Multiple sequence alignment - TraesCS1A01G147700

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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 TraesCS1A01G147700 chr1A 100.000 2465 0 0 1 2465 254997671 254995207 0.000000e+00 4553.0
1 TraesCS1A01G147700 chr1A 90.756 119 6 4 91 207 254997276 254997161 1.180000e-33 154.0
2 TraesCS1A01G147700 chr1A 90.756 119 6 4 396 511 254997581 254997465 1.180000e-33 154.0
3 TraesCS1A01G147700 chr1D 97.497 2477 41 9 1 2465 201058283 201055816 0.000000e+00 4211.0
4 TraesCS1A01G147700 chr1D 92.437 119 5 2 396 511 201058193 201058076 1.520000e-37 167.0
5 TraesCS1A01G147700 chr1D 89.167 120 6 6 91 207 201057888 201057773 2.560000e-30 143.0
6 TraesCS1A01G147700 chr1B 92.795 1027 58 7 529 1543 288960763 288959741 0.000000e+00 1472.0
7 TraesCS1A01G147700 chr1B 89.844 384 33 6 4 384 288961140 288960760 2.850000e-134 488.0
8 TraesCS1A01G147700 chr1B 91.195 318 22 4 1561 1874 288959752 288959437 6.300000e-116 427.0
9 TraesCS1A01G147700 chr1B 88.660 291 26 4 2177 2465 288954290 288954005 5.050000e-92 348.0
10 TraesCS1A01G147700 chr1B 78.472 144 15 10 1928 2055 288958581 288958438 2.030000e-11 80.5
11 TraesCS1A01G147700 chr5A 81.855 496 87 3 973 1465 675958368 675957873 4.900000e-112 414.0


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 TraesCS1A01G147700 chr1A 254995207 254997671 2464 True 1620.333333 4553 93.837333 1 2465 3 chr1A.!!$R1 2464
1 TraesCS1A01G147700 chr1D 201055816 201058283 2467 True 1507.000000 4211 93.033667 1 2465 3 chr1D.!!$R1 2464
2 TraesCS1A01G147700 chr1B 288958438 288961140 2702 True 616.875000 1472 88.076500 4 2055 4 chr1B.!!$R2 2051

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
279 281 0.324943 CTCGCTTCTTCCCTTTCCCA 59.675 55.000 0.0 0.0 0.0 4.37 F
1344 1362 1.723003 CTAACACTCCGCCACGTTTAC 59.277 52.381 0.0 0.0 0.0 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1392 1410 0.884704 ATTTGCACAACGCCTCGAGT 60.885 50.0 12.31 0.0 41.33 4.18 R
2307 3161 5.297029 CGAGATTTTAGGTTCAGATTTCCCC 59.703 44.0 0.00 0.0 0.00 4.81 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
52 53 2.556144 TGAGACTGTTTGCAGAGCAT 57.444 45.000 1.30 0.0 45.28 3.79
100 101 6.655078 ACAAGTTGTCTGCCTGAATAAAAT 57.345 33.333 1.64 0.0 0.00 1.82
137 138 6.042552 TGGTCTCCTCATCTGAAATAGATTCC 59.957 42.308 0.00 0.0 43.68 3.01
139 140 4.887748 TCCTCATCTGAAATAGATTCCGC 58.112 43.478 0.00 0.0 43.68 5.54
279 281 0.324943 CTCGCTTCTTCCCTTTCCCA 59.675 55.000 0.00 0.0 0.00 4.37
307 309 4.584874 TGAACAATCTTGGATCGGCTTTA 58.415 39.130 0.00 0.0 0.00 1.85
313 315 8.918202 ACAATCTTGGATCGGCTTTATATTTA 57.082 30.769 0.00 0.0 0.00 1.40
468 472 3.990318 GCTGACAAGCCAAGTAACTTT 57.010 42.857 0.00 0.0 44.22 2.66
476 480 8.637986 TGACAAGCCAAGTAACTTTATGAAAAT 58.362 29.630 0.00 0.0 0.00 1.82
525 529 9.010029 TGTATCTTTGGAAAAACAATAGAGGAC 57.990 33.333 0.00 0.0 0.00 3.85
624 636 3.550820 TGACTGCTTGTAACCACATGTT 58.449 40.909 0.00 0.0 41.11 2.71
821 835 4.716784 AGTGTATCTTTGGCATCTAGTGGA 59.283 41.667 0.00 0.0 0.00 4.02
1134 1152 5.437289 TTTATAGGCTCAATTTGATGGCG 57.563 39.130 0.00 0.0 0.00 5.69
1344 1362 1.723003 CTAACACTCCGCCACGTTTAC 59.277 52.381 0.00 0.0 0.00 2.01
1392 1410 2.646930 CCCTTCTGCAAGCATATGTCA 58.353 47.619 4.29 0.0 0.00 3.58
1507 1525 1.763545 CTACCAAGCTCCTACCTTCCC 59.236 57.143 0.00 0.0 0.00 3.97
1561 1579 2.348472 TGTGGGAGAAGATGGGAGTTT 58.652 47.619 0.00 0.0 0.00 2.66
1567 1585 4.218635 GGGAGAAGATGGGAGTTTTTCAAC 59.781 45.833 0.00 0.0 0.00 3.18
1986 2838 6.882656 ACAGTCATACTCAACAGATATTGCT 58.117 36.000 0.00 0.0 0.00 3.91
1987 2839 7.334090 ACAGTCATACTCAACAGATATTGCTT 58.666 34.615 0.00 0.0 0.00 3.91
1988 2840 7.493971 ACAGTCATACTCAACAGATATTGCTTC 59.506 37.037 0.00 0.0 0.00 3.86
1989 2841 7.710044 CAGTCATACTCAACAGATATTGCTTCT 59.290 37.037 0.00 0.0 0.00 2.85
1990 2842 8.263640 AGTCATACTCAACAGATATTGCTTCTT 58.736 33.333 0.00 0.0 0.00 2.52
2080 2934 4.378459 CCCTCTGTTCAAAATACTTGTCGC 60.378 45.833 0.00 0.0 0.00 5.19
2200 3054 1.203288 TGTTCCAAGGGAATGGCCAAT 60.203 47.619 10.96 0.0 44.04 3.16
2307 3161 4.963276 TTTGGGATTTACAATCAGCTCG 57.037 40.909 0.00 0.0 0.00 5.03
2343 3197 7.073342 ACCTAAAATCTCGCACAGTAAATTC 57.927 36.000 0.00 0.0 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 4.507710 GACACTGACTTGCAATATCTGGA 58.492 43.478 16.85 0.00 0.00 3.86
100 101 5.105567 TGAGGAGACCAACTAAAACAACA 57.894 39.130 0.00 0.00 0.00 3.33
137 138 3.020026 CTTGGCTTGTCAGCTCGCG 62.020 63.158 0.00 0.00 46.44 5.87
139 140 1.461127 GTTACTTGGCTTGTCAGCTCG 59.539 52.381 0.00 0.00 46.44 5.03
212 214 4.093998 ACTGTAGATGCTCGCAATTGAAAG 59.906 41.667 10.34 6.39 0.00 2.62
217 219 2.283298 CCACTGTAGATGCTCGCAATT 58.717 47.619 0.00 0.00 0.00 2.32
245 247 3.366392 CGAGTTCAACGCACCAATG 57.634 52.632 0.00 0.00 0.00 2.82
279 281 4.444022 CCGATCCAAGATTGTTCAGGAGAT 60.444 45.833 0.00 0.00 33.50 2.75
307 309 9.950680 CTTTCCATTGAAGCATAACGTAAATAT 57.049 29.630 0.00 0.00 0.00 1.28
313 315 3.443681 CCCTTTCCATTGAAGCATAACGT 59.556 43.478 0.00 0.00 0.00 3.99
520 524 4.223032 TGAACCTTCTGGAACTATGTCCTC 59.777 45.833 0.00 0.00 38.62 3.71
525 529 5.500234 TCCAATGAACCTTCTGGAACTATG 58.500 41.667 0.00 0.00 37.04 2.23
844 858 0.107993 CTGCAATCTGCCTCCTCGAA 60.108 55.000 0.00 0.00 44.23 3.71
1134 1152 3.916761 TGCATTGAAATCCTTGCAGAAC 58.083 40.909 3.97 0.00 39.98 3.01
1344 1362 5.687285 AGCTTGTTTAAGTTTTGCAATCTCG 59.313 36.000 0.00 0.00 36.27 4.04
1392 1410 0.884704 ATTTGCACAACGCCTCGAGT 60.885 50.000 12.31 0.00 41.33 4.18
1487 1505 1.763545 GGGAAGGTAGGAGCTTGGTAG 59.236 57.143 0.00 0.00 35.86 3.18
1507 1525 2.224606 ACAGCTCACAAATGTCACCTG 58.775 47.619 0.00 0.00 0.00 4.00
1561 1579 5.470098 GCTCAGTAAGGATCAACAGTTGAAA 59.530 40.000 19.92 0.00 43.95 2.69
1567 1585 4.734398 AGAGCTCAGTAAGGATCAACAG 57.266 45.455 17.77 0.00 0.00 3.16
1837 1859 6.800543 TGCAAGTAAAAGTCATGTAAAAGCA 58.199 32.000 0.00 0.00 0.00 3.91
2055 2909 5.643777 CGACAAGTATTTTGAACAGAGGGAT 59.356 40.000 0.00 0.00 0.00 3.85
2080 2934 6.515043 TCAGTTAAGTTCGAACTAAAACCG 57.485 37.500 32.20 27.23 38.57 4.44
2200 3054 9.986157 TTCTAACTCTAAATTCCTACTCTGGTA 57.014 33.333 0.00 0.00 0.00 3.25
2307 3161 5.297029 CGAGATTTTAGGTTCAGATTTCCCC 59.703 44.000 0.00 0.00 0.00 4.81
2370 3224 5.998363 ACAGTACCTTGTTCTTGAGGAAATC 59.002 40.000 0.00 0.00 36.84 2.17


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

AutoCloner maintained by Alex Coulton.