Multiple sequence alignment - TraesCS3D01G267800

Loading Multiple Alignment...

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 TraesCS3D01G267800 chr3D 100.000 2279 0 0 1 2279 371868810 371871088 0.000000e+00 4209
1 TraesCS3D01G267800 chr3A 96.452 2283 73 6 1 2279 492735568 492737846 0.000000e+00 3760
2 TraesCS3D01G267800 chr3B 95.684 2294 65 12 1 2279 482783390 482785664 0.000000e+00 3657
3 TraesCS3D01G267800 chr1B 78.490 967 182 20 870 1826 638782832 638783782 5.380000e-171 610
4 TraesCS3D01G267800 chr1B 78.323 978 178 23 870 1831 638820932 638821891 3.240000e-168 601
5 TraesCS3D01G267800 chr1A 78.413 945 175 22 873 1806 555534505 555533579 2.520000e-164 588
6 TraesCS3D01G267800 chr1A 77.812 978 183 23 870 1831 555522152 555523111 7.060000e-160 573
7 TraesCS3D01G267800 chr1A 77.310 974 183 32 870 1827 555484043 555484994 7.160000e-150 540
8 TraesCS3D01G267800 chr1D 78.330 946 174 25 873 1806 463342360 463341434 1.170000e-162 582
9 TraesCS3D01G267800 chr1D 77.710 978 184 23 870 1831 463325447 463326406 3.290000e-158 568


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 TraesCS3D01G267800 chr3D 371868810 371871088 2278 False 4209 4209 100.000 1 2279 1 chr3D.!!$F1 2278
1 TraesCS3D01G267800 chr3A 492735568 492737846 2278 False 3760 3760 96.452 1 2279 1 chr3A.!!$F1 2278
2 TraesCS3D01G267800 chr3B 482783390 482785664 2274 False 3657 3657 95.684 1 2279 1 chr3B.!!$F1 2278
3 TraesCS3D01G267800 chr1B 638782832 638783782 950 False 610 610 78.490 870 1826 1 chr1B.!!$F1 956
4 TraesCS3D01G267800 chr1B 638820932 638821891 959 False 601 601 78.323 870 1831 1 chr1B.!!$F2 961
5 TraesCS3D01G267800 chr1A 555533579 555534505 926 True 588 588 78.413 873 1806 1 chr1A.!!$R1 933
6 TraesCS3D01G267800 chr1A 555522152 555523111 959 False 573 573 77.812 870 1831 1 chr1A.!!$F2 961
7 TraesCS3D01G267800 chr1A 555484043 555484994 951 False 540 540 77.310 870 1827 1 chr1A.!!$F1 957
8 TraesCS3D01G267800 chr1D 463341434 463342360 926 True 582 582 78.330 873 1806 1 chr1D.!!$R1 933
9 TraesCS3D01G267800 chr1D 463325447 463326406 959 False 568 568 77.710 870 1831 1 chr1D.!!$F1 961

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
259 260 0.522626 TCCACAATGACGCAAGCATG 59.477 50.0 0.0 0.0 45.62 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1587 1596 1.220749 GAGGCGGTTGCTCATGGTA 59.779 57.895 0.0 0.0 42.25 3.25 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
130 131 7.335422 CAGAGAAGAGGCTACATTACAAAACAT 59.665 37.037 0.00 0.00 0.00 2.71
135 136 6.493458 AGAGGCTACATTACAAAACATGGTTT 59.507 34.615 1.93 1.93 0.00 3.27
259 260 0.522626 TCCACAATGACGCAAGCATG 59.477 50.000 0.00 0.00 45.62 4.06
261 262 1.333115 CACAATGACGCAAGCATGTG 58.667 50.000 0.04 0.04 45.62 3.21
317 318 2.159037 TGACGCGTGTACACAAAACAAA 59.841 40.909 20.70 2.12 0.00 2.83
323 324 2.529894 GTGTACACAAAACAAAGCAGCG 59.470 45.455 21.14 0.00 0.00 5.18
354 355 5.508153 GCAGTCGAGCAGAGGAATATTTCTA 60.508 44.000 0.00 0.00 0.00 2.10
362 363 8.489676 AGCAGAGGAATATTTCTATCTTCTGA 57.510 34.615 15.53 0.00 0.00 3.27
426 428 7.450074 TGTGAAGATTGTTAGTCCATGTTACT 58.550 34.615 3.70 3.70 0.00 2.24
427 429 8.590204 TGTGAAGATTGTTAGTCCATGTTACTA 58.410 33.333 1.96 1.96 0.00 1.82
428 430 9.601217 GTGAAGATTGTTAGTCCATGTTACTAT 57.399 33.333 6.12 0.00 29.86 2.12
471 473 7.069085 ACTCCATAATCAAACATCCTTCCATTG 59.931 37.037 0.00 0.00 0.00 2.82
531 533 0.527385 CAAGCAACCACCAAACCACG 60.527 55.000 0.00 0.00 0.00 4.94
775 784 1.059584 TTCAACTGCACCTCCTCCCA 61.060 55.000 0.00 0.00 0.00 4.37
780 789 4.394712 GCACCTCCTCCCACACCG 62.395 72.222 0.00 0.00 0.00 4.94
1029 1038 2.127003 CTGTGCAGCGACGACGTA 60.127 61.111 9.33 0.00 41.98 3.57
1341 1350 1.139095 GAAGTACCTCGTCCGGCTG 59.861 63.158 0.00 0.00 0.00 4.85
1587 1596 3.399181 ACCCCGATGACCACGCAT 61.399 61.111 0.00 0.00 0.00 4.73
1938 1961 4.733542 TTAGCGCTGGGTTGGGGC 62.734 66.667 22.90 0.00 41.87 5.80
2063 2090 1.960689 CGAACCTTTTTGTGATGGGGT 59.039 47.619 0.00 0.00 0.00 4.95
2169 2196 8.826710 TCAACACAAATTCGAATATATGTCCTC 58.173 33.333 11.83 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 7.500720 TGTGATATAAATCATGGCAAGTGAG 57.499 36.000 0.00 0.00 43.87 3.51
130 131 8.528044 AAAAGGTGATTAGTAAGTTGAAACCA 57.472 30.769 0.00 0.00 0.00 3.67
259 260 7.202526 AGCACAACCACAATTTATATATGCAC 58.797 34.615 0.00 0.00 0.00 4.57
261 262 8.783093 TCTAGCACAACCACAATTTATATATGC 58.217 33.333 0.00 0.00 0.00 3.14
317 318 1.963338 GACTGCTCCAAACGCTGCT 60.963 57.895 0.00 0.00 0.00 4.24
323 324 0.319900 TCTGCTCGACTGCTCCAAAC 60.320 55.000 0.00 0.00 0.00 2.93
367 368 0.179001 TCGGAGCCTATCGGTGATCA 60.179 55.000 0.00 0.00 0.00 2.92
426 428 5.838521 TGGAGTGCTACCTTATGTGATGATA 59.161 40.000 0.00 0.00 0.00 2.15
427 429 4.655649 TGGAGTGCTACCTTATGTGATGAT 59.344 41.667 0.00 0.00 0.00 2.45
428 430 4.030216 TGGAGTGCTACCTTATGTGATGA 58.970 43.478 0.00 0.00 0.00 2.92
471 473 3.493129 TGCTATAATGTTTCGATGGACGC 59.507 43.478 0.00 0.00 42.26 5.19
531 533 2.487934 CGATCCATGAGGTTGGTGATC 58.512 52.381 0.00 0.00 38.01 2.92
645 647 6.769512 AGTCTAGTTGCACCTATTTCTCAAA 58.230 36.000 0.00 0.00 0.00 2.69
750 759 0.586802 GAGGTGCAGTTGAAACCGTC 59.413 55.000 0.00 0.00 39.07 4.79
775 784 3.908081 AAGTGGCGACGTCGGTGT 61.908 61.111 36.13 4.11 40.23 4.16
780 789 0.505655 GTGTTACAAGTGGCGACGTC 59.494 55.000 5.18 5.18 0.00 4.34
1029 1038 2.676265 GGCCGGGATGGTGTACCTT 61.676 63.158 2.18 0.00 41.21 3.50
1587 1596 1.220749 GAGGCGGTTGCTCATGGTA 59.779 57.895 0.00 0.00 42.25 3.25
1938 1961 2.670148 CCTTTCCCTCCTCACCCCG 61.670 68.421 0.00 0.00 0.00 5.73
2169 2196 6.879458 ACTACTAGTTTGCATTAACAAGGAGG 59.121 38.462 0.00 0.00 0.00 4.30
2222 2249 7.805071 CGCTCTATCTTCAAGTTGAACAAAAAT 59.195 33.333 14.35 6.18 32.21 1.82
2223 2250 7.132213 CGCTCTATCTTCAAGTTGAACAAAAA 58.868 34.615 14.35 0.48 32.21 1.94


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

AutoCloner maintained by Alex Coulton.