Multiple sequence alignment - TraesCS1B01G200500

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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 TraesCS1B01G200500 chr1B 100.000 2639 0 0 1 2639 359220719 359218081 0.000000e+00 4874.0
1 TraesCS1B01G200500 chr2B 96.634 2644 73 9 1 2639 225325803 225323171 0.000000e+00 4375.0
2 TraesCS1B01G200500 chr2B 88.462 1846 173 33 812 2639 664329675 664327852 0.000000e+00 2193.0
3 TraesCS1B01G200500 chr4B 93.380 1858 82 21 812 2639 622502469 622500623 0.000000e+00 2712.0
4 TraesCS1B01G200500 chr4B 95.732 820 34 1 1 820 622503321 622502503 0.000000e+00 1319.0
5 TraesCS1B01G200500 chr6B 93.369 1855 80 11 814 2636 717731239 717733082 0.000000e+00 2704.0
6 TraesCS1B01G200500 chr6B 93.914 1216 48 3 812 2002 147949876 147948662 0.000000e+00 1812.0
7 TraesCS1B01G200500 chr6B 87.898 1413 134 26 812 2197 567117376 567115974 0.000000e+00 1628.0
8 TraesCS1B01G200500 chr6B 96.220 820 30 1 1 820 147950728 147949910 0.000000e+00 1341.0
9 TraesCS1B01G200500 chr6B 81.609 174 23 8 1904 2072 717732479 717732648 4.580000e-28 135.0
10 TraesCS1B01G200500 chr5B 88.063 1843 177 36 812 2636 529281267 529283084 0.000000e+00 2145.0
11 TraesCS1B01G200500 chr5B 88.467 1448 130 27 812 2253 575036921 575035505 0.000000e+00 1714.0
12 TraesCS1B01G200500 chr5B 96.711 821 24 2 1 820 659536099 659536917 0.000000e+00 1363.0
13 TraesCS1B01G200500 chr5B 95.122 820 38 1 1 820 649874453 649875270 0.000000e+00 1291.0
14 TraesCS1B01G200500 chr5B 88.372 516 32 2 1725 2214 659546441 659546954 1.750000e-166 595.0
15 TraesCS1B01G200500 chr5B 93.275 342 21 2 2300 2639 575025503 575025162 1.090000e-138 503.0
16 TraesCS1B01G200500 chr5B 92.128 343 26 1 2295 2636 649895559 649895901 1.420000e-132 483.0
17 TraesCS1B01G200500 chr5B 81.633 196 27 8 1882 2072 659546746 659546937 1.260000e-33 154.0
18 TraesCS1B01G200500 chr3D 87.554 1856 187 22 812 2636 558680114 558681956 0.000000e+00 2108.0
19 TraesCS1B01G200500 chr3D 95.833 816 33 1 1 816 558679262 558680076 0.000000e+00 1317.0
20 TraesCS1B01G200500 chr2D 88.600 1421 119 26 812 2199 12315260 12313850 0.000000e+00 1687.0
21 TraesCS1B01G200500 chr2D 95.488 820 36 1 1 820 12316100 12315282 0.000000e+00 1308.0
22 TraesCS1B01G200500 chr7B 91.156 1176 81 15 812 1983 36427258 36426102 0.000000e+00 1574.0
23 TraesCS1B01G200500 chr7B 91.908 346 27 1 2295 2639 36425868 36425523 1.420000e-132 483.0
24 TraesCS1B01G200500 chr7B 100.000 31 0 0 1882 1912 380703615 380703645 1.020000e-04 58.4
25 TraesCS1B01G200500 chr3B 95.610 820 35 1 1 820 71793798 71792980 0.000000e+00 1314.0
26 TraesCS1B01G200500 chr3B 90.000 720 46 3 1377 2072 10032856 10032139 0.000000e+00 907.0
27 TraesCS1B01G200500 chr3B 81.992 472 57 22 2011 2473 10032322 10031870 2.480000e-100 375.0
28 TraesCS1B01G200500 chr5D 95.343 816 37 1 1 816 387241738 387242552 0.000000e+00 1295.0
29 TraesCS1B01G200500 chr4D 83.518 813 105 21 1843 2639 473876286 473875487 0.000000e+00 732.0


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 TraesCS1B01G200500 chr1B 359218081 359220719 2638 True 4874.0 4874 100.0000 1 2639 1 chr1B.!!$R1 2638
1 TraesCS1B01G200500 chr2B 225323171 225325803 2632 True 4375.0 4375 96.6340 1 2639 1 chr2B.!!$R1 2638
2 TraesCS1B01G200500 chr2B 664327852 664329675 1823 True 2193.0 2193 88.4620 812 2639 1 chr2B.!!$R2 1827
3 TraesCS1B01G200500 chr4B 622500623 622503321 2698 True 2015.5 2712 94.5560 1 2639 2 chr4B.!!$R1 2638
4 TraesCS1B01G200500 chr6B 567115974 567117376 1402 True 1628.0 1628 87.8980 812 2197 1 chr6B.!!$R1 1385
5 TraesCS1B01G200500 chr6B 147948662 147950728 2066 True 1576.5 1812 95.0670 1 2002 2 chr6B.!!$R2 2001
6 TraesCS1B01G200500 chr6B 717731239 717733082 1843 False 1419.5 2704 87.4890 814 2636 2 chr6B.!!$F1 1822
7 TraesCS1B01G200500 chr5B 529281267 529283084 1817 False 2145.0 2145 88.0630 812 2636 1 chr5B.!!$F1 1824
8 TraesCS1B01G200500 chr5B 575035505 575036921 1416 True 1714.0 1714 88.4670 812 2253 1 chr5B.!!$R2 1441
9 TraesCS1B01G200500 chr5B 659536099 659536917 818 False 1363.0 1363 96.7110 1 820 1 chr5B.!!$F4 819
10 TraesCS1B01G200500 chr5B 649874453 649875270 817 False 1291.0 1291 95.1220 1 820 1 chr5B.!!$F2 819
11 TraesCS1B01G200500 chr5B 659546441 659546954 513 False 374.5 595 85.0025 1725 2214 2 chr5B.!!$F5 489
12 TraesCS1B01G200500 chr3D 558679262 558681956 2694 False 1712.5 2108 91.6935 1 2636 2 chr3D.!!$F1 2635
13 TraesCS1B01G200500 chr2D 12313850 12316100 2250 True 1497.5 1687 92.0440 1 2199 2 chr2D.!!$R1 2198
14 TraesCS1B01G200500 chr7B 36425523 36427258 1735 True 1028.5 1574 91.5320 812 2639 2 chr7B.!!$R1 1827
15 TraesCS1B01G200500 chr3B 71792980 71793798 818 True 1314.0 1314 95.6100 1 820 1 chr3B.!!$R1 819
16 TraesCS1B01G200500 chr3B 10031870 10032856 986 True 641.0 907 85.9960 1377 2473 2 chr3B.!!$R2 1096
17 TraesCS1B01G200500 chr5D 387241738 387242552 814 False 1295.0 1295 95.3430 1 816 1 chr5D.!!$F1 815
18 TraesCS1B01G200500 chr4D 473875487 473876286 799 True 732.0 732 83.5180 1843 2639 1 chr4D.!!$R1 796


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
413 414 0.606401 AAGCCACGAGGTTGACATGG 60.606 55.0 0.0 0.0 34.07 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2149 2264 0.320771 CAGCATACCCTACCGCCATC 60.321 60.0 0.0 0.0 0.0 3.51 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
413 414 0.606401 AAGCCACGAGGTTGACATGG 60.606 55.000 0.00 0.00 34.07 3.66
691 692 2.046285 CCAAGGACCGATGCCAACC 61.046 63.158 0.00 0.00 0.00 3.77
693 694 2.231380 AAGGACCGATGCCAACCCT 61.231 57.895 0.00 0.00 0.00 4.34
694 695 2.124695 GGACCGATGCCAACCCTC 60.125 66.667 0.00 0.00 0.00 4.30
729 730 2.169330 GGTGTTCGTAGAGGAGGTTCT 58.831 52.381 0.00 0.00 38.43 3.01
731 732 2.818432 GTGTTCGTAGAGGAGGTTCTGA 59.182 50.000 0.00 0.00 38.43 3.27
915 959 9.463443 GGTTGAAATAATATGAATGGTACTTGC 57.537 33.333 0.00 0.00 0.00 4.01
1029 1073 2.668632 GGTTCCATGACGAGGCCA 59.331 61.111 5.01 0.00 0.00 5.36
1100 1145 1.539712 GGACGAGGTGACGGAAAAAGT 60.540 52.381 0.00 0.00 37.61 2.66
1103 1148 3.795877 ACGAGGTGACGGAAAAAGTTAA 58.204 40.909 0.00 0.00 37.61 2.01
1104 1149 3.557185 ACGAGGTGACGGAAAAAGTTAAC 59.443 43.478 0.00 0.00 37.61 2.01
1169 1214 1.597027 CCACCGACCGCAAGAAGTT 60.597 57.895 0.00 0.00 43.02 2.66
1239 1284 0.887387 GGAGGCTACCAACAAACGCA 60.887 55.000 0.00 0.00 0.00 5.24
1894 1997 3.046374 AGATATTTGAACCCTACCGCCT 58.954 45.455 0.00 0.00 0.00 5.52
2009 2114 2.844451 GCGCAACAGCAAGGGAACA 61.844 57.895 0.30 0.00 37.05 3.18
2086 2192 0.828343 GTAGGCCCCTCATACTCGCT 60.828 60.000 0.00 0.00 0.00 4.93
2089 2195 2.491022 GCCCCTCATACTCGCTCGT 61.491 63.158 0.00 0.00 0.00 4.18
2253 2372 5.835280 AGAGATGGGAGTCAAAAACAATGTT 59.165 36.000 0.00 0.00 0.00 2.71
2254 2373 6.015940 AGAGATGGGAGTCAAAAACAATGTTC 60.016 38.462 0.00 0.00 0.00 3.18
2256 2375 5.667539 TGGGAGTCAAAAACAATGTTCAA 57.332 34.783 0.00 0.00 0.00 2.69
2257 2376 5.659463 TGGGAGTCAAAAACAATGTTCAAG 58.341 37.500 0.00 0.00 0.00 3.02
2258 2377 5.186797 TGGGAGTCAAAAACAATGTTCAAGT 59.813 36.000 0.00 0.00 0.00 3.16
2259 2378 5.519927 GGGAGTCAAAAACAATGTTCAAGTG 59.480 40.000 0.00 0.00 0.00 3.16
2260 2379 6.329496 GGAGTCAAAAACAATGTTCAAGTGA 58.671 36.000 0.00 0.00 0.00 3.41
2262 2381 7.330700 GGAGTCAAAAACAATGTTCAAGTGAAA 59.669 33.333 0.00 0.00 35.58 2.69
2263 2382 8.776376 AGTCAAAAACAATGTTCAAGTGAAAT 57.224 26.923 0.00 0.00 35.58 2.17
2264 2383 9.868277 AGTCAAAAACAATGTTCAAGTGAAATA 57.132 25.926 0.00 0.00 35.58 1.40
2271 2390 9.868277 AACAATGTTCAAGTGAAATAAGAAACA 57.132 25.926 0.00 0.00 35.58 2.83
2272 2391 9.868277 ACAATGTTCAAGTGAAATAAGAAACAA 57.132 25.926 0.00 0.00 35.58 2.83
2282 2401 9.520204 AGTGAAATAAGAAACAATGTTCAAGTG 57.480 29.630 0.00 0.00 0.00 3.16
2283 2402 9.515020 GTGAAATAAGAAACAATGTTCAAGTGA 57.485 29.630 0.00 0.00 0.00 3.41
2288 2407 9.868277 ATAAGAAACAATGTTCAAGTGAAACAA 57.132 25.926 0.00 0.00 41.43 2.83
2289 2408 8.776376 AAGAAACAATGTTCAAGTGAAACAAT 57.224 26.923 0.00 0.00 41.43 2.71
2290 2409 8.188531 AGAAACAATGTTCAAGTGAAACAATG 57.811 30.769 0.00 3.24 41.43 2.82
2291 2410 7.818930 AGAAACAATGTTCAAGTGAAACAATGT 59.181 29.630 0.00 4.35 41.43 2.71
2292 2411 7.903995 AACAATGTTCAAGTGAAACAATGTT 57.096 28.000 13.72 13.72 41.43 2.71
2293 2412 7.524294 ACAATGTTCAAGTGAAACAATGTTC 57.476 32.000 0.00 0.00 41.43 3.18
2611 2735 0.742505 CGCCAATGGATCATGCAACT 59.257 50.000 2.05 0.00 0.00 3.16
2636 2760 3.901797 CTCACGGAACCAGGCCCAC 62.902 68.421 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 108 4.892345 TGAAACCTCAACCAATCATCAACA 59.108 37.500 0.00 0.00 0.00 3.33
267 268 0.034059 CTCTCACACTGACACCACCC 59.966 60.000 0.00 0.00 0.00 4.61
413 414 0.105039 AGGATGAAATCGAGACGCCC 59.895 55.000 0.00 0.00 46.86 6.13
691 692 1.689273 ACCTATTTGGCTAGAGCGAGG 59.311 52.381 0.00 0.38 43.26 4.63
693 694 2.108168 ACACCTATTTGGCTAGAGCGA 58.892 47.619 0.00 0.00 43.26 4.93
694 695 2.604046 ACACCTATTTGGCTAGAGCG 57.396 50.000 0.00 0.00 43.26 5.03
729 730 0.613572 TACCTCCTCGTGTGCCATCA 60.614 55.000 0.00 0.00 0.00 3.07
731 732 1.330655 CCTACCTCCTCGTGTGCCAT 61.331 60.000 0.00 0.00 0.00 4.40
870 913 3.426615 ACCATCCGGATTAAGCAAAACA 58.573 40.909 16.19 0.00 35.59 2.83
1029 1073 0.667487 CTTCACGATCAGCACACGGT 60.667 55.000 0.00 0.00 0.00 4.83
1100 1145 6.097554 ACACCAACATGATGGAGTTTTGTTAA 59.902 34.615 27.18 0.00 40.77 2.01
1103 1148 3.960102 ACACCAACATGATGGAGTTTTGT 59.040 39.130 27.18 17.22 40.77 2.83
1104 1149 4.300803 CACACCAACATGATGGAGTTTTG 58.699 43.478 27.18 16.61 40.77 2.44
1169 1214 2.840640 TCTTCTCCCTTCCGTCCATA 57.159 50.000 0.00 0.00 0.00 2.74
1239 1284 2.559668 CCATACCGGTGGTACGTCATAT 59.440 50.000 19.93 0.00 41.31 1.78
1894 1997 2.239400 CATCCTACCGCCATAGTCTGA 58.761 52.381 0.00 0.00 0.00 3.27
2089 2195 2.842462 ACACGGTGTCTGGGCAGA 60.842 61.111 8.21 0.00 34.56 4.26
2149 2264 0.320771 CAGCATACCCTACCGCCATC 60.321 60.000 0.00 0.00 0.00 3.51
2256 2375 9.520204 CACTTGAACATTGTTTCTTATTTCACT 57.480 29.630 3.08 0.00 0.00 3.41
2257 2376 9.515020 TCACTTGAACATTGTTTCTTATTTCAC 57.485 29.630 3.08 0.00 0.00 3.18
2262 2381 9.868277 TTGTTTCACTTGAACATTGTTTCTTAT 57.132 25.926 3.08 0.00 33.13 1.73
2263 2382 9.868277 ATTGTTTCACTTGAACATTGTTTCTTA 57.132 25.926 3.08 0.00 33.13 2.10
2264 2383 8.658609 CATTGTTTCACTTGAACATTGTTTCTT 58.341 29.630 3.08 0.00 33.13 2.52
2265 2384 7.818930 ACATTGTTTCACTTGAACATTGTTTCT 59.181 29.630 3.08 0.00 32.57 2.52
2267 2386 7.903995 ACATTGTTTCACTTGAACATTGTTT 57.096 28.000 3.08 0.00 32.57 2.83
2270 2389 7.522901 TGAACATTGTTTCACTTGAACATTG 57.477 32.000 3.08 9.16 33.13 2.82
2271 2390 8.545229 TTTGAACATTGTTTCACTTGAACATT 57.455 26.923 3.08 0.00 35.18 2.71
2272 2391 8.605746 CATTTGAACATTGTTTCACTTGAACAT 58.394 29.630 3.08 0.00 35.18 2.71
2274 2393 8.183830 TCATTTGAACATTGTTTCACTTGAAC 57.816 30.769 3.08 0.00 35.18 3.18
2275 2394 8.768957 TTCATTTGAACATTGTTTCACTTGAA 57.231 26.923 3.08 10.67 35.87 2.69
2277 2396 9.823098 TTTTTCATTTGAACATTGTTTCACTTG 57.177 25.926 3.08 4.49 35.18 3.16
2353 2476 7.706607 GGGTGTTGCTTCTTATTTCATTTATCC 59.293 37.037 0.00 0.00 0.00 2.59



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

AutoCloner maintained by Alex Coulton.