Multiple sequence alignment - TraesCS3A01G085300

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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 TraesCS3A01G085300 chr3A 100.000 6157 0 0 1 6157 55030272 55036428 0.000000e+00 11370.0
1 TraesCS3A01G085300 chr3A 79.594 1181 167 42 4071 5187 509542599 509543769 0.000000e+00 778.0
2 TraesCS3A01G085300 chr3A 85.714 721 78 12 2945 3654 54937938 54938644 0.000000e+00 737.0
3 TraesCS3A01G085300 chr3A 77.158 1309 233 45 2753 4024 509541343 509542622 0.000000e+00 701.0
4 TraesCS3A01G085300 chr3A 81.728 602 91 13 1922 2518 509540367 509540954 9.280000e-133 484.0
5 TraesCS3A01G085300 chr3A 84.434 212 27 5 235 445 170737609 170737815 2.910000e-48 204.0
6 TraesCS3A01G085300 chr3A 82.328 232 32 6 226 454 700416137 700416362 6.300000e-45 193.0
7 TraesCS3A01G085300 chr3B 92.063 2646 142 20 3554 6157 66875927 66878546 0.000000e+00 3661.0
8 TraesCS3A01G085300 chr3B 87.136 2542 202 51 887 3359 66873179 66875664 0.000000e+00 2767.0
9 TraesCS3A01G085300 chr3B 79.547 1193 171 40 4071 5198 505267340 505268524 0.000000e+00 784.0
10 TraesCS3A01G085300 chr3B 78.411 1070 182 33 2983 4024 505266315 505267363 0.000000e+00 651.0
11 TraesCS3A01G085300 chr3B 79.253 723 123 20 1802 2518 505264913 505265614 4.320000e-131 479.0
12 TraesCS3A01G085300 chr3B 85.714 168 21 2 1007 1174 505263833 505263997 2.280000e-39 174.0
13 TraesCS3A01G085300 chr3D 93.609 2222 93 21 3949 6157 43009274 43011459 0.000000e+00 3271.0
14 TraesCS3A01G085300 chr3D 88.570 2091 151 32 849 2922 43006262 43008281 0.000000e+00 2457.0
15 TraesCS3A01G085300 chr3D 88.100 1000 82 14 2947 3913 43008278 43009273 0.000000e+00 1153.0
16 TraesCS3A01G085300 chr3D 77.515 1312 223 56 2753 4024 388446461 388447740 0.000000e+00 723.0
17 TraesCS3A01G085300 chr3D 84.601 539 76 3 4638 5169 388448335 388448873 4.230000e-146 529.0
18 TraesCS3A01G085300 chr3D 79.778 722 120 20 1802 2518 388445404 388446104 9.210000e-138 501.0
19 TraesCS3A01G085300 chr3D 82.780 482 55 17 4071 4530 388447717 388448192 7.430000e-109 405.0
20 TraesCS3A01G085300 chr3D 84.971 173 20 3 1005 1174 388444393 388444562 2.950000e-38 171.0
21 TraesCS3A01G085300 chr4D 90.312 640 47 6 1383 2018 509552377 509553005 0.000000e+00 824.0
22 TraesCS3A01G085300 chr6B 89.688 640 55 5 1383 2018 139414013 139414645 0.000000e+00 806.0
23 TraesCS3A01G085300 chr6B 85.714 126 13 2 450 570 680740115 680740240 1.800000e-25 128.0
24 TraesCS3A01G085300 chr4B 89.219 640 58 4 1383 2018 488091667 488091035 0.000000e+00 789.0
25 TraesCS3A01G085300 chr4B 89.062 640 59 3 1383 2018 469360682 469360050 0.000000e+00 784.0
26 TraesCS3A01G085300 chr4B 85.714 126 9 4 450 572 55753500 55753619 2.330000e-24 124.0
27 TraesCS3A01G085300 chr1B 89.219 640 58 4 1383 2018 546249155 546249787 0.000000e+00 789.0
28 TraesCS3A01G085300 chr1B 85.345 232 28 2 4296 4524 428108897 428109125 1.030000e-57 235.0
29 TraesCS3A01G085300 chr1B 85.227 176 22 3 3757 3928 428108494 428108669 1.760000e-40 178.0
30 TraesCS3A01G085300 chr5B 89.097 642 57 6 1383 2018 327987338 327987972 0.000000e+00 785.0
31 TraesCS3A01G085300 chr5B 89.062 640 54 5 1383 2018 245728699 245729326 0.000000e+00 780.0
32 TraesCS3A01G085300 chr5B 84.360 211 30 3 235 445 659301312 659301519 2.910000e-48 204.0
33 TraesCS3A01G085300 chr6A 78.214 459 89 10 3571 4021 148530817 148530362 3.630000e-72 283.0
34 TraesCS3A01G085300 chr6A 80.548 365 44 14 3016 3361 148531394 148531038 7.920000e-64 255.0
35 TraesCS3A01G085300 chr6A 83.673 245 32 7 4287 4528 148530190 148529951 2.230000e-54 224.0
36 TraesCS3A01G085300 chr6A 83.412 211 32 2 235 445 558457703 558457496 6.300000e-45 193.0
37 TraesCS3A01G085300 chr6A 83.412 211 32 2 235 445 558461023 558460816 6.300000e-45 193.0
38 TraesCS3A01G085300 chr6A 95.122 41 1 1 152 192 580790022 580789983 5.150000e-06 63.9
39 TraesCS3A01G085300 chr1D 86.207 232 26 2 4296 4524 316010132 316010360 4.770000e-61 246.0
40 TraesCS3A01G085300 chr1D 84.434 212 28 3 235 445 18864560 18864767 2.910000e-48 204.0
41 TraesCS3A01G085300 chr1D 84.181 177 22 5 3757 3928 316009722 316009897 3.820000e-37 167.0
42 TraesCS3A01G085300 chr2B 84.112 214 32 2 235 448 174594124 174593913 8.090000e-49 206.0
43 TraesCS3A01G085300 chr2B 83.796 216 26 6 235 446 626881475 626881265 4.870000e-46 196.0
44 TraesCS3A01G085300 chrUn 83.491 212 31 3 235 445 171112599 171112391 1.750000e-45 195.0
45 TraesCS3A01G085300 chr1A 83.708 178 21 6 3757 3928 396450857 396451032 1.780000e-35 161.0


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 TraesCS3A01G085300 chr3A 55030272 55036428 6156 False 11370.000000 11370 100.000000 1 6157 1 chr3A.!!$F2 6156
1 TraesCS3A01G085300 chr3A 54937938 54938644 706 False 737.000000 737 85.714000 2945 3654 1 chr3A.!!$F1 709
2 TraesCS3A01G085300 chr3A 509540367 509543769 3402 False 654.333333 778 79.493333 1922 5187 3 chr3A.!!$F5 3265
3 TraesCS3A01G085300 chr3B 66873179 66878546 5367 False 3214.000000 3661 89.599500 887 6157 2 chr3B.!!$F1 5270
4 TraesCS3A01G085300 chr3B 505263833 505268524 4691 False 522.000000 784 80.731250 1007 5198 4 chr3B.!!$F2 4191
5 TraesCS3A01G085300 chr3D 43006262 43011459 5197 False 2293.666667 3271 90.093000 849 6157 3 chr3D.!!$F1 5308
6 TraesCS3A01G085300 chr3D 388444393 388448873 4480 False 465.800000 723 81.929000 1005 5169 5 chr3D.!!$F2 4164
7 TraesCS3A01G085300 chr4D 509552377 509553005 628 False 824.000000 824 90.312000 1383 2018 1 chr4D.!!$F1 635
8 TraesCS3A01G085300 chr6B 139414013 139414645 632 False 806.000000 806 89.688000 1383 2018 1 chr6B.!!$F1 635
9 TraesCS3A01G085300 chr4B 488091035 488091667 632 True 789.000000 789 89.219000 1383 2018 1 chr4B.!!$R2 635
10 TraesCS3A01G085300 chr4B 469360050 469360682 632 True 784.000000 784 89.062000 1383 2018 1 chr4B.!!$R1 635
11 TraesCS3A01G085300 chr1B 546249155 546249787 632 False 789.000000 789 89.219000 1383 2018 1 chr1B.!!$F1 635
12 TraesCS3A01G085300 chr1B 428108494 428109125 631 False 206.500000 235 85.286000 3757 4524 2 chr1B.!!$F2 767
13 TraesCS3A01G085300 chr5B 327987338 327987972 634 False 785.000000 785 89.097000 1383 2018 1 chr5B.!!$F2 635
14 TraesCS3A01G085300 chr5B 245728699 245729326 627 False 780.000000 780 89.062000 1383 2018 1 chr5B.!!$F1 635
15 TraesCS3A01G085300 chr6A 148529951 148531394 1443 True 254.000000 283 80.811667 3016 4528 3 chr6A.!!$R2 1512
16 TraesCS3A01G085300 chr1D 316009722 316010360 638 False 206.500000 246 85.194000 3757 4524 2 chr1D.!!$F2 767


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
433 434 0.034670 AGCATGGGAAGAGAACAGGC 60.035 55.000 0.0 0.0 41.70 4.85 F
1401 1416 0.030638 TGCTCGCAAGGTTCTTTTGC 59.969 50.000 0.1 0.1 45.64 3.68 F
1908 2332 0.593128 ATTCGTCACAGCAACCAAGC 59.407 50.000 0.0 0.0 0.00 4.01 F
2608 3066 2.368439 GCATACTGCAATCACCCAGAA 58.632 47.619 0.0 0.0 44.26 3.02 F
2811 3523 0.248907 GCAGTCATGTGCCATGCATC 60.249 55.000 0.0 0.0 41.91 3.91 F
4692 5717 0.029267 ATCCCTGCCTCCTCCAGATT 60.029 55.000 0.0 0.0 32.03 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1429 1445 0.106521 CCAGCAAAACCACCCAAAGG 59.893 55.000 0.0 0.0 40.04 3.11 R
2730 3210 0.258774 AACAAGTCACCAGGCAACCT 59.741 50.000 0.0 0.0 37.17 3.50 R
2731 3211 0.668535 GAACAAGTCACCAGGCAACC 59.331 55.000 0.0 0.0 37.17 3.77 R
4381 5370 0.878961 GCCAATGGGGACGACGATAC 60.879 60.000 0.0 0.0 40.01 2.24 R
4782 5810 0.617413 AGGATCTGAGCTGTGGGTTG 59.383 55.000 0.0 0.0 0.00 3.77 R
5516 6581 1.066858 TGCTGGTTCCTAGAGAAAGCG 60.067 52.381 0.0 0.0 40.01 4.68 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)



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AutoCloner maintained by Alex Coulton.