Multiple sequence alignment - TraesCS7A01G377700

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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 TraesCS7A01G377700 chr7A 100.000 2950 0 0 1 2950 553227860 553230809 0.000000e+00 5448.0
1 TraesCS7A01G377700 chr7B 90.282 2593 127 52 440 2950 512352450 512354999 0.000000e+00 3277.0
2 TraesCS7A01G377700 chr7D 86.673 1981 96 60 311 2213 484922465 484924355 0.000000e+00 2041.0
3 TraesCS7A01G377700 chr7D 93.048 748 34 11 2205 2950 484924718 484925449 0.000000e+00 1077.0
4 TraesCS7A01G377700 chr1D 75.439 228 46 8 1508 1730 279234756 279234534 5.200000e-18 102.0
5 TraesCS7A01G377700 chr1A 74.561 228 48 9 1508 1730 351475681 351475459 1.130000e-14 91.6


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 TraesCS7A01G377700 chr7A 553227860 553230809 2949 False 5448 5448 100.0000 1 2950 1 chr7A.!!$F1 2949
1 TraesCS7A01G377700 chr7B 512352450 512354999 2549 False 3277 3277 90.2820 440 2950 1 chr7B.!!$F1 2510
2 TraesCS7A01G377700 chr7D 484922465 484925449 2984 False 1559 2041 89.8605 311 2950 2 chr7D.!!$F1 2639

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
238 239 0.032540 GAATGCCCGATTGCCCATTC 59.967 55.0 7.59 7.59 37.48 2.67 F
331 332 0.039798 GTACACGGAGAGACGCAACA 60.040 55.0 0.00 0.00 37.37 3.33 F
427 442 0.603065 AAGATTTTGCGCCCCAGAAC 59.397 50.0 4.18 0.00 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1762 1842 0.108804 CATGCCAAGCAAGGAAGCAG 60.109 55.000 0.00 0.0 43.62 4.24 R
1795 1881 1.496393 CTGCAAGAGAAGCACAGCG 59.504 57.895 0.00 0.0 37.02 5.18 R
2409 2919 1.264288 CAAGCCGCGAGACTTCTTTTT 59.736 47.619 8.23 0.0 0.00 1.94 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
27 28 8.732746 AAGTGTGTGTACTTGAATTCTTAAGT 57.267 30.769 13.79 13.79 39.33 2.24
28 29 8.732746 AGTGTGTGTACTTGAATTCTTAAGTT 57.267 30.769 14.35 0.00 38.11 2.66
29 30 9.174166 AGTGTGTGTACTTGAATTCTTAAGTTT 57.826 29.630 14.35 0.00 38.11 2.66
30 31 9.434559 GTGTGTGTACTTGAATTCTTAAGTTTC 57.565 33.333 14.35 7.94 38.11 2.78
31 32 8.332464 TGTGTGTACTTGAATTCTTAAGTTTCG 58.668 33.333 14.35 0.00 38.11 3.46
32 33 8.545420 GTGTGTACTTGAATTCTTAAGTTTCGA 58.455 33.333 14.35 6.54 38.11 3.71
33 34 9.100554 TGTGTACTTGAATTCTTAAGTTTCGAA 57.899 29.630 14.35 0.00 38.11 3.71
38 39 9.884465 ACTTGAATTCTTAAGTTTCGAATCAAG 57.116 29.630 20.74 20.74 37.72 3.02
44 45 9.831737 ATTCTTAAGTTTCGAATCAAGATGTTG 57.168 29.630 8.83 0.00 34.67 3.33
45 46 8.378172 TCTTAAGTTTCGAATCAAGATGTTGT 57.622 30.769 8.83 0.00 34.98 3.32
46 47 8.282592 TCTTAAGTTTCGAATCAAGATGTTGTG 58.717 33.333 8.83 0.00 34.98 3.33
47 48 6.618287 AAGTTTCGAATCAAGATGTTGTGA 57.382 33.333 8.83 0.00 34.98 3.58
48 49 6.808008 AGTTTCGAATCAAGATGTTGTGAT 57.192 33.333 8.83 0.00 36.00 3.06
49 50 7.905604 AGTTTCGAATCAAGATGTTGTGATA 57.094 32.000 8.83 0.00 33.31 2.15
50 51 8.322906 AGTTTCGAATCAAGATGTTGTGATAA 57.677 30.769 8.83 0.00 33.31 1.75
51 52 8.950210 AGTTTCGAATCAAGATGTTGTGATAAT 58.050 29.630 8.83 0.00 33.31 1.28
109 110 3.641437 TTTTGAGAGCGTGAAAATGGG 57.359 42.857 0.00 0.00 0.00 4.00
110 111 1.533625 TTGAGAGCGTGAAAATGGGG 58.466 50.000 0.00 0.00 0.00 4.96
111 112 0.960364 TGAGAGCGTGAAAATGGGGC 60.960 55.000 0.00 0.00 0.00 5.80
112 113 1.982073 GAGAGCGTGAAAATGGGGCG 61.982 60.000 0.00 0.00 0.00 6.13
113 114 2.282180 AGCGTGAAAATGGGGCGT 60.282 55.556 0.00 0.00 0.00 5.68
114 115 2.178273 GCGTGAAAATGGGGCGTC 59.822 61.111 0.00 0.00 0.00 5.19
115 116 2.622011 GCGTGAAAATGGGGCGTCA 61.622 57.895 0.00 0.00 0.00 4.35
116 117 1.933115 GCGTGAAAATGGGGCGTCAT 61.933 55.000 0.00 0.00 0.00 3.06
117 118 0.525761 CGTGAAAATGGGGCGTCATT 59.474 50.000 0.00 0.00 38.84 2.57
118 119 1.732077 CGTGAAAATGGGGCGTCATTG 60.732 52.381 5.65 0.00 37.42 2.82
119 120 1.543802 GTGAAAATGGGGCGTCATTGA 59.456 47.619 5.65 0.00 37.42 2.57
120 121 1.818060 TGAAAATGGGGCGTCATTGAG 59.182 47.619 5.65 0.00 37.42 3.02
121 122 0.532115 AAAATGGGGCGTCATTGAGC 59.468 50.000 5.65 0.00 37.42 4.26
128 129 3.905900 GCGTCATTGAGCCTAAAGC 57.094 52.632 0.00 0.00 44.25 3.51
141 142 4.907879 GCCTAAAGCTGCAGTATTCATT 57.092 40.909 16.64 0.12 38.99 2.57
143 144 5.995055 GCCTAAAGCTGCAGTATTCATTAG 58.005 41.667 16.64 10.63 38.99 1.73
144 145 5.760253 GCCTAAAGCTGCAGTATTCATTAGA 59.240 40.000 16.64 0.00 38.99 2.10
145 146 6.073331 GCCTAAAGCTGCAGTATTCATTAGAG 60.073 42.308 16.64 6.81 38.99 2.43
146 147 6.426328 CCTAAAGCTGCAGTATTCATTAGAGG 59.574 42.308 16.64 9.04 0.00 3.69
147 148 5.365021 AAGCTGCAGTATTCATTAGAGGT 57.635 39.130 16.64 0.00 0.00 3.85
148 149 4.701765 AGCTGCAGTATTCATTAGAGGTG 58.298 43.478 16.64 0.00 0.00 4.00
149 150 4.163078 AGCTGCAGTATTCATTAGAGGTGT 59.837 41.667 16.64 0.00 0.00 4.16
150 151 4.272018 GCTGCAGTATTCATTAGAGGTGTG 59.728 45.833 16.64 0.00 0.00 3.82
151 152 4.191544 TGCAGTATTCATTAGAGGTGTGC 58.808 43.478 0.00 0.00 0.00 4.57
152 153 4.191544 GCAGTATTCATTAGAGGTGTGCA 58.808 43.478 0.00 0.00 0.00 4.57
153 154 4.034510 GCAGTATTCATTAGAGGTGTGCAC 59.965 45.833 10.75 10.75 0.00 4.57
154 155 5.423015 CAGTATTCATTAGAGGTGTGCACT 58.577 41.667 19.41 0.00 0.00 4.40
155 156 5.877012 CAGTATTCATTAGAGGTGTGCACTT 59.123 40.000 19.41 3.42 0.00 3.16
156 157 6.036517 CAGTATTCATTAGAGGTGTGCACTTC 59.963 42.308 19.41 12.78 37.65 3.01
158 159 5.738619 TTCATTAGAGGTGTGCACTTCTA 57.261 39.130 19.41 17.83 44.52 2.10
163 164 4.199432 AGAGGTGTGCACTTCTAATGAG 57.801 45.455 19.41 0.00 44.52 2.90
164 165 3.834813 AGAGGTGTGCACTTCTAATGAGA 59.165 43.478 19.41 0.00 44.52 3.27
165 166 4.469227 AGAGGTGTGCACTTCTAATGAGAT 59.531 41.667 19.41 0.00 44.52 2.75
166 167 4.511527 AGGTGTGCACTTCTAATGAGATG 58.488 43.478 19.41 0.00 33.92 2.90
167 168 3.064545 GGTGTGCACTTCTAATGAGATGC 59.935 47.826 19.41 0.00 36.22 3.91
168 169 3.686241 GTGTGCACTTCTAATGAGATGCA 59.314 43.478 19.41 4.47 40.33 3.96
169 170 4.334759 GTGTGCACTTCTAATGAGATGCAT 59.665 41.667 19.41 0.00 42.62 3.96
171 172 5.416639 TGTGCACTTCTAATGAGATGCATTT 59.583 36.000 19.41 0.00 44.68 2.32
172 173 5.970023 GTGCACTTCTAATGAGATGCATTTC 59.030 40.000 10.32 10.23 44.68 2.17
173 174 5.884232 TGCACTTCTAATGAGATGCATTTCT 59.116 36.000 17.28 4.06 44.68 2.52
174 175 7.011763 GTGCACTTCTAATGAGATGCATTTCTA 59.988 37.037 17.28 5.50 44.68 2.10
175 176 7.226128 TGCACTTCTAATGAGATGCATTTCTAG 59.774 37.037 17.28 11.65 44.68 2.43
176 177 7.226325 GCACTTCTAATGAGATGCATTTCTAGT 59.774 37.037 17.28 6.78 44.68 2.57
177 178 9.107177 CACTTCTAATGAGATGCATTTCTAGTT 57.893 33.333 17.28 11.78 44.68 2.24
178 179 9.678260 ACTTCTAATGAGATGCATTTCTAGTTT 57.322 29.630 17.28 8.88 44.68 2.66
179 180 9.932699 CTTCTAATGAGATGCATTTCTAGTTTG 57.067 33.333 17.28 10.60 44.68 2.93
180 181 9.453572 TTCTAATGAGATGCATTTCTAGTTTGT 57.546 29.630 17.28 0.00 44.68 2.83
183 184 6.668541 TGAGATGCATTTCTAGTTTGTAGC 57.331 37.500 17.28 0.00 0.00 3.58
184 185 6.409704 TGAGATGCATTTCTAGTTTGTAGCT 58.590 36.000 17.28 0.00 0.00 3.32
185 186 6.881065 TGAGATGCATTTCTAGTTTGTAGCTT 59.119 34.615 17.28 0.00 0.00 3.74
186 187 8.040727 TGAGATGCATTTCTAGTTTGTAGCTTA 58.959 33.333 17.28 0.00 0.00 3.09
187 188 8.970859 AGATGCATTTCTAGTTTGTAGCTTAT 57.029 30.769 0.00 0.00 0.00 1.73
203 204 8.812147 TGTAGCTTATATACGAACTGATTTGG 57.188 34.615 0.00 0.00 0.00 3.28
204 205 8.635328 TGTAGCTTATATACGAACTGATTTGGA 58.365 33.333 0.00 0.00 0.00 3.53
205 206 9.130312 GTAGCTTATATACGAACTGATTTGGAG 57.870 37.037 0.00 0.00 0.00 3.86
206 207 7.952671 AGCTTATATACGAACTGATTTGGAGA 58.047 34.615 0.00 0.00 0.00 3.71
207 208 8.421784 AGCTTATATACGAACTGATTTGGAGAA 58.578 33.333 0.00 0.00 0.00 2.87
208 209 8.488764 GCTTATATACGAACTGATTTGGAGAAC 58.511 37.037 0.00 0.00 0.00 3.01
209 210 8.570096 TTATATACGAACTGATTTGGAGAACG 57.430 34.615 0.00 0.00 0.00 3.95
210 211 3.380479 ACGAACTGATTTGGAGAACGA 57.620 42.857 0.00 0.00 0.00 3.85
211 212 3.926616 ACGAACTGATTTGGAGAACGAT 58.073 40.909 0.00 0.00 0.00 3.73
212 213 4.315803 ACGAACTGATTTGGAGAACGATT 58.684 39.130 0.00 0.00 0.00 3.34
213 214 5.475719 ACGAACTGATTTGGAGAACGATTA 58.524 37.500 0.00 0.00 0.00 1.75
214 215 6.106673 ACGAACTGATTTGGAGAACGATTAT 58.893 36.000 0.00 0.00 0.00 1.28
215 216 6.594159 ACGAACTGATTTGGAGAACGATTATT 59.406 34.615 0.00 0.00 0.00 1.40
216 217 6.901887 CGAACTGATTTGGAGAACGATTATTG 59.098 38.462 0.00 0.00 0.00 1.90
217 218 7.413000 CGAACTGATTTGGAGAACGATTATTGT 60.413 37.037 0.00 0.00 0.00 2.71
218 219 7.687941 ACTGATTTGGAGAACGATTATTGTT 57.312 32.000 0.00 0.00 0.00 2.83
219 220 7.530010 ACTGATTTGGAGAACGATTATTGTTG 58.470 34.615 2.09 0.00 0.00 3.33
220 221 7.390440 ACTGATTTGGAGAACGATTATTGTTGA 59.610 33.333 2.09 0.00 0.00 3.18
221 222 8.105097 TGATTTGGAGAACGATTATTGTTGAA 57.895 30.769 2.09 0.00 0.00 2.69
222 223 8.739039 TGATTTGGAGAACGATTATTGTTGAAT 58.261 29.630 2.09 0.00 0.00 2.57
223 224 8.915871 ATTTGGAGAACGATTATTGTTGAATG 57.084 30.769 2.09 0.00 0.00 2.67
224 225 5.879237 TGGAGAACGATTATTGTTGAATGC 58.121 37.500 2.09 0.00 0.00 3.56
225 226 5.163663 TGGAGAACGATTATTGTTGAATGCC 60.164 40.000 2.09 0.00 0.00 4.40
226 227 5.248870 AGAACGATTATTGTTGAATGCCC 57.751 39.130 2.09 0.00 0.00 5.36
227 228 3.691049 ACGATTATTGTTGAATGCCCG 57.309 42.857 0.00 0.00 0.00 6.13
228 229 3.275143 ACGATTATTGTTGAATGCCCGA 58.725 40.909 0.00 0.00 0.00 5.14
229 230 3.882888 ACGATTATTGTTGAATGCCCGAT 59.117 39.130 0.00 0.00 0.00 4.18
230 231 4.338118 ACGATTATTGTTGAATGCCCGATT 59.662 37.500 0.00 0.00 0.00 3.34
231 232 4.676471 CGATTATTGTTGAATGCCCGATTG 59.324 41.667 0.00 0.00 0.00 2.67
232 233 2.298411 ATTGTTGAATGCCCGATTGC 57.702 45.000 0.00 0.00 0.00 3.56
233 234 0.246086 TTGTTGAATGCCCGATTGCC 59.754 50.000 0.00 0.00 0.00 4.52
234 235 1.141665 GTTGAATGCCCGATTGCCC 59.858 57.895 0.00 0.00 0.00 5.36
235 236 1.304796 TTGAATGCCCGATTGCCCA 60.305 52.632 0.00 0.00 0.00 5.36
236 237 0.687098 TTGAATGCCCGATTGCCCAT 60.687 50.000 0.00 0.00 0.00 4.00
237 238 0.687098 TGAATGCCCGATTGCCCATT 60.687 50.000 0.00 0.00 0.00 3.16
238 239 0.032540 GAATGCCCGATTGCCCATTC 59.967 55.000 7.59 7.59 37.48 2.67
239 240 0.687098 AATGCCCGATTGCCCATTCA 60.687 50.000 0.00 0.00 0.00 2.57
240 241 0.470456 ATGCCCGATTGCCCATTCAT 60.470 50.000 0.00 0.00 0.00 2.57
241 242 0.687098 TGCCCGATTGCCCATTCATT 60.687 50.000 0.00 0.00 0.00 2.57
242 243 0.032540 GCCCGATTGCCCATTCATTC 59.967 55.000 0.00 0.00 0.00 2.67
243 244 0.311790 CCCGATTGCCCATTCATTCG 59.688 55.000 0.00 0.00 38.68 3.34
244 245 1.024271 CCGATTGCCCATTCATTCGT 58.976 50.000 0.00 0.00 37.84 3.85
245 246 2.217750 CCGATTGCCCATTCATTCGTA 58.782 47.619 0.00 0.00 37.84 3.43
246 247 2.032030 CCGATTGCCCATTCATTCGTAC 60.032 50.000 0.00 0.00 37.84 3.67
247 248 2.348498 CGATTGCCCATTCATTCGTACG 60.348 50.000 9.53 9.53 36.01 3.67
248 249 1.374560 TTGCCCATTCATTCGTACGG 58.625 50.000 16.52 0.00 0.00 4.02
249 250 1.092921 TGCCCATTCATTCGTACGGC 61.093 55.000 16.52 7.89 35.44 5.68
250 251 0.814010 GCCCATTCATTCGTACGGCT 60.814 55.000 16.52 0.00 32.09 5.52
251 252 1.663695 CCCATTCATTCGTACGGCTT 58.336 50.000 16.52 0.00 0.00 4.35
252 253 2.828877 CCCATTCATTCGTACGGCTTA 58.171 47.619 16.52 0.00 0.00 3.09
253 254 2.800544 CCCATTCATTCGTACGGCTTAG 59.199 50.000 16.52 1.75 0.00 2.18
254 255 2.221055 CCATTCATTCGTACGGCTTAGC 59.779 50.000 16.52 0.00 0.00 3.09
255 256 2.658373 TTCATTCGTACGGCTTAGCA 57.342 45.000 16.52 0.00 0.00 3.49
256 257 2.882927 TCATTCGTACGGCTTAGCAT 57.117 45.000 16.52 0.00 0.00 3.79
257 258 2.469826 TCATTCGTACGGCTTAGCATG 58.530 47.619 16.52 0.00 0.00 4.06
258 259 2.100087 TCATTCGTACGGCTTAGCATGA 59.900 45.455 16.52 8.86 0.00 3.07
259 260 2.882927 TTCGTACGGCTTAGCATGAT 57.117 45.000 16.52 0.00 0.00 2.45
260 261 2.882927 TCGTACGGCTTAGCATGATT 57.117 45.000 16.52 0.00 0.00 2.57
261 262 3.173668 TCGTACGGCTTAGCATGATTT 57.826 42.857 16.52 0.00 0.00 2.17
262 263 3.120792 TCGTACGGCTTAGCATGATTTC 58.879 45.455 16.52 0.00 0.00 2.17
263 264 2.863740 CGTACGGCTTAGCATGATTTCA 59.136 45.455 7.57 0.00 0.00 2.69
264 265 3.308595 CGTACGGCTTAGCATGATTTCAA 59.691 43.478 7.57 0.00 0.00 2.69
265 266 4.550831 CGTACGGCTTAGCATGATTTCAAG 60.551 45.833 7.57 0.00 0.00 3.02
266 267 2.098117 ACGGCTTAGCATGATTTCAAGC 59.902 45.455 6.53 8.16 40.51 4.01
267 268 2.097954 CGGCTTAGCATGATTTCAAGCA 59.902 45.455 16.41 0.00 42.43 3.91
268 269 3.427909 CGGCTTAGCATGATTTCAAGCAA 60.428 43.478 16.41 2.70 42.43 3.91
269 270 4.110482 GGCTTAGCATGATTTCAAGCAAG 58.890 43.478 16.41 11.13 42.43 4.01
270 271 4.381292 GGCTTAGCATGATTTCAAGCAAGT 60.381 41.667 16.41 0.00 42.43 3.16
271 272 4.797349 GCTTAGCATGATTTCAAGCAAGTC 59.203 41.667 11.16 5.29 42.43 3.01
272 273 5.620654 GCTTAGCATGATTTCAAGCAAGTCA 60.621 40.000 11.16 0.00 42.43 3.41
273 274 6.519679 TTAGCATGATTTCAAGCAAGTCAT 57.480 33.333 10.07 0.00 41.04 3.06
279 280 5.716094 TGATTTCAAGCAAGTCATGAATGG 58.284 37.500 0.00 0.00 33.09 3.16
280 281 5.477637 TGATTTCAAGCAAGTCATGAATGGA 59.522 36.000 0.63 0.00 33.09 3.41
281 282 4.771590 TTCAAGCAAGTCATGAATGGAC 57.228 40.909 0.63 0.00 35.50 4.02
282 283 3.753815 TCAAGCAAGTCATGAATGGACA 58.246 40.909 0.63 0.00 37.74 4.02
283 284 4.143543 TCAAGCAAGTCATGAATGGACAA 58.856 39.130 0.63 0.00 37.74 3.18
284 285 4.768448 TCAAGCAAGTCATGAATGGACAAT 59.232 37.500 0.63 0.00 37.74 2.71
285 286 4.978083 AGCAAGTCATGAATGGACAATC 57.022 40.909 0.63 0.00 37.74 2.67
286 287 3.698040 AGCAAGTCATGAATGGACAATCC 59.302 43.478 0.63 0.00 37.74 3.01
298 299 4.764050 TGGACAATCCATACAACGGTAT 57.236 40.909 0.00 0.00 42.67 2.73
299 300 4.699637 TGGACAATCCATACAACGGTATC 58.300 43.478 0.00 0.00 42.67 2.24
300 301 4.407621 TGGACAATCCATACAACGGTATCT 59.592 41.667 0.00 0.00 42.67 1.98
301 302 4.750098 GGACAATCCATACAACGGTATCTG 59.250 45.833 0.00 0.00 38.14 2.90
302 303 4.703897 ACAATCCATACAACGGTATCTGG 58.296 43.478 0.00 0.00 38.14 3.86
303 304 2.902705 TCCATACAACGGTATCTGGC 57.097 50.000 0.00 0.00 38.14 4.85
304 305 1.414919 TCCATACAACGGTATCTGGCC 59.585 52.381 0.00 0.00 38.14 5.36
305 306 1.416401 CCATACAACGGTATCTGGCCT 59.584 52.381 3.32 0.00 38.14 5.19
306 307 2.483876 CATACAACGGTATCTGGCCTG 58.516 52.381 3.32 2.92 38.14 4.85
307 308 0.828022 TACAACGGTATCTGGCCTGG 59.172 55.000 10.07 0.00 0.00 4.45
308 309 1.819632 CAACGGTATCTGGCCTGGC 60.820 63.158 11.05 11.05 0.00 4.85
309 310 3.385749 AACGGTATCTGGCCTGGCG 62.386 63.158 13.40 0.00 0.00 5.69
331 332 0.039798 GTACACGGAGAGACGCAACA 60.040 55.000 0.00 0.00 37.37 3.33
361 364 3.968568 CACCGTCCGTCCGTCACA 61.969 66.667 0.00 0.00 0.00 3.58
387 392 4.218722 GGTACGCAACCCATCAGG 57.781 61.111 0.00 0.00 43.16 3.86
427 442 0.603065 AAGATTTTGCGCCCCAGAAC 59.397 50.000 4.18 0.00 0.00 3.01
428 443 1.215382 GATTTTGCGCCCCAGAACC 59.785 57.895 4.18 0.00 0.00 3.62
429 444 1.531739 GATTTTGCGCCCCAGAACCA 61.532 55.000 4.18 0.00 0.00 3.67
430 445 0.904394 ATTTTGCGCCCCAGAACCAT 60.904 50.000 4.18 0.00 0.00 3.55
431 446 1.118356 TTTTGCGCCCCAGAACCATT 61.118 50.000 4.18 0.00 0.00 3.16
432 447 1.814772 TTTGCGCCCCAGAACCATTG 61.815 55.000 4.18 0.00 0.00 2.82
433 448 3.451894 GCGCCCCAGAACCATTGG 61.452 66.667 0.00 0.00 35.41 3.16
489 504 1.151777 CGTTCCTTCGCGCCACATAT 61.152 55.000 0.00 0.00 0.00 1.78
496 511 1.954146 CGCGCCACATATAACCGCT 60.954 57.895 0.00 0.00 42.21 5.52
559 574 1.881602 CAAAGCCAAGCTGGAGAGC 59.118 57.895 6.40 0.00 46.64 4.09
832 880 2.029828 CCCTGCTCGCCGGATATATATC 60.030 54.545 5.05 13.50 0.00 1.63
833 881 2.887783 CCTGCTCGCCGGATATATATCT 59.112 50.000 19.72 0.00 33.28 1.98
923 972 2.760374 CCAGTCCGCCTGAGATATTTC 58.240 52.381 2.22 0.00 44.49 2.17
924 973 2.366916 CCAGTCCGCCTGAGATATTTCT 59.633 50.000 2.22 0.00 44.49 2.52
939 988 8.770438 GAGATATTTCTCTCTCTCTCTCTCTC 57.230 42.308 5.97 0.00 44.29 3.20
940 989 8.503428 AGATATTTCTCTCTCTCTCTCTCTCT 57.497 38.462 0.00 0.00 0.00 3.10
941 990 8.592809 AGATATTTCTCTCTCTCTCTCTCTCTC 58.407 40.741 0.00 0.00 0.00 3.20
942 991 6.821616 ATTTCTCTCTCTCTCTCTCTCTCT 57.178 41.667 0.00 0.00 0.00 3.10
943 992 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
944 993 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
945 994 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
969 1018 1.079256 CTCTCTGGGGTGAGGGTGA 59.921 63.158 0.00 0.00 34.98 4.02
973 1026 3.537506 TGGGGTGAGGGTGAGGGA 61.538 66.667 0.00 0.00 0.00 4.20
974 1027 3.009714 GGGGTGAGGGTGAGGGAC 61.010 72.222 0.00 0.00 0.00 4.46
1075 1128 2.890474 CGGCGGTGGAGCATGTAC 60.890 66.667 0.00 0.00 39.27 2.90
1337 1411 3.412408 GGGGGAGGAACAGGAGGC 61.412 72.222 0.00 0.00 0.00 4.70
1742 1822 3.403936 ACTGGTCAGTCAGCCAAAC 57.596 52.632 0.00 0.00 36.92 2.93
1744 1824 1.064758 ACTGGTCAGTCAGCCAAACAA 60.065 47.619 0.00 0.00 36.92 2.83
1795 1881 0.166814 GGCATGCGTGACAGTTTCTC 59.833 55.000 12.44 0.00 31.88 2.87
1867 1953 4.194720 CGCCGAGGAGGAAGACGG 62.195 72.222 0.00 0.00 45.00 4.79
1943 2029 1.459158 ATCCTCCATCAGAGCGGCT 60.459 57.895 0.00 0.00 41.74 5.52
1984 2070 8.644216 TCAATCTCACTACCAGTAAACAAACTA 58.356 33.333 0.00 0.00 0.00 2.24
2026 2112 2.100031 GCGACATGCCACGATCACA 61.100 57.895 10.79 0.00 37.76 3.58
2028 2114 1.717937 GACATGCCACGATCACAGC 59.282 57.895 0.00 0.00 0.00 4.40
2035 2121 3.071206 ACGATCACAGCGGCCTCT 61.071 61.111 0.00 0.00 0.00 3.69
2042 2128 3.847602 CAGCGGCCTCTGAGGGAG 61.848 72.222 24.43 0.38 41.51 4.30
2121 2237 0.895530 GGCTACCTGTGTGAGCAGTA 59.104 55.000 0.00 0.00 37.98 2.74
2191 2330 3.676049 GCCTAATAAGGTTTTGCTGTGCC 60.676 47.826 0.00 0.00 45.64 5.01
2226 2736 6.823689 AGAATGTTCCTGATAACATGGTGTAC 59.176 38.462 0.00 0.00 46.72 2.90
2229 2739 4.118093 TCCTGATAACATGGTGTACGTG 57.882 45.455 0.00 0.00 41.98 4.49
2354 2864 4.397420 ACACTGAATGCACCAAGTTCATA 58.603 39.130 0.39 0.00 32.05 2.15
2355 2865 4.456911 ACACTGAATGCACCAAGTTCATAG 59.543 41.667 0.39 0.23 32.05 2.23
2366 2876 4.567971 CCAAGTTCATAGCAAAATTGGCA 58.432 39.130 0.00 0.00 42.68 4.92
2389 2899 7.201600 GGCACAAATTTTGCAGTAAAAGAAGAA 60.202 33.333 19.78 0.00 41.26 2.52
2400 2910 7.093509 TGCAGTAAAAGAAGAAAAGGGAAAACT 60.094 33.333 0.00 0.00 0.00 2.66
2406 2916 4.895297 AGAAGAAAAGGGAAAACTCATGCA 59.105 37.500 0.00 0.00 0.00 3.96
2409 2919 2.978156 AAGGGAAAACTCATGCAGGA 57.022 45.000 0.00 0.00 0.00 3.86
2425 2935 1.461127 CAGGAAAAAGAAGTCTCGCGG 59.539 52.381 6.13 0.00 0.00 6.46
2427 2937 1.149148 GAAAAAGAAGTCTCGCGGCT 58.851 50.000 6.13 0.00 0.00 5.52
2612 3122 4.522789 AGCCACAAGTTTACTACCCAAATG 59.477 41.667 0.00 0.00 0.00 2.32
2633 3143 3.256383 TGACAAAAATGCAGACATGGGAG 59.744 43.478 0.00 0.00 36.36 4.30
2673 3183 2.548067 GCTTTCCGAAAGACTGGACTCA 60.548 50.000 22.55 0.00 41.02 3.41
2674 3184 3.728845 CTTTCCGAAAGACTGGACTCAA 58.271 45.455 14.72 0.00 41.02 3.02
2755 3265 1.442526 CGGATGGGATCTGCAGTTGC 61.443 60.000 14.67 10.88 42.50 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.732746 ACTTAAGAATTCAAGTACACACACTT 57.267 30.769 10.09 0.00 39.34 3.16
3 4 8.732746 AACTTAAGAATTCAAGTACACACACT 57.267 30.769 10.09 0.00 33.92 3.55
4 5 9.434559 GAAACTTAAGAATTCAAGTACACACAC 57.565 33.333 10.09 0.00 33.92 3.82
5 6 8.332464 CGAAACTTAAGAATTCAAGTACACACA 58.668 33.333 10.09 0.00 33.92 3.72
6 7 8.545420 TCGAAACTTAAGAATTCAAGTACACAC 58.455 33.333 10.09 1.07 33.92 3.82
7 8 8.651391 TCGAAACTTAAGAATTCAAGTACACA 57.349 30.769 10.09 0.00 33.92 3.72
12 13 9.884465 CTTGATTCGAAACTTAAGAATTCAAGT 57.116 29.630 10.09 6.78 36.38 3.16
18 19 9.831737 CAACATCTTGATTCGAAACTTAAGAAT 57.168 29.630 10.09 0.00 37.32 2.40
19 20 8.836413 ACAACATCTTGATTCGAAACTTAAGAA 58.164 29.630 10.09 0.00 0.00 2.52
20 21 8.282592 CACAACATCTTGATTCGAAACTTAAGA 58.717 33.333 10.09 10.13 0.00 2.10
21 22 8.282592 TCACAACATCTTGATTCGAAACTTAAG 58.717 33.333 0.00 0.00 0.00 1.85
22 23 8.148807 TCACAACATCTTGATTCGAAACTTAA 57.851 30.769 0.00 0.00 0.00 1.85
23 24 7.722795 TCACAACATCTTGATTCGAAACTTA 57.277 32.000 0.00 0.00 0.00 2.24
24 25 6.618287 TCACAACATCTTGATTCGAAACTT 57.382 33.333 0.00 0.00 0.00 2.66
25 26 6.808008 ATCACAACATCTTGATTCGAAACT 57.192 33.333 0.00 0.00 0.00 2.66
88 89 3.243704 CCCCATTTTCACGCTCTCAAAAA 60.244 43.478 0.00 0.00 0.00 1.94
89 90 2.295909 CCCCATTTTCACGCTCTCAAAA 59.704 45.455 0.00 0.00 0.00 2.44
90 91 1.885887 CCCCATTTTCACGCTCTCAAA 59.114 47.619 0.00 0.00 0.00 2.69
91 92 1.533625 CCCCATTTTCACGCTCTCAA 58.466 50.000 0.00 0.00 0.00 3.02
92 93 0.960364 GCCCCATTTTCACGCTCTCA 60.960 55.000 0.00 0.00 0.00 3.27
93 94 1.803289 GCCCCATTTTCACGCTCTC 59.197 57.895 0.00 0.00 0.00 3.20
94 95 2.040544 CGCCCCATTTTCACGCTCT 61.041 57.895 0.00 0.00 0.00 4.09
95 96 2.253414 GACGCCCCATTTTCACGCTC 62.253 60.000 0.00 0.00 0.00 5.03
96 97 2.282180 ACGCCCCATTTTCACGCT 60.282 55.556 0.00 0.00 0.00 5.07
97 98 1.933115 ATGACGCCCCATTTTCACGC 61.933 55.000 0.00 0.00 0.00 5.34
98 99 0.525761 AATGACGCCCCATTTTCACG 59.474 50.000 0.00 0.00 33.29 4.35
99 100 1.543802 TCAATGACGCCCCATTTTCAC 59.456 47.619 0.00 0.00 34.77 3.18
100 101 1.818060 CTCAATGACGCCCCATTTTCA 59.182 47.619 0.00 0.00 34.77 2.69
101 102 1.469767 GCTCAATGACGCCCCATTTTC 60.470 52.381 0.00 0.00 34.77 2.29
102 103 0.532115 GCTCAATGACGCCCCATTTT 59.468 50.000 0.00 0.00 34.77 1.82
103 104 1.322538 GGCTCAATGACGCCCCATTT 61.323 55.000 11.11 0.00 40.43 2.32
104 105 1.754234 GGCTCAATGACGCCCCATT 60.754 57.895 11.11 0.00 40.43 3.16
105 106 2.124151 GGCTCAATGACGCCCCAT 60.124 61.111 11.11 0.00 40.43 4.00
109 110 0.378610 GCTTTAGGCTCAATGACGCC 59.621 55.000 13.42 13.42 46.65 5.68
110 111 3.905900 GCTTTAGGCTCAATGACGC 57.094 52.632 0.00 0.00 38.06 5.19
120 121 4.907879 AATGAATACTGCAGCTTTAGGC 57.092 40.909 15.27 0.00 42.19 3.93
121 122 6.426328 CCTCTAATGAATACTGCAGCTTTAGG 59.574 42.308 15.27 6.38 0.00 2.69
122 123 6.989169 ACCTCTAATGAATACTGCAGCTTTAG 59.011 38.462 15.27 14.26 0.00 1.85
123 124 6.763135 CACCTCTAATGAATACTGCAGCTTTA 59.237 38.462 15.27 5.06 0.00 1.85
124 125 5.587844 CACCTCTAATGAATACTGCAGCTTT 59.412 40.000 15.27 7.61 0.00 3.51
125 126 5.121811 CACCTCTAATGAATACTGCAGCTT 58.878 41.667 15.27 7.83 0.00 3.74
126 127 4.163078 ACACCTCTAATGAATACTGCAGCT 59.837 41.667 15.27 3.67 0.00 4.24
127 128 4.272018 CACACCTCTAATGAATACTGCAGC 59.728 45.833 15.27 0.00 0.00 5.25
128 129 4.272018 GCACACCTCTAATGAATACTGCAG 59.728 45.833 13.48 13.48 0.00 4.41
129 130 4.191544 GCACACCTCTAATGAATACTGCA 58.808 43.478 0.00 0.00 0.00 4.41
130 131 4.034510 GTGCACACCTCTAATGAATACTGC 59.965 45.833 13.17 0.00 0.00 4.40
131 132 5.423015 AGTGCACACCTCTAATGAATACTG 58.577 41.667 21.04 0.00 0.00 2.74
132 133 5.683876 AGTGCACACCTCTAATGAATACT 57.316 39.130 21.04 0.00 0.00 2.12
133 134 6.109359 AGAAGTGCACACCTCTAATGAATAC 58.891 40.000 21.04 0.00 30.79 1.89
134 135 6.299805 AGAAGTGCACACCTCTAATGAATA 57.700 37.500 21.04 0.00 30.79 1.75
135 136 5.171339 AGAAGTGCACACCTCTAATGAAT 57.829 39.130 21.04 0.00 30.79 2.57
136 137 4.623932 AGAAGTGCACACCTCTAATGAA 57.376 40.909 21.04 0.00 30.79 2.57
137 138 5.738619 TTAGAAGTGCACACCTCTAATGA 57.261 39.130 21.04 4.79 38.64 2.57
140 141 5.480422 TCTCATTAGAAGTGCACACCTCTAA 59.520 40.000 25.56 25.56 44.05 2.10
141 142 5.016831 TCTCATTAGAAGTGCACACCTCTA 58.983 41.667 21.04 17.62 34.27 2.43
142 143 3.834813 TCTCATTAGAAGTGCACACCTCT 59.165 43.478 21.04 18.62 36.24 3.69
143 144 4.193826 TCTCATTAGAAGTGCACACCTC 57.806 45.455 21.04 12.27 0.00 3.85
144 145 4.511527 CATCTCATTAGAAGTGCACACCT 58.488 43.478 21.04 16.97 34.73 4.00
145 146 3.064545 GCATCTCATTAGAAGTGCACACC 59.935 47.826 21.04 10.04 35.47 4.16
146 147 3.686241 TGCATCTCATTAGAAGTGCACAC 59.314 43.478 21.04 12.64 38.50 3.82
147 148 3.941573 TGCATCTCATTAGAAGTGCACA 58.058 40.909 21.04 0.00 38.50 4.57
148 149 5.496133 AATGCATCTCATTAGAAGTGCAC 57.504 39.130 9.40 9.40 43.24 4.57
149 150 5.884232 AGAAATGCATCTCATTAGAAGTGCA 59.116 36.000 2.24 7.46 44.23 4.57
150 151 6.374565 AGAAATGCATCTCATTAGAAGTGC 57.625 37.500 2.24 0.00 44.23 4.40
151 152 8.659925 ACTAGAAATGCATCTCATTAGAAGTG 57.340 34.615 2.24 0.00 44.23 3.16
152 153 9.678260 AAACTAGAAATGCATCTCATTAGAAGT 57.322 29.630 2.24 0.00 44.23 3.01
153 154 9.932699 CAAACTAGAAATGCATCTCATTAGAAG 57.067 33.333 2.24 0.00 44.23 2.85
154 155 9.453572 ACAAACTAGAAATGCATCTCATTAGAA 57.546 29.630 2.24 0.00 44.23 2.10
157 158 8.830580 GCTACAAACTAGAAATGCATCTCATTA 58.169 33.333 2.24 0.00 44.23 1.90
158 159 7.555554 AGCTACAAACTAGAAATGCATCTCATT 59.444 33.333 2.24 0.00 46.82 2.57
159 160 7.052873 AGCTACAAACTAGAAATGCATCTCAT 58.947 34.615 2.24 0.00 36.87 2.90
160 161 6.409704 AGCTACAAACTAGAAATGCATCTCA 58.590 36.000 2.24 0.00 0.00 3.27
161 162 6.917217 AGCTACAAACTAGAAATGCATCTC 57.083 37.500 0.00 0.00 0.00 2.75
162 163 8.970859 ATAAGCTACAAACTAGAAATGCATCT 57.029 30.769 0.00 0.00 0.00 2.90
177 178 9.256477 CCAAATCAGTTCGTATATAAGCTACAA 57.744 33.333 0.00 0.00 0.00 2.41
178 179 8.635328 TCCAAATCAGTTCGTATATAAGCTACA 58.365 33.333 0.00 0.00 0.00 2.74
179 180 9.130312 CTCCAAATCAGTTCGTATATAAGCTAC 57.870 37.037 0.00 0.00 0.00 3.58
180 181 9.074576 TCTCCAAATCAGTTCGTATATAAGCTA 57.925 33.333 0.00 0.00 0.00 3.32
181 182 7.952671 TCTCCAAATCAGTTCGTATATAAGCT 58.047 34.615 0.00 0.00 0.00 3.74
182 183 8.488764 GTTCTCCAAATCAGTTCGTATATAAGC 58.511 37.037 0.00 0.00 0.00 3.09
183 184 8.691727 CGTTCTCCAAATCAGTTCGTATATAAG 58.308 37.037 0.00 0.00 0.00 1.73
184 185 8.407832 TCGTTCTCCAAATCAGTTCGTATATAA 58.592 33.333 0.00 0.00 0.00 0.98
185 186 7.933396 TCGTTCTCCAAATCAGTTCGTATATA 58.067 34.615 0.00 0.00 0.00 0.86
186 187 6.802608 TCGTTCTCCAAATCAGTTCGTATAT 58.197 36.000 0.00 0.00 0.00 0.86
187 188 6.198650 TCGTTCTCCAAATCAGTTCGTATA 57.801 37.500 0.00 0.00 0.00 1.47
188 189 5.068234 TCGTTCTCCAAATCAGTTCGTAT 57.932 39.130 0.00 0.00 0.00 3.06
189 190 4.508461 TCGTTCTCCAAATCAGTTCGTA 57.492 40.909 0.00 0.00 0.00 3.43
190 191 3.380479 TCGTTCTCCAAATCAGTTCGT 57.620 42.857 0.00 0.00 0.00 3.85
191 192 4.928661 AATCGTTCTCCAAATCAGTTCG 57.071 40.909 0.00 0.00 0.00 3.95
192 193 7.752695 ACAATAATCGTTCTCCAAATCAGTTC 58.247 34.615 0.00 0.00 0.00 3.01
193 194 7.687941 ACAATAATCGTTCTCCAAATCAGTT 57.312 32.000 0.00 0.00 0.00 3.16
194 195 7.390440 TCAACAATAATCGTTCTCCAAATCAGT 59.610 33.333 0.00 0.00 0.00 3.41
195 196 7.751732 TCAACAATAATCGTTCTCCAAATCAG 58.248 34.615 0.00 0.00 0.00 2.90
196 197 7.680442 TCAACAATAATCGTTCTCCAAATCA 57.320 32.000 0.00 0.00 0.00 2.57
197 198 9.013490 CATTCAACAATAATCGTTCTCCAAATC 57.987 33.333 0.00 0.00 0.00 2.17
198 199 7.489113 GCATTCAACAATAATCGTTCTCCAAAT 59.511 33.333 0.00 0.00 0.00 2.32
199 200 6.806249 GCATTCAACAATAATCGTTCTCCAAA 59.194 34.615 0.00 0.00 0.00 3.28
200 201 6.321717 GCATTCAACAATAATCGTTCTCCAA 58.678 36.000 0.00 0.00 0.00 3.53
201 202 5.163663 GGCATTCAACAATAATCGTTCTCCA 60.164 40.000 0.00 0.00 0.00 3.86
202 203 5.273944 GGCATTCAACAATAATCGTTCTCC 58.726 41.667 0.00 0.00 0.00 3.71
203 204 5.273944 GGGCATTCAACAATAATCGTTCTC 58.726 41.667 0.00 0.00 0.00 2.87
204 205 4.201910 CGGGCATTCAACAATAATCGTTCT 60.202 41.667 0.00 0.00 0.00 3.01
205 206 4.035017 CGGGCATTCAACAATAATCGTTC 58.965 43.478 0.00 0.00 0.00 3.95
206 207 3.692101 TCGGGCATTCAACAATAATCGTT 59.308 39.130 0.00 0.00 0.00 3.85
207 208 3.275143 TCGGGCATTCAACAATAATCGT 58.725 40.909 0.00 0.00 0.00 3.73
208 209 3.961477 TCGGGCATTCAACAATAATCG 57.039 42.857 0.00 0.00 0.00 3.34
209 210 4.445385 GCAATCGGGCATTCAACAATAATC 59.555 41.667 0.00 0.00 0.00 1.75
210 211 4.370917 GCAATCGGGCATTCAACAATAAT 58.629 39.130 0.00 0.00 0.00 1.28
211 212 3.430098 GGCAATCGGGCATTCAACAATAA 60.430 43.478 0.00 0.00 42.77 1.40
212 213 2.100584 GGCAATCGGGCATTCAACAATA 59.899 45.455 0.00 0.00 42.77 1.90
213 214 1.134729 GGCAATCGGGCATTCAACAAT 60.135 47.619 0.00 0.00 42.77 2.71
214 215 0.246086 GGCAATCGGGCATTCAACAA 59.754 50.000 0.00 0.00 42.77 2.83
215 216 1.603236 GGGCAATCGGGCATTCAACA 61.603 55.000 0.00 0.00 45.66 3.33
216 217 1.141665 GGGCAATCGGGCATTCAAC 59.858 57.895 0.00 0.00 45.66 3.18
217 218 0.687098 ATGGGCAATCGGGCATTCAA 60.687 50.000 0.00 0.00 45.66 2.69
218 219 0.687098 AATGGGCAATCGGGCATTCA 60.687 50.000 0.00 0.00 45.66 2.57
219 220 0.032540 GAATGGGCAATCGGGCATTC 59.967 55.000 0.00 0.00 45.66 2.67
220 221 0.687098 TGAATGGGCAATCGGGCATT 60.687 50.000 0.00 0.00 45.66 3.56
221 222 0.470456 ATGAATGGGCAATCGGGCAT 60.470 50.000 0.00 0.00 45.66 4.40
222 223 0.687098 AATGAATGGGCAATCGGGCA 60.687 50.000 0.00 0.00 45.66 5.36
223 224 0.032540 GAATGAATGGGCAATCGGGC 59.967 55.000 0.00 0.00 42.44 6.13
224 225 0.311790 CGAATGAATGGGCAATCGGG 59.688 55.000 0.00 0.00 37.49 5.14
225 226 1.024271 ACGAATGAATGGGCAATCGG 58.976 50.000 0.00 0.00 43.47 4.18
226 227 2.348498 CGTACGAATGAATGGGCAATCG 60.348 50.000 10.44 0.00 44.42 3.34
227 228 2.032030 CCGTACGAATGAATGGGCAATC 60.032 50.000 18.76 0.00 0.00 2.67
228 229 1.946768 CCGTACGAATGAATGGGCAAT 59.053 47.619 18.76 0.00 0.00 3.56
229 230 1.374560 CCGTACGAATGAATGGGCAA 58.625 50.000 18.76 0.00 0.00 4.52
230 231 1.092921 GCCGTACGAATGAATGGGCA 61.093 55.000 18.76 0.00 38.88 5.36
231 232 0.814010 AGCCGTACGAATGAATGGGC 60.814 55.000 18.76 8.07 39.33 5.36
232 233 1.663695 AAGCCGTACGAATGAATGGG 58.336 50.000 18.76 0.00 0.00 4.00
233 234 2.221055 GCTAAGCCGTACGAATGAATGG 59.779 50.000 18.76 0.00 0.00 3.16
234 235 2.863740 TGCTAAGCCGTACGAATGAATG 59.136 45.455 18.76 0.00 0.00 2.67
235 236 3.173668 TGCTAAGCCGTACGAATGAAT 57.826 42.857 18.76 0.00 0.00 2.57
236 237 2.658373 TGCTAAGCCGTACGAATGAA 57.342 45.000 18.76 0.00 0.00 2.57
237 238 2.100087 TCATGCTAAGCCGTACGAATGA 59.900 45.455 18.76 10.53 0.00 2.57
238 239 2.469826 TCATGCTAAGCCGTACGAATG 58.530 47.619 18.76 8.51 0.00 2.67
239 240 2.882927 TCATGCTAAGCCGTACGAAT 57.117 45.000 18.76 4.71 0.00 3.34
240 241 2.882927 ATCATGCTAAGCCGTACGAA 57.117 45.000 18.76 0.00 0.00 3.85
241 242 2.882927 AATCATGCTAAGCCGTACGA 57.117 45.000 18.76 0.00 0.00 3.43
242 243 2.863740 TGAAATCATGCTAAGCCGTACG 59.136 45.455 8.69 8.69 0.00 3.67
243 244 4.786609 GCTTGAAATCATGCTAAGCCGTAC 60.787 45.833 12.51 0.00 41.90 3.67
244 245 3.312421 GCTTGAAATCATGCTAAGCCGTA 59.688 43.478 12.51 0.00 41.90 4.02
245 246 2.098117 GCTTGAAATCATGCTAAGCCGT 59.902 45.455 12.51 0.00 41.90 5.68
246 247 2.097954 TGCTTGAAATCATGCTAAGCCG 59.902 45.455 18.42 0.00 44.41 5.52
247 248 3.788333 TGCTTGAAATCATGCTAAGCC 57.212 42.857 18.42 0.00 44.41 4.35
248 249 4.741342 ACTTGCTTGAAATCATGCTAAGC 58.259 39.130 18.42 9.24 44.41 3.09
249 250 5.946298 TGACTTGCTTGAAATCATGCTAAG 58.054 37.500 18.42 19.07 44.41 2.18
250 251 5.963176 TGACTTGCTTGAAATCATGCTAA 57.037 34.783 18.42 11.71 44.41 3.09
251 252 5.648960 TCATGACTTGCTTGAAATCATGCTA 59.351 36.000 18.42 12.10 44.08 3.49
252 253 4.461431 TCATGACTTGCTTGAAATCATGCT 59.539 37.500 18.42 2.94 44.08 3.79
253 254 4.740268 TCATGACTTGCTTGAAATCATGC 58.260 39.130 12.80 12.80 44.08 4.06
254 255 6.255670 CCATTCATGACTTGCTTGAAATCATG 59.744 38.462 0.00 6.24 45.22 3.07
255 256 6.153851 TCCATTCATGACTTGCTTGAAATCAT 59.846 34.615 0.00 0.00 41.97 2.45
256 257 5.477637 TCCATTCATGACTTGCTTGAAATCA 59.522 36.000 0.00 0.00 41.97 2.57
257 258 5.803967 GTCCATTCATGACTTGCTTGAAATC 59.196 40.000 0.00 0.00 41.97 2.17
258 259 5.244402 TGTCCATTCATGACTTGCTTGAAAT 59.756 36.000 0.00 0.00 41.97 2.17
259 260 4.583907 TGTCCATTCATGACTTGCTTGAAA 59.416 37.500 0.00 0.00 41.97 2.69
260 261 4.143543 TGTCCATTCATGACTTGCTTGAA 58.856 39.130 0.00 0.00 42.59 2.69
261 262 3.753815 TGTCCATTCATGACTTGCTTGA 58.246 40.909 0.00 0.00 0.00 3.02
262 263 4.508461 TTGTCCATTCATGACTTGCTTG 57.492 40.909 0.00 0.00 0.00 4.01
263 264 4.159135 GGATTGTCCATTCATGACTTGCTT 59.841 41.667 0.00 0.00 36.28 3.91
264 265 3.698040 GGATTGTCCATTCATGACTTGCT 59.302 43.478 0.00 0.00 36.28 3.91
265 266 3.444742 TGGATTGTCCATTCATGACTTGC 59.555 43.478 0.00 0.00 42.67 4.01
278 279 4.750098 CAGATACCGTTGTATGGATTGTCC 59.250 45.833 0.00 0.00 37.80 4.02
279 280 4.750098 CCAGATACCGTTGTATGGATTGTC 59.250 45.833 0.00 0.00 37.80 3.18
280 281 4.703897 CCAGATACCGTTGTATGGATTGT 58.296 43.478 0.00 0.00 37.80 2.71
281 282 3.498397 GCCAGATACCGTTGTATGGATTG 59.502 47.826 0.00 0.00 37.80 2.67
282 283 3.496160 GGCCAGATACCGTTGTATGGATT 60.496 47.826 0.00 0.00 37.80 3.01
283 284 2.038557 GGCCAGATACCGTTGTATGGAT 59.961 50.000 0.00 0.00 37.80 3.41
284 285 1.414919 GGCCAGATACCGTTGTATGGA 59.585 52.381 0.00 0.00 37.80 3.41
285 286 1.416401 AGGCCAGATACCGTTGTATGG 59.584 52.381 5.01 0.00 37.80 2.74
286 287 2.483876 CAGGCCAGATACCGTTGTATG 58.516 52.381 5.01 0.00 37.80 2.39
287 288 1.416401 CCAGGCCAGATACCGTTGTAT 59.584 52.381 5.01 0.00 40.41 2.29
288 289 0.828022 CCAGGCCAGATACCGTTGTA 59.172 55.000 5.01 0.00 0.00 2.41
289 290 1.602237 CCAGGCCAGATACCGTTGT 59.398 57.895 5.01 0.00 0.00 3.32
290 291 1.819632 GCCAGGCCAGATACCGTTG 60.820 63.158 5.01 0.00 0.00 4.10
291 292 2.590092 GCCAGGCCAGATACCGTT 59.410 61.111 5.01 0.00 0.00 4.44
292 293 3.849951 CGCCAGGCCAGATACCGT 61.850 66.667 5.01 0.00 0.00 4.83
293 294 2.421877 CTACGCCAGGCCAGATACCG 62.422 65.000 5.01 0.71 0.00 4.02
294 295 1.367840 CTACGCCAGGCCAGATACC 59.632 63.158 5.01 0.00 0.00 2.73
295 296 1.000496 GTACTACGCCAGGCCAGATAC 60.000 57.143 5.01 5.04 0.00 2.24
296 297 1.325355 GTACTACGCCAGGCCAGATA 58.675 55.000 5.01 0.00 0.00 1.98
297 298 0.686441 TGTACTACGCCAGGCCAGAT 60.686 55.000 5.01 0.00 0.00 2.90
298 299 1.304630 TGTACTACGCCAGGCCAGA 60.305 57.895 5.01 0.00 0.00 3.86
299 300 1.153628 GTGTACTACGCCAGGCCAG 60.154 63.158 5.01 5.97 0.00 4.85
300 301 2.975536 GTGTACTACGCCAGGCCA 59.024 61.111 5.01 0.00 0.00 5.36
301 302 2.202703 CGTGTACTACGCCAGGCC 60.203 66.667 5.63 0.00 46.92 5.19
309 310 1.081892 TGCGTCTCTCCGTGTACTAC 58.918 55.000 0.00 0.00 0.00 2.73
356 359 1.291272 GTACCCCTCCGTGTGTGAC 59.709 63.158 0.00 0.00 0.00 3.67
359 362 3.688159 GCGTACCCCTCCGTGTGT 61.688 66.667 0.00 0.00 0.00 3.72
361 364 2.918802 TTGCGTACCCCTCCGTGT 60.919 61.111 0.00 0.00 0.00 4.49
371 376 2.112815 GGCCTGATGGGTTGCGTAC 61.113 63.158 0.00 0.00 37.43 3.67
380 385 4.256180 GTAGGGGCGGCCTGATGG 62.256 72.222 28.80 0.00 0.00 3.51
381 386 3.479203 TGTAGGGGCGGCCTGATG 61.479 66.667 28.80 0.00 0.00 3.07
382 387 3.480133 GTGTAGGGGCGGCCTGAT 61.480 66.667 28.80 16.36 0.00 2.90
383 388 4.715130 AGTGTAGGGGCGGCCTGA 62.715 66.667 28.80 13.30 0.00 3.86
387 392 3.682292 CTTGGAGTGTAGGGGCGGC 62.682 68.421 0.00 0.00 0.00 6.53
403 418 1.257750 GGGGCGCAAAATCTTCCCTT 61.258 55.000 10.83 0.00 37.16 3.95
427 442 1.288932 AGGGAAGATCCAACCCAATGG 59.711 52.381 17.79 0.00 45.43 3.16
428 443 2.762327 CAAGGGAAGATCCAACCCAATG 59.238 50.000 17.79 13.18 45.43 2.82
429 444 2.889756 GCAAGGGAAGATCCAACCCAAT 60.890 50.000 17.79 6.96 45.43 3.16
430 445 1.549950 GCAAGGGAAGATCCAACCCAA 60.550 52.381 17.79 0.00 45.43 4.12
431 446 0.039618 GCAAGGGAAGATCCAACCCA 59.960 55.000 17.79 0.00 45.43 4.51
432 447 0.684479 GGCAAGGGAAGATCCAACCC 60.684 60.000 10.38 10.38 38.64 4.11
433 448 1.032114 CGGCAAGGGAAGATCCAACC 61.032 60.000 0.00 0.00 38.64 3.77
434 449 0.035439 TCGGCAAGGGAAGATCCAAC 60.035 55.000 0.00 0.00 38.64 3.77
435 450 0.918983 ATCGGCAAGGGAAGATCCAA 59.081 50.000 0.00 0.00 38.64 3.53
436 451 0.181114 CATCGGCAAGGGAAGATCCA 59.819 55.000 0.00 0.00 38.64 3.41
437 452 0.469917 TCATCGGCAAGGGAAGATCC 59.530 55.000 0.00 0.00 35.23 3.36
489 504 2.579201 GCAGGAGAGCAGCGGTTA 59.421 61.111 0.00 0.00 0.00 2.85
573 588 1.754234 CTGTGGGCAGCCATTACCC 60.754 63.158 15.19 0.00 44.52 3.69
709 730 3.162154 GGGCCCGGGTAGGAAGAG 61.162 72.222 24.63 0.00 45.00 2.85
867 916 1.794003 CGTCGCGTCACTCACTGAG 60.794 63.158 5.77 4.36 35.52 3.35
868 917 2.251371 CGTCGCGTCACTCACTGA 59.749 61.111 5.77 0.00 0.00 3.41
869 918 3.461982 GCGTCGCGTCACTCACTG 61.462 66.667 5.77 0.00 0.00 3.66
923 972 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
924 973 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
925 974 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
926 975 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
927 976 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
928 977 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
929 978 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
930 979 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
931 980 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
932 981 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
933 982 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
934 983 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
935 984 4.039004 CCAGAGAGAGAGAGAGAGAGAGAG 59.961 54.167 0.00 0.00 0.00 3.20
936 985 3.963374 CCAGAGAGAGAGAGAGAGAGAGA 59.037 52.174 0.00 0.00 0.00 3.10
937 986 3.070734 CCCAGAGAGAGAGAGAGAGAGAG 59.929 56.522 0.00 0.00 0.00 3.20
938 987 3.041211 CCCAGAGAGAGAGAGAGAGAGA 58.959 54.545 0.00 0.00 0.00 3.10
939 988 2.105477 CCCCAGAGAGAGAGAGAGAGAG 59.895 59.091 0.00 0.00 0.00 3.20
940 989 2.126882 CCCCAGAGAGAGAGAGAGAGA 58.873 57.143 0.00 0.00 0.00 3.10
941 990 1.846439 ACCCCAGAGAGAGAGAGAGAG 59.154 57.143 0.00 0.00 0.00 3.20
942 991 1.563879 CACCCCAGAGAGAGAGAGAGA 59.436 57.143 0.00 0.00 0.00 3.10
943 992 1.563879 TCACCCCAGAGAGAGAGAGAG 59.436 57.143 0.00 0.00 0.00 3.20
944 993 1.563879 CTCACCCCAGAGAGAGAGAGA 59.436 57.143 0.00 0.00 37.87 3.10
945 994 1.410083 CCTCACCCCAGAGAGAGAGAG 60.410 61.905 0.00 0.00 37.87 3.20
969 1018 1.306970 CGGTCTACCCTCAGTCCCT 59.693 63.158 0.00 0.00 0.00 4.20
973 1026 2.754658 CCGCGGTCTACCCTCAGT 60.755 66.667 19.50 0.00 0.00 3.41
974 1027 3.528370 CCCGCGGTCTACCCTCAG 61.528 72.222 26.12 0.00 0.00 3.35
975 1028 4.371417 ACCCGCGGTCTACCCTCA 62.371 66.667 26.12 0.00 0.00 3.86
1740 1820 3.649986 GTGGCGCGCTGAGTTGTT 61.650 61.111 32.29 0.00 0.00 2.83
1741 1821 4.609018 AGTGGCGCGCTGAGTTGT 62.609 61.111 32.29 5.92 0.00 3.32
1742 1822 3.300667 GAAGTGGCGCGCTGAGTTG 62.301 63.158 32.29 0.00 0.00 3.16
1762 1842 0.108804 CATGCCAAGCAAGGAAGCAG 60.109 55.000 0.00 0.00 43.62 4.24
1768 1848 2.126228 CACGCATGCCAAGCAAGG 60.126 61.111 13.15 0.00 43.62 3.61
1795 1881 1.496393 CTGCAAGAGAAGCACAGCG 59.504 57.895 0.00 0.00 37.02 5.18
1867 1953 3.112709 GCTGCCCGTCGTTGAGAC 61.113 66.667 0.00 0.00 46.16 3.36
1958 2044 7.506114 AGTTTGTTTACTGGTAGTGAGATTGA 58.494 34.615 0.00 0.00 0.00 2.57
1984 2070 1.980765 TCCTTGCAGAGTTCCAGATGT 59.019 47.619 0.00 0.00 0.00 3.06
2068 2158 1.597027 AGTTTACAAGCTGCCGCGT 60.597 52.632 4.92 0.00 42.32 6.01
2079 2169 5.470777 CCGGACTTGGTTTATTCAGTTTACA 59.529 40.000 0.00 0.00 0.00 2.41
2121 2237 2.532843 TCCTACCAACCTTAGAAGCGT 58.467 47.619 0.00 0.00 0.00 5.07
2191 2330 9.035607 GTTATCAGGAACATTCTACATGTACAG 57.964 37.037 0.08 0.00 0.00 2.74
2229 2739 6.651643 TGTAATTCACAAGTGGTACATACACC 59.348 38.462 0.00 0.00 35.33 4.16
2323 2833 5.288015 TGGTGCATTCAGTGTAATTTTGTG 58.712 37.500 0.00 0.00 0.00 3.33
2377 2887 8.589701 TGAGTTTTCCCTTTTCTTCTTTTACT 57.410 30.769 0.00 0.00 0.00 2.24
2380 2890 6.763135 GCATGAGTTTTCCCTTTTCTTCTTTT 59.237 34.615 0.00 0.00 0.00 2.27
2389 2899 3.243359 TCCTGCATGAGTTTTCCCTTT 57.757 42.857 0.00 0.00 0.00 3.11
2400 2910 3.748048 CGAGACTTCTTTTTCCTGCATGA 59.252 43.478 0.00 0.00 0.00 3.07
2406 2916 1.797025 CCGCGAGACTTCTTTTTCCT 58.203 50.000 8.23 0.00 0.00 3.36
2409 2919 1.264288 CAAGCCGCGAGACTTCTTTTT 59.736 47.619 8.23 0.00 0.00 1.94
2425 2935 7.520614 GCATATGACTACCTTGTATTTCCAAGC 60.521 40.741 6.97 0.00 40.40 4.01
2427 2937 7.342581 TGCATATGACTACCTTGTATTTCCAA 58.657 34.615 6.97 0.00 0.00 3.53
2612 3122 3.367703 CCTCCCATGTCTGCATTTTTGTC 60.368 47.826 0.00 0.00 31.99 3.18
2633 3143 0.179078 CTGAGAGTCATGCCTCAGCC 60.179 60.000 19.34 5.62 46.48 4.85
2673 3183 4.083802 GCTCAACGCATAGAAAACAGTCTT 60.084 41.667 0.00 0.00 38.92 3.01
2674 3184 3.433615 GCTCAACGCATAGAAAACAGTCT 59.566 43.478 0.00 0.00 38.92 3.24
2755 3265 6.148480 ACAGCTAGAAATTAGCAAGTCAACTG 59.852 38.462 8.69 0.00 42.68 3.16
2756 3266 6.234177 ACAGCTAGAAATTAGCAAGTCAACT 58.766 36.000 8.69 0.00 42.68 3.16
2757 3267 6.487689 ACAGCTAGAAATTAGCAAGTCAAC 57.512 37.500 8.69 0.00 42.68 3.18
2758 3268 6.936900 AGAACAGCTAGAAATTAGCAAGTCAA 59.063 34.615 8.69 0.00 42.68 3.18
2759 3269 6.369890 CAGAACAGCTAGAAATTAGCAAGTCA 59.630 38.462 8.69 0.00 42.68 3.41
2760 3270 6.674278 GCAGAACAGCTAGAAATTAGCAAGTC 60.674 42.308 8.69 2.95 42.68 3.01
2795 3305 3.607422 TCTGTTGACATTGCAACTTCG 57.393 42.857 0.00 0.00 46.31 3.79


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

AutoCloner maintained by Alex Coulton.