Multiple sequence alignment - TraesCS2A01G205800

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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 TraesCS2A01G205800 chr2A 100.000 2549 0 0 1 2549 184516992 184514444 0.000000e+00 4708.0
1 TraesCS2A01G205800 chr2A 93.142 2581 123 5 1 2549 202211746 202214304 0.000000e+00 3736.0
2 TraesCS2A01G205800 chr2A 93.753 1841 73 10 1 1820 751417320 751415501 0.000000e+00 2724.0
3 TraesCS2A01G205800 chr2A 94.365 1739 98 0 1 1739 54414786 54416524 0.000000e+00 2669.0
4 TraesCS2A01G205800 chr2A 94.028 921 55 0 1 921 54411459 54412379 0.000000e+00 1397.0
5 TraesCS2A01G205800 chr2A 92.275 699 39 2 1851 2549 751415515 751414832 0.000000e+00 977.0
6 TraesCS2A01G205800 chr5B 87.418 2607 209 53 4 2549 547624623 547622075 0.000000e+00 2887.0
7 TraesCS2A01G205800 chr5B 84.179 828 97 23 1737 2549 692429150 692429958 0.000000e+00 773.0
8 TraesCS2A01G205800 chr5B 93.860 342 20 1 1302 1642 659491596 659491937 4.860000e-142 514.0
9 TraesCS2A01G205800 chrUn 94.545 1760 66 9 1 1739 112556537 112554787 0.000000e+00 2691.0
10 TraesCS2A01G205800 chr3D 94.152 1710 77 3 1 1687 447609767 447608058 0.000000e+00 2582.0
11 TraesCS2A01G205800 chr3D 89.052 1909 113 43 691 2549 580651490 580649628 0.000000e+00 2279.0
12 TraesCS2A01G205800 chr3D 92.704 699 51 0 1851 2549 447607938 447607240 0.000000e+00 1009.0
13 TraesCS2A01G205800 chr3D 90.629 747 52 14 1817 2549 374009039 374008297 0.000000e+00 976.0
14 TraesCS2A01G205800 chr3D 90.094 747 56 14 1817 2549 155677686 155678428 0.000000e+00 953.0
15 TraesCS2A01G205800 chr3D 85.870 184 13 7 1782 1953 603108001 603107819 1.560000e-42 183.0
16 TraesCS2A01G205800 chr3D 97.436 39 1 0 1737 1775 603108026 603107988 1.640000e-07 67.6
17 TraesCS2A01G205800 chr6A 92.216 1760 88 21 1 1739 454845739 454844008 0.000000e+00 2446.0
18 TraesCS2A01G205800 chr6A 88.257 826 68 12 1734 2549 68887039 68887845 0.000000e+00 961.0
19 TraesCS2A01G205800 chr6D 89.979 1906 118 37 663 2549 387623988 387622137 0.000000e+00 2394.0
20 TraesCS2A01G205800 chr6D 88.889 747 65 14 1817 2549 445208166 445207424 0.000000e+00 904.0
21 TraesCS2A01G205800 chr2D 89.827 1730 113 21 1 1687 633747131 633748840 0.000000e+00 2161.0
22 TraesCS2A01G205800 chr2D 89.558 747 60 14 1817 2549 535664157 535664899 0.000000e+00 931.0
23 TraesCS2A01G205800 chr7B 92.601 1257 55 9 465 1687 66321419 66322671 0.000000e+00 1772.0
24 TraesCS2A01G205800 chr7B 89.744 702 66 1 1851 2546 11699689 11698988 0.000000e+00 893.0
25 TraesCS2A01G205800 chr1B 82.309 1724 248 39 1 1687 605987019 605988722 0.000000e+00 1441.0
26 TraesCS2A01G205800 chr5A 92.497 813 50 7 1 811 395004115 395004918 0.000000e+00 1153.0
27 TraesCS2A01G205800 chr5A 74.249 1732 318 90 1 1680 18811955 18810300 6.030000e-171 610.0
28 TraesCS2A01G205800 chr3A 90.064 785 73 4 862 1645 658001530 658000750 0.000000e+00 1013.0
29 TraesCS2A01G205800 chr3A 79.699 133 9 10 1851 1970 721547742 721547869 2.100000e-11 80.5
30 TraesCS2A01G205800 chr6B 82.798 779 81 27 1774 2549 564054338 564053610 0.000000e+00 647.0
31 TraesCS2A01G205800 chr4B 78.025 719 127 18 929 1643 509580346 509579655 8.430000e-115 424.0
32 TraesCS2A01G205800 chr4D 82.979 141 11 1 1739 1866 43371853 43371993 5.760000e-22 115.0


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 TraesCS2A01G205800 chr2A 184514444 184516992 2548 True 4708.0 4708 100.0000 1 2549 1 chr2A.!!$R1 2548
1 TraesCS2A01G205800 chr2A 202211746 202214304 2558 False 3736.0 3736 93.1420 1 2549 1 chr2A.!!$F1 2548
2 TraesCS2A01G205800 chr2A 54411459 54416524 5065 False 2033.0 2669 94.1965 1 1739 2 chr2A.!!$F2 1738
3 TraesCS2A01G205800 chr2A 751414832 751417320 2488 True 1850.5 2724 93.0140 1 2549 2 chr2A.!!$R2 2548
4 TraesCS2A01G205800 chr5B 547622075 547624623 2548 True 2887.0 2887 87.4180 4 2549 1 chr5B.!!$R1 2545
5 TraesCS2A01G205800 chr5B 692429150 692429958 808 False 773.0 773 84.1790 1737 2549 1 chr5B.!!$F2 812
6 TraesCS2A01G205800 chrUn 112554787 112556537 1750 True 2691.0 2691 94.5450 1 1739 1 chrUn.!!$R1 1738
7 TraesCS2A01G205800 chr3D 580649628 580651490 1862 True 2279.0 2279 89.0520 691 2549 1 chr3D.!!$R2 1858
8 TraesCS2A01G205800 chr3D 447607240 447609767 2527 True 1795.5 2582 93.4280 1 2549 2 chr3D.!!$R3 2548
9 TraesCS2A01G205800 chr3D 374008297 374009039 742 True 976.0 976 90.6290 1817 2549 1 chr3D.!!$R1 732
10 TraesCS2A01G205800 chr3D 155677686 155678428 742 False 953.0 953 90.0940 1817 2549 1 chr3D.!!$F1 732
11 TraesCS2A01G205800 chr6A 454844008 454845739 1731 True 2446.0 2446 92.2160 1 1739 1 chr6A.!!$R1 1738
12 TraesCS2A01G205800 chr6A 68887039 68887845 806 False 961.0 961 88.2570 1734 2549 1 chr6A.!!$F1 815
13 TraesCS2A01G205800 chr6D 387622137 387623988 1851 True 2394.0 2394 89.9790 663 2549 1 chr6D.!!$R1 1886
14 TraesCS2A01G205800 chr6D 445207424 445208166 742 True 904.0 904 88.8890 1817 2549 1 chr6D.!!$R2 732
15 TraesCS2A01G205800 chr2D 633747131 633748840 1709 False 2161.0 2161 89.8270 1 1687 1 chr2D.!!$F2 1686
16 TraesCS2A01G205800 chr2D 535664157 535664899 742 False 931.0 931 89.5580 1817 2549 1 chr2D.!!$F1 732
17 TraesCS2A01G205800 chr7B 66321419 66322671 1252 False 1772.0 1772 92.6010 465 1687 1 chr7B.!!$F1 1222
18 TraesCS2A01G205800 chr7B 11698988 11699689 701 True 893.0 893 89.7440 1851 2546 1 chr7B.!!$R1 695
19 TraesCS2A01G205800 chr1B 605987019 605988722 1703 False 1441.0 1441 82.3090 1 1687 1 chr1B.!!$F1 1686
20 TraesCS2A01G205800 chr5A 395004115 395004918 803 False 1153.0 1153 92.4970 1 811 1 chr5A.!!$F1 810
21 TraesCS2A01G205800 chr5A 18810300 18811955 1655 True 610.0 610 74.2490 1 1680 1 chr5A.!!$R1 1679
22 TraesCS2A01G205800 chr3A 658000750 658001530 780 True 1013.0 1013 90.0640 862 1645 1 chr3A.!!$R1 783
23 TraesCS2A01G205800 chr6B 564053610 564054338 728 True 647.0 647 82.7980 1774 2549 1 chr6B.!!$R1 775
24 TraesCS2A01G205800 chr4B 509579655 509580346 691 True 424.0 424 78.0250 929 1643 1 chr4B.!!$R1 714

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
273 306 0.681564 TCCTCTCCTCTTCAGTCGCC 60.682 60.0 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2145 5920 0.179187 CAGAGCTCGTCGTCGTGAAT 60.179 55.0 8.37 0.0 38.33 2.57 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
98 99 0.971386 GAGGGTGTTTCCGACAGGTA 59.029 55.000 0.00 0.0 39.39 3.08
123 125 1.313772 CAATTTGGGTGACGTGTCCA 58.686 50.000 0.00 0.0 0.00 4.02
191 193 3.062466 CGAGAGACAGACCGCCCA 61.062 66.667 0.00 0.0 0.00 5.36
207 215 1.695114 CCCATGCCCGACCACATCTA 61.695 60.000 0.00 0.0 0.00 1.98
232 244 0.810648 CTCTCTCTGCTCTCACGCTT 59.189 55.000 0.00 0.0 0.00 4.68
265 298 1.622173 CCCTCTTGCTCCTCTCCTCTT 60.622 57.143 0.00 0.0 0.00 2.85
266 299 1.756538 CCTCTTGCTCCTCTCCTCTTC 59.243 57.143 0.00 0.0 0.00 2.87
267 300 2.455557 CTCTTGCTCCTCTCCTCTTCA 58.544 52.381 0.00 0.0 0.00 3.02
268 301 2.428171 CTCTTGCTCCTCTCCTCTTCAG 59.572 54.545 0.00 0.0 0.00 3.02
269 302 2.178580 CTTGCTCCTCTCCTCTTCAGT 58.821 52.381 0.00 0.0 0.00 3.41
270 303 1.846007 TGCTCCTCTCCTCTTCAGTC 58.154 55.000 0.00 0.0 0.00 3.51
271 304 0.738389 GCTCCTCTCCTCTTCAGTCG 59.262 60.000 0.00 0.0 0.00 4.18
272 305 0.738389 CTCCTCTCCTCTTCAGTCGC 59.262 60.000 0.00 0.0 0.00 5.19
273 306 0.681564 TCCTCTCCTCTTCAGTCGCC 60.682 60.000 0.00 0.0 0.00 5.54
274 307 1.431440 CTCTCCTCTTCAGTCGCCG 59.569 63.158 0.00 0.0 0.00 6.46
487 571 2.151202 ACAATTGATGAGCCGTCGTTT 58.849 42.857 13.59 0.0 0.00 3.60
573 657 3.624777 CATTTGAGGGGATAAGCACTGT 58.375 45.455 0.00 0.0 0.00 3.55
1196 4775 5.250982 TGATGCTGAGAACATTTCAGTGAT 58.749 37.500 0.00 0.0 43.12 3.06
1359 4938 6.843333 TGATCTCTGATAAGAGGACTTTGGAT 59.157 38.462 7.28 0.0 37.53 3.41
1428 5049 3.376234 GCATTGCTGAGCTGATGAAACTA 59.624 43.478 20.13 0.0 0.00 2.24
1431 5052 6.561614 CATTGCTGAGCTGATGAAACTAAAT 58.438 36.000 5.83 0.0 0.00 1.40
1785 5434 7.836842 TGATAACACTGACAGCAAGTAGATAA 58.163 34.615 1.25 0.0 0.00 1.75
1788 5437 5.230942 ACACTGACAGCAAGTAGATAACAC 58.769 41.667 1.25 0.0 0.00 3.32
2107 5882 2.231478 CTCTTCTTCTTGGTCGGCACTA 59.769 50.000 0.00 0.0 0.00 2.74
2145 5920 2.660064 GCCGCCCTCCTCTTCTTGA 61.660 63.158 0.00 0.0 0.00 3.02
2171 5946 1.006102 CGACGAGCTCTGGGTTGTT 60.006 57.895 12.85 0.0 37.65 2.83
2172 5947 0.242825 CGACGAGCTCTGGGTTGTTA 59.757 55.000 12.85 0.0 37.65 2.41
2214 5989 3.070015 CCACTTCAATTGGGCTGTTCTTT 59.930 43.478 5.42 0.0 0.00 2.52
2252 6027 3.075005 GACGGGTGCCAGGAGCTA 61.075 66.667 0.00 0.0 44.23 3.32
2270 6045 3.136077 AGCTACACATCAGGCTCATCATT 59.864 43.478 0.00 0.0 0.00 2.57
2294 6096 1.406614 GGAGTCGGAGGAGAGTACGAA 60.407 57.143 0.00 0.0 37.08 3.85
2307 6109 2.753452 GAGTACGAAGACCTCATCCACA 59.247 50.000 0.00 0.0 0.00 4.17
2423 6237 0.395311 CGCCTCTCCCAGTAGGTGTA 60.395 60.000 0.00 0.0 38.36 2.90
2440 6254 2.006415 TAGTTGATGGGGGCTGGGG 61.006 63.158 0.00 0.0 0.00 4.96
2498 6312 1.940883 GACGGCGTGGTGGATGAGTA 61.941 60.000 21.19 0.0 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 143 1.067635 GTCGGTCTTAAGGTAACGGCA 60.068 52.381 1.85 0.0 46.39 5.69
191 193 1.050988 AGCTAGATGTGGTCGGGCAT 61.051 55.000 0.00 0.0 33.71 4.40
207 215 1.077501 AGAGCAGAGAGAGCGAGCT 60.078 57.895 0.00 0.0 38.43 4.09
288 338 2.659063 CGCTCCAGGACACCATGGA 61.659 63.158 21.47 0.0 43.34 3.41
447 531 4.033009 TGTAGCTGGGATCTGAGAAATCA 58.967 43.478 0.00 0.0 0.00 2.57
487 571 2.557056 CAAGTCGTCAGTAAGACCCTCA 59.443 50.000 0.00 0.0 44.66 3.86
497 581 4.816385 ACAAATCACATTCAAGTCGTCAGT 59.184 37.500 0.00 0.0 0.00 3.41
573 657 1.067295 ACAGGCAATGAACCTCCTCA 58.933 50.000 0.00 0.0 34.42 3.86
1196 4775 1.689984 TGTCATGCTGCTTTCCACAA 58.310 45.000 0.00 0.0 0.00 3.33
1359 4938 5.357742 TCTTCAGGTCAGCATAGCAAATA 57.642 39.130 0.00 0.0 0.00 1.40
1428 5049 5.246981 TCTCCATGGTCAACTTCTCATTT 57.753 39.130 12.58 0.0 0.00 2.32
1431 5052 3.903714 TCTTCTCCATGGTCAACTTCTCA 59.096 43.478 12.58 0.0 0.00 3.27
1479 5100 6.070824 TGTTGCTATCACCTATTGTCTTGAGA 60.071 38.462 0.00 0.0 0.00 3.27
1785 5434 5.692204 GCTATCTATGTTCAGTTATGCGTGT 59.308 40.000 0.00 0.0 0.00 4.49
1788 5437 6.422100 ACTTGCTATCTATGTTCAGTTATGCG 59.578 38.462 0.00 0.0 0.00 4.73
1970 5737 7.141100 AGAAGAAAAAGTTCAGTTTCGTCAA 57.859 32.000 13.39 0.0 41.66 3.18
2107 5882 0.326264 GGTGAAGATGTGGTGGAGCT 59.674 55.000 0.00 0.0 0.00 4.09
2145 5920 0.179187 CAGAGCTCGTCGTCGTGAAT 60.179 55.000 8.37 0.0 38.33 2.57
2241 6016 0.538584 CTGATGTGTAGCTCCTGGCA 59.461 55.000 0.00 0.0 44.79 4.92
2252 6027 2.240414 TCCAATGATGAGCCTGATGTGT 59.760 45.455 0.00 0.0 0.00 3.72
2270 6045 1.208844 ACTCTCCTCCGACTCCTCCA 61.209 60.000 0.00 0.0 0.00 3.86
2294 6096 0.741326 CGACGATGTGGATGAGGTCT 59.259 55.000 0.00 0.0 0.00 3.85
2307 6109 2.695127 ACTACTCCTCTGACGACGAT 57.305 50.000 0.00 0.0 0.00 3.73
2423 6237 3.350163 CCCCAGCCCCCATCAACT 61.350 66.667 0.00 0.0 0.00 3.16
2440 6254 4.517703 CGACGTCGTCCTCGCTCC 62.518 72.222 29.08 0.0 36.96 4.70
2498 6312 0.394938 TGCACGTTGGTGGATGTACT 59.605 50.000 0.00 0.0 44.54 2.73


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

AutoCloner maintained by Alex Coulton.