58.705 33.333 0.00 0.00 0.00 3.01
1499 1507 8.160106 AGATTTTGAACTTGACTTACCAGATCT 58.840 33.333 0.00 0.00 0.00 2.75
1894 1907 3.515901 AGGAGGACATGTTCTACACCTTC 59.484 47.826 19.10 9.03 0.00 3.46
2366 2380 7.800380 CGTAGTTTACTTCTGTTAGAACGAAGA 59.200 37.037 22.24 6.29 39.55 2.87
2515 2529 9.738832 TTTGAAGTAGTAATGTTGCTTTTTACC 57.261 29.630 0.00 0.00 0.00 2.85
2833 2848 2.255252 GTTGTGCGACACCATGGC 59.745 61.111 13.04 0.00 32.73 4.40
2857 2872 3.064545 GCATGTAAGAGTCATGGCAAGTC 59.935 47.826 0.00 0.00 41.77 3.01
2980 2995 0.889994 GGCATGTGTTGGAATGCTCA 59.110 50.000 7.49 0.00 46.72 4.26
3031 3046 1.895020 GAGACATGGGCGTGGTACCA 61.895 60.000 11.60 11.60 41.76 3.25
3047 3062 3.056322 GGTACCACGACCATGTAAGAGTT 60.056 47.826 7.15 0.00 39.51 3.01
3051 3066 1.271379 ACGACCATGTAAGAGTTGCGA 59.729 47.619 0.00 0.00 0.00 5.10
3078 3093 4.590487 CGTTAGGCACGTGGATGT 57.410 55.556 18.88 0.00 44.49 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
249 255 3.951680 CACTACTCTCTTCCTTCCTCTCC 59.048 52.174 0.00 0.00 0.00 3.71
340 346 4.251246 AAAAAGCCAGGCGACACA 57.749 50.000 5.55 0.00 0.00 3.72
358 365 9.758651 TCTATTAAGATGCTATAGCGAACAAAA 57.241 29.630 19.55 9.84 45.83 2.44
652 659 0.890542 ACACGACCAATGCTGCACAT 60.891 50.000 3.57 0.00 42.30 3.21
691 698 2.084546 GTTATTGCTCGCACCTTTCCT 58.915 47.619 0.00 0.00 0.00 3.36
811 819 2.268920 GAGGGCGGAAGACATGCA 59.731 61.111 0.00 0.00 45.40 3.96
873 881 0.980231 TGCCCTTTTGTGCCAAGGTT 60.980 50.000 0.00 0.00 39.50 3.50
1200 1208 1.302832 CAAGCCGCAGACCCTCTTT 60.303 57.895 0.00 0.00 0.00 2.52
1490 1498 9.056005 GCATCAAATACATAAACAGATCTGGTA 57.944 33.333 26.08 17.28 34.19 3.25
1707 1715 8.795786 TCAGAAATAAAATACAAGCACAACAC 57.204 30.769 0.00 0.00 0.00 3.32
1759 1767 8.961294 ATAGTACGTATAATTCATGGACGAAC 57.039 34.615 0.00 0.00 37.00 3.95
1881 1894 1.290955 CCGGCGAAGGTGTAGAACA 59.709 57.895 9.30 0.00 0.00 3.18
1894 1907 2.762360 TTCAATACTGAAGCCGGCG 58.238 52.632 23.20 9.47 36.62 6.46
2366 2380 8.543774 ACCTGATACAGATGACATTAGAAACTT 58.456 33.333 0.00 0.00 32.44 2.66
2515 2529 8.878769 ACTGCTTTGTATTTTGTTGTTTTTAGG 58.121 29.630 0.00 0.00 0.00 2.69
2582 2596 0.324285 CTGCCACTCCTCAAGAAGCT 59.676 55.000 0.00 0.00 0.00 3.74
2833 2848 0.940126 GCCATGACTCTTACATGCCG 59.060 55.000 0.00 0.00 42.31 5.69
2857 2872 1.134759 CAGGTGCCTCTCTCACATGAG 60.135 57.143 0.00 2.24 45.71 2.90
2890 2905 1.448893 GTCGCAATCCCGTGCCTTA 60.449 57.895 0.00 0.00 41.73 2.69
2980 2995 4.310769 GTCACAACAGTGCATCTCTAACT 58.689 43.478 0.00 0.00 33.28 2.24
3031 3046 1.271379 TCGCAACTCTTACATGGTCGT 59.729 47.619 0.00 0.00 0.00 4.34
3078 3093 0.813184 CTCCGTGCCTTCCGTAACTA 59.187 55.000 0.00 0.00 0.00 2.24
3126 3141 3.520569 AGCTGTTCGCAACAACAAAAAT 58.479 36.364 0.00 0.00 41.61 1.82
3157 3172 6.009589 TGGTATCACACTTTTGAACATCCAT 58.990 36.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.