Multiple sequence alignment - TraesCS3B01G121700

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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 TraesCS3B01G121700 chr3B 100.000 2447 0 0 1 2447 92236950 92239396 0 4519
1 TraesCS3B01G121700 chr3B 98.121 2448 44 2 1 2447 201584602 201582156 0 4265
2 TraesCS3B01G121700 chr3B 98.039 2448 44 3 1 2447 92227466 92225022 0 4252
3 TraesCS3B01G121700 chr2B 97.712 2448 46 3 1 2447 87959280 87961718 0 4202
4 TraesCS3B01G121700 chr2B 98.783 2301 27 1 1 2300 449203847 449201547 0 4093
5 TraesCS3B01G121700 chr1B 96.982 2452 62 6 1 2447 135100555 135098111 0 4108
6 TraesCS3B01G121700 chr1B 97.474 1821 39 3 1 1816 135059518 135057700 0 3101
7 TraesCS3B01G121700 chr1B 98.058 927 11 4 1 922 339012800 339013724 0 1605
8 TraesCS3B01G121700 chr1B 97.735 927 12 5 1 922 338937103 338938025 0 1587
9 TraesCS3B01G121700 chr7B 98.086 1933 37 0 515 2447 742964755 742966687 0 3365
10 TraesCS3B01G121700 chr6D 98.071 1607 30 1 842 2447 430466784 430465178 0 2795
11 TraesCS3B01G121700 chr3D 98.070 1606 31 0 842 2447 202625480 202623875 0 2795
12 TraesCS3B01G121700 chr5A 97.634 1606 38 0 842 2447 162145416 162143811 0 2756
13 TraesCS3B01G121700 chr6B 97.519 927 14 4 1 922 388026212 388027134 0 1576


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 TraesCS3B01G121700 chr3B 92236950 92239396 2446 False 4519 4519 100.000 1 2447 1 chr3B.!!$F1 2446
1 TraesCS3B01G121700 chr3B 201582156 201584602 2446 True 4265 4265 98.121 1 2447 1 chr3B.!!$R2 2446
2 TraesCS3B01G121700 chr3B 92225022 92227466 2444 True 4252 4252 98.039 1 2447 1 chr3B.!!$R1 2446
3 TraesCS3B01G121700 chr2B 87959280 87961718 2438 False 4202 4202 97.712 1 2447 1 chr2B.!!$F1 2446
4 TraesCS3B01G121700 chr2B 449201547 449203847 2300 True 4093 4093 98.783 1 2300 1 chr2B.!!$R1 2299
5 TraesCS3B01G121700 chr1B 135098111 135100555 2444 True 4108 4108 96.982 1 2447 1 chr1B.!!$R2 2446
6 TraesCS3B01G121700 chr1B 135057700 135059518 1818 True 3101 3101 97.474 1 1816 1 chr1B.!!$R1 1815
7 TraesCS3B01G121700 chr1B 339012800 339013724 924 False 1605 1605 98.058 1 922 1 chr1B.!!$F2 921
8 TraesCS3B01G121700 chr1B 338937103 338938025 922 False 1587 1587 97.735 1 922 1 chr1B.!!$F1 921
9 TraesCS3B01G121700 chr7B 742964755 742966687 1932 False 3365 3365 98.086 515 2447 1 chr7B.!!$F1 1932
10 TraesCS3B01G121700 chr6D 430465178 430466784 1606 True 2795 2795 98.071 842 2447 1 chr6D.!!$R1 1605
11 TraesCS3B01G121700 chr3D 202623875 202625480 1605 True 2795 2795 98.070 842 2447 1 chr3D.!!$R1 1605
12 TraesCS3B01G121700 chr5A 162143811 162145416 1605 True 2756 2756 97.634 842 2447 1 chr5A.!!$R1 1605
13 TraesCS3B01G121700 chr6B 388026212 388027134 922 False 1576 1576 97.519 1 922 1 chr6B.!!$F1 921

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
277 279 0.867753 CCGGAGATGAAGAAGCGACG 60.868 60.000 0.0 0.0 0.00 5.12 F
910 916 1.478510 CTCTTTTCGGGAGCAGAGCTA 59.521 52.381 0.0 0.0 39.88 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1412 1419 0.739462 ATGCGCGAAACTCCGATTGA 60.739 50.0 12.1 0.0 0.00 2.57 R
2116 2132 0.923358 AGGACCAGTGAAAACCCACA 59.077 50.0 0.0 0.0 39.42 4.17 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
277 279 0.867753 CCGGAGATGAAGAAGCGACG 60.868 60.000 0.00 0.00 0.00 5.12
910 916 1.478510 CTCTTTTCGGGAGCAGAGCTA 59.521 52.381 0.00 0.00 39.88 3.32
911 917 1.478510 TCTTTTCGGGAGCAGAGCTAG 59.521 52.381 0.00 0.00 39.88 3.42
1165 1171 3.633525 ACTTATGGTTGACGCCGTAGATA 59.366 43.478 0.00 0.00 32.21 1.98
1176 1183 4.418392 ACGCCGTAGATAATATAAAGCCG 58.582 43.478 0.00 0.00 0.00 5.52
1223 1230 5.230942 AGTCGCAGGTACTATTTATGATGC 58.769 41.667 0.00 0.00 36.02 3.91
1304 1311 4.449743 AGCAGCTTTCAAACGACGTATAAA 59.550 37.500 0.00 1.67 0.00 1.40
1466 1473 7.120923 GGTAAAGTGATACCACATAAGGAGA 57.879 40.000 0.00 0.00 45.54 3.71
1832 1847 1.303561 AAGCAAGGGATGAGCGCAA 60.304 52.632 11.47 0.00 0.00 4.85
2055 2071 0.179043 AGCATCTGAGGCTGCATCAG 60.179 55.000 31.93 31.93 44.57 2.90
2116 2132 1.134220 TGAACTTCGCCTTCACCAAGT 60.134 47.619 0.00 0.00 0.00 3.16
2142 2158 5.073965 TGGGTTTTCACTGGTCCTAACTAAT 59.926 40.000 0.00 0.00 0.00 1.73
2189 2205 2.427245 CCCGAAGATCAGACGGCCT 61.427 63.158 16.09 0.00 44.45 5.19
2223 2239 5.390885 GCGATCATTCAAGCAAGTTACTCAA 60.391 40.000 0.00 0.00 0.00 3.02
2272 2288 8.000780 AGATTGTGCAGTTTCTTAGTCTTTTT 57.999 30.769 0.00 0.00 0.00 1.94
2354 2370 5.201243 TCAGAAACCATCCGAGATCTTCTA 58.799 41.667 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
277 279 8.276252 ACATAACATTGTATAAGTCAACCCAC 57.724 34.615 0.00 0.0 0.00 4.61
910 916 5.122396 GCGATTGTTACTGTCCATCTTTTCT 59.878 40.000 0.00 0.0 0.00 2.52
911 917 5.324697 GCGATTGTTACTGTCCATCTTTTC 58.675 41.667 0.00 0.0 0.00 2.29
1165 1171 5.351465 CCACTTCGCATATCGGCTTTATATT 59.649 40.000 0.00 0.0 39.05 1.28
1176 1183 4.508124 CCTACTTTGACCACTTCGCATATC 59.492 45.833 0.00 0.0 0.00 1.63
1304 1311 8.312669 ACATTTCTCTAAGCTTATCCTGTAGT 57.687 34.615 6.64 0.0 0.00 2.73
1412 1419 0.739462 ATGCGCGAAACTCCGATTGA 60.739 50.000 12.10 0.0 0.00 2.57
1466 1473 7.093156 TGTTGAGTATGACTGAATGAGGAAGAT 60.093 37.037 0.00 0.0 0.00 2.40
1832 1847 1.745489 GCAACGGATTTCGCTCCCT 60.745 57.895 0.00 0.0 43.89 4.20
2116 2132 0.923358 AGGACCAGTGAAAACCCACA 59.077 50.000 0.00 0.0 39.42 4.17
2142 2158 2.361104 GGGATCGCTTGCCAACCA 60.361 61.111 1.84 0.0 35.48 3.67
2189 2205 2.310538 TGAATGATCGCTCTGGCTCTA 58.689 47.619 0.00 0.0 36.09 2.43
2223 2239 9.342308 TCTATTGATTGACTGAAAAACTCAAGT 57.658 29.630 0.00 0.0 32.17 3.16
2354 2370 6.480981 CCTTTGATGCAACATTTCTTGTTTCT 59.519 34.615 0.00 0.0 46.51 2.52


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

AutoCloner maintained by Alex Coulton.