Multiple sequence alignment - TraesCS6D01G249000

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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 TraesCS6D01G249000 chr6D 100.000 3408 0 0 1 3408 352358022 352361429 0.000000e+00 6294
1 TraesCS6D01G249000 chr6D 95.107 327 14 2 1277 1602 448792800 448792475 6.520000e-142 514
2 TraesCS6D01G249000 chr6B 97.524 2706 55 9 29 2728 526718071 526715372 0.000000e+00 4615
3 TraesCS6D01G249000 chr6B 92.259 633 14 7 2796 3408 526715370 526714753 0.000000e+00 865
4 TraesCS6D01G249000 chr6A 93.743 2749 100 24 684 3408 490492311 490489611 0.000000e+00 4058
5 TraesCS6D01G249000 chr6A 89.250 400 24 6 276 668 490492772 490492385 1.840000e-132 483


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 TraesCS6D01G249000 chr6D 352358022 352361429 3407 False 6294.0 6294 100.0000 1 3408 1 chr6D.!!$F1 3407
1 TraesCS6D01G249000 chr6B 526714753 526718071 3318 True 2740.0 4615 94.8915 29 3408 2 chr6B.!!$R1 3379
2 TraesCS6D01G249000 chr6A 490489611 490492772 3161 True 2270.5 4058 91.4965 276 3408 2 chr6A.!!$R1 3132

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
19 20 0.481128 ACGTCCCAACCCTGGAAATT 59.519 50.0 0.0 0.0 46.92 1.82 F
136 138 1.009829 GTCTGGGCTTGCATACTTCG 58.990 55.0 0.0 0.0 0.00 3.79 F
2011 2084 1.155042 CAGGACAAGAGAGCAAGTGC 58.845 55.0 0.0 0.0 42.49 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1663 1736 3.045601 ACTTTAGCACTTGCAGTCGAT 57.954 42.857 3.62 0.0 45.16 3.59 R
2085 2158 2.814336 GGTTTGTTGGTCTCTGGACATC 59.186 50.000 0.00 0.0 43.77 3.06 R
2871 2951 0.035056 GCCTTGCCTCCTTGCTTCTA 60.035 55.000 0.00 0.0 0.00 2.10 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
17 18 3.663419 ACGTCCCAACCCTGGAAA 58.337 55.556 0.00 0.00 46.92 3.13
18 19 2.160646 ACGTCCCAACCCTGGAAAT 58.839 52.632 0.00 0.00 46.92 2.17
19 20 0.481128 ACGTCCCAACCCTGGAAATT 59.519 50.000 0.00 0.00 46.92 1.82
20 21 1.133294 ACGTCCCAACCCTGGAAATTT 60.133 47.619 0.00 0.00 46.92 1.82
21 22 1.544246 CGTCCCAACCCTGGAAATTTC 59.456 52.381 9.83 9.83 46.92 2.17
22 23 1.899814 GTCCCAACCCTGGAAATTTCC 59.100 52.381 27.39 27.39 46.92 3.13
23 24 1.203250 TCCCAACCCTGGAAATTTCCC 60.203 52.381 30.04 15.29 46.92 3.97
24 25 1.203300 CCCAACCCTGGAAATTTCCCT 60.203 52.381 30.04 10.62 46.92 4.20
25 26 2.619931 CCAACCCTGGAAATTTCCCTT 58.380 47.619 30.04 15.27 46.92 3.95
26 27 2.978978 CCAACCCTGGAAATTTCCCTTT 59.021 45.455 30.04 16.45 46.92 3.11
27 28 3.244526 CCAACCCTGGAAATTTCCCTTTG 60.245 47.826 30.04 24.18 46.92 2.77
43 44 1.475682 CTTTGCTTTGCCAGAGGATCC 59.524 52.381 2.48 2.48 33.66 3.36
54 55 4.210331 GCCAGAGGATCCAATGTGTATTT 58.790 43.478 15.82 0.00 33.66 1.40
60 61 4.776837 AGGATCCAATGTGTATTTTTGCCA 59.223 37.500 15.82 0.00 0.00 4.92
66 67 8.316640 TCCAATGTGTATTTTTGCCAATAAAC 57.683 30.769 0.00 0.00 30.20 2.01
71 72 8.304202 TGTGTATTTTTGCCAATAAACATGAC 57.696 30.769 0.00 0.00 33.58 3.06
92 93 1.825090 CACCATGGCTTGAACTGCTA 58.175 50.000 13.04 0.00 0.00 3.49
94 95 2.095059 CACCATGGCTTGAACTGCTAAC 60.095 50.000 13.04 0.00 0.00 2.34
97 98 3.568538 CATGGCTTGAACTGCTAACAAC 58.431 45.455 0.00 0.00 0.00 3.32
98 99 1.601903 TGGCTTGAACTGCTAACAACG 59.398 47.619 0.00 0.00 0.00 4.10
124 126 8.066000 GTGTAATTTATTATACGTTGTCTGGGC 58.934 37.037 0.00 0.00 0.00 5.36
126 128 7.875327 AATTTATTATACGTTGTCTGGGCTT 57.125 32.000 0.00 0.00 0.00 4.35
136 138 1.009829 GTCTGGGCTTGCATACTTCG 58.990 55.000 0.00 0.00 0.00 3.79
148 150 4.495422 TGCATACTTCGAAGAGGAAGAAC 58.505 43.478 31.08 11.81 44.93 3.01
165 167 6.796705 GAAGAACTCTTCCGGTTTATTTCA 57.203 37.500 0.00 0.00 44.93 2.69
166 168 7.379098 GAAGAACTCTTCCGGTTTATTTCAT 57.621 36.000 0.00 0.00 44.93 2.57
167 169 7.761038 AAGAACTCTTCCGGTTTATTTCATT 57.239 32.000 0.00 0.00 0.00 2.57
168 170 8.857694 AAGAACTCTTCCGGTTTATTTCATTA 57.142 30.769 0.00 0.00 0.00 1.90
169 171 8.857694 AGAACTCTTCCGGTTTATTTCATTAA 57.142 30.769 0.00 0.00 0.00 1.40
193 195 8.408043 AATAATTCTGATCCATTTCGGCATTA 57.592 30.769 0.00 0.00 29.00 1.90
205 207 5.670149 TTTCGGCATTAACAGTTTCGTAA 57.330 34.783 0.00 0.00 0.00 3.18
233 235 9.565213 CTAATGAAAGTTCTTTATTCTGGCAAG 57.435 33.333 0.00 0.00 0.00 4.01
279 281 3.266510 TGGATCCGGATCTTTCACTTG 57.733 47.619 36.72 0.00 37.92 3.16
566 573 2.637872 AGACTTTGGCTAGCTTGGTGTA 59.362 45.455 15.72 0.00 0.00 2.90
868 935 4.142838 CGTTTAGAAAACCCCGGACAATAC 60.143 45.833 0.73 0.00 0.00 1.89
1278 1351 3.848019 GCAATGCTTTTGACAGTACGATG 59.152 43.478 0.00 0.00 0.00 3.84
1663 1736 2.524569 TGAAACACATCAGCTCACGA 57.475 45.000 0.00 0.00 0.00 4.35
2011 2084 1.155042 CAGGACAAGAGAGCAAGTGC 58.845 55.000 0.00 0.00 42.49 4.40
2085 2158 4.247380 GGCTGATCAGGAGGGCGG 62.247 72.222 23.89 0.00 0.00 6.13
2093 2166 2.765807 AGGAGGGCGGATGTCCAG 60.766 66.667 0.00 0.00 44.71 3.86
2128 2201 6.415573 ACCAGAAGATACTGAAATGGGTAAC 58.584 40.000 0.00 0.00 39.94 2.50
2142 2215 2.435069 TGGGTAACGGTGAACAGAAAGA 59.565 45.455 0.00 0.00 37.60 2.52
2145 2218 3.367025 GGTAACGGTGAACAGAAAGATCG 59.633 47.826 0.00 0.00 0.00 3.69
2152 2225 3.308323 GTGAACAGAAAGATCGAGATGCC 59.692 47.826 0.00 0.00 0.00 4.40
2610 2684 7.515998 CGCGGTGTATTTTCATTTGTTCTTTTT 60.516 33.333 0.00 0.00 0.00 1.94
2777 2857 7.944061 CATAATTGCATCTATTTCACCTTGGA 58.056 34.615 0.00 0.00 0.00 3.53
2778 2858 8.582437 CATAATTGCATCTATTTCACCTTGGAT 58.418 33.333 0.00 0.00 0.00 3.41
2793 2873 5.586243 CACCTTGGATCACGTCAAATTATCT 59.414 40.000 0.00 0.00 0.00 1.98
2865 2945 3.799035 CAACTCAAACGACCAAGAATCG 58.201 45.455 0.00 0.00 45.17 3.34
3145 3255 1.281899 GCGAATCGTCAGAAGGGAAG 58.718 55.000 4.07 0.00 0.00 3.46
3305 3415 2.764128 TGGATGGACCTCTCCGGC 60.764 66.667 0.00 0.00 39.88 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.481128 AATTTCCAGGGTTGGGACGT 59.519 50.000 0.00 0.00 45.10 4.34
1 2 1.544246 GAAATTTCCAGGGTTGGGACG 59.456 52.381 6.95 0.00 45.10 4.79
2 3 1.899814 GGAAATTTCCAGGGTTGGGAC 59.100 52.381 28.76 0.08 46.76 4.46
3 4 2.319025 GGAAATTTCCAGGGTTGGGA 57.681 50.000 28.76 0.00 46.76 4.37
13 14 2.813754 GGCAAAGCAAAGGGAAATTTCC 59.186 45.455 26.41 26.41 46.82 3.13
14 15 3.475575 TGGCAAAGCAAAGGGAAATTTC 58.524 40.909 9.83 9.83 0.00 2.17
15 16 3.136260 TCTGGCAAAGCAAAGGGAAATTT 59.864 39.130 0.00 0.00 0.00 1.82
16 17 2.705127 TCTGGCAAAGCAAAGGGAAATT 59.295 40.909 0.00 0.00 0.00 1.82
17 18 2.301009 CTCTGGCAAAGCAAAGGGAAAT 59.699 45.455 0.00 0.00 0.00 2.17
18 19 1.688197 CTCTGGCAAAGCAAAGGGAAA 59.312 47.619 0.00 0.00 0.00 3.13
19 20 1.331214 CTCTGGCAAAGCAAAGGGAA 58.669 50.000 0.00 0.00 0.00 3.97
20 21 0.540365 CCTCTGGCAAAGCAAAGGGA 60.540 55.000 0.00 0.00 0.00 4.20
21 22 0.540365 TCCTCTGGCAAAGCAAAGGG 60.540 55.000 0.00 0.00 0.00 3.95
22 23 1.475682 GATCCTCTGGCAAAGCAAAGG 59.524 52.381 0.00 0.00 0.00 3.11
23 24 1.475682 GGATCCTCTGGCAAAGCAAAG 59.524 52.381 3.84 0.00 0.00 2.77
24 25 1.203038 TGGATCCTCTGGCAAAGCAAA 60.203 47.619 14.23 0.00 0.00 3.68
25 26 0.405198 TGGATCCTCTGGCAAAGCAA 59.595 50.000 14.23 0.00 0.00 3.91
26 27 0.405198 TTGGATCCTCTGGCAAAGCA 59.595 50.000 14.23 0.00 0.00 3.91
27 28 1.407979 CATTGGATCCTCTGGCAAAGC 59.592 52.381 14.23 0.00 0.00 3.51
43 44 9.544314 CATGTTTATTGGCAAAAATACACATTG 57.456 29.630 3.01 0.16 39.59 2.82
54 55 3.312828 GTGCGTCATGTTTATTGGCAAA 58.687 40.909 3.01 0.00 0.00 3.68
60 61 2.159254 GCCATGGTGCGTCATGTTTATT 60.159 45.455 14.67 0.00 42.02 1.40
66 67 1.138036 CAAGCCATGGTGCGTCATG 59.862 57.895 14.67 10.91 42.92 3.07
71 72 1.210931 CAGTTCAAGCCATGGTGCG 59.789 57.895 14.67 1.63 36.02 5.34
97 98 8.270799 CCCAGACAACGTATAATAAATTACACG 58.729 37.037 10.98 10.98 45.59 4.49
98 99 8.066000 GCCCAGACAACGTATAATAAATTACAC 58.934 37.037 0.00 0.00 0.00 2.90
110 111 0.036164 TGCAAGCCCAGACAACGTAT 59.964 50.000 0.00 0.00 0.00 3.06
111 112 0.036164 ATGCAAGCCCAGACAACGTA 59.964 50.000 0.00 0.00 0.00 3.57
124 126 4.748892 TCTTCCTCTTCGAAGTATGCAAG 58.251 43.478 23.85 17.74 40.21 4.01
126 128 4.220821 AGTTCTTCCTCTTCGAAGTATGCA 59.779 41.667 23.85 4.22 40.21 3.96
164 166 8.298854 TGCCGAAATGGATCAGAATTATTAATG 58.701 33.333 0.00 0.00 42.00 1.90
165 167 8.408043 TGCCGAAATGGATCAGAATTATTAAT 57.592 30.769 0.00 0.00 42.00 1.40
166 168 7.815840 TGCCGAAATGGATCAGAATTATTAA 57.184 32.000 0.00 0.00 42.00 1.40
167 169 8.408043 AATGCCGAAATGGATCAGAATTATTA 57.592 30.769 0.00 0.00 42.00 0.98
168 170 6.906157 ATGCCGAAATGGATCAGAATTATT 57.094 33.333 0.00 0.00 42.00 1.40
169 171 6.906157 AATGCCGAAATGGATCAGAATTAT 57.094 33.333 0.00 0.00 42.00 1.28
175 177 4.336433 ACTGTTAATGCCGAAATGGATCAG 59.664 41.667 0.00 0.00 42.00 2.90
179 181 4.378978 CGAAACTGTTAATGCCGAAATGGA 60.379 41.667 0.00 0.00 42.00 3.41
205 207 9.466497 TGCCAGAATAAAGAACTTTCATTAGAT 57.534 29.630 2.99 0.00 34.23 1.98
868 935 5.743872 GCCAAATAAAGAACAAATAGCGAGG 59.256 40.000 0.00 0.00 0.00 4.63
1278 1351 7.819900 ACAATGATTGTGTTAAGAGGTAGAGAC 59.180 37.037 10.45 0.00 43.48 3.36
1663 1736 3.045601 ACTTTAGCACTTGCAGTCGAT 57.954 42.857 3.62 0.00 45.16 3.59
2011 2084 3.539604 CTTAGCTGGATCACTTTCCTGG 58.460 50.000 0.00 0.00 36.68 4.45
2085 2158 2.814336 GGTTTGTTGGTCTCTGGACATC 59.186 50.000 0.00 0.00 43.77 3.06
2093 2166 5.409826 CAGTATCTTCTGGTTTGTTGGTCTC 59.590 44.000 0.00 0.00 0.00 3.36
2128 2201 3.217599 TCTCGATCTTTCTGTTCACCG 57.782 47.619 0.00 0.00 0.00 4.94
2142 2215 0.249447 TGCGATTTCGGCATCTCGAT 60.249 50.000 1.75 0.00 39.03 3.59
2145 2218 1.268234 CCTTTGCGATTTCGGCATCTC 60.268 52.381 1.75 0.00 40.23 2.75
2152 2225 0.038709 TTTGGGCCTTTGCGATTTCG 60.039 50.000 4.53 0.00 43.27 3.46
2542 2616 4.220602 AGAAAATAAACAGACACCATGGCC 59.779 41.667 13.04 0.00 0.00 5.36
2543 2617 5.391312 AGAAAATAAACAGACACCATGGC 57.609 39.130 13.04 0.00 0.00 4.40
2610 2684 1.243342 CCATTTGTGGCAAGGCTCGA 61.243 55.000 0.00 0.00 0.00 4.04
2768 2848 2.920724 TTTGACGTGATCCAAGGTGA 57.079 45.000 0.00 0.00 0.00 4.02
2865 2945 2.233922 TGCCTCCTTGCTTCTACAGTAC 59.766 50.000 0.00 0.00 0.00 2.73
2867 2947 1.352083 TGCCTCCTTGCTTCTACAGT 58.648 50.000 0.00 0.00 0.00 3.55
2868 2948 2.354259 CTTGCCTCCTTGCTTCTACAG 58.646 52.381 0.00 0.00 0.00 2.74
2869 2949 1.003580 CCTTGCCTCCTTGCTTCTACA 59.996 52.381 0.00 0.00 0.00 2.74
2870 2950 1.743996 CCTTGCCTCCTTGCTTCTAC 58.256 55.000 0.00 0.00 0.00 2.59
2871 2951 0.035056 GCCTTGCCTCCTTGCTTCTA 60.035 55.000 0.00 0.00 0.00 2.10
2872 2952 1.303970 GCCTTGCCTCCTTGCTTCT 60.304 57.895 0.00 0.00 0.00 2.85
2947 3047 2.017138 TTCAATCCAACAGCGCGATA 57.983 45.000 12.10 0.00 0.00 2.92
3145 3255 1.074319 TGAAATAGTCGTCGCGTGCC 61.074 55.000 5.77 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.