Multiple sequence alignment - TraesCS6D01G117300

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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 TraesCS6D01G117300 chr6D 100.000 2399 0 0 1 2399 83123288 83125686 0.000000e+00 4431
1 TraesCS6D01G117300 chr6D 93.324 1498 100 0 1 1498 83542044 83540547 0.000000e+00 2213
2 TraesCS6D01G117300 chr6D 88.227 1410 161 5 3 1410 83045428 83046834 0.000000e+00 1679
3 TraesCS6D01G117300 chr6D 88.028 1420 164 5 3 1419 83158962 83160378 0.000000e+00 1676
4 TraesCS6D01G117300 chr6D 84.746 236 19 10 1576 1806 83827507 83827284 1.120000e-53 220
5 TraesCS6D01G117300 chr6D 84.255 235 19 11 1576 1804 83540156 83539934 1.870000e-51 213
6 TraesCS6D01G117300 chr6D 87.903 124 9 3 2275 2397 83827910 83827792 8.940000e-30 141
7 TraesCS6D01G117300 chr6B 96.106 2414 69 8 1 2397 158148357 158150762 0.000000e+00 3914
8 TraesCS6D01G117300 chr6B 93.124 1498 103 0 1 1498 159403512 159402015 0.000000e+00 2196
9 TraesCS6D01G117300 chr6B 87.764 1422 160 13 3 1419 158161576 158162988 0.000000e+00 1650
10 TraesCS6D01G117300 chr6B 87.732 269 25 6 1306 1572 158150419 158150681 8.330000e-80 307
11 TraesCS6D01G117300 chr6B 92.857 126 6 3 2275 2397 159402021 159401896 1.890000e-41 180
12 TraesCS6D01G117300 chr6A 95.712 1539 65 1 1 1538 100183645 100185183 0.000000e+00 2475
13 TraesCS6D01G117300 chr6A 93.258 1498 101 0 1 1498 100762418 100760921 0.000000e+00 2207
14 TraesCS6D01G117300 chr6A 92.790 1498 99 3 1 1498 100804479 100802991 0.000000e+00 2159
15 TraesCS6D01G117300 chr6A 94.110 815 31 6 1596 2397 100185185 100185995 0.000000e+00 1223
16 TraesCS6D01G117300 chr6A 92.800 125 7 2 2275 2397 100760927 100760803 1.890000e-41 180
17 TraesCS6D01G117300 chr6A 79.762 252 20 12 1584 1806 100760537 100760288 1.150000e-33 154
18 TraesCS6D01G117300 chr6A 92.000 100 8 0 1707 1806 100802464 100802365 8.940000e-30 141


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 TraesCS6D01G117300 chr6D 83123288 83125686 2398 False 4431.0 4431 100.000000 1 2399 1 chr6D.!!$F2 2398
1 TraesCS6D01G117300 chr6D 83045428 83046834 1406 False 1679.0 1679 88.227000 3 1410 1 chr6D.!!$F1 1407
2 TraesCS6D01G117300 chr6D 83158962 83160378 1416 False 1676.0 1676 88.028000 3 1419 1 chr6D.!!$F3 1416
3 TraesCS6D01G117300 chr6D 83539934 83542044 2110 True 1213.0 2213 88.789500 1 1804 2 chr6D.!!$R1 1803
4 TraesCS6D01G117300 chr6B 158148357 158150762 2405 False 2110.5 3914 91.919000 1 2397 2 chr6B.!!$F2 2396
5 TraesCS6D01G117300 chr6B 158161576 158162988 1412 False 1650.0 1650 87.764000 3 1419 1 chr6B.!!$F1 1416
6 TraesCS6D01G117300 chr6B 159401896 159403512 1616 True 1188.0 2196 92.990500 1 2397 2 chr6B.!!$R1 2396
7 TraesCS6D01G117300 chr6A 100183645 100185995 2350 False 1849.0 2475 94.911000 1 2397 2 chr6A.!!$F1 2396
8 TraesCS6D01G117300 chr6A 100802365 100804479 2114 True 1150.0 2159 92.395000 1 1806 2 chr6A.!!$R2 1805
9 TraesCS6D01G117300 chr6A 100760288 100762418 2130 True 847.0 2207 88.606667 1 2397 3 chr6A.!!$R1 2396

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
875 877 1.174712 AGCACAGCAAAAGATGGCGT 61.175 50.0 0.0 0.0 34.54 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2040 2412 0.534412 CAGCCTCACGAGAATCCAGT 59.466 55.0 0.0 0.0 0.0 4.0 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
150 151 4.290722 ACCTGGAGATTCTTGAAACCATCT 59.709 41.667 0.00 0.00 0.00 2.90
151 152 4.639310 CCTGGAGATTCTTGAAACCATCTG 59.361 45.833 0.00 0.00 0.00 2.90
300 301 5.366768 TGATAGGAATAACAGGGACTTCAGG 59.633 44.000 0.00 0.00 34.60 3.86
730 731 1.819903 AGAGGTGCTCTAACGAGGTTC 59.180 52.381 0.00 0.00 39.28 3.62
875 877 1.174712 AGCACAGCAAAAGATGGCGT 61.175 50.000 0.00 0.00 34.54 5.68
1040 1042 1.091771 CGCGCAGGGATTGAAGATGT 61.092 55.000 8.75 0.00 46.37 3.06
1137 1139 2.386864 TGGCAAGCCACCAGATAGT 58.613 52.632 10.24 0.00 41.89 2.12
1186 1188 2.672996 CGGTGAGGTTGCCAAGGG 60.673 66.667 0.00 0.00 0.00 3.95
1188 1190 1.384191 GGTGAGGTTGCCAAGGGAT 59.616 57.895 0.00 0.00 0.00 3.85
1289 1291 1.962822 ATGTGCAGCAGTCGGTGTG 60.963 57.895 0.00 0.00 42.79 3.82
1435 1437 1.133025 CCAAGCTAAACGAAGGCATGG 59.867 52.381 0.00 0.00 38.22 3.66
1448 1450 3.893326 AGGCATGGTAAAATTCTTGGC 57.107 42.857 0.00 0.00 35.07 4.52
1574 1928 4.217334 TGTTGTTTGACAGTTTCTGAAGCA 59.783 37.500 7.01 0.00 35.18 3.91
1691 2051 5.279506 CCACTTTAGGACTTTGTGAGAGCTA 60.280 44.000 0.00 0.00 0.00 3.32
1989 2357 5.007136 GGAGGCGATTTCAGAGTCAAATAAG 59.993 44.000 0.00 0.00 0.00 1.73
2040 2412 6.983307 GCTCTCTCAACTTCAATAGAATGCTA 59.017 38.462 0.00 0.00 32.31 3.49
2058 2430 2.028130 CTACTGGATTCTCGTGAGGCT 58.972 52.381 0.00 0.00 0.00 4.58
2153 2527 2.880890 GAGAGACCAAAAAGAGCAGCAA 59.119 45.455 0.00 0.00 0.00 3.91
2175 2549 2.421424 CACCAGAGCCAAGCTAAATGAC 59.579 50.000 0.00 0.00 39.88 3.06
2229 2609 2.489938 AATAGTGGATGCACGGTGTT 57.510 45.000 12.02 3.08 0.00 3.32
2250 2630 1.944709 GTGGTGAAACTAGCAACGGTT 59.055 47.619 0.00 0.00 36.74 4.44
2265 2645 4.272748 GCAACGGTTTAGTGAAGAAAGAGT 59.727 41.667 0.00 0.00 0.00 3.24
2331 2712 2.484264 CCTGAAACTGTCCATTCCGAAC 59.516 50.000 0.00 0.00 0.00 3.95
2397 2778 3.896648 TTCGGATTCTGTCAGTTTTGC 57.103 42.857 0.00 0.00 0.00 3.68
2398 2779 2.151202 TCGGATTCTGTCAGTTTTGCC 58.849 47.619 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
150 151 1.297689 GCCAGAGGATGTCAGCACA 59.702 57.895 0.00 0.0 36.78 4.57
151 152 0.107312 ATGCCAGAGGATGTCAGCAC 60.107 55.000 0.00 0.0 38.95 4.40
300 301 6.803807 GTCAATTGTCAGAAGAAATAGGCAAC 59.196 38.462 5.13 0.0 0.00 4.17
730 731 3.988976 TCCAGATGAACTCTTCAAGGG 57.011 47.619 0.00 0.0 43.95 3.95
875 877 2.073056 CAACTACGCCATGTGTTAGCA 58.927 47.619 0.00 0.0 0.00 3.49
1030 1032 2.306805 TGGGTGAGCTGACATCTTCAAT 59.693 45.455 5.47 0.0 32.21 2.57
1040 1042 3.005539 GAGGCCTGGGTGAGCTGA 61.006 66.667 12.00 0.0 0.00 4.26
1137 1139 0.761323 TCAACCTGTCCCGGAACTCA 60.761 55.000 0.73 0.0 0.00 3.41
1335 1337 1.271127 GCTCCCTTCTCCAGCTCCTT 61.271 60.000 0.00 0.0 0.00 3.36
1435 1437 3.638484 ACAAGCACGCCAAGAATTTTAC 58.362 40.909 0.00 0.0 0.00 2.01
1448 1450 7.113404 GCCATTATATTTCATACAACAAGCACG 59.887 37.037 0.00 0.0 0.00 5.34
1574 1928 2.149578 GCAAGATGCATCCGATTAGCT 58.850 47.619 23.06 0.0 44.26 3.32
1691 2051 1.823797 AAGAACTCGAGTAGCTCCGT 58.176 50.000 20.39 0.0 0.00 4.69
1935 2295 5.650283 TCTTATTCCATGTCCAAAGGGTTT 58.350 37.500 0.00 0.0 34.93 3.27
2040 2412 0.534412 CAGCCTCACGAGAATCCAGT 59.466 55.000 0.00 0.0 0.00 4.00
2058 2430 3.531207 CGCTCTCTCGGGATGGCA 61.531 66.667 9.69 0.0 0.00 4.92
2143 2517 0.888285 GCTCTGGTGTTGCTGCTCTT 60.888 55.000 0.00 0.0 0.00 2.85
2153 2527 2.040278 TCATTTAGCTTGGCTCTGGTGT 59.960 45.455 0.00 0.0 40.44 4.16
2175 2549 7.748847 AGTACACTAAGAATTTTAACATGCCG 58.251 34.615 0.00 0.0 0.00 5.69
2229 2609 1.134340 ACCGTTGCTAGTTTCACCACA 60.134 47.619 0.00 0.0 0.00 4.17
2250 2630 4.316205 TCGCACACTCTTTCTTCACTAA 57.684 40.909 0.00 0.0 0.00 2.24
2265 2645 1.593209 GGACAGTTCCGTTCGCACA 60.593 57.895 0.00 0.0 29.98 4.57
2331 2712 3.627577 AGGAAATGGCAGTTTAGTATGCG 59.372 43.478 0.19 0.0 43.49 4.73


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

AutoCloner maintained by Alex Coulton.