Multiple sequence alignment - TraesCS3D01G428500

Loading Multiple Alignment...

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 TraesCS3D01G428500 chr3D 100.000 2264 0 0 1 2264 542834696 542836959 0.000000e+00 4181
1 TraesCS3D01G428500 chr7D 96.296 2187 65 9 1 2179 116648207 116650385 0.000000e+00 3576
2 TraesCS3D01G428500 chr2D 96.208 2189 76 6 1 2182 634063059 634060871 0.000000e+00 3576
3 TraesCS3D01G428500 chr1A 96.016 2184 81 4 1 2179 254401241 254403423 0.000000e+00 3546
4 TraesCS3D01G428500 chr1A 95.801 2191 80 5 1 2179 47184079 47181889 0.000000e+00 3526
5 TraesCS3D01G428500 chr5D 95.837 2186 78 7 1 2179 238122176 238124355 0.000000e+00 3520
6 TraesCS3D01G428500 chr4D 95.598 2181 85 4 1 2179 130442933 130440762 0.000000e+00 3485
7 TraesCS3D01G428500 chr4D 94.614 2191 104 9 1 2179 303073155 303075343 0.000000e+00 3380
8 TraesCS3D01G428500 chr5B 95.142 2182 97 7 1 2179 278890060 278892235 0.000000e+00 3434
9 TraesCS3D01G428500 chr2A 95.011 2185 100 8 1 2179 240856331 240858512 0.000000e+00 3422
10 TraesCS3D01G428500 chr3A 96.203 79 3 0 2181 2259 679645459 679645537 1.820000e-26 130


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 TraesCS3D01G428500 chr3D 542834696 542836959 2263 False 4181 4181 100.000 1 2264 1 chr3D.!!$F1 2263
1 TraesCS3D01G428500 chr7D 116648207 116650385 2178 False 3576 3576 96.296 1 2179 1 chr7D.!!$F1 2178
2 TraesCS3D01G428500 chr2D 634060871 634063059 2188 True 3576 3576 96.208 1 2182 1 chr2D.!!$R1 2181
3 TraesCS3D01G428500 chr1A 254401241 254403423 2182 False 3546 3546 96.016 1 2179 1 chr1A.!!$F1 2178
4 TraesCS3D01G428500 chr1A 47181889 47184079 2190 True 3526 3526 95.801 1 2179 1 chr1A.!!$R1 2178
5 TraesCS3D01G428500 chr5D 238122176 238124355 2179 False 3520 3520 95.837 1 2179 1 chr5D.!!$F1 2178
6 TraesCS3D01G428500 chr4D 130440762 130442933 2171 True 3485 3485 95.598 1 2179 1 chr4D.!!$R1 2178
7 TraesCS3D01G428500 chr4D 303073155 303075343 2188 False 3380 3380 94.614 1 2179 1 chr4D.!!$F1 2178
8 TraesCS3D01G428500 chr5B 278890060 278892235 2175 False 3434 3434 95.142 1 2179 1 chr5B.!!$F1 2178
9 TraesCS3D01G428500 chr2A 240856331 240858512 2181 False 3422 3422 95.011 1 2179 1 chr2A.!!$F1 2178

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
931 954 1.065709 GTCCTCGATGGCCCTAACAAA 60.066 52.381 0.0 0.0 35.26 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2190 2234 0.03392 TGCTGATATGCAGGTAGGCG 59.966 55.0 0.0 0.0 45.03 5.52 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
188 189 1.284982 CTTGTCTTGTCCGACAGCCG 61.285 60.000 0.64 0.00 44.02 5.52
247 248 1.341285 CCCAGATGGCACCTGATTCAA 60.341 52.381 11.42 0.00 33.65 2.69
310 314 3.119602 CGTTGAGCCAACTACTACTGCTA 60.120 47.826 13.76 0.00 41.62 3.49
382 401 1.872952 CGAACAACATGAAGTGGCAGA 59.127 47.619 0.00 0.00 0.00 4.26
384 403 2.346766 ACAACATGAAGTGGCAGACA 57.653 45.000 0.00 0.00 0.00 3.41
472 492 1.242076 CTTCAAGGAGGTGCACTTGG 58.758 55.000 17.98 1.16 43.20 3.61
581 602 1.204146 GGATCCAAGTGTCCAGGCTA 58.796 55.000 6.95 0.00 34.57 3.93
733 754 4.927425 TCCTAATCGCAACTAACAACACTC 59.073 41.667 0.00 0.00 0.00 3.51
931 954 1.065709 GTCCTCGATGGCCCTAACAAA 60.066 52.381 0.00 0.00 35.26 2.83
1278 1305 0.820871 ACTAGAGTAGTGCTGCCTGC 59.179 55.000 0.00 0.00 37.69 4.85
1418 1448 5.102956 AGGTGGTATATACTAACCCCTCACA 60.103 44.000 23.55 6.06 33.62 3.58
1420 1450 5.011431 GTGGTATATACTAACCCCTCACACC 59.989 48.000 12.54 0.00 34.69 4.16
1454 1484 1.190178 GGTGGTAGGACGACACCCTT 61.190 60.000 0.00 0.00 46.90 3.95
1593 1630 1.135575 GCTACTTGTGTGCTCCATTGC 60.136 52.381 0.00 0.00 0.00 3.56
1754 1797 1.002544 GTTCAAGACTAGGCAGGCAGT 59.997 52.381 0.00 0.00 28.86 4.40
1834 1877 1.444933 TGGAGGTGTCAAGGTGGATT 58.555 50.000 0.00 0.00 0.00 3.01
1998 2041 3.353029 CGCCGTGTTCATGTGCCA 61.353 61.111 0.00 0.00 0.00 4.92
2135 2179 0.404040 CCAGGCTGGTTTGGGAAGTA 59.596 55.000 25.74 0.00 31.35 2.24
2179 2223 3.532155 GGCAACCAAACACGCCCA 61.532 61.111 0.00 0.00 38.67 5.36
2182 2226 0.741221 GCAACCAAACACGCCCAAAA 60.741 50.000 0.00 0.00 0.00 2.44
2183 2227 1.726853 CAACCAAACACGCCCAAAAA 58.273 45.000 0.00 0.00 0.00 1.94
2184 2228 1.663135 CAACCAAACACGCCCAAAAAG 59.337 47.619 0.00 0.00 0.00 2.27
2185 2229 1.187087 ACCAAACACGCCCAAAAAGA 58.813 45.000 0.00 0.00 0.00 2.52
2186 2230 1.134936 ACCAAACACGCCCAAAAAGAC 60.135 47.619 0.00 0.00 0.00 3.01
2187 2231 1.196200 CAAACACGCCCAAAAAGACG 58.804 50.000 0.00 0.00 0.00 4.18
2188 2232 1.096416 AAACACGCCCAAAAAGACGA 58.904 45.000 0.00 0.00 0.00 4.20
2189 2233 0.379316 AACACGCCCAAAAAGACGAC 59.621 50.000 0.00 0.00 0.00 4.34
2190 2234 1.281656 CACGCCCAAAAAGACGACC 59.718 57.895 0.00 0.00 0.00 4.79
2191 2235 2.248835 ACGCCCAAAAAGACGACCG 61.249 57.895 0.00 0.00 0.00 4.79
2192 2236 2.254350 GCCCAAAAAGACGACCGC 59.746 61.111 0.00 0.00 0.00 5.68
2193 2237 2.951458 CCCAAAAAGACGACCGCC 59.049 61.111 0.00 0.00 0.00 6.13
2194 2238 1.599797 CCCAAAAAGACGACCGCCT 60.600 57.895 0.00 0.00 0.00 5.52
2195 2239 0.320946 CCCAAAAAGACGACCGCCTA 60.321 55.000 0.00 0.00 0.00 3.93
2196 2240 0.794473 CCAAAAAGACGACCGCCTAC 59.206 55.000 0.00 0.00 0.00 3.18
2197 2241 0.794473 CAAAAAGACGACCGCCTACC 59.206 55.000 0.00 0.00 0.00 3.18
2198 2242 0.683412 AAAAAGACGACCGCCTACCT 59.317 50.000 0.00 0.00 0.00 3.08
2199 2243 0.037605 AAAAGACGACCGCCTACCTG 60.038 55.000 0.00 0.00 0.00 4.00
2200 2244 2.502692 AAAGACGACCGCCTACCTGC 62.503 60.000 0.00 0.00 0.00 4.85
2201 2245 3.755628 GACGACCGCCTACCTGCA 61.756 66.667 0.00 0.00 0.00 4.41
2202 2246 3.075005 ACGACCGCCTACCTGCAT 61.075 61.111 0.00 0.00 0.00 3.96
2203 2247 1.731433 GACGACCGCCTACCTGCATA 61.731 60.000 0.00 0.00 0.00 3.14
2204 2248 1.113517 ACGACCGCCTACCTGCATAT 61.114 55.000 0.00 0.00 0.00 1.78
2205 2249 0.388649 CGACCGCCTACCTGCATATC 60.389 60.000 0.00 0.00 0.00 1.63
2206 2250 0.679505 GACCGCCTACCTGCATATCA 59.320 55.000 0.00 0.00 0.00 2.15
2207 2251 0.681733 ACCGCCTACCTGCATATCAG 59.318 55.000 0.00 0.00 42.49 2.90
2208 2252 0.671781 CCGCCTACCTGCATATCAGC 60.672 60.000 0.00 0.00 41.50 4.26
2209 2253 0.033920 CGCCTACCTGCATATCAGCA 59.966 55.000 0.00 0.00 41.50 4.41
2210 2254 1.338484 CGCCTACCTGCATATCAGCAT 60.338 52.381 0.00 0.00 44.68 3.79
2211 2255 2.094026 CGCCTACCTGCATATCAGCATA 60.094 50.000 0.00 0.00 44.68 3.14
2212 2256 3.431346 CGCCTACCTGCATATCAGCATAT 60.431 47.826 0.00 0.00 44.68 1.78
2213 2257 3.875727 GCCTACCTGCATATCAGCATATG 59.124 47.826 0.00 0.00 44.68 1.78
2219 2263 2.430828 CATATCAGCATATGCACGCG 57.569 50.000 28.62 14.10 45.16 6.01
2220 2264 0.723414 ATATCAGCATATGCACGCGC 59.277 50.000 28.62 0.00 45.16 6.86
2235 2279 4.079446 CGCAGCTTTCCTTGGGAA 57.921 55.556 0.00 0.00 40.27 3.97
2236 2280 2.571548 CGCAGCTTTCCTTGGGAAT 58.428 52.632 0.00 0.00 41.71 3.01
2237 2281 0.890683 CGCAGCTTTCCTTGGGAATT 59.109 50.000 0.00 0.00 41.71 2.17
2238 2282 2.091541 CGCAGCTTTCCTTGGGAATTA 58.908 47.619 0.00 0.00 41.71 1.40
2239 2283 2.689983 CGCAGCTTTCCTTGGGAATTAT 59.310 45.455 0.00 0.00 41.71 1.28
2240 2284 3.243201 CGCAGCTTTCCTTGGGAATTATC 60.243 47.826 0.00 0.00 41.71 1.75
2241 2285 3.701040 GCAGCTTTCCTTGGGAATTATCA 59.299 43.478 0.00 0.00 41.71 2.15
2242 2286 4.160252 GCAGCTTTCCTTGGGAATTATCAA 59.840 41.667 0.00 0.00 41.71 2.57
2243 2287 5.163374 GCAGCTTTCCTTGGGAATTATCAAT 60.163 40.000 0.00 0.00 41.71 2.57
2244 2288 6.278363 CAGCTTTCCTTGGGAATTATCAATG 58.722 40.000 0.00 0.00 41.71 2.82
2245 2289 5.364735 AGCTTTCCTTGGGAATTATCAATGG 59.635 40.000 0.00 0.00 41.71 3.16
2246 2290 5.604565 CTTTCCTTGGGAATTATCAATGGC 58.395 41.667 0.00 0.00 41.71 4.40
2247 2291 4.262891 TCCTTGGGAATTATCAATGGCA 57.737 40.909 0.00 0.00 0.00 4.92
2248 2292 3.960102 TCCTTGGGAATTATCAATGGCAC 59.040 43.478 0.00 0.00 0.00 5.01
2249 2293 6.048157 TTCCTTGGGAATTATCAATGGCACA 61.048 40.000 0.00 0.00 39.05 4.57
2250 2294 7.321017 TTCCTTGGGAATTATCAATGGCACAT 61.321 38.462 0.00 0.00 39.22 3.21
2251 2295 8.735066 TTCCTTGGGAATTATCAATGGCACATT 61.735 37.037 0.00 0.00 39.22 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
188 189 1.399727 CGACAAACGATGGAGCAAACC 60.400 52.381 0.00 0.00 45.77 3.27
216 217 1.135094 CCATCTGGGACATAGGCTGT 58.865 55.000 0.00 0.00 42.15 4.40
247 248 1.339151 GGAATCAGAGGCGAACACCTT 60.339 52.381 0.00 0.00 41.32 3.50
382 401 1.798223 CACGAACGTGGACATGAATGT 59.202 47.619 17.83 0.00 42.00 2.71
384 403 0.796312 GCACGAACGTGGACATGAAT 59.204 50.000 24.71 0.00 45.49 2.57
472 492 2.551270 CTGCTTCGCAACGGTGTC 59.449 61.111 0.66 0.00 38.41 3.67
552 573 2.093447 ACACTTGGATCCATCGACTTCC 60.093 50.000 17.06 0.00 0.00 3.46
733 754 3.435671 GGTGGTCCTAAGAATGAAACACG 59.564 47.826 0.00 0.00 0.00 4.49
1278 1305 2.969238 GGGGATCATGCACGCTCG 60.969 66.667 0.00 0.00 0.00 5.03
1418 1448 0.971386 ACCGTAAGTTCACCATCGGT 59.029 50.000 0.00 0.00 44.87 4.69
1420 1450 1.337447 ACCACCGTAAGTTCACCATCG 60.337 52.381 0.00 0.00 0.00 3.84
1433 1463 2.270986 GGTGTCGTCCTACCACCGT 61.271 63.158 0.00 0.00 39.29 4.83
1454 1484 3.603965 ACCTACCACCACATCCAAAAA 57.396 42.857 0.00 0.00 0.00 1.94
1593 1630 2.034305 AGCAAGAGTTGAAGCAGCAAAG 59.966 45.455 0.00 0.00 0.00 2.77
1754 1797 3.192844 CCAGTCGGAGTAAGCTTGTTCTA 59.807 47.826 9.86 0.00 0.00 2.10
1834 1877 0.183492 AGCTTCAGCCCAAACTGACA 59.817 50.000 0.00 0.00 46.13 3.58
1998 2041 2.045926 GCCTGCATTGACCCGAGT 60.046 61.111 0.00 0.00 0.00 4.18
2135 2179 1.303074 CAGGGCCTGCATCGCATAT 60.303 57.895 22.68 0.00 38.13 1.78
2179 2223 0.683412 AGGTAGGCGGTCGTCTTTTT 59.317 50.000 2.01 0.00 0.00 1.94
2182 2226 3.003113 GCAGGTAGGCGGTCGTCTT 62.003 63.158 2.01 0.00 0.00 3.01
2183 2227 3.450115 GCAGGTAGGCGGTCGTCT 61.450 66.667 2.37 2.37 0.00 4.18
2184 2228 1.731433 TATGCAGGTAGGCGGTCGTC 61.731 60.000 0.00 0.00 36.28 4.20
2185 2229 1.113517 ATATGCAGGTAGGCGGTCGT 61.114 55.000 0.00 0.00 36.28 4.34
2186 2230 0.388649 GATATGCAGGTAGGCGGTCG 60.389 60.000 0.00 0.00 36.28 4.79
2187 2231 0.679505 TGATATGCAGGTAGGCGGTC 59.320 55.000 0.00 0.00 36.28 4.79
2188 2232 0.681733 CTGATATGCAGGTAGGCGGT 59.318 55.000 0.00 0.00 41.07 5.68
2189 2233 0.671781 GCTGATATGCAGGTAGGCGG 60.672 60.000 0.00 0.00 45.03 6.13
2190 2234 0.033920 TGCTGATATGCAGGTAGGCG 59.966 55.000 0.00 0.00 45.03 5.52
2191 2235 2.486472 ATGCTGATATGCAGGTAGGC 57.514 50.000 0.00 0.00 46.71 3.93
2200 2244 1.528400 GCGCGTGCATATGCTGATATG 60.528 52.381 27.13 13.87 43.12 1.78
2201 2245 0.723414 GCGCGTGCATATGCTGATAT 59.277 50.000 27.13 0.00 42.66 1.63
2202 2246 2.153039 GCGCGTGCATATGCTGATA 58.847 52.632 27.13 5.26 42.66 2.15
2203 2247 2.941333 GCGCGTGCATATGCTGAT 59.059 55.556 27.13 0.00 42.66 2.90
2213 2257 4.030452 AAGGAAAGCTGCGCGTGC 62.030 61.111 15.48 15.48 43.20 5.34
2214 2258 2.127118 CAAGGAAAGCTGCGCGTG 60.127 61.111 8.43 1.88 0.00 5.34
2215 2259 3.357079 CCAAGGAAAGCTGCGCGT 61.357 61.111 8.43 0.00 0.00 6.01
2216 2260 4.107051 CCCAAGGAAAGCTGCGCG 62.107 66.667 0.00 0.00 0.00 6.86
2217 2261 1.598701 ATTCCCAAGGAAAGCTGCGC 61.599 55.000 0.00 0.00 45.41 6.09
2218 2262 0.890683 AATTCCCAAGGAAAGCTGCG 59.109 50.000 0.00 0.00 45.41 5.18
2219 2263 3.701040 TGATAATTCCCAAGGAAAGCTGC 59.299 43.478 0.00 0.00 45.41 5.25
2220 2264 5.920193 TTGATAATTCCCAAGGAAAGCTG 57.080 39.130 0.00 0.00 45.41 4.24
2221 2265 5.364735 CCATTGATAATTCCCAAGGAAAGCT 59.635 40.000 0.00 0.00 45.41 3.74
2222 2266 5.604565 CCATTGATAATTCCCAAGGAAAGC 58.395 41.667 0.00 0.00 45.41 3.51
2223 2267 5.129155 TGCCATTGATAATTCCCAAGGAAAG 59.871 40.000 0.00 0.00 45.41 2.62
2224 2268 5.028802 TGCCATTGATAATTCCCAAGGAAA 58.971 37.500 0.00 0.00 45.41 3.13
2225 2269 4.405358 GTGCCATTGATAATTCCCAAGGAA 59.595 41.667 0.00 0.00 46.39 3.36
2226 2270 3.960102 GTGCCATTGATAATTCCCAAGGA 59.040 43.478 6.11 0.00 0.00 3.36
2227 2271 3.705579 TGTGCCATTGATAATTCCCAAGG 59.294 43.478 0.00 0.00 0.00 3.61
2228 2272 5.540400 ATGTGCCATTGATAATTCCCAAG 57.460 39.130 0.00 0.00 0.00 3.61
2229 2273 5.396548 CCAATGTGCCATTGATAATTCCCAA 60.397 40.000 22.11 0.00 0.00 4.12
2230 2274 4.101274 CCAATGTGCCATTGATAATTCCCA 59.899 41.667 22.11 0.00 0.00 4.37
2231 2275 4.634199 CCAATGTGCCATTGATAATTCCC 58.366 43.478 22.11 0.00 0.00 3.97
2232 2276 4.060205 GCCAATGTGCCATTGATAATTCC 58.940 43.478 22.11 5.15 0.00 3.01
2233 2277 3.737266 CGCCAATGTGCCATTGATAATTC 59.263 43.478 22.11 8.55 0.00 2.17
2234 2278 3.719924 CGCCAATGTGCCATTGATAATT 58.280 40.909 22.11 0.00 0.00 1.40
2235 2279 2.546373 GCGCCAATGTGCCATTGATAAT 60.546 45.455 22.11 0.00 42.25 1.28
2236 2280 1.202394 GCGCCAATGTGCCATTGATAA 60.202 47.619 22.11 0.00 42.25 1.75
2237 2281 0.385029 GCGCCAATGTGCCATTGATA 59.615 50.000 22.11 0.00 42.25 2.15
2238 2282 1.142314 GCGCCAATGTGCCATTGAT 59.858 52.632 22.11 0.00 42.25 2.57
2239 2283 2.572812 GCGCCAATGTGCCATTGA 59.427 55.556 22.11 0.00 42.25 2.57


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

AutoCloner maintained by Alex Coulton.