Multiple sequence alignment - TraesCS4A01G084000

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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 TraesCS4A01G084000 chr4A 100.000 2357 0 0 1 2357 88457682 88460038 0.000000e+00 4353
1 TraesCS4A01G084000 chr4B 97.246 2360 43 5 1 2357 628610447 628608107 0.000000e+00 3978
2 TraesCS4A01G084000 chr4B 96.907 2360 49 11 1 2357 47032346 47034684 0.000000e+00 3932
3 TraesCS4A01G084000 chr3B 97.119 2360 44 5 1 2357 499755777 499758115 0.000000e+00 3960
4 TraesCS4A01G084000 chr1B 96.739 2361 54 5 1 2357 93968434 93970775 0.000000e+00 3912
5 TraesCS4A01G084000 chr1B 96.612 2361 53 10 1 2357 446715641 446717978 0.000000e+00 3892
6 TraesCS4A01G084000 chr1B 96.877 1825 33 6 1 1821 3208668 3206864 0.000000e+00 3033
7 TraesCS4A01G084000 chr6A 97.420 2248 35 5 113 2357 579417420 579415193 0.000000e+00 3808
8 TraesCS4A01G084000 chr6B 95.975 2360 56 9 1 2357 30325266 30327589 0.000000e+00 3795
9 TraesCS4A01G084000 chr5A 96.774 2077 42 6 1 2072 679766169 679764113 0.000000e+00 3441
10 TraesCS4A01G084000 chr5A 97.877 1978 39 2 383 2357 705322433 705320456 0.000000e+00 3417
11 TraesCS4A01G084000 chr5A 97.534 365 9 0 1 365 705322777 705322413 1.990000e-175 625
12 TraesCS4A01G084000 chrUn 97.169 1978 49 4 383 2357 118925054 118923081 0.000000e+00 3336
13 TraesCS4A01G084000 chr5B 95.180 1556 40 4 1 1554 387148248 387149770 0.000000e+00 2425


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 TraesCS4A01G084000 chr4A 88457682 88460038 2356 False 4353 4353 100.0000 1 2357 1 chr4A.!!$F1 2356
1 TraesCS4A01G084000 chr4B 628608107 628610447 2340 True 3978 3978 97.2460 1 2357 1 chr4B.!!$R1 2356
2 TraesCS4A01G084000 chr4B 47032346 47034684 2338 False 3932 3932 96.9070 1 2357 1 chr4B.!!$F1 2356
3 TraesCS4A01G084000 chr3B 499755777 499758115 2338 False 3960 3960 97.1190 1 2357 1 chr3B.!!$F1 2356
4 TraesCS4A01G084000 chr1B 93968434 93970775 2341 False 3912 3912 96.7390 1 2357 1 chr1B.!!$F1 2356
5 TraesCS4A01G084000 chr1B 446715641 446717978 2337 False 3892 3892 96.6120 1 2357 1 chr1B.!!$F2 2356
6 TraesCS4A01G084000 chr1B 3206864 3208668 1804 True 3033 3033 96.8770 1 1821 1 chr1B.!!$R1 1820
7 TraesCS4A01G084000 chr6A 579415193 579417420 2227 True 3808 3808 97.4200 113 2357 1 chr6A.!!$R1 2244
8 TraesCS4A01G084000 chr6B 30325266 30327589 2323 False 3795 3795 95.9750 1 2357 1 chr6B.!!$F1 2356
9 TraesCS4A01G084000 chr5A 679764113 679766169 2056 True 3441 3441 96.7740 1 2072 1 chr5A.!!$R1 2071
10 TraesCS4A01G084000 chr5A 705320456 705322777 2321 True 2021 3417 97.7055 1 2357 2 chr5A.!!$R2 2356
11 TraesCS4A01G084000 chrUn 118923081 118925054 1973 True 3336 3336 97.1690 383 2357 1 chrUn.!!$R1 1974
12 TraesCS4A01G084000 chr5B 387148248 387149770 1522 False 2425 2425 95.1800 1 1554 1 chr5B.!!$F1 1553

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
812 815 0.108585 GCAAGGTGAAGGAGGTGACA 59.891 55.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1904 1915 0.46729 GGACTGAGGAGAGCGAGGAT 60.467 60.0 0.0 0.0 0.0 3.24 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
360 361 2.509336 ACGGCGCTGATTTCGAGG 60.509 61.111 25.98 0.00 0.00 4.63
361 362 2.509336 CGGCGCTGATTTCGAGGT 60.509 61.111 11.90 0.00 0.00 3.85
362 363 2.802667 CGGCGCTGATTTCGAGGTG 61.803 63.158 11.90 0.00 0.00 4.00
363 364 2.401195 GCGCTGATTTCGAGGTGC 59.599 61.111 0.00 0.00 0.00 5.01
364 365 2.697425 CGCTGATTTCGAGGTGCG 59.303 61.111 0.00 0.00 42.69 5.34
365 366 2.802667 CGCTGATTTCGAGGTGCGG 61.803 63.158 10.78 0.00 41.33 5.69
366 367 1.741770 GCTGATTTCGAGGTGCGGT 60.742 57.895 0.00 0.00 41.33 5.68
367 368 1.970917 GCTGATTTCGAGGTGCGGTG 61.971 60.000 0.00 0.00 41.33 4.94
368 369 1.970917 CTGATTTCGAGGTGCGGTGC 61.971 60.000 0.00 0.00 41.33 5.01
375 376 1.796796 GAGGTGCGGTGCTGATTTC 59.203 57.895 0.00 0.00 0.00 2.17
378 379 1.421485 GTGCGGTGCTGATTTCGAG 59.579 57.895 0.00 0.00 0.00 4.04
812 815 0.108585 GCAAGGTGAAGGAGGTGACA 59.891 55.000 0.00 0.00 0.00 3.58
939 942 9.825109 TTAACCATCACGAATAGATATTGTTGA 57.175 29.630 0.00 0.00 0.00 3.18
1032 1037 0.036388 GGATTGACACGGAGAAGCCA 60.036 55.000 0.00 0.00 35.94 4.75
1033 1038 1.610624 GGATTGACACGGAGAAGCCAA 60.611 52.381 0.00 0.00 35.94 4.52
1201 1211 4.642445 TTTGAGGAAACGGGAAAGAAAC 57.358 40.909 0.00 0.00 0.00 2.78
1227 1237 1.888436 AAGAGGCTCGTCGCATGGAA 61.888 55.000 9.22 0.00 41.67 3.53
1339 1349 5.682212 GCTGGCGATGGAAAAGGAAAATATT 60.682 40.000 0.00 0.00 0.00 1.28
1388 1398 9.915629 TGTGGTAGTATTTTTAATTTCGCAATT 57.084 25.926 0.00 0.00 36.52 2.32
1514 1524 9.478768 TGTCGTGTTGTATCTTATTTTCAGTTA 57.521 29.630 0.00 0.00 0.00 2.24
2026 2037 7.295322 ACCTAAGAAGTTCTTTACGTACCTT 57.705 36.000 22.66 0.00 37.89 3.50
2153 2164 6.116126 GTCCATCTTGAAATTGGTAGCTAGT 58.884 40.000 0.00 0.00 0.00 2.57
2340 2351 0.323816 TTGGCGGGAACATATGGCAA 60.324 50.000 7.80 0.47 43.43 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
360 361 1.421485 CTCGAAATCAGCACCGCAC 59.579 57.895 0.00 0.0 0.00 5.34
361 362 1.741401 CCTCGAAATCAGCACCGCA 60.741 57.895 0.00 0.0 0.00 5.69
362 363 1.741770 ACCTCGAAATCAGCACCGC 60.742 57.895 0.00 0.0 0.00 5.68
363 364 1.970917 GCACCTCGAAATCAGCACCG 61.971 60.000 0.00 0.0 0.00 4.94
364 365 1.796796 GCACCTCGAAATCAGCACC 59.203 57.895 0.00 0.0 0.00 5.01
365 366 1.421485 CGCACCTCGAAATCAGCAC 59.579 57.895 0.00 0.0 41.67 4.40
366 367 1.741401 CCGCACCTCGAAATCAGCA 60.741 57.895 0.00 0.0 41.67 4.41
367 368 1.741770 ACCGCACCTCGAAATCAGC 60.742 57.895 0.00 0.0 41.67 4.26
368 369 1.970917 GCACCGCACCTCGAAATCAG 61.971 60.000 0.00 0.0 41.67 2.90
375 376 1.970917 GAAATCAGCACCGCACCTCG 61.971 60.000 0.00 0.0 38.08 4.63
378 379 1.970917 CTCGAAATCAGCACCGCACC 61.971 60.000 0.00 0.0 0.00 5.01
812 815 3.903090 TGCCCAACCAATCTGAAAAATCT 59.097 39.130 0.00 0.0 0.00 2.40
1032 1037 1.131638 TCTCAGTCACTGCCCAAGTT 58.868 50.000 0.00 0.0 36.83 2.66
1033 1038 1.356124 ATCTCAGTCACTGCCCAAGT 58.644 50.000 0.00 0.0 40.93 3.16
1190 1200 1.880027 CTTCCCTGTGTTTCTTTCCCG 59.120 52.381 0.00 0.0 0.00 5.14
1201 1211 1.216710 GACGAGCCTCTTCCCTGTG 59.783 63.158 0.00 0.0 0.00 3.66
1227 1237 1.806461 TTCGCTGTCGTTCCTGCTCT 61.806 55.000 0.00 0.0 36.96 4.09
1339 1349 4.436242 GAATCTACTGAGTCCAACGTGA 57.564 45.455 0.00 0.0 31.78 4.35
1569 1579 5.984725 TGCTCGATAATTAGTGGAGGAAAA 58.015 37.500 10.45 0.0 0.00 2.29
1904 1915 0.467290 GGACTGAGGAGAGCGAGGAT 60.467 60.000 0.00 0.0 0.00 3.24
2153 2164 3.951037 GGATGAGTAGCACTCTTCTGAGA 59.049 47.826 20.74 0.0 45.27 3.27


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

AutoCloner maintained by Alex Coulton.