Multiple sequence alignment - TraesCS5A01G120700

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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 TraesCS5A01G120700 chr5A 100.000 3982 0 0 1 3982 258085137 258089118 0 7354
1 TraesCS5A01G120700 chr5A 96.991 3988 110 4 1 3982 93990703 93994686 0 6691
2 TraesCS5A01G120700 chr3A 97.442 3987 96 3 1 3982 111792161 111788176 0 6793
3 TraesCS5A01G120700 chr3A 96.991 3988 113 3 1 3982 673191360 673187374 0 6693
4 TraesCS5A01G120700 chr1A 97.369 3991 94 5 1 3982 552093516 552097504 0 6778
5 TraesCS5A01G120700 chr1A 96.990 3987 108 4 1 3982 392057043 392061022 0 6687
6 TraesCS5A01G120700 chr1A 96.915 3987 113 5 1 3982 53203204 53207185 0 6673
7 TraesCS5A01G120700 chr1A 96.842 3990 115 6 1 3982 479844218 479848204 0 6660
8 TraesCS5A01G120700 chr7A 97.340 3985 102 3 1 3982 447290200 447294183 0 6769
9 TraesCS5A01G120700 chr2A 96.916 3988 114 7 1 3982 409606934 409602950 0 6674


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 TraesCS5A01G120700 chr5A 258085137 258089118 3981 False 7354 7354 100.000 1 3982 1 chr5A.!!$F2 3981
1 TraesCS5A01G120700 chr5A 93990703 93994686 3983 False 6691 6691 96.991 1 3982 1 chr5A.!!$F1 3981
2 TraesCS5A01G120700 chr3A 111788176 111792161 3985 True 6793 6793 97.442 1 3982 1 chr3A.!!$R1 3981
3 TraesCS5A01G120700 chr3A 673187374 673191360 3986 True 6693 6693 96.991 1 3982 1 chr3A.!!$R2 3981
4 TraesCS5A01G120700 chr1A 552093516 552097504 3988 False 6778 6778 97.369 1 3982 1 chr1A.!!$F4 3981
5 TraesCS5A01G120700 chr1A 392057043 392061022 3979 False 6687 6687 96.990 1 3982 1 chr1A.!!$F2 3981
6 TraesCS5A01G120700 chr1A 53203204 53207185 3981 False 6673 6673 96.915 1 3982 1 chr1A.!!$F1 3981
7 TraesCS5A01G120700 chr1A 479844218 479848204 3986 False 6660 6660 96.842 1 3982 1 chr1A.!!$F3 3981
8 TraesCS5A01G120700 chr7A 447290200 447294183 3983 False 6769 6769 97.340 1 3982 1 chr7A.!!$F1 3981
9 TraesCS5A01G120700 chr2A 409602950 409606934 3984 True 6674 6674 96.916 1 3982 1 chr2A.!!$R1 3981

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
804 810 0.179051 ACCTTTTTCGCCACGTACCA 60.179 50.0 0.0 0.0 0.0 3.25 F
1914 1928 0.621571 AGATGCTGGAAGGGTGGCTA 60.622 55.0 0.0 0.0 0.0 3.93 F
2776 2796 0.250338 GTGAGGCGGAACAGGAAAGT 60.250 55.0 0.0 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2199 2213 0.677098 CGTCGTCTCCCTCTCCTTCA 60.677 60.000 0.00 0.00 0.00 3.02 R
2979 2999 1.350019 CTCCATCATGATGCCTGCCTA 59.650 52.381 27.24 7.41 37.49 3.93 R
3638 3665 3.005472 TCGTCAAGAATGAGAAACCTCGT 59.995 43.478 0.00 0.00 35.88 4.18 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
32 33 1.134788 CCTTCGCGGAGGAAGTAACAT 60.135 52.381 30.66 0.00 41.44 2.71
110 112 2.044946 GCCAACCCCTGCTACTGG 60.045 66.667 0.00 0.00 0.00 4.00
269 272 2.252260 CGTTTGCTTGCGGAGTGG 59.748 61.111 0.00 0.00 0.00 4.00
605 611 3.588842 ACCTTGATCCATTCTTGGTCTCA 59.411 43.478 0.00 0.00 44.06 3.27
723 729 2.178912 TTGAATTTCGGGAAGCGAGT 57.821 45.000 0.00 0.00 0.00 4.18
747 753 1.834301 GGGGGCAGCCGAAGTAATA 59.166 57.895 5.00 0.00 0.00 0.98
804 810 0.179051 ACCTTTTTCGCCACGTACCA 60.179 50.000 0.00 0.00 0.00 3.25
1200 1214 1.213926 GGAGTCATTCCCCATGAAGCT 59.786 52.381 0.00 0.00 43.93 3.74
1201 1215 2.295885 GAGTCATTCCCCATGAAGCTG 58.704 52.381 0.00 0.00 43.93 4.24
1202 1216 0.743097 GTCATTCCCCATGAAGCTGC 59.257 55.000 0.00 0.00 43.93 5.25
1330 1344 3.315191 CCGGAGCTTTTTGAACTTCTTCA 59.685 43.478 0.00 0.00 34.39 3.02
1914 1928 0.621571 AGATGCTGGAAGGGTGGCTA 60.622 55.000 0.00 0.00 0.00 3.93
2041 2055 5.069501 AGATCTTGCTTTCTTCATTTGCC 57.930 39.130 0.00 0.00 0.00 4.52
2119 2133 2.230508 GAGATGTACTCGACACCCAACA 59.769 50.000 0.00 0.00 42.17 3.33
2199 2213 1.606889 GGAGTGGGAGTCTGACGGT 60.607 63.158 1.52 0.00 0.00 4.83
2467 2484 1.351017 TGACTGTCCCCACCATTTCTC 59.649 52.381 5.17 0.00 0.00 2.87
2482 2499 6.202954 CACCATTTCTCGGTAATGATAGAACC 59.797 42.308 0.00 0.00 35.49 3.62
2776 2796 0.250338 GTGAGGCGGAACAGGAAAGT 60.250 55.000 0.00 0.00 0.00 2.66
3109 3129 4.224147 TGCTTGTTCTGTTAGGGTATGCTA 59.776 41.667 0.00 0.00 0.00 3.49
3504 3531 1.070134 TCTTGGACCTTTGTCGACTGG 59.930 52.381 17.92 17.37 42.73 4.00
3638 3665 3.153369 TGAAGCAAAAGGTATGGCTGA 57.847 42.857 0.00 0.00 36.58 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.753043 GGCACCGAGACGTAGGGA 60.753 66.667 6.06 0.00 0.00 4.20
110 112 1.382914 ATATAAGCCACCCCCATCCC 58.617 55.000 0.00 0.00 0.00 3.85
114 116 3.648683 ACTCTATATAAGCCACCCCCA 57.351 47.619 0.00 0.00 0.00 4.96
269 272 3.378742 TCGACTGACAGGAGATCTAAAGC 59.621 47.826 7.51 0.00 0.00 3.51
605 611 4.516365 AGTAAGGAAATTCACTCGACGT 57.484 40.909 0.00 0.00 0.00 4.34
649 655 1.346395 TCAAACTAAAGAGCCCGCTCA 59.654 47.619 18.44 0.00 44.99 4.26
692 698 3.122780 CCGAAATTCAAATCCCGCAAAAC 59.877 43.478 0.00 0.00 0.00 2.43
747 753 2.157880 AGCTTCCATCCTATCCCATCCT 60.158 50.000 0.00 0.00 0.00 3.24
938 946 3.706373 GCGGAGGTGGCAGAGGAA 61.706 66.667 0.00 0.00 0.00 3.36
1492 1506 1.375908 GCTGGATCACTTGCGTCCA 60.376 57.895 0.00 0.00 39.61 4.02
1762 1776 1.750399 GCAAGTCCATGCCGGTCAT 60.750 57.895 1.90 4.20 40.49 3.06
1914 1928 0.904649 TGTTCCCTGTGATGCTCGAT 59.095 50.000 0.00 0.00 0.00 3.59
2041 2055 2.094700 TCAGTCGACCGATTCAAAGAGG 60.095 50.000 13.01 0.00 0.00 3.69
2199 2213 0.677098 CGTCGTCTCCCTCTCCTTCA 60.677 60.000 0.00 0.00 0.00 3.02
2272 2289 2.488153 GTGTAAGCTTGGATCGCCTTTT 59.512 45.455 9.86 0.00 34.31 2.27
2482 2499 1.269621 ACGGTCGACAAAGGAGAACAG 60.270 52.381 18.91 0.00 0.00 3.16
2776 2796 3.749064 GAGTCTCGCCAGCCGACA 61.749 66.667 8.76 0.00 41.89 4.35
2979 2999 1.350019 CTCCATCATGATGCCTGCCTA 59.650 52.381 27.24 7.41 37.49 3.93
3109 3129 6.940739 TCTTCGGAAAAGAGATTCTTCAGAT 58.059 36.000 0.00 0.00 35.27 2.90
3638 3665 3.005472 TCGTCAAGAATGAGAAACCTCGT 59.995 43.478 0.00 0.00 35.88 4.18


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

AutoCloner maintained by Alex Coulton.