Multiple sequence alignment - TraesCS5A01G077000

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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 TraesCS5A01G077000 chr5A 100.000 2639 0 0 1 2639 93187456 93190094 0.000000e+00 4874.0
1 TraesCS5A01G077000 chr5A 92.837 726 48 2 895 1619 106855930 106855208 0.000000e+00 1050.0
2 TraesCS5A01G077000 chr5D 94.511 838 39 4 789 1619 104398580 104397743 0.000000e+00 1286.0
3 TraesCS5A01G077000 chr5D 92.857 728 44 5 895 1619 104447168 104446446 0.000000e+00 1050.0
4 TraesCS5A01G077000 chr5D 86.577 298 31 7 1903 2197 138896481 138896772 1.180000e-83 320.0
5 TraesCS5A01G077000 chr5D 87.931 232 16 8 2313 2535 104446453 104446225 2.010000e-66 263.0
6 TraesCS5A01G077000 chr5D 94.737 152 5 1 2313 2461 104397750 104397599 1.580000e-57 233.0
7 TraesCS5A01G077000 chr5D 95.489 133 3 1 2507 2639 104397600 104397471 2.660000e-50 209.0
8 TraesCS5A01G077000 chr5D 86.567 67 6 2 2246 2312 138896776 138896839 1.310000e-08 71.3
9 TraesCS5A01G077000 chr5B 93.357 858 45 7 765 1619 113806012 113805164 0.000000e+00 1258.0
10 TraesCS5A01G077000 chr5B 92.720 728 45 6 895 1619 113823570 113822848 0.000000e+00 1044.0
11 TraesCS5A01G077000 chr5B 96.061 330 7 2 2313 2639 113805171 113804845 1.390000e-147 532.0
12 TraesCS5A01G077000 chr6A 99.135 694 6 0 1620 2313 604442428 604441735 0.000000e+00 1249.0
13 TraesCS5A01G077000 chr6A 91.746 739 48 9 2 733 539166536 539167268 0.000000e+00 1014.0
14 TraesCS5A01G077000 chr2B 98.420 696 9 1 1620 2315 790365760 790366453 0.000000e+00 1223.0
15 TraesCS5A01G077000 chr2B 84.185 411 41 15 1908 2312 531049327 531048935 6.900000e-101 377.0
16 TraesCS5A01G077000 chr2B 90.187 214 18 3 1620 1832 531049778 531049567 2.590000e-70 276.0
17 TraesCS5A01G077000 chr6D 92.463 743 41 11 1 733 402412050 402412787 0.000000e+00 1048.0
18 TraesCS5A01G077000 chr6D 91.588 737 49 9 7 733 147647219 147646486 0.000000e+00 1005.0
19 TraesCS5A01G077000 chr6D 91.180 737 48 13 6 733 428602443 428603171 0.000000e+00 985.0
20 TraesCS5A01G077000 chr2D 92.527 736 39 12 6 733 103169749 103170476 0.000000e+00 1040.0
21 TraesCS5A01G077000 chr2D 92.244 722 41 11 6 720 497917977 497917264 0.000000e+00 1009.0
22 TraesCS5A01G077000 chr2D 91.069 739 48 14 4 733 160320371 160319642 0.000000e+00 983.0
23 TraesCS5A01G077000 chr2D 83.721 430 37 12 1903 2312 7406085 7406501 2.480000e-100 375.0
24 TraesCS5A01G077000 chr3D 91.316 737 46 12 6 732 603118890 603118162 0.000000e+00 990.0
25 TraesCS5A01G077000 chr3D 91.081 740 53 9 6 735 596657717 596656981 0.000000e+00 989.0
26 TraesCS5A01G077000 chr3D 80.737 353 31 15 1962 2310 604231498 604231179 9.440000e-60 241.0
27 TraesCS5A01G077000 chr3D 89.706 136 9 5 1663 1796 604231977 604231845 4.520000e-38 169.0
28 TraesCS5A01G077000 chr3B 88.620 413 42 4 1903 2312 609325076 609325486 5.070000e-137 497.0
29 TraesCS5A01G077000 chr3B 91.844 282 19 3 1620 1897 609324395 609324676 8.860000e-105 390.0
30 TraesCS5A01G077000 chr3B 84.071 113 18 0 1613 1725 817195285 817195173 2.780000e-20 110.0
31 TraesCS5A01G077000 chr1A 87.198 414 43 9 1903 2311 532457402 532456994 1.850000e-126 462.0
32 TraesCS5A01G077000 chr1A 94.884 215 10 1 1620 1833 532457830 532457616 4.210000e-88 335.0
33 TraesCS5A01G077000 chr1A 97.143 70 2 0 1833 1902 532457584 532457515 4.610000e-23 119.0
34 TraesCS5A01G077000 chr6B 85.577 416 46 9 1903 2314 46771863 46771458 8.730000e-115 424.0
35 TraesCS5A01G077000 chr6B 91.628 215 15 3 1620 1832 46781278 46781065 7.140000e-76 294.0
36 TraesCS5A01G077000 chr4B 86.188 362 41 8 1955 2312 584505228 584504872 1.480000e-102 383.0
37 TraesCS5A01G077000 chr7B 89.732 224 11 4 1620 1832 80071135 80071357 2.590000e-70 276.0
38 TraesCS5A01G077000 chr4A 81.967 122 19 2 1620 1740 323404508 323404389 1.670000e-17 100.0


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 TraesCS5A01G077000 chr5A 93187456 93190094 2638 False 4874.000000 4874 100.000000 1 2639 1 chr5A.!!$F1 2638
1 TraesCS5A01G077000 chr5A 106855208 106855930 722 True 1050.000000 1050 92.837000 895 1619 1 chr5A.!!$R1 724
2 TraesCS5A01G077000 chr5D 104446225 104447168 943 True 656.500000 1050 90.394000 895 2535 2 chr5D.!!$R2 1640
3 TraesCS5A01G077000 chr5D 104397471 104398580 1109 True 576.000000 1286 94.912333 789 2639 3 chr5D.!!$R1 1850
4 TraesCS5A01G077000 chr5B 113822848 113823570 722 True 1044.000000 1044 92.720000 895 1619 1 chr5B.!!$R1 724
5 TraesCS5A01G077000 chr5B 113804845 113806012 1167 True 895.000000 1258 94.709000 765 2639 2 chr5B.!!$R2 1874
6 TraesCS5A01G077000 chr6A 604441735 604442428 693 True 1249.000000 1249 99.135000 1620 2313 1 chr6A.!!$R1 693
7 TraesCS5A01G077000 chr6A 539166536 539167268 732 False 1014.000000 1014 91.746000 2 733 1 chr6A.!!$F1 731
8 TraesCS5A01G077000 chr2B 790365760 790366453 693 False 1223.000000 1223 98.420000 1620 2315 1 chr2B.!!$F1 695
9 TraesCS5A01G077000 chr2B 531048935 531049778 843 True 326.500000 377 87.186000 1620 2312 2 chr2B.!!$R1 692
10 TraesCS5A01G077000 chr6D 402412050 402412787 737 False 1048.000000 1048 92.463000 1 733 1 chr6D.!!$F1 732
11 TraesCS5A01G077000 chr6D 147646486 147647219 733 True 1005.000000 1005 91.588000 7 733 1 chr6D.!!$R1 726
12 TraesCS5A01G077000 chr6D 428602443 428603171 728 False 985.000000 985 91.180000 6 733 1 chr6D.!!$F2 727
13 TraesCS5A01G077000 chr2D 103169749 103170476 727 False 1040.000000 1040 92.527000 6 733 1 chr2D.!!$F2 727
14 TraesCS5A01G077000 chr2D 497917264 497917977 713 True 1009.000000 1009 92.244000 6 720 1 chr2D.!!$R2 714
15 TraesCS5A01G077000 chr2D 160319642 160320371 729 True 983.000000 983 91.069000 4 733 1 chr2D.!!$R1 729
16 TraesCS5A01G077000 chr3D 603118162 603118890 728 True 990.000000 990 91.316000 6 732 1 chr3D.!!$R2 726
17 TraesCS5A01G077000 chr3D 596656981 596657717 736 True 989.000000 989 91.081000 6 735 1 chr3D.!!$R1 729
18 TraesCS5A01G077000 chr3D 604231179 604231977 798 True 205.000000 241 85.221500 1663 2310 2 chr3D.!!$R3 647
19 TraesCS5A01G077000 chr3B 609324395 609325486 1091 False 443.500000 497 90.232000 1620 2312 2 chr3B.!!$F1 692
20 TraesCS5A01G077000 chr1A 532456994 532457830 836 True 305.333333 462 93.075000 1620 2311 3 chr1A.!!$R1 691

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
822 846 0.319083 TACCAAACATGTCTCGGCGT 59.681 50.0 6.85 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2408 2955 1.373748 GTACGGCAAAGCGAGGACA 60.374 57.895 0.0 0.0 0.0 4.02 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
55 57 1.070786 TTTTGCTTCCGCGAGAGGT 59.929 52.632 8.23 0.00 39.65 3.85
128 130 6.449448 AACAAAACGCGTTTTCTGTTTTTA 57.551 29.167 38.94 0.00 42.20 1.52
139 144 8.105742 GCGTTTTCTGTTTTTATTTCTTTCGTT 58.894 29.630 0.00 0.00 0.00 3.85
267 276 1.295792 GTGAGAGTCACGGTTTTGCA 58.704 50.000 0.00 0.00 37.67 4.08
287 296 2.807631 TTCGCGAGAGGCACGGTTAC 62.808 60.000 9.59 0.00 43.84 2.50
309 318 2.166130 TTTCGCGAGAGTCATGGCCA 62.166 55.000 8.56 8.56 43.69 5.36
535 557 6.325028 TGGGATCTAGTTTTGAAGATCTCGAT 59.675 38.462 11.05 0.00 40.21 3.59
586 608 2.879646 AGATTTGGACGCACGGTTTAAA 59.120 40.909 0.00 0.00 0.00 1.52
684 708 4.681978 GCCACTTGTCGCGACCCT 62.682 66.667 34.34 15.12 0.00 4.34
685 709 2.967397 CCACTTGTCGCGACCCTA 59.033 61.111 34.34 19.24 0.00 3.53
700 724 5.123936 GCGACCCTAGAAAATGGAGTATTT 58.876 41.667 0.00 0.00 40.67 1.40
785 809 4.933064 CTTCTCGCGCGGGCCTAG 62.933 72.222 31.69 19.61 35.02 3.02
805 829 4.810191 AGCTAAGGTATATGCAGCCTAC 57.190 45.455 0.00 0.00 32.58 3.18
811 835 3.458118 AGGTATATGCAGCCTACCAAACA 59.542 43.478 18.91 0.00 37.88 2.83
817 841 1.740025 GCAGCCTACCAAACATGTCTC 59.260 52.381 0.00 0.00 0.00 3.36
818 842 2.002586 CAGCCTACCAAACATGTCTCG 58.997 52.381 0.00 0.00 0.00 4.04
820 844 1.369625 CCTACCAAACATGTCTCGGC 58.630 55.000 0.00 0.00 0.00 5.54
821 845 0.999406 CTACCAAACATGTCTCGGCG 59.001 55.000 0.00 0.00 0.00 6.46
822 846 0.319083 TACCAAACATGTCTCGGCGT 59.681 50.000 6.85 0.00 0.00 5.68
823 847 0.319083 ACCAAACATGTCTCGGCGTA 59.681 50.000 6.85 0.00 0.00 4.42
824 848 0.719465 CCAAACATGTCTCGGCGTAC 59.281 55.000 6.85 7.51 0.00 3.67
827 852 0.601558 AACATGTCTCGGCGTACTGT 59.398 50.000 6.85 9.85 0.00 3.55
831 856 0.669619 TGTCTCGGCGTACTGTGAAA 59.330 50.000 6.85 0.00 0.00 2.69
835 860 1.662446 CGGCGTACTGTGAAACCGT 60.662 57.895 0.00 0.00 38.12 4.83
852 877 0.320421 CGTTGCTTTTCCTCCCTCGA 60.320 55.000 0.00 0.00 0.00 4.04
853 878 1.876416 CGTTGCTTTTCCTCCCTCGAA 60.876 52.381 0.00 0.00 0.00 3.71
855 880 1.892209 TGCTTTTCCTCCCTCGAAAC 58.108 50.000 0.00 0.00 0.00 2.78
920 951 3.204827 CCGAGCGGCAATCCTTGG 61.205 66.667 1.45 0.00 0.00 3.61
938 969 7.253905 TCCTTGGCTACAAAAGTACTAGAAT 57.746 36.000 0.00 0.00 35.89 2.40
1059 1093 3.064987 GCTAGCCGCCTTCTCGTCA 62.065 63.158 2.29 0.00 0.00 4.35
1146 1180 1.956629 GCCTTCCGTCCATCTCCGAA 61.957 60.000 0.00 0.00 0.00 4.30
1194 1228 0.491823 TTCTCTCCCTCACCTTCCCA 59.508 55.000 0.00 0.00 0.00 4.37
1195 1229 0.252284 TCTCTCCCTCACCTTCCCAC 60.252 60.000 0.00 0.00 0.00 4.61
1608 1642 2.691011 GGAGCTTAAGATCGTCCTCTGT 59.309 50.000 14.22 0.00 0.00 3.41
1611 1645 3.764434 AGCTTAAGATCGTCCTCTGTCAA 59.236 43.478 6.67 0.00 0.00 3.18
1997 2537 1.226746 GGCTAATCGGCTTTACGCAT 58.773 50.000 0.00 0.00 41.67 4.73
2113 2654 2.426738 CGCTATCATTTGCCCCTTTGAA 59.573 45.455 0.00 0.00 0.00 2.69
2143 2684 7.201626 GGGTTTGGTAGCGTTAAATTTTGTTTT 60.202 33.333 0.00 0.00 0.00 2.43
2318 2864 4.436998 CTCCGCCACTGGTCGTCC 62.437 72.222 9.94 0.00 0.00 4.79
2320 2866 4.082523 CCGCCACTGGTCGTCCAT 62.083 66.667 0.73 0.00 43.43 3.41
2321 2867 2.815211 CGCCACTGGTCGTCCATG 60.815 66.667 0.73 3.35 43.43 3.66
2322 2868 3.127533 GCCACTGGTCGTCCATGC 61.128 66.667 0.73 2.22 43.43 4.06
2323 2869 2.665000 CCACTGGTCGTCCATGCT 59.335 61.111 0.73 0.00 43.43 3.79
2324 2870 1.448540 CCACTGGTCGTCCATGCTC 60.449 63.158 0.73 0.00 43.43 4.26
2325 2871 1.448540 CACTGGTCGTCCATGCTCC 60.449 63.158 0.73 0.00 43.43 4.70
2326 2872 1.913262 ACTGGTCGTCCATGCTCCA 60.913 57.895 0.73 0.00 43.43 3.86
2327 2873 1.153489 CTGGTCGTCCATGCTCCAG 60.153 63.158 0.73 0.00 43.43 3.86
2328 2874 1.892819 CTGGTCGTCCATGCTCCAGT 61.893 60.000 0.73 0.00 43.43 4.00
2329 2875 1.448540 GGTCGTCCATGCTCCAGTG 60.449 63.158 0.00 0.00 0.00 3.66
2330 2876 2.103042 GTCGTCCATGCTCCAGTGC 61.103 63.158 0.00 0.00 0.00 4.40
2331 2877 3.190849 CGTCCATGCTCCAGTGCG 61.191 66.667 0.00 0.00 35.36 5.34
2332 2878 2.821366 GTCCATGCTCCAGTGCGG 60.821 66.667 0.00 0.00 35.36 5.69
2333 2879 4.783621 TCCATGCTCCAGTGCGGC 62.784 66.667 0.00 0.00 35.36 6.53
2485 3039 3.408288 AGATAAGAGTTCGTGAGCGTC 57.592 47.619 0.00 0.00 39.49 5.19
2498 3052 1.003118 TGAGCGTCAATTAAGTGGCCT 59.997 47.619 3.32 0.21 0.00 5.19
2562 3117 7.341256 AGACCTTAGGTTTCGTCATCTGTAATA 59.659 37.037 4.99 0.00 35.25 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 130 4.879598 ACCGTGACTCTAACGAAAGAAAT 58.120 39.130 0.00 0.00 43.68 2.17
139 144 2.762745 GGAAGCAAAACCGTGACTCTA 58.237 47.619 0.00 0.00 0.00 2.43
249 258 2.254546 ATGCAAAACCGTGACTCTCA 57.745 45.000 0.00 0.00 0.00 3.27
347 360 3.060602 GTGACTCTCGTGGAAGGAAAAG 58.939 50.000 0.00 0.00 0.00 2.27
535 557 2.378445 TCACGATTGGATTTCTCGCA 57.622 45.000 0.00 0.00 35.89 5.10
541 563 5.008217 TCGAACTGTTTTCACGATTGGATTT 59.992 36.000 0.00 0.00 0.00 2.17
550 572 4.025229 TCCAAATCTCGAACTGTTTTCACG 60.025 41.667 0.00 0.00 0.00 4.35
700 724 6.870971 AATTAAGGAGTACTCGTTGCAAAA 57.129 33.333 31.33 21.33 38.07 2.44
763 787 2.961669 GCCCGCGCGAGAAGAAAAA 61.962 57.895 34.63 0.00 0.00 1.94
764 788 3.419759 GCCCGCGCGAGAAGAAAA 61.420 61.111 34.63 0.00 0.00 2.29
768 792 4.933064 CTAGGCCCGCGCGAGAAG 62.933 72.222 34.63 17.75 35.02 2.85
784 808 3.515901 GGTAGGCTGCATATACCTTAGCT 59.484 47.826 16.25 0.00 36.76 3.32
785 809 3.260884 TGGTAGGCTGCATATACCTTAGC 59.739 47.826 21.11 2.67 39.78 3.09
794 818 3.054434 AGACATGTTTGGTAGGCTGCATA 60.054 43.478 0.00 0.00 0.00 3.14
805 829 0.719465 GTACGCCGAGACATGTTTGG 59.281 55.000 0.00 3.57 0.00 3.28
811 835 0.885879 TTCACAGTACGCCGAGACAT 59.114 50.000 0.00 0.00 0.00 3.06
817 841 1.216941 AACGGTTTCACAGTACGCCG 61.217 55.000 0.00 0.00 44.10 6.46
818 842 0.233848 CAACGGTTTCACAGTACGCC 59.766 55.000 0.00 0.00 0.00 5.68
820 844 1.214367 AGCAACGGTTTCACAGTACG 58.786 50.000 0.00 0.00 0.00 3.67
821 845 3.685836 AAAGCAACGGTTTCACAGTAC 57.314 42.857 0.00 0.00 0.00 2.73
822 846 3.065648 GGAAAAGCAACGGTTTCACAGTA 59.934 43.478 0.00 0.00 35.80 2.74
823 847 2.159296 GGAAAAGCAACGGTTTCACAGT 60.159 45.455 0.00 0.00 35.80 3.55
824 848 2.099098 AGGAAAAGCAACGGTTTCACAG 59.901 45.455 0.00 0.00 35.80 3.66
827 852 1.679153 GGAGGAAAAGCAACGGTTTCA 59.321 47.619 0.00 0.00 35.80 2.69
831 856 0.250770 GAGGGAGGAAAAGCAACGGT 60.251 55.000 0.00 0.00 0.00 4.83
835 860 2.227194 GTTTCGAGGGAGGAAAAGCAA 58.773 47.619 0.00 0.00 35.36 3.91
918 949 6.614694 TGGATTCTAGTACTTTTGTAGCCA 57.385 37.500 0.00 1.94 35.28 4.75
920 951 5.524281 GGCTGGATTCTAGTACTTTTGTAGC 59.476 44.000 0.00 3.41 35.28 3.58
938 969 1.038130 GTTAGAGAGGAGCGGCTGGA 61.038 60.000 7.50 0.00 0.00 3.86
1059 1093 1.078848 GATGGTCAGCTTGGTCGCT 60.079 57.895 0.00 0.00 41.90 4.93
1134 1168 1.076332 CGGTGTTTTCGGAGATGGAC 58.924 55.000 0.00 0.00 35.04 4.02
1433 1467 2.197605 TCGCAGTTGAGGTCCACGA 61.198 57.895 0.00 0.00 0.00 4.35
1593 1627 3.945921 ACGATTGACAGAGGACGATCTTA 59.054 43.478 0.00 0.00 30.35 2.10
1608 1642 2.668632 GCCCCTGTGGACGATTGA 59.331 61.111 0.00 0.00 35.39 2.57
2113 2654 2.955342 TAACGCTACCAAACCCCTTT 57.045 45.000 0.00 0.00 0.00 3.11
2315 2861 2.821366 CCGCACTGGAGCATGGAC 60.821 66.667 0.00 0.00 42.00 4.02
2316 2862 4.783621 GCCGCACTGGAGCATGGA 62.784 66.667 0.00 0.00 42.00 3.41
2408 2955 1.373748 GTACGGCAAAGCGAGGACA 60.374 57.895 0.00 0.00 0.00 4.02
2485 3039 6.686630 TGTATGAAAACAGGCCACTTAATTG 58.313 36.000 5.01 0.00 0.00 2.32
2498 3052 8.932945 TTAACTGCAACATTTGTATGAAAACA 57.067 26.923 0.00 0.00 35.65 2.83
2578 3133 3.304794 CGGATGGCTTAGCTCAGTACTAC 60.305 52.174 3.59 0.00 0.00 2.73
2579 3134 2.885266 CGGATGGCTTAGCTCAGTACTA 59.115 50.000 3.59 0.00 0.00 1.82
2580 3135 1.683917 CGGATGGCTTAGCTCAGTACT 59.316 52.381 3.59 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.