Multiple sequence alignment - TraesCS1D01G231100

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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 TraesCS1D01G231100 chr1D 100.000 2482 0 0 663 3144 319528362 319525881 0.000000e+00 4584.0
1 TraesCS1D01G231100 chr1D 90.532 1785 112 15 663 2425 242558520 242560269 0.000000e+00 2307.0
2 TraesCS1D01G231100 chr1D 94.349 407 20 3 2424 2828 242560431 242560836 3.440000e-174 621.0
3 TraesCS1D01G231100 chr1D 100.000 177 0 0 1 177 319529024 319528848 8.410000e-86 327.0
4 TraesCS1D01G231100 chr1D 92.857 42 1 2 2830 2869 242561131 242561172 3.390000e-05 60.2
5 TraesCS1D01G231100 chr1D 92.683 41 2 1 2825 2865 319526168 319526129 1.220000e-04 58.4
6 TraesCS1D01G231100 chr1D 92.683 41 2 1 2857 2896 319526200 319526160 1.220000e-04 58.4
7 TraesCS1D01G231100 chr2D 98.946 2466 10 5 663 3112 327321670 327324135 0.000000e+00 4396.0
8 TraesCS1D01G231100 chr2D 98.824 2466 24 5 663 3126 299657240 299654778 0.000000e+00 4388.0
9 TraesCS1D01G231100 chr2D 99.435 177 1 0 1 177 299657460 299657284 3.910000e-84 322.0
10 TraesCS1D01G231100 chr2D 99.435 177 1 0 1 177 327321337 327321513 3.910000e-84 322.0
11 TraesCS1D01G231100 chr2D 92.683 41 2 1 2825 2865 299655047 299655008 1.220000e-04 58.4
12 TraesCS1D01G231100 chr2D 92.683 41 2 1 2857 2896 299655079 299655039 1.220000e-04 58.4
13 TraesCS1D01G231100 chr2D 92.683 41 2 1 2857 2896 327323838 327323878 1.220000e-04 58.4
14 TraesCS1D01G231100 chr2D 92.683 41 2 1 2825 2865 327323870 327323909 1.220000e-04 58.4
15 TraesCS1D01G231100 chr4A 91.171 2186 136 28 663 2828 146048274 146046126 0.000000e+00 2915.0
16 TraesCS1D01G231100 chr4A 91.590 1308 92 10 663 1956 53752376 53753679 0.000000e+00 1790.0
17 TraesCS1D01G231100 chr4A 92.361 1152 75 4 663 1802 12668932 12667782 0.000000e+00 1628.0
18 TraesCS1D01G231100 chr4A 93.785 177 11 0 1 177 12669153 12668977 1.860000e-67 267.0
19 TraesCS1D01G231100 chr4A 87.395 119 10 2 3007 3125 146045782 146045669 7.080000e-27 132.0
20 TraesCS1D01G231100 chr4A 100.000 35 0 0 2835 2869 146045824 146045790 7.280000e-07 65.8
21 TraesCS1D01G231100 chr4A 100.000 30 0 0 2867 2896 146045823 146045794 4.380000e-04 56.5
22 TraesCS1D01G231100 chr4B 90.851 2186 144 23 663 2828 417374727 417372578 0.000000e+00 2878.0
23 TraesCS1D01G231100 chr4B 94.318 176 10 0 1 176 417374948 417374773 1.440000e-68 270.0
24 TraesCS1D01G231100 chr4B 86.331 139 10 6 3007 3140 417372234 417372100 3.270000e-30 143.0
25 TraesCS1D01G231100 chr4B 100.000 35 0 0 2835 2869 417372276 417372242 7.280000e-07 65.8
26 TraesCS1D01G231100 chr4B 100.000 30 0 0 2867 2896 417372275 417372246 4.380000e-04 56.5
27 TraesCS1D01G231100 chr3A 90.668 2186 147 23 663 2828 667661201 667663349 0.000000e+00 2854.0
28 TraesCS1D01G231100 chr3A 94.318 176 10 0 1 176 667660980 667661155 1.440000e-68 270.0
29 TraesCS1D01G231100 chr3A 88.281 128 9 3 3004 3129 667663690 667663813 7.030000e-32 148.0
30 TraesCS1D01G231100 chr3A 95.238 42 0 2 2830 2869 667663644 667663685 7.280000e-07 65.8
31 TraesCS1D01G231100 chr3A 100.000 30 0 0 2867 2896 667663652 667663681 4.380000e-04 56.5
32 TraesCS1D01G231100 chr6A 85.484 2170 229 38 668 2776 241737926 241740070 0.000000e+00 2183.0
33 TraesCS1D01G231100 chr6A 85.166 1773 212 24 663 2398 261024482 261026240 0.000000e+00 1770.0
34 TraesCS1D01G231100 chr6A 86.902 397 27 13 2404 2777 261026804 261027198 3.750000e-114 422.0
35 TraesCS1D01G231100 chr7A 92.361 1152 75 4 663 1802 67563324 67564474 0.000000e+00 1628.0
36 TraesCS1D01G231100 chr7A 92.188 1152 76 5 663 1802 2540642 2541791 0.000000e+00 1616.0
37 TraesCS1D01G231100 chr7A 93.785 177 11 0 1 177 2540421 2540597 1.860000e-67 267.0
38 TraesCS1D01G231100 chr7A 93.785 177 11 0 1 177 67563103 67563279 1.860000e-67 267.0
39 TraesCS1D01G231100 chr1A 92.274 1152 76 4 663 1802 502837215 502836065 0.000000e+00 1622.0
40 TraesCS1D01G231100 chr1A 93.785 177 11 0 1 177 502837436 502837260 1.860000e-67 267.0
41 TraesCS1D01G231100 chr1A 87.097 62 0 8 3078 3135 565273417 565273360 2.620000e-06 63.9
42 TraesCS1D01G231100 chr5A 93.785 177 11 0 1 177 280764740 280764916 1.860000e-67 267.0
43 TraesCS1D01G231100 chr2B 90.323 62 1 5 3083 3140 706801438 706801378 3.360000e-10 76.8
44 TraesCS1D01G231100 chr3B 86.567 67 4 3 3083 3144 145880745 145880679 5.630000e-08 69.4
45 TraesCS1D01G231100 chr2A 89.286 56 2 4 3083 3135 216745534 216745480 2.020000e-07 67.6


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 TraesCS1D01G231100 chr1D 319525881 319529024 3143 True 1256.950000 4584 96.341500 1 3144 4 chr1D.!!$R1 3143
1 TraesCS1D01G231100 chr1D 242558520 242561172 2652 False 996.066667 2307 92.579333 663 2869 3 chr1D.!!$F1 2206
2 TraesCS1D01G231100 chr2D 327321337 327324135 2798 False 1208.700000 4396 95.936750 1 3112 4 chr2D.!!$F1 3111
3 TraesCS1D01G231100 chr2D 299654778 299657460 2682 True 1206.700000 4388 95.906250 1 3126 4 chr2D.!!$R1 3125
4 TraesCS1D01G231100 chr4A 53752376 53753679 1303 False 1790.000000 1790 91.590000 663 1956 1 chr4A.!!$F1 1293
5 TraesCS1D01G231100 chr4A 12667782 12669153 1371 True 947.500000 1628 93.073000 1 1802 2 chr4A.!!$R1 1801
6 TraesCS1D01G231100 chr4A 146045669 146048274 2605 True 792.325000 2915 94.641500 663 3125 4 chr4A.!!$R2 2462
7 TraesCS1D01G231100 chr4B 417372100 417374948 2848 True 682.660000 2878 94.300000 1 3140 5 chr4B.!!$R1 3139
8 TraesCS1D01G231100 chr3A 667660980 667663813 2833 False 678.860000 2854 93.701000 1 3129 5 chr3A.!!$F1 3128
9 TraesCS1D01G231100 chr6A 241737926 241740070 2144 False 2183.000000 2183 85.484000 668 2776 1 chr6A.!!$F1 2108
10 TraesCS1D01G231100 chr6A 261024482 261027198 2716 False 1096.000000 1770 86.034000 663 2777 2 chr6A.!!$F2 2114
11 TraesCS1D01G231100 chr7A 67563103 67564474 1371 False 947.500000 1628 93.073000 1 1802 2 chr7A.!!$F2 1801
12 TraesCS1D01G231100 chr7A 2540421 2541791 1370 False 941.500000 1616 92.986500 1 1802 2 chr7A.!!$F1 1801
13 TraesCS1D01G231100 chr1A 502836065 502837436 1371 True 944.500000 1622 93.029500 1 1802 2 chr1A.!!$R2 1801

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
1234 1273 6.327934 GCTATTCAGCTGACAATTTCAACAT 58.672 36.0 18.03 5.66 44.93 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2810 3673 5.705905 ACCATGTAAGTTCAAGTAGGCTTTC 59.294 40.0 0.0 0.0 31.49 2.62 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
1234 1273 6.327934 GCTATTCAGCTGACAATTTCAACAT 58.672 36.000 18.03 5.66 44.93 2.71
1408 1458 2.000447 GTGGCTACGAAATCTCACACC 59.000 52.381 0.00 0.00 0.00 4.16
2033 2122 2.164422 CACACATCGTCTCCAAGCTCTA 59.836 50.000 0.00 0.00 0.00 2.43
2292 2401 0.107703 CCCGATGCCACAGTACATGT 60.108 55.000 2.69 2.69 45.43 3.21
2810 3673 1.273327 CCCCTGCAAGCAAAGTAAAGG 59.727 52.381 0.00 0.00 0.00 3.11
2930 4087 2.684881 CGTTGCCTCTCCTATTGCAAAT 59.315 45.455 1.71 0.00 44.44 2.32
3117 4285 2.361789 ACGCACGGGCATTTTTACTAT 58.638 42.857 11.77 0.00 41.24 2.12
3118 4286 3.533547 ACGCACGGGCATTTTTACTATA 58.466 40.909 11.77 0.00 41.24 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1408 1458 4.831307 CCCGACCGAAGCGACTCG 62.831 72.222 0.0 0.0 38.58 4.18
2033 2122 4.107051 GCCTGCGTTGCTTGCGAT 62.107 61.111 0.0 0.0 34.24 4.58
2810 3673 5.705905 ACCATGTAAGTTCAAGTAGGCTTTC 59.294 40.000 0.0 0.0 31.49 2.62
2930 4087 8.691661 AGAGGCTTTTGAGTATTTTTGAGTAA 57.308 30.769 0.0 0.0 0.00 2.24


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

AutoCloner maintained by Alex Coulton.