Multiple sequence alignment - TraesCS3A01G505800

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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 TraesCS3A01G505800 chr3A 100.000 2252 0 0 1 2252 727477626 727479877 0.000000e+00 4159
1 TraesCS3A01G505800 chr3B 92.132 2275 134 20 1 2252 804247655 804249907 0.000000e+00 3168
2 TraesCS3A01G505800 chr3D 94.108 1222 51 7 434 1640 597420736 597421951 0.000000e+00 1838
3 TraesCS3A01G505800 chr3D 81.955 1330 119 43 717 1981 597546746 597548019 0.000000e+00 1014
4 TraesCS3A01G505800 chr3D 86.149 296 28 5 1 284 597546203 597546497 7.810000e-80 307
5 TraesCS3A01G505800 chr3D 89.540 239 10 3 1 239 597420333 597420556 2.830000e-74 289
6 TraesCS3A01G505800 chr3D 87.421 159 11 3 223 374 597420572 597420728 8.270000e-40 174
7 TraesCS3A01G505800 chr3D 84.270 178 27 1 2065 2241 597548067 597548244 2.970000e-39 172
8 TraesCS3A01G505800 chr2A 97.070 1024 19 4 435 1447 605116273 605115250 0.000000e+00 1714
9 TraesCS3A01G505800 chr2A 98.853 436 5 0 1 436 605120313 605119878 0.000000e+00 778
10 TraesCS3A01G505800 chr2A 95.349 258 11 1 1585 1842 605114922 605114666 2.080000e-110 409


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 TraesCS3A01G505800 chr3A 727477626 727479877 2251 False 4159.000000 4159 100.000000 1 2252 1 chr3A.!!$F1 2251
1 TraesCS3A01G505800 chr3B 804247655 804249907 2252 False 3168.000000 3168 92.132000 1 2252 1 chr3B.!!$F1 2251
2 TraesCS3A01G505800 chr3D 597420333 597421951 1618 False 767.000000 1838 90.356333 1 1640 3 chr3D.!!$F1 1639
3 TraesCS3A01G505800 chr3D 597546203 597548244 2041 False 497.666667 1014 84.124667 1 2241 3 chr3D.!!$F2 2240
4 TraesCS3A01G505800 chr2A 605114666 605120313 5647 True 967.000000 1714 97.090667 1 1842 3 chr2A.!!$R1 1841

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
777 4443 0.389556 CCCGCATCGATCCATCAGAG 60.39 60.0 0.0 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2201 6124 1.711824 GTTATTTCGCAACCAACGCAC 59.288 47.619 0.0 0.0 0.0 5.34 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
321 363 2.826128 TGTGCTCGAAACTACTCCATCT 59.174 45.455 0.00 0.00 0.00 2.90
593 4258 8.218488 ACTACCTAAATGTTCTGGAAAGAAAGT 58.782 33.333 0.00 0.00 0.00 2.66
777 4443 0.389556 CCCGCATCGATCCATCAGAG 60.390 60.000 0.00 0.00 0.00 3.35
882 4553 0.669012 GCCGCAAGCTAGCTAGATCC 60.669 60.000 25.15 11.71 38.99 3.36
1018 4698 0.108186 GATGTCGTCCATGGACTGCA 60.108 55.000 35.84 31.74 42.54 4.41
1361 5079 5.525012 AGCTACACATGTGCACTGTATATTG 59.475 40.000 25.68 7.68 0.00 1.90
1411 5129 5.301805 TCGGCATAGTAATTGATCACTCTCA 59.698 40.000 0.00 0.00 0.00 3.27
1452 5172 6.966534 ATGGTGGTGATTAATTGGATCTTC 57.033 37.500 0.00 0.00 0.00 2.87
1583 5492 9.716531 TGAGGATTCATGATTCACTATTATGTC 57.283 33.333 17.08 0.00 33.25 3.06
1669 5582 9.308318 CAGATATGAGATATCAGAAGCAGAATG 57.692 37.037 5.32 0.00 43.20 2.67
1775 5691 3.685756 TCCATGTTTTATCGTTCGGGTTC 59.314 43.478 0.00 0.00 0.00 3.62
1845 5764 8.732746 ATATTGCTCGTAGTCCAACTAATTTT 57.267 30.769 0.00 0.00 31.62 1.82
1858 5777 8.352942 GTCCAACTAATTTTGTTCACTGAGAAT 58.647 33.333 0.00 0.00 38.76 2.40
1875 5794 8.893727 CACTGAGAATTAATTACCGGATTCTTT 58.106 33.333 9.46 0.00 38.56 2.52
1902 5821 7.320324 GTGTGTTGTTTCTGTATATTGTTCACG 59.680 37.037 0.00 0.00 0.00 4.35
1907 5826 7.380536 TGTTTCTGTATATTGTTCACGGTACT 58.619 34.615 0.00 0.00 0.00 2.73
1938 5857 9.678260 ATTTCTGAAATGTTTGATCTACTAGCT 57.322 29.630 14.47 0.00 0.00 3.32
1971 5890 9.546909 CAAAGATAGTAATGCACTAGTTTGTTG 57.453 33.333 0.00 0.00 43.01 3.33
1983 5902 8.462811 TGCACTAGTTTGTTGTAAGAAAATTGA 58.537 29.630 0.00 0.00 0.00 2.57
1993 5912 9.255304 TGTTGTAAGAAAATTGAACATAAAGCC 57.745 29.630 0.00 0.00 0.00 4.35
2000 5919 8.370182 AGAAAATTGAACATAAAGCCTCACAAT 58.630 29.630 0.00 0.00 0.00 2.71
2051 5973 6.891908 ACCACTTAGGATTGTAAGCATTCATT 59.108 34.615 0.00 0.00 41.22 2.57
2134 6056 9.485206 GGTTTCTCTAAGTTGTATCAAAGTACA 57.515 33.333 0.00 0.00 32.99 2.90
2185 6108 5.573380 ACCTGATGTGCCATGTAATCTAT 57.427 39.130 0.00 0.00 0.00 1.98
2201 6124 2.076100 TCTATTTGCAACAGCTCGTGG 58.924 47.619 0.00 0.00 0.00 4.94
2213 6136 3.521308 CTCGTGGTGCGTTGGTTGC 62.521 63.158 0.00 0.00 42.13 4.17
2247 6170 9.459276 CAAACTGTTCAACTTTATTTTTGTTCG 57.541 29.630 0.00 0.00 0.00 3.95
2248 6171 7.216920 ACTGTTCAACTTTATTTTTGTTCGC 57.783 32.000 0.00 0.00 0.00 4.70
2249 6172 6.809196 ACTGTTCAACTTTATTTTTGTTCGCA 59.191 30.769 0.00 0.00 0.00 5.10
2251 6174 6.035112 TGTTCAACTTTATTTTTGTTCGCACC 59.965 34.615 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
321 363 6.014755 TGGAATATGTGCATGTCTTGGAAAAA 60.015 34.615 0.00 0.00 0.00 1.94
504 4168 2.097791 GGTGTACACGGCAACAGAAAAA 59.902 45.455 19.41 0.00 0.00 1.94
882 4553 0.110688 CTGGCGTTGTGTGTTCGATG 60.111 55.000 0.00 0.00 0.00 3.84
1018 4698 1.078214 CCAGCACCACATGGATCGT 60.078 57.895 4.53 0.00 39.02 3.73
1390 5108 7.654923 TGATGTGAGAGTGATCAATTACTATGC 59.345 37.037 0.00 0.00 0.00 3.14
1411 5129 3.583966 ACCATTTGCTCCCAAATTGATGT 59.416 39.130 0.00 0.00 46.66 3.06
1583 5492 9.120538 AGGCTTAGTTACCATTTACACATAATG 57.879 33.333 0.00 0.00 33.72 1.90
1669 5582 6.930731 ACTAATTCTTGTCTGTTCTCTCTCC 58.069 40.000 0.00 0.00 0.00 3.71
1725 5641 5.219739 AGCAAGGAAGAAGATCCACCTATA 58.780 41.667 0.00 0.00 42.27 1.31
1775 5691 6.798476 CACATGCATAACCAGCGATTAATAAG 59.202 38.462 0.00 0.00 33.85 1.73
1845 5764 6.703319 TCCGGTAATTAATTCTCAGTGAACA 58.297 36.000 3.39 0.00 37.52 3.18
1858 5777 7.013464 ACAACACACAAAGAATCCGGTAATTAA 59.987 33.333 0.00 0.00 0.00 1.40
1875 5794 8.126074 GTGAACAATATACAGAAACAACACACA 58.874 33.333 0.00 0.00 0.00 3.72
1902 5821 8.134895 TCAAACATTTCAGAAATCACAAGTACC 58.865 33.333 5.32 0.00 0.00 3.34
1907 5826 9.897744 GTAGATCAAACATTTCAGAAATCACAA 57.102 29.630 5.32 0.00 0.00 3.33
1952 5871 8.671384 TTCTTACAACAAACTAGTGCATTACT 57.329 30.769 0.00 0.00 43.56 2.24
1953 5872 9.724839 TTTTCTTACAACAAACTAGTGCATTAC 57.275 29.630 0.00 0.00 0.00 1.89
1971 5890 9.129209 GTGAGGCTTTATGTTCAATTTTCTTAC 57.871 33.333 0.00 0.00 0.00 2.34
1983 5902 9.040939 GTAACAAAAATTGTGAGGCTTTATGTT 57.959 29.630 0.00 0.00 44.59 2.71
1991 5910 7.437862 TGAATCAAGTAACAAAAATTGTGAGGC 59.562 33.333 0.00 0.00 44.59 4.70
1993 5912 9.520204 ACTGAATCAAGTAACAAAAATTGTGAG 57.480 29.630 0.00 0.00 44.59 3.51
2023 5945 7.498900 TGAATGCTTACAATCCTAAGTGGTATG 59.501 37.037 0.00 0.00 37.07 2.39
2149 6072 6.974622 GGCACATCAGGTAATTAATGAAACAG 59.025 38.462 5.90 1.46 0.00 3.16
2169 6092 6.625520 CTGTTGCAAATAGATTACATGGCACA 60.626 38.462 0.00 0.00 39.53 4.57
2185 6108 1.726865 CACCACGAGCTGTTGCAAA 59.273 52.632 0.00 0.00 42.74 3.68
2201 6124 1.711824 GTTATTTCGCAACCAACGCAC 59.288 47.619 0.00 0.00 0.00 5.34
2205 6128 4.801516 ACAGTTTGTTATTTCGCAACCAAC 59.198 37.500 0.00 0.00 33.80 3.77


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

AutoCloner maintained by Alex Coulton.