Multiple sequence alignment - TraesCS3A01G473100

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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 TraesCS3A01G473100 chr3A 100.000 3161 0 0 1 3161 703938125 703941285 0.000000e+00 5838.0
1 TraesCS3A01G473100 chr3D 93.437 2377 146 7 1 2372 571676587 571678958 0.000000e+00 3517.0
2 TraesCS3A01G473100 chr3D 93.852 2212 127 5 836 3045 571117326 571119530 0.000000e+00 3323.0
3 TraesCS3A01G473100 chr3D 87.234 2585 272 27 395 2956 571512931 571515480 0.000000e+00 2892.0
4 TraesCS3A01G473100 chr3D 82.024 1235 176 18 1071 2297 571208066 571209262 0.000000e+00 1009.0
5 TraesCS3A01G473100 chr3D 90.387 749 48 14 2414 3159 571678964 571679691 0.000000e+00 963.0
6 TraesCS3A01G473100 chr3D 88.889 450 43 5 2548 2993 571492794 571493240 5.960000e-152 547.0
7 TraesCS3A01G473100 chr3D 80.082 487 66 11 1818 2301 571490567 571491025 1.820000e-87 333.0
8 TraesCS3A01G473100 chr3D 91.860 86 5 1 2638 2723 571210155 571210238 5.540000e-23 119.0
9 TraesCS3A01G473100 chr3D 78.358 134 17 7 3028 3150 571493254 571493386 3.380000e-10 76.8
10 TraesCS3A01G473100 chrUn 97.099 2034 40 7 1128 3161 352871305 352873319 0.000000e+00 3411.0
11 TraesCS3A01G473100 chrUn 96.777 1365 25 7 1128 2492 409139747 409141092 0.000000e+00 2259.0
12 TraesCS3A01G473100 chrUn 98.121 1171 22 0 1164 2334 427478523 427479693 0.000000e+00 2041.0
13 TraesCS3A01G473100 chrUn 96.905 1163 33 2 1 1162 408639509 408638349 0.000000e+00 1945.0
14 TraesCS3A01G473100 chrUn 96.733 1163 35 2 1 1162 408637088 408638248 0.000000e+00 1934.0
15 TraesCS3A01G473100 chrUn 96.450 986 31 3 1 985 380839122 380838140 0.000000e+00 1624.0
16 TraesCS3A01G473100 chrUn 98.217 785 14 0 2377 3161 349530663 349529879 0.000000e+00 1373.0
17 TraesCS3A01G473100 chrUn 98.529 612 9 0 2550 3161 357850997 357851608 0.000000e+00 1081.0
18 TraesCS3A01G473100 chrUn 91.071 56 5 0 1964 2019 41526058 41526113 3.380000e-10 76.8
19 TraesCS3A01G473100 chr3B 91.487 2314 180 6 838 3141 758435304 758437610 0.000000e+00 3166.0
20 TraesCS3A01G473100 chr3B 87.361 269 29 3 2896 3159 758165801 758166069 1.420000e-78 303.0
21 TraesCS3A01G473100 chr3B 88.500 200 23 0 838 1037 758339536 758339735 3.150000e-60 243.0
22 TraesCS3A01G473100 chr3B 75.839 298 55 13 653 942 715003147 715003435 5.500000e-28 135.0
23 TraesCS3A01G473100 chr3B 84.932 73 10 1 2977 3048 758371951 758372023 4.370000e-09 73.1
24 TraesCS3A01G473100 chr3B 84.615 65 6 3 440 504 821214383 821214443 9.470000e-06 62.1
25 TraesCS3A01G473100 chr5D 85.169 236 31 1 1 232 34210686 34210451 4.070000e-59 239.0


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 TraesCS3A01G473100 chr3A 703938125 703941285 3160 False 5838.000000 5838 100.000 1 3161 1 chr3A.!!$F1 3160
1 TraesCS3A01G473100 chr3D 571117326 571119530 2204 False 3323.000000 3323 93.852 836 3045 1 chr3D.!!$F1 2209
2 TraesCS3A01G473100 chr3D 571512931 571515480 2549 False 2892.000000 2892 87.234 395 2956 1 chr3D.!!$F2 2561
3 TraesCS3A01G473100 chr3D 571676587 571679691 3104 False 2240.000000 3517 91.912 1 3159 2 chr3D.!!$F5 3158
4 TraesCS3A01G473100 chr3D 571208066 571210238 2172 False 564.000000 1009 86.942 1071 2723 2 chr3D.!!$F3 1652
5 TraesCS3A01G473100 chr3D 571490567 571493386 2819 False 318.933333 547 82.443 1818 3150 3 chr3D.!!$F4 1332
6 TraesCS3A01G473100 chrUn 352871305 352873319 2014 False 3411.000000 3411 97.099 1128 3161 1 chrUn.!!$F2 2033
7 TraesCS3A01G473100 chrUn 409139747 409141092 1345 False 2259.000000 2259 96.777 1128 2492 1 chrUn.!!$F5 1364
8 TraesCS3A01G473100 chrUn 427478523 427479693 1170 False 2041.000000 2041 98.121 1164 2334 1 chrUn.!!$F6 1170
9 TraesCS3A01G473100 chrUn 408638349 408639509 1160 True 1945.000000 1945 96.905 1 1162 1 chrUn.!!$R3 1161
10 TraesCS3A01G473100 chrUn 408637088 408638248 1160 False 1934.000000 1934 96.733 1 1162 1 chrUn.!!$F4 1161
11 TraesCS3A01G473100 chrUn 380838140 380839122 982 True 1624.000000 1624 96.450 1 985 1 chrUn.!!$R2 984
12 TraesCS3A01G473100 chrUn 349529879 349530663 784 True 1373.000000 1373 98.217 2377 3161 1 chrUn.!!$R1 784
13 TraesCS3A01G473100 chrUn 357850997 357851608 611 False 1081.000000 1081 98.529 2550 3161 1 chrUn.!!$F3 611
14 TraesCS3A01G473100 chr3B 758435304 758437610 2306 False 3166.000000 3166 91.487 838 3141 1 chr3B.!!$F5 2303

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
582 587 0.108662 CGCCATCTGTAGCAGTGTCA 60.109 55.0 0.0 0.0 32.61 3.58 F
1177 1189 0.108138 ACTCCAGGATTTCTTCGCCG 60.108 55.0 0.0 0.0 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1385 1406 0.251354 GAAGCTGAGCTCATGGTGGA 59.749 55.000 18.63 0.0 38.25 4.02 R
2729 4518 2.093890 TCAGCGTGAACGATTACCCTA 58.906 47.619 7.10 0.0 43.02 3.53 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
102 107 1.989864 TCAACTGCGTATGTACTTGCG 59.010 47.619 13.64 13.64 0.00 4.85
311 316 1.064208 CGATATAGTCGCATCCGAGGG 59.936 57.143 0.00 0.00 45.38 4.30
339 344 0.179205 GGTCGTCGTACTTCGGTGAG 60.179 60.000 6.70 0.00 40.32 3.51
582 587 0.108662 CGCCATCTGTAGCAGTGTCA 60.109 55.000 0.00 0.00 32.61 3.58
710 715 2.817839 CGGGAAAGAAGTGGAATTGGGT 60.818 50.000 0.00 0.00 0.00 4.51
813 818 1.710013 AGTCGCACTTGACGGTATTG 58.290 50.000 0.00 0.00 43.70 1.90
858 868 6.039829 AGTGTCAAGGAAGGAAGAAAATGAAC 59.960 38.462 0.00 0.00 0.00 3.18
1050 1062 2.642996 TATCGCTGTCGGCCACCATG 62.643 60.000 2.24 0.00 37.74 3.66
1158 1170 2.280797 GCGAGTTGCCTGACCACA 60.281 61.111 0.00 0.00 37.76 4.17
1177 1189 0.108138 ACTCCAGGATTTCTTCGCCG 60.108 55.000 0.00 0.00 0.00 6.46
1337 1358 5.399497 CCCTCCATGATTTTGATCCTAACCT 60.399 44.000 0.00 0.00 0.00 3.50
1583 1605 2.482326 GCACTGAACCCTATGTGCC 58.518 57.895 5.75 0.00 46.84 5.01
1833 1855 4.515191 CCAGAAGAGTTTCATGTTTTCCGA 59.485 41.667 0.00 0.00 35.70 4.55
2075 2099 0.590195 GCCGATGGATCTTGTGATGC 59.410 55.000 0.00 0.00 40.78 3.91
2367 2394 0.534652 GCTGCTAAGCTGATCCCTGG 60.535 60.000 0.00 0.00 46.60 4.45
2910 4717 4.634004 CGACAAGCATAATACTGTTTCCCA 59.366 41.667 0.00 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 7.843490 AGTACATACGCAGTTGATATTTTGT 57.157 32.000 0.00 0.00 37.78 2.83
339 344 4.740822 ATGGACGGTGGCCAAGGC 62.741 66.667 7.24 6.95 39.21 4.35
582 587 1.925455 CATGGAGGAGGGTGTGGGT 60.925 63.158 0.00 0.00 0.00 4.51
710 715 1.001974 CCGAACAGTCCCACATTCTCA 59.998 52.381 0.00 0.00 0.00 3.27
1050 1062 1.841103 GGAGGAGGAGGAGGCCATC 60.841 68.421 5.01 0.00 0.00 3.51
1158 1170 0.108138 CGGCGAAGAAATCCTGGAGT 60.108 55.000 0.00 0.00 0.00 3.85
1337 1358 2.151202 CAAAAGAGTAGAAGGCGGCAA 58.849 47.619 13.08 0.00 0.00 4.52
1385 1406 0.251354 GAAGCTGAGCTCATGGTGGA 59.749 55.000 18.63 0.00 38.25 4.02
1583 1605 4.574013 CCTTGAGAAAGATCAAATCCTCCG 59.426 45.833 0.00 0.00 38.66 4.63
1833 1855 0.920763 TCCCCTCCATTGACTGCCAT 60.921 55.000 0.00 0.00 0.00 4.40
1917 1939 1.666700 CCTTTCGTCGGAACAACACAA 59.333 47.619 0.00 0.00 0.00 3.33
2075 2099 5.106396 CCCTCTAAGTTCTCAGCAACAAATG 60.106 44.000 0.00 0.00 0.00 2.32
2729 4518 2.093890 TCAGCGTGAACGATTACCCTA 58.906 47.619 7.10 0.00 43.02 3.53
2786 4575 9.008965 TGCGGATAAAATGCTTTGTATATGTAT 57.991 29.630 0.00 0.00 0.00 2.29
2946 4753 9.158233 CGGTAAACCAACATTATTTCTCTAAGA 57.842 33.333 0.00 0.00 35.14 2.10
3084 4892 6.260714 GCATGATGATGTATTACAACTGGTCA 59.739 38.462 0.00 0.36 31.50 4.02


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

AutoCloner maintained by Alex Coulton.