Multiple sequence alignment - TraesCS1A01G174300

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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 TraesCS1A01G174300 chr1A 100.000 2264 0 0 1 2264 311772641 311770378 0.000000e+00 4181
1 TraesCS1A01G174300 chr4D 93.692 1934 114 6 338 2264 470196300 470194368 0.000000e+00 2889
2 TraesCS1A01G174300 chr4D 95.549 337 15 0 1 337 161392578 161392914 7.110000e-150 540
3 TraesCS1A01G174300 chr4D 95.549 337 15 0 1 337 325869964 325869628 7.110000e-150 540
4 TraesCS1A01G174300 chr2D 94.722 1819 92 4 338 2154 619853969 619855785 0.000000e+00 2824
5 TraesCS1A01G174300 chr2D 96.142 337 13 0 1 337 191080188 191080524 3.290000e-153 551
6 TraesCS1A01G174300 chr2D 95.575 339 13 2 1 338 49984900 49985237 1.980000e-150 542
7 TraesCS1A01G174300 chr2D 85.294 102 14 1 2163 2264 152003244 152003144 1.110000e-18 104
8 TraesCS1A01G174300 chr7D 92.122 1904 135 14 338 2235 131689732 131691626 0.000000e+00 2671
9 TraesCS1A01G174300 chr7D 92.794 1818 123 8 338 2151 528561525 528563338 0.000000e+00 2625
10 TraesCS1A01G174300 chr7D 88.182 1540 104 31 741 2264 460800557 460802034 0.000000e+00 1764
11 TraesCS1A01G174300 chr7D 83.475 236 35 3 2030 2264 460802058 460801826 1.360000e-52 217
12 TraesCS1A01G174300 chrUn 92.904 1832 122 8 338 2165 10399511 10401338 0.000000e+00 2656
13 TraesCS1A01G174300 chr6D 95.714 1610 68 1 338 1946 377212543 377214152 0.000000e+00 2590
14 TraesCS1A01G174300 chr6D 88.372 86 10 0 2179 2264 62143251 62143166 1.110000e-18 104
15 TraesCS1A01G174300 chr3D 94.921 1654 75 3 338 1990 446922762 446924407 0.000000e+00 2580
16 TraesCS1A01G174300 chr3D 96.142 337 13 0 1 337 578083187 578083523 3.290000e-153 551
17 TraesCS1A01G174300 chr3D 95.562 338 14 1 1 337 160720448 160720111 7.110000e-150 540
18 TraesCS1A01G174300 chr3D 95.308 341 15 1 1 341 264588953 264588614 7.110000e-150 540
19 TraesCS1A01G174300 chr6B 91.283 1847 144 17 338 2176 599876438 599878275 0.000000e+00 2503
20 TraesCS1A01G174300 chr2B 93.849 1642 97 4 338 1977 454449562 454451201 0.000000e+00 2470
21 TraesCS1A01G174300 chr3B 89.787 1929 158 25 338 2260 558278035 558276140 0.000000e+00 2435
22 TraesCS1A01G174300 chr5D 96.439 337 11 1 1 337 246998742 246998407 2.540000e-154 555
23 TraesCS1A01G174300 chr1D 95.575 339 15 0 1 339 87698314 87698652 5.500000e-151 544
24 TraesCS1A01G174300 chr6A 80.085 236 45 2 2030 2264 23006936 23006702 8.310000e-40 174


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 TraesCS1A01G174300 chr1A 311770378 311772641 2263 True 4181 4181 100.000 1 2264 1 chr1A.!!$R1 2263
1 TraesCS1A01G174300 chr4D 470194368 470196300 1932 True 2889 2889 93.692 338 2264 1 chr4D.!!$R2 1926
2 TraesCS1A01G174300 chr2D 619853969 619855785 1816 False 2824 2824 94.722 338 2154 1 chr2D.!!$F3 1816
3 TraesCS1A01G174300 chr7D 131689732 131691626 1894 False 2671 2671 92.122 338 2235 1 chr7D.!!$F1 1897
4 TraesCS1A01G174300 chr7D 528561525 528563338 1813 False 2625 2625 92.794 338 2151 1 chr7D.!!$F3 1813
5 TraesCS1A01G174300 chr7D 460800557 460802034 1477 False 1764 1764 88.182 741 2264 1 chr7D.!!$F2 1523
6 TraesCS1A01G174300 chrUn 10399511 10401338 1827 False 2656 2656 92.904 338 2165 1 chrUn.!!$F1 1827
7 TraesCS1A01G174300 chr6D 377212543 377214152 1609 False 2590 2590 95.714 338 1946 1 chr6D.!!$F1 1608
8 TraesCS1A01G174300 chr3D 446922762 446924407 1645 False 2580 2580 94.921 338 1990 1 chr3D.!!$F1 1652
9 TraesCS1A01G174300 chr6B 599876438 599878275 1837 False 2503 2503 91.283 338 2176 1 chr6B.!!$F1 1838
10 TraesCS1A01G174300 chr2B 454449562 454451201 1639 False 2470 2470 93.849 338 1977 1 chr2B.!!$F1 1639
11 TraesCS1A01G174300 chr3B 558276140 558278035 1895 True 2435 2435 89.787 338 2260 1 chr3B.!!$R1 1922

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
190 191 0.10576 TTTGCTCCTTTTCCAGCCCA 60.106 50.0 0.0 0.0 34.47 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2079 2219 0.616679 ACACCACCCTACCGCTATGT 60.617 55.0 0.0 0.0 0.0 2.29 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
63 64 2.343758 CACCCTCGTGGACAGGTG 59.656 66.667 4.76 0.63 43.50 4.00
64 65 2.923035 ACCCTCGTGGACAGGTGG 60.923 66.667 4.76 6.22 38.00 4.61
65 66 2.603473 CCCTCGTGGACAGGTGGA 60.603 66.667 4.76 0.00 35.39 4.02
66 67 2.650116 CCCTCGTGGACAGGTGGAG 61.650 68.421 4.76 2.37 35.39 3.86
67 68 2.650116 CCTCGTGGACAGGTGGAGG 61.650 68.421 0.00 1.87 38.43 4.30
68 69 3.302347 CTCGTGGACAGGTGGAGGC 62.302 68.421 0.00 0.00 0.00 4.70
69 70 4.742201 CGTGGACAGGTGGAGGCG 62.742 72.222 0.00 0.00 0.00 5.52
81 82 3.537874 GAGGCGCCCCTGACGTAT 61.538 66.667 26.15 0.00 43.12 3.06
82 83 3.081409 AGGCGCCCCTGACGTATT 61.081 61.111 26.15 0.00 40.94 1.89
83 84 2.124860 GGCGCCCCTGACGTATTT 60.125 61.111 18.11 0.00 0.00 1.40
84 85 2.178235 GGCGCCCCTGACGTATTTC 61.178 63.158 18.11 0.00 0.00 2.17
85 86 1.153429 GCGCCCCTGACGTATTTCT 60.153 57.895 0.00 0.00 0.00 2.52
86 87 0.743345 GCGCCCCTGACGTATTTCTT 60.743 55.000 0.00 0.00 0.00 2.52
87 88 1.287425 CGCCCCTGACGTATTTCTTC 58.713 55.000 0.00 0.00 0.00 2.87
88 89 1.664873 GCCCCTGACGTATTTCTTCC 58.335 55.000 0.00 0.00 0.00 3.46
89 90 1.935933 CCCCTGACGTATTTCTTCCG 58.064 55.000 0.00 0.00 0.00 4.30
90 91 1.287425 CCCTGACGTATTTCTTCCGC 58.713 55.000 0.00 0.00 0.00 5.54
91 92 1.134788 CCCTGACGTATTTCTTCCGCT 60.135 52.381 0.00 0.00 0.00 5.52
92 93 2.194271 CCTGACGTATTTCTTCCGCTC 58.806 52.381 0.00 0.00 0.00 5.03
93 94 2.416836 CCTGACGTATTTCTTCCGCTCA 60.417 50.000 0.00 0.00 0.00 4.26
94 95 2.854777 CTGACGTATTTCTTCCGCTCAG 59.145 50.000 0.00 0.00 0.00 3.35
95 96 2.230508 TGACGTATTTCTTCCGCTCAGT 59.769 45.455 0.00 0.00 0.00 3.41
96 97 3.441222 TGACGTATTTCTTCCGCTCAGTA 59.559 43.478 0.00 0.00 0.00 2.74
97 98 4.097437 TGACGTATTTCTTCCGCTCAGTAT 59.903 41.667 0.00 0.00 0.00 2.12
98 99 5.007385 ACGTATTTCTTCCGCTCAGTATT 57.993 39.130 0.00 0.00 0.00 1.89
99 100 5.416947 ACGTATTTCTTCCGCTCAGTATTT 58.583 37.500 0.00 0.00 0.00 1.40
100 101 5.873164 ACGTATTTCTTCCGCTCAGTATTTT 59.127 36.000 0.00 0.00 0.00 1.82
101 102 6.370718 ACGTATTTCTTCCGCTCAGTATTTTT 59.629 34.615 0.00 0.00 0.00 1.94
130 131 9.685828 TTATTTCCAAAAATAACTTTCGTGGAG 57.314 29.630 0.43 0.00 40.65 3.86
131 132 6.702716 TTCCAAAAATAACTTTCGTGGAGT 57.297 33.333 0.00 0.00 38.60 3.85
132 133 6.702716 TCCAAAAATAACTTTCGTGGAGTT 57.297 33.333 6.21 6.21 40.28 3.01
133 134 7.102847 TCCAAAAATAACTTTCGTGGAGTTT 57.897 32.000 6.24 0.00 38.28 2.66
134 135 7.197703 TCCAAAAATAACTTTCGTGGAGTTTC 58.802 34.615 6.24 0.00 38.28 2.78
135 136 6.975772 CCAAAAATAACTTTCGTGGAGTTTCA 59.024 34.615 6.24 0.00 38.28 2.69
136 137 7.651704 CCAAAAATAACTTTCGTGGAGTTTCAT 59.348 33.333 6.24 0.00 38.28 2.57
137 138 8.479280 CAAAAATAACTTTCGTGGAGTTTCATG 58.521 33.333 6.24 0.00 38.28 3.07
138 139 7.504924 AAATAACTTTCGTGGAGTTTCATGA 57.495 32.000 0.00 0.00 38.28 3.07
139 140 4.813296 AACTTTCGTGGAGTTTCATGAC 57.187 40.909 0.00 0.00 33.76 3.06
140 141 4.073293 ACTTTCGTGGAGTTTCATGACT 57.927 40.909 0.00 0.00 32.97 3.41
141 142 4.451900 ACTTTCGTGGAGTTTCATGACTT 58.548 39.130 0.00 0.00 32.97 3.01
142 143 4.881850 ACTTTCGTGGAGTTTCATGACTTT 59.118 37.500 0.00 0.00 32.97 2.66
143 144 5.357032 ACTTTCGTGGAGTTTCATGACTTTT 59.643 36.000 0.00 0.00 32.97 2.27
144 145 4.811555 TCGTGGAGTTTCATGACTTTTG 57.188 40.909 0.00 0.00 0.00 2.44
145 146 3.563808 TCGTGGAGTTTCATGACTTTTGG 59.436 43.478 0.00 0.00 0.00 3.28
146 147 3.563808 CGTGGAGTTTCATGACTTTTGGA 59.436 43.478 0.00 0.00 0.00 3.53
147 148 4.319766 CGTGGAGTTTCATGACTTTTGGAG 60.320 45.833 0.00 0.00 0.00 3.86
148 149 4.580580 GTGGAGTTTCATGACTTTTGGAGT 59.419 41.667 0.00 0.00 42.70 3.85
149 150 5.067805 GTGGAGTTTCATGACTTTTGGAGTT 59.932 40.000 0.00 0.00 39.19 3.01
150 151 5.067674 TGGAGTTTCATGACTTTTGGAGTTG 59.932 40.000 0.00 0.00 39.19 3.16
151 152 5.067805 GGAGTTTCATGACTTTTGGAGTTGT 59.932 40.000 0.00 0.00 39.19 3.32
152 153 5.894807 AGTTTCATGACTTTTGGAGTTGTG 58.105 37.500 0.00 0.00 39.19 3.33
153 154 3.988379 TCATGACTTTTGGAGTTGTGC 57.012 42.857 0.00 0.00 39.19 4.57
154 155 3.286353 TCATGACTTTTGGAGTTGTGCA 58.714 40.909 0.00 0.00 39.19 4.57
155 156 3.316029 TCATGACTTTTGGAGTTGTGCAG 59.684 43.478 0.00 0.00 39.19 4.41
156 157 2.997980 TGACTTTTGGAGTTGTGCAGA 58.002 42.857 0.00 0.00 39.19 4.26
157 158 3.351740 TGACTTTTGGAGTTGTGCAGAA 58.648 40.909 0.00 0.00 39.19 3.02
158 159 3.953612 TGACTTTTGGAGTTGTGCAGAAT 59.046 39.130 0.00 0.00 39.19 2.40
159 160 5.129634 TGACTTTTGGAGTTGTGCAGAATA 58.870 37.500 0.00 0.00 39.19 1.75
160 161 5.239306 TGACTTTTGGAGTTGTGCAGAATAG 59.761 40.000 0.00 0.00 39.19 1.73
161 162 4.520492 ACTTTTGGAGTTGTGCAGAATAGG 59.480 41.667 0.00 0.00 33.92 2.57
162 163 3.788227 TTGGAGTTGTGCAGAATAGGT 57.212 42.857 0.00 0.00 0.00 3.08
163 164 3.334583 TGGAGTTGTGCAGAATAGGTC 57.665 47.619 0.00 0.00 0.00 3.85
164 165 2.906389 TGGAGTTGTGCAGAATAGGTCT 59.094 45.455 0.00 0.00 36.88 3.85
165 166 3.055819 TGGAGTTGTGCAGAATAGGTCTC 60.056 47.826 0.00 1.06 32.70 3.36
166 167 3.196685 GGAGTTGTGCAGAATAGGTCTCT 59.803 47.826 0.00 0.00 32.70 3.10
167 168 4.402793 GGAGTTGTGCAGAATAGGTCTCTA 59.597 45.833 0.00 0.00 32.70 2.43
168 169 5.105310 GGAGTTGTGCAGAATAGGTCTCTAA 60.105 44.000 0.00 0.00 32.70 2.10
169 170 6.407525 GGAGTTGTGCAGAATAGGTCTCTAAT 60.408 42.308 0.00 0.00 32.70 1.73
170 171 7.201920 GGAGTTGTGCAGAATAGGTCTCTAATA 60.202 40.741 0.00 0.00 32.70 0.98
171 172 8.256356 AGTTGTGCAGAATAGGTCTCTAATAT 57.744 34.615 0.00 0.00 32.70 1.28
172 173 8.709308 AGTTGTGCAGAATAGGTCTCTAATATT 58.291 33.333 0.00 0.00 32.70 1.28
173 174 9.331282 GTTGTGCAGAATAGGTCTCTAATATTT 57.669 33.333 0.00 0.00 32.70 1.40
174 175 8.893219 TGTGCAGAATAGGTCTCTAATATTTG 57.107 34.615 0.00 0.00 32.70 2.32
175 176 7.442364 TGTGCAGAATAGGTCTCTAATATTTGC 59.558 37.037 0.00 0.00 32.70 3.68
176 177 7.659390 GTGCAGAATAGGTCTCTAATATTTGCT 59.341 37.037 0.00 0.00 32.70 3.91
177 178 7.875041 TGCAGAATAGGTCTCTAATATTTGCTC 59.125 37.037 0.00 0.00 32.70 4.26
178 179 7.333174 GCAGAATAGGTCTCTAATATTTGCTCC 59.667 40.741 0.00 0.00 32.70 4.70
179 180 8.592809 CAGAATAGGTCTCTAATATTTGCTCCT 58.407 37.037 0.00 3.47 32.70 3.69
180 181 9.165057 AGAATAGGTCTCTAATATTTGCTCCTT 57.835 33.333 0.00 0.00 0.00 3.36
181 182 9.785982 GAATAGGTCTCTAATATTTGCTCCTTT 57.214 33.333 0.00 0.00 0.00 3.11
183 184 9.785982 ATAGGTCTCTAATATTTGCTCCTTTTC 57.214 33.333 0.00 0.00 0.00 2.29
184 185 7.057264 AGGTCTCTAATATTTGCTCCTTTTCC 58.943 38.462 0.00 0.00 0.00 3.13
185 186 6.828785 GGTCTCTAATATTTGCTCCTTTTCCA 59.171 38.462 0.00 0.00 0.00 3.53
186 187 7.012799 GGTCTCTAATATTTGCTCCTTTTCCAG 59.987 40.741 0.00 0.00 0.00 3.86
187 188 6.543831 TCTCTAATATTTGCTCCTTTTCCAGC 59.456 38.462 0.00 0.00 36.08 4.85
188 189 4.743057 AATATTTGCTCCTTTTCCAGCC 57.257 40.909 0.00 0.00 34.47 4.85
189 190 1.269958 ATTTGCTCCTTTTCCAGCCC 58.730 50.000 0.00 0.00 34.47 5.19
190 191 0.105760 TTTGCTCCTTTTCCAGCCCA 60.106 50.000 0.00 0.00 34.47 5.36
191 192 0.540365 TTGCTCCTTTTCCAGCCCAG 60.540 55.000 0.00 0.00 34.47 4.45
192 193 1.380302 GCTCCTTTTCCAGCCCAGA 59.620 57.895 0.00 0.00 0.00 3.86
193 194 0.251341 GCTCCTTTTCCAGCCCAGAA 60.251 55.000 0.00 0.00 0.00 3.02
194 195 1.618074 GCTCCTTTTCCAGCCCAGAAT 60.618 52.381 0.00 0.00 0.00 2.40
195 196 2.812658 CTCCTTTTCCAGCCCAGAATT 58.187 47.619 0.00 0.00 0.00 2.17
196 197 2.757314 CTCCTTTTCCAGCCCAGAATTC 59.243 50.000 0.00 0.00 0.00 2.17
197 198 1.827344 CCTTTTCCAGCCCAGAATTCC 59.173 52.381 0.65 0.00 0.00 3.01
198 199 2.528564 CTTTTCCAGCCCAGAATTCCA 58.471 47.619 0.65 0.00 0.00 3.53
199 200 2.692709 TTTCCAGCCCAGAATTCCAA 57.307 45.000 0.65 0.00 0.00 3.53
200 201 1.923356 TTCCAGCCCAGAATTCCAAC 58.077 50.000 0.65 0.00 0.00 3.77
201 202 1.075601 TCCAGCCCAGAATTCCAACT 58.924 50.000 0.65 0.00 0.00 3.16
202 203 1.180029 CCAGCCCAGAATTCCAACTG 58.820 55.000 0.65 5.24 0.00 3.16
203 204 0.529378 CAGCCCAGAATTCCAACTGC 59.471 55.000 0.65 0.00 33.40 4.40
204 205 0.613012 AGCCCAGAATTCCAACTGCC 60.613 55.000 0.65 0.00 33.40 4.85
205 206 1.937546 GCCCAGAATTCCAACTGCCG 61.938 60.000 0.65 0.00 33.40 5.69
206 207 1.315257 CCCAGAATTCCAACTGCCGG 61.315 60.000 0.65 0.00 33.40 6.13
207 208 1.508088 CAGAATTCCAACTGCCGGC 59.492 57.895 22.73 22.73 0.00 6.13
208 209 1.074775 AGAATTCCAACTGCCGGCA 59.925 52.632 30.59 30.59 0.00 5.69
209 210 0.323725 AGAATTCCAACTGCCGGCAT 60.324 50.000 32.87 14.47 0.00 4.40
210 211 0.532115 GAATTCCAACTGCCGGCATT 59.468 50.000 32.87 23.63 0.00 3.56
211 212 0.532115 AATTCCAACTGCCGGCATTC 59.468 50.000 32.87 0.00 0.00 2.67
212 213 0.323725 ATTCCAACTGCCGGCATTCT 60.324 50.000 32.87 14.79 0.00 2.40
213 214 0.960364 TTCCAACTGCCGGCATTCTC 60.960 55.000 32.87 0.00 0.00 2.87
214 215 2.409870 CCAACTGCCGGCATTCTCC 61.410 63.158 32.87 0.00 0.00 3.71
215 216 2.044946 AACTGCCGGCATTCTCCC 60.045 61.111 32.87 0.00 0.00 4.30
216 217 2.606587 AACTGCCGGCATTCTCCCT 61.607 57.895 32.87 5.72 0.00 4.20
217 218 2.203126 CTGCCGGCATTCTCCCTC 60.203 66.667 32.87 0.00 0.00 4.30
218 219 3.764160 CTGCCGGCATTCTCCCTCC 62.764 68.421 32.87 0.00 0.00 4.30
219 220 3.483869 GCCGGCATTCTCCCTCCT 61.484 66.667 24.80 0.00 0.00 3.69
220 221 3.049080 GCCGGCATTCTCCCTCCTT 62.049 63.158 24.80 0.00 0.00 3.36
221 222 1.696097 GCCGGCATTCTCCCTCCTTA 61.696 60.000 24.80 0.00 0.00 2.69
222 223 1.059913 CCGGCATTCTCCCTCCTTAT 58.940 55.000 0.00 0.00 0.00 1.73
223 224 1.271054 CCGGCATTCTCCCTCCTTATG 60.271 57.143 0.00 0.00 0.00 1.90
224 225 1.417890 CGGCATTCTCCCTCCTTATGT 59.582 52.381 0.00 0.00 0.00 2.29
225 226 2.632996 CGGCATTCTCCCTCCTTATGTA 59.367 50.000 0.00 0.00 0.00 2.29
226 227 3.071023 CGGCATTCTCCCTCCTTATGTAA 59.929 47.826 0.00 0.00 0.00 2.41
227 228 4.444306 CGGCATTCTCCCTCCTTATGTAAA 60.444 45.833 0.00 0.00 0.00 2.01
228 229 4.822350 GGCATTCTCCCTCCTTATGTAAAC 59.178 45.833 0.00 0.00 0.00 2.01
229 230 4.822350 GCATTCTCCCTCCTTATGTAAACC 59.178 45.833 0.00 0.00 0.00 3.27
230 231 5.398012 GCATTCTCCCTCCTTATGTAAACCT 60.398 44.000 0.00 0.00 0.00 3.50
231 232 6.663734 CATTCTCCCTCCTTATGTAAACCTT 58.336 40.000 0.00 0.00 0.00 3.50
232 233 5.693769 TCTCCCTCCTTATGTAAACCTTG 57.306 43.478 0.00 0.00 0.00 3.61
233 234 5.098663 TCTCCCTCCTTATGTAAACCTTGT 58.901 41.667 0.00 0.00 0.00 3.16
234 235 6.266080 TCTCCCTCCTTATGTAAACCTTGTA 58.734 40.000 0.00 0.00 0.00 2.41
235 236 6.731919 TCTCCCTCCTTATGTAAACCTTGTAA 59.268 38.462 0.00 0.00 0.00 2.41
236 237 7.238096 TCTCCCTCCTTATGTAAACCTTGTAAA 59.762 37.037 0.00 0.00 0.00 2.01
237 238 7.757611 TCCCTCCTTATGTAAACCTTGTAAAA 58.242 34.615 0.00 0.00 0.00 1.52
238 239 8.395605 TCCCTCCTTATGTAAACCTTGTAAAAT 58.604 33.333 0.00 0.00 0.00 1.82
239 240 9.689501 CCCTCCTTATGTAAACCTTGTAAAATA 57.310 33.333 0.00 0.00 0.00 1.40
252 253 8.966069 ACCTTGTAAAATAAGAGAGAATAGGC 57.034 34.615 0.00 0.00 0.00 3.93
253 254 8.548877 ACCTTGTAAAATAAGAGAGAATAGGCA 58.451 33.333 0.00 0.00 0.00 4.75
254 255 9.566432 CCTTGTAAAATAAGAGAGAATAGGCAT 57.434 33.333 0.00 0.00 0.00 4.40
286 287 7.944729 ATGACATAATGTGGAATAATAGCCC 57.055 36.000 0.00 0.00 0.00 5.19
287 288 6.846988 TGACATAATGTGGAATAATAGCCCA 58.153 36.000 0.00 0.00 0.00 5.36
288 289 7.293828 TGACATAATGTGGAATAATAGCCCAA 58.706 34.615 0.00 0.00 0.00 4.12
289 290 7.782168 TGACATAATGTGGAATAATAGCCCAAA 59.218 33.333 0.00 0.00 0.00 3.28
290 291 8.546083 ACATAATGTGGAATAATAGCCCAAAA 57.454 30.769 0.00 0.00 0.00 2.44
291 292 9.158097 ACATAATGTGGAATAATAGCCCAAAAT 57.842 29.630 0.00 0.00 0.00 1.82
292 293 9.426837 CATAATGTGGAATAATAGCCCAAAATG 57.573 33.333 0.00 0.00 0.00 2.32
293 294 5.275067 TGTGGAATAATAGCCCAAAATGC 57.725 39.130 0.00 0.00 0.00 3.56
294 295 4.713814 TGTGGAATAATAGCCCAAAATGCA 59.286 37.500 0.00 0.00 0.00 3.96
295 296 5.188555 TGTGGAATAATAGCCCAAAATGCAA 59.811 36.000 0.00 0.00 0.00 4.08
296 297 6.126825 TGTGGAATAATAGCCCAAAATGCAAT 60.127 34.615 0.00 0.00 0.00 3.56
297 298 7.070447 TGTGGAATAATAGCCCAAAATGCAATA 59.930 33.333 0.00 0.00 0.00 1.90
298 299 7.930865 GTGGAATAATAGCCCAAAATGCAATAA 59.069 33.333 0.00 0.00 0.00 1.40
299 300 8.489489 TGGAATAATAGCCCAAAATGCAATAAA 58.511 29.630 0.00 0.00 0.00 1.40
300 301 9.506018 GGAATAATAGCCCAAAATGCAATAAAT 57.494 29.630 0.00 0.00 0.00 1.40
336 337 8.887036 AAGTATGATGCAAAATAGACGTATCA 57.113 30.769 0.00 0.00 36.43 2.15
365 366 3.206964 TGCACGAGTTTACATTGGAACA 58.793 40.909 0.00 0.00 0.00 3.18
388 389 1.847798 AAGGTTGACATGGGCGCCTA 61.848 55.000 28.56 23.38 0.00 3.93
409 410 6.634955 GCCTAGGTTCAATCCTTTCCTTGATA 60.635 42.308 11.31 0.00 38.86 2.15
415 416 6.581388 TCAATCCTTTCCTTGATACCTCAT 57.419 37.500 0.00 0.00 0.00 2.90
456 457 1.064906 CCAGACATTGTGCCAGATCCT 60.065 52.381 0.00 0.00 0.00 3.24
534 535 4.482990 TGGATGATCTAGCTGGATACACA 58.517 43.478 13.16 7.45 46.17 3.72
610 611 3.423749 TGTGGAGAATGCAATGACACAT 58.576 40.909 9.55 0.00 39.09 3.21
877 879 2.930040 CCTATCGACGTGTTGCTCAATT 59.070 45.455 0.00 0.00 0.00 2.32
878 880 3.370978 CCTATCGACGTGTTGCTCAATTT 59.629 43.478 0.00 0.00 0.00 1.82
895 897 8.756927 TGCTCAATTTGGATGGTTGAAATAATA 58.243 29.630 0.00 0.00 32.08 0.98
976 978 9.230122 ACATGTCAATGTGTTCATATTTAGACA 57.770 29.630 13.30 13.30 45.51 3.41
1010 1015 1.745087 CGTTGTAGGCATGGCTTCATT 59.255 47.619 28.30 5.01 0.00 2.57
1013 1018 0.308993 GTAGGCATGGCTTCATTCGC 59.691 55.000 28.30 5.71 0.00 4.70
1016 1021 0.526954 GGCATGGCTTCATTCGCTTG 60.527 55.000 12.86 0.00 0.00 4.01
1095 1100 3.208747 TCTTTGGACAAGGTGAAGGAC 57.791 47.619 0.00 0.00 0.00 3.85
1177 1182 1.003233 ACCGAAAGAAGTCATGGACCC 59.997 52.381 0.00 0.00 32.18 4.46
1279 1284 8.082852 CGGTATGCTAGAGAAGTAACATGTTAT 58.917 37.037 20.72 6.50 0.00 1.89
1325 1330 5.182487 ACATCCGTTTTATATGCAGTCACA 58.818 37.500 0.00 0.00 0.00 3.58
1418 1423 4.580356 AAGATTGTCTTAGGCGCCAGCA 62.580 50.000 31.54 16.70 39.09 4.41
1460 1465 0.546267 AGAGGCTTGGAGGAAGAGCA 60.546 55.000 0.00 0.00 38.14 4.26
1734 1740 2.098934 GCCATGTGTTGTGAACTTGTCA 59.901 45.455 0.00 0.00 0.00 3.58
1890 1920 4.421131 AGGGATAGAACAGAACAGAGTGT 58.579 43.478 0.00 0.00 0.00 3.55
1970 2108 2.659063 CCTCCAGACCACATGGCGA 61.659 63.158 0.00 0.00 37.76 5.54
1997 2136 4.263068 GGGGGTGTATATCTTCTGTGATGG 60.263 50.000 0.00 0.00 0.00 3.51
2002 2141 6.708054 GGTGTATATCTTCTGTGATGGGAAAG 59.292 42.308 0.00 0.00 0.00 2.62
2005 2144 1.988107 TCTTCTGTGATGGGAAAGGCT 59.012 47.619 0.00 0.00 0.00 4.58
2056 2196 2.688666 CAGGGCCTGGCAGTAGGA 60.689 66.667 26.34 0.00 40.42 2.94
2079 2219 1.206132 CTGTACCATACCGCCAGACAA 59.794 52.381 0.00 0.00 0.00 3.18
2083 2223 1.834896 ACCATACCGCCAGACAACATA 59.165 47.619 0.00 0.00 0.00 2.29
2108 2250 5.319453 CGGTAGGGTGGTGTATATCTTCTA 58.681 45.833 0.00 0.00 0.00 2.10
2122 2264 6.732896 ATATCTTCTATGACGGGAAACACT 57.267 37.500 0.00 0.00 0.00 3.55
2165 2310 2.819984 CTACCGCCACAGCCAATGGT 62.820 60.000 0.00 0.00 39.63 3.55
2204 2352 4.309950 AGGGCGCCGTCGTTTCTT 62.310 61.111 22.54 0.00 38.14 2.52
2205 2353 2.432972 GGGCGCCGTCGTTTCTTA 60.433 61.111 22.54 0.00 38.14 2.10
2223 2372 8.969267 CGTTTCTTATCACAGAAGATATACACC 58.031 37.037 0.00 0.00 34.22 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.619320 TGCCCCTTGCCTTGTGGG 62.619 66.667 0.00 0.00 40.16 4.61
4 5 3.305516 GTGCCCCTTGCCTTGTGG 61.306 66.667 0.00 0.00 40.16 4.17
5 6 3.673484 CGTGCCCCTTGCCTTGTG 61.673 66.667 0.00 0.00 40.16 3.33
46 47 2.343758 CACCTGTCCACGAGGGTG 59.656 66.667 0.00 0.00 43.99 4.61
47 48 2.923035 CCACCTGTCCACGAGGGT 60.923 66.667 0.00 0.00 38.11 4.34
48 49 2.603473 TCCACCTGTCCACGAGGG 60.603 66.667 0.00 0.00 34.56 4.30
49 50 2.650116 CCTCCACCTGTCCACGAGG 61.650 68.421 0.00 0.00 34.56 4.63
50 51 2.973899 CCTCCACCTGTCCACGAG 59.026 66.667 0.00 0.00 0.00 4.18
51 52 3.311110 GCCTCCACCTGTCCACGA 61.311 66.667 0.00 0.00 0.00 4.35
52 53 4.742201 CGCCTCCACCTGTCCACG 62.742 72.222 0.00 0.00 0.00 4.94
64 65 2.588856 AAATACGTCAGGGGCGCCTC 62.589 60.000 28.56 25.59 0.00 4.70
65 66 2.588856 GAAATACGTCAGGGGCGCCT 62.589 60.000 28.56 18.22 0.00 5.52
66 67 2.124860 AAATACGTCAGGGGCGCC 60.125 61.111 21.18 21.18 0.00 6.53
67 68 0.743345 AAGAAATACGTCAGGGGCGC 60.743 55.000 0.00 0.00 0.00 6.53
68 69 1.287425 GAAGAAATACGTCAGGGGCG 58.713 55.000 0.00 0.00 0.00 6.13
69 70 1.664873 GGAAGAAATACGTCAGGGGC 58.335 55.000 0.00 0.00 0.00 5.80
70 71 1.935933 CGGAAGAAATACGTCAGGGG 58.064 55.000 0.00 0.00 0.00 4.79
71 72 1.134788 AGCGGAAGAAATACGTCAGGG 60.135 52.381 0.00 0.00 37.81 4.45
72 73 2.194271 GAGCGGAAGAAATACGTCAGG 58.806 52.381 0.00 0.00 37.81 3.86
73 74 2.854777 CTGAGCGGAAGAAATACGTCAG 59.145 50.000 0.00 0.00 37.81 3.51
74 75 2.230508 ACTGAGCGGAAGAAATACGTCA 59.769 45.455 0.00 0.00 37.81 4.35
75 76 2.877335 ACTGAGCGGAAGAAATACGTC 58.123 47.619 0.00 0.00 37.81 4.34
76 77 4.650754 ATACTGAGCGGAAGAAATACGT 57.349 40.909 0.00 0.00 37.81 3.57
77 78 5.968387 AAATACTGAGCGGAAGAAATACG 57.032 39.130 0.00 0.00 38.88 3.06
104 105 9.685828 CTCCACGAAAGTTATTTTTGGAAATAA 57.314 29.630 0.00 1.36 46.40 1.40
105 106 8.852135 ACTCCACGAAAGTTATTTTTGGAAATA 58.148 29.630 0.00 0.00 46.40 1.40
106 107 7.722363 ACTCCACGAAAGTTATTTTTGGAAAT 58.278 30.769 0.00 0.00 46.40 2.17
107 108 7.102847 ACTCCACGAAAGTTATTTTTGGAAA 57.897 32.000 0.00 0.00 46.40 3.13
108 109 6.702716 ACTCCACGAAAGTTATTTTTGGAA 57.297 33.333 0.00 0.00 46.40 3.53
109 110 6.702716 AACTCCACGAAAGTTATTTTTGGA 57.297 33.333 0.00 0.00 46.40 3.53
110 111 6.975772 TGAAACTCCACGAAAGTTATTTTTGG 59.024 34.615 0.00 0.00 46.40 3.28
111 112 7.979115 TGAAACTCCACGAAAGTTATTTTTG 57.021 32.000 0.00 0.00 46.40 2.44
112 113 8.410141 TCATGAAACTCCACGAAAGTTATTTTT 58.590 29.630 0.00 0.00 46.40 1.94
113 114 7.860872 GTCATGAAACTCCACGAAAGTTATTTT 59.139 33.333 0.00 0.00 46.40 1.82
114 115 7.228706 AGTCATGAAACTCCACGAAAGTTATTT 59.771 33.333 0.00 0.00 46.40 1.40
115 116 6.710744 AGTCATGAAACTCCACGAAAGTTATT 59.289 34.615 0.00 0.00 46.40 1.40
116 117 6.231211 AGTCATGAAACTCCACGAAAGTTAT 58.769 36.000 0.00 0.00 46.40 1.89
117 118 5.607477 AGTCATGAAACTCCACGAAAGTTA 58.393 37.500 0.00 0.00 46.40 2.24
118 119 4.451900 AGTCATGAAACTCCACGAAAGTT 58.548 39.130 0.00 0.00 46.40 2.66
120 121 5.424121 AAAGTCATGAAACTCCACGAAAG 57.576 39.130 0.00 0.00 0.00 2.62
121 122 5.449862 CCAAAAGTCATGAAACTCCACGAAA 60.450 40.000 0.00 0.00 0.00 3.46
122 123 4.036262 CCAAAAGTCATGAAACTCCACGAA 59.964 41.667 0.00 0.00 0.00 3.85
123 124 3.563808 CCAAAAGTCATGAAACTCCACGA 59.436 43.478 0.00 0.00 0.00 4.35
124 125 3.563808 TCCAAAAGTCATGAAACTCCACG 59.436 43.478 0.00 0.00 0.00 4.94
125 126 4.580580 ACTCCAAAAGTCATGAAACTCCAC 59.419 41.667 0.00 0.00 30.02 4.02
126 127 4.792068 ACTCCAAAAGTCATGAAACTCCA 58.208 39.130 0.00 0.00 30.02 3.86
127 128 5.067805 ACAACTCCAAAAGTCATGAAACTCC 59.932 40.000 0.00 0.00 37.17 3.85
128 129 5.973565 CACAACTCCAAAAGTCATGAAACTC 59.026 40.000 0.00 0.00 37.17 3.01
129 130 5.679638 GCACAACTCCAAAAGTCATGAAACT 60.680 40.000 0.00 0.00 37.17 2.66
130 131 4.504097 GCACAACTCCAAAAGTCATGAAAC 59.496 41.667 0.00 0.00 37.17 2.78
131 132 4.159321 TGCACAACTCCAAAAGTCATGAAA 59.841 37.500 0.00 0.00 37.17 2.69
132 133 3.698539 TGCACAACTCCAAAAGTCATGAA 59.301 39.130 0.00 0.00 37.17 2.57
133 134 3.286353 TGCACAACTCCAAAAGTCATGA 58.714 40.909 0.00 0.00 37.17 3.07
134 135 3.316029 TCTGCACAACTCCAAAAGTCATG 59.684 43.478 0.00 0.00 37.17 3.07
135 136 3.554934 TCTGCACAACTCCAAAAGTCAT 58.445 40.909 0.00 0.00 37.17 3.06
136 137 2.997980 TCTGCACAACTCCAAAAGTCA 58.002 42.857 0.00 0.00 37.17 3.41
137 138 4.574599 ATTCTGCACAACTCCAAAAGTC 57.425 40.909 0.00 0.00 37.17 3.01
138 139 4.520492 CCTATTCTGCACAACTCCAAAAGT 59.480 41.667 0.00 0.00 41.10 2.66
139 140 4.520492 ACCTATTCTGCACAACTCCAAAAG 59.480 41.667 0.00 0.00 0.00 2.27
140 141 4.469657 ACCTATTCTGCACAACTCCAAAA 58.530 39.130 0.00 0.00 0.00 2.44
141 142 4.072131 GACCTATTCTGCACAACTCCAAA 58.928 43.478 0.00 0.00 0.00 3.28
142 143 3.327757 AGACCTATTCTGCACAACTCCAA 59.672 43.478 0.00 0.00 31.12 3.53
143 144 2.906389 AGACCTATTCTGCACAACTCCA 59.094 45.455 0.00 0.00 31.12 3.86
144 145 3.196685 AGAGACCTATTCTGCACAACTCC 59.803 47.826 0.00 0.00 33.22 3.85
145 146 4.464069 AGAGACCTATTCTGCACAACTC 57.536 45.455 0.00 0.00 33.22 3.01
146 147 6.552445 ATTAGAGACCTATTCTGCACAACT 57.448 37.500 0.00 0.00 33.22 3.16
147 148 8.894768 AATATTAGAGACCTATTCTGCACAAC 57.105 34.615 0.00 0.00 33.22 3.32
148 149 9.330063 CAAATATTAGAGACCTATTCTGCACAA 57.670 33.333 0.00 0.00 33.22 3.33
149 150 7.442364 GCAAATATTAGAGACCTATTCTGCACA 59.558 37.037 0.00 0.00 33.22 4.57
150 151 7.659390 AGCAAATATTAGAGACCTATTCTGCAC 59.341 37.037 0.00 0.00 33.22 4.57
151 152 7.739825 AGCAAATATTAGAGACCTATTCTGCA 58.260 34.615 0.00 0.00 33.22 4.41
152 153 7.333174 GGAGCAAATATTAGAGACCTATTCTGC 59.667 40.741 0.00 0.00 33.22 4.26
153 154 8.592809 AGGAGCAAATATTAGAGACCTATTCTG 58.407 37.037 0.00 0.00 33.22 3.02
154 155 8.734593 AGGAGCAAATATTAGAGACCTATTCT 57.265 34.615 0.00 0.00 37.23 2.40
155 156 9.785982 AAAGGAGCAAATATTAGAGACCTATTC 57.214 33.333 0.00 0.00 0.00 1.75
157 158 9.785982 GAAAAGGAGCAAATATTAGAGACCTAT 57.214 33.333 0.00 0.00 0.00 2.57
158 159 8.211629 GGAAAAGGAGCAAATATTAGAGACCTA 58.788 37.037 0.00 0.00 0.00 3.08
159 160 7.057264 GGAAAAGGAGCAAATATTAGAGACCT 58.943 38.462 0.00 0.00 0.00 3.85
160 161 6.828785 TGGAAAAGGAGCAAATATTAGAGACC 59.171 38.462 0.00 0.00 0.00 3.85
161 162 7.467947 GCTGGAAAAGGAGCAAATATTAGAGAC 60.468 40.741 0.00 0.00 35.15 3.36
162 163 6.543831 GCTGGAAAAGGAGCAAATATTAGAGA 59.456 38.462 0.00 0.00 35.15 3.10
163 164 6.238869 GGCTGGAAAAGGAGCAAATATTAGAG 60.239 42.308 0.00 0.00 36.90 2.43
164 165 5.594317 GGCTGGAAAAGGAGCAAATATTAGA 59.406 40.000 0.00 0.00 36.90 2.10
165 166 5.221322 GGGCTGGAAAAGGAGCAAATATTAG 60.221 44.000 0.00 0.00 36.90 1.73
166 167 4.649218 GGGCTGGAAAAGGAGCAAATATTA 59.351 41.667 0.00 0.00 36.90 0.98
167 168 3.452264 GGGCTGGAAAAGGAGCAAATATT 59.548 43.478 0.00 0.00 36.90 1.28
168 169 3.033909 GGGCTGGAAAAGGAGCAAATAT 58.966 45.455 0.00 0.00 36.90 1.28
169 170 2.225242 TGGGCTGGAAAAGGAGCAAATA 60.225 45.455 0.00 0.00 36.90 1.40
170 171 1.269958 GGGCTGGAAAAGGAGCAAAT 58.730 50.000 0.00 0.00 36.90 2.32
171 172 0.105760 TGGGCTGGAAAAGGAGCAAA 60.106 50.000 0.00 0.00 36.90 3.68
172 173 0.540365 CTGGGCTGGAAAAGGAGCAA 60.540 55.000 0.00 0.00 36.90 3.91
173 174 1.075482 CTGGGCTGGAAAAGGAGCA 59.925 57.895 0.00 0.00 36.90 4.26
174 175 0.251341 TTCTGGGCTGGAAAAGGAGC 60.251 55.000 0.00 0.00 34.23 4.70
175 176 2.521547 ATTCTGGGCTGGAAAAGGAG 57.478 50.000 0.00 0.00 0.00 3.69
176 177 2.557452 GGAATTCTGGGCTGGAAAAGGA 60.557 50.000 5.23 0.00 0.00 3.36
177 178 1.827344 GGAATTCTGGGCTGGAAAAGG 59.173 52.381 5.23 0.00 0.00 3.11
178 179 2.528564 TGGAATTCTGGGCTGGAAAAG 58.471 47.619 5.23 0.00 0.00 2.27
179 180 2.632512 GTTGGAATTCTGGGCTGGAAAA 59.367 45.455 5.23 0.00 0.00 2.29
180 181 2.158325 AGTTGGAATTCTGGGCTGGAAA 60.158 45.455 5.23 0.00 0.00 3.13
181 182 1.428912 AGTTGGAATTCTGGGCTGGAA 59.571 47.619 5.23 0.00 0.00 3.53
182 183 1.075601 AGTTGGAATTCTGGGCTGGA 58.924 50.000 5.23 0.00 0.00 3.86
183 184 1.180029 CAGTTGGAATTCTGGGCTGG 58.820 55.000 5.23 0.00 0.00 4.85
184 185 0.529378 GCAGTTGGAATTCTGGGCTG 59.471 55.000 5.23 9.73 32.94 4.85
185 186 0.613012 GGCAGTTGGAATTCTGGGCT 60.613 55.000 5.23 0.00 32.94 5.19
186 187 1.893062 GGCAGTTGGAATTCTGGGC 59.107 57.895 5.23 2.91 32.94 5.36
187 188 1.315257 CCGGCAGTTGGAATTCTGGG 61.315 60.000 5.23 0.00 32.94 4.45
188 189 1.937546 GCCGGCAGTTGGAATTCTGG 61.938 60.000 24.80 0.00 32.94 3.86
189 190 1.243342 TGCCGGCAGTTGGAATTCTG 61.243 55.000 29.03 0.00 35.12 3.02
190 191 0.323725 ATGCCGGCAGTTGGAATTCT 60.324 50.000 35.36 11.04 0.00 2.40
191 192 0.532115 AATGCCGGCAGTTGGAATTC 59.468 50.000 35.36 0.00 27.68 2.17
192 193 0.532115 GAATGCCGGCAGTTGGAATT 59.468 50.000 35.36 21.97 37.45 2.17
193 194 0.323725 AGAATGCCGGCAGTTGGAAT 60.324 50.000 35.36 13.63 0.00 3.01
194 195 0.960364 GAGAATGCCGGCAGTTGGAA 60.960 55.000 35.36 9.43 0.00 3.53
195 196 1.377202 GAGAATGCCGGCAGTTGGA 60.377 57.895 35.36 10.32 0.00 3.53
196 197 2.409870 GGAGAATGCCGGCAGTTGG 61.410 63.158 35.36 0.00 0.00 3.77
197 198 2.409870 GGGAGAATGCCGGCAGTTG 61.410 63.158 35.36 0.00 36.28 3.16
198 199 2.044946 GGGAGAATGCCGGCAGTT 60.045 61.111 35.36 26.44 36.28 3.16
206 207 4.822350 GGTTTACATAAGGAGGGAGAATGC 59.178 45.833 0.00 0.00 0.00 3.56
207 208 6.253946 AGGTTTACATAAGGAGGGAGAATG 57.746 41.667 0.00 0.00 0.00 2.67
208 209 6.217693 ACAAGGTTTACATAAGGAGGGAGAAT 59.782 38.462 0.00 0.00 0.00 2.40
209 210 5.550403 ACAAGGTTTACATAAGGAGGGAGAA 59.450 40.000 0.00 0.00 0.00 2.87
210 211 5.098663 ACAAGGTTTACATAAGGAGGGAGA 58.901 41.667 0.00 0.00 0.00 3.71
211 212 5.437191 ACAAGGTTTACATAAGGAGGGAG 57.563 43.478 0.00 0.00 0.00 4.30
212 213 6.956102 TTACAAGGTTTACATAAGGAGGGA 57.044 37.500 0.00 0.00 0.00 4.20
213 214 8.589701 ATTTTACAAGGTTTACATAAGGAGGG 57.410 34.615 0.00 0.00 0.00 4.30
226 227 9.397280 GCCTATTCTCTCTTATTTTACAAGGTT 57.603 33.333 0.00 0.00 0.00 3.50
227 228 8.548877 TGCCTATTCTCTCTTATTTTACAAGGT 58.451 33.333 0.00 0.00 0.00 3.50
228 229 8.964476 TGCCTATTCTCTCTTATTTTACAAGG 57.036 34.615 0.00 0.00 0.00 3.61
249 250 9.453572 CCACATTATGTCATAATACTTATGCCT 57.546 33.333 16.07 0.00 42.12 4.75
250 251 9.448438 TCCACATTATGTCATAATACTTATGCC 57.552 33.333 16.07 0.00 42.12 4.40
260 261 9.461312 GGGCTATTATTCCACATTATGTCATAA 57.539 33.333 7.72 7.72 0.00 1.90
261 262 8.610369 TGGGCTATTATTCCACATTATGTCATA 58.390 33.333 0.00 0.00 0.00 2.15
262 263 7.469343 TGGGCTATTATTCCACATTATGTCAT 58.531 34.615 0.00 0.00 0.00 3.06
263 264 6.846988 TGGGCTATTATTCCACATTATGTCA 58.153 36.000 0.00 0.00 0.00 3.58
264 265 7.759489 TTGGGCTATTATTCCACATTATGTC 57.241 36.000 0.00 0.00 0.00 3.06
265 266 8.546083 TTTTGGGCTATTATTCCACATTATGT 57.454 30.769 0.00 0.00 0.00 2.29
266 267 9.426837 CATTTTGGGCTATTATTCCACATTATG 57.573 33.333 0.00 0.00 0.00 1.90
267 268 8.096414 GCATTTTGGGCTATTATTCCACATTAT 58.904 33.333 0.00 0.00 0.00 1.28
268 269 7.070447 TGCATTTTGGGCTATTATTCCACATTA 59.930 33.333 0.00 0.00 0.00 1.90
269 270 6.126825 TGCATTTTGGGCTATTATTCCACATT 60.127 34.615 0.00 0.00 0.00 2.71
270 271 5.366186 TGCATTTTGGGCTATTATTCCACAT 59.634 36.000 0.00 0.00 0.00 3.21
271 272 4.713814 TGCATTTTGGGCTATTATTCCACA 59.286 37.500 0.00 0.00 0.00 4.17
272 273 5.275067 TGCATTTTGGGCTATTATTCCAC 57.725 39.130 0.00 0.00 0.00 4.02
273 274 5.946942 TTGCATTTTGGGCTATTATTCCA 57.053 34.783 0.00 0.00 0.00 3.53
274 275 8.900983 TTTATTGCATTTTGGGCTATTATTCC 57.099 30.769 0.00 0.00 0.00 3.01
310 311 9.325198 TGATACGTCTATTTTGCATCATACTTT 57.675 29.630 0.00 0.00 0.00 2.66
311 312 8.887036 TGATACGTCTATTTTGCATCATACTT 57.113 30.769 0.00 0.00 0.00 2.24
312 313 8.144478 ACTGATACGTCTATTTTGCATCATACT 58.856 33.333 0.00 0.00 0.00 2.12
313 314 8.217115 CACTGATACGTCTATTTTGCATCATAC 58.783 37.037 0.00 0.00 0.00 2.39
314 315 7.095649 GCACTGATACGTCTATTTTGCATCATA 60.096 37.037 0.00 0.00 0.00 2.15
315 316 6.293081 GCACTGATACGTCTATTTTGCATCAT 60.293 38.462 0.00 0.00 0.00 2.45
316 317 5.006649 GCACTGATACGTCTATTTTGCATCA 59.993 40.000 0.00 0.00 0.00 3.07
317 318 5.435557 GCACTGATACGTCTATTTTGCATC 58.564 41.667 0.00 0.00 0.00 3.91
318 319 4.025730 CGCACTGATACGTCTATTTTGCAT 60.026 41.667 0.00 0.00 0.00 3.96
319 320 3.305897 CGCACTGATACGTCTATTTTGCA 59.694 43.478 0.00 0.00 0.00 4.08
320 321 3.302480 CCGCACTGATACGTCTATTTTGC 60.302 47.826 0.00 0.00 0.00 3.68
321 322 3.863424 ACCGCACTGATACGTCTATTTTG 59.137 43.478 0.00 0.00 0.00 2.44
322 323 4.119442 ACCGCACTGATACGTCTATTTT 57.881 40.909 0.00 0.00 0.00 1.82
323 324 3.795623 ACCGCACTGATACGTCTATTT 57.204 42.857 0.00 0.00 0.00 1.40
324 325 3.444916 CAACCGCACTGATACGTCTATT 58.555 45.455 0.00 0.00 0.00 1.73
325 326 2.798499 GCAACCGCACTGATACGTCTAT 60.798 50.000 0.00 0.00 38.36 1.98
326 327 1.468565 GCAACCGCACTGATACGTCTA 60.469 52.381 0.00 0.00 38.36 2.59
327 328 0.736325 GCAACCGCACTGATACGTCT 60.736 55.000 0.00 0.00 38.36 4.18
328 329 1.011968 TGCAACCGCACTGATACGTC 61.012 55.000 0.00 0.00 45.36 4.34
329 330 1.005512 TGCAACCGCACTGATACGT 60.006 52.632 0.00 0.00 45.36 3.57
330 331 3.869187 TGCAACCGCACTGATACG 58.131 55.556 0.00 0.00 45.36 3.06
365 366 0.673437 CGCCCATGTCAACCTTGTTT 59.327 50.000 0.00 0.00 0.00 2.83
388 389 5.254032 AGGTATCAAGGAAAGGATTGAACCT 59.746 40.000 12.15 12.15 39.45 3.50
409 410 2.848678 TACTCAGGCCACTATGAGGT 57.151 50.000 20.43 10.73 45.86 3.85
415 416 1.837439 CCCAACATACTCAGGCCACTA 59.163 52.381 5.01 0.00 0.00 2.74
534 535 4.463891 CCACTACCAAATTGCTTCATTCCT 59.536 41.667 0.00 0.00 0.00 3.36
610 611 2.139917 GCATGTCCTAACGTTGTGTCA 58.860 47.619 11.99 6.19 0.00 3.58
738 739 0.683504 GGCTAGTCCTTCCTCCACGA 60.684 60.000 0.00 0.00 0.00 4.35
877 879 9.211410 ACCATTCATATTATTTCAACCATCCAA 57.789 29.630 0.00 0.00 0.00 3.53
878 880 8.780616 ACCATTCATATTATTTCAACCATCCA 57.219 30.769 0.00 0.00 0.00 3.41
976 978 8.559536 CATGCCTACAACGAATAAAGATGTTAT 58.440 33.333 0.00 0.00 0.00 1.89
990 992 1.382522 ATGAAGCCATGCCTACAACG 58.617 50.000 0.00 0.00 0.00 4.10
1010 1015 2.815211 GCCTCGTCATGCAAGCGA 60.815 61.111 9.59 9.59 0.00 4.93
1013 1018 2.401766 GGTGGCCTCGTCATGCAAG 61.402 63.158 3.32 0.00 0.00 4.01
1016 1021 2.124570 ATGGTGGCCTCGTCATGC 60.125 61.111 3.32 0.00 0.00 4.06
1095 1100 2.749076 TGGCGGAATCTTCACATCTTTG 59.251 45.455 0.00 0.00 0.00 2.77
1177 1182 6.101997 GGCAAACAAAATATCTCCTTCCTTG 58.898 40.000 0.00 0.00 0.00 3.61
1325 1330 3.039252 AGTACTTGCATAGAGGAGGCT 57.961 47.619 0.00 0.00 35.30 4.58
1418 1423 5.659440 TTGAAACCTTTCTTTGAACAGCT 57.341 34.783 0.00 0.00 38.02 4.24
1426 1431 5.395657 CCAAGCCTCTTTGAAACCTTTCTTT 60.396 40.000 0.00 0.00 38.02 2.52
1460 1465 3.636300 CTCCATCCTCTCTTTCTGACGAT 59.364 47.826 0.00 0.00 0.00 3.73
1531 1536 0.987294 TTTCTTGCCCTCTCCTCCTG 59.013 55.000 0.00 0.00 0.00 3.86
1565 1570 1.004044 CATCCTCCTCTTGTGCCTTGT 59.996 52.381 0.00 0.00 0.00 3.16
1722 1728 6.421501 GCAAATTCATTCATGACAAGTTCACA 59.578 34.615 0.00 0.00 36.92 3.58
1734 1740 9.451002 TTCAATACAAATGGCAAATTCATTCAT 57.549 25.926 0.00 0.00 34.15 2.57
1837 1856 3.556775 CCCAGCACAACAGTTTTTCAATG 59.443 43.478 0.00 0.00 0.00 2.82
1890 1920 6.184789 AGGGTTGTGAACTCTAAAAACAGAA 58.815 36.000 0.00 0.00 41.41 3.02
1954 2092 0.752658 CTATCGCCATGTGGTCTGGA 59.247 55.000 0.35 0.00 35.70 3.86
2066 2206 1.538204 CGCTATGTTGTCTGGCGGTAT 60.538 52.381 0.00 0.00 41.77 2.73
2079 2219 0.616679 ACACCACCCTACCGCTATGT 60.617 55.000 0.00 0.00 0.00 2.29
2083 2223 2.158355 AGATATACACCACCCTACCGCT 60.158 50.000 0.00 0.00 0.00 5.52
2108 2250 0.739813 GCGCTAGTGTTTCCCGTCAT 60.740 55.000 0.00 0.00 0.00 3.06
2194 2342 7.916128 ATATCTTCTGTGATAAGAAACGACG 57.084 36.000 0.00 0.00 36.60 5.12
2196 2344 9.731819 GTGTATATCTTCTGTGATAAGAAACGA 57.268 33.333 0.00 0.00 36.60 3.85
2204 2352 5.977533 AGGGGGTGTATATCTTCTGTGATA 58.022 41.667 0.00 0.00 33.99 2.15
2205 2353 4.832492 AGGGGGTGTATATCTTCTGTGAT 58.168 43.478 0.00 0.00 0.00 3.06
2223 2372 3.945304 GACAACGTGGCGGTAGGGG 62.945 68.421 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.