Multiple sequence alignment - TraesCS7A01G198000

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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 TraesCS7A01G198000 chr7A 100.000 2744 0 0 1 2744 158633383 158630640 0 5068
1 TraesCS7A01G198000 chr7A 95.022 2752 125 7 1 2744 557401733 557398986 0 4313
2 TraesCS7A01G198000 chr5A 95.198 2749 121 8 1 2744 306514218 306516960 0 4335
3 TraesCS7A01G198000 chr3A 95.084 2746 130 5 1 2744 464513228 464510486 0 4318
4 TraesCS7A01G198000 chr3A 94.936 2745 136 3 1 2744 615335598 615338340 0 4296
5 TraesCS7A01G198000 chr3A 94.904 2747 129 8 1 2744 259992109 259994847 0 4287
6 TraesCS7A01G198000 chr3A 94.756 2746 139 5 1 2744 251098963 251101705 0 4268
7 TraesCS7A01G198000 chr1A 95.084 2746 127 6 1 2744 100434556 100437295 0 4316
8 TraesCS7A01G198000 chr1A 94.762 2749 134 8 1 2744 357466444 357463701 0 4270
9 TraesCS7A01G198000 chr6A 95.015 2748 131 4 1 2744 83698864 83696119 0 4311


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 TraesCS7A01G198000 chr7A 158630640 158633383 2743 True 5068 5068 100.000 1 2744 1 chr7A.!!$R1 2743
1 TraesCS7A01G198000 chr7A 557398986 557401733 2747 True 4313 4313 95.022 1 2744 1 chr7A.!!$R2 2743
2 TraesCS7A01G198000 chr5A 306514218 306516960 2742 False 4335 4335 95.198 1 2744 1 chr5A.!!$F1 2743
3 TraesCS7A01G198000 chr3A 464510486 464513228 2742 True 4318 4318 95.084 1 2744 1 chr3A.!!$R1 2743
4 TraesCS7A01G198000 chr3A 615335598 615338340 2742 False 4296 4296 94.936 1 2744 1 chr3A.!!$F3 2743
5 TraesCS7A01G198000 chr3A 259992109 259994847 2738 False 4287 4287 94.904 1 2744 1 chr3A.!!$F2 2743
6 TraesCS7A01G198000 chr3A 251098963 251101705 2742 False 4268 4268 94.756 1 2744 1 chr3A.!!$F1 2743
7 TraesCS7A01G198000 chr1A 100434556 100437295 2739 False 4316 4316 95.084 1 2744 1 chr1A.!!$F1 2743
8 TraesCS7A01G198000 chr1A 357463701 357466444 2743 True 4270 4270 94.762 1 2744 1 chr1A.!!$R1 2743
9 TraesCS7A01G198000 chr6A 83696119 83698864 2745 True 4311 4311 95.015 1 2744 1 chr6A.!!$R1 2743

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
921 925 0.108615 GCACACGCTGACTGTAGGAT 60.109 55.0 0.0 0.0 34.3 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2713 2728 0.735978 TGTGATTGTGCGAGCTACCG 60.736 55.0 0.0 0.0 0.0 4.02 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
51 52 7.387948 AGTTGATTAAGTTGTGCGAACTCTTAT 59.612 33.333 10.81 4.38 0.00 1.73
84 85 3.995636 AGCAGATGTAGGGGAAAGTAGA 58.004 45.455 0.00 0.00 0.00 2.59
149 151 3.566351 ACTATGTCTCGGTCATCCATCA 58.434 45.455 0.00 0.00 0.00 3.07
191 193 0.879090 GAAACCAAACGGAGGCGATT 59.121 50.000 0.00 0.00 0.00 3.34
226 228 1.174712 AAGTGCGCAAACCTCTGCAT 61.175 50.000 14.00 0.00 42.77 3.96
259 261 6.169557 ACTAATCATAATTAGCCGTGTCCA 57.830 37.500 0.00 0.00 45.60 4.02
278 280 2.035961 CCACGGTTATGGACATCTCGAT 59.964 50.000 0.00 0.00 43.02 3.59
465 469 2.243810 AGGGAAAAATGGCTTTACGCA 58.756 42.857 0.00 0.00 41.67 5.24
575 579 2.579873 GCATATTCCATGTGCTGACCT 58.420 47.619 0.00 0.00 43.11 3.85
643 647 3.397849 AGGAGTTTTTAGGTCGTGGTC 57.602 47.619 0.00 0.00 0.00 4.02
775 779 9.996554 TCTTTTGAGACACTTGATGTAATAAGA 57.003 29.630 0.00 0.00 43.56 2.10
810 814 9.384764 GCTACTCTGTTATAAATCCTTCAAGTT 57.615 33.333 0.00 0.00 0.00 2.66
921 925 0.108615 GCACACGCTGACTGTAGGAT 60.109 55.000 0.00 0.00 34.30 3.24
982 986 7.888021 ACTCTCTTCTCTTTCTGACTTCTCATA 59.112 37.037 0.00 0.00 0.00 2.15
1032 1036 1.021968 GGAACAAGTTCACGCAACCT 58.978 50.000 14.25 0.00 41.20 3.50
1036 1040 1.873591 ACAAGTTCACGCAACCTGATC 59.126 47.619 3.98 0.00 35.28 2.92
1075 1079 3.053455 CGTCACTTGAAGGAAGTCACTC 58.947 50.000 0.00 0.00 43.52 3.51
1225 1229 6.321181 AGAGTTTTCTTTTGATGCACCAACTA 59.679 34.615 0.00 0.00 0.00 2.24
1428 1432 2.014857 CGACGTCAGGAGAACCAGATA 58.985 52.381 17.16 0.00 38.94 1.98
1502 1506 2.972713 AGGAAGAACTCAAGGCTACACA 59.027 45.455 0.00 0.00 0.00 3.72
1548 1552 8.239038 TCGAAGTATTAGTGGAGAAGAATGAT 57.761 34.615 0.00 0.00 0.00 2.45
1590 1594 1.348064 TATTCATGGGAGGCCCTACG 58.652 55.000 0.00 0.00 45.70 3.51
1635 1639 2.074729 AGGAGATTCGTCCGGAAGAT 57.925 50.000 21.05 10.98 42.05 2.40
2041 2046 7.482169 TGATGTAGTTGTTAGTCCAGAATCT 57.518 36.000 0.00 0.00 0.00 2.40
2145 2159 1.414919 TGTTTTCCAGTAGCACCGAGT 59.585 47.619 0.00 0.00 0.00 4.18
2165 2179 5.106908 CGAGTCGATAGTAGCAGATGATTGA 60.107 44.000 6.73 0.00 37.40 2.57
2240 2254 1.068333 GTGAAGTTTGCCGCACATCAT 60.068 47.619 0.00 0.00 0.00 2.45
2287 2301 2.489722 GGGAGAATTTCACAGCCACTTC 59.510 50.000 0.00 0.00 0.00 3.01
2295 2309 1.770110 ACAGCCACTTCCCCTGTCA 60.770 57.895 0.00 0.00 34.99 3.58
2298 2312 1.966451 GCCACTTCCCCTGTCAACG 60.966 63.158 0.00 0.00 0.00 4.10
2331 2345 1.043022 CCAGTTTCAGCAGGCCTTTT 58.957 50.000 0.00 0.00 0.00 2.27
2594 2609 3.520721 TGCTCTCATGATTGAAGGGAAGA 59.479 43.478 0.00 0.00 0.00 2.87
2713 2728 0.183492 TTCAGCATACCCATGGAGGC 59.817 55.000 15.22 7.77 35.39 4.70
2737 2752 0.523072 GCTCGCACAATCACAATGGT 59.477 50.000 0.00 0.00 0.00 3.55
2739 2754 2.223112 GCTCGCACAATCACAATGGTAG 60.223 50.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 5.456330 CCCTACATCTGCTAGTCTACCACTA 60.456 48.000 0.00 0.00 36.43 2.74
149 151 3.002791 CGCACTACATGGTGTTTGAGAT 58.997 45.455 0.00 0.00 39.21 2.75
191 193 2.930950 CACTTTTCCCCACAAGACTCA 58.069 47.619 0.00 0.00 0.00 3.41
259 261 5.477291 AGATAATCGAGATGTCCATAACCGT 59.523 40.000 0.00 0.00 0.00 4.83
275 277 9.958234 CATGATAATCCAGGTACTAGATAATCG 57.042 37.037 0.00 0.00 35.34 3.34
278 280 9.822727 TGACATGATAATCCAGGTACTAGATAA 57.177 33.333 0.00 0.00 35.34 1.75
336 339 7.222872 AGCATCATCATTAAACAAAACCCAAA 58.777 30.769 0.00 0.00 0.00 3.28
465 469 6.775629 TGGAAAGCTCTATGGTTACAGTTTTT 59.224 34.615 0.00 0.00 35.02 1.94
575 579 0.814410 TAACGTTGCAGCCCGAAACA 60.814 50.000 11.99 0.00 0.00 2.83
643 647 3.384668 CAACGGCATCACTGAGTATAGG 58.615 50.000 0.00 0.00 0.00 2.57
738 742 7.475137 AGTGTCTCAAAAGAGAGCTTACTAT 57.525 36.000 0.00 0.00 35.59 2.12
741 745 5.986135 TCAAGTGTCTCAAAAGAGAGCTTAC 59.014 40.000 10.08 0.00 35.59 2.34
746 750 7.953158 TTACATCAAGTGTCTCAAAAGAGAG 57.047 36.000 0.00 0.00 42.29 3.20
763 767 8.478066 AGTAGCAATCACACTCTTATTACATCA 58.522 33.333 0.00 0.00 0.00 3.07
775 779 9.319143 GATTTATAACAGAGTAGCAATCACACT 57.681 33.333 0.00 0.00 0.00 3.55
810 814 2.368548 AGTAATGCTGACACCACACAGA 59.631 45.455 0.00 0.00 36.38 3.41
880 884 5.163269 TGCTCTGATACCATCTTGTAGCAAT 60.163 40.000 0.00 0.00 36.75 3.56
882 886 3.706086 TGCTCTGATACCATCTTGTAGCA 59.294 43.478 0.00 0.00 34.95 3.49
921 925 4.338879 AGGTCTTTAGCTTAGTGGTCGTA 58.661 43.478 0.00 0.00 0.00 3.43
982 986 5.823045 CCGCCATCCTAAAAGAGTAGAAAAT 59.177 40.000 0.00 0.00 0.00 1.82
1032 1036 3.624707 GCCCAAAGGGTGTATCTTGATCA 60.625 47.826 3.68 0.00 46.51 2.92
1053 1057 1.527311 GTGACTTCCTTCAAGTGACGC 59.473 52.381 0.00 0.00 46.10 5.19
1075 1079 4.825634 TGGTACTCCTATGTTCAGGTATCG 59.174 45.833 0.00 0.00 36.99 2.92
1225 1229 3.037549 CCATGCTCTTTCCTAGACTCCT 58.962 50.000 0.00 0.00 0.00 3.69
1428 1432 1.547820 AGATCTATCATGTCGGCGCAT 59.452 47.619 10.83 6.50 0.00 4.73
1502 1506 6.806751 TCGATTTCCTCTTCGTAATCTTCAT 58.193 36.000 0.00 0.00 36.74 2.57
1590 1594 3.851976 TCTTCGTCTTCTTCTACTGGC 57.148 47.619 0.00 0.00 0.00 4.85
1635 1639 3.702330 GGTGTCGTCGATGATGATGTAA 58.298 45.455 11.16 0.00 29.93 2.41
1668 1672 6.260870 ACATAGTCATCATCACTATCGTCC 57.739 41.667 0.00 0.00 35.28 4.79
2041 2046 3.304911 TGTTGTTGTTCCCCTGATTCA 57.695 42.857 0.00 0.00 0.00 2.57
2145 2159 5.182190 GGAGTCAATCATCTGCTACTATCGA 59.818 44.000 0.00 0.00 0.00 3.59
2165 2179 0.814457 CTCTAGCTGTCTTGCGGAGT 59.186 55.000 0.00 0.00 38.13 3.85
2208 2222 3.716601 CAAACTTCACCTTTTCCGCATT 58.283 40.909 0.00 0.00 0.00 3.56
2240 2254 1.841302 ATGCTGCGGGTCCTTCAAGA 61.841 55.000 0.00 0.00 0.00 3.02
2287 2301 1.961277 GTGACAGCGTTGACAGGGG 60.961 63.158 6.16 0.00 29.85 4.79
2327 2341 3.052036 CTGAAACATGGGCGTTCAAAAG 58.948 45.455 0.00 0.00 0.00 2.27
2331 2345 0.821301 TGCTGAAACATGGGCGTTCA 60.821 50.000 0.00 0.67 0.00 3.18
2594 2609 3.076621 TGCGATTCTCAATCTGCTGTTT 58.923 40.909 11.56 0.00 37.87 2.83
2713 2728 0.735978 TGTGATTGTGCGAGCTACCG 60.736 55.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.