Multiple sequence alignment - TraesCS1A01G046700

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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 TraesCS1A01G046700 chr1A 100.000 3684 0 0 1 3684 28629097 28632780 0 6804
1 TraesCS1A01G046700 chr7A 98.426 3685 55 3 1 3684 529302100 529305782 0 6481
2 TraesCS1A01G046700 chr1D 95.232 3691 144 21 1 3684 414533676 414537341 0 5812
3 TraesCS1A01G046700 chr6A 95.256 3689 137 23 1 3684 552550188 552553843 0 5808
4 TraesCS1A01G046700 chr5D 94.911 3694 154 22 1 3684 408809473 408813142 0 5749
5 TraesCS1A01G046700 chr4D 94.932 3690 151 22 1 3684 45314344 45318003 0 5746
6 TraesCS1A01G046700 chr4B 94.264 3696 176 23 1 3684 255645485 255649156 0 5618
7 TraesCS1A01G046700 chr5A 92.643 3711 219 29 1 3684 95526541 95522858 0 5291
8 TraesCS1A01G046700 chr4A 94.848 3125 127 20 1 3124 175481765 175484856 0 4848
9 TraesCS1A01G046700 chr2A 92.013 2842 186 30 13 2836 511248920 511251738 0 3952
10 TraesCS1A01G046700 chr2A 91.316 1520 89 30 16 1510 511265691 511267192 0 2036
11 TraesCS1A01G046700 chr7B 92.105 684 46 6 3001 3684 355726871 355726196 0 957


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 TraesCS1A01G046700 chr1A 28629097 28632780 3683 False 6804 6804 100.000 1 3684 1 chr1A.!!$F1 3683
1 TraesCS1A01G046700 chr7A 529302100 529305782 3682 False 6481 6481 98.426 1 3684 1 chr7A.!!$F1 3683
2 TraesCS1A01G046700 chr1D 414533676 414537341 3665 False 5812 5812 95.232 1 3684 1 chr1D.!!$F1 3683
3 TraesCS1A01G046700 chr6A 552550188 552553843 3655 False 5808 5808 95.256 1 3684 1 chr6A.!!$F1 3683
4 TraesCS1A01G046700 chr5D 408809473 408813142 3669 False 5749 5749 94.911 1 3684 1 chr5D.!!$F1 3683
5 TraesCS1A01G046700 chr4D 45314344 45318003 3659 False 5746 5746 94.932 1 3684 1 chr4D.!!$F1 3683
6 TraesCS1A01G046700 chr4B 255645485 255649156 3671 False 5618 5618 94.264 1 3684 1 chr4B.!!$F1 3683
7 TraesCS1A01G046700 chr5A 95522858 95526541 3683 True 5291 5291 92.643 1 3684 1 chr5A.!!$R1 3683
8 TraesCS1A01G046700 chr4A 175481765 175484856 3091 False 4848 4848 94.848 1 3124 1 chr4A.!!$F1 3123
9 TraesCS1A01G046700 chr2A 511248920 511251738 2818 False 3952 3952 92.013 13 2836 1 chr2A.!!$F1 2823
10 TraesCS1A01G046700 chr2A 511265691 511267192 1501 False 2036 2036 91.316 16 1510 1 chr2A.!!$F2 1494
11 TraesCS1A01G046700 chr7B 355726196 355726871 675 True 957 957 92.105 3001 3684 1 chr7B.!!$R1 683

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
180 185 0.606604 GCAAACTGAGTCCGGGTCTA 59.393 55.000 0.0 0.0 0.00 2.59 F
397 408 2.285442 GGTGGGTAGAGGGTGCCT 60.285 66.667 0.0 0.0 36.03 4.75 F
892 910 2.380084 TTGGTGGTCTATCTCGCAAC 57.620 50.000 0.0 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1873 1908 0.608856 ATGACCGCTGCATTGTGGAA 60.609 50.000 12.16 1.18 39.82 3.53 R
2079 2114 1.292223 GAAGCGACAGGTGTAGGCA 59.708 57.895 7.99 0.00 32.13 4.75 R
2809 2844 1.613520 GGGGACAAACTCTACCTTGCC 60.614 57.143 0.00 0.00 0.00 4.52 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
180 185 0.606604 GCAAACTGAGTCCGGGTCTA 59.393 55.000 0.00 0.00 0.00 2.59
397 408 2.285442 GGTGGGTAGAGGGTGCCT 60.285 66.667 0.00 0.00 36.03 4.75
792 810 5.808366 ATTATGGTTTCGAGCTCTATGGA 57.192 39.130 12.85 0.00 0.00 3.41
892 910 2.380084 TTGGTGGTCTATCTCGCAAC 57.620 50.000 0.00 0.00 0.00 4.17
1570 1605 6.940831 AGTTAGAGACGGTAGGAATACTTC 57.059 41.667 0.00 0.00 0.00 3.01
1865 1900 6.070021 TGTTCCATCAGACATGGACTTCTATT 60.070 38.462 2.66 0.00 46.90 1.73
1873 1908 5.045286 AGACATGGACTTCTATTTGGAGCTT 60.045 40.000 0.00 0.00 0.00 3.74
2079 2114 1.980765 TGTTGGGTCTTCATCAGCTCT 59.019 47.619 0.00 0.00 0.00 4.09
2109 2144 2.738846 CTGTCGCTTCAACAGTTAGCAT 59.261 45.455 8.48 0.00 39.42 3.79
2370 2405 1.349357 ACAGGAAGAAGTTGAGGGAGC 59.651 52.381 0.00 0.00 0.00 4.70
2881 2917 4.202315 TGGTGTGTGCTCTAGTTGTAATGT 60.202 41.667 0.00 0.00 0.00 2.71
2979 3015 4.281941 TGTGCATTAGGAGGCTCATAGTAG 59.718 45.833 17.69 8.32 32.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
180 185 0.963962 TTGCCCGAGTTCTCGTACTT 59.036 50.000 18.59 0.00 0.00 2.24
194 199 0.254178 TGATCAAGGAGAGCTTGCCC 59.746 55.000 0.00 0.00 32.67 5.36
397 408 3.054434 CACCTTCCAGTATGTCCATCCAA 60.054 47.826 0.00 0.00 0.00 3.53
792 810 7.840342 CTCTGCAGAGTTTGTATCACTTTAT 57.160 36.000 31.71 0.00 37.40 1.40
1032 1063 6.163135 AGCAAGAGTGAGTACAAAGTACTT 57.837 37.500 10.79 1.12 0.00 2.24
1570 1605 7.765695 ATATAGCAAGTATGGGTTCCAATTG 57.234 36.000 0.00 0.00 36.95 2.32
1873 1908 0.608856 ATGACCGCTGCATTGTGGAA 60.609 50.000 12.16 1.18 39.82 3.53
2079 2114 1.292223 GAAGCGACAGGTGTAGGCA 59.708 57.895 7.99 0.00 32.13 4.75
2109 2144 7.493645 CAGCAATCATTGTCATACTAGAAGTGA 59.506 37.037 0.00 0.00 0.00 3.41
2370 2405 1.815003 GTGGCTCATTTGGGTTCTCTG 59.185 52.381 0.00 0.00 0.00 3.35
2809 2844 1.613520 GGGGACAAACTCTACCTTGCC 60.614 57.143 0.00 0.00 0.00 4.52
2881 2917 5.693769 AGTCTTGCTTAAGGGCATAACTA 57.306 39.130 4.29 0.00 42.09 2.24
2979 3015 6.369065 ACTCACTAAAGCACACAATAGTAAGC 59.631 38.462 0.00 0.00 0.00 3.09
3178 3218 5.999205 AACCATTGTTATTCATCCTGCAA 57.001 34.783 0.00 0.00 31.36 4.08


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

AutoCloner maintained by Alex Coulton.