Multiple sequence alignment - TraesCS5B01G187100

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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 TraesCS5B01G187100 chr5B 100.000 2913 0 0 1 2913 339360876 339357964 0 5380
1 TraesCS5B01G187100 chr5B 94.130 2913 158 7 1 2911 326457272 326454371 0 4420
2 TraesCS5B01G187100 chr1B 94.505 2912 154 2 1 2911 116279630 116282536 0 4486
3 TraesCS5B01G187100 chr1B 94.702 2888 146 4 24 2911 146922199 146919319 0 4479
4 TraesCS5B01G187100 chr1B 94.297 2911 155 4 1 2911 640095981 640093082 0 4446
5 TraesCS5B01G187100 chr6B 94.505 2912 150 6 1 2911 148662147 148659245 0 4482
6 TraesCS5B01G187100 chr6B 94.162 2912 162 5 1 2911 590698035 590700939 0 4429
7 TraesCS5B01G187100 chr7B 94.271 2915 153 9 1 2911 504526765 504529669 0 4446
8 TraesCS5B01G187100 chr7B 94.229 2911 161 3 1 2911 279084337 279087240 0 4438
9 TraesCS5B01G187100 chr4B 94.091 2911 166 3 1 2911 604371986 604369082 0 4418


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 TraesCS5B01G187100 chr5B 339357964 339360876 2912 True 5380 5380 100.000 1 2913 1 chr5B.!!$R2 2912
1 TraesCS5B01G187100 chr5B 326454371 326457272 2901 True 4420 4420 94.130 1 2911 1 chr5B.!!$R1 2910
2 TraesCS5B01G187100 chr1B 116279630 116282536 2906 False 4486 4486 94.505 1 2911 1 chr1B.!!$F1 2910
3 TraesCS5B01G187100 chr1B 146919319 146922199 2880 True 4479 4479 94.702 24 2911 1 chr1B.!!$R1 2887
4 TraesCS5B01G187100 chr1B 640093082 640095981 2899 True 4446 4446 94.297 1 2911 1 chr1B.!!$R2 2910
5 TraesCS5B01G187100 chr6B 148659245 148662147 2902 True 4482 4482 94.505 1 2911 1 chr6B.!!$R1 2910
6 TraesCS5B01G187100 chr6B 590698035 590700939 2904 False 4429 4429 94.162 1 2911 1 chr6B.!!$F1 2910
7 TraesCS5B01G187100 chr7B 504526765 504529669 2904 False 4446 4446 94.271 1 2911 1 chr7B.!!$F2 2910
8 TraesCS5B01G187100 chr7B 279084337 279087240 2903 False 4438 4438 94.229 1 2911 1 chr7B.!!$F1 2910
9 TraesCS5B01G187100 chr4B 604369082 604371986 2904 True 4418 4418 94.091 1 2911 1 chr4B.!!$R1 2910

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
721 726 1.564348 AGTTCTGCCCCCATTAATCGT 59.436 47.619 0.00 0.0 0.00 3.73 F
1008 1013 1.207089 CCCAAGCGAGAGATGGTTGTA 59.793 52.381 4.49 0.0 41.86 2.41 F
1764 1769 0.108329 CCTAAAGGCATGACCGACGT 60.108 55.000 0.00 0.0 46.52 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1747 1752 0.457166 CGACGTCGGTCATGCCTTTA 60.457 55.0 29.70 0.0 43.61 1.85 R
1817 1822 0.767375 AAGAAGGTCAGCTCCTGCAA 59.233 50.0 2.33 0.0 42.74 4.08 R
2846 2854 2.553028 GGAGTTGAGGAGGAATGTGCAA 60.553 50.0 0.00 0.0 0.00 4.08 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
96 100 3.993920 ACATGCATGATACACGCTATCA 58.006 40.909 32.75 5.99 38.20 2.15
104 108 7.067494 TGCATGATACACGCTATCATAGACTAT 59.933 37.037 13.29 0.00 41.29 2.12
200 204 2.041216 TGGAGTACTACTGCACTGGAGA 59.959 50.000 6.66 0.00 41.73 3.71
415 420 1.826385 CCAAAGGGAGGTGCAGTTAG 58.174 55.000 0.00 0.00 35.59 2.34
721 726 1.564348 AGTTCTGCCCCCATTAATCGT 59.436 47.619 0.00 0.00 0.00 3.73
730 735 3.283751 CCCCATTAATCGTGCCAGTTTA 58.716 45.455 0.00 0.00 0.00 2.01
833 838 4.299796 GGAGGGCCAGCCAACCAA 62.300 66.667 11.50 0.00 37.98 3.67
853 858 4.381185 CCAATGCATGCACATTTACTGTCT 60.381 41.667 25.37 0.00 38.19 3.41
975 980 9.859692 GTATAAAATATGTGACGGTAAAGCTTC 57.140 33.333 0.00 0.00 0.00 3.86
1008 1013 1.207089 CCCAAGCGAGAGATGGTTGTA 59.793 52.381 4.49 0.00 41.86 2.41
1041 1046 2.621338 GAGATCATGCAGACGGAACAA 58.379 47.619 0.00 0.00 0.00 2.83
1120 1125 4.699522 GCCTTCGCCCCTTGACGT 62.700 66.667 0.00 0.00 0.00 4.34
1363 1368 3.625897 TCGCTGAGGGTGGTGTGG 61.626 66.667 0.00 0.00 0.00 4.17
1568 1573 1.677966 CTCCAGCTGCAAGTGCCAT 60.678 57.895 8.66 0.00 41.18 4.40
1636 1641 2.712325 TTTTCTTGGTCGGCGGCGTA 62.712 55.000 31.06 15.10 0.00 4.42
1639 1644 3.927163 CTTGGTCGGCGGCGTACTT 62.927 63.158 31.06 0.00 0.00 2.24
1711 1716 2.357034 CCACTGCCGCACTACGTT 60.357 61.111 0.00 0.00 41.42 3.99
1718 1723 1.959226 CCGCACTACGTTGCCAAGT 60.959 57.895 6.64 0.00 39.53 3.16
1764 1769 0.108329 CCTAAAGGCATGACCGACGT 60.108 55.000 0.00 0.00 46.52 4.34
1931 1936 6.877322 GTCCTAAATGTTTCTACAGTGCCTTA 59.123 38.462 0.00 0.00 37.77 2.69
2005 2010 5.686387 GCTTAAGAAATGGTGGGTTTTGGTT 60.686 40.000 6.67 0.00 0.00 3.67
2057 2062 8.258007 AGATCAGTAATTTCCAATAGTCGAACA 58.742 33.333 0.00 0.00 0.00 3.18
2390 2397 1.213013 GACGCGTGTGTGAGAGGAT 59.787 57.895 20.70 0.00 0.00 3.24
2429 2436 5.125739 ACCTCTTCTCTTCCTGTATAACGTG 59.874 44.000 0.00 0.00 0.00 4.49
2430 2437 5.450688 CCTCTTCTCTTCCTGTATAACGTGG 60.451 48.000 0.00 0.00 0.00 4.94
2431 2438 5.258841 TCTTCTCTTCCTGTATAACGTGGA 58.741 41.667 0.00 0.00 0.00 4.02
2432 2439 5.357314 TCTTCTCTTCCTGTATAACGTGGAG 59.643 44.000 0.00 0.00 0.00 3.86
2433 2440 4.597004 TCTCTTCCTGTATAACGTGGAGT 58.403 43.478 0.00 0.00 0.00 3.85
2555 2562 3.100545 CCATGCGGCTATTCCTGTT 57.899 52.632 0.00 0.00 0.00 3.16
2572 2579 1.249407 GTTGAACGCCCCATTAACCA 58.751 50.000 0.00 0.00 0.00 3.67
2912 2920 0.700564 TCAGCATCCTTCCCTTGCTT 59.299 50.000 0.00 0.00 43.94 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 100 7.928706 GGCAGTTTCATGTGTAGAATAGTCTAT 59.071 37.037 2.81 0.00 38.62 1.98
104 108 3.563808 GTGTGGCAGTTTCATGTGTAGAA 59.436 43.478 0.00 0.00 0.00 2.10
200 204 3.119566 GCCAGAAGCGTACTGTAGTACTT 60.120 47.826 17.33 8.09 46.43 2.24
415 420 2.693896 TATCCTCTCCCTCGCGGACC 62.694 65.000 6.13 0.00 34.86 4.46
548 553 5.240891 TGCAAGTATCAAAAGGAGAGTCAG 58.759 41.667 0.00 0.00 0.00 3.51
721 726 4.727507 TTTTCTGCTTTGTAAACTGGCA 57.272 36.364 0.00 0.00 0.00 4.92
730 735 3.256631 CCTGTAGCCATTTTCTGCTTTGT 59.743 43.478 0.00 0.00 39.00 2.83
787 792 0.613012 GCTTGAGTTGGCTTCCCCAT 60.613 55.000 0.00 0.00 44.89 4.00
833 838 7.991084 ATATAGACAGTAAATGTGCATGCAT 57.009 32.000 25.64 10.48 44.17 3.96
853 858 9.336171 TGCACATGAGTAAGTTGCATAAATATA 57.664 29.630 0.00 0.00 0.00 0.86
865 870 0.035056 GCCCCTGCACATGAGTAAGT 60.035 55.000 0.00 0.00 37.47 2.24
896 901 5.937111 AGGAAGGCAGTAGTTTGAGTTTTA 58.063 37.500 0.00 0.00 0.00 1.52
975 980 4.805768 TTGGGCCGGGGCATTACG 62.806 66.667 23.10 0.00 44.11 3.18
1008 1013 2.043852 ATCTCGCCCTCCTCGTGT 60.044 61.111 0.00 0.00 0.00 4.49
1041 1046 2.035940 AGCTCCCTCGTCGGTTCT 59.964 61.111 0.00 0.00 0.00 3.01
1120 1125 7.012138 GTGTATTCGAACCTCATACACTAGAGA 59.988 40.741 22.68 0.00 45.22 3.10
1301 1306 0.957395 CTCCGCATGTCAAAGCCACT 60.957 55.000 0.00 0.00 0.00 4.00
1377 1382 1.755380 GGTAAGTGACGTAGAGCCCAT 59.245 52.381 0.00 0.00 0.00 4.00
1639 1644 3.841379 GATAGGCGCGCCGATGTCA 62.841 63.158 43.71 25.93 41.95 3.58
1747 1752 0.457166 CGACGTCGGTCATGCCTTTA 60.457 55.000 29.70 0.00 43.61 1.85
1755 1760 2.188829 ACCTTGACGACGTCGGTCA 61.189 57.895 37.89 31.92 43.61 4.02
1764 1769 1.003118 CCTCCATTTCCACCTTGACGA 59.997 52.381 0.00 0.00 0.00 4.20
1817 1822 0.767375 AAGAAGGTCAGCTCCTGCAA 59.233 50.000 2.33 0.00 42.74 4.08
1861 1866 2.602676 GGACACCAGCTTAGCCCCA 61.603 63.158 0.00 0.00 0.00 4.96
2005 2010 3.125146 GTCGAAGTAATTGCTGCATCACA 59.875 43.478 1.84 0.00 0.00 3.58
2371 2378 2.214181 ATCCTCTCACACACGCGTCC 62.214 60.000 9.86 0.00 0.00 4.79
2433 2440 9.880157 ACAAAAACTTGTACTCTGAGTTTAGTA 57.120 29.630 16.53 0.00 41.36 1.82
2555 2562 3.054287 TCTTATGGTTAATGGGGCGTTCA 60.054 43.478 0.00 0.00 0.00 3.18
2572 2579 7.124298 ACTGGCACCATCGTATACATATCTTAT 59.876 37.037 3.32 0.00 0.00 1.73
2796 2804 5.530543 ACCGAGTACTAATACACTCCTAAGC 59.469 44.000 0.00 0.00 38.35 3.09
2846 2854 2.553028 GGAGTTGAGGAGGAATGTGCAA 60.553 50.000 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.