Multiple sequence alignment - TraesCS6B01G264800

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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 TraesCS6B01G264800 chr6B 100.000 2930 0 0 1 2930 476147035 476144106 0 5411
1 TraesCS6B01G264800 chr6B 94.619 2936 142 11 2 2930 224783232 224786158 0 4532
2 TraesCS6B01G264800 chr6B 94.549 2935 145 12 2 2930 157703780 157706705 0 4519
3 TraesCS6B01G264800 chr2D 95.501 2934 123 7 2 2930 594918620 594915691 0 4678
4 TraesCS6B01G264800 chr2D 94.986 2932 135 9 2 2930 105261319 105258397 0 4590
5 TraesCS6B01G264800 chr5B 94.894 2938 125 14 2 2930 330590534 330587613 0 4571
6 TraesCS6B01G264800 chr5D 94.499 2945 141 10 2 2930 248428002 248425063 0 4521
7 TraesCS6B01G264800 chr2B 94.486 2938 150 7 1 2930 371055174 371058107 0 4518
8 TraesCS6B01G264800 chr3B 94.484 2937 149 9 1 2930 572240810 572237880 0 4514
9 TraesCS6B01G264800 chr3B 94.480 2935 150 10 2 2930 180018672 180015744 0 4512


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 TraesCS6B01G264800 chr6B 476144106 476147035 2929 True 5411 5411 100.000 1 2930 1 chr6B.!!$R1 2929
1 TraesCS6B01G264800 chr6B 224783232 224786158 2926 False 4532 4532 94.619 2 2930 1 chr6B.!!$F2 2928
2 TraesCS6B01G264800 chr6B 157703780 157706705 2925 False 4519 4519 94.549 2 2930 1 chr6B.!!$F1 2928
3 TraesCS6B01G264800 chr2D 594915691 594918620 2929 True 4678 4678 95.501 2 2930 1 chr2D.!!$R2 2928
4 TraesCS6B01G264800 chr2D 105258397 105261319 2922 True 4590 4590 94.986 2 2930 1 chr2D.!!$R1 2928
5 TraesCS6B01G264800 chr5B 330587613 330590534 2921 True 4571 4571 94.894 2 2930 1 chr5B.!!$R1 2928
6 TraesCS6B01G264800 chr5D 248425063 248428002 2939 True 4521 4521 94.499 2 2930 1 chr5D.!!$R1 2928
7 TraesCS6B01G264800 chr2B 371055174 371058107 2933 False 4518 4518 94.486 1 2930 1 chr2B.!!$F1 2929
8 TraesCS6B01G264800 chr3B 572237880 572240810 2930 True 4514 4514 94.484 1 2930 1 chr3B.!!$R2 2929
9 TraesCS6B01G264800 chr3B 180015744 180018672 2928 True 4512 4512 94.480 2 2930 1 chr3B.!!$R1 2928

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
293 294 1.138661 GGCTAGCTCTTGCATGAGAGT 59.861 52.381 28.50 18.17 44.03 3.24 F
1397 1412 0.412244 TACACCACAGTCCTAGGGCT 59.588 55.000 11.08 11.08 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1913 1929 1.031029 ACCTTACTCGGAGTCCTCGC 61.031 60.0 15.05 0.0 0.0 5.03 R
2758 2787 0.523072 GCCGCATGTGTCATGTTCTT 59.477 50.0 5.38 0.0 0.0 2.52 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
193 194 8.500753 ACTTGCCATTATCATTTTAACTACGA 57.499 30.769 0.00 0.00 0.00 3.43
201 202 4.097714 TCATTTTAACTACGACGCTACGG 58.902 43.478 0.00 0.00 37.61 4.02
230 231 3.037549 GAGTCTCCTGATTCCTGACCAT 58.962 50.000 0.00 0.00 0.00 3.55
255 256 1.204146 TACAGGTGCCTCTCCCAATC 58.796 55.000 0.00 0.00 0.00 2.67
293 294 1.138661 GGCTAGCTCTTGCATGAGAGT 59.861 52.381 28.50 18.17 44.03 3.24
338 339 3.388308 CTCTCTTTCCTCCACATATGCG 58.612 50.000 1.58 0.00 0.00 4.73
395 399 3.618690 CTCCTACAGGTGCTAAGCTTT 57.381 47.619 3.20 0.00 36.34 3.51
617 624 7.447238 GGCAAATGCAATAAATACTACTCCCTA 59.553 37.037 7.80 0.00 44.36 3.53
637 644 9.273137 CTCCCTATGTCCCATAATATAAGAACT 57.727 37.037 0.00 0.00 0.00 3.01
838 853 2.374170 ACCGTGTTAAATCTCCAAGGGT 59.626 45.455 0.00 0.00 32.83 4.34
937 952 4.633175 TCAAACGGTCACATGCTAAGTTA 58.367 39.130 0.00 0.00 0.00 2.24
959 974 8.860088 AGTTACTGAAAATTTGCAGAATAACCT 58.140 29.630 29.41 15.24 36.07 3.50
1072 1087 3.263425 GGAGAATGGAAAGACACTACCCA 59.737 47.826 0.00 0.00 0.00 4.51
1094 1109 2.899838 TTCGCACGCTGGCAGTTT 60.900 55.556 17.16 0.00 0.00 2.66
1157 1172 2.124983 TCCTAGTCGTCCCGTCCG 60.125 66.667 0.00 0.00 0.00 4.79
1182 1197 2.277084 CATTACGGCAGTCCCACTAAC 58.723 52.381 0.00 0.00 0.00 2.34
1208 1223 1.225373 CCTCCTCCCAAATCCATGGA 58.775 55.000 18.88 18.88 43.54 3.41
1395 1410 2.100989 GAGTACACCACAGTCCTAGGG 58.899 57.143 9.46 0.00 0.00 3.53
1397 1412 0.412244 TACACCACAGTCCTAGGGCT 59.588 55.000 11.08 11.08 0.00 5.19
1630 1645 2.237392 CCCTTCGACCTCCAGAAGAATT 59.763 50.000 6.76 0.00 44.76 2.17
1635 1650 2.168521 CGACCTCCAGAAGAATTGGCTA 59.831 50.000 0.00 0.00 35.62 3.93
1703 1718 3.025978 TGGTTCATCCTTCGTACGGTAT 58.974 45.455 16.52 1.20 37.07 2.73
1792 1807 0.659427 CCACTACGCTGCAATGGATG 59.341 55.000 0.00 0.00 31.69 3.51
1793 1808 0.659427 CACTACGCTGCAATGGATGG 59.341 55.000 0.00 0.00 0.00 3.51
1794 1809 0.541392 ACTACGCTGCAATGGATGGA 59.459 50.000 0.00 0.00 0.00 3.41
1795 1810 1.141657 ACTACGCTGCAATGGATGGAT 59.858 47.619 0.00 0.00 0.00 3.41
1913 1929 2.178521 CGAAGTCGAGGACGTGGG 59.821 66.667 0.00 0.00 43.02 4.61
1939 1959 1.272313 ACTCCGAGTAAGGTGGCAGTA 60.272 52.381 0.00 0.00 0.00 2.74
1942 1962 1.754803 CCGAGTAAGGTGGCAGTATCA 59.245 52.381 0.00 0.00 0.00 2.15
2099 2122 8.786898 ACTTTAACTCTTCAGTACGTACATACA 58.213 33.333 26.55 7.50 30.14 2.29
2284 2308 1.063070 TTGAGGGGTGGGTTGTGCTA 61.063 55.000 0.00 0.00 0.00 3.49
2410 2436 2.263077 GGCGCAATCCATCGATACTAG 58.737 52.381 10.83 0.00 0.00 2.57
2471 2499 1.811679 GCAGTCTAGCTTGGTCGGC 60.812 63.158 0.00 0.00 0.00 5.54
2504 2532 3.882888 GTGAGGACCTTTGTGATTTGACA 59.117 43.478 0.00 0.00 0.00 3.58
2582 2611 0.539051 CGACCTGAGGAGGAGCAAAT 59.461 55.000 4.99 0.00 42.93 2.32
2592 2621 0.036765 AGGAGCAAATAACCGTGCGA 60.037 50.000 0.00 0.00 45.62 5.10
2665 2694 1.228228 CAGCCCAGTGCCATATGGT 59.772 57.895 22.79 0.06 42.71 3.55
2758 2787 2.984562 TGTTCTATTCATGCCTCGCAA 58.015 42.857 0.00 0.00 43.62 4.85
2771 2800 1.872952 CCTCGCAAAGAACATGACACA 59.127 47.619 0.00 0.00 0.00 3.72
2784 2813 1.233950 TGACACATGCGGCGAAACAT 61.234 50.000 12.98 0.90 0.00 2.71
2857 2886 2.290367 CCAAATGATCTAATTCGCCGCA 59.710 45.455 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
201 202 4.803426 CAGGAGACTCACGCCGGC 62.803 72.222 19.07 19.07 43.25 6.13
230 231 1.689575 GGAGAGGCACCTGTATGGAGA 60.690 57.143 0.00 0.00 39.71 3.71
293 294 4.207165 CAAGGAAAAAGTGGAGAAGTGGA 58.793 43.478 0.00 0.00 0.00 4.02
338 339 2.345341 GTGCGCTTTACATGGCATTTTC 59.655 45.455 9.73 0.00 37.77 2.29
395 399 5.130975 ACATCAGACTTTATGCCTATGTGGA 59.869 40.000 0.00 0.00 38.35 4.02
525 529 8.709386 TTTTTGTTGCTAAGTTTGCTTCATTA 57.291 26.923 10.60 0.33 36.22 1.90
937 952 7.955918 AGAAGGTTATTCTGCAAATTTTCAGT 58.044 30.769 15.93 2.60 0.00 3.41
959 974 8.068110 CCTATGGGTGAATATCCTATCCTAGAA 58.932 40.741 0.00 0.00 0.00 2.10
1157 1172 1.084289 GGGACTGCCGTAATGTGAAC 58.916 55.000 0.00 0.00 33.83 3.18
1174 1189 1.210538 GGAGGGTTAGGGTTAGTGGG 58.789 60.000 0.00 0.00 0.00 4.61
1182 1197 1.495148 GATTTGGGAGGAGGGTTAGGG 59.505 57.143 0.00 0.00 0.00 3.53
1208 1223 4.150359 GCTGATCATGGAGATTTGGGATT 58.850 43.478 0.00 0.00 37.00 3.01
1395 1410 4.822896 TCGTCCTTTAGATCCTTCTCTAGC 59.177 45.833 0.00 0.00 33.17 3.42
1397 1412 6.660800 TCTTCGTCCTTTAGATCCTTCTCTA 58.339 40.000 0.00 0.00 33.17 2.43
1703 1718 6.620877 ACATGTATTGAGGTTTCTCCAGTA 57.379 37.500 0.00 0.00 39.23 2.74
1792 1807 6.547510 AGATATTGAAACAAAGGTAGCCATCC 59.452 38.462 0.00 0.00 0.00 3.51
1793 1808 7.573968 AGATATTGAAACAAAGGTAGCCATC 57.426 36.000 0.00 0.00 0.00 3.51
1794 1809 8.052748 TGTAGATATTGAAACAAAGGTAGCCAT 58.947 33.333 0.00 0.00 0.00 4.40
1795 1810 7.398829 TGTAGATATTGAAACAAAGGTAGCCA 58.601 34.615 0.00 0.00 0.00 4.75
1913 1929 1.031029 ACCTTACTCGGAGTCCTCGC 61.031 60.000 15.05 0.00 0.00 5.03
1939 1959 3.377253 AGAACCACCATGAGCAATGAT 57.623 42.857 0.00 0.00 38.72 2.45
1942 1962 3.382546 GCATTAGAACCACCATGAGCAAT 59.617 43.478 0.00 0.00 0.00 3.56
2140 2163 8.565416 ACGTATATGATATGAAGAAACGAGTGA 58.435 33.333 9.39 0.00 0.00 3.41
2284 2308 4.471386 AGGCTAGTCACAATAATGGTGTCT 59.529 41.667 0.00 0.00 38.07 3.41
2488 2516 3.554934 TGAGCTGTCAAATCACAAAGGT 58.445 40.909 0.00 0.00 0.00 3.50
2504 2532 2.484417 CGCCTTCCATCAGTAATGAGCT 60.484 50.000 0.00 0.00 37.59 4.09
2582 2611 4.906065 ACTTGAGTATATCGCACGGTTA 57.094 40.909 0.00 0.00 0.00 2.85
2758 2787 0.523072 GCCGCATGTGTCATGTTCTT 59.477 50.000 5.38 0.00 0.00 2.52
2771 2800 0.729116 CTTCAGATGTTTCGCCGCAT 59.271 50.000 0.00 0.00 0.00 4.73
2784 2813 5.221106 CCTGTGTTTCATCTTTTGCTTCAGA 60.221 40.000 0.00 0.00 0.00 3.27
2857 2886 4.673061 CGATGAAGAAGCAGTTACGACTCT 60.673 45.833 0.00 0.00 32.54 3.24


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

AutoCloner maintained by Alex Coulton.