Multiple sequence alignment - TraesCS4B01G379900

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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 TraesCS4B01G379900 chr4B 100.000 3281 0 0 1 3281 660596698 660593418 0.000000e+00 6059.0
1 TraesCS4B01G379900 chr5A 89.925 2541 132 55 620 3076 700450503 700448003 0.000000e+00 3160.0
2 TraesCS4B01G379900 chr5A 95.189 291 9 2 2991 3281 11183489 11183204 3.860000e-124 455.0
3 TraesCS4B01G379900 chr5A 99.346 153 0 1 173 324 463611144 463610992 3.220000e-70 276.0
4 TraesCS4B01G379900 chr5A 100.000 148 0 0 171 318 164066723 164066870 1.160000e-69 274.0
5 TraesCS4B01G379900 chr5A 83.256 215 20 6 3071 3281 700447973 700447771 2.010000e-42 183.0
6 TraesCS4B01G379900 chr5A 99.020 102 1 0 321 422 700452581 700452480 2.010000e-42 183.0
7 TraesCS4B01G379900 chr5A 86.145 166 16 4 1 165 700452733 700452574 4.350000e-39 172.0
8 TraesCS4B01G379900 chr5A 95.349 43 2 0 551 593 503267987 503268029 5.870000e-08 69.4
9 TraesCS4B01G379900 chrUn 92.738 2217 105 24 900 3076 110527762 110525562 0.000000e+00 3151.0
10 TraesCS4B01G379900 chrUn 82.779 331 37 10 595 911 110528107 110527783 8.970000e-71 278.0
11 TraesCS4B01G379900 chrUn 89.474 228 7 7 321 544 110528310 110528096 4.170000e-69 272.0
12 TraesCS4B01G379900 chrUn 93.064 173 7 3 1 172 110528470 110528302 7.030000e-62 248.0
13 TraesCS4B01G379900 chrUn 85.047 214 16 6 3072 3281 110525531 110525330 1.540000e-48 204.0
14 TraesCS4B01G379900 chr2A 89.599 548 41 9 1087 1622 510441976 510442519 0.000000e+00 682.0
15 TraesCS4B01G379900 chr2A 97.872 47 1 0 549 595 721671022 721671068 7.550000e-12 82.4
16 TraesCS4B01G379900 chr2B 95.533 291 8 2 2991 3281 755118683 755118398 8.300000e-126 460.0
17 TraesCS4B01G379900 chr2B 94.502 291 11 2 2991 3281 535432836 535433121 8.350000e-121 444.0
18 TraesCS4B01G379900 chr2B 91.026 78 4 1 1286 1363 254695655 254695729 5.790000e-18 102.0
19 TraesCS4B01G379900 chr5B 95.189 291 9 2 2991 3281 34369770 34370055 3.860000e-124 455.0
20 TraesCS4B01G379900 chr3A 95.189 291 9 2 2991 3281 722603943 722604228 3.860000e-124 455.0
21 TraesCS4B01G379900 chr7B 81.818 429 53 14 1096 1516 679845021 679844610 1.460000e-88 337.0
22 TraesCS4B01G379900 chr7B 98.639 147 2 0 169 315 58640112 58640258 9.030000e-66 261.0
23 TraesCS4B01G379900 chr4A 99.342 152 0 1 168 318 615017628 615017779 1.160000e-69 274.0
24 TraesCS4B01G379900 chr4A 93.617 47 2 1 550 595 667032452 667032498 5.870000e-08 69.4
25 TraesCS4B01G379900 chr7A 100.000 147 0 0 172 318 675045964 675046110 4.170000e-69 272.0
26 TraesCS4B01G379900 chr7A 92.593 54 4 0 541 594 734051365 734051418 9.760000e-11 78.7
27 TraesCS4B01G379900 chr3B 99.333 150 0 1 173 321 692965679 692965828 1.500000e-68 270.0
28 TraesCS4B01G379900 chr1A 86.620 142 19 0 178 319 7187066 7186925 1.220000e-34 158.0
29 TraesCS4B01G379900 chr1A 100.000 46 0 0 549 594 549170601 549170556 5.830000e-13 86.1
30 TraesCS4B01G379900 chr4D 91.667 84 7 0 1238 1321 494358746 494358829 2.070000e-22 117.0
31 TraesCS4B01G379900 chr1D 97.059 34 1 0 561 594 61393659 61393626 1.270000e-04 58.4


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 TraesCS4B01G379900 chr4B 660593418 660596698 3280 True 6059.0 6059 100.0000 1 3281 1 chr4B.!!$R1 3280
1 TraesCS4B01G379900 chr5A 700447771 700452733 4962 True 924.5 3160 89.5865 1 3281 4 chr5A.!!$R3 3280
2 TraesCS4B01G379900 chrUn 110525330 110528470 3140 True 830.6 3151 88.6204 1 3281 5 chrUn.!!$R1 3280
3 TraesCS4B01G379900 chr2A 510441976 510442519 543 False 682.0 682 89.5990 1087 1622 1 chr2A.!!$F1 535

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
242 243 0.038166 AAATCCAGCCGGACATGTGT 59.962 50.0 5.05 0.0 46.79 3.72 F
596 2440 0.038166 CACCCATGCCAAGTGGTACT 59.962 55.0 0.00 0.0 37.57 2.73 F
597 2441 0.328258 ACCCATGCCAAGTGGTACTC 59.672 55.0 0.00 0.0 37.57 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1071 2986 0.854218 AGCCGGATAAGGGAGAGAGA 59.146 55.000 5.05 0.0 0.00 3.10 R
1902 3852 1.874019 CTTGTCGACGATGGCGAGG 60.874 63.158 11.62 0.0 41.64 4.63 R
2334 4285 4.261363 GCCCTCTGAAGAACAAAACAGAAG 60.261 45.833 0.00 0.0 38.60 2.85 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
152 153 0.453282 GCTTGCTGTGTGTGTATGCG 60.453 55.000 0.00 0.00 0.00 4.73
172 173 6.115450 TGCGTAGTAGAGTACATGTACAAG 57.885 41.667 32.02 16.55 38.48 3.16
173 174 5.876460 TGCGTAGTAGAGTACATGTACAAGA 59.124 40.000 32.02 16.67 38.48 3.02
174 175 6.372381 TGCGTAGTAGAGTACATGTACAAGAA 59.628 38.462 32.02 15.23 38.48 2.52
175 176 7.066645 TGCGTAGTAGAGTACATGTACAAGAAT 59.933 37.037 32.02 19.41 38.48 2.40
176 177 7.587028 GCGTAGTAGAGTACATGTACAAGAATC 59.413 40.741 32.02 21.72 38.48 2.52
177 178 8.610035 CGTAGTAGAGTACATGTACAAGAATCA 58.390 37.037 32.02 12.72 38.48 2.57
180 181 7.923344 AGTAGAGTACATGTACAAGAATCATGC 59.077 37.037 32.02 16.07 41.51 4.06
181 182 6.882656 AGAGTACATGTACAAGAATCATGCT 58.117 36.000 32.02 11.43 41.51 3.79
182 183 8.011844 AGAGTACATGTACAAGAATCATGCTA 57.988 34.615 32.02 0.00 41.51 3.49
183 184 8.646004 AGAGTACATGTACAAGAATCATGCTAT 58.354 33.333 32.02 10.85 41.51 2.97
184 185 9.914131 GAGTACATGTACAAGAATCATGCTATA 57.086 33.333 32.02 0.00 41.51 1.31
185 186 9.698309 AGTACATGTACAAGAATCATGCTATAC 57.302 33.333 32.02 6.68 41.51 1.47
186 187 9.476202 GTACATGTACAAGAATCATGCTATACA 57.524 33.333 27.37 0.00 41.51 2.29
187 188 8.370493 ACATGTACAAGAATCATGCTATACAC 57.630 34.615 4.87 0.00 41.51 2.90
188 189 7.986889 ACATGTACAAGAATCATGCTATACACA 59.013 33.333 4.87 0.00 41.51 3.72
189 190 7.770801 TGTACAAGAATCATGCTATACACAC 57.229 36.000 0.00 0.00 0.00 3.82
190 191 5.973651 ACAAGAATCATGCTATACACACG 57.026 39.130 0.00 0.00 0.00 4.49
191 192 5.660460 ACAAGAATCATGCTATACACACGA 58.340 37.500 0.00 0.00 0.00 4.35
192 193 5.520288 ACAAGAATCATGCTATACACACGAC 59.480 40.000 0.00 0.00 0.00 4.34
193 194 5.262588 AGAATCATGCTATACACACGACA 57.737 39.130 0.00 0.00 0.00 4.35
194 195 5.660460 AGAATCATGCTATACACACGACAA 58.340 37.500 0.00 0.00 0.00 3.18
195 196 5.750547 AGAATCATGCTATACACACGACAAG 59.249 40.000 0.00 0.00 0.00 3.16
196 197 4.712122 TCATGCTATACACACGACAAGA 57.288 40.909 0.00 0.00 0.00 3.02
197 198 5.262588 TCATGCTATACACACGACAAGAT 57.737 39.130 0.00 0.00 0.00 2.40
198 199 5.660460 TCATGCTATACACACGACAAGATT 58.340 37.500 0.00 0.00 0.00 2.40
199 200 5.748630 TCATGCTATACACACGACAAGATTC 59.251 40.000 0.00 0.00 0.00 2.52
200 201 4.102649 TGCTATACACACGACAAGATTCG 58.897 43.478 0.00 0.00 44.87 3.34
201 202 3.486108 GCTATACACACGACAAGATTCGG 59.514 47.826 0.00 0.00 43.58 4.30
202 203 3.861276 ATACACACGACAAGATTCGGA 57.139 42.857 0.00 0.00 43.58 4.55
203 204 1.779569 ACACACGACAAGATTCGGAC 58.220 50.000 0.00 0.00 43.58 4.79
204 205 0.708370 CACACGACAAGATTCGGACG 59.292 55.000 0.00 0.00 43.58 4.79
205 206 0.594602 ACACGACAAGATTCGGACGA 59.405 50.000 9.28 0.00 43.58 4.20
206 207 1.001048 ACACGACAAGATTCGGACGAA 60.001 47.619 9.75 9.75 43.58 3.85
207 208 1.385743 CACGACAAGATTCGGACGAAC 59.614 52.381 9.52 4.40 43.58 3.95
208 209 0.989890 CGACAAGATTCGGACGAACC 59.010 55.000 9.52 0.00 36.91 3.62
209 210 1.667756 CGACAAGATTCGGACGAACCA 60.668 52.381 9.52 0.00 36.91 3.67
210 211 2.618053 GACAAGATTCGGACGAACCAT 58.382 47.619 9.52 0.00 36.91 3.55
211 212 3.732774 CGACAAGATTCGGACGAACCATA 60.733 47.826 9.52 0.00 36.91 2.74
212 213 3.782046 ACAAGATTCGGACGAACCATAG 58.218 45.455 9.52 2.36 36.91 2.23
213 214 3.446161 ACAAGATTCGGACGAACCATAGA 59.554 43.478 9.52 0.00 36.91 1.98
214 215 3.712091 AGATTCGGACGAACCATAGAC 57.288 47.619 9.52 0.00 36.91 2.59
215 216 2.033049 AGATTCGGACGAACCATAGACG 59.967 50.000 9.52 0.00 36.91 4.18
216 217 1.452110 TTCGGACGAACCATAGACGA 58.548 50.000 2.62 0.00 38.90 4.20
217 218 1.671979 TCGGACGAACCATAGACGAT 58.328 50.000 0.00 0.00 38.90 3.73
218 219 1.332686 TCGGACGAACCATAGACGATG 59.667 52.381 0.00 0.00 38.90 3.84
231 232 5.990408 CATAGACGATGGTTAAAATCCAGC 58.010 41.667 0.00 0.00 38.42 4.85
232 233 3.279434 AGACGATGGTTAAAATCCAGCC 58.721 45.455 0.00 0.00 38.01 4.85
233 234 2.014128 ACGATGGTTAAAATCCAGCCG 58.986 47.619 0.00 0.00 38.01 5.52
234 235 1.333619 CGATGGTTAAAATCCAGCCGG 59.666 52.381 0.00 0.00 38.01 6.13
236 237 1.828979 TGGTTAAAATCCAGCCGGAC 58.171 50.000 5.05 0.00 46.79 4.79
237 238 1.074084 TGGTTAAAATCCAGCCGGACA 59.926 47.619 5.05 0.00 46.79 4.02
238 239 2.291282 TGGTTAAAATCCAGCCGGACAT 60.291 45.455 5.05 0.00 46.79 3.06
239 240 2.099098 GGTTAAAATCCAGCCGGACATG 59.901 50.000 5.05 0.00 46.79 3.21
240 241 2.752903 GTTAAAATCCAGCCGGACATGT 59.247 45.455 5.05 0.00 46.79 3.21
241 242 1.176527 AAAATCCAGCCGGACATGTG 58.823 50.000 5.05 0.00 46.79 3.21
242 243 0.038166 AAATCCAGCCGGACATGTGT 59.962 50.000 5.05 0.00 46.79 3.72
243 244 0.677731 AATCCAGCCGGACATGTGTG 60.678 55.000 5.05 0.00 46.79 3.82
244 245 3.434319 CCAGCCGGACATGTGTGC 61.434 66.667 5.05 2.53 0.00 4.57
245 246 2.669229 CAGCCGGACATGTGTGCA 60.669 61.111 5.05 0.00 36.05 4.57
246 247 2.042259 CAGCCGGACATGTGTGCAT 61.042 57.895 5.05 0.00 36.05 3.96
247 248 0.744057 CAGCCGGACATGTGTGCATA 60.744 55.000 5.05 0.00 36.05 3.14
248 249 0.744414 AGCCGGACATGTGTGCATAC 60.744 55.000 5.05 6.65 36.05 2.39
249 250 1.024046 GCCGGACATGTGTGCATACA 61.024 55.000 19.10 19.10 36.05 2.29
250 251 1.667236 CCGGACATGTGTGCATACAT 58.333 50.000 21.95 21.95 41.77 2.29
251 252 2.016318 CCGGACATGTGTGCATACATT 58.984 47.619 24.63 16.26 39.17 2.71
252 253 2.223317 CCGGACATGTGTGCATACATTG 60.223 50.000 24.63 20.58 39.17 2.82
253 254 2.677337 CGGACATGTGTGCATACATTGA 59.323 45.455 24.63 0.00 39.17 2.57
254 255 3.126686 CGGACATGTGTGCATACATTGAA 59.873 43.478 24.63 0.00 39.17 2.69
255 256 4.414852 GGACATGTGTGCATACATTGAAC 58.585 43.478 24.63 15.45 39.17 3.18
256 257 4.082841 GGACATGTGTGCATACATTGAACA 60.083 41.667 24.63 0.00 41.91 3.18
261 262 2.228582 TGTGCATACATTGAACACCAGC 59.771 45.455 0.00 0.00 39.09 4.85
262 263 1.818060 TGCATACATTGAACACCAGCC 59.182 47.619 0.00 0.00 0.00 4.85
263 264 1.134946 GCATACATTGAACACCAGCCC 59.865 52.381 0.00 0.00 0.00 5.19
264 265 1.750778 CATACATTGAACACCAGCCCC 59.249 52.381 0.00 0.00 0.00 5.80
265 266 1.072266 TACATTGAACACCAGCCCCT 58.928 50.000 0.00 0.00 0.00 4.79
266 267 0.540365 ACATTGAACACCAGCCCCTG 60.540 55.000 0.00 0.00 0.00 4.45
277 278 1.856629 CAGCCCCTGGATTTTCATGT 58.143 50.000 0.00 0.00 0.00 3.21
278 279 1.753073 CAGCCCCTGGATTTTCATGTC 59.247 52.381 0.00 0.00 0.00 3.06
279 280 0.740737 GCCCCTGGATTTTCATGTCG 59.259 55.000 0.00 0.00 0.00 4.35
280 281 1.955208 GCCCCTGGATTTTCATGTCGT 60.955 52.381 0.00 0.00 0.00 4.34
281 282 1.745087 CCCCTGGATTTTCATGTCGTG 59.255 52.381 0.00 0.00 0.00 4.35
282 283 1.133025 CCCTGGATTTTCATGTCGTGC 59.867 52.381 0.00 0.00 0.00 5.34
283 284 1.811965 CCTGGATTTTCATGTCGTGCA 59.188 47.619 0.00 0.00 0.00 4.57
284 285 2.424601 CCTGGATTTTCATGTCGTGCAT 59.575 45.455 0.00 0.00 38.60 3.96
285 286 3.627123 CCTGGATTTTCATGTCGTGCATA 59.373 43.478 0.00 0.00 35.74 3.14
286 287 4.496341 CCTGGATTTTCATGTCGTGCATAC 60.496 45.833 0.00 0.00 35.74 2.39
287 288 4.006319 TGGATTTTCATGTCGTGCATACA 58.994 39.130 7.24 7.24 35.74 2.29
288 289 4.639755 TGGATTTTCATGTCGTGCATACAT 59.360 37.500 10.85 10.85 38.08 2.29
289 290 5.207768 GGATTTTCATGTCGTGCATACATC 58.792 41.667 13.11 4.35 35.39 3.06
290 291 3.923827 TTTCATGTCGTGCATACATCG 57.076 42.857 13.11 9.92 35.39 3.84
291 292 2.577449 TCATGTCGTGCATACATCGT 57.423 45.000 13.11 0.00 35.39 3.73
292 293 2.192624 TCATGTCGTGCATACATCGTG 58.807 47.619 13.11 6.36 35.39 4.35
293 294 1.926510 CATGTCGTGCATACATCGTGT 59.073 47.619 13.11 0.00 35.39 4.49
294 295 2.923605 TGTCGTGCATACATCGTGTA 57.076 45.000 0.00 1.30 37.24 2.90
295 296 2.521996 TGTCGTGCATACATCGTGTAC 58.478 47.619 0.00 0.00 35.42 2.90
296 297 1.850441 GTCGTGCATACATCGTGTACC 59.150 52.381 0.00 0.00 35.42 3.34
297 298 1.473278 TCGTGCATACATCGTGTACCA 59.527 47.619 0.00 0.31 35.42 3.25
298 299 1.852280 CGTGCATACATCGTGTACCAG 59.148 52.381 0.00 0.00 35.42 4.00
299 300 2.201732 GTGCATACATCGTGTACCAGG 58.798 52.381 0.00 0.00 35.42 4.45
300 301 2.104170 TGCATACATCGTGTACCAGGA 58.896 47.619 0.00 0.00 35.42 3.86
301 302 2.698274 TGCATACATCGTGTACCAGGAT 59.302 45.455 0.00 0.00 39.16 3.24
302 303 3.243737 TGCATACATCGTGTACCAGGATC 60.244 47.826 0.00 0.00 36.94 3.36
303 304 3.565516 CATACATCGTGTACCAGGATCG 58.434 50.000 0.00 0.00 36.94 3.69
304 305 1.471119 ACATCGTGTACCAGGATCGT 58.529 50.000 0.00 0.00 36.94 3.73
305 306 1.134367 ACATCGTGTACCAGGATCGTG 59.866 52.381 8.47 8.47 36.94 4.35
306 307 0.102481 ATCGTGTACCAGGATCGTGC 59.898 55.000 9.95 0.00 34.48 5.34
307 308 1.214325 CGTGTACCAGGATCGTGCA 59.786 57.895 9.95 0.27 0.00 4.57
308 309 0.179111 CGTGTACCAGGATCGTGCAT 60.179 55.000 9.95 3.10 0.00 3.96
309 310 1.290203 GTGTACCAGGATCGTGCATG 58.710 55.000 9.95 0.00 0.00 4.06
310 311 1.134818 GTGTACCAGGATCGTGCATGA 60.135 52.381 11.83 11.83 0.00 3.07
311 312 1.552792 TGTACCAGGATCGTGCATGAA 59.447 47.619 13.65 0.00 0.00 2.57
312 313 2.205074 GTACCAGGATCGTGCATGAAG 58.795 52.381 13.65 3.56 0.00 3.02
313 314 0.745845 ACCAGGATCGTGCATGAAGC 60.746 55.000 13.65 8.10 45.96 3.86
358 359 4.551702 TGGAACAGTAGTGCATGTACAT 57.448 40.909 16.62 1.41 0.00 2.29
420 2263 0.531532 CATCCGGCTGCTGTCTTAGG 60.532 60.000 7.82 0.00 0.00 2.69
446 2289 6.598753 TTACTTGTGTCAAGAACTTGCTAC 57.401 37.500 15.04 10.47 40.24 3.58
543 2387 4.844349 TGCCTGGATACTCTAGCTTTTT 57.156 40.909 0.00 0.00 37.61 1.94
577 2421 9.109393 TGTTCATTGTTTCTGATATAGCTTACC 57.891 33.333 0.00 0.00 0.00 2.85
578 2422 9.109393 GTTCATTGTTTCTGATATAGCTTACCA 57.891 33.333 0.00 0.00 0.00 3.25
579 2423 8.662781 TCATTGTTTCTGATATAGCTTACCAC 57.337 34.615 0.00 0.00 0.00 4.16
580 2424 7.715249 TCATTGTTTCTGATATAGCTTACCACC 59.285 37.037 0.00 0.00 0.00 4.61
581 2425 5.925509 TGTTTCTGATATAGCTTACCACCC 58.074 41.667 0.00 0.00 0.00 4.61
582 2426 5.427157 TGTTTCTGATATAGCTTACCACCCA 59.573 40.000 0.00 0.00 0.00 4.51
583 2427 6.101150 TGTTTCTGATATAGCTTACCACCCAT 59.899 38.462 0.00 0.00 0.00 4.00
584 2428 5.745312 TCTGATATAGCTTACCACCCATG 57.255 43.478 0.00 0.00 0.00 3.66
585 2429 4.020218 TCTGATATAGCTTACCACCCATGC 60.020 45.833 0.00 0.00 0.00 4.06
586 2430 3.009033 TGATATAGCTTACCACCCATGCC 59.991 47.826 0.00 0.00 0.00 4.40
587 2431 1.221635 ATAGCTTACCACCCATGCCA 58.778 50.000 0.00 0.00 0.00 4.92
588 2432 0.995803 TAGCTTACCACCCATGCCAA 59.004 50.000 0.00 0.00 0.00 4.52
589 2433 0.323725 AGCTTACCACCCATGCCAAG 60.324 55.000 0.00 0.00 0.00 3.61
590 2434 0.611896 GCTTACCACCCATGCCAAGT 60.612 55.000 0.00 0.00 0.00 3.16
591 2435 1.176527 CTTACCACCCATGCCAAGTG 58.823 55.000 0.00 0.00 0.00 3.16
593 2437 2.118076 CCACCCATGCCAAGTGGT 59.882 61.111 12.00 0.00 44.95 4.16
594 2438 1.382240 CCACCCATGCCAAGTGGTA 59.618 57.895 12.00 0.00 44.95 3.25
595 2439 0.965363 CCACCCATGCCAAGTGGTAC 60.965 60.000 12.00 0.00 44.95 3.34
596 2440 0.038166 CACCCATGCCAAGTGGTACT 59.962 55.000 0.00 0.00 37.57 2.73
597 2441 0.328258 ACCCATGCCAAGTGGTACTC 59.672 55.000 0.00 0.00 37.57 2.59
598 2442 0.620556 CCCATGCCAAGTGGTACTCT 59.379 55.000 0.00 0.00 37.57 3.24
599 2443 1.837439 CCCATGCCAAGTGGTACTCTA 59.163 52.381 0.00 0.00 37.57 2.43
600 2444 2.158900 CCCATGCCAAGTGGTACTCTAG 60.159 54.545 0.00 0.00 37.57 2.43
601 2445 2.555199 CATGCCAAGTGGTACTCTAGC 58.445 52.381 0.00 0.64 37.57 3.42
602 2446 1.938585 TGCCAAGTGGTACTCTAGCT 58.061 50.000 0.00 0.00 37.57 3.32
603 2447 2.257207 TGCCAAGTGGTACTCTAGCTT 58.743 47.619 0.00 0.00 37.57 3.74
604 2448 2.637872 TGCCAAGTGGTACTCTAGCTTT 59.362 45.455 0.00 0.00 37.57 3.51
605 2449 3.072476 TGCCAAGTGGTACTCTAGCTTTT 59.928 43.478 0.00 0.00 37.57 2.27
607 2451 5.045869 TGCCAAGTGGTACTCTAGCTTTTAT 60.046 40.000 0.00 0.00 37.57 1.40
613 2457 8.998277 AGTGGTACTCTAGCTTTTATCTATGA 57.002 34.615 0.00 0.00 0.00 2.15
614 2458 9.422681 AGTGGTACTCTAGCTTTTATCTATGAA 57.577 33.333 0.00 0.00 0.00 2.57
615 2459 9.465985 GTGGTACTCTAGCTTTTATCTATGAAC 57.534 37.037 0.00 0.00 0.00 3.18
616 2460 9.422681 TGGTACTCTAGCTTTTATCTATGAACT 57.577 33.333 0.00 0.00 0.00 3.01
631 2475 1.557371 TGAACTTGTGTCAGTGGTGGA 59.443 47.619 0.00 0.00 0.00 4.02
666 2510 4.500127 TCGCTTTGCTTGCAGTAAGTATA 58.500 39.130 0.00 0.00 38.70 1.47
723 2580 3.484407 AGGAGCTATGCACATGGATTTC 58.516 45.455 0.00 0.00 0.00 2.17
756 2618 6.936968 ATCAGAGGGTTGTAACTTTAGAGT 57.063 37.500 0.00 0.00 37.87 3.24
757 2619 8.431910 AATCAGAGGGTTGTAACTTTAGAGTA 57.568 34.615 0.00 0.00 34.21 2.59
809 2674 3.689161 CAGTCACAACAAGGTCAACAGAA 59.311 43.478 0.00 0.00 0.00 3.02
810 2675 3.689649 AGTCACAACAAGGTCAACAGAAC 59.310 43.478 0.00 0.00 0.00 3.01
907 2788 2.277628 CGCTCGCCGTTCTCTCTC 60.278 66.667 0.00 0.00 0.00 3.20
922 2835 2.164219 CTCTCTCTGTGTTGCTCTCTCC 59.836 54.545 0.00 0.00 0.00 3.71
925 2838 1.891811 CTCTGTGTTGCTCTCTCCTGA 59.108 52.381 0.00 0.00 0.00 3.86
926 2839 2.496871 CTCTGTGTTGCTCTCTCCTGAT 59.503 50.000 0.00 0.00 0.00 2.90
929 2842 3.698539 CTGTGTTGCTCTCTCCTGATCTA 59.301 47.826 0.00 0.00 0.00 1.98
958 2871 3.256879 GGAGGAGGCCAGAAAAAGAAAAG 59.743 47.826 5.01 0.00 0.00 2.27
959 2872 3.234353 AGGAGGCCAGAAAAAGAAAAGG 58.766 45.455 5.01 0.00 0.00 3.11
960 2873 2.289072 GGAGGCCAGAAAAAGAAAAGGC 60.289 50.000 5.01 0.00 41.29 4.35
961 2874 2.365293 GAGGCCAGAAAAAGAAAAGGCA 59.635 45.455 5.01 0.00 43.72 4.75
962 2875 2.103094 AGGCCAGAAAAAGAAAAGGCAC 59.897 45.455 5.01 0.00 43.72 5.01
963 2876 2.127251 GCCAGAAAAAGAAAAGGCACG 58.873 47.619 0.00 0.00 41.63 5.34
964 2877 2.223711 GCCAGAAAAAGAAAAGGCACGA 60.224 45.455 0.00 0.00 41.63 4.35
965 2878 3.632189 CCAGAAAAAGAAAAGGCACGAG 58.368 45.455 0.00 0.00 0.00 4.18
967 2880 3.315191 CAGAAAAAGAAAAGGCACGAGGA 59.685 43.478 0.00 0.00 0.00 3.71
1012 2925 0.810648 TTCATTCATGGGCTTCGCAC 59.189 50.000 0.00 0.00 0.00 5.34
1023 2936 1.448540 CTTCGCACGAGGAGGCAAT 60.449 57.895 0.00 0.00 0.00 3.56
1024 2937 1.003839 TTCGCACGAGGAGGCAATT 60.004 52.632 0.00 0.00 0.00 2.32
1029 2944 1.084370 CACGAGGAGGCAATTCCGTC 61.084 60.000 0.00 0.00 42.29 4.79
1054 2969 2.092103 TGGCGGCCCACTAATAAAGAAT 60.092 45.455 17.97 0.00 35.79 2.40
1148 3077 3.060615 GGCCACCTGCTTCTGCTG 61.061 66.667 0.00 0.00 40.92 4.41
1161 3093 0.975040 TCTGCTGCTCCTCCTTCTCC 60.975 60.000 0.00 0.00 0.00 3.71
1201 3133 0.533755 CCATTCACCGCCATCTCCTC 60.534 60.000 0.00 0.00 0.00 3.71
1217 3149 4.689549 TCCCCCTTCTCGCCGTCA 62.690 66.667 0.00 0.00 0.00 4.35
1275 3219 2.325082 CCACAACCCGCTGCTACAC 61.325 63.158 0.00 0.00 0.00 2.90
1823 3773 1.751927 GCAAGACCATCTGCCCCAG 60.752 63.158 0.00 0.00 0.00 4.45
2283 4233 3.630769 TCAGCAGCATCTTCCAATGAATC 59.369 43.478 0.00 0.00 0.00 2.52
2286 4236 4.278669 AGCAGCATCTTCCAATGAATCATC 59.721 41.667 0.00 0.00 0.00 2.92
2289 4239 6.382608 CAGCATCTTCCAATGAATCATCATC 58.617 40.000 0.00 0.00 45.60 2.92
2290 4240 6.207614 CAGCATCTTCCAATGAATCATCATCT 59.792 38.462 0.00 0.00 45.60 2.90
2291 4241 6.431543 AGCATCTTCCAATGAATCATCATCTC 59.568 38.462 0.00 0.00 45.60 2.75
2308 4259 9.086758 TCATCATCTCACTACATTCATCATACT 57.913 33.333 0.00 0.00 0.00 2.12
2389 4347 1.860950 CACCCGACATTCATCGACATC 59.139 52.381 0.00 0.00 45.13 3.06
2427 4385 7.977818 TGCTGACATAAATAAGATCCCTATGT 58.022 34.615 0.00 0.00 36.23 2.29
2480 4438 5.353956 TCAAAGATGTATTCACCGTGATTGG 59.646 40.000 1.09 0.00 0.00 3.16
2481 4439 4.753516 AGATGTATTCACCGTGATTGGA 57.246 40.909 1.09 0.00 0.00 3.53
2482 4440 5.296151 AGATGTATTCACCGTGATTGGAT 57.704 39.130 1.09 0.00 0.00 3.41
2483 4441 5.059161 AGATGTATTCACCGTGATTGGATG 58.941 41.667 1.09 0.00 0.00 3.51
2524 4482 8.213518 TGATTACATGAAAGGATTAGTTGCTC 57.786 34.615 0.00 0.00 0.00 4.26
2640 4598 3.437795 CTTGCCTTCCCTGCTGCG 61.438 66.667 0.00 0.00 0.00 5.18
2661 4619 4.595116 CGCCTTGCATCTTCTTAATCTTG 58.405 43.478 0.00 0.00 0.00 3.02
2664 4622 4.497006 CCTTGCATCTTCTTAATCTTGCCG 60.497 45.833 0.00 0.00 0.00 5.69
2700 4658 2.518949 GCTGCAACAACATAACATCCG 58.481 47.619 0.00 0.00 0.00 4.18
2743 4735 7.909641 TGCACACACATATTCATCGAAAATAAG 59.090 33.333 7.46 6.28 0.00 1.73
2747 4739 9.162793 CACACATATTCATCGAAAATAAGAAGC 57.837 33.333 11.03 0.00 0.00 3.86
2774 4766 1.606224 GGCAAATGTTGTGGCAGGAAG 60.606 52.381 0.00 0.00 41.05 3.46
2805 4797 4.095782 GGCATTCAGTAAAATTGCTACCGA 59.904 41.667 0.00 0.00 0.00 4.69
2827 4819 7.875041 ACCGATTGATACTTCTAATCCATGAAG 59.125 37.037 0.00 0.00 43.63 3.02
2936 4928 2.605366 GCGAGAATCTTCCAGTAGCAAC 59.395 50.000 0.00 0.00 0.00 4.17
2957 4949 2.237143 CTCTTCCACCTGTGCCAAGATA 59.763 50.000 9.19 0.00 31.69 1.98
2976 4968 7.797123 CCAAGATACAAGTTCAGTAACGAAAAC 59.203 37.037 0.00 0.00 40.73 2.43
3033 5025 7.437862 GTGTCATGCAAGTTCAATAAGGAAAAA 59.562 33.333 0.00 0.00 0.00 1.94
3067 5059 6.220930 GTTTGATTGCCGTATATGGAGAGTA 58.779 40.000 15.58 0.00 0.00 2.59
3068 5060 5.386958 TGATTGCCGTATATGGAGAGTAC 57.613 43.478 15.58 0.00 0.00 2.73
3077 5104 6.382608 CGTATATGGAGAGTACCAATGTCTG 58.617 44.000 0.00 0.00 43.47 3.51
3096 5123 6.245408 TGTCTGGCCTTTGATAGTAACAATT 58.755 36.000 3.32 0.00 0.00 2.32
3150 5177 5.010112 TCCGTGCAACTTTCCATCATTAAAA 59.990 36.000 0.00 0.00 31.75 1.52
3182 5213 5.468746 GTGCTAACCAATATAAATCAGCGGA 59.531 40.000 0.00 0.00 0.00 5.54
3195 5226 4.691860 ATCAGCGGATGCATAATTAAGC 57.308 40.909 0.00 5.74 46.23 3.09
3197 5228 1.806542 AGCGGATGCATAATTAAGCGG 59.193 47.619 0.00 0.00 46.23 5.52
3198 5229 1.729149 GCGGATGCATAATTAAGCGGC 60.729 52.381 0.00 5.43 42.15 6.53
3199 5230 1.535028 CGGATGCATAATTAAGCGGCA 59.465 47.619 0.00 7.40 39.03 5.69
3200 5231 2.162208 CGGATGCATAATTAAGCGGCAT 59.838 45.455 0.00 13.63 46.91 4.40
3201 5232 3.373748 CGGATGCATAATTAAGCGGCATA 59.626 43.478 0.00 0.00 44.52 3.14
3202 5233 4.035558 CGGATGCATAATTAAGCGGCATAT 59.964 41.667 0.00 1.22 44.52 1.78
3203 5234 5.514279 GGATGCATAATTAAGCGGCATATC 58.486 41.667 0.00 8.49 44.52 1.63
3215 5246 4.645535 AGCGGCATATCAGATATGTTGTT 58.354 39.130 25.21 15.82 43.52 2.83
3222 5253 9.056005 GGCATATCAGATATGTTGTTACAGAAA 57.944 33.333 25.21 0.00 43.52 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 143 5.475273 TGTACTCTACTACGCATACACAC 57.525 43.478 0.00 0.00 0.00 3.82
143 144 5.587443 ACATGTACTCTACTACGCATACACA 59.413 40.000 0.00 0.00 0.00 3.72
172 173 5.748630 TCTTGTCGTGTGTATAGCATGATTC 59.251 40.000 0.00 0.00 34.82 2.52
173 174 5.660460 TCTTGTCGTGTGTATAGCATGATT 58.340 37.500 0.00 0.00 34.82 2.57
174 175 5.262588 TCTTGTCGTGTGTATAGCATGAT 57.737 39.130 0.00 0.00 34.82 2.45
175 176 4.712122 TCTTGTCGTGTGTATAGCATGA 57.288 40.909 0.00 0.00 0.00 3.07
176 177 5.331830 CGAATCTTGTCGTGTGTATAGCATG 60.332 44.000 0.00 0.00 36.26 4.06
177 178 4.740205 CGAATCTTGTCGTGTGTATAGCAT 59.260 41.667 0.00 0.00 36.26 3.79
178 179 4.102649 CGAATCTTGTCGTGTGTATAGCA 58.897 43.478 0.00 0.00 36.26 3.49
179 180 3.486108 CCGAATCTTGTCGTGTGTATAGC 59.514 47.826 0.00 0.00 39.43 2.97
180 181 4.733887 GTCCGAATCTTGTCGTGTGTATAG 59.266 45.833 0.00 0.00 39.43 1.31
181 182 4.665212 GTCCGAATCTTGTCGTGTGTATA 58.335 43.478 0.00 0.00 39.43 1.47
182 183 3.508762 GTCCGAATCTTGTCGTGTGTAT 58.491 45.455 0.00 0.00 39.43 2.29
183 184 2.666344 CGTCCGAATCTTGTCGTGTGTA 60.666 50.000 0.00 0.00 39.43 2.90
184 185 1.779569 GTCCGAATCTTGTCGTGTGT 58.220 50.000 0.00 0.00 39.43 3.72
185 186 0.708370 CGTCCGAATCTTGTCGTGTG 59.292 55.000 0.00 0.00 39.43 3.82
186 187 0.594602 TCGTCCGAATCTTGTCGTGT 59.405 50.000 0.00 0.00 39.43 4.49
187 188 1.385743 GTTCGTCCGAATCTTGTCGTG 59.614 52.381 5.33 0.00 39.43 4.35
188 189 1.668047 GGTTCGTCCGAATCTTGTCGT 60.668 52.381 5.33 0.00 39.43 4.34
189 190 0.989890 GGTTCGTCCGAATCTTGTCG 59.010 55.000 5.33 0.00 40.77 4.35
190 191 2.074547 TGGTTCGTCCGAATCTTGTC 57.925 50.000 13.24 0.00 36.30 3.18
191 192 2.762535 ATGGTTCGTCCGAATCTTGT 57.237 45.000 13.24 0.00 36.30 3.16
192 193 3.797256 GTCTATGGTTCGTCCGAATCTTG 59.203 47.826 13.24 4.59 36.30 3.02
193 194 3.488721 CGTCTATGGTTCGTCCGAATCTT 60.489 47.826 13.24 9.67 36.30 2.40
194 195 2.033049 CGTCTATGGTTCGTCCGAATCT 59.967 50.000 13.24 2.92 36.30 2.40
195 196 2.032550 TCGTCTATGGTTCGTCCGAATC 59.967 50.000 5.33 5.55 39.52 2.52
196 197 2.019249 TCGTCTATGGTTCGTCCGAAT 58.981 47.619 5.33 0.00 39.52 3.34
197 198 1.452110 TCGTCTATGGTTCGTCCGAA 58.548 50.000 0.00 0.00 39.52 4.30
198 199 1.332686 CATCGTCTATGGTTCGTCCGA 59.667 52.381 0.00 0.00 39.52 4.55
199 200 1.755161 CATCGTCTATGGTTCGTCCG 58.245 55.000 0.00 0.00 39.52 4.79
208 209 5.049405 GGCTGGATTTTAACCATCGTCTATG 60.049 44.000 0.00 0.00 36.79 2.23
209 210 5.063880 GGCTGGATTTTAACCATCGTCTAT 58.936 41.667 0.00 0.00 36.79 1.98
210 211 4.448210 GGCTGGATTTTAACCATCGTCTA 58.552 43.478 0.00 0.00 36.79 2.59
211 212 3.279434 GGCTGGATTTTAACCATCGTCT 58.721 45.455 0.00 0.00 36.79 4.18
212 213 2.031683 CGGCTGGATTTTAACCATCGTC 59.968 50.000 0.00 0.00 36.79 4.20
213 214 2.014128 CGGCTGGATTTTAACCATCGT 58.986 47.619 0.00 0.00 36.79 3.73
214 215 1.333619 CCGGCTGGATTTTAACCATCG 59.666 52.381 5.28 0.00 37.49 3.84
215 216 2.650322 TCCGGCTGGATTTTAACCATC 58.350 47.619 11.27 0.00 40.17 3.51
216 217 2.818751 TCCGGCTGGATTTTAACCAT 57.181 45.000 11.27 0.00 40.17 3.55
226 227 2.347114 CACACATGTCCGGCTGGA 59.653 61.111 11.27 11.27 43.88 3.86
227 228 3.434319 GCACACATGTCCGGCTGG 61.434 66.667 4.71 4.71 0.00 4.85
228 229 0.744057 TATGCACACATGTCCGGCTG 60.744 55.000 12.50 0.00 37.04 4.85
229 230 0.744414 GTATGCACACATGTCCGGCT 60.744 55.000 12.50 3.54 37.04 5.52
230 231 1.024046 TGTATGCACACATGTCCGGC 61.024 55.000 0.00 0.07 37.04 6.13
231 232 1.667236 ATGTATGCACACATGTCCGG 58.333 50.000 10.42 0.00 37.74 5.14
232 233 2.677337 TCAATGTATGCACACATGTCCG 59.323 45.455 12.16 1.22 39.10 4.79
233 234 4.082841 TGTTCAATGTATGCACACATGTCC 60.083 41.667 12.16 1.14 39.10 4.02
234 235 5.045668 TGTTCAATGTATGCACACATGTC 57.954 39.130 12.16 3.58 39.10 3.06
240 241 2.228582 GCTGGTGTTCAATGTATGCACA 59.771 45.455 0.00 0.00 39.52 4.57
241 242 2.415893 GGCTGGTGTTCAATGTATGCAC 60.416 50.000 0.00 0.00 0.00 4.57
242 243 1.818060 GGCTGGTGTTCAATGTATGCA 59.182 47.619 0.00 0.00 0.00 3.96
243 244 1.134946 GGGCTGGTGTTCAATGTATGC 59.865 52.381 0.00 0.00 0.00 3.14
244 245 1.750778 GGGGCTGGTGTTCAATGTATG 59.249 52.381 0.00 0.00 0.00 2.39
245 246 1.640670 AGGGGCTGGTGTTCAATGTAT 59.359 47.619 0.00 0.00 0.00 2.29
246 247 1.072266 AGGGGCTGGTGTTCAATGTA 58.928 50.000 0.00 0.00 0.00 2.29
247 248 0.540365 CAGGGGCTGGTGTTCAATGT 60.540 55.000 0.00 0.00 0.00 2.71
248 249 1.252904 CCAGGGGCTGGTGTTCAATG 61.253 60.000 0.00 0.00 45.82 2.82
249 250 1.077265 CCAGGGGCTGGTGTTCAAT 59.923 57.895 0.00 0.00 45.82 2.57
250 251 2.520458 CCAGGGGCTGGTGTTCAA 59.480 61.111 0.00 0.00 45.82 2.69
258 259 1.753073 GACATGAAAATCCAGGGGCTG 59.247 52.381 0.00 0.00 0.00 4.85
259 260 1.683011 CGACATGAAAATCCAGGGGCT 60.683 52.381 0.00 0.00 0.00 5.19
260 261 0.740737 CGACATGAAAATCCAGGGGC 59.259 55.000 0.00 0.00 0.00 5.80
261 262 1.745087 CACGACATGAAAATCCAGGGG 59.255 52.381 0.00 0.00 0.00 4.79
262 263 1.133025 GCACGACATGAAAATCCAGGG 59.867 52.381 0.00 0.00 0.00 4.45
263 264 1.811965 TGCACGACATGAAAATCCAGG 59.188 47.619 0.00 0.00 0.00 4.45
264 265 3.770263 ATGCACGACATGAAAATCCAG 57.230 42.857 0.00 0.00 37.70 3.86
265 266 4.006319 TGTATGCACGACATGAAAATCCA 58.994 39.130 0.00 0.00 40.06 3.41
266 267 4.614555 TGTATGCACGACATGAAAATCC 57.385 40.909 0.00 0.00 40.06 3.01
267 268 4.900182 CGATGTATGCACGACATGAAAATC 59.100 41.667 18.32 5.48 40.06 2.17
268 269 4.332543 ACGATGTATGCACGACATGAAAAT 59.667 37.500 18.32 0.00 40.06 1.82
269 270 3.682377 ACGATGTATGCACGACATGAAAA 59.318 39.130 18.32 0.00 40.06 2.29
270 271 3.061965 CACGATGTATGCACGACATGAAA 59.938 43.478 18.32 0.00 40.06 2.69
271 272 2.602660 CACGATGTATGCACGACATGAA 59.397 45.455 18.32 0.00 40.06 2.57
272 273 2.192624 CACGATGTATGCACGACATGA 58.807 47.619 18.32 0.00 40.06 3.07
273 274 1.926510 ACACGATGTATGCACGACATG 59.073 47.619 18.32 13.20 40.06 3.21
274 275 2.293677 ACACGATGTATGCACGACAT 57.706 45.000 14.37 14.37 43.18 3.06
275 276 2.521996 GTACACGATGTATGCACGACA 58.478 47.619 5.78 5.78 35.05 4.35
276 277 1.850441 GGTACACGATGTATGCACGAC 59.150 52.381 11.33 0.00 35.05 4.34
277 278 1.473278 TGGTACACGATGTATGCACGA 59.527 47.619 11.33 0.00 35.05 4.35
278 279 1.852280 CTGGTACACGATGTATGCACG 59.148 52.381 0.00 0.00 35.05 5.34
279 280 2.159156 TCCTGGTACACGATGTATGCAC 60.159 50.000 0.00 0.00 35.05 4.57
280 281 2.104170 TCCTGGTACACGATGTATGCA 58.896 47.619 0.00 0.00 35.05 3.96
281 282 2.882927 TCCTGGTACACGATGTATGC 57.117 50.000 0.00 0.00 35.05 3.14
282 283 3.004419 ACGATCCTGGTACACGATGTATG 59.996 47.826 0.00 0.00 34.42 2.39
283 284 3.004419 CACGATCCTGGTACACGATGTAT 59.996 47.826 0.00 0.00 34.42 2.29
284 285 2.356695 CACGATCCTGGTACACGATGTA 59.643 50.000 0.00 0.00 34.42 2.29
285 286 1.134367 CACGATCCTGGTACACGATGT 59.866 52.381 0.00 0.00 34.42 3.06
286 287 1.840181 CACGATCCTGGTACACGATG 58.160 55.000 0.00 0.00 34.42 3.84
287 288 0.102481 GCACGATCCTGGTACACGAT 59.898 55.000 0.00 0.00 36.83 3.73
288 289 1.245376 TGCACGATCCTGGTACACGA 61.245 55.000 0.00 0.00 0.00 4.35
289 290 0.179111 ATGCACGATCCTGGTACACG 60.179 55.000 0.00 0.00 0.00 4.49
290 291 1.134818 TCATGCACGATCCTGGTACAC 60.135 52.381 0.00 0.00 0.00 2.90
291 292 1.190643 TCATGCACGATCCTGGTACA 58.809 50.000 0.00 0.00 0.00 2.90
292 293 2.205074 CTTCATGCACGATCCTGGTAC 58.795 52.381 0.00 0.00 0.00 3.34
293 294 1.473257 GCTTCATGCACGATCCTGGTA 60.473 52.381 0.00 0.00 42.31 3.25
294 295 0.745845 GCTTCATGCACGATCCTGGT 60.746 55.000 0.00 0.00 42.31 4.00
295 296 2.020131 GCTTCATGCACGATCCTGG 58.980 57.895 0.00 0.00 42.31 4.45
305 306 0.169672 ACATGCGAACTGCTTCATGC 59.830 50.000 0.00 0.00 46.63 4.06
306 307 2.416202 TGTACATGCGAACTGCTTCATG 59.584 45.455 0.00 0.00 46.63 3.07
307 308 2.698803 TGTACATGCGAACTGCTTCAT 58.301 42.857 0.00 0.00 46.63 2.57
308 309 2.162319 TGTACATGCGAACTGCTTCA 57.838 45.000 0.00 0.00 46.63 3.02
309 310 2.412847 GGTTGTACATGCGAACTGCTTC 60.413 50.000 0.00 0.00 46.63 3.86
310 311 1.535462 GGTTGTACATGCGAACTGCTT 59.465 47.619 0.00 0.00 46.63 3.91
311 312 1.156736 GGTTGTACATGCGAACTGCT 58.843 50.000 0.00 0.00 46.63 4.24
312 313 1.135972 CAGGTTGTACATGCGAACTGC 60.136 52.381 0.00 0.00 46.70 4.40
313 314 1.135972 GCAGGTTGTACATGCGAACTG 60.136 52.381 6.04 6.04 46.04 3.16
314 315 1.156736 GCAGGTTGTACATGCGAACT 58.843 50.000 4.29 0.00 46.04 3.01
315 316 3.676091 GCAGGTTGTACATGCGAAC 57.324 52.632 4.29 0.00 46.04 3.95
358 359 0.252103 GTACTGTCCCAGGTGGAGGA 60.252 60.000 0.00 0.00 46.38 3.71
420 2263 5.034797 GCAAGTTCTTGACACAAGTAAACC 58.965 41.667 15.52 0.00 0.00 3.27
457 2300 0.401738 TTCCAGTTCCAGCCTTCCAG 59.598 55.000 0.00 0.00 0.00 3.86
458 2301 0.401738 CTTCCAGTTCCAGCCTTCCA 59.598 55.000 0.00 0.00 0.00 3.53
459 2302 0.693049 TCTTCCAGTTCCAGCCTTCC 59.307 55.000 0.00 0.00 0.00 3.46
460 2303 1.625818 TCTCTTCCAGTTCCAGCCTTC 59.374 52.381 0.00 0.00 0.00 3.46
461 2304 1.734655 TCTCTTCCAGTTCCAGCCTT 58.265 50.000 0.00 0.00 0.00 4.35
462 2305 1.349357 GTTCTCTTCCAGTTCCAGCCT 59.651 52.381 0.00 0.00 0.00 4.58
463 2306 1.072331 TGTTCTCTTCCAGTTCCAGCC 59.928 52.381 0.00 0.00 0.00 4.85
464 2307 2.147150 GTGTTCTCTTCCAGTTCCAGC 58.853 52.381 0.00 0.00 0.00 4.85
551 2395 9.109393 GGTAAGCTATATCAGAAACAATGAACA 57.891 33.333 0.00 0.00 0.00 3.18
552 2396 9.109393 TGGTAAGCTATATCAGAAACAATGAAC 57.891 33.333 0.00 0.00 0.00 3.18
553 2397 9.109393 GTGGTAAGCTATATCAGAAACAATGAA 57.891 33.333 0.00 0.00 0.00 2.57
554 2398 7.715249 GGTGGTAAGCTATATCAGAAACAATGA 59.285 37.037 0.00 0.00 0.00 2.57
555 2399 7.041098 GGGTGGTAAGCTATATCAGAAACAATG 60.041 40.741 0.00 0.00 0.00 2.82
556 2400 6.998673 GGGTGGTAAGCTATATCAGAAACAAT 59.001 38.462 0.00 0.00 0.00 2.71
557 2401 6.069905 TGGGTGGTAAGCTATATCAGAAACAA 60.070 38.462 0.00 0.00 0.00 2.83
558 2402 5.427157 TGGGTGGTAAGCTATATCAGAAACA 59.573 40.000 0.00 0.00 0.00 2.83
559 2403 5.925509 TGGGTGGTAAGCTATATCAGAAAC 58.074 41.667 0.00 0.00 0.00 2.78
560 2404 6.533730 CATGGGTGGTAAGCTATATCAGAAA 58.466 40.000 0.00 0.00 0.00 2.52
561 2405 5.513094 GCATGGGTGGTAAGCTATATCAGAA 60.513 44.000 0.00 0.00 0.00 3.02
562 2406 4.020218 GCATGGGTGGTAAGCTATATCAGA 60.020 45.833 0.00 0.00 0.00 3.27
563 2407 4.256920 GCATGGGTGGTAAGCTATATCAG 58.743 47.826 0.00 0.00 0.00 2.90
564 2408 3.009033 GGCATGGGTGGTAAGCTATATCA 59.991 47.826 0.00 0.00 0.00 2.15
565 2409 3.009033 TGGCATGGGTGGTAAGCTATATC 59.991 47.826 0.00 0.00 0.00 1.63
566 2410 2.986019 TGGCATGGGTGGTAAGCTATAT 59.014 45.455 0.00 0.00 0.00 0.86
567 2411 2.413601 TGGCATGGGTGGTAAGCTATA 58.586 47.619 0.00 0.00 0.00 1.31
568 2412 1.221635 TGGCATGGGTGGTAAGCTAT 58.778 50.000 0.00 0.00 0.00 2.97
569 2413 0.995803 TTGGCATGGGTGGTAAGCTA 59.004 50.000 0.00 0.00 0.00 3.32
570 2414 0.323725 CTTGGCATGGGTGGTAAGCT 60.324 55.000 0.00 0.00 0.00 3.74
571 2415 0.611896 ACTTGGCATGGGTGGTAAGC 60.612 55.000 5.31 0.00 0.00 3.09
572 2416 1.176527 CACTTGGCATGGGTGGTAAG 58.823 55.000 5.31 0.00 0.00 2.34
573 2417 0.251564 CCACTTGGCATGGGTGGTAA 60.252 55.000 19.75 0.00 43.72 2.85
574 2418 1.382240 CCACTTGGCATGGGTGGTA 59.618 57.895 19.75 0.00 43.72 3.25
575 2419 2.118076 CCACTTGGCATGGGTGGT 59.882 61.111 19.75 0.00 43.72 4.16
577 2421 0.038166 AGTACCACTTGGCATGGGTG 59.962 55.000 11.62 9.75 41.97 4.61
578 2422 0.328258 GAGTACCACTTGGCATGGGT 59.672 55.000 11.62 13.39 41.97 4.51
579 2423 0.620556 AGAGTACCACTTGGCATGGG 59.379 55.000 11.62 3.78 41.97 4.00
580 2424 2.743183 GCTAGAGTACCACTTGGCATGG 60.743 54.545 5.58 5.58 43.43 3.66
581 2425 2.169352 AGCTAGAGTACCACTTGGCATG 59.831 50.000 0.00 0.00 39.32 4.06
582 2426 2.472029 AGCTAGAGTACCACTTGGCAT 58.528 47.619 0.00 0.00 39.32 4.40
583 2427 1.938585 AGCTAGAGTACCACTTGGCA 58.061 50.000 0.00 0.00 39.32 4.92
584 2428 3.336138 AAAGCTAGAGTACCACTTGGC 57.664 47.619 0.00 0.00 39.32 4.52
585 2429 6.879400 AGATAAAAGCTAGAGTACCACTTGG 58.121 40.000 0.00 0.00 42.17 3.61
586 2430 9.469807 CATAGATAAAAGCTAGAGTACCACTTG 57.530 37.037 0.00 0.00 0.00 3.16
587 2431 9.422681 TCATAGATAAAAGCTAGAGTACCACTT 57.577 33.333 0.00 0.00 0.00 3.16
588 2432 8.998277 TCATAGATAAAAGCTAGAGTACCACT 57.002 34.615 0.00 0.00 0.00 4.00
589 2433 9.465985 GTTCATAGATAAAAGCTAGAGTACCAC 57.534 37.037 0.00 0.00 0.00 4.16
590 2434 9.422681 AGTTCATAGATAAAAGCTAGAGTACCA 57.577 33.333 0.00 0.00 0.00 3.25
594 2438 9.593134 CACAAGTTCATAGATAAAAGCTAGAGT 57.407 33.333 0.00 0.00 0.00 3.24
595 2439 9.593134 ACACAAGTTCATAGATAAAAGCTAGAG 57.407 33.333 0.00 0.00 0.00 2.43
596 2440 9.587772 GACACAAGTTCATAGATAAAAGCTAGA 57.412 33.333 0.00 0.00 0.00 2.43
597 2441 9.371136 TGACACAAGTTCATAGATAAAAGCTAG 57.629 33.333 0.00 0.00 0.00 3.42
598 2442 9.371136 CTGACACAAGTTCATAGATAAAAGCTA 57.629 33.333 0.00 0.00 0.00 3.32
599 2443 7.880195 ACTGACACAAGTTCATAGATAAAAGCT 59.120 33.333 0.00 0.00 0.00 3.74
600 2444 7.959651 CACTGACACAAGTTCATAGATAAAAGC 59.040 37.037 0.00 0.00 0.00 3.51
601 2445 8.446273 CCACTGACACAAGTTCATAGATAAAAG 58.554 37.037 0.00 0.00 0.00 2.27
602 2446 7.936847 ACCACTGACACAAGTTCATAGATAAAA 59.063 33.333 0.00 0.00 0.00 1.52
603 2447 7.387673 CACCACTGACACAAGTTCATAGATAAA 59.612 37.037 0.00 0.00 0.00 1.40
604 2448 6.873605 CACCACTGACACAAGTTCATAGATAA 59.126 38.462 0.00 0.00 0.00 1.75
605 2449 6.398095 CACCACTGACACAAGTTCATAGATA 58.602 40.000 0.00 0.00 0.00 1.98
607 2451 4.503123 CCACCACTGACACAAGTTCATAGA 60.503 45.833 0.00 0.00 0.00 1.98
613 2457 2.092429 ACATCCACCACTGACACAAGTT 60.092 45.455 0.00 0.00 0.00 2.66
614 2458 1.490490 ACATCCACCACTGACACAAGT 59.510 47.619 0.00 0.00 0.00 3.16
615 2459 1.875514 CACATCCACCACTGACACAAG 59.124 52.381 0.00 0.00 0.00 3.16
616 2460 1.211703 ACACATCCACCACTGACACAA 59.788 47.619 0.00 0.00 0.00 3.33
618 2462 2.037251 AGTACACATCCACCACTGACAC 59.963 50.000 0.00 0.00 0.00 3.67
631 2475 2.350772 GCAAAGCGAGCAAAGTACACAT 60.351 45.455 0.00 0.00 0.00 3.21
809 2674 2.092753 CCAGTAATCCTCATGCAGGTGT 60.093 50.000 0.00 4.01 43.95 4.16
810 2675 2.171237 TCCAGTAATCCTCATGCAGGTG 59.829 50.000 0.00 0.00 43.95 4.00
907 2788 2.496871 AGATCAGGAGAGAGCAACACAG 59.503 50.000 0.00 0.00 0.00 3.66
925 2838 2.724672 TGGCCTCCTCCTACTGATAGAT 59.275 50.000 3.32 0.00 0.00 1.98
926 2839 2.109128 CTGGCCTCCTCCTACTGATAGA 59.891 54.545 3.32 0.00 0.00 1.98
929 2842 0.937441 TCTGGCCTCCTCCTACTGAT 59.063 55.000 3.32 0.00 0.00 2.90
943 2856 2.127251 CGTGCCTTTTCTTTTTCTGGC 58.873 47.619 0.00 0.00 40.62 4.85
986 2899 1.364901 CCCATGAATGAATGCGGCC 59.635 57.895 0.00 0.00 0.00 6.13
1012 2925 1.878522 CGACGGAATTGCCTCCTCG 60.879 63.158 0.00 0.00 33.18 4.63
1066 2981 2.554344 CGGATAAGGGAGAGAGAGAGGG 60.554 59.091 0.00 0.00 0.00 4.30
1067 2982 2.554344 CCGGATAAGGGAGAGAGAGAGG 60.554 59.091 0.00 0.00 0.00 3.69
1068 2983 2.790433 CCGGATAAGGGAGAGAGAGAG 58.210 57.143 0.00 0.00 0.00 3.20
1069 2984 1.202952 GCCGGATAAGGGAGAGAGAGA 60.203 57.143 5.05 0.00 0.00 3.10
1070 2985 1.203001 AGCCGGATAAGGGAGAGAGAG 60.203 57.143 5.05 0.00 0.00 3.20
1071 2986 0.854218 AGCCGGATAAGGGAGAGAGA 59.146 55.000 5.05 0.00 0.00 3.10
1148 3077 2.371259 GGTGGGGAGAAGGAGGAGC 61.371 68.421 0.00 0.00 0.00 4.70
1201 3133 4.452733 GTGACGGCGAGAAGGGGG 62.453 72.222 16.62 0.00 0.00 5.40
1902 3852 1.874019 CTTGTCGACGATGGCGAGG 60.874 63.158 11.62 0.00 41.64 4.63
2283 4233 9.708092 AAGTATGATGAATGTAGTGAGATGATG 57.292 33.333 0.00 0.00 0.00 3.07
2334 4285 4.261363 GCCCTCTGAAGAACAAAACAGAAG 60.261 45.833 0.00 0.00 38.60 2.85
2425 4383 5.323371 TGTAGATGACACGATGATCAACA 57.677 39.130 0.00 0.00 31.20 3.33
2480 4438 8.415553 TGTAATCAATCAACCAATCAATCCATC 58.584 33.333 0.00 0.00 0.00 3.51
2481 4439 8.308851 TGTAATCAATCAACCAATCAATCCAT 57.691 30.769 0.00 0.00 0.00 3.41
2482 4440 7.715266 TGTAATCAATCAACCAATCAATCCA 57.285 32.000 0.00 0.00 0.00 3.41
2483 4441 8.415553 TCATGTAATCAATCAACCAATCAATCC 58.584 33.333 0.00 0.00 0.00 3.01
2524 4482 4.919754 GCATTGTTCTTCAACTAGCAAAGG 59.080 41.667 0.00 0.00 38.97 3.11
2640 4598 4.357996 GCAAGATTAAGAAGATGCAAGGC 58.642 43.478 0.00 0.00 34.10 4.35
2679 4637 2.731968 CGGATGTTATGTTGTTGCAGCC 60.732 50.000 0.00 0.00 32.86 4.85
2687 4645 5.601662 AGATAGTCACCGGATGTTATGTTG 58.398 41.667 9.46 0.00 0.00 3.33
2700 4658 1.479323 TGCACCGGTAAGATAGTCACC 59.521 52.381 6.87 0.00 0.00 4.02
2715 4684 2.935849 TCGATGAATATGTGTGTGCACC 59.064 45.455 15.69 6.37 44.65 5.01
2716 4685 4.598406 TTCGATGAATATGTGTGTGCAC 57.402 40.909 10.75 10.75 45.44 4.57
2735 4727 2.790387 CCGCTGCTGCTTCTTATTTTC 58.210 47.619 14.03 0.00 36.97 2.29
2743 4735 1.804326 CATTTGCCGCTGCTGCTTC 60.804 57.895 16.81 5.60 38.71 3.86
2747 4739 1.007038 ACAACATTTGCCGCTGCTG 60.007 52.632 0.70 0.00 38.71 4.41
2754 4746 0.392336 TTCCTGCCACAACATTTGCC 59.608 50.000 0.00 0.00 0.00 4.52
2755 4747 1.787012 CTTCCTGCCACAACATTTGC 58.213 50.000 0.00 0.00 0.00 3.68
2774 4766 3.302365 TTTACTGAATGCCTTTGCTGC 57.698 42.857 0.00 0.00 38.71 5.25
2827 4819 2.276740 CCCCTCCCTGCACCATTC 59.723 66.667 0.00 0.00 0.00 2.67
2936 4928 0.397941 TCTTGGCACAGGTGGAAGAG 59.602 55.000 1.10 0.00 42.39 2.85
2957 4949 5.783100 TTCGTTTTCGTTACTGAACTTGT 57.217 34.783 0.00 0.00 44.46 3.16
3033 5025 3.576550 ACGGCAATCAAACCCATTTTACT 59.423 39.130 0.00 0.00 0.00 2.24
3114 5141 3.692593 AGTTGCACGGAGTTACTGTTTTT 59.307 39.130 0.00 0.00 41.61 1.94
3115 5142 3.275999 AGTTGCACGGAGTTACTGTTTT 58.724 40.909 0.00 0.00 41.61 2.43
3116 5143 2.914059 AGTTGCACGGAGTTACTGTTT 58.086 42.857 0.00 0.00 41.61 2.83
3117 5144 2.614829 AGTTGCACGGAGTTACTGTT 57.385 45.000 0.00 0.00 41.61 3.16
3119 5146 2.223377 GGAAAGTTGCACGGAGTTACTG 59.777 50.000 0.00 0.00 41.61 2.74
3120 5147 2.158871 TGGAAAGTTGCACGGAGTTACT 60.159 45.455 0.00 0.00 41.61 2.24
3121 5148 2.215196 TGGAAAGTTGCACGGAGTTAC 58.785 47.619 0.00 0.00 41.61 2.50
3122 5149 2.623878 TGGAAAGTTGCACGGAGTTA 57.376 45.000 0.00 0.00 41.61 2.24
3123 5150 1.880027 GATGGAAAGTTGCACGGAGTT 59.120 47.619 0.00 0.00 41.61 3.01
3125 5152 1.522668 TGATGGAAAGTTGCACGGAG 58.477 50.000 0.00 0.00 0.00 4.63
3126 5153 2.198827 ATGATGGAAAGTTGCACGGA 57.801 45.000 0.00 0.00 0.00 4.69
3127 5154 4.433186 TTAATGATGGAAAGTTGCACGG 57.567 40.909 0.00 0.00 0.00 4.94
3128 5155 6.949578 ATTTTAATGATGGAAAGTTGCACG 57.050 33.333 0.00 0.00 0.00 5.34
3131 5158 7.903995 TCCAATTTTAATGATGGAAAGTTGC 57.096 32.000 2.17 0.00 38.95 4.17
3171 5202 6.611381 GCTTAATTATGCATCCGCTGATTTA 58.389 36.000 16.25 0.00 39.64 1.40
3182 5213 5.882000 TCTGATATGCCGCTTAATTATGCAT 59.118 36.000 19.79 16.29 44.28 3.96
3195 5226 6.868339 TCTGTAACAACATATCTGATATGCCG 59.132 38.462 28.81 23.17 45.05 5.69
3215 5246 6.833041 TGTTGTGGAAGAAGGTATTTCTGTA 58.167 36.000 0.00 0.00 45.41 2.74
3222 5253 5.445964 ACACTTTGTTGTGGAAGAAGGTAT 58.554 37.500 0.00 0.00 41.84 2.73


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

AutoCloner maintained by Alex Coulton.