Multiple sequence alignment - TraesCS6D01G165000

Loading Multiple Alignment...

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 TraesCS6D01G165000 chr6D 100.000 2186 0 0 667 2852 144060398 144058213 0.000000e+00 4037.0
1 TraesCS6D01G165000 chr6D 88.928 1409 149 6 668 2072 285196894 285198299 0.000000e+00 1731.0
2 TraesCS6D01G165000 chr6D 97.423 776 18 1 2077 2852 144052979 144052206 0.000000e+00 1321.0
3 TraesCS6D01G165000 chr6D 96.654 777 24 2 2077 2852 27083347 27082572 0.000000e+00 1290.0
4 TraesCS6D01G165000 chr6D 100.000 189 0 0 1 189 144061064 144060876 1.630000e-92 350.0
5 TraesCS6D01G165000 chr1B 91.725 1293 104 3 782 2072 246765852 246764561 0.000000e+00 1792.0
6 TraesCS6D01G165000 chr1B 89.478 1302 100 11 667 1964 146954760 146956028 0.000000e+00 1611.0
7 TraesCS6D01G165000 chr1B 92.366 131 10 0 1 131 116137301 116137171 1.350000e-43 187.0
8 TraesCS6D01G165000 chr1B 88.889 90 6 3 1 90 146954169 146954254 1.080000e-19 108.0
9 TraesCS6D01G165000 chr7B 89.704 1418 125 9 667 2066 165207670 165209084 0.000000e+00 1790.0
10 TraesCS6D01G165000 chr3A 91.390 1266 100 7 710 1970 308702642 308701381 0.000000e+00 1725.0
11 TraesCS6D01G165000 chr3A 92.424 66 5 0 124 189 308702747 308702682 8.410000e-16 95.3
12 TraesCS6D01G165000 chr4A 88.127 1415 157 11 667 2072 384351627 384353039 0.000000e+00 1672.0
13 TraesCS6D01G165000 chr4A 88.582 1340 144 8 667 2000 384333382 384334718 0.000000e+00 1618.0
14 TraesCS6D01G165000 chr4A 79.787 188 38 0 2 189 700981270 700981083 1.380000e-28 137.0
15 TraesCS6D01G165000 chr2B 85.920 1392 183 10 667 2050 402672716 402671330 0.000000e+00 1472.0
16 TraesCS6D01G165000 chr2A 88.683 1131 123 5 945 2072 537010292 537009164 0.000000e+00 1375.0
17 TraesCS6D01G165000 chr5D 97.036 776 23 0 2077 2852 536513598 536512823 0.000000e+00 1306.0
18 TraesCS6D01G165000 chr5D 96.649 776 26 0 2077 2852 479663865 479664640 0.000000e+00 1290.0
19 TraesCS6D01G165000 chr5D 96.178 785 29 1 2068 2852 243783620 243784403 0.000000e+00 1282.0
20 TraesCS6D01G165000 chr6A 96.778 776 25 0 2077 2852 617618571 617619346 0.000000e+00 1295.0
21 TraesCS6D01G165000 chr7D 96.433 785 25 3 2070 2852 436428019 436427236 0.000000e+00 1291.0
22 TraesCS6D01G165000 chr4D 96.649 776 26 0 2077 2852 508715477 508714702 0.000000e+00 1290.0
23 TraesCS6D01G165000 chr3D 96.649 776 26 0 2077 2852 16400475 16399700 0.000000e+00 1290.0


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 TraesCS6D01G165000 chr6D 144058213 144061064 2851 True 2193.50 4037 100.0000 1 2852 2 chr6D.!!$R3 2851
1 TraesCS6D01G165000 chr6D 285196894 285198299 1405 False 1731.00 1731 88.9280 668 2072 1 chr6D.!!$F1 1404
2 TraesCS6D01G165000 chr6D 144052206 144052979 773 True 1321.00 1321 97.4230 2077 2852 1 chr6D.!!$R2 775
3 TraesCS6D01G165000 chr6D 27082572 27083347 775 True 1290.00 1290 96.6540 2077 2852 1 chr6D.!!$R1 775
4 TraesCS6D01G165000 chr1B 246764561 246765852 1291 True 1792.00 1792 91.7250 782 2072 1 chr1B.!!$R2 1290
5 TraesCS6D01G165000 chr1B 146954169 146956028 1859 False 859.50 1611 89.1835 1 1964 2 chr1B.!!$F1 1963
6 TraesCS6D01G165000 chr7B 165207670 165209084 1414 False 1790.00 1790 89.7040 667 2066 1 chr7B.!!$F1 1399
7 TraesCS6D01G165000 chr3A 308701381 308702747 1366 True 910.15 1725 91.9070 124 1970 2 chr3A.!!$R1 1846
8 TraesCS6D01G165000 chr4A 384351627 384353039 1412 False 1672.00 1672 88.1270 667 2072 1 chr4A.!!$F2 1405
9 TraesCS6D01G165000 chr4A 384333382 384334718 1336 False 1618.00 1618 88.5820 667 2000 1 chr4A.!!$F1 1333
10 TraesCS6D01G165000 chr2B 402671330 402672716 1386 True 1472.00 1472 85.9200 667 2050 1 chr2B.!!$R1 1383
11 TraesCS6D01G165000 chr2A 537009164 537010292 1128 True 1375.00 1375 88.6830 945 2072 1 chr2A.!!$R1 1127
12 TraesCS6D01G165000 chr5D 536512823 536513598 775 True 1306.00 1306 97.0360 2077 2852 1 chr5D.!!$R1 775
13 TraesCS6D01G165000 chr5D 479663865 479664640 775 False 1290.00 1290 96.6490 2077 2852 1 chr5D.!!$F2 775
14 TraesCS6D01G165000 chr5D 243783620 243784403 783 False 1282.00 1282 96.1780 2068 2852 1 chr5D.!!$F1 784
15 TraesCS6D01G165000 chr6A 617618571 617619346 775 False 1295.00 1295 96.7780 2077 2852 1 chr6A.!!$F1 775
16 TraesCS6D01G165000 chr7D 436427236 436428019 783 True 1291.00 1291 96.4330 2070 2852 1 chr7D.!!$R1 782
17 TraesCS6D01G165000 chr4D 508714702 508715477 775 True 1290.00 1290 96.6490 2077 2852 1 chr4D.!!$R1 775
18 TraesCS6D01G165000 chr3D 16399700 16400475 775 True 1290.00 1290 96.6490 2077 2852 1 chr3D.!!$R1 775

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
871 1284 0.609406 GAAGAAGAAAGGGCCGGCTT 60.609 55.0 28.56 13.58 0.00 4.35 F
1526 1942 0.244994 GAGCTCTCACTTCGCAAGGA 59.755 55.0 6.43 0.00 38.47 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1791 2215 1.532238 GTGGGTTAGATGGCTCCCC 59.468 63.158 0.0 0.0 39.2 4.81 R
2680 3109 4.357947 GGTGCTCTCCGTGTCGCA 62.358 66.667 0.0 0.0 0.0 5.10 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
106 503 4.099170 CGAGTCCCGTCGTTCGCT 62.099 66.667 0.00 0.00 38.35 4.93
861 1274 6.234177 CCAAGGAGCTAAGAAGAAGAAGAAA 58.766 40.000 0.00 0.00 0.00 2.52
871 1284 0.609406 GAAGAAGAAAGGGCCGGCTT 60.609 55.000 28.56 13.58 0.00 4.35
898 1311 3.716195 CTCCCGCCACATCCACCA 61.716 66.667 0.00 0.00 0.00 4.17
1082 1497 2.814336 CCGAGGAGATCATGATGTACGA 59.186 50.000 14.30 0.00 0.00 3.43
1240 1656 0.396435 CCTGTGTAGGTGCAAGTGGA 59.604 55.000 0.00 0.00 39.39 4.02
1290 1706 1.481056 CCTTCACGGTGGTCTTCCCT 61.481 60.000 8.50 0.00 0.00 4.20
1331 1747 4.374702 CACTCGCAGCGGCAACAC 62.375 66.667 16.42 0.00 41.24 3.32
1526 1942 0.244994 GAGCTCTCACTTCGCAAGGA 59.755 55.000 6.43 0.00 38.47 3.36
1649 2071 3.053291 GCCGCCAAACCATGTCGA 61.053 61.111 0.00 0.00 0.00 4.20
1654 2076 1.671054 CCAAACCATGTCGACCGCT 60.671 57.895 14.12 0.00 0.00 5.52
1791 2215 4.787280 ACTCCTGCTCCCCCTCCG 62.787 72.222 0.00 0.00 0.00 4.63
1908 2332 2.123077 CTCCTCCGGCCTCTCCAT 60.123 66.667 0.00 0.00 34.01 3.41
2075 2503 2.509336 CCACGGGCAGCGACTAAG 60.509 66.667 0.00 0.00 0.00 2.18
2221 2649 1.765674 CGCTTAACGTTCGCTTTACG 58.234 50.000 2.82 0.00 44.20 3.18
2308 2736 4.571176 AGAGCACGTAAATAAAAGCTAGGC 59.429 41.667 0.00 0.00 31.61 3.93
2475 2904 7.743749 ACTTTCTCTACTTGGATCATATGCAT 58.256 34.615 3.79 3.79 0.00 3.96
2680 3109 1.299976 GGGAATCCCTCACGCTTGT 59.700 57.895 11.95 0.00 41.34 3.16
2704 3133 1.043816 CACGGAGAGCACCATAGGAT 58.956 55.000 0.00 0.00 0.00 3.24
2795 3224 9.914131 CGAATCTACTCAAACATCATAGGATAA 57.086 33.333 0.00 0.00 30.87 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.554363 CGTAGGTCTGCCTCGCGG 62.554 72.222 6.13 0.0 45.64 6.46
90 91 2.504244 CAGCGAACGACGGGACTC 60.504 66.667 0.00 0.0 42.83 3.36
91 92 4.052229 CCAGCGAACGACGGGACT 62.052 66.667 0.00 0.0 42.83 3.85
733 1131 0.607762 TTGCCGGATTGCTGCTGTTA 60.608 50.000 5.05 0.0 0.00 2.41
1082 1497 3.286694 ATGCCCTCAATGCCGTGGT 62.287 57.895 0.00 0.0 0.00 4.16
1257 1673 2.156098 GTGAAGGTGTTGGCGGAAATA 58.844 47.619 0.00 0.0 0.00 1.40
1259 1675 1.440938 CGTGAAGGTGTTGGCGGAAA 61.441 55.000 0.00 0.0 0.00 3.13
1447 1863 1.191535 CGGATAACCCACTCAGACCA 58.808 55.000 0.00 0.0 34.14 4.02
1526 1942 0.323908 CTTCACTCGGACCTCCTCCT 60.324 60.000 0.00 0.0 36.80 3.69
1527 1943 1.324005 CCTTCACTCGGACCTCCTCC 61.324 65.000 0.00 0.0 35.33 4.30
1528 1944 0.612453 ACCTTCACTCGGACCTCCTC 60.612 60.000 0.00 0.0 0.00 3.71
1539 1961 2.040412 GTCCAGGGATTTCACCTTCACT 59.960 50.000 0.00 0.0 35.78 3.41
1638 2060 1.375523 GGAGCGGTCGACATGGTTT 60.376 57.895 18.91 0.0 0.00 3.27
1654 2076 1.742146 CATCATCGGAGAAGCGGGA 59.258 57.895 0.00 0.0 43.58 5.14
1791 2215 1.532238 GTGGGTTAGATGGCTCCCC 59.468 63.158 0.00 0.0 39.20 4.81
2075 2503 3.714798 TGATCCCCTATACTTGTGGGTTC 59.285 47.826 0.00 0.0 39.31 3.62
2221 2649 9.974750 GCATTTCTAGTTTCATACTTGTTCTAC 57.025 33.333 0.00 0.0 38.33 2.59
2244 2672 3.482436 TCCGAAAACACCTACAAAGCAT 58.518 40.909 0.00 0.0 0.00 3.79
2246 2674 4.094442 CCTATCCGAAAACACCTACAAAGC 59.906 45.833 0.00 0.0 0.00 3.51
2308 2736 8.851960 TTAGTTGTGTCTTTATCTATACAGCG 57.148 34.615 0.00 0.0 0.00 5.18
2435 2864 8.696374 AGTAGAGAAAGTATGTTAGCTTATGCA 58.304 33.333 0.00 0.0 42.74 3.96
2475 2904 6.179756 TGCTTGCTAGAGTTCCAATCATAAA 58.820 36.000 0.00 0.0 0.00 1.40
2680 3109 4.357947 GGTGCTCTCCGTGTCGCA 62.358 66.667 0.00 0.0 0.00 5.10
2704 3133 7.835822 AGTTGCATGTTTTATTATTGGTGCTA 58.164 30.769 0.00 0.0 32.87 3.49


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

AutoCloner maintained by Alex Coulton.