Multiple sequence alignment - TraesCS7A01G299100

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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 TraesCS7A01G299100 chr7A 100.000 2855 0 0 1 2855 408687442 408690296 0.000000e+00 5236
1 TraesCS7A01G299100 chr7A 98.573 911 3 2 1 911 693382329 693383229 0.000000e+00 1604
2 TraesCS7A01G299100 chr7D 97.765 1387 26 1 911 2297 368809388 368810769 0.000000e+00 2385
3 TraesCS7A01G299100 chr7D 93.276 580 15 5 2294 2855 368811090 368811663 0.000000e+00 833
4 TraesCS7A01G299100 chr7B 98.298 999 17 0 911 1909 313773558 313772560 0.000000e+00 1751
5 TraesCS7A01G299100 chr7B 91.684 938 38 7 1944 2855 313772556 313771633 0.000000e+00 1264
6 TraesCS7A01G299100 chr7B 87.708 960 56 32 1 909 164496191 164495243 0.000000e+00 1064
7 TraesCS7A01G299100 chr7B 89.934 457 25 5 320 761 557456051 557456501 1.150000e-158 569
8 TraesCS7A01G299100 chr7B 97.078 308 9 0 1 308 557451753 557452060 1.170000e-143 520
9 TraesCS7A01G299100 chr7B 89.216 306 31 2 4 308 697278069 697278373 5.770000e-102 381
10 TraesCS7A01G299100 chr7B 90.058 171 17 0 381 551 725392511 725392341 3.700000e-54 222
11 TraesCS7A01G299100 chr6B 100.000 909 0 0 1 909 37067349 37068257 0.000000e+00 1642
12 TraesCS7A01G299100 chr5A 98.900 909 1 1 1 909 670540456 670539557 0.000000e+00 1616
13 TraesCS7A01G299100 chr3B 93.209 913 44 6 1 904 715051823 715050920 0.000000e+00 1328
14 TraesCS7A01G299100 chr3B 79.044 272 25 19 399 656 533019296 533019549 1.060000e-34 158
15 TraesCS7A01G299100 chr2B 92.717 920 47 4 1 909 369028303 369027393 0.000000e+00 1312
16 TraesCS7A01G299100 chr6A 92.387 683 27 9 1 675 9259182 9258517 0.000000e+00 952
17 TraesCS7A01G299100 chr6A 93.893 131 8 0 779 909 9258032 9257902 6.240000e-47 198
18 TraesCS7A01G299100 chr6D 82.680 306 52 1 4 308 55431083 55431388 1.300000e-68 270
19 TraesCS7A01G299100 chr3D 82.680 306 52 1 4 308 577427379 577427684 1.300000e-68 270
20 TraesCS7A01G299100 chr1D 96.183 131 5 0 779 909 379845496 379845366 6.200000e-52 215
21 TraesCS7A01G299100 chr5D 92.481 133 8 2 779 910 276923741 276923872 3.750000e-44 189


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 TraesCS7A01G299100 chr7A 408687442 408690296 2854 False 5236.0 5236 100.0000 1 2855 1 chr7A.!!$F1 2854
1 TraesCS7A01G299100 chr7A 693382329 693383229 900 False 1604.0 1604 98.5730 1 911 1 chr7A.!!$F2 910
2 TraesCS7A01G299100 chr7D 368809388 368811663 2275 False 1609.0 2385 95.5205 911 2855 2 chr7D.!!$F1 1944
3 TraesCS7A01G299100 chr7B 313771633 313773558 1925 True 1507.5 1751 94.9910 911 2855 2 chr7B.!!$R3 1944
4 TraesCS7A01G299100 chr7B 164495243 164496191 948 True 1064.0 1064 87.7080 1 909 1 chr7B.!!$R1 908
5 TraesCS7A01G299100 chr7B 557451753 557456501 4748 False 544.5 569 93.5060 1 761 2 chr7B.!!$F2 760
6 TraesCS7A01G299100 chr6B 37067349 37068257 908 False 1642.0 1642 100.0000 1 909 1 chr6B.!!$F1 908
7 TraesCS7A01G299100 chr5A 670539557 670540456 899 True 1616.0 1616 98.9000 1 909 1 chr5A.!!$R1 908
8 TraesCS7A01G299100 chr3B 715050920 715051823 903 True 1328.0 1328 93.2090 1 904 1 chr3B.!!$R1 903
9 TraesCS7A01G299100 chr2B 369027393 369028303 910 True 1312.0 1312 92.7170 1 909 1 chr2B.!!$R1 908
10 TraesCS7A01G299100 chr6A 9257902 9259182 1280 True 575.0 952 93.1400 1 909 2 chr6A.!!$R1 908

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
998 5391 9.884814 ATAATTAGCTCTTCTTCTACCCTAGAA 57.115 33.333 0.0 0.0 42.19 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2024 6421 1.111277 ACAAACAGGGACCAGCAAAC 58.889 50.0 0.0 0.0 0.0 2.93 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
998 5391 9.884814 ATAATTAGCTCTTCTTCTACCCTAGAA 57.115 33.333 0.0 0.0 42.19 2.10
2024 6421 7.227049 ACCTGATAAATTTGGTTGGTGTTAG 57.773 36.000 0.0 0.0 0.00 2.34
2032 6429 2.028130 TGGTTGGTGTTAGTTTGCTGG 58.972 47.619 0.0 0.0 0.00 4.85
2141 6538 7.773489 TGGAATGGTTTGATGATGAGTTAAA 57.227 32.000 0.0 0.0 0.00 1.52
2251 6648 9.691362 ACTTGTTTGATTTGGTTGAACATATAC 57.309 29.630 0.0 0.0 31.15 1.47
2252 6649 9.689976 CTTGTTTGATTTGGTTGAACATATACA 57.310 29.630 0.0 0.0 31.15 2.29
2300 7021 5.428253 TGGATGTCAGTTTTGCTACTATCC 58.572 41.667 0.0 0.0 33.30 2.59
2306 7027 7.112122 TGTCAGTTTTGCTACTATCCATTCAT 58.888 34.615 0.0 0.0 0.00 2.57
2308 7029 8.125448 GTCAGTTTTGCTACTATCCATTCATTC 58.875 37.037 0.0 0.0 0.00 2.67
2349 7070 7.481275 TTTCTTTTTGCTTCTTAATGCTTGG 57.519 32.000 0.0 0.0 0.00 3.61
2393 7114 7.543947 TGTTGACTGAGATTGTTGCTATATG 57.456 36.000 0.0 0.0 0.00 1.78
2473 7198 6.475596 AATCCCAGCTTAATCATTTCCTTG 57.524 37.500 0.0 0.0 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
998 5391 2.181975 CCAAATCCAGTCCTGCCATTT 58.818 47.619 0.00 0.00 0.00 2.32
1434 5827 0.538977 TCTCGAACCTTCCGTGGAGT 60.539 55.000 0.00 0.00 31.15 3.85
1754 6147 1.611673 CCATCGGCAGGTTGAAGAACT 60.612 52.381 0.00 0.00 32.15 3.01
2024 6421 1.111277 ACAAACAGGGACCAGCAAAC 58.889 50.000 0.00 0.00 0.00 2.93
2238 6635 6.912591 GCTGCTTGTATTGTATATGTTCAACC 59.087 38.462 0.00 0.00 0.00 3.77
2250 6647 4.760530 TGGATCTAGCTGCTTGTATTGT 57.239 40.909 7.79 0.00 0.00 2.71
2251 6648 4.388165 CGATGGATCTAGCTGCTTGTATTG 59.612 45.833 7.79 1.25 0.00 1.90
2252 6649 4.281941 TCGATGGATCTAGCTGCTTGTATT 59.718 41.667 7.79 0.00 0.00 1.89
2253 6650 3.829026 TCGATGGATCTAGCTGCTTGTAT 59.171 43.478 7.79 1.69 0.00 2.29
2254 6651 3.222603 TCGATGGATCTAGCTGCTTGTA 58.777 45.455 7.79 0.00 0.00 2.41
2283 6680 7.011389 CGAATGAATGGATAGTAGCAAAACTGA 59.989 37.037 0.00 0.00 0.00 3.41
2286 6683 6.260050 TCCGAATGAATGGATAGTAGCAAAAC 59.740 38.462 0.00 0.00 0.00 2.43
2323 7044 8.397148 CCAAGCATTAAGAAGCAAAAAGAAAAA 58.603 29.630 0.00 0.00 0.00 1.94
2324 7045 7.768120 TCCAAGCATTAAGAAGCAAAAAGAAAA 59.232 29.630 0.00 0.00 0.00 2.29
2325 7046 7.224557 GTCCAAGCATTAAGAAGCAAAAAGAAA 59.775 33.333 0.00 0.00 0.00 2.52
2326 7047 6.701400 GTCCAAGCATTAAGAAGCAAAAAGAA 59.299 34.615 0.00 0.00 0.00 2.52
2327 7048 6.040842 AGTCCAAGCATTAAGAAGCAAAAAGA 59.959 34.615 0.00 0.00 0.00 2.52
2328 7049 6.218746 AGTCCAAGCATTAAGAAGCAAAAAG 58.781 36.000 0.00 0.00 0.00 2.27
2349 7070 5.262588 ACAAATGACAGGAAAACCAAGTC 57.737 39.130 0.00 0.00 0.00 3.01
2383 7104 3.677121 CCAGATGCGAGACATATAGCAAC 59.323 47.826 0.00 0.00 43.19 4.17
2384 7105 3.573967 TCCAGATGCGAGACATATAGCAA 59.426 43.478 0.00 0.00 43.19 3.91
2393 7114 3.521560 TGTAAACATCCAGATGCGAGAC 58.478 45.455 7.56 2.42 42.39 3.36
2559 7285 8.254508 CAGGGAATAGGAACTTGTATATAGCTC 58.745 40.741 0.00 0.00 41.75 4.09
2647 7389 1.474077 GCTTCGGGCAAACTTCATCAT 59.526 47.619 0.00 0.00 41.35 2.45


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

AutoCloner maintained by Alex Coulton.