Multiple sequence alignment - TraesCS6B01G234300

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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 TraesCS6B01G234300 chr6B 100.000 2258 0 0 1 2258 394295360 394293103 0 4170
1 TraesCS6B01G234300 chr4B 95.215 2257 106 1 2 2258 347874187 347876441 0 3568
2 TraesCS6B01G234300 chr7A 94.993 2257 113 0 2 2258 389127410 389129666 0 3542
3 TraesCS6B01G234300 chr7A 94.860 2257 116 0 2 2258 163924986 163922730 0 3526
4 TraesCS6B01G234300 chr5A 95.033 2255 111 1 4 2258 662055472 662057725 0 3542
5 TraesCS6B01G234300 chr2A 94.996 2258 111 2 2 2258 429131860 429134116 0 3542
6 TraesCS6B01G234300 chr7D 94.949 2257 113 1 2 2258 572699831 572702086 0 3535
7 TraesCS6B01G234300 chr4A 94.863 2258 114 2 2 2258 566108783 566111039 0 3526
8 TraesCS6B01G234300 chr2D 94.914 2261 102 6 5 2258 460769302 460767048 0 3526
9 TraesCS6B01G234300 chr1A 94.860 2257 115 1 2 2258 239821235 239823490 0 3524


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 TraesCS6B01G234300 chr6B 394293103 394295360 2257 True 4170 4170 100.000 1 2258 1 chr6B.!!$R1 2257
1 TraesCS6B01G234300 chr4B 347874187 347876441 2254 False 3568 3568 95.215 2 2258 1 chr4B.!!$F1 2256
2 TraesCS6B01G234300 chr7A 389127410 389129666 2256 False 3542 3542 94.993 2 2258 1 chr7A.!!$F1 2256
3 TraesCS6B01G234300 chr7A 163922730 163924986 2256 True 3526 3526 94.860 2 2258 1 chr7A.!!$R1 2256
4 TraesCS6B01G234300 chr5A 662055472 662057725 2253 False 3542 3542 95.033 4 2258 1 chr5A.!!$F1 2254
5 TraesCS6B01G234300 chr2A 429131860 429134116 2256 False 3542 3542 94.996 2 2258 1 chr2A.!!$F1 2256
6 TraesCS6B01G234300 chr7D 572699831 572702086 2255 False 3535 3535 94.949 2 2258 1 chr7D.!!$F1 2256
7 TraesCS6B01G234300 chr4A 566108783 566111039 2256 False 3526 3526 94.863 2 2258 1 chr4A.!!$F1 2256
8 TraesCS6B01G234300 chr2D 460767048 460769302 2254 True 3526 3526 94.914 5 2258 1 chr2D.!!$R1 2253
9 TraesCS6B01G234300 chr1A 239821235 239823490 2255 False 3524 3524 94.860 2 2258 1 chr1A.!!$F1 2256

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
31 32 1.004560 TGCCGCTGAGTGAAAGAGG 60.005 57.895 0.0 0.0 37.64 3.69 F
547 554 1.137086 GCTGCCGAGACCTAAGAATCA 59.863 52.381 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1215 1226 0.321653 GGTTCGGATGCTTCACCAGT 60.322 55.0 1.64 0.0 0.0 4.00 R
2132 2143 0.324943 TGCCCTTCCCTTCTTTCTCG 59.675 55.0 0.00 0.0 0.0 4.04 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
31 32 1.004560 TGCCGCTGAGTGAAAGAGG 60.005 57.895 0.00 0.00 37.64 3.69
140 145 9.665719 TTAGATAAGTCATATTGTGAACTGCAA 57.334 29.630 0.00 0.00 38.90 4.08
281 288 6.490566 AAATCTGAATTTTTACTACGGCGT 57.509 33.333 19.64 19.64 30.79 5.68
328 335 3.756963 GGGGTTTGATCTTAGCGAGTTTT 59.243 43.478 0.00 0.00 0.00 2.43
450 457 5.490159 TCTGTCAGTATTCATGCATTGTGA 58.510 37.500 0.00 0.00 0.00 3.58
500 507 3.511477 AGTTGATGCCGGTAGATAGGAT 58.489 45.455 1.90 0.00 0.00 3.24
539 546 1.248785 TTAAGACGCTGCCGAGACCT 61.249 55.000 0.00 0.00 38.29 3.85
547 554 1.137086 GCTGCCGAGACCTAAGAATCA 59.863 52.381 0.00 0.00 0.00 2.57
759 767 1.203063 ACTGGGCAGAGTAGTCAGTCA 60.203 52.381 0.00 0.00 34.00 3.41
777 785 8.486210 AGTCAGTCAATAATATTAGCTGGTTCA 58.514 33.333 0.00 0.00 0.00 3.18
814 823 3.117360 GGATGAGGAAGGGGATGAAATGT 60.117 47.826 0.00 0.00 0.00 2.71
835 844 1.364328 AGAGGGTGATGGAGGAAGAGT 59.636 52.381 0.00 0.00 0.00 3.24
916 925 1.139654 CGATTCCTTCTGCATGGGAGA 59.860 52.381 0.00 0.00 0.00 3.71
949 958 2.519377 CGGCCTTACGGTCAATGATA 57.481 50.000 0.00 0.00 33.27 2.15
950 959 2.828877 CGGCCTTACGGTCAATGATAA 58.171 47.619 0.00 0.00 33.27 1.75
997 1006 5.836024 TCTGAACCAAGTACAAATAGGGT 57.164 39.130 0.00 0.00 0.00 4.34
1059 1070 3.611766 AAGTGGGCTATGTCTACACAC 57.388 47.619 0.00 0.00 34.48 3.82
1106 1117 6.704493 TCAAGTCCAACAAACTATACTGTGAC 59.296 38.462 0.00 0.00 0.00 3.67
1215 1226 7.016153 ACATAATTGTGTGAGGAAGAACCTA 57.984 36.000 7.08 0.00 41.32 3.08
1255 1266 3.062763 CTGACTTCAAGTCTCATTGCGT 58.937 45.455 18.49 0.00 45.27 5.24
1256 1267 2.802247 TGACTTCAAGTCTCATTGCGTG 59.198 45.455 18.49 0.00 45.27 5.34
1276 1287 6.262273 TGCGTGACTCATGTATACAGAGATAA 59.738 38.462 25.93 14.69 33.69 1.75
1397 1408 2.649816 AGGCTATGGAGGAAAGGTTTGT 59.350 45.455 0.00 0.00 0.00 2.83
1731 1742 1.146263 GGTATGGTTCCTCCGGCAG 59.854 63.158 0.00 0.00 39.52 4.85
1749 1760 3.924144 GCAGGTGAAAATTGCCATTGTA 58.076 40.909 0.00 0.00 31.79 2.41
1764 1775 3.761752 CCATTGTAAAGGACCGACCAAAT 59.238 43.478 0.00 0.00 42.04 2.32
1834 1845 4.703575 AGACACTACGTAATCCAGCAGTTA 59.296 41.667 0.00 0.00 0.00 2.24
2132 2143 5.992217 CAGCAATTGACCCTCCTAATACTAC 59.008 44.000 10.34 0.00 0.00 2.73
2154 2165 3.435275 GAGAAAGAAGGGAAGGGCAATT 58.565 45.455 0.00 0.00 0.00 2.32
2215 2226 0.961019 TTGGTCTTTGCTGCATGACC 59.039 50.000 31.12 31.12 46.53 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 3.443329 TGGTTATACCTTCGAAGCGTGTA 59.557 43.478 19.99 15.95 39.58 2.90
135 140 8.981647 GCCTCCAAAAATATATTAACATTGCAG 58.018 33.333 0.00 0.00 0.00 4.41
154 159 4.599041 ACTATGCACTAAAATGCCTCCAA 58.401 39.130 0.00 0.00 45.50 3.53
281 288 9.051679 CCAACTCATTATATCGAACATTACCAA 57.948 33.333 0.00 0.00 0.00 3.67
328 335 4.637977 TGCTAATGTCATGACGCCATTTTA 59.362 37.500 20.54 10.06 31.63 1.52
346 353 0.251653 AGTCTGTCCGGGTCTGCTAA 60.252 55.000 0.00 0.00 0.00 3.09
450 457 7.710475 CACTTGACATTTTTACAGGATTTGGTT 59.290 33.333 0.00 0.00 0.00 3.67
500 507 0.251297 CAGGGACAACCAATGCTGGA 60.251 55.000 0.00 0.00 46.92 3.86
539 546 6.095300 CACAAGTGCATATGGGTTGATTCTTA 59.905 38.462 4.56 0.00 0.00 2.10
585 592 2.694628 ACTGTGGAGTTGTACGGTGTTA 59.305 45.455 0.00 0.00 35.22 2.41
686 694 0.601558 CGACTCTTTCTCGGGTTGGA 59.398 55.000 0.00 0.00 0.00 3.53
728 736 0.467384 CTGCCCAGTATCAGGACCAG 59.533 60.000 0.00 0.00 0.00 4.00
759 767 8.197439 GCAAAACCTGAACCAGCTAATATTATT 58.803 33.333 0.00 0.00 0.00 1.40
777 785 1.358787 TCATCCCCATCAGCAAAACCT 59.641 47.619 0.00 0.00 0.00 3.50
814 823 2.587777 ACTCTTCCTCCATCACCCTCTA 59.412 50.000 0.00 0.00 0.00 2.43
835 844 2.509548 CCTCCACCAATCCATCCTTGTA 59.490 50.000 0.00 0.00 0.00 2.41
916 925 0.694444 AGGCCGGTGGATATGTCCTT 60.694 55.000 10.16 0.00 45.32 3.36
1059 1070 0.464735 TGTGTGTCCGGAAAACCCTG 60.465 55.000 5.23 0.00 0.00 4.45
1106 1117 3.381272 AGGACAACCTGTTTCAACACATG 59.619 43.478 0.00 0.00 45.92 3.21
1146 1157 1.552792 TGGATGTCATACTTCGGCACA 59.447 47.619 0.00 0.00 0.00 4.57
1215 1226 0.321653 GGTTCGGATGCTTCACCAGT 60.322 55.000 1.64 0.00 0.00 4.00
1276 1287 9.911788 TTTTGCTTCCATATCTTTCTTCTCTAT 57.088 29.630 0.00 0.00 0.00 1.98
1360 1371 1.657751 GCCTTTTGCTTAGCCCTCCG 61.658 60.000 0.29 0.00 36.87 4.63
1397 1408 4.957759 TCATATGAGTCGAAGAACGTCA 57.042 40.909 0.00 0.00 39.69 4.35
1731 1742 5.408299 GTCCTTTACAATGGCAATTTTCACC 59.592 40.000 0.00 0.00 0.00 4.02
1749 1760 1.953686 CACACATTTGGTCGGTCCTTT 59.046 47.619 0.00 0.00 37.07 3.11
2132 2143 0.324943 TGCCCTTCCCTTCTTTCTCG 59.675 55.000 0.00 0.00 0.00 4.04
2215 2226 1.271054 GCCATACCTAGCTCCATGTGG 60.271 57.143 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.