Multiple sequence alignment - TraesCS2B01G543700

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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 TraesCS2B01G543700 chr2B 100.000 8642 0 0 1 8642 741219771 741211130 0.000000e+00 15886.0
1 TraesCS2B01G543700 chr2B 99.384 4867 27 2 1 4865 741249344 741244479 0.000000e+00 8818.0
2 TraesCS2B01G543700 chr2B 99.241 2636 18 2 6008 8642 741243497 741240863 0.000000e+00 4756.0
3 TraesCS2B01G543700 chr2B 99.792 961 2 0 4912 5872 741244468 741243508 0.000000e+00 1764.0
4 TraesCS2B01G543700 chr2B 97.196 749 21 0 7894 8642 318083052 318083800 0.000000e+00 1267.0
5 TraesCS2B01G543700 chr2B 97.323 747 19 1 7896 8642 564815993 564815248 0.000000e+00 1267.0
6 TraesCS2B01G543700 chr2B 97.185 746 21 0 7896 8641 615587889 615587144 0.000000e+00 1262.0
7 TraesCS2B01G543700 chr2B 95.730 281 12 0 2666 2946 511849661 511849941 3.680000e-123 453.0
8 TraesCS2B01G543700 chr2B 93.907 279 13 1 3222 3500 737765304 737765030 1.340000e-112 418.0
9 TraesCS2B01G543700 chr2B 93.286 283 15 1 3220 3502 27626142 27625864 1.740000e-111 414.0
10 TraesCS2B01G543700 chr2B 92.657 286 17 1 3220 3505 242971041 242970760 8.080000e-110 409.0
11 TraesCS2B01G543700 chr2B 83.616 177 28 1 5690 5866 481459273 481459098 1.930000e-36 165.0
12 TraesCS2B01G543700 chr2B 87.681 138 15 1 5687 5822 801156716 801156853 8.980000e-35 159.0
13 TraesCS2B01G543700 chr2B 75.410 305 55 14 7085 7374 636779903 636780202 7.040000e-26 130.0
14 TraesCS2B01G543700 chr2A 91.375 1229 65 13 153 1358 739491861 739490651 0.000000e+00 1644.0
15 TraesCS2B01G543700 chr2A 87.573 1199 122 18 6187 7368 739482936 739481748 0.000000e+00 1363.0
16 TraesCS2B01G543700 chr2A 93.767 722 40 2 1373 2091 739490667 739489948 0.000000e+00 1079.0
17 TraesCS2B01G543700 chr2A 91.713 543 39 4 4082 4621 739485237 739484698 0.000000e+00 749.0
18 TraesCS2B01G543700 chr2A 93.534 464 28 2 7435 7897 739481464 739481002 0.000000e+00 689.0
19 TraesCS2B01G543700 chr2A 87.091 550 37 13 2131 2672 739489952 739489429 7.470000e-165 592.0
20 TraesCS2B01G543700 chr2A 87.119 295 31 3 3800 4088 739489298 739489005 2.330000e-85 327.0
21 TraesCS2B01G543700 chr2A 96.296 108 4 0 3692 3799 449280138 449280031 2.480000e-40 178.0
22 TraesCS2B01G543700 chr2A 96.330 109 3 1 3584 3692 739489407 739489300 2.480000e-40 178.0
23 TraesCS2B01G543700 chr2A 89.683 126 13 0 2 127 739492363 739492238 2.500000e-35 161.0
24 TraesCS2B01G543700 chr2A 88.636 132 13 2 5692 5822 726576102 726576232 8.980000e-35 159.0
25 TraesCS2B01G543700 chr2A 86.466 133 18 0 5552 5684 739484694 739484562 6.990000e-31 147.0
26 TraesCS2B01G543700 chr2A 82.468 154 24 3 7222 7373 678675606 678675758 1.960000e-26 132.0
27 TraesCS2B01G543700 chr2A 77.570 214 36 9 7222 7431 164709600 164709395 1.520000e-22 119.0
28 TraesCS2B01G543700 chr6B 98.525 746 11 0 7897 8642 131695262 131696007 0.000000e+00 1317.0
29 TraesCS2B01G543700 chr6B 97.992 747 15 0 7896 8642 712550669 712549923 0.000000e+00 1297.0
30 TraesCS2B01G543700 chr6B 96.296 108 4 0 3692 3799 506127983 506128090 2.480000e-40 178.0
31 TraesCS2B01G543700 chr6B 79.429 175 26 1 5692 5866 642913256 642913092 1.970000e-21 115.0
32 TraesCS2B01G543700 chr1B 98.396 748 10 2 7896 8642 20558422 20559168 0.000000e+00 1314.0
33 TraesCS2B01G543700 chr1B 98.123 746 14 0 7897 8642 321011904 321011159 0.000000e+00 1301.0
34 TraesCS2B01G543700 chr1B 95.070 284 14 0 2663 2946 391329976 391330259 1.710000e-121 448.0
35 TraesCS2B01G543700 chr1B 94.624 279 11 1 3222 3500 612400491 612400217 6.200000e-116 429.0
36 TraesCS2B01G543700 chr1B 86.420 162 22 0 5692 5853 49318968 49319129 2.480000e-40 178.0
37 TraesCS2B01G543700 chr1B 76.151 239 48 8 7199 7433 561301967 561301734 5.480000e-22 117.0
38 TraesCS2B01G543700 chr5B 97.594 748 17 1 7895 8642 610024102 610024848 0.000000e+00 1280.0
39 TraesCS2B01G543700 chr5B 94.645 747 38 2 7897 8642 589823572 589824317 0.000000e+00 1157.0
40 TraesCS2B01G543700 chr5B 96.703 273 9 0 2674 2946 522895060 522895332 1.020000e-123 455.0
41 TraesCS2B01G543700 chr5B 94.265 279 11 2 3222 3500 578920093 578920366 1.040000e-113 422.0
42 TraesCS2B01G543700 chr2D 90.405 740 48 17 1373 2096 607996685 607995953 0.000000e+00 952.0
43 TraesCS2B01G543700 chr2D 88.000 725 46 21 1 686 607999395 607998673 0.000000e+00 819.0
44 TraesCS2B01G543700 chr2D 92.704 466 15 5 903 1358 607997125 607996669 0.000000e+00 654.0
45 TraesCS2B01G543700 chr2D 79.471 945 99 46 5914 6832 607990140 607989265 4.500000e-162 582.0
46 TraesCS2B01G543700 chr2D 79.511 859 117 35 3798 4635 607993684 607992864 2.730000e-154 556.0
47 TraesCS2B01G543700 chr2D 93.627 204 7 1 696 899 607997422 607997225 5.070000e-77 300.0
48 TraesCS2B01G543700 chrUn 96.727 275 9 0 2672 2946 36437383 36437109 7.910000e-125 459.0
49 TraesCS2B01G543700 chrUn 83.750 160 25 1 5707 5866 264105672 264105830 5.400000e-32 150.0
50 TraesCS2B01G543700 chrUn 80.000 165 27 4 7199 7361 49987644 49987804 5.480000e-22 117.0
51 TraesCS2B01G543700 chr7B 96.727 275 9 0 2672 2946 589400747 589400473 7.910000e-125 459.0
52 TraesCS2B01G543700 chr7B 96.715 274 9 0 2673 2946 636357188 636356915 2.840000e-124 457.0
53 TraesCS2B01G543700 chr7B 93.662 284 14 2 3220 3503 83906604 83906883 1.040000e-113 422.0
54 TraesCS2B01G543700 chr7B 94.574 258 13 1 2966 3222 138014865 138014608 1.750000e-106 398.0
55 TraesCS2B01G543700 chr7B 84.868 152 23 0 5716 5867 570411326 570411175 4.180000e-33 154.0
56 TraesCS2B01G543700 chr7B 92.045 88 6 1 3500 3587 138014610 138014524 1.180000e-23 122.0
57 TraesCS2B01G543700 chr4B 96.715 274 9 0 2673 2946 418491294 418491021 2.840000e-124 457.0
58 TraesCS2B01G543700 chr4B 96.364 275 10 0 2672 2946 212051630 212051356 3.680000e-123 453.0
59 TraesCS2B01G543700 chr4B 94.624 279 11 1 3222 3500 70104405 70104679 6.200000e-116 429.0
60 TraesCS2B01G543700 chr4B 95.238 42 2 0 161 202 172315854 172315895 5.600000e-07 67.6
61 TraesCS2B01G543700 chr4A 93.548 279 14 3 3222 3500 689946772 689947046 6.240000e-111 412.0
62 TraesCS2B01G543700 chr4A 85.946 185 23 3 5684 5866 52619292 52619109 2.460000e-45 195.0
63 TraesCS2B01G543700 chr7D 77.748 373 46 22 7085 7438 15237366 15237012 2.460000e-45 195.0
64 TraesCS2B01G543700 chr7D 85.393 178 26 0 5692 5869 17234594 17234417 1.480000e-42 185.0
65 TraesCS2B01G543700 chr7D 95.370 108 4 1 3692 3799 60693373 60693479 4.150000e-38 171.0
66 TraesCS2B01G543700 chr7D 83.616 177 29 0 5692 5868 23526371 23526195 5.370000e-37 167.0
67 TraesCS2B01G543700 chr7D 75.916 382 50 25 7085 7438 15233359 15232992 3.230000e-34 158.0
68 TraesCS2B01G543700 chr6D 95.370 108 5 0 3692 3799 388543030 388542923 1.150000e-38 172.0
69 TraesCS2B01G543700 chr3D 94.595 111 6 0 3692 3802 104404937 104404827 1.150000e-38 172.0
70 TraesCS2B01G543700 chr3D 79.255 188 36 3 7247 7433 374397461 374397646 2.530000e-25 128.0
71 TraesCS2B01G543700 chr1D 95.370 108 5 0 3692 3799 465596804 465596911 1.150000e-38 172.0
72 TraesCS2B01G543700 chr1A 93.860 114 7 0 3692 3805 13308423 13308536 1.150000e-38 172.0
73 TraesCS2B01G543700 chr5A 94.444 108 6 0 3692 3799 658993803 658993696 5.370000e-37 167.0
74 TraesCS2B01G543700 chr3B 82.857 140 20 3 7222 7359 809044573 809044436 1.180000e-23 122.0
75 TraesCS2B01G543700 chr4D 97.297 37 1 0 166 202 111134767 111134803 7.240000e-06 63.9


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 TraesCS2B01G543700 chr2B 741211130 741219771 8641 True 15886.000000 15886 100.000000 1 8642 1 chr2B.!!$R7 8641
1 TraesCS2B01G543700 chr2B 741240863 741249344 8481 True 5112.666667 8818 99.472333 1 8642 3 chr2B.!!$R8 8641
2 TraesCS2B01G543700 chr2B 318083052 318083800 748 False 1267.000000 1267 97.196000 7894 8642 1 chr2B.!!$F1 748
3 TraesCS2B01G543700 chr2B 564815248 564815993 745 True 1267.000000 1267 97.323000 7896 8642 1 chr2B.!!$R4 746
4 TraesCS2B01G543700 chr2B 615587144 615587889 745 True 1262.000000 1262 97.185000 7896 8641 1 chr2B.!!$R5 745
5 TraesCS2B01G543700 chr2A 739481002 739492363 11361 True 692.900000 1644 90.465100 2 7897 10 chr2A.!!$R3 7895
6 TraesCS2B01G543700 chr6B 131695262 131696007 745 False 1317.000000 1317 98.525000 7897 8642 1 chr6B.!!$F1 745
7 TraesCS2B01G543700 chr6B 712549923 712550669 746 True 1297.000000 1297 97.992000 7896 8642 1 chr6B.!!$R2 746
8 TraesCS2B01G543700 chr1B 20558422 20559168 746 False 1314.000000 1314 98.396000 7896 8642 1 chr1B.!!$F1 746
9 TraesCS2B01G543700 chr1B 321011159 321011904 745 True 1301.000000 1301 98.123000 7897 8642 1 chr1B.!!$R1 745
10 TraesCS2B01G543700 chr5B 610024102 610024848 746 False 1280.000000 1280 97.594000 7895 8642 1 chr5B.!!$F4 747
11 TraesCS2B01G543700 chr5B 589823572 589824317 745 False 1157.000000 1157 94.645000 7897 8642 1 chr5B.!!$F3 745
12 TraesCS2B01G543700 chr2D 607989265 607999395 10130 True 643.833333 952 87.286333 1 6832 6 chr2D.!!$R1 6831

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
301 659 1.001293 CTCTGTGGCACTGCTAAGACA 59.999 52.381 19.83 0.0 0.00 3.41 F
683 1048 5.108187 ACTGCATGACATCTCTAACCAAT 57.892 39.130 0.00 0.0 0.00 3.16 F
688 1053 6.875726 TGCATGACATCTCTAACCAATATAGC 59.124 38.462 0.00 0.0 0.00 2.97 F
1959 3683 3.932822 TCGTCTAGCCTTTGCATAACAA 58.067 40.909 0.00 0.0 41.13 2.83 F
3237 6543 1.348036 GGTAAGGCTAGCCATAGTGGG 59.652 57.143 34.70 0.0 38.19 4.61 F
3310 6616 5.055812 GGCATGAAGTTAATGAGGAGAGAG 58.944 45.833 4.20 0.0 0.00 3.20 F
4903 12036 4.589675 GGGGTTTGGCGGTGGTGA 62.590 66.667 0.00 0.0 0.00 4.02 F
5904 13230 1.202879 TGGTGGTTCCTTTCGCAAGAT 60.203 47.619 0.00 0.0 41.40 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1173 2892 4.147449 CGGAGCCTGACGATGCCA 62.147 66.667 0.00 0.0 0.00 4.92 R
1777 3496 9.620259 AAAGATTTACCTGAAGATGGAGATTAC 57.380 33.333 0.00 0.0 0.00 1.89 R
3183 6489 2.755650 CAGCGTATCCACCAATACCTC 58.244 52.381 0.00 0.0 0.00 3.85 R
3864 7179 4.249661 TGAACGTATTATGAAGTGCAGCA 58.750 39.130 0.00 0.0 0.00 4.41 R
4903 12036 0.174389 CGCTGGCACATCAGAGTAGT 59.826 55.000 0.00 0.0 38.20 2.73 R
5884 13210 0.181587 TCTTGCGAAAGGAACCACCA 59.818 50.000 2.54 0.0 42.04 4.17 R
5887 13213 3.596214 GAGTATCTTGCGAAAGGAACCA 58.404 45.455 2.54 0.0 36.14 3.67 R
8242 18729 0.179124 GAAGCGGAACTGAGAGCGAT 60.179 55.000 0.00 0.0 34.34 4.58 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
301 659 1.001293 CTCTGTGGCACTGCTAAGACA 59.999 52.381 19.83 0.00 0.00 3.41
683 1048 5.108187 ACTGCATGACATCTCTAACCAAT 57.892 39.130 0.00 0.00 0.00 3.16
688 1053 6.875726 TGCATGACATCTCTAACCAATATAGC 59.124 38.462 0.00 0.00 0.00 2.97
1959 3683 3.932822 TCGTCTAGCCTTTGCATAACAA 58.067 40.909 0.00 0.00 41.13 2.83
2826 6132 7.880195 GTCCCAATGCAATATGAGTCTATAACT 59.120 37.037 0.00 0.00 42.42 2.24
3183 6489 1.630244 GCAGCAGTTACCACTCAGCG 61.630 60.000 0.00 0.00 29.15 5.18
3237 6543 1.348036 GGTAAGGCTAGCCATAGTGGG 59.652 57.143 34.70 0.00 38.19 4.61
3310 6616 5.055812 GGCATGAAGTTAATGAGGAGAGAG 58.944 45.833 4.20 0.00 0.00 3.20
3498 6804 6.334102 AGTTACTATGCACTATGACTAGCC 57.666 41.667 0.00 0.00 0.00 3.93
3864 7179 5.182570 CCATCCGCATTCATCTCATAATTGT 59.817 40.000 0.00 0.00 0.00 2.71
4903 12036 4.589675 GGGGTTTGGCGGTGGTGA 62.590 66.667 0.00 0.00 0.00 4.02
5904 13230 1.202879 TGGTGGTTCCTTTCGCAAGAT 60.203 47.619 0.00 0.00 41.40 2.40
5926 14729 4.834406 ACTCCATAGATGGTAGGGAGAA 57.166 45.455 17.33 0.00 45.47 2.87
5933 14736 6.183361 CCATAGATGGTAGGGAGAAAATGACA 60.183 42.308 0.00 0.00 43.05 3.58
5943 14746 6.251471 AGGGAGAAAATGACAAGATTGTGAT 58.749 36.000 2.31 0.00 42.43 3.06
5993 14797 7.342026 AGTTTTGAGAGGGTTTTGTGTAGAAAT 59.658 33.333 0.00 0.00 0.00 2.17
7700 18187 8.783833 TTCCTTAAATAGCTATGAGATGCATC 57.216 34.615 19.37 19.37 38.44 3.91
8158 18645 6.098124 AGGAGACCTGTCTAGAAGATCATTTG 59.902 42.308 0.00 0.00 40.61 2.32
8333 18820 3.976704 CAGTATGGTTCCTGGCCAA 57.023 52.632 7.01 0.00 39.72 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
301 659 6.134535 TCTTAGGGAACATACAATGGTGTT 57.865 37.500 6.08 6.08 40.97 3.32
1173 2892 4.147449 CGGAGCCTGACGATGCCA 62.147 66.667 0.00 0.00 0.00 4.92
1777 3496 9.620259 AAAGATTTACCTGAAGATGGAGATTAC 57.380 33.333 0.00 0.00 0.00 1.89
3183 6489 2.755650 CAGCGTATCCACCAATACCTC 58.244 52.381 0.00 0.00 0.00 3.85
3237 6543 8.680903 TGTGCTATGTTACTACCTAAGTTACTC 58.319 37.037 0.00 0.00 38.33 2.59
3310 6616 6.683974 ACATCTTATGTTACCACAAGCATC 57.316 37.500 0.00 0.00 41.63 3.91
3864 7179 4.249661 TGAACGTATTATGAAGTGCAGCA 58.750 39.130 0.00 0.00 0.00 4.41
4875 11997 1.416030 GCCAAACCCCTTGTCATTGTT 59.584 47.619 0.00 0.00 32.65 2.83
4876 11998 1.047801 GCCAAACCCCTTGTCATTGT 58.952 50.000 0.00 0.00 32.65 2.71
4894 12027 0.818296 ATCAGAGTAGTCACCACCGC 59.182 55.000 0.00 0.00 0.00 5.68
4903 12036 0.174389 CGCTGGCACATCAGAGTAGT 59.826 55.000 0.00 0.00 38.20 2.73
5884 13210 0.181587 TCTTGCGAAAGGAACCACCA 59.818 50.000 2.54 0.00 42.04 4.17
5887 13213 3.596214 GAGTATCTTGCGAAAGGAACCA 58.404 45.455 2.54 0.00 36.14 3.67
5890 13216 3.973206 TGGAGTATCTTGCGAAAGGAA 57.027 42.857 2.54 0.00 39.89 3.36
5891 13217 4.893524 TCTATGGAGTATCTTGCGAAAGGA 59.106 41.667 2.54 0.00 33.73 3.36
5926 14729 9.754382 GCCATAATAATCACAATCTTGTCATTT 57.246 29.630 0.00 0.00 39.91 2.32
5933 14736 7.232127 CCCTTGAGCCATAATAATCACAATCTT 59.768 37.037 0.00 0.00 0.00 2.40
5943 14746 4.532834 GGTTGTCCCTTGAGCCATAATAA 58.467 43.478 0.00 0.00 0.00 1.40
7003 17255 9.638239 ATTATTTAAATCTTGTGTGCGTGAAAT 57.362 25.926 3.39 0.00 0.00 2.17
7004 17256 9.123709 GATTATTTAAATCTTGTGTGCGTGAAA 57.876 29.630 3.39 0.00 0.00 2.69
7438 17925 4.723879 ACACAAAAGCAACACAAACAAC 57.276 36.364 0.00 0.00 0.00 3.32
8158 18645 3.636764 TCTTTTGTGGCTTCTTTCCTTCC 59.363 43.478 0.00 0.00 0.00 3.46
8242 18729 0.179124 GAAGCGGAACTGAGAGCGAT 60.179 55.000 0.00 0.00 34.34 4.58
8333 18820 2.281070 CTGCAAGTGTGGGCGTCT 60.281 61.111 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.