Multiple sequence alignment - TraesCS5B01G164000

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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 TraesCS5B01G164000 chr5B 100.000 2414 0 0 1 2414 303914251 303911838 0 4458
1 TraesCS5B01G164000 chr5A 96.002 2426 75 12 1 2414 355847734 355845319 0 3923
2 TraesCS5B01G164000 chr5D 95.998 2424 74 14 1 2414 268480173 268477763 0 3917


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 TraesCS5B01G164000 chr5B 303911838 303914251 2413 True 4458 4458 100.000 1 2414 1 chr5B.!!$R1 2413
1 TraesCS5B01G164000 chr5A 355845319 355847734 2415 True 3923 3923 96.002 1 2414 1 chr5A.!!$R1 2413
2 TraesCS5B01G164000 chr5D 268477763 268480173 2410 True 3917 3917 95.998 1 2414 1 chr5D.!!$R1 2413

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
380 381 1.666011 GCCTCTTCCTGTGTCGTGA 59.334 57.895 0.0 0.0 0.0 4.35 F
1212 1213 0.824759 GTGTGAATACCTCCTCCGCT 59.175 55.000 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1353 1354 0.247460 GGGATCTTTGTTTGGGCAGC 59.753 55.0 0.00 0.0 0.0 5.25 R
2248 2258 0.322187 GGCCCACGGTGTTGATAGTT 60.322 55.0 7.45 0.0 0.0 2.24 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
272 273 6.256539 ACATAAGAGTGCTCATATTGTTGTCG 59.743 38.462 1.82 0.00 0.00 4.35
380 381 1.666011 GCCTCTTCCTGTGTCGTGA 59.334 57.895 0.00 0.00 0.00 4.35
714 715 4.532834 TGTGCCTACCTTTTGTTCTCTTT 58.467 39.130 0.00 0.00 0.00 2.52
764 765 6.097554 TCCTCTTCTTCACTATCTCCATTCAC 59.902 42.308 0.00 0.00 0.00 3.18
1023 1024 9.760926 TCAATGAGTACTATAGCATTATCCTCT 57.239 33.333 7.09 0.00 30.45 3.69
1047 1048 4.321452 GGTTTCCATGCCATGCTACATATG 60.321 45.833 0.00 0.00 0.00 1.78
1212 1213 0.824759 GTGTGAATACCTCCTCCGCT 59.175 55.000 0.00 0.00 0.00 5.52
1353 1354 1.347817 GAGTCAAGCTTCGTGCCTCG 61.348 60.000 0.00 0.00 44.23 4.63
1491 1492 0.242825 TGGAGATCGTGTTGTCGACC 59.757 55.000 14.12 0.00 42.56 4.79
1615 1616 1.880894 CTCTGGAACGTGCCGTCTA 59.119 57.895 8.41 0.00 39.99 2.59
1657 1658 7.657761 ACATTTACAGATCTCGAAGTGAAAACT 59.342 33.333 12.89 0.00 32.30 2.66
1705 1706 4.794439 CGCGCATCAGGACGGTCA 62.794 66.667 8.75 0.00 0.00 4.02
1760 1761 1.447314 GTGGTCGATGGAACCGGAC 60.447 63.158 9.46 0.76 0.00 4.79
2061 2062 0.380378 GCGAGAGAGAGATGCTTCGT 59.620 55.000 0.00 0.00 0.00 3.85
2064 2065 2.159448 CGAGAGAGAGATGCTTCGTGTT 60.159 50.000 0.00 0.00 0.00 3.32
2070 2071 0.603569 AGATGCTTCGTGTTCGAGGT 59.396 50.000 2.26 0.00 46.81 3.85
2086 2087 1.268079 GAGGTTTTCTTGGTGAGCTGC 59.732 52.381 0.00 0.00 0.00 5.25
2096 2099 0.255890 GGTGAGCTGCTGGGGATTTA 59.744 55.000 7.01 0.00 0.00 1.40
2098 2101 0.107017 TGAGCTGCTGGGGATTTAGC 60.107 55.000 7.01 0.00 40.29 3.09
2139 2144 2.354196 GCGAGCGTTTATGTTTCGATG 58.646 47.619 0.00 0.00 33.38 3.84
2248 2258 1.807886 GACTCCTCGCGGAAAGCTA 59.192 57.895 6.13 0.00 45.59 3.32
2252 2262 1.404391 CTCCTCGCGGAAAGCTAACTA 59.596 52.381 6.13 0.00 45.59 2.24
2255 2265 2.223735 CCTCGCGGAAAGCTAACTATCA 60.224 50.000 6.13 0.00 45.59 2.15
2256 2266 3.444916 CTCGCGGAAAGCTAACTATCAA 58.555 45.455 6.13 0.00 45.59 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
272 273 4.526770 GCAAATCCATGCAAGGGC 57.473 55.556 8.36 0.00 45.70 5.19
714 715 1.834188 TACACGAGATGCAGTCAGGA 58.166 50.000 0.00 0.00 0.00 3.86
764 765 0.171007 GGCCACATTTGATGACCACG 59.829 55.000 0.00 0.00 0.00 4.94
1023 1024 1.272369 TGTAGCATGGCATGGAAACCA 60.272 47.619 27.48 4.04 41.06 3.67
1047 1048 3.505293 AGAGGCAGAAGTTTGATGAAAGC 59.495 43.478 0.00 0.00 0.00 3.51
1179 1180 5.179555 GGTATTCACACTGAAAGGAGAACAC 59.820 44.000 0.00 0.00 40.12 3.32
1353 1354 0.247460 GGGATCTTTGTTTGGGCAGC 59.753 55.000 0.00 0.00 0.00 5.25
1615 1616 7.878127 TCTGTAAATGTCTCCGAATTTCTTTCT 59.122 33.333 0.00 0.00 31.73 2.52
1666 1667 7.847078 GCGCGATATCTTATCTTAGTAGTACAG 59.153 40.741 12.10 0.00 0.00 2.74
1667 1668 7.332678 TGCGCGATATCTTATCTTAGTAGTACA 59.667 37.037 12.10 0.00 0.00 2.90
1669 1670 7.838771 TGCGCGATATCTTATCTTAGTAGTA 57.161 36.000 12.10 0.00 0.00 1.82
1670 1671 6.738832 TGCGCGATATCTTATCTTAGTAGT 57.261 37.500 12.10 0.00 0.00 2.73
1671 1672 7.410485 TGATGCGCGATATCTTATCTTAGTAG 58.590 38.462 12.10 0.00 0.00 2.57
1676 1677 4.158579 TCCTGATGCGCGATATCTTATCTT 59.841 41.667 12.10 0.00 0.00 2.40
1687 1688 4.492160 GACCGTCCTGATGCGCGA 62.492 66.667 12.10 0.00 0.00 5.87
1705 1706 0.396811 CTTCCCAGGTTCGTGGTTCT 59.603 55.000 10.05 0.00 35.60 3.01
2044 2045 3.434637 GAACACGAAGCATCTCTCTCTC 58.565 50.000 0.00 0.00 0.00 3.20
2045 2046 2.159448 CGAACACGAAGCATCTCTCTCT 60.159 50.000 0.00 0.00 0.00 3.10
2061 2062 3.202906 CTCACCAAGAAAACCTCGAACA 58.797 45.455 0.00 0.00 0.00 3.18
2064 2065 1.416401 AGCTCACCAAGAAAACCTCGA 59.584 47.619 0.00 0.00 0.00 4.04
2070 2071 1.321474 CCAGCAGCTCACCAAGAAAA 58.679 50.000 0.00 0.00 0.00 2.29
2086 2087 2.498167 CCAATCTCGCTAAATCCCCAG 58.502 52.381 0.00 0.00 0.00 4.45
2096 2099 1.099879 GCATCTTGGCCAATCTCGCT 61.100 55.000 20.85 0.00 0.00 4.93
2098 2101 1.645455 CGCATCTTGGCCAATCTCG 59.355 57.895 20.85 15.81 0.00 4.04
2122 2125 2.742053 AGCACATCGAAACATAAACGCT 59.258 40.909 0.00 0.00 0.00 5.07
2139 2144 1.003718 ACTCGTTTAGCCCCAGCAC 60.004 57.895 0.00 0.00 43.56 4.40
2248 2258 0.322187 GGCCCACGGTGTTGATAGTT 60.322 55.000 7.45 0.00 0.00 2.24
2252 2262 1.901464 GTTGGCCCACGGTGTTGAT 60.901 57.895 7.45 0.00 0.00 2.57
2255 2265 3.999297 AACGTTGGCCCACGGTGTT 62.999 57.895 30.35 15.00 44.82 3.32
2256 2266 4.493049 AACGTTGGCCCACGGTGT 62.493 61.111 30.35 14.36 44.82 4.16
2364 2374 9.045223 GTCAGAACATTGCACAGATATATTACA 57.955 33.333 0.00 0.00 0.00 2.41
2365 2375 8.499162 GGTCAGAACATTGCACAGATATATTAC 58.501 37.037 0.00 0.00 0.00 1.89
2366 2376 8.210265 TGGTCAGAACATTGCACAGATATATTA 58.790 33.333 0.00 0.00 0.00 0.98
2367 2377 7.056006 TGGTCAGAACATTGCACAGATATATT 58.944 34.615 0.00 0.00 0.00 1.28
2368 2378 6.594744 TGGTCAGAACATTGCACAGATATAT 58.405 36.000 0.00 0.00 0.00 0.86
2371 2381 4.284829 TGGTCAGAACATTGCACAGATA 57.715 40.909 0.00 0.00 0.00 1.98
2372 2382 3.144657 TGGTCAGAACATTGCACAGAT 57.855 42.857 0.00 0.00 0.00 2.90
2373 2383 2.636647 TGGTCAGAACATTGCACAGA 57.363 45.000 0.00 0.00 0.00 3.41
2374 2384 5.106038 ACAATATGGTCAGAACATTGCACAG 60.106 40.000 6.18 0.00 31.28 3.66


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

AutoCloner maintained by Alex Coulton.