Multiple sequence alignment - TraesCS5A01G555500

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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 TraesCS5A01G555500 chr5A 100.000 2297 0 0 1 2297 706864912 706862616 0 4242
1 TraesCS5A01G555500 chrUn 96.346 2299 81 3 1 2297 274341283 274338986 0 3777
2 TraesCS5A01G555500 chrUn 96.345 2298 82 2 1 2297 291535439 291537735 0 3777
3 TraesCS5A01G555500 chrUn 96.345 2298 81 3 1 2297 245706067 245708362 0 3775
4 TraesCS5A01G555500 chrUn 96.301 2298 83 2 1 2297 199874823 199877119 0 3771
5 TraesCS5A01G555500 chrUn 96.301 2298 83 2 1 2297 229310228 229307932 0 3771
6 TraesCS5A01G555500 chrUn 96.214 2298 85 2 1 2297 3845815 3843519 0 3760
7 TraesCS5A01G555500 chrUn 96.214 2298 85 2 1 2297 199904743 199907039 0 3760
8 TraesCS5A01G555500 chr1B 96.301 2298 81 3 1 2297 544593696 544595990 0 3770
9 TraesCS5A01G555500 chr1B 96.214 2298 85 2 1 2297 544623635 544625931 0 3760


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 TraesCS5A01G555500 chr5A 706862616 706864912 2296 True 4242 4242 100.000 1 2297 1 chr5A.!!$R1 2296
1 TraesCS5A01G555500 chrUn 274338986 274341283 2297 True 3777 3777 96.346 1 2297 1 chrUn.!!$R3 2296
2 TraesCS5A01G555500 chrUn 291535439 291537735 2296 False 3777 3777 96.345 1 2297 1 chrUn.!!$F4 2296
3 TraesCS5A01G555500 chrUn 245706067 245708362 2295 False 3775 3775 96.345 1 2297 1 chrUn.!!$F3 2296
4 TraesCS5A01G555500 chrUn 199874823 199877119 2296 False 3771 3771 96.301 1 2297 1 chrUn.!!$F1 2296
5 TraesCS5A01G555500 chrUn 229307932 229310228 2296 True 3771 3771 96.301 1 2297 1 chrUn.!!$R2 2296
6 TraesCS5A01G555500 chrUn 3843519 3845815 2296 True 3760 3760 96.214 1 2297 1 chrUn.!!$R1 2296
7 TraesCS5A01G555500 chrUn 199904743 199907039 2296 False 3760 3760 96.214 1 2297 1 chrUn.!!$F2 2296
8 TraesCS5A01G555500 chr1B 544593696 544595990 2294 False 3770 3770 96.301 1 2297 1 chr1B.!!$F1 2296
9 TraesCS5A01G555500 chr1B 544623635 544625931 2296 False 3760 3760 96.214 1 2297 1 chr1B.!!$F2 2296

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
328 329 0.318784 GCGCTAACCTAGATCCCACG 60.319 60.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1594 1596 0.250945 TGGTATTTCACTTGCGCCCA 60.251 50.0 4.18 0.0 0.0 5.36 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
73 74 3.206866 ACCATCTAGTAGCTGGTTCCCTA 59.793 47.826 18.12 0.00 41.58 3.53
74 75 4.140663 ACCATCTAGTAGCTGGTTCCCTAT 60.141 45.833 18.12 0.00 41.58 2.57
271 272 1.676014 GGTAAGCAGAACTGGCGATGT 60.676 52.381 3.99 0.00 36.08 3.06
322 323 2.418746 CCAACTGTGCGCTAACCTAGAT 60.419 50.000 9.73 0.00 0.00 1.98
328 329 0.318784 GCGCTAACCTAGATCCCACG 60.319 60.000 0.00 0.00 0.00 4.94
352 353 3.071892 AGGGTGTTGGTCGATTAAGACAA 59.928 43.478 11.90 0.00 42.62 3.18
355 356 4.454504 GGTGTTGGTCGATTAAGACAACAT 59.545 41.667 11.08 0.00 42.62 2.71
374 375 3.625745 GACGGTGGTCATGGAAGTT 57.374 52.632 0.00 0.00 42.91 2.66
416 417 3.329929 AACAACTCACCTACCGAATCC 57.670 47.619 0.00 0.00 0.00 3.01
624 625 2.354203 CCGAAGAGGAGAAAGGTTCCAG 60.354 54.545 0.00 0.00 45.00 3.86
659 660 0.469917 ACATGGGTAAGCCGATCCTG 59.530 55.000 0.00 0.00 30.32 3.86
686 687 1.752833 GGTAACCCCGGCAGATAGG 59.247 63.158 0.00 0.00 0.00 2.57
731 732 4.166246 GGGAATCGGGTTAAGATTTCCT 57.834 45.455 8.58 0.00 45.83 3.36
755 757 2.358247 GATGTGGCGGTTGACGGT 60.358 61.111 0.00 0.00 44.51 4.83
758 760 2.358247 GTGGCGGTTGACGGTGAT 60.358 61.111 0.00 0.00 44.51 3.06
777 779 2.297698 TGTTAGGAAGTCCGGAGACA 57.702 50.000 3.06 0.00 46.15 3.41
878 880 4.021925 GTGGCCGGAAGAGCACCT 62.022 66.667 5.05 0.00 0.00 4.00
881 883 2.586792 GCCGGAAGAGCACCTCAT 59.413 61.111 5.05 0.00 32.06 2.90
924 926 0.684153 CCGGTGGCCCATGAAAATCT 60.684 55.000 0.00 0.00 0.00 2.40
938 940 4.030913 TGAAAATCTGGAGGACCGAGTAT 58.969 43.478 0.00 0.00 39.42 2.12
989 991 2.123589 TCAGGTCTCCAAGGTGAACAA 58.876 47.619 8.73 0.00 0.00 2.83
1040 1042 0.250553 AAGTCGGCAAAACGGATCCA 60.251 50.000 13.41 0.00 0.00 3.41
1078 1080 2.297129 GGCTCTGAGGACTGGGCTT 61.297 63.158 6.83 0.00 40.52 4.35
1082 1084 2.121963 TGAGGACTGGGCTTGGGT 60.122 61.111 0.00 0.00 0.00 4.51
1135 1137 1.587043 TTGCTCGAGCTACTCACGCT 61.587 55.000 35.27 0.00 42.66 5.07
1137 1139 1.797441 CTCGAGCTACTCACGCTGT 59.203 57.895 0.00 0.00 37.96 4.40
1218 1220 1.618343 TCCTCGAGCATGAAACAGTCA 59.382 47.619 6.99 0.00 41.67 3.41
1263 1265 6.120220 AGGGGAATCCGACTGTTTAATTAAG 58.880 40.000 0.00 0.00 41.52 1.85
1316 1318 0.523968 CGCAATGTGATTTCTGCCCG 60.524 55.000 0.00 0.00 0.00 6.13
1357 1359 1.234821 AGAAATTCAACCAAGCGCGA 58.765 45.000 12.10 0.00 0.00 5.87
1421 1423 4.322080 TGCCTCGTCATCTAATTAGTGG 57.678 45.455 12.19 6.16 0.00 4.00
1425 1427 2.100087 TCGTCATCTAATTAGTGGCGCA 59.900 45.455 24.54 16.23 40.46 6.09
1520 1522 0.918983 TGGAATCAGCGGGGAAAGAT 59.081 50.000 0.00 0.00 0.00 2.40
1538 1540 2.373169 AGATGACCCTGTTGAGCTTGAA 59.627 45.455 0.00 0.00 0.00 2.69
1594 1596 1.061033 AGGATAAGTGGGAGCCCTCAT 60.061 52.381 7.16 0.00 36.94 2.90
1806 1810 5.134202 TGAGCTCAACGAGAACAGAAATA 57.866 39.130 15.67 0.00 0.00 1.40
1855 1859 6.037610 GCTCGTTTGATTCTGATTTCCAGTAT 59.962 38.462 0.00 0.00 43.38 2.12
1884 1888 1.024579 CCGTGAAAGCGTGGCCTATT 61.025 55.000 3.32 0.00 0.00 1.73
1994 1998 3.628017 CGACGTTGCTTTTTGATCCTTT 58.372 40.909 0.00 0.00 0.00 3.11
2013 2017 3.459232 TTGATGTCGGCTCTTCCTATG 57.541 47.619 0.00 0.00 0.00 2.23
2274 2278 2.169789 CAAGCTAGCATGCGACGCT 61.170 57.895 22.08 20.58 43.62 5.07
2277 2281 2.456119 GCTAGCATGCGACGCTTGT 61.456 57.895 29.21 20.42 40.96 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.438087 CCAAGTCAGATGAACGATTTGCT 59.562 43.478 0.00 0.00 30.04 3.91
16 17 2.339769 GCCCCTATACCCAAGTCAGAT 58.660 52.381 0.00 0.00 0.00 2.90
73 74 4.043596 AGCTATCCTGAGGGAAACTTCAT 58.956 43.478 0.00 0.00 46.26 2.57
74 75 3.198635 CAGCTATCCTGAGGGAAACTTCA 59.801 47.826 0.00 0.00 45.78 3.02
271 272 2.674754 GGCTTCCGGTTCATCCCA 59.325 61.111 0.00 0.00 0.00 4.37
308 309 0.750850 GTGGGATCTAGGTTAGCGCA 59.249 55.000 11.47 0.00 0.00 6.09
328 329 3.683340 GTCTTAATCGACCAACACCCTTC 59.317 47.826 0.00 0.00 0.00 3.46
374 375 2.301870 ACACACTCCTTAGCGGATTTCA 59.698 45.455 0.00 0.00 42.12 2.69
408 409 2.432300 CGGGGCTAGTGGATTCGGT 61.432 63.158 0.00 0.00 0.00 4.69
416 417 1.949525 CATCCATTTTCGGGGCTAGTG 59.050 52.381 0.00 0.00 0.00 2.74
478 479 1.410850 CCTACTCATCGGGGCATGGT 61.411 60.000 0.00 0.00 0.00 3.55
546 547 2.942796 AAGATCTGCACCGACGGCA 61.943 57.895 15.39 6.18 39.32 5.69
602 603 1.900486 GGAACCTTTCTCCTCTTCGGA 59.100 52.381 0.00 0.00 40.30 4.55
632 633 1.247567 GCTTACCCATGTGCAAGTGT 58.752 50.000 0.00 0.00 0.00 3.55
755 757 2.758979 GTCTCCGGACTTCCTAACATCA 59.241 50.000 0.00 0.00 39.24 3.07
758 760 1.891150 GTGTCTCCGGACTTCCTAACA 59.109 52.381 0.00 0.00 42.54 2.41
783 785 2.177529 TAACTCTTCCCGAGGCCCCT 62.178 60.000 0.00 0.00 44.33 4.79
909 911 1.342275 CCTCCAGATTTTCATGGGCCA 60.342 52.381 9.61 9.61 37.19 5.36
924 926 3.583054 AACGATACTCGGTCCTCCA 57.417 52.632 1.29 0.00 45.59 3.86
938 940 2.260154 TACGACCAGGCGTGAACGA 61.260 57.895 23.41 10.54 45.23 3.85
949 951 1.175654 TGCGGTTATGAGTACGACCA 58.824 50.000 0.00 0.00 32.41 4.02
989 991 0.482446 TTGTTCCATTGGCCAGAGGT 59.518 50.000 21.07 1.32 0.00 3.85
1040 1042 3.699538 GCCAATCCTTTTCCCGAAGTTAT 59.300 43.478 0.00 0.00 0.00 1.89
1112 1114 1.135139 GTGAGTAGCTCGAGCAATCCA 59.865 52.381 36.87 24.95 45.16 3.41
1163 1165 0.978146 CGATTCCCAGTCTGTCCCCT 60.978 60.000 0.00 0.00 0.00 4.79
1201 1203 3.059884 GAGTTGACTGTTTCATGCTCGA 58.940 45.455 0.00 0.00 32.84 4.04
1218 1220 2.313317 TGTCCGTACCAGTTCTGAGTT 58.687 47.619 1.00 0.00 0.00 3.01
1263 1265 1.468054 GGACCATCGCAATGCTTTGTC 60.468 52.381 13.29 4.73 35.17 3.18
1316 1318 3.141398 TCACTTTGACATTCAGAGCACC 58.859 45.455 0.00 0.00 32.38 5.01
1357 1359 1.260544 AGTTACTCCCGCCGTTTACT 58.739 50.000 0.00 0.00 0.00 2.24
1421 1423 2.031560 TCGTTAATCCATTCATGTGCGC 59.968 45.455 0.00 0.00 0.00 6.09
1425 1427 5.765182 GGGAATCTCGTTAATCCATTCATGT 59.235 40.000 0.00 0.00 33.48 3.21
1520 1522 2.373169 AGATTCAAGCTCAACAGGGTCA 59.627 45.455 0.00 0.00 0.00 4.02
1538 1540 5.869888 GTCATTTCACAAAGTCGGACTAGAT 59.130 40.000 11.71 0.00 0.00 1.98
1594 1596 0.250945 TGGTATTTCACTTGCGCCCA 60.251 50.000 4.18 0.00 0.00 5.36
1668 1672 2.270959 GCCTTGGAGCCAAAAGGAG 58.729 57.895 10.72 0.00 44.93 3.69
1688 1692 2.364579 ATCGGCCCGGTAAGACCA 60.365 61.111 1.90 0.00 38.47 4.02
1806 1810 2.358322 ACCCTTTTGTTCCACACGAT 57.642 45.000 0.00 0.00 0.00 3.73
1855 1859 3.124466 CACGCTTTCACGGTTCATATTCA 59.876 43.478 0.00 0.00 37.37 2.57
1861 1865 2.539338 GCCACGCTTTCACGGTTCA 61.539 57.895 0.00 0.00 37.37 3.18
1901 1905 5.775701 TCTGACACCTCTAGCTTTAAACTCT 59.224 40.000 0.00 0.00 0.00 3.24
1908 1912 5.297569 ACTTTTCTGACACCTCTAGCTTT 57.702 39.130 0.00 0.00 0.00 3.51
1965 1969 4.083537 TCAAAAAGCAACGTCGCTATGAAT 60.084 37.500 0.00 0.00 42.89 2.57
1994 1998 2.666317 TCATAGGAAGAGCCGACATCA 58.334 47.619 0.00 0.00 43.43 3.07
2085 2089 5.476614 GGTAAAACTAACCTGTCTCACGAT 58.523 41.667 0.00 0.00 33.97 3.73
2199 2203 2.886124 GGTAGCTTCGCGCCACTC 60.886 66.667 0.00 0.00 40.39 3.51
2217 2221 3.873361 CGTTCAGTCATAATCCAGCACAT 59.127 43.478 0.00 0.00 0.00 3.21
2223 2227 2.766263 AGAGGCGTTCAGTCATAATCCA 59.234 45.455 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.