Multiple sequence alignment - TraesCS5D01G180400

Loading Multiple Alignment...

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 TraesCS5D01G180400 chr5D 100.000 2581 0 0 1 2581 280782128 280784708 0.000000e+00 4767
1 TraesCS5D01G180400 chr5B 93.825 2494 85 32 108 2581 318399574 318402018 0.000000e+00 3688
2 TraesCS5D01G180400 chr5A 98.567 977 14 0 1605 2581 371031145 371030169 0.000000e+00 1727
3 TraesCS5D01G180400 chr5A 88.655 1331 119 14 108 1416 371032945 371031625 0.000000e+00 1592
4 TraesCS5D01G180400 chr5A 91.228 114 8 2 4 115 371033081 371032968 1.240000e-33 154
5 TraesCS5D01G180400 chr5A 79.121 182 34 3 11 190 558241798 558241977 3.490000e-24 122


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 TraesCS5D01G180400 chr5D 280782128 280784708 2580 False 4767.000000 4767 100.000000 1 2581 1 chr5D.!!$F1 2580
1 TraesCS5D01G180400 chr5B 318399574 318402018 2444 False 3688.000000 3688 93.825000 108 2581 1 chr5B.!!$F1 2473
2 TraesCS5D01G180400 chr5A 371030169 371033081 2912 True 1157.666667 1727 92.816667 4 2581 3 chr5A.!!$R1 2577

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
267 301 0.810648 CCGGTGTGTCATGAAATGGG 59.189 55.0 0.0 0.0 46.73 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1603 1966 1.067354 GCCCAAAGCTGTTCTTCATGG 60.067 52.381 0.0 0.0 38.99 3.66 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
70 72 5.012046 TCAGAGAGAATACTTTCAACCTGCA 59.988 40.000 0.00 0.00 34.08 4.41
75 77 7.168219 AGAGAATACTTTCAACCTGCACATAA 58.832 34.615 0.00 0.00 34.08 1.90
78 80 9.632638 AGAATACTTTCAACCTGCACATAATAT 57.367 29.630 0.00 0.00 34.08 1.28
79 81 9.669353 GAATACTTTCAACCTGCACATAATATG 57.331 33.333 0.00 0.00 0.00 1.78
85 87 5.535783 TCAACCTGCACATAATATGGATTGG 59.464 40.000 5.16 4.55 33.60 3.16
119 152 5.335976 GGTGATTCACTTGAGGGAAATTGTC 60.336 44.000 16.02 0.00 34.40 3.18
130 163 3.118371 AGGGAAATTGTCGATGTCCTACC 60.118 47.826 8.94 0.00 41.36 3.18
146 179 2.146342 CTACCATCTTATGCGCTTGGG 58.854 52.381 9.73 3.07 0.00 4.12
154 187 2.418368 TATGCGCTTGGGAGACAAAT 57.582 45.000 9.73 0.00 38.91 2.32
205 239 3.495331 ACATCAGGCGAGTCTAGATCAT 58.505 45.455 0.00 0.00 0.00 2.45
207 241 4.699735 ACATCAGGCGAGTCTAGATCATAG 59.300 45.833 0.00 0.00 0.00 2.23
260 294 1.448540 GAGAGGCCGGTGTGTCATG 60.449 63.158 1.90 0.00 0.00 3.07
267 301 0.810648 CCGGTGTGTCATGAAATGGG 59.189 55.000 0.00 0.00 46.73 4.00
285 319 1.676006 GGGTATCAAAGCCAACCATCG 59.324 52.381 0.00 0.00 45.71 3.84
292 326 2.128771 AAGCCAACCATCGCAGTTAT 57.871 45.000 0.00 0.00 0.00 1.89
317 351 2.434336 GACATGTGCAGATAGGGGTACA 59.566 50.000 1.15 0.00 34.21 2.90
327 361 4.593206 CAGATAGGGGTACATACATGTGGT 59.407 45.833 9.11 9.36 41.89 4.16
372 418 3.434319 CACCGCATGGCACTGGAC 61.434 66.667 8.33 0.00 39.70 4.02
395 443 5.057843 ACATGGATGTGCTAAGATGGAAT 57.942 39.130 0.00 0.00 40.03 3.01
437 485 3.265995 GGGTGTCAGATCCTTTTAAGGGA 59.734 47.826 8.60 0.00 46.47 4.20
454 502 2.768527 AGGGAGTGTATGTGACATCCTG 59.231 50.000 0.00 0.00 41.14 3.86
466 514 5.741011 TGTGACATCCTGGTTAAATAGGAC 58.259 41.667 10.30 1.37 45.30 3.85
470 518 6.127054 TGACATCCTGGTTAAATAGGACTGAG 60.127 42.308 10.30 5.28 45.30 3.35
526 577 6.879458 ACTCATATTAACAAGGTGTGTCTTCC 59.121 38.462 0.00 0.00 40.60 3.46
531 582 6.844097 TTAACAAGGTGTGTCTTCCTTTTT 57.156 33.333 0.00 0.00 40.60 1.94
533 584 4.340617 ACAAGGTGTGTCTTCCTTTTTGA 58.659 39.130 0.00 0.00 41.44 2.69
550 601 8.774586 TCCTTTTTGAAAGATCGTCTCTAAAAG 58.225 33.333 20.76 20.76 39.49 2.27
567 621 9.148879 TCTCTAAAAGACCTCTGGATTATAAGG 57.851 37.037 0.00 0.00 34.94 2.69
605 659 6.903883 ACAATTTAGACGCTCGTATTGATT 57.096 33.333 17.30 7.02 0.00 2.57
611 665 3.924686 AGACGCTCGTATTGATTTTCGTT 59.075 39.130 0.00 0.00 0.00 3.85
736 791 2.550606 TGTATGAAGCCGGTGTGTTTTC 59.449 45.455 1.90 0.00 0.00 2.29
926 983 3.633116 TGCTCTCAGCTGCAGCCA 61.633 61.111 34.39 21.00 42.97 4.75
1007 1064 1.002134 AAGGTGCGACAATGGGGAG 60.002 57.895 0.00 0.00 0.00 4.30
1501 1651 3.000825 GTCATATGAACGCATGTAACGCA 59.999 43.478 7.07 0.00 35.94 5.24
1594 1747 2.310538 CAGGTGAAATAGAATGGGGGC 58.689 52.381 0.00 0.00 0.00 5.80
1596 1749 2.091665 AGGTGAAATAGAATGGGGGCAG 60.092 50.000 0.00 0.00 0.00 4.85
1603 1966 0.332972 AGAATGGGGGCAGACCTTTC 59.667 55.000 0.00 10.65 40.53 2.62
1704 2067 9.553064 AGATACAATCACTTTAATGACAGATCC 57.447 33.333 0.00 0.00 0.00 3.36
1978 2341 3.077088 TCTCTACCCCTTCACCTACACTT 59.923 47.826 0.00 0.00 0.00 3.16
2363 2726 2.159037 CCATCGATCAAAGATGATGCGG 59.841 50.000 9.81 0.00 46.30 5.69
2542 2905 2.102925 TCGGGAAAACTGGTAAACGACT 59.897 45.455 0.00 0.00 0.00 4.18
2543 2906 2.477754 CGGGAAAACTGGTAAACGACTC 59.522 50.000 0.00 0.00 0.00 3.36
2546 2909 4.212847 GGGAAAACTGGTAAACGACTCTTC 59.787 45.833 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 45 7.572168 GCAGGTTGAAAGTATTCTCTCTGAAAC 60.572 40.741 0.00 0.00 38.29 2.78
47 49 5.121454 GTGCAGGTTGAAAGTATTCTCTCTG 59.879 44.000 0.00 0.00 36.48 3.35
78 80 7.556275 GTGAATCACCTTAGATTTACCAATCCA 59.444 37.037 1.10 0.00 39.95 3.41
79 81 7.775561 AGTGAATCACCTTAGATTTACCAATCC 59.224 37.037 10.12 0.00 42.30 3.01
85 87 7.281100 CCCTCAAGTGAATCACCTTAGATTTAC 59.719 40.741 10.12 0.00 41.91 2.01
98 100 4.695455 TCGACAATTTCCCTCAAGTGAATC 59.305 41.667 0.00 0.00 0.00 2.52
130 163 1.869767 GTCTCCCAAGCGCATAAGATG 59.130 52.381 11.47 0.00 0.00 2.90
146 179 8.709386 TCTATTCTTGCAGACTTATTTGTCTC 57.291 34.615 0.00 0.00 44.56 3.36
154 187 5.874810 ACGCATTTCTATTCTTGCAGACTTA 59.125 36.000 0.00 0.00 34.80 2.24
161 195 6.018751 TGTCTATCACGCATTTCTATTCTTGC 60.019 38.462 0.00 0.00 0.00 4.01
170 204 3.059325 GCCTGATGTCTATCACGCATTTC 60.059 47.826 0.00 0.00 41.81 2.17
176 210 1.335182 ACTCGCCTGATGTCTATCACG 59.665 52.381 0.00 0.00 38.37 4.35
205 239 4.833380 GTCATTACTCCTGGCTATCACCTA 59.167 45.833 0.00 0.00 0.00 3.08
207 241 3.244249 GGTCATTACTCCTGGCTATCACC 60.244 52.174 0.00 0.00 0.00 4.02
260 294 3.513515 TGGTTGGCTTTGATACCCATTTC 59.486 43.478 0.00 0.00 0.00 2.17
267 301 1.742831 TGCGATGGTTGGCTTTGATAC 59.257 47.619 0.00 0.00 0.00 2.24
282 316 3.748048 GCACATGTCCATATAACTGCGAT 59.252 43.478 0.00 0.00 0.00 4.58
285 319 4.129380 TCTGCACATGTCCATATAACTGC 58.871 43.478 0.00 0.00 0.00 4.40
292 326 2.639347 CCCCTATCTGCACATGTCCATA 59.361 50.000 0.00 0.00 0.00 2.74
390 438 1.342819 CGGCCCAAAAGAAACATTCCA 59.657 47.619 0.00 0.00 0.00 3.53
395 443 0.464013 TCGTCGGCCCAAAAGAAACA 60.464 50.000 0.00 0.00 0.00 2.83
437 485 5.755409 TTAACCAGGATGTCACATACACT 57.245 39.130 1.88 0.00 42.09 3.55
454 502 9.668497 ATGAAAACTACTCAGTCCTATTTAACC 57.332 33.333 0.00 0.00 32.29 2.85
466 514 9.838339 ATCCTATTAACCATGAAAACTACTCAG 57.162 33.333 0.00 0.00 0.00 3.35
509 560 5.946972 TCAAAAAGGAAGACACACCTTGTTA 59.053 36.000 0.00 0.00 44.44 2.41
526 577 9.587461 GTCTTTTAGAGACGATCTTTCAAAAAG 57.413 33.333 14.82 14.82 44.90 2.27
605 659 5.499139 AGTTGAATGCTTGAAGAACGAAA 57.501 34.783 0.00 0.00 0.00 3.46
611 665 3.254166 GCCAGAAGTTGAATGCTTGAAGA 59.746 43.478 0.00 0.00 0.00 2.87
736 791 3.118261 TGTTCTGCTTTAGCTGGATAGGG 60.118 47.826 0.00 0.00 42.66 3.53
926 983 8.566979 ACATACCCCTACTACTGCATATATAGT 58.433 37.037 0.00 0.00 33.73 2.12
1501 1651 5.144100 TCTGAGAAAACAGAGAAGGAGTCT 58.856 41.667 0.00 0.00 41.21 3.24
1556 1709 2.709475 GATTGTGTCCGCGGATGC 59.291 61.111 33.58 25.80 37.91 3.91
1588 1741 1.856873 ATGGAAAGGTCTGCCCCCA 60.857 57.895 0.00 0.00 35.00 4.96
1594 1747 3.190118 GCTGTTCTTCATGGAAAGGTCTG 59.810 47.826 0.00 0.00 0.00 3.51
1596 1749 3.416156 AGCTGTTCTTCATGGAAAGGTC 58.584 45.455 0.00 0.00 0.00 3.85
1603 1966 1.067354 GCCCAAAGCTGTTCTTCATGG 60.067 52.381 0.00 0.00 38.99 3.66
1704 2067 6.403636 GGAATAGGTGTAGAACAATGTTGCTG 60.404 42.308 2.20 0.00 0.00 4.41
1826 2189 8.709646 ACGTTCTGTATAATCTTTTGACACTTC 58.290 33.333 0.00 0.00 0.00 3.01
1978 2341 8.439993 TGTCACAGCTGTTGTAAAATTACTAA 57.560 30.769 18.94 0.00 38.16 2.24
2178 2541 2.813754 AGCGCTCAAGCAATTGTTTCTA 59.186 40.909 2.64 0.00 42.21 2.10
2542 2905 3.327757 ACCAGTTCCACTGCAATAGAAGA 59.672 43.478 0.00 0.00 44.63 2.87
2543 2906 3.679389 ACCAGTTCCACTGCAATAGAAG 58.321 45.455 0.00 0.00 44.63 2.85
2546 2909 3.375299 GCTTACCAGTTCCACTGCAATAG 59.625 47.826 0.00 0.00 44.63 1.73


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

AutoCloner maintained by Alex Coulton.