Multiple sequence alignment - TraesCS2B01G560500

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2B01G560500 chr2B 100.000 3063 0 0 1 3063 753833789 753836851 0.000000e+00 5657.0
1 TraesCS2B01G560500 chr7D 89.410 2153 156 33 954 3058 426496444 426498572 0.000000e+00 2647.0
2 TraesCS2B01G560500 chr7D 88.945 2171 153 38 937 3063 426632545 426634672 0.000000e+00 2599.0
3 TraesCS2B01G560500 chr7D 87.488 2070 152 45 304 2314 426449748 426451769 0.000000e+00 2289.0
4 TraesCS2B01G560500 chr7D 85.892 1772 174 36 996 2739 426517893 426519616 0.000000e+00 1818.0
5 TraesCS2B01G560500 chr7D 84.356 1483 161 40 1275 2722 426553861 426555307 0.000000e+00 1387.0
6 TraesCS2B01G560500 chr7D 84.737 190 17 7 578 758 426643774 426643960 2.430000e-41 180.0
7 TraesCS2B01G560500 chr7D 85.841 113 9 4 578 690 426637971 426638076 2.500000e-21 113.0
8 TraesCS2B01G560500 chr7A 88.383 1954 141 40 304 2225 507023527 507021628 0.000000e+00 2272.0
9 TraesCS2B01G560500 chr7A 83.472 2402 241 80 578 2890 507014776 507012442 0.000000e+00 2093.0
10 TraesCS2B01G560500 chr7A 78.657 923 109 39 2176 3059 506853535 506852662 1.620000e-147 532.0
11 TraesCS2B01G560500 chr7A 86.607 112 9 4 579 690 507018932 507018827 5.370000e-23 119.0
12 TraesCS2B01G560500 chr7A 90.909 66 6 0 2888 2953 506985804 506985739 4.210000e-14 89.8
13 TraesCS2B01G560500 chr7B 87.358 1930 158 38 430 2314 443689669 443691557 0.000000e+00 2134.0
14 TraesCS2B01G560500 chr7B 84.286 1820 190 47 996 2786 443696516 443698268 0.000000e+00 1688.0
15 TraesCS2B01G560500 chr7B 90.615 927 64 11 935 1846 443702214 443703132 0.000000e+00 1208.0
16 TraesCS2B01G560500 chr7B 90.411 511 36 6 2556 3057 443704460 443704966 0.000000e+00 660.0
17 TraesCS2B01G560500 chr7B 88.172 93 7 3 578 668 443730444 443730534 1.160000e-19 108.0
18 TraesCS2B01G560500 chrUn 87.671 73 9 0 2895 2967 18116239 18116311 5.440000e-13 86.1


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 TraesCS2B01G560500 chr2B 753833789 753836851 3062 False 5657.000000 5657 100.000000 1 3063 1 chr2B.!!$F1 3062
1 TraesCS2B01G560500 chr7D 426496444 426498572 2128 False 2647.000000 2647 89.410000 954 3058 1 chr7D.!!$F2 2104
2 TraesCS2B01G560500 chr7D 426449748 426451769 2021 False 2289.000000 2289 87.488000 304 2314 1 chr7D.!!$F1 2010
3 TraesCS2B01G560500 chr7D 426517893 426519616 1723 False 1818.000000 1818 85.892000 996 2739 1 chr7D.!!$F3 1743
4 TraesCS2B01G560500 chr7D 426553861 426555307 1446 False 1387.000000 1387 84.356000 1275 2722 1 chr7D.!!$F4 1447
5 TraesCS2B01G560500 chr7D 426632545 426638076 5531 False 1356.000000 2599 87.393000 578 3063 2 chr7D.!!$F6 2485
6 TraesCS2B01G560500 chr7A 507012442 507014776 2334 True 2093.000000 2093 83.472000 578 2890 1 chr7A.!!$R3 2312
7 TraesCS2B01G560500 chr7A 507018827 507023527 4700 True 1195.500000 2272 87.495000 304 2225 2 chr7A.!!$R4 1921
8 TraesCS2B01G560500 chr7A 506852662 506853535 873 True 532.000000 532 78.657000 2176 3059 1 chr7A.!!$R1 883
9 TraesCS2B01G560500 chr7B 443689669 443691557 1888 False 2134.000000 2134 87.358000 430 2314 1 chr7B.!!$F1 1884
10 TraesCS2B01G560500 chr7B 443696516 443704966 8450 False 1185.333333 1688 88.437333 935 3057 3 chr7B.!!$F3 2122

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
32 33 0.170561 GCTCGGAGCTTCTGAACGTA 59.829 55.0 22.32 0.0 38.45 3.57 F
255 256 0.179000 AGCGAACCTCAAGGCCATAG 59.821 55.0 5.01 0.0 39.32 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 7102 0.173481 TGCTGTACATCTCCACGAGC 59.827 55.000 0.0 0.0 0.0 5.03 R
2070 7259 1.131126 CATGACGCACTTGGGATCAAC 59.869 52.381 0.0 0.0 0.0 3.18 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
26 27 2.511145 GCTGGCTCGGAGCTTCTG 60.511 66.667 27.47 16.83 41.99 3.02
27 28 3.011635 GCTGGCTCGGAGCTTCTGA 62.012 63.158 27.47 7.76 41.99 3.27
28 29 1.593787 CTGGCTCGGAGCTTCTGAA 59.406 57.895 27.47 7.67 41.99 3.02
29 30 0.739112 CTGGCTCGGAGCTTCTGAAC 60.739 60.000 27.47 11.04 41.99 3.18
31 32 1.080434 GCTCGGAGCTTCTGAACGT 60.080 57.895 22.32 0.00 38.45 3.99
32 33 0.170561 GCTCGGAGCTTCTGAACGTA 59.829 55.000 22.32 0.00 38.45 3.57
35 36 3.488721 GCTCGGAGCTTCTGAACGTATTA 60.489 47.826 22.32 0.00 38.45 0.98
36 37 4.669318 CTCGGAGCTTCTGAACGTATTAA 58.331 43.478 0.00 0.00 30.21 1.40
37 38 5.258456 TCGGAGCTTCTGAACGTATTAAT 57.742 39.130 0.00 0.00 0.00 1.40
39 40 4.444720 CGGAGCTTCTGAACGTATTAATCC 59.555 45.833 0.00 0.00 0.00 3.01
40 41 4.444720 GGAGCTTCTGAACGTATTAATCCG 59.555 45.833 0.00 0.00 0.00 4.18
41 42 5.258456 AGCTTCTGAACGTATTAATCCGA 57.742 39.130 7.48 0.00 0.00 4.55
42 43 5.657474 AGCTTCTGAACGTATTAATCCGAA 58.343 37.500 7.48 0.00 0.00 4.30
43 44 6.103997 AGCTTCTGAACGTATTAATCCGAAA 58.896 36.000 7.48 0.00 0.00 3.46
44 45 6.761714 AGCTTCTGAACGTATTAATCCGAAAT 59.238 34.615 7.48 0.00 0.00 2.17
45 46 7.924412 AGCTTCTGAACGTATTAATCCGAAATA 59.076 33.333 7.48 0.00 0.00 1.40
46 47 8.709646 GCTTCTGAACGTATTAATCCGAAATAT 58.290 33.333 7.48 0.00 0.00 1.28
48 49 9.752961 TTCTGAACGTATTAATCCGAAATATGA 57.247 29.630 7.48 0.00 32.51 2.15
50 51 8.874744 TGAACGTATTAATCCGAAATATGACA 57.125 30.769 7.48 0.00 32.51 3.58
51 52 8.974408 TGAACGTATTAATCCGAAATATGACAG 58.026 33.333 7.48 0.00 32.51 3.51
54 55 9.706691 ACGTATTAATCCGAAATATGACAGATT 57.293 29.630 7.48 0.00 32.51 2.40
70 71 8.812513 ATGACAGATTTAATGATTTGGACAGA 57.187 30.769 0.00 0.00 0.00 3.41
71 72 8.634335 TGACAGATTTAATGATTTGGACAGAA 57.366 30.769 0.00 0.00 0.00 3.02
72 73 9.076781 TGACAGATTTAATGATTTGGACAGAAA 57.923 29.630 0.00 0.00 0.00 2.52
83 84 8.463930 TGATTTGGACAGAAATCTAAGTTGTT 57.536 30.769 0.00 0.00 41.21 2.83
84 85 8.912988 TGATTTGGACAGAAATCTAAGTTGTTT 58.087 29.630 0.00 0.00 41.21 2.83
85 86 9.750125 GATTTGGACAGAAATCTAAGTTGTTTT 57.250 29.630 0.00 0.00 38.69 2.43
140 141 8.261492 AGATGAGATGTGACAACTTATTGAAC 57.739 34.615 1.90 0.00 39.30 3.18
141 142 7.879677 AGATGAGATGTGACAACTTATTGAACA 59.120 33.333 1.90 0.00 39.30 3.18
142 143 7.800155 TGAGATGTGACAACTTATTGAACAA 57.200 32.000 0.00 0.00 38.50 2.83
144 145 7.281999 TGAGATGTGACAACTTATTGAACAACA 59.718 33.333 0.00 0.00 38.50 3.33
145 146 7.417612 AGATGTGACAACTTATTGAACAACAC 58.582 34.615 0.00 0.00 38.50 3.32
146 147 6.502136 TGTGACAACTTATTGAACAACACA 57.498 33.333 0.00 0.00 39.30 3.72
149 150 6.804295 GTGACAACTTATTGAACAACACACAA 59.196 34.615 0.00 0.00 39.30 3.33
151 152 7.700234 TGACAACTTATTGAACAACACACAATC 59.300 33.333 0.00 0.00 39.30 2.67
152 153 6.690957 ACAACTTATTGAACAACACACAATCG 59.309 34.615 0.00 0.00 39.30 3.34
154 155 6.427150 ACTTATTGAACAACACACAATCGTC 58.573 36.000 0.00 0.00 36.06 4.20
155 156 4.891627 ATTGAACAACACACAATCGTCA 57.108 36.364 0.00 0.00 29.89 4.35
156 157 4.686839 TTGAACAACACACAATCGTCAA 57.313 36.364 0.00 0.00 0.00 3.18
157 158 4.686839 TGAACAACACACAATCGTCAAA 57.313 36.364 0.00 0.00 0.00 2.69
158 159 4.407818 TGAACAACACACAATCGTCAAAC 58.592 39.130 0.00 0.00 0.00 2.93
159 160 3.414549 ACAACACACAATCGTCAAACC 57.585 42.857 0.00 0.00 0.00 3.27
160 161 2.223157 ACAACACACAATCGTCAAACCG 60.223 45.455 0.00 0.00 0.00 4.44
164 165 2.073816 ACACAATCGTCAAACCGATCC 58.926 47.619 0.00 0.00 46.23 3.36
165 166 2.073056 CACAATCGTCAAACCGATCCA 58.927 47.619 0.00 0.00 46.23 3.41
166 167 2.677836 CACAATCGTCAAACCGATCCAT 59.322 45.455 0.00 0.00 46.23 3.41
167 168 2.936498 ACAATCGTCAAACCGATCCATC 59.064 45.455 0.00 0.00 46.23 3.51
168 169 2.935849 CAATCGTCAAACCGATCCATCA 59.064 45.455 0.00 0.00 46.23 3.07
169 170 2.979814 TCGTCAAACCGATCCATCAT 57.020 45.000 0.00 0.00 30.63 2.45
170 171 3.260475 TCGTCAAACCGATCCATCATT 57.740 42.857 0.00 0.00 30.63 2.57
171 172 3.605634 TCGTCAAACCGATCCATCATTT 58.394 40.909 0.00 0.00 30.63 2.32
172 173 4.760878 TCGTCAAACCGATCCATCATTTA 58.239 39.130 0.00 0.00 30.63 1.40
173 174 4.808895 TCGTCAAACCGATCCATCATTTAG 59.191 41.667 0.00 0.00 30.63 1.85
174 175 4.552767 CGTCAAACCGATCCATCATTTAGC 60.553 45.833 0.00 0.00 0.00 3.09
175 176 4.576463 GTCAAACCGATCCATCATTTAGCT 59.424 41.667 0.00 0.00 0.00 3.32
176 177 5.066505 GTCAAACCGATCCATCATTTAGCTT 59.933 40.000 0.00 0.00 0.00 3.74
177 178 5.652014 TCAAACCGATCCATCATTTAGCTTT 59.348 36.000 0.00 0.00 0.00 3.51
178 179 6.152661 TCAAACCGATCCATCATTTAGCTTTT 59.847 34.615 0.00 0.00 0.00 2.27
180 181 6.619801 ACCGATCCATCATTTAGCTTTTAC 57.380 37.500 0.00 0.00 0.00 2.01
181 182 5.531287 ACCGATCCATCATTTAGCTTTTACC 59.469 40.000 0.00 0.00 0.00 2.85
182 183 5.765182 CCGATCCATCATTTAGCTTTTACCT 59.235 40.000 0.00 0.00 0.00 3.08
184 185 7.201821 CCGATCCATCATTTAGCTTTTACCTTT 60.202 37.037 0.00 0.00 0.00 3.11
185 186 7.857885 CGATCCATCATTTAGCTTTTACCTTTC 59.142 37.037 0.00 0.00 0.00 2.62
186 187 8.829373 ATCCATCATTTAGCTTTTACCTTTCT 57.171 30.769 0.00 0.00 0.00 2.52
187 188 8.281212 TCCATCATTTAGCTTTTACCTTTCTC 57.719 34.615 0.00 0.00 0.00 2.87
190 191 6.790319 TCATTTAGCTTTTACCTTTCTCCCT 58.210 36.000 0.00 0.00 0.00 4.20
191 192 6.884836 TCATTTAGCTTTTACCTTTCTCCCTC 59.115 38.462 0.00 0.00 0.00 4.30
192 193 5.836024 TTAGCTTTTACCTTTCTCCCTCA 57.164 39.130 0.00 0.00 0.00 3.86
193 194 4.936685 AGCTTTTACCTTTCTCCCTCAT 57.063 40.909 0.00 0.00 0.00 2.90
194 195 5.262455 AGCTTTTACCTTTCTCCCTCATT 57.738 39.130 0.00 0.00 0.00 2.57
196 197 6.077993 AGCTTTTACCTTTCTCCCTCATTTT 58.922 36.000 0.00 0.00 0.00 1.82
197 198 7.238710 AGCTTTTACCTTTCTCCCTCATTTTA 58.761 34.615 0.00 0.00 0.00 1.52
201 202 7.525158 TTACCTTTCTCCCTCATTTTATCCT 57.475 36.000 0.00 0.00 0.00 3.24
202 203 6.408770 ACCTTTCTCCCTCATTTTATCCTT 57.591 37.500 0.00 0.00 0.00 3.36
204 205 5.830457 CCTTTCTCCCTCATTTTATCCTTCC 59.170 44.000 0.00 0.00 0.00 3.46
206 207 5.896073 TCTCCCTCATTTTATCCTTCCTC 57.104 43.478 0.00 0.00 0.00 3.71
207 208 4.345257 TCTCCCTCATTTTATCCTTCCTCG 59.655 45.833 0.00 0.00 0.00 4.63
211 212 5.396884 CCCTCATTTTATCCTTCCTCGTTCT 60.397 44.000 0.00 0.00 0.00 3.01
212 213 6.116126 CCTCATTTTATCCTTCCTCGTTCTT 58.884 40.000 0.00 0.00 0.00 2.52
215 216 4.796038 TTTATCCTTCCTCGTTCTTCGT 57.204 40.909 0.00 0.00 40.80 3.85
216 217 4.796038 TTATCCTTCCTCGTTCTTCGTT 57.204 40.909 0.00 0.00 40.80 3.85
217 218 2.433868 TCCTTCCTCGTTCTTCGTTG 57.566 50.000 0.00 0.00 40.80 4.10
218 219 1.684983 TCCTTCCTCGTTCTTCGTTGT 59.315 47.619 0.00 0.00 40.80 3.32
219 220 2.101917 TCCTTCCTCGTTCTTCGTTGTT 59.898 45.455 0.00 0.00 40.80 2.83
222 223 4.201881 CCTTCCTCGTTCTTCGTTGTTTTT 60.202 41.667 0.00 0.00 40.80 1.94
223 224 4.525411 TCCTCGTTCTTCGTTGTTTTTC 57.475 40.909 0.00 0.00 40.80 2.29
224 225 3.000523 TCCTCGTTCTTCGTTGTTTTTCG 59.999 43.478 0.00 0.00 40.80 3.46
225 226 3.242188 CCTCGTTCTTCGTTGTTTTTCGT 60.242 43.478 0.00 0.00 40.80 3.85
226 227 3.661819 TCGTTCTTCGTTGTTTTTCGTG 58.338 40.909 0.00 0.00 40.80 4.35
227 228 3.123284 TCGTTCTTCGTTGTTTTTCGTGT 59.877 39.130 0.00 0.00 40.80 4.49
228 229 3.841872 CGTTCTTCGTTGTTTTTCGTGTT 59.158 39.130 0.00 0.00 34.52 3.32
229 230 4.318854 CGTTCTTCGTTGTTTTTCGTGTTT 59.681 37.500 0.00 0.00 34.52 2.83
230 231 5.525819 GTTCTTCGTTGTTTTTCGTGTTTG 58.474 37.500 0.00 0.00 0.00 2.93
233 234 5.509972 TCTTCGTTGTTTTTCGTGTTTGATG 59.490 36.000 0.00 0.00 0.00 3.07
234 235 4.971008 TCGTTGTTTTTCGTGTTTGATGA 58.029 34.783 0.00 0.00 0.00 2.92
235 236 4.789119 TCGTTGTTTTTCGTGTTTGATGAC 59.211 37.500 0.00 0.00 0.00 3.06
236 237 4.555360 CGTTGTTTTTCGTGTTTGATGACA 59.445 37.500 0.00 0.00 0.00 3.58
239 240 2.661504 TTTCGTGTTTGATGACAGCG 57.338 45.000 0.00 0.00 0.00 5.18
240 241 1.859383 TTCGTGTTTGATGACAGCGA 58.141 45.000 0.00 0.00 34.09 4.93
241 242 1.859383 TCGTGTTTGATGACAGCGAA 58.141 45.000 0.00 0.00 33.50 4.70
242 243 1.525197 TCGTGTTTGATGACAGCGAAC 59.475 47.619 15.53 15.53 33.50 3.95
245 246 2.096218 GTGTTTGATGACAGCGAACCTC 60.096 50.000 18.77 9.88 0.00 3.85
246 247 2.143122 GTTTGATGACAGCGAACCTCA 58.857 47.619 12.03 0.00 0.00 3.86
247 248 2.542020 TTGATGACAGCGAACCTCAA 57.458 45.000 0.00 0.00 0.00 3.02
248 249 2.084610 TGATGACAGCGAACCTCAAG 57.915 50.000 0.00 0.00 0.00 3.02
249 250 1.338105 TGATGACAGCGAACCTCAAGG 60.338 52.381 0.00 0.00 42.17 3.61
250 251 0.674895 ATGACAGCGAACCTCAAGGC 60.675 55.000 0.00 0.00 39.32 4.35
251 252 2.032681 ACAGCGAACCTCAAGGCC 59.967 61.111 0.00 0.00 39.32 5.19
252 253 2.032528 CAGCGAACCTCAAGGCCA 59.967 61.111 5.01 0.00 39.32 5.36
253 254 1.377725 CAGCGAACCTCAAGGCCAT 60.378 57.895 5.01 0.00 39.32 4.40
255 256 0.179000 AGCGAACCTCAAGGCCATAG 59.821 55.000 5.01 0.00 39.32 2.23
257 258 0.179045 CGAACCTCAAGGCCATAGGG 60.179 60.000 19.00 11.87 39.32 3.53
285 286 2.034799 GCAGACCTAGGGCAGTCCATA 61.035 57.143 19.45 0.00 38.24 2.74
286 287 1.967066 CAGACCTAGGGCAGTCCATAG 59.033 57.143 19.45 0.00 44.24 2.23
287 288 0.682292 GACCTAGGGCAGTCCATAGC 59.318 60.000 10.77 0.00 43.52 2.97
293 294 2.584608 GCAGTCCATAGCCACCGT 59.415 61.111 0.00 0.00 0.00 4.83
294 295 1.815421 GCAGTCCATAGCCACCGTG 60.815 63.158 0.00 0.00 0.00 4.94
295 296 1.815421 CAGTCCATAGCCACCGTGC 60.815 63.158 0.00 0.00 0.00 5.34
296 297 2.890474 GTCCATAGCCACCGTGCG 60.890 66.667 0.00 0.00 36.02 5.34
297 298 3.387091 TCCATAGCCACCGTGCGT 61.387 61.111 0.00 0.00 36.02 5.24
298 299 2.890474 CCATAGCCACCGTGCGTC 60.890 66.667 0.00 0.00 36.02 5.19
299 300 2.890474 CATAGCCACCGTGCGTCC 60.890 66.667 0.00 0.00 36.02 4.79
300 301 4.157120 ATAGCCACCGTGCGTCCC 62.157 66.667 0.00 0.00 36.02 4.46
404 421 2.589157 CCAGTTCCAGCGGGGTGTA 61.589 63.158 2.05 0.00 38.11 2.90
408 425 1.910671 AGTTCCAGCGGGGTGTATTTA 59.089 47.619 2.05 0.00 38.11 1.40
431 448 2.105821 AGGATGTTTTCTGGAACCGTGA 59.894 45.455 0.00 0.00 0.00 4.35
495 513 1.067516 CAAAACAGCCCAAGTGGACAG 59.932 52.381 0.00 0.00 37.39 3.51
520 538 3.058983 TGCATCTTTGTGTTTCTACAGCG 60.059 43.478 0.00 0.00 34.24 5.18
521 539 3.482786 CATCTTTGTGTTTCTACAGCGC 58.517 45.455 0.00 0.00 34.24 5.92
522 540 1.525197 TCTTTGTGTTTCTACAGCGCG 59.475 47.619 0.00 0.00 34.24 6.86
523 541 1.525197 CTTTGTGTTTCTACAGCGCGA 59.475 47.619 12.10 0.00 34.24 5.87
540 565 1.062880 GCGAGTTTCAACGGTTTGTGA 59.937 47.619 0.00 0.00 34.02 3.58
541 566 2.286772 GCGAGTTTCAACGGTTTGTGAT 60.287 45.455 0.00 0.00 34.02 3.06
542 567 3.059461 GCGAGTTTCAACGGTTTGTGATA 60.059 43.478 0.00 0.00 34.02 2.15
543 568 4.378046 GCGAGTTTCAACGGTTTGTGATAT 60.378 41.667 0.00 0.00 34.02 1.63
544 569 5.079406 CGAGTTTCAACGGTTTGTGATATG 58.921 41.667 0.00 0.00 34.02 1.78
545 570 5.333798 CGAGTTTCAACGGTTTGTGATATGT 60.334 40.000 0.00 0.00 34.02 2.29
560 585 3.332187 TGATATGTCCCAACACCCTTTGA 59.668 43.478 0.00 0.00 38.48 2.69
576 602 4.475944 CCTTTGAATTCAGCGAACGATTT 58.524 39.130 8.41 0.00 0.00 2.17
680 716 5.824624 AGCTAGGTACGTGTATTAGTTAGCA 59.175 40.000 0.00 0.00 34.86 3.49
705 741 2.438868 ATTCCCTGCGCTTTTGTTTC 57.561 45.000 9.73 0.00 0.00 2.78
706 742 1.398692 TTCCCTGCGCTTTTGTTTCT 58.601 45.000 9.73 0.00 0.00 2.52
707 743 0.951558 TCCCTGCGCTTTTGTTTCTC 59.048 50.000 9.73 0.00 0.00 2.87
708 744 0.954452 CCCTGCGCTTTTGTTTCTCT 59.046 50.000 9.73 0.00 0.00 3.10
710 746 2.605580 CCCTGCGCTTTTGTTTCTCTTC 60.606 50.000 9.73 0.00 0.00 2.87
711 747 2.301787 CTGCGCTTTTGTTTCTCTTCG 58.698 47.619 9.73 0.00 0.00 3.79
713 749 2.867368 TGCGCTTTTGTTTCTCTTCGTA 59.133 40.909 9.73 0.00 0.00 3.43
714 750 3.216031 GCGCTTTTGTTTCTCTTCGTAC 58.784 45.455 0.00 0.00 0.00 3.67
715 751 3.457596 CGCTTTTGTTTCTCTTCGTACG 58.542 45.455 9.53 9.53 0.00 3.67
758 794 3.869272 CGGCCAAGATGCACGAGC 61.869 66.667 2.24 0.00 42.57 5.03
820 856 3.004734 GAGCAGAGCGTTCGCACAC 62.005 63.158 18.95 9.24 0.00 3.82
869 908 5.696724 CCCAAACCGAAGTCTATATAAGCAG 59.303 44.000 0.00 0.00 0.00 4.24
892 932 9.628016 GCAGATGCTTACTACTGGATCATCCAT 62.628 44.444 6.90 0.23 41.22 3.41
900 940 2.832643 TGGATCATCCATTGCAACCT 57.167 45.000 0.66 0.00 42.67 3.50
901 941 3.949586 TGGATCATCCATTGCAACCTA 57.050 42.857 0.66 0.00 42.67 3.08
902 942 3.824133 TGGATCATCCATTGCAACCTAG 58.176 45.455 0.66 0.00 42.67 3.02
906 946 4.077300 TCATCCATTGCAACCTAGCTAG 57.923 45.455 14.20 14.20 34.99 3.42
908 948 1.559219 TCCATTGCAACCTAGCTAGCA 59.441 47.619 18.83 8.28 34.99 3.49
913 953 2.838736 TGCAACCTAGCTAGCAATAGC 58.161 47.619 18.83 13.00 43.12 2.97
915 955 3.181451 TGCAACCTAGCTAGCAATAGCAT 60.181 43.478 18.83 0.00 45.11 3.79
937 977 7.338475 GCATTAAGCTATAAGCATCTCGCTCT 61.338 42.308 1.22 0.00 46.28 4.09
938 978 9.036422 GCATTAAGCTATAAGCATCTCGCTCTC 62.036 44.444 1.22 0.00 46.28 3.20
946 5711 0.249405 CATCTCGCTCTCTCCTTGCC 60.249 60.000 0.00 0.00 0.00 4.52
947 5712 1.733402 ATCTCGCTCTCTCCTTGCCG 61.733 60.000 0.00 0.00 0.00 5.69
952 5717 1.298014 CTCTCTCCTTGCCGGCTTT 59.702 57.895 29.70 0.00 0.00 3.51
994 5767 3.456280 GCTCTCATCATCAGTCAACCTC 58.544 50.000 0.00 0.00 0.00 3.85
1013 5786 2.374830 CTAGGCATGGCGTCCTCCAG 62.375 65.000 14.30 0.35 39.89 3.86
1029 5802 2.048127 AGCGTCGTCCCTTCTTGC 60.048 61.111 0.00 0.00 0.00 4.01
1296 6097 9.726438 ACTATATGGTTCCATTTGCTAATACTC 57.274 33.333 9.70 0.00 0.00 2.59
1339 6156 2.639347 TGATGCTTCTGTTCTCCTGGAA 59.361 45.455 0.00 0.00 0.00 3.53
1345 6162 1.072331 TCTGTTCTCCTGGAAGCAACC 59.928 52.381 0.00 0.00 34.23 3.77
1426 6243 2.158959 CGACGACATCAAGTCCGCC 61.159 63.158 0.00 0.00 44.66 6.13
1654 6471 4.415332 AACCTCGACGCGCGTGAT 62.415 61.111 42.90 17.52 41.80 3.06
1805 6622 0.323957 GGGTCCTTCTGGTAAAGCGT 59.676 55.000 0.00 0.00 34.23 5.07
1913 7091 2.283388 TCTACGGCGGTGGAGGTT 60.283 61.111 13.24 0.00 0.00 3.50
1924 7102 0.954452 GTGGAGGTTTGCAGGACAAG 59.046 55.000 4.91 0.00 40.06 3.16
2014 7192 0.603439 GAAACGTACCTCCGCCCAAA 60.603 55.000 0.00 0.00 0.00 3.28
2048 7226 1.739562 GTGAGGCTCAAGTGCTCCG 60.740 63.158 20.62 0.00 0.00 4.63
2051 7229 3.426568 GGCTCAAGTGCTCCGTGC 61.427 66.667 0.00 0.00 43.25 5.34
2058 7239 1.764571 AAGTGCTCCGTGCCCAACTA 61.765 55.000 0.00 0.00 42.00 2.24
2059 7240 1.078426 GTGCTCCGTGCCCAACTAT 60.078 57.895 0.00 0.00 42.00 2.12
2060 7241 0.676782 GTGCTCCGTGCCCAACTATT 60.677 55.000 0.00 0.00 42.00 1.73
2061 7242 0.676466 TGCTCCGTGCCCAACTATTG 60.676 55.000 0.00 0.00 42.00 1.90
2070 7259 4.685924 GTGCCCAACTATTGATTGATTGG 58.314 43.478 0.00 0.00 39.67 3.16
2085 7274 2.639970 TTGGTTGATCCCAAGTGCG 58.360 52.632 0.00 0.00 39.56 5.34
2144 7353 6.935741 TTAGATGTGCAAGTTGTAACAGTT 57.064 33.333 15.62 10.31 0.00 3.16
2218 7441 6.968263 TTGACAAAATGTTCCCTTACATGA 57.032 33.333 0.00 0.00 38.69 3.07
2242 7493 7.095397 TGAGTGTGTAATAAATGGTGTTTCTCG 60.095 37.037 0.00 0.00 0.00 4.04
2332 7609 0.867746 TCAGTGACGCTTCAACATGC 59.132 50.000 0.00 0.00 31.90 4.06
2358 7635 6.255215 CAAACGGCTATTATGTCGAATTGTT 58.745 36.000 0.00 0.00 38.54 2.83
2359 7636 5.403897 ACGGCTATTATGTCGAATTGTTG 57.596 39.130 0.00 0.00 38.54 3.33
2452 7739 1.611977 CAGAAGGTGACCGTGACACTA 59.388 52.381 3.68 0.00 38.20 2.74
2453 7740 2.035449 CAGAAGGTGACCGTGACACTAA 59.965 50.000 3.68 0.00 38.20 2.24
2454 7741 2.035576 AGAAGGTGACCGTGACACTAAC 59.964 50.000 3.68 0.00 38.20 2.34
2455 7742 1.405872 AGGTGACCGTGACACTAACA 58.594 50.000 3.68 0.00 38.20 2.41
2456 7743 1.068127 AGGTGACCGTGACACTAACAC 59.932 52.381 3.68 9.96 38.20 3.32
2457 7744 1.068127 GGTGACCGTGACACTAACACT 59.932 52.381 18.09 0.00 38.20 3.55
2507 7796 7.455891 TGCAGATATGACACATGGATATCTTT 58.544 34.615 2.05 0.00 37.33 2.52
2550 7847 3.787476 GCACAAAAGTGTTCGTCGATGTT 60.787 43.478 4.21 0.00 35.07 2.71
2551 7848 3.718864 CACAAAAGTGTTCGTCGATGTTG 59.281 43.478 4.21 2.66 35.07 3.33
2552 7849 2.663279 AAAGTGTTCGTCGATGTTGC 57.337 45.000 4.21 0.00 0.00 4.17
2553 7850 1.577468 AAGTGTTCGTCGATGTTGCA 58.423 45.000 4.21 0.00 0.00 4.08
2580 8123 4.721776 AGGGTTCATGGAGCTCAGTATTTA 59.278 41.667 17.19 0.00 0.00 1.40
2606 8154 1.004745 ACCCAATGCCGATGAAAGAGT 59.995 47.619 0.00 0.00 0.00 3.24
2614 8164 5.147330 TGCCGATGAAAGAGTCTTTTAGA 57.853 39.130 18.96 7.37 0.00 2.10
2699 8249 3.785887 AGGTGGAATAATTGCCTGGTAGA 59.214 43.478 0.00 0.00 0.00 2.59
2725 8277 0.530288 CGGGCAATTCATCGGGTTTT 59.470 50.000 0.00 0.00 0.00 2.43
2764 8316 4.874970 TCTTGTAAGTTGTTACCTCCGAC 58.125 43.478 0.00 0.00 38.24 4.79
2770 8322 3.999046 AGTTGTTACCTCCGACGATTTT 58.001 40.909 0.00 0.00 0.00 1.82
2793 8346 3.755905 TGGATTTCGCATTGCTACTTTGA 59.244 39.130 7.12 0.00 0.00 2.69
2829 8382 4.081917 TCACAATGACATCAATGCTTGCAT 60.082 37.500 1.81 1.81 30.12 3.96
2839 8392 8.349568 ACATCAATGCTTGCATATATCTCATT 57.650 30.769 8.61 0.00 0.00 2.57
2842 8404 6.943718 TCAATGCTTGCATATATCTCATTGGA 59.056 34.615 8.61 3.78 39.53 3.53
3042 8618 2.485038 GGGCATTTGGAATTGTGCAAAG 59.515 45.455 0.00 0.00 46.58 2.77
3049 8625 4.846779 TGGAATTGTGCAAAGTAGGTTC 57.153 40.909 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.140599 AGAAGCTCCGAGCCAGCG 62.141 66.667 16.99 0.00 43.77 5.18
9 10 2.511145 CAGAAGCTCCGAGCCAGC 60.511 66.667 16.99 6.69 43.77 4.85
10 11 0.739112 GTTCAGAAGCTCCGAGCCAG 60.739 60.000 16.99 4.86 43.77 4.85
12 13 1.807573 CGTTCAGAAGCTCCGAGCC 60.808 63.158 16.99 2.61 43.77 4.70
13 14 0.170561 TACGTTCAGAAGCTCCGAGC 59.829 55.000 12.80 12.80 42.84 5.03
14 15 2.853731 ATACGTTCAGAAGCTCCGAG 57.146 50.000 0.00 0.00 0.00 4.63
15 16 4.707030 TTAATACGTTCAGAAGCTCCGA 57.293 40.909 0.00 0.00 0.00 4.55
17 18 4.444720 CGGATTAATACGTTCAGAAGCTCC 59.555 45.833 12.12 0.00 0.00 4.70
19 20 5.258456 TCGGATTAATACGTTCAGAAGCT 57.742 39.130 19.27 0.00 35.15 3.74
22 23 9.752961 TCATATTTCGGATTAATACGTTCAGAA 57.247 29.630 19.27 3.63 35.15 3.02
23 24 9.188588 GTCATATTTCGGATTAATACGTTCAGA 57.811 33.333 19.27 8.78 35.15 3.27
24 25 8.974408 TGTCATATTTCGGATTAATACGTTCAG 58.026 33.333 19.27 6.78 35.15 3.02
26 27 9.188588 TCTGTCATATTTCGGATTAATACGTTC 57.811 33.333 19.27 4.03 35.15 3.95
27 28 9.706691 ATCTGTCATATTTCGGATTAATACGTT 57.293 29.630 19.27 8.68 35.15 3.99
28 29 9.706691 AATCTGTCATATTTCGGATTAATACGT 57.293 29.630 19.27 3.51 37.73 3.57
44 45 9.904198 TCTGTCCAAATCATTAAATCTGTCATA 57.096 29.630 0.00 0.00 0.00 2.15
45 46 8.812513 TCTGTCCAAATCATTAAATCTGTCAT 57.187 30.769 0.00 0.00 0.00 3.06
46 47 8.634335 TTCTGTCCAAATCATTAAATCTGTCA 57.366 30.769 0.00 0.00 0.00 3.58
56 57 9.082313 ACAACTTAGATTTCTGTCCAAATCATT 57.918 29.630 8.28 0.00 42.86 2.57
57 58 8.641498 ACAACTTAGATTTCTGTCCAAATCAT 57.359 30.769 8.28 0.00 42.86 2.45
58 59 8.463930 AACAACTTAGATTTCTGTCCAAATCA 57.536 30.769 8.28 0.00 42.86 2.57
114 115 9.371136 GTTCAATAAGTTGTCACATCTCATCTA 57.629 33.333 0.00 0.00 36.69 1.98
115 116 7.879677 TGTTCAATAAGTTGTCACATCTCATCT 59.120 33.333 0.00 0.00 36.69 2.90
116 117 8.032952 TGTTCAATAAGTTGTCACATCTCATC 57.967 34.615 0.00 0.00 36.69 2.92
117 118 7.984422 TGTTCAATAAGTTGTCACATCTCAT 57.016 32.000 0.00 0.00 36.69 2.90
118 119 7.281999 TGTTGTTCAATAAGTTGTCACATCTCA 59.718 33.333 0.00 0.00 36.69 3.27
119 120 7.587757 GTGTTGTTCAATAAGTTGTCACATCTC 59.412 37.037 0.00 0.00 36.69 2.75
120 121 7.066887 TGTGTTGTTCAATAAGTTGTCACATCT 59.933 33.333 0.00 0.00 36.69 2.90
121 122 7.165812 GTGTGTTGTTCAATAAGTTGTCACATC 59.834 37.037 0.00 0.00 36.69 3.06
122 123 6.972328 GTGTGTTGTTCAATAAGTTGTCACAT 59.028 34.615 0.00 0.00 36.69 3.21
123 124 6.072452 TGTGTGTTGTTCAATAAGTTGTCACA 60.072 34.615 0.00 0.00 36.69 3.58
124 125 6.318628 TGTGTGTTGTTCAATAAGTTGTCAC 58.681 36.000 0.00 0.00 36.69 3.67
125 126 6.502136 TGTGTGTTGTTCAATAAGTTGTCA 57.498 33.333 0.00 0.00 36.69 3.58
126 127 7.097047 CGATTGTGTGTTGTTCAATAAGTTGTC 60.097 37.037 0.00 0.00 36.69 3.18
127 128 6.690957 CGATTGTGTGTTGTTCAATAAGTTGT 59.309 34.615 0.00 0.00 36.69 3.32
128 129 6.690957 ACGATTGTGTGTTGTTCAATAAGTTG 59.309 34.615 0.00 0.00 36.65 3.16
129 130 6.791303 ACGATTGTGTGTTGTTCAATAAGTT 58.209 32.000 0.00 0.00 32.90 2.66
130 131 6.037720 TGACGATTGTGTGTTGTTCAATAAGT 59.962 34.615 0.00 0.00 32.90 2.24
132 133 6.364945 TGACGATTGTGTGTTGTTCAATAA 57.635 33.333 0.00 0.00 32.90 1.40
133 134 5.993106 TGACGATTGTGTGTTGTTCAATA 57.007 34.783 0.00 0.00 32.90 1.90
134 135 4.891627 TGACGATTGTGTGTTGTTCAAT 57.108 36.364 0.00 0.00 35.00 2.57
135 136 4.686839 TTGACGATTGTGTGTTGTTCAA 57.313 36.364 0.00 0.00 0.00 2.69
136 137 4.407818 GTTTGACGATTGTGTGTTGTTCA 58.592 39.130 0.00 0.00 0.00 3.18
138 139 3.729462 CGGTTTGACGATTGTGTGTTGTT 60.729 43.478 0.00 0.00 35.47 2.83
139 140 2.223157 CGGTTTGACGATTGTGTGTTGT 60.223 45.455 0.00 0.00 35.47 3.32
140 141 2.031068 TCGGTTTGACGATTGTGTGTTG 59.969 45.455 0.00 0.00 38.06 3.33
141 142 2.281517 TCGGTTTGACGATTGTGTGTT 58.718 42.857 0.00 0.00 38.06 3.32
142 143 1.942677 TCGGTTTGACGATTGTGTGT 58.057 45.000 0.00 0.00 38.06 3.72
151 152 4.552767 GCTAAATGATGGATCGGTTTGACG 60.553 45.833 0.00 0.00 0.00 4.35
152 153 4.576463 AGCTAAATGATGGATCGGTTTGAC 59.424 41.667 0.00 0.00 0.00 3.18
154 155 5.505173 AAGCTAAATGATGGATCGGTTTG 57.495 39.130 0.00 0.00 0.00 2.93
155 156 6.530019 AAAAGCTAAATGATGGATCGGTTT 57.470 33.333 0.00 0.00 0.00 3.27
156 157 6.039382 GGTAAAAGCTAAATGATGGATCGGTT 59.961 38.462 0.00 0.00 0.00 4.44
157 158 5.531287 GGTAAAAGCTAAATGATGGATCGGT 59.469 40.000 0.00 0.00 0.00 4.69
158 159 5.765182 AGGTAAAAGCTAAATGATGGATCGG 59.235 40.000 0.00 0.00 0.00 4.18
159 160 6.867662 AGGTAAAAGCTAAATGATGGATCG 57.132 37.500 0.00 0.00 0.00 3.69
160 161 8.907885 AGAAAGGTAAAAGCTAAATGATGGATC 58.092 33.333 0.00 0.00 0.00 3.36
162 163 7.339466 GGAGAAAGGTAAAAGCTAAATGATGGA 59.661 37.037 0.00 0.00 0.00 3.41
164 165 7.340487 AGGGAGAAAGGTAAAAGCTAAATGATG 59.660 37.037 0.00 0.00 0.00 3.07
165 166 7.414266 AGGGAGAAAGGTAAAAGCTAAATGAT 58.586 34.615 0.00 0.00 0.00 2.45
166 167 6.790319 AGGGAGAAAGGTAAAAGCTAAATGA 58.210 36.000 0.00 0.00 0.00 2.57
167 168 6.659242 TGAGGGAGAAAGGTAAAAGCTAAATG 59.341 38.462 0.00 0.00 0.00 2.32
168 169 6.790319 TGAGGGAGAAAGGTAAAAGCTAAAT 58.210 36.000 0.00 0.00 0.00 1.40
169 170 6.195600 TGAGGGAGAAAGGTAAAAGCTAAA 57.804 37.500 0.00 0.00 0.00 1.85
170 171 5.836024 TGAGGGAGAAAGGTAAAAGCTAA 57.164 39.130 0.00 0.00 0.00 3.09
171 172 6.388619 AATGAGGGAGAAAGGTAAAAGCTA 57.611 37.500 0.00 0.00 0.00 3.32
172 173 4.936685 ATGAGGGAGAAAGGTAAAAGCT 57.063 40.909 0.00 0.00 0.00 3.74
173 174 5.984695 AAATGAGGGAGAAAGGTAAAAGC 57.015 39.130 0.00 0.00 0.00 3.51
174 175 8.687242 GGATAAAATGAGGGAGAAAGGTAAAAG 58.313 37.037 0.00 0.00 0.00 2.27
175 176 8.398743 AGGATAAAATGAGGGAGAAAGGTAAAA 58.601 33.333 0.00 0.00 0.00 1.52
176 177 7.939781 AGGATAAAATGAGGGAGAAAGGTAAA 58.060 34.615 0.00 0.00 0.00 2.01
177 178 7.525158 AGGATAAAATGAGGGAGAAAGGTAA 57.475 36.000 0.00 0.00 0.00 2.85
178 179 7.366551 GGAAGGATAAAATGAGGGAGAAAGGTA 60.367 40.741 0.00 0.00 0.00 3.08
180 181 5.830457 GGAAGGATAAAATGAGGGAGAAAGG 59.170 44.000 0.00 0.00 0.00 3.11
181 182 6.667661 AGGAAGGATAAAATGAGGGAGAAAG 58.332 40.000 0.00 0.00 0.00 2.62
182 183 6.632672 CGAGGAAGGATAAAATGAGGGAGAAA 60.633 42.308 0.00 0.00 0.00 2.52
184 185 4.345257 CGAGGAAGGATAAAATGAGGGAGA 59.655 45.833 0.00 0.00 0.00 3.71
185 186 4.101741 ACGAGGAAGGATAAAATGAGGGAG 59.898 45.833 0.00 0.00 0.00 4.30
186 187 4.037927 ACGAGGAAGGATAAAATGAGGGA 58.962 43.478 0.00 0.00 0.00 4.20
187 188 4.423625 ACGAGGAAGGATAAAATGAGGG 57.576 45.455 0.00 0.00 0.00 4.30
190 191 5.810587 CGAAGAACGAGGAAGGATAAAATGA 59.189 40.000 0.00 0.00 45.77 2.57
191 192 5.581085 ACGAAGAACGAGGAAGGATAAAATG 59.419 40.000 0.00 0.00 45.77 2.32
192 193 5.731591 ACGAAGAACGAGGAAGGATAAAAT 58.268 37.500 0.00 0.00 45.77 1.82
193 194 5.143376 ACGAAGAACGAGGAAGGATAAAA 57.857 39.130 0.00 0.00 45.77 1.52
194 195 4.796038 ACGAAGAACGAGGAAGGATAAA 57.204 40.909 0.00 0.00 45.77 1.40
196 197 3.508793 ACAACGAAGAACGAGGAAGGATA 59.491 43.478 0.00 0.00 45.77 2.59
197 198 2.299297 ACAACGAAGAACGAGGAAGGAT 59.701 45.455 0.00 0.00 45.77 3.24
201 202 4.492895 CGAAAAACAACGAAGAACGAGGAA 60.493 41.667 0.00 0.00 45.77 3.36
202 203 3.000523 CGAAAAACAACGAAGAACGAGGA 59.999 43.478 0.00 0.00 45.77 3.71
204 205 3.712572 CACGAAAAACAACGAAGAACGAG 59.287 43.478 0.00 0.00 45.77 4.18
207 208 5.340138 TCAAACACGAAAAACAACGAAGAAC 59.660 36.000 0.00 0.00 0.00 3.01
211 212 5.284188 GTCATCAAACACGAAAAACAACGAA 59.716 36.000 0.00 0.00 0.00 3.85
212 213 4.789119 GTCATCAAACACGAAAAACAACGA 59.211 37.500 0.00 0.00 0.00 3.85
215 216 4.560819 GCTGTCATCAAACACGAAAAACAA 59.439 37.500 0.00 0.00 0.00 2.83
216 217 4.101942 GCTGTCATCAAACACGAAAAACA 58.898 39.130 0.00 0.00 0.00 2.83
217 218 3.177643 CGCTGTCATCAAACACGAAAAAC 59.822 43.478 0.00 0.00 0.00 2.43
218 219 3.064134 TCGCTGTCATCAAACACGAAAAA 59.936 39.130 0.00 0.00 33.22 1.94
219 220 2.609916 TCGCTGTCATCAAACACGAAAA 59.390 40.909 0.00 0.00 33.22 2.29
222 223 1.525197 GTTCGCTGTCATCAAACACGA 59.475 47.619 0.00 0.00 33.82 4.35
223 224 1.398451 GGTTCGCTGTCATCAAACACG 60.398 52.381 0.00 0.00 0.00 4.49
224 225 1.873591 AGGTTCGCTGTCATCAAACAC 59.126 47.619 0.00 0.00 0.00 3.32
225 226 2.143122 GAGGTTCGCTGTCATCAAACA 58.857 47.619 0.00 0.00 0.00 2.83
226 227 2.143122 TGAGGTTCGCTGTCATCAAAC 58.857 47.619 0.00 0.00 0.00 2.93
227 228 2.542020 TGAGGTTCGCTGTCATCAAA 57.458 45.000 0.00 0.00 0.00 2.69
228 229 2.416747 CTTGAGGTTCGCTGTCATCAA 58.583 47.619 0.00 0.00 34.19 2.57
229 230 1.338105 CCTTGAGGTTCGCTGTCATCA 60.338 52.381 0.00 0.00 0.00 3.07
230 231 1.363744 CCTTGAGGTTCGCTGTCATC 58.636 55.000 0.00 0.00 0.00 2.92
233 234 2.035442 GGCCTTGAGGTTCGCTGTC 61.035 63.158 0.00 0.00 37.57 3.51
234 235 2.032681 GGCCTTGAGGTTCGCTGT 59.967 61.111 0.00 0.00 37.57 4.40
235 236 0.107703 TATGGCCTTGAGGTTCGCTG 60.108 55.000 3.32 0.00 37.57 5.18
236 237 0.179000 CTATGGCCTTGAGGTTCGCT 59.821 55.000 3.32 0.00 37.57 4.93
239 240 3.808984 CCCTATGGCCTTGAGGTTC 57.191 57.895 3.32 0.00 37.57 3.62
250 251 1.071471 CTGCCTTACCGCCCTATGG 59.929 63.158 0.00 0.00 0.00 2.74
251 252 0.249911 GTCTGCCTTACCGCCCTATG 60.250 60.000 0.00 0.00 0.00 2.23
252 253 1.408453 GGTCTGCCTTACCGCCCTAT 61.408 60.000 0.00 0.00 0.00 2.57
253 254 2.062177 GGTCTGCCTTACCGCCCTA 61.062 63.158 0.00 0.00 0.00 3.53
255 256 2.029307 CTAGGTCTGCCTTACCGCCC 62.029 65.000 0.00 0.00 44.18 6.13
257 258 1.442148 CCTAGGTCTGCCTTACCGC 59.558 63.158 0.00 0.00 44.18 5.68
258 259 2.029307 GCCCTAGGTCTGCCTTACCG 62.029 65.000 8.29 0.00 44.18 4.02
259 260 0.981277 TGCCCTAGGTCTGCCTTACC 60.981 60.000 8.29 0.00 44.18 2.85
260 261 0.466124 CTGCCCTAGGTCTGCCTTAC 59.534 60.000 8.29 0.00 44.18 2.34
262 263 1.229658 ACTGCCCTAGGTCTGCCTT 60.230 57.895 8.29 0.00 44.18 4.35
264 265 2.736826 GGACTGCCCTAGGTCTGCC 61.737 68.421 8.29 1.45 33.46 4.85
265 266 1.341156 ATGGACTGCCCTAGGTCTGC 61.341 60.000 8.29 4.69 35.38 4.26
266 267 1.967066 CTATGGACTGCCCTAGGTCTG 59.033 57.143 8.29 0.83 35.38 3.51
267 268 1.759562 GCTATGGACTGCCCTAGGTCT 60.760 57.143 8.29 0.00 34.15 3.85
268 269 0.682292 GCTATGGACTGCCCTAGGTC 59.318 60.000 8.29 0.00 34.15 3.85
269 270 0.764752 GGCTATGGACTGCCCTAGGT 60.765 60.000 8.29 0.00 43.11 3.08
270 271 2.062070 GGCTATGGACTGCCCTAGG 58.938 63.158 0.06 0.06 43.11 3.02
276 277 1.815421 CACGGTGGCTATGGACTGC 60.815 63.158 0.00 0.00 0.00 4.40
277 278 1.815421 GCACGGTGGCTATGGACTG 60.815 63.158 10.60 0.00 0.00 3.51
278 279 2.584608 GCACGGTGGCTATGGACT 59.415 61.111 10.60 0.00 0.00 3.85
279 280 2.890474 CGCACGGTGGCTATGGAC 60.890 66.667 10.60 0.00 0.00 4.02
296 297 1.340697 ACCTAAGAATTTGCCCGGGAC 60.341 52.381 29.31 16.95 0.00 4.46
297 298 0.996583 ACCTAAGAATTTGCCCGGGA 59.003 50.000 29.31 2.74 0.00 5.14
298 299 1.749063 GAACCTAAGAATTTGCCCGGG 59.251 52.381 19.09 19.09 0.00 5.73
299 300 2.683362 GAGAACCTAAGAATTTGCCCGG 59.317 50.000 0.00 0.00 0.00 5.73
300 301 2.351726 CGAGAACCTAAGAATTTGCCCG 59.648 50.000 0.00 0.00 0.00 6.13
301 302 3.606687 TCGAGAACCTAAGAATTTGCCC 58.393 45.455 0.00 0.00 0.00 5.36
302 303 6.931840 AGATATCGAGAACCTAAGAATTTGCC 59.068 38.462 0.00 0.00 0.00 4.52
358 371 4.509616 TGGTATGTATGCACACCTTACAC 58.490 43.478 12.70 0.00 42.49 2.90
383 400 2.045926 CCCCGCTGGAACTGGAAG 60.046 66.667 0.00 0.00 36.41 3.46
404 421 6.266786 ACGGTTCCAGAAAACATCCTTTAAAT 59.733 34.615 0.00 0.00 0.00 1.40
408 425 3.317993 CACGGTTCCAGAAAACATCCTTT 59.682 43.478 0.00 0.00 0.00 3.11
431 448 3.650139 ACGAGTTAGCAGACGATTTTGT 58.350 40.909 0.00 0.00 0.00 2.83
495 513 4.797471 TGTAGAAACACAAAGATGCATGC 58.203 39.130 11.82 11.82 0.00 4.06
520 538 1.062880 TCACAAACCGTTGAAACTCGC 59.937 47.619 0.00 0.00 38.20 5.03
521 539 3.602390 ATCACAAACCGTTGAAACTCG 57.398 42.857 0.00 0.00 38.20 4.18
522 540 5.997385 ACATATCACAAACCGTTGAAACTC 58.003 37.500 0.00 0.00 38.20 3.01
523 541 5.048991 GGACATATCACAAACCGTTGAAACT 60.049 40.000 0.00 0.00 38.20 2.66
540 565 4.396357 TTCAAAGGGTGTTGGGACATAT 57.604 40.909 0.00 0.00 39.30 1.78
541 566 3.885976 TTCAAAGGGTGTTGGGACATA 57.114 42.857 0.00 0.00 39.30 2.29
542 567 2.765689 TTCAAAGGGTGTTGGGACAT 57.234 45.000 0.00 0.00 39.30 3.06
543 568 2.765689 ATTCAAAGGGTGTTGGGACA 57.234 45.000 0.00 0.00 0.00 4.02
544 569 2.962421 TGAATTCAAAGGGTGTTGGGAC 59.038 45.455 5.45 0.00 0.00 4.46
545 570 3.230134 CTGAATTCAAAGGGTGTTGGGA 58.770 45.455 9.88 0.00 0.00 4.37
560 585 5.551760 AGAATCAAATCGTTCGCTGAATT 57.448 34.783 0.00 0.00 0.00 2.17
576 602 0.249120 ATTGTCCACGCCGAGAATCA 59.751 50.000 0.00 0.00 33.17 2.57
680 716 1.549203 AAAGCGCAGGGAATTGACAT 58.451 45.000 11.47 0.00 0.00 3.06
705 741 1.139095 GGGCAGGACGTACGAAGAG 59.861 63.158 24.41 10.02 0.00 2.85
706 742 1.303888 AGGGCAGGACGTACGAAGA 60.304 57.895 24.41 0.00 0.00 2.87
707 743 1.153823 CAGGGCAGGACGTACGAAG 60.154 63.158 24.41 9.29 0.00 3.79
708 744 1.604308 TCAGGGCAGGACGTACGAA 60.604 57.895 24.41 0.00 0.00 3.85
710 746 2.181021 GTCAGGGCAGGACGTACG 59.819 66.667 15.01 15.01 0.00 3.67
711 747 2.577593 GGTCAGGGCAGGACGTAC 59.422 66.667 0.00 0.00 36.12 3.67
846 885 6.513180 TCTGCTTATATAGACTTCGGTTTGG 58.487 40.000 0.00 0.00 0.00 3.28
869 908 5.474578 TGGATGATCCAGTAGTAAGCATC 57.525 43.478 10.75 0.00 42.67 3.91
882 922 2.555757 GCTAGGTTGCAATGGATGATCC 59.444 50.000 4.05 4.05 36.96 3.36
892 932 3.206150 GCTATTGCTAGCTAGGTTGCAA 58.794 45.455 34.21 34.21 45.78 4.08
933 973 2.811542 AAAGCCGGCAAGGAGAGAGC 62.812 60.000 31.54 0.00 45.00 4.09
935 975 0.110486 AAAAAGCCGGCAAGGAGAGA 59.890 50.000 31.54 0.00 45.00 3.10
937 977 0.110486 AGAAAAAGCCGGCAAGGAGA 59.890 50.000 31.54 0.00 45.00 3.71
938 978 0.242017 CAGAAAAAGCCGGCAAGGAG 59.758 55.000 31.54 8.12 45.00 3.69
939 979 1.805428 GCAGAAAAAGCCGGCAAGGA 61.805 55.000 31.54 0.00 45.00 3.36
940 980 1.373371 GCAGAAAAAGCCGGCAAGG 60.373 57.895 31.54 11.43 44.97 3.61
946 5711 1.370414 CACGGTGCAGAAAAAGCCG 60.370 57.895 8.00 8.00 46.83 5.52
947 5712 1.661509 GCACGGTGCAGAAAAAGCC 60.662 57.895 27.10 0.00 44.26 4.35
994 5767 2.374830 CTGGAGGACGCCATGCCTAG 62.375 65.000 0.00 0.00 37.30 3.02
1013 5786 3.479269 CGCAAGAAGGGACGACGC 61.479 66.667 0.00 0.00 43.02 5.19
1014 5787 1.663702 AACGCAAGAAGGGACGACG 60.664 57.895 0.00 0.00 43.62 5.12
1015 5788 1.860078 CAACGCAAGAAGGGACGAC 59.140 57.895 0.00 0.00 43.62 4.34
1029 5802 4.318021 AGCAGCGCAAGTGCAACG 62.318 61.111 20.47 0.00 45.86 4.10
1270 6061 9.726438 GAGTATTAGCAAATGGAACCATATAGT 57.274 33.333 6.77 3.55 35.31 2.12
1271 6062 9.950496 AGAGTATTAGCAAATGGAACCATATAG 57.050 33.333 6.77 1.99 35.31 1.31
1293 6093 2.365617 CCCTGTCACGCCATATAAGAGT 59.634 50.000 0.00 0.00 0.00 3.24
1296 6097 3.244215 ACATCCCTGTCACGCCATATAAG 60.244 47.826 0.00 0.00 0.00 1.73
1339 6156 2.941583 GGGGAGAAGGGGGTTGCT 60.942 66.667 0.00 0.00 0.00 3.91
1555 6372 4.083862 GTGGACTCTGGGTCGGCC 62.084 72.222 0.00 0.00 45.35 6.13
1564 6381 1.492993 GGCCCTTCTTGGTGGACTCT 61.493 60.000 0.00 0.00 0.00 3.24
1654 6471 3.592814 CCGGAGAGCGCGGTCATA 61.593 66.667 36.38 0.00 0.00 2.15
1675 6492 4.388499 GCCATCCCGACGGTGTGT 62.388 66.667 13.94 0.00 0.00 3.72
1805 6622 0.596600 GGAGTCTGCACGTCAAACGA 60.597 55.000 6.48 0.00 46.05 3.85
1913 7091 1.597854 CCACGAGCTTGTCCTGCAA 60.598 57.895 2.72 0.00 35.50 4.08
1924 7102 0.173481 TGCTGTACATCTCCACGAGC 59.827 55.000 0.00 0.00 0.00 5.03
2014 7192 2.610859 ACCTCCACGGGCATTCCT 60.611 61.111 0.00 0.00 36.97 3.36
2048 7226 4.160252 ACCAATCAATCAATAGTTGGGCAC 59.840 41.667 7.29 0.00 42.73 5.01
2051 7229 6.528537 TCAACCAATCAATCAATAGTTGGG 57.471 37.500 7.29 0.00 42.73 4.12
2070 7259 1.131126 CATGACGCACTTGGGATCAAC 59.869 52.381 0.00 0.00 0.00 3.18
2124 7333 5.424121 AGAACTGTTACAACTTGCACATC 57.576 39.130 0.00 0.00 0.00 3.06
2129 7338 3.308866 ACACGAGAACTGTTACAACTTGC 59.691 43.478 0.00 0.00 0.00 4.01
2133 7342 5.459110 TTGAACACGAGAACTGTTACAAC 57.541 39.130 0.00 0.00 31.83 3.32
2171 7392 5.965922 ACATTCTGTTGAGACGACATGATA 58.034 37.500 0.00 0.00 0.00 2.15
2172 7393 4.825422 ACATTCTGTTGAGACGACATGAT 58.175 39.130 0.00 0.00 0.00 2.45
2173 7394 4.257267 ACATTCTGTTGAGACGACATGA 57.743 40.909 0.00 0.00 0.00 3.07
2174 7395 4.997905 AACATTCTGTTGAGACGACATG 57.002 40.909 0.00 0.00 39.45 3.21
2218 7441 6.932400 TCGAGAAACACCATTTATTACACACT 59.068 34.615 0.00 0.00 0.00 3.55
2332 7609 2.828877 TCGACATAATAGCCGTTTGGG 58.171 47.619 0.00 0.00 39.58 4.12
2358 7635 6.183361 ACGGTCCATTAGATTCCATGTTATCA 60.183 38.462 6.96 0.00 0.00 2.15
2359 7636 6.231211 ACGGTCCATTAGATTCCATGTTATC 58.769 40.000 0.00 0.00 0.00 1.75
2378 7659 3.729004 CGTTGCTTGAAGAACGGTC 57.271 52.632 16.55 0.00 40.96 4.79
2452 7739 6.600427 TGTCATATGCAATCATCTGAAGTGTT 59.400 34.615 0.00 0.00 37.49 3.32
2453 7740 6.037940 GTGTCATATGCAATCATCTGAAGTGT 59.962 38.462 0.00 0.00 37.49 3.55
2454 7741 6.260271 AGTGTCATATGCAATCATCTGAAGTG 59.740 38.462 0.00 0.00 37.49 3.16
2455 7742 6.354938 AGTGTCATATGCAATCATCTGAAGT 58.645 36.000 0.00 0.00 37.49 3.01
2456 7743 6.073167 GGAGTGTCATATGCAATCATCTGAAG 60.073 42.308 20.85 0.00 37.49 3.02
2457 7744 5.761726 GGAGTGTCATATGCAATCATCTGAA 59.238 40.000 20.85 0.00 37.49 3.02
2475 7764 2.833943 TGTGTCATATCTGCAGGAGTGT 59.166 45.455 15.13 0.00 0.00 3.55
2507 7796 8.800370 TGTGCACTTTATGGTTATATCTTTCA 57.200 30.769 19.41 0.00 0.00 2.69
2550 7847 1.340017 GCTCCATGAACCCTAACTGCA 60.340 52.381 0.00 0.00 0.00 4.41
2551 7848 1.065126 AGCTCCATGAACCCTAACTGC 60.065 52.381 0.00 0.00 0.00 4.40
2552 7849 2.237143 TGAGCTCCATGAACCCTAACTG 59.763 50.000 12.15 0.00 0.00 3.16
2553 7850 2.503356 CTGAGCTCCATGAACCCTAACT 59.497 50.000 12.15 0.00 0.00 2.24
2614 8164 6.663523 CACCCTCTTACTTCACCCATTAATTT 59.336 38.462 0.00 0.00 0.00 1.82
2699 8249 1.401552 CGATGAATTGCCCGTGTCATT 59.598 47.619 0.00 0.00 30.94 2.57
2764 8316 3.613737 AGCAATGCGAAATCCAAAAATCG 59.386 39.130 0.00 0.00 38.28 3.34
2770 8322 4.217334 TCAAAGTAGCAATGCGAAATCCAA 59.783 37.500 0.00 0.00 0.00 3.53
2793 8346 3.755378 GTCATTGTGAGATTCAGGCAAGT 59.245 43.478 0.00 0.00 0.00 3.16
2829 8382 8.713971 AGTACCACATGTTTCCAATGAGATATA 58.286 33.333 0.00 0.00 0.00 0.86
2839 8392 3.904965 TGGAGTAGTACCACATGTTTCCA 59.095 43.478 0.00 0.00 32.03 3.53
2842 8404 4.164981 TCCTGGAGTAGTACCACATGTTT 58.835 43.478 0.00 0.00 33.57 2.83
2909 8482 5.885352 AGATGGATAGATGTCATCGACTAGG 59.115 44.000 7.18 0.00 41.35 3.02
2914 8490 4.835056 ACCAAGATGGATAGATGTCATCGA 59.165 41.667 7.18 2.50 40.96 3.59
3018 8594 2.496871 TGCACAATTCCAAATGCCCTAG 59.503 45.455 0.00 0.00 37.26 3.02
3034 8610 3.388272 TGCGAACCTACTTTGCACA 57.612 47.368 0.00 0.00 43.36 4.57
3042 8618 2.423577 ACTGGACAATTGCGAACCTAC 58.576 47.619 5.05 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.