Multiple sequence alignment - TraesCS5D01G345200

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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 TraesCS5D01G345200 chr5D 100.000 2255 0 0 1 2255 432393296 432395550 0 4165
1 TraesCS5D01G345200 chr5D 97.120 2257 61 4 1 2255 503239095 503236841 0 3805
2 TraesCS5D01G345200 chr5D 97.076 2257 59 5 1 2255 503243341 503241090 0 3795
3 TraesCS5D01G345200 chr5D 97.031 2257 61 4 1 2255 503229314 503227062 0 3792
4 TraesCS5D01G345200 chr5D 96.987 2257 59 4 1 2255 503267233 503269482 0 3783
5 TraesCS5D01G345200 chr6D 97.297 2257 58 3 1 2255 389255238 389252983 0 3827
6 TraesCS5D01G345200 chr6D 97.209 2257 60 3 1 2255 389250443 389248188 0 3816
7 TraesCS5D01G345200 chr3D 97.076 2257 62 4 1 2255 589265454 589267708 0 3799
8 TraesCS5D01G345200 chr3A 97.076 2257 62 4 1 2255 66007063 66009317 0 3799
9 TraesCS5D01G345200 chr7B 96.943 2257 66 3 1 2255 662724473 662722218 0 3783


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 TraesCS5D01G345200 chr5D 432393296 432395550 2254 False 4165.0 4165 100.000 1 2255 1 chr5D.!!$F1 2254
1 TraesCS5D01G345200 chr5D 503236841 503243341 6500 True 3800.0 3805 97.098 1 2255 2 chr5D.!!$R2 2254
2 TraesCS5D01G345200 chr5D 503227062 503229314 2252 True 3792.0 3792 97.031 1 2255 1 chr5D.!!$R1 2254
3 TraesCS5D01G345200 chr5D 503267233 503269482 2249 False 3783.0 3783 96.987 1 2255 1 chr5D.!!$F2 2254
4 TraesCS5D01G345200 chr6D 389248188 389255238 7050 True 3821.5 3827 97.253 1 2255 2 chr6D.!!$R1 2254
5 TraesCS5D01G345200 chr3D 589265454 589267708 2254 False 3799.0 3799 97.076 1 2255 1 chr3D.!!$F1 2254
6 TraesCS5D01G345200 chr3A 66007063 66009317 2254 False 3799.0 3799 97.076 1 2255 1 chr3A.!!$F1 2254
7 TraesCS5D01G345200 chr7B 662722218 662724473 2255 True 3783.0 3783 96.943 1 2255 1 chr7B.!!$R1 2254

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
849 5100 0.036875 CTTCCTCCGGGCTGTCTTTT 59.963 55.0 0.0 0.0 0.0 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1737 10783 0.928229 CACGGTAGCAATAGAACGGC 59.072 55.0 0.0 0.0 0.0 5.68 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
37 38 6.266786 TGCTTATTCCTCAGATACCGTCATTA 59.733 38.462 0.00 0.00 0.00 1.90
46 47 7.928706 CCTCAGATACCGTCATTATTTCTTCTT 59.071 37.037 0.00 0.00 0.00 2.52
53 54 6.310711 ACCGTCATTATTTCTTCTTCGAGAAC 59.689 38.462 0.00 0.00 35.50 3.01
113 114 2.094757 TTGCTCCGTCAGGCTTTCGA 62.095 55.000 9.22 0.00 37.47 3.71
145 146 4.980592 TCCCCACTGCTGCCTCCA 62.981 66.667 0.00 0.00 0.00 3.86
353 355 1.566231 CTCCCAAGGGCAGGTTCTTAT 59.434 52.381 0.00 0.00 34.68 1.73
377 379 1.466025 TACTCACCCGTTCGCCACTT 61.466 55.000 0.00 0.00 0.00 3.16
396 398 4.030216 ACTTGAAACACCACTTCCCATTT 58.970 39.130 0.00 0.00 0.00 2.32
450 452 4.844420 CTGAGCCAGGATCGAACC 57.156 61.111 2.97 2.97 0.00 3.62
511 513 7.389330 TCCTTATTCGTAAACAAAGCAGATTCA 59.611 33.333 0.00 0.00 0.00 2.57
529 531 5.645497 AGATTCAGAATTGTCTTTCCTTCCG 59.355 40.000 0.00 0.00 28.78 4.30
532 534 4.283467 TCAGAATTGTCTTTCCTTCCGAGA 59.717 41.667 0.00 0.00 28.78 4.04
568 570 4.600692 TGCGCTTCAGATTATTAGCCTA 57.399 40.909 9.73 0.00 0.00 3.93
583 585 1.605058 GCCTAGAGTTCGCCACCAGA 61.605 60.000 0.00 0.00 0.00 3.86
606 608 4.426704 AGTATAGCCAACCCTACCCTATG 58.573 47.826 0.00 0.00 0.00 2.23
644 646 2.102588 CCTCTTATCCATTCCCGTTCGT 59.897 50.000 0.00 0.00 0.00 3.85
727 729 2.567169 TCGAACTGATGACTTCCACCAT 59.433 45.455 0.00 0.00 0.00 3.55
780 5031 1.075525 TTCCCCGTCCCATCGAGAT 60.076 57.895 0.00 0.00 0.00 2.75
808 5059 7.110155 AGAATTAACGAATCCTAAGGCAAAGA 58.890 34.615 0.00 0.00 0.00 2.52
843 5094 2.581354 CACTCTTCCTCCGGGCTG 59.419 66.667 0.00 0.00 0.00 4.85
849 5100 0.036875 CTTCCTCCGGGCTGTCTTTT 59.963 55.000 0.00 0.00 0.00 2.27
916 5167 4.819105 TGTCAACTGGTCCTATCGAAAT 57.181 40.909 0.00 0.00 0.00 2.17
1054 5305 2.715763 ACTGGTAGGAGAAGAACCCA 57.284 50.000 0.00 0.00 31.97 4.51
1223 5474 1.593196 CACGCCCTTTTCTTGAGACA 58.407 50.000 0.00 0.00 0.00 3.41
1255 5506 8.816894 ACATGAGGACAAATTACTTCTCTTAGA 58.183 33.333 0.00 0.00 0.00 2.10
1427 10473 6.697395 TGTAGAAAGACTGATTCATTCGGAA 58.303 36.000 0.00 0.00 37.08 4.30
1755 10801 0.526954 CGCCGTTCTATTGCTACCGT 60.527 55.000 0.00 0.00 0.00 4.83
1779 10825 3.997021 GGTCTTATGCAATCGATCGGATT 59.003 43.478 16.41 10.72 46.29 3.01
1843 10889 0.670546 CGGACGACTCACCAAAGCAT 60.671 55.000 0.00 0.00 0.00 3.79
1923 10969 5.768317 CTCACATTAACCCGTCAATTTTGT 58.232 37.500 0.00 0.00 0.00 2.83
1955 11001 4.038642 CGGGATTTTTCTTGGGAAGTTTCA 59.961 41.667 0.00 0.00 32.61 2.69
2021 11067 4.832248 AGGTTCTCTATTGATGCAAACGA 58.168 39.130 0.00 0.00 0.00 3.85
2167 11214 5.523188 CGAAAAGGATCCTTCTGATTCTCAG 59.477 44.000 27.20 10.60 45.59 3.35
2201 11248 4.718961 CAAGGGGATTGATACCGAGAAAT 58.281 43.478 0.00 0.00 41.83 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 2.287427 GGTCGTCAACTTCTGTTCTCGA 60.287 50.000 0.00 0.00 36.63 4.04
53 54 1.402456 CCTACGGGTCGTCAACTTCTG 60.402 57.143 0.00 0.00 41.54 3.02
145 146 0.624785 ACACGGCCTAGACTCCTACT 59.375 55.000 0.00 0.00 0.00 2.57
156 157 2.997897 GGGACTGAGACACGGCCT 60.998 66.667 0.00 0.00 0.00 5.19
190 191 2.025155 GATCAGTAGCTGGTCCGAGAA 58.975 52.381 0.00 0.00 35.74 2.87
267 268 0.451783 CAAAAGGAGAAATCCGCCCG 59.548 55.000 0.00 0.00 35.03 6.13
353 355 1.372004 CGAACGGGTGAGTAACGCA 60.372 57.895 0.00 0.00 41.73 5.24
377 379 3.383185 GTCAAATGGGAAGTGGTGTTTCA 59.617 43.478 0.00 0.00 0.00 2.69
396 398 4.163458 CATGCTTAACACATGCAAGTCA 57.837 40.909 0.00 0.00 40.37 3.41
450 452 4.711399 TGCAACTATGAATCTCATGGAGG 58.289 43.478 6.97 0.73 37.52 4.30
497 499 6.645790 AGACAATTCTGAATCTGCTTTGTT 57.354 33.333 2.92 0.00 0.00 2.83
511 513 4.891992 TCTCGGAAGGAAAGACAATTCT 57.108 40.909 0.00 0.00 0.00 2.40
568 570 1.629043 TACTTCTGGTGGCGAACTCT 58.371 50.000 0.00 0.00 0.00 3.24
583 585 3.433088 AGGGTAGGGTTGGCTATACTT 57.567 47.619 0.00 0.00 0.00 2.24
606 608 0.321653 AGGCTTGTGGGATTGACGTC 60.322 55.000 9.11 9.11 0.00 4.34
644 646 2.604079 TTACTCCCCCGCCACGAA 60.604 61.111 0.00 0.00 0.00 3.85
780 5031 7.356089 TGCCTTAGGATTCGTTAATTCTCTA 57.644 36.000 0.69 0.00 32.81 2.43
808 5059 1.003233 GGCCTTGAGTTTCTCGCCT 60.003 57.895 0.00 0.00 33.70 5.52
916 5167 5.279506 GGCTCGAATCCATAGTCAATCCTAA 60.280 44.000 0.00 0.00 0.00 2.69
1022 5273 5.699915 TCTCCTACCAGTATCGAATAGAACG 59.300 44.000 0.00 0.00 0.00 3.95
1223 5474 7.607991 AGAAGTAATTTGTCCTCATGTTTCGAT 59.392 33.333 0.00 0.00 0.00 3.59
1255 5506 8.079809 CCGTTATCCTTTTTCTTGTATGTGTTT 58.920 33.333 0.00 0.00 0.00 2.83
1392 5643 5.775195 TCAGTCTTTCTACAGAGGTCAATCA 59.225 40.000 0.00 0.00 0.00 2.57
1427 10473 2.040178 GGAGTTGGGTCCTCATATCGT 58.960 52.381 0.00 0.00 33.30 3.73
1526 10572 0.912006 GAGGAGAAAGGGGGCTCAGT 60.912 60.000 0.00 0.00 32.83 3.41
1718 10764 5.416947 ACGGCGAAAGTATACAGAAAAGAT 58.583 37.500 16.62 0.00 0.00 2.40
1737 10783 0.928229 CACGGTAGCAATAGAACGGC 59.072 55.000 0.00 0.00 0.00 5.68
1755 10801 2.547855 CCGATCGATTGCATAAGACCCA 60.548 50.000 18.66 0.00 0.00 4.51
1800 10846 7.139392 CGAGATCTTTTCGATGACCTATGTTA 58.861 38.462 0.00 0.00 40.36 2.41
1843 10889 6.071391 GGAATCCATTTTCTAACTGGCTTTCA 60.071 38.462 0.00 0.00 0.00 2.69
1881 10927 3.324846 TGAGCTTATCCATGCGGTTAGAT 59.675 43.478 0.00 0.00 0.00 1.98
1882 10928 2.698274 TGAGCTTATCCATGCGGTTAGA 59.302 45.455 0.00 0.00 0.00 2.10
1923 10969 5.362430 CCCAAGAAAAATCCCGAATTGGATA 59.638 40.000 2.72 0.00 44.49 2.59
2021 11067 6.391649 CCTCTATCCCTATCCTCTAGGTACAT 59.608 46.154 0.00 0.00 36.34 2.29
2094 11141 5.141182 TGGGCTCTTCTATCTTCGACTTAT 58.859 41.667 0.00 0.00 0.00 1.73
2167 11214 1.228510 CCCCTTGCCCCTCATTCTC 59.771 63.158 0.00 0.00 0.00 2.87
2220 11267 7.036829 CCAAACATATGCAGATCAAATCACAA 58.963 34.615 1.58 0.00 0.00 3.33
2221 11268 6.153170 ACCAAACATATGCAGATCAAATCACA 59.847 34.615 1.58 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.