Multiple sequence alignment - TraesCS7A01G424400

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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 TraesCS7A01G424400 chr7A 100.000 2414 0 0 1 2414 617597569 617599982 0.000000e+00 4458.0
1 TraesCS7A01G424400 chr7A 97.727 2420 29 2 1 2414 41465715 41463316 0.000000e+00 4141.0
2 TraesCS7A01G424400 chr2A 98.467 2414 37 0 1 2414 756523536 756525949 0.000000e+00 4253.0
3 TraesCS7A01G424400 chr7D 92.981 1097 51 9 1293 2387 449503417 449502345 0.000000e+00 1576.0
4 TraesCS7A01G424400 chr7D 92.890 1097 51 10 1293 2387 621797432 621798503 0.000000e+00 1568.0
5 TraesCS7A01G424400 chr7D 95.000 40 2 0 99 138 55126291 55126330 2.000000e-06 63.9
6 TraesCS7A01G424400 chr3D 92.974 1096 52 8 1293 2387 583596393 583597464 0.000000e+00 1574.0
7 TraesCS7A01G424400 chr3D 95.812 191 8 0 352 542 553215157 553214967 2.330000e-80 309.0
8 TraesCS7A01G424400 chr3D 94.231 156 7 1 698 851 553214395 553214240 1.120000e-58 237.0
9 TraesCS7A01G424400 chr3D 95.283 106 5 0 543 648 553214933 553214828 4.130000e-38 169.0
10 TraesCS7A01G424400 chr3A 92.707 1097 55 8 1293 2387 703814313 703815386 0.000000e+00 1559.0
11 TraesCS7A01G424400 chr3A 91.304 299 21 4 848 1141 662597936 662597638 1.040000e-108 403.0
12 TraesCS7A01G424400 chr3A 89.355 310 15 5 543 851 689496439 689496147 8.150000e-100 374.0
13 TraesCS7A01G424400 chr3A 96.859 191 6 0 352 542 689496663 689496473 1.080000e-83 320.0
14 TraesCS7A01G424400 chr3A 88.235 204 22 2 149 351 662598134 662597932 2.400000e-60 243.0
15 TraesCS7A01G424400 chrUn 92.257 1072 58 8 1293 2362 344422306 344423354 0.000000e+00 1496.0
16 TraesCS7A01G424400 chrUn 92.141 1018 56 7 1371 2387 314367743 314368737 0.000000e+00 1415.0
17 TraesCS7A01G424400 chrUn 92.246 993 53 7 1371 2362 455429912 455430881 0.000000e+00 1386.0
18 TraesCS7A01G424400 chr2B 89.806 824 58 14 921 1729 134341437 134342249 0.000000e+00 1033.0
19 TraesCS7A01G424400 chr2B 91.639 299 20 5 848 1141 100101772 100101474 2.230000e-110 409.0
20 TraesCS7A01G424400 chr2B 91.000 200 16 2 146 344 759994051 759994249 3.960000e-68 268.0
21 TraesCS7A01G424400 chr5D 89.769 821 60 14 921 1729 27280867 27281675 0.000000e+00 1029.0
22 TraesCS7A01G424400 chr5D 92.715 151 11 0 2237 2387 27284964 27285114 4.040000e-53 219.0
23 TraesCS7A01G424400 chr5D 95.745 47 2 0 848 894 27280823 27280869 2.570000e-10 76.8
24 TraesCS7A01G424400 chr1B 93.491 676 35 6 848 1521 675900497 675901165 0.000000e+00 996.0
25 TraesCS7A01G424400 chr1B 91.133 203 10 6 149 351 675900307 675900501 3.960000e-68 268.0
26 TraesCS7A01G424400 chr6D 88.727 825 66 16 921 1729 440673450 440674263 0.000000e+00 983.0
27 TraesCS7A01G424400 chr6D 92.357 157 12 0 2231 2387 440675727 440675883 8.680000e-55 224.0
28 TraesCS7A01G424400 chr2D 88.299 829 69 17 921 1732 606091321 606090504 0.000000e+00 968.0
29 TraesCS7A01G424400 chr2D 85.802 162 9 2 2 149 23117077 23116916 2.480000e-35 159.0
30 TraesCS7A01G424400 chr2D 97.222 36 1 0 101 136 245668081 245668046 7.210000e-06 62.1
31 TraesCS7A01G424400 chr6A 88.087 831 69 16 921 1732 163168091 163167272 0.000000e+00 959.0
32 TraesCS7A01G424400 chr4A 87.485 831 62 22 921 1729 658381529 658382339 0.000000e+00 920.0
33 TraesCS7A01G424400 chr4A 91.275 298 22 4 848 1141 742008686 742008389 1.040000e-108 403.0
34 TraesCS7A01G424400 chr4A 91.262 206 18 0 146 351 658381284 658381489 5.080000e-72 281.0
35 TraesCS7A01G424400 chr4A 87.745 204 23 2 149 351 742008884 742008682 1.120000e-58 237.0
36 TraesCS7A01G424400 chr4A 83.521 267 23 7 2101 2348 31395895 31395631 1.870000e-56 230.0
37 TraesCS7A01G424400 chr5A 92.230 296 18 5 848 1138 470930907 470931202 4.800000e-112 414.0
38 TraesCS7A01G424400 chr5A 87.143 210 25 2 143 351 470930703 470930911 1.120000e-58 237.0
39 TraesCS7A01G424400 chr7B 91.246 297 22 4 848 1141 593348547 593348252 3.740000e-108 401.0
40 TraesCS7A01G424400 chr7B 87.850 214 18 1 146 351 228800481 228800694 6.670000e-61 244.0
41 TraesCS7A01G424400 chr3B 89.644 309 15 6 543 851 734429039 734428748 6.300000e-101 377.0
42 TraesCS7A01G424400 chr3B 96.335 191 7 0 352 542 734429263 734429073 5.010000e-82 315.0
43 TraesCS7A01G424400 chr3B 85.276 163 10 3 1 149 775660079 775659917 3.210000e-34 156.0
44 TraesCS7A01G424400 chr3B 97.368 38 1 0 101 138 816273579 816273616 5.570000e-07 65.8
45 TraesCS7A01G424400 chr4D 92.105 152 10 1 2238 2387 85850332 85850181 1.880000e-51 213.0


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 TraesCS7A01G424400 chr7A 617597569 617599982 2413 False 4458.000000 4458 100.000000 1 2414 1 chr7A.!!$F1 2413
1 TraesCS7A01G424400 chr7A 41463316 41465715 2399 True 4141.000000 4141 97.727000 1 2414 1 chr7A.!!$R1 2413
2 TraesCS7A01G424400 chr2A 756523536 756525949 2413 False 4253.000000 4253 98.467000 1 2414 1 chr2A.!!$F1 2413
3 TraesCS7A01G424400 chr7D 449502345 449503417 1072 True 1576.000000 1576 92.981000 1293 2387 1 chr7D.!!$R1 1094
4 TraesCS7A01G424400 chr7D 621797432 621798503 1071 False 1568.000000 1568 92.890000 1293 2387 1 chr7D.!!$F2 1094
5 TraesCS7A01G424400 chr3D 583596393 583597464 1071 False 1574.000000 1574 92.974000 1293 2387 1 chr3D.!!$F1 1094
6 TraesCS7A01G424400 chr3D 553214240 553215157 917 True 238.333333 309 95.108667 352 851 3 chr3D.!!$R1 499
7 TraesCS7A01G424400 chr3A 703814313 703815386 1073 False 1559.000000 1559 92.707000 1293 2387 1 chr3A.!!$F1 1094
8 TraesCS7A01G424400 chr3A 689496147 689496663 516 True 347.000000 374 93.107000 352 851 2 chr3A.!!$R2 499
9 TraesCS7A01G424400 chrUn 344422306 344423354 1048 False 1496.000000 1496 92.257000 1293 2362 1 chrUn.!!$F2 1069
10 TraesCS7A01G424400 chrUn 314367743 314368737 994 False 1415.000000 1415 92.141000 1371 2387 1 chrUn.!!$F1 1016
11 TraesCS7A01G424400 chrUn 455429912 455430881 969 False 1386.000000 1386 92.246000 1371 2362 1 chrUn.!!$F3 991
12 TraesCS7A01G424400 chr2B 134341437 134342249 812 False 1033.000000 1033 89.806000 921 1729 1 chr2B.!!$F1 808
13 TraesCS7A01G424400 chr5D 27280823 27285114 4291 False 441.600000 1029 92.743000 848 2387 3 chr5D.!!$F1 1539
14 TraesCS7A01G424400 chr1B 675900307 675901165 858 False 632.000000 996 92.312000 149 1521 2 chr1B.!!$F1 1372
15 TraesCS7A01G424400 chr6D 440673450 440675883 2433 False 603.500000 983 90.542000 921 2387 2 chr6D.!!$F1 1466
16 TraesCS7A01G424400 chr2D 606090504 606091321 817 True 968.000000 968 88.299000 921 1732 1 chr2D.!!$R3 811
17 TraesCS7A01G424400 chr6A 163167272 163168091 819 True 959.000000 959 88.087000 921 1732 1 chr6A.!!$R1 811
18 TraesCS7A01G424400 chr4A 658381284 658382339 1055 False 600.500000 920 89.373500 146 1729 2 chr4A.!!$F1 1583
19 TraesCS7A01G424400 chr3B 734428748 734429263 515 True 346.000000 377 92.989500 352 851 2 chr3B.!!$R2 499

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
39 40 0.543174 GGTGCGGGGGAGATATCTCT 60.543 60.000 27.65 0.0 42.48 3.10 F
178 179 1.299976 GATTTGTGGAGAGCCCGGT 59.700 57.895 0.00 0.0 37.93 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1201 1654 4.851843 TCTGGCATCATCTTCATGTTCTT 58.148 39.13 0.0 0.0 0.0 2.52 R
2051 4952 5.886474 CACTACCTACTGACTCCAATCACTA 59.114 44.00 0.0 0.0 0.0 2.74 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
39 40 0.543174 GGTGCGGGGGAGATATCTCT 60.543 60.000 27.65 0.00 42.48 3.10
97 98 4.157120 GTAGTCCGCCCATGCCGT 62.157 66.667 3.81 0.00 0.00 5.68
178 179 1.299976 GATTTGTGGAGAGCCCGGT 59.700 57.895 0.00 0.00 37.93 5.28
257 258 2.163211 GCTTCCATTGCTCTTCAGTTCC 59.837 50.000 0.00 0.00 0.00 3.62
299 300 8.454106 ACTGTAAAAATATCTGATGAAGCACAC 58.546 33.333 0.00 0.00 0.00 3.82
604 638 2.159462 GGAACTATTGCTTGCACTCTGC 60.159 50.000 0.00 0.00 45.29 4.26
662 696 2.752030 TCAGAGATGGTCTTACAGGGG 58.248 52.381 0.00 0.00 30.64 4.79
772 1191 9.992910 GAAATTCAAATTCTTCAAGTTGCTTTT 57.007 25.926 0.00 0.00 37.48 2.27
985 1404 4.587584 TGATTTTGCAGTTGCTGATTCA 57.412 36.364 5.62 3.93 42.66 2.57
1201 1654 3.165875 AGGAAACTGAGGAACGATCTGA 58.834 45.455 0.00 0.00 41.13 3.27
1393 1847 2.162208 TGCAAGATTCTGTCGATTTGGC 59.838 45.455 0.00 0.00 0.00 4.52
2051 4952 6.902974 AGTTATTTCCCCCTGCTTTTGATTAT 59.097 34.615 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.613520 CGTAGAGATATCTCCCCCGCA 60.614 57.143 25.88 5.17 43.88 5.69
97 98 2.441164 GCTGCTCCCTCTCCTCGA 60.441 66.667 0.00 0.00 0.00 4.04
178 179 2.154798 GACCTGTAGACGGTGCTGCA 62.155 60.000 0.00 0.00 34.19 4.41
257 258 7.481275 TTTTACAGTTTCCAACTAGTAACCG 57.519 36.000 0.00 0.00 40.46 4.44
299 300 2.270986 GGCCACTGTGGAAAGCTGG 61.271 63.158 30.23 1.38 40.96 4.85
604 638 3.200593 GCAGATGCTCCTGTGCCG 61.201 66.667 0.00 0.00 36.57 5.69
662 696 7.065803 GGCTTTTTCCCCTATAAATGCTTTTTC 59.934 37.037 2.59 0.00 35.76 2.29
1201 1654 4.851843 TCTGGCATCATCTTCATGTTCTT 58.148 39.130 0.00 0.00 0.00 2.52
2051 4952 5.886474 CACTACCTACTGACTCCAATCACTA 59.114 44.000 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.