Multiple sequence alignment - TraesCS4A01G092200

Loading Multiple Alignment...

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 TraesCS4A01G092200 chr4A 100.000 2474 0 0 1 2474 99004047 99006520 0.000000e+00 4569.0
1 TraesCS4A01G092200 chr4A 93.950 595 22 7 888 1478 98785411 98785995 0.000000e+00 887.0
2 TraesCS4A01G092200 chr4A 91.597 476 33 1 884 1352 98787386 98787861 0.000000e+00 651.0
3 TraesCS4A01G092200 chr4A 90.566 477 42 2 1001 1474 100551358 100550882 1.610000e-176 628.0
4 TraesCS4A01G092200 chr6A 98.977 880 9 0 1 880 389571971 389572850 0.000000e+00 1576.0
5 TraesCS4A01G092200 chr7A 98.864 880 10 0 1 880 31000202 30999323 0.000000e+00 1570.0
6 TraesCS4A01G092200 chr7A 98.636 880 12 0 1 880 299538670 299539549 0.000000e+00 1559.0
7 TraesCS4A01G092200 chr4B 96.237 930 30 2 888 1817 450483352 450482428 0.000000e+00 1519.0
8 TraesCS4A01G092200 chr4B 89.300 757 46 20 884 1625 450105617 450106353 0.000000e+00 917.0
9 TraesCS4A01G092200 chr4B 89.362 705 33 18 888 1569 450686458 450685773 0.000000e+00 848.0
10 TraesCS4A01G092200 chr4B 89.851 670 30 6 1811 2474 450482305 450481668 0.000000e+00 826.0
11 TraesCS4A01G092200 chr3B 96.498 828 29 0 1 828 43597486 43598313 0.000000e+00 1369.0
12 TraesCS4A01G092200 chr3B 96.667 60 2 0 821 880 43604088 43604147 1.570000e-17 100.0
13 TraesCS4A01G092200 chr4D 94.145 871 27 7 888 1753 365865095 365864244 0.000000e+00 1304.0
14 TraesCS4A01G092200 chr4D 95.122 615 27 2 1862 2474 365864232 365863619 0.000000e+00 966.0
15 TraesCS4A01G092200 chr4D 94.247 591 23 4 888 1478 365217450 365218029 0.000000e+00 893.0
16 TraesCS4A01G092200 chr4D 88.363 782 37 24 890 1633 366219736 366218971 0.000000e+00 891.0
17 TraesCS4A01G092200 chr4D 96.875 32 0 1 2244 2275 507732565 507732595 4.000000e-03 52.8
18 TraesCS4A01G092200 chr2A 96.000 700 24 3 184 880 11792622 11791924 0.000000e+00 1134.0
19 TraesCS4A01G092200 chr2A 98.462 65 1 0 1 65 11792991 11792927 5.590000e-22 115.0
20 TraesCS4A01G092200 chr7B 97.742 310 6 1 571 880 721810608 721810300 1.300000e-147 532.0
21 TraesCS4A01G092200 chr1B 89.552 134 12 2 630 761 266948271 266948404 4.230000e-38 169.0
22 TraesCS4A01G092200 chr5D 86.885 61 8 0 1692 1752 460449122 460449182 4.410000e-08 69.4
23 TraesCS4A01G092200 chr6B 96.875 32 0 1 2244 2275 213319601 213319571 4.000000e-03 52.8


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 TraesCS4A01G092200 chr4A 99004047 99006520 2473 False 4569.0 4569 100.0000 1 2474 1 chr4A.!!$F1 2473
1 TraesCS4A01G092200 chr4A 98785411 98787861 2450 False 769.0 887 92.7735 884 1478 2 chr4A.!!$F2 594
2 TraesCS4A01G092200 chr6A 389571971 389572850 879 False 1576.0 1576 98.9770 1 880 1 chr6A.!!$F1 879
3 TraesCS4A01G092200 chr7A 30999323 31000202 879 True 1570.0 1570 98.8640 1 880 1 chr7A.!!$R1 879
4 TraesCS4A01G092200 chr7A 299538670 299539549 879 False 1559.0 1559 98.6360 1 880 1 chr7A.!!$F1 879
5 TraesCS4A01G092200 chr4B 450481668 450483352 1684 True 1172.5 1519 93.0440 888 2474 2 chr4B.!!$R2 1586
6 TraesCS4A01G092200 chr4B 450105617 450106353 736 False 917.0 917 89.3000 884 1625 1 chr4B.!!$F1 741
7 TraesCS4A01G092200 chr4B 450685773 450686458 685 True 848.0 848 89.3620 888 1569 1 chr4B.!!$R1 681
8 TraesCS4A01G092200 chr3B 43597486 43598313 827 False 1369.0 1369 96.4980 1 828 1 chr3B.!!$F1 827
9 TraesCS4A01G092200 chr4D 365863619 365865095 1476 True 1135.0 1304 94.6335 888 2474 2 chr4D.!!$R2 1586
10 TraesCS4A01G092200 chr4D 365217450 365218029 579 False 893.0 893 94.2470 888 1478 1 chr4D.!!$F1 590
11 TraesCS4A01G092200 chr4D 366218971 366219736 765 True 891.0 891 88.3630 890 1633 1 chr4D.!!$R1 743
12 TraesCS4A01G092200 chr2A 11791924 11792991 1067 True 624.5 1134 97.2310 1 880 2 chr2A.!!$R1 879

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
992 1196 0.039437 CTCGAATCCCCACCGATACG 60.039 60.0 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2203 3527 0.30289 GTTGCATCGCGAATGAGGAG 59.697 55.0 15.24 0.0 37.59 3.69 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
410 597 4.760047 CCTGCTAACGCCCGCACT 62.760 66.667 0.00 0.00 34.43 4.40
518 705 3.129462 CGACTGGATCTGCTAAGAACTCA 59.871 47.826 0.00 0.00 35.59 3.41
541 728 2.687566 ATCCCCCACCGTCTCCAC 60.688 66.667 0.00 0.00 0.00 4.02
670 859 3.928343 TTTTTCCACCTCAAACGCG 57.072 47.368 3.53 3.53 0.00 6.01
880 1070 1.807573 CGCTCTTTCGCCACTCTCC 60.808 63.158 0.00 0.00 0.00 3.71
881 1071 1.293498 GCTCTTTCGCCACTCTCCA 59.707 57.895 0.00 0.00 0.00 3.86
882 1072 0.739112 GCTCTTTCGCCACTCTCCAG 60.739 60.000 0.00 0.00 0.00 3.86
883 1073 0.891373 CTCTTTCGCCACTCTCCAGA 59.109 55.000 0.00 0.00 0.00 3.86
884 1074 1.273606 CTCTTTCGCCACTCTCCAGAA 59.726 52.381 0.00 0.00 0.00 3.02
885 1075 1.691976 TCTTTCGCCACTCTCCAGAAA 59.308 47.619 0.00 0.00 0.00 2.52
886 1076 2.072298 CTTTCGCCACTCTCCAGAAAG 58.928 52.381 2.50 2.50 40.84 2.62
920 1114 2.768527 AGAGCTCCCAGAAATCAATCGA 59.231 45.455 10.93 0.00 0.00 3.59
972 1167 0.911769 TCGATTCCTTCCACCAGCAT 59.088 50.000 0.00 0.00 0.00 3.79
985 1189 0.533755 CCAGCATCTCGAATCCCCAC 60.534 60.000 0.00 0.00 0.00 4.61
986 1190 0.533755 CAGCATCTCGAATCCCCACC 60.534 60.000 0.00 0.00 0.00 4.61
987 1191 1.595382 GCATCTCGAATCCCCACCG 60.595 63.158 0.00 0.00 0.00 4.94
988 1192 2.028125 GCATCTCGAATCCCCACCGA 62.028 60.000 0.00 0.00 0.00 4.69
989 1193 0.681733 CATCTCGAATCCCCACCGAT 59.318 55.000 0.00 0.00 0.00 4.18
990 1194 1.893137 CATCTCGAATCCCCACCGATA 59.107 52.381 0.00 0.00 0.00 2.92
991 1195 1.325355 TCTCGAATCCCCACCGATAC 58.675 55.000 0.00 0.00 0.00 2.24
992 1196 0.039437 CTCGAATCCCCACCGATACG 60.039 60.000 0.00 0.00 0.00 3.06
993 1197 0.466007 TCGAATCCCCACCGATACGA 60.466 55.000 0.00 0.00 0.00 3.43
1074 1278 3.391382 CCCTTCGACGGCTTCCCT 61.391 66.667 1.55 0.00 0.00 4.20
1308 1521 1.194781 AGAAGACCGACACCTGGCAT 61.195 55.000 0.00 0.00 0.00 4.40
1487 1718 1.517242 GGCTAGAGCGATGAAATGGG 58.483 55.000 0.00 0.00 43.26 4.00
1488 1726 1.070758 GGCTAGAGCGATGAAATGGGA 59.929 52.381 0.00 0.00 43.26 4.37
1491 1729 3.805108 GCTAGAGCGATGAAATGGGATGT 60.805 47.826 0.00 0.00 0.00 3.06
1513 1751 1.004440 GCAGTGGTGTGGAGTCTCC 60.004 63.158 12.40 12.40 36.96 3.71
1631 1893 2.422127 CAGTGTTTTGAGTCCGGTTTGT 59.578 45.455 0.00 0.00 0.00 2.83
1854 2331 2.084546 GTCTTGCCCGAGCTATGTTTT 58.915 47.619 0.00 0.00 40.80 2.43
1855 2332 2.488153 GTCTTGCCCGAGCTATGTTTTT 59.512 45.455 0.00 0.00 40.80 1.94
1878 2357 1.014352 GCCAGCGTTCCGTATTCAAT 58.986 50.000 0.00 0.00 0.00 2.57
2036 2737 3.810896 GCGACGGTTCCATTGCCC 61.811 66.667 0.00 0.00 0.00 5.36
2203 3527 1.360911 GGAGATCTCGGCTCCGTTC 59.639 63.158 16.46 4.71 42.22 3.95
2356 3680 3.770666 TCAGCTAATCACGTCTACTTGC 58.229 45.455 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.471617 CTGGCCTAGGCTGTATGCTT 59.528 55.000 32.18 0.00 42.39 3.91
182 369 2.193087 GATGGGGTTGTAGGCACCGT 62.193 60.000 0.00 0.00 0.00 4.83
410 597 2.598787 CCCGTTGGCTAGGTTCCCA 61.599 63.158 0.00 0.00 0.00 4.37
518 705 2.861974 ACGGTGGGGGATGGGTTT 60.862 61.111 0.00 0.00 0.00 3.27
541 728 1.376037 GGCTTGAGAGGGTTGACGG 60.376 63.158 0.00 0.00 0.00 4.79
670 859 2.734670 GTTTACCGGCTTTCACAAACC 58.265 47.619 0.00 0.00 0.00 3.27
706 895 1.618876 ATGATGGCCCGTCCGTACAA 61.619 55.000 0.00 0.00 37.80 2.41
880 1070 3.329386 TCTTTGATCGGTGCTCTTTCTG 58.671 45.455 0.00 0.00 0.00 3.02
881 1071 3.594134 CTCTTTGATCGGTGCTCTTTCT 58.406 45.455 0.00 0.00 0.00 2.52
882 1072 2.095053 GCTCTTTGATCGGTGCTCTTTC 59.905 50.000 0.00 0.00 0.00 2.62
883 1073 2.079925 GCTCTTTGATCGGTGCTCTTT 58.920 47.619 0.00 0.00 0.00 2.52
884 1074 1.277557 AGCTCTTTGATCGGTGCTCTT 59.722 47.619 4.62 0.00 0.00 2.85
885 1075 0.901124 AGCTCTTTGATCGGTGCTCT 59.099 50.000 4.62 0.00 0.00 4.09
886 1076 1.285578 GAGCTCTTTGATCGGTGCTC 58.714 55.000 6.43 15.80 40.25 4.26
920 1114 0.322546 GTTGGAAGCGGAAGGGTGAT 60.323 55.000 0.00 0.00 0.00 3.06
972 1167 1.325355 GTATCGGTGGGGATTCGAGA 58.675 55.000 0.00 0.00 36.34 4.04
985 1189 1.474017 GACATTGTCGGTCGTATCGG 58.526 55.000 0.13 0.00 0.00 4.18
1206 1419 2.704190 TCACCTCCTCCTTCTTCAGT 57.296 50.000 0.00 0.00 0.00 3.41
1487 1718 1.550524 TCCACACCACTGCTCTACATC 59.449 52.381 0.00 0.00 0.00 3.06
1488 1726 1.552337 CTCCACACCACTGCTCTACAT 59.448 52.381 0.00 0.00 0.00 2.29
1491 1729 1.203063 AGACTCCACACCACTGCTCTA 60.203 52.381 0.00 0.00 0.00 2.43
1513 1751 4.508128 CATCACGACGACCGGGGG 62.508 72.222 6.32 0.00 43.16 5.40
1631 1893 5.895636 ACAGACTGATGAACAAACAACAA 57.104 34.783 10.08 0.00 0.00 2.83
1817 2162 1.160137 GACATGGCTGACAAGACACC 58.840 55.000 0.00 0.00 46.98 4.16
1910 2389 3.121030 CGAGCGAACTTGGGCCAG 61.121 66.667 6.23 3.69 0.00 4.85
1911 2390 3.936203 ACGAGCGAACTTGGGCCA 61.936 61.111 0.00 0.00 0.00 5.36
2076 2808 4.388499 CGGTCTGGAACGGTGGGG 62.388 72.222 0.00 0.00 37.98 4.96
2203 3527 0.302890 GTTGCATCGCGAATGAGGAG 59.697 55.000 15.24 0.00 37.59 3.69
2346 3670 1.071605 GCACAAGGAGCAAGTAGACG 58.928 55.000 0.00 0.00 0.00 4.18
2356 3680 1.595109 TGCACGACAGCACAAGGAG 60.595 57.895 0.00 0.00 40.11 3.69


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

AutoCloner maintained by Alex Coulton.