Multiple sequence alignment - TraesCS3D01G188300

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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 TraesCS3D01G188300 chr3D 100.000 4102 0 0 1 4102 174927307 174923206 0.000000e+00 7576.0
1 TraesCS3D01G188300 chr3A 97.836 4113 56 14 1 4102 214291312 214287222 0.000000e+00 7071.0
2 TraesCS3D01G188300 chr3B 96.603 3415 75 18 4 3400 253897585 253894194 0.000000e+00 5626.0
3 TraesCS3D01G188300 chr3B 91.259 286 14 3 3413 3688 253893172 253892888 2.990000e-101 379.0
4 TraesCS3D01G188300 chr3B 82.902 193 18 10 3717 3896 253892906 253892716 4.240000e-35 159.0
5 TraesCS3D01G188300 chr5A 96.875 32 1 0 3381 3412 580265395 580265426 2.000000e-03 54.7


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 TraesCS3D01G188300 chr3D 174923206 174927307 4101 True 7576.000000 7576 100.000000 1 4102 1 chr3D.!!$R1 4101
1 TraesCS3D01G188300 chr3A 214287222 214291312 4090 True 7071.000000 7071 97.836000 1 4102 1 chr3A.!!$R1 4101
2 TraesCS3D01G188300 chr3B 253892716 253897585 4869 True 2054.666667 5626 90.254667 4 3896 3 chr3B.!!$R1 3892

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
302 304 3.003173 CTGGACTGGGGAGGCGAA 61.003 66.667 0.00 0.00 0.00 4.70 F
1014 1023 1.005215 ACAGAGATGGCTGGAAAAGGG 59.995 52.381 0.00 0.00 40.20 3.95 F
2303 2316 3.424703 AGACACATTAAGCCTGCAATGT 58.575 40.909 2.91 2.91 44.21 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 1942 1.656652 CAATCCTCTGGCAGTAACCG 58.343 55.000 15.27 0.00 0.00 4.44 R
2597 2610 0.811219 GCGTAGTGCATGATCCAGCA 60.811 55.000 0.00 5.18 45.45 4.41 R
3257 3277 1.154543 GGTTACACCTTTTCGCGCG 60.155 57.895 26.76 26.76 34.73 6.86 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
302 304 3.003173 CTGGACTGGGGAGGCGAA 61.003 66.667 0.00 0.00 0.00 4.70
557 563 5.528043 TTCTATCTTGAGTCATGAGCCTC 57.472 43.478 13.52 0.39 0.00 4.70
898 907 7.630242 ACAATCCGAAATGTCATCACTAAAT 57.370 32.000 0.00 0.00 0.00 1.40
1014 1023 1.005215 ACAGAGATGGCTGGAAAAGGG 59.995 52.381 0.00 0.00 40.20 3.95
1365 1374 9.802039 TTTGATGTTCCCTTAGTTTTAGTACAT 57.198 29.630 0.00 0.00 0.00 2.29
1366 1375 9.802039 TTGATGTTCCCTTAGTTTTAGTACATT 57.198 29.630 0.00 0.00 0.00 2.71
1367 1376 9.226606 TGATGTTCCCTTAGTTTTAGTACATTG 57.773 33.333 0.00 0.00 0.00 2.82
1916 1929 4.412075 GCTTCCTGCTGCCTTCTT 57.588 55.556 0.00 0.00 38.95 2.52
1929 1942 4.513318 GCTGCCTTCTTGTATATGGACTTC 59.487 45.833 0.00 0.00 0.00 3.01
2303 2316 3.424703 AGACACATTAAGCCTGCAATGT 58.575 40.909 2.91 2.91 44.21 2.71
2597 2610 3.913163 AGTTCTTGGGATCTGGAACTCTT 59.087 43.478 13.20 0.00 42.92 2.85
2792 2805 2.744202 GTGCCAGTCTGTTGTTATCCTG 59.256 50.000 0.00 0.00 0.00 3.86
2794 2807 2.744202 GCCAGTCTGTTGTTATCCTGTG 59.256 50.000 0.00 0.00 0.00 3.66
3257 3277 8.803397 AAAGATAACCTGTAAACTAATGGACC 57.197 34.615 0.00 0.00 0.00 4.46
3460 4493 8.203485 TGAATGTTCTACTTCCTGCAAAATTTT 58.797 29.630 0.00 0.00 0.00 1.82
3596 4631 7.492669 AGTCACGAACGATATCTTGATGAAAAT 59.507 33.333 0.34 0.00 31.34 1.82
3797 4842 7.030768 GTGTTCTCCTCTTATGTGAAGTAGAC 58.969 42.308 0.00 0.00 0.00 2.59
3858 4914 6.325028 ACCTGCAAGCTAAGAGAACTATATGA 59.675 38.462 0.00 0.00 0.00 2.15
4018 5074 3.053291 GCGTGGTTGCGGATCCAA 61.053 61.111 13.41 0.00 35.38 3.53
4041 5097 0.108992 TTTCCGGATCGAGTTGACCG 60.109 55.000 4.15 12.09 39.47 4.79
4083 5140 9.716507 GAATACTTACATGCATTTACGTGATTT 57.283 29.630 11.18 4.03 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
280 282 2.284921 CTCCCCAGTCCAGGAGCA 60.285 66.667 0.00 0.00 43.11 4.26
302 304 0.178068 ATTGGTGCTTATCCGCGACT 59.822 50.000 8.23 0.00 0.00 4.18
557 563 2.293122 TCAAGCTTTCCAATTCGGTGTG 59.707 45.455 0.00 0.00 35.57 3.82
732 739 6.061441 TGGCATGTCATAATTCCGATAACTT 58.939 36.000 0.00 0.00 0.00 2.66
898 907 2.626780 CGTGGTGCAGAGACCGAGA 61.627 63.158 0.00 0.00 39.07 4.04
1014 1023 2.202878 TGCGGCGGAACATAGCTC 60.203 61.111 9.78 0.00 0.00 4.09
1365 1374 7.343574 TCCTACTTCCTTATGCACTATGTACAA 59.656 37.037 0.00 0.00 0.00 2.41
1366 1375 6.837048 TCCTACTTCCTTATGCACTATGTACA 59.163 38.462 0.00 0.00 0.00 2.90
1367 1376 7.286215 TCCTACTTCCTTATGCACTATGTAC 57.714 40.000 0.00 0.00 0.00 2.90
1916 1929 4.202182 GGCAGTAACCGAAGTCCATATACA 60.202 45.833 0.00 0.00 0.00 2.29
1929 1942 1.656652 CAATCCTCTGGCAGTAACCG 58.343 55.000 15.27 0.00 0.00 4.44
2303 2316 1.707106 TGGACGTAGGACCAACTCAA 58.293 50.000 4.11 0.00 35.50 3.02
2597 2610 0.811219 GCGTAGTGCATGATCCAGCA 60.811 55.000 0.00 5.18 45.45 4.41
3257 3277 1.154543 GGTTACACCTTTTCGCGCG 60.155 57.895 26.76 26.76 34.73 6.86
3460 4493 7.660112 AGCACATCAAATGTTATTTCTTCACA 58.340 30.769 0.00 0.00 42.70 3.58
3536 4569 9.757227 AAAACACTAAACATGCAGCTTAAAATA 57.243 25.926 0.00 0.00 0.00 1.40
3596 4631 9.681062 CCTTGAGTTCTTTCCCTACATATAAAA 57.319 33.333 0.00 0.00 0.00 1.52
3797 4842 2.304516 CTAATTGGCGCAACGGGTCG 62.305 60.000 10.83 0.00 0.00 4.79
3871 4927 7.004086 TCCATCCAAATAGTTCACTTGACTTT 58.996 34.615 0.00 0.00 0.00 2.66
3976 5032 2.307768 CCCTCCGCACTATAGAGACAA 58.692 52.381 6.78 0.00 0.00 3.18
4041 5097 2.998316 ATTCACTAGCTCAAGGAGGC 57.002 50.000 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.