Multiple sequence alignment - TraesCS2D01G448700

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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 TraesCS2D01G448700 chr2D 100.000 2942 0 0 1 2942 558481280 558484221 0 5433
1 TraesCS2D01G448700 chr2B 97.322 2203 45 8 1 2202 666934338 666936527 0 3729
2 TraesCS2D01G448700 chr2B 92.578 768 30 11 2185 2942 666936480 666937230 0 1077
3 TraesCS2D01G448700 chr2A 96.964 2207 43 10 1 2193 699129057 699131253 0 3683
4 TraesCS2D01G448700 chr2A 98.141 753 9 3 2191 2942 699131212 699131960 0 1308


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 TraesCS2D01G448700 chr2D 558481280 558484221 2941 False 5433.0 5433 100.0000 1 2942 1 chr2D.!!$F1 2941
1 TraesCS2D01G448700 chr2B 666934338 666937230 2892 False 2403.0 3729 94.9500 1 2942 2 chr2B.!!$F1 2941
2 TraesCS2D01G448700 chr2A 699129057 699131960 2903 False 2495.5 3683 97.5525 1 2942 2 chr2A.!!$F1 2941

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
109 111 1.004044 CACTCAACAAGGGCCAGATCT 59.996 52.381 6.18 0.0 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 1998 0.030101 GTGATCTCGCCTTCTCTCCG 59.97 60.0 0.0 0.0 0.0 4.63 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
39 40 5.938322 AGCATATACAAAACAAAGACCACG 58.062 37.500 0.00 0.00 0.00 4.94
109 111 1.004044 CACTCAACAAGGGCCAGATCT 59.996 52.381 6.18 0.00 0.00 2.75
111 113 3.118112 CACTCAACAAGGGCCAGATCTAT 60.118 47.826 6.18 0.00 0.00 1.98
113 115 2.103094 TCAACAAGGGCCAGATCTATCG 59.897 50.000 6.18 0.00 0.00 2.92
138 140 1.064389 AGCAAAGGATCCTAGGGCAAC 60.064 52.381 25.37 9.75 0.00 4.17
212 214 3.641906 CCCTAAGTCGTATCAATCCTGGT 59.358 47.826 0.00 0.00 0.00 4.00
227 229 4.895668 TCCTGGTTTAGTGGTCGTTAAT 57.104 40.909 0.00 0.00 0.00 1.40
514 516 3.261897 TGTTCTCCCATCCAAACTCTCTC 59.738 47.826 0.00 0.00 0.00 3.20
515 517 3.481559 TCTCCCATCCAAACTCTCTCT 57.518 47.619 0.00 0.00 0.00 3.10
516 518 3.370104 TCTCCCATCCAAACTCTCTCTC 58.630 50.000 0.00 0.00 0.00 3.20
517 519 3.012274 TCTCCCATCCAAACTCTCTCTCT 59.988 47.826 0.00 0.00 0.00 3.10
756 765 4.006319 AGCACTATCTTCTTGCACCTTTC 58.994 43.478 0.00 0.00 38.81 2.62
1158 1167 3.993584 AACGGCGGCAACTACGGA 61.994 61.111 13.24 0.00 37.62 4.69
1368 1377 2.187946 CACATCCTGGAGGTCGGC 59.812 66.667 11.66 0.00 36.34 5.54
1983 1998 1.017177 TCGGTGTAATTGCTGTCGGC 61.017 55.000 0.00 0.00 42.22 5.54
2191 2206 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
2192 2207 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
2193 2208 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
2194 2209 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
2195 2210 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
2196 2211 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
2197 2212 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
2198 2213 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
2199 2214 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
2200 2215 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
2201 2216 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
2202 2217 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
2203 2218 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
2204 2219 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
2205 2220 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
2206 2221 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
2207 2222 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
2208 2223 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
2209 2224 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
2210 2225 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
2211 2226 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
2212 2227 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
2213 2228 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
2214 2229 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
2215 2230 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
2216 2231 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
2217 2232 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
2218 2233 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
2340 2355 2.341257 CGAGCATATGCATGGGTCTAC 58.659 52.381 28.62 7.81 45.16 2.59
2512 2529 7.195839 TGCTTTTGGGTAATTATTTTTGTGC 57.804 32.000 0.00 0.00 0.00 4.57
2791 2809 2.775890 ACTGCATCCTCACAGAAACAG 58.224 47.619 0.00 0.00 37.35 3.16
2799 2817 3.133003 TCCTCACAGAAACAGGCTATAGC 59.867 47.826 16.78 16.78 41.14 2.97
2895 2921 3.380637 TCGCTCCTTGTCCTATTGAGTAC 59.619 47.826 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.594603 AATCGATCTCGTGGTCTTTGT 57.405 42.857 0.00 0.00 40.80 2.83
29 30 3.926527 TCAAATCGATCTCGTGGTCTTTG 59.073 43.478 0.00 6.26 40.80 2.77
30 31 4.188247 TCAAATCGATCTCGTGGTCTTT 57.812 40.909 0.00 0.00 40.80 2.52
31 32 3.868757 TCAAATCGATCTCGTGGTCTT 57.131 42.857 0.00 0.00 40.80 3.01
33 34 2.603560 GGTTCAAATCGATCTCGTGGTC 59.396 50.000 0.00 0.00 40.80 4.02
35 36 2.348666 GTGGTTCAAATCGATCTCGTGG 59.651 50.000 0.00 0.00 40.80 4.94
36 37 2.348666 GGTGGTTCAAATCGATCTCGTG 59.651 50.000 0.00 0.00 40.80 4.35
37 38 2.028476 TGGTGGTTCAAATCGATCTCGT 60.028 45.455 0.00 0.00 40.80 4.18
38 39 2.616960 TGGTGGTTCAAATCGATCTCG 58.383 47.619 0.00 0.00 41.45 4.04
39 40 4.455877 AGTTTGGTGGTTCAAATCGATCTC 59.544 41.667 0.00 0.00 38.64 2.75
94 96 1.417890 CCGATAGATCTGGCCCTTGTT 59.582 52.381 5.18 0.00 39.76 2.83
96 98 0.321122 GCCGATAGATCTGGCCCTTG 60.321 60.000 10.77 0.00 39.15 3.61
97 99 1.821061 CGCCGATAGATCTGGCCCTT 61.821 60.000 15.07 0.00 40.71 3.95
109 111 0.033504 GATCCTTTGCTCCGCCGATA 59.966 55.000 0.00 0.00 0.00 2.92
111 113 2.186903 GATCCTTTGCTCCGCCGA 59.813 61.111 0.00 0.00 0.00 5.54
113 115 0.250081 CTAGGATCCTTTGCTCCGCC 60.250 60.000 22.03 0.00 36.62 6.13
138 140 4.100084 TCCCACCTCCAGCGCATG 62.100 66.667 11.47 4.88 0.00 4.06
212 214 5.733620 ACCTGAGATTAACGACCACTAAA 57.266 39.130 0.00 0.00 0.00 1.85
514 516 3.600448 AATGGGAGGAGAGAGAGAGAG 57.400 52.381 0.00 0.00 0.00 3.20
515 517 5.678142 AATAATGGGAGGAGAGAGAGAGA 57.322 43.478 0.00 0.00 0.00 3.10
516 518 6.745794 AAAATAATGGGAGGAGAGAGAGAG 57.254 41.667 0.00 0.00 0.00 3.20
517 519 7.791766 ACATAAAATAATGGGAGGAGAGAGAGA 59.208 37.037 0.00 0.00 0.00 3.10
756 765 5.774498 AGCAAACAGGGAAGAAACTAAAG 57.226 39.130 0.00 0.00 0.00 1.85
1122 1131 2.897846 CCGTTGCCGTTGTGGTCA 60.898 61.111 0.00 0.00 41.21 4.02
1983 1998 0.030101 GTGATCTCGCCTTCTCTCCG 59.970 60.000 0.00 0.00 0.00 4.63
2184 2199 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
2186 2201 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
2187 2202 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
2191 2206 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
2192 2207 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
2213 2228 9.495572 GGAGAGACAAGAAAAGAAAATAGAAGA 57.504 33.333 0.00 0.00 0.00 2.87
2214 2229 9.500785 AGGAGAGACAAGAAAAGAAAATAGAAG 57.499 33.333 0.00 0.00 0.00 2.85
2215 2230 9.277783 CAGGAGAGACAAGAAAAGAAAATAGAA 57.722 33.333 0.00 0.00 0.00 2.10
2216 2231 8.651389 TCAGGAGAGACAAGAAAAGAAAATAGA 58.349 33.333 0.00 0.00 0.00 1.98
2217 2232 8.839310 TCAGGAGAGACAAGAAAAGAAAATAG 57.161 34.615 0.00 0.00 0.00 1.73
2218 2233 9.057089 GTTCAGGAGAGACAAGAAAAGAAAATA 57.943 33.333 0.00 0.00 0.00 1.40
2340 2355 2.486472 ACCAGCAAGACCAAGATGAG 57.514 50.000 0.00 0.00 0.00 2.90
2512 2529 3.632145 GGGCATCTAACACCTTTGTATGG 59.368 47.826 0.00 0.00 33.55 2.74
2799 2817 4.762289 GGGTTCCCCATGAGCTATATAG 57.238 50.000 5.30 5.30 44.65 1.31


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

AutoCloner maintained by Alex Coulton.