Multiple sequence alignment - TraesCS5A01G133700

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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 TraesCS5A01G133700 chr5A 100.000 2264 0 0 1 2264 300954917 300957180 0 4181
1 TraesCS5A01G133700 chr5B 98.660 1791 18 1 474 2264 281832380 281830596 0 3169
2 TraesCS5A01G133700 chr5B 98.438 1792 21 5 474 2264 433002040 433000255 0 3147
3 TraesCS5A01G133700 chr5B 98.382 1792 22 2 474 2264 351469143 351467358 0 3142
4 TraesCS5A01G133700 chr5B 98.381 1791 23 4 474 2264 471294460 471292676 0 3142
5 TraesCS5A01G133700 chr5B 98.958 480 3 2 1 478 436483810 436483331 0 857
6 TraesCS5A01G133700 chr2A 98.548 1791 20 1 474 2264 728934145 728935929 0 3158
7 TraesCS5A01G133700 chr2A 99.167 480 2 2 1 478 148608228 148608707 0 863
8 TraesCS5A01G133700 chr2A 99.167 480 2 2 1 478 728940963 728940484 0 863
9 TraesCS5A01G133700 chr7A 98.548 1791 19 2 474 2264 16005485 16007268 0 3157
10 TraesCS5A01G133700 chr7B 98.270 1792 24 2 474 2264 102653085 102654870 0 3131
11 TraesCS5A01G133700 chr7B 98.213 1791 26 1 474 2264 133432180 133430396 0 3125
12 TraesCS5A01G133700 chr7B 98.958 480 3 2 1 478 102657565 102657086 0 857
13 TraesCS5A01G133700 chr7B 98.958 480 3 2 1 478 133424042 133424521 0 857
14 TraesCS5A01G133700 chr4B 98.270 1792 24 2 474 2264 649623640 649625425 0 3131
15 TraesCS5A01G133700 chr3B 99.167 480 2 2 1 478 798605344 798605823 0 863
16 TraesCS5A01G133700 chr3A 99.167 480 2 2 1 478 69954862 69954383 0 863
17 TraesCS5A01G133700 chr2B 99.167 480 2 2 1 478 770078268 770078747 0 863
18 TraesCS5A01G133700 chr1B 99.165 479 2 2 2 478 443571930 443571452 0 861


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 TraesCS5A01G133700 chr5A 300954917 300957180 2263 False 4181 4181 100.000 1 2264 1 chr5A.!!$F1 2263
1 TraesCS5A01G133700 chr5B 281830596 281832380 1784 True 3169 3169 98.660 474 2264 1 chr5B.!!$R1 1790
2 TraesCS5A01G133700 chr5B 433000255 433002040 1785 True 3147 3147 98.438 474 2264 1 chr5B.!!$R3 1790
3 TraesCS5A01G133700 chr5B 351467358 351469143 1785 True 3142 3142 98.382 474 2264 1 chr5B.!!$R2 1790
4 TraesCS5A01G133700 chr5B 471292676 471294460 1784 True 3142 3142 98.381 474 2264 1 chr5B.!!$R5 1790
5 TraesCS5A01G133700 chr2A 728934145 728935929 1784 False 3158 3158 98.548 474 2264 1 chr2A.!!$F2 1790
6 TraesCS5A01G133700 chr7A 16005485 16007268 1783 False 3157 3157 98.548 474 2264 1 chr7A.!!$F1 1790
7 TraesCS5A01G133700 chr7B 102653085 102654870 1785 False 3131 3131 98.270 474 2264 1 chr7B.!!$F1 1790
8 TraesCS5A01G133700 chr7B 133430396 133432180 1784 True 3125 3125 98.213 474 2264 1 chr7B.!!$R2 1790
9 TraesCS5A01G133700 chr4B 649623640 649625425 1785 False 3131 3131 98.270 474 2264 1 chr4B.!!$F1 1790

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
333 334 0.039618 TCCCCTCTTTGGTTGGATGC 59.96 55.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 1946 0.68908 TCTGGATCTGGGAGGCAGAC 60.689 60.0 0.0 0.0 0.0 3.51 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
19 20 4.742201 CACGGTCCCTGGCGTCTG 62.742 72.222 0.00 0.00 0.00 3.51
58 59 4.335647 CCTGCCCGTTGACCTGCT 62.336 66.667 0.00 0.00 0.00 4.24
59 60 3.052082 CTGCCCGTTGACCTGCTG 61.052 66.667 0.00 0.00 0.00 4.41
60 61 3.535629 CTGCCCGTTGACCTGCTGA 62.536 63.158 0.00 0.00 0.00 4.26
61 62 3.050275 GCCCGTTGACCTGCTGAC 61.050 66.667 0.00 0.00 0.00 3.51
62 63 2.738521 CCCGTTGACCTGCTGACG 60.739 66.667 0.00 0.00 35.44 4.35
63 64 2.029073 CCGTTGACCTGCTGACGT 59.971 61.111 0.00 0.00 33.95 4.34
64 65 2.310233 CCGTTGACCTGCTGACGTG 61.310 63.158 0.00 0.00 33.95 4.49
65 66 2.310233 CGTTGACCTGCTGACGTGG 61.310 63.158 0.00 0.00 0.00 4.94
66 67 2.280797 TTGACCTGCTGACGTGGC 60.281 61.111 0.00 0.00 0.00 5.01
67 68 3.100503 TTGACCTGCTGACGTGGCA 62.101 57.895 11.48 11.48 38.10 4.92
68 69 2.280797 GACCTGCTGACGTGGCAA 60.281 61.111 12.75 0.09 39.30 4.52
69 70 1.891919 GACCTGCTGACGTGGCAAA 60.892 57.895 12.75 0.00 39.30 3.68
70 71 1.845809 GACCTGCTGACGTGGCAAAG 61.846 60.000 12.75 9.98 39.30 2.77
71 72 2.620112 CCTGCTGACGTGGCAAAGG 61.620 63.158 12.75 8.52 39.30 3.11
72 73 2.594303 TGCTGACGTGGCAAAGGG 60.594 61.111 9.89 0.00 36.71 3.95
73 74 3.365265 GCTGACGTGGCAAAGGGG 61.365 66.667 0.00 0.00 0.00 4.79
74 75 3.365265 CTGACGTGGCAAAGGGGC 61.365 66.667 0.00 0.00 43.73 5.80
110 111 4.832608 GCGTCTGGCCCCGGTAAG 62.833 72.222 0.00 0.00 34.80 2.34
111 112 3.387947 CGTCTGGCCCCGGTAAGT 61.388 66.667 0.00 0.00 0.00 2.24
112 113 2.267961 GTCTGGCCCCGGTAAGTG 59.732 66.667 0.00 0.00 0.00 3.16
113 114 3.006728 TCTGGCCCCGGTAAGTGG 61.007 66.667 0.00 0.00 0.00 4.00
114 115 3.006728 CTGGCCCCGGTAAGTGGA 61.007 66.667 0.00 0.00 0.00 4.02
115 116 2.285818 TGGCCCCGGTAAGTGGAT 60.286 61.111 0.00 0.00 0.00 3.41
116 117 1.003182 TGGCCCCGGTAAGTGGATA 59.997 57.895 0.00 0.00 0.00 2.59
117 118 0.620990 TGGCCCCGGTAAGTGGATAA 60.621 55.000 0.00 0.00 0.00 1.75
118 119 0.179037 GGCCCCGGTAAGTGGATAAC 60.179 60.000 0.00 0.00 0.00 1.89
119 120 0.179037 GCCCCGGTAAGTGGATAACC 60.179 60.000 0.00 0.00 0.00 2.85
145 146 3.432335 CAGCCCACCCATCCCCAT 61.432 66.667 0.00 0.00 0.00 4.00
146 147 3.105928 AGCCCACCCATCCCCATC 61.106 66.667 0.00 0.00 0.00 3.51
147 148 3.105928 GCCCACCCATCCCCATCT 61.106 66.667 0.00 0.00 0.00 2.90
148 149 2.704424 GCCCACCCATCCCCATCTT 61.704 63.158 0.00 0.00 0.00 2.40
149 150 2.018447 CCCACCCATCCCCATCTTT 58.982 57.895 0.00 0.00 0.00 2.52
150 151 0.106015 CCCACCCATCCCCATCTTTC 60.106 60.000 0.00 0.00 0.00 2.62
151 152 0.929244 CCACCCATCCCCATCTTTCT 59.071 55.000 0.00 0.00 0.00 2.52
152 153 1.133668 CCACCCATCCCCATCTTTCTC 60.134 57.143 0.00 0.00 0.00 2.87
153 154 1.133668 CACCCATCCCCATCTTTCTCC 60.134 57.143 0.00 0.00 0.00 3.71
154 155 1.275238 ACCCATCCCCATCTTTCTCCT 60.275 52.381 0.00 0.00 0.00 3.69
155 156 1.144503 CCCATCCCCATCTTTCTCCTG 59.855 57.143 0.00 0.00 0.00 3.86
156 157 1.144503 CCATCCCCATCTTTCTCCTGG 59.855 57.143 0.00 0.00 0.00 4.45
157 158 0.849417 ATCCCCATCTTTCTCCTGGC 59.151 55.000 0.00 0.00 0.00 4.85
158 159 1.153086 CCCCATCTTTCTCCTGGCG 60.153 63.158 0.00 0.00 0.00 5.69
159 160 1.153086 CCCATCTTTCTCCTGGCGG 60.153 63.158 0.00 0.00 0.00 6.13
160 161 1.821332 CCATCTTTCTCCTGGCGGC 60.821 63.158 0.00 0.00 0.00 6.53
161 162 2.176273 CATCTTTCTCCTGGCGGCG 61.176 63.158 0.51 0.51 0.00 6.46
162 163 4.760047 TCTTTCTCCTGGCGGCGC 62.760 66.667 26.17 26.17 0.00 6.53
178 179 3.112709 GCACGACGAACAGAGGGC 61.113 66.667 0.00 0.00 0.00 5.19
179 180 2.651361 CACGACGAACAGAGGGCT 59.349 61.111 0.00 0.00 0.00 5.19
180 181 1.444553 CACGACGAACAGAGGGCTC 60.445 63.158 0.00 0.00 0.00 4.70
181 182 1.604023 ACGACGAACAGAGGGCTCT 60.604 57.895 0.00 0.00 41.37 4.09
190 191 1.594310 AGAGGGCTCTGTTCTTCGC 59.406 57.895 0.00 0.00 38.75 4.70
191 192 1.448717 GAGGGCTCTGTTCTTCGCC 60.449 63.158 0.00 0.00 41.75 5.54
193 194 2.436824 GGCTCTGTTCTTCGCCCC 60.437 66.667 0.00 0.00 36.56 5.80
194 195 2.665603 GCTCTGTTCTTCGCCCCT 59.334 61.111 0.00 0.00 0.00 4.79
195 196 1.003233 GCTCTGTTCTTCGCCCCTT 60.003 57.895 0.00 0.00 0.00 3.95
196 197 1.021920 GCTCTGTTCTTCGCCCCTTC 61.022 60.000 0.00 0.00 0.00 3.46
197 198 0.610687 CTCTGTTCTTCGCCCCTTCT 59.389 55.000 0.00 0.00 0.00 2.85
198 199 0.608640 TCTGTTCTTCGCCCCTTCTC 59.391 55.000 0.00 0.00 0.00 2.87
199 200 0.610687 CTGTTCTTCGCCCCTTCTCT 59.389 55.000 0.00 0.00 0.00 3.10
200 201 0.608640 TGTTCTTCGCCCCTTCTCTC 59.391 55.000 0.00 0.00 0.00 3.20
201 202 0.108089 GTTCTTCGCCCCTTCTCTCC 60.108 60.000 0.00 0.00 0.00 3.71
202 203 1.265454 TTCTTCGCCCCTTCTCTCCC 61.265 60.000 0.00 0.00 0.00 4.30
203 204 1.687493 CTTCGCCCCTTCTCTCCCT 60.687 63.158 0.00 0.00 0.00 4.20
204 205 1.681486 CTTCGCCCCTTCTCTCCCTC 61.681 65.000 0.00 0.00 0.00 4.30
205 206 3.157949 CGCCCCTTCTCTCCCTCC 61.158 72.222 0.00 0.00 0.00 4.30
206 207 2.770475 GCCCCTTCTCTCCCTCCC 60.770 72.222 0.00 0.00 0.00 4.30
207 208 2.787866 CCCCTTCTCTCCCTCCCA 59.212 66.667 0.00 0.00 0.00 4.37
208 209 1.690985 CCCCTTCTCTCCCTCCCAC 60.691 68.421 0.00 0.00 0.00 4.61
209 210 1.690985 CCCTTCTCTCCCTCCCACC 60.691 68.421 0.00 0.00 0.00 4.61
210 211 1.081092 CCTTCTCTCCCTCCCACCA 59.919 63.158 0.00 0.00 0.00 4.17
211 212 1.268283 CCTTCTCTCCCTCCCACCAC 61.268 65.000 0.00 0.00 0.00 4.16
212 213 1.229529 TTCTCTCCCTCCCACCACC 60.230 63.158 0.00 0.00 0.00 4.61
213 214 2.043527 TTCTCTCCCTCCCACCACCA 62.044 60.000 0.00 0.00 0.00 4.17
214 215 2.203938 TCTCCCTCCCACCACCAC 60.204 66.667 0.00 0.00 0.00 4.16
215 216 3.330720 CTCCCTCCCACCACCACC 61.331 72.222 0.00 0.00 0.00 4.61
216 217 4.995058 TCCCTCCCACCACCACCC 62.995 72.222 0.00 0.00 0.00 4.61
235 236 2.694397 CCCCCTTGATCTACTCCATCA 58.306 52.381 0.00 0.00 0.00 3.07
236 237 3.048600 CCCCCTTGATCTACTCCATCAA 58.951 50.000 0.00 0.00 37.82 2.57
237 238 3.181450 CCCCCTTGATCTACTCCATCAAC 60.181 52.174 0.00 0.00 35.71 3.18
238 239 3.181450 CCCCTTGATCTACTCCATCAACC 60.181 52.174 0.00 0.00 35.71 3.77
239 240 3.181450 CCCTTGATCTACTCCATCAACCC 60.181 52.174 0.00 0.00 35.71 4.11
240 241 3.181450 CCTTGATCTACTCCATCAACCCC 60.181 52.174 0.00 0.00 35.71 4.95
241 242 3.421394 TGATCTACTCCATCAACCCCT 57.579 47.619 0.00 0.00 0.00 4.79
242 243 3.309296 TGATCTACTCCATCAACCCCTC 58.691 50.000 0.00 0.00 0.00 4.30
243 244 2.940514 TCTACTCCATCAACCCCTCA 57.059 50.000 0.00 0.00 0.00 3.86
244 245 3.199442 TCTACTCCATCAACCCCTCAA 57.801 47.619 0.00 0.00 0.00 3.02
245 246 3.526899 TCTACTCCATCAACCCCTCAAA 58.473 45.455 0.00 0.00 0.00 2.69
246 247 2.586648 ACTCCATCAACCCCTCAAAC 57.413 50.000 0.00 0.00 0.00 2.93
247 248 2.065799 ACTCCATCAACCCCTCAAACT 58.934 47.619 0.00 0.00 0.00 2.66
248 249 2.040412 ACTCCATCAACCCCTCAAACTC 59.960 50.000 0.00 0.00 0.00 3.01
249 250 2.040278 CTCCATCAACCCCTCAAACTCA 59.960 50.000 0.00 0.00 0.00 3.41
250 251 2.162681 CCATCAACCCCTCAAACTCAC 58.837 52.381 0.00 0.00 0.00 3.51
251 252 2.488891 CCATCAACCCCTCAAACTCACA 60.489 50.000 0.00 0.00 0.00 3.58
252 253 2.638480 TCAACCCCTCAAACTCACAG 57.362 50.000 0.00 0.00 0.00 3.66
253 254 2.123589 TCAACCCCTCAAACTCACAGA 58.876 47.619 0.00 0.00 0.00 3.41
254 255 2.711009 TCAACCCCTCAAACTCACAGAT 59.289 45.455 0.00 0.00 0.00 2.90
255 256 3.077359 CAACCCCTCAAACTCACAGATC 58.923 50.000 0.00 0.00 0.00 2.75
256 257 1.276421 ACCCCTCAAACTCACAGATCG 59.724 52.381 0.00 0.00 0.00 3.69
257 258 1.406069 CCCCTCAAACTCACAGATCGG 60.406 57.143 0.00 0.00 0.00 4.18
258 259 1.550524 CCCTCAAACTCACAGATCGGA 59.449 52.381 0.00 0.00 0.00 4.55
259 260 2.611518 CCTCAAACTCACAGATCGGAC 58.388 52.381 0.00 0.00 0.00 4.79
260 261 2.611518 CTCAAACTCACAGATCGGACC 58.388 52.381 0.00 0.00 0.00 4.46
261 262 1.275291 TCAAACTCACAGATCGGACCC 59.725 52.381 0.00 0.00 0.00 4.46
262 263 0.613777 AAACTCACAGATCGGACCCC 59.386 55.000 0.00 0.00 0.00 4.95
263 264 1.265454 AACTCACAGATCGGACCCCC 61.265 60.000 0.00 0.00 0.00 5.40
279 280 2.967270 CCCCCAAGCTTCTTTGAGG 58.033 57.895 0.00 0.00 0.00 3.86
280 281 0.113190 CCCCCAAGCTTCTTTGAGGT 59.887 55.000 0.00 0.00 0.00 3.85
281 282 1.354368 CCCCCAAGCTTCTTTGAGGTA 59.646 52.381 0.00 0.00 0.00 3.08
282 283 2.024941 CCCCCAAGCTTCTTTGAGGTAT 60.025 50.000 0.00 0.00 0.00 2.73
283 284 3.564352 CCCCCAAGCTTCTTTGAGGTATT 60.564 47.826 0.00 0.00 0.00 1.89
284 285 3.696548 CCCCAAGCTTCTTTGAGGTATTC 59.303 47.826 0.00 0.00 0.00 1.75
285 286 4.568592 CCCCAAGCTTCTTTGAGGTATTCT 60.569 45.833 0.00 0.00 0.00 2.40
286 287 4.637977 CCCAAGCTTCTTTGAGGTATTCTC 59.362 45.833 0.00 0.00 42.74 2.87
287 288 4.637977 CCAAGCTTCTTTGAGGTATTCTCC 59.362 45.833 0.00 0.00 41.76 3.71
288 289 4.495690 AGCTTCTTTGAGGTATTCTCCC 57.504 45.455 0.00 0.00 41.76 4.30
289 290 3.201045 AGCTTCTTTGAGGTATTCTCCCC 59.799 47.826 0.00 0.00 41.76 4.81
290 291 3.685835 GCTTCTTTGAGGTATTCTCCCCC 60.686 52.174 0.00 0.00 41.76 5.40
291 292 3.214694 TCTTTGAGGTATTCTCCCCCA 57.785 47.619 0.00 0.00 41.76 4.96
292 293 3.747852 TCTTTGAGGTATTCTCCCCCAT 58.252 45.455 0.00 0.00 41.76 4.00
293 294 4.119155 TCTTTGAGGTATTCTCCCCCATT 58.881 43.478 0.00 0.00 41.76 3.16
294 295 4.166144 TCTTTGAGGTATTCTCCCCCATTC 59.834 45.833 0.00 0.00 41.76 2.67
295 296 2.418669 TGAGGTATTCTCCCCCATTCC 58.581 52.381 0.00 0.00 41.76 3.01
296 297 1.705745 GAGGTATTCTCCCCCATTCCC 59.294 57.143 0.00 0.00 36.52 3.97
297 298 1.301511 AGGTATTCTCCCCCATTCCCT 59.698 52.381 0.00 0.00 0.00 4.20
298 299 1.705745 GGTATTCTCCCCCATTCCCTC 59.294 57.143 0.00 0.00 0.00 4.30
299 300 1.705745 GTATTCTCCCCCATTCCCTCC 59.294 57.143 0.00 0.00 0.00 4.30
300 301 0.047802 ATTCTCCCCCATTCCCTCCA 59.952 55.000 0.00 0.00 0.00 3.86
301 302 0.178816 TTCTCCCCCATTCCCTCCAA 60.179 55.000 0.00 0.00 0.00 3.53
302 303 0.047802 TCTCCCCCATTCCCTCCAAT 59.952 55.000 0.00 0.00 0.00 3.16
303 304 0.936691 CTCCCCCATTCCCTCCAATT 59.063 55.000 0.00 0.00 0.00 2.32
304 305 1.291939 CTCCCCCATTCCCTCCAATTT 59.708 52.381 0.00 0.00 0.00 1.82
305 306 1.727525 TCCCCCATTCCCTCCAATTTT 59.272 47.619 0.00 0.00 0.00 1.82
306 307 2.115238 TCCCCCATTCCCTCCAATTTTT 59.885 45.455 0.00 0.00 0.00 1.94
327 328 5.506730 TTTTTGTTTTCCCCTCTTTGGTT 57.493 34.783 0.00 0.00 0.00 3.67
328 329 4.479786 TTTGTTTTCCCCTCTTTGGTTG 57.520 40.909 0.00 0.00 0.00 3.77
329 330 2.393646 TGTTTTCCCCTCTTTGGTTGG 58.606 47.619 0.00 0.00 0.00 3.77
330 331 2.023888 TGTTTTCCCCTCTTTGGTTGGA 60.024 45.455 0.00 0.00 0.00 3.53
331 332 3.239449 GTTTTCCCCTCTTTGGTTGGAT 58.761 45.455 0.00 0.00 0.00 3.41
332 333 2.603075 TTCCCCTCTTTGGTTGGATG 57.397 50.000 0.00 0.00 0.00 3.51
333 334 0.039618 TCCCCTCTTTGGTTGGATGC 59.960 55.000 0.00 0.00 0.00 3.91
334 335 0.251742 CCCCTCTTTGGTTGGATGCA 60.252 55.000 0.00 0.00 0.00 3.96
335 336 1.620524 CCCCTCTTTGGTTGGATGCAT 60.621 52.381 0.00 0.00 0.00 3.96
336 337 2.181975 CCCTCTTTGGTTGGATGCATT 58.818 47.619 0.00 0.00 0.00 3.56
337 338 3.364549 CCCTCTTTGGTTGGATGCATTA 58.635 45.455 0.00 0.00 0.00 1.90
338 339 3.962718 CCCTCTTTGGTTGGATGCATTAT 59.037 43.478 0.00 0.00 0.00 1.28
339 340 4.406649 CCCTCTTTGGTTGGATGCATTATT 59.593 41.667 0.00 0.00 0.00 1.40
340 341 5.452356 CCCTCTTTGGTTGGATGCATTATTC 60.452 44.000 0.00 0.00 0.00 1.75
341 342 5.127519 CCTCTTTGGTTGGATGCATTATTCA 59.872 40.000 0.00 0.00 0.00 2.57
342 343 6.351202 CCTCTTTGGTTGGATGCATTATTCAA 60.351 38.462 0.00 1.23 31.68 2.69
349 350 6.698008 TTGGATGCATTATTCAACACTAGG 57.302 37.500 0.00 0.00 29.04 3.02
350 351 5.754782 TGGATGCATTATTCAACACTAGGT 58.245 37.500 0.00 0.00 0.00 3.08
351 352 5.589855 TGGATGCATTATTCAACACTAGGTG 59.410 40.000 0.00 0.00 39.75 4.00
352 353 5.822519 GGATGCATTATTCAACACTAGGTGA 59.177 40.000 0.00 0.00 36.96 4.02
353 354 6.488006 GGATGCATTATTCAACACTAGGTGAT 59.512 38.462 0.00 0.00 36.96 3.06
354 355 6.682423 TGCATTATTCAACACTAGGTGATG 57.318 37.500 4.62 3.34 37.61 3.07
355 356 6.179756 TGCATTATTCAACACTAGGTGATGT 58.820 36.000 4.62 0.00 37.54 3.06
356 357 6.658816 TGCATTATTCAACACTAGGTGATGTT 59.341 34.615 4.62 0.00 39.63 2.71
357 358 7.826744 TGCATTATTCAACACTAGGTGATGTTA 59.173 33.333 4.62 0.00 36.92 2.41
358 359 8.338259 GCATTATTCAACACTAGGTGATGTTAG 58.662 37.037 4.62 0.00 36.92 2.34
359 360 9.599866 CATTATTCAACACTAGGTGATGTTAGA 57.400 33.333 4.62 0.00 36.92 2.10
361 362 9.599866 TTATTCAACACTAGGTGATGTTAGATG 57.400 33.333 4.62 0.00 36.92 2.90
362 363 6.850752 TCAACACTAGGTGATGTTAGATGA 57.149 37.500 4.62 0.00 36.92 2.92
363 364 6.867550 TCAACACTAGGTGATGTTAGATGAG 58.132 40.000 4.62 0.00 36.92 2.90
364 365 6.437477 TCAACACTAGGTGATGTTAGATGAGT 59.563 38.462 4.62 0.00 36.92 3.41
365 366 7.614192 TCAACACTAGGTGATGTTAGATGAGTA 59.386 37.037 4.62 0.00 36.92 2.59
366 367 7.575414 ACACTAGGTGATGTTAGATGAGTAG 57.425 40.000 4.62 0.00 36.96 2.57
367 368 7.347252 ACACTAGGTGATGTTAGATGAGTAGA 58.653 38.462 4.62 0.00 36.96 2.59
368 369 8.001875 ACACTAGGTGATGTTAGATGAGTAGAT 58.998 37.037 4.62 0.00 36.96 1.98
369 370 8.296000 CACTAGGTGATGTTAGATGAGTAGATG 58.704 40.741 0.00 0.00 35.23 2.90
370 371 6.662865 AGGTGATGTTAGATGAGTAGATGG 57.337 41.667 0.00 0.00 0.00 3.51
371 372 6.139671 AGGTGATGTTAGATGAGTAGATGGT 58.860 40.000 0.00 0.00 0.00 3.55
372 373 6.613271 AGGTGATGTTAGATGAGTAGATGGTT 59.387 38.462 0.00 0.00 0.00 3.67
373 374 7.126421 AGGTGATGTTAGATGAGTAGATGGTTT 59.874 37.037 0.00 0.00 0.00 3.27
374 375 7.439655 GGTGATGTTAGATGAGTAGATGGTTTC 59.560 40.741 0.00 0.00 0.00 2.78
375 376 8.200792 GTGATGTTAGATGAGTAGATGGTTTCT 58.799 37.037 0.00 0.00 38.57 2.52
376 377 8.762645 TGATGTTAGATGAGTAGATGGTTTCTT 58.237 33.333 0.00 0.00 35.79 2.52
425 426 9.533831 TTGATAGATGATTAGGTATGCAGTAGA 57.466 33.333 0.00 0.00 0.00 2.59
426 427 9.706529 TGATAGATGATTAGGTATGCAGTAGAT 57.293 33.333 0.00 0.00 0.00 1.98
427 428 9.964303 GATAGATGATTAGGTATGCAGTAGATG 57.036 37.037 0.00 0.00 0.00 2.90
428 429 9.706529 ATAGATGATTAGGTATGCAGTAGATGA 57.293 33.333 0.00 0.00 0.00 2.92
429 430 8.606754 AGATGATTAGGTATGCAGTAGATGAT 57.393 34.615 0.00 0.00 0.00 2.45
430 431 8.476447 AGATGATTAGGTATGCAGTAGATGATG 58.524 37.037 0.00 0.00 0.00 3.07
431 432 7.544804 TGATTAGGTATGCAGTAGATGATGT 57.455 36.000 0.00 0.00 0.00 3.06
432 433 7.381323 TGATTAGGTATGCAGTAGATGATGTG 58.619 38.462 0.00 0.00 0.00 3.21
433 434 6.731292 TTAGGTATGCAGTAGATGATGTGT 57.269 37.500 0.00 0.00 0.00 3.72
434 435 7.833285 TTAGGTATGCAGTAGATGATGTGTA 57.167 36.000 0.00 0.00 0.00 2.90
435 436 6.338214 AGGTATGCAGTAGATGATGTGTAG 57.662 41.667 0.00 0.00 0.00 2.74
436 437 5.835819 AGGTATGCAGTAGATGATGTGTAGT 59.164 40.000 0.00 0.00 0.00 2.73
437 438 6.325028 AGGTATGCAGTAGATGATGTGTAGTT 59.675 38.462 0.00 0.00 0.00 2.24
438 439 6.422100 GGTATGCAGTAGATGATGTGTAGTTG 59.578 42.308 0.00 0.00 0.00 3.16
439 440 5.659440 TGCAGTAGATGATGTGTAGTTGA 57.341 39.130 0.00 0.00 0.00 3.18
440 441 6.036577 TGCAGTAGATGATGTGTAGTTGAA 57.963 37.500 0.00 0.00 0.00 2.69
441 442 5.869344 TGCAGTAGATGATGTGTAGTTGAAC 59.131 40.000 0.00 0.00 0.00 3.18
442 443 5.869344 GCAGTAGATGATGTGTAGTTGAACA 59.131 40.000 0.00 0.00 0.00 3.18
443 444 6.536582 GCAGTAGATGATGTGTAGTTGAACAT 59.463 38.462 0.00 0.00 39.69 2.71
444 445 7.465111 GCAGTAGATGATGTGTAGTTGAACATG 60.465 40.741 0.00 0.00 37.15 3.21
445 446 7.547019 CAGTAGATGATGTGTAGTTGAACATGT 59.453 37.037 0.00 0.00 37.15 3.21
446 447 8.749354 AGTAGATGATGTGTAGTTGAACATGTA 58.251 33.333 0.00 0.00 37.15 2.29
447 448 9.025020 GTAGATGATGTGTAGTTGAACATGTAG 57.975 37.037 0.00 0.00 37.15 2.74
448 449 7.044181 AGATGATGTGTAGTTGAACATGTAGG 58.956 38.462 0.00 0.00 37.15 3.18
449 450 6.109156 TGATGTGTAGTTGAACATGTAGGT 57.891 37.500 0.00 0.00 37.15 3.08
450 451 7.234661 TGATGTGTAGTTGAACATGTAGGTA 57.765 36.000 0.00 0.00 37.15 3.08
451 452 7.672240 TGATGTGTAGTTGAACATGTAGGTAA 58.328 34.615 0.00 0.00 37.15 2.85
452 453 8.151596 TGATGTGTAGTTGAACATGTAGGTAAA 58.848 33.333 0.00 0.00 37.15 2.01
453 454 8.911918 ATGTGTAGTTGAACATGTAGGTAAAA 57.088 30.769 0.00 0.00 35.71 1.52
454 455 8.911918 TGTGTAGTTGAACATGTAGGTAAAAT 57.088 30.769 0.00 0.00 0.00 1.82
455 456 9.344772 TGTGTAGTTGAACATGTAGGTAAAATT 57.655 29.630 0.00 0.00 0.00 1.82
463 464 9.233649 TGAACATGTAGGTAAAATTAATTCGGT 57.766 29.630 0.00 0.00 0.00 4.69
469 470 9.680315 TGTAGGTAAAATTAATTCGGTTTTGTG 57.320 29.630 0.10 0.00 0.00 3.33
470 471 9.681692 GTAGGTAAAATTAATTCGGTTTTGTGT 57.318 29.630 0.10 0.00 0.00 3.72
1195 1198 5.104277 TGGACAGAAGGTAGAAGGTTTTTCA 60.104 40.000 0.00 0.00 0.00 2.69
1802 1805 6.209361 GTCATTCGAGACTAGTTGATATGCA 58.791 40.000 0.00 0.00 35.65 3.96
1945 1948 4.152625 GTGCATGGCGTCTGCGTC 62.153 66.667 6.90 0.00 42.62 5.19
1946 1949 4.377708 TGCATGGCGTCTGCGTCT 62.378 61.111 6.90 0.00 44.07 4.18
1947 1950 3.857854 GCATGGCGTCTGCGTCTG 61.858 66.667 0.00 0.00 44.07 3.51
1948 1951 3.857854 CATGGCGTCTGCGTCTGC 61.858 66.667 0.00 0.00 44.07 4.26
2115 2118 1.208614 GTCTGGCTTGCTTTGCTCG 59.791 57.895 0.00 0.00 0.00 5.03
2201 2204 2.060980 GCCTCCCAGATCCAGACGT 61.061 63.158 0.00 0.00 0.00 4.34
2232 2235 1.656441 CGTCTGGCTTGCTTTGCTT 59.344 52.632 0.00 0.00 0.00 3.91
2234 2237 1.470098 CGTCTGGCTTGCTTTGCTTAT 59.530 47.619 0.00 0.00 0.00 1.73
2250 2253 2.681976 GCTTATGCAGGTGACCAGACAT 60.682 50.000 3.63 6.83 39.41 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.742201 CAGACGCCAGGGACCGTG 62.742 72.222 7.23 7.23 37.87 4.94
41 42 4.335647 AGCAGGTCAACGGGCAGG 62.336 66.667 0.00 0.00 0.00 4.85
42 43 3.052082 CAGCAGGTCAACGGGCAG 61.052 66.667 0.00 0.00 0.00 4.85
43 44 3.555324 TCAGCAGGTCAACGGGCA 61.555 61.111 0.00 0.00 0.00 5.36
44 45 3.050275 GTCAGCAGGTCAACGGGC 61.050 66.667 0.00 0.00 0.00 6.13
45 46 2.738521 CGTCAGCAGGTCAACGGG 60.739 66.667 0.00 0.00 0.00 5.28
46 47 2.029073 ACGTCAGCAGGTCAACGG 59.971 61.111 8.49 0.00 39.35 4.44
47 48 2.310233 CCACGTCAGCAGGTCAACG 61.310 63.158 3.15 3.15 40.77 4.10
48 49 2.607892 GCCACGTCAGCAGGTCAAC 61.608 63.158 2.25 0.00 0.00 3.18
49 50 2.280797 GCCACGTCAGCAGGTCAA 60.281 61.111 2.25 0.00 0.00 3.18
50 51 2.601194 TTTGCCACGTCAGCAGGTCA 62.601 55.000 9.53 0.00 42.17 4.02
51 52 1.845809 CTTTGCCACGTCAGCAGGTC 61.846 60.000 9.53 0.00 42.17 3.85
52 53 1.893808 CTTTGCCACGTCAGCAGGT 60.894 57.895 9.53 0.00 42.17 4.00
53 54 2.620112 CCTTTGCCACGTCAGCAGG 61.620 63.158 9.53 5.63 42.17 4.85
54 55 2.620112 CCCTTTGCCACGTCAGCAG 61.620 63.158 9.53 0.58 42.17 4.24
55 56 2.594303 CCCTTTGCCACGTCAGCA 60.594 61.111 5.70 5.70 38.81 4.41
56 57 3.365265 CCCCTTTGCCACGTCAGC 61.365 66.667 0.04 0.04 0.00 4.26
57 58 3.365265 GCCCCTTTGCCACGTCAG 61.365 66.667 0.00 0.00 0.00 3.51
93 94 4.832608 CTTACCGGGGCCAGACGC 62.833 72.222 6.32 0.00 0.00 5.19
94 95 3.387947 ACTTACCGGGGCCAGACG 61.388 66.667 6.32 5.83 0.00 4.18
95 96 2.267961 CACTTACCGGGGCCAGAC 59.732 66.667 6.32 0.00 0.00 3.51
96 97 2.833151 ATCCACTTACCGGGGCCAGA 62.833 60.000 6.32 0.00 0.00 3.86
97 98 1.052124 TATCCACTTACCGGGGCCAG 61.052 60.000 6.32 0.00 0.00 4.85
98 99 0.620990 TTATCCACTTACCGGGGCCA 60.621 55.000 6.32 0.00 0.00 5.36
99 100 0.179037 GTTATCCACTTACCGGGGCC 60.179 60.000 6.32 0.00 0.00 5.80
100 101 0.179037 GGTTATCCACTTACCGGGGC 60.179 60.000 6.32 0.00 0.00 5.80
105 106 1.485032 CGCGCGGTTATCCACTTACC 61.485 60.000 24.84 0.00 0.00 2.85
106 107 1.485032 CCGCGCGGTTATCCACTTAC 61.485 60.000 39.71 0.00 0.00 2.34
107 108 1.227031 CCGCGCGGTTATCCACTTA 60.227 57.895 39.71 0.00 0.00 2.24
108 109 2.510691 CCGCGCGGTTATCCACTT 60.511 61.111 39.71 0.00 0.00 3.16
109 110 4.524318 CCCGCGCGGTTATCCACT 62.524 66.667 43.12 0.00 0.00 4.00
128 129 3.432335 ATGGGGATGGGTGGGCTG 61.432 66.667 0.00 0.00 0.00 4.85
129 130 3.105928 GATGGGGATGGGTGGGCT 61.106 66.667 0.00 0.00 0.00 5.19
130 131 2.242408 AAAGATGGGGATGGGTGGGC 62.242 60.000 0.00 0.00 0.00 5.36
131 132 0.106015 GAAAGATGGGGATGGGTGGG 60.106 60.000 0.00 0.00 0.00 4.61
132 133 0.929244 AGAAAGATGGGGATGGGTGG 59.071 55.000 0.00 0.00 0.00 4.61
133 134 1.133668 GGAGAAAGATGGGGATGGGTG 60.134 57.143 0.00 0.00 0.00 4.61
134 135 1.226311 GGAGAAAGATGGGGATGGGT 58.774 55.000 0.00 0.00 0.00 4.51
135 136 1.144503 CAGGAGAAAGATGGGGATGGG 59.855 57.143 0.00 0.00 0.00 4.00
136 137 1.144503 CCAGGAGAAAGATGGGGATGG 59.855 57.143 0.00 0.00 0.00 3.51
137 138 1.478288 GCCAGGAGAAAGATGGGGATG 60.478 57.143 0.00 0.00 34.52 3.51
138 139 0.849417 GCCAGGAGAAAGATGGGGAT 59.151 55.000 0.00 0.00 34.52 3.85
139 140 1.626356 CGCCAGGAGAAAGATGGGGA 61.626 60.000 1.59 0.00 46.86 4.81
140 141 1.153086 CGCCAGGAGAAAGATGGGG 60.153 63.158 0.00 0.00 40.16 4.96
141 142 1.153086 CCGCCAGGAGAAAGATGGG 60.153 63.158 0.00 0.00 41.02 4.00
142 143 1.821332 GCCGCCAGGAGAAAGATGG 60.821 63.158 0.00 0.00 41.02 3.51
143 144 2.176273 CGCCGCCAGGAGAAAGATG 61.176 63.158 0.00 0.00 39.96 2.90
144 145 2.187946 CGCCGCCAGGAGAAAGAT 59.812 61.111 0.00 0.00 39.96 2.40
145 146 4.760047 GCGCCGCCAGGAGAAAGA 62.760 66.667 0.00 0.00 39.96 2.52
158 159 3.470567 CTCTGTTCGTCGTGCGCC 61.471 66.667 4.18 0.00 41.07 6.53
159 160 3.470567 CCTCTGTTCGTCGTGCGC 61.471 66.667 0.00 0.00 41.07 6.09
160 161 2.805353 CCCTCTGTTCGTCGTGCG 60.805 66.667 0.00 0.00 43.01 5.34
161 162 3.112709 GCCCTCTGTTCGTCGTGC 61.113 66.667 0.00 0.00 0.00 5.34
162 163 1.444553 GAGCCCTCTGTTCGTCGTG 60.445 63.158 0.00 0.00 0.00 4.35
163 164 1.604023 AGAGCCCTCTGTTCGTCGT 60.604 57.895 0.00 0.00 38.75 4.34
164 165 3.279183 AGAGCCCTCTGTTCGTCG 58.721 61.111 0.00 0.00 38.75 5.12
172 173 1.594310 GCGAAGAACAGAGCCCTCT 59.406 57.895 0.00 0.00 41.37 3.69
173 174 1.448717 GGCGAAGAACAGAGCCCTC 60.449 63.158 0.00 0.00 43.54 4.30
174 175 2.665603 GGCGAAGAACAGAGCCCT 59.334 61.111 0.00 0.00 43.54 5.19
177 178 1.003233 AAGGGGCGAAGAACAGAGC 60.003 57.895 0.00 0.00 0.00 4.09
178 179 0.610687 AGAAGGGGCGAAGAACAGAG 59.389 55.000 0.00 0.00 0.00 3.35
179 180 0.608640 GAGAAGGGGCGAAGAACAGA 59.391 55.000 0.00 0.00 0.00 3.41
180 181 0.610687 AGAGAAGGGGCGAAGAACAG 59.389 55.000 0.00 0.00 0.00 3.16
181 182 0.608640 GAGAGAAGGGGCGAAGAACA 59.391 55.000 0.00 0.00 0.00 3.18
182 183 0.108089 GGAGAGAAGGGGCGAAGAAC 60.108 60.000 0.00 0.00 0.00 3.01
183 184 1.265454 GGGAGAGAAGGGGCGAAGAA 61.265 60.000 0.00 0.00 0.00 2.52
184 185 1.686110 GGGAGAGAAGGGGCGAAGA 60.686 63.158 0.00 0.00 0.00 2.87
185 186 1.681486 GAGGGAGAGAAGGGGCGAAG 61.681 65.000 0.00 0.00 0.00 3.79
186 187 1.686110 GAGGGAGAGAAGGGGCGAA 60.686 63.158 0.00 0.00 0.00 4.70
187 188 2.042843 GAGGGAGAGAAGGGGCGA 60.043 66.667 0.00 0.00 0.00 5.54
188 189 3.157949 GGAGGGAGAGAAGGGGCG 61.158 72.222 0.00 0.00 0.00 6.13
189 190 2.770475 GGGAGGGAGAGAAGGGGC 60.770 72.222 0.00 0.00 0.00 5.80
190 191 1.690985 GTGGGAGGGAGAGAAGGGG 60.691 68.421 0.00 0.00 0.00 4.79
191 192 1.690985 GGTGGGAGGGAGAGAAGGG 60.691 68.421 0.00 0.00 0.00 3.95
192 193 1.081092 TGGTGGGAGGGAGAGAAGG 59.919 63.158 0.00 0.00 0.00 3.46
193 194 1.268283 GGTGGTGGGAGGGAGAGAAG 61.268 65.000 0.00 0.00 0.00 2.85
194 195 1.229529 GGTGGTGGGAGGGAGAGAA 60.230 63.158 0.00 0.00 0.00 2.87
195 196 2.450243 GGTGGTGGGAGGGAGAGA 59.550 66.667 0.00 0.00 0.00 3.10
196 197 2.122729 TGGTGGTGGGAGGGAGAG 59.877 66.667 0.00 0.00 0.00 3.20
197 198 2.203938 GTGGTGGTGGGAGGGAGA 60.204 66.667 0.00 0.00 0.00 3.71
198 199 3.330720 GGTGGTGGTGGGAGGGAG 61.331 72.222 0.00 0.00 0.00 4.30
199 200 4.995058 GGGTGGTGGTGGGAGGGA 62.995 72.222 0.00 0.00 0.00 4.20
215 216 2.694397 TGATGGAGTAGATCAAGGGGG 58.306 52.381 0.00 0.00 0.00 5.40
216 217 3.181450 GGTTGATGGAGTAGATCAAGGGG 60.181 52.174 0.00 0.00 39.83 4.79
217 218 3.181450 GGGTTGATGGAGTAGATCAAGGG 60.181 52.174 0.00 0.00 39.83 3.95
218 219 3.181450 GGGGTTGATGGAGTAGATCAAGG 60.181 52.174 0.00 0.00 39.83 3.61
219 220 3.713764 AGGGGTTGATGGAGTAGATCAAG 59.286 47.826 0.00 0.00 39.83 3.02
220 221 3.711704 GAGGGGTTGATGGAGTAGATCAA 59.288 47.826 0.00 0.00 37.46 2.57
221 222 3.309296 GAGGGGTTGATGGAGTAGATCA 58.691 50.000 0.00 0.00 0.00 2.92
222 223 3.309296 TGAGGGGTTGATGGAGTAGATC 58.691 50.000 0.00 0.00 0.00 2.75
223 224 3.421394 TGAGGGGTTGATGGAGTAGAT 57.579 47.619 0.00 0.00 0.00 1.98
224 225 2.940514 TGAGGGGTTGATGGAGTAGA 57.059 50.000 0.00 0.00 0.00 2.59
225 226 3.264450 AGTTTGAGGGGTTGATGGAGTAG 59.736 47.826 0.00 0.00 0.00 2.57
226 227 3.256704 AGTTTGAGGGGTTGATGGAGTA 58.743 45.455 0.00 0.00 0.00 2.59
227 228 2.040412 GAGTTTGAGGGGTTGATGGAGT 59.960 50.000 0.00 0.00 0.00 3.85
228 229 2.040278 TGAGTTTGAGGGGTTGATGGAG 59.960 50.000 0.00 0.00 0.00 3.86
229 230 2.061848 TGAGTTTGAGGGGTTGATGGA 58.938 47.619 0.00 0.00 0.00 3.41
230 231 2.162681 GTGAGTTTGAGGGGTTGATGG 58.837 52.381 0.00 0.00 0.00 3.51
231 232 2.816087 CTGTGAGTTTGAGGGGTTGATG 59.184 50.000 0.00 0.00 0.00 3.07
232 233 2.711009 TCTGTGAGTTTGAGGGGTTGAT 59.289 45.455 0.00 0.00 0.00 2.57
233 234 2.123589 TCTGTGAGTTTGAGGGGTTGA 58.876 47.619 0.00 0.00 0.00 3.18
234 235 2.638480 TCTGTGAGTTTGAGGGGTTG 57.362 50.000 0.00 0.00 0.00 3.77
235 236 2.289694 CGATCTGTGAGTTTGAGGGGTT 60.290 50.000 0.00 0.00 0.00 4.11
236 237 1.276421 CGATCTGTGAGTTTGAGGGGT 59.724 52.381 0.00 0.00 0.00 4.95
237 238 1.406069 CCGATCTGTGAGTTTGAGGGG 60.406 57.143 0.00 0.00 0.00 4.79
238 239 1.550524 TCCGATCTGTGAGTTTGAGGG 59.449 52.381 0.00 0.00 0.00 4.30
239 240 2.611518 GTCCGATCTGTGAGTTTGAGG 58.388 52.381 0.00 0.00 0.00 3.86
240 241 2.611518 GGTCCGATCTGTGAGTTTGAG 58.388 52.381 0.00 0.00 0.00 3.02
241 242 1.275291 GGGTCCGATCTGTGAGTTTGA 59.725 52.381 0.00 0.00 0.00 2.69
242 243 1.676014 GGGGTCCGATCTGTGAGTTTG 60.676 57.143 0.00 0.00 0.00 2.93
243 244 0.613777 GGGGTCCGATCTGTGAGTTT 59.386 55.000 0.00 0.00 0.00 2.66
244 245 1.265454 GGGGGTCCGATCTGTGAGTT 61.265 60.000 0.00 0.00 0.00 3.01
245 246 1.686110 GGGGGTCCGATCTGTGAGT 60.686 63.158 0.00 0.00 0.00 3.41
246 247 3.221222 GGGGGTCCGATCTGTGAG 58.779 66.667 0.00 0.00 0.00 3.51
261 262 2.967270 CCTCAAAGAAGCTTGGGGG 58.033 57.895 2.10 0.00 42.46 5.40
263 264 4.593956 AGAATACCTCAAAGAAGCTTGGG 58.406 43.478 2.10 0.00 0.00 4.12
264 265 4.637977 GGAGAATACCTCAAAGAAGCTTGG 59.362 45.833 2.10 0.00 43.76 3.61
265 266 4.637977 GGGAGAATACCTCAAAGAAGCTTG 59.362 45.833 2.10 0.00 43.76 4.01
266 267 4.324641 GGGGAGAATACCTCAAAGAAGCTT 60.325 45.833 0.00 0.00 43.76 3.74
267 268 3.201045 GGGGAGAATACCTCAAAGAAGCT 59.799 47.826 0.00 0.00 43.76 3.74
268 269 3.546724 GGGGAGAATACCTCAAAGAAGC 58.453 50.000 0.00 0.00 43.76 3.86
269 270 3.523564 TGGGGGAGAATACCTCAAAGAAG 59.476 47.826 0.00 0.00 43.76 2.85
270 271 3.537337 TGGGGGAGAATACCTCAAAGAA 58.463 45.455 0.00 0.00 43.76 2.52
271 272 3.214694 TGGGGGAGAATACCTCAAAGA 57.785 47.619 0.00 0.00 43.76 2.52
272 273 4.464947 GAATGGGGGAGAATACCTCAAAG 58.535 47.826 0.00 0.00 42.85 2.77
273 274 3.204382 GGAATGGGGGAGAATACCTCAAA 59.796 47.826 0.00 0.00 42.85 2.69
274 275 2.783510 GGAATGGGGGAGAATACCTCAA 59.216 50.000 0.00 0.00 42.85 3.02
275 276 2.418669 GGAATGGGGGAGAATACCTCA 58.581 52.381 0.00 0.00 43.95 3.86
276 277 1.705745 GGGAATGGGGGAGAATACCTC 59.294 57.143 0.00 0.00 41.22 3.85
277 278 1.301511 AGGGAATGGGGGAGAATACCT 59.698 52.381 0.00 0.00 0.00 3.08
278 279 1.705745 GAGGGAATGGGGGAGAATACC 59.294 57.143 0.00 0.00 0.00 2.73
279 280 1.705745 GGAGGGAATGGGGGAGAATAC 59.294 57.143 0.00 0.00 0.00 1.89
280 281 1.299942 TGGAGGGAATGGGGGAGAATA 59.700 52.381 0.00 0.00 0.00 1.75
281 282 0.047802 TGGAGGGAATGGGGGAGAAT 59.952 55.000 0.00 0.00 0.00 2.40
282 283 0.178816 TTGGAGGGAATGGGGGAGAA 60.179 55.000 0.00 0.00 0.00 2.87
283 284 0.047802 ATTGGAGGGAATGGGGGAGA 59.952 55.000 0.00 0.00 0.00 3.71
284 285 0.936691 AATTGGAGGGAATGGGGGAG 59.063 55.000 0.00 0.00 0.00 4.30
285 286 1.403089 AAATTGGAGGGAATGGGGGA 58.597 50.000 0.00 0.00 0.00 4.81
286 287 2.268796 AAAATTGGAGGGAATGGGGG 57.731 50.000 0.00 0.00 0.00 5.40
305 306 5.249420 CAACCAAAGAGGGGAAAACAAAAA 58.751 37.500 0.00 0.00 43.89 1.94
306 307 4.323868 CCAACCAAAGAGGGGAAAACAAAA 60.324 41.667 0.00 0.00 43.89 2.44
307 308 3.198853 CCAACCAAAGAGGGGAAAACAAA 59.801 43.478 0.00 0.00 43.89 2.83
308 309 2.769095 CCAACCAAAGAGGGGAAAACAA 59.231 45.455 0.00 0.00 43.89 2.83
309 310 2.023888 TCCAACCAAAGAGGGGAAAACA 60.024 45.455 0.00 0.00 43.89 2.83
310 311 2.673258 TCCAACCAAAGAGGGGAAAAC 58.327 47.619 0.00 0.00 43.89 2.43
311 312 3.238597 CATCCAACCAAAGAGGGGAAAA 58.761 45.455 0.00 0.00 43.89 2.29
312 313 2.888212 CATCCAACCAAAGAGGGGAAA 58.112 47.619 0.00 0.00 43.89 3.13
313 314 1.549950 GCATCCAACCAAAGAGGGGAA 60.550 52.381 0.00 0.00 43.89 3.97
314 315 0.039618 GCATCCAACCAAAGAGGGGA 59.960 55.000 0.00 0.00 43.89 4.81
315 316 0.251742 TGCATCCAACCAAAGAGGGG 60.252 55.000 0.00 0.00 43.89 4.79
316 317 1.856629 ATGCATCCAACCAAAGAGGG 58.143 50.000 0.00 0.00 43.89 4.30
317 318 5.127519 TGAATAATGCATCCAACCAAAGAGG 59.872 40.000 0.00 0.00 45.67 3.69
318 319 6.211587 TGAATAATGCATCCAACCAAAGAG 57.788 37.500 0.00 0.00 0.00 2.85
319 320 6.014755 TGTTGAATAATGCATCCAACCAAAGA 60.015 34.615 21.04 8.32 37.04 2.52
320 321 6.091169 GTGTTGAATAATGCATCCAACCAAAG 59.909 38.462 21.04 0.00 37.04 2.77
321 322 5.931146 GTGTTGAATAATGCATCCAACCAAA 59.069 36.000 21.04 8.79 37.04 3.28
322 323 5.245751 AGTGTTGAATAATGCATCCAACCAA 59.754 36.000 21.04 11.81 37.04 3.67
323 324 4.771577 AGTGTTGAATAATGCATCCAACCA 59.228 37.500 21.04 12.46 37.04 3.67
324 325 5.329035 AGTGTTGAATAATGCATCCAACC 57.671 39.130 21.04 15.63 37.04 3.77
325 326 6.095440 ACCTAGTGTTGAATAATGCATCCAAC 59.905 38.462 18.91 18.91 38.00 3.77
326 327 6.095300 CACCTAGTGTTGAATAATGCATCCAA 59.905 38.462 0.00 0.00 0.00 3.53
327 328 5.589855 CACCTAGTGTTGAATAATGCATCCA 59.410 40.000 0.00 0.00 0.00 3.41
328 329 5.822519 TCACCTAGTGTTGAATAATGCATCC 59.177 40.000 0.00 0.00 34.79 3.51
329 330 6.925610 TCACCTAGTGTTGAATAATGCATC 57.074 37.500 0.00 0.00 34.79 3.91
330 331 6.830324 ACATCACCTAGTGTTGAATAATGCAT 59.170 34.615 11.65 0.00 36.91 3.96
331 332 6.179756 ACATCACCTAGTGTTGAATAATGCA 58.820 36.000 11.65 0.00 36.91 3.96
332 333 6.683974 ACATCACCTAGTGTTGAATAATGC 57.316 37.500 11.65 0.00 36.91 3.56
333 334 9.599866 TCTAACATCACCTAGTGTTGAATAATG 57.400 33.333 11.65 1.92 38.84 1.90
335 336 9.599866 CATCTAACATCACCTAGTGTTGAATAA 57.400 33.333 11.65 0.00 38.84 1.40
336 337 8.977412 TCATCTAACATCACCTAGTGTTGAATA 58.023 33.333 11.65 5.04 38.84 1.75
337 338 7.851228 TCATCTAACATCACCTAGTGTTGAAT 58.149 34.615 11.65 4.31 38.84 2.57
338 339 7.039011 ACTCATCTAACATCACCTAGTGTTGAA 60.039 37.037 11.65 1.01 38.84 2.69
339 340 6.437477 ACTCATCTAACATCACCTAGTGTTGA 59.563 38.462 11.65 0.00 38.84 3.18
340 341 6.634805 ACTCATCTAACATCACCTAGTGTTG 58.365 40.000 6.69 4.63 38.84 3.33
341 342 6.859112 ACTCATCTAACATCACCTAGTGTT 57.141 37.500 2.46 2.46 41.16 3.32
342 343 7.347252 TCTACTCATCTAACATCACCTAGTGT 58.653 38.462 0.00 0.00 34.79 3.55
343 344 7.809546 TCTACTCATCTAACATCACCTAGTG 57.190 40.000 0.00 0.00 34.45 2.74
344 345 7.450014 CCATCTACTCATCTAACATCACCTAGT 59.550 40.741 0.00 0.00 0.00 2.57
345 346 7.450014 ACCATCTACTCATCTAACATCACCTAG 59.550 40.741 0.00 0.00 0.00 3.02
346 347 7.298374 ACCATCTACTCATCTAACATCACCTA 58.702 38.462 0.00 0.00 0.00 3.08
347 348 6.139671 ACCATCTACTCATCTAACATCACCT 58.860 40.000 0.00 0.00 0.00 4.00
348 349 6.412362 ACCATCTACTCATCTAACATCACC 57.588 41.667 0.00 0.00 0.00 4.02
349 350 8.200792 AGAAACCATCTACTCATCTAACATCAC 58.799 37.037 0.00 0.00 36.32 3.06
350 351 8.311395 AGAAACCATCTACTCATCTAACATCA 57.689 34.615 0.00 0.00 36.32 3.07
399 400 9.533831 TCTACTGCATACCTAATCATCTATCAA 57.466 33.333 0.00 0.00 0.00 2.57
400 401 9.706529 ATCTACTGCATACCTAATCATCTATCA 57.293 33.333 0.00 0.00 0.00 2.15
401 402 9.964303 CATCTACTGCATACCTAATCATCTATC 57.036 37.037 0.00 0.00 0.00 2.08
402 403 9.706529 TCATCTACTGCATACCTAATCATCTAT 57.293 33.333 0.00 0.00 0.00 1.98
403 404 9.706529 ATCATCTACTGCATACCTAATCATCTA 57.293 33.333 0.00 0.00 0.00 1.98
404 405 8.476447 CATCATCTACTGCATACCTAATCATCT 58.524 37.037 0.00 0.00 0.00 2.90
405 406 8.256605 ACATCATCTACTGCATACCTAATCATC 58.743 37.037 0.00 0.00 0.00 2.92
406 407 8.039538 CACATCATCTACTGCATACCTAATCAT 58.960 37.037 0.00 0.00 0.00 2.45
407 408 7.015584 ACACATCATCTACTGCATACCTAATCA 59.984 37.037 0.00 0.00 0.00 2.57
408 409 7.382110 ACACATCATCTACTGCATACCTAATC 58.618 38.462 0.00 0.00 0.00 1.75
409 410 7.308450 ACACATCATCTACTGCATACCTAAT 57.692 36.000 0.00 0.00 0.00 1.73
410 411 6.731292 ACACATCATCTACTGCATACCTAA 57.269 37.500 0.00 0.00 0.00 2.69
411 412 7.004691 ACTACACATCATCTACTGCATACCTA 58.995 38.462 0.00 0.00 0.00 3.08
412 413 5.835819 ACTACACATCATCTACTGCATACCT 59.164 40.000 0.00 0.00 0.00 3.08
413 414 6.090483 ACTACACATCATCTACTGCATACC 57.910 41.667 0.00 0.00 0.00 2.73
414 415 7.203218 TCAACTACACATCATCTACTGCATAC 58.797 38.462 0.00 0.00 0.00 2.39
415 416 7.346751 TCAACTACACATCATCTACTGCATA 57.653 36.000 0.00 0.00 0.00 3.14
416 417 6.225981 TCAACTACACATCATCTACTGCAT 57.774 37.500 0.00 0.00 0.00 3.96
417 418 5.659440 TCAACTACACATCATCTACTGCA 57.341 39.130 0.00 0.00 0.00 4.41
418 419 5.869344 TGTTCAACTACACATCATCTACTGC 59.131 40.000 0.00 0.00 0.00 4.40
419 420 7.547019 ACATGTTCAACTACACATCATCTACTG 59.453 37.037 0.00 0.00 30.90 2.74
420 421 7.615403 ACATGTTCAACTACACATCATCTACT 58.385 34.615 0.00 0.00 30.90 2.57
421 422 7.834068 ACATGTTCAACTACACATCATCTAC 57.166 36.000 0.00 0.00 30.90 2.59
422 423 8.197439 CCTACATGTTCAACTACACATCATCTA 58.803 37.037 2.30 0.00 30.90 1.98
423 424 7.044181 CCTACATGTTCAACTACACATCATCT 58.956 38.462 2.30 0.00 30.90 2.90
424 425 6.818644 ACCTACATGTTCAACTACACATCATC 59.181 38.462 2.30 0.00 30.90 2.92
425 426 6.711277 ACCTACATGTTCAACTACACATCAT 58.289 36.000 2.30 0.00 30.90 2.45
426 427 6.109156 ACCTACATGTTCAACTACACATCA 57.891 37.500 2.30 0.00 30.90 3.07
427 428 8.542497 TTTACCTACATGTTCAACTACACATC 57.458 34.615 2.30 0.00 30.90 3.06
428 429 8.911918 TTTTACCTACATGTTCAACTACACAT 57.088 30.769 2.30 0.00 33.72 3.21
429 430 8.911918 ATTTTACCTACATGTTCAACTACACA 57.088 30.769 2.30 0.00 0.00 3.72
437 438 9.233649 ACCGAATTAATTTTACCTACATGTTCA 57.766 29.630 2.30 0.00 0.00 3.18
443 444 9.680315 CACAAAACCGAATTAATTTTACCTACA 57.320 29.630 1.43 0.00 0.00 2.74
444 445 9.681692 ACACAAAACCGAATTAATTTTACCTAC 57.318 29.630 1.43 0.00 0.00 3.18
456 457 7.971722 GCTACCAAATATACACAAAACCGAATT 59.028 33.333 0.00 0.00 0.00 2.17
457 458 7.477494 GCTACCAAATATACACAAAACCGAAT 58.523 34.615 0.00 0.00 0.00 3.34
458 459 6.402334 CGCTACCAAATATACACAAAACCGAA 60.402 38.462 0.00 0.00 0.00 4.30
459 460 5.063691 CGCTACCAAATATACACAAAACCGA 59.936 40.000 0.00 0.00 0.00 4.69
460 461 5.260140 CGCTACCAAATATACACAAAACCG 58.740 41.667 0.00 0.00 0.00 4.44
461 462 5.124297 ACCGCTACCAAATATACACAAAACC 59.876 40.000 0.00 0.00 0.00 3.27
462 463 6.128227 TGACCGCTACCAAATATACACAAAAC 60.128 38.462 0.00 0.00 0.00 2.43
463 464 5.938710 TGACCGCTACCAAATATACACAAAA 59.061 36.000 0.00 0.00 0.00 2.44
464 465 5.489249 TGACCGCTACCAAATATACACAAA 58.511 37.500 0.00 0.00 0.00 2.83
465 466 5.087391 TGACCGCTACCAAATATACACAA 57.913 39.130 0.00 0.00 0.00 3.33
466 467 4.739587 TGACCGCTACCAAATATACACA 57.260 40.909 0.00 0.00 0.00 3.72
467 468 6.259167 TGAAATGACCGCTACCAAATATACAC 59.741 38.462 0.00 0.00 0.00 2.90
468 469 6.350103 TGAAATGACCGCTACCAAATATACA 58.650 36.000 0.00 0.00 0.00 2.29
469 470 6.854496 TGAAATGACCGCTACCAAATATAC 57.146 37.500 0.00 0.00 0.00 1.47
1126 1129 2.295349 CCTTCAGCTTGCAAACATCACT 59.705 45.455 0.00 0.00 0.00 3.41
1195 1198 2.877097 TGTGCATAGTTGGGACACAT 57.123 45.000 0.00 0.00 39.29 3.21
1943 1946 0.689080 TCTGGATCTGGGAGGCAGAC 60.689 60.000 0.00 0.00 0.00 3.51
1944 1947 0.689080 GTCTGGATCTGGGAGGCAGA 60.689 60.000 0.00 0.00 0.00 4.26
1945 1948 1.828768 GTCTGGATCTGGGAGGCAG 59.171 63.158 0.00 0.00 0.00 4.85
1946 1949 2.060383 CGTCTGGATCTGGGAGGCA 61.060 63.158 0.00 0.00 0.00 4.75
1947 1950 2.818132 CGTCTGGATCTGGGAGGC 59.182 66.667 0.00 0.00 0.00 4.70
1948 1951 2.801631 GGCGTCTGGATCTGGGAGG 61.802 68.421 0.00 0.00 0.00 4.30
2115 2118 2.740055 CTGTCTGGTCACCTGCGC 60.740 66.667 0.00 0.00 0.00 6.09
2232 2235 1.407299 GCATGTCTGGTCACCTGCATA 60.407 52.381 9.31 0.00 37.72 3.14
2234 2237 1.302752 GCATGTCTGGTCACCTGCA 60.303 57.895 0.00 0.00 37.72 4.41


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

AutoCloner maintained by Alex Coulton.