Multiple sequence alignment - TraesCS2D01G376800

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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 TraesCS2D01G376800 chr2D 100.000 5109 0 0 1 5109 481055605 481050497 0 9435
1 TraesCS2D01G376800 chr2A 97.656 5120 98 11 1 5109 623945413 623940305 0 8770
2 TraesCS2D01G376800 chr2B 96.937 5126 123 16 1 5109 564236623 564231515 0 8565


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 TraesCS2D01G376800 chr2D 481050497 481055605 5108 True 9435 9435 100.000 1 5109 1 chr2D.!!$R1 5108
1 TraesCS2D01G376800 chr2A 623940305 623945413 5108 True 8770 8770 97.656 1 5109 1 chr2A.!!$R1 5108
2 TraesCS2D01G376800 chr2B 564231515 564236623 5108 True 8565 8565 96.937 1 5109 1 chr2B.!!$R1 5108

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
612 617 0.250727 TTGTGACTTGGGCCAGCTAC 60.251 55.000 6.23 5.85 0.00 3.58 F
752 758 1.507140 ACTTGGACCCACTGTTCTCA 58.493 50.000 0.00 0.00 0.00 3.27 F
2402 2418 0.681733 TCTCCTCAACGCAGCTTCTT 59.318 50.000 0.00 0.00 0.00 2.52 F
2861 2881 1.075536 ACCCAGTGATTTGAAGGGGAC 59.924 52.381 0.00 0.00 43.96 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2402 2418 1.210722 TGGTATGGCGCAGATTGGTAA 59.789 47.619 10.83 0.00 0.00 2.85 R
2870 2890 9.046296 AGCAGTAGTTACATGCATAAAATCTAC 57.954 33.333 0.00 9.09 42.45 2.59 R
3249 3269 2.231478 CTGGTATGTGACTGGAGACGTT 59.769 50.000 0.00 0.00 0.00 3.99 R
4710 4734 2.159240 GGCTTTGCCCTGCAGTAAATAC 60.159 50.000 13.81 6.49 44.06 1.89 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
287 288 4.725790 AGTTAGGTTGGGTATGACGTAC 57.274 45.455 0.00 0.00 0.00 3.67
612 617 0.250727 TTGTGACTTGGGCCAGCTAC 60.251 55.000 6.23 5.85 0.00 3.58
752 758 1.507140 ACTTGGACCCACTGTTCTCA 58.493 50.000 0.00 0.00 0.00 3.27
1147 1153 4.612264 AGCCTTCATGTTTGCAAGATTT 57.388 36.364 0.00 0.00 0.00 2.17
1240 1247 5.118050 TCTGTTGTTTTCGAATGTAGCTACG 59.882 40.000 18.74 7.25 0.00 3.51
1790 1799 9.083080 ACTTTAAATGTGTTCTTTTACAAGCAC 57.917 29.630 0.00 0.00 0.00 4.40
1834 1843 9.241317 GATGAAAAGCTAATCACACATAAATGG 57.759 33.333 3.68 0.00 0.00 3.16
2117 2126 9.750125 AAACTGCAGGTTAAAAGAAAAGAATAG 57.250 29.630 17.30 0.00 37.12 1.73
2402 2418 0.681733 TCTCCTCAACGCAGCTTCTT 59.318 50.000 0.00 0.00 0.00 2.52
2719 2735 4.580167 CCAAAGTTCTGAAACCTGACATCA 59.420 41.667 0.00 0.00 35.92 3.07
2720 2736 5.067674 CCAAAGTTCTGAAACCTGACATCAA 59.932 40.000 0.00 0.00 35.92 2.57
2721 2737 6.239120 CCAAAGTTCTGAAACCTGACATCAAT 60.239 38.462 0.00 0.00 35.92 2.57
2722 2738 7.040478 CCAAAGTTCTGAAACCTGACATCAATA 60.040 37.037 0.00 0.00 35.92 1.90
2861 2881 1.075536 ACCCAGTGATTTGAAGGGGAC 59.924 52.381 0.00 0.00 43.96 4.46
2870 2890 6.211384 AGTGATTTGAAGGGGACAAAATAAGG 59.789 38.462 0.00 0.00 39.95 2.69
2907 2927 8.704234 GCATGTAACTACTGCTAGATTTCATAC 58.296 37.037 0.00 0.00 33.15 2.39
3126 3146 4.323417 ACGCTCTCAGAGATATACCTCAG 58.677 47.826 5.62 0.00 35.68 3.35
3249 3269 6.770303 TCAGTACATTTCTTGTGATTGGAACA 59.230 34.615 0.00 0.00 39.48 3.18
3294 3314 2.795329 CTTGGCCACCTTAAGACATGT 58.205 47.619 3.88 0.00 0.00 3.21
3978 3998 5.698832 TGAAATACAGTTCAATTTGCTCCG 58.301 37.500 0.00 0.00 34.59 4.63
4096 4116 3.689161 TCAAGAAGGCAAATGGTGTATCG 59.311 43.478 0.00 0.00 0.00 2.92
4250 4274 8.301720 TCGTAGAGTGTATATTTTGACACAACT 58.698 33.333 8.75 9.17 46.83 3.16
4336 4360 1.285280 CTTCCTGTGACATACCCCCA 58.715 55.000 0.00 0.00 0.00 4.96
4450 4474 5.475909 AGGGACGAGATGTAAAGCGATATAA 59.524 40.000 0.00 0.00 0.00 0.98
4585 4609 7.506114 ACCTGTCAGAAATGTTTGTTAGACTA 58.494 34.615 0.00 0.00 0.00 2.59
4815 4839 8.454894 CAAAAGAAAGGAAGAATCTAACTAGGC 58.545 37.037 0.00 0.00 0.00 3.93
4978 5004 3.067461 CCTGATAGACTGCTGGTGACTAC 59.933 52.174 0.00 0.00 0.00 2.73
5010 5036 7.443302 TCTGAGGAAAATAATGAGGTGAGAT 57.557 36.000 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 7.123997 TGAATAAAATGGTCACAATACATGCCT 59.876 33.333 0.00 0.00 0.00 4.75
43 44 5.428253 TCCTAAGCAACATGTTAGATGGAC 58.572 41.667 11.53 0.00 0.00 4.02
45 46 5.882557 ACTTCCTAAGCAACATGTTAGATGG 59.117 40.000 11.53 10.09 0.00 3.51
371 372 8.518151 CTATGACTAGCAAGTGAGACATTATG 57.482 38.462 0.00 0.00 35.56 1.90
450 451 0.037697 TAGCACCTACTTGCACACCG 60.038 55.000 0.00 0.00 45.62 4.94
593 598 0.250727 GTAGCTGGCCCAAGTCACAA 60.251 55.000 0.00 0.00 0.00 3.33
612 617 4.989279 AGAATGGAATGGGTCAAATTCG 57.011 40.909 0.00 0.00 36.58 3.34
1147 1153 8.030106 CCTTTGGTTTGTTGTTAAGTTCTGTTA 58.970 33.333 0.00 0.00 0.00 2.41
1212 1219 5.846473 GCTACATTCGAAAACAACAGAGTTC 59.154 40.000 0.00 0.00 0.00 3.01
1240 1247 3.691118 TGAGATGCCAGCTTGTTAATGTC 59.309 43.478 0.00 0.00 0.00 3.06
1807 1816 9.791820 CATTTATGTGTGATTAGCTTTTCATCA 57.208 29.630 0.00 0.66 0.00 3.07
1834 1843 7.865889 CCAGGAAAACTAAACAAGTAAATGACC 59.134 37.037 0.00 0.00 37.50 4.02
2077 2086 4.431809 CTGCAGTTTTTGGAATGTCAACA 58.568 39.130 5.25 0.00 0.00 3.33
2251 2267 6.506500 AGTTCATGCAACCTAATTCAGAAG 57.493 37.500 0.00 0.00 35.28 2.85
2402 2418 1.210722 TGGTATGGCGCAGATTGGTAA 59.789 47.619 10.83 0.00 0.00 2.85
2870 2890 9.046296 AGCAGTAGTTACATGCATAAAATCTAC 57.954 33.333 0.00 9.09 42.45 2.59
2956 2976 6.696441 ACTTCTTTAGGACTGTAGGTATCG 57.304 41.667 0.00 0.00 0.00 2.92
3126 3146 5.422666 TGCATGTATTGTCCATCGAAATC 57.577 39.130 0.00 0.00 0.00 2.17
3249 3269 2.231478 CTGGTATGTGACTGGAGACGTT 59.769 50.000 0.00 0.00 0.00 3.99
3294 3314 5.057149 GTGTAGCCAAAAGAGAGAACAAGA 58.943 41.667 0.00 0.00 0.00 3.02
3297 3317 4.345257 AGAGTGTAGCCAAAAGAGAGAACA 59.655 41.667 0.00 0.00 0.00 3.18
3530 3550 5.968254 TGTTAGTATAACTGCCATTCGTCA 58.032 37.500 1.76 0.00 0.00 4.35
3900 3920 8.893219 TCATCATACAAACTATGCTTAAGAGG 57.107 34.615 6.67 0.00 0.00 3.69
4336 4360 8.034804 GCATATAAGAACTGGGTTTTGACAAAT 58.965 33.333 0.50 0.00 0.00 2.32
4450 4474 2.969821 TGCAGTTAAACAGATGGGGT 57.030 45.000 0.00 0.00 0.00 4.95
4487 4511 9.846248 GCGATTGGATTAATCATTTTATAGCTT 57.154 29.630 17.07 0.00 44.42 3.74
4585 4609 4.827692 TGCTAATTCACAGGACGTGTAAT 58.172 39.130 0.00 0.00 46.44 1.89
4600 4624 4.735578 GCTGTGCTACAATGCATGCTAATT 60.736 41.667 20.33 8.40 45.23 1.40
4710 4734 2.159240 GGCTTTGCCCTGCAGTAAATAC 60.159 50.000 13.81 6.49 44.06 1.89
4815 4839 9.078990 TGATCATGTATTCAGTAGGTAAGTAGG 57.921 37.037 0.00 0.00 0.00 3.18
4882 4906 9.185680 GTGTTTACATCATAGGGTTAAGGATTT 57.814 33.333 0.00 0.00 0.00 2.17
4978 5004 7.363268 CCTCATTATTTTCCTCAGAAGGTTTGG 60.363 40.741 0.00 0.00 43.82 3.28
5010 5036 8.141268 GGTGGACTGTTCAAAAATTCAATAGAA 58.859 33.333 0.00 0.00 38.31 2.10
5062 5088 5.935945 TGAATTCACAAGGGAGTAACAGAA 58.064 37.500 3.38 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.