Multiple sequence alignment - TraesCS4D01G244500

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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 TraesCS4D01G244500 chr4D 100.000 2849 0 0 1 2849 409170794 409167946 0.000000e+00 5262.0
1 TraesCS4D01G244500 chr4A 95.626 2858 75 17 1 2841 80858694 80855870 0.000000e+00 4540.0
2 TraesCS4D01G244500 chr4B 93.624 2886 105 29 1 2842 506908950 506911800 0.000000e+00 4237.0
3 TraesCS4D01G244500 chr5D 86.957 115 15 0 1303 1417 344885063 344884949 2.300000e-26 130.0
4 TraesCS4D01G244500 chr5D 84.270 89 10 3 1303 1389 436971839 436971925 1.820000e-12 84.2
5 TraesCS4D01G244500 chr5A 88.073 109 13 0 1303 1411 447305063 447305171 2.300000e-26 130.0
6 TraesCS4D01G244500 chr7D 89.691 97 10 0 1303 1399 117792114 117792210 1.070000e-24 124.0
7 TraesCS4D01G244500 chr7B 88.660 97 11 0 1303 1399 79051426 79051522 4.990000e-23 119.0
8 TraesCS4D01G244500 chr7A 88.660 97 11 0 1303 1399 122207649 122207745 4.990000e-23 119.0
9 TraesCS4D01G244500 chr5B 84.270 89 10 3 1303 1389 531187513 531187599 1.820000e-12 84.2


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 TraesCS4D01G244500 chr4D 409167946 409170794 2848 True 5262 5262 100.000 1 2849 1 chr4D.!!$R1 2848
1 TraesCS4D01G244500 chr4A 80855870 80858694 2824 True 4540 4540 95.626 1 2841 1 chr4A.!!$R1 2840
2 TraesCS4D01G244500 chr4B 506908950 506911800 2850 False 4237 4237 93.624 1 2842 1 chr4B.!!$F1 2841

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
710 718 1.013596 TGCGATGCGAAACCTATTGG 58.986 50.000 0.00 0.0 39.83 3.16 F
1196 1209 1.153309 CGCATGCATCACCTGAGGA 60.153 57.895 19.57 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1540 1553 0.835941 AACTGCTGGCCATAGGAGAG 59.164 55.000 18.67 0.95 38.28 3.2 R
2446 2473 2.025981 TGGCAGCTAATTGATGACTGGT 60.026 45.455 0.00 0.00 41.50 4.0 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
322 323 7.924947 AGAAATGAAGAAAGCAAAGAAAAGAGG 59.075 33.333 0.00 0.00 0.00 3.69
326 327 4.148079 AGAAAGCAAAGAAAAGAGGGAGG 58.852 43.478 0.00 0.00 0.00 4.30
327 328 3.884037 AAGCAAAGAAAAGAGGGAGGA 57.116 42.857 0.00 0.00 0.00 3.71
328 329 3.431673 AGCAAAGAAAAGAGGGAGGAG 57.568 47.619 0.00 0.00 0.00 3.69
329 330 2.982488 AGCAAAGAAAAGAGGGAGGAGA 59.018 45.455 0.00 0.00 0.00 3.71
330 331 3.008923 AGCAAAGAAAAGAGGGAGGAGAG 59.991 47.826 0.00 0.00 0.00 3.20
331 332 3.008485 GCAAAGAAAAGAGGGAGGAGAGA 59.992 47.826 0.00 0.00 0.00 3.10
332 333 4.574892 CAAAGAAAAGAGGGAGGAGAGAC 58.425 47.826 0.00 0.00 0.00 3.36
333 334 3.551635 AGAAAAGAGGGAGGAGAGACA 57.448 47.619 0.00 0.00 0.00 3.41
334 335 3.863086 AGAAAAGAGGGAGGAGAGACAA 58.137 45.455 0.00 0.00 0.00 3.18
335 336 4.235372 AGAAAAGAGGGAGGAGAGACAAA 58.765 43.478 0.00 0.00 0.00 2.83
369 370 3.177291 TCGTGAGAGTGAGGGGGA 58.823 61.111 0.00 0.00 34.84 4.81
675 683 2.497770 CATCCGTCGGTACCCCAC 59.502 66.667 11.88 2.22 0.00 4.61
710 718 1.013596 TGCGATGCGAAACCTATTGG 58.986 50.000 0.00 0.00 39.83 3.16
748 756 1.205655 TCCTCCTTTGAGCGACATGAG 59.794 52.381 0.00 0.00 37.29 2.90
782 790 5.990668 TCTTCTTGCCCTTTCTATTCCTAC 58.009 41.667 0.00 0.00 0.00 3.18
1120 1133 3.565961 TTGCCATTCCTGCGCTCCA 62.566 57.895 9.73 0.00 0.00 3.86
1196 1209 1.153309 CGCATGCATCACCTGAGGA 60.153 57.895 19.57 0.00 0.00 3.71
1344 1357 1.675310 CTGCAGGCATTTCCCGACA 60.675 57.895 5.57 0.00 34.51 4.35
1566 1579 0.254178 ATGGCCAGCAGTTCTACAGG 59.746 55.000 13.05 0.00 0.00 4.00
1576 1589 1.074775 TTCTACAGGGGGATCGGGG 60.075 63.158 0.00 0.00 0.00 5.73
1730 1743 1.566211 CAGAGAGCTTCCCCTTCTCA 58.434 55.000 0.00 0.00 39.79 3.27
1852 1865 7.658982 TGAGCTTAGATTTGCATCTATAAGTGG 59.341 37.037 10.38 0.00 40.97 4.00
2010 2031 5.084818 ACACGTGAGAAATATGTCCATCA 57.915 39.130 25.01 0.00 0.00 3.07
2127 2148 8.450964 GCAGCAAGACAACTTTATACTCAATTA 58.549 33.333 0.00 0.00 33.70 1.40
2180 2202 6.846325 AAGCTGAGTTACACACTAAAACTC 57.154 37.500 7.35 7.35 45.99 3.01
2186 2208 7.883217 TGAGTTACACACTAAAACTCTAGGAG 58.117 38.462 13.70 0.00 45.98 3.69
2302 2325 7.994425 TTAGGCATAAAGAAGTGATGAACAA 57.006 32.000 0.00 0.00 0.00 2.83
2370 2393 9.431887 TGGTGAATAAAACAGATTGTAGTCTAC 57.568 33.333 2.81 2.81 0.00 2.59
2474 2502 1.350684 TCAATTAGCTGCCACAGGTCA 59.649 47.619 2.05 0.00 41.50 4.02
2523 2555 8.240682 AGCAAATACAAGTGAACGCATATAAAA 58.759 29.630 0.00 0.00 0.00 1.52
2679 2725 4.393371 GGTAGATTCAGCTTTCTGGTGTTC 59.607 45.833 0.00 0.00 43.97 3.18
2702 2748 5.350365 TCATTCAAGATAGTTTGCACGTACC 59.650 40.000 0.00 0.00 0.00 3.34
2711 2757 8.181573 AGATAGTTTGCACGTACCAAAAATATG 58.818 33.333 13.18 0.00 34.33 1.78
2713 2759 6.508777 AGTTTGCACGTACCAAAAATATGTT 58.491 32.000 13.18 0.00 34.33 2.71
2803 2851 8.786826 TCTCTATCTAGAAAGCTGAGCTATAC 57.213 38.462 7.68 2.15 38.25 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
234 235 3.241530 TCTGAGCGTGGGCCTGTT 61.242 61.111 4.53 0.00 41.24 3.16
322 323 3.947834 CTCTCTCTCTTTGTCTCTCCTCC 59.052 52.174 0.00 0.00 0.00 4.30
326 327 4.333926 GCTCTCTCTCTCTCTTTGTCTCTC 59.666 50.000 0.00 0.00 0.00 3.20
327 328 4.265073 GCTCTCTCTCTCTCTTTGTCTCT 58.735 47.826 0.00 0.00 0.00 3.10
328 329 3.063997 CGCTCTCTCTCTCTCTTTGTCTC 59.936 52.174 0.00 0.00 0.00 3.36
329 330 3.009723 CGCTCTCTCTCTCTCTTTGTCT 58.990 50.000 0.00 0.00 0.00 3.41
330 331 2.477863 GCGCTCTCTCTCTCTCTTTGTC 60.478 54.545 0.00 0.00 0.00 3.18
331 332 1.472480 GCGCTCTCTCTCTCTCTTTGT 59.528 52.381 0.00 0.00 0.00 2.83
332 333 1.745087 AGCGCTCTCTCTCTCTCTTTG 59.255 52.381 2.64 0.00 0.00 2.77
333 334 2.017049 GAGCGCTCTCTCTCTCTCTTT 58.983 52.381 29.88 0.00 36.42 2.52
334 335 1.668419 GAGCGCTCTCTCTCTCTCTT 58.332 55.000 29.88 0.00 36.42 2.85
335 336 0.530650 CGAGCGCTCTCTCTCTCTCT 60.531 60.000 32.88 0.00 37.19 3.10
367 368 3.772025 TGAGGAAAACCATCTCTCTCTCC 59.228 47.826 0.00 0.00 0.00 3.71
369 370 4.466015 GTCTGAGGAAAACCATCTCTCTCT 59.534 45.833 0.00 0.00 0.00 3.10
675 683 2.758089 GCATGCTTGGTGAGGCGAG 61.758 63.158 11.37 0.00 0.00 5.03
708 716 4.227300 AGGAGTGCCAAATGTATAGAACCA 59.773 41.667 0.00 0.00 36.29 3.67
710 718 4.816925 GGAGGAGTGCCAAATGTATAGAAC 59.183 45.833 0.00 0.00 36.29 3.01
748 756 1.916697 GCAAGAAGAAGGTCTGGCGC 61.917 60.000 0.00 0.00 34.91 6.53
782 790 2.693074 GAGCCAAGGAGAGAGAAGGTAG 59.307 54.545 0.00 0.00 0.00 3.18
1196 1209 4.174411 GCGGTGGCTTCTTTAATTCTTT 57.826 40.909 0.00 0.00 35.83 2.52
1395 1408 4.393155 ATCTGCACCCGCTTCGCA 62.393 61.111 0.00 0.00 39.64 5.10
1498 1511 0.389426 GACGGGTACAATGTCGCACT 60.389 55.000 0.00 0.00 0.00 4.40
1540 1553 0.835941 AACTGCTGGCCATAGGAGAG 59.164 55.000 18.67 0.95 38.28 3.20
1852 1865 6.723131 ATCTACTAAAAACAACGGAGAAGC 57.277 37.500 0.00 0.00 0.00 3.86
2010 2031 2.996631 AGCAGGATCGAAGCTTTGATT 58.003 42.857 26.52 12.04 34.37 2.57
2212 2235 9.851686 AATGTGCATCTGAATCCTAAAAGTATA 57.148 29.630 0.00 0.00 0.00 1.47
2213 2236 8.757982 AATGTGCATCTGAATCCTAAAAGTAT 57.242 30.769 0.00 0.00 0.00 2.12
2216 2239 8.767478 AAAAATGTGCATCTGAATCCTAAAAG 57.233 30.769 0.00 0.00 0.00 2.27
2232 2255 6.407475 AAATGGCGAGAAATAAAAATGTGC 57.593 33.333 0.00 0.00 0.00 4.57
2276 2299 8.579850 TGTTCATCACTTCTTTATGCCTAATT 57.420 30.769 0.00 0.00 0.00 1.40
2384 2407 4.705023 CCCACCGAAATGAAGATAACCTTT 59.295 41.667 0.00 0.00 34.68 3.11
2401 2424 5.447624 AATGAAAAAGTAAACTCCCACCG 57.552 39.130 0.00 0.00 0.00 4.94
2446 2473 2.025981 TGGCAGCTAATTGATGACTGGT 60.026 45.455 0.00 0.00 41.50 4.00
2474 2502 7.559590 CTTAATTAAGCTGCAGGTTCATACT 57.440 36.000 32.76 16.41 37.00 2.12
2505 2535 8.894409 TTCAGAATTTTATATGCGTTCACTTG 57.106 30.769 0.00 0.00 0.00 3.16
2507 2537 8.946085 TCTTTCAGAATTTTATATGCGTTCACT 58.054 29.630 0.00 0.00 0.00 3.41
2523 2555 5.940192 TTGCGTGTGTATTCTTTCAGAAT 57.060 34.783 4.47 4.47 46.01 2.40
2679 2725 5.121611 TGGTACGTGCAAACTATCTTGAATG 59.878 40.000 5.86 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.