Multiple sequence alignment - TraesCS2B01G169800

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 TraesCS2B01G169800 chr2B 100.000 2888 0 0 1 2888 142887444 142890331 0.000000e+00 5334
1 TraesCS2B01G169800 chr5B 96.182 2017 59 7 1 2002 701465082 701467095 0.000000e+00 3282
2 TraesCS2B01G169800 chr7A 96.524 1985 55 4 1 1971 206573714 206575698 0.000000e+00 3271
3 TraesCS2B01G169800 chr1B 95.721 2010 73 3 6 2002 23816108 23818117 0.000000e+00 3223
4 TraesCS2B01G169800 chr2D 96.429 1568 48 6 1325 2888 197521669 197520106 0.000000e+00 2579
5 TraesCS2B01G169800 chr2D 93.960 1341 68 3 1 1328 197523147 197521807 0.000000e+00 2015
6 TraesCS2B01G169800 chr5A 96.041 1566 57 4 1325 2888 670475032 670473470 0.000000e+00 2543
7 TraesCS2B01G169800 chr5A 94.381 1566 79 6 1325 2888 696327132 696325574 0.000000e+00 2396
8 TraesCS2B01G169800 chr5A 95.131 1335 53 2 6 1328 670476504 670475170 0.000000e+00 2095
9 TraesCS2B01G169800 chr5A 93.933 1335 67 4 6 1328 696328602 696327270 0.000000e+00 2004
10 TraesCS2B01G169800 chr1A 95.785 1566 61 4 1325 2888 374209501 374211063 0.000000e+00 2521
11 TraesCS2B01G169800 chr1A 95.716 1564 61 5 1325 2885 449451784 449453344 0.000000e+00 2512
12 TraesCS2B01G169800 chr1A 94.831 1335 55 4 6 1328 374208031 374209363 0.000000e+00 2071
13 TraesCS2B01G169800 chr1A 94.113 1342 64 5 1 1328 449450306 449451646 0.000000e+00 2026
14 TraesCS2B01G169800 chr3A 95.275 1566 65 6 1325 2888 1715090 1713532 0.000000e+00 2473
15 TraesCS2B01G169800 chr3A 91.398 93 8 0 2796 2888 218167708 218167616 8.400000e-26 128
16 TraesCS2B01G169800 chr3B 95.030 1348 55 2 6 1342 607522811 607521465 0.000000e+00 2108
17 TraesCS2B01G169800 chr3B 92.473 93 7 0 2796 2888 338596437 338596529 1.810000e-27 134
18 TraesCS2B01G169800 chr3D 90.986 1542 108 17 1325 2841 303481143 303479608 0.000000e+00 2049
19 TraesCS2B01G169800 chr3D 92.756 635 34 8 2216 2838 241395839 241396473 0.000000e+00 907
20 TraesCS2B01G169800 chr5D 88.499 913 78 12 1961 2848 51750724 51749814 0.000000e+00 1079
21 TraesCS2B01G169800 chr5D 91.398 93 8 0 2796 2888 51749909 51749817 8.400000e-26 128


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 TraesCS2B01G169800 chr2B 142887444 142890331 2887 False 5334.0 5334 100.0000 1 2888 1 chr2B.!!$F1 2887
1 TraesCS2B01G169800 chr5B 701465082 701467095 2013 False 3282.0 3282 96.1820 1 2002 1 chr5B.!!$F1 2001
2 TraesCS2B01G169800 chr7A 206573714 206575698 1984 False 3271.0 3271 96.5240 1 1971 1 chr7A.!!$F1 1970
3 TraesCS2B01G169800 chr1B 23816108 23818117 2009 False 3223.0 3223 95.7210 6 2002 1 chr1B.!!$F1 1996
4 TraesCS2B01G169800 chr2D 197520106 197523147 3041 True 2297.0 2579 95.1945 1 2888 2 chr2D.!!$R1 2887
5 TraesCS2B01G169800 chr5A 670473470 670476504 3034 True 2319.0 2543 95.5860 6 2888 2 chr5A.!!$R1 2882
6 TraesCS2B01G169800 chr5A 696325574 696328602 3028 True 2200.0 2396 94.1570 6 2888 2 chr5A.!!$R2 2882
7 TraesCS2B01G169800 chr1A 374208031 374211063 3032 False 2296.0 2521 95.3080 6 2888 2 chr1A.!!$F1 2882
8 TraesCS2B01G169800 chr1A 449450306 449453344 3038 False 2269.0 2512 94.9145 1 2885 2 chr1A.!!$F2 2884
9 TraesCS2B01G169800 chr3A 1713532 1715090 1558 True 2473.0 2473 95.2750 1325 2888 1 chr3A.!!$R1 1563
10 TraesCS2B01G169800 chr3B 607521465 607522811 1346 True 2108.0 2108 95.0300 6 1342 1 chr3B.!!$R1 1336
11 TraesCS2B01G169800 chr3D 303479608 303481143 1535 True 2049.0 2049 90.9860 1325 2841 1 chr3D.!!$R1 1516
12 TraesCS2B01G169800 chr3D 241395839 241396473 634 False 907.0 907 92.7560 2216 2838 1 chr3D.!!$F1 622
13 TraesCS2B01G169800 chr5D 51749814 51750724 910 True 603.5 1079 89.9485 1961 2888 2 chr5D.!!$R1 927

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
244 247 0.384669 CGAGGAGTTCGGTATCACCC 59.615 60.000 0.0 0.0 45.54 4.61 F
346 349 1.609580 CCGGAACCACATCGAAAGGAA 60.610 52.381 0.0 0.0 0.00 3.36 F
447 450 2.159254 GCGGCATGTGTTGTATTCCATT 60.159 45.455 0.0 0.0 0.00 3.16 F
1083 1098 2.772568 TGTTTGTTCACTGCCATTCG 57.227 45.000 0.0 0.0 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1511 1811 1.496429 CCCCTTGCCCTTGTAGATCAT 59.504 52.381 0.00 0.00 0.00 2.45 R
1709 2010 3.686726 ACAGTTTCCAATCGAGAAGATGC 59.313 43.478 0.00 0.00 40.02 3.91 R
1713 2014 4.034510 GCCATACAGTTTCCAATCGAGAAG 59.965 45.833 0.00 0.00 0.00 2.85 R
2500 2823 1.202879 ACTTTCGAACAAGATGGGCCA 60.203 47.619 9.61 9.61 0.00 5.36 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
172 175 6.921857 GGATTTCATGTGCTAGATGGAAAATG 59.078 38.462 0.00 0.00 0.00 2.32
244 247 0.384669 CGAGGAGTTCGGTATCACCC 59.615 60.000 0.00 0.00 45.54 4.61
265 268 3.334691 CAAGTGAATTTAGGAGGCGACA 58.665 45.455 0.00 0.00 0.00 4.35
287 290 3.832490 ACTCATCTAATACGGGCTATGCA 59.168 43.478 0.00 0.00 0.00 3.96
346 349 1.609580 CCGGAACCACATCGAAAGGAA 60.610 52.381 0.00 0.00 0.00 3.36
351 354 4.022329 GGAACCACATCGAAAGGAACATTT 60.022 41.667 7.99 0.00 0.00 2.32
423 426 7.671398 ACCCAATAGAGTCACAAATCAAGATTT 59.329 33.333 2.31 2.31 41.33 2.17
447 450 2.159254 GCGGCATGTGTTGTATTCCATT 60.159 45.455 0.00 0.00 0.00 3.16
606 609 2.811431 ACTCTTAGAGATCAGATCGCGG 59.189 50.000 16.95 4.10 34.06 6.46
788 791 3.126831 CCATGCATACGAGAAAGGTCTC 58.873 50.000 0.00 0.00 46.01 3.36
826 829 5.328565 TGACCACAACAATCCCATTTATCA 58.671 37.500 0.00 0.00 0.00 2.15
866 869 4.712337 ACTACTGAAGGGTGGACTAGAATG 59.288 45.833 0.00 0.00 0.00 2.67
1030 1045 5.364778 TCGTTGAACCTGTAATATGGGATG 58.635 41.667 0.00 0.00 0.00 3.51
1083 1098 2.772568 TGTTTGTTCACTGCCATTCG 57.227 45.000 0.00 0.00 0.00 3.34
1226 1241 5.071250 ACACTACATGAAGGTGTGTTTCCTA 59.929 40.000 17.09 0.00 41.75 2.94
1511 1811 6.745794 TGTTGATGATGGTATGTCCTCATA 57.254 37.500 0.00 0.00 35.66 2.15
1709 2010 5.395682 TTGAAGGAATCAAAGCAAGATGG 57.604 39.130 0.00 0.00 44.94 3.51
1713 2014 3.383825 AGGAATCAAAGCAAGATGGCATC 59.616 43.478 19.78 19.78 35.83 3.91
1887 2188 6.669591 TGAAGGAGGAGATTTCTGAGATGTAA 59.330 38.462 0.00 0.00 0.00 2.41
1890 2191 7.507829 AGGAGGAGATTTCTGAGATGTAAATG 58.492 38.462 0.00 0.00 0.00 2.32
2089 2396 4.747810 CATTTGGAGAAATGTTACTGCCC 58.252 43.478 0.00 0.00 42.43 5.36
2101 2408 3.633065 TGTTACTGCCCTTTGTTTGGTAC 59.367 43.478 0.00 0.00 0.00 3.34
2185 2504 5.708736 TTCACCTCCTATTGCCTCATAAA 57.291 39.130 0.00 0.00 0.00 1.40
2192 2511 6.013379 CCTCCTATTGCCTCATAAATCACCTA 60.013 42.308 0.00 0.00 0.00 3.08
2228 2547 3.604582 CCCTGTTCATCTGGAGACTTTC 58.395 50.000 0.00 0.00 37.33 2.62
2257 2576 6.780522 AGTAAACAAATTGGGTTACTGGACAT 59.219 34.615 20.40 0.00 33.73 3.06
2275 2594 1.086696 ATCCTTGTGATTGCGTTCCG 58.913 50.000 0.00 0.00 0.00 4.30
2500 2823 2.297701 AGGACGTGATTGTTGCTTTGT 58.702 42.857 0.00 0.00 0.00 2.83
2584 2910 7.892778 TTTATAGTGCACAAACTTGACGATA 57.107 32.000 21.04 0.00 0.00 2.92
2671 2997 0.179240 CGTCGTGAAATGCAGACTGC 60.179 55.000 20.86 20.86 45.29 4.40
2685 3011 3.559242 GCAGACTGCTATCTTAAGCTTGG 59.441 47.826 20.41 1.84 43.19 3.61
2771 3099 5.911752 TGTTATGTGCCTGTGATTTTTGTT 58.088 33.333 0.00 0.00 0.00 2.83
2778 3106 5.351189 GTGCCTGTGATTTTTGTTGTTTCTT 59.649 36.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
149 152 7.414222 ACATTTTCCATCTAGCACATGAAAT 57.586 32.000 0.00 0.00 0.00 2.17
172 175 7.559486 TGCATATCCACCATCTATGAGATAAC 58.441 38.462 0.00 0.00 32.12 1.89
244 247 3.125316 GTGTCGCCTCCTAAATTCACTTG 59.875 47.826 0.00 0.00 0.00 3.16
265 268 3.832490 TGCATAGCCCGTATTAGATGAGT 59.168 43.478 0.00 0.00 0.00 3.41
287 290 3.456277 GGTTGAACATCTCCCTATGGTCT 59.544 47.826 0.00 0.00 42.89 3.85
300 303 3.098774 TGCATGGGTATGGTTGAACAT 57.901 42.857 0.00 0.00 34.79 2.71
368 371 3.282885 GCCCACTTTCAAGATAGGGAAG 58.717 50.000 15.87 0.00 37.92 3.46
423 426 0.675208 AATACAACACATGCCGCCGA 60.675 50.000 0.00 0.00 0.00 5.54
447 450 6.070824 TCACCACTTTGAGCTCTAATGATGTA 60.071 38.462 16.19 0.00 0.00 2.29
606 609 3.806625 ATAATCAGCCCACATTTGCAC 57.193 42.857 0.00 0.00 0.00 4.57
788 791 3.687212 TGTGGTCAAGCATTATACCAACG 59.313 43.478 0.00 0.00 42.68 4.10
793 796 6.265577 GGATTGTTGTGGTCAAGCATTATAC 58.734 40.000 0.00 0.00 33.61 1.47
826 829 3.397955 AGTAGTCCACCCATTTTGACCTT 59.602 43.478 0.00 0.00 0.00 3.50
1030 1045 8.554835 AGAAAAGAGCTAACCTTGATAAGTTC 57.445 34.615 0.00 0.00 0.00 3.01
1083 1098 3.375782 AAACAATGCCTTGAAGAGCAC 57.624 42.857 8.84 0.00 42.84 4.40
1226 1241 3.454375 GGTCGACGGAAACACATGATAT 58.546 45.455 9.92 0.00 0.00 1.63
1511 1811 1.496429 CCCCTTGCCCTTGTAGATCAT 59.504 52.381 0.00 0.00 0.00 2.45
1709 2010 3.686726 ACAGTTTCCAATCGAGAAGATGC 59.313 43.478 0.00 0.00 40.02 3.91
1713 2014 4.034510 GCCATACAGTTTCCAATCGAGAAG 59.965 45.833 0.00 0.00 0.00 2.85
1827 2128 6.346096 CCGAAGATTTGAGTCCTTGGTATTA 58.654 40.000 0.00 0.00 0.00 0.98
1946 2252 7.276218 CCAGTCAATAATGCCACAAAGTAAATG 59.724 37.037 0.00 0.00 0.00 2.32
2101 2408 7.480810 ACAAGCTTTTAAAGGTACACAGAAAG 58.519 34.615 9.90 0.00 38.49 2.62
2185 2504 7.231317 CAGGGCAATATATTGTTGTTAGGTGAT 59.769 37.037 23.14 0.00 39.88 3.06
2192 2511 6.849085 TGAACAGGGCAATATATTGTTGTT 57.151 33.333 26.77 26.77 39.34 2.83
2228 2547 7.013846 TCCAGTAACCCAATTTGTTTACTTGAG 59.986 37.037 13.89 8.93 0.00 3.02
2500 2823 1.202879 ACTTTCGAACAAGATGGGCCA 60.203 47.619 9.61 9.61 0.00 5.36
2609 2935 5.175856 CCGTTTTCATGTGCGGAAATAAAAA 59.824 36.000 12.14 0.00 46.33 1.94
2671 2997 6.259608 CCATCACTTCACCAAGCTTAAGATAG 59.740 42.308 12.56 0.00 32.09 2.08
2685 3011 8.997621 TTACTACAACTTATCCATCACTTCAC 57.002 34.615 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.