Multiple sequence alignment - TraesCS6D01G402200

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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 TraesCS6D01G402200 chr6D 100.000 2326 0 0 1 2326 470854682 470857007 0.000000e+00 4296
1 TraesCS6D01G402200 chr6D 85.917 1477 174 18 360 1826 470816482 470817934 0.000000e+00 1544
2 TraesCS6D01G402200 chr6D 87.162 148 18 1 44 190 470816346 470816493 1.430000e-37 167
3 TraesCS6D01G402200 chr6A 94.584 1717 88 4 360 2075 615670836 615672548 0.000000e+00 2651
4 TraesCS6D01G402200 chr6A 85.348 1754 199 25 360 2093 615632978 615634693 0.000000e+00 1762
5 TraesCS6D01G402200 chr6A 97.340 188 5 0 1 188 615670658 615670845 1.040000e-83 320
6 TraesCS6D01G402200 chr6A 96.237 186 7 0 2072 2257 615672860 615673045 2.900000e-79 305
7 TraesCS6D01G402200 chr6A 90.857 175 9 4 192 359 200352656 200352482 6.470000e-56 228
8 TraesCS6D01G402200 chr6A 81.743 241 22 7 2029 2247 615634694 615634934 5.110000e-42 182
9 TraesCS6D01G402200 chr6A 92.958 71 5 0 2256 2326 615673097 615673167 1.140000e-18 104
10 TraesCS6D01G402200 chr3D 98.225 169 3 0 191 359 434157564 434157396 1.750000e-76 296
11 TraesCS6D01G402200 chr5D 95.135 185 7 2 174 357 537679462 537679645 8.130000e-75 291
12 TraesCS6D01G402200 chr2D 98.726 157 2 0 192 348 637017312 637017156 1.760000e-71 279
13 TraesCS6D01G402200 chr1D 95.833 168 6 1 192 359 323617895 323617729 1.060000e-68 270
14 TraesCS6D01G402200 chr7A 92.614 176 6 6 190 359 150053416 150053242 1.790000e-61 246
15 TraesCS6D01G402200 chr1B 92.486 173 5 5 193 359 538422086 538421916 8.310000e-60 241
16 TraesCS6D01G402200 chr2A 91.765 170 9 5 192 356 67094107 67094276 5.000000e-57 231
17 TraesCS6D01G402200 chr3B 91.279 172 9 3 193 359 109442307 109442137 1.800000e-56 230


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 TraesCS6D01G402200 chr6D 470854682 470857007 2325 False 4296.0 4296 100.00000 1 2326 1 chr6D.!!$F1 2325
1 TraesCS6D01G402200 chr6D 470816346 470817934 1588 False 855.5 1544 86.53950 44 1826 2 chr6D.!!$F2 1782
2 TraesCS6D01G402200 chr6A 615632978 615634934 1956 False 972.0 1762 83.54550 360 2247 2 chr6A.!!$F1 1887
3 TraesCS6D01G402200 chr6A 615670658 615673167 2509 False 845.0 2651 95.27975 1 2326 4 chr6A.!!$F2 2325

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
293 295 0.397941 TGTTGGGAGAGCAACCAGAG 59.602 55.0 0.0 0.0 38.16 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1656 1674 1.543429 GCAGCACAACACTTCTAGGGT 60.543 52.381 0.0 0.0 29.33 4.34 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
121 123 4.494410 GCGGTATTGATTTTGACGTAAAGC 59.506 41.667 0.00 0.00 0.00 3.51
190 192 9.394477 CACAAATGCAAGATATATCAACATCAG 57.606 33.333 15.08 11.74 0.00 2.90
191 193 9.128404 ACAAATGCAAGATATATCAACATCAGT 57.872 29.630 15.08 12.23 0.00 3.41
192 194 9.961265 CAAATGCAAGATATATCAACATCAGTT 57.039 29.630 15.08 7.61 38.88 3.16
222 224 8.634335 TTACCATAAAACAGTAGGGTAAAACC 57.366 34.615 6.14 0.00 43.71 3.27
235 237 4.075963 GGTAAAACCCTACTGTGTGTCA 57.924 45.455 0.00 0.00 30.04 3.58
236 238 4.648651 GGTAAAACCCTACTGTGTGTCAT 58.351 43.478 0.00 0.00 30.04 3.06
237 239 5.067954 GGTAAAACCCTACTGTGTGTCATT 58.932 41.667 0.00 0.00 30.04 2.57
238 240 5.533528 GGTAAAACCCTACTGTGTGTCATTT 59.466 40.000 0.00 0.00 30.04 2.32
239 241 6.040054 GGTAAAACCCTACTGTGTGTCATTTT 59.960 38.462 0.00 0.00 30.04 1.82
240 242 5.767816 AAACCCTACTGTGTGTCATTTTC 57.232 39.130 0.00 0.00 0.00 2.29
241 243 4.431416 ACCCTACTGTGTGTCATTTTCA 57.569 40.909 0.00 0.00 0.00 2.69
242 244 4.985538 ACCCTACTGTGTGTCATTTTCAT 58.014 39.130 0.00 0.00 0.00 2.57
243 245 5.385198 ACCCTACTGTGTGTCATTTTCATT 58.615 37.500 0.00 0.00 0.00 2.57
244 246 6.539173 ACCCTACTGTGTGTCATTTTCATTA 58.461 36.000 0.00 0.00 0.00 1.90
245 247 7.175104 ACCCTACTGTGTGTCATTTTCATTAT 58.825 34.615 0.00 0.00 0.00 1.28
246 248 8.325787 ACCCTACTGTGTGTCATTTTCATTATA 58.674 33.333 0.00 0.00 0.00 0.98
247 249 9.173021 CCCTACTGTGTGTCATTTTCATTATAA 57.827 33.333 0.00 0.00 0.00 0.98
273 275 8.574251 TGAATAAAAGTGCATAGTACAATGGT 57.426 30.769 0.00 0.00 0.00 3.55
274 276 9.019656 TGAATAAAAGTGCATAGTACAATGGTT 57.980 29.630 0.00 0.00 0.00 3.67
275 277 9.289303 GAATAAAAGTGCATAGTACAATGGTTG 57.711 33.333 0.00 0.00 0.00 3.77
277 279 6.648879 AAAGTGCATAGTACAATGGTTGTT 57.351 33.333 0.20 0.00 42.22 2.83
278 280 5.627499 AGTGCATAGTACAATGGTTGTTG 57.373 39.130 0.20 0.00 42.22 3.33
279 281 4.458989 AGTGCATAGTACAATGGTTGTTGG 59.541 41.667 0.20 0.00 42.22 3.77
280 282 3.761218 TGCATAGTACAATGGTTGTTGGG 59.239 43.478 0.20 0.00 42.22 4.12
281 283 4.013728 GCATAGTACAATGGTTGTTGGGA 58.986 43.478 0.20 0.00 42.22 4.37
282 284 4.096382 GCATAGTACAATGGTTGTTGGGAG 59.904 45.833 0.20 0.00 42.22 4.30
283 285 5.496556 CATAGTACAATGGTTGTTGGGAGA 58.503 41.667 0.20 0.00 42.22 3.71
284 286 4.021102 AGTACAATGGTTGTTGGGAGAG 57.979 45.455 0.20 0.00 42.22 3.20
285 287 1.620822 ACAATGGTTGTTGGGAGAGC 58.379 50.000 0.00 0.00 42.22 4.09
286 288 1.133513 ACAATGGTTGTTGGGAGAGCA 60.134 47.619 0.00 0.00 42.22 4.26
287 289 1.962807 CAATGGTTGTTGGGAGAGCAA 59.037 47.619 0.00 0.00 0.00 3.91
288 290 1.620822 ATGGTTGTTGGGAGAGCAAC 58.379 50.000 0.00 0.00 41.02 4.17
290 292 3.109847 GTTGTTGGGAGAGCAACCA 57.890 52.632 0.00 0.00 37.20 3.67
291 293 0.954452 GTTGTTGGGAGAGCAACCAG 59.046 55.000 0.00 0.00 38.16 4.00
292 294 0.843309 TTGTTGGGAGAGCAACCAGA 59.157 50.000 0.00 0.00 38.16 3.86
293 295 0.397941 TGTTGGGAGAGCAACCAGAG 59.602 55.000 0.00 0.00 38.16 3.35
294 296 0.398318 GTTGGGAGAGCAACCAGAGT 59.602 55.000 0.00 0.00 38.16 3.24
295 297 0.397941 TTGGGAGAGCAACCAGAGTG 59.602 55.000 0.00 0.00 38.16 3.51
296 298 1.298014 GGGAGAGCAACCAGAGTGG 59.702 63.158 0.00 0.00 45.02 4.00
297 299 1.194781 GGGAGAGCAACCAGAGTGGA 61.195 60.000 0.00 0.00 40.96 4.02
298 300 0.687354 GGAGAGCAACCAGAGTGGAA 59.313 55.000 0.00 0.00 40.96 3.53
299 301 1.338579 GGAGAGCAACCAGAGTGGAAG 60.339 57.143 0.00 0.00 40.96 3.46
300 302 1.620819 GAGAGCAACCAGAGTGGAAGA 59.379 52.381 0.00 0.00 40.96 2.87
301 303 1.622811 AGAGCAACCAGAGTGGAAGAG 59.377 52.381 0.00 0.00 40.96 2.85
302 304 1.346068 GAGCAACCAGAGTGGAAGAGT 59.654 52.381 0.00 0.00 40.96 3.24
303 305 1.771255 AGCAACCAGAGTGGAAGAGTT 59.229 47.619 0.00 0.00 40.96 3.01
304 306 2.173569 AGCAACCAGAGTGGAAGAGTTT 59.826 45.455 0.00 0.00 40.96 2.66
305 307 3.391296 AGCAACCAGAGTGGAAGAGTTTA 59.609 43.478 0.00 0.00 40.96 2.01
306 308 3.498777 GCAACCAGAGTGGAAGAGTTTAC 59.501 47.826 0.00 0.00 40.96 2.01
307 309 4.703897 CAACCAGAGTGGAAGAGTTTACA 58.296 43.478 0.00 0.00 40.96 2.41
308 310 4.608948 ACCAGAGTGGAAGAGTTTACAG 57.391 45.455 0.00 0.00 40.96 2.74
309 311 3.967987 ACCAGAGTGGAAGAGTTTACAGT 59.032 43.478 0.00 0.00 40.96 3.55
310 312 5.145564 ACCAGAGTGGAAGAGTTTACAGTA 58.854 41.667 0.00 0.00 40.96 2.74
311 313 5.601313 ACCAGAGTGGAAGAGTTTACAGTAA 59.399 40.000 0.00 0.00 40.96 2.24
312 314 6.099269 ACCAGAGTGGAAGAGTTTACAGTAAA 59.901 38.462 1.26 1.26 40.96 2.01
313 315 6.647067 CCAGAGTGGAAGAGTTTACAGTAAAG 59.353 42.308 5.96 0.00 40.96 1.85
314 316 7.434492 CAGAGTGGAAGAGTTTACAGTAAAGA 58.566 38.462 5.96 0.00 30.69 2.52
315 317 7.926555 CAGAGTGGAAGAGTTTACAGTAAAGAA 59.073 37.037 5.96 0.00 30.69 2.52
316 318 8.483758 AGAGTGGAAGAGTTTACAGTAAAGAAA 58.516 33.333 5.96 0.00 30.69 2.52
317 319 9.106070 GAGTGGAAGAGTTTACAGTAAAGAAAA 57.894 33.333 5.96 0.00 30.69 2.29
318 320 9.110502 AGTGGAAGAGTTTACAGTAAAGAAAAG 57.889 33.333 5.96 0.00 28.64 2.27
319 321 9.106070 GTGGAAGAGTTTACAGTAAAGAAAAGA 57.894 33.333 5.96 0.00 0.00 2.52
320 322 9.675464 TGGAAGAGTTTACAGTAAAGAAAAGAA 57.325 29.630 5.96 0.00 0.00 2.52
371 373 8.667076 TGTTGTCTATCCAATATCAACATCAG 57.333 34.615 0.00 0.00 39.65 2.90
435 438 7.452880 TCTATGCAAATATTATTGTGCCTCC 57.547 36.000 7.25 0.00 36.12 4.30
713 716 9.751542 ATAGACTGACTCGGAAATTAATAGTTG 57.248 33.333 0.00 0.00 0.00 3.16
896 899 7.828508 ATATTTGTGCAAGATATGGATGTGT 57.171 32.000 0.00 0.00 0.00 3.72
1014 1017 2.173356 TCTCCTCATGGCACCCATAAAG 59.827 50.000 0.00 0.00 43.15 1.85
1037 1040 0.469144 GGAAACACAAGGAGGGCCAA 60.469 55.000 6.18 0.00 36.29 4.52
1111 1114 0.391661 CCATGCACGAGGTAAGCACT 60.392 55.000 0.00 0.00 41.60 4.40
1160 1163 9.846248 ATAATCTTGTCTTGTTGAATTGCTAAC 57.154 29.630 0.00 0.00 0.00 2.34
1249 1252 1.020437 GAGCCTAGTTGCATGGAAGC 58.980 55.000 0.00 0.00 0.00 3.86
1253 1256 2.372264 CCTAGTTGCATGGAAGCATGT 58.628 47.619 0.00 0.00 45.19 3.21
1401 1404 4.694982 TGATCGTGCTTGTGTGATGTAATT 59.305 37.500 0.00 0.00 0.00 1.40
1434 1437 2.309755 ACTCCTTGAATGGAATGAGCCA 59.690 45.455 0.00 0.00 43.23 4.75
1549 1557 9.632638 TTTCAATCCAACCCAATGATTTTAAAA 57.367 25.926 2.51 2.51 0.00 1.52
1632 1650 2.939460 AATTTCCGCCAAAATCCGAG 57.061 45.000 0.00 0.00 0.00 4.63
1656 1674 2.824936 CTCAACATTGTGGCCATGGTTA 59.175 45.455 9.72 0.00 0.00 2.85
1685 1703 1.078848 GTTGTGCTGCCTCTCGGAT 60.079 57.895 0.00 0.00 0.00 4.18
1702 1721 2.724174 CGGATGCGAGAAAAACCAAAAC 59.276 45.455 0.00 0.00 0.00 2.43
1745 1764 0.464373 AGTTGGCACCATAGCATCCG 60.464 55.000 0.00 0.00 35.83 4.18
1785 1804 8.150296 TGATCTCTGAAGAAATTAAGTGTGACA 58.850 33.333 0.00 0.00 34.49 3.58
1886 1905 3.845178 TGAACTGGCTTACATACACTCG 58.155 45.455 0.00 0.00 0.00 4.18
1909 1928 6.043358 TCGATGGTGGTTGGGTATAATCATTA 59.957 38.462 0.00 0.00 0.00 1.90
1971 1994 3.547746 GTCTACCCAAACCAACACTCAA 58.452 45.455 0.00 0.00 0.00 3.02
1987 2010 4.776837 ACACTCAAGATCACTCTTCTCCAT 59.223 41.667 0.00 0.00 39.78 3.41
2015 2038 3.507162 TTATGGGGATCGATGCATTGT 57.493 42.857 19.14 4.15 0.00 2.71
2041 2064 2.443887 AGCTTTCATTGCGCAAACAT 57.556 40.000 28.81 8.12 35.28 2.71
2111 2449 9.197306 ACACGATAGGTAATAATATAGCCATGA 57.803 33.333 0.00 0.00 43.77 3.07
2151 2499 2.102925 TGTTGTCTCATGCACTCACTCA 59.897 45.455 0.00 0.00 0.00 3.41
2154 2502 2.564062 TGTCTCATGCACTCACTCATGA 59.436 45.455 0.00 0.00 44.62 3.07
2302 2715 6.326843 AGAAATCCACACCCCTAGTAATCTAC 59.673 42.308 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 7.712205 GTGGAATATTTATTGGCTCTTGCATTT 59.288 33.333 0.00 0.00 41.91 2.32
151 153 4.626042 TGCATTTGTGTTCCATTTACACC 58.374 39.130 0.00 0.00 44.05 4.16
196 198 9.076781 GGTTTTACCCTACTGTTTTATGGTAAA 57.923 33.333 7.41 7.41 43.09 2.01
197 199 8.634335 GGTTTTACCCTACTGTTTTATGGTAA 57.366 34.615 0.00 0.00 36.75 2.85
214 216 4.075963 TGACACACAGTAGGGTTTTACC 57.924 45.455 0.00 0.00 37.60 2.85
215 217 6.628919 AAATGACACACAGTAGGGTTTTAC 57.371 37.500 0.00 0.00 0.00 2.01
216 218 6.829298 TGAAAATGACACACAGTAGGGTTTTA 59.171 34.615 0.00 0.00 0.00 1.52
217 219 5.654650 TGAAAATGACACACAGTAGGGTTTT 59.345 36.000 0.00 0.00 0.00 2.43
218 220 5.197451 TGAAAATGACACACAGTAGGGTTT 58.803 37.500 0.00 0.00 0.00 3.27
219 221 4.787551 TGAAAATGACACACAGTAGGGTT 58.212 39.130 0.00 0.00 0.00 4.11
220 222 4.431416 TGAAAATGACACACAGTAGGGT 57.569 40.909 0.00 0.00 0.00 4.34
221 223 5.964958 AATGAAAATGACACACAGTAGGG 57.035 39.130 0.00 0.00 0.00 3.53
247 249 9.189156 ACCATTGTACTATGCACTTTTATTCAT 57.811 29.630 11.30 0.00 0.00 2.57
248 250 8.574251 ACCATTGTACTATGCACTTTTATTCA 57.426 30.769 11.30 0.00 0.00 2.57
249 251 9.289303 CAACCATTGTACTATGCACTTTTATTC 57.711 33.333 11.30 0.00 0.00 1.75
250 252 8.802267 ACAACCATTGTACTATGCACTTTTATT 58.198 29.630 11.30 0.00 43.27 1.40
251 253 8.348285 ACAACCATTGTACTATGCACTTTTAT 57.652 30.769 11.30 0.00 43.27 1.40
252 254 7.753309 ACAACCATTGTACTATGCACTTTTA 57.247 32.000 11.30 0.00 43.27 1.52
253 255 6.648879 ACAACCATTGTACTATGCACTTTT 57.351 33.333 11.30 0.00 43.27 2.27
254 256 6.446318 CAACAACCATTGTACTATGCACTTT 58.554 36.000 11.30 0.62 44.59 2.66
255 257 5.048083 CCAACAACCATTGTACTATGCACTT 60.048 40.000 11.30 0.82 44.59 3.16
256 258 4.458989 CCAACAACCATTGTACTATGCACT 59.541 41.667 11.30 0.00 44.59 4.40
257 259 4.380444 CCCAACAACCATTGTACTATGCAC 60.380 45.833 11.30 0.00 44.59 4.57
258 260 3.761218 CCCAACAACCATTGTACTATGCA 59.239 43.478 11.30 0.00 44.59 3.96
259 261 4.013728 TCCCAACAACCATTGTACTATGC 58.986 43.478 11.30 0.00 44.59 3.14
260 262 5.496556 TCTCCCAACAACCATTGTACTATG 58.503 41.667 9.98 9.98 44.59 2.23
261 263 5.745227 CTCTCCCAACAACCATTGTACTAT 58.255 41.667 0.00 0.00 44.59 2.12
262 264 4.564821 GCTCTCCCAACAACCATTGTACTA 60.565 45.833 0.00 0.00 44.59 1.82
263 265 3.810743 GCTCTCCCAACAACCATTGTACT 60.811 47.826 0.00 0.00 44.59 2.73
264 266 2.488153 GCTCTCCCAACAACCATTGTAC 59.512 50.000 0.00 0.00 44.59 2.90
265 267 2.107378 TGCTCTCCCAACAACCATTGTA 59.893 45.455 0.00 0.00 44.59 2.41
267 269 1.619654 TGCTCTCCCAACAACCATTG 58.380 50.000 0.00 0.00 0.00 2.82
268 270 1.963515 GTTGCTCTCCCAACAACCATT 59.036 47.619 0.57 0.00 43.45 3.16
269 271 1.620822 GTTGCTCTCCCAACAACCAT 58.379 50.000 0.57 0.00 43.45 3.55
270 272 3.109847 GTTGCTCTCCCAACAACCA 57.890 52.632 0.57 0.00 43.45 3.67
272 274 0.954452 CTGGTTGCTCTCCCAACAAC 59.046 55.000 7.26 0.00 45.25 3.32
273 275 0.843309 TCTGGTTGCTCTCCCAACAA 59.157 50.000 7.26 0.00 45.25 2.83
274 276 0.397941 CTCTGGTTGCTCTCCCAACA 59.602 55.000 7.26 0.00 45.25 3.33
275 277 0.398318 ACTCTGGTTGCTCTCCCAAC 59.602 55.000 0.00 0.00 43.29 3.77
276 278 0.397941 CACTCTGGTTGCTCTCCCAA 59.602 55.000 0.00 0.00 0.00 4.12
277 279 1.483595 CCACTCTGGTTGCTCTCCCA 61.484 60.000 0.00 0.00 31.35 4.37
278 280 1.194781 TCCACTCTGGTTGCTCTCCC 61.195 60.000 0.00 0.00 39.03 4.30
279 281 0.687354 TTCCACTCTGGTTGCTCTCC 59.313 55.000 0.00 0.00 39.03 3.71
280 282 1.620819 TCTTCCACTCTGGTTGCTCTC 59.379 52.381 0.00 0.00 39.03 3.20
281 283 1.622811 CTCTTCCACTCTGGTTGCTCT 59.377 52.381 0.00 0.00 39.03 4.09
282 284 1.346068 ACTCTTCCACTCTGGTTGCTC 59.654 52.381 0.00 0.00 39.03 4.26
283 285 1.428869 ACTCTTCCACTCTGGTTGCT 58.571 50.000 0.00 0.00 39.03 3.91
284 286 2.262423 AACTCTTCCACTCTGGTTGC 57.738 50.000 0.00 0.00 39.03 4.17
285 287 4.703897 TGTAAACTCTTCCACTCTGGTTG 58.296 43.478 0.00 0.00 39.03 3.77
286 288 4.409247 ACTGTAAACTCTTCCACTCTGGTT 59.591 41.667 0.00 0.00 39.03 3.67
287 289 3.967987 ACTGTAAACTCTTCCACTCTGGT 59.032 43.478 0.00 0.00 39.03 4.00
288 290 4.608948 ACTGTAAACTCTTCCACTCTGG 57.391 45.455 0.00 0.00 39.43 3.86
289 291 7.434492 TCTTTACTGTAAACTCTTCCACTCTG 58.566 38.462 8.84 0.00 0.00 3.35
290 292 7.598759 TCTTTACTGTAAACTCTTCCACTCT 57.401 36.000 8.84 0.00 0.00 3.24
291 293 8.658499 TTTCTTTACTGTAAACTCTTCCACTC 57.342 34.615 8.84 0.00 0.00 3.51
292 294 9.110502 CTTTTCTTTACTGTAAACTCTTCCACT 57.889 33.333 8.84 0.00 0.00 4.00
293 295 9.106070 TCTTTTCTTTACTGTAAACTCTTCCAC 57.894 33.333 8.84 0.00 0.00 4.02
294 296 9.675464 TTCTTTTCTTTACTGTAAACTCTTCCA 57.325 29.630 8.84 0.00 0.00 3.53
341 343 9.460019 TGTTGATATTGGATAGACAACATTTGA 57.540 29.630 0.00 0.00 39.08 2.69
344 346 9.631257 TGATGTTGATATTGGATAGACAACATT 57.369 29.630 22.03 13.96 45.35 2.71
345 347 9.281371 CTGATGTTGATATTGGATAGACAACAT 57.719 33.333 21.69 21.69 46.44 2.71
346 348 8.267183 ACTGATGTTGATATTGGATAGACAACA 58.733 33.333 17.23 17.23 43.18 3.33
347 349 8.668510 ACTGATGTTGATATTGGATAGACAAC 57.331 34.615 0.00 0.00 36.95 3.32
353 355 9.559732 CCACTTAACTGATGTTGATATTGGATA 57.440 33.333 0.00 0.00 37.59 2.59
354 356 8.274322 TCCACTTAACTGATGTTGATATTGGAT 58.726 33.333 0.00 0.00 37.59 3.41
355 357 7.629157 TCCACTTAACTGATGTTGATATTGGA 58.371 34.615 0.00 0.00 37.59 3.53
356 358 7.864108 TCCACTTAACTGATGTTGATATTGG 57.136 36.000 0.00 0.00 37.59 3.16
370 372 9.125026 CTTCCTGCATTAATTATCCACTTAACT 57.875 33.333 0.00 0.00 0.00 2.24
371 373 7.862873 GCTTCCTGCATTAATTATCCACTTAAC 59.137 37.037 0.00 0.00 42.31 2.01
690 693 6.535508 AGCAACTATTAATTTCCGAGTCAGTC 59.464 38.462 0.00 0.00 0.00 3.51
725 728 4.530553 TGCCACACAAATCTTCCTAGTCTA 59.469 41.667 0.00 0.00 0.00 2.59
727 730 3.674997 TGCCACACAAATCTTCCTAGTC 58.325 45.455 0.00 0.00 0.00 2.59
729 732 5.416952 AGAAATGCCACACAAATCTTCCTAG 59.583 40.000 0.00 0.00 0.00 3.02
732 735 4.525912 AGAAATGCCACACAAATCTTCC 57.474 40.909 0.00 0.00 0.00 3.46
942 945 3.146066 TCCTTGTGTTCTTATGGTGTGC 58.854 45.455 0.00 0.00 0.00 4.57
1014 1017 0.961753 CCCTCCTTGTGTTTCCTTGC 59.038 55.000 0.00 0.00 0.00 4.01
1037 1040 2.108952 AGGACAAGGAAAGCAATGGACT 59.891 45.455 0.00 0.00 0.00 3.85
1111 1114 9.747898 TTATTCTAGATTAGCCCTTTCAAACAA 57.252 29.630 0.00 0.00 0.00 2.83
1160 1163 7.112565 GCAGATGCAATAAAGTTGTATTCATCG 59.887 37.037 0.00 0.00 41.59 3.84
1362 1365 2.285220 CGATCAAGATTCATTCGGCGTT 59.715 45.455 6.85 0.00 0.00 4.84
1366 1369 2.868583 AGCACGATCAAGATTCATTCGG 59.131 45.455 0.00 0.00 34.28 4.30
1401 1404 5.414454 CCATTCAAGGAGTTTATTCACCGAA 59.586 40.000 0.00 0.00 0.00 4.30
1563 1571 7.283329 AGACCCATACAATGAAATCTAGGAAC 58.717 38.462 0.00 0.00 0.00 3.62
1656 1674 1.543429 GCAGCACAACACTTCTAGGGT 60.543 52.381 0.00 0.00 29.33 4.34
1685 1703 2.161808 TGACGTTTTGGTTTTTCTCGCA 59.838 40.909 0.00 0.00 0.00 5.10
1702 1721 7.492669 ACTCTATGTTTCATGGAGTTATTGACG 59.507 37.037 18.28 0.00 36.64 4.35
1745 1764 6.872628 TCAGAGATCATATCAAATTGCACC 57.127 37.500 0.00 0.00 0.00 5.01
1785 1804 6.477360 CGCCCATTTTGTTACTAACTGTTTTT 59.523 34.615 0.00 0.00 0.00 1.94
1886 1905 7.122650 CCATAATGATTATACCCAACCACCATC 59.877 40.741 0.00 0.00 0.00 3.51
1971 1994 7.615039 AATGATGTATGGAGAAGAGTGATCT 57.385 36.000 0.00 0.00 0.00 2.75
1987 2010 5.185454 GCATCGATCCCCATAAATGATGTA 58.815 41.667 0.00 0.00 35.40 2.29
2015 2038 3.078097 TGCGCAATGAAAGCTTTACCTA 58.922 40.909 12.68 0.00 0.00 3.08
2151 2499 2.886523 CACATTACGGGGCAATGATCAT 59.113 45.455 1.18 1.18 36.95 2.45
2154 2502 2.023673 CACACATTACGGGGCAATGAT 58.976 47.619 2.66 0.00 36.95 2.45
2257 2617 9.903682 GATTTCTTCATGATTTCTTGACAAAGA 57.096 29.630 0.00 0.00 40.76 2.52
2267 2680 5.394553 GGGGTGTGGATTTCTTCATGATTTC 60.395 44.000 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.