Multiple sequence alignment - TraesCS3A01G106300

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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 TraesCS3A01G106300 chr3A 100.000 2807 0 0 1 2807 70711397 70714203 0.000000e+00 5184
1 TraesCS3A01G106300 chr3D 96.497 2826 70 11 3 2807 61685493 61688310 0.000000e+00 4643
2 TraesCS3A01G106300 chr3D 76.168 1049 196 44 910 1945 61680265 61681272 1.160000e-138 503
3 TraesCS3A01G106300 chr3B 95.755 2073 59 6 5 2074 99125766 99127812 0.000000e+00 3314
4 TraesCS3A01G106300 chr3B 89.895 762 26 11 2073 2807 99129731 99130468 0.000000e+00 933
5 TraesCS3A01G106300 chr3B 75.603 1037 201 36 910 1935 99117852 99118847 1.520000e-127 466


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 TraesCS3A01G106300 chr3A 70711397 70714203 2806 False 5184.0 5184 100.000 1 2807 1 chr3A.!!$F1 2806
1 TraesCS3A01G106300 chr3D 61685493 61688310 2817 False 4643.0 4643 96.497 3 2807 1 chr3D.!!$F2 2804
2 TraesCS3A01G106300 chr3D 61680265 61681272 1007 False 503.0 503 76.168 910 1945 1 chr3D.!!$F1 1035
3 TraesCS3A01G106300 chr3B 99125766 99130468 4702 False 2123.5 3314 92.825 5 2807 2 chr3B.!!$F2 2802
4 TraesCS3A01G106300 chr3B 99117852 99118847 995 False 466.0 466 75.603 910 1935 1 chr3B.!!$F1 1025

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
846 855 1.394917 GTTAAGGCTGCATCTGTCACG 59.605 52.381 0.5 0.0 0.00 4.35 F
1125 1135 0.535797 GAGTCGGGGGTCTCGAAAAT 59.464 55.000 0.0 0.0 38.42 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1744 1758 1.054406 GGGAGTCCCCGAATGGATGA 61.054 60.000 18.55 0.0 44.02 2.92 R
2573 4539 1.067212 GACCGTGCTTGATCGATACCT 59.933 52.381 0.00 0.0 0.00 3.08 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
66 67 3.750371 CATGTTACCAGTGGAAACTCCA 58.250 45.455 18.40 3.77 45.98 3.86
202 203 1.543607 TGTCAGTCTCTCTCTGGCAG 58.456 55.000 8.58 8.58 41.62 4.85
335 336 9.387123 CTTATTCACAAAGCTTACTGTTTCTTC 57.613 33.333 0.00 0.00 0.00 2.87
561 562 4.098894 AGGGGATCATGTTGATTTTGCTT 58.901 39.130 0.00 0.00 37.20 3.91
587 588 7.748847 TGTCTAAAGCTTGAAACCGATATTTC 58.251 34.615 0.00 0.00 38.77 2.17
746 747 7.331687 GGTCATAGATGAAAACATTTTTGGGTG 59.668 37.037 0.00 0.00 38.75 4.61
846 855 1.394917 GTTAAGGCTGCATCTGTCACG 59.605 52.381 0.50 0.00 0.00 4.35
1125 1135 0.535797 GAGTCGGGGGTCTCGAAAAT 59.464 55.000 0.00 0.00 38.42 1.82
1569 1580 3.071602 GCCTCCTATGCCTCTGTATGAAA 59.928 47.826 0.00 0.00 0.00 2.69
1574 1585 4.214971 CCTATGCCTCTGTATGAAACATGC 59.785 45.833 0.00 0.00 37.50 4.06
1706 1720 5.076182 TGTTCTTTTCCATGCTGATACCAA 58.924 37.500 0.00 0.00 0.00 3.67
1744 1758 1.453379 GCTGCATCAGTCTGGCCAT 60.453 57.895 5.51 0.00 33.43 4.40
1748 1762 1.236628 GCATCAGTCTGGCCATCATC 58.763 55.000 5.51 0.00 0.00 2.92
1749 1763 1.893544 CATCAGTCTGGCCATCATCC 58.106 55.000 5.51 0.00 0.00 3.51
1750 1764 1.142262 CATCAGTCTGGCCATCATCCA 59.858 52.381 5.51 0.00 0.00 3.41
1805 1819 0.744414 CGATGGGGTACTTGGCAGTG 60.744 60.000 0.00 0.00 34.06 3.66
1968 1983 3.338676 GTGCCTACTATGCGCCGC 61.339 66.667 4.18 0.00 33.19 6.53
2032 2047 9.712305 ATATGGTTGTCTTGCTAGATTATGTAC 57.288 33.333 0.05 0.00 31.86 2.90
2034 2049 7.620880 TGGTTGTCTTGCTAGATTATGTACTT 58.379 34.615 0.05 0.00 31.86 2.24
2064 2081 5.952526 TGATGCATATGACCTGCTAAATG 57.047 39.130 6.97 0.00 40.34 2.32
2314 4263 2.262915 CAGGTCGGACAGGAGCAC 59.737 66.667 10.76 0.00 36.90 4.40
2573 4539 3.153024 GCCAGTCTGCGGATGTAAA 57.847 52.632 0.00 0.00 0.00 2.01
2683 4649 4.166888 GAGCTGCCGATGGAGCCA 62.167 66.667 0.00 0.00 35.69 4.75
2684 4650 3.472943 GAGCTGCCGATGGAGCCAT 62.473 63.158 0.71 0.71 39.69 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.657237 CTCCTCCACCCACGTCAC 59.343 66.667 0.00 0.00 0.00 3.67
106 107 0.107459 GTCAGCAATCTCCACCTCCC 60.107 60.000 0.00 0.00 0.00 4.30
119 120 1.071987 CTGTGGCCAGAAGTCAGCA 59.928 57.895 5.11 0.00 41.50 4.41
202 203 9.846248 ACTTTTCAATGCAGAGAACATAAATAC 57.154 29.630 3.34 0.00 0.00 1.89
536 537 5.721000 AGCAAAATCAACATGATCCCCTAAA 59.279 36.000 0.00 0.00 35.76 1.85
541 542 5.240121 ACAAAGCAAAATCAACATGATCCC 58.760 37.500 0.00 0.00 35.76 3.85
561 562 7.681939 AATATCGGTTTCAAGCTTTAGACAA 57.318 32.000 0.00 0.00 0.00 3.18
587 588 5.258456 TCTTAAGCCACTGTAATCTACCG 57.742 43.478 0.00 0.00 0.00 4.02
746 747 1.016627 TTCCACATTGCAGCGCTATC 58.983 50.000 10.99 5.63 0.00 2.08
846 855 6.543831 ACCAAATAGACCATCATAAACTCAGC 59.456 38.462 0.00 0.00 0.00 4.26
1125 1135 3.190383 TGAGAGAGGTGAATCTTGGGA 57.810 47.619 0.00 0.00 0.00 4.37
1574 1585 3.726517 CCAAACGGCCTGCAGACG 61.727 66.667 23.23 23.23 0.00 4.18
1622 1636 0.166814 GAACGGACAAGCAGTGATGC 59.833 55.000 0.00 0.00 0.00 3.91
1744 1758 1.054406 GGGAGTCCCCGAATGGATGA 61.054 60.000 18.55 0.00 44.02 2.92
1805 1819 3.281727 TGAAGTATGGATGCAAGGGTC 57.718 47.619 0.00 0.00 0.00 4.46
1937 1952 3.576356 GCACACATCCGGCCATCG 61.576 66.667 2.24 0.00 38.88 3.84
2032 2047 6.148976 CAGGTCATATGCATCATACAAGGAAG 59.851 42.308 0.19 0.00 0.00 3.46
2034 2049 5.554070 CAGGTCATATGCATCATACAAGGA 58.446 41.667 0.19 0.00 0.00 3.36
2064 2081 5.359756 ACAAAGCAAAAGGATTCAGAAACC 58.640 37.500 0.99 0.99 0.00 3.27
2218 4160 4.965814 AGAACACAGAGCTGATCTTTCAA 58.034 39.130 4.21 0.00 35.47 2.69
2219 4161 4.613925 AGAACACAGAGCTGATCTTTCA 57.386 40.909 4.21 0.00 35.47 2.69
2573 4539 1.067212 GACCGTGCTTGATCGATACCT 59.933 52.381 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.