Multiple sequence alignment - TraesCS5A01G311100

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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 TraesCS5A01G311100 chr5A 100.000 1794 0 0 912 2705 522883534 522881741 0.000000e+00 3314.0
1 TraesCS5A01G311100 chr5A 91.146 881 67 4 968 1846 522956871 522956000 0.000000e+00 1184.0
2 TraesCS5A01G311100 chr5A 100.000 633 0 0 1 633 522884445 522883813 0.000000e+00 1170.0
3 TraesCS5A01G311100 chr5A 84.438 347 48 3 1087 1433 523148703 523148363 1.200000e-88 337.0
4 TraesCS5A01G311100 chr5B 92.683 1394 70 8 939 2317 493481235 493479859 0.000000e+00 1980.0
5 TraesCS5A01G311100 chr5B 90.814 762 68 1 968 1727 493516810 493516049 0.000000e+00 1018.0
6 TraesCS5A01G311100 chr5B 82.564 390 56 8 1047 1433 493695478 493695098 1.550000e-87 333.0
7 TraesCS5A01G311100 chr5B 94.410 161 7 1 259 419 493481858 493481700 2.080000e-61 246.0
8 TraesCS5A01G311100 chr5B 84.120 233 6 11 418 620 493481503 493481272 2.120000e-46 196.0
9 TraesCS5A01G311100 chr5B 81.481 162 8 13 418 559 493517024 493516865 2.200000e-21 113.0
10 TraesCS5A01G311100 chr5B 100.000 30 0 0 1713 1742 493516034 493516005 3.760000e-04 56.5
11 TraesCS5A01G311100 chr5D 96.349 986 35 1 939 1924 410953074 410952090 0.000000e+00 1620.0
12 TraesCS5A01G311100 chr5D 91.383 824 60 3 974 1797 411149415 411148603 0.000000e+00 1118.0
13 TraesCS5A01G311100 chr5D 85.845 438 27 9 1921 2357 410952004 410951601 1.490000e-117 433.0
14 TraesCS5A01G311100 chr5D 85.303 347 45 3 1087 1433 411225757 411225417 1.190000e-93 353.0
15 TraesCS5A01G311100 chr5D 83.285 347 47 7 1093 1438 411790599 411790263 2.620000e-80 309.0
16 TraesCS5A01G311100 chr5D 95.597 159 4 2 261 419 410953705 410953550 4.470000e-63 252.0
17 TraesCS5A01G311100 chr5D 86.809 235 11 2 418 632 410953354 410953120 7.480000e-61 244.0
18 TraesCS5A01G311100 chr5D 82.609 207 16 6 418 604 411149651 411149445 5.990000e-37 165.0
19 TraesCS5A01G311100 chr5D 100.000 37 0 0 1787 1823 411142678 411142642 4.830000e-08 69.4
20 TraesCS5A01G311100 chr5D 87.755 49 4 2 2659 2705 410950949 410950901 3.760000e-04 56.5


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 TraesCS5A01G311100 chr5A 522881741 522884445 2704 True 2242.000000 3314 100.000000 1 2705 2 chr5A.!!$R3 2704
1 TraesCS5A01G311100 chr5A 522956000 522956871 871 True 1184.000000 1184 91.146000 968 1846 1 chr5A.!!$R1 878
2 TraesCS5A01G311100 chr5B 493479859 493481858 1999 True 807.333333 1980 90.404333 259 2317 3 chr5B.!!$R2 2058
3 TraesCS5A01G311100 chr5B 493516005 493517024 1019 True 395.833333 1018 90.765000 418 1742 3 chr5B.!!$R3 1324
4 TraesCS5A01G311100 chr5D 411148603 411149651 1048 True 641.500000 1118 86.996000 418 1797 2 chr5D.!!$R5 1379
5 TraesCS5A01G311100 chr5D 410950901 410953705 2804 True 521.100000 1620 90.471000 261 2705 5 chr5D.!!$R4 2444

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
207 208 0.030638 CACTGGGTTTTTCTGCACCG 59.969 55.0 0.0 0.0 33.34 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1938 2321 0.788391 GTGAACGAACGGCACCTTAG 59.212 55.0 9.89 0.0 0.0 2.18 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
22 23 5.385396 CCTTTGTTGTATCGGTATTCGTC 57.615 43.478 0.00 0.00 40.32 4.20
23 24 4.269363 CCTTTGTTGTATCGGTATTCGTCC 59.731 45.833 0.00 0.00 40.32 4.79
25 26 2.223548 TGTTGTATCGGTATTCGTCCGG 60.224 50.000 0.00 0.00 46.82 5.14
26 27 1.679139 TGTATCGGTATTCGTCCGGT 58.321 50.000 0.00 0.00 46.82 5.28
27 28 2.023673 TGTATCGGTATTCGTCCGGTT 58.976 47.619 0.00 0.00 46.82 4.44
28 29 2.426738 TGTATCGGTATTCGTCCGGTTT 59.573 45.455 0.00 0.00 46.82 3.27
29 30 2.678471 ATCGGTATTCGTCCGGTTTT 57.322 45.000 0.00 0.00 46.82 2.43
30 31 2.453983 TCGGTATTCGTCCGGTTTTT 57.546 45.000 0.00 0.00 46.82 1.94
31 32 2.336667 TCGGTATTCGTCCGGTTTTTC 58.663 47.619 0.00 0.00 46.82 2.29
32 33 2.067766 CGGTATTCGTCCGGTTTTTCA 58.932 47.619 0.00 0.00 43.68 2.69
33 34 2.159801 CGGTATTCGTCCGGTTTTTCAC 60.160 50.000 0.00 0.00 43.68 3.18
34 35 3.069289 GGTATTCGTCCGGTTTTTCACT 58.931 45.455 0.00 0.00 0.00 3.41
35 36 4.244862 GGTATTCGTCCGGTTTTTCACTA 58.755 43.478 0.00 0.00 0.00 2.74
36 37 4.690280 GGTATTCGTCCGGTTTTTCACTAA 59.310 41.667 0.00 0.00 0.00 2.24
37 38 4.737353 ATTCGTCCGGTTTTTCACTAAC 57.263 40.909 0.00 0.00 0.00 2.34
38 39 3.457610 TCGTCCGGTTTTTCACTAACT 57.542 42.857 0.00 0.00 0.00 2.24
39 40 4.582701 TCGTCCGGTTTTTCACTAACTA 57.417 40.909 0.00 0.00 0.00 2.24
40 41 4.942852 TCGTCCGGTTTTTCACTAACTAA 58.057 39.130 0.00 0.00 0.00 2.24
41 42 5.355596 TCGTCCGGTTTTTCACTAACTAAA 58.644 37.500 0.00 0.00 0.00 1.85
42 43 5.990996 TCGTCCGGTTTTTCACTAACTAAAT 59.009 36.000 0.00 0.00 0.00 1.40
43 44 6.073657 TCGTCCGGTTTTTCACTAACTAAATG 60.074 38.462 0.00 0.00 0.00 2.32
44 45 6.376177 GTCCGGTTTTTCACTAACTAAATGG 58.624 40.000 0.00 0.00 0.00 3.16
45 46 6.205270 GTCCGGTTTTTCACTAACTAAATGGA 59.795 38.462 0.00 0.00 0.00 3.41
46 47 6.205270 TCCGGTTTTTCACTAACTAAATGGAC 59.795 38.462 0.00 0.00 0.00 4.02
47 48 6.016943 CCGGTTTTTCACTAACTAAATGGACA 60.017 38.462 0.00 0.00 0.00 4.02
48 49 7.419204 CGGTTTTTCACTAACTAAATGGACAA 58.581 34.615 0.00 0.00 0.00 3.18
49 50 8.079809 CGGTTTTTCACTAACTAAATGGACAAT 58.920 33.333 0.00 0.00 0.00 2.71
50 51 9.758651 GGTTTTTCACTAACTAAATGGACAATT 57.241 29.630 0.00 0.00 0.00 2.32
57 58 9.965824 CACTAACTAAATGGACAATTTTCTTGT 57.034 29.630 0.00 0.00 39.29 3.16
92 93 6.765915 AGATGAGATAAAGTTTTTGCCTCC 57.234 37.500 0.00 0.00 0.00 4.30
93 94 5.355350 AGATGAGATAAAGTTTTTGCCTCCG 59.645 40.000 0.00 0.00 0.00 4.63
94 95 4.394729 TGAGATAAAGTTTTTGCCTCCGT 58.605 39.130 0.00 0.00 0.00 4.69
95 96 4.825085 TGAGATAAAGTTTTTGCCTCCGTT 59.175 37.500 0.00 0.00 0.00 4.44
96 97 5.300792 TGAGATAAAGTTTTTGCCTCCGTTT 59.699 36.000 0.00 0.00 0.00 3.60
97 98 5.769367 AGATAAAGTTTTTGCCTCCGTTTC 58.231 37.500 0.00 0.00 0.00 2.78
98 99 3.878160 AAAGTTTTTGCCTCCGTTTCA 57.122 38.095 0.00 0.00 0.00 2.69
99 100 3.878160 AAGTTTTTGCCTCCGTTTCAA 57.122 38.095 0.00 0.00 0.00 2.69
100 101 3.878160 AGTTTTTGCCTCCGTTTCAAA 57.122 38.095 0.00 0.00 0.00 2.69
101 102 4.195225 AGTTTTTGCCTCCGTTTCAAAA 57.805 36.364 0.00 0.00 37.75 2.44
102 103 4.570930 AGTTTTTGCCTCCGTTTCAAAAA 58.429 34.783 7.69 7.69 43.27 1.94
128 129 7.496529 AATATTAAGGATGATGTTGGACACG 57.503 36.000 0.00 0.00 0.00 4.49
129 130 2.859165 AAGGATGATGTTGGACACGT 57.141 45.000 0.00 0.00 0.00 4.49
130 131 2.099141 AGGATGATGTTGGACACGTG 57.901 50.000 15.48 15.48 0.00 4.49
131 132 1.086696 GGATGATGTTGGACACGTGG 58.913 55.000 21.57 1.66 0.00 4.94
132 133 0.447801 GATGATGTTGGACACGTGGC 59.552 55.000 21.57 18.48 0.00 5.01
133 134 0.250684 ATGATGTTGGACACGTGGCA 60.251 50.000 25.47 12.08 0.00 4.92
134 135 0.884259 TGATGTTGGACACGTGGCAG 60.884 55.000 25.47 0.00 0.00 4.85
135 136 0.884704 GATGTTGGACACGTGGCAGT 60.885 55.000 25.47 3.08 0.00 4.40
136 137 0.884704 ATGTTGGACACGTGGCAGTC 60.885 55.000 25.47 12.60 0.00 3.51
137 138 1.522806 GTTGGACACGTGGCAGTCA 60.523 57.895 25.47 9.50 36.50 3.41
138 139 0.884704 GTTGGACACGTGGCAGTCAT 60.885 55.000 25.47 0.00 36.50 3.06
139 140 0.682292 TTGGACACGTGGCAGTCATA 59.318 50.000 25.47 0.00 36.50 2.15
140 141 0.901827 TGGACACGTGGCAGTCATAT 59.098 50.000 25.47 0.00 36.50 1.78
141 142 1.277842 TGGACACGTGGCAGTCATATT 59.722 47.619 25.47 0.00 36.50 1.28
142 143 1.665679 GGACACGTGGCAGTCATATTG 59.334 52.381 25.47 0.00 36.50 1.90
143 144 2.616960 GACACGTGGCAGTCATATTGA 58.383 47.619 18.77 0.00 34.93 2.57
144 145 3.198068 GACACGTGGCAGTCATATTGAT 58.802 45.455 18.77 0.00 34.93 2.57
145 146 4.368315 GACACGTGGCAGTCATATTGATA 58.632 43.478 18.77 0.00 34.93 2.15
146 147 4.371786 ACACGTGGCAGTCATATTGATAG 58.628 43.478 21.57 0.00 0.00 2.08
147 148 4.141937 ACACGTGGCAGTCATATTGATAGT 60.142 41.667 21.57 0.00 0.00 2.12
148 149 4.209911 CACGTGGCAGTCATATTGATAGTG 59.790 45.833 7.95 0.00 0.00 2.74
149 150 4.141937 ACGTGGCAGTCATATTGATAGTGT 60.142 41.667 0.00 0.00 0.00 3.55
150 151 4.811024 CGTGGCAGTCATATTGATAGTGTT 59.189 41.667 0.00 0.00 0.00 3.32
151 152 5.277011 CGTGGCAGTCATATTGATAGTGTTG 60.277 44.000 0.00 0.00 0.00 3.33
152 153 5.008019 GTGGCAGTCATATTGATAGTGTTGG 59.992 44.000 0.00 0.00 0.00 3.77
153 154 5.104569 TGGCAGTCATATTGATAGTGTTGGA 60.105 40.000 0.00 0.00 0.00 3.53
154 155 6.000219 GGCAGTCATATTGATAGTGTTGGAT 59.000 40.000 0.00 0.00 0.00 3.41
155 156 6.072838 GGCAGTCATATTGATAGTGTTGGATG 60.073 42.308 0.00 0.00 0.00 3.51
156 157 6.567321 GCAGTCATATTGATAGTGTTGGATGC 60.567 42.308 0.00 0.00 0.00 3.91
157 158 6.000219 AGTCATATTGATAGTGTTGGATGCC 59.000 40.000 0.00 0.00 0.00 4.40
158 159 5.764686 GTCATATTGATAGTGTTGGATGCCA 59.235 40.000 0.00 0.00 0.00 4.92
159 160 6.262944 GTCATATTGATAGTGTTGGATGCCAA 59.737 38.462 0.00 0.00 41.69 4.52
169 170 4.481112 GATGCCAACGCCGCCAAG 62.481 66.667 0.00 0.00 0.00 3.61
179 180 3.763671 CCGCCAAGGCTCTTGTTT 58.236 55.556 9.73 0.00 39.32 2.83
180 181 1.581447 CCGCCAAGGCTCTTGTTTC 59.419 57.895 9.73 3.16 39.32 2.78
181 182 0.890996 CCGCCAAGGCTCTTGTTTCT 60.891 55.000 9.73 0.00 39.32 2.52
182 183 0.519077 CGCCAAGGCTCTTGTTTCTC 59.481 55.000 9.73 0.00 39.32 2.87
183 184 0.519077 GCCAAGGCTCTTGTTTCTCG 59.481 55.000 3.29 0.44 38.26 4.04
184 185 1.884235 CCAAGGCTCTTGTTTCTCGT 58.116 50.000 12.18 0.00 0.00 4.18
185 186 1.801178 CCAAGGCTCTTGTTTCTCGTC 59.199 52.381 12.18 0.00 0.00 4.20
186 187 2.483876 CAAGGCTCTTGTTTCTCGTCA 58.516 47.619 6.74 0.00 0.00 4.35
187 188 2.447244 AGGCTCTTGTTTCTCGTCAG 57.553 50.000 0.00 0.00 0.00 3.51
188 189 0.793250 GGCTCTTGTTTCTCGTCAGC 59.207 55.000 0.00 0.00 0.00 4.26
189 190 1.502231 GCTCTTGTTTCTCGTCAGCA 58.498 50.000 0.00 0.00 0.00 4.41
190 191 1.193426 GCTCTTGTTTCTCGTCAGCAC 59.807 52.381 0.00 0.00 0.00 4.40
191 192 2.748605 CTCTTGTTTCTCGTCAGCACT 58.251 47.619 0.00 0.00 0.00 4.40
192 193 2.473816 TCTTGTTTCTCGTCAGCACTG 58.526 47.619 0.00 0.00 0.00 3.66
193 194 1.528586 CTTGTTTCTCGTCAGCACTGG 59.471 52.381 0.00 0.00 0.00 4.00
194 195 0.249868 TGTTTCTCGTCAGCACTGGG 60.250 55.000 0.00 0.00 0.00 4.45
195 196 0.249911 GTTTCTCGTCAGCACTGGGT 60.250 55.000 0.00 0.00 0.00 4.51
196 197 0.468226 TTTCTCGTCAGCACTGGGTT 59.532 50.000 0.00 0.00 0.00 4.11
197 198 0.468226 TTCTCGTCAGCACTGGGTTT 59.532 50.000 0.00 0.00 0.00 3.27
198 199 0.468226 TCTCGTCAGCACTGGGTTTT 59.532 50.000 0.00 0.00 0.00 2.43
199 200 1.134220 TCTCGTCAGCACTGGGTTTTT 60.134 47.619 0.00 0.00 0.00 1.94
200 201 1.264288 CTCGTCAGCACTGGGTTTTTC 59.736 52.381 0.00 0.00 0.00 2.29
201 202 1.134220 TCGTCAGCACTGGGTTTTTCT 60.134 47.619 0.00 0.00 0.00 2.52
202 203 1.002468 CGTCAGCACTGGGTTTTTCTG 60.002 52.381 0.00 0.00 0.00 3.02
203 204 1.032014 TCAGCACTGGGTTTTTCTGC 58.968 50.000 0.00 0.00 0.00 4.26
204 205 0.746063 CAGCACTGGGTTTTTCTGCA 59.254 50.000 0.00 0.00 0.00 4.41
205 206 0.746659 AGCACTGGGTTTTTCTGCAC 59.253 50.000 0.00 0.00 0.00 4.57
206 207 0.249447 GCACTGGGTTTTTCTGCACC 60.249 55.000 0.00 0.00 0.00 5.01
207 208 0.030638 CACTGGGTTTTTCTGCACCG 59.969 55.000 0.00 0.00 33.34 4.94
208 209 1.106944 ACTGGGTTTTTCTGCACCGG 61.107 55.000 0.00 0.00 33.34 5.28
209 210 1.076632 TGGGTTTTTCTGCACCGGT 60.077 52.632 0.00 0.00 33.34 5.28
210 211 1.362355 GGGTTTTTCTGCACCGGTG 59.638 57.895 30.66 30.66 33.34 4.94
211 212 1.104577 GGGTTTTTCTGCACCGGTGA 61.105 55.000 38.30 20.99 33.34 4.02
212 213 0.958822 GGTTTTTCTGCACCGGTGAT 59.041 50.000 38.30 0.00 0.00 3.06
213 214 1.068541 GGTTTTTCTGCACCGGTGATC 60.069 52.381 38.30 21.43 0.00 2.92
214 215 1.880027 GTTTTTCTGCACCGGTGATCT 59.120 47.619 38.30 0.00 0.00 2.75
215 216 1.522668 TTTTCTGCACCGGTGATCTG 58.477 50.000 38.30 23.06 0.00 2.90
216 217 0.396435 TTTCTGCACCGGTGATCTGT 59.604 50.000 38.30 0.00 0.00 3.41
217 218 0.396435 TTCTGCACCGGTGATCTGTT 59.604 50.000 38.30 0.00 0.00 3.16
218 219 0.037326 TCTGCACCGGTGATCTGTTC 60.037 55.000 38.30 18.37 0.00 3.18
219 220 1.354337 CTGCACCGGTGATCTGTTCG 61.354 60.000 38.30 8.74 0.00 3.95
220 221 1.080093 GCACCGGTGATCTGTTCGA 60.080 57.895 38.30 0.00 0.00 3.71
221 222 0.460284 GCACCGGTGATCTGTTCGAT 60.460 55.000 38.30 0.00 34.25 3.59
222 223 1.280982 CACCGGTGATCTGTTCGATG 58.719 55.000 31.31 0.00 30.84 3.84
223 224 0.175760 ACCGGTGATCTGTTCGATGG 59.824 55.000 6.12 0.00 30.84 3.51
224 225 0.175760 CCGGTGATCTGTTCGATGGT 59.824 55.000 0.00 0.00 30.84 3.55
225 226 1.280982 CGGTGATCTGTTCGATGGTG 58.719 55.000 0.00 0.00 30.84 4.17
226 227 1.009829 GGTGATCTGTTCGATGGTGC 58.990 55.000 0.00 0.00 30.84 5.01
227 228 0.647410 GTGATCTGTTCGATGGTGCG 59.353 55.000 0.00 0.00 30.84 5.34
228 229 0.246360 TGATCTGTTCGATGGTGCGT 59.754 50.000 0.00 0.00 30.84 5.24
229 230 0.647410 GATCTGTTCGATGGTGCGTG 59.353 55.000 0.00 0.00 30.84 5.34
230 231 1.361668 ATCTGTTCGATGGTGCGTGC 61.362 55.000 0.00 0.00 0.00 5.34
231 232 2.280457 TGTTCGATGGTGCGTGCA 60.280 55.556 0.00 0.00 0.00 4.57
232 233 2.231745 CTGTTCGATGGTGCGTGCAG 62.232 60.000 0.00 0.00 0.00 4.41
233 234 2.741985 TTCGATGGTGCGTGCAGG 60.742 61.111 1.01 1.01 0.00 4.85
234 235 4.758251 TCGATGGTGCGTGCAGGG 62.758 66.667 8.72 0.00 0.00 4.45
244 245 3.134127 GTGCAGGGCCAACCGATC 61.134 66.667 6.18 0.00 46.96 3.69
245 246 4.776322 TGCAGGGCCAACCGATCG 62.776 66.667 8.51 8.51 46.96 3.69
246 247 4.467084 GCAGGGCCAACCGATCGA 62.467 66.667 18.66 0.00 46.96 3.59
247 248 2.202932 CAGGGCCAACCGATCGAG 60.203 66.667 18.66 9.42 46.96 4.04
248 249 4.162690 AGGGCCAACCGATCGAGC 62.163 66.667 18.66 13.28 46.96 5.03
249 250 4.162690 GGGCCAACCGATCGAGCT 62.163 66.667 18.66 0.00 36.48 4.09
250 251 2.892425 GGCCAACCGATCGAGCTG 60.892 66.667 18.66 10.18 0.00 4.24
251 252 2.892425 GCCAACCGATCGAGCTGG 60.892 66.667 18.66 19.31 0.00 4.85
252 253 2.892425 CCAACCGATCGAGCTGGC 60.892 66.667 18.66 0.00 0.00 4.85
253 254 2.892425 CAACCGATCGAGCTGGCC 60.892 66.667 18.66 0.00 0.00 5.36
254 255 4.514577 AACCGATCGAGCTGGCCG 62.515 66.667 18.66 0.00 0.00 6.13
256 257 4.207281 CCGATCGAGCTGGCCGAA 62.207 66.667 18.66 0.00 39.62 4.30
257 258 2.028190 CGATCGAGCTGGCCGAAT 59.972 61.111 10.26 0.00 39.62 3.34
276 277 0.034186 TCCTGGTCACATGCCAATCC 60.034 55.000 0.00 0.00 35.32 3.01
314 315 7.787725 GGGACGTTGAAACTTCTTCATATAT 57.212 36.000 0.00 0.00 0.00 0.86
331 332 9.971922 CTTCATATATTTCCTGTCAAAAATCCC 57.028 33.333 0.00 0.00 0.00 3.85
363 364 0.319900 ATATGTCGCGTCCATCTGGC 60.320 55.000 15.32 0.00 34.44 4.85
459 662 3.044305 GTCGACCAGCAGCACCAC 61.044 66.667 3.51 0.00 0.00 4.16
599 847 0.947244 CAACACCTCAAGCACACTCC 59.053 55.000 0.00 0.00 0.00 3.85
632 883 0.533308 TGCCCAACACGTACCTCAAC 60.533 55.000 0.00 0.00 0.00 3.18
935 1186 7.728847 AAGAAGAAGAAGAAGAAGAAGAAGC 57.271 36.000 0.00 0.00 0.00 3.86
936 1187 7.066307 AGAAGAAGAAGAAGAAGAAGAAGCT 57.934 36.000 0.00 0.00 0.00 3.74
937 1188 7.154656 AGAAGAAGAAGAAGAAGAAGAAGCTC 58.845 38.462 0.00 0.00 0.00 4.09
1011 1262 2.440409 CAGCTAGCAATGGACTTTGGT 58.560 47.619 18.83 7.60 40.25 3.67
1662 1913 0.733729 CGTACTGGGAGAACGGAGAG 59.266 60.000 0.00 0.00 33.13 3.20
1742 2022 3.636764 GTGGGTTCACACTGAGGATTTTT 59.363 43.478 0.00 0.00 43.13 1.94
1765 2045 1.002624 TCCCGATTGGACCAACTGC 60.003 57.895 9.67 1.22 38.61 4.40
1895 2189 1.067142 GCCTGAATGTCACTGTCGGTA 60.067 52.381 0.00 0.00 0.00 4.02
1898 2192 3.428180 CCTGAATGTCACTGTCGGTAGAG 60.428 52.174 0.00 0.00 0.00 2.43
1938 2321 3.130633 GGTTTGCAGAATGGTTCCAAAC 58.869 45.455 12.25 12.25 42.55 2.93
1977 2360 1.002366 GTGTGCTCATCATGACGGAC 58.998 55.000 0.00 1.76 0.00 4.79
1988 2371 0.320421 ATGACGGACCAACCAGAACG 60.320 55.000 0.00 0.00 38.90 3.95
1989 2372 1.068585 GACGGACCAACCAGAACGT 59.931 57.895 0.00 0.00 38.90 3.99
1990 2373 0.314935 GACGGACCAACCAGAACGTA 59.685 55.000 0.00 0.00 38.90 3.57
1991 2374 0.032540 ACGGACCAACCAGAACGTAC 59.967 55.000 0.00 0.00 38.90 3.67
2016 2399 7.438459 ACCAGAAATATCTTACGAGTAATGCAC 59.562 37.037 0.00 0.00 32.03 4.57
2085 2468 1.325943 GCTGTCGCTTCACTCATTAGC 59.674 52.381 0.00 0.00 0.00 3.09
2105 2488 2.831526 GCCATTAGTGGGGTTGTTGAAT 59.168 45.455 6.38 0.00 46.14 2.57
2110 2493 6.406849 CCATTAGTGGGGTTGTTGAATAATGG 60.407 42.308 0.00 0.00 42.11 3.16
2146 2529 0.250081 GCTCTCGCCAATTAGAGGGG 60.250 60.000 5.36 0.00 39.73 4.79
2153 2536 1.879796 GCCAATTAGAGGGGAGATGCG 60.880 57.143 0.00 0.00 0.00 4.73
2172 2555 2.540515 CGAAAGATGTGGTATGTCGCT 58.459 47.619 0.00 0.00 0.00 4.93
2173 2556 2.930040 CGAAAGATGTGGTATGTCGCTT 59.070 45.455 0.00 0.00 0.00 4.68
2217 2600 9.587772 TTGATACTACAGTGCTAGATTTTCTTC 57.412 33.333 0.00 0.00 0.00 2.87
2222 2605 3.619038 CAGTGCTAGATTTTCTTCGGGAC 59.381 47.826 0.00 0.00 0.00 4.46
2259 2642 2.543383 CGCGAATGATCTGCGAGC 59.457 61.111 0.00 4.14 45.06 5.03
2261 2644 1.563655 GCGAATGATCTGCGAGCAG 59.436 57.895 18.20 18.20 44.86 4.24
2263 2646 1.284657 CGAATGATCTGCGAGCAGTT 58.715 50.000 22.47 15.61 43.96 3.16
2268 2651 1.273327 TGATCTGCGAGCAGTTCTTGA 59.727 47.619 26.54 11.89 43.96 3.02
2269 2652 2.289010 TGATCTGCGAGCAGTTCTTGAA 60.289 45.455 26.54 11.62 43.96 2.69
2270 2653 2.462456 TCTGCGAGCAGTTCTTGAAT 57.538 45.000 22.47 0.00 43.96 2.57
2271 2654 2.771089 TCTGCGAGCAGTTCTTGAATT 58.229 42.857 22.47 0.00 43.96 2.17
2272 2655 2.738846 TCTGCGAGCAGTTCTTGAATTC 59.261 45.455 22.47 0.00 43.96 2.17
2273 2656 1.806542 TGCGAGCAGTTCTTGAATTCC 59.193 47.619 2.27 0.00 0.00 3.01
2278 2661 3.594134 AGCAGTTCTTGAATTCCGAGAG 58.406 45.455 2.27 0.00 36.68 3.20
2317 2700 8.122472 AGGTTGATCCGAAAATAGATTTTGTT 57.878 30.769 4.98 0.00 39.86 2.83
2318 2701 8.028938 AGGTTGATCCGAAAATAGATTTTGTTG 58.971 33.333 4.98 0.00 39.86 3.33
2326 2709 7.596995 CCGAAAATAGATTTTGTTGTAAGCCAA 59.403 33.333 4.98 0.00 39.86 4.52
2328 2711 9.691362 GAAAATAGATTTTGTTGTAAGCCAAGA 57.309 29.630 4.98 0.00 39.86 3.02
2338 2721 2.881513 TGTAAGCCAAGACAAATCGCAA 59.118 40.909 0.00 0.00 0.00 4.85
2339 2722 2.422276 AAGCCAAGACAAATCGCAAC 57.578 45.000 0.00 0.00 0.00 4.17
2357 2740 1.228675 CCTGAAGGGTGGCAAAGCT 60.229 57.895 0.00 0.00 0.00 3.74
2358 2741 0.829182 CCTGAAGGGTGGCAAAGCTT 60.829 55.000 0.00 0.00 0.00 3.74
2359 2742 1.043022 CTGAAGGGTGGCAAAGCTTT 58.957 50.000 5.69 5.69 0.00 3.51
2360 2743 1.413812 CTGAAGGGTGGCAAAGCTTTT 59.586 47.619 9.53 0.00 0.00 2.27
2362 2745 0.469494 AAGGGTGGCAAAGCTTTTGG 59.531 50.000 9.53 0.00 0.00 3.28
2363 2746 1.597854 GGGTGGCAAAGCTTTTGGC 60.598 57.895 20.55 20.55 44.16 4.52
2365 2748 1.447217 GTGGCAAAGCTTTTGGCCT 59.553 52.632 30.09 1.43 46.53 5.19
2366 2749 0.881600 GTGGCAAAGCTTTTGGCCTG 60.882 55.000 30.09 13.92 46.53 4.85
2367 2750 1.301953 GGCAAAGCTTTTGGCCTGG 60.302 57.895 25.74 9.15 43.09 4.45
2368 2751 1.301953 GCAAAGCTTTTGGCCTGGG 60.302 57.895 9.53 0.00 43.05 4.45
2369 2752 2.043604 GCAAAGCTTTTGGCCTGGGT 62.044 55.000 9.53 0.00 43.05 4.51
2371 2754 1.691434 CAAAGCTTTTGGCCTGGGTTA 59.309 47.619 9.53 0.00 43.05 2.85
2372 2755 2.302733 CAAAGCTTTTGGCCTGGGTTAT 59.697 45.455 9.53 0.00 43.05 1.89
2375 2758 3.096852 AGCTTTTGGCCTGGGTTATAAC 58.903 45.455 3.32 7.09 43.05 1.89
2377 2760 4.383897 GCTTTTGGCCTGGGTTATAACCA 61.384 47.826 30.94 18.19 42.19 3.67
2433 3250 6.670695 AAAAACATAAAATCTGGGCTGAGT 57.329 33.333 0.00 0.00 0.00 3.41
2434 3251 6.670695 AAAACATAAAATCTGGGCTGAGTT 57.329 33.333 0.00 0.00 0.00 3.01
2435 3252 5.904362 AACATAAAATCTGGGCTGAGTTC 57.096 39.130 0.00 0.00 0.00 3.01
2436 3253 4.922206 ACATAAAATCTGGGCTGAGTTCA 58.078 39.130 0.00 0.00 0.00 3.18
2437 3254 5.513233 ACATAAAATCTGGGCTGAGTTCAT 58.487 37.500 0.00 0.00 0.00 2.57
2438 3255 6.662755 ACATAAAATCTGGGCTGAGTTCATA 58.337 36.000 0.00 0.00 0.00 2.15
2439 3256 7.118723 ACATAAAATCTGGGCTGAGTTCATAA 58.881 34.615 0.00 0.00 0.00 1.90
2440 3257 7.615365 ACATAAAATCTGGGCTGAGTTCATAAA 59.385 33.333 0.00 0.00 0.00 1.40
2441 3258 6.916360 AAAATCTGGGCTGAGTTCATAAAA 57.084 33.333 0.00 0.00 0.00 1.52
2442 3259 7.486407 AAAATCTGGGCTGAGTTCATAAAAT 57.514 32.000 0.00 0.00 0.00 1.82
2443 3260 7.486407 AAATCTGGGCTGAGTTCATAAAATT 57.514 32.000 0.00 0.00 0.00 1.82
2444 3261 7.486407 AATCTGGGCTGAGTTCATAAAATTT 57.514 32.000 0.00 0.00 0.00 1.82
2445 3262 6.271488 TCTGGGCTGAGTTCATAAAATTTG 57.729 37.500 0.00 0.00 0.00 2.32
2446 3263 6.009589 TCTGGGCTGAGTTCATAAAATTTGA 58.990 36.000 0.00 0.00 0.00 2.69
2447 3264 6.664816 TCTGGGCTGAGTTCATAAAATTTGAT 59.335 34.615 0.00 0.00 0.00 2.57
2448 3265 7.178983 TCTGGGCTGAGTTCATAAAATTTGATT 59.821 33.333 0.00 0.00 0.00 2.57
2449 3266 8.359875 TGGGCTGAGTTCATAAAATTTGATTA 57.640 30.769 0.00 0.00 0.00 1.75
2450 3267 8.811017 TGGGCTGAGTTCATAAAATTTGATTAA 58.189 29.630 0.00 0.00 0.00 1.40
2451 3268 9.651913 GGGCTGAGTTCATAAAATTTGATTAAA 57.348 29.630 0.00 0.00 0.00 1.52
2517 3334 4.670227 ATGCTAGTTGAGAAAAGTTCGC 57.330 40.909 0.00 0.00 34.02 4.70
2526 3343 6.797033 AGTTGAGAAAAGTTCGCGAATATTTG 59.203 34.615 28.14 0.00 31.63 2.32
2531 3348 6.419413 AGAAAAGTTCGCGAATATTTGCAAAA 59.581 30.769 28.14 15.72 37.43 2.44
2532 3349 5.745653 AAGTTCGCGAATATTTGCAAAAG 57.254 34.783 26.23 10.40 37.43 2.27
2535 3352 5.918011 AGTTCGCGAATATTTGCAAAAGAAA 59.082 32.000 26.23 2.69 37.43 2.52
2536 3353 6.419413 AGTTCGCGAATATTTGCAAAAGAAAA 59.581 30.769 26.23 0.10 37.43 2.29
2537 3354 6.134787 TCGCGAATATTTGCAAAAGAAAAC 57.865 33.333 24.18 4.38 37.43 2.43
2538 3355 5.000296 CGCGAATATTTGCAAAAGAAAACG 59.000 37.500 24.18 16.62 37.43 3.60
2539 3356 5.386933 CGCGAATATTTGCAAAAGAAAACGT 60.387 36.000 24.18 0.00 37.43 3.99
2541 3358 6.345408 GCGAATATTTGCAAAAGAAAACGTGA 60.345 34.615 20.76 0.00 37.52 4.35
2654 3471 8.647143 AAAAGTTCATGTTGGAAATACTTGTG 57.353 30.769 0.00 0.00 0.00 3.33
2655 3472 7.581213 AAGTTCATGTTGGAAATACTTGTGA 57.419 32.000 0.00 0.00 0.00 3.58
2656 3473 6.970484 AGTTCATGTTGGAAATACTTGTGAC 58.030 36.000 0.00 0.00 0.00 3.67
2657 3474 6.545666 AGTTCATGTTGGAAATACTTGTGACA 59.454 34.615 0.00 0.00 0.00 3.58
2658 3475 7.231317 AGTTCATGTTGGAAATACTTGTGACAT 59.769 33.333 0.00 0.00 0.00 3.06
2659 3476 7.523293 TCATGTTGGAAATACTTGTGACATT 57.477 32.000 0.00 0.00 0.00 2.71
2660 3477 7.950512 TCATGTTGGAAATACTTGTGACATTT 58.049 30.769 0.00 0.00 0.00 2.32
2661 3478 8.420222 TCATGTTGGAAATACTTGTGACATTTT 58.580 29.630 0.00 0.00 0.00 1.82
2662 3479 8.489559 CATGTTGGAAATACTTGTGACATTTTG 58.510 33.333 0.00 0.00 0.00 2.44
2663 3480 7.776107 TGTTGGAAATACTTGTGACATTTTGA 58.224 30.769 0.00 0.00 0.00 2.69
2664 3481 8.253810 TGTTGGAAATACTTGTGACATTTTGAA 58.746 29.630 0.00 0.00 0.00 2.69
2665 3482 9.092876 GTTGGAAATACTTGTGACATTTTGAAA 57.907 29.630 0.00 0.00 0.00 2.69
2666 3483 9.658799 TTGGAAATACTTGTGACATTTTGAAAA 57.341 25.926 0.00 0.00 0.00 2.29
2667 3484 9.658799 TGGAAATACTTGTGACATTTTGAAAAA 57.341 25.926 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.269363 GGACGAATACCGATACAACAAAGG 59.731 45.833 0.00 0.00 41.76 3.11
1 2 5.385396 GGACGAATACCGATACAACAAAG 57.615 43.478 0.00 0.00 41.76 2.77
13 14 3.069289 AGTGAAAAACCGGACGAATACC 58.931 45.455 9.46 0.00 0.00 2.73
14 15 5.406477 AGTTAGTGAAAAACCGGACGAATAC 59.594 40.000 9.46 0.00 0.00 1.89
15 16 5.540911 AGTTAGTGAAAAACCGGACGAATA 58.459 37.500 9.46 0.00 0.00 1.75
16 17 4.383173 AGTTAGTGAAAAACCGGACGAAT 58.617 39.130 9.46 0.00 0.00 3.34
17 18 3.795877 AGTTAGTGAAAAACCGGACGAA 58.204 40.909 9.46 0.00 0.00 3.85
18 19 3.457610 AGTTAGTGAAAAACCGGACGA 57.542 42.857 9.46 0.00 0.00 4.20
19 20 5.655893 TTTAGTTAGTGAAAAACCGGACG 57.344 39.130 9.46 0.00 0.00 4.79
20 21 6.205270 TCCATTTAGTTAGTGAAAAACCGGAC 59.795 38.462 9.46 0.00 0.00 4.79
21 22 6.205270 GTCCATTTAGTTAGTGAAAAACCGGA 59.795 38.462 9.46 0.00 0.00 5.14
22 23 6.016943 TGTCCATTTAGTTAGTGAAAAACCGG 60.017 38.462 0.00 0.00 0.00 5.28
23 24 6.961576 TGTCCATTTAGTTAGTGAAAAACCG 58.038 36.000 0.00 0.00 0.00 4.44
24 25 9.758651 AATTGTCCATTTAGTTAGTGAAAAACC 57.241 29.630 0.00 0.00 0.00 3.27
31 32 9.965824 ACAAGAAAATTGTCCATTTAGTTAGTG 57.034 29.630 0.00 0.00 33.60 2.74
66 67 8.907885 GGAGGCAAAAACTTTATCTCATCTATT 58.092 33.333 0.00 0.00 0.00 1.73
67 68 7.227512 CGGAGGCAAAAACTTTATCTCATCTAT 59.772 37.037 0.00 0.00 0.00 1.98
68 69 6.538742 CGGAGGCAAAAACTTTATCTCATCTA 59.461 38.462 0.00 0.00 0.00 1.98
69 70 5.355350 CGGAGGCAAAAACTTTATCTCATCT 59.645 40.000 0.00 0.00 0.00 2.90
70 71 5.123979 ACGGAGGCAAAAACTTTATCTCATC 59.876 40.000 0.00 0.00 0.00 2.92
71 72 5.010282 ACGGAGGCAAAAACTTTATCTCAT 58.990 37.500 0.00 0.00 0.00 2.90
72 73 4.394729 ACGGAGGCAAAAACTTTATCTCA 58.605 39.130 0.00 0.00 0.00 3.27
73 74 5.372547 AACGGAGGCAAAAACTTTATCTC 57.627 39.130 0.00 0.00 0.00 2.75
74 75 5.300792 TGAAACGGAGGCAAAAACTTTATCT 59.699 36.000 0.00 0.00 0.00 1.98
75 76 5.525199 TGAAACGGAGGCAAAAACTTTATC 58.475 37.500 0.00 0.00 0.00 1.75
76 77 5.523438 TGAAACGGAGGCAAAAACTTTAT 57.477 34.783 0.00 0.00 0.00 1.40
77 78 4.985538 TGAAACGGAGGCAAAAACTTTA 57.014 36.364 0.00 0.00 0.00 1.85
78 79 3.878160 TGAAACGGAGGCAAAAACTTT 57.122 38.095 0.00 0.00 0.00 2.66
79 80 3.878160 TTGAAACGGAGGCAAAAACTT 57.122 38.095 0.00 0.00 0.00 2.66
80 81 3.878160 TTTGAAACGGAGGCAAAAACT 57.122 38.095 0.00 0.00 0.00 2.66
81 82 4.930463 TTTTTGAAACGGAGGCAAAAAC 57.070 36.364 12.95 0.00 42.89 2.43
102 103 8.405531 CGTGTCCAACATCATCCTTAATATTTT 58.594 33.333 0.00 0.00 0.00 1.82
103 104 7.556275 ACGTGTCCAACATCATCCTTAATATTT 59.444 33.333 0.00 0.00 0.00 1.40
104 105 7.012327 CACGTGTCCAACATCATCCTTAATATT 59.988 37.037 7.58 0.00 0.00 1.28
105 106 6.483307 CACGTGTCCAACATCATCCTTAATAT 59.517 38.462 7.58 0.00 0.00 1.28
106 107 5.815222 CACGTGTCCAACATCATCCTTAATA 59.185 40.000 7.58 0.00 0.00 0.98
107 108 4.635765 CACGTGTCCAACATCATCCTTAAT 59.364 41.667 7.58 0.00 0.00 1.40
108 109 4.000325 CACGTGTCCAACATCATCCTTAA 59.000 43.478 7.58 0.00 0.00 1.85
109 110 3.595173 CACGTGTCCAACATCATCCTTA 58.405 45.455 7.58 0.00 0.00 2.69
110 111 2.426522 CACGTGTCCAACATCATCCTT 58.573 47.619 7.58 0.00 0.00 3.36
111 112 1.339055 CCACGTGTCCAACATCATCCT 60.339 52.381 15.65 0.00 0.00 3.24
112 113 1.086696 CCACGTGTCCAACATCATCC 58.913 55.000 15.65 0.00 0.00 3.51
113 114 0.447801 GCCACGTGTCCAACATCATC 59.552 55.000 15.65 0.00 0.00 2.92
114 115 0.250684 TGCCACGTGTCCAACATCAT 60.251 50.000 15.65 0.00 0.00 2.45
115 116 0.884259 CTGCCACGTGTCCAACATCA 60.884 55.000 15.65 0.00 0.00 3.07
116 117 0.884704 ACTGCCACGTGTCCAACATC 60.885 55.000 15.65 0.00 0.00 3.06
117 118 0.884704 GACTGCCACGTGTCCAACAT 60.885 55.000 15.65 0.14 0.00 2.71
118 119 1.522806 GACTGCCACGTGTCCAACA 60.523 57.895 15.65 3.73 0.00 3.33
119 120 0.884704 ATGACTGCCACGTGTCCAAC 60.885 55.000 15.65 8.59 32.67 3.77
120 121 0.682292 TATGACTGCCACGTGTCCAA 59.318 50.000 15.65 0.00 32.67 3.53
121 122 0.901827 ATATGACTGCCACGTGTCCA 59.098 50.000 15.65 10.20 32.67 4.02
122 123 1.665679 CAATATGACTGCCACGTGTCC 59.334 52.381 15.65 5.64 32.67 4.02
123 124 2.616960 TCAATATGACTGCCACGTGTC 58.383 47.619 15.65 0.98 0.00 3.67
124 125 2.760634 TCAATATGACTGCCACGTGT 57.239 45.000 15.65 0.00 0.00 4.49
125 126 4.209911 CACTATCAATATGACTGCCACGTG 59.790 45.833 9.08 9.08 0.00 4.49
126 127 4.141937 ACACTATCAATATGACTGCCACGT 60.142 41.667 0.00 0.00 0.00 4.49
127 128 4.371786 ACACTATCAATATGACTGCCACG 58.628 43.478 0.00 0.00 0.00 4.94
128 129 5.008019 CCAACACTATCAATATGACTGCCAC 59.992 44.000 0.00 0.00 0.00 5.01
129 130 5.104569 TCCAACACTATCAATATGACTGCCA 60.105 40.000 0.00 0.00 0.00 4.92
130 131 5.368145 TCCAACACTATCAATATGACTGCC 58.632 41.667 0.00 0.00 0.00 4.85
131 132 6.567321 GCATCCAACACTATCAATATGACTGC 60.567 42.308 0.00 0.00 0.00 4.40
132 133 6.072838 GGCATCCAACACTATCAATATGACTG 60.073 42.308 0.00 0.00 0.00 3.51
133 134 6.000219 GGCATCCAACACTATCAATATGACT 59.000 40.000 0.00 0.00 0.00 3.41
134 135 5.764686 TGGCATCCAACACTATCAATATGAC 59.235 40.000 0.00 0.00 0.00 3.06
135 136 5.939447 TGGCATCCAACACTATCAATATGA 58.061 37.500 0.00 0.00 0.00 2.15
136 137 6.638096 TTGGCATCCAACACTATCAATATG 57.362 37.500 0.00 0.00 38.75 1.78
152 153 4.481112 CTTGGCGGCGTTGGCATC 62.481 66.667 9.37 0.00 44.53 3.91
162 163 0.890996 AGAAACAAGAGCCTTGGCGG 60.891 55.000 16.21 0.62 0.00 6.13
163 164 0.519077 GAGAAACAAGAGCCTTGGCG 59.481 55.000 16.21 0.00 0.00 5.69
164 165 0.519077 CGAGAAACAAGAGCCTTGGC 59.481 55.000 16.21 2.97 0.00 4.52
165 166 1.801178 GACGAGAAACAAGAGCCTTGG 59.199 52.381 16.21 3.63 0.00 3.61
166 167 2.478134 CTGACGAGAAACAAGAGCCTTG 59.522 50.000 11.87 11.87 0.00 3.61
167 168 2.760374 CTGACGAGAAACAAGAGCCTT 58.240 47.619 0.00 0.00 0.00 4.35
168 169 1.606737 GCTGACGAGAAACAAGAGCCT 60.607 52.381 0.00 0.00 0.00 4.58
169 170 0.793250 GCTGACGAGAAACAAGAGCC 59.207 55.000 0.00 0.00 0.00 4.70
170 171 1.193426 GTGCTGACGAGAAACAAGAGC 59.807 52.381 0.00 0.00 0.00 4.09
171 172 2.474359 CAGTGCTGACGAGAAACAAGAG 59.526 50.000 0.00 0.00 0.00 2.85
172 173 2.473816 CAGTGCTGACGAGAAACAAGA 58.526 47.619 0.00 0.00 0.00 3.02
173 174 1.528586 CCAGTGCTGACGAGAAACAAG 59.471 52.381 0.02 0.00 0.00 3.16
174 175 1.581934 CCAGTGCTGACGAGAAACAA 58.418 50.000 0.02 0.00 0.00 2.83
175 176 0.249868 CCCAGTGCTGACGAGAAACA 60.250 55.000 0.02 0.00 0.00 2.83
176 177 0.249911 ACCCAGTGCTGACGAGAAAC 60.250 55.000 0.02 0.00 0.00 2.78
177 178 0.468226 AACCCAGTGCTGACGAGAAA 59.532 50.000 0.02 0.00 0.00 2.52
178 179 0.468226 AAACCCAGTGCTGACGAGAA 59.532 50.000 0.02 0.00 0.00 2.87
179 180 0.468226 AAAACCCAGTGCTGACGAGA 59.532 50.000 0.02 0.00 0.00 4.04
180 181 1.264288 GAAAAACCCAGTGCTGACGAG 59.736 52.381 0.02 0.00 0.00 4.18
181 182 1.134220 AGAAAAACCCAGTGCTGACGA 60.134 47.619 0.02 0.00 0.00 4.20
182 183 1.002468 CAGAAAAACCCAGTGCTGACG 60.002 52.381 0.02 0.00 0.00 4.35
183 184 1.269257 GCAGAAAAACCCAGTGCTGAC 60.269 52.381 0.02 0.00 0.00 3.51
184 185 1.032014 GCAGAAAAACCCAGTGCTGA 58.968 50.000 0.02 0.00 0.00 4.26
185 186 0.746063 TGCAGAAAAACCCAGTGCTG 59.254 50.000 0.00 0.00 35.11 4.41
186 187 0.746659 GTGCAGAAAAACCCAGTGCT 59.253 50.000 0.00 0.00 35.11 4.40
187 188 0.249447 GGTGCAGAAAAACCCAGTGC 60.249 55.000 0.00 0.00 34.62 4.40
188 189 0.030638 CGGTGCAGAAAAACCCAGTG 59.969 55.000 0.00 0.00 32.44 3.66
189 190 1.106944 CCGGTGCAGAAAAACCCAGT 61.107 55.000 0.00 0.00 32.44 4.00
190 191 1.106944 ACCGGTGCAGAAAAACCCAG 61.107 55.000 6.12 0.00 32.44 4.45
191 192 1.076632 ACCGGTGCAGAAAAACCCA 60.077 52.632 6.12 0.00 32.44 4.51
192 193 1.104577 TCACCGGTGCAGAAAAACCC 61.105 55.000 30.25 0.00 32.44 4.11
193 194 0.958822 ATCACCGGTGCAGAAAAACC 59.041 50.000 30.25 0.00 0.00 3.27
194 195 1.880027 AGATCACCGGTGCAGAAAAAC 59.120 47.619 30.25 10.21 0.00 2.43
195 196 1.879380 CAGATCACCGGTGCAGAAAAA 59.121 47.619 30.25 11.28 0.00 1.94
196 197 1.202758 ACAGATCACCGGTGCAGAAAA 60.203 47.619 30.25 12.09 0.00 2.29
197 198 0.396435 ACAGATCACCGGTGCAGAAA 59.604 50.000 30.25 12.91 0.00 2.52
198 199 0.396435 AACAGATCACCGGTGCAGAA 59.604 50.000 30.25 13.34 0.00 3.02
199 200 0.037326 GAACAGATCACCGGTGCAGA 60.037 55.000 30.25 13.75 0.00 4.26
200 201 1.354337 CGAACAGATCACCGGTGCAG 61.354 60.000 30.25 19.62 0.00 4.41
201 202 1.374125 CGAACAGATCACCGGTGCA 60.374 57.895 30.25 18.56 0.00 4.57
202 203 0.460284 ATCGAACAGATCACCGGTGC 60.460 55.000 30.25 16.85 33.45 5.01
203 204 1.280982 CATCGAACAGATCACCGGTG 58.719 55.000 29.26 29.26 37.52 4.94
204 205 0.175760 CCATCGAACAGATCACCGGT 59.824 55.000 0.00 0.00 37.52 5.28
205 206 0.175760 ACCATCGAACAGATCACCGG 59.824 55.000 0.00 0.00 37.52 5.28
206 207 1.280982 CACCATCGAACAGATCACCG 58.719 55.000 0.00 0.00 37.52 4.94
207 208 1.009829 GCACCATCGAACAGATCACC 58.990 55.000 0.00 0.00 37.52 4.02
208 209 0.647410 CGCACCATCGAACAGATCAC 59.353 55.000 0.00 0.00 37.52 3.06
209 210 0.246360 ACGCACCATCGAACAGATCA 59.754 50.000 0.00 0.00 37.52 2.92
210 211 0.647410 CACGCACCATCGAACAGATC 59.353 55.000 0.00 0.00 37.52 2.75
211 212 1.361668 GCACGCACCATCGAACAGAT 61.362 55.000 0.00 0.00 41.01 2.90
212 213 2.027073 GCACGCACCATCGAACAGA 61.027 57.895 0.00 0.00 0.00 3.41
213 214 2.231745 CTGCACGCACCATCGAACAG 62.232 60.000 0.00 0.00 32.93 3.16
214 215 2.280457 TGCACGCACCATCGAACA 60.280 55.556 0.00 0.00 0.00 3.18
215 216 2.476051 CTGCACGCACCATCGAAC 59.524 61.111 0.00 0.00 0.00 3.95
216 217 2.741985 CCTGCACGCACCATCGAA 60.742 61.111 0.00 0.00 0.00 3.71
217 218 4.758251 CCCTGCACGCACCATCGA 62.758 66.667 0.00 0.00 0.00 3.59
227 228 3.134127 GATCGGTTGGCCCTGCAC 61.134 66.667 0.00 0.00 0.00 4.57
228 229 4.776322 CGATCGGTTGGCCCTGCA 62.776 66.667 7.38 0.00 0.00 4.41
229 230 4.467084 TCGATCGGTTGGCCCTGC 62.467 66.667 16.41 0.00 0.00 4.85
230 231 2.202932 CTCGATCGGTTGGCCCTG 60.203 66.667 16.41 0.00 0.00 4.45
231 232 4.162690 GCTCGATCGGTTGGCCCT 62.163 66.667 16.41 0.00 0.00 5.19
232 233 4.162690 AGCTCGATCGGTTGGCCC 62.163 66.667 16.41 0.00 0.00 5.80
233 234 2.892425 CAGCTCGATCGGTTGGCC 60.892 66.667 16.41 0.00 0.00 5.36
234 235 2.892425 CCAGCTCGATCGGTTGGC 60.892 66.667 20.30 16.50 0.00 4.52
235 236 2.892425 GCCAGCTCGATCGGTTGG 60.892 66.667 24.73 24.73 0.00 3.77
236 237 2.892425 GGCCAGCTCGATCGGTTG 60.892 66.667 16.41 13.44 0.00 3.77
237 238 4.514577 CGGCCAGCTCGATCGGTT 62.515 66.667 16.41 0.94 0.00 4.44
239 240 3.506059 ATTCGGCCAGCTCGATCGG 62.506 63.158 16.41 7.26 36.49 4.18
240 241 2.018866 GATTCGGCCAGCTCGATCG 61.019 63.158 9.36 9.36 36.49 3.69
241 242 1.666234 GGATTCGGCCAGCTCGATC 60.666 63.158 2.24 0.00 36.49 3.69
242 243 2.136878 AGGATTCGGCCAGCTCGAT 61.137 57.895 2.24 0.00 36.49 3.59
243 244 2.759973 AGGATTCGGCCAGCTCGA 60.760 61.111 2.24 0.00 34.62 4.04
244 245 2.587194 CAGGATTCGGCCAGCTCG 60.587 66.667 2.24 0.00 0.00 5.03
245 246 2.203126 CCAGGATTCGGCCAGCTC 60.203 66.667 2.24 0.00 0.00 4.09
246 247 3.011517 ACCAGGATTCGGCCAGCT 61.012 61.111 2.24 0.00 0.00 4.24
247 248 2.514824 GACCAGGATTCGGCCAGC 60.515 66.667 2.24 0.00 0.00 4.85
248 249 1.450312 GTGACCAGGATTCGGCCAG 60.450 63.158 2.24 0.00 0.00 4.85
249 250 1.561769 ATGTGACCAGGATTCGGCCA 61.562 55.000 2.24 0.00 0.00 5.36
250 251 1.097547 CATGTGACCAGGATTCGGCC 61.098 60.000 0.00 0.00 0.00 6.13
251 252 1.718757 GCATGTGACCAGGATTCGGC 61.719 60.000 0.00 0.00 0.00 5.54
252 253 1.097547 GGCATGTGACCAGGATTCGG 61.098 60.000 0.00 0.00 0.00 4.30
253 254 0.392863 TGGCATGTGACCAGGATTCG 60.393 55.000 0.00 0.00 32.06 3.34
254 255 1.838112 TTGGCATGTGACCAGGATTC 58.162 50.000 0.00 0.00 38.73 2.52
255 256 2.381911 GATTGGCATGTGACCAGGATT 58.618 47.619 0.00 0.00 38.73 3.01
256 257 1.410648 GGATTGGCATGTGACCAGGAT 60.411 52.381 0.00 0.00 38.73 3.24
257 258 0.034186 GGATTGGCATGTGACCAGGA 60.034 55.000 0.00 0.00 38.73 3.86
276 277 1.278238 CGTCCCGCTAGCTTTTACAG 58.722 55.000 13.93 0.00 0.00 2.74
313 314 3.903090 TGCAGGGATTTTTGACAGGAAAT 59.097 39.130 0.00 0.13 0.00 2.17
314 315 3.303938 TGCAGGGATTTTTGACAGGAAA 58.696 40.909 0.00 0.00 0.00 3.13
363 364 3.819188 GGCTGCTTCCCGAATCAG 58.181 61.111 0.00 4.32 37.54 2.90
439 638 2.807045 GTGCTGCTGGTCGACGAG 60.807 66.667 21.82 21.82 0.00 4.18
459 662 2.549754 AGAATGCGCCTGATATTTTCGG 59.450 45.455 4.18 0.00 0.00 4.30
599 847 3.406361 GGCAGTCGAGTGTGTGCG 61.406 66.667 20.92 0.00 36.76 5.34
911 1162 7.508687 AGCTTCTTCTTCTTCTTCTTCTTCTT 58.491 34.615 0.00 0.00 0.00 2.52
912 1163 7.066307 AGCTTCTTCTTCTTCTTCTTCTTCT 57.934 36.000 0.00 0.00 0.00 2.85
913 1164 6.928492 TGAGCTTCTTCTTCTTCTTCTTCTTC 59.072 38.462 0.00 0.00 0.00 2.87
914 1165 6.825610 TGAGCTTCTTCTTCTTCTTCTTCTT 58.174 36.000 0.00 0.00 0.00 2.52
915 1166 6.418057 TGAGCTTCTTCTTCTTCTTCTTCT 57.582 37.500 0.00 0.00 0.00 2.85
916 1167 6.347644 GCTTGAGCTTCTTCTTCTTCTTCTTC 60.348 42.308 0.00 0.00 38.21 2.87
917 1168 5.469760 GCTTGAGCTTCTTCTTCTTCTTCTT 59.530 40.000 0.00 0.00 38.21 2.52
918 1169 4.996758 GCTTGAGCTTCTTCTTCTTCTTCT 59.003 41.667 0.00 0.00 38.21 2.85
919 1170 5.281693 GCTTGAGCTTCTTCTTCTTCTTC 57.718 43.478 0.00 0.00 38.21 2.87
951 1202 2.567615 GGTGGAATGTGGTCACTCTAGT 59.432 50.000 2.66 0.00 0.00 2.57
1006 1257 2.026729 TGATCCAGCCGTTGATACCAAA 60.027 45.455 0.00 0.00 33.49 3.28
1008 1259 1.138859 CTGATCCAGCCGTTGATACCA 59.861 52.381 0.00 0.00 0.00 3.25
1264 1515 4.794439 CATGGCGGCGTCGTGAGA 62.794 66.667 28.34 0.00 38.89 3.27
1473 1724 4.367023 GGCGACGGCAGGTACACA 62.367 66.667 17.49 0.00 42.47 3.72
1503 1754 1.228657 GCACCTGGAACACTTCGTCC 61.229 60.000 0.00 0.00 0.00 4.79
1641 1892 1.303888 TCCGTTCTCCCAGTACGCT 60.304 57.895 0.00 0.00 37.62 5.07
1938 2321 0.788391 GTGAACGAACGGCACCTTAG 59.212 55.000 9.89 0.00 0.00 2.18
1977 2360 2.536761 TTCTGGTACGTTCTGGTTGG 57.463 50.000 0.00 0.00 0.00 3.77
2016 2399 1.228245 CCCAGACACACACCCCTTG 60.228 63.158 0.00 0.00 0.00 3.61
2085 2468 6.406849 CCATTATTCAACAACCCCACTAATGG 60.407 42.308 0.00 0.00 46.81 3.16
2105 2488 1.207089 CGTGCTTCCTCACCTCCATTA 59.793 52.381 0.00 0.00 33.57 1.90
2110 2493 2.029844 GCACGTGCTTCCTCACCTC 61.030 63.158 32.55 0.00 38.21 3.85
2135 2518 3.475566 TTCGCATCTCCCCTCTAATTG 57.524 47.619 0.00 0.00 0.00 2.32
2136 2519 3.711704 TCTTTCGCATCTCCCCTCTAATT 59.288 43.478 0.00 0.00 0.00 1.40
2146 2529 4.122776 ACATACCACATCTTTCGCATCTC 58.877 43.478 0.00 0.00 0.00 2.75
2153 2536 4.437390 CCAAAGCGACATACCACATCTTTC 60.437 45.833 0.00 0.00 0.00 2.62
2172 2555 6.694445 ATCAAAATATCCAACCCAACCAAA 57.306 33.333 0.00 0.00 0.00 3.28
2173 2556 6.957020 AGTATCAAAATATCCAACCCAACCAA 59.043 34.615 0.00 0.00 0.00 3.67
2217 2600 2.295253 ACGCTAGATCTTTTGTCCCG 57.705 50.000 0.00 0.00 0.00 5.14
2222 2605 2.540101 CGGGCTAACGCTAGATCTTTTG 59.460 50.000 0.00 0.00 36.09 2.44
2259 2642 4.193826 TCCTCTCGGAATTCAAGAACTG 57.806 45.455 7.93 2.23 36.03 3.16
2261 2644 5.674820 GCAAATCCTCTCGGAATTCAAGAAC 60.675 44.000 7.93 0.00 44.02 3.01
2263 2646 3.941483 GCAAATCCTCTCGGAATTCAAGA 59.059 43.478 7.93 8.50 44.02 3.02
2268 2651 5.934781 AGAATAGCAAATCCTCTCGGAATT 58.065 37.500 0.00 0.00 44.02 2.17
2269 2652 5.559148 AGAATAGCAAATCCTCTCGGAAT 57.441 39.130 0.00 0.00 44.02 3.01
2270 2653 5.011125 CCTAGAATAGCAAATCCTCTCGGAA 59.989 44.000 0.00 0.00 39.23 4.30
2271 2654 4.524714 CCTAGAATAGCAAATCCTCTCGGA 59.475 45.833 0.00 0.00 39.79 4.55
2272 2655 4.282195 ACCTAGAATAGCAAATCCTCTCGG 59.718 45.833 0.00 0.00 37.37 4.63
2273 2656 5.461032 ACCTAGAATAGCAAATCCTCTCG 57.539 43.478 0.00 0.00 37.37 4.04
2278 2661 5.409826 CGGATCAACCTAGAATAGCAAATCC 59.590 44.000 0.00 0.00 37.37 3.01
2293 2676 7.812669 ACAACAAAATCTATTTTCGGATCAACC 59.187 33.333 0.00 0.00 37.86 3.77
2317 2700 2.499197 TGCGATTTGTCTTGGCTTACA 58.501 42.857 0.00 0.00 0.00 2.41
2318 2701 3.234386 GTTGCGATTTGTCTTGGCTTAC 58.766 45.455 0.00 0.00 0.00 2.34
2322 2705 0.598065 AGGTTGCGATTTGTCTTGGC 59.402 50.000 0.00 0.00 0.00 4.52
2326 2709 2.154462 CCTTCAGGTTGCGATTTGTCT 58.846 47.619 0.00 0.00 0.00 3.41
2328 2711 1.247567 CCCTTCAGGTTGCGATTTGT 58.752 50.000 0.00 0.00 0.00 2.83
2339 2722 0.829182 AAGCTTTGCCACCCTTCAGG 60.829 55.000 0.00 0.00 43.78 3.86
2368 2751 6.817140 ACTCAAAGTTCGGATCTGGTTATAAC 59.183 38.462 7.09 7.09 0.00 1.89
2369 2752 6.942976 ACTCAAAGTTCGGATCTGGTTATAA 58.057 36.000 0.62 0.00 0.00 0.98
2371 2754 5.422214 ACTCAAAGTTCGGATCTGGTTAT 57.578 39.130 0.62 0.00 0.00 1.89
2372 2755 4.884668 ACTCAAAGTTCGGATCTGGTTA 57.115 40.909 0.62 0.00 0.00 2.85
2415 3232 7.572523 TTATGAACTCAGCCCAGATTTTATG 57.427 36.000 0.00 0.00 0.00 1.90
2416 3233 8.593945 TTTTATGAACTCAGCCCAGATTTTAT 57.406 30.769 0.00 0.00 0.00 1.40
2417 3234 8.593945 ATTTTATGAACTCAGCCCAGATTTTA 57.406 30.769 0.00 0.00 0.00 1.52
2418 3235 6.916360 TTTTATGAACTCAGCCCAGATTTT 57.084 33.333 0.00 0.00 0.00 1.82
2419 3236 7.486407 AATTTTATGAACTCAGCCCAGATTT 57.514 32.000 0.00 0.00 0.00 2.17
2420 3237 7.178983 TCAAATTTTATGAACTCAGCCCAGATT 59.821 33.333 0.00 0.00 0.00 2.40
2421 3238 6.664816 TCAAATTTTATGAACTCAGCCCAGAT 59.335 34.615 0.00 0.00 0.00 2.90
2422 3239 6.009589 TCAAATTTTATGAACTCAGCCCAGA 58.990 36.000 0.00 0.00 0.00 3.86
2423 3240 6.271488 TCAAATTTTATGAACTCAGCCCAG 57.729 37.500 0.00 0.00 0.00 4.45
2424 3241 6.855763 ATCAAATTTTATGAACTCAGCCCA 57.144 33.333 0.00 0.00 0.00 5.36
2425 3242 9.651913 TTTAATCAAATTTTATGAACTCAGCCC 57.348 29.630 0.00 0.00 0.00 5.19
2492 3309 7.075741 GCGAACTTTTCTCAACTAGCATTTTA 58.924 34.615 0.00 0.00 0.00 1.52
2493 3310 5.915196 GCGAACTTTTCTCAACTAGCATTTT 59.085 36.000 0.00 0.00 0.00 1.82
2494 3311 5.452777 GCGAACTTTTCTCAACTAGCATTT 58.547 37.500 0.00 0.00 0.00 2.32
2496 3313 3.123621 CGCGAACTTTTCTCAACTAGCAT 59.876 43.478 0.00 0.00 0.00 3.79
2497 3314 2.475111 CGCGAACTTTTCTCAACTAGCA 59.525 45.455 0.00 0.00 0.00 3.49
2498 3315 2.729882 TCGCGAACTTTTCTCAACTAGC 59.270 45.455 6.20 0.00 0.00 3.42
2499 3316 4.966850 TTCGCGAACTTTTCTCAACTAG 57.033 40.909 19.38 0.00 0.00 2.57
2500 3317 7.591006 AATATTCGCGAACTTTTCTCAACTA 57.409 32.000 26.00 8.28 0.00 2.24
2505 3322 5.086058 TGCAAATATTCGCGAACTTTTCTC 58.914 37.500 26.00 17.91 0.00 2.87
2507 3324 5.739237 TTGCAAATATTCGCGAACTTTTC 57.261 34.783 26.00 19.72 0.00 2.29
2517 3334 7.088097 TCACGTTTTCTTTTGCAAATATTCG 57.912 32.000 13.65 14.57 0.00 3.34
2629 3446 8.474025 TCACAAGTATTTCCAACATGAACTTTT 58.526 29.630 0.00 0.00 0.00 2.27
2633 3450 6.734137 TGTCACAAGTATTTCCAACATGAAC 58.266 36.000 0.00 0.00 0.00 3.18
2640 3457 9.658799 TTTTCAAAATGTCACAAGTATTTCCAA 57.341 25.926 0.00 0.00 0.00 3.53
2641 3458 9.658799 TTTTTCAAAATGTCACAAGTATTTCCA 57.341 25.926 0.00 0.00 0.00 3.53
2666 3483 9.533253 ACGAGATGTTTTCAAATTCAAGATTTT 57.467 25.926 0.00 0.00 0.00 1.82
2667 3484 8.971321 CACGAGATGTTTTCAAATTCAAGATTT 58.029 29.630 0.00 0.00 0.00 2.17
2668 3485 8.352201 TCACGAGATGTTTTCAAATTCAAGATT 58.648 29.630 0.00 0.00 0.00 2.40
2669 3486 7.874940 TCACGAGATGTTTTCAAATTCAAGAT 58.125 30.769 0.00 0.00 0.00 2.40
2670 3487 7.258022 TCACGAGATGTTTTCAAATTCAAGA 57.742 32.000 0.00 0.00 0.00 3.02
2671 3488 7.912949 TTCACGAGATGTTTTCAAATTCAAG 57.087 32.000 0.00 0.00 0.00 3.02
2672 3489 8.870160 ATTTCACGAGATGTTTTCAAATTCAA 57.130 26.923 0.00 0.00 0.00 2.69
2673 3490 8.870160 AATTTCACGAGATGTTTTCAAATTCA 57.130 26.923 0.00 0.00 0.00 2.57
2674 3491 9.571804 CAAATTTCACGAGATGTTTTCAAATTC 57.428 29.630 0.00 0.00 0.00 2.17
2675 3492 9.311916 TCAAATTTCACGAGATGTTTTCAAATT 57.688 25.926 0.00 0.00 0.00 1.82
2676 3493 8.870160 TCAAATTTCACGAGATGTTTTCAAAT 57.130 26.923 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.