Multiple sequence alignment - TraesCS6D01G214000

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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 TraesCS6D01G214000 chr6D 100.000 3389 0 0 1 3389 304286882 304290270 0.000000e+00 6259.0
1 TraesCS6D01G214000 chr6A 97.507 3329 63 10 78 3389 410895922 410892597 0.000000e+00 5670.0
2 TraesCS6D01G214000 chr6A 93.850 2000 81 23 1130 3122 441435761 441437725 0.000000e+00 2974.0
3 TraesCS6D01G214000 chr6A 95.697 1069 29 8 1 1061 441434376 441435435 0.000000e+00 1703.0
4 TraesCS6D01G214000 chr6B 96.067 3407 99 18 1 3389 470131020 470134409 0.000000e+00 5517.0
5 TraesCS6D01G214000 chr3A 83.696 92 11 3 3290 3381 275567740 275567653 2.170000e-12 84.2
6 TraesCS6D01G214000 chr1B 82.653 98 13 3 3284 3381 518875764 518875671 2.170000e-12 84.2
7 TraesCS6D01G214000 chr4A 90.323 62 6 0 3320 3381 546004067 546004006 7.790000e-12 82.4
8 TraesCS6D01G214000 chr4A 94.444 36 2 0 3346 3381 603355726 603355691 4.720000e-04 56.5
9 TraesCS6D01G214000 chr7A 97.222 36 1 0 3346 3381 310303892 310303927 1.020000e-05 62.1
10 TraesCS6D01G214000 chr5B 97.222 36 1 0 3346 3381 692810586 692810551 1.020000e-05 62.1
11 TraesCS6D01G214000 chr5B 97.222 36 1 0 3346 3381 692812666 692812631 1.020000e-05 62.1


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 TraesCS6D01G214000 chr6D 304286882 304290270 3388 False 6259.0 6259 100.0000 1 3389 1 chr6D.!!$F1 3388
1 TraesCS6D01G214000 chr6A 410892597 410895922 3325 True 5670.0 5670 97.5070 78 3389 1 chr6A.!!$R1 3311
2 TraesCS6D01G214000 chr6A 441434376 441437725 3349 False 2338.5 2974 94.7735 1 3122 2 chr6A.!!$F1 3121
3 TraesCS6D01G214000 chr6B 470131020 470134409 3389 False 5517.0 5517 96.0670 1 3389 1 chr6B.!!$F1 3388

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
978 1005 0.180171 AAAACCCCAAACCTTGCTGC 59.82 50.0 0.0 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2482 2766 1.22603 AACGGCAACACCTTAGCGTC 61.226 55.0 0.0 0.0 35.61 5.19 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
109 111 7.907389 AGAATTACAAGATCACAGGTAAGTCA 58.093 34.615 18.99 0.00 40.97 3.41
126 132 7.336931 AGGTAAGTCAGGCATAAATGTACAAAG 59.663 37.037 0.00 0.00 0.00 2.77
142 149 1.842381 AAAGACGAAGGGGGCCAGAG 61.842 60.000 4.39 0.00 0.00 3.35
211 218 7.205297 ACCAATATGATACTTTGCTCAAATGC 58.795 34.615 0.00 0.00 0.00 3.56
289 298 1.003839 AGCTCCGATTTGGCGAACA 60.004 52.632 0.00 0.00 37.80 3.18
854 863 1.309950 GGGCTTAGGATTTCGGCTTC 58.690 55.000 0.00 0.00 0.00 3.86
927 954 3.321497 CAAGACTCCTCTTGTGCTGTAC 58.679 50.000 2.79 0.00 45.94 2.90
929 956 2.823154 AGACTCCTCTTGTGCTGTACTC 59.177 50.000 0.00 0.00 0.00 2.59
930 957 2.823154 GACTCCTCTTGTGCTGTACTCT 59.177 50.000 0.00 0.00 0.00 3.24
931 958 2.560542 ACTCCTCTTGTGCTGTACTCTG 59.439 50.000 0.00 0.00 0.00 3.35
932 959 2.560542 CTCCTCTTGTGCTGTACTCTGT 59.439 50.000 0.00 0.00 0.00 3.41
933 960 2.297315 TCCTCTTGTGCTGTACTCTGTG 59.703 50.000 0.00 0.00 0.00 3.66
934 961 2.064762 CTCTTGTGCTGTACTCTGTGC 58.935 52.381 0.00 0.00 0.00 4.57
935 962 1.688735 TCTTGTGCTGTACTCTGTGCT 59.311 47.619 0.00 0.00 0.00 4.40
936 963 2.103094 TCTTGTGCTGTACTCTGTGCTT 59.897 45.455 0.00 0.00 0.00 3.91
937 964 2.620251 TGTGCTGTACTCTGTGCTTT 57.380 45.000 0.00 0.00 0.00 3.51
938 965 2.212652 TGTGCTGTACTCTGTGCTTTG 58.787 47.619 0.00 0.00 0.00 2.77
978 1005 0.180171 AAAACCCCAAACCTTGCTGC 59.820 50.000 0.00 0.00 0.00 5.25
1431 1715 2.045926 CCCTTCAACGCCCTCCTG 60.046 66.667 0.00 0.00 0.00 3.86
1434 1718 1.371183 CTTCAACGCCCTCCTGTCA 59.629 57.895 0.00 0.00 0.00 3.58
1764 2048 3.434319 GCCATGCACCACGGACTG 61.434 66.667 0.00 0.00 0.00 3.51
2070 2354 5.857268 ACAATGAAAGGATTTGTTGAAGGG 58.143 37.500 0.00 0.00 39.27 3.95
2115 2399 4.743955 GCTGAGGCGAAGGAGGTTATTTAT 60.744 45.833 0.00 0.00 0.00 1.40
2461 2745 9.897744 TCATTCTCAACATTGAAGAATTGTTAC 57.102 29.630 12.62 0.00 35.18 2.50
2482 2766 0.107459 GCTGCTTTGGGGAGAGGTAG 60.107 60.000 0.00 0.00 35.24 3.18
2485 2769 0.175989 GCTTTGGGGAGAGGTAGACG 59.824 60.000 0.00 0.00 0.00 4.18
2523 2807 1.202964 TCGATAAGGGCTCGTGGGATA 60.203 52.381 0.00 0.00 37.40 2.59
2605 2889 2.100631 AGTGTGCGCGATGTTAGGC 61.101 57.895 12.10 0.00 0.00 3.93
2809 3099 4.556699 GCTTCACCATTAACAGTGTTGGTC 60.557 45.833 18.90 2.93 40.44 4.02
3197 3491 2.821991 AGGGACAGAAAGTGACGAAG 57.178 50.000 0.00 0.00 0.00 3.79
3299 3603 5.808366 TGTAGGAGATGGTATGCCTTTAG 57.192 43.478 0.16 0.00 35.27 1.85
3300 3604 5.216622 TGTAGGAGATGGTATGCCTTTAGT 58.783 41.667 0.16 0.00 35.27 2.24
3327 3632 6.821665 TCTGGTTAGTGGTAATCTATTTGTGC 59.178 38.462 0.00 0.00 0.00 4.57
3328 3633 6.717289 TGGTTAGTGGTAATCTATTTGTGCT 58.283 36.000 0.00 0.00 0.00 4.40
3329 3634 7.172342 TGGTTAGTGGTAATCTATTTGTGCTT 58.828 34.615 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 6.588756 TCAGTTATTTTACATGTCTCCGTGAC 59.411 38.462 0.00 0.0 45.54 3.67
109 111 5.354234 CCTTCGTCTTTGTACATTTATGCCT 59.646 40.000 0.00 0.0 0.00 4.75
126 132 1.627297 AATCTCTGGCCCCCTTCGTC 61.627 60.000 0.00 0.0 0.00 4.20
142 149 6.846283 CGTTTTCTATTAATCTGTGCCGAATC 59.154 38.462 0.00 0.0 0.00 2.52
211 218 3.190849 CAGGTGCGCTCCGATGTG 61.191 66.667 21.85 11.5 0.00 3.21
289 298 3.122480 TCCTTGGGATGTATGACCACAT 58.878 45.455 0.00 0.0 41.83 3.21
854 863 3.806316 ACTGTACCAATTTTCTTCGCG 57.194 42.857 0.00 0.0 0.00 5.87
927 954 2.983136 CGACAGAGTACAAAGCACAGAG 59.017 50.000 0.00 0.0 0.00 3.35
929 956 1.457303 GCGACAGAGTACAAAGCACAG 59.543 52.381 0.00 0.0 0.00 3.66
930 957 1.497991 GCGACAGAGTACAAAGCACA 58.502 50.000 0.00 0.0 0.00 4.57
931 958 0.790814 GGCGACAGAGTACAAAGCAC 59.209 55.000 0.00 0.0 0.00 4.40
932 959 0.320421 GGGCGACAGAGTACAAAGCA 60.320 55.000 0.00 0.0 0.00 3.91
933 960 0.320421 TGGGCGACAGAGTACAAAGC 60.320 55.000 0.00 0.0 0.00 3.51
934 961 2.163818 TTGGGCGACAGAGTACAAAG 57.836 50.000 0.00 0.0 0.00 2.77
935 962 2.614983 GTTTTGGGCGACAGAGTACAAA 59.385 45.455 0.00 0.0 0.00 2.83
936 963 2.215196 GTTTTGGGCGACAGAGTACAA 58.785 47.619 0.00 0.0 0.00 2.41
937 964 1.541670 GGTTTTGGGCGACAGAGTACA 60.542 52.381 0.00 0.0 0.00 2.90
938 965 1.154197 GGTTTTGGGCGACAGAGTAC 58.846 55.000 0.00 0.0 0.00 2.73
978 1005 1.525995 CGGGGGTGGAATTGGATCG 60.526 63.158 0.00 0.0 0.00 3.69
1395 1679 2.203847 ATCGGCGAGATGGGGGAT 60.204 61.111 17.22 0.0 38.36 3.85
1431 1715 2.432628 CACCGGACGAAGGCTGAC 60.433 66.667 9.46 0.0 0.00 3.51
1764 2048 1.678970 ACCTTCCGGCTTGCCATTC 60.679 57.895 12.45 0.0 0.00 2.67
2070 2354 2.747855 CTGCCTCCCTTCGCCAAC 60.748 66.667 0.00 0.0 0.00 3.77
2115 2399 2.711009 AGGGAACTTCTTCATCACCACA 59.289 45.455 0.00 0.0 37.44 4.17
2461 2745 1.378250 CCTCTCCCCAAAGCAGCAG 60.378 63.158 0.00 0.0 0.00 4.24
2482 2766 1.226030 AACGGCAACACCTTAGCGTC 61.226 55.000 0.00 0.0 35.61 5.19
2485 2769 1.662026 CGAAAACGGCAACACCTTAGC 60.662 52.381 0.00 0.0 35.61 3.09
2605 2889 2.483876 AGCATCACCGGAACAATATCG 58.516 47.619 9.46 0.0 0.00 2.92
2809 3099 5.583495 CGATAGAGAAGACAAAGTACCAGG 58.417 45.833 0.00 0.0 39.76 4.45
3197 3491 9.039870 CAATTCACTTGTGAAGTAGGATATCTC 57.960 37.037 18.99 0.0 40.46 2.75
3299 3603 7.822822 ACAAATAGATTACCACTAACCAGACAC 59.177 37.037 0.00 0.0 0.00 3.67
3300 3604 7.822334 CACAAATAGATTACCACTAACCAGACA 59.178 37.037 0.00 0.0 0.00 3.41
3329 3634 7.686434 AGAGCTAACACTGTATTAGGGAAAAA 58.314 34.615 7.85 0.0 32.67 1.94


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

AutoCloner maintained by Alex Coulton.