Multiple sequence alignment - TraesCS5D01G209400

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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 TraesCS5D01G209400 chr5D 100.000 6488 0 0 1 6488 316240509 316246996 0.000000e+00 11982.0
1 TraesCS5D01G209400 chr5B 94.985 3071 76 28 2977 6036 366007559 366010562 0.000000e+00 4747.0
2 TraesCS5D01G209400 chr5B 94.016 2189 85 23 822 2985 366005288 366007455 0.000000e+00 3275.0
3 TraesCS5D01G209400 chr5B 85.370 540 38 14 5985 6488 366010549 366011083 7.450000e-144 521.0
4 TraesCS5D01G209400 chr5B 89.474 171 10 1 669 831 366003992 366004162 6.590000e-50 209.0
5 TraesCS5D01G209400 chr5A 97.623 2482 37 7 2642 5104 410800878 410803356 0.000000e+00 4237.0
6 TraesCS5D01G209400 chr5A 93.805 1469 67 14 1192 2647 410799164 410800621 0.000000e+00 2187.0
7 TraesCS5D01G209400 chr5A 95.846 987 23 5 5136 6119 410803350 410804321 0.000000e+00 1580.0
8 TraesCS5D01G209400 chr5A 90.694 634 29 16 540 1166 410798560 410799170 0.000000e+00 817.0
9 TraesCS5D01G209400 chr5A 88.818 313 24 5 6117 6421 410804434 410804743 2.210000e-99 374.0
10 TraesCS5D01G209400 chr7D 98.141 269 5 0 1 269 231194181 231194449 2.740000e-128 470.0
11 TraesCS5D01G209400 chr7D 98.141 269 5 0 1 269 231211179 231211447 2.740000e-128 470.0
12 TraesCS5D01G209400 chr4D 97.786 271 4 1 1 269 457114728 457114458 3.540000e-127 466.0
13 TraesCS5D01G209400 chr4D 97.778 270 5 1 1 269 204297462 204297193 1.270000e-126 464.0
14 TraesCS5D01G209400 chr4D 97.778 270 5 1 1 269 230188384 230188653 1.270000e-126 464.0
15 TraesCS5D01G209400 chr4D 97.417 271 6 1 1 270 192008126 192008396 1.650000e-125 460.0
16 TraesCS5D01G209400 chr2D 97.778 270 5 1 1 269 287528486 287528755 1.270000e-126 464.0
17 TraesCS5D01G209400 chr1D 97.770 269 6 0 1 269 189025160 189024892 1.270000e-126 464.0
18 TraesCS5D01G209400 chr1D 83.621 232 31 6 288 517 23250848 23251074 1.830000e-50 211.0
19 TraesCS5D01G209400 chr1D 83.784 148 15 7 380 526 74909805 74909666 1.470000e-26 132.0
20 TraesCS5D01G209400 chr1D 87.143 70 9 0 464 533 289573812 289573881 5.390000e-11 80.5
21 TraesCS5D01G209400 chr1D 87.143 70 9 0 464 533 289596038 289596107 5.390000e-11 80.5
22 TraesCS5D01G209400 chr6D 97.417 271 5 2 1 269 431590475 431590745 1.650000e-125 460.0
23 TraesCS5D01G209400 chr6D 82.609 230 34 6 288 516 352826385 352826609 1.430000e-46 198.0
24 TraesCS5D01G209400 chr6D 91.111 45 4 0 271 315 472760668 472760712 1.950000e-05 62.1
25 TraesCS5D01G209400 chr3B 82.258 248 36 7 288 533 163167561 163167802 2.370000e-49 207.0
26 TraesCS5D01G209400 chr6B 81.641 256 32 11 280 526 712187196 712187445 1.430000e-46 198.0
27 TraesCS5D01G209400 chr6B 91.111 45 4 0 271 315 178666413 178666369 1.950000e-05 62.1
28 TraesCS5D01G209400 chr1B 81.081 259 33 13 270 526 7919015 7919259 6.640000e-45 193.0
29 TraesCS5D01G209400 chr1B 80.328 244 33 8 288 530 118485093 118484864 3.110000e-38 171.0
30 TraesCS5D01G209400 chr7B 79.623 265 45 9 272 533 726892621 726892363 1.440000e-41 182.0
31 TraesCS5D01G209400 chr1A 80.816 245 36 10 288 527 53677863 53677625 1.440000e-41 182.0
32 TraesCS5D01G209400 chr7A 78.824 255 31 17 288 535 562321746 562321984 4.050000e-32 150.0


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 TraesCS5D01G209400 chr5D 316240509 316246996 6487 False 11982 11982 100.00000 1 6488 1 chr5D.!!$F1 6487
1 TraesCS5D01G209400 chr5B 366003992 366011083 7091 False 2188 4747 90.96125 669 6488 4 chr5B.!!$F1 5819
2 TraesCS5D01G209400 chr5A 410798560 410804743 6183 False 1839 4237 93.35720 540 6421 5 chr5A.!!$F1 5881

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
161 162 0.033405 CCCAACTCTCTCCGAGGGTA 60.033 60.000 0.0 0.0 43.29 3.69 F
283 284 0.035036 TTACACCGCCACCATCGAAA 59.965 50.000 0.0 0.0 0.00 3.46 F
389 390 0.107945 CCAAAGAGAGAAGGGGCGAG 60.108 60.000 0.0 0.0 0.00 5.03 F
1975 3136 0.368907 CGAAAGTAATCCGCCGTGTG 59.631 55.000 0.0 0.0 0.00 3.82 F
2924 4360 0.677288 GTTTTGGCCCCAAGTACCAC 59.323 55.000 0.0 0.0 37.24 4.16 F
3660 5217 4.716784 AGTCTATGTTATGCCAGTCCTCAA 59.283 41.667 0.0 0.0 0.00 3.02 F
4461 6018 0.166814 GCTGTTGCTTCTGCTTACCG 59.833 55.000 0.0 0.0 40.48 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2067 3228 0.394216 CATGTGGATCCCGGCTTTCA 60.394 55.000 9.90 0.0 0.00 2.69 R
2132 3293 2.045524 TGGTTTTGTCAACCATGGCAT 58.954 42.857 13.04 0.0 44.74 4.40 R
2306 3467 1.006639 TGGGGGAGGCTGATTTTTACC 59.993 52.381 0.00 0.0 0.00 2.85 R
3324 4881 0.316204 ACCCTGTAAGACCAACGACG 59.684 55.000 0.00 0.0 34.07 5.12 R
4168 5725 2.121948 AGGAAGACCATGCAGCAGATA 58.878 47.619 0.00 0.0 38.94 1.98 R
5415 6988 1.002430 TCGGAATGGATAGCATCAGCC 59.998 52.381 0.00 0.0 43.56 4.85 R
6422 8176 0.036022 AGGCCTCACACTCTCAAAGC 59.964 55.000 0.00 0.0 0.00 3.51 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
45 46 9.612066 GAGAAGTCATATTTTCTCCTCTCATTT 57.388 33.333 8.98 0.00 42.10 2.32
105 106 9.693739 AATTAAAACCAAAATCCTTGTTTCCTT 57.306 25.926 0.00 0.00 0.00 3.36
109 110 9.693739 AAAACCAAAATCCTTGTTTCCTTATTT 57.306 25.926 0.00 0.00 0.00 1.40
110 111 8.675705 AACCAAAATCCTTGTTTCCTTATTTG 57.324 30.769 0.00 0.00 0.00 2.32
111 112 8.028652 ACCAAAATCCTTGTTTCCTTATTTGA 57.971 30.769 0.00 0.00 0.00 2.69
112 113 8.659527 ACCAAAATCCTTGTTTCCTTATTTGAT 58.340 29.630 0.00 0.00 0.00 2.57
142 143 7.703058 TCAAATAGGAAGGTCAAGAAAATCC 57.297 36.000 0.00 0.00 0.00 3.01
143 144 6.663523 TCAAATAGGAAGGTCAAGAAAATCCC 59.336 38.462 0.00 0.00 0.00 3.85
144 145 3.458044 AGGAAGGTCAAGAAAATCCCC 57.542 47.619 0.00 0.00 0.00 4.81
145 146 2.721906 AGGAAGGTCAAGAAAATCCCCA 59.278 45.455 0.00 0.00 0.00 4.96
146 147 3.142028 AGGAAGGTCAAGAAAATCCCCAA 59.858 43.478 0.00 0.00 0.00 4.12
147 148 3.258372 GGAAGGTCAAGAAAATCCCCAAC 59.742 47.826 0.00 0.00 0.00 3.77
148 149 3.903530 AGGTCAAGAAAATCCCCAACT 57.096 42.857 0.00 0.00 0.00 3.16
149 150 3.767711 AGGTCAAGAAAATCCCCAACTC 58.232 45.455 0.00 0.00 0.00 3.01
150 151 3.399305 AGGTCAAGAAAATCCCCAACTCT 59.601 43.478 0.00 0.00 0.00 3.24
151 152 3.759086 GGTCAAGAAAATCCCCAACTCTC 59.241 47.826 0.00 0.00 0.00 3.20
152 153 4.507512 GGTCAAGAAAATCCCCAACTCTCT 60.508 45.833 0.00 0.00 0.00 3.10
153 154 4.697828 GTCAAGAAAATCCCCAACTCTCTC 59.302 45.833 0.00 0.00 0.00 3.20
154 155 4.013050 CAAGAAAATCCCCAACTCTCTCC 58.987 47.826 0.00 0.00 0.00 3.71
155 156 2.237392 AGAAAATCCCCAACTCTCTCCG 59.763 50.000 0.00 0.00 0.00 4.63
156 157 1.952621 AAATCCCCAACTCTCTCCGA 58.047 50.000 0.00 0.00 0.00 4.55
157 158 1.490574 AATCCCCAACTCTCTCCGAG 58.509 55.000 0.00 0.00 45.56 4.63
158 159 0.397816 ATCCCCAACTCTCTCCGAGG 60.398 60.000 0.00 0.00 44.33 4.63
159 160 2.060980 CCCCAACTCTCTCCGAGGG 61.061 68.421 0.00 0.00 44.33 4.30
160 161 1.305381 CCCAACTCTCTCCGAGGGT 60.305 63.158 0.00 0.00 46.42 4.34
161 162 0.033405 CCCAACTCTCTCCGAGGGTA 60.033 60.000 0.00 0.00 43.29 3.69
162 163 1.104630 CCAACTCTCTCCGAGGGTAC 58.895 60.000 0.00 0.00 43.29 3.34
163 164 1.341187 CCAACTCTCTCCGAGGGTACT 60.341 57.143 0.00 0.00 43.29 2.73
164 165 2.448453 CAACTCTCTCCGAGGGTACTT 58.552 52.381 0.00 0.00 43.29 2.24
165 166 2.131776 ACTCTCTCCGAGGGTACTTG 57.868 55.000 0.00 0.00 42.15 3.16
166 167 1.634459 ACTCTCTCCGAGGGTACTTGA 59.366 52.381 0.00 0.00 42.15 3.02
167 168 2.294074 CTCTCTCCGAGGGTACTTGAG 58.706 57.143 0.00 0.00 36.06 3.02
168 169 1.634459 TCTCTCCGAGGGTACTTGAGT 59.366 52.381 0.00 0.00 31.53 3.41
169 170 2.041350 TCTCTCCGAGGGTACTTGAGTT 59.959 50.000 0.00 0.00 31.53 3.01
170 171 2.164624 CTCTCCGAGGGTACTTGAGTTG 59.835 54.545 0.00 0.00 31.53 3.16
171 172 0.606604 TCCGAGGGTACTTGAGTTGC 59.393 55.000 0.00 0.00 0.00 4.17
172 173 0.608640 CCGAGGGTACTTGAGTTGCT 59.391 55.000 0.00 0.00 0.00 3.91
173 174 1.002087 CCGAGGGTACTTGAGTTGCTT 59.998 52.381 0.00 0.00 0.00 3.91
174 175 2.232941 CCGAGGGTACTTGAGTTGCTTA 59.767 50.000 0.00 0.00 0.00 3.09
175 176 3.512680 CGAGGGTACTTGAGTTGCTTAG 58.487 50.000 0.00 0.00 0.00 2.18
176 177 3.676324 CGAGGGTACTTGAGTTGCTTAGG 60.676 52.174 0.00 0.00 0.00 2.69
177 178 2.572104 AGGGTACTTGAGTTGCTTAGGG 59.428 50.000 0.00 0.00 0.00 3.53
178 179 2.305052 GGGTACTTGAGTTGCTTAGGGT 59.695 50.000 0.00 0.00 0.00 4.34
179 180 3.244805 GGGTACTTGAGTTGCTTAGGGTT 60.245 47.826 0.00 0.00 0.00 4.11
180 181 4.395625 GGTACTTGAGTTGCTTAGGGTTT 58.604 43.478 0.00 0.00 0.00 3.27
181 182 4.825634 GGTACTTGAGTTGCTTAGGGTTTT 59.174 41.667 0.00 0.00 0.00 2.43
182 183 5.301045 GGTACTTGAGTTGCTTAGGGTTTTT 59.699 40.000 0.00 0.00 0.00 1.94
183 184 5.515797 ACTTGAGTTGCTTAGGGTTTTTC 57.484 39.130 0.00 0.00 0.00 2.29
184 185 4.036380 ACTTGAGTTGCTTAGGGTTTTTCG 59.964 41.667 0.00 0.00 0.00 3.46
185 186 3.811083 TGAGTTGCTTAGGGTTTTTCGA 58.189 40.909 0.00 0.00 0.00 3.71
186 187 3.813166 TGAGTTGCTTAGGGTTTTTCGAG 59.187 43.478 0.00 0.00 0.00 4.04
187 188 3.146847 AGTTGCTTAGGGTTTTTCGAGG 58.853 45.455 0.00 0.00 0.00 4.63
188 189 3.143728 GTTGCTTAGGGTTTTTCGAGGA 58.856 45.455 0.00 0.00 0.00 3.71
189 190 3.713826 TGCTTAGGGTTTTTCGAGGAT 57.286 42.857 0.00 0.00 0.00 3.24
190 191 4.028993 TGCTTAGGGTTTTTCGAGGATT 57.971 40.909 0.00 0.00 0.00 3.01
191 192 4.403734 TGCTTAGGGTTTTTCGAGGATTT 58.596 39.130 0.00 0.00 0.00 2.17
192 193 4.217550 TGCTTAGGGTTTTTCGAGGATTTG 59.782 41.667 0.00 0.00 0.00 2.32
193 194 4.733850 CTTAGGGTTTTTCGAGGATTTGC 58.266 43.478 0.00 0.00 0.00 3.68
194 195 1.893137 AGGGTTTTTCGAGGATTTGCC 59.107 47.619 0.00 0.00 0.00 4.52
195 196 1.616374 GGGTTTTTCGAGGATTTGCCA 59.384 47.619 0.00 0.00 40.02 4.92
196 197 2.036604 GGGTTTTTCGAGGATTTGCCAA 59.963 45.455 0.00 0.00 40.02 4.52
197 198 3.493524 GGGTTTTTCGAGGATTTGCCAAA 60.494 43.478 0.00 0.00 40.02 3.28
198 199 4.123506 GGTTTTTCGAGGATTTGCCAAAA 58.876 39.130 0.00 0.00 40.02 2.44
199 200 4.754618 GGTTTTTCGAGGATTTGCCAAAAT 59.245 37.500 0.00 0.00 38.74 1.82
200 201 5.334028 GGTTTTTCGAGGATTTGCCAAAATG 60.334 40.000 0.00 0.00 36.10 2.32
201 202 2.652941 TCGAGGATTTGCCAAAATGC 57.347 45.000 0.00 0.00 42.66 3.56
202 203 1.891811 TCGAGGATTTGCCAAAATGCA 59.108 42.857 0.00 0.00 44.23 3.96
214 215 7.627298 TTGCCAAAATGCAATAAAATATGCT 57.373 28.000 0.00 0.00 45.77 3.79
215 216 8.728337 TTGCCAAAATGCAATAAAATATGCTA 57.272 26.923 0.00 0.00 45.77 3.49
216 217 8.905660 TGCCAAAATGCAATAAAATATGCTAT 57.094 26.923 0.00 0.00 42.97 2.97
217 218 8.775527 TGCCAAAATGCAATAAAATATGCTATG 58.224 29.630 0.00 0.00 42.97 2.23
218 219 7.747357 GCCAAAATGCAATAAAATATGCTATGC 59.253 33.333 0.00 0.00 42.97 3.14
219 220 8.775527 CCAAAATGCAATAAAATATGCTATGCA 58.224 29.630 0.00 0.00 44.86 3.96
223 224 9.713713 AATGCAATAAAATATGCTATGCAATGA 57.286 25.926 1.40 0.00 43.62 2.57
224 225 9.884636 ATGCAATAAAATATGCTATGCAATGAT 57.115 25.926 1.40 0.00 43.62 2.45
225 226 9.145865 TGCAATAAAATATGCTATGCAATGATG 57.854 29.630 0.00 0.00 43.62 3.07
226 227 9.361315 GCAATAAAATATGCTATGCAATGATGA 57.639 29.630 0.00 0.00 43.62 2.92
234 235 7.939784 ATGCTATGCAATGATGATCTAATGT 57.060 32.000 0.00 0.00 43.62 2.71
236 237 9.628500 ATGCTATGCAATGATGATCTAATGTAT 57.372 29.630 0.00 0.00 43.62 2.29
271 272 8.541133 AATTAAAAATTTGGGATGTTACACCG 57.459 30.769 0.00 0.00 0.00 4.94
272 273 3.586100 AAATTTGGGATGTTACACCGC 57.414 42.857 0.00 0.00 0.00 5.68
273 274 1.470051 ATTTGGGATGTTACACCGCC 58.530 50.000 0.00 0.00 0.00 6.13
274 275 0.110678 TTTGGGATGTTACACCGCCA 59.889 50.000 0.00 0.00 0.00 5.69
275 276 0.606944 TTGGGATGTTACACCGCCAC 60.607 55.000 0.00 0.00 0.00 5.01
276 277 1.747745 GGGATGTTACACCGCCACC 60.748 63.158 0.00 0.00 0.00 4.61
277 278 1.003112 GGATGTTACACCGCCACCA 60.003 57.895 0.00 0.00 0.00 4.17
278 279 0.393808 GGATGTTACACCGCCACCAT 60.394 55.000 0.00 0.00 0.00 3.55
279 280 1.014352 GATGTTACACCGCCACCATC 58.986 55.000 0.00 0.00 0.00 3.51
280 281 0.742990 ATGTTACACCGCCACCATCG 60.743 55.000 0.00 0.00 0.00 3.84
281 282 1.079681 GTTACACCGCCACCATCGA 60.080 57.895 0.00 0.00 0.00 3.59
282 283 0.671163 GTTACACCGCCACCATCGAA 60.671 55.000 0.00 0.00 0.00 3.71
283 284 0.035036 TTACACCGCCACCATCGAAA 59.965 50.000 0.00 0.00 0.00 3.46
284 285 0.390603 TACACCGCCACCATCGAAAG 60.391 55.000 0.00 0.00 0.00 2.62
285 286 1.671054 CACCGCCACCATCGAAAGT 60.671 57.895 0.00 0.00 0.00 2.66
286 287 1.671054 ACCGCCACCATCGAAAGTG 60.671 57.895 10.41 10.41 0.00 3.16
287 288 2.480555 CGCCACCATCGAAAGTGC 59.519 61.111 11.61 7.34 32.48 4.40
288 289 2.877691 GCCACCATCGAAAGTGCC 59.122 61.111 11.61 0.00 32.48 5.01
289 290 1.675641 GCCACCATCGAAAGTGCCT 60.676 57.895 11.61 0.00 32.48 4.75
290 291 1.926511 GCCACCATCGAAAGTGCCTG 61.927 60.000 11.61 1.86 32.48 4.85
291 292 1.308069 CCACCATCGAAAGTGCCTGG 61.308 60.000 11.61 5.19 32.48 4.45
292 293 1.002134 ACCATCGAAAGTGCCTGGG 60.002 57.895 4.14 0.00 0.00 4.45
293 294 1.750399 CCATCGAAAGTGCCTGGGG 60.750 63.158 0.00 0.00 0.00 4.96
330 331 4.807039 GCTCCGCCGAAACGCCTA 62.807 66.667 0.00 0.00 0.00 3.93
331 332 2.582498 CTCCGCCGAAACGCCTAG 60.582 66.667 0.00 0.00 0.00 3.02
332 333 4.807039 TCCGCCGAAACGCCTAGC 62.807 66.667 0.00 0.00 0.00 3.42
363 364 4.977126 GTCGCGTATCGGCCGGAG 62.977 72.222 27.83 15.07 36.67 4.63
380 381 3.717294 GGGCGCCCCAAAGAGAGA 61.717 66.667 36.64 0.00 44.65 3.10
381 382 2.351276 GGCGCCCCAAAGAGAGAA 59.649 61.111 18.11 0.00 0.00 2.87
382 383 1.746991 GGCGCCCCAAAGAGAGAAG 60.747 63.158 18.11 0.00 0.00 2.85
383 384 1.746991 GCGCCCCAAAGAGAGAAGG 60.747 63.158 0.00 0.00 0.00 3.46
384 385 1.078143 CGCCCCAAAGAGAGAAGGG 60.078 63.158 0.00 0.00 41.02 3.95
387 388 1.078143 CCCAAAGAGAGAAGGGGCG 60.078 63.158 0.00 0.00 37.66 6.13
388 389 1.553690 CCCAAAGAGAGAAGGGGCGA 61.554 60.000 0.00 0.00 37.66 5.54
389 390 0.107945 CCAAAGAGAGAAGGGGCGAG 60.108 60.000 0.00 0.00 0.00 5.03
390 391 0.742635 CAAAGAGAGAAGGGGCGAGC 60.743 60.000 0.00 0.00 0.00 5.03
391 392 1.904990 AAAGAGAGAAGGGGCGAGCC 61.905 60.000 5.37 5.37 0.00 4.70
430 431 2.745492 GAGCTTTGCTCGCCAGCT 60.745 61.111 4.57 11.26 45.85 4.24
431 432 2.331132 GAGCTTTGCTCGCCAGCTT 61.331 57.895 4.57 0.16 45.85 3.74
432 433 2.250841 GAGCTTTGCTCGCCAGCTTC 62.251 60.000 4.57 4.83 45.85 3.86
437 438 3.191539 GCTCGCCAGCTTCTTCCG 61.192 66.667 0.00 0.00 43.09 4.30
438 439 2.510238 CTCGCCAGCTTCTTCCGG 60.510 66.667 0.00 0.00 0.00 5.14
439 440 4.760047 TCGCCAGCTTCTTCCGGC 62.760 66.667 0.00 0.41 41.30 6.13
466 467 3.721706 GAGGGTGCAGGGGAGGTG 61.722 72.222 0.00 0.00 0.00 4.00
470 471 3.580319 GTGCAGGGGAGGTGGGTT 61.580 66.667 0.00 0.00 0.00 4.11
471 472 3.579302 TGCAGGGGAGGTGGGTTG 61.579 66.667 0.00 0.00 0.00 3.77
472 473 4.366684 GCAGGGGAGGTGGGTTGG 62.367 72.222 0.00 0.00 0.00 3.77
473 474 3.661648 CAGGGGAGGTGGGTTGGG 61.662 72.222 0.00 0.00 0.00 4.12
492 493 4.125695 GCGACGACGGCTAGGGTT 62.126 66.667 9.67 0.00 40.15 4.11
493 494 2.101770 CGACGACGGCTAGGGTTC 59.898 66.667 0.00 0.00 35.72 3.62
494 495 2.101770 GACGACGGCTAGGGTTCG 59.898 66.667 0.00 0.00 0.00 3.95
495 496 4.125695 ACGACGGCTAGGGTTCGC 62.126 66.667 0.00 0.00 0.00 4.70
496 497 4.867599 CGACGGCTAGGGTTCGCC 62.868 72.222 0.00 0.00 42.86 5.54
522 523 4.278513 CCCCTTGGGGCAACGTGA 62.279 66.667 12.40 0.00 42.67 4.35
523 524 2.672996 CCCTTGGGGCAACGTGAG 60.673 66.667 0.00 0.00 35.35 3.51
524 525 3.365265 CCTTGGGGCAACGTGAGC 61.365 66.667 4.77 4.77 37.60 4.26
525 526 3.726517 CTTGGGGCAACGTGAGCG 61.727 66.667 7.10 0.00 44.93 5.03
526 527 4.243008 TTGGGGCAACGTGAGCGA 62.243 61.111 7.10 0.00 42.00 4.93
527 528 4.680237 TGGGGCAACGTGAGCGAG 62.680 66.667 7.10 0.00 42.00 5.03
528 529 4.681978 GGGGCAACGTGAGCGAGT 62.682 66.667 7.10 0.00 42.00 4.18
529 530 3.112709 GGGCAACGTGAGCGAGTC 61.113 66.667 7.10 0.00 42.00 3.36
530 531 3.470567 GGCAACGTGAGCGAGTCG 61.471 66.667 8.54 8.54 42.00 4.18
531 532 3.470567 GCAACGTGAGCGAGTCGG 61.471 66.667 15.52 0.00 42.00 4.79
532 533 2.805353 CAACGTGAGCGAGTCGGG 60.805 66.667 15.52 0.00 42.00 5.14
533 534 3.292936 AACGTGAGCGAGTCGGGT 61.293 61.111 15.52 0.14 42.00 5.28
534 535 2.853290 AACGTGAGCGAGTCGGGTT 61.853 57.895 15.52 0.00 42.00 4.11
535 536 1.518056 AACGTGAGCGAGTCGGGTTA 61.518 55.000 15.52 0.00 42.00 2.85
536 537 1.513586 CGTGAGCGAGTCGGGTTAC 60.514 63.158 15.52 6.81 41.33 2.50
537 538 1.153881 GTGAGCGAGTCGGGTTACC 60.154 63.158 15.52 0.00 0.00 2.85
573 574 3.586470 TGCTTGAAAGTAGGGGTTCAA 57.414 42.857 0.00 0.00 40.52 2.69
584 585 2.250924 AGGGGTTCAAATTGAAGGCTG 58.749 47.619 8.88 0.00 37.00 4.85
608 609 2.862541 CTGTCAAAATGTGAGGGGTCA 58.137 47.619 0.00 0.00 36.74 4.02
616 617 5.628797 AAATGTGAGGGGTCAAAACAAAT 57.371 34.783 0.00 0.00 0.00 2.32
618 619 5.722021 ATGTGAGGGGTCAAAACAAATAC 57.278 39.130 0.00 0.00 0.00 1.89
620 621 4.339814 TGTGAGGGGTCAAAACAAATACAC 59.660 41.667 0.00 0.00 0.00 2.90
622 623 4.193240 AGGGGTCAAAACAAATACACCT 57.807 40.909 0.00 0.00 40.99 4.00
623 624 5.163077 TGAGGGGTCAAAACAAATACACCTA 60.163 40.000 0.00 0.00 45.79 3.08
655 657 1.525995 CTGTGCACGTTTGAGGGGT 60.526 57.895 13.13 0.00 0.00 4.95
657 659 0.533308 TGTGCACGTTTGAGGGGTAC 60.533 55.000 13.13 0.00 0.00 3.34
678 680 1.202734 CGTGATTGGGGATGCTCTCAT 60.203 52.381 0.00 0.00 35.17 2.90
718 720 0.605319 GACGTGGAGGTCAATTGGCA 60.605 55.000 12.93 0.00 36.91 4.92
720 722 0.734889 CGTGGAGGTCAATTGGCATC 59.265 55.000 16.06 16.06 0.00 3.91
726 728 1.139520 GTCAATTGGCATCACGGGC 59.860 57.895 4.85 0.00 0.00 6.13
751 761 4.803426 CGACGGACTCAGCTGCCC 62.803 72.222 9.47 9.11 0.00 5.36
1159 2309 1.067212 CCGATTCGGTTGGAGACTAGG 59.933 57.143 17.08 0.00 42.73 3.02
1160 2310 1.067212 CGATTCGGTTGGAGACTAGGG 59.933 57.143 0.00 0.00 0.00 3.53
1161 2311 2.108970 GATTCGGTTGGAGACTAGGGT 58.891 52.381 0.00 0.00 0.00 4.34
1162 2312 2.905415 TTCGGTTGGAGACTAGGGTA 57.095 50.000 0.00 0.00 0.00 3.69
1163 2313 2.905415 TCGGTTGGAGACTAGGGTAA 57.095 50.000 0.00 0.00 0.00 2.85
1164 2314 2.731572 TCGGTTGGAGACTAGGGTAAG 58.268 52.381 0.00 0.00 0.00 2.34
1165 2315 1.136500 CGGTTGGAGACTAGGGTAAGC 59.864 57.143 0.00 0.00 0.00 3.09
1166 2316 1.136500 GGTTGGAGACTAGGGTAAGCG 59.864 57.143 0.00 0.00 0.00 4.68
1197 2347 0.970937 TTAGCCGGTCTCAGGTGAGG 60.971 60.000 1.90 0.00 42.30 3.86
1217 2367 1.153997 GACGAGCTGGAGGAACGTC 60.154 63.158 1.44 4.29 44.19 4.34
1283 2433 2.443255 ACTCAGTGGTCAAAAGGGATGT 59.557 45.455 0.00 0.00 0.00 3.06
1287 2437 2.305927 AGTGGTCAAAAGGGATGTCGAT 59.694 45.455 0.00 0.00 0.00 3.59
1305 2455 7.931578 TGTCGATCCCTTACATTTATTTTGT 57.068 32.000 0.00 0.00 0.00 2.83
1353 2503 8.050778 TCTGGTTGATGTGGATTTGTTATTAC 57.949 34.615 0.00 0.00 0.00 1.89
1454 2611 1.290324 CACCGACTGAGGACCTGTG 59.710 63.158 0.00 0.00 34.73 3.66
1467 2624 1.618837 GACCTGTGTCTTGACCTGCTA 59.381 52.381 0.00 0.00 38.53 3.49
1470 2627 2.625737 CTGTGTCTTGACCTGCTATGG 58.374 52.381 0.00 0.00 0.00 2.74
1515 2672 3.963374 CTGATATGAGGTCAAGGAGGACA 59.037 47.826 0.00 0.00 39.59 4.02
1895 3056 8.574737 CAATGAAAGTCTTCCTCTTCAGAAAAT 58.425 33.333 0.00 0.00 0.00 1.82
1975 3136 0.368907 CGAAAGTAATCCGCCGTGTG 59.631 55.000 0.00 0.00 0.00 3.82
2067 3228 2.486191 CCTTTGTCTTGTCACTGCTCCT 60.486 50.000 0.00 0.00 0.00 3.69
2132 3293 3.869912 GCTGAAGTGAAGTCCTGCCATAA 60.870 47.826 0.00 0.00 0.00 1.90
2146 3307 1.755959 GCCATAATGCCATGGTTGACA 59.244 47.619 14.67 2.53 46.21 3.58
2270 3431 2.574006 TGCTGGCTGATTTTGTCTCT 57.426 45.000 0.00 0.00 0.00 3.10
2288 3449 6.711277 TGTCTCTGCTATAACCAAGACAATT 58.289 36.000 0.81 0.00 39.92 2.32
2290 3451 8.486210 TGTCTCTGCTATAACCAAGACAATTAT 58.514 33.333 0.81 0.00 39.92 1.28
2291 3452 9.331282 GTCTCTGCTATAACCAAGACAATTATT 57.669 33.333 0.00 0.00 34.64 1.40
2295 3456 9.831737 CTGCTATAACCAAGACAATTATTATGC 57.168 33.333 0.00 0.00 0.00 3.14
2296 3457 9.573166 TGCTATAACCAAGACAATTATTATGCT 57.427 29.630 0.00 0.00 0.00 3.79
2297 3458 9.831737 GCTATAACCAAGACAATTATTATGCTG 57.168 33.333 0.00 0.00 0.00 4.41
2300 3461 5.203528 ACCAAGACAATTATTATGCTGGCT 58.796 37.500 0.00 0.00 0.00 4.75
2301 3462 5.068198 ACCAAGACAATTATTATGCTGGCTG 59.932 40.000 0.00 0.00 0.00 4.85
2304 3465 7.431249 CAAGACAATTATTATGCTGGCTGATT 58.569 34.615 0.00 0.00 0.00 2.57
2306 3467 7.431249 AGACAATTATTATGCTGGCTGATTTG 58.569 34.615 0.00 0.00 0.00 2.32
2424 3596 6.878923 TGATTACTGGTATTCTGGTTCACAAG 59.121 38.462 4.89 0.00 0.00 3.16
2595 3767 8.747538 ATAGAAAAGGAAAGTTGTGTACAAGT 57.252 30.769 0.00 0.00 40.96 3.16
2924 4360 0.677288 GTTTTGGCCCCAAGTACCAC 59.323 55.000 0.00 0.00 37.24 4.16
3000 4547 9.823647 CTAGTACCATACATTTGAGAAGACAAT 57.176 33.333 0.00 0.00 0.00 2.71
3452 5009 7.907389 ACTATGTATTCTGAGGAACTTTCACA 58.093 34.615 0.00 0.00 41.55 3.58
3572 5129 8.364142 ACTAGCTGAAGAGGTATGCTTAATTAG 58.636 37.037 0.00 0.00 35.47 1.73
3660 5217 4.716784 AGTCTATGTTATGCCAGTCCTCAA 59.283 41.667 0.00 0.00 0.00 3.02
4420 5977 2.591571 TCATCCGCATCTTCACTGAG 57.408 50.000 0.00 0.00 0.00 3.35
4461 6018 0.166814 GCTGTTGCTTCTGCTTACCG 59.833 55.000 0.00 0.00 40.48 4.02
4734 6298 7.643569 TTATTTGATATCAAGAGGCAAGCAA 57.356 32.000 17.28 0.36 37.15 3.91
4848 6419 4.102524 AGTTTCTGATTGCCCCATCGTATA 59.897 41.667 0.00 0.00 0.00 1.47
4896 6467 7.873719 TGACTCTTGAATTTCCTTGTTTACA 57.126 32.000 0.00 0.00 0.00 2.41
5103 6674 6.501805 TCATTATGGGAATATGCTACCAGACT 59.498 38.462 0.00 0.00 36.27 3.24
5168 6741 6.861065 ACATGAATTGACCGATAACCATAC 57.139 37.500 0.00 0.00 0.00 2.39
5233 6806 8.660373 CGCTTCTATTTTGTTTATCTCTGACTT 58.340 33.333 0.00 0.00 0.00 3.01
5415 6988 7.687005 TTACAAGAAATACAAAAAGCCGTTG 57.313 32.000 0.00 0.00 0.00 4.10
5511 7084 3.492102 ATGTTCACTGGTGCTACTGTT 57.508 42.857 0.00 0.00 0.00 3.16
5542 7115 5.562298 ACCCGCTTACATATTAAGATGGT 57.438 39.130 14.27 3.33 0.00 3.55
5709 7282 3.144506 CATCACTGTGTTCTGGAGCTTT 58.855 45.455 7.79 0.00 0.00 3.51
5833 7406 5.068067 TCCATCTTTCATGGCATGTGTTATG 59.932 40.000 25.62 21.72 39.01 1.90
6002 7609 4.019681 CCAAGTAACAGGATCCTGGTTACA 60.020 45.833 36.50 24.13 41.95 2.41
6003 7610 5.339200 CCAAGTAACAGGATCCTGGTTACAT 60.339 44.000 36.50 30.68 41.95 2.29
6004 7611 6.126883 CCAAGTAACAGGATCCTGGTTACATA 60.127 42.308 36.50 23.60 41.95 2.29
6005 7612 7.335627 CAAGTAACAGGATCCTGGTTACATAA 58.664 38.462 36.50 23.07 41.95 1.90
6006 7613 7.504926 AGTAACAGGATCCTGGTTACATAAA 57.495 36.000 36.50 22.55 41.95 1.40
6007 7614 7.924541 AGTAACAGGATCCTGGTTACATAAAA 58.075 34.615 36.50 22.02 41.95 1.52
6080 7687 6.127479 GGTGGGTGTTTCATATGCAGAAAATA 60.127 38.462 0.00 0.00 36.80 1.40
6081 7688 7.319646 GTGGGTGTTTCATATGCAGAAAATAA 58.680 34.615 0.00 0.00 36.80 1.40
6082 7689 7.816995 GTGGGTGTTTCATATGCAGAAAATAAA 59.183 33.333 0.00 0.00 36.80 1.40
6083 7690 8.370940 TGGGTGTTTCATATGCAGAAAATAAAA 58.629 29.630 0.00 0.00 36.80 1.52
6084 7691 9.213799 GGGTGTTTCATATGCAGAAAATAAAAA 57.786 29.630 0.00 0.00 36.80 1.94
6087 7694 9.213799 TGTTTCATATGCAGAAAATAAAAACCC 57.786 29.630 0.00 0.00 36.80 4.11
6120 7735 6.157645 ACCTCTGGTTCTGAATTCTGATACAT 59.842 38.462 14.89 1.80 27.29 2.29
6274 8009 3.890147 GTGTTAGACCCTGGATATCTCGT 59.110 47.826 2.05 0.00 0.00 4.18
6292 8027 0.392461 GTCGCATCCCTTGGCTAACA 60.392 55.000 0.00 0.00 0.00 2.41
6358 8112 0.890683 GAAGGTTTGCCCTGATGGTG 59.109 55.000 0.00 0.00 45.47 4.17
6384 8138 2.913777 TCGAGAGAATGTGGTGTACG 57.086 50.000 0.00 0.00 37.03 3.67
6419 8173 4.642429 GTGGAGGATACACACAAAAGAGT 58.358 43.478 0.00 0.00 43.60 3.24
6420 8174 5.063880 GTGGAGGATACACACAAAAGAGTT 58.936 41.667 0.00 0.00 43.60 3.01
6421 8175 5.179555 GTGGAGGATACACACAAAAGAGTTC 59.820 44.000 0.00 0.00 43.60 3.01
6422 8176 4.389077 GGAGGATACACACAAAAGAGTTCG 59.611 45.833 0.00 0.00 41.41 3.95
6423 8177 3.746492 AGGATACACACAAAAGAGTTCGC 59.254 43.478 0.00 0.00 41.41 4.70
6424 8178 3.746492 GGATACACACAAAAGAGTTCGCT 59.254 43.478 0.00 0.00 0.00 4.93
6425 8179 4.213482 GGATACACACAAAAGAGTTCGCTT 59.787 41.667 0.00 0.00 0.00 4.68
6426 8180 5.277828 GGATACACACAAAAGAGTTCGCTTT 60.278 40.000 0.00 0.00 39.65 3.51
6427 8181 3.758300 ACACACAAAAGAGTTCGCTTTG 58.242 40.909 2.68 7.67 38.08 2.77
6439 8205 0.319900 TCGCTTTGAGAGTGTGAGGC 60.320 55.000 0.00 0.00 37.18 4.70
6468 8234 7.174413 TCCATGTTTTCTCAGGATCAACATTA 58.826 34.615 3.33 0.00 35.40 1.90
6469 8235 7.121168 TCCATGTTTTCTCAGGATCAACATTAC 59.879 37.037 3.33 0.00 35.40 1.89
6473 8239 3.785486 TCTCAGGATCAACATTACGCTG 58.215 45.455 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 9.612066 AAATGAGAGGAGAAAATATGACTTCTC 57.388 33.333 11.45 11.45 44.53 2.87
79 80 9.693739 AAGGAAACAAGGATTTTGGTTTTAATT 57.306 25.926 0.00 0.00 33.92 1.40
83 84 9.693739 AAATAAGGAAACAAGGATTTTGGTTTT 57.306 25.926 0.00 0.00 33.92 2.43
84 85 9.119418 CAAATAAGGAAACAAGGATTTTGGTTT 57.881 29.630 0.00 0.00 36.27 3.27
85 86 8.490311 TCAAATAAGGAAACAAGGATTTTGGTT 58.510 29.630 0.00 0.00 31.00 3.67
86 87 8.028652 TCAAATAAGGAAACAAGGATTTTGGT 57.971 30.769 0.00 0.00 0.00 3.67
116 117 8.753133 GGATTTTCTTGACCTTCCTATTTGATT 58.247 33.333 0.00 0.00 0.00 2.57
117 118 7.343057 GGGATTTTCTTGACCTTCCTATTTGAT 59.657 37.037 0.00 0.00 0.00 2.57
118 119 6.663523 GGGATTTTCTTGACCTTCCTATTTGA 59.336 38.462 0.00 0.00 0.00 2.69
119 120 6.127338 GGGGATTTTCTTGACCTTCCTATTTG 60.127 42.308 0.00 0.00 0.00 2.32
120 121 5.958380 GGGGATTTTCTTGACCTTCCTATTT 59.042 40.000 0.00 0.00 0.00 1.40
121 122 5.016245 TGGGGATTTTCTTGACCTTCCTATT 59.984 40.000 0.00 0.00 0.00 1.73
122 123 4.544152 TGGGGATTTTCTTGACCTTCCTAT 59.456 41.667 0.00 0.00 0.00 2.57
123 124 3.920197 TGGGGATTTTCTTGACCTTCCTA 59.080 43.478 0.00 0.00 0.00 2.94
124 125 2.721906 TGGGGATTTTCTTGACCTTCCT 59.278 45.455 0.00 0.00 0.00 3.36
125 126 3.169512 TGGGGATTTTCTTGACCTTCC 57.830 47.619 0.00 0.00 0.00 3.46
126 127 4.152647 AGTTGGGGATTTTCTTGACCTTC 58.847 43.478 0.00 0.00 0.00 3.46
127 128 4.140924 AGAGTTGGGGATTTTCTTGACCTT 60.141 41.667 0.00 0.00 0.00 3.50
128 129 3.399305 AGAGTTGGGGATTTTCTTGACCT 59.601 43.478 0.00 0.00 0.00 3.85
129 130 3.759086 GAGAGTTGGGGATTTTCTTGACC 59.241 47.826 0.00 0.00 0.00 4.02
130 131 4.657013 AGAGAGTTGGGGATTTTCTTGAC 58.343 43.478 0.00 0.00 0.00 3.18
131 132 4.263506 GGAGAGAGTTGGGGATTTTCTTGA 60.264 45.833 0.00 0.00 0.00 3.02
132 133 4.013050 GGAGAGAGTTGGGGATTTTCTTG 58.987 47.826 0.00 0.00 0.00 3.02
133 134 3.307762 CGGAGAGAGTTGGGGATTTTCTT 60.308 47.826 0.00 0.00 0.00 2.52
134 135 2.237392 CGGAGAGAGTTGGGGATTTTCT 59.763 50.000 0.00 0.00 0.00 2.52
135 136 2.236395 TCGGAGAGAGTTGGGGATTTTC 59.764 50.000 0.00 0.00 0.00 2.29
136 137 2.266279 TCGGAGAGAGTTGGGGATTTT 58.734 47.619 0.00 0.00 0.00 1.82
137 138 1.952621 TCGGAGAGAGTTGGGGATTT 58.047 50.000 0.00 0.00 0.00 2.17
138 139 3.711849 TCGGAGAGAGTTGGGGATT 57.288 52.632 0.00 0.00 0.00 3.01
150 151 2.168496 CAACTCAAGTACCCTCGGAGA 58.832 52.381 6.58 0.00 0.00 3.71
151 152 1.404315 GCAACTCAAGTACCCTCGGAG 60.404 57.143 0.00 0.00 0.00 4.63
152 153 0.606604 GCAACTCAAGTACCCTCGGA 59.393 55.000 0.00 0.00 0.00 4.55
153 154 0.608640 AGCAACTCAAGTACCCTCGG 59.391 55.000 0.00 0.00 0.00 4.63
154 155 2.457366 AAGCAACTCAAGTACCCTCG 57.543 50.000 0.00 0.00 0.00 4.63
155 156 3.369576 CCCTAAGCAACTCAAGTACCCTC 60.370 52.174 0.00 0.00 0.00 4.30
156 157 2.572104 CCCTAAGCAACTCAAGTACCCT 59.428 50.000 0.00 0.00 0.00 4.34
157 158 2.305052 ACCCTAAGCAACTCAAGTACCC 59.695 50.000 0.00 0.00 0.00 3.69
158 159 3.697619 ACCCTAAGCAACTCAAGTACC 57.302 47.619 0.00 0.00 0.00 3.34
159 160 6.387041 AAAAACCCTAAGCAACTCAAGTAC 57.613 37.500 0.00 0.00 0.00 2.73
160 161 5.237779 CGAAAAACCCTAAGCAACTCAAGTA 59.762 40.000 0.00 0.00 0.00 2.24
161 162 4.036380 CGAAAAACCCTAAGCAACTCAAGT 59.964 41.667 0.00 0.00 0.00 3.16
162 163 4.274950 TCGAAAAACCCTAAGCAACTCAAG 59.725 41.667 0.00 0.00 0.00 3.02
163 164 4.200874 TCGAAAAACCCTAAGCAACTCAA 58.799 39.130 0.00 0.00 0.00 3.02
164 165 3.811083 TCGAAAAACCCTAAGCAACTCA 58.189 40.909 0.00 0.00 0.00 3.41
165 166 3.188667 CCTCGAAAAACCCTAAGCAACTC 59.811 47.826 0.00 0.00 0.00 3.01
166 167 3.146847 CCTCGAAAAACCCTAAGCAACT 58.853 45.455 0.00 0.00 0.00 3.16
167 168 3.143728 TCCTCGAAAAACCCTAAGCAAC 58.856 45.455 0.00 0.00 0.00 4.17
168 169 3.495434 TCCTCGAAAAACCCTAAGCAA 57.505 42.857 0.00 0.00 0.00 3.91
169 170 3.713826 ATCCTCGAAAAACCCTAAGCA 57.286 42.857 0.00 0.00 0.00 3.91
170 171 4.733850 CAAATCCTCGAAAAACCCTAAGC 58.266 43.478 0.00 0.00 0.00 3.09
171 172 4.380550 GGCAAATCCTCGAAAAACCCTAAG 60.381 45.833 0.00 0.00 0.00 2.18
172 173 3.508402 GGCAAATCCTCGAAAAACCCTAA 59.492 43.478 0.00 0.00 0.00 2.69
173 174 3.086282 GGCAAATCCTCGAAAAACCCTA 58.914 45.455 0.00 0.00 0.00 3.53
174 175 1.893137 GGCAAATCCTCGAAAAACCCT 59.107 47.619 0.00 0.00 0.00 4.34
175 176 1.616374 TGGCAAATCCTCGAAAAACCC 59.384 47.619 0.00 0.00 35.26 4.11
176 177 3.378911 TTGGCAAATCCTCGAAAAACC 57.621 42.857 0.00 0.00 35.26 3.27
177 178 5.678921 CATTTTGGCAAATCCTCGAAAAAC 58.321 37.500 14.29 0.00 35.26 2.43
178 179 4.213059 GCATTTTGGCAAATCCTCGAAAAA 59.787 37.500 14.29 0.00 35.26 1.94
179 180 3.745458 GCATTTTGGCAAATCCTCGAAAA 59.255 39.130 14.29 0.00 35.26 2.29
180 181 3.244009 TGCATTTTGGCAAATCCTCGAAA 60.244 39.130 14.29 0.00 41.65 3.46
181 182 2.298446 TGCATTTTGGCAAATCCTCGAA 59.702 40.909 14.29 0.00 41.65 3.71
182 183 1.891811 TGCATTTTGGCAAATCCTCGA 59.108 42.857 14.29 0.00 41.65 4.04
183 184 2.367030 TGCATTTTGGCAAATCCTCG 57.633 45.000 14.29 2.25 41.65 4.63
191 192 8.775527 CATAGCATATTTTATTGCATTTTGGCA 58.224 29.630 0.00 0.00 41.35 4.92
192 193 7.747357 GCATAGCATATTTTATTGCATTTTGGC 59.253 33.333 0.00 0.00 41.35 4.52
193 194 8.775527 TGCATAGCATATTTTATTGCATTTTGG 58.224 29.630 0.00 0.00 41.35 3.28
197 198 9.713713 TCATTGCATAGCATATTTTATTGCATT 57.286 25.926 0.00 0.00 41.35 3.56
198 199 9.884636 ATCATTGCATAGCATATTTTATTGCAT 57.115 25.926 0.00 0.00 41.35 3.96
199 200 9.145865 CATCATTGCATAGCATATTTTATTGCA 57.854 29.630 0.00 0.00 41.35 4.08
200 201 9.361315 TCATCATTGCATAGCATATTTTATTGC 57.639 29.630 0.00 0.00 38.76 3.56
208 209 9.628500 ACATTAGATCATCATTGCATAGCATAT 57.372 29.630 0.00 0.00 38.76 1.78
210 211 7.939784 ACATTAGATCATCATTGCATAGCAT 57.060 32.000 0.00 0.00 38.76 3.79
245 246 8.994170 CGGTGTAACATCCCAAATTTTTAATTT 58.006 29.630 0.00 0.00 39.98 1.82
246 247 7.118535 GCGGTGTAACATCCCAAATTTTTAATT 59.881 33.333 0.00 0.00 39.98 1.40
247 248 6.592220 GCGGTGTAACATCCCAAATTTTTAAT 59.408 34.615 0.00 0.00 39.98 1.40
248 249 5.927115 GCGGTGTAACATCCCAAATTTTTAA 59.073 36.000 0.00 0.00 39.98 1.52
249 250 5.471257 GCGGTGTAACATCCCAAATTTTTA 58.529 37.500 0.00 0.00 39.98 1.52
250 251 4.311606 GCGGTGTAACATCCCAAATTTTT 58.688 39.130 0.00 0.00 39.98 1.94
251 252 3.306433 GGCGGTGTAACATCCCAAATTTT 60.306 43.478 0.00 0.00 39.98 1.82
252 253 2.232696 GGCGGTGTAACATCCCAAATTT 59.767 45.455 0.00 0.00 39.98 1.82
253 254 1.822371 GGCGGTGTAACATCCCAAATT 59.178 47.619 0.00 0.00 39.98 1.82
254 255 1.272203 TGGCGGTGTAACATCCCAAAT 60.272 47.619 0.00 0.00 39.98 2.32
255 256 0.110678 TGGCGGTGTAACATCCCAAA 59.889 50.000 0.00 0.00 39.98 3.28
256 257 0.606944 GTGGCGGTGTAACATCCCAA 60.607 55.000 0.00 0.00 39.98 4.12
257 258 1.003112 GTGGCGGTGTAACATCCCA 60.003 57.895 0.00 0.00 39.98 4.37
258 259 1.747745 GGTGGCGGTGTAACATCCC 60.748 63.158 0.00 0.00 39.98 3.85
259 260 0.393808 ATGGTGGCGGTGTAACATCC 60.394 55.000 0.00 0.00 39.98 3.51
260 261 1.014352 GATGGTGGCGGTGTAACATC 58.986 55.000 0.00 0.00 39.98 3.06
261 262 0.742990 CGATGGTGGCGGTGTAACAT 60.743 55.000 0.00 0.00 39.98 2.71
262 263 1.374885 CGATGGTGGCGGTGTAACA 60.375 57.895 0.00 0.00 39.98 2.41
263 264 0.671163 TTCGATGGTGGCGGTGTAAC 60.671 55.000 0.00 0.00 0.00 2.50
264 265 0.035036 TTTCGATGGTGGCGGTGTAA 59.965 50.000 0.00 0.00 0.00 2.41
265 266 0.390603 CTTTCGATGGTGGCGGTGTA 60.391 55.000 0.00 0.00 0.00 2.90
266 267 1.671054 CTTTCGATGGTGGCGGTGT 60.671 57.895 0.00 0.00 0.00 4.16
267 268 1.671054 ACTTTCGATGGTGGCGGTG 60.671 57.895 0.00 0.00 0.00 4.94
268 269 1.671054 CACTTTCGATGGTGGCGGT 60.671 57.895 9.52 0.00 0.00 5.68
269 270 3.039202 GCACTTTCGATGGTGGCGG 62.039 63.158 16.37 0.00 34.41 6.13
270 271 2.480555 GCACTTTCGATGGTGGCG 59.519 61.111 16.37 0.00 34.41 5.69
272 273 1.308069 CCAGGCACTTTCGATGGTGG 61.308 60.000 16.37 1.55 34.60 4.61
273 274 1.308069 CCCAGGCACTTTCGATGGTG 61.308 60.000 12.15 12.15 34.60 4.17
274 275 1.002134 CCCAGGCACTTTCGATGGT 60.002 57.895 0.00 0.00 34.60 3.55
275 276 1.750399 CCCCAGGCACTTTCGATGG 60.750 63.158 0.00 0.00 34.60 3.51
276 277 3.909662 CCCCAGGCACTTTCGATG 58.090 61.111 0.00 0.00 34.60 3.84
299 300 4.811364 GAGCCAGGAAGCTGGGGC 62.811 72.222 9.48 9.48 45.15 5.80
300 301 4.120755 GGAGCCAGGAAGCTGGGG 62.121 72.222 0.00 0.00 45.15 4.96
301 302 4.479993 CGGAGCCAGGAAGCTGGG 62.480 72.222 0.00 0.00 45.15 4.45
346 347 4.977126 CTCCGGCCGATACGCGAC 62.977 72.222 30.73 2.51 44.57 5.19
360 361 4.803908 CTCTTTGGGGCGCCCTCC 62.804 72.222 42.70 28.63 45.70 4.30
361 362 3.689002 CTCTCTTTGGGGCGCCCTC 62.689 68.421 42.70 32.00 45.70 4.30
362 363 3.721706 CTCTCTTTGGGGCGCCCT 61.722 66.667 42.70 0.00 45.70 5.19
363 364 3.268103 TTCTCTCTTTGGGGCGCCC 62.268 63.158 38.57 38.57 45.71 6.13
364 365 1.746991 CTTCTCTCTTTGGGGCGCC 60.747 63.158 21.18 21.18 0.00 6.53
365 366 1.746991 CCTTCTCTCTTTGGGGCGC 60.747 63.158 0.00 0.00 0.00 6.53
366 367 1.078143 CCCTTCTCTCTTTGGGGCG 60.078 63.158 0.00 0.00 36.15 6.13
369 370 1.078143 CGCCCCTTCTCTCTTTGGG 60.078 63.158 0.00 0.00 39.37 4.12
370 371 0.107945 CTCGCCCCTTCTCTCTTTGG 60.108 60.000 0.00 0.00 0.00 3.28
371 372 0.742635 GCTCGCCCCTTCTCTCTTTG 60.743 60.000 0.00 0.00 0.00 2.77
372 373 1.599576 GCTCGCCCCTTCTCTCTTT 59.400 57.895 0.00 0.00 0.00 2.52
373 374 2.363172 GGCTCGCCCCTTCTCTCTT 61.363 63.158 0.00 0.00 0.00 2.85
374 375 2.762043 GGCTCGCCCCTTCTCTCT 60.762 66.667 0.00 0.00 0.00 3.10
401 402 4.514577 AAGCTCGTCCGGCGGATG 62.515 66.667 36.30 36.30 39.89 3.51
402 403 3.771160 AAAGCTCGTCCGGCGGAT 61.771 61.111 33.54 13.28 41.72 4.18
403 404 4.735132 CAAAGCTCGTCCGGCGGA 62.735 66.667 27.46 27.46 41.72 5.54
406 407 3.491652 GAGCAAAGCTCGTCCGGC 61.492 66.667 0.00 0.00 45.85 6.13
420 421 3.191539 CGGAAGAAGCTGGCGAGC 61.192 66.667 13.51 13.51 46.64 5.03
421 422 2.510238 CCGGAAGAAGCTGGCGAG 60.510 66.667 0.00 0.00 0.00 5.03
449 450 3.721706 CACCTCCCCTGCACCCTC 61.722 72.222 0.00 0.00 0.00 4.30
453 454 3.580319 AACCCACCTCCCCTGCAC 61.580 66.667 0.00 0.00 0.00 4.57
454 455 3.579302 CAACCCACCTCCCCTGCA 61.579 66.667 0.00 0.00 0.00 4.41
455 456 4.366684 CCAACCCACCTCCCCTGC 62.367 72.222 0.00 0.00 0.00 4.85
456 457 3.661648 CCCAACCCACCTCCCCTG 61.662 72.222 0.00 0.00 0.00 4.45
475 476 4.125695 AACCCTAGCCGTCGTCGC 62.126 66.667 0.00 0.00 35.54 5.19
476 477 2.101770 GAACCCTAGCCGTCGTCG 59.898 66.667 0.00 0.00 0.00 5.12
477 478 2.101770 CGAACCCTAGCCGTCGTC 59.898 66.667 0.00 0.00 0.00 4.20
478 479 4.125695 GCGAACCCTAGCCGTCGT 62.126 66.667 8.39 0.00 0.00 4.34
479 480 4.867599 GGCGAACCCTAGCCGTCG 62.868 72.222 0.00 3.58 44.22 5.12
507 508 3.365265 GCTCACGTTGCCCCAAGG 61.365 66.667 0.00 0.00 35.67 3.61
508 509 3.726517 CGCTCACGTTGCCCCAAG 61.727 66.667 4.93 0.00 33.53 3.61
509 510 4.243008 TCGCTCACGTTGCCCCAA 62.243 61.111 4.93 0.00 41.18 4.12
510 511 4.680237 CTCGCTCACGTTGCCCCA 62.680 66.667 4.93 0.00 41.18 4.96
511 512 4.681978 ACTCGCTCACGTTGCCCC 62.682 66.667 4.93 0.00 41.18 5.80
512 513 3.112709 GACTCGCTCACGTTGCCC 61.113 66.667 4.93 0.00 41.18 5.36
513 514 3.470567 CGACTCGCTCACGTTGCC 61.471 66.667 4.93 0.00 41.18 4.52
514 515 3.470567 CCGACTCGCTCACGTTGC 61.471 66.667 0.00 0.00 41.18 4.17
515 516 2.805353 CCCGACTCGCTCACGTTG 60.805 66.667 0.00 0.00 41.18 4.10
516 517 1.518056 TAACCCGACTCGCTCACGTT 61.518 55.000 0.00 0.00 41.18 3.99
517 518 1.968017 TAACCCGACTCGCTCACGT 60.968 57.895 0.00 0.00 41.18 4.49
518 519 1.513586 GTAACCCGACTCGCTCACG 60.514 63.158 0.00 0.00 42.01 4.35
519 520 1.153881 GGTAACCCGACTCGCTCAC 60.154 63.158 0.00 0.00 0.00 3.51
520 521 3.281240 GGTAACCCGACTCGCTCA 58.719 61.111 0.00 0.00 0.00 4.26
530 531 5.945466 TTTCAAAGAATACACGGTAACCC 57.055 39.130 0.00 0.00 0.00 4.11
531 532 5.798434 GCATTTCAAAGAATACACGGTAACC 59.202 40.000 0.00 0.00 0.00 2.85
532 533 6.608610 AGCATTTCAAAGAATACACGGTAAC 58.391 36.000 0.00 0.00 0.00 2.50
533 534 6.811253 AGCATTTCAAAGAATACACGGTAA 57.189 33.333 0.00 0.00 0.00 2.85
534 535 6.428465 TCAAGCATTTCAAAGAATACACGGTA 59.572 34.615 0.00 0.00 0.00 4.02
535 536 5.240623 TCAAGCATTTCAAAGAATACACGGT 59.759 36.000 0.00 0.00 0.00 4.83
536 537 5.698832 TCAAGCATTTCAAAGAATACACGG 58.301 37.500 0.00 0.00 0.00 4.94
537 538 7.379529 ACTTTCAAGCATTTCAAAGAATACACG 59.620 33.333 0.00 0.00 32.35 4.49
538 539 8.579682 ACTTTCAAGCATTTCAAAGAATACAC 57.420 30.769 0.00 0.00 32.35 2.90
573 574 3.423539 TGACAGCTACAGCCTTCAATT 57.576 42.857 0.00 0.00 43.38 2.32
584 585 2.749621 CCCCTCACATTTTGACAGCTAC 59.250 50.000 0.00 0.00 0.00 3.58
608 609 8.524487 TGTTCAGTGTTTAGGTGTATTTGTTTT 58.476 29.630 0.00 0.00 0.00 2.43
616 617 6.481976 CACAGATTGTTCAGTGTTTAGGTGTA 59.518 38.462 0.00 0.00 35.34 2.90
618 619 5.751680 CACAGATTGTTCAGTGTTTAGGTG 58.248 41.667 0.00 0.00 35.34 4.00
620 621 4.275689 TGCACAGATTGTTCAGTGTTTAGG 59.724 41.667 0.00 0.00 40.46 2.69
622 623 4.260579 CGTGCACAGATTGTTCAGTGTTTA 60.261 41.667 18.64 0.00 40.46 2.01
623 624 3.487376 CGTGCACAGATTGTTCAGTGTTT 60.487 43.478 18.64 0.00 40.46 2.83
655 657 0.468226 GAGCATCCCCAATCACGGTA 59.532 55.000 0.00 0.00 0.00 4.02
657 659 0.533755 GAGAGCATCCCCAATCACGG 60.534 60.000 0.00 0.00 33.66 4.94
667 669 2.175878 AATACGCCATGAGAGCATCC 57.824 50.000 0.00 0.00 33.66 3.51
678 680 2.843669 GGGAACGACAAATACGCCA 58.156 52.632 0.00 0.00 0.00 5.69
751 761 1.717791 TATCTCCACGTGGCGTACCG 61.718 60.000 30.25 12.67 38.32 4.02
972 2122 3.487202 GTTCGATGCGCGCTTCCA 61.487 61.111 32.96 22.97 40.61 3.53
1112 2262 2.230130 AAAGCGGGATTGAAATGGGA 57.770 45.000 0.00 0.00 0.00 4.37
1149 2299 1.381928 CGCGCTTACCCTAGTCTCCA 61.382 60.000 5.56 0.00 0.00 3.86
1166 2316 3.030882 GGCTAATCTCGCGGTCGC 61.031 66.667 6.13 5.16 35.26 5.19
1197 2347 1.444553 CGTTCCTCCAGCTCGTCAC 60.445 63.158 0.00 0.00 0.00 3.67
1217 2367 2.755103 GGAACAGCAATTTCTACCTGGG 59.245 50.000 0.00 0.00 0.00 4.45
1257 2407 3.066760 CCCTTTTGACCACTGAGTTCAAC 59.933 47.826 0.00 0.00 0.00 3.18
1283 2433 9.621629 ACATACAAAATAAATGTAAGGGATCGA 57.378 29.630 0.00 0.00 36.88 3.59
1353 2503 3.181505 ACATCTGACGCTCTAAAGTCTCG 60.182 47.826 0.00 0.00 38.16 4.04
1454 2611 7.573968 AATTAAATCCATAGCAGGTCAAGAC 57.426 36.000 0.00 0.00 0.00 3.01
1467 2624 5.104817 CCACTTGGCTCCAAATTAAATCCAT 60.105 40.000 2.69 0.00 35.33 3.41
1470 2627 5.185828 AGTCCACTTGGCTCCAAATTAAATC 59.814 40.000 2.69 0.00 35.33 2.17
1858 3019 3.319122 AGACTTTCATTGGTCTGTTTGGC 59.681 43.478 0.00 0.00 40.71 4.52
1895 3056 9.209175 GCTAGAGAAGTAATTCAAGAGTTTTGA 57.791 33.333 5.62 0.00 0.00 2.69
1936 3097 3.495377 TCGTGGTTGATTTTAACGGACTG 59.505 43.478 0.00 0.00 35.08 3.51
1975 3136 1.155155 TTTTCCTGGTTCTGCCCCC 59.845 57.895 0.00 0.00 36.04 5.40
2048 3209 2.170397 TCAGGAGCAGTGACAAGACAAA 59.830 45.455 0.00 0.00 0.00 2.83
2067 3228 0.394216 CATGTGGATCCCGGCTTTCA 60.394 55.000 9.90 0.00 0.00 2.69
2132 3293 2.045524 TGGTTTTGTCAACCATGGCAT 58.954 42.857 13.04 0.00 44.74 4.40
2146 3307 2.703536 GGGGTTCCAGAAATGTGGTTTT 59.296 45.455 0.00 0.00 38.88 2.43
2270 3431 9.573166 AGCATAATAATTGTCTTGGTTATAGCA 57.427 29.630 0.00 0.00 0.00 3.49
2288 3449 7.652524 TTTTACCAAATCAGCCAGCATAATA 57.347 32.000 0.00 0.00 0.00 0.98
2290 3451 5.991933 TTTTACCAAATCAGCCAGCATAA 57.008 34.783 0.00 0.00 0.00 1.90
2291 3452 5.991933 TTTTTACCAAATCAGCCAGCATA 57.008 34.783 0.00 0.00 0.00 3.14
2293 3454 4.282957 TGATTTTTACCAAATCAGCCAGCA 59.717 37.500 6.00 0.00 40.53 4.41
2294 3455 4.819769 TGATTTTTACCAAATCAGCCAGC 58.180 39.130 6.00 0.00 40.53 4.85
2300 3461 4.466015 GGGAGGCTGATTTTTACCAAATCA 59.534 41.667 9.15 9.15 42.44 2.57
2301 3462 4.141937 GGGGAGGCTGATTTTTACCAAATC 60.142 45.833 0.00 1.10 37.21 2.17
2304 3465 2.558800 GGGGGAGGCTGATTTTTACCAA 60.559 50.000 0.00 0.00 0.00 3.67
2306 3467 1.006639 TGGGGGAGGCTGATTTTTACC 59.993 52.381 0.00 0.00 0.00 2.85
2424 3596 7.607250 AGGAAATCAGGAGACGATATATCAAC 58.393 38.462 13.11 5.90 0.00 3.18
2595 3767 0.772124 AGGTCTGGCCCTTCTTTGGA 60.772 55.000 0.00 0.00 38.26 3.53
3000 4547 6.014755 TGGTCACTAAATGGAAAATGATGCAA 60.015 34.615 0.00 0.00 0.00 4.08
3324 4881 0.316204 ACCCTGTAAGACCAACGACG 59.684 55.000 0.00 0.00 34.07 5.12
3379 4936 0.678950 TGCATTGAGTCACGGTGAGA 59.321 50.000 11.83 0.00 0.00 3.27
3452 5009 5.049336 CCACTGAGTTCAGACGATATACGAT 60.049 44.000 15.63 0.00 46.59 3.73
3572 5129 4.184079 ACTCGGTGAATACTGGTACAAC 57.816 45.455 0.00 0.00 38.70 3.32
4168 5725 2.121948 AGGAAGACCATGCAGCAGATA 58.878 47.619 0.00 0.00 38.94 1.98
4461 6018 3.079960 ACGACCGATCATACATGTGAC 57.920 47.619 9.11 0.00 0.00 3.67
4545 6109 7.827819 TCAGTGAAGGAAACTCATTATTACG 57.172 36.000 0.00 0.00 42.68 3.18
4734 6298 7.986889 ACTTTATCAAAAACATGAAAGCTTGGT 59.013 29.630 0.00 0.00 32.06 3.67
4745 6309 9.225436 ACAAAAACACCACTTTATCAAAAACAT 57.775 25.926 0.00 0.00 0.00 2.71
4806 6370 8.116753 CAGAAACTAAGAAATAATAGTGTGGCG 58.883 37.037 0.00 0.00 0.00 5.69
4896 6467 8.194769 ACTGAAAATAGGAAACGTGAAAACAAT 58.805 29.630 0.00 0.00 0.00 2.71
4990 6561 2.558359 ACAGGTACCAAAGCAATCAAGC 59.442 45.455 15.94 0.00 0.00 4.01
5201 6774 7.331791 AGATAAACAAAATAGAAGCGAGGTCT 58.668 34.615 0.00 0.00 0.00 3.85
5233 6806 6.882140 TGACAAGTACCAAAGAAAGAGAACAA 59.118 34.615 0.00 0.00 0.00 2.83
5415 6988 1.002430 TCGGAATGGATAGCATCAGCC 59.998 52.381 0.00 0.00 43.56 4.85
5542 7115 5.420725 ACACAAGGTCAATATGAGCACTA 57.579 39.130 11.61 0.00 46.52 2.74
5709 7282 5.065914 AGAAAGCAGAAATAGTTGTCAGCA 58.934 37.500 0.00 0.00 0.00 4.41
5833 7406 4.232221 CAATCATCAAACCAACTGCACTC 58.768 43.478 0.00 0.00 0.00 3.51
6019 7626 2.305927 ACACCCAAGGATCCTGTTAGTG 59.694 50.000 17.02 21.05 0.00 2.74
6058 7665 8.770438 TTTTATTTTCTGCATATGAAACACCC 57.230 30.769 6.97 0.00 33.77 4.61
6197 7927 9.988350 ATCGACACACATAACTTTCATAATTTC 57.012 29.630 0.00 0.00 0.00 2.17
6214 7944 0.512952 GCAGAACACCATCGACACAC 59.487 55.000 0.00 0.00 0.00 3.82
6215 7945 0.392706 AGCAGAACACCATCGACACA 59.607 50.000 0.00 0.00 0.00 3.72
6274 8009 0.392461 GTGTTAGCCAAGGGATGCGA 60.392 55.000 0.00 0.00 0.00 5.10
6324 8060 1.577922 CTTCCGACCACTCGACGAA 59.422 57.895 0.00 0.00 43.06 3.85
6333 8069 2.114411 GGGCAAACCTTCCGACCA 59.886 61.111 0.00 0.00 35.85 4.02
6358 8112 4.142359 ACACCACATTCTCTCGATAGTGTC 60.142 45.833 0.00 0.00 30.54 3.67
6374 8128 0.038983 CCACATCGACGTACACCACA 60.039 55.000 0.00 0.00 0.00 4.17
6381 8135 1.214325 CACAGCCCACATCGACGTA 59.786 57.895 0.00 0.00 0.00 3.57
6384 8138 1.448540 CTCCACAGCCCACATCGAC 60.449 63.158 0.00 0.00 0.00 4.20
6413 8167 3.557595 CACACTCTCAAAGCGAACTCTTT 59.442 43.478 0.00 0.00 36.78 2.52
6416 8170 2.728839 CTCACACTCTCAAAGCGAACTC 59.271 50.000 0.00 0.00 0.00 3.01
6419 8173 1.873903 GCCTCACACTCTCAAAGCGAA 60.874 52.381 0.00 0.00 0.00 4.70
6420 8174 0.319900 GCCTCACACTCTCAAAGCGA 60.320 55.000 0.00 0.00 0.00 4.93
6421 8175 1.294659 GGCCTCACACTCTCAAAGCG 61.295 60.000 0.00 0.00 0.00 4.68
6422 8176 0.036022 AGGCCTCACACTCTCAAAGC 59.964 55.000 0.00 0.00 0.00 3.51
6423 8177 3.431486 GGATAGGCCTCACACTCTCAAAG 60.431 52.174 9.68 0.00 0.00 2.77
6424 8178 2.501723 GGATAGGCCTCACACTCTCAAA 59.498 50.000 9.68 0.00 0.00 2.69
6425 8179 2.111384 GGATAGGCCTCACACTCTCAA 58.889 52.381 9.68 0.00 0.00 3.02
6426 8180 1.007118 TGGATAGGCCTCACACTCTCA 59.993 52.381 9.68 0.00 37.63 3.27
6427 8181 1.781786 TGGATAGGCCTCACACTCTC 58.218 55.000 9.68 0.00 37.63 3.20
6439 8205 5.933617 TGATCCTGAGAAAACATGGATAGG 58.066 41.667 0.00 0.00 37.62 2.57
6468 8234 3.557903 ATGGCTCCAGCAACAGCGT 62.558 57.895 0.03 0.00 44.36 5.07
6469 8235 2.749044 ATGGCTCCAGCAACAGCG 60.749 61.111 0.03 0.00 44.36 5.18


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

AutoCloner maintained by Alex Coulton.