Multiple sequence alignment - TraesCS7D01G213000

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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 TraesCS7D01G213000 chr7D 100.000 4030 0 0 1 4030 171311196 171315225 0.000000e+00 7443
1 TraesCS7D01G213000 chr7B 93.170 4070 204 33 1 4030 137792988 137797023 0.000000e+00 5908
2 TraesCS7D01G213000 chr7A 97.633 3295 43 7 86 3369 174202503 174205773 0.000000e+00 5620
3 TraesCS7D01G213000 chr7A 88.732 355 26 4 3676 4030 174206189 174206529 4.820000e-114 422
4 TraesCS7D01G213000 chr7A 94.017 234 14 0 3361 3594 174205947 174206180 4.950000e-94 355
5 TraesCS7D01G213000 chr6D 78.283 396 61 14 2655 3030 379573524 379573914 8.710000e-57 231
6 TraesCS7D01G213000 chr6A 78.141 398 62 13 2655 3032 521452099 521451707 3.130000e-56 230
7 TraesCS7D01G213000 chr6B 77.889 398 63 13 2655 3032 567398104 567397712 1.460000e-54 224


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 TraesCS7D01G213000 chr7D 171311196 171315225 4029 False 7443.000000 7443 100.000000 1 4030 1 chr7D.!!$F1 4029
1 TraesCS7D01G213000 chr7B 137792988 137797023 4035 False 5908.000000 5908 93.170000 1 4030 1 chr7B.!!$F1 4029
2 TraesCS7D01G213000 chr7A 174202503 174206529 4026 False 2132.333333 5620 93.460667 86 4030 3 chr7A.!!$F1 3944

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
947 949 4.439837 GGGAAACAGTAGCTACTACCTTCG 60.440 50.0 25.63 14.62 37.65 3.79 F
1671 1679 0.178929 ACGTGGAGAAGGAAGGGAGT 60.179 55.0 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2371 2381 2.228103 GTGTGTGTATGGAGTGAGTCGA 59.772 50.0 0.0 0.0 0.0 4.20 R
3429 3632 1.104577 TTGTTCTTTGGTGTCCGGCC 61.105 55.0 0.0 0.0 0.0 6.13 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
462 464 5.357742 TCAAATTAGCTGGCATCTGAGTA 57.642 39.130 0.14 0.00 0.00 2.59
947 949 4.439837 GGGAAACAGTAGCTACTACCTTCG 60.440 50.000 25.63 14.62 37.65 3.79
1288 1290 2.717580 TGAAGCACAGGTACACTACG 57.282 50.000 0.00 0.00 0.00 3.51
1671 1679 0.178929 ACGTGGAGAAGGAAGGGAGT 60.179 55.000 0.00 0.00 0.00 3.85
1973 1982 3.425625 GCAAGTGAAAGTGTGAAACGTCA 60.426 43.478 0.00 0.00 42.39 4.35
2098 2107 5.066505 AGCCACTTCAAAGAAAAGTACACAG 59.933 40.000 0.00 0.00 35.25 3.66
2109 2118 0.541863 AGTACACAGCCCATGCCTAC 59.458 55.000 0.00 0.00 38.69 3.18
2132 2141 7.016361 ACGCAGATTAATGGATTAGTTTGTC 57.984 36.000 0.00 0.00 0.00 3.18
2134 2143 7.011482 ACGCAGATTAATGGATTAGTTTGTCTC 59.989 37.037 0.00 0.00 0.00 3.36
2367 2377 9.457436 TTCAAGTTTTCTCAGTAACTAAAAGGT 57.543 29.630 0.00 0.00 33.66 3.50
2368 2378 9.106070 TCAAGTTTTCTCAGTAACTAAAAGGTC 57.894 33.333 0.00 0.00 33.66 3.85
2369 2379 8.889717 CAAGTTTTCTCAGTAACTAAAAGGTCA 58.110 33.333 0.00 0.00 33.66 4.02
2370 2380 8.434733 AGTTTTCTCAGTAACTAAAAGGTCAC 57.565 34.615 0.00 0.00 33.06 3.67
2371 2381 8.265764 AGTTTTCTCAGTAACTAAAAGGTCACT 58.734 33.333 0.00 0.00 33.06 3.41
2372 2382 8.549548 GTTTTCTCAGTAACTAAAAGGTCACTC 58.450 37.037 0.00 0.00 0.00 3.51
2373 2383 6.010294 TCTCAGTAACTAAAAGGTCACTCG 57.990 41.667 0.00 0.00 0.00 4.18
2374 2384 5.766670 TCTCAGTAACTAAAAGGTCACTCGA 59.233 40.000 0.00 0.00 0.00 4.04
2375 2385 5.766222 TCAGTAACTAAAAGGTCACTCGAC 58.234 41.667 0.00 0.00 41.80 4.20
2767 2784 2.685017 AGCTGGAGCCATCGGTCA 60.685 61.111 0.00 0.00 43.38 4.02
3149 3166 9.169592 GTGCAACTTAATCATAAGGTACCTTAA 57.830 33.333 32.74 20.70 42.39 1.85
3150 3167 9.742144 TGCAACTTAATCATAAGGTACCTTAAA 57.258 29.630 32.74 24.62 42.39 1.52
3354 3375 3.958798 AGCTGATTTCATTGATGAAGGGG 59.041 43.478 6.53 1.79 46.34 4.79
3418 3621 1.000896 CTGAAAAGGGTGCGGGGAT 60.001 57.895 0.00 0.00 0.00 3.85
3465 3668 5.423886 AGAACAAGAAGCCTAGCTAATCAC 58.576 41.667 0.00 0.00 38.25 3.06
3495 3699 6.620877 TTGAATAGGTCTTCCAGCTAAGAA 57.379 37.500 0.42 0.00 38.60 2.52
3500 3704 5.707066 AGGTCTTCCAGCTAAGAATGAAT 57.293 39.130 0.42 0.00 37.24 2.57
3545 3749 1.414550 GGCTTGTTTTTGCTAACCCCA 59.585 47.619 0.00 0.00 0.00 4.96
3550 3754 4.599047 TGTTTTTGCTAACCCCAATCAG 57.401 40.909 0.00 0.00 0.00 2.90
3553 3757 0.679640 TTGCTAACCCCAATCAGCCG 60.680 55.000 0.00 0.00 32.97 5.52
3562 3766 1.084370 CCAATCAGCCGAACGAGGTC 61.084 60.000 0.00 0.00 0.00 3.85
3627 3831 6.151648 TCAAAGCTTGTTTCCTTATCAGATGG 59.848 38.462 0.00 0.00 0.00 3.51
3666 3870 4.935808 GGTTGAGTGTGTCCAGGTATTTAG 59.064 45.833 0.00 0.00 0.00 1.85
3670 3874 5.305902 TGAGTGTGTCCAGGTATTTAGTTGA 59.694 40.000 0.00 0.00 0.00 3.18
3712 3916 2.766313 TCTGATTGGAGTTTCACCGTG 58.234 47.619 0.00 0.00 0.00 4.94
3753 3957 3.076621 CACCACTTTTGCTCATCTGCTA 58.923 45.455 0.00 0.00 0.00 3.49
3779 3983 3.181423 TGCTTGTAGTCCCCAAAATCCTT 60.181 43.478 0.00 0.00 0.00 3.36
3786 3990 6.717997 TGTAGTCCCCAAAATCCTTCTAAAAC 59.282 38.462 0.00 0.00 0.00 2.43
3828 4054 5.049267 GGAGAACTGTCCGATAGAGATACAC 60.049 48.000 0.00 0.00 39.76 2.90
3845 4071 1.001815 ACACCATTTTTCTTGCGTCCG 60.002 47.619 0.00 0.00 0.00 4.79
3947 4176 4.956700 TCAGATAGTTCTACAGTCCCCAAG 59.043 45.833 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 4.780815 TGCCGTCCTATTCATCTGAAAAT 58.219 39.130 0.00 0.00 37.61 1.82
51 52 6.037610 CCATGTCACTAGATAGTTTCTTTGCC 59.962 42.308 0.00 0.00 35.79 4.52
175 177 6.071952 TGTTAGATTCCAAAGCATGAGGTTTC 60.072 38.462 0.00 0.00 43.10 2.78
462 464 5.802956 CCGTGTGTTCACTTTTTACATTTGT 59.197 36.000 4.59 0.00 41.89 2.83
947 949 2.158608 AGACCATGCAAGGGGTATTAGC 60.159 50.000 13.45 0.00 46.47 3.09
1158 1160 2.904866 GAGGCCACACGGTTTGCA 60.905 61.111 5.01 0.00 33.28 4.08
1671 1679 1.822371 TGCGAAGGTACTATGCACTCA 59.178 47.619 0.00 0.00 42.40 3.41
2109 2118 7.251704 AGACAAACTAATCCATTAATCTGCG 57.748 36.000 0.00 0.00 0.00 5.18
2132 2141 5.556915 TGGGTGTTCTATGTGTAAAAGGAG 58.443 41.667 0.00 0.00 0.00 3.69
2134 2143 5.768164 AGTTGGGTGTTCTATGTGTAAAAGG 59.232 40.000 0.00 0.00 0.00 3.11
2367 2377 2.747989 GTGTATGGAGTGAGTCGAGTGA 59.252 50.000 0.00 0.00 0.00 3.41
2368 2378 2.488153 TGTGTATGGAGTGAGTCGAGTG 59.512 50.000 0.00 0.00 0.00 3.51
2369 2379 2.488545 GTGTGTATGGAGTGAGTCGAGT 59.511 50.000 0.00 0.00 0.00 4.18
2370 2380 2.488153 TGTGTGTATGGAGTGAGTCGAG 59.512 50.000 0.00 0.00 0.00 4.04
2371 2381 2.228103 GTGTGTGTATGGAGTGAGTCGA 59.772 50.000 0.00 0.00 0.00 4.20
2372 2382 2.229062 AGTGTGTGTATGGAGTGAGTCG 59.771 50.000 0.00 0.00 0.00 4.18
2373 2383 3.508012 AGAGTGTGTGTATGGAGTGAGTC 59.492 47.826 0.00 0.00 0.00 3.36
2374 2384 3.501349 AGAGTGTGTGTATGGAGTGAGT 58.499 45.455 0.00 0.00 0.00 3.41
2375 2385 3.507622 TGAGAGTGTGTGTATGGAGTGAG 59.492 47.826 0.00 0.00 0.00 3.51
2500 2510 8.849543 TTAGGGATAAAACCTACACTAGACAT 57.150 34.615 0.00 0.00 40.18 3.06
2501 2511 7.147776 GCTTAGGGATAAAACCTACACTAGACA 60.148 40.741 0.00 0.00 40.18 3.41
2767 2784 4.954875 CTGAAGTGAAGGACTTGAGAAGT 58.045 43.478 0.00 0.00 45.95 3.01
3354 3375 6.460664 AAATTTGCTTTGTAACATTACCGC 57.539 33.333 0.00 1.31 32.72 5.68
3429 3632 1.104577 TTGTTCTTTGGTGTCCGGCC 61.105 55.000 0.00 0.00 0.00 6.13
3465 3668 2.280628 GAAGACCTATTCAAGCCACCG 58.719 52.381 0.00 0.00 0.00 4.94
3495 3699 4.020573 TGAGTGAGTTACGGTTCCATTCAT 60.021 41.667 0.00 0.00 0.00 2.57
3500 3704 2.696707 AGTTGAGTGAGTTACGGTTCCA 59.303 45.455 0.00 0.00 0.00 3.53
3545 3749 1.218316 GGACCTCGTTCGGCTGATT 59.782 57.895 0.00 0.00 0.00 2.57
3550 3754 2.126031 GTGAGGACCTCGTTCGGC 60.126 66.667 16.81 0.00 32.35 5.54
3562 3766 3.744660 AGTTAGCAGAAACAAGGTGAGG 58.255 45.455 0.00 0.00 0.00 3.86
3602 3806 6.151648 CCATCTGATAAGGAAACAAGCTTTGA 59.848 38.462 0.00 0.00 0.00 2.69
3606 3810 3.950395 GCCATCTGATAAGGAAACAAGCT 59.050 43.478 0.00 0.00 0.00 3.74
3627 3831 6.039047 ACACTCAACCATGATCTTTCATATGC 59.961 38.462 0.00 0.00 40.70 3.14
3712 3916 1.152673 GGATGCCATCACTTCCCCC 60.153 63.158 7.06 0.00 0.00 5.40
3753 3957 1.136828 TTGGGGACTACAAGCACACT 58.863 50.000 0.00 0.00 0.00 3.55
3786 3990 4.101856 TCTCCTACCCCCTAAAACTCTTG 58.898 47.826 0.00 0.00 0.00 3.02
3828 4054 2.724403 GCGGACGCAAGAAAAATGG 58.276 52.632 12.31 0.00 41.49 3.16
3845 4071 0.388391 TAGGCTTTTGTGCGCATTGC 60.388 50.000 15.91 13.53 46.70 3.56
3849 4075 0.310543 CAAGTAGGCTTTTGTGCGCA 59.689 50.000 5.66 5.66 31.49 6.09
3859 4085 7.141758 TCATTCTGGAAATATCAAGTAGGCT 57.858 36.000 0.00 0.00 0.00 4.58
3900 4126 0.325272 GAGAGAGGGCCTTTCGGTTT 59.675 55.000 17.54 0.79 0.00 3.27
3902 4128 0.545548 AAGAGAGAGGGCCTTTCGGT 60.546 55.000 17.54 6.89 31.75 4.69
3903 4129 0.615850 AAAGAGAGAGGGCCTTTCGG 59.384 55.000 17.54 0.00 31.75 4.30
3904 4130 1.552792 AGAAAGAGAGAGGGCCTTTCG 59.447 52.381 17.54 0.00 46.10 3.46
3905 4131 2.569404 TGAGAAAGAGAGAGGGCCTTTC 59.431 50.000 16.03 16.03 43.51 2.62
3912 4141 7.773224 TGTAGAACTATCTGAGAAAGAGAGAGG 59.227 40.741 4.13 0.00 45.53 3.69
3920 4149 5.657302 GGGGACTGTAGAACTATCTGAGAAA 59.343 44.000 0.00 0.00 37.10 2.52
3947 4176 2.124942 CCCTTCCTTGAGCTCGGC 60.125 66.667 9.64 0.00 0.00 5.54
4010 4239 2.653234 CCCAAGAGATTCCTGGATGG 57.347 55.000 0.00 0.46 37.10 3.51


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

AutoCloner maintained by Alex Coulton.