Multiple sequence alignment - TraesCS5B01G250100

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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 TraesCS5B01G250100 chr5B 100.000 2229 0 0 1 2229 432720291 432718063 0 4117
1 TraesCS5B01G250100 chr6D 98.061 2218 34 5 1 2210 389255240 389253024 0 3849
2 TraesCS5B01G250100 chr6D 97.971 2218 36 5 1 2210 389250445 389248229 0 3838
3 TraesCS5B01G250100 chr5D 98.016 2218 34 6 1 2210 503239097 503236882 0 3843
4 TraesCS5B01G250100 chr5D 97.926 2218 33 7 1 2210 503243343 503241131 0 3829
5 TraesCS5B01G250100 chr5D 97.881 2218 35 6 1 2210 503229316 503227103 0 3825
6 TraesCS5B01G250100 chr5D 97.791 2218 34 6 1 2210 503267231 503269441 0 3810
7 TraesCS5B01G250100 chr3A 97.836 2218 38 6 1 2210 66007061 66009276 0 3821
8 TraesCS5B01G250100 chr7B 97.791 2218 40 5 1 2210 662724475 662722259 0 3816
9 TraesCS5B01G250100 chr3D 97.791 2218 39 6 1 2210 589265452 589267667 0 3816


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 TraesCS5B01G250100 chr5B 432718063 432720291 2228 True 4117.0 4117 100.000 1 2229 1 chr5B.!!$R1 2228
1 TraesCS5B01G250100 chr6D 389248229 389255240 7011 True 3843.5 3849 98.016 1 2210 2 chr6D.!!$R1 2209
2 TraesCS5B01G250100 chr5D 503236882 503243343 6461 True 3836.0 3843 97.971 1 2210 2 chr5D.!!$R2 2209
3 TraesCS5B01G250100 chr5D 503227103 503229316 2213 True 3825.0 3825 97.881 1 2210 1 chr5D.!!$R1 2209
4 TraesCS5B01G250100 chr5D 503267231 503269441 2210 False 3810.0 3810 97.791 1 2210 1 chr5D.!!$F1 2209
5 TraesCS5B01G250100 chr3A 66007061 66009276 2215 False 3821.0 3821 97.836 1 2210 1 chr3A.!!$F1 2209
6 TraesCS5B01G250100 chr7B 662722259 662724475 2216 True 3816.0 3816 97.791 1 2210 1 chr7B.!!$R1 2209
7 TraesCS5B01G250100 chr3D 589265452 589267667 2215 False 3816.0 3816 97.791 1 2210 1 chr3D.!!$F1 2209

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
183 184 0.398522 TGTCTCAGTCCCAGTGTGGT 60.399 55.0 0.0 0.0 35.17 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1604 6405 2.89264 CGATCCCGGCTCTGTGAA 59.107 61.111 0.0 0.0 0.0 3.18 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
68 69 4.049186 CTCCGAGAAAAGAAGTTGACGAA 58.951 43.478 0.00 0.00 0.00 3.85
183 184 0.398522 TGTCTCAGTCCCAGTGTGGT 60.399 55.000 0.00 0.00 35.17 4.16
199 200 1.123077 TGGTTGATCATCCTCTCGGG 58.877 55.000 20.87 0.00 0.00 5.14
257 258 3.762288 TCACCAACTAGCTAATCAGACGT 59.238 43.478 0.00 0.00 0.00 4.34
288 289 3.903714 CCTTGGGTGGATTTCTCCTTTTT 59.096 43.478 0.00 0.00 42.59 1.94
374 378 1.372004 CGCGTTACTCACCCGTTCA 60.372 57.895 0.00 0.00 0.00 3.18
557 561 4.275936 GGATAACTTGTATCCATGCGCTTT 59.724 41.667 9.73 0.00 42.29 3.51
578 582 6.992715 GCTTTAGATTATTAGCCTGGAGTTCA 59.007 38.462 0.00 0.00 0.00 3.18
701 706 5.112129 ACTCACATTGGGTTTAGGGATAC 57.888 43.478 0.00 0.00 0.00 2.24
794 799 6.106673 GTCCCATCGAGAAAGAGAATTAACA 58.893 40.000 0.00 0.00 0.00 2.41
968 975 7.066887 TCGCACATGGTTTCATAAAATCTGTAT 59.933 33.333 0.00 0.00 31.33 2.29
1226 6027 1.143073 ACGCCCTTTTCTTGAGACCTT 59.857 47.619 0.00 0.00 0.00 3.50
1280 6081 9.533831 AGGAACACATACAAGAAAAAGGATAAT 57.466 29.630 0.00 0.00 0.00 1.28
1372 6173 5.163913 CCGAGACAGAATTTAGAACTTGCTG 60.164 44.000 0.00 0.00 0.00 4.41
1440 6241 5.722021 TTCATTCGGATCGATATGAGGAA 57.278 39.130 0.00 4.94 36.08 3.36
1554 6355 1.215647 CCTTTCTCCTCGGTCCACG 59.784 63.158 0.00 0.00 46.11 4.94
1604 6405 6.477033 CGATAGTTCATCACGGAAGAAAGAAT 59.523 38.462 0.00 0.00 32.71 2.40
1951 6757 4.651962 TCGGGATTTTTCTTGGGAAGTTTT 59.348 37.500 0.00 0.00 32.61 2.43
2197 7004 4.523083 CAAGGGGATTGATACCGAGAAAA 58.477 43.478 0.00 0.00 41.83 2.29
2213 7020 8.270080 ACCGAGAAAAATTTCTTCTTATCTCC 57.730 34.615 9.60 0.00 46.84 3.71
2214 7021 7.883311 ACCGAGAAAAATTTCTTCTTATCTCCA 59.117 33.333 9.60 0.00 46.84 3.86
2215 7022 8.897752 CCGAGAAAAATTTCTTCTTATCTCCAT 58.102 33.333 9.60 0.00 46.84 3.41
2224 7031 9.927081 ATTTCTTCTTATCTCCATATGTTTGGT 57.073 29.630 1.24 0.00 38.01 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 1.988406 GAGGTGGAAGGCCTACGGT 60.988 63.158 5.16 0.00 36.29 4.83
124 125 0.686789 GGCAGCAGTGGGGAATTTTT 59.313 50.000 0.00 0.00 0.00 1.94
161 162 0.467474 ACACTGGGACTGAGACACGA 60.467 55.000 0.00 0.00 0.00 4.35
199 200 0.948141 GGCGATGATCAGTAGCTGGC 60.948 60.000 16.06 5.90 31.51 4.85
273 274 5.564550 CTGAGGAGAAAAAGGAGAAATCCA 58.435 41.667 0.00 0.00 0.00 3.41
557 561 5.903010 TGGTGAACTCCAGGCTAATAATCTA 59.097 40.000 0.00 0.00 33.19 1.98
578 582 1.065418 GTTGGCTATACTGCTGGTGGT 60.065 52.381 0.00 0.00 0.00 4.16
701 706 1.476085 AGTCATCAGTTCGAGCCTGAG 59.524 52.381 18.15 12.10 41.91 3.35
741 746 3.576648 GGATATAACTCAGCGGTACAGC 58.423 50.000 10.25 10.25 37.41 4.40
744 749 4.321824 GGAAGGGATATAACTCAGCGGTAC 60.322 50.000 0.00 0.00 0.00 3.34
794 799 1.866015 GCCCCTTTGCCTTAGGATTT 58.134 50.000 0.69 0.00 34.56 2.17
1226 6027 7.939039 AGAGAAGTAATTTGTCCTCATGTTTCA 59.061 33.333 0.00 0.00 29.54 2.69
1604 6405 2.892640 CGATCCCGGCTCTGTGAA 59.107 61.111 0.00 0.00 0.00 3.18
1725 6526 5.803237 ATAGAACGGGGAAAGTATACAGG 57.197 43.478 5.50 0.00 0.00 4.00
1951 6757 7.993349 ATTATTCCATTCCAATTTCTTCCCA 57.007 32.000 0.00 0.00 0.00 4.37
2111 6918 7.779754 TTCCATTTCTTCATTTGGAATCTGA 57.220 32.000 0.00 0.00 41.95 3.27


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

AutoCloner maintained by Alex Coulton.