Multiple sequence alignment - TraesCS7A01G272700

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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 TraesCS7A01G272700 chr7A 100.000 2417 0 0 1 2417 286148159 286150575 0.000000e+00 4464
1 TraesCS7A01G272700 chr7A 96.154 104 2 2 249 351 286119384 286119486 4.130000e-38 169
2 TraesCS7A01G272700 chr7B 90.566 1431 90 21 336 1758 242910047 242911440 0.000000e+00 1853
3 TraesCS7A01G272700 chr7B 93.128 553 32 2 1797 2346 242911443 242911992 0.000000e+00 806
4 TraesCS7A01G272700 chr7D 94.421 1165 50 5 757 1917 263450196 263451349 0.000000e+00 1777
5 TraesCS7A01G272700 chr7D 89.264 503 27 6 1915 2417 263451672 263452147 2.660000e-169 604
6 TraesCS7A01G272700 chr7D 87.892 446 43 9 290 730 263449762 263450201 4.610000e-142 514
7 TraesCS7A01G272700 chr7D 93.469 245 16 0 10 254 440040945 440040701 4.910000e-97 364
8 TraesCS7A01G272700 chr4D 93.254 252 17 0 3 254 11504108 11504359 2.930000e-99 372
9 TraesCS7A01G272700 chr4D 93.145 248 16 1 10 257 30506426 30506672 1.770000e-96 363
10 TraesCS7A01G272700 chr4D 93.416 243 16 0 9 251 76611942 76612184 6.350000e-96 361
11 TraesCS7A01G272700 chr2D 92.549 255 17 1 8 260 459810943 459810689 4.910000e-97 364
12 TraesCS7A01G272700 chr6A 93.089 246 17 0 10 255 97699049 97698804 6.350000e-96 361
13 TraesCS7A01G272700 chr3A 92.400 250 19 0 10 259 601373403 601373652 8.220000e-95 357
14 TraesCS7A01G272700 chr4A 92.400 250 18 1 3 251 521308509 521308758 2.960000e-94 355
15 TraesCS7A01G272700 chr3D 90.909 264 22 1 10 271 129016584 129016847 1.060000e-93 353
16 TraesCS7A01G272700 chr5B 88.679 106 11 1 2067 2172 383920105 383920001 7.010000e-26 128


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 TraesCS7A01G272700 chr7A 286148159 286150575 2416 False 4464.0 4464 100.000000 1 2417 1 chr7A.!!$F2 2416
1 TraesCS7A01G272700 chr7B 242910047 242911992 1945 False 1329.5 1853 91.847000 336 2346 2 chr7B.!!$F1 2010
2 TraesCS7A01G272700 chr7D 263449762 263452147 2385 False 965.0 1777 90.525667 290 2417 3 chr7D.!!$F1 2127

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
178 179 0.039617 TTCCGCTGCAATCGGTTTTG 60.04 50.0 21.74 2.06 46.49 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2157 2552 0.108992 TGTGGAACTACGATGCGGAC 60.109 55.0 0.0 0.0 38.04 4.79 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
23 24 6.636454 TGTAGTTCATACTCCCTCCATTTT 57.364 37.500 0.00 0.00 35.78 1.82
24 25 7.743116 TGTAGTTCATACTCCCTCCATTTTA 57.257 36.000 0.00 0.00 35.78 1.52
25 26 8.153221 TGTAGTTCATACTCCCTCCATTTTAA 57.847 34.615 0.00 0.00 35.78 1.52
26 27 8.607713 TGTAGTTCATACTCCCTCCATTTTAAA 58.392 33.333 0.00 0.00 35.78 1.52
27 28 9.457436 GTAGTTCATACTCCCTCCATTTTAAAA 57.543 33.333 2.51 2.51 35.78 1.52
35 36 8.465273 ACTCCCTCCATTTTAAAATATAGTGC 57.535 34.615 12.98 0.00 0.00 4.40
36 37 7.228706 ACTCCCTCCATTTTAAAATATAGTGCG 59.771 37.037 12.98 3.65 0.00 5.34
37 38 6.016610 TCCCTCCATTTTAAAATATAGTGCGC 60.017 38.462 12.98 0.00 0.00 6.09
38 39 6.149633 CCTCCATTTTAAAATATAGTGCGCC 58.850 40.000 12.98 0.00 0.00 6.53
39 40 6.079424 TCCATTTTAAAATATAGTGCGCCC 57.921 37.500 12.98 0.00 0.00 6.13
40 41 4.915085 CCATTTTAAAATATAGTGCGCCCG 59.085 41.667 12.98 0.00 0.00 6.13
41 42 3.612472 TTTAAAATATAGTGCGCCCGC 57.388 42.857 4.18 5.60 42.35 6.13
42 43 1.141645 TAAAATATAGTGCGCCCGCG 58.858 50.000 4.18 4.36 45.51 6.46
43 44 0.812412 AAAATATAGTGCGCCCGCGT 60.812 50.000 4.18 0.52 45.51 6.01
44 45 0.812412 AAATATAGTGCGCCCGCGTT 60.812 50.000 4.18 1.35 45.51 4.84
45 46 0.812412 AATATAGTGCGCCCGCGTTT 60.812 50.000 4.18 0.00 45.51 3.60
46 47 1.219522 ATATAGTGCGCCCGCGTTTC 61.220 55.000 4.18 2.02 45.51 2.78
56 57 2.356553 CGCGTTTCCCGAGGTCAA 60.357 61.111 0.00 0.00 39.56 3.18
57 58 1.957186 CGCGTTTCCCGAGGTCAAA 60.957 57.895 0.00 0.00 39.56 2.69
58 59 1.572941 GCGTTTCCCGAGGTCAAAC 59.427 57.895 0.00 4.65 39.56 2.93
59 60 0.883370 GCGTTTCCCGAGGTCAAACT 60.883 55.000 10.39 0.00 39.56 2.66
60 61 1.589803 CGTTTCCCGAGGTCAAACTT 58.410 50.000 10.39 0.00 39.56 2.66
61 62 1.944709 CGTTTCCCGAGGTCAAACTTT 59.055 47.619 10.39 0.00 39.56 2.66
62 63 2.286772 CGTTTCCCGAGGTCAAACTTTG 60.287 50.000 10.39 0.00 39.56 2.77
63 64 2.946990 GTTTCCCGAGGTCAAACTTTGA 59.053 45.455 0.00 0.00 37.33 2.69
82 83 9.804758 AACTTTGACCATAAATTTAACAAACGA 57.195 25.926 1.21 0.00 0.00 3.85
83 84 9.458374 ACTTTGACCATAAATTTAACAAACGAG 57.542 29.630 1.21 4.89 0.00 4.18
84 85 9.672086 CTTTGACCATAAATTTAACAAACGAGA 57.328 29.630 1.21 0.00 0.00 4.04
85 86 9.453325 TTTGACCATAAATTTAACAAACGAGAC 57.547 29.630 1.21 0.00 0.00 3.36
86 87 7.586747 TGACCATAAATTTAACAAACGAGACC 58.413 34.615 1.21 0.00 0.00 3.85
87 88 6.604930 ACCATAAATTTAACAAACGAGACCG 58.395 36.000 1.21 0.00 42.50 4.79
88 89 6.427547 ACCATAAATTTAACAAACGAGACCGA 59.572 34.615 1.21 0.00 39.50 4.69
89 90 6.739550 CCATAAATTTAACAAACGAGACCGAC 59.260 38.462 1.21 0.00 39.50 4.79
90 91 5.996669 AAATTTAACAAACGAGACCGACT 57.003 34.783 0.00 0.00 39.50 4.18
91 92 4.985044 ATTTAACAAACGAGACCGACTG 57.015 40.909 0.00 0.00 39.50 3.51
92 93 3.441496 TTAACAAACGAGACCGACTGT 57.559 42.857 0.00 0.00 39.50 3.55
93 94 1.567504 AACAAACGAGACCGACTGTG 58.432 50.000 0.00 0.00 39.50 3.66
94 95 0.249322 ACAAACGAGACCGACTGTGG 60.249 55.000 0.00 0.00 39.50 4.17
95 96 1.300697 AAACGAGACCGACTGTGGC 60.301 57.895 0.00 0.00 39.50 5.01
96 97 3.553437 AACGAGACCGACTGTGGCG 62.553 63.158 0.00 0.00 39.50 5.69
102 103 3.691342 CCGACTGTGGCGGGAGAA 61.691 66.667 3.58 0.00 44.87 2.87
103 104 2.342279 CGACTGTGGCGGGAGAAA 59.658 61.111 0.00 0.00 0.00 2.52
104 105 1.301401 CGACTGTGGCGGGAGAAAA 60.301 57.895 0.00 0.00 0.00 2.29
105 106 0.882927 CGACTGTGGCGGGAGAAAAA 60.883 55.000 0.00 0.00 0.00 1.94
159 160 8.268850 ACGAATTCACTGATATAACTTTTGCT 57.731 30.769 6.22 0.00 0.00 3.91
160 161 8.730680 ACGAATTCACTGATATAACTTTTGCTT 58.269 29.630 6.22 0.00 0.00 3.91
161 162 9.214953 CGAATTCACTGATATAACTTTTGCTTC 57.785 33.333 6.22 0.00 0.00 3.86
162 163 9.508567 GAATTCACTGATATAACTTTTGCTTCC 57.491 33.333 0.00 0.00 0.00 3.46
163 164 6.662414 TCACTGATATAACTTTTGCTTCCG 57.338 37.500 0.00 0.00 0.00 4.30
164 165 5.064707 TCACTGATATAACTTTTGCTTCCGC 59.935 40.000 0.00 0.00 0.00 5.54
165 166 5.065218 CACTGATATAACTTTTGCTTCCGCT 59.935 40.000 0.00 0.00 36.97 5.52
166 167 5.065218 ACTGATATAACTTTTGCTTCCGCTG 59.935 40.000 0.00 0.00 36.97 5.18
167 168 2.636768 ATAACTTTTGCTTCCGCTGC 57.363 45.000 0.00 0.00 36.97 5.25
168 169 1.313772 TAACTTTTGCTTCCGCTGCA 58.686 45.000 0.00 0.00 38.80 4.41
169 170 0.459489 AACTTTTGCTTCCGCTGCAA 59.541 45.000 0.00 0.00 46.90 4.08
172 173 2.869646 TTGCTTCCGCTGCAATCG 59.130 55.556 0.00 1.43 44.24 3.34
173 174 2.689785 TTGCTTCCGCTGCAATCGG 61.690 57.895 18.05 18.05 44.24 4.18
174 175 3.127533 GCTTCCGCTGCAATCGGT 61.128 61.111 21.74 0.00 46.49 4.69
175 176 2.690778 GCTTCCGCTGCAATCGGTT 61.691 57.895 21.74 0.00 46.49 4.44
176 177 1.875963 CTTCCGCTGCAATCGGTTT 59.124 52.632 21.74 0.00 46.49 3.27
177 178 0.240945 CTTCCGCTGCAATCGGTTTT 59.759 50.000 21.74 0.00 46.49 2.43
178 179 0.039617 TTCCGCTGCAATCGGTTTTG 60.040 50.000 21.74 2.06 46.49 2.44
189 190 6.944557 GCAATCGGTTTTGCTAGTTAAATT 57.055 33.333 10.19 0.00 46.66 1.82
190 191 7.346208 GCAATCGGTTTTGCTAGTTAAATTT 57.654 32.000 10.19 0.00 46.66 1.82
191 192 8.455598 GCAATCGGTTTTGCTAGTTAAATTTA 57.544 30.769 10.19 0.00 46.66 1.40
192 193 8.370321 GCAATCGGTTTTGCTAGTTAAATTTAC 58.630 33.333 0.00 0.00 46.66 2.01
193 194 8.572151 CAATCGGTTTTGCTAGTTAAATTTACG 58.428 33.333 0.00 0.00 0.00 3.18
194 195 6.601264 TCGGTTTTGCTAGTTAAATTTACGG 58.399 36.000 0.00 0.00 0.00 4.02
195 196 6.204495 TCGGTTTTGCTAGTTAAATTTACGGT 59.796 34.615 0.00 0.00 0.00 4.83
196 197 6.520790 CGGTTTTGCTAGTTAAATTTACGGTC 59.479 38.462 0.00 0.00 0.00 4.79
197 198 7.361894 GGTTTTGCTAGTTAAATTTACGGTCA 58.638 34.615 0.00 0.00 0.00 4.02
198 199 7.861872 GGTTTTGCTAGTTAAATTTACGGTCAA 59.138 33.333 0.00 0.00 0.00 3.18
199 200 9.235537 GTTTTGCTAGTTAAATTTACGGTCAAA 57.764 29.630 0.00 3.29 0.00 2.69
200 201 9.453325 TTTTGCTAGTTAAATTTACGGTCAAAG 57.547 29.630 0.00 0.00 0.00 2.77
201 202 7.733402 TGCTAGTTAAATTTACGGTCAAAGT 57.267 32.000 0.00 0.00 0.00 2.66
202 203 8.156994 TGCTAGTTAAATTTACGGTCAAAGTT 57.843 30.769 0.00 0.00 31.36 2.66
203 204 8.071368 TGCTAGTTAAATTTACGGTCAAAGTTG 58.929 33.333 0.00 0.00 29.44 3.16
204 205 8.284693 GCTAGTTAAATTTACGGTCAAAGTTGA 58.715 33.333 0.00 0.00 34.20 3.18
207 208 8.680001 AGTTAAATTTACGGTCAAAGTTGAAGT 58.320 29.630 0.00 2.51 39.21 3.01
208 209 9.934190 GTTAAATTTACGGTCAAAGTTGAAGTA 57.066 29.630 0.00 1.61 39.21 2.24
209 210 9.934190 TTAAATTTACGGTCAAAGTTGAAGTAC 57.066 29.630 0.00 0.00 39.21 2.73
210 211 5.640218 TTTACGGTCAAAGTTGAAGTACG 57.360 39.130 9.02 7.98 39.21 3.67
211 212 2.476821 ACGGTCAAAGTTGAAGTACGG 58.523 47.619 0.00 0.00 39.21 4.02
212 213 1.796459 CGGTCAAAGTTGAAGTACGGG 59.204 52.381 0.00 0.00 39.21 5.28
213 214 2.148768 GGTCAAAGTTGAAGTACGGGG 58.851 52.381 0.00 0.00 39.21 5.73
214 215 2.224354 GGTCAAAGTTGAAGTACGGGGA 60.224 50.000 0.00 0.00 39.21 4.81
215 216 3.558533 GGTCAAAGTTGAAGTACGGGGAT 60.559 47.826 0.00 0.00 39.21 3.85
216 217 4.322953 GGTCAAAGTTGAAGTACGGGGATA 60.323 45.833 0.00 0.00 39.21 2.59
217 218 4.868734 GTCAAAGTTGAAGTACGGGGATAG 59.131 45.833 0.00 0.00 39.21 2.08
218 219 4.773674 TCAAAGTTGAAGTACGGGGATAGA 59.226 41.667 0.00 0.00 33.55 1.98
219 220 4.732672 AAGTTGAAGTACGGGGATAGAC 57.267 45.455 0.00 0.00 0.00 2.59
220 221 2.686915 AGTTGAAGTACGGGGATAGACG 59.313 50.000 0.00 0.00 0.00 4.18
221 222 2.684881 GTTGAAGTACGGGGATAGACGA 59.315 50.000 0.00 0.00 0.00 4.20
222 223 3.003394 TGAAGTACGGGGATAGACGAA 57.997 47.619 0.00 0.00 0.00 3.85
223 224 3.355378 TGAAGTACGGGGATAGACGAAA 58.645 45.455 0.00 0.00 0.00 3.46
224 225 3.129287 TGAAGTACGGGGATAGACGAAAC 59.871 47.826 0.00 0.00 0.00 2.78
225 226 2.726821 AGTACGGGGATAGACGAAACA 58.273 47.619 0.00 0.00 0.00 2.83
226 227 2.424956 AGTACGGGGATAGACGAAACAC 59.575 50.000 0.00 0.00 0.00 3.32
227 228 1.553706 ACGGGGATAGACGAAACACT 58.446 50.000 0.00 0.00 0.00 3.55
228 229 2.726821 ACGGGGATAGACGAAACACTA 58.273 47.619 0.00 0.00 0.00 2.74
229 230 2.424956 ACGGGGATAGACGAAACACTAC 59.575 50.000 0.00 0.00 0.00 2.73
230 231 2.424601 CGGGGATAGACGAAACACTACA 59.575 50.000 0.00 0.00 0.00 2.74
231 232 3.067742 CGGGGATAGACGAAACACTACAT 59.932 47.826 0.00 0.00 0.00 2.29
232 233 4.441079 CGGGGATAGACGAAACACTACATT 60.441 45.833 0.00 0.00 0.00 2.71
233 234 4.809426 GGGGATAGACGAAACACTACATTG 59.191 45.833 0.00 0.00 0.00 2.82
234 235 5.416947 GGGATAGACGAAACACTACATTGT 58.583 41.667 0.00 0.00 0.00 2.71
235 236 5.291128 GGGATAGACGAAACACTACATTGTG 59.709 44.000 0.00 0.00 43.07 3.33
236 237 5.291128 GGATAGACGAAACACTACATTGTGG 59.709 44.000 0.00 0.00 41.84 4.17
237 238 4.330944 AGACGAAACACTACATTGTGGA 57.669 40.909 7.20 0.00 41.84 4.02
238 239 4.699637 AGACGAAACACTACATTGTGGAA 58.300 39.130 7.20 0.00 41.84 3.53
239 240 5.305585 AGACGAAACACTACATTGTGGAAT 58.694 37.500 7.20 0.00 41.84 3.01
240 241 5.179368 AGACGAAACACTACATTGTGGAATG 59.821 40.000 7.20 0.00 44.11 2.67
241 242 4.215399 ACGAAACACTACATTGTGGAATGG 59.785 41.667 7.20 0.00 43.00 3.16
242 243 4.454161 CGAAACACTACATTGTGGAATGGA 59.546 41.667 7.20 0.00 43.00 3.41
246 247 3.931907 CTACATTGTGGAATGGAGGGA 57.068 47.619 0.00 0.00 44.23 4.20
247 248 2.814805 ACATTGTGGAATGGAGGGAG 57.185 50.000 0.00 0.00 43.00 4.30
248 249 1.995542 ACATTGTGGAATGGAGGGAGT 59.004 47.619 0.00 0.00 43.00 3.85
249 250 3.189606 ACATTGTGGAATGGAGGGAGTA 58.810 45.455 0.00 0.00 43.00 2.59
250 251 3.788142 ACATTGTGGAATGGAGGGAGTAT 59.212 43.478 0.00 0.00 43.00 2.12
251 252 4.230502 ACATTGTGGAATGGAGGGAGTATT 59.769 41.667 0.00 0.00 43.00 1.89
252 253 5.431731 ACATTGTGGAATGGAGGGAGTATTA 59.568 40.000 0.00 0.00 43.00 0.98
253 254 5.630415 TTGTGGAATGGAGGGAGTATTAG 57.370 43.478 0.00 0.00 0.00 1.73
254 255 4.890988 TGTGGAATGGAGGGAGTATTAGA 58.109 43.478 0.00 0.00 0.00 2.10
255 256 5.285401 TGTGGAATGGAGGGAGTATTAGAA 58.715 41.667 0.00 0.00 0.00 2.10
256 257 5.911178 TGTGGAATGGAGGGAGTATTAGAAT 59.089 40.000 0.00 0.00 0.00 2.40
257 258 6.043243 TGTGGAATGGAGGGAGTATTAGAATC 59.957 42.308 0.00 0.00 0.00 2.52
258 259 6.271159 GTGGAATGGAGGGAGTATTAGAATCT 59.729 42.308 0.00 0.00 0.00 2.40
259 260 6.851836 TGGAATGGAGGGAGTATTAGAATCTT 59.148 38.462 0.00 0.00 0.00 2.40
260 261 8.016652 TGGAATGGAGGGAGTATTAGAATCTTA 58.983 37.037 0.00 0.00 0.00 2.10
261 262 8.881262 GGAATGGAGGGAGTATTAGAATCTTAA 58.119 37.037 0.00 0.00 0.00 1.85
286 287 5.924769 AAAAGACTTTTAGGAAGGAGGGA 57.075 39.130 11.51 0.00 0.00 4.20
287 288 5.506730 AAAGACTTTTAGGAAGGAGGGAG 57.493 43.478 0.00 0.00 0.00 4.30
288 289 3.455849 AGACTTTTAGGAAGGAGGGAGG 58.544 50.000 0.00 0.00 0.00 4.30
292 293 1.405243 TTAGGAAGGAGGGAGGGAGT 58.595 55.000 0.00 0.00 0.00 3.85
307 308 2.135933 GGGAGTATGTGCGTATGAAGC 58.864 52.381 0.00 0.00 0.00 3.86
315 316 0.248336 TGCGTATGAAGCGTCTACGG 60.248 55.000 22.25 11.57 38.84 4.02
319 320 0.306840 TATGAAGCGTCTACGGAGCG 59.693 55.000 4.49 7.06 40.23 5.03
325 326 1.796355 CGTCTACGGAGCGTGTGTG 60.796 63.158 3.67 0.00 41.39 3.82
371 374 9.778993 CATTTTGGAACATAGAAGAATAGTGTG 57.221 33.333 0.00 0.00 39.30 3.82
382 385 5.482175 AGAAGAATAGTGTGTTGCTAGTCCT 59.518 40.000 0.00 0.00 35.04 3.85
409 412 2.425143 ACCGAGTACCTGGTCGATTA 57.575 50.000 0.63 0.00 38.50 1.75
459 462 1.205055 GGCAGCTATATACCCCTCCC 58.795 60.000 0.00 0.00 0.00 4.30
548 551 4.503296 CGCATAGCCCCTCAAAGTTATACT 60.503 45.833 0.00 0.00 0.00 2.12
549 552 4.998033 GCATAGCCCCTCAAAGTTATACTC 59.002 45.833 0.00 0.00 0.00 2.59
550 553 3.821421 AGCCCCTCAAAGTTATACTCG 57.179 47.619 0.00 0.00 0.00 4.18
551 554 3.105283 AGCCCCTCAAAGTTATACTCGT 58.895 45.455 0.00 0.00 0.00 4.18
552 555 4.284178 AGCCCCTCAAAGTTATACTCGTA 58.716 43.478 0.00 0.00 0.00 3.43
553 556 4.099113 AGCCCCTCAAAGTTATACTCGTAC 59.901 45.833 0.00 0.00 0.00 3.67
554 557 4.142093 GCCCCTCAAAGTTATACTCGTACA 60.142 45.833 0.00 0.00 0.00 2.90
555 558 5.452917 GCCCCTCAAAGTTATACTCGTACAT 60.453 44.000 0.00 0.00 0.00 2.29
556 559 6.239120 GCCCCTCAAAGTTATACTCGTACATA 60.239 42.308 0.00 0.00 0.00 2.29
557 560 7.368833 CCCCTCAAAGTTATACTCGTACATAG 58.631 42.308 0.00 0.00 0.00 2.23
558 561 7.014038 CCCCTCAAAGTTATACTCGTACATAGT 59.986 40.741 3.59 3.59 0.00 2.12
559 562 8.411683 CCCTCAAAGTTATACTCGTACATAGTT 58.588 37.037 3.41 0.00 0.00 2.24
560 563 9.448294 CCTCAAAGTTATACTCGTACATAGTTC 57.552 37.037 3.41 0.00 0.00 3.01
590 596 3.245519 GCGTACTAATTTCTACTGCTGCC 59.754 47.826 0.00 0.00 0.00 4.85
632 638 3.057969 TGGCAGTGTCTTTATGTGGAG 57.942 47.619 0.00 0.00 0.00 3.86
646 652 7.439356 TCTTTATGTGGAGAGATTTGCTAATCG 59.561 37.037 13.95 0.00 43.99 3.34
720 727 2.158449 GCAACTGACATCGAAAGTGGAG 59.842 50.000 0.00 0.00 0.00 3.86
725 732 2.560981 TGACATCGAAAGTGGAGCACTA 59.439 45.455 0.00 0.00 44.62 2.74
726 733 2.924290 GACATCGAAAGTGGAGCACTAC 59.076 50.000 0.00 0.00 44.62 2.73
727 734 1.920574 CATCGAAAGTGGAGCACTACG 59.079 52.381 0.00 0.00 44.62 3.51
728 735 0.388134 TCGAAAGTGGAGCACTACGC 60.388 55.000 0.71 0.00 44.62 4.42
737 744 3.400007 GCACTACGCTTAGCCTGC 58.600 61.111 0.00 0.00 37.77 4.85
738 745 1.447838 GCACTACGCTTAGCCTGCA 60.448 57.895 7.65 0.00 37.77 4.41
739 746 1.696832 GCACTACGCTTAGCCTGCAC 61.697 60.000 7.65 0.00 37.77 4.57
740 747 0.108615 CACTACGCTTAGCCTGCACT 60.109 55.000 0.00 0.00 0.00 4.40
741 748 0.173708 ACTACGCTTAGCCTGCACTC 59.826 55.000 0.00 0.00 0.00 3.51
742 749 0.173481 CTACGCTTAGCCTGCACTCA 59.827 55.000 0.00 0.00 0.00 3.41
743 750 0.606096 TACGCTTAGCCTGCACTCAA 59.394 50.000 0.00 0.00 0.00 3.02
744 751 0.951040 ACGCTTAGCCTGCACTCAAC 60.951 55.000 0.00 0.00 0.00 3.18
745 752 1.790387 GCTTAGCCTGCACTCAACG 59.210 57.895 0.00 0.00 0.00 4.10
746 753 0.670546 GCTTAGCCTGCACTCAACGA 60.671 55.000 0.00 0.00 0.00 3.85
747 754 1.795768 CTTAGCCTGCACTCAACGAA 58.204 50.000 0.00 0.00 0.00 3.85
748 755 2.143122 CTTAGCCTGCACTCAACGAAA 58.857 47.619 0.00 0.00 0.00 3.46
749 756 2.248280 TAGCCTGCACTCAACGAAAA 57.752 45.000 0.00 0.00 0.00 2.29
750 757 1.388547 AGCCTGCACTCAACGAAAAA 58.611 45.000 0.00 0.00 0.00 1.94
751 758 1.065551 AGCCTGCACTCAACGAAAAAC 59.934 47.619 0.00 0.00 0.00 2.43
752 759 1.202245 GCCTGCACTCAACGAAAAACA 60.202 47.619 0.00 0.00 0.00 2.83
753 760 2.733858 GCCTGCACTCAACGAAAAACAA 60.734 45.455 0.00 0.00 0.00 2.83
754 761 3.506810 CCTGCACTCAACGAAAAACAAA 58.493 40.909 0.00 0.00 0.00 2.83
755 762 3.547468 CCTGCACTCAACGAAAAACAAAG 59.453 43.478 0.00 0.00 0.00 2.77
792 831 5.221422 CCTTGGGTTTCTTGTAATTCTGCAA 60.221 40.000 0.00 0.00 0.00 4.08
927 966 1.802365 GCACACGAAATTAACCGGAGT 59.198 47.619 9.46 0.00 0.00 3.85
1157 1196 2.997897 GCCGCTAGGATCGGGGAT 60.998 66.667 9.01 0.00 46.51 3.85
1191 1230 4.382541 TGCTCCTCCTCCTCGCCA 62.383 66.667 0.00 0.00 0.00 5.69
1207 1246 3.767230 CACGCTCCGTCAACGCTG 61.767 66.667 0.00 0.00 38.32 5.18
1282 1321 3.404141 GAGGACGACGAGCAGGAGC 62.404 68.421 0.00 0.00 42.56 4.70
1350 1389 0.462581 TGTACGACGCTACGGATCCT 60.463 55.000 10.75 0.00 37.61 3.24
1458 1497 1.691196 TGCCTGTAATTATGGGCTGC 58.309 50.000 23.04 0.00 44.36 5.25
1483 1522 0.688087 GCAGGGACTAGTAGCCTGGT 60.688 60.000 19.65 0.00 36.02 4.00
1549 1588 2.539344 CGGTGTACGTATGTGTATCGCA 60.539 50.000 0.00 0.00 37.93 5.10
1564 1603 8.748380 TGTGTATCGCATAGATCAAGAAATAG 57.252 34.615 0.00 0.00 40.66 1.73
1581 1620 9.212641 CAAGAAATAGTGATCTTCTCTTCACAA 57.787 33.333 5.91 0.00 43.72 3.33
1594 1636 4.327982 TCTTCACAAGAGGAGTCACAAG 57.672 45.455 0.00 0.00 32.71 3.16
1692 1736 1.469703 TGTGCTTGGATCGATTTGCAG 59.530 47.619 13.16 3.95 0.00 4.41
1740 1784 7.956420 ACGTACTTTCATCTGAATTACAACA 57.044 32.000 0.00 0.00 33.54 3.33
1741 1785 8.373048 ACGTACTTTCATCTGAATTACAACAA 57.627 30.769 0.00 0.00 33.54 2.83
1742 1786 8.280497 ACGTACTTTCATCTGAATTACAACAAC 58.720 33.333 0.00 0.00 33.54 3.32
1779 1823 0.323816 GAGCCTTTTCTCCCCCTTGG 60.324 60.000 0.00 0.00 0.00 3.61
1780 1824 1.074296 AGCCTTTTCTCCCCCTTGGT 61.074 55.000 0.00 0.00 34.77 3.67
1782 1826 0.777446 CCTTTTCTCCCCCTTGGTGA 59.223 55.000 0.00 0.00 34.85 4.02
1783 1827 1.359130 CCTTTTCTCCCCCTTGGTGAT 59.641 52.381 0.00 0.00 36.54 3.06
1792 1837 4.757692 TCCCCCTTGGTGATTTTTAACAT 58.242 39.130 0.00 0.00 34.77 2.71
1844 1889 5.513141 GCGCTTTTAGACTTGAAATGGAATC 59.487 40.000 0.00 0.00 0.00 2.52
1861 1906 5.775686 TGGAATCTGATTTGTTCTTGCTTG 58.224 37.500 4.11 0.00 0.00 4.01
2041 2427 3.731547 TCCAGGAGGCAGGACATG 58.268 61.111 0.00 0.00 33.74 3.21
2042 2428 1.997311 TCCAGGAGGCAGGACATGG 60.997 63.158 0.00 0.00 38.99 3.66
2049 2435 2.046892 GCAGGACATGGCAGACGT 60.047 61.111 0.00 0.00 0.00 4.34
2050 2436 1.672356 GCAGGACATGGCAGACGTT 60.672 57.895 0.00 0.00 0.00 3.99
2079 2465 3.771491 CGAGCGACTGCAGCACAC 61.771 66.667 15.27 2.35 46.23 3.82
2080 2466 3.418068 GAGCGACTGCAGCACACC 61.418 66.667 15.27 2.64 46.23 4.16
2081 2467 4.240103 AGCGACTGCAGCACACCA 62.240 61.111 15.27 0.00 46.23 4.17
2082 2468 3.279116 GCGACTGCAGCACACCAA 61.279 61.111 15.27 0.00 42.15 3.67
2083 2469 2.941333 CGACTGCAGCACACCAAG 59.059 61.111 15.27 0.00 0.00 3.61
2084 2470 2.641559 GACTGCAGCACACCAAGC 59.358 61.111 15.27 0.00 0.00 4.01
2085 2471 2.908940 ACTGCAGCACACCAAGCC 60.909 61.111 15.27 0.00 0.00 4.35
2086 2472 2.908428 CTGCAGCACACCAAGCCA 60.908 61.111 0.00 0.00 0.00 4.75
2087 2473 2.203523 TGCAGCACACCAAGCCAT 60.204 55.556 0.00 0.00 0.00 4.40
2088 2474 2.209064 CTGCAGCACACCAAGCCATC 62.209 60.000 0.00 0.00 0.00 3.51
2098 2493 0.184451 CCAAGCCATCCATGCCTAGT 59.816 55.000 0.00 0.00 0.00 2.57
2116 2511 3.434940 AGTGGAAAACTGGGTATCACC 57.565 47.619 0.00 0.00 37.88 4.02
2120 2515 2.745821 GGAAAACTGGGTATCACCGTTC 59.254 50.000 0.00 0.00 39.83 3.95
2130 2525 0.460311 ATCACCGTTCGATCCTCCAC 59.540 55.000 0.00 0.00 0.00 4.02
2141 2536 0.836400 ATCCTCCACCGTCCACAGTT 60.836 55.000 0.00 0.00 0.00 3.16
2157 2552 0.249322 AGTTCGTCCACACCAAGTCG 60.249 55.000 0.00 0.00 0.00 4.18
2165 2560 1.374252 ACACCAAGTCGTCCGCATC 60.374 57.895 0.00 0.00 0.00 3.91
2176 2571 0.108992 GTCCGCATCGTAGTTCCACA 60.109 55.000 0.00 0.00 0.00 4.17
2225 2620 3.502595 GGAAGGTAGCCAGAAAGACAAAC 59.497 47.826 0.00 0.00 0.00 2.93
2231 2626 3.084786 AGCCAGAAAGACAAACATAGGC 58.915 45.455 0.00 0.00 39.82 3.93
2342 2737 1.210155 GTGCTGTGAACGGGATTGC 59.790 57.895 0.00 0.00 0.00 3.56
2347 2742 2.106683 GTGAACGGGATTGCGAGGG 61.107 63.158 0.00 0.00 0.00 4.30
2348 2743 2.513897 GAACGGGATTGCGAGGGG 60.514 66.667 0.00 0.00 0.00 4.79
2349 2744 4.109675 AACGGGATTGCGAGGGGG 62.110 66.667 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.636454 AAAATGGAGGGAGTATGAACTACA 57.364 37.500 0.00 0.00 38.45 2.74
1 2 9.457436 TTTTAAAATGGAGGGAGTATGAACTAC 57.543 33.333 0.00 0.00 35.56 2.73
9 10 9.569122 GCACTATATTTTAAAATGGAGGGAGTA 57.431 33.333 21.19 0.80 0.00 2.59
10 11 7.228706 CGCACTATATTTTAAAATGGAGGGAGT 59.771 37.037 21.19 12.23 0.00 3.85
11 12 7.584987 CGCACTATATTTTAAAATGGAGGGAG 58.415 38.462 21.19 16.08 0.00 4.30
12 13 6.016610 GCGCACTATATTTTAAAATGGAGGGA 60.017 38.462 21.19 2.85 0.00 4.20
13 14 6.149633 GCGCACTATATTTTAAAATGGAGGG 58.850 40.000 21.19 18.41 0.00 4.30
14 15 6.149633 GGCGCACTATATTTTAAAATGGAGG 58.850 40.000 21.19 11.71 0.00 4.30
15 16 6.149633 GGGCGCACTATATTTTAAAATGGAG 58.850 40.000 21.19 18.49 0.00 3.86
16 17 5.278071 CGGGCGCACTATATTTTAAAATGGA 60.278 40.000 21.19 9.38 0.00 3.41
17 18 4.915085 CGGGCGCACTATATTTTAAAATGG 59.085 41.667 21.19 13.72 0.00 3.16
18 19 4.381566 GCGGGCGCACTATATTTTAAAATG 59.618 41.667 21.19 8.59 41.49 2.32
19 20 4.542735 GCGGGCGCACTATATTTTAAAAT 58.457 39.130 17.18 17.18 41.49 1.82
20 21 3.546417 CGCGGGCGCACTATATTTTAAAA 60.546 43.478 8.62 2.51 42.06 1.52
21 22 2.032722 CGCGGGCGCACTATATTTTAAA 60.033 45.455 8.62 0.00 42.06 1.52
22 23 1.527736 CGCGGGCGCACTATATTTTAA 59.472 47.619 8.62 0.00 42.06 1.52
23 24 1.141645 CGCGGGCGCACTATATTTTA 58.858 50.000 8.62 0.00 42.06 1.52
24 25 0.812412 ACGCGGGCGCACTATATTTT 60.812 50.000 12.47 0.00 44.19 1.82
25 26 0.812412 AACGCGGGCGCACTATATTT 60.812 50.000 12.47 0.00 44.19 1.40
26 27 0.812412 AAACGCGGGCGCACTATATT 60.812 50.000 12.47 0.00 44.19 1.28
27 28 1.219522 GAAACGCGGGCGCACTATAT 61.220 55.000 12.47 0.00 44.19 0.86
28 29 1.879430 GAAACGCGGGCGCACTATA 60.879 57.895 12.47 0.00 44.19 1.31
29 30 3.192922 GAAACGCGGGCGCACTAT 61.193 61.111 12.47 0.00 44.19 2.12
39 40 1.957186 TTTGACCTCGGGAAACGCG 60.957 57.895 3.53 3.53 43.86 6.01
40 41 0.883370 AGTTTGACCTCGGGAAACGC 60.883 55.000 0.00 0.00 43.86 4.84
41 42 1.589803 AAGTTTGACCTCGGGAAACG 58.410 50.000 0.00 0.00 46.11 3.60
42 43 2.946990 TCAAAGTTTGACCTCGGGAAAC 59.053 45.455 14.35 0.00 34.08 2.78
43 44 3.284793 TCAAAGTTTGACCTCGGGAAA 57.715 42.857 14.35 0.00 34.08 3.13
56 57 9.804758 TCGTTTGTTAAATTTATGGTCAAAGTT 57.195 25.926 0.00 0.00 31.36 2.66
57 58 9.458374 CTCGTTTGTTAAATTTATGGTCAAAGT 57.542 29.630 0.00 0.00 0.00 2.66
58 59 9.672086 TCTCGTTTGTTAAATTTATGGTCAAAG 57.328 29.630 0.00 4.73 0.00 2.77
59 60 9.453325 GTCTCGTTTGTTAAATTTATGGTCAAA 57.547 29.630 0.00 6.53 0.00 2.69
60 61 8.077386 GGTCTCGTTTGTTAAATTTATGGTCAA 58.923 33.333 0.00 1.18 0.00 3.18
61 62 7.571613 CGGTCTCGTTTGTTAAATTTATGGTCA 60.572 37.037 0.00 0.00 0.00 4.02
62 63 6.739550 CGGTCTCGTTTGTTAAATTTATGGTC 59.260 38.462 0.00 0.00 0.00 4.02
63 64 6.427547 TCGGTCTCGTTTGTTAAATTTATGGT 59.572 34.615 0.00 0.00 37.69 3.55
64 65 6.739550 GTCGGTCTCGTTTGTTAAATTTATGG 59.260 38.462 0.00 0.00 37.69 2.74
65 66 7.477422 CAGTCGGTCTCGTTTGTTAAATTTATG 59.523 37.037 0.00 0.00 37.69 1.90
66 67 7.172019 ACAGTCGGTCTCGTTTGTTAAATTTAT 59.828 33.333 0.00 0.00 37.69 1.40
67 68 6.479660 ACAGTCGGTCTCGTTTGTTAAATTTA 59.520 34.615 0.00 0.00 37.69 1.40
68 69 5.295045 ACAGTCGGTCTCGTTTGTTAAATTT 59.705 36.000 0.00 0.00 37.69 1.82
69 70 4.812626 ACAGTCGGTCTCGTTTGTTAAATT 59.187 37.500 0.00 0.00 37.69 1.82
70 71 4.210537 CACAGTCGGTCTCGTTTGTTAAAT 59.789 41.667 0.00 0.00 37.69 1.40
71 72 3.552699 CACAGTCGGTCTCGTTTGTTAAA 59.447 43.478 0.00 0.00 37.69 1.52
72 73 3.117794 CACAGTCGGTCTCGTTTGTTAA 58.882 45.455 0.00 0.00 37.69 2.01
73 74 2.544277 CCACAGTCGGTCTCGTTTGTTA 60.544 50.000 0.00 0.00 37.69 2.41
74 75 1.567504 CACAGTCGGTCTCGTTTGTT 58.432 50.000 0.00 0.00 37.69 2.83
75 76 0.249322 CCACAGTCGGTCTCGTTTGT 60.249 55.000 0.00 0.00 37.69 2.83
76 77 1.557443 GCCACAGTCGGTCTCGTTTG 61.557 60.000 0.00 0.00 37.69 2.93
77 78 1.300697 GCCACAGTCGGTCTCGTTT 60.301 57.895 0.00 0.00 37.69 3.60
78 79 2.338984 GCCACAGTCGGTCTCGTT 59.661 61.111 0.00 0.00 37.69 3.85
79 80 4.039357 CGCCACAGTCGGTCTCGT 62.039 66.667 0.00 0.00 37.69 4.18
80 81 4.778415 CCGCCACAGTCGGTCTCG 62.778 72.222 0.00 0.00 41.85 4.04
81 82 4.436998 CCCGCCACAGTCGGTCTC 62.437 72.222 0.35 0.00 45.09 3.36
82 83 4.988716 TCCCGCCACAGTCGGTCT 62.989 66.667 0.35 0.00 45.09 3.85
83 84 4.436998 CTCCCGCCACAGTCGGTC 62.437 72.222 0.35 0.00 45.09 4.79
84 85 4.988716 TCTCCCGCCACAGTCGGT 62.989 66.667 0.35 0.00 45.09 4.69
85 86 2.725203 TTTTCTCCCGCCACAGTCGG 62.725 60.000 0.00 0.00 46.05 4.79
86 87 0.882927 TTTTTCTCCCGCCACAGTCG 60.883 55.000 0.00 0.00 0.00 4.18
87 88 3.015516 TTTTTCTCCCGCCACAGTC 57.984 52.632 0.00 0.00 0.00 3.51
133 134 9.378551 AGCAAAAGTTATATCAGTGAATTCGTA 57.621 29.630 0.00 0.00 0.00 3.43
134 135 8.268850 AGCAAAAGTTATATCAGTGAATTCGT 57.731 30.769 0.00 0.00 0.00 3.85
135 136 9.214953 GAAGCAAAAGTTATATCAGTGAATTCG 57.785 33.333 0.00 0.00 0.00 3.34
136 137 9.508567 GGAAGCAAAAGTTATATCAGTGAATTC 57.491 33.333 0.00 0.00 0.00 2.17
137 138 8.184192 CGGAAGCAAAAGTTATATCAGTGAATT 58.816 33.333 0.00 0.00 0.00 2.17
138 139 7.697691 CGGAAGCAAAAGTTATATCAGTGAAT 58.302 34.615 0.00 0.00 0.00 2.57
139 140 7.072177 CGGAAGCAAAAGTTATATCAGTGAA 57.928 36.000 0.00 0.00 0.00 3.18
140 141 6.662414 CGGAAGCAAAAGTTATATCAGTGA 57.338 37.500 0.00 0.00 0.00 3.41
167 168 8.572151 CGTAAATTTAACTAGCAAAACCGATTG 58.428 33.333 0.00 0.00 0.00 2.67
168 169 7.751793 CCGTAAATTTAACTAGCAAAACCGATT 59.248 33.333 0.00 0.00 0.00 3.34
169 170 7.094677 ACCGTAAATTTAACTAGCAAAACCGAT 60.095 33.333 0.00 0.00 0.00 4.18
170 171 6.204495 ACCGTAAATTTAACTAGCAAAACCGA 59.796 34.615 0.00 0.00 0.00 4.69
171 172 6.372981 ACCGTAAATTTAACTAGCAAAACCG 58.627 36.000 0.00 0.00 0.00 4.44
172 173 7.361894 TGACCGTAAATTTAACTAGCAAAACC 58.638 34.615 0.00 0.00 0.00 3.27
173 174 8.785468 TTGACCGTAAATTTAACTAGCAAAAC 57.215 30.769 0.00 0.00 0.00 2.43
174 175 9.453325 CTTTGACCGTAAATTTAACTAGCAAAA 57.547 29.630 0.00 0.00 0.00 2.44
175 176 8.623030 ACTTTGACCGTAAATTTAACTAGCAAA 58.377 29.630 0.00 6.84 0.00 3.68
176 177 8.156994 ACTTTGACCGTAAATTTAACTAGCAA 57.843 30.769 0.00 0.00 0.00 3.91
177 178 7.733402 ACTTTGACCGTAAATTTAACTAGCA 57.267 32.000 0.00 0.00 0.00 3.49
178 179 8.284693 TCAACTTTGACCGTAAATTTAACTAGC 58.715 33.333 0.00 0.00 31.01 3.42
181 182 8.680001 ACTTCAACTTTGACCGTAAATTTAACT 58.320 29.630 0.00 0.00 36.83 2.24
182 183 8.845942 ACTTCAACTTTGACCGTAAATTTAAC 57.154 30.769 0.00 0.00 36.83 2.01
183 184 9.934190 GTACTTCAACTTTGACCGTAAATTTAA 57.066 29.630 0.00 0.00 36.83 1.52
184 185 8.274939 CGTACTTCAACTTTGACCGTAAATTTA 58.725 33.333 0.00 0.00 36.83 1.40
185 186 7.127686 CGTACTTCAACTTTGACCGTAAATTT 58.872 34.615 0.00 0.00 36.83 1.82
186 187 6.293027 CCGTACTTCAACTTTGACCGTAAATT 60.293 38.462 0.00 0.00 36.83 1.82
187 188 5.178067 CCGTACTTCAACTTTGACCGTAAAT 59.822 40.000 0.00 0.00 36.83 1.40
188 189 4.507388 CCGTACTTCAACTTTGACCGTAAA 59.493 41.667 0.00 0.00 36.83 2.01
189 190 4.050553 CCGTACTTCAACTTTGACCGTAA 58.949 43.478 0.00 0.00 36.83 3.18
190 191 3.552684 CCCGTACTTCAACTTTGACCGTA 60.553 47.826 0.00 0.00 36.83 4.02
191 192 2.476821 CCGTACTTCAACTTTGACCGT 58.523 47.619 0.00 0.00 36.83 4.83
192 193 1.796459 CCCGTACTTCAACTTTGACCG 59.204 52.381 0.00 0.00 36.83 4.79
193 194 2.148768 CCCCGTACTTCAACTTTGACC 58.851 52.381 0.00 0.00 36.83 4.02
194 195 3.116079 TCCCCGTACTTCAACTTTGAC 57.884 47.619 0.00 0.00 36.83 3.18
195 196 4.773674 TCTATCCCCGTACTTCAACTTTGA 59.226 41.667 0.00 0.00 34.92 2.69
196 197 4.868734 GTCTATCCCCGTACTTCAACTTTG 59.131 45.833 0.00 0.00 0.00 2.77
197 198 4.381292 CGTCTATCCCCGTACTTCAACTTT 60.381 45.833 0.00 0.00 0.00 2.66
198 199 3.129988 CGTCTATCCCCGTACTTCAACTT 59.870 47.826 0.00 0.00 0.00 2.66
199 200 2.686915 CGTCTATCCCCGTACTTCAACT 59.313 50.000 0.00 0.00 0.00 3.16
200 201 2.684881 TCGTCTATCCCCGTACTTCAAC 59.315 50.000 0.00 0.00 0.00 3.18
201 202 3.003394 TCGTCTATCCCCGTACTTCAA 57.997 47.619 0.00 0.00 0.00 2.69
202 203 2.715749 TCGTCTATCCCCGTACTTCA 57.284 50.000 0.00 0.00 0.00 3.02
203 204 3.129287 TGTTTCGTCTATCCCCGTACTTC 59.871 47.826 0.00 0.00 0.00 3.01
204 205 3.091545 TGTTTCGTCTATCCCCGTACTT 58.908 45.455 0.00 0.00 0.00 2.24
205 206 2.424956 GTGTTTCGTCTATCCCCGTACT 59.575 50.000 0.00 0.00 0.00 2.73
206 207 2.424956 AGTGTTTCGTCTATCCCCGTAC 59.575 50.000 0.00 0.00 0.00 3.67
207 208 2.726821 AGTGTTTCGTCTATCCCCGTA 58.273 47.619 0.00 0.00 0.00 4.02
208 209 1.553706 AGTGTTTCGTCTATCCCCGT 58.446 50.000 0.00 0.00 0.00 5.28
209 210 2.424601 TGTAGTGTTTCGTCTATCCCCG 59.575 50.000 0.00 0.00 0.00 5.73
210 211 4.667519 ATGTAGTGTTTCGTCTATCCCC 57.332 45.455 0.00 0.00 0.00 4.81
211 212 5.291128 CACAATGTAGTGTTTCGTCTATCCC 59.709 44.000 0.00 0.00 34.83 3.85
212 213 5.291128 CCACAATGTAGTGTTTCGTCTATCC 59.709 44.000 0.00 0.00 37.82 2.59
213 214 6.097356 TCCACAATGTAGTGTTTCGTCTATC 58.903 40.000 0.00 0.00 37.82 2.08
214 215 6.032956 TCCACAATGTAGTGTTTCGTCTAT 57.967 37.500 0.00 0.00 37.82 1.98
215 216 5.456548 TCCACAATGTAGTGTTTCGTCTA 57.543 39.130 0.00 0.00 37.82 2.59
216 217 4.330944 TCCACAATGTAGTGTTTCGTCT 57.669 40.909 0.00 0.00 37.82 4.18
217 218 5.382303 CATTCCACAATGTAGTGTTTCGTC 58.618 41.667 0.00 0.00 37.82 4.20
218 219 4.215399 CCATTCCACAATGTAGTGTTTCGT 59.785 41.667 0.00 0.00 38.22 3.85
219 220 4.454161 TCCATTCCACAATGTAGTGTTTCG 59.546 41.667 0.00 0.00 38.22 3.46
220 221 5.106157 CCTCCATTCCACAATGTAGTGTTTC 60.106 44.000 0.00 0.00 38.22 2.78
221 222 4.766891 CCTCCATTCCACAATGTAGTGTTT 59.233 41.667 0.00 0.00 38.22 2.83
222 223 4.335416 CCTCCATTCCACAATGTAGTGTT 58.665 43.478 0.00 0.00 38.22 3.32
223 224 3.308402 CCCTCCATTCCACAATGTAGTGT 60.308 47.826 0.00 0.00 38.22 3.55
224 225 3.054434 TCCCTCCATTCCACAATGTAGTG 60.054 47.826 0.00 0.00 38.22 2.74
225 226 3.189606 TCCCTCCATTCCACAATGTAGT 58.810 45.455 0.00 0.00 38.22 2.73
226 227 3.200825 ACTCCCTCCATTCCACAATGTAG 59.799 47.826 0.00 0.00 38.22 2.74
227 228 3.189606 ACTCCCTCCATTCCACAATGTA 58.810 45.455 0.00 0.00 38.22 2.29
228 229 1.995542 ACTCCCTCCATTCCACAATGT 59.004 47.619 0.00 0.00 38.22 2.71
229 230 2.814805 ACTCCCTCCATTCCACAATG 57.185 50.000 0.00 0.00 39.45 2.82
230 231 5.911178 TCTAATACTCCCTCCATTCCACAAT 59.089 40.000 0.00 0.00 0.00 2.71
231 232 5.285401 TCTAATACTCCCTCCATTCCACAA 58.715 41.667 0.00 0.00 0.00 3.33
232 233 4.890988 TCTAATACTCCCTCCATTCCACA 58.109 43.478 0.00 0.00 0.00 4.17
233 234 5.888982 TTCTAATACTCCCTCCATTCCAC 57.111 43.478 0.00 0.00 0.00 4.02
234 235 6.393897 AGATTCTAATACTCCCTCCATTCCA 58.606 40.000 0.00 0.00 0.00 3.53
235 236 6.943899 AGATTCTAATACTCCCTCCATTCC 57.056 41.667 0.00 0.00 0.00 3.01
263 264 6.275692 TCCCTCCTTCCTAAAAGTCTTTTT 57.724 37.500 15.53 3.15 39.69 1.94
264 265 5.222151 CCTCCCTCCTTCCTAAAAGTCTTTT 60.222 44.000 14.76 14.76 36.67 2.27
265 266 4.289934 CCTCCCTCCTTCCTAAAAGTCTTT 59.710 45.833 0.00 0.00 0.00 2.52
266 267 3.847184 CCTCCCTCCTTCCTAAAAGTCTT 59.153 47.826 0.00 0.00 0.00 3.01
267 268 3.455849 CCTCCCTCCTTCCTAAAAGTCT 58.544 50.000 0.00 0.00 0.00 3.24
268 269 2.506231 CCCTCCCTCCTTCCTAAAAGTC 59.494 54.545 0.00 0.00 0.00 3.01
269 270 2.115605 TCCCTCCCTCCTTCCTAAAAGT 59.884 50.000 0.00 0.00 0.00 2.66
270 271 2.774809 CTCCCTCCCTCCTTCCTAAAAG 59.225 54.545 0.00 0.00 0.00 2.27
271 272 2.115605 ACTCCCTCCCTCCTTCCTAAAA 59.884 50.000 0.00 0.00 0.00 1.52
272 273 1.728701 ACTCCCTCCCTCCTTCCTAAA 59.271 52.381 0.00 0.00 0.00 1.85
273 274 1.405243 ACTCCCTCCCTCCTTCCTAA 58.595 55.000 0.00 0.00 0.00 2.69
274 275 2.315503 TACTCCCTCCCTCCTTCCTA 57.684 55.000 0.00 0.00 0.00 2.94
275 276 1.221781 CATACTCCCTCCCTCCTTCCT 59.778 57.143 0.00 0.00 0.00 3.36
276 277 1.062044 ACATACTCCCTCCCTCCTTCC 60.062 57.143 0.00 0.00 0.00 3.46
277 278 2.043227 CACATACTCCCTCCCTCCTTC 58.957 57.143 0.00 0.00 0.00 3.46
278 279 1.972207 GCACATACTCCCTCCCTCCTT 60.972 57.143 0.00 0.00 0.00 3.36
279 280 0.399233 GCACATACTCCCTCCCTCCT 60.399 60.000 0.00 0.00 0.00 3.69
280 281 1.749334 CGCACATACTCCCTCCCTCC 61.749 65.000 0.00 0.00 0.00 4.30
281 282 1.043673 ACGCACATACTCCCTCCCTC 61.044 60.000 0.00 0.00 0.00 4.30
282 283 0.260816 TACGCACATACTCCCTCCCT 59.739 55.000 0.00 0.00 0.00 4.20
283 284 1.000955 CATACGCACATACTCCCTCCC 59.999 57.143 0.00 0.00 0.00 4.30
284 285 1.961394 TCATACGCACATACTCCCTCC 59.039 52.381 0.00 0.00 0.00 4.30
285 286 3.643763 CTTCATACGCACATACTCCCTC 58.356 50.000 0.00 0.00 0.00 4.30
286 287 2.224066 GCTTCATACGCACATACTCCCT 60.224 50.000 0.00 0.00 0.00 4.20
287 288 2.135933 GCTTCATACGCACATACTCCC 58.864 52.381 0.00 0.00 0.00 4.30
288 289 1.787155 CGCTTCATACGCACATACTCC 59.213 52.381 0.00 0.00 0.00 3.85
292 293 2.863401 AGACGCTTCATACGCACATA 57.137 45.000 0.00 0.00 0.00 2.29
307 308 1.796355 CACACACGCTCCGTAGACG 60.796 63.158 0.00 0.00 38.32 4.18
315 316 0.228742 CACGTTACACACACACGCTC 59.771 55.000 0.00 0.00 37.44 5.03
319 320 4.955617 TGTTTAACACGTTACACACACAC 58.044 39.130 5.11 0.00 32.66 3.82
325 326 9.240742 CAAAATGTTTTGTTTAACACGTTACAC 57.759 29.630 9.48 0.32 41.87 2.90
356 357 7.343316 AGGACTAGCAACACACTATTCTTCTAT 59.657 37.037 0.00 0.00 0.00 1.98
371 374 1.041447 TAGGGCCGAGGACTAGCAAC 61.041 60.000 0.00 0.00 0.00 4.17
409 412 2.203153 GCACTTCACGTGGTGGGT 60.203 61.111 21.43 11.02 43.97 4.51
411 414 3.345808 CCGCACTTCACGTGGTGG 61.346 66.667 21.43 15.09 43.97 4.61
459 462 7.168302 GTGATATTTCTGTGGACGAGATAACTG 59.832 40.741 0.00 0.00 0.00 3.16
508 511 3.880846 GAAAGATGGCTGCCGGCG 61.881 66.667 23.90 17.75 42.94 6.46
509 512 3.880846 CGAAAGATGGCTGCCGGC 61.881 66.667 22.73 22.73 40.90 6.13
524 527 0.618458 AACTTTGAGGGGCTATGCGA 59.382 50.000 0.00 0.00 0.00 5.10
548 551 4.507756 ACGCGTATGTAGAACTATGTACGA 59.492 41.667 11.67 0.00 35.36 3.43
549 552 4.766007 ACGCGTATGTAGAACTATGTACG 58.234 43.478 11.67 16.68 35.89 3.67
550 553 6.882072 AGTACGCGTATGTAGAACTATGTAC 58.118 40.000 23.56 5.87 0.00 2.90
551 554 8.587952 TTAGTACGCGTATGTAGAACTATGTA 57.412 34.615 23.56 2.29 0.00 2.29
552 555 5.998454 AGTACGCGTATGTAGAACTATGT 57.002 39.130 23.56 0.00 0.00 2.29
553 556 8.945758 AATTAGTACGCGTATGTAGAACTATG 57.054 34.615 23.56 0.00 0.00 2.23
554 557 9.604626 GAAATTAGTACGCGTATGTAGAACTAT 57.395 33.333 23.56 4.92 0.00 2.12
555 558 8.830580 AGAAATTAGTACGCGTATGTAGAACTA 58.169 33.333 23.56 16.32 0.00 2.24
556 559 7.701445 AGAAATTAGTACGCGTATGTAGAACT 58.299 34.615 23.56 17.40 0.00 3.01
557 560 7.905031 AGAAATTAGTACGCGTATGTAGAAC 57.095 36.000 23.56 10.27 0.00 3.01
558 561 8.830580 AGTAGAAATTAGTACGCGTATGTAGAA 58.169 33.333 23.56 12.16 0.00 2.10
559 562 8.278408 CAGTAGAAATTAGTACGCGTATGTAGA 58.722 37.037 23.56 7.66 0.00 2.59
560 563 7.059260 GCAGTAGAAATTAGTACGCGTATGTAG 59.941 40.741 23.56 3.83 0.00 2.74
561 564 6.852853 GCAGTAGAAATTAGTACGCGTATGTA 59.147 38.462 23.56 14.16 0.00 2.29
562 565 5.684626 GCAGTAGAAATTAGTACGCGTATGT 59.315 40.000 23.56 15.21 0.00 2.29
563 566 5.913514 AGCAGTAGAAATTAGTACGCGTATG 59.086 40.000 23.56 12.54 0.00 2.39
590 596 8.087750 TGCCAAAAGTTCCATTTTGTAGAATAG 58.912 33.333 10.13 0.00 44.85 1.73
632 638 3.531538 TGGGACACGATTAGCAAATCTC 58.468 45.455 0.00 0.00 39.56 2.75
720 727 1.447838 TGCAGGCTAAGCGTAGTGC 60.448 57.895 13.09 13.09 46.98 4.40
724 731 0.606096 TTGAGTGCAGGCTAAGCGTA 59.394 50.000 0.00 0.00 33.85 4.42
725 732 0.951040 GTTGAGTGCAGGCTAAGCGT 60.951 55.000 0.00 0.00 33.85 5.07
726 733 1.790387 GTTGAGTGCAGGCTAAGCG 59.210 57.895 0.00 0.00 33.85 4.68
727 734 0.670546 TCGTTGAGTGCAGGCTAAGC 60.671 55.000 0.00 0.00 0.00 3.09
728 735 1.795768 TTCGTTGAGTGCAGGCTAAG 58.204 50.000 0.00 0.00 0.00 2.18
729 736 2.248280 TTTCGTTGAGTGCAGGCTAA 57.752 45.000 0.00 0.00 0.00 3.09
730 737 2.248280 TTTTCGTTGAGTGCAGGCTA 57.752 45.000 0.00 0.00 0.00 3.93
731 738 1.065551 GTTTTTCGTTGAGTGCAGGCT 59.934 47.619 0.00 0.00 0.00 4.58
732 739 1.202245 TGTTTTTCGTTGAGTGCAGGC 60.202 47.619 0.00 0.00 0.00 4.85
733 740 2.842208 TGTTTTTCGTTGAGTGCAGG 57.158 45.000 0.00 0.00 0.00 4.85
734 741 4.165779 ACTTTGTTTTTCGTTGAGTGCAG 58.834 39.130 0.00 0.00 0.00 4.41
735 742 4.167554 ACTTTGTTTTTCGTTGAGTGCA 57.832 36.364 0.00 0.00 0.00 4.57
736 743 4.201558 CGTACTTTGTTTTTCGTTGAGTGC 59.798 41.667 0.00 0.00 0.00 4.40
737 744 4.201558 GCGTACTTTGTTTTTCGTTGAGTG 59.798 41.667 0.00 0.00 0.00 3.51
738 745 4.093850 AGCGTACTTTGTTTTTCGTTGAGT 59.906 37.500 0.00 0.00 0.00 3.41
739 746 4.584394 AGCGTACTTTGTTTTTCGTTGAG 58.416 39.130 0.00 0.00 0.00 3.02
740 747 4.093115 TGAGCGTACTTTGTTTTTCGTTGA 59.907 37.500 0.00 0.00 0.00 3.18
741 748 4.336101 TGAGCGTACTTTGTTTTTCGTTG 58.664 39.130 0.00 0.00 0.00 4.10
742 749 4.584394 CTGAGCGTACTTTGTTTTTCGTT 58.416 39.130 0.00 0.00 0.00 3.85
743 750 3.545426 GCTGAGCGTACTTTGTTTTTCGT 60.545 43.478 0.00 0.00 0.00 3.85
744 751 2.964768 GCTGAGCGTACTTTGTTTTTCG 59.035 45.455 0.00 0.00 0.00 3.46
745 752 3.297472 GGCTGAGCGTACTTTGTTTTTC 58.703 45.455 0.00 0.00 0.00 2.29
746 753 2.034179 GGGCTGAGCGTACTTTGTTTTT 59.966 45.455 0.00 0.00 0.00 1.94
747 754 1.607148 GGGCTGAGCGTACTTTGTTTT 59.393 47.619 0.00 0.00 0.00 2.43
748 755 1.235724 GGGCTGAGCGTACTTTGTTT 58.764 50.000 0.00 0.00 0.00 2.83
749 756 0.605589 GGGGCTGAGCGTACTTTGTT 60.606 55.000 0.00 0.00 0.00 2.83
750 757 1.003718 GGGGCTGAGCGTACTTTGT 60.004 57.895 0.00 0.00 0.00 2.83
751 758 1.745489 GGGGGCTGAGCGTACTTTG 60.745 63.158 0.00 0.00 0.00 2.77
752 759 1.489560 AAGGGGGCTGAGCGTACTTT 61.490 55.000 0.00 0.00 0.00 2.66
753 760 1.918800 AAGGGGGCTGAGCGTACTT 60.919 57.895 0.00 0.00 0.00 2.24
754 761 2.284699 AAGGGGGCTGAGCGTACT 60.285 61.111 0.00 0.00 0.00 2.73
755 762 2.125106 CAAGGGGGCTGAGCGTAC 60.125 66.667 0.00 0.00 0.00 3.67
792 831 3.692406 GACTTCGACCGGGGTGCT 61.692 66.667 6.32 0.00 0.00 4.40
991 1030 4.856801 CTGTTCCATCCCCGGCGG 62.857 72.222 21.46 21.46 0.00 6.13
992 1031 4.856801 CCTGTTCCATCCCCGGCG 62.857 72.222 0.00 0.00 0.00 6.46
994 1033 4.506255 GGCCTGTTCCATCCCCGG 62.506 72.222 0.00 0.00 0.00 5.73
995 1034 4.506255 GGGCCTGTTCCATCCCCG 62.506 72.222 0.84 0.00 32.60 5.73
996 1035 3.023735 AGGGCCTGTTCCATCCCC 61.024 66.667 4.50 0.00 39.59 4.81
999 1038 2.190578 CGGAGGGCCTGTTCCATC 59.809 66.667 12.95 0.00 36.27 3.51
1098 1137 2.999485 GCTGCTCTCGCTGAGGTGA 61.999 63.158 7.24 0.00 42.87 4.02
1256 1295 3.878519 CGTCGTCCTCCTCCTCGC 61.879 72.222 0.00 0.00 0.00 5.03
1400 1439 3.622630 TCTTTCTACTTCCTCCTCTCCG 58.377 50.000 0.00 0.00 0.00 4.63
1458 1497 2.362717 GGCTACTAGTCCCTGCTAACAG 59.637 54.545 0.00 0.00 44.05 3.16
1471 1510 3.312973 CGTTCTCTACACCAGGCTACTAG 59.687 52.174 0.00 0.00 0.00 2.57
1483 1522 5.223382 CAAAGCTTCTCTTCGTTCTCTACA 58.777 41.667 0.00 0.00 32.88 2.74
1581 1620 3.261818 AACTACCCTTGTGACTCCTCT 57.738 47.619 0.00 0.00 0.00 3.69
1592 1634 7.622479 TGATTAAGCTCCTAACTAACTACCCTT 59.378 37.037 0.00 0.00 0.00 3.95
1594 1636 7.357429 TGATTAAGCTCCTAACTAACTACCC 57.643 40.000 0.00 0.00 0.00 3.69
1692 1736 0.251354 TCAATGGAGTCTCTGCTGCC 59.749 55.000 0.00 0.00 0.00 4.85
1761 1805 1.074296 ACCAAGGGGGAGAAAAGGCT 61.074 55.000 0.00 0.00 41.15 4.58
1773 1817 7.598493 CAGTACAATGTTAAAAATCACCAAGGG 59.402 37.037 0.00 0.00 0.00 3.95
1844 1889 3.068590 ACCACCAAGCAAGAACAAATCAG 59.931 43.478 0.00 0.00 0.00 2.90
1861 1906 2.229062 GCTGGCTCTTCTAAAAACCACC 59.771 50.000 0.00 0.00 0.00 4.61
1966 2336 0.179225 TACTCGTTTCGTCGTACGGC 60.179 55.000 16.52 13.62 42.81 5.68
2033 2419 1.300971 CCAACGTCTGCCATGTCCTG 61.301 60.000 0.00 0.00 0.00 3.86
2034 2420 1.003355 CCAACGTCTGCCATGTCCT 60.003 57.895 0.00 0.00 0.00 3.85
2035 2421 1.302511 ACCAACGTCTGCCATGTCC 60.303 57.895 0.00 0.00 0.00 4.02
2036 2422 0.884704 ACACCAACGTCTGCCATGTC 60.885 55.000 0.00 0.00 0.00 3.06
2037 2423 0.465460 AACACCAACGTCTGCCATGT 60.465 50.000 0.00 0.00 0.00 3.21
2038 2424 0.238289 GAACACCAACGTCTGCCATG 59.762 55.000 0.00 0.00 0.00 3.66
2039 2425 1.227999 CGAACACCAACGTCTGCCAT 61.228 55.000 0.00 0.00 0.00 4.40
2040 2426 1.885388 CGAACACCAACGTCTGCCA 60.885 57.895 0.00 0.00 0.00 4.92
2041 2427 1.885850 ACGAACACCAACGTCTGCC 60.886 57.895 0.00 0.00 38.34 4.85
2042 2428 3.713963 ACGAACACCAACGTCTGC 58.286 55.556 0.00 0.00 38.34 4.26
2084 2470 2.689983 GTTTTCCACTAGGCATGGATGG 59.310 50.000 6.05 0.00 45.71 3.51
2085 2471 3.379372 CAGTTTTCCACTAGGCATGGATG 59.621 47.826 6.05 0.00 45.71 3.51
2086 2472 3.624777 CAGTTTTCCACTAGGCATGGAT 58.375 45.455 6.05 0.00 45.71 3.41
2087 2473 2.290896 CCAGTTTTCCACTAGGCATGGA 60.291 50.000 0.00 1.40 44.74 3.41
2088 2474 2.094675 CCAGTTTTCCACTAGGCATGG 58.905 52.381 0.00 0.00 38.71 3.66
2098 2493 1.700739 ACGGTGATACCCAGTTTTCCA 59.299 47.619 0.00 0.00 33.75 3.53
2120 2515 2.284798 CTGTGGACGGTGGAGGATCG 62.285 65.000 0.00 0.00 34.37 3.69
2130 2525 1.663702 GTGGACGAACTGTGGACGG 60.664 63.158 0.00 0.00 0.00 4.79
2141 2536 1.361271 GACGACTTGGTGTGGACGA 59.639 57.895 0.00 0.00 0.00 4.20
2157 2552 0.108992 TGTGGAACTACGATGCGGAC 60.109 55.000 0.00 0.00 38.04 4.79
2165 2560 3.181530 CGCTTTGAGATTGTGGAACTACG 60.182 47.826 0.00 0.00 38.04 3.51
2176 2571 3.010420 GACCCTTAAGCGCTTTGAGATT 58.990 45.455 30.13 15.26 0.00 2.40
2225 2620 0.314302 CGAACCCCTCGTAGCCTATG 59.686 60.000 0.00 0.00 42.89 2.23
2231 2626 1.664321 CCAGACCGAACCCCTCGTAG 61.664 65.000 0.00 0.00 46.65 3.51
2309 2704 1.015109 AGCACACGTAGATCGATCGT 58.985 50.000 19.33 12.00 42.86 3.73
2359 2754 1.881973 TGTTTCTGATGCAGTTCAGCC 59.118 47.619 11.73 4.19 42.37 4.85


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

AutoCloner maintained by Alex Coulton.