Multiple sequence alignment - TraesCS6A01G012500

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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 TraesCS6A01G012500 chr6A 100.000 2942 0 0 1 2942 5858535 5855594 0.000000e+00 5433.0
1 TraesCS6A01G012500 chr6A 97.164 2962 41 9 1 2942 5650911 5647973 0.000000e+00 4964.0
2 TraesCS6A01G012500 chr6A 97.379 1450 28 4 1494 2942 5752179 5750739 0.000000e+00 2459.0
3 TraesCS6A01G012500 chr6A 97.026 1177 14 6 1 1156 5753330 5752154 0.000000e+00 1960.0
4 TraesCS6A01G012500 chr6D 90.783 1302 54 11 1 1252 6317764 6316479 0.000000e+00 1679.0
5 TraesCS6A01G012500 chr6D 92.439 820 34 11 1307 2098 6316174 6315355 0.000000e+00 1146.0
6 TraesCS6A01G012500 chr6D 96.135 207 8 0 2151 2357 6312451 6312245 3.630000e-89 339.0
7 TraesCS6A01G012500 chr6D 98.333 60 1 0 2092 2151 6314763 6314704 4.010000e-19 106.0
8 TraesCS6A01G012500 chr6B 94.686 621 28 3 1307 1922 11573034 11572414 0.000000e+00 959.0
9 TraesCS6A01G012500 chr6B 94.118 272 13 3 986 1254 11573461 11573190 7.590000e-111 411.0
10 TraesCS6A01G012500 chr3D 86.851 578 65 7 2355 2928 28454501 28455071 1.150000e-178 636.0
11 TraesCS6A01G012500 chr3D 80.721 638 98 17 998 1618 497809794 497809165 9.540000e-130 473.0
12 TraesCS6A01G012500 chr3D 92.150 293 22 1 1331 1623 497820096 497819805 2.110000e-111 412.0
13 TraesCS6A01G012500 chr2D 86.332 578 68 6 2355 2928 224923325 224923895 1.160000e-173 619.0
14 TraesCS6A01G012500 chr2D 81.933 238 33 8 2113 2344 113489628 113489395 2.990000e-45 193.0
15 TraesCS6A01G012500 chr3A 81.860 645 86 24 998 1627 636693993 636694621 5.620000e-142 514.0
16 TraesCS6A01G012500 chr3A 79.289 647 102 26 998 1618 636697926 636698566 9.750000e-115 424.0
17 TraesCS6A01G012500 chrUn 87.354 427 50 3 2355 2777 56377130 56376704 1.230000e-133 486.0
18 TraesCS6A01G012500 chrUn 87.354 427 50 3 2355 2777 276428933 276429359 1.230000e-133 486.0
19 TraesCS6A01G012500 chr3B 80.936 577 92 11 1332 1906 658063215 658062655 9.680000e-120 440.0
20 TraesCS6A01G012500 chr3B 90.604 298 27 1 1326 1623 658059833 658059537 7.640000e-106 394.0
21 TraesCS6A01G012500 chr4D 83.152 368 56 4 2355 2716 364618156 364617789 6.080000e-87 331.0
22 TraesCS6A01G012500 chr5D 86.496 274 31 4 2355 2622 6477335 6477062 2.220000e-76 296.0
23 TraesCS6A01G012500 chr5D 100.000 31 0 0 576 606 450531629 450531599 1.140000e-04 58.4
24 TraesCS6A01G012500 chr5A 83.983 231 27 6 2113 2337 185651047 185651273 2.300000e-51 213.0
25 TraesCS6A01G012500 chr5A 100.000 31 0 0 576 606 569708342 569708312 1.140000e-04 58.4
26 TraesCS6A01G012500 chr7B 81.538 195 26 8 2113 2304 409424361 409424174 5.080000e-33 152.0
27 TraesCS6A01G012500 chr7D 75.299 251 50 6 2355 2602 51813362 51813121 3.100000e-20 110.0
28 TraesCS6A01G012500 chr2A 100.000 28 0 0 239 266 380430697 380430670 5.000000e-03 52.8


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 TraesCS6A01G012500 chr6A 5855594 5858535 2941 True 5433.0 5433 100.0000 1 2942 1 chr6A.!!$R2 2941
1 TraesCS6A01G012500 chr6A 5647973 5650911 2938 True 4964.0 4964 97.1640 1 2942 1 chr6A.!!$R1 2941
2 TraesCS6A01G012500 chr6A 5750739 5753330 2591 True 2209.5 2459 97.2025 1 2942 2 chr6A.!!$R3 2941
3 TraesCS6A01G012500 chr6D 6312245 6317764 5519 True 817.5 1679 94.4225 1 2357 4 chr6D.!!$R1 2356
4 TraesCS6A01G012500 chr6B 11572414 11573461 1047 True 685.0 959 94.4020 986 1922 2 chr6B.!!$R1 936
5 TraesCS6A01G012500 chr3D 28454501 28455071 570 False 636.0 636 86.8510 2355 2928 1 chr3D.!!$F1 573
6 TraesCS6A01G012500 chr3D 497809165 497809794 629 True 473.0 473 80.7210 998 1618 1 chr3D.!!$R1 620
7 TraesCS6A01G012500 chr2D 224923325 224923895 570 False 619.0 619 86.3320 2355 2928 1 chr2D.!!$F1 573
8 TraesCS6A01G012500 chr3A 636693993 636698566 4573 False 469.0 514 80.5745 998 1627 2 chr3A.!!$F1 629
9 TraesCS6A01G012500 chr3B 658059537 658063215 3678 True 417.0 440 85.7700 1326 1906 2 chr3B.!!$R1 580

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
606 641 3.004002 TCTTAGTCTCGTTCTTCGTGCAA 59.996 43.478 0.0 0.0 40.8 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2324 10896 1.810151 GAAAATCAGCCCGCTACAACA 59.19 47.619 0.0 0.0 0.0 3.33 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
121 123 9.199645 TCTAGCCATTTTAAATGGAAATGATGA 57.800 29.630 33.34 18.97 43.71 2.92
179 209 5.723295 ACAATCATATGTTTGTTCTTGGGC 58.277 37.500 21.29 0.00 35.19 5.36
279 310 8.560903 ACAGGAATAGGAAAACATAAGAATCCT 58.439 33.333 0.00 0.00 42.89 3.24
539 574 6.633500 TTTCTGTTCTTATGTGTTCCCTTG 57.367 37.500 0.00 0.00 0.00 3.61
587 622 5.358160 GCCTTATTGTTGCACTAAGGATCTT 59.642 40.000 21.64 0.00 44.37 2.40
606 641 3.004002 TCTTAGTCTCGTTCTTCGTGCAA 59.996 43.478 0.00 0.00 40.80 4.08
1287 1552 4.213694 CCTATATACGAATCCGCGAGCTAT 59.786 45.833 8.23 0.00 39.95 2.97
1292 1557 2.222976 ACGAATCCGCGAGCTATATACG 60.223 50.000 8.23 3.31 39.95 3.06
2324 10896 0.601558 AGGACGTACATGCGTGAGTT 59.398 50.000 14.17 0.00 45.79 3.01
2337 10909 0.602905 GTGAGTTGTTGTAGCGGGCT 60.603 55.000 0.00 0.00 0.00 5.19
2693 11269 1.344114 CTATCTTCTGAGGGGCAGCTC 59.656 57.143 0.00 0.00 44.52 4.09
2772 11348 0.107017 CCACGAAAGCCCAGATCCAT 60.107 55.000 0.00 0.00 0.00 3.41
2928 11504 1.612146 TCTCCAGGACGGGATGCAA 60.612 57.895 0.00 0.00 36.09 4.08
2932 11508 1.811266 CAGGACGGGATGCAAGACG 60.811 63.158 0.00 0.00 0.00 4.18
2933 11509 1.982395 AGGACGGGATGCAAGACGA 60.982 57.895 13.09 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 123 5.063312 CACGAACTTTTGCCACTCAAATTTT 59.937 36.000 0.00 0.00 43.53 1.82
179 209 8.810427 GTTTTATACATGCATTCCTCAAATGTG 58.190 33.333 0.00 0.00 45.55 3.21
539 574 5.975344 CCTCCTTTGGTTTAAACGAAAAGTC 59.025 40.000 26.78 10.93 36.43 3.01
587 622 3.358707 TTTGCACGAAGAACGAGACTA 57.641 42.857 0.00 0.00 45.77 2.59
1287 1552 4.193865 TCACCTCGTGACAGATTCGTATA 58.806 43.478 0.00 0.00 37.67 1.47
2324 10896 1.810151 GAAAATCAGCCCGCTACAACA 59.190 47.619 0.00 0.00 0.00 3.33
2337 10909 7.342799 CCCTGATGAAAAATAGGAGGAAAATCA 59.657 37.037 0.00 0.00 31.91 2.57
2655 11231 0.176680 AGTACATGGCCTCTTGAGCG 59.823 55.000 3.32 0.00 0.00 5.03
2693 11269 3.200483 TGTCGAATTCAGATCAGCCATG 58.800 45.455 6.22 0.00 0.00 3.66
2893 11469 2.665185 AGCCGGTTCACGCTTCAC 60.665 61.111 1.90 0.00 42.52 3.18
2894 11470 2.357034 GAGCCGGTTCACGCTTCA 60.357 61.111 14.14 0.00 42.52 3.02
2895 11471 2.048127 AGAGCCGGTTCACGCTTC 60.048 61.111 21.22 0.00 42.52 3.86
2896 11472 2.048127 GAGAGCCGGTTCACGCTT 60.048 61.111 21.22 0.00 42.52 4.68
2897 11473 4.070552 GGAGAGCCGGTTCACGCT 62.071 66.667 21.22 1.45 42.52 5.07
2898 11474 4.373116 TGGAGAGCCGGTTCACGC 62.373 66.667 21.22 9.00 42.52 5.34
2899 11475 2.125912 CTGGAGAGCCGGTTCACG 60.126 66.667 21.22 5.91 43.80 4.35


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

AutoCloner maintained by Alex Coulton.