Multiple sequence alignment - TraesCS1A01G206800

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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 TraesCS1A01G206800 chr1A 100.000 2426 0 0 1 2426 368833324 368830899 0.000000e+00 4481.0
1 TraesCS1A01G206800 chr1A 92.925 212 13 2 36 246 286461359 286461149 8.430000e-80 307.0
2 TraesCS1A01G206800 chr1A 95.000 40 0 2 6 44 9091375 9091413 7.240000e-06 62.1
3 TraesCS1A01G206800 chr1D 91.320 1993 83 34 513 2426 295974476 295972495 0.000000e+00 2639.0
4 TraesCS1A01G206800 chr1D 93.878 49 3 0 2 50 295975086 295975038 9.300000e-10 75.0
5 TraesCS1A01G206800 chr1D 97.059 34 1 0 410 443 295974503 295974470 9.370000e-05 58.4
6 TraesCS1A01G206800 chr1B 92.374 813 23 9 855 1634 397456817 397456011 0.000000e+00 1122.0
7 TraesCS1A01G206800 chr1B 91.882 813 49 10 1626 2426 397453655 397452848 0.000000e+00 1120.0
8 TraesCS1A01G206800 chr1B 91.756 279 16 2 1009 1287 626422252 626421981 4.890000e-102 381.0
9 TraesCS1A01G206800 chr1B 95.000 200 9 1 48 246 534113542 534113741 1.810000e-81 313.0
10 TraesCS1A01G206800 chr1B 90.204 245 13 8 1 245 671743656 671743423 2.340000e-80 309.0
11 TraesCS1A01G206800 chr6B 94.286 210 10 2 39 246 132706035 132705826 1.080000e-83 320.0
12 TraesCS1A01G206800 chr6B 94.686 207 10 1 41 246 321415733 321415527 1.080000e-83 320.0
13 TraesCS1A01G206800 chr3B 95.025 201 10 0 46 246 699229656 699229456 1.400000e-82 316.0
14 TraesCS1A01G206800 chr3A 93.868 212 10 3 36 246 717202571 717202362 1.400000e-82 316.0
15 TraesCS1A01G206800 chr7B 95.025 201 9 1 46 246 456510852 456510653 5.040000e-82 315.0
16 TraesCS1A01G206800 chr7B 93.333 60 4 0 1009 1068 643391473 643391414 3.320000e-14 89.8
17 TraesCS1A01G206800 chr4B 93.301 209 12 2 38 246 426640111 426640317 8.430000e-80 307.0
18 TraesCS1A01G206800 chr4B 95.349 43 0 2 6 47 159627315 159627274 1.560000e-07 67.6
19 TraesCS1A01G206800 chr7A 95.349 43 0 2 6 47 68233052 68233093 1.560000e-07 67.6
20 TraesCS1A01G206800 chr4D 93.333 45 3 0 6 50 315568767 315568811 1.560000e-07 67.6
21 TraesCS1A01G206800 chr4D 93.023 43 1 2 6 47 170223912 170223953 7.240000e-06 62.1
22 TraesCS1A01G206800 chr4A 93.478 46 1 2 6 50 425994444 425994400 1.560000e-07 67.6
23 TraesCS1A01G206800 chr2B 95.349 43 0 2 6 47 200644632 200644673 1.560000e-07 67.6


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 TraesCS1A01G206800 chr1A 368830899 368833324 2425 True 4481.000000 4481 100.000000 1 2426 1 chr1A.!!$R2 2425
1 TraesCS1A01G206800 chr1D 295972495 295975086 2591 True 924.133333 2639 94.085667 2 2426 3 chr1D.!!$R1 2424
2 TraesCS1A01G206800 chr1B 397452848 397456817 3969 True 1121.000000 1122 92.128000 855 2426 2 chr1B.!!$R3 1571

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
756 1195 0.313987 AAAAGTGCGGCTACAAAGGC 59.686 50.0 0.0 0.0 44.69 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2213 5085 0.609662 CCAGGGTTGCAATCAAAGGG 59.39 55.0 12.67 2.98 33.37 3.95 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
58 59 8.904099 AAATGAATAAAGTAATACTCCCTCCG 57.096 34.615 0.00 0.00 0.00 4.63
59 60 7.613551 ATGAATAAAGTAATACTCCCTCCGT 57.386 36.000 0.00 0.00 0.00 4.69
60 61 7.427989 TGAATAAAGTAATACTCCCTCCGTT 57.572 36.000 0.00 0.00 0.00 4.44
61 62 7.495055 TGAATAAAGTAATACTCCCTCCGTTC 58.505 38.462 0.00 0.00 0.00 3.95
62 63 4.750021 AAAGTAATACTCCCTCCGTTCC 57.250 45.455 0.00 0.00 0.00 3.62
63 64 3.684408 AGTAATACTCCCTCCGTTCCT 57.316 47.619 0.00 0.00 0.00 3.36
64 65 3.991683 AGTAATACTCCCTCCGTTCCTT 58.008 45.455 0.00 0.00 0.00 3.36
65 66 3.705072 AGTAATACTCCCTCCGTTCCTTG 59.295 47.826 0.00 0.00 0.00 3.61
66 67 2.544844 ATACTCCCTCCGTTCCTTGA 57.455 50.000 0.00 0.00 0.00 3.02
67 68 2.544844 TACTCCCTCCGTTCCTTGAT 57.455 50.000 0.00 0.00 0.00 2.57
68 69 2.544844 ACTCCCTCCGTTCCTTGATA 57.455 50.000 0.00 0.00 0.00 2.15
69 70 3.047695 ACTCCCTCCGTTCCTTGATAT 57.952 47.619 0.00 0.00 0.00 1.63
70 71 4.194678 ACTCCCTCCGTTCCTTGATATA 57.805 45.455 0.00 0.00 0.00 0.86
71 72 4.553678 ACTCCCTCCGTTCCTTGATATAA 58.446 43.478 0.00 0.00 0.00 0.98
72 73 4.589374 ACTCCCTCCGTTCCTTGATATAAG 59.411 45.833 0.00 0.00 0.00 1.73
73 74 3.901844 TCCCTCCGTTCCTTGATATAAGG 59.098 47.826 0.00 0.00 38.78 2.69
74 75 3.646637 CCCTCCGTTCCTTGATATAAGGT 59.353 47.826 5.67 0.00 38.55 3.50
75 76 4.836736 CCCTCCGTTCCTTGATATAAGGTA 59.163 45.833 5.67 0.00 38.55 3.08
76 77 5.484290 CCCTCCGTTCCTTGATATAAGGTAT 59.516 44.000 5.67 0.00 38.55 2.73
77 78 6.666546 CCCTCCGTTCCTTGATATAAGGTATA 59.333 42.308 5.67 0.00 38.55 1.47
78 79 7.344871 CCCTCCGTTCCTTGATATAAGGTATAT 59.655 40.741 5.67 0.00 38.55 0.86
79 80 9.417561 CCTCCGTTCCTTGATATAAGGTATATA 57.582 37.037 5.67 0.00 38.55 0.86
118 119 9.744468 AAAAATCCGAAATATAAGGTGTATTGC 57.256 29.630 0.00 0.00 0.00 3.56
119 120 6.721571 ATCCGAAATATAAGGTGTATTGCG 57.278 37.500 0.00 0.00 39.29 4.85
120 121 5.603596 TCCGAAATATAAGGTGTATTGCGT 58.396 37.500 5.76 0.00 38.38 5.24
121 122 6.050432 TCCGAAATATAAGGTGTATTGCGTT 58.950 36.000 5.76 0.00 38.38 4.84
122 123 6.018588 TCCGAAATATAAGGTGTATTGCGTTG 60.019 38.462 5.76 0.00 38.38 4.10
123 124 6.238266 CCGAAATATAAGGTGTATTGCGTTGT 60.238 38.462 5.76 0.00 38.38 3.32
124 125 7.042590 CCGAAATATAAGGTGTATTGCGTTGTA 60.043 37.037 5.76 0.00 38.38 2.41
125 126 7.790673 CGAAATATAAGGTGTATTGCGTTGTAC 59.209 37.037 0.00 0.00 36.36 2.90
126 127 7.486802 AATATAAGGTGTATTGCGTTGTACC 57.513 36.000 0.00 0.00 0.00 3.34
127 128 2.843401 AGGTGTATTGCGTTGTACCA 57.157 45.000 0.00 0.00 0.00 3.25
128 129 2.419667 AGGTGTATTGCGTTGTACCAC 58.580 47.619 0.00 0.00 0.00 4.16
129 130 2.038033 AGGTGTATTGCGTTGTACCACT 59.962 45.455 0.00 0.00 0.00 4.00
130 131 2.414138 GGTGTATTGCGTTGTACCACTC 59.586 50.000 0.00 0.00 0.00 3.51
131 132 2.091588 GTGTATTGCGTTGTACCACTCG 59.908 50.000 0.00 0.00 0.00 4.18
132 133 2.288334 TGTATTGCGTTGTACCACTCGT 60.288 45.455 0.00 0.00 0.00 4.18
133 134 1.425412 ATTGCGTTGTACCACTCGTC 58.575 50.000 0.00 0.00 0.00 4.20
134 135 0.386476 TTGCGTTGTACCACTCGTCT 59.614 50.000 0.00 0.00 0.00 4.18
135 136 0.318360 TGCGTTGTACCACTCGTCTG 60.318 55.000 0.00 0.00 0.00 3.51
136 137 1.007336 GCGTTGTACCACTCGTCTGG 61.007 60.000 0.00 0.22 37.33 3.86
137 138 0.594602 CGTTGTACCACTCGTCTGGA 59.405 55.000 7.95 0.00 35.04 3.86
138 139 1.201647 CGTTGTACCACTCGTCTGGAT 59.798 52.381 7.95 0.00 35.04 3.41
139 140 2.421073 CGTTGTACCACTCGTCTGGATA 59.579 50.000 7.95 0.00 35.04 2.59
140 141 3.119743 CGTTGTACCACTCGTCTGGATAA 60.120 47.826 7.95 0.00 35.04 1.75
141 142 4.439700 CGTTGTACCACTCGTCTGGATAAT 60.440 45.833 7.95 0.00 35.04 1.28
142 143 4.649088 TGTACCACTCGTCTGGATAATG 57.351 45.455 7.95 0.00 35.04 1.90
143 144 4.021229 TGTACCACTCGTCTGGATAATGT 58.979 43.478 7.95 0.00 35.04 2.71
144 145 4.464951 TGTACCACTCGTCTGGATAATGTT 59.535 41.667 7.95 0.00 35.04 2.71
145 146 4.553330 ACCACTCGTCTGGATAATGTTT 57.447 40.909 7.95 0.00 35.04 2.83
146 147 4.906618 ACCACTCGTCTGGATAATGTTTT 58.093 39.130 7.95 0.00 35.04 2.43
147 148 5.313712 ACCACTCGTCTGGATAATGTTTTT 58.686 37.500 7.95 0.00 35.04 1.94
148 149 6.469410 ACCACTCGTCTGGATAATGTTTTTA 58.531 36.000 7.95 0.00 35.04 1.52
149 150 6.594159 ACCACTCGTCTGGATAATGTTTTTAG 59.406 38.462 7.95 0.00 35.04 1.85
150 151 6.037172 CCACTCGTCTGGATAATGTTTTTAGG 59.963 42.308 0.00 0.00 32.30 2.69
151 152 6.037172 CACTCGTCTGGATAATGTTTTTAGGG 59.963 42.308 0.00 0.00 0.00 3.53
152 153 6.070424 ACTCGTCTGGATAATGTTTTTAGGGA 60.070 38.462 0.00 0.00 0.00 4.20
153 154 6.713276 TCGTCTGGATAATGTTTTTAGGGAA 58.287 36.000 0.00 0.00 0.00 3.97
154 155 7.343357 TCGTCTGGATAATGTTTTTAGGGAAT 58.657 34.615 0.00 0.00 0.00 3.01
155 156 7.832187 TCGTCTGGATAATGTTTTTAGGGAATT 59.168 33.333 0.00 0.00 0.00 2.17
156 157 7.915397 CGTCTGGATAATGTTTTTAGGGAATTG 59.085 37.037 0.00 0.00 0.00 2.32
157 158 8.966868 GTCTGGATAATGTTTTTAGGGAATTGA 58.033 33.333 0.00 0.00 0.00 2.57
158 159 9.713684 TCTGGATAATGTTTTTAGGGAATTGAT 57.286 29.630 0.00 0.00 0.00 2.57
167 168 9.936759 TGTTTTTAGGGAATTGATTACATTTCC 57.063 29.630 12.52 12.52 46.84 3.13
183 184 9.813826 ATTACATTTCCTTATATTAGGCAAGCT 57.186 29.630 2.71 0.00 35.15 3.74
184 185 7.751768 ACATTTCCTTATATTAGGCAAGCTC 57.248 36.000 2.71 0.00 35.15 4.09
185 186 6.717084 ACATTTCCTTATATTAGGCAAGCTCC 59.283 38.462 2.71 0.00 35.15 4.70
186 187 6.515512 TTTCCTTATATTAGGCAAGCTCCT 57.484 37.500 2.71 0.00 40.21 3.69
187 188 5.746990 TCCTTATATTAGGCAAGCTCCTC 57.253 43.478 2.71 0.00 37.66 3.71
188 189 5.407049 TCCTTATATTAGGCAAGCTCCTCT 58.593 41.667 2.71 0.00 37.66 3.69
189 190 6.562228 TCCTTATATTAGGCAAGCTCCTCTA 58.438 40.000 2.71 0.00 37.66 2.43
190 191 7.192628 TCCTTATATTAGGCAAGCTCCTCTAT 58.807 38.462 2.71 0.59 37.66 1.98
191 192 7.680310 TCCTTATATTAGGCAAGCTCCTCTATT 59.320 37.037 2.71 0.00 37.66 1.73
192 193 8.325046 CCTTATATTAGGCAAGCTCCTCTATTT 58.675 37.037 0.00 0.00 37.66 1.40
193 194 9.732130 CTTATATTAGGCAAGCTCCTCTATTTT 57.268 33.333 0.00 0.00 37.66 1.82
194 195 7.992754 ATATTAGGCAAGCTCCTCTATTTTG 57.007 36.000 0.00 0.00 37.66 2.44
195 196 3.728385 AGGCAAGCTCCTCTATTTTGT 57.272 42.857 0.00 0.00 0.00 2.83
196 197 3.615155 AGGCAAGCTCCTCTATTTTGTC 58.385 45.455 0.00 0.00 0.00 3.18
197 198 3.009473 AGGCAAGCTCCTCTATTTTGTCA 59.991 43.478 0.00 0.00 0.00 3.58
198 199 3.950395 GGCAAGCTCCTCTATTTTGTCAT 59.050 43.478 0.00 0.00 0.00 3.06
199 200 4.201990 GGCAAGCTCCTCTATTTTGTCATG 60.202 45.833 0.00 0.00 0.00 3.07
200 201 4.397417 GCAAGCTCCTCTATTTTGTCATGT 59.603 41.667 0.00 0.00 0.00 3.21
201 202 5.448360 GCAAGCTCCTCTATTTTGTCATGTC 60.448 44.000 0.00 0.00 0.00 3.06
202 203 5.426689 AGCTCCTCTATTTTGTCATGTCA 57.573 39.130 0.00 0.00 0.00 3.58
203 204 5.809001 AGCTCCTCTATTTTGTCATGTCAA 58.191 37.500 0.98 0.98 0.00 3.18
204 205 6.421485 AGCTCCTCTATTTTGTCATGTCAAT 58.579 36.000 6.21 0.00 0.00 2.57
205 206 6.888632 AGCTCCTCTATTTTGTCATGTCAATT 59.111 34.615 6.21 0.97 0.00 2.32
206 207 8.049117 AGCTCCTCTATTTTGTCATGTCAATTA 58.951 33.333 6.21 2.00 0.00 1.40
207 208 8.341173 GCTCCTCTATTTTGTCATGTCAATTAG 58.659 37.037 6.21 10.28 0.00 1.73
208 209 9.388506 CTCCTCTATTTTGTCATGTCAATTAGT 57.611 33.333 6.21 0.00 0.00 2.24
209 210 9.739276 TCCTCTATTTTGTCATGTCAATTAGTT 57.261 29.630 6.21 0.00 0.00 2.24
215 216 8.458573 TTTTGTCATGTCAATTAGTTAGGTGT 57.541 30.769 6.21 0.00 0.00 4.16
216 217 9.562408 TTTTGTCATGTCAATTAGTTAGGTGTA 57.438 29.630 6.21 0.00 0.00 2.90
217 218 9.562408 TTTGTCATGTCAATTAGTTAGGTGTAA 57.438 29.630 6.21 0.00 0.00 2.41
218 219 9.733556 TTGTCATGTCAATTAGTTAGGTGTAAT 57.266 29.630 0.98 0.00 0.00 1.89
219 220 9.378551 TGTCATGTCAATTAGTTAGGTGTAATC 57.621 33.333 0.00 0.00 0.00 1.75
220 221 9.601217 GTCATGTCAATTAGTTAGGTGTAATCT 57.399 33.333 0.00 0.00 0.00 2.40
221 222 9.817809 TCATGTCAATTAGTTAGGTGTAATCTC 57.182 33.333 0.00 0.00 0.00 2.75
222 223 8.755941 CATGTCAATTAGTTAGGTGTAATCTCG 58.244 37.037 0.00 0.00 0.00 4.04
223 224 6.755141 TGTCAATTAGTTAGGTGTAATCTCGC 59.245 38.462 0.00 0.00 0.00 5.03
224 225 6.200475 GTCAATTAGTTAGGTGTAATCTCGCC 59.800 42.308 0.00 0.00 38.17 5.54
225 226 4.660789 TTAGTTAGGTGTAATCTCGCCC 57.339 45.455 0.00 0.00 38.61 6.13
226 227 2.463752 AGTTAGGTGTAATCTCGCCCA 58.536 47.619 0.00 0.00 38.61 5.36
227 228 2.835764 AGTTAGGTGTAATCTCGCCCAA 59.164 45.455 0.00 0.00 38.61 4.12
228 229 3.262405 AGTTAGGTGTAATCTCGCCCAAA 59.738 43.478 0.00 0.00 38.61 3.28
229 230 2.871096 AGGTGTAATCTCGCCCAAAA 57.129 45.000 0.00 0.00 38.61 2.44
230 231 2.433436 AGGTGTAATCTCGCCCAAAAC 58.567 47.619 0.00 0.00 38.61 2.43
231 232 2.039879 AGGTGTAATCTCGCCCAAAACT 59.960 45.455 0.00 0.00 38.61 2.66
232 233 2.817844 GGTGTAATCTCGCCCAAAACTT 59.182 45.455 0.00 0.00 32.43 2.66
233 234 4.004982 GGTGTAATCTCGCCCAAAACTTA 58.995 43.478 0.00 0.00 32.43 2.24
234 235 4.638865 GGTGTAATCTCGCCCAAAACTTAT 59.361 41.667 0.00 0.00 32.43 1.73
235 236 5.448632 GGTGTAATCTCGCCCAAAACTTATG 60.449 44.000 0.00 0.00 32.43 1.90
236 237 5.353123 GTGTAATCTCGCCCAAAACTTATGA 59.647 40.000 0.00 0.00 0.00 2.15
237 238 5.941058 TGTAATCTCGCCCAAAACTTATGAA 59.059 36.000 0.00 0.00 0.00 2.57
238 239 5.975693 AATCTCGCCCAAAACTTATGAAA 57.024 34.783 0.00 0.00 0.00 2.69
239 240 6.530019 AATCTCGCCCAAAACTTATGAAAT 57.470 33.333 0.00 0.00 0.00 2.17
240 241 5.975693 TCTCGCCCAAAACTTATGAAATT 57.024 34.783 0.00 0.00 0.00 1.82
241 242 6.339587 TCTCGCCCAAAACTTATGAAATTT 57.660 33.333 0.00 0.00 0.00 1.82
242 243 6.754193 TCTCGCCCAAAACTTATGAAATTTT 58.246 32.000 0.00 0.00 0.00 1.82
243 244 6.866248 TCTCGCCCAAAACTTATGAAATTTTC 59.134 34.615 2.05 2.05 0.00 2.29
244 245 5.929415 TCGCCCAAAACTTATGAAATTTTCC 59.071 36.000 6.68 0.00 0.00 3.13
245 246 5.121611 CGCCCAAAACTTATGAAATTTTCCC 59.878 40.000 6.68 0.00 0.00 3.97
246 247 6.000840 GCCCAAAACTTATGAAATTTTCCCA 58.999 36.000 6.68 0.00 0.00 4.37
247 248 6.488344 GCCCAAAACTTATGAAATTTTCCCAA 59.512 34.615 6.68 0.57 0.00 4.12
248 249 7.013750 GCCCAAAACTTATGAAATTTTCCCAAA 59.986 33.333 6.68 0.00 0.00 3.28
249 250 8.907885 CCCAAAACTTATGAAATTTTCCCAAAA 58.092 29.630 6.68 0.00 34.41 2.44
259 260 9.719355 ATGAAATTTTCCCAAAAACTATACACC 57.281 29.630 6.68 0.00 37.20 4.16
260 261 8.151596 TGAAATTTTCCCAAAAACTATACACCC 58.848 33.333 6.68 0.00 37.20 4.61
261 262 7.865530 AATTTTCCCAAAAACTATACACCCT 57.134 32.000 0.00 0.00 37.20 4.34
262 263 7.865530 ATTTTCCCAAAAACTATACACCCTT 57.134 32.000 0.00 0.00 37.20 3.95
263 264 7.678207 TTTTCCCAAAAACTATACACCCTTT 57.322 32.000 0.00 0.00 29.44 3.11
264 265 8.779096 TTTTCCCAAAAACTATACACCCTTTA 57.221 30.769 0.00 0.00 29.44 1.85
265 266 8.959676 TTTCCCAAAAACTATACACCCTTTAT 57.040 30.769 0.00 0.00 0.00 1.40
266 267 8.959676 TTCCCAAAAACTATACACCCTTTATT 57.040 30.769 0.00 0.00 0.00 1.40
295 296 9.193806 GGAACGGAGGAAGTATATATTACCATA 57.806 37.037 0.00 0.00 0.00 2.74
317 385 8.388589 CCATATGATAGTACGGAGGGGTATATA 58.611 40.741 3.65 0.00 0.00 0.86
326 394 5.338632 ACGGAGGGGTATATATGACATGAA 58.661 41.667 0.00 0.00 0.00 2.57
328 396 5.163405 CGGAGGGGTATATATGACATGAAGG 60.163 48.000 0.00 0.00 0.00 3.46
340 409 2.486592 GACATGAAGGTAAAACCACCGG 59.513 50.000 0.00 0.00 43.84 5.28
368 437 7.124599 TGGTAGGATATGTTTTCCTCGTTAGAA 59.875 37.037 0.00 0.00 42.69 2.10
379 448 9.434559 GTTTTCCTCGTTAGAAAATATGTATGC 57.565 33.333 11.22 0.00 43.14 3.14
380 449 7.724305 TTCCTCGTTAGAAAATATGTATGCC 57.276 36.000 0.00 0.00 0.00 4.40
381 450 7.062749 TCCTCGTTAGAAAATATGTATGCCT 57.937 36.000 0.00 0.00 0.00 4.75
382 451 7.506114 TCCTCGTTAGAAAATATGTATGCCTT 58.494 34.615 0.00 0.00 0.00 4.35
383 452 7.990886 TCCTCGTTAGAAAATATGTATGCCTTT 59.009 33.333 0.00 0.00 0.00 3.11
384 453 8.621286 CCTCGTTAGAAAATATGTATGCCTTTT 58.379 33.333 0.00 0.00 0.00 2.27
385 454 9.651718 CTCGTTAGAAAATATGTATGCCTTTTC 57.348 33.333 0.00 0.00 37.69 2.29
386 455 8.332464 TCGTTAGAAAATATGTATGCCTTTTCG 58.668 33.333 0.00 0.00 40.69 3.46
387 456 7.586300 CGTTAGAAAATATGTATGCCTTTTCGG 59.414 37.037 0.00 0.00 40.69 4.30
388 457 8.617809 GTTAGAAAATATGTATGCCTTTTCGGA 58.382 33.333 0.00 0.00 40.69 4.55
389 458 7.639113 AGAAAATATGTATGCCTTTTCGGAA 57.361 32.000 0.00 0.00 40.69 4.30
390 459 8.062065 AGAAAATATGTATGCCTTTTCGGAAA 57.938 30.769 0.00 0.00 40.69 3.13
391 460 8.527810 AGAAAATATGTATGCCTTTTCGGAAAA 58.472 29.630 14.64 14.64 40.69 2.29
392 461 9.145865 GAAAATATGTATGCCTTTTCGGAAAAA 57.854 29.630 15.99 3.30 30.60 1.94
455 865 4.452890 CGTTATGCGTTATGAAAGAGGG 57.547 45.455 0.00 0.00 35.54 4.30
456 866 4.116961 CGTTATGCGTTATGAAAGAGGGA 58.883 43.478 0.00 0.00 35.54 4.20
457 867 4.209288 CGTTATGCGTTATGAAAGAGGGAG 59.791 45.833 0.00 0.00 35.54 4.30
458 868 5.357257 GTTATGCGTTATGAAAGAGGGAGA 58.643 41.667 0.00 0.00 0.00 3.71
459 869 3.526931 TGCGTTATGAAAGAGGGAGAG 57.473 47.619 0.00 0.00 0.00 3.20
460 870 2.832129 TGCGTTATGAAAGAGGGAGAGT 59.168 45.455 0.00 0.00 0.00 3.24
461 871 3.190874 GCGTTATGAAAGAGGGAGAGTG 58.809 50.000 0.00 0.00 0.00 3.51
462 872 3.190874 CGTTATGAAAGAGGGAGAGTGC 58.809 50.000 0.00 0.00 0.00 4.40
463 873 3.368427 CGTTATGAAAGAGGGAGAGTGCA 60.368 47.826 0.00 0.00 0.00 4.57
464 874 4.187694 GTTATGAAAGAGGGAGAGTGCAG 58.812 47.826 0.00 0.00 0.00 4.41
465 875 2.015456 TGAAAGAGGGAGAGTGCAGA 57.985 50.000 0.00 0.00 0.00 4.26
466 876 1.620819 TGAAAGAGGGAGAGTGCAGAC 59.379 52.381 0.00 0.00 0.00 3.51
467 877 1.899142 GAAAGAGGGAGAGTGCAGACT 59.101 52.381 0.00 0.00 33.98 3.24
468 878 2.022718 AAGAGGGAGAGTGCAGACTT 57.977 50.000 0.00 0.00 30.16 3.01
469 879 2.022718 AGAGGGAGAGTGCAGACTTT 57.977 50.000 0.00 0.00 30.16 2.66
470 880 3.176924 AGAGGGAGAGTGCAGACTTTA 57.823 47.619 0.00 0.00 30.16 1.85
471 881 3.096092 AGAGGGAGAGTGCAGACTTTAG 58.904 50.000 0.00 0.00 30.16 1.85
472 882 2.829120 GAGGGAGAGTGCAGACTTTAGT 59.171 50.000 0.00 0.00 30.16 2.24
473 883 3.243724 AGGGAGAGTGCAGACTTTAGTT 58.756 45.455 0.00 0.00 30.16 2.24
474 884 4.417437 AGGGAGAGTGCAGACTTTAGTTA 58.583 43.478 0.00 0.00 30.16 2.24
475 885 4.464597 AGGGAGAGTGCAGACTTTAGTTAG 59.535 45.833 0.00 0.00 30.16 2.34
476 886 4.463186 GGGAGAGTGCAGACTTTAGTTAGA 59.537 45.833 0.00 0.00 30.16 2.10
477 887 5.404096 GGAGAGTGCAGACTTTAGTTAGAC 58.596 45.833 0.00 0.00 30.16 2.59
478 888 5.049398 AGAGTGCAGACTTTAGTTAGACG 57.951 43.478 0.00 0.00 30.16 4.18
479 889 4.082679 AGAGTGCAGACTTTAGTTAGACGG 60.083 45.833 0.00 0.00 30.16 4.79
480 890 3.573110 AGTGCAGACTTTAGTTAGACGGT 59.427 43.478 0.00 0.00 0.00 4.83
481 891 4.038883 AGTGCAGACTTTAGTTAGACGGTT 59.961 41.667 0.00 0.00 0.00 4.44
482 892 4.150098 GTGCAGACTTTAGTTAGACGGTTG 59.850 45.833 0.00 0.00 0.00 3.77
483 893 4.038282 TGCAGACTTTAGTTAGACGGTTGA 59.962 41.667 0.00 0.00 0.00 3.18
484 894 4.621886 GCAGACTTTAGTTAGACGGTTGAG 59.378 45.833 0.00 0.00 0.00 3.02
485 895 5.564259 GCAGACTTTAGTTAGACGGTTGAGA 60.564 44.000 0.00 0.00 0.00 3.27
486 896 6.087522 CAGACTTTAGTTAGACGGTTGAGAG 58.912 44.000 0.00 0.00 0.00 3.20
487 897 5.769162 AGACTTTAGTTAGACGGTTGAGAGT 59.231 40.000 0.00 0.00 0.00 3.24
488 898 5.770417 ACTTTAGTTAGACGGTTGAGAGTG 58.230 41.667 0.00 0.00 0.00 3.51
489 899 5.301298 ACTTTAGTTAGACGGTTGAGAGTGT 59.699 40.000 0.00 0.00 0.00 3.55
490 900 6.488006 ACTTTAGTTAGACGGTTGAGAGTGTA 59.512 38.462 0.00 0.00 0.00 2.90
491 901 6.492007 TTAGTTAGACGGTTGAGAGTGTAG 57.508 41.667 0.00 0.00 0.00 2.74
492 902 4.396522 AGTTAGACGGTTGAGAGTGTAGT 58.603 43.478 0.00 0.00 0.00 2.73
493 903 4.215827 AGTTAGACGGTTGAGAGTGTAGTG 59.784 45.833 0.00 0.00 0.00 2.74
494 904 2.584236 AGACGGTTGAGAGTGTAGTGT 58.416 47.619 0.00 0.00 0.00 3.55
495 905 2.957006 AGACGGTTGAGAGTGTAGTGTT 59.043 45.455 0.00 0.00 0.00 3.32
496 906 4.139786 AGACGGTTGAGAGTGTAGTGTTA 58.860 43.478 0.00 0.00 0.00 2.41
497 907 4.581824 AGACGGTTGAGAGTGTAGTGTTAA 59.418 41.667 0.00 0.00 0.00 2.01
498 908 5.068198 AGACGGTTGAGAGTGTAGTGTTAAA 59.932 40.000 0.00 0.00 0.00 1.52
499 909 5.663456 ACGGTTGAGAGTGTAGTGTTAAAA 58.337 37.500 0.00 0.00 0.00 1.52
500 910 6.108015 ACGGTTGAGAGTGTAGTGTTAAAAA 58.892 36.000 0.00 0.00 0.00 1.94
537 947 2.498078 GAGACAGAGGGAGTAGTTTGGG 59.502 54.545 0.00 0.00 0.00 4.12
581 991 2.745515 AGTGAAGCGGAGTTTAGGTC 57.254 50.000 0.00 0.00 0.00 3.85
597 1007 2.588620 AGGTCAAATACGGCCAACAAA 58.411 42.857 2.24 0.00 0.00 2.83
607 1046 4.597032 CCAACAAAGGCTCCACCA 57.403 55.556 0.00 0.00 43.14 4.17
625 1064 4.649674 CCACCACCTGTATCTGTATGTACT 59.350 45.833 0.00 0.00 0.00 2.73
628 1067 6.320418 CACCACCTGTATCTGTATGTACTACA 59.680 42.308 0.00 0.04 38.02 2.74
630 1069 7.147949 ACCACCTGTATCTGTATGTACTACAAC 60.148 40.741 0.00 0.00 39.82 3.32
631 1070 7.068348 CCACCTGTATCTGTATGTACTACAACT 59.932 40.741 0.00 0.00 39.82 3.16
632 1071 9.117183 CACCTGTATCTGTATGTACTACAACTA 57.883 37.037 0.00 0.00 39.82 2.24
633 1072 9.690913 ACCTGTATCTGTATGTACTACAACTAA 57.309 33.333 0.00 0.00 39.82 2.24
686 1125 4.075963 AGTACAAGGACCTAAACGCAAA 57.924 40.909 0.00 0.00 0.00 3.68
733 1172 2.978010 AAAAGGACACGCGCCCAG 60.978 61.111 5.73 0.00 0.00 4.45
756 1195 0.313987 AAAAGTGCGGCTACAAAGGC 59.686 50.000 0.00 0.00 44.69 4.35
805 1244 1.078426 CCCAGCTAAACCCACCTCG 60.078 63.158 0.00 0.00 0.00 4.63
850 1289 3.412408 GCAACCTCCCCTCCTCCC 61.412 72.222 0.00 0.00 0.00 4.30
923 1370 1.152546 ACCACCAACCCAAGAAGCC 60.153 57.895 0.00 0.00 0.00 4.35
943 1402 1.562008 CCCCTCTTCCTTCTTCCTTCC 59.438 57.143 0.00 0.00 0.00 3.46
1544 2008 1.530323 TACTGCTGTACTCGTGCTCA 58.470 50.000 0.00 0.00 0.00 4.26
1659 4505 7.146648 GTGGTCAATGGAGTAATAGTAGTAGC 58.853 42.308 0.00 0.00 0.00 3.58
1660 4506 6.837048 TGGTCAATGGAGTAATAGTAGTAGCA 59.163 38.462 0.00 0.00 0.00 3.49
1661 4507 7.146648 GGTCAATGGAGTAATAGTAGTAGCAC 58.853 42.308 0.00 0.00 0.00 4.40
1838 4693 3.118038 TCCCAATACAAGCACTCCATACC 60.118 47.826 0.00 0.00 0.00 2.73
1864 4719 6.483640 ACTTATTTGTTCTTCAGTCCTGTGTC 59.516 38.462 0.00 0.00 0.00 3.67
1876 4731 5.047021 TCAGTCCTGTGTCTATTTTCTCTGG 60.047 44.000 0.00 0.00 0.00 3.86
1928 4791 5.072600 GGGGTTAATAAATCCAAAATCCCCC 59.927 44.000 0.00 0.00 43.49 5.40
1963 4828 3.576118 ACCATCTCGAGTCTAATCCCATG 59.424 47.826 13.13 5.22 0.00 3.66
1986 4851 3.500680 GCAAGAGGATTGTTAACCGAACA 59.499 43.478 2.48 0.00 46.56 3.18
1993 4858 1.600023 TGTTAACCGAACAAGGCCAG 58.400 50.000 5.01 0.00 45.23 4.85
2017 4883 2.903855 CGCTGCCATGCTTAGGGG 60.904 66.667 0.00 0.00 0.00 4.79
2150 5016 3.241530 CCGGCCCTATGCTGCCTA 61.242 66.667 0.00 0.00 45.58 3.93
2157 5029 1.018226 CCTATGCTGCCTATGCGAGC 61.018 60.000 0.00 7.23 41.78 5.03
2191 5063 2.017783 TCGTTGTCGCCTACGTTGC 61.018 57.895 0.00 0.00 40.10 4.17
2213 5085 0.317854 GCTTGGTGGCGTTCTGTTTC 60.318 55.000 0.00 0.00 0.00 2.78
2237 5113 0.893270 TGATTGCAACCCTGGTTCCG 60.893 55.000 0.00 0.00 36.00 4.30
2259 5135 4.816925 CGAATGGATTCTTAACTCCTTCCC 59.183 45.833 0.00 0.00 34.69 3.97
2270 5146 2.192263 ACTCCTTCCCTTCAGTGGATC 58.808 52.381 0.00 0.00 0.00 3.36
2284 5160 2.182842 GGATCACACAGCGATGGCC 61.183 63.158 5.32 0.00 41.24 5.36
2307 5183 7.255139 GGCCGCATCTTGTTACTATAAAAATCT 60.255 37.037 0.00 0.00 0.00 2.40
2318 5194 1.653094 TAAAAATCTGGCCCTGCGCG 61.653 55.000 0.00 0.00 38.94 6.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 8.030913 ACGGAGGGAGTATTACTTTATTCATT 57.969 34.615 0.00 0.00 0.00 2.57
37 38 6.927936 GGAACGGAGGGAGTATTACTTTATTC 59.072 42.308 0.00 0.00 0.00 1.75
38 39 6.614496 AGGAACGGAGGGAGTATTACTTTATT 59.386 38.462 0.00 0.00 0.00 1.40
46 47 2.829023 TCAAGGAACGGAGGGAGTATT 58.171 47.619 0.00 0.00 0.00 1.89
47 48 2.544844 TCAAGGAACGGAGGGAGTAT 57.455 50.000 0.00 0.00 0.00 2.12
48 49 2.544844 ATCAAGGAACGGAGGGAGTA 57.455 50.000 0.00 0.00 0.00 2.59
49 50 2.544844 TATCAAGGAACGGAGGGAGT 57.455 50.000 0.00 0.00 0.00 3.85
50 51 4.021016 CCTTATATCAAGGAACGGAGGGAG 60.021 50.000 0.00 0.00 39.81 4.30
51 52 3.901844 CCTTATATCAAGGAACGGAGGGA 59.098 47.826 0.00 0.00 39.81 4.20
52 53 3.646637 ACCTTATATCAAGGAACGGAGGG 59.353 47.826 9.96 0.00 39.81 4.30
53 54 4.957684 ACCTTATATCAAGGAACGGAGG 57.042 45.455 9.96 0.00 39.81 4.30
92 93 9.744468 GCAATACACCTTATATTTCGGATTTTT 57.256 29.630 0.00 0.00 0.00 1.94
93 94 8.073768 CGCAATACACCTTATATTTCGGATTTT 58.926 33.333 0.00 0.00 28.90 1.82
94 95 7.227910 ACGCAATACACCTTATATTTCGGATTT 59.772 33.333 0.00 0.00 34.36 2.17
95 96 6.708949 ACGCAATACACCTTATATTTCGGATT 59.291 34.615 0.00 0.00 34.36 3.01
96 97 6.228258 ACGCAATACACCTTATATTTCGGAT 58.772 36.000 0.00 0.00 34.36 4.18
97 98 5.603596 ACGCAATACACCTTATATTTCGGA 58.396 37.500 0.00 0.00 34.36 4.55
98 99 5.917541 ACGCAATACACCTTATATTTCGG 57.082 39.130 0.00 0.00 34.36 4.30
99 100 6.711579 ACAACGCAATACACCTTATATTTCG 58.288 36.000 0.00 0.00 35.61 3.46
100 101 8.066000 GGTACAACGCAATACACCTTATATTTC 58.934 37.037 0.00 0.00 0.00 2.17
101 102 7.553402 TGGTACAACGCAATACACCTTATATTT 59.447 33.333 0.00 0.00 31.92 1.40
102 103 7.011669 GTGGTACAACGCAATACACCTTATATT 59.988 37.037 0.00 0.00 44.16 1.28
103 104 6.480981 GTGGTACAACGCAATACACCTTATAT 59.519 38.462 0.00 0.00 44.16 0.86
104 105 5.811613 GTGGTACAACGCAATACACCTTATA 59.188 40.000 0.00 0.00 44.16 0.98
105 106 4.632688 GTGGTACAACGCAATACACCTTAT 59.367 41.667 0.00 0.00 44.16 1.73
106 107 3.995705 GTGGTACAACGCAATACACCTTA 59.004 43.478 0.00 0.00 44.16 2.69
107 108 2.809696 GTGGTACAACGCAATACACCTT 59.190 45.455 0.00 0.00 44.16 3.50
108 109 2.038033 AGTGGTACAACGCAATACACCT 59.962 45.455 0.00 0.00 44.16 4.00
109 110 2.414138 GAGTGGTACAACGCAATACACC 59.586 50.000 0.00 0.00 44.16 4.16
110 111 2.091588 CGAGTGGTACAACGCAATACAC 59.908 50.000 4.92 0.00 44.16 2.90
111 112 2.288334 ACGAGTGGTACAACGCAATACA 60.288 45.455 4.92 0.00 44.16 2.29
112 113 2.331194 ACGAGTGGTACAACGCAATAC 58.669 47.619 4.92 0.00 44.16 1.89
113 114 2.229543 AGACGAGTGGTACAACGCAATA 59.770 45.455 4.92 0.00 44.16 1.90
114 115 1.000506 AGACGAGTGGTACAACGCAAT 59.999 47.619 4.92 0.00 44.16 3.56
115 116 0.386476 AGACGAGTGGTACAACGCAA 59.614 50.000 4.92 0.00 44.16 4.85
116 117 0.318360 CAGACGAGTGGTACAACGCA 60.318 55.000 4.92 0.00 44.16 5.24
117 118 1.007336 CCAGACGAGTGGTACAACGC 61.007 60.000 0.00 0.00 44.16 4.84
118 119 0.594602 TCCAGACGAGTGGTACAACG 59.405 55.000 7.53 0.00 44.16 4.10
119 120 4.445452 TTATCCAGACGAGTGGTACAAC 57.555 45.455 7.53 0.00 44.16 3.32
120 121 4.464951 ACATTATCCAGACGAGTGGTACAA 59.535 41.667 7.53 0.00 44.16 2.41
121 122 4.021229 ACATTATCCAGACGAGTGGTACA 58.979 43.478 7.53 0.00 38.88 2.90
122 123 4.650754 ACATTATCCAGACGAGTGGTAC 57.349 45.455 7.53 0.00 38.88 3.34
123 124 5.670792 AAACATTATCCAGACGAGTGGTA 57.329 39.130 7.53 0.00 38.88 3.25
124 125 4.553330 AAACATTATCCAGACGAGTGGT 57.447 40.909 7.53 0.00 38.88 4.16
125 126 5.880054 AAAAACATTATCCAGACGAGTGG 57.120 39.130 0.00 0.00 39.19 4.00
126 127 6.037172 CCCTAAAAACATTATCCAGACGAGTG 59.963 42.308 0.00 0.00 0.00 3.51
127 128 6.070424 TCCCTAAAAACATTATCCAGACGAGT 60.070 38.462 0.00 0.00 0.00 4.18
128 129 6.346096 TCCCTAAAAACATTATCCAGACGAG 58.654 40.000 0.00 0.00 0.00 4.18
129 130 6.302535 TCCCTAAAAACATTATCCAGACGA 57.697 37.500 0.00 0.00 0.00 4.20
130 131 6.995511 TTCCCTAAAAACATTATCCAGACG 57.004 37.500 0.00 0.00 0.00 4.18
131 132 8.966868 TCAATTCCCTAAAAACATTATCCAGAC 58.033 33.333 0.00 0.00 0.00 3.51
132 133 9.713684 ATCAATTCCCTAAAAACATTATCCAGA 57.286 29.630 0.00 0.00 0.00 3.86
141 142 9.936759 GGAAATGTAATCAATTCCCTAAAAACA 57.063 29.630 4.31 0.00 43.86 2.83
157 158 9.813826 AGCTTGCCTAATATAAGGAAATGTAAT 57.186 29.630 0.00 0.00 39.15 1.89
158 159 9.284968 GAGCTTGCCTAATATAAGGAAATGTAA 57.715 33.333 0.00 0.00 39.15 2.41
159 160 7.883311 GGAGCTTGCCTAATATAAGGAAATGTA 59.117 37.037 0.00 0.00 39.15 2.29
160 161 6.717084 GGAGCTTGCCTAATATAAGGAAATGT 59.283 38.462 0.00 0.00 39.15 2.71
161 162 6.944862 AGGAGCTTGCCTAATATAAGGAAATG 59.055 38.462 0.00 0.00 39.15 2.32
162 163 7.018049 AGAGGAGCTTGCCTAATATAAGGAAAT 59.982 37.037 0.00 0.00 38.73 2.17
163 164 6.330250 AGAGGAGCTTGCCTAATATAAGGAAA 59.670 38.462 0.00 0.00 38.73 3.13
164 165 5.846714 AGAGGAGCTTGCCTAATATAAGGAA 59.153 40.000 0.00 0.00 38.73 3.36
165 166 5.407049 AGAGGAGCTTGCCTAATATAAGGA 58.593 41.667 0.00 0.00 38.73 3.36
166 167 5.753721 AGAGGAGCTTGCCTAATATAAGG 57.246 43.478 0.00 0.00 38.73 2.69
167 168 9.732130 AAAATAGAGGAGCTTGCCTAATATAAG 57.268 33.333 0.00 0.00 38.73 1.73
168 169 9.507329 CAAAATAGAGGAGCTTGCCTAATATAA 57.493 33.333 0.00 0.00 38.73 0.98
169 170 8.660435 ACAAAATAGAGGAGCTTGCCTAATATA 58.340 33.333 0.00 0.00 38.73 0.86
170 171 7.521669 ACAAAATAGAGGAGCTTGCCTAATAT 58.478 34.615 0.00 0.00 38.73 1.28
171 172 6.900194 ACAAAATAGAGGAGCTTGCCTAATA 58.100 36.000 0.00 0.00 38.73 0.98
172 173 5.760131 ACAAAATAGAGGAGCTTGCCTAAT 58.240 37.500 0.00 0.00 38.73 1.73
173 174 5.179452 ACAAAATAGAGGAGCTTGCCTAA 57.821 39.130 0.00 0.00 38.73 2.69
174 175 4.225042 TGACAAAATAGAGGAGCTTGCCTA 59.775 41.667 0.00 0.00 38.73 3.93
175 176 3.009473 TGACAAAATAGAGGAGCTTGCCT 59.991 43.478 0.00 0.00 42.17 4.75
176 177 3.347216 TGACAAAATAGAGGAGCTTGCC 58.653 45.455 0.00 0.00 0.00 4.52
177 178 4.397417 ACATGACAAAATAGAGGAGCTTGC 59.603 41.667 0.00 0.00 0.00 4.01
178 179 5.645067 TGACATGACAAAATAGAGGAGCTTG 59.355 40.000 0.00 0.00 0.00 4.01
179 180 5.809001 TGACATGACAAAATAGAGGAGCTT 58.191 37.500 0.00 0.00 0.00 3.74
180 181 5.426689 TGACATGACAAAATAGAGGAGCT 57.573 39.130 0.00 0.00 0.00 4.09
181 182 6.690194 ATTGACATGACAAAATAGAGGAGC 57.310 37.500 14.36 0.00 33.44 4.70
182 183 9.388506 ACTAATTGACATGACAAAATAGAGGAG 57.611 33.333 25.68 13.86 32.62 3.69
183 184 9.739276 AACTAATTGACATGACAAAATAGAGGA 57.261 29.630 25.68 3.12 32.62 3.71
189 190 9.077885 ACACCTAACTAATTGACATGACAAAAT 57.922 29.630 14.36 9.21 33.44 1.82
190 191 8.458573 ACACCTAACTAATTGACATGACAAAA 57.541 30.769 14.36 5.60 33.44 2.44
191 192 9.562408 TTACACCTAACTAATTGACATGACAAA 57.438 29.630 14.36 0.00 33.44 2.83
192 193 9.733556 ATTACACCTAACTAATTGACATGACAA 57.266 29.630 12.85 12.85 0.00 3.18
193 194 9.378551 GATTACACCTAACTAATTGACATGACA 57.621 33.333 0.00 0.00 0.00 3.58
194 195 9.601217 AGATTACACCTAACTAATTGACATGAC 57.399 33.333 0.00 0.00 0.00 3.06
195 196 9.817809 GAGATTACACCTAACTAATTGACATGA 57.182 33.333 0.00 0.00 0.00 3.07
196 197 8.755941 CGAGATTACACCTAACTAATTGACATG 58.244 37.037 0.00 0.00 0.00 3.21
197 198 7.438459 GCGAGATTACACCTAACTAATTGACAT 59.562 37.037 0.00 0.00 0.00 3.06
198 199 6.755141 GCGAGATTACACCTAACTAATTGACA 59.245 38.462 0.00 0.00 0.00 3.58
199 200 6.200475 GGCGAGATTACACCTAACTAATTGAC 59.800 42.308 0.00 0.00 0.00 3.18
200 201 6.278363 GGCGAGATTACACCTAACTAATTGA 58.722 40.000 0.00 0.00 0.00 2.57
201 202 5.465724 GGGCGAGATTACACCTAACTAATTG 59.534 44.000 0.00 0.00 0.00 2.32
202 203 5.129815 TGGGCGAGATTACACCTAACTAATT 59.870 40.000 0.00 0.00 0.00 1.40
203 204 4.652421 TGGGCGAGATTACACCTAACTAAT 59.348 41.667 0.00 0.00 0.00 1.73
204 205 4.025360 TGGGCGAGATTACACCTAACTAA 58.975 43.478 0.00 0.00 0.00 2.24
205 206 3.634504 TGGGCGAGATTACACCTAACTA 58.365 45.455 0.00 0.00 0.00 2.24
206 207 2.463752 TGGGCGAGATTACACCTAACT 58.536 47.619 0.00 0.00 0.00 2.24
207 208 2.973694 TGGGCGAGATTACACCTAAC 57.026 50.000 0.00 0.00 0.00 2.34
208 209 3.985019 TTTGGGCGAGATTACACCTAA 57.015 42.857 0.00 0.00 0.00 2.69
209 210 3.262405 AGTTTTGGGCGAGATTACACCTA 59.738 43.478 0.00 0.00 0.00 3.08
210 211 2.039879 AGTTTTGGGCGAGATTACACCT 59.960 45.455 0.00 0.00 0.00 4.00
211 212 2.433436 AGTTTTGGGCGAGATTACACC 58.567 47.619 0.00 0.00 0.00 4.16
212 213 5.353123 TCATAAGTTTTGGGCGAGATTACAC 59.647 40.000 0.00 0.00 0.00 2.90
213 214 5.492895 TCATAAGTTTTGGGCGAGATTACA 58.507 37.500 0.00 0.00 0.00 2.41
214 215 6.431198 TTCATAAGTTTTGGGCGAGATTAC 57.569 37.500 0.00 0.00 0.00 1.89
215 216 7.639113 ATTTCATAAGTTTTGGGCGAGATTA 57.361 32.000 0.00 0.00 0.00 1.75
216 217 5.975693 TTTCATAAGTTTTGGGCGAGATT 57.024 34.783 0.00 0.00 0.00 2.40
217 218 6.530019 AATTTCATAAGTTTTGGGCGAGAT 57.470 33.333 0.00 0.00 0.00 2.75
218 219 5.975693 AATTTCATAAGTTTTGGGCGAGA 57.024 34.783 0.00 0.00 0.00 4.04
219 220 6.090763 GGAAAATTTCATAAGTTTTGGGCGAG 59.909 38.462 8.09 0.00 32.23 5.03
220 221 5.929415 GGAAAATTTCATAAGTTTTGGGCGA 59.071 36.000 8.09 0.00 32.23 5.54
221 222 5.121611 GGGAAAATTTCATAAGTTTTGGGCG 59.878 40.000 8.09 0.00 32.23 6.13
222 223 6.000840 TGGGAAAATTTCATAAGTTTTGGGC 58.999 36.000 8.09 0.00 32.23 5.36
223 224 8.457238 TTTGGGAAAATTTCATAAGTTTTGGG 57.543 30.769 8.09 0.00 32.23 4.12
233 234 9.719355 GGTGTATAGTTTTTGGGAAAATTTCAT 57.281 29.630 8.09 0.00 37.12 2.57
234 235 8.151596 GGGTGTATAGTTTTTGGGAAAATTTCA 58.848 33.333 8.09 0.00 37.12 2.69
235 236 8.372459 AGGGTGTATAGTTTTTGGGAAAATTTC 58.628 33.333 0.00 0.00 37.12 2.17
236 237 8.270137 AGGGTGTATAGTTTTTGGGAAAATTT 57.730 30.769 0.00 0.00 37.12 1.82
237 238 7.865530 AGGGTGTATAGTTTTTGGGAAAATT 57.134 32.000 0.00 0.00 37.12 1.82
238 239 7.865530 AAGGGTGTATAGTTTTTGGGAAAAT 57.134 32.000 0.00 0.00 37.12 1.82
239 240 7.678207 AAAGGGTGTATAGTTTTTGGGAAAA 57.322 32.000 0.00 0.00 32.53 2.29
240 241 8.959676 ATAAAGGGTGTATAGTTTTTGGGAAA 57.040 30.769 0.00 0.00 0.00 3.13
241 242 8.959676 AATAAAGGGTGTATAGTTTTTGGGAA 57.040 30.769 0.00 0.00 0.00 3.97
266 267 9.247861 GGTAATATATACTTCCTCCGTTCCTTA 57.752 37.037 0.00 0.00 0.00 2.69
267 268 7.731688 TGGTAATATATACTTCCTCCGTTCCTT 59.268 37.037 0.00 0.00 0.00 3.36
268 269 7.243824 TGGTAATATATACTTCCTCCGTTCCT 58.756 38.462 0.00 0.00 0.00 3.36
269 270 7.472334 TGGTAATATATACTTCCTCCGTTCC 57.528 40.000 0.00 0.00 0.00 3.62
272 273 9.931698 TCATATGGTAATATATACTTCCTCCGT 57.068 33.333 2.13 0.00 0.00 4.69
285 286 7.728981 CCCCTCCGTACTATCATATGGTAATAT 59.271 40.741 2.13 0.00 33.52 1.28
288 289 5.222400 ACCCCTCCGTACTATCATATGGTAA 60.222 44.000 2.13 0.00 33.52 2.85
295 296 7.943447 GTCATATATACCCCTCCGTACTATCAT 59.057 40.741 0.00 0.00 0.00 2.45
305 306 5.726793 ACCTTCATGTCATATATACCCCTCC 59.273 44.000 0.00 0.00 0.00 4.30
306 307 6.875972 ACCTTCATGTCATATATACCCCTC 57.124 41.667 0.00 0.00 0.00 4.30
307 308 8.751215 TTTACCTTCATGTCATATATACCCCT 57.249 34.615 0.00 0.00 0.00 4.79
317 385 3.756434 CGGTGGTTTTACCTTCATGTCAT 59.244 43.478 0.00 0.00 39.58 3.06
326 394 3.970205 CCATCCGGTGGTTTTACCT 57.030 52.632 13.21 0.00 43.44 3.08
443 853 4.081420 GTCTGCACTCTCCCTCTTTCATAA 60.081 45.833 0.00 0.00 0.00 1.90
444 854 3.449018 GTCTGCACTCTCCCTCTTTCATA 59.551 47.826 0.00 0.00 0.00 2.15
445 855 2.235898 GTCTGCACTCTCCCTCTTTCAT 59.764 50.000 0.00 0.00 0.00 2.57
446 856 1.620819 GTCTGCACTCTCCCTCTTTCA 59.379 52.381 0.00 0.00 0.00 2.69
447 857 1.899142 AGTCTGCACTCTCCCTCTTTC 59.101 52.381 0.00 0.00 0.00 2.62
448 858 2.022718 AGTCTGCACTCTCCCTCTTT 57.977 50.000 0.00 0.00 0.00 2.52
449 859 2.022718 AAGTCTGCACTCTCCCTCTT 57.977 50.000 0.00 0.00 29.93 2.85
450 860 2.022718 AAAGTCTGCACTCTCCCTCT 57.977 50.000 0.00 0.00 29.93 3.69
451 861 2.829120 ACTAAAGTCTGCACTCTCCCTC 59.171 50.000 0.00 0.00 29.93 4.30
452 862 2.896039 ACTAAAGTCTGCACTCTCCCT 58.104 47.619 0.00 0.00 29.93 4.20
453 863 3.686916 AACTAAAGTCTGCACTCTCCC 57.313 47.619 0.00 0.00 29.93 4.30
454 864 5.404096 GTCTAACTAAAGTCTGCACTCTCC 58.596 45.833 0.00 0.00 29.93 3.71
455 865 5.090083 CGTCTAACTAAAGTCTGCACTCTC 58.910 45.833 0.00 0.00 29.93 3.20
456 866 4.082679 CCGTCTAACTAAAGTCTGCACTCT 60.083 45.833 0.00 0.00 29.93 3.24
457 867 4.167268 CCGTCTAACTAAAGTCTGCACTC 58.833 47.826 0.00 0.00 29.93 3.51
458 868 3.573110 ACCGTCTAACTAAAGTCTGCACT 59.427 43.478 0.00 0.00 0.00 4.40
459 869 3.910648 ACCGTCTAACTAAAGTCTGCAC 58.089 45.455 0.00 0.00 0.00 4.57
460 870 4.038282 TCAACCGTCTAACTAAAGTCTGCA 59.962 41.667 0.00 0.00 0.00 4.41
461 871 4.553323 TCAACCGTCTAACTAAAGTCTGC 58.447 43.478 0.00 0.00 0.00 4.26
462 872 6.010294 TCTCAACCGTCTAACTAAAGTCTG 57.990 41.667 0.00 0.00 0.00 3.51
463 873 5.769162 ACTCTCAACCGTCTAACTAAAGTCT 59.231 40.000 0.00 0.00 0.00 3.24
464 874 5.857517 CACTCTCAACCGTCTAACTAAAGTC 59.142 44.000 0.00 0.00 0.00 3.01
465 875 5.301298 ACACTCTCAACCGTCTAACTAAAGT 59.699 40.000 0.00 0.00 0.00 2.66
466 876 5.770417 ACACTCTCAACCGTCTAACTAAAG 58.230 41.667 0.00 0.00 0.00 1.85
467 877 5.779529 ACACTCTCAACCGTCTAACTAAA 57.220 39.130 0.00 0.00 0.00 1.85
468 878 6.000219 ACTACACTCTCAACCGTCTAACTAA 59.000 40.000 0.00 0.00 0.00 2.24
469 879 5.410746 CACTACACTCTCAACCGTCTAACTA 59.589 44.000 0.00 0.00 0.00 2.24
470 880 4.215827 CACTACACTCTCAACCGTCTAACT 59.784 45.833 0.00 0.00 0.00 2.24
471 881 4.023365 ACACTACACTCTCAACCGTCTAAC 60.023 45.833 0.00 0.00 0.00 2.34
472 882 4.139786 ACACTACACTCTCAACCGTCTAA 58.860 43.478 0.00 0.00 0.00 2.10
473 883 3.748083 ACACTACACTCTCAACCGTCTA 58.252 45.455 0.00 0.00 0.00 2.59
474 884 2.584236 ACACTACACTCTCAACCGTCT 58.416 47.619 0.00 0.00 0.00 4.18
475 885 3.366440 AACACTACACTCTCAACCGTC 57.634 47.619 0.00 0.00 0.00 4.79
476 886 4.924305 TTAACACTACACTCTCAACCGT 57.076 40.909 0.00 0.00 0.00 4.83
477 887 6.592798 TTTTTAACACTACACTCTCAACCG 57.407 37.500 0.00 0.00 0.00 4.44
497 907 8.816894 TCTGTCTCATAATAGAGGAGTGTTTTT 58.183 33.333 0.00 0.00 37.26 1.94
498 908 8.367660 TCTGTCTCATAATAGAGGAGTGTTTT 57.632 34.615 0.00 0.00 37.26 2.43
499 909 7.962995 TCTGTCTCATAATAGAGGAGTGTTT 57.037 36.000 0.00 0.00 37.26 2.83
500 910 7.581213 CTCTGTCTCATAATAGAGGAGTGTT 57.419 40.000 0.00 0.00 37.26 3.32
507 917 7.458397 ACTACTCCCTCTGTCTCATAATAGAG 58.542 42.308 0.00 0.00 37.11 2.43
508 918 7.395525 ACTACTCCCTCTGTCTCATAATAGA 57.604 40.000 0.00 0.00 0.00 1.98
509 919 8.356657 CAAACTACTCCCTCTGTCTCATAATAG 58.643 40.741 0.00 0.00 0.00 1.73
510 920 7.287927 CCAAACTACTCCCTCTGTCTCATAATA 59.712 40.741 0.00 0.00 0.00 0.98
511 921 6.098982 CCAAACTACTCCCTCTGTCTCATAAT 59.901 42.308 0.00 0.00 0.00 1.28
512 922 5.422331 CCAAACTACTCCCTCTGTCTCATAA 59.578 44.000 0.00 0.00 0.00 1.90
513 923 4.956700 CCAAACTACTCCCTCTGTCTCATA 59.043 45.833 0.00 0.00 0.00 2.15
514 924 3.772025 CCAAACTACTCCCTCTGTCTCAT 59.228 47.826 0.00 0.00 0.00 2.90
515 925 3.165875 CCAAACTACTCCCTCTGTCTCA 58.834 50.000 0.00 0.00 0.00 3.27
516 926 2.498078 CCCAAACTACTCCCTCTGTCTC 59.502 54.545 0.00 0.00 0.00 3.36
517 927 2.158143 ACCCAAACTACTCCCTCTGTCT 60.158 50.000 0.00 0.00 0.00 3.41
518 928 2.258109 ACCCAAACTACTCCCTCTGTC 58.742 52.381 0.00 0.00 0.00 3.51
519 929 2.372172 CAACCCAAACTACTCCCTCTGT 59.628 50.000 0.00 0.00 0.00 3.41
520 930 2.876079 GCAACCCAAACTACTCCCTCTG 60.876 54.545 0.00 0.00 0.00 3.35
521 931 1.351350 GCAACCCAAACTACTCCCTCT 59.649 52.381 0.00 0.00 0.00 3.69
537 947 8.732746 TTTTACCTCATCTTATCCTAAGCAAC 57.267 34.615 0.00 0.00 0.00 4.17
581 991 1.708822 GCCTTTGTTGGCCGTATTTG 58.291 50.000 0.00 0.00 46.82 2.32
597 1007 0.043334 AGATACAGGTGGTGGAGCCT 59.957 55.000 0.00 0.00 38.35 4.58
607 1046 9.690913 TTAGTTGTAGTACATACAGATACAGGT 57.309 33.333 3.28 0.00 45.05 4.00
638 1077 9.352191 ACTGTTTCTCTTCTCTTTGTACTACTA 57.648 33.333 0.00 0.00 0.00 1.82
639 1078 8.240267 ACTGTTTCTCTTCTCTTTGTACTACT 57.760 34.615 0.00 0.00 0.00 2.57
641 1080 9.352191 ACTACTGTTTCTCTTCTCTTTGTACTA 57.648 33.333 0.00 0.00 0.00 1.82
643 1082 9.396938 GTACTACTGTTTCTCTTCTCTTTGTAC 57.603 37.037 0.00 0.00 0.00 2.90
644 1083 9.128404 TGTACTACTGTTTCTCTTCTCTTTGTA 57.872 33.333 0.00 0.00 0.00 2.41
645 1084 8.008513 TGTACTACTGTTTCTCTTCTCTTTGT 57.991 34.615 0.00 0.00 0.00 2.83
646 1085 8.873215 TTGTACTACTGTTTCTCTTCTCTTTG 57.127 34.615 0.00 0.00 0.00 2.77
647 1086 8.145122 CCTTGTACTACTGTTTCTCTTCTCTTT 58.855 37.037 0.00 0.00 0.00 2.52
648 1087 7.506261 TCCTTGTACTACTGTTTCTCTTCTCTT 59.494 37.037 0.00 0.00 0.00 2.85
649 1088 7.005296 TCCTTGTACTACTGTTTCTCTTCTCT 58.995 38.462 0.00 0.00 0.00 3.10
650 1089 7.085746 GTCCTTGTACTACTGTTTCTCTTCTC 58.914 42.308 0.00 0.00 0.00 2.87
651 1090 6.015265 GGTCCTTGTACTACTGTTTCTCTTCT 60.015 42.308 0.00 0.00 0.00 2.85
652 1091 6.015265 AGGTCCTTGTACTACTGTTTCTCTTC 60.015 42.308 0.00 0.00 0.00 2.87
686 1125 2.410730 CACGGCTAGTTCGATTTCGTTT 59.589 45.455 13.08 0.00 40.80 3.60
733 1172 3.551551 CTTTGTAGCCGCACTTTTGTAC 58.448 45.455 0.00 0.00 0.00 2.90
805 1244 1.265568 CTTTGTTGCTGATGCGATGC 58.734 50.000 0.00 0.00 43.34 3.91
893 1340 3.496131 GGTGGTGCGTGGCGTATG 61.496 66.667 0.00 0.00 0.00 2.39
894 1341 3.538785 TTGGTGGTGCGTGGCGTAT 62.539 57.895 0.00 0.00 0.00 3.06
895 1342 4.237207 TTGGTGGTGCGTGGCGTA 62.237 61.111 0.00 0.00 0.00 4.42
900 1347 2.830827 TTGGGTTGGTGGTGCGTG 60.831 61.111 0.00 0.00 0.00 5.34
901 1348 2.518349 CTTGGGTTGGTGGTGCGT 60.518 61.111 0.00 0.00 0.00 5.24
902 1349 1.795170 CTTCTTGGGTTGGTGGTGCG 61.795 60.000 0.00 0.00 0.00 5.34
903 1350 2.041153 CTTCTTGGGTTGGTGGTGC 58.959 57.895 0.00 0.00 0.00 5.01
923 1370 1.562008 GGAAGGAAGAAGGAAGAGGGG 59.438 57.143 0.00 0.00 0.00 4.79
943 1402 0.683973 ACTCTTGTGCCTGTGAGAGG 59.316 55.000 0.00 0.00 46.13 3.69
1109 1572 4.834453 CTGCTCCTCCTGCTGCCG 62.834 72.222 0.00 0.00 0.00 5.69
1110 1573 3.397439 TCTGCTCCTCCTGCTGCC 61.397 66.667 0.00 0.00 0.00 4.85
1115 1578 2.241479 CTGCTGGTCTGCTCCTCCTG 62.241 65.000 1.84 0.00 0.00 3.86
1118 1581 2.583520 CCTGCTGGTCTGCTCCTC 59.416 66.667 0.51 0.00 0.00 3.71
1119 1582 3.715097 GCCTGCTGGTCTGCTCCT 61.715 66.667 11.69 0.00 35.27 3.69
1120 1583 3.972971 CTGCCTGCTGGTCTGCTCC 62.973 68.421 11.69 0.00 35.27 4.70
1299 1762 4.140599 AAGAGGCGCTCCAGCTCG 62.141 66.667 7.64 0.00 39.32 5.03
1347 1810 0.326264 TGAGCTTGGCCTTCTTCTCC 59.674 55.000 3.32 0.00 0.00 3.71
1544 2008 4.198028 GGTACCACGAACTGACCTAATT 57.802 45.455 7.15 0.00 0.00 1.40
1709 4555 5.343307 CCATGGAAGGGAATTTAAACCTG 57.657 43.478 5.56 0.00 43.46 4.00
1838 4693 6.260936 ACACAGGACTGAAGAACAAATAAGTG 59.739 38.462 6.29 0.00 0.00 3.16
1864 4719 8.743714 ACAAGGCTAAAATTCCAGAGAAAATAG 58.256 33.333 0.00 0.00 35.09 1.73
1876 4731 6.512297 TCCAAACAGAACAAGGCTAAAATTC 58.488 36.000 0.00 0.00 0.00 2.17
1928 4791 2.659428 GAGATGGTTGGAGGGAATTGG 58.341 52.381 0.00 0.00 0.00 3.16
1963 4828 2.706890 TCGGTTAACAATCCTCTTGCC 58.293 47.619 8.10 0.00 0.00 4.52
2017 4883 1.036707 ATCTCTCGTGCCCTAGCTTC 58.963 55.000 0.00 0.00 40.80 3.86
2149 5015 1.439228 GGAGACAGCAGCTCGCATA 59.561 57.895 10.16 0.00 46.13 3.14
2150 5016 2.186384 GGAGACAGCAGCTCGCAT 59.814 61.111 10.16 0.00 46.13 4.73
2157 5029 2.179517 GACGGACGGAGACAGCAG 59.820 66.667 0.00 0.00 0.00 4.24
2213 5085 0.609662 CCAGGGTTGCAATCAAAGGG 59.390 55.000 12.67 2.98 33.37 3.95
2237 5113 6.007485 AGGGAAGGAGTTAAGAATCCATTC 57.993 41.667 4.57 0.00 38.12 2.67
2259 5135 1.073964 CGCTGTGTGATCCACTGAAG 58.926 55.000 18.64 9.24 44.81 3.02
2280 5156 4.409718 TTATAGTAACAAGATGCGGCCA 57.590 40.909 2.24 0.00 0.00 5.36
2284 5160 7.587757 GCCAGATTTTTATAGTAACAAGATGCG 59.412 37.037 0.00 0.00 0.00 4.73
2287 5163 8.282256 AGGGCCAGATTTTTATAGTAACAAGAT 58.718 33.333 6.18 0.00 0.00 2.40
2288 5164 7.556275 CAGGGCCAGATTTTTATAGTAACAAGA 59.444 37.037 6.18 0.00 0.00 3.02
2290 5166 6.096282 GCAGGGCCAGATTTTTATAGTAACAA 59.904 38.462 6.18 0.00 0.00 2.83
2292 5168 5.277828 CGCAGGGCCAGATTTTTATAGTAAC 60.278 44.000 6.18 0.00 0.00 2.50
2293 5169 4.819630 CGCAGGGCCAGATTTTTATAGTAA 59.180 41.667 6.18 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.