Multiple sequence alignment - TraesCS5D01G307000

Loading Multiple Alignment...

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 TraesCS5D01G307000 chr5D 100.000 3061 0 0 1 3061 403416470 403413410 0.000000e+00 5653.0
1 TraesCS5D01G307000 chr5D 82.485 982 140 25 1003 1967 358825586 358824620 0.000000e+00 832.0
2 TraesCS5D01G307000 chr5B 92.463 2481 93 34 221 2654 485153429 485155862 0.000000e+00 3459.0
3 TraesCS5D01G307000 chr5B 82.096 983 142 28 1003 1967 423901515 423900549 0.000000e+00 809.0
4 TraesCS5D01G307000 chr5B 90.843 415 32 4 2651 3061 485158212 485158624 4.460000e-153 551.0
5 TraesCS5D01G307000 chr5A 94.261 1638 59 19 749 2368 510078941 510077321 0.000000e+00 2471.0
6 TraesCS5D01G307000 chr5A 82.688 982 138 25 1003 1967 459677081 459676115 0.000000e+00 843.0
7 TraesCS5D01G307000 chr5A 89.354 263 15 7 2434 2696 510077294 510077045 4.930000e-83 318.0
8 TraesCS5D01G307000 chr5A 89.912 228 6 4 468 695 510079397 510079187 8.360000e-71 278.0
9 TraesCS5D01G307000 chr5A 89.773 176 12 3 247 418 510080989 510080816 1.430000e-53 220.0
10 TraesCS5D01G307000 chr5A 91.803 61 5 0 3001 3061 510076797 510076737 5.440000e-13 86.1
11 TraesCS5D01G307000 chrUn 96.281 242 7 1 1 242 61000419 61000180 2.210000e-106 396.0
12 TraesCS5D01G307000 chrUn 96.653 239 6 1 1 239 330692084 330692320 2.210000e-106 396.0
13 TraesCS5D01G307000 chrUn 95.726 234 7 1 9 242 60999833 60999603 1.040000e-99 374.0
14 TraesCS5D01G307000 chr3D 94.779 249 10 1 1 249 518169294 518169049 4.790000e-103 385.0
15 TraesCS5D01G307000 chr3D 93.776 241 12 2 1 241 583271253 583271016 2.900000e-95 359.0
16 TraesCS5D01G307000 chr7B 95.000 240 10 2 1 239 57266279 57266041 2.880000e-100 375.0
17 TraesCS5D01G307000 chr7D 95.000 240 7 2 1 240 46832836 46833070 3.730000e-99 372.0
18 TraesCS5D01G307000 chr2D 94.215 242 8 2 1 242 12767002 12766767 6.240000e-97 364.0
19 TraesCS5D01G307000 chr3A 94.142 239 10 1 1 239 20208528 20208294 8.070000e-96 361.0


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 TraesCS5D01G307000 chr5D 403413410 403416470 3060 True 5653.00 5653 100.0000 1 3061 1 chr5D.!!$R2 3060
1 TraesCS5D01G307000 chr5D 358824620 358825586 966 True 832.00 832 82.4850 1003 1967 1 chr5D.!!$R1 964
2 TraesCS5D01G307000 chr5B 485153429 485158624 5195 False 2005.00 3459 91.6530 221 3061 2 chr5B.!!$F1 2840
3 TraesCS5D01G307000 chr5B 423900549 423901515 966 True 809.00 809 82.0960 1003 1967 1 chr5B.!!$R1 964
4 TraesCS5D01G307000 chr5A 459676115 459677081 966 True 843.00 843 82.6880 1003 1967 1 chr5A.!!$R1 964
5 TraesCS5D01G307000 chr5A 510076737 510080989 4252 True 674.62 2471 91.0206 247 3061 5 chr5A.!!$R2 2814
6 TraesCS5D01G307000 chrUn 60999603 61000419 816 True 385.00 396 96.0035 1 242 2 chrUn.!!$R1 241

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
290 292 0.036306 AAACCCTAGACACCGCCAAG 59.964 55.0 0.00 0.00 0.0 3.61 F
964 2564 0.767998 CTAGATCTTTGGGGGCCTCC 59.232 60.0 17.64 17.64 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1498 3553 2.261671 CACGCTGCGGTAGTTCCT 59.738 61.111 26.95 0.0 0.0 3.36 R
2924 7366 0.328258 CCTCTTGACACCCCCGATTT 59.672 55.000 0.00 0.0 0.0 2.17 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
129 130 0.960861 GAAGAAGAAGTTGGGGGCGG 60.961 60.000 0.00 0.00 0.00 6.13
137 138 1.830847 GTTGGGGGCGGTCTGTTTT 60.831 57.895 0.00 0.00 0.00 2.43
138 139 1.075896 TTGGGGGCGGTCTGTTTTT 60.076 52.632 0.00 0.00 0.00 1.94
161 162 0.965439 TTTTTGCCTGGATCCAACGG 59.035 50.000 17.00 15.58 0.00 4.44
162 163 1.531739 TTTTGCCTGGATCCAACGGC 61.532 55.000 29.70 29.70 37.66 5.68
163 164 2.424842 TTTGCCTGGATCCAACGGCT 62.425 55.000 33.43 0.00 37.91 5.52
164 165 2.825836 GCCTGGATCCAACGGCTG 60.826 66.667 29.30 12.55 35.28 4.85
165 166 2.825836 CCTGGATCCAACGGCTGC 60.826 66.667 17.00 0.00 0.00 5.25
166 167 3.197790 CTGGATCCAACGGCTGCG 61.198 66.667 17.00 0.00 0.00 5.18
167 168 3.958147 CTGGATCCAACGGCTGCGT 62.958 63.158 17.00 0.00 0.00 5.24
168 169 3.499737 GGATCCAACGGCTGCGTG 61.500 66.667 6.95 0.00 0.00 5.34
169 170 3.499737 GATCCAACGGCTGCGTGG 61.500 66.667 9.20 9.20 0.00 4.94
174 175 4.704833 AACGGCTGCGTGGCTCAT 62.705 61.111 0.00 0.00 39.32 2.90
175 176 3.309436 AACGGCTGCGTGGCTCATA 62.309 57.895 0.00 0.00 39.32 2.15
176 177 2.280389 CGGCTGCGTGGCTCATAT 60.280 61.111 0.00 0.00 39.32 1.78
177 178 2.313172 CGGCTGCGTGGCTCATATC 61.313 63.158 0.00 0.00 39.32 1.63
178 179 1.963338 GGCTGCGTGGCTCATATCC 60.963 63.158 0.00 0.00 38.32 2.59
179 180 1.227645 GCTGCGTGGCTCATATCCA 60.228 57.895 0.00 0.00 0.00 3.41
180 181 0.815213 GCTGCGTGGCTCATATCCAA 60.815 55.000 0.00 0.00 35.01 3.53
181 182 1.888215 CTGCGTGGCTCATATCCAAT 58.112 50.000 0.00 0.00 35.01 3.16
182 183 1.534163 CTGCGTGGCTCATATCCAATG 59.466 52.381 0.00 0.00 35.01 2.82
183 184 0.877071 GCGTGGCTCATATCCAATGG 59.123 55.000 0.00 0.00 35.01 3.16
184 185 0.877071 CGTGGCTCATATCCAATGGC 59.123 55.000 0.00 0.00 35.01 4.40
185 186 1.251251 GTGGCTCATATCCAATGGCC 58.749 55.000 0.00 0.00 35.01 5.36
186 187 1.151760 TGGCTCATATCCAATGGCCT 58.848 50.000 3.32 0.00 36.76 5.19
187 188 1.202964 TGGCTCATATCCAATGGCCTG 60.203 52.381 3.32 0.00 36.76 4.85
188 189 1.542492 GCTCATATCCAATGGCCTGG 58.458 55.000 3.32 4.05 37.87 4.45
189 190 1.889699 GCTCATATCCAATGGCCTGGG 60.890 57.143 11.00 6.39 37.06 4.45
190 191 0.112995 TCATATCCAATGGCCTGGGC 59.887 55.000 14.23 14.23 37.06 5.36
191 192 0.113776 CATATCCAATGGCCTGGGCT 59.886 55.000 21.72 4.10 41.60 5.19
192 193 0.113776 ATATCCAATGGCCTGGGCTG 59.886 55.000 21.72 11.90 41.60 4.85
193 194 2.010412 TATCCAATGGCCTGGGCTGG 62.010 60.000 21.72 20.24 41.60 4.85
194 195 4.064768 CCAATGGCCTGGGCTGGA 62.065 66.667 20.09 1.94 41.60 3.86
195 196 2.757099 CAATGGCCTGGGCTGGAC 60.757 66.667 21.72 0.00 41.60 4.02
196 197 4.066139 AATGGCCTGGGCTGGACC 62.066 66.667 21.72 0.00 41.60 4.46
242 243 3.876300 GCCTATAAGCGCCCATCG 58.124 61.111 2.29 0.00 42.12 3.84
245 246 0.317160 CCTATAAGCGCCCATCGTCA 59.683 55.000 2.29 0.00 41.07 4.35
255 256 3.672241 GCGCCCATCGTCAAACTATTTTT 60.672 43.478 0.00 0.00 41.07 1.94
285 287 3.072211 GGAAAGAAAACCCTAGACACCG 58.928 50.000 0.00 0.00 0.00 4.94
290 292 0.036306 AAACCCTAGACACCGCCAAG 59.964 55.000 0.00 0.00 0.00 3.61
300 302 1.603739 ACCGCCAAGAAGGGAAAGC 60.604 57.895 0.00 0.00 38.09 3.51
359 364 4.389576 CAAACACGGCAGCGGCTC 62.390 66.667 9.17 0.00 40.87 4.70
418 423 2.027929 TGTTCCGATTCTTTCGCCCTAA 60.028 45.455 0.00 0.00 46.71 2.69
433 1819 3.017442 GCCCTAAATGACTTTCCCACTC 58.983 50.000 0.00 0.00 0.00 3.51
692 2105 3.839432 CTCCTTCCTCCCGTCCGC 61.839 72.222 0.00 0.00 0.00 5.54
729 2144 2.286425 CCCTCCTCCCCCACACAT 60.286 66.667 0.00 0.00 0.00 3.21
883 2481 5.087323 CTCCTACTGGGAATAGAATAGCCA 58.913 45.833 0.00 0.00 44.58 4.75
884 2482 4.838986 TCCTACTGGGAATAGAATAGCCAC 59.161 45.833 0.00 0.00 41.91 5.01
885 2483 4.020128 CCTACTGGGAATAGAATAGCCACC 60.020 50.000 0.00 0.00 37.23 4.61
886 2484 2.711547 ACTGGGAATAGAATAGCCACCC 59.288 50.000 0.00 0.00 36.72 4.61
887 2485 2.040412 CTGGGAATAGAATAGCCACCCC 59.960 54.545 0.00 0.00 35.48 4.95
910 2508 2.549992 GCCCAAATCCCACACCTTTTTC 60.550 50.000 0.00 0.00 0.00 2.29
918 2518 3.510360 TCCCACACCTTTTTCGTTTTTGA 59.490 39.130 0.00 0.00 0.00 2.69
960 2560 3.366052 TGTTTCTAGATCTTTGGGGGC 57.634 47.619 0.00 0.00 0.00 5.80
964 2564 0.767998 CTAGATCTTTGGGGGCCTCC 59.232 60.000 17.64 17.64 0.00 4.30
977 2577 1.814169 GCCTCCAATTCGTCCGTCC 60.814 63.158 0.00 0.00 0.00 4.79
2078 4155 2.345124 ACTAGTAGTACCGCTGGAGG 57.655 55.000 0.00 0.00 37.30 4.30
2100 4177 1.734655 TTTCTCCAGTTCCTGCCTCT 58.265 50.000 0.00 0.00 0.00 3.69
2105 4182 1.988107 TCCAGTTCCTGCCTCTCATTT 59.012 47.619 0.00 0.00 0.00 2.32
2256 4333 8.469309 ACTATTACTGGCATGCTTTCAATTAT 57.531 30.769 18.92 0.00 0.00 1.28
2257 4334 9.573166 ACTATTACTGGCATGCTTTCAATTATA 57.427 29.630 18.92 0.50 0.00 0.98
2260 4337 6.780457 ACTGGCATGCTTTCAATTATAAGT 57.220 33.333 18.92 0.00 0.00 2.24
2261 4338 7.880160 ACTGGCATGCTTTCAATTATAAGTA 57.120 32.000 18.92 0.00 0.00 2.24
2306 4392 9.178427 GAAACGGTAGTATAGTATAAGCAACAG 57.822 37.037 0.00 0.00 0.00 3.16
2362 4448 4.808414 AGCAGTAAGTAAGATGTGCTGA 57.192 40.909 0.00 0.00 39.73 4.26
2391 4477 4.850680 TGCCCCTCGACTTATTACAAAAT 58.149 39.130 0.00 0.00 0.00 1.82
2392 4478 5.991861 TGCCCCTCGACTTATTACAAAATA 58.008 37.500 0.00 0.00 0.00 1.40
2393 4479 6.053005 TGCCCCTCGACTTATTACAAAATAG 58.947 40.000 0.00 0.00 0.00 1.73
2394 4480 6.126997 TGCCCCTCGACTTATTACAAAATAGA 60.127 38.462 0.00 0.00 0.00 1.98
2395 4481 6.424207 GCCCCTCGACTTATTACAAAATAGAG 59.576 42.308 0.00 0.00 0.00 2.43
2409 4495 5.012148 ACAAAATAGAGTACTCCACTGCTGT 59.988 40.000 19.38 12.57 37.72 4.40
2411 4497 6.852420 AAATAGAGTACTCCACTGCTGTAA 57.148 37.500 19.38 0.00 37.72 2.41
2416 4502 4.015084 AGTACTCCACTGCTGTAATACGT 58.985 43.478 0.00 0.00 35.62 3.57
2421 4507 4.740268 TCCACTGCTGTAATACGTACAAG 58.260 43.478 0.00 0.00 42.23 3.16
2424 4510 3.118884 ACTGCTGTAATACGTACAAGGGG 60.119 47.826 0.00 0.00 42.23 4.79
2431 4517 5.533903 TGTAATACGTACAAGGGGAGATCTC 59.466 44.000 14.75 14.75 39.85 2.75
2592 4678 5.240183 CAGGAACATATTCATGCCAAGTAGG 59.760 44.000 0.00 0.00 39.55 3.18
2621 4707 1.593006 CCACGAGAACGCCATTATCAC 59.407 52.381 0.00 0.00 43.96 3.06
2631 4720 2.656947 CCATTATCACCCCGAATGGT 57.343 50.000 4.96 0.00 43.09 3.55
2641 4730 4.776322 CGAATGGTGCCCGCCTCA 62.776 66.667 0.00 0.00 0.00 3.86
2654 4743 0.951040 CGCCTCAGTTCCAACCTCAC 60.951 60.000 0.00 0.00 0.00 3.51
2739 7181 5.100259 CGAAAAGAAGCATCAATCAGCAAT 58.900 37.500 0.00 0.00 0.00 3.56
2741 7183 3.438297 AGAAGCATCAATCAGCAATGC 57.562 42.857 0.00 0.00 44.80 3.56
2787 7229 4.201881 GCATGTTACCGGACCTAATTTCAC 60.202 45.833 9.46 0.00 0.00 3.18
2796 7238 3.244112 GGACCTAATTTCACGATCCCGAT 60.244 47.826 0.00 0.00 39.50 4.18
2811 7253 4.220693 TCCCGATAGCCCAATAATGATG 57.779 45.455 0.00 0.00 0.00 3.07
2834 7276 4.603131 ACCTAATTTCCACATCAGCACAT 58.397 39.130 0.00 0.00 0.00 3.21
2837 7279 6.663093 ACCTAATTTCCACATCAGCACATAAA 59.337 34.615 0.00 0.00 0.00 1.40
2860 7302 0.107214 ACATGTACCGGCCCAAGATG 60.107 55.000 0.00 1.61 0.00 2.90
2878 7320 3.820467 AGATGGACGAATTGTTCTTTGCA 59.180 39.130 0.00 0.00 0.00 4.08
2896 7338 2.736721 TGCAAAATCGACAGTGAGTAGC 59.263 45.455 0.00 0.00 0.00 3.58
2915 7357 1.741401 ACACGATGTGATGCCGGTG 60.741 57.895 1.90 0.00 36.96 4.94
2916 7358 2.819595 ACGATGTGATGCCGGTGC 60.820 61.111 1.90 0.00 38.26 5.01
2928 7370 2.953020 TGCCGGTGCAAATGTTAAATC 58.047 42.857 1.90 0.00 46.66 2.17
2929 7371 1.917303 GCCGGTGCAAATGTTAAATCG 59.083 47.619 1.90 0.00 37.47 3.34
2930 7372 2.525055 CCGGTGCAAATGTTAAATCGG 58.475 47.619 0.00 0.00 0.00 4.18
2941 7385 2.372504 TGTTAAATCGGGGGTGTCAAGA 59.627 45.455 0.00 0.00 0.00 3.02
2968 7412 2.573340 CACCAAAAGCCGGCCATC 59.427 61.111 26.15 0.00 0.00 3.51
3005 7481 2.571212 CAGTTAAGGTTGACAGTGCCA 58.429 47.619 0.00 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 2.108250 CCCCAACTTCTTCTTCCTTGGA 59.892 50.000 0.00 0.00 34.41 3.53
161 162 0.815213 TTGGATATGAGCCACGCAGC 60.815 55.000 0.00 0.00 34.56 5.25
162 163 1.534163 CATTGGATATGAGCCACGCAG 59.466 52.381 0.00 0.00 34.56 5.18
163 164 1.596603 CATTGGATATGAGCCACGCA 58.403 50.000 0.00 0.00 34.56 5.24
164 165 0.877071 CCATTGGATATGAGCCACGC 59.123 55.000 0.00 0.00 34.56 5.34
165 166 0.877071 GCCATTGGATATGAGCCACG 59.123 55.000 6.95 0.00 34.56 4.94
166 167 1.202976 AGGCCATTGGATATGAGCCAC 60.203 52.381 5.01 0.00 37.63 5.01
167 168 1.151760 AGGCCATTGGATATGAGCCA 58.848 50.000 5.01 0.00 37.63 4.75
168 169 1.542492 CAGGCCATTGGATATGAGCC 58.458 55.000 5.01 0.05 36.37 4.70
169 170 1.542492 CCAGGCCATTGGATATGAGC 58.458 55.000 5.01 0.00 40.87 4.26
170 171 1.889699 GCCCAGGCCATTGGATATGAG 60.890 57.143 12.62 0.00 40.87 2.90
171 172 0.112995 GCCCAGGCCATTGGATATGA 59.887 55.000 12.62 0.00 40.87 2.15
172 173 0.113776 AGCCCAGGCCATTGGATATG 59.886 55.000 12.62 1.09 40.87 1.78
173 174 0.113776 CAGCCCAGGCCATTGGATAT 59.886 55.000 12.62 0.00 40.87 1.63
174 175 1.538167 CAGCCCAGGCCATTGGATA 59.462 57.895 12.62 0.00 40.87 2.59
175 176 2.281091 CAGCCCAGGCCATTGGAT 59.719 61.111 12.62 1.06 40.87 3.41
176 177 4.064768 CCAGCCCAGGCCATTGGA 62.065 66.667 12.62 0.00 40.87 3.53
177 178 4.064768 TCCAGCCCAGGCCATTGG 62.065 66.667 5.01 4.39 43.17 3.16
178 179 2.757099 GTCCAGCCCAGGCCATTG 60.757 66.667 5.01 0.00 43.17 2.82
179 180 4.066139 GGTCCAGCCCAGGCCATT 62.066 66.667 5.01 0.00 43.17 3.16
225 226 1.004918 ACGATGGGCGCTTATAGGC 60.005 57.895 7.64 0.00 46.04 3.93
226 227 0.317160 TGACGATGGGCGCTTATAGG 59.683 55.000 7.64 0.77 46.04 2.57
227 228 2.148916 TTGACGATGGGCGCTTATAG 57.851 50.000 7.64 5.19 46.04 1.31
228 229 2.159014 AGTTTGACGATGGGCGCTTATA 60.159 45.455 7.64 0.00 46.04 0.98
229 230 1.014352 GTTTGACGATGGGCGCTTAT 58.986 50.000 7.64 1.25 46.04 1.73
230 231 0.036765 AGTTTGACGATGGGCGCTTA 60.037 50.000 7.64 0.00 46.04 3.09
231 232 0.036765 TAGTTTGACGATGGGCGCTT 60.037 50.000 7.64 0.00 46.04 4.68
232 233 0.178068 ATAGTTTGACGATGGGCGCT 59.822 50.000 7.64 0.00 46.04 5.92
233 234 1.014352 AATAGTTTGACGATGGGCGC 58.986 50.000 0.00 0.00 46.04 6.53
235 236 4.095610 CGAAAAATAGTTTGACGATGGGC 58.904 43.478 8.93 0.00 32.65 5.36
236 237 4.095610 GCGAAAAATAGTTTGACGATGGG 58.904 43.478 15.75 0.00 32.65 4.00
237 238 4.095610 GGCGAAAAATAGTTTGACGATGG 58.904 43.478 15.75 0.00 32.65 3.51
238 239 3.778718 CGGCGAAAAATAGTTTGACGATG 59.221 43.478 0.00 6.44 44.84 3.84
242 243 4.435651 CCTCTCGGCGAAAAATAGTTTGAC 60.436 45.833 12.13 0.00 0.00 3.18
245 246 3.934068 TCCTCTCGGCGAAAAATAGTTT 58.066 40.909 12.13 0.00 0.00 2.66
255 256 1.607251 GGTTTTCTTTCCTCTCGGCGA 60.607 52.381 10.14 10.14 0.00 5.54
285 287 2.908688 TTTTGCTTTCCCTTCTTGGC 57.091 45.000 0.00 0.00 0.00 4.52
307 309 0.610232 CTGCCTTGGGAGAGGGTTTG 60.610 60.000 1.71 0.00 37.29 2.93
311 313 3.041469 GCTCTGCCTTGGGAGAGGG 62.041 68.421 30.18 14.34 36.91 4.30
312 314 2.588989 GCTCTGCCTTGGGAGAGG 59.411 66.667 30.18 17.18 36.91 3.69
418 423 3.009584 GGAAGGAGAGTGGGAAAGTCATT 59.990 47.826 0.00 0.00 0.00 2.57
487 1876 2.029964 GTTTGCTGTCCGGACGGA 59.970 61.111 41.26 27.50 42.90 4.69
488 1877 3.411351 CGTTTGCTGTCCGGACGG 61.411 66.667 34.82 34.82 40.59 4.79
606 1995 4.373116 TCGCAGGCTGACGGGTTC 62.373 66.667 20.86 0.00 0.00 3.62
607 1996 4.681978 GTCGCAGGCTGACGGGTT 62.682 66.667 20.86 0.00 0.00 4.11
692 2105 1.890510 GGCGCCGTTTATAGGTGGG 60.891 63.158 12.58 0.00 39.52 4.61
729 2144 3.253061 TCAATGGTGGGTGCGGGA 61.253 61.111 0.00 0.00 0.00 5.14
885 2483 4.374584 TGTGGGATTTGGGCGGGG 62.375 66.667 0.00 0.00 0.00 5.73
886 2484 3.068064 GTGTGGGATTTGGGCGGG 61.068 66.667 0.00 0.00 0.00 6.13
887 2485 3.068064 GGTGTGGGATTTGGGCGG 61.068 66.667 0.00 0.00 0.00 6.13
899 2497 6.312672 AGGAAATCAAAAACGAAAAAGGTGTG 59.687 34.615 0.00 0.00 0.00 3.82
910 2508 8.774586 TCTAAAGAAGAGAGGAAATCAAAAACG 58.225 33.333 0.00 0.00 0.00 3.60
960 2560 1.518572 CGGACGGACGAATTGGAGG 60.519 63.158 0.00 0.00 35.47 4.30
964 2564 2.505337 TCGCGGACGGACGAATTG 60.505 61.111 6.13 0.00 40.63 2.32
988 2588 3.483869 GCCCATCTTCCCCTCGCT 61.484 66.667 0.00 0.00 0.00 4.93
990 2590 3.447025 GACGCCCATCTTCCCCTCG 62.447 68.421 0.00 0.00 0.00 4.63
992 2592 1.915078 CTTGACGCCCATCTTCCCCT 61.915 60.000 0.00 0.00 0.00 4.79
994 2594 1.452108 CCTTGACGCCCATCTTCCC 60.452 63.158 0.00 0.00 0.00 3.97
995 2595 1.452108 CCCTTGACGCCCATCTTCC 60.452 63.158 0.00 0.00 0.00 3.46
996 2596 1.452108 CCCCTTGACGCCCATCTTC 60.452 63.158 0.00 0.00 0.00 2.87
1498 3553 2.261671 CACGCTGCGGTAGTTCCT 59.738 61.111 26.95 0.00 0.00 3.36
2100 4177 8.835439 TCGATCAAATTCATCCGAATAAAATGA 58.165 29.630 0.00 0.00 41.12 2.57
2105 4182 9.449550 CAAAATCGATCAAATTCATCCGAATAA 57.550 29.630 0.00 0.00 41.12 1.40
2157 4234 4.631377 TCTCAAAGTTGACATTCATAGCCG 59.369 41.667 0.00 0.00 32.90 5.52
2199 4276 3.574284 TTGGTACATTGTCAATGCTGC 57.426 42.857 22.79 13.97 42.69 5.25
2261 4338 9.449719 ACCGTTTCAGAATTCTCAAATTAGTAT 57.550 29.630 7.82 0.00 35.21 2.12
2297 4383 1.614051 CCAGCACATCCCTGTTGCTTA 60.614 52.381 0.00 0.00 37.53 3.09
2298 4384 0.896940 CCAGCACATCCCTGTTGCTT 60.897 55.000 0.00 0.00 37.53 3.91
2306 4392 3.446570 GCACTGCCAGCACATCCC 61.447 66.667 0.00 0.00 0.00 3.85
2362 4448 1.755393 AAGTCGAGGGGCAAAGTCGT 61.755 55.000 0.00 0.00 35.22 4.34
2391 4477 5.526479 CGTATTACAGCAGTGGAGTACTCTA 59.474 44.000 21.88 14.08 37.60 2.43
2392 4478 4.335874 CGTATTACAGCAGTGGAGTACTCT 59.664 45.833 21.88 0.00 37.60 3.24
2393 4479 4.096081 ACGTATTACAGCAGTGGAGTACTC 59.904 45.833 14.87 14.87 37.60 2.59
2394 4480 4.015084 ACGTATTACAGCAGTGGAGTACT 58.985 43.478 0.00 0.00 41.36 2.73
2395 4481 4.367386 ACGTATTACAGCAGTGGAGTAC 57.633 45.455 0.00 0.00 0.00 2.73
2409 4495 5.950023 AGAGATCTCCCCTTGTACGTATTA 58.050 41.667 19.30 0.00 0.00 0.98
2411 4497 4.456662 AGAGATCTCCCCTTGTACGTAT 57.543 45.455 19.30 0.00 0.00 3.06
2416 4502 3.533907 AGAGGAAGAGATCTCCCCTTGTA 59.466 47.826 26.16 0.00 34.62 2.41
2421 4507 2.814097 CGAGAGAGGAAGAGATCTCCCC 60.814 59.091 19.30 19.18 42.45 4.81
2631 4720 3.565214 TTGGAACTGAGGCGGGCA 61.565 61.111 3.78 0.00 0.00 5.36
2632 4721 3.056328 GTTGGAACTGAGGCGGGC 61.056 66.667 0.00 0.00 0.00 6.13
2641 4730 2.702592 TCGTTTGTGAGGTTGGAACT 57.297 45.000 0.00 0.00 0.00 3.01
2654 4743 1.226379 GGCCATCACGCATCGTTTG 60.226 57.895 0.00 0.00 38.32 2.93
2711 7153 4.216042 TGATTGATGCTTCTTTTCGCTGAA 59.784 37.500 0.88 0.00 0.00 3.02
2741 7183 4.697756 TTTGCAGCCCGGGAGACG 62.698 66.667 29.31 9.85 43.80 4.18
2787 7229 3.118775 TCATTATTGGGCTATCGGGATCG 60.119 47.826 0.00 0.00 37.82 3.69
2796 7238 7.669722 GGAAATTAGGTCATCATTATTGGGCTA 59.330 37.037 0.00 0.00 0.00 3.93
2811 7253 4.009675 TGTGCTGATGTGGAAATTAGGTC 58.990 43.478 0.00 0.00 0.00 3.85
2834 7276 1.202557 GGGCCGGTACATGTCGATTTA 60.203 52.381 0.00 0.00 0.00 1.40
2837 7279 1.618876 TTGGGCCGGTACATGTCGAT 61.619 55.000 0.00 0.00 0.00 3.59
2860 7302 5.387342 CGATTTTGCAAAGAACAATTCGTCC 60.387 40.000 12.41 0.00 32.67 4.79
2878 7320 3.741344 GTGTGCTACTCACTGTCGATTTT 59.259 43.478 0.00 0.00 45.81 1.82
2913 7355 2.232696 ACCCCCGATTTAACATTTGCAC 59.767 45.455 0.00 0.00 0.00 4.57
2915 7357 2.232696 ACACCCCCGATTTAACATTTGC 59.767 45.455 0.00 0.00 0.00 3.68
2916 7358 3.508012 TGACACCCCCGATTTAACATTTG 59.492 43.478 0.00 0.00 0.00 2.32
2918 7360 3.443145 TGACACCCCCGATTTAACATT 57.557 42.857 0.00 0.00 0.00 2.71
2919 7361 3.009695 TCTTGACACCCCCGATTTAACAT 59.990 43.478 0.00 0.00 0.00 2.71
2920 7362 2.372504 TCTTGACACCCCCGATTTAACA 59.627 45.455 0.00 0.00 0.00 2.41
2921 7363 3.007635 CTCTTGACACCCCCGATTTAAC 58.992 50.000 0.00 0.00 0.00 2.01
2922 7364 2.026636 CCTCTTGACACCCCCGATTTAA 60.027 50.000 0.00 0.00 0.00 1.52
2923 7365 1.557832 CCTCTTGACACCCCCGATTTA 59.442 52.381 0.00 0.00 0.00 1.40
2924 7366 0.328258 CCTCTTGACACCCCCGATTT 59.672 55.000 0.00 0.00 0.00 2.17
2925 7367 0.546747 TCCTCTTGACACCCCCGATT 60.547 55.000 0.00 0.00 0.00 3.34
2926 7368 0.978146 CTCCTCTTGACACCCCCGAT 60.978 60.000 0.00 0.00 0.00 4.18
2928 7370 2.660064 CCTCCTCTTGACACCCCCG 61.660 68.421 0.00 0.00 0.00 5.73
2929 7371 2.972819 GCCTCCTCTTGACACCCCC 61.973 68.421 0.00 0.00 0.00 5.40
2930 7372 1.779061 TTGCCTCCTCTTGACACCCC 61.779 60.000 0.00 0.00 0.00 4.95
2941 7385 1.115326 GCTTTTGGTGGTTGCCTCCT 61.115 55.000 7.64 0.00 37.97 3.69
2968 7412 1.647545 CTGCACTTACCGCCACCATG 61.648 60.000 0.00 0.00 0.00 3.66
3005 7481 3.055719 CCGCAACCAAGTCGGCAT 61.056 61.111 0.00 0.00 39.03 4.40


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

AutoCloner maintained by Alex Coulton.