Multiple sequence alignment - TraesCS1B01G355100

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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 TraesCS1B01G355100 chr1B 100.000 2517 0 0 1 2517 584636727 584634211 0.000000e+00 4649
1 TraesCS1B01G355100 chr1B 95.970 2432 92 5 1 2427 83652243 83654673 0.000000e+00 3943
2 TraesCS1B01G355100 chr1B 95.636 2452 102 5 1 2450 661028329 661030777 0.000000e+00 3930
3 TraesCS1B01G355100 chr3B 96.983 2519 72 4 1 2517 48679970 48682486 0.000000e+00 4228
4 TraesCS1B01G355100 chr3B 87.172 1637 144 42 900 2517 725531380 725532969 0.000000e+00 1799
5 TraesCS1B01G355100 chr3B 86.544 1635 160 37 900 2517 709814608 709816199 0.000000e+00 1746
6 TraesCS1B01G355100 chr6B 96.471 2522 83 6 1 2517 439424251 439421731 0.000000e+00 4159
7 TraesCS1B01G355100 chr6B 86.064 1636 167 39 900 2517 49207564 49209156 0.000000e+00 1701
8 TraesCS1B01G355100 chr7B 96.900 2452 73 3 1 2450 112898387 112900837 0.000000e+00 4104
9 TraesCS1B01G355100 chr7B 94.764 2521 120 9 1 2515 610536334 610538848 0.000000e+00 3914
10 TraesCS1B01G355100 chr5B 95.399 2521 106 8 1 2517 541962817 541965331 0.000000e+00 4004
11 TraesCS1B01G355100 chr2B 95.923 2453 92 5 1 2450 87791490 87793937 0.000000e+00 3969
12 TraesCS1B01G355100 chr2B 84.083 289 39 5 2231 2515 499574873 499574588 3.190000e-69 272
13 TraesCS1B01G355100 chr4B 96.049 2430 88 8 1 2427 554204779 554207203 0.000000e+00 3949
14 TraesCS1B01G355100 chr4B 84.138 290 41 4 2231 2517 523192825 523193112 2.470000e-70 276


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 TraesCS1B01G355100 chr1B 584634211 584636727 2516 True 4649 4649 100.000 1 2517 1 chr1B.!!$R1 2516
1 TraesCS1B01G355100 chr1B 83652243 83654673 2430 False 3943 3943 95.970 1 2427 1 chr1B.!!$F1 2426
2 TraesCS1B01G355100 chr1B 661028329 661030777 2448 False 3930 3930 95.636 1 2450 1 chr1B.!!$F2 2449
3 TraesCS1B01G355100 chr3B 48679970 48682486 2516 False 4228 4228 96.983 1 2517 1 chr3B.!!$F1 2516
4 TraesCS1B01G355100 chr3B 725531380 725532969 1589 False 1799 1799 87.172 900 2517 1 chr3B.!!$F3 1617
5 TraesCS1B01G355100 chr3B 709814608 709816199 1591 False 1746 1746 86.544 900 2517 1 chr3B.!!$F2 1617
6 TraesCS1B01G355100 chr6B 439421731 439424251 2520 True 4159 4159 96.471 1 2517 1 chr6B.!!$R1 2516
7 TraesCS1B01G355100 chr6B 49207564 49209156 1592 False 1701 1701 86.064 900 2517 1 chr6B.!!$F1 1617
8 TraesCS1B01G355100 chr7B 112898387 112900837 2450 False 4104 4104 96.900 1 2450 1 chr7B.!!$F1 2449
9 TraesCS1B01G355100 chr7B 610536334 610538848 2514 False 3914 3914 94.764 1 2515 1 chr7B.!!$F2 2514
10 TraesCS1B01G355100 chr5B 541962817 541965331 2514 False 4004 4004 95.399 1 2517 1 chr5B.!!$F1 2516
11 TraesCS1B01G355100 chr2B 87791490 87793937 2447 False 3969 3969 95.923 1 2450 1 chr2B.!!$F1 2449
12 TraesCS1B01G355100 chr4B 554204779 554207203 2424 False 3949 3949 96.049 1 2427 1 chr4B.!!$F2 2426

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
51 52 1.034838 AAGTTCCAACGTGCCTGCAA 61.035 50.000 0.00 0.0 0.00 4.08 F
218 220 2.044946 GGAAATGCGAGGGCCAGT 60.045 61.111 6.18 0.0 38.85 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1035 1053 1.209261 TGACCACACTTGTCTTGCTGA 59.791 47.619 0.0 0.0 33.83 4.26 R
1845 1871 2.351253 CGGGTGATGCAAACGATGAAAA 60.351 45.455 0.0 0.0 0.00 2.29 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
51 52 1.034838 AAGTTCCAACGTGCCTGCAA 61.035 50.000 0.00 0.00 0.00 4.08
147 149 2.707849 GCGGAAGACTACGAGCCCA 61.708 63.158 3.89 0.00 0.00 5.36
218 220 2.044946 GGAAATGCGAGGGCCAGT 60.045 61.111 6.18 0.00 38.85 4.00
258 260 4.481930 CTGAAAGCGTAAATGACCACAA 57.518 40.909 0.00 0.00 0.00 3.33
287 291 3.759581 TCTCTCATTTTGCTTTGCTCCT 58.240 40.909 0.00 0.00 0.00 3.69
508 514 5.163972 CCAAACGGTAAAATGTCGACGAATA 60.164 40.000 11.62 0.00 0.00 1.75
591 597 5.357742 TCATGCATTATAGTGTGACCTGT 57.642 39.130 0.00 0.00 0.00 4.00
646 653 3.445096 CCCGAGGAAGAATTTTGCTCAAT 59.555 43.478 16.16 0.00 36.80 2.57
854 867 7.831690 TGGCAACTTGATAGTAAAATACATGGA 59.168 33.333 0.00 0.00 33.17 3.41
855 868 8.129211 GGCAACTTGATAGTAAAATACATGGAC 58.871 37.037 0.00 0.00 33.17 4.02
964 980 4.946157 CCCTCTGCTGTTCTTTATGTGAAT 59.054 41.667 0.00 0.00 0.00 2.57
1035 1053 0.330604 AGGAGCTTGCACCACATGAT 59.669 50.000 11.34 0.00 0.00 2.45
1148 1166 3.801114 TGCAGATCTTACTACGCATGT 57.199 42.857 0.00 0.00 0.00 3.21
1291 1309 2.053747 TAACCCCCTCCTTCATGTGT 57.946 50.000 0.00 0.00 0.00 3.72
1311 1329 6.009589 TGTGTCATTTACATCAATCCAACCT 58.990 36.000 0.00 0.00 41.10 3.50
1570 1592 1.337823 GCGAGTTTGTGGAGGAAGCTA 60.338 52.381 0.00 0.00 0.00 3.32
1626 1648 1.872234 CGATACACACCGGACGCAG 60.872 63.158 9.46 0.00 0.00 5.18
1652 1674 5.416952 CCTTACATTCTGTTGCTGAGGAATT 59.583 40.000 0.00 0.00 0.00 2.17
1803 1827 5.822519 GTGTGGATGTGAATCTAATTAGGCA 59.177 40.000 12.54 6.15 0.00 4.75
2014 2047 2.565841 CCAGCTAGCATGGTAGGTTTC 58.434 52.381 28.87 14.69 32.85 2.78
2115 2149 3.257375 ACACTATGTGTCTCTAAACCGCA 59.743 43.478 0.00 0.00 43.92 5.69
2252 2287 3.887621 ACACGGCAGATACAGTACAAT 57.112 42.857 0.00 0.00 0.00 2.71
2402 2471 6.106673 GCAGACTAACTACACATAACATGGT 58.893 40.000 0.00 0.00 33.60 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 149 3.181423 TGTTCCTTAGTGGCCCTGAATTT 60.181 43.478 0.00 0.00 35.26 1.82
218 220 1.280133 AGCTCCTTCATGTGCTTGCTA 59.720 47.619 0.00 0.00 30.96 3.49
258 260 6.628844 GCAAAGCAAAATGAGAGATTATGGGT 60.629 38.462 0.00 0.00 0.00 4.51
508 514 0.392706 TCGATCCCGCATGCAACTAT 59.607 50.000 19.57 4.99 35.37 2.12
591 597 6.126409 GTGGAAGTCACCATCCCATATTTTA 58.874 40.000 0.00 0.00 42.17 1.52
646 653 2.299013 AGTGTGAGCTTGATTCACCGTA 59.701 45.455 3.24 0.00 43.32 4.02
854 867 3.119173 CGCCCATGTATGAACAAAATGGT 60.119 43.478 0.00 0.00 39.58 3.55
855 868 3.446799 CGCCCATGTATGAACAAAATGG 58.553 45.455 0.00 0.00 39.58 3.16
964 980 6.949352 AAAGTGAAGAAATGAGAAGCAGAA 57.051 33.333 0.00 0.00 0.00 3.02
1035 1053 1.209261 TGACCACACTTGTCTTGCTGA 59.791 47.619 0.00 0.00 33.83 4.26
1291 1309 6.962182 AGAGAGGTTGGATTGATGTAAATGA 58.038 36.000 0.00 0.00 0.00 2.57
1419 1440 3.005684 CCACTTTGCAAAGTATTCCAGCA 59.994 43.478 37.19 1.64 46.89 4.41
1471 1492 2.668280 GGAGCTCAACGACGTTGCC 61.668 63.158 30.96 23.04 42.55 4.52
1570 1592 7.009179 TGTACCTCTTGATGACTTTCTTGAT 57.991 36.000 0.00 0.00 0.00 2.57
1652 1674 8.800332 ACGAGAACAAAAGAGATAGTACCTTAA 58.200 33.333 0.00 0.00 0.00 1.85
1792 1814 5.557576 ATCTGCTGTCATGCCTAATTAGA 57.442 39.130 14.28 0.00 0.00 2.10
1796 1820 5.238624 ACATATCTGCTGTCATGCCTAAT 57.761 39.130 0.00 0.00 0.00 1.73
1845 1871 2.351253 CGGGTGATGCAAACGATGAAAA 60.351 45.455 0.00 0.00 0.00 2.29
2014 2047 3.674138 GCAAAGGTTGTGGCTACATGATG 60.674 47.826 2.83 1.01 36.53 3.07
2115 2149 6.312918 GGCATATATTTCCGTGACAATACGAT 59.687 38.462 0.00 0.00 46.46 3.73
2286 2321 5.862678 TGCCATGCTAGTTGTACTACATA 57.137 39.130 10.09 0.00 0.00 2.29
2290 2325 8.647796 ACTAAATATGCCATGCTAGTTGTACTA 58.352 33.333 0.00 0.00 0.00 1.82
2402 2471 8.700973 TCTGCCATGTTATGTGTAGTTAATCTA 58.299 33.333 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.