Multiple sequence alignment - TraesCS6D01G121100

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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 TraesCS6D01G121100 chr6D 100.000 2615 0 0 1 2615 86143922 86141308 0.000000e+00 4830.0
1 TraesCS6D01G121100 chr6A 92.417 2545 91 33 2 2479 103759990 103757481 0.000000e+00 3537.0
2 TraesCS6D01G121100 chr6A 93.103 58 3 1 2559 2615 103757450 103757393 1.670000e-12 84.2
3 TraesCS6D01G121100 chr6B 93.372 2082 80 23 441 2511 163230634 163228600 0.000000e+00 3027.0
4 TraesCS6D01G121100 chr6B 88.771 472 27 3 2 448 163231130 163230660 2.940000e-154 555.0
5 TraesCS6D01G121100 chr6B 96.226 106 3 1 2510 2615 163228571 163228467 3.460000e-39 172.0
6 TraesCS6D01G121100 chr5A 90.094 424 34 5 2 418 323084342 323084764 6.360000e-151 544.0
7 TraesCS6D01G121100 chr4A 89.614 414 38 2 2 410 113486339 113486752 2.980000e-144 521.0
8 TraesCS6D01G121100 chr7D 80.500 400 58 17 1053 1448 547681351 547680968 3.290000e-74 289.0
9 TraesCS6D01G121100 chr7A 79.950 399 59 17 1053 1448 630869780 630870160 9.220000e-70 274.0
10 TraesCS6D01G121100 chr7B 79.699 399 57 19 1053 1448 590842642 590842265 1.540000e-67 267.0
11 TraesCS6D01G121100 chr2D 83.696 92 11 3 1531 1622 606198801 606198714 1.670000e-12 84.2
12 TraesCS6D01G121100 chr1B 81.522 92 13 2 1531 1622 641140312 641140399 3.610000e-09 73.1


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 TraesCS6D01G121100 chr6D 86141308 86143922 2614 True 4830.000000 4830 100.000000 1 2615 1 chr6D.!!$R1 2614
1 TraesCS6D01G121100 chr6A 103757393 103759990 2597 True 1810.600000 3537 92.760000 2 2615 2 chr6A.!!$R1 2613
2 TraesCS6D01G121100 chr6B 163228467 163231130 2663 True 1251.333333 3027 92.789667 2 2615 3 chr6B.!!$R1 2613

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
286 318 0.185901 ATACATGGATTGGCCGGCTT 59.814 50.0 28.56 11.93 40.66 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2268 2383 0.033601 ACAGAGATCCAGAGCCGAGT 60.034 55.0 0.0 0.0 0.0 4.18 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
119 142 5.049474 GTGTAACACAATGTTCAGAGATGCA 60.049 40.000 0.00 0.00 40.22 3.96
123 146 4.763279 ACACAATGTTCAGAGATGCATTGA 59.237 37.500 18.90 0.00 46.39 2.57
183 206 5.565439 GCCTATGCATCTTTGACAACTGTTT 60.565 40.000 0.19 0.00 37.47 2.83
211 234 5.365021 AGATACTTGGTGGGAGAATTCAG 57.635 43.478 8.44 0.00 0.00 3.02
244 267 5.581085 GGCACTATAGTAGGACTTGTGTTTG 59.419 44.000 4.74 0.00 30.85 2.93
247 270 7.360101 GCACTATAGTAGGACTTGTGTTTGTTG 60.360 40.741 4.74 0.00 30.85 3.33
251 274 1.006639 AGGACTTGTGTTTGTTGGGGT 59.993 47.619 0.00 0.00 0.00 4.95
252 275 1.136110 GGACTTGTGTTTGTTGGGGTG 59.864 52.381 0.00 0.00 0.00 4.61
278 310 4.987408 TGGCAGAAACATACATGGATTG 57.013 40.909 0.00 0.00 0.00 2.67
279 311 3.700539 TGGCAGAAACATACATGGATTGG 59.299 43.478 0.00 0.00 0.00 3.16
280 312 3.491447 GGCAGAAACATACATGGATTGGC 60.491 47.826 0.00 0.00 0.00 4.52
281 313 3.491447 GCAGAAACATACATGGATTGGCC 60.491 47.826 0.00 0.00 37.10 5.36
282 314 2.951642 AGAAACATACATGGATTGGCCG 59.048 45.455 0.00 0.00 40.66 6.13
283 315 1.691196 AACATACATGGATTGGCCGG 58.309 50.000 0.00 0.00 40.66 6.13
284 316 0.823356 ACATACATGGATTGGCCGGC 60.823 55.000 21.18 21.18 40.66 6.13
285 317 0.538057 CATACATGGATTGGCCGGCT 60.538 55.000 28.56 6.33 40.66 5.52
286 318 0.185901 ATACATGGATTGGCCGGCTT 59.814 50.000 28.56 11.93 40.66 4.35
287 319 0.840617 TACATGGATTGGCCGGCTTA 59.159 50.000 28.56 15.26 40.66 3.09
320 352 7.805542 GCAGAAATGAAGTTTAGAAGGAAGAAC 59.194 37.037 0.00 0.00 0.00 3.01
603 673 1.348064 TCCGTCCATCACAGAAAGGT 58.652 50.000 0.00 0.00 0.00 3.50
604 674 1.697432 TCCGTCCATCACAGAAAGGTT 59.303 47.619 0.00 0.00 0.00 3.50
605 675 2.105821 TCCGTCCATCACAGAAAGGTTT 59.894 45.455 0.00 0.00 0.00 3.27
606 676 2.884639 CCGTCCATCACAGAAAGGTTTT 59.115 45.455 0.00 0.00 0.00 2.43
607 677 3.317993 CCGTCCATCACAGAAAGGTTTTT 59.682 43.478 0.00 0.00 0.00 1.94
608 678 4.537015 CGTCCATCACAGAAAGGTTTTTC 58.463 43.478 0.00 0.00 42.44 2.29
609 679 4.556699 CGTCCATCACAGAAAGGTTTTTCC 60.557 45.833 0.00 0.00 42.99 3.13
1859 1962 7.282224 TCCACGGGAAATAGACTGATAATTTTG 59.718 37.037 0.00 0.00 0.00 2.44
1900 2003 0.461163 TTGTGTATCATCCACGGGCG 60.461 55.000 0.00 0.00 35.56 6.13
1901 2004 1.594293 GTGTATCATCCACGGGCGG 60.594 63.158 0.00 0.00 0.00 6.13
1902 2005 2.665185 GTATCATCCACGGGCGGC 60.665 66.667 0.00 0.00 0.00 6.53
1903 2006 4.293648 TATCATCCACGGGCGGCG 62.294 66.667 0.51 0.51 0.00 6.46
1932 2036 4.035909 TGCTGCTGCTGTTATGTTGATATG 59.964 41.667 17.00 0.00 40.48 1.78
1981 2088 8.940397 TGGAAGAAATCAAGAGGAAATTTACT 57.060 30.769 1.41 1.41 0.00 2.24
2005 2119 2.622942 TGTGAACTGGGTCATTTGCTTC 59.377 45.455 0.00 0.00 0.00 3.86
2030 2144 1.266718 GATTGTTGGCTGCTGAACGAA 59.733 47.619 0.00 2.04 0.00 3.85
2062 2176 0.248843 GCTCCTGGAAGAGTGTCTGG 59.751 60.000 0.00 0.00 36.20 3.86
2068 2182 1.230324 GGAAGAGTGTCTGGTTGTGC 58.770 55.000 0.00 0.00 0.00 4.57
2069 2183 1.202698 GGAAGAGTGTCTGGTTGTGCT 60.203 52.381 0.00 0.00 0.00 4.40
2070 2184 1.869767 GAAGAGTGTCTGGTTGTGCTG 59.130 52.381 0.00 0.00 0.00 4.41
2071 2185 0.833287 AGAGTGTCTGGTTGTGCTGT 59.167 50.000 0.00 0.00 0.00 4.40
2072 2186 1.210478 AGAGTGTCTGGTTGTGCTGTT 59.790 47.619 0.00 0.00 0.00 3.16
2117 2231 0.737367 GCATGGCCGGAAAGCTTTTC 60.737 55.000 14.05 10.70 0.00 2.29
2121 2235 2.566529 CCGGAAAGCTTTTCGCCC 59.433 61.111 30.52 17.67 37.83 6.13
2126 2240 1.792118 GAAAGCTTTTCGCCCGTGGT 61.792 55.000 14.05 0.00 40.39 4.16
2150 2264 3.252484 GCCGACACGATACGCCAC 61.252 66.667 0.00 0.00 0.00 5.01
2155 2269 0.933509 GACACGATACGCCACCGATC 60.934 60.000 0.00 0.00 38.29 3.69
2196 2310 5.041191 AGGAATTTGGATCATAACGCTCT 57.959 39.130 0.00 0.00 0.00 4.09
2198 2312 5.297776 AGGAATTTGGATCATAACGCTCTTG 59.702 40.000 0.00 0.00 0.00 3.02
2215 2329 3.599343 TCTTGTGATGTGTGTATGCTCC 58.401 45.455 0.00 0.00 0.00 4.70
2217 2331 3.251479 TGTGATGTGTGTATGCTCCTC 57.749 47.619 0.00 0.00 0.00 3.71
2219 2333 3.007831 TGTGATGTGTGTATGCTCCTCAA 59.992 43.478 0.00 0.00 0.00 3.02
2252 2367 7.060421 TCACACTAAAGAAGAACCCAAAATCT 58.940 34.615 0.00 0.00 0.00 2.40
2424 2541 5.279910 GGATTAGCACAAGAGCAGGATATCT 60.280 44.000 2.05 0.00 36.85 1.98
2505 2623 1.024271 TGCGCATTCTCCATTAAGGC 58.976 50.000 5.66 0.00 37.29 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.991121 GAGCAACACTAGAGGAACAAGTC 59.009 47.826 0.00 0.00 0.00 3.01
5 6 2.229302 AGACGAGCAACACTAGAGGAAC 59.771 50.000 0.00 0.00 0.00 3.62
12 13 0.608130 ATGGCAGACGAGCAACACTA 59.392 50.000 0.00 0.00 35.83 2.74
20 21 1.135721 TCATGAGTCATGGCAGACGAG 59.864 52.381 28.54 4.35 41.66 4.18
119 142 6.830838 ACTGAAGACAAAAGGAAAGAGTCAAT 59.169 34.615 0.00 0.00 0.00 2.57
123 146 4.336713 GCACTGAAGACAAAAGGAAAGAGT 59.663 41.667 0.00 0.00 0.00 3.24
157 180 3.693085 AGTTGTCAAAGATGCATAGGCTG 59.307 43.478 0.00 0.00 41.91 4.85
183 206 4.890988 TCTCCCACCAAGTATCTATTCCA 58.109 43.478 0.00 0.00 0.00 3.53
211 234 6.893005 AGTCCTACTATAGTGCCTATTCATCC 59.107 42.308 15.90 0.00 0.00 3.51
244 267 1.337118 TCTGCCAAAATCACCCCAAC 58.663 50.000 0.00 0.00 0.00 3.77
247 270 1.691434 TGTTTCTGCCAAAATCACCCC 59.309 47.619 0.00 0.00 0.00 4.95
251 274 5.479724 TCCATGTATGTTTCTGCCAAAATCA 59.520 36.000 0.00 0.00 0.00 2.57
252 275 5.964758 TCCATGTATGTTTCTGCCAAAATC 58.035 37.500 0.00 0.00 0.00 2.17
292 324 7.667219 TCTTCCTTCTAAACTTCATTTCTGCAT 59.333 33.333 0.00 0.00 0.00 3.96
865 939 0.453793 TTTGTGTGTTTGGTCGGCAG 59.546 50.000 0.00 0.00 0.00 4.85
1859 1962 4.837972 AGTAAGAACAGAGAAAGATGGCC 58.162 43.478 0.00 0.00 0.00 5.36
1905 2008 0.098905 CATAACAGCAGCAGCAGCAG 59.901 55.000 12.92 6.60 45.49 4.24
1906 2009 0.607217 ACATAACAGCAGCAGCAGCA 60.607 50.000 12.92 0.00 45.49 4.41
1907 2010 0.524862 AACATAACAGCAGCAGCAGC 59.475 50.000 3.17 0.46 45.49 5.25
1908 2011 1.808343 TCAACATAACAGCAGCAGCAG 59.192 47.619 3.17 0.00 45.49 4.24
1915 2018 6.836242 TCCATACCATATCAACATAACAGCA 58.164 36.000 0.00 0.00 0.00 4.41
1932 2036 8.612619 CCATTACGCATCTAATTAATCCATACC 58.387 37.037 0.00 0.00 0.00 2.73
1965 2072 7.556275 AGTTCACACAAGTAAATTTCCTCTTGA 59.444 33.333 24.26 7.91 39.39 3.02
1981 2088 2.100584 GCAAATGACCCAGTTCACACAA 59.899 45.455 0.00 0.00 0.00 3.33
2005 2119 0.809385 CAGCAGCCAACAATCTCAGG 59.191 55.000 0.00 0.00 0.00 3.86
2030 2144 2.443255 TCCAGGAGCCAAAACTTCTCTT 59.557 45.455 0.00 0.00 0.00 2.85
2062 2176 4.752101 AGATACAGAACAGAACAGCACAAC 59.248 41.667 0.00 0.00 0.00 3.32
2068 2182 4.814147 TGCAGAGATACAGAACAGAACAG 58.186 43.478 0.00 0.00 0.00 3.16
2069 2183 4.871933 TGCAGAGATACAGAACAGAACA 57.128 40.909 0.00 0.00 0.00 3.18
2070 2184 7.518052 GCATAATGCAGAGATACAGAACAGAAC 60.518 40.741 0.00 0.00 44.26 3.01
2071 2185 6.481313 GCATAATGCAGAGATACAGAACAGAA 59.519 38.462 0.00 0.00 44.26 3.02
2072 2186 5.987953 GCATAATGCAGAGATACAGAACAGA 59.012 40.000 0.00 0.00 44.26 3.41
2121 2235 2.432628 GTCGGCAGGAAGACCACG 60.433 66.667 0.00 0.00 38.94 4.94
2126 2240 0.454600 GTATCGTGTCGGCAGGAAGA 59.545 55.000 17.13 5.05 41.92 2.87
2150 2264 1.742761 ATTCTTGTGGTGCAGATCGG 58.257 50.000 0.00 0.00 0.00 4.18
2155 2269 3.318839 TCCTTGAAATTCTTGTGGTGCAG 59.681 43.478 0.00 0.00 0.00 4.41
2196 2310 3.007831 TGAGGAGCATACACACATCACAA 59.992 43.478 0.00 0.00 0.00 3.33
2198 2312 3.251479 TGAGGAGCATACACACATCAC 57.749 47.619 0.00 0.00 0.00 3.06
2215 2329 8.777413 TCTTCTTTAGTGTGATGATTTGTTGAG 58.223 33.333 0.00 0.00 0.00 3.02
2217 2331 9.173939 GTTCTTCTTTAGTGTGATGATTTGTTG 57.826 33.333 0.00 0.00 0.00 3.33
2219 2333 7.040409 GGGTTCTTCTTTAGTGTGATGATTTGT 60.040 37.037 0.00 0.00 0.00 2.83
2268 2383 0.033601 ACAGAGATCCAGAGCCGAGT 60.034 55.000 0.00 0.00 0.00 4.18
2424 2541 2.829206 CGTGCGGCACCACTTTGAA 61.829 57.895 26.00 0.00 33.60 2.69
2491 2609 6.916360 TGTTCTTTTGCCTTAATGGAGAAT 57.084 33.333 0.00 0.00 38.35 2.40
2505 2623 5.613358 AAGTTAGCTCGGATGTTCTTTTG 57.387 39.130 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.