Multiple sequence alignment - TraesCS2B01G152200

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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 TraesCS2B01G152200 chr2B 100.000 2787 0 0 1 2787 118840950 118843736 0 5147
1 TraesCS2B01G152200 chr1D 98.350 2788 45 1 1 2787 315624662 315627449 0 4892
2 TraesCS2B01G152200 chr2D 98.350 2788 43 3 1 2787 107007488 107004703 0 4891
3 TraesCS2B01G152200 chr2D 98.279 2789 46 2 1 2787 66137612 66140400 0 4883
4 TraesCS2B01G152200 chr3D 98.314 2788 46 1 1 2787 380104427 380101640 0 4887
5 TraesCS2B01G152200 chr3D 98.279 2789 46 2 1 2787 442860329 442857541 0 4883
6 TraesCS2B01G152200 chr3D 98.278 2788 47 1 1 2787 38236218 38233431 0 4881
7 TraesCS2B01G152200 chr3D 98.278 2788 47 1 1 2787 302922731 302919944 0 4881
8 TraesCS2B01G152200 chr5D 98.314 2788 44 2 1 2787 443513890 443516675 0 4885
9 TraesCS2B01G152200 chr6D 98.278 2788 46 2 1 2787 237393876 237391090 0 4881


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 TraesCS2B01G152200 chr2B 118840950 118843736 2786 False 5147 5147 100.000 1 2787 1 chr2B.!!$F1 2786
1 TraesCS2B01G152200 chr1D 315624662 315627449 2787 False 4892 4892 98.350 1 2787 1 chr1D.!!$F1 2786
2 TraesCS2B01G152200 chr2D 107004703 107007488 2785 True 4891 4891 98.350 1 2787 1 chr2D.!!$R1 2786
3 TraesCS2B01G152200 chr2D 66137612 66140400 2788 False 4883 4883 98.279 1 2787 1 chr2D.!!$F1 2786
4 TraesCS2B01G152200 chr3D 380101640 380104427 2787 True 4887 4887 98.314 1 2787 1 chr3D.!!$R3 2786
5 TraesCS2B01G152200 chr3D 442857541 442860329 2788 True 4883 4883 98.279 1 2787 1 chr3D.!!$R4 2786
6 TraesCS2B01G152200 chr3D 38233431 38236218 2787 True 4881 4881 98.278 1 2787 1 chr3D.!!$R1 2786
7 TraesCS2B01G152200 chr3D 302919944 302922731 2787 True 4881 4881 98.278 1 2787 1 chr3D.!!$R2 2786
8 TraesCS2B01G152200 chr5D 443513890 443516675 2785 False 4885 4885 98.314 1 2787 1 chr5D.!!$F1 2786
9 TraesCS2B01G152200 chr6D 237391090 237393876 2786 True 4881 4881 98.278 1 2787 1 chr6D.!!$R1 2786

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
215 217 0.457166 CAACTTGCGCCACCATCATG 60.457 55.000 4.18 0.0 0.0 3.07 F
901 904 1.134521 TGAGTGTTCTTGCTGACCGTT 60.135 47.619 0.00 0.0 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1349 1353 4.976540 AGTAGTCTTGGTAGGCTTGTTT 57.023 40.909 0.0 0.0 37.55 2.83 R
2474 2479 2.030805 GGCATTCACCAAGTCAGTCAAC 60.031 50.000 0.0 0.0 0.00 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
65 67 6.790285 TTTGATTTCTTGTCCGGTAAGTAC 57.210 37.500 16.82 2.67 0.00 2.73
80 82 5.863397 CGGTAAGTACACGAATTAGAAACCA 59.137 40.000 0.00 0.00 0.00 3.67
165 167 3.231889 CTGCGGCCAGAGACACACT 62.232 63.158 2.24 0.00 41.77 3.55
213 215 1.528076 ACAACTTGCGCCACCATCA 60.528 52.632 4.18 0.00 0.00 3.07
215 217 0.457166 CAACTTGCGCCACCATCATG 60.457 55.000 4.18 0.00 0.00 3.07
234 236 2.626785 TGGTCTACTCCATCCCAAACA 58.373 47.619 0.00 0.00 31.96 2.83
440 442 1.878522 AGATCGTCGCCAACATCGC 60.879 57.895 0.00 0.00 0.00 4.58
552 555 2.163010 GCTGCTGTTATGCATGTCTTGT 59.837 45.455 10.16 0.00 42.48 3.16
572 575 7.224949 GTCTTGTTGTTCTTCTAGTTTGCTAGT 59.775 37.037 0.00 0.00 43.86 2.57
717 720 2.045634 GCTGATGCACTGAGGCCA 60.046 61.111 5.01 0.00 39.41 5.36
751 754 2.572290 GTGTGCACTTTAAGAGGTGGT 58.428 47.619 19.41 0.00 34.41 4.16
901 904 1.134521 TGAGTGTTCTTGCTGACCGTT 60.135 47.619 0.00 0.00 0.00 4.44
1068 1071 5.412594 GGTTGAACAAGCTCATGAGATACAA 59.587 40.000 27.04 19.14 36.02 2.41
1075 1078 6.769341 ACAAGCTCATGAGATACAATGCATTA 59.231 34.615 27.04 0.00 0.00 1.90
1183 1186 2.613026 TTTCGCCACAACTCTGAAGA 57.387 45.000 0.00 0.00 0.00 2.87
1317 1320 1.758592 GGTGCAGAGGTACCCACAA 59.241 57.895 17.46 0.00 43.33 3.33
1349 1353 6.211785 ACAAAGGGAAGAACAAACCTGTTTTA 59.788 34.615 0.00 0.00 45.98 1.52
1375 1379 5.198965 CAAGCCTACCAAGACTACTACCTA 58.801 45.833 0.00 0.00 0.00 3.08
1754 1758 1.535462 GTGCAACTAAGGAACGTGCAT 59.465 47.619 0.00 0.00 33.32 3.96
1984 1988 3.138884 TGCAAGTATTTGGCACTCTCA 57.861 42.857 0.00 0.00 34.79 3.27
2370 2375 4.181578 CGATCGTGGTGGAGAGTATTTTT 58.818 43.478 7.03 0.00 0.00 1.94
2474 2479 1.491563 CGAGAGGAAAAACCGCACG 59.508 57.895 0.00 0.00 43.77 5.34
2666 2671 2.038820 CACTTGGGGATGTTTGGCAAAT 59.961 45.455 16.74 0.01 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 67 4.322101 CCGACTTGGTTTCTAATTCGTG 57.678 45.455 0.00 0.00 31.04 4.35
80 82 1.133606 ACCACAATCCCAAACCGACTT 60.134 47.619 0.00 0.00 0.00 3.01
165 167 3.133183 GGCAAAACCCTAGGTGTTTTTCA 59.867 43.478 25.98 0.00 42.38 2.69
215 217 2.355818 GGTGTTTGGGATGGAGTAGACC 60.356 54.545 0.00 0.00 0.00 3.85
353 355 1.153628 GGAAGACGACCCGTGATGG 60.154 63.158 0.00 0.00 41.37 3.51
440 442 1.577328 GGGTGCGACAGTGTTGATGG 61.577 60.000 15.07 0.00 0.00 3.51
572 575 9.920133 CTAGAAGAGATACTAGCATGCAATAAA 57.080 33.333 21.98 1.00 31.50 1.40
717 720 3.007614 AGTGCACACCGGTAAACTTATCT 59.992 43.478 21.04 0.00 0.00 1.98
751 754 0.888619 CAGAGCGTGGTCTTCACCTA 59.111 55.000 0.00 0.00 44.17 3.08
772 775 5.220777 CGTGGAAAACTTTCAGAGCAGTAAA 60.221 40.000 4.67 0.00 38.92 2.01
901 904 3.209410 TGTGCATGTACACATCACACAA 58.791 40.909 13.02 8.19 45.36 3.33
984 987 5.952347 ACTCTCCATGATGTACAGTTCACTA 59.048 40.000 0.33 0.00 0.00 2.74
1068 1071 6.096001 GGAGTTCAAGTTCCTTCATAATGCAT 59.904 38.462 0.00 0.00 0.00 3.96
1183 1186 8.774546 TCAACTGATATCTCCTGTCTCTTATT 57.225 34.615 3.98 0.00 0.00 1.40
1317 1320 5.993748 TTGTTCTTCCCTTTGTCTTGTTT 57.006 34.783 0.00 0.00 0.00 2.83
1349 1353 4.976540 AGTAGTCTTGGTAGGCTTGTTT 57.023 40.909 0.00 0.00 37.55 2.83
1375 1379 5.163612 GCCTTGTTGAACTTCTTCTTCTTGT 60.164 40.000 0.00 0.00 0.00 3.16
1754 1758 6.867519 TTCTTGTTCATAGTAGGGACATGA 57.132 37.500 7.53 7.53 0.00 3.07
2474 2479 2.030805 GGCATTCACCAAGTCAGTCAAC 60.031 50.000 0.00 0.00 0.00 3.18
2687 2692 6.347696 TGTCTTTGATCCAAGTTTGCATTTT 58.652 32.000 6.45 0.00 0.00 1.82
2691 2696 3.953612 ACTGTCTTTGATCCAAGTTTGCA 59.046 39.130 6.45 0.00 0.00 4.08
2703 2708 4.422073 AGACACAATCCACTGTCTTTGA 57.578 40.909 0.00 0.00 43.81 2.69


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

AutoCloner maintained by Alex Coulton.