Multiple sequence alignment - TraesCS3D01G174900

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 TraesCS3D01G174900 chr3D 100.000 2773 0 0 1 2773 156973101 156970329 0.000000e+00 5121.0
1 TraesCS3D01G174900 chr3D 83.686 331 42 8 4 327 586212062 586212387 4.490000e-78 302.0
2 TraesCS3D01G174900 chr3A 92.558 2271 103 36 541 2773 171255234 171257476 0.000000e+00 3197.0
3 TraesCS3D01G174900 chr3B 87.354 1969 126 64 450 2362 228089988 228088087 0.000000e+00 2143.0
4 TraesCS3D01G174900 chr3B 90.106 283 21 5 2370 2649 228087841 228087563 7.300000e-96 361.0
5 TraesCS3D01G174900 chr3B 88.596 114 11 1 327 438 228090086 228089973 1.340000e-28 137.0
6 TraesCS3D01G174900 chr3B 74.522 157 34 5 2500 2652 542516720 542516566 2.310000e-06 63.9
7 TraesCS3D01G174900 chr6B 85.030 334 36 11 1 327 688197606 688197932 7.410000e-86 327.0
8 TraesCS3D01G174900 chr6B 83.871 341 37 15 1 329 131288214 131287880 2.680000e-80 309.0
9 TraesCS3D01G174900 chr6B 83.728 338 35 15 1 329 94191636 94191310 4.490000e-78 302.0
10 TraesCS3D01G174900 chr2D 84.570 337 30 15 1 327 515072111 515072435 5.770000e-82 315.0
11 TraesCS3D01G174900 chr4A 84.179 335 34 13 1 327 510644183 510643860 9.650000e-80 307.0
12 TraesCS3D01G174900 chr1D 84.084 333 38 10 1 327 307468764 307468441 9.650000e-80 307.0
13 TraesCS3D01G174900 chr5B 84.036 332 36 13 2 327 51474756 51475076 1.250000e-78 303.0
14 TraesCS3D01G174900 chr4B 83.631 336 36 15 1 330 215088117 215087795 5.810000e-77 298.0
15 TraesCS3D01G174900 chr5D 78.548 303 58 6 2390 2688 409005448 409005747 2.820000e-45 193.0


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 TraesCS3D01G174900 chr3D 156970329 156973101 2772 True 5121.000000 5121 100.000000 1 2773 1 chr3D.!!$R1 2772
1 TraesCS3D01G174900 chr3A 171255234 171257476 2242 False 3197.000000 3197 92.558000 541 2773 1 chr3A.!!$F1 2232
2 TraesCS3D01G174900 chr3B 228087563 228090086 2523 True 880.333333 2143 88.685333 327 2649 3 chr3B.!!$R2 2322

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
942 986 0.24899 CATCAGCGACAGAGAGCTCC 60.249 60.0 10.93 1.7 42.52 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2317 2413 0.46729 TGGGTTTGGAGTCTGTTGGC 60.467 55.0 0.0 0.0 0.0 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
22 23 3.437049 GGGAAAAGACTCTTGATCAACCG 59.563 47.826 3.38 0.83 0.00 4.44
23 24 3.437049 GGAAAAGACTCTTGATCAACCGG 59.563 47.826 3.38 0.00 0.00 5.28
24 25 3.771577 AAAGACTCTTGATCAACCGGT 57.228 42.857 0.00 0.00 0.00 5.28
25 26 3.320673 AAGACTCTTGATCAACCGGTC 57.679 47.619 8.04 12.19 0.00 4.79
26 27 2.248248 AGACTCTTGATCAACCGGTCA 58.752 47.619 8.04 0.00 0.00 4.02
27 28 2.632996 AGACTCTTGATCAACCGGTCAA 59.367 45.455 8.04 6.95 33.63 3.18
28 29 2.737252 GACTCTTGATCAACCGGTCAAC 59.263 50.000 8.04 0.31 31.55 3.18
29 30 2.104111 ACTCTTGATCAACCGGTCAACA 59.896 45.455 8.04 3.36 31.55 3.33
30 31 2.480419 CTCTTGATCAACCGGTCAACAC 59.520 50.000 8.04 0.00 31.55 3.32
31 32 1.194547 CTTGATCAACCGGTCAACACG 59.805 52.381 8.04 0.26 31.55 4.49
32 33 0.389757 TGATCAACCGGTCAACACGA 59.610 50.000 8.04 0.00 0.00 4.35
33 34 0.788391 GATCAACCGGTCAACACGAC 59.212 55.000 8.04 0.00 44.57 4.34
40 41 4.979204 GTCAACACGACCGATGGA 57.021 55.556 0.00 0.00 38.85 3.41
41 42 2.442084 GTCAACACGACCGATGGAC 58.558 57.895 0.00 0.00 38.85 4.02
42 43 1.081041 TCAACACGACCGATGGACG 60.081 57.895 6.18 6.18 45.28 4.79
43 44 1.081041 CAACACGACCGATGGACGA 60.081 57.895 14.14 0.00 42.79 4.20
44 45 0.665068 CAACACGACCGATGGACGAA 60.665 55.000 14.14 0.00 42.79 3.85
45 46 0.665369 AACACGACCGATGGACGAAC 60.665 55.000 14.14 0.00 42.79 3.95
46 47 1.804326 CACGACCGATGGACGAACC 60.804 63.158 14.14 0.00 42.79 3.62
47 48 2.202703 CGACCGATGGACGAACCC 60.203 66.667 1.52 0.00 42.79 4.11
48 49 2.707849 CGACCGATGGACGAACCCT 61.708 63.158 1.52 0.00 42.79 4.34
49 50 1.378882 CGACCGATGGACGAACCCTA 61.379 60.000 1.52 0.00 42.79 3.53
50 51 0.384669 GACCGATGGACGAACCCTAG 59.615 60.000 0.00 0.00 45.77 3.02
51 52 1.041447 ACCGATGGACGAACCCTAGG 61.041 60.000 0.06 0.06 45.77 3.02
52 53 1.041447 CCGATGGACGAACCCTAGGT 61.041 60.000 8.29 0.00 45.77 3.08
53 54 1.683943 CGATGGACGAACCCTAGGTA 58.316 55.000 8.29 0.00 45.77 3.08
54 55 1.336125 CGATGGACGAACCCTAGGTAC 59.664 57.143 8.29 0.00 45.77 3.34
55 56 1.336125 GATGGACGAACCCTAGGTACG 59.664 57.143 8.29 12.32 33.12 3.67
56 57 0.680921 TGGACGAACCCTAGGTACGG 60.681 60.000 18.63 3.39 33.12 4.02
94 95 4.530857 GGTCATGGAGGCCGACCG 62.531 72.222 10.54 1.66 39.86 4.79
143 144 4.832608 GGACGGCGGCTAGGGTTG 62.833 72.222 14.66 0.00 0.00 3.77
144 145 4.832608 GACGGCGGCTAGGGTTGG 62.833 72.222 13.24 0.00 0.00 3.77
146 147 3.861797 CGGCGGCTAGGGTTGGAT 61.862 66.667 7.61 0.00 0.00 3.41
147 148 2.111251 GGCGGCTAGGGTTGGATC 59.889 66.667 0.00 0.00 0.00 3.36
148 149 2.280186 GCGGCTAGGGTTGGATCG 60.280 66.667 0.00 0.00 0.00 3.69
149 150 2.421739 CGGCTAGGGTTGGATCGG 59.578 66.667 0.00 0.00 0.00 4.18
150 151 2.432300 CGGCTAGGGTTGGATCGGT 61.432 63.158 0.00 0.00 0.00 4.69
151 152 1.912971 GGCTAGGGTTGGATCGGTT 59.087 57.895 0.00 0.00 0.00 4.44
152 153 1.125633 GGCTAGGGTTGGATCGGTTA 58.874 55.000 0.00 0.00 0.00 2.85
153 154 1.070289 GGCTAGGGTTGGATCGGTTAG 59.930 57.143 0.00 0.00 0.00 2.34
154 155 2.037144 GCTAGGGTTGGATCGGTTAGA 58.963 52.381 0.00 0.00 0.00 2.10
155 156 2.223994 GCTAGGGTTGGATCGGTTAGAC 60.224 54.545 0.00 0.00 0.00 2.59
156 157 2.249309 AGGGTTGGATCGGTTAGACT 57.751 50.000 0.00 0.00 0.00 3.24
157 158 1.831736 AGGGTTGGATCGGTTAGACTG 59.168 52.381 0.00 0.00 0.00 3.51
158 159 1.829222 GGGTTGGATCGGTTAGACTGA 59.171 52.381 0.00 0.00 37.97 3.41
159 160 2.434702 GGGTTGGATCGGTTAGACTGAT 59.565 50.000 2.19 2.19 46.28 2.90
160 161 3.640029 GGGTTGGATCGGTTAGACTGATA 59.360 47.826 2.56 0.00 43.82 2.15
161 162 4.501058 GGGTTGGATCGGTTAGACTGATAC 60.501 50.000 5.36 5.36 43.82 2.24
162 163 4.501058 GGTTGGATCGGTTAGACTGATACC 60.501 50.000 9.11 6.99 42.89 2.73
163 164 3.905968 TGGATCGGTTAGACTGATACCA 58.094 45.455 9.11 11.24 42.89 3.25
164 165 4.480115 TGGATCGGTTAGACTGATACCAT 58.520 43.478 9.11 0.00 42.89 3.55
165 166 4.280929 TGGATCGGTTAGACTGATACCATG 59.719 45.833 9.11 0.00 42.89 3.66
166 167 4.281182 GGATCGGTTAGACTGATACCATGT 59.719 45.833 2.56 0.00 43.82 3.21
167 168 5.221461 GGATCGGTTAGACTGATACCATGTT 60.221 44.000 2.56 0.00 43.82 2.71
168 169 6.015688 GGATCGGTTAGACTGATACCATGTTA 60.016 42.308 2.56 0.00 43.82 2.41
169 170 6.387041 TCGGTTAGACTGATACCATGTTAG 57.613 41.667 0.00 0.00 32.12 2.34
170 171 6.124340 TCGGTTAGACTGATACCATGTTAGA 58.876 40.000 0.00 0.00 32.12 2.10
171 172 6.604396 TCGGTTAGACTGATACCATGTTAGAA 59.396 38.462 0.00 0.00 32.12 2.10
172 173 6.918569 CGGTTAGACTGATACCATGTTAGAAG 59.081 42.308 0.00 0.00 32.12 2.85
173 174 7.210873 GGTTAGACTGATACCATGTTAGAAGG 58.789 42.308 0.00 0.00 32.12 3.46
174 175 5.878406 AGACTGATACCATGTTAGAAGGG 57.122 43.478 0.00 0.00 0.00 3.95
175 176 5.529289 AGACTGATACCATGTTAGAAGGGA 58.471 41.667 0.00 0.00 0.00 4.20
176 177 5.600484 AGACTGATACCATGTTAGAAGGGAG 59.400 44.000 0.00 0.00 0.00 4.30
177 178 5.529289 ACTGATACCATGTTAGAAGGGAGA 58.471 41.667 0.00 0.00 0.00 3.71
178 179 5.600484 ACTGATACCATGTTAGAAGGGAGAG 59.400 44.000 0.00 0.00 0.00 3.20
179 180 5.777449 TGATACCATGTTAGAAGGGAGAGA 58.223 41.667 0.00 0.00 0.00 3.10
180 181 6.385443 TGATACCATGTTAGAAGGGAGAGAT 58.615 40.000 0.00 0.00 0.00 2.75
181 182 6.268617 TGATACCATGTTAGAAGGGAGAGATG 59.731 42.308 0.00 0.00 0.00 2.90
182 183 3.713764 ACCATGTTAGAAGGGAGAGATGG 59.286 47.826 0.00 0.00 38.50 3.51
183 184 3.969976 CCATGTTAGAAGGGAGAGATGGA 59.030 47.826 0.00 0.00 35.56 3.41
184 185 4.596643 CCATGTTAGAAGGGAGAGATGGAT 59.403 45.833 0.00 0.00 35.56 3.41
185 186 5.072872 CCATGTTAGAAGGGAGAGATGGATT 59.927 44.000 0.00 0.00 35.56 3.01
186 187 6.410157 CCATGTTAGAAGGGAGAGATGGATTT 60.410 42.308 0.00 0.00 35.56 2.17
187 188 5.994250 TGTTAGAAGGGAGAGATGGATTTG 58.006 41.667 0.00 0.00 0.00 2.32
188 189 5.488919 TGTTAGAAGGGAGAGATGGATTTGT 59.511 40.000 0.00 0.00 0.00 2.83
189 190 4.500499 AGAAGGGAGAGATGGATTTGTG 57.500 45.455 0.00 0.00 0.00 3.33
190 191 4.107072 AGAAGGGAGAGATGGATTTGTGA 58.893 43.478 0.00 0.00 0.00 3.58
191 192 4.537688 AGAAGGGAGAGATGGATTTGTGAA 59.462 41.667 0.00 0.00 0.00 3.18
192 193 4.934797 AGGGAGAGATGGATTTGTGAAA 57.065 40.909 0.00 0.00 0.00 2.69
193 194 5.463051 AGGGAGAGATGGATTTGTGAAAT 57.537 39.130 0.00 0.00 0.00 2.17
194 195 6.581388 AGGGAGAGATGGATTTGTGAAATA 57.419 37.500 0.00 0.00 0.00 1.40
195 196 6.599445 AGGGAGAGATGGATTTGTGAAATAG 58.401 40.000 0.00 0.00 0.00 1.73
196 197 6.159398 AGGGAGAGATGGATTTGTGAAATAGT 59.841 38.462 0.00 0.00 0.00 2.12
197 198 6.830838 GGGAGAGATGGATTTGTGAAATAGTT 59.169 38.462 0.00 0.00 0.00 2.24
198 199 7.012799 GGGAGAGATGGATTTGTGAAATAGTTC 59.987 40.741 0.00 0.00 0.00 3.01
199 200 7.254590 GGAGAGATGGATTTGTGAAATAGTTCG 60.255 40.741 0.00 0.00 36.46 3.95
200 201 7.106239 AGAGATGGATTTGTGAAATAGTTCGT 58.894 34.615 0.00 0.00 36.46 3.85
201 202 7.607991 AGAGATGGATTTGTGAAATAGTTCGTT 59.392 33.333 0.00 0.00 36.46 3.85
202 203 7.752695 AGATGGATTTGTGAAATAGTTCGTTC 58.247 34.615 0.00 0.00 36.46 3.95
203 204 5.922546 TGGATTTGTGAAATAGTTCGTTCG 58.077 37.500 0.00 0.00 36.46 3.95
204 205 5.467399 TGGATTTGTGAAATAGTTCGTTCGT 59.533 36.000 0.00 0.00 36.46 3.85
205 206 6.017770 TGGATTTGTGAAATAGTTCGTTCGTT 60.018 34.615 0.00 0.00 36.46 3.85
206 207 6.302313 GGATTTGTGAAATAGTTCGTTCGTTG 59.698 38.462 0.00 0.00 36.46 4.10
207 208 5.721876 TTGTGAAATAGTTCGTTCGTTGT 57.278 34.783 0.00 0.00 36.46 3.32
208 209 6.825284 TTGTGAAATAGTTCGTTCGTTGTA 57.175 33.333 0.00 0.00 36.46 2.41
209 210 7.410800 TTGTGAAATAGTTCGTTCGTTGTAT 57.589 32.000 0.00 0.00 36.46 2.29
210 211 7.410800 TGTGAAATAGTTCGTTCGTTGTATT 57.589 32.000 0.00 0.00 36.46 1.89
211 212 7.285069 TGTGAAATAGTTCGTTCGTTGTATTG 58.715 34.615 0.00 0.00 36.46 1.90
212 213 6.245710 GTGAAATAGTTCGTTCGTTGTATTGC 59.754 38.462 0.00 0.00 36.46 3.56
213 214 6.146510 TGAAATAGTTCGTTCGTTGTATTGCT 59.853 34.615 0.00 0.00 36.46 3.91
214 215 6.476243 AATAGTTCGTTCGTTGTATTGCTT 57.524 33.333 0.00 0.00 0.00 3.91
215 216 4.128554 AGTTCGTTCGTTGTATTGCTTG 57.871 40.909 0.00 0.00 0.00 4.01
216 217 3.805422 AGTTCGTTCGTTGTATTGCTTGA 59.195 39.130 0.00 0.00 0.00 3.02
217 218 4.084537 AGTTCGTTCGTTGTATTGCTTGAG 60.085 41.667 0.00 0.00 0.00 3.02
218 219 2.156891 TCGTTCGTTGTATTGCTTGAGC 59.843 45.455 0.00 0.00 42.50 4.26
219 220 2.724839 CGTTCGTTGTATTGCTTGAGCC 60.725 50.000 0.00 0.00 41.18 4.70
220 221 2.472695 TCGTTGTATTGCTTGAGCCT 57.527 45.000 0.00 0.00 41.18 4.58
221 222 2.346803 TCGTTGTATTGCTTGAGCCTC 58.653 47.619 0.00 0.00 41.18 4.70
222 223 2.076100 CGTTGTATTGCTTGAGCCTCA 58.924 47.619 0.00 0.00 41.18 3.86
223 224 2.679837 CGTTGTATTGCTTGAGCCTCAT 59.320 45.455 0.00 0.00 41.18 2.90
224 225 3.486375 CGTTGTATTGCTTGAGCCTCATG 60.486 47.826 0.00 0.00 41.18 3.07
225 226 2.646930 TGTATTGCTTGAGCCTCATGG 58.353 47.619 9.39 0.96 41.18 3.66
226 227 1.952296 GTATTGCTTGAGCCTCATGGG 59.048 52.381 9.39 0.00 41.18 4.00
258 259 9.911788 ATATATAGGAATACAAAGGCCATCTTG 57.088 33.333 5.01 8.17 35.55 3.02
259 260 4.591321 AGGAATACAAAGGCCATCTTGA 57.409 40.909 16.54 3.94 35.55 3.02
260 261 4.934356 AGGAATACAAAGGCCATCTTGAA 58.066 39.130 16.54 0.00 35.55 2.69
261 262 4.952335 AGGAATACAAAGGCCATCTTGAAG 59.048 41.667 16.54 0.00 35.55 3.02
262 263 4.706962 GGAATACAAAGGCCATCTTGAAGT 59.293 41.667 16.54 1.96 35.55 3.01
263 264 5.885912 GGAATACAAAGGCCATCTTGAAGTA 59.114 40.000 16.54 3.90 35.55 2.24
264 265 6.183360 GGAATACAAAGGCCATCTTGAAGTAC 60.183 42.308 16.54 0.00 35.55 2.73
265 266 4.098914 ACAAAGGCCATCTTGAAGTACA 57.901 40.909 16.54 0.00 35.55 2.90
266 267 4.469657 ACAAAGGCCATCTTGAAGTACAA 58.530 39.130 16.54 0.00 35.55 2.41
267 268 4.892934 ACAAAGGCCATCTTGAAGTACAAA 59.107 37.500 16.54 0.00 38.08 2.83
268 269 5.362430 ACAAAGGCCATCTTGAAGTACAAAA 59.638 36.000 16.54 0.00 38.08 2.44
269 270 5.453567 AAGGCCATCTTGAAGTACAAAAC 57.546 39.130 5.01 0.00 38.08 2.43
270 271 4.469657 AGGCCATCTTGAAGTACAAAACA 58.530 39.130 5.01 0.00 38.08 2.83
271 272 4.892934 AGGCCATCTTGAAGTACAAAACAA 59.107 37.500 5.01 0.00 38.08 2.83
272 273 5.010012 AGGCCATCTTGAAGTACAAAACAAG 59.990 40.000 5.01 12.01 40.37 3.16
273 274 5.222631 GCCATCTTGAAGTACAAAACAAGG 58.777 41.667 15.63 7.24 39.74 3.61
274 275 5.222631 CCATCTTGAAGTACAAAACAAGGC 58.777 41.667 15.63 0.00 39.74 4.35
275 276 5.221224 CCATCTTGAAGTACAAAACAAGGCA 60.221 40.000 15.63 4.55 39.74 4.75
276 277 5.499139 TCTTGAAGTACAAAACAAGGCAG 57.501 39.130 15.63 0.00 39.74 4.85
277 278 4.338118 TCTTGAAGTACAAAACAAGGCAGG 59.662 41.667 15.63 0.00 39.74 4.85
278 279 3.892284 TGAAGTACAAAACAAGGCAGGA 58.108 40.909 0.00 0.00 0.00 3.86
279 280 4.469657 TGAAGTACAAAACAAGGCAGGAT 58.530 39.130 0.00 0.00 0.00 3.24
280 281 4.518970 TGAAGTACAAAACAAGGCAGGATC 59.481 41.667 0.00 0.00 0.00 3.36
281 282 4.098914 AGTACAAAACAAGGCAGGATCA 57.901 40.909 0.00 0.00 0.00 2.92
282 283 4.469657 AGTACAAAACAAGGCAGGATCAA 58.530 39.130 0.00 0.00 0.00 2.57
283 284 4.892934 AGTACAAAACAAGGCAGGATCAAA 59.107 37.500 0.00 0.00 0.00 2.69
284 285 4.961438 ACAAAACAAGGCAGGATCAAAT 57.039 36.364 0.00 0.00 0.00 2.32
285 286 4.886579 ACAAAACAAGGCAGGATCAAATC 58.113 39.130 0.00 0.00 0.00 2.17
305 306 9.702253 TCAAATCCTACTCTATCATATACTCCC 57.298 37.037 0.00 0.00 0.00 4.30
306 307 9.707957 CAAATCCTACTCTATCATATACTCCCT 57.292 37.037 0.00 0.00 0.00 4.20
309 310 9.752940 ATCCTACTCTATCATATACTCCCTAGT 57.247 37.037 0.00 0.00 39.91 2.57
325 326 8.709272 ACTCCCTAGTAATCCTTATACTCAAC 57.291 38.462 0.00 0.00 35.34 3.18
392 393 7.847711 TCTCCAAAAATCAAATAAACCTCCA 57.152 32.000 0.00 0.00 0.00 3.86
394 395 6.764379 TCCAAAAATCAAATAAACCTCCACC 58.236 36.000 0.00 0.00 0.00 4.61
409 412 0.734889 CCACCGCTCCATCATTTGTC 59.265 55.000 0.00 0.00 0.00 3.18
438 441 7.014326 TCGACATATCAGGTTTGCTTCTAGTAT 59.986 37.037 0.00 0.00 0.00 2.12
439 442 7.327275 CGACATATCAGGTTTGCTTCTAGTATC 59.673 40.741 0.00 0.00 0.00 2.24
440 443 7.445945 ACATATCAGGTTTGCTTCTAGTATCC 58.554 38.462 0.00 0.00 0.00 2.59
441 444 4.755266 TCAGGTTTGCTTCTAGTATCCC 57.245 45.455 0.00 0.00 0.00 3.85
443 446 5.525484 TCAGGTTTGCTTCTAGTATCCCTA 58.475 41.667 0.00 0.00 0.00 3.53
445 448 6.442564 TCAGGTTTGCTTCTAGTATCCCTAAA 59.557 38.462 0.00 0.00 0.00 1.85
446 449 7.037873 TCAGGTTTGCTTCTAGTATCCCTAAAA 60.038 37.037 0.00 0.00 0.00 1.52
447 450 7.610305 CAGGTTTGCTTCTAGTATCCCTAAAAA 59.390 37.037 0.00 0.00 0.00 1.94
469 472 7.436430 AAAAAGGTTTGCTTCTAGTAGTAGC 57.564 36.000 18.96 18.96 38.84 3.58
470 473 6.361768 AAAGGTTTGCTTCTAGTAGTAGCT 57.638 37.500 24.06 6.11 39.09 3.32
471 474 6.361768 AAGGTTTGCTTCTAGTAGTAGCTT 57.638 37.500 24.06 10.96 39.09 3.74
477 480 5.844004 TGCTTCTAGTAGTAGCTTATTGCC 58.156 41.667 24.06 0.18 44.23 4.52
491 494 3.662866 TATTGCCCCGTGCGAAGGAAA 62.663 52.381 5.10 1.63 45.60 3.13
493 496 3.419759 CCCCGTGCGAAGGAAACG 61.420 66.667 0.00 0.00 37.07 3.60
499 502 1.201812 CGTGCGAAGGAAACGAATCAG 60.202 52.381 0.00 0.00 39.64 2.90
510 513 7.886405 AGGAAACGAATCAGTAGAAAGTTAC 57.114 36.000 0.00 0.00 0.00 2.50
513 516 8.718734 GGAAACGAATCAGTAGAAAGTTACATT 58.281 33.333 0.00 0.00 0.00 2.71
645 672 2.893398 CGTAGGGAGAGGCACCAC 59.107 66.667 0.00 0.00 0.00 4.16
646 673 2.893398 GTAGGGAGAGGCACCACG 59.107 66.667 0.00 0.00 0.00 4.94
648 675 3.976490 TAGGGAGAGGCACCACGGG 62.976 68.421 0.00 0.00 0.00 5.28
652 679 2.607750 AGAGGCACCACGGGACAT 60.608 61.111 0.00 0.00 0.00 3.06
656 683 2.347490 GCACCACGGGACATGACT 59.653 61.111 0.00 0.00 0.00 3.41
697 724 1.811679 CGCTCGGCTCCTTTCCTTC 60.812 63.158 0.00 0.00 0.00 3.46
701 728 0.898789 TCGGCTCCTTTCCTTCGTCT 60.899 55.000 0.00 0.00 0.00 4.18
718 753 2.288825 CGTCTGCAAGTCCCACTCTTTA 60.289 50.000 0.00 0.00 33.76 1.85
719 754 3.740115 GTCTGCAAGTCCCACTCTTTAA 58.260 45.455 0.00 0.00 33.76 1.52
720 755 3.498777 GTCTGCAAGTCCCACTCTTTAAC 59.501 47.826 0.00 0.00 33.76 2.01
721 756 3.391296 TCTGCAAGTCCCACTCTTTAACT 59.609 43.478 0.00 0.00 33.76 2.24
722 757 3.476552 TGCAAGTCCCACTCTTTAACTG 58.523 45.455 0.00 0.00 0.00 3.16
786 822 1.418373 GCAAGCAACGAACAAATCCC 58.582 50.000 0.00 0.00 0.00 3.85
820 856 2.253154 CCGCGCCACATGCATATG 59.747 61.111 0.00 0.00 41.33 1.78
843 879 6.883129 TGCATTCGTTCATGTATATAAACCG 58.117 36.000 0.00 0.00 0.00 4.44
844 880 5.788531 GCATTCGTTCATGTATATAAACCGC 59.211 40.000 0.00 0.00 0.00 5.68
845 881 5.564213 TTCGTTCATGTATATAAACCGCG 57.436 39.130 0.00 0.00 0.00 6.46
846 882 4.857799 TCGTTCATGTATATAAACCGCGA 58.142 39.130 8.23 0.00 0.00 5.87
847 883 5.280164 TCGTTCATGTATATAAACCGCGAA 58.720 37.500 8.23 0.00 0.00 4.70
848 884 5.400188 TCGTTCATGTATATAAACCGCGAAG 59.600 40.000 8.23 0.00 0.00 3.79
894 933 3.017323 CGCGTCAGGCATTCCATC 58.983 61.111 0.00 0.00 43.84 3.51
942 986 0.248990 CATCAGCGACAGAGAGCTCC 60.249 60.000 10.93 1.70 42.52 4.70
1004 1048 1.015607 GTACGTCCGGCGAAAATGGT 61.016 55.000 22.10 0.00 44.77 3.55
1066 1110 3.701205 ACTTGTGCATGTACCTCATCA 57.299 42.857 11.66 0.00 34.09 3.07
1137 1181 3.320256 TCATCATAGGTACTGCTCTGCTG 59.680 47.826 0.00 0.00 41.52 4.41
1194 1247 1.451028 CTAGAGCCTGCCCAGTTGC 60.451 63.158 0.00 0.00 0.00 4.17
1216 1269 0.899720 ATTTGTGATTGCCTGCAGGG 59.100 50.000 33.46 15.81 35.18 4.45
1348 1401 1.446792 CTGCATCGTCGGCTTCACT 60.447 57.895 0.00 0.00 0.00 3.41
1454 1507 2.712918 TAAGCACGCGCGTTTCTCG 61.713 57.895 35.90 22.89 45.49 4.04
1472 1545 7.558137 GTTTCTCGAATTACACAACTCGTTTA 58.442 34.615 0.00 0.00 33.15 2.01
1481 1554 4.751060 ACACAACTCGTTTAGTCTGACAA 58.249 39.130 10.88 0.00 37.50 3.18
1482 1555 5.172934 ACACAACTCGTTTAGTCTGACAAA 58.827 37.500 10.88 6.02 37.50 2.83
1486 1559 6.370718 ACAACTCGTTTAGTCTGACAAACTTT 59.629 34.615 21.81 14.42 37.50 2.66
1487 1560 7.546667 ACAACTCGTTTAGTCTGACAAACTTTA 59.453 33.333 21.81 12.86 37.50 1.85
1488 1561 8.548721 CAACTCGTTTAGTCTGACAAACTTTAT 58.451 33.333 21.81 11.08 37.50 1.40
1489 1562 8.073355 ACTCGTTTAGTCTGACAAACTTTATG 57.927 34.615 21.81 12.83 30.33 1.90
1501 1574 8.177119 TGACAAACTTTATGCTGAACCTTATT 57.823 30.769 0.00 0.00 0.00 1.40
1502 1575 9.290988 TGACAAACTTTATGCTGAACCTTATTA 57.709 29.630 0.00 0.00 0.00 0.98
1607 1685 1.139095 CTCGCCCTGTACTTCGTCC 59.861 63.158 0.00 0.00 0.00 4.79
1611 1689 1.214589 CCCTGTACTTCGTCCGGTG 59.785 63.158 0.00 0.00 0.00 4.94
1620 1702 0.179094 TTCGTCCGGTGCATATGGTC 60.179 55.000 0.00 0.00 0.00 4.02
1621 1703 1.949133 CGTCCGGTGCATATGGTCG 60.949 63.158 0.00 0.00 0.00 4.79
1635 1717 2.455674 TGGTCGGTGAACTGATCAAG 57.544 50.000 2.67 0.00 39.27 3.02
1636 1718 1.001974 TGGTCGGTGAACTGATCAAGG 59.998 52.381 2.67 0.00 39.27 3.61
1678 1760 1.945354 ATGGAGGCGTTCACGATCGT 61.945 55.000 16.60 16.60 43.02 3.73
1710 1792 0.741326 GCAGCTCGTCTACATCCTCA 59.259 55.000 0.00 0.00 0.00 3.86
1831 1923 0.310854 CGCCGGAGAAAGTTTGCTTT 59.689 50.000 5.05 0.00 46.63 3.51
1838 1930 4.112634 GGAGAAAGTTTGCTTTGTTGTCC 58.887 43.478 0.00 0.00 44.25 4.02
1889 1981 2.170166 TGAGTGGGATTGGTGAAATGC 58.830 47.619 0.00 0.00 35.94 3.56
1993 2085 3.206964 TGATTTGTTAGGACGTGCAACA 58.793 40.909 10.52 14.39 35.74 3.33
2001 2093 2.968179 GACGTGCAACAAATCGTCG 58.032 52.632 9.15 0.00 41.89 5.12
2007 2099 1.666189 TGCAACAAATCGTCGTCACAA 59.334 42.857 0.00 0.00 0.00 3.33
2022 2114 6.005289 GTCGTCACAATACATACGTGTTTTC 58.995 40.000 0.00 0.00 39.77 2.29
2106 2201 8.223100 GCTACCAAAACAAGCAGAAAATAAATG 58.777 33.333 0.00 0.00 36.26 2.32
2114 2209 9.986833 AACAAGCAGAAAATAAATGAAAACAAC 57.013 25.926 0.00 0.00 0.00 3.32
2232 2328 2.609747 TCAGTCCCTGTGAAGTAAGCT 58.390 47.619 0.00 0.00 32.61 3.74
2277 2373 0.114364 ACCCATCAACCCCCAAAGAC 59.886 55.000 0.00 0.00 0.00 3.01
2311 2407 4.996788 AATCGACAAACTACCGATACCT 57.003 40.909 0.00 0.00 41.49 3.08
2317 2413 4.817517 ACAAACTACCGATACCTCACAAG 58.182 43.478 0.00 0.00 0.00 3.16
2333 2429 2.024414 ACAAGCCAACAGACTCCAAAC 58.976 47.619 0.00 0.00 0.00 2.93
2345 2441 1.850345 ACTCCAAACCCACCTTTCTCA 59.150 47.619 0.00 0.00 0.00 3.27
2362 2458 2.149578 CTCAGAGTCCACAAGCCAAAG 58.850 52.381 0.00 0.00 0.00 2.77
2368 2464 2.523902 CACAAGCCAAAGCCCCCA 60.524 61.111 0.00 0.00 41.25 4.96
2453 2789 4.527816 TGCCTTAAAGACTTCATTGGCAAT 59.472 37.500 6.96 6.96 44.86 3.56
2499 2835 6.563422 TCACTTCATTGTTCCTTGTCTTTTG 58.437 36.000 0.00 0.00 0.00 2.44
2652 2989 4.843728 CAGATACACCAACCATAACCAGT 58.156 43.478 0.00 0.00 0.00 4.00
2653 2990 5.253330 CAGATACACCAACCATAACCAGTT 58.747 41.667 0.00 0.00 0.00 3.16
2654 2991 5.710099 CAGATACACCAACCATAACCAGTTT 59.290 40.000 0.00 0.00 0.00 2.66
2696 3033 7.923414 ACCTCAGTATCCAAAGATTAAACAC 57.077 36.000 0.00 0.00 33.67 3.32
2713 3050 3.581024 ACACATCATGAACATTGCCAC 57.419 42.857 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.437049 CGGTTGATCAAGAGTCTTTTCCC 59.563 47.826 8.80 1.37 0.00 3.97
1 2 3.437049 CCGGTTGATCAAGAGTCTTTTCC 59.563 47.826 8.80 2.13 0.00 3.13
2 3 4.065789 ACCGGTTGATCAAGAGTCTTTTC 58.934 43.478 8.80 4.26 0.00 2.29
3 4 4.065789 GACCGGTTGATCAAGAGTCTTTT 58.934 43.478 9.42 0.00 0.00 2.27
4 5 3.071023 TGACCGGTTGATCAAGAGTCTTT 59.929 43.478 22.94 0.00 0.00 2.52
5 6 2.632996 TGACCGGTTGATCAAGAGTCTT 59.367 45.455 22.94 0.00 0.00 3.01
6 7 2.248248 TGACCGGTTGATCAAGAGTCT 58.752 47.619 22.94 0.00 0.00 3.24
7 8 2.737252 GTTGACCGGTTGATCAAGAGTC 59.263 50.000 9.42 15.36 35.55 3.36
8 9 2.104111 TGTTGACCGGTTGATCAAGAGT 59.896 45.455 9.42 6.52 35.55 3.24
9 10 2.480419 GTGTTGACCGGTTGATCAAGAG 59.520 50.000 9.42 5.76 35.55 2.85
10 11 2.489971 GTGTTGACCGGTTGATCAAGA 58.510 47.619 9.42 3.70 35.55 3.02
11 12 1.194547 CGTGTTGACCGGTTGATCAAG 59.805 52.381 9.42 5.12 35.55 3.02
12 13 1.202545 TCGTGTTGACCGGTTGATCAA 60.203 47.619 9.42 5.26 32.44 2.57
13 14 0.389757 TCGTGTTGACCGGTTGATCA 59.610 50.000 9.42 0.00 0.00 2.92
14 15 0.788391 GTCGTGTTGACCGGTTGATC 59.212 55.000 9.42 0.00 42.04 2.92
15 16 2.908817 GTCGTGTTGACCGGTTGAT 58.091 52.632 9.42 0.00 42.04 2.57
16 17 4.423764 GTCGTGTTGACCGGTTGA 57.576 55.556 9.42 0.00 42.04 3.18
24 25 1.081041 CGTCCATCGGTCGTGTTGA 60.081 57.895 0.00 0.00 35.71 3.18
25 26 0.665068 TTCGTCCATCGGTCGTGTTG 60.665 55.000 0.00 0.00 40.32 3.33
26 27 0.665369 GTTCGTCCATCGGTCGTGTT 60.665 55.000 0.00 0.00 40.32 3.32
27 28 1.080974 GTTCGTCCATCGGTCGTGT 60.081 57.895 0.00 0.00 40.32 4.49
28 29 1.804326 GGTTCGTCCATCGGTCGTG 60.804 63.158 0.00 0.00 40.32 4.35
29 30 2.570181 GGTTCGTCCATCGGTCGT 59.430 61.111 0.00 0.00 40.32 4.34
30 31 1.378882 TAGGGTTCGTCCATCGGTCG 61.379 60.000 0.00 0.00 40.32 4.79
31 32 0.384669 CTAGGGTTCGTCCATCGGTC 59.615 60.000 2.42 0.00 40.32 4.79
32 33 1.041447 CCTAGGGTTCGTCCATCGGT 61.041 60.000 0.00 0.00 40.32 4.69
33 34 1.041447 ACCTAGGGTTCGTCCATCGG 61.041 60.000 14.81 3.98 38.55 4.18
34 35 1.336125 GTACCTAGGGTTCGTCCATCG 59.664 57.143 14.81 0.00 37.09 3.84
35 36 1.336125 CGTACCTAGGGTTCGTCCATC 59.664 57.143 14.81 0.00 40.63 3.51
36 37 1.396653 CGTACCTAGGGTTCGTCCAT 58.603 55.000 14.81 0.00 40.63 3.41
37 38 0.680921 CCGTACCTAGGGTTCGTCCA 60.681 60.000 14.81 0.00 43.23 4.02
38 39 1.387295 CCCGTACCTAGGGTTCGTCC 61.387 65.000 14.81 0.00 43.23 4.79
39 40 2.110296 CCCGTACCTAGGGTTCGTC 58.890 63.158 14.81 0.00 43.23 4.20
40 41 4.344237 CCCGTACCTAGGGTTCGT 57.656 61.111 14.81 0.00 43.23 3.85
46 47 2.803479 GCGTCACCCGTACCTAGG 59.197 66.667 7.41 7.41 39.32 3.02
47 48 2.406401 CGCGTCACCCGTACCTAG 59.594 66.667 0.00 0.00 39.32 3.02
48 49 3.133464 CCGCGTCACCCGTACCTA 61.133 66.667 4.92 0.00 39.32 3.08
77 78 4.530857 CGGTCGGCCTCCATGACC 62.531 72.222 14.89 14.89 46.91 4.02
126 127 4.832608 CAACCCTAGCCGCCGTCC 62.833 72.222 0.00 0.00 0.00 4.79
127 128 4.832608 CCAACCCTAGCCGCCGTC 62.833 72.222 0.00 0.00 0.00 4.79
129 130 3.809374 GATCCAACCCTAGCCGCCG 62.809 68.421 0.00 0.00 0.00 6.46
130 131 2.111251 GATCCAACCCTAGCCGCC 59.889 66.667 0.00 0.00 0.00 6.13
131 132 2.280186 CGATCCAACCCTAGCCGC 60.280 66.667 0.00 0.00 0.00 6.53
132 133 1.968050 AACCGATCCAACCCTAGCCG 61.968 60.000 0.00 0.00 0.00 5.52
133 134 1.070289 CTAACCGATCCAACCCTAGCC 59.930 57.143 0.00 0.00 0.00 3.93
134 135 2.037144 TCTAACCGATCCAACCCTAGC 58.963 52.381 0.00 0.00 0.00 3.42
135 136 3.068307 CAGTCTAACCGATCCAACCCTAG 59.932 52.174 0.00 0.00 0.00 3.02
136 137 3.028850 CAGTCTAACCGATCCAACCCTA 58.971 50.000 0.00 0.00 0.00 3.53
137 138 1.831736 CAGTCTAACCGATCCAACCCT 59.168 52.381 0.00 0.00 0.00 4.34
138 139 1.829222 TCAGTCTAACCGATCCAACCC 59.171 52.381 0.00 0.00 0.00 4.11
139 140 3.821421 ATCAGTCTAACCGATCCAACC 57.179 47.619 0.00 0.00 0.00 3.77
140 141 4.098960 TGGTATCAGTCTAACCGATCCAAC 59.901 45.833 0.00 0.00 35.98 3.77
141 142 4.283337 TGGTATCAGTCTAACCGATCCAA 58.717 43.478 0.00 0.00 35.98 3.53
142 143 3.905968 TGGTATCAGTCTAACCGATCCA 58.094 45.455 0.00 0.00 35.98 3.41
143 144 4.281182 ACATGGTATCAGTCTAACCGATCC 59.719 45.833 0.00 0.00 35.98 3.36
144 145 5.455056 ACATGGTATCAGTCTAACCGATC 57.545 43.478 0.00 0.00 35.98 3.69
145 146 5.871396 AACATGGTATCAGTCTAACCGAT 57.129 39.130 0.00 0.00 35.98 4.18
146 147 6.124340 TCTAACATGGTATCAGTCTAACCGA 58.876 40.000 0.00 0.00 35.98 4.69
147 148 6.387041 TCTAACATGGTATCAGTCTAACCG 57.613 41.667 0.00 0.00 35.98 4.44
148 149 7.210873 CCTTCTAACATGGTATCAGTCTAACC 58.789 42.308 0.00 0.00 0.00 2.85
149 150 7.069578 TCCCTTCTAACATGGTATCAGTCTAAC 59.930 40.741 0.00 0.00 0.00 2.34
150 151 7.130099 TCCCTTCTAACATGGTATCAGTCTAA 58.870 38.462 0.00 0.00 0.00 2.10
151 152 6.679542 TCCCTTCTAACATGGTATCAGTCTA 58.320 40.000 0.00 0.00 0.00 2.59
152 153 5.529289 TCCCTTCTAACATGGTATCAGTCT 58.471 41.667 0.00 0.00 0.00 3.24
153 154 5.598830 TCTCCCTTCTAACATGGTATCAGTC 59.401 44.000 0.00 0.00 0.00 3.51
154 155 5.529289 TCTCCCTTCTAACATGGTATCAGT 58.471 41.667 0.00 0.00 0.00 3.41
155 156 5.835819 TCTCTCCCTTCTAACATGGTATCAG 59.164 44.000 0.00 0.00 0.00 2.90
156 157 5.777449 TCTCTCCCTTCTAACATGGTATCA 58.223 41.667 0.00 0.00 0.00 2.15
157 158 6.295575 CCATCTCTCCCTTCTAACATGGTATC 60.296 46.154 0.00 0.00 0.00 2.24
158 159 5.545723 CCATCTCTCCCTTCTAACATGGTAT 59.454 44.000 0.00 0.00 0.00 2.73
159 160 4.901849 CCATCTCTCCCTTCTAACATGGTA 59.098 45.833 0.00 0.00 0.00 3.25
160 161 3.713764 CCATCTCTCCCTTCTAACATGGT 59.286 47.826 0.00 0.00 0.00 3.55
161 162 3.969976 TCCATCTCTCCCTTCTAACATGG 59.030 47.826 0.00 0.00 0.00 3.66
162 163 5.822132 ATCCATCTCTCCCTTCTAACATG 57.178 43.478 0.00 0.00 0.00 3.21
163 164 6.159398 ACAAATCCATCTCTCCCTTCTAACAT 59.841 38.462 0.00 0.00 0.00 2.71
164 165 5.488919 ACAAATCCATCTCTCCCTTCTAACA 59.511 40.000 0.00 0.00 0.00 2.41
165 166 5.819901 CACAAATCCATCTCTCCCTTCTAAC 59.180 44.000 0.00 0.00 0.00 2.34
166 167 5.726308 TCACAAATCCATCTCTCCCTTCTAA 59.274 40.000 0.00 0.00 0.00 2.10
167 168 5.280499 TCACAAATCCATCTCTCCCTTCTA 58.720 41.667 0.00 0.00 0.00 2.10
168 169 4.107072 TCACAAATCCATCTCTCCCTTCT 58.893 43.478 0.00 0.00 0.00 2.85
169 170 4.494091 TCACAAATCCATCTCTCCCTTC 57.506 45.455 0.00 0.00 0.00 3.46
170 171 4.934797 TTCACAAATCCATCTCTCCCTT 57.065 40.909 0.00 0.00 0.00 3.95
171 172 4.934797 TTTCACAAATCCATCTCTCCCT 57.065 40.909 0.00 0.00 0.00 4.20
172 173 6.360618 ACTATTTCACAAATCCATCTCTCCC 58.639 40.000 0.00 0.00 32.38 4.30
173 174 7.254590 CGAACTATTTCACAAATCCATCTCTCC 60.255 40.741 0.00 0.00 32.38 3.71
174 175 7.278868 ACGAACTATTTCACAAATCCATCTCTC 59.721 37.037 0.00 0.00 32.38 3.20
175 176 7.106239 ACGAACTATTTCACAAATCCATCTCT 58.894 34.615 0.00 0.00 32.38 3.10
176 177 7.308782 ACGAACTATTTCACAAATCCATCTC 57.691 36.000 0.00 0.00 32.38 2.75
177 178 7.413000 CGAACGAACTATTTCACAAATCCATCT 60.413 37.037 0.00 0.00 32.38 2.90
178 179 6.682863 CGAACGAACTATTTCACAAATCCATC 59.317 38.462 0.00 0.00 32.38 3.51
179 180 6.148811 ACGAACGAACTATTTCACAAATCCAT 59.851 34.615 0.14 0.00 32.38 3.41
180 181 5.467399 ACGAACGAACTATTTCACAAATCCA 59.533 36.000 0.14 0.00 32.38 3.41
181 182 5.923665 ACGAACGAACTATTTCACAAATCC 58.076 37.500 0.14 0.00 32.38 3.01
182 183 6.849305 ACAACGAACGAACTATTTCACAAATC 59.151 34.615 0.14 0.00 32.38 2.17
183 184 6.721321 ACAACGAACGAACTATTTCACAAAT 58.279 32.000 0.14 0.00 34.90 2.32
184 185 6.109320 ACAACGAACGAACTATTTCACAAA 57.891 33.333 0.14 0.00 0.00 2.83
185 186 5.721876 ACAACGAACGAACTATTTCACAA 57.278 34.783 0.14 0.00 0.00 3.33
186 187 7.285069 CAATACAACGAACGAACTATTTCACA 58.715 34.615 0.14 0.00 0.00 3.58
187 188 6.245710 GCAATACAACGAACGAACTATTTCAC 59.754 38.462 0.14 0.00 0.00 3.18
188 189 6.146510 AGCAATACAACGAACGAACTATTTCA 59.853 34.615 0.14 0.00 0.00 2.69
189 190 6.531439 AGCAATACAACGAACGAACTATTTC 58.469 36.000 0.14 0.00 0.00 2.17
190 191 6.476243 AGCAATACAACGAACGAACTATTT 57.524 33.333 0.14 0.00 0.00 1.40
191 192 6.146510 TCAAGCAATACAACGAACGAACTATT 59.853 34.615 0.14 0.00 0.00 1.73
192 193 5.636121 TCAAGCAATACAACGAACGAACTAT 59.364 36.000 0.14 0.00 0.00 2.12
193 194 4.983538 TCAAGCAATACAACGAACGAACTA 59.016 37.500 0.14 0.00 0.00 2.24
194 195 3.805422 TCAAGCAATACAACGAACGAACT 59.195 39.130 0.14 0.00 0.00 3.01
195 196 4.123276 TCAAGCAATACAACGAACGAAC 57.877 40.909 0.14 0.00 0.00 3.95
196 197 3.363575 GCTCAAGCAATACAACGAACGAA 60.364 43.478 0.14 0.00 41.59 3.85
197 198 2.156891 GCTCAAGCAATACAACGAACGA 59.843 45.455 0.14 0.00 41.59 3.85
198 199 2.495939 GCTCAAGCAATACAACGAACG 58.504 47.619 0.00 0.00 41.59 3.95
199 200 2.484264 AGGCTCAAGCAATACAACGAAC 59.516 45.455 4.13 0.00 44.36 3.95
200 201 2.742053 GAGGCTCAAGCAATACAACGAA 59.258 45.455 10.25 0.00 44.36 3.85
201 202 2.289382 TGAGGCTCAAGCAATACAACGA 60.289 45.455 16.28 0.00 44.36 3.85
202 203 2.076100 TGAGGCTCAAGCAATACAACG 58.924 47.619 16.28 0.00 44.36 4.10
203 204 3.181493 CCATGAGGCTCAAGCAATACAAC 60.181 47.826 22.84 0.00 44.36 3.32
204 205 3.018856 CCATGAGGCTCAAGCAATACAA 58.981 45.455 22.84 0.00 44.36 2.41
205 206 2.646930 CCATGAGGCTCAAGCAATACA 58.353 47.619 22.84 0.00 44.36 2.29
206 207 1.952296 CCCATGAGGCTCAAGCAATAC 59.048 52.381 22.84 0.00 44.36 1.89
207 208 2.353357 CCCATGAGGCTCAAGCAATA 57.647 50.000 22.84 0.00 44.36 1.90
208 209 3.202548 CCCATGAGGCTCAAGCAAT 57.797 52.632 22.84 0.66 44.36 3.56
209 210 4.749323 CCCATGAGGCTCAAGCAA 57.251 55.556 22.84 0.00 44.36 3.91
232 233 9.911788 CAAGATGGCCTTTGTATTCCTATATAT 57.088 33.333 3.32 0.00 31.42 0.86
233 234 9.111519 TCAAGATGGCCTTTGTATTCCTATATA 57.888 33.333 3.32 0.00 31.42 0.86
234 235 7.988937 TCAAGATGGCCTTTGTATTCCTATAT 58.011 34.615 3.32 0.00 31.42 0.86
235 236 7.387265 TCAAGATGGCCTTTGTATTCCTATA 57.613 36.000 3.32 0.00 31.42 1.31
236 237 6.266131 TCAAGATGGCCTTTGTATTCCTAT 57.734 37.500 3.32 0.00 31.42 2.57
237 238 5.708736 TCAAGATGGCCTTTGTATTCCTA 57.291 39.130 3.32 0.00 31.42 2.94
238 239 4.591321 TCAAGATGGCCTTTGTATTCCT 57.409 40.909 3.32 0.00 31.42 3.36
239 240 4.706962 ACTTCAAGATGGCCTTTGTATTCC 59.293 41.667 3.32 0.00 31.42 3.01
240 241 5.904362 ACTTCAAGATGGCCTTTGTATTC 57.096 39.130 3.32 0.00 31.42 1.75
241 242 6.245408 TGTACTTCAAGATGGCCTTTGTATT 58.755 36.000 3.32 0.00 31.42 1.89
242 243 5.815581 TGTACTTCAAGATGGCCTTTGTAT 58.184 37.500 3.32 0.00 31.42 2.29
243 244 5.235850 TGTACTTCAAGATGGCCTTTGTA 57.764 39.130 3.32 0.00 31.42 2.41
244 245 4.098914 TGTACTTCAAGATGGCCTTTGT 57.901 40.909 3.32 0.00 31.42 2.83
245 246 5.452078 TTTGTACTTCAAGATGGCCTTTG 57.548 39.130 3.32 6.59 37.35 2.77
246 247 5.362430 TGTTTTGTACTTCAAGATGGCCTTT 59.638 36.000 3.32 0.00 37.35 3.11
247 248 4.892934 TGTTTTGTACTTCAAGATGGCCTT 59.107 37.500 3.32 0.00 37.35 4.35
248 249 4.469657 TGTTTTGTACTTCAAGATGGCCT 58.530 39.130 3.32 0.00 37.35 5.19
249 250 4.846779 TGTTTTGTACTTCAAGATGGCC 57.153 40.909 0.00 0.00 37.35 5.36
250 251 5.222631 CCTTGTTTTGTACTTCAAGATGGC 58.777 41.667 15.64 0.00 39.39 4.40
251 252 5.221224 TGCCTTGTTTTGTACTTCAAGATGG 60.221 40.000 15.64 8.26 39.39 3.51
252 253 5.830912 TGCCTTGTTTTGTACTTCAAGATG 58.169 37.500 15.64 6.63 39.39 2.90
253 254 5.010012 CCTGCCTTGTTTTGTACTTCAAGAT 59.990 40.000 15.64 0.00 39.39 2.40
254 255 4.338118 CCTGCCTTGTTTTGTACTTCAAGA 59.662 41.667 15.64 0.00 39.39 3.02
255 256 4.338118 TCCTGCCTTGTTTTGTACTTCAAG 59.662 41.667 0.00 4.08 37.35 3.02
256 257 4.274147 TCCTGCCTTGTTTTGTACTTCAA 58.726 39.130 0.00 0.00 0.00 2.69
257 258 3.892284 TCCTGCCTTGTTTTGTACTTCA 58.108 40.909 0.00 0.00 0.00 3.02
258 259 4.518970 TGATCCTGCCTTGTTTTGTACTTC 59.481 41.667 0.00 0.00 0.00 3.01
259 260 4.469657 TGATCCTGCCTTGTTTTGTACTT 58.530 39.130 0.00 0.00 0.00 2.24
260 261 4.098914 TGATCCTGCCTTGTTTTGTACT 57.901 40.909 0.00 0.00 0.00 2.73
261 262 4.846779 TTGATCCTGCCTTGTTTTGTAC 57.153 40.909 0.00 0.00 0.00 2.90
262 263 5.047377 GGATTTGATCCTGCCTTGTTTTGTA 60.047 40.000 0.00 0.00 46.19 2.41
263 264 4.262592 GGATTTGATCCTGCCTTGTTTTGT 60.263 41.667 0.00 0.00 46.19 2.83
264 265 4.248058 GGATTTGATCCTGCCTTGTTTTG 58.752 43.478 0.00 0.00 46.19 2.44
265 266 4.541973 GGATTTGATCCTGCCTTGTTTT 57.458 40.909 0.00 0.00 46.19 2.43
279 280 9.702253 GGGAGTATATGATAGAGTAGGATTTGA 57.298 37.037 0.00 0.00 0.00 2.69
280 281 9.707957 AGGGAGTATATGATAGAGTAGGATTTG 57.292 37.037 0.00 0.00 0.00 2.32
283 284 9.752940 ACTAGGGAGTATATGATAGAGTAGGAT 57.247 37.037 0.00 0.00 32.65 3.24
299 300 9.804977 GTTGAGTATAAGGATTACTAGGGAGTA 57.195 37.037 0.00 0.00 37.10 2.59
300 301 8.287350 TGTTGAGTATAAGGATTACTAGGGAGT 58.713 37.037 0.00 0.00 39.92 3.85
301 302 8.578151 GTGTTGAGTATAAGGATTACTAGGGAG 58.422 40.741 0.00 0.00 30.46 4.30
302 303 8.287350 AGTGTTGAGTATAAGGATTACTAGGGA 58.713 37.037 0.00 0.00 30.46 4.20
303 304 8.480133 AGTGTTGAGTATAAGGATTACTAGGG 57.520 38.462 0.00 0.00 30.46 3.53
345 346 9.809096 GAGATATGGAAGATAAGCGAATCATTA 57.191 33.333 4.46 0.00 0.00 1.90
347 348 7.093156 TGGAGATATGGAAGATAAGCGAATCAT 60.093 37.037 4.46 0.00 0.00 2.45
352 353 6.419484 TTTGGAGATATGGAAGATAAGCGA 57.581 37.500 0.00 0.00 0.00 4.93
367 368 8.314021 GTGGAGGTTTATTTGATTTTTGGAGAT 58.686 33.333 0.00 0.00 0.00 2.75
370 371 6.517529 CGGTGGAGGTTTATTTGATTTTTGGA 60.518 38.462 0.00 0.00 0.00 3.53
392 393 0.327924 TGGACAAATGATGGAGCGGT 59.672 50.000 0.00 0.00 0.00 5.68
394 395 1.262417 CGATGGACAAATGATGGAGCG 59.738 52.381 0.00 0.00 0.00 5.03
409 412 3.470709 AGCAAACCTGATATGTCGATGG 58.529 45.455 0.00 0.00 0.00 3.51
445 448 7.225011 AGCTACTACTAGAAGCAAACCTTTTT 58.775 34.615 0.00 0.00 38.75 1.94
446 449 6.770542 AGCTACTACTAGAAGCAAACCTTTT 58.229 36.000 0.00 0.00 38.75 2.27
447 450 6.361768 AGCTACTACTAGAAGCAAACCTTT 57.638 37.500 0.00 0.00 38.75 3.11
448 451 6.361768 AAGCTACTACTAGAAGCAAACCTT 57.638 37.500 0.00 0.00 38.75 3.50
449 452 7.663043 ATAAGCTACTACTAGAAGCAAACCT 57.337 36.000 0.00 0.00 38.75 3.50
450 453 7.254488 GCAATAAGCTACTACTAGAAGCAAACC 60.254 40.741 0.00 0.00 41.15 3.27
451 454 7.254488 GGCAATAAGCTACTACTAGAAGCAAAC 60.254 40.741 0.00 0.00 44.79 2.93
452 455 6.761714 GGCAATAAGCTACTACTAGAAGCAAA 59.238 38.462 0.00 0.00 44.79 3.68
453 456 6.281405 GGCAATAAGCTACTACTAGAAGCAA 58.719 40.000 0.00 0.00 44.79 3.91
454 457 5.221461 GGGCAATAAGCTACTACTAGAAGCA 60.221 44.000 0.00 0.00 44.79 3.91
455 458 5.231702 GGGCAATAAGCTACTACTAGAAGC 58.768 45.833 0.00 0.00 44.79 3.86
456 459 5.565045 CGGGGCAATAAGCTACTACTAGAAG 60.565 48.000 0.00 0.00 44.79 2.85
457 460 4.280174 CGGGGCAATAAGCTACTACTAGAA 59.720 45.833 0.00 0.00 44.79 2.10
458 461 3.825014 CGGGGCAATAAGCTACTACTAGA 59.175 47.826 0.00 0.00 44.79 2.43
459 462 3.573110 ACGGGGCAATAAGCTACTACTAG 59.427 47.826 0.00 0.00 44.79 2.57
460 463 3.319972 CACGGGGCAATAAGCTACTACTA 59.680 47.826 0.00 0.00 44.79 1.82
461 464 2.102588 CACGGGGCAATAAGCTACTACT 59.897 50.000 0.00 0.00 44.79 2.57
462 465 2.480845 CACGGGGCAATAAGCTACTAC 58.519 52.381 0.00 0.00 44.79 2.73
463 466 1.202604 GCACGGGGCAATAAGCTACTA 60.203 52.381 0.00 0.00 44.79 1.82
464 467 0.463833 GCACGGGGCAATAAGCTACT 60.464 55.000 0.00 0.00 44.79 2.57
465 468 1.772063 CGCACGGGGCAATAAGCTAC 61.772 60.000 1.92 0.00 45.17 3.58
466 469 1.522806 CGCACGGGGCAATAAGCTA 60.523 57.895 1.92 0.00 45.17 3.32
467 470 2.813226 TTCGCACGGGGCAATAAGCT 62.813 55.000 1.92 0.00 45.17 3.74
468 471 2.322999 CTTCGCACGGGGCAATAAGC 62.323 60.000 1.92 0.00 45.17 3.09
469 472 1.714899 CCTTCGCACGGGGCAATAAG 61.715 60.000 1.92 2.50 45.17 1.73
470 473 1.747367 CCTTCGCACGGGGCAATAA 60.747 57.895 1.92 0.00 45.17 1.40
471 474 2.124901 CCTTCGCACGGGGCAATA 60.125 61.111 1.92 0.00 45.17 1.90
477 480 1.296056 ATTCGTTTCCTTCGCACGGG 61.296 55.000 0.00 0.00 34.61 5.28
536 539 9.503399 CCAATGTAGAGTAACTTTCTAGGTTTT 57.497 33.333 0.00 0.00 0.00 2.43
537 540 7.606839 GCCAATGTAGAGTAACTTTCTAGGTTT 59.393 37.037 0.00 0.00 0.00 3.27
538 541 7.104290 GCCAATGTAGAGTAACTTTCTAGGTT 58.896 38.462 0.00 0.00 0.00 3.50
539 542 6.212791 TGCCAATGTAGAGTAACTTTCTAGGT 59.787 38.462 0.00 0.00 0.00 3.08
550 553 2.946990 TCGTCGATGCCAATGTAGAGTA 59.053 45.455 0.00 0.00 0.00 2.59
551 554 1.749063 TCGTCGATGCCAATGTAGAGT 59.251 47.619 0.00 0.00 0.00 3.24
552 555 2.492019 TCGTCGATGCCAATGTAGAG 57.508 50.000 0.00 0.00 0.00 2.43
553 556 2.165641 AGTTCGTCGATGCCAATGTAGA 59.834 45.455 0.00 0.00 0.00 2.59
554 557 2.540515 AGTTCGTCGATGCCAATGTAG 58.459 47.619 0.00 0.00 0.00 2.74
645 672 2.046988 TGCTGCAGTCATGTCCCG 60.047 61.111 16.64 0.00 0.00 5.14
646 673 2.404995 GCTGCTGCAGTCATGTCCC 61.405 63.158 28.50 7.62 39.41 4.46
648 675 3.976758 TGCTGCTGCAGTCATGTC 58.023 55.556 28.50 12.81 45.31 3.06
697 724 0.034059 AAGAGTGGGACTTGCAGACG 59.966 55.000 0.00 0.00 0.00 4.18
701 728 3.135712 TCAGTTAAAGAGTGGGACTTGCA 59.864 43.478 0.00 0.00 0.00 4.08
718 753 2.847234 TCCGGGTGGCTGTCAGTT 60.847 61.111 0.00 0.00 34.14 3.16
719 754 3.314331 CTCCGGGTGGCTGTCAGT 61.314 66.667 0.00 0.00 34.14 3.41
720 755 2.883828 AACTCCGGGTGGCTGTCAG 61.884 63.158 0.00 0.00 34.14 3.51
721 756 2.847234 AACTCCGGGTGGCTGTCA 60.847 61.111 0.00 0.00 34.14 3.58
722 757 2.358737 CAACTCCGGGTGGCTGTC 60.359 66.667 0.00 0.00 34.14 3.51
820 856 5.788531 GCGGTTTATATACATGAACGAATGC 59.211 40.000 0.00 0.00 32.74 3.56
850 886 2.668550 AAACTGGACGGCTTCGGC 60.669 61.111 0.00 0.00 42.17 5.54
851 887 1.004918 AGAAACTGGACGGCTTCGG 60.005 57.895 0.00 0.00 38.38 4.30
852 888 0.319555 TCAGAAACTGGACGGCTTCG 60.320 55.000 0.00 0.00 34.42 3.79
853 889 1.878953 TTCAGAAACTGGACGGCTTC 58.121 50.000 0.00 0.00 31.51 3.86
942 986 1.931172 CGCCACTCGGGTTATTTACAG 59.069 52.381 0.00 0.00 39.65 2.74
982 1026 1.346378 ATTTTCGCCGGACGTACGTG 61.346 55.000 28.16 12.97 44.19 4.49
1004 1048 0.878523 CACGGGCTTCAAGTTGTCGA 60.879 55.000 2.11 0.00 0.00 4.20
1151 1200 3.656559 TGTTACTACGGCTTTGAGGTTC 58.343 45.455 0.00 0.00 0.00 3.62
1194 1247 2.416836 CCTGCAGGCAATCACAAATCAG 60.417 50.000 22.33 0.00 0.00 2.90
1348 1401 1.006571 GTTCCAGAAGCGGACGTGA 60.007 57.895 0.00 0.00 33.75 4.35
1454 1507 7.168637 TGTCAGACTAAACGAGTTGTGTAATTC 59.831 37.037 1.31 0.00 39.06 2.17
1472 1545 5.239525 GGTTCAGCATAAAGTTTGTCAGACT 59.760 40.000 1.31 0.00 0.00 3.24
1488 1561 9.748708 GCAATTTATCAATAATAAGGTTCAGCA 57.251 29.630 0.00 0.00 31.52 4.41
1489 1562 9.971922 AGCAATTTATCAATAATAAGGTTCAGC 57.028 29.630 0.00 0.00 31.52 4.26
1607 1685 0.461163 TTCACCGACCATATGCACCG 60.461 55.000 0.00 0.16 0.00 4.94
1611 1689 2.309528 TCAGTTCACCGACCATATGC 57.690 50.000 0.00 0.00 0.00 3.14
1620 1702 1.970917 GCGCCTTGATCAGTTCACCG 61.971 60.000 0.00 0.00 32.84 4.94
1621 1703 0.674895 AGCGCCTTGATCAGTTCACC 60.675 55.000 2.29 0.00 32.84 4.02
1678 1760 2.147315 GAGCTGCGTCAGTGACAGGA 62.147 60.000 22.66 14.80 33.43 3.86
1745 1827 1.278637 CAAGGCGTTGTGTCGTTCC 59.721 57.895 10.97 0.00 0.00 3.62
1831 1923 2.088423 ACGAAAAGCACAAGGACAACA 58.912 42.857 0.00 0.00 0.00 3.33
1838 1930 4.350346 TCACATCAAACGAAAAGCACAAG 58.650 39.130 0.00 0.00 0.00 3.16
1889 1981 1.729284 ATTACTACAACGCCAACCCG 58.271 50.000 0.00 0.00 0.00 5.28
1993 2085 5.004061 CACGTATGTATTGTGACGACGATTT 59.996 40.000 0.00 0.00 38.63 2.17
2022 2114 8.380743 TCGGAGTAGTAGCTCTCTTTATAAAG 57.619 38.462 17.60 17.60 35.89 1.85
2072 2167 4.582656 TGCTTGTTTTGGTAGCTGTAACAT 59.417 37.500 0.00 0.00 35.93 2.71
2106 2201 3.455619 AGATCATGCGTCGTTGTTTTC 57.544 42.857 0.00 0.00 0.00 2.29
2232 2328 4.096681 TCTCATCTTGCTCCTTTAGGACA 58.903 43.478 0.00 0.00 39.78 4.02
2277 2373 5.183140 AGTTTGTCGATTTATCCCTTTGTGG 59.817 40.000 0.00 0.00 0.00 4.17
2311 2407 0.836606 TGGAGTCTGTTGGCTTGTGA 59.163 50.000 0.00 0.00 0.00 3.58
2317 2413 0.467290 TGGGTTTGGAGTCTGTTGGC 60.467 55.000 0.00 0.00 0.00 4.52
2333 2429 1.002544 GTGGACTCTGAGAAAGGTGGG 59.997 57.143 12.44 0.00 0.00 4.61
2345 2441 0.538287 GGCTTTGGCTTGTGGACTCT 60.538 55.000 0.00 0.00 38.73 3.24
2453 2789 3.054139 AGGCATAAGAATGGTTGAGCTGA 60.054 43.478 0.00 0.00 33.38 4.26
2499 2835 6.478512 TGGAATATTTTGCAGATAAACCCC 57.521 37.500 0.00 0.00 0.00 4.95
2677 3014 9.685276 TCATGATGTGTTTAATCTTTGGATACT 57.315 29.630 0.00 0.00 37.61 2.12
2696 3033 7.822658 TGATATATGTGGCAATGTTCATGATG 58.177 34.615 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.