Multiple sequence alignment - TraesCS3D01G511100

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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 TraesCS3D01G511100 chr3D 100.000 3887 0 0 1 3887 595943439 595939553 0.000000e+00 7179
1 TraesCS3D01G511100 chr3D 83.741 3186 388 61 624 3728 596848315 596851451 0.000000e+00 2894
2 TraesCS3D01G511100 chr3D 77.005 848 180 9 2515 3349 32280415 32281260 4.550000e-129 472
3 TraesCS3D01G511100 chr3B 88.588 3216 300 31 562 3731 799104680 799101486 0.000000e+00 3843
4 TraesCS3D01G511100 chr3B 84.961 3165 385 43 624 3728 803049461 803046328 0.000000e+00 3123
5 TraesCS3D01G511100 chr3B 83.730 3190 388 61 624 3728 801196146 801193003 0.000000e+00 2894
6 TraesCS3D01G511100 chr3B 85.758 1952 210 24 1812 3728 802610470 802608552 0.000000e+00 2002
7 TraesCS3D01G511100 chr3B 72.201 1036 235 43 1185 2195 54785030 54786037 6.400000e-68 268
8 TraesCS3D01G511100 chr3A 86.235 2194 215 45 561 2703 726743296 726741139 0.000000e+00 2298
9 TraesCS3D01G511100 chr3A 86.656 607 64 9 3135 3728 726726465 726725863 0.000000e+00 656
10 TraesCS3D01G511100 chr3A 90.732 410 27 1 2698 3096 726726871 726726462 1.590000e-148 536
11 TraesCS3D01G511100 chr3A 72.604 1033 243 33 1185 2198 44710042 44711053 1.750000e-78 303
12 TraesCS3D01G511100 chr3A 79.420 345 50 13 670 997 704984491 704984151 1.410000e-54 224
13 TraesCS3D01G511100 chr2B 88.525 244 21 7 316 556 416816067 416815828 4.910000e-74 289
14 TraesCS3D01G511100 chr2D 88.115 244 22 7 316 556 350746845 350746606 2.290000e-72 283
15 TraesCS3D01G511100 chr2A 86.770 257 20 9 316 563 468290645 468290394 1.380000e-69 274
16 TraesCS3D01G511100 chr5A 86.275 255 23 12 316 561 160082162 160081911 2.300000e-67 267
17 TraesCS3D01G511100 chr7D 86.111 252 23 10 316 556 16394480 16394230 1.070000e-65 261
18 TraesCS3D01G511100 chr4D 86.475 244 22 8 326 560 136764756 136764997 1.390000e-64 257
19 TraesCS3D01G511100 chr4D 85.656 244 26 8 316 551 267858163 267858405 8.340000e-62 248
20 TraesCS3D01G511100 chr4D 85.597 243 26 8 316 551 81466342 81466582 3.000000e-61 246
21 TraesCS3D01G511100 chr1D 85.366 246 25 10 316 552 275046663 275046420 1.080000e-60 244
22 TraesCS3D01G511100 chr4B 79.420 345 50 13 670 997 140984725 140985065 1.410000e-54 224
23 TraesCS3D01G511100 chr4B 79.130 345 51 13 670 997 602066857 602066517 6.540000e-53 219
24 TraesCS3D01G511100 chr4B 78.841 345 52 14 670 997 186920548 186920208 3.040000e-51 213
25 TraesCS3D01G511100 chr4B 71.412 850 204 33 1188 2014 2337038 2336205 1.840000e-43 187
26 TraesCS3D01G511100 chrUn 78.551 345 53 13 670 997 298363226 298363566 1.420000e-49 207
27 TraesCS3D01G511100 chrUn 78.551 345 53 13 670 997 308961737 308961397 1.420000e-49 207
28 TraesCS3D01G511100 chr7A 83.043 230 32 7 772 997 590219996 590220222 6.590000e-48 202
29 TraesCS3D01G511100 chr7B 82.251 231 34 7 771 997 636183386 636183159 3.960000e-45 193


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 TraesCS3D01G511100 chr3D 595939553 595943439 3886 True 7179 7179 100.000 1 3887 1 chr3D.!!$R1 3886
1 TraesCS3D01G511100 chr3D 596848315 596851451 3136 False 2894 2894 83.741 624 3728 1 chr3D.!!$F2 3104
2 TraesCS3D01G511100 chr3D 32280415 32281260 845 False 472 472 77.005 2515 3349 1 chr3D.!!$F1 834
3 TraesCS3D01G511100 chr3B 799101486 799104680 3194 True 3843 3843 88.588 562 3731 1 chr3B.!!$R1 3169
4 TraesCS3D01G511100 chr3B 803046328 803049461 3133 True 3123 3123 84.961 624 3728 1 chr3B.!!$R4 3104
5 TraesCS3D01G511100 chr3B 801193003 801196146 3143 True 2894 2894 83.730 624 3728 1 chr3B.!!$R2 3104
6 TraesCS3D01G511100 chr3B 802608552 802610470 1918 True 2002 2002 85.758 1812 3728 1 chr3B.!!$R3 1916
7 TraesCS3D01G511100 chr3B 54785030 54786037 1007 False 268 268 72.201 1185 2195 1 chr3B.!!$F1 1010
8 TraesCS3D01G511100 chr3A 726741139 726743296 2157 True 2298 2298 86.235 561 2703 1 chr3A.!!$R2 2142
9 TraesCS3D01G511100 chr3A 726725863 726726871 1008 True 596 656 88.694 2698 3728 2 chr3A.!!$R3 1030
10 TraesCS3D01G511100 chr3A 44710042 44711053 1011 False 303 303 72.604 1185 2198 1 chr3A.!!$F1 1013


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
845 863 0.034574 TGTGGTCCTGTTGTGCAACT 60.035 50.0 14.97 0.0 41.67 3.16 F
1168 1227 0.033109 AGGGGATGCTAACTTTGGGC 60.033 55.0 0.00 0.0 0.00 5.36 F
2143 2214 0.174389 CCACCCTGATCTCAGTGTCG 59.826 60.0 6.46 0.0 42.27 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 2030 0.107643 GCCTCTGGCCTATCTTGGTC 59.892 60.0 3.32 0.0 44.06 4.02 R
2709 2798 0.738975 CGGACTCCTCATCGCAGTAA 59.261 55.0 0.00 0.0 0.00 2.24 R
3832 3944 0.242017 GGGCAGTCACATTCAAGTGC 59.758 55.0 0.00 0.0 40.39 4.40 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)



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AutoCloner maintained by Alex Coulton.