Multiple sequence alignment - TraesCS6D01G074800

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 TraesCS6D01G074800 chr6D 100.000 2597 0 0 1 2597 38564074 38566670 0.000000e+00 4796
1 TraesCS6D01G074800 chr4A 94.262 2614 124 14 2 2597 350847096 350844491 0.000000e+00 3973
2 TraesCS6D01G074800 chr4A 97.043 1623 33 8 725 2336 466147605 466145987 0.000000e+00 2717
3 TraesCS6D01G074800 chr4A 96.721 1464 37 7 1141 2597 309476171 309474712 0.000000e+00 2427
4 TraesCS6D01G074800 chr4A 88.580 1909 142 40 1 1859 621289586 621287704 0.000000e+00 2248
5 TraesCS6D01G074800 chr4A 93.956 1125 51 8 5 1115 309477284 309476163 0.000000e+00 1685
6 TraesCS6D01G074800 chr4A 97.758 446 8 1 251 696 466148035 466147592 0.000000e+00 767
7 TraesCS6D01G074800 chr6B 97.271 2345 50 7 3 2336 280037699 280035358 0.000000e+00 3964
8 TraesCS6D01G074800 chr6B 87.175 1848 169 37 1 1792 90024079 90025914 0.000000e+00 2037
9 TraesCS6D01G074800 chr6B 90.289 968 56 15 1 931 266830531 266829565 0.000000e+00 1232
10 TraesCS6D01G074800 chr3D 97.170 2332 51 7 278 2595 141474550 141472220 0.000000e+00 3927
11 TraesCS6D01G074800 chr3D 95.671 1594 35 15 1 1579 405523639 405522065 0.000000e+00 2531
12 TraesCS6D01G074800 chr3D 97.573 989 18 4 1609 2595 405522071 405521087 0.000000e+00 1688
13 TraesCS6D01G074800 chr7B 96.418 2345 62 9 3 2336 78125441 78123108 0.000000e+00 3845
14 TraesCS6D01G074800 chr7B 82.759 580 57 21 630 1170 218533364 218532789 6.500000e-131 477
15 TraesCS6D01G074800 chr7A 94.495 1435 72 4 1168 2597 455697505 455698937 0.000000e+00 2206
16 TraesCS6D01G074800 chr7A 88.898 1234 66 22 3 1169 455696114 455697343 0.000000e+00 1454
17 TraesCS6D01G074800 chr4B 86.210 1211 102 32 377 1531 429608816 429607615 0.000000e+00 1251
18 TraesCS6D01G074800 chr4B 91.968 884 59 4 1723 2597 552767620 552768500 0.000000e+00 1229
19 TraesCS6D01G074800 chrUn 87.093 860 70 16 525 1349 235690576 235689723 0.000000e+00 935
20 TraesCS6D01G074800 chr5B 94.467 488 23 2 1 485 61559058 61559544 0.000000e+00 749


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 TraesCS6D01G074800 chr6D 38564074 38566670 2596 False 4796.0 4796 100.0000 1 2597 1 chr6D.!!$F1 2596
1 TraesCS6D01G074800 chr4A 350844491 350847096 2605 True 3973.0 3973 94.2620 2 2597 1 chr4A.!!$R1 2595
2 TraesCS6D01G074800 chr4A 621287704 621289586 1882 True 2248.0 2248 88.5800 1 1859 1 chr4A.!!$R2 1858
3 TraesCS6D01G074800 chr4A 309474712 309477284 2572 True 2056.0 2427 95.3385 5 2597 2 chr4A.!!$R3 2592
4 TraesCS6D01G074800 chr4A 466145987 466148035 2048 True 1742.0 2717 97.4005 251 2336 2 chr4A.!!$R4 2085
5 TraesCS6D01G074800 chr6B 280035358 280037699 2341 True 3964.0 3964 97.2710 3 2336 1 chr6B.!!$R2 2333
6 TraesCS6D01G074800 chr6B 90024079 90025914 1835 False 2037.0 2037 87.1750 1 1792 1 chr6B.!!$F1 1791
7 TraesCS6D01G074800 chr6B 266829565 266830531 966 True 1232.0 1232 90.2890 1 931 1 chr6B.!!$R1 930
8 TraesCS6D01G074800 chr3D 141472220 141474550 2330 True 3927.0 3927 97.1700 278 2595 1 chr3D.!!$R1 2317
9 TraesCS6D01G074800 chr3D 405521087 405523639 2552 True 2109.5 2531 96.6220 1 2595 2 chr3D.!!$R2 2594
10 TraesCS6D01G074800 chr7B 78123108 78125441 2333 True 3845.0 3845 96.4180 3 2336 1 chr7B.!!$R1 2333
11 TraesCS6D01G074800 chr7B 218532789 218533364 575 True 477.0 477 82.7590 630 1170 1 chr7B.!!$R2 540
12 TraesCS6D01G074800 chr7A 455696114 455698937 2823 False 1830.0 2206 91.6965 3 2597 2 chr7A.!!$F1 2594
13 TraesCS6D01G074800 chr4B 429607615 429608816 1201 True 1251.0 1251 86.2100 377 1531 1 chr4B.!!$R1 1154
14 TraesCS6D01G074800 chr4B 552767620 552768500 880 False 1229.0 1229 91.9680 1723 2597 1 chr4B.!!$F1 874
15 TraesCS6D01G074800 chrUn 235689723 235690576 853 True 935.0 935 87.0930 525 1349 1 chrUn.!!$R1 824

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
786 934 0.941463 ACGCGACTGCAGAACTTGAG 60.941 55.0 23.35 6.48 42.97 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 2029 1.860676 GTCAGTGTTCAACTACGCCA 58.139 50.0 0.0 0.0 36.83 5.69 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
196 199 7.716799 TTAGCAAGTTGGATGGAAATTGTAT 57.283 32.000 4.75 0.00 34.24 2.29
218 222 9.508642 TGTATACTGTAATTTCATGTCCAACAA 57.491 29.630 4.17 0.00 0.00 2.83
610 694 7.414222 AATCAGCATCACCTGTAAATCAAAT 57.586 32.000 0.00 0.00 34.47 2.32
707 792 2.731217 GTGCATCCATATTTTGCGGAC 58.269 47.619 0.00 0.00 39.23 4.79
779 927 4.700365 CGACCACGCGACTGCAGA 62.700 66.667 23.35 0.00 42.97 4.26
781 929 2.658707 GACCACGCGACTGCAGAAC 61.659 63.158 23.35 12.87 42.97 3.01
782 930 2.356313 CCACGCGACTGCAGAACT 60.356 61.111 23.35 0.00 42.97 3.01
783 931 1.956170 CCACGCGACTGCAGAACTT 60.956 57.895 23.35 0.00 42.97 2.66
784 932 1.202568 CACGCGACTGCAGAACTTG 59.797 57.895 23.35 8.94 42.97 3.16
785 933 1.067416 ACGCGACTGCAGAACTTGA 59.933 52.632 23.35 0.00 42.97 3.02
786 934 0.941463 ACGCGACTGCAGAACTTGAG 60.941 55.000 23.35 6.48 42.97 3.02
923 1085 5.734720 CACGCATATTATAGACCTGGGAAT 58.265 41.667 0.00 0.00 0.00 3.01
979 1151 3.559238 AATCTTTGCTTGGTTGTAGCG 57.441 42.857 0.00 0.00 41.54 4.26
1110 1301 9.950680 GATTTCAGTGTGAGAATTCTACAAAAA 57.049 29.630 8.25 12.94 0.00 1.94
1223 1589 4.818546 AGCGTCCCTTCTGAATAATCATTG 59.181 41.667 0.00 0.00 34.37 2.82
1249 1615 7.660208 GGATCACTAAACTGTTAACAGAAGGAA 59.340 37.037 36.14 21.52 46.59 3.36
1505 1887 0.034476 CTGCACTCTGTCAGCTTCCA 59.966 55.000 0.00 0.00 0.00 3.53
1817 2203 2.360350 CCTGGTTCGGCTGCATGT 60.360 61.111 0.50 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
196 199 7.667635 TGGATTGTTGGACATGAAATTACAGTA 59.332 33.333 0.00 0.0 0.00 2.74
218 222 1.568504 TGGAGCCGTCTAAGTTGGAT 58.431 50.000 0.00 0.0 0.00 3.41
610 694 2.637872 CACTCTGTGGAAGAAACCCCTA 59.362 50.000 0.00 0.0 33.37 3.53
778 926 4.938226 CCCAAGATAAGTGACCTCAAGTTC 59.062 45.833 0.00 0.0 0.00 3.01
779 927 4.807643 GCCCAAGATAAGTGACCTCAAGTT 60.808 45.833 0.00 0.0 0.00 2.66
781 929 3.274288 GCCCAAGATAAGTGACCTCAAG 58.726 50.000 0.00 0.0 0.00 3.02
782 930 2.642311 TGCCCAAGATAAGTGACCTCAA 59.358 45.455 0.00 0.0 0.00 3.02
783 931 2.027192 GTGCCCAAGATAAGTGACCTCA 60.027 50.000 0.00 0.0 0.00 3.86
784 932 2.633488 GTGCCCAAGATAAGTGACCTC 58.367 52.381 0.00 0.0 0.00 3.85
785 933 1.282157 GGTGCCCAAGATAAGTGACCT 59.718 52.381 0.00 0.0 0.00 3.85
786 934 1.004277 TGGTGCCCAAGATAAGTGACC 59.996 52.381 0.00 0.0 0.00 4.02
944 1107 8.885722 CAAGCAAAGATTTTTACATGCCATAAT 58.114 29.630 0.00 0.0 34.44 1.28
949 1120 4.996758 ACCAAGCAAAGATTTTTACATGCC 59.003 37.500 0.00 0.0 34.44 4.40
959 1131 2.884639 ACGCTACAACCAAGCAAAGATT 59.115 40.909 0.00 0.0 40.08 2.40
979 1151 5.464168 CATTCTTCTGGTGATTTGGTCAAC 58.536 41.667 0.00 0.0 45.15 3.18
1223 1589 7.159372 TCCTTCTGTTAACAGTTTAGTGATCC 58.841 38.462 29.83 0.0 44.12 3.36
1249 1615 2.598565 TGTCCTCTCTGTGCACTTACT 58.401 47.619 19.41 0.0 0.00 2.24
1505 1887 3.074675 TCTCTTCCTCGTACTTCTGCT 57.925 47.619 0.00 0.0 0.00 4.24
1646 2029 1.860676 GTCAGTGTTCAACTACGCCA 58.139 50.000 0.00 0.0 36.83 5.69
1705 2089 4.421131 CCTCTATAATCCCTGGCTACAGT 58.579 47.826 0.00 0.0 43.36 3.55
1817 2203 4.097892 GTCCTCTGAAAACTTTTGCCAGAA 59.902 41.667 6.95 0.0 33.40 3.02


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

AutoCloner maintained by Alex Coulton.