Multiple sequence alignment - TraesCS4D01G043100

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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 TraesCS4D01G043100 chr4D 100.000 2513 0 0 1 2513 19911575 19914087 0 4641
1 TraesCS4D01G043100 chr3D 97.112 2528 57 8 1 2513 21899151 21901677 0 4250
2 TraesCS4D01G043100 chr5D 97.075 2530 57 9 1 2513 240132764 240135293 0 4246
3 TraesCS4D01G043100 chr5D 96.283 2529 72 14 1 2513 6206211 6203689 0 4130
4 TraesCS4D01G043100 chr5D 96.835 2370 58 9 159 2513 449153933 449151566 0 3945
5 TraesCS4D01G043100 chr3B 96.559 2528 71 8 1 2513 201508190 201510716 0 4172
6 TraesCS4D01G043100 chr2D 94.879 2558 81 14 1 2513 334227528 334230080 0 3952
7 TraesCS4D01G043100 chr1D 96.943 2192 52 7 337 2513 483919206 483917015 0 3663
8 TraesCS4D01G043100 chr1D 96.736 1930 47 8 597 2513 254493672 254495598 0 3201
9 TraesCS4D01G043100 chr1D 96.790 1464 28 11 1 1447 254491274 254492735 0 2425
10 TraesCS4D01G043100 chr1D 96.446 1238 28 8 1 1222 483921346 483920109 0 2028
11 TraesCS4D01G043100 chr2B 97.134 1291 37 0 1216 2506 474899819 474898529 0 2180
12 TraesCS4D01G043100 chrUn 96.269 1099 25 8 1 1083 317471574 317470476 0 1788
13 TraesCS4D01G043100 chrUn 96.324 1061 22 9 1 1044 412876894 412877954 0 1727
14 TraesCS4D01G043100 chr2A 95.944 789 24 5 515 1297 42773842 42773056 0 1273


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 TraesCS4D01G043100 chr4D 19911575 19914087 2512 False 4641.0 4641 100.0000 1 2513 1 chr4D.!!$F1 2512
1 TraesCS4D01G043100 chr3D 21899151 21901677 2526 False 4250.0 4250 97.1120 1 2513 1 chr3D.!!$F1 2512
2 TraesCS4D01G043100 chr5D 240132764 240135293 2529 False 4246.0 4246 97.0750 1 2513 1 chr5D.!!$F1 2512
3 TraesCS4D01G043100 chr5D 6203689 6206211 2522 True 4130.0 4130 96.2830 1 2513 1 chr5D.!!$R1 2512
4 TraesCS4D01G043100 chr5D 449151566 449153933 2367 True 3945.0 3945 96.8350 159 2513 1 chr5D.!!$R2 2354
5 TraesCS4D01G043100 chr3B 201508190 201510716 2526 False 4172.0 4172 96.5590 1 2513 1 chr3B.!!$F1 2512
6 TraesCS4D01G043100 chr2D 334227528 334230080 2552 False 3952.0 3952 94.8790 1 2513 1 chr2D.!!$F1 2512
7 TraesCS4D01G043100 chr1D 483917015 483921346 4331 True 2845.5 3663 96.6945 1 2513 2 chr1D.!!$R1 2512
8 TraesCS4D01G043100 chr1D 254491274 254495598 4324 False 2813.0 3201 96.7630 1 2513 2 chr1D.!!$F1 2512
9 TraesCS4D01G043100 chr2B 474898529 474899819 1290 True 2180.0 2180 97.1340 1216 2506 1 chr2B.!!$R1 1290
10 TraesCS4D01G043100 chrUn 317470476 317471574 1098 True 1788.0 1788 96.2690 1 1083 1 chrUn.!!$R1 1082
11 TraesCS4D01G043100 chrUn 412876894 412877954 1060 False 1727.0 1727 96.3240 1 1044 1 chrUn.!!$F1 1043
12 TraesCS4D01G043100 chr2A 42773056 42773842 786 True 1273.0 1273 95.9440 515 1297 1 chr2A.!!$R1 782

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
549 558 1.1862 GAAAAGGAGGTTCATGGCCC 58.814 55.0 0.0 0.0 0.0 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2246 5902 1.066645 GGAAACGACGGAACCCACTAT 60.067 52.381 0.0 0.0 0.0 2.12 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
164 166 8.183536 TCGTGATATGACAAAATTTGATCCTTG 58.816 33.333 13.19 0.00 0.00 3.61
224 228 2.017049 GATGGATTGGGTTGAACCTCG 58.983 52.381 14.87 0.00 38.64 4.63
327 333 3.550437 ATCAGAGCATAGAAAAGGCGT 57.450 42.857 0.00 0.00 0.00 5.68
549 558 1.186200 GAAAAGGAGGTTCATGGCCC 58.814 55.000 0.00 0.00 0.00 5.80
621 630 2.351738 CGAAAAGGTGCCAATGAGGAAC 60.352 50.000 0.00 0.00 46.41 3.62
692 701 6.364976 CACCCGGACAATTAGAATTCAAAAAC 59.635 38.462 0.73 0.00 0.00 2.43
779 2592 5.418310 TCGATCTTTCCAAACAACAGAAC 57.582 39.130 0.00 0.00 0.00 3.01
780 2593 4.878971 TCGATCTTTCCAAACAACAGAACA 59.121 37.500 0.00 0.00 0.00 3.18
789 2602 7.083875 TCCAAACAACAGAACAAGTAAGAAG 57.916 36.000 0.00 0.00 0.00 2.85
944 2784 7.510549 TGGATCAAAGAAAAACTACTTCTGG 57.489 36.000 0.00 0.00 33.40 3.86
1250 3103 9.443323 TGAACAAGGAAAAATATTATCGAGACA 57.557 29.630 0.00 0.00 0.00 3.41
1346 4998 6.779117 TCTTACCGTTTCGTAACTATGAGAG 58.221 40.000 3.36 0.00 31.89 3.20
1523 5176 7.881142 AGTTCCGATTGTTGATGTTTTATTCA 58.119 30.769 0.00 0.00 0.00 2.57
1746 5399 6.349280 GGATTTGATACAGCTACTTGTGCAAA 60.349 38.462 0.00 0.00 39.10 3.68
1859 5512 6.604396 TGCATTTATCTGAGTGATCCACAAAT 59.396 34.615 0.00 0.00 36.74 2.32
1923 5576 6.806751 AGGAAACAAAAGCTCTTTTTACCTC 58.193 36.000 4.97 1.43 40.45 3.85
1979 5632 4.158579 CCCCTCTAAAGTTTGAGGCAAATC 59.841 45.833 20.21 0.00 45.15 2.17
1994 5647 4.335037 AGGCAAATCAACGCATTTTTGTTT 59.665 33.333 0.00 0.00 32.88 2.83
2004 5657 3.701241 GCATTTTTGTTTGTCGTCTCCA 58.299 40.909 0.00 0.00 0.00 3.86
2165 5818 6.238759 CCAATGGCTTTTGCTATAGTAACCTC 60.239 42.308 2.39 0.00 46.15 3.85
2266 5922 0.318120 TAGTGGGTTCCGTCGTTTCC 59.682 55.000 0.00 0.00 0.00 3.13
2297 5953 0.323629 TTAAACGGTGAGGCCCTCTG 59.676 55.000 12.94 4.53 0.00 3.35
2309 5965 0.388294 GCCCTCTGTATACACCGGAC 59.612 60.000 9.46 0.00 0.00 4.79
2366 6022 3.515602 AGTCCACATTCTTTGGCTCTT 57.484 42.857 0.00 0.00 33.71 2.85
2448 6104 8.188139 ACGGTATTTAATTATGAAAGTTGGCTG 58.812 33.333 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
184 186 8.539117 TCCATCTTTTCTTTCTTTTTCCTTCT 57.461 30.769 0.00 0.00 0.00 2.85
224 228 7.604927 GGGGTTTACCAAATTTTTAATGACTCC 59.395 37.037 0.69 0.00 42.91 3.85
327 333 5.268387 TCCTTTCATTTAATTAGCCAGCCA 58.732 37.500 0.00 0.00 0.00 4.75
549 558 7.108847 ACTCTGATTCTAACATCTTTTCCCTG 58.891 38.462 0.00 0.00 0.00 4.45
621 630 7.830201 AGTACTATATCTAGAAATCCCTGTCGG 59.170 40.741 0.00 0.00 0.00 4.79
692 701 3.297979 GCTTGCGACAATAACGACAAATG 59.702 43.478 0.00 0.00 0.00 2.32
1030 2883 5.131067 GGATTTACTAAAGGGTTGCCTAGG 58.869 45.833 3.67 3.67 0.00 3.02
1034 2887 4.381612 GCTTGGATTTACTAAAGGGTTGCC 60.382 45.833 0.00 0.00 0.00 4.52
1272 3125 6.314784 AGCAAGAGTAATTAATCGTTGTTGC 58.685 36.000 20.84 20.84 37.44 4.17
1346 4998 1.460743 GGGCTTGAAATTGCTTTTCGC 59.539 47.619 7.78 6.28 45.63 4.70
1523 5176 1.075536 AGGTCTGGCCCTTTCGAATTT 59.924 47.619 0.00 0.00 38.26 1.82
1570 5223 5.733620 TTAAGTGGTAGGAATCAACGAGT 57.266 39.130 0.00 0.00 0.00 4.18
1810 5463 6.810182 CAGCTACGCGGGTATATAAAGTATTT 59.190 38.462 12.47 0.00 43.42 1.40
1831 5484 4.141551 TGGATCACTCAGATAAATGCAGCT 60.142 41.667 0.00 0.00 37.00 4.24
1859 5512 2.556622 GGCAAAAGAGGGATTTTCGTCA 59.443 45.455 0.00 0.00 30.01 4.35
1923 5576 8.438676 AAGACTTAATCGAATGATTACCCAAG 57.561 34.615 0.00 0.00 44.64 3.61
1979 5632 3.545873 AGACGACAAACAAAAATGCGTTG 59.454 39.130 0.00 0.00 32.42 4.10
1994 5647 4.018324 AGGATATATAGCCTGGAGACGACA 60.018 45.833 18.77 0.00 41.28 4.35
2066 5719 6.388619 AGGGTGGCTAAAAGAAGAGAAATA 57.611 37.500 0.00 0.00 0.00 1.40
2246 5902 1.066645 GGAAACGACGGAACCCACTAT 60.067 52.381 0.00 0.00 0.00 2.12
2297 5953 2.113807 AGAAAGGGGTCCGGTGTATAC 58.886 52.381 0.00 0.00 0.00 1.47
2448 6104 2.427812 GGACTAACAGGGTCAGCTACTC 59.572 54.545 0.00 0.00 35.61 2.59


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

AutoCloner maintained by Alex Coulton.