Multiple sequence alignment - TraesCS1D01G193300

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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 TraesCS1D01G193300 chr1D 100.000 2718 0 0 1 2718 269410272 269407555 0 5020
1 TraesCS1D01G193300 chr5A 98.860 2720 29 2 1 2718 19245369 19248088 0 4850
2 TraesCS1D01G193300 chr7D 98.676 2719 34 2 1 2718 382053551 382050834 0 4820
3 TraesCS1D01G193300 chr7D 98.527 2716 38 2 4 2718 381927470 381924756 0 4793
4 TraesCS1D01G193300 chr7D 98.455 2719 40 2 1 2718 203503471 203500754 0 4787
5 TraesCS1D01G193300 chr7D 98.348 2724 36 3 1 2718 381970292 381973012 0 4772
6 TraesCS1D01G193300 chr6D 98.419 2720 41 2 1 2718 124520996 124518277 0 4783
7 TraesCS1D01G193300 chr7B 98.419 2720 36 3 1 2718 716875312 716878026 0 4778
8 TraesCS1D01G193300 chr7A 98.235 2719 42 2 1 2718 60282781 60280068 0 4750
9 TraesCS1D01G193300 chr1A 98.235 2719 42 2 1 2718 498687759 498690472 0 4750


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 TraesCS1D01G193300 chr1D 269407555 269410272 2717 True 5020 5020 100.000 1 2718 1 chr1D.!!$R1 2717
1 TraesCS1D01G193300 chr5A 19245369 19248088 2719 False 4850 4850 98.860 1 2718 1 chr5A.!!$F1 2717
2 TraesCS1D01G193300 chr7D 382050834 382053551 2717 True 4820 4820 98.676 1 2718 1 chr7D.!!$R3 2717
3 TraesCS1D01G193300 chr7D 381924756 381927470 2714 True 4793 4793 98.527 4 2718 1 chr7D.!!$R2 2714
4 TraesCS1D01G193300 chr7D 203500754 203503471 2717 True 4787 4787 98.455 1 2718 1 chr7D.!!$R1 2717
5 TraesCS1D01G193300 chr7D 381970292 381973012 2720 False 4772 4772 98.348 1 2718 1 chr7D.!!$F1 2717
6 TraesCS1D01G193300 chr6D 124518277 124520996 2719 True 4783 4783 98.419 1 2718 1 chr6D.!!$R1 2717
7 TraesCS1D01G193300 chr7B 716875312 716878026 2714 False 4778 4778 98.419 1 2718 1 chr7B.!!$F1 2717
8 TraesCS1D01G193300 chr7A 60280068 60282781 2713 True 4750 4750 98.235 1 2718 1 chr7A.!!$R1 2717
9 TraesCS1D01G193300 chr1A 498687759 498690472 2713 False 4750 4750 98.235 1 2718 1 chr1A.!!$F1 2717

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
262 265 3.488489 CCTTTGTAAGCGAAAATGTCCG 58.512 45.455 0.0 0.0 0.0 4.79 F
1191 1196 1.035385 CATCCATTGCAGCAGAGCCA 61.035 55.000 0.0 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 1657 0.107081 TCCACGTCGGTTGTTGGAAT 59.893 50.0 0.00 0.0 35.57 3.01 R
2548 2558 0.608640 TCTCTCGAGCCCCAAGAAAC 59.391 55.0 7.81 0.0 0.00 2.78 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
117 118 6.897986 TCCTTTAATCGGAGACTAGACTAGT 58.102 40.000 15.13 15.13 42.51 2.57
126 127 6.056884 CGGAGACTAGACTAGTGTTAGGAAT 58.943 44.000 19.90 0.00 39.59 3.01
262 265 3.488489 CCTTTGTAAGCGAAAATGTCCG 58.512 45.455 0.00 0.00 0.00 4.79
331 334 7.212274 CCTTTCTTTGAACCTTGTCAATGATT 58.788 34.615 4.86 0.00 39.81 2.57
740 744 6.459066 AGATGATTCTTTCTTTGTCGAGACA 58.541 36.000 1.24 1.24 39.98 3.41
785 790 7.431960 TCGATTGAAAAATGTGAGTCTGTTTTG 59.568 33.333 0.00 0.00 0.00 2.44
862 867 7.148306 GCTTCTTATTCCCGTGTTTGATCTTAA 60.148 37.037 0.00 0.00 0.00 1.85
914 919 4.689062 AGACCCCTGTAGAGAATGAAGAA 58.311 43.478 0.00 0.00 0.00 2.52
1191 1196 1.035385 CATCCATTGCAGCAGAGCCA 61.035 55.000 0.00 0.00 0.00 4.75
1201 1206 2.640184 CAGCAGAGCCATTTCATGAGA 58.360 47.619 0.00 0.00 0.00 3.27
1663 1673 1.223187 GTCATTCCAACAACCGACGT 58.777 50.000 0.00 0.00 0.00 4.34
1696 1706 0.997226 ATACGATCGCGCGCAGTAAG 60.997 55.000 32.61 19.33 42.48 2.34
1874 1884 2.488937 TGATTCGGTAAGCTACGTGTCA 59.511 45.455 0.00 7.81 0.00 3.58
2053 2063 0.834612 CTAACGGGGGTATTCCTGCA 59.165 55.000 0.00 0.00 36.66 4.41
2460 2470 3.281727 AGGCGCAATAGAAAGGAATGA 57.718 42.857 10.83 0.00 0.00 2.57
2498 2508 5.308237 GGTGAACCCTCATAGATATCAGGTT 59.692 44.000 5.32 7.58 38.78 3.50
2533 2543 5.253330 AGAGTCAAAAGAGAGATCGAGTCT 58.747 41.667 0.00 0.00 40.81 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 0.668535 GAAACTTCGCTTTGCCACCT 59.331 50.000 0.00 0.00 0.00 4.00
117 118 5.306937 TCTGTCTCCTTTGTCATTCCTAACA 59.693 40.000 0.00 0.00 0.00 2.41
126 127 4.963318 ATTCTGTCTGTCTCCTTTGTCA 57.037 40.909 0.00 0.00 0.00 3.58
331 334 7.599171 TCAGTTCATATCTGTAAGTTCGTTCA 58.401 34.615 0.00 0.00 34.86 3.18
539 542 2.064242 CTTGGTTTCGGGGTGGACCT 62.064 60.000 0.00 0.00 40.03 3.85
657 661 1.488705 AAGTGATCCGAACCTGCCCA 61.489 55.000 0.00 0.00 0.00 5.36
785 790 0.853530 AGGGGGATGGATAAAGTGGC 59.146 55.000 0.00 0.00 0.00 5.01
862 867 3.011517 AAGCGGGGCAGAGATGGT 61.012 61.111 0.00 0.00 0.00 3.55
914 919 3.987745 TGAGAGTAAGATCCTTGGCTCT 58.012 45.455 12.14 12.14 36.20 4.09
1317 1327 1.870064 AATCAAGGATTTGGGGCTGG 58.130 50.000 0.00 0.00 34.97 4.85
1463 1473 7.147585 CCTCCAATGAAGAAATAAGAGGAGAGA 60.148 40.741 0.00 0.00 41.82 3.10
1647 1657 0.107081 TCCACGTCGGTTGTTGGAAT 59.893 50.000 0.00 0.00 35.57 3.01
1663 1673 2.430248 TCGTATACTGAGGTGCTCCA 57.570 50.000 7.70 0.00 35.89 3.86
1696 1706 4.344390 CCTTAGGTGTAATAGGACTCCCAC 59.656 50.000 0.00 0.00 34.17 4.61
1874 1884 2.193536 GGCAGTTTTCCGTGCACCT 61.194 57.895 12.15 0.00 41.75 4.00
2053 2063 8.497745 ACCTTCTCCATTACAATGTTCTCATAT 58.502 33.333 0.00 0.00 34.60 1.78
2498 2508 9.083422 CTCTCTTTTGACTCTATATATGTGGGA 57.917 37.037 0.00 0.00 0.00 4.37
2527 2537 1.454847 CCCCTCTCCCTCAGACTCG 60.455 68.421 0.00 0.00 0.00 4.18
2548 2558 0.608640 TCTCTCGAGCCCCAAGAAAC 59.391 55.000 7.81 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.