Multiple sequence alignment - TraesCS4B01G128100

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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 TraesCS4B01G128100 chr4B 100.000 2168 0 0 1 2168 167912692 167914859 0.000000e+00 4004
1 TraesCS4B01G128100 chr4B 93.972 282 14 2 1874 2155 37398589 37398311 9.430000e-115 424
2 TraesCS4B01G128100 chr4B 100.000 177 0 0 2671 2847 167915362 167915538 7.610000e-86 327
3 TraesCS4B01G128100 chr4B 97.740 177 4 0 2671 2847 37397796 37397620 3.560000e-79 305
4 TraesCS4B01G128100 chr4D 96.136 1061 35 3 806 1862 108907440 108906382 0.000000e+00 1727
5 TraesCS4B01G128100 chr4D 87.935 431 49 3 12 442 483120002 483120429 3.270000e-139 505
6 TraesCS4B01G128100 chrUn 95.913 1052 34 4 807 1852 414079930 414080978 0.000000e+00 1696
7 TraesCS4B01G128100 chr4A 95.913 1052 34 4 807 1852 467306953 467308001 0.000000e+00 1696
8 TraesCS4B01G128100 chr4A 86.996 446 54 4 1 444 573883172 573883615 1.520000e-137 499
9 TraesCS4B01G128100 chr4A 94.576 295 13 2 1874 2168 615453861 615453570 1.200000e-123 453
10 TraesCS4B01G128100 chr1B 96.093 819 29 3 1 816 53054989 53054171 0.000000e+00 1332
11 TraesCS4B01G128100 chr3B 95.961 817 29 3 1 813 716457674 716456858 0.000000e+00 1323
12 TraesCS4B01G128100 chr3B 95.116 819 34 4 1 813 716425549 716424731 0.000000e+00 1286
13 TraesCS4B01G128100 chr3B 97.175 177 5 0 2671 2847 773737599 773737423 1.660000e-77 300
14 TraesCS4B01G128100 chr2B 95.721 818 28 6 1 813 4938939 4938124 0.000000e+00 1310
15 TraesCS4B01G128100 chr2B 94.295 298 14 2 1871 2168 738503340 738503634 1.200000e-123 453
16 TraesCS4B01G128100 chr7A 83.676 827 112 22 1 814 7790637 7789821 0.000000e+00 758
17 TraesCS4B01G128100 chr3A 83.636 825 108 21 1 806 732084522 732085338 0.000000e+00 750
18 TraesCS4B01G128100 chr5A 83.678 821 106 22 1 800 523881867 523882680 0.000000e+00 749
19 TraesCS4B01G128100 chr5A 82.936 838 111 23 1 812 378782464 378781633 0.000000e+00 726
20 TraesCS4B01G128100 chr2A 82.950 827 107 24 1 805 422112953 422113767 0.000000e+00 715
21 TraesCS4B01G128100 chr2A 82.557 837 107 30 1 813 642583935 642583114 0.000000e+00 701
22 TraesCS4B01G128100 chr2A 92.953 298 18 2 1871 2168 756125420 756125714 5.630000e-117 431
23 TraesCS4B01G128100 chr2A 96.610 177 6 0 2671 2847 756126269 756126445 7.710000e-76 294
24 TraesCS4B01G128100 chr3D 81.522 828 112 25 1 806 75923761 75924569 0.000000e+00 643
25 TraesCS4B01G128100 chr1A 94.631 298 13 2 1871 2168 532382688 532382982 2.580000e-125 459
26 TraesCS4B01G128100 chr1A 97.740 177 4 0 2671 2847 532383319 532383495 3.560000e-79 305
27 TraesCS4B01G128100 chr7B 94.158 291 13 3 1871 2160 485615113 485615400 9.360000e-120 440
28 TraesCS4B01G128100 chr7B 92.542 295 19 2 1874 2168 580611995 580611704 1.220000e-113 420
29 TraesCS4B01G128100 chr7B 96.610 177 6 0 2671 2847 580611149 580610973 7.710000e-76 294
30 TraesCS4B01G128100 chr5B 92.953 298 18 2 1871 2168 118541926 118542220 5.630000e-117 431
31 TraesCS4B01G128100 chr5B 94.286 280 13 2 1874 2153 349387527 349387251 2.620000e-115 425
32 TraesCS4B01G128100 chr5B 98.870 177 2 0 2671 2847 349386842 349386666 1.650000e-82 316
33 TraesCS4B01G128100 chr5B 97.740 177 4 0 2671 2847 118542740 118542916 3.560000e-79 305
34 TraesCS4B01G128100 chr5B 97.740 177 4 0 2671 2847 620823767 620823591 3.560000e-79 305
35 TraesCS4B01G128100 chr5B 95.480 177 8 0 2671 2847 583307551 583307375 1.670000e-72 283


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 TraesCS4B01G128100 chr4B 167912692 167915538 2846 False 2165.5 4004 100.0000 1 2847 2 chr4B.!!$F1 2846
1 TraesCS4B01G128100 chr4B 37397620 37398589 969 True 364.5 424 95.8560 1874 2847 2 chr4B.!!$R1 973
2 TraesCS4B01G128100 chr4D 108906382 108907440 1058 True 1727.0 1727 96.1360 806 1862 1 chr4D.!!$R1 1056
3 TraesCS4B01G128100 chrUn 414079930 414080978 1048 False 1696.0 1696 95.9130 807 1852 1 chrUn.!!$F1 1045
4 TraesCS4B01G128100 chr4A 467306953 467308001 1048 False 1696.0 1696 95.9130 807 1852 1 chr4A.!!$F1 1045
5 TraesCS4B01G128100 chr1B 53054171 53054989 818 True 1332.0 1332 96.0930 1 816 1 chr1B.!!$R1 815
6 TraesCS4B01G128100 chr3B 716456858 716457674 816 True 1323.0 1323 95.9610 1 813 1 chr3B.!!$R2 812
7 TraesCS4B01G128100 chr3B 716424731 716425549 818 True 1286.0 1286 95.1160 1 813 1 chr3B.!!$R1 812
8 TraesCS4B01G128100 chr2B 4938124 4938939 815 True 1310.0 1310 95.7210 1 813 1 chr2B.!!$R1 812
9 TraesCS4B01G128100 chr7A 7789821 7790637 816 True 758.0 758 83.6760 1 814 1 chr7A.!!$R1 813
10 TraesCS4B01G128100 chr3A 732084522 732085338 816 False 750.0 750 83.6360 1 806 1 chr3A.!!$F1 805
11 TraesCS4B01G128100 chr5A 523881867 523882680 813 False 749.0 749 83.6780 1 800 1 chr5A.!!$F1 799
12 TraesCS4B01G128100 chr5A 378781633 378782464 831 True 726.0 726 82.9360 1 812 1 chr5A.!!$R1 811
13 TraesCS4B01G128100 chr2A 422112953 422113767 814 False 715.0 715 82.9500 1 805 1 chr2A.!!$F1 804
14 TraesCS4B01G128100 chr2A 642583114 642583935 821 True 701.0 701 82.5570 1 813 1 chr2A.!!$R1 812
15 TraesCS4B01G128100 chr2A 756125420 756126445 1025 False 362.5 431 94.7815 1871 2847 2 chr2A.!!$F2 976
16 TraesCS4B01G128100 chr3D 75923761 75924569 808 False 643.0 643 81.5220 1 806 1 chr3D.!!$F1 805
17 TraesCS4B01G128100 chr1A 532382688 532383495 807 False 382.0 459 96.1855 1871 2847 2 chr1A.!!$F1 976
18 TraesCS4B01G128100 chr7B 580610973 580611995 1022 True 357.0 420 94.5760 1874 2847 2 chr7B.!!$R1 973
19 TraesCS4B01G128100 chr5B 349386666 349387527 861 True 370.5 425 96.5780 1874 2847 2 chr5B.!!$R3 973
20 TraesCS4B01G128100 chr5B 118541926 118542916 990 False 368.0 431 95.3465 1871 2847 2 chr5B.!!$F1 976

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
996 1073 1.000646 GGTCTCTCACCCCGTCTCT 60.001 63.158 0.0 0.0 39.69 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 2054 1.39839 GCGGTCAGATTTGTGCTTAGG 59.602 52.381 0.0 0.0 0.0 2.69 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
377 390 1.804748 GACCACGATTTCACAGGTTCC 59.195 52.381 0.00 0.00 31.57 3.62
524 589 4.013728 CTGGTATTGGGTTCGAAATCCAA 58.986 43.478 26.29 26.29 43.62 3.53
597 664 5.652994 AAGGTGTGTGCTTTTCTACAAAA 57.347 34.783 0.00 0.00 0.00 2.44
729 797 1.237285 ATGCAAGTTCGTGGACCAGC 61.237 55.000 0.00 0.00 0.00 4.85
783 852 1.148310 CCGCCACACACAAGTTCTAG 58.852 55.000 0.00 0.00 0.00 2.43
891 967 1.609208 GGCACTCTTGTGTGGTTGAT 58.391 50.000 5.22 0.00 45.44 2.57
965 1042 1.334869 ACACGAGCCTTGCTTTCTTTG 59.665 47.619 0.00 0.00 39.88 2.77
996 1073 1.000646 GGTCTCTCACCCCGTCTCT 60.001 63.158 0.00 0.00 39.69 3.10
1014 1091 4.408821 GGCATGGACGTCCTGGCA 62.409 66.667 34.47 20.63 38.56 4.92
1356 1433 1.272147 GGCTTCCACCACCTCTTCAAT 60.272 52.381 0.00 0.00 0.00 2.57
1587 1667 3.611766 ACCTACCAATTCTGACGAAGG 57.388 47.619 0.00 0.00 31.60 3.46
1592 1672 4.819105 ACCAATTCTGACGAAGGTATGA 57.181 40.909 0.00 0.00 28.91 2.15
1738 1818 1.388065 CGAGCATCCTCTTCTCCGGT 61.388 60.000 0.00 0.00 35.90 5.28
1859 1939 6.448207 AGTACTCGTAGTTAGTCCCATTTC 57.552 41.667 0.00 0.00 0.00 2.17
1862 1942 5.014858 ACTCGTAGTTAGTCCCATTTCTGA 58.985 41.667 0.00 0.00 0.00 3.27
1863 1943 5.125739 ACTCGTAGTTAGTCCCATTTCTGAG 59.874 44.000 0.00 0.00 0.00 3.35
1864 1944 5.014858 TCGTAGTTAGTCCCATTTCTGAGT 58.985 41.667 0.00 0.00 0.00 3.41
1865 1945 6.182627 TCGTAGTTAGTCCCATTTCTGAGTA 58.817 40.000 0.00 0.00 0.00 2.59
1866 1946 6.832384 TCGTAGTTAGTCCCATTTCTGAGTAT 59.168 38.462 0.00 0.00 0.00 2.12
1867 1947 7.341256 TCGTAGTTAGTCCCATTTCTGAGTATT 59.659 37.037 0.00 0.00 0.00 1.89
1868 1948 7.980099 CGTAGTTAGTCCCATTTCTGAGTATTT 59.020 37.037 0.00 0.00 0.00 1.40
1872 1952 8.890718 GTTAGTCCCATTTCTGAGTATTTAACC 58.109 37.037 0.00 0.00 0.00 2.85
1885 1965 8.749026 TGAGTATTTAACCAAAAACTACCACA 57.251 30.769 0.00 0.00 0.00 4.17
1886 1966 9.186837 TGAGTATTTAACCAAAAACTACCACAA 57.813 29.630 0.00 0.00 0.00 3.33
1891 1971 8.705048 TTTAACCAAAAACTACCACAATTCAC 57.295 30.769 0.00 0.00 0.00 3.18
1892 1972 4.927422 ACCAAAAACTACCACAATTCACG 58.073 39.130 0.00 0.00 0.00 4.35
1893 1973 4.641094 ACCAAAAACTACCACAATTCACGA 59.359 37.500 0.00 0.00 0.00 4.35
1894 1974 5.125739 ACCAAAAACTACCACAATTCACGAA 59.874 36.000 0.00 0.00 0.00 3.85
1895 1975 6.037098 CCAAAAACTACCACAATTCACGAAA 58.963 36.000 0.00 0.00 0.00 3.46
1896 1976 6.020201 CCAAAAACTACCACAATTCACGAAAC 60.020 38.462 0.00 0.00 0.00 2.78
1897 1977 4.823790 AACTACCACAATTCACGAAACC 57.176 40.909 0.00 0.00 0.00 3.27
1899 1979 1.670791 ACCACAATTCACGAAACCGT 58.329 45.000 0.00 0.00 41.53 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
208 214 2.905085 ACCATCCAAAAATGTCCATGCA 59.095 40.909 0.00 0.00 0.00 3.96
377 390 4.485163 GAAAAACAGGATCCCGACAATTG 58.515 43.478 8.55 3.24 0.00 2.32
597 664 7.712639 CCACAGTAATAGTTCTTGCATGATAGT 59.287 37.037 2.75 0.00 0.00 2.12
729 797 8.495554 TGCATAAACTTGTAAAATACGTGTTG 57.504 30.769 0.00 0.00 30.89 3.33
836 905 7.781763 AAAAACTGAAAGAGCGAAAATATCG 57.218 32.000 0.00 0.00 46.68 2.92
864 940 2.032528 CAAGAGTGCCCGCCTGAA 59.967 61.111 0.00 0.00 0.00 3.02
865 941 3.241530 ACAAGAGTGCCCGCCTGA 61.242 61.111 0.00 0.00 0.00 3.86
980 1057 1.000771 CCAGAGACGGGGTGAGAGA 60.001 63.158 0.00 0.00 0.00 3.10
996 1073 4.408821 GCCAGGACGTCCATGCCA 62.409 66.667 35.00 0.00 38.89 4.92
1062 1139 1.141019 GAGAACGTATGGGCGAGCA 59.859 57.895 0.00 0.00 35.59 4.26
1386 1463 2.858476 TTGCAGAGGCCTTCCCCA 60.858 61.111 6.77 0.00 40.13 4.96
1431 1508 2.852075 AAGGGCCCTTGGTCGTCA 60.852 61.111 36.80 0.00 34.60 4.35
1571 1651 4.504858 GTCATACCTTCGTCAGAATTGGT 58.495 43.478 0.00 0.00 38.18 3.67
1579 1659 1.533129 CGATGCGTCATACCTTCGTCA 60.533 52.381 6.75 0.00 0.00 4.35
1587 1667 2.423926 ACCTGATCGATGCGTCATAC 57.576 50.000 0.54 0.00 0.00 2.39
1592 1672 0.736636 TCGTTACCTGATCGATGCGT 59.263 50.000 0.54 0.00 0.00 5.24
1847 1927 8.607713 TGGTTAAATACTCAGAAATGGGACTAA 58.392 33.333 0.00 0.00 0.00 2.24
1852 1932 9.203421 GTTTTTGGTTAAATACTCAGAAATGGG 57.797 33.333 0.00 0.00 0.00 4.00
1859 1939 8.842280 TGTGGTAGTTTTTGGTTAAATACTCAG 58.158 33.333 0.00 0.00 38.47 3.35
1865 1945 9.320352 GTGAATTGTGGTAGTTTTTGGTTAAAT 57.680 29.630 0.00 0.00 0.00 1.40
1866 1946 7.488471 CGTGAATTGTGGTAGTTTTTGGTTAAA 59.512 33.333 0.00 0.00 0.00 1.52
1867 1947 6.973474 CGTGAATTGTGGTAGTTTTTGGTTAA 59.027 34.615 0.00 0.00 0.00 2.01
1868 1948 6.318144 TCGTGAATTGTGGTAGTTTTTGGTTA 59.682 34.615 0.00 0.00 0.00 2.85
1869 1949 5.125739 TCGTGAATTGTGGTAGTTTTTGGTT 59.874 36.000 0.00 0.00 0.00 3.67
1872 1952 6.020201 GGTTTCGTGAATTGTGGTAGTTTTTG 60.020 38.462 0.00 0.00 0.00 2.44
1891 1971 4.024725 TGGTAGTTTTTCATCACGGTTTCG 60.025 41.667 0.00 0.00 43.02 3.46
1892 1972 5.008316 AGTGGTAGTTTTTCATCACGGTTTC 59.992 40.000 0.00 0.00 0.00 2.78
1893 1973 4.885325 AGTGGTAGTTTTTCATCACGGTTT 59.115 37.500 0.00 0.00 0.00 3.27
1894 1974 4.457466 AGTGGTAGTTTTTCATCACGGTT 58.543 39.130 0.00 0.00 0.00 4.44
1895 1975 4.081322 AGTGGTAGTTTTTCATCACGGT 57.919 40.909 0.00 0.00 0.00 4.83
1896 1976 5.432885 AAAGTGGTAGTTTTTCATCACGG 57.567 39.130 0.00 0.00 0.00 4.94
1952 2032 2.398554 GGCCAAGCGAGCGATTTCA 61.399 57.895 0.00 0.00 0.00 2.69
1974 2054 1.398390 GCGGTCAGATTTGTGCTTAGG 59.602 52.381 0.00 0.00 0.00 2.69
2098 2178 2.047274 CTTGGTGGGCACGACGAT 60.047 61.111 0.00 0.00 38.18 3.73


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

AutoCloner maintained by Alex Coulton.