Multiple sequence alignment - TraesCS5D01G294900

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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 TraesCS5D01G294900 chr5D 100.000 2894 0 0 1 2894 391985977 391988870 0.000000e+00 5345
1 TraesCS5D01G294900 chr5D 91.870 984 62 13 1894 2868 395726001 395726975 0.000000e+00 1358
2 TraesCS5D01G294900 chr5D 90.438 1004 82 8 1894 2888 395924269 395925267 0.000000e+00 1310
3 TraesCS5D01G294900 chr5B 98.447 2897 30 7 1 2894 472747866 472750750 0.000000e+00 5086
4 TraesCS5D01G294900 chr5B 92.325 456 33 2 2435 2888 475991164 475991619 0.000000e+00 647
5 TraesCS5D01G294900 chr5B 89.723 506 39 10 1894 2391 475990661 475991161 4.070000e-178 634
6 TraesCS5D01G294900 chr5A 89.573 1007 90 11 1894 2891 501819228 501820228 0.000000e+00 1264
7 TraesCS5D01G294900 chr5A 89.641 1004 89 11 1894 2888 501827584 501828581 0.000000e+00 1264
8 TraesCS5D01G294900 chr2D 89.595 519 46 5 2382 2894 549927969 549927453 0.000000e+00 652
9 TraesCS5D01G294900 chr2D 89.662 503 43 6 2401 2894 549737338 549736836 1.460000e-177 632
10 TraesCS5D01G294900 chr2D 89.662 503 43 6 2401 2894 550250097 550249595 1.460000e-177 632
11 TraesCS5D01G294900 chr2D 86.907 527 42 21 1894 2404 549928520 549928005 1.510000e-157 566
12 TraesCS5D01G294900 chr2D 86.266 466 52 8 1894 2352 574906220 574905760 2.000000e-136 496
13 TraesCS5D01G294900 chr2B 87.023 524 47 16 1894 2404 656237731 656237216 3.240000e-159 571


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 TraesCS5D01G294900 chr5D 391985977 391988870 2893 False 5345.0 5345 100.000 1 2894 1 chr5D.!!$F1 2893
1 TraesCS5D01G294900 chr5D 395726001 395726975 974 False 1358.0 1358 91.870 1894 2868 1 chr5D.!!$F2 974
2 TraesCS5D01G294900 chr5D 395924269 395925267 998 False 1310.0 1310 90.438 1894 2888 1 chr5D.!!$F3 994
3 TraesCS5D01G294900 chr5B 472747866 472750750 2884 False 5086.0 5086 98.447 1 2894 1 chr5B.!!$F1 2893
4 TraesCS5D01G294900 chr5B 475990661 475991619 958 False 640.5 647 91.024 1894 2888 2 chr5B.!!$F2 994
5 TraesCS5D01G294900 chr5A 501819228 501820228 1000 False 1264.0 1264 89.573 1894 2891 1 chr5A.!!$F1 997
6 TraesCS5D01G294900 chr5A 501827584 501828581 997 False 1264.0 1264 89.641 1894 2888 1 chr5A.!!$F2 994
7 TraesCS5D01G294900 chr2D 549736836 549737338 502 True 632.0 632 89.662 2401 2894 1 chr2D.!!$R1 493
8 TraesCS5D01G294900 chr2D 550249595 550250097 502 True 632.0 632 89.662 2401 2894 1 chr2D.!!$R2 493
9 TraesCS5D01G294900 chr2D 549927453 549928520 1067 True 609.0 652 88.251 1894 2894 2 chr2D.!!$R4 1000
10 TraesCS5D01G294900 chr2B 656237216 656237731 515 True 571.0 571 87.023 1894 2404 1 chr2B.!!$R1 510

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
357 358 0.673644 GCAACACCACCGTCTGCTAT 60.674 55.0 0.0 0.0 0.0 2.97 F
358 359 1.078709 CAACACCACCGTCTGCTATG 58.921 55.0 0.0 0.0 0.0 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1167 1168 1.599171 GCCACATCTCTCTCATCGTCG 60.599 57.143 0.0 0.0 0.0 5.12 R
2207 2215 3.201266 ACCCTGACTACCTGACAACAAAA 59.799 43.478 0.0 0.0 0.0 2.44 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 1.289066 CGACTTCTCGGTTGAGGCA 59.711 57.895 0.00 0.00 42.79 4.75
310 311 1.870055 CTGCTGCAAACCGCCTCATT 61.870 55.000 3.02 0.00 41.33 2.57
334 335 1.228245 TTCAGAGCTTGCCACCCAC 60.228 57.895 0.00 0.00 0.00 4.61
357 358 0.673644 GCAACACCACCGTCTGCTAT 60.674 55.000 0.00 0.00 0.00 2.97
358 359 1.078709 CAACACCACCGTCTGCTATG 58.921 55.000 0.00 0.00 0.00 2.23
424 425 1.303888 ATGAGCAAGGGTGGCTGTG 60.304 57.895 0.00 0.00 42.78 3.66
453 454 1.135774 GTGTCACGATCGACTGCTGTA 60.136 52.381 24.34 0.55 36.82 2.74
538 539 4.421446 AGCGTCGTCGTCGTCGTC 62.421 66.667 19.72 13.26 46.29 4.20
540 541 4.400776 CGTCGTCGTCGTCGTCGT 62.401 66.667 18.87 0.00 45.27 4.34
541 542 2.857992 GTCGTCGTCGTCGTCGTG 60.858 66.667 18.44 6.23 45.27 4.35
542 543 4.707840 TCGTCGTCGTCGTCGTGC 62.708 66.667 18.44 5.67 45.27 5.34
925 926 8.062065 AGTTCTCTCTAGGAATTGACTTACAG 57.938 38.462 0.00 0.00 0.00 2.74
1061 1062 5.836821 AGACGTCTTATCTTGACATGCTA 57.163 39.130 13.58 0.00 34.37 3.49
1077 1078 1.299926 CTACCATGTCGTAGCGGGC 60.300 63.158 0.00 0.00 29.96 6.13
1167 1168 1.762957 TCTGGCCAGATACTACTTGCC 59.237 52.381 32.00 0.00 45.26 4.52
1275 1276 2.289444 TGATCGGGTTGTCAAGAAGGAC 60.289 50.000 0.00 0.00 38.29 3.85
1299 1300 6.795399 CATGGAATTAGTCATGTTGGGTAAC 58.205 40.000 0.00 0.00 36.82 2.50
1338 1339 5.184479 GGGTGTAATTAAAGAACCAGGAACC 59.816 44.000 0.00 0.00 32.28 3.62
1508 1509 3.751518 GGTGTCATATGTATCAACCCCC 58.248 50.000 1.90 0.00 0.00 5.40
1735 1736 4.080526 ACCGTGTATATTTTCAGAAGGGCT 60.081 41.667 0.00 0.00 0.00 5.19
1775 1776 2.983229 TGAGAAGATCCTTTCAGCAGC 58.017 47.619 0.00 0.00 0.00 5.25
2207 2215 3.642848 ACATTTGCCTTGTGAGGTTCATT 59.357 39.130 0.00 0.00 45.44 2.57
2815 2890 4.407621 TCCATGTACACGGATGATTACCTT 59.592 41.667 6.56 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
225 226 3.615811 AGGCTGTGGGGGAGGAGA 61.616 66.667 0.00 0.00 0.00 3.71
226 227 3.406200 CAGGCTGTGGGGGAGGAG 61.406 72.222 6.28 0.00 0.00 3.69
227 228 3.940480 TCAGGCTGTGGGGGAGGA 61.940 66.667 15.27 0.00 0.00 3.71
228 229 3.721706 GTCAGGCTGTGGGGGAGG 61.722 72.222 15.27 0.00 0.00 4.30
229 230 2.930019 TGTCAGGCTGTGGGGGAG 60.930 66.667 15.27 0.00 0.00 4.30
283 284 4.016629 TTTGCAGCAGCTCGCACG 62.017 61.111 16.27 0.00 46.13 5.34
334 335 2.177580 AGACGGTGGTGTTGCAACG 61.178 57.895 23.79 13.60 0.00 4.10
357 358 2.685017 AGCACTCGCATCCCCTCA 60.685 61.111 0.00 0.00 42.27 3.86
358 359 2.202987 CAGCACTCGCATCCCCTC 60.203 66.667 0.00 0.00 42.27 4.30
424 425 0.025513 GATCGTGACACAATCGCAGC 59.974 55.000 6.37 0.00 37.73 5.25
430 431 1.067565 AGCAGTCGATCGTGACACAAT 60.068 47.619 15.94 0.00 41.41 2.71
661 662 2.229784 CTCACCCCTCACTGCATTTTTC 59.770 50.000 0.00 0.00 0.00 2.29
662 663 2.158475 TCTCACCCCTCACTGCATTTTT 60.158 45.455 0.00 0.00 0.00 1.94
663 664 1.425066 TCTCACCCCTCACTGCATTTT 59.575 47.619 0.00 0.00 0.00 1.82
1061 1062 3.371097 CTGCCCGCTACGACATGGT 62.371 63.158 0.00 0.00 0.00 3.55
1167 1168 1.599171 GCCACATCTCTCTCATCGTCG 60.599 57.143 0.00 0.00 0.00 5.12
1275 1276 6.376864 TGTTACCCAACATGACTAATTCCATG 59.623 38.462 0.00 11.53 44.12 3.66
1297 1298 4.159557 ACACCCTTAGGCATGAAAATGTT 58.840 39.130 0.00 0.00 36.11 2.71
1299 1300 5.913137 TTACACCCTTAGGCATGAAAATG 57.087 39.130 0.00 0.00 36.11 2.32
1338 1339 5.739161 GCATTACTTTGATTTGCCGTAAGAG 59.261 40.000 0.00 0.00 43.02 2.85
1508 1509 4.452733 GGTGCTCCCGAAGTCCCG 62.453 72.222 0.00 0.00 0.00 5.14
1775 1776 4.331717 ACAAGAACACTTTTACTCACCACG 59.668 41.667 0.00 0.00 0.00 4.94
1819 1820 6.070078 ACCATGAGTATTTGGGAAATGCATTT 60.070 34.615 24.33 24.33 36.15 2.32
1863 1864 7.156000 TCATTCGACTGAAAACAGTTGGTATA 58.844 34.615 14.87 3.00 37.71 1.47
1886 1887 6.299805 AGTGTATGAGCAATTCCTACTTCA 57.700 37.500 0.00 0.00 30.74 3.02
2207 2215 3.201266 ACCCTGACTACCTGACAACAAAA 59.799 43.478 0.00 0.00 0.00 2.44
2815 2890 3.516700 TCTCCACTCTCTTGCAATGATCA 59.483 43.478 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.