Multiple sequence alignment - TraesCS6B01G237200

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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 TraesCS6B01G237200 chr6B 100.000 2935 0 0 1 2935 410229765 410232699 0.000000e+00 5421
1 TraesCS6B01G237200 chr6B 98.402 2942 26 3 1 2935 410679134 410682061 0.000000e+00 5153
2 TraesCS6B01G237200 chr3B 94.667 150 7 1 1 150 636430695 636430547 6.330000e-57 231
3 TraesCS6B01G237200 chr3B 92.715 151 10 1 1 151 48082229 48082378 1.770000e-52 217
4 TraesCS6B01G237200 chr3B 92.053 151 11 1 1 151 47744644 47744793 8.240000e-51 211
5 TraesCS6B01G237200 chr3B 92.053 151 11 1 1 151 47812400 47812549 8.240000e-51 211
6 TraesCS6B01G237200 chr3B 92.053 151 11 1 1 151 47866294 47866443 8.240000e-51 211
7 TraesCS6B01G237200 chr2B 92.715 151 10 1 1 151 598487962 598488111 1.770000e-52 217
8 TraesCS6B01G237200 chr2B 92.053 151 11 1 1 151 772648889 772648740 8.240000e-51 211
9 TraesCS6B01G237200 chr5B 92.157 153 11 1 1 153 396137607 396137456 6.370000e-52 215


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 TraesCS6B01G237200 chr6B 410229765 410232699 2934 False 5421 5421 100.000 1 2935 1 chr6B.!!$F1 2934
1 TraesCS6B01G237200 chr6B 410679134 410682061 2927 False 5153 5153 98.402 1 2935 1 chr6B.!!$F2 2934

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
109 110 2.245159 TTCACTGGCAGTTCACTCTG 57.755 50.0 19.43 4.94 38.35 3.35 F
129 130 4.752604 TCTGTGAATTGATTTCGTTCCGAA 59.247 37.5 0.00 0.00 44.28 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1538 1546 5.908341 AGCTAGTAAAAGGAGATGCAGTAC 58.092 41.667 0.0 0.0 0.0 2.73 R
2350 2358 3.366985 GCACCCCAAATAACAACTAGCAC 60.367 47.826 0.0 0.0 0.0 4.40 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
76 77 2.742053 GGCGCTACACAAAAAGATCAGA 59.258 45.455 7.64 0.00 0.00 3.27
103 104 5.689383 TGAAATAGTTTCACTGGCAGTTC 57.311 39.130 19.43 10.24 44.21 3.01
109 110 2.245159 TTCACTGGCAGTTCACTCTG 57.755 50.000 19.43 4.94 38.35 3.35
124 125 6.618287 TTCACTCTGTGAATTGATTTCGTT 57.382 33.333 8.81 0.00 45.88 3.85
129 130 4.752604 TCTGTGAATTGATTTCGTTCCGAA 59.247 37.500 0.00 0.00 44.28 4.30
130 131 5.029650 TGTGAATTGATTTCGTTCCGAAG 57.970 39.130 0.00 0.00 46.43 3.79
792 800 6.825944 TTTTGCTGCTGTTATGGTAATGTA 57.174 33.333 0.00 0.00 0.00 2.29
1440 1448 6.154203 TGCATTTGGTGATGTTGTTAGAAA 57.846 33.333 0.00 0.00 0.00 2.52
1538 1546 4.368874 TTTCTTGAACATGTGTGTGTGG 57.631 40.909 0.00 0.00 38.92 4.17
2350 2358 7.889589 TTGTCTATTGTGACATGTCAAGTAG 57.110 36.000 29.42 25.99 45.03 2.57
2711 2719 9.685276 ACAATATTGGAGTACTTCATCATCAAA 57.315 29.630 19.37 0.00 0.00 2.69
2715 2723 7.815840 TTGGAGTACTTCATCATCAAAAACA 57.184 32.000 4.23 0.00 0.00 2.83
2716 2724 8.408043 TTGGAGTACTTCATCATCAAAAACAT 57.592 30.769 4.23 0.00 0.00 2.71
2717 2725 9.513906 TTGGAGTACTTCATCATCAAAAACATA 57.486 29.630 4.23 0.00 0.00 2.29
2718 2726 9.513906 TGGAGTACTTCATCATCAAAAACATAA 57.486 29.630 0.00 0.00 0.00 1.90
2796 2804 8.234525 AGATTTATAATAACTTGGGGGCATTCT 58.765 33.333 0.00 0.00 0.00 2.40
2818 2826 5.071384 TCTGATAATGTCCACATGAGATGCT 59.929 40.000 0.00 0.00 36.56 3.79
2827 2835 3.118702 CCACATGAGATGCTGAGTCTCTT 60.119 47.826 0.00 3.10 42.04 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 1.442017 CTTTTTGTGTAGCGCCCGC 60.442 57.895 2.29 4.20 42.33 6.13
56 57 3.679980 TCTCTGATCTTTTTGTGTAGCGC 59.320 43.478 0.00 0.00 0.00 5.92
103 104 5.385617 GGAACGAAATCAATTCACAGAGTG 58.614 41.667 0.00 0.00 37.96 3.51
121 122 7.253950 AAATTTGACAATTTTGACTTCGGAACG 60.254 33.333 7.15 0.00 46.37 3.95
124 125 6.019156 GCAAATTTGACAATTTTGACTTCGGA 60.019 34.615 27.56 0.00 40.09 4.55
129 130 5.355596 TCGGCAAATTTGACAATTTTGACT 58.644 33.333 27.56 0.86 40.09 3.41
130 131 5.234116 ACTCGGCAAATTTGACAATTTTGAC 59.766 36.000 27.56 25.28 40.09 3.18
792 800 0.754472 ACAGCAAAAATGTGGCAGCT 59.246 45.000 0.00 0.00 0.00 4.24
1440 1448 6.924913 TGCATATTAGGATAAGCTCAGAGT 57.075 37.500 0.00 0.00 34.42 3.24
1538 1546 5.908341 AGCTAGTAAAAGGAGATGCAGTAC 58.092 41.667 0.00 0.00 0.00 2.73
2350 2358 3.366985 GCACCCCAAATAACAACTAGCAC 60.367 47.826 0.00 0.00 0.00 4.40
2513 2521 5.163713 GCTTTGTGCCTAGGAATTAAGACTG 60.164 44.000 14.75 0.00 35.15 3.51
2711 2719 9.657419 CAAGGCTTTAATCCTCAAATTATGTTT 57.343 29.630 0.00 0.00 32.45 2.83
2712 2720 8.815912 ACAAGGCTTTAATCCTCAAATTATGTT 58.184 29.630 0.00 0.00 32.45 2.71
2713 2721 8.253113 CACAAGGCTTTAATCCTCAAATTATGT 58.747 33.333 0.00 0.00 32.45 2.29
2714 2722 8.253113 ACACAAGGCTTTAATCCTCAAATTATG 58.747 33.333 0.00 0.00 32.45 1.90
2715 2723 8.366359 ACACAAGGCTTTAATCCTCAAATTAT 57.634 30.769 0.00 0.00 32.45 1.28
2716 2724 7.775053 ACACAAGGCTTTAATCCTCAAATTA 57.225 32.000 0.00 0.00 32.45 1.40
2717 2725 6.670695 ACACAAGGCTTTAATCCTCAAATT 57.329 33.333 0.00 0.00 32.45 1.82
2718 2726 6.267471 TGAACACAAGGCTTTAATCCTCAAAT 59.733 34.615 0.00 0.00 32.45 2.32
2719 2727 5.596361 TGAACACAAGGCTTTAATCCTCAAA 59.404 36.000 0.00 0.00 32.45 2.69
2720 2728 5.136828 TGAACACAAGGCTTTAATCCTCAA 58.863 37.500 0.00 0.00 32.45 3.02
2721 2729 4.724399 TGAACACAAGGCTTTAATCCTCA 58.276 39.130 0.00 0.00 32.45 3.86
2722 2730 4.762251 ACTGAACACAAGGCTTTAATCCTC 59.238 41.667 0.00 0.00 32.45 3.71
2723 2731 4.520492 CACTGAACACAAGGCTTTAATCCT 59.480 41.667 0.00 0.00 34.90 3.24
2796 2804 5.061179 CAGCATCTCATGTGGACATTATCA 58.939 41.667 0.00 0.00 33.61 2.15
2818 2826 4.824479 TCACATGCCATAAAGAGACTCA 57.176 40.909 5.02 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.