Multiple sequence alignment - TraesCS6B01G226500

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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 TraesCS6B01G226500 chr6B 100.000 2312 0 0 1 2312 348687218 348689529 0.000000e+00 4270
1 TraesCS6B01G226500 chr6B 99.222 1929 15 0 1 1929 348659341 348657413 0.000000e+00 3480
2 TraesCS6B01G226500 chr6A 89.618 1310 60 24 467 1732 322984638 322985915 0.000000e+00 1596
3 TraesCS6B01G226500 chr6A 89.169 397 27 7 1915 2311 322993797 322994177 4.470000e-132 481
4 TraesCS6B01G226500 chr6A 83.019 477 61 10 1 458 322982320 322982795 4.600000e-112 414
5 TraesCS6B01G226500 chr6A 94.382 178 10 0 1736 1913 322993587 322993764 8.140000e-70 274
6 TraesCS6B01G226500 chr6D 89.286 1260 45 31 466 1669 262290482 262289257 0.000000e+00 1496
7 TraesCS6B01G226500 chr6D 88.834 403 24 9 1915 2311 262277930 262277543 2.080000e-130 475
8 TraesCS6B01G226500 chr6D 90.458 262 21 1 1654 1915 262278218 262277961 2.200000e-90 342
9 TraesCS6B01G226500 chr6D 82.507 343 55 3 2 339 461525388 461525046 1.740000e-76 296
10 TraesCS6B01G226500 chr6D 84.942 259 36 3 87 342 305268722 305268980 2.280000e-65 259
11 TraesCS6B01G226500 chr2A 85.088 342 47 4 1 340 656840461 656840122 1.700000e-91 346
12 TraesCS6B01G226500 chr5D 83.871 341 51 4 2 340 360549743 360549405 2.870000e-84 322
13 TraesCS6B01G226500 chr4A 83.140 344 49 6 1 341 690190995 690190658 2.890000e-79 305
14 TraesCS6B01G226500 chr5B 82.421 347 53 3 1 341 496814192 496814536 1.740000e-76 296
15 TraesCS6B01G226500 chr5B 82.515 326 52 5 2 324 478410919 478410596 4.860000e-72 281
16 TraesCS6B01G226500 chr3B 89.744 78 7 1 1 78 719919807 719919883 5.260000e-17 99


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 TraesCS6B01G226500 chr6B 348687218 348689529 2311 False 4270.0 4270 100.0000 1 2312 1 chr6B.!!$F1 2311
1 TraesCS6B01G226500 chr6B 348657413 348659341 1928 True 3480.0 3480 99.2220 1 1929 1 chr6B.!!$R1 1928
2 TraesCS6B01G226500 chr6A 322982320 322985915 3595 False 1005.0 1596 86.3185 1 1732 2 chr6A.!!$F1 1731
3 TraesCS6B01G226500 chr6A 322993587 322994177 590 False 377.5 481 91.7755 1736 2311 2 chr6A.!!$F2 575
4 TraesCS6B01G226500 chr6D 262289257 262290482 1225 True 1496.0 1496 89.2860 466 1669 1 chr6D.!!$R1 1203
5 TraesCS6B01G226500 chr6D 262277543 262278218 675 True 408.5 475 89.6460 1654 2311 2 chr6D.!!$R3 657

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
1325 3223 4.644103 ACGCGTAGGATTGTGTAAGTAT 57.356 40.909 11.67 0.0 0.0 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2269 4234 0.694196 GGGGTTGCTGGTAGGTTGTA 59.306 55.0 0.0 0.0 0.0 2.41 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
1325 3223 4.644103 ACGCGTAGGATTGTGTAAGTAT 57.356 40.909 11.67 0.00 0.00 2.12
1506 3408 5.122512 AGCCTATGTTATGTACTGTAGCG 57.877 43.478 0.00 0.00 0.00 4.26
1868 3796 3.590824 CCGGGCTGGTGAATTCAC 58.409 61.111 27.16 27.16 45.72 3.18
1947 3906 3.600388 ACATAACCACTAGCAAGCACTC 58.400 45.455 0.00 0.00 0.00 3.51
1987 3946 3.953712 ATGACACTTGACCATACGACA 57.046 42.857 0.00 0.00 0.00 4.35
2002 3961 3.100862 GACATTTCAGAGGCGCGCC 62.101 63.158 42.34 42.34 0.00 6.53
2020 3984 1.359848 CCTGTGCTGTCCGTACATTC 58.640 55.000 0.00 0.00 37.60 2.67
2021 3985 1.066858 CCTGTGCTGTCCGTACATTCT 60.067 52.381 0.00 0.00 37.60 2.40
2159 4123 4.361783 TGATACTTGAGATCCCAACCTGA 58.638 43.478 0.00 0.00 0.00 3.86
2222 4187 4.871933 TGAGGATCATGTACGTATGCAT 57.128 40.909 3.79 3.79 42.56 3.96
2223 4188 5.975693 TGAGGATCATGTACGTATGCATA 57.024 39.130 1.16 1.16 42.56 3.14
2224 4189 5.954335 TGAGGATCATGTACGTATGCATAG 58.046 41.667 6.67 4.25 42.56 2.23
2225 4190 5.476945 TGAGGATCATGTACGTATGCATAGT 59.523 40.000 6.67 9.94 42.56 2.12
2226 4191 5.714047 AGGATCATGTACGTATGCATAGTG 58.286 41.667 6.67 5.50 28.86 2.74
2227 4192 4.864806 GGATCATGTACGTATGCATAGTGG 59.135 45.833 6.67 2.27 28.86 4.00
2249 4214 5.780282 TGGTAGTGGTATCCAGATATCCAAG 59.220 44.000 0.00 0.00 32.34 3.61
2264 4229 1.699656 CCAAGATCGCGCCACTTCAG 61.700 60.000 0.00 0.00 0.00 3.02
2265 4230 1.016130 CAAGATCGCGCCACTTCAGT 61.016 55.000 0.00 0.00 0.00 3.41
2266 4231 0.530744 AAGATCGCGCCACTTCAGTA 59.469 50.000 0.00 0.00 0.00 2.74
2267 4232 0.530744 AGATCGCGCCACTTCAGTAA 59.469 50.000 0.00 0.00 0.00 2.24
2268 4233 0.924090 GATCGCGCCACTTCAGTAAG 59.076 55.000 0.00 0.00 38.77 2.34
2277 4242 4.321452 CGCCACTTCAGTAAGTACAACCTA 60.321 45.833 0.00 0.00 44.28 3.08
2281 4246 6.157211 CACTTCAGTAAGTACAACCTACCAG 58.843 44.000 0.00 0.00 44.28 4.00
2292 4257 2.125106 CTACCAGCAACCCCGCTC 60.125 66.667 0.00 0.00 41.38 5.03
2311 4276 1.686587 TCCGGATATGCGACAATGACT 59.313 47.619 19.02 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1325 3223 0.607112 TACGCAACCCCAATCGTACA 59.393 50.000 0.00 0.00 36.50 2.90
1506 3408 6.157211 TCAGAAGTTGAGATTAACCGAGAAC 58.843 40.000 0.00 0.00 0.00 3.01
1868 3796 1.614903 TGAAGCTTTCTGTTGCCATGG 59.385 47.619 7.63 7.63 0.00 3.66
1947 3906 2.188837 TTGCGTCTACTACATGCTCG 57.811 50.000 0.00 0.00 0.00 5.03
2002 3961 1.995484 CAGAATGTACGGACAGCACAG 59.005 52.381 6.62 0.00 39.50 3.66
2003 3962 1.616374 TCAGAATGTACGGACAGCACA 59.384 47.619 6.62 0.00 39.50 4.57
2004 3963 2.363788 TCAGAATGTACGGACAGCAC 57.636 50.000 6.62 0.00 39.50 4.40
2020 3984 3.829948 GTGATGTCACAATGGCTTTCAG 58.170 45.455 8.22 0.00 45.75 3.02
2021 3985 3.921119 GTGATGTCACAATGGCTTTCA 57.079 42.857 8.22 0.00 45.75 2.69
2159 4123 7.921304 TGATCATGGTCACAGGCTATATATTT 58.079 34.615 4.01 0.00 0.00 1.40
2214 4179 3.728076 ACCACTACCACTATGCATACG 57.272 47.619 1.16 2.13 0.00 3.06
2216 4181 5.399113 TGGATACCACTACCACTATGCATA 58.601 41.667 6.20 6.20 0.00 3.14
2218 4183 3.641436 CTGGATACCACTACCACTATGCA 59.359 47.826 0.00 0.00 0.00 3.96
2219 4184 3.895656 TCTGGATACCACTACCACTATGC 59.104 47.826 0.00 0.00 0.00 3.14
2220 4185 7.068839 GGATATCTGGATACCACTACCACTATG 59.931 44.444 2.05 0.00 0.00 2.23
2221 4186 7.126733 GGATATCTGGATACCACTACCACTAT 58.873 42.308 2.05 0.00 0.00 2.12
2222 4187 6.046286 TGGATATCTGGATACCACTACCACTA 59.954 42.308 2.05 0.00 0.00 2.74
2223 4188 5.162870 TGGATATCTGGATACCACTACCACT 60.163 44.000 2.05 0.00 0.00 4.00
2224 4189 5.084519 TGGATATCTGGATACCACTACCAC 58.915 45.833 2.05 0.00 0.00 4.16
2225 4190 5.348259 TGGATATCTGGATACCACTACCA 57.652 43.478 2.05 0.00 0.00 3.25
2226 4191 6.017192 TCTTGGATATCTGGATACCACTACC 58.983 44.000 2.05 0.00 30.09 3.18
2227 4192 7.415765 CGATCTTGGATATCTGGATACCACTAC 60.416 44.444 2.05 0.00 30.09 2.73
2249 4214 0.924090 CTTACTGAAGTGGCGCGATC 59.076 55.000 12.10 0.51 0.00 3.69
2264 4229 3.999001 GGTTGCTGGTAGGTTGTACTTAC 59.001 47.826 0.00 0.00 30.79 2.34
2265 4230 3.008266 GGGTTGCTGGTAGGTTGTACTTA 59.992 47.826 0.00 0.00 0.00 2.24
2266 4231 2.224695 GGGTTGCTGGTAGGTTGTACTT 60.225 50.000 0.00 0.00 0.00 2.24
2267 4232 1.350019 GGGTTGCTGGTAGGTTGTACT 59.650 52.381 0.00 0.00 0.00 2.73
2268 4233 1.612462 GGGGTTGCTGGTAGGTTGTAC 60.612 57.143 0.00 0.00 0.00 2.90
2269 4234 0.694196 GGGGTTGCTGGTAGGTTGTA 59.306 55.000 0.00 0.00 0.00 2.41
2292 4257 2.154854 AGTCATTGTCGCATATCCGG 57.845 50.000 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.