Multiple sequence alignment - TraesCS6D01G340000

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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 TraesCS6D01G340000 chr6D 100.000 3038 0 0 1 3038 439602068 439599031 0.000000e+00 5611.0
1 TraesCS6D01G340000 chr6D 83.077 845 112 15 1221 2065 439642329 439641516 0.000000e+00 739.0
2 TraesCS6D01G340000 chr6D 77.511 667 142 8 768 1430 439510828 439510166 7.890000e-106 394.0
3 TraesCS6D01G340000 chr6D 75.959 678 144 16 768 1434 439614355 439613686 6.280000e-87 331.0
4 TraesCS6D01G340000 chr6B 96.307 2735 89 8 313 3038 664305570 664302839 0.000000e+00 4481.0
5 TraesCS6D01G340000 chr6B 81.326 739 130 4 768 1498 664497204 664496466 7.250000e-166 593.0
6 TraesCS6D01G340000 chr6B 90.176 397 38 1 2641 3036 714617941 714618337 1.610000e-142 516.0
7 TraesCS6D01G340000 chr6B 83.908 522 72 8 1547 2065 664496462 664495950 3.520000e-134 488.0
8 TraesCS6D01G340000 chr6B 82.885 520 81 6 1547 2065 664511299 664510787 7.670000e-126 460.0
9 TraesCS6D01G340000 chr6B 75.851 646 137 15 768 1402 664406955 664406318 8.180000e-81 311.0
10 TraesCS6D01G340000 chr6B 87.607 234 26 1 1679 1909 664413938 664413705 4.990000e-68 268.0
11 TraesCS6D01G340000 chr6B 95.238 63 3 0 921 983 664415833 664415771 1.930000e-17 100.0
12 TraesCS6D01G340000 chr6A 79.199 1173 212 17 769 1940 587955649 587954508 0.000000e+00 785.0
13 TraesCS6D01G340000 chr6A 78.383 532 113 2 768 1298 587883911 587883381 8.060000e-91 344.0
14 TraesCS6D01G340000 chr7A 90.977 399 34 2 2640 3036 39150199 39149801 1.240000e-148 536.0
15 TraesCS6D01G340000 chr2A 90.909 396 31 3 2642 3036 648336430 648336039 7.460000e-146 527.0
16 TraesCS6D01G340000 chr2A 78.974 390 69 10 2642 3028 114820510 114820889 1.400000e-63 254.0
17 TraesCS6D01G340000 chr1B 89.578 403 39 3 2636 3036 285325801 285326202 2.700000e-140 508.0
18 TraesCS6D01G340000 chr4D 90.981 377 33 1 2661 3036 202679289 202678913 9.720000e-140 507.0
19 TraesCS6D01G340000 chr4B 86.813 273 28 6 2766 3032 435433310 435433040 6.370000e-77 298.0
20 TraesCS6D01G340000 chr4A 78.061 392 74 11 2642 3028 1734004 1733620 1.410000e-58 237.0
21 TraesCS6D01G340000 chr3B 92.308 39 3 0 1010 1048 62708758 62708796 4.230000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G340000 chr6D 439599031 439602068 3037 True 5611.0 5611 100.000 1 3038 1 chr6D.!!$R2 3037
1 TraesCS6D01G340000 chr6D 439641516 439642329 813 True 739.0 739 83.077 1221 2065 1 chr6D.!!$R4 844
2 TraesCS6D01G340000 chr6D 439510166 439510828 662 True 394.0 394 77.511 768 1430 1 chr6D.!!$R1 662
3 TraesCS6D01G340000 chr6D 439613686 439614355 669 True 331.0 331 75.959 768 1434 1 chr6D.!!$R3 666
4 TraesCS6D01G340000 chr6B 664302839 664305570 2731 True 4481.0 4481 96.307 313 3038 1 chr6B.!!$R1 2725
5 TraesCS6D01G340000 chr6B 664495950 664497204 1254 True 540.5 593 82.617 768 2065 2 chr6B.!!$R5 1297
6 TraesCS6D01G340000 chr6B 664510787 664511299 512 True 460.0 460 82.885 1547 2065 1 chr6B.!!$R3 518
7 TraesCS6D01G340000 chr6B 664406318 664406955 637 True 311.0 311 75.851 768 1402 1 chr6B.!!$R2 634
8 TraesCS6D01G340000 chr6A 587954508 587955649 1141 True 785.0 785 79.199 769 1940 1 chr6A.!!$R2 1171
9 TraesCS6D01G340000 chr6A 587883381 587883911 530 True 344.0 344 78.383 768 1298 1 chr6A.!!$R1 530

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
301 302 0.318614 CGCGGGATTGTTGTGCTTTT 60.319 50.000 0.0 0.0 0.0 2.27 F
1110 1131 1.215382 CCACTTCCTCGATGTCGCA 59.785 57.895 0.0 0.0 39.6 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1591 1615 1.137872 AGAGGAGCGGTCATTGTCATC 59.862 52.381 17.59 0.0 0.00 2.92 R
2896 2920 0.327480 TATGGCCTCCCTCACCATGT 60.327 55.000 3.32 0.0 43.93 3.21 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
18 19 2.917172 CTGCCAAAATGGTGTTGCC 58.083 52.632 0.00 0.00 40.46 4.52
19 20 0.603439 CTGCCAAAATGGTGTTGCCC 60.603 55.000 0.00 0.00 40.46 5.36
20 21 1.053264 TGCCAAAATGGTGTTGCCCT 61.053 50.000 0.00 0.00 40.46 5.19
21 22 0.603439 GCCAAAATGGTGTTGCCCTG 60.603 55.000 0.00 0.00 40.46 4.45
22 23 0.603439 CCAAAATGGTGTTGCCCTGC 60.603 55.000 0.00 0.00 36.04 4.85
23 24 0.603439 CAAAATGGTGTTGCCCTGCC 60.603 55.000 0.00 0.00 36.04 4.85
24 25 2.098426 AAAATGGTGTTGCCCTGCCG 62.098 55.000 0.00 0.00 36.04 5.69
31 32 4.722700 TTGCCCTGCCGGAGCTTC 62.723 66.667 5.05 0.00 40.80 3.86
44 45 4.148645 GCTTCGCCGAAAGCCGTC 62.149 66.667 0.00 0.00 44.75 4.79
45 46 3.838795 CTTCGCCGAAAGCCGTCG 61.839 66.667 0.00 0.00 41.38 5.12
102 103 3.732892 CGCGCCACCCGAAAACAT 61.733 61.111 0.00 0.00 40.02 2.71
103 104 2.178273 GCGCCACCCGAAAACATC 59.822 61.111 0.00 0.00 40.02 3.06
104 105 2.622011 GCGCCACCCGAAAACATCA 61.622 57.895 0.00 0.00 40.02 3.07
105 106 1.209127 CGCCACCCGAAAACATCAC 59.791 57.895 0.00 0.00 40.02 3.06
106 107 1.511318 CGCCACCCGAAAACATCACA 61.511 55.000 0.00 0.00 40.02 3.58
107 108 0.887933 GCCACCCGAAAACATCACAT 59.112 50.000 0.00 0.00 0.00 3.21
108 109 1.272212 GCCACCCGAAAACATCACATT 59.728 47.619 0.00 0.00 0.00 2.71
109 110 2.490115 GCCACCCGAAAACATCACATTA 59.510 45.455 0.00 0.00 0.00 1.90
110 111 3.130340 GCCACCCGAAAACATCACATTAT 59.870 43.478 0.00 0.00 0.00 1.28
111 112 4.336993 GCCACCCGAAAACATCACATTATA 59.663 41.667 0.00 0.00 0.00 0.98
112 113 5.163602 GCCACCCGAAAACATCACATTATAA 60.164 40.000 0.00 0.00 0.00 0.98
113 114 6.626181 GCCACCCGAAAACATCACATTATAAA 60.626 38.462 0.00 0.00 0.00 1.40
114 115 7.316640 CCACCCGAAAACATCACATTATAAAA 58.683 34.615 0.00 0.00 0.00 1.52
115 116 7.815068 CCACCCGAAAACATCACATTATAAAAA 59.185 33.333 0.00 0.00 0.00 1.94
144 145 9.959749 AAAACACTTTTCTTTTCTATAATGCGA 57.040 25.926 0.00 0.00 0.00 5.10
155 156 9.398170 CTTTTCTATAATGCGATATTTTGGTGG 57.602 33.333 0.00 0.00 0.00 4.61
156 157 7.447374 TTCTATAATGCGATATTTTGGTGGG 57.553 36.000 0.00 0.00 0.00 4.61
157 158 6.539173 TCTATAATGCGATATTTTGGTGGGT 58.461 36.000 0.00 0.00 0.00 4.51
158 159 7.001674 TCTATAATGCGATATTTTGGTGGGTT 58.998 34.615 0.00 0.00 0.00 4.11
159 160 4.817318 AATGCGATATTTTGGTGGGTTT 57.183 36.364 0.00 0.00 0.00 3.27
160 161 4.817318 ATGCGATATTTTGGTGGGTTTT 57.183 36.364 0.00 0.00 0.00 2.43
161 162 4.608948 TGCGATATTTTGGTGGGTTTTT 57.391 36.364 0.00 0.00 0.00 1.94
180 181 5.860941 TTTTTGGGTGTGTGATTACATGT 57.139 34.783 2.69 2.69 39.39 3.21
181 182 5.860941 TTTTGGGTGTGTGATTACATGTT 57.139 34.783 2.30 0.00 39.39 2.71
182 183 5.860941 TTTGGGTGTGTGATTACATGTTT 57.139 34.783 2.30 0.00 39.39 2.83
183 184 5.446143 TTGGGTGTGTGATTACATGTTTC 57.554 39.130 2.30 2.36 39.39 2.78
184 185 3.823873 TGGGTGTGTGATTACATGTTTCC 59.176 43.478 2.30 0.00 39.39 3.13
185 186 4.079253 GGGTGTGTGATTACATGTTTCCT 58.921 43.478 2.30 0.00 39.39 3.36
186 187 4.082787 GGGTGTGTGATTACATGTTTCCTG 60.083 45.833 2.30 0.00 39.39 3.86
187 188 4.518970 GGTGTGTGATTACATGTTTCCTGT 59.481 41.667 2.30 0.00 39.39 4.00
188 189 5.009610 GGTGTGTGATTACATGTTTCCTGTT 59.990 40.000 2.30 0.00 39.39 3.16
189 190 6.205853 GGTGTGTGATTACATGTTTCCTGTTA 59.794 38.462 2.30 0.00 39.39 2.41
190 191 7.255312 GGTGTGTGATTACATGTTTCCTGTTAA 60.255 37.037 2.30 0.00 39.39 2.01
191 192 8.296713 GTGTGTGATTACATGTTTCCTGTTAAT 58.703 33.333 2.30 0.00 39.39 1.40
192 193 8.511321 TGTGTGATTACATGTTTCCTGTTAATC 58.489 33.333 2.30 5.23 39.39 1.75
193 194 8.511321 GTGTGATTACATGTTTCCTGTTAATCA 58.489 33.333 2.30 7.96 39.39 2.57
194 195 9.072375 TGTGATTACATGTTTCCTGTTAATCAA 57.928 29.630 14.74 6.36 33.54 2.57
195 196 9.341899 GTGATTACATGTTTCCTGTTAATCAAC 57.658 33.333 14.74 8.30 33.54 3.18
196 197 9.295825 TGATTACATGTTTCCTGTTAATCAACT 57.704 29.630 2.30 0.00 35.56 3.16
197 198 9.774742 GATTACATGTTTCCTGTTAATCAACTC 57.225 33.333 2.30 0.00 35.56 3.01
198 199 6.241207 ACATGTTTCCTGTTAATCAACTCG 57.759 37.500 0.00 0.00 35.56 4.18
199 200 5.763204 ACATGTTTCCTGTTAATCAACTCGT 59.237 36.000 0.00 0.00 35.56 4.18
200 201 6.932400 ACATGTTTCCTGTTAATCAACTCGTA 59.068 34.615 0.00 0.00 35.56 3.43
201 202 7.117812 ACATGTTTCCTGTTAATCAACTCGTAG 59.882 37.037 0.00 0.00 35.56 3.51
202 203 6.518493 TGTTTCCTGTTAATCAACTCGTAGT 58.482 36.000 0.00 0.00 35.56 2.73
203 204 6.987992 TGTTTCCTGTTAATCAACTCGTAGTT 59.012 34.615 0.00 0.00 39.39 2.24
204 205 8.143193 TGTTTCCTGTTAATCAACTCGTAGTTA 58.857 33.333 0.87 0.00 36.03 2.24
205 206 9.148104 GTTTCCTGTTAATCAACTCGTAGTTAT 57.852 33.333 0.87 0.00 36.03 1.89
206 207 8.697846 TTCCTGTTAATCAACTCGTAGTTATG 57.302 34.615 0.87 0.00 36.03 1.90
207 208 7.833786 TCCTGTTAATCAACTCGTAGTTATGT 58.166 34.615 0.87 0.00 36.03 2.29
208 209 7.758076 TCCTGTTAATCAACTCGTAGTTATGTG 59.242 37.037 0.87 0.00 36.03 3.21
209 210 7.010183 CCTGTTAATCAACTCGTAGTTATGTGG 59.990 40.741 0.87 0.00 36.03 4.17
210 211 6.814644 TGTTAATCAACTCGTAGTTATGTGGG 59.185 38.462 0.87 0.00 36.03 4.61
211 212 5.670792 AATCAACTCGTAGTTATGTGGGA 57.329 39.130 0.87 0.00 36.03 4.37
212 213 5.670792 ATCAACTCGTAGTTATGTGGGAA 57.329 39.130 0.87 0.00 36.03 3.97
213 214 5.670792 TCAACTCGTAGTTATGTGGGAAT 57.329 39.130 0.87 0.00 36.03 3.01
214 215 6.045072 TCAACTCGTAGTTATGTGGGAATT 57.955 37.500 0.87 0.00 36.03 2.17
215 216 6.469410 TCAACTCGTAGTTATGTGGGAATTT 58.531 36.000 0.87 0.00 36.03 1.82
216 217 6.370442 TCAACTCGTAGTTATGTGGGAATTTG 59.630 38.462 0.87 0.00 36.03 2.32
217 218 5.183228 ACTCGTAGTTATGTGGGAATTTGG 58.817 41.667 0.00 0.00 0.00 3.28
218 219 5.168647 TCGTAGTTATGTGGGAATTTGGT 57.831 39.130 0.00 0.00 0.00 3.67
219 220 5.180271 TCGTAGTTATGTGGGAATTTGGTC 58.820 41.667 0.00 0.00 0.00 4.02
220 221 4.033587 CGTAGTTATGTGGGAATTTGGTCG 59.966 45.833 0.00 0.00 0.00 4.79
221 222 2.752903 AGTTATGTGGGAATTTGGTCGC 59.247 45.455 0.00 0.00 0.00 5.19
222 223 2.490115 GTTATGTGGGAATTTGGTCGCA 59.510 45.455 0.00 0.00 38.06 5.10
223 224 1.851304 ATGTGGGAATTTGGTCGCAT 58.149 45.000 0.00 0.00 41.82 4.73
224 225 0.887247 TGTGGGAATTTGGTCGCATG 59.113 50.000 0.00 0.00 41.82 4.06
225 226 0.887933 GTGGGAATTTGGTCGCATGT 59.112 50.000 0.00 0.00 41.82 3.21
226 227 2.088423 GTGGGAATTTGGTCGCATGTA 58.912 47.619 0.00 0.00 41.82 2.29
227 228 2.687935 GTGGGAATTTGGTCGCATGTAT 59.312 45.455 0.00 0.00 41.82 2.29
228 229 2.948979 TGGGAATTTGGTCGCATGTATC 59.051 45.455 0.00 0.00 35.72 2.24
229 230 2.948979 GGGAATTTGGTCGCATGTATCA 59.051 45.455 0.00 0.00 0.00 2.15
230 231 3.569701 GGGAATTTGGTCGCATGTATCAT 59.430 43.478 0.00 0.00 0.00 2.45
231 232 4.539870 GGAATTTGGTCGCATGTATCATG 58.460 43.478 5.49 5.49 0.00 3.07
232 233 4.036734 GGAATTTGGTCGCATGTATCATGT 59.963 41.667 10.68 0.00 0.00 3.21
233 234 5.450412 GGAATTTGGTCGCATGTATCATGTT 60.450 40.000 10.68 0.00 0.00 2.71
234 235 4.354071 TTTGGTCGCATGTATCATGTTG 57.646 40.909 10.68 5.14 0.00 3.33
235 236 2.984562 TGGTCGCATGTATCATGTTGT 58.015 42.857 10.68 0.00 0.00 3.32
236 237 3.342719 TGGTCGCATGTATCATGTTGTT 58.657 40.909 10.68 0.00 0.00 2.83
237 238 3.126686 TGGTCGCATGTATCATGTTGTTG 59.873 43.478 10.68 0.00 0.00 3.33
238 239 3.100817 GTCGCATGTATCATGTTGTTGC 58.899 45.455 10.68 0.00 0.00 4.17
239 240 3.009026 TCGCATGTATCATGTTGTTGCT 58.991 40.909 10.68 0.00 0.00 3.91
240 241 4.033932 GTCGCATGTATCATGTTGTTGCTA 59.966 41.667 10.68 0.00 0.00 3.49
241 242 4.033932 TCGCATGTATCATGTTGTTGCTAC 59.966 41.667 10.68 0.00 0.00 3.58
242 243 4.201802 CGCATGTATCATGTTGTTGCTACA 60.202 41.667 10.68 0.00 33.99 2.74
243 244 5.268544 GCATGTATCATGTTGTTGCTACAG 58.731 41.667 10.68 0.00 33.25 2.74
244 245 5.163723 GCATGTATCATGTTGTTGCTACAGT 60.164 40.000 10.68 0.00 33.25 3.55
245 246 5.861222 TGTATCATGTTGTTGCTACAGTG 57.139 39.130 0.37 3.07 35.28 3.66
246 247 5.304778 TGTATCATGTTGTTGCTACAGTGT 58.695 37.500 0.00 0.00 35.28 3.55
247 248 5.762711 TGTATCATGTTGTTGCTACAGTGTT 59.237 36.000 0.00 1.37 35.28 3.32
248 249 6.931840 TGTATCATGTTGTTGCTACAGTGTTA 59.068 34.615 0.00 0.55 35.28 2.41
249 250 5.922739 TCATGTTGTTGCTACAGTGTTAG 57.077 39.130 0.00 0.00 35.28 2.34
250 251 5.606505 TCATGTTGTTGCTACAGTGTTAGA 58.393 37.500 0.00 0.00 35.28 2.10
251 252 6.230472 TCATGTTGTTGCTACAGTGTTAGAT 58.770 36.000 0.00 0.00 35.28 1.98
252 253 5.922739 TGTTGTTGCTACAGTGTTAGATG 57.077 39.130 0.00 0.00 35.28 2.90
253 254 5.364778 TGTTGTTGCTACAGTGTTAGATGT 58.635 37.500 0.00 0.00 35.28 3.06
254 255 5.820423 TGTTGTTGCTACAGTGTTAGATGTT 59.180 36.000 0.00 0.00 35.28 2.71
255 256 5.922739 TGTTGCTACAGTGTTAGATGTTG 57.077 39.130 0.00 0.00 0.00 3.33
256 257 5.606505 TGTTGCTACAGTGTTAGATGTTGA 58.393 37.500 0.00 0.00 0.00 3.18
257 258 6.230472 TGTTGCTACAGTGTTAGATGTTGAT 58.770 36.000 0.00 0.00 0.00 2.57
258 259 6.710295 TGTTGCTACAGTGTTAGATGTTGATT 59.290 34.615 0.00 0.00 0.00 2.57
259 260 7.228507 TGTTGCTACAGTGTTAGATGTTGATTT 59.771 33.333 0.00 0.00 0.00 2.17
260 261 7.744087 TGCTACAGTGTTAGATGTTGATTTT 57.256 32.000 0.00 0.00 0.00 1.82
261 262 8.165239 TGCTACAGTGTTAGATGTTGATTTTT 57.835 30.769 0.00 0.00 0.00 1.94
282 283 3.764237 TTTTAGGTGGTGAGAGGACAC 57.236 47.619 0.00 0.00 39.70 3.67
283 284 1.254026 TTAGGTGGTGAGAGGACACG 58.746 55.000 0.00 0.00 41.12 4.49
284 285 1.248785 TAGGTGGTGAGAGGACACGC 61.249 60.000 0.00 0.00 41.12 5.34
285 286 2.430921 GTGGTGAGAGGACACGCG 60.431 66.667 3.53 3.53 41.12 6.01
286 287 3.680786 TGGTGAGAGGACACGCGG 61.681 66.667 12.47 1.27 41.12 6.46
287 288 4.436998 GGTGAGAGGACACGCGGG 62.437 72.222 6.92 6.92 41.12 6.13
288 289 3.371063 GTGAGAGGACACGCGGGA 61.371 66.667 19.19 0.00 0.00 5.14
289 290 2.362503 TGAGAGGACACGCGGGAT 60.363 61.111 19.19 0.00 0.00 3.85
290 291 1.982395 TGAGAGGACACGCGGGATT 60.982 57.895 19.19 0.00 0.00 3.01
291 292 1.519455 GAGAGGACACGCGGGATTG 60.519 63.158 19.19 3.50 0.00 2.67
292 293 2.227089 GAGAGGACACGCGGGATTGT 62.227 60.000 19.19 7.82 0.00 2.71
293 294 1.375523 GAGGACACGCGGGATTGTT 60.376 57.895 19.19 0.00 0.00 2.83
294 295 1.635663 GAGGACACGCGGGATTGTTG 61.636 60.000 19.19 1.15 0.00 3.33
295 296 1.964373 GGACACGCGGGATTGTTGT 60.964 57.895 19.19 5.44 0.00 3.32
296 297 1.206578 GACACGCGGGATTGTTGTG 59.793 57.895 19.19 0.00 36.64 3.33
297 298 2.126888 CACGCGGGATTGTTGTGC 60.127 61.111 12.47 0.00 0.00 4.57
298 299 2.281484 ACGCGGGATTGTTGTGCT 60.281 55.556 12.47 0.00 0.00 4.40
299 300 1.896660 ACGCGGGATTGTTGTGCTT 60.897 52.632 12.47 0.00 0.00 3.91
300 301 1.285641 CGCGGGATTGTTGTGCTTT 59.714 52.632 0.00 0.00 0.00 3.51
301 302 0.318614 CGCGGGATTGTTGTGCTTTT 60.319 50.000 0.00 0.00 0.00 2.27
302 303 1.864565 GCGGGATTGTTGTGCTTTTT 58.135 45.000 0.00 0.00 0.00 1.94
303 304 2.605823 CGCGGGATTGTTGTGCTTTTTA 60.606 45.455 0.00 0.00 0.00 1.52
304 305 3.584834 GCGGGATTGTTGTGCTTTTTAT 58.415 40.909 0.00 0.00 0.00 1.40
305 306 3.367630 GCGGGATTGTTGTGCTTTTTATG 59.632 43.478 0.00 0.00 0.00 1.90
306 307 4.804108 CGGGATTGTTGTGCTTTTTATGA 58.196 39.130 0.00 0.00 0.00 2.15
307 308 5.410067 CGGGATTGTTGTGCTTTTTATGAT 58.590 37.500 0.00 0.00 0.00 2.45
308 309 5.289193 CGGGATTGTTGTGCTTTTTATGATG 59.711 40.000 0.00 0.00 0.00 3.07
309 310 6.397272 GGGATTGTTGTGCTTTTTATGATGA 58.603 36.000 0.00 0.00 0.00 2.92
310 311 7.043565 GGGATTGTTGTGCTTTTTATGATGAT 58.956 34.615 0.00 0.00 0.00 2.45
311 312 8.196771 GGGATTGTTGTGCTTTTTATGATGATA 58.803 33.333 0.00 0.00 0.00 2.15
330 331 9.223099 TGATGATATTTTACGATGATTGATGCT 57.777 29.630 0.00 0.00 0.00 3.79
478 479 9.636789 AAATAAAAACACCTTAACTACTCCAGT 57.363 29.630 0.00 0.00 40.05 4.00
480 481 9.716531 ATAAAAACACCTTAACTACTCCAGTAC 57.283 33.333 0.00 0.00 36.04 2.73
481 482 6.990908 AAACACCTTAACTACTCCAGTACT 57.009 37.500 0.00 0.00 36.04 2.73
482 483 5.979288 ACACCTTAACTACTCCAGTACTG 57.021 43.478 16.34 16.34 36.04 2.74
576 586 2.102553 GTCGAGCTAGGCACCGAC 59.897 66.667 16.39 16.39 44.15 4.79
599 609 1.300963 CAGGCTTCCAGGCAGCTAA 59.699 57.895 11.24 0.00 44.19 3.09
684 694 4.202172 GCCGCTATATATTTCTCTCTCCCC 60.202 50.000 0.00 0.00 0.00 4.81
703 713 4.043200 GGCCAGCACGGAAGCAAC 62.043 66.667 0.00 0.00 36.56 4.17
706 716 1.234615 GCCAGCACGGAAGCAACTTA 61.235 55.000 0.00 0.00 36.56 2.24
726 736 1.416813 GCAGATCGCACAGACCTTCG 61.417 60.000 4.93 0.00 41.79 3.79
739 749 2.231478 AGACCTTCGTCATTCATCACGT 59.769 45.455 0.00 0.00 41.87 4.49
975 988 4.135153 CTGACGCCCTCGGACAGG 62.135 72.222 0.00 0.00 43.01 4.00
992 1005 2.031163 GGGAATCCATCGCCTCCG 59.969 66.667 0.09 0.00 35.03 4.63
1110 1131 1.215382 CCACTTCCTCGATGTCGCA 59.785 57.895 0.00 0.00 39.60 5.10
1115 1136 1.877576 TTCCTCGATGTCGCAGTGCT 61.878 55.000 14.33 0.00 39.60 4.40
1528 1552 4.829968 CAGTGAGGATGAAGATGACAACT 58.170 43.478 0.00 0.00 0.00 3.16
1591 1615 2.604914 GGTGATGCTAGTGACATTGACG 59.395 50.000 0.00 0.00 0.00 4.35
2086 2110 2.827921 GTTGACTTGCCAATCTGGGAAT 59.172 45.455 0.00 0.00 46.83 3.01
2140 2164 2.862536 CCTGCGACATCATTAGTCACTG 59.137 50.000 0.00 0.00 35.77 3.66
2411 2435 1.808411 TCAAGTGCTCCGGACAAATC 58.192 50.000 0.00 0.00 0.00 2.17
2418 2442 3.557595 GTGCTCCGGACAAATCTTCTATG 59.442 47.826 0.00 0.00 0.00 2.23
2607 2631 3.731867 GCTGGACAAACAAACTGACAGTG 60.732 47.826 9.33 0.00 0.00 3.66
2614 2638 1.765314 ACAAACTGACAGTGAGAGGCT 59.235 47.619 9.33 0.00 0.00 4.58
2619 2643 2.435805 ACTGACAGTGAGAGGCTTTGAA 59.564 45.455 7.47 0.00 0.00 2.69
2672 2696 7.071014 TCAAAACAAAGACAAAAGATTTGCC 57.929 32.000 2.88 0.00 37.42 4.52
2725 2749 2.940410 AGAGTTTTACAACACACCCACG 59.060 45.455 0.00 0.00 35.05 4.94
2780 2804 0.551879 TCCCTAGTCTCTTAGCGCCT 59.448 55.000 2.29 0.00 0.00 5.52
2836 2860 3.070590 GTGGTAAGGATAATAGGCGGTGT 59.929 47.826 0.00 0.00 0.00 4.16
2939 2963 7.316393 AGTATGCCAATTAGGATTGCTACTA 57.684 36.000 0.00 0.00 41.06 1.82
2969 2993 1.663702 GTCCCACCACTCGTTGACG 60.664 63.158 0.00 0.00 41.45 4.35
3034 3058 3.497640 CCAATCTTCTCGATGATGGCTTC 59.502 47.826 0.00 0.00 31.20 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.917172 GGCAACACCATTTTGGCAG 58.083 52.632 3.96 0.00 46.16 4.85
2 3 0.603439 CAGGGCAACACCATTTTGGC 60.603 55.000 0.25 0.25 42.67 4.52
3 4 0.603439 GCAGGGCAACACCATTTTGG 60.603 55.000 0.00 0.00 45.02 3.28
4 5 0.603439 GGCAGGGCAACACCATTTTG 60.603 55.000 0.00 0.00 42.05 2.44
5 6 1.754107 GGCAGGGCAACACCATTTT 59.246 52.632 0.00 0.00 42.05 1.82
6 7 2.573083 CGGCAGGGCAACACCATTT 61.573 57.895 0.00 0.00 42.05 2.32
7 8 2.990967 CGGCAGGGCAACACCATT 60.991 61.111 0.00 0.00 42.05 3.16
14 15 4.722700 GAAGCTCCGGCAGGGCAA 62.723 66.667 16.12 0.00 41.70 4.52
85 86 3.661025 GATGTTTTCGGGTGGCGCG 62.661 63.158 0.00 0.00 41.10 6.86
86 87 2.178273 GATGTTTTCGGGTGGCGC 59.822 61.111 0.00 0.00 0.00 6.53
87 88 1.209127 GTGATGTTTTCGGGTGGCG 59.791 57.895 0.00 0.00 0.00 5.69
88 89 0.887933 ATGTGATGTTTTCGGGTGGC 59.112 50.000 0.00 0.00 0.00 5.01
89 90 4.981806 ATAATGTGATGTTTTCGGGTGG 57.018 40.909 0.00 0.00 0.00 4.61
90 91 8.749841 TTTTTATAATGTGATGTTTTCGGGTG 57.250 30.769 0.00 0.00 0.00 4.61
118 119 9.959749 TCGCATTATAGAAAAGAAAAGTGTTTT 57.040 25.926 0.00 0.00 33.18 2.43
129 130 9.398170 CCACCAAAATATCGCATTATAGAAAAG 57.602 33.333 0.00 0.00 0.00 2.27
130 131 8.356657 CCCACCAAAATATCGCATTATAGAAAA 58.643 33.333 0.00 0.00 0.00 2.29
131 132 7.504238 ACCCACCAAAATATCGCATTATAGAAA 59.496 33.333 0.00 0.00 0.00 2.52
132 133 7.001674 ACCCACCAAAATATCGCATTATAGAA 58.998 34.615 0.00 0.00 0.00 2.10
133 134 6.539173 ACCCACCAAAATATCGCATTATAGA 58.461 36.000 0.00 0.00 0.00 1.98
134 135 6.817765 ACCCACCAAAATATCGCATTATAG 57.182 37.500 0.00 0.00 0.00 1.31
135 136 7.589958 AAACCCACCAAAATATCGCATTATA 57.410 32.000 0.00 0.00 0.00 0.98
136 137 6.478512 AAACCCACCAAAATATCGCATTAT 57.521 33.333 0.00 0.00 0.00 1.28
137 138 5.923733 AAACCCACCAAAATATCGCATTA 57.076 34.783 0.00 0.00 0.00 1.90
138 139 4.817318 AAACCCACCAAAATATCGCATT 57.183 36.364 0.00 0.00 0.00 3.56
139 140 4.817318 AAAACCCACCAAAATATCGCAT 57.183 36.364 0.00 0.00 0.00 4.73
140 141 4.608948 AAAAACCCACCAAAATATCGCA 57.391 36.364 0.00 0.00 0.00 5.10
158 159 5.860941 ACATGTAATCACACACCCAAAAA 57.139 34.783 0.00 0.00 37.54 1.94
159 160 5.860941 AACATGTAATCACACACCCAAAA 57.139 34.783 0.00 0.00 37.54 2.44
160 161 5.221342 GGAAACATGTAATCACACACCCAAA 60.221 40.000 0.00 0.00 37.54 3.28
161 162 4.279671 GGAAACATGTAATCACACACCCAA 59.720 41.667 0.00 0.00 37.54 4.12
162 163 3.823873 GGAAACATGTAATCACACACCCA 59.176 43.478 0.00 0.00 37.54 4.51
163 164 4.079253 AGGAAACATGTAATCACACACCC 58.921 43.478 0.00 0.00 37.54 4.61
164 165 4.518970 ACAGGAAACATGTAATCACACACC 59.481 41.667 0.00 0.00 37.54 4.16
165 166 5.689383 ACAGGAAACATGTAATCACACAC 57.311 39.130 0.00 0.00 37.54 3.82
166 167 7.809546 TTAACAGGAAACATGTAATCACACA 57.190 32.000 0.00 0.00 37.54 3.72
167 168 8.511321 TGATTAACAGGAAACATGTAATCACAC 58.489 33.333 10.80 0.00 37.54 3.82
168 169 8.628630 TGATTAACAGGAAACATGTAATCACA 57.371 30.769 10.80 0.00 39.52 3.58
169 170 9.341899 GTTGATTAACAGGAAACATGTAATCAC 57.658 33.333 13.37 7.65 34.35 3.06
170 171 9.295825 AGTTGATTAACAGGAAACATGTAATCA 57.704 29.630 10.80 10.80 39.30 2.57
171 172 9.774742 GAGTTGATTAACAGGAAACATGTAATC 57.225 33.333 0.00 2.76 39.30 1.75
172 173 8.450964 CGAGTTGATTAACAGGAAACATGTAAT 58.549 33.333 0.00 0.00 39.30 1.89
173 174 7.442969 ACGAGTTGATTAACAGGAAACATGTAA 59.557 33.333 0.00 0.00 39.30 2.41
174 175 6.932400 ACGAGTTGATTAACAGGAAACATGTA 59.068 34.615 0.00 0.00 39.30 2.29
175 176 5.763204 ACGAGTTGATTAACAGGAAACATGT 59.237 36.000 2.93 0.00 39.30 3.21
176 177 6.241207 ACGAGTTGATTAACAGGAAACATG 57.759 37.500 2.93 0.00 39.30 3.21
177 178 7.159372 ACTACGAGTTGATTAACAGGAAACAT 58.841 34.615 2.93 0.00 39.30 2.71
178 179 6.518493 ACTACGAGTTGATTAACAGGAAACA 58.482 36.000 2.93 0.00 39.30 2.83
179 180 7.417496 AACTACGAGTTGATTAACAGGAAAC 57.583 36.000 2.93 0.00 37.00 2.78
180 181 9.146984 CATAACTACGAGTTGATTAACAGGAAA 57.853 33.333 2.93 0.00 39.11 3.13
181 182 8.308931 ACATAACTACGAGTTGATTAACAGGAA 58.691 33.333 2.93 0.00 39.11 3.36
182 183 7.758076 CACATAACTACGAGTTGATTAACAGGA 59.242 37.037 2.93 0.00 39.11 3.86
183 184 7.010183 CCACATAACTACGAGTTGATTAACAGG 59.990 40.741 2.93 0.00 39.11 4.00
184 185 7.010183 CCCACATAACTACGAGTTGATTAACAG 59.990 40.741 2.93 0.00 39.11 3.16
185 186 6.814644 CCCACATAACTACGAGTTGATTAACA 59.185 38.462 2.93 0.00 39.11 2.41
186 187 7.037438 TCCCACATAACTACGAGTTGATTAAC 58.963 38.462 9.58 0.00 39.11 2.01
187 188 7.172868 TCCCACATAACTACGAGTTGATTAA 57.827 36.000 9.58 0.00 39.11 1.40
188 189 6.778834 TCCCACATAACTACGAGTTGATTA 57.221 37.500 9.58 0.00 39.11 1.75
189 190 5.670792 TCCCACATAACTACGAGTTGATT 57.329 39.130 9.58 0.00 39.11 2.57
190 191 5.670792 TTCCCACATAACTACGAGTTGAT 57.329 39.130 9.58 0.12 39.11 2.57
191 192 5.670792 ATTCCCACATAACTACGAGTTGA 57.329 39.130 9.58 0.00 39.11 3.18
192 193 6.403200 CCAAATTCCCACATAACTACGAGTTG 60.403 42.308 9.58 0.00 39.11 3.16
193 194 5.646360 CCAAATTCCCACATAACTACGAGTT 59.354 40.000 0.00 0.00 41.97 3.01
194 195 5.183228 CCAAATTCCCACATAACTACGAGT 58.817 41.667 0.00 0.00 0.00 4.18
195 196 5.183228 ACCAAATTCCCACATAACTACGAG 58.817 41.667 0.00 0.00 0.00 4.18
196 197 5.168647 ACCAAATTCCCACATAACTACGA 57.831 39.130 0.00 0.00 0.00 3.43
197 198 4.033587 CGACCAAATTCCCACATAACTACG 59.966 45.833 0.00 0.00 0.00 3.51
198 199 4.201881 GCGACCAAATTCCCACATAACTAC 60.202 45.833 0.00 0.00 0.00 2.73
199 200 3.942748 GCGACCAAATTCCCACATAACTA 59.057 43.478 0.00 0.00 0.00 2.24
200 201 2.752903 GCGACCAAATTCCCACATAACT 59.247 45.455 0.00 0.00 0.00 2.24
201 202 2.490115 TGCGACCAAATTCCCACATAAC 59.510 45.455 0.00 0.00 0.00 1.89
202 203 2.796557 TGCGACCAAATTCCCACATAA 58.203 42.857 0.00 0.00 0.00 1.90
203 204 2.498644 TGCGACCAAATTCCCACATA 57.501 45.000 0.00 0.00 0.00 2.29
204 205 1.477700 CATGCGACCAAATTCCCACAT 59.522 47.619 0.00 0.00 0.00 3.21
205 206 0.887247 CATGCGACCAAATTCCCACA 59.113 50.000 0.00 0.00 0.00 4.17
206 207 0.887933 ACATGCGACCAAATTCCCAC 59.112 50.000 0.00 0.00 0.00 4.61
207 208 2.498644 TACATGCGACCAAATTCCCA 57.501 45.000 0.00 0.00 0.00 4.37
208 209 2.948979 TGATACATGCGACCAAATTCCC 59.051 45.455 0.00 0.00 0.00 3.97
209 210 4.036734 ACATGATACATGCGACCAAATTCC 59.963 41.667 0.00 0.00 0.00 3.01
210 211 5.173774 ACATGATACATGCGACCAAATTC 57.826 39.130 0.00 0.00 0.00 2.17
211 212 5.105797 ACAACATGATACATGCGACCAAATT 60.106 36.000 0.00 0.00 0.00 1.82
212 213 4.398988 ACAACATGATACATGCGACCAAAT 59.601 37.500 0.00 0.00 0.00 2.32
213 214 3.755905 ACAACATGATACATGCGACCAAA 59.244 39.130 0.00 0.00 0.00 3.28
214 215 3.342719 ACAACATGATACATGCGACCAA 58.657 40.909 0.00 0.00 0.00 3.67
215 216 2.984562 ACAACATGATACATGCGACCA 58.015 42.857 0.00 0.00 0.00 4.02
216 217 3.683989 CAACAACATGATACATGCGACC 58.316 45.455 0.00 0.00 0.00 4.79
217 218 3.100817 GCAACAACATGATACATGCGAC 58.899 45.455 0.00 0.00 0.00 5.19
218 219 3.009026 AGCAACAACATGATACATGCGA 58.991 40.909 0.00 0.00 37.40 5.10
219 220 3.409851 AGCAACAACATGATACATGCG 57.590 42.857 0.00 6.07 37.40 4.73
220 221 5.233957 TGTAGCAACAACATGATACATGC 57.766 39.130 0.00 3.44 44.61 4.06
223 224 5.304778 ACACTGTAGCAACAACATGATACA 58.695 37.500 0.00 5.44 46.55 2.29
224 225 5.862924 ACACTGTAGCAACAACATGATAC 57.137 39.130 0.00 0.00 41.39 2.24
225 226 7.382898 TCTAACACTGTAGCAACAACATGATA 58.617 34.615 0.00 0.00 34.49 2.15
226 227 6.230472 TCTAACACTGTAGCAACAACATGAT 58.770 36.000 0.00 0.00 34.49 2.45
227 228 5.606505 TCTAACACTGTAGCAACAACATGA 58.393 37.500 0.00 0.00 34.49 3.07
228 229 5.922739 TCTAACACTGTAGCAACAACATG 57.077 39.130 0.00 0.00 34.49 3.21
229 230 5.997746 ACATCTAACACTGTAGCAACAACAT 59.002 36.000 0.00 0.00 34.49 2.71
230 231 5.364778 ACATCTAACACTGTAGCAACAACA 58.635 37.500 0.00 0.00 34.49 3.33
231 232 5.924475 ACATCTAACACTGTAGCAACAAC 57.076 39.130 0.00 0.00 34.49 3.32
232 233 6.052360 TCAACATCTAACACTGTAGCAACAA 58.948 36.000 0.00 0.00 34.49 2.83
233 234 5.606505 TCAACATCTAACACTGTAGCAACA 58.393 37.500 0.00 0.00 0.00 3.33
234 235 6.727824 ATCAACATCTAACACTGTAGCAAC 57.272 37.500 0.00 0.00 0.00 4.17
235 236 7.744087 AAATCAACATCTAACACTGTAGCAA 57.256 32.000 0.00 0.00 0.00 3.91
236 237 7.744087 AAAATCAACATCTAACACTGTAGCA 57.256 32.000 0.00 0.00 0.00 3.49
261 262 3.493699 CGTGTCCTCTCACCACCTAAAAA 60.494 47.826 0.00 0.00 35.18 1.94
262 263 2.036733 CGTGTCCTCTCACCACCTAAAA 59.963 50.000 0.00 0.00 35.18 1.52
263 264 1.616865 CGTGTCCTCTCACCACCTAAA 59.383 52.381 0.00 0.00 35.18 1.85
264 265 1.254026 CGTGTCCTCTCACCACCTAA 58.746 55.000 0.00 0.00 35.18 2.69
265 266 1.248785 GCGTGTCCTCTCACCACCTA 61.249 60.000 0.00 0.00 35.18 3.08
266 267 2.574955 GCGTGTCCTCTCACCACCT 61.575 63.158 0.00 0.00 35.18 4.00
267 268 2.048127 GCGTGTCCTCTCACCACC 60.048 66.667 0.00 0.00 35.18 4.61
268 269 2.430921 CGCGTGTCCTCTCACCAC 60.431 66.667 0.00 0.00 35.18 4.16
269 270 3.680786 CCGCGTGTCCTCTCACCA 61.681 66.667 4.92 0.00 35.18 4.17
270 271 4.436998 CCCGCGTGTCCTCTCACC 62.437 72.222 4.92 0.00 35.18 4.02
271 272 2.227089 AATCCCGCGTGTCCTCTCAC 62.227 60.000 4.92 0.00 35.28 3.51
272 273 1.982395 AATCCCGCGTGTCCTCTCA 60.982 57.895 4.92 0.00 0.00 3.27
273 274 1.519455 CAATCCCGCGTGTCCTCTC 60.519 63.158 4.92 0.00 0.00 3.20
274 275 1.827399 AACAATCCCGCGTGTCCTCT 61.827 55.000 4.92 0.00 0.00 3.69
275 276 1.375523 AACAATCCCGCGTGTCCTC 60.376 57.895 4.92 0.00 0.00 3.71
276 277 1.671054 CAACAATCCCGCGTGTCCT 60.671 57.895 4.92 0.00 0.00 3.85
277 278 1.964373 ACAACAATCCCGCGTGTCC 60.964 57.895 4.92 0.00 0.00 4.02
278 279 1.206578 CACAACAATCCCGCGTGTC 59.793 57.895 4.92 0.00 0.00 3.67
279 280 2.903547 GCACAACAATCCCGCGTGT 61.904 57.895 4.92 0.00 0.00 4.49
280 281 2.126888 GCACAACAATCCCGCGTG 60.127 61.111 4.92 0.00 0.00 5.34
281 282 1.452145 AAAGCACAACAATCCCGCGT 61.452 50.000 4.92 0.00 0.00 6.01
282 283 0.318614 AAAAGCACAACAATCCCGCG 60.319 50.000 0.00 0.00 0.00 6.46
283 284 1.864565 AAAAAGCACAACAATCCCGC 58.135 45.000 0.00 0.00 0.00 6.13
284 285 4.804108 TCATAAAAAGCACAACAATCCCG 58.196 39.130 0.00 0.00 0.00 5.14
285 286 6.397272 TCATCATAAAAAGCACAACAATCCC 58.603 36.000 0.00 0.00 0.00 3.85
286 287 9.754382 ATATCATCATAAAAAGCACAACAATCC 57.246 29.630 0.00 0.00 0.00 3.01
303 304 9.999009 GCATCAATCATCGTAAAATATCATCAT 57.001 29.630 0.00 0.00 0.00 2.45
304 305 9.223099 AGCATCAATCATCGTAAAATATCATCA 57.777 29.630 0.00 0.00 0.00 3.07
305 306 9.486857 CAGCATCAATCATCGTAAAATATCATC 57.513 33.333 0.00 0.00 0.00 2.92
306 307 9.223099 TCAGCATCAATCATCGTAAAATATCAT 57.777 29.630 0.00 0.00 0.00 2.45
307 308 8.606040 TCAGCATCAATCATCGTAAAATATCA 57.394 30.769 0.00 0.00 0.00 2.15
386 387 7.854166 AGCTCTCTCATTCAGGTAAGATATT 57.146 36.000 0.00 0.00 0.00 1.28
407 408 5.355350 CACCGGATTGATTTCTTAAGAAGCT 59.645 40.000 17.05 9.58 35.21 3.74
465 466 5.047519 GCCTTGACAGTACTGGAGTAGTTAA 60.048 44.000 26.12 6.85 40.89 2.01
472 473 0.976641 TGGCCTTGACAGTACTGGAG 59.023 55.000 26.12 18.81 34.19 3.86
473 474 0.976641 CTGGCCTTGACAGTACTGGA 59.023 55.000 26.12 10.12 33.29 3.86
474 475 0.036010 CCTGGCCTTGACAGTACTGG 60.036 60.000 26.12 9.72 36.87 4.00
475 476 0.976641 TCCTGGCCTTGACAGTACTG 59.023 55.000 21.44 21.44 36.87 2.74
476 477 1.625818 CTTCCTGGCCTTGACAGTACT 59.374 52.381 3.32 0.00 36.87 2.73
477 478 1.946283 GCTTCCTGGCCTTGACAGTAC 60.946 57.143 3.32 0.00 36.87 2.73
478 479 0.324943 GCTTCCTGGCCTTGACAGTA 59.675 55.000 3.32 0.00 36.87 2.74
479 480 1.073897 GCTTCCTGGCCTTGACAGT 59.926 57.895 3.32 0.00 36.87 3.55
480 481 0.323178 ATGCTTCCTGGCCTTGACAG 60.323 55.000 3.32 0.00 38.64 3.51
481 482 0.322816 GATGCTTCCTGGCCTTGACA 60.323 55.000 3.32 0.00 0.00 3.58
482 483 1.034292 GGATGCTTCCTGGCCTTGAC 61.034 60.000 11.34 0.00 39.14 3.18
576 586 2.743928 GCCTGGAAGCCTGTCGTG 60.744 66.667 0.00 0.00 0.00 4.35
643 653 2.915659 AAGGCTGTCCGGTCGTGA 60.916 61.111 0.00 0.00 37.47 4.35
698 708 1.338105 TGTGCGATCTGCTAAGTTGCT 60.338 47.619 10.16 0.00 46.63 3.91
703 713 1.135915 AGGTCTGTGCGATCTGCTAAG 59.864 52.381 10.16 7.87 46.63 2.18
706 716 0.108424 GAAGGTCTGTGCGATCTGCT 60.108 55.000 10.16 0.00 46.63 4.24
726 736 4.201758 CGTTCGTACTACGTGATGAATGAC 59.798 45.833 8.42 0.00 43.14 3.06
739 749 0.930310 CGATCCGGTCGTTCGTACTA 59.070 55.000 15.48 0.00 45.19 1.82
760 770 3.140141 CGCCGCCATGGGAATTGT 61.140 61.111 15.13 0.00 38.63 2.71
975 988 2.031163 CGGAGGCGATGGATTCCC 59.969 66.667 0.00 0.00 0.00 3.97
992 1005 3.119708 GCATCTTGTGTTCATGGGAAGTC 60.120 47.826 0.00 0.00 32.62 3.01
1110 1131 3.946201 AGCTCCGGCAACAGCACT 61.946 61.111 14.64 0.00 38.05 4.40
1115 1136 1.301716 GAGTTCAGCTCCGGCAACA 60.302 57.895 0.00 0.00 41.70 3.33
1528 1552 5.072040 TCTTCTTGACTCAACGCATCATA 57.928 39.130 0.00 0.00 0.00 2.15
1591 1615 1.137872 AGAGGAGCGGTCATTGTCATC 59.862 52.381 17.59 0.00 0.00 2.92
1944 1968 5.531287 AGTTCTAATAATCCCGGTTTGCATC 59.469 40.000 0.00 0.00 0.00 3.91
2140 2164 7.981789 TGTCTACAACATGATTCTCATAGTTCC 59.018 37.037 0.00 0.00 34.28 3.62
2164 2188 9.784531 AAATAGACCGAAGAATGATTGATATGT 57.215 29.630 0.00 0.00 0.00 2.29
2177 2201 6.263344 CAACTCGTCATAAATAGACCGAAGA 58.737 40.000 0.00 0.00 32.41 2.87
2393 2417 1.813513 AGATTTGTCCGGAGCACTTG 58.186 50.000 3.06 0.00 0.00 3.16
2411 2435 3.120752 CCGAAGAATCATGCGCATAGAAG 60.121 47.826 24.84 11.09 0.00 2.85
2418 2442 2.052766 CGCCGAAGAATCATGCGC 60.053 61.111 0.00 0.00 38.88 6.09
2476 2500 6.899393 AAATCCTTTTCTGCTGAACATACA 57.101 33.333 5.41 0.00 31.02 2.29
2524 2548 7.337942 AGAAACATAGCTTCCTTGGTATGAAAG 59.662 37.037 17.02 0.00 45.76 2.62
2529 2553 6.599638 GTCAAGAAACATAGCTTCCTTGGTAT 59.400 38.462 0.00 0.00 0.00 2.73
2655 2679 5.305128 TGGATGAGGCAAATCTTTTGTCTTT 59.695 36.000 8.35 0.76 34.05 2.52
2725 2749 4.651994 CGAGTAATTGTCATGCCACTTTC 58.348 43.478 0.00 0.00 0.00 2.62
2780 2804 2.336341 CAAGCTTTGGGTTACCGCA 58.664 52.632 0.00 0.00 40.75 5.69
2802 2826 1.613928 TTACCACCATCCTGGGCGA 60.614 57.895 0.00 0.00 43.37 5.54
2805 2829 1.522900 ATCCTTACCACCATCCTGGG 58.477 55.000 0.00 0.00 43.37 4.45
2836 2860 1.228094 TTCCGCCACAAGTGCATGA 60.228 52.632 0.00 0.00 0.00 3.07
2896 2920 0.327480 TATGGCCTCCCTCACCATGT 60.327 55.000 3.32 0.00 43.93 3.21
2939 2963 0.613777 GGTGGGACAAGAGAACCGAT 59.386 55.000 0.00 0.00 44.16 4.18
2969 2993 1.327303 TGTGGCACCTTCATGAAACC 58.673 50.000 16.26 9.19 0.00 3.27
3003 3027 7.232118 TCATCGAGAAGATTGGCTTATATCA 57.768 36.000 0.00 0.00 37.52 2.15
3005 3029 7.046652 CCATCATCGAGAAGATTGGCTTATAT 58.953 38.462 0.00 0.00 37.52 0.86


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

AutoCloner maintained by Alex Coulton.