Multiple sequence alignment - TraesCS2D01G542900

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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 TraesCS2D01G542900 chr2D 100.000 2354 0 0 1 2354 621128458 621126105 0.000000e+00 4348
1 TraesCS2D01G542900 chr2D 95.981 647 20 4 693 1333 621309114 621308468 0.000000e+00 1046
2 TraesCS2D01G542900 chr2D 95.565 451 17 1 886 1333 621135236 621134786 0.000000e+00 719
3 TraesCS2D01G542900 chr2D 82.432 518 74 8 819 1332 621313595 621313091 9.990000e-119 436
4 TraesCS2D01G542900 chr2D 82.745 510 69 12 827 1329 621315454 621315951 9.990000e-119 436
5 TraesCS2D01G542900 chr2D 78.895 507 58 26 270 741 621137051 621136559 4.920000e-77 298
6 TraesCS2D01G542900 chr2D 83.439 314 35 11 153 457 621312063 621311758 2.300000e-70 276
7 TraesCS2D01G542900 chr2D 98.131 107 2 0 1330 1436 621308012 621307906 1.110000e-43 187
8 TraesCS2D01G542900 chr2D 90.654 107 10 0 1330 1436 621134404 621134298 2.440000e-30 143
9 TraesCS2D01G542900 chr2D 92.000 100 4 3 797 896 621135737 621135642 1.130000e-28 137
10 TraesCS2D01G542900 chr2B 96.260 1337 46 2 1 1333 762050013 762048677 0.000000e+00 2189
11 TraesCS2D01G542900 chr2B 92.958 213 13 1 680 892 762067783 762067573 2.270000e-80 309
12 TraesCS2D01G542900 chr2B 98.113 106 2 0 1331 1436 762048220 762048115 4.000000e-43 185
13 TraesCS2D01G542900 chr7D 97.428 933 16 6 1425 2354 612975459 612976386 0.000000e+00 1583
14 TraesCS2D01G542900 chr7D 85.246 122 9 8 1426 1547 219566737 219566625 1.480000e-22 117
15 TraesCS2D01G542900 chr7A 95.054 930 31 7 1426 2354 704379073 704379988 0.000000e+00 1448
16 TraesCS2D01G542900 chr7A 89.194 546 46 10 1426 1969 45821354 45820820 0.000000e+00 669
17 TraesCS2D01G542900 chr7A 92.448 384 23 5 1973 2354 45820108 45819729 5.720000e-151 544
18 TraesCS2D01G542900 chr7A 89.147 387 36 5 1973 2354 29700794 29700409 5.890000e-131 477
19 TraesCS2D01G542900 chr7A 89.894 188 16 2 1433 1620 29702139 29701955 3.020000e-59 239
20 TraesCS2D01G542900 chrUn 93.645 598 26 7 1 592 314617337 314616746 0.000000e+00 883
21 TraesCS2D01G542900 chrUn 92.857 210 13 1 680 889 307392208 307392415 1.060000e-78 303
22 TraesCS2D01G542900 chrUn 95.536 112 5 0 590 701 314616362 314616251 1.860000e-41 180
23 TraesCS2D01G542900 chr4A 86.322 541 48 9 1432 1969 567294631 567295148 1.220000e-157 566
24 TraesCS2D01G542900 chr4A 93.305 239 14 2 2117 2354 567295838 567296075 3.720000e-93 351
25 TraesCS2D01G542900 chr4A 92.357 157 8 3 1973 2128 567295666 567295819 1.100000e-53 220
26 TraesCS2D01G542900 chr2A 94.231 364 13 2 460 815 752975768 752975405 1.230000e-152 549
27 TraesCS2D01G542900 chr2A 90.888 428 9 3 1 428 752976165 752975768 4.420000e-152 547
28 TraesCS2D01G542900 chr2A 90.404 396 16 5 810 1202 752975150 752974774 3.490000e-138 501
29 TraesCS2D01G542900 chr2A 80.091 658 72 29 264 889 753040023 753039393 3.590000e-118 435
30 TraesCS2D01G542900 chr2A 82.353 510 71 15 827 1329 753060742 753061239 2.160000e-115 425
31 TraesCS2D01G542900 chr2A 81.818 506 79 11 831 1332 752996725 752996229 1.680000e-111 412
32 TraesCS2D01G542900 chr2A 81.818 506 79 11 831 1332 753004610 753004114 1.680000e-111 412
33 TraesCS2D01G542900 chr2A 77.609 594 96 25 760 1329 753017627 753018207 2.260000e-85 326
34 TraesCS2D01G542900 chr2A 93.213 221 10 3 679 894 753002462 753002242 1.050000e-83 320
35 TraesCS2D01G542900 chr2A 81.424 323 42 9 153 466 752994940 752994627 5.020000e-62 248
36 TraesCS2D01G542900 chr2A 81.115 323 43 9 153 466 753003076 753002763 2.340000e-60 243
37 TraesCS2D01G542900 chr2A 97.196 107 3 0 1330 1436 752925941 752925835 5.170000e-42 182
38 TraesCS2D01G542900 chr2A 92.553 94 4 1 679 769 752994326 752994233 5.280000e-27 132
39 TraesCS2D01G542900 chr4B 91.927 384 25 5 1973 2354 630972433 630972054 1.240000e-147 532
40 TraesCS2D01G542900 chr4B 86.593 455 39 10 1526 1969 630973477 630973034 1.270000e-132 483
41 TraesCS2D01G542900 chr7B 83.704 540 66 10 1432 1969 415231720 415231201 7.560000e-135 490
42 TraesCS2D01G542900 chr7B 87.047 386 44 5 1973 2354 415230664 415230281 4.650000e-117 431
43 TraesCS2D01G542900 chr6B 89.583 384 34 5 1973 2354 159942192 159942571 1.270000e-132 483
44 TraesCS2D01G542900 chr6B 89.172 314 27 5 1432 1744 159941214 159941521 3.670000e-103 385
45 TraesCS2D01G542900 chr1B 84.170 518 57 13 1426 1936 543885969 543886468 1.640000e-131 479
46 TraesCS2D01G542900 chr1B 88.012 342 29 8 2021 2354 543887028 543887365 6.100000e-106 394
47 TraesCS2D01G542900 chr1B 84.861 251 21 8 1426 1670 543885585 543885824 1.090000e-58 237


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 TraesCS2D01G542900 chr2D 621126105 621128458 2353 True 4348.000000 4348 100.000000 1 2354 1 chr2D.!!$R1 2353
1 TraesCS2D01G542900 chr2D 621307906 621313595 5689 True 486.250000 1046 89.995750 153 1436 4 chr2D.!!$R3 1283
2 TraesCS2D01G542900 chr2D 621134298 621137051 2753 True 324.250000 719 89.278500 270 1436 4 chr2D.!!$R2 1166
3 TraesCS2D01G542900 chr2B 762048115 762050013 1898 True 1187.000000 2189 97.186500 1 1436 2 chr2B.!!$R2 1435
4 TraesCS2D01G542900 chr7D 612975459 612976386 927 False 1583.000000 1583 97.428000 1425 2354 1 chr7D.!!$F1 929
5 TraesCS2D01G542900 chr7A 704379073 704379988 915 False 1448.000000 1448 95.054000 1426 2354 1 chr7A.!!$F1 928
6 TraesCS2D01G542900 chr7A 45819729 45821354 1625 True 606.500000 669 90.821000 1426 2354 2 chr7A.!!$R2 928
7 TraesCS2D01G542900 chr7A 29700409 29702139 1730 True 358.000000 477 89.520500 1433 2354 2 chr7A.!!$R1 921
8 TraesCS2D01G542900 chrUn 314616251 314617337 1086 True 531.500000 883 94.590500 1 701 2 chrUn.!!$R1 700
9 TraesCS2D01G542900 chr4A 567294631 567296075 1444 False 379.000000 566 90.661333 1432 2354 3 chr4A.!!$F1 922
10 TraesCS2D01G542900 chr2A 752974774 752976165 1391 True 532.333333 549 91.841000 1 1202 3 chr2A.!!$R3 1201
11 TraesCS2D01G542900 chr2A 753039393 753040023 630 True 435.000000 435 80.091000 264 889 1 chr2A.!!$R2 625
12 TraesCS2D01G542900 chr2A 753017627 753018207 580 False 326.000000 326 77.609000 760 1329 1 chr2A.!!$F1 569
13 TraesCS2D01G542900 chr2A 753002242 753004610 2368 True 325.000000 412 85.382000 153 1332 3 chr2A.!!$R5 1179
14 TraesCS2D01G542900 chr2A 752994233 752996725 2492 True 264.000000 412 85.265000 153 1332 3 chr2A.!!$R4 1179
15 TraesCS2D01G542900 chr4B 630972054 630973477 1423 True 507.500000 532 89.260000 1526 2354 2 chr4B.!!$R1 828
16 TraesCS2D01G542900 chr7B 415230281 415231720 1439 True 460.500000 490 85.375500 1432 2354 2 chr7B.!!$R1 922
17 TraesCS2D01G542900 chr6B 159941214 159942571 1357 False 434.000000 483 89.377500 1432 2354 2 chr6B.!!$F1 922
18 TraesCS2D01G542900 chr1B 543885585 543887365 1780 False 370.000000 479 85.681000 1426 2354 3 chr1B.!!$F1 928

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
803 5917 0.103026 CTGCATGCCTAGCTCGTGTA 59.897 55.0 16.68 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2050 10302 0.326595 TTAGACGGAAGCATTGGCCA 59.673 50.0 0.0 0.0 42.56 5.36 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
668 2568 1.084370 GCGTCGGTATTGAAGCAGCT 61.084 55.000 0.00 0.00 42.01 4.24
803 5917 0.103026 CTGCATGCCTAGCTCGTGTA 59.897 55.000 16.68 0.00 0.00 2.90
841 6223 0.533491 TACGCTTTCACCTACCGCAT 59.467 50.000 0.00 0.00 0.00 4.73
1006 6811 2.679342 GGTCCTACTGCCATGGCCA 61.679 63.158 33.44 19.88 41.09 5.36
1335 7385 1.034292 GCTTCCCTGGCCATTGTCTC 61.034 60.000 5.51 0.00 0.00 3.36
1337 7387 1.198094 TTCCCTGGCCATTGTCTCGA 61.198 55.000 5.51 0.00 0.00 4.04
1340 7390 1.533625 CCTGGCCATTGTCTCGAAAA 58.466 50.000 5.51 0.00 0.00 2.29
1344 7394 4.261322 CCTGGCCATTGTCTCGAAAATATG 60.261 45.833 5.51 0.00 0.00 1.78
1348 7398 6.545666 TGGCCATTGTCTCGAAAATATGTATT 59.454 34.615 0.00 0.00 0.00 1.89
1468 7761 1.574428 GCAAGGTGCGTTTCGTCAT 59.426 52.632 0.00 0.00 31.71 3.06
1863 8856 1.229625 ATCAGTGAGCCACCTGGGA 60.230 57.895 0.00 0.00 40.01 4.37
2105 10366 3.691118 TCAATCTTTCTCCCGATGCAAAG 59.309 43.478 0.00 0.00 0.00 2.77
2167 10650 9.935241 TTTTCTATATCTTCATGTCATAGGAGC 57.065 33.333 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
266 1668 8.430801 AGTGATGAAAGATTTTCGAAGGATAG 57.569 34.615 0.00 0.00 0.00 2.08
308 1711 2.248280 TATACAATGGCGCCAACGAT 57.752 45.000 36.33 24.67 43.93 3.73
439 1853 2.166459 TCTCAGACCACGGATTAAGCAG 59.834 50.000 0.00 0.00 0.00 4.24
566 2080 1.150986 AGTAGATCCATAGGGCCAGCT 59.849 52.381 6.18 0.00 0.00 4.24
766 5388 2.751806 GCAGGTAGTACGTACTTGGTCT 59.248 50.000 31.58 19.75 38.80 3.85
803 5917 3.681897 CGTAGAATATAGAGTACGCGGGT 59.318 47.826 12.47 10.91 32.65 5.28
1006 6811 2.169352 CGAGGAGAATGGTTCTGGTGAT 59.831 50.000 0.00 0.00 40.87 3.06
1106 6914 1.597027 GTGCTGTAGTTGGTGCCGT 60.597 57.895 0.00 0.00 0.00 5.68
1863 8856 1.618343 CGGGATGGCTTTCCACTTTTT 59.382 47.619 8.90 0.00 46.92 1.94
2050 10302 0.326595 TTAGACGGAAGCATTGGCCA 59.673 50.000 0.00 0.00 42.56 5.36


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

AutoCloner maintained by Alex Coulton.