Multiple sequence alignment - TraesCS3D01G410800

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 TraesCS3D01G410800 chr3D 100.000 2192 0 0 1 2192 523752691 523754882 0 4048
1 TraesCS3D01G410800 chr3A 97.629 2193 51 1 1 2192 495104760 495102568 0 3760
2 TraesCS3D01G410800 chrUn 97.538 2193 52 2 1 2192 217907668 217909859 0 3749
3 TraesCS3D01G410800 chr3B 97.538 2193 52 2 1 2192 6010766 6008575 0 3749
4 TraesCS3D01G410800 chr3B 97.312 2195 53 4 1 2192 92296732 92294541 0 3722
5 TraesCS3D01G410800 chr2B 97.538 2193 53 1 1 2192 234541160 234538968 0 3749
6 TraesCS3D01G410800 chr1A 97.446 2193 54 2 1 2192 278521194 278523385 0 3738
7 TraesCS3D01G410800 chr1B 97.264 2193 58 2 1 2192 619195331 619193140 0 3716
8 TraesCS3D01G410800 chr7D 97.036 2193 62 3 1 2192 307146623 307144433 0 3687


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 TraesCS3D01G410800 chr3D 523752691 523754882 2191 False 4048 4048 100.000 1 2192 1 chr3D.!!$F1 2191
1 TraesCS3D01G410800 chr3A 495102568 495104760 2192 True 3760 3760 97.629 1 2192 1 chr3A.!!$R1 2191
2 TraesCS3D01G410800 chrUn 217907668 217909859 2191 False 3749 3749 97.538 1 2192 1 chrUn.!!$F1 2191
3 TraesCS3D01G410800 chr3B 6008575 6010766 2191 True 3749 3749 97.538 1 2192 1 chr3B.!!$R1 2191
4 TraesCS3D01G410800 chr3B 92294541 92296732 2191 True 3722 3722 97.312 1 2192 1 chr3B.!!$R2 2191
5 TraesCS3D01G410800 chr2B 234538968 234541160 2192 True 3749 3749 97.538 1 2192 1 chr2B.!!$R1 2191
6 TraesCS3D01G410800 chr1A 278521194 278523385 2191 False 3738 3738 97.446 1 2192 1 chr1A.!!$F1 2191
7 TraesCS3D01G410800 chr1B 619193140 619195331 2191 True 3716 3716 97.264 1 2192 1 chr1B.!!$R1 2191
8 TraesCS3D01G410800 chr7D 307144433 307146623 2190 True 3687 3687 97.036 1 2192 1 chr7D.!!$R1 2191

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
85 86 1.355381 TGGATGTGGGAGCATCAACTT 59.645 47.619 8.11 0.0 45.11 2.66 F
944 947 1.792006 ACGTCGAATGAAAGTGGTCC 58.208 50.000 0.00 0.0 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1012 1015 0.250513 GTCGTTCTTGGGCAGATCCT 59.749 55.000 0.0 0.0 34.39 3.24 R
1821 1828 2.637872 AGTTGATTCCTCCGAAGAACCA 59.362 45.455 0.0 0.0 0.00 3.67 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
85 86 1.355381 TGGATGTGGGAGCATCAACTT 59.645 47.619 8.11 0.0 45.11 2.66
295 296 2.203015 CCGGCAACCGTATCTGGG 60.203 66.667 5.17 0.0 46.80 4.45
322 323 7.562135 ACAACGATTAGTGGATATTGGTACTT 58.438 34.615 0.00 0.0 0.00 2.24
410 411 4.338879 AGACATTGATAGCAATATGGGGC 58.661 43.478 5.78 0.0 42.66 5.80
471 472 4.925054 ACAAAAGCATGCATATGTTGTCAC 59.075 37.500 21.98 0.0 36.65 3.67
479 480 5.806366 TGCATATGTTGTCACTGAAGATG 57.194 39.130 4.29 0.0 0.00 2.90
724 725 2.930826 AATCGGCATAGGTTAGGTGG 57.069 50.000 0.00 0.0 0.00 4.61
768 769 5.595952 GCCCATCTTTCTCCATATGAAAGTT 59.404 40.000 3.65 0.0 46.08 2.66
944 947 1.792006 ACGTCGAATGAAAGTGGTCC 58.208 50.000 0.00 0.0 0.00 4.46
1012 1015 2.777692 CCCTCCCTTATGTTTAGGAGCA 59.222 50.000 0.00 0.0 43.86 4.26
1126 1129 7.097192 TCACAAGATAAAGAAGTATGACGCTT 58.903 34.615 0.00 0.0 0.00 4.68
1319 1326 0.545548 AGGGTCCCCTCACTGACTTC 60.546 60.000 3.51 0.0 44.43 3.01
1511 1518 3.876914 TGAAGAGATGCGACAAAGTGTTT 59.123 39.130 0.00 0.0 0.00 2.83
1542 1549 4.220163 TGTGCAATGTCCTAATCAAATGCA 59.780 37.500 0.00 0.0 38.43 3.96
1560 1567 3.888583 TGCATAGTGGCATGATCAAAGA 58.111 40.909 0.00 0.0 39.25 2.52
1662 1669 0.387622 CGCCGTTCTTAACCGAGACA 60.388 55.000 0.00 0.0 0.00 3.41
1736 1743 3.545124 TTGGCGCATCTCGTTGGGT 62.545 57.895 10.83 0.0 41.07 4.51
1802 1809 4.995058 TTCCCGTCCCCTTGCCCT 62.995 66.667 0.00 0.0 0.00 5.19
2052 2060 1.645034 CAATGTACTGCGTCCAGGAG 58.355 55.000 0.00 0.0 43.53 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 5.466728 TGAGTAGTTGAAGCAAGTGAATGAC 59.533 40.000 0.00 0.00 0.00 3.06
85 86 1.953686 CTCAAAAGCCCAAAGGAACGA 59.046 47.619 0.00 0.00 33.47 3.85
295 296 6.920569 ACCAATATCCACTAATCGTTGTTC 57.079 37.500 0.00 0.00 0.00 3.18
322 323 0.816373 TTTGCTTGCTGTGCAGTGAA 59.184 45.000 0.00 0.00 40.61 3.18
471 472 3.144506 AGGCTTCACACAACATCTTCAG 58.855 45.455 0.00 0.00 0.00 3.02
479 480 1.604278 GTCTCCAAGGCTTCACACAAC 59.396 52.381 0.00 0.00 0.00 3.32
653 654 4.973055 CGGTTCCGACGTGCCCAA 62.973 66.667 5.19 0.00 0.00 4.12
724 725 4.278419 GGGCTTACCATGTTCCATCAATAC 59.722 45.833 0.00 0.00 39.85 1.89
768 769 0.390492 CATCTCTATGTGCCCGCAGA 59.610 55.000 0.00 0.00 0.00 4.26
844 845 0.178992 CCCAGTCAGCCACCTTTTCA 60.179 55.000 0.00 0.00 0.00 2.69
917 918 2.125673 CATTCGACGTTCCGGGCT 60.126 61.111 0.00 0.00 0.00 5.19
1012 1015 0.250513 GTCGTTCTTGGGCAGATCCT 59.749 55.000 0.00 0.00 34.39 3.24
1080 1083 5.532779 GTGATGGTTGAGGAGTTTCTTTCTT 59.467 40.000 0.00 0.00 0.00 2.52
1126 1129 5.745312 ATGACCAATAGAGTCAGACACAA 57.255 39.130 2.66 0.00 46.76 3.33
1309 1316 3.691342 CCCGGGCGAAGTCAGTGA 61.691 66.667 8.08 0.00 0.00 3.41
1319 1326 3.615509 TTTCACTTAGGCCCGGGCG 62.616 63.158 38.22 26.65 43.06 6.13
1479 1486 5.220381 GTCGCATCTCTTCAATACGGATAA 58.780 41.667 0.00 0.00 0.00 1.75
1542 1549 4.406648 TCGTCTTTGATCATGCCACTAT 57.593 40.909 0.00 0.00 0.00 2.12
1560 1567 8.871851 ATGGAGGACATAGTTTACGATCATCGT 61.872 40.741 18.45 18.45 46.67 3.73
1573 1580 3.823873 GAGATCGTGATGGAGGACATAGT 59.176 47.826 0.00 0.00 40.72 2.12
1662 1669 0.526662 CGAGACGGAGCTTAACCTGT 59.473 55.000 0.00 0.00 0.00 4.00
1686 1693 0.544833 TTACTCCTAACCCCACGGCA 60.545 55.000 0.00 0.00 0.00 5.69
1736 1743 1.547675 GGTTCCCAATGCTTCTCCACA 60.548 52.381 0.00 0.00 0.00 4.17
1821 1828 2.637872 AGTTGATTCCTCCGAAGAACCA 59.362 45.455 0.00 0.00 0.00 3.67
2052 2060 3.793144 CCGGCAAGCTCGTTCTGC 61.793 66.667 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.