Multiple sequence alignment - TraesCS7D01G276500

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 TraesCS7D01G276500 chr7D 100.000 3238 0 0 1 3238 264763087 264766324 0.000000e+00 5980
1 TraesCS7D01G276500 chr2D 99.109 2133 19 0 1106 3238 33018316 33020448 0.000000e+00 3834
2 TraesCS7D01G276500 chr2D 97.362 834 16 1 235 1068 33017491 33018318 0.000000e+00 1413
3 TraesCS7D01G276500 chr7A 88.977 3021 303 23 236 3237 176256562 176259571 0.000000e+00 3707
4 TraesCS7D01G276500 chr7A 97.458 236 6 0 1 236 288935651 288935886 1.400000e-108 403
5 TraesCS7D01G276500 chr2A 88.929 3026 302 24 233 3237 642924703 642921690 0.000000e+00 3701
6 TraesCS7D01G276500 chr2A 88.973 2240 240 6 999 3237 208560475 208558242 0.000000e+00 2761
7 TraesCS7D01G276500 chr5B 88.841 3029 310 21 228 3237 161074836 161077855 0.000000e+00 3696
8 TraesCS7D01G276500 chr7B 89.092 2246 234 10 996 3237 418742059 418744297 0.000000e+00 2780
9 TraesCS7D01G276500 chr7B 88.760 2242 246 6 999 3237 291563025 291560787 0.000000e+00 2739
10 TraesCS7D01G276500 chr7B 97.890 237 4 1 1 236 245078784 245079020 3.010000e-110 409
11 TraesCS7D01G276500 chr3B 89.107 2240 238 6 999 3237 470052992 470050758 0.000000e+00 2780
12 TraesCS7D01G276500 chr6A 88.973 2240 238 7 999 3237 189558650 189556419 0.000000e+00 2760
13 TraesCS7D01G276500 chr6A 90.633 758 44 22 231 970 466092182 466092930 0.000000e+00 981
14 TraesCS7D01G276500 chr2B 88.731 2245 248 5 996 3237 309476631 309478873 0.000000e+00 2739
15 TraesCS7D01G276500 chr1A 88.725 2244 249 4 996 3237 440450177 440452418 0.000000e+00 2739
16 TraesCS7D01G276500 chr6B 87.829 2317 266 13 930 3237 698115628 698117937 0.000000e+00 2702
17 TraesCS7D01G276500 chr6B 91.777 754 37 20 232 970 698114880 698115623 0.000000e+00 1026
18 TraesCS7D01G276500 chr6B 90.921 749 45 17 236 970 458495685 458496424 0.000000e+00 985
19 TraesCS7D01G276500 chr4B 91.345 751 40 18 236 970 439195477 439196218 0.000000e+00 1003
20 TraesCS7D01G276500 chr4A 91.079 751 40 19 236 970 548526247 548525508 0.000000e+00 990


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 TraesCS7D01G276500 chr7D 264763087 264766324 3237 False 5980.0 5980 100.0000 1 3238 1 chr7D.!!$F1 3237
1 TraesCS7D01G276500 chr2D 33017491 33020448 2957 False 2623.5 3834 98.2355 235 3238 2 chr2D.!!$F1 3003
2 TraesCS7D01G276500 chr7A 176256562 176259571 3009 False 3707.0 3707 88.9770 236 3237 1 chr7A.!!$F1 3001
3 TraesCS7D01G276500 chr2A 642921690 642924703 3013 True 3701.0 3701 88.9290 233 3237 1 chr2A.!!$R2 3004
4 TraesCS7D01G276500 chr2A 208558242 208560475 2233 True 2761.0 2761 88.9730 999 3237 1 chr2A.!!$R1 2238
5 TraesCS7D01G276500 chr5B 161074836 161077855 3019 False 3696.0 3696 88.8410 228 3237 1 chr5B.!!$F1 3009
6 TraesCS7D01G276500 chr7B 418742059 418744297 2238 False 2780.0 2780 89.0920 996 3237 1 chr7B.!!$F2 2241
7 TraesCS7D01G276500 chr7B 291560787 291563025 2238 True 2739.0 2739 88.7600 999 3237 1 chr7B.!!$R1 2238
8 TraesCS7D01G276500 chr3B 470050758 470052992 2234 True 2780.0 2780 89.1070 999 3237 1 chr3B.!!$R1 2238
9 TraesCS7D01G276500 chr6A 189556419 189558650 2231 True 2760.0 2760 88.9730 999 3237 1 chr6A.!!$R1 2238
10 TraesCS7D01G276500 chr6A 466092182 466092930 748 False 981.0 981 90.6330 231 970 1 chr6A.!!$F1 739
11 TraesCS7D01G276500 chr2B 309476631 309478873 2242 False 2739.0 2739 88.7310 996 3237 1 chr2B.!!$F1 2241
12 TraesCS7D01G276500 chr1A 440450177 440452418 2241 False 2739.0 2739 88.7250 996 3237 1 chr1A.!!$F1 2241
13 TraesCS7D01G276500 chr6B 698114880 698117937 3057 False 1864.0 2702 89.8030 232 3237 2 chr6B.!!$F2 3005
14 TraesCS7D01G276500 chr6B 458495685 458496424 739 False 985.0 985 90.9210 236 970 1 chr6B.!!$F1 734
15 TraesCS7D01G276500 chr4B 439195477 439196218 741 False 1003.0 1003 91.3450 236 970 1 chr4B.!!$F1 734
16 TraesCS7D01G276500 chr4A 548525508 548526247 739 True 990.0 990 91.0790 236 970 1 chr4A.!!$R1 734

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
194 195 0.533755 ATGCAGGCATTCTCTACGCC 60.534 55.000 0.00 0.0 46.62 5.68 F
200 201 1.138266 GGCATTCTCTACGCCCTAACA 59.862 52.381 0.00 0.0 40.07 2.41 F
1069 1127 1.004394 TCCTCGCTGAGTCCAACTCTA 59.996 52.381 8.44 0.0 45.27 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1069 1127 1.299976 GTCGAGGAACAATGGCCCT 59.700 57.895 0.0 0.0 0.0 5.19 R
1101 1159 1.906574 AGGGGTGACATTTCGAGCTTA 59.093 47.619 0.0 0.0 0.0 3.09 R
2300 2360 2.293122 GCTGGCACATGTAAAACTGACA 59.707 45.455 0.0 0.0 38.2 3.58 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
22 23 4.481368 TTGTTCACCACTGTTACACTCT 57.519 40.909 0.00 0.00 0.00 3.24
23 24 4.054780 TGTTCACCACTGTTACACTCTC 57.945 45.455 0.00 0.00 0.00 3.20
24 25 3.704566 TGTTCACCACTGTTACACTCTCT 59.295 43.478 0.00 0.00 0.00 3.10
25 26 4.051922 GTTCACCACTGTTACACTCTCTG 58.948 47.826 0.00 0.00 0.00 3.35
26 27 2.035961 TCACCACTGTTACACTCTCTGC 59.964 50.000 0.00 0.00 0.00 4.26
27 28 2.039418 ACCACTGTTACACTCTCTGCA 58.961 47.619 0.00 0.00 0.00 4.41
28 29 2.634940 ACCACTGTTACACTCTCTGCAT 59.365 45.455 0.00 0.00 0.00 3.96
29 30 3.071602 ACCACTGTTACACTCTCTGCATT 59.928 43.478 0.00 0.00 0.00 3.56
30 31 4.283467 ACCACTGTTACACTCTCTGCATTA 59.717 41.667 0.00 0.00 0.00 1.90
31 32 5.046304 ACCACTGTTACACTCTCTGCATTAT 60.046 40.000 0.00 0.00 0.00 1.28
32 33 5.877012 CCACTGTTACACTCTCTGCATTATT 59.123 40.000 0.00 0.00 0.00 1.40
33 34 7.041721 CCACTGTTACACTCTCTGCATTATTA 58.958 38.462 0.00 0.00 0.00 0.98
34 35 7.549134 CCACTGTTACACTCTCTGCATTATTAA 59.451 37.037 0.00 0.00 0.00 1.40
35 36 8.935844 CACTGTTACACTCTCTGCATTATTAAA 58.064 33.333 0.00 0.00 0.00 1.52
36 37 9.502091 ACTGTTACACTCTCTGCATTATTAAAA 57.498 29.630 0.00 0.00 0.00 1.52
112 113 9.774413 AAAAAGTAAGTATTGTGTAGTGTAGCT 57.226 29.630 0.00 0.00 0.00 3.32
113 114 8.983307 AAAGTAAGTATTGTGTAGTGTAGCTC 57.017 34.615 0.00 0.00 0.00 4.09
114 115 7.941431 AGTAAGTATTGTGTAGTGTAGCTCT 57.059 36.000 0.00 0.00 0.00 4.09
115 116 9.458727 AAGTAAGTATTGTGTAGTGTAGCTCTA 57.541 33.333 0.00 0.00 0.00 2.43
116 117 8.891720 AGTAAGTATTGTGTAGTGTAGCTCTAC 58.108 37.037 0.00 0.00 38.45 2.59
117 118 7.941431 AAGTATTGTGTAGTGTAGCTCTACT 57.059 36.000 11.21 9.57 38.67 2.57
118 119 7.941431 AGTATTGTGTAGTGTAGCTCTACTT 57.059 36.000 11.21 0.69 38.67 2.24
119 120 7.987649 AGTATTGTGTAGTGTAGCTCTACTTC 58.012 38.462 11.21 6.37 38.67 3.01
120 121 5.640189 TTGTGTAGTGTAGCTCTACTTCC 57.360 43.478 11.21 3.75 38.67 3.46
121 122 4.919793 TGTGTAGTGTAGCTCTACTTCCT 58.080 43.478 11.21 4.78 38.67 3.36
122 123 5.322754 TGTGTAGTGTAGCTCTACTTCCTT 58.677 41.667 11.21 0.00 38.67 3.36
123 124 5.773680 TGTGTAGTGTAGCTCTACTTCCTTT 59.226 40.000 11.21 0.00 38.67 3.11
124 125 6.267014 TGTGTAGTGTAGCTCTACTTCCTTTT 59.733 38.462 11.21 0.00 38.67 2.27
125 126 6.807720 GTGTAGTGTAGCTCTACTTCCTTTTC 59.192 42.308 11.21 0.06 38.67 2.29
126 127 6.720288 TGTAGTGTAGCTCTACTTCCTTTTCT 59.280 38.462 11.21 0.00 38.67 2.52
127 128 6.275494 AGTGTAGCTCTACTTCCTTTTCTC 57.725 41.667 8.34 0.00 37.00 2.87
128 129 5.096849 GTGTAGCTCTACTTCCTTTTCTCG 58.903 45.833 8.34 0.00 37.00 4.04
129 130 5.008331 TGTAGCTCTACTTCCTTTTCTCGA 58.992 41.667 8.34 0.00 37.00 4.04
130 131 5.652891 TGTAGCTCTACTTCCTTTTCTCGAT 59.347 40.000 8.34 0.00 37.00 3.59
131 132 5.669164 AGCTCTACTTCCTTTTCTCGATT 57.331 39.130 0.00 0.00 0.00 3.34
132 133 6.043854 AGCTCTACTTCCTTTTCTCGATTT 57.956 37.500 0.00 0.00 0.00 2.17
133 134 6.103330 AGCTCTACTTCCTTTTCTCGATTTC 58.897 40.000 0.00 0.00 0.00 2.17
134 135 6.071051 AGCTCTACTTCCTTTTCTCGATTTCT 60.071 38.462 0.00 0.00 0.00 2.52
135 136 6.254804 GCTCTACTTCCTTTTCTCGATTTCTC 59.745 42.308 0.00 0.00 0.00 2.87
136 137 7.228314 TCTACTTCCTTTTCTCGATTTCTCA 57.772 36.000 0.00 0.00 0.00 3.27
137 138 7.091443 TCTACTTCCTTTTCTCGATTTCTCAC 58.909 38.462 0.00 0.00 0.00 3.51
138 139 5.611374 ACTTCCTTTTCTCGATTTCTCACA 58.389 37.500 0.00 0.00 0.00 3.58
139 140 6.055588 ACTTCCTTTTCTCGATTTCTCACAA 58.944 36.000 0.00 0.00 0.00 3.33
140 141 6.542370 ACTTCCTTTTCTCGATTTCTCACAAA 59.458 34.615 0.00 0.00 0.00 2.83
141 142 6.935741 TCCTTTTCTCGATTTCTCACAAAA 57.064 33.333 0.00 0.00 0.00 2.44
142 143 6.725246 TCCTTTTCTCGATTTCTCACAAAAC 58.275 36.000 0.00 0.00 0.00 2.43
143 144 6.317642 TCCTTTTCTCGATTTCTCACAAAACA 59.682 34.615 0.00 0.00 0.00 2.83
144 145 7.013274 TCCTTTTCTCGATTTCTCACAAAACAT 59.987 33.333 0.00 0.00 0.00 2.71
145 146 7.113965 CCTTTTCTCGATTTCTCACAAAACATG 59.886 37.037 0.00 0.00 0.00 3.21
146 147 6.859420 TTCTCGATTTCTCACAAAACATGA 57.141 33.333 0.00 0.00 0.00 3.07
147 148 6.859420 TCTCGATTTCTCACAAAACATGAA 57.141 33.333 0.00 0.00 0.00 2.57
148 149 6.658831 TCTCGATTTCTCACAAAACATGAAC 58.341 36.000 0.00 0.00 0.00 3.18
149 150 5.757886 TCGATTTCTCACAAAACATGAACC 58.242 37.500 0.00 0.00 0.00 3.62
150 151 5.298026 TCGATTTCTCACAAAACATGAACCA 59.702 36.000 0.00 0.00 0.00 3.67
151 152 5.976534 CGATTTCTCACAAAACATGAACCAA 59.023 36.000 0.00 0.00 0.00 3.67
152 153 6.142798 CGATTTCTCACAAAACATGAACCAAG 59.857 38.462 0.00 0.00 0.00 3.61
153 154 5.913137 TTCTCACAAAACATGAACCAAGT 57.087 34.783 0.00 0.00 0.00 3.16
154 155 5.913137 TCTCACAAAACATGAACCAAGTT 57.087 34.783 0.00 0.00 0.00 2.66
155 156 7.397892 TTCTCACAAAACATGAACCAAGTTA 57.602 32.000 0.00 0.00 0.00 2.24
156 157 7.026631 TCTCACAAAACATGAACCAAGTTAG 57.973 36.000 0.00 0.00 0.00 2.34
157 158 5.587289 TCACAAAACATGAACCAAGTTAGC 58.413 37.500 0.00 0.00 0.00 3.09
158 159 5.126222 TCACAAAACATGAACCAAGTTAGCA 59.874 36.000 0.00 0.00 0.00 3.49
159 160 5.809562 CACAAAACATGAACCAAGTTAGCAA 59.190 36.000 0.00 0.00 0.00 3.91
160 161 6.479660 CACAAAACATGAACCAAGTTAGCAAT 59.520 34.615 0.00 0.00 0.00 3.56
161 162 6.479660 ACAAAACATGAACCAAGTTAGCAATG 59.520 34.615 0.00 0.00 0.00 2.82
162 163 4.178545 ACATGAACCAAGTTAGCAATGC 57.821 40.909 0.00 0.00 0.00 3.56
163 164 3.573538 ACATGAACCAAGTTAGCAATGCA 59.426 39.130 8.35 0.00 0.00 3.96
164 165 4.039004 ACATGAACCAAGTTAGCAATGCAA 59.961 37.500 8.35 0.00 0.00 4.08
165 166 4.662468 TGAACCAAGTTAGCAATGCAAA 57.338 36.364 8.35 0.00 0.00 3.68
166 167 5.212532 TGAACCAAGTTAGCAATGCAAAT 57.787 34.783 8.35 0.00 0.00 2.32
167 168 6.338214 TGAACCAAGTTAGCAATGCAAATA 57.662 33.333 8.35 0.00 0.00 1.40
168 169 6.753180 TGAACCAAGTTAGCAATGCAAATAA 58.247 32.000 8.35 0.00 0.00 1.40
169 170 7.212976 TGAACCAAGTTAGCAATGCAAATAAA 58.787 30.769 8.35 0.00 0.00 1.40
170 171 7.712639 TGAACCAAGTTAGCAATGCAAATAAAA 59.287 29.630 8.35 0.00 0.00 1.52
171 172 8.620116 AACCAAGTTAGCAATGCAAATAAAAT 57.380 26.923 8.35 0.00 0.00 1.82
172 173 9.717942 AACCAAGTTAGCAATGCAAATAAAATA 57.282 25.926 8.35 0.00 0.00 1.40
173 174 9.717942 ACCAAGTTAGCAATGCAAATAAAATAA 57.282 25.926 8.35 0.00 0.00 1.40
181 182 8.185505 AGCAATGCAAATAAAATAAAATGCAGG 58.814 29.630 8.35 0.99 45.69 4.85
182 183 7.043920 GCAATGCAAATAAAATAAAATGCAGGC 60.044 33.333 0.00 6.78 45.69 4.85
183 184 7.627298 ATGCAAATAAAATAAAATGCAGGCA 57.373 28.000 0.00 0.00 45.69 4.75
184 185 7.627298 TGCAAATAAAATAAAATGCAGGCAT 57.373 28.000 0.00 0.00 38.73 4.40
185 186 8.688151 ATGCAAATAAAATAAAATGCAGGCATT 58.312 25.926 13.44 13.44 45.69 3.56
186 187 8.182881 TGCAAATAAAATAAAATGCAGGCATTC 58.817 29.630 18.81 3.78 44.86 2.67
187 188 8.400186 GCAAATAAAATAAAATGCAGGCATTCT 58.600 29.630 18.81 8.90 44.86 2.40
188 189 9.925268 CAAATAAAATAAAATGCAGGCATTCTC 57.075 29.630 18.81 0.00 44.86 2.87
189 190 9.895138 AAATAAAATAAAATGCAGGCATTCTCT 57.105 25.926 18.81 9.86 44.86 3.10
191 192 9.971922 ATAAAATAAAATGCAGGCATTCTCTAC 57.028 29.630 18.81 0.00 44.86 2.59
192 193 5.679734 ATAAAATGCAGGCATTCTCTACG 57.320 39.130 18.81 0.00 44.86 3.51
193 194 1.303309 AATGCAGGCATTCTCTACGC 58.697 50.000 13.44 0.00 42.32 4.42
194 195 0.533755 ATGCAGGCATTCTCTACGCC 60.534 55.000 0.00 0.00 46.62 5.68
199 200 1.867166 GGCATTCTCTACGCCCTAAC 58.133 55.000 0.00 0.00 40.07 2.34
200 201 1.138266 GGCATTCTCTACGCCCTAACA 59.862 52.381 0.00 0.00 40.07 2.41
201 202 2.419574 GGCATTCTCTACGCCCTAACAA 60.420 50.000 0.00 0.00 40.07 2.83
202 203 3.267483 GCATTCTCTACGCCCTAACAAA 58.733 45.455 0.00 0.00 0.00 2.83
203 204 3.687698 GCATTCTCTACGCCCTAACAAAA 59.312 43.478 0.00 0.00 0.00 2.44
204 205 4.201822 GCATTCTCTACGCCCTAACAAAAG 60.202 45.833 0.00 0.00 0.00 2.27
205 206 4.612264 TTCTCTACGCCCTAACAAAAGT 57.388 40.909 0.00 0.00 0.00 2.66
206 207 4.612264 TCTCTACGCCCTAACAAAAGTT 57.388 40.909 0.00 0.00 0.00 2.66
207 208 4.964593 TCTCTACGCCCTAACAAAAGTTT 58.035 39.130 0.00 0.00 0.00 2.66
208 209 4.753107 TCTCTACGCCCTAACAAAAGTTTG 59.247 41.667 2.22 2.22 43.62 2.93
209 210 4.706035 TCTACGCCCTAACAAAAGTTTGA 58.294 39.130 10.66 0.00 40.55 2.69
210 211 5.124645 TCTACGCCCTAACAAAAGTTTGAA 58.875 37.500 10.66 0.00 40.55 2.69
211 212 4.301637 ACGCCCTAACAAAAGTTTGAAG 57.698 40.909 10.66 7.20 40.55 3.02
212 213 3.697542 ACGCCCTAACAAAAGTTTGAAGT 59.302 39.130 10.66 0.00 40.55 3.01
213 214 4.883006 ACGCCCTAACAAAAGTTTGAAGTA 59.117 37.500 10.66 0.12 40.55 2.24
214 215 5.209977 CGCCCTAACAAAAGTTTGAAGTAC 58.790 41.667 10.66 0.00 40.55 2.73
215 216 5.220892 CGCCCTAACAAAAGTTTGAAGTACA 60.221 40.000 10.66 0.00 40.55 2.90
216 217 6.566141 GCCCTAACAAAAGTTTGAAGTACAA 58.434 36.000 10.66 0.00 40.55 2.41
217 218 6.695713 GCCCTAACAAAAGTTTGAAGTACAAG 59.304 38.462 10.66 0.00 40.55 3.16
218 219 7.415877 GCCCTAACAAAAGTTTGAAGTACAAGA 60.416 37.037 10.66 0.00 40.55 3.02
219 220 8.129211 CCCTAACAAAAGTTTGAAGTACAAGAG 58.871 37.037 10.66 0.00 40.55 2.85
220 221 8.674607 CCTAACAAAAGTTTGAAGTACAAGAGT 58.325 33.333 10.66 0.00 40.55 3.24
221 222 9.704098 CTAACAAAAGTTTGAAGTACAAGAGTC 57.296 33.333 10.66 0.00 40.55 3.36
222 223 7.681939 ACAAAAGTTTGAAGTACAAGAGTCA 57.318 32.000 10.66 0.00 40.55 3.41
223 224 7.527457 ACAAAAGTTTGAAGTACAAGAGTCAC 58.473 34.615 10.66 0.00 40.55 3.67
224 225 7.390718 ACAAAAGTTTGAAGTACAAGAGTCACT 59.609 33.333 10.66 0.00 40.55 3.41
225 226 7.923414 AAAGTTTGAAGTACAAGAGTCACTT 57.077 32.000 0.00 0.00 39.77 3.16
251 252 7.610692 TGTAAATAATTGTTGAACCGGTATGGA 59.389 33.333 8.00 0.00 42.00 3.41
873 885 2.094494 GCTGACTCTGTTGCTGCTACTA 60.094 50.000 14.81 3.30 0.00 1.82
1069 1127 1.004394 TCCTCGCTGAGTCCAACTCTA 59.996 52.381 8.44 0.00 45.27 2.43
1077 1135 1.840635 GAGTCCAACTCTAGGGCCATT 59.159 52.381 6.18 0.00 41.88 3.16
1101 1159 0.534412 CTCGACAGGAAGTGGCTCAT 59.466 55.000 0.00 0.00 27.93 2.90
2300 2360 6.006449 AGTGCACTTCAAACATCTCCTTATT 58.994 36.000 15.25 0.00 0.00 1.40
2816 2877 6.037062 CGTATGACTTGGATTTACTTGATGCA 59.963 38.462 0.00 0.00 0.00 3.96
3115 3179 2.614057 GCAGTTATGACAGCCACATACC 59.386 50.000 0.00 0.00 32.65 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.051922 CAGAGAGTGTAACAGTGGTGAAC 58.948 47.826 0.00 0.00 41.43 3.18
6 7 2.224042 TGCAGAGAGTGTAACAGTGGTG 60.224 50.000 0.00 0.00 41.43 4.17
7 8 2.039418 TGCAGAGAGTGTAACAGTGGT 58.961 47.619 0.00 0.00 41.43 4.16
8 9 2.820059 TGCAGAGAGTGTAACAGTGG 57.180 50.000 0.00 0.00 41.43 4.00
10 11 9.502091 TTTTAATAATGCAGAGAGTGTAACAGT 57.498 29.630 0.00 0.00 41.43 3.55
86 87 9.774413 AGCTACACTACACAATACTTACTTTTT 57.226 29.630 0.00 0.00 0.00 1.94
87 88 9.420551 GAGCTACACTACACAATACTTACTTTT 57.579 33.333 0.00 0.00 0.00 2.27
88 89 8.804204 AGAGCTACACTACACAATACTTACTTT 58.196 33.333 0.00 0.00 0.00 2.66
89 90 8.350852 AGAGCTACACTACACAATACTTACTT 57.649 34.615 0.00 0.00 0.00 2.24
90 91 7.941431 AGAGCTACACTACACAATACTTACT 57.059 36.000 0.00 0.00 0.00 2.24
91 92 8.891720 AGTAGAGCTACACTACACAATACTTAC 58.108 37.037 12.22 0.00 41.56 2.34
92 93 9.458727 AAGTAGAGCTACACTACACAATACTTA 57.541 33.333 12.22 0.00 41.56 2.24
93 94 7.941431 AGTAGAGCTACACTACACAATACTT 57.059 36.000 12.22 0.00 41.56 2.24
94 95 7.067251 GGAAGTAGAGCTACACTACACAATACT 59.933 40.741 12.22 0.00 41.56 2.12
95 96 7.067251 AGGAAGTAGAGCTACACTACACAATAC 59.933 40.741 12.22 0.00 41.56 1.89
96 97 7.117397 AGGAAGTAGAGCTACACTACACAATA 58.883 38.462 12.22 0.00 41.56 1.90
97 98 5.952947 AGGAAGTAGAGCTACACTACACAAT 59.047 40.000 12.22 0.00 41.56 2.71
98 99 5.322754 AGGAAGTAGAGCTACACTACACAA 58.677 41.667 12.22 0.00 41.56 3.33
99 100 4.919793 AGGAAGTAGAGCTACACTACACA 58.080 43.478 12.22 0.00 41.56 3.72
100 101 5.900865 AAGGAAGTAGAGCTACACTACAC 57.099 43.478 12.22 6.74 41.56 2.90
101 102 6.720288 AGAAAAGGAAGTAGAGCTACACTACA 59.280 38.462 12.22 0.00 41.56 2.74
102 103 7.160547 AGAAAAGGAAGTAGAGCTACACTAC 57.839 40.000 10.04 3.43 40.04 2.73
103 104 6.093771 CGAGAAAAGGAAGTAGAGCTACACTA 59.906 42.308 10.04 0.00 38.48 2.74
104 105 5.106078 CGAGAAAAGGAAGTAGAGCTACACT 60.106 44.000 10.04 0.00 38.48 3.55
105 106 5.096849 CGAGAAAAGGAAGTAGAGCTACAC 58.903 45.833 10.04 4.00 38.48 2.90
106 107 5.008331 TCGAGAAAAGGAAGTAGAGCTACA 58.992 41.667 10.04 0.00 38.48 2.74
107 108 5.564048 TCGAGAAAAGGAAGTAGAGCTAC 57.436 43.478 0.00 0.00 36.35 3.58
108 109 6.777213 AATCGAGAAAAGGAAGTAGAGCTA 57.223 37.500 0.00 0.00 0.00 3.32
109 110 5.669164 AATCGAGAAAAGGAAGTAGAGCT 57.331 39.130 0.00 0.00 0.00 4.09
110 111 6.103330 AGAAATCGAGAAAAGGAAGTAGAGC 58.897 40.000 0.00 0.00 0.00 4.09
111 112 7.274686 GTGAGAAATCGAGAAAAGGAAGTAGAG 59.725 40.741 0.00 0.00 0.00 2.43
112 113 7.091443 GTGAGAAATCGAGAAAAGGAAGTAGA 58.909 38.462 0.00 0.00 0.00 2.59
113 114 6.868864 TGTGAGAAATCGAGAAAAGGAAGTAG 59.131 38.462 0.00 0.00 0.00 2.57
114 115 6.755206 TGTGAGAAATCGAGAAAAGGAAGTA 58.245 36.000 0.00 0.00 0.00 2.24
115 116 5.611374 TGTGAGAAATCGAGAAAAGGAAGT 58.389 37.500 0.00 0.00 0.00 3.01
116 117 6.545504 TTGTGAGAAATCGAGAAAAGGAAG 57.454 37.500 0.00 0.00 0.00 3.46
117 118 6.935741 TTTGTGAGAAATCGAGAAAAGGAA 57.064 33.333 0.00 0.00 0.00 3.36
118 119 6.317642 TGTTTTGTGAGAAATCGAGAAAAGGA 59.682 34.615 0.00 0.00 0.00 3.36
119 120 6.494842 TGTTTTGTGAGAAATCGAGAAAAGG 58.505 36.000 0.00 0.00 0.00 3.11
120 121 7.857389 TCATGTTTTGTGAGAAATCGAGAAAAG 59.143 33.333 0.00 0.00 0.00 2.27
121 122 7.702386 TCATGTTTTGTGAGAAATCGAGAAAA 58.298 30.769 0.00 0.00 0.00 2.29
122 123 7.258022 TCATGTTTTGTGAGAAATCGAGAAA 57.742 32.000 0.00 0.00 0.00 2.52
123 124 6.859420 TCATGTTTTGTGAGAAATCGAGAA 57.141 33.333 0.00 0.00 0.00 2.87
124 125 6.293407 GGTTCATGTTTTGTGAGAAATCGAGA 60.293 38.462 0.00 0.00 0.00 4.04
125 126 5.853282 GGTTCATGTTTTGTGAGAAATCGAG 59.147 40.000 0.00 0.00 0.00 4.04
126 127 5.298026 TGGTTCATGTTTTGTGAGAAATCGA 59.702 36.000 0.00 0.00 0.00 3.59
127 128 5.518812 TGGTTCATGTTTTGTGAGAAATCG 58.481 37.500 0.00 0.00 0.00 3.34
128 129 6.980397 ACTTGGTTCATGTTTTGTGAGAAATC 59.020 34.615 0.00 0.00 0.00 2.17
129 130 6.877236 ACTTGGTTCATGTTTTGTGAGAAAT 58.123 32.000 0.00 0.00 0.00 2.17
130 131 6.279513 ACTTGGTTCATGTTTTGTGAGAAA 57.720 33.333 0.00 0.00 0.00 2.52
131 132 5.913137 ACTTGGTTCATGTTTTGTGAGAA 57.087 34.783 0.00 0.00 0.00 2.87
132 133 5.913137 AACTTGGTTCATGTTTTGTGAGA 57.087 34.783 0.00 0.00 29.47 3.27
133 134 5.687285 GCTAACTTGGTTCATGTTTTGTGAG 59.313 40.000 4.87 0.00 34.43 3.51
134 135 5.126222 TGCTAACTTGGTTCATGTTTTGTGA 59.874 36.000 4.87 0.00 34.43 3.58
135 136 5.347342 TGCTAACTTGGTTCATGTTTTGTG 58.653 37.500 4.87 0.00 34.43 3.33
136 137 5.590530 TGCTAACTTGGTTCATGTTTTGT 57.409 34.783 4.87 0.00 34.43 2.83
137 138 6.564499 GCATTGCTAACTTGGTTCATGTTTTG 60.564 38.462 0.16 1.79 34.43 2.44
138 139 5.466393 GCATTGCTAACTTGGTTCATGTTTT 59.534 36.000 0.16 0.00 34.43 2.43
139 140 4.990426 GCATTGCTAACTTGGTTCATGTTT 59.010 37.500 0.16 0.00 34.43 2.83
140 141 4.039004 TGCATTGCTAACTTGGTTCATGTT 59.961 37.500 10.49 4.92 36.14 2.71
141 142 3.573538 TGCATTGCTAACTTGGTTCATGT 59.426 39.130 10.49 0.00 0.00 3.21
142 143 4.177165 TGCATTGCTAACTTGGTTCATG 57.823 40.909 10.49 0.00 0.00 3.07
143 144 4.870123 TTGCATTGCTAACTTGGTTCAT 57.130 36.364 10.49 0.00 0.00 2.57
144 145 4.662468 TTTGCATTGCTAACTTGGTTCA 57.338 36.364 10.49 0.00 0.00 3.18
145 146 7.650834 TTTATTTGCATTGCTAACTTGGTTC 57.349 32.000 10.49 0.00 0.00 3.62
146 147 8.620116 ATTTTATTTGCATTGCTAACTTGGTT 57.380 26.923 10.49 0.00 0.00 3.67
147 148 9.717942 TTATTTTATTTGCATTGCTAACTTGGT 57.282 25.926 10.49 0.00 0.00 3.67
155 156 8.185505 CCTGCATTTTATTTTATTTGCATTGCT 58.814 29.630 10.49 0.00 39.16 3.91
156 157 7.043920 GCCTGCATTTTATTTTATTTGCATTGC 60.044 33.333 0.46 0.46 39.16 3.56
157 158 7.968956 TGCCTGCATTTTATTTTATTTGCATTG 59.031 29.630 0.00 0.00 39.16 2.82
158 159 8.053026 TGCCTGCATTTTATTTTATTTGCATT 57.947 26.923 0.00 0.00 39.16 3.56
159 160 7.627298 TGCCTGCATTTTATTTTATTTGCAT 57.373 28.000 0.00 0.00 39.16 3.96
160 161 7.627298 ATGCCTGCATTTTATTTTATTTGCA 57.373 28.000 0.00 0.00 37.73 4.08
161 162 8.400186 AGAATGCCTGCATTTTATTTTATTTGC 58.600 29.630 17.66 1.83 45.50 3.68
162 163 9.925268 GAGAATGCCTGCATTTTATTTTATTTG 57.075 29.630 17.66 0.00 45.50 2.32
163 164 9.895138 AGAGAATGCCTGCATTTTATTTTATTT 57.105 25.926 17.66 0.00 45.50 1.40
165 166 9.971922 GTAGAGAATGCCTGCATTTTATTTTAT 57.028 29.630 17.66 0.00 45.50 1.40
166 167 8.128582 CGTAGAGAATGCCTGCATTTTATTTTA 58.871 33.333 17.66 4.31 45.50 1.52
167 168 6.974622 CGTAGAGAATGCCTGCATTTTATTTT 59.025 34.615 17.66 5.10 45.50 1.82
168 169 6.498304 CGTAGAGAATGCCTGCATTTTATTT 58.502 36.000 17.66 6.43 45.50 1.40
169 170 5.506317 GCGTAGAGAATGCCTGCATTTTATT 60.506 40.000 17.66 7.67 45.50 1.40
170 171 4.023707 GCGTAGAGAATGCCTGCATTTTAT 60.024 41.667 17.66 12.27 45.50 1.40
171 172 3.312421 GCGTAGAGAATGCCTGCATTTTA 59.688 43.478 17.66 8.99 45.50 1.52
172 173 2.098117 GCGTAGAGAATGCCTGCATTTT 59.902 45.455 17.66 12.65 45.50 1.82
173 174 1.672881 GCGTAGAGAATGCCTGCATTT 59.327 47.619 17.66 8.59 45.50 2.32
175 176 2.997899 GCGTAGAGAATGCCTGCAT 58.002 52.632 0.00 0.00 38.46 3.96
176 177 4.521075 GCGTAGAGAATGCCTGCA 57.479 55.556 0.00 0.00 33.68 4.41
181 182 2.596904 TGTTAGGGCGTAGAGAATGC 57.403 50.000 0.00 0.00 39.58 3.56
182 183 4.935808 ACTTTTGTTAGGGCGTAGAGAATG 59.064 41.667 0.00 0.00 0.00 2.67
183 184 5.161943 ACTTTTGTTAGGGCGTAGAGAAT 57.838 39.130 0.00 0.00 0.00 2.40
184 185 4.612264 ACTTTTGTTAGGGCGTAGAGAA 57.388 40.909 0.00 0.00 0.00 2.87
185 186 4.612264 AACTTTTGTTAGGGCGTAGAGA 57.388 40.909 0.00 0.00 41.50 3.10
186 187 4.753107 TCAAACTTTTGTTAGGGCGTAGAG 59.247 41.667 1.75 0.00 42.67 2.43
187 188 4.706035 TCAAACTTTTGTTAGGGCGTAGA 58.294 39.130 1.75 0.00 42.67 2.59
188 189 5.008316 ACTTCAAACTTTTGTTAGGGCGTAG 59.992 40.000 1.75 0.00 42.67 3.51
189 190 4.883006 ACTTCAAACTTTTGTTAGGGCGTA 59.117 37.500 1.75 0.00 42.67 4.42
190 191 3.697542 ACTTCAAACTTTTGTTAGGGCGT 59.302 39.130 1.75 0.00 42.67 5.68
191 192 4.301637 ACTTCAAACTTTTGTTAGGGCG 57.698 40.909 1.75 0.00 42.67 6.13
192 193 6.139048 TGTACTTCAAACTTTTGTTAGGGC 57.861 37.500 1.75 0.00 42.67 5.19
193 194 7.992008 TCTTGTACTTCAAACTTTTGTTAGGG 58.008 34.615 1.75 0.00 42.67 3.53
194 195 8.674607 ACTCTTGTACTTCAAACTTTTGTTAGG 58.325 33.333 1.75 0.00 42.67 2.69
195 196 9.704098 GACTCTTGTACTTCAAACTTTTGTTAG 57.296 33.333 1.75 4.03 42.67 2.34
196 197 9.221933 TGACTCTTGTACTTCAAACTTTTGTTA 57.778 29.630 1.75 0.00 42.67 2.41
197 198 8.021396 GTGACTCTTGTACTTCAAACTTTTGTT 58.979 33.333 1.75 0.00 45.94 2.83
198 199 7.390718 AGTGACTCTTGTACTTCAAACTTTTGT 59.609 33.333 1.75 0.00 39.18 2.83
199 200 7.752695 AGTGACTCTTGTACTTCAAACTTTTG 58.247 34.615 0.00 0.00 39.48 2.44
200 201 7.923414 AGTGACTCTTGTACTTCAAACTTTT 57.077 32.000 0.00 0.00 35.48 2.27
201 202 7.752695 CAAGTGACTCTTGTACTTCAAACTTT 58.247 34.615 8.75 0.00 45.89 2.66
202 203 7.308782 CAAGTGACTCTTGTACTTCAAACTT 57.691 36.000 8.75 0.00 45.89 2.66
203 204 6.910536 CAAGTGACTCTTGTACTTCAAACT 57.089 37.500 8.75 0.00 45.89 2.66
217 218 9.394477 GGTTCAACAATTATTTACAAGTGACTC 57.606 33.333 0.00 0.00 0.00 3.36
218 219 8.073768 CGGTTCAACAATTATTTACAAGTGACT 58.926 33.333 0.00 0.00 0.00 3.41
219 220 7.325097 CCGGTTCAACAATTATTTACAAGTGAC 59.675 37.037 0.00 0.00 0.00 3.67
220 221 7.013464 ACCGGTTCAACAATTATTTACAAGTGA 59.987 33.333 0.00 0.00 0.00 3.41
221 222 7.142680 ACCGGTTCAACAATTATTTACAAGTG 58.857 34.615 0.00 0.00 0.00 3.16
222 223 7.279750 ACCGGTTCAACAATTATTTACAAGT 57.720 32.000 0.00 0.00 0.00 3.16
223 224 9.284594 CATACCGGTTCAACAATTATTTACAAG 57.715 33.333 15.04 0.00 0.00 3.16
224 225 8.244802 CCATACCGGTTCAACAATTATTTACAA 58.755 33.333 15.04 0.00 0.00 2.41
225 226 7.610692 TCCATACCGGTTCAACAATTATTTACA 59.389 33.333 15.04 0.00 35.57 2.41
226 227 7.911727 GTCCATACCGGTTCAACAATTATTTAC 59.088 37.037 15.04 0.00 35.57 2.01
227 228 7.067251 GGTCCATACCGGTTCAACAATTATTTA 59.933 37.037 15.04 0.00 35.62 1.40
228 229 6.127563 GGTCCATACCGGTTCAACAATTATTT 60.128 38.462 15.04 0.00 35.62 1.40
229 230 5.358725 GGTCCATACCGGTTCAACAATTATT 59.641 40.000 15.04 0.00 35.62 1.40
230 231 4.885325 GGTCCATACCGGTTCAACAATTAT 59.115 41.667 15.04 0.00 35.62 1.28
231 232 4.263435 GGTCCATACCGGTTCAACAATTA 58.737 43.478 15.04 0.00 35.62 1.40
232 233 3.086282 GGTCCATACCGGTTCAACAATT 58.914 45.455 15.04 0.00 35.62 2.32
233 234 2.718563 GGTCCATACCGGTTCAACAAT 58.281 47.619 15.04 0.00 35.62 2.71
251 252 3.126453 AGATAAGAAGATGGGCTTGGGT 58.874 45.455 0.00 0.00 36.83 4.51
316 318 2.190578 GAACGGGAGGGCTGGATG 59.809 66.667 0.00 0.00 0.00 3.51
772 784 4.445735 CGATCTCTCCCCTTTCTACTCTCT 60.446 50.000 0.00 0.00 0.00 3.10
873 885 3.644606 CCCCTCAGCAGCACCAGT 61.645 66.667 0.00 0.00 0.00 4.00
1069 1127 1.299976 GTCGAGGAACAATGGCCCT 59.700 57.895 0.00 0.00 0.00 5.19
1101 1159 1.906574 AGGGGTGACATTTCGAGCTTA 59.093 47.619 0.00 0.00 0.00 3.09
1986 2044 3.118038 TGTCCCCTTCAACTACCATATGC 60.118 47.826 0.00 0.00 0.00 3.14
2300 2360 2.293122 GCTGGCACATGTAAAACTGACA 59.707 45.455 0.00 0.00 38.20 3.58
2816 2877 4.018960 AGCTAAACACCTCATCCTTGTGAT 60.019 41.667 0.00 0.00 34.18 3.06
2927 2988 4.387598 CATGAAAGCCCCAAAAATGTTGA 58.612 39.130 0.00 0.00 0.00 3.18
3115 3179 2.629051 GGAAGGTGTCCGGTTTATCAG 58.371 52.381 0.00 0.00 36.40 2.90
3214 3278 2.605837 TCACGAACAAAGCAGGTACA 57.394 45.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.