Multiple sequence alignment - TraesCS3B01G544800

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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 TraesCS3B01G544800 chr3B 100.000 3237 0 0 1 3237 782173537 782170301 0.000000e+00 5978
1 TraesCS3B01G544800 chr3B 99.012 3238 31 1 1 3237 782256039 782252802 0.000000e+00 5801
2 TraesCS3B01G544800 chr3B 98.950 3238 27 2 1 3237 782214630 782211399 0.000000e+00 5784
3 TraesCS3B01G544800 chr3B 98.888 3238 25 4 1 3237 782297852 782294625 0.000000e+00 5770
4 TraesCS3B01G544800 chr5A 95.976 2187 51 20 663 2845 457099661 457101814 0.000000e+00 3517
5 TraesCS3B01G544800 chr5A 98.204 668 11 1 1 667 457098964 457099631 0.000000e+00 1166
6 TraesCS3B01G544800 chr5A 91.031 669 58 2 1 667 390556910 390557578 0.000000e+00 902
7 TraesCS3B01G544800 chr5A 87.835 485 50 7 1080 1558 390558240 390558721 7.840000e-156 560
8 TraesCS3B01G544800 chr7B 95.932 2188 51 21 663 2846 505221664 505219511 0.000000e+00 3513
9 TraesCS3B01G544800 chr7B 98.054 668 12 1 1 667 505222361 505221694 0.000000e+00 1160
10 TraesCS3B01G544800 chr2A 89.055 2211 172 32 663 2848 21632184 21634349 0.000000e+00 2678
11 TraesCS3B01G544800 chr2A 91.330 669 56 2 1 667 180214796 180214128 0.000000e+00 913
12 TraesCS3B01G544800 chr4A 97.937 1406 28 1 1440 2845 27194815 27193411 0.000000e+00 2435
13 TraesCS3B01G544800 chr4A 90.939 1810 131 18 1047 2844 698013234 698011446 0.000000e+00 2403
14 TraesCS3B01G544800 chr4D 97.597 1165 27 1 1682 2846 505348746 505347583 0.000000e+00 1995
15 TraesCS3B01G544800 chr4D 97.902 143 3 0 885 1027 505348908 505348766 6.930000e-62 248
16 TraesCS3B01G544800 chr4B 97.517 1168 28 1 1679 2846 42255569 42256735 0.000000e+00 1995
17 TraesCS3B01G544800 chr4B 97.902 143 3 0 885 1027 42255410 42255552 6.930000e-62 248
18 TraesCS3B01G544800 chr3D 97.597 1165 27 1 1682 2846 562176038 562174875 0.000000e+00 1995
19 TraesCS3B01G544800 chr3D 92.417 211 10 2 3033 3237 585878463 585878253 2.440000e-76 296
20 TraesCS3B01G544800 chr3D 95.506 178 8 0 2845 3022 585878710 585878533 5.290000e-73 285
21 TraesCS3B01G544800 chr6B 91.181 669 57 2 1 667 532351327 532351995 0.000000e+00 907
22 TraesCS3B01G544800 chr7A 91.031 669 58 2 1 667 31808115 31808783 0.000000e+00 902
23 TraesCS3B01G544800 chr7A 87.423 485 52 7 1080 1558 31809315 31809796 1.700000e-152 549
24 TraesCS3B01G544800 chr1B 88.796 714 74 4 1568 2280 150371624 150370916 0.000000e+00 870
25 TraesCS3B01G544800 chr5D 97.902 143 3 0 885 1027 468179801 468179659 6.930000e-62 248


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 TraesCS3B01G544800 chr3B 782170301 782173537 3236 True 5978.0 5978 100.0000 1 3237 1 chr3B.!!$R1 3236
1 TraesCS3B01G544800 chr3B 782252802 782256039 3237 True 5801.0 5801 99.0120 1 3237 1 chr3B.!!$R3 3236
2 TraesCS3B01G544800 chr3B 782211399 782214630 3231 True 5784.0 5784 98.9500 1 3237 1 chr3B.!!$R2 3236
3 TraesCS3B01G544800 chr3B 782294625 782297852 3227 True 5770.0 5770 98.8880 1 3237 1 chr3B.!!$R4 3236
4 TraesCS3B01G544800 chr5A 457098964 457101814 2850 False 2341.5 3517 97.0900 1 2845 2 chr5A.!!$F2 2844
5 TraesCS3B01G544800 chr5A 390556910 390558721 1811 False 731.0 902 89.4330 1 1558 2 chr5A.!!$F1 1557
6 TraesCS3B01G544800 chr7B 505219511 505222361 2850 True 2336.5 3513 96.9930 1 2846 2 chr7B.!!$R1 2845
7 TraesCS3B01G544800 chr2A 21632184 21634349 2165 False 2678.0 2678 89.0550 663 2848 1 chr2A.!!$F1 2185
8 TraesCS3B01G544800 chr2A 180214128 180214796 668 True 913.0 913 91.3300 1 667 1 chr2A.!!$R1 666
9 TraesCS3B01G544800 chr4A 27193411 27194815 1404 True 2435.0 2435 97.9370 1440 2845 1 chr4A.!!$R1 1405
10 TraesCS3B01G544800 chr4A 698011446 698013234 1788 True 2403.0 2403 90.9390 1047 2844 1 chr4A.!!$R2 1797
11 TraesCS3B01G544800 chr4D 505347583 505348908 1325 True 1121.5 1995 97.7495 885 2846 2 chr4D.!!$R1 1961
12 TraesCS3B01G544800 chr4B 42255410 42256735 1325 False 1121.5 1995 97.7095 885 2846 2 chr4B.!!$F1 1961
13 TraesCS3B01G544800 chr3D 562174875 562176038 1163 True 1995.0 1995 97.5970 1682 2846 1 chr3D.!!$R1 1164
14 TraesCS3B01G544800 chr6B 532351327 532351995 668 False 907.0 907 91.1810 1 667 1 chr6B.!!$F1 666
15 TraesCS3B01G544800 chr7A 31808115 31809796 1681 False 725.5 902 89.2270 1 1558 2 chr7A.!!$F1 1557
16 TraesCS3B01G544800 chr1B 150370916 150371624 708 True 870.0 870 88.7960 1568 2280 1 chr1B.!!$R1 712


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
428 431 1.903404 GCAAGGCCGGGGATATTGG 60.903 63.158 2.18 0.0 0.0 3.16 F
1010 1228 2.622942 TGTTGCTGAAGATGGGTGTTTC 59.377 45.455 0.00 0.0 0.0 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 2477 1.405661 CGAAGAAGCTAAGGACCCACC 60.406 57.143 0.0 0.0 39.35 4.61 R
2716 3044 2.602257 AGCACTTGCCAACTTTTTCC 57.398 45.000 0.0 0.0 43.38 3.13 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
68 70 7.881232 TGAACTTCCCTTTTTCATATTCGTAGT 59.119 33.333 0.00 0.0 0.00 2.73
428 431 1.903404 GCAAGGCCGGGGATATTGG 60.903 63.158 2.18 0.0 0.00 3.16
1010 1228 2.622942 TGTTGCTGAAGATGGGTGTTTC 59.377 45.455 0.00 0.0 0.00 2.78
2163 2477 4.161333 GCTGATGAAACAATTCTTGGACG 58.839 43.478 0.00 0.0 36.48 4.79
2553 2877 1.819928 ACAGTTTGTGTCTGTGTGCA 58.180 45.000 0.00 0.0 43.32 4.57
2716 3044 1.374505 CGCTGGCCAATGGTTTTGG 60.375 57.895 7.01 0.0 42.37 3.28
2964 3292 1.768684 GCACAAGGACCTCCAGGACA 61.769 60.000 0.00 0.0 38.89 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 10 5.593679 GGCTAGGCCGATCTTGTATAATA 57.406 43.478 4.61 0.0 39.62 0.98
68 70 2.101640 TCTAGTGCCCCTATGCATCA 57.898 50.000 0.19 0.0 44.30 3.07
428 431 2.607892 GCACACCACGACAAGGAGC 61.608 63.158 0.00 0.0 0.00 4.70
967 1143 9.382244 CAACACTTGAAGCTTACATACTAAAAC 57.618 33.333 0.00 0.0 0.00 2.43
1010 1228 3.753294 AATAAGTCCGGACCAGCATAG 57.247 47.619 30.82 0.0 0.00 2.23
2163 2477 1.405661 CGAAGAAGCTAAGGACCCACC 60.406 57.143 0.00 0.0 39.35 4.61
2401 2719 7.876068 CACATAGTAACCAAGTCTTTACCAGAA 59.124 37.037 0.00 0.0 31.28 3.02
2716 3044 2.602257 AGCACTTGCCAACTTTTTCC 57.398 45.000 0.00 0.0 43.38 3.13



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

AutoCloner maintained by Alex Coulton.