Multiple sequence alignment - TraesCS5D01G090900

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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 TraesCS5D01G090900 chr5D 100.000 3083 0 0 1 3083 97831557 97834639 0.000000e+00 5694.0
1 TraesCS5D01G090900 chr5A 95.270 2685 59 22 283 2933 105689975 105687325 0.000000e+00 4193.0
2 TraesCS5D01G090900 chr5A 94.857 175 4 3 1 172 105690111 105689939 5.070000e-68 268.0
3 TraesCS5D01G090900 chr5A 91.195 159 4 1 2935 3083 105687263 105687105 1.120000e-49 207.0
4 TraesCS5D01G090900 chr5B 95.650 2138 57 10 283 2395 107196198 107198324 0.000000e+00 3400.0
5 TraesCS5D01G090900 chr5B 96.056 710 10 4 2388 3083 107198509 107199214 0.000000e+00 1140.0
6 TraesCS5D01G090900 chr5B 93.143 175 8 2 1 172 107196062 107196235 1.420000e-63 254.0
7 TraesCS5D01G090900 chr4D 94.074 135 6 2 160 293 105237797 105237930 1.450000e-48 204.0
8 TraesCS5D01G090900 chr2D 94.615 130 6 1 167 295 116827424 116827295 1.870000e-47 200.0
9 TraesCS5D01G090900 chr2B 96.639 119 4 0 169 287 723434349 723434231 6.740000e-47 198.0
10 TraesCS5D01G090900 chr4A 95.200 125 5 1 169 292 702148909 702148785 2.430000e-46 196.0
11 TraesCS5D01G090900 chr1D 93.284 134 8 1 168 301 469813518 469813386 2.430000e-46 196.0
12 TraesCS5D01G090900 chr6D 93.846 130 6 2 167 295 39092682 39092810 8.720000e-46 195.0
13 TraesCS5D01G090900 chr6D 95.833 120 5 0 169 288 108860765 108860646 8.720000e-46 195.0
14 TraesCS5D01G090900 chr3B 95.798 119 5 0 168 286 694025133 694025015 3.140000e-45 193.0
15 TraesCS5D01G090900 chr1B 91.912 136 11 0 161 296 613246053 613245918 1.130000e-44 191.0
16 TraesCS5D01G090900 chr1B 100.000 30 0 0 2964 2993 517896807 517896778 4.290000e-04 56.5


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 TraesCS5D01G090900 chr5D 97831557 97834639 3082 False 5694 5694 100.000000 1 3083 1 chr5D.!!$F1 3082
1 TraesCS5D01G090900 chr5A 105687105 105690111 3006 True 1556 4193 93.774000 1 3083 3 chr5A.!!$R1 3082
2 TraesCS5D01G090900 chr5B 107196062 107199214 3152 False 1598 3400 94.949667 1 3083 3 chr5B.!!$F1 3082

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
184 191 0.033796 ATGTACTCCCTCCGTCCGAA 60.034 55.0 0.0 0.0 0.0 4.30 F
694 718 0.178918 TCCAAACCCCCATCAAACCC 60.179 55.0 0.0 0.0 0.0 4.11 F
695 719 0.472734 CCAAACCCCCATCAAACCCA 60.473 55.0 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1137 1167 1.432657 GTAGCGGAGAAGGACGTCC 59.567 63.158 27.67 27.67 0.00 4.79 R
1679 1709 1.521450 CTTGCTCCCAGCTGGTTGTG 61.521 60.000 30.63 17.64 42.97 3.33 R
2110 2143 1.948834 TCGCCATAATGCAACTCCATG 59.051 47.619 0.00 0.00 0.00 3.66 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
74 75 6.539649 TTTGTTCTTTCTCATACCGTCTTG 57.460 37.500 0.00 0.00 0.00 3.02
114 121 9.436957 TGGATAACAGAACAGAATCTAGTTTTC 57.563 33.333 0.00 0.00 0.00 2.29
173 180 6.509418 TTTTGAGGCAAATGTATGTACTCC 57.491 37.500 0.00 0.00 33.19 3.85
174 181 4.150897 TGAGGCAAATGTATGTACTCCC 57.849 45.455 0.00 0.00 0.00 4.30
175 182 3.780294 TGAGGCAAATGTATGTACTCCCT 59.220 43.478 0.00 0.00 0.00 4.20
176 183 4.141711 TGAGGCAAATGTATGTACTCCCTC 60.142 45.833 0.00 0.00 37.45 4.30
177 184 3.136626 AGGCAAATGTATGTACTCCCTCC 59.863 47.826 0.00 0.00 0.00 4.30
178 185 3.131396 GCAAATGTATGTACTCCCTCCG 58.869 50.000 0.00 0.00 0.00 4.63
179 186 3.431766 GCAAATGTATGTACTCCCTCCGT 60.432 47.826 0.00 0.00 0.00 4.69
180 187 4.369182 CAAATGTATGTACTCCCTCCGTC 58.631 47.826 0.00 0.00 0.00 4.79
181 188 2.062971 TGTATGTACTCCCTCCGTCC 57.937 55.000 0.00 0.00 0.00 4.79
182 189 0.950116 GTATGTACTCCCTCCGTCCG 59.050 60.000 0.00 0.00 0.00 4.79
183 190 0.839277 TATGTACTCCCTCCGTCCGA 59.161 55.000 0.00 0.00 0.00 4.55
184 191 0.033796 ATGTACTCCCTCCGTCCGAA 60.034 55.000 0.00 0.00 0.00 4.30
185 192 0.251297 TGTACTCCCTCCGTCCGAAA 60.251 55.000 0.00 0.00 0.00 3.46
186 193 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
187 194 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
188 195 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
189 196 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
190 197 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
191 198 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
192 199 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
193 200 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
194 201 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
195 202 2.597305 CTCCGTCCGAAAATACTTGTCG 59.403 50.000 0.00 0.00 34.58 4.35
204 211 5.560148 CGAAAATACTTGTCGGAGAAATGG 58.440 41.667 0.00 0.00 39.69 3.16
205 212 5.350365 CGAAAATACTTGTCGGAGAAATGGA 59.650 40.000 0.00 0.00 39.69 3.41
206 213 6.037172 CGAAAATACTTGTCGGAGAAATGGAT 59.963 38.462 0.00 0.00 39.69 3.41
207 214 7.223971 CGAAAATACTTGTCGGAGAAATGGATA 59.776 37.037 0.00 0.00 39.69 2.59
208 215 8.801882 AAAATACTTGTCGGAGAAATGGATAA 57.198 30.769 0.00 0.00 39.69 1.75
209 216 8.801882 AAATACTTGTCGGAGAAATGGATAAA 57.198 30.769 0.00 0.00 39.69 1.40
210 217 8.801882 AATACTTGTCGGAGAAATGGATAAAA 57.198 30.769 0.00 0.00 39.69 1.52
211 218 8.801882 ATACTTGTCGGAGAAATGGATAAAAA 57.198 30.769 0.00 0.00 39.69 1.94
212 219 7.703058 ACTTGTCGGAGAAATGGATAAAAAT 57.297 32.000 0.00 0.00 39.69 1.82
213 220 7.538575 ACTTGTCGGAGAAATGGATAAAAATG 58.461 34.615 0.00 0.00 39.69 2.32
214 221 6.449635 TGTCGGAGAAATGGATAAAAATGG 57.550 37.500 0.00 0.00 39.69 3.16
215 222 6.184068 TGTCGGAGAAATGGATAAAAATGGA 58.816 36.000 0.00 0.00 39.69 3.41
216 223 6.833416 TGTCGGAGAAATGGATAAAAATGGAT 59.167 34.615 0.00 0.00 39.69 3.41
217 224 7.141363 GTCGGAGAAATGGATAAAAATGGATG 58.859 38.462 0.00 0.00 39.69 3.51
218 225 6.833416 TCGGAGAAATGGATAAAAATGGATGT 59.167 34.615 0.00 0.00 0.00 3.06
219 226 7.996066 TCGGAGAAATGGATAAAAATGGATGTA 59.004 33.333 0.00 0.00 0.00 2.29
220 227 8.796475 CGGAGAAATGGATAAAAATGGATGTAT 58.204 33.333 0.00 0.00 0.00 2.29
257 264 9.915629 AATACGTCTAGATACATTCATTTCTCC 57.084 33.333 0.00 0.00 0.00 3.71
258 265 6.439599 ACGTCTAGATACATTCATTTCTCCG 58.560 40.000 0.00 0.00 0.00 4.63
259 266 6.262496 ACGTCTAGATACATTCATTTCTCCGA 59.738 38.462 0.00 0.00 0.00 4.55
260 267 7.040340 ACGTCTAGATACATTCATTTCTCCGAT 60.040 37.037 0.00 0.00 0.00 4.18
261 268 8.451748 CGTCTAGATACATTCATTTCTCCGATA 58.548 37.037 0.00 0.00 0.00 2.92
270 277 9.057089 ACATTCATTTCTCCGATAAGTATTTCC 57.943 33.333 0.00 0.00 0.00 3.13
271 278 7.709269 TTCATTTCTCCGATAAGTATTTCCG 57.291 36.000 0.00 0.00 0.00 4.30
272 279 6.812998 TCATTTCTCCGATAAGTATTTCCGT 58.187 36.000 0.00 0.00 0.00 4.69
273 280 7.944061 TCATTTCTCCGATAAGTATTTCCGTA 58.056 34.615 0.00 0.00 0.00 4.02
274 281 7.864379 TCATTTCTCCGATAAGTATTTCCGTAC 59.136 37.037 0.00 0.00 0.00 3.67
275 282 5.348418 TCTCCGATAAGTATTTCCGTACG 57.652 43.478 8.69 8.69 0.00 3.67
276 283 4.214119 TCTCCGATAAGTATTTCCGTACGG 59.786 45.833 28.66 28.66 39.30 4.02
277 284 4.133820 TCCGATAAGTATTTCCGTACGGA 58.866 43.478 32.61 32.61 43.35 4.69
278 285 4.214119 TCCGATAAGTATTTCCGTACGGAG 59.786 45.833 33.67 19.18 46.06 4.63
279 286 4.470462 CGATAAGTATTTCCGTACGGAGG 58.530 47.826 33.67 10.36 46.06 4.30
280 287 4.614535 CGATAAGTATTTCCGTACGGAGGG 60.615 50.000 33.67 9.98 46.06 4.30
281 288 2.442236 AGTATTTCCGTACGGAGGGA 57.558 50.000 33.67 24.13 46.06 4.20
282 289 2.305009 AGTATTTCCGTACGGAGGGAG 58.695 52.381 33.67 8.83 46.06 4.30
283 290 2.027385 GTATTTCCGTACGGAGGGAGT 58.973 52.381 33.67 20.06 46.06 3.85
284 291 2.442236 ATTTCCGTACGGAGGGAGTA 57.558 50.000 33.67 17.87 46.06 2.59
285 292 1.463674 TTTCCGTACGGAGGGAGTAC 58.536 55.000 33.67 0.00 46.06 2.73
286 293 0.620556 TTCCGTACGGAGGGAGTACT 59.379 55.000 33.67 0.00 46.06 2.73
287 294 1.496060 TCCGTACGGAGGGAGTACTA 58.504 55.000 32.61 6.92 41.51 1.82
288 295 2.050144 TCCGTACGGAGGGAGTACTAT 58.950 52.381 32.61 0.00 41.51 2.12
289 296 2.439507 TCCGTACGGAGGGAGTACTATT 59.560 50.000 32.61 0.00 41.51 1.73
290 297 3.117888 TCCGTACGGAGGGAGTACTATTT 60.118 47.826 32.61 0.00 41.51 1.40
291 298 3.633986 CCGTACGGAGGGAGTACTATTTT 59.366 47.826 30.64 0.00 41.51 1.82
292 299 4.821805 CCGTACGGAGGGAGTACTATTTTA 59.178 45.833 30.64 0.00 41.51 1.52
293 300 5.049129 CCGTACGGAGGGAGTACTATTTTAG 60.049 48.000 30.64 0.00 41.51 1.85
337 344 8.923683 GTCTGTACTATTTTAGTGTTGTCCTTC 58.076 37.037 0.00 0.00 39.81 3.46
338 345 8.092687 TCTGTACTATTTTAGTGTTGTCCTTCC 58.907 37.037 0.00 0.00 39.81 3.46
464 472 3.719144 GGCGAAACCAACCGTCCG 61.719 66.667 0.00 0.00 38.86 4.79
465 473 3.719144 GCGAAACCAACCGTCCGG 61.719 66.667 3.76 3.76 42.03 5.14
592 600 2.284405 TTCGTCTCCACCTCCCCC 60.284 66.667 0.00 0.00 0.00 5.40
593 601 2.807036 CTTCGTCTCCACCTCCCCCT 62.807 65.000 0.00 0.00 0.00 4.79
597 608 4.787280 CTCCACCTCCCCCTCGCT 62.787 72.222 0.00 0.00 0.00 4.93
627 643 4.227134 CGGATCAGAGCCCACCCG 62.227 72.222 0.00 0.00 0.00 5.28
684 708 0.609406 GTCTCCTGCTTCCAAACCCC 60.609 60.000 0.00 0.00 0.00 4.95
686 710 2.080336 CTCCTGCTTCCAAACCCCCA 62.080 60.000 0.00 0.00 0.00 4.96
687 711 1.079073 CCTGCTTCCAAACCCCCAT 59.921 57.895 0.00 0.00 0.00 4.00
688 712 0.972471 CCTGCTTCCAAACCCCCATC 60.972 60.000 0.00 0.00 0.00 3.51
689 713 0.251742 CTGCTTCCAAACCCCCATCA 60.252 55.000 0.00 0.00 0.00 3.07
690 714 0.189574 TGCTTCCAAACCCCCATCAA 59.810 50.000 0.00 0.00 0.00 2.57
691 715 1.347062 GCTTCCAAACCCCCATCAAA 58.653 50.000 0.00 0.00 0.00 2.69
692 716 1.001974 GCTTCCAAACCCCCATCAAAC 59.998 52.381 0.00 0.00 0.00 2.93
693 717 1.623311 CTTCCAAACCCCCATCAAACC 59.377 52.381 0.00 0.00 0.00 3.27
694 718 0.178918 TCCAAACCCCCATCAAACCC 60.179 55.000 0.00 0.00 0.00 4.11
695 719 0.472734 CCAAACCCCCATCAAACCCA 60.473 55.000 0.00 0.00 0.00 4.51
696 720 1.655372 CAAACCCCCATCAAACCCAT 58.345 50.000 0.00 0.00 0.00 4.00
702 726 2.127232 CCATCAAACCCATCCCGCC 61.127 63.158 0.00 0.00 0.00 6.13
1146 1176 4.719369 GCGCTCGTGGACGTCCTT 62.719 66.667 33.39 0.00 40.80 3.36
1374 1404 4.147322 GTGCCATTCACGCGTCCG 62.147 66.667 9.86 0.00 35.76 4.79
1643 1673 1.002134 CTGATGGGTTTCGGCCAGT 60.002 57.895 2.24 0.00 0.00 4.00
1679 1709 1.628846 TGTAGCCAAAGGGAAGGAGAC 59.371 52.381 0.00 0.00 35.59 3.36
1823 1853 0.245539 CCAGCAATTCAGGGTGCAAG 59.754 55.000 0.00 0.00 43.42 4.01
2110 2143 1.003355 TAGAAGTGCAGTGCCCAGC 60.003 57.895 13.72 0.00 0.00 4.85
2135 2168 0.734889 GTTGCATTATGGCGAGCTGT 59.265 50.000 0.00 0.00 36.28 4.40
2260 2293 3.263170 TGGCTATCAGTTCCTTACTTGCA 59.737 43.478 0.00 0.00 33.85 4.08
2310 2343 2.821378 CAAATGAGATTGAGCCCACACA 59.179 45.455 0.00 0.00 31.84 3.72
2364 2397 3.842007 TTGGTTACCTGAAAGTCGGAA 57.158 42.857 2.07 0.00 0.00 4.30
2386 2419 6.822170 GGAAAAGGATACCCAACTGTAGTAAG 59.178 42.308 0.00 0.00 33.88 2.34
2466 2691 5.478233 TTTATGTGTTGATATGCGTCACC 57.522 39.130 0.00 0.00 0.00 4.02
2603 2830 6.014242 AGTCATGATTACTCTCTGTTGTTGGA 60.014 38.462 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 5.070770 TGTTATCCATGGTTGCAATGAAC 57.929 39.130 12.58 4.44 0.00 3.18
149 156 6.071616 GGGAGTACATACATTTGCCTCAAAAA 60.072 38.462 0.00 0.00 36.90 1.94
150 157 5.417580 GGGAGTACATACATTTGCCTCAAAA 59.582 40.000 0.00 0.00 36.90 2.44
151 158 4.947388 GGGAGTACATACATTTGCCTCAAA 59.053 41.667 0.00 0.00 37.75 2.69
152 159 4.227300 AGGGAGTACATACATTTGCCTCAA 59.773 41.667 0.00 0.00 0.00 3.02
153 160 3.780294 AGGGAGTACATACATTTGCCTCA 59.220 43.478 0.00 0.00 0.00 3.86
154 161 4.381411 GAGGGAGTACATACATTTGCCTC 58.619 47.826 0.00 0.00 38.83 4.70
155 162 3.136626 GGAGGGAGTACATACATTTGCCT 59.863 47.826 0.00 0.00 31.82 4.75
156 163 3.477530 GGAGGGAGTACATACATTTGCC 58.522 50.000 0.00 0.00 0.00 4.52
157 164 3.131396 CGGAGGGAGTACATACATTTGC 58.869 50.000 0.00 0.00 0.00 3.68
158 165 4.369182 GACGGAGGGAGTACATACATTTG 58.631 47.826 0.00 0.00 0.00 2.32
159 166 3.387050 GGACGGAGGGAGTACATACATTT 59.613 47.826 0.00 0.00 0.00 2.32
160 167 2.963782 GGACGGAGGGAGTACATACATT 59.036 50.000 0.00 0.00 0.00 2.71
161 168 2.595238 GGACGGAGGGAGTACATACAT 58.405 52.381 0.00 0.00 0.00 2.29
162 169 1.748244 CGGACGGAGGGAGTACATACA 60.748 57.143 0.00 0.00 0.00 2.29
163 170 0.950116 CGGACGGAGGGAGTACATAC 59.050 60.000 0.00 0.00 0.00 2.39
164 171 0.839277 TCGGACGGAGGGAGTACATA 59.161 55.000 0.00 0.00 0.00 2.29
165 172 0.033796 TTCGGACGGAGGGAGTACAT 60.034 55.000 0.00 0.00 0.00 2.29
166 173 0.251297 TTTCGGACGGAGGGAGTACA 60.251 55.000 0.00 0.00 0.00 2.90
167 174 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.000 0.00 0.00 0.00 2.73
168 175 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
169 176 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
170 177 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
171 178 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
172 179 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
173 180 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
174 181 2.597305 CGACAAGTATTTTCGGACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
175 182 2.598589 CGACAAGTATTTTCGGACGGA 58.401 47.619 0.00 0.00 0.00 4.69
181 188 5.350365 TCCATTTCTCCGACAAGTATTTTCG 59.650 40.000 0.00 0.00 0.00 3.46
182 189 6.737254 TCCATTTCTCCGACAAGTATTTTC 57.263 37.500 0.00 0.00 0.00 2.29
183 190 8.801882 TTATCCATTTCTCCGACAAGTATTTT 57.198 30.769 0.00 0.00 0.00 1.82
184 191 8.801882 TTTATCCATTTCTCCGACAAGTATTT 57.198 30.769 0.00 0.00 0.00 1.40
185 192 8.801882 TTTTATCCATTTCTCCGACAAGTATT 57.198 30.769 0.00 0.00 0.00 1.89
186 193 8.801882 TTTTTATCCATTTCTCCGACAAGTAT 57.198 30.769 0.00 0.00 0.00 2.12
187 194 8.673711 CATTTTTATCCATTTCTCCGACAAGTA 58.326 33.333 0.00 0.00 0.00 2.24
188 195 7.362920 CCATTTTTATCCATTTCTCCGACAAGT 60.363 37.037 0.00 0.00 0.00 3.16
189 196 6.974622 CCATTTTTATCCATTTCTCCGACAAG 59.025 38.462 0.00 0.00 0.00 3.16
190 197 6.661377 TCCATTTTTATCCATTTCTCCGACAA 59.339 34.615 0.00 0.00 0.00 3.18
191 198 6.184068 TCCATTTTTATCCATTTCTCCGACA 58.816 36.000 0.00 0.00 0.00 4.35
192 199 6.693315 TCCATTTTTATCCATTTCTCCGAC 57.307 37.500 0.00 0.00 0.00 4.79
193 200 6.833416 ACATCCATTTTTATCCATTTCTCCGA 59.167 34.615 0.00 0.00 0.00 4.55
194 201 7.042797 ACATCCATTTTTATCCATTTCTCCG 57.957 36.000 0.00 0.00 0.00 4.63
231 238 9.915629 GGAGAAATGAATGTATCTAGACGTATT 57.084 33.333 0.00 0.00 0.00 1.89
232 239 8.237949 CGGAGAAATGAATGTATCTAGACGTAT 58.762 37.037 0.00 0.00 0.00 3.06
233 240 7.443272 TCGGAGAAATGAATGTATCTAGACGTA 59.557 37.037 0.00 0.00 0.00 3.57
234 241 6.262496 TCGGAGAAATGAATGTATCTAGACGT 59.738 38.462 0.00 0.00 0.00 4.34
235 242 6.669278 TCGGAGAAATGAATGTATCTAGACG 58.331 40.000 0.00 0.00 0.00 4.18
244 251 9.057089 GGAAATACTTATCGGAGAAATGAATGT 57.943 33.333 0.00 0.00 43.58 2.71
245 252 8.223769 CGGAAATACTTATCGGAGAAATGAATG 58.776 37.037 0.00 0.00 43.58 2.67
246 253 7.931948 ACGGAAATACTTATCGGAGAAATGAAT 59.068 33.333 0.00 0.00 43.58 2.57
247 254 7.270047 ACGGAAATACTTATCGGAGAAATGAA 58.730 34.615 0.00 0.00 43.58 2.57
248 255 6.812998 ACGGAAATACTTATCGGAGAAATGA 58.187 36.000 0.00 0.00 43.58 2.57
249 256 7.149015 CGTACGGAAATACTTATCGGAGAAATG 60.149 40.741 7.57 0.00 43.58 2.32
250 257 6.860023 CGTACGGAAATACTTATCGGAGAAAT 59.140 38.462 7.57 0.00 43.58 2.17
251 258 6.201517 CGTACGGAAATACTTATCGGAGAAA 58.798 40.000 7.57 0.00 43.58 2.52
252 259 5.277974 CCGTACGGAAATACTTATCGGAGAA 60.278 44.000 30.64 0.00 37.57 2.87
253 260 4.214119 CCGTACGGAAATACTTATCGGAGA 59.786 45.833 30.64 0.00 38.34 3.71
254 261 4.214119 TCCGTACGGAAATACTTATCGGAG 59.786 45.833 33.96 2.10 42.05 4.63
255 262 4.133820 TCCGTACGGAAATACTTATCGGA 58.866 43.478 33.96 6.50 42.05 4.55
256 263 4.470462 CTCCGTACGGAAATACTTATCGG 58.530 47.826 34.77 16.58 44.66 4.18
257 264 4.470462 CCTCCGTACGGAAATACTTATCG 58.530 47.826 34.77 19.73 44.66 2.92
258 265 4.520492 TCCCTCCGTACGGAAATACTTATC 59.480 45.833 34.77 0.00 44.66 1.75
259 266 4.473444 TCCCTCCGTACGGAAATACTTAT 58.527 43.478 34.77 0.00 44.66 1.73
260 267 3.885297 CTCCCTCCGTACGGAAATACTTA 59.115 47.826 34.77 16.25 44.66 2.24
261 268 2.692041 CTCCCTCCGTACGGAAATACTT 59.308 50.000 34.77 0.00 44.66 2.24
262 269 2.305009 CTCCCTCCGTACGGAAATACT 58.695 52.381 34.77 0.00 44.66 2.12
263 270 2.027385 ACTCCCTCCGTACGGAAATAC 58.973 52.381 34.77 0.00 44.66 1.89
264 271 2.442236 ACTCCCTCCGTACGGAAATA 57.558 50.000 34.77 21.70 44.66 1.40
265 272 2.027385 GTACTCCCTCCGTACGGAAAT 58.973 52.381 34.77 20.78 44.66 2.17
266 273 1.004745 AGTACTCCCTCCGTACGGAAA 59.995 52.381 34.77 22.33 44.66 3.13
267 274 0.620556 AGTACTCCCTCCGTACGGAA 59.379 55.000 34.77 21.09 44.66 4.30
268 275 1.496060 TAGTACTCCCTCCGTACGGA 58.504 55.000 33.55 33.55 41.51 4.69
269 276 2.557920 ATAGTACTCCCTCCGTACGG 57.442 55.000 28.66 28.66 41.51 4.02
270 277 4.907879 AAAATAGTACTCCCTCCGTACG 57.092 45.455 8.69 8.69 41.51 3.67
271 278 6.951062 ACTAAAATAGTACTCCCTCCGTAC 57.049 41.667 0.00 0.00 37.23 3.67
272 279 7.961326 AAACTAAAATAGTACTCCCTCCGTA 57.039 36.000 0.00 0.00 38.26 4.02
273 280 6.864151 AAACTAAAATAGTACTCCCTCCGT 57.136 37.500 0.00 0.00 38.26 4.69
337 344 4.201910 CCCAGTTACAAGTGAAATATGCGG 60.202 45.833 0.00 0.00 0.00 5.69
338 345 4.730613 GCCCAGTTACAAGTGAAATATGCG 60.731 45.833 0.00 0.00 0.00 4.73
395 402 3.047877 CCACGCGGGGTTCTGTTC 61.048 66.667 22.33 0.00 0.00 3.18
503 511 1.964373 GTGGAAATCCCGTGTGCGT 60.964 57.895 0.00 0.00 37.93 5.24
638 655 1.006639 GGATTTAGGGTTTGGGGAGCA 59.993 52.381 0.00 0.00 0.00 4.26
684 708 2.127232 GGCGGGATGGGTTTGATGG 61.127 63.158 0.00 0.00 0.00 3.51
686 710 2.278738 GGGCGGGATGGGTTTGAT 59.721 61.111 0.00 0.00 0.00 2.57
687 711 2.938798 AGGGCGGGATGGGTTTGA 60.939 61.111 0.00 0.00 0.00 2.69
688 712 2.440247 GAGGGCGGGATGGGTTTG 60.440 66.667 0.00 0.00 0.00 2.93
689 713 4.109675 CGAGGGCGGGATGGGTTT 62.110 66.667 0.00 0.00 0.00 3.27
691 715 4.880426 ATCGAGGGCGGGATGGGT 62.880 66.667 0.00 0.00 38.28 4.51
692 716 3.120086 AAATCGAGGGCGGGATGGG 62.120 63.158 0.00 0.00 38.28 4.00
693 717 1.598130 GAAATCGAGGGCGGGATGG 60.598 63.158 0.00 0.00 38.28 3.51
694 718 1.598130 GGAAATCGAGGGCGGGATG 60.598 63.158 0.00 0.00 38.28 3.51
695 719 2.819284 GGGAAATCGAGGGCGGGAT 61.819 63.158 0.00 0.00 38.28 3.85
696 720 3.476419 GGGAAATCGAGGGCGGGA 61.476 66.667 0.00 0.00 38.28 5.14
702 726 1.152963 ATTGGGCGGGAAATCGAGG 60.153 57.895 0.00 0.00 0.00 4.63
896 920 4.169068 AGCTAGGGTTAGATCTCTCCTTCA 59.831 45.833 14.20 0.89 0.00 3.02
897 921 4.736473 AGCTAGGGTTAGATCTCTCCTTC 58.264 47.826 14.20 8.69 0.00 3.46
898 922 4.448640 GGAGCTAGGGTTAGATCTCTCCTT 60.449 50.000 14.20 10.17 41.12 3.36
901 925 3.078837 CGGAGCTAGGGTTAGATCTCTC 58.921 54.545 0.00 0.00 41.12 3.20
1137 1167 1.432657 GTAGCGGAGAAGGACGTCC 59.567 63.158 27.67 27.67 0.00 4.79
1146 1176 2.360726 TGCGTGAGGTAGCGGAGA 60.361 61.111 0.00 0.00 35.87 3.71
1374 1404 2.651455 GGTATAGGGAACTTGGGCAAC 58.349 52.381 0.00 0.00 43.67 4.17
1479 1509 1.909781 GTAGGTGTGTGGGTCCGGA 60.910 63.158 0.00 0.00 0.00 5.14
1643 1673 3.451178 GGCTACACTATCCTCAGAAACCA 59.549 47.826 0.00 0.00 0.00 3.67
1679 1709 1.521450 CTTGCTCCCAGCTGGTTGTG 61.521 60.000 30.63 17.64 42.97 3.33
2110 2143 1.948834 TCGCCATAATGCAACTCCATG 59.051 47.619 0.00 0.00 0.00 3.66
2135 2168 4.170053 TCATAGATCCCTTCTCCCACACTA 59.830 45.833 0.00 0.00 35.79 2.74
2310 2343 1.962807 TGCATTGCCTAGCACAAACTT 59.037 42.857 6.12 0.00 38.71 2.66
2318 2351 3.511595 TGCGCTGCATTGCCTAGC 61.512 61.111 9.73 8.48 31.71 3.42
2364 2397 6.947376 ACTTACTACAGTTGGGTATCCTTT 57.053 37.500 0.00 0.00 0.00 3.11
2386 2419 9.582431 TGTAGTGCAAAGTCTACATAAGATTAC 57.418 33.333 10.05 0.00 40.66 1.89
2466 2691 2.415491 GCCCTTAGTTTAAAAGCAGGCG 60.415 50.000 0.00 0.00 0.00 5.52
2603 2830 9.099071 AGGACTATGCTTACTATCATCAGAAAT 57.901 33.333 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.