Multiple sequence alignment - TraesCS3D01G293000

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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 TraesCS3D01G293000 chr3D 100.000 2228 0 0 1 2228 402797259 402795032 0.000000e+00 4115.0
1 TraesCS3D01G293000 chr3B 92.137 2124 121 24 129 2224 528632180 528630075 0.000000e+00 2955.0
2 TraesCS3D01G293000 chr3B 96.591 88 3 0 1 88 528632270 528632183 1.780000e-31 147.0
3 TraesCS3D01G293000 chr3A 92.582 2022 96 25 229 2224 523747078 523745085 0.000000e+00 2854.0
4 TraesCS3D01G293000 chr3A 96.667 150 4 1 58 207 523747213 523747065 4.750000e-62 248.0
5 TraesCS3D01G293000 chr3A 100.000 41 0 0 1 41 523747248 523747208 2.370000e-10 76.8


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 TraesCS3D01G293000 chr3D 402795032 402797259 2227 True 4115.0 4115 100.000000 1 2228 1 chr3D.!!$R1 2227
1 TraesCS3D01G293000 chr3B 528630075 528632270 2195 True 1551.0 2955 94.364000 1 2224 2 chr3B.!!$R1 2223
2 TraesCS3D01G293000 chr3A 523745085 523747248 2163 True 1059.6 2854 96.416333 1 2224 3 chr3A.!!$R1 2223

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
580 584 0.886563 GTACTATCGCCGGGCATACT 59.113 55.0 20.71 7.6 0.0 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 1818 0.459411 AGTTGGTGTTTTTGGCGCAC 60.459 50.0 10.83 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
41 42 3.139397 ACCCATTGAGTGTGGAAGGTTAA 59.861 43.478 0.00 0.00 39.12 2.01
209 210 1.206371 GGCTCAACCATACACCTACGT 59.794 52.381 0.00 0.00 38.86 3.57
290 291 2.890945 CCCCTTTTCTTCCATTCGTTGT 59.109 45.455 0.00 0.00 0.00 3.32
331 332 3.385193 TGCGTGTATCGAATCATGGAT 57.615 42.857 12.18 0.00 42.86 3.41
447 451 4.404654 GCAAAGGCGCCTGAACCG 62.405 66.667 33.60 17.57 0.00 4.44
451 455 1.515521 AAAGGCGCCTGAACCGAAAG 61.516 55.000 33.60 0.00 0.00 2.62
455 459 1.503818 GCGCCTGAACCGAAAGACAA 61.504 55.000 0.00 0.00 0.00 3.18
580 584 0.886563 GTACTATCGCCGGGCATACT 59.113 55.000 20.71 7.60 0.00 2.12
657 661 2.818132 CACTCAGGAGATCGGCCC 59.182 66.667 2.79 0.00 0.00 5.80
660 664 4.458829 TCAGGAGATCGGCCCGGT 62.459 66.667 1.90 0.00 0.00 5.28
761 765 3.925090 GTCTATCCCACCGGCCGG 61.925 72.222 42.17 42.17 42.03 6.13
819 826 2.095567 CCCCGTGTATATAAGTCGGTCG 60.096 54.545 15.43 6.29 39.62 4.79
861 868 2.243736 ACTTCCTAGCTAGCTCCAGAGT 59.756 50.000 23.26 17.68 0.00 3.24
874 889 1.651240 CCAGAGTCCATTGCCTTGCG 61.651 60.000 0.00 0.00 0.00 4.85
878 893 3.372730 TCCATTGCCTTGCGGTGC 61.373 61.111 0.00 0.00 0.00 5.01
1146 1161 1.771255 GAGGTATCCATGAAGGTGCCT 59.229 52.381 0.00 0.00 36.65 4.75
1173 1188 2.997315 CAGAGGCAGGTCGGGACA 60.997 66.667 0.75 0.00 0.00 4.02
1372 1390 2.480555 CCATTCGTTCGGTGCTGC 59.519 61.111 0.00 0.00 0.00 5.25
1428 1454 5.651576 AGGGCGCTTTCCTACTATATACTAC 59.348 44.000 7.64 0.00 31.86 2.73
1429 1455 5.651576 GGGCGCTTTCCTACTATATACTACT 59.348 44.000 7.64 0.00 0.00 2.57
1430 1456 6.825721 GGGCGCTTTCCTACTATATACTACTA 59.174 42.308 7.64 0.00 0.00 1.82
1431 1457 7.012232 GGGCGCTTTCCTACTATATACTACTAG 59.988 44.444 7.64 0.00 0.00 2.57
1474 1512 5.830000 ATGTCATCATGTCCACAGAAATG 57.170 39.130 0.00 0.00 38.88 2.32
1662 1702 1.137872 GGCATGATAGGCTAGCGCTAT 59.862 52.381 19.19 19.57 36.09 2.97
1664 1704 2.819115 CATGATAGGCTAGCGCTATGG 58.181 52.381 19.19 8.56 36.09 2.74
1713 1753 4.217983 ACGTACCAACCTCTGTTCTCTAAG 59.782 45.833 0.00 0.00 30.42 2.18
1918 1959 1.934399 GCGGCAGCTATGATCTGACTC 60.934 57.143 0.00 0.00 37.44 3.36
2001 2045 5.053811 TGACTTCGATACAGCTTCACAAAA 58.946 37.500 0.00 0.00 0.00 2.44
2002 2046 5.700832 TGACTTCGATACAGCTTCACAAAAT 59.299 36.000 0.00 0.00 0.00 1.82
2137 2181 0.102481 ATACGACGTGGAGATGGTGC 59.898 55.000 11.56 0.00 0.00 5.01
2155 2200 4.192317 GGTGCTATCTTGTGTAAGAAGGG 58.808 47.826 0.00 0.00 45.47 3.95
2184 2229 2.202570 CGGCTCAAATGCAGCTGC 60.203 61.111 31.89 31.89 36.47 5.25
2196 2241 1.222936 CAGCTGCCGGGAGAAAGAT 59.777 57.895 29.09 3.06 0.00 2.40
2218 2264 4.611310 AAACGATGCATCACATTCTCAG 57.389 40.909 25.70 8.95 39.84 3.35
2219 2265 3.257469 ACGATGCATCACATTCTCAGT 57.743 42.857 25.70 9.58 39.84 3.41
2224 2270 2.270923 GCATCACATTCTCAGTACGCA 58.729 47.619 0.00 0.00 0.00 5.24
2225 2271 2.029728 GCATCACATTCTCAGTACGCAC 59.970 50.000 0.00 0.00 0.00 5.34
2226 2272 3.253230 CATCACATTCTCAGTACGCACA 58.747 45.455 0.00 0.00 0.00 4.57
2227 2273 3.378911 TCACATTCTCAGTACGCACAA 57.621 42.857 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 6.238759 GCGATAACCTCTTTTAATTCCAGCAT 60.239 38.462 0.00 0.00 0.00 3.79
95 96 0.820074 CCAACGTTGGTGTGGCCTTA 60.820 55.000 34.48 0.00 43.43 2.69
105 106 3.375922 ACTCACAAGTAAACCAACGTTGG 59.624 43.478 39.20 39.20 43.55 3.77
209 210 0.599204 GTCACAACGAAGCGAAGGGA 60.599 55.000 0.00 0.00 0.00 4.20
290 291 5.653507 GCATTCAACCTTTTGCTGATGATA 58.346 37.500 0.00 0.00 32.17 2.15
331 332 5.458595 TCCTTCTGGATGCTAGTTATCTCA 58.541 41.667 8.41 5.30 37.46 3.27
580 584 0.320683 CAGAGGCGACCAATGTGTGA 60.321 55.000 0.00 0.00 0.00 3.58
758 762 5.824904 AAGATTTTGATGAATCACTCCGG 57.175 39.130 0.00 0.00 38.27 5.14
759 763 6.036083 ACGTAAGATTTTGATGAATCACTCCG 59.964 38.462 0.00 0.00 38.27 4.63
761 765 7.064609 TCCACGTAAGATTTTGATGAATCACTC 59.935 37.037 0.00 0.00 38.27 3.51
769 773 4.935205 TGGACTCCACGTAAGATTTTGATG 59.065 41.667 4.28 0.00 43.62 3.07
819 826 5.715070 AGTACGAATCATGCCTAAGCTATC 58.285 41.667 0.00 0.00 40.80 2.08
878 893 3.186047 GGGTCGTCGATGCAACGG 61.186 66.667 16.74 1.27 40.45 4.44
904 919 2.346803 GTGCAAAGATGAGCTAACCGA 58.653 47.619 0.00 0.00 0.00 4.69
906 921 2.346803 TCGTGCAAAGATGAGCTAACC 58.653 47.619 0.00 0.00 0.00 2.85
932 947 0.747644 CAGCGACAATGTATGCCCCA 60.748 55.000 6.48 0.00 0.00 4.96
963 978 4.537433 GGCGCTTGATCGGAGGCT 62.537 66.667 7.64 0.00 0.00 4.58
1067 1082 2.344203 AAGACCCGAGCTGACTCCG 61.344 63.158 0.00 0.00 40.03 4.63
1074 1089 1.181786 CTTCTCTCAAGACCCGAGCT 58.818 55.000 0.00 0.00 0.00 4.09
1170 1185 1.739562 CTTGGACTCTGCCGCTGTC 60.740 63.158 0.00 0.00 0.00 3.51
1173 1188 4.749310 CGCTTGGACTCTGCCGCT 62.749 66.667 0.00 0.00 0.00 5.52
1235 1250 0.668706 CACGGGAGAGCTCAACACAG 60.669 60.000 17.77 9.40 0.00 3.66
1372 1390 6.870965 AGAGACAAAGTGAAAGCATACAGTAG 59.129 38.462 0.00 0.00 0.00 2.57
1447 1485 8.667076 TTTCTGTGGACATGATGACATTATAG 57.333 34.615 0.00 0.00 34.15 1.31
1474 1512 2.415357 CCAAACGTGCATGGTCCAATAC 60.415 50.000 11.36 0.00 31.84 1.89
1662 1702 7.985184 GTGGATGACTTTGTGTATTAGATACCA 59.015 37.037 0.00 0.00 34.86 3.25
1713 1753 2.355756 ACAGCAAATACATCGCATGGAC 59.644 45.455 0.00 0.00 33.60 4.02
1746 1786 1.808133 GCTGGATGCACTACAGGCTAC 60.808 57.143 13.87 0.00 42.31 3.58
1778 1818 0.459411 AGTTGGTGTTTTTGGCGCAC 60.459 50.000 10.83 0.00 0.00 5.34
1944 1985 3.740128 CTTGGCCGGTGCGAGCTAT 62.740 63.158 1.90 0.00 38.85 2.97
1987 2031 4.633175 TCACCGTATTTTGTGAAGCTGTA 58.367 39.130 0.00 0.00 38.48 2.74
1996 2040 2.224426 TGCCTCACTCACCGTATTTTGT 60.224 45.455 0.00 0.00 0.00 2.83
2001 2045 0.537188 CCTTGCCTCACTCACCGTAT 59.463 55.000 0.00 0.00 0.00 3.06
2002 2046 1.541310 CCCTTGCCTCACTCACCGTA 61.541 60.000 0.00 0.00 0.00 4.02
2137 2181 5.059833 GCATCCCCTTCTTACACAAGATAG 58.940 45.833 0.00 0.00 40.47 2.08
2155 2200 1.144716 TGAGCCGTCTCATGCATCC 59.855 57.895 0.00 0.00 43.95 3.51
2184 2229 2.544267 GCATCGTTTATCTTTCTCCCGG 59.456 50.000 0.00 0.00 0.00 5.73
2196 2241 5.178061 ACTGAGAATGTGATGCATCGTTTA 58.822 37.500 21.34 8.16 36.67 2.01


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

AutoCloner maintained by Alex Coulton.