Multiple sequence alignment - TraesCS7D01G014100

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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 TraesCS7D01G014100 chr7D 100.000 2765 0 0 1 2765 6354816 6352052 0.000000e+00 5107.0
1 TraesCS7D01G014100 chr3D 98.090 1885 21 2 292 2161 415662841 415660957 0.000000e+00 3267.0
2 TraesCS7D01G014100 chr3D 94.976 617 30 1 2147 2763 415659782 415659167 0.000000e+00 966.0
3 TraesCS7D01G014100 chr3D 97.643 297 7 0 1 297 415665543 415665247 6.830000e-141 510.0
4 TraesCS7D01G014100 chr3D 84.211 285 43 1 1 283 2408200 2408484 2.710000e-70 276.0
5 TraesCS7D01G014100 chr3D 81.122 196 27 10 123 312 360577551 360577360 6.170000e-32 148.0
6 TraesCS7D01G014100 chr3B 89.072 970 51 23 886 1814 542494295 542493340 0.000000e+00 1153.0
7 TraesCS7D01G014100 chr3B 93.168 161 10 1 1874 2033 542491394 542491234 4.600000e-58 235.0
8 TraesCS7D01G014100 chr3B 81.622 185 19 8 643 821 542494569 542494394 3.710000e-29 139.0
9 TraesCS7D01G014100 chr3A 86.393 926 55 26 880 1797 534477856 534478718 0.000000e+00 946.0
10 TraesCS7D01G014100 chr3A 85.433 913 80 28 1789 2696 534484243 534485107 0.000000e+00 900.0
11 TraesCS7D01G014100 chr3A 83.392 283 34 9 52 328 1704805 1704530 1.640000e-62 250.0
12 TraesCS7D01G014100 chr1A 78.344 314 41 18 53 351 234238021 234237720 7.870000e-41 178.0
13 TraesCS7D01G014100 chr1D 80.451 133 26 0 1 133 236443136 236443268 4.870000e-18 102.0
14 TraesCS7D01G014100 chr1D 85.714 56 8 0 73 128 332685866 332685811 2.970000e-05 60.2
15 TraesCS7D01G014100 chr7A 90.385 52 5 0 75 126 25105826 25105775 4.940000e-08 69.4
16 TraesCS7D01G014100 chr4A 84.000 75 8 4 271 344 676535237 676535166 4.940000e-08 69.4
17 TraesCS7D01G014100 chrUn 100.000 28 0 0 161 188 132039407 132039434 5.000000e-03 52.8


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 TraesCS7D01G014100 chr7D 6352052 6354816 2764 True 5107 5107 100.000 1 2765 1 chr7D.!!$R1 2764
1 TraesCS7D01G014100 chr3D 415659167 415665543 6376 True 1581 3267 96.903 1 2763 3 chr3D.!!$R2 2762
2 TraesCS7D01G014100 chr3B 542491234 542494569 3335 True 509 1153 87.954 643 2033 3 chr3B.!!$R1 1390
3 TraesCS7D01G014100 chr3A 534477856 534478718 862 False 946 946 86.393 880 1797 1 chr3A.!!$F1 917
4 TraesCS7D01G014100 chr3A 534484243 534485107 864 False 900 900 85.433 1789 2696 1 chr3A.!!$F2 907

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
442 2854 2.857483 TGGCATTTCGAAGGTTCTCAA 58.143 42.857 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2376 7981 1.07505 ACCACCCGTCTAGAGAGTTGA 59.925 52.381 0.0 0.0 0.0 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
204 205 4.609018 CGGCGGGCTGGAGTATGG 62.609 72.222 0.00 0.00 0.00 2.74
260 261 7.054124 AGGATAAATTTGCCTTCACTATTCGA 58.946 34.615 0.00 0.00 0.00 3.71
268 269 5.084519 TGCCTTCACTATTCGATATAGGGT 58.915 41.667 13.20 0.00 0.00 4.34
269 270 5.542635 TGCCTTCACTATTCGATATAGGGTT 59.457 40.000 13.20 0.00 0.00 4.11
275 276 6.266103 TCACTATTCGATATAGGGTTTCGGTT 59.734 38.462 13.20 0.00 33.82 4.44
409 2821 5.891551 AGGGGCGAAATGTTCAGTATTTAAT 59.108 36.000 0.00 0.00 0.00 1.40
442 2854 2.857483 TGGCATTTCGAAGGTTCTCAA 58.143 42.857 0.00 0.00 0.00 3.02
473 2885 5.702209 CAGGGGACAAAATGAATGGAAAAAG 59.298 40.000 0.00 0.00 0.00 2.27
477 2889 5.333263 GGACAAAATGAATGGAAAAAGCACG 60.333 40.000 0.00 0.00 0.00 5.34
942 3395 3.243267 ACAAAAGTCGGGTGAAATTTCCG 60.243 43.478 15.48 12.46 44.59 4.30
2039 6455 3.587797 TTTTGAACTATCTCGCGAGGT 57.412 42.857 33.98 30.74 0.00 3.85
2193 7798 3.963129 AGGTCTCTCTCTACCTCAACAG 58.037 50.000 0.00 0.00 42.60 3.16
2198 7803 3.357203 TCTCTCTACCTCAACAGCGATT 58.643 45.455 0.00 0.00 0.00 3.34
2334 7939 0.727398 GCTATTGGTGTGGCGACTTC 59.273 55.000 0.00 0.00 0.00 3.01
2337 7942 2.391724 ATTGGTGTGGCGACTTCGGT 62.392 55.000 0.00 0.00 40.23 4.69
2360 7965 1.532868 CTTCTTCCTGTTGTTCTGCGG 59.467 52.381 0.00 0.00 0.00 5.69
2376 7981 0.668535 GCGGCCTGTTTCAGTTTCTT 59.331 50.000 0.00 0.00 0.00 2.52
2457 8062 8.918961 TCAAACTTATGTGTTTCAACGATTTT 57.081 26.923 0.00 0.00 37.98 1.82
2474 8079 9.731519 CAACGATTTTTAAATCTCATTTCAAGC 57.268 29.630 12.05 0.00 41.99 4.01
2513 8118 4.320870 GGTGTTTAAAGCCTAGTGTAGCA 58.679 43.478 0.00 0.00 0.00 3.49
2543 8148 2.224670 TGCAGGTGTCCCTTTCGTTTAT 60.225 45.455 0.00 0.00 39.89 1.40
2613 8218 2.703007 AGGAAGAAGCAGGCTAGTATGG 59.297 50.000 0.00 0.00 0.00 2.74
2629 8234 6.931281 GCTAGTATGGTTCTCAATGCTATTGA 59.069 38.462 10.01 10.01 0.00 2.57
2718 8323 9.732130 AAGATGCTCTTTCTAGTGTATTTCTTT 57.268 29.630 0.00 0.00 31.57 2.52
2748 8353 2.036733 TGTTACAAAGCCGCACTAGAGT 59.963 45.455 0.00 0.00 0.00 3.24
2763 8368 4.081586 CACTAGAGTGGGAAGAAAGGTACC 60.082 50.000 2.73 2.73 42.10 3.34
2764 8369 1.900486 AGAGTGGGAAGAAAGGTACCG 59.100 52.381 6.18 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 112 4.082523 CCGCCACCACCGATGACT 62.083 66.667 0.00 0.00 0.00 3.41
194 195 4.040952 CCAATCTCCCTAACCATACTCCAG 59.959 50.000 0.00 0.00 0.00 3.86
204 205 4.731313 AATCCCATCCAATCTCCCTAAC 57.269 45.455 0.00 0.00 0.00 2.34
260 261 3.243975 CGCACCTAACCGAAACCCTATAT 60.244 47.826 0.00 0.00 0.00 0.86
268 269 2.522836 TACAACGCACCTAACCGAAA 57.477 45.000 0.00 0.00 0.00 3.46
269 270 2.406130 CTTACAACGCACCTAACCGAA 58.594 47.619 0.00 0.00 0.00 4.30
275 276 0.899720 CCTCCCTTACAACGCACCTA 59.100 55.000 0.00 0.00 0.00 3.08
336 2748 3.275999 GCTTTCGGGGCATTTCTAACTA 58.724 45.455 0.00 0.00 0.00 2.24
348 2760 3.830192 GGCTGCATGCTTTCGGGG 61.830 66.667 20.33 1.71 42.39 5.73
409 2821 7.973388 CCTTCGAAATGCCAATTTTATGAGTTA 59.027 33.333 0.00 0.00 36.10 2.24
442 2854 3.575805 TCATTTTGTCCCCTGCTCTTTT 58.424 40.909 0.00 0.00 0.00 2.27
473 2885 4.487412 GCAGAAGCATGGCCGTGC 62.487 66.667 37.83 37.83 45.38 5.34
477 2889 3.512516 GACGGCAGAAGCATGGCC 61.513 66.667 0.00 0.00 44.61 5.36
865 3300 3.515286 CCATGCCCGCTTGCTGAG 61.515 66.667 0.00 0.00 0.00 3.35
1548 4033 4.426313 TCCTCGCGCTCCTCCTCA 62.426 66.667 5.56 0.00 0.00 3.86
2193 7798 2.602322 GCGGCTCCAGATCAATCGC 61.602 63.158 0.00 0.00 35.12 4.58
2198 7803 2.895680 GACAGCGGCTCCAGATCA 59.104 61.111 0.00 0.00 0.00 2.92
2334 7939 4.627467 CAGAACAACAGGAAGAAGATACCG 59.373 45.833 0.00 0.00 0.00 4.02
2337 7942 4.245660 CGCAGAACAACAGGAAGAAGATA 58.754 43.478 0.00 0.00 0.00 1.98
2376 7981 1.075050 ACCACCCGTCTAGAGAGTTGA 59.925 52.381 0.00 0.00 0.00 3.18
2457 8062 3.761218 TGGCCGCTTGAAATGAGATTTAA 59.239 39.130 0.00 0.00 31.47 1.52
2474 8079 2.173669 CCGCAATAGTCACTGGCCG 61.174 63.158 0.00 0.00 0.00 6.13
2513 8118 1.187567 GGACACCTGCAAATGCCCTT 61.188 55.000 2.46 0.00 41.18 3.95
2543 8148 5.201713 TGAAAATTGCACCGAACCAATAA 57.798 34.783 0.00 0.00 31.82 1.40
2613 8218 7.856398 CACAGATTGATCAATAGCATTGAGAAC 59.144 37.037 20.75 4.31 0.00 3.01
2629 8234 6.016777 GGAAAGACAACTTGACACAGATTGAT 60.017 38.462 0.00 0.00 36.39 2.57
2725 8330 2.036733 TCTAGTGCGGCTTTGTAACACT 59.963 45.455 0.00 0.00 43.60 3.55
2729 8334 2.611971 CCACTCTAGTGCGGCTTTGTAA 60.612 50.000 4.53 0.00 44.34 2.41
2735 8340 1.608717 CTTCCCACTCTAGTGCGGCT 61.609 60.000 4.53 0.00 44.34 5.52


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

AutoCloner maintained by Alex Coulton.