Multiple sequence alignment - TraesCS2A01G182000

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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 TraesCS2A01G182000 chr2A 100.000 2747 0 0 1 2747 141284422 141281676 0.000000e+00 5073
1 TraesCS2A01G182000 chr2D 94.811 2679 80 24 1 2648 133273997 133271347 0.000000e+00 4122
2 TraesCS2A01G182000 chr2D 97.030 101 3 0 2647 2747 133271196 133271096 1.310000e-38 171
3 TraesCS2A01G182000 chr2B 93.483 2762 135 23 1 2747 189746816 189744085 0.000000e+00 4061


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 TraesCS2A01G182000 chr2A 141281676 141284422 2746 True 5073.0 5073 100.0000 1 2747 1 chr2A.!!$R1 2746
1 TraesCS2A01G182000 chr2D 133271096 133273997 2901 True 2146.5 4122 95.9205 1 2747 2 chr2D.!!$R1 2746
2 TraesCS2A01G182000 chr2B 189744085 189746816 2731 True 4061.0 4061 93.4830 1 2747 1 chr2B.!!$R1 2746

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
303 325 1.069500 CCCGAATGACCACACGAAAAC 60.069 52.381 0.0 0.0 0.0 2.43 F
350 372 1.997311 CTCAGCCCTCCATCCACCA 60.997 63.158 0.0 0.0 0.0 4.17 F
449 473 2.200955 GTCCCTTTCCTCTTCATCCCT 58.799 52.381 0.0 0.0 0.0 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1173 1206 1.071385 CAGAACTCCTTCCACAGCACT 59.929 52.381 0.00 0.0 0.00 4.40 R
1446 1479 1.133809 CACCTTCTTCCCCCTGGTCA 61.134 60.000 0.00 0.0 0.00 4.02 R
2177 2210 1.427020 GCAACTGCTCGCTGATTCC 59.573 57.895 2.72 0.0 38.21 3.01 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
27 28 8.886719 TCTTATCAAAGACATGCACTTCATTAG 58.113 33.333 6.28 5.89 36.80 1.73
41 43 9.890629 TGCACTTCATTAGATTCTACTTAATGT 57.109 29.630 6.73 0.00 31.97 2.71
56 58 9.567776 TCTACTTAATGTGGATTTGTCTTTTGA 57.432 29.630 0.00 0.00 31.00 2.69
60 62 6.713762 AATGTGGATTTGTCTTTTGAGTGA 57.286 33.333 0.00 0.00 0.00 3.41
67 69 5.772825 TTTGTCTTTTGAGTGATCAAGGG 57.227 39.130 0.00 0.00 0.00 3.95
82 88 2.281484 GGGAGAGTTTGCGTGGCA 60.281 61.111 0.00 0.00 36.47 4.92
101 107 4.776837 TGGCATGAATGTGGGTAAAGAAAT 59.223 37.500 0.00 0.00 0.00 2.17
110 116 6.531503 TGTGGGTAAAGAAATTTGTTCACA 57.468 33.333 13.14 13.14 0.00 3.58
121 127 7.725251 AGAAATTTGTTCACAGGCTGATAAAA 58.275 30.769 23.66 13.55 0.00 1.52
130 136 9.982651 GTTCACAGGCTGATAAAACTATATCTA 57.017 33.333 23.66 0.00 34.14 1.98
131 137 9.982651 TTCACAGGCTGATAAAACTATATCTAC 57.017 33.333 23.66 0.00 34.14 2.59
137 143 8.512956 GGCTGATAAAACTATATCTACGAGTCA 58.487 37.037 0.00 0.00 34.14 3.41
192 202 6.761099 TTTTATGCGGAAATTACCAAGCTA 57.239 33.333 0.00 0.00 0.00 3.32
193 203 6.761099 TTTATGCGGAAATTACCAAGCTAA 57.239 33.333 0.00 0.00 0.00 3.09
194 204 6.952773 TTATGCGGAAATTACCAAGCTAAT 57.047 33.333 0.00 0.00 0.00 1.73
195 205 8.453238 TTTATGCGGAAATTACCAAGCTAATA 57.547 30.769 0.00 0.00 0.00 0.98
222 232 5.977489 AAAGTAACTAAATGAACCCCTGC 57.023 39.130 0.00 0.00 0.00 4.85
223 233 4.650972 AGTAACTAAATGAACCCCTGCA 57.349 40.909 0.00 0.00 0.00 4.41
224 234 4.589908 AGTAACTAAATGAACCCCTGCAG 58.410 43.478 6.78 6.78 0.00 4.41
225 235 3.806949 AACTAAATGAACCCCTGCAGA 57.193 42.857 17.39 0.00 0.00 4.26
233 255 7.732222 AAATGAACCCCTGCAGAAAATAATA 57.268 32.000 17.39 0.00 0.00 0.98
236 258 6.930731 TGAACCCCTGCAGAAAATAATAAAC 58.069 36.000 17.39 0.00 0.00 2.01
259 281 2.697431 TTGATGAAAACGGCGAAAGG 57.303 45.000 16.62 0.00 0.00 3.11
265 287 2.114056 GAAAACGGCGAAAGGAAACAC 58.886 47.619 16.62 0.00 0.00 3.32
303 325 1.069500 CCCGAATGACCACACGAAAAC 60.069 52.381 0.00 0.00 0.00 2.43
350 372 1.997311 CTCAGCCCTCCATCCACCA 60.997 63.158 0.00 0.00 0.00 4.17
449 473 2.200955 GTCCCTTTCCTCTTCATCCCT 58.799 52.381 0.00 0.00 0.00 4.20
914 941 2.360553 ATGCTCTTCGTGTGACTGAG 57.639 50.000 0.00 0.00 0.00 3.35
983 1016 4.056125 CGGTCGCTGCTGGAGTGA 62.056 66.667 8.42 8.42 38.97 3.41
1173 1206 2.357034 GACGAGGTCGCCAAGCAA 60.357 61.111 0.00 0.00 44.43 3.91
1446 1479 0.806102 CCGATCCGTGCGAACATCTT 60.806 55.000 0.00 0.00 0.00 2.40
1464 1497 0.402861 TTGACCAGGGGGAAGAAGGT 60.403 55.000 0.00 0.00 38.05 3.50
1759 1792 4.500545 CGGAGGAGTAATCATCAGGAACAG 60.501 50.000 7.18 0.00 0.00 3.16
1810 1843 7.739498 TCTTGGTTCCTGTCATTAGTTTAAC 57.261 36.000 0.00 0.00 0.00 2.01
1846 1879 5.883115 AGCTTAGCCTTATCTTCAAAGGTTC 59.117 40.000 0.00 0.00 44.56 3.62
2032 2065 3.891049 GACCAATTTCTATGGGCTGACT 58.109 45.455 0.00 0.00 43.09 3.41
2144 2177 2.545537 TGCATACGTGTGGTTTACCA 57.454 45.000 14.49 0.00 45.30 3.25
2177 2210 7.341769 TGATATTTACATCCTGAAACCCCAAAG 59.658 37.037 0.00 0.00 0.00 2.77
2186 2219 1.202348 GAAACCCCAAAGGAATCAGCG 59.798 52.381 0.00 0.00 39.89 5.18
2370 2403 4.090090 TCAGTAAGAAAGCTCACTAGGCT 58.910 43.478 0.00 0.00 42.31 4.58
2412 2445 7.425224 ACTAATCTTAGTGCATGGTACTTCT 57.575 36.000 1.87 0.00 42.13 2.85
2628 2662 6.544928 TGTGTGATGTATCAACCTCATAGT 57.455 37.500 0.00 0.00 38.75 2.12
2632 2666 8.391106 GTGTGATGTATCAACCTCATAGTTTTC 58.609 37.037 0.00 0.00 38.75 2.29
2693 2879 7.011109 GCGATAAAACTGCCAGTTAGAATAAGA 59.989 37.037 11.10 0.00 37.47 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 43 6.016024 CCTTGATCACTCAAAAGACAAATCCA 60.016 38.462 0.00 0.00 40.78 3.41
48 50 4.899502 TCTCCCTTGATCACTCAAAAGAC 58.100 43.478 0.00 0.00 40.78 3.01
56 58 2.613977 CGCAAACTCTCCCTTGATCACT 60.614 50.000 0.00 0.00 0.00 3.41
60 62 1.611673 CCACGCAAACTCTCCCTTGAT 60.612 52.381 0.00 0.00 0.00 2.57
67 69 0.874390 TTCATGCCACGCAAACTCTC 59.126 50.000 0.00 0.00 43.62 3.20
82 88 8.428063 TGAACAAATTTCTTTACCCACATTCAT 58.572 29.630 0.00 0.00 0.00 2.57
101 107 7.759489 ATAGTTTTATCAGCCTGTGAACAAA 57.241 32.000 0.00 0.00 39.19 2.83
110 116 8.638629 ACTCGTAGATATAGTTTTATCAGCCT 57.361 34.615 0.00 0.00 33.89 4.58
121 127 8.569641 GGATTTTGTCTGACTCGTAGATATAGT 58.430 37.037 9.51 0.00 33.89 2.12
130 136 2.557056 TCTCGGATTTTGTCTGACTCGT 59.443 45.455 9.51 0.00 37.31 4.18
131 137 3.217599 TCTCGGATTTTGTCTGACTCG 57.782 47.619 9.51 4.15 37.31 4.18
233 255 4.363999 TCGCCGTTTTCATCAATTTGTTT 58.636 34.783 0.00 0.00 0.00 2.83
236 258 4.143347 CCTTTCGCCGTTTTCATCAATTTG 60.143 41.667 0.00 0.00 0.00 2.32
259 281 5.392380 GGATGGATGAGTTCATGTGTGTTTC 60.392 44.000 0.00 0.00 36.57 2.78
265 287 2.579873 GGGGATGGATGAGTTCATGTG 58.420 52.381 0.00 0.00 36.57 3.21
449 473 1.602237 GTGCGGAAGGAAGGGATCA 59.398 57.895 0.00 0.00 0.00 2.92
475 499 2.592308 GGTAGGGCAGGAGCTTGG 59.408 66.667 0.00 0.00 41.70 3.61
983 1016 1.338960 CCATTTCCGGCAGCCAAAATT 60.339 47.619 13.30 0.00 0.00 1.82
1173 1206 1.071385 CAGAACTCCTTCCACAGCACT 59.929 52.381 0.00 0.00 0.00 4.40
1446 1479 1.133809 CACCTTCTTCCCCCTGGTCA 61.134 60.000 0.00 0.00 0.00 4.02
1759 1792 6.404708 ACATAGCATATCATCACCTGATCAC 58.595 40.000 0.00 0.00 43.70 3.06
2144 2177 8.408601 GTTTCAGGATGTAAATATCATGTGCTT 58.591 33.333 0.00 0.00 39.26 3.91
2177 2210 1.427020 GCAACTGCTCGCTGATTCC 59.573 57.895 2.72 0.00 38.21 3.01
2311 2344 5.113383 ACTGATCGTTGTTTGAACAGTGTA 58.887 37.500 0.00 0.00 44.58 2.90
2370 2403 1.860240 AGTAGATGAGGGGTAGAGCCA 59.140 52.381 0.00 0.00 39.65 4.75
2412 2445 3.636300 CCATGATCCCGGCTTCATTTAAA 59.364 43.478 13.07 0.00 30.24 1.52
2693 2879 9.396022 ACATAAGTAAGCTTACATTTATGCTGT 57.604 29.630 32.95 23.46 39.70 4.40


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

AutoCloner maintained by Alex Coulton.