Multiple sequence alignment - TraesCS5B01G272300

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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 TraesCS5B01G272300 chr5B 100.000 3292 0 0 1 3292 457931902 457928611 0.000000e+00 6080.0
1 TraesCS5B01G272300 chr5B 97.913 2540 47 4 1 2538 458049542 458052077 0.000000e+00 4392.0
2 TraesCS5B01G272300 chr5B 98.243 740 13 0 2553 3292 457922360 457921621 0.000000e+00 1295.0
3 TraesCS5B01G272300 chr5B 92.913 127 8 1 42 168 644943018 644943143 2.020000e-42 183.0
4 TraesCS5B01G272300 chr5B 88.811 143 14 2 42 182 588885995 588885853 1.210000e-39 174.0
5 TraesCS5B01G272300 chr5A 88.549 2419 174 54 169 2538 481935387 481937751 0.000000e+00 2837.0
6 TraesCS5B01G272300 chr1B 98.111 741 12 2 2552 3292 684268289 684267551 0.000000e+00 1290.0
7 TraesCS5B01G272300 chr1B 97.973 740 15 0 2553 3292 684006397 684007136 0.000000e+00 1284.0
8 TraesCS5B01G272300 chr1B 74.930 359 82 8 1422 1776 673865100 673864746 1.220000e-34 158.0
9 TraesCS5B01G272300 chr7B 97.981 743 14 1 2551 3292 697468096 697467354 0.000000e+00 1288.0
10 TraesCS5B01G272300 chr2B 97.976 741 15 0 2552 3292 135623118 135622378 0.000000e+00 1286.0
11 TraesCS5B01G272300 chr2B 97.973 740 15 0 2553 3292 178785900 178785161 0.000000e+00 1284.0
12 TraesCS5B01G272300 chr3B 97.973 740 15 0 2553 3292 64346709 64345970 0.000000e+00 1284.0
13 TraesCS5B01G272300 chr3B 97.973 740 15 0 2553 3292 116201907 116201168 0.000000e+00 1284.0
14 TraesCS5B01G272300 chr3B 91.603 131 11 0 38 168 595555456 595555326 7.260000e-42 182.0
15 TraesCS5B01G272300 chr4A 97.718 745 16 1 2549 3292 743735030 743734286 0.000000e+00 1280.0
16 TraesCS5B01G272300 chr4A 82.143 252 36 5 1351 1599 729530915 729530670 1.200000e-49 207.0
17 TraesCS5B01G272300 chr6A 83.439 791 124 6 1005 1791 15656113 15655326 0.000000e+00 728.0
18 TraesCS5B01G272300 chr6A 82.353 238 40 2 2155 2391 15646423 15646187 4.310000e-49 206.0
19 TraesCS5B01G272300 chr6A 73.927 303 70 7 2240 2538 587692488 587692191 2.680000e-21 113.0
20 TraesCS5B01G272300 chr6B 80.000 730 136 9 1018 1745 26304733 26304012 6.250000e-147 531.0
21 TraesCS5B01G272300 chr6B 81.088 386 67 6 2155 2537 26290455 26290073 1.480000e-78 303.0
22 TraesCS5B01G272300 chr6B 74.917 303 67 7 2240 2538 664023784 664023487 2.670000e-26 130.0
23 TraesCS5B01G272300 chr6B 74.587 303 68 7 2240 2538 664064481 664064184 1.240000e-24 124.0
24 TraesCS5B01G272300 chr3A 78.996 757 153 4 1007 1763 690711171 690710421 2.270000e-141 512.0
25 TraesCS5B01G272300 chr3A 78.947 760 148 9 1007 1763 690712293 690711543 1.050000e-139 507.0
26 TraesCS5B01G272300 chr3A 90.977 133 12 0 42 174 735609682 735609550 2.610000e-41 180.0
27 TraesCS5B01G272300 chr3A 89.781 137 14 0 42 178 501568318 501568454 3.380000e-40 176.0
28 TraesCS5B01G272300 chr6D 80.183 656 121 8 1092 1745 14468965 14468317 1.780000e-132 483.0
29 TraesCS5B01G272300 chr5D 83.721 301 48 1 2238 2538 27951300 27951599 1.930000e-72 283.0
30 TraesCS5B01G272300 chr7D 74.394 578 133 13 1028 1599 10480540 10479972 1.980000e-57 233.0
31 TraesCS5B01G272300 chr7D 78.594 313 65 2 2226 2537 10038707 10039018 4.310000e-49 206.0
32 TraesCS5B01G272300 chr3D 93.939 132 8 0 43 174 30764589 30764720 2.000000e-47 200.0
33 TraesCS5B01G272300 chrUn 72.561 656 152 25 1022 1663 268323898 268324539 4.340000e-44 189.0
34 TraesCS5B01G272300 chr2A 92.913 127 9 0 42 168 437969933 437969807 5.610000e-43 185.0
35 TraesCS5B01G272300 chr4D 91.538 130 11 0 42 171 476194113 476193984 2.610000e-41 180.0
36 TraesCS5B01G272300 chr1A 80.275 218 41 2 1022 1238 580743627 580743411 2.630000e-36 163.0
37 TraesCS5B01G272300 chr4B 72.881 295 70 8 2248 2537 646578596 646578307 3.500000e-15 93.5


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 TraesCS5B01G272300 chr5B 457928611 457931902 3291 True 6080.0 6080 100.0000 1 3292 1 chr5B.!!$R2 3291
1 TraesCS5B01G272300 chr5B 458049542 458052077 2535 False 4392.0 4392 97.9130 1 2538 1 chr5B.!!$F1 2537
2 TraesCS5B01G272300 chr5B 457921621 457922360 739 True 1295.0 1295 98.2430 2553 3292 1 chr5B.!!$R1 739
3 TraesCS5B01G272300 chr5A 481935387 481937751 2364 False 2837.0 2837 88.5490 169 2538 1 chr5A.!!$F1 2369
4 TraesCS5B01G272300 chr1B 684267551 684268289 738 True 1290.0 1290 98.1110 2552 3292 1 chr1B.!!$R2 740
5 TraesCS5B01G272300 chr1B 684006397 684007136 739 False 1284.0 1284 97.9730 2553 3292 1 chr1B.!!$F1 739
6 TraesCS5B01G272300 chr7B 697467354 697468096 742 True 1288.0 1288 97.9810 2551 3292 1 chr7B.!!$R1 741
7 TraesCS5B01G272300 chr2B 135622378 135623118 740 True 1286.0 1286 97.9760 2552 3292 1 chr2B.!!$R1 740
8 TraesCS5B01G272300 chr2B 178785161 178785900 739 True 1284.0 1284 97.9730 2553 3292 1 chr2B.!!$R2 739
9 TraesCS5B01G272300 chr3B 64345970 64346709 739 True 1284.0 1284 97.9730 2553 3292 1 chr3B.!!$R1 739
10 TraesCS5B01G272300 chr3B 116201168 116201907 739 True 1284.0 1284 97.9730 2553 3292 1 chr3B.!!$R2 739
11 TraesCS5B01G272300 chr4A 743734286 743735030 744 True 1280.0 1280 97.7180 2549 3292 1 chr4A.!!$R2 743
12 TraesCS5B01G272300 chr6A 15655326 15656113 787 True 728.0 728 83.4390 1005 1791 1 chr6A.!!$R2 786
13 TraesCS5B01G272300 chr6B 26304012 26304733 721 True 531.0 531 80.0000 1018 1745 1 chr6B.!!$R2 727
14 TraesCS5B01G272300 chr3A 690710421 690712293 1872 True 509.5 512 78.9715 1007 1763 2 chr3A.!!$R2 756
15 TraesCS5B01G272300 chr6D 14468317 14468965 648 True 483.0 483 80.1830 1092 1745 1 chr6D.!!$R1 653
16 TraesCS5B01G272300 chr7D 10479972 10480540 568 True 233.0 233 74.3940 1028 1599 1 chr7D.!!$R1 571

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
108 109 5.788531 GGATTCGTGTAAAACAGAATCAACG 59.211 40.000 20.79 0.0 43.24 4.10 F
1143 1155 1.686052 GCTCTCCTTGACGAGATGGAT 59.314 52.381 0.00 0.0 38.22 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1413 2547 0.249405 CCACAACCACAACACCATGC 60.249 55.0 0.0 0.0 0.00 4.06 R
2516 3697 0.169009 GCAATCCGCCACACTTCTTC 59.831 55.0 0.0 0.0 32.94 2.87 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
108 109 5.788531 GGATTCGTGTAAAACAGAATCAACG 59.211 40.000 20.79 0.00 43.24 4.10
1032 1044 2.347490 GACCTGCTCCTCGGCAAA 59.653 61.111 0.00 0.00 41.94 3.68
1042 1054 2.280524 TCGGCAAACTCACCACGG 60.281 61.111 0.00 0.00 0.00 4.94
1135 1147 2.005451 CCATGAAAGCTCTCCTTGACG 58.995 52.381 0.00 0.00 33.01 4.35
1143 1155 1.686052 GCTCTCCTTGACGAGATGGAT 59.314 52.381 0.00 0.00 38.22 3.41
1463 2597 1.067212 GTCGGCGATCTACAAGGATGT 59.933 52.381 14.79 0.00 43.74 3.06
1723 2862 2.233186 CAGGAGTCTTCTCATGCTCACA 59.767 50.000 0.00 0.00 43.66 3.58
1763 2902 2.564947 ACCAGCTTAGAGAACACCTCAG 59.435 50.000 0.00 0.00 44.40 3.35
1809 2948 6.665680 TCTCTAGATAGCTGTATGATTTCCCC 59.334 42.308 0.00 0.00 0.00 4.81
1825 2992 9.671279 ATGATTTCCCCAAAGACATTTAATTTC 57.329 29.630 0.00 0.00 0.00 2.17
1891 3058 3.374678 CCAATGCAAAATATTGTGTGGCC 59.625 43.478 7.46 0.00 38.85 5.36
2166 3346 8.792633 CATCCTTTACTATGTTTGTTTCCTTCA 58.207 33.333 0.00 0.00 0.00 3.02
2182 3362 8.203485 TGTTTCCTTCATTTTAGTTTTGATGCT 58.797 29.630 0.00 0.00 0.00 3.79
2291 3472 3.055167 ACTTGTGGGATCAATCGACATGA 60.055 43.478 0.00 5.31 0.00 3.07
2503 3684 9.132521 CTGCTCGATACAATTCAAAGAAATTTT 57.867 29.630 0.00 0.00 0.00 1.82
2547 3728 3.936372 GCGGATTGCCATACTAGTAGA 57.064 47.619 8.85 0.00 37.76 2.59
2548 3729 4.252971 GCGGATTGCCATACTAGTAGAA 57.747 45.455 8.85 0.00 37.76 2.10
2549 3730 4.628074 GCGGATTGCCATACTAGTAGAAA 58.372 43.478 8.85 0.00 37.76 2.52
2996 4179 2.712709 CTCTACAGGTGTCTCCGAAGA 58.287 52.381 0.00 0.00 41.99 2.87
3284 4467 7.713750 TGACCGATAAAGATCTTCGTAGAATT 58.286 34.615 8.78 0.00 45.90 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.415672 AAAACTGCCCTCCCGAGTCA 61.416 55.000 0.00 0.00 0.00 3.41
787 799 0.323178 CATGGCCAGAGACTGCCTTT 60.323 55.000 13.05 0.00 32.01 3.11
996 1008 1.228831 CAACACCCCTGCCATTCCA 60.229 57.895 0.00 0.00 0.00 3.53
1042 1054 0.386858 TTGTACTCGTCGCTGAGCAC 60.387 55.000 4.88 0.92 39.68 4.40
1135 1147 5.226194 AGCTTGTCCATAAGATCCATCTC 57.774 43.478 0.00 0.00 35.76 2.75
1143 1155 3.782523 AGGGATCAAGCTTGTCCATAAGA 59.217 43.478 31.44 14.01 33.12 2.10
1413 2547 0.249405 CCACAACCACAACACCATGC 60.249 55.000 0.00 0.00 0.00 4.06
1463 2597 1.873178 AATACCCACCAGGCATGCCA 61.873 55.000 37.18 15.60 40.58 4.92
1723 2862 2.555757 GGTCAATGAAGTCTTGCAGCTT 59.444 45.455 0.00 0.80 0.00 3.74
1789 2928 5.912149 TTGGGGAAATCATACAGCTATCT 57.088 39.130 0.00 0.00 0.00 1.98
1825 2992 4.133820 TGACTCATGGGTACAACTGTTTG 58.866 43.478 0.00 0.00 38.83 2.93
2291 3472 7.232534 TCAGGAAAGGCACAACTAATAATGTTT 59.767 33.333 0.00 0.00 0.00 2.83
2476 3657 6.801539 TTTCTTTGAATTGTATCGAGCAGT 57.198 33.333 0.00 0.00 0.00 4.40
2503 3684 6.017109 GCCACACTTCTTCAGAATTTCAACTA 60.017 38.462 0.00 0.00 33.01 2.24
2516 3697 0.169009 GCAATCCGCCACACTTCTTC 59.831 55.000 0.00 0.00 32.94 2.87
2539 3720 9.384764 GCATATTTCCTTCACTTTTCTACTAGT 57.615 33.333 0.00 0.00 0.00 2.57
2540 3721 8.831550 GGCATATTTCCTTCACTTTTCTACTAG 58.168 37.037 0.00 0.00 0.00 2.57
2541 3722 7.773690 GGGCATATTTCCTTCACTTTTCTACTA 59.226 37.037 0.00 0.00 0.00 1.82
2542 3723 6.603599 GGGCATATTTCCTTCACTTTTCTACT 59.396 38.462 0.00 0.00 0.00 2.57
2543 3724 6.603599 AGGGCATATTTCCTTCACTTTTCTAC 59.396 38.462 0.00 0.00 0.00 2.59
2544 3725 6.731467 AGGGCATATTTCCTTCACTTTTCTA 58.269 36.000 0.00 0.00 0.00 2.10
2545 3726 5.583932 AGGGCATATTTCCTTCACTTTTCT 58.416 37.500 0.00 0.00 0.00 2.52
2546 3727 5.921962 AGGGCATATTTCCTTCACTTTTC 57.078 39.130 0.00 0.00 0.00 2.29
2547 3728 6.731467 TCTAGGGCATATTTCCTTCACTTTT 58.269 36.000 0.00 0.00 34.75 2.27
2548 3729 6.327386 TCTAGGGCATATTTCCTTCACTTT 57.673 37.500 0.00 0.00 34.75 2.66
2549 3730 5.163152 CCTCTAGGGCATATTTCCTTCACTT 60.163 44.000 0.00 0.00 34.75 3.16
2996 4179 5.221224 CGAATTATGCCAACCCAACATGTAT 60.221 40.000 0.00 0.00 0.00 2.29
3195 4378 2.787473 ACTTGCCCGAGATTTGATCA 57.213 45.000 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.