Multiple sequence alignment - TraesCS4D01G344700

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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 TraesCS4D01G344700 chr4D 100.000 2954 0 0 1 2954 499713928 499710975 0.000000e+00 5456.0
1 TraesCS4D01G344700 chr4D 88.238 2100 215 21 865 2950 499694324 499696405 0.000000e+00 2481.0
2 TraesCS4D01G344700 chr4D 84.980 2217 219 64 333 2481 499702559 499700389 0.000000e+00 2145.0
3 TraesCS4D01G344700 chr4D 90.230 522 46 3 1723 2241 499830833 499831352 0.000000e+00 676.0
4 TraesCS4D01G344700 chr4D 80.301 731 95 27 2220 2941 499833646 499834336 9.450000e-140 507.0
5 TraesCS4D01G344700 chr4D 84.848 396 53 5 1923 2314 499844655 499845047 2.760000e-105 392.0
6 TraesCS4D01G344700 chr4D 89.313 262 11 3 1466 1727 499794184 499794428 2.210000e-81 313.0
7 TraesCS4D01G344700 chr4D 93.452 168 11 0 169 336 499713596 499713429 1.760000e-62 250.0
8 TraesCS4D01G344700 chr4D 93.452 168 11 0 333 500 499713760 499713593 1.760000e-62 250.0
9 TraesCS4D01G344700 chr5A 94.939 2055 75 5 567 2620 680697265 680695239 0.000000e+00 3192.0
10 TraesCS4D01G344700 chr5A 90.781 1909 160 10 730 2629 680748797 680750698 0.000000e+00 2536.0
11 TraesCS4D01G344700 chr5A 90.560 339 19 6 3 336 680697706 680697376 1.260000e-118 436.0
12 TraesCS4D01G344700 chr5A 90.706 269 19 3 333 597 680697547 680697281 1.300000e-93 353.0
13 TraesCS4D01G344700 chr5A 82.075 424 53 17 630 1035 680663229 680662811 1.010000e-89 340.0
14 TraesCS4D01G344700 chr5A 94.118 85 4 1 113 197 680748410 680748493 8.590000e-26 128.0
15 TraesCS4D01G344700 chr4B 89.411 1766 155 22 730 2475 642963498 642965251 0.000000e+00 2196.0
16 TraesCS4D01G344700 chr4B 88.530 1735 168 14 865 2587 642750862 642749147 0.000000e+00 2073.0
17 TraesCS4D01G344700 chr4B 96.146 1012 31 2 696 1700 642781119 642780109 0.000000e+00 1646.0
18 TraesCS4D01G344700 chr4B 95.103 919 44 1 1684 2602 642779700 642778783 0.000000e+00 1447.0
19 TraesCS4D01G344700 chr4B 91.270 252 21 1 55 305 486974116 486974367 2.820000e-90 342.0
20 TraesCS4D01G344700 chr4B 89.091 220 15 4 4 222 642781582 642781371 6.280000e-67 265.0
21 TraesCS4D01G344700 chr4B 84.477 277 28 6 616 892 642751128 642750867 2.920000e-65 259.0
22 TraesCS4D01G344700 chr4B 83.594 256 26 9 346 586 642751758 642751504 2.960000e-55 226.0
23 TraesCS4D01G344700 chr4B 92.701 137 10 0 333 469 486974231 486974367 6.460000e-47 198.0
24 TraesCS4D01G344700 chr4B 88.571 140 7 1 447 586 642781350 642781220 8.470000e-36 161.0
25 TraesCS4D01G344700 chr4B 95.652 92 4 0 244 335 642963222 642963313 6.600000e-32 148.0
26 TraesCS4D01G344700 chr4B 93.750 96 6 0 798 893 486974438 486974533 8.530000e-31 145.0
27 TraesCS4D01G344700 chr4B 90.426 94 8 1 113 206 642963129 642963221 4.000000e-24 122.0
28 TraesCS4D01G344700 chr4B 87.640 89 7 1 865 949 486974537 486974625 1.870000e-17 100.0
29 TraesCS4D01G344700 chr4B 95.122 41 0 2 333 372 642963184 642963223 2.460000e-06 63.9
30 TraesCS4D01G344700 chr4B 100.000 33 0 0 238 270 642781374 642781342 8.840000e-06 62.1
31 TraesCS4D01G344700 chr3D 83.871 155 24 1 113 266 578589857 578590011 2.370000e-31 147.0
32 TraesCS4D01G344700 chr3D 85.859 99 12 2 333 430 578589914 578590011 1.450000e-18 104.0


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 TraesCS4D01G344700 chr4D 499710975 499713928 2953 True 1985.333333 5456 95.634667 1 2954 3 chr4D.!!$R2 2953
1 TraesCS4D01G344700 chr4D 499694324 499696405 2081 False 2481.000000 2481 88.238000 865 2950 1 chr4D.!!$F1 2085
2 TraesCS4D01G344700 chr4D 499700389 499702559 2170 True 2145.000000 2145 84.980000 333 2481 1 chr4D.!!$R1 2148
3 TraesCS4D01G344700 chr4D 499830833 499834336 3503 False 591.500000 676 85.265500 1723 2941 2 chr4D.!!$F4 1218
4 TraesCS4D01G344700 chr5A 680748410 680750698 2288 False 1332.000000 2536 92.449500 113 2629 2 chr5A.!!$F1 2516
5 TraesCS4D01G344700 chr5A 680695239 680697706 2467 True 1327.000000 3192 92.068333 3 2620 3 chr5A.!!$R2 2617
6 TraesCS4D01G344700 chr4B 642749147 642751758 2611 True 852.666667 2073 85.533667 346 2587 3 chr4B.!!$R1 2241
7 TraesCS4D01G344700 chr4B 642778783 642781582 2799 True 716.220000 1646 93.782200 4 2602 5 chr4B.!!$R2 2598
8 TraesCS4D01G344700 chr4B 642963129 642965251 2122 False 632.475000 2196 92.652750 113 2475 4 chr4B.!!$F2 2362

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
192 194 0.03563 AGTGCATGCCAAGTCTCTCC 60.036 55.0 16.68 0.0 0.0 3.71 F
193 195 0.03563 GTGCATGCCAAGTCTCTCCT 60.036 55.0 16.68 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1284 1814 0.321671 ACACGACCCCAGATTGACTG 59.678 55.0 0.00 0.00 45.36 3.51 R
2151 3127 0.392863 TTCACACGGATGCATCCCAG 60.393 55.0 34.76 28.69 44.24 4.45 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
44 46 9.539825 GTATCCACTCCATCAATATCATGATAC 57.460 37.037 17.60 0.00 37.96 2.24
45 47 7.557875 TCCACTCCATCAATATCATGATACA 57.442 36.000 17.60 5.54 37.96 2.29
46 48 7.976712 TCCACTCCATCAATATCATGATACAA 58.023 34.615 17.60 6.75 37.96 2.41
47 49 8.608598 TCCACTCCATCAATATCATGATACAAT 58.391 33.333 17.60 8.67 37.96 2.71
48 50 8.890718 CCACTCCATCAATATCATGATACAATC 58.109 37.037 17.60 0.00 37.96 2.67
49 51 9.444600 CACTCCATCAATATCATGATACAATCA 57.555 33.333 17.60 0.00 44.55 2.57
171 173 4.900054 ACTGAAACTGTAGTAGGACTTGGT 59.100 41.667 0.00 0.00 0.00 3.67
172 174 5.010820 ACTGAAACTGTAGTAGGACTTGGTC 59.989 44.000 0.00 0.00 0.00 4.02
173 175 4.897076 TGAAACTGTAGTAGGACTTGGTCA 59.103 41.667 0.14 0.00 33.68 4.02
174 176 5.010719 TGAAACTGTAGTAGGACTTGGTCAG 59.989 44.000 0.14 0.00 33.68 3.51
175 177 4.115398 ACTGTAGTAGGACTTGGTCAGT 57.885 45.455 0.14 0.00 39.07 3.41
176 178 3.827302 ACTGTAGTAGGACTTGGTCAGTG 59.173 47.826 0.00 0.00 35.01 3.66
177 179 2.561419 TGTAGTAGGACTTGGTCAGTGC 59.439 50.000 0.14 0.00 44.22 4.40
178 180 1.717032 AGTAGGACTTGGTCAGTGCA 58.283 50.000 0.14 0.00 46.30 4.57
179 181 2.260822 AGTAGGACTTGGTCAGTGCAT 58.739 47.619 0.00 0.00 46.30 3.96
180 182 2.027745 AGTAGGACTTGGTCAGTGCATG 60.028 50.000 0.00 0.00 46.30 4.06
181 183 0.607489 AGGACTTGGTCAGTGCATGC 60.607 55.000 11.82 11.82 46.30 4.06
182 184 1.589716 GGACTTGGTCAGTGCATGCC 61.590 60.000 16.68 6.65 43.36 4.40
183 185 0.890542 GACTTGGTCAGTGCATGCCA 60.891 55.000 16.68 0.96 35.01 4.92
184 186 0.467844 ACTTGGTCAGTGCATGCCAA 60.468 50.000 16.68 9.81 40.51 4.52
185 187 0.242825 CTTGGTCAGTGCATGCCAAG 59.757 55.000 16.68 21.98 46.79 3.61
186 188 0.467844 TTGGTCAGTGCATGCCAAGT 60.468 50.000 16.68 0.00 38.99 3.16
187 189 0.890542 TGGTCAGTGCATGCCAAGTC 60.891 55.000 16.68 3.01 33.77 3.01
188 190 0.607489 GGTCAGTGCATGCCAAGTCT 60.607 55.000 16.68 3.04 0.00 3.24
189 191 0.801251 GTCAGTGCATGCCAAGTCTC 59.199 55.000 16.68 0.00 0.00 3.36
190 192 0.689055 TCAGTGCATGCCAAGTCTCT 59.311 50.000 16.68 0.00 0.00 3.10
191 193 1.085091 CAGTGCATGCCAAGTCTCTC 58.915 55.000 16.68 0.00 0.00 3.20
192 194 0.035630 AGTGCATGCCAAGTCTCTCC 60.036 55.000 16.68 0.00 0.00 3.71
193 195 0.035630 GTGCATGCCAAGTCTCTCCT 60.036 55.000 16.68 0.00 0.00 3.69
194 196 0.694771 TGCATGCCAAGTCTCTCCTT 59.305 50.000 16.68 0.00 0.00 3.36
195 197 1.093159 GCATGCCAAGTCTCTCCTTG 58.907 55.000 6.36 0.00 41.21 3.61
196 198 1.339438 GCATGCCAAGTCTCTCCTTGA 60.339 52.381 6.36 0.00 43.65 3.02
197 199 2.354259 CATGCCAAGTCTCTCCTTGAC 58.646 52.381 2.62 0.00 43.65 3.18
198 200 1.423584 TGCCAAGTCTCTCCTTGACA 58.576 50.000 2.62 0.00 43.65 3.58
199 201 1.768275 TGCCAAGTCTCTCCTTGACAA 59.232 47.619 2.62 0.00 43.65 3.18
200 202 2.172505 TGCCAAGTCTCTCCTTGACAAA 59.827 45.455 2.62 0.00 43.65 2.83
201 203 3.181440 TGCCAAGTCTCTCCTTGACAAAT 60.181 43.478 2.62 0.00 43.65 2.32
202 204 4.041567 TGCCAAGTCTCTCCTTGACAAATA 59.958 41.667 2.62 0.00 43.65 1.40
203 205 4.393371 GCCAAGTCTCTCCTTGACAAATAC 59.607 45.833 2.62 0.00 43.65 1.89
204 206 4.627467 CCAAGTCTCTCCTTGACAAATACG 59.373 45.833 2.62 0.00 43.65 3.06
205 207 3.851098 AGTCTCTCCTTGACAAATACGC 58.149 45.455 0.00 0.00 36.94 4.42
206 208 3.258372 AGTCTCTCCTTGACAAATACGCA 59.742 43.478 0.00 0.00 36.94 5.24
207 209 3.994392 GTCTCTCCTTGACAAATACGCAA 59.006 43.478 0.00 0.00 34.80 4.85
208 210 4.631813 GTCTCTCCTTGACAAATACGCAAT 59.368 41.667 0.00 0.00 34.80 3.56
209 211 4.631377 TCTCTCCTTGACAAATACGCAATG 59.369 41.667 0.00 0.00 0.00 2.82
210 212 3.126858 TCTCCTTGACAAATACGCAATGC 59.873 43.478 0.00 0.00 0.00 3.56
211 213 3.081061 TCCTTGACAAATACGCAATGCT 58.919 40.909 2.94 0.00 0.00 3.79
212 214 3.505680 TCCTTGACAAATACGCAATGCTT 59.494 39.130 2.94 0.00 0.00 3.91
213 215 3.609373 CCTTGACAAATACGCAATGCTTG 59.391 43.478 2.94 3.45 0.00 4.01
214 216 4.475028 CTTGACAAATACGCAATGCTTGA 58.525 39.130 11.12 0.00 0.00 3.02
215 217 4.700268 TGACAAATACGCAATGCTTGAT 57.300 36.364 11.12 0.00 0.00 2.57
216 218 5.058149 TGACAAATACGCAATGCTTGATT 57.942 34.783 11.12 1.88 0.00 2.57
217 219 5.468592 TGACAAATACGCAATGCTTGATTT 58.531 33.333 11.12 7.31 0.00 2.17
218 220 5.345472 TGACAAATACGCAATGCTTGATTTG 59.655 36.000 22.83 22.83 36.52 2.32
219 221 5.229423 ACAAATACGCAATGCTTGATTTGT 58.771 33.333 23.70 23.70 37.62 2.83
220 222 5.695816 ACAAATACGCAATGCTTGATTTGTT 59.304 32.000 23.70 14.61 38.39 2.83
221 223 5.766702 AATACGCAATGCTTGATTTGTTG 57.233 34.783 2.94 0.00 0.00 3.33
222 224 3.096489 ACGCAATGCTTGATTTGTTGT 57.904 38.095 2.94 0.00 0.00 3.32
223 225 3.456280 ACGCAATGCTTGATTTGTTGTT 58.544 36.364 2.94 0.00 0.00 2.83
224 226 3.490526 ACGCAATGCTTGATTTGTTGTTC 59.509 39.130 2.94 0.00 0.00 3.18
225 227 3.490155 CGCAATGCTTGATTTGTTGTTCA 59.510 39.130 2.94 0.00 0.00 3.18
226 228 4.025896 CGCAATGCTTGATTTGTTGTTCAA 60.026 37.500 2.94 0.00 0.00 2.69
227 229 5.199726 GCAATGCTTGATTTGTTGTTCAAC 58.800 37.500 8.52 8.52 35.61 3.18
228 230 5.006941 GCAATGCTTGATTTGTTGTTCAACT 59.993 36.000 15.18 0.00 35.61 3.16
229 231 6.457257 GCAATGCTTGATTTGTTGTTCAACTT 60.457 34.615 15.18 2.66 35.61 2.66
230 232 6.833342 ATGCTTGATTTGTTGTTCAACTTC 57.167 33.333 15.18 10.42 35.61 3.01
231 233 4.797868 TGCTTGATTTGTTGTTCAACTTCG 59.202 37.500 15.18 0.00 35.61 3.79
232 234 4.207019 GCTTGATTTGTTGTTCAACTTCGG 59.793 41.667 15.18 8.57 35.61 4.30
233 235 4.300189 TGATTTGTTGTTCAACTTCGGG 57.700 40.909 15.18 0.00 35.61 5.14
234 236 2.570442 TTTGTTGTTCAACTTCGGGC 57.430 45.000 15.18 0.00 35.61 6.13
235 237 1.757682 TTGTTGTTCAACTTCGGGCT 58.242 45.000 15.18 0.00 0.00 5.19
236 238 2.623878 TGTTGTTCAACTTCGGGCTA 57.376 45.000 15.18 0.00 0.00 3.93
237 239 2.489971 TGTTGTTCAACTTCGGGCTAG 58.510 47.619 15.18 0.00 0.00 3.42
238 240 2.158871 TGTTGTTCAACTTCGGGCTAGT 60.159 45.455 15.18 0.00 0.00 2.57
239 241 2.876550 GTTGTTCAACTTCGGGCTAGTT 59.123 45.455 8.23 0.00 36.31 2.24
246 248 4.820894 AACTTCGGGCTAGTTGAATACT 57.179 40.909 0.00 0.00 41.04 2.12
247 249 5.927281 AACTTCGGGCTAGTTGAATACTA 57.073 39.130 0.00 0.00 38.33 1.82
272 274 5.885230 TTCAGATAATGAAGTGTTGGCAG 57.115 39.130 0.00 0.00 43.09 4.85
273 275 3.691118 TCAGATAATGAAGTGTTGGCAGC 59.309 43.478 0.00 0.00 34.02 5.25
274 276 3.693085 CAGATAATGAAGTGTTGGCAGCT 59.307 43.478 2.28 0.00 0.00 4.24
275 277 4.877823 CAGATAATGAAGTGTTGGCAGCTA 59.122 41.667 2.28 0.00 0.00 3.32
276 278 5.355071 CAGATAATGAAGTGTTGGCAGCTAA 59.645 40.000 2.28 0.00 0.00 3.09
277 279 5.587844 AGATAATGAAGTGTTGGCAGCTAAG 59.412 40.000 2.28 0.00 0.00 2.18
278 280 2.928801 TGAAGTGTTGGCAGCTAAGA 57.071 45.000 2.28 0.00 0.00 2.10
279 281 3.207265 TGAAGTGTTGGCAGCTAAGAA 57.793 42.857 2.28 0.00 0.00 2.52
280 282 2.878406 TGAAGTGTTGGCAGCTAAGAAC 59.122 45.455 2.28 0.00 0.00 3.01
281 283 1.897560 AGTGTTGGCAGCTAAGAACC 58.102 50.000 2.28 0.00 0.00 3.62
282 284 1.142870 AGTGTTGGCAGCTAAGAACCA 59.857 47.619 2.28 0.00 0.00 3.67
283 285 1.953686 GTGTTGGCAGCTAAGAACCAA 59.046 47.619 2.28 0.00 39.81 3.67
284 286 2.030805 GTGTTGGCAGCTAAGAACCAAG 60.031 50.000 2.28 0.00 42.60 3.61
285 287 2.158682 TGTTGGCAGCTAAGAACCAAGA 60.159 45.455 2.28 2.21 42.60 3.02
286 288 2.479566 TGGCAGCTAAGAACCAAGAG 57.520 50.000 0.00 0.00 0.00 2.85
287 289 1.699634 TGGCAGCTAAGAACCAAGAGT 59.300 47.619 0.00 0.00 0.00 3.24
288 290 2.106511 TGGCAGCTAAGAACCAAGAGTT 59.893 45.455 0.00 0.00 43.07 3.01
289 291 2.485814 GGCAGCTAAGAACCAAGAGTTG 59.514 50.000 0.00 0.00 39.40 3.16
302 304 5.931441 CCAAGAGTTGGTTCTCAGTTAAG 57.069 43.478 0.00 0.00 45.93 1.85
303 305 5.368989 CCAAGAGTTGGTTCTCAGTTAAGT 58.631 41.667 0.00 0.00 45.93 2.24
304 306 5.467063 CCAAGAGTTGGTTCTCAGTTAAGTC 59.533 44.000 0.00 0.00 45.93 3.01
305 307 5.871396 AGAGTTGGTTCTCAGTTAAGTCA 57.129 39.130 0.00 0.00 36.97 3.41
306 308 5.848406 AGAGTTGGTTCTCAGTTAAGTCAG 58.152 41.667 0.00 0.00 36.97 3.51
307 309 5.364157 AGAGTTGGTTCTCAGTTAAGTCAGT 59.636 40.000 0.00 0.00 36.97 3.41
308 310 5.990668 AGTTGGTTCTCAGTTAAGTCAGTT 58.009 37.500 0.00 0.00 0.00 3.16
309 311 6.415573 AGTTGGTTCTCAGTTAAGTCAGTTT 58.584 36.000 0.00 0.00 0.00 2.66
310 312 6.316390 AGTTGGTTCTCAGTTAAGTCAGTTTG 59.684 38.462 0.00 0.00 0.00 2.93
311 313 5.984725 TGGTTCTCAGTTAAGTCAGTTTGA 58.015 37.500 0.00 0.00 0.00 2.69
312 314 6.591935 TGGTTCTCAGTTAAGTCAGTTTGAT 58.408 36.000 0.00 0.00 0.00 2.57
313 315 7.054124 TGGTTCTCAGTTAAGTCAGTTTGATT 58.946 34.615 0.00 0.00 0.00 2.57
314 316 7.012327 TGGTTCTCAGTTAAGTCAGTTTGATTG 59.988 37.037 0.00 0.00 0.00 2.67
315 317 7.226720 GGTTCTCAGTTAAGTCAGTTTGATTGA 59.773 37.037 0.00 0.00 0.00 2.57
316 318 8.778358 GTTCTCAGTTAAGTCAGTTTGATTGAT 58.222 33.333 0.00 0.00 0.00 2.57
317 319 8.315391 TCTCAGTTAAGTCAGTTTGATTGATG 57.685 34.615 0.00 0.00 0.00 3.07
318 320 6.902341 TCAGTTAAGTCAGTTTGATTGATGC 58.098 36.000 0.00 0.00 0.00 3.91
319 321 6.486320 TCAGTTAAGTCAGTTTGATTGATGCA 59.514 34.615 0.00 0.00 0.00 3.96
320 322 6.800408 CAGTTAAGTCAGTTTGATTGATGCAG 59.200 38.462 0.00 0.00 0.00 4.41
321 323 6.712095 AGTTAAGTCAGTTTGATTGATGCAGA 59.288 34.615 0.00 0.00 0.00 4.26
322 324 5.624344 AAGTCAGTTTGATTGATGCAGAG 57.376 39.130 0.00 0.00 0.00 3.35
323 325 4.903054 AGTCAGTTTGATTGATGCAGAGA 58.097 39.130 0.00 0.00 0.00 3.10
324 326 5.311265 AGTCAGTTTGATTGATGCAGAGAA 58.689 37.500 0.00 0.00 0.00 2.87
325 327 5.766670 AGTCAGTTTGATTGATGCAGAGAAA 59.233 36.000 0.00 0.00 0.00 2.52
326 328 6.263842 AGTCAGTTTGATTGATGCAGAGAAAA 59.736 34.615 0.00 0.00 0.00 2.29
327 329 6.919662 GTCAGTTTGATTGATGCAGAGAAAAA 59.080 34.615 0.00 0.00 0.00 1.94
328 330 7.597743 GTCAGTTTGATTGATGCAGAGAAAAAT 59.402 33.333 0.00 0.00 0.00 1.82
329 331 8.795513 TCAGTTTGATTGATGCAGAGAAAAATA 58.204 29.630 0.00 0.00 0.00 1.40
330 332 9.582431 CAGTTTGATTGATGCAGAGAAAAATAT 57.418 29.630 0.00 0.00 0.00 1.28
331 333 9.582431 AGTTTGATTGATGCAGAGAAAAATATG 57.418 29.630 0.00 0.00 0.00 1.78
376 378 3.384789 TCCTTGACAGATACGCTATGCTT 59.615 43.478 0.00 0.00 0.00 3.91
391 394 5.091431 GCTATGCTTGATCTGTTGTTCAAC 58.909 41.667 8.52 8.52 31.13 3.18
401 404 3.074412 CTGTTGTTCAACTTCGGGCTAT 58.926 45.455 15.18 0.00 0.00 2.97
441 450 6.867816 CAGATAATAAAGTGTTGGCAGCAAAA 59.132 34.615 5.34 0.00 0.00 2.44
549 569 2.034685 TGGTTCTCAGTCAAGTCTGTCG 59.965 50.000 0.00 0.00 36.85 4.35
586 1011 0.517316 GGTGATGGCTCGTCAACAAC 59.483 55.000 7.36 0.00 37.09 3.32
600 1025 0.400213 AACAACGGCCCAAGAGATCA 59.600 50.000 0.00 0.00 0.00 2.92
601 1026 0.036010 ACAACGGCCCAAGAGATCAG 60.036 55.000 0.00 0.00 0.00 2.90
606 1031 0.179936 GGCCCAAGAGATCAGAGTGG 59.820 60.000 0.00 0.00 0.00 4.00
778 1229 2.623416 AAGGTTGACTTTGCTAACCAGC 59.377 45.455 7.96 0.00 44.86 4.85
789 1240 2.408271 CTAACCAGCAGAGGCATCAA 57.592 50.000 0.00 0.00 44.61 2.57
790 1241 2.012673 CTAACCAGCAGAGGCATCAAC 58.987 52.381 0.00 0.00 44.61 3.18
791 1242 0.403271 AACCAGCAGAGGCATCAACT 59.597 50.000 0.00 0.00 44.61 3.16
792 1243 0.403271 ACCAGCAGAGGCATCAACTT 59.597 50.000 0.00 0.00 44.61 2.66
793 1244 1.093159 CCAGCAGAGGCATCAACTTC 58.907 55.000 0.00 0.00 44.61 3.01
794 1245 1.093159 CAGCAGAGGCATCAACTTCC 58.907 55.000 0.00 0.00 44.61 3.46
795 1246 0.694771 AGCAGAGGCATCAACTTCCA 59.305 50.000 0.00 0.00 44.61 3.53
796 1247 1.074405 AGCAGAGGCATCAACTTCCAA 59.926 47.619 0.00 0.00 44.61 3.53
797 1248 1.471684 GCAGAGGCATCAACTTCCAAG 59.528 52.381 0.00 0.00 40.72 3.61
798 1249 1.471684 CAGAGGCATCAACTTCCAAGC 59.528 52.381 0.00 0.00 0.00 4.01
799 1250 1.353694 AGAGGCATCAACTTCCAAGCT 59.646 47.619 0.00 0.00 0.00 3.74
800 1251 1.742268 GAGGCATCAACTTCCAAGCTC 59.258 52.381 0.00 0.00 0.00 4.09
801 1252 1.074405 AGGCATCAACTTCCAAGCTCA 59.926 47.619 0.00 0.00 0.00 4.26
802 1253 1.471684 GGCATCAACTTCCAAGCTCAG 59.528 52.381 0.00 0.00 0.00 3.35
816 1267 3.777106 AGCTCAGTGTTCATTCCTGAA 57.223 42.857 0.00 0.00 39.07 3.02
926 1435 4.270008 GGGCAGAGCATAAAAGGAGTTTA 58.730 43.478 0.00 0.00 36.14 2.01
1142 1672 2.111878 GGGGCAGGTCATCATCGG 59.888 66.667 0.00 0.00 0.00 4.18
1173 1703 1.371635 GCGGCACATCACAAACCAC 60.372 57.895 0.00 0.00 0.00 4.16
1261 1791 0.447801 CAGATGCCAAGCGTACCAAC 59.552 55.000 0.00 0.00 0.00 3.77
1284 1814 4.953940 AGAGGAGAATATTCAGGCTGTC 57.046 45.455 17.56 4.06 0.00 3.51
1380 1910 1.072159 ACAAGCGCTTGAAGAGGCT 59.928 52.632 46.69 26.01 42.93 4.58
1461 1991 0.108186 ATCCTCGCTTGCATCGTCAA 60.108 50.000 8.42 0.00 0.00 3.18
1817 2790 1.064017 TCTGTGGGAAAACCTGTGCTT 60.064 47.619 0.00 0.00 41.11 3.91
1827 2800 1.286880 CCTGTGCTTTCTTTGCCGG 59.713 57.895 0.00 0.00 0.00 6.13
1840 2813 2.184020 TTGCCGGCAGAGCACTACAT 62.184 55.000 30.75 0.00 40.69 2.29
2151 3127 2.549754 TGCAAAAGCAGCTCTGTAAGTC 59.450 45.455 0.00 0.00 33.76 3.01
2156 3132 0.898320 GCAGCTCTGTAAGTCTGGGA 59.102 55.000 0.00 0.00 36.60 4.37
2181 3157 0.861837 CCGTGTGAACTTCTCAGTGC 59.138 55.000 0.00 0.00 33.60 4.40
2212 3188 4.503910 CTGTGTATCTTCAACGAATGGGA 58.496 43.478 0.00 0.00 0.00 4.37
2597 5893 3.251004 GGCCAAGTTTGTTCAGAGTGTAG 59.749 47.826 0.00 0.00 0.00 2.74
2602 5898 3.561725 AGTTTGTTCAGAGTGTAGCAAGC 59.438 43.478 0.00 0.00 0.00 4.01
2604 5900 3.475566 TGTTCAGAGTGTAGCAAGCTT 57.524 42.857 0.00 0.00 0.00 3.74
2626 5922 5.523438 TTGCCCTTTTGTTCGAAAACTAT 57.477 34.783 0.00 0.00 36.30 2.12
2633 5929 7.248437 CCTTTTGTTCGAAAACTATCCATACC 58.752 38.462 0.00 0.00 36.30 2.73
2653 5955 2.554142 CAGTGTGTCTTGCTTGTCAGA 58.446 47.619 0.00 0.00 0.00 3.27
2657 5959 3.059325 GTGTGTCTTGCTTGTCAGACATC 60.059 47.826 3.45 0.20 42.25 3.06
2663 5965 1.814394 TGCTTGTCAGACATCAATGGC 59.186 47.619 3.45 3.61 35.53 4.40
2670 5972 3.947196 GTCAGACATCAATGGCCAACATA 59.053 43.478 10.96 0.00 39.40 2.29
2677 5979 5.244402 ACATCAATGGCCAACATATATGTGG 59.756 40.000 18.94 20.20 40.61 4.17
2689 5991 8.999431 CCAACATATATGTGGGTAATCTTGTAC 58.001 37.037 25.87 0.00 45.12 2.90
2690 5992 9.778741 CAACATATATGTGGGTAATCTTGTACT 57.221 33.333 18.94 0.00 41.61 2.73
2691 5993 9.778741 AACATATATGTGGGTAATCTTGTACTG 57.221 33.333 18.94 0.00 41.61 2.74
2692 5994 8.934697 ACATATATGTGGGTAATCTTGTACTGT 58.065 33.333 17.60 0.00 40.03 3.55
2704 6006 5.018539 TCTTGTACTGTATATGTGGTGGC 57.981 43.478 0.00 0.00 0.00 5.01
2706 6008 4.665833 TGTACTGTATATGTGGTGGCTC 57.334 45.455 0.00 0.00 0.00 4.70
2737 6039 3.944422 AAGCACTTTACACTGAACACG 57.056 42.857 0.00 0.00 0.00 4.49
2740 6042 4.435425 AGCACTTTACACTGAACACGTAA 58.565 39.130 0.00 0.00 0.00 3.18
2741 6043 4.269363 AGCACTTTACACTGAACACGTAAC 59.731 41.667 0.00 0.00 0.00 2.50
2742 6044 4.743839 CACTTTACACTGAACACGTAACG 58.256 43.478 0.00 0.00 0.00 3.18
2743 6045 4.266029 CACTTTACACTGAACACGTAACGT 59.734 41.667 0.00 0.00 42.36 3.99
2744 6046 5.455201 CACTTTACACTGAACACGTAACGTA 59.545 40.000 0.00 0.00 38.32 3.57
2745 6047 6.142798 CACTTTACACTGAACACGTAACGTAT 59.857 38.462 0.00 0.00 38.32 3.06
2751 6053 4.917415 ACTGAACACGTAACGTATAACACC 59.083 41.667 0.00 0.00 38.32 4.16
2753 6055 5.468592 TGAACACGTAACGTATAACACCAT 58.531 37.500 0.00 0.00 38.32 3.55
2769 6071 2.068181 ACCATGATGCCACCCTATGAT 58.932 47.619 0.00 0.00 0.00 2.45
2776 6078 1.202842 TGCCACCCTATGATGCTCATG 60.203 52.381 8.40 0.00 37.70 3.07
2779 6081 3.344515 CCACCCTATGATGCTCATGATG 58.655 50.000 0.00 0.00 37.70 3.07
2783 6085 3.271729 CCTATGATGCTCATGATGCCTC 58.728 50.000 12.62 12.43 37.70 4.70
2802 6104 5.009610 TGCCTCCATTTACTGTTTCTGAAAC 59.990 40.000 22.94 22.94 41.73 2.78
2823 6127 9.787435 TGAAACTAATACTCCACAACATAGTTT 57.213 29.630 7.51 7.51 41.92 2.66
2838 6144 7.769044 ACAACATAGTTTCGAGCCTTATGTAAT 59.231 33.333 11.69 4.32 0.00 1.89
2840 6146 8.142994 ACATAGTTTCGAGCCTTATGTAATTG 57.857 34.615 10.35 0.00 0.00 2.32
2844 6150 5.888691 TTCGAGCCTTATGTAATTGCAAA 57.111 34.783 1.71 0.00 0.00 3.68
2846 6152 5.636837 TCGAGCCTTATGTAATTGCAAAAC 58.363 37.500 1.71 5.74 0.00 2.43
2848 6154 5.393027 CGAGCCTTATGTAATTGCAAAACCT 60.393 40.000 1.71 0.74 0.00 3.50
2861 6167 2.033424 GCAAAACCTGAGTGTGGTCTTC 59.967 50.000 0.00 0.00 36.69 2.87
2867 6174 4.223953 ACCTGAGTGTGGTCTTCTTCTTA 58.776 43.478 0.00 0.00 31.03 2.10
2871 6178 2.364324 AGTGTGGTCTTCTTCTTACGCA 59.636 45.455 0.00 0.00 0.00 5.24
2894 6201 7.427606 CGCAGAAAAGAACAATTGTATGATCTC 59.572 37.037 12.39 4.52 32.00 2.75
2902 6209 5.253330 ACAATTGTATGATCTCGTGGGTTT 58.747 37.500 9.97 0.00 0.00 3.27
2912 6219 2.364970 TCTCGTGGGTTTTCGGTTCTTA 59.635 45.455 0.00 0.00 0.00 2.10
2917 6224 4.913345 CGTGGGTTTTCGGTTCTTAATTTC 59.087 41.667 0.00 0.00 0.00 2.17
2918 6225 5.224888 GTGGGTTTTCGGTTCTTAATTTCC 58.775 41.667 0.00 0.00 0.00 3.13
2919 6226 4.281435 TGGGTTTTCGGTTCTTAATTTCCC 59.719 41.667 0.00 0.00 0.00 3.97
2926 6233 3.126343 CGGTTCTTAATTTCCCGGTTCTG 59.874 47.826 0.00 0.00 35.11 3.02
2942 6249 7.935210 TCCCGGTTCTGATTATTAAATCTTACC 59.065 37.037 0.00 0.00 41.83 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.204882 GTGGATACTTTTATTCTCCGAATGGG 59.795 42.308 0.00 0.00 34.09 4.00
1 2 6.992715 AGTGGATACTTTTATTCTCCGAATGG 59.007 38.462 0.00 0.00 31.66 3.16
171 173 0.689055 AGAGACTTGGCATGCACTGA 59.311 50.000 21.36 0.52 0.00 3.41
172 174 1.085091 GAGAGACTTGGCATGCACTG 58.915 55.000 21.36 10.60 0.00 3.66
173 175 0.035630 GGAGAGACTTGGCATGCACT 60.036 55.000 21.36 9.90 0.00 4.40
174 176 0.035630 AGGAGAGACTTGGCATGCAC 60.036 55.000 21.36 9.64 0.00 4.57
175 177 0.694771 AAGGAGAGACTTGGCATGCA 59.305 50.000 21.36 2.54 0.00 3.96
176 178 1.093159 CAAGGAGAGACTTGGCATGC 58.907 55.000 9.90 9.90 43.14 4.06
177 179 2.775911 TCAAGGAGAGACTTGGCATG 57.224 50.000 6.15 0.00 46.04 4.06
181 183 4.627467 CGTATTTGTCAAGGAGAGACTTGG 59.373 45.833 6.15 0.00 46.04 3.61
183 185 4.246458 GCGTATTTGTCAAGGAGAGACTT 58.754 43.478 0.00 0.00 36.94 3.01
184 186 3.258372 TGCGTATTTGTCAAGGAGAGACT 59.742 43.478 0.00 0.00 36.94 3.24
185 187 3.585862 TGCGTATTTGTCAAGGAGAGAC 58.414 45.455 0.00 0.00 36.55 3.36
186 188 3.953712 TGCGTATTTGTCAAGGAGAGA 57.046 42.857 0.00 0.00 0.00 3.10
187 189 4.728882 GCATTGCGTATTTGTCAAGGAGAG 60.729 45.833 0.00 0.00 0.00 3.20
188 190 3.126858 GCATTGCGTATTTGTCAAGGAGA 59.873 43.478 0.00 0.00 0.00 3.71
189 191 3.127548 AGCATTGCGTATTTGTCAAGGAG 59.872 43.478 2.38 0.00 0.00 3.69
190 192 3.081061 AGCATTGCGTATTTGTCAAGGA 58.919 40.909 2.38 0.00 0.00 3.36
191 193 3.492421 AGCATTGCGTATTTGTCAAGG 57.508 42.857 2.38 0.00 0.00 3.61
192 194 4.811158 CAAGCATTGCGTATTTGTCAAG 57.189 40.909 2.38 0.00 40.39 3.02
196 198 5.229423 ACAAATCAAGCATTGCGTATTTGT 58.771 33.333 27.55 27.55 46.79 2.83
200 202 8.422462 TTGAACAACAAATCAAGCATTGCGTAT 61.422 33.333 2.38 0.00 39.83 3.06
201 203 7.171991 TTGAACAACAAATCAAGCATTGCGTA 61.172 34.615 2.38 0.00 39.83 4.42
202 204 6.417492 TTGAACAACAAATCAAGCATTGCGT 61.417 36.000 2.38 0.00 39.83 5.24
203 205 4.025896 TTGAACAACAAATCAAGCATTGCG 60.026 37.500 2.38 0.00 39.83 4.85
204 206 5.006941 AGTTGAACAACAAATCAAGCATTGC 59.993 36.000 17.85 0.00 44.08 3.56
205 207 6.592798 AGTTGAACAACAAATCAAGCATTG 57.407 33.333 17.85 0.00 45.01 2.82
206 208 6.019640 CGAAGTTGAACAACAAATCAAGCATT 60.020 34.615 17.85 1.89 43.47 3.56
207 209 5.459762 CGAAGTTGAACAACAAATCAAGCAT 59.540 36.000 17.85 0.00 43.47 3.79
208 210 4.797868 CGAAGTTGAACAACAAATCAAGCA 59.202 37.500 17.85 0.00 43.47 3.91
209 211 4.207019 CCGAAGTTGAACAACAAATCAAGC 59.793 41.667 17.85 0.00 43.47 4.01
210 212 4.739716 CCCGAAGTTGAACAACAAATCAAG 59.260 41.667 17.85 8.41 43.47 3.02
211 213 4.677584 CCCGAAGTTGAACAACAAATCAA 58.322 39.130 17.85 0.00 43.47 2.57
212 214 3.490078 GCCCGAAGTTGAACAACAAATCA 60.490 43.478 17.85 0.00 43.47 2.57
213 215 3.049912 GCCCGAAGTTGAACAACAAATC 58.950 45.455 17.85 12.06 43.47 2.17
214 216 2.693074 AGCCCGAAGTTGAACAACAAAT 59.307 40.909 17.85 5.64 43.47 2.32
215 217 2.096248 AGCCCGAAGTTGAACAACAAA 58.904 42.857 17.85 0.00 43.47 2.83
216 218 1.757682 AGCCCGAAGTTGAACAACAA 58.242 45.000 17.85 0.00 43.47 2.83
217 219 2.158871 ACTAGCCCGAAGTTGAACAACA 60.159 45.455 17.85 0.00 43.47 3.33
218 220 2.490991 ACTAGCCCGAAGTTGAACAAC 58.509 47.619 9.33 9.33 41.45 3.32
219 221 2.922740 ACTAGCCCGAAGTTGAACAA 57.077 45.000 0.00 0.00 0.00 2.83
220 222 2.922740 AACTAGCCCGAAGTTGAACA 57.077 45.000 0.00 0.00 35.87 3.18
225 227 4.820894 AGTATTCAACTAGCCCGAAGTT 57.179 40.909 0.00 0.00 36.36 2.66
244 246 7.497249 GCCAACACTTCATTATCTGAATCTAGT 59.503 37.037 0.00 0.00 42.87 2.57
245 247 7.496920 TGCCAACACTTCATTATCTGAATCTAG 59.503 37.037 0.00 0.00 42.87 2.43
246 248 7.337938 TGCCAACACTTCATTATCTGAATCTA 58.662 34.615 0.00 0.00 42.87 1.98
247 249 6.182627 TGCCAACACTTCATTATCTGAATCT 58.817 36.000 0.00 0.00 42.87 2.40
248 250 6.441093 TGCCAACACTTCATTATCTGAATC 57.559 37.500 0.00 0.00 42.87 2.52
249 251 5.163581 GCTGCCAACACTTCATTATCTGAAT 60.164 40.000 0.00 0.00 42.87 2.57
250 252 4.156556 GCTGCCAACACTTCATTATCTGAA 59.843 41.667 0.00 0.00 41.61 3.02
251 253 3.691118 GCTGCCAACACTTCATTATCTGA 59.309 43.478 0.00 0.00 0.00 3.27
252 254 3.693085 AGCTGCCAACACTTCATTATCTG 59.307 43.478 0.00 0.00 0.00 2.90
253 255 3.960571 AGCTGCCAACACTTCATTATCT 58.039 40.909 0.00 0.00 0.00 1.98
254 256 5.586243 TCTTAGCTGCCAACACTTCATTATC 59.414 40.000 0.00 0.00 0.00 1.75
255 257 5.500234 TCTTAGCTGCCAACACTTCATTAT 58.500 37.500 0.00 0.00 0.00 1.28
256 258 4.905429 TCTTAGCTGCCAACACTTCATTA 58.095 39.130 0.00 0.00 0.00 1.90
257 259 3.754965 TCTTAGCTGCCAACACTTCATT 58.245 40.909 0.00 0.00 0.00 2.57
258 260 3.423539 TCTTAGCTGCCAACACTTCAT 57.576 42.857 0.00 0.00 0.00 2.57
259 261 2.878406 GTTCTTAGCTGCCAACACTTCA 59.122 45.455 0.00 0.00 0.00 3.02
260 262 2.226674 GGTTCTTAGCTGCCAACACTTC 59.773 50.000 0.00 0.00 0.00 3.01
261 263 2.230660 GGTTCTTAGCTGCCAACACTT 58.769 47.619 0.00 0.00 0.00 3.16
262 264 1.142870 TGGTTCTTAGCTGCCAACACT 59.857 47.619 0.00 0.00 0.00 3.55
263 265 1.604604 TGGTTCTTAGCTGCCAACAC 58.395 50.000 0.00 0.00 0.00 3.32
264 266 2.158682 TCTTGGTTCTTAGCTGCCAACA 60.159 45.455 0.00 0.00 36.23 3.33
265 267 2.485814 CTCTTGGTTCTTAGCTGCCAAC 59.514 50.000 0.00 0.00 36.23 3.77
266 268 2.106511 ACTCTTGGTTCTTAGCTGCCAA 59.893 45.455 0.00 2.58 38.51 4.52
267 269 1.699634 ACTCTTGGTTCTTAGCTGCCA 59.300 47.619 0.00 0.00 0.00 4.92
268 270 2.481289 ACTCTTGGTTCTTAGCTGCC 57.519 50.000 0.00 0.00 0.00 4.85
269 271 2.485814 CCAACTCTTGGTTCTTAGCTGC 59.514 50.000 0.00 0.00 45.93 5.25
281 283 6.049149 TGACTTAACTGAGAACCAACTCTTG 58.951 40.000 0.00 0.00 37.73 3.02
282 284 6.127026 ACTGACTTAACTGAGAACCAACTCTT 60.127 38.462 0.00 0.00 37.73 2.85
283 285 5.364157 ACTGACTTAACTGAGAACCAACTCT 59.636 40.000 0.00 0.00 37.73 3.24
284 286 5.602628 ACTGACTTAACTGAGAACCAACTC 58.397 41.667 0.00 0.00 37.42 3.01
285 287 5.615925 ACTGACTTAACTGAGAACCAACT 57.384 39.130 0.00 0.00 0.00 3.16
286 288 6.315393 TCAAACTGACTTAACTGAGAACCAAC 59.685 38.462 0.00 0.00 0.00 3.77
287 289 6.411376 TCAAACTGACTTAACTGAGAACCAA 58.589 36.000 0.00 0.00 0.00 3.67
288 290 5.984725 TCAAACTGACTTAACTGAGAACCA 58.015 37.500 0.00 0.00 0.00 3.67
289 291 7.226720 TCAATCAAACTGACTTAACTGAGAACC 59.773 37.037 0.00 0.00 0.00 3.62
290 292 8.142994 TCAATCAAACTGACTTAACTGAGAAC 57.857 34.615 0.00 0.00 0.00 3.01
291 293 8.777413 CATCAATCAAACTGACTTAACTGAGAA 58.223 33.333 0.00 0.00 0.00 2.87
292 294 7.095060 GCATCAATCAAACTGACTTAACTGAGA 60.095 37.037 0.00 0.00 0.00 3.27
293 295 7.020010 GCATCAATCAAACTGACTTAACTGAG 58.980 38.462 0.00 0.00 0.00 3.35
294 296 6.486320 TGCATCAATCAAACTGACTTAACTGA 59.514 34.615 0.00 0.00 0.00 3.41
295 297 6.671190 TGCATCAATCAAACTGACTTAACTG 58.329 36.000 0.00 0.00 0.00 3.16
296 298 6.712095 TCTGCATCAATCAAACTGACTTAACT 59.288 34.615 0.00 0.00 0.00 2.24
297 299 6.902341 TCTGCATCAATCAAACTGACTTAAC 58.098 36.000 0.00 0.00 0.00 2.01
298 300 6.936335 TCTCTGCATCAATCAAACTGACTTAA 59.064 34.615 0.00 0.00 0.00 1.85
299 301 6.466812 TCTCTGCATCAATCAAACTGACTTA 58.533 36.000 0.00 0.00 0.00 2.24
300 302 5.311265 TCTCTGCATCAATCAAACTGACTT 58.689 37.500 0.00 0.00 0.00 3.01
301 303 4.903054 TCTCTGCATCAATCAAACTGACT 58.097 39.130 0.00 0.00 0.00 3.41
302 304 5.618056 TTCTCTGCATCAATCAAACTGAC 57.382 39.130 0.00 0.00 0.00 3.51
303 305 6.638096 TTTTCTCTGCATCAATCAAACTGA 57.362 33.333 0.00 0.00 0.00 3.41
304 306 7.884816 ATTTTTCTCTGCATCAATCAAACTG 57.115 32.000 0.00 0.00 0.00 3.16
305 307 9.582431 CATATTTTTCTCTGCATCAATCAAACT 57.418 29.630 0.00 0.00 0.00 2.66
306 308 9.362539 ACATATTTTTCTCTGCATCAATCAAAC 57.637 29.630 0.00 0.00 0.00 2.93
307 309 9.361315 CACATATTTTTCTCTGCATCAATCAAA 57.639 29.630 0.00 0.00 0.00 2.69
308 310 7.977293 CCACATATTTTTCTCTGCATCAATCAA 59.023 33.333 0.00 0.00 0.00 2.57
309 311 7.123098 ACCACATATTTTTCTCTGCATCAATCA 59.877 33.333 0.00 0.00 0.00 2.57
310 312 7.486647 ACCACATATTTTTCTCTGCATCAATC 58.513 34.615 0.00 0.00 0.00 2.67
311 313 7.123098 TGACCACATATTTTTCTCTGCATCAAT 59.877 33.333 0.00 0.00 0.00 2.57
312 314 6.433716 TGACCACATATTTTTCTCTGCATCAA 59.566 34.615 0.00 0.00 0.00 2.57
313 315 5.945191 TGACCACATATTTTTCTCTGCATCA 59.055 36.000 0.00 0.00 0.00 3.07
314 316 6.094603 ACTGACCACATATTTTTCTCTGCATC 59.905 38.462 0.00 0.00 0.00 3.91
315 317 5.948162 ACTGACCACATATTTTTCTCTGCAT 59.052 36.000 0.00 0.00 0.00 3.96
316 318 5.181811 CACTGACCACATATTTTTCTCTGCA 59.818 40.000 0.00 0.00 0.00 4.41
317 319 5.634896 CACTGACCACATATTTTTCTCTGC 58.365 41.667 0.00 0.00 0.00 4.26
318 320 5.181811 TGCACTGACCACATATTTTTCTCTG 59.818 40.000 0.00 0.00 0.00 3.35
319 321 5.316167 TGCACTGACCACATATTTTTCTCT 58.684 37.500 0.00 0.00 0.00 3.10
320 322 5.627499 TGCACTGACCACATATTTTTCTC 57.373 39.130 0.00 0.00 0.00 2.87
321 323 5.622914 GCATGCACTGACCACATATTTTTCT 60.623 40.000 14.21 0.00 0.00 2.52
322 324 4.563976 GCATGCACTGACCACATATTTTTC 59.436 41.667 14.21 0.00 0.00 2.29
323 325 4.497300 GCATGCACTGACCACATATTTTT 58.503 39.130 14.21 0.00 0.00 1.94
324 326 3.119029 GGCATGCACTGACCACATATTTT 60.119 43.478 21.36 0.00 0.00 1.82
325 327 2.428171 GGCATGCACTGACCACATATTT 59.572 45.455 21.36 0.00 0.00 1.40
326 328 2.026641 GGCATGCACTGACCACATATT 58.973 47.619 21.36 0.00 0.00 1.28
327 329 1.064537 TGGCATGCACTGACCACATAT 60.065 47.619 21.36 0.00 28.32 1.78
328 330 0.327591 TGGCATGCACTGACCACATA 59.672 50.000 21.36 0.00 28.32 2.29
329 331 0.540133 TTGGCATGCACTGACCACAT 60.540 50.000 21.36 0.00 32.85 3.21
330 332 1.152798 TTGGCATGCACTGACCACA 60.153 52.632 21.36 2.10 32.85 4.17
331 333 1.174712 ACTTGGCATGCACTGACCAC 61.175 55.000 21.36 0.00 32.85 4.16
376 378 3.138304 CCCGAAGTTGAACAACAGATCA 58.862 45.455 17.85 0.00 43.47 2.92
391 394 5.855045 ACCTAGTATTCAAATAGCCCGAAG 58.145 41.667 0.00 0.00 0.00 3.79
454 463 6.994496 TCAATCAAACTGACTTGACTGAGAAT 59.006 34.615 4.96 0.00 36.82 2.40
549 569 7.365741 CCATCACCATGTATTTCTTTCTATGC 58.634 38.462 0.00 0.00 0.00 3.14
586 1011 0.179089 CACTCTGATCTCTTGGGCCG 60.179 60.000 0.00 0.00 0.00 6.13
600 1025 1.362224 AATGGCAGGTACACCACTCT 58.638 50.000 0.38 0.00 39.60 3.24
601 1026 2.420129 CCTAATGGCAGGTACACCACTC 60.420 54.545 0.38 0.00 39.60 3.51
606 1031 4.130118 CTGATTCCTAATGGCAGGTACAC 58.870 47.826 0.00 0.00 36.99 2.90
778 1229 1.471684 GCTTGGAAGTTGATGCCTCTG 59.528 52.381 0.00 0.00 0.00 3.35
779 1230 1.353694 AGCTTGGAAGTTGATGCCTCT 59.646 47.619 0.00 0.00 0.00 3.69
780 1231 1.742268 GAGCTTGGAAGTTGATGCCTC 59.258 52.381 0.00 0.00 0.00 4.70
781 1232 1.074405 TGAGCTTGGAAGTTGATGCCT 59.926 47.619 0.00 0.00 0.00 4.75
782 1233 1.471684 CTGAGCTTGGAAGTTGATGCC 59.528 52.381 0.00 0.00 0.00 4.40
783 1234 2.095364 CACTGAGCTTGGAAGTTGATGC 60.095 50.000 0.00 0.00 0.00 3.91
784 1235 3.144506 ACACTGAGCTTGGAAGTTGATG 58.855 45.455 0.00 0.00 0.00 3.07
785 1236 3.498774 ACACTGAGCTTGGAAGTTGAT 57.501 42.857 0.00 0.00 0.00 2.57
786 1237 3.206150 GAACACTGAGCTTGGAAGTTGA 58.794 45.455 0.00 0.00 0.00 3.18
787 1238 2.945008 TGAACACTGAGCTTGGAAGTTG 59.055 45.455 0.00 0.00 0.00 3.16
788 1239 3.281727 TGAACACTGAGCTTGGAAGTT 57.718 42.857 0.00 0.00 0.00 2.66
789 1240 3.498774 ATGAACACTGAGCTTGGAAGT 57.501 42.857 0.00 0.00 0.00 3.01
790 1241 3.190118 GGAATGAACACTGAGCTTGGAAG 59.810 47.826 0.00 0.00 0.00 3.46
791 1242 3.149196 GGAATGAACACTGAGCTTGGAA 58.851 45.455 0.00 0.00 0.00 3.53
792 1243 2.373169 AGGAATGAACACTGAGCTTGGA 59.627 45.455 0.00 0.00 0.00 3.53
793 1244 2.486982 CAGGAATGAACACTGAGCTTGG 59.513 50.000 0.00 0.00 34.21 3.61
794 1245 3.405831 TCAGGAATGAACACTGAGCTTG 58.594 45.455 0.00 0.00 36.41 4.01
795 1246 3.777106 TCAGGAATGAACACTGAGCTT 57.223 42.857 0.00 0.00 36.41 3.74
796 1247 3.326006 TCTTCAGGAATGAACACTGAGCT 59.674 43.478 0.00 0.00 41.71 4.09
797 1248 3.668447 TCTTCAGGAATGAACACTGAGC 58.332 45.455 0.00 0.00 41.71 4.26
798 1249 6.401394 TGTATCTTCAGGAATGAACACTGAG 58.599 40.000 0.00 0.00 41.71 3.35
799 1250 6.358974 TGTATCTTCAGGAATGAACACTGA 57.641 37.500 0.00 0.00 39.31 3.41
800 1251 6.652481 ACTTGTATCTTCAGGAATGAACACTG 59.348 38.462 0.00 0.00 0.00 3.66
801 1252 6.773638 ACTTGTATCTTCAGGAATGAACACT 58.226 36.000 0.00 0.00 0.00 3.55
802 1253 6.092807 GGACTTGTATCTTCAGGAATGAACAC 59.907 42.308 0.00 0.00 0.00 3.32
816 1267 2.090663 GGGACTAGGGGGACTTGTATCT 60.091 54.545 0.00 0.00 35.27 1.98
926 1435 6.876257 GGAAGTTGAATAGTTCATGTCTCTGT 59.124 38.462 0.00 0.00 39.84 3.41
1194 1724 3.007940 GGTACATGGCATACCTCAGCATA 59.992 47.826 11.43 0.00 39.30 3.14
1261 1791 5.033589 ACAGCCTGAATATTCTCCTCTTG 57.966 43.478 16.24 9.46 0.00 3.02
1284 1814 0.321671 ACACGACCCCAGATTGACTG 59.678 55.000 0.00 0.00 45.36 3.51
1380 1910 1.541379 TGGATCTCAAACCGTCGAGA 58.459 50.000 0.00 3.73 42.25 4.04
1461 1991 3.276857 CAAGAGATGCATGCTGTAAGGT 58.723 45.455 20.33 0.00 0.00 3.50
1817 2790 2.112928 TGCTCTGCCGGCAAAGAA 59.887 55.556 33.66 21.97 36.71 2.52
1840 2813 8.673711 GCTTGTGATAATGATTTTACTACCACA 58.326 33.333 0.00 0.00 0.00 4.17
1950 2923 7.215789 TGTACTTCCAAACGTAATCACCTTAA 58.784 34.615 0.00 0.00 0.00 1.85
2068 3044 8.538409 AATTGATGTTAAAATTGGCTCTCAAC 57.462 30.769 0.00 0.00 38.31 3.18
2151 3127 0.392863 TTCACACGGATGCATCCCAG 60.393 55.000 34.76 28.69 44.24 4.45
2156 3132 2.289631 TGAGAAGTTCACACGGATGCAT 60.290 45.455 0.00 0.00 0.00 3.96
2181 3157 5.455849 CGTTGAAGATACACAGGTCTATTCG 59.544 44.000 0.00 0.00 0.00 3.34
2413 5704 0.739112 GCTTCCTCTTCACCGCTCTG 60.739 60.000 0.00 0.00 0.00 3.35
2602 5898 4.180817 AGTTTTCGAACAAAAGGGCAAAG 58.819 39.130 0.00 0.00 0.00 2.77
2604 5900 3.878160 AGTTTTCGAACAAAAGGGCAA 57.122 38.095 0.00 0.00 0.00 4.52
2617 5913 5.175859 ACACACTGGTATGGATAGTTTTCG 58.824 41.667 0.00 0.00 0.00 3.46
2626 5922 1.977854 AGCAAGACACACTGGTATGGA 59.022 47.619 0.00 0.00 0.00 3.41
2633 5929 2.286294 GTCTGACAAGCAAGACACACTG 59.714 50.000 2.24 0.00 0.00 3.66
2653 5955 5.244402 CCACATATATGTTGGCCATTGATGT 59.756 40.000 15.85 8.26 39.39 3.06
2657 5959 3.896888 ACCCACATATATGTTGGCCATTG 59.103 43.478 27.79 15.77 44.90 2.82
2663 5965 8.999431 GTACAAGATTACCCACATATATGTTGG 58.001 37.037 26.74 26.74 46.06 3.77
2677 5979 7.656137 CCACCACATATACAGTACAAGATTACC 59.344 40.741 0.00 0.00 0.00 2.85
2678 5980 7.170998 GCCACCACATATACAGTACAAGATTAC 59.829 40.741 0.00 0.00 0.00 1.89
2689 5991 2.808202 GCCAGAGCCACCACATATACAG 60.808 54.545 0.00 0.00 0.00 2.74
2690 5992 1.140852 GCCAGAGCCACCACATATACA 59.859 52.381 0.00 0.00 0.00 2.29
2691 5993 1.417890 AGCCAGAGCCACCACATATAC 59.582 52.381 0.00 0.00 41.25 1.47
2692 5994 1.806496 AGCCAGAGCCACCACATATA 58.194 50.000 0.00 0.00 41.25 0.86
2693 5995 1.806496 TAGCCAGAGCCACCACATAT 58.194 50.000 0.00 0.00 41.25 1.78
2694 5996 1.806496 ATAGCCAGAGCCACCACATA 58.194 50.000 0.00 0.00 41.25 2.29
2704 6006 7.928706 AGTGTAAAGTGCTTATAATAGCCAGAG 59.071 37.037 0.00 0.00 40.49 3.35
2706 6008 7.710907 TCAGTGTAAAGTGCTTATAATAGCCAG 59.289 37.037 0.00 0.00 40.49 4.85
2737 6039 4.812091 TGGCATCATGGTGTTATACGTTAC 59.188 41.667 8.00 0.00 0.00 2.50
2740 6042 3.202906 GTGGCATCATGGTGTTATACGT 58.797 45.455 8.00 0.00 0.00 3.57
2741 6043 2.548057 GGTGGCATCATGGTGTTATACG 59.452 50.000 8.00 0.00 0.00 3.06
2742 6044 2.884639 GGGTGGCATCATGGTGTTATAC 59.115 50.000 8.00 2.08 0.00 1.47
2743 6045 2.782925 AGGGTGGCATCATGGTGTTATA 59.217 45.455 8.00 0.00 0.00 0.98
2744 6046 1.570501 AGGGTGGCATCATGGTGTTAT 59.429 47.619 8.00 0.00 0.00 1.89
2745 6047 0.998928 AGGGTGGCATCATGGTGTTA 59.001 50.000 8.00 0.00 0.00 2.41
2751 6053 1.816835 GCATCATAGGGTGGCATCATG 59.183 52.381 0.00 0.00 0.00 3.07
2753 6055 1.072806 GAGCATCATAGGGTGGCATCA 59.927 52.381 0.00 0.00 33.17 3.07
2769 6071 2.447408 AAATGGAGGCATCATGAGCA 57.553 45.000 15.83 0.00 0.00 4.26
2776 6078 4.943705 TCAGAAACAGTAAATGGAGGCATC 59.056 41.667 0.00 0.00 0.00 3.91
2779 6081 5.241728 AGTTTCAGAAACAGTAAATGGAGGC 59.758 40.000 24.85 0.00 43.79 4.70
2802 6104 7.043325 GCTCGAAACTATGTTGTGGAGTATTAG 60.043 40.741 0.00 0.00 0.00 1.73
2808 6112 2.673368 GGCTCGAAACTATGTTGTGGAG 59.327 50.000 0.00 0.00 0.00 3.86
2810 6114 2.699954 AGGCTCGAAACTATGTTGTGG 58.300 47.619 0.00 0.00 0.00 4.17
2823 6127 5.392595 GGTTTTGCAATTACATAAGGCTCGA 60.393 40.000 0.00 0.00 0.00 4.04
2838 6144 1.748493 GACCACACTCAGGTTTTGCAA 59.252 47.619 0.00 0.00 40.09 4.08
2840 6146 1.680338 AGACCACACTCAGGTTTTGC 58.320 50.000 0.00 0.00 40.09 3.68
2844 6150 3.041946 AGAAGAAGACCACACTCAGGTT 58.958 45.455 0.00 0.00 40.09 3.50
2846 6152 3.760580 AAGAAGAAGACCACACTCAGG 57.239 47.619 0.00 0.00 0.00 3.86
2848 6154 3.552273 GCGTAAGAAGAAGACCACACTCA 60.552 47.826 0.00 0.00 43.02 3.41
2861 6167 6.912591 ACAATTGTTCTTTTCTGCGTAAGAAG 59.087 34.615 4.92 0.00 45.64 2.85
2867 6174 6.312399 TCATACAATTGTTCTTTTCTGCGT 57.688 33.333 17.78 0.00 0.00 5.24
2871 6178 8.446273 CACGAGATCATACAATTGTTCTTTTCT 58.554 33.333 17.78 12.43 0.00 2.52
2894 6201 4.492791 AATTAAGAACCGAAAACCCACG 57.507 40.909 0.00 0.00 0.00 4.94
2912 6219 9.421399 AGATTTAATAATCAGAACCGGGAAATT 57.579 29.630 6.32 0.64 42.18 1.82
2917 6224 7.717875 TGGTAAGATTTAATAATCAGAACCGGG 59.282 37.037 6.32 0.00 42.18 5.73
2918 6225 8.557029 GTGGTAAGATTTAATAATCAGAACCGG 58.443 37.037 0.00 0.00 42.18 5.28
2919 6226 9.326413 AGTGGTAAGATTTAATAATCAGAACCG 57.674 33.333 0.00 0.00 42.18 4.44


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

AutoCloner maintained by Alex Coulton.