Multiple sequence alignment - TraesCS2B01G302700

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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 TraesCS2B01G302700 chr2B 100.000 2405 0 0 1 2405 427247835 427245431 0 4442
1 TraesCS2B01G302700 chr2D 96.883 2406 57 10 1 2400 359398354 359400747 0 4012
2 TraesCS2B01G302700 chr2A 96.395 2413 67 12 1 2405 483602755 483600355 0 3956


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 TraesCS2B01G302700 chr2B 427245431 427247835 2404 True 4442 4442 100.000 1 2405 1 chr2B.!!$R1 2404
1 TraesCS2B01G302700 chr2D 359398354 359400747 2393 False 4012 4012 96.883 1 2400 1 chr2D.!!$F1 2399
2 TraesCS2B01G302700 chr2A 483600355 483602755 2400 True 3956 3956 96.395 1 2405 1 chr2A.!!$R1 2404

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
723 732 0.80338 TGCATGCGTCTCGTGAGATG 60.803 55.0 14.09 13.54 45.04 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1546 1557 1.180029 GACGGAGGCAGTAGTGGTAA 58.82 55.0 0.0 0.0 0.0 2.85 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
18 19 1.217244 GCCAGCAAAATGAGCCAGG 59.783 57.895 0.00 0.00 0.00 4.45
65 66 1.000233 GCGTCGCGTGAAGTGAACTA 61.000 55.000 13.34 0.00 41.58 2.24
165 167 8.644216 TCACTCAACTGTCAACTTATTAACCTA 58.356 33.333 0.00 0.00 0.00 3.08
228 232 1.226773 GCCCTTTCATCATGCGCAC 60.227 57.895 14.90 0.00 0.00 5.34
294 298 6.916360 TTTGCCTAAAGAAAAGGACATCAT 57.084 33.333 0.00 0.00 36.08 2.45
464 471 3.366440 AGTAGTCAACACCGACAAGTC 57.634 47.619 0.00 0.00 38.43 3.01
540 547 8.934825 TGCAAAAATCCTAATTTGTGAAATAGC 58.065 29.630 5.45 0.00 41.01 2.97
541 548 9.154847 GCAAAAATCCTAATTTGTGAAATAGCT 57.845 29.630 5.45 0.00 41.01 3.32
559 566 1.661112 GCTAGGCTTGACTTTGTAGCG 59.339 52.381 0.00 0.00 35.77 4.26
563 570 1.871039 GGCTTGACTTTGTAGCGTTGA 59.129 47.619 0.00 0.00 35.77 3.18
583 590 4.326826 TGATGTGGCCTCTTTAAACAGAG 58.673 43.478 3.32 0.00 40.23 3.35
619 626 1.442769 TCGAGCTGCTGAAACAATCC 58.557 50.000 7.01 0.00 0.00 3.01
700 709 6.428295 TCAAAGAGGTTTTCAGGGTCTAAAA 58.572 36.000 0.00 0.00 0.00 1.52
701 710 6.893005 TCAAAGAGGTTTTCAGGGTCTAAAAA 59.107 34.615 0.00 0.00 0.00 1.94
723 732 0.803380 TGCATGCGTCTCGTGAGATG 60.803 55.000 14.09 13.54 45.04 2.90
734 743 5.057819 GTCTCGTGAGATGGTCTAGTATCA 58.942 45.833 2.42 0.00 39.97 2.15
772 781 4.605640 TCCTGGAAAAGAAAAAGGCATG 57.394 40.909 0.00 0.00 0.00 4.06
773 782 3.069289 CCTGGAAAAGAAAAAGGCATGC 58.931 45.455 9.90 9.90 0.00 4.06
774 783 3.494749 CCTGGAAAAGAAAAAGGCATGCA 60.495 43.478 21.36 0.00 0.00 3.96
775 784 4.320870 CTGGAAAAGAAAAAGGCATGCAT 58.679 39.130 21.36 10.32 0.00 3.96
1124 1133 3.645975 CGCCGTGGTGGTGTTCAC 61.646 66.667 0.00 0.00 43.63 3.18
1203 1212 4.063967 CCCACCGTGCACGAGCTA 62.064 66.667 39.10 0.00 43.02 3.32
1722 1733 6.455513 GCTTGCCTTGTTTAAAACTTCTGTTG 60.456 38.462 0.00 0.00 36.39 3.33
1993 2005 3.857157 TTTTGTAGAGACAAGTGGGCT 57.143 42.857 0.00 0.00 46.11 5.19
2106 2118 1.081309 GCATTGCGTGTGTGCATGA 60.081 52.632 0.00 0.00 45.78 3.07
2129 2141 8.357796 TGATATCTTTATGCTTTGTTCGAGAG 57.642 34.615 3.98 0.00 0.00 3.20
2268 2280 1.715585 CATGGCCGTGTAAAGCTCG 59.284 57.895 17.42 0.00 0.00 5.03
2321 2333 2.299297 AGTTAGCTTGGCTTCTACGTGT 59.701 45.455 0.00 0.00 40.44 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 6.318396 AGACCTCGTACTCCAAGTTAGAATAC 59.682 42.308 0.00 0.00 0.00 1.89
65 66 1.005630 GCTAGCGATGGAGGCGATT 60.006 57.895 0.00 0.00 35.00 3.34
188 192 3.557595 CAGCGGACTGGAAATAAGCTTAG 59.442 47.826 12.54 1.05 40.48 2.18
274 278 5.904362 ACATGATGTCCTTTTCTTTAGGC 57.096 39.130 0.00 0.00 32.59 3.93
318 325 0.180406 ACAGTGAAAGTCGCACCCTT 59.820 50.000 0.00 0.00 36.95 3.95
377 384 6.073167 TGCATTTGTTCTATTTTGCCACAATG 60.073 34.615 0.00 0.00 0.00 2.82
381 388 5.921004 TTGCATTTGTTCTATTTTGCCAC 57.079 34.783 0.00 0.00 0.00 5.01
464 471 7.759465 AGAAATACAGAATGAATTGCAGTCAG 58.241 34.615 8.03 0.00 43.75 3.51
540 547 2.960819 ACGCTACAAAGTCAAGCCTAG 58.039 47.619 0.00 0.00 32.50 3.02
541 548 3.064207 CAACGCTACAAAGTCAAGCCTA 58.936 45.455 0.00 0.00 32.50 3.93
542 549 1.873591 CAACGCTACAAAGTCAAGCCT 59.126 47.619 0.00 0.00 32.50 4.58
543 550 1.871039 TCAACGCTACAAAGTCAAGCC 59.129 47.619 0.00 0.00 32.50 4.35
559 566 4.518970 TCTGTTTAAAGAGGCCACATCAAC 59.481 41.667 12.06 0.86 0.00 3.18
563 570 3.084786 GCTCTGTTTAAAGAGGCCACAT 58.915 45.455 12.06 0.00 43.37 3.21
583 590 4.743644 AGCTCGAAGTTAAACCGTATATGC 59.256 41.667 0.00 0.00 0.00 3.14
700 709 0.599991 TCACGAGACGCATGCAACTT 60.600 50.000 19.57 0.00 0.00 2.66
701 710 1.006220 TCACGAGACGCATGCAACT 60.006 52.632 19.57 15.57 0.00 3.16
723 732 5.648092 ACATGCAGGTTTTTGATACTAGACC 59.352 40.000 0.00 0.00 0.00 3.85
734 743 3.511146 CCAGGATGTACATGCAGGTTTTT 59.489 43.478 26.61 3.83 32.49 1.94
772 781 1.740025 CACGGAAAGGAGAAGGAATGC 59.260 52.381 0.00 0.00 0.00 3.56
773 782 3.334583 TCACGGAAAGGAGAAGGAATG 57.665 47.619 0.00 0.00 0.00 2.67
774 783 3.583086 TCTTCACGGAAAGGAGAAGGAAT 59.417 43.478 0.00 0.00 37.00 3.01
775 784 2.969950 TCTTCACGGAAAGGAGAAGGAA 59.030 45.455 0.00 0.00 37.00 3.36
805 814 3.552132 TTTTTCTTTTGGGGTCCAAGC 57.448 42.857 0.00 0.00 44.84 4.01
1411 1420 3.953712 ACGGTGTCACTGACAATATGA 57.046 42.857 18.86 0.00 44.49 2.15
1546 1557 1.180029 GACGGAGGCAGTAGTGGTAA 58.820 55.000 0.00 0.00 0.00 2.85
1722 1733 3.380004 TGTCAAAGGATGAACACACAACC 59.620 43.478 0.00 0.00 40.50 3.77
1993 2005 2.668001 CGACCATTGGTACGAACACGTA 60.668 50.000 8.70 0.00 40.72 3.57
2106 2118 7.170658 GCTCTCTCGAACAAAGCATAAAGATAT 59.829 37.037 4.43 0.00 33.21 1.63
2129 2141 3.545633 CGAAGCAAACAGTGTAAAGCTC 58.454 45.455 14.86 9.29 0.00 4.09
2227 2239 1.501604 TGTTAACAAAAGGGAGGGCCT 59.498 47.619 5.25 5.25 0.00 5.19
2268 2280 9.922305 GCTGTGTTCAAAGTATAATATCTGTTC 57.078 33.333 0.00 0.00 0.00 3.18
2321 2333 4.260985 CAGTATGGTCCACAGTTTGCATA 58.739 43.478 0.00 0.00 0.00 3.14


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

AutoCloner maintained by Alex Coulton.