Multiple sequence alignment - TraesCS1B01G200900

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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 TraesCS1B01G200900 chr1B 100.000 2432 0 0 1 2432 359894080 359896511 0 4492
1 TraesCS1B01G200900 chr1D 95.689 2459 72 10 1 2432 252924626 252922175 0 3923
2 TraesCS1B01G200900 chr1A 94.898 2450 82 19 1 2432 324501937 324499513 0 3792


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 TraesCS1B01G200900 chr1B 359894080 359896511 2431 False 4492 4492 100.000 1 2432 1 chr1B.!!$F1 2431
1 TraesCS1B01G200900 chr1D 252922175 252924626 2451 True 3923 3923 95.689 1 2432 1 chr1D.!!$R1 2431
2 TraesCS1B01G200900 chr1A 324499513 324501937 2424 True 3792 3792 94.898 1 2432 1 chr1A.!!$R1 2431

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
227 247 1.080974 GGCGTTTCGACGAGGAGAA 60.081 57.895 2.79 0.0 34.64 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1705 1738 0.884704 GAGGAAACAAGAGCACCGCA 60.885 55.0 0.0 0.0 0.0 5.69 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
113 132 2.256158 GCCGCGGTGTTTTTACCC 59.744 61.111 28.70 0.93 37.44 3.69
120 139 1.270465 CGGTGTTTTTACCCCGTCTCT 60.270 52.381 0.00 0.00 37.44 3.10
138 157 2.232298 CTTCCTCCGCCTTCGAGCTT 62.232 60.000 0.00 0.00 38.10 3.74
160 179 2.679082 ACTGGTATGTATCCTCGCCTT 58.321 47.619 0.00 0.00 0.00 4.35
211 231 2.038387 TCGCTTCAGATTTTAGGGGC 57.962 50.000 0.00 0.00 0.00 5.80
227 247 1.080974 GGCGTTTCGACGAGGAGAA 60.081 57.895 2.79 0.00 34.64 2.87
396 416 7.255208 GGTTTCACCGTTTAGATCTGGTAAAAA 60.255 37.037 5.18 5.71 32.29 1.94
412 432 4.746115 GGTAAAAATTTGTGAACCGGGAAC 59.254 41.667 6.32 0.74 0.00 3.62
539 566 5.689961 CCTTTTGGATTCGTTTGTAGTTTGG 59.310 40.000 0.00 0.00 44.07 3.28
740 769 6.755141 GCAAATCTGTGATAAATCTTGCATGT 59.245 34.615 0.00 0.00 38.20 3.21
812 841 5.743026 TTCTTGTGTTCGATGCAAAAGTA 57.257 34.783 15.61 7.56 33.93 2.24
850 880 7.026631 TGCAATTTATTCTAGGAATGGTTCG 57.973 36.000 3.37 0.00 0.00 3.95
860 890 4.073293 AGGAATGGTTCGGTAATAGCAG 57.927 45.455 0.00 0.00 0.00 4.24
970 1000 3.461831 TCTCAGAAACCAAGAAAAGGGGA 59.538 43.478 0.00 0.00 0.00 4.81
1146 1176 2.264005 TTGGAAACATGTACCGCTGT 57.736 45.000 14.48 0.00 42.32 4.40
1167 1197 5.620206 TGTAAACTGACTGGAATGACACAT 58.380 37.500 0.00 0.00 0.00 3.21
1254 1284 2.383527 GCAGTTGTTCCCGCTCTCG 61.384 63.158 0.00 0.00 0.00 4.04
1458 1491 5.931441 AACGAGACTTCCATCTTTTCTTG 57.069 39.130 0.00 0.00 0.00 3.02
1507 1540 3.496331 TCCATTTCCCCTTCTTTGACAC 58.504 45.455 0.00 0.00 0.00 3.67
1721 1754 1.508632 TAGTGCGGTGCTCTTGTTTC 58.491 50.000 0.00 0.00 34.22 2.78
1791 1824 6.121590 TGAGGTTCATTATCTGCTGCATTTA 58.878 36.000 1.31 0.00 0.00 1.40
1838 1871 5.744171 TGCTTGACATAGTTGGTGATGTAT 58.256 37.500 0.00 0.00 36.42 2.29
1858 1894 5.861787 TGTATATCCGTTGCAGACATTATCG 59.138 40.000 0.00 0.00 0.00 2.92
2044 2080 4.817318 TGCTTCCTCCTGTTTTGTTTTT 57.183 36.364 0.00 0.00 0.00 1.94
2065 2101 3.214328 TGACTTGCTTCTTTCCTTGACC 58.786 45.455 0.00 0.00 0.00 4.02
2154 2190 6.500041 TGTTCCCTTTGTTAAGTTGATTTCG 58.500 36.000 0.00 0.00 0.00 3.46
2177 2213 5.324697 GTTTGTTCTGAGTGTTCACTTGTC 58.675 41.667 6.91 0.00 0.00 3.18
2180 2216 5.245531 TGTTCTGAGTGTTCACTTGTCTTT 58.754 37.500 6.91 0.00 0.00 2.52
2204 2240 1.603678 GCTTGTGCAGGTGAATTGGTG 60.604 52.381 0.00 0.00 39.41 4.17
2205 2241 1.682854 CTTGTGCAGGTGAATTGGTGT 59.317 47.619 0.00 0.00 0.00 4.16
2206 2242 1.774110 TGTGCAGGTGAATTGGTGTT 58.226 45.000 0.00 0.00 0.00 3.32
2207 2243 1.680735 TGTGCAGGTGAATTGGTGTTC 59.319 47.619 0.00 0.00 0.00 3.18
2261 2297 5.618236 CAGGAGCTATGGAAGATCATTGAA 58.382 41.667 0.00 0.00 42.69 2.69
2287 2323 2.133281 TGCAGCAGTGGAATAGCAAT 57.867 45.000 0.00 0.00 0.00 3.56
2308 2344 2.301870 TGTACCATCAAAGTCTTCGGCT 59.698 45.455 0.00 0.00 0.00 5.52
2334 2370 1.886886 TGCTTTTCAGGTAACCGTCC 58.113 50.000 0.00 0.00 37.17 4.79
2361 2397 5.858581 GCGCTTGTCAGTTTATTTTGAAGAT 59.141 36.000 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 132 2.286127 GAAGGCGGAGGAAGAGACGG 62.286 65.000 0.00 0.00 0.00 4.79
120 139 1.827399 AAAGCTCGAAGGCGGAGGAA 61.827 55.000 0.00 0.00 38.28 3.36
138 157 3.840991 AGGCGAGGATACATACCAGTAA 58.159 45.455 0.00 0.00 41.41 2.24
160 179 3.262405 AGGAACAACGTAATAGAGGGCAA 59.738 43.478 0.00 0.00 0.00 4.52
196 216 2.745281 CGAAACGCCCCTAAAATCTGAA 59.255 45.455 0.00 0.00 0.00 3.02
227 247 1.305381 CCTCTCACGGTCTCCCCTT 60.305 63.158 0.00 0.00 0.00 3.95
282 302 6.183360 CCAAAATCTACGCCAATTAGGGATTT 60.183 38.462 0.00 0.00 38.09 2.17
412 432 2.040544 CAAACACCTAGCTGCCCCG 61.041 63.158 0.00 0.00 0.00 5.73
516 543 6.198216 CACCAAACTACAAACGAATCCAAAAG 59.802 38.462 0.00 0.00 0.00 2.27
539 566 1.263356 TAGTACAGTCCACCTGGCAC 58.737 55.000 0.00 0.00 46.06 5.01
676 705 9.449719 ACAATTTTCTACAGATAAATCTCGGTT 57.550 29.630 0.00 0.00 34.22 4.44
740 769 6.207810 ACCTCACGAAATTGCCACTAAATTTA 59.792 34.615 0.00 0.00 37.35 1.40
812 841 9.678260 AGAATAAATTGCAGTAAATCTGAGAGT 57.322 29.630 0.00 0.00 46.27 3.24
840 869 2.548480 GCTGCTATTACCGAACCATTCC 59.452 50.000 0.00 0.00 0.00 3.01
850 880 4.093556 GTGACAGTTCTTGCTGCTATTACC 59.906 45.833 0.00 0.00 39.96 2.85
860 890 2.244651 ACGCGGTGACAGTTCTTGC 61.245 57.895 12.47 0.00 0.00 4.01
970 1000 2.672478 CGCGAGAAACCTCTTCACAGAT 60.672 50.000 0.00 0.00 29.54 2.90
1146 1176 8.729756 CAAATATGTGTCATTCCAGTCAGTTTA 58.270 33.333 0.00 0.00 0.00 2.01
1167 1197 8.282455 TCTGGTTACAGTTTTTGTCACAAATA 57.718 30.769 3.17 0.00 45.14 1.40
1458 1491 2.281553 GCATAAGGTAGCCGGGGC 60.282 66.667 2.18 0.18 42.33 5.80
1705 1738 0.884704 GAGGAAACAAGAGCACCGCA 60.885 55.000 0.00 0.00 0.00 5.69
1721 1754 7.396540 AGCTACAATAATGAAAAGTTGGAGG 57.603 36.000 0.00 0.00 33.97 4.30
1791 1824 1.034356 TGCACAGCTTGAATGCACTT 58.966 45.000 7.45 0.00 44.17 3.16
1838 1871 4.316205 ACGATAATGTCTGCAACGGATA 57.684 40.909 0.00 0.00 0.00 2.59
1858 1894 2.433436 AGTTCACGCCCCAAGAAATAC 58.567 47.619 0.00 0.00 0.00 1.89
2044 2080 3.214328 GGTCAAGGAAAGAAGCAAGTCA 58.786 45.455 0.00 0.00 0.00 3.41
2154 2190 5.122396 AGACAAGTGAACACTCAGAACAAAC 59.878 40.000 7.93 0.00 41.58 2.93
2204 2240 3.363084 CCAAGAAGAGCGAAAGAACGAAC 60.363 47.826 0.00 0.00 35.09 3.95
2205 2241 2.800544 CCAAGAAGAGCGAAAGAACGAA 59.199 45.455 0.00 0.00 35.09 3.85
2206 2242 2.223971 ACCAAGAAGAGCGAAAGAACGA 60.224 45.455 0.00 0.00 35.09 3.85
2207 2243 2.135933 ACCAAGAAGAGCGAAAGAACG 58.864 47.619 0.00 0.00 0.00 3.95
2261 2297 1.999648 TTCCACTGCTGCAAAGGATT 58.000 45.000 19.47 0.00 0.00 3.01
2330 2366 3.175240 CTGACAAGCGCTCGGACG 61.175 66.667 12.06 0.00 0.00 4.79
2334 2370 3.455619 AAATAAACTGACAAGCGCTCG 57.544 42.857 12.06 0.00 0.00 5.03
2387 2423 6.296026 TGCACTGGAAAAGACTAATGTAAGT 58.704 36.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.