Multiple sequence alignment - TraesCS5B01G250300

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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 TraesCS5B01G250300 chr5B 100.000 2240 0 0 1 2240 432868648 432870887 0 4137
1 TraesCS5B01G250300 chr2A 96.967 2242 66 2 1 2240 726903962 726901721 0 3762
2 TraesCS5B01G250300 chr2A 95.491 2240 97 4 1 2238 335803579 335801342 0 3574
3 TraesCS5B01G250300 chr3B 96.699 2242 72 2 1 2240 201572294 201570053 0 3729
4 TraesCS5B01G250300 chr3D 96.655 2242 72 3 1 2240 589261034 589258794 0 3722
5 TraesCS5B01G250300 chr7B 96.564 2241 76 1 1 2240 662729407 662731647 0 3711
6 TraesCS5B01G250300 chr2D 96.476 2242 73 5 1 2240 272809753 272807516 0 3698
7 TraesCS5B01G250300 chr3A 96.386 2241 79 2 1 2240 695642878 695645117 0 3688
8 TraesCS5B01G250300 chr4A 96.382 2239 78 3 1 2238 583866413 583864177 0 3683
9 TraesCS5B01G250300 chr2B 95.230 2243 104 2 1 2240 474923427 474925669 0 3546


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 TraesCS5B01G250300 chr5B 432868648 432870887 2239 False 4137 4137 100.000 1 2240 1 chr5B.!!$F1 2239
1 TraesCS5B01G250300 chr2A 726901721 726903962 2241 True 3762 3762 96.967 1 2240 1 chr2A.!!$R2 2239
2 TraesCS5B01G250300 chr2A 335801342 335803579 2237 True 3574 3574 95.491 1 2238 1 chr2A.!!$R1 2237
3 TraesCS5B01G250300 chr3B 201570053 201572294 2241 True 3729 3729 96.699 1 2240 1 chr3B.!!$R1 2239
4 TraesCS5B01G250300 chr3D 589258794 589261034 2240 True 3722 3722 96.655 1 2240 1 chr3D.!!$R1 2239
5 TraesCS5B01G250300 chr7B 662729407 662731647 2240 False 3711 3711 96.564 1 2240 1 chr7B.!!$F1 2239
6 TraesCS5B01G250300 chr2D 272807516 272809753 2237 True 3698 3698 96.476 1 2240 1 chr2D.!!$R1 2239
7 TraesCS5B01G250300 chr3A 695642878 695645117 2239 False 3688 3688 96.386 1 2240 1 chr3A.!!$F1 2239
8 TraesCS5B01G250300 chr4A 583864177 583866413 2236 True 3683 3683 96.382 1 2238 1 chr4A.!!$R1 2237
9 TraesCS5B01G250300 chr2B 474923427 474925669 2242 False 3546 3546 95.230 1 2240 1 chr2B.!!$F1 2239

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
524 525 0.033503 TCCACGAGGCTCATACCAGA 60.034 55.0 15.95 0.0 33.74 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 1781 0.395862 CGGAGGCTCTAGGGAAGTCA 60.396 60.0 15.23 0.0 0.0 3.41 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
56 57 1.386533 CCCTTGCGCTGAAGATGAAT 58.613 50.000 9.73 0.00 0.00 2.57
73 74 0.839946 AATGGGGCTAAGCGATCTGT 59.160 50.000 0.00 0.00 0.00 3.41
145 146 1.008995 GAAGCAACCGCAAAAGCGA 60.009 52.632 11.83 0.00 42.27 4.93
164 165 2.506438 GGTCGACGAAGCGGAAGG 60.506 66.667 9.92 0.00 0.00 3.46
168 169 2.184579 GACGAAGCGGAAGGGAGG 59.815 66.667 0.00 0.00 0.00 4.30
212 213 2.905415 TTGGTGAGAATCCAATGCCT 57.095 45.000 0.00 0.00 39.62 4.75
524 525 0.033503 TCCACGAGGCTCATACCAGA 60.034 55.000 15.95 0.00 33.74 3.86
533 534 1.022735 CTCATACCAGACGCTACGGT 58.977 55.000 0.00 0.00 36.79 4.83
563 564 5.841237 AGTATGTAACTGATGCCATACTCCT 59.159 40.000 5.56 0.00 43.93 3.69
648 649 3.406498 AGGTAGAGAATACCTAGGGGCAT 59.594 47.826 14.81 0.00 45.47 4.40
673 674 5.636123 AGACAACTCTCTCTAAGGAACTCA 58.364 41.667 0.00 0.00 38.49 3.41
690 691 2.213499 CTCAGCAAAATAGCCCCGTAG 58.787 52.381 0.00 0.00 34.23 3.51
865 866 4.162690 GACAGGGAAGCCGGCGAT 62.163 66.667 23.20 15.02 0.00 4.58
911 912 6.136541 CGTAACTATAACGGTCCTAAGGTT 57.863 41.667 0.00 0.00 36.71 3.50
937 938 4.635699 AATTCCTTGTCGGGTAAGTTCT 57.364 40.909 0.00 0.00 0.00 3.01
1023 1024 2.164624 GTCTGTGAAGATGCGGACTACT 59.835 50.000 0.00 0.00 37.84 2.57
1059 1060 7.180408 ACAGAAAGACCCTATGAAGCTTTACTA 59.820 37.037 0.00 0.00 0.00 1.82
1091 1092 2.209315 GCTTTGGGCCTTTCCTGCA 61.209 57.895 4.53 0.00 34.39 4.41
1117 1118 1.377333 GGTGGAAGGCGAAGAAGGG 60.377 63.158 0.00 0.00 0.00 3.95
1296 1299 2.668632 GGGCCAGACGGACATTGA 59.331 61.111 4.39 0.00 45.55 2.57
1517 1522 0.976641 CACTTGGAGCTGTAGGTGGA 59.023 55.000 0.00 0.00 0.00 4.02
1549 1554 1.203523 GGTTGTTCGCCCATTAATGCA 59.796 47.619 10.11 0.00 0.00 3.96
1563 1568 1.386533 AATGCAGTACATGAGCTGGC 58.613 50.000 17.88 12.52 39.60 4.85
1566 1571 1.271543 TGCAGTACATGAGCTGGCTTT 60.272 47.619 17.88 0.00 33.62 3.51
1581 1586 2.230508 TGGCTTTAGAACGTCGTGAGAT 59.769 45.455 0.00 0.00 45.19 2.75
1644 1649 3.624456 GGACCTTTCCCTAGTACGAGAGT 60.624 52.174 4.34 0.00 41.63 3.24
1763 1768 1.005450 GTAAGCCCACCCCAAGATGAA 59.995 52.381 0.00 0.00 0.00 2.57
1776 1781 3.388676 CCAAGATGAATGCTCTCTCCTCT 59.611 47.826 0.00 0.00 0.00 3.69
1878 1883 4.228824 TGGAAATAGGATAAGGTAGCGGT 58.771 43.478 0.00 0.00 0.00 5.68
1949 1954 1.134670 GCTGAGGCATCCTAACGAACT 60.135 52.381 0.00 0.00 38.54 3.01
1979 1984 1.373435 CCTTGTTCCTACACGGCCA 59.627 57.895 2.24 0.00 36.94 5.36
2093 2100 6.134535 TCTCTTGGATAGATAGAGAGGGAC 57.865 45.833 0.00 0.00 39.46 4.46
2206 2213 2.628178 CGATATTCTGGTGTCCTAGGCA 59.372 50.000 2.96 2.51 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 1.823295 GACAGATCGCTTAGCCCCA 59.177 57.895 0.00 0.00 0.00 4.96
73 74 3.904800 TTTGACATCCCATAGCTTCGA 57.095 42.857 0.00 0.00 0.00 3.71
145 146 2.987547 TTCCGCTTCGTCGACCCT 60.988 61.111 10.58 0.00 0.00 4.34
164 165 1.112113 TACTCAAGCCGACATCCTCC 58.888 55.000 0.00 0.00 0.00 4.30
168 169 2.273370 TCGTTACTCAAGCCGACATC 57.727 50.000 0.00 0.00 0.00 3.06
280 281 2.093306 TGTCCATCAACTACGCCTTG 57.907 50.000 0.00 0.00 0.00 3.61
303 304 5.789535 AGGGGTAGTACAGGAATATTGACT 58.210 41.667 2.06 0.00 0.00 3.41
524 525 0.815734 ATACTTCAGCACCGTAGCGT 59.184 50.000 0.00 0.00 40.15 5.07
533 534 4.191544 GGCATCAGTTACATACTTCAGCA 58.808 43.478 0.00 0.00 33.85 4.41
563 564 1.891150 AGGTCGTTCGAGCTTTTCCTA 59.109 47.619 18.85 0.00 39.59 2.94
673 674 0.916809 ACCTACGGGGCTATTTTGCT 59.083 50.000 0.00 0.00 39.10 3.91
690 691 2.669240 CACCCCTTCTCCCGAACC 59.331 66.667 0.00 0.00 0.00 3.62
691 692 2.046217 GCACCCCTTCTCCCGAAC 60.046 66.667 0.00 0.00 0.00 3.95
810 811 3.637273 GACCTTCCGGCACTGGGT 61.637 66.667 0.00 0.00 0.00 4.51
865 866 4.367023 CGTTCACCGGGGCTTCGA 62.367 66.667 6.32 0.00 0.00 3.71
911 912 1.698506 ACCCGACAAGGAATTTTGCA 58.301 45.000 0.00 0.00 45.00 4.08
955 956 0.036952 AGACAGTGCCCAGATCGTTG 60.037 55.000 0.00 0.00 0.00 4.10
988 989 6.997655 TCTTCACAGACATGTCTATTTCACT 58.002 36.000 27.44 0.74 37.65 3.41
1023 1024 1.476833 GGTCTTTCTGTCCAGGTGCAA 60.477 52.381 0.00 0.00 0.00 4.08
1059 1060 1.623279 CCAAAGCCAATCCCAGGGAAT 60.623 52.381 13.94 0.00 34.34 3.01
1091 1092 1.192146 TCGCCTTCCACCTAAGCTGT 61.192 55.000 0.00 0.00 0.00 4.40
1132 1134 4.227134 CTCACGGATGGCTCGGGG 62.227 72.222 0.00 0.00 0.00 5.73
1144 1147 3.017442 TCTTCCAGAGTGGTATCTCACG 58.983 50.000 0.00 0.00 42.10 4.35
1296 1299 0.392193 CTGCCTTTGCACTCGAGGAT 60.392 55.000 18.41 0.00 44.23 3.24
1342 1345 2.159448 CGACTTTCATCTCTGCTCGACT 60.159 50.000 0.00 0.00 0.00 4.18
1501 1506 1.204146 GGATCCACCTACAGCTCCAA 58.796 55.000 6.95 0.00 35.41 3.53
1549 1554 4.508662 GTTCTAAAGCCAGCTCATGTACT 58.491 43.478 0.00 0.00 0.00 2.73
1563 1568 5.448479 CGAACTATCTCACGACGTTCTAAAG 59.552 44.000 0.00 0.00 33.86 1.85
1566 1571 3.308053 CCGAACTATCTCACGACGTTCTA 59.692 47.826 0.00 0.00 33.86 2.10
1644 1649 3.384532 GGTGCGTCCTTCCCGGTA 61.385 66.667 0.00 0.00 0.00 4.02
1763 1768 2.387757 GGAAGTCAGAGGAGAGAGCAT 58.612 52.381 0.00 0.00 0.00 3.79
1776 1781 0.395862 CGGAGGCTCTAGGGAAGTCA 60.396 60.000 15.23 0.00 0.00 3.41
1878 1883 5.116180 CACCTATTTAAACGGCTCATCTCA 58.884 41.667 5.50 0.00 0.00 3.27
1949 1954 6.203338 GTGTAGGAACAAGGTTCAAATCGTTA 59.797 38.462 10.86 0.00 37.36 3.18
1979 1984 5.746638 GCAAGTGCCTGATCGATTTGATCT 61.747 45.833 13.79 0.00 43.61 2.75
2007 2012 8.294577 TCATCAAAGAGTTGAACAATGAAGATG 58.705 33.333 0.00 4.52 46.66 2.90
2206 2213 3.189606 TGGATTGGTGTGGTTCCTCTAT 58.810 45.455 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.