Multiple sequence alignment - TraesCS2A01G153900

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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 TraesCS2A01G153900 chr2A 100.000 2948 0 0 1 2948 101835320 101838267 0.000000e+00 5445.0
1 TraesCS2A01G153900 chr2D 93.943 1585 58 16 307 1874 102724576 102726139 0.000000e+00 2361.0
2 TraesCS2A01G153900 chr2D 93.243 148 5 2 1 143 102724439 102724586 2.300000e-51 213.0
3 TraesCS2A01G153900 chr1A 95.238 1071 49 1 1878 2948 572729356 572728288 0.000000e+00 1694.0
4 TraesCS2A01G153900 chr4A 94.967 1073 51 2 1877 2948 514799052 514800122 0.000000e+00 1679.0
5 TraesCS2A01G153900 chr4A 93.536 1083 58 7 1876 2948 605870005 605871085 0.000000e+00 1602.0
6 TraesCS2A01G153900 chr7A 94.527 1078 55 3 1873 2948 238594099 238595174 0.000000e+00 1661.0
7 TraesCS2A01G153900 chr7A 94.331 1076 58 2 1874 2948 454162609 454163682 0.000000e+00 1646.0
8 TraesCS2A01G153900 chr7A 94.347 1079 50 7 1877 2948 719498421 719499495 0.000000e+00 1644.0
9 TraesCS2A01G153900 chr7A 95.358 1034 43 3 1916 2948 603329325 603328296 0.000000e+00 1639.0
10 TraesCS2A01G153900 chr6A 93.698 1079 59 6 1875 2948 93427777 93428851 0.000000e+00 1607.0
11 TraesCS2A01G153900 chr6A 85.974 549 70 6 1138 1681 96772390 96772936 5.480000e-162 580.0
12 TraesCS2A01G153900 chr5A 93.663 1073 60 3 1876 2948 18849544 18850608 0.000000e+00 1598.0
13 TraesCS2A01G153900 chr2B 96.736 674 22 0 1029 1702 153903487 153904160 0.000000e+00 1123.0
14 TraesCS2A01G153900 chr2B 90.027 371 24 7 700 1065 153903119 153903481 4.450000e-128 468.0
15 TraesCS2A01G153900 chr2B 95.758 165 7 0 142 306 772209257 772209421 1.740000e-67 267.0
16 TraesCS2A01G153900 chr2B 97.222 72 2 0 1803 1874 153904211 153904282 3.990000e-24 122.0
17 TraesCS2A01G153900 chr6D 85.844 551 71 6 1139 1684 79934139 79933591 1.970000e-161 579.0
18 TraesCS2A01G153900 chr6D 85.636 550 70 8 1138 1681 80061438 80061984 1.190000e-158 569.0
19 TraesCS2A01G153900 chr6D 95.783 166 7 0 142 307 470319825 470319990 4.840000e-68 268.0
20 TraesCS2A01G153900 chr6D 79.255 188 35 4 1146 1331 472997883 472998068 8.580000e-26 128.0
21 TraesCS2A01G153900 chr6D 79.255 188 35 4 1146 1331 473056062 473056247 8.580000e-26 128.0
22 TraesCS2A01G153900 chr6B 85.145 552 75 6 1138 1684 152631073 152630524 2.570000e-155 558.0
23 TraesCS2A01G153900 chr6B 91.667 204 12 4 1138 1337 152695870 152695668 8.050000e-71 278.0
24 TraesCS2A01G153900 chr6B 95.882 170 7 0 140 309 152213162 152212993 2.890000e-70 276.0
25 TraesCS2A01G153900 chr3D 96.407 167 6 0 142 308 489278332 489278166 2.890000e-70 276.0
26 TraesCS2A01G153900 chr4B 96.364 165 6 0 142 306 345955396 345955232 3.740000e-69 272.0
27 TraesCS2A01G153900 chr5B 95.783 166 7 0 142 307 443181792 443181627 4.840000e-68 268.0
28 TraesCS2A01G153900 chr5B 82.692 104 17 1 344 447 669550001 669549899 1.130000e-14 91.6
29 TraesCS2A01G153900 chr7B 95.238 168 8 0 141 308 119792585 119792418 1.740000e-67 267.0
30 TraesCS2A01G153900 chr5D 95.238 168 8 0 141 308 344794551 344794384 1.740000e-67 267.0
31 TraesCS2A01G153900 chr3B 95.266 169 7 1 142 309 131538782 131538614 1.740000e-67 267.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G153900 chr2A 101835320 101838267 2947 False 5445 5445 100.000000 1 2948 1 chr2A.!!$F1 2947
1 TraesCS2A01G153900 chr2D 102724439 102726139 1700 False 1287 2361 93.593000 1 1874 2 chr2D.!!$F1 1873
2 TraesCS2A01G153900 chr1A 572728288 572729356 1068 True 1694 1694 95.238000 1878 2948 1 chr1A.!!$R1 1070
3 TraesCS2A01G153900 chr4A 514799052 514800122 1070 False 1679 1679 94.967000 1877 2948 1 chr4A.!!$F1 1071
4 TraesCS2A01G153900 chr4A 605870005 605871085 1080 False 1602 1602 93.536000 1876 2948 1 chr4A.!!$F2 1072
5 TraesCS2A01G153900 chr7A 238594099 238595174 1075 False 1661 1661 94.527000 1873 2948 1 chr7A.!!$F1 1075
6 TraesCS2A01G153900 chr7A 454162609 454163682 1073 False 1646 1646 94.331000 1874 2948 1 chr7A.!!$F2 1074
7 TraesCS2A01G153900 chr7A 719498421 719499495 1074 False 1644 1644 94.347000 1877 2948 1 chr7A.!!$F3 1071
8 TraesCS2A01G153900 chr7A 603328296 603329325 1029 True 1639 1639 95.358000 1916 2948 1 chr7A.!!$R1 1032
9 TraesCS2A01G153900 chr6A 93427777 93428851 1074 False 1607 1607 93.698000 1875 2948 1 chr6A.!!$F1 1073
10 TraesCS2A01G153900 chr6A 96772390 96772936 546 False 580 580 85.974000 1138 1681 1 chr6A.!!$F2 543
11 TraesCS2A01G153900 chr5A 18849544 18850608 1064 False 1598 1598 93.663000 1876 2948 1 chr5A.!!$F1 1072
12 TraesCS2A01G153900 chr2B 153903119 153904282 1163 False 571 1123 94.661667 700 1874 3 chr2B.!!$F2 1174
13 TraesCS2A01G153900 chr6D 79933591 79934139 548 True 579 579 85.844000 1139 1684 1 chr6D.!!$R1 545
14 TraesCS2A01G153900 chr6D 80061438 80061984 546 False 569 569 85.636000 1138 1681 1 chr6D.!!$F1 543
15 TraesCS2A01G153900 chr6B 152630524 152631073 549 True 558 558 85.145000 1138 1684 1 chr6B.!!$R2 546

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
147 152 0.107848 CAAACCTACCCCTAGTGGCG 60.108 60.0 0.0 0.0 0.0 5.69 F
165 170 0.109132 CGGCTCCAGGAATTTGCAAC 60.109 55.0 0.0 0.0 0.0 4.17 F
376 381 0.175760 CTCCCACATACCCACTCACG 59.824 60.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1787 1851 1.402194 GCTAGCTAGCTAGTGATGGCG 60.402 57.143 39.05 21.44 45.67 5.69 R
1788 1852 2.362169 GCTAGCTAGCTAGTGATGGC 57.638 55.000 39.05 27.07 45.67 4.40 R
2289 2371 1.339055 TGCGCTTTGCTCTGGACTATT 60.339 47.619 9.73 0.00 46.63 1.73 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
17 18 3.947173 CACTGGATCCGCCTCTCT 58.053 61.111 7.39 0.00 37.63 3.10
50 51 0.613260 CATGGAAGAACACCTCGGGA 59.387 55.000 0.00 0.00 0.00 5.14
98 103 2.997315 CACTGGGACGGAGCTCCA 60.997 66.667 31.67 12.23 38.67 3.86
144 149 3.875865 GGCAAACCTACCCCTAGTG 57.124 57.895 0.00 0.00 0.00 2.74
145 150 0.255033 GGCAAACCTACCCCTAGTGG 59.745 60.000 0.00 0.00 0.00 4.00
146 151 0.393944 GCAAACCTACCCCTAGTGGC 60.394 60.000 0.00 0.00 0.00 5.01
147 152 0.107848 CAAACCTACCCCTAGTGGCG 60.108 60.000 0.00 0.00 0.00 5.69
148 153 1.269703 AAACCTACCCCTAGTGGCGG 61.270 60.000 0.00 0.00 0.00 6.13
149 154 3.547513 CCTACCCCTAGTGGCGGC 61.548 72.222 0.00 0.00 0.00 6.53
150 155 2.444140 CTACCCCTAGTGGCGGCT 60.444 66.667 11.43 0.00 0.00 5.52
151 156 2.443390 TACCCCTAGTGGCGGCTC 60.443 66.667 11.43 6.75 0.00 4.70
160 165 2.763215 TGGCGGCTCCAGGAATTT 59.237 55.556 11.43 0.00 40.72 1.82
161 166 1.678635 TGGCGGCTCCAGGAATTTG 60.679 57.895 11.43 0.00 40.72 2.32
162 167 2.491621 GCGGCTCCAGGAATTTGC 59.508 61.111 0.00 0.00 0.00 3.68
163 168 2.342650 GCGGCTCCAGGAATTTGCA 61.343 57.895 1.09 0.00 0.00 4.08
164 169 1.876497 GCGGCTCCAGGAATTTGCAA 61.876 55.000 0.00 0.00 0.00 4.08
165 170 0.109132 CGGCTCCAGGAATTTGCAAC 60.109 55.000 0.00 0.00 0.00 4.17
166 171 0.247460 GGCTCCAGGAATTTGCAACC 59.753 55.000 0.00 0.00 0.00 3.77
167 172 0.968405 GCTCCAGGAATTTGCAACCA 59.032 50.000 0.00 0.00 0.00 3.67
168 173 1.067354 GCTCCAGGAATTTGCAACCAG 60.067 52.381 0.00 0.00 0.00 4.00
169 174 1.547372 CTCCAGGAATTTGCAACCAGG 59.453 52.381 0.00 3.96 0.00 4.45
170 175 1.133199 TCCAGGAATTTGCAACCAGGT 60.133 47.619 13.56 0.00 33.13 4.00
171 176 2.109128 TCCAGGAATTTGCAACCAGGTA 59.891 45.455 13.56 1.72 33.13 3.08
172 177 3.099141 CCAGGAATTTGCAACCAGGTAT 58.901 45.455 0.00 0.00 0.00 2.73
173 178 3.515104 CCAGGAATTTGCAACCAGGTATT 59.485 43.478 0.00 0.00 0.00 1.89
174 179 4.381932 CCAGGAATTTGCAACCAGGTATTC 60.382 45.833 0.00 4.64 0.00 1.75
175 180 4.220382 CAGGAATTTGCAACCAGGTATTCA 59.780 41.667 16.90 0.47 0.00 2.57
176 181 5.025453 AGGAATTTGCAACCAGGTATTCAT 58.975 37.500 16.90 9.99 0.00 2.57
177 182 5.105228 AGGAATTTGCAACCAGGTATTCATG 60.105 40.000 16.90 0.00 0.00 3.07
178 183 5.337491 GGAATTTGCAACCAGGTATTCATGT 60.337 40.000 16.90 0.00 0.00 3.21
179 184 4.517952 TTTGCAACCAGGTATTCATGTG 57.482 40.909 0.00 0.00 0.00 3.21
180 185 3.153369 TGCAACCAGGTATTCATGTGT 57.847 42.857 0.00 0.00 0.00 3.72
181 186 4.293662 TGCAACCAGGTATTCATGTGTA 57.706 40.909 0.00 0.00 0.00 2.90
182 187 4.854173 TGCAACCAGGTATTCATGTGTAT 58.146 39.130 0.00 0.00 0.00 2.29
183 188 5.260424 TGCAACCAGGTATTCATGTGTATT 58.740 37.500 0.00 0.00 0.00 1.89
184 189 5.356751 TGCAACCAGGTATTCATGTGTATTC 59.643 40.000 0.00 0.00 0.00 1.75
185 190 5.356751 GCAACCAGGTATTCATGTGTATTCA 59.643 40.000 0.00 0.00 0.00 2.57
186 191 6.039717 GCAACCAGGTATTCATGTGTATTCAT 59.960 38.462 0.00 0.00 0.00 2.57
187 192 7.416664 GCAACCAGGTATTCATGTGTATTCATT 60.417 37.037 0.00 0.00 0.00 2.57
188 193 8.469200 CAACCAGGTATTCATGTGTATTCATTT 58.531 33.333 0.00 0.00 0.00 2.32
189 194 8.593945 ACCAGGTATTCATGTGTATTCATTTT 57.406 30.769 0.00 0.00 0.00 1.82
190 195 8.469200 ACCAGGTATTCATGTGTATTCATTTTG 58.531 33.333 0.00 0.00 0.00 2.44
191 196 7.436080 CCAGGTATTCATGTGTATTCATTTTGC 59.564 37.037 0.00 0.00 0.00 3.68
192 197 8.192774 CAGGTATTCATGTGTATTCATTTTGCT 58.807 33.333 0.00 0.00 0.00 3.91
193 198 9.407380 AGGTATTCATGTGTATTCATTTTGCTA 57.593 29.630 0.00 0.00 0.00 3.49
203 208 9.693157 GTGTATTCATTTTGCTAAAATCATTGC 57.307 29.630 0.00 0.00 38.97 3.56
204 209 8.881743 TGTATTCATTTTGCTAAAATCATTGCC 58.118 29.630 0.00 0.00 38.97 4.52
205 210 6.406093 TTCATTTTGCTAAAATCATTGCCG 57.594 33.333 0.00 0.00 38.97 5.69
206 211 5.477510 TCATTTTGCTAAAATCATTGCCGT 58.522 33.333 0.00 0.00 38.97 5.68
207 212 5.931146 TCATTTTGCTAAAATCATTGCCGTT 59.069 32.000 0.00 0.00 38.97 4.44
208 213 6.426328 TCATTTTGCTAAAATCATTGCCGTTT 59.574 30.769 0.00 0.00 38.97 3.60
209 214 6.610741 TTTTGCTAAAATCATTGCCGTTTT 57.389 29.167 0.00 0.00 0.00 2.43
210 215 6.610741 TTTGCTAAAATCATTGCCGTTTTT 57.389 29.167 0.00 0.00 0.00 1.94
211 216 5.837586 TGCTAAAATCATTGCCGTTTTTC 57.162 34.783 0.00 0.00 0.00 2.29
212 217 4.384247 TGCTAAAATCATTGCCGTTTTTCG 59.616 37.500 0.00 0.00 39.52 3.46
213 218 4.619336 GCTAAAATCATTGCCGTTTTTCGA 59.381 37.500 0.00 0.00 42.86 3.71
214 219 5.117897 GCTAAAATCATTGCCGTTTTTCGAA 59.882 36.000 0.00 0.00 42.86 3.71
215 220 5.975410 AAAATCATTGCCGTTTTTCGAAA 57.025 30.435 6.47 6.47 42.86 3.46
216 221 5.975410 AAATCATTGCCGTTTTTCGAAAA 57.025 30.435 19.08 19.08 42.86 2.29
217 222 6.538189 AAATCATTGCCGTTTTTCGAAAAT 57.462 29.167 23.05 4.56 42.86 1.82
218 223 6.538189 AATCATTGCCGTTTTTCGAAAATT 57.462 29.167 23.05 8.32 42.86 1.82
219 224 5.321983 TCATTGCCGTTTTTCGAAAATTG 57.678 34.783 23.05 17.33 42.86 2.32
220 225 4.806247 TCATTGCCGTTTTTCGAAAATTGT 59.194 33.333 23.05 4.22 42.86 2.71
221 226 4.763594 TTGCCGTTTTTCGAAAATTGTC 57.236 36.364 23.05 13.43 42.86 3.18
222 227 3.770666 TGCCGTTTTTCGAAAATTGTCA 58.229 36.364 23.05 15.51 42.86 3.58
223 228 3.548268 TGCCGTTTTTCGAAAATTGTCAC 59.452 39.130 23.05 16.25 42.86 3.67
224 229 3.794564 GCCGTTTTTCGAAAATTGTCACT 59.205 39.130 23.05 0.00 42.86 3.41
225 230 4.085772 GCCGTTTTTCGAAAATTGTCACTC 60.086 41.667 23.05 9.17 42.86 3.51
226 231 5.270853 CCGTTTTTCGAAAATTGTCACTCT 58.729 37.500 23.05 0.00 42.86 3.24
227 232 5.741982 CCGTTTTTCGAAAATTGTCACTCTT 59.258 36.000 23.05 0.00 42.86 2.85
228 233 6.252655 CCGTTTTTCGAAAATTGTCACTCTTT 59.747 34.615 23.05 0.00 42.86 2.52
229 234 7.201401 CCGTTTTTCGAAAATTGTCACTCTTTT 60.201 33.333 23.05 0.00 42.86 2.27
230 235 7.626815 CGTTTTTCGAAAATTGTCACTCTTTTG 59.373 33.333 23.05 2.16 42.86 2.44
231 236 6.567769 TTTCGAAAATTGTCACTCTTTTGC 57.432 33.333 8.44 0.00 0.00 3.68
232 237 5.499139 TCGAAAATTGTCACTCTTTTGCT 57.501 34.783 0.00 0.00 0.00 3.91
233 238 6.612247 TCGAAAATTGTCACTCTTTTGCTA 57.388 33.333 0.00 0.00 0.00 3.49
234 239 7.022055 TCGAAAATTGTCACTCTTTTGCTAA 57.978 32.000 0.00 0.00 0.00 3.09
235 240 7.476667 TCGAAAATTGTCACTCTTTTGCTAAA 58.523 30.769 0.00 0.00 0.00 1.85
236 241 7.971168 TCGAAAATTGTCACTCTTTTGCTAAAA 59.029 29.630 0.00 0.00 0.00 1.52
237 242 8.755018 CGAAAATTGTCACTCTTTTGCTAAAAT 58.245 29.630 0.00 0.00 0.00 1.82
239 244 9.598517 AAAATTGTCACTCTTTTGCTAAAATCA 57.401 25.926 0.00 0.00 0.00 2.57
240 245 9.598517 AAATTGTCACTCTTTTGCTAAAATCAA 57.401 25.926 0.00 0.00 0.00 2.57
241 246 7.985634 TTGTCACTCTTTTGCTAAAATCAAC 57.014 32.000 0.00 0.00 0.00 3.18
242 247 7.094508 TGTCACTCTTTTGCTAAAATCAACA 57.905 32.000 0.00 0.00 0.00 3.33
243 248 7.715657 TGTCACTCTTTTGCTAAAATCAACAT 58.284 30.769 0.00 0.00 0.00 2.71
244 249 8.196771 TGTCACTCTTTTGCTAAAATCAACATT 58.803 29.630 0.00 0.00 0.00 2.71
245 250 8.482429 GTCACTCTTTTGCTAAAATCAACATTG 58.518 33.333 0.00 0.00 0.00 2.82
246 251 8.196771 TCACTCTTTTGCTAAAATCAACATTGT 58.803 29.630 0.00 0.00 0.00 2.71
247 252 8.819974 CACTCTTTTGCTAAAATCAACATTGTT 58.180 29.630 0.00 0.00 0.00 2.83
248 253 9.382275 ACTCTTTTGCTAAAATCAACATTGTTT 57.618 25.926 0.00 0.00 0.00 2.83
250 255 9.985318 TCTTTTGCTAAAATCAACATTGTTTTG 57.015 25.926 0.00 0.00 32.24 2.44
251 256 9.771915 CTTTTGCTAAAATCAACATTGTTTTGT 57.228 25.926 0.00 0.00 32.24 2.83
263 268 8.834465 TCAACATTGTTTTGTAAAAATCATGGG 58.166 29.630 0.00 4.60 0.00 4.00
264 269 8.619546 CAACATTGTTTTGTAAAAATCATGGGT 58.380 29.630 0.00 0.00 0.00 4.51
265 270 9.838339 AACATTGTTTTGTAAAAATCATGGGTA 57.162 25.926 0.00 0.00 0.00 3.69
270 275 9.482627 TGTTTTGTAAAAATCATGGGTATTCAC 57.517 29.630 0.00 0.00 0.00 3.18
271 276 9.482627 GTTTTGTAAAAATCATGGGTATTCACA 57.517 29.630 0.00 0.00 0.00 3.58
288 293 7.920738 GTATTCACATGAAGACCCAAGAATAC 58.079 38.462 7.95 0.00 39.58 1.89
289 294 4.843728 TCACATGAAGACCCAAGAATACC 58.156 43.478 0.00 0.00 0.00 2.73
290 295 3.947834 CACATGAAGACCCAAGAATACCC 59.052 47.826 0.00 0.00 0.00 3.69
291 296 3.053619 ACATGAAGACCCAAGAATACCCC 60.054 47.826 0.00 0.00 0.00 4.95
292 297 2.929301 TGAAGACCCAAGAATACCCCT 58.071 47.619 0.00 0.00 0.00 4.79
293 298 4.083080 TGAAGACCCAAGAATACCCCTA 57.917 45.455 0.00 0.00 0.00 3.53
294 299 4.037927 TGAAGACCCAAGAATACCCCTAG 58.962 47.826 0.00 0.00 0.00 3.02
295 300 2.409570 AGACCCAAGAATACCCCTAGC 58.590 52.381 0.00 0.00 0.00 3.42
296 301 1.070289 GACCCAAGAATACCCCTAGCG 59.930 57.143 0.00 0.00 0.00 4.26
297 302 0.250338 CCCAAGAATACCCCTAGCGC 60.250 60.000 0.00 0.00 0.00 5.92
298 303 0.250338 CCAAGAATACCCCTAGCGCC 60.250 60.000 2.29 0.00 0.00 6.53
299 304 0.600255 CAAGAATACCCCTAGCGCCG 60.600 60.000 2.29 0.00 0.00 6.46
300 305 2.357154 GAATACCCCTAGCGCCGC 60.357 66.667 2.29 0.00 0.00 6.53
301 306 3.878374 GAATACCCCTAGCGCCGCC 62.878 68.421 4.98 0.00 0.00 6.13
336 341 3.123273 AGCCCTACACCTAATGGACAAT 58.877 45.455 0.00 0.00 37.04 2.71
337 342 3.527665 AGCCCTACACCTAATGGACAATT 59.472 43.478 0.00 0.00 37.04 2.32
338 343 4.724798 AGCCCTACACCTAATGGACAATTA 59.275 41.667 0.00 0.00 37.04 1.40
339 344 5.192923 AGCCCTACACCTAATGGACAATTAA 59.807 40.000 0.00 0.00 37.04 1.40
342 347 7.629866 GCCCTACACCTAATGGACAATTAAAAC 60.630 40.741 0.00 0.00 37.04 2.43
362 367 0.617820 GAGTACCTGGCTTCCTCCCA 60.618 60.000 0.00 0.00 0.00 4.37
369 374 1.279025 TGGCTTCCTCCCACATACCC 61.279 60.000 0.00 0.00 0.00 3.69
376 381 0.175760 CTCCCACATACCCACTCACG 59.824 60.000 0.00 0.00 0.00 4.35
378 383 0.830648 CCCACATACCCACTCACGAT 59.169 55.000 0.00 0.00 0.00 3.73
442 447 4.407296 AGATTTTCCTAGGCGACTCTCAAT 59.593 41.667 2.96 0.00 43.67 2.57
461 466 4.687215 GTGGCGAGCAGGCTCACA 62.687 66.667 20.18 15.03 46.88 3.58
472 477 0.337773 AGGCTCACATCTCTCTCCCA 59.662 55.000 0.00 0.00 0.00 4.37
475 480 2.037901 GCTCACATCTCTCTCCCATCA 58.962 52.381 0.00 0.00 0.00 3.07
487 492 4.288105 TCTCTCCCATCAAAGCTTTCTCTT 59.712 41.667 9.23 0.00 0.00 2.85
516 521 2.558378 AGATCGGTGCAGTTCATGATG 58.442 47.619 0.00 0.00 0.00 3.07
517 522 1.600957 GATCGGTGCAGTTCATGATGG 59.399 52.381 0.00 0.00 0.00 3.51
518 523 1.026182 TCGGTGCAGTTCATGATGGC 61.026 55.000 0.00 1.26 0.00 4.40
568 573 4.518217 CGTAGCATTTAAATCGAGCCAAG 58.482 43.478 0.00 0.00 0.00 3.61
590 595 4.522789 AGCACCACAATTTAGGGTTTGTAG 59.477 41.667 0.00 0.00 34.42 2.74
797 805 1.072505 TCTGGCCCAACCGTTTCTC 59.927 57.895 0.00 0.00 43.94 2.87
798 806 1.971695 CTGGCCCAACCGTTTCTCC 60.972 63.158 0.00 0.00 43.94 3.71
816 824 4.433615 TCTCCGTGCAGTTTCTTATCATC 58.566 43.478 0.00 0.00 0.00 2.92
880 888 4.131649 TCGAAAGGCCGAGAATATTTCA 57.868 40.909 10.81 0.00 34.19 2.69
921 929 1.805945 GTGTAGCTCCGAGCAACCG 60.806 63.158 22.29 0.00 45.56 4.44
923 931 4.143333 TAGCTCCGAGCAACCGCC 62.143 66.667 22.29 0.00 45.56 6.13
949 958 2.629656 GCTTGTCGCAGGTTGGCAT 61.630 57.895 0.00 0.00 38.92 4.40
1025 1078 2.055100 GCTCATAAATCTCCTCGTCGC 58.945 52.381 0.00 0.00 0.00 5.19
1026 1079 2.543861 GCTCATAAATCTCCTCGTCGCA 60.544 50.000 0.00 0.00 0.00 5.10
1027 1080 3.046390 CTCATAAATCTCCTCGTCGCAC 58.954 50.000 0.00 0.00 0.00 5.34
1028 1081 2.688446 TCATAAATCTCCTCGTCGCACT 59.312 45.455 0.00 0.00 0.00 4.40
1029 1082 2.846039 TAAATCTCCTCGTCGCACTC 57.154 50.000 0.00 0.00 0.00 3.51
1030 1083 0.179161 AAATCTCCTCGTCGCACTCG 60.179 55.000 0.00 0.00 0.00 4.18
1031 1084 2.600122 AATCTCCTCGTCGCACTCGC 62.600 60.000 0.00 0.00 35.26 5.03
1465 1521 3.706373 TTCAGGCTCACCGGGCTC 61.706 66.667 6.32 0.00 42.76 4.70
1717 1773 1.587034 GAAGCTCGTACCAACATACGC 59.413 52.381 0.55 0.00 46.00 4.42
1719 1775 1.136305 AGCTCGTACCAACATACGCAT 59.864 47.619 0.55 0.00 46.00 4.73
1720 1776 1.521423 GCTCGTACCAACATACGCATC 59.479 52.381 0.55 0.00 46.00 3.91
1722 1778 3.043586 CTCGTACCAACATACGCATCTC 58.956 50.000 0.55 0.00 46.00 2.75
1724 1780 2.480587 CGTACCAACATACGCATCTCCA 60.481 50.000 0.00 0.00 41.28 3.86
1725 1781 2.779755 ACCAACATACGCATCTCCAA 57.220 45.000 0.00 0.00 0.00 3.53
1726 1782 3.281727 ACCAACATACGCATCTCCAAT 57.718 42.857 0.00 0.00 0.00 3.16
1751 1815 6.414732 TCTCCATCGGAAACATATGAAAACT 58.585 36.000 10.38 0.00 0.00 2.66
1752 1816 6.538742 TCTCCATCGGAAACATATGAAAACTC 59.461 38.462 10.38 0.00 0.00 3.01
1754 1818 5.356751 CCATCGGAAACATATGAAAACTCCA 59.643 40.000 10.38 0.45 0.00 3.86
1833 1897 6.871844 TCATGAGAGAGTGAAAAGGATAGTG 58.128 40.000 0.00 0.00 0.00 2.74
1929 1994 2.473816 CATCAGAACGATGCATACGGT 58.526 47.619 18.34 13.97 44.95 4.83
2115 2197 1.377463 CCGCCATCCAAACCGGTTA 60.377 57.895 22.60 5.30 36.18 2.85
2289 2371 5.867330 ACCAAATCATTTCTGCAATTCCAA 58.133 33.333 0.00 0.00 0.00 3.53
2481 2563 2.418976 GTGTTTAATTGTCTCCTCCCGC 59.581 50.000 0.00 0.00 0.00 6.13
2543 2625 5.705905 GCTTTGTCAGGTTGTCCTTAGTTAT 59.294 40.000 0.00 0.00 43.07 1.89
2544 2626 6.877322 GCTTTGTCAGGTTGTCCTTAGTTATA 59.123 38.462 0.00 0.00 43.07 0.98
2619 2701 0.961019 GACAGCCCAAACATGCTTGA 59.039 50.000 10.43 0.00 0.00 3.02
2718 2800 3.549423 CCAGCATAATTCATCTGGTTGCG 60.549 47.826 10.14 0.00 40.79 4.85
2725 2807 0.111446 TCATCTGGTTGCGGGGAAAA 59.889 50.000 0.00 0.00 0.00 2.29
2755 2837 3.052869 TCCATCAGCCTCCTAACTAGACA 60.053 47.826 0.00 0.00 0.00 3.41
2795 2877 4.554363 CCCGCTAGCGACCGTCTG 62.554 72.222 37.39 18.56 42.83 3.51
2928 3010 3.028850 CAAGTATCCTCCCAGAACCGTA 58.971 50.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 81 2.109126 GCTCCGTCCCAGTGCATTC 61.109 63.158 0.00 0.00 0.00 2.67
128 133 0.107848 CGCCACTAGGGGTAGGTTTG 60.108 60.000 13.95 0.00 42.60 2.93
137 142 3.854669 CTGGAGCCGCCACTAGGG 61.855 72.222 0.00 0.00 43.33 3.53
138 143 3.854669 CCTGGAGCCGCCACTAGG 61.855 72.222 0.00 3.85 43.33 3.02
139 144 1.690219 ATTCCTGGAGCCGCCACTAG 61.690 60.000 0.00 0.00 43.33 2.57
140 145 1.271840 AATTCCTGGAGCCGCCACTA 61.272 55.000 0.00 0.00 43.33 2.74
141 146 2.142292 AAATTCCTGGAGCCGCCACT 62.142 55.000 0.00 0.00 43.33 4.00
142 147 1.678970 AAATTCCTGGAGCCGCCAC 60.679 57.895 0.00 0.00 43.33 5.01
143 148 1.678635 CAAATTCCTGGAGCCGCCA 60.679 57.895 0.00 0.00 46.96 5.69
144 149 3.068729 GCAAATTCCTGGAGCCGCC 62.069 63.158 0.00 0.00 37.10 6.13
145 150 1.876497 TTGCAAATTCCTGGAGCCGC 61.876 55.000 0.00 0.00 0.00 6.53
146 151 0.109132 GTTGCAAATTCCTGGAGCCG 60.109 55.000 0.00 0.00 0.00 5.52
147 152 0.247460 GGTTGCAAATTCCTGGAGCC 59.753 55.000 0.00 0.00 31.24 4.70
148 153 0.968405 TGGTTGCAAATTCCTGGAGC 59.032 50.000 0.00 0.00 0.00 4.70
149 154 1.547372 CCTGGTTGCAAATTCCTGGAG 59.453 52.381 19.86 4.60 41.02 3.86
150 155 1.133199 ACCTGGTTGCAAATTCCTGGA 60.133 47.619 27.11 0.00 41.02 3.86
151 156 1.341080 ACCTGGTTGCAAATTCCTGG 58.659 50.000 21.77 21.77 43.11 4.45
152 157 4.220382 TGAATACCTGGTTGCAAATTCCTG 59.780 41.667 3.84 9.64 0.00 3.86
153 158 4.415596 TGAATACCTGGTTGCAAATTCCT 58.584 39.130 3.84 0.00 0.00 3.36
154 159 4.799564 TGAATACCTGGTTGCAAATTCC 57.200 40.909 3.84 7.12 0.00 3.01
155 160 5.577945 CACATGAATACCTGGTTGCAAATTC 59.422 40.000 3.84 8.44 0.00 2.17
156 161 5.011943 ACACATGAATACCTGGTTGCAAATT 59.988 36.000 3.84 0.00 0.00 1.82
157 162 4.527816 ACACATGAATACCTGGTTGCAAAT 59.472 37.500 3.84 0.00 0.00 2.32
158 163 3.894427 ACACATGAATACCTGGTTGCAAA 59.106 39.130 3.84 0.00 0.00 3.68
159 164 3.495331 ACACATGAATACCTGGTTGCAA 58.505 40.909 3.84 0.00 0.00 4.08
160 165 3.153369 ACACATGAATACCTGGTTGCA 57.847 42.857 3.84 1.24 0.00 4.08
161 166 5.356751 TGAATACACATGAATACCTGGTTGC 59.643 40.000 3.84 0.00 0.00 4.17
162 167 7.572523 ATGAATACACATGAATACCTGGTTG 57.427 36.000 3.84 0.00 0.00 3.77
163 168 8.593945 AAATGAATACACATGAATACCTGGTT 57.406 30.769 3.84 0.00 0.00 3.67
164 169 8.469200 CAAAATGAATACACATGAATACCTGGT 58.531 33.333 4.05 4.05 0.00 4.00
165 170 7.436080 GCAAAATGAATACACATGAATACCTGG 59.564 37.037 0.00 0.00 0.00 4.45
166 171 8.192774 AGCAAAATGAATACACATGAATACCTG 58.807 33.333 0.00 0.00 0.00 4.00
167 172 8.297470 AGCAAAATGAATACACATGAATACCT 57.703 30.769 0.00 0.00 0.00 3.08
177 182 9.693157 GCAATGATTTTAGCAAAATGAATACAC 57.307 29.630 10.33 0.00 40.97 2.90
178 183 8.881743 GGCAATGATTTTAGCAAAATGAATACA 58.118 29.630 10.33 4.39 40.97 2.29
179 184 8.057742 CGGCAATGATTTTAGCAAAATGAATAC 58.942 33.333 10.33 0.06 40.97 1.89
180 185 7.763528 ACGGCAATGATTTTAGCAAAATGAATA 59.236 29.630 10.33 0.00 40.97 1.75
181 186 6.594937 ACGGCAATGATTTTAGCAAAATGAAT 59.405 30.769 10.33 3.81 40.97 2.57
182 187 5.931146 ACGGCAATGATTTTAGCAAAATGAA 59.069 32.000 10.33 2.12 40.97 2.57
183 188 5.477510 ACGGCAATGATTTTAGCAAAATGA 58.522 33.333 10.33 4.46 40.97 2.57
184 189 5.783100 ACGGCAATGATTTTAGCAAAATG 57.217 34.783 10.33 1.85 40.97 2.32
185 190 6.799926 AAACGGCAATGATTTTAGCAAAAT 57.200 29.167 6.57 6.57 43.43 1.82
186 191 6.610741 AAAACGGCAATGATTTTAGCAAAA 57.389 29.167 0.00 0.00 34.41 2.44
187 192 6.563010 CGAAAAACGGCAATGATTTTAGCAAA 60.563 34.615 0.00 0.00 38.46 3.68
188 193 5.107683 CGAAAAACGGCAATGATTTTAGCAA 60.108 36.000 0.00 0.00 38.46 3.91
189 194 4.384247 CGAAAAACGGCAATGATTTTAGCA 59.616 37.500 0.00 0.00 38.46 3.49
190 195 4.619336 TCGAAAAACGGCAATGATTTTAGC 59.381 37.500 0.00 0.00 42.82 3.09
191 196 6.683090 TTCGAAAAACGGCAATGATTTTAG 57.317 33.333 0.00 0.00 42.82 1.85
192 197 7.464830 TTTTCGAAAAACGGCAATGATTTTA 57.535 28.000 20.56 0.00 42.82 1.52
193 198 5.975410 TTTCGAAAAACGGCAATGATTTT 57.025 30.435 8.44 0.00 42.82 1.82
194 199 5.975410 TTTTCGAAAAACGGCAATGATTT 57.025 30.435 20.56 0.00 42.82 2.17
195 200 6.018343 ACAATTTTCGAAAAACGGCAATGATT 60.018 30.769 25.77 9.73 42.82 2.57
196 201 5.465056 ACAATTTTCGAAAAACGGCAATGAT 59.535 32.000 25.77 3.96 42.82 2.45
197 202 4.806247 ACAATTTTCGAAAAACGGCAATGA 59.194 33.333 25.77 0.65 42.82 2.57
198 203 5.076911 ACAATTTTCGAAAAACGGCAATG 57.923 34.783 25.77 16.81 42.82 2.82
199 204 4.806247 TGACAATTTTCGAAAAACGGCAAT 59.194 33.333 25.77 6.14 42.82 3.56
200 205 4.031878 GTGACAATTTTCGAAAAACGGCAA 59.968 37.500 25.77 10.72 42.82 4.52
201 206 3.548268 GTGACAATTTTCGAAAAACGGCA 59.452 39.130 25.77 23.11 42.82 5.69
202 207 3.794564 AGTGACAATTTTCGAAAAACGGC 59.205 39.130 25.77 21.02 42.82 5.68
203 208 5.270853 AGAGTGACAATTTTCGAAAAACGG 58.729 37.500 25.77 19.13 42.82 4.44
204 209 6.790336 AAGAGTGACAATTTTCGAAAAACG 57.210 33.333 25.77 20.61 44.09 3.60
205 210 7.422462 GCAAAAGAGTGACAATTTTCGAAAAAC 59.578 33.333 25.77 18.40 0.00 2.43
206 211 7.330700 AGCAAAAGAGTGACAATTTTCGAAAAA 59.669 29.630 25.77 7.60 0.00 1.94
207 212 6.811170 AGCAAAAGAGTGACAATTTTCGAAAA 59.189 30.769 24.43 24.43 0.00 2.29
208 213 6.329496 AGCAAAAGAGTGACAATTTTCGAAA 58.671 32.000 6.47 6.47 0.00 3.46
209 214 5.890334 AGCAAAAGAGTGACAATTTTCGAA 58.110 33.333 0.00 0.00 0.00 3.71
210 215 5.499139 AGCAAAAGAGTGACAATTTTCGA 57.501 34.783 0.00 0.00 0.00 3.71
211 216 7.678194 TTTAGCAAAAGAGTGACAATTTTCG 57.322 32.000 0.00 0.00 0.00 3.46
213 218 9.598517 TGATTTTAGCAAAAGAGTGACAATTTT 57.401 25.926 0.00 0.00 33.22 1.82
214 219 9.598517 TTGATTTTAGCAAAAGAGTGACAATTT 57.401 25.926 0.00 0.00 33.22 1.82
215 220 9.034544 GTTGATTTTAGCAAAAGAGTGACAATT 57.965 29.630 0.00 0.00 33.22 2.32
216 221 8.196771 TGTTGATTTTAGCAAAAGAGTGACAAT 58.803 29.630 0.00 0.00 33.22 2.71
217 222 7.542890 TGTTGATTTTAGCAAAAGAGTGACAA 58.457 30.769 0.00 0.00 33.22 3.18
218 223 7.094508 TGTTGATTTTAGCAAAAGAGTGACA 57.905 32.000 0.00 0.00 33.22 3.58
219 224 8.482429 CAATGTTGATTTTAGCAAAAGAGTGAC 58.518 33.333 0.00 0.00 33.22 3.67
220 225 8.196771 ACAATGTTGATTTTAGCAAAAGAGTGA 58.803 29.630 0.00 0.00 33.22 3.41
221 226 8.356533 ACAATGTTGATTTTAGCAAAAGAGTG 57.643 30.769 0.00 0.00 33.22 3.51
222 227 8.947055 AACAATGTTGATTTTAGCAAAAGAGT 57.053 26.923 0.00 0.00 33.22 3.24
224 229 9.985318 CAAAACAATGTTGATTTTAGCAAAAGA 57.015 25.926 0.00 0.00 31.90 2.52
225 230 9.771915 ACAAAACAATGTTGATTTTAGCAAAAG 57.228 25.926 0.00 0.00 31.90 2.27
237 242 8.834465 CCCATGATTTTTACAAAACAATGTTGA 58.166 29.630 0.00 0.00 34.75 3.18
238 243 8.619546 ACCCATGATTTTTACAAAACAATGTTG 58.380 29.630 0.00 0.00 34.75 3.33
239 244 8.744568 ACCCATGATTTTTACAAAACAATGTT 57.255 26.923 0.00 0.00 34.75 2.71
244 249 9.482627 GTGAATACCCATGATTTTTACAAAACA 57.517 29.630 0.00 0.00 0.00 2.83
245 250 9.482627 TGTGAATACCCATGATTTTTACAAAAC 57.517 29.630 0.00 0.00 0.00 2.43
247 252 9.650539 CATGTGAATACCCATGATTTTTACAAA 57.349 29.630 0.00 0.00 40.70 2.83
248 253 9.029368 TCATGTGAATACCCATGATTTTTACAA 57.971 29.630 0.00 0.00 41.77 2.41
249 254 8.586879 TCATGTGAATACCCATGATTTTTACA 57.413 30.769 0.00 0.00 41.77 2.41
250 255 9.520204 CTTCATGTGAATACCCATGATTTTTAC 57.480 33.333 0.00 0.00 44.93 2.01
251 256 9.473007 TCTTCATGTGAATACCCATGATTTTTA 57.527 29.630 0.00 0.00 44.93 1.52
252 257 8.253113 GTCTTCATGTGAATACCCATGATTTTT 58.747 33.333 0.00 0.00 44.93 1.94
253 258 7.147846 GGTCTTCATGTGAATACCCATGATTTT 60.148 37.037 15.62 0.00 44.93 1.82
254 259 6.322201 GGTCTTCATGTGAATACCCATGATTT 59.678 38.462 15.62 0.00 44.93 2.17
255 260 5.829924 GGTCTTCATGTGAATACCCATGATT 59.170 40.000 15.62 0.00 44.93 2.57
256 261 5.380043 GGTCTTCATGTGAATACCCATGAT 58.620 41.667 15.62 0.00 44.93 2.45
257 262 4.780815 GGTCTTCATGTGAATACCCATGA 58.219 43.478 15.62 1.95 42.26 3.07
262 267 4.843728 TCTTGGGTCTTCATGTGAATACC 58.156 43.478 17.36 17.36 45.31 2.73
263 268 7.012421 GGTATTCTTGGGTCTTCATGTGAATAC 59.988 40.741 0.00 0.00 41.52 1.89
264 269 7.054124 GGTATTCTTGGGTCTTCATGTGAATA 58.946 38.462 0.00 0.00 33.01 1.75
265 270 5.888161 GGTATTCTTGGGTCTTCATGTGAAT 59.112 40.000 0.00 0.00 33.01 2.57
266 271 5.253330 GGTATTCTTGGGTCTTCATGTGAA 58.747 41.667 0.00 0.00 0.00 3.18
267 272 4.324254 GGGTATTCTTGGGTCTTCATGTGA 60.324 45.833 0.00 0.00 0.00 3.58
268 273 3.947834 GGGTATTCTTGGGTCTTCATGTG 59.052 47.826 0.00 0.00 0.00 3.21
269 274 3.053619 GGGGTATTCTTGGGTCTTCATGT 60.054 47.826 0.00 0.00 0.00 3.21
270 275 3.203040 AGGGGTATTCTTGGGTCTTCATG 59.797 47.826 0.00 0.00 0.00 3.07
271 276 3.474920 AGGGGTATTCTTGGGTCTTCAT 58.525 45.455 0.00 0.00 0.00 2.57
272 277 2.929301 AGGGGTATTCTTGGGTCTTCA 58.071 47.619 0.00 0.00 0.00 3.02
273 278 3.181453 GCTAGGGGTATTCTTGGGTCTTC 60.181 52.174 0.00 0.00 0.00 2.87
274 279 2.778270 GCTAGGGGTATTCTTGGGTCTT 59.222 50.000 0.00 0.00 0.00 3.01
275 280 2.409570 GCTAGGGGTATTCTTGGGTCT 58.590 52.381 0.00 0.00 0.00 3.85
276 281 1.070289 CGCTAGGGGTATTCTTGGGTC 59.930 57.143 0.00 0.00 0.00 4.46
277 282 1.129058 CGCTAGGGGTATTCTTGGGT 58.871 55.000 0.00 0.00 0.00 4.51
278 283 0.250338 GCGCTAGGGGTATTCTTGGG 60.250 60.000 9.09 0.00 0.00 4.12
279 284 0.250338 GGCGCTAGGGGTATTCTTGG 60.250 60.000 7.64 0.00 0.00 3.61
280 285 0.600255 CGGCGCTAGGGGTATTCTTG 60.600 60.000 7.64 0.00 0.00 3.02
281 286 1.746517 CGGCGCTAGGGGTATTCTT 59.253 57.895 7.64 0.00 0.00 2.52
282 287 2.868986 GCGGCGCTAGGGGTATTCT 61.869 63.158 26.86 0.00 0.00 2.40
283 288 2.357154 GCGGCGCTAGGGGTATTC 60.357 66.667 26.86 0.00 0.00 1.75
284 289 3.937447 GGCGGCGCTAGGGGTATT 61.937 66.667 32.30 0.00 0.00 1.89
298 303 4.872574 TAGGGGTAGGCAGGGGCG 62.873 72.222 0.00 0.00 42.47 6.13
299 304 2.849646 CTAGGGGTAGGCAGGGGC 60.850 72.222 0.00 0.00 40.13 5.80
300 305 2.849646 GCTAGGGGTAGGCAGGGG 60.850 72.222 0.00 0.00 0.00 4.79
301 306 2.849646 GGCTAGGGGTAGGCAGGG 60.850 72.222 1.35 0.00 41.65 4.45
302 307 2.032356 TAGGGCTAGGGGTAGGCAGG 62.032 65.000 8.11 0.00 43.55 4.85
303 308 0.832559 GTAGGGCTAGGGGTAGGCAG 60.833 65.000 8.11 0.00 43.55 4.85
304 309 1.235112 GTAGGGCTAGGGGTAGGCA 59.765 63.158 8.11 0.00 43.55 4.75
305 310 1.120184 GTGTAGGGCTAGGGGTAGGC 61.120 65.000 0.00 0.00 41.35 3.93
336 341 3.325716 AGGAAGCCAGGTACTCGTTTTAA 59.674 43.478 0.00 0.00 34.60 1.52
337 342 2.901839 AGGAAGCCAGGTACTCGTTTTA 59.098 45.455 0.00 0.00 34.60 1.52
338 343 1.697982 AGGAAGCCAGGTACTCGTTTT 59.302 47.619 0.00 0.00 34.60 2.43
339 344 1.275573 GAGGAAGCCAGGTACTCGTTT 59.724 52.381 0.00 0.00 34.60 3.60
342 347 1.677637 GGGAGGAAGCCAGGTACTCG 61.678 65.000 0.00 0.00 34.60 4.18
369 374 1.448540 GGTGCTCCCATCGTGAGTG 60.449 63.158 0.00 0.00 32.31 3.51
417 422 4.142138 TGAGAGTCGCCTAGGAAAATCTTC 60.142 45.833 14.75 8.02 0.00 2.87
460 465 3.842007 AGCTTTGATGGGAGAGAGATG 57.158 47.619 0.00 0.00 0.00 2.90
461 466 4.474287 AGAAAGCTTTGATGGGAGAGAGAT 59.526 41.667 18.30 0.00 0.00 2.75
472 477 4.464008 TGACACCAAGAGAAAGCTTTGAT 58.536 39.130 18.30 4.65 0.00 2.57
475 480 4.949856 TCTTTGACACCAAGAGAAAGCTTT 59.050 37.500 12.53 12.53 33.23 3.51
487 492 0.107643 TGCACCGATCTTTGACACCA 59.892 50.000 0.00 0.00 0.00 4.17
543 548 3.535860 GCTCGATTTAAATGCTACGCTG 58.464 45.455 5.17 1.49 0.00 5.18
547 552 4.201910 TGCTTGGCTCGATTTAAATGCTAC 60.202 41.667 5.17 0.00 0.00 3.58
564 569 2.247358 ACCCTAAATTGTGGTGCTTGG 58.753 47.619 0.00 0.00 0.00 3.61
568 573 3.744238 ACAAACCCTAAATTGTGGTGC 57.256 42.857 0.00 0.00 38.29 5.01
590 595 3.808174 AGCTTTTCGTTGTTGGAGAGTAC 59.192 43.478 0.00 0.00 0.00 2.73
716 722 5.993106 ATTATCGCTTAAGAAGTTGAGCC 57.007 39.130 6.67 0.00 41.23 4.70
797 805 2.285834 GCGATGATAAGAAACTGCACGG 60.286 50.000 0.00 0.00 0.00 4.94
798 806 2.348362 TGCGATGATAAGAAACTGCACG 59.652 45.455 0.00 0.00 0.00 5.34
816 824 1.875963 CCAAGGTAGCTTGGTTGCG 59.124 57.895 35.43 16.88 46.45 4.85
921 929 3.257933 CGACAAGCAACAGGAGGC 58.742 61.111 0.00 0.00 0.00 4.70
998 1007 4.002316 GAGGAGATTTATGAGCCAGATGC 58.998 47.826 0.00 0.00 41.71 3.91
999 1008 4.244066 CGAGGAGATTTATGAGCCAGATG 58.756 47.826 0.00 0.00 0.00 2.90
1000 1009 3.900601 ACGAGGAGATTTATGAGCCAGAT 59.099 43.478 0.00 0.00 0.00 2.90
1002 1011 3.648009 GACGAGGAGATTTATGAGCCAG 58.352 50.000 0.00 0.00 0.00 4.85
1003 1012 2.034685 CGACGAGGAGATTTATGAGCCA 59.965 50.000 0.00 0.00 0.00 4.75
1009 1020 2.287069 CGAGTGCGACGAGGAGATTTAT 60.287 50.000 0.00 0.00 40.82 1.40
1419 1475 2.434884 CGCTGAACATGGCGTCCT 60.435 61.111 5.98 0.00 45.34 3.85
1716 1772 2.149578 CCGATGGAGAATTGGAGATGC 58.850 52.381 0.00 0.00 42.03 3.91
1717 1773 3.758755 TCCGATGGAGAATTGGAGATG 57.241 47.619 0.00 0.00 43.09 2.90
1722 1778 5.764686 TCATATGTTTCCGATGGAGAATTGG 59.235 40.000 1.90 0.00 40.91 3.16
1724 1780 7.880160 TTTCATATGTTTCCGATGGAGAATT 57.120 32.000 1.90 0.00 31.21 2.17
1725 1781 7.557719 AGTTTTCATATGTTTCCGATGGAGAAT 59.442 33.333 1.90 0.00 31.21 2.40
1726 1782 6.884295 AGTTTTCATATGTTTCCGATGGAGAA 59.116 34.615 1.90 0.00 31.21 2.87
1782 1846 2.729467 GCTAGCTAGTGATGGCGATACG 60.729 54.545 21.62 0.00 0.00 3.06
1783 1847 2.490115 AGCTAGCTAGTGATGGCGATAC 59.510 50.000 17.69 0.88 41.02 2.24
1785 1849 1.626686 AGCTAGCTAGTGATGGCGAT 58.373 50.000 17.69 0.00 41.02 4.58
1786 1850 2.155279 CTAGCTAGCTAGTGATGGCGA 58.845 52.381 34.41 9.61 41.02 5.54
1787 1851 1.402194 GCTAGCTAGCTAGTGATGGCG 60.402 57.143 39.05 21.44 45.67 5.69
1788 1852 2.362169 GCTAGCTAGCTAGTGATGGC 57.638 55.000 39.05 27.07 45.67 4.40
1833 1897 2.518949 CGTTTGTTGCCATGTAGATGC 58.481 47.619 0.00 0.00 0.00 3.91
2115 2197 4.421131 AGATGGTAGCTCGGGATATCTTT 58.579 43.478 2.05 0.00 0.00 2.52
2289 2371 1.339055 TGCGCTTTGCTCTGGACTATT 60.339 47.619 9.73 0.00 46.63 1.73
2425 2507 1.548269 CCCGCTGGCCAAAATTCTTTA 59.452 47.619 7.01 0.00 0.00 1.85
2475 2557 1.272490 TGTAGTTTCTGTGAGCGGGAG 59.728 52.381 0.00 0.00 0.00 4.30
2481 2563 7.633193 ATCTACTAGGTGTAGTTTCTGTGAG 57.367 40.000 0.00 0.00 46.50 3.51
2506 2588 3.734463 TGACAAAGCGTAATTGGACAGA 58.266 40.909 0.00 0.00 32.02 3.41
2619 2701 4.762289 ATTCGAGCTTCATTCCTACCTT 57.238 40.909 0.00 0.00 0.00 3.50
2718 2800 2.225017 TGATGGAGGTTCAGTTTTCCCC 60.225 50.000 0.00 0.00 0.00 4.81
2725 2807 0.908198 GAGGCTGATGGAGGTTCAGT 59.092 55.000 0.00 0.00 42.12 3.41
2755 2837 0.984230 TCGTTGGGAAGAATGGCTCT 59.016 50.000 0.00 0.00 35.13 4.09
2795 2877 9.454859 CAATCTATCCCCCTTAATATTCAGTTC 57.545 37.037 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.