Multiple sequence alignment - TraesCS3B01G165600

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 TraesCS3B01G165600 chr3B 100.000 2324 0 0 1 2324 164412680 164415003 0.000000e+00 4292.0
1 TraesCS3B01G165600 chr3B 82.337 368 56 6 969 1335 156862788 156862429 6.240000e-81 311.0
2 TraesCS3B01G165600 chr3B 94.915 59 3 0 2266 2324 164452564 164452622 2.460000e-15 93.5
3 TraesCS3B01G165600 chr3B 80.159 126 14 9 623 740 132400435 132400557 1.480000e-12 84.2
4 TraesCS3B01G165600 chr3B 100.000 32 0 0 1438 1469 164414085 164414116 2.490000e-05 60.2
5 TraesCS3B01G165600 chr3B 100.000 32 0 0 1406 1437 164414117 164414148 2.490000e-05 60.2
6 TraesCS3B01G165600 chr3D 96.774 1705 32 20 14 1712 118536809 118535122 0.000000e+00 2822.0
7 TraesCS3B01G165600 chr3D 91.564 972 63 13 736 1704 119119213 119120168 0.000000e+00 1323.0
8 TraesCS3B01G165600 chr3D 96.237 558 15 3 1769 2324 118534963 118534410 0.000000e+00 909.0
9 TraesCS3B01G165600 chr3D 88.415 656 48 16 14 657 119118574 119119213 0.000000e+00 765.0
10 TraesCS3B01G165600 chr3D 83.480 569 49 20 1710 2260 119120135 119120676 2.680000e-134 488.0
11 TraesCS3B01G165600 chr3D 94.915 59 3 0 2266 2324 118534366 118534308 2.460000e-15 93.5
12 TraesCS3B01G165600 chr3D 97.778 45 1 0 1711 1755 118534998 118534954 6.880000e-11 78.7
13 TraesCS3B01G165600 chr3D 100.000 32 0 0 1406 1437 118535396 118535365 2.490000e-05 60.2
14 TraesCS3B01G165600 chr3D 100.000 32 0 0 1438 1469 118535428 118535397 2.490000e-05 60.2
15 TraesCS3B01G165600 chr3A 81.771 384 53 11 966 1343 550496571 550496943 2.900000e-79 305.0
16 TraesCS3B01G165600 chr5D 85.714 98 11 3 651 746 481806104 481806200 1.470000e-17 100.0
17 TraesCS3B01G165600 chr7A 86.364 88 11 1 654 740 285604 285691 6.840000e-16 95.3
18 TraesCS3B01G165600 chr7A 86.364 88 11 1 651 737 78670884 78670971 6.840000e-16 95.3
19 TraesCS3B01G165600 chr7A 86.364 88 7 4 654 738 67001085 67001000 8.840000e-15 91.6
20 TraesCS3B01G165600 chr2D 86.747 83 10 1 654 735 63371712 63371630 8.840000e-15 91.6
21 TraesCS3B01G165600 chr1D 85.882 85 11 1 654 737 381978372 381978288 3.180000e-14 89.8
22 TraesCS3B01G165600 chr1D 84.444 90 13 1 654 743 488953918 488954006 1.140000e-13 87.9


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 TraesCS3B01G165600 chr3B 164412680 164415003 2323 False 1470.800000 4292 100.000000 1 2324 3 chr3B.!!$F3 2323
1 TraesCS3B01G165600 chr3D 119118574 119120676 2102 False 858.666667 1323 87.819667 14 2260 3 chr3D.!!$F1 2246
2 TraesCS3B01G165600 chr3D 118534308 118536809 2501 True 670.600000 2822 97.617333 14 2324 6 chr3D.!!$R1 2310

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
203 209 1.303317 GTGCCCCCACAACTACAGG 60.303 63.158 0.00 0.0 41.67 4.00 F
348 354 4.630505 GGAGAAATTCCGACTTAAGGTGAC 59.369 45.833 7.53 0.0 35.91 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1040 1051 0.321346 TCTCCTTGCATGTTCGAGCA 59.679 50.000 3.86 3.86 39.32 4.26 R
2185 2342 1.262683 GCCATCGCTGAACTTCTATGC 59.737 52.381 0.00 0.00 0.00 3.14 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
158 164 5.348986 ACTAGTGTATAAATGTGAGCACCG 58.651 41.667 0.00 0.00 0.00 4.94
165 171 2.799126 AATGTGAGCACCGGGATTTA 57.201 45.000 6.32 0.00 0.00 1.40
199 205 1.823169 GAGTCGTGCCCCCACAACTA 61.823 60.000 0.00 0.00 39.25 2.24
200 206 1.670083 GTCGTGCCCCCACAACTAC 60.670 63.158 0.00 0.00 42.17 2.73
201 207 2.141448 TCGTGCCCCCACAACTACA 61.141 57.895 0.00 0.00 42.17 2.74
202 208 1.671054 CGTGCCCCCACAACTACAG 60.671 63.158 0.00 0.00 42.17 2.74
203 209 1.303317 GTGCCCCCACAACTACAGG 60.303 63.158 0.00 0.00 41.67 4.00
348 354 4.630505 GGAGAAATTCCGACTTAAGGTGAC 59.369 45.833 7.53 0.00 35.91 3.67
1040 1051 5.104318 GGAAGAAACAACCTAGAGGATGGAT 60.104 44.000 10.28 0.00 41.68 3.41
1701 1715 2.434185 TGGCTTGCTCCTAACGCG 60.434 61.111 3.53 3.53 0.00 6.01
1755 1894 3.650139 CTTAAGCGCGTATGTATCCCTT 58.350 45.455 8.43 1.18 0.00 3.95
1777 1918 4.508551 ACATTTGCCTGGATGTATCTCA 57.491 40.909 0.00 0.00 34.88 3.27
1931 2078 3.007723 TGCTTGGGTTACCGTACATGTAA 59.992 43.478 7.25 0.00 40.75 2.41
1990 2145 7.148239 CCAGTGCTAAAAATTTCTACGGATCTT 60.148 37.037 0.00 0.00 0.00 2.40
2154 2310 0.324614 TCGCATGCCAGGAAAAGAGA 59.675 50.000 13.15 0.00 0.00 3.10
2163 2319 2.504996 CCAGGAAAAGAGAGATCTGCCT 59.495 50.000 0.00 0.00 0.00 4.75
2272 2430 3.119849 AGGCGACATCAAACACAATAAGC 60.120 43.478 0.00 0.00 0.00 3.09
2276 2434 5.390461 GCGACATCAAACACAATAAGCTGTA 60.390 40.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.501892 TGATGTTAGGTGCTGCATTATTTATGA 59.498 33.333 5.27 0.00 36.26 2.15
1 2 7.592533 GTGATGTTAGGTGCTGCATTATTTATG 59.407 37.037 5.27 0.00 37.31 1.90
2 3 7.285172 TGTGATGTTAGGTGCTGCATTATTTAT 59.715 33.333 5.27 0.00 0.00 1.40
3 4 6.601217 TGTGATGTTAGGTGCTGCATTATTTA 59.399 34.615 5.27 0.00 0.00 1.40
5 6 4.949238 TGTGATGTTAGGTGCTGCATTATT 59.051 37.500 5.27 0.00 0.00 1.40
6 7 4.525996 TGTGATGTTAGGTGCTGCATTAT 58.474 39.130 5.27 0.00 0.00 1.28
7 8 3.940852 CTGTGATGTTAGGTGCTGCATTA 59.059 43.478 5.27 0.00 0.00 1.90
8 9 2.751259 CTGTGATGTTAGGTGCTGCATT 59.249 45.455 5.27 0.00 0.00 3.56
9 10 2.290514 ACTGTGATGTTAGGTGCTGCAT 60.291 45.455 5.27 0.00 0.00 3.96
10 11 1.072173 ACTGTGATGTTAGGTGCTGCA 59.928 47.619 0.00 0.00 0.00 4.41
11 12 1.466167 CACTGTGATGTTAGGTGCTGC 59.534 52.381 0.32 0.00 0.00 5.25
12 13 1.466167 GCACTGTGATGTTAGGTGCTG 59.534 52.381 12.86 0.00 46.39 4.41
13 14 1.813513 GCACTGTGATGTTAGGTGCT 58.186 50.000 12.86 0.00 46.39 4.40
15 16 2.481568 CAGTGCACTGTGATGTTAGGTG 59.518 50.000 34.04 8.95 39.09 4.00
16 17 2.771089 CAGTGCACTGTGATGTTAGGT 58.229 47.619 34.04 0.00 39.09 3.08
130 132 6.607600 TGCTCACATTTATACACTAGTCTCCT 59.392 38.462 0.00 0.00 0.00 3.69
131 133 6.697892 GTGCTCACATTTATACACTAGTCTCC 59.302 42.308 0.00 0.00 0.00 3.71
158 164 2.565391 CACCAACCAGGGTTTAAATCCC 59.435 50.000 14.12 14.40 43.89 3.85
165 171 0.185175 GACTCCACCAACCAGGGTTT 59.815 55.000 0.00 0.00 43.89 3.27
199 205 4.742201 CGCGGTGCTGTAGCCTGT 62.742 66.667 0.00 0.00 41.18 4.00
342 348 4.453480 TTTCATTTTCCCTCTGTCACCT 57.547 40.909 0.00 0.00 0.00 4.00
348 354 8.579863 ACTATTCACTTTTTCATTTTCCCTCTG 58.420 33.333 0.00 0.00 0.00 3.35
430 438 2.183478 AATGTCATCGGCACTGAACA 57.817 45.000 0.00 0.00 0.00 3.18
439 450 7.009999 TGTTTCTTCAAAAACAAATGTCATCGG 59.990 33.333 0.01 0.00 44.02 4.18
705 716 8.080417 CCTCCGTAAAGAAATACTTATCATCGA 58.920 37.037 0.00 0.00 37.93 3.59
976 987 9.976511 CATGGATCAATAAAGTTGATGCTAAAT 57.023 29.630 18.54 6.03 44.33 1.40
1040 1051 0.321346 TCTCCTTGCATGTTCGAGCA 59.679 50.000 3.86 3.86 39.32 4.26
1391 1404 7.881232 AGAAAATTGCCATTCTTTCATGATGTT 59.119 29.630 0.00 0.00 32.05 2.71
1392 1405 7.333423 CAGAAAATTGCCATTCTTTCATGATGT 59.667 33.333 0.00 0.00 33.73 3.06
1508 1521 5.360714 TCTGAGGAACTGCAAAATGAAAAGT 59.639 36.000 0.00 0.00 41.55 2.66
1509 1522 5.835257 TCTGAGGAACTGCAAAATGAAAAG 58.165 37.500 0.00 0.00 41.55 2.27
1720 1859 1.939974 CTTAAGCGAGCATGCCACTA 58.060 50.000 15.66 0.00 34.65 2.74
1755 1894 5.104569 TGTGAGATACATCCAGGCAAATGTA 60.105 40.000 8.44 8.44 41.28 2.29
1777 1918 5.105351 GGTAGCTTTAAATCCAGGCAAATGT 60.105 40.000 0.00 0.00 0.00 2.71
1884 2031 6.637254 ACAGAGAGTAAAATCATATACACGCG 59.363 38.462 3.53 3.53 0.00 6.01
1931 2078 6.800072 TTAAGGTCAAAAGTTGGGATGTTT 57.200 33.333 0.00 0.00 0.00 2.83
2183 2340 3.800261 GCCATCGCTGAACTTCTATGCTA 60.800 47.826 0.00 0.00 0.00 3.49
2184 2341 2.831333 CCATCGCTGAACTTCTATGCT 58.169 47.619 0.00 0.00 0.00 3.79
2185 2342 1.262683 GCCATCGCTGAACTTCTATGC 59.737 52.381 0.00 0.00 0.00 3.14
2186 2343 1.869767 GGCCATCGCTGAACTTCTATG 59.130 52.381 0.00 0.00 34.44 2.23
2187 2344 1.765314 AGGCCATCGCTGAACTTCTAT 59.235 47.619 5.01 0.00 34.44 1.98


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

AutoCloner maintained by Alex Coulton.