Multiple sequence alignment - TraesCS1B01G199200

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 TraesCS1B01G199200 chr1B 100.000 5825 0 0 2315 8139 357424001 357418177 0.000000e+00 10757.0
1 TraesCS1B01G199200 chr1B 100.000 2013 0 0 1 2013 357426315 357424303 0.000000e+00 3718.0
2 TraesCS1B01G199200 chr1B 82.528 269 24 9 7887 8134 329909406 329909672 1.780000e-51 215.0
3 TraesCS1B01G199200 chr1B 87.654 162 17 2 7981 8139 575139493 575139654 1.390000e-42 185.0
4 TraesCS1B01G199200 chr1B 88.199 161 9 6 7982 8134 603564443 603564285 5.020000e-42 183.0
5 TraesCS1B01G199200 chr1A 95.256 1834 71 6 5924 7742 327536339 327538171 0.000000e+00 2891.0
6 TraesCS1B01G199200 chr1A 95.430 1466 35 11 4456 5895 327534887 327536346 0.000000e+00 2307.0
7 TraesCS1B01G199200 chr1A 94.422 1004 49 4 2326 3323 327532959 327533961 0.000000e+00 1537.0
8 TraesCS1B01G199200 chr1A 95.851 940 29 5 1078 2013 327531759 327532692 0.000000e+00 1511.0
9 TraesCS1B01G199200 chr1A 92.949 936 53 9 3434 4359 327533957 327534889 0.000000e+00 1351.0
10 TraesCS1B01G199200 chr1A 85.278 1080 61 41 15 1034 327530713 327531754 0.000000e+00 1024.0
11 TraesCS1B01G199200 chr1A 79.639 388 40 18 7781 8139 327538284 327538661 8.160000e-60 243.0
12 TraesCS1B01G199200 chr1A 86.957 161 19 2 7981 8139 520858689 520858849 6.490000e-41 180.0
13 TraesCS1B01G199200 chr1D 92.480 1835 87 23 4456 6255 255498644 255500462 0.000000e+00 2577.0
14 TraesCS1B01G199200 chr1D 95.704 1513 55 6 6256 7765 255500506 255502011 0.000000e+00 2425.0
15 TraesCS1B01G199200 chr1D 93.031 1564 58 25 1 1538 255493237 255494775 0.000000e+00 2237.0
16 TraesCS1B01G199200 chr1D 91.471 938 40 14 3434 4359 255497737 255498646 0.000000e+00 1253.0
17 TraesCS1B01G199200 chr1D 95.223 649 28 2 2535 3180 255496440 255497088 0.000000e+00 1024.0
18 TraesCS1B01G199200 chr1D 93.182 484 12 4 1538 2013 255495676 255496146 0.000000e+00 691.0
19 TraesCS1B01G199200 chr1D 92.072 391 20 6 7756 8139 255502029 255502415 2.580000e-149 540.0
20 TraesCS1B01G199200 chr1D 97.653 213 5 0 2337 2549 255496188 255496400 4.640000e-97 366.0
21 TraesCS1B01G199200 chr1D 93.548 155 7 1 3172 3323 255497587 255497741 2.290000e-55 228.0
22 TraesCS1B01G199200 chr1D 78.415 366 40 21 7807 8139 34949689 34950048 1.390000e-47 202.0
23 TraesCS1B01G199200 chr1D 95.161 124 5 1 3322 3445 28313637 28313515 2.320000e-45 195.0
24 TraesCS1B01G199200 chr1D 92.562 121 7 2 4356 4475 445993578 445993697 1.090000e-38 172.0
25 TraesCS1B01G199200 chr5A 83.065 248 24 11 7906 8139 6481712 6481469 8.280000e-50 209.0
26 TraesCS1B01G199200 chr3D 77.500 400 53 15 7774 8139 30290227 30289831 1.070000e-48 206.0
27 TraesCS1B01G199200 chr3D 89.032 155 17 0 7985 8139 457907567 457907413 8.340000e-45 193.0
28 TraesCS1B01G199200 chr3D 98.113 106 2 0 4356 4461 529790944 529790839 1.390000e-42 185.0
29 TraesCS1B01G199200 chr4B 97.479 119 3 0 3320 3438 628068095 628067977 3.850000e-48 204.0
30 TraesCS1B01G199200 chr4B 91.200 125 7 4 4356 4479 272861393 272861272 5.050000e-37 167.0
31 TraesCS1B01G199200 chr5B 95.902 122 5 0 3320 3441 403545836 403545715 1.790000e-46 198.0
32 TraesCS1B01G199200 chr5B 95.161 124 6 0 3315 3438 611922696 611922819 6.440000e-46 196.0
33 TraesCS1B01G199200 chr5B 95.161 124 5 1 3320 3443 571209384 571209262 2.320000e-45 195.0
34 TraesCS1B01G199200 chr5B 95.122 123 5 1 3320 3442 451432869 451432990 8.340000e-45 193.0
35 TraesCS1B01G199200 chr5B 94.690 113 4 2 4356 4466 138779427 138779315 3.020000e-39 174.0
36 TraesCS1B01G199200 chr5B 81.043 211 32 7 7905 8108 17569566 17569775 2.350000e-35 161.0
37 TraesCS1B01G199200 chr2D 93.939 132 5 3 3319 3448 158283412 158283282 6.440000e-46 196.0
38 TraesCS1B01G199200 chr4D 93.798 129 6 2 3315 3441 72256255 72256127 8.340000e-45 193.0
39 TraesCS1B01G199200 chr4D 93.913 115 6 1 4356 4469 195030545 195030659 1.090000e-38 172.0
40 TraesCS1B01G199200 chr4D 79.781 183 33 4 7800 7980 55714924 55714744 6.630000e-26 130.0
41 TraesCS1B01G199200 chr4A 91.367 139 9 2 3303 3438 544199299 544199437 3.880000e-43 187.0
42 TraesCS1B01G199200 chr4A 98.077 104 2 0 4356 4459 362098359 362098462 1.800000e-41 182.0
43 TraesCS1B01G199200 chr4A 91.667 132 7 4 4356 4486 596221223 596221351 6.490000e-41 180.0
44 TraesCS1B01G199200 chr7A 77.874 348 43 16 7821 8139 241740867 241741209 1.390000e-42 185.0
45 TraesCS1B01G199200 chr7A 79.085 153 19 10 7830 7980 63441114 63441255 8.700000e-15 93.5
46 TraesCS1B01G199200 chr3B 92.437 119 7 2 4356 4474 809849029 809849145 1.400000e-37 169.0
47 TraesCS1B01G199200 chr3B 91.200 125 8 3 4356 4480 272137348 272137469 5.050000e-37 167.0
48 TraesCS1B01G199200 chr3B 79.524 210 33 9 7774 7980 24357535 24357737 3.060000e-29 141.0
49 TraesCS1B01G199200 chr3B 79.426 209 34 8 7774 7980 24378906 24379107 1.100000e-28 139.0
50 TraesCS1B01G199200 chr5D 79.310 116 15 5 5403 5512 543310973 543310861 1.130000e-08 73.1


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 TraesCS1B01G199200 chr1B 357418177 357426315 8138 True 7237.500000 10757 100.000000 1 8139 2 chr1B.!!$R2 8138
1 TraesCS1B01G199200 chr1A 327530713 327538661 7948 False 1552.000000 2891 91.260714 15 8139 7 chr1A.!!$F2 8124
2 TraesCS1B01G199200 chr1D 255493237 255502415 9178 False 1260.111111 2577 93.818222 1 8139 9 chr1D.!!$F3 8138


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
583 625 0.107606 CCGAGACCGAGAGAGAAGGA 60.108 60.000 0.00 0.0 38.22 3.36 F
586 628 1.404035 GAGACCGAGAGAGAAGGAAGC 59.596 57.143 0.00 0.0 0.00 3.86 F
1488 1566 2.490903 GCCCATGCCATCTATGTGAATC 59.509 50.000 0.00 0.0 0.00 2.52 F
2725 3766 0.036294 GAAGCTACCCGACTTTGCCT 60.036 55.000 0.00 0.0 0.00 4.75 F
3338 4892 0.032813 AATACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.0 44.66 4.30 F
3341 4895 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.0 44.66 1.40 F
3343 4897 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.0 44.66 2.12 F
4373 5945 0.330604 AATGTGCCAGAGCCATGAGT 59.669 50.000 0.00 0.0 38.69 3.41 F
5047 6645 0.109827 CGGCACACATTTTGATGCGA 60.110 50.000 0.00 0.0 39.02 5.10 F
6348 8009 0.390492 AACTGCTTTTGCCAAGCTCC 59.610 50.000 16.39 0.0 46.87 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1488 1566 1.225475 GCAACGACTCGAATGCACG 60.225 57.895 21.07 0.00 40.55 5.34 R
1513 1591 1.896220 TTTCAGCAGCTAACCACCAG 58.104 50.000 0.00 0.00 0.00 4.00 R
3321 4875 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59 R
4356 5928 0.607217 CAACTCATGGCTCTGGCACA 60.607 55.000 0.00 0.00 41.84 4.57 R
4395 5967 0.714180 TGGGGTAGGCTAGAGGTGAA 59.286 55.000 0.00 0.00 0.00 3.18 R
4396 5968 0.714180 TTGGGGTAGGCTAGAGGTGA 59.286 55.000 0.00 0.00 0.00 4.02 R
4398 5970 0.717196 AGTTGGGGTAGGCTAGAGGT 59.283 55.000 0.00 0.00 0.00 3.85 R
5990 7600 1.971357 CATTAGGGGATACGTCTGGCT 59.029 52.381 0.00 0.00 37.60 4.75 R
6784 8453 0.106819 GATTGTGATGGAGGCTGGCT 60.107 55.000 2.24 2.24 0.00 4.75 R
7787 9560 0.469331 ACCGTTCCCTCTGTCTCACA 60.469 55.000 0.00 0.00 0.00 3.58 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)



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

AutoCloner maintained by Alex Coulton.