Multiple sequence alignment - TraesCS7A01G095000

Loading Multiple Alignment...

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 TraesCS7A01G095000 chr7A 100.000 2688 0 0 1 2688 57964024 57961337 0.000000e+00 4964
1 TraesCS7A01G095000 chr6A 97.593 2701 45 8 1 2688 315406070 315408763 0.000000e+00 4610
2 TraesCS7A01G095000 chr6A 87.769 1161 92 23 1220 2344 70063906 70065052 0.000000e+00 1312
3 TraesCS7A01G095000 chr6A 89.866 671 42 14 396 1047 70063245 70063908 0.000000e+00 839
4 TraesCS7A01G095000 chr4B 96.213 1637 55 5 1057 2688 633178312 633176678 0.000000e+00 2673
5 TraesCS7A01G095000 chr4B 96.993 1031 24 1 1 1024 633179339 633178309 0.000000e+00 1725
6 TraesCS7A01G095000 chr4B 87.166 1161 99 23 1220 2344 125739564 125740710 0.000000e+00 1273
7 TraesCS7A01G095000 chr3D 87.984 2222 168 47 396 2561 33867197 33865019 0.000000e+00 2532
8 TraesCS7A01G095000 chr2A 86.461 2105 195 45 502 2557 552865042 552862979 0.000000e+00 2226
9 TraesCS7A01G095000 chr2A 85.913 575 46 19 1831 2373 445929320 445928749 4.990000e-162 580
10 TraesCS7A01G095000 chr2A 96.721 122 4 0 2562 2683 552862569 552862448 1.260000e-48 204
11 TraesCS7A01G095000 chr7B 88.881 1484 105 19 396 1855 1757851 1759298 0.000000e+00 1772
12 TraesCS7A01G095000 chr7B 88.538 1012 79 19 1395 2373 693933330 693932323 0.000000e+00 1192
13 TraesCS7A01G095000 chr7B 95.935 123 5 0 2561 2683 693932036 693931914 1.630000e-47 200
14 TraesCS7A01G095000 chr5A 98.138 913 9 2 1 905 436605109 436606021 0.000000e+00 1585
15 TraesCS7A01G095000 chr5A 98.049 615 10 2 2076 2688 436608120 436608734 0.000000e+00 1068
16 TraesCS7A01G095000 chr1A 87.931 1102 98 23 505 1595 517327301 517328378 0.000000e+00 1266
17 TraesCS7A01G095000 chr1A 96.000 125 5 0 2559 2683 517330339 517330463 1.260000e-48 204
18 TraesCS7A01G095000 chr1A 90.833 120 8 1 396 512 517325761 517325880 9.960000e-35 158
19 TraesCS7A01G095000 chr4D 86.524 1165 90 32 1220 2344 487999872 488001009 0.000000e+00 1219
20 TraesCS7A01G095000 chr4D 89.655 667 45 15 396 1047 487999217 487999874 0.000000e+00 828
21 TraesCS7A01G095000 chr3B 87.587 1007 79 16 1395 2366 8745307 8744312 0.000000e+00 1125
22 TraesCS7A01G095000 chr3B 96.748 123 4 0 2561 2683 8744019 8743897 3.510000e-49 206
23 TraesCS7A01G095000 chr3B 93.333 75 5 0 1 75 778415504 778415578 7.870000e-21 111
24 TraesCS7A01G095000 chr3A 88.213 806 80 11 798 1596 36801821 36801024 0.000000e+00 948
25 TraesCS7A01G095000 chr3A 85.692 643 55 15 1780 2390 324102842 324102205 0.000000e+00 643
26 TraesCS7A01G095000 chr3A 83.709 577 62 16 2014 2561 36800548 36799975 1.430000e-142 516
27 TraesCS7A01G095000 chr4A 87.219 579 50 17 1809 2373 293331393 293330825 2.920000e-179 638
28 TraesCS7A01G095000 chr2B 92.058 277 19 3 2288 2563 541601751 541602025 1.170000e-103 387
29 TraesCS7A01G095000 chr2B 94.444 126 7 0 2563 2688 541602343 541602468 7.590000e-46 195
30 TraesCS7A01G095000 chr5D 97.541 122 3 0 2562 2683 548609866 548609987 2.710000e-50 209


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 TraesCS7A01G095000 chr7A 57961337 57964024 2687 True 4964.000000 4964 100.0000 1 2688 1 chr7A.!!$R1 2687
1 TraesCS7A01G095000 chr6A 315406070 315408763 2693 False 4610.000000 4610 97.5930 1 2688 1 chr6A.!!$F1 2687
2 TraesCS7A01G095000 chr6A 70063245 70065052 1807 False 1075.500000 1312 88.8175 396 2344 2 chr6A.!!$F2 1948
3 TraesCS7A01G095000 chr4B 633176678 633179339 2661 True 2199.000000 2673 96.6030 1 2688 2 chr4B.!!$R1 2687
4 TraesCS7A01G095000 chr4B 125739564 125740710 1146 False 1273.000000 1273 87.1660 1220 2344 1 chr4B.!!$F1 1124
5 TraesCS7A01G095000 chr3D 33865019 33867197 2178 True 2532.000000 2532 87.9840 396 2561 1 chr3D.!!$R1 2165
6 TraesCS7A01G095000 chr2A 552862448 552865042 2594 True 1215.000000 2226 91.5910 502 2683 2 chr2A.!!$R2 2181
7 TraesCS7A01G095000 chr2A 445928749 445929320 571 True 580.000000 580 85.9130 1831 2373 1 chr2A.!!$R1 542
8 TraesCS7A01G095000 chr7B 1757851 1759298 1447 False 1772.000000 1772 88.8810 396 1855 1 chr7B.!!$F1 1459
9 TraesCS7A01G095000 chr7B 693931914 693933330 1416 True 696.000000 1192 92.2365 1395 2683 2 chr7B.!!$R1 1288
10 TraesCS7A01G095000 chr5A 436605109 436608734 3625 False 1326.500000 1585 98.0935 1 2688 2 chr5A.!!$F1 2687
11 TraesCS7A01G095000 chr1A 517325761 517330463 4702 False 542.666667 1266 91.5880 396 2683 3 chr1A.!!$F1 2287
12 TraesCS7A01G095000 chr4D 487999217 488001009 1792 False 1023.500000 1219 88.0895 396 2344 2 chr4D.!!$F1 1948
13 TraesCS7A01G095000 chr3B 8743897 8745307 1410 True 665.500000 1125 92.1675 1395 2683 2 chr3B.!!$R1 1288
14 TraesCS7A01G095000 chr3A 36799975 36801821 1846 True 732.000000 948 85.9610 798 2561 2 chr3A.!!$R2 1763
15 TraesCS7A01G095000 chr3A 324102205 324102842 637 True 643.000000 643 85.6920 1780 2390 1 chr3A.!!$R1 610
16 TraesCS7A01G095000 chr4A 293330825 293331393 568 True 638.000000 638 87.2190 1809 2373 1 chr4A.!!$R1 564
17 TraesCS7A01G095000 chr2B 541601751 541602468 717 False 291.000000 387 93.2510 2288 2688 2 chr2B.!!$F1 400


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
92 93 2.819608 ACATGCATTTCCGTAACAGCTT 59.180 40.909 0.00 0.0 0.00 3.74 F
714 2167 6.092670 TGGAAAATTGCATTTCTCTAGTCTCG 59.907 38.462 11.51 0.0 38.92 4.04 F
1344 3404 0.670162 TTGCAGGCTGAAGAACTTGC 59.330 50.000 20.86 0.0 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1122 2606 0.035056 AGGGCCTCATGTTTTCTCCG 60.035 55.000 0.00 0.0 0.00 4.63 R
1562 3632 5.398603 TCTTCAGGTTGTTTCTGCAAAAA 57.601 34.783 0.00 0.0 32.63 1.94 R
2159 5960 7.063308 CCGTATTTGAACAAATAGCAAGCAAAT 59.937 33.333 16.86 0.0 42.09 2.32 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
92 93 2.819608 ACATGCATTTCCGTAACAGCTT 59.180 40.909 0.00 0.00 0.00 3.74
714 2167 6.092670 TGGAAAATTGCATTTCTCTAGTCTCG 59.907 38.462 11.51 0.00 38.92 4.04
1344 3404 0.670162 TTGCAGGCTGAAGAACTTGC 59.330 50.000 20.86 0.00 0.00 4.01
1454 3520 8.091449 TTGTTAGTCACACATACACATCATGTA 58.909 33.333 0.00 0.00 40.89 2.29
1562 3632 4.347607 AGGTGCCTCATTTGCTCTATTTT 58.652 39.130 0.00 0.00 0.00 1.82
1563 3633 4.774200 AGGTGCCTCATTTGCTCTATTTTT 59.226 37.500 0.00 0.00 0.00 1.94
2159 5960 8.712285 ATTTAGTACGCAAGCTAAACTGAATA 57.288 30.769 0.00 0.00 39.18 1.75
2258 6065 7.229306 TGAAGCTTGCTCTCTTTTAAAGATCAA 59.771 33.333 2.10 11.02 36.82 2.57
2435 6254 4.133820 CAACATATGCGAACCCCTATTGA 58.866 43.478 1.58 0.00 0.00 2.57
2538 6357 8.833231 ACACTATTACATATATGACTGTTGGC 57.167 34.615 19.63 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 7.487484 TGTGCAAATTAATTGTCAGAGTTTGA 58.513 30.769 0.39 0.0 41.32 2.69
714 2167 0.318699 GCGCCAAGGAAGAACAAACC 60.319 55.000 0.00 0.0 0.00 3.27
1064 2548 8.732746 AGCTCTCAACTTACTTTTGTTTTCTA 57.267 30.769 0.00 0.0 0.00 2.10
1122 2606 0.035056 AGGGCCTCATGTTTTCTCCG 60.035 55.000 0.00 0.0 0.00 4.63
1344 3404 4.868314 TCATCTCTCTGCATGTCATAGG 57.132 45.455 0.00 0.0 0.00 2.57
1454 3520 6.389906 GTGCATGGCTGTACTAAAGAAAAAT 58.610 36.000 0.00 0.0 35.36 1.82
1562 3632 5.398603 TCTTCAGGTTGTTTCTGCAAAAA 57.601 34.783 0.00 0.0 32.63 1.94
1563 3633 5.398603 TTCTTCAGGTTGTTTCTGCAAAA 57.601 34.783 0.00 0.0 32.63 2.44
2159 5960 7.063308 CCGTATTTGAACAAATAGCAAGCAAAT 59.937 33.333 16.86 0.0 42.09 2.32



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

AutoCloner maintained by Alex Coulton.