Multiple sequence alignment - TraesCS3A01G505700

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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 TraesCS3A01G505700 chr3A 100.000 4900 0 0 1 4900 727468525 727473424 0.000000e+00 9049.0
1 TraesCS3A01G505700 chr3A 87.164 2493 284 24 910 3384 727397544 727400018 0.000000e+00 2798.0
2 TraesCS3A01G505700 chr2A 98.486 4161 62 1 1 4161 605130739 605126580 0.000000e+00 7334.0
3 TraesCS3A01G505700 chr2A 86.850 2943 342 32 970 3887 605398590 605401512 0.000000e+00 3249.0
4 TraesCS3A01G505700 chr2A 99.441 358 2 0 4150 4507 605125143 605124786 0.000000e+00 651.0
5 TraesCS3A01G505700 chr2A 82.948 692 99 15 3217 3900 605355066 605354386 1.510000e-169 606.0
6 TraesCS3A01G505700 chr2A 98.225 338 4 1 4507 4842 605124754 605124417 1.520000e-164 590.0
7 TraesCS3A01G505700 chr2A 83.709 577 78 13 3217 3785 605355834 605355266 9.340000e-147 531.0
8 TraesCS3A01G505700 chr3B 93.449 3984 225 22 552 4516 804237378 804241344 0.000000e+00 5879.0
9 TraesCS3A01G505700 chr3B 85.940 3101 374 49 837 3898 804129992 804133069 0.000000e+00 3254.0
10 TraesCS3A01G505700 chr3B 86.373 1996 252 13 1892 3877 804228291 804230276 0.000000e+00 2161.0
11 TraesCS3A01G505700 chr3B 85.471 2051 267 25 1857 3887 804170642 804172681 0.000000e+00 2108.0
12 TraesCS3A01G505700 chr3B 86.424 987 119 8 865 1838 804167822 804168806 0.000000e+00 1066.0
13 TraesCS3A01G505700 chr3B 85.671 984 115 18 873 1838 804214233 804215208 0.000000e+00 1013.0
14 TraesCS3A01G505700 chr3B 86.197 355 31 7 4551 4896 804241423 804241768 7.750000e-98 368.0
15 TraesCS3A01G505700 chr3B 77.800 509 87 19 3993 4484 804172834 804173333 1.730000e-74 291.0
16 TraesCS3A01G505700 chr3B 77.337 353 53 18 4552 4900 804232932 804233261 3.010000e-42 183.0
17 TraesCS3A01G505700 chr3B 81.301 123 14 2 58 173 804237252 804237372 1.880000e-14 91.6
18 TraesCS3A01G505700 chr3D 94.642 3621 175 10 808 4415 597486607 597490221 0.000000e+00 5594.0
19 TraesCS3A01G505700 chr3D 85.970 1953 242 24 1936 3877 597295750 597297681 0.000000e+00 2060.0
20 TraesCS3A01G505700 chr3D 86.678 1216 157 5 1902 3114 597409428 597410641 0.000000e+00 1343.0
21 TraesCS3A01G505700 chr3D 86.492 918 120 4 903 1818 597407601 597408516 0.000000e+00 1005.0
22 TraesCS3A01G505700 chr3D 90.041 492 35 11 4413 4900 597490421 597490902 4.160000e-175 625.0
23 TraesCS3A01G505700 chr3D 93.088 217 14 1 3 219 597486274 597486489 2.850000e-82 316.0
24 TraesCS3A01G505700 chr3D 97.701 87 2 0 251 337 597486484 597486570 3.060000e-32 150.0


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 TraesCS3A01G505700 chr3A 727468525 727473424 4899 False 9049.000000 9049 100.000000 1 4900 1 chr3A.!!$F2 4899
1 TraesCS3A01G505700 chr3A 727397544 727400018 2474 False 2798.000000 2798 87.164000 910 3384 1 chr3A.!!$F1 2474
2 TraesCS3A01G505700 chr2A 605398590 605401512 2922 False 3249.000000 3249 86.850000 970 3887 1 chr2A.!!$F1 2917
3 TraesCS3A01G505700 chr2A 605124417 605130739 6322 True 2858.333333 7334 98.717333 1 4842 3 chr2A.!!$R1 4841
4 TraesCS3A01G505700 chr2A 605354386 605355834 1448 True 568.500000 606 83.328500 3217 3900 2 chr2A.!!$R2 683
5 TraesCS3A01G505700 chr3B 804129992 804133069 3077 False 3254.000000 3254 85.940000 837 3898 1 chr3B.!!$F1 3061
6 TraesCS3A01G505700 chr3B 804228291 804241768 13477 False 1736.520000 5879 84.931400 58 4900 5 chr3B.!!$F4 4842
7 TraesCS3A01G505700 chr3B 804167822 804173333 5511 False 1155.000000 2108 83.231667 865 4484 3 chr3B.!!$F3 3619
8 TraesCS3A01G505700 chr3B 804214233 804215208 975 False 1013.000000 1013 85.671000 873 1838 1 chr3B.!!$F2 965
9 TraesCS3A01G505700 chr3D 597295750 597297681 1931 False 2060.000000 2060 85.970000 1936 3877 1 chr3D.!!$F1 1941
10 TraesCS3A01G505700 chr3D 597486274 597490902 4628 False 1671.250000 5594 93.868000 3 4900 4 chr3D.!!$F3 4897
11 TraesCS3A01G505700 chr3D 597407601 597410641 3040 False 1174.000000 1343 86.585000 903 3114 2 chr3D.!!$F2 2211

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
325 9237 0.250727 TGCTGTTCCTGTAAGTGGCC 60.251 55.000 0.0 0.0 0.00 5.36 F
1119 10061 1.558756 CTGAGGAAGGAGGTGAAGCAT 59.441 52.381 0.0 0.0 0.00 3.79 F
1358 10300 0.879400 CATCAGATCGCTGGGCAGAC 60.879 60.000 0.0 0.0 42.53 3.51 F
2703 14330 2.695359 TCCTGTACAAATCTGCGGAAC 58.305 47.619 0.0 0.0 0.00 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1210 10152 0.034767 TACGACATCTCCCTGACCGT 60.035 55.000 0.00 0.0 34.96 4.83 R
2211 13838 2.092429 TGAGTTGACCTGGACAAGCTTT 60.092 45.455 11.78 0.0 0.00 3.51 R
2705 14332 9.227777 GGGTTGTCTACTACAGTGATAAAATTT 57.772 33.333 0.00 0.0 39.87 1.82 R
4313 18240 3.179830 CTGAAAATCGGTGTCTCTACGG 58.820 50.000 0.00 0.0 0.00 4.02 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
147 9059 4.385825 ACTTGTAACGAAAATCCAGCTGA 58.614 39.130 17.39 1.21 0.00 4.26
186 9098 2.121963 AAGGACCTGACAGCCCCA 60.122 61.111 12.16 0.00 0.00 4.96
325 9237 0.250727 TGCTGTTCCTGTAAGTGGCC 60.251 55.000 0.00 0.00 0.00 5.36
652 9566 5.717178 GCCATATAGTCAAGGTCTCCTATCA 59.283 44.000 0.00 0.00 31.13 2.15
779 9693 6.192234 GCAAAGAGAATGATGCCCTATATG 57.808 41.667 0.00 0.00 32.73 1.78
780 9694 5.125097 GCAAAGAGAATGATGCCCTATATGG 59.875 44.000 0.00 0.00 32.73 2.74
781 9695 6.479006 CAAAGAGAATGATGCCCTATATGGA 58.521 40.000 0.00 0.00 38.35 3.41
782 9696 6.905067 AAGAGAATGATGCCCTATATGGAT 57.095 37.500 0.00 0.00 38.35 3.41
783 9697 6.249911 AGAGAATGATGCCCTATATGGATG 57.750 41.667 0.00 0.00 38.35 3.51
784 9698 4.789807 AGAATGATGCCCTATATGGATGC 58.210 43.478 0.00 0.00 38.35 3.91
785 9699 4.477581 AGAATGATGCCCTATATGGATGCT 59.522 41.667 0.00 0.00 38.35 3.79
787 9701 3.457836 TGATGCCCTATATGGATGCTCT 58.542 45.455 0.00 0.00 38.35 4.09
788 9702 3.199289 TGATGCCCTATATGGATGCTCTG 59.801 47.826 0.00 0.00 38.35 3.35
1119 10061 1.558756 CTGAGGAAGGAGGTGAAGCAT 59.441 52.381 0.00 0.00 0.00 3.79
1210 10152 2.759973 CCGCTAGCTGGAGGGACA 60.760 66.667 12.24 0.00 0.00 4.02
1358 10300 0.879400 CATCAGATCGCTGGGCAGAC 60.879 60.000 0.00 0.00 42.53 3.51
2211 13838 8.415950 TTTTGGTAGGATATTTTGCTCTGAAA 57.584 30.769 0.00 0.00 0.00 2.69
2703 14330 2.695359 TCCTGTACAAATCTGCGGAAC 58.305 47.619 0.00 0.00 0.00 3.62
2705 14332 2.811431 CCTGTACAAATCTGCGGAACAA 59.189 45.455 0.00 0.00 0.00 2.83
2894 14521 5.006165 GGCAGAATTCAAGTATCTTCGAGTG 59.994 44.000 8.44 0.00 0.00 3.51
4049 16521 5.519927 CACCTTTCTTTTTGTTGTAGCAAGG 59.480 40.000 0.00 0.00 35.39 3.61
4313 18240 7.886338 AGTAATTTTGAGAGTTCAACCATTCC 58.114 34.615 0.00 0.00 42.79 3.01
4724 18912 7.752239 GTGTTGGATCACTGATTGTTTTCTATG 59.248 37.037 0.00 0.00 35.68 2.23
4799 18987 2.820197 TGCTGTGTAGACACTAGACAGG 59.180 50.000 25.80 14.51 46.55 4.00
4806 18994 2.227089 GACACTAGACAGGGCACGGG 62.227 65.000 0.00 0.00 0.00 5.28
4862 19055 6.624423 CAGGGGAAAGTTTCTGAATATGTTG 58.376 40.000 15.05 0.00 0.00 3.33
4866 19059 7.084486 GGGAAAGTTTCTGAATATGTTGTGTC 58.916 38.462 15.05 0.00 0.00 3.67
4870 19063 5.118664 AGTTTCTGAATATGTTGTGTCGACG 59.881 40.000 11.62 0.00 0.00 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
325 9237 0.459237 GCCCACGACATCTCAGTCTG 60.459 60.000 0.00 0.00 36.38 3.51
652 9566 8.265165 AGACAGAGTTTTAGACGTTTTTCTTT 57.735 30.769 0.00 0.00 0.00 2.52
777 9691 4.091549 ACCATGTTTTTCAGAGCATCCAT 58.908 39.130 0.00 0.00 33.66 3.41
778 9692 3.499338 ACCATGTTTTTCAGAGCATCCA 58.501 40.909 0.00 0.00 33.66 3.41
779 9693 3.119352 GGACCATGTTTTTCAGAGCATCC 60.119 47.826 0.00 0.00 33.66 3.51
780 9694 3.760684 AGGACCATGTTTTTCAGAGCATC 59.239 43.478 0.00 0.00 0.00 3.91
781 9695 3.760684 GAGGACCATGTTTTTCAGAGCAT 59.239 43.478 0.00 0.00 0.00 3.79
782 9696 3.149196 GAGGACCATGTTTTTCAGAGCA 58.851 45.455 0.00 0.00 0.00 4.26
783 9697 2.489722 GGAGGACCATGTTTTTCAGAGC 59.510 50.000 0.00 0.00 35.97 4.09
784 9698 3.755378 CAGGAGGACCATGTTTTTCAGAG 59.245 47.826 0.00 0.00 38.94 3.35
785 9699 3.754965 CAGGAGGACCATGTTTTTCAGA 58.245 45.455 0.00 0.00 38.94 3.27
787 9701 2.238521 GCAGGAGGACCATGTTTTTCA 58.761 47.619 0.00 0.00 38.94 2.69
788 9702 1.546029 GGCAGGAGGACCATGTTTTTC 59.454 52.381 0.00 0.00 38.94 2.29
1119 10061 2.800985 GCTGCTCAGTTCATCGCTGATA 60.801 50.000 0.00 0.00 41.49 2.15
1210 10152 0.034767 TACGACATCTCCCTGACCGT 60.035 55.000 0.00 0.00 34.96 4.83
1358 10300 3.254166 CACAAGTTTCTTGATGTCCCCAG 59.746 47.826 15.04 0.00 0.00 4.45
2211 13838 2.092429 TGAGTTGACCTGGACAAGCTTT 60.092 45.455 11.78 0.00 0.00 3.51
2705 14332 9.227777 GGGTTGTCTACTACAGTGATAAAATTT 57.772 33.333 0.00 0.00 39.87 1.82
4049 16521 3.924918 TCTGCATAGATCTACGGAAGC 57.075 47.619 4.10 5.44 0.00 3.86
4313 18240 3.179830 CTGAAAATCGGTGTCTCTACGG 58.820 50.000 0.00 0.00 0.00 4.02
4724 18912 9.048446 TGAAATTATTTAGTATGCCTTCCGTAC 57.952 33.333 0.00 0.00 36.39 3.67
4799 18987 0.953960 CTGTAGGAAACACCCGTGCC 60.954 60.000 0.00 0.00 40.05 5.01
4806 18994 1.348036 ACTGCTCCCTGTAGGAAACAC 59.652 52.381 0.00 0.00 46.94 3.32
4862 19055 3.400590 GGTTGCGTCCGTCGACAC 61.401 66.667 17.16 6.15 42.86 3.67
4866 19059 3.708734 GGTTGGTTGCGTCCGTCG 61.709 66.667 0.00 0.00 43.12 5.12
4870 19063 1.816074 TATTCAGGTTGGTTGCGTCC 58.184 50.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.