Multiple sequence alignment - TraesCS7A01G199800

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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 TraesCS7A01G199800 chr7A 100.000 3600 0 0 1 3600 162529875 162526276 0.000000e+00 6649
1 TraesCS7A01G199800 chr7D 96.017 3063 105 7 550 3600 161289473 161286416 0.000000e+00 4964
2 TraesCS7A01G199800 chr7D 91.765 170 8 5 321 489 161290416 161290252 7.770000e-57 231
3 TraesCS7A01G199800 chr7D 95.312 64 3 0 493 556 161290268 161290205 6.360000e-18 102
4 TraesCS7A01G199800 chr7B 94.552 2368 105 12 321 2672 123438044 123435685 0.000000e+00 3637
5 TraesCS7A01G199800 chr6D 93.146 321 15 4 1 318 40537317 40537001 7.040000e-127 464
6 TraesCS7A01G199800 chr3A 92.790 319 18 5 3 318 585062369 585062685 1.180000e-124 457
7 TraesCS7A01G199800 chr3A 92.000 325 21 4 1 322 738732444 738732122 5.480000e-123 451
8 TraesCS7A01G199800 chr2D 92.260 323 23 2 3 324 450874961 450875282 1.180000e-124 457
9 TraesCS7A01G199800 chr1A 92.260 323 22 3 3 324 455016211 455016531 4.240000e-124 455
10 TraesCS7A01G199800 chr1A 91.793 329 21 5 3 329 494811332 494811008 1.520000e-123 453
11 TraesCS7A01G199800 chr5A 92.453 318 21 3 3 318 296306731 296307047 5.480000e-123 451
12 TraesCS7A01G199800 chr4A 92.476 319 18 6 3 318 709847190 709847505 5.480000e-123 451
13 TraesCS7A01G199800 chr5D 92.429 317 21 3 3 318 170318620 170318934 1.970000e-122 449


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 TraesCS7A01G199800 chr7A 162526276 162529875 3599 True 6649.000000 6649 100.000000 1 3600 1 chr7A.!!$R1 3599
1 TraesCS7A01G199800 chr7D 161286416 161290416 4000 True 1765.666667 4964 94.364667 321 3600 3 chr7D.!!$R1 3279
2 TraesCS7A01G199800 chr7B 123435685 123438044 2359 True 3637.000000 3637 94.552000 321 2672 1 chr7B.!!$R1 2351

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
273 274 0.037326 GCCACTTGTCGTGATCTGGA 60.037 55.0 0.0 0.0 46.81 3.86 F
1749 2511 0.250901 TCTGGTTCAGGCTTTGCTCC 60.251 55.0 0.0 0.0 31.51 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1795 2557 0.178992 TGGTGGTTGCCCTTCTTCTG 60.179 55.0 0.0 0.0 0.00 3.02 R
3286 4049 0.390998 GTCAGCCAGACTTCAGGAGC 60.391 60.0 0.0 0.0 44.09 4.70 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
99 100 9.840427 AAAAGTTCGTCAAAACCTATCAATATG 57.160 29.630 0.00 0.00 0.00 1.78
100 101 7.553881 AGTTCGTCAAAACCTATCAATATGG 57.446 36.000 0.00 0.00 0.00 2.74
101 102 6.542370 AGTTCGTCAAAACCTATCAATATGGG 59.458 38.462 0.00 0.00 39.60 4.00
102 103 6.241882 TCGTCAAAACCTATCAATATGGGA 57.758 37.500 0.00 0.00 37.20 4.37
103 104 6.837312 TCGTCAAAACCTATCAATATGGGAT 58.163 36.000 0.00 0.00 37.20 3.85
104 105 6.934645 TCGTCAAAACCTATCAATATGGGATC 59.065 38.462 0.00 0.00 37.20 3.36
105 106 6.936900 CGTCAAAACCTATCAATATGGGATCT 59.063 38.462 0.00 0.00 37.20 2.75
106 107 8.094548 CGTCAAAACCTATCAATATGGGATCTA 58.905 37.037 0.00 0.00 37.20 1.98
107 108 9.442047 GTCAAAACCTATCAATATGGGATCTAG 57.558 37.037 0.00 0.00 37.20 2.43
108 109 9.170890 TCAAAACCTATCAATATGGGATCTAGT 57.829 33.333 0.00 0.00 37.20 2.57
109 110 9.799106 CAAAACCTATCAATATGGGATCTAGTT 57.201 33.333 0.00 0.00 37.20 2.24
112 113 9.799106 AACCTATCAATATGGGATCTAGTTTTG 57.201 33.333 0.00 0.00 37.20 2.44
113 114 9.170890 ACCTATCAATATGGGATCTAGTTTTGA 57.829 33.333 0.00 0.00 37.20 2.69
118 119 9.784531 TCAATATGGGATCTAGTTTTGAAGATC 57.215 33.333 4.15 4.15 37.15 2.75
119 120 9.790344 CAATATGGGATCTAGTTTTGAAGATCT 57.210 33.333 11.05 0.00 37.77 2.75
121 122 5.907207 TGGGATCTAGTTTTGAAGATCTCG 58.093 41.667 11.05 0.00 40.21 4.04
122 123 5.656859 TGGGATCTAGTTTTGAAGATCTCGA 59.343 40.000 11.05 0.00 40.21 4.04
123 124 5.980715 GGGATCTAGTTTTGAAGATCTCGAC 59.019 44.000 11.05 0.00 37.77 4.20
124 125 5.683743 GGATCTAGTTTTGAAGATCTCGACG 59.316 44.000 11.05 0.00 37.77 5.12
125 126 5.624344 TCTAGTTTTGAAGATCTCGACGT 57.376 39.130 0.00 0.00 0.00 4.34
126 127 5.391449 TCTAGTTTTGAAGATCTCGACGTG 58.609 41.667 0.00 0.00 0.00 4.49
127 128 4.238761 AGTTTTGAAGATCTCGACGTGA 57.761 40.909 0.00 1.62 0.00 4.35
128 129 4.230657 AGTTTTGAAGATCTCGACGTGAG 58.769 43.478 0.00 0.00 46.72 3.51
129 130 2.921634 TTGAAGATCTCGACGTGAGG 57.078 50.000 12.89 0.00 45.32 3.86
130 131 2.109425 TGAAGATCTCGACGTGAGGA 57.891 50.000 12.89 0.40 45.32 3.71
131 132 2.433436 TGAAGATCTCGACGTGAGGAA 58.567 47.619 12.89 0.00 45.32 3.36
132 133 3.017442 TGAAGATCTCGACGTGAGGAAT 58.983 45.455 12.89 3.22 45.32 3.01
133 134 3.065510 TGAAGATCTCGACGTGAGGAATC 59.934 47.826 12.89 10.10 45.32 2.52
134 135 1.950909 AGATCTCGACGTGAGGAATCC 59.049 52.381 12.89 0.00 45.32 3.01
135 136 1.676529 GATCTCGACGTGAGGAATCCA 59.323 52.381 0.61 0.00 45.32 3.41
136 137 1.541379 TCTCGACGTGAGGAATCCAA 58.459 50.000 0.61 0.00 45.32 3.53
137 138 2.100197 TCTCGACGTGAGGAATCCAAT 58.900 47.619 0.61 0.00 45.32 3.16
138 139 3.284617 TCTCGACGTGAGGAATCCAATA 58.715 45.455 0.61 0.00 45.32 1.90
139 140 3.315470 TCTCGACGTGAGGAATCCAATAG 59.685 47.826 0.61 0.00 45.32 1.73
140 141 3.021695 TCGACGTGAGGAATCCAATAGT 58.978 45.455 0.61 0.00 0.00 2.12
141 142 3.116300 CGACGTGAGGAATCCAATAGTG 58.884 50.000 0.61 0.00 0.00 2.74
142 143 3.181490 CGACGTGAGGAATCCAATAGTGA 60.181 47.826 0.61 0.00 0.00 3.41
143 144 4.676986 CGACGTGAGGAATCCAATAGTGAA 60.677 45.833 0.61 0.00 0.00 3.18
144 145 5.160607 ACGTGAGGAATCCAATAGTGAAA 57.839 39.130 0.61 0.00 0.00 2.69
145 146 5.556915 ACGTGAGGAATCCAATAGTGAAAA 58.443 37.500 0.61 0.00 0.00 2.29
146 147 5.411669 ACGTGAGGAATCCAATAGTGAAAAC 59.588 40.000 0.61 0.00 0.00 2.43
147 148 5.445939 CGTGAGGAATCCAATAGTGAAAACG 60.446 44.000 0.61 0.00 0.00 3.60
148 149 4.941263 TGAGGAATCCAATAGTGAAAACGG 59.059 41.667 0.61 0.00 0.00 4.44
149 150 4.918588 AGGAATCCAATAGTGAAAACGGT 58.081 39.130 0.61 0.00 0.00 4.83
150 151 5.321927 AGGAATCCAATAGTGAAAACGGTT 58.678 37.500 0.61 0.00 0.00 4.44
151 152 5.414765 AGGAATCCAATAGTGAAAACGGTTC 59.585 40.000 0.61 0.00 0.00 3.62
152 153 5.182380 GGAATCCAATAGTGAAAACGGTTCA 59.818 40.000 0.00 0.00 0.00 3.18
153 154 6.294286 GGAATCCAATAGTGAAAACGGTTCAA 60.294 38.462 5.48 0.00 0.00 2.69
154 155 5.682943 TCCAATAGTGAAAACGGTTCAAG 57.317 39.130 5.48 0.00 0.00 3.02
155 156 5.369833 TCCAATAGTGAAAACGGTTCAAGA 58.630 37.500 5.48 0.00 0.00 3.02
156 157 6.001460 TCCAATAGTGAAAACGGTTCAAGAT 58.999 36.000 5.48 0.77 0.00 2.40
157 158 6.488683 TCCAATAGTGAAAACGGTTCAAGATT 59.511 34.615 5.48 5.89 0.00 2.40
158 159 7.013846 TCCAATAGTGAAAACGGTTCAAGATTT 59.986 33.333 5.48 0.00 0.00 2.17
159 160 7.114811 CCAATAGTGAAAACGGTTCAAGATTTG 59.885 37.037 5.48 7.46 0.00 2.32
160 161 4.932146 AGTGAAAACGGTTCAAGATTTGG 58.068 39.130 5.48 0.00 0.00 3.28
161 162 4.642885 AGTGAAAACGGTTCAAGATTTGGA 59.357 37.500 5.48 0.00 0.00 3.53
162 163 4.738252 GTGAAAACGGTTCAAGATTTGGAC 59.262 41.667 5.48 0.00 38.49 4.02
163 164 3.619233 AAACGGTTCAAGATTTGGACG 57.381 42.857 0.00 0.00 40.19 4.79
164 165 0.872388 ACGGTTCAAGATTTGGACGC 59.128 50.000 0.00 0.00 40.19 5.19
165 166 0.871722 CGGTTCAAGATTTGGACGCA 59.128 50.000 0.00 0.00 40.19 5.24
166 167 1.399727 CGGTTCAAGATTTGGACGCAC 60.400 52.381 0.00 0.00 40.19 5.34
167 168 1.399727 GGTTCAAGATTTGGACGCACG 60.400 52.381 0.00 0.00 40.19 5.34
168 169 0.871722 TTCAAGATTTGGACGCACGG 59.128 50.000 0.00 0.00 0.00 4.94
169 170 0.250124 TCAAGATTTGGACGCACGGT 60.250 50.000 0.00 0.00 0.00 4.83
170 171 0.591170 CAAGATTTGGACGCACGGTT 59.409 50.000 0.00 0.00 0.00 4.44
171 172 1.001815 CAAGATTTGGACGCACGGTTT 60.002 47.619 0.00 0.00 0.00 3.27
172 173 2.172851 AGATTTGGACGCACGGTTTA 57.827 45.000 0.00 0.00 0.00 2.01
173 174 2.496111 AGATTTGGACGCACGGTTTAA 58.504 42.857 0.00 0.00 0.00 1.52
174 175 2.879646 AGATTTGGACGCACGGTTTAAA 59.120 40.909 0.00 0.00 0.00 1.52
175 176 3.315749 AGATTTGGACGCACGGTTTAAAA 59.684 39.130 0.00 0.00 0.00 1.52
176 177 2.759538 TTGGACGCACGGTTTAAAAG 57.240 45.000 0.00 0.00 0.00 2.27
177 178 1.950828 TGGACGCACGGTTTAAAAGA 58.049 45.000 0.00 0.00 0.00 2.52
178 179 2.496111 TGGACGCACGGTTTAAAAGAT 58.504 42.857 0.00 0.00 0.00 2.40
179 180 3.661944 TGGACGCACGGTTTAAAAGATA 58.338 40.909 0.00 0.00 0.00 1.98
180 181 4.063689 TGGACGCACGGTTTAAAAGATAA 58.936 39.130 0.00 0.00 0.00 1.75
181 182 4.514441 TGGACGCACGGTTTAAAAGATAAA 59.486 37.500 0.00 0.00 0.00 1.40
182 183 5.008415 TGGACGCACGGTTTAAAAGATAAAA 59.992 36.000 0.00 0.00 0.00 1.52
183 184 5.340403 GGACGCACGGTTTAAAAGATAAAAC 59.660 40.000 0.00 0.00 35.34 2.43
206 207 6.321873 CGTTTTGAATAAACGGATCTACGA 57.678 37.500 13.31 0.00 46.39 3.43
207 208 6.754206 CGTTTTGAATAAACGGATCTACGAA 58.246 36.000 13.31 0.00 46.39 3.85
208 209 7.228840 CGTTTTGAATAAACGGATCTACGAAA 58.771 34.615 13.31 0.00 46.39 3.46
209 210 7.741216 CGTTTTGAATAAACGGATCTACGAAAA 59.259 33.333 13.31 0.00 46.39 2.29
210 211 9.384682 GTTTTGAATAAACGGATCTACGAAAAA 57.615 29.630 0.00 0.00 37.61 1.94
229 230 4.753516 AAAAAGGAAAACTCCCAGGTTG 57.246 40.909 0.00 0.00 0.00 3.77
230 231 1.704641 AAGGAAAACTCCCAGGTTGC 58.295 50.000 0.00 0.00 0.00 4.17
231 232 0.555769 AGGAAAACTCCCAGGTTGCA 59.444 50.000 0.00 0.00 0.00 4.08
232 233 1.063266 AGGAAAACTCCCAGGTTGCAA 60.063 47.619 0.00 0.00 0.00 4.08
233 234 1.068588 GGAAAACTCCCAGGTTGCAAC 59.931 52.381 21.59 21.59 0.00 4.17
234 235 1.754226 GAAAACTCCCAGGTTGCAACA 59.246 47.619 29.55 9.07 0.00 3.33
235 236 1.859302 AAACTCCCAGGTTGCAACAA 58.141 45.000 29.55 9.35 0.00 2.83
236 237 1.402787 AACTCCCAGGTTGCAACAAG 58.597 50.000 29.55 20.28 0.00 3.16
237 238 0.258774 ACTCCCAGGTTGCAACAAGT 59.741 50.000 29.55 19.60 0.00 3.16
238 239 0.670162 CTCCCAGGTTGCAACAAGTG 59.330 55.000 29.55 21.64 0.00 3.16
239 240 0.754957 TCCCAGGTTGCAACAAGTGG 60.755 55.000 29.55 27.78 0.00 4.00
240 241 1.067916 CCAGGTTGCAACAAGTGGC 59.932 57.895 29.55 12.10 0.00 5.01
241 242 1.299316 CAGGTTGCAACAAGTGGCG 60.299 57.895 29.55 6.78 0.00 5.69
242 243 2.658268 GGTTGCAACAAGTGGCGC 60.658 61.111 29.55 0.00 0.00 6.53
243 244 3.024043 GTTGCAACAAGTGGCGCG 61.024 61.111 24.52 0.00 0.00 6.86
244 245 4.921847 TTGCAACAAGTGGCGCGC 62.922 61.111 25.94 25.94 0.00 6.86
258 259 4.520846 GCGCTGCATGTACGCCAC 62.521 66.667 15.78 0.48 46.63 5.01
259 260 2.815211 CGCTGCATGTACGCCACT 60.815 61.111 0.00 0.00 0.00 4.00
260 261 2.390599 CGCTGCATGTACGCCACTT 61.391 57.895 0.00 0.00 0.00 3.16
261 262 1.135315 GCTGCATGTACGCCACTTG 59.865 57.895 0.00 0.00 35.82 3.16
262 263 1.577328 GCTGCATGTACGCCACTTGT 61.577 55.000 0.00 0.00 35.30 3.16
263 264 0.443869 CTGCATGTACGCCACTTGTC 59.556 55.000 0.00 0.95 35.30 3.18
264 265 1.288419 TGCATGTACGCCACTTGTCG 61.288 55.000 0.00 0.00 35.30 4.35
265 266 1.289109 GCATGTACGCCACTTGTCGT 61.289 55.000 0.00 0.00 42.09 4.34
266 267 0.438445 CATGTACGCCACTTGTCGTG 59.562 55.000 0.00 0.00 43.41 4.35
267 268 0.315886 ATGTACGCCACTTGTCGTGA 59.684 50.000 0.00 0.00 46.81 4.35
268 269 0.315886 TGTACGCCACTTGTCGTGAT 59.684 50.000 0.00 0.00 46.81 3.06
269 270 0.989890 GTACGCCACTTGTCGTGATC 59.010 55.000 0.00 0.00 46.81 2.92
270 271 0.885879 TACGCCACTTGTCGTGATCT 59.114 50.000 0.00 0.00 46.81 2.75
271 272 0.667487 ACGCCACTTGTCGTGATCTG 60.667 55.000 0.00 0.00 46.81 2.90
272 273 1.354337 CGCCACTTGTCGTGATCTGG 61.354 60.000 0.00 0.00 46.81 3.86
273 274 0.037326 GCCACTTGTCGTGATCTGGA 60.037 55.000 0.00 0.00 46.81 3.86
274 275 1.608025 GCCACTTGTCGTGATCTGGAA 60.608 52.381 0.00 0.00 46.81 3.53
275 276 2.766313 CCACTTGTCGTGATCTGGAAA 58.234 47.619 0.00 0.00 46.81 3.13
276 277 3.138304 CCACTTGTCGTGATCTGGAAAA 58.862 45.455 0.00 0.00 46.81 2.29
277 278 3.753272 CCACTTGTCGTGATCTGGAAAAT 59.247 43.478 0.00 0.00 46.81 1.82
278 279 4.378770 CCACTTGTCGTGATCTGGAAAATG 60.379 45.833 0.00 0.00 46.81 2.32
279 280 3.753272 ACTTGTCGTGATCTGGAAAATGG 59.247 43.478 0.00 0.00 0.00 3.16
280 281 3.694043 TGTCGTGATCTGGAAAATGGA 57.306 42.857 0.00 0.00 0.00 3.41
281 282 3.599343 TGTCGTGATCTGGAAAATGGAG 58.401 45.455 0.00 0.00 0.00 3.86
282 283 3.007940 TGTCGTGATCTGGAAAATGGAGT 59.992 43.478 0.00 0.00 0.00 3.85
283 284 3.372206 GTCGTGATCTGGAAAATGGAGTG 59.628 47.826 0.00 0.00 0.00 3.51
284 285 3.007940 TCGTGATCTGGAAAATGGAGTGT 59.992 43.478 0.00 0.00 0.00 3.55
285 286 3.753272 CGTGATCTGGAAAATGGAGTGTT 59.247 43.478 0.00 0.00 0.00 3.32
286 287 4.142816 CGTGATCTGGAAAATGGAGTGTTC 60.143 45.833 0.00 0.00 0.00 3.18
287 288 5.006386 GTGATCTGGAAAATGGAGTGTTCT 58.994 41.667 0.00 0.00 0.00 3.01
288 289 5.474876 GTGATCTGGAAAATGGAGTGTTCTT 59.525 40.000 0.00 0.00 0.00 2.52
289 290 6.015940 GTGATCTGGAAAATGGAGTGTTCTTT 60.016 38.462 0.00 0.00 0.00 2.52
290 291 5.772825 TCTGGAAAATGGAGTGTTCTTTG 57.227 39.130 0.00 0.00 0.00 2.77
291 292 4.037923 TCTGGAAAATGGAGTGTTCTTTGC 59.962 41.667 0.00 0.00 0.00 3.68
292 293 3.703556 TGGAAAATGGAGTGTTCTTTGCA 59.296 39.130 0.00 0.00 0.00 4.08
293 294 4.161189 TGGAAAATGGAGTGTTCTTTGCAA 59.839 37.500 0.00 0.00 0.00 4.08
294 295 4.507756 GGAAAATGGAGTGTTCTTTGCAAC 59.492 41.667 0.00 0.00 0.00 4.17
295 296 4.734398 AAATGGAGTGTTCTTTGCAACA 57.266 36.364 0.00 0.00 33.75 3.33
296 297 4.734398 AATGGAGTGTTCTTTGCAACAA 57.266 36.364 0.00 0.00 38.01 2.83
297 298 3.781079 TGGAGTGTTCTTTGCAACAAG 57.219 42.857 0.00 0.00 38.01 3.16
298 299 3.088532 TGGAGTGTTCTTTGCAACAAGT 58.911 40.909 0.00 0.00 38.01 3.16
299 300 4.265893 TGGAGTGTTCTTTGCAACAAGTA 58.734 39.130 0.00 0.00 38.01 2.24
300 301 4.095782 TGGAGTGTTCTTTGCAACAAGTAC 59.904 41.667 0.00 0.00 38.01 2.73
301 302 4.335594 GGAGTGTTCTTTGCAACAAGTACT 59.664 41.667 0.00 1.28 38.01 2.73
302 303 5.485662 AGTGTTCTTTGCAACAAGTACTC 57.514 39.130 0.00 0.37 38.01 2.59
303 304 5.186198 AGTGTTCTTTGCAACAAGTACTCT 58.814 37.500 0.00 2.80 38.01 3.24
304 305 5.648092 AGTGTTCTTTGCAACAAGTACTCTT 59.352 36.000 0.00 0.00 38.01 2.85
305 306 6.151144 AGTGTTCTTTGCAACAAGTACTCTTT 59.849 34.615 0.00 0.00 38.01 2.52
306 307 7.335924 AGTGTTCTTTGCAACAAGTACTCTTTA 59.664 33.333 0.00 0.00 38.01 1.85
307 308 7.966204 GTGTTCTTTGCAACAAGTACTCTTTAA 59.034 33.333 0.00 0.00 38.01 1.52
308 309 8.682710 TGTTCTTTGCAACAAGTACTCTTTAAT 58.317 29.630 0.00 0.00 33.21 1.40
309 310 9.516314 GTTCTTTGCAACAAGTACTCTTTAATT 57.484 29.630 0.00 0.00 0.00 1.40
313 314 9.944663 TTTGCAACAAGTACTCTTTAATTAGTG 57.055 29.630 0.00 0.00 0.00 2.74
314 315 8.896320 TGCAACAAGTACTCTTTAATTAGTGA 57.104 30.769 0.00 0.00 0.00 3.41
315 316 9.502091 TGCAACAAGTACTCTTTAATTAGTGAT 57.498 29.630 0.00 0.00 0.00 3.06
343 344 6.094048 TGCCTTGTTCAATTCAGTATAGCTTC 59.906 38.462 0.00 0.00 0.00 3.86
443 450 0.466922 GTAGGGGATCTCCGGTCGAA 60.467 60.000 5.81 0.00 36.71 3.71
542 549 3.243704 GGTCGATTCTCTCTGGAGATTGG 60.244 52.174 0.48 0.00 46.51 3.16
568 1313 1.558294 GGAAGGAAATGAGGTACCGGT 59.442 52.381 13.98 13.98 0.00 5.28
1026 1787 3.223589 GCGCTCCTCCTCTCCCTC 61.224 72.222 0.00 0.00 0.00 4.30
1243 2005 2.690497 CGAGAATGACCCAGCTCTTCTA 59.310 50.000 0.00 0.00 0.00 2.10
1327 2089 2.745884 CAAATCTGGCCGCGTGGA 60.746 61.111 21.76 0.00 37.49 4.02
1445 2207 3.412408 GGGAGGGTCCAAGAGGCC 61.412 72.222 0.00 0.00 38.64 5.19
1511 2273 4.155280 GCACCCGACACATTTACTTACAAT 59.845 41.667 0.00 0.00 0.00 2.71
1537 2299 2.160221 CCGATGCATTTTGCCGTGC 61.160 57.895 0.00 0.00 44.23 5.34
1627 2389 3.076621 TCACTCTGAACATGATTGTGGC 58.923 45.455 0.00 0.00 35.83 5.01
1696 2458 4.039609 CAGGGAGAAAAGAACAATTTGGCT 59.960 41.667 0.78 0.00 0.00 4.75
1749 2511 0.250901 TCTGGTTCAGGCTTTGCTCC 60.251 55.000 0.00 0.00 31.51 4.70
1776 2538 2.779755 AAATGTGGACGTAGCCATGA 57.220 45.000 0.00 0.00 40.68 3.07
1795 2557 5.163683 CCATGAAGTTGTTCCATGAGATGAC 60.164 44.000 0.00 0.00 0.00 3.06
1965 2727 5.515106 TGATTGGTGGGTTTTATAAGGAGG 58.485 41.667 0.00 0.00 0.00 4.30
2198 2960 4.260784 GGTAAAATAGATGAGGCGTTGCAG 60.261 45.833 0.00 0.00 0.00 4.41
2205 2967 1.896220 TGAGGCGTTGCAGATTTTCT 58.104 45.000 0.00 0.00 0.00 2.52
2800 3562 5.412904 GGTACTCATCAGTTCCTTTTTCTGG 59.587 44.000 0.00 0.00 37.17 3.86
2870 3632 0.605083 CAGTGCTCAGCTGGTCAGTA 59.395 55.000 15.13 0.08 0.00 2.74
2909 3671 3.304861 GCAGCAACACATTCTTGACATGA 60.305 43.478 0.00 0.00 0.00 3.07
2910 3672 4.793678 GCAGCAACACATTCTTGACATGAA 60.794 41.667 0.00 6.26 0.00 2.57
2914 3676 3.489355 ACACATTCTTGACATGAAGCCA 58.511 40.909 0.00 0.00 0.00 4.75
2930 3692 5.748402 TGAAGCCATCTACATCAAATGAGT 58.252 37.500 0.00 0.00 0.00 3.41
2972 3735 9.907576 GATAATTATTGTTGAAGAGACTTCGTG 57.092 33.333 0.00 0.00 0.00 4.35
2973 3736 7.962964 AATTATTGTTGAAGAGACTTCGTGA 57.037 32.000 0.00 0.00 0.00 4.35
2974 3737 8.553459 AATTATTGTTGAAGAGACTTCGTGAT 57.447 30.769 0.00 0.00 0.00 3.06
3032 3795 2.959030 TCGTATGATGGAAGAGAGGTGG 59.041 50.000 0.00 0.00 0.00 4.61
3077 3840 6.240894 TGATATTCTTATGGAATGGCTGACC 58.759 40.000 6.15 0.00 43.68 4.02
3078 3841 3.297134 TTCTTATGGAATGGCTGACCC 57.703 47.619 0.00 0.00 33.59 4.46
3180 3943 2.386661 ATGCTTAGTCGACACCAAGG 57.613 50.000 19.50 1.80 0.00 3.61
3260 4023 3.831911 ACCAAGGTGTAATTTGTGATGGG 59.168 43.478 0.00 0.00 0.00 4.00
3267 4030 4.702131 GTGTAATTTGTGATGGGAAGAGCT 59.298 41.667 0.00 0.00 0.00 4.09
3269 4032 1.538047 TTTGTGATGGGAAGAGCTGC 58.462 50.000 0.00 0.00 0.00 5.25
3270 4033 0.401356 TTGTGATGGGAAGAGCTGCA 59.599 50.000 1.02 0.00 0.00 4.41
3275 4038 1.041447 ATGGGAAGAGCTGCATTGGC 61.041 55.000 1.02 0.00 41.68 4.52
3286 4049 2.416431 GCTGCATTGGCTAGAAAACCAG 60.416 50.000 0.00 0.06 41.91 4.00
3296 4059 3.558109 GCTAGAAAACCAGCTCCTGAAGT 60.558 47.826 0.00 0.00 34.86 3.01
3315 4078 6.817184 TGAAGTCTGGCTGACCTAATATAAC 58.183 40.000 19.33 3.67 46.46 1.89
3318 4081 4.038883 GTCTGGCTGACCTAATATAACGGT 59.961 45.833 13.00 0.00 39.69 4.83
3340 4103 2.225091 TGCCCCTGTGATCAGAATTGTT 60.225 45.455 0.00 0.00 43.76 2.83
3373 4136 2.456577 TCATAGACAGCCAGCAGTACA 58.543 47.619 0.00 0.00 0.00 2.90
3440 4203 4.142534 ACATATGTGATTTGTGACAGCTGC 60.143 41.667 15.27 7.45 0.00 5.25
3451 4214 1.408702 TGACAGCTGCCCAAGTTTTTC 59.591 47.619 15.27 0.00 0.00 2.29
3456 4219 1.538849 GCTGCCCAAGTTTTTCTGTGG 60.539 52.381 0.00 0.00 0.00 4.17
3473 4236 2.158534 TGTGGTAATCAGGGCACTGTTT 60.159 45.455 17.28 16.67 45.14 2.83
3478 4241 0.478072 ATCAGGGCACTGTTTGGTCA 59.522 50.000 17.28 0.00 45.14 4.02
3489 4252 0.038166 GTTTGGTCAGGGGCTCATCA 59.962 55.000 0.00 0.00 0.00 3.07
3536 4299 2.870411 ACCTGCGTTACAACTGAAGAAC 59.130 45.455 0.00 0.00 0.00 3.01
3581 4345 6.714810 ACATTTACAACCTAATCACTTCAGCA 59.285 34.615 0.00 0.00 0.00 4.41
3594 4358 3.561310 CACTTCAGCACTCAACTGCTTAA 59.439 43.478 0.00 0.00 45.64 1.85
3595 4359 4.214971 CACTTCAGCACTCAACTGCTTAAT 59.785 41.667 0.00 0.00 45.64 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 9.840427 CATATTGATAGGTTTTGACGAACTTTT 57.160 29.630 0.00 0.00 0.00 2.27
74 75 8.458843 CCATATTGATAGGTTTTGACGAACTTT 58.541 33.333 0.00 0.00 0.00 2.66
75 76 7.067008 CCCATATTGATAGGTTTTGACGAACTT 59.933 37.037 0.00 0.00 0.00 2.66
76 77 6.542370 CCCATATTGATAGGTTTTGACGAACT 59.458 38.462 0.00 0.00 0.00 3.01
77 78 6.540914 TCCCATATTGATAGGTTTTGACGAAC 59.459 38.462 0.00 0.00 0.00 3.95
78 79 6.654959 TCCCATATTGATAGGTTTTGACGAA 58.345 36.000 0.00 0.00 0.00 3.85
79 80 6.241882 TCCCATATTGATAGGTTTTGACGA 57.758 37.500 0.00 0.00 0.00 4.20
80 81 6.936900 AGATCCCATATTGATAGGTTTTGACG 59.063 38.462 0.00 0.00 0.00 4.35
81 82 9.442047 CTAGATCCCATATTGATAGGTTTTGAC 57.558 37.037 0.00 0.00 0.00 3.18
82 83 9.170890 ACTAGATCCCATATTGATAGGTTTTGA 57.829 33.333 0.00 0.00 0.00 2.69
83 84 9.799106 AACTAGATCCCATATTGATAGGTTTTG 57.201 33.333 0.00 0.00 0.00 2.44
86 87 9.799106 CAAAACTAGATCCCATATTGATAGGTT 57.201 33.333 0.00 0.00 0.00 3.50
87 88 9.170890 TCAAAACTAGATCCCATATTGATAGGT 57.829 33.333 0.00 0.00 0.00 3.08
92 93 9.784531 GATCTTCAAAACTAGATCCCATATTGA 57.215 33.333 0.00 0.00 33.15 2.57
93 94 9.790344 AGATCTTCAAAACTAGATCCCATATTG 57.210 33.333 0.00 0.00 38.24 1.90
95 96 8.310382 CGAGATCTTCAAAACTAGATCCCATAT 58.690 37.037 0.00 0.00 38.24 1.78
96 97 7.505923 TCGAGATCTTCAAAACTAGATCCCATA 59.494 37.037 0.00 0.00 38.24 2.74
97 98 6.325028 TCGAGATCTTCAAAACTAGATCCCAT 59.675 38.462 0.00 0.00 38.24 4.00
98 99 5.656859 TCGAGATCTTCAAAACTAGATCCCA 59.343 40.000 0.00 0.00 38.24 4.37
99 100 5.980715 GTCGAGATCTTCAAAACTAGATCCC 59.019 44.000 0.00 0.00 38.24 3.85
100 101 5.683743 CGTCGAGATCTTCAAAACTAGATCC 59.316 44.000 0.00 1.33 38.24 3.36
101 102 6.195613 CACGTCGAGATCTTCAAAACTAGATC 59.804 42.308 0.00 0.00 37.89 2.75
102 103 6.030849 CACGTCGAGATCTTCAAAACTAGAT 58.969 40.000 0.00 0.00 0.00 1.98
103 104 5.180680 TCACGTCGAGATCTTCAAAACTAGA 59.819 40.000 0.00 0.00 0.00 2.43
104 105 5.391449 TCACGTCGAGATCTTCAAAACTAG 58.609 41.667 0.00 0.00 0.00 2.57
105 106 5.366829 TCACGTCGAGATCTTCAAAACTA 57.633 39.130 0.00 0.00 0.00 2.24
106 107 4.230657 CTCACGTCGAGATCTTCAAAACT 58.769 43.478 0.00 0.00 45.45 2.66
107 108 3.365220 CCTCACGTCGAGATCTTCAAAAC 59.635 47.826 14.19 0.00 45.45 2.43
108 109 3.254903 TCCTCACGTCGAGATCTTCAAAA 59.745 43.478 14.19 0.00 45.45 2.44
109 110 2.817844 TCCTCACGTCGAGATCTTCAAA 59.182 45.455 14.19 0.00 45.45 2.69
110 111 2.433436 TCCTCACGTCGAGATCTTCAA 58.567 47.619 14.19 0.00 45.45 2.69
111 112 2.109425 TCCTCACGTCGAGATCTTCA 57.891 50.000 14.19 0.00 45.45 3.02
112 113 3.549221 GGATTCCTCACGTCGAGATCTTC 60.549 52.174 14.19 7.26 45.45 2.87
113 114 2.359531 GGATTCCTCACGTCGAGATCTT 59.640 50.000 14.19 0.36 45.45 2.40
114 115 1.950909 GGATTCCTCACGTCGAGATCT 59.049 52.381 14.19 0.00 45.45 2.75
115 116 1.676529 TGGATTCCTCACGTCGAGATC 59.323 52.381 14.19 10.47 45.45 2.75
116 117 1.763968 TGGATTCCTCACGTCGAGAT 58.236 50.000 14.19 3.69 45.45 2.75
117 118 1.541379 TTGGATTCCTCACGTCGAGA 58.459 50.000 14.19 0.00 45.45 4.04
118 119 2.586258 ATTGGATTCCTCACGTCGAG 57.414 50.000 3.95 7.72 41.89 4.04
119 120 3.021695 ACTATTGGATTCCTCACGTCGA 58.978 45.455 3.95 0.00 0.00 4.20
120 121 3.116300 CACTATTGGATTCCTCACGTCG 58.884 50.000 3.95 0.00 0.00 5.12
121 122 4.386867 TCACTATTGGATTCCTCACGTC 57.613 45.455 3.95 0.00 0.00 4.34
122 123 4.819105 TTCACTATTGGATTCCTCACGT 57.181 40.909 3.95 0.00 0.00 4.49
123 124 5.445939 CGTTTTCACTATTGGATTCCTCACG 60.446 44.000 3.95 0.00 0.00 4.35
124 125 5.163754 CCGTTTTCACTATTGGATTCCTCAC 60.164 44.000 3.95 0.00 0.00 3.51
125 126 4.941263 CCGTTTTCACTATTGGATTCCTCA 59.059 41.667 3.95 0.00 0.00 3.86
126 127 4.941873 ACCGTTTTCACTATTGGATTCCTC 59.058 41.667 3.95 0.00 0.00 3.71
127 128 4.918588 ACCGTTTTCACTATTGGATTCCT 58.081 39.130 3.95 0.00 0.00 3.36
128 129 5.182380 TGAACCGTTTTCACTATTGGATTCC 59.818 40.000 0.00 0.00 0.00 3.01
129 130 6.249035 TGAACCGTTTTCACTATTGGATTC 57.751 37.500 0.00 0.00 0.00 2.52
130 131 6.488683 TCTTGAACCGTTTTCACTATTGGATT 59.511 34.615 0.00 0.00 0.00 3.01
131 132 6.001460 TCTTGAACCGTTTTCACTATTGGAT 58.999 36.000 0.00 0.00 0.00 3.41
132 133 5.369833 TCTTGAACCGTTTTCACTATTGGA 58.630 37.500 0.00 0.00 0.00 3.53
133 134 5.682943 TCTTGAACCGTTTTCACTATTGG 57.317 39.130 0.00 0.00 0.00 3.16
134 135 7.114811 CCAAATCTTGAACCGTTTTCACTATTG 59.885 37.037 0.00 1.97 0.00 1.90
135 136 7.013846 TCCAAATCTTGAACCGTTTTCACTATT 59.986 33.333 0.00 0.00 0.00 1.73
136 137 6.488683 TCCAAATCTTGAACCGTTTTCACTAT 59.511 34.615 0.00 0.00 0.00 2.12
137 138 5.823570 TCCAAATCTTGAACCGTTTTCACTA 59.176 36.000 0.00 0.00 0.00 2.74
138 139 4.642885 TCCAAATCTTGAACCGTTTTCACT 59.357 37.500 0.00 0.00 0.00 3.41
139 140 4.738252 GTCCAAATCTTGAACCGTTTTCAC 59.262 41.667 0.00 0.00 0.00 3.18
140 141 4.496673 CGTCCAAATCTTGAACCGTTTTCA 60.497 41.667 0.00 0.00 0.00 2.69
141 142 3.972502 CGTCCAAATCTTGAACCGTTTTC 59.027 43.478 0.00 0.00 0.00 2.29
142 143 3.794138 GCGTCCAAATCTTGAACCGTTTT 60.794 43.478 0.00 0.00 0.00 2.43
143 144 2.287368 GCGTCCAAATCTTGAACCGTTT 60.287 45.455 0.00 0.00 0.00 3.60
144 145 1.265905 GCGTCCAAATCTTGAACCGTT 59.734 47.619 0.00 0.00 0.00 4.44
145 146 0.872388 GCGTCCAAATCTTGAACCGT 59.128 50.000 0.00 0.00 0.00 4.83
146 147 0.871722 TGCGTCCAAATCTTGAACCG 59.128 50.000 0.00 0.00 0.00 4.44
147 148 1.399727 CGTGCGTCCAAATCTTGAACC 60.400 52.381 0.00 0.00 0.00 3.62
148 149 1.399727 CCGTGCGTCCAAATCTTGAAC 60.400 52.381 0.00 0.00 0.00 3.18
149 150 0.871722 CCGTGCGTCCAAATCTTGAA 59.128 50.000 0.00 0.00 0.00 2.69
150 151 0.250124 ACCGTGCGTCCAAATCTTGA 60.250 50.000 0.00 0.00 0.00 3.02
151 152 0.591170 AACCGTGCGTCCAAATCTTG 59.409 50.000 0.00 0.00 0.00 3.02
152 153 1.314730 AAACCGTGCGTCCAAATCTT 58.685 45.000 0.00 0.00 0.00 2.40
153 154 2.172851 TAAACCGTGCGTCCAAATCT 57.827 45.000 0.00 0.00 0.00 2.40
154 155 2.973419 TTAAACCGTGCGTCCAAATC 57.027 45.000 0.00 0.00 0.00 2.17
155 156 3.315749 TCTTTTAAACCGTGCGTCCAAAT 59.684 39.130 0.00 0.00 0.00 2.32
156 157 2.681848 TCTTTTAAACCGTGCGTCCAAA 59.318 40.909 0.00 0.00 0.00 3.28
157 158 2.286872 TCTTTTAAACCGTGCGTCCAA 58.713 42.857 0.00 0.00 0.00 3.53
158 159 1.950828 TCTTTTAAACCGTGCGTCCA 58.049 45.000 0.00 0.00 0.00 4.02
159 160 4.666928 TTATCTTTTAAACCGTGCGTCC 57.333 40.909 0.00 0.00 0.00 4.79
160 161 5.057166 CGTTTTATCTTTTAAACCGTGCGTC 59.943 40.000 0.00 0.00 32.05 5.19
161 162 4.905295 CGTTTTATCTTTTAAACCGTGCGT 59.095 37.500 0.00 0.00 32.05 5.24
162 163 4.905295 ACGTTTTATCTTTTAAACCGTGCG 59.095 37.500 0.86 0.00 32.05 5.34
163 164 6.736807 AACGTTTTATCTTTTAAACCGTGC 57.263 33.333 0.00 0.00 32.05 5.34
164 165 8.796278 TCAAAACGTTTTATCTTTTAAACCGTG 58.204 29.630 24.79 8.65 32.05 4.94
165 166 8.908172 TCAAAACGTTTTATCTTTTAAACCGT 57.092 26.923 24.79 0.00 32.05 4.83
181 182 7.095691 TTCGTAGATCCGTTTATTCAAAACGTT 60.096 33.333 18.32 0.00 43.53 3.99
182 183 6.365789 TTCGTAGATCCGTTTATTCAAAACGT 59.634 34.615 18.32 4.51 43.53 3.99
183 184 6.754206 TTCGTAGATCCGTTTATTCAAAACG 58.246 36.000 14.30 14.30 44.14 3.60
184 185 8.938047 TTTTCGTAGATCCGTTTATTCAAAAC 57.062 30.769 0.00 0.00 35.04 2.43
208 209 3.118408 GCAACCTGGGAGTTTTCCTTTTT 60.118 43.478 0.00 0.00 43.49 1.94
209 210 2.434336 GCAACCTGGGAGTTTTCCTTTT 59.566 45.455 0.00 0.00 43.49 2.27
210 211 2.039418 GCAACCTGGGAGTTTTCCTTT 58.961 47.619 0.00 0.00 43.49 3.11
211 212 1.063266 TGCAACCTGGGAGTTTTCCTT 60.063 47.619 0.00 0.00 43.49 3.36
212 213 0.555769 TGCAACCTGGGAGTTTTCCT 59.444 50.000 0.00 0.00 43.49 3.36
213 214 1.068588 GTTGCAACCTGGGAGTTTTCC 59.931 52.381 19.15 0.00 43.23 3.13
214 215 1.754226 TGTTGCAACCTGGGAGTTTTC 59.246 47.619 26.14 0.00 0.00 2.29
215 216 1.859302 TGTTGCAACCTGGGAGTTTT 58.141 45.000 26.14 0.00 0.00 2.43
216 217 1.756538 CTTGTTGCAACCTGGGAGTTT 59.243 47.619 26.14 0.00 0.00 2.66
217 218 1.341976 ACTTGTTGCAACCTGGGAGTT 60.342 47.619 26.14 0.77 0.00 3.01
218 219 0.258774 ACTTGTTGCAACCTGGGAGT 59.741 50.000 26.14 17.48 0.00 3.85
219 220 0.670162 CACTTGTTGCAACCTGGGAG 59.330 55.000 26.14 16.91 0.00 4.30
220 221 0.754957 CCACTTGTTGCAACCTGGGA 60.755 55.000 26.14 4.69 0.00 4.37
221 222 1.741525 CCACTTGTTGCAACCTGGG 59.258 57.895 26.14 18.61 0.00 4.45
222 223 1.067916 GCCACTTGTTGCAACCTGG 59.932 57.895 26.14 24.88 0.00 4.45
223 224 1.299316 CGCCACTTGTTGCAACCTG 60.299 57.895 26.14 19.75 0.00 4.00
224 225 3.119193 CGCCACTTGTTGCAACCT 58.881 55.556 26.14 6.41 0.00 3.50
225 226 2.658268 GCGCCACTTGTTGCAACC 60.658 61.111 26.14 9.01 0.00 3.77
226 227 3.024043 CGCGCCACTTGTTGCAAC 61.024 61.111 22.83 22.83 0.00 4.17
227 228 4.921847 GCGCGCCACTTGTTGCAA 62.922 61.111 23.24 0.00 0.00 4.08
235 236 4.758251 TACATGCAGCGCGCCACT 62.758 61.111 30.33 6.46 41.33 4.00
236 237 4.520846 GTACATGCAGCGCGCCAC 62.521 66.667 30.33 21.15 41.33 5.01
242 243 2.390599 AAGTGGCGTACATGCAGCG 61.391 57.895 0.00 0.00 36.28 5.18
243 244 1.135315 CAAGTGGCGTACATGCAGC 59.865 57.895 0.00 0.00 36.28 5.25
244 245 0.443869 GACAAGTGGCGTACATGCAG 59.556 55.000 0.00 0.00 36.28 4.41
245 246 1.288419 CGACAAGTGGCGTACATGCA 61.288 55.000 0.00 0.00 42.66 3.96
246 247 1.419922 CGACAAGTGGCGTACATGC 59.580 57.895 0.00 0.00 42.66 4.06
257 258 3.753272 CCATTTTCCAGATCACGACAAGT 59.247 43.478 0.00 0.00 0.00 3.16
258 259 4.002982 TCCATTTTCCAGATCACGACAAG 58.997 43.478 0.00 0.00 0.00 3.16
259 260 4.002982 CTCCATTTTCCAGATCACGACAA 58.997 43.478 0.00 0.00 0.00 3.18
260 261 3.007940 ACTCCATTTTCCAGATCACGACA 59.992 43.478 0.00 0.00 0.00 4.35
261 262 3.372206 CACTCCATTTTCCAGATCACGAC 59.628 47.826 0.00 0.00 0.00 4.34
262 263 3.007940 ACACTCCATTTTCCAGATCACGA 59.992 43.478 0.00 0.00 0.00 4.35
263 264 3.338249 ACACTCCATTTTCCAGATCACG 58.662 45.455 0.00 0.00 0.00 4.35
264 265 5.006386 AGAACACTCCATTTTCCAGATCAC 58.994 41.667 0.00 0.00 0.00 3.06
265 266 5.246981 AGAACACTCCATTTTCCAGATCA 57.753 39.130 0.00 0.00 0.00 2.92
266 267 6.385033 CAAAGAACACTCCATTTTCCAGATC 58.615 40.000 0.00 0.00 0.00 2.75
267 268 5.279156 GCAAAGAACACTCCATTTTCCAGAT 60.279 40.000 0.00 0.00 0.00 2.90
268 269 4.037923 GCAAAGAACACTCCATTTTCCAGA 59.962 41.667 0.00 0.00 0.00 3.86
269 270 4.202141 TGCAAAGAACACTCCATTTTCCAG 60.202 41.667 0.00 0.00 0.00 3.86
270 271 3.703556 TGCAAAGAACACTCCATTTTCCA 59.296 39.130 0.00 0.00 0.00 3.53
271 272 4.320608 TGCAAAGAACACTCCATTTTCC 57.679 40.909 0.00 0.00 0.00 3.13
272 273 5.108517 TGTTGCAAAGAACACTCCATTTTC 58.891 37.500 0.00 0.00 30.75 2.29
273 274 5.083533 TGTTGCAAAGAACACTCCATTTT 57.916 34.783 0.00 0.00 30.75 1.82
274 275 4.734398 TGTTGCAAAGAACACTCCATTT 57.266 36.364 0.00 0.00 30.75 2.32
275 276 4.160252 ACTTGTTGCAAAGAACACTCCATT 59.840 37.500 0.00 0.00 35.56 3.16
276 277 3.701040 ACTTGTTGCAAAGAACACTCCAT 59.299 39.130 0.00 0.00 35.56 3.41
277 278 3.088532 ACTTGTTGCAAAGAACACTCCA 58.911 40.909 0.00 0.00 35.56 3.86
278 279 3.782889 ACTTGTTGCAAAGAACACTCC 57.217 42.857 0.00 0.00 35.56 3.85
279 280 5.294552 AGAGTACTTGTTGCAAAGAACACTC 59.705 40.000 17.54 17.54 35.56 3.51
280 281 5.186198 AGAGTACTTGTTGCAAAGAACACT 58.814 37.500 0.00 2.09 35.56 3.55
281 282 5.485662 AGAGTACTTGTTGCAAAGAACAC 57.514 39.130 0.00 0.00 35.56 3.32
282 283 6.509418 AAAGAGTACTTGTTGCAAAGAACA 57.491 33.333 0.00 0.00 36.39 3.18
283 284 9.516314 AATTAAAGAGTACTTGTTGCAAAGAAC 57.484 29.630 0.00 0.00 36.39 3.01
287 288 9.944663 CACTAATTAAAGAGTACTTGTTGCAAA 57.055 29.630 0.00 0.00 36.39 3.68
288 289 9.332502 TCACTAATTAAAGAGTACTTGTTGCAA 57.667 29.630 0.00 0.00 36.39 4.08
289 290 8.896320 TCACTAATTAAAGAGTACTTGTTGCA 57.104 30.769 0.00 0.00 36.39 4.08
296 297 9.740710 AGGCAAAATCACTAATTAAAGAGTACT 57.259 29.630 0.00 0.00 0.00 2.73
299 300 8.860088 ACAAGGCAAAATCACTAATTAAAGAGT 58.140 29.630 0.00 0.00 0.00 3.24
300 301 9.696917 AACAAGGCAAAATCACTAATTAAAGAG 57.303 29.630 0.00 0.00 0.00 2.85
301 302 9.691362 GAACAAGGCAAAATCACTAATTAAAGA 57.309 29.630 0.00 0.00 0.00 2.52
302 303 9.474920 TGAACAAGGCAAAATCACTAATTAAAG 57.525 29.630 0.00 0.00 0.00 1.85
303 304 9.823647 TTGAACAAGGCAAAATCACTAATTAAA 57.176 25.926 0.00 0.00 0.00 1.52
304 305 9.995003 ATTGAACAAGGCAAAATCACTAATTAA 57.005 25.926 0.00 0.00 0.00 1.40
305 306 9.995003 AATTGAACAAGGCAAAATCACTAATTA 57.005 25.926 0.00 0.00 0.00 1.40
306 307 8.907222 AATTGAACAAGGCAAAATCACTAATT 57.093 26.923 0.00 0.00 0.00 1.40
307 308 8.149647 TGAATTGAACAAGGCAAAATCACTAAT 58.850 29.630 0.00 0.00 0.00 1.73
308 309 7.495901 TGAATTGAACAAGGCAAAATCACTAA 58.504 30.769 0.00 0.00 0.00 2.24
309 310 7.048629 TGAATTGAACAAGGCAAAATCACTA 57.951 32.000 0.00 0.00 0.00 2.74
310 311 5.916318 TGAATTGAACAAGGCAAAATCACT 58.084 33.333 0.00 0.00 0.00 3.41
311 312 5.754890 ACTGAATTGAACAAGGCAAAATCAC 59.245 36.000 0.00 0.00 0.00 3.06
312 313 5.916318 ACTGAATTGAACAAGGCAAAATCA 58.084 33.333 0.00 0.00 0.00 2.57
313 314 9.294030 CTATACTGAATTGAACAAGGCAAAATC 57.706 33.333 0.00 0.00 0.00 2.17
314 315 7.761249 GCTATACTGAATTGAACAAGGCAAAAT 59.239 33.333 0.00 0.00 0.00 1.82
315 316 7.039784 AGCTATACTGAATTGAACAAGGCAAAA 60.040 33.333 0.00 0.00 0.00 2.44
316 317 6.434028 AGCTATACTGAATTGAACAAGGCAAA 59.566 34.615 0.00 0.00 0.00 3.68
317 318 5.945784 AGCTATACTGAATTGAACAAGGCAA 59.054 36.000 0.00 0.00 0.00 4.52
318 319 5.500234 AGCTATACTGAATTGAACAAGGCA 58.500 37.500 0.00 0.00 0.00 4.75
319 320 6.442513 AAGCTATACTGAATTGAACAAGGC 57.557 37.500 0.00 0.00 0.00 4.35
542 549 5.126779 GGTACCTCATTTCCTTCCAATCTC 58.873 45.833 4.06 0.00 0.00 2.75
568 1313 1.473258 CGGCCCAAAATGGATCAAGA 58.527 50.000 0.00 0.00 40.96 3.02
1295 2057 1.820519 GATTTGCAGAGGCCATTGACA 59.179 47.619 5.01 2.66 40.13 3.58
1388 2150 1.487452 CCACCGTGTTCACAGTGACG 61.487 60.000 17.46 4.45 31.79 4.35
1445 2207 0.798776 GCTCCTCCACAAATGTCACG 59.201 55.000 0.00 0.00 0.00 4.35
1511 2273 0.321021 AAAATGCATCGGCCAAGCAA 59.679 45.000 16.40 2.55 42.15 3.91
1556 2318 2.671070 CTCCCAACCACCTCGCAT 59.329 61.111 0.00 0.00 0.00 4.73
1559 2321 1.221840 CATCCTCCCAACCACCTCG 59.778 63.158 0.00 0.00 0.00 4.63
1642 2404 2.036256 CAGCCCAAACCCTCCCTG 59.964 66.667 0.00 0.00 0.00 4.45
1712 2474 2.154798 GAGTGCTGTAGGTCACCGCA 62.155 60.000 0.00 0.00 44.06 5.69
1749 2511 2.961522 ACGTCCACATTTTTAGTGCG 57.038 45.000 0.00 0.00 35.69 5.34
1766 2528 2.422597 TGGAACAACTTCATGGCTACG 58.577 47.619 0.00 0.00 31.92 3.51
1795 2557 0.178992 TGGTGGTTGCCCTTCTTCTG 60.179 55.000 0.00 0.00 0.00 3.02
1841 2603 0.899720 CTGCTTGTGCCAATCCCAAT 59.100 50.000 0.00 0.00 38.71 3.16
1957 2719 3.766591 CTCACACAGTCTGTCCTCCTTAT 59.233 47.826 1.37 0.00 0.00 1.73
1960 2722 1.626686 CTCACACAGTCTGTCCTCCT 58.373 55.000 1.37 0.00 0.00 3.69
1965 2727 0.676184 TGAGCCTCACACAGTCTGTC 59.324 55.000 1.37 0.00 0.00 3.51
2198 2960 7.174599 CCAGATTCATCCATAGACCAGAAAATC 59.825 40.741 0.00 0.00 0.00 2.17
2205 2967 4.040047 ACACCAGATTCATCCATAGACCA 58.960 43.478 0.00 0.00 0.00 4.02
2586 3348 9.905713 ATGCCTACATAATTTGAGAAAGACTAA 57.094 29.630 0.00 0.00 33.67 2.24
2606 3368 3.765511 AGCTGAAGCAAAATTCATGCCTA 59.234 39.130 11.39 0.51 44.91 3.93
2800 3562 0.799534 GCGCTCATGGATGCAAACAC 60.800 55.000 0.00 0.00 0.00 3.32
2855 3617 2.955660 ACTATCTACTGACCAGCTGAGC 59.044 50.000 17.39 7.08 0.00 4.26
2870 3632 4.023980 TGCTGCCTGTTACACTACTATCT 58.976 43.478 0.00 0.00 0.00 1.98
2909 3671 5.999044 AGACTCATTTGATGTAGATGGCTT 58.001 37.500 0.00 0.00 0.00 4.35
2910 3672 5.366186 AGAGACTCATTTGATGTAGATGGCT 59.634 40.000 5.02 0.00 0.00 4.75
3032 3795 0.535335 TGGCCACGTAATCTGGAGTC 59.465 55.000 0.00 0.00 0.00 3.36
3077 3840 3.250762 TCTTTCTGTTTCAGCAATGACGG 59.749 43.478 0.00 0.00 0.00 4.79
3078 3841 4.472691 TCTTTCTGTTTCAGCAATGACG 57.527 40.909 0.00 0.00 0.00 4.35
3180 3943 1.889170 CTCCCTCCTTTGAGCAAAACC 59.111 52.381 0.00 0.00 37.29 3.27
3240 4003 5.476599 TCTTCCCATCACAAATTACACCTTG 59.523 40.000 0.00 0.00 0.00 3.61
3260 4023 2.322355 TCTAGCCAATGCAGCTCTTC 57.678 50.000 1.69 0.00 41.83 2.87
3267 4030 1.545582 GCTGGTTTTCTAGCCAATGCA 59.454 47.619 0.00 0.00 46.51 3.96
3275 4038 4.020662 AGACTTCAGGAGCTGGTTTTCTAG 60.021 45.833 0.00 0.00 31.51 2.43
3286 4049 0.390998 GTCAGCCAGACTTCAGGAGC 60.391 60.000 0.00 0.00 44.09 4.70
3296 4059 4.220724 ACCGTTATATTAGGTCAGCCAGA 58.779 43.478 0.00 0.00 37.19 3.86
3318 4081 2.225091 ACAATTCTGATCACAGGGGCAA 60.225 45.455 0.00 0.00 43.60 4.52
3358 4121 2.005451 CTGAATGTACTGCTGGCTGTC 58.995 52.381 8.29 2.78 0.00 3.51
3373 4136 8.664079 AGAATTCAGTATGGCCTATAACTGAAT 58.336 33.333 29.55 29.55 43.05 2.57
3440 4203 5.278957 CCTGATTACCACAGAAAAACTTGGG 60.279 44.000 0.00 0.00 37.54 4.12
3451 4214 1.003580 ACAGTGCCCTGATTACCACAG 59.996 52.381 2.19 0.00 41.50 3.66
3456 4219 2.488153 GACCAAACAGTGCCCTGATTAC 59.512 50.000 2.19 0.00 41.50 1.89
3473 4236 0.842030 AACTGATGAGCCCCTGACCA 60.842 55.000 0.00 0.00 0.00 4.02
3478 4241 1.283321 GAAAGGAACTGATGAGCCCCT 59.717 52.381 0.00 0.00 40.86 4.79
3521 4284 4.270325 ACTTCTGCGTTCTTCAGTTGTAAC 59.730 41.667 0.00 0.00 33.48 2.50
3525 4288 2.097202 CGACTTCTGCGTTCTTCAGTTG 60.097 50.000 0.00 0.00 33.48 3.16
3536 4299 1.926510 TGCAATGTATCGACTTCTGCG 59.073 47.619 0.00 0.00 0.00 5.18


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

AutoCloner maintained by Alex Coulton.