Multiple sequence alignment - TraesCS4A01G069900

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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 TraesCS4A01G069900 chr4A 100.000 2486 0 0 1 2486 67576685 67574200 0 4591
1 TraesCS4A01G069900 chr4A 96.275 2443 82 6 1 2441 633467260 633469695 0 3999
2 TraesCS4A01G069900 chr6B 98.193 2490 35 6 1 2486 596620323 596622806 0 4340
3 TraesCS4A01G069900 chrUn 98.072 2490 38 6 1 2486 282364697 282362214 0 4324
4 TraesCS4A01G069900 chrUn 98.032 2490 39 6 1 2486 86510013 86507530 0 4318
5 TraesCS4A01G069900 chr6A 97.831 2490 47 6 1 2486 84434143 84436629 0 4292
6 TraesCS4A01G069900 chr2B 97.711 2490 42 9 1 2486 30670612 30668134 0 4268
7 TraesCS4A01G069900 chr1A 97.150 2491 60 7 1 2486 94783306 94785790 0 4196
8 TraesCS4A01G069900 chr3A 97.028 2490 62 8 1 2486 694375571 694373090 0 4178
9 TraesCS4A01G069900 chr5B 96.988 2490 58 7 1 2486 567270596 567268120 0 4167


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 TraesCS4A01G069900 chr4A 67574200 67576685 2485 True 4591 4591 100.000 1 2486 1 chr4A.!!$R1 2485
1 TraesCS4A01G069900 chr4A 633467260 633469695 2435 False 3999 3999 96.275 1 2441 1 chr4A.!!$F1 2440
2 TraesCS4A01G069900 chr6B 596620323 596622806 2483 False 4340 4340 98.193 1 2486 1 chr6B.!!$F1 2485
3 TraesCS4A01G069900 chrUn 282362214 282364697 2483 True 4324 4324 98.072 1 2486 1 chrUn.!!$R2 2485
4 TraesCS4A01G069900 chrUn 86507530 86510013 2483 True 4318 4318 98.032 1 2486 1 chrUn.!!$R1 2485
5 TraesCS4A01G069900 chr6A 84434143 84436629 2486 False 4292 4292 97.831 1 2486 1 chr6A.!!$F1 2485
6 TraesCS4A01G069900 chr2B 30668134 30670612 2478 True 4268 4268 97.711 1 2486 1 chr2B.!!$R1 2485
7 TraesCS4A01G069900 chr1A 94783306 94785790 2484 False 4196 4196 97.150 1 2486 1 chr1A.!!$F1 2485
8 TraesCS4A01G069900 chr3A 694373090 694375571 2481 True 4178 4178 97.028 1 2486 1 chr3A.!!$R1 2485
9 TraesCS4A01G069900 chr5B 567268120 567270596 2476 True 4167 4167 96.988 1 2486 1 chr5B.!!$R1 2485

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
138 140 1.685765 GCCCCCTCAATTCAACCCC 60.686 63.158 0.0 0.0 0.0 4.95 F
221 223 4.165779 CGCCAAGTCCATAATTCACAAAC 58.834 43.478 0.0 0.0 0.0 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1313 1321 1.544691 GTCCGTATATCATGGGCGACT 59.455 52.381 0.00 0.0 33.62 4.18 R
2195 2210 0.300789 GAAACACCGATTCGATCCGC 59.699 55.000 7.83 0.0 0.00 5.54 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
138 140 1.685765 GCCCCCTCAATTCAACCCC 60.686 63.158 0.00 0.0 0.00 4.95
190 192 6.477688 GCATTTAGACGGTGCAGTTAGTATTA 59.522 38.462 0.00 0.0 38.68 0.98
221 223 4.165779 CGCCAAGTCCATAATTCACAAAC 58.834 43.478 0.00 0.0 0.00 2.93
737 741 6.070251 TGCTTAGTCAAGTGAGGATTCCATTA 60.070 38.462 5.29 0.0 34.00 1.90
775 779 4.279420 GGAGCACCATCTTCAAAACTTCTT 59.721 41.667 0.00 0.0 35.97 2.52
1218 1225 7.625498 TTATGGTATGGTATTGTCAGATCCA 57.375 36.000 0.00 0.0 0.00 3.41
1551 1559 2.843701 CTTGTCAAGCTGGTCTCACTT 58.156 47.619 0.00 0.0 0.00 3.16
1840 1849 4.258702 ACACAAAGTCACTTAGCTCGAT 57.741 40.909 0.00 0.0 0.00 3.59
1945 1954 0.606096 TAAGCTGCTTCGCACCACTA 59.394 50.000 19.62 0.0 33.79 2.74
1946 1955 0.036010 AAGCTGCTTCGCACCACTAT 60.036 50.000 9.53 0.0 33.79 2.12
2209 2224 3.925090 GGGGCGGATCGAATCGGT 61.925 66.667 1.76 0.0 32.76 4.69
2273 2288 2.689983 CTGTGCTTGGTGGAAAAGAAGT 59.310 45.455 0.00 0.0 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 4.743955 GCCTGTTCTGTCCTAAACTGTTCT 60.744 45.833 0.00 0.0 0.00 3.01
130 132 1.580942 CGTACTCGTCGGGGTTGAA 59.419 57.895 0.00 0.0 0.00 2.69
138 140 0.433492 CCAAGTTTGCGTACTCGTCG 59.567 55.000 0.00 0.0 39.49 5.12
190 192 1.373812 GGACTTGGCGGTAGTGGTT 59.626 57.895 0.00 0.0 0.00 3.67
550 554 4.624015 TCTTGACTCGTTTTCGGTGTATT 58.376 39.130 0.00 0.0 44.25 1.89
620 624 6.206634 TGCGAAAGAAAGTGAAATGTCCTATT 59.793 34.615 0.00 0.0 0.00 1.73
737 741 3.305881 GGTGCTCCTGTTACGTTACTTCT 60.306 47.826 6.24 0.0 0.00 2.85
775 779 0.978151 TCGAAAAACTCCGGATCCCA 59.022 50.000 3.57 0.0 0.00 4.37
1218 1225 7.817478 GCAAACAAATAAAGTAGCCCTATGTTT 59.183 33.333 0.00 0.0 38.56 2.83
1313 1321 1.544691 GTCCGTATATCATGGGCGACT 59.455 52.381 0.00 0.0 33.62 4.18
2193 2208 2.661866 CACCGATTCGATCCGCCC 60.662 66.667 7.83 0.0 0.00 6.13
2194 2209 1.087771 AAACACCGATTCGATCCGCC 61.088 55.000 7.83 0.0 0.00 6.13
2195 2210 0.300789 GAAACACCGATTCGATCCGC 59.699 55.000 7.83 0.0 0.00 5.54
2209 2224 1.276989 CGGTGGCTACCTAAGGAAACA 59.723 52.381 18.03 0.0 45.22 2.83
2273 2288 0.032952 AGCGAGCGTACCTTTGTTCA 59.967 50.000 0.00 0.0 0.00 3.18
2452 2467 3.963428 AACAAGAAGTCACGCCTAGAT 57.037 42.857 0.00 0.0 0.00 1.98


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

AutoCloner maintained by Alex Coulton.