Multiple sequence alignment - TraesCS2A01G014700

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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 TraesCS2A01G014700 chr2A 100.000 2375 0 0 1 2375 5900042 5902416 0.000000e+00 4386
1 TraesCS2A01G014700 chr2A 79.570 465 68 16 253 711 548999693 548999250 8.250000e-80 307
2 TraesCS2A01G014700 chr2A 79.355 465 69 15 253 711 549011558 549011115 3.840000e-78 302
3 TraesCS2A01G014700 chr4A 97.938 2376 44 5 1 2375 208839133 208836762 0.000000e+00 4111
4 TraesCS2A01G014700 chr4A 94.699 2377 114 9 1 2375 202603957 202601591 0.000000e+00 3681
5 TraesCS2A01G014700 chr5B 91.400 2128 160 18 253 2375 63988201 63986092 0.000000e+00 2894
6 TraesCS2A01G014700 chr5B 88.998 1327 114 19 1059 2375 652562237 652563541 0.000000e+00 1613
7 TraesCS2A01G014700 chr5B 84.151 795 102 13 253 1046 652561387 652562158 0.000000e+00 749
8 TraesCS2A01G014700 chr3A 98.092 1363 25 1 1013 2375 732714183 732712822 0.000000e+00 2372
9 TraesCS2A01G014700 chr3A 97.736 1016 20 3 1 1015 732715319 732714306 0.000000e+00 1746
10 TraesCS2A01G014700 chr3A 88.182 1320 122 21 1067 2375 672319603 672320899 0.000000e+00 1543
11 TraesCS2A01G014700 chr7A 88.404 1328 120 21 1059 2375 668179611 668180915 0.000000e+00 1568
12 TraesCS2A01G014700 chr7A 88.213 1332 121 20 1059 2375 468297868 468299178 0.000000e+00 1557
13 TraesCS2A01G014700 chr7A 88.235 1326 126 22 1059 2375 537033703 537035007 0.000000e+00 1557
14 TraesCS2A01G014700 chr7A 87.552 241 27 3 1 239 468296794 468297033 2.330000e-70 276
15 TraesCS2A01G014700 chr3B 87.943 1327 127 17 1062 2375 292166018 292164712 0.000000e+00 1533
16 TraesCS2A01G014700 chr6D 95.420 917 37 4 253 1168 429952376 429953288 0.000000e+00 1456
17 TraesCS2A01G014700 chr6D 95.213 376 18 0 1164 1539 429960648 429961023 1.570000e-166 595
18 TraesCS2A01G014700 chr6D 92.917 240 15 1 1 240 429952155 429952392 4.860000e-92 348
19 TraesCS2A01G014700 chr6D 85.124 242 32 4 1 239 464459824 464459584 6.560000e-61 244
20 TraesCS2A01G014700 chr2B 79.104 469 61 23 253 711 483175350 483175791 2.990000e-74 289
21 TraesCS2A01G014700 chr5A 85.950 242 31 3 1 239 117113534 117113775 3.030000e-64 255
22 TraesCS2A01G014700 chr2D 85.124 242 32 4 1 239 25665457 25665697 6.560000e-61 244
23 TraesCS2A01G014700 chr1D 85.124 242 32 4 1 239 58931561 58931321 6.560000e-61 244


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 TraesCS2A01G014700 chr2A 5900042 5902416 2374 False 4386.0 4386 100.0000 1 2375 1 chr2A.!!$F1 2374
1 TraesCS2A01G014700 chr4A 208836762 208839133 2371 True 4111.0 4111 97.9380 1 2375 1 chr4A.!!$R2 2374
2 TraesCS2A01G014700 chr4A 202601591 202603957 2366 True 3681.0 3681 94.6990 1 2375 1 chr4A.!!$R1 2374
3 TraesCS2A01G014700 chr5B 63986092 63988201 2109 True 2894.0 2894 91.4000 253 2375 1 chr5B.!!$R1 2122
4 TraesCS2A01G014700 chr5B 652561387 652563541 2154 False 1181.0 1613 86.5745 253 2375 2 chr5B.!!$F1 2122
5 TraesCS2A01G014700 chr3A 732712822 732715319 2497 True 2059.0 2372 97.9140 1 2375 2 chr3A.!!$R1 2374
6 TraesCS2A01G014700 chr3A 672319603 672320899 1296 False 1543.0 1543 88.1820 1067 2375 1 chr3A.!!$F1 1308
7 TraesCS2A01G014700 chr7A 668179611 668180915 1304 False 1568.0 1568 88.4040 1059 2375 1 chr7A.!!$F2 1316
8 TraesCS2A01G014700 chr7A 537033703 537035007 1304 False 1557.0 1557 88.2350 1059 2375 1 chr7A.!!$F1 1316
9 TraesCS2A01G014700 chr7A 468296794 468299178 2384 False 916.5 1557 87.8825 1 2375 2 chr7A.!!$F3 2374
10 TraesCS2A01G014700 chr3B 292164712 292166018 1306 True 1533.0 1533 87.9430 1062 2375 1 chr3B.!!$R1 1313
11 TraesCS2A01G014700 chr6D 429952155 429953288 1133 False 902.0 1456 94.1685 1 1168 2 chr6D.!!$F2 1167

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
31 32 8.267183 TCTGTGACAGTATGGTATTTTCATGAT 58.733 33.333 12.93 0.0 43.62 2.45 F
1101 1313 0.786435 ACCCAGCCAAATTCCTCCTT 59.214 50.000 0.00 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1132 1345 0.984230 TCGGGGCAGAAGAAAGATGT 59.016 50.0 0.0 0.0 0.0 3.06 R
2244 2477 1.999648 ATGCTTGTGGGCTTCAGAAA 58.000 45.0 0.0 0.0 0.0 2.52 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
31 32 8.267183 TCTGTGACAGTATGGTATTTTCATGAT 58.733 33.333 12.93 0.00 43.62 2.45
1101 1313 0.786435 ACCCAGCCAAATTCCTCCTT 59.214 50.000 0.00 0.00 0.00 3.36
1111 1324 2.215942 ATTCCTCCTTTTTCACCCGG 57.784 50.000 0.00 0.00 0.00 5.73
1132 1345 3.009115 GAGCCACTGCCTACCCCA 61.009 66.667 0.00 0.00 38.69 4.96
1201 1414 0.974010 AGCCCCGATTGGAACGACTA 60.974 55.000 0.00 0.00 37.49 2.59
1356 1572 2.928396 CCGAGGTTGGACCCACCT 60.928 66.667 17.14 17.14 39.75 4.00
1559 1790 5.313280 TGTTAAAAAGCCTGAACCTCCTA 57.687 39.130 0.00 0.00 0.00 2.94
1650 1883 7.815840 TTGCATTTGTTATAGCCTGCTATTA 57.184 32.000 16.20 5.43 39.65 0.98
2244 2477 9.561069 CTAATTTAGCTACCCATGATGTTAAGT 57.439 33.333 0.00 0.00 0.00 2.24
2245 2478 8.823220 AATTTAGCTACCCATGATGTTAAGTT 57.177 30.769 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 0.888736 CGGTGACACTGGCAAATCCA 60.889 55.000 6.51 0.00 44.18 3.41
177 180 4.618489 CGCTCAATAGCCTTTGAAAAACTG 59.382 41.667 1.15 0.00 46.68 3.16
179 182 4.546570 ACGCTCAATAGCCTTTGAAAAAC 58.453 39.130 1.15 0.00 46.68 2.43
368 374 1.174783 TCTTGCCGAGTCACTACCTC 58.825 55.000 0.00 0.00 0.00 3.85
441 448 3.695830 TGCCCGTTCACTCTCTTATTT 57.304 42.857 0.00 0.00 0.00 1.40
743 756 7.450074 TCATTTGTATCTGTTGTAGAACTGGT 58.550 34.615 9.32 5.38 39.30 4.00
1101 1313 1.074248 GGCTCTTCCCGGGTGAAAA 59.926 57.895 22.86 6.23 0.00 2.29
1111 1324 1.222113 GGTAGGCAGTGGCTCTTCC 59.778 63.158 24.23 18.98 39.70 3.46
1132 1345 0.984230 TCGGGGCAGAAGAAAGATGT 59.016 50.000 0.00 0.00 0.00 3.06
1356 1572 2.184020 CTCACTGGGCGGGTTGATGA 62.184 60.000 0.00 0.00 0.00 2.92
1458 1675 6.989155 ATGCATGAACCCTAATCATTGAAT 57.011 33.333 0.00 0.00 35.38 2.57
1650 1883 9.305555 CATATATTCAGGTTCATCCCTTTTGAT 57.694 33.333 0.00 0.00 36.75 2.57
1857 2090 4.990426 TGATTATGACACCATACAGCGATG 59.010 41.667 0.00 0.00 35.16 3.84
2140 2373 9.803315 CAAAAGTACACTGATACAGAGCTATAA 57.197 33.333 5.76 0.00 35.18 0.98
2209 2442 4.102681 GGGTAGCTAAATTAGGAGAGGCAA 59.897 45.833 0.00 0.00 0.00 4.52
2244 2477 1.999648 ATGCTTGTGGGCTTCAGAAA 58.000 45.000 0.00 0.00 0.00 2.52
2245 2478 1.999648 AATGCTTGTGGGCTTCAGAA 58.000 45.000 0.00 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.