Multiple sequence alignment - TraesCS3B01G500800

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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 TraesCS3B01G500800 chr3B 100.000 2282 0 0 1 2282 745196490 745194209 0 4215
1 TraesCS3B01G500800 chr3B 85.101 2282 335 5 1 2281 181313060 181310783 0 2326
2 TraesCS3B01G500800 chr7B 95.048 2282 110 3 1 2281 244414560 244412281 0 3585
3 TraesCS3B01G500800 chr7D 93.602 2282 139 4 1 2281 383219418 383217143 0 3398
4 TraesCS3B01G500800 chr5B 94.365 1881 103 3 1 1880 137974837 137972959 0 2883
5 TraesCS3B01G500800 chr3D 86.128 2278 309 6 7 2281 126962316 126964589 0 2449
6 TraesCS3B01G500800 chr2B 94.757 1564 75 3 718 2281 250260887 250259331 0 2427
7 TraesCS3B01G500800 chr6B 92.608 1664 122 1 618 2281 195286478 195284816 0 2390
8 TraesCS3B01G500800 chr1A 85.589 2283 320 6 1 2281 242788930 242786655 0 2385
9 TraesCS3B01G500800 chr2D 85.573 2017 286 5 267 2281 239717902 239715889 0 2108


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 TraesCS3B01G500800 chr3B 745194209 745196490 2281 True 4215 4215 100.000 1 2282 1 chr3B.!!$R2 2281
1 TraesCS3B01G500800 chr3B 181310783 181313060 2277 True 2326 2326 85.101 1 2281 1 chr3B.!!$R1 2280
2 TraesCS3B01G500800 chr7B 244412281 244414560 2279 True 3585 3585 95.048 1 2281 1 chr7B.!!$R1 2280
3 TraesCS3B01G500800 chr7D 383217143 383219418 2275 True 3398 3398 93.602 1 2281 1 chr7D.!!$R1 2280
4 TraesCS3B01G500800 chr5B 137972959 137974837 1878 True 2883 2883 94.365 1 1880 1 chr5B.!!$R1 1879
5 TraesCS3B01G500800 chr3D 126962316 126964589 2273 False 2449 2449 86.128 7 2281 1 chr3D.!!$F1 2274
6 TraesCS3B01G500800 chr2B 250259331 250260887 1556 True 2427 2427 94.757 718 2281 1 chr2B.!!$R1 1563
7 TraesCS3B01G500800 chr6B 195284816 195286478 1662 True 2390 2390 92.608 618 2281 1 chr6B.!!$R1 1663
8 TraesCS3B01G500800 chr1A 242786655 242788930 2275 True 2385 2385 85.589 1 2281 1 chr1A.!!$R1 2280
9 TraesCS3B01G500800 chr2D 239715889 239717902 2013 True 2108 2108 85.573 267 2281 1 chr2D.!!$R1 2014

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
905 907 0.03438 CTCCCAGTCACCTACCTCGA 60.034 60.0 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1757 1763 1.143183 GGCGATCCAGGTTAGCGAA 59.857 57.895 0.0 0.0 0.0 4.7 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
132 134 2.974489 CTGCAAGCTCAACCAGGCG 61.974 63.158 0.00 0.00 0.00 5.52
396 398 0.469494 TGCTCAAGCTTGACCTCACA 59.531 50.000 25.16 14.54 42.66 3.58
431 433 3.618351 CCATATCATGGCCATTCCTCTC 58.382 50.000 17.92 0.00 44.70 3.20
528 530 0.035820 GGGTCCTGTTGAATGGCGTA 60.036 55.000 0.00 0.00 0.00 4.42
611 613 0.241749 TTCGTACTCGCGGTTGACAT 59.758 50.000 6.13 0.00 36.96 3.06
842 844 3.145551 CTTGCATGGGGAGCAGGC 61.146 66.667 0.00 0.00 43.75 4.85
874 876 3.567579 ATCACCGGCCTGGGTTGTG 62.568 63.158 16.44 7.00 44.64 3.33
875 877 4.579384 CACCGGCCTGGGTTGTGT 62.579 66.667 16.44 0.00 44.64 3.72
905 907 0.034380 CTCCCAGTCACCTACCTCGA 60.034 60.000 0.00 0.00 0.00 4.04
1125 1127 3.055385 TCGAGAAGATTCAACGGGGATTT 60.055 43.478 10.50 0.00 32.96 2.17
1126 1128 3.689649 CGAGAAGATTCAACGGGGATTTT 59.310 43.478 0.00 0.00 0.00 1.82
1372 1374 1.227943 CGTCATGGCCATCGGGAAT 60.228 57.895 17.61 0.00 35.59 3.01
1406 1408 0.394565 GTTCTGGGAGGATCGATGGG 59.605 60.000 0.54 0.00 34.37 4.00
1444 1446 1.144716 CGAGCTCATGCCCTTGCTA 59.855 57.895 15.40 0.00 40.80 3.49
1578 1580 4.340246 CCTGCAGCTCTGGCACCA 62.340 66.667 8.66 0.00 41.70 4.17
1579 1581 2.045242 CTGCAGCTCTGGCACCAT 60.045 61.111 0.00 0.00 41.70 3.55
1757 1763 3.641436 GAGGGTCAAGTTTTTCCATTGGT 59.359 43.478 1.86 0.00 0.00 3.67
1775 1781 1.143183 TTCGCTAACCTGGATCGCC 59.857 57.895 0.00 0.00 0.00 5.54
1834 1840 1.748329 ATCATCCGCGCTGCCTTCTA 61.748 55.000 5.56 0.00 0.00 2.10
1909 1915 2.046988 CAGGCATGGCACGAGACA 60.047 61.111 22.64 0.00 37.03 3.41
1919 1925 3.224324 ACGAGACACTGGCGTGGT 61.224 61.111 12.66 1.65 45.50 4.16
1933 1939 4.657408 TGGTTGCGCATCCCAGCA 62.657 61.111 29.76 19.57 42.15 4.41
1945 1951 0.399949 TCCCAGCACCGATCCCTAAT 60.400 55.000 0.00 0.00 0.00 1.73
2202 2208 1.293179 CATGGGACGTGCACTGAGA 59.707 57.895 16.19 0.00 0.00 3.27
2281 2287 5.276348 CCTGTTCAATGAAAAGAAACGCAAC 60.276 40.000 14.45 0.00 28.86 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 0.451783 GCAAGGAATTCGGCGTTGAT 59.548 50.000 6.85 0.00 34.12 2.57
132 134 2.099431 CGGCAGCAGAGTGAGAAGC 61.099 63.158 0.00 0.00 0.00 3.86
156 158 4.824515 AGCTCTAGGGCGTCGGCT 62.825 66.667 19.00 7.32 39.81 5.52
396 398 0.032130 ATATGGAGTCGAATGCGCGT 59.968 50.000 8.43 0.00 37.46 6.01
431 433 0.107456 ATATTGGCGCAGGACCTCAG 59.893 55.000 10.83 0.00 0.00 3.35
528 530 1.378762 CCAAATCGGTGGTCCTGGT 59.621 57.895 0.00 0.00 33.63 4.00
611 613 3.849951 GAATCAGCCGGCCGAGGA 61.850 66.667 30.73 20.92 0.00 3.71
788 790 4.157289 TCTTCGCGTAATTAACTCTGAGGT 59.843 41.667 5.77 4.80 0.00 3.85
794 796 3.178033 CGAGCTCTTCGCGTAATTAACTC 59.822 47.826 12.85 5.21 43.22 3.01
842 844 1.805495 CGGTGATGATCTCAGTGGCAG 60.805 57.143 0.00 0.00 33.51 4.85
905 907 1.153901 CGCGTCGTCAAGGGTATGT 60.154 57.895 0.00 0.00 0.00 2.29
1020 1022 3.966026 GACCGACTTGACGAGGGCG 62.966 68.421 0.00 0.00 44.79 6.13
1125 1127 1.752694 GCTCGCCCAGCCCATAAAA 60.753 57.895 0.00 0.00 43.17 1.52
1126 1128 2.124320 GCTCGCCCAGCCCATAAA 60.124 61.111 0.00 0.00 43.17 1.40
1690 1696 1.077993 AGCTTCCAGGAGTAGGAGTGT 59.922 52.381 0.00 0.00 36.33 3.55
1757 1763 1.143183 GGCGATCCAGGTTAGCGAA 59.857 57.895 0.00 0.00 0.00 4.70
1933 1939 1.343069 GCTCCTGATTAGGGATCGGT 58.657 55.000 3.28 0.00 44.70 4.69
1945 1951 1.997311 CATGAGGGTGGGCTCCTGA 60.997 63.158 0.00 0.00 34.21 3.86
1986 1992 4.012895 GTGCTTGTGGCGTGTCGG 62.013 66.667 0.00 0.00 45.43 4.79
2202 2208 7.595502 CGAATAAAGCGAGGATAAGATACAAGT 59.404 37.037 0.00 0.00 0.00 3.16
2240 2246 3.853207 ACAGGTAGGGAGTCAGTTACAA 58.147 45.455 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.