Multiple sequence alignment - TraesCS5D01G100700

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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 TraesCS5D01G100700 chr5D 100.000 1870 0 0 605 2474 113392093 113390224 0.000000e+00 3454.0
1 TraesCS5D01G100700 chr5D 100.000 304 0 0 1 304 113392697 113392394 1.660000e-156 562.0
2 TraesCS5D01G100700 chr5A 95.268 1902 52 10 605 2474 118671338 118669443 0.000000e+00 2979.0
3 TraesCS5D01G100700 chr5A 94.754 305 12 2 1 304 118671738 118671437 2.880000e-129 472.0
4 TraesCS5D01G100700 chr5B 94.391 1658 54 15 605 2236 123761293 123759649 0.000000e+00 2510.0
5 TraesCS5D01G100700 chr5B 91.961 311 15 3 1 304 123761699 123761392 6.320000e-116 427.0
6 TraesCS5D01G100700 chr5B 97.189 249 7 0 2226 2474 123759239 123758991 2.940000e-114 422.0
7 TraesCS5D01G100700 chr5B 94.444 36 2 0 797 832 322858710 322858745 3.440000e-04 56.5
8 TraesCS5D01G100700 chr6A 85.526 76 9 2 1107 1181 520869922 520869996 7.340000e-11 78.7
9 TraesCS5D01G100700 chr6A 90.000 50 5 0 803 852 63610630 63610581 5.710000e-07 65.8
10 TraesCS5D01G100700 chr6D 84.416 77 10 2 1109 1184 379723987 379723912 9.490000e-10 75.0
11 TraesCS5D01G100700 chr6D 90.000 50 5 0 803 852 52724690 52724641 5.710000e-07 65.8
12 TraesCS5D01G100700 chr6D 84.375 64 8 2 1107 1169 115021148 115021086 7.390000e-06 62.1
13 TraesCS5D01G100700 chr7D 88.333 60 7 0 1109 1168 136253322 136253263 3.410000e-09 73.1
14 TraesCS5D01G100700 chr7B 88.333 60 7 0 1109 1168 99130768 99130709 3.410000e-09 73.1
15 TraesCS5D01G100700 chr6B 90.000 50 5 0 803 852 119849602 119849553 5.710000e-07 65.8
16 TraesCS5D01G100700 chr6B 84.375 64 8 2 1107 1169 204333994 204333932 7.390000e-06 62.1
17 TraesCS5D01G100700 chr3D 87.037 54 7 0 800 853 252334801 252334854 7.390000e-06 62.1
18 TraesCS5D01G100700 chr3B 87.037 54 7 0 800 853 313808034 313808087 7.390000e-06 62.1
19 TraesCS5D01G100700 chr3A 88.235 51 6 0 803 853 332220134 332220084 7.390000e-06 62.1


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 TraesCS5D01G100700 chr5D 113390224 113392697 2473 True 2008.000000 3454 100.000000 1 2474 2 chr5D.!!$R1 2473
1 TraesCS5D01G100700 chr5A 118669443 118671738 2295 True 1725.500000 2979 95.011000 1 2474 2 chr5A.!!$R1 2473
2 TraesCS5D01G100700 chr5B 123758991 123761699 2708 True 1119.666667 2510 94.513667 1 2474 3 chr5B.!!$R1 2473

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
138 140 0.322322 ATTACGGAAACACCCTCGCA 59.678 50.0 0.0 0.0 34.64 5.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1656 1696 0.684805 AGGACATGGAGGACGAGGAC 60.685 60.0 0.0 0.0 0.0 3.85 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
34 35 4.463879 CGGAGAGCCACCCAGCAG 62.464 72.222 0.00 0.00 34.23 4.24
35 36 4.792804 GGAGAGCCACCCAGCAGC 62.793 72.222 0.00 0.00 34.23 5.25
36 37 4.025858 GAGAGCCACCCAGCAGCA 62.026 66.667 0.00 0.00 34.23 4.41
102 104 1.787155 CTAGAATGCACATACGCCGTC 59.213 52.381 0.00 0.00 0.00 4.79
137 139 1.445871 AATTACGGAAACACCCTCGC 58.554 50.000 0.00 0.00 34.64 5.03
138 140 0.322322 ATTACGGAAACACCCTCGCA 59.678 50.000 0.00 0.00 34.64 5.10
190 192 4.101448 CAGGAGTGCCCTTCCCCG 62.101 72.222 0.00 0.00 44.85 5.73
283 285 1.035932 GCTGCCATTGCTCTCCACAT 61.036 55.000 0.00 0.00 38.71 3.21
653 667 2.980246 TGCTAGGCTAGGCTAGATCA 57.020 50.000 42.16 31.75 0.00 2.92
893 908 4.206609 CCGTCGCTAGCAGTAAACTATTTC 59.793 45.833 16.45 0.00 0.00 2.17
912 930 8.100164 ACTATTTCCTCCTTCTTCTTCTTCTTG 58.900 37.037 0.00 0.00 0.00 3.02
976 1009 2.107292 CAGCAGCAGCAGTAGCCAG 61.107 63.158 3.17 0.00 45.49 4.85
996 1029 1.479323 GGTAGTAGTGATTCCGGTGCA 59.521 52.381 0.00 0.00 0.00 4.57
1522 1555 1.152440 AGGATCCCCTGTAGGAGCG 60.152 63.158 8.55 0.00 43.53 5.03
1624 1657 8.055279 AGTTTGCTGCTATATGTTGTGTTTAT 57.945 30.769 0.00 0.00 0.00 1.40
1625 1658 8.522830 AGTTTGCTGCTATATGTTGTGTTTATT 58.477 29.630 0.00 0.00 0.00 1.40
1626 1659 9.781834 GTTTGCTGCTATATGTTGTGTTTATTA 57.218 29.630 0.00 0.00 0.00 0.98
1648 1688 5.796350 ATTATGTTTCAGTAAGTGTCCGC 57.204 39.130 0.00 0.00 0.00 5.54
1656 1696 3.313007 TAAGTGTCCGCCGTCGTCG 62.313 63.158 0.00 0.00 0.00 5.12
1819 1868 6.714810 TGTAAATTCTGCTGTGTTCCAAGTAT 59.285 34.615 0.00 0.00 0.00 2.12
1849 1898 8.322906 TCAAGTGTTTGATCAGATTTTACGAT 57.677 30.769 0.00 0.00 38.37 3.73
1892 1941 9.650539 TTTCTTGTTGAATTGAATGAAGAACAA 57.349 25.926 11.66 0.00 34.24 2.83
1960 2010 3.069729 AGTCGTATAAATCTGTGGGCTCC 59.930 47.826 0.00 0.00 0.00 4.70
1974 2024 4.016444 GTGGGCTCCTATCAAATCACAAA 58.984 43.478 0.00 0.00 0.00 2.83
2071 2121 4.435137 TTCAAGGTTCCTCCTGGATTCTA 58.565 43.478 0.00 0.00 44.97 2.10
2170 2225 7.016153 ACAAGAATCAAATGGTACCACTAGA 57.984 36.000 19.09 15.18 0.00 2.43
2295 2776 3.399330 GGTAGTGTAAGCAAGCAGAACA 58.601 45.455 0.00 0.00 0.00 3.18
2411 2892 6.825213 CCAAATGACATCACCAGATAGAAGAA 59.175 38.462 0.00 0.00 31.88 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.244019 AATCTTTGCTGGTCCGGTGC 61.244 55.000 0.00 2.82 0.00 5.01
35 36 0.804989 GAATCTTTGCTGGTCCGGTG 59.195 55.000 0.00 0.00 0.00 4.94
36 37 0.322546 GGAATCTTTGCTGGTCCGGT 60.323 55.000 0.00 0.00 0.00 5.28
113 115 2.297880 AGGGTGTTTCCGTAATTTTGCC 59.702 45.455 0.00 0.00 37.00 4.52
137 139 1.676006 GGGCGTTCTGGTAATTCCATG 59.324 52.381 0.00 0.00 46.12 3.66
138 140 1.564348 AGGGCGTTCTGGTAATTCCAT 59.436 47.619 0.00 0.00 46.12 3.41
190 192 2.235891 CGGAGGGGTTATTTATTGGCC 58.764 52.381 0.00 0.00 0.00 5.36
893 908 5.471797 GGAAACAAGAAGAAGAAGAAGGAGG 59.528 44.000 0.00 0.00 0.00 4.30
912 930 2.098443 TGTTGACGCAGGAAAAGGAAAC 59.902 45.455 0.00 0.00 0.00 2.78
967 1000 4.038162 GGAATCACTACTACCTGGCTACTG 59.962 50.000 0.00 0.00 0.00 2.74
976 1009 1.479323 TGCACCGGAATCACTACTACC 59.521 52.381 9.46 0.00 0.00 3.18
996 1029 1.063951 GCGACGACGACGACATCTTT 61.064 55.000 22.94 0.00 42.66 2.52
1185 1218 3.491652 GCGTTCTCGGCCTTGAGC 61.492 66.667 0.00 0.00 42.60 4.26
1624 1657 6.314400 GGCGGACACTTACTGAAACATAATAA 59.686 38.462 0.00 0.00 0.00 1.40
1625 1658 5.813672 GGCGGACACTTACTGAAACATAATA 59.186 40.000 0.00 0.00 0.00 0.98
1626 1659 4.634443 GGCGGACACTTACTGAAACATAAT 59.366 41.667 0.00 0.00 0.00 1.28
1648 1688 4.157958 GGACGAGGACGACGACGG 62.158 72.222 12.58 0.00 44.46 4.79
1656 1696 0.684805 AGGACATGGAGGACGAGGAC 60.685 60.000 0.00 0.00 0.00 3.85
1660 1700 2.454336 ACATAGGACATGGAGGACGA 57.546 50.000 0.00 0.00 0.00 4.20
1661 1701 4.039245 ACATTACATAGGACATGGAGGACG 59.961 45.833 0.00 0.00 0.00 4.79
1662 1702 5.552870 ACATTACATAGGACATGGAGGAC 57.447 43.478 0.00 0.00 0.00 3.85
1849 1898 2.635915 AGAAACCAACATCCGGTGACTA 59.364 45.455 0.00 0.00 36.67 2.59
1892 1941 3.071312 TGAATCTGCAAAACTGGCCAAAT 59.929 39.130 7.01 0.00 0.00 2.32
1960 2010 8.408601 CCTTCCACCTTATTTGTGATTTGATAG 58.591 37.037 0.00 0.00 35.74 2.08
1974 2024 3.136443 TGATTCGATGCCTTCCACCTTAT 59.864 43.478 0.00 0.00 0.00 1.73
2170 2225 2.238521 GGTTGTGACATGGGTTGTGAT 58.761 47.619 0.00 0.00 39.18 3.06
2224 2285 7.285566 ACTGATCAAAGGTGCTGATGTATATT 58.714 34.615 0.00 0.00 33.63 1.28
2295 2776 7.162082 AGTTTAGTTTTCTGATGACGGATCTT 58.838 34.615 0.00 0.00 31.55 2.40
2411 2892 8.494433 ACCATCATTATGACTTATAACTGGTGT 58.506 33.333 10.80 0.00 38.79 4.16


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

AutoCloner maintained by Alex Coulton.