Multiple sequence alignment - TraesCS1B01G154300

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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 TraesCS1B01G154300 chr1B 100.000 2285 0 0 1 2285 256213354 256211070 0.000000e+00 4220
1 TraesCS1B01G154300 chr1B 78.070 342 71 3 1917 2256 670967802 670968141 1.780000e-51 213
2 TraesCS1B01G154300 chr1B 82.011 189 30 4 1994 2180 50810787 50810601 8.450000e-35 158
3 TraesCS1B01G154300 chr2B 97.900 2286 44 2 1 2285 429178884 429176602 0.000000e+00 3952
4 TraesCS1B01G154300 chr6D 96.799 1937 60 2 1 1936 235785364 235783429 0.000000e+00 3232
5 TraesCS1B01G154300 chr6D 96.011 351 11 1 1935 2285 235780968 235780621 3.290000e-158 568
6 TraesCS1B01G154300 chr4B 98.065 155 3 0 2131 2285 479405124 479404970 1.040000e-68 270
7 TraesCS1B01G154300 chr4B 75.066 381 87 8 1804 2180 393411489 393411113 1.090000e-38 171
8 TraesCS1B01G154300 chr1A 75.000 456 108 5 1804 2256 521911740 521911288 2.980000e-49 206
9 TraesCS1B01G154300 chr3D 77.820 266 53 6 1918 2180 284927963 284927701 2.350000e-35 159
10 TraesCS1B01G154300 chr5B 74.352 386 88 10 1819 2199 115380035 115379656 1.090000e-33 154
11 TraesCS1B01G154300 chr7B 77.391 230 48 4 1917 2144 439628321 439628548 1.420000e-27 134


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 TraesCS1B01G154300 chr1B 256211070 256213354 2284 True 4220 4220 100.000 1 2285 1 chr1B.!!$R2 2284
1 TraesCS1B01G154300 chr2B 429176602 429178884 2282 True 3952 3952 97.900 1 2285 1 chr2B.!!$R1 2284
2 TraesCS1B01G154300 chr6D 235780621 235785364 4743 True 1900 3232 96.405 1 2285 2 chr6D.!!$R1 2284

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
282 283 0.401738 CTCAGGTTCAGGGGCTTTCA 59.598 55.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 1822 0.905809 TGCTCCTAGTTGGGCCGTAA 60.906 55.0 0.0 0.0 36.2 3.18 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
50 51 3.795639 CGCAACAACAATGTTCAACATCA 59.204 39.130 2.74 0.00 46.78 3.07
282 283 0.401738 CTCAGGTTCAGGGGCTTTCA 59.598 55.000 0.00 0.00 0.00 2.69
300 301 2.276201 TCATGCGGTGTTATTTCCTCG 58.724 47.619 0.00 0.00 0.00 4.63
324 325 4.241555 GATCGCAGGGTCCGCCAT 62.242 66.667 0.00 0.00 36.17 4.40
362 363 3.329542 GATGCCAGGAGGTCCGCAA 62.330 63.158 3.12 0.00 42.08 4.85
509 510 0.976641 TCTGCATCCTTGACGAGGTT 59.023 50.000 8.69 0.00 46.39 3.50
734 735 2.846532 CTTTGGGTCCCAGGTGCT 59.153 61.111 11.40 0.00 33.81 4.40
878 879 1.738099 CCTTGTTCGTGCCTCTCCG 60.738 63.158 0.00 0.00 0.00 4.63
973 974 1.425066 TCACCAGCTTCAACCTTGGAT 59.575 47.619 0.00 0.00 34.76 3.41
1262 1263 3.438087 CAGATGCAAGGAAATGAAGACGT 59.562 43.478 0.00 0.00 0.00 4.34
1496 1497 6.152661 TGGTTTCCAATGAGTAATCACAATCC 59.847 38.462 0.00 0.00 0.00 3.01
1655 1656 0.764369 TCTTCACTGGGTGGTCTGCT 60.764 55.000 0.00 0.00 33.87 4.24
1677 1678 4.162690 GGGAGCTTCGCCCATCGT 62.163 66.667 4.06 0.00 43.17 3.73
1794 1796 3.062639 CGATGTTCAGCTTGCTAATTCGT 59.937 43.478 0.00 0.00 0.00 3.85
1820 1822 6.927381 ACGTTATGTTCAAGCTAACTACAGTT 59.073 34.615 0.00 0.00 41.73 3.16
1835 1837 1.002773 ACAGTTTACGGCCCAACTAGG 59.997 52.381 8.87 2.33 31.78 3.02
1915 1917 2.283173 GTGGCTGGTTCTTGGGGG 60.283 66.667 0.00 0.00 0.00 5.40
2130 4594 0.958822 GGACGTTGAGTTTGGGCATT 59.041 50.000 0.00 0.00 0.00 3.56
2226 4690 4.553330 AGAACTAAATCCTTCCGCTTCA 57.447 40.909 0.00 0.00 0.00 3.02
2249 4713 3.896888 AGAACTTTTGGATCAACATGCCA 59.103 39.130 0.00 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 1.076533 GTCACGGTCATCATCGCGTT 61.077 55.000 5.77 0.00 0.00 4.84
158 159 2.081462 CATGATGCTCTGAAGTGCACA 58.919 47.619 21.04 9.66 45.57 4.57
282 283 1.663695 CCGAGGAAATAACACCGCAT 58.336 50.000 0.00 0.00 0.00 4.73
300 301 4.241555 ACCCTGCGATCGGATGCC 62.242 66.667 18.30 0.00 0.00 4.40
308 309 4.552365 CATGGCGGACCCTGCGAT 62.552 66.667 0.00 0.00 30.86 4.58
346 347 4.020617 CTTGCGGACCTCCTGGCA 62.021 66.667 0.00 0.00 36.63 4.92
509 510 3.071206 GAGGAGCTGGTCGAGGCA 61.071 66.667 0.00 0.00 0.00 4.75
682 683 1.040646 CTGGCAATAGGCGTCCTCTA 58.959 55.000 1.46 0.00 46.16 2.43
1496 1497 3.310774 CACATTCCAGTTTAGGATGCTCG 59.689 47.826 0.00 0.00 37.56 5.03
1677 1678 0.976641 CCACAGTACCAGAAGCAGGA 59.023 55.000 0.00 0.00 0.00 3.86
1794 1796 7.596494 ACTGTAGTTAGCTTGAACATAACGTA 58.404 34.615 0.00 0.00 35.14 3.57
1820 1822 0.905809 TGCTCCTAGTTGGGCCGTAA 60.906 55.000 0.00 0.00 36.20 3.18
1835 1837 6.765915 AAGAAAATATCCTTGAGGTTGCTC 57.234 37.500 0.00 0.00 36.34 4.26
1915 1917 6.982141 TCTGGCATGATAAATTTGATTGAAGC 59.018 34.615 0.00 0.00 0.00 3.86
2130 4594 3.920231 AGCAAGAGCATGGAGAATGTA 57.080 42.857 0.00 0.00 45.49 2.29
2226 4690 4.344679 TGGCATGTTGATCCAAAAGTTCTT 59.655 37.500 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.