Multiple sequence alignment - TraesCS4D01G088600

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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 TraesCS4D01G088600 chr4D 100.000 2511 0 0 1 2511 64218119 64220629 0 4638
1 TraesCS4D01G088600 chr4D 96.976 2513 74 1 1 2511 173590073 173587561 0 4218
2 TraesCS4D01G088600 chr4D 96.937 2514 69 5 1 2511 444104988 444102480 0 4209
3 TraesCS4D01G088600 chr7D 97.452 2512 61 3 1 2511 369872047 369874556 0 4281
4 TraesCS4D01G088600 chr7D 97.177 2515 63 5 3 2511 611022523 611025035 0 4244
5 TraesCS4D01G088600 chr7D 96.937 2514 73 4 1 2511 251579412 251576900 0 4213
6 TraesCS4D01G088600 chr6D 97.216 2514 66 4 1 2511 340961292 340958780 0 4252
7 TraesCS4D01G088600 chr6D 96.859 2515 75 4 1 2511 53650164 53647650 0 4204
8 TraesCS4D01G088600 chr3D 97.214 2513 68 1 1 2511 213976085 213973573 0 4252
9 TraesCS4D01G088600 chr5D 97.096 2514 68 4 1 2511 212869875 212872386 0 4233


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 TraesCS4D01G088600 chr4D 64218119 64220629 2510 False 4638 4638 100.000 1 2511 1 chr4D.!!$F1 2510
1 TraesCS4D01G088600 chr4D 173587561 173590073 2512 True 4218 4218 96.976 1 2511 1 chr4D.!!$R1 2510
2 TraesCS4D01G088600 chr4D 444102480 444104988 2508 True 4209 4209 96.937 1 2511 1 chr4D.!!$R2 2510
3 TraesCS4D01G088600 chr7D 369872047 369874556 2509 False 4281 4281 97.452 1 2511 1 chr7D.!!$F1 2510
4 TraesCS4D01G088600 chr7D 611022523 611025035 2512 False 4244 4244 97.177 3 2511 1 chr7D.!!$F2 2508
5 TraesCS4D01G088600 chr7D 251576900 251579412 2512 True 4213 4213 96.937 1 2511 1 chr7D.!!$R1 2510
6 TraesCS4D01G088600 chr6D 340958780 340961292 2512 True 4252 4252 97.216 1 2511 1 chr6D.!!$R2 2510
7 TraesCS4D01G088600 chr6D 53647650 53650164 2514 True 4204 4204 96.859 1 2511 1 chr6D.!!$R1 2510
8 TraesCS4D01G088600 chr3D 213973573 213976085 2512 True 4252 4252 97.214 1 2511 1 chr3D.!!$R1 2510
9 TraesCS4D01G088600 chr5D 212869875 212872386 2511 False 4233 4233 97.096 1 2511 1 chr5D.!!$F1 2510

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
30 31 0.464452 GGCAGCGTAGGGTAGTTCAT 59.536 55.0 0.00 0.00 0.0 2.57 F
1438 1455 0.249741 CAAAGTGGGAAGGTCGACGT 60.250 55.0 9.92 7.31 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1447 1464 1.229975 CGACCATTGCAGCTGTGACA 61.230 55.0 16.64 1.46 0.0 3.58 R
2475 2501 4.962362 ACACAAGAAACCAAAGAAAGGGAT 59.038 37.5 0.00 0.00 0.0 3.85 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
30 31 0.464452 GGCAGCGTAGGGTAGTTCAT 59.536 55.000 0.00 0.00 0.00 2.57
40 41 1.376683 GTAGTTCATGCGCCACCCA 60.377 57.895 4.18 0.00 0.00 4.51
150 151 3.054875 ACAGCAATCACATGAAGGAGCTA 60.055 43.478 0.00 0.00 0.00 3.32
319 321 6.951062 TTCATACAGTTCATGTTTGGACAA 57.049 33.333 0.00 0.00 39.96 3.18
401 403 1.349688 AGGCCACTCGGTAAAATGTCA 59.650 47.619 5.01 0.00 33.28 3.58
586 589 7.800155 TCACAATGAAGAAATGTGTGAGTAA 57.200 32.000 0.85 0.00 42.63 2.24
747 754 6.069905 TGCTTTCCTAATACAACCTATGTGGA 60.070 38.462 0.00 0.00 43.77 4.02
798 805 5.394224 TGTTCATACATGGACGTCAACTA 57.606 39.130 18.91 0.00 39.20 2.24
1008 1020 2.593026 GTCTTGTTCCCCATGTTCCAA 58.407 47.619 0.00 0.00 0.00 3.53
1134 1147 3.099905 AGCTGATGCAGACCTTACTACA 58.900 45.455 0.00 0.00 42.74 2.74
1219 1232 3.944015 GGTCCAGATCAGACATTTTCCAG 59.056 47.826 15.39 0.00 35.89 3.86
1404 1421 2.434884 CGACTGCGGCTTCCACAT 60.435 61.111 0.00 0.00 0.00 3.21
1438 1455 0.249741 CAAAGTGGGAAGGTCGACGT 60.250 55.000 9.92 7.31 0.00 4.34
1447 1464 0.462789 AAGGTCGACGTGTTCCTGTT 59.537 50.000 12.13 0.00 0.00 3.16
1507 1524 3.569701 ACACATGGAACTGGTTGATGAAC 59.430 43.478 0.00 0.00 0.00 3.18
1508 1525 3.822735 CACATGGAACTGGTTGATGAACT 59.177 43.478 0.00 0.00 32.15 3.01
1615 1632 1.303888 TCCTGACCGAACGCCTACT 60.304 57.895 0.00 0.00 0.00 2.57
1651 1668 4.202284 GCCGAGGAATGTAAGGTATTACCA 60.202 45.833 15.19 0.00 41.95 3.25
1690 1707 9.856488 ACTATGTCCTTGTAATATGCTATTACG 57.144 33.333 15.31 0.00 37.32 3.18
1865 1882 1.393603 TGGTGTTTTGAATGCGTCCA 58.606 45.000 0.00 0.00 0.00 4.02
2386 2405 2.886081 CACCTGAAGAGTCATTCTCCG 58.114 52.381 0.00 0.00 43.71 4.63
2475 2501 1.982660 TGTTGTTTACGGATTGCCCA 58.017 45.000 0.00 0.00 34.14 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.570774 AATCATCCATGGGTGGCGCA 62.571 55.000 24.94 5.82 45.63 6.09
40 41 5.072736 TGACTTCTGGCTCATAATCATCCAT 59.927 40.000 0.00 0.00 0.00 3.41
150 151 1.883926 GGGTGTGGTCATTACGCTTTT 59.116 47.619 0.00 0.00 0.00 2.27
305 307 5.667539 TCTTGGTTTTGTCCAAACATGAA 57.332 34.783 0.00 0.00 46.01 2.57
319 321 6.567050 GCATCACATTGTATGATCTTGGTTT 58.433 36.000 0.00 0.00 34.49 3.27
401 403 4.406456 TCCCACATGCAACTACATTCTTT 58.594 39.130 0.00 0.00 0.00 2.52
747 754 9.040939 GTTGCCATGTATTTTAGTTTGAAGTTT 57.959 29.630 0.00 0.00 0.00 2.66
847 855 1.004745 ACGAAAGCATCAAGGGTCCAT 59.995 47.619 0.00 0.00 0.00 3.41
1008 1020 1.595382 GTCGTGTGGTGCAAGCTCT 60.595 57.895 0.00 0.00 33.76 4.09
1056 1068 3.416156 GTTCTTCAGGTCAAGGCAGATT 58.584 45.455 0.00 0.00 0.00 2.40
1219 1232 1.611043 GTAGTCGCCACGTACTCAAC 58.389 55.000 0.00 0.00 0.00 3.18
1266 1279 5.011023 GGTTTGGAGGACACATGAAGAAAAT 59.989 40.000 0.00 0.00 0.00 1.82
1404 1421 3.320541 CCACTTTGCAAGGTATTCCAACA 59.679 43.478 14.45 0.00 35.89 3.33
1447 1464 1.229975 CGACCATTGCAGCTGTGACA 61.230 55.000 16.64 1.46 0.00 3.58
1507 1524 2.093783 GGACCGCGTGTTGAAATCTTAG 59.906 50.000 4.92 0.00 0.00 2.18
1508 1525 2.070783 GGACCGCGTGTTGAAATCTTA 58.929 47.619 4.92 0.00 0.00 2.10
1687 1704 2.198287 GCTACGGGGAGATGCCGTA 61.198 63.158 0.00 0.00 40.66 4.02
1690 1707 1.533273 TAGGCTACGGGGAGATGCC 60.533 63.158 0.00 0.00 40.17 4.40
1865 1882 5.471556 TTTGCCATGTTTTCAGACATCAT 57.528 34.783 0.00 0.00 38.15 2.45
1959 1978 3.711704 ACCATGCTAGCCAGTACAGTTAT 59.288 43.478 13.29 0.00 0.00 1.89
2475 2501 4.962362 ACACAAGAAACCAAAGAAAGGGAT 59.038 37.500 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.