Multiple sequence alignment - TraesCS6B01G155300

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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 TraesCS6B01G155300 chr6B 100.000 3215 0 0 1 3215 158163125 158159911 0.000000e+00 5938.0
1 TraesCS6B01G155300 chr6B 84.665 2465 335 31 1 2445 159377885 159380326 0.000000e+00 2418.0
2 TraesCS6B01G155300 chr6B 84.381 2228 327 19 119 2336 159395984 159398200 0.000000e+00 2167.0
3 TraesCS6B01G155300 chr6D 96.124 2451 85 7 1 2444 83160515 83158068 0.000000e+00 3991.0
4 TraesCS6B01G155300 chr6D 83.285 2405 370 25 23 2402 83046957 83044560 0.000000e+00 2185.0
5 TraesCS6B01G155300 chr6D 84.064 1826 271 17 54 1869 83525237 83527052 0.000000e+00 1742.0
6 TraesCS6B01G155300 chr6A 96.453 2340 79 2 1 2336 100228985 100226646 0.000000e+00 3858.0
7 TraesCS6B01G155300 chr6A 85.708 2421 307 28 54 2444 100797485 100799896 0.000000e+00 2518.0
8 TraesCS6B01G155300 chr6A 85.163 2460 328 26 1 2441 100738147 100740588 0.000000e+00 2486.0
9 TraesCS6B01G155300 chr6A 83.677 2426 355 20 54 2444 100755377 100757796 0.000000e+00 2248.0
10 TraesCS6B01G155300 chr2B 96.253 774 27 2 2443 3215 385137120 385137892 0.000000e+00 1267.0
11 TraesCS6B01G155300 chr1B 94.703 774 37 3 2443 3215 130106123 130105353 0.000000e+00 1199.0
12 TraesCS6B01G155300 chr3B 93.694 777 40 7 2442 3215 541576538 541575768 0.000000e+00 1155.0
13 TraesCS6B01G155300 chr3B 93.979 764 42 4 2443 3205 466660779 466660019 0.000000e+00 1153.0
14 TraesCS6B01G155300 chr3B 92.885 773 51 4 2444 3215 386975704 386974935 0.000000e+00 1120.0
15 TraesCS6B01G155300 chr3B 96.087 230 9 0 2106 2335 680860917 680860688 3.030000e-100 375.0
16 TraesCS6B01G155300 chr7B 93.565 777 43 5 2443 3215 479926462 479927235 0.000000e+00 1151.0
17 TraesCS6B01G155300 chr5A 92.298 779 47 9 2439 3215 211644892 211644125 0.000000e+00 1094.0
18 TraesCS6B01G155300 chr7D 92.000 775 53 8 2443 3215 181004478 181003711 0.000000e+00 1079.0
19 TraesCS6B01G155300 chr7D 85.714 77 2 7 2410 2483 544781043 544781113 4.450000e-09 73.1
20 TraesCS6B01G155300 chr4B 90.698 774 61 8 2443 3215 613938597 613937834 0.000000e+00 1020.0


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 TraesCS6B01G155300 chr6B 158159911 158163125 3214 True 5938 5938 100.000 1 3215 1 chr6B.!!$R1 3214
1 TraesCS6B01G155300 chr6B 159377885 159380326 2441 False 2418 2418 84.665 1 2445 1 chr6B.!!$F1 2444
2 TraesCS6B01G155300 chr6B 159395984 159398200 2216 False 2167 2167 84.381 119 2336 1 chr6B.!!$F2 2217
3 TraesCS6B01G155300 chr6D 83158068 83160515 2447 True 3991 3991 96.124 1 2444 1 chr6D.!!$R2 2443
4 TraesCS6B01G155300 chr6D 83044560 83046957 2397 True 2185 2185 83.285 23 2402 1 chr6D.!!$R1 2379
5 TraesCS6B01G155300 chr6D 83525237 83527052 1815 False 1742 1742 84.064 54 1869 1 chr6D.!!$F1 1815
6 TraesCS6B01G155300 chr6A 100226646 100228985 2339 True 3858 3858 96.453 1 2336 1 chr6A.!!$R1 2335
7 TraesCS6B01G155300 chr6A 100797485 100799896 2411 False 2518 2518 85.708 54 2444 1 chr6A.!!$F3 2390
8 TraesCS6B01G155300 chr6A 100738147 100740588 2441 False 2486 2486 85.163 1 2441 1 chr6A.!!$F1 2440
9 TraesCS6B01G155300 chr6A 100755377 100757796 2419 False 2248 2248 83.677 54 2444 1 chr6A.!!$F2 2390
10 TraesCS6B01G155300 chr2B 385137120 385137892 772 False 1267 1267 96.253 2443 3215 1 chr2B.!!$F1 772
11 TraesCS6B01G155300 chr1B 130105353 130106123 770 True 1199 1199 94.703 2443 3215 1 chr1B.!!$R1 772
12 TraesCS6B01G155300 chr3B 541575768 541576538 770 True 1155 1155 93.694 2442 3215 1 chr3B.!!$R3 773
13 TraesCS6B01G155300 chr3B 466660019 466660779 760 True 1153 1153 93.979 2443 3205 1 chr3B.!!$R2 762
14 TraesCS6B01G155300 chr3B 386974935 386975704 769 True 1120 1120 92.885 2444 3215 1 chr3B.!!$R1 771
15 TraesCS6B01G155300 chr7B 479926462 479927235 773 False 1151 1151 93.565 2443 3215 1 chr7B.!!$F1 772
16 TraesCS6B01G155300 chr5A 211644125 211644892 767 True 1094 1094 92.298 2439 3215 1 chr5A.!!$R1 776
17 TraesCS6B01G155300 chr7D 181003711 181004478 767 True 1079 1079 92.000 2443 3215 1 chr7D.!!$R1 772
18 TraesCS6B01G155300 chr4B 613937834 613938597 763 True 1020 1020 90.698 2443 3215 1 chr4B.!!$R1 772

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
466 468 0.179702 TGTCATCCAGCAGCATCCTC 59.820 55.000 0.0 0.0 0.0 3.71 F
790 793 1.134250 TCAGTGCTGGCTACAACAACA 60.134 47.619 0.0 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1663 1670 3.129988 GCATAAACAGGCAGCTCAAAGAT 59.87 43.478 0.0 0.0 0.0 2.40 R
2513 2561 0.109964 GTGTGTTTGTGTGCGTGTGT 60.11 50.000 0.0 0.0 0.0 3.72 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
117 119 0.319211 CGCTCACACAGGAACGGTTA 60.319 55.000 0.00 0.00 31.98 2.85
149 151 1.134220 TCTTCGGTTTGGCTCTTGTGT 60.134 47.619 0.00 0.00 0.00 3.72
164 166 4.265893 TCTTGTGTTACTGGTTTGCTTGA 58.734 39.130 0.00 0.00 0.00 3.02
466 468 0.179702 TGTCATCCAGCAGCATCCTC 59.820 55.000 0.00 0.00 0.00 3.71
567 569 6.692486 AGGTACTGAACATCTCAAGTAACTG 58.308 40.000 0.00 0.00 35.82 3.16
790 793 1.134250 TCAGTGCTGGCTACAACAACA 60.134 47.619 0.00 0.00 0.00 3.33
799 802 1.812571 GCTACAACAACATCAGTGGGG 59.187 52.381 0.00 0.00 0.00 4.96
849 852 3.850273 GGTCGTTACAGTACATCTCGTTG 59.150 47.826 0.00 0.00 0.00 4.10
928 932 4.044571 TCACCCTTGATCTTGGGAAGAATT 59.955 41.667 24.03 4.15 46.15 2.17
929 933 4.774200 CACCCTTGATCTTGGGAAGAATTT 59.226 41.667 24.03 3.56 46.15 1.82
1164 1171 1.197721 GACTTCACTGGCACAATTCCG 59.802 52.381 0.00 0.00 38.70 4.30
1287 1294 7.903145 TCTGCTTTCTATCACTTGTTAACCTA 58.097 34.615 2.48 0.00 0.00 3.08
1455 1462 6.764308 ATGAGTTATTGTTCAATGTCTGGG 57.236 37.500 8.11 0.00 0.00 4.45
1642 1649 4.022589 CGGAGATGCCAATGCTAAAATCAT 60.023 41.667 0.00 0.00 38.71 2.45
1663 1670 1.921982 TAAGATTGCAGCAAAGGCCA 58.078 45.000 12.97 0.00 42.56 5.36
1711 1719 6.187727 TCAGTCCATTTATCCAATACCTCC 57.812 41.667 0.00 0.00 0.00 4.30
1758 1766 9.403110 GTGCTTAATCTAGCCATCAATAAATTG 57.597 33.333 0.00 0.00 40.49 2.32
1801 1809 2.515854 TCGGTCAACTAAGAGCACTCT 58.484 47.619 0.00 0.00 42.75 3.24
2191 2200 8.052141 CAGTAGGAGTCCTATATGATCAGATGA 58.948 40.741 21.88 0.00 38.48 2.92
2381 2426 3.599343 ACATGATTAGCGAGTGAGCAAA 58.401 40.909 0.00 0.00 40.15 3.68
2397 2442 4.697828 TGAGCAAAGTCAACAGTGTGTAAA 59.302 37.500 0.00 0.00 0.00 2.01
2402 2447 9.062524 AGCAAAGTCAACAGTGTGTAAATATTA 57.937 29.630 0.00 0.00 0.00 0.98
2411 2456 9.906660 AACAGTGTGTAAATATTATTGTTGTGG 57.093 29.630 0.00 0.00 0.00 4.17
2499 2546 1.821936 CAACTGCCCAAGCCAACAA 59.178 52.632 0.00 0.00 38.69 2.83
2519 2567 0.376852 CCAACACAGGTTCACACACG 59.623 55.000 0.00 0.00 34.21 4.49
2569 2624 2.298610 GTAGCCAAGAGGGTTAATGCC 58.701 52.381 0.00 0.00 45.14 4.40
2588 2643 1.021202 CGAGGGCACAACTCAACAAA 58.979 50.000 0.00 0.00 34.66 2.83
2760 2818 0.392461 CTAAGTGGCCGCCAAAGCTA 60.392 55.000 15.39 2.43 34.18 3.32
2798 2858 1.726853 AAAGATGGTGTCAGTAGCGC 58.273 50.000 0.00 0.00 0.00 5.92
2799 2859 0.458543 AAGATGGTGTCAGTAGCGCG 60.459 55.000 0.00 0.00 0.00 6.86
2800 2860 1.153823 GATGGTGTCAGTAGCGCGT 60.154 57.895 8.43 0.00 0.00 6.01
2801 2861 0.736325 GATGGTGTCAGTAGCGCGTT 60.736 55.000 8.43 3.54 0.00 4.84
2921 2982 1.301558 GAGGCATGGATCTCCGCAG 60.302 63.158 0.00 0.00 39.43 5.18
2991 3052 3.006537 CGGAAACTGGACCAGAGAAACTA 59.993 47.826 28.56 0.00 35.18 2.24
3154 3215 0.251121 TGATTTTCAGGGGCAAGCGA 60.251 50.000 0.00 0.00 0.00 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 119 3.855159 CCGAAGAAAGGAACGGGAT 57.145 52.632 0.00 0.0 41.41 3.85
149 151 4.522789 GGGAGAATTCAAGCAAACCAGTAA 59.477 41.667 8.44 0.0 0.00 2.24
349 351 0.840722 ACGGTGAGATGGACCCCTTT 60.841 55.000 0.00 0.0 0.00 3.11
388 390 0.465460 ACAGGTTGAGGCGCAAAAGA 60.465 50.000 10.83 0.0 38.44 2.52
466 468 3.496130 AGTTGAAGCTGACATCAAGAACG 59.504 43.478 0.00 0.0 34.39 3.95
790 793 0.842030 TCTGGAAGTGCCCCACTGAT 60.842 55.000 0.00 0.0 44.62 2.90
799 802 5.123027 CCTTAAAGAGTTCATCTGGAAGTGC 59.877 44.000 0.00 0.0 39.28 4.40
1164 1171 2.810852 GCTGCAGGAGTATATGCTTTCC 59.189 50.000 17.12 0.0 42.98 3.13
1287 1294 6.761714 GTGTTCTCGTGATATTTGTAAGGGAT 59.238 38.462 0.00 0.0 0.00 3.85
1642 1649 3.630168 TGGCCTTTGCTGCAATCTTATA 58.370 40.909 16.77 0.0 37.74 0.98
1663 1670 3.129988 GCATAAACAGGCAGCTCAAAGAT 59.870 43.478 0.00 0.0 0.00 2.40
1729 1737 6.874288 ATTGATGGCTAGATTAAGCACTTC 57.126 37.500 0.00 0.0 44.64 3.01
1801 1809 7.106439 TGTTGGAGCTCAAATTAAGTGAAAA 57.894 32.000 17.19 0.0 37.08 2.29
2354 2398 4.183865 TCACTCGCTAATCATGTTTCAGG 58.816 43.478 0.00 0.0 0.00 3.86
2356 2400 3.618594 GCTCACTCGCTAATCATGTTTCA 59.381 43.478 0.00 0.0 0.00 2.69
2499 2546 1.459450 GTGTGTGAACCTGTGTTGGT 58.541 50.000 0.00 0.0 43.11 3.67
2512 2560 0.110010 TGTGTTTGTGTGCGTGTGTG 60.110 50.000 0.00 0.0 0.00 3.82
2513 2561 0.109964 GTGTGTTTGTGTGCGTGTGT 60.110 50.000 0.00 0.0 0.00 3.72
2519 2567 1.094785 AGACCTGTGTGTTTGTGTGC 58.905 50.000 0.00 0.0 0.00 4.57
2569 2624 1.021202 TTTGTTGAGTTGTGCCCTCG 58.979 50.000 0.00 0.0 0.00 4.63
2588 2643 4.503910 GTGCTTTTTCTGTTTTTCAGGGT 58.496 39.130 0.00 0.0 43.76 4.34
2760 2818 7.255801 CCATCTTTAAAATGTGTGGGTACTTGT 60.256 37.037 0.00 0.0 0.00 3.16
2798 2858 0.671781 CAGAAGGTGCCTCTCCAACG 60.672 60.000 0.00 0.0 0.00 4.10
2799 2859 0.322008 CCAGAAGGTGCCTCTCCAAC 60.322 60.000 0.00 0.0 0.00 3.77
2800 2860 0.473694 TCCAGAAGGTGCCTCTCCAA 60.474 55.000 0.00 0.0 35.89 3.53
2801 2861 0.252881 ATCCAGAAGGTGCCTCTCCA 60.253 55.000 0.00 0.0 35.89 3.86
2840 2900 0.962356 CTTGCCTGGACGCTTTGGAT 60.962 55.000 0.00 0.0 0.00 3.41
2921 2982 1.303643 CCAACTTCCCTGACCTGCC 60.304 63.158 0.00 0.0 0.00 4.85
3065 3126 1.207329 GGTCCTCAAGCGTAATGGACT 59.793 52.381 14.87 0.0 44.60 3.85
3154 3215 4.338879 CCTTCAGTCTGATTTGGGACATT 58.661 43.478 2.68 0.0 39.30 2.71


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

AutoCloner maintained by Alex Coulton.