Multiple sequence alignment - TraesCS5A01G290900

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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 TraesCS5A01G290900 chr5A 100.000 2728 0 0 1 2728 501834669 501837396 0 5038
1 TraesCS5A01G290900 chr2D 97.656 2730 50 8 1 2728 178274771 178272054 0 4674
2 TraesCS5A01G290900 chr2D 97.217 2623 54 6 1 2617 511935116 511932507 0 4421
3 TraesCS5A01G290900 chr2B 96.770 2755 62 6 1 2728 640105741 640108495 0 4569
4 TraesCS5A01G290900 chr2B 96.078 2754 82 6 1 2728 683669800 683672553 0 4464
5 TraesCS5A01G290900 chr1B 96.659 2754 66 6 1 2728 313093405 313090652 0 4553
6 TraesCS5A01G290900 chr1B 96.587 2754 63 10 1 2728 277434044 277436792 0 4536
7 TraesCS5A01G290900 chr3B 96.623 2754 64 7 1 2728 312175331 312172581 0 4543
8 TraesCS5A01G290900 chr4A 96.520 2759 65 7 1 2728 647219007 647216249 0 4534
9 TraesCS5A01G290900 chr6B 96.403 2752 71 7 3 2728 646622909 646625658 0 4508
10 TraesCS5A01G290900 chr7D 94.928 1518 42 4 1 1489 510009189 510010700 0 2344


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 TraesCS5A01G290900 chr5A 501834669 501837396 2727 False 5038 5038 100.000 1 2728 1 chr5A.!!$F1 2727
1 TraesCS5A01G290900 chr2D 178272054 178274771 2717 True 4674 4674 97.656 1 2728 1 chr2D.!!$R1 2727
2 TraesCS5A01G290900 chr2D 511932507 511935116 2609 True 4421 4421 97.217 1 2617 1 chr2D.!!$R2 2616
3 TraesCS5A01G290900 chr2B 640105741 640108495 2754 False 4569 4569 96.770 1 2728 1 chr2B.!!$F1 2727
4 TraesCS5A01G290900 chr2B 683669800 683672553 2753 False 4464 4464 96.078 1 2728 1 chr2B.!!$F2 2727
5 TraesCS5A01G290900 chr1B 313090652 313093405 2753 True 4553 4553 96.659 1 2728 1 chr1B.!!$R1 2727
6 TraesCS5A01G290900 chr1B 277434044 277436792 2748 False 4536 4536 96.587 1 2728 1 chr1B.!!$F1 2727
7 TraesCS5A01G290900 chr3B 312172581 312175331 2750 True 4543 4543 96.623 1 2728 1 chr3B.!!$R1 2727
8 TraesCS5A01G290900 chr4A 647216249 647219007 2758 True 4534 4534 96.520 1 2728 1 chr4A.!!$R1 2727
9 TraesCS5A01G290900 chr6B 646622909 646625658 2749 False 4508 4508 96.403 3 2728 1 chr6B.!!$F1 2725
10 TraesCS5A01G290900 chr7D 510009189 510010700 1511 False 2344 2344 94.928 1 1489 1 chr7D.!!$F1 1488

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
969 1013 0.514255 CTGGTTGTGAGTCATGTGCG 59.486 55.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2285 2359 0.680921 GCACCAGGGCATGAAAGCTA 60.681 55.0 0.0 0.0 34.17 3.32 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
143 147 2.051518 GCCGCCACCCATGAAATCA 61.052 57.895 0.00 0.00 0.00 2.57
215 219 1.925120 CTGCCCCATCCCATCTTCA 59.075 57.895 0.00 0.00 0.00 3.02
407 412 2.102252 GCTCCACCTTCTATCCAGTGAG 59.898 54.545 0.00 0.00 31.79 3.51
408 413 3.636679 CTCCACCTTCTATCCAGTGAGA 58.363 50.000 0.00 0.00 31.79 3.27
409 414 4.222336 CTCCACCTTCTATCCAGTGAGAT 58.778 47.826 0.00 0.00 31.79 2.75
410 415 4.219115 TCCACCTTCTATCCAGTGAGATC 58.781 47.826 0.00 0.00 31.79 2.75
411 416 3.323403 CCACCTTCTATCCAGTGAGATCC 59.677 52.174 0.00 0.00 31.79 3.36
412 417 3.963374 CACCTTCTATCCAGTGAGATCCA 59.037 47.826 0.00 0.00 31.79 3.41
453 487 2.094286 GCTGTCTGCTGCTCTTCTCTTA 60.094 50.000 0.00 0.00 38.95 2.10
498 542 1.228245 GGGTGTTTCCAGCTGCTGA 60.228 57.895 30.10 13.74 39.09 4.26
694 738 4.104383 AGGAAGTCTTGGCAAAAGATCA 57.896 40.909 0.00 0.00 0.00 2.92
800 844 2.928801 TGGAAGTACTTTGAGCAGCA 57.071 45.000 10.02 0.00 0.00 4.41
969 1013 0.514255 CTGGTTGTGAGTCATGTGCG 59.486 55.000 0.00 0.00 0.00 5.34
991 1035 4.082245 CGGCAAAGGAAAAGTATGACCATT 60.082 41.667 0.00 0.00 0.00 3.16
1109 1154 1.363744 GCACTTGCTAGCTTGATCGT 58.636 50.000 17.23 1.11 38.21 3.73
1224 1269 0.532862 CCACACCTTCAGCTGTCGTT 60.533 55.000 14.67 0.00 0.00 3.85
1287 1332 2.687700 TCAAGCTTCATCCAGAGCTC 57.312 50.000 5.27 5.27 36.51 4.09
1310 1355 2.251818 AGCTGAGTTTCAGGCTAGACA 58.748 47.619 0.00 0.00 44.43 3.41
1458 1521 3.685139 TCTTTCCATGTGACCTCTGAC 57.315 47.619 0.00 0.00 0.00 3.51
1490 1553 2.595463 GTCTTGCCAGCCAGTGCA 60.595 61.111 0.00 0.00 41.13 4.57
1555 1618 7.589958 TCTATTACTCATCAGGGTTCTCTTC 57.410 40.000 0.00 0.00 0.00 2.87
1829 1895 4.641396 TCAACATCAAGATCCACTTCGTT 58.359 39.130 0.00 0.00 36.61 3.85
1956 2022 6.130569 TGGTTTTCACTGTAAGGGTTGTAAT 58.869 36.000 0.00 0.00 39.54 1.89
2142 2209 8.201464 TGGTCTATTTTATGAAGCATCGTTCTA 58.799 33.333 0.00 0.00 0.00 2.10
2329 2403 1.376543 CTCAGAATGGCGTTGCTGAT 58.623 50.000 16.53 0.00 36.85 2.90
2461 2535 2.289444 CCAACCTTCTACTCGCCTTGAA 60.289 50.000 0.00 0.00 0.00 2.69
2654 2728 1.455030 GCTATGATTCTTCTGCTCGCG 59.545 52.381 0.00 0.00 0.00 5.87
2683 2758 4.552767 CGCTTTTCTCACGATGTCACTTTT 60.553 41.667 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 7.042335 CCGAACAGTTTTCTATATTGAGGAGT 58.958 38.462 0.00 0.00 0.00 3.85
43 47 6.015350 AGAGAGAATGACCGAACAGTTTTCTA 60.015 38.462 0.00 0.00 0.00 2.10
143 147 3.310860 GAATCACCTCACCGGCGGT 62.311 63.158 28.83 28.83 35.62 5.68
188 192 3.704231 GATGGGGCAGCGATGTGGT 62.704 63.158 1.22 0.00 0.00 4.16
215 219 2.158842 GCAGCTCCTACAGGTTGATGAT 60.159 50.000 11.36 0.00 36.34 2.45
308 312 1.174712 GCACCAAGAGCTTGCTGGAA 61.175 55.000 14.62 0.00 39.16 3.53
407 412 1.422531 ACAGGAGCTGGATCTGGATC 58.577 55.000 0.00 2.24 35.51 3.36
408 413 1.890552 AACAGGAGCTGGATCTGGAT 58.109 50.000 0.00 0.00 35.51 3.41
409 414 1.280133 CAAACAGGAGCTGGATCTGGA 59.720 52.381 0.00 0.00 35.51 3.86
410 415 1.004044 ACAAACAGGAGCTGGATCTGG 59.996 52.381 0.00 0.00 35.51 3.86
411 416 2.082231 CACAAACAGGAGCTGGATCTG 58.918 52.381 0.00 0.00 35.51 2.90
412 417 1.004044 CCACAAACAGGAGCTGGATCT 59.996 52.381 0.00 0.00 35.51 2.75
498 542 1.836999 TTGCCATAGTGGTGAGCGGT 61.837 55.000 0.00 0.00 40.46 5.68
599 643 0.540830 AGCCGTCCTCAAGACAGTCT 60.541 55.000 0.00 0.00 46.69 3.24
694 738 3.634397 AACTCCCATCACACGATCATT 57.366 42.857 0.00 0.00 0.00 2.57
800 844 0.838122 ACTGCTGGGCTGAAGGTAGT 60.838 55.000 3.60 0.00 0.00 2.73
969 1013 5.405935 AATGGTCATACTTTTCCTTTGCC 57.594 39.130 0.00 0.00 0.00 4.52
991 1035 6.816136 TCACAAACTGAAACATGAGAGTCTA 58.184 36.000 0.00 0.00 0.00 2.59
1287 1332 4.081972 TGTCTAGCCTGAAACTCAGCTAAG 60.082 45.833 0.00 0.00 42.98 2.18
1310 1355 2.274760 GCTGCTGATTGAGGGCCT 59.725 61.111 5.25 5.25 0.00 5.19
1458 1521 2.141517 CAAGACACAAGCTGAGAGTGG 58.858 52.381 11.83 0.00 37.58 4.00
1490 1553 0.617413 CTGAACAGAGGCACCATCCT 59.383 55.000 0.00 0.00 39.67 3.24
1555 1618 3.300009 GAACAGAAAACTTGGATGTGCG 58.700 45.455 0.00 0.00 0.00 5.34
1724 1790 4.358310 TGTAGAGGGATGTGGATCCTCTAT 59.642 45.833 14.23 4.49 46.88 1.98
1829 1895 2.977772 CCACTGGGCAAAAGAAAACA 57.022 45.000 0.00 0.00 0.00 2.83
1956 2022 5.013704 TGGAAGCTGTATTTGTTTCCCTAGA 59.986 40.000 6.84 0.00 41.91 2.43
2285 2359 0.680921 GCACCAGGGCATGAAAGCTA 60.681 55.000 0.00 0.00 34.17 3.32
2329 2403 3.106242 ACAATATGGCGATGCTTACGA 57.894 42.857 0.00 0.00 0.00 3.43
2461 2535 1.757306 CTCACCAGGACACTTGCCT 59.243 57.895 0.00 0.00 35.75 4.75
2654 2728 0.796312 TCGTGAGAAAAGCGAATGCC 59.204 50.000 0.00 0.00 38.77 4.40
2670 2744 3.804036 TCCTCAACAAAAGTGACATCGT 58.196 40.909 0.00 0.00 0.00 3.73


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

AutoCloner maintained by Alex Coulton.