Multiple sequence alignment - TraesCS6B01G000600

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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 TraesCS6B01G000600 chr6B 100.000 2300 0 0 1 2300 261755 259456 0.000000e+00 4248
1 TraesCS6B01G000600 chr6B 93.662 2272 95 22 1 2249 551634323 551632078 0.000000e+00 3352
2 TraesCS6B01G000600 chr6B 93.486 2272 100 21 1 2249 551414312 551412066 0.000000e+00 3332
3 TraesCS6B01G000600 chr6B 93.046 2272 109 20 1 2249 551318647 551316402 0.000000e+00 3275
4 TraesCS6B01G000600 chr6B 92.917 2273 112 23 1 2249 551257912 551255665 0.000000e+00 3260
5 TraesCS6B01G000600 chr6B 92.694 2272 116 22 1 2249 551161121 551158877 0.000000e+00 3230
6 TraesCS6B01G000600 chr6B 92.565 2273 118 23 1 2249 551503967 551501722 0.000000e+00 3214
7 TraesCS6B01G000600 chr6B 92.606 2272 108 23 1 2249 551565451 551563217 0.000000e+00 3210
8 TraesCS6B01G000600 chr6A 95.757 2239 68 9 1 2223 1403432 1405659 0.000000e+00 3583
9 TraesCS6B01G000600 chr6A 91.543 473 20 4 1790 2242 53912301 53912773 3.220000e-178 634
10 TraesCS6B01G000600 chr5B 94.996 2258 76 15 8 2241 526525324 526523080 0.000000e+00 3509
11 TraesCS6B01G000600 chr5B 90.698 473 22 6 1790 2240 47284855 47284383 5.430000e-171 610
12 TraesCS6B01G000600 chr4B 94.902 2256 86 10 1 2236 28261899 28259653 0.000000e+00 3502
13 TraesCS6B01G000600 chr4B 91.026 468 21 5 1790 2236 245488767 245489234 1.510000e-171 612
14 TraesCS6B01G000600 chr4A 91.405 477 20 5 1790 2245 706654289 706653813 3.220000e-178 634
15 TraesCS6B01G000600 chr1B 91.045 469 21 5 1790 2237 588241276 588240808 4.200000e-172 614


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 TraesCS6B01G000600 chr6B 259456 261755 2299 True 4248 4248 100.000 1 2300 1 chr6B.!!$R1 2299
1 TraesCS6B01G000600 chr6B 551632078 551634323 2245 True 3352 3352 93.662 1 2249 1 chr6B.!!$R8 2248
2 TraesCS6B01G000600 chr6B 551412066 551414312 2246 True 3332 3332 93.486 1 2249 1 chr6B.!!$R5 2248
3 TraesCS6B01G000600 chr6B 551316402 551318647 2245 True 3275 3275 93.046 1 2249 1 chr6B.!!$R4 2248
4 TraesCS6B01G000600 chr6B 551255665 551257912 2247 True 3260 3260 92.917 1 2249 1 chr6B.!!$R3 2248
5 TraesCS6B01G000600 chr6B 551158877 551161121 2244 True 3230 3230 92.694 1 2249 1 chr6B.!!$R2 2248
6 TraesCS6B01G000600 chr6B 551501722 551503967 2245 True 3214 3214 92.565 1 2249 1 chr6B.!!$R6 2248
7 TraesCS6B01G000600 chr6B 551563217 551565451 2234 True 3210 3210 92.606 1 2249 1 chr6B.!!$R7 2248
8 TraesCS6B01G000600 chr6A 1403432 1405659 2227 False 3583 3583 95.757 1 2223 1 chr6A.!!$F1 2222
9 TraesCS6B01G000600 chr5B 526523080 526525324 2244 True 3509 3509 94.996 8 2241 1 chr5B.!!$R2 2233
10 TraesCS6B01G000600 chr4B 28259653 28261899 2246 True 3502 3502 94.902 1 2236 1 chr4B.!!$R1 2235

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
158 162 0.179026 CGATGTAGGAGGACGAGGGA 60.179 60.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1475 1487 0.468226 ACTCAACTTTGTCAGCCCGA 59.532 50.0 0.0 0.0 0.0 5.14 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
158 162 0.179026 CGATGTAGGAGGACGAGGGA 60.179 60.000 0.00 0.00 0.00 4.20
289 293 1.748879 GCGGCTGCCATGAAGGTTA 60.749 57.895 20.29 0.00 40.61 2.85
290 294 1.312371 GCGGCTGCCATGAAGGTTAA 61.312 55.000 20.29 0.00 40.61 2.01
512 521 2.368221 AGATGCTACTGAGAAGGATGGC 59.632 50.000 0.00 0.00 0.00 4.40
572 581 5.783111 AGGTTGGTATTTTTGCATGACTTC 58.217 37.500 0.00 0.00 0.00 3.01
642 651 0.464452 GGGACCGACAGGAGTTATGG 59.536 60.000 0.00 0.00 41.02 2.74
841 850 5.968848 GCGACTTGATTTTCTGTGTTGTTAA 59.031 36.000 0.00 0.00 0.00 2.01
1132 1143 7.978414 GCGAAGATCATCTTATCTATCCATCAA 59.022 37.037 0.00 0.00 36.73 2.57
1475 1487 0.769247 AACTAACCTGGCCCTTTCGT 59.231 50.000 0.00 0.00 0.00 3.85
1534 1547 5.651387 GCTGAGGAGTCTGCATACATATA 57.349 43.478 4.92 0.00 44.81 0.86
1535 1548 6.219417 GCTGAGGAGTCTGCATACATATAT 57.781 41.667 4.92 0.00 44.81 0.86
1536 1549 7.340122 GCTGAGGAGTCTGCATACATATATA 57.660 40.000 4.92 0.00 44.81 0.86
1537 1550 7.950512 GCTGAGGAGTCTGCATACATATATAT 58.049 38.462 4.92 0.00 44.81 0.86
1538 1551 9.072375 GCTGAGGAGTCTGCATACATATATATA 57.928 37.037 4.92 0.00 44.81 0.86
1846 1871 9.408648 TGTGTATGAGAACTGATTCAGAGTATA 57.591 33.333 20.33 8.23 37.29 1.47
1868 1893 2.571212 TGGTCATTTGCGTTCTCAAGT 58.429 42.857 0.00 0.00 0.00 3.16
1916 1941 4.830046 AGAGAATGATACACGAGCCAGTAT 59.170 41.667 0.00 0.00 33.85 2.12
1969 1994 8.682710 TCATTACAAAATGGTTGGCTAGATAAC 58.317 33.333 0.00 0.00 42.40 1.89
2100 2137 7.739825 TCTATTTGTTGATCTTCTATCCCCTG 58.260 38.462 0.00 0.00 0.00 4.45
2113 2150 2.225596 CCCCTGTCCACCCCGTTTA 61.226 63.158 0.00 0.00 0.00 2.01
2184 2221 8.954950 TTGAACATGTTTTGATGTTTATTGGT 57.045 26.923 13.36 0.00 44.78 3.67
2191 2228 6.426328 TGTTTTGATGTTTATTGGTGGCATTC 59.574 34.615 0.00 0.00 0.00 2.67
2277 2316 9.877178 ATAATCTCTCCCTAATAATAAAGCACG 57.123 33.333 0.00 0.00 0.00 5.34
2278 2317 6.097915 TCTCTCCCTAATAATAAAGCACGG 57.902 41.667 0.00 0.00 0.00 4.94
2279 2318 5.836898 TCTCTCCCTAATAATAAAGCACGGA 59.163 40.000 0.00 0.00 0.00 4.69
2280 2319 6.497259 TCTCTCCCTAATAATAAAGCACGGAT 59.503 38.462 0.00 0.00 0.00 4.18
2281 2320 7.016268 TCTCTCCCTAATAATAAAGCACGGATT 59.984 37.037 0.00 0.00 0.00 3.01
2282 2321 6.934645 TCTCCCTAATAATAAAGCACGGATTG 59.065 38.462 0.00 0.00 0.00 2.67
2283 2322 6.001460 TCCCTAATAATAAAGCACGGATTGG 58.999 40.000 0.00 0.00 0.00 3.16
2284 2323 5.183140 CCCTAATAATAAAGCACGGATTGGG 59.817 44.000 0.00 0.00 0.00 4.12
2285 2324 5.768164 CCTAATAATAAAGCACGGATTGGGT 59.232 40.000 0.00 0.00 0.00 4.51
2286 2325 6.264518 CCTAATAATAAAGCACGGATTGGGTT 59.735 38.462 0.00 0.00 0.00 4.11
2287 2326 6.538945 AATAATAAAGCACGGATTGGGTTT 57.461 33.333 0.00 0.00 38.21 3.27
2288 2327 4.450082 AATAAAGCACGGATTGGGTTTC 57.550 40.909 0.00 0.00 36.30 2.78
2289 2328 0.966179 AAAGCACGGATTGGGTTTCC 59.034 50.000 0.00 0.00 29.48 3.13
2296 2335 1.611519 GGATTGGGTTTCCGTGTTCA 58.388 50.000 0.00 0.00 35.24 3.18
2297 2336 1.268625 GGATTGGGTTTCCGTGTTCAC 59.731 52.381 0.00 0.00 35.24 3.18
2298 2337 1.268625 GATTGGGTTTCCGTGTTCACC 59.731 52.381 0.00 0.00 35.24 4.02
2299 2338 1.096386 TTGGGTTTCCGTGTTCACCG 61.096 55.000 0.00 0.00 35.24 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 90 3.741830 TTGACTGCGGGCGAACACA 62.742 57.895 0.00 0.00 0.00 3.72
88 92 2.031919 ATTGACTGCGGGCGAACA 59.968 55.556 0.00 0.00 0.00 3.18
572 581 8.757164 ATGCAACAGAATTTATATCATGCATG 57.243 30.769 21.07 21.07 36.85 4.06
642 651 0.109597 CACAATGCTTCCAACCGCTC 60.110 55.000 0.00 0.00 0.00 5.03
1132 1143 2.885135 TGTTGTGCTGGGATGATTCT 57.115 45.000 0.00 0.00 0.00 2.40
1312 1324 9.128107 ACTTGTCATCTTAATTATGCAAAAACG 57.872 29.630 0.00 0.00 0.00 3.60
1409 1421 5.981088 AAAACATGGAGCAATGACACATA 57.019 34.783 0.00 0.00 0.00 2.29
1475 1487 0.468226 ACTCAACTTTGTCAGCCCGA 59.532 50.000 0.00 0.00 0.00 5.14
1503 1516 3.254166 GCAGACTCCTCAGCAAAATTGAA 59.746 43.478 0.00 0.00 0.00 2.69
1534 1547 3.159070 CGCGCACGCAGCATATAT 58.841 55.556 16.04 0.00 46.13 0.86
1553 1568 2.930562 GGTGTCTGGGCAGAGGGT 60.931 66.667 0.00 0.00 38.27 4.34
1562 1577 1.374758 GAGCCTTGACGGTGTCTGG 60.375 63.158 0.00 2.53 33.15 3.86
1815 1836 5.928264 TGAATCAGTTCTCATACACACACTG 59.072 40.000 0.00 0.00 35.33 3.66
1846 1871 3.569701 ACTTGAGAACGCAAATGACCAAT 59.430 39.130 0.00 0.00 0.00 3.16
1880 1905 7.543868 GTGTATCATTCTCTCCCATAGAAATCG 59.456 40.741 0.00 0.00 36.60 3.34
1969 1994 9.371333 GTGATCATATATAGTAGAATGCGTACG 57.629 37.037 11.84 11.84 0.00 3.67
2079 2116 5.339200 GGACAGGGGATAGAAGATCAACAAA 60.339 44.000 0.00 0.00 0.00 2.83
2100 2137 2.081462 CATGAGTTAAACGGGGTGGAC 58.919 52.381 0.00 0.00 0.00 4.02
2113 2150 5.200483 TCTTTGAAAGTGGGAACATGAGTT 58.800 37.500 4.68 0.00 46.14 3.01
2251 2290 9.877178 CGTGCTTTATTATTAGGGAGAGATTAT 57.123 33.333 0.00 0.00 0.00 1.28
2252 2291 8.311836 CCGTGCTTTATTATTAGGGAGAGATTA 58.688 37.037 0.00 0.00 0.00 1.75
2253 2292 7.016268 TCCGTGCTTTATTATTAGGGAGAGATT 59.984 37.037 0.00 0.00 0.00 2.40
2254 2293 6.497259 TCCGTGCTTTATTATTAGGGAGAGAT 59.503 38.462 0.00 0.00 0.00 2.75
2255 2294 5.836898 TCCGTGCTTTATTATTAGGGAGAGA 59.163 40.000 0.00 0.00 0.00 3.10
2256 2295 6.097915 TCCGTGCTTTATTATTAGGGAGAG 57.902 41.667 0.00 0.00 0.00 3.20
2257 2296 6.681729 ATCCGTGCTTTATTATTAGGGAGA 57.318 37.500 0.00 0.00 0.00 3.71
2258 2297 6.149474 CCAATCCGTGCTTTATTATTAGGGAG 59.851 42.308 0.00 0.00 0.00 4.30
2259 2298 6.001460 CCAATCCGTGCTTTATTATTAGGGA 58.999 40.000 0.00 0.00 0.00 4.20
2260 2299 5.183140 CCCAATCCGTGCTTTATTATTAGGG 59.817 44.000 0.00 0.00 0.00 3.53
2261 2300 5.768164 ACCCAATCCGTGCTTTATTATTAGG 59.232 40.000 0.00 0.00 0.00 2.69
2262 2301 6.877611 ACCCAATCCGTGCTTTATTATTAG 57.122 37.500 0.00 0.00 0.00 1.73
2263 2302 7.201839 GGAAACCCAATCCGTGCTTTATTATTA 60.202 37.037 0.00 0.00 0.00 0.98
2264 2303 6.406512 GGAAACCCAATCCGTGCTTTATTATT 60.407 38.462 0.00 0.00 0.00 1.40
2265 2304 5.068591 GGAAACCCAATCCGTGCTTTATTAT 59.931 40.000 0.00 0.00 0.00 1.28
2266 2305 4.399934 GGAAACCCAATCCGTGCTTTATTA 59.600 41.667 0.00 0.00 0.00 0.98
2267 2306 3.194755 GGAAACCCAATCCGTGCTTTATT 59.805 43.478 0.00 0.00 0.00 1.40
2268 2307 2.758423 GGAAACCCAATCCGTGCTTTAT 59.242 45.455 0.00 0.00 0.00 1.40
2269 2308 2.164338 GGAAACCCAATCCGTGCTTTA 58.836 47.619 0.00 0.00 0.00 1.85
2270 2309 0.966179 GGAAACCCAATCCGTGCTTT 59.034 50.000 0.00 0.00 0.00 3.51
2271 2310 2.653557 GGAAACCCAATCCGTGCTT 58.346 52.632 0.00 0.00 0.00 3.91
2272 2311 4.415783 GGAAACCCAATCCGTGCT 57.584 55.556 0.00 0.00 0.00 4.40
2277 2316 1.268625 GTGAACACGGAAACCCAATCC 59.731 52.381 0.00 0.00 0.00 3.01
2278 2317 1.268625 GGTGAACACGGAAACCCAATC 59.731 52.381 0.00 0.00 0.00 2.67
2279 2318 1.324383 GGTGAACACGGAAACCCAAT 58.676 50.000 0.00 0.00 0.00 3.16
2280 2319 1.096386 CGGTGAACACGGAAACCCAA 61.096 55.000 6.66 0.00 34.05 4.12
2281 2320 1.524165 CGGTGAACACGGAAACCCA 60.524 57.895 6.66 0.00 34.05 4.51
2282 2321 3.336566 CGGTGAACACGGAAACCC 58.663 61.111 6.66 0.00 34.05 4.11


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

AutoCloner maintained by Alex Coulton.