Multiple sequence alignment - TraesCS5B01G019100

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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 TraesCS5B01G019100 chr5B 100.000 2942 0 0 1 2942 18191132 18188191 0 5433
1 TraesCS5B01G019100 chr5B 98.708 2942 37 1 1 2942 353923716 353926656 0 5221
2 TraesCS5B01G019100 chr5B 96.991 2958 62 6 1 2942 123794088 123791142 0 4944
3 TraesCS5B01G019100 chr5B 97.009 2942 77 2 1 2942 34300376 34297446 0 4935
4 TraesCS5B01G019100 chr3B 98.640 2942 39 1 1 2942 734220047 734222987 0 5210
5 TraesCS5B01G019100 chr7B 98.232 2942 40 3 1 2942 379918554 379915625 0 5134
6 TraesCS5B01G019100 chr7B 97.925 2940 51 1 1 2940 666623095 666620166 0 5083
7 TraesCS5B01G019100 chr7B 97.692 2946 53 9 1 2942 664945264 664948198 0 5049
8 TraesCS5B01G019100 chr4B 97.420 2946 61 3 1 2942 522410880 522407946 0 5005
9 TraesCS5B01G019100 chr1B 98.440 2757 40 1 1 2757 643575225 643572472 0 4850
10 TraesCS5B01G019100 chr2D 93.788 2946 167 6 1 2942 126682551 126685484 0 4412


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 TraesCS5B01G019100 chr5B 18188191 18191132 2941 True 5433 5433 100.000 1 2942 1 chr5B.!!$R1 2941
1 TraesCS5B01G019100 chr5B 353923716 353926656 2940 False 5221 5221 98.708 1 2942 1 chr5B.!!$F1 2941
2 TraesCS5B01G019100 chr5B 123791142 123794088 2946 True 4944 4944 96.991 1 2942 1 chr5B.!!$R3 2941
3 TraesCS5B01G019100 chr5B 34297446 34300376 2930 True 4935 4935 97.009 1 2942 1 chr5B.!!$R2 2941
4 TraesCS5B01G019100 chr3B 734220047 734222987 2940 False 5210 5210 98.640 1 2942 1 chr3B.!!$F1 2941
5 TraesCS5B01G019100 chr7B 379915625 379918554 2929 True 5134 5134 98.232 1 2942 1 chr7B.!!$R1 2941
6 TraesCS5B01G019100 chr7B 666620166 666623095 2929 True 5083 5083 97.925 1 2940 1 chr7B.!!$R2 2939
7 TraesCS5B01G019100 chr7B 664945264 664948198 2934 False 5049 5049 97.692 1 2942 1 chr7B.!!$F1 2941
8 TraesCS5B01G019100 chr4B 522407946 522410880 2934 True 5005 5005 97.420 1 2942 1 chr4B.!!$R1 2941
9 TraesCS5B01G019100 chr1B 643572472 643575225 2753 True 4850 4850 98.440 1 2757 1 chr1B.!!$R1 2756
10 TraesCS5B01G019100 chr2D 126682551 126685484 2933 False 4412 4412 93.788 1 2942 1 chr2D.!!$F1 2941

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
884 917 0.249699 ACGACAAAGACCATCGTGCA 60.250 50.0 0.0 0.0 46.68 4.57 F
885 918 1.078709 CGACAAAGACCATCGTGCAT 58.921 50.0 0.0 0.0 0.00 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1843 1880 1.414181 CATCTCCCAACAGTAGGCGAT 59.586 52.381 0.0 0.0 0.0 4.58 R
2096 2133 2.052468 AGCATATCAGTGGGCATCTCA 58.948 47.619 0.0 0.0 0.0 3.27 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
34 35 1.540267 CCATGGGTCTTGGCGTTTAA 58.460 50.000 2.85 0.0 0.00 1.52
187 192 4.159693 ACCCCAAATCGCTTATTTTCTTCC 59.840 41.667 0.00 0.0 35.54 3.46
820 853 8.883954 TGTTTCATTTGTTCATGCTTGATTTA 57.116 26.923 2.75 0.0 0.00 1.40
825 858 8.970020 TCATTTGTTCATGCTTGATTTATAGGT 58.030 29.630 2.75 0.0 0.00 3.08
884 917 0.249699 ACGACAAAGACCATCGTGCA 60.250 50.000 0.00 0.0 46.68 4.57
885 918 1.078709 CGACAAAGACCATCGTGCAT 58.921 50.000 0.00 0.0 0.00 3.96
1538 1575 2.111255 ACCTACTAAGTGACTGGGACCA 59.889 50.000 0.00 0.0 0.00 4.02
1939 1976 6.491714 AGCTGGATATGTTGACTCATAAGT 57.508 37.500 0.00 0.0 38.88 2.24
1993 2030 5.947228 ATTGTGATGGAACTGTGTACTTG 57.053 39.130 0.00 0.0 0.00 3.16
2096 2133 1.283613 TGACAGGAATATTTGGCGGGT 59.716 47.619 0.00 0.0 0.00 5.28
2143 2180 0.902984 TGTCGAGTGGCACTACCCAT 60.903 55.000 22.11 0.0 37.20 4.00
2296 2333 6.187125 TCTTGCTAATGCTTTCATCTTGTC 57.813 37.500 0.00 0.0 40.48 3.18
2406 2443 1.222113 GTGGCCCTAGTGGAGAAGC 59.778 63.158 0.00 0.0 35.39 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 0.402121 GGTTTTCTGCTCTCCAGGGT 59.598 55.000 0.00 0.00 42.05 4.34
187 192 2.746362 GGCTCAGATCCACACTTTTGAG 59.254 50.000 0.00 0.00 36.13 3.02
266 273 8.789825 ATGAATTAATGCTGCCAAAATACAAA 57.210 26.923 0.00 0.00 0.00 2.83
820 853 3.004090 GTTCCCCCGCCAACCTAT 58.996 61.111 0.00 0.00 0.00 2.57
884 917 3.435026 CCCCGTTATTCTCAATGTCCCAT 60.435 47.826 0.00 0.00 0.00 4.00
885 918 2.092646 CCCCGTTATTCTCAATGTCCCA 60.093 50.000 0.00 0.00 0.00 4.37
1193 1230 0.608130 CTCCAAGGTCACGGTCATCA 59.392 55.000 0.00 0.00 0.00 3.07
1538 1575 4.172807 TCCTGAACCCCAACTGTACTTAT 58.827 43.478 0.00 0.00 0.00 1.73
1843 1880 1.414181 CATCTCCCAACAGTAGGCGAT 59.586 52.381 0.00 0.00 0.00 4.58
1993 2030 7.773149 ACCTACAACACAAGATGATACTAGTC 58.227 38.462 0.00 0.00 0.00 2.59
2096 2133 2.052468 AGCATATCAGTGGGCATCTCA 58.948 47.619 0.00 0.00 0.00 3.27
2296 2333 8.397906 TCTTTCGACTAATTCTGCAAATTATGG 58.602 33.333 11.78 6.73 0.00 2.74
2406 2443 8.092521 ACTGAATCACTATGTTGTCTTCTTTG 57.907 34.615 0.00 0.00 0.00 2.77
2497 2534 4.301072 TCCAACTCTTCCAATTCCGAAT 57.699 40.909 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.