Multiple sequence alignment - TraesCS6D01G118200

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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 TraesCS6D01G118200 chr6D 100.000 3959 0 0 1 3959 83955602 83951644 0.000000e+00 7312
1 TraesCS6D01G118200 chr2D 97.407 3972 87 7 1 3959 635037252 635041220 0.000000e+00 6750
2 TraesCS6D01G118200 chr5A 97.333 3975 89 6 1 3959 16623283 16619310 0.000000e+00 6737
3 TraesCS6D01G118200 chr7B 97.307 3973 90 8 1 3959 743066297 743070266 0.000000e+00 6728
4 TraesCS6D01G118200 chr3D 97.306 3972 92 7 1 3959 202611938 202615907 0.000000e+00 6728
5 TraesCS6D01G118200 chr4D 97.207 3974 93 8 1 3959 123367634 123371604 0.000000e+00 6708
6 TraesCS6D01G118200 chr7A 97.205 3972 96 7 1 3959 671960576 671956607 0.000000e+00 6706
7 TraesCS6D01G118200 chr7A 97.128 3970 99 7 1 3959 120828856 120824891 0.000000e+00 6685
8 TraesCS6D01G118200 chr7A 96.953 3971 108 4 1 3959 120925849 120921880 0.000000e+00 6650
9 TraesCS6D01G118200 chr7A 95.915 3256 116 9 1 3243 575306385 575309636 0.000000e+00 5260
10 TraesCS6D01G118200 chr7A 96.739 92 3 0 3868 3959 734970773 734970682 1.910000e-33 154


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 TraesCS6D01G118200 chr6D 83951644 83955602 3958 True 7312 7312 100.000 1 3959 1 chr6D.!!$R1 3958
1 TraesCS6D01G118200 chr2D 635037252 635041220 3968 False 6750 6750 97.407 1 3959 1 chr2D.!!$F1 3958
2 TraesCS6D01G118200 chr5A 16619310 16623283 3973 True 6737 6737 97.333 1 3959 1 chr5A.!!$R1 3958
3 TraesCS6D01G118200 chr7B 743066297 743070266 3969 False 6728 6728 97.307 1 3959 1 chr7B.!!$F1 3958
4 TraesCS6D01G118200 chr3D 202611938 202615907 3969 False 6728 6728 97.306 1 3959 1 chr3D.!!$F1 3958
5 TraesCS6D01G118200 chr4D 123367634 123371604 3970 False 6708 6708 97.207 1 3959 1 chr4D.!!$F1 3958
6 TraesCS6D01G118200 chr7A 671956607 671960576 3969 True 6706 6706 97.205 1 3959 1 chr7A.!!$R3 3958
7 TraesCS6D01G118200 chr7A 120824891 120828856 3965 True 6685 6685 97.128 1 3959 1 chr7A.!!$R1 3958
8 TraesCS6D01G118200 chr7A 120921880 120925849 3969 True 6650 6650 96.953 1 3959 1 chr7A.!!$R2 3958
9 TraesCS6D01G118200 chr7A 575306385 575309636 3251 False 5260 5260 95.915 1 3243 1 chr7A.!!$F1 3242

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
464 469 2.105821 TGGGTCCGTTGATGACTTTCTT 59.894 45.455 0.0 0.0 33.22 2.52 F
1057 1075 2.044492 AGTGGTCCTATTCTCTGTCCCA 59.956 50.000 0.0 0.0 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1482 1500 1.457346 AAAGCTTGATCCCAGCGAAG 58.543 50.0 0.0 0.0 0.0 3.79 R
3028 3060 1.391157 GGCCTTGCTTGTGTGTCCAA 61.391 55.0 0.0 0.0 0.0 3.53 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
52 53 3.848272 TTACGTTAAACTCCGTCCGAT 57.152 42.857 0.00 0.00 38.43 4.18
320 325 4.202305 GCCTTCAGATAGGTGCTCAACTAT 60.202 45.833 7.13 7.13 43.58 2.12
397 402 6.463049 GCAATAGATAGTTGCTCCTTCCACTA 60.463 42.308 3.77 0.00 46.34 2.74
446 451 7.316640 GCACACTACTAGATAGATTGTATGGG 58.683 42.308 0.00 0.00 34.65 4.00
454 459 4.899457 AGATAGATTGTATGGGTCCGTTGA 59.101 41.667 0.00 0.00 0.00 3.18
464 469 2.105821 TGGGTCCGTTGATGACTTTCTT 59.894 45.455 0.00 0.00 33.22 2.52
672 677 4.082949 GGCGTAACAAAGCTACCTGAAAAT 60.083 41.667 0.00 0.00 0.00 1.82
740 745 7.501892 GCCAGATGGATTCTTTAGAAAGATTCT 59.498 37.037 18.99 9.61 41.58 2.40
792 797 8.770828 GTTAGAATCTAAATAAAGGCGCATACA 58.229 33.333 10.83 0.00 0.00 2.29
1057 1075 2.044492 AGTGGTCCTATTCTCTGTCCCA 59.956 50.000 0.00 0.00 0.00 4.37
1099 1117 7.889469 TCCTCTTTTCATTCCAAATTCTTCAG 58.111 34.615 0.00 0.00 0.00 3.02
1353 1371 6.552008 TGGTATGAGAAGTTTTGGGAAAGAT 58.448 36.000 0.00 0.00 0.00 2.40
1482 1500 3.271142 CGGAGCTGAGCATCTTCTC 57.729 57.895 7.39 0.00 34.85 2.87
1557 1575 4.415332 CGGTCCCCTGTCGTCGTG 62.415 72.222 0.00 0.00 0.00 4.35
1984 2006 2.288886 GGTTAGTTCCTCTGTCGTTGCT 60.289 50.000 0.00 0.00 0.00 3.91
1986 2008 1.040646 AGTTCCTCTGTCGTTGCTGA 58.959 50.000 0.00 0.00 0.00 4.26
1999 2021 1.949525 GTTGCTGAAGAGTTCTTGGCA 59.050 47.619 12.19 12.19 38.54 4.92
2047 2070 0.616679 AAACGGAGGGGAGGATCGAA 60.617 55.000 0.00 0.00 34.37 3.71
2084 2107 7.447419 ATTCTGAAGAAGGACTGTTGGCAGT 62.447 44.000 0.00 0.00 46.65 4.40
2103 2126 5.488341 GCAGTAGGTGGAGACATTTCTTTA 58.512 41.667 0.00 0.00 46.14 1.85
2146 2169 1.112315 CAGGGTAGAGCTCGGCAGAT 61.112 60.000 8.37 0.00 0.00 2.90
2241 2264 1.077716 GCAGGCCTAAACGATGGGT 60.078 57.895 3.98 0.00 0.00 4.51
2252 2275 2.446848 CGATGGGTGGGCATCTCCT 61.447 63.158 0.00 0.00 34.39 3.69
2458 2481 2.290071 CCAACTACCACCGGTCAATTCT 60.290 50.000 2.59 0.00 37.09 2.40
2460 2483 1.975680 ACTACCACCGGTCAATTCTGT 59.024 47.619 2.59 0.00 37.09 3.41
2508 2531 4.845541 TCATTATAGGGGTATGGGGTTCA 58.154 43.478 0.00 0.00 0.00 3.18
3028 3060 5.704053 CCGTTAGGTCACCTATTTTGAGTTT 59.296 40.000 3.76 0.00 35.87 2.66
3094 3126 4.969359 ACCCATCAACCTACTAGCAATAGT 59.031 41.667 0.00 0.00 0.00 2.12
3273 3305 2.586648 ATCTTTCGGTTGGCTTTCCT 57.413 45.000 0.00 0.00 0.00 3.36
3286 3318 6.325596 GTTGGCTTTCCTGTGAATAAGAATC 58.674 40.000 0.00 0.00 0.00 2.52
3377 3409 3.514645 GCATGGCTGAAATGAACGAAAT 58.485 40.909 0.00 0.00 0.00 2.17
3525 3557 6.931281 TGGATCCATCAGAAAGAAATCGATAC 59.069 38.462 11.44 0.00 0.00 2.24
3561 3593 4.204799 TCTACATCGTATGTACAGTGCCT 58.795 43.478 0.33 0.00 44.38 4.75
3830 3863 4.624364 CACGTGCCCAGTCCAGCA 62.624 66.667 0.82 0.00 36.44 4.41
3878 3911 0.470456 TGCTATACCGAATCCCCCGT 60.470 55.000 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 0.885879 TGTCTGTACTGCGTCGGATT 59.114 50.000 0.00 0.00 0.00 3.01
155 158 2.595655 GGGGCGGCTATGAAAGGT 59.404 61.111 9.56 0.00 0.00 3.50
320 325 7.093465 CGTCTCCCCATAAAATAGATAAGCCTA 60.093 40.741 0.00 0.00 0.00 3.93
380 385 1.822990 CGGTAGTGGAAGGAGCAACTA 59.177 52.381 0.00 0.00 0.00 2.24
446 451 4.259850 GCGATAAGAAAGTCATCAACGGAC 60.260 45.833 0.00 0.00 35.50 4.79
454 459 2.981859 ACCCGCGATAAGAAAGTCAT 57.018 45.000 8.23 0.00 0.00 3.06
464 469 4.768130 TTTTCAAATGAAACCCGCGATA 57.232 36.364 8.23 0.00 43.01 2.92
1099 1117 7.168302 CAGACCAATCAATCGTATCAGTCTTAC 59.832 40.741 0.00 0.00 29.97 2.34
1482 1500 1.457346 AAAGCTTGATCCCAGCGAAG 58.543 50.000 0.00 0.00 0.00 3.79
1548 1566 3.565482 ACCTTTACTACTTCACGACGACA 59.435 43.478 0.00 0.00 0.00 4.35
1984 2006 4.130118 GTCTCTTTGCCAAGAACTCTTCA 58.870 43.478 1.45 0.00 38.63 3.02
1986 2008 3.137360 AGGTCTCTTTGCCAAGAACTCTT 59.863 43.478 1.45 0.00 34.44 2.85
1999 2021 6.628644 AGCAACTTATCCTAAGGTCTCTTT 57.371 37.500 0.00 0.00 34.59 2.52
2047 2070 5.723672 TCTTCAGAATTCTACTGAACGGT 57.276 39.130 7.86 0.00 45.44 4.83
2084 2107 4.080526 GGGCTAAAGAAATGTCTCCACCTA 60.081 45.833 0.00 0.00 30.70 3.08
2103 2126 2.118679 GCATTTATTTGGAAGGGGGCT 58.881 47.619 0.00 0.00 0.00 5.19
2146 2169 2.023695 ACCCTACCCTATTCTCGAACCA 60.024 50.000 0.00 0.00 0.00 3.67
2478 2501 6.676632 CCCATACCCCTATAATGATGGTAGAA 59.323 42.308 0.00 0.00 35.20 2.10
2508 2531 4.022503 GCTGCCTTGATCTTTCTTTGTCTT 60.023 41.667 0.00 0.00 0.00 3.01
3028 3060 1.391157 GGCCTTGCTTGTGTGTCCAA 61.391 55.000 0.00 0.00 0.00 3.53
3094 3126 2.742053 GCGACATGCTAAGTTTTCTCCA 59.258 45.455 0.00 0.00 41.73 3.86
3148 3180 1.255882 TTTAGGAACAGACGGCGGTA 58.744 50.000 13.24 0.00 0.00 4.02
3214 3246 2.281345 GGTGCTGCTGCTGTCTGT 60.281 61.111 17.00 0.00 40.48 3.41
3377 3409 4.810491 TCAATCGATTTGAATCATCTCGCA 59.190 37.500 8.21 1.81 41.38 5.10
3407 3439 5.625150 TCGATCTATCAGAACAGATCAGGA 58.375 41.667 18.72 10.30 44.93 3.86
3561 3593 0.955428 CTGAGCTGGCCAAACGCTTA 60.955 55.000 18.17 13.53 37.74 3.09
3878 3911 2.041430 TAGGTCCCCGATGGCCAA 59.959 61.111 10.96 0.00 33.97 4.52


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

AutoCloner maintained by Alex Coulton.