Multiple sequence alignment - TraesCS1D01G119200

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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 TraesCS1D01G119200 chr1D 100.000 2617 0 0 1 2617 115569322 115566706 0.000000e+00 4833
1 TraesCS1D01G119200 chr1D 80.275 218 35 4 988 1204 468745819 468746029 9.700000e-35 158
2 TraesCS1D01G119200 chr7D 97.790 2624 33 6 1 2617 29884540 29881935 0.000000e+00 4501
3 TraesCS1D01G119200 chr6D 98.491 1988 27 3 1 1985 454644195 454642208 0.000000e+00 3502
4 TraesCS1D01G119200 chr6D 98.493 531 8 0 2086 2616 454642214 454641684 0.000000e+00 937
5 TraesCS1D01G119200 chr1A 89.351 385 34 4 826 1204 16477972 16477589 6.550000e-131 477
6 TraesCS1D01G119200 chr1A 88.971 136 11 4 2 136 6071801 6071669 5.790000e-37 165
7 TraesCS1D01G119200 chr1A 80.734 218 34 4 988 1204 561587018 561587228 2.080000e-36 163
8 TraesCS1D01G119200 chr1A 92.391 92 7 0 4 95 16478074 16477983 5.880000e-27 132
9 TraesCS1D01G119200 chr6B 88.095 168 16 4 3 167 712293847 712294013 2.050000e-46 196
10 TraesCS1D01G119200 chr7A 88.971 136 10 5 2 136 84693527 84693658 2.080000e-36 163
11 TraesCS1D01G119200 chr3A 88.971 136 10 5 2 136 93565952 93566083 2.080000e-36 163
12 TraesCS1D01G119200 chr4A 88.406 138 11 4 2 136 636121797 636121662 7.500000e-36 161
13 TraesCS1D01G119200 chr4A 97.222 72 1 1 826 897 598522295 598522225 1.270000e-23 121
14 TraesCS1D01G119200 chr5B 88.722 133 12 3 5 136 315244521 315244391 2.700000e-35 159
15 TraesCS1D01G119200 chr3D 83.226 155 11 5 160 300 528126667 528126514 7.600000e-26 128
16 TraesCS1D01G119200 chr3D 83.007 153 11 5 162 300 553219851 553219700 9.830000e-25 124


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 TraesCS1D01G119200 chr1D 115566706 115569322 2616 True 4833.0 4833 100.000 1 2617 1 chr1D.!!$R1 2616
1 TraesCS1D01G119200 chr7D 29881935 29884540 2605 True 4501.0 4501 97.790 1 2617 1 chr7D.!!$R1 2616
2 TraesCS1D01G119200 chr6D 454641684 454644195 2511 True 2219.5 3502 98.492 1 2616 2 chr6D.!!$R1 2615

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
334 337 1.678728 CCTTACTTGCCAATCAGCCGA 60.679 52.381 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2285 2295 2.588731 CGTCTTGAACGTCTGCACA 58.411 52.632 0.0 0.0 46.42 4.57 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
334 337 1.678728 CCTTACTTGCCAATCAGCCGA 60.679 52.381 0.00 0.00 0.00 5.54
502 506 3.253230 GCAAATTTTCACGCTATGCCTT 58.747 40.909 0.00 0.00 0.00 4.35
741 745 7.442364 CAGTGAGAAAGAGAAGAAAATGTACCA 59.558 37.037 0.00 0.00 0.00 3.25
991 995 8.795786 TTCTAACTGAATTTTTCAAACCGATG 57.204 30.769 0.00 0.00 39.58 3.84
1064 1068 3.579709 TCGACACTGAGAAGAAGATTGC 58.420 45.455 0.00 0.00 0.00 3.56
1071 1075 5.048224 CACTGAGAAGAAGATTGCAATGGTT 60.048 40.000 18.59 10.03 0.00 3.67
1097 1101 4.472470 TGATCCAACAGAGACAGATCCATT 59.528 41.667 0.00 0.00 33.86 3.16
1876 1881 5.714806 AGTGGTTATTTGATCCCGTGATTTT 59.285 36.000 0.00 0.00 0.00 1.82
2010 2015 0.457851 AAGGCGTACTAGAGCAGCAG 59.542 55.000 0.00 0.00 34.54 4.24
2285 2295 7.002879 ACCTAGCTGAATATGATCAAAGCAAT 58.997 34.615 0.00 0.00 0.00 3.56
2332 2342 8.607459 CATAACTTCTGTTTGGAGATACATGAC 58.393 37.037 0.00 0.00 37.59 3.06
2391 2401 0.752376 CCGACTAGTCTCTGGTCCCC 60.752 65.000 20.34 0.00 38.48 4.81
2424 2434 0.318699 CTCGAGCTCGTCACCACAAA 60.319 55.000 33.33 11.82 40.80 2.83
2425 2435 0.317160 TCGAGCTCGTCACCACAAAT 59.683 50.000 33.33 0.00 40.80 2.32
2426 2436 0.439985 CGAGCTCGTCACCACAAATG 59.560 55.000 27.79 0.00 34.11 2.32
2427 2437 2.851966 CGAGCTCGTCACCACAAATGG 61.852 57.143 27.79 0.00 42.51 3.16
2474 2494 3.093057 GAGGAGGAAGTCAGCTAGAACA 58.907 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
502 506 3.487626 TCTGGTGGTGCACTGCCA 61.488 61.111 24.04 24.04 34.40 4.92
741 745 0.107508 CCATCTGTCAAGCCATCCGT 60.108 55.000 0.00 0.00 0.00 4.69
931 935 4.142838 CGAAGCATGCAGTTCATTACTTCA 60.143 41.667 21.98 0.00 41.45 3.02
991 995 3.476552 TCACAGGGAACATGAACTGAAC 58.523 45.455 0.00 0.00 35.08 3.18
1064 1068 5.005740 TCTCTGTTGGATCAAGAACCATTG 58.994 41.667 0.00 0.00 36.02 2.82
1071 1075 4.161189 GGATCTGTCTCTGTTGGATCAAGA 59.839 45.833 0.00 0.00 35.76 3.02
1097 1101 5.837438 TCATGCTTCCTCTTCATCTCATCTA 59.163 40.000 0.00 0.00 0.00 1.98
1876 1881 5.187772 ACACAGCTACTCAATTCTGGTATGA 59.812 40.000 0.00 0.00 0.00 2.15
2285 2295 2.588731 CGTCTTGAACGTCTGCACA 58.411 52.632 0.00 0.00 46.42 4.57
2308 2318 7.602644 GTGTCATGTATCTCCAAACAGAAGTTA 59.397 37.037 0.00 0.00 36.84 2.24
2391 2401 3.467119 CGAGACGAACGTTGCGGG 61.467 66.667 5.00 0.00 0.00 6.13
2424 2434 3.184628 TCTCTTGTCCATGTTCCTCCAT 58.815 45.455 0.00 0.00 0.00 3.41
2425 2435 2.619931 TCTCTTGTCCATGTTCCTCCA 58.380 47.619 0.00 0.00 0.00 3.86
2426 2436 3.198635 TCATCTCTTGTCCATGTTCCTCC 59.801 47.826 0.00 0.00 0.00 4.30
2427 2437 4.161189 TCTCATCTCTTGTCCATGTTCCTC 59.839 45.833 0.00 0.00 0.00 3.71
2428 2438 4.099633 TCTCATCTCTTGTCCATGTTCCT 58.900 43.478 0.00 0.00 0.00 3.36
2429 2439 4.440880 CTCTCATCTCTTGTCCATGTTCC 58.559 47.826 0.00 0.00 0.00 3.62
2430 2440 4.440880 CCTCTCATCTCTTGTCCATGTTC 58.559 47.826 0.00 0.00 0.00 3.18
2431 2441 3.199508 CCCTCTCATCTCTTGTCCATGTT 59.800 47.826 0.00 0.00 0.00 2.71
2432 2442 2.770802 CCCTCTCATCTCTTGTCCATGT 59.229 50.000 0.00 0.00 0.00 3.21
2433 2443 3.036819 TCCCTCTCATCTCTTGTCCATG 58.963 50.000 0.00 0.00 0.00 3.66
2474 2494 1.680522 CTAGTCCTGCCGCCATGTCT 61.681 60.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.