Multiple sequence alignment - TraesCS2A01G048400

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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 TraesCS2A01G048400 chr2A 100.000 2392 0 0 1 2392 18647479 18645088 0.000000e+00 4418.0
1 TraesCS2A01G048400 chr2A 87.643 1481 150 16 1 1462 18614808 18613342 0.000000e+00 1690.0
2 TraesCS2A01G048400 chr2A 86.269 1158 113 20 590 1713 18675171 18674026 0.000000e+00 1216.0
3 TraesCS2A01G048400 chr2A 87.654 648 60 8 317 946 18676048 18675403 0.000000e+00 736.0
4 TraesCS2A01G048400 chr2A 93.307 254 17 0 1460 1713 18613219 18612966 2.240000e-100 375.0
5 TraesCS2A01G048400 chr2A 73.373 338 51 28 1870 2177 517929422 517929750 3.280000e-14 89.8
6 TraesCS2A01G048400 chr2D 95.641 2409 83 7 1 2392 17183368 17180965 0.000000e+00 3847.0
7 TraesCS2A01G048400 chr2D 95.475 2409 82 11 1 2392 17327700 17325302 0.000000e+00 3819.0
8 TraesCS2A01G048400 chr2D 85.689 1146 91 31 590 1704 17237728 17236625 0.000000e+00 1140.0
9 TraesCS2A01G048400 chr2D 79.710 138 17 4 1919 2047 383354761 383354896 3.280000e-14 89.8
10 TraesCS2A01G048400 chr2B 87.341 1730 186 17 1 1713 29055896 29054183 0.000000e+00 1951.0
11 TraesCS2A01G048400 chr2B 87.031 1704 180 26 1 1676 29979732 29981422 0.000000e+00 1884.0
12 TraesCS2A01G048400 chr2B 88.374 1144 101 15 170 1292 28996224 28995092 0.000000e+00 1347.0
13 TraesCS2A01G048400 chr2B 84.370 1158 117 36 590 1713 29871897 29873024 0.000000e+00 1077.0
14 TraesCS2A01G048400 chr2B 82.870 683 83 19 1740 2392 28992549 28991871 1.230000e-162 582.0
15 TraesCS2A01G048400 chr2B 90.094 424 32 4 1290 1713 28993419 28993006 2.090000e-150 542.0
16 TraesCS2A01G048400 chr2B 84.483 290 36 8 317 598 29871442 29871730 6.510000e-71 278.0
17 TraesCS2A01G048400 chr2B 86.486 185 18 6 1740 1918 29053780 29053597 1.880000e-46 196.0
18 TraesCS2A01G048400 chr4B 80.364 275 38 12 1912 2174 41756041 41755771 6.750000e-46 195.0
19 TraesCS2A01G048400 chr1D 79.842 253 37 9 1919 2160 435753724 435753475 3.160000e-39 172.0
20 TraesCS2A01G048400 chr1D 82.558 172 27 3 1913 2083 255822751 255822920 5.330000e-32 148.0
21 TraesCS2A01G048400 chr1A 83.140 172 26 3 1913 2083 328242319 328242488 1.150000e-33 154.0
22 TraesCS2A01G048400 chr1A 97.436 39 0 1 1881 1918 22070264 22070302 5.520000e-07 65.8
23 TraesCS2A01G048400 chr7D 76.534 277 40 15 1919 2187 555056836 555057095 6.940000e-26 128.0
24 TraesCS2A01G048400 chr7D 73.962 265 37 14 1864 2103 590193396 590193139 7.090000e-11 78.7
25 TraesCS2A01G048400 chr3D 81.944 144 23 3 1993 2135 607903499 607903640 4.180000e-23 119.0
26 TraesCS2A01G048400 chr3B 79.195 149 23 4 1919 2059 789220039 789219891 1.960000e-16 97.1


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 TraesCS2A01G048400 chr2A 18645088 18647479 2391 True 4418.000000 4418 100.000000 1 2392 1 chr2A.!!$R1 2391
1 TraesCS2A01G048400 chr2A 18612966 18614808 1842 True 1032.500000 1690 90.475000 1 1713 2 chr2A.!!$R2 1712
2 TraesCS2A01G048400 chr2A 18674026 18676048 2022 True 976.000000 1216 86.961500 317 1713 2 chr2A.!!$R3 1396
3 TraesCS2A01G048400 chr2D 17180965 17183368 2403 True 3847.000000 3847 95.641000 1 2392 1 chr2D.!!$R1 2391
4 TraesCS2A01G048400 chr2D 17325302 17327700 2398 True 3819.000000 3819 95.475000 1 2392 1 chr2D.!!$R3 2391
5 TraesCS2A01G048400 chr2D 17236625 17237728 1103 True 1140.000000 1140 85.689000 590 1704 1 chr2D.!!$R2 1114
6 TraesCS2A01G048400 chr2B 29979732 29981422 1690 False 1884.000000 1884 87.031000 1 1676 1 chr2B.!!$F1 1675
7 TraesCS2A01G048400 chr2B 29053597 29055896 2299 True 1073.500000 1951 86.913500 1 1918 2 chr2B.!!$R2 1917
8 TraesCS2A01G048400 chr2B 28991871 28996224 4353 True 823.666667 1347 87.112667 170 2392 3 chr2B.!!$R1 2222
9 TraesCS2A01G048400 chr2B 29871442 29873024 1582 False 677.500000 1077 84.426500 317 1713 2 chr2B.!!$F2 1396

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
953 1595 3.507622 AGGTGAATGACAAGCTTTTAGCC 59.492 43.478 0.0 0.0 43.77 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 5107 3.983533 ACTAGAGCCAAGAGGATACCT 57.016 47.619 0.0 0.0 36.89 3.08 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
66 67 6.265196 GCCACAATTCCCTTAATATGTCATCA 59.735 38.462 0.00 0.00 0.00 3.07
136 139 6.485171 ACTAGAACCAAGATTACCATTTGCT 58.515 36.000 0.00 0.00 0.00 3.91
279 286 7.557358 TCCAAAAAGATTAGCAAGATCATAGCA 59.443 33.333 0.00 0.00 0.00 3.49
431 448 6.401367 GCAAATGATGAAACAAATAGTGTGGC 60.401 38.462 0.00 0.00 40.60 5.01
550 568 6.595716 GCTGATATGTAGTTTCAAAGTCACCT 59.404 38.462 0.00 0.00 0.00 4.00
740 1378 8.764524 AGAGACACATGATAAAGTCTAACAAC 57.235 34.615 0.00 0.00 41.10 3.32
953 1595 3.507622 AGGTGAATGACAAGCTTTTAGCC 59.492 43.478 0.00 0.00 43.77 3.93
978 1620 5.565439 GCACTTCAGCAATATCCTTGTTTGT 60.565 40.000 0.00 0.00 0.00 2.83
1028 1670 8.736742 GTGCATTCGATGTTGTATTATTTCAAG 58.263 33.333 0.00 0.00 0.00 3.02
1054 1699 9.654663 GAACCCTTACCATATCAATCTATGTAC 57.345 37.037 0.00 0.00 0.00 2.90
1085 1731 9.836864 TTTTATACAGACTGCATAAGATGATGT 57.163 29.630 1.25 0.00 0.00 3.06
1240 1886 3.248266 GGAATGCAATGCAAGTGAAGAC 58.752 45.455 13.45 0.00 43.62 3.01
1246 1892 1.913778 ATGCAAGTGAAGACCATGCA 58.086 45.000 0.88 0.88 44.78 3.96
1282 1931 5.413309 AGTTCTGTTGATGGAAGGAGTAG 57.587 43.478 0.00 0.00 0.00 2.57
1676 4146 8.294954 TCAAATGTGAAGGGTTAAACAAGTAA 57.705 30.769 0.00 0.00 0.00 2.24
1874 4786 8.888579 AAACGGAGGATTGTAAGATAACTATG 57.111 34.615 0.00 0.00 0.00 2.23
1943 4884 3.819368 CATGCCACCTCACCATACAATA 58.181 45.455 0.00 0.00 0.00 1.90
2004 4945 5.612725 AAATCAACCACAACATTCAACCT 57.387 34.783 0.00 0.00 0.00 3.50
2007 4948 3.131933 TCAACCACAACATTCAACCTTGG 59.868 43.478 0.00 0.00 0.00 3.61
2372 5322 1.202830 ACTCGCCAAATGTACCAACCA 60.203 47.619 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 84 9.483489 TGAATCACTAGGGAAAACTATGTACTA 57.517 33.333 0.00 0.0 0.00 1.82
295 303 3.947910 ACATTGGCCATGTTCTTGAAG 57.052 42.857 6.09 0.0 44.40 3.02
431 448 1.205655 TCCTTGATCTCTTCAGCACCG 59.794 52.381 0.00 0.0 35.27 4.94
550 568 7.324935 TGCAATTCGAGGTGTACTTATTTAGA 58.675 34.615 0.00 0.0 0.00 2.10
953 1595 2.679837 ACAAGGATATTGCTGAAGTGCG 59.320 45.455 0.00 0.0 35.36 5.34
1028 1670 9.654663 GTACATAGATTGATATGGTAAGGGTTC 57.345 37.037 0.00 0.0 37.45 3.62
1240 1886 4.067896 ACTAGAAGTCAGTTTGTGCATGG 58.932 43.478 0.00 0.0 0.00 3.66
1246 1892 6.640518 TCAACAGAACTAGAAGTCAGTTTGT 58.359 36.000 0.00 0.0 36.38 2.83
1282 1931 0.613012 AATTTCCTCACCAGCAGGGC 60.613 55.000 0.00 0.0 42.05 5.19
1415 3745 4.611943 TCGCACTATGACTTATCTTCAGC 58.388 43.478 0.00 0.0 0.00 4.26
2163 5107 3.983533 ACTAGAGCCAAGAGGATACCT 57.016 47.619 0.00 0.0 36.89 3.08
2226 5175 5.341872 TTTCATATGCCCACTTTCCAATG 57.658 39.130 0.00 0.0 0.00 2.82
2337 5287 5.461032 TGGCGAGTTTACATTGGAAATTT 57.539 34.783 0.00 0.0 0.00 1.82


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

AutoCloner maintained by Alex Coulton.