Multiple sequence alignment - TraesCS1D01G226300

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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 TraesCS1D01G226300 chr1D 100.000 2690 0 0 1 2690 314575514 314572825 0.000000e+00 4968.0
1 TraesCS1D01G226300 chr1A 93.546 2572 112 15 4 2536 394853697 394851141 0.000000e+00 3781.0
2 TraesCS1D01G226300 chr1A 96.000 150 6 0 2541 2690 394850979 394850830 7.440000e-61 244.0
3 TraesCS1D01G226300 chr1B 94.732 2316 81 12 408 2690 426073280 426070973 0.000000e+00 3563.0
4 TraesCS1D01G226300 chr7A 83.196 726 112 7 699 1414 642253383 642254108 0.000000e+00 656.0
5 TraesCS1D01G226300 chr7D 82.735 724 115 4 701 1414 556639524 556640247 1.050000e-178 636.0
6 TraesCS1D01G226300 chr6B 83.114 456 50 6 1166 1621 22711663 22711235 9.030000e-105 390.0
7 TraesCS1D01G226300 chr6B 87.850 321 35 2 1719 2039 22711178 22710862 9.090000e-100 374.0
8 TraesCS1D01G226300 chr6B 94.118 51 3 0 2590 2640 22710777 22710727 7.980000e-11 78.7
9 TraesCS1D01G226300 chr6D 88.474 321 37 0 1719 2039 12345466 12345146 3.250000e-104 388.0
10 TraesCS1D01G226300 chr6D 94.000 50 3 0 2590 2639 12345076 12345027 2.870000e-10 76.8


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 TraesCS1D01G226300 chr1D 314572825 314575514 2689 True 4968.0 4968 100.000000 1 2690 1 chr1D.!!$R1 2689
1 TraesCS1D01G226300 chr1A 394850830 394853697 2867 True 2012.5 3781 94.773000 4 2690 2 chr1A.!!$R1 2686
2 TraesCS1D01G226300 chr1B 426070973 426073280 2307 True 3563.0 3563 94.732000 408 2690 1 chr1B.!!$R1 2282
3 TraesCS1D01G226300 chr7A 642253383 642254108 725 False 656.0 656 83.196000 699 1414 1 chr7A.!!$F1 715
4 TraesCS1D01G226300 chr7D 556639524 556640247 723 False 636.0 636 82.735000 701 1414 1 chr7D.!!$F1 713
5 TraesCS1D01G226300 chr6B 22710727 22711663 936 True 280.9 390 88.360667 1166 2640 3 chr6B.!!$R1 1474

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
53 54 0.379316 AAAGCGACCCACGTGAAAAC 59.621 50.0 19.30 4.59 44.6 2.43 F
361 377 0.882042 CATCCAGCGCCATAGTCCAC 60.882 60.0 2.29 0.00 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1437 1469 2.433604 TGGATCATCTGAGCAGAAGGAC 59.566 50.0 4.06 0.0 41.36 3.85 R
2298 2382 0.450184 CGCCAACCCAGAAATTACCG 59.550 55.0 0.00 0.0 0.00 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
25 26 5.362717 ACGGGAAAGGAAAATTCTTTTGAGT 59.637 36.000 7.83 3.35 36.73 3.41
50 51 1.952133 CGAAAGCGACCCACGTGAA 60.952 57.895 19.30 0.00 44.60 3.18
53 54 0.379316 AAAGCGACCCACGTGAAAAC 59.621 50.000 19.30 4.59 44.60 2.43
59 60 1.003223 GACCCACGTGAAAACTTTCCG 60.003 52.381 19.30 9.87 36.36 4.30
69 70 5.407387 CGTGAAAACTTTCCGAGGATTCTAA 59.593 40.000 0.00 0.00 36.36 2.10
100 101 5.514274 ACCAAACAAGTTCAATACCACAG 57.486 39.130 0.00 0.00 0.00 3.66
128 129 7.468141 AAGAATTGGATCAAAAGGGTTCTAC 57.532 36.000 0.00 0.00 0.00 2.59
132 133 5.779241 TGGATCAAAAGGGTTCTACAGAT 57.221 39.130 0.00 0.00 0.00 2.90
135 136 6.214615 TGGATCAAAAGGGTTCTACAGATACA 59.785 38.462 0.00 0.00 0.00 2.29
144 145 5.188359 GGGTTCTACAGATACACCCAAGTTA 59.812 44.000 11.28 0.00 40.63 2.24
150 151 8.212312 TCTACAGATACACCCAAGTTAAAACAA 58.788 33.333 0.00 0.00 0.00 2.83
174 177 1.107538 AGCCCGCGCTTGATAGAGTA 61.108 55.000 5.56 0.00 45.55 2.59
191 194 1.339610 AGTATGCAGATGCTCGACCTC 59.660 52.381 6.35 0.00 42.66 3.85
192 195 1.067669 GTATGCAGATGCTCGACCTCA 59.932 52.381 6.35 0.00 42.66 3.86
206 209 6.183360 TGCTCGACCTCATAAAAACACTTTTT 60.183 34.615 0.00 0.00 44.43 1.94
245 248 8.970691 ATATAAACAAAGACTCATGTTGCAAC 57.029 30.769 22.83 22.83 39.57 4.17
253 256 6.152932 AGACTCATGTTGCAACTTCAAAAT 57.847 33.333 28.61 11.23 0.00 1.82
257 260 7.264221 ACTCATGTTGCAACTTCAAAATAACA 58.736 30.769 28.61 6.52 0.00 2.41
330 346 5.530915 TGGTAAAACCAGACTGAATTCACAG 59.469 40.000 3.38 0.00 44.79 3.66
351 367 2.515523 AGACATGCCATCCAGCGC 60.516 61.111 0.00 0.00 34.65 5.92
361 377 0.882042 CATCCAGCGCCATAGTCCAC 60.882 60.000 2.29 0.00 0.00 4.02
423 444 1.914634 AAAAACATGTGCAAACGCGA 58.085 40.000 15.93 0.00 0.00 5.87
428 449 1.954146 ATGTGCAAACGCGACGACT 60.954 52.632 15.93 0.00 0.00 4.18
442 463 4.550063 CGCGACGACTAACATGCATAAAAT 60.550 41.667 0.00 0.00 0.00 1.82
513 538 4.263018 TCGCATAGCAGAAGAAGCATAT 57.737 40.909 0.00 0.00 0.00 1.78
514 539 5.391312 TCGCATAGCAGAAGAAGCATATA 57.609 39.130 0.00 0.00 0.00 0.86
601 626 2.425592 CACCGTTCCAGACCAGCA 59.574 61.111 0.00 0.00 0.00 4.41
1437 1469 1.398390 GACTGCCCTTTGTTATCAGCG 59.602 52.381 0.00 0.00 0.00 5.18
1612 1644 5.227569 TGTCTTGCTGTTATCTTCCTTGA 57.772 39.130 0.00 0.00 0.00 3.02
1764 1824 3.287222 AGGCTCTGAGACTGTGATACTC 58.713 50.000 13.36 0.00 27.71 2.59
1783 1843 2.617308 CTCGCTTGAGCAATGGAATCAT 59.383 45.455 3.65 0.00 42.21 2.45
2066 2126 9.139174 GAAAAACATCAACAAACTGAAGAGAAA 57.861 29.630 0.00 0.00 0.00 2.52
2140 2219 9.364989 CACAGTTTTGATTCCTTCTTTTTGTAA 57.635 29.630 0.00 0.00 0.00 2.41
2154 2233 2.073252 TTGTAATGCACCAACCCACA 57.927 45.000 0.00 0.00 0.00 4.17
2215 2299 6.963322 AGGGAAGCTAACATGAATACTTTCT 58.037 36.000 0.00 0.00 32.78 2.52
2216 2300 7.406104 AGGGAAGCTAACATGAATACTTTCTT 58.594 34.615 0.00 0.00 32.78 2.52
2225 2309 8.682936 AACATGAATACTTTCTTGACTTCACT 57.317 30.769 0.00 0.00 38.60 3.41
2281 2365 3.572255 TGTGAAGGAAAACTATGTTGCCC 59.428 43.478 0.00 0.00 0.00 5.36
2298 2382 4.250116 TGCCCATAACAACATGTCAAAC 57.750 40.909 0.00 0.00 0.00 2.93
2319 2403 0.172578 GTAATTTCTGGGTTGGCGCC 59.827 55.000 22.73 22.73 0.00 6.53
2335 2419 1.877367 GCCGCGTGGGAAACAAATA 59.123 52.632 18.41 0.00 38.47 1.40
2348 2432 6.927933 GGAAACAAATATTTTCCTGTGACG 57.072 37.500 9.32 0.00 45.94 4.35
2422 2506 1.344953 TAGAAGCCATGCGTCCCCAT 61.345 55.000 0.00 0.00 37.75 4.00
2457 2541 2.650116 AACTCCCGCTGTCTCGCAT 61.650 57.895 0.00 0.00 0.00 4.73
2643 2892 1.663702 GCCAAGCTGCAGTGCAAAG 60.664 57.895 20.22 9.72 38.41 2.77
2660 2909 2.739913 CAAAGTTGATTGGCATGGCAAG 59.260 45.455 34.07 17.66 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 0.675083 TGGGTCGCTTTCGTACTCAA 59.325 50.000 0.00 0.00 36.96 3.02
69 70 9.758651 GTATTGAACTTGTTTGGTTTTAAGGAT 57.241 29.630 0.00 0.00 0.00 3.24
74 75 7.837863 TGTGGTATTGAACTTGTTTGGTTTTA 58.162 30.769 0.00 0.00 0.00 1.52
75 76 6.702329 TGTGGTATTGAACTTGTTTGGTTTT 58.298 32.000 0.00 0.00 0.00 2.43
86 87 8.143835 CCAATTCTTTTTCTGTGGTATTGAACT 58.856 33.333 0.00 0.00 0.00 3.01
100 101 7.933577 AGAACCCTTTTGATCCAATTCTTTTTC 59.066 33.333 0.00 0.00 0.00 2.29
128 129 6.016276 AGCTTGTTTTAACTTGGGTGTATCTG 60.016 38.462 0.00 0.00 0.00 2.90
132 133 5.194432 TGAGCTTGTTTTAACTTGGGTGTA 58.806 37.500 0.00 0.00 0.00 2.90
135 136 3.068165 GCTGAGCTTGTTTTAACTTGGGT 59.932 43.478 0.00 0.00 0.00 4.51
144 145 2.908073 CGCGGGCTGAGCTTGTTTT 61.908 57.895 3.72 0.00 0.00 2.43
174 177 0.757512 ATGAGGTCGAGCATCTGCAT 59.242 50.000 18.15 8.90 45.16 3.96
215 218 9.069078 CAACATGAGTCTTTGTTTATATTGCAG 57.931 33.333 0.00 0.00 33.93 4.41
218 221 8.969121 TGCAACATGAGTCTTTGTTTATATTG 57.031 30.769 0.00 1.36 33.93 1.90
221 224 8.165239 AGTTGCAACATGAGTCTTTGTTTATA 57.835 30.769 30.11 0.00 33.93 0.98
223 226 6.449635 AGTTGCAACATGAGTCTTTGTTTA 57.550 33.333 30.11 1.29 33.93 2.01
231 234 7.434897 TGTTATTTTGAAGTTGCAACATGAGTC 59.565 33.333 30.11 18.09 0.00 3.36
253 256 7.466725 GCACTAGTTTTGACACACTTCATGTTA 60.467 37.037 0.00 0.00 40.64 2.41
257 260 4.881273 TGCACTAGTTTTGACACACTTCAT 59.119 37.500 0.00 0.00 0.00 2.57
319 335 4.093998 GGCATGTCTGTACTGTGAATTCAG 59.906 45.833 8.80 0.24 40.80 3.02
330 346 1.303309 GCTGGATGGCATGTCTGTAC 58.697 55.000 3.81 0.00 0.00 2.90
339 355 2.111669 CTATGGCGCTGGATGGCA 59.888 61.111 7.64 0.00 46.52 4.92
351 367 5.878406 ACTTCAGAATAGGTGGACTATGG 57.122 43.478 0.00 0.00 41.54 2.74
361 377 5.006165 CGCAGCTTTTCTACTTCAGAATAGG 59.994 44.000 6.60 0.00 42.88 2.57
419 440 1.472990 TATGCATGTTAGTCGTCGCG 58.527 50.000 10.16 0.00 0.00 5.87
420 441 3.918258 TTTATGCATGTTAGTCGTCGC 57.082 42.857 10.16 0.00 0.00 5.19
421 442 7.043656 TCACTATTTTATGCATGTTAGTCGTCG 60.044 37.037 10.16 0.00 0.00 5.12
422 443 8.126871 TCACTATTTTATGCATGTTAGTCGTC 57.873 34.615 10.16 0.00 0.00 4.20
423 444 8.551205 CATCACTATTTTATGCATGTTAGTCGT 58.449 33.333 10.16 0.00 0.00 4.34
428 449 8.404765 CACCACATCACTATTTTATGCATGTTA 58.595 33.333 10.16 0.00 0.00 2.41
513 538 1.568504 ATGGGACTCGTTTCAGGCTA 58.431 50.000 0.00 0.00 0.00 3.93
514 539 0.693049 AATGGGACTCGTTTCAGGCT 59.307 50.000 0.00 0.00 0.00 4.58
566 591 1.947456 GTGGGTGGTCTGTTGAACTTC 59.053 52.381 0.00 0.00 0.00 3.01
601 626 0.818040 GGTTTCTGGCGTGTCCTGTT 60.818 55.000 0.00 0.00 35.49 3.16
666 691 2.048222 CGAGGCGTTCCTTGCTCA 60.048 61.111 0.00 0.00 44.46 4.26
1437 1469 2.433604 TGGATCATCTGAGCAGAAGGAC 59.566 50.000 4.06 0.00 41.36 3.85
1764 1824 3.431922 AATGATTCCATTGCTCAAGCG 57.568 42.857 0.00 0.00 41.18 4.68
1783 1843 3.011144 TCTGCAATTAGATTCACCCCCAA 59.989 43.478 0.00 0.00 0.00 4.12
2038 2098 8.469200 TCTCTTCAGTTTGTTGATGTTTTTCAT 58.531 29.630 0.00 0.00 39.77 2.57
2039 2099 7.825681 TCTCTTCAGTTTGTTGATGTTTTTCA 58.174 30.769 0.00 0.00 0.00 2.69
2040 2100 8.687824 TTCTCTTCAGTTTGTTGATGTTTTTC 57.312 30.769 0.00 0.00 0.00 2.29
2140 2219 1.354031 TCTGTATGTGGGTTGGTGCAT 59.646 47.619 0.00 0.00 0.00 3.96
2185 2264 7.836183 AGTATTCATGTTAGCTTCCCTTTCAAT 59.164 33.333 0.00 0.00 0.00 2.57
2199 2283 9.778741 AGTGAAGTCAAGAAAGTATTCATGTTA 57.221 29.630 0.00 0.00 38.06 2.41
2215 2299 1.895798 AGAGATGCCGAGTGAAGTCAA 59.104 47.619 0.00 0.00 0.00 3.18
2216 2300 1.203287 CAGAGATGCCGAGTGAAGTCA 59.797 52.381 0.00 0.00 0.00 3.41
2225 2309 4.705507 AGTCTTTAGTTACAGAGATGCCGA 59.294 41.667 0.00 0.00 0.00 5.54
2257 2341 4.982295 GGCAACATAGTTTTCCTTCACAAC 59.018 41.667 0.00 0.00 0.00 3.32
2281 2365 8.514136 AAATTACCGTTTGACATGTTGTTATG 57.486 30.769 0.00 0.00 0.00 1.90
2298 2382 0.450184 CGCCAACCCAGAAATTACCG 59.550 55.000 0.00 0.00 0.00 4.02
2319 2403 3.610677 GGAAAATATTTGTTTCCCACGCG 59.389 43.478 3.53 3.53 45.62 6.01
2457 2541 5.357596 AGCATAATGTTGCACACATGACATA 59.642 36.000 13.05 5.10 46.23 2.29
2539 2780 8.692110 TCTGATTGAATATTTGTGATTGTTGC 57.308 30.769 0.00 0.00 0.00 4.17
2583 2824 8.453681 TCCTCTACATCAGTATATTTGGGTAGA 58.546 37.037 0.00 0.00 34.64 2.59
2643 2892 2.028748 ACTTCTTGCCATGCCAATCAAC 60.029 45.455 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.