Multiple sequence alignment - TraesCS5D01G401200

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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 TraesCS5D01G401200 chr5D 100.000 3153 0 0 1 3153 466232744 466229592 0.000000e+00 5823
1 TraesCS5D01G401200 chr5B 94.714 3178 118 19 2 3153 573228449 573225296 0.000000e+00 4892
2 TraesCS5D01G401200 chr5A 91.936 3187 154 34 16 3152 586606691 586603558 0.000000e+00 4366
3 TraesCS5D01G401200 chr5A 87.850 535 29 16 2205 2720 538232499 538233016 2.090000e-166 595
4 TraesCS5D01G401200 chr1B 96.040 505 17 1 183 687 22642865 22643366 0.000000e+00 819
5 TraesCS5D01G401200 chr6A 86.059 538 39 15 2201 2719 218850529 218851049 2.140000e-151 545
6 TraesCS5D01G401200 chr3A 85.981 535 37 17 2205 2720 380636526 380636011 3.580000e-149 538


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 TraesCS5D01G401200 chr5D 466229592 466232744 3152 True 5823 5823 100.000 1 3153 1 chr5D.!!$R1 3152
1 TraesCS5D01G401200 chr5B 573225296 573228449 3153 True 4892 4892 94.714 2 3153 1 chr5B.!!$R1 3151
2 TraesCS5D01G401200 chr5A 586603558 586606691 3133 True 4366 4366 91.936 16 3152 1 chr5A.!!$R1 3136
3 TraesCS5D01G401200 chr5A 538232499 538233016 517 False 595 595 87.850 2205 2720 1 chr5A.!!$F1 515
4 TraesCS5D01G401200 chr1B 22642865 22643366 501 False 819 819 96.040 183 687 1 chr1B.!!$F1 504
5 TraesCS5D01G401200 chr6A 218850529 218851049 520 False 545 545 86.059 2201 2719 1 chr6A.!!$F1 518
6 TraesCS5D01G401200 chr3A 380636011 380636526 515 True 538 538 85.981 2205 2720 1 chr3A.!!$R1 515

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
49 50 0.527817 GCCAACACGTAGAGATCCGG 60.528 60.0 0.0 0.0 0.00 5.14 F
50 51 0.527817 CCAACACGTAGAGATCCGGC 60.528 60.0 0.0 0.0 0.00 6.13 F
1077 1116 0.667993 TCCAAACAAAGCCTTCGCAG 59.332 50.0 0.0 0.0 37.52 5.18 F
1497 1536 0.953727 TCAAGGCACTGCACATGAAC 59.046 50.0 0.0 0.0 40.86 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1356 1395 0.594602 TCGTCGTGTCTGTGTTAGGG 59.405 55.000 0.00 0.0 0.00 3.53 R
1497 1536 3.181367 GCCTCGCCACACTTCATG 58.819 61.111 0.00 0.0 0.00 3.07 R
2093 2134 2.047274 CGTGCCGGACTGGTCAAT 60.047 61.111 5.05 0.0 41.21 2.57 R
2926 3003 2.079170 TGCTGGAAATGGGTGTCAAA 57.921 45.000 0.00 0.0 0.00 2.69 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
46 47 1.146358 GGCGCCAACACGTAGAGATC 61.146 60.000 24.80 0.00 34.88 2.75
47 48 1.146358 GCGCCAACACGTAGAGATCC 61.146 60.000 0.00 0.00 34.88 3.36
48 49 0.866061 CGCCAACACGTAGAGATCCG 60.866 60.000 0.00 0.00 0.00 4.18
49 50 0.527817 GCCAACACGTAGAGATCCGG 60.528 60.000 0.00 0.00 0.00 5.14
50 51 0.527817 CCAACACGTAGAGATCCGGC 60.528 60.000 0.00 0.00 0.00 6.13
51 52 0.866061 CAACACGTAGAGATCCGGCG 60.866 60.000 0.00 0.00 0.00 6.46
52 53 2.353607 CACGTAGAGATCCGGCGC 60.354 66.667 0.00 0.00 0.00 6.53
53 54 3.950254 ACGTAGAGATCCGGCGCG 61.950 66.667 0.00 0.00 0.00 6.86
96 97 3.610669 CTCCATCTCCGCCCCTCG 61.611 72.222 0.00 0.00 38.08 4.63
143 144 0.757188 GCGGAGAGGGAGGAGATCAA 60.757 60.000 0.00 0.00 0.00 2.57
206 220 1.443828 GCGCCCTCAAACCCAAAAA 59.556 52.632 0.00 0.00 0.00 1.94
254 268 2.442056 CGGAGGGAGGTAAGGGATG 58.558 63.158 0.00 0.00 0.00 3.51
257 271 2.707554 GGAGGGAGGTAAGGGATGATT 58.292 52.381 0.00 0.00 0.00 2.57
301 317 2.075338 CTCTGTTCTCTGCTTGCTTCC 58.925 52.381 0.00 0.00 0.00 3.46
467 483 2.229784 CTCAAGGTTGGTTTCCAGCATC 59.770 50.000 5.15 0.00 36.44 3.91
674 713 5.904362 ATTCAAGATAACAGCCAAGGAAC 57.096 39.130 0.00 0.00 0.00 3.62
805 844 4.391830 ACACGTATAATTCACACAAGCTGG 59.608 41.667 0.00 0.00 0.00 4.85
854 893 2.689471 GCAATTCAGTGCATATCCACCA 59.311 45.455 0.00 0.00 44.29 4.17
1008 1047 3.117776 TCCAGCATAAGCCAATGTCTGAT 60.118 43.478 15.54 0.00 43.56 2.90
1020 1059 7.112122 AGCCAATGTCTGATAACAGTATTCAA 58.888 34.615 0.00 0.00 43.81 2.69
1044 1083 2.780010 AGCATTGCTACCTGATAACCCT 59.220 45.455 10.00 0.00 36.99 4.34
1064 1103 1.273048 TGATGCCAATGTGCTCCAAAC 59.727 47.619 0.00 0.00 0.00 2.93
1071 1110 1.708341 ATGTGCTCCAAACAAAGCCT 58.292 45.000 0.00 0.00 37.73 4.58
1077 1116 0.667993 TCCAAACAAAGCCTTCGCAG 59.332 50.000 0.00 0.00 37.52 5.18
1230 1269 5.439059 AGGGTTCCTCCTATTTCTCTACCTA 59.561 44.000 0.00 0.00 34.92 3.08
1236 1275 6.332103 TCCTCCTATTTCTCTACCTACTAGCA 59.668 42.308 0.00 0.00 0.00 3.49
1243 1282 1.211212 TCTACCTACTAGCAGGCGTCA 59.789 52.381 9.10 0.00 39.53 4.35
1356 1395 2.633488 GTTGGCTATGGAGACCTTGTC 58.367 52.381 0.00 0.00 0.00 3.18
1497 1536 0.953727 TCAAGGCACTGCACATGAAC 59.046 50.000 0.00 0.00 40.86 3.18
1907 1946 3.279434 GGAAAGTGGGGTAAGCACATAG 58.721 50.000 0.00 0.00 0.00 2.23
1935 1974 4.672587 TTCAGTATTCTTCCCTCCATCG 57.327 45.455 0.00 0.00 0.00 3.84
1963 2002 5.185635 CCCTTGAGATTTTGCAGGTAATGAA 59.814 40.000 0.00 0.00 0.00 2.57
1966 2005 6.012658 TGAGATTTTGCAGGTAATGAACAC 57.987 37.500 0.00 0.00 0.00 3.32
1992 2033 9.681692 CTGATGTTGATTTGTGAACTTTGATAA 57.318 29.630 0.00 0.00 0.00 1.75
2177 2218 6.260050 ACGAACATATGGGCTTGTACTTAATG 59.740 38.462 7.80 0.00 0.00 1.90
2203 2249 6.909550 ACAGCTTAAATGGTTGAATGGTTA 57.090 33.333 0.00 0.00 0.00 2.85
2301 2361 1.303309 GCTCATATGCACCTGGACAC 58.697 55.000 0.00 0.00 0.00 3.67
2371 2431 6.067263 TGTGTACATGAAGTTTGTTAAGCC 57.933 37.500 0.00 0.00 0.00 4.35
2616 2680 2.054799 TCACTTCTAACAGGTTGCCCT 58.945 47.619 0.00 0.00 44.02 5.19
2926 3003 5.047590 TGCTGACAATGCTTCAATCTCAAAT 60.048 36.000 0.00 0.00 0.00 2.32
3097 3174 0.536006 ACTGACCAGGTGAAAGCAGC 60.536 55.000 0.00 0.00 42.72 5.25
3137 3214 2.806434 TGGAGTACCTACTGCCGTTAA 58.194 47.619 1.93 0.00 43.07 2.01
3146 3223 1.245732 ACTGCCGTTAAGAGTCGACT 58.754 50.000 20.18 20.18 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 144 1.606885 GCTCTCCTGCTCTGCTCAGT 61.607 60.000 0.00 0.00 0.00 3.41
252 266 7.271511 GGTTGAGAAGACACAGAGATAATCAT 58.728 38.462 0.00 0.00 0.00 2.45
253 267 6.625960 CGGTTGAGAAGACACAGAGATAATCA 60.626 42.308 0.00 0.00 0.00 2.57
254 268 5.746245 CGGTTGAGAAGACACAGAGATAATC 59.254 44.000 0.00 0.00 0.00 1.75
257 271 4.079970 ACGGTTGAGAAGACACAGAGATA 58.920 43.478 0.00 0.00 0.00 1.98
301 317 4.845580 AGCTCCGGCCATTCGCAG 62.846 66.667 2.24 0.00 40.31 5.18
674 713 4.615588 TTTGGTCAAAAATAAGGGCCAG 57.384 40.909 6.18 0.00 0.00 4.85
805 844 3.181474 CCACCGAGAAACTCTATTCCTCC 60.181 52.174 0.00 0.00 0.00 4.30
883 922 4.623595 CGAGGAAGAAGTTTAGAAGCTCAC 59.376 45.833 0.00 0.00 0.00 3.51
1008 1047 4.935205 AGCAATGCTCGTTGAATACTGTTA 59.065 37.500 0.00 0.00 30.62 2.41
1020 1059 3.458189 GTTATCAGGTAGCAATGCTCGT 58.542 45.455 12.53 2.47 40.44 4.18
1044 1083 1.273048 GTTTGGAGCACATTGGCATCA 59.727 47.619 0.00 0.00 35.83 3.07
1064 1103 2.694760 GCTCCCTGCGAAGGCTTTG 61.695 63.158 2.84 10.27 40.82 2.77
1230 1269 1.032657 AGACGATGACGCCTGCTAGT 61.033 55.000 0.00 0.00 43.96 2.57
1236 1275 1.549170 AGGTAAAAGACGATGACGCCT 59.451 47.619 0.00 0.00 43.96 5.52
1243 1282 5.160607 TCCATGACAAGGTAAAAGACGAT 57.839 39.130 0.00 0.00 0.00 3.73
1356 1395 0.594602 TCGTCGTGTCTGTGTTAGGG 59.405 55.000 0.00 0.00 0.00 3.53
1497 1536 3.181367 GCCTCGCCACACTTCATG 58.819 61.111 0.00 0.00 0.00 3.07
1907 1946 3.751698 AGGGAAGAATACTGAAAACGCAC 59.248 43.478 0.00 0.00 0.00 5.34
1935 1974 4.273318 ACCTGCAAAATCTCAAGGGATAC 58.727 43.478 0.00 0.00 0.00 2.24
1963 2002 6.455360 AAGTTCACAAATCAACATCAGTGT 57.545 33.333 0.00 0.00 41.28 3.55
1966 2005 9.681692 TTATCAAAGTTCACAAATCAACATCAG 57.318 29.630 0.00 0.00 0.00 2.90
2093 2134 2.047274 CGTGCCGGACTGGTCAAT 60.047 61.111 5.05 0.00 41.21 2.57
2177 2218 6.687604 ACCATTCAACCATTTAAGCTGTAAC 58.312 36.000 0.00 0.00 0.00 2.50
2191 2232 6.267496 ACAGCATTAACTAACCATTCAACC 57.733 37.500 0.00 0.00 0.00 3.77
2239 2285 4.957296 ACAAGGTCGTATCTTTTGACACT 58.043 39.130 0.00 0.00 34.32 3.55
2301 2361 7.416154 TCACCAAATACTTCTTTCTTACACG 57.584 36.000 0.00 0.00 0.00 4.49
2371 2431 9.309516 CTGGAAATATTTCATGACTGGAAAATG 57.690 33.333 25.55 0.00 37.74 2.32
2480 2542 4.934001 CACTTGCCGAGCATCATTAGATAT 59.066 41.667 0.00 0.00 38.76 1.63
2616 2680 9.778741 TTTGGGTTTATTATGTTAATGTGCAAA 57.221 25.926 0.00 0.00 0.00 3.68
2926 3003 2.079170 TGCTGGAAATGGGTGTCAAA 57.921 45.000 0.00 0.00 0.00 2.69
3097 3174 6.107901 TCCATTGTTCCAAAAGGTTTATGG 57.892 37.500 0.00 0.00 35.49 2.74
3122 3199 2.679837 CGACTCTTAACGGCAGTAGGTA 59.320 50.000 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.