Multiple sequence alignment - TraesCS5D01G382300

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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 TraesCS5D01G382300 chr5D 100.000 2670 0 0 1 2670 452215576 452218245 0.000000e+00 4931
1 TraesCS5D01G382300 chr5D 85.421 487 33 17 484 951 451978646 451979113 3.110000e-129 472
2 TraesCS5D01G382300 chr5B 92.089 2705 102 34 1 2670 552292154 552294781 0.000000e+00 3707
3 TraesCS5D01G382300 chr5B 85.283 530 52 12 469 973 551807735 551808263 8.470000e-145 523
4 TraesCS5D01G382300 chr5B 80.285 492 56 24 1 466 551807222 551807698 1.530000e-87 333
5 TraesCS5D01G382300 chr5A 89.695 2232 143 40 467 2670 570936600 570938772 0.000000e+00 2767
6 TraesCS5D01G382300 chr5A 82.025 484 58 23 5 466 570936087 570936563 4.170000e-103 385
7 TraesCS5D01G382300 chr5A 87.086 302 28 6 1 301 33312027 33312318 5.510000e-87 331
8 TraesCS5D01G382300 chr7A 87.625 299 26 6 1 298 315704460 315704748 1.180000e-88 337
9 TraesCS5D01G382300 chr1A 87.797 295 26 5 7 301 191561235 191560951 1.180000e-88 337
10 TraesCS5D01G382300 chrUn 87.291 299 26 6 1 298 62126558 62126845 5.510000e-87 331
11 TraesCS5D01G382300 chr6A 87.086 302 28 6 1 301 204398541 204398250 5.510000e-87 331
12 TraesCS5D01G382300 chr2A 86.424 302 30 6 1 301 108313880 108314171 1.190000e-83 320
13 TraesCS5D01G382300 chr4A 86.093 302 31 6 1 301 216408482 216408773 5.550000e-82 315


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 TraesCS5D01G382300 chr5D 452215576 452218245 2669 False 4931 4931 100.000 1 2670 1 chr5D.!!$F2 2669
1 TraesCS5D01G382300 chr5B 552292154 552294781 2627 False 3707 3707 92.089 1 2670 1 chr5B.!!$F1 2669
2 TraesCS5D01G382300 chr5B 551807222 551808263 1041 False 428 523 82.784 1 973 2 chr5B.!!$F2 972
3 TraesCS5D01G382300 chr5A 570936087 570938772 2685 False 1576 2767 85.860 5 2670 2 chr5A.!!$F2 2665

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
181 184 0.031994 ATCAGGCGGCACAAACAAAC 59.968 50.0 13.08 0.0 0.0 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2110 2239 0.817654 ATGAATGCGAGGAGACGACA 59.182 50.0 0.0 0.0 35.09 4.35 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
120 123 8.363390 TCAAAGAGAAGCATATGAGTATACCTG 58.637 37.037 6.97 0.00 0.00 4.00
133 136 4.855340 AGTATACCTGGGTTTGGAACATG 58.145 43.478 0.00 0.00 39.30 3.21
139 142 0.603065 GGGTTTGGAACATGAGTGCC 59.397 55.000 0.00 0.00 44.61 5.01
181 184 0.031994 ATCAGGCGGCACAAACAAAC 59.968 50.000 13.08 0.00 0.00 2.93
187 190 1.668237 GCGGCACAAACAAACCATTTT 59.332 42.857 0.00 0.00 0.00 1.82
190 193 4.024472 GCGGCACAAACAAACCATTTTTAT 60.024 37.500 0.00 0.00 0.00 1.40
249 252 2.416547 ACGAGAAACATTGAATCTGCCG 59.583 45.455 0.00 0.00 0.00 5.69
270 282 5.742926 GCCGACTTAGAGTAATCACAAGTAC 59.257 44.000 9.34 0.00 29.89 2.73
271 283 6.404513 GCCGACTTAGAGTAATCACAAGTACT 60.405 42.308 9.34 0.00 38.92 2.73
272 284 7.201679 GCCGACTTAGAGTAATCACAAGTACTA 60.202 40.741 9.34 0.00 36.47 1.82
316 329 1.440353 GTCGCGCGCAGAAACAAAT 60.440 52.632 32.61 0.00 0.00 2.32
324 337 0.598065 GCAGAAACAAATCCCGCACT 59.402 50.000 0.00 0.00 0.00 4.40
325 338 1.401539 GCAGAAACAAATCCCGCACTC 60.402 52.381 0.00 0.00 0.00 3.51
326 339 2.154462 CAGAAACAAATCCCGCACTCT 58.846 47.619 0.00 0.00 0.00 3.24
329 342 4.396166 CAGAAACAAATCCCGCACTCTAAT 59.604 41.667 0.00 0.00 0.00 1.73
343 374 4.985409 GCACTCTAATTCATCCCTCGTAAG 59.015 45.833 0.00 0.00 0.00 2.34
382 413 2.879826 ACTTGTTTTCACAGCAGTTGC 58.120 42.857 0.00 0.00 42.49 4.17
412 443 7.361286 GCAATTAGAGCAGGCAATAATACTACC 60.361 40.741 0.00 0.00 0.00 3.18
482 549 2.049156 TGAGACGGAGCAAGCACG 60.049 61.111 7.45 7.45 0.00 5.34
541 616 2.544685 CGAGTCACAAGCTATGAAGGG 58.455 52.381 2.28 0.00 0.00 3.95
647 738 2.364448 AAGAGGAGGCGGGGAGAC 60.364 66.667 0.00 0.00 0.00 3.36
873 968 2.250188 CCCATGAATTGCGTTTCGTTC 58.750 47.619 0.00 0.00 0.00 3.95
982 1080 0.386985 GTTCCTTCGCGACTCGTCTT 60.387 55.000 9.15 0.00 39.67 3.01
1586 1703 6.014647 TCCTTTCAACTGCTACTCCTACTAA 58.985 40.000 0.00 0.00 0.00 2.24
1740 1860 3.797184 GCTTTGCAAAATTGTCCACGGTA 60.797 43.478 13.84 0.00 0.00 4.02
1773 1893 4.955925 ACGTATTCAGAGAGACAGACAG 57.044 45.455 0.00 0.00 0.00 3.51
1775 1895 4.393680 ACGTATTCAGAGAGACAGACAGAC 59.606 45.833 0.00 0.00 0.00 3.51
1915 2041 2.809446 TCAGCTTCATCGATAACACCG 58.191 47.619 0.00 0.00 0.00 4.94
1927 2056 0.396695 TAACACCGCCAAAACCCCAA 60.397 50.000 0.00 0.00 0.00 4.12
1982 2111 0.040204 AAGCTTGCTGCCCAACCTAT 59.960 50.000 0.00 0.00 44.23 2.57
2101 2230 1.186200 TCTCCTCCTCCATGTTGACG 58.814 55.000 0.00 0.00 0.00 4.35
2110 2239 2.421073 CTCCATGTTGACGTCATGCATT 59.579 45.455 24.42 13.02 40.63 3.56
2128 2257 0.601057 TTGTCGTCTCCTCGCATTCA 59.399 50.000 0.00 0.00 0.00 2.57
2260 2389 2.592102 AGAGCTTGCCCTTCATGAAA 57.408 45.000 9.88 0.00 0.00 2.69
2363 2494 9.448438 TCAGCAAGTACATTTTTACATCAGTAT 57.552 29.630 0.00 0.00 0.00 2.12
2375 2506 9.952030 TTTTTACATCAGTATACAGATTGGTCA 57.048 29.630 7.97 0.00 0.00 4.02
2532 2663 3.037549 AGAAGAGATCATCGCCCTTTCT 58.962 45.455 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 123 0.603065 GGCACTCATGTTCCAAACCC 59.397 55.000 0.00 0.00 29.71 4.11
133 136 1.150536 TGTTTCCTGGGTGGCACTC 59.849 57.895 18.45 15.20 35.26 3.51
139 142 5.160607 TGATTACTAGTGTTTCCTGGGTG 57.839 43.478 5.39 0.00 0.00 4.61
200 203 7.156000 TCGAATACAACTATGAACCACTTTGA 58.844 34.615 0.00 0.00 0.00 2.69
270 282 6.574350 AGACTCGGTTGTATTCAGGAAATAG 58.426 40.000 0.00 0.00 30.39 1.73
271 283 6.540438 AGACTCGGTTGTATTCAGGAAATA 57.460 37.500 0.00 0.00 0.00 1.40
272 284 5.422214 AGACTCGGTTGTATTCAGGAAAT 57.578 39.130 0.00 0.00 0.00 2.17
279 291 4.341099 CGACAGTAGACTCGGTTGTATTC 58.659 47.826 0.00 0.00 0.00 1.75
316 329 1.416401 GGGATGAATTAGAGTGCGGGA 59.584 52.381 0.00 0.00 0.00 5.14
324 337 4.039245 CCAGCTTACGAGGGATGAATTAGA 59.961 45.833 0.00 0.00 0.00 2.10
325 338 4.202264 ACCAGCTTACGAGGGATGAATTAG 60.202 45.833 0.00 0.00 0.00 1.73
326 339 3.709653 ACCAGCTTACGAGGGATGAATTA 59.290 43.478 0.00 0.00 0.00 1.40
329 342 1.480954 GACCAGCTTACGAGGGATGAA 59.519 52.381 0.00 0.00 0.00 2.57
343 374 2.007608 GTTCCCATTTCGTAGACCAGC 58.992 52.381 0.00 0.00 34.32 4.85
382 413 1.466856 TGCCTGCTCTAATTGCCTTG 58.533 50.000 0.00 0.00 0.00 3.61
482 549 0.747255 TTCCTAGTCAGATCTGCGGC 59.253 55.000 18.36 10.29 0.00 6.53
541 616 2.028883 CGTCGCCTAGGTTTTCGATTTC 59.971 50.000 11.31 0.00 33.37 2.17
840 935 1.526917 CATGGGCCTTAGAAGCGGG 60.527 63.158 4.53 0.00 0.00 6.13
913 1011 4.465512 CATGCAACAGCGGGCGTC 62.466 66.667 0.00 0.00 0.00 5.19
1553 1670 8.779354 AGTAGCAGTTGAAAGGAGTTTATTAG 57.221 34.615 0.00 0.00 0.00 1.73
1610 1730 5.294306 TGTCGATCTAAGCACAATTCCATTC 59.706 40.000 0.00 0.00 0.00 2.67
1740 1860 5.183331 TCTCTGAATACGTTGTCTAAGCAGT 59.817 40.000 0.00 0.00 0.00 4.40
1773 1893 1.259507 TGAAAACTAACGCACGCTGTC 59.740 47.619 0.00 0.00 0.00 3.51
1775 1895 1.004398 TGTGAAAACTAACGCACGCTG 60.004 47.619 0.00 0.00 34.12 5.18
1915 2041 1.006220 CGCTCTTTGGGGTTTTGGC 60.006 57.895 0.00 0.00 0.00 4.52
1927 2056 2.976490 AAGATGCCTGCCCGCTCTT 61.976 57.895 0.00 0.00 0.00 2.85
1982 2111 1.217001 CAGTGCGCACAACAGTAAGA 58.783 50.000 39.21 0.00 0.00 2.10
2101 2230 1.929836 GAGGAGACGACAATGCATGAC 59.070 52.381 0.00 0.00 0.00 3.06
2110 2239 0.817654 ATGAATGCGAGGAGACGACA 59.182 50.000 0.00 0.00 35.09 4.35
2128 2257 1.037579 TGACCGACATGGAGCTCGAT 61.038 55.000 7.83 6.51 42.00 3.59
2218 2347 3.888930 ACATTCATTTCACGGTGGAGTTT 59.111 39.130 8.50 0.00 0.00 2.66
2260 2389 2.435693 GCCGATGTACCAGAGGCCT 61.436 63.158 3.86 3.86 41.81 5.19
2323 2452 8.177119 TGTACTTGCTGATAATCTTTGGTTTT 57.823 30.769 0.00 0.00 0.00 2.43
2358 2489 6.456795 TCTCAGTGACCAATCTGTATACTG 57.543 41.667 4.17 3.79 36.03 2.74
2363 2494 7.062957 TCATAGATCTCAGTGACCAATCTGTA 58.937 38.462 0.00 1.54 33.89 2.74
2375 2506 4.093011 GGTATGGCCTCATAGATCTCAGT 58.907 47.826 3.32 0.00 36.62 3.41
2409 2540 6.588719 TCATTAAATCAAACCCTGGTGAAG 57.411 37.500 0.00 0.00 0.00 3.02
2532 2663 1.766496 AGGAACACCCGAAGTTCAAGA 59.234 47.619 3.32 0.00 45.45 3.02


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

AutoCloner maintained by Alex Coulton.