Multiple sequence alignment - TraesCS5A01G058300

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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 TraesCS5A01G058300 chr5A 100.000 2608 0 0 1 2608 56839910 56837303 0 4817
1 TraesCS5A01G058300 chr5B 93.278 2648 85 38 1 2602 73346862 73349462 0 3818
2 TraesCS5A01G058300 chr5D 93.150 2657 80 37 1 2599 67323371 67325983 0 3805


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 TraesCS5A01G058300 chr5A 56837303 56839910 2607 True 4817 4817 100.000 1 2608 1 chr5A.!!$R1 2607
1 TraesCS5A01G058300 chr5B 73346862 73349462 2600 False 3818 3818 93.278 1 2602 1 chr5B.!!$F1 2601
2 TraesCS5A01G058300 chr5D 67323371 67325983 2612 False 3805 3805 93.150 1 2599 1 chr5D.!!$F1 2598

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
531 536 1.119684 GGCTCTCCTCCTTTCTCTCC 58.88 60.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1666 1709 1.498576 CTCTCATCTCTCTCCCTCCCA 59.501 57.143 0.0 0.0 0.0 4.37 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
28 29 3.580319 AAGGGGTGGTGGAGTGGC 61.580 66.667 0.00 0.00 0.00 5.01
53 54 7.017645 CGTACAGACCAAATCATTCAAAGAAG 58.982 38.462 0.00 0.00 0.00 2.85
86 87 5.105756 CCAGCCTCCCTACACAAATAAAAAG 60.106 44.000 0.00 0.00 0.00 2.27
90 91 6.866770 GCCTCCCTACACAAATAAAAAGAAAC 59.133 38.462 0.00 0.00 0.00 2.78
91 92 7.375834 CCTCCCTACACAAATAAAAAGAAACC 58.624 38.462 0.00 0.00 0.00 3.27
144 147 4.411013 AGGAAGAAAAAGGTCCCATCTTG 58.589 43.478 0.00 0.00 30.89 3.02
343 348 8.702163 AAATAACAATATTTGCCACTTGCTAC 57.298 30.769 0.00 0.00 39.64 3.58
406 411 2.621115 GCCTCCCATCCCCTCCTA 59.379 66.667 0.00 0.00 0.00 2.94
531 536 1.119684 GGCTCTCCTCCTTTCTCTCC 58.880 60.000 0.00 0.00 0.00 3.71
617 622 6.607198 CCCCATCTCTCTATTTATCTCTCTCC 59.393 46.154 0.00 0.00 0.00 3.71
724 747 5.535030 AGGTTTTGTTACAGATCTTGGGAAC 59.465 40.000 0.00 0.00 0.00 3.62
750 773 4.402155 ACCACATGTTCTTGCAAAAAGAGA 59.598 37.500 0.00 0.00 0.00 3.10
754 777 6.921857 CACATGTTCTTGCAAAAAGAGAGAAT 59.078 34.615 0.00 0.00 0.00 2.40
757 780 9.467258 CATGTTCTTGCAAAAAGAGAGAATAAA 57.533 29.630 0.00 0.00 0.00 1.40
760 783 8.755941 GTTCTTGCAAAAAGAGAGAATAAAACC 58.244 33.333 0.00 0.00 0.00 3.27
764 787 6.485313 TGCAAAAAGAGAGAATAAAACCGAGA 59.515 34.615 0.00 0.00 0.00 4.04
782 805 4.560128 CGAGAGGATTTGTTCTTCTGTGA 58.440 43.478 0.00 0.00 40.63 3.58
797 820 5.994054 TCTTCTGTGACAAATCTTCTGGAAG 59.006 40.000 4.13 4.13 39.71 3.46
798 821 4.645535 TCTGTGACAAATCTTCTGGAAGG 58.354 43.478 10.01 0.00 38.88 3.46
799 822 4.103153 TCTGTGACAAATCTTCTGGAAGGT 59.897 41.667 10.01 0.50 38.88 3.50
860 884 9.860898 GGAAAAATCAGATTAGTTAGCAAATGT 57.139 29.630 0.00 0.00 0.00 2.71
947 984 2.291741 CTGTTCTTGTTCTTGCAGGGTC 59.708 50.000 0.00 0.00 0.00 4.46
978 1015 4.579454 TCCGGATCTAATCAACTAACCG 57.421 45.455 0.00 0.00 39.02 4.44
1179 1216 0.847373 ATCTGCTCGACCTCCTCCTA 59.153 55.000 0.00 0.00 0.00 2.94
1222 1259 0.399454 CTCGGCCCAAGATCCATGAT 59.601 55.000 0.00 0.00 0.00 2.45
1298 1340 0.647925 GCGACGAGAGCAATCTTTCC 59.352 55.000 0.00 0.00 34.19 3.13
1666 1709 2.887152 CCCTCAGTAGTGCAAAAGCTTT 59.113 45.455 5.69 5.69 0.00 3.51
1667 1710 3.304928 CCCTCAGTAGTGCAAAAGCTTTG 60.305 47.826 13.54 8.26 0.00 2.77
1843 1889 1.001764 CAGATGCAGGTGCCCTTCA 60.002 57.895 0.00 0.00 41.18 3.02
1894 1941 4.648307 GGACGGGGTAGAAGAAATCTAGAA 59.352 45.833 0.00 0.00 41.31 2.10
1897 1944 4.039366 CGGGGTAGAAGAAATCTAGAAGGG 59.961 50.000 0.00 0.00 41.31 3.95
1928 1976 1.006102 AGAGGGCACGAGAAACACG 60.006 57.895 0.00 0.00 0.00 4.49
2158 2212 3.735591 TGTGTACAAAAGAGTGGCTACC 58.264 45.455 0.00 0.00 0.00 3.18
2234 2288 5.180868 GTGAGAGGCATGAATGATGTATTCC 59.819 44.000 0.00 0.00 43.72 3.01
2315 2369 5.251182 TCTCATGCCATGATTATCACCAT 57.749 39.130 8.03 0.00 38.85 3.55
2461 2532 6.377996 TGACTAGCCAATGACTAATGCAAAAT 59.622 34.615 0.00 0.00 0.00 1.82
2467 2538 6.211515 CCAATGACTAATGCAAAATAGCCTC 58.788 40.000 0.00 0.00 0.00 4.70
2533 2604 3.070015 GGGCCAAAGATGAAATACCATGG 59.930 47.826 11.19 11.19 0.00 3.66
2557 2631 1.152567 CTTGTGGCCTTCACCCCAA 60.153 57.895 3.32 0.00 45.48 4.12
2558 2632 1.152567 TTGTGGCCTTCACCCCAAG 60.153 57.895 3.32 0.00 45.48 3.61
2559 2633 1.943730 TTGTGGCCTTCACCCCAAGT 61.944 55.000 3.32 0.00 45.48 3.16
2597 2671 8.447924 TTGAGATGTACTAGATGTGGTACTAC 57.552 38.462 15.92 1.77 40.43 2.73
2604 2678 9.206690 TGTACTAGATGTGGTACTACTACTAGT 57.793 37.037 29.91 29.91 40.43 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 6.480524 TCTTTGAATGATTTGGTCTGTACG 57.519 37.500 0.00 0.00 0.00 3.67
53 54 2.626780 GGGAGGCTGGTTTTCGTGC 61.627 63.158 0.00 0.00 0.00 5.34
86 87 2.545113 GGCCACCTTTTCTTTCGGTTTC 60.545 50.000 0.00 0.00 0.00 2.78
90 91 0.881796 GAGGCCACCTTTTCTTTCGG 59.118 55.000 5.01 0.00 31.76 4.30
91 92 0.881796 GGAGGCCACCTTTTCTTTCG 59.118 55.000 12.67 0.00 31.76 3.46
144 147 5.811613 TGCTGCCATAATTGAAGCAATAAAC 59.188 36.000 0.00 0.00 38.56 2.01
208 211 1.035139 AGGTTGAGCAAAAGCTGGTG 58.965 50.000 0.00 0.00 36.56 4.17
406 411 1.299939 GATGGGAGGAAGGAAAGGGT 58.700 55.000 0.00 0.00 0.00 4.34
617 622 6.105333 CCAACAGAAGATGAGAAACTAGAGG 58.895 44.000 0.00 0.00 0.00 3.69
724 747 1.039068 TTGCAAGAACATGTGGTGGG 58.961 50.000 0.00 0.00 0.00 4.61
726 749 4.431809 TCTTTTTGCAAGAACATGTGGTG 58.568 39.130 0.00 0.00 0.00 4.17
750 773 7.168905 AGAACAAATCCTCTCGGTTTTATTCT 58.831 34.615 3.74 3.74 39.31 2.40
754 777 6.426937 CAGAAGAACAAATCCTCTCGGTTTTA 59.573 38.462 0.00 0.00 32.34 1.52
757 780 4.202367 ACAGAAGAACAAATCCTCTCGGTT 60.202 41.667 0.00 0.00 25.59 4.44
760 783 4.387256 GTCACAGAAGAACAAATCCTCTCG 59.613 45.833 0.00 0.00 25.59 4.04
764 787 6.966534 ATTTGTCACAGAAGAACAAATCCT 57.033 33.333 6.82 0.00 36.62 3.24
769 792 6.038603 CCAGAAGATTTGTCACAGAAGAACAA 59.961 38.462 0.00 0.00 0.00 2.83
797 820 7.981789 AGAAAGAAATCAAAAGAAACTGGAACC 59.018 33.333 0.00 0.00 0.00 3.62
798 821 8.811378 CAGAAAGAAATCAAAAGAAACTGGAAC 58.189 33.333 0.00 0.00 0.00 3.62
799 822 8.531146 ACAGAAAGAAATCAAAAGAAACTGGAA 58.469 29.630 0.00 0.00 0.00 3.53
807 830 5.656416 ACCCACACAGAAAGAAATCAAAAGA 59.344 36.000 0.00 0.00 0.00 2.52
808 831 5.750067 CACCCACACAGAAAGAAATCAAAAG 59.250 40.000 0.00 0.00 0.00 2.27
810 833 4.099266 CCACCCACACAGAAAGAAATCAAA 59.901 41.667 0.00 0.00 0.00 2.69
894 931 7.530426 AATTGCTCAGTTTCACCTCTAAAAT 57.470 32.000 0.00 0.00 0.00 1.82
947 984 8.893727 AGTTGATTAGATCCGGAAAATTTACAG 58.106 33.333 9.01 0.00 0.00 2.74
1179 1216 4.319177 CGGAGAAAGAACTCACCTTTGAT 58.681 43.478 0.00 0.00 38.51 2.57
1222 1259 1.374252 GAGAAGCCACGCGAGGAAA 60.374 57.895 27.39 0.00 0.00 3.13
1409 1451 2.272146 GACATCACCGGCCACCAT 59.728 61.111 0.00 0.00 0.00 3.55
1666 1709 1.498576 CTCTCATCTCTCTCCCTCCCA 59.501 57.143 0.00 0.00 0.00 4.37
1667 1710 1.499007 ACTCTCATCTCTCTCCCTCCC 59.501 57.143 0.00 0.00 0.00 4.30
1843 1889 6.378280 CCAAACTAGAGCTCCCAAATTTACAT 59.622 38.462 10.93 0.00 0.00 2.29
1874 1921 4.039366 CCCTTCTAGATTTCTTCTACCCCG 59.961 50.000 0.00 0.00 35.79 5.73
1897 1944 1.768077 CCCTCTGTCCCAGATCCCC 60.768 68.421 0.00 0.00 39.92 4.81
1904 1952 2.997315 CTCGTGCCCTCTGTCCCA 60.997 66.667 0.00 0.00 0.00 4.37
1919 1967 3.400255 AGGGCTAAACTTCGTGTTTCTC 58.600 45.455 11.24 6.27 44.81 2.87
1928 1976 7.336931 TGATTCATACAAAGAGGGCTAAACTTC 59.663 37.037 0.00 0.00 0.00 3.01
2158 2212 2.756760 AGCTGCTCTCTCTTCTCTTCTG 59.243 50.000 0.00 0.00 0.00 3.02
2343 2397 6.884280 AGAAATTGAGAGGTGACGAAAAAT 57.116 33.333 0.00 0.00 0.00 1.82
2412 2483 3.880047 TCCTTATCACCTACGTGTTGG 57.120 47.619 0.00 0.00 41.09 3.77
2435 2506 4.445453 TGCATTAGTCATTGGCTAGTCAG 58.555 43.478 0.00 0.00 0.00 3.51
2467 2538 4.963318 TGAGATTATTAGCCACTCAGGG 57.037 45.455 0.00 0.00 38.09 4.45
2557 2631 5.440610 ACATCTCAAAGAAAAGGACACACT 58.559 37.500 0.00 0.00 0.00 3.55
2558 2632 5.757850 ACATCTCAAAGAAAAGGACACAC 57.242 39.130 0.00 0.00 0.00 3.82
2559 2633 6.591935 AGTACATCTCAAAGAAAAGGACACA 58.408 36.000 0.00 0.00 0.00 3.72
2560 2634 8.088981 TCTAGTACATCTCAAAGAAAAGGACAC 58.911 37.037 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.