Multiple sequence alignment - TraesCS5A01G153700

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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 TraesCS5A01G153700 chr5A 100.000 2668 0 0 1 2668 331111934 331114601 0 4927
1 TraesCS5A01G153700 chr5A 100.000 1924 0 0 2912 4835 331114845 331116768 0 3554
2 TraesCS5A01G153700 chr5B 94.672 2684 95 22 1 2668 281582632 281579981 0 4120
3 TraesCS5A01G153700 chr5B 96.405 1947 44 8 2914 4835 281579937 281577992 0 3184
4 TraesCS5A01G153700 chr5D 95.368 1943 39 17 2918 4835 247074629 247076545 0 3042
5 TraesCS5A01G153700 chr5D 94.746 1808 64 10 877 2668 247072525 247074317 0 2784
6 TraesCS5A01G153700 chr5D 95.311 853 25 7 1 847 247071372 247072215 0 1339
7 TraesCS5A01G153700 chr3A 88.282 1007 77 13 2983 3967 95945629 95944642 0 1168
8 TraesCS5A01G153700 chr3A 85.015 1021 115 13 1003 1987 95948627 95947609 0 1003
9 TraesCS5A01G153700 chr3B 87.972 1006 83 15 2988 3974 127856285 127855299 0 1153
10 TraesCS5A01G153700 chr3B 85.927 1009 105 11 1015 1987 127862489 127861482 0 1042
11 TraesCS5A01G153700 chr3D 87.071 1021 92 16 2964 3963 81693299 81692298 0 1118
12 TraesCS5A01G153700 chr3D 85.658 1011 109 10 1003 1979 81696319 81695311 0 1031


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 TraesCS5A01G153700 chr5A 331111934 331116768 4834 False 4240.500000 4927 100.000000 1 4835 2 chr5A.!!$F1 4834
1 TraesCS5A01G153700 chr5B 281577992 281582632 4640 True 3652.000000 4120 95.538500 1 4835 2 chr5B.!!$R1 4834
2 TraesCS5A01G153700 chr5D 247071372 247076545 5173 False 2388.333333 3042 95.141667 1 4835 3 chr5D.!!$F1 4834
3 TraesCS5A01G153700 chr3A 95944642 95948627 3985 True 1085.500000 1168 86.648500 1003 3967 2 chr3A.!!$R1 2964
4 TraesCS5A01G153700 chr3B 127855299 127856285 986 True 1153.000000 1153 87.972000 2988 3974 1 chr3B.!!$R1 986
5 TraesCS5A01G153700 chr3B 127861482 127862489 1007 True 1042.000000 1042 85.927000 1015 1987 1 chr3B.!!$R2 972
6 TraesCS5A01G153700 chr3D 81692298 81696319 4021 True 1074.500000 1118 86.364500 1003 3963 2 chr3D.!!$R1 2960

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
326 330 0.108662 GCAAAGAAGGGGGCGATTTG 60.109 55.0 0.0 0.0 34.70 2.32 F
859 1145 0.180406 GCGCTTAATCTCTTGGGGGA 59.820 55.0 0.0 0.0 0.00 4.81 F
1677 2011 0.693430 AGGAGGAGATGCTGATGCCA 60.693 55.0 0.0 0.0 38.71 4.92 F
3331 4785 0.178873 AAAGACTCCACCCCCAGCTA 60.179 55.0 0.0 0.0 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1417 1751 1.376424 CGAGGATGTGCCACTTGCT 60.376 57.895 4.41 4.41 42.00 3.91 R
2393 3176 0.389817 TCGGATCTTGCTGGTGTTCG 60.390 55.000 0.00 0.00 0.00 3.95 R
3400 4854 1.355381 TCCTCCATGGATTGCAACTGT 59.645 47.619 16.63 0.00 40.56 3.55 R
4160 5634 1.677052 GGTACAACAACAAAAGGCGGA 59.323 47.619 0.00 0.00 0.00 5.54 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
65 66 5.297547 TGTTTGACGCCTCTTATATGGATC 58.702 41.667 0.00 0.00 0.00 3.36
260 264 2.503356 AGAAGACACTTGCTATGGAGGG 59.497 50.000 0.00 0.00 0.00 4.30
326 330 0.108662 GCAAAGAAGGGGGCGATTTG 60.109 55.000 0.00 0.00 34.70 2.32
434 438 1.291877 CGTTCTTCTGCTTCGGGGTG 61.292 60.000 0.00 0.00 0.00 4.61
699 704 8.482429 GCATCACAAGAGAAATTTTTGTTAGTG 58.518 33.333 4.37 8.54 33.06 2.74
702 707 9.173021 TCACAAGAGAAATTTTTGTTAGTGAGA 57.827 29.630 14.00 4.14 33.06 3.27
749 755 6.647481 GCCATCATCATGCTGATCTATCTATC 59.353 42.308 9.07 0.00 34.28 2.08
750 756 7.472240 GCCATCATCATGCTGATCTATCTATCT 60.472 40.741 9.07 0.00 34.28 1.98
751 757 9.080097 CCATCATCATGCTGATCTATCTATCTA 57.920 37.037 9.07 0.00 34.28 1.98
788 794 6.971602 TGATAATGGTTAGCACAAACGAAAA 58.028 32.000 0.00 0.00 0.00 2.29
854 1140 1.643832 GGCCGCGCTTAATCTCTTG 59.356 57.895 5.56 0.00 0.00 3.02
859 1145 0.180406 GCGCTTAATCTCTTGGGGGA 59.820 55.000 0.00 0.00 0.00 4.81
941 1229 4.492611 GGACCGGATCTAATCGATTTACC 58.507 47.826 17.19 12.90 30.84 2.85
961 1249 4.400251 CCCACCTCTCCCTCCCGT 62.400 72.222 0.00 0.00 0.00 5.28
999 1288 1.685224 CTGCCTCTAAACCCCAGCA 59.315 57.895 0.00 0.00 0.00 4.41
1202 1536 2.126307 CAGCCTCCTCGTCACGTG 60.126 66.667 9.94 9.94 0.00 4.49
1548 1882 4.738998 CAGCCCACGCCCATCCAA 62.739 66.667 0.00 0.00 34.57 3.53
1677 2011 0.693430 AGGAGGAGATGCTGATGCCA 60.693 55.000 0.00 0.00 38.71 4.92
1949 2286 5.590259 ACCTTGACAATTGCAGGTATGTATC 59.410 40.000 18.58 1.57 0.00 2.24
1957 2295 7.334421 ACAATTGCAGGTATGTATCGGATATTC 59.666 37.037 5.05 0.00 0.00 1.75
2140 2912 1.382240 CATTAGTGTGGGTGGGCCA 59.618 57.895 0.00 0.00 36.17 5.36
2208 2983 8.110612 GCGTGTCTATAATTATCGAATGAATGG 58.889 37.037 0.00 0.00 0.00 3.16
2223 2998 8.593679 TCGAATGAATGGGATGTACACTTATAT 58.406 33.333 0.00 0.00 0.00 0.86
2242 3025 2.112279 TGTCAGGTAGGGGTGACTTT 57.888 50.000 4.27 0.00 43.03 2.66
2393 3176 4.019321 TGTTATATTGCAGGCCCTCCTATC 60.019 45.833 0.00 0.00 41.93 2.08
2507 3358 6.375455 CAGTGTCCTTCTTAGTTAATGCCAAT 59.625 38.462 0.00 0.00 0.00 3.16
2541 3417 9.745018 ATAGGCATTGTTATATAGACAGCAATT 57.255 29.630 0.00 0.00 0.00 2.32
2559 3435 7.393234 ACAGCAATTTAGATGTAAACTTGCCTA 59.607 33.333 23.29 0.00 39.85 3.93
2560 3436 8.243426 CAGCAATTTAGATGTAAACTTGCCTAA 58.757 33.333 23.29 0.00 39.85 2.69
2561 3437 8.462016 AGCAATTTAGATGTAAACTTGCCTAAG 58.538 33.333 23.29 0.00 39.85 2.18
2594 3470 2.919602 ACAACTAATCCCCATCACTGGT 59.080 45.455 0.00 0.00 41.37 4.00
2659 3535 6.268847 GGTAGAACCATTCTGATCCTAGATGT 59.731 42.308 1.26 0.00 40.94 3.06
2955 4406 8.352942 ACTTCTTTTAAATGCAAGTAGAACCTG 58.647 33.333 12.76 1.35 0.00 4.00
3065 4519 4.080695 AGCTGATAGGCTTGTTGATCTTGA 60.081 41.667 0.00 0.00 39.86 3.02
3088 4542 2.159179 TGAGGATGACATTCGGGAGA 57.841 50.000 0.00 0.00 0.00 3.71
3324 4778 1.248486 GCCTTCAAAAGACTCCACCC 58.752 55.000 0.00 0.00 0.00 4.61
3331 4785 0.178873 AAAGACTCCACCCCCAGCTA 60.179 55.000 0.00 0.00 0.00 3.32
3362 4816 4.431809 TGTGAAAACAAAGCTGATGTTGG 58.568 39.130 16.37 0.00 39.98 3.77
3400 4854 8.437575 AGTATCTTCTTCTAAAGGGTGTTGAAA 58.562 33.333 0.00 0.00 0.00 2.69
3546 5000 7.332926 CCTGATATCCAGCATGTGATTAACTAC 59.667 40.741 0.00 0.00 41.57 2.73
3602 5056 0.828022 ATTGGTCGAACTGGCCGATA 59.172 50.000 0.33 0.00 38.38 2.92
3829 5283 0.036952 TGCTGACTGTCCTAAGCTGC 60.037 55.000 16.47 0.00 36.60 5.25
3832 5302 1.185618 TGACTGTCCTAAGCTGCGGT 61.186 55.000 5.17 0.00 0.00 5.68
3884 5354 1.104630 GTGGAGGTTACCGAGGAGAG 58.895 60.000 0.00 0.00 0.00 3.20
3963 5437 2.094894 CGTGAGTTCATCCATGCTTGAC 59.905 50.000 0.22 0.00 0.00 3.18
4066 5540 5.843019 TTCTTTTCTGGAGGGTATTCACT 57.157 39.130 0.00 0.00 0.00 3.41
4088 5562 8.755028 TCACTAGTCAAAACCTAGTAATGCATA 58.245 33.333 0.00 0.00 42.42 3.14
4093 5567 7.557719 AGTCAAAACCTAGTAATGCATATTGCT 59.442 33.333 0.00 0.00 45.31 3.91
4194 5668 6.478344 TGTTGTTGTACCAAATGATGCTTTTC 59.522 34.615 0.00 0.00 0.00 2.29
4236 5710 3.576550 GGGCCCACAAAGAAATTTGTAGA 59.423 43.478 19.95 0.00 42.69 2.59
4264 5738 2.729028 AAGGCATACTATGGGCGTTT 57.271 45.000 0.00 0.00 32.35 3.60
4278 5752 4.664392 TGGGCGTTTCTTTCCCTTTATTA 58.336 39.130 0.00 0.00 40.69 0.98
4335 5818 7.173907 AGGTACATCAAGACATTTCAAACTGAG 59.826 37.037 0.00 0.00 0.00 3.35
4553 6036 3.087031 AGCTCCATTTGACCACATCTTG 58.913 45.455 0.00 0.00 0.00 3.02
4738 6221 7.454260 AAAATTGCTCTAGGACCTAAACAAG 57.546 36.000 2.08 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 7.792925 TGTGTCGTATACAAAGAAAGATTGTG 58.207 34.615 3.32 0.00 40.95 3.33
65 66 0.457035 AACAGCTGCACTTGTGTTGG 59.543 50.000 15.27 0.00 31.94 3.77
265 269 2.487428 CCCAGTGAGAGAGACGCG 59.513 66.667 3.53 3.53 0.00 6.01
309 313 0.407918 TCCAAATCGCCCCCTTCTTT 59.592 50.000 0.00 0.00 0.00 2.52
326 330 2.292292 GCTCTACACGAGGATCTTCTCC 59.708 54.545 3.09 0.00 45.33 3.71
404 408 2.678324 CAGAAGAACGACCCTCAGAAC 58.322 52.381 0.00 0.00 0.00 3.01
409 413 1.715993 GAAGCAGAAGAACGACCCTC 58.284 55.000 0.00 0.00 0.00 4.30
629 633 2.408835 CACGGGATCAAATGCGCC 59.591 61.111 4.18 0.00 0.00 6.53
699 704 5.587844 ACACACATTTCCTTATGCATCTCTC 59.412 40.000 0.19 0.00 0.00 3.20
702 707 4.142315 GCACACACATTTCCTTATGCATCT 60.142 41.667 0.19 0.00 0.00 2.90
751 757 8.416329 GCTAACCATTATCAGGTTTTGAATCAT 58.584 33.333 2.64 0.00 46.85 2.45
752 758 7.395772 TGCTAACCATTATCAGGTTTTGAATCA 59.604 33.333 2.64 0.00 46.85 2.57
769 775 8.649973 TTTTATTTTTCGTTTGTGCTAACCAT 57.350 26.923 0.00 0.00 0.00 3.55
770 776 8.475331 TTTTTATTTTTCGTTTGTGCTAACCA 57.525 26.923 0.00 0.00 0.00 3.67
811 817 1.202806 ACCAGACCCAACAGTGTCATG 60.203 52.381 0.00 0.00 33.89 3.07
854 1140 3.607370 GAGTCGGTTGCTGTCCCCC 62.607 68.421 0.00 0.00 0.00 5.40
859 1145 1.202758 TGGAATTGAGTCGGTTGCTGT 60.203 47.619 0.00 0.00 0.00 4.40
906 1194 3.400054 GGTCCGACCCTGGGAAGG 61.400 72.222 22.23 20.92 34.80 3.46
941 1229 1.075151 GGGAGGGAGAGGTGGGTAG 60.075 68.421 0.00 0.00 0.00 3.18
961 1249 3.582358 GGGGGTTTTCGTGGGGGA 61.582 66.667 0.00 0.00 0.00 4.81
1296 1630 3.966543 CCCACGGGCTTGAGGGTT 61.967 66.667 5.00 0.00 35.26 4.11
1396 1730 2.103340 GAGCTCGTCGGCCTTCTC 59.897 66.667 0.00 0.00 0.00 2.87
1398 1732 4.856607 CGGAGCTCGTCGGCCTTC 62.857 72.222 7.83 0.00 0.00 3.46
1417 1751 1.376424 CGAGGATGTGCCACTTGCT 60.376 57.895 4.41 4.41 42.00 3.91
1467 1801 2.962569 CGGAGGTCGCAGAAGTCA 59.037 61.111 0.00 0.00 39.69 3.41
1677 2011 2.772924 CCCTCCCCAGGCACAATT 59.227 61.111 0.00 0.00 38.72 2.32
1949 2286 5.059161 ACACCACATTGATCAGAATATCCG 58.941 41.667 0.00 0.00 0.00 4.18
1957 2295 7.993101 AGATATGAAAACACCACATTGATCAG 58.007 34.615 0.00 0.00 0.00 2.90
2140 2912 9.227777 GTTTTACCCATTAGAAATACACTCACT 57.772 33.333 0.00 0.00 0.00 3.41
2208 2983 7.309867 CCCTACCTGACATATAAGTGTACATCC 60.310 44.444 0.00 0.00 31.16 3.51
2223 2998 1.975680 GAAAGTCACCCCTACCTGACA 59.024 52.381 0.00 0.00 39.49 3.58
2242 3025 1.688735 CCCATCAGCCGTATCTTCTGA 59.311 52.381 0.00 0.00 40.62 3.27
2393 3176 0.389817 TCGGATCTTGCTGGTGTTCG 60.390 55.000 0.00 0.00 0.00 3.95
2463 3307 7.148407 GGACACTGAAATTGTCGTTATCTCATT 60.148 37.037 0.00 0.00 43.75 2.57
2590 3466 7.837863 TCCTACAGAGTTTGATTACTTACCAG 58.162 38.462 0.00 0.00 0.00 4.00
2955 4406 4.044426 CACTGCTTTTTAAAGGCACTGAC 58.956 43.478 10.40 0.00 40.86 3.51
3065 4519 2.571653 TCCCGAATGTCATCCTCAAACT 59.428 45.455 0.00 0.00 0.00 2.66
3324 4778 9.868277 TTGTTTTCACAAAATATAATAGCTGGG 57.132 29.630 0.00 0.00 40.10 4.45
3362 4816 6.991938 AGAAGAAGATACTCATGGATGTAGC 58.008 40.000 0.00 0.00 0.00 3.58
3400 4854 1.355381 TCCTCCATGGATTGCAACTGT 59.645 47.619 16.63 0.00 40.56 3.55
3546 5000 1.745653 TCTATCTCGGCAGGCATATCG 59.254 52.381 0.00 0.00 0.00 2.92
3602 5056 4.677182 AGTTGCTATTCCAGTTTTCCCAT 58.323 39.130 0.00 0.00 0.00 4.00
3723 5177 0.987294 CATCCTCCAGTGGGTCAACT 59.013 55.000 9.92 0.00 34.93 3.16
3829 5283 1.746615 CTGGAACCAGCCATCACCG 60.747 63.158 7.95 0.00 37.30 4.94
3832 5302 1.280133 CTCTTCTGGAACCAGCCATCA 59.720 52.381 15.20 0.00 43.31 3.07
3963 5437 5.155278 TGTAAGGTAAGGTGTGGTGTATG 57.845 43.478 0.00 0.00 0.00 2.39
4066 5540 8.836413 GCAATATGCATTACTAGGTTTTGACTA 58.164 33.333 3.54 0.00 44.26 2.59
4088 5562 1.206610 TGTGCACCACAACAAAGCAAT 59.793 42.857 15.69 0.00 41.69 3.56
4160 5634 1.677052 GGTACAACAACAAAAGGCGGA 59.323 47.619 0.00 0.00 0.00 5.54
4194 5668 3.815401 CCCGGCTACCAAATAGAAGATTG 59.185 47.826 0.00 0.00 31.83 2.67
4236 5710 6.241645 GCCCATAGTATGCCTTTAAAGATCT 58.758 40.000 16.98 9.09 0.00 2.75
4264 5738 9.374711 ACTGAAACCATTTAATAAAGGGAAAGA 57.625 29.630 21.42 3.82 44.82 2.52
4278 5752 6.403866 TTCACATGCTAACTGAAACCATTT 57.596 33.333 0.00 0.00 0.00 2.32
4335 5818 4.789012 TGAACCAGATGGATTTGAAAGC 57.211 40.909 5.72 0.00 38.94 3.51
4378 5861 7.041644 GCTTGGTATCGGCACTTAATATTTACA 60.042 37.037 0.00 0.00 0.00 2.41
4738 6221 4.132336 GGTTCATTAAGGTCCCCGATAAC 58.868 47.826 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.