Multiple sequence alignment - TraesCS6B01G294700

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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 TraesCS6B01G294700 chr6B 100.00 3886 0 0 1 3886 528912481 528916366 0 7177
1 TraesCS6B01G294700 chr6A 94.78 3908 142 30 1 3886 492802950 492806817 0 6030
2 TraesCS6B01G294700 chr6D 96.90 3194 76 12 10 3196 350931204 350928027 0 5328
3 TraesCS6B01G294700 chr6D 92.99 699 34 4 3192 3886 350915305 350914618 0 1005


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 TraesCS6B01G294700 chr6B 528912481 528916366 3885 False 7177 7177 100.00 1 3886 1 chr6B.!!$F1 3885
1 TraesCS6B01G294700 chr6A 492802950 492806817 3867 False 6030 6030 94.78 1 3886 1 chr6A.!!$F1 3885
2 TraesCS6B01G294700 chr6D 350928027 350931204 3177 True 5328 5328 96.90 10 3196 1 chr6D.!!$R2 3186
3 TraesCS6B01G294700 chr6D 350914618 350915305 687 True 1005 1005 92.99 3192 3886 1 chr6D.!!$R1 694

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
141 148 0.603065 GGAGGGTGCATGTGAAAACC 59.397 55.0 0.0 0.0 0.0 3.27 F
1748 1791 2.093128 ACAGTTAGCAGTATTTCCCCGG 60.093 50.0 0.0 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1822 1865 2.119801 TGCTGAAATCAAGGAGCTCC 57.880 50.000 26.22 26.22 32.41 4.70 R
2904 2948 2.073056 TGGTGATGAAACGATTCGTGG 58.927 47.619 13.22 0.00 39.99 4.94 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
31 38 3.128938 CCGATTCCTTCGTCTTACTCTGT 59.871 47.826 0.00 0.00 46.65 3.41
65 72 6.096141 GTGTCTCTATTCTCCTCTGATCAACA 59.904 42.308 0.00 0.00 0.00 3.33
120 127 4.894784 AGCGAGTCAAAAGGAATTCTACA 58.105 39.130 5.23 0.00 0.00 2.74
141 148 0.603065 GGAGGGTGCATGTGAAAACC 59.397 55.000 0.00 0.00 0.00 3.27
151 158 3.730715 GCATGTGAAAACCGTTTCTTCAG 59.269 43.478 0.00 0.00 43.13 3.02
159 166 7.486870 GTGAAAACCGTTTCTTCAGTTTAATGT 59.513 33.333 0.00 0.00 43.13 2.71
534 541 4.093850 GCAGGACATTAAATCGTAAACGGT 59.906 41.667 2.24 0.00 40.29 4.83
546 553 4.992688 TCGTAAACGGTGTATACGGAATT 58.007 39.130 16.28 2.25 41.89 2.17
555 562 6.650390 ACGGTGTATACGGAATTTTTAAGTGT 59.350 34.615 4.18 0.00 35.23 3.55
560 567 9.287373 TGTATACGGAATTTTTAAGTGTCCTTT 57.713 29.630 0.00 0.00 31.89 3.11
747 761 4.695928 GTCCAGGGAAAGAATACAGACAAC 59.304 45.833 0.00 0.00 0.00 3.32
760 792 8.443160 AGAATACAGACAACATACGATTGTTTG 58.557 33.333 6.80 6.80 43.95 2.93
761 793 5.356882 ACAGACAACATACGATTGTTTGG 57.643 39.130 11.59 6.57 43.13 3.28
762 794 5.060506 ACAGACAACATACGATTGTTTGGA 58.939 37.500 11.59 0.00 43.13 3.53
763 795 5.529430 ACAGACAACATACGATTGTTTGGAA 59.471 36.000 11.59 0.00 43.13 3.53
764 796 6.206634 ACAGACAACATACGATTGTTTGGAAT 59.793 34.615 11.59 0.00 43.13 3.01
765 797 7.083858 CAGACAACATACGATTGTTTGGAATT 58.916 34.615 8.23 0.00 40.36 2.17
766 798 8.233868 CAGACAACATACGATTGTTTGGAATTA 58.766 33.333 8.23 0.00 40.36 1.40
767 799 8.956426 AGACAACATACGATTGTTTGGAATTAT 58.044 29.630 8.23 0.00 40.36 1.28
770 802 9.663904 CAACATACGATTGTTTGGAATTATAGG 57.336 33.333 8.23 0.00 37.73 2.57
771 803 9.621629 AACATACGATTGTTTGGAATTATAGGA 57.378 29.630 8.23 0.00 36.43 2.94
772 804 9.621629 ACATACGATTGTTTGGAATTATAGGAA 57.378 29.630 8.23 0.00 32.09 3.36
775 807 8.801882 ACGATTGTTTGGAATTATAGGAAGAA 57.198 30.769 0.00 0.00 0.00 2.52
776 808 9.408648 ACGATTGTTTGGAATTATAGGAAGAAT 57.591 29.630 0.00 0.00 0.00 2.40
828 860 7.066766 CCCTGATATCACCAGAAAAGAAAAGAG 59.933 40.741 0.00 0.00 33.65 2.85
1254 1297 2.594592 AGCGTGTTTGGAGGTGCC 60.595 61.111 0.00 0.00 37.10 5.01
1746 1789 5.066117 GCTTAACAGTTAGCAGTATTTCCCC 59.934 44.000 8.89 0.00 0.00 4.81
1748 1791 2.093128 ACAGTTAGCAGTATTTCCCCGG 60.093 50.000 0.00 0.00 0.00 5.73
1760 1803 5.595542 AGTATTTCCCCGGCTAAAATAAACC 59.404 40.000 12.79 4.96 29.37 3.27
1782 1825 5.186409 ACCTGATCATTTTGCAAGCTGTAAT 59.814 36.000 0.00 0.00 0.00 1.89
1932 1975 8.829612 GTTCAGATGTTTCAATGGATTTTGTTT 58.170 29.630 0.00 0.00 0.00 2.83
2085 2129 7.122204 GGTACTGCCTTTTTACCAACTAATCAT 59.878 37.037 0.00 0.00 36.12 2.45
2280 2324 4.112634 AGGCATTAAGTTCTTCAACCCA 57.887 40.909 0.00 0.00 32.22 4.51
2614 2658 6.935167 TCAGACAATGCTGTACAATCTTAGA 58.065 36.000 0.00 0.00 35.30 2.10
2904 2948 3.091545 TGATCAGCCCCAAATTCAAGTC 58.908 45.455 0.00 0.00 0.00 3.01
2913 2957 3.426159 CCCAAATTCAAGTCCACGAATCG 60.426 47.826 0.00 0.00 30.64 3.34
2929 2973 3.679980 CGAATCGTTTCATCACCAACTCT 59.320 43.478 7.00 0.00 0.00 3.24
3011 3055 3.430218 CGGTAGAAAGTTCACTGCAGAAG 59.570 47.826 23.35 12.71 0.00 2.85
3091 3135 9.996554 TCTTATGTCTCTTCTTAACACATTTCA 57.003 29.630 0.00 0.00 0.00 2.69
3147 3191 6.615264 AATACATGTGCTTGCTAGAATCAG 57.385 37.500 9.11 0.00 0.00 2.90
3276 3320 8.968242 GGATTTGTAGACAGAATTGTGAAAAAC 58.032 33.333 9.96 2.94 37.76 2.43
3277 3321 8.871686 ATTTGTAGACAGAATTGTGAAAAACC 57.128 30.769 9.96 0.00 37.76 3.27
3323 3367 3.067106 ACAGTGTTCTAGCAAATCACCG 58.933 45.455 0.00 0.00 0.00 4.94
3395 3439 6.403049 TCATCCACTAACAAACGTATCATGT 58.597 36.000 0.00 0.00 0.00 3.21
3421 3465 5.872617 TGATAACAGGAATGGTTACGAACTG 59.127 40.000 0.00 0.00 33.89 3.16
3446 3490 9.571816 TGAAGGCATAACAATCATGTCATTATA 57.428 29.630 0.00 0.00 39.40 0.98
3523 3568 3.755378 GGAACTGCTGATGTGAAACTGAT 59.245 43.478 0.00 0.00 38.04 2.90
3662 3707 5.126869 TCACTTTCTCAGCCAAAATTCAACA 59.873 36.000 0.00 0.00 0.00 3.33
3828 3878 5.723295 CAACAATTGGCAAGCTAAGGTAAT 58.277 37.500 10.83 0.00 0.00 1.89
3863 3913 1.000843 TGCTCAGTGTGTAAGTGCGAT 59.999 47.619 0.00 0.00 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 38 3.378512 AGAATAGAGACACAGCCATGGA 58.621 45.455 18.40 0.00 0.00 3.41
65 72 8.157476 ACAGAAGTTACAGAACCATAACTCATT 58.843 33.333 0.00 0.00 40.04 2.57
120 127 1.895131 GTTTTCACATGCACCCTCCAT 59.105 47.619 0.00 0.00 0.00 3.41
141 148 9.210426 GCATATACACATTAAACTGAAGAAACG 57.790 33.333 0.00 0.00 0.00 3.60
159 166 6.389906 CACGAGACATTCCATAGCATATACA 58.610 40.000 0.00 0.00 0.00 2.29
522 529 4.630894 TCCGTATACACCGTTTACGATT 57.369 40.909 15.55 0.00 42.70 3.34
534 541 8.851541 AAGGACACTTAAAAATTCCGTATACA 57.148 30.769 3.32 0.00 34.49 2.29
546 553 3.942748 ACACGAGCAAAGGACACTTAAAA 59.057 39.130 0.00 0.00 35.41 1.52
555 562 1.810151 GCCAAATACACGAGCAAAGGA 59.190 47.619 0.00 0.00 0.00 3.36
560 567 0.321564 AGCTGCCAAATACACGAGCA 60.322 50.000 0.00 0.00 0.00 4.26
597 604 6.424812 AGCGCTCTTTGCTGAAAATTAATTTT 59.575 30.769 22.95 22.95 42.14 1.82
683 691 5.763204 ACGAAAAGCTTCTGATTCCACTTTA 59.237 36.000 0.00 0.00 0.00 1.85
687 701 4.691216 ACTACGAAAAGCTTCTGATTCCAC 59.309 41.667 0.00 0.00 0.00 4.02
766 798 9.917887 AGTGATCTGAAAATGAATTCTTCCTAT 57.082 29.630 7.05 0.00 0.00 2.57
768 800 9.917887 ATAGTGATCTGAAAATGAATTCTTCCT 57.082 29.630 7.05 0.00 0.00 3.36
775 807 8.566260 GCAGCTTATAGTGATCTGAAAATGAAT 58.434 33.333 0.00 0.00 0.00 2.57
776 808 7.012704 GGCAGCTTATAGTGATCTGAAAATGAA 59.987 37.037 0.00 0.00 0.00 2.57
777 809 6.484643 GGCAGCTTATAGTGATCTGAAAATGA 59.515 38.462 0.00 0.00 0.00 2.57
1710 1753 4.574674 ACTGTTAAGCATCAGGGAATCA 57.425 40.909 0.00 0.00 36.17 2.57
1746 1789 7.254084 GCAAAATGATCAGGTTTATTTTAGCCG 60.254 37.037 0.09 0.00 33.01 5.52
1748 1791 8.477984 TGCAAAATGATCAGGTTTATTTTAGC 57.522 30.769 0.09 8.79 33.01 3.09
1760 1803 8.589629 GTTTATTACAGCTTGCAAAATGATCAG 58.410 33.333 15.44 0.00 0.00 2.90
1782 1825 8.776470 CGTACCTGGTTTAAAAATCTCTGTTTA 58.224 33.333 3.84 0.00 0.00 2.01
1790 1833 6.739550 CGTTCATCGTACCTGGTTTAAAAATC 59.260 38.462 3.84 0.00 34.52 2.17
1822 1865 2.119801 TGCTGAAATCAAGGAGCTCC 57.880 50.000 26.22 26.22 32.41 4.70
1909 1952 8.492748 CAGAAACAAAATCCATTGAAACATCTG 58.507 33.333 0.00 0.00 34.38 2.90
2085 2129 9.720769 TTTTTGGTTTATGGAAAACACTTGTTA 57.279 25.926 0.00 0.00 42.01 2.41
2117 2161 4.009675 TGGTCAGTTTACATGCCATCTTC 58.990 43.478 0.00 0.00 0.00 2.87
2280 2324 5.422331 TGATCCTTCATCGAAGAGGTAAACT 59.578 40.000 5.31 0.00 43.63 2.66
2614 2658 6.073222 CGATACCTGAAGTAAACAAGCAAACT 60.073 38.462 0.00 0.00 33.70 2.66
2904 2948 2.073056 TGGTGATGAAACGATTCGTGG 58.927 47.619 13.22 0.00 39.99 4.94
2913 2957 7.550551 TCATTCTCATAGAGTTGGTGATGAAAC 59.449 37.037 0.00 0.00 0.00 2.78
2929 2973 2.629617 TGCGAGGATGCTCATTCTCATA 59.370 45.455 15.10 3.86 42.39 2.15
3011 3055 5.754890 AGTTCAAAATGCAGGTTTTCATGAC 59.245 36.000 0.00 0.00 32.95 3.06
3091 3135 6.484288 TGAAACATGGGAGAAGATGTACATT 58.516 36.000 10.30 0.00 32.40 2.71
3246 3290 5.707298 CACAATTCTGTCTACAAATCCACCT 59.293 40.000 0.00 0.00 31.64 4.00
3323 3367 5.577164 GTCAGATATACAGTTCCACACACAC 59.423 44.000 0.00 0.00 0.00 3.82
3395 3439 5.408880 TCGTAACCATTCCTGTTATCACA 57.591 39.130 0.00 0.00 31.41 3.58
3446 3490 6.010219 AGTAGCACAATGTACCTTTTCCATT 58.990 36.000 0.00 0.00 0.00 3.16
3798 3848 1.862201 CTTGCCAATTGTTGCACTGTG 59.138 47.619 8.65 2.76 37.18 3.66
3863 3913 1.527148 TTGCGTGGCCTGCAACTTA 60.527 52.632 25.69 9.58 46.62 2.24


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

AutoCloner maintained by Alex Coulton.