Multiple sequence alignment - TraesCS2D01G378900

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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 TraesCS2D01G378900 chr2D 100.000 2606 0 0 1 2606 483257426 483254821 0.000000e+00 4813
1 TraesCS2D01G378900 chr2B 97.746 2617 29 11 1 2606 568274049 568276646 0.000000e+00 4479
2 TraesCS2D01G378900 chr2A 95.283 2035 59 14 1 2025 626590787 626588780 0.000000e+00 3192
3 TraesCS2D01G378900 chr2A 97.479 595 15 0 2006 2600 626588751 626588157 0.000000e+00 1016
4 TraesCS2D01G378900 chr6B 89.183 453 46 2 1097 1549 460928684 460929133 1.750000e-156 562
5 TraesCS2D01G378900 chr6B 86.861 411 52 2 1107 1516 687525408 687524999 2.360000e-125 459
6 TraesCS2D01G378900 chr6D 89.111 450 46 3 1100 1549 296348060 296347614 8.150000e-155 556
7 TraesCS2D01G378900 chr6A 88.889 450 47 3 1100 1549 422328681 422328235 3.790000e-153 551
8 TraesCS2D01G378900 chr6A 87.105 411 51 2 1107 1516 598619731 598619322 5.080000e-127 464
9 TraesCS2D01G378900 chr1D 86.150 426 56 2 1095 1517 214068359 214067934 8.500000e-125 457
10 TraesCS2D01G378900 chr1A 86.183 427 54 4 1095 1517 271620276 271619851 8.500000e-125 457


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 TraesCS2D01G378900 chr2D 483254821 483257426 2605 True 4813 4813 100.000 1 2606 1 chr2D.!!$R1 2605
1 TraesCS2D01G378900 chr2B 568274049 568276646 2597 False 4479 4479 97.746 1 2606 1 chr2B.!!$F1 2605
2 TraesCS2D01G378900 chr2A 626588157 626590787 2630 True 2104 3192 96.381 1 2600 2 chr2A.!!$R1 2599

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
595 600 0.326264 AGAGCGCCAAACCAAGATCT 59.674 50.0 2.29 0.0 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 2029 0.096281 CGAACCACACACACACACAC 59.904 55.0 0.0 0.0 0.0 3.82 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
575 580 1.555967 GGCTTTGCCCTGTAATTCCA 58.444 50.000 0.00 0.00 44.06 3.53
594 599 1.135575 CAAGAGCGCCAAACCAAGATC 60.136 52.381 2.29 0.00 0.00 2.75
595 600 0.326264 AGAGCGCCAAACCAAGATCT 59.674 50.000 2.29 0.00 0.00 2.75
740 749 0.976641 TGGCGAATGGTGAGAGAACT 59.023 50.000 0.00 0.00 0.00 3.01
772 785 3.601443 AACAGATCGCTAGCTCAAGTT 57.399 42.857 13.93 10.34 0.00 2.66
776 789 6.392625 ACAGATCGCTAGCTCAAGTTTATA 57.607 37.500 13.93 0.00 0.00 0.98
777 790 6.987386 ACAGATCGCTAGCTCAAGTTTATAT 58.013 36.000 13.93 0.00 0.00 0.86
778 791 8.112016 ACAGATCGCTAGCTCAAGTTTATATA 57.888 34.615 13.93 0.00 0.00 0.86
779 792 8.744652 ACAGATCGCTAGCTCAAGTTTATATAT 58.255 33.333 13.93 0.00 0.00 0.86
831 844 6.157820 TCATGGTTCTGGAATATGTAGGAACA 59.842 38.462 0.00 0.00 40.69 3.18
832 845 5.989477 TGGTTCTGGAATATGTAGGAACAG 58.011 41.667 0.00 0.00 39.49 3.16
833 846 5.487488 TGGTTCTGGAATATGTAGGAACAGT 59.513 40.000 0.00 0.00 39.49 3.55
1422 1437 2.943978 CGAGTCCAACCCCTTCGCT 61.944 63.158 0.00 0.00 0.00 4.93
1615 1630 1.144565 CGGTTGCTGAGCTGATCGAG 61.145 60.000 5.83 0.00 0.00 4.04
1655 1670 3.066190 AGCCGGTGGTCGATCGAA 61.066 61.111 21.31 1.56 42.43 3.71
1967 1982 2.600790 CATGCAGGGAGAGAGAGAGAT 58.399 52.381 0.00 0.00 0.00 2.75
1969 1984 3.961484 TGCAGGGAGAGAGAGAGATAA 57.039 47.619 0.00 0.00 0.00 1.75
2011 2030 2.850439 CAGCTAGCTGCATGTGTGT 58.150 52.632 30.62 0.00 45.94 3.72
2012 2031 0.446616 CAGCTAGCTGCATGTGTGTG 59.553 55.000 30.62 5.33 45.94 3.82
2013 2032 0.035881 AGCTAGCTGCATGTGTGTGT 59.964 50.000 18.57 0.00 45.94 3.72
2014 2033 0.167470 GCTAGCTGCATGTGTGTGTG 59.833 55.000 7.70 0.00 42.31 3.82
2015 2034 1.516161 CTAGCTGCATGTGTGTGTGT 58.484 50.000 1.02 0.00 0.00 3.72
2336 2409 0.108992 GATGCATGTGGCTTGTGGTG 60.109 55.000 2.46 0.00 45.15 4.17
2464 2543 3.225104 CATGTGATAGGGGGTTGAATGG 58.775 50.000 0.00 0.00 0.00 3.16
2489 2568 7.417797 GGGTTGCATATGTTATTCTTGTTGGAT 60.418 37.037 4.29 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.027469 GGGGTGTCGACCTGTTTCTAAT 60.027 50.000 14.12 0.0 42.66 1.73
575 580 1.168714 GATCTTGGTTTGGCGCTCTT 58.831 50.000 7.64 0.0 0.00 2.85
594 599 2.263741 GGTGGTGTTGGCAGCTGAG 61.264 63.158 20.43 0.0 43.05 3.35
595 600 2.203337 GGTGGTGTTGGCAGCTGA 60.203 61.111 20.43 0.0 43.05 4.26
740 749 1.134699 CGATCTGTTTGGGAGCAGCTA 60.135 52.381 0.00 0.0 34.45 3.32
776 789 8.733458 GGTCAATGATTACATGTGTGCATATAT 58.267 33.333 9.11 0.0 36.79 0.86
777 790 7.938490 AGGTCAATGATTACATGTGTGCATATA 59.062 33.333 9.11 0.0 36.79 0.86
778 791 6.774170 AGGTCAATGATTACATGTGTGCATAT 59.226 34.615 9.11 0.0 36.79 1.78
779 792 6.121590 AGGTCAATGATTACATGTGTGCATA 58.878 36.000 9.11 0.0 36.79 3.14
885 898 4.827835 GGCTTTCCCTTACACTTCTCTTTT 59.172 41.667 0.00 0.0 0.00 2.27
1655 1670 0.393077 CCGGCCAAATAGGAGATCGT 59.607 55.000 2.24 0.0 41.22 3.73
1967 1982 7.609097 AGCAAGAGAGATCTCCATACATTTA 57.391 36.000 19.30 0.0 43.88 1.40
1969 1984 6.552725 TGTAGCAAGAGAGATCTCCATACATT 59.447 38.462 19.30 0.0 43.88 2.71
2010 2029 0.096281 CGAACCACACACACACACAC 59.904 55.000 0.00 0.0 0.00 3.82
2011 2030 0.320858 ACGAACCACACACACACACA 60.321 50.000 0.00 0.0 0.00 3.72
2012 2031 0.096281 CACGAACCACACACACACAC 59.904 55.000 0.00 0.0 0.00 3.82
2013 2032 1.640210 GCACGAACCACACACACACA 61.640 55.000 0.00 0.0 0.00 3.72
2014 2033 1.061887 GCACGAACCACACACACAC 59.938 57.895 0.00 0.0 0.00 3.82
2015 2034 0.955919 TTGCACGAACCACACACACA 60.956 50.000 0.00 0.0 0.00 3.72
2336 2409 7.277539 CAGAAGTACTCAGAAATCCATGAGAAC 59.722 40.741 9.06 0.0 44.68 3.01
2464 2543 6.862209 TCCAACAAGAATAACATATGCAACC 58.138 36.000 1.58 0.0 0.00 3.77


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

AutoCloner maintained by Alex Coulton.