Multiple sequence alignment - TraesCS3A01G110100

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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 TraesCS3A01G110100 chr3A 100.000 3232 0 0 1 3232 77470296 77473527 0.000000e+00 5969.0
1 TraesCS3A01G110100 chr3A 92.308 78 6 0 2264 2341 77472636 77472559 9.480000e-21 111.0
2 TraesCS3A01G110100 chr3D 93.561 2050 67 22 268 2267 66339165 66341199 0.000000e+00 2994.0
3 TraesCS3A01G110100 chr3D 98.281 931 13 2 2302 3232 66341183 66342110 0.000000e+00 1628.0
4 TraesCS3A01G110100 chr3D 92.098 367 16 8 1 364 66338367 66338723 3.720000e-139 505.0
5 TraesCS3A01G110100 chr3D 100.000 35 0 0 2264 2298 66341222 66341188 7.480000e-07 65.8
6 TraesCS3A01G110100 chr3B 91.566 1909 67 25 426 2264 109941842 109943726 0.000000e+00 2547.0
7 TraesCS3A01G110100 chr3B 88.720 789 55 15 2457 3232 109944014 109944781 0.000000e+00 933.0
8 TraesCS3A01G110100 chr3B 91.395 430 24 8 1 424 109941257 109941679 7.780000e-161 577.0


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 TraesCS3A01G110100 chr3A 77470296 77473527 3231 False 5969.000000 5969 100.000000 1 3232 1 chr3A.!!$F1 3231
1 TraesCS3A01G110100 chr3D 66338367 66342110 3743 False 1709.000000 2994 94.646667 1 3232 3 chr3D.!!$F1 3231
2 TraesCS3A01G110100 chr3B 109941257 109944781 3524 False 1352.333333 2547 90.560333 1 3232 3 chr3B.!!$F1 3231

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
201 203 0.100503 GCACCACAAGTCCACAACAC 59.899 55.0 0.0 0.0 0.0 3.32 F
717 1433 0.843309 TCAAAGCTCCAGTGTTCCCA 59.157 50.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1041 1776 0.533531 CTCTCAGTGTGTGCAGGCAA 60.534 55.0 0.00 0.00 0.0 4.52 R
2490 3449 0.308993 GAAGTGTCTGCTTGCCACAC 59.691 55.0 13.71 13.71 40.7 3.82 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
191 193 4.111916 CAAAAAGTTACAGGCACCACAAG 58.888 43.478 0.00 0.0 0.00 3.16
192 194 2.729028 AAGTTACAGGCACCACAAGT 57.271 45.000 0.00 0.0 0.00 3.16
194 196 1.202770 AGTTACAGGCACCACAAGTCC 60.203 52.381 0.00 0.0 0.00 3.85
196 198 0.107831 TACAGGCACCACAAGTCCAC 59.892 55.000 0.00 0.0 0.00 4.02
198 200 0.751277 CAGGCACCACAAGTCCACAA 60.751 55.000 0.00 0.0 0.00 3.33
199 201 0.751643 AGGCACCACAAGTCCACAAC 60.752 55.000 0.00 0.0 0.00 3.32
200 202 1.034838 GGCACCACAAGTCCACAACA 61.035 55.000 0.00 0.0 0.00 3.33
201 203 0.100503 GCACCACAAGTCCACAACAC 59.899 55.000 0.00 0.0 0.00 3.32
202 204 1.750193 CACCACAAGTCCACAACACT 58.250 50.000 0.00 0.0 0.00 3.55
203 205 2.912771 CACCACAAGTCCACAACACTA 58.087 47.619 0.00 0.0 0.00 2.74
204 206 2.872245 CACCACAAGTCCACAACACTAG 59.128 50.000 0.00 0.0 0.00 2.57
205 207 2.769663 ACCACAAGTCCACAACACTAGA 59.230 45.455 0.00 0.0 0.00 2.43
206 208 3.131396 CCACAAGTCCACAACACTAGAC 58.869 50.000 0.00 0.0 0.00 2.59
383 933 2.027192 AGCAAAAGCAGACCGAATCCTA 60.027 45.455 0.00 0.0 0.00 2.94
494 1205 5.123027 CCAGATTCCAGTAGAAGCAAGAAAC 59.877 44.000 0.00 0.0 43.58 2.78
544 1256 4.009675 TCCCAAATTCAATTCTGGAGTCG 58.990 43.478 11.04 0.0 0.00 4.18
681 1393 3.437049 GTCCAAAACACAGTGAGGCTATC 59.563 47.826 7.81 0.0 0.00 2.08
690 1402 1.482182 AGTGAGGCTATCAATGCGACA 59.518 47.619 0.00 0.0 40.43 4.35
691 1403 2.103771 AGTGAGGCTATCAATGCGACAT 59.896 45.455 0.00 0.0 40.43 3.06
693 1405 2.072298 GAGGCTATCAATGCGACATCC 58.928 52.381 0.00 0.0 0.00 3.51
698 1410 4.310769 GCTATCAATGCGACATCCTTACT 58.689 43.478 0.00 0.0 0.00 2.24
712 1424 2.972713 TCCTTACTCAAAGCTCCAGTGT 59.027 45.455 0.00 0.0 33.49 3.55
717 1433 0.843309 TCAAAGCTCCAGTGTTCCCA 59.157 50.000 0.00 0.0 0.00 4.37
732 1448 3.117474 TGTTCCCAACCATCTACCAACAA 60.117 43.478 0.00 0.0 0.00 2.83
733 1449 4.086457 GTTCCCAACCATCTACCAACAAT 58.914 43.478 0.00 0.0 0.00 2.71
734 1450 5.222151 TGTTCCCAACCATCTACCAACAATA 60.222 40.000 0.00 0.0 0.00 1.90
787 1503 3.412237 TTGGGTTAACACAGGCTCTAC 57.588 47.619 11.03 0.0 0.00 2.59
946 1676 3.365868 GCAATGGAATCAACGCAACTGTA 60.366 43.478 0.00 0.0 0.00 2.74
967 1697 3.992260 GAGTGCCACTCTCGTGTATAT 57.008 47.619 17.57 0.0 41.88 0.86
985 1715 6.836527 GTGTATATATAGGCATCCAGAGACCT 59.163 42.308 0.00 0.0 36.27 3.85
1016 1746 1.808945 CAACTCAAGCATCTCCACCAC 59.191 52.381 0.00 0.0 0.00 4.16
1041 1776 5.858381 TCAGTTCAGTTGCTTATTCTGTCT 58.142 37.500 0.00 0.0 0.00 3.41
1044 1779 5.049129 AGTTCAGTTGCTTATTCTGTCTTGC 60.049 40.000 0.00 0.0 0.00 4.01
1469 2221 1.501582 GGTCAGGAGGAGGCTACAAT 58.498 55.000 0.00 0.0 0.00 2.71
2072 2877 7.175104 AGAAGGCAAATGAATTCCACTACTAA 58.825 34.615 2.27 0.0 0.00 2.24
2113 2918 4.044065 TCTTGGCTAAATTTCTTCCTCCCA 59.956 41.667 0.00 0.0 0.00 4.37
2225 3030 4.898829 TTGAGTGCAATAAATCCATCCG 57.101 40.909 0.00 0.0 0.00 4.18
2299 3104 8.718102 TTTTCTATGTGTTACTAATCCAGCTC 57.282 34.615 0.00 0.0 0.00 4.09
2300 3105 6.406692 TCTATGTGTTACTAATCCAGCTCC 57.593 41.667 0.00 0.0 0.00 4.70
2301 3106 5.897250 TCTATGTGTTACTAATCCAGCTCCA 59.103 40.000 0.00 0.0 0.00 3.86
2302 3107 5.636903 ATGTGTTACTAATCCAGCTCCAT 57.363 39.130 0.00 0.0 0.00 3.41
2303 3108 5.435686 TGTGTTACTAATCCAGCTCCATT 57.564 39.130 0.00 0.0 0.00 3.16
2304 3109 6.553953 TGTGTTACTAATCCAGCTCCATTA 57.446 37.500 0.00 0.0 0.00 1.90
2305 3110 7.136822 TGTGTTACTAATCCAGCTCCATTAT 57.863 36.000 0.00 0.0 0.00 1.28
2306 3111 6.992123 TGTGTTACTAATCCAGCTCCATTATG 59.008 38.462 0.00 0.0 0.00 1.90
2307 3112 5.997746 TGTTACTAATCCAGCTCCATTATGC 59.002 40.000 0.00 0.0 0.00 3.14
2308 3113 4.989875 ACTAATCCAGCTCCATTATGCT 57.010 40.909 0.00 0.0 40.54 3.79
2316 3121 4.989875 AGCTCCATTATGCTGGATTAGT 57.010 40.909 0.00 0.0 44.23 2.24
2502 3461 4.331356 GCAAAGTGTGGCAAGCAG 57.669 55.556 0.00 0.0 0.00 4.24
2707 3667 8.077836 AGTTAGTTATTCTTCGATTGCATAGC 57.922 34.615 0.00 0.0 0.00 2.97
2782 3742 6.101223 ACCATCTTTTCCCCTGATATCCTAT 58.899 40.000 0.00 0.0 0.00 2.57
2980 3941 6.239345 GGTGTTTGATACCACATAAACCCAAA 60.239 38.462 0.00 0.0 38.12 3.28
3111 4072 3.742433 ACCTCACTTGAAGTCAGTCAG 57.258 47.619 0.00 0.0 0.00 3.51
3181 4142 4.696877 GCATTGGATGTGCTATGTGCTATA 59.303 41.667 0.00 0.0 43.37 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.336427 GGAGCCAATAATAGAAGAATGATCCAG 59.664 40.741 0.00 0.00 0.00 3.86
228 233 5.351465 TCGCTTCTACCTTCATCAATGAAAC 59.649 40.000 6.85 0.00 45.26 2.78
316 321 8.338259 GTGTCGTGCATTTCATCTTTAGATATT 58.662 33.333 0.00 0.00 32.63 1.28
383 933 1.214175 TCCAACTGGAATGTGGTGTGT 59.786 47.619 0.00 0.00 42.18 3.72
494 1205 1.006519 TGGAAACATGGTGGGGTATGG 59.993 52.381 0.00 0.00 33.40 2.74
544 1256 0.942962 CGAGCTGGATTTGATGCTCC 59.057 55.000 0.00 0.00 46.32 4.70
681 1393 4.728882 GCTTTGAGTAAGGATGTCGCATTG 60.729 45.833 0.00 0.00 34.26 2.82
690 1402 3.584848 ACACTGGAGCTTTGAGTAAGGAT 59.415 43.478 0.00 0.00 34.26 3.24
691 1403 2.972713 ACACTGGAGCTTTGAGTAAGGA 59.027 45.455 0.00 0.00 34.26 3.36
693 1405 3.748568 GGAACACTGGAGCTTTGAGTAAG 59.251 47.826 0.00 0.00 36.90 2.34
698 1410 0.843309 TGGGAACACTGGAGCTTTGA 59.157 50.000 0.00 0.00 33.40 2.69
712 1424 3.885976 TTGTTGGTAGATGGTTGGGAA 57.114 42.857 0.00 0.00 0.00 3.97
717 1433 5.133221 GCCTCATATTGTTGGTAGATGGTT 58.867 41.667 0.00 0.00 0.00 3.67
787 1503 3.005554 CAAGCTCCCACTGTGAGTATTG 58.994 50.000 9.86 5.93 32.31 1.90
825 1555 1.750399 GCCAGGCATGACGGTGATT 60.750 57.895 6.55 0.00 0.00 2.57
901 1631 2.795973 CATGCATGGACCTGTGCG 59.204 61.111 19.40 0.00 44.11 5.34
902 1632 1.879737 TTGCATGCATGGACCTGTGC 61.880 55.000 27.34 13.02 41.61 4.57
967 1697 4.556697 TGAAAGGTCTCTGGATGCCTATA 58.443 43.478 0.00 0.00 0.00 1.31
985 1715 5.766670 AGATGCTTGAGTTGATGAACTGAAA 59.233 36.000 1.00 0.00 42.80 2.69
1016 1746 6.426328 AGACAGAATAAGCAACTGAACTGAAG 59.574 38.462 0.00 0.00 35.85 3.02
1041 1776 0.533531 CTCTCAGTGTGTGCAGGCAA 60.534 55.000 0.00 0.00 0.00 4.52
1044 1779 0.533531 TTGCTCTCAGTGTGTGCAGG 60.534 55.000 18.06 0.00 35.02 4.85
1229 1969 2.938451 TGTAATAGATGCAGTGCAGTGC 59.062 45.455 34.65 34.65 43.65 4.40
1469 2221 1.678598 AAGTTGGTGTCGGTGTCGGA 61.679 55.000 0.00 0.00 36.95 4.55
2072 2877 6.041979 AGCCAAGAAACACCAATGACTAAAAT 59.958 34.615 0.00 0.00 0.00 1.82
2083 2888 6.462347 GGAAGAAATTTAGCCAAGAAACACCA 60.462 38.462 0.00 0.00 0.00 4.17
2113 2918 4.813027 AGCATCAATCAAGAAAAATGCGT 58.187 34.783 0.00 0.00 43.17 5.24
2273 3078 9.162764 GAGCTGGATTAGTAACACATAGAAAAA 57.837 33.333 0.00 0.00 0.00 1.94
2274 3079 7.769044 GGAGCTGGATTAGTAACACATAGAAAA 59.231 37.037 0.00 0.00 0.00 2.29
2275 3080 7.093068 TGGAGCTGGATTAGTAACACATAGAAA 60.093 37.037 0.00 0.00 0.00 2.52
2276 3081 6.382859 TGGAGCTGGATTAGTAACACATAGAA 59.617 38.462 0.00 0.00 0.00 2.10
2277 3082 5.897250 TGGAGCTGGATTAGTAACACATAGA 59.103 40.000 0.00 0.00 0.00 1.98
2278 3083 6.161855 TGGAGCTGGATTAGTAACACATAG 57.838 41.667 0.00 0.00 0.00 2.23
2279 3084 6.747414 ATGGAGCTGGATTAGTAACACATA 57.253 37.500 0.00 0.00 0.00 2.29
2280 3085 5.636903 ATGGAGCTGGATTAGTAACACAT 57.363 39.130 0.00 0.00 0.00 3.21
2281 3086 5.435686 AATGGAGCTGGATTAGTAACACA 57.564 39.130 0.00 0.00 0.00 3.72
2282 3087 6.073003 GCATAATGGAGCTGGATTAGTAACAC 60.073 42.308 0.00 0.00 0.00 3.32
2283 3088 5.997746 GCATAATGGAGCTGGATTAGTAACA 59.002 40.000 0.00 0.00 0.00 2.41
2284 3089 6.234177 AGCATAATGGAGCTGGATTAGTAAC 58.766 40.000 0.00 0.00 40.13 2.50
2285 3090 6.439636 AGCATAATGGAGCTGGATTAGTAA 57.560 37.500 0.00 0.00 40.13 2.24
2287 3092 4.989875 AGCATAATGGAGCTGGATTAGT 57.010 40.909 0.00 0.00 40.13 2.24
2299 3104 7.750229 ATGTGTTACTAATCCAGCATAATGG 57.250 36.000 0.00 0.00 42.11 3.16
2300 3105 9.710900 TCTATGTGTTACTAATCCAGCATAATG 57.289 33.333 0.00 0.00 0.00 1.90
2304 3109 9.461312 TTTTTCTATGTGTTACTAATCCAGCAT 57.539 29.630 0.00 0.00 0.00 3.79
2305 3110 8.856153 TTTTTCTATGTGTTACTAATCCAGCA 57.144 30.769 0.00 0.00 0.00 4.41
2341 3146 7.667043 ATTATTGCTCTTTTGTAGTGTTCGA 57.333 32.000 0.00 0.00 0.00 3.71
2490 3449 0.308993 GAAGTGTCTGCTTGCCACAC 59.691 55.000 13.71 13.71 40.70 3.82
2502 3461 5.682862 CAGTTTGTTAGCAACATGAAGTGTC 59.317 40.000 0.00 0.00 41.14 3.67
2707 3667 6.712276 AGAACAAGGTTCATAGGTCCTTTAG 58.288 40.000 11.28 0.00 39.22 1.85
2802 3762 7.899648 TTTTTGGGGTTCAACAGTAAGATTA 57.100 32.000 0.00 0.00 34.67 1.75
2980 3941 5.136105 AGCTTCAACTCATCTTGGAAGTTT 58.864 37.500 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.