Multiple sequence alignment - TraesCS3D01G344300

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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 TraesCS3D01G344300 chr3D 100.000 2915 0 0 1 2915 456090685 456093599 0.000000e+00 5384.0
1 TraesCS3D01G344300 chr3D 87.345 1130 101 23 385 1503 481063084 481061986 0.000000e+00 1256.0
2 TraesCS3D01G344300 chr7D 91.051 1855 94 25 385 2186 573371885 573373720 0.000000e+00 2440.0
3 TraesCS3D01G344300 chrUn 90.865 1850 113 22 378 2188 93144025 93142193 0.000000e+00 2429.0
4 TraesCS3D01G344300 chr5D 91.536 1784 83 19 379 2116 470036865 470038626 0.000000e+00 2396.0
5 TraesCS3D01G344300 chr5D 90.490 1777 91 37 439 2190 529800839 529799116 0.000000e+00 2274.0
6 TraesCS3D01G344300 chr5D 90.247 1456 113 7 385 1813 294049164 294047711 0.000000e+00 1875.0
7 TraesCS3D01G344300 chr5D 88.364 825 37 23 1403 2186 8952041 8952847 0.000000e+00 937.0
8 TraesCS3D01G344300 chr2D 90.622 1834 112 28 391 2189 649601854 649600046 0.000000e+00 2379.0
9 TraesCS3D01G344300 chr2D 87.996 1891 125 35 373 2186 638636446 638638311 0.000000e+00 2141.0
10 TraesCS3D01G344300 chr1D 90.054 1860 88 25 378 2188 342068172 342066361 0.000000e+00 2320.0
11 TraesCS3D01G344300 chr1D 93.347 1428 55 12 792 2190 485240056 485238640 0.000000e+00 2074.0
12 TraesCS3D01G344300 chr1D 89.585 1181 59 19 1047 2192 92205186 92204035 0.000000e+00 1441.0
13 TraesCS3D01G344300 chr1D 87.143 350 25 1 378 707 485240644 485240295 2.120000e-101 379.0
14 TraesCS3D01G344300 chr1D 93.902 82 4 1 2109 2189 483670743 483670824 3.940000e-24 122.0
15 TraesCS3D01G344300 chr4D 90.330 1696 103 31 530 2186 488325640 488327313 0.000000e+00 2167.0
16 TraesCS3D01G344300 chr4D 96.104 77 3 0 2114 2190 501676082 501676006 3.050000e-25 126.0
17 TraesCS3D01G344300 chr6D 93.333 1275 56 13 853 2116 466744725 466743469 0.000000e+00 1857.0
18 TraesCS3D01G344300 chr6D 90.970 742 35 8 385 1098 225141950 225142687 0.000000e+00 970.0
19 TraesCS3D01G344300 chr6D 83.333 210 12 11 1998 2186 225143419 225143626 3.860000e-39 172.0
20 TraesCS3D01G344300 chr6D 94.937 79 4 0 2114 2192 352843733 352843655 1.100000e-24 124.0
21 TraesCS3D01G344300 chr1B 86.556 1629 156 38 520 2114 231351895 231350296 0.000000e+00 1736.0
22 TraesCS3D01G344300 chr1B 92.857 84 5 1 2114 2197 13068318 13068400 1.420000e-23 121.0
23 TraesCS3D01G344300 chr3A 89.556 1082 65 17 385 1450 10966309 10965260 0.000000e+00 1328.0
24 TraesCS3D01G344300 chr3A 86.802 788 44 17 1427 2186 710842435 710841680 0.000000e+00 824.0
25 TraesCS3D01G344300 chr3A 89.251 307 26 3 2609 2915 598947992 598948291 7.630000e-101 377.0
26 TraesCS3D01G344300 chr3A 87.636 275 23 4 2184 2455 598947692 598947958 2.820000e-80 309.0
27 TraesCS3D01G344300 chr3A 81.818 407 29 15 1 381 598947309 598947696 1.700000e-77 300.0
28 TraesCS3D01G344300 chr3B 87.288 354 21 8 2223 2575 602490688 602491018 1.640000e-102 383.0
29 TraesCS3D01G344300 chr3B 84.840 343 21 15 70 383 602490356 602490696 1.690000e-82 316.0
30 TraesCS3D01G344300 chr3B 85.538 325 18 11 2559 2883 602491033 602491328 2.180000e-81 313.0
31 TraesCS3D01G344300 chr3B 96.154 78 2 1 2116 2193 467880182 467880258 3.050000e-25 126.0
32 TraesCS3D01G344300 chr3B 90.909 88 6 2 2107 2193 797124337 797124251 1.840000e-22 117.0
33 TraesCS3D01G344300 chr3B 93.333 75 2 2 1 72 602490253 602490327 1.100000e-19 108.0
34 TraesCS3D01G344300 chr6B 85.511 352 40 9 379 729 703089088 703089429 9.930000e-95 357.0
35 TraesCS3D01G344300 chr6B 84.091 352 46 7 379 729 703039463 703039805 6.020000e-87 331.0
36 TraesCS3D01G344300 chr6B 76.260 754 93 38 1488 2195 95441743 95441030 3.620000e-84 322.0
37 TraesCS3D01G344300 chr6B 96.053 76 3 0 2116 2191 262269109 262269034 1.100000e-24 124.0
38 TraesCS3D01G344300 chr4A 82.482 274 33 8 385 644 574200856 574200584 2.920000e-55 226.0
39 TraesCS3D01G344300 chr4B 86.538 52 3 4 2865 2915 506904154 506904202 1.000000e-03 54.7


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 TraesCS3D01G344300 chr3D 456090685 456093599 2914 False 5384.000000 5384 100.00000 1 2915 1 chr3D.!!$F1 2914
1 TraesCS3D01G344300 chr3D 481061986 481063084 1098 True 1256.000000 1256 87.34500 385 1503 1 chr3D.!!$R1 1118
2 TraesCS3D01G344300 chr7D 573371885 573373720 1835 False 2440.000000 2440 91.05100 385 2186 1 chr7D.!!$F1 1801
3 TraesCS3D01G344300 chrUn 93142193 93144025 1832 True 2429.000000 2429 90.86500 378 2188 1 chrUn.!!$R1 1810
4 TraesCS3D01G344300 chr5D 470036865 470038626 1761 False 2396.000000 2396 91.53600 379 2116 1 chr5D.!!$F2 1737
5 TraesCS3D01G344300 chr5D 529799116 529800839 1723 True 2274.000000 2274 90.49000 439 2190 1 chr5D.!!$R2 1751
6 TraesCS3D01G344300 chr5D 294047711 294049164 1453 True 1875.000000 1875 90.24700 385 1813 1 chr5D.!!$R1 1428
7 TraesCS3D01G344300 chr5D 8952041 8952847 806 False 937.000000 937 88.36400 1403 2186 1 chr5D.!!$F1 783
8 TraesCS3D01G344300 chr2D 649600046 649601854 1808 True 2379.000000 2379 90.62200 391 2189 1 chr2D.!!$R1 1798
9 TraesCS3D01G344300 chr2D 638636446 638638311 1865 False 2141.000000 2141 87.99600 373 2186 1 chr2D.!!$F1 1813
10 TraesCS3D01G344300 chr1D 342066361 342068172 1811 True 2320.000000 2320 90.05400 378 2188 1 chr1D.!!$R2 1810
11 TraesCS3D01G344300 chr1D 92204035 92205186 1151 True 1441.000000 1441 89.58500 1047 2192 1 chr1D.!!$R1 1145
12 TraesCS3D01G344300 chr1D 485238640 485240644 2004 True 1226.500000 2074 90.24500 378 2190 2 chr1D.!!$R3 1812
13 TraesCS3D01G344300 chr4D 488325640 488327313 1673 False 2167.000000 2167 90.33000 530 2186 1 chr4D.!!$F1 1656
14 TraesCS3D01G344300 chr6D 466743469 466744725 1256 True 1857.000000 1857 93.33300 853 2116 1 chr6D.!!$R2 1263
15 TraesCS3D01G344300 chr6D 225141950 225143626 1676 False 571.000000 970 87.15150 385 2186 2 chr6D.!!$F1 1801
16 TraesCS3D01G344300 chr1B 231350296 231351895 1599 True 1736.000000 1736 86.55600 520 2114 1 chr1B.!!$R1 1594
17 TraesCS3D01G344300 chr3A 10965260 10966309 1049 True 1328.000000 1328 89.55600 385 1450 1 chr3A.!!$R1 1065
18 TraesCS3D01G344300 chr3A 710841680 710842435 755 True 824.000000 824 86.80200 1427 2186 1 chr3A.!!$R2 759
19 TraesCS3D01G344300 chr3A 598947309 598948291 982 False 328.666667 377 86.23500 1 2915 3 chr3A.!!$F1 2914
20 TraesCS3D01G344300 chr3B 602490253 602491328 1075 False 280.000000 383 87.74975 1 2883 4 chr3B.!!$F2 2882
21 TraesCS3D01G344300 chr6B 95441030 95441743 713 True 322.000000 322 76.26000 1488 2195 1 chr6B.!!$R1 707

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
253 294 0.098376 GGTCTCTACTGTACCGTGCG 59.902 60.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 2303 1.025041 ATAAAAGCCTAAGCCGCTGC 58.975 50.0 0.0 0.0 41.25 5.25 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
100 137 1.654220 GCTGTTGCCGCAAAGAAGA 59.346 52.632 7.54 0.00 0.00 2.87
119 160 0.108329 ATCTTTGGACGACGCGGATT 60.108 50.000 12.47 0.00 0.00 3.01
120 161 0.527113 TCTTTGGACGACGCGGATTA 59.473 50.000 12.47 0.00 0.00 1.75
124 165 0.593008 TGGACGACGCGGATTAATCG 60.593 55.000 12.47 12.33 40.39 3.34
142 183 4.537135 ATCGCTTTTCTCTGTTCTGGTA 57.463 40.909 0.00 0.00 0.00 3.25
143 184 3.914312 TCGCTTTTCTCTGTTCTGGTAG 58.086 45.455 0.00 0.00 0.00 3.18
144 185 2.996621 CGCTTTTCTCTGTTCTGGTAGG 59.003 50.000 0.00 0.00 0.00 3.18
145 186 3.555168 CGCTTTTCTCTGTTCTGGTAGGT 60.555 47.826 0.00 0.00 0.00 3.08
146 187 3.748568 GCTTTTCTCTGTTCTGGTAGGTG 59.251 47.826 0.00 0.00 0.00 4.00
147 188 4.319177 CTTTTCTCTGTTCTGGTAGGTGG 58.681 47.826 0.00 0.00 0.00 4.61
148 189 1.267121 TCTCTGTTCTGGTAGGTGGC 58.733 55.000 0.00 0.00 0.00 5.01
149 190 0.250513 CTCTGTTCTGGTAGGTGGCC 59.749 60.000 0.00 0.00 0.00 5.36
150 191 1.079127 CTGTTCTGGTAGGTGGCCG 60.079 63.158 0.00 0.00 0.00 6.13
151 192 2.267961 GTTCTGGTAGGTGGCCGG 59.732 66.667 0.00 0.00 0.00 6.13
152 193 3.712907 TTCTGGTAGGTGGCCGGC 61.713 66.667 21.18 21.18 32.54 6.13
161 202 4.382320 GTGGCCGGCCGAACAGTA 62.382 66.667 39.00 18.71 39.42 2.74
162 203 4.077184 TGGCCGGCCGAACAGTAG 62.077 66.667 39.00 9.14 39.42 2.57
163 204 3.766691 GGCCGGCCGAACAGTAGA 61.767 66.667 33.60 0.00 0.00 2.59
164 205 2.263540 GCCGGCCGAACAGTAGAA 59.736 61.111 30.73 0.00 0.00 2.10
165 206 2.098831 GCCGGCCGAACAGTAGAAC 61.099 63.158 30.73 0.00 0.00 3.01
166 207 1.290955 CCGGCCGAACAGTAGAACA 59.709 57.895 30.73 0.00 0.00 3.18
167 208 0.736325 CCGGCCGAACAGTAGAACAG 60.736 60.000 30.73 0.00 0.00 3.16
168 209 0.242825 CGGCCGAACAGTAGAACAGA 59.757 55.000 24.07 0.00 0.00 3.41
169 210 1.135083 CGGCCGAACAGTAGAACAGAT 60.135 52.381 24.07 0.00 0.00 2.90
170 211 2.098607 CGGCCGAACAGTAGAACAGATA 59.901 50.000 24.07 0.00 0.00 1.98
171 212 3.445857 GGCCGAACAGTAGAACAGATAC 58.554 50.000 0.00 0.00 0.00 2.24
172 213 3.119245 GGCCGAACAGTAGAACAGATACA 60.119 47.826 0.00 0.00 0.00 2.29
173 214 4.441634 GGCCGAACAGTAGAACAGATACAT 60.442 45.833 0.00 0.00 0.00 2.29
174 215 4.504461 GCCGAACAGTAGAACAGATACATG 59.496 45.833 0.00 0.00 0.00 3.21
175 216 5.043903 CCGAACAGTAGAACAGATACATGG 58.956 45.833 0.00 0.00 0.00 3.66
176 217 4.504461 CGAACAGTAGAACAGATACATGGC 59.496 45.833 0.00 0.00 0.00 4.40
177 218 5.665459 GAACAGTAGAACAGATACATGGCT 58.335 41.667 0.00 0.00 0.00 4.75
178 219 5.269505 ACAGTAGAACAGATACATGGCTC 57.730 43.478 0.00 0.00 0.00 4.70
179 220 4.202060 ACAGTAGAACAGATACATGGCTCG 60.202 45.833 0.00 0.00 0.00 5.03
180 221 2.898729 AGAACAGATACATGGCTCGG 57.101 50.000 0.00 0.00 0.00 4.63
181 222 2.388735 AGAACAGATACATGGCTCGGA 58.611 47.619 0.00 0.00 0.00 4.55
182 223 2.968574 AGAACAGATACATGGCTCGGAT 59.031 45.455 0.00 0.00 0.00 4.18
183 224 2.827800 ACAGATACATGGCTCGGATG 57.172 50.000 0.00 0.00 0.00 3.51
184 225 1.270518 ACAGATACATGGCTCGGATGC 60.271 52.381 0.00 0.00 0.00 3.91
185 226 1.051008 AGATACATGGCTCGGATGCA 58.949 50.000 0.00 0.00 34.04 3.96
186 227 1.001746 AGATACATGGCTCGGATGCAG 59.998 52.381 0.00 0.00 34.04 4.41
187 228 1.001293 GATACATGGCTCGGATGCAGA 59.999 52.381 0.00 0.00 34.04 4.26
188 229 0.390492 TACATGGCTCGGATGCAGAG 59.610 55.000 0.00 0.00 38.68 3.35
189 230 1.145598 CATGGCTCGGATGCAGAGT 59.854 57.895 3.67 0.00 37.99 3.24
190 231 1.145598 ATGGCTCGGATGCAGAGTG 59.854 57.895 3.67 0.00 37.99 3.51
191 232 2.202987 GGCTCGGATGCAGAGTGG 60.203 66.667 3.67 0.00 37.99 4.00
192 233 2.894387 GCTCGGATGCAGAGTGGC 60.894 66.667 3.67 0.00 37.99 5.01
193 234 2.584418 CTCGGATGCAGAGTGGCG 60.584 66.667 0.00 0.00 36.28 5.69
194 235 4.819761 TCGGATGCAGAGTGGCGC 62.820 66.667 0.00 0.00 36.28 6.53
195 236 4.827087 CGGATGCAGAGTGGCGCT 62.827 66.667 7.64 0.00 36.28 5.92
196 237 3.200593 GGATGCAGAGTGGCGCTG 61.201 66.667 4.71 0.79 36.28 5.18
197 238 3.200593 GATGCAGAGTGGCGCTGG 61.201 66.667 4.71 0.00 36.28 4.85
198 239 3.670637 GATGCAGAGTGGCGCTGGA 62.671 63.158 4.71 1.35 36.09 3.86
199 240 2.937379 GATGCAGAGTGGCGCTGGAT 62.937 60.000 4.71 6.93 43.57 3.41
200 241 3.200593 GCAGAGTGGCGCTGGATG 61.201 66.667 4.71 2.54 32.10 3.51
201 242 2.513204 CAGAGTGGCGCTGGATGG 60.513 66.667 4.71 0.00 0.00 3.51
202 243 4.479993 AGAGTGGCGCTGGATGGC 62.480 66.667 4.71 0.00 0.00 4.40
203 244 4.479993 GAGTGGCGCTGGATGGCT 62.480 66.667 4.71 0.00 0.00 4.75
204 245 4.790962 AGTGGCGCTGGATGGCTG 62.791 66.667 7.64 0.00 0.00 4.85
205 246 4.783621 GTGGCGCTGGATGGCTGA 62.784 66.667 7.64 0.00 0.00 4.26
206 247 4.783621 TGGCGCTGGATGGCTGAC 62.784 66.667 7.64 0.00 0.00 3.51
207 248 4.783621 GGCGCTGGATGGCTGACA 62.784 66.667 7.64 0.00 0.00 3.58
208 249 2.747460 GCGCTGGATGGCTGACAA 60.747 61.111 0.00 0.00 0.00 3.18
209 250 3.044059 GCGCTGGATGGCTGACAAC 62.044 63.158 0.00 0.00 0.00 3.32
210 251 2.743752 CGCTGGATGGCTGACAACG 61.744 63.158 0.00 0.00 0.00 4.10
211 252 1.375908 GCTGGATGGCTGACAACGA 60.376 57.895 0.00 0.00 0.00 3.85
212 253 1.639298 GCTGGATGGCTGACAACGAC 61.639 60.000 0.00 0.00 0.00 4.34
213 254 1.354337 CTGGATGGCTGACAACGACG 61.354 60.000 0.00 0.00 0.00 5.12
214 255 1.080093 GGATGGCTGACAACGACGA 60.080 57.895 0.00 0.00 0.00 4.20
215 256 1.352156 GGATGGCTGACAACGACGAC 61.352 60.000 0.00 0.00 0.00 4.34
216 257 1.674611 GATGGCTGACAACGACGACG 61.675 60.000 5.58 5.58 45.75 5.12
217 258 3.103911 GGCTGACAACGACGACGG 61.104 66.667 12.58 0.00 44.46 4.79
218 259 3.764049 GCTGACAACGACGACGGC 61.764 66.667 12.58 0.00 44.46 5.68
219 260 3.458579 CTGACAACGACGACGGCG 61.459 66.667 23.84 23.84 44.46 6.46
220 261 4.986587 TGACAACGACGACGGCGG 62.987 66.667 28.89 13.21 44.46 6.13
227 268 4.072088 GACGACGGCGGCTTGTTG 62.072 66.667 18.49 5.01 43.91 3.33
228 269 4.903010 ACGACGGCGGCTTGTTGT 62.903 61.111 18.49 5.71 43.17 3.32
229 270 4.072088 CGACGGCGGCTTGTTGTC 62.072 66.667 12.58 5.62 0.00 3.18
230 271 2.970324 GACGGCGGCTTGTTGTCA 60.970 61.111 13.24 0.00 0.00 3.58
231 272 2.281484 ACGGCGGCTTGTTGTCAT 60.281 55.556 13.24 0.00 0.00 3.06
232 273 1.852067 GACGGCGGCTTGTTGTCATT 61.852 55.000 13.24 0.00 0.00 2.57
233 274 1.442520 CGGCGGCTTGTTGTCATTG 60.443 57.895 7.61 0.00 0.00 2.82
234 275 1.080569 GGCGGCTTGTTGTCATTGG 60.081 57.895 0.00 0.00 0.00 3.16
235 276 1.080569 GCGGCTTGTTGTCATTGGG 60.081 57.895 0.00 0.00 0.00 4.12
236 277 1.805428 GCGGCTTGTTGTCATTGGGT 61.805 55.000 0.00 0.00 0.00 4.51
237 278 0.240945 CGGCTTGTTGTCATTGGGTC 59.759 55.000 0.00 0.00 0.00 4.46
238 279 1.620822 GGCTTGTTGTCATTGGGTCT 58.379 50.000 0.00 0.00 0.00 3.85
239 280 1.541588 GGCTTGTTGTCATTGGGTCTC 59.458 52.381 0.00 0.00 0.00 3.36
240 281 2.508526 GCTTGTTGTCATTGGGTCTCT 58.491 47.619 0.00 0.00 0.00 3.10
241 282 3.559171 GGCTTGTTGTCATTGGGTCTCTA 60.559 47.826 0.00 0.00 0.00 2.43
242 283 3.437049 GCTTGTTGTCATTGGGTCTCTAC 59.563 47.826 0.00 0.00 0.00 2.59
243 284 4.804261 GCTTGTTGTCATTGGGTCTCTACT 60.804 45.833 0.00 0.00 0.00 2.57
244 285 4.271696 TGTTGTCATTGGGTCTCTACTG 57.728 45.455 0.00 0.00 0.00 2.74
245 286 3.646162 TGTTGTCATTGGGTCTCTACTGT 59.354 43.478 0.00 0.00 0.00 3.55
246 287 4.836175 TGTTGTCATTGGGTCTCTACTGTA 59.164 41.667 0.00 0.00 0.00 2.74
247 288 5.169295 GTTGTCATTGGGTCTCTACTGTAC 58.831 45.833 0.00 0.00 0.00 2.90
248 289 3.767673 TGTCATTGGGTCTCTACTGTACC 59.232 47.826 0.00 0.00 0.00 3.34
249 290 3.021695 TCATTGGGTCTCTACTGTACCG 58.978 50.000 0.00 0.00 33.89 4.02
250 291 2.592102 TTGGGTCTCTACTGTACCGT 57.408 50.000 0.00 0.00 33.89 4.83
251 292 1.830279 TGGGTCTCTACTGTACCGTG 58.170 55.000 0.00 0.00 33.89 4.94
252 293 0.455005 GGGTCTCTACTGTACCGTGC 59.545 60.000 0.00 0.00 33.89 5.34
253 294 0.098376 GGTCTCTACTGTACCGTGCG 59.902 60.000 0.00 0.00 0.00 5.34
254 295 0.522915 GTCTCTACTGTACCGTGCGC 60.523 60.000 0.00 0.00 0.00 6.09
255 296 1.226603 CTCTACTGTACCGTGCGCC 60.227 63.158 4.18 0.00 0.00 6.53
256 297 1.654954 CTCTACTGTACCGTGCGCCT 61.655 60.000 4.18 0.00 0.00 5.52
257 298 1.516386 CTACTGTACCGTGCGCCTG 60.516 63.158 4.18 0.00 0.00 4.85
258 299 3.636313 TACTGTACCGTGCGCCTGC 62.636 63.158 4.18 0.00 43.20 4.85
268 309 2.186384 GCGCCTGCAGATGAGACT 59.814 61.111 17.39 0.00 42.15 3.24
269 310 1.449246 GCGCCTGCAGATGAGACTT 60.449 57.895 17.39 0.00 42.15 3.01
270 311 0.179100 GCGCCTGCAGATGAGACTTA 60.179 55.000 17.39 0.00 42.15 2.24
271 312 1.850377 CGCCTGCAGATGAGACTTAG 58.150 55.000 17.39 0.00 0.00 2.18
272 313 1.406898 CGCCTGCAGATGAGACTTAGA 59.593 52.381 17.39 0.00 0.00 2.10
273 314 2.797792 CGCCTGCAGATGAGACTTAGAC 60.798 54.545 17.39 0.00 0.00 2.59
274 315 2.797792 GCCTGCAGATGAGACTTAGACG 60.798 54.545 17.39 0.00 0.00 4.18
275 316 2.223688 CCTGCAGATGAGACTTAGACGG 60.224 54.545 17.39 0.00 0.00 4.79
276 317 1.135139 TGCAGATGAGACTTAGACGGC 59.865 52.381 0.00 0.00 0.00 5.68
277 318 1.135139 GCAGATGAGACTTAGACGGCA 59.865 52.381 0.00 0.00 0.00 5.69
278 319 2.797792 GCAGATGAGACTTAGACGGCAG 60.798 54.545 0.00 0.00 0.00 4.85
279 320 2.425312 CAGATGAGACTTAGACGGCAGT 59.575 50.000 0.00 0.00 0.00 4.40
280 321 3.093057 AGATGAGACTTAGACGGCAGTT 58.907 45.455 0.00 0.00 0.00 3.16
281 322 3.129638 AGATGAGACTTAGACGGCAGTTC 59.870 47.826 0.00 0.00 0.00 3.01
282 323 1.199327 TGAGACTTAGACGGCAGTTCG 59.801 52.381 0.00 0.00 0.00 3.95
283 324 0.526662 AGACTTAGACGGCAGTTCGG 59.473 55.000 0.00 0.00 0.00 4.30
284 325 1.077089 GACTTAGACGGCAGTTCGGC 61.077 60.000 0.00 0.00 38.69 5.54
286 327 0.802607 CTTAGACGGCAGTTCGGCTC 60.803 60.000 0.00 0.00 46.93 4.70
287 328 2.537792 TTAGACGGCAGTTCGGCTCG 62.538 60.000 0.00 0.00 46.93 5.03
291 332 4.090057 GGCAGTTCGGCTCGCAAC 62.090 66.667 0.00 0.00 37.17 4.17
292 333 3.044305 GCAGTTCGGCTCGCAACT 61.044 61.111 0.00 0.00 32.87 3.16
293 334 2.856032 CAGTTCGGCTCGCAACTG 59.144 61.111 16.69 16.69 42.62 3.16
294 335 2.734591 AGTTCGGCTCGCAACTGA 59.265 55.556 9.65 0.00 31.42 3.41
295 336 1.293498 AGTTCGGCTCGCAACTGAT 59.707 52.632 9.65 0.00 31.42 2.90
296 337 0.737715 AGTTCGGCTCGCAACTGATC 60.738 55.000 9.65 0.00 31.42 2.92
297 338 1.014044 GTTCGGCTCGCAACTGATCA 61.014 55.000 0.00 0.00 0.00 2.92
298 339 0.108186 TTCGGCTCGCAACTGATCAT 60.108 50.000 0.00 0.00 0.00 2.45
299 340 0.528466 TCGGCTCGCAACTGATCATC 60.528 55.000 0.00 0.00 0.00 2.92
300 341 1.815212 CGGCTCGCAACTGATCATCG 61.815 60.000 0.00 0.00 0.00 3.84
301 342 1.275066 GCTCGCAACTGATCATCGC 59.725 57.895 0.00 0.00 0.00 4.58
302 343 1.556958 CTCGCAACTGATCATCGCG 59.443 57.895 21.06 21.06 46.92 5.87
303 344 1.142185 CTCGCAACTGATCATCGCGT 61.142 55.000 24.07 6.49 45.77 6.01
304 345 0.735978 TCGCAACTGATCATCGCGTT 60.736 50.000 24.07 11.48 45.77 4.84
305 346 0.920664 CGCAACTGATCATCGCGTTA 59.079 50.000 19.61 0.00 40.99 3.18
306 347 1.071894 CGCAACTGATCATCGCGTTAG 60.072 52.381 19.61 0.00 40.99 2.34
307 348 1.258982 GCAACTGATCATCGCGTTAGG 59.741 52.381 5.77 0.00 0.00 2.69
308 349 2.540515 CAACTGATCATCGCGTTAGGT 58.459 47.619 5.77 0.00 0.00 3.08
309 350 2.930040 CAACTGATCATCGCGTTAGGTT 59.070 45.455 5.77 1.08 0.00 3.50
310 351 2.810650 ACTGATCATCGCGTTAGGTTC 58.189 47.619 5.77 0.00 0.00 3.62
311 352 2.128035 CTGATCATCGCGTTAGGTTCC 58.872 52.381 5.77 0.00 0.00 3.62
312 353 1.202486 TGATCATCGCGTTAGGTTCCC 60.202 52.381 5.77 0.00 0.00 3.97
313 354 0.249322 ATCATCGCGTTAGGTTCCCG 60.249 55.000 5.77 0.00 0.00 5.14
314 355 1.140161 CATCGCGTTAGGTTCCCGA 59.860 57.895 5.77 0.00 0.00 5.14
315 356 1.140375 ATCGCGTTAGGTTCCCGAC 59.860 57.895 5.77 0.00 0.00 4.79
316 357 2.603135 ATCGCGTTAGGTTCCCGACG 62.603 60.000 5.77 9.25 39.55 5.12
317 358 2.507769 GCGTTAGGTTCCCGACGG 60.508 66.667 6.99 6.99 38.00 4.79
318 359 2.182537 CGTTAGGTTCCCGACGGG 59.817 66.667 27.86 27.86 46.11 5.28
319 360 2.639327 CGTTAGGTTCCCGACGGGT 61.639 63.158 31.54 15.71 44.74 5.28
320 361 1.216444 GTTAGGTTCCCGACGGGTC 59.784 63.158 31.54 23.71 44.74 4.46
341 382 2.202401 GTCCGTGGAGACGTACGC 60.202 66.667 16.72 8.42 44.54 4.42
342 383 2.669229 TCCGTGGAGACGTACGCA 60.669 61.111 16.72 1.65 44.54 5.24
343 384 2.042259 TCCGTGGAGACGTACGCAT 61.042 57.895 16.72 3.40 44.54 4.73
344 385 1.872234 CCGTGGAGACGTACGCATG 60.872 63.158 16.72 10.29 44.54 4.06
345 386 2.505498 CGTGGAGACGTACGCATGC 61.505 63.158 16.72 7.91 40.91 4.06
346 387 1.153823 GTGGAGACGTACGCATGCT 60.154 57.895 16.72 7.72 0.00 3.79
347 388 0.736325 GTGGAGACGTACGCATGCTT 60.736 55.000 16.72 9.37 0.00 3.91
348 389 0.735978 TGGAGACGTACGCATGCTTG 60.736 55.000 16.72 3.27 0.00 4.01
349 390 1.421410 GGAGACGTACGCATGCTTGG 61.421 60.000 16.72 5.84 0.00 3.61
350 391 2.025359 GAGACGTACGCATGCTTGGC 62.025 60.000 16.72 4.56 0.00 4.52
357 398 3.803082 GCATGCTTGGCGCTCGAA 61.803 61.111 11.37 0.00 40.11 3.71
358 399 2.402388 CATGCTTGGCGCTCGAAG 59.598 61.111 7.64 8.65 40.11 3.79
359 400 3.503363 ATGCTTGGCGCTCGAAGC 61.503 61.111 23.62 23.62 44.10 3.86
361 402 4.157958 GCTTGGCGCTCGAAGCAG 62.158 66.667 24.71 5.48 42.58 4.24
362 403 4.157958 CTTGGCGCTCGAAGCAGC 62.158 66.667 7.64 12.51 42.58 5.25
363 404 4.986645 TTGGCGCTCGAAGCAGCA 62.987 61.111 7.64 2.03 42.58 4.41
381 422 1.469423 GCAGGCTCGTCAGGTACTTAC 60.469 57.143 0.00 0.00 34.60 2.34
401 442 4.845580 CATCTCCAGCCGCGCCTT 62.846 66.667 0.00 0.00 0.00 4.35
505 548 1.586154 CTTGGGCCGAAATCAACGCT 61.586 55.000 0.54 0.00 0.00 5.07
633 698 2.828095 CCCGCGGGAATCAATGCA 60.828 61.111 41.82 0.00 37.50 3.96
1383 1644 2.363795 AGTTCCTGGATCCCGCGA 60.364 61.111 8.23 0.00 0.00 5.87
2111 2518 3.755628 GCGGGCACGTGACTAGGA 61.756 66.667 23.08 0.00 43.45 2.94
2199 2607 0.461548 TGCTCTTAGTGCCCGATCAG 59.538 55.000 3.76 0.00 0.00 2.90
2209 2617 1.743321 GCCCGATCAGCAGCTAGTCT 61.743 60.000 0.00 0.00 0.00 3.24
2215 2623 5.398169 CCGATCAGCAGCTAGTCTAAATAG 58.602 45.833 0.00 0.00 0.00 1.73
2248 2656 3.509575 TGACAAAGTGTGGCAAAGAAGTT 59.490 39.130 0.00 0.00 44.65 2.66
2249 2657 4.702612 TGACAAAGTGTGGCAAAGAAGTTA 59.297 37.500 0.00 0.00 44.65 2.24
2250 2658 4.993905 ACAAAGTGTGGCAAAGAAGTTAC 58.006 39.130 0.00 0.00 0.00 2.50
2251 2659 3.963383 AAGTGTGGCAAAGAAGTTACG 57.037 42.857 0.00 0.00 0.00 3.18
2306 2714 3.474600 CTTAGATTCATCCACAGCCCAG 58.525 50.000 0.00 0.00 0.00 4.45
2374 2783 5.751586 ACAAAACAGAGAAGAAAGGGTGTA 58.248 37.500 0.00 0.00 0.00 2.90
2379 2788 3.686726 CAGAGAAGAAAGGGTGTATGTGC 59.313 47.826 0.00 0.00 0.00 4.57
2383 2792 2.577763 GAAAGGGTGTATGTGCGCGC 62.578 60.000 27.26 27.26 0.00 6.86
2423 2832 2.992273 GCCGGCAATGCACACATCA 61.992 57.895 24.80 0.00 34.62 3.07
2471 2882 1.134818 TGCCGTACAGATAGTGCCTTG 60.135 52.381 0.00 0.00 0.00 3.61
2473 2884 1.137086 CCGTACAGATAGTGCCTTGCT 59.863 52.381 0.00 0.00 0.00 3.91
2530 2941 4.757149 ACAGCCTAAATTCACTGACTGAAC 59.243 41.667 0.00 0.00 41.87 3.18
2543 2954 8.018677 TCACTGACTGAACGATTCTTATTTTC 57.981 34.615 0.00 0.00 0.00 2.29
2602 3044 0.028505 CGCGAGATGATTGGGCAAAG 59.971 55.000 0.00 0.00 0.00 2.77
2603 3045 0.383231 GCGAGATGATTGGGCAAAGG 59.617 55.000 0.00 0.00 0.00 3.11
2604 3046 0.383231 CGAGATGATTGGGCAAAGGC 59.617 55.000 0.00 0.00 40.13 4.35
2605 3047 1.477553 GAGATGATTGGGCAAAGGCA 58.522 50.000 0.00 0.00 43.71 4.75
2606 3048 2.037144 GAGATGATTGGGCAAAGGCAT 58.963 47.619 0.00 0.00 43.71 4.40
2607 3049 2.433239 GAGATGATTGGGCAAAGGCATT 59.567 45.455 0.00 0.00 43.71 3.56
2608 3050 3.638160 GAGATGATTGGGCAAAGGCATTA 59.362 43.478 0.00 0.00 43.71 1.90
2609 3051 4.032310 AGATGATTGGGCAAAGGCATTAA 58.968 39.130 0.00 0.00 43.71 1.40
2631 3073 1.152963 AATGCAGCGGGGATGGTAC 60.153 57.895 0.00 0.00 0.00 3.34
2645 3087 1.989706 TGGTACCTGCCAAAGAAACC 58.010 50.000 14.36 0.00 35.25 3.27
2685 3127 5.049405 GGCATAATCAGGGACAAATAAGTCG 60.049 44.000 0.00 0.00 39.42 4.18
2705 3147 6.570692 AGTCGTCTGAGAAAACTTAGTCAAA 58.429 36.000 0.00 0.00 0.00 2.69
2706 3148 7.210873 AGTCGTCTGAGAAAACTTAGTCAAAT 58.789 34.615 0.00 0.00 0.00 2.32
2740 3182 1.516161 TGCACATTGAGAGCACTGAC 58.484 50.000 0.00 0.00 38.96 3.51
2771 3213 0.324738 TGGTGGACAAAACCCAAGCA 60.325 50.000 0.00 0.00 36.83 3.91
2772 3214 1.047801 GGTGGACAAAACCCAAGCAT 58.952 50.000 0.00 0.00 35.12 3.79
2773 3215 1.416030 GGTGGACAAAACCCAAGCATT 59.584 47.619 0.00 0.00 35.12 3.56
2774 3216 2.630580 GGTGGACAAAACCCAAGCATTA 59.369 45.455 0.00 0.00 35.12 1.90
2844 3286 9.136323 GAAGAGACAATGTTTATTGGGGATATT 57.864 33.333 5.17 0.00 46.33 1.28
2846 3288 9.574516 AGAGACAATGTTTATTGGGGATATTAC 57.425 33.333 5.17 0.00 46.33 1.89
2847 3289 9.349713 GAGACAATGTTTATTGGGGATATTACA 57.650 33.333 5.17 0.00 46.33 2.41
2848 3290 9.131791 AGACAATGTTTATTGGGGATATTACAC 57.868 33.333 5.17 0.00 46.33 2.90
2850 3292 9.432982 ACAATGTTTATTGGGGATATTACACAT 57.567 29.630 5.17 0.00 46.33 3.21
2886 3328 6.959606 AGGCCCAAATATATCATGTACTCT 57.040 37.500 0.00 0.00 0.00 3.24
2889 3331 7.885399 AGGCCCAAATATATCATGTACTCTTTC 59.115 37.037 0.00 0.00 0.00 2.62
2894 3336 8.926710 CAAATATATCATGTACTCTTTCCGTCC 58.073 37.037 0.00 0.00 0.00 4.79
2899 3341 4.712829 TCATGTACTCTTTCCGTCCCATAA 59.287 41.667 0.00 0.00 0.00 1.90
2907 3349 7.668492 ACTCTTTCCGTCCCATAATATAAGAC 58.332 38.462 0.00 0.00 0.00 3.01
2908 3350 7.509659 ACTCTTTCCGTCCCATAATATAAGACT 59.490 37.037 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 77 1.154150 GGCAACAGCGATGTTCTGC 60.154 57.895 17.51 18.63 35.04 4.26
73 78 1.133253 CGGCAACAGCGATGTTCTG 59.867 57.895 17.51 8.73 37.56 3.02
74 79 2.680913 GCGGCAACAGCGATGTTCT 61.681 57.895 17.51 0.00 0.00 3.01
100 137 0.108329 AATCCGCGTCGTCCAAAGAT 60.108 50.000 4.92 0.00 0.00 2.40
119 160 4.894784 ACCAGAACAGAGAAAAGCGATTA 58.105 39.130 0.00 0.00 0.00 1.75
120 161 3.744660 ACCAGAACAGAGAAAAGCGATT 58.255 40.909 0.00 0.00 0.00 3.34
124 165 3.748568 CACCTACCAGAACAGAGAAAAGC 59.251 47.826 0.00 0.00 0.00 3.51
131 172 1.541310 CGGCCACCTACCAGAACAGA 61.541 60.000 2.24 0.00 0.00 3.41
144 185 4.382320 TACTGTTCGGCCGGCCAC 62.382 66.667 42.78 33.69 35.37 5.01
145 186 4.077184 CTACTGTTCGGCCGGCCA 62.077 66.667 42.78 27.76 35.37 5.36
146 187 3.305177 TTCTACTGTTCGGCCGGCC 62.305 63.158 36.69 36.69 0.00 6.13
147 188 2.098831 GTTCTACTGTTCGGCCGGC 61.099 63.158 27.83 21.18 0.00 6.13
148 189 0.736325 CTGTTCTACTGTTCGGCCGG 60.736 60.000 27.83 11.94 0.00 6.13
149 190 0.242825 TCTGTTCTACTGTTCGGCCG 59.757 55.000 22.12 22.12 0.00 6.13
150 191 2.674796 ATCTGTTCTACTGTTCGGCC 57.325 50.000 0.00 0.00 0.00 6.13
151 192 4.106029 TGTATCTGTTCTACTGTTCGGC 57.894 45.455 0.00 0.00 0.00 5.54
152 193 5.043903 CCATGTATCTGTTCTACTGTTCGG 58.956 45.833 0.00 0.00 0.00 4.30
153 194 4.504461 GCCATGTATCTGTTCTACTGTTCG 59.496 45.833 0.00 0.00 0.00 3.95
154 195 5.665459 AGCCATGTATCTGTTCTACTGTTC 58.335 41.667 0.00 0.00 0.00 3.18
155 196 5.665459 GAGCCATGTATCTGTTCTACTGTT 58.335 41.667 0.00 0.00 0.00 3.16
156 197 4.202060 CGAGCCATGTATCTGTTCTACTGT 60.202 45.833 0.00 0.00 0.00 3.55
157 198 4.294232 CGAGCCATGTATCTGTTCTACTG 58.706 47.826 0.00 0.00 0.00 2.74
158 199 3.319405 CCGAGCCATGTATCTGTTCTACT 59.681 47.826 0.00 0.00 0.00 2.57
159 200 3.318275 TCCGAGCCATGTATCTGTTCTAC 59.682 47.826 0.00 0.00 0.00 2.59
160 201 3.562182 TCCGAGCCATGTATCTGTTCTA 58.438 45.455 0.00 0.00 0.00 2.10
161 202 2.388735 TCCGAGCCATGTATCTGTTCT 58.611 47.619 0.00 0.00 0.00 3.01
162 203 2.890808 TCCGAGCCATGTATCTGTTC 57.109 50.000 0.00 0.00 0.00 3.18
163 204 2.808202 GCATCCGAGCCATGTATCTGTT 60.808 50.000 0.00 0.00 0.00 3.16
164 205 1.270518 GCATCCGAGCCATGTATCTGT 60.271 52.381 0.00 0.00 0.00 3.41
165 206 1.270465 TGCATCCGAGCCATGTATCTG 60.270 52.381 0.00 0.00 0.00 2.90
166 207 1.001746 CTGCATCCGAGCCATGTATCT 59.998 52.381 0.00 0.00 0.00 1.98
167 208 1.001293 TCTGCATCCGAGCCATGTATC 59.999 52.381 0.00 0.00 0.00 2.24
168 209 1.001746 CTCTGCATCCGAGCCATGTAT 59.998 52.381 0.00 0.00 0.00 2.29
169 210 0.390492 CTCTGCATCCGAGCCATGTA 59.610 55.000 0.00 0.00 0.00 2.29
170 211 1.145598 CTCTGCATCCGAGCCATGT 59.854 57.895 0.00 0.00 0.00 3.21
171 212 1.145598 ACTCTGCATCCGAGCCATG 59.854 57.895 1.55 0.00 31.71 3.66
172 213 1.145598 CACTCTGCATCCGAGCCAT 59.854 57.895 1.55 0.00 31.71 4.40
173 214 2.580815 CACTCTGCATCCGAGCCA 59.419 61.111 1.55 0.00 31.71 4.75
174 215 2.202987 CCACTCTGCATCCGAGCC 60.203 66.667 1.55 0.00 31.71 4.70
175 216 2.894387 GCCACTCTGCATCCGAGC 60.894 66.667 1.55 0.00 31.71 5.03
176 217 2.584418 CGCCACTCTGCATCCGAG 60.584 66.667 0.14 0.14 34.70 4.63
177 218 4.819761 GCGCCACTCTGCATCCGA 62.820 66.667 0.00 0.00 0.00 4.55
178 219 4.827087 AGCGCCACTCTGCATCCG 62.827 66.667 2.29 0.00 0.00 4.18
179 220 3.200593 CAGCGCCACTCTGCATCC 61.201 66.667 2.29 0.00 0.00 3.51
180 221 2.937379 ATCCAGCGCCACTCTGCATC 62.937 60.000 2.29 0.00 0.00 3.91
181 222 3.040206 ATCCAGCGCCACTCTGCAT 62.040 57.895 2.29 0.00 0.00 3.96
182 223 3.709633 ATCCAGCGCCACTCTGCA 61.710 61.111 2.29 0.00 0.00 4.41
183 224 3.200593 CATCCAGCGCCACTCTGC 61.201 66.667 2.29 0.00 0.00 4.26
184 225 2.513204 CCATCCAGCGCCACTCTG 60.513 66.667 2.29 0.00 0.00 3.35
185 226 4.479993 GCCATCCAGCGCCACTCT 62.480 66.667 2.29 0.00 0.00 3.24
186 227 4.479993 AGCCATCCAGCGCCACTC 62.480 66.667 2.29 0.00 38.01 3.51
187 228 4.790962 CAGCCATCCAGCGCCACT 62.791 66.667 2.29 0.00 38.01 4.00
188 229 4.783621 TCAGCCATCCAGCGCCAC 62.784 66.667 2.29 0.00 38.01 5.01
189 230 4.783621 GTCAGCCATCCAGCGCCA 62.784 66.667 2.29 0.00 38.01 5.69
190 231 4.783621 TGTCAGCCATCCAGCGCC 62.784 66.667 2.29 0.00 38.01 6.53
191 232 2.747460 TTGTCAGCCATCCAGCGC 60.747 61.111 0.00 0.00 38.01 5.92
192 233 2.743752 CGTTGTCAGCCATCCAGCG 61.744 63.158 0.00 0.00 38.01 5.18
193 234 1.375908 TCGTTGTCAGCCATCCAGC 60.376 57.895 0.00 0.00 0.00 4.85
194 235 1.354337 CGTCGTTGTCAGCCATCCAG 61.354 60.000 0.00 0.00 0.00 3.86
195 236 1.374125 CGTCGTTGTCAGCCATCCA 60.374 57.895 0.00 0.00 0.00 3.41
196 237 1.080093 TCGTCGTTGTCAGCCATCC 60.080 57.895 0.00 0.00 0.00 3.51
197 238 1.674611 CGTCGTCGTTGTCAGCCATC 61.675 60.000 0.00 0.00 0.00 3.51
198 239 1.733041 CGTCGTCGTTGTCAGCCAT 60.733 57.895 0.00 0.00 0.00 4.40
199 240 2.354188 CGTCGTCGTTGTCAGCCA 60.354 61.111 0.00 0.00 0.00 4.75
200 241 3.103911 CCGTCGTCGTTGTCAGCC 61.104 66.667 0.71 0.00 35.01 4.85
201 242 3.764049 GCCGTCGTCGTTGTCAGC 61.764 66.667 0.71 0.00 35.01 4.26
202 243 3.458579 CGCCGTCGTCGTTGTCAG 61.459 66.667 0.71 0.00 35.01 3.51
203 244 4.986587 CCGCCGTCGTCGTTGTCA 62.987 66.667 0.71 0.00 35.01 3.58
210 251 4.072088 CAACAAGCCGCCGTCGTC 62.072 66.667 0.00 0.00 0.00 4.20
211 252 4.903010 ACAACAAGCCGCCGTCGT 62.903 61.111 0.00 0.00 0.00 4.34
212 253 4.072088 GACAACAAGCCGCCGTCG 62.072 66.667 0.00 0.00 0.00 5.12
213 254 1.852067 AATGACAACAAGCCGCCGTC 61.852 55.000 0.00 0.00 0.00 4.79
214 255 1.896660 AATGACAACAAGCCGCCGT 60.897 52.632 0.00 0.00 0.00 5.68
215 256 1.442520 CAATGACAACAAGCCGCCG 60.443 57.895 0.00 0.00 0.00 6.46
216 257 1.080569 CCAATGACAACAAGCCGCC 60.081 57.895 0.00 0.00 0.00 6.13
217 258 1.080569 CCCAATGACAACAAGCCGC 60.081 57.895 0.00 0.00 0.00 6.53
218 259 0.240945 GACCCAATGACAACAAGCCG 59.759 55.000 0.00 0.00 0.00 5.52
219 260 1.541588 GAGACCCAATGACAACAAGCC 59.458 52.381 0.00 0.00 0.00 4.35
220 261 2.508526 AGAGACCCAATGACAACAAGC 58.491 47.619 0.00 0.00 0.00 4.01
221 262 4.692625 CAGTAGAGACCCAATGACAACAAG 59.307 45.833 0.00 0.00 0.00 3.16
222 263 4.102524 ACAGTAGAGACCCAATGACAACAA 59.897 41.667 0.00 0.00 0.00 2.83
223 264 3.646162 ACAGTAGAGACCCAATGACAACA 59.354 43.478 0.00 0.00 0.00 3.33
224 265 4.273148 ACAGTAGAGACCCAATGACAAC 57.727 45.455 0.00 0.00 0.00 3.32
225 266 4.222145 GGTACAGTAGAGACCCAATGACAA 59.778 45.833 0.00 0.00 0.00 3.18
226 267 3.767673 GGTACAGTAGAGACCCAATGACA 59.232 47.826 0.00 0.00 0.00 3.58
227 268 3.181489 CGGTACAGTAGAGACCCAATGAC 60.181 52.174 0.00 0.00 0.00 3.06
228 269 3.021695 CGGTACAGTAGAGACCCAATGA 58.978 50.000 0.00 0.00 0.00 2.57
229 270 2.758979 ACGGTACAGTAGAGACCCAATG 59.241 50.000 0.00 0.00 0.00 2.82
230 271 2.758979 CACGGTACAGTAGAGACCCAAT 59.241 50.000 0.00 0.00 0.00 3.16
231 272 2.165167 CACGGTACAGTAGAGACCCAA 58.835 52.381 0.00 0.00 0.00 4.12
232 273 1.830279 CACGGTACAGTAGAGACCCA 58.170 55.000 0.00 0.00 0.00 4.51
233 274 0.455005 GCACGGTACAGTAGAGACCC 59.545 60.000 0.00 0.00 0.00 4.46
234 275 0.098376 CGCACGGTACAGTAGAGACC 59.902 60.000 0.00 0.00 0.00 3.85
235 276 0.522915 GCGCACGGTACAGTAGAGAC 60.523 60.000 0.30 0.00 0.00 3.36
236 277 1.651240 GGCGCACGGTACAGTAGAGA 61.651 60.000 10.83 0.00 0.00 3.10
237 278 1.226603 GGCGCACGGTACAGTAGAG 60.227 63.158 10.83 0.00 0.00 2.43
238 279 1.676635 AGGCGCACGGTACAGTAGA 60.677 57.895 10.83 0.00 0.00 2.59
239 280 1.516386 CAGGCGCACGGTACAGTAG 60.516 63.158 10.83 0.00 0.00 2.57
240 281 2.569657 CAGGCGCACGGTACAGTA 59.430 61.111 10.83 0.00 0.00 2.74
244 285 4.735132 TCTGCAGGCGCACGGTAC 62.735 66.667 15.13 0.00 45.36 3.34
245 286 3.770040 ATCTGCAGGCGCACGGTA 61.770 61.111 15.13 0.00 45.36 4.02
248 289 3.561213 CTCATCTGCAGGCGCACG 61.561 66.667 15.13 0.00 45.36 5.34
249 290 2.125391 TCTCATCTGCAGGCGCAC 60.125 61.111 15.13 0.00 45.36 5.34
251 292 0.179100 TAAGTCTCATCTGCAGGCGC 60.179 55.000 15.13 0.00 39.24 6.53
252 293 1.406898 TCTAAGTCTCATCTGCAGGCG 59.593 52.381 15.13 5.35 0.00 5.52
253 294 2.797792 CGTCTAAGTCTCATCTGCAGGC 60.798 54.545 15.13 0.00 0.00 4.85
254 295 2.223688 CCGTCTAAGTCTCATCTGCAGG 60.224 54.545 15.13 0.00 0.00 4.85
255 296 2.797792 GCCGTCTAAGTCTCATCTGCAG 60.798 54.545 7.63 7.63 0.00 4.41
256 297 1.135139 GCCGTCTAAGTCTCATCTGCA 59.865 52.381 0.00 0.00 0.00 4.41
257 298 1.135139 TGCCGTCTAAGTCTCATCTGC 59.865 52.381 0.00 0.00 0.00 4.26
258 299 2.425312 ACTGCCGTCTAAGTCTCATCTG 59.575 50.000 0.00 0.00 0.00 2.90
259 300 2.729194 ACTGCCGTCTAAGTCTCATCT 58.271 47.619 0.00 0.00 0.00 2.90
260 301 3.440228 GAACTGCCGTCTAAGTCTCATC 58.560 50.000 0.00 0.00 0.00 2.92
261 302 2.159366 CGAACTGCCGTCTAAGTCTCAT 60.159 50.000 0.00 0.00 0.00 2.90
262 303 1.199327 CGAACTGCCGTCTAAGTCTCA 59.801 52.381 0.00 0.00 0.00 3.27
263 304 1.467713 CCGAACTGCCGTCTAAGTCTC 60.468 57.143 0.00 0.00 0.00 3.36
264 305 0.526662 CCGAACTGCCGTCTAAGTCT 59.473 55.000 0.00 0.00 0.00 3.24
265 306 1.077089 GCCGAACTGCCGTCTAAGTC 61.077 60.000 0.00 0.00 0.00 3.01
266 307 1.080025 GCCGAACTGCCGTCTAAGT 60.080 57.895 0.00 0.00 0.00 2.24
267 308 0.802607 GAGCCGAACTGCCGTCTAAG 60.803 60.000 0.00 0.00 0.00 2.18
268 309 1.214589 GAGCCGAACTGCCGTCTAA 59.785 57.895 0.00 0.00 0.00 2.10
269 310 2.882876 GAGCCGAACTGCCGTCTA 59.117 61.111 0.00 0.00 0.00 2.59
270 311 4.421479 CGAGCCGAACTGCCGTCT 62.421 66.667 0.00 0.00 0.00 4.18
274 315 4.090057 GTTGCGAGCCGAACTGCC 62.090 66.667 0.00 0.00 0.00 4.85
275 316 3.044305 AGTTGCGAGCCGAACTGC 61.044 61.111 0.84 0.00 30.73 4.40
276 317 1.016130 ATCAGTTGCGAGCCGAACTG 61.016 55.000 17.10 17.10 41.45 3.16
277 318 0.737715 GATCAGTTGCGAGCCGAACT 60.738 55.000 0.00 0.00 31.49 3.01
278 319 1.014044 TGATCAGTTGCGAGCCGAAC 61.014 55.000 0.00 0.00 0.00 3.95
279 320 0.108186 ATGATCAGTTGCGAGCCGAA 60.108 50.000 0.09 0.00 0.00 4.30
280 321 0.528466 GATGATCAGTTGCGAGCCGA 60.528 55.000 0.09 0.00 0.00 5.54
281 322 1.815212 CGATGATCAGTTGCGAGCCG 61.815 60.000 0.09 0.00 0.00 5.52
282 323 1.930100 CGATGATCAGTTGCGAGCC 59.070 57.895 0.09 0.00 0.00 4.70
283 324 1.275066 GCGATGATCAGTTGCGAGC 59.725 57.895 0.09 0.00 0.00 5.03
287 328 1.258982 CCTAACGCGATGATCAGTTGC 59.741 52.381 15.93 4.04 0.00 4.17
288 329 2.540515 ACCTAACGCGATGATCAGTTG 58.459 47.619 15.93 0.00 0.00 3.16
289 330 2.961526 ACCTAACGCGATGATCAGTT 57.038 45.000 15.93 2.36 0.00 3.16
290 331 2.481449 GGAACCTAACGCGATGATCAGT 60.481 50.000 15.93 0.00 0.00 3.41
291 332 2.128035 GGAACCTAACGCGATGATCAG 58.872 52.381 15.93 0.00 0.00 2.90
292 333 2.218953 GGAACCTAACGCGATGATCA 57.781 50.000 15.93 0.00 0.00 2.92
318 359 4.773117 GTCTCCACGGACGGCGAC 62.773 72.222 16.62 7.58 33.87 5.19
328 369 0.736325 AAGCATGCGTACGTCTCCAC 60.736 55.000 17.90 0.00 0.00 4.02
329 370 0.735978 CAAGCATGCGTACGTCTCCA 60.736 55.000 17.90 6.44 0.00 3.86
330 371 1.421410 CCAAGCATGCGTACGTCTCC 61.421 60.000 17.90 0.00 0.00 3.71
331 372 1.999051 CCAAGCATGCGTACGTCTC 59.001 57.895 17.90 0.27 0.00 3.36
332 373 2.100631 GCCAAGCATGCGTACGTCT 61.101 57.895 17.90 6.41 0.00 4.18
333 374 2.399611 GCCAAGCATGCGTACGTC 59.600 61.111 17.90 9.82 0.00 4.34
334 375 3.487202 CGCCAAGCATGCGTACGT 61.487 61.111 17.90 0.00 46.59 3.57
344 385 4.157958 CTGCTTCGAGCGCCAAGC 62.158 66.667 22.92 22.92 46.26 4.01
345 386 4.157958 GCTGCTTCGAGCGCCAAG 62.158 66.667 2.29 5.28 46.26 3.61
346 387 4.986645 TGCTGCTTCGAGCGCCAA 62.987 61.111 2.29 0.00 46.26 4.52
358 399 3.006756 TACCTGACGAGCCTGCTGC 62.007 63.158 0.00 0.00 41.71 5.25
359 400 1.153745 GTACCTGACGAGCCTGCTG 60.154 63.158 0.00 0.00 0.00 4.41
360 401 0.900647 AAGTACCTGACGAGCCTGCT 60.901 55.000 0.00 0.00 0.00 4.24
361 402 0.815734 TAAGTACCTGACGAGCCTGC 59.184 55.000 0.00 0.00 0.00 4.85
362 403 1.816835 TGTAAGTACCTGACGAGCCTG 59.183 52.381 0.00 0.00 0.00 4.85
363 404 1.817447 GTGTAAGTACCTGACGAGCCT 59.183 52.381 0.00 0.00 0.00 4.58
364 405 1.135170 GGTGTAAGTACCTGACGAGCC 60.135 57.143 0.00 0.00 37.74 4.70
365 406 1.542915 TGGTGTAAGTACCTGACGAGC 59.457 52.381 0.00 0.00 41.43 5.03
366 407 3.695060 AGATGGTGTAAGTACCTGACGAG 59.305 47.826 0.00 0.00 41.43 4.18
367 408 3.693085 GAGATGGTGTAAGTACCTGACGA 59.307 47.826 0.00 0.00 41.43 4.20
368 409 3.181489 GGAGATGGTGTAAGTACCTGACG 60.181 52.174 0.00 0.00 41.43 4.35
369 410 3.767673 TGGAGATGGTGTAAGTACCTGAC 59.232 47.826 0.00 0.00 41.43 3.51
370 411 4.023980 CTGGAGATGGTGTAAGTACCTGA 58.976 47.826 0.00 0.00 41.43 3.86
371 412 3.430929 GCTGGAGATGGTGTAAGTACCTG 60.431 52.174 0.00 0.00 41.43 4.00
401 442 1.535444 TCTGGGAAGGCGGTTCTGA 60.535 57.895 0.00 0.00 35.25 3.27
465 508 1.595093 CGGCGAAAAATGGGCTCCTT 61.595 55.000 0.00 0.00 0.00 3.36
970 1226 1.895707 CGGGTACTCGGCCTCGTAT 60.896 63.158 7.42 0.00 37.69 3.06
1383 1644 3.782443 GACCCCGGCTCCATTCGT 61.782 66.667 0.00 0.00 0.00 3.85
1949 2301 2.771328 AAAAGCCTAAGCCGCTGCCT 62.771 55.000 0.00 0.00 41.25 4.75
1951 2303 1.025041 ATAAAAGCCTAAGCCGCTGC 58.975 50.000 0.00 0.00 41.25 5.25
1952 2304 3.877508 ACTAATAAAAGCCTAAGCCGCTG 59.122 43.478 0.00 0.00 41.25 5.18
1954 2306 4.552184 CGAACTAATAAAAGCCTAAGCCGC 60.552 45.833 0.00 0.00 41.25 6.53
2023 2385 1.600023 AGTTCGGCCAATTTTCGACA 58.400 45.000 2.24 0.00 32.39 4.35
2111 2518 3.854669 AGCCGGCGCTAGATTGCT 61.855 61.111 23.20 0.00 46.08 3.91
2199 2607 6.877611 AGAGAGACTATTTAGACTAGCTGC 57.122 41.667 0.00 0.00 0.00 5.25
2209 2617 9.698309 CACTTTGTCAAGAAGAGAGACTATTTA 57.302 33.333 0.00 0.00 33.72 1.40
2215 2623 4.509600 CCACACTTTGTCAAGAAGAGAGAC 59.490 45.833 0.00 0.00 33.72 3.36
2248 2656 2.033675 CAGACCGTGGTGCATATACGTA 59.966 50.000 15.74 0.00 36.17 3.57
2249 2657 1.108776 AGACCGTGGTGCATATACGT 58.891 50.000 15.74 0.00 36.17 3.57
2250 2658 1.202371 ACAGACCGTGGTGCATATACG 60.202 52.381 11.76 11.76 37.55 3.06
2251 2659 2.100916 AGACAGACCGTGGTGCATATAC 59.899 50.000 0.00 0.00 0.00 1.47
2306 2714 0.598562 TCGAGAGGAGTTCACAGTGC 59.401 55.000 0.00 0.00 0.00 4.40
2418 2827 2.595750 TCCACCGGGAAAAATGATGT 57.404 45.000 6.32 0.00 41.32 3.06
2448 2859 1.134788 GGCACTATCTGTACGGCAACT 60.135 52.381 0.00 0.00 0.00 3.16
2471 2882 2.932498 TGCGACATCATTTTCAACAGC 58.068 42.857 0.00 0.00 0.00 4.40
2473 2884 3.067320 TGGTTGCGACATCATTTTCAACA 59.933 39.130 6.39 0.00 36.48 3.33
2505 2916 5.479306 TCAGTCAGTGAATTTAGGCTGTAC 58.521 41.667 0.00 0.00 29.64 2.90
2507 2918 4.623932 TCAGTCAGTGAATTTAGGCTGT 57.376 40.909 0.00 0.00 29.64 4.40
2512 2923 7.588143 AGAATCGTTCAGTCAGTGAATTTAG 57.412 36.000 0.00 0.00 46.99 1.85
2516 2927 8.553459 AAATAAGAATCGTTCAGTCAGTGAAT 57.447 30.769 0.00 0.00 46.99 2.57
2530 2941 1.937899 ACGCCGGGAAAATAAGAATCG 59.062 47.619 2.18 0.00 0.00 3.34
2605 3047 1.394266 CCCCGCTGCATTGCCTTAAT 61.394 55.000 6.12 0.00 0.00 1.40
2606 3048 2.051518 CCCCGCTGCATTGCCTTAA 61.052 57.895 6.12 0.00 0.00 1.85
2607 3049 2.283143 ATCCCCGCTGCATTGCCTTA 62.283 55.000 6.12 0.00 0.00 2.69
2608 3050 3.667217 ATCCCCGCTGCATTGCCTT 62.667 57.895 6.12 0.00 0.00 4.35
2609 3051 4.133373 ATCCCCGCTGCATTGCCT 62.133 61.111 6.12 0.00 0.00 4.75
2620 3062 2.204865 TTTGGCAGGTACCATCCCCG 62.205 60.000 15.94 0.00 40.13 5.73
2631 3073 1.667722 GCCTGGTTTCTTTGGCAGG 59.332 57.895 0.00 0.00 44.34 4.85
2657 3099 3.565764 TTGTCCCTGATTATGCCAGAG 57.434 47.619 0.00 0.00 33.65 3.35
2685 3127 8.178313 GCCATATTTGACTAAGTTTTCTCAGAC 58.822 37.037 0.00 0.00 0.00 3.51
2705 3147 6.661805 TCAATGTGCATATGATTGAGCCATAT 59.338 34.615 6.97 0.00 37.62 1.78
2706 3148 6.005198 TCAATGTGCATATGATTGAGCCATA 58.995 36.000 6.97 0.00 32.44 2.74
2740 3182 1.229428 GTCCACCACATGACACTGTG 58.771 55.000 6.19 6.19 44.92 3.66
2771 3213 5.300286 GTGGAGCATACAAGCCTGAATTAAT 59.700 40.000 0.00 0.00 34.23 1.40
2772 3214 4.640201 GTGGAGCATACAAGCCTGAATTAA 59.360 41.667 0.00 0.00 34.23 1.40
2773 3215 4.080356 AGTGGAGCATACAAGCCTGAATTA 60.080 41.667 0.00 0.00 34.23 1.40
2774 3216 3.019564 GTGGAGCATACAAGCCTGAATT 58.980 45.455 0.00 0.00 34.23 2.17
2785 3227 2.361119 TCGACATACCAGTGGAGCATAC 59.639 50.000 18.40 1.75 0.00 2.39
2844 3286 7.460071 TGGGCCTTTAGTACTTTAAATGTGTA 58.540 34.615 4.53 0.00 0.00 2.90
2845 3287 6.308566 TGGGCCTTTAGTACTTTAAATGTGT 58.691 36.000 4.53 0.00 0.00 3.72
2846 3288 6.827586 TGGGCCTTTAGTACTTTAAATGTG 57.172 37.500 4.53 0.00 0.00 3.21
2847 3289 7.842887 TTTGGGCCTTTAGTACTTTAAATGT 57.157 32.000 4.53 0.00 0.00 2.71
2867 3309 8.833231 ACGGAAAGAGTACATGATATATTTGG 57.167 34.615 0.00 0.00 0.00 3.28
2886 3328 7.369551 ACAGTCTTATATTATGGGACGGAAA 57.630 36.000 13.34 0.00 32.86 3.13
2889 3331 8.446599 AAAAACAGTCTTATATTATGGGACGG 57.553 34.615 0.00 0.00 32.86 4.79


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

AutoCloner maintained by Alex Coulton.