Multiple sequence alignment - TraesCS3A01G430500

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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 TraesCS3A01G430500 chr3A 100.000 2372 0 0 1 2372 672888703 672886332 0.000000e+00 4381
1 TraesCS3A01G430500 chr3A 98.253 2289 38 2 1 2288 66004937 66002650 0.000000e+00 4004
2 TraesCS3A01G430500 chr6D 98.037 2292 42 2 1 2289 389245626 389243335 0.000000e+00 3980
3 TraesCS3A01G430500 chr6D 96.739 92 3 0 2281 2372 389243258 389243167 1.140000e-33 154
4 TraesCS3A01G430500 chr5D 97.993 2292 43 2 1 2289 503264580 503262289 0.000000e+00 3975
5 TraesCS3A01G430500 chr5D 97.987 2285 45 1 1 2284 503245468 503247752 0.000000e+00 3964
6 TraesCS3A01G430500 chr2A 97.949 2292 44 2 1 2289 726906259 726903968 0.000000e+00 3969
7 TraesCS3A01G430500 chr3D 97.906 2292 44 3 1 2289 589263330 589261040 0.000000e+00 3964
8 TraesCS3A01G430500 chr3D 96.739 92 3 0 2281 2372 80427179 80427088 1.140000e-33 154
9 TraesCS3A01G430500 chr2D 97.987 2285 45 1 1 2284 591984805 591987089 0.000000e+00 3964
10 TraesCS3A01G430500 chr7B 97.818 2292 47 2 1 2289 663099229 663096938 0.000000e+00 3952
11 TraesCS3A01G430500 chr1D 97.775 2292 48 2 1 2289 459904521 459902230 0.000000e+00 3947
12 TraesCS3A01G430500 chr1D 96.739 92 3 0 2281 2372 459902153 459902062 1.140000e-33 154
13 TraesCS3A01G430500 chrUn 96.739 92 3 0 2281 2372 414708681 414708772 1.140000e-33 154
14 TraesCS3A01G430500 chrUn 96.739 92 3 0 2281 2372 428084328 428084237 1.140000e-33 154
15 TraesCS3A01G430500 chrUn 96.739 92 3 0 2281 2372 461211080 461210989 1.140000e-33 154
16 TraesCS3A01G430500 chr7D 96.739 92 3 0 2281 2372 231543574 231543665 1.140000e-33 154
17 TraesCS3A01G430500 chr7D 96.739 92 3 0 2281 2372 231551374 231551465 1.140000e-33 154
18 TraesCS3A01G430500 chr6B 95.789 95 4 0 2278 2372 450080150 450080244 1.140000e-33 154


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 TraesCS3A01G430500 chr3A 672886332 672888703 2371 True 4381.0 4381 100.000 1 2372 1 chr3A.!!$R2 2371
1 TraesCS3A01G430500 chr3A 66002650 66004937 2287 True 4004.0 4004 98.253 1 2288 1 chr3A.!!$R1 2287
2 TraesCS3A01G430500 chr6D 389243167 389245626 2459 True 2067.0 3980 97.388 1 2372 2 chr6D.!!$R1 2371
3 TraesCS3A01G430500 chr5D 503262289 503264580 2291 True 3975.0 3975 97.993 1 2289 1 chr5D.!!$R1 2288
4 TraesCS3A01G430500 chr5D 503245468 503247752 2284 False 3964.0 3964 97.987 1 2284 1 chr5D.!!$F1 2283
5 TraesCS3A01G430500 chr2A 726903968 726906259 2291 True 3969.0 3969 97.949 1 2289 1 chr2A.!!$R1 2288
6 TraesCS3A01G430500 chr3D 589261040 589263330 2290 True 3964.0 3964 97.906 1 2289 1 chr3D.!!$R2 2288
7 TraesCS3A01G430500 chr2D 591984805 591987089 2284 False 3964.0 3964 97.987 1 2284 1 chr2D.!!$F1 2283
8 TraesCS3A01G430500 chr7B 663096938 663099229 2291 True 3952.0 3952 97.818 1 2289 1 chr7B.!!$R1 2288
9 TraesCS3A01G430500 chr1D 459902062 459904521 2459 True 2050.5 3947 97.257 1 2372 2 chr1D.!!$R1 2371

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
691 693 1.379527 CTCTCCGGTTGGGCATTAAC 58.62 55.0 0.0 0.0 35.24 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2148 2150 1.07975 GTCTCACTGGCCGACCTTC 60.08 63.158 0.0 0.0 36.63 3.46 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
142 144 3.525537 ACTCTTTCATGCATACTCCACG 58.474 45.455 0.00 0.0 0.00 4.94
239 241 3.808174 GTCTAATTGTCCAGGCGGTAATC 59.192 47.826 0.00 0.0 0.00 1.75
309 311 3.350833 GAAGAGGACTGAAACATGCCAT 58.649 45.455 0.00 0.0 0.00 4.40
425 427 2.029623 GATAGTTGGAGTCGGTGGCTA 58.970 52.381 0.00 0.0 0.00 3.93
687 689 4.473520 CGCTCTCCGGTTGGGCAT 62.474 66.667 18.83 0.0 35.24 4.40
691 693 1.379527 CTCTCCGGTTGGGCATTAAC 58.620 55.000 0.00 0.0 35.24 2.01
902 904 3.119459 GGAGAGCACAGTACGATGAAAGA 60.119 47.826 3.82 0.0 0.00 2.52
916 918 5.470098 ACGATGAAAGATGTAAGCTGTGTTT 59.530 36.000 0.00 0.0 24.31 2.83
1117 1119 7.172019 CGATCTATGATTTCACATTCATGGACA 59.828 37.037 1.78 0.0 40.97 4.02
1237 1239 1.984570 CCAGAGACGAGGAAGGGCA 60.985 63.158 0.00 0.0 0.00 5.36
1361 1363 0.951040 GAGACAACCTGGCGAACTGG 60.951 60.000 0.00 0.0 43.37 4.00
1471 1473 2.084546 GGTTGTGGGAGAGCAATACAC 58.915 52.381 0.00 0.0 0.00 2.90
1708 1710 6.370718 GTGGGTAGTGAAATAGAACGTGAAAT 59.629 38.462 0.00 0.0 0.00 2.17
1812 1814 0.766131 TGGCTTGGTTAAGGGAACGA 59.234 50.000 0.00 0.0 39.12 3.85
1830 1832 2.453379 GAAACCCACCGGAGCCGTAA 62.453 60.000 9.46 0.0 37.81 3.18
1851 1853 4.978083 ACGAAAGCGAGTCTTAATAGGA 57.022 40.909 0.00 0.0 41.64 2.94
1901 1903 3.392285 CTGGGTGATCTATCCATGACCAA 59.608 47.826 0.00 0.0 0.00 3.67
2065 2067 4.264668 TGACTGGACATCTAGGGGTAAAGA 60.265 45.833 0.00 0.0 0.00 2.52
2084 2086 3.423154 CTGTTTCGGTGCGGGCTC 61.423 66.667 0.00 0.0 0.00 4.70
2200 2202 2.482142 GCTTCATCGTCGAGAGGGAAAT 60.482 50.000 0.00 0.0 0.00 2.17
2234 2236 2.173569 CAGCTAAGGCCCCTAAATGACT 59.826 50.000 0.00 0.0 39.73 3.41
2290 2379 0.036388 CAGGAGGTTTGCCGAAGCTA 60.036 55.000 0.00 0.0 45.64 3.32
2363 2452 4.367023 CGAAAGCGGGGGTCGACA 62.367 66.667 18.91 0.0 42.43 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.257936 CGTGAAGTAAATCATCGCCCG 59.742 52.381 0.00 0.00 0.00 6.13
239 241 5.068723 ACCGGTTCAGGTACAAGATACTATG 59.931 44.000 0.00 0.00 43.89 2.23
309 311 8.258007 TCTTTTTGTCTCAGTAGAGTCTTTCAA 58.742 33.333 0.00 0.00 42.66 2.69
425 427 2.618794 CAGATGAGGGAAGCCTAGGAT 58.381 52.381 14.75 1.88 0.00 3.24
611 613 2.687566 GGTCCGTGACCCCTGGAT 60.688 66.667 10.92 0.00 46.19 3.41
665 667 3.744719 CAACCGGAGAGCGGACGA 61.745 66.667 9.46 0.00 0.00 4.20
687 689 1.186917 TGCCCTTCTCCGACCGTTAA 61.187 55.000 0.00 0.00 0.00 2.01
691 693 1.521681 GATTGCCCTTCTCCGACCG 60.522 63.158 0.00 0.00 0.00 4.79
902 904 1.923356 CCCCCAAACACAGCTTACAT 58.077 50.000 0.00 0.00 0.00 2.29
938 940 2.711547 GGGTTCTACCATAGAGGCCAAT 59.288 50.000 5.01 0.00 41.02 3.16
1117 1119 9.732130 GCTACTAAATGGAAGGATCTTATCAAT 57.268 33.333 0.00 0.00 0.00 2.57
1237 1239 1.656652 AGCATTTCGTCGCTTGCTAT 58.343 45.000 12.66 0.00 43.28 2.97
1272 1274 3.594134 GGAATCTCCGGATCTATGCTTG 58.406 50.000 3.57 0.00 0.00 4.01
1361 1363 5.599999 TTCCTCTGGCTACTAAGATGTTC 57.400 43.478 0.00 0.00 0.00 3.18
1708 1710 2.659016 CTTGGGAGCTCAGCACGA 59.341 61.111 17.19 1.57 0.00 4.35
1812 1814 2.518709 TTACGGCTCCGGTGGGTTT 61.519 57.895 13.31 0.00 44.69 3.27
1830 1832 4.670347 GTCCTATTAAGACTCGCTTTCGT 58.330 43.478 0.00 0.00 38.05 3.85
1851 1853 3.262420 GTCCATAAGCAGTGACAATCGT 58.738 45.455 0.00 0.00 0.00 3.73
1901 1903 5.356470 GCTTAGTTTCATCCAAGCTTCATCT 59.644 40.000 0.00 0.00 40.16 2.90
2065 2067 3.284449 GCCCGCACCGAAACAGTT 61.284 61.111 0.00 0.00 0.00 3.16
2148 2150 1.079750 GTCTCACTGGCCGACCTTC 60.080 63.158 0.00 0.00 36.63 3.46
2200 2202 2.042464 CTTAGCTGGTGATCTGGGCTA 58.958 52.381 0.00 0.61 34.88 3.93
2234 2236 2.237143 CCACCTCCTTTATCACTGAGCA 59.763 50.000 0.00 0.00 0.00 4.26
2290 2379 2.363038 CCGATGCATTTTGACATCCCAT 59.637 45.455 0.00 0.00 39.63 4.00


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

AutoCloner maintained by Alex Coulton.