Multiple sequence alignment - TraesCS4B01G118600

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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 TraesCS4B01G118600 chr4B 100.000 2699 0 0 1 2699 139105060 139107758 0.000000e+00 4985.0
1 TraesCS4B01G118600 chr4B 94.553 257 14 0 1 257 27782156 27782412 6.480000e-107 398.0
2 TraesCS4B01G118600 chr4B 92.776 263 18 1 1 263 335937485 335937746 2.350000e-101 379.0
3 TraesCS4B01G118600 chr4B 100.000 120 0 0 3104 3223 139108163 139108282 4.190000e-54 222.0
4 TraesCS4B01G118600 chr4B 77.778 279 52 8 1918 2191 455011312 455011039 2.570000e-36 163.0
5 TraesCS4B01G118600 chr4D 94.154 1950 83 14 437 2375 97382533 97384462 0.000000e+00 2940.0
6 TraesCS4B01G118600 chr4D 94.400 250 7 4 2392 2637 97384447 97384693 8.440000e-101 377.0
7 TraesCS4B01G118600 chr4D 81.164 292 52 3 1912 2203 97379107 97379395 6.950000e-57 231.0
8 TraesCS4B01G118600 chr4D 86.243 189 26 0 258 446 1845557 1845745 4.210000e-49 206.0
9 TraesCS4B01G118600 chr4D 77.143 280 52 10 1918 2191 369861333 369861060 5.570000e-33 152.0
10 TraesCS4B01G118600 chr4D 76.817 289 55 10 1909 2191 369875238 369875520 5.570000e-33 152.0
11 TraesCS4B01G118600 chr4A 94.145 854 42 4 1529 2375 478751781 478750929 0.000000e+00 1293.0
12 TraesCS4B01G118600 chr4A 93.537 882 34 10 566 1442 478752838 478751975 0.000000e+00 1291.0
13 TraesCS4B01G118600 chr4A 88.083 193 13 6 2392 2579 478750944 478750757 1.510000e-53 220.0
14 TraesCS4B01G118600 chr4A 83.333 198 31 2 254 449 700626674 700626871 7.100000e-42 182.0
15 TraesCS4B01G118600 chr4A 77.431 288 55 8 1909 2191 94824700 94824982 2.570000e-36 163.0
16 TraesCS4B01G118600 chr4A 89.167 120 6 2 461 580 478752991 478752879 3.350000e-30 143.0
17 TraesCS4B01G118600 chr4A 95.588 68 2 1 3157 3223 712882634 712882567 1.220000e-19 108.0
18 TraesCS4B01G118600 chr4A 100.000 39 0 0 3104 3142 712883232 712883194 4.460000e-09 73.1
19 TraesCS4B01G118600 chr2B 94.553 257 14 0 1 257 83550023 83549767 6.480000e-107 398.0
20 TraesCS4B01G118600 chr2B 94.862 253 13 0 1 253 24650074 24649822 2.330000e-106 396.0
21 TraesCS4B01G118600 chr2B 90.833 120 10 1 3105 3223 672339883 672340002 3.330000e-35 159.0
22 TraesCS4B01G118600 chr2B 89.655 87 0 4 3138 3223 107118880 107118958 5.690000e-18 102.0
23 TraesCS4B01G118600 chr1B 93.870 261 16 0 1 261 32432151 32431891 8.380000e-106 394.0
24 TraesCS4B01G118600 chr1B 90.323 93 9 0 260 352 10930900 10930992 4.370000e-24 122.0
25 TraesCS4B01G118600 chr1B 90.323 93 9 0 260 352 24668928 24668836 4.370000e-24 122.0
26 TraesCS4B01G118600 chr3B 94.466 253 14 0 1 253 726423248 726423500 1.080000e-104 390.0
27 TraesCS4B01G118600 chr3B 92.776 263 19 0 1 263 139361120 139360858 6.520000e-102 381.0
28 TraesCS4B01G118600 chr3B 95.890 73 3 0 3104 3176 612295250 612295178 5.650000e-23 119.0
29 TraesCS4B01G118600 chr3B 98.462 65 1 0 2635 2699 51953864 51953800 7.310000e-22 115.0
30 TraesCS4B01G118600 chr6B 92.803 264 19 0 1 264 683150500 683150763 1.810000e-102 383.0
31 TraesCS4B01G118600 chr6B 92.045 264 21 0 1 264 683180959 683181222 3.930000e-99 372.0
32 TraesCS4B01G118600 chr5A 89.005 191 20 1 258 447 458272181 458272371 5.380000e-58 235.0
33 TraesCS4B01G118600 chr7B 85.864 191 27 0 258 448 736612910 736613100 1.520000e-48 204.0
34 TraesCS4B01G118600 chr7B 91.398 93 8 0 260 352 25340253 25340345 9.390000e-26 128.0
35 TraesCS4B01G118600 chr7A 83.163 196 32 1 258 453 40804769 40804575 9.190000e-41 178.0
36 TraesCS4B01G118600 chr7A 86.441 118 16 0 328 445 148807050 148807167 2.610000e-26 130.0
37 TraesCS4B01G118600 chr3D 84.000 175 26 2 272 445 562374885 562375058 1.990000e-37 167.0
38 TraesCS4B01G118600 chr7D 96.429 84 2 1 3141 3223 55446353 55446270 1.560000e-28 137.0
39 TraesCS4B01G118600 chr5B 95.122 41 1 1 3184 3223 586529252 586529292 2.680000e-06 63.9


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 TraesCS4B01G118600 chr4B 139105060 139108282 3222 False 2603.500000 4985 100.000 1 3223 2 chr4B.!!$F3 3222
1 TraesCS4B01G118600 chr4D 97379107 97384693 5586 False 1182.666667 2940 89.906 437 2637 3 chr4D.!!$F3 2200
2 TraesCS4B01G118600 chr4A 478750757 478752991 2234 True 736.750000 1293 91.233 461 2579 4 chr4A.!!$R1 2118

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
228 229 0.038618 TGTGGTCGAGATGGTGAACG 60.039 55.0 0.00 0.00 0.00 3.95 F
588 3581 0.043053 CGACACGAGTTGCACAAGTG 60.043 55.0 8.62 8.62 35.13 3.16 F
1173 4221 0.179018 AAGTGGACCCTGCACAAGAC 60.179 55.0 0.00 0.00 41.46 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1340 4388 1.068472 GCCAGTACGCACTATATCGCT 60.068 52.381 0.0 0.0 32.21 4.93 R
1915 5097 1.137086 CATCGTCGGAGTCCCATTCTT 59.863 52.381 2.8 0.0 0.00 2.52 R
2640 5836 0.815615 GGGCTTAACGGCTGGAGATG 60.816 60.000 0.0 0.0 38.46 2.90 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
53 54 2.813179 CGCATAGCAGTTCCACCGC 61.813 63.158 0.00 0.00 0.00 5.68
54 55 1.745115 GCATAGCAGTTCCACCGCA 60.745 57.895 0.00 0.00 0.00 5.69
55 56 1.982073 GCATAGCAGTTCCACCGCAC 61.982 60.000 0.00 0.00 0.00 5.34
56 57 1.447838 ATAGCAGTTCCACCGCACG 60.448 57.895 0.00 0.00 0.00 5.34
77 78 4.680237 CCGAGTGGCAACCGCTGA 62.680 66.667 4.05 0.00 45.19 4.26
78 79 3.414700 CGAGTGGCAACCGCTGAC 61.415 66.667 4.05 0.00 45.19 3.51
79 80 3.050275 GAGTGGCAACCGCTGACC 61.050 66.667 4.05 0.00 45.19 4.02
80 81 4.988598 AGTGGCAACCGCTGACCG 62.989 66.667 0.00 0.00 43.37 4.79
104 105 4.645921 GGCAACCAACGTGCAGGC 62.646 66.667 6.26 0.00 44.07 4.85
106 107 3.276091 CAACCAACGTGCAGGCGA 61.276 61.111 6.26 0.00 35.59 5.54
107 108 2.515057 AACCAACGTGCAGGCGAA 60.515 55.556 6.26 0.00 35.59 4.70
108 109 2.830285 AACCAACGTGCAGGCGAAC 61.830 57.895 6.26 0.00 35.59 3.95
121 122 3.084579 CGAACTGTCTCGCATGCC 58.915 61.111 13.15 0.00 31.04 4.40
122 123 2.792290 CGAACTGTCTCGCATGCCG 61.792 63.158 13.15 7.68 38.61 5.69
123 124 3.088500 GAACTGTCTCGCATGCCGC 62.089 63.158 13.15 0.16 36.73 6.53
124 125 3.881952 AACTGTCTCGCATGCCGCA 62.882 57.895 13.15 0.00 42.60 5.69
125 126 3.857854 CTGTCTCGCATGCCGCAC 61.858 66.667 13.15 6.36 42.60 5.34
126 127 4.678499 TGTCTCGCATGCCGCACA 62.678 61.111 13.15 9.09 42.60 4.57
127 128 4.152625 GTCTCGCATGCCGCACAC 62.153 66.667 13.15 0.00 42.60 3.82
144 145 2.202440 CGTGCCTCGTCCTACGTG 60.202 66.667 0.00 0.00 43.14 4.49
148 149 4.849329 CCTCGTCCTACGTGGCGC 62.849 72.222 0.00 0.00 46.16 6.53
149 150 4.111016 CTCGTCCTACGTGGCGCA 62.111 66.667 10.83 0.00 43.14 6.09
150 151 4.111016 TCGTCCTACGTGGCGCAG 62.111 66.667 10.83 1.82 43.14 5.18
154 155 0.947180 GTCCTACGTGGCGCAGAAAA 60.947 55.000 10.83 0.00 35.26 2.29
155 156 0.249953 TCCTACGTGGCGCAGAAAAA 60.250 50.000 10.83 0.00 35.26 1.94
156 157 0.110373 CCTACGTGGCGCAGAAAAAC 60.110 55.000 10.83 0.00 0.00 2.43
157 158 0.450482 CTACGTGGCGCAGAAAAACG 60.450 55.000 10.83 11.29 40.00 3.60
159 160 1.721133 CGTGGCGCAGAAAAACGAC 60.721 57.895 10.83 0.00 36.38 4.34
160 161 1.370051 GTGGCGCAGAAAAACGACC 60.370 57.895 10.83 0.00 36.12 4.79
163 164 2.600475 GCGCAGAAAAACGACCGGA 61.600 57.895 9.46 0.00 0.00 5.14
165 166 0.515564 CGCAGAAAAACGACCGGATT 59.484 50.000 9.46 0.00 0.00 3.01
166 167 1.724654 CGCAGAAAAACGACCGGATTG 60.725 52.381 9.46 0.00 0.00 2.67
167 168 1.265905 GCAGAAAAACGACCGGATTGT 59.734 47.619 9.46 0.00 0.00 2.71
168 169 2.916111 CAGAAAAACGACCGGATTGTG 58.084 47.619 9.46 0.00 0.00 3.33
169 170 1.265905 AGAAAAACGACCGGATTGTGC 59.734 47.619 9.46 0.00 0.00 4.57
170 171 0.312729 AAAAACGACCGGATTGTGCC 59.687 50.000 9.46 0.00 0.00 5.01
171 172 0.820074 AAAACGACCGGATTGTGCCA 60.820 50.000 9.46 0.00 0.00 4.92
172 173 0.820074 AAACGACCGGATTGTGCCAA 60.820 50.000 9.46 0.00 0.00 4.52
173 174 1.234615 AACGACCGGATTGTGCCAAG 61.235 55.000 9.46 0.00 0.00 3.61
174 175 1.375396 CGACCGGATTGTGCCAAGA 60.375 57.895 9.46 0.00 0.00 3.02
175 176 0.744414 CGACCGGATTGTGCCAAGAT 60.744 55.000 9.46 0.00 0.00 2.40
177 178 1.401905 GACCGGATTGTGCCAAGATTC 59.598 52.381 9.46 0.00 0.00 2.52
178 179 0.378257 CCGGATTGTGCCAAGATTCG 59.622 55.000 0.00 0.00 0.00 3.34
179 180 1.086696 CGGATTGTGCCAAGATTCGT 58.913 50.000 0.00 0.00 0.00 3.85
180 181 1.202065 CGGATTGTGCCAAGATTCGTG 60.202 52.381 0.00 0.00 0.00 4.35
181 182 1.468054 GGATTGTGCCAAGATTCGTGC 60.468 52.381 0.00 0.00 0.00 5.34
182 183 1.199789 GATTGTGCCAAGATTCGTGCA 59.800 47.619 0.00 0.00 0.00 4.57
184 185 4.471761 TGCCAAGATTCGTGCACA 57.528 50.000 18.64 0.00 0.00 4.57
185 186 2.712984 TGCCAAGATTCGTGCACAA 58.287 47.368 18.64 10.71 0.00 3.33
186 187 1.028130 TGCCAAGATTCGTGCACAAA 58.972 45.000 18.64 4.80 0.00 2.83
187 188 1.001487 TGCCAAGATTCGTGCACAAAG 60.001 47.619 18.64 0.04 0.00 2.77
188 189 1.001378 GCCAAGATTCGTGCACAAAGT 60.001 47.619 18.64 0.25 0.00 2.66
190 191 3.810373 CCAAGATTCGTGCACAAAGTAC 58.190 45.455 18.64 0.95 0.00 2.73
192 193 4.377431 CCAAGATTCGTGCACAAAGTACTC 60.377 45.833 18.64 0.00 0.00 2.59
194 195 4.377021 AGATTCGTGCACAAAGTACTCAA 58.623 39.130 18.64 0.00 0.00 3.02
195 196 3.936902 TTCGTGCACAAAGTACTCAAC 57.063 42.857 18.64 0.00 0.00 3.18
197 198 3.263261 TCGTGCACAAAGTACTCAACAA 58.737 40.909 18.64 0.00 0.00 2.83
199 200 3.968096 CGTGCACAAAGTACTCAACAATG 59.032 43.478 18.64 0.00 0.00 2.82
200 201 4.260579 CGTGCACAAAGTACTCAACAATGA 60.261 41.667 18.64 0.00 0.00 2.57
201 202 5.560760 CGTGCACAAAGTACTCAACAATGAT 60.561 40.000 18.64 0.00 34.37 2.45
202 203 5.626543 GTGCACAAAGTACTCAACAATGATG 59.373 40.000 13.17 0.00 34.37 3.07
203 204 4.618489 GCACAAAGTACTCAACAATGATGC 59.382 41.667 0.00 0.00 34.37 3.91
205 206 5.854866 CACAAAGTACTCAACAATGATGCTG 59.145 40.000 0.00 0.00 34.37 4.41
206 207 5.048504 ACAAAGTACTCAACAATGATGCTGG 60.049 40.000 0.00 0.00 34.37 4.85
208 209 0.806868 ACTCAACAATGATGCTGGCG 59.193 50.000 0.00 0.00 34.37 5.69
209 210 0.806868 CTCAACAATGATGCTGGCGT 59.193 50.000 0.00 0.00 34.37 5.68
210 211 0.522626 TCAACAATGATGCTGGCGTG 59.477 50.000 0.00 0.00 0.00 5.34
211 212 0.241749 CAACAATGATGCTGGCGTGT 59.758 50.000 0.00 0.00 0.00 4.49
212 213 0.241749 AACAATGATGCTGGCGTGTG 59.758 50.000 0.00 0.00 0.00 3.82
213 214 1.138036 CAATGATGCTGGCGTGTGG 59.862 57.895 0.00 0.00 0.00 4.17
214 215 1.303561 AATGATGCTGGCGTGTGGT 60.304 52.632 0.00 0.00 0.00 4.16
215 216 1.308069 AATGATGCTGGCGTGTGGTC 61.308 55.000 0.00 0.00 0.00 4.02
217 218 3.932580 GATGCTGGCGTGTGGTCGA 62.933 63.158 0.00 0.00 0.00 4.20
218 219 3.939837 ATGCTGGCGTGTGGTCGAG 62.940 63.158 0.00 0.00 0.00 4.04
221 222 1.807165 CTGGCGTGTGGTCGAGATG 60.807 63.158 0.00 0.00 0.00 2.90
222 223 2.509336 GGCGTGTGGTCGAGATGG 60.509 66.667 0.00 0.00 0.00 3.51
223 224 2.261671 GCGTGTGGTCGAGATGGT 59.738 61.111 0.00 0.00 0.00 3.55
224 225 2.094659 GCGTGTGGTCGAGATGGTG 61.095 63.158 0.00 0.00 0.00 4.17
225 226 1.584495 CGTGTGGTCGAGATGGTGA 59.416 57.895 0.00 0.00 0.00 4.02
227 228 1.429463 GTGTGGTCGAGATGGTGAAC 58.571 55.000 0.00 0.00 0.00 3.18
228 229 0.038618 TGTGGTCGAGATGGTGAACG 60.039 55.000 0.00 0.00 0.00 3.95
230 231 1.810030 GGTCGAGATGGTGAACGCC 60.810 63.158 0.00 0.00 0.00 5.68
231 232 1.810030 GTCGAGATGGTGAACGCCC 60.810 63.158 1.86 0.00 0.00 6.13
232 233 2.264480 CGAGATGGTGAACGCCCA 59.736 61.111 1.86 0.00 36.16 5.36
233 234 2.100631 CGAGATGGTGAACGCCCAC 61.101 63.158 1.86 0.00 34.07 4.61
234 235 1.003839 GAGATGGTGAACGCCCACA 60.004 57.895 9.52 0.00 38.74 4.17
248 249 3.720531 CACACGTGTGGGCGTTAA 58.279 55.556 35.65 0.00 43.83 2.01
249 250 1.277440 CACACGTGTGGGCGTTAAC 59.723 57.895 35.65 0.00 43.83 2.01
250 251 1.153409 ACACGTGTGGGCGTTAACA 60.153 52.632 22.71 0.00 43.83 2.41
251 252 0.533308 ACACGTGTGGGCGTTAACAT 60.533 50.000 22.71 0.00 43.83 2.71
252 253 0.589223 CACGTGTGGGCGTTAACATT 59.411 50.000 7.58 0.00 43.83 2.71
253 254 1.799403 CACGTGTGGGCGTTAACATTA 59.201 47.619 7.58 0.00 43.83 1.90
255 256 2.674357 ACGTGTGGGCGTTAACATTATC 59.326 45.455 6.39 0.00 43.04 1.75
257 258 2.931325 GTGTGGGCGTTAACATTATCGA 59.069 45.455 6.39 0.00 0.00 3.59
258 259 3.371591 GTGTGGGCGTTAACATTATCGAA 59.628 43.478 6.39 0.00 0.00 3.71
259 260 3.619483 TGTGGGCGTTAACATTATCGAAG 59.381 43.478 6.39 0.00 0.00 3.79
260 261 3.866910 GTGGGCGTTAACATTATCGAAGA 59.133 43.478 6.39 0.00 45.75 2.87
261 262 4.510340 GTGGGCGTTAACATTATCGAAGAT 59.490 41.667 6.39 0.00 45.12 2.40
264 265 6.762187 TGGGCGTTAACATTATCGAAGATTTA 59.238 34.615 6.39 0.00 45.12 1.40
265 266 7.442969 TGGGCGTTAACATTATCGAAGATTTAT 59.557 33.333 6.39 0.00 45.12 1.40
266 267 7.955864 GGGCGTTAACATTATCGAAGATTTATC 59.044 37.037 6.39 0.00 45.12 1.75
293 294 7.365840 AGATTCTAGTTAGAAAGTTTTGCCG 57.634 36.000 5.75 0.00 44.63 5.69
294 295 5.352643 TTCTAGTTAGAAAGTTTTGCCGC 57.647 39.130 0.00 0.00 39.22 6.53
295 296 2.681152 AGTTAGAAAGTTTTGCCGCG 57.319 45.000 0.00 0.00 0.00 6.46
296 297 1.050009 GTTAGAAAGTTTTGCCGCGC 58.950 50.000 0.00 0.00 0.00 6.86
298 299 0.237235 TAGAAAGTTTTGCCGCGCTG 59.763 50.000 5.56 0.00 0.00 5.18
299 300 2.648318 GAAAGTTTTGCCGCGCTGC 61.648 57.895 17.60 17.60 0.00 5.25
300 301 3.423162 AAAGTTTTGCCGCGCTGCA 62.423 52.632 23.14 23.14 40.07 4.41
301 302 2.697992 AAAGTTTTGCCGCGCTGCAT 62.698 50.000 27.12 9.66 41.70 3.96
302 303 1.861542 AAGTTTTGCCGCGCTGCATA 61.862 50.000 27.12 19.60 41.70 3.14
303 304 1.869132 GTTTTGCCGCGCTGCATAG 60.869 57.895 27.12 0.00 41.70 2.23
304 305 3.050166 TTTTGCCGCGCTGCATAGG 62.050 57.895 27.12 10.01 41.70 2.57
305 306 4.776322 TTGCCGCGCTGCATAGGT 62.776 61.111 27.12 0.00 41.70 3.08
306 307 4.776322 TGCCGCGCTGCATAGGTT 62.776 61.111 23.14 0.00 36.04 3.50
307 308 3.508840 GCCGCGCTGCATAGGTTT 61.509 61.111 19.50 0.00 0.00 3.27
308 309 2.404789 CCGCGCTGCATAGGTTTG 59.595 61.111 5.56 0.00 0.00 2.93
309 310 2.106074 CCGCGCTGCATAGGTTTGA 61.106 57.895 5.56 0.00 0.00 2.69
310 311 1.643868 CCGCGCTGCATAGGTTTGAA 61.644 55.000 5.56 0.00 0.00 2.69
311 312 0.521242 CGCGCTGCATAGGTTTGAAC 60.521 55.000 5.56 0.00 0.00 3.18
312 313 0.804989 GCGCTGCATAGGTTTGAACT 59.195 50.000 0.00 0.00 0.00 3.01
313 314 1.200020 GCGCTGCATAGGTTTGAACTT 59.800 47.619 0.00 0.00 0.00 2.66
315 316 2.744202 CGCTGCATAGGTTTGAACTTCT 59.256 45.455 0.00 0.00 0.00 2.85
316 317 3.932710 CGCTGCATAGGTTTGAACTTCTA 59.067 43.478 0.00 0.00 0.00 2.10
317 318 4.033358 CGCTGCATAGGTTTGAACTTCTAG 59.967 45.833 0.00 0.00 0.00 2.43
318 319 5.178797 GCTGCATAGGTTTGAACTTCTAGA 58.821 41.667 0.00 0.00 0.00 2.43
319 320 5.819901 GCTGCATAGGTTTGAACTTCTAGAT 59.180 40.000 0.00 0.00 0.00 1.98
320 321 6.986817 GCTGCATAGGTTTGAACTTCTAGATA 59.013 38.462 0.00 0.00 0.00 1.98
321 322 7.659390 GCTGCATAGGTTTGAACTTCTAGATAT 59.341 37.037 0.00 0.00 0.00 1.63
322 323 8.893219 TGCATAGGTTTGAACTTCTAGATATG 57.107 34.615 0.00 0.00 0.00 1.78
323 324 8.486210 TGCATAGGTTTGAACTTCTAGATATGT 58.514 33.333 0.00 0.00 0.00 2.29
324 325 9.331282 GCATAGGTTTGAACTTCTAGATATGTT 57.669 33.333 0.00 0.00 0.00 2.71
336 337 9.634021 ACTTCTAGATATGTTCTATGTGAGACA 57.366 33.333 0.00 0.00 36.35 3.41
342 343 9.725019 AGATATGTTCTATGTGAGACAAACAAA 57.275 29.630 0.00 0.00 32.29 2.83
379 380 7.372451 TCATATACAAAGTTAGTTGTGTGGC 57.628 36.000 0.92 0.00 41.75 5.01
380 381 6.937465 TCATATACAAAGTTAGTTGTGTGGCA 59.063 34.615 0.92 0.00 41.75 4.92
381 382 3.775661 ACAAAGTTAGTTGTGTGGCAC 57.224 42.857 11.55 11.55 40.22 5.01
383 384 2.319136 AAGTTAGTTGTGTGGCACGA 57.681 45.000 13.77 0.00 37.14 4.35
384 385 2.319136 AGTTAGTTGTGTGGCACGAA 57.681 45.000 13.77 5.45 37.14 3.85
385 386 2.846193 AGTTAGTTGTGTGGCACGAAT 58.154 42.857 13.77 3.49 37.14 3.34
386 387 2.806244 AGTTAGTTGTGTGGCACGAATC 59.194 45.455 13.77 3.99 37.14 2.52
387 388 1.803334 TAGTTGTGTGGCACGAATCC 58.197 50.000 13.77 0.00 37.14 3.01
388 389 0.108585 AGTTGTGTGGCACGAATCCT 59.891 50.000 13.77 2.06 37.14 3.24
389 390 1.346395 AGTTGTGTGGCACGAATCCTA 59.654 47.619 13.77 0.00 37.14 2.94
390 391 2.147958 GTTGTGTGGCACGAATCCTAA 58.852 47.619 13.77 0.00 37.14 2.69
392 393 2.422597 TGTGTGGCACGAATCCTAAAG 58.577 47.619 13.77 0.00 37.14 1.85
393 394 1.130561 GTGTGGCACGAATCCTAAAGC 59.869 52.381 13.77 0.00 0.00 3.51
394 395 0.373716 GTGGCACGAATCCTAAAGCG 59.626 55.000 0.00 0.00 0.00 4.68
397 398 2.101750 TGGCACGAATCCTAAAGCGATA 59.898 45.455 0.00 0.00 0.00 2.92
398 399 3.244078 TGGCACGAATCCTAAAGCGATAT 60.244 43.478 0.00 0.00 0.00 1.63
399 400 3.746492 GGCACGAATCCTAAAGCGATATT 59.254 43.478 0.00 0.00 0.00 1.28
401 402 4.447724 GCACGAATCCTAAAGCGATATTGA 59.552 41.667 0.00 0.00 0.00 2.57
402 403 5.050363 GCACGAATCCTAAAGCGATATTGAA 60.050 40.000 0.00 0.00 0.00 2.69
404 405 6.420903 CACGAATCCTAAAGCGATATTGAAGA 59.579 38.462 0.00 0.00 0.00 2.87
405 406 6.642950 ACGAATCCTAAAGCGATATTGAAGAG 59.357 38.462 0.00 0.00 0.00 2.85
406 407 6.400515 CGAATCCTAAAGCGATATTGAAGAGC 60.401 42.308 0.00 0.00 0.00 4.09
407 408 5.537300 TCCTAAAGCGATATTGAAGAGCT 57.463 39.130 0.00 0.00 40.20 4.09
410 411 7.671302 TCCTAAAGCGATATTGAAGAGCTAAT 58.329 34.615 0.00 0.00 37.15 1.73
427 428 0.773644 AATATAGCAGGGCCTGGGTG 59.226 55.000 33.43 11.08 31.21 4.61
428 429 1.783250 ATATAGCAGGGCCTGGGTGC 61.783 60.000 33.43 20.80 37.48 5.01
436 437 4.047125 GCCTGGGTGCAAGGGCTA 62.047 66.667 5.09 0.00 41.20 3.93
437 438 3.010144 CCTGGGTGCAAGGGCTAT 58.990 61.111 0.00 0.00 41.91 2.97
440 441 1.064017 CCTGGGTGCAAGGGCTATAAA 60.064 52.381 0.00 0.00 41.91 1.40
441 442 2.622977 CCTGGGTGCAAGGGCTATAAAA 60.623 50.000 0.00 0.00 41.91 1.52
442 443 3.096092 CTGGGTGCAAGGGCTATAAAAA 58.904 45.455 0.00 0.00 41.91 1.94
453 3444 3.493503 GGGCTATAAAAATCCACGACTCG 59.506 47.826 0.00 0.00 0.00 4.18
561 3554 4.752101 CAGCCTTTCTCTTCTTTTCTCGAA 59.248 41.667 0.00 0.00 0.00 3.71
562 3555 4.752604 AGCCTTTCTCTTCTTTTCTCGAAC 59.247 41.667 0.00 0.00 0.00 3.95
564 3557 5.007724 GCCTTTCTCTTCTTTTCTCGAACAA 59.992 40.000 0.00 0.00 0.00 2.83
570 3563 3.955771 TCTTTTCTCGAACAAAACCCG 57.044 42.857 0.00 0.00 0.00 5.28
580 3573 1.011333 ACAAAACCCGACACGAGTTG 58.989 50.000 0.00 0.00 0.00 3.16
581 3574 0.316689 CAAAACCCGACACGAGTTGC 60.317 55.000 0.00 0.00 0.00 4.17
582 3575 0.745128 AAAACCCGACACGAGTTGCA 60.745 50.000 0.00 0.00 0.00 4.08
583 3576 1.433837 AAACCCGACACGAGTTGCAC 61.434 55.000 0.00 0.00 0.00 4.57
584 3577 2.279851 CCCGACACGAGTTGCACA 60.280 61.111 0.00 0.00 0.00 4.57
585 3578 1.885388 CCCGACACGAGTTGCACAA 60.885 57.895 0.00 0.00 0.00 3.33
586 3579 1.564622 CCGACACGAGTTGCACAAG 59.435 57.895 0.00 0.00 0.00 3.16
588 3581 0.043053 CGACACGAGTTGCACAAGTG 60.043 55.000 8.62 8.62 35.13 3.16
701 3744 1.686110 CCAGACCGAAGCCCTACCT 60.686 63.158 0.00 0.00 0.00 3.08
713 3756 2.683859 CCTACCTGACGACACGCGA 61.684 63.158 15.93 0.00 44.57 5.87
744 3792 2.125326 CCTCCCGCCGTGTGATCTA 61.125 63.158 0.00 0.00 0.00 1.98
904 3952 3.710722 CCTCCGCACAGAAGCCCT 61.711 66.667 0.00 0.00 0.00 5.19
905 3953 2.348998 CTCCGCACAGAAGCCCTT 59.651 61.111 0.00 0.00 0.00 3.95
921 3969 1.611673 CCCTTGATCGACTGCAACCTT 60.612 52.381 0.00 0.00 0.00 3.50
1017 4065 3.525537 CGACATGAACTTGTGCTCCTAT 58.474 45.455 0.00 0.00 0.00 2.57
1173 4221 0.179018 AAGTGGACCCTGCACAAGAC 60.179 55.000 0.00 0.00 41.46 3.01
1176 4224 0.764369 TGGACCCTGCACAAGACTCT 60.764 55.000 0.00 0.00 0.00 3.24
1304 4352 1.599667 CGATGTTCGGGTAGATCCACG 60.600 57.143 0.00 0.00 36.00 4.94
1323 4371 3.310774 CACGAGAGCCAAAATCTATGTGG 59.689 47.826 0.00 0.00 33.14 4.17
1458 4640 7.303998 TCTACTTCTTGTCTTAGTAGCGTTTC 58.696 38.462 0.00 0.00 40.59 2.78
1459 4641 6.086785 ACTTCTTGTCTTAGTAGCGTTTCT 57.913 37.500 0.00 0.00 0.00 2.52
1460 4642 6.151004 ACTTCTTGTCTTAGTAGCGTTTCTC 58.849 40.000 0.00 0.00 0.00 2.87
1461 4643 5.961396 TCTTGTCTTAGTAGCGTTTCTCT 57.039 39.130 0.00 0.00 0.00 3.10
1463 4645 7.444629 TCTTGTCTTAGTAGCGTTTCTCTTA 57.555 36.000 0.00 0.00 0.00 2.10
1464 4646 8.053026 TCTTGTCTTAGTAGCGTTTCTCTTAT 57.947 34.615 0.00 0.00 0.00 1.73
1465 4647 9.170734 TCTTGTCTTAGTAGCGTTTCTCTTATA 57.829 33.333 0.00 0.00 0.00 0.98
1466 4648 9.224058 CTTGTCTTAGTAGCGTTTCTCTTATAC 57.776 37.037 0.00 0.00 0.00 1.47
1530 4712 8.292448 AGCTGTGAAGTTGTTGACATATTTTAG 58.708 33.333 0.00 0.00 28.67 1.85
1597 4779 7.625828 AGTACCAAGTAATTAAGATGCCAAC 57.374 36.000 0.00 0.00 0.00 3.77
1722 4904 3.548587 CTTGTTGAATCAAGCAGACACG 58.451 45.455 0.00 0.00 38.35 4.49
1846 5028 1.835494 AATGGAGGACGACGAGAAGA 58.165 50.000 0.00 0.00 0.00 2.87
1915 5097 6.291377 GTGGAATGCTAATACCAGAGAATCA 58.709 40.000 0.00 0.00 37.82 2.57
1952 5134 6.346120 CCGACGATGATAATGTTCTGAATGTC 60.346 42.308 0.00 0.00 0.00 3.06
2131 5313 4.341366 ACTATCATGGACATGCGAATGA 57.659 40.909 11.32 7.11 38.65 2.57
2136 5318 3.809279 TCATGGACATGCGAATGACATAC 59.191 43.478 11.32 0.00 38.65 2.39
2179 5361 0.396139 TGCATGATTGGGGAGCTTCC 60.396 55.000 0.70 0.70 35.23 3.46
2183 5365 2.692709 TGATTGGGGAGCTTCCAAAA 57.307 45.000 21.21 12.53 45.99 2.44
2290 5478 4.286549 TCCTCGGTTTTACCTTTGATGGTA 59.713 41.667 0.00 0.00 41.22 3.25
2312 5500 1.160137 CTCTTTGAAACTGCTCCGGG 58.840 55.000 0.00 0.00 0.00 5.73
2359 5547 7.333174 TGCGTTCTGTGTCATTTAGATTATTCA 59.667 33.333 0.00 0.00 0.00 2.57
2360 5548 8.175069 GCGTTCTGTGTCATTTAGATTATTCAA 58.825 33.333 0.00 0.00 0.00 2.69
2361 5549 9.694520 CGTTCTGTGTCATTTAGATTATTCAAG 57.305 33.333 0.00 0.00 0.00 3.02
2362 5550 9.994432 GTTCTGTGTCATTTAGATTATTCAAGG 57.006 33.333 0.00 0.00 0.00 3.61
2363 5551 9.739276 TTCTGTGTCATTTAGATTATTCAAGGT 57.261 29.630 0.00 0.00 0.00 3.50
2364 5552 9.739276 TCTGTGTCATTTAGATTATTCAAGGTT 57.261 29.630 0.00 0.00 0.00 3.50
2365 5553 9.994432 CTGTGTCATTTAGATTATTCAAGGTTC 57.006 33.333 0.00 0.00 0.00 3.62
2366 5554 9.739276 TGTGTCATTTAGATTATTCAAGGTTCT 57.261 29.630 0.00 0.00 0.00 3.01
2380 5568 7.486802 TTCAAGGTTCTAGTTAAGTTTTCCG 57.513 36.000 0.00 0.00 0.00 4.30
2381 5569 5.467735 TCAAGGTTCTAGTTAAGTTTTCCGC 59.532 40.000 0.00 0.00 0.00 5.54
2382 5570 4.964593 AGGTTCTAGTTAAGTTTTCCGCA 58.035 39.130 0.00 0.00 0.00 5.69
2383 5571 5.370679 AGGTTCTAGTTAAGTTTTCCGCAA 58.629 37.500 0.00 0.00 0.00 4.85
2384 5572 5.824097 AGGTTCTAGTTAAGTTTTCCGCAAA 59.176 36.000 0.00 0.00 0.00 3.68
2385 5573 6.319405 AGGTTCTAGTTAAGTTTTCCGCAAAA 59.681 34.615 0.00 0.00 0.00 2.44
2386 5574 6.974048 GGTTCTAGTTAAGTTTTCCGCAAAAA 59.026 34.615 0.00 0.00 33.17 1.94
2421 5609 7.927048 TCTAGTTAAGTGCCAAGAAGTTTTTC 58.073 34.615 0.00 0.00 0.00 2.29
2468 5660 8.730680 TGGTTTCTTCAGCTATTTGATAACTTC 58.269 33.333 0.00 0.00 0.00 3.01
2488 5680 3.317150 TCTGCAGTTGTATGAACGAGTG 58.683 45.455 14.67 0.00 41.65 3.51
2590 5786 4.141482 GGATGGATGTATGGTGTGTAGGTT 60.141 45.833 0.00 0.00 0.00 3.50
2637 5833 1.156736 CACACAGAAACGGGCCTAAG 58.843 55.000 0.84 0.00 0.00 2.18
2638 5834 0.036306 ACACAGAAACGGGCCTAAGG 59.964 55.000 0.84 0.00 0.00 2.69
2639 5835 0.676782 CACAGAAACGGGCCTAAGGG 60.677 60.000 0.84 0.00 0.00 3.95
2655 5851 4.954933 GGCATCTCCAGCCGTTAA 57.045 55.556 0.00 0.00 43.15 2.01
2656 5852 2.695314 GGCATCTCCAGCCGTTAAG 58.305 57.895 0.00 0.00 43.15 1.85
2657 5853 1.440145 GGCATCTCCAGCCGTTAAGC 61.440 60.000 0.00 0.00 43.15 3.09
2658 5854 1.440145 GCATCTCCAGCCGTTAAGCC 61.440 60.000 0.00 0.00 0.00 4.35
2659 5855 0.815615 CATCTCCAGCCGTTAAGCCC 60.816 60.000 0.00 0.00 0.00 5.19
2660 5856 1.984288 ATCTCCAGCCGTTAAGCCCC 61.984 60.000 0.00 0.00 0.00 5.80
2661 5857 3.699134 CTCCAGCCGTTAAGCCCCC 62.699 68.421 0.00 0.00 0.00 5.40
2663 5859 4.090588 CAGCCGTTAAGCCCCCGA 62.091 66.667 0.00 0.00 0.00 5.14
2664 5860 3.782443 AGCCGTTAAGCCCCCGAG 61.782 66.667 0.00 0.00 0.00 4.63
2665 5861 4.851179 GCCGTTAAGCCCCCGAGG 62.851 72.222 0.00 0.00 39.47 4.63
2666 5862 3.078836 CCGTTAAGCCCCCGAGGA 61.079 66.667 0.00 0.00 38.24 3.71
2667 5863 2.499685 CGTTAAGCCCCCGAGGAG 59.500 66.667 0.00 0.00 38.24 3.69
2668 5864 2.908796 GTTAAGCCCCCGAGGAGG 59.091 66.667 0.00 0.00 38.24 4.30
2674 5870 2.683475 CCCCCGAGGAGGCATTTT 59.317 61.111 0.00 0.00 38.24 1.82
2675 5871 1.000359 CCCCCGAGGAGGCATTTTT 60.000 57.895 0.00 0.00 38.24 1.94
3120 6316 4.168291 CCTGGCCGGCTCCTTCTC 62.168 72.222 28.56 8.18 0.00 2.87
3121 6317 4.521062 CTGGCCGGCTCCTTCTCG 62.521 72.222 28.56 1.96 0.00 4.04
3129 6325 4.856607 CTCCTTCTCGCGCCCGTC 62.857 72.222 0.00 0.00 35.54 4.79
3209 6405 4.465446 CGCTCTCCCTCCCTCCCA 62.465 72.222 0.00 0.00 0.00 4.37
3210 6406 2.041265 GCTCTCCCTCCCTCCCAA 59.959 66.667 0.00 0.00 0.00 4.12
3211 6407 2.069430 GCTCTCCCTCCCTCCCAAG 61.069 68.421 0.00 0.00 0.00 3.61
3212 6408 2.041265 TCTCCCTCCCTCCCAAGC 59.959 66.667 0.00 0.00 0.00 4.01
3213 6409 3.093172 CTCCCTCCCTCCCAAGCC 61.093 72.222 0.00 0.00 0.00 4.35
3214 6410 4.760220 TCCCTCCCTCCCAAGCCC 62.760 72.222 0.00 0.00 0.00 5.19
3217 6413 3.732849 CTCCCTCCCAAGCCCCAC 61.733 72.222 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.659244 GACCGCGGTTGACGTCAA 60.659 61.111 34.65 26.53 46.52 3.18
1 2 4.986587 CGACCGCGGTTGACGTCA 62.987 66.667 37.46 15.76 46.52 4.35
27 28 3.030308 CTGCTATGCGCCCGTACG 61.030 66.667 8.69 8.69 38.05 3.67
28 29 1.488261 GAACTGCTATGCGCCCGTAC 61.488 60.000 4.18 0.00 38.05 3.67
30 31 2.511600 GAACTGCTATGCGCCCGT 60.512 61.111 4.18 0.00 38.05 5.28
31 32 3.272334 GGAACTGCTATGCGCCCG 61.272 66.667 4.18 0.00 38.05 6.13
32 33 2.124736 TGGAACTGCTATGCGCCC 60.125 61.111 4.18 0.00 38.05 6.13
33 34 2.472909 GGTGGAACTGCTATGCGCC 61.473 63.158 4.18 0.00 38.05 6.53
34 35 2.813179 CGGTGGAACTGCTATGCGC 61.813 63.158 0.00 0.00 35.75 6.09
35 36 3.398920 CGGTGGAACTGCTATGCG 58.601 61.111 0.00 0.00 35.75 4.73
60 61 4.680237 TCAGCGGTTGCCACTCGG 62.680 66.667 0.00 0.00 44.31 4.63
61 62 3.414700 GTCAGCGGTTGCCACTCG 61.415 66.667 0.00 0.00 44.31 4.18
62 63 3.050275 GGTCAGCGGTTGCCACTC 61.050 66.667 0.00 0.00 44.31 3.51
63 64 4.988598 CGGTCAGCGGTTGCCACT 62.989 66.667 5.26 0.00 44.31 4.00
82 83 2.983592 CACGTTGGTTGCCCTCCC 60.984 66.667 0.00 0.00 0.00 4.30
83 84 3.670377 GCACGTTGGTTGCCCTCC 61.670 66.667 0.00 0.00 0.00 4.30
85 86 2.906897 CTGCACGTTGGTTGCCCT 60.907 61.111 0.00 0.00 0.00 5.19
86 87 3.977244 CCTGCACGTTGGTTGCCC 61.977 66.667 0.00 0.00 0.00 5.36
87 88 4.645921 GCCTGCACGTTGGTTGCC 62.646 66.667 0.00 0.00 0.00 4.52
88 89 4.980903 CGCCTGCACGTTGGTTGC 62.981 66.667 0.00 0.00 0.00 4.17
89 90 2.829206 TTCGCCTGCACGTTGGTTG 61.829 57.895 0.00 0.00 0.00 3.77
90 91 2.515057 TTCGCCTGCACGTTGGTT 60.515 55.556 0.00 0.00 0.00 3.67
94 95 2.203015 ACAGTTCGCCTGCACGTT 60.203 55.556 0.00 0.00 45.68 3.99
95 96 2.661866 GACAGTTCGCCTGCACGT 60.662 61.111 2.29 0.00 45.68 4.49
96 97 2.356313 AGACAGTTCGCCTGCACG 60.356 61.111 2.29 0.00 45.68 5.34
97 98 2.375766 CGAGACAGTTCGCCTGCAC 61.376 63.158 2.29 0.00 45.68 4.57
98 99 2.049156 CGAGACAGTTCGCCTGCA 60.049 61.111 2.29 0.00 45.68 4.41
104 105 2.792290 CGGCATGCGAGACAGTTCG 61.792 63.158 12.44 1.95 43.23 3.95
106 107 3.121030 GCGGCATGCGAGACAGTT 61.121 61.111 12.44 0.00 0.00 3.16
127 128 2.202440 CACGTAGGACGAGGCACG 60.202 66.667 5.94 1.94 46.05 5.34
128 129 2.181021 CCACGTAGGACGAGGCAC 59.819 66.667 5.94 0.00 44.58 5.01
132 133 4.111016 TGCGCCACGTAGGACGAG 62.111 66.667 4.18 0.00 46.05 4.18
137 138 0.110373 GTTTTTCTGCGCCACGTAGG 60.110 55.000 4.18 0.00 39.84 3.18
138 139 0.450482 CGTTTTTCTGCGCCACGTAG 60.450 55.000 4.18 0.00 40.69 3.51
139 140 0.875040 TCGTTTTTCTGCGCCACGTA 60.875 50.000 4.18 0.00 32.65 3.57
140 141 2.174969 TCGTTTTTCTGCGCCACGT 61.175 52.632 4.18 0.00 32.65 4.49
141 142 1.721133 GTCGTTTTTCTGCGCCACG 60.721 57.895 4.18 3.93 0.00 4.94
142 143 1.370051 GGTCGTTTTTCTGCGCCAC 60.370 57.895 4.18 0.00 0.00 5.01
144 145 2.127383 CGGTCGTTTTTCTGCGCC 60.127 61.111 4.18 0.00 0.00 6.53
145 146 1.908066 ATCCGGTCGTTTTTCTGCGC 61.908 55.000 0.00 0.00 0.00 6.09
146 147 0.515564 AATCCGGTCGTTTTTCTGCG 59.484 50.000 0.00 0.00 0.00 5.18
147 148 1.265905 ACAATCCGGTCGTTTTTCTGC 59.734 47.619 0.00 0.00 0.00 4.26
148 149 2.916111 CACAATCCGGTCGTTTTTCTG 58.084 47.619 0.00 0.00 0.00 3.02
149 150 1.265905 GCACAATCCGGTCGTTTTTCT 59.734 47.619 0.00 0.00 0.00 2.52
150 151 1.664874 GGCACAATCCGGTCGTTTTTC 60.665 52.381 0.00 0.00 0.00 2.29
154 155 2.428187 TGGCACAATCCGGTCGTT 59.572 55.556 0.00 0.00 31.92 3.85
165 166 4.471761 TGCACGAATCTTGGCACA 57.528 50.000 0.00 0.00 0.00 4.57
167 168 1.001487 CTTTGTGCACGAATCTTGGCA 60.001 47.619 19.77 0.00 0.00 4.92
168 169 1.001378 ACTTTGTGCACGAATCTTGGC 60.001 47.619 19.77 0.00 0.00 4.52
169 170 3.498397 AGTACTTTGTGCACGAATCTTGG 59.502 43.478 19.77 10.32 0.00 3.61
170 171 4.211164 TGAGTACTTTGTGCACGAATCTTG 59.789 41.667 19.77 10.67 0.00 3.02
171 172 4.377021 TGAGTACTTTGTGCACGAATCTT 58.623 39.130 19.77 9.92 0.00 2.40
172 173 3.990092 TGAGTACTTTGTGCACGAATCT 58.010 40.909 19.77 16.81 0.00 2.40
173 174 4.025229 TGTTGAGTACTTTGTGCACGAATC 60.025 41.667 19.77 14.34 0.00 2.52
174 175 3.874543 TGTTGAGTACTTTGTGCACGAAT 59.125 39.130 19.77 12.26 0.00 3.34
175 176 3.263261 TGTTGAGTACTTTGTGCACGAA 58.737 40.909 18.49 18.49 0.00 3.85
177 178 3.666883 TTGTTGAGTACTTTGTGCACG 57.333 42.857 13.13 0.00 0.00 5.34
178 179 5.168526 TCATTGTTGAGTACTTTGTGCAC 57.831 39.130 10.75 10.75 0.00 4.57
179 180 5.761003 CATCATTGTTGAGTACTTTGTGCA 58.239 37.500 0.00 0.00 34.73 4.57
180 181 4.618489 GCATCATTGTTGAGTACTTTGTGC 59.382 41.667 0.00 0.00 34.73 4.57
181 182 5.854866 CAGCATCATTGTTGAGTACTTTGTG 59.145 40.000 0.00 0.00 36.26 3.33
182 183 5.048504 CCAGCATCATTGTTGAGTACTTTGT 60.049 40.000 0.00 0.00 36.26 2.83
184 185 4.082571 GCCAGCATCATTGTTGAGTACTTT 60.083 41.667 0.00 0.00 36.26 2.66
185 186 3.441572 GCCAGCATCATTGTTGAGTACTT 59.558 43.478 0.00 0.00 36.26 2.24
186 187 3.012518 GCCAGCATCATTGTTGAGTACT 58.987 45.455 0.00 0.00 36.26 2.73
187 188 2.223112 CGCCAGCATCATTGTTGAGTAC 60.223 50.000 0.00 0.00 36.26 2.73
188 189 2.009051 CGCCAGCATCATTGTTGAGTA 58.991 47.619 0.00 0.00 36.26 2.59
190 191 0.806868 ACGCCAGCATCATTGTTGAG 59.193 50.000 0.00 0.00 36.26 3.02
192 193 0.241749 ACACGCCAGCATCATTGTTG 59.758 50.000 0.00 0.00 34.16 3.33
194 195 1.588824 CCACACGCCAGCATCATTGT 61.589 55.000 0.00 0.00 0.00 2.71
195 196 1.138036 CCACACGCCAGCATCATTG 59.862 57.895 0.00 0.00 0.00 2.82
197 198 1.746615 GACCACACGCCAGCATCAT 60.747 57.895 0.00 0.00 0.00 2.45
199 200 3.490759 CGACCACACGCCAGCATC 61.491 66.667 0.00 0.00 0.00 3.91
200 201 3.939837 CTCGACCACACGCCAGCAT 62.940 63.158 0.00 0.00 0.00 3.79
201 202 4.662961 CTCGACCACACGCCAGCA 62.663 66.667 0.00 0.00 0.00 4.41
202 203 3.649277 ATCTCGACCACACGCCAGC 62.649 63.158 0.00 0.00 0.00 4.85
203 204 1.807165 CATCTCGACCACACGCCAG 60.807 63.158 0.00 0.00 0.00 4.85
205 206 2.509336 CCATCTCGACCACACGCC 60.509 66.667 0.00 0.00 0.00 5.68
206 207 2.094659 CACCATCTCGACCACACGC 61.095 63.158 0.00 0.00 0.00 5.34
208 209 1.429463 GTTCACCATCTCGACCACAC 58.571 55.000 0.00 0.00 0.00 3.82
209 210 0.038618 CGTTCACCATCTCGACCACA 60.039 55.000 0.00 0.00 0.00 4.17
210 211 1.352156 GCGTTCACCATCTCGACCAC 61.352 60.000 0.00 0.00 0.00 4.16
211 212 1.080093 GCGTTCACCATCTCGACCA 60.080 57.895 0.00 0.00 0.00 4.02
212 213 1.810030 GGCGTTCACCATCTCGACC 60.810 63.158 0.00 0.00 0.00 4.79
213 214 1.810030 GGGCGTTCACCATCTCGAC 60.810 63.158 0.00 0.00 0.00 4.20
214 215 2.279810 TGGGCGTTCACCATCTCGA 61.280 57.895 0.00 0.00 31.83 4.04
215 216 2.100631 GTGGGCGTTCACCATCTCG 61.101 63.158 0.00 0.00 40.70 4.04
217 218 1.302511 GTGTGGGCGTTCACCATCT 60.303 57.895 7.58 0.00 40.70 2.90
218 219 2.677003 CGTGTGGGCGTTCACCATC 61.677 63.158 7.58 0.00 40.70 3.51
221 222 3.645975 CACGTGTGGGCGTTCACC 61.646 66.667 7.58 0.00 43.83 4.02
222 223 2.893404 ACACGTGTGGGCGTTCAC 60.893 61.111 22.71 3.83 43.83 3.18
223 224 2.892914 CACACGTGTGGGCGTTCA 60.893 61.111 35.65 0.00 43.83 3.18
238 239 3.866910 TCTTCGATAATGTTAACGCCCAC 59.133 43.478 0.26 0.00 0.00 4.61
239 240 4.126208 TCTTCGATAATGTTAACGCCCA 57.874 40.909 0.26 0.00 0.00 5.36
240 241 5.668558 AATCTTCGATAATGTTAACGCCC 57.331 39.130 0.26 0.00 0.00 6.13
241 242 8.492748 TGATAAATCTTCGATAATGTTAACGCC 58.507 33.333 0.26 0.00 0.00 5.68
268 269 7.064253 GCGGCAAAACTTTCTAACTAGAATCTA 59.936 37.037 0.00 0.00 41.52 1.98
269 270 6.128254 GCGGCAAAACTTTCTAACTAGAATCT 60.128 38.462 0.00 0.00 41.52 2.40
270 271 6.022208 GCGGCAAAACTTTCTAACTAGAATC 58.978 40.000 0.00 0.00 41.52 2.52
272 273 4.084223 CGCGGCAAAACTTTCTAACTAGAA 60.084 41.667 0.00 0.00 40.33 2.10
273 274 3.430895 CGCGGCAAAACTTTCTAACTAGA 59.569 43.478 0.00 0.00 0.00 2.43
276 277 1.334689 GCGCGGCAAAACTTTCTAACT 60.335 47.619 8.83 0.00 0.00 2.24
277 278 1.050009 GCGCGGCAAAACTTTCTAAC 58.950 50.000 8.83 0.00 0.00 2.34
278 279 0.948678 AGCGCGGCAAAACTTTCTAA 59.051 45.000 8.83 0.00 0.00 2.10
279 280 0.237235 CAGCGCGGCAAAACTTTCTA 59.763 50.000 8.83 0.00 0.00 2.10
280 281 1.008538 CAGCGCGGCAAAACTTTCT 60.009 52.632 8.83 0.00 0.00 2.52
283 284 3.898509 TGCAGCGCGGCAAAACTT 61.899 55.556 32.59 0.00 41.65 2.66
290 291 3.508840 AAACCTATGCAGCGCGGC 61.509 61.111 26.08 26.08 0.00 6.53
291 292 1.643868 TTCAAACCTATGCAGCGCGG 61.644 55.000 8.83 2.11 0.00 6.46
292 293 0.521242 GTTCAAACCTATGCAGCGCG 60.521 55.000 0.00 0.00 0.00 6.86
293 294 0.804989 AGTTCAAACCTATGCAGCGC 59.195 50.000 0.00 0.00 0.00 5.92
294 295 2.744202 AGAAGTTCAAACCTATGCAGCG 59.256 45.455 5.50 0.00 0.00 5.18
295 296 5.178797 TCTAGAAGTTCAAACCTATGCAGC 58.821 41.667 5.50 0.00 0.00 5.25
296 297 8.986847 CATATCTAGAAGTTCAAACCTATGCAG 58.013 37.037 5.50 0.00 0.00 4.41
298 299 8.894768 ACATATCTAGAAGTTCAAACCTATGC 57.105 34.615 5.50 0.00 0.00 3.14
310 311 9.634021 TGTCTCACATAGAACATATCTAGAAGT 57.366 33.333 0.00 0.00 43.75 3.01
316 317 9.725019 TTTGTTTGTCTCACATAGAACATATCT 57.275 29.630 0.00 0.00 42.48 1.98
355 356 6.937465 TGCCACACAACTAACTTTGTATATGA 59.063 34.615 0.00 0.00 37.62 2.15
357 358 6.128391 CGTGCCACACAACTAACTTTGTATAT 60.128 38.462 0.00 0.00 37.62 0.86
359 360 4.024387 CGTGCCACACAACTAACTTTGTAT 60.024 41.667 0.00 0.00 37.62 2.29
362 363 2.353269 TCGTGCCACACAACTAACTTTG 59.647 45.455 0.00 0.00 33.40 2.77
363 364 2.634600 TCGTGCCACACAACTAACTTT 58.365 42.857 0.00 0.00 33.40 2.66
366 367 2.095919 GGATTCGTGCCACACAACTAAC 60.096 50.000 0.00 0.00 33.40 2.34
367 368 2.147958 GGATTCGTGCCACACAACTAA 58.852 47.619 0.00 0.00 33.40 2.24
368 369 1.346395 AGGATTCGTGCCACACAACTA 59.654 47.619 0.00 0.00 33.40 2.24
369 370 0.108585 AGGATTCGTGCCACACAACT 59.891 50.000 0.00 0.00 33.40 3.16
370 371 1.803334 TAGGATTCGTGCCACACAAC 58.197 50.000 0.00 0.00 33.40 3.32
371 372 2.552599 TTAGGATTCGTGCCACACAA 57.447 45.000 0.00 0.00 33.40 3.33
372 373 2.422597 CTTTAGGATTCGTGCCACACA 58.577 47.619 0.00 0.00 33.40 3.72
373 374 1.130561 GCTTTAGGATTCGTGCCACAC 59.869 52.381 0.00 0.00 0.00 3.82
375 376 0.373716 CGCTTTAGGATTCGTGCCAC 59.626 55.000 0.00 0.00 0.00 5.01
376 377 0.248012 TCGCTTTAGGATTCGTGCCA 59.752 50.000 0.00 0.00 0.00 4.92
377 378 1.583054 ATCGCTTTAGGATTCGTGCC 58.417 50.000 0.00 0.00 0.00 5.01
378 379 4.447724 TCAATATCGCTTTAGGATTCGTGC 59.552 41.667 0.00 0.00 0.00 5.34
379 380 6.420903 TCTTCAATATCGCTTTAGGATTCGTG 59.579 38.462 0.00 0.00 0.00 4.35
380 381 6.513180 TCTTCAATATCGCTTTAGGATTCGT 58.487 36.000 0.00 0.00 0.00 3.85
381 382 6.400515 GCTCTTCAATATCGCTTTAGGATTCG 60.401 42.308 0.00 0.00 0.00 3.34
383 384 6.529220 AGCTCTTCAATATCGCTTTAGGATT 58.471 36.000 0.00 0.00 0.00 3.01
384 385 6.107901 AGCTCTTCAATATCGCTTTAGGAT 57.892 37.500 0.00 0.00 0.00 3.24
385 386 5.537300 AGCTCTTCAATATCGCTTTAGGA 57.463 39.130 0.00 0.00 0.00 2.94
386 387 7.897575 ATTAGCTCTTCAATATCGCTTTAGG 57.102 36.000 0.00 0.00 32.49 2.69
406 407 2.026822 CACCCAGGCCCTGCTATATTAG 60.027 54.545 4.81 0.00 0.00 1.73
407 408 1.985159 CACCCAGGCCCTGCTATATTA 59.015 52.381 4.81 0.00 0.00 0.98
410 411 2.452064 GCACCCAGGCCCTGCTATA 61.452 63.158 4.81 0.00 0.00 1.31
419 420 1.994885 TATAGCCCTTGCACCCAGGC 61.995 60.000 7.26 7.26 46.13 4.85
420 421 0.550914 TTATAGCCCTTGCACCCAGG 59.449 55.000 0.00 0.00 41.13 4.45
421 422 2.435372 TTTATAGCCCTTGCACCCAG 57.565 50.000 0.00 0.00 41.13 4.45
422 423 2.909504 TTTTATAGCCCTTGCACCCA 57.090 45.000 0.00 0.00 41.13 4.51
423 424 3.069586 GGATTTTTATAGCCCTTGCACCC 59.930 47.826 0.00 0.00 41.13 4.61
424 425 3.704061 TGGATTTTTATAGCCCTTGCACC 59.296 43.478 0.00 0.00 41.13 5.01
425 426 4.682787 GTGGATTTTTATAGCCCTTGCAC 58.317 43.478 0.00 0.00 41.13 4.57
427 428 3.630312 TCGTGGATTTTTATAGCCCTTGC 59.370 43.478 0.00 0.00 37.95 4.01
428 429 4.881850 AGTCGTGGATTTTTATAGCCCTTG 59.118 41.667 0.00 0.00 0.00 3.61
430 431 4.704965 GAGTCGTGGATTTTTATAGCCCT 58.295 43.478 0.00 0.00 0.00 5.19
431 432 3.493503 CGAGTCGTGGATTTTTATAGCCC 59.506 47.826 3.82 0.00 0.00 5.19
432 433 3.059800 GCGAGTCGTGGATTTTTATAGCC 60.060 47.826 15.08 0.00 0.00 3.93
433 434 3.361724 CGCGAGTCGTGGATTTTTATAGC 60.362 47.826 18.26 0.00 33.47 2.97
434 435 4.356162 CGCGAGTCGTGGATTTTTATAG 57.644 45.455 18.26 0.00 33.47 1.31
453 3444 1.389106 GTAGAAACACCACGATCACGC 59.611 52.381 0.00 0.00 43.96 5.34
456 3447 4.916870 CGATAGTAGAAACACCACGATCA 58.083 43.478 0.00 0.00 0.00 2.92
521 3512 0.945743 CTGCGGCGCTGCTTATATGA 60.946 55.000 38.42 18.13 35.36 2.15
543 3536 7.248437 GGTTTTGTTCGAGAAAAGAAGAGAAA 58.752 34.615 5.03 0.00 0.00 2.52
544 3537 6.183360 GGGTTTTGTTCGAGAAAAGAAGAGAA 60.183 38.462 5.03 0.00 0.00 2.87
570 3563 0.316196 GCACTTGTGCAACTCGTGTC 60.316 55.000 19.36 0.00 39.01 3.67
701 3744 2.126618 GGATGTCGCGTGTCGTCA 60.127 61.111 15.51 1.16 40.19 4.35
712 3755 4.593864 GAGGCGGCCGAGGATGTC 62.594 72.222 33.48 9.05 0.00 3.06
892 3940 0.391661 TCGATCAAGGGCTTCTGTGC 60.392 55.000 0.00 0.00 0.00 4.57
904 3952 2.143122 GTCAAGGTTGCAGTCGATCAA 58.857 47.619 0.00 0.00 0.00 2.57
905 3953 1.344438 AGTCAAGGTTGCAGTCGATCA 59.656 47.619 0.00 0.00 0.00 2.92
921 3969 0.320374 CGTAACCAGGCAGGAAGTCA 59.680 55.000 1.67 0.00 41.22 3.41
954 4002 0.668535 TGCAGTGATCTACGATCGGG 59.331 55.000 20.98 11.83 0.00 5.14
955 4003 2.120232 GTTGCAGTGATCTACGATCGG 58.880 52.381 20.98 2.12 0.00 4.18
957 4005 2.120232 CCGTTGCAGTGATCTACGATC 58.880 52.381 6.42 0.00 35.35 3.69
1324 4372 4.101448 CTGCCTTGGACCTCCCCG 62.101 72.222 0.00 0.00 34.29 5.73
1340 4388 1.068472 GCCAGTACGCACTATATCGCT 60.068 52.381 0.00 0.00 32.21 4.93
1429 4477 7.605691 ACGCTACTAAGACAAGAAGTAGAAGTA 59.394 37.037 11.81 0.00 43.49 2.24
1484 4666 4.997395 AGCTATAGTGGTGAAGTTGTTGTG 59.003 41.667 0.84 0.00 0.00 3.33
1487 4669 4.997395 CACAGCTATAGTGGTGAAGTTGTT 59.003 41.667 16.34 0.00 38.63 2.83
1530 4712 6.230849 TCTGCAAAATTGTCAATTCATTGC 57.769 33.333 26.64 26.64 41.54 3.56
1597 4779 7.149569 TCCTGTTTTCTTTCTGCAATATCTG 57.850 36.000 0.00 0.00 0.00 2.90
1722 4904 6.823689 ACATGATACTTCAACACCCAATCTAC 59.176 38.462 0.00 0.00 34.96 2.59
1776 4958 1.153823 CACCTGTGTCGATCCGGAC 60.154 63.158 6.12 0.00 37.45 4.79
1827 5009 1.835494 TCTTCTCGTCGTCCTCCATT 58.165 50.000 0.00 0.00 0.00 3.16
1846 5028 1.493871 CATCTGCTTCTCCCCATCCTT 59.506 52.381 0.00 0.00 0.00 3.36
1915 5097 1.137086 CATCGTCGGAGTCCCATTCTT 59.863 52.381 2.80 0.00 0.00 2.52
1952 5134 5.769484 AGAAGCATCCATAATCAGCTTTG 57.231 39.130 0.00 0.00 44.73 2.77
2131 5313 3.587797 ACGGAAATGAGTCGTGTATGT 57.412 42.857 0.00 0.00 35.70 2.29
2136 5318 1.990563 GGTGTACGGAAATGAGTCGTG 59.009 52.381 0.00 0.00 38.19 4.35
2179 5361 3.003689 ACGACTCCTTGAAGCATGTTTTG 59.996 43.478 0.00 0.00 0.00 2.44
2183 5365 1.670087 CGACGACTCCTTGAAGCATGT 60.670 52.381 0.00 0.00 0.00 3.21
2290 5478 3.077359 CCGGAGCAGTTTCAAAGAGAAT 58.923 45.455 0.00 0.00 35.83 2.40
2312 5500 4.207841 GCATGTTAATACGTAACCGACCTC 59.792 45.833 0.00 0.00 41.35 3.85
2359 5547 5.370679 TGCGGAAAACTTAACTAGAACCTT 58.629 37.500 0.00 0.00 0.00 3.50
2360 5548 4.964593 TGCGGAAAACTTAACTAGAACCT 58.035 39.130 0.00 0.00 0.00 3.50
2361 5549 5.678132 TTGCGGAAAACTTAACTAGAACC 57.322 39.130 0.00 0.00 0.00 3.62
2362 5550 7.974243 TTTTTGCGGAAAACTTAACTAGAAC 57.026 32.000 14.81 0.00 32.44 3.01
2388 5576 6.831868 TCTTGGCACTTAACTAGAACCTTTTT 59.168 34.615 0.00 0.00 0.00 1.94
2389 5577 6.362248 TCTTGGCACTTAACTAGAACCTTTT 58.638 36.000 0.00 0.00 0.00 2.27
2390 5578 5.937111 TCTTGGCACTTAACTAGAACCTTT 58.063 37.500 0.00 0.00 0.00 3.11
2428 5616 6.638610 TGAAGAAACCAGAGAAATGCAAAAA 58.361 32.000 0.00 0.00 0.00 1.94
2468 5660 2.159787 GCACTCGTTCATACAACTGCAG 60.160 50.000 13.48 13.48 0.00 4.41
2488 5680 4.151070 CACGAATTCAGTTGTACATGTGC 58.849 43.478 9.11 8.01 0.00 4.57
2590 5786 8.741603 ACACATGATGATCATTGTAATTCAGA 57.258 30.769 10.14 0.00 34.28 3.27
2638 5834 1.440145 GCTTAACGGCTGGAGATGCC 61.440 60.000 0.00 0.00 46.42 4.40
2639 5835 1.440145 GGCTTAACGGCTGGAGATGC 61.440 60.000 0.00 0.00 34.85 3.91
2640 5836 0.815615 GGGCTTAACGGCTGGAGATG 60.816 60.000 0.00 0.00 38.46 2.90
2641 5837 1.527370 GGGCTTAACGGCTGGAGAT 59.473 57.895 0.00 0.00 38.46 2.75
2642 5838 2.666098 GGGGCTTAACGGCTGGAGA 61.666 63.158 0.00 0.00 38.46 3.71
2643 5839 2.124695 GGGGCTTAACGGCTGGAG 60.125 66.667 0.00 0.00 38.46 3.86
2644 5840 3.723922 GGGGGCTTAACGGCTGGA 61.724 66.667 0.00 0.00 38.46 3.86
2646 5842 4.090588 TCGGGGGCTTAACGGCTG 62.091 66.667 0.00 0.00 38.46 4.85
2647 5843 3.782443 CTCGGGGGCTTAACGGCT 61.782 66.667 0.00 0.00 38.46 5.52
2648 5844 4.851179 CCTCGGGGGCTTAACGGC 62.851 72.222 0.00 0.00 37.49 5.68
2649 5845 3.078836 TCCTCGGGGGCTTAACGG 61.079 66.667 0.00 0.00 34.39 4.44
2650 5846 2.499685 CTCCTCGGGGGCTTAACG 59.500 66.667 0.00 0.00 34.39 3.18
2651 5847 2.908796 CCTCCTCGGGGGCTTAAC 59.091 66.667 0.00 0.00 34.39 2.01
2652 5848 3.087906 GCCTCCTCGGGGGCTTAA 61.088 66.667 19.70 0.00 44.48 1.85
2657 5853 1.000359 AAAAATGCCTCCTCGGGGG 60.000 57.895 0.00 0.00 0.00 5.40
2658 5854 4.764143 AAAAATGCCTCCTCGGGG 57.236 55.556 0.00 0.00 0.00 5.73
3103 6299 4.168291 GAGAAGGAGCCGGCCAGG 62.168 72.222 26.15 6.38 44.97 4.45
3104 6300 4.521062 CGAGAAGGAGCCGGCCAG 62.521 72.222 26.15 1.61 0.00 4.85
3112 6308 4.856607 GACGGGCGCGAGAAGGAG 62.857 72.222 30.98 0.00 0.00 3.69
3192 6388 3.984186 TTGGGAGGGAGGGAGAGCG 62.984 68.421 0.00 0.00 0.00 5.03
3193 6389 2.041265 TTGGGAGGGAGGGAGAGC 59.959 66.667 0.00 0.00 0.00 4.09
3194 6390 2.069430 GCTTGGGAGGGAGGGAGAG 61.069 68.421 0.00 0.00 0.00 3.20
3195 6391 2.041265 GCTTGGGAGGGAGGGAGA 59.959 66.667 0.00 0.00 0.00 3.71
3196 6392 3.093172 GGCTTGGGAGGGAGGGAG 61.093 72.222 0.00 0.00 0.00 4.30
3197 6393 4.760220 GGGCTTGGGAGGGAGGGA 62.760 72.222 0.00 0.00 0.00 4.20
3200 6396 3.732849 GTGGGGCTTGGGAGGGAG 61.733 72.222 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.