Multiple sequence alignment - TraesCS2D01G111900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G111900 chr2D 100.000 3368 0 0 1 3368 62066014 62062647 0.000000e+00 6220
1 TraesCS2D01G111900 chr2D 94.215 484 27 1 2 485 113482711 113483193 0.000000e+00 737
2 TraesCS2D01G111900 chr2D 93.621 486 30 1 1 486 630346841 630347325 0.000000e+00 725
3 TraesCS2D01G111900 chr2A 95.325 2460 77 13 922 3368 62390177 62387743 0.000000e+00 3871
4 TraesCS2D01G111900 chr2A 94.915 472 14 5 483 952 62392129 62391666 0.000000e+00 730
5 TraesCS2D01G111900 chr2A 88.693 283 22 8 2808 3085 15610791 15611068 1.500000e-88 337
6 TraesCS2D01G111900 chr2B 96.227 2200 59 17 1187 3368 97437532 97435339 0.000000e+00 3581
7 TraesCS2D01G111900 chr2B 93.568 482 30 1 2 483 697662025 697662505 0.000000e+00 717
8 TraesCS2D01G111900 chr2B 88.421 285 24 9 2808 3085 24241786 24242068 5.380000e-88 335
9 TraesCS2D01G111900 chr2B 91.860 172 11 3 952 1122 97437711 97437542 1.560000e-58 237
10 TraesCS2D01G111900 chr7D 95.359 474 19 2 10 483 116128248 116127778 0.000000e+00 750
11 TraesCS2D01G111900 chr7D 90.262 267 22 4 2811 3074 199607138 199606873 2.490000e-91 346
12 TraesCS2D01G111900 chr7D 91.373 255 19 3 2808 3060 485106455 485106708 2.490000e-91 346
13 TraesCS2D01G111900 chr3B 94.639 485 25 1 1 485 730173538 730173055 0.000000e+00 750
14 TraesCS2D01G111900 chr7A 94.227 485 26 2 1 485 679240357 679239875 0.000000e+00 739
15 TraesCS2D01G111900 chr7A 88.192 271 27 5 2806 3072 150586751 150587020 5.420000e-83 318
16 TraesCS2D01G111900 chr5D 94.227 485 27 1 1 485 292683844 292684327 0.000000e+00 739
17 TraesCS2D01G111900 chr1D 94.227 485 27 1 1 485 474017730 474017247 0.000000e+00 739
18 TraesCS2D01G111900 chr3A 93.725 494 27 4 1 493 741737157 741736667 0.000000e+00 737
19 TraesCS2D01G111900 chr7B 90.672 268 20 5 2811 3075 540063197 540063462 5.350000e-93 351
20 TraesCS2D01G111900 chr6D 89.474 266 18 7 2812 3072 411402239 411402499 9.010000e-86 327


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 TraesCS2D01G111900 chr2D 62062647 62066014 3367 True 6220.0 6220 100.0000 1 3368 1 chr2D.!!$R1 3367
1 TraesCS2D01G111900 chr2A 62387743 62392129 4386 True 2300.5 3871 95.1200 483 3368 2 chr2A.!!$R1 2885
2 TraesCS2D01G111900 chr2B 97435339 97437711 2372 True 1909.0 3581 94.0435 952 3368 2 chr2B.!!$R1 2416

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
453 454 0.035598 TCTTCGATTTTGGACCGCCA 59.964 50.000 0.00 0.00 44.17 5.69 F
1294 2812 1.153168 CATCCGCGGAACCCTCATT 60.153 57.895 34.66 10.38 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2094 3613 1.222936 CGGCAGCTCCTTCTCCAAT 59.777 57.895 0.0 0.0 0.00 3.16 R
2739 4258 1.804151 CACATCGACCCAACAACGAAT 59.196 47.619 0.0 0.0 39.38 3.34 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 4.972733 TGTTGGCCCGTGCAGCAT 62.973 61.111 0.00 0.00 40.13 3.79
23 24 4.424566 GTTGGCCCGTGCAGCATG 62.425 66.667 7.74 7.74 40.13 4.06
47 48 3.414700 CCGCTGCTCGTGGTGTTC 61.415 66.667 0.00 0.00 38.52 3.18
48 49 3.767230 CGCTGCTCGTGGTGTTCG 61.767 66.667 0.00 0.00 0.00 3.95
49 50 4.077188 GCTGCTCGTGGTGTTCGC 62.077 66.667 0.00 0.00 0.00 4.70
98 99 2.047655 CCGGCAAAGGAGCACGTA 60.048 61.111 0.00 0.00 35.83 3.57
99 100 2.388232 CCGGCAAAGGAGCACGTAC 61.388 63.158 0.00 0.00 35.83 3.67
100 101 1.666553 CGGCAAAGGAGCACGTACA 60.667 57.895 0.00 0.00 35.83 2.90
101 102 1.225376 CGGCAAAGGAGCACGTACAA 61.225 55.000 0.00 0.00 35.83 2.41
102 103 0.517316 GGCAAAGGAGCACGTACAAG 59.483 55.000 0.00 0.00 35.83 3.16
103 104 0.517316 GCAAAGGAGCACGTACAAGG 59.483 55.000 0.00 0.00 0.00 3.61
104 105 1.156736 CAAAGGAGCACGTACAAGGG 58.843 55.000 0.00 0.00 0.00 3.95
105 106 1.053424 AAAGGAGCACGTACAAGGGA 58.947 50.000 0.00 0.00 0.00 4.20
106 107 0.608640 AAGGAGCACGTACAAGGGAG 59.391 55.000 0.00 0.00 0.00 4.30
107 108 1.448013 GGAGCACGTACAAGGGAGC 60.448 63.158 0.00 0.00 0.00 4.70
108 109 1.592223 GAGCACGTACAAGGGAGCT 59.408 57.895 0.00 0.00 34.61 4.09
109 110 0.458716 GAGCACGTACAAGGGAGCTC 60.459 60.000 4.71 4.71 41.21 4.09
110 111 1.805945 GCACGTACAAGGGAGCTCG 60.806 63.158 7.83 0.00 0.00 5.03
111 112 1.153823 CACGTACAAGGGAGCTCGG 60.154 63.158 7.83 0.00 0.00 4.63
112 113 2.348888 ACGTACAAGGGAGCTCGGG 61.349 63.158 7.83 0.00 0.00 5.14
113 114 2.187163 GTACAAGGGAGCTCGGGC 59.813 66.667 7.83 0.00 39.06 6.13
130 131 4.738998 CTCCGGCCATGGCAACCA 62.739 66.667 36.56 16.78 44.11 3.67
135 136 3.747976 GCCATGGCAACCACGGAC 61.748 66.667 32.08 0.00 39.54 4.79
136 137 3.430862 CCATGGCAACCACGGACG 61.431 66.667 0.00 0.00 39.54 4.79
137 138 2.358125 CATGGCAACCACGGACGA 60.358 61.111 0.00 0.00 35.80 4.20
138 139 2.047274 ATGGCAACCACGGACGAG 60.047 61.111 0.00 0.00 35.80 4.18
139 140 4.980805 TGGCAACCACGGACGAGC 62.981 66.667 0.00 0.00 0.00 5.03
140 141 4.980805 GGCAACCACGGACGAGCA 62.981 66.667 0.00 0.00 0.00 4.26
141 142 3.712881 GCAACCACGGACGAGCAC 61.713 66.667 0.00 0.00 0.00 4.40
142 143 3.403057 CAACCACGGACGAGCACG 61.403 66.667 0.76 0.76 45.75 5.34
143 144 3.598715 AACCACGGACGAGCACGA 61.599 61.111 11.40 0.00 42.66 4.35
144 145 3.553437 AACCACGGACGAGCACGAG 62.553 63.158 11.40 3.79 42.66 4.18
145 146 3.733960 CCACGGACGAGCACGAGA 61.734 66.667 11.40 0.00 42.66 4.04
146 147 2.202362 CACGGACGAGCACGAGAG 60.202 66.667 11.40 3.05 42.66 3.20
147 148 4.104417 ACGGACGAGCACGAGAGC 62.104 66.667 11.40 0.00 42.66 4.09
149 150 4.838486 GGACGAGCACGAGAGCGG 62.838 72.222 11.40 0.00 43.17 5.52
150 151 4.104417 GACGAGCACGAGAGCGGT 62.104 66.667 11.40 0.00 43.17 5.68
151 152 4.406173 ACGAGCACGAGAGCGGTG 62.406 66.667 11.40 0.00 43.17 4.94
156 157 2.664851 CACGAGAGCGGTGGCAAA 60.665 61.111 0.00 0.00 43.41 3.68
157 158 2.665185 ACGAGAGCGGTGGCAAAC 60.665 61.111 0.00 0.00 43.41 2.93
158 159 3.777925 CGAGAGCGGTGGCAAACG 61.778 66.667 0.00 0.00 43.41 3.60
159 160 2.357034 GAGAGCGGTGGCAAACGA 60.357 61.111 0.45 0.00 43.41 3.85
160 161 2.665185 AGAGCGGTGGCAAACGAC 60.665 61.111 0.45 0.00 43.41 4.34
161 162 2.970324 GAGCGGTGGCAAACGACA 60.970 61.111 0.45 0.00 43.41 4.35
162 163 3.236618 GAGCGGTGGCAAACGACAC 62.237 63.158 0.45 0.00 42.15 3.67
167 168 3.472263 GTGGCAAACGACACCAATC 57.528 52.632 0.00 0.00 36.31 2.67
169 170 0.533085 TGGCAAACGACACCAATCGA 60.533 50.000 1.63 0.00 45.13 3.59
170 171 0.589223 GGCAAACGACACCAATCGAA 59.411 50.000 1.63 0.00 45.13 3.71
171 172 1.399727 GGCAAACGACACCAATCGAAG 60.400 52.381 1.63 0.00 45.13 3.79
172 173 1.399727 GCAAACGACACCAATCGAAGG 60.400 52.381 1.63 5.78 45.13 3.46
173 174 1.196808 CAAACGACACCAATCGAAGGG 59.803 52.381 11.44 8.04 45.13 3.95
174 175 0.321298 AACGACACCAATCGAAGGGG 60.321 55.000 7.89 7.89 45.13 4.79
175 176 1.189524 ACGACACCAATCGAAGGGGA 61.190 55.000 15.64 0.00 45.13 4.81
176 177 0.036765 CGACACCAATCGAAGGGGAA 60.037 55.000 15.64 0.00 45.13 3.97
177 178 1.609580 CGACACCAATCGAAGGGGAAA 60.610 52.381 15.64 0.00 45.13 3.13
178 179 2.510613 GACACCAATCGAAGGGGAAAA 58.489 47.619 15.64 0.00 32.49 2.29
179 180 2.888414 GACACCAATCGAAGGGGAAAAA 59.112 45.455 15.64 0.00 32.49 1.94
197 198 4.542906 AAAAATAGGGGGATTGGGAGAG 57.457 45.455 0.00 0.00 0.00 3.20
198 199 2.140098 AATAGGGGGATTGGGAGAGG 57.860 55.000 0.00 0.00 0.00 3.69
199 200 1.264869 ATAGGGGGATTGGGAGAGGA 58.735 55.000 0.00 0.00 0.00 3.71
200 201 0.568192 TAGGGGGATTGGGAGAGGAG 59.432 60.000 0.00 0.00 0.00 3.69
201 202 2.456443 GGGGGATTGGGAGAGGAGC 61.456 68.421 0.00 0.00 0.00 4.70
202 203 1.385206 GGGGATTGGGAGAGGAGCT 60.385 63.158 0.00 0.00 0.00 4.09
203 204 1.414866 GGGGATTGGGAGAGGAGCTC 61.415 65.000 4.71 4.71 43.17 4.09
204 205 0.692419 GGGATTGGGAGAGGAGCTCA 60.692 60.000 17.19 0.00 45.81 4.26
205 206 1.433121 GGATTGGGAGAGGAGCTCAT 58.567 55.000 17.19 8.81 45.81 2.90
206 207 1.347378 GGATTGGGAGAGGAGCTCATC 59.653 57.143 20.50 20.50 45.81 2.92
207 208 2.045524 GATTGGGAGAGGAGCTCATCA 58.954 52.381 28.45 9.39 45.81 3.07
208 209 1.198713 TTGGGAGAGGAGCTCATCAC 58.801 55.000 28.45 22.33 45.81 3.06
209 210 1.039785 TGGGAGAGGAGCTCATCACG 61.040 60.000 28.45 0.00 45.81 4.35
210 211 1.739049 GGAGAGGAGCTCATCACGG 59.261 63.158 28.45 0.00 45.81 4.94
211 212 1.739049 GAGAGGAGCTCATCACGGG 59.261 63.158 28.45 0.00 43.38 5.28
212 213 1.743321 GAGAGGAGCTCATCACGGGG 61.743 65.000 28.45 0.00 43.38 5.73
213 214 1.758514 GAGGAGCTCATCACGGGGA 60.759 63.158 22.87 0.00 0.00 4.81
214 215 1.743321 GAGGAGCTCATCACGGGGAG 61.743 65.000 22.87 0.00 0.00 4.30
215 216 2.801631 GGAGCTCATCACGGGGAGG 61.802 68.421 17.19 0.00 0.00 4.30
216 217 1.758514 GAGCTCATCACGGGGAGGA 60.759 63.158 9.40 0.00 34.66 3.71
217 218 1.074926 AGCTCATCACGGGGAGGAT 60.075 57.895 0.00 0.00 35.47 3.24
218 219 1.070445 GCTCATCACGGGGAGGATG 59.930 63.158 0.00 0.00 41.73 3.51
219 220 1.750930 CTCATCACGGGGAGGATGG 59.249 63.158 0.00 0.00 40.94 3.51
220 221 2.111878 CATCACGGGGAGGATGGC 59.888 66.667 0.00 0.00 37.77 4.40
221 222 3.550431 ATCACGGGGAGGATGGCG 61.550 66.667 0.00 0.00 0.00 5.69
241 242 3.148279 CTCGGGGAGGTCGGGAAG 61.148 72.222 0.00 0.00 0.00 3.46
242 243 3.657038 CTCGGGGAGGTCGGGAAGA 62.657 68.421 0.00 0.00 0.00 2.87
243 244 3.148279 CGGGGAGGTCGGGAAGAG 61.148 72.222 0.00 0.00 0.00 2.85
250 251 3.071580 GGTCGGGAAGAGCTTGATG 57.928 57.895 0.00 0.00 43.62 3.07
251 252 0.462759 GGTCGGGAAGAGCTTGATGG 60.463 60.000 0.00 0.00 43.62 3.51
252 253 1.092345 GTCGGGAAGAGCTTGATGGC 61.092 60.000 0.00 0.00 0.00 4.40
253 254 2.176273 CGGGAAGAGCTTGATGGCG 61.176 63.158 0.00 0.00 37.29 5.69
254 255 1.221840 GGGAAGAGCTTGATGGCGA 59.778 57.895 0.00 0.00 37.29 5.54
255 256 1.092345 GGGAAGAGCTTGATGGCGAC 61.092 60.000 0.00 0.00 37.29 5.19
256 257 1.424493 GGAAGAGCTTGATGGCGACG 61.424 60.000 0.00 0.00 37.29 5.12
257 258 1.424493 GAAGAGCTTGATGGCGACGG 61.424 60.000 0.00 0.00 37.29 4.79
258 259 1.888436 AAGAGCTTGATGGCGACGGA 61.888 55.000 0.00 0.00 37.29 4.69
259 260 1.227380 GAGCTTGATGGCGACGGAT 60.227 57.895 0.00 0.00 37.29 4.18
260 261 0.811616 GAGCTTGATGGCGACGGATT 60.812 55.000 0.00 0.00 37.29 3.01
261 262 0.392998 AGCTTGATGGCGACGGATTT 60.393 50.000 0.00 0.00 37.29 2.17
262 263 0.248215 GCTTGATGGCGACGGATTTG 60.248 55.000 0.00 0.00 0.00 2.32
263 264 1.368641 CTTGATGGCGACGGATTTGA 58.631 50.000 0.00 0.00 0.00 2.69
264 265 1.062587 CTTGATGGCGACGGATTTGAC 59.937 52.381 0.00 0.00 0.00 3.18
265 266 1.081556 TGATGGCGACGGATTTGACG 61.082 55.000 0.00 0.00 37.36 4.35
266 267 0.804544 GATGGCGACGGATTTGACGA 60.805 55.000 0.00 0.00 34.93 4.20
267 268 0.390603 ATGGCGACGGATTTGACGAA 60.391 50.000 0.00 0.00 34.93 3.85
268 269 1.011968 TGGCGACGGATTTGACGAAG 61.012 55.000 0.00 0.00 34.93 3.79
269 270 1.693083 GGCGACGGATTTGACGAAGG 61.693 60.000 0.00 0.00 34.93 3.46
270 271 1.708027 CGACGGATTTGACGAAGGC 59.292 57.895 0.00 0.00 34.93 4.35
271 272 1.708027 GACGGATTTGACGAAGGCG 59.292 57.895 0.00 0.00 44.79 5.52
272 273 1.693083 GACGGATTTGACGAAGGCGG 61.693 60.000 0.00 0.00 43.17 6.13
290 291 3.367743 CCGACGTCCCGAGGTTGA 61.368 66.667 10.58 0.00 33.59 3.18
291 292 2.646719 CGACGTCCCGAGGTTGAA 59.353 61.111 10.58 0.00 33.59 2.69
292 293 1.443872 CGACGTCCCGAGGTTGAAG 60.444 63.158 10.58 0.00 33.59 3.02
293 294 1.859427 CGACGTCCCGAGGTTGAAGA 61.859 60.000 10.58 0.00 33.59 2.87
294 295 0.316204 GACGTCCCGAGGTTGAAGAA 59.684 55.000 3.51 0.00 0.00 2.52
295 296 0.317479 ACGTCCCGAGGTTGAAGAAG 59.683 55.000 0.00 0.00 0.00 2.85
296 297 0.601558 CGTCCCGAGGTTGAAGAAGA 59.398 55.000 0.00 0.00 0.00 2.87
297 298 1.669211 CGTCCCGAGGTTGAAGAAGAC 60.669 57.143 0.00 0.00 0.00 3.01
298 299 0.601558 TCCCGAGGTTGAAGAAGACG 59.398 55.000 0.00 0.00 0.00 4.18
299 300 0.601558 CCCGAGGTTGAAGAAGACGA 59.398 55.000 0.00 0.00 0.00 4.20
300 301 1.204941 CCCGAGGTTGAAGAAGACGAT 59.795 52.381 0.00 0.00 0.00 3.73
301 302 2.531206 CCGAGGTTGAAGAAGACGATC 58.469 52.381 0.00 0.00 0.00 3.69
302 303 2.094700 CCGAGGTTGAAGAAGACGATCA 60.095 50.000 0.00 0.00 0.00 2.92
303 304 3.575630 CGAGGTTGAAGAAGACGATCAA 58.424 45.455 0.00 0.00 0.00 2.57
304 305 3.610242 CGAGGTTGAAGAAGACGATCAAG 59.390 47.826 0.00 0.00 34.02 3.02
305 306 3.929610 GAGGTTGAAGAAGACGATCAAGG 59.070 47.826 0.00 0.00 34.02 3.61
306 307 2.416893 GGTTGAAGAAGACGATCAAGGC 59.583 50.000 0.00 0.00 34.02 4.35
307 308 1.996292 TGAAGAAGACGATCAAGGCG 58.004 50.000 0.00 0.00 0.00 5.52
308 309 1.544246 TGAAGAAGACGATCAAGGCGA 59.456 47.619 0.00 0.00 0.00 5.54
309 310 2.166459 TGAAGAAGACGATCAAGGCGAT 59.834 45.455 0.00 0.00 36.91 4.58
310 311 2.969628 AGAAGACGATCAAGGCGATT 57.030 45.000 0.00 0.00 33.17 3.34
311 312 2.815478 AGAAGACGATCAAGGCGATTC 58.185 47.619 0.00 0.00 33.17 2.52
312 313 2.428890 AGAAGACGATCAAGGCGATTCT 59.571 45.455 0.00 0.00 35.34 2.40
313 314 3.632604 AGAAGACGATCAAGGCGATTCTA 59.367 43.478 0.00 0.00 36.95 2.10
314 315 3.357166 AGACGATCAAGGCGATTCTAC 57.643 47.619 0.00 0.00 33.17 2.59
315 316 2.688446 AGACGATCAAGGCGATTCTACA 59.312 45.455 0.00 0.00 33.17 2.74
316 317 3.319405 AGACGATCAAGGCGATTCTACAT 59.681 43.478 0.00 0.00 33.17 2.29
317 318 3.643763 ACGATCAAGGCGATTCTACATC 58.356 45.455 0.00 0.00 33.17 3.06
318 319 3.319405 ACGATCAAGGCGATTCTACATCT 59.681 43.478 0.00 0.00 33.17 2.90
319 320 4.202161 ACGATCAAGGCGATTCTACATCTT 60.202 41.667 0.00 0.00 33.17 2.40
320 321 4.384247 CGATCAAGGCGATTCTACATCTTC 59.616 45.833 0.00 0.00 33.17 2.87
321 322 4.736126 TCAAGGCGATTCTACATCTTCA 57.264 40.909 0.00 0.00 0.00 3.02
322 323 5.282055 TCAAGGCGATTCTACATCTTCAT 57.718 39.130 0.00 0.00 0.00 2.57
323 324 5.674525 TCAAGGCGATTCTACATCTTCATT 58.325 37.500 0.00 0.00 0.00 2.57
324 325 6.115446 TCAAGGCGATTCTACATCTTCATTT 58.885 36.000 0.00 0.00 0.00 2.32
325 326 6.599244 TCAAGGCGATTCTACATCTTCATTTT 59.401 34.615 0.00 0.00 0.00 1.82
326 327 6.369059 AGGCGATTCTACATCTTCATTTTG 57.631 37.500 0.00 0.00 0.00 2.44
327 328 5.297776 AGGCGATTCTACATCTTCATTTTGG 59.702 40.000 0.00 0.00 0.00 3.28
328 329 5.296780 GGCGATTCTACATCTTCATTTTGGA 59.703 40.000 0.00 0.00 0.00 3.53
329 330 6.195165 GCGATTCTACATCTTCATTTTGGAC 58.805 40.000 0.00 0.00 0.00 4.02
330 331 6.719365 CGATTCTACATCTTCATTTTGGACC 58.281 40.000 0.00 0.00 0.00 4.46
331 332 6.316140 CGATTCTACATCTTCATTTTGGACCA 59.684 38.462 0.00 0.00 0.00 4.02
332 333 7.012704 CGATTCTACATCTTCATTTTGGACCAT 59.987 37.037 0.00 0.00 0.00 3.55
333 334 7.630242 TTCTACATCTTCATTTTGGACCATC 57.370 36.000 0.00 0.00 0.00 3.51
334 335 6.962182 TCTACATCTTCATTTTGGACCATCT 58.038 36.000 0.00 0.00 0.00 2.90
335 336 5.909621 ACATCTTCATTTTGGACCATCTG 57.090 39.130 0.00 0.00 0.00 2.90
336 337 5.327732 ACATCTTCATTTTGGACCATCTGT 58.672 37.500 0.00 0.00 0.00 3.41
337 338 5.776716 ACATCTTCATTTTGGACCATCTGTT 59.223 36.000 0.00 0.00 0.00 3.16
338 339 5.710513 TCTTCATTTTGGACCATCTGTTG 57.289 39.130 0.00 0.00 0.00 3.33
351 352 4.843220 CATCTGTTGGAGTTGCTCTTTT 57.157 40.909 0.00 0.00 0.00 2.27
352 353 4.543692 CATCTGTTGGAGTTGCTCTTTTG 58.456 43.478 0.00 0.00 0.00 2.44
353 354 2.951642 TCTGTTGGAGTTGCTCTTTTGG 59.048 45.455 0.00 0.00 0.00 3.28
354 355 2.951642 CTGTTGGAGTTGCTCTTTTGGA 59.048 45.455 0.00 0.00 0.00 3.53
355 356 2.687935 TGTTGGAGTTGCTCTTTTGGAC 59.312 45.455 0.00 0.00 0.00 4.02
356 357 1.981256 TGGAGTTGCTCTTTTGGACC 58.019 50.000 0.00 0.00 0.00 4.46
357 358 1.214175 TGGAGTTGCTCTTTTGGACCA 59.786 47.619 0.00 0.00 0.00 4.02
358 359 2.158475 TGGAGTTGCTCTTTTGGACCAT 60.158 45.455 0.00 0.00 0.00 3.55
359 360 2.489722 GGAGTTGCTCTTTTGGACCATC 59.510 50.000 0.00 0.00 0.00 3.51
360 361 3.149196 GAGTTGCTCTTTTGGACCATCA 58.851 45.455 0.00 0.00 0.00 3.07
361 362 3.565307 AGTTGCTCTTTTGGACCATCAA 58.435 40.909 0.00 0.00 0.00 2.57
362 363 4.154942 AGTTGCTCTTTTGGACCATCAAT 58.845 39.130 0.00 0.00 0.00 2.57
363 364 4.590222 AGTTGCTCTTTTGGACCATCAATT 59.410 37.500 0.00 0.00 0.00 2.32
364 365 5.070847 AGTTGCTCTTTTGGACCATCAATTT 59.929 36.000 0.00 0.00 0.00 1.82
365 366 4.885413 TGCTCTTTTGGACCATCAATTTG 58.115 39.130 0.00 0.00 0.00 2.32
366 367 4.248058 GCTCTTTTGGACCATCAATTTGG 58.752 43.478 0.00 0.00 42.82 3.28
367 368 4.021192 GCTCTTTTGGACCATCAATTTGGA 60.021 41.667 3.10 0.00 39.25 3.53
368 369 5.467035 TCTTTTGGACCATCAATTTGGAC 57.533 39.130 3.10 0.00 39.25 4.02
373 374 3.635591 GGACCATCAATTTGGACCATCT 58.364 45.455 11.42 0.00 46.78 2.90
374 375 3.382546 GGACCATCAATTTGGACCATCTG 59.617 47.826 11.42 0.00 46.78 2.90
375 376 4.019174 GACCATCAATTTGGACCATCTGT 58.981 43.478 3.10 0.00 39.25 3.41
376 377 4.419282 ACCATCAATTTGGACCATCTGTT 58.581 39.130 3.10 0.00 39.25 3.16
377 378 4.221262 ACCATCAATTTGGACCATCTGTTG 59.779 41.667 3.10 0.00 39.25 3.33
378 379 6.796646 ACCATCAATTTGGACCATCTGTTGG 61.797 44.000 18.12 18.12 44.65 3.77
379 380 8.907229 ACCATCAATTTGGACCATCTGTTGGA 62.907 42.308 22.75 7.30 42.98 3.53
390 391 4.843220 CATCTGTTGGAGTTCAGCTTTT 57.157 40.909 0.00 0.00 0.00 2.27
391 392 5.192327 CATCTGTTGGAGTTCAGCTTTTT 57.808 39.130 0.00 0.00 0.00 1.94
408 409 3.430333 TTTTTCGGAGCTCCAAAACAC 57.570 42.857 31.67 3.61 35.14 3.32
409 410 2.045561 TTTCGGAGCTCCAAAACACA 57.954 45.000 31.67 2.12 35.14 3.72
410 411 2.270352 TTCGGAGCTCCAAAACACAT 57.730 45.000 31.67 0.00 35.14 3.21
411 412 2.270352 TCGGAGCTCCAAAACACATT 57.730 45.000 31.67 0.00 35.14 2.71
412 413 2.582052 TCGGAGCTCCAAAACACATTT 58.418 42.857 31.67 0.00 35.14 2.32
413 414 2.955660 TCGGAGCTCCAAAACACATTTT 59.044 40.909 31.67 0.00 38.61 1.82
414 415 3.383185 TCGGAGCTCCAAAACACATTTTT 59.617 39.130 31.67 0.00 35.79 1.94
435 436 3.859411 TGGCGGTCCAAATTTTACATC 57.141 42.857 0.00 0.00 39.99 3.06
436 437 3.426615 TGGCGGTCCAAATTTTACATCT 58.573 40.909 0.00 0.00 39.99 2.90
437 438 3.829601 TGGCGGTCCAAATTTTACATCTT 59.170 39.130 0.00 0.00 39.99 2.40
438 439 4.082463 TGGCGGTCCAAATTTTACATCTTC 60.082 41.667 0.00 0.00 39.99 2.87
439 440 4.095610 GCGGTCCAAATTTTACATCTTCG 58.904 43.478 0.00 0.00 0.00 3.79
440 441 4.142773 GCGGTCCAAATTTTACATCTTCGA 60.143 41.667 0.00 0.00 0.00 3.71
441 442 5.448632 GCGGTCCAAATTTTACATCTTCGAT 60.449 40.000 0.00 0.00 0.00 3.59
442 443 6.551736 CGGTCCAAATTTTACATCTTCGATT 58.448 36.000 0.00 0.00 0.00 3.34
443 444 7.027161 CGGTCCAAATTTTACATCTTCGATTT 58.973 34.615 0.00 0.00 0.00 2.17
444 445 7.540745 CGGTCCAAATTTTACATCTTCGATTTT 59.459 33.333 0.00 0.00 0.00 1.82
445 446 8.647226 GGTCCAAATTTTACATCTTCGATTTTG 58.353 33.333 0.00 0.00 0.00 2.44
446 447 8.647226 GTCCAAATTTTACATCTTCGATTTTGG 58.353 33.333 0.00 0.00 0.00 3.28
447 448 8.580720 TCCAAATTTTACATCTTCGATTTTGGA 58.419 29.630 8.73 8.73 0.00 3.53
448 449 8.647226 CCAAATTTTACATCTTCGATTTTGGAC 58.353 33.333 4.95 0.00 0.00 4.02
449 450 8.647226 CAAATTTTACATCTTCGATTTTGGACC 58.353 33.333 0.00 0.00 0.00 4.46
450 451 5.539582 TTTACATCTTCGATTTTGGACCG 57.460 39.130 0.00 0.00 0.00 4.79
451 452 1.737793 ACATCTTCGATTTTGGACCGC 59.262 47.619 0.00 0.00 0.00 5.68
452 453 1.064060 CATCTTCGATTTTGGACCGCC 59.936 52.381 0.00 0.00 0.00 6.13
453 454 0.035598 TCTTCGATTTTGGACCGCCA 59.964 50.000 0.00 0.00 44.17 5.69
572 573 9.599322 GATAATAAGCTGTGCATACAATTACAC 57.401 33.333 0.00 0.00 36.14 2.90
610 611 6.698008 TGTGGCAATAATTCCAGTATTCAG 57.302 37.500 0.00 0.00 32.15 3.02
650 651 1.359130 CCCACCCTCCATCTTTCCTTT 59.641 52.381 0.00 0.00 0.00 3.11
721 722 9.101655 AGAATCCAACAAATTCAAACTTTCAAG 57.898 29.630 0.00 0.00 35.92 3.02
841 844 7.663081 ACAAGTGATCTGATGTCTGTGTATTTT 59.337 33.333 0.00 0.00 0.00 1.82
892 895 7.436118 TCACACTCGTTATAACCAGTAAGTTT 58.564 34.615 14.46 0.72 29.10 2.66
893 896 7.927629 TCACACTCGTTATAACCAGTAAGTTTT 59.072 33.333 14.46 0.00 29.10 2.43
894 897 8.553696 CACACTCGTTATAACCAGTAAGTTTTT 58.446 33.333 14.46 0.00 29.10 1.94
919 922 6.394025 TTTTTGAGGCAACGTTATAACCTT 57.606 33.333 10.01 2.22 46.39 3.50
955 2473 9.577110 TGAGAAATACGTTATAACCAGTAAGTG 57.423 33.333 10.01 0.00 0.00 3.16
1122 2640 7.704047 GCACAGACTCTTCTCAAAAAGAAAAAT 59.296 33.333 0.00 0.00 43.39 1.82
1208 2726 1.699054 CGCATCATCCTTCTCCCCCA 61.699 60.000 0.00 0.00 0.00 4.96
1247 2765 2.512515 GAGCCATGTCCGCCTCAC 60.513 66.667 0.00 0.00 0.00 3.51
1294 2812 1.153168 CATCCGCGGAACCCTCATT 60.153 57.895 34.66 10.38 0.00 2.57
1617 3136 3.584052 CTCTACCTCGTCGGCGGG 61.584 72.222 10.62 5.65 38.89 6.13
1743 3262 4.500116 GTCCTCTCCGGCGTGCTC 62.500 72.222 6.01 0.00 0.00 4.26
1927 3446 2.978824 GCGGAGGCTTGGTCTACA 59.021 61.111 0.00 0.00 35.83 2.74
2028 3547 2.657143 GTCGGTGGAATCCTCTACTCT 58.343 52.381 0.00 0.00 33.68 3.24
2074 3593 3.072184 GGGCTATGATCCAGACACTGATT 59.928 47.826 0.00 0.00 32.44 2.57
2094 3613 1.752198 CTGGAACACGGTGGAAGGA 59.248 57.895 13.48 0.00 0.00 3.36
2172 3691 1.962807 CTGCTCTACCTGATCTGGGAG 59.037 57.143 22.10 22.10 39.42 4.30
2196 3715 2.498644 AGTGGAAAGGGAAAGCTAGC 57.501 50.000 6.62 6.62 0.00 3.42
2739 4258 4.289934 TGTATTGGTAATGGACACAGGGAA 59.710 41.667 0.00 0.00 0.00 3.97
2839 4367 3.437049 GCTCCGTTTTCATTTACTCTGCT 59.563 43.478 0.00 0.00 0.00 4.24
2841 4369 5.121768 GCTCCGTTTTCATTTACTCTGCTTA 59.878 40.000 0.00 0.00 0.00 3.09
2985 4528 9.120538 GTATTGACTTGGTATTGTGGATGTTAT 57.879 33.333 0.00 0.00 0.00 1.89
3318 4862 7.961326 ATCTTATGTCCAGTTAAATGCCTTT 57.039 32.000 0.00 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.972733 ATGCTGCACGGGCCAACA 62.973 61.111 7.46 2.23 40.13 3.33
6 7 4.424566 CATGCTGCACGGGCCAAC 62.425 66.667 7.46 0.00 40.13 3.77
30 31 3.414700 GAACACCACGAGCAGCGG 61.415 66.667 4.06 0.00 46.49 5.52
32 33 4.077188 GCGAACACCACGAGCAGC 62.077 66.667 0.00 0.00 0.00 5.25
33 34 3.767230 CGCGAACACCACGAGCAG 61.767 66.667 0.00 0.00 0.00 4.24
34 35 4.578898 ACGCGAACACCACGAGCA 62.579 61.111 15.93 0.00 34.29 4.26
35 36 3.764049 GACGCGAACACCACGAGC 61.764 66.667 15.93 0.00 34.29 5.03
36 37 3.458579 CGACGCGAACACCACGAG 61.459 66.667 15.93 0.00 36.71 4.18
37 38 4.986587 CCGACGCGAACACCACGA 62.987 66.667 15.93 0.00 0.00 4.35
81 82 2.047655 TACGTGCTCCTTTGCCGG 60.048 61.111 0.00 0.00 33.33 6.13
82 83 1.225376 TTGTACGTGCTCCTTTGCCG 61.225 55.000 4.97 0.00 34.52 5.69
83 84 0.517316 CTTGTACGTGCTCCTTTGCC 59.483 55.000 4.97 0.00 0.00 4.52
84 85 0.517316 CCTTGTACGTGCTCCTTTGC 59.483 55.000 4.97 0.00 0.00 3.68
85 86 1.156736 CCCTTGTACGTGCTCCTTTG 58.843 55.000 4.97 0.00 0.00 2.77
86 87 1.002087 CTCCCTTGTACGTGCTCCTTT 59.998 52.381 4.97 0.00 0.00 3.11
87 88 0.608640 CTCCCTTGTACGTGCTCCTT 59.391 55.000 4.97 0.00 0.00 3.36
88 89 1.889530 GCTCCCTTGTACGTGCTCCT 61.890 60.000 4.97 0.00 0.00 3.69
89 90 1.448013 GCTCCCTTGTACGTGCTCC 60.448 63.158 4.97 0.00 0.00 4.70
90 91 0.458716 GAGCTCCCTTGTACGTGCTC 60.459 60.000 0.87 4.84 39.74 4.26
91 92 1.592223 GAGCTCCCTTGTACGTGCT 59.408 57.895 0.87 0.00 0.00 4.40
92 93 1.805945 CGAGCTCCCTTGTACGTGC 60.806 63.158 8.47 0.00 0.00 5.34
93 94 1.153823 CCGAGCTCCCTTGTACGTG 60.154 63.158 8.47 0.00 0.00 4.49
94 95 2.348888 CCCGAGCTCCCTTGTACGT 61.349 63.158 8.47 0.00 0.00 3.57
95 96 2.494918 CCCGAGCTCCCTTGTACG 59.505 66.667 8.47 0.00 0.00 3.67
96 97 2.187163 GCCCGAGCTCCCTTGTAC 59.813 66.667 8.47 0.00 35.50 2.90
113 114 4.738998 TGGTTGCCATGGCCGGAG 62.739 66.667 33.44 0.00 41.09 4.63
120 121 2.358125 TCGTCCGTGGTTGCCATG 60.358 61.111 0.58 0.58 40.02 3.66
121 122 2.047274 CTCGTCCGTGGTTGCCAT 60.047 61.111 0.00 0.00 35.28 4.40
122 123 4.980805 GCTCGTCCGTGGTTGCCA 62.981 66.667 0.00 0.00 0.00 4.92
123 124 4.980805 TGCTCGTCCGTGGTTGCC 62.981 66.667 0.00 0.00 0.00 4.52
124 125 3.712881 GTGCTCGTCCGTGGTTGC 61.713 66.667 0.00 0.00 0.00 4.17
125 126 3.403057 CGTGCTCGTCCGTGGTTG 61.403 66.667 0.00 0.00 0.00 3.77
126 127 3.553437 CTCGTGCTCGTCCGTGGTT 62.553 63.158 8.17 0.00 38.33 3.67
127 128 4.039357 CTCGTGCTCGTCCGTGGT 62.039 66.667 8.17 0.00 38.33 4.16
128 129 3.669036 CTCTCGTGCTCGTCCGTGG 62.669 68.421 8.17 0.00 38.33 4.94
129 130 2.202362 CTCTCGTGCTCGTCCGTG 60.202 66.667 8.17 0.00 38.33 4.94
130 131 4.104417 GCTCTCGTGCTCGTCCGT 62.104 66.667 8.17 0.00 38.33 4.69
132 133 4.838486 CCGCTCTCGTGCTCGTCC 62.838 72.222 8.17 0.00 38.33 4.79
133 134 4.104417 ACCGCTCTCGTGCTCGTC 62.104 66.667 8.17 0.00 38.33 4.20
134 135 4.406173 CACCGCTCTCGTGCTCGT 62.406 66.667 8.17 0.00 38.33 4.18
139 140 2.664851 TTTGCCACCGCTCTCGTG 60.665 61.111 0.00 0.00 35.36 4.35
140 141 2.665185 GTTTGCCACCGCTCTCGT 60.665 61.111 0.00 0.00 35.36 4.18
141 142 3.777925 CGTTTGCCACCGCTCTCG 61.778 66.667 0.00 0.00 35.36 4.04
142 143 2.357034 TCGTTTGCCACCGCTCTC 60.357 61.111 0.00 0.00 35.36 3.20
143 144 2.665185 GTCGTTTGCCACCGCTCT 60.665 61.111 0.00 0.00 35.36 4.09
144 145 2.970324 TGTCGTTTGCCACCGCTC 60.970 61.111 0.00 0.00 35.36 5.03
145 146 3.276846 GTGTCGTTTGCCACCGCT 61.277 61.111 0.00 0.00 35.36 5.52
146 147 4.322385 GGTGTCGTTTGCCACCGC 62.322 66.667 0.00 0.00 41.55 5.68
149 150 0.385473 CGATTGGTGTCGTTTGCCAC 60.385 55.000 0.00 0.00 36.88 5.01
150 151 0.533085 TCGATTGGTGTCGTTTGCCA 60.533 50.000 0.00 0.00 42.07 4.92
151 152 0.589223 TTCGATTGGTGTCGTTTGCC 59.411 50.000 0.00 0.00 42.07 4.52
152 153 1.399727 CCTTCGATTGGTGTCGTTTGC 60.400 52.381 0.00 0.00 42.07 3.68
153 154 1.196808 CCCTTCGATTGGTGTCGTTTG 59.803 52.381 4.59 0.00 42.07 2.93
154 155 1.519408 CCCTTCGATTGGTGTCGTTT 58.481 50.000 4.59 0.00 42.07 3.60
155 156 0.321298 CCCCTTCGATTGGTGTCGTT 60.321 55.000 4.59 0.00 42.07 3.85
156 157 1.189524 TCCCCTTCGATTGGTGTCGT 61.190 55.000 4.59 0.00 42.07 4.34
157 158 0.036765 TTCCCCTTCGATTGGTGTCG 60.037 55.000 4.59 0.00 42.74 4.35
158 159 2.194201 TTTCCCCTTCGATTGGTGTC 57.806 50.000 4.59 0.00 0.00 3.67
159 160 2.668144 TTTTCCCCTTCGATTGGTGT 57.332 45.000 4.59 0.00 0.00 4.16
176 177 3.207549 CCTCTCCCAATCCCCCTATTTTT 59.792 47.826 0.00 0.00 0.00 1.94
177 178 2.791774 CCTCTCCCAATCCCCCTATTTT 59.208 50.000 0.00 0.00 0.00 1.82
178 179 2.020037 TCCTCTCCCAATCCCCCTATTT 60.020 50.000 0.00 0.00 0.00 1.40
179 180 1.590590 TCCTCTCCCAATCCCCCTATT 59.409 52.381 0.00 0.00 0.00 1.73
180 181 1.153132 CTCCTCTCCCAATCCCCCTAT 59.847 57.143 0.00 0.00 0.00 2.57
181 182 0.568192 CTCCTCTCCCAATCCCCCTA 59.432 60.000 0.00 0.00 0.00 3.53
182 183 1.319799 CTCCTCTCCCAATCCCCCT 59.680 63.158 0.00 0.00 0.00 4.79
183 184 2.456443 GCTCCTCTCCCAATCCCCC 61.456 68.421 0.00 0.00 0.00 5.40
184 185 1.385206 AGCTCCTCTCCCAATCCCC 60.385 63.158 0.00 0.00 0.00 4.81
185 186 0.692419 TGAGCTCCTCTCCCAATCCC 60.692 60.000 12.15 0.00 41.18 3.85
186 187 1.347378 GATGAGCTCCTCTCCCAATCC 59.653 57.143 12.15 0.00 41.18 3.01
187 188 2.045524 TGATGAGCTCCTCTCCCAATC 58.954 52.381 18.28 9.45 41.18 2.67
188 189 1.767681 GTGATGAGCTCCTCTCCCAAT 59.232 52.381 18.28 0.00 41.18 3.16
189 190 1.198713 GTGATGAGCTCCTCTCCCAA 58.801 55.000 18.28 0.00 41.18 4.12
190 191 1.039785 CGTGATGAGCTCCTCTCCCA 61.040 60.000 18.28 0.00 41.18 4.37
191 192 1.739049 CGTGATGAGCTCCTCTCCC 59.261 63.158 18.28 7.06 41.18 4.30
192 193 1.739049 CCGTGATGAGCTCCTCTCC 59.261 63.158 18.28 9.16 41.18 3.71
193 194 1.739049 CCCGTGATGAGCTCCTCTC 59.261 63.158 18.28 14.07 42.23 3.20
194 195 1.760086 CCCCGTGATGAGCTCCTCT 60.760 63.158 18.28 0.57 0.00 3.69
195 196 1.743321 CTCCCCGTGATGAGCTCCTC 61.743 65.000 12.15 11.90 0.00 3.71
196 197 1.760086 CTCCCCGTGATGAGCTCCT 60.760 63.158 12.15 0.00 0.00 3.69
197 198 2.801631 CCTCCCCGTGATGAGCTCC 61.802 68.421 12.15 0.00 0.00 4.70
198 199 1.118356 ATCCTCCCCGTGATGAGCTC 61.118 60.000 6.82 6.82 0.00 4.09
199 200 1.074926 ATCCTCCCCGTGATGAGCT 60.075 57.895 0.00 0.00 0.00 4.09
200 201 1.070445 CATCCTCCCCGTGATGAGC 59.930 63.158 0.00 0.00 40.64 4.26
201 202 1.750930 CCATCCTCCCCGTGATGAG 59.249 63.158 0.00 0.00 40.64 2.90
202 203 2.443394 GCCATCCTCCCCGTGATGA 61.443 63.158 0.00 0.00 40.64 2.92
203 204 2.111878 GCCATCCTCCCCGTGATG 59.888 66.667 0.00 0.00 38.45 3.07
204 205 3.550431 CGCCATCCTCCCCGTGAT 61.550 66.667 0.00 0.00 0.00 3.06
224 225 3.148279 CTTCCCGACCTCCCCGAG 61.148 72.222 0.00 0.00 0.00 4.63
225 226 3.657038 CTCTTCCCGACCTCCCCGA 62.657 68.421 0.00 0.00 0.00 5.14
226 227 3.148279 CTCTTCCCGACCTCCCCG 61.148 72.222 0.00 0.00 0.00 5.73
227 228 3.471806 GCTCTTCCCGACCTCCCC 61.472 72.222 0.00 0.00 0.00 4.81
228 229 1.990614 AAGCTCTTCCCGACCTCCC 60.991 63.158 0.00 0.00 0.00 4.30
229 230 1.219393 CAAGCTCTTCCCGACCTCC 59.781 63.158 0.00 0.00 0.00 4.30
230 231 0.827368 ATCAAGCTCTTCCCGACCTC 59.173 55.000 0.00 0.00 0.00 3.85
231 232 0.539051 CATCAAGCTCTTCCCGACCT 59.461 55.000 0.00 0.00 0.00 3.85
232 233 0.462759 CCATCAAGCTCTTCCCGACC 60.463 60.000 0.00 0.00 0.00 4.79
233 234 1.092345 GCCATCAAGCTCTTCCCGAC 61.092 60.000 0.00 0.00 0.00 4.79
234 235 1.221840 GCCATCAAGCTCTTCCCGA 59.778 57.895 0.00 0.00 0.00 5.14
235 236 2.176273 CGCCATCAAGCTCTTCCCG 61.176 63.158 0.00 0.00 0.00 5.14
236 237 1.092345 GTCGCCATCAAGCTCTTCCC 61.092 60.000 0.00 0.00 0.00 3.97
237 238 1.424493 CGTCGCCATCAAGCTCTTCC 61.424 60.000 0.00 0.00 0.00 3.46
238 239 1.424493 CCGTCGCCATCAAGCTCTTC 61.424 60.000 0.00 0.00 0.00 2.87
239 240 1.448540 CCGTCGCCATCAAGCTCTT 60.449 57.895 0.00 0.00 0.00 2.85
240 241 1.680522 ATCCGTCGCCATCAAGCTCT 61.681 55.000 0.00 0.00 0.00 4.09
241 242 0.811616 AATCCGTCGCCATCAAGCTC 60.812 55.000 0.00 0.00 0.00 4.09
242 243 0.392998 AAATCCGTCGCCATCAAGCT 60.393 50.000 0.00 0.00 0.00 3.74
243 244 0.248215 CAAATCCGTCGCCATCAAGC 60.248 55.000 0.00 0.00 0.00 4.01
244 245 1.062587 GTCAAATCCGTCGCCATCAAG 59.937 52.381 0.00 0.00 0.00 3.02
245 246 1.083489 GTCAAATCCGTCGCCATCAA 58.917 50.000 0.00 0.00 0.00 2.57
246 247 1.081556 CGTCAAATCCGTCGCCATCA 61.082 55.000 0.00 0.00 0.00 3.07
247 248 0.804544 TCGTCAAATCCGTCGCCATC 60.805 55.000 0.00 0.00 0.00 3.51
248 249 0.390603 TTCGTCAAATCCGTCGCCAT 60.391 50.000 0.00 0.00 0.00 4.40
249 250 1.005984 TTCGTCAAATCCGTCGCCA 60.006 52.632 0.00 0.00 0.00 5.69
250 251 1.693083 CCTTCGTCAAATCCGTCGCC 61.693 60.000 0.00 0.00 0.00 5.54
251 252 1.708027 CCTTCGTCAAATCCGTCGC 59.292 57.895 0.00 0.00 0.00 5.19
252 253 1.708027 GCCTTCGTCAAATCCGTCG 59.292 57.895 0.00 0.00 0.00 5.12
253 254 1.693083 CCGCCTTCGTCAAATCCGTC 61.693 60.000 0.00 0.00 0.00 4.79
254 255 1.740296 CCGCCTTCGTCAAATCCGT 60.740 57.895 0.00 0.00 0.00 4.69
255 256 3.089784 CCGCCTTCGTCAAATCCG 58.910 61.111 0.00 0.00 0.00 4.18
256 257 2.761195 GGCCGCCTTCGTCAAATCC 61.761 63.158 0.71 0.00 0.00 3.01
257 258 2.791927 GGCCGCCTTCGTCAAATC 59.208 61.111 0.71 0.00 0.00 2.17
258 259 3.124921 CGGCCGCCTTCGTCAAAT 61.125 61.111 14.67 0.00 0.00 2.32
259 260 4.302509 TCGGCCGCCTTCGTCAAA 62.303 61.111 23.51 0.00 0.00 2.69
278 279 1.669211 CGTCTTCTTCAACCTCGGGAC 60.669 57.143 0.00 0.00 0.00 4.46
279 280 0.601558 CGTCTTCTTCAACCTCGGGA 59.398 55.000 0.00 0.00 0.00 5.14
280 281 0.601558 TCGTCTTCTTCAACCTCGGG 59.398 55.000 0.00 0.00 0.00 5.14
281 282 2.094700 TGATCGTCTTCTTCAACCTCGG 60.095 50.000 0.00 0.00 0.00 4.63
282 283 3.217599 TGATCGTCTTCTTCAACCTCG 57.782 47.619 0.00 0.00 0.00 4.63
283 284 3.929610 CCTTGATCGTCTTCTTCAACCTC 59.070 47.826 0.00 0.00 0.00 3.85
284 285 3.866449 GCCTTGATCGTCTTCTTCAACCT 60.866 47.826 0.00 0.00 0.00 3.50
285 286 2.416893 GCCTTGATCGTCTTCTTCAACC 59.583 50.000 0.00 0.00 0.00 3.77
286 287 2.092838 CGCCTTGATCGTCTTCTTCAAC 59.907 50.000 0.00 0.00 0.00 3.18
287 288 2.029380 TCGCCTTGATCGTCTTCTTCAA 60.029 45.455 0.00 0.00 0.00 2.69
288 289 1.544246 TCGCCTTGATCGTCTTCTTCA 59.456 47.619 0.00 0.00 0.00 3.02
289 290 2.279582 TCGCCTTGATCGTCTTCTTC 57.720 50.000 0.00 0.00 0.00 2.87
290 291 2.969628 ATCGCCTTGATCGTCTTCTT 57.030 45.000 0.00 0.00 28.49 2.52
291 292 2.428890 AGAATCGCCTTGATCGTCTTCT 59.571 45.455 0.00 0.00 35.84 2.85
292 293 2.815478 AGAATCGCCTTGATCGTCTTC 58.185 47.619 0.00 0.00 35.84 2.87
293 294 2.969628 AGAATCGCCTTGATCGTCTT 57.030 45.000 0.00 0.00 35.84 3.01
294 295 2.688446 TGTAGAATCGCCTTGATCGTCT 59.312 45.455 0.00 0.00 35.84 4.18
295 296 3.079960 TGTAGAATCGCCTTGATCGTC 57.920 47.619 0.00 0.00 35.84 4.20
296 297 3.319405 AGATGTAGAATCGCCTTGATCGT 59.681 43.478 0.00 0.00 35.84 3.73
297 298 3.906998 AGATGTAGAATCGCCTTGATCG 58.093 45.455 0.00 0.00 35.84 3.69
298 299 5.292765 TGAAGATGTAGAATCGCCTTGATC 58.707 41.667 0.00 0.00 35.84 2.92
299 300 5.282055 TGAAGATGTAGAATCGCCTTGAT 57.718 39.130 0.00 0.00 39.67 2.57
300 301 4.736126 TGAAGATGTAGAATCGCCTTGA 57.264 40.909 0.00 0.00 0.00 3.02
301 302 5.998454 AATGAAGATGTAGAATCGCCTTG 57.002 39.130 0.00 0.00 0.00 3.61
302 303 6.183360 CCAAAATGAAGATGTAGAATCGCCTT 60.183 38.462 0.00 0.00 0.00 4.35
303 304 5.297776 CCAAAATGAAGATGTAGAATCGCCT 59.702 40.000 0.00 0.00 0.00 5.52
304 305 5.296780 TCCAAAATGAAGATGTAGAATCGCC 59.703 40.000 0.00 0.00 0.00 5.54
305 306 6.195165 GTCCAAAATGAAGATGTAGAATCGC 58.805 40.000 0.00 0.00 0.00 4.58
306 307 6.316140 TGGTCCAAAATGAAGATGTAGAATCG 59.684 38.462 0.00 0.00 0.00 3.34
307 308 7.630242 TGGTCCAAAATGAAGATGTAGAATC 57.370 36.000 0.00 0.00 0.00 2.52
308 309 8.057623 AGATGGTCCAAAATGAAGATGTAGAAT 58.942 33.333 0.00 0.00 0.00 2.40
309 310 7.337689 CAGATGGTCCAAAATGAAGATGTAGAA 59.662 37.037 0.00 0.00 0.00 2.10
310 311 6.825213 CAGATGGTCCAAAATGAAGATGTAGA 59.175 38.462 0.00 0.00 0.00 2.59
311 312 6.600822 ACAGATGGTCCAAAATGAAGATGTAG 59.399 38.462 0.00 0.00 0.00 2.74
312 313 6.484288 ACAGATGGTCCAAAATGAAGATGTA 58.516 36.000 0.00 0.00 0.00 2.29
313 314 5.327732 ACAGATGGTCCAAAATGAAGATGT 58.672 37.500 0.00 0.00 0.00 3.06
314 315 5.909621 ACAGATGGTCCAAAATGAAGATG 57.090 39.130 0.00 0.00 0.00 2.90
315 316 5.186409 CCAACAGATGGTCCAAAATGAAGAT 59.814 40.000 0.00 0.00 44.85 2.40
316 317 4.523943 CCAACAGATGGTCCAAAATGAAGA 59.476 41.667 0.00 0.00 44.85 2.87
317 318 4.813027 CCAACAGATGGTCCAAAATGAAG 58.187 43.478 0.00 0.00 44.85 3.02
318 319 4.870123 CCAACAGATGGTCCAAAATGAA 57.130 40.909 0.00 0.00 44.85 2.57
330 331 4.543692 CAAAAGAGCAACTCCAACAGATG 58.456 43.478 0.00 0.00 0.00 2.90
331 332 3.571401 CCAAAAGAGCAACTCCAACAGAT 59.429 43.478 0.00 0.00 0.00 2.90
332 333 2.951642 CCAAAAGAGCAACTCCAACAGA 59.048 45.455 0.00 0.00 0.00 3.41
333 334 2.951642 TCCAAAAGAGCAACTCCAACAG 59.048 45.455 0.00 0.00 0.00 3.16
334 335 2.687935 GTCCAAAAGAGCAACTCCAACA 59.312 45.455 0.00 0.00 0.00 3.33
335 336 2.034685 GGTCCAAAAGAGCAACTCCAAC 59.965 50.000 0.00 0.00 42.81 3.77
336 337 2.306847 GGTCCAAAAGAGCAACTCCAA 58.693 47.619 0.00 0.00 42.81 3.53
337 338 1.981256 GGTCCAAAAGAGCAACTCCA 58.019 50.000 0.00 0.00 42.81 3.86
344 345 4.021192 TCCAAATTGATGGTCCAAAAGAGC 60.021 41.667 0.00 0.00 41.46 4.09
345 346 5.473039 GTCCAAATTGATGGTCCAAAAGAG 58.527 41.667 0.00 0.00 41.46 2.85
346 347 4.283212 GGTCCAAATTGATGGTCCAAAAGA 59.717 41.667 0.00 0.00 44.93 2.52
347 348 4.568956 GGTCCAAATTGATGGTCCAAAAG 58.431 43.478 0.00 0.00 44.93 2.27
348 349 4.615588 GGTCCAAATTGATGGTCCAAAA 57.384 40.909 0.00 0.00 44.93 2.44
352 353 3.382546 CAGATGGTCCAAATTGATGGTCC 59.617 47.826 0.00 5.71 45.54 4.46
353 354 4.019174 ACAGATGGTCCAAATTGATGGTC 58.981 43.478 0.00 0.00 41.46 4.02
354 355 4.051661 ACAGATGGTCCAAATTGATGGT 57.948 40.909 0.00 0.00 41.46 3.55
355 356 4.382254 CCAACAGATGGTCCAAATTGATGG 60.382 45.833 12.44 12.44 44.85 3.51
356 357 4.751060 CCAACAGATGGTCCAAATTGATG 58.249 43.478 0.00 0.12 44.85 3.07
369 370 4.843220 AAAAGCTGAACTCCAACAGATG 57.157 40.909 0.00 0.00 36.38 2.90
390 391 2.045561 TGTGTTTTGGAGCTCCGAAA 57.954 45.000 35.12 35.12 44.84 3.46
391 392 2.270352 ATGTGTTTTGGAGCTCCGAA 57.730 45.000 28.68 28.68 39.43 4.30
392 393 2.270352 AATGTGTTTTGGAGCTCCGA 57.730 45.000 27.43 23.72 39.43 4.55
393 394 3.369546 AAAATGTGTTTTGGAGCTCCG 57.630 42.857 27.43 0.00 36.24 4.63
415 416 3.426615 AGATGTAAAATTTGGACCGCCA 58.573 40.909 0.00 0.00 44.17 5.69
416 417 4.421058 GAAGATGTAAAATTTGGACCGCC 58.579 43.478 0.00 0.00 0.00 6.13
417 418 4.095610 CGAAGATGTAAAATTTGGACCGC 58.904 43.478 0.00 0.00 0.00 5.68
418 419 5.539582 TCGAAGATGTAAAATTTGGACCG 57.460 39.130 0.00 0.00 0.00 4.79
419 420 8.647226 CAAAATCGAAGATGTAAAATTTGGACC 58.353 33.333 0.00 0.00 45.12 4.46
420 421 8.647226 CCAAAATCGAAGATGTAAAATTTGGAC 58.353 33.333 12.65 0.00 44.29 4.02
421 422 8.580720 TCCAAAATCGAAGATGTAAAATTTGGA 58.419 29.630 15.01 15.01 46.46 3.53
422 423 8.647226 GTCCAAAATCGAAGATGTAAAATTTGG 58.353 33.333 12.11 12.11 45.12 3.28
423 424 8.647226 GGTCCAAAATCGAAGATGTAAAATTTG 58.353 33.333 0.00 0.00 45.12 2.32
424 425 7.540745 CGGTCCAAAATCGAAGATGTAAAATTT 59.459 33.333 0.00 0.00 45.12 1.82
425 426 7.027161 CGGTCCAAAATCGAAGATGTAAAATT 58.973 34.615 0.00 0.00 45.12 1.82
426 427 6.551736 CGGTCCAAAATCGAAGATGTAAAAT 58.448 36.000 0.00 0.00 45.12 1.82
427 428 5.618195 GCGGTCCAAAATCGAAGATGTAAAA 60.618 40.000 0.00 0.00 45.12 1.52
428 429 4.142773 GCGGTCCAAAATCGAAGATGTAAA 60.143 41.667 0.00 0.00 45.12 2.01
429 430 3.372822 GCGGTCCAAAATCGAAGATGTAA 59.627 43.478 0.00 0.00 45.12 2.41
430 431 2.933906 GCGGTCCAAAATCGAAGATGTA 59.066 45.455 0.00 0.00 45.12 2.29
431 432 1.737793 GCGGTCCAAAATCGAAGATGT 59.262 47.619 0.00 0.00 45.12 3.06
432 433 1.064060 GGCGGTCCAAAATCGAAGATG 59.936 52.381 0.00 0.00 45.12 2.90
433 434 1.339631 TGGCGGTCCAAAATCGAAGAT 60.340 47.619 0.00 0.00 40.00 2.40
434 435 0.035598 TGGCGGTCCAAAATCGAAGA 59.964 50.000 0.00 0.00 39.99 2.87
435 436 2.550487 TGGCGGTCCAAAATCGAAG 58.450 52.632 0.00 0.00 39.99 3.79
436 437 4.802678 TGGCGGTCCAAAATCGAA 57.197 50.000 0.00 0.00 39.99 3.71
449 450 6.192480 CCAATAGATGGTCCAAAATTTGGCG 61.192 44.000 19.37 0.00 44.95 5.69
450 451 5.118286 CCAATAGATGGTCCAAAATTTGGC 58.882 41.667 19.37 13.88 44.95 4.52
475 476 4.877823 TCCATCACACAATGTAAGAGCATC 59.122 41.667 0.00 0.00 0.00 3.91
476 477 4.847198 TCCATCACACAATGTAAGAGCAT 58.153 39.130 0.00 0.00 0.00 3.79
477 478 4.256110 CTCCATCACACAATGTAAGAGCA 58.744 43.478 0.00 0.00 0.00 4.26
478 479 4.093998 CACTCCATCACACAATGTAAGAGC 59.906 45.833 0.00 0.00 0.00 4.09
479 480 5.121298 CACACTCCATCACACAATGTAAGAG 59.879 44.000 0.00 0.00 0.00 2.85
480 481 4.996758 CACACTCCATCACACAATGTAAGA 59.003 41.667 0.00 0.00 0.00 2.10
481 482 4.996758 TCACACTCCATCACACAATGTAAG 59.003 41.667 0.00 0.00 0.00 2.34
586 587 6.663093 ACTGAATACTGGAATTATTGCCACAA 59.337 34.615 0.00 0.00 0.00 3.33
587 588 6.186957 ACTGAATACTGGAATTATTGCCACA 58.813 36.000 0.00 0.00 0.00 4.17
588 589 6.699575 ACTGAATACTGGAATTATTGCCAC 57.300 37.500 0.00 0.00 0.00 5.01
589 590 7.831690 TGTAACTGAATACTGGAATTATTGCCA 59.168 33.333 0.00 0.00 0.00 4.92
610 611 5.236695 GTGGGTCTTCAAGAGAAAGTGTAAC 59.763 44.000 0.00 0.00 35.79 2.50
663 664 7.455058 ACCCAGAACACTATGTACAACAAATA 58.545 34.615 0.00 0.00 0.00 1.40
676 677 8.677865 TGGATTCTGTATGAACCCAGAACACTA 61.678 40.741 4.38 0.00 43.27 2.74
818 821 6.533012 CGAAAATACACAGACATCAGATCACT 59.467 38.462 0.00 0.00 0.00 3.41
841 844 3.994392 GGTCTCTTGCAAATTCTACACGA 59.006 43.478 0.00 0.00 0.00 4.35
929 932 9.577110 CACTTACTGGTTATAACGTATTTCTCA 57.423 33.333 9.46 0.00 0.00 3.27
930 933 8.538039 GCACTTACTGGTTATAACGTATTTCTC 58.462 37.037 9.46 0.00 0.00 2.87
933 936 7.820872 AGTGCACTTACTGGTTATAACGTATTT 59.179 33.333 15.25 0.00 0.00 1.40
935 938 6.870769 AGTGCACTTACTGGTTATAACGTAT 58.129 36.000 15.25 0.13 0.00 3.06
936 939 6.151648 AGAGTGCACTTACTGGTTATAACGTA 59.848 38.462 22.65 4.66 0.00 3.57
937 940 5.047519 AGAGTGCACTTACTGGTTATAACGT 60.048 40.000 22.65 5.58 0.00 3.99
938 941 5.408356 AGAGTGCACTTACTGGTTATAACG 58.592 41.667 22.65 0.00 0.00 3.18
939 942 6.092259 CCAAGAGTGCACTTACTGGTTATAAC 59.908 42.308 22.65 7.09 0.00 1.89
942 2460 4.286032 TCCAAGAGTGCACTTACTGGTTAT 59.714 41.667 28.14 5.39 0.00 1.89
955 2473 0.391793 GTGGCCTAGTCCAAGAGTGC 60.392 60.000 3.32 0.00 37.96 4.40
970 2488 3.117794 GTTTTGGGAACTTAAACGTGGC 58.882 45.455 0.00 0.00 0.00 5.01
1208 2726 1.590147 GTCGTCGTTGGGGATGAGT 59.410 57.895 0.00 0.00 32.85 3.41
1731 3250 4.421479 ACGAAGAGCACGCCGGAG 62.421 66.667 5.05 3.72 0.00 4.63
1732 3251 4.415332 GACGAAGAGCACGCCGGA 62.415 66.667 5.05 0.00 0.00 5.14
1755 3274 2.737376 GACGACGGAACACAGCCC 60.737 66.667 0.00 0.00 0.00 5.19
2028 3547 1.841277 ACCTGCCCCATGTAATCGTAA 59.159 47.619 0.00 0.00 0.00 3.18
2074 3593 1.752198 CTTCCACCGTGTTCCAGGA 59.248 57.895 0.00 0.00 0.00 3.86
2094 3613 1.222936 CGGCAGCTCCTTCTCCAAT 59.777 57.895 0.00 0.00 0.00 3.16
2172 3691 1.924731 CTTTCCCTTTCCACTTCCCC 58.075 55.000 0.00 0.00 0.00 4.81
2196 3715 2.276732 TCACTTTGCCTTCTCCCTTG 57.723 50.000 0.00 0.00 0.00 3.61
2541 4060 7.014134 TCTCAGCCAACAATTAATCTGAAACAA 59.986 33.333 4.44 0.00 31.24 2.83
2739 4258 1.804151 CACATCGACCCAACAACGAAT 59.196 47.619 0.00 0.00 39.38 3.34
3318 4862 7.197703 TCAACTATGTCAACGCTCGATATTAA 58.802 34.615 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.