Multiple sequence alignment - TraesCS4A01G477300

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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 TraesCS4A01G477300 chr4A 100.000 3943 0 0 1 3943 735315317 735319259 0.000000e+00 7282
1 TraesCS4A01G477300 chr4A 89.309 3199 306 25 754 3928 735562948 735559762 0.000000e+00 3980
2 TraesCS4A01G477300 chr4A 86.147 2974 374 27 974 3936 734585118 734588064 0.000000e+00 3175
3 TraesCS4A01G477300 chr4A 86.378 2907 368 26 1041 3936 735747182 735750071 0.000000e+00 3149
4 TraesCS4A01G477300 chr4A 85.970 2958 396 12 974 3928 736756305 736759246 0.000000e+00 3145
5 TraesCS4A01G477300 chr4A 89.249 2502 261 6 1445 3943 735689506 735692002 0.000000e+00 3123
6 TraesCS4A01G477300 chr4A 86.135 2921 367 26 1038 3942 734730701 734733599 0.000000e+00 3116
7 TraesCS4A01G477300 chr4A 83.929 2912 443 23 1039 3936 735733913 735736813 0.000000e+00 2761
8 TraesCS4A01G477300 chr4A 83.819 2917 449 21 1039 3942 736433809 736430903 0.000000e+00 2750
9 TraesCS4A01G477300 chr4A 84.430 456 56 9 1004 1458 735687716 735688157 6.050000e-118 435
10 TraesCS4A01G477300 chr7D 85.363 3457 446 35 512 3936 5638558 5635130 0.000000e+00 3526
11 TraesCS4A01G477300 chr7D 87.050 2973 361 20 975 3936 5649405 5646446 0.000000e+00 3336
12 TraesCS4A01G477300 chr7D 86.232 2622 327 23 1329 3936 5486537 5483936 0.000000e+00 2811
13 TraesCS4A01G477300 chr7D 84.162 2917 439 21 1039 3942 5788110 5785204 0.000000e+00 2806
14 TraesCS4A01G477300 chr7D 86.410 1479 170 9 513 1968 5557744 5556274 0.000000e+00 1589
15 TraesCS4A01G477300 chr7D 87.578 161 13 5 335 493 5558007 5557852 3.130000e-41 180


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 TraesCS4A01G477300 chr4A 735315317 735319259 3942 False 7282.0 7282 100.0000 1 3943 1 chr4A.!!$F3 3942
1 TraesCS4A01G477300 chr4A 735559762 735562948 3186 True 3980.0 3980 89.3090 754 3928 1 chr4A.!!$R1 3174
2 TraesCS4A01G477300 chr4A 734585118 734588064 2946 False 3175.0 3175 86.1470 974 3936 1 chr4A.!!$F1 2962
3 TraesCS4A01G477300 chr4A 735747182 735750071 2889 False 3149.0 3149 86.3780 1041 3936 1 chr4A.!!$F5 2895
4 TraesCS4A01G477300 chr4A 736756305 736759246 2941 False 3145.0 3145 85.9700 974 3928 1 chr4A.!!$F6 2954
5 TraesCS4A01G477300 chr4A 734730701 734733599 2898 False 3116.0 3116 86.1350 1038 3942 1 chr4A.!!$F2 2904
6 TraesCS4A01G477300 chr4A 735733913 735736813 2900 False 2761.0 2761 83.9290 1039 3936 1 chr4A.!!$F4 2897
7 TraesCS4A01G477300 chr4A 736430903 736433809 2906 True 2750.0 2750 83.8190 1039 3942 1 chr4A.!!$R2 2903
8 TraesCS4A01G477300 chr4A 735687716 735692002 4286 False 1779.0 3123 86.8395 1004 3943 2 chr4A.!!$F7 2939
9 TraesCS4A01G477300 chr7D 5635130 5638558 3428 True 3526.0 3526 85.3630 512 3936 1 chr7D.!!$R2 3424
10 TraesCS4A01G477300 chr7D 5646446 5649405 2959 True 3336.0 3336 87.0500 975 3936 1 chr7D.!!$R3 2961
11 TraesCS4A01G477300 chr7D 5483936 5486537 2601 True 2811.0 2811 86.2320 1329 3936 1 chr7D.!!$R1 2607
12 TraesCS4A01G477300 chr7D 5785204 5788110 2906 True 2806.0 2806 84.1620 1039 3942 1 chr7D.!!$R4 2903
13 TraesCS4A01G477300 chr7D 5556274 5558007 1733 True 884.5 1589 86.9940 335 1968 2 chr7D.!!$R5 1633

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
165 166 0.033228 GATCTGCGAGACCAGGGATG 59.967 60.0 0.0 0.0 33.64 3.51 F
386 387 0.034337 TTGGTACAGAACAGCCCGTC 59.966 55.0 0.0 0.0 42.39 4.79 F
489 490 0.248843 AGCAAGTCCAGCTCAGCTAC 59.751 55.0 0.0 0.0 38.01 3.58 F
569 658 0.322816 TACCGGCTCCTACGACAGTT 60.323 55.0 0.0 0.0 0.00 3.16 F
1680 3179 0.323725 GAGCTGGAGGCATGGGAAAA 60.324 55.0 0.0 0.0 44.79 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 3495 0.674534 ATGTATCCCGCCGAGAAGTC 59.325 55.000 0.0 0.0 0.0 3.01 R
2125 3632 1.063912 CAACTTTTCACACAGCAGCGA 59.936 47.619 0.0 0.0 0.0 4.93 R
2193 3700 1.326951 AACCCACAACTTTTGCCGCT 61.327 50.000 0.0 0.0 0.0 5.52 R
2418 3925 1.927487 TGCATGAATCAACAAGGCCT 58.073 45.000 0.0 0.0 0.0 5.19 R
3341 4873 0.402504 ACCGTGAATTGTAAGGCCCA 59.597 50.000 0.0 0.0 0.0 5.36 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.603075 TTAGGCTGTGCAAAATCCCT 57.397 45.000 0.00 0.00 0.00 4.20
21 22 2.603075 TAGGCTGTGCAAAATCCCTT 57.397 45.000 0.00 0.00 0.00 3.95
22 23 1.720781 AGGCTGTGCAAAATCCCTTT 58.279 45.000 0.00 0.00 0.00 3.11
23 24 1.620323 AGGCTGTGCAAAATCCCTTTC 59.380 47.619 0.00 0.00 0.00 2.62
24 25 1.620323 GGCTGTGCAAAATCCCTTTCT 59.380 47.619 0.00 0.00 0.00 2.52
25 26 2.037641 GGCTGTGCAAAATCCCTTTCTT 59.962 45.455 0.00 0.00 0.00 2.52
26 27 3.494924 GGCTGTGCAAAATCCCTTTCTTT 60.495 43.478 0.00 0.00 0.00 2.52
27 28 4.129380 GCTGTGCAAAATCCCTTTCTTTT 58.871 39.130 0.00 0.00 0.00 2.27
28 29 4.576053 GCTGTGCAAAATCCCTTTCTTTTT 59.424 37.500 0.00 0.00 0.00 1.94
100 101 4.540359 TTTTTCATGATTTCCCTGCAGG 57.460 40.909 26.87 26.87 0.00 4.85
101 102 2.905415 TTCATGATTTCCCTGCAGGT 57.095 45.000 30.63 13.02 36.75 4.00
102 103 2.905415 TCATGATTTCCCTGCAGGTT 57.095 45.000 30.63 12.87 36.75 3.50
103 104 2.449464 TCATGATTTCCCTGCAGGTTG 58.551 47.619 30.63 16.96 36.75 3.77
104 105 2.041485 TCATGATTTCCCTGCAGGTTGA 59.959 45.455 30.63 19.08 36.75 3.18
105 106 2.205022 TGATTTCCCTGCAGGTTGAG 57.795 50.000 30.63 15.82 36.75 3.02
106 107 1.704628 TGATTTCCCTGCAGGTTGAGA 59.295 47.619 30.63 17.96 36.75 3.27
107 108 2.108075 TGATTTCCCTGCAGGTTGAGAA 59.892 45.455 30.63 22.51 36.75 2.87
108 109 2.978156 TTTCCCTGCAGGTTGAGAAT 57.022 45.000 30.63 0.00 36.75 2.40
109 110 2.496899 TTCCCTGCAGGTTGAGAATC 57.503 50.000 30.63 0.00 36.75 2.52
148 149 7.707624 TTTTTCTTGGTCATAGCATTCTGAT 57.292 32.000 0.00 0.00 0.00 2.90
149 150 6.932356 TTTCTTGGTCATAGCATTCTGATC 57.068 37.500 0.00 0.00 0.00 2.92
150 151 5.883685 TCTTGGTCATAGCATTCTGATCT 57.116 39.130 0.00 0.00 0.00 2.75
151 152 5.608449 TCTTGGTCATAGCATTCTGATCTG 58.392 41.667 0.00 0.00 0.00 2.90
152 153 3.736720 TGGTCATAGCATTCTGATCTGC 58.263 45.455 4.97 4.97 38.69 4.26
153 154 2.735663 GGTCATAGCATTCTGATCTGCG 59.264 50.000 0.00 0.00 43.17 5.18
154 155 3.553715 GGTCATAGCATTCTGATCTGCGA 60.554 47.826 0.00 3.41 43.17 5.10
155 156 3.674281 GTCATAGCATTCTGATCTGCGAG 59.326 47.826 0.00 2.99 43.17 5.03
156 157 3.571401 TCATAGCATTCTGATCTGCGAGA 59.429 43.478 0.00 4.74 43.17 4.04
157 158 2.222007 AGCATTCTGATCTGCGAGAC 57.778 50.000 0.00 0.00 43.17 3.36
158 159 1.202510 AGCATTCTGATCTGCGAGACC 60.203 52.381 0.00 0.00 43.17 3.85
159 160 1.472201 GCATTCTGATCTGCGAGACCA 60.472 52.381 0.00 0.00 0.00 4.02
160 161 2.471818 CATTCTGATCTGCGAGACCAG 58.528 52.381 2.11 2.11 0.00 4.00
161 162 0.820226 TTCTGATCTGCGAGACCAGG 59.180 55.000 7.44 0.00 33.64 4.45
162 163 1.039785 TCTGATCTGCGAGACCAGGG 61.040 60.000 7.44 0.00 33.64 4.45
163 164 1.000359 TGATCTGCGAGACCAGGGA 60.000 57.895 0.00 0.00 33.64 4.20
164 165 0.397675 TGATCTGCGAGACCAGGGAT 60.398 55.000 0.00 0.00 33.64 3.85
165 166 0.033228 GATCTGCGAGACCAGGGATG 59.967 60.000 0.00 0.00 33.64 3.51
166 167 1.406065 ATCTGCGAGACCAGGGATGG 61.406 60.000 0.00 0.00 33.64 3.51
167 168 2.284625 TGCGAGACCAGGGATGGT 60.285 61.111 0.00 0.00 46.40 3.55
168 169 2.187946 GCGAGACCAGGGATGGTG 59.812 66.667 4.31 0.00 43.24 4.17
169 170 2.359169 GCGAGACCAGGGATGGTGA 61.359 63.158 4.31 0.00 43.24 4.02
170 171 1.690219 GCGAGACCAGGGATGGTGAT 61.690 60.000 4.31 0.00 43.24 3.06
171 172 0.105593 CGAGACCAGGGATGGTGATG 59.894 60.000 4.31 0.00 43.24 3.07
172 173 0.471617 GAGACCAGGGATGGTGATGG 59.528 60.000 4.31 0.00 43.24 3.51
173 174 0.044702 AGACCAGGGATGGTGATGGA 59.955 55.000 4.31 0.00 43.24 3.41
174 175 0.471617 GACCAGGGATGGTGATGGAG 59.528 60.000 4.31 0.00 43.24 3.86
175 176 0.044702 ACCAGGGATGGTGATGGAGA 59.955 55.000 0.00 0.00 41.33 3.71
176 177 0.763652 CCAGGGATGGTGATGGAGAG 59.236 60.000 0.00 0.00 34.60 3.20
177 178 1.693726 CCAGGGATGGTGATGGAGAGA 60.694 57.143 0.00 0.00 34.60 3.10
178 179 1.693062 CAGGGATGGTGATGGAGAGAG 59.307 57.143 0.00 0.00 0.00 3.20
179 180 1.577729 AGGGATGGTGATGGAGAGAGA 59.422 52.381 0.00 0.00 0.00 3.10
180 181 2.181865 AGGGATGGTGATGGAGAGAGAT 59.818 50.000 0.00 0.00 0.00 2.75
181 182 2.978278 GGGATGGTGATGGAGAGAGATT 59.022 50.000 0.00 0.00 0.00 2.40
182 183 3.393941 GGGATGGTGATGGAGAGAGATTT 59.606 47.826 0.00 0.00 0.00 2.17
183 184 4.141298 GGGATGGTGATGGAGAGAGATTTT 60.141 45.833 0.00 0.00 0.00 1.82
184 185 5.444176 GGATGGTGATGGAGAGAGATTTTT 58.556 41.667 0.00 0.00 0.00 1.94
208 209 2.683211 GGGGGCTAACATCATTCCAT 57.317 50.000 0.00 0.00 0.00 3.41
209 210 2.242043 GGGGGCTAACATCATTCCATG 58.758 52.381 0.00 0.00 0.00 3.66
210 211 2.158475 GGGGGCTAACATCATTCCATGA 60.158 50.000 0.00 0.00 44.55 3.07
211 212 3.152341 GGGGCTAACATCATTCCATGAG 58.848 50.000 0.00 0.00 43.53 2.90
212 213 3.152341 GGGCTAACATCATTCCATGAGG 58.848 50.000 0.00 0.00 45.82 3.86
213 214 3.181440 GGGCTAACATCATTCCATGAGGA 60.181 47.826 5.45 0.00 43.29 3.71
214 215 4.508047 GGGCTAACATCATTCCATGAGGAT 60.508 45.833 5.45 0.00 45.26 3.24
215 216 5.280676 GGGCTAACATCATTCCATGAGGATA 60.281 44.000 5.45 0.00 45.26 2.59
216 217 5.879223 GGCTAACATCATTCCATGAGGATAG 59.121 44.000 5.45 8.03 45.26 2.08
217 218 6.296087 GGCTAACATCATTCCATGAGGATAGA 60.296 42.308 15.69 0.84 44.19 1.98
218 219 7.164122 GCTAACATCATTCCATGAGGATAGAA 58.836 38.462 15.69 0.00 44.19 2.10
219 220 7.118971 GCTAACATCATTCCATGAGGATAGAAC 59.881 40.741 15.69 1.08 44.19 3.01
220 221 5.545588 ACATCATTCCATGAGGATAGAACG 58.454 41.667 5.45 0.00 45.26 3.95
221 222 4.607293 TCATTCCATGAGGATAGAACGG 57.393 45.455 0.00 0.00 45.26 4.44
222 223 3.324846 TCATTCCATGAGGATAGAACGGG 59.675 47.826 0.00 0.00 45.26 5.28
223 224 1.717032 TCCATGAGGATAGAACGGGG 58.283 55.000 0.00 0.00 39.61 5.73
224 225 1.219469 TCCATGAGGATAGAACGGGGA 59.781 52.381 0.00 0.00 39.61 4.81
225 226 2.047061 CCATGAGGATAGAACGGGGAA 58.953 52.381 0.00 0.00 36.89 3.97
226 227 2.037772 CCATGAGGATAGAACGGGGAAG 59.962 54.545 0.00 0.00 36.89 3.46
227 228 2.840640 TGAGGATAGAACGGGGAAGA 57.159 50.000 0.00 0.00 0.00 2.87
228 229 3.110293 TGAGGATAGAACGGGGAAGAA 57.890 47.619 0.00 0.00 0.00 2.52
229 230 3.654273 TGAGGATAGAACGGGGAAGAAT 58.346 45.455 0.00 0.00 0.00 2.40
230 231 3.388024 TGAGGATAGAACGGGGAAGAATG 59.612 47.826 0.00 0.00 0.00 2.67
231 232 2.706190 AGGATAGAACGGGGAAGAATGG 59.294 50.000 0.00 0.00 0.00 3.16
232 233 2.224548 GGATAGAACGGGGAAGAATGGG 60.225 54.545 0.00 0.00 0.00 4.00
233 234 1.209621 TAGAACGGGGAAGAATGGGG 58.790 55.000 0.00 0.00 0.00 4.96
234 235 0.845102 AGAACGGGGAAGAATGGGGT 60.845 55.000 0.00 0.00 0.00 4.95
235 236 0.039180 GAACGGGGAAGAATGGGGTT 59.961 55.000 0.00 0.00 0.00 4.11
236 237 0.039180 AACGGGGAAGAATGGGGTTC 59.961 55.000 0.00 0.00 37.08 3.62
238 239 1.209621 CGGGGAAGAATGGGGTTCTA 58.790 55.000 0.00 0.00 46.39 2.10
239 240 1.562475 CGGGGAAGAATGGGGTTCTAA 59.438 52.381 0.00 0.00 46.39 2.10
240 241 2.682858 CGGGGAAGAATGGGGTTCTAAC 60.683 54.545 0.00 0.00 46.39 2.34
241 242 2.581246 GGGGAAGAATGGGGTTCTAACT 59.419 50.000 0.00 0.00 46.39 2.24
242 243 3.371702 GGGGAAGAATGGGGTTCTAACTC 60.372 52.174 0.00 0.00 46.39 3.01
243 244 3.532542 GGAAGAATGGGGTTCTAACTCG 58.467 50.000 0.00 0.00 46.39 4.18
244 245 3.055312 GGAAGAATGGGGTTCTAACTCGT 60.055 47.826 0.00 0.00 46.39 4.18
245 246 3.611766 AGAATGGGGTTCTAACTCGTG 57.388 47.619 0.00 0.00 45.28 4.35
246 247 3.170717 AGAATGGGGTTCTAACTCGTGA 58.829 45.455 0.00 0.00 45.28 4.35
247 248 3.775316 AGAATGGGGTTCTAACTCGTGAT 59.225 43.478 0.00 0.00 45.28 3.06
248 249 3.543680 ATGGGGTTCTAACTCGTGATG 57.456 47.619 0.00 0.00 0.00 3.07
249 250 1.066430 TGGGGTTCTAACTCGTGATGC 60.066 52.381 0.00 0.00 0.00 3.91
250 251 1.207329 GGGGTTCTAACTCGTGATGCT 59.793 52.381 0.00 0.00 0.00 3.79
251 252 2.354805 GGGGTTCTAACTCGTGATGCTT 60.355 50.000 0.00 0.00 0.00 3.91
252 253 2.930682 GGGTTCTAACTCGTGATGCTTC 59.069 50.000 0.00 0.00 0.00 3.86
253 254 3.585862 GGTTCTAACTCGTGATGCTTCA 58.414 45.455 0.00 0.00 0.00 3.02
254 255 3.614616 GGTTCTAACTCGTGATGCTTCAG 59.385 47.826 1.91 0.00 30.85 3.02
255 256 3.510388 TCTAACTCGTGATGCTTCAGG 57.490 47.619 14.31 14.31 38.75 3.86
256 257 3.089284 TCTAACTCGTGATGCTTCAGGA 58.911 45.455 19.92 19.92 42.76 3.86
261 262 3.232213 TCGTGATGCTTCAGGAGTTAC 57.768 47.619 17.97 0.00 40.76 2.50
262 263 2.560981 TCGTGATGCTTCAGGAGTTACA 59.439 45.455 17.97 0.00 40.76 2.41
263 264 3.006430 TCGTGATGCTTCAGGAGTTACAA 59.994 43.478 17.97 0.00 40.76 2.41
264 265 3.745975 CGTGATGCTTCAGGAGTTACAAA 59.254 43.478 15.13 0.00 39.56 2.83
265 266 4.393062 CGTGATGCTTCAGGAGTTACAAAT 59.607 41.667 15.13 0.00 39.56 2.32
266 267 5.106555 CGTGATGCTTCAGGAGTTACAAATT 60.107 40.000 15.13 0.00 39.56 1.82
267 268 6.088824 GTGATGCTTCAGGAGTTACAAATTG 58.911 40.000 1.91 0.00 30.85 2.32
268 269 5.183713 TGATGCTTCAGGAGTTACAAATTGG 59.816 40.000 0.00 0.00 0.00 3.16
269 270 3.255642 TGCTTCAGGAGTTACAAATTGGC 59.744 43.478 0.00 0.00 0.00 4.52
270 271 3.367395 GCTTCAGGAGTTACAAATTGGCC 60.367 47.826 0.00 0.00 0.00 5.36
271 272 3.806949 TCAGGAGTTACAAATTGGCCT 57.193 42.857 3.32 0.00 0.00 5.19
272 273 4.112634 TCAGGAGTTACAAATTGGCCTT 57.887 40.909 3.32 0.00 0.00 4.35
273 274 4.479158 TCAGGAGTTACAAATTGGCCTTT 58.521 39.130 3.32 0.00 0.00 3.11
274 275 4.898861 TCAGGAGTTACAAATTGGCCTTTT 59.101 37.500 3.32 0.74 0.00 2.27
275 276 4.990426 CAGGAGTTACAAATTGGCCTTTTG 59.010 41.667 22.46 22.46 39.43 2.44
276 277 4.653801 AGGAGTTACAAATTGGCCTTTTGT 59.346 37.500 28.44 28.44 46.18 2.83
277 278 5.836358 AGGAGTTACAAATTGGCCTTTTGTA 59.164 36.000 26.95 26.95 43.52 2.41
278 279 6.496911 AGGAGTTACAAATTGGCCTTTTGTAT 59.503 34.615 29.16 21.43 44.56 2.29
279 280 7.016170 AGGAGTTACAAATTGGCCTTTTGTATT 59.984 33.333 29.16 23.50 44.56 1.89
280 281 7.659799 GGAGTTACAAATTGGCCTTTTGTATTT 59.340 33.333 29.16 23.28 44.56 1.40
281 282 9.699703 GAGTTACAAATTGGCCTTTTGTATTTA 57.300 29.630 29.16 19.37 44.56 1.40
282 283 9.483916 AGTTACAAATTGGCCTTTTGTATTTAC 57.516 29.630 29.16 25.35 44.56 2.01
283 284 8.714179 GTTACAAATTGGCCTTTTGTATTTACC 58.286 33.333 29.16 18.01 44.56 2.85
284 285 6.234920 ACAAATTGGCCTTTTGTATTTACCC 58.765 36.000 26.11 0.00 43.52 3.69
285 286 6.183361 ACAAATTGGCCTTTTGTATTTACCCA 60.183 34.615 26.11 0.00 43.52 4.51
286 287 4.875561 TTGGCCTTTTGTATTTACCCAC 57.124 40.909 3.32 0.00 0.00 4.61
287 288 3.845860 TGGCCTTTTGTATTTACCCACA 58.154 40.909 3.32 0.00 0.00 4.17
288 289 3.574826 TGGCCTTTTGTATTTACCCACAC 59.425 43.478 3.32 0.00 0.00 3.82
289 290 3.574826 GGCCTTTTGTATTTACCCACACA 59.425 43.478 0.00 0.00 0.00 3.72
290 291 4.039366 GGCCTTTTGTATTTACCCACACAA 59.961 41.667 0.00 0.00 0.00 3.33
291 292 5.279758 GGCCTTTTGTATTTACCCACACAAT 60.280 40.000 0.00 0.00 31.45 2.71
292 293 5.637387 GCCTTTTGTATTTACCCACACAATG 59.363 40.000 0.00 0.00 31.45 2.82
308 309 4.869215 CACAATGGTGTTGTATTTGCAGA 58.131 39.130 0.00 0.00 40.24 4.26
309 310 4.919168 CACAATGGTGTTGTATTTGCAGAG 59.081 41.667 0.00 0.00 40.24 3.35
310 311 4.584325 ACAATGGTGTTGTATTTGCAGAGT 59.416 37.500 0.00 0.00 32.58 3.24
311 312 5.767665 ACAATGGTGTTGTATTTGCAGAGTA 59.232 36.000 0.00 0.00 32.58 2.59
312 313 6.072508 ACAATGGTGTTGTATTTGCAGAGTAG 60.073 38.462 0.00 0.00 32.58 2.57
313 314 4.968259 TGGTGTTGTATTTGCAGAGTAGT 58.032 39.130 0.00 0.00 0.00 2.73
314 315 4.994852 TGGTGTTGTATTTGCAGAGTAGTC 59.005 41.667 0.00 0.00 0.00 2.59
315 316 4.392138 GGTGTTGTATTTGCAGAGTAGTCC 59.608 45.833 0.00 0.00 0.00 3.85
316 317 5.238583 GTGTTGTATTTGCAGAGTAGTCCT 58.761 41.667 0.00 0.00 0.00 3.85
317 318 5.348997 GTGTTGTATTTGCAGAGTAGTCCTC 59.651 44.000 0.00 0.00 40.80 3.71
327 328 3.124578 GAGTAGTCCTCTACCCTACGG 57.875 57.143 2.36 0.00 45.36 4.02
328 329 2.703007 GAGTAGTCCTCTACCCTACGGA 59.297 54.545 2.36 0.00 45.36 4.69
329 330 3.325605 AGTAGTCCTCTACCCTACGGAT 58.674 50.000 2.36 0.00 45.36 4.18
330 331 2.955342 AGTCCTCTACCCTACGGATC 57.045 55.000 0.00 0.00 0.00 3.36
331 332 2.420705 AGTCCTCTACCCTACGGATCT 58.579 52.381 0.00 0.00 0.00 2.75
332 333 2.106857 AGTCCTCTACCCTACGGATCTG 59.893 54.545 0.00 0.00 0.00 2.90
333 334 2.106166 GTCCTCTACCCTACGGATCTGA 59.894 54.545 9.00 0.00 0.00 3.27
341 342 2.420642 CCTACGGATCTGATTGCATGG 58.579 52.381 9.00 0.00 0.00 3.66
363 364 1.929836 GTTATCTGTCCGCTGCTGAAG 59.070 52.381 0.00 0.00 0.00 3.02
378 379 3.315191 TGCTGAAGCTTTTGGTACAGAAC 59.685 43.478 13.21 0.00 40.59 3.01
379 380 3.315191 GCTGAAGCTTTTGGTACAGAACA 59.685 43.478 13.21 0.00 37.69 3.18
380 381 4.555511 GCTGAAGCTTTTGGTACAGAACAG 60.556 45.833 13.21 6.84 37.69 3.16
382 383 2.230660 AGCTTTTGGTACAGAACAGCC 58.769 47.619 10.01 0.00 42.39 4.85
383 384 1.269723 GCTTTTGGTACAGAACAGCCC 59.730 52.381 0.00 0.00 42.39 5.19
384 385 1.535462 CTTTTGGTACAGAACAGCCCG 59.465 52.381 0.00 0.00 42.39 6.13
385 386 0.470766 TTTGGTACAGAACAGCCCGT 59.529 50.000 0.00 0.00 42.39 5.28
386 387 0.034337 TTGGTACAGAACAGCCCGTC 59.966 55.000 0.00 0.00 42.39 4.79
387 388 1.116536 TGGTACAGAACAGCCCGTCA 61.117 55.000 0.00 0.00 0.00 4.35
391 392 0.603707 ACAGAACAGCCCGTCATGTG 60.604 55.000 0.00 0.00 0.00 3.21
407 408 5.393461 CGTCATGTGATATGCATCTAGCCTA 60.393 44.000 0.19 0.00 44.83 3.93
410 411 6.212187 TCATGTGATATGCATCTAGCCTACTT 59.788 38.462 0.19 0.00 44.83 2.24
415 416 8.037758 GTGATATGCATCTAGCCTACTTTATGT 58.962 37.037 0.19 0.00 44.83 2.29
446 447 3.692791 TCGATCAGTGAACTATGTCCG 57.307 47.619 0.00 0.00 0.00 4.79
485 486 5.181748 AGTTTATTAGCAAGTCCAGCTCAG 58.818 41.667 0.00 0.00 42.32 3.35
489 490 0.248843 AGCAAGTCCAGCTCAGCTAC 59.751 55.000 0.00 0.00 38.01 3.58
493 515 2.493675 CAAGTCCAGCTCAGCTACACTA 59.506 50.000 0.00 0.00 36.40 2.74
495 517 2.025793 AGTCCAGCTCAGCTACACTAGA 60.026 50.000 0.00 0.00 36.40 2.43
503 525 4.761739 GCTCAGCTACACTAGATCAGATCT 59.238 45.833 17.34 17.34 43.33 2.75
551 640 0.613260 AACCTTGCCTCATCGCTGTA 59.387 50.000 0.00 0.00 0.00 2.74
567 656 1.028330 TGTACCGGCTCCTACGACAG 61.028 60.000 0.00 0.00 0.00 3.51
569 658 0.322816 TACCGGCTCCTACGACAGTT 60.323 55.000 0.00 0.00 0.00 3.16
606 698 4.093556 GTGTAAGCTCACCACTATTCTTGC 59.906 45.833 0.00 0.00 32.81 4.01
609 701 3.539604 AGCTCACCACTATTCTTGCATC 58.460 45.455 0.00 0.00 0.00 3.91
625 717 3.565307 TGCATCTTTTCCTCCACAAGTT 58.435 40.909 0.00 0.00 0.00 2.66
627 719 4.037923 TGCATCTTTTCCTCCACAAGTTTC 59.962 41.667 0.00 0.00 0.00 2.78
704 796 2.341846 TTCCCACTTCAACAGGTGTC 57.658 50.000 0.00 0.00 0.00 3.67
730 826 6.000246 TCCATTGCTATATTCACTGGTTGA 58.000 37.500 11.28 0.00 36.17 3.18
738 834 6.651225 GCTATATTCACTGGTTGATTCTACCC 59.349 42.308 13.65 0.00 34.66 3.69
740 836 1.913419 TCACTGGTTGATTCTACCCCC 59.087 52.381 13.65 0.00 34.66 5.40
751 847 0.635009 TCTACCCCCGATCCAGAAGT 59.365 55.000 0.00 0.00 0.00 3.01
773 870 4.337555 GTGCTTTCATTGCTGGTCTATCAT 59.662 41.667 0.00 0.00 0.00 2.45
774 871 4.577693 TGCTTTCATTGCTGGTCTATCATC 59.422 41.667 0.00 0.00 0.00 2.92
793 896 6.183810 TCATCTATTCAGGTCATTGCTCAT 57.816 37.500 0.00 0.00 0.00 2.90
808 911 6.537660 TCATTGCTCATTCTCAGAACAGTATG 59.462 38.462 0.00 0.00 46.00 2.39
810 913 4.186926 GCTCATTCTCAGAACAGTATGCA 58.813 43.478 0.00 0.00 42.53 3.96
819 922 6.015434 TCTCAGAACAGTATGCACAGTCTTTA 60.015 38.462 0.00 0.00 42.53 1.85
825 928 9.582431 GAACAGTATGCACAGTCTTTACTATTA 57.418 33.333 0.00 0.00 42.53 0.98
926 1047 4.473444 ACAGGTTTTTCATCCATCACTGT 58.527 39.130 0.00 0.00 32.37 3.55
927 1048 4.520492 ACAGGTTTTTCATCCATCACTGTC 59.480 41.667 0.00 0.00 31.68 3.51
928 1049 4.082125 AGGTTTTTCATCCATCACTGTCC 58.918 43.478 0.00 0.00 0.00 4.02
929 1050 3.826157 GGTTTTTCATCCATCACTGTCCA 59.174 43.478 0.00 0.00 0.00 4.02
946 1070 3.130633 GTCCAAAAACAATTCCAGTGCC 58.869 45.455 0.00 0.00 0.00 5.01
954 1078 3.499338 ACAATTCCAGTGCCATCTTCAA 58.501 40.909 0.00 0.00 0.00 2.69
967 1091 5.066375 TGCCATCTTCAATTTATTCAGACCG 59.934 40.000 0.00 0.00 0.00 4.79
1071 1196 0.804989 CATCACCGGCCTTGAAGAAC 59.195 55.000 0.00 0.00 0.00 3.01
1078 1203 1.278127 CGGCCTTGAAGAACCTCCTTA 59.722 52.381 0.00 0.00 0.00 2.69
1095 1220 7.806180 ACCTCCTTACTAATGCTTCAACATAT 58.194 34.615 0.00 0.00 0.00 1.78
1209 1334 0.468029 ACAGGCCCAAGTTGGACAAG 60.468 55.000 24.06 10.29 40.96 3.16
1248 1373 2.411904 GAAGCATTCTATCTGGCCGAG 58.588 52.381 0.00 0.00 43.23 4.63
1257 1382 1.557269 ATCTGGCCGAGGACTTGCTT 61.557 55.000 0.00 0.00 0.00 3.91
1262 1387 1.738099 CCGAGGACTTGCTTGACGG 60.738 63.158 0.00 0.00 0.00 4.79
1274 1399 1.359848 CTTGACGGGCATGAGTACAC 58.640 55.000 0.00 0.00 0.00 2.90
1281 1406 0.912486 GGCATGAGTACACCCTCCTT 59.088 55.000 0.00 0.00 0.00 3.36
1335 1460 2.621407 GGACAATGCCTCCTCCATCAAA 60.621 50.000 0.00 0.00 0.00 2.69
1480 2967 2.038952 TGTGAACTGCTCTGCTTACCAT 59.961 45.455 0.00 0.00 0.00 3.55
1499 2992 3.755378 CCATCTGGTTATAATGCAGAGGC 59.245 47.826 0.00 0.00 41.68 4.70
1505 2998 1.759101 TATAATGCAGAGGCCCCCAT 58.241 50.000 0.00 0.00 40.13 4.00
1510 3003 0.773305 TGCAGAGGCCCCCATCATAT 60.773 55.000 0.00 0.00 40.13 1.78
1527 3020 4.122046 TCATATCATCAGCTGTTGTTCCG 58.878 43.478 21.24 11.06 0.00 4.30
1545 3038 1.448540 GGAGACCACATCACTGCCG 60.449 63.158 0.00 0.00 0.00 5.69
1601 3094 8.630917 CCGGGATCGTATAATAGATCAACTTAT 58.369 37.037 12.99 0.00 43.61 1.73
1680 3179 0.323725 GAGCTGGAGGCATGGGAAAA 60.324 55.000 0.00 0.00 44.79 2.29
1712 3211 5.221402 TGGCACAACATGTTTACAATGACAT 60.221 36.000 8.77 0.00 33.76 3.06
1809 3308 1.269448 GAGATCATCGAGTCTGCCTCC 59.731 57.143 0.00 0.00 36.82 4.30
1995 3495 2.977772 TGGGAAGCAAAGTTTTGGTG 57.022 45.000 9.75 0.00 46.98 4.17
2105 3612 4.022589 ACTCTTCAAACACCATGCATTCTG 60.023 41.667 0.00 0.00 0.00 3.02
2110 3617 2.291209 ACACCATGCATTCTGTGGAA 57.709 45.000 19.42 0.00 36.82 3.53
2193 3700 4.657814 AAGGCTTGGACAATCTCCTTTA 57.342 40.909 0.00 0.00 40.26 1.85
2226 3733 1.133606 GTGGGTTCCCAGTTGAAAGGA 60.134 52.381 11.21 0.00 36.70 3.36
2403 3910 1.534163 GGCGTTGAGGAGTTGGTTTAC 59.466 52.381 0.00 0.00 0.00 2.01
2418 3925 3.161866 GGTTTACCTTTGGATGGCAGAA 58.838 45.455 0.00 0.00 0.00 3.02
2462 3969 8.405531 CAACAAAAACAAGAGAGTGGAAGATAA 58.594 33.333 0.00 0.00 0.00 1.75
2531 4050 5.941788 ACCTGTTTATGAGGAAGACACTTT 58.058 37.500 0.00 0.00 34.37 2.66
2565 4084 3.725490 TGATCTCCTTCATGATCTTGCG 58.275 45.455 0.00 0.00 39.63 4.85
2647 4166 6.776116 ACCATCAACTGTTCGATACCTATCTA 59.224 38.462 0.00 0.00 0.00 1.98
2697 4216 4.688021 AGCTAAGTATCTGCAAGCTACAC 58.312 43.478 5.02 0.00 41.56 2.90
2701 4220 5.614324 AAGTATCTGCAAGCTACACCATA 57.386 39.130 0.00 0.00 37.99 2.74
3088 4619 4.795308 AGCTGACTTTGCTTCAAGAATTGC 60.795 41.667 0.00 0.00 36.97 3.56
3129 4660 6.521151 AAGAAAAAGGGATATGAGTTGCAG 57.479 37.500 0.00 0.00 0.00 4.41
3306 4838 6.480763 TGCAGAGGATAGTTTACATTTGGAA 58.519 36.000 0.00 0.00 0.00 3.53
3340 4872 0.392461 GATGCCACCGCCTCAACTTA 60.392 55.000 0.00 0.00 30.61 2.24
3341 4873 0.255890 ATGCCACCGCCTCAACTTAT 59.744 50.000 0.00 0.00 0.00 1.73
3390 4922 6.916360 TCTTCAAAATATCCAAGCTGGTTT 57.084 33.333 0.00 0.00 39.03 3.27
3462 4994 2.325082 CGCGTTGCAAAGCCTACCT 61.325 57.895 27.79 0.00 0.00 3.08
3473 5005 4.589908 CAAAGCCTACCTTCCAATACTGT 58.410 43.478 0.00 0.00 31.99 3.55
3480 5012 5.414765 CCTACCTTCCAATACTGTGGTTTTC 59.585 44.000 0.00 0.00 39.88 2.29
3496 5028 3.193479 GGTTTTCCGGAATTGCTCTTCAT 59.807 43.478 19.62 0.00 0.00 2.57
3498 5030 5.105917 GGTTTTCCGGAATTGCTCTTCATTA 60.106 40.000 19.62 0.00 0.00 1.90
3500 5032 3.808728 TCCGGAATTGCTCTTCATTAGG 58.191 45.455 0.00 0.00 0.00 2.69
3502 5034 2.945008 CGGAATTGCTCTTCATTAGGCA 59.055 45.455 0.00 0.00 0.00 4.75
3525 5057 7.600065 GCATCATCAATATGCTAAACCTGAAT 58.400 34.615 0.00 0.00 45.05 2.57
3556 5088 4.553330 TGTCTTCCACTAGGCCTTAAAG 57.447 45.455 12.58 4.64 33.74 1.85
3678 5210 4.156556 GCATCACAGCTTGGTTTAATCTGA 59.843 41.667 0.00 0.00 36.32 3.27
3768 5300 9.273016 CTGATGATATTGATGCATGCTGATATA 57.727 33.333 20.33 11.62 0.00 0.86
3854 5386 5.768662 GGGATATCATCAAGGCATGGATATG 59.231 44.000 4.83 0.00 37.36 1.78
3942 5474 4.279671 TCAGGACTTTGTGAACTCTCTCTC 59.720 45.833 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.105959 AGGGATTTTGCACAGCCTAAT 57.894 42.857 0.00 0.00 0.00 1.73
1 2 2.603075 AGGGATTTTGCACAGCCTAA 57.397 45.000 0.00 0.00 0.00 2.69
2 3 2.603075 AAGGGATTTTGCACAGCCTA 57.397 45.000 0.00 0.00 0.00 3.93
3 4 1.620323 GAAAGGGATTTTGCACAGCCT 59.380 47.619 0.00 0.00 0.00 4.58
4 5 1.620323 AGAAAGGGATTTTGCACAGCC 59.380 47.619 0.00 0.00 0.00 4.85
5 6 3.391506 AAGAAAGGGATTTTGCACAGC 57.608 42.857 0.00 0.00 0.00 4.40
74 75 8.591072 CCTGCAGGGAAATCATGAAAAATATAT 58.409 33.333 26.14 0.00 37.23 0.86
75 76 7.564660 ACCTGCAGGGAAATCATGAAAAATATA 59.435 33.333 35.42 0.00 40.27 0.86
76 77 6.384886 ACCTGCAGGGAAATCATGAAAAATAT 59.615 34.615 35.42 5.83 40.27 1.28
77 78 5.721000 ACCTGCAGGGAAATCATGAAAAATA 59.279 36.000 35.42 0.00 40.27 1.40
78 79 4.533311 ACCTGCAGGGAAATCATGAAAAAT 59.467 37.500 35.42 6.62 40.27 1.82
79 80 3.903090 ACCTGCAGGGAAATCATGAAAAA 59.097 39.130 35.42 0.00 40.27 1.94
80 81 3.509442 ACCTGCAGGGAAATCATGAAAA 58.491 40.909 35.42 0.00 40.27 2.29
81 82 3.173953 ACCTGCAGGGAAATCATGAAA 57.826 42.857 35.42 0.00 40.27 2.69
82 83 2.827322 CAACCTGCAGGGAAATCATGAA 59.173 45.455 35.42 0.00 40.27 2.57
83 84 2.041485 TCAACCTGCAGGGAAATCATGA 59.959 45.455 35.42 22.07 40.27 3.07
84 85 2.426024 CTCAACCTGCAGGGAAATCATG 59.574 50.000 35.42 20.40 40.27 3.07
85 86 2.309755 TCTCAACCTGCAGGGAAATCAT 59.690 45.455 35.42 11.03 40.27 2.45
86 87 1.704628 TCTCAACCTGCAGGGAAATCA 59.295 47.619 35.42 12.72 40.27 2.57
87 88 2.496899 TCTCAACCTGCAGGGAAATC 57.503 50.000 35.42 0.00 40.27 2.17
88 89 2.978156 TTCTCAACCTGCAGGGAAAT 57.022 45.000 35.42 16.45 40.27 2.17
89 90 2.108075 TGATTCTCAACCTGCAGGGAAA 59.892 45.455 35.42 20.80 40.27 3.13
90 91 1.704628 TGATTCTCAACCTGCAGGGAA 59.295 47.619 35.42 27.03 40.27 3.97
91 92 1.361204 TGATTCTCAACCTGCAGGGA 58.639 50.000 35.42 22.63 40.27 4.20
92 93 2.205022 TTGATTCTCAACCTGCAGGG 57.795 50.000 35.42 19.57 40.27 4.45
93 94 2.426024 CCATTGATTCTCAACCTGCAGG 59.574 50.000 31.60 31.60 39.45 4.85
94 95 2.426024 CCCATTGATTCTCAACCTGCAG 59.574 50.000 6.78 6.78 39.45 4.41
95 96 2.449464 CCCATTGATTCTCAACCTGCA 58.551 47.619 0.00 0.00 39.45 4.41
96 97 1.753073 CCCCATTGATTCTCAACCTGC 59.247 52.381 0.00 0.00 39.45 4.85
97 98 3.019564 GACCCCATTGATTCTCAACCTG 58.980 50.000 0.00 0.00 39.45 4.00
98 99 2.922283 AGACCCCATTGATTCTCAACCT 59.078 45.455 0.00 0.00 39.45 3.50
99 100 3.372440 AGACCCCATTGATTCTCAACC 57.628 47.619 0.00 0.00 39.45 3.77
100 101 7.410120 AAATAAGACCCCATTGATTCTCAAC 57.590 36.000 0.00 0.00 39.45 3.18
101 102 8.434589 AAAAATAAGACCCCATTGATTCTCAA 57.565 30.769 0.00 0.00 41.09 3.02
124 125 7.613022 AGATCAGAATGCTATGACCAAGAAAAA 59.387 33.333 0.00 0.00 34.76 1.94
125 126 7.066645 CAGATCAGAATGCTATGACCAAGAAAA 59.933 37.037 0.00 0.00 34.76 2.29
126 127 6.541278 CAGATCAGAATGCTATGACCAAGAAA 59.459 38.462 0.00 0.00 34.76 2.52
127 128 6.053650 CAGATCAGAATGCTATGACCAAGAA 58.946 40.000 0.00 0.00 34.76 2.52
128 129 5.608449 CAGATCAGAATGCTATGACCAAGA 58.392 41.667 0.00 0.00 34.76 3.02
129 130 4.213694 GCAGATCAGAATGCTATGACCAAG 59.786 45.833 0.00 0.00 39.38 3.61
130 131 4.132336 GCAGATCAGAATGCTATGACCAA 58.868 43.478 0.00 0.00 39.38 3.67
131 132 3.736720 GCAGATCAGAATGCTATGACCA 58.263 45.455 0.00 0.00 39.38 4.02
132 133 2.735663 CGCAGATCAGAATGCTATGACC 59.264 50.000 8.83 0.00 40.34 4.02
133 134 3.646946 TCGCAGATCAGAATGCTATGAC 58.353 45.455 8.83 0.00 40.34 3.06
134 135 3.571401 TCTCGCAGATCAGAATGCTATGA 59.429 43.478 8.83 2.86 40.34 2.15
135 136 3.674281 GTCTCGCAGATCAGAATGCTATG 59.326 47.826 8.83 1.01 40.34 2.23
136 137 3.305950 GGTCTCGCAGATCAGAATGCTAT 60.306 47.826 8.83 0.00 40.34 2.97
137 138 2.035193 GGTCTCGCAGATCAGAATGCTA 59.965 50.000 8.83 0.00 40.34 3.49
138 139 1.202510 GGTCTCGCAGATCAGAATGCT 60.203 52.381 8.83 0.00 40.34 3.79
139 140 1.216122 GGTCTCGCAGATCAGAATGC 58.784 55.000 0.00 0.00 39.09 3.56
140 141 2.591571 TGGTCTCGCAGATCAGAATG 57.408 50.000 0.00 0.00 28.68 2.67
145 146 0.397675 ATCCCTGGTCTCGCAGATCA 60.398 55.000 0.00 0.25 33.63 2.92
146 147 0.033228 CATCCCTGGTCTCGCAGATC 59.967 60.000 0.00 0.00 33.89 2.75
147 148 1.406065 CCATCCCTGGTCTCGCAGAT 61.406 60.000 0.00 0.00 37.79 2.90
148 149 2.060383 CCATCCCTGGTCTCGCAGA 61.060 63.158 0.00 0.00 37.79 4.26
149 150 2.503061 CCATCCCTGGTCTCGCAG 59.497 66.667 0.00 0.00 37.79 5.18
158 159 1.693062 CTCTCTCCATCACCATCCCTG 59.307 57.143 0.00 0.00 0.00 4.45
159 160 1.577729 TCTCTCTCCATCACCATCCCT 59.422 52.381 0.00 0.00 0.00 4.20
160 161 2.094100 TCTCTCTCCATCACCATCCC 57.906 55.000 0.00 0.00 0.00 3.85
161 162 4.703379 AAATCTCTCTCCATCACCATCC 57.297 45.455 0.00 0.00 0.00 3.51
189 190 2.683211 ATGGAATGATGTTAGCCCCC 57.317 50.000 0.00 0.00 0.00 5.40
201 202 3.557898 CCCCGTTCTATCCTCATGGAATG 60.558 52.174 0.00 0.00 46.80 2.67
202 203 2.639839 CCCCGTTCTATCCTCATGGAAT 59.360 50.000 0.00 0.00 46.80 3.01
203 204 2.047061 CCCCGTTCTATCCTCATGGAA 58.953 52.381 0.00 0.00 46.80 3.53
205 206 1.717032 TCCCCGTTCTATCCTCATGG 58.283 55.000 0.00 0.00 0.00 3.66
206 207 2.965831 TCTTCCCCGTTCTATCCTCATG 59.034 50.000 0.00 0.00 0.00 3.07
207 208 3.330126 TCTTCCCCGTTCTATCCTCAT 57.670 47.619 0.00 0.00 0.00 2.90
208 209 2.840640 TCTTCCCCGTTCTATCCTCA 57.159 50.000 0.00 0.00 0.00 3.86
209 210 3.244249 CCATTCTTCCCCGTTCTATCCTC 60.244 52.174 0.00 0.00 0.00 3.71
210 211 2.706190 CCATTCTTCCCCGTTCTATCCT 59.294 50.000 0.00 0.00 0.00 3.24
211 212 2.224548 CCCATTCTTCCCCGTTCTATCC 60.225 54.545 0.00 0.00 0.00 2.59
212 213 2.224548 CCCCATTCTTCCCCGTTCTATC 60.225 54.545 0.00 0.00 0.00 2.08
213 214 1.774856 CCCCATTCTTCCCCGTTCTAT 59.225 52.381 0.00 0.00 0.00 1.98
214 215 1.209621 CCCCATTCTTCCCCGTTCTA 58.790 55.000 0.00 0.00 0.00 2.10
215 216 0.845102 ACCCCATTCTTCCCCGTTCT 60.845 55.000 0.00 0.00 0.00 3.01
216 217 0.039180 AACCCCATTCTTCCCCGTTC 59.961 55.000 0.00 0.00 0.00 3.95
217 218 0.039180 GAACCCCATTCTTCCCCGTT 59.961 55.000 0.00 0.00 34.15 4.44
218 219 0.845102 AGAACCCCATTCTTCCCCGT 60.845 55.000 0.00 0.00 46.05 5.28
219 220 1.209621 TAGAACCCCATTCTTCCCCG 58.790 55.000 0.00 0.00 46.05 5.73
220 221 2.581246 AGTTAGAACCCCATTCTTCCCC 59.419 50.000 0.00 0.00 46.05 4.81
221 222 3.681874 CGAGTTAGAACCCCATTCTTCCC 60.682 52.174 0.00 0.00 46.05 3.97
222 223 3.055312 ACGAGTTAGAACCCCATTCTTCC 60.055 47.826 0.00 0.00 46.05 3.46
223 224 3.933332 CACGAGTTAGAACCCCATTCTTC 59.067 47.826 0.00 0.00 46.05 2.87
224 225 3.581332 TCACGAGTTAGAACCCCATTCTT 59.419 43.478 0.00 0.00 46.05 2.52
226 227 3.604875 TCACGAGTTAGAACCCCATTC 57.395 47.619 0.00 0.00 37.62 2.67
227 228 3.873910 CATCACGAGTTAGAACCCCATT 58.126 45.455 0.00 0.00 0.00 3.16
228 229 2.420129 GCATCACGAGTTAGAACCCCAT 60.420 50.000 0.00 0.00 0.00 4.00
229 230 1.066430 GCATCACGAGTTAGAACCCCA 60.066 52.381 0.00 0.00 0.00 4.96
230 231 1.207329 AGCATCACGAGTTAGAACCCC 59.793 52.381 0.00 0.00 0.00 4.95
231 232 2.674796 AGCATCACGAGTTAGAACCC 57.325 50.000 0.00 0.00 0.00 4.11
232 233 3.585862 TGAAGCATCACGAGTTAGAACC 58.414 45.455 0.00 0.00 0.00 3.62
233 234 3.614616 CCTGAAGCATCACGAGTTAGAAC 59.385 47.826 0.00 0.00 0.00 3.01
234 235 3.509967 TCCTGAAGCATCACGAGTTAGAA 59.490 43.478 0.00 0.00 0.00 2.10
235 236 3.089284 TCCTGAAGCATCACGAGTTAGA 58.911 45.455 0.00 0.00 0.00 2.10
236 237 3.119316 ACTCCTGAAGCATCACGAGTTAG 60.119 47.826 15.06 0.00 44.43 2.34
237 238 2.826128 ACTCCTGAAGCATCACGAGTTA 59.174 45.455 15.06 0.00 44.43 2.24
238 239 1.620819 ACTCCTGAAGCATCACGAGTT 59.379 47.619 15.06 3.61 44.43 3.01
239 240 1.261480 ACTCCTGAAGCATCACGAGT 58.739 50.000 15.06 15.06 43.04 4.18
240 241 2.376808 AACTCCTGAAGCATCACGAG 57.623 50.000 13.98 13.98 41.63 4.18
241 242 2.560981 TGTAACTCCTGAAGCATCACGA 59.439 45.455 0.00 0.00 0.00 4.35
242 243 2.959516 TGTAACTCCTGAAGCATCACG 58.040 47.619 0.00 0.00 0.00 4.35
243 244 5.886960 ATTTGTAACTCCTGAAGCATCAC 57.113 39.130 0.00 0.00 0.00 3.06
244 245 5.183713 CCAATTTGTAACTCCTGAAGCATCA 59.816 40.000 0.00 0.00 0.00 3.07
245 246 5.644644 CCAATTTGTAACTCCTGAAGCATC 58.355 41.667 0.00 0.00 0.00 3.91
246 247 4.082026 GCCAATTTGTAACTCCTGAAGCAT 60.082 41.667 0.00 0.00 0.00 3.79
247 248 3.255642 GCCAATTTGTAACTCCTGAAGCA 59.744 43.478 0.00 0.00 0.00 3.91
248 249 3.367395 GGCCAATTTGTAACTCCTGAAGC 60.367 47.826 0.00 0.00 0.00 3.86
249 250 4.082125 AGGCCAATTTGTAACTCCTGAAG 58.918 43.478 5.01 0.00 0.00 3.02
250 251 4.112634 AGGCCAATTTGTAACTCCTGAA 57.887 40.909 5.01 0.00 0.00 3.02
251 252 3.806949 AGGCCAATTTGTAACTCCTGA 57.193 42.857 5.01 0.00 0.00 3.86
252 253 4.871933 AAAGGCCAATTTGTAACTCCTG 57.128 40.909 5.01 0.00 0.00 3.86
253 254 4.653801 ACAAAAGGCCAATTTGTAACTCCT 59.346 37.500 28.25 10.23 46.21 3.69
254 255 4.956085 ACAAAAGGCCAATTTGTAACTCC 58.044 39.130 28.25 0.00 46.21 3.85
261 262 6.148645 GTGGGTAAATACAAAAGGCCAATTTG 59.851 38.462 24.50 24.50 42.18 2.32
262 263 6.183361 TGTGGGTAAATACAAAAGGCCAATTT 60.183 34.615 5.01 2.57 0.00 1.82
263 264 5.308237 TGTGGGTAAATACAAAAGGCCAATT 59.692 36.000 5.01 0.00 0.00 2.32
264 265 4.841246 TGTGGGTAAATACAAAAGGCCAAT 59.159 37.500 5.01 0.00 0.00 3.16
265 266 4.039366 GTGTGGGTAAATACAAAAGGCCAA 59.961 41.667 5.01 0.00 0.00 4.52
266 267 3.574826 GTGTGGGTAAATACAAAAGGCCA 59.425 43.478 5.01 0.00 0.00 5.36
267 268 3.574826 TGTGTGGGTAAATACAAAAGGCC 59.425 43.478 0.00 0.00 0.00 5.19
268 269 4.857509 TGTGTGGGTAAATACAAAAGGC 57.142 40.909 0.00 0.00 0.00 4.35
269 270 6.162777 CCATTGTGTGGGTAAATACAAAAGG 58.837 40.000 0.00 0.00 44.79 3.11
287 288 4.584325 ACTCTGCAAATACAACACCATTGT 59.416 37.500 0.00 0.00 37.67 2.71
288 289 5.125100 ACTCTGCAAATACAACACCATTG 57.875 39.130 0.00 0.00 0.00 2.82
289 290 6.003950 ACTACTCTGCAAATACAACACCATT 58.996 36.000 0.00 0.00 0.00 3.16
290 291 5.560724 ACTACTCTGCAAATACAACACCAT 58.439 37.500 0.00 0.00 0.00 3.55
291 292 4.968259 ACTACTCTGCAAATACAACACCA 58.032 39.130 0.00 0.00 0.00 4.17
292 293 4.392138 GGACTACTCTGCAAATACAACACC 59.608 45.833 0.00 0.00 0.00 4.16
293 294 5.238583 AGGACTACTCTGCAAATACAACAC 58.761 41.667 0.00 0.00 0.00 3.32
294 295 5.479306 GAGGACTACTCTGCAAATACAACA 58.521 41.667 0.00 0.00 43.14 3.33
305 306 6.979186 ATCCGTAGGGTAGAGGACTACTCTG 61.979 52.000 16.85 4.49 43.57 3.35
306 307 4.945172 ATCCGTAGGGTAGAGGACTACTCT 60.945 50.000 13.17 13.17 43.57 3.24
307 308 3.327464 ATCCGTAGGGTAGAGGACTACTC 59.673 52.174 0.53 0.00 43.57 2.59
308 309 3.325605 ATCCGTAGGGTAGAGGACTACT 58.674 50.000 0.53 0.00 43.57 2.57
309 310 3.786368 ATCCGTAGGGTAGAGGACTAC 57.214 52.381 0.53 0.00 43.57 2.73
322 323 3.244009 ACTCCATGCAATCAGATCCGTAG 60.244 47.826 0.00 0.00 0.00 3.51
323 324 2.700371 ACTCCATGCAATCAGATCCGTA 59.300 45.455 0.00 0.00 0.00 4.02
324 325 1.487976 ACTCCATGCAATCAGATCCGT 59.512 47.619 0.00 0.00 0.00 4.69
325 326 2.251409 ACTCCATGCAATCAGATCCG 57.749 50.000 0.00 0.00 0.00 4.18
326 327 5.411977 CAGATAACTCCATGCAATCAGATCC 59.588 44.000 0.00 0.00 0.00 3.36
327 328 5.996513 ACAGATAACTCCATGCAATCAGATC 59.003 40.000 0.00 0.00 0.00 2.75
328 329 5.938279 ACAGATAACTCCATGCAATCAGAT 58.062 37.500 0.00 0.00 0.00 2.90
329 330 5.363101 GACAGATAACTCCATGCAATCAGA 58.637 41.667 0.00 0.00 0.00 3.27
330 331 4.514441 GGACAGATAACTCCATGCAATCAG 59.486 45.833 0.00 0.00 0.00 2.90
331 332 4.454678 GGACAGATAACTCCATGCAATCA 58.545 43.478 0.00 0.00 0.00 2.57
332 333 3.496130 CGGACAGATAACTCCATGCAATC 59.504 47.826 0.00 0.00 0.00 2.67
333 334 3.470709 CGGACAGATAACTCCATGCAAT 58.529 45.455 0.00 0.00 0.00 3.56
341 342 1.135139 TCAGCAGCGGACAGATAACTC 59.865 52.381 0.00 0.00 0.00 3.01
363 364 1.269723 GGGCTGTTCTGTACCAAAAGC 59.730 52.381 7.90 7.90 0.00 3.51
364 365 1.535462 CGGGCTGTTCTGTACCAAAAG 59.465 52.381 0.00 0.00 0.00 2.27
370 371 1.337823 ACATGACGGGCTGTTCTGTAC 60.338 52.381 11.72 0.00 0.00 2.90
378 379 0.870393 GCATATCACATGACGGGCTG 59.130 55.000 0.00 0.00 0.00 4.85
379 380 0.469494 TGCATATCACATGACGGGCT 59.531 50.000 0.00 0.00 0.00 5.19
380 381 1.466167 GATGCATATCACATGACGGGC 59.534 52.381 0.00 0.00 33.38 6.13
382 383 3.615937 GCTAGATGCATATCACATGACGG 59.384 47.826 0.00 0.00 42.31 4.79
383 384 3.615937 GGCTAGATGCATATCACATGACG 59.384 47.826 0.00 0.00 45.15 4.35
384 385 4.829968 AGGCTAGATGCATATCACATGAC 58.170 43.478 0.00 0.00 45.15 3.06
385 386 5.718607 AGTAGGCTAGATGCATATCACATGA 59.281 40.000 0.00 0.00 45.15 3.07
386 387 5.975282 AGTAGGCTAGATGCATATCACATG 58.025 41.667 0.00 0.00 45.15 3.21
387 388 6.617782 AAGTAGGCTAGATGCATATCACAT 57.382 37.500 0.00 0.00 45.15 3.21
391 392 9.522804 GTACATAAAGTAGGCTAGATGCATATC 57.477 37.037 0.00 0.00 45.15 1.63
425 426 3.551046 GCGGACATAGTTCACTGATCGAT 60.551 47.826 0.00 0.00 0.00 3.59
437 438 3.531538 CACTAACCAATGCGGACATAGT 58.468 45.455 0.00 0.00 38.63 2.12
446 447 7.913821 GCTAATAAACTAACCACTAACCAATGC 59.086 37.037 0.00 0.00 0.00 3.56
485 486 6.757897 ATAGCAGATCTGATCTAGTGTAGC 57.242 41.667 27.04 16.34 37.58 3.58
489 490 5.047164 AGGCAATAGCAGATCTGATCTAGTG 60.047 44.000 27.04 24.39 44.61 2.74
493 515 5.085920 AGTAGGCAATAGCAGATCTGATCT 58.914 41.667 27.04 16.44 44.61 2.75
495 517 6.896860 AGATAGTAGGCAATAGCAGATCTGAT 59.103 38.462 27.04 22.97 44.61 2.90
503 525 5.398236 AGAGGAAGATAGTAGGCAATAGCA 58.602 41.667 0.00 0.00 44.61 3.49
551 640 1.593296 GAACTGTCGTAGGAGCCGGT 61.593 60.000 1.90 0.00 0.00 5.28
606 698 4.787598 CGAAACTTGTGGAGGAAAAGATG 58.212 43.478 0.00 0.00 0.00 2.90
609 701 2.618709 AGCGAAACTTGTGGAGGAAAAG 59.381 45.455 0.00 0.00 0.00 2.27
625 717 1.053424 AAACAGGACCCTACAGCGAA 58.947 50.000 0.00 0.00 0.00 4.70
627 719 2.981859 ATAAACAGGACCCTACAGCG 57.018 50.000 0.00 0.00 0.00 5.18
730 826 2.330216 CTTCTGGATCGGGGGTAGAAT 58.670 52.381 0.00 0.00 0.00 2.40
738 834 1.339055 TGAAAGCACTTCTGGATCGGG 60.339 52.381 0.00 0.00 34.86 5.14
740 836 3.730061 GCAATGAAAGCACTTCTGGATCG 60.730 47.826 0.00 0.00 34.86 3.69
751 847 3.954200 TGATAGACCAGCAATGAAAGCA 58.046 40.909 0.00 0.00 0.00 3.91
773 870 6.126968 TGAGAATGAGCAATGACCTGAATAGA 60.127 38.462 0.00 0.00 0.00 1.98
774 871 6.053650 TGAGAATGAGCAATGACCTGAATAG 58.946 40.000 0.00 0.00 0.00 1.73
793 896 4.281941 AGACTGTGCATACTGTTCTGAGAA 59.718 41.667 0.00 0.00 38.83 2.87
819 922 9.019656 CCTAGTTGCAGATCTGTAGATAATAGT 57.980 37.037 23.38 8.72 34.37 2.12
825 928 6.382570 AGAAACCTAGTTGCAGATCTGTAGAT 59.617 38.462 23.38 13.53 37.51 1.98
895 1016 4.082733 GGATGAAAAACCTGTTGGAGTAGC 60.083 45.833 0.00 0.00 37.04 3.58
926 1047 2.768527 TGGCACTGGAATTGTTTTTGGA 59.231 40.909 0.00 0.00 0.00 3.53
927 1048 3.191078 TGGCACTGGAATTGTTTTTGG 57.809 42.857 0.00 0.00 0.00 3.28
928 1049 4.634199 AGATGGCACTGGAATTGTTTTTG 58.366 39.130 0.00 0.00 0.00 2.44
929 1050 4.961438 AGATGGCACTGGAATTGTTTTT 57.039 36.364 0.00 0.00 0.00 1.94
946 1070 7.148255 TGGAACGGTCTGAATAAATTGAAGATG 60.148 37.037 0.00 0.00 0.00 2.90
954 1078 4.014406 GGGTTGGAACGGTCTGAATAAAT 58.986 43.478 0.00 0.00 0.00 1.40
1071 1196 8.153550 AGATATGTTGAAGCATTAGTAAGGAGG 58.846 37.037 0.00 0.00 0.00 4.30
1078 1203 7.281774 CACTCCAAGATATGTTGAAGCATTAGT 59.718 37.037 13.90 3.54 0.00 2.24
1095 1220 1.296392 CGCCATGTCCACTCCAAGA 59.704 57.895 0.00 0.00 0.00 3.02
1139 1264 1.640428 CTCGAACTGCGGCAAGATTA 58.360 50.000 3.44 0.00 41.33 1.75
1140 1265 1.639298 GCTCGAACTGCGGCAAGATT 61.639 55.000 3.44 0.00 41.33 2.40
1209 1334 2.851195 TCTTTGAGTTCCTGAAGCCAC 58.149 47.619 0.00 0.00 0.00 5.01
1248 1373 1.675641 ATGCCCGTCAAGCAAGTCC 60.676 57.895 0.00 0.00 44.83 3.85
1257 1382 1.594833 GGTGTACTCATGCCCGTCA 59.405 57.895 0.00 0.00 0.00 4.35
1262 1387 0.912486 AAGGAGGGTGTACTCATGCC 59.088 55.000 0.00 0.00 39.27 4.40
1274 1399 2.115291 GCTTGGCGCTTAAGGAGGG 61.115 63.158 20.75 3.08 41.05 4.30
1281 1406 1.976474 CCCCTTTGCTTGGCGCTTA 60.976 57.895 7.64 0.00 40.11 3.09
1312 1437 0.982852 ATGGAGGAGGCATTGTCCGA 60.983 55.000 0.00 0.00 39.30 4.55
1316 1441 2.905415 TTTGATGGAGGAGGCATTGT 57.095 45.000 0.00 0.00 0.00 2.71
1335 1460 3.192212 GCAGAGGCTTCATAAAAGTGCTT 59.808 43.478 0.00 0.00 36.96 3.91
1373 1498 1.066358 CAGAGCTCAGAATGGACAGCA 60.066 52.381 17.77 0.00 36.07 4.41
1459 2946 1.416030 TGGTAAGCAGAGCAGTTCACA 59.584 47.619 0.00 0.00 0.00 3.58
1480 2967 2.106511 GGGCCTCTGCATTATAACCAGA 59.893 50.000 0.84 13.88 40.13 3.86
1498 2991 1.284198 AGCTGATGATATGATGGGGGC 59.716 52.381 0.00 0.00 0.00 5.80
1499 2992 2.307980 ACAGCTGATGATATGATGGGGG 59.692 50.000 23.35 0.00 0.00 5.40
1505 2998 4.122046 CGGAACAACAGCTGATGATATGA 58.878 43.478 28.46 0.00 0.00 2.15
1510 3003 0.684535 TCCGGAACAACAGCTGATGA 59.315 50.000 28.46 3.89 0.00 2.92
1527 3020 1.448540 CGGCAGTGATGTGGTCTCC 60.449 63.158 0.00 0.00 0.00 3.71
1545 3038 1.734465 CGACCAATCACTTTCAGAGGC 59.266 52.381 0.00 0.00 0.00 4.70
1601 3094 4.286032 ACTTGGTAATAGCAGTTGTCCTGA 59.714 41.667 0.00 0.00 44.49 3.86
1604 3097 4.833390 AGACTTGGTAATAGCAGTTGTCC 58.167 43.478 13.97 0.00 0.00 4.02
1680 3179 1.259609 CATGTTGTGCCAAGGTGGAT 58.740 50.000 0.00 0.00 40.96 3.41
1712 3211 9.527157 TCACATCAAAATATTCTTTTACCCTCA 57.473 29.630 0.00 0.00 0.00 3.86
1809 3308 2.272146 CGTGGACATTCCCCCTGG 59.728 66.667 0.00 0.00 35.03 4.45
1862 3362 3.209410 CCTGATTCTTGCAGTATGTCCC 58.791 50.000 0.00 0.00 39.31 4.46
1863 3363 3.118261 TCCCTGATTCTTGCAGTATGTCC 60.118 47.826 0.00 0.00 39.31 4.02
1925 3425 1.619363 TCCCATTCCCTCCCACTGG 60.619 63.158 0.00 0.00 0.00 4.00
1995 3495 0.674534 ATGTATCCCGCCGAGAAGTC 59.325 55.000 0.00 0.00 0.00 3.01
2105 3612 4.385748 GCGAATTTCCAATTTCTGTTCCAC 59.614 41.667 0.00 0.00 0.00 4.02
2110 3617 3.256631 AGCAGCGAATTTCCAATTTCTGT 59.743 39.130 0.00 1.64 0.00 3.41
2125 3632 1.063912 CAACTTTTCACACAGCAGCGA 59.936 47.619 0.00 0.00 0.00 4.93
2193 3700 1.326951 AACCCACAACTTTTGCCGCT 61.327 50.000 0.00 0.00 0.00 5.52
2226 3733 3.890756 TCCATGCAGTGACATCTGTTTTT 59.109 39.130 0.00 0.00 37.70 1.94
2301 3808 8.041323 GGATCTAACTTCTCATAACTCCACAAA 58.959 37.037 0.00 0.00 0.00 2.83
2386 3893 4.037565 CCAAAGGTAAACCAACTCCTCAAC 59.962 45.833 1.26 0.00 38.89 3.18
2391 3898 3.509967 CCATCCAAAGGTAAACCAACTCC 59.490 47.826 1.26 0.00 38.89 3.85
2403 3910 2.196319 GCCTTCTGCCATCCAAAGG 58.804 57.895 0.00 0.00 41.03 3.11
2418 3925 1.927487 TGCATGAATCAACAAGGCCT 58.073 45.000 0.00 0.00 0.00 5.19
2531 4050 7.307131 TGAAGGAGATCATGCATAACATAGA 57.693 36.000 0.00 0.00 36.64 1.98
2565 4084 3.009584 AGTTCCCTTTGGAGAGTGATTCC 59.990 47.826 0.00 0.00 43.07 3.01
2628 4147 7.013083 ACACGAATAGATAGGTATCGAACAGTT 59.987 37.037 0.00 0.00 37.76 3.16
2647 4166 6.593770 TGTTGCTTCATACTATCAACACGAAT 59.406 34.615 0.00 0.00 41.12 3.34
2697 4216 5.878332 TGCAAATAATAGTGCGGATATGG 57.122 39.130 0.00 0.00 43.93 2.74
2701 4220 5.643777 GGTCTATGCAAATAATAGTGCGGAT 59.356 40.000 0.00 0.00 43.93 4.18
3088 4619 6.907206 TTTCTTTTGCACAGAAAATTCCTG 57.093 33.333 15.06 6.33 37.33 3.86
3129 4660 1.364626 CGTTCATGTCCCTCAGCTGC 61.365 60.000 9.47 0.00 0.00 5.25
3340 4872 1.005450 ACCGTGAATTGTAAGGCCCAT 59.995 47.619 0.00 0.00 0.00 4.00
3341 4873 0.402504 ACCGTGAATTGTAAGGCCCA 59.597 50.000 0.00 0.00 0.00 5.36
3462 4994 3.150767 CCGGAAAACCACAGTATTGGAA 58.849 45.455 0.00 0.00 39.24 3.53
3473 5005 2.286365 AGAGCAATTCCGGAAAACCA 57.714 45.000 23.08 0.00 0.00 3.67
3480 5012 2.291741 GCCTAATGAAGAGCAATTCCGG 59.708 50.000 0.00 0.00 0.00 5.14
3502 5034 9.797642 TGTATTCAGGTTTAGCATATTGATGAT 57.202 29.630 0.00 0.00 34.73 2.45
3515 5047 9.444600 GAAGACAAGGTAATGTATTCAGGTTTA 57.555 33.333 9.25 0.00 45.95 2.01
3525 5057 5.105064 GCCTAGTGGAAGACAAGGTAATGTA 60.105 44.000 0.00 0.00 31.72 2.29
3556 5088 8.730680 CAGTGGGCAATTGGATATACTTAATAC 58.269 37.037 7.72 0.00 0.00 1.89
3678 5210 3.411454 TCTGATCCTGAATCCACCTCT 57.589 47.619 0.00 0.00 33.01 3.69
3830 5362 3.726557 TCCATGCCTTGATGATATCCC 57.273 47.619 0.00 0.00 0.00 3.85
3854 5386 0.527385 GATCCTCTGCTCGTGACAGC 60.527 60.000 1.00 1.00 40.13 4.40


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

AutoCloner maintained by Alex Coulton.