Multiple sequence alignment - TraesCS6A01G183500

Loading Multiple Alignment...

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 TraesCS6A01G183500 chr6A 100.000 2648 0 0 1 2648 213994448 213991801 0.000000e+00 4891
1 TraesCS6A01G183500 chr6A 96.021 2438 83 8 224 2648 204306933 204304497 0.000000e+00 3952
2 TraesCS6A01G183500 chr6A 95.281 2458 102 9 202 2648 136164340 136161886 0.000000e+00 3884
3 TraesCS6A01G183500 chr6A 95.412 2441 102 5 217 2648 518075644 518073205 0.000000e+00 3879
4 TraesCS6A01G183500 chr6A 95.102 2450 106 9 212 2648 328875916 328878364 0.000000e+00 3847
5 TraesCS6A01G183500 chr6A 95.744 2185 80 8 473 2648 473515388 473517568 0.000000e+00 3507
6 TraesCS6A01G183500 chr5A 96.223 2436 78 7 221 2648 109667608 109670037 0.000000e+00 3976
7 TraesCS6A01G183500 chr5A 95.786 2444 84 6 214 2648 268344297 268346730 0.000000e+00 3925
8 TraesCS6A01G183500 chr5A 94.667 225 10 2 1 224 631391344 631391567 5.420000e-92 348
9 TraesCS6A01G183500 chr5A 94.643 224 10 2 2 224 297899463 297899685 1.950000e-91 346
10 TraesCS6A01G183500 chr5A 94.595 222 10 2 4 224 648983824 648983604 2.520000e-90 342
11 TraesCS6A01G183500 chr2A 95.343 2448 102 8 212 2648 616456362 616453916 0.000000e+00 3879
12 TraesCS6A01G183500 chr3A 93.970 2471 109 19 212 2647 134617324 134619789 0.000000e+00 3701
13 TraesCS6A01G183500 chr3A 94.222 225 11 2 1 224 279654737 279654960 2.520000e-90 342
14 TraesCS6A01G183500 chr3A 86.478 318 33 9 1 314 465659756 465660067 9.080000e-90 340
15 TraesCS6A01G183500 chr1A 95.821 2034 74 6 623 2648 465251795 465253825 0.000000e+00 3275
16 TraesCS6A01G183500 chr4A 95.982 224 8 1 1 224 65793477 65793699 1.940000e-96 363
17 TraesCS6A01G183500 chr4A 95.536 224 9 1 1 224 58662086 58661864 9.010000e-95 357
18 TraesCS6A01G183500 chr4A 94.222 225 11 2 1 224 293103791 293103568 2.520000e-90 342
19 TraesCS6A01G183500 chr7A 94.222 225 11 2 1 224 592817504 592817727 2.520000e-90 342


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 TraesCS6A01G183500 chr6A 213991801 213994448 2647 True 4891 4891 100.000 1 2648 1 chr6A.!!$R3 2647
1 TraesCS6A01G183500 chr6A 204304497 204306933 2436 True 3952 3952 96.021 224 2648 1 chr6A.!!$R2 2424
2 TraesCS6A01G183500 chr6A 136161886 136164340 2454 True 3884 3884 95.281 202 2648 1 chr6A.!!$R1 2446
3 TraesCS6A01G183500 chr6A 518073205 518075644 2439 True 3879 3879 95.412 217 2648 1 chr6A.!!$R4 2431
4 TraesCS6A01G183500 chr6A 328875916 328878364 2448 False 3847 3847 95.102 212 2648 1 chr6A.!!$F1 2436
5 TraesCS6A01G183500 chr6A 473515388 473517568 2180 False 3507 3507 95.744 473 2648 1 chr6A.!!$F2 2175
6 TraesCS6A01G183500 chr5A 109667608 109670037 2429 False 3976 3976 96.223 221 2648 1 chr5A.!!$F1 2427
7 TraesCS6A01G183500 chr5A 268344297 268346730 2433 False 3925 3925 95.786 214 2648 1 chr5A.!!$F2 2434
8 TraesCS6A01G183500 chr2A 616453916 616456362 2446 True 3879 3879 95.343 212 2648 1 chr2A.!!$R1 2436
9 TraesCS6A01G183500 chr3A 134617324 134619789 2465 False 3701 3701 93.970 212 2647 1 chr3A.!!$F1 2435
10 TraesCS6A01G183500 chr1A 465251795 465253825 2030 False 3275 3275 95.821 623 2648 1 chr1A.!!$F1 2025

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
69 70 0.035458 ATGCTATAAGCTCGGGGTGC 59.965 55.0 0.00 0.0 42.97 5.01 F
152 153 0.038343 TCGGCCGTACCAAAGTGTAC 60.038 55.0 27.15 0.0 39.03 2.90 F
166 167 0.168128 GTGTACGGTTGCAAGGCATC 59.832 55.0 0.00 0.0 38.76 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1220 1252 0.548031 GGATGATGTCCTCCTGCCAA 59.452 55.000 0.0 0.00 44.16 4.52 R
1273 1305 1.227943 GCACTTCTGCAGGGTGTCA 60.228 57.895 28.0 4.82 43.62 3.58 R
2052 2100 1.305201 TTGGTGAAGTTCGACTTGGC 58.695 50.000 5.2 0.00 38.80 4.52 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
20 21 1.877637 GGCAAACCCAACATTTGACC 58.122 50.000 1.76 0.00 38.87 4.02
21 22 1.139853 GGCAAACCCAACATTTGACCA 59.860 47.619 1.76 0.00 38.87 4.02
22 23 2.420687 GGCAAACCCAACATTTGACCAA 60.421 45.455 1.76 0.00 38.87 3.67
23 24 3.274288 GCAAACCCAACATTTGACCAAA 58.726 40.909 1.76 0.00 39.01 3.28
24 25 3.312146 GCAAACCCAACATTTGACCAAAG 59.688 43.478 1.76 0.00 39.01 2.77
25 26 4.764172 CAAACCCAACATTTGACCAAAGA 58.236 39.130 1.57 0.00 39.01 2.52
26 27 4.400529 AACCCAACATTTGACCAAAGAC 57.599 40.909 1.57 0.00 33.32 3.01
27 28 3.370104 ACCCAACATTTGACCAAAGACA 58.630 40.909 1.57 0.00 33.32 3.41
28 29 3.966665 ACCCAACATTTGACCAAAGACAT 59.033 39.130 1.57 0.00 33.32 3.06
29 30 4.202243 ACCCAACATTTGACCAAAGACATG 60.202 41.667 1.57 0.00 33.32 3.21
30 31 4.039004 CCCAACATTTGACCAAAGACATGA 59.961 41.667 0.00 0.00 33.32 3.07
31 32 5.279607 CCCAACATTTGACCAAAGACATGAT 60.280 40.000 0.00 0.00 33.32 2.45
32 33 6.225318 CCAACATTTGACCAAAGACATGATT 58.775 36.000 0.00 0.00 33.32 2.57
33 34 6.366877 CCAACATTTGACCAAAGACATGATTC 59.633 38.462 0.00 0.00 33.32 2.52
34 35 5.702865 ACATTTGACCAAAGACATGATTCG 58.297 37.500 0.00 0.00 33.32 3.34
35 36 4.764679 TTTGACCAAAGACATGATTCGG 57.235 40.909 0.00 0.00 0.00 4.30
36 37 3.694043 TGACCAAAGACATGATTCGGA 57.306 42.857 0.00 0.00 0.00 4.55
37 38 3.599343 TGACCAAAGACATGATTCGGAG 58.401 45.455 0.00 0.00 0.00 4.63
38 39 2.352960 GACCAAAGACATGATTCGGAGC 59.647 50.000 0.00 0.00 0.00 4.70
39 40 1.672881 CCAAAGACATGATTCGGAGCC 59.327 52.381 0.00 0.00 0.00 4.70
40 41 1.328680 CAAAGACATGATTCGGAGCCG 59.671 52.381 0.00 1.74 41.35 5.52
52 53 2.892374 TCGGAGCCGATGCATATAATG 58.108 47.619 7.66 0.00 44.01 1.90
67 68 5.918608 CATATAATGCTATAAGCTCGGGGT 58.081 41.667 0.03 0.00 42.97 4.95
68 69 2.550830 AATGCTATAAGCTCGGGGTG 57.449 50.000 0.00 0.00 42.97 4.61
69 70 0.035458 ATGCTATAAGCTCGGGGTGC 59.965 55.000 0.00 0.00 42.97 5.01
70 71 1.301795 GCTATAAGCTCGGGGTGCC 60.302 63.158 0.00 0.00 38.45 5.01
71 72 1.006102 CTATAAGCTCGGGGTGCCG 60.006 63.158 0.00 0.00 0.00 5.69
72 73 3.159858 TATAAGCTCGGGGTGCCGC 62.160 63.158 0.00 0.00 0.00 6.53
80 81 3.977244 GGGGTGCCGCACTTTGTG 61.977 66.667 22.41 0.00 34.40 3.33
81 82 2.904866 GGGTGCCGCACTTTGTGA 60.905 61.111 22.41 0.00 35.23 3.58
82 83 2.485795 GGGTGCCGCACTTTGTGAA 61.486 57.895 22.41 0.00 35.23 3.18
83 84 1.435515 GGTGCCGCACTTTGTGAAA 59.564 52.632 22.41 0.00 35.23 2.69
84 85 0.594796 GGTGCCGCACTTTGTGAAAG 60.595 55.000 22.41 0.00 44.10 2.62
97 98 5.869350 CTTTGTGAAAGTGTTCGAACTTCT 58.131 37.500 27.32 21.27 39.48 2.85
98 99 5.464965 TTGTGAAAGTGTTCGAACTTCTC 57.535 39.130 27.32 21.35 39.48 2.87
99 100 4.500127 TGTGAAAGTGTTCGAACTTCTCA 58.500 39.130 27.32 23.23 39.48 3.27
100 101 4.328983 TGTGAAAGTGTTCGAACTTCTCAC 59.671 41.667 27.32 27.48 41.80 3.51
101 102 4.328983 GTGAAAGTGTTCGAACTTCTCACA 59.671 41.667 28.41 23.10 41.52 3.58
102 103 4.328983 TGAAAGTGTTCGAACTTCTCACAC 59.671 41.667 27.32 16.64 39.48 3.82
103 104 2.822764 AGTGTTCGAACTTCTCACACC 58.177 47.619 27.32 0.00 0.00 4.16
104 105 2.167693 AGTGTTCGAACTTCTCACACCA 59.832 45.455 27.32 1.78 0.00 4.17
105 106 3.131396 GTGTTCGAACTTCTCACACCAT 58.869 45.455 27.32 0.00 0.00 3.55
106 107 4.038763 AGTGTTCGAACTTCTCACACCATA 59.961 41.667 27.32 0.97 0.00 2.74
107 108 4.929808 GTGTTCGAACTTCTCACACCATAT 59.070 41.667 27.32 0.00 0.00 1.78
108 109 5.408604 GTGTTCGAACTTCTCACACCATATT 59.591 40.000 27.32 0.00 0.00 1.28
109 110 6.588756 GTGTTCGAACTTCTCACACCATATTA 59.411 38.462 27.32 0.00 0.00 0.98
110 111 7.277981 GTGTTCGAACTTCTCACACCATATTAT 59.722 37.037 27.32 0.00 0.00 1.28
111 112 7.277760 TGTTCGAACTTCTCACACCATATTATG 59.722 37.037 27.32 0.00 0.00 1.90
125 126 5.506708 CCATATTATGGGTACTTAAGCCCC 58.493 45.833 19.48 19.48 46.86 5.80
126 127 5.253096 CCATATTATGGGTACTTAAGCCCCT 59.747 44.000 24.16 13.99 46.86 4.79
127 128 4.724279 ATTATGGGTACTTAAGCCCCTG 57.276 45.455 24.16 0.00 45.86 4.45
128 129 1.222567 ATGGGTACTTAAGCCCCTGG 58.777 55.000 24.16 0.00 45.86 4.45
129 130 0.178855 TGGGTACTTAAGCCCCTGGT 60.179 55.000 24.16 0.33 45.86 4.00
130 131 0.255033 GGGTACTTAAGCCCCTGGTG 59.745 60.000 19.16 0.00 40.09 4.17
131 132 0.989602 GGTACTTAAGCCCCTGGTGT 59.010 55.000 1.29 0.00 0.00 4.16
132 133 2.190538 GGTACTTAAGCCCCTGGTGTA 58.809 52.381 1.29 0.00 0.00 2.90
133 134 2.775960 GGTACTTAAGCCCCTGGTGTAT 59.224 50.000 1.29 0.00 0.00 2.29
134 135 3.181457 GGTACTTAAGCCCCTGGTGTATC 60.181 52.174 1.29 0.00 0.00 2.24
135 136 1.485066 ACTTAAGCCCCTGGTGTATCG 59.515 52.381 1.29 0.00 0.00 2.92
136 137 0.834612 TTAAGCCCCTGGTGTATCGG 59.165 55.000 0.00 0.00 0.00 4.18
137 138 1.692173 TAAGCCCCTGGTGTATCGGC 61.692 60.000 1.60 1.60 40.03 5.54
138 139 4.564110 GCCCCTGGTGTATCGGCC 62.564 72.222 0.00 0.00 33.30 6.13
139 140 4.235762 CCCCTGGTGTATCGGCCG 62.236 72.222 22.12 22.12 0.00 6.13
140 141 3.467226 CCCTGGTGTATCGGCCGT 61.467 66.667 27.15 15.22 0.00 5.68
141 142 2.129146 CCCTGGTGTATCGGCCGTA 61.129 63.158 27.15 14.11 0.00 4.02
142 143 1.066918 CCTGGTGTATCGGCCGTAC 59.933 63.158 27.15 24.47 0.00 3.67
143 144 1.066918 CTGGTGTATCGGCCGTACC 59.933 63.158 27.15 26.12 0.00 3.34
144 145 1.669049 CTGGTGTATCGGCCGTACCA 61.669 60.000 29.58 29.58 38.98 3.25
145 146 1.256361 TGGTGTATCGGCCGTACCAA 61.256 55.000 29.60 19.27 38.39 3.67
146 147 0.108233 GGTGTATCGGCCGTACCAAA 60.108 55.000 27.15 4.32 39.03 3.28
147 148 1.283736 GTGTATCGGCCGTACCAAAG 58.716 55.000 27.15 0.00 39.03 2.77
148 149 0.896923 TGTATCGGCCGTACCAAAGT 59.103 50.000 27.15 4.81 39.03 2.66
149 150 1.283736 GTATCGGCCGTACCAAAGTG 58.716 55.000 27.15 0.00 39.03 3.16
150 151 0.896923 TATCGGCCGTACCAAAGTGT 59.103 50.000 27.15 2.21 39.03 3.55
151 152 0.896923 ATCGGCCGTACCAAAGTGTA 59.103 50.000 27.15 0.03 39.03 2.90
152 153 0.038343 TCGGCCGTACCAAAGTGTAC 60.038 55.000 27.15 0.00 39.03 2.90
158 159 2.955607 GTACCAAAGTGTACGGTTGC 57.044 50.000 0.00 0.00 32.51 4.17
159 160 2.211806 GTACCAAAGTGTACGGTTGCA 58.788 47.619 0.00 0.00 32.51 4.08
160 161 1.752683 ACCAAAGTGTACGGTTGCAA 58.247 45.000 0.00 0.00 0.00 4.08
161 162 1.673920 ACCAAAGTGTACGGTTGCAAG 59.326 47.619 0.00 0.00 0.00 4.01
162 163 1.001815 CCAAAGTGTACGGTTGCAAGG 60.002 52.381 0.00 0.00 0.00 3.61
163 164 0.666374 AAAGTGTACGGTTGCAAGGC 59.334 50.000 0.00 0.00 0.00 4.35
164 165 0.464735 AAGTGTACGGTTGCAAGGCA 60.465 50.000 0.00 0.00 36.47 4.75
165 166 0.250727 AGTGTACGGTTGCAAGGCAT 60.251 50.000 0.00 0.00 38.76 4.40
166 167 0.168128 GTGTACGGTTGCAAGGCATC 59.832 55.000 0.00 0.00 38.76 3.91
167 168 1.295357 TGTACGGTTGCAAGGCATCG 61.295 55.000 0.00 11.11 38.76 3.84
168 169 1.004320 TACGGTTGCAAGGCATCGT 60.004 52.632 18.58 18.58 45.11 3.73
169 170 0.604243 TACGGTTGCAAGGCATCGTT 60.604 50.000 19.35 8.83 42.47 3.85
170 171 0.604243 ACGGTTGCAAGGCATCGTTA 60.604 50.000 0.00 0.00 42.47 3.18
171 172 0.519519 CGGTTGCAAGGCATCGTTAA 59.480 50.000 0.00 0.00 38.76 2.01
172 173 1.132262 CGGTTGCAAGGCATCGTTAAT 59.868 47.619 0.00 0.00 38.76 1.40
173 174 2.529151 GGTTGCAAGGCATCGTTAATG 58.471 47.619 0.00 0.00 38.76 1.90
174 175 2.163412 GGTTGCAAGGCATCGTTAATGA 59.837 45.455 0.00 0.00 38.76 2.57
175 176 3.366883 GGTTGCAAGGCATCGTTAATGAA 60.367 43.478 0.00 0.00 38.76 2.57
176 177 3.485947 TGCAAGGCATCGTTAATGAAC 57.514 42.857 0.55 0.00 37.59 3.18
177 178 2.816672 TGCAAGGCATCGTTAATGAACA 59.183 40.909 0.55 0.00 37.59 3.18
178 179 3.171277 GCAAGGCATCGTTAATGAACAC 58.829 45.455 0.55 0.00 37.59 3.32
179 180 3.365868 GCAAGGCATCGTTAATGAACACA 60.366 43.478 0.55 0.00 37.59 3.72
180 181 4.158384 CAAGGCATCGTTAATGAACACAC 58.842 43.478 0.55 0.00 37.59 3.82
181 182 3.407698 AGGCATCGTTAATGAACACACA 58.592 40.909 0.55 0.00 37.59 3.72
182 183 3.188460 AGGCATCGTTAATGAACACACAC 59.812 43.478 0.55 0.00 37.59 3.82
183 184 3.058570 GGCATCGTTAATGAACACACACA 60.059 43.478 0.55 0.00 37.59 3.72
184 185 3.906008 GCATCGTTAATGAACACACACAC 59.094 43.478 0.55 0.00 37.59 3.82
185 186 4.553742 GCATCGTTAATGAACACACACACA 60.554 41.667 0.55 0.00 37.59 3.72
186 187 4.523853 TCGTTAATGAACACACACACAC 57.476 40.909 0.00 0.00 35.06 3.82
187 188 3.933332 TCGTTAATGAACACACACACACA 59.067 39.130 0.00 0.00 35.06 3.72
188 189 4.025750 CGTTAATGAACACACACACACAC 58.974 43.478 0.00 0.00 35.06 3.82
189 190 4.436183 CGTTAATGAACACACACACACACA 60.436 41.667 0.00 0.00 35.06 3.72
190 191 3.485947 AATGAACACACACACACACAC 57.514 42.857 0.00 0.00 0.00 3.82
191 192 1.884235 TGAACACACACACACACACA 58.116 45.000 0.00 0.00 0.00 3.72
192 193 1.533299 TGAACACACACACACACACAC 59.467 47.619 0.00 0.00 0.00 3.82
193 194 1.533299 GAACACACACACACACACACA 59.467 47.619 0.00 0.00 0.00 3.72
194 195 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
195 196 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
196 197 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
197 198 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
198 199 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
199 200 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
200 201 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
201 202 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
202 203 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
203 204 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
204 205 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
205 206 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
206 207 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
207 208 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
208 209 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
764 774 4.796231 GTCCGCCGCGATGTCACT 62.796 66.667 15.93 0.00 0.00 3.41
771 781 0.740868 CCGCGATGTCACTGTCCATT 60.741 55.000 8.23 0.00 0.00 3.16
919 951 3.049674 CGTGCGGCATGAACCTGT 61.050 61.111 17.10 0.00 0.00 4.00
929 961 1.001974 CATGAACCTGTCCTTCGACCA 59.998 52.381 0.00 0.00 38.32 4.02
993 1025 2.499205 CAGCCCATCGGACGCTAA 59.501 61.111 0.00 0.00 0.00 3.09
1120 1152 3.513515 TGTGTATGTGTGCAGGTGATCTA 59.486 43.478 0.00 0.00 0.00 1.98
1166 1198 2.203266 GGGCTGCCCTACATCTGC 60.203 66.667 30.42 0.00 41.34 4.26
1220 1252 3.330701 TGAAGGAGTACAAGGGCATCTTT 59.669 43.478 0.00 0.00 32.41 2.52
1280 1312 2.154462 CTGACAAGGAATGTGACACCC 58.846 52.381 2.45 0.00 44.12 4.61
1336 1368 0.908198 AGGAGAAGCTCGGCAAGATT 59.092 50.000 0.00 0.00 35.97 2.40
1736 1782 6.206395 TGACATTTCACAACAACTGACAAT 57.794 33.333 0.00 0.00 0.00 2.71
1826 1872 0.108585 TCTCCTCGGCAGCAAAAAGT 59.891 50.000 0.00 0.00 0.00 2.66
1870 1916 5.526479 TCGTATGCTACTAGTAGGTCAACTG 59.474 44.000 27.24 13.08 33.87 3.16
1935 1982 8.416329 CCCCATGTGAAATTCTATAAAAAGGAG 58.584 37.037 0.00 0.00 0.00 3.69
1952 1999 3.103080 GGAGGGAACAGTCTCCTTCTA 57.897 52.381 11.25 0.00 44.54 2.10
2037 2085 4.691216 ACTAGAAAAAGATGAGCACGTTCC 59.309 41.667 0.00 0.00 0.00 3.62
2214 2264 2.880443 AGCAATTCAAAAGGAGCAGGA 58.120 42.857 0.00 0.00 0.00 3.86
2360 2411 3.452627 GTGTGGTGAGGAATGAGAGGTAT 59.547 47.826 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.139853 TGGTCAAATGTTGGGTTTGCC 59.860 47.619 0.00 0.00 36.69 4.52
2 3 2.611225 TGGTCAAATGTTGGGTTTGC 57.389 45.000 0.00 0.00 36.69 3.68
3 4 4.570369 GTCTTTGGTCAAATGTTGGGTTTG 59.430 41.667 0.00 0.00 37.79 2.93
4 5 4.223923 TGTCTTTGGTCAAATGTTGGGTTT 59.776 37.500 0.00 0.00 0.00 3.27
6 7 3.370104 TGTCTTTGGTCAAATGTTGGGT 58.630 40.909 0.00 0.00 0.00 4.51
7 8 4.039004 TCATGTCTTTGGTCAAATGTTGGG 59.961 41.667 0.00 0.00 0.00 4.12
8 9 5.199024 TCATGTCTTTGGTCAAATGTTGG 57.801 39.130 0.00 0.00 0.00 3.77
9 10 6.088483 CGAATCATGTCTTTGGTCAAATGTTG 59.912 38.462 0.00 0.00 0.00 3.33
10 11 6.151691 CGAATCATGTCTTTGGTCAAATGTT 58.848 36.000 0.00 0.00 0.00 2.71
11 12 5.335897 CCGAATCATGTCTTTGGTCAAATGT 60.336 40.000 8.21 0.00 0.00 2.71
12 13 5.097529 CCGAATCATGTCTTTGGTCAAATG 58.902 41.667 8.21 0.00 0.00 2.32
13 14 5.009631 TCCGAATCATGTCTTTGGTCAAAT 58.990 37.500 13.41 0.00 0.00 2.32
14 15 4.393834 TCCGAATCATGTCTTTGGTCAAA 58.606 39.130 13.41 0.00 0.00 2.69
15 16 4.002982 CTCCGAATCATGTCTTTGGTCAA 58.997 43.478 13.41 0.00 0.00 3.18
16 17 3.599343 CTCCGAATCATGTCTTTGGTCA 58.401 45.455 13.41 0.43 0.00 4.02
17 18 2.352960 GCTCCGAATCATGTCTTTGGTC 59.647 50.000 13.41 6.62 0.00 4.02
18 19 2.359900 GCTCCGAATCATGTCTTTGGT 58.640 47.619 13.41 0.00 0.00 3.67
19 20 1.672881 GGCTCCGAATCATGTCTTTGG 59.327 52.381 9.52 9.52 0.00 3.28
20 21 1.328680 CGGCTCCGAATCATGTCTTTG 59.671 52.381 1.35 0.00 42.83 2.77
21 22 1.207089 TCGGCTCCGAATCATGTCTTT 59.793 47.619 8.76 0.00 46.01 2.52
22 23 0.824109 TCGGCTCCGAATCATGTCTT 59.176 50.000 8.76 0.00 46.01 3.01
23 24 2.504920 TCGGCTCCGAATCATGTCT 58.495 52.632 8.76 0.00 46.01 3.41
44 45 5.755375 CACCCCGAGCTTATAGCATTATATG 59.245 44.000 1.09 0.00 45.56 1.78
45 46 5.685075 GCACCCCGAGCTTATAGCATTATAT 60.685 44.000 1.09 0.00 45.56 0.86
46 47 4.382685 GCACCCCGAGCTTATAGCATTATA 60.383 45.833 1.09 0.00 45.56 0.98
47 48 3.619979 GCACCCCGAGCTTATAGCATTAT 60.620 47.826 1.09 0.00 45.56 1.28
48 49 2.289444 GCACCCCGAGCTTATAGCATTA 60.289 50.000 1.09 0.00 45.56 1.90
49 50 1.543429 GCACCCCGAGCTTATAGCATT 60.543 52.381 1.09 0.00 45.56 3.56
50 51 0.035458 GCACCCCGAGCTTATAGCAT 59.965 55.000 1.09 0.00 45.56 3.79
51 52 1.445942 GCACCCCGAGCTTATAGCA 59.554 57.895 1.09 0.00 45.56 3.49
52 53 1.301795 GGCACCCCGAGCTTATAGC 60.302 63.158 0.00 0.00 42.84 2.97
63 64 3.977244 CACAAAGTGCGGCACCCC 61.977 66.667 28.14 5.16 34.49 4.95
64 65 2.010582 TTTCACAAAGTGCGGCACCC 62.011 55.000 28.14 5.96 34.49 4.61
65 66 0.594796 CTTTCACAAAGTGCGGCACC 60.595 55.000 28.14 11.55 34.49 5.01
66 67 2.872028 CTTTCACAAAGTGCGGCAC 58.128 52.632 25.00 25.00 33.80 5.01
74 75 5.869350 AGAAGTTCGAACACTTTCACAAAG 58.131 37.500 28.78 0.00 44.10 2.77
75 76 5.410132 TGAGAAGTTCGAACACTTTCACAAA 59.590 36.000 28.78 9.07 37.11 2.83
76 77 4.932799 TGAGAAGTTCGAACACTTTCACAA 59.067 37.500 28.78 11.14 37.11 3.33
77 78 4.328983 GTGAGAAGTTCGAACACTTTCACA 59.671 41.667 29.34 24.30 40.27 3.58
78 79 4.328983 TGTGAGAAGTTCGAACACTTTCAC 59.671 41.667 28.50 28.50 40.55 3.18
79 80 4.328983 GTGTGAGAAGTTCGAACACTTTCA 59.671 41.667 28.78 21.08 37.11 2.69
80 81 4.260253 GGTGTGAGAAGTTCGAACACTTTC 60.260 45.833 28.78 22.10 37.11 2.62
81 82 3.621715 GGTGTGAGAAGTTCGAACACTTT 59.378 43.478 28.78 15.32 37.11 2.66
82 83 3.195661 GGTGTGAGAAGTTCGAACACTT 58.804 45.455 28.78 16.21 39.84 3.16
83 84 2.167693 TGGTGTGAGAAGTTCGAACACT 59.832 45.455 28.78 24.82 37.57 3.55
84 85 2.546778 TGGTGTGAGAAGTTCGAACAC 58.453 47.619 28.78 24.55 37.08 3.32
85 86 2.971660 TGGTGTGAGAAGTTCGAACA 57.028 45.000 28.78 6.18 0.00 3.18
86 87 7.254455 CCATAATATGGTGTGAGAAGTTCGAAC 60.254 40.741 20.71 20.71 45.54 3.95
87 88 6.761242 CCATAATATGGTGTGAGAAGTTCGAA 59.239 38.462 11.07 0.00 45.54 3.71
88 89 6.280643 CCATAATATGGTGTGAGAAGTTCGA 58.719 40.000 11.07 0.00 45.54 3.71
89 90 6.530913 CCATAATATGGTGTGAGAAGTTCG 57.469 41.667 11.07 0.00 45.54 3.95
111 112 0.255033 CACCAGGGGCTTAAGTACCC 59.745 60.000 22.62 22.62 46.24 3.69
112 113 0.989602 ACACCAGGGGCTTAAGTACC 59.010 55.000 4.02 7.04 0.00 3.34
113 114 3.492137 CGATACACCAGGGGCTTAAGTAC 60.492 52.174 4.02 0.00 0.00 2.73
114 115 2.696707 CGATACACCAGGGGCTTAAGTA 59.303 50.000 4.02 0.00 0.00 2.24
115 116 1.485066 CGATACACCAGGGGCTTAAGT 59.515 52.381 4.02 0.00 0.00 2.24
116 117 1.202651 CCGATACACCAGGGGCTTAAG 60.203 57.143 0.00 0.00 0.00 1.85
117 118 0.834612 CCGATACACCAGGGGCTTAA 59.165 55.000 0.00 0.00 0.00 1.85
118 119 1.692173 GCCGATACACCAGGGGCTTA 61.692 60.000 0.00 0.00 40.59 3.09
119 120 3.043999 GCCGATACACCAGGGGCTT 62.044 63.158 0.00 0.00 40.59 4.35
120 121 3.480133 GCCGATACACCAGGGGCT 61.480 66.667 0.00 0.00 40.59 5.19
121 122 4.564110 GGCCGATACACCAGGGGC 62.564 72.222 0.00 0.00 43.01 5.80
122 123 4.235762 CGGCCGATACACCAGGGG 62.236 72.222 24.07 0.00 0.00 4.79
123 124 2.129146 TACGGCCGATACACCAGGG 61.129 63.158 35.90 0.00 0.00 4.45
124 125 1.066918 GTACGGCCGATACACCAGG 59.933 63.158 35.90 0.00 0.00 4.45
125 126 1.066918 GGTACGGCCGATACACCAG 59.933 63.158 35.90 0.00 0.00 4.00
126 127 1.256361 TTGGTACGGCCGATACACCA 61.256 55.000 35.90 31.26 41.21 4.17
127 128 0.108233 TTTGGTACGGCCGATACACC 60.108 55.000 35.90 29.21 41.21 4.16
128 129 1.283736 CTTTGGTACGGCCGATACAC 58.716 55.000 35.90 21.98 41.21 2.90
129 130 0.896923 ACTTTGGTACGGCCGATACA 59.103 50.000 35.90 23.25 41.21 2.29
130 131 1.283736 CACTTTGGTACGGCCGATAC 58.716 55.000 35.90 27.20 41.21 2.24
131 132 0.896923 ACACTTTGGTACGGCCGATA 59.103 50.000 35.90 17.76 41.21 2.92
132 133 0.896923 TACACTTTGGTACGGCCGAT 59.103 50.000 35.90 18.92 41.21 4.18
133 134 0.038343 GTACACTTTGGTACGGCCGA 60.038 55.000 35.90 13.31 41.21 5.54
134 135 2.448477 GTACACTTTGGTACGGCCG 58.552 57.895 26.86 26.86 41.21 6.13
139 140 2.211806 TGCAACCGTACACTTTGGTAC 58.788 47.619 0.00 0.00 40.14 3.34
140 141 2.616634 TGCAACCGTACACTTTGGTA 57.383 45.000 0.00 0.00 34.11 3.25
141 142 1.673920 CTTGCAACCGTACACTTTGGT 59.326 47.619 0.00 0.00 37.68 3.67
142 143 1.001815 CCTTGCAACCGTACACTTTGG 60.002 52.381 0.00 0.00 0.00 3.28
143 144 1.599419 GCCTTGCAACCGTACACTTTG 60.599 52.381 0.00 0.00 0.00 2.77
144 145 0.666374 GCCTTGCAACCGTACACTTT 59.334 50.000 0.00 0.00 0.00 2.66
145 146 0.464735 TGCCTTGCAACCGTACACTT 60.465 50.000 0.00 0.00 34.76 3.16
146 147 0.250727 ATGCCTTGCAACCGTACACT 60.251 50.000 0.00 0.00 43.62 3.55
147 148 0.168128 GATGCCTTGCAACCGTACAC 59.832 55.000 0.00 0.00 43.62 2.90
148 149 1.295357 CGATGCCTTGCAACCGTACA 61.295 55.000 0.00 0.00 43.62 2.90
149 150 1.296056 ACGATGCCTTGCAACCGTAC 61.296 55.000 14.91 0.00 43.62 3.67
150 151 0.604243 AACGATGCCTTGCAACCGTA 60.604 50.000 16.19 0.00 43.62 4.02
151 152 0.604243 TAACGATGCCTTGCAACCGT 60.604 50.000 12.02 12.02 43.62 4.83
152 153 0.519519 TTAACGATGCCTTGCAACCG 59.480 50.000 0.00 11.00 43.62 4.44
153 154 2.163412 TCATTAACGATGCCTTGCAACC 59.837 45.455 0.00 0.00 43.62 3.77
154 155 3.485947 TCATTAACGATGCCTTGCAAC 57.514 42.857 0.00 0.00 43.62 4.17
155 156 3.254411 TGTTCATTAACGATGCCTTGCAA 59.746 39.130 0.00 0.00 39.28 4.08
156 157 2.816672 TGTTCATTAACGATGCCTTGCA 59.183 40.909 0.00 0.00 39.81 4.08
157 158 3.171277 GTGTTCATTAACGATGCCTTGC 58.829 45.455 0.00 0.00 38.53 4.01
158 159 4.158384 GTGTGTTCATTAACGATGCCTTG 58.842 43.478 0.00 0.00 38.53 3.61
159 160 3.818210 TGTGTGTTCATTAACGATGCCTT 59.182 39.130 0.00 0.00 38.53 4.35
160 161 3.188460 GTGTGTGTTCATTAACGATGCCT 59.812 43.478 0.00 0.00 38.53 4.75
161 162 3.058570 TGTGTGTGTTCATTAACGATGCC 60.059 43.478 0.00 0.00 38.53 4.40
162 163 3.906008 GTGTGTGTGTTCATTAACGATGC 59.094 43.478 0.00 0.00 38.53 3.91
163 164 4.903585 GTGTGTGTGTGTTCATTAACGATG 59.096 41.667 0.00 0.00 38.53 3.84
164 165 4.572795 TGTGTGTGTGTGTTCATTAACGAT 59.427 37.500 0.00 0.00 38.53 3.73
165 166 3.933332 TGTGTGTGTGTGTTCATTAACGA 59.067 39.130 0.00 0.00 38.53 3.85
166 167 4.025750 GTGTGTGTGTGTGTTCATTAACG 58.974 43.478 0.00 0.00 38.53 3.18
167 168 4.791163 GTGTGTGTGTGTGTGTTCATTAAC 59.209 41.667 0.00 0.00 36.07 2.01
168 169 4.455877 TGTGTGTGTGTGTGTGTTCATTAA 59.544 37.500 0.00 0.00 0.00 1.40
169 170 4.003648 TGTGTGTGTGTGTGTGTTCATTA 58.996 39.130 0.00 0.00 0.00 1.90
170 171 2.816672 TGTGTGTGTGTGTGTGTTCATT 59.183 40.909 0.00 0.00 0.00 2.57
171 172 2.161410 GTGTGTGTGTGTGTGTGTTCAT 59.839 45.455 0.00 0.00 0.00 2.57
172 173 1.533299 GTGTGTGTGTGTGTGTGTTCA 59.467 47.619 0.00 0.00 0.00 3.18
173 174 1.533299 TGTGTGTGTGTGTGTGTGTTC 59.467 47.619 0.00 0.00 0.00 3.18
174 175 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32
175 176 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
176 177 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
177 178 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
178 179 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
179 180 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
180 181 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
181 182 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
182 183 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
183 184 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
184 185 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
185 186 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
186 187 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
187 188 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
188 189 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
189 190 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
190 191 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
191 192 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
192 193 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
193 194 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
194 195 5.861222 ATATATGTGTGTGTGTGTGTGTG 57.139 39.130 0.00 0.00 0.00 3.82
287 288 1.183030 TTCAGGAACGCCTCTTCGGA 61.183 55.000 0.00 0.00 44.80 4.55
303 304 2.158667 GGTGGGTTTTCTCAGGAGTTCA 60.159 50.000 0.00 0.00 0.00 3.18
519 525 4.752879 GAACCTGGCACGGCGCTA 62.753 66.667 6.90 0.00 41.91 4.26
598 606 3.736224 TAGGAGGAGACCGGCGGT 61.736 66.667 34.81 34.81 39.44 5.68
748 758 4.794439 CAGTGACATCGCGGCGGA 62.794 66.667 23.46 9.74 0.00 5.54
764 774 3.575247 ACCACCGGGCAATGGACA 61.575 61.111 15.35 0.00 39.46 4.02
919 951 0.965866 ATGAGCTCGTGGTCGAAGGA 60.966 55.000 7.89 0.00 45.61 3.36
993 1025 0.037882 CAGTCAGCCACATGTCGTCT 60.038 55.000 0.00 0.00 0.00 4.18
1120 1152 2.291043 CCTAGCCCAAGGTGGTCGT 61.291 63.158 0.00 0.00 35.17 4.34
1166 1198 2.913578 TTGCTGGCCTTGCTGTGG 60.914 61.111 19.10 0.00 0.00 4.17
1220 1252 0.548031 GGATGATGTCCTCCTGCCAA 59.452 55.000 0.00 0.00 44.16 4.52
1273 1305 1.227943 GCACTTCTGCAGGGTGTCA 60.228 57.895 28.00 4.82 43.62 3.58
1280 1312 2.191802 CGAGATGTAGCACTTCTGCAG 58.808 52.381 7.63 7.63 46.97 4.41
1336 1368 3.432186 CGAGCTTGATGAAATAGGGGTCA 60.432 47.826 0.00 0.00 0.00 4.02
1736 1782 1.605457 CGCTCTATCCAGCCGCAATTA 60.605 52.381 0.00 0.00 35.84 1.40
1826 1872 8.869897 CATACGAATTGAACTTCAGTTAAGCTA 58.130 33.333 0.00 0.00 38.93 3.32
1870 1916 1.521580 AAGAACTCTGCTGCTGCTTC 58.478 50.000 17.00 11.46 40.48 3.86
1935 1982 2.429250 GAGCTAGAAGGAGACTGTTCCC 59.571 54.545 0.00 0.00 42.68 3.97
1952 1999 1.445095 GATCACCGATGGCTGAGCT 59.555 57.895 3.72 0.00 0.00 4.09
1977 2024 4.621747 CGACTTGGTCTTTAGGAGAAGCAT 60.622 45.833 0.00 0.00 35.79 3.79
2052 2100 1.305201 TTGGTGAAGTTCGACTTGGC 58.695 50.000 5.20 0.00 38.80 4.52
2214 2264 4.453751 TGTACTTTAGGCAAACGAAACCT 58.546 39.130 0.00 0.00 37.61 3.50


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

AutoCloner maintained by Alex Coulton.