Multiple sequence alignment - TraesCS4A01G154200

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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 TraesCS4A01G154200 chr4A 100.000 2111 0 0 1 2111 310730855 310728745 0.000000e+00 3899
1 TraesCS4A01G154200 chr4A 90.148 944 92 1 1169 2111 298298517 298297574 0.000000e+00 1227
2 TraesCS4A01G154200 chr4A 87.656 964 114 5 1150 2111 200264366 200265326 0.000000e+00 1116
3 TraesCS4A01G154200 chr4A 87.447 940 114 4 1175 2111 299108088 299109026 0.000000e+00 1079
4 TraesCS4A01G154200 chr4A 86.411 964 128 3 1150 2111 414692041 414691079 0.000000e+00 1051
5 TraesCS4A01G154200 chr4A 86.397 963 130 1 1150 2111 459998795 459999757 0.000000e+00 1051
6 TraesCS4A01G154200 chr4A 95.918 196 7 1 1 195 15182254 15182059 1.220000e-82 316
7 TraesCS4A01G154200 chr6D 96.364 1155 35 7 1 1149 45511827 45510674 0.000000e+00 1893
8 TraesCS4A01G154200 chr5D 96.364 1155 35 7 1 1149 6181202 6180049 0.000000e+00 1893
9 TraesCS4A01G154200 chr5D 96.104 1155 39 5 1 1149 503287044 503288198 0.000000e+00 1879
10 TraesCS4A01G154200 chr5D 96.097 1153 38 7 1 1149 120799616 120800765 0.000000e+00 1873
11 TraesCS4A01G154200 chr5D 94.883 1153 55 4 1 1149 167071678 167072830 0.000000e+00 1799
12 TraesCS4A01G154200 chr5D 96.451 648 18 4 507 1149 512416234 512415587 0.000000e+00 1064
13 TraesCS4A01G154200 chr1D 95.924 1153 42 5 1 1149 51878329 51877178 0.000000e+00 1864
14 TraesCS4A01G154200 chr1D 93.576 1152 70 4 1 1149 260891851 260893001 0.000000e+00 1714
15 TraesCS4A01G154200 chr2A 95.702 1047 39 6 1 1045 335830883 335829841 0.000000e+00 1679
16 TraesCS4A01G154200 chr2A 94.038 738 29 6 417 1149 334595896 334595169 0.000000e+00 1105
17 TraesCS4A01G154200 chr2D 95.486 997 32 3 156 1149 9785044 9786030 0.000000e+00 1580
18 TraesCS4A01G154200 chr7A 88.785 963 107 1 1150 2111 301966841 301967803 0.000000e+00 1179
19 TraesCS4A01G154200 chr7A 86.749 966 121 7 1150 2111 145707457 145708419 0.000000e+00 1068
20 TraesCS4A01G154200 chr3A 87.656 964 116 3 1150 2111 391343691 391344653 0.000000e+00 1118
21 TraesCS4A01G154200 chr5A 87.047 965 124 1 1148 2111 158101335 158100371 0.000000e+00 1088


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 TraesCS4A01G154200 chr4A 310728745 310730855 2110 True 3899 3899 100.000 1 2111 1 chr4A.!!$R3 2110
1 TraesCS4A01G154200 chr4A 298297574 298298517 943 True 1227 1227 90.148 1169 2111 1 chr4A.!!$R2 942
2 TraesCS4A01G154200 chr4A 200264366 200265326 960 False 1116 1116 87.656 1150 2111 1 chr4A.!!$F1 961
3 TraesCS4A01G154200 chr4A 299108088 299109026 938 False 1079 1079 87.447 1175 2111 1 chr4A.!!$F2 936
4 TraesCS4A01G154200 chr4A 414691079 414692041 962 True 1051 1051 86.411 1150 2111 1 chr4A.!!$R4 961
5 TraesCS4A01G154200 chr4A 459998795 459999757 962 False 1051 1051 86.397 1150 2111 1 chr4A.!!$F3 961
6 TraesCS4A01G154200 chr6D 45510674 45511827 1153 True 1893 1893 96.364 1 1149 1 chr6D.!!$R1 1148
7 TraesCS4A01G154200 chr5D 6180049 6181202 1153 True 1893 1893 96.364 1 1149 1 chr5D.!!$R1 1148
8 TraesCS4A01G154200 chr5D 503287044 503288198 1154 False 1879 1879 96.104 1 1149 1 chr5D.!!$F3 1148
9 TraesCS4A01G154200 chr5D 120799616 120800765 1149 False 1873 1873 96.097 1 1149 1 chr5D.!!$F1 1148
10 TraesCS4A01G154200 chr5D 167071678 167072830 1152 False 1799 1799 94.883 1 1149 1 chr5D.!!$F2 1148
11 TraesCS4A01G154200 chr5D 512415587 512416234 647 True 1064 1064 96.451 507 1149 1 chr5D.!!$R2 642
12 TraesCS4A01G154200 chr1D 51877178 51878329 1151 True 1864 1864 95.924 1 1149 1 chr1D.!!$R1 1148
13 TraesCS4A01G154200 chr1D 260891851 260893001 1150 False 1714 1714 93.576 1 1149 1 chr1D.!!$F1 1148
14 TraesCS4A01G154200 chr2A 335829841 335830883 1042 True 1679 1679 95.702 1 1045 1 chr2A.!!$R2 1044
15 TraesCS4A01G154200 chr2A 334595169 334595896 727 True 1105 1105 94.038 417 1149 1 chr2A.!!$R1 732
16 TraesCS4A01G154200 chr2D 9785044 9786030 986 False 1580 1580 95.486 156 1149 1 chr2D.!!$F1 993
17 TraesCS4A01G154200 chr7A 301966841 301967803 962 False 1179 1179 88.785 1150 2111 1 chr7A.!!$F2 961
18 TraesCS4A01G154200 chr7A 145707457 145708419 962 False 1068 1068 86.749 1150 2111 1 chr7A.!!$F1 961
19 TraesCS4A01G154200 chr3A 391343691 391344653 962 False 1118 1118 87.656 1150 2111 1 chr3A.!!$F1 961
20 TraesCS4A01G154200 chr5A 158100371 158101335 964 True 1088 1088 87.047 1148 2111 1 chr5A.!!$R1 963

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
585 590 1.340889 CCTTTGTTTGGCAAGCTGCTA 59.659 47.619 15.19 0.0 44.28 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1577 1599 0.950836 CGCACCCAACTGAATGAACA 59.049 50.0 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
188 190 5.800941 GCTAGTATTCTACACATGCGGATAC 59.199 44.000 0.00 0.00 0.00 2.24
195 197 6.986904 TCTACACATGCGGATACTATAGAG 57.013 41.667 6.78 0.00 0.00 2.43
197 199 6.940867 TCTACACATGCGGATACTATAGAGTT 59.059 38.462 6.78 0.00 37.10 3.01
291 294 5.779241 TTTGAGAGTGGGAATACAAGGAT 57.221 39.130 0.00 0.00 0.00 3.24
346 349 5.411831 AGATTTTGAATCTGCCTTTTCCC 57.588 39.130 2.56 0.00 0.00 3.97
361 364 5.279506 GCCTTTTCCCTCTTTCCCTTAAAAG 60.280 44.000 0.00 0.00 37.55 2.27
585 590 1.340889 CCTTTGTTTGGCAAGCTGCTA 59.659 47.619 15.19 0.00 44.28 3.49
746 753 7.618019 TCTTCTACATTGAATGGGTAGCTAT 57.382 36.000 10.27 0.00 35.58 2.97
854 861 8.352942 CACCTAACCCTATTTTTGCTATTGATC 58.647 37.037 0.00 0.00 0.00 2.92
1016 1031 9.331282 AGATTATGTAATGCTTACTCTCAAACC 57.669 33.333 7.33 0.00 37.06 3.27
1021 1036 7.871853 TGTAATGCTTACTCTCAAACCTTTTC 58.128 34.615 7.33 0.00 37.06 2.29
1091 1106 6.896021 TTTATCTAATGACCTAGGACGGAG 57.104 41.667 17.98 8.06 0.00 4.63
1109 1124 3.062466 TCCTGGACGCGAGGAGTG 61.062 66.667 15.93 0.00 33.54 3.51
1274 1295 1.452651 CAACAGGGCCGCATCTCAT 60.453 57.895 0.00 0.00 0.00 2.90
1279 1300 2.976903 GGCCGCATCTCATGAGCC 60.977 66.667 18.36 11.64 41.78 4.70
1328 1349 2.609046 GGGTCCACCTCACAGCTAT 58.391 57.895 0.00 0.00 35.85 2.97
1429 1451 2.046988 CATCACGCTGTCCTGGCA 60.047 61.111 0.00 0.00 0.00 4.92
1434 1456 2.210013 ACGCTGTCCTGGCAGAGAA 61.210 57.895 17.94 0.00 38.32 2.87
1570 1592 1.084289 GGCAACGTTATCAGGTGACC 58.916 55.000 0.00 0.00 0.00 4.02
1577 1599 3.326880 ACGTTATCAGGTGACCCTTTTCT 59.673 43.478 0.00 0.00 39.89 2.52
1593 1615 4.342092 CCTTTTCTGTTCATTCAGTTGGGT 59.658 41.667 0.00 0.00 36.85 4.51
1597 1619 0.951558 GTTCATTCAGTTGGGTGCGT 59.048 50.000 0.00 0.00 0.00 5.24
1620 1642 1.153061 CTGGCTGCATCATCCCCAT 59.847 57.895 0.50 0.00 0.00 4.00
1624 1646 0.466739 GCTGCATCATCCCCATGTCA 60.467 55.000 0.00 0.00 0.00 3.58
1750 1773 3.016031 TGGCATGTATCGTTCTTGCATT 58.984 40.909 0.00 0.00 37.59 3.56
1756 1779 7.095229 GGCATGTATCGTTCTTGCATTTATCTA 60.095 37.037 0.00 0.00 37.59 1.98
1899 1922 0.747255 CATGAGTAGGCTAGGCACGT 59.253 55.000 19.70 1.18 0.00 4.49
1903 1926 0.964358 AGTAGGCTAGGCACGTCGTT 60.964 55.000 19.70 0.00 0.00 3.85
1924 1947 3.458163 GCTCGGGTCCGTCCATGA 61.458 66.667 9.36 0.00 40.74 3.07
1927 1950 1.304630 TCGGGTCCGTCCATGAAGA 60.305 57.895 9.36 0.00 40.74 2.87
1931 1954 0.895530 GGTCCGTCCATGAAGAGTCA 59.104 55.000 0.00 0.00 38.41 3.41
1935 1958 4.113354 GTCCGTCCATGAAGAGTCAATAC 58.887 47.826 0.00 0.00 37.30 1.89
1939 1962 4.620567 CGTCCATGAAGAGTCAATACACCA 60.621 45.833 0.00 0.00 37.30 4.17
2007 2030 2.110213 GGTCGTTGGTGTCTGGCA 59.890 61.111 0.00 0.00 0.00 4.92
2071 2094 3.099141 CCTAACCATTTTGCAGGACCAT 58.901 45.455 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.751924 CTCGGAGGTTCGAATCCTTCT 59.248 52.381 16.93 4.72 38.77 2.85
35 36 1.302993 TGGTAAGGCAGCGGGTTTC 60.303 57.895 0.00 0.00 0.00 2.78
149 151 8.734593 AGAATACTAGCAAGAGAATATCCCTT 57.265 34.615 0.00 0.00 0.00 3.95
291 294 5.450688 CGGACTTTCCCAAACACAAAATACA 60.451 40.000 0.00 0.00 31.13 2.29
650 655 8.350852 TCTCGGCTTTTACCCATTTTTAAATA 57.649 30.769 0.00 0.00 0.00 1.40
746 753 9.034800 AGAAAGGTTGATCCAAATTTATTGCTA 57.965 29.630 0.00 0.00 39.02 3.49
765 772 0.984995 GTGCAGGGGAGTAGAAAGGT 59.015 55.000 0.00 0.00 0.00 3.50
1068 1083 6.371278 ACTCCGTCCTAGGTCATTAGATAAA 58.629 40.000 9.08 0.00 0.00 1.40
1091 1106 3.063084 ACTCCTCGCGTCCAGGAC 61.063 66.667 9.92 9.92 34.91 3.85
1400 1422 1.447217 CGTGATGCATGGCCTCCTA 59.553 57.895 2.46 0.00 0.00 2.94
1429 1451 1.561643 TGAAGACCATCGCCTTCTCT 58.438 50.000 0.00 0.00 39.47 3.10
1434 1456 0.984230 TTCCTTGAAGACCATCGCCT 59.016 50.000 0.00 0.00 0.00 5.52
1570 1592 4.342092 ACCCAACTGAATGAACAGAAAAGG 59.658 41.667 0.00 0.00 40.63 3.11
1577 1599 0.950836 CGCACCCAACTGAATGAACA 59.049 50.000 0.00 0.00 0.00 3.18
1597 1619 1.703014 GGATGATGCAGCCAGAGGGA 61.703 60.000 0.00 0.00 40.02 4.20
1603 1625 1.152631 CATGGGGATGATGCAGCCA 60.153 57.895 0.00 0.00 42.36 4.75
1899 1922 2.029964 GGACCCGAGCACAAACGA 59.970 61.111 0.00 0.00 0.00 3.85
1903 1926 3.998672 GGACGGACCCGAGCACAA 61.999 66.667 16.07 0.00 42.83 3.33
1924 1947 6.533730 TCAGTCATTTGGTGTATTGACTCTT 58.466 36.000 1.65 0.00 45.19 2.85
1931 1954 4.940046 CAGAGCTCAGTCATTTGGTGTATT 59.060 41.667 17.77 0.00 0.00 1.89
1935 1958 2.740981 GACAGAGCTCAGTCATTTGGTG 59.259 50.000 28.54 11.71 33.29 4.17
1939 1962 3.428725 CGCTAGACAGAGCTCAGTCATTT 60.429 47.826 32.82 19.41 40.51 2.32
2007 2030 1.836166 CTGAGGTGGTCACATGAGGAT 59.164 52.381 0.00 0.00 0.00 3.24
2071 2094 6.475504 TGGTCTTGATTCTTGATAGCTTCAA 58.524 36.000 0.00 1.07 42.09 2.69


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

AutoCloner maintained by Alex Coulton.