Multiple sequence alignment - TraesCS6D01G275800

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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 TraesCS6D01G275800 chr6D 100.000 3284 0 0 1 3284 384433923 384430640 0.000000e+00 6065.0
1 TraesCS6D01G275800 chr6A 84.512 2602 189 77 262 2702 529003159 529000611 0.000000e+00 2375.0
2 TraesCS6D01G275800 chr6A 95.400 587 25 2 2699 3284 529000317 528999732 0.000000e+00 933.0
3 TraesCS6D01G275800 chr6A 87.243 243 15 1 25 267 529014945 529014719 2.510000e-66 263.0
4 TraesCS6D01G275800 chr6A 100.000 34 0 0 2925 2958 102449584 102449617 2.740000e-06 63.9
5 TraesCS6D01G275800 chr6A 97.222 36 1 0 2925 2960 479441490 479441525 9.840000e-06 62.1
6 TraesCS6D01G275800 chr6B 91.491 1140 51 30 590 1691 574665951 574664820 0.000000e+00 1526.0
7 TraesCS6D01G275800 chr6B 93.863 554 34 0 2112 2665 574664279 574663726 0.000000e+00 835.0
8 TraesCS6D01G275800 chr6B 87.268 377 31 13 1689 2056 574664728 574664360 6.560000e-112 414.0
9 TraesCS6D01G275800 chr7D 89.091 55 4 2 2903 2956 40673747 40673800 2.110000e-07 67.6
10 TraesCS6D01G275800 chr3A 97.222 36 1 0 2925 2960 703927742 703927707 9.840000e-06 62.1
11 TraesCS6D01G275800 chr2B 93.023 43 1 2 2925 2967 609285120 609285080 9.840000e-06 62.1
12 TraesCS6D01G275800 chrUn 100.000 32 0 0 2925 2956 295889694 295889725 3.540000e-05 60.2
13 TraesCS6D01G275800 chr7A 100.000 32 0 0 2925 2956 499905095 499905126 3.540000e-05 60.2
14 TraesCS6D01G275800 chr1B 92.500 40 3 0 2917 2956 553942068 553942107 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 TraesCS6D01G275800 chr6D 384430640 384433923 3283 True 6065 6065 100.000 1 3284 1 chr6D.!!$R1 3283
1 TraesCS6D01G275800 chr6A 528999732 529003159 3427 True 1654 2375 89.956 262 3284 2 chr6A.!!$R2 3022
2 TraesCS6D01G275800 chr6B 574663726 574665951 2225 True 925 1526 90.874 590 2665 3 chr6B.!!$R1 2075

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
550 560 0.038251 TGAACTGTAGTCAGCTGCGG 60.038 55.0 9.47 2.28 44.77 5.69 F
1542 1652 0.316196 GTATGCATTTCGGCGACTGC 60.316 55.0 27.49 27.49 41.71 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1939 2192 0.031585 CCACAGAACGGTCGACTGAA 59.968 55.0 30.55 0.0 35.85 3.02 R
2613 2913 0.244721 GCCTTGCACAACAGGAATCC 59.755 55.0 6.34 0.0 0.00 3.01 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
41 42 7.448588 TCAAAATGTGTTTCAAGATTGTTCG 57.551 32.000 0.00 0.00 0.00 3.95
42 43 7.032580 TCAAAATGTGTTTCAAGATTGTTCGT 58.967 30.769 0.00 0.00 0.00 3.85
43 44 6.810888 AAATGTGTTTCAAGATTGTTCGTG 57.189 33.333 0.00 0.00 33.23 4.35
44 45 4.955925 TGTGTTTCAAGATTGTTCGTGT 57.044 36.364 0.00 0.00 33.63 4.49
45 46 5.303747 TGTGTTTCAAGATTGTTCGTGTT 57.696 34.783 0.00 0.00 33.63 3.32
46 47 5.704888 TGTGTTTCAAGATTGTTCGTGTTT 58.295 33.333 0.00 0.00 33.63 2.83
47 48 6.153067 TGTGTTTCAAGATTGTTCGTGTTTT 58.847 32.000 0.00 0.00 33.63 2.43
48 49 6.088749 TGTGTTTCAAGATTGTTCGTGTTTTG 59.911 34.615 0.00 0.00 33.63 2.44
49 50 6.306837 GTGTTTCAAGATTGTTCGTGTTTTGA 59.693 34.615 0.00 0.00 33.63 2.69
50 51 6.863645 TGTTTCAAGATTGTTCGTGTTTTGAA 59.136 30.769 0.00 0.00 33.63 2.69
51 52 7.382488 TGTTTCAAGATTGTTCGTGTTTTGAAA 59.618 29.630 5.64 5.64 39.39 2.69
52 53 7.875316 TTCAAGATTGTTCGTGTTTTGAAAA 57.125 28.000 0.00 0.00 33.63 2.29
53 54 7.875316 TCAAGATTGTTCGTGTTTTGAAAAA 57.125 28.000 0.00 0.00 33.63 1.94
54 55 7.725142 TCAAGATTGTTCGTGTTTTGAAAAAC 58.275 30.769 10.96 10.96 46.40 2.43
161 162 9.971744 AATTCAAAATTTCAAAAGACGTTCAAG 57.028 25.926 0.00 0.00 0.00 3.02
162 163 8.527567 TTCAAAATTTCAAAAGACGTTCAAGT 57.472 26.923 0.00 0.00 0.00 3.16
163 164 7.948137 TCAAAATTTCAAAAGACGTTCAAGTG 58.052 30.769 0.00 0.00 0.00 3.16
164 165 7.596995 TCAAAATTTCAAAAGACGTTCAAGTGT 59.403 29.630 0.00 0.00 0.00 3.55
165 166 8.855279 CAAAATTTCAAAAGACGTTCAAGTGTA 58.145 29.630 0.00 0.00 0.00 2.90
166 167 7.964545 AATTTCAAAAGACGTTCAAGTGTAC 57.035 32.000 0.00 0.00 0.00 2.90
167 168 4.765281 TCAAAAGACGTTCAAGTGTACG 57.235 40.909 8.65 8.65 43.06 3.67
168 169 3.552699 TCAAAAGACGTTCAAGTGTACGG 59.447 43.478 13.80 0.00 41.98 4.02
169 170 1.494824 AAGACGTTCAAGTGTACGGC 58.505 50.000 13.80 11.17 45.44 5.68
170 171 3.190337 GACGTTCAAGTGTACGGCT 57.810 52.632 13.80 0.00 42.46 5.52
171 172 0.782384 GACGTTCAAGTGTACGGCTG 59.218 55.000 13.80 0.00 42.46 4.85
172 173 0.386476 ACGTTCAAGTGTACGGCTGA 59.614 50.000 13.80 0.00 41.98 4.26
173 174 1.000506 ACGTTCAAGTGTACGGCTGAT 59.999 47.619 13.80 0.00 41.98 2.90
174 175 1.654105 CGTTCAAGTGTACGGCTGATC 59.346 52.381 0.00 0.00 35.61 2.92
175 176 2.683968 GTTCAAGTGTACGGCTGATCA 58.316 47.619 0.00 0.00 0.00 2.92
176 177 2.654749 TCAAGTGTACGGCTGATCAG 57.345 50.000 18.84 18.84 0.00 2.90
177 178 2.167662 TCAAGTGTACGGCTGATCAGA 58.832 47.619 27.04 1.88 0.00 3.27
178 179 2.164422 TCAAGTGTACGGCTGATCAGAG 59.836 50.000 27.04 19.95 0.00 3.35
179 180 1.840737 AGTGTACGGCTGATCAGAGT 58.159 50.000 27.04 24.11 0.00 3.24
180 181 2.171840 AGTGTACGGCTGATCAGAGTT 58.828 47.619 27.04 10.88 0.00 3.01
181 182 2.164624 AGTGTACGGCTGATCAGAGTTC 59.835 50.000 27.04 20.31 0.00 3.01
182 183 2.164624 GTGTACGGCTGATCAGAGTTCT 59.835 50.000 27.04 5.58 0.00 3.01
183 184 2.826128 TGTACGGCTGATCAGAGTTCTT 59.174 45.455 27.04 8.18 0.00 2.52
184 185 4.014406 TGTACGGCTGATCAGAGTTCTTA 58.986 43.478 27.04 7.29 0.00 2.10
185 186 4.461431 TGTACGGCTGATCAGAGTTCTTAA 59.539 41.667 27.04 6.95 0.00 1.85
186 187 3.851098 ACGGCTGATCAGAGTTCTTAAC 58.149 45.455 27.04 4.81 0.00 2.01
187 188 3.258372 ACGGCTGATCAGAGTTCTTAACA 59.742 43.478 27.04 0.00 0.00 2.41
188 189 3.614616 CGGCTGATCAGAGTTCTTAACAC 59.385 47.826 27.04 3.54 0.00 3.32
189 190 4.619394 CGGCTGATCAGAGTTCTTAACACT 60.619 45.833 27.04 0.00 32.34 3.55
190 191 4.867608 GGCTGATCAGAGTTCTTAACACTC 59.132 45.833 27.04 2.89 41.02 3.51
191 192 4.867608 GCTGATCAGAGTTCTTAACACTCC 59.132 45.833 27.04 0.00 41.55 3.85
192 193 5.060662 TGATCAGAGTTCTTAACACTCCG 57.939 43.478 0.00 0.00 41.55 4.63
193 194 3.299340 TCAGAGTTCTTAACACTCCGC 57.701 47.619 6.48 0.00 41.55 5.54
194 195 1.986378 CAGAGTTCTTAACACTCCGCG 59.014 52.381 0.00 0.00 41.55 6.46
195 196 0.714439 GAGTTCTTAACACTCCGCGC 59.286 55.000 0.00 0.00 35.53 6.86
196 197 0.317479 AGTTCTTAACACTCCGCGCT 59.683 50.000 5.56 0.00 0.00 5.92
197 198 1.542915 AGTTCTTAACACTCCGCGCTA 59.457 47.619 5.56 0.00 0.00 4.26
198 199 1.652619 GTTCTTAACACTCCGCGCTAC 59.347 52.381 5.56 0.00 0.00 3.58
199 200 1.171308 TCTTAACACTCCGCGCTACT 58.829 50.000 5.56 0.00 0.00 2.57
200 201 1.131883 TCTTAACACTCCGCGCTACTC 59.868 52.381 5.56 0.00 0.00 2.59
201 202 0.883153 TTAACACTCCGCGCTACTCA 59.117 50.000 5.56 0.00 0.00 3.41
202 203 1.100510 TAACACTCCGCGCTACTCAT 58.899 50.000 5.56 0.00 0.00 2.90
203 204 0.246635 AACACTCCGCGCTACTCATT 59.753 50.000 5.56 0.00 0.00 2.57
204 205 1.100510 ACACTCCGCGCTACTCATTA 58.899 50.000 5.56 0.00 0.00 1.90
205 206 1.065701 ACACTCCGCGCTACTCATTAG 59.934 52.381 5.56 0.00 0.00 1.73
206 207 1.065701 CACTCCGCGCTACTCATTAGT 59.934 52.381 5.56 0.00 39.91 2.24
207 208 1.334243 ACTCCGCGCTACTCATTAGTC 59.666 52.381 5.56 0.00 37.15 2.59
208 209 1.333931 CTCCGCGCTACTCATTAGTCA 59.666 52.381 5.56 0.00 37.15 3.41
209 210 1.065102 TCCGCGCTACTCATTAGTCAC 59.935 52.381 5.56 0.00 37.15 3.67
210 211 1.202256 CCGCGCTACTCATTAGTCACA 60.202 52.381 5.56 0.00 37.15 3.58
211 212 2.526077 CGCGCTACTCATTAGTCACAA 58.474 47.619 5.56 0.00 37.15 3.33
212 213 2.921121 CGCGCTACTCATTAGTCACAAA 59.079 45.455 5.56 0.00 37.15 2.83
213 214 3.366724 CGCGCTACTCATTAGTCACAAAA 59.633 43.478 5.56 0.00 37.15 2.44
214 215 4.490959 CGCGCTACTCATTAGTCACAAAAG 60.491 45.833 5.56 0.00 37.15 2.27
215 216 4.389077 GCGCTACTCATTAGTCACAAAAGT 59.611 41.667 0.00 0.00 37.15 2.66
216 217 5.107065 GCGCTACTCATTAGTCACAAAAGTT 60.107 40.000 0.00 0.00 37.15 2.66
217 218 6.526222 CGCTACTCATTAGTCACAAAAGTTC 58.474 40.000 0.00 0.00 37.15 3.01
218 219 6.526222 GCTACTCATTAGTCACAAAAGTTCG 58.474 40.000 0.00 0.00 37.15 3.95
219 220 6.145696 GCTACTCATTAGTCACAAAAGTTCGT 59.854 38.462 0.00 0.00 37.15 3.85
220 221 6.920569 ACTCATTAGTCACAAAAGTTCGTT 57.079 33.333 0.00 0.00 0.00 3.85
221 222 9.188588 CTACTCATTAGTCACAAAAGTTCGTTA 57.811 33.333 0.00 0.00 37.15 3.18
222 223 8.073355 ACTCATTAGTCACAAAAGTTCGTTAG 57.927 34.615 0.00 0.00 0.00 2.34
223 224 7.924412 ACTCATTAGTCACAAAAGTTCGTTAGA 59.076 33.333 0.00 0.00 0.00 2.10
224 225 8.827177 TCATTAGTCACAAAAGTTCGTTAGAT 57.173 30.769 0.00 0.00 0.00 1.98
225 226 9.268268 TCATTAGTCACAAAAGTTCGTTAGATT 57.732 29.630 0.00 0.00 0.00 2.40
226 227 9.530129 CATTAGTCACAAAAGTTCGTTAGATTC 57.470 33.333 0.00 0.00 0.00 2.52
227 228 8.651391 TTAGTCACAAAAGTTCGTTAGATTCA 57.349 30.769 0.00 0.00 0.00 2.57
228 229 7.178712 AGTCACAAAAGTTCGTTAGATTCAG 57.821 36.000 0.00 0.00 0.00 3.02
229 230 6.761714 AGTCACAAAAGTTCGTTAGATTCAGT 59.238 34.615 0.00 0.00 0.00 3.41
230 231 7.280205 AGTCACAAAAGTTCGTTAGATTCAGTT 59.720 33.333 0.00 0.00 0.00 3.16
231 232 7.373441 GTCACAAAAGTTCGTTAGATTCAGTTG 59.627 37.037 0.00 0.00 0.00 3.16
232 233 6.140737 CACAAAAGTTCGTTAGATTCAGTTGC 59.859 38.462 0.00 0.00 0.00 4.17
233 234 6.038271 ACAAAAGTTCGTTAGATTCAGTTGCT 59.962 34.615 0.00 0.00 0.00 3.91
234 235 7.225931 ACAAAAGTTCGTTAGATTCAGTTGCTA 59.774 33.333 0.00 0.00 0.00 3.49
235 236 6.952935 AAGTTCGTTAGATTCAGTTGCTAG 57.047 37.500 0.00 0.00 0.00 3.42
236 237 5.411781 AGTTCGTTAGATTCAGTTGCTAGG 58.588 41.667 0.00 0.00 0.00 3.02
237 238 3.782046 TCGTTAGATTCAGTTGCTAGGC 58.218 45.455 0.00 0.00 0.00 3.93
238 239 3.447586 TCGTTAGATTCAGTTGCTAGGCT 59.552 43.478 0.00 0.00 0.00 4.58
239 240 3.799420 CGTTAGATTCAGTTGCTAGGCTC 59.201 47.826 0.00 0.00 0.00 4.70
240 241 2.593346 AGATTCAGTTGCTAGGCTCG 57.407 50.000 0.00 0.00 0.00 5.03
241 242 0.933796 GATTCAGTTGCTAGGCTCGC 59.066 55.000 3.71 3.71 0.00 5.03
242 243 0.462759 ATTCAGTTGCTAGGCTCGCC 60.463 55.000 8.68 0.00 0.00 5.54
243 244 1.826340 TTCAGTTGCTAGGCTCGCCA 61.826 55.000 11.02 0.00 38.92 5.69
244 245 1.375908 CAGTTGCTAGGCTCGCCAA 60.376 57.895 11.02 0.00 38.92 4.52
245 246 1.376037 AGTTGCTAGGCTCGCCAAC 60.376 57.895 11.02 11.69 38.92 3.77
246 247 2.434185 TTGCTAGGCTCGCCAACG 60.434 61.111 11.02 0.00 38.92 4.10
314 315 3.364621 CGGAATTCATTTTGCTGGTTTCG 59.635 43.478 7.93 0.00 0.00 3.46
315 316 4.306600 GGAATTCATTTTGCTGGTTTCGT 58.693 39.130 7.93 0.00 0.00 3.85
344 345 1.461268 TGGAACCAGGTGCTCCTCA 60.461 57.895 11.13 0.00 43.07 3.86
345 346 0.842030 TGGAACCAGGTGCTCCTCAT 60.842 55.000 11.13 0.00 43.07 2.90
353 354 2.437281 CAGGTGCTCCTCATTCCATAGT 59.563 50.000 3.81 0.00 43.07 2.12
365 366 7.072328 TCCTCATTCCATAGTTTCATACCATGA 59.928 37.037 0.00 0.00 37.55 3.07
404 405 0.722469 CACGCATTGCACAACTCGAC 60.722 55.000 9.69 0.00 0.00 4.20
407 408 1.507713 CATTGCACAACTCGACGCG 60.508 57.895 3.53 3.53 0.00 6.01
415 416 1.400846 ACAACTCGACGCGTCTCATAT 59.599 47.619 33.94 15.37 0.00 1.78
425 426 3.551890 ACGCGTCTCATATTTCATCACAC 59.448 43.478 5.58 0.00 0.00 3.82
431 432 5.643348 GTCTCATATTTCATCACACACACCA 59.357 40.000 0.00 0.00 0.00 4.17
445 446 0.895100 ACACCATGCCATGTTTCGCT 60.895 50.000 3.63 0.00 0.00 4.93
446 447 1.093972 CACCATGCCATGTTTCGCTA 58.906 50.000 3.63 0.00 0.00 4.26
447 448 1.472082 CACCATGCCATGTTTCGCTAA 59.528 47.619 3.63 0.00 0.00 3.09
448 449 1.472480 ACCATGCCATGTTTCGCTAAC 59.528 47.619 3.63 0.00 37.26 2.34
496 503 0.962489 AAGCAGCAGTCAGTCGTAGT 59.038 50.000 0.00 0.00 0.00 2.73
522 529 1.202580 CCTCACATGGCCTACTGTAGC 60.203 57.143 3.32 5.21 0.00 3.58
527 534 1.123928 ATGGCCTACTGTAGCACTCC 58.876 55.000 3.32 7.73 0.00 3.85
544 554 4.380023 GCACTCCTACTGAACTGTAGTCAG 60.380 50.000 7.73 7.73 46.18 3.51
550 560 0.038251 TGAACTGTAGTCAGCTGCGG 60.038 55.000 9.47 2.28 44.77 5.69
887 911 4.518970 ACAGCGTTCACAAAGAAATACCAT 59.481 37.500 0.00 0.00 38.13 3.55
903 927 0.882042 CCATAGCACACTCGCCATCC 60.882 60.000 0.00 0.00 0.00 3.51
905 929 1.337384 ATAGCACACTCGCCATCCCA 61.337 55.000 0.00 0.00 0.00 4.37
1115 1158 2.184579 GAAGAAGGAGGACGGCGG 59.815 66.667 13.24 0.00 0.00 6.13
1401 1473 3.261951 CGGCGGATTGGCAGTACG 61.262 66.667 10.63 10.63 45.16 3.67
1402 1474 2.125269 GGCGGATTGGCAGTACGT 60.125 61.111 16.30 0.00 44.08 3.57
1403 1475 1.142314 GGCGGATTGGCAGTACGTA 59.858 57.895 16.30 0.00 44.08 3.57
1404 1476 1.149964 GGCGGATTGGCAGTACGTAC 61.150 60.000 18.10 18.10 44.08 3.67
1475 1552 4.644103 TCTAGCCGCCGATTATAATACC 57.356 45.455 0.00 0.00 0.00 2.73
1516 1593 1.742761 GCATCTTGCTAGCTTGTGGA 58.257 50.000 17.23 7.14 40.96 4.02
1517 1594 1.669779 GCATCTTGCTAGCTTGTGGAG 59.330 52.381 17.23 4.62 40.96 3.86
1518 1595 4.139302 GCATCTTGCTAGCTTGTGGAGC 62.139 54.545 17.23 7.73 45.51 4.70
1542 1652 0.316196 GTATGCATTTCGGCGACTGC 60.316 55.000 27.49 27.49 41.71 4.40
1543 1653 0.461870 TATGCATTTCGGCGACTGCT 60.462 50.000 31.22 22.64 42.25 4.24
1596 1706 5.523552 CGATGTACTTCTGCATTTGTATCCA 59.476 40.000 7.13 0.00 0.00 3.41
1685 1803 3.005367 CCACTCCCATTTTGTGTGTTACC 59.995 47.826 0.00 0.00 0.00 2.85
1935 2188 4.741676 GCACAGAAGTTTGACCAGAAAATG 59.258 41.667 0.00 0.00 0.00 2.32
1939 2192 1.956477 AGTTTGACCAGAAAATGCGCT 59.044 42.857 9.73 0.00 0.00 5.92
1943 2196 1.536766 TGACCAGAAAATGCGCTTCAG 59.463 47.619 9.73 0.72 0.00 3.02
1956 2218 0.318784 GCTTCAGTCGACCGTTCTGT 60.319 55.000 13.01 0.00 0.00 3.41
1961 2223 1.728426 GTCGACCGTTCTGTGGACG 60.728 63.158 3.51 0.00 44.18 4.79
1983 2245 2.978452 ATACTCACATCTGCCGCGCC 62.978 60.000 0.00 0.00 0.00 6.53
1988 2251 4.520846 CATCTGCCGCGCCGAAAC 62.521 66.667 0.00 0.00 0.00 2.78
2012 2275 0.469705 ACCAATGCCTGCCAACTTCA 60.470 50.000 0.00 0.00 0.00 3.02
2022 2285 1.761784 TGCCAACTTCACCATTGCTTT 59.238 42.857 0.00 0.00 0.00 3.51
2029 2293 7.601856 CCAACTTCACCATTGCTTTTCTAATA 58.398 34.615 0.00 0.00 0.00 0.98
2030 2294 8.087750 CCAACTTCACCATTGCTTTTCTAATAA 58.912 33.333 0.00 0.00 0.00 1.40
2031 2295 9.643693 CAACTTCACCATTGCTTTTCTAATAAT 57.356 29.630 0.00 0.00 0.00 1.28
2032 2296 9.643693 AACTTCACCATTGCTTTTCTAATAATG 57.356 29.630 0.00 0.00 0.00 1.90
2033 2297 7.761249 ACTTCACCATTGCTTTTCTAATAATGC 59.239 33.333 0.00 0.00 0.00 3.56
2034 2298 6.572519 TCACCATTGCTTTTCTAATAATGCC 58.427 36.000 0.00 0.00 0.00 4.40
2035 2299 6.154192 TCACCATTGCTTTTCTAATAATGCCA 59.846 34.615 0.00 0.00 0.00 4.92
2036 2300 6.256321 CACCATTGCTTTTCTAATAATGCCAC 59.744 38.462 0.00 0.00 0.00 5.01
2037 2301 6.070881 ACCATTGCTTTTCTAATAATGCCACA 60.071 34.615 0.00 0.00 0.00 4.17
2056 2320 5.040635 CCACACACAATTTAACCAGACAAC 58.959 41.667 0.00 0.00 0.00 3.32
2057 2321 5.393569 CCACACACAATTTAACCAGACAACA 60.394 40.000 0.00 0.00 0.00 3.33
2058 2322 6.096036 CACACACAATTTAACCAGACAACAA 58.904 36.000 0.00 0.00 0.00 2.83
2068 2332 4.882671 ACCAGACAACAATCGCATTATC 57.117 40.909 0.00 0.00 0.00 1.75
2085 2349 6.301687 CATTATCTGCTGGAACATTCTCAG 57.698 41.667 6.00 6.00 38.20 3.35
2086 2350 2.775911 TCTGCTGGAACATTCTCAGG 57.224 50.000 10.29 0.00 38.20 3.86
2099 2363 1.229428 TCTCAGGCTTTGCGTTTCTG 58.771 50.000 0.00 0.00 0.00 3.02
2100 2364 1.202639 TCTCAGGCTTTGCGTTTCTGA 60.203 47.619 0.00 0.00 33.96 3.27
2142 2436 2.432628 CAGGAGTTCGACACCGCC 60.433 66.667 0.00 0.00 33.85 6.13
2196 2490 1.544691 AGCTTCGGTTCATACGTCACT 59.455 47.619 0.00 0.00 0.00 3.41
2300 2594 0.250124 TGACGACGGCCAGACAAATT 60.250 50.000 2.24 0.00 0.00 1.82
2334 2628 1.026718 GTATGCACCTGTGTGGGAGC 61.027 60.000 0.00 0.00 42.99 4.70
2335 2629 3.487626 TGCACCTGTGTGGGAGCA 61.488 61.111 1.82 1.82 44.70 4.26
2376 2670 1.577328 ATGCAAACGGTTCGGCTGAG 61.577 55.000 15.50 0.00 0.00 3.35
2399 2698 4.032786 GCAAGCCCTTGTAATTAAATTGCG 59.967 41.667 9.53 0.00 42.31 4.85
2414 2713 4.481930 AATTGCGTTGTTTCTTCGATGA 57.518 36.364 0.00 0.00 0.00 2.92
2440 2739 2.749621 GGAGACTCCATTTTTGCGTCAT 59.250 45.455 17.10 0.00 36.28 3.06
2462 2762 1.879380 TCTACGGTTCGAAACTCCGAA 59.121 47.619 26.62 12.29 46.05 4.30
2560 2860 4.455533 TGTTCTGTAGATGTCCAAACATGC 59.544 41.667 0.00 0.00 46.20 4.06
2613 2913 6.798959 GCAAGCTTTCAGAATGTACTAAACAG 59.201 38.462 0.00 0.00 42.70 3.16
2618 2918 8.178313 GCTTTCAGAATGTACTAAACAGGATTC 58.822 37.037 0.00 0.00 42.70 2.52
2962 3562 3.453353 GGGCATGTTTCCTAGTGGTAGTA 59.547 47.826 0.00 0.00 34.23 1.82
2971 3571 5.927281 TCCTAGTGGTAGTACAATTCACC 57.073 43.478 2.06 0.00 34.23 4.02
2972 3572 4.713321 TCCTAGTGGTAGTACAATTCACCC 59.287 45.833 2.06 0.00 34.23 4.61
3036 3636 3.370953 GCTTAGGTCATGGGATGAGTGTT 60.371 47.826 0.00 0.00 40.53 3.32
3062 3662 3.820467 TGAAGCTCTTGTATGTTTGTGGG 59.180 43.478 0.00 0.00 0.00 4.61
3072 3672 0.754957 TGTTTGTGGGCTCCAGTTGG 60.755 55.000 0.00 0.00 32.34 3.77
3091 3691 5.711976 AGTTGGAACATGAATTGGAGGTTAG 59.288 40.000 0.00 0.00 39.30 2.34
3134 3734 7.801104 TCATGGTAAGCCTTTATCTGACATTA 58.199 34.615 0.00 0.00 35.27 1.90
3177 3777 8.445275 TTCCTATGTGCGTAAATGACATAAAT 57.555 30.769 0.00 0.00 33.32 1.40
3198 3798 0.623723 ACATAGCCCATGGTTTCGGT 59.376 50.000 11.73 3.19 39.13 4.69
3206 3806 0.602562 CATGGTTTCGGTTGTGCCAT 59.397 50.000 0.00 0.00 40.22 4.40
3210 3810 0.939106 GTTTCGGTTGTGCCATGTGC 60.939 55.000 0.00 0.00 41.77 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 8.379161 CGAACAATCTTGAAACACATTTTGAAA 58.621 29.630 0.00 0.00 0.00 2.69
16 17 7.543868 ACGAACAATCTTGAAACACATTTTGAA 59.456 29.630 0.00 0.00 0.00 2.69
17 18 7.009083 CACGAACAATCTTGAAACACATTTTGA 59.991 33.333 0.00 0.00 0.00 2.69
18 19 7.112397 CACGAACAATCTTGAAACACATTTTG 58.888 34.615 0.00 0.00 0.00 2.44
19 20 6.811170 ACACGAACAATCTTGAAACACATTTT 59.189 30.769 0.00 0.00 0.00 1.82
20 21 6.329496 ACACGAACAATCTTGAAACACATTT 58.671 32.000 0.00 0.00 0.00 2.32
21 22 5.890334 ACACGAACAATCTTGAAACACATT 58.110 33.333 0.00 0.00 0.00 2.71
22 23 5.499139 ACACGAACAATCTTGAAACACAT 57.501 34.783 0.00 0.00 0.00 3.21
23 24 4.955925 ACACGAACAATCTTGAAACACA 57.044 36.364 0.00 0.00 0.00 3.72
24 25 6.306837 TCAAAACACGAACAATCTTGAAACAC 59.693 34.615 0.00 0.00 0.00 3.32
25 26 6.382608 TCAAAACACGAACAATCTTGAAACA 58.617 32.000 0.00 0.00 0.00 2.83
26 27 6.862944 TCAAAACACGAACAATCTTGAAAC 57.137 33.333 0.00 0.00 0.00 2.78
27 28 7.875316 TTTCAAAACACGAACAATCTTGAAA 57.125 28.000 0.00 0.00 38.37 2.69
28 29 7.875316 TTTTCAAAACACGAACAATCTTGAA 57.125 28.000 0.00 0.00 31.41 2.69
29 30 7.409874 CGTTTTTCAAAACACGAACAATCTTGA 60.410 33.333 14.05 0.00 46.52 3.02
30 31 6.672439 CGTTTTTCAAAACACGAACAATCTTG 59.328 34.615 14.05 0.00 46.52 3.02
31 32 6.363896 ACGTTTTTCAAAACACGAACAATCTT 59.636 30.769 17.95 0.00 46.52 2.40
32 33 5.859648 ACGTTTTTCAAAACACGAACAATCT 59.140 32.000 17.95 0.00 46.52 2.40
33 34 5.943573 CACGTTTTTCAAAACACGAACAATC 59.056 36.000 17.95 0.00 46.52 2.67
34 35 5.402867 ACACGTTTTTCAAAACACGAACAAT 59.597 32.000 17.95 0.00 46.52 2.71
35 36 4.738740 ACACGTTTTTCAAAACACGAACAA 59.261 33.333 17.95 0.00 46.52 2.83
36 37 4.288531 ACACGTTTTTCAAAACACGAACA 58.711 34.783 17.95 0.00 46.52 3.18
37 38 4.872051 ACACGTTTTTCAAAACACGAAC 57.128 36.364 17.95 0.69 46.52 3.95
38 39 4.974275 TGAACACGTTTTTCAAAACACGAA 59.026 33.333 17.95 0.00 46.52 3.85
39 40 4.534168 TGAACACGTTTTTCAAAACACGA 58.466 34.783 17.95 0.00 46.52 4.35
40 41 4.870315 TGAACACGTTTTTCAAAACACG 57.130 36.364 14.05 11.42 46.52 4.49
135 136 9.971744 CTTGAACGTCTTTTGAAATTTTGAATT 57.028 25.926 0.00 0.00 0.00 2.17
136 137 9.150348 ACTTGAACGTCTTTTGAAATTTTGAAT 57.850 25.926 0.00 0.00 0.00 2.57
137 138 8.431593 CACTTGAACGTCTTTTGAAATTTTGAA 58.568 29.630 0.00 0.00 0.00 2.69
138 139 7.596995 ACACTTGAACGTCTTTTGAAATTTTGA 59.403 29.630 0.00 0.00 0.00 2.69
139 140 7.728895 ACACTTGAACGTCTTTTGAAATTTTG 58.271 30.769 0.00 0.00 0.00 2.44
140 141 7.883229 ACACTTGAACGTCTTTTGAAATTTT 57.117 28.000 0.00 0.00 0.00 1.82
141 142 7.217447 CGTACACTTGAACGTCTTTTGAAATTT 59.783 33.333 0.00 0.00 34.48 1.82
142 143 6.685403 CGTACACTTGAACGTCTTTTGAAATT 59.315 34.615 0.00 0.00 34.48 1.82
143 144 6.189567 CGTACACTTGAACGTCTTTTGAAAT 58.810 36.000 0.00 0.00 34.48 2.17
144 145 5.446206 CCGTACACTTGAACGTCTTTTGAAA 60.446 40.000 0.00 0.00 37.40 2.69
145 146 4.033129 CCGTACACTTGAACGTCTTTTGAA 59.967 41.667 0.00 0.00 37.40 2.69
146 147 3.552699 CCGTACACTTGAACGTCTTTTGA 59.447 43.478 0.00 0.00 37.40 2.69
147 148 3.843510 GCCGTACACTTGAACGTCTTTTG 60.844 47.826 0.00 0.00 37.40 2.44
148 149 2.286025 GCCGTACACTTGAACGTCTTTT 59.714 45.455 0.00 0.00 37.40 2.27
149 150 1.862827 GCCGTACACTTGAACGTCTTT 59.137 47.619 0.00 0.00 37.40 2.52
150 151 1.068127 AGCCGTACACTTGAACGTCTT 59.932 47.619 0.00 0.00 37.40 3.01
151 152 0.672342 AGCCGTACACTTGAACGTCT 59.328 50.000 0.00 0.00 37.40 4.18
152 153 0.782384 CAGCCGTACACTTGAACGTC 59.218 55.000 0.00 0.00 37.40 4.34
153 154 0.386476 TCAGCCGTACACTTGAACGT 59.614 50.000 0.00 0.00 37.40 3.99
154 155 1.654105 GATCAGCCGTACACTTGAACG 59.346 52.381 0.00 0.00 38.80 3.95
155 156 2.668457 CTGATCAGCCGTACACTTGAAC 59.332 50.000 10.38 0.00 0.00 3.18
156 157 2.560981 TCTGATCAGCCGTACACTTGAA 59.439 45.455 18.36 0.00 0.00 2.69
157 158 2.164422 CTCTGATCAGCCGTACACTTGA 59.836 50.000 18.36 0.00 0.00 3.02
158 159 2.094494 ACTCTGATCAGCCGTACACTTG 60.094 50.000 18.36 0.00 0.00 3.16
159 160 2.171840 ACTCTGATCAGCCGTACACTT 58.828 47.619 18.36 0.00 0.00 3.16
160 161 1.840737 ACTCTGATCAGCCGTACACT 58.159 50.000 18.36 0.00 0.00 3.55
161 162 2.164624 AGAACTCTGATCAGCCGTACAC 59.835 50.000 18.36 11.44 0.00 2.90
162 163 2.447443 AGAACTCTGATCAGCCGTACA 58.553 47.619 18.36 0.00 0.00 2.90
163 164 3.512033 AAGAACTCTGATCAGCCGTAC 57.488 47.619 18.36 8.01 0.00 3.67
164 165 4.461431 TGTTAAGAACTCTGATCAGCCGTA 59.539 41.667 18.36 6.78 0.00 4.02
165 166 3.258372 TGTTAAGAACTCTGATCAGCCGT 59.742 43.478 18.36 13.88 0.00 5.68
166 167 3.614616 GTGTTAAGAACTCTGATCAGCCG 59.385 47.826 18.36 13.25 0.00 5.52
167 168 4.826556 AGTGTTAAGAACTCTGATCAGCC 58.173 43.478 18.36 6.95 34.25 4.85
168 169 4.867608 GGAGTGTTAAGAACTCTGATCAGC 59.132 45.833 18.36 3.87 43.03 4.26
175 176 1.669211 GCGCGGAGTGTTAAGAACTCT 60.669 52.381 8.83 0.00 43.03 3.24
176 177 0.714439 GCGCGGAGTGTTAAGAACTC 59.286 55.000 8.83 8.98 42.79 3.01
177 178 0.317479 AGCGCGGAGTGTTAAGAACT 59.683 50.000 8.83 0.00 41.96 3.01
178 179 1.652619 GTAGCGCGGAGTGTTAAGAAC 59.347 52.381 8.83 0.00 41.96 3.01
179 180 1.542915 AGTAGCGCGGAGTGTTAAGAA 59.457 47.619 8.83 0.00 41.96 2.52
180 181 1.131883 GAGTAGCGCGGAGTGTTAAGA 59.868 52.381 8.83 0.00 41.96 2.10
181 182 1.135489 TGAGTAGCGCGGAGTGTTAAG 60.135 52.381 8.83 0.00 41.96 1.85
182 183 0.883153 TGAGTAGCGCGGAGTGTTAA 59.117 50.000 8.83 0.00 41.96 2.01
183 184 1.100510 ATGAGTAGCGCGGAGTGTTA 58.899 50.000 8.83 0.00 41.96 2.41
184 185 0.246635 AATGAGTAGCGCGGAGTGTT 59.753 50.000 8.83 0.00 41.96 3.32
185 186 1.065701 CTAATGAGTAGCGCGGAGTGT 59.934 52.381 8.83 0.00 41.96 3.55
186 187 1.065701 ACTAATGAGTAGCGCGGAGTG 59.934 52.381 8.83 0.00 35.77 3.51
187 188 1.334243 GACTAATGAGTAGCGCGGAGT 59.666 52.381 8.83 0.00 35.45 3.85
188 189 1.333931 TGACTAATGAGTAGCGCGGAG 59.666 52.381 8.83 0.00 35.45 4.63
189 190 1.065102 GTGACTAATGAGTAGCGCGGA 59.935 52.381 8.83 0.00 35.45 5.54
190 191 1.202256 TGTGACTAATGAGTAGCGCGG 60.202 52.381 8.83 0.00 35.45 6.46
191 192 2.188837 TGTGACTAATGAGTAGCGCG 57.811 50.000 0.00 0.00 35.45 6.86
192 193 4.389077 ACTTTTGTGACTAATGAGTAGCGC 59.611 41.667 0.00 0.00 35.45 5.92
193 194 6.467723 AACTTTTGTGACTAATGAGTAGCG 57.532 37.500 0.29 0.00 35.45 4.26
194 195 6.145696 ACGAACTTTTGTGACTAATGAGTAGC 59.854 38.462 0.00 0.00 35.45 3.58
195 196 7.639162 ACGAACTTTTGTGACTAATGAGTAG 57.361 36.000 0.00 0.00 35.45 2.57
196 197 9.188588 CTAACGAACTTTTGTGACTAATGAGTA 57.811 33.333 0.00 0.00 35.45 2.59
197 198 6.920569 AACGAACTTTTGTGACTAATGAGT 57.079 33.333 0.00 0.00 39.20 3.41
198 199 8.294341 TCTAACGAACTTTTGTGACTAATGAG 57.706 34.615 0.00 0.00 0.00 2.90
199 200 8.827177 ATCTAACGAACTTTTGTGACTAATGA 57.173 30.769 0.00 0.00 0.00 2.57
200 201 9.530129 GAATCTAACGAACTTTTGTGACTAATG 57.470 33.333 0.00 0.00 0.00 1.90
201 202 9.268268 TGAATCTAACGAACTTTTGTGACTAAT 57.732 29.630 0.00 0.00 0.00 1.73
202 203 8.651391 TGAATCTAACGAACTTTTGTGACTAA 57.349 30.769 0.00 0.00 0.00 2.24
203 204 7.924412 ACTGAATCTAACGAACTTTTGTGACTA 59.076 33.333 0.00 0.00 0.00 2.59
204 205 6.761714 ACTGAATCTAACGAACTTTTGTGACT 59.238 34.615 0.00 0.00 0.00 3.41
205 206 6.945072 ACTGAATCTAACGAACTTTTGTGAC 58.055 36.000 0.00 0.00 0.00 3.67
206 207 7.406553 CAACTGAATCTAACGAACTTTTGTGA 58.593 34.615 0.00 0.00 0.00 3.58
207 208 6.140737 GCAACTGAATCTAACGAACTTTTGTG 59.859 38.462 0.00 0.00 0.00 3.33
208 209 6.038271 AGCAACTGAATCTAACGAACTTTTGT 59.962 34.615 0.00 0.00 0.00 2.83
209 210 6.430451 AGCAACTGAATCTAACGAACTTTTG 58.570 36.000 0.00 0.00 0.00 2.44
210 211 6.619801 AGCAACTGAATCTAACGAACTTTT 57.380 33.333 0.00 0.00 0.00 2.27
211 212 6.369065 CCTAGCAACTGAATCTAACGAACTTT 59.631 38.462 0.00 0.00 0.00 2.66
212 213 5.869888 CCTAGCAACTGAATCTAACGAACTT 59.130 40.000 0.00 0.00 0.00 2.66
213 214 5.411781 CCTAGCAACTGAATCTAACGAACT 58.588 41.667 0.00 0.00 0.00 3.01
214 215 4.033014 GCCTAGCAACTGAATCTAACGAAC 59.967 45.833 0.00 0.00 0.00 3.95
215 216 4.081642 AGCCTAGCAACTGAATCTAACGAA 60.082 41.667 0.00 0.00 0.00 3.85
216 217 3.447586 AGCCTAGCAACTGAATCTAACGA 59.552 43.478 0.00 0.00 0.00 3.85
217 218 3.786635 AGCCTAGCAACTGAATCTAACG 58.213 45.455 0.00 0.00 0.00 3.18
218 219 3.799420 CGAGCCTAGCAACTGAATCTAAC 59.201 47.826 0.00 0.00 0.00 2.34
219 220 3.738281 GCGAGCCTAGCAACTGAATCTAA 60.738 47.826 0.00 0.00 34.19 2.10
220 221 2.223829 GCGAGCCTAGCAACTGAATCTA 60.224 50.000 0.00 0.00 34.19 1.98
221 222 1.472376 GCGAGCCTAGCAACTGAATCT 60.472 52.381 0.00 0.00 34.19 2.40
222 223 0.933796 GCGAGCCTAGCAACTGAATC 59.066 55.000 0.00 0.00 34.19 2.52
223 224 0.462759 GGCGAGCCTAGCAACTGAAT 60.463 55.000 6.90 0.00 36.08 2.57
224 225 1.079127 GGCGAGCCTAGCAACTGAA 60.079 57.895 6.90 0.00 36.08 3.02
225 226 1.826340 TTGGCGAGCCTAGCAACTGA 61.826 55.000 15.75 0.00 36.94 3.41
226 227 1.375908 TTGGCGAGCCTAGCAACTG 60.376 57.895 15.75 0.00 36.94 3.16
227 228 1.376037 GTTGGCGAGCCTAGCAACT 60.376 57.895 15.75 0.00 36.94 3.16
228 229 2.740714 CGTTGGCGAGCCTAGCAAC 61.741 63.158 15.75 9.89 41.33 4.17
229 230 2.434185 CGTTGGCGAGCCTAGCAA 60.434 61.111 15.75 0.00 41.33 3.91
230 231 3.378602 TCGTTGGCGAGCCTAGCA 61.379 61.111 15.75 0.00 42.81 3.49
245 246 2.486636 TATTAGCAGCCGGGCGATCG 62.487 60.000 14.39 11.69 39.27 3.69
246 247 0.737715 CTATTAGCAGCCGGGCGATC 60.738 60.000 14.39 6.73 39.27 3.69
247 248 1.293498 CTATTAGCAGCCGGGCGAT 59.707 57.895 14.39 10.02 39.27 4.58
248 249 2.734591 CTATTAGCAGCCGGGCGA 59.265 61.111 14.39 0.00 39.27 5.54
249 250 2.357517 CCTATTAGCAGCCGGGCG 60.358 66.667 14.39 9.89 39.27 6.13
250 251 1.004440 CTCCTATTAGCAGCCGGGC 60.004 63.158 12.11 12.11 0.00 6.13
251 252 1.004440 GCTCCTATTAGCAGCCGGG 60.004 63.158 2.18 0.00 42.30 5.73
252 253 0.037790 GAGCTCCTATTAGCAGCCGG 60.038 60.000 0.87 0.00 45.30 6.13
253 254 0.037790 GGAGCTCCTATTAGCAGCCG 60.038 60.000 26.25 0.00 45.30 5.52
254 255 0.323302 GGGAGCTCCTATTAGCAGCC 59.677 60.000 31.36 7.64 45.30 4.85
255 256 0.037790 CGGGAGCTCCTATTAGCAGC 60.038 60.000 31.36 11.02 45.30 5.25
256 257 0.605589 CCGGGAGCTCCTATTAGCAG 59.394 60.000 31.36 12.47 45.30 4.24
257 258 0.832135 CCCGGGAGCTCCTATTAGCA 60.832 60.000 31.36 0.00 45.30 3.49
258 259 1.545706 CCCCGGGAGCTCCTATTAGC 61.546 65.000 31.36 13.24 43.11 3.09
259 260 0.114560 TCCCCGGGAGCTCCTATTAG 59.885 60.000 31.36 16.66 35.95 1.73
260 261 0.114560 CTCCCCGGGAGCTCCTATTA 59.885 60.000 31.36 12.99 43.29 0.98
291 292 3.317603 AACCAGCAAAATGAATTCCGG 57.682 42.857 2.27 0.00 0.00 5.14
314 315 2.076863 CTGGTTCCAGGTTTGATCGAC 58.923 52.381 10.71 0.00 0.00 4.20
315 316 1.003118 CCTGGTTCCAGGTTTGATCGA 59.997 52.381 25.10 0.00 46.22 3.59
388 389 1.793613 GCGTCGAGTTGTGCAATGC 60.794 57.895 0.00 0.00 0.00 3.56
391 392 2.582265 GACGCGTCGAGTTGTGCAA 61.582 57.895 25.19 0.00 0.00 4.08
404 405 3.551485 TGTGTGATGAAATATGAGACGCG 59.449 43.478 3.53 3.53 0.00 6.01
407 408 5.643348 TGGTGTGTGTGATGAAATATGAGAC 59.357 40.000 0.00 0.00 0.00 3.36
415 416 1.612950 GGCATGGTGTGTGTGATGAAA 59.387 47.619 0.00 0.00 0.00 2.69
425 426 0.733566 GCGAAACATGGCATGGTGTG 60.734 55.000 29.49 20.19 33.60 3.82
445 446 2.560981 TCCTCGCTTCACTGTGATGTTA 59.439 45.455 20.52 10.93 0.00 2.41
446 447 1.344438 TCCTCGCTTCACTGTGATGTT 59.656 47.619 20.52 0.00 0.00 2.71
447 448 0.969149 TCCTCGCTTCACTGTGATGT 59.031 50.000 20.52 0.00 0.00 3.06
448 449 1.354040 GTCCTCGCTTCACTGTGATG 58.646 55.000 11.86 14.72 0.00 3.07
450 451 1.285950 CGTCCTCGCTTCACTGTGA 59.714 57.895 6.36 6.36 0.00 3.58
451 452 1.734477 CCGTCCTCGCTTCACTGTG 60.734 63.158 0.17 0.17 35.54 3.66
452 453 1.901948 TCCGTCCTCGCTTCACTGT 60.902 57.895 0.00 0.00 35.54 3.55
455 456 2.126031 GGTCCGTCCTCGCTTCAC 60.126 66.667 0.00 0.00 35.54 3.18
475 482 0.109735 TACGACTGACTGCTGCTTCG 60.110 55.000 0.00 2.42 0.00 3.79
496 503 2.047061 GTAGGCCATGTGAGGATGGTA 58.953 52.381 5.01 0.00 44.37 3.25
522 529 4.380023 GCTGACTACAGTTCAGTAGGAGTG 60.380 50.000 4.50 0.00 44.49 3.51
527 534 3.506810 GCAGCTGACTACAGTTCAGTAG 58.493 50.000 20.43 0.00 45.04 2.57
872 896 6.500684 AGTGTGCTATGGTATTTCTTTGTG 57.499 37.500 0.00 0.00 0.00 3.33
887 911 1.549243 TTGGGATGGCGAGTGTGCTA 61.549 55.000 0.00 0.00 34.52 3.49
1289 1332 0.744771 GGAGACGGCAATGGAGTTCC 60.745 60.000 0.00 0.00 0.00 3.62
1401 1473 8.341173 AGTACTAGCAATCATGTAAGTACGTAC 58.659 37.037 18.10 18.10 43.78 3.67
1402 1474 8.442632 AGTACTAGCAATCATGTAAGTACGTA 57.557 34.615 0.00 0.00 43.78 3.57
1403 1475 7.330900 AGTACTAGCAATCATGTAAGTACGT 57.669 36.000 0.00 0.00 43.78 3.57
1404 1476 8.557864 ACTAGTACTAGCAATCATGTAAGTACG 58.442 37.037 26.54 1.30 43.78 3.67
1409 1481 9.286170 CTCCTACTAGTACTAGCAATCATGTAA 57.714 37.037 26.54 4.16 36.66 2.41
1475 1552 2.029288 ACTCGCTGCACAATCACGG 61.029 57.895 0.00 0.00 0.00 4.94
1513 1590 2.419673 CGAAATGCATACACTTGCTCCA 59.580 45.455 0.00 0.00 43.18 3.86
1514 1591 2.223340 CCGAAATGCATACACTTGCTCC 60.223 50.000 0.00 0.00 43.18 4.70
1515 1592 2.792542 GCCGAAATGCATACACTTGCTC 60.793 50.000 0.00 0.00 43.18 4.26
1516 1593 1.133025 GCCGAAATGCATACACTTGCT 59.867 47.619 0.00 0.00 43.18 3.91
1517 1594 1.548986 GCCGAAATGCATACACTTGC 58.451 50.000 0.00 0.00 43.07 4.01
1518 1595 1.396648 TCGCCGAAATGCATACACTTG 59.603 47.619 0.00 0.00 0.00 3.16
1519 1596 1.396996 GTCGCCGAAATGCATACACTT 59.603 47.619 0.00 0.00 0.00 3.16
1520 1597 1.006832 GTCGCCGAAATGCATACACT 58.993 50.000 0.00 0.00 0.00 3.55
1521 1598 1.006832 AGTCGCCGAAATGCATACAC 58.993 50.000 0.00 0.00 0.00 2.90
1522 1599 1.006086 CAGTCGCCGAAATGCATACA 58.994 50.000 0.00 0.00 0.00 2.29
1524 1601 0.461870 AGCAGTCGCCGAAATGCATA 60.462 50.000 22.60 0.00 41.14 3.14
1526 1603 2.358615 AGCAGTCGCCGAAATGCA 60.359 55.556 22.60 0.00 41.14 3.96
1527 1604 2.029904 GAGAGCAGTCGCCGAAATGC 62.030 60.000 15.51 15.51 39.83 3.56
1542 1652 2.510012 TGCATTGCCGCGAGAGAG 60.510 61.111 8.23 0.00 33.35 3.20
1543 1653 2.510012 CTGCATTGCCGCGAGAGA 60.510 61.111 8.23 0.00 33.35 3.10
1596 1706 1.074405 TGCAGCTCAATCCTTCAAGGT 59.926 47.619 2.50 0.00 36.53 3.50
1685 1803 5.306394 TCGATACACTCCATCTAGGTAGTG 58.694 45.833 4.63 4.63 44.37 2.74
1935 2188 2.717809 GAACGGTCGACTGAAGCGC 61.718 63.158 30.55 0.00 41.07 5.92
1939 2192 0.031585 CCACAGAACGGTCGACTGAA 59.968 55.000 30.55 0.00 35.85 3.02
1943 2196 1.728426 CGTCCACAGAACGGTCGAC 60.728 63.158 7.13 7.13 37.26 4.20
1956 2218 2.159099 GCAGATGTGAGTATTCCGTCCA 60.159 50.000 0.00 0.00 0.00 4.02
1961 2223 1.221414 GCGGCAGATGTGAGTATTCC 58.779 55.000 0.00 0.00 0.00 3.01
1983 2245 1.154225 GGCATTGGTGAGCGTTTCG 60.154 57.895 0.00 0.00 0.00 3.46
1984 2246 0.109597 CAGGCATTGGTGAGCGTTTC 60.110 55.000 0.00 0.00 0.00 2.78
1988 2251 3.818787 GGCAGGCATTGGTGAGCG 61.819 66.667 0.00 0.00 0.00 5.03
1992 2255 0.037975 GAAGTTGGCAGGCATTGGTG 60.038 55.000 0.00 0.00 0.00 4.17
1993 2256 0.469705 TGAAGTTGGCAGGCATTGGT 60.470 50.000 0.00 0.00 0.00 3.67
1994 2257 0.037975 GTGAAGTTGGCAGGCATTGG 60.038 55.000 0.00 0.00 0.00 3.16
2012 2275 6.070881 TGTGGCATTATTAGAAAAGCAATGGT 60.071 34.615 0.00 0.00 0.00 3.55
2022 2285 9.632807 GTTAAATTGTGTGTGGCATTATTAGAA 57.367 29.630 0.00 0.00 0.00 2.10
2029 2293 4.343526 TCTGGTTAAATTGTGTGTGGCATT 59.656 37.500 0.00 0.00 0.00 3.56
2030 2294 3.894427 TCTGGTTAAATTGTGTGTGGCAT 59.106 39.130 0.00 0.00 0.00 4.40
2031 2295 3.067461 GTCTGGTTAAATTGTGTGTGGCA 59.933 43.478 0.00 0.00 0.00 4.92
2032 2296 3.067461 TGTCTGGTTAAATTGTGTGTGGC 59.933 43.478 0.00 0.00 0.00 5.01
2033 2297 4.909696 TGTCTGGTTAAATTGTGTGTGG 57.090 40.909 0.00 0.00 0.00 4.17
2034 2298 5.645624 TGTTGTCTGGTTAAATTGTGTGTG 58.354 37.500 0.00 0.00 0.00 3.82
2035 2299 5.906113 TGTTGTCTGGTTAAATTGTGTGT 57.094 34.783 0.00 0.00 0.00 3.72
2036 2300 6.142161 CGATTGTTGTCTGGTTAAATTGTGTG 59.858 38.462 0.00 0.00 0.00 3.82
2037 2301 6.205784 CGATTGTTGTCTGGTTAAATTGTGT 58.794 36.000 0.00 0.00 0.00 3.72
2068 2332 1.093159 GCCTGAGAATGTTCCAGCAG 58.907 55.000 0.00 0.00 0.00 4.24
2071 2335 2.094854 GCAAAGCCTGAGAATGTTCCAG 60.095 50.000 0.00 0.00 0.00 3.86
2073 2337 1.135575 CGCAAAGCCTGAGAATGTTCC 60.136 52.381 0.00 0.00 0.00 3.62
2085 2349 4.515107 CGTCAGAAACGCAAAGCC 57.485 55.556 0.00 0.00 45.76 4.35
2099 2363 2.678336 CAAAGGATAACAAGCTCCCGTC 59.322 50.000 0.00 0.00 0.00 4.79
2100 2364 2.711542 CAAAGGATAACAAGCTCCCGT 58.288 47.619 0.00 0.00 0.00 5.28
2102 2366 2.424956 CAGCAAAGGATAACAAGCTCCC 59.575 50.000 0.00 0.00 0.00 4.30
2103 2367 3.127721 GTCAGCAAAGGATAACAAGCTCC 59.872 47.826 0.00 0.00 0.00 4.70
2104 2368 3.753272 TGTCAGCAAAGGATAACAAGCTC 59.247 43.478 0.00 0.00 0.00 4.09
2106 2370 3.119708 CCTGTCAGCAAAGGATAACAAGC 60.120 47.826 0.00 0.00 35.40 4.01
2107 2371 4.326826 TCCTGTCAGCAAAGGATAACAAG 58.673 43.478 0.00 0.00 37.68 3.16
2211 2505 8.837389 ACCTTATCAACAGAAAAGTACAAGAAC 58.163 33.333 0.00 0.00 0.00 3.01
2287 2581 0.591170 AACGACAATTTGTCTGGCCG 59.409 50.000 23.29 14.73 44.85 6.13
2300 2594 4.390603 GGTGCATACAATTAGTGAACGACA 59.609 41.667 0.00 0.00 0.00 4.35
2334 2628 1.142748 GAGCTGGGACGTCCTCATG 59.857 63.158 32.52 20.07 36.20 3.07
2335 2629 2.060980 GGAGCTGGGACGTCCTCAT 61.061 63.158 32.52 16.96 36.20 2.90
2376 2670 4.032786 CGCAATTTAATTACAAGGGCTTGC 59.967 41.667 0.00 0.00 44.03 4.01
2399 2698 5.179368 TCTCCATTGTCATCGAAGAAACAAC 59.821 40.000 0.00 0.00 44.75 3.32
2440 2739 1.069022 CGGAGTTTCGAACCGTAGACA 60.069 52.381 15.44 0.00 41.47 3.41
2462 2762 2.070783 ACACATTACGCCGTCGAATTT 58.929 42.857 0.00 0.00 39.41 1.82
2560 2860 7.011016 TCACTTCAATATACACCAAACTATGCG 59.989 37.037 0.00 0.00 0.00 4.73
2613 2913 0.244721 GCCTTGCACAACAGGAATCC 59.755 55.000 6.34 0.00 0.00 3.01
2618 2918 3.045142 CCTGCCTTGCACAACAGG 58.955 61.111 12.33 12.33 43.45 4.00
2823 3423 5.123820 TGTTTCCACATGCTAGTCAATTAGC 59.876 40.000 0.00 0.00 44.97 3.09
2830 3430 5.181690 TGTTTTGTTTCCACATGCTAGTC 57.818 39.130 0.00 0.00 31.06 2.59
2902 3502 6.481644 GGGATTGCAAGTACAACAATTTTCAA 59.518 34.615 4.94 0.00 34.28 2.69
2936 3536 0.676782 ACTAGGAAACATGCCCGTGC 60.677 55.000 0.00 0.00 38.26 5.34
2962 3562 3.157087 GACAAGATGGTGGGTGAATTGT 58.843 45.455 0.00 0.00 32.46 2.71
2971 3571 2.840651 AGGTCTAAGGACAAGATGGTGG 59.159 50.000 0.00 0.00 43.77 4.61
2972 3572 3.429547 CGAGGTCTAAGGACAAGATGGTG 60.430 52.174 0.00 0.00 43.77 4.17
3036 3636 4.520111 ACAAACATACAAGAGCTTCATGCA 59.480 37.500 0.00 0.00 45.94 3.96
3062 3662 3.367703 CCAATTCATGTTCCAACTGGAGC 60.368 47.826 5.69 5.69 46.36 4.70
3072 3672 4.273318 AGCCTAACCTCCAATTCATGTTC 58.727 43.478 0.00 0.00 0.00 3.18
3091 3691 4.024556 CCATGAAATCGTCAACTATGAGCC 60.025 45.833 0.00 0.00 40.50 4.70
3134 3734 9.936329 ACATAGGAAACCACATATAAGGAATTT 57.064 29.630 0.00 0.00 0.00 1.82
3177 3777 1.408127 CCGAAACCATGGGCTATGTCA 60.408 52.381 18.09 0.00 34.87 3.58
3206 3806 1.476891 GAGTTAGATGTCTCCGGCACA 59.523 52.381 8.36 8.36 0.00 4.57
3210 3810 4.208746 AGGTTAGAGTTAGATGTCTCCGG 58.791 47.826 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.