Multiple sequence alignment - TraesCS4A01G272400

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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 TraesCS4A01G272400 chr4A 100.000 2222 0 0 1 2222 583870366 583868145 0 4104
1 TraesCS4A01G272400 chr5D 97.931 2223 38 3 1 2222 503243818 503246033 0 3843
2 TraesCS4A01G272400 chr6D 97.886 2223 39 3 1 2222 389247276 389245061 0 3838
3 TraesCS4A01G272400 chr3D 97.796 2223 38 4 1 2222 589264977 589262765 0 3823
4 TraesCS4A01G272400 chr7B 97.751 2223 42 3 1 2222 663100879 663098664 0 3821
5 TraesCS4A01G272400 chr7B 97.481 2223 48 3 1 2222 662724950 662727165 0 3788
6 TraesCS4A01G272400 chr2A 97.706 2223 43 3 1 2222 726907909 726905694 0 3816
7 TraesCS4A01G272400 chr3A 97.661 2223 43 3 1 2222 66006586 66004372 0 3808
8 TraesCS4A01G272400 chr3A 97.076 2223 54 6 1 2222 650015966 650013754 0 3735
9 TraesCS4A01G272400 chr3A 96.941 2223 59 4 1 2222 695638934 695641148 0 3720


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 TraesCS4A01G272400 chr4A 583868145 583870366 2221 True 4104 4104 100.000 1 2222 1 chr4A.!!$R1 2221
1 TraesCS4A01G272400 chr5D 503243818 503246033 2215 False 3843 3843 97.931 1 2222 1 chr5D.!!$F1 2221
2 TraesCS4A01G272400 chr6D 389245061 389247276 2215 True 3838 3838 97.886 1 2222 1 chr6D.!!$R1 2221
3 TraesCS4A01G272400 chr3D 589262765 589264977 2212 True 3823 3823 97.796 1 2222 1 chr3D.!!$R1 2221
4 TraesCS4A01G272400 chr7B 663098664 663100879 2215 True 3821 3821 97.751 1 2222 1 chr7B.!!$R1 2221
5 TraesCS4A01G272400 chr7B 662724950 662727165 2215 False 3788 3788 97.481 1 2222 1 chr7B.!!$F1 2221
6 TraesCS4A01G272400 chr2A 726905694 726907909 2215 True 3816 3816 97.706 1 2222 1 chr2A.!!$R1 2221
7 TraesCS4A01G272400 chr3A 66004372 66006586 2214 True 3808 3808 97.661 1 2222 1 chr3A.!!$R1 2221
8 TraesCS4A01G272400 chr3A 650013754 650015966 2212 True 3735 3735 97.076 1 2222 1 chr3A.!!$R2 2221
9 TraesCS4A01G272400 chr3A 695638934 695641148 2214 False 3720 3720 96.941 1 2222 1 chr3A.!!$F1 2221

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
201 202 1.133637 CGGAGGAAGGAGAGGATGAGA 60.134 57.143 0.0 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1504 1508 0.10576 TGGGCAGAAAAAGGAAGGCA 60.106 50.0 0.0 0.0 0.0 4.75 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
23 24 2.168313 TGACATGCAGCGAATCCTCTTA 59.832 45.455 0.00 0.0 0.00 2.10
109 110 4.501915 CGTAAGGTGTTGGGTTAAGTCTCA 60.502 45.833 0.00 0.0 0.00 3.27
117 118 2.696707 TGGGTTAAGTCTCACAACGAGT 59.303 45.455 0.00 0.0 42.88 4.18
166 167 3.138283 TGAGTTTGGAACCCTGAACAGAT 59.862 43.478 3.19 0.0 0.00 2.90
201 202 1.133637 CGGAGGAAGGAGAGGATGAGA 60.134 57.143 0.00 0.0 0.00 3.27
672 674 5.305128 TGGAAGTCTTCTTTCGTTTAGGGTA 59.695 40.000 12.31 0.0 32.08 3.69
790 792 2.043752 TGGCAGCATGGGGATGTG 60.044 61.111 0.00 0.0 34.68 3.21
960 962 6.653020 TGGATAGTTCAATGTGCTTATCAGT 58.347 36.000 0.00 0.0 0.00 3.41
1058 1060 4.207165 CCAAACAAACTTCTCCTCAGGAA 58.793 43.478 0.00 0.0 0.00 3.36
1481 1485 7.455008 TGAAAAAGGATCTTAGAGTGTCTAGGT 59.545 37.037 0.00 0.0 29.56 3.08
1504 1508 1.512735 GGCCAGGAGGGTCTCTTAAT 58.487 55.000 0.00 0.0 38.65 1.40
1689 1693 1.303898 TTGGTTGGATCATAGGGGCA 58.696 50.000 0.00 0.0 0.00 5.36
1802 1806 0.811616 GCATACTCCACTTGGCTCGG 60.812 60.000 0.00 0.0 34.44 4.63
1803 1807 0.179073 CATACTCCACTTGGCTCGGG 60.179 60.000 0.00 0.0 34.44 5.14
1804 1808 1.338136 ATACTCCACTTGGCTCGGGG 61.338 60.000 0.00 0.0 34.44 5.73
1805 1809 4.101448 CTCCACTTGGCTCGGGGG 62.101 72.222 0.00 0.0 34.44 5.40
1874 1878 0.249676 TTGCGATTACGGGTTGGCTA 59.750 50.000 0.00 0.0 40.15 3.93
1882 1886 6.392354 CGATTACGGGTTGGCTATCTAATTA 58.608 40.000 0.00 0.0 35.72 1.40
2062 2066 5.627135 TCTAGTATGGATCGTACATGGACA 58.373 41.667 9.21 0.0 0.00 4.02
2130 2134 2.307098 CTGGGGAAGAGGATCAAGTTGT 59.693 50.000 2.11 0.0 37.82 3.32
2161 2165 5.117745 CGAATAACTTGATGCACTATCTCCG 59.882 44.000 0.00 0.0 36.71 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 1.069765 CACCTGTGTCTGCGTTCCT 59.930 57.895 0.00 0.00 0.00 3.36
109 110 4.456806 GAGGGTTGCACTCGTTGT 57.543 55.556 0.00 0.00 0.00 3.32
117 118 1.944024 CAACTAAACACGAGGGTTGCA 59.056 47.619 0.00 0.00 32.50 4.08
201 202 0.706433 AAGGGGCATGATGACTTGGT 59.294 50.000 0.00 0.00 0.00 3.67
232 233 1.234821 CCCATTGTAGCACGTGTGTT 58.765 50.000 18.38 6.02 0.00 3.32
777 779 1.358787 TCCTTTTCACATCCCCATGCT 59.641 47.619 0.00 0.00 32.57 3.79
790 792 5.808366 AAAACTCCATCCCTTTCCTTTTC 57.192 39.130 0.00 0.00 0.00 2.29
960 962 1.296392 CACATCTTCGGGTCAGGCA 59.704 57.895 0.00 0.00 0.00 4.75
1058 1060 1.905215 CCTGAATCGCCCCATCTATCT 59.095 52.381 0.00 0.00 0.00 1.98
1142 1146 4.459089 GAGAGGAGCCGTGGTGCC 62.459 72.222 0.00 0.00 0.00 5.01
1481 1485 2.121506 AGACCCTCCTGGCCCAAA 60.122 61.111 0.00 0.00 37.83 3.28
1504 1508 0.105760 TGGGCAGAAAAAGGAAGGCA 60.106 50.000 0.00 0.00 0.00 4.75
1681 1685 4.821805 CGTGAAGTAAATCATTGCCCCTAT 59.178 41.667 0.00 0.00 0.00 2.57
1689 1693 2.936498 CTCGCCCGTGAAGTAAATCATT 59.064 45.455 0.00 0.00 0.00 2.57
1874 1878 6.620877 TCATTACCGCCTGGATAATTAGAT 57.379 37.500 0.00 0.00 39.21 1.98
1882 1886 5.273208 AGATACTATCATTACCGCCTGGAT 58.727 41.667 0.00 0.00 39.21 3.41
2062 2066 1.153429 GCCGCCGACTCCAACTATT 60.153 57.895 0.00 0.00 0.00 1.73
2130 2134 2.682856 GCATCAAGTTATTCGCAAGGGA 59.317 45.455 0.00 0.00 38.47 4.20
2161 2165 3.243401 ACATTTCGCTCAAAGGGTTGAAC 60.243 43.478 0.00 0.00 43.18 3.18


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

AutoCloner maintained by Alex Coulton.