Multiple sequence alignment - TraesCS4D01G229800

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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 TraesCS4D01G229800 chr4D 100.000 2780 0 0 1 2780 389490679 389493458 0.000000e+00 5134.0
1 TraesCS4D01G229800 chr2D 99.900 2003 2 0 1 2003 628169297 628171299 0.000000e+00 3688.0
2 TraesCS4D01G229800 chr2D 84.111 1800 253 19 1 1795 203441941 203443712 0.000000e+00 1709.0
3 TraesCS4D01G229800 chr2D 76.730 838 186 9 11 846 291874910 291874080 2.520000e-125 459.0
4 TraesCS4D01G229800 chr7A 98.101 2001 37 1 1 2001 711168955 711170954 0.000000e+00 3483.0
5 TraesCS4D01G229800 chr1D 93.812 2004 117 5 1 2001 463533178 463531179 0.000000e+00 3007.0
6 TraesCS4D01G229800 chr1D 93.470 2006 122 6 1 2001 47641027 47639026 0.000000e+00 2970.0
7 TraesCS4D01G229800 chr5D 93.762 2004 118 5 1 2001 322187734 322189733 0.000000e+00 3001.0
8 TraesCS4D01G229800 chr3D 93.563 2004 122 5 1 2001 538179882 538177883 0.000000e+00 2979.0
9 TraesCS4D01G229800 chr5B 90.564 2003 169 7 1 2001 448041233 448039249 0.000000e+00 2634.0
10 TraesCS4D01G229800 chr3A 97.220 1439 36 3 568 2006 747056716 747055282 0.000000e+00 2433.0
11 TraesCS4D01G229800 chr7D 93.939 1584 95 1 215 1798 574676019 574674437 0.000000e+00 2392.0
12 TraesCS4D01G229800 chr4B 87.443 661 54 13 2142 2780 479396493 479397146 0.000000e+00 734.0
13 TraesCS4D01G229800 chr4B 95.238 147 3 3 2002 2145 479396142 479396287 2.150000e-56 230.0
14 TraesCS4D01G229800 chr4A 89.112 597 50 9 2194 2780 71164724 71165315 0.000000e+00 728.0
15 TraesCS4D01G229800 chr4A 86.486 148 12 4 2002 2149 71164267 71164406 3.710000e-34 156.0
16 TraesCS4D01G229800 chr2B 86.667 60 7 1 2025 2084 406446474 406446416 6.430000e-07 65.8


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 TraesCS4D01G229800 chr4D 389490679 389493458 2779 False 5134 5134 100.0000 1 2780 1 chr4D.!!$F1 2779
1 TraesCS4D01G229800 chr2D 628169297 628171299 2002 False 3688 3688 99.9000 1 2003 1 chr2D.!!$F2 2002
2 TraesCS4D01G229800 chr2D 203441941 203443712 1771 False 1709 1709 84.1110 1 1795 1 chr2D.!!$F1 1794
3 TraesCS4D01G229800 chr2D 291874080 291874910 830 True 459 459 76.7300 11 846 1 chr2D.!!$R1 835
4 TraesCS4D01G229800 chr7A 711168955 711170954 1999 False 3483 3483 98.1010 1 2001 1 chr7A.!!$F1 2000
5 TraesCS4D01G229800 chr1D 463531179 463533178 1999 True 3007 3007 93.8120 1 2001 1 chr1D.!!$R2 2000
6 TraesCS4D01G229800 chr1D 47639026 47641027 2001 True 2970 2970 93.4700 1 2001 1 chr1D.!!$R1 2000
7 TraesCS4D01G229800 chr5D 322187734 322189733 1999 False 3001 3001 93.7620 1 2001 1 chr5D.!!$F1 2000
8 TraesCS4D01G229800 chr3D 538177883 538179882 1999 True 2979 2979 93.5630 1 2001 1 chr3D.!!$R1 2000
9 TraesCS4D01G229800 chr5B 448039249 448041233 1984 True 2634 2634 90.5640 1 2001 1 chr5B.!!$R1 2000
10 TraesCS4D01G229800 chr3A 747055282 747056716 1434 True 2433 2433 97.2200 568 2006 1 chr3A.!!$R1 1438
11 TraesCS4D01G229800 chr7D 574674437 574676019 1582 True 2392 2392 93.9390 215 1798 1 chr7D.!!$R1 1583
12 TraesCS4D01G229800 chr4B 479396142 479397146 1004 False 482 734 91.3405 2002 2780 2 chr4B.!!$F1 778
13 TraesCS4D01G229800 chr4A 71164267 71165315 1048 False 442 728 87.7990 2002 2780 2 chr4A.!!$F1 778

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
626 639 9.926751 CATAGTCTGAATTTGACAATATGTGAC 57.073 33.333 12.82 0.0 36.94 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2278 2568 2.037902 TCCACGTGCCTAGTTTTCATCA 59.962 45.455 10.91 0.0 0.0 3.07 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
626 639 9.926751 CATAGTCTGAATTTGACAATATGTGAC 57.073 33.333 12.82 0.00 36.94 3.67
1591 1605 0.249826 TGTGACAGTTGCATCTGCGA 60.250 50.000 21.97 8.19 45.83 5.10
2090 2106 2.653890 CCAAAGTCATCAACGTGCAAG 58.346 47.619 0.00 0.00 0.00 4.01
2213 2503 9.806203 TTTGCATCAGGATATTAATTTCTTGTG 57.194 29.630 14.61 13.06 0.00 3.33
2228 2518 2.035632 CTTGTGCACCCCCTACAAAAA 58.964 47.619 15.69 0.00 34.30 1.94
2232 2522 5.194473 TGTGCACCCCCTACAAAAATATA 57.806 39.130 15.69 0.00 0.00 0.86
2270 2560 2.871096 ATGACCCTTGGCGAAAACTA 57.129 45.000 0.00 0.00 0.00 2.24
2311 2601 2.609459 GGCACGTGGATGAACTCTATTG 59.391 50.000 18.88 0.00 0.00 1.90
2455 2747 4.279922 GCTACCTCCTCTCAACCTATTCTC 59.720 50.000 0.00 0.00 0.00 2.87
2466 2758 1.054406 CCTATTCTCCCTTGCCCCGA 61.054 60.000 0.00 0.00 0.00 5.14
2469 2761 1.208165 ATTCTCCCTTGCCCCGAACT 61.208 55.000 0.00 0.00 0.00 3.01
2471 2763 2.528127 TCCCTTGCCCCGAACTGA 60.528 61.111 0.00 0.00 0.00 3.41
2474 2766 1.002134 CCTTGCCCCGAACTGACAT 60.002 57.895 0.00 0.00 0.00 3.06
2496 2788 6.442564 ACATGTTTGGAACCTAGGTGTAGATA 59.557 38.462 17.14 0.09 0.00 1.98
2501 2793 7.989947 TTGGAACCTAGGTGTAGATAAATCT 57.010 36.000 17.14 0.00 40.86 2.40
2502 2794 7.361457 TGGAACCTAGGTGTAGATAAATCTG 57.639 40.000 17.14 0.00 37.76 2.90
2637 2932 4.974368 TTTATGGTATTGTGGGCGAAAG 57.026 40.909 0.00 0.00 0.00 2.62
2644 2942 5.477291 TGGTATTGTGGGCGAAAGAAAAATA 59.523 36.000 0.00 0.00 0.00 1.40
2645 2943 6.015350 TGGTATTGTGGGCGAAAGAAAAATAA 60.015 34.615 0.00 0.00 0.00 1.40
2646 2944 6.869388 GGTATTGTGGGCGAAAGAAAAATAAA 59.131 34.615 0.00 0.00 0.00 1.40
2647 2945 7.547722 GGTATTGTGGGCGAAAGAAAAATAAAT 59.452 33.333 0.00 0.00 0.00 1.40
2648 2946 6.777526 TTGTGGGCGAAAGAAAAATAAATG 57.222 33.333 0.00 0.00 0.00 2.32
2689 2987 3.904136 ATTCACTCCTTTTGTTCGCAG 57.096 42.857 0.00 0.00 0.00 5.18
2734 3040 7.222000 TGGGAGTTCGCAAAACTTTTTATAT 57.778 32.000 3.24 0.00 35.80 0.86
2735 3041 7.087639 TGGGAGTTCGCAAAACTTTTTATATG 58.912 34.615 3.24 0.00 35.80 1.78
2764 3070 4.070009 CCAGTAGGTCAAGTTTGTTACCC 58.930 47.826 0.00 0.00 32.10 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
626 639 4.466828 CTTTACGACAAGACTTTGCCATG 58.533 43.478 0.00 0.00 37.85 3.66
1591 1605 7.646548 ACTTGAGTTTAGAAAAGCTCCTTTT 57.353 32.000 2.84 2.84 44.92 2.27
2213 2503 6.724893 ACAATATATTTTTGTAGGGGGTGC 57.275 37.500 0.00 0.00 35.61 5.01
2278 2568 2.037902 TCCACGTGCCTAGTTTTCATCA 59.962 45.455 10.91 0.00 0.00 3.07
2352 2642 5.298276 TCTTGTTGTTCTTTGCTCGGTAAAT 59.702 36.000 0.00 0.00 0.00 1.40
2455 2747 2.359975 GTCAGTTCGGGGCAAGGG 60.360 66.667 0.00 0.00 0.00 3.95
2466 2758 4.141251 ACCTAGGTTCCAAACATGTCAGTT 60.141 41.667 9.21 0.00 0.00 3.16
2469 2761 3.137544 ACACCTAGGTTCCAAACATGTCA 59.862 43.478 13.15 0.00 0.00 3.58
2471 2763 3.876309 ACACCTAGGTTCCAAACATGT 57.124 42.857 13.15 0.22 0.00 3.21
2474 2766 6.938698 TTATCTACACCTAGGTTCCAAACA 57.061 37.500 13.15 0.00 0.00 2.83
2595 2888 6.375945 AAAAAGCATTCTTCCGCAATTTTT 57.624 29.167 0.00 0.00 30.25 1.94
2596 2889 7.361116 CCATAAAAAGCATTCTTCCGCAATTTT 60.361 33.333 0.00 0.00 35.23 1.82
2597 2890 6.092533 CCATAAAAAGCATTCTTCCGCAATTT 59.907 34.615 0.00 0.00 0.00 1.82
2598 2891 5.581874 CCATAAAAAGCATTCTTCCGCAATT 59.418 36.000 0.00 0.00 0.00 2.32
2599 2892 5.111293 CCATAAAAAGCATTCTTCCGCAAT 58.889 37.500 0.00 0.00 0.00 3.56
2613 2908 4.974368 TCGCCCACAATACCATAAAAAG 57.026 40.909 0.00 0.00 0.00 2.27
2647 2945 9.131791 TGAATAGTAACTATGATGTAGTGCTCA 57.868 33.333 0.00 0.00 0.00 4.26
2648 2946 9.400638 GTGAATAGTAACTATGATGTAGTGCTC 57.599 37.037 0.00 0.00 0.00 4.26
2661 2959 7.330208 GCGAACAAAAGGAGTGAATAGTAACTA 59.670 37.037 0.00 0.00 0.00 2.24
2710 3008 3.878160 AAAAAGTTTTGCGAACTCCCA 57.122 38.095 0.61 0.00 0.00 4.37
2718 3016 8.018520 TGGTGTACTCATATAAAAAGTTTTGCG 58.981 33.333 0.61 0.00 0.00 4.85
2719 3017 9.341899 CTGGTGTACTCATATAAAAAGTTTTGC 57.658 33.333 0.61 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.