Multiple sequence alignment - TraesCS3D01G069800

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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 TraesCS3D01G069800 chr3D 100.000 2844 0 0 1 2844 30928935 30926092 0.000000e+00 5252
1 TraesCS3D01G069800 chr3B 97.686 2723 48 10 1 2711 53472535 53469816 0.000000e+00 4665
2 TraesCS3D01G069800 chr3B 96.324 136 5 0 2709 2844 53469781 53469646 1.030000e-54 224


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 TraesCS3D01G069800 chr3D 30926092 30928935 2843 True 5252.0 5252 100.000 1 2844 1 chr3D.!!$R1 2843
1 TraesCS3D01G069800 chr3B 53469646 53472535 2889 True 2444.5 4665 97.005 1 2844 2 chr3B.!!$R1 2843

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
249 250 0.102663 GTAGTGCTAAGCTCCGTCCC 59.897 60.0 0.0 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1852 1865 0.679505 CCTCCTTGACGAGAACCACA 59.32 55.0 0.0 0.0 30.97 4.17 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
238 239 6.351881 CCATTCCTCTGTTTTAGGTAGTGCTA 60.352 42.308 0.00 0.00 35.48 3.49
246 247 2.431954 TAGGTAGTGCTAAGCTCCGT 57.568 50.000 0.00 0.00 0.00 4.69
249 250 0.102663 GTAGTGCTAAGCTCCGTCCC 59.897 60.000 0.00 0.00 0.00 4.46
273 274 1.326213 ACATCTCTCCAGTCCAGCCG 61.326 60.000 0.00 0.00 0.00 5.52
331 332 3.255379 GTGCGCCTCCGACGATTC 61.255 66.667 4.18 0.00 36.29 2.52
335 336 1.586564 CGCCTCCGACGATTCTGTC 60.587 63.158 0.00 0.44 36.29 3.51
371 372 1.268896 CCGTGTACGCCTAATCGATGT 60.269 52.381 0.00 0.00 38.18 3.06
487 490 1.679977 ATGGCATGGCACCACTGAC 60.680 57.895 25.84 0.00 40.82 3.51
701 704 1.606668 CGTTGTAGTGCAAACCATGGT 59.393 47.619 13.00 13.00 39.03 3.55
747 750 1.522355 CTAGCTCCACACGCATGGG 60.522 63.158 8.44 8.44 40.49 4.00
795 799 2.357517 CGGTCTTGCCAAGTCGCT 60.358 61.111 4.04 0.00 36.97 4.93
889 893 1.187087 AGGTAGCTGGAGTAGTGCAC 58.813 55.000 9.40 9.40 0.00 4.57
1088 1092 0.453950 CGTCTGCATTCTGTTGCTGC 60.454 55.000 0.00 0.00 43.18 5.25
1099 1103 5.910637 TTCTGTTGCTGCAAATGATTTTC 57.089 34.783 17.80 2.50 0.00 2.29
1103 1107 2.060284 TGCTGCAAATGATTTTCGTGC 58.940 42.857 0.00 0.00 35.75 5.34
1333 1337 3.926616 AGGTTCTTTGACTCACCGTATG 58.073 45.455 0.00 0.00 34.19 2.39
1359 1363 1.398390 GGATGGAATGTTGTCGCACTC 59.602 52.381 0.00 0.00 0.00 3.51
1484 1488 5.811399 TTGTCCCTATTTTATCAGCGTTG 57.189 39.130 0.00 0.00 0.00 4.10
1566 1570 3.600388 AGTTGTTCATCTAAGGAAGCGG 58.400 45.455 0.00 0.00 0.00 5.52
1851 1864 2.590007 GCAGGCATAGCACGAGGG 60.590 66.667 0.00 0.00 0.00 4.30
1852 1865 2.903357 CAGGCATAGCACGAGGGT 59.097 61.111 0.00 0.00 0.00 4.34
1896 1909 7.545615 GGTAAATTTAGTGCCCTTTCTGAAATG 59.454 37.037 2.88 0.83 0.00 2.32
2024 2037 5.607939 TTACCCCATGACACATGTAGTAG 57.392 43.478 0.00 0.00 0.00 2.57
2111 2124 3.134574 ACAATTACTTTGGACAGGCGA 57.865 42.857 0.00 0.00 39.80 5.54
2194 2207 3.073062 TCACTTTTTCCCCTCTCCTTCAG 59.927 47.826 0.00 0.00 0.00 3.02
2284 2297 8.383175 TGAGAAGTTGTAGGAAATGGTCTTAAT 58.617 33.333 0.00 0.00 0.00 1.40
2329 2342 7.616313 ACATAGTCCTAGGCTTCATAATTAGC 58.384 38.462 2.96 0.00 36.66 3.09
2503 2516 6.670695 ATTTTCTCTGTTTGTTTAGGGCAT 57.329 33.333 0.00 0.00 0.00 4.40
2599 2612 5.315195 GGCATAATTTGTTTCATTGTTGCG 58.685 37.500 0.00 0.00 30.53 4.85
2629 2642 4.935352 TTGCTTTTGGTCATAGTTGCTT 57.065 36.364 0.00 0.00 0.00 3.91
2641 2654 7.093509 TGGTCATAGTTGCTTGAGTATCTACAA 60.094 37.037 0.00 0.00 34.92 2.41
2677 2690 2.110420 GGCACCTATACGCCCCAC 59.890 66.667 0.00 0.00 42.82 4.61
2723 2773 3.609853 GCACTGACCTCAAATCCATACA 58.390 45.455 0.00 0.00 0.00 2.29
2763 2813 5.936686 ACATATGTACTGCGTACGTATCT 57.063 39.130 17.90 12.82 44.44 1.98
2827 2877 0.811616 CCGAGTAGATGGGCAACTGC 60.812 60.000 0.00 0.00 41.14 4.40
2836 2886 3.056328 GGCAACTGCGGGAACTCC 61.056 66.667 0.00 0.00 43.26 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 0.919710 GTTATGACAAGAGGCCCCCT 59.080 55.000 0.00 0.00 36.03 4.79
100 101 0.543883 AGCAGGTGGAGAGAAGCTGA 60.544 55.000 6.80 0.00 44.14 4.26
146 147 3.267860 CGGCCAGATTCGCTCAGC 61.268 66.667 2.24 0.00 0.00 4.26
148 149 4.838152 GCCGGCCAGATTCGCTCA 62.838 66.667 18.11 0.00 0.00 4.26
249 250 1.341156 GGACTGGAGAGATGTGGGGG 61.341 65.000 0.00 0.00 0.00 5.40
331 332 0.905357 CCAGGGACTTACCAGGACAG 59.095 60.000 0.00 0.00 41.20 3.51
335 336 2.998949 GGCCAGGGACTTACCAGG 59.001 66.667 0.00 0.00 41.20 4.45
371 372 3.763057 TCCTGACTACTGACTAAGCACA 58.237 45.455 0.00 0.00 0.00 4.57
487 490 2.125912 CTCACCGGGCGTTCTCTG 60.126 66.667 6.32 0.00 0.00 3.35
701 704 1.377987 GGAGCGGTGCCATGGTAAA 60.378 57.895 14.67 0.00 0.00 2.01
747 750 1.065102 CTGCTGTGCATATTGCTGGAC 59.935 52.381 0.00 0.00 45.31 4.02
1088 1092 4.587211 CCATTGGCACGAAAATCATTTG 57.413 40.909 0.00 0.00 0.00 2.32
1103 1107 6.319658 ACTGTGATAGACAATAAAGCCATTGG 59.680 38.462 0.00 0.00 39.71 3.16
1195 1199 5.580691 CGACACTGTTGGAGAAATAAGCATA 59.419 40.000 0.00 0.00 0.00 3.14
1333 1337 2.096496 CGACAACATTCCATCCAGAAGC 59.904 50.000 0.00 0.00 0.00 3.86
1359 1363 5.649395 TGAAGCACCCAATGAGATAAAAGAG 59.351 40.000 0.00 0.00 0.00 2.85
1637 1641 1.133790 ACCGGAACAGCGTATACAGAC 59.866 52.381 9.46 0.00 0.00 3.51
1683 1687 2.743928 GACTCCACCAAGGCGCTG 60.744 66.667 7.64 0.00 37.29 5.18
1726 1730 7.974482 AACCAAAAGGCGGTATTATATACTC 57.026 36.000 0.00 0.00 34.99 2.59
1738 1751 1.001378 CTCAGTCAAACCAAAAGGCGG 60.001 52.381 0.00 0.00 0.00 6.13
1851 1864 1.605712 CCTCCTTGACGAGAACCACAC 60.606 57.143 0.00 0.00 30.97 3.82
1852 1865 0.679505 CCTCCTTGACGAGAACCACA 59.320 55.000 0.00 0.00 30.97 4.17
1896 1909 7.894376 ATCAATTGACACATGATGGTTTTTC 57.106 32.000 11.07 0.00 32.77 2.29
2024 2037 4.159120 GCGTTTTCAGTTTTGAGATAGCC 58.841 43.478 0.00 0.00 34.15 3.93
2111 2124 2.030893 GTGTACATGCACATGCTGTTGT 60.031 45.455 10.50 8.73 42.39 3.32
2134 2147 9.903682 AATAAAAAGATGAGAAATGCATATCCG 57.096 29.630 0.00 0.00 0.00 4.18
2181 2194 8.852671 AATATATTAGATCTGAAGGAGAGGGG 57.147 38.462 5.18 0.00 32.80 4.79
2194 2207 8.103305 TCCTGCCACCAAAGAATATATTAGATC 58.897 37.037 0.00 0.00 0.00 2.75
2284 2297 3.810148 GTGCGCACGACAACTTTTA 57.190 47.368 26.77 0.00 0.00 1.52
2304 2317 7.235606 TGCTAATTATGAAGCCTAGGACTATGT 59.764 37.037 14.75 1.85 37.97 2.29
2329 2342 9.650539 CTAGTAGGATCAGAATATTCCAACATG 57.349 37.037 11.92 3.78 31.65 3.21
2503 2516 8.442632 TTCATGGCAATTAACAATGAAACAAA 57.557 26.923 7.63 0.00 0.00 2.83
2599 2612 0.317519 ACCAAAAGCAAACTACGCGC 60.318 50.000 5.73 0.00 0.00 6.86
2629 2642 4.055710 TGACCAGGGTTGTAGATACTCA 57.944 45.455 0.00 0.00 0.00 3.41
2641 2654 2.358195 GCCCAAATTAGATGACCAGGGT 60.358 50.000 0.00 0.00 37.38 4.34
2701 2714 2.134789 ATGGATTTGAGGTCAGTGCC 57.865 50.000 0.00 0.00 0.00 5.01
2754 2804 8.237282 TGACGATGAGTAGATAAGATACGTAC 57.763 38.462 0.00 0.00 0.00 3.67
2763 2813 6.590677 CGATACCTCTGACGATGAGTAGATAA 59.409 42.308 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.