Multiple sequence alignment - TraesCS3D01G045000

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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 TraesCS3D01G045000 chr3D 100.000 6802 0 0 1 6802 17352565 17359366 0.000000e+00 12562.0
1 TraesCS3D01G045000 chr3D 83.323 1643 153 62 4574 6132 17538372 17536767 0.000000e+00 1404.0
2 TraesCS3D01G045000 chr3D 89.159 618 61 3 1256 1871 17541258 17540645 0.000000e+00 765.0
3 TraesCS3D01G045000 chr3D 80.819 1001 129 42 4654 5622 17671034 17670065 0.000000e+00 726.0
4 TraesCS3D01G045000 chr3D 78.049 861 133 29 3365 4205 17355075 17355899 6.130000e-135 492.0
5 TraesCS3D01G045000 chr3D 78.049 861 133 29 2511 3335 17355929 17356769 6.130000e-135 492.0
6 TraesCS3D01G045000 chr3D 77.551 784 133 26 1044 1814 17538072 17537319 3.770000e-117 433.0
7 TraesCS3D01G045000 chr3D 77.452 785 127 30 1037 1811 17357428 17358172 2.270000e-114 424.0
8 TraesCS3D01G045000 chr3D 85.287 401 56 2 4870 5270 18793228 18793625 1.770000e-110 411.0
9 TraesCS3D01G045000 chr3D 95.500 200 9 0 6279 6478 1876473 1876274 3.060000e-83 320.0
10 TraesCS3D01G045000 chr3D 95.050 202 9 1 6279 6479 378782479 378782680 3.960000e-82 316.0
11 TraesCS3D01G045000 chr3D 76.224 715 78 50 4268 4949 11331494 11332149 1.860000e-75 294.0
12 TraesCS3D01G045000 chr3D 76.726 391 74 13 1073 1462 18793251 18793625 1.160000e-47 202.0
13 TraesCS3D01G045000 chr3D 91.667 144 9 1 1114 1257 17541743 17541603 5.380000e-46 196.0
14 TraesCS3D01G045000 chr3D 83.516 182 23 3 4362 4543 17671468 17671294 5.460000e-36 163.0
15 TraesCS3D01G045000 chr3D 80.925 173 21 3 6484 6645 595079857 595079686 7.160000e-25 126.0
16 TraesCS3D01G045000 chr3B 81.779 2294 270 79 3517 5718 24927294 24929531 0.000000e+00 1784.0
17 TraesCS3D01G045000 chr3B 87.666 1281 97 27 619 1868 24925189 24926439 0.000000e+00 1434.0
18 TraesCS3D01G045000 chr3B 83.890 689 107 4 4896 5582 30498358 30499044 0.000000e+00 654.0
19 TraesCS3D01G045000 chr3B 83.309 695 103 9 4896 5582 30200045 30200734 4.480000e-176 628.0
20 TraesCS3D01G045000 chr3B 82.663 721 112 8 4870 5582 29776931 29777646 1.610000e-175 627.0
21 TraesCS3D01G045000 chr3B 80.725 690 115 12 4870 5550 30508987 30509667 7.820000e-144 521.0
22 TraesCS3D01G045000 chr3B 91.099 191 15 2 341 529 24924899 24925089 2.430000e-64 257.0
23 TraesCS3D01G045000 chr3B 82.520 246 31 8 6482 6718 821480270 821480028 8.940000e-49 206.0
24 TraesCS3D01G045000 chr3B 82.648 219 31 4 3353 3569 24927096 24927309 3.240000e-43 187.0
25 TraesCS3D01G045000 chr3B 94.737 95 5 0 162 256 24924740 24924834 1.530000e-31 148.0
26 TraesCS3D01G045000 chr3A 87.795 1483 108 31 4277 5720 19492160 19490712 0.000000e+00 1668.0
27 TraesCS3D01G045000 chr3A 87.932 1185 100 23 905 2055 19494786 19493611 0.000000e+00 1356.0
28 TraesCS3D01G045000 chr3A 85.128 1096 115 27 2281 3335 19493293 19492205 0.000000e+00 1077.0
29 TraesCS3D01G045000 chr3A 81.105 1032 146 30 4574 5584 19275343 19276346 0.000000e+00 780.0
30 TraesCS3D01G045000 chr3A 77.808 1469 173 81 4303 5718 25994495 25993127 0.000000e+00 765.0
31 TraesCS3D01G045000 chr3A 80.599 902 149 17 3365 4247 19493057 19492163 0.000000e+00 673.0
32 TraesCS3D01G045000 chr3A 75.979 970 163 40 845 1787 19491773 19490847 2.910000e-118 436.0
33 TraesCS3D01G045000 chr3A 83.232 495 44 17 5717 6192 19490681 19490207 1.060000e-112 418.0
34 TraesCS3D01G045000 chr3A 95.025 201 9 1 6279 6478 690792772 690792972 1.420000e-81 315.0
35 TraesCS3D01G045000 chr3A 90.173 173 11 3 5716 5886 19352833 19353001 3.190000e-53 220.0
36 TraesCS3D01G045000 chr3A 86.842 76 8 2 5722 5796 25993094 25993020 4.370000e-12 84.2
37 TraesCS3D01G045000 chr6D 96.040 202 6 2 6276 6476 155841818 155841618 1.830000e-85 327.0
38 TraesCS3D01G045000 chr6D 95.522 201 9 0 6279 6479 389653552 389653352 8.510000e-84 322.0
39 TraesCS3D01G045000 chr6D 80.081 246 39 8 6479 6716 10420115 10420358 2.520000e-39 174.0
40 TraesCS3D01G045000 chr6D 78.571 252 32 14 6482 6718 292373851 292374095 5.500000e-31 147.0
41 TraesCS3D01G045000 chr2D 95.074 203 10 0 6276 6478 458171872 458172074 3.060000e-83 320.0
42 TraesCS3D01G045000 chr2D 79.435 248 39 10 6482 6721 422881367 422881124 1.520000e-36 165.0
43 TraesCS3D01G045000 chr2A 95.025 201 9 1 6279 6478 769618682 769618482 1.420000e-81 315.0
44 TraesCS3D01G045000 chr1A 95.025 201 9 1 6279 6478 586372725 586372925 1.420000e-81 315.0
45 TraesCS3D01G045000 chr1A 83.468 248 29 8 6483 6721 533318239 533317995 3.190000e-53 220.0
46 TraesCS3D01G045000 chr5D 93.720 207 12 1 6270 6476 487979075 487979280 6.630000e-80 309.0
47 TraesCS3D01G045000 chr5A 82.540 252 29 9 6479 6718 702190684 702190932 2.490000e-49 207.0
48 TraesCS3D01G045000 chr5A 79.116 249 40 8 6482 6721 563220536 563220291 1.960000e-35 161.0
49 TraesCS3D01G045000 chr7D 79.681 251 34 7 6479 6714 610805281 610805529 1.520000e-36 165.0
50 TraesCS3D01G045000 chr6B 80.085 236 36 8 6489 6716 19132016 19132248 1.520000e-36 165.0
51 TraesCS3D01G045000 chr2B 78.000 250 29 16 6482 6722 662899997 662899765 4.280000e-27 134.0
52 TraesCS3D01G045000 chr4B 93.333 60 3 1 6663 6722 604867435 604867493 3.380000e-13 87.9


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 TraesCS3D01G045000 chr3D 17352565 17359366 6801 False 12562.000000 12562 100.000000 1 6802 1 chr3D.!!$F2 6801
1 TraesCS3D01G045000 chr3D 17536767 17541743 4976 True 699.500000 1404 85.425000 1044 6132 4 chr3D.!!$R3 5088
2 TraesCS3D01G045000 chr3D 17355075 17358172 3097 False 469.333333 492 77.850000 1037 4205 3 chr3D.!!$F4 3168
3 TraesCS3D01G045000 chr3D 17670065 17671468 1403 True 444.500000 726 82.167500 4362 5622 2 chr3D.!!$R4 1260
4 TraesCS3D01G045000 chr3D 11331494 11332149 655 False 294.000000 294 76.224000 4268 4949 1 chr3D.!!$F1 681
5 TraesCS3D01G045000 chr3B 24924740 24929531 4791 False 762.000000 1784 87.585800 162 5718 5 chr3B.!!$F5 5556
6 TraesCS3D01G045000 chr3B 30498358 30499044 686 False 654.000000 654 83.890000 4896 5582 1 chr3B.!!$F3 686
7 TraesCS3D01G045000 chr3B 30200045 30200734 689 False 628.000000 628 83.309000 4896 5582 1 chr3B.!!$F2 686
8 TraesCS3D01G045000 chr3B 29776931 29777646 715 False 627.000000 627 82.663000 4870 5582 1 chr3B.!!$F1 712
9 TraesCS3D01G045000 chr3B 30508987 30509667 680 False 521.000000 521 80.725000 4870 5550 1 chr3B.!!$F4 680
10 TraesCS3D01G045000 chr3A 19490207 19494786 4579 True 938.000000 1668 83.444167 845 6192 6 chr3A.!!$R1 5347
11 TraesCS3D01G045000 chr3A 19275343 19276346 1003 False 780.000000 780 81.105000 4574 5584 1 chr3A.!!$F1 1010
12 TraesCS3D01G045000 chr3A 25993020 25994495 1475 True 424.600000 765 82.325000 4303 5796 2 chr3A.!!$R2 1493


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
882 948 0.035598 TTCGCATTCCCCTTTCGTCA 59.964 50.0 0.00 0.0 0.00 4.35 F
1878 2322 0.096976 CTTTCGCGGTATGGTTGCAG 59.903 55.0 6.13 0.0 0.00 4.41 F
1910 2354 0.108756 GTTGCACTAGTCGGGAGGTC 60.109 60.0 0.00 0.0 0.00 3.85 F
1915 2359 0.179051 ACTAGTCGGGAGGTCTAGCG 60.179 60.0 0.00 0.0 37.87 4.26 F
1916 2360 0.179051 CTAGTCGGGAGGTCTAGCGT 60.179 60.0 0.00 0.0 32.05 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 2325 0.652592 CTAGTGCAACGCTGGTATGC 59.347 55.000 0.00 0.0 45.86 3.14 R
5632 7598 1.660575 GATATGGCCGTCCACGTCG 60.661 63.158 0.00 0.0 46.92 5.12 R
5678 7648 0.905357 ACGAACCAGGGAGGAAGATG 59.095 55.000 0.00 0.0 41.22 2.90 R
5731 7742 0.179018 AAATCTCCATGGGCCTACGC 60.179 55.000 13.02 0.0 0.00 4.42 R
5803 7826 0.109458 TGTACTCAGCGTGTTAGCCG 60.109 55.000 0.00 0.0 38.01 5.52 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.