Multiple sequence alignment - TraesCS4A01G228700

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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 TraesCS4A01G228700 chr4A 100.000 3561 0 0 1 3561 537233890 537230330 0 6577
1 TraesCS4A01G228700 chr4A 98.484 3561 48 1 1 3561 377592563 377596117 0 6272
2 TraesCS4A01G228700 chr4A 98.430 3568 49 2 1 3561 446472546 446476113 0 6272
3 TraesCS4A01G228700 chr4A 98.764 2913 30 1 1 2907 72015305 72018217 0 5175
4 TraesCS4A01G228700 chr2B 98.545 3573 39 2 1 3561 39425839 39429410 0 6298
5 TraesCS4A01G228700 chr2B 98.351 2729 35 3 1 2719 673932097 673929369 0 4782
6 TraesCS4A01G228700 chr3B 98.265 3573 48 3 1 3561 85118157 85114587 0 6242
7 TraesCS4A01G228700 chr3B 98.713 2720 34 1 1 2719 766970462 766973181 0 4828
8 TraesCS4A01G228700 chr6B 98.287 3561 56 3 1 3561 663847347 663850902 0 6233
9 TraesCS4A01G228700 chr5A 98.114 3552 43 2 34 3561 403293655 403297206 0 6167
10 TraesCS4A01G228700 chr1A 98.214 3528 54 1 34 3561 552374927 552378445 0 6157
11 TraesCS4A01G228700 chr1A 97.741 3585 37 2 1 3561 449181555 449185119 0 6131
12 TraesCS4A01G228700 chr2A 97.872 3571 42 5 1 3561 69201673 69198127 0 6143
13 TraesCS4A01G228700 chr7B 98.338 3188 47 1 34 3215 147534475 147537662 0 5589
14 TraesCS4A01G228700 chr4B 98.713 2720 34 1 1 2719 237023875 237021156 0 4828


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 TraesCS4A01G228700 chr4A 537230330 537233890 3560 True 6577 6577 100.000 1 3561 1 chr4A.!!$R1 3560
1 TraesCS4A01G228700 chr4A 377592563 377596117 3554 False 6272 6272 98.484 1 3561 1 chr4A.!!$F2 3560
2 TraesCS4A01G228700 chr4A 446472546 446476113 3567 False 6272 6272 98.430 1 3561 1 chr4A.!!$F3 3560
3 TraesCS4A01G228700 chr4A 72015305 72018217 2912 False 5175 5175 98.764 1 2907 1 chr4A.!!$F1 2906
4 TraesCS4A01G228700 chr2B 39425839 39429410 3571 False 6298 6298 98.545 1 3561 1 chr2B.!!$F1 3560
5 TraesCS4A01G228700 chr2B 673929369 673932097 2728 True 4782 4782 98.351 1 2719 1 chr2B.!!$R1 2718
6 TraesCS4A01G228700 chr3B 85114587 85118157 3570 True 6242 6242 98.265 1 3561 1 chr3B.!!$R1 3560
7 TraesCS4A01G228700 chr3B 766970462 766973181 2719 False 4828 4828 98.713 1 2719 1 chr3B.!!$F1 2718
8 TraesCS4A01G228700 chr6B 663847347 663850902 3555 False 6233 6233 98.287 1 3561 1 chr6B.!!$F1 3560
9 TraesCS4A01G228700 chr5A 403293655 403297206 3551 False 6167 6167 98.114 34 3561 1 chr5A.!!$F1 3527
10 TraesCS4A01G228700 chr1A 552374927 552378445 3518 False 6157 6157 98.214 34 3561 1 chr1A.!!$F2 3527
11 TraesCS4A01G228700 chr1A 449181555 449185119 3564 False 6131 6131 97.741 1 3561 1 chr1A.!!$F1 3560
12 TraesCS4A01G228700 chr2A 69198127 69201673 3546 True 6143 6143 97.872 1 3561 1 chr2A.!!$R1 3560
13 TraesCS4A01G228700 chr7B 147534475 147537662 3187 False 5589 5589 98.338 34 3215 1 chr7B.!!$F1 3181
14 TraesCS4A01G228700 chr4B 237021156 237023875 2719 True 4828 4828 98.713 1 2719 1 chr4B.!!$R1 2718

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
129 130 0.465097 TCGGTATCACGGGGTCTCTC 60.465 60.0 0.0 0.0 0.0 3.20 F
1221 1222 1.259142 TTCCGCCTCAACCCGATGTA 61.259 55.0 0.0 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 2119 1.714787 TGGTGTACCAGACCTAGAGGT 59.285 52.381 0.00 0.0 46.55 3.85 R
3220 3292 1.664649 CTTCGCTTCGGTGCACTCA 60.665 57.895 17.98 0.0 0.00 3.41 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
129 130 0.465097 TCGGTATCACGGGGTCTCTC 60.465 60.000 0.00 0.00 0.00 3.20
353 354 1.399714 TCACCGGTCTTGCTATCGAT 58.600 50.000 2.59 2.16 0.00 3.59
916 917 3.621805 TTGGACGCCCGAAGAGCA 61.622 61.111 0.00 0.00 34.29 4.26
1221 1222 1.259142 TTCCGCCTCAACCCGATGTA 61.259 55.000 0.00 0.00 0.00 2.29
1389 1390 4.711846 TCATAGGTAAGAGAGCATGTGTGT 59.288 41.667 0.00 0.00 0.00 3.72
1799 1820 3.135994 TCTTTACTTTCCTGTTGACCGC 58.864 45.455 0.00 0.00 0.00 5.68
1938 1959 4.512944 GCAATGATGATGGTTCACTACGAT 59.487 41.667 0.00 0.00 33.85 3.73
1978 1999 2.168313 TCGCATTCACTATGAGAGCCAA 59.832 45.455 0.00 0.00 38.02 4.52
2097 2119 8.316946 GTGATCCTGAATATGATGAACCATCTA 58.683 37.037 8.22 0.36 41.06 1.98
2353 2375 2.814805 ATGTGTTCAAGCCTAGGCAT 57.185 45.000 34.70 22.07 44.88 4.40
2951 3022 1.153289 CTGTCCTTAGGCGCTGCAT 60.153 57.895 7.64 0.00 0.00 3.96
2961 3032 0.525761 GGCGCTGCATTACTTCCAAA 59.474 50.000 7.64 0.00 0.00 3.28
3156 3228 2.049888 GCAGCTTGCCCTAGAAGATT 57.950 50.000 0.00 0.00 37.42 2.40
3295 3367 2.600769 ACGTGCCGAGTCCTCCTT 60.601 61.111 1.50 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 130 2.173669 CGTAAGGCATGGCAGGACG 61.174 63.158 22.64 21.30 0.00 4.79
353 354 2.894731 CTCATACATAGAGGCCTCCCA 58.105 52.381 29.54 17.98 0.00 4.37
916 917 4.210331 GCATACCAAGGATCAAACCTGAT 58.790 43.478 0.00 0.00 45.34 2.90
1221 1222 2.366916 CAGAGATCCTTATCCCGCAAGT 59.633 50.000 0.00 0.00 31.98 3.16
1389 1390 5.010719 GGAGTCCCGATGATTAGACAATACA 59.989 44.000 0.00 0.00 0.00 2.29
1799 1820 6.251163 CGTTAGCCATTCAAACATGTGTAATG 59.749 38.462 15.87 15.87 0.00 1.90
1938 1959 4.343814 TGCGATATGTACCTTGAGGAATGA 59.656 41.667 3.59 0.00 38.94 2.57
1978 1999 8.668510 AAGATATCAAACTTCGCAACATAGAT 57.331 30.769 5.32 0.00 0.00 1.98
2097 2119 1.714787 TGGTGTACCAGACCTAGAGGT 59.285 52.381 0.00 0.00 46.55 3.85
2353 2375 3.376078 GTGTACCGGCGTCTGGGA 61.376 66.667 6.01 0.00 0.00 4.37
2951 3022 6.778821 TCTGGATGTGAGATTTTGGAAGTAA 58.221 36.000 0.00 0.00 0.00 2.24
2961 3032 2.170187 GTGGCTCTCTGGATGTGAGATT 59.830 50.000 0.00 0.00 39.49 2.40
3059 3131 6.005583 TGTCTTAAGTTATGAACTCGTCGT 57.994 37.500 1.63 0.00 41.91 4.34
3156 3228 2.553602 GCATGTGAGATGTTGGTGAACA 59.446 45.455 0.00 0.00 46.13 3.18
3220 3292 1.664649 CTTCGCTTCGGTGCACTCA 60.665 57.895 17.98 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.