Multiple sequence alignment - TraesCS4B01G067000

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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 TraesCS4B01G067000 chr4B 100.000 2321 0 0 1 2321 59865358 59867678 0.000000e+00 4287.0
1 TraesCS4B01G067000 chr4B 86.496 859 86 20 10 861 592271221 592270386 0.000000e+00 917.0
2 TraesCS4B01G067000 chr4B 92.322 547 41 1 1775 2321 175671381 175670836 0.000000e+00 776.0
3 TraesCS4B01G067000 chr4D 93.362 919 47 4 860 1768 40824336 40825250 0.000000e+00 1347.0
4 TraesCS4B01G067000 chr4D 92.932 863 45 5 10 861 164020720 164021577 0.000000e+00 1242.0
5 TraesCS4B01G067000 chr4D 94.022 552 28 3 1767 2318 473177114 473177660 0.000000e+00 832.0
6 TraesCS4B01G067000 chr5B 93.880 866 33 9 10 864 594469787 594470643 0.000000e+00 1288.0
7 TraesCS4B01G067000 chr5B 80.488 82 6 5 1454 1525 27832925 27833006 1.000000e-03 54.7
8 TraesCS4B01G067000 chr3D 93.371 875 44 4 6 870 185851474 185850604 0.000000e+00 1282.0
9 TraesCS4B01G067000 chr3D 93.171 864 43 7 9 861 487918810 487919668 0.000000e+00 1254.0
10 TraesCS4B01G067000 chr3D 92.123 876 51 7 5 870 359230091 359229224 0.000000e+00 1219.0
11 TraesCS4B01G067000 chr3D 91.506 883 43 9 4 874 364043061 364042199 0.000000e+00 1186.0
12 TraesCS4B01G067000 chr3D 90.857 875 50 8 5 868 478204388 478205243 0.000000e+00 1146.0
13 TraesCS4B01G067000 chr3D 92.000 550 38 4 1769 2318 213248898 213249441 0.000000e+00 767.0
14 TraesCS4B01G067000 chr3D 91.636 550 42 2 1769 2318 67328947 67329492 0.000000e+00 758.0
15 TraesCS4B01G067000 chr7D 93.519 864 39 6 13 865 555709375 555708518 0.000000e+00 1269.0
16 TraesCS4B01G067000 chr7D 93.005 872 45 5 10 870 443447556 443446690 0.000000e+00 1258.0
17 TraesCS4B01G067000 chr7D 92.935 552 33 4 1767 2318 230720962 230721507 0.000000e+00 798.0
18 TraesCS4B01G067000 chr7D 97.059 34 1 0 1457 1490 51418409 51418376 8.960000e-05 58.4
19 TraesCS4B01G067000 chr6D 93.044 877 41 10 5 868 289763372 289764241 0.000000e+00 1264.0
20 TraesCS4B01G067000 chr6D 92.513 561 34 6 1759 2318 338115488 338114935 0.000000e+00 797.0
21 TraesCS4B01G067000 chr6D 91.773 547 31 6 340 876 391092850 391093392 0.000000e+00 749.0
22 TraesCS4B01G067000 chr4A 91.830 918 53 4 860 1768 558676478 558675574 0.000000e+00 1260.0
23 TraesCS4B01G067000 chr4A 92.754 552 36 2 1767 2318 714894300 714893753 0.000000e+00 795.0
24 TraesCS4B01G067000 chr1D 92.816 877 45 8 4 870 486670409 486671277 0.000000e+00 1254.0
25 TraesCS4B01G067000 chr1D 100.000 29 0 0 1489 1517 247506543 247506571 1.000000e-03 54.7
26 TraesCS4B01G067000 chr7B 93.240 858 44 3 13 861 244936318 244937170 0.000000e+00 1251.0
27 TraesCS4B01G067000 chr5D 92.972 868 44 6 4 861 214261070 214261930 0.000000e+00 1249.0
28 TraesCS4B01G067000 chr5D 90.493 873 59 10 6 867 107734378 107733519 0.000000e+00 1131.0
29 TraesCS4B01G067000 chr5D 93.514 555 32 3 1768 2321 515318178 515317627 0.000000e+00 822.0
30 TraesCS4B01G067000 chr6B 92.218 861 48 7 13 863 244608624 244609475 0.000000e+00 1201.0
31 TraesCS4B01G067000 chr6B 80.505 872 133 28 8 866 464043003 464043850 3.250000e-178 634.0
32 TraesCS4B01G067000 chr6B 89.831 59 5 1 1468 1525 586516615 586516673 8.890000e-10 75.0
33 TraesCS4B01G067000 chr1A 91.676 877 56 6 4 869 235712757 235713627 0.000000e+00 1199.0
34 TraesCS4B01G067000 chr2D 89.055 868 58 15 10 861 611723329 611724175 0.000000e+00 1042.0
35 TraesCS4B01G067000 chr2D 87.115 877 91 12 7 870 539973761 539972894 0.000000e+00 974.0
36 TraesCS4B01G067000 chr2D 86.636 868 98 13 11 870 277157714 277156857 0.000000e+00 944.0
37 TraesCS4B01G067000 chr2D 86.319 307 38 2 1027 1329 74986456 74986150 4.780000e-87 331.0
38 TraesCS4B01G067000 chr7A 87.007 862 81 17 13 862 224439851 224440693 0.000000e+00 942.0
39 TraesCS4B01G067000 chr1B 92.647 544 39 1 1775 2318 649017185 649016643 0.000000e+00 782.0
40 TraesCS4B01G067000 chr3B 93.950 281 16 1 581 861 483953441 483953720 7.670000e-115 424.0
41 TraesCS4B01G067000 chr2A 85.621 306 41 1 1027 1329 74562036 74561731 3.720000e-83 318.0
42 TraesCS4B01G067000 chr2B 77.989 527 88 16 884 1382 114431180 114430654 2.900000e-79 305.0
43 TraesCS4B01G067000 chr2B 96.970 33 1 0 1459 1491 600001772 600001740 3.220000e-04 56.5
44 TraesCS4B01G067000 chrUn 84.524 84 11 2 1686 1768 83954317 83954399 5.320000e-12 82.4
45 TraesCS4B01G067000 chrUn 94.444 36 1 1 1463 1498 321212702 321212736 1.000000e-03 54.7
46 TraesCS4B01G067000 chr5A 94.444 36 1 1 1463 1498 555236913 555236879 1.000000e-03 54.7
47 TraesCS4B01G067000 chr5A 94.444 36 1 1 1463 1498 555251121 555251087 1.000000e-03 54.7


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 TraesCS4B01G067000 chr4B 59865358 59867678 2320 False 4287 4287 100.000 1 2321 1 chr4B.!!$F1 2320
1 TraesCS4B01G067000 chr4B 592270386 592271221 835 True 917 917 86.496 10 861 1 chr4B.!!$R2 851
2 TraesCS4B01G067000 chr4B 175670836 175671381 545 True 776 776 92.322 1775 2321 1 chr4B.!!$R1 546
3 TraesCS4B01G067000 chr4D 40824336 40825250 914 False 1347 1347 93.362 860 1768 1 chr4D.!!$F1 908
4 TraesCS4B01G067000 chr4D 164020720 164021577 857 False 1242 1242 92.932 10 861 1 chr4D.!!$F2 851
5 TraesCS4B01G067000 chr4D 473177114 473177660 546 False 832 832 94.022 1767 2318 1 chr4D.!!$F3 551
6 TraesCS4B01G067000 chr5B 594469787 594470643 856 False 1288 1288 93.880 10 864 1 chr5B.!!$F2 854
7 TraesCS4B01G067000 chr3D 185850604 185851474 870 True 1282 1282 93.371 6 870 1 chr3D.!!$R1 864
8 TraesCS4B01G067000 chr3D 487918810 487919668 858 False 1254 1254 93.171 9 861 1 chr3D.!!$F4 852
9 TraesCS4B01G067000 chr3D 359229224 359230091 867 True 1219 1219 92.123 5 870 1 chr3D.!!$R2 865
10 TraesCS4B01G067000 chr3D 364042199 364043061 862 True 1186 1186 91.506 4 874 1 chr3D.!!$R3 870
11 TraesCS4B01G067000 chr3D 478204388 478205243 855 False 1146 1146 90.857 5 868 1 chr3D.!!$F3 863
12 TraesCS4B01G067000 chr3D 213248898 213249441 543 False 767 767 92.000 1769 2318 1 chr3D.!!$F2 549
13 TraesCS4B01G067000 chr3D 67328947 67329492 545 False 758 758 91.636 1769 2318 1 chr3D.!!$F1 549
14 TraesCS4B01G067000 chr7D 555708518 555709375 857 True 1269 1269 93.519 13 865 1 chr7D.!!$R3 852
15 TraesCS4B01G067000 chr7D 443446690 443447556 866 True 1258 1258 93.005 10 870 1 chr7D.!!$R2 860
16 TraesCS4B01G067000 chr7D 230720962 230721507 545 False 798 798 92.935 1767 2318 1 chr7D.!!$F1 551
17 TraesCS4B01G067000 chr6D 289763372 289764241 869 False 1264 1264 93.044 5 868 1 chr6D.!!$F1 863
18 TraesCS4B01G067000 chr6D 338114935 338115488 553 True 797 797 92.513 1759 2318 1 chr6D.!!$R1 559
19 TraesCS4B01G067000 chr6D 391092850 391093392 542 False 749 749 91.773 340 876 1 chr6D.!!$F2 536
20 TraesCS4B01G067000 chr4A 558675574 558676478 904 True 1260 1260 91.830 860 1768 1 chr4A.!!$R1 908
21 TraesCS4B01G067000 chr4A 714893753 714894300 547 True 795 795 92.754 1767 2318 1 chr4A.!!$R2 551
22 TraesCS4B01G067000 chr1D 486670409 486671277 868 False 1254 1254 92.816 4 870 1 chr1D.!!$F2 866
23 TraesCS4B01G067000 chr7B 244936318 244937170 852 False 1251 1251 93.240 13 861 1 chr7B.!!$F1 848
24 TraesCS4B01G067000 chr5D 214261070 214261930 860 False 1249 1249 92.972 4 861 1 chr5D.!!$F1 857
25 TraesCS4B01G067000 chr5D 107733519 107734378 859 True 1131 1131 90.493 6 867 1 chr5D.!!$R1 861
26 TraesCS4B01G067000 chr5D 515317627 515318178 551 True 822 822 93.514 1768 2321 1 chr5D.!!$R2 553
27 TraesCS4B01G067000 chr6B 244608624 244609475 851 False 1201 1201 92.218 13 863 1 chr6B.!!$F1 850
28 TraesCS4B01G067000 chr6B 464043003 464043850 847 False 634 634 80.505 8 866 1 chr6B.!!$F2 858
29 TraesCS4B01G067000 chr1A 235712757 235713627 870 False 1199 1199 91.676 4 869 1 chr1A.!!$F1 865
30 TraesCS4B01G067000 chr2D 611723329 611724175 846 False 1042 1042 89.055 10 861 1 chr2D.!!$F1 851
31 TraesCS4B01G067000 chr2D 539972894 539973761 867 True 974 974 87.115 7 870 1 chr2D.!!$R3 863
32 TraesCS4B01G067000 chr2D 277156857 277157714 857 True 944 944 86.636 11 870 1 chr2D.!!$R2 859
33 TraesCS4B01G067000 chr7A 224439851 224440693 842 False 942 942 87.007 13 862 1 chr7A.!!$F1 849
34 TraesCS4B01G067000 chr1B 649016643 649017185 542 True 782 782 92.647 1775 2318 1 chr1B.!!$R1 543
35 TraesCS4B01G067000 chr2B 114430654 114431180 526 True 305 305 77.989 884 1382 1 chr2B.!!$R1 498

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
919 976 2.057922 ACACAATCACTCCCTTCCAGT 58.942 47.619 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1856 1938 0.396811 CTGTTCTGAGGGTTTCGGGT 59.603 55.0 0.0 0.0 32.69 5.28 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
45 47 2.263895 TATGCCCCTAGTTGTGTCCT 57.736 50.000 0.00 0.00 0.00 3.85
87 89 2.421751 TTCCAAAAGTCACCGGTTCA 57.578 45.000 2.97 0.00 0.00 3.18
283 290 3.402628 AGTGCACATCCGAGTTTTAGT 57.597 42.857 21.04 0.00 0.00 2.24
291 298 6.725246 CACATCCGAGTTTTAGTTCTTTTGT 58.275 36.000 0.00 0.00 0.00 2.83
916 973 3.610911 CCTTACACAATCACTCCCTTCC 58.389 50.000 0.00 0.00 0.00 3.46
919 976 2.057922 ACACAATCACTCCCTTCCAGT 58.942 47.619 0.00 0.00 0.00 4.00
979 1040 2.419198 GACTCTCCATGGCGCGAT 59.581 61.111 12.10 0.00 0.00 4.58
1023 1096 4.426112 CTCGCAGTCGCCTCAGCA 62.426 66.667 0.00 0.00 39.83 4.41
1053 1126 2.279069 CCACAGTGAGAGGCTCGGT 61.279 63.158 9.22 1.10 32.35 4.69
1200 1276 1.139058 GTGGTCTCCGGCATGAACTAT 59.861 52.381 0.00 0.00 0.00 2.12
1215 1291 1.595466 ACTATCGCCTCTTCGTCGAT 58.405 50.000 0.00 0.00 44.05 3.59
1309 1385 2.559668 CAGCTCAAATCCTTCAAGCCAA 59.440 45.455 0.00 0.00 33.43 4.52
1387 1467 6.662616 CCGCTCTGGTTAATTTCATTATCTG 58.337 40.000 0.00 0.00 0.00 2.90
1414 1494 8.515414 GTCCTTTGAAGCACTAATAAATGAGTT 58.485 33.333 0.00 0.00 0.00 3.01
1437 1517 6.097915 TGAATATTACTCCCTCGTTCCATC 57.902 41.667 0.00 0.00 0.00 3.51
1519 1600 4.825634 ACGATCTTATATTGTGGGACGAGA 59.174 41.667 0.00 0.00 0.00 4.04
1535 1616 3.741249 ACGAGAGAGTACTCAAGTGTCA 58.259 45.455 24.44 0.00 44.79 3.58
1553 1634 2.805671 GTCATGTGGTTTGATCGTGACA 59.194 45.455 10.53 0.00 43.39 3.58
1575 1656 2.034812 CCTACGGTTCATCCTCACTAGC 59.965 54.545 0.00 0.00 0.00 3.42
1584 1665 5.230323 TCATCCTCACTAGCGACTACTAT 57.770 43.478 0.00 0.00 0.00 2.12
1665 1746 0.538118 ATTGTTGTGATGGCCCATGC 59.462 50.000 0.00 0.00 0.00 4.06
1666 1747 0.830866 TTGTTGTGATGGCCCATGCA 60.831 50.000 0.00 0.00 40.13 3.96
1667 1748 1.252215 TGTTGTGATGGCCCATGCAG 61.252 55.000 0.00 0.00 40.13 4.41
1668 1749 1.683025 TTGTGATGGCCCATGCAGG 60.683 57.895 0.00 0.00 40.13 4.85
1712 1793 1.228124 AGTTGGGCGTGCTTTGCTA 60.228 52.632 0.00 0.00 0.00 3.49
1714 1795 1.527148 TTGGGCGTGCTTTGCTACA 60.527 52.632 0.00 0.00 0.00 2.74
1773 1854 8.986929 ACTCCCTCTATTTCAAAATAGGATTG 57.013 34.615 17.98 10.14 45.00 2.67
1790 1871 3.118775 GGATTGTTTATTTCTGTGCCCCC 60.119 47.826 0.00 0.00 0.00 5.40
1795 1876 0.406361 TATTTCTGTGCCCCCGGTTT 59.594 50.000 0.00 0.00 0.00 3.27
1821 1902 2.224402 GCTCTACTCATTCATCCCCACC 60.224 54.545 0.00 0.00 0.00 4.61
1851 1933 2.452600 TTGCTCACTTTTCCCCACTT 57.547 45.000 0.00 0.00 0.00 3.16
1856 1938 3.497942 GCTCACTTTTCCCCACTTCCTTA 60.498 47.826 0.00 0.00 0.00 2.69
1882 1964 5.109903 CGAAACCCTCAGAACAGGTTATAG 58.890 45.833 0.00 0.00 43.06 1.31
2017 2107 0.258484 TCCATGGACATGCCCGAAAT 59.742 50.000 11.44 0.00 37.49 2.17
2031 2121 4.018506 TGCCCGAAATGTCCCATCATATAT 60.019 41.667 0.00 0.00 0.00 0.86
2318 2409 0.112412 AAGATGGTGCGGGGAAACTT 59.888 50.000 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 47 6.610075 AATTAGGGGTAAAACAGACGAGTA 57.390 37.500 0.00 0.00 0.00 2.59
87 89 3.073650 AGAGGAGCAAAGTGACTTGGATT 59.926 43.478 3.37 0.00 0.00 3.01
182 186 7.500992 TGAACATTTTGGTACCTTATTTGCAA 58.499 30.769 14.36 0.00 0.00 4.08
674 726 7.026631 TCAGAAAAATGCCAATAAGATACCG 57.973 36.000 0.00 0.00 0.00 4.02
726 778 0.179051 ACCGTTTGACCGCCAGTTTA 60.179 50.000 0.00 0.00 0.00 2.01
916 973 0.686441 TGGGGACGGTGGATCTACTG 60.686 60.000 15.93 15.93 0.00 2.74
919 976 0.979187 GGTTGGGGACGGTGGATCTA 60.979 60.000 0.00 0.00 0.00 1.98
1119 1195 2.503061 CTAGCCAGGCTCGCATGT 59.497 61.111 20.38 0.00 40.44 3.21
1254 1330 0.328592 AGGACTGCTCGTAGACCTCA 59.671 55.000 0.79 0.00 38.21 3.86
1309 1385 0.247736 GGGACAGATCAGTTCGCAGT 59.752 55.000 0.00 0.00 0.00 4.40
1414 1494 5.600898 TGATGGAACGAGGGAGTAATATTCA 59.399 40.000 0.00 0.00 0.00 2.57
1519 1600 3.898123 ACCACATGACACTTGAGTACTCT 59.102 43.478 23.01 2.71 0.00 3.24
1535 1616 2.151202 GGTGTCACGATCAAACCACAT 58.849 47.619 0.00 0.00 0.00 3.21
1575 1656 5.931146 ACACTATCCGGAGTAATAGTAGTCG 59.069 44.000 11.34 8.29 36.74 4.18
1620 1701 6.893958 AGAGAACTCACAACTTTATATGCG 57.106 37.500 4.64 0.00 0.00 4.73
1676 1757 7.048512 GCCCAACTCTTCTAGTACACATTAAT 58.951 38.462 0.00 0.00 37.50 1.40
1712 1793 6.487331 TGAAAACCCAATAACACTAACGATGT 59.513 34.615 0.00 0.00 0.00 3.06
1714 1795 7.392113 TCATGAAAACCCAATAACACTAACGAT 59.608 33.333 0.00 0.00 0.00 3.73
1770 1851 2.495669 CGGGGGCACAGAAATAAACAAT 59.504 45.455 0.00 0.00 0.00 2.71
1773 1854 0.815095 CCGGGGGCACAGAAATAAAC 59.185 55.000 0.00 0.00 0.00 2.01
1790 1871 5.651530 TGAATGAGTAGAGCTAAGAAACCG 58.348 41.667 0.00 0.00 0.00 4.44
1795 1876 4.835615 GGGGATGAATGAGTAGAGCTAAGA 59.164 45.833 0.00 0.00 0.00 2.10
1821 1902 3.982576 AAGTGAGCAAAAGTTAACCGG 57.017 42.857 0.00 0.00 0.00 5.28
1851 1933 1.203212 TCTGAGGGTTTCGGGTAAGGA 60.203 52.381 0.00 0.00 32.69 3.36
1856 1938 0.396811 CTGTTCTGAGGGTTTCGGGT 59.603 55.000 0.00 0.00 32.69 5.28
1972 2058 0.815213 CTACCCCATGACCGTGCATG 60.815 60.000 0.00 0.00 44.05 4.06
1973 2059 1.526887 CTACCCCATGACCGTGCAT 59.473 57.895 0.00 0.00 0.00 3.96
1977 2063 2.987125 GTGCTACCCCATGACCGT 59.013 61.111 0.00 0.00 0.00 4.83
1983 2073 1.271840 ATGGACACGTGCTACCCCAT 61.272 55.000 17.22 16.58 0.00 4.00
2031 2121 1.615424 GGAGGTGGTTGCCCCTCTA 60.615 63.158 16.60 0.00 45.46 2.43
2240 2331 1.985614 CAGCTCCACCACATCTCCA 59.014 57.895 0.00 0.00 0.00 3.86
2300 2391 0.609131 CAAGTTTCCCCGCACCATCT 60.609 55.000 0.00 0.00 0.00 2.90
2302 2393 2.275380 GCAAGTTTCCCCGCACCAT 61.275 57.895 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.