Multiple sequence alignment - TraesCS5A01G017300

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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 TraesCS5A01G017300 chr5A 100.000 2512 0 0 1 2512 13143402 13140891 0.000000e+00 4639
1 TraesCS5A01G017300 chr4A 96.206 2530 70 12 1 2512 45631395 45633916 0.000000e+00 4117
2 TraesCS5A01G017300 chr2A 95.965 2528 79 13 1 2512 677262023 677264543 0.000000e+00 4082
3 TraesCS5A01G017300 chr7D 95.251 2548 77 13 1 2510 421675283 421677824 0.000000e+00 3995
4 TraesCS5A01G017300 chr7D 92.258 465 16 8 2049 2493 510256860 510257324 2.110000e-180 641
5 TraesCS5A01G017300 chr6A 95.332 2528 94 14 1 2512 484784652 484782133 0.000000e+00 3993
6 TraesCS5A01G017300 chr6D 94.973 2546 84 14 1 2510 451600148 451597611 0.000000e+00 3952
7 TraesCS5A01G017300 chr6D 95.272 2517 75 15 1 2482 459129171 459131678 0.000000e+00 3949
8 TraesCS5A01G017300 chr6D 94.625 2549 80 16 1 2510 397854471 397851941 0.000000e+00 3895
9 TraesCS5A01G017300 chr6D 92.473 465 15 8 2049 2493 434427969 434428433 0.000000e+00 647
10 TraesCS5A01G017300 chr2D 94.939 2549 83 15 1 2510 54047557 54045016 0.000000e+00 3951
11 TraesCS5A01G017300 chr5D 95.002 2381 73 14 1 2344 58009616 58007245 0.000000e+00 3696
12 TraesCS5A01G017300 chr5D 93.352 2527 117 20 1 2493 391883823 391881314 0.000000e+00 3688
13 TraesCS5A01G017300 chr4B 92.473 465 15 1 2049 2493 379062664 379063128 0.000000e+00 647
14 TraesCS5A01G017300 chr3D 92.258 465 16 8 2049 2493 360442088 360441624 2.110000e-180 641
15 TraesCS5A01G017300 chr3D 92.043 465 16 9 2049 2493 384997389 384997852 3.530000e-178 634
16 TraesCS5A01G017300 chr3B 91.845 466 17 7 2049 2493 497580954 497580489 4.560000e-177 630
17 TraesCS5A01G017300 chr7B 91.398 465 20 8 2049 2493 432968975 432969439 9.870000e-174 619
18 TraesCS5A01G017300 chr6B 96.970 330 10 0 2164 2493 658001857 658002186 2.820000e-154 555


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 TraesCS5A01G017300 chr5A 13140891 13143402 2511 True 4639 4639 100.000 1 2512 1 chr5A.!!$R1 2511
1 TraesCS5A01G017300 chr4A 45631395 45633916 2521 False 4117 4117 96.206 1 2512 1 chr4A.!!$F1 2511
2 TraesCS5A01G017300 chr2A 677262023 677264543 2520 False 4082 4082 95.965 1 2512 1 chr2A.!!$F1 2511
3 TraesCS5A01G017300 chr7D 421675283 421677824 2541 False 3995 3995 95.251 1 2510 1 chr7D.!!$F1 2509
4 TraesCS5A01G017300 chr6A 484782133 484784652 2519 True 3993 3993 95.332 1 2512 1 chr6A.!!$R1 2511
5 TraesCS5A01G017300 chr6D 451597611 451600148 2537 True 3952 3952 94.973 1 2510 1 chr6D.!!$R2 2509
6 TraesCS5A01G017300 chr6D 459129171 459131678 2507 False 3949 3949 95.272 1 2482 1 chr6D.!!$F2 2481
7 TraesCS5A01G017300 chr6D 397851941 397854471 2530 True 3895 3895 94.625 1 2510 1 chr6D.!!$R1 2509
8 TraesCS5A01G017300 chr2D 54045016 54047557 2541 True 3951 3951 94.939 1 2510 1 chr2D.!!$R1 2509
9 TraesCS5A01G017300 chr5D 58007245 58009616 2371 True 3696 3696 95.002 1 2344 1 chr5D.!!$R1 2343
10 TraesCS5A01G017300 chr5D 391881314 391883823 2509 True 3688 3688 93.352 1 2493 1 chr5D.!!$R2 2492

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
657 676 0.038251 GATCCGCGTGATGCATCCTA 60.038 55.0 23.67 3.18 46.97 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2258 2334 2.234143 GGCTTTGGTTTGAGAGCTCTT 58.766 47.619 19.36 0.91 35.53 2.85 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
43 46 9.582431 TTTAATTCAAAACCGTCAAATAACACA 57.418 25.926 0.00 0.00 0.00 3.72
177 184 4.901785 AACCCTCTCTCCCTATTCTACA 57.098 45.455 0.00 0.00 0.00 2.74
309 318 4.411327 GCTATGTGCGCAAGAATTACAAA 58.589 39.130 14.00 0.00 43.02 2.83
527 545 2.239402 GGTCAAACCCTAATAACCCCGA 59.761 50.000 0.00 0.00 30.04 5.14
548 566 2.658593 CTCGCTCATAACCCCGCG 60.659 66.667 0.00 0.00 46.28 6.46
657 676 0.038251 GATCCGCGTGATGCATCCTA 60.038 55.000 23.67 3.18 46.97 2.94
682 701 1.273606 GCTACTGCACTGTCCTTCTCA 59.726 52.381 0.00 0.00 39.41 3.27
847 866 4.835056 TCTTCTCCATCTGACAGACAAAGA 59.165 41.667 7.47 7.75 0.00 2.52
874 895 2.961741 AGCAGATCGAGCAATTCCTCTA 59.038 45.455 2.38 0.00 0.00 2.43
876 897 3.925913 GCAGATCGAGCAATTCCTCTATC 59.074 47.826 2.38 3.25 35.44 2.08
944 965 1.030457 TTCTTCCTCTCGGGCGATAC 58.970 55.000 0.00 0.00 34.39 2.24
948 969 2.184830 CCTCTCGGGCGATACGTCA 61.185 63.158 0.00 0.00 30.88 4.35
998 1019 1.596934 CGGTGTATGGTCCAGTGCT 59.403 57.895 0.00 0.00 0.00 4.40
1080 1101 3.399305 AGGAGAAGAATGGGAACTTTGGT 59.601 43.478 0.00 0.00 0.00 3.67
1092 1113 0.311790 ACTTTGGTCGCGAGTTCGTA 59.688 50.000 10.24 0.00 42.22 3.43
1129 1150 1.480683 CGGAGGGGCAGGTTAGATCTA 60.481 57.143 0.00 0.00 0.00 1.98
1161 1185 6.420903 CGTCGCATCCTTTATCTAATTTCTCA 59.579 38.462 0.00 0.00 0.00 3.27
1285 1311 1.194121 GGGTTGGGCTTGCTGGATTT 61.194 55.000 0.00 0.00 0.00 2.17
1317 1343 2.744202 GCAATCCGTGAGTTCAATCTGT 59.256 45.455 0.00 0.00 0.00 3.41
1404 1430 4.319177 ACTGAAGACGGAATTGAAGAAGG 58.681 43.478 0.00 0.00 0.00 3.46
1610 1636 5.843673 ACTGTCGATCTCTGAATGTATGT 57.156 39.130 0.00 0.00 0.00 2.29
1750 1776 5.712446 AGATGACAGTAAGCAGTACTTGAGA 59.288 40.000 0.00 0.00 41.37 3.27
1835 1861 4.162812 GAGTTCGTCAGTTCTGCTAGAAG 58.837 47.826 0.00 0.00 34.42 2.85
1836 1862 3.821600 AGTTCGTCAGTTCTGCTAGAAGA 59.178 43.478 0.00 0.00 34.42 2.87
1911 1942 7.944554 ACAAAGGATAAATGAGGAGAAACAAGA 59.055 33.333 0.00 0.00 0.00 3.02
2007 2042 4.679373 TGCCCAATCTCTTCTATCTCAC 57.321 45.455 0.00 0.00 0.00 3.51
2381 2466 0.036306 AGCCGTGTCTAAACTTGGGG 59.964 55.000 0.00 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
177 184 4.695455 CACCTATGAACATGTTCGGAGTTT 59.305 41.667 27.68 16.36 42.28 2.66
417 434 8.211629 GTCCATTTATGAGACCTAGTTACCATT 58.788 37.037 0.00 0.00 0.00 3.16
548 566 1.751351 GCTAGGGTTTGGAGCATTTCC 59.249 52.381 0.00 0.00 46.98 3.13
657 676 1.352352 AGGACAGTGCAGTAGCCATTT 59.648 47.619 12.80 0.00 41.13 2.32
682 701 1.353022 TGGGGCAGATCGTAAAAACCT 59.647 47.619 0.00 0.00 0.00 3.50
874 895 2.703007 CGAGAAGATGGGGGAAAGAGAT 59.297 50.000 0.00 0.00 0.00 2.75
876 897 1.834263 ACGAGAAGATGGGGGAAAGAG 59.166 52.381 0.00 0.00 0.00 2.85
944 965 1.444553 GCTGACGAGGAGGTTGACG 60.445 63.158 0.00 0.00 0.00 4.35
948 969 3.003763 GGGGCTGACGAGGAGGTT 61.004 66.667 0.00 0.00 0.00 3.50
998 1019 3.332034 CAGTCAGTGCATTGAGTCATCA 58.668 45.455 16.01 0.00 0.00 3.07
1080 1101 0.364180 CGCATTTTACGAACTCGCGA 59.636 50.000 9.26 9.26 43.64 5.87
1129 1150 4.935808 AGATAAAGGATGCGACGAAAACTT 59.064 37.500 0.00 0.00 0.00 2.66
1285 1311 1.227102 CGGATTGCATTCCCCCTCA 59.773 57.895 19.46 0.00 31.61 3.86
1317 1343 3.315142 GAGCGGCACTGTCATGGGA 62.315 63.158 1.45 0.00 0.00 4.37
1404 1430 4.622701 ACTGCTTGAAGTTCTTGTTCAC 57.377 40.909 4.17 0.00 33.63 3.18
1433 1459 6.845758 ATCAGATTGGATTGCTTCTTCAAA 57.154 33.333 0.00 0.00 0.00 2.69
1610 1636 6.567050 AGTGTCGAAACTTGACAGTAAACTA 58.433 36.000 1.19 0.00 45.63 2.24
1750 1776 6.006275 ACTTGATGTATATCCCTTGTGCTT 57.994 37.500 0.00 0.00 32.09 3.91
1857 1885 6.093219 GTCTATTGCAGCTTGATTCTCTTTGA 59.907 38.462 0.00 0.00 0.00 2.69
2258 2334 2.234143 GGCTTTGGTTTGAGAGCTCTT 58.766 47.619 19.36 0.91 35.53 2.85
2381 2466 8.942924 GCTTTGTTATGTTTGTATTTTGTTTGC 58.057 29.630 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.