Multiple sequence alignment - TraesCS3B01G186000

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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 TraesCS3B01G186000 chr3B 100.000 3497 0 0 1 3497 201498278 201494782 0.000000e+00 6458
1 TraesCS3B01G186000 chr5D 98.260 3505 53 3 1 3497 483802493 483805997 0.000000e+00 6128
2 TraesCS3B01G186000 chr5D 97.767 2150 47 1 1349 3497 6232320 6234469 0.000000e+00 3703
3 TraesCS3B01G186000 chr1D 97.568 3495 69 10 1 3483 254482260 254478770 0.000000e+00 5969
4 TraesCS3B01G186000 chr1D 97.410 1853 46 2 1645 3497 180352115 180353965 0.000000e+00 3155
5 TraesCS3B01G186000 chr2D 97.982 2825 49 3 1 2818 643858624 643855801 0.000000e+00 4894
6 TraesCS3B01G186000 chr2D 97.883 2456 45 3 138 2588 359629753 359632206 0.000000e+00 4241
7 TraesCS3B01G186000 chr2D 98.339 1927 28 4 1 1924 628291233 628293158 0.000000e+00 3378
8 TraesCS3B01G186000 chr2D 89.604 202 20 1 1 202 400049722 400049922 4.480000e-64 255
9 TraesCS3B01G186000 chr2B 97.877 2826 51 2 95 2919 474940033 474937216 0.000000e+00 4878
10 TraesCS3B01G186000 chr7A 93.776 2876 166 10 625 3497 352292166 352295031 0.000000e+00 4307
11 TraesCS3B01G186000 chr7A 97.674 86 2 0 1252 1337 428893255 428893170 7.820000e-32 148
12 TraesCS3B01G186000 chr6D 95.144 2430 100 10 883 3311 210720972 210723384 0.000000e+00 3818
13 TraesCS3B01G186000 chr4A 95.716 1984 79 6 164 2142 309270913 309272895 0.000000e+00 3188
14 TraesCS3B01G186000 chrUn 98.867 1589 18 0 1885 3473 386522348 386523936 0.000000e+00 2835
15 TraesCS3B01G186000 chrUn 99.016 508 4 1 2977 3483 397678312 397677805 0.000000e+00 909
16 TraesCS3B01G186000 chr1A 98.072 1141 21 1 3 1142 554473317 554474457 0.000000e+00 1984
17 TraesCS3B01G186000 chr7B 97.059 136 4 0 1 136 745252159 745252024 2.720000e-56 230
18 TraesCS3B01G186000 chr7B 93.258 89 6 0 1 89 23996315 23996403 7.880000e-27 132


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 TraesCS3B01G186000 chr3B 201494782 201498278 3496 True 6458 6458 100.000 1 3497 1 chr3B.!!$R1 3496
1 TraesCS3B01G186000 chr5D 483802493 483805997 3504 False 6128 6128 98.260 1 3497 1 chr5D.!!$F2 3496
2 TraesCS3B01G186000 chr5D 6232320 6234469 2149 False 3703 3703 97.767 1349 3497 1 chr5D.!!$F1 2148
3 TraesCS3B01G186000 chr1D 254478770 254482260 3490 True 5969 5969 97.568 1 3483 1 chr1D.!!$R1 3482
4 TraesCS3B01G186000 chr1D 180352115 180353965 1850 False 3155 3155 97.410 1645 3497 1 chr1D.!!$F1 1852
5 TraesCS3B01G186000 chr2D 643855801 643858624 2823 True 4894 4894 97.982 1 2818 1 chr2D.!!$R1 2817
6 TraesCS3B01G186000 chr2D 359629753 359632206 2453 False 4241 4241 97.883 138 2588 1 chr2D.!!$F1 2450
7 TraesCS3B01G186000 chr2D 628291233 628293158 1925 False 3378 3378 98.339 1 1924 1 chr2D.!!$F3 1923
8 TraesCS3B01G186000 chr2B 474937216 474940033 2817 True 4878 4878 97.877 95 2919 1 chr2B.!!$R1 2824
9 TraesCS3B01G186000 chr7A 352292166 352295031 2865 False 4307 4307 93.776 625 3497 1 chr7A.!!$F1 2872
10 TraesCS3B01G186000 chr6D 210720972 210723384 2412 False 3818 3818 95.144 883 3311 1 chr6D.!!$F1 2428
11 TraesCS3B01G186000 chr4A 309270913 309272895 1982 False 3188 3188 95.716 164 2142 1 chr4A.!!$F1 1978
12 TraesCS3B01G186000 chrUn 386522348 386523936 1588 False 2835 2835 98.867 1885 3473 1 chrUn.!!$F1 1588
13 TraesCS3B01G186000 chrUn 397677805 397678312 507 True 909 909 99.016 2977 3483 1 chrUn.!!$R1 506
14 TraesCS3B01G186000 chr1A 554473317 554474457 1140 False 1984 1984 98.072 3 1142 1 chr1A.!!$F1 1139

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
101 102 1.134965 CAAGCTGAGGACTTACTCGGG 60.135 57.143 0.0 0.0 42.78 5.14 F
1115 1136 0.251787 GTCACTTTTCCCCCAGGCAT 60.252 55.000 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1596 1621 1.611261 CCGTTCCCCTACTCCACCA 60.611 63.158 0.0 0.0 0.0 4.17 R
2646 2675 0.321564 CATTGGTCGTTGAGGAGGCA 60.322 55.000 0.0 0.0 0.0 4.75 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
101 102 1.134965 CAAGCTGAGGACTTACTCGGG 60.135 57.143 0.00 0.00 42.78 5.14
248 249 8.661345 GTCCCTCCCTATAACTCTTGAATTAAT 58.339 37.037 0.00 0.00 0.00 1.40
275 276 8.783660 ATTCTCACAATAATAGGGTCTACTCA 57.216 34.615 0.00 0.00 0.00 3.41
1115 1136 0.251787 GTCACTTTTCCCCCAGGCAT 60.252 55.000 0.00 0.00 0.00 4.40
1546 1571 6.127814 TGGAGTAGGTAAAACAGTACTGATCG 60.128 42.308 29.30 2.86 0.00 3.69
1596 1621 1.061546 ATGGGGGCGTATCCGTATTT 58.938 50.000 0.00 0.00 36.15 1.40
1700 1727 3.914426 TGAGGAATCAAAGGTAGCTCC 57.086 47.619 0.00 0.00 0.00 4.70
1822 1849 9.864034 AAGACGTGCTTTTATTTATCGATAATG 57.136 29.630 18.18 2.96 31.11 1.90
1848 1875 3.476552 TCGTTTTGTTCAAGCAGGATCT 58.523 40.909 0.00 0.00 0.00 2.75
2005 2032 0.396435 ACCTGCAGACGATTTGACCA 59.604 50.000 17.39 0.00 0.00 4.02
2646 2675 8.820831 CAGTAGATATGGGTCCTTTGAGAATAT 58.179 37.037 0.00 0.00 0.00 1.28
2745 2774 7.781324 ATTTTAGGAAATGATGTGGAACTGT 57.219 32.000 0.00 0.00 33.98 3.55
3317 3346 5.147767 TGATAAGGGCTATAGCTCAGTTCA 58.852 41.667 26.23 20.00 46.01 3.18
3453 3482 3.584848 AGGAGAACAGTAGCCTGACAAAT 59.415 43.478 0.00 0.00 41.50 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 6.250711 TCTTCTACTGGTACATGGACAACTA 58.749 40.000 10.99 0.00 38.20 2.24
83 84 0.331954 TCCCGAGTAAGTCCTCAGCT 59.668 55.000 0.00 0.00 0.00 4.24
101 102 4.874966 GGATACTGATATCTTGGCAGCATC 59.125 45.833 3.98 0.00 37.85 3.91
263 264 7.470981 CGCCTAATTAACATTGAGTAGACCCTA 60.471 40.741 0.00 0.00 0.00 3.53
419 423 6.663953 TCCTATAGGATAGAACATACACAGGC 59.336 42.308 18.00 0.00 39.78 4.85
780 797 5.858581 CCGTTGGAAAGTTCAATCAATCTTC 59.141 40.000 0.00 0.00 0.00 2.87
1142 1163 3.572255 GTCAGTGTCTCTTCTCTGGACTT 59.428 47.826 0.00 0.00 32.14 3.01
1152 1173 7.516198 AATTTGCTTATTGTCAGTGTCTCTT 57.484 32.000 0.00 0.00 0.00 2.85
1596 1621 1.611261 CCGTTCCCCTACTCCACCA 60.611 63.158 0.00 0.00 0.00 4.17
1700 1727 5.450965 GGTTCATTCATTTGGCCATAGACTG 60.451 44.000 6.09 9.75 0.00 3.51
1822 1849 3.791353 CCTGCTTGAACAAAACGAAAGAC 59.209 43.478 0.00 0.00 0.00 3.01
1848 1875 4.485875 TCCCTAATAAAGCGGATACCTCA 58.514 43.478 0.00 0.00 0.00 3.86
2249 2276 5.862924 TGCTCTTGCTACAGTTTAATGAC 57.137 39.130 0.00 0.00 40.48 3.06
2255 2282 5.835113 TTTTCTTGCTCTTGCTACAGTTT 57.165 34.783 0.00 0.00 40.48 2.66
2646 2675 0.321564 CATTGGTCGTTGAGGAGGCA 60.322 55.000 0.00 0.00 0.00 4.75
2737 2766 6.582636 GGATCAATATCACTACACAGTTCCA 58.417 40.000 0.00 0.00 33.41 3.53
2745 2774 6.724893 TTCTTCCGGATCAATATCACTACA 57.275 37.500 4.15 0.00 33.41 2.74
3317 3346 3.004106 ACGTGTAAACGAGTTGCTCTACT 59.996 43.478 13.54 0.00 36.85 2.57


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

AutoCloner maintained by Alex Coulton.