Multiple sequence alignment - TraesCS2D01G173600

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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 TraesCS2D01G173600 chr2D 100.000 2276 0 0 1 2276 117220830 117218555 0.000000e+00 4204.0
1 TraesCS2D01G173600 chr2D 96.356 247 8 1 1 247 542729088 542729333 2.720000e-109 405.0
2 TraesCS2D01G173600 chr2D 79.294 425 65 18 783 1189 117197075 117196656 2.230000e-70 276.0
3 TraesCS2D01G173600 chr2D 87.440 207 26 0 1071 1277 117200013 117199807 2.920000e-59 239.0
4 TraesCS2D01G173600 chr2B 89.991 1099 64 17 428 1497 167796924 167795843 0.000000e+00 1378.0
5 TraesCS2D01G173600 chr2B 78.320 512 79 25 783 1277 167497775 167497279 3.670000e-78 302.0
6 TraesCS2D01G173600 chr2B 85.990 207 29 0 1071 1277 167499556 167499350 2.940000e-54 222.0
7 TraesCS2D01G173600 chr2B 90.141 71 6 1 1374 1444 167499290 167499221 8.660000e-15 91.6
8 TraesCS2D01G173600 chr2A 93.283 923 47 7 1353 2275 118667906 118666999 0.000000e+00 1347.0
9 TraesCS2D01G173600 chr2A 91.196 920 35 15 421 1307 118669098 118668192 0.000000e+00 1208.0
10 TraesCS2D01G173600 chr2A 86.957 207 27 0 1071 1277 118489067 118488861 1.360000e-57 233.0
11 TraesCS2D01G173600 chr6D 97.984 248 5 0 1 248 126417874 126417627 4.490000e-117 431.0
12 TraesCS2D01G173600 chr6D 97.571 247 6 0 1 247 46863142 46863388 7.520000e-115 424.0
13 TraesCS2D01G173600 chr6D 97.571 247 6 0 1 247 126423042 126422796 7.520000e-115 424.0
14 TraesCS2D01G173600 chr6D 97.177 248 7 0 1 248 46868412 46868659 9.720000e-114 420.0
15 TraesCS2D01G173600 chr3D 97.177 248 6 1 1 248 11408566 11408812 3.500000e-113 418.0
16 TraesCS2D01G173600 chr3D 96.761 247 7 1 1 247 11403206 11403451 5.850000e-111 411.0
17 TraesCS2D01G173600 chr5D 96.356 247 8 1 1 247 361345031 361344786 2.720000e-109 405.0
18 TraesCS2D01G173600 chr4D 96.356 247 8 1 1 247 401787244 401787489 2.720000e-109 405.0
19 TraesCS2D01G173600 chrUn 87.805 82 6 3 1632 1710 352613241 352613161 2.410000e-15 93.5
20 TraesCS2D01G173600 chrUn 87.805 82 6 3 1632 1710 352725674 352725754 2.410000e-15 93.5
21 TraesCS2D01G173600 chrUn 87.805 82 6 3 1632 1710 352782797 352782717 2.410000e-15 93.5
22 TraesCS2D01G173600 chr7A 87.805 82 6 3 1632 1710 707543167 707543247 2.410000e-15 93.5
23 TraesCS2D01G173600 chr7A 87.805 82 6 3 1632 1710 710477421 710477501 2.410000e-15 93.5
24 TraesCS2D01G173600 chr4B 88.000 50 6 0 1796 1845 633672918 633672869 2.440000e-05 60.2


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 TraesCS2D01G173600 chr2D 117218555 117220830 2275 True 4204.0 4204 100.0000 1 2276 1 chr2D.!!$R1 2275
1 TraesCS2D01G173600 chr2D 117196656 117200013 3357 True 257.5 276 83.3670 783 1277 2 chr2D.!!$R2 494
2 TraesCS2D01G173600 chr2B 167795843 167796924 1081 True 1378.0 1378 89.9910 428 1497 1 chr2B.!!$R1 1069
3 TraesCS2D01G173600 chr2B 167497279 167499556 2277 True 205.2 302 84.8170 783 1444 3 chr2B.!!$R2 661
4 TraesCS2D01G173600 chr2A 118666999 118669098 2099 True 1277.5 1347 92.2395 421 2275 2 chr2A.!!$R2 1854

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
75 76 0.030501 CACCCCACCTACATCCCCTA 60.031 60.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2065 4514 0.378962 CGCTCCACTCTCCTTACTCG 59.621 60.0 0.0 0.0 0.0 4.18 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
20 21 1.064825 ATATAAAGAGGTGGGGGCCG 58.935 55.000 0.00 0.00 0.00 6.13
66 67 3.069946 CGCCGTACACCCCACCTA 61.070 66.667 0.00 0.00 0.00 3.08
68 69 2.285024 GCCGTACACCCCACCTACA 61.285 63.158 0.00 0.00 0.00 2.74
69 70 1.619807 GCCGTACACCCCACCTACAT 61.620 60.000 0.00 0.00 0.00 2.29
70 71 0.462789 CCGTACACCCCACCTACATC 59.537 60.000 0.00 0.00 0.00 3.06
71 72 0.462789 CGTACACCCCACCTACATCC 59.537 60.000 0.00 0.00 0.00 3.51
72 73 0.835276 GTACACCCCACCTACATCCC 59.165 60.000 0.00 0.00 0.00 3.85
74 75 1.307866 CACCCCACCTACATCCCCT 60.308 63.158 0.00 0.00 0.00 4.79
75 76 0.030501 CACCCCACCTACATCCCCTA 60.031 60.000 0.00 0.00 0.00 3.53
77 78 0.767060 CCCCACCTACATCCCCTACC 60.767 65.000 0.00 0.00 0.00 3.18
78 79 1.119574 CCCACCTACATCCCCTACCG 61.120 65.000 0.00 0.00 0.00 4.02
79 80 0.105862 CCACCTACATCCCCTACCGA 60.106 60.000 0.00 0.00 0.00 4.69
80 81 1.482553 CCACCTACATCCCCTACCGAT 60.483 57.143 0.00 0.00 0.00 4.18
81 82 1.893801 CACCTACATCCCCTACCGATC 59.106 57.143 0.00 0.00 0.00 3.69
85 86 3.266254 CCTACATCCCCTACCGATCTAGA 59.734 52.174 0.00 0.00 0.00 2.43
87 88 2.717515 ACATCCCCTACCGATCTAGAGT 59.282 50.000 0.00 0.00 0.00 3.24
88 89 3.140519 ACATCCCCTACCGATCTAGAGTT 59.859 47.826 0.00 0.00 0.00 3.01
89 90 4.353191 ACATCCCCTACCGATCTAGAGTTA 59.647 45.833 0.00 0.00 0.00 2.24
91 92 3.979347 TCCCCTACCGATCTAGAGTTAGT 59.021 47.826 0.00 0.00 0.00 2.24
92 93 4.073549 CCCCTACCGATCTAGAGTTAGTG 58.926 52.174 0.00 0.00 0.00 2.74
93 94 3.502979 CCCTACCGATCTAGAGTTAGTGC 59.497 52.174 0.00 0.00 0.00 4.40
94 95 4.135306 CCTACCGATCTAGAGTTAGTGCA 58.865 47.826 0.00 0.00 0.00 4.57
96 97 3.622630 ACCGATCTAGAGTTAGTGCAGT 58.377 45.455 0.00 0.00 0.00 4.40
97 98 3.378742 ACCGATCTAGAGTTAGTGCAGTG 59.621 47.826 3.69 0.00 0.00 3.66
98 99 3.367607 CGATCTAGAGTTAGTGCAGTGC 58.632 50.000 8.58 8.58 0.00 4.40
100 101 3.857549 TCTAGAGTTAGTGCAGTGCTG 57.142 47.619 17.60 0.00 0.00 4.41
101 102 3.421844 TCTAGAGTTAGTGCAGTGCTGA 58.578 45.455 17.60 0.00 0.00 4.26
102 103 2.447244 AGAGTTAGTGCAGTGCTGAC 57.553 50.000 17.60 7.10 0.00 3.51
103 104 1.063806 GAGTTAGTGCAGTGCTGACG 58.936 55.000 17.60 0.00 0.00 4.35
104 105 0.319900 AGTTAGTGCAGTGCTGACGG 60.320 55.000 17.60 0.00 0.00 4.79
106 107 1.468506 TTAGTGCAGTGCTGACGGGA 61.469 55.000 17.60 0.00 0.00 5.14
107 108 1.468506 TAGTGCAGTGCTGACGGGAA 61.469 55.000 17.60 0.00 0.00 3.97
108 109 2.031012 TGCAGTGCTGACGGGAAG 59.969 61.111 17.60 0.00 0.00 3.46
126 127 3.760035 CACCGCCACCGCTACTCT 61.760 66.667 0.00 0.00 0.00 3.24
127 128 3.760035 ACCGCCACCGCTACTCTG 61.760 66.667 0.00 0.00 0.00 3.35
130 131 4.082523 GCCACCGCTACTCTGCCA 62.083 66.667 0.00 0.00 0.00 4.92
131 132 2.903357 CCACCGCTACTCTGCCAT 59.097 61.111 0.00 0.00 0.00 4.40
133 134 0.464036 CCACCGCTACTCTGCCATTA 59.536 55.000 0.00 0.00 0.00 1.90
134 135 1.571919 CACCGCTACTCTGCCATTAC 58.428 55.000 0.00 0.00 0.00 1.89
135 136 0.464452 ACCGCTACTCTGCCATTACC 59.536 55.000 0.00 0.00 0.00 2.85
136 137 0.597637 CCGCTACTCTGCCATTACCG 60.598 60.000 0.00 0.00 0.00 4.02
144 145 4.789123 GCCATTACCGGCCACCGT 62.789 66.667 0.00 0.00 46.80 4.83
145 146 2.512974 CCATTACCGGCCACCGTC 60.513 66.667 0.00 0.00 46.80 4.79
146 147 2.266372 CATTACCGGCCACCGTCA 59.734 61.111 0.00 0.00 46.80 4.35
147 148 2.104253 CATTACCGGCCACCGTCAC 61.104 63.158 0.00 0.00 46.80 3.67
171 172 4.292178 CGGCATCGGGAGCTCCTC 62.292 72.222 31.36 20.09 35.95 3.71
173 174 3.219928 GCATCGGGAGCTCCTCGA 61.220 66.667 33.75 33.75 40.85 4.04
174 175 3.038280 CATCGGGAGCTCCTCGAG 58.962 66.667 34.15 25.99 40.27 4.04
184 185 3.432517 CTCCTCGAGCCACAAGAAG 57.567 57.895 6.99 0.00 0.00 2.85
186 187 1.273606 CTCCTCGAGCCACAAGAAGAA 59.726 52.381 6.99 0.00 0.00 2.52
188 189 1.674221 CCTCGAGCCACAAGAAGAAGG 60.674 57.143 6.99 0.00 0.00 3.46
189 190 1.001406 CTCGAGCCACAAGAAGAAGGT 59.999 52.381 0.00 0.00 0.00 3.50
190 191 2.231478 CTCGAGCCACAAGAAGAAGGTA 59.769 50.000 0.00 0.00 0.00 3.08
193 194 4.464951 TCGAGCCACAAGAAGAAGGTAATA 59.535 41.667 0.00 0.00 0.00 0.98
194 195 4.567159 CGAGCCACAAGAAGAAGGTAATAC 59.433 45.833 0.00 0.00 0.00 1.89
211 212 0.688487 TACCTACCACCACTGTTGCC 59.312 55.000 0.00 0.00 0.00 4.52
212 213 1.671054 CCTACCACCACTGTTGCCG 60.671 63.158 0.00 0.00 0.00 5.69
214 215 2.107041 CTACCACCACTGTTGCCGGA 62.107 60.000 5.05 0.00 0.00 5.14
215 216 1.697082 TACCACCACTGTTGCCGGAA 61.697 55.000 5.05 0.00 0.00 4.30
216 217 1.603455 CCACCACTGTTGCCGGAAT 60.603 57.895 5.05 0.00 0.00 3.01
217 218 1.586154 CCACCACTGTTGCCGGAATC 61.586 60.000 5.05 0.00 0.00 2.52
218 219 1.303317 ACCACTGTTGCCGGAATCC 60.303 57.895 5.05 0.00 0.00 3.01
219 220 1.002134 CCACTGTTGCCGGAATCCT 60.002 57.895 5.05 0.00 0.00 3.24
220 221 0.251916 CCACTGTTGCCGGAATCCTA 59.748 55.000 5.05 0.00 0.00 2.94
222 223 0.107654 ACTGTTGCCGGAATCCTAGC 60.108 55.000 5.05 0.57 0.00 3.42
224 225 1.271840 TGTTGCCGGAATCCTAGCCT 61.272 55.000 5.05 0.00 0.00 4.58
225 226 0.756903 GTTGCCGGAATCCTAGCCTA 59.243 55.000 5.05 0.00 0.00 3.93
226 227 1.140252 GTTGCCGGAATCCTAGCCTAA 59.860 52.381 5.05 0.00 0.00 2.69
227 228 0.756903 TGCCGGAATCCTAGCCTAAC 59.243 55.000 5.05 0.00 0.00 2.34
228 229 0.035036 GCCGGAATCCTAGCCTAACC 59.965 60.000 5.05 0.00 0.00 2.85
229 230 0.317479 CCGGAATCCTAGCCTAACCG 59.683 60.000 0.00 0.00 38.83 4.44
230 231 1.325355 CGGAATCCTAGCCTAACCGA 58.675 55.000 0.00 0.00 41.09 4.69
231 232 1.893801 CGGAATCCTAGCCTAACCGAT 59.106 52.381 0.00 0.00 41.09 4.18
232 233 2.094649 CGGAATCCTAGCCTAACCGATC 60.095 54.545 0.00 0.00 41.09 3.69
233 234 2.234168 GGAATCCTAGCCTAACCGATCC 59.766 54.545 0.00 0.00 0.00 3.36
236 237 1.063492 TCCTAGCCTAACCGATCCACA 60.063 52.381 0.00 0.00 0.00 4.17
237 238 1.341531 CCTAGCCTAACCGATCCACAG 59.658 57.143 0.00 0.00 0.00 3.66
239 240 1.568504 AGCCTAACCGATCCACAGAA 58.431 50.000 0.00 0.00 0.00 3.02
240 241 2.119495 AGCCTAACCGATCCACAGAAT 58.881 47.619 0.00 0.00 0.00 2.40
242 243 2.103263 GCCTAACCGATCCACAGAATCT 59.897 50.000 0.00 0.00 0.00 2.40
243 244 3.321111 GCCTAACCGATCCACAGAATCTA 59.679 47.826 0.00 0.00 0.00 1.98
244 245 4.021016 GCCTAACCGATCCACAGAATCTAT 60.021 45.833 0.00 0.00 0.00 1.98
245 246 5.715070 CCTAACCGATCCACAGAATCTATC 58.285 45.833 0.00 0.00 0.00 2.08
246 247 5.243954 CCTAACCGATCCACAGAATCTATCA 59.756 44.000 0.00 0.00 0.00 2.15
247 248 4.592485 ACCGATCCACAGAATCTATCAC 57.408 45.455 0.00 0.00 0.00 3.06
248 249 3.322254 ACCGATCCACAGAATCTATCACC 59.678 47.826 0.00 0.00 0.00 4.02
249 250 3.576118 CCGATCCACAGAATCTATCACCT 59.424 47.826 0.00 0.00 0.00 4.00
250 251 4.039730 CCGATCCACAGAATCTATCACCTT 59.960 45.833 0.00 0.00 0.00 3.50
257 258 6.259608 CCACAGAATCTATCACCTTCAACATC 59.740 42.308 0.00 0.00 0.00 3.06
258 259 7.046652 CACAGAATCTATCACCTTCAACATCT 58.953 38.462 0.00 0.00 0.00 2.90
261 262 9.258826 CAGAATCTATCACCTTCAACATCTTAG 57.741 37.037 0.00 0.00 0.00 2.18
263 264 5.918608 TCTATCACCTTCAACATCTTAGCC 58.081 41.667 0.00 0.00 0.00 3.93
264 265 3.350219 TCACCTTCAACATCTTAGCCC 57.650 47.619 0.00 0.00 0.00 5.19
266 267 3.073798 TCACCTTCAACATCTTAGCCCAA 59.926 43.478 0.00 0.00 0.00 4.12
268 269 3.074538 ACCTTCAACATCTTAGCCCAACT 59.925 43.478 0.00 0.00 0.00 3.16
269 270 3.441572 CCTTCAACATCTTAGCCCAACTG 59.558 47.826 0.00 0.00 0.00 3.16
270 271 3.788227 TCAACATCTTAGCCCAACTGT 57.212 42.857 0.00 0.00 0.00 3.55
271 272 4.098914 TCAACATCTTAGCCCAACTGTT 57.901 40.909 0.00 0.00 0.00 3.16
272 273 5.235850 TCAACATCTTAGCCCAACTGTTA 57.764 39.130 0.00 0.00 0.00 2.41
274 275 3.610911 ACATCTTAGCCCAACTGTTAGC 58.389 45.455 6.62 6.62 0.00 3.09
275 276 3.264450 ACATCTTAGCCCAACTGTTAGCT 59.736 43.478 17.85 17.85 39.37 3.32
276 277 3.611766 TCTTAGCCCAACTGTTAGCTC 57.388 47.619 17.42 0.00 36.79 4.09
279 280 1.352083 AGCCCAACTGTTAGCTCTGA 58.648 50.000 10.48 0.00 0.00 3.27
280 281 1.699634 AGCCCAACTGTTAGCTCTGAA 59.300 47.619 10.48 0.00 0.00 3.02
281 282 2.307098 AGCCCAACTGTTAGCTCTGAAT 59.693 45.455 10.48 0.00 0.00 2.57
282 283 2.421424 GCCCAACTGTTAGCTCTGAATG 59.579 50.000 0.00 0.00 0.00 2.67
283 284 3.869912 GCCCAACTGTTAGCTCTGAATGA 60.870 47.826 0.00 0.00 0.00 2.57
284 285 4.326826 CCCAACTGTTAGCTCTGAATGAA 58.673 43.478 0.00 0.00 0.00 2.57
285 286 4.946157 CCCAACTGTTAGCTCTGAATGAAT 59.054 41.667 0.00 0.00 0.00 2.57
286 287 5.163683 CCCAACTGTTAGCTCTGAATGAATG 60.164 44.000 0.00 0.00 0.00 2.67
287 288 5.163683 CCAACTGTTAGCTCTGAATGAATGG 60.164 44.000 0.00 0.00 0.00 3.16
288 289 5.426689 ACTGTTAGCTCTGAATGAATGGA 57.573 39.130 0.00 0.00 0.00 3.41
289 290 5.999044 ACTGTTAGCTCTGAATGAATGGAT 58.001 37.500 0.00 0.00 0.00 3.41
292 293 3.292492 AGCTCTGAATGAATGGATGCA 57.708 42.857 0.00 0.00 0.00 3.96
293 294 3.215151 AGCTCTGAATGAATGGATGCAG 58.785 45.455 0.00 0.00 30.84 4.41
295 296 2.293677 CTCTGAATGAATGGATGCAGGC 59.706 50.000 0.00 0.00 30.60 4.85
296 297 2.028876 CTGAATGAATGGATGCAGGCA 58.971 47.619 0.00 0.00 0.00 4.75
297 298 2.628178 CTGAATGAATGGATGCAGGCAT 59.372 45.455 6.44 6.44 39.69 4.40
298 299 2.364002 TGAATGAATGGATGCAGGCATG 59.636 45.455 12.12 0.00 36.70 4.06
301 302 1.117150 GAATGGATGCAGGCATGGTT 58.883 50.000 12.12 3.53 36.70 3.67
305 306 0.746659 GGATGCAGGCATGGTTAACC 59.253 55.000 18.27 18.27 36.70 2.85
306 307 0.746659 GATGCAGGCATGGTTAACCC 59.253 55.000 21.97 6.51 36.70 4.11
307 308 0.336048 ATGCAGGCATGGTTAACCCT 59.664 50.000 21.97 9.56 35.03 4.34
308 309 0.611618 TGCAGGCATGGTTAACCCTG 60.612 55.000 21.97 21.88 45.93 4.45
319 320 6.507023 CATGGTTAACCCTGCATATTTTCTC 58.493 40.000 21.97 0.00 34.29 2.87
320 321 5.826643 TGGTTAACCCTGCATATTTTCTCT 58.173 37.500 21.97 0.00 34.29 3.10
321 322 5.652014 TGGTTAACCCTGCATATTTTCTCTG 59.348 40.000 21.97 0.00 34.29 3.35
322 323 5.885912 GGTTAACCCTGCATATTTTCTCTGA 59.114 40.000 14.16 0.00 0.00 3.27
323 324 6.038714 GGTTAACCCTGCATATTTTCTCTGAG 59.961 42.308 14.16 0.00 0.00 3.35
325 326 5.441718 ACCCTGCATATTTTCTCTGAGAA 57.558 39.130 15.82 15.82 31.28 2.87
329 330 6.544931 CCCTGCATATTTTCTCTGAGAAATGA 59.455 38.462 27.93 20.23 43.06 2.57
330 331 7.067859 CCCTGCATATTTTCTCTGAGAAATGAA 59.932 37.037 27.93 18.83 43.06 2.57
331 332 8.129840 CCTGCATATTTTCTCTGAGAAATGAAG 58.870 37.037 27.93 24.78 43.06 3.02
332 333 8.571461 TGCATATTTTCTCTGAGAAATGAAGT 57.429 30.769 27.93 16.18 43.06 3.01
333 334 9.017509 TGCATATTTTCTCTGAGAAATGAAGTT 57.982 29.630 27.93 14.08 43.06 2.66
334 335 9.286946 GCATATTTTCTCTGAGAAATGAAGTTG 57.713 33.333 27.93 20.05 43.06 3.16
335 336 9.784680 CATATTTTCTCTGAGAAATGAAGTTGG 57.215 33.333 27.93 12.29 43.06 3.77
336 337 7.830099 ATTTTCTCTGAGAAATGAAGTTGGT 57.170 32.000 27.93 8.08 43.06 3.67
337 338 8.924511 ATTTTCTCTGAGAAATGAAGTTGGTA 57.075 30.769 27.93 13.17 43.06 3.25
339 340 7.730364 TTCTCTGAGAAATGAAGTTGGTAAC 57.270 36.000 17.32 0.00 29.99 2.50
340 341 7.279615 TTCTCTGAGAAATGAAGTTGGTAACA 58.720 34.615 17.32 0.00 36.44 2.41
355 356 3.649073 GGTAACAAAACCATGGCAGAAC 58.351 45.455 13.04 1.10 39.50 3.01
356 357 2.908688 AACAAAACCATGGCAGAACC 57.091 45.000 13.04 0.00 39.84 3.62
370 371 3.859386 GGCAGAACCAAATCAAATAAGCG 59.141 43.478 0.00 0.00 38.86 4.68
371 372 3.859386 GCAGAACCAAATCAAATAAGCGG 59.141 43.478 0.00 0.00 0.00 5.52
372 373 4.618227 GCAGAACCAAATCAAATAAGCGGT 60.618 41.667 0.00 0.00 0.00 5.68
374 375 5.925969 CAGAACCAAATCAAATAAGCGGTTT 59.074 36.000 4.64 0.00 35.47 3.27
375 376 5.925969 AGAACCAAATCAAATAAGCGGTTTG 59.074 36.000 4.64 0.00 35.47 2.93
378 379 3.951775 AATCAAATAAGCGGTTTGGCA 57.048 38.095 4.64 0.00 37.22 4.92
379 380 3.508744 ATCAAATAAGCGGTTTGGCAG 57.491 42.857 4.64 0.00 37.22 4.85
380 381 1.543802 TCAAATAAGCGGTTTGGCAGG 59.456 47.619 4.64 0.00 37.22 4.85
382 383 1.627864 AATAAGCGGTTTGGCAGGTT 58.372 45.000 4.64 0.00 36.92 3.50
383 384 0.887933 ATAAGCGGTTTGGCAGGTTG 59.112 50.000 4.64 0.00 34.95 3.77
385 386 4.662961 GCGGTTTGGCAGGTTGGC 62.663 66.667 0.00 0.00 44.03 4.52
393 394 2.657297 GGCAGGTTGGCATTCTTGA 58.343 52.632 6.52 0.00 43.14 3.02
395 396 0.529378 GCAGGTTGGCATTCTTGAGG 59.471 55.000 6.52 0.00 0.00 3.86
396 397 1.180029 CAGGTTGGCATTCTTGAGGG 58.820 55.000 0.00 0.00 0.00 4.30
397 398 1.075601 AGGTTGGCATTCTTGAGGGA 58.924 50.000 0.00 0.00 0.00 4.20
399 400 1.821136 GGTTGGCATTCTTGAGGGAAG 59.179 52.381 0.00 0.00 0.00 3.46
400 401 2.555227 GGTTGGCATTCTTGAGGGAAGA 60.555 50.000 0.00 0.00 39.05 2.87
409 410 3.744660 TCTTGAGGGAAGAACTTTCAGC 58.255 45.455 0.00 0.00 37.78 4.26
410 411 3.136443 TCTTGAGGGAAGAACTTTCAGCA 59.864 43.478 0.00 0.00 37.78 4.41
412 413 4.104383 TGAGGGAAGAACTTTCAGCATT 57.896 40.909 0.00 0.00 0.00 3.56
413 414 4.074970 TGAGGGAAGAACTTTCAGCATTC 58.925 43.478 0.00 0.00 0.00 2.67
414 415 4.202503 TGAGGGAAGAACTTTCAGCATTCT 60.203 41.667 0.00 0.00 34.11 2.40
415 416 4.734266 AGGGAAGAACTTTCAGCATTCTT 58.266 39.130 0.00 0.00 43.62 2.52
416 417 4.522022 AGGGAAGAACTTTCAGCATTCTTG 59.478 41.667 3.33 0.00 41.58 3.02
418 419 4.321527 GGAAGAACTTTCAGCATTCTTGGG 60.322 45.833 3.33 0.00 41.58 4.12
419 420 2.560105 AGAACTTTCAGCATTCTTGGGC 59.440 45.455 0.00 0.00 28.03 5.36
422 423 2.036346 ACTTTCAGCATTCTTGGGCAAC 59.964 45.455 0.00 0.00 0.00 4.17
424 425 2.877097 TCAGCATTCTTGGGCAACTA 57.123 45.000 0.00 0.00 0.00 2.24
425 426 2.436417 TCAGCATTCTTGGGCAACTAC 58.564 47.619 0.00 0.00 0.00 2.73
524 525 5.377478 CACTTCCCCCACTAGGAATTTATC 58.623 45.833 0.00 0.00 42.44 1.75
576 580 7.392494 TCGGAATATAATCTGGCAGTAGTAG 57.608 40.000 15.27 0.00 0.00 2.57
577 581 6.946583 TCGGAATATAATCTGGCAGTAGTAGT 59.053 38.462 15.27 3.31 0.00 2.73
578 582 8.105197 TCGGAATATAATCTGGCAGTAGTAGTA 58.895 37.037 15.27 0.00 0.00 1.82
579 583 8.399425 CGGAATATAATCTGGCAGTAGTAGTAG 58.601 40.741 15.27 0.00 0.00 2.57
583 587 3.733883 TCTGGCAGTAGTAGTAGTGGT 57.266 47.619 15.27 0.00 31.04 4.16
584 588 4.849813 TCTGGCAGTAGTAGTAGTGGTA 57.150 45.455 15.27 0.00 31.04 3.25
585 589 4.521146 TCTGGCAGTAGTAGTAGTGGTAC 58.479 47.826 15.27 0.00 31.04 3.34
586 590 3.273434 TGGCAGTAGTAGTAGTGGTACG 58.727 50.000 13.22 0.00 33.97 3.67
587 591 3.055167 TGGCAGTAGTAGTAGTGGTACGA 60.055 47.826 13.22 0.00 33.97 3.43
666 671 7.944061 TGCATGATTTATTAGGAAATGTCAGG 58.056 34.615 0.00 0.00 0.00 3.86
690 695 5.509622 GCAAAGACTAAGAATCGAACAATGC 59.490 40.000 0.00 0.00 0.00 3.56
695 700 6.978659 AGACTAAGAATCGAACAATGCGATAA 59.021 34.615 0.00 0.00 46.67 1.75
710 715 3.939592 TGCGATAAGTCTCTCGAGAAAGA 59.060 43.478 17.36 8.48 39.48 2.52
814 2991 1.078848 CTCGCCCTCCACCAAGAAG 60.079 63.158 0.00 0.00 0.00 2.85
815 2992 1.535444 TCGCCCTCCACCAAGAAGA 60.535 57.895 0.00 0.00 0.00 2.87
986 3178 3.485431 CTGCGTCCTGAGCTTGCG 61.485 66.667 0.00 0.00 35.28 4.85
1314 3511 3.181483 GCTCCATGGGTTTTTATCTGCTG 60.181 47.826 13.02 0.00 0.00 4.41
1326 3523 0.749049 ATCTGCTGTGCTATGCTCGA 59.251 50.000 0.00 0.00 0.00 4.04
1353 3550 9.706691 CCTACTGAATGAAAACTACTCAAGTAA 57.293 33.333 0.00 0.00 37.50 2.24
1356 3553 7.990886 ACTGAATGAAAACTACTCAAGTAACCA 59.009 33.333 0.00 0.00 37.50 3.67
1374 3822 2.764572 ACCACCATAGTACAGTACCTGC 59.235 50.000 7.13 0.00 34.37 4.85
1398 3847 1.588404 GCGTCGTGTGATATGGTTGAG 59.412 52.381 0.00 0.00 0.00 3.02
1497 3946 6.560253 ACTTCATTATGGAGTGTTTGTGTC 57.440 37.500 5.18 0.00 0.00 3.67
1531 3980 2.675371 GCCCCCTTAGGCGAACTT 59.325 61.111 0.00 0.00 44.57 2.66
1537 3986 1.134788 CCCTTAGGCGAACTTCACGAT 60.135 52.381 0.00 0.00 0.00 3.73
1551 4000 3.193757 CGATCCCGTTCTGTCCGA 58.806 61.111 0.00 0.00 0.00 4.55
1559 4008 3.067742 TCCCGTTCTGTCCGAATTCTATC 59.932 47.826 3.52 0.00 33.45 2.08
1560 4009 3.381949 CCGTTCTGTCCGAATTCTATCC 58.618 50.000 3.52 0.00 33.45 2.59
1562 4011 3.488721 CGTTCTGTCCGAATTCTATCCGT 60.489 47.826 3.52 0.00 33.45 4.69
1563 4012 4.430908 GTTCTGTCCGAATTCTATCCGTT 58.569 43.478 3.52 0.00 33.45 4.44
1565 4014 4.430007 TCTGTCCGAATTCTATCCGTTTG 58.570 43.478 3.52 0.00 0.00 2.93
1568 4017 4.081862 TGTCCGAATTCTATCCGTTTGAGT 60.082 41.667 3.52 0.00 0.00 3.41
1570 4019 4.158949 TCCGAATTCTATCCGTTTGAGTCA 59.841 41.667 3.52 0.00 0.00 3.41
1571 4020 4.504461 CCGAATTCTATCCGTTTGAGTCAG 59.496 45.833 3.52 0.00 0.00 3.51
1572 4021 4.026475 CGAATTCTATCCGTTTGAGTCAGC 60.026 45.833 3.52 0.00 0.00 4.26
1573 4022 2.961526 TCTATCCGTTTGAGTCAGCC 57.038 50.000 0.00 0.00 0.00 4.85
1574 4023 2.176045 TCTATCCGTTTGAGTCAGCCA 58.824 47.619 0.00 0.00 0.00 4.75
1579 4028 1.001378 CCGTTTGAGTCAGCCAAAAGG 60.001 52.381 0.00 0.00 43.07 3.11
1581 4030 2.306847 GTTTGAGTCAGCCAAAAGGGA 58.693 47.619 0.00 0.00 40.01 4.20
1602 4051 1.213013 CCGTCCGACCTCTTCTGTG 59.787 63.158 0.00 0.00 0.00 3.66
1605 4054 1.269621 CGTCCGACCTCTTCTGTGTTT 60.270 52.381 0.00 0.00 0.00 2.83
1612 4061 0.588252 CTCTTCTGTGTTTGCGTGGG 59.412 55.000 0.00 0.00 0.00 4.61
1619 4068 2.248135 TGTTTGCGTGGGTAGTGCG 61.248 57.895 0.00 0.00 0.00 5.34
1641 4090 2.870435 GCCGAGCGGACCAAATGTATAT 60.870 50.000 13.94 0.00 37.50 0.86
1643 4092 4.755411 CCGAGCGGACCAAATGTATATAT 58.245 43.478 2.00 0.00 37.50 0.86
1779 4228 8.964420 AACTTAAATTGTCACAAATACATCGG 57.036 30.769 0.00 0.00 0.00 4.18
1783 4232 9.967346 TTAAATTGTCACAAATACATCGGAAAA 57.033 25.926 0.00 0.00 0.00 2.29
1849 4298 3.316029 TGTGCTCAACCAAGTCATTTCAG 59.684 43.478 0.00 0.00 0.00 3.02
1863 4312 9.237846 CAAGTCATTTCAGAAAAGAAAGGTAAC 57.762 33.333 2.38 0.00 40.49 2.50
1920 4369 8.903820 AGATAACATAATTGCCCTGTTAGTTTC 58.096 33.333 0.00 0.00 38.39 2.78
1996 4445 1.327303 TCAACCAAGCCAACACCATC 58.673 50.000 0.00 0.00 0.00 3.51
2000 4449 2.397597 ACCAAGCCAACACCATCTTTT 58.602 42.857 0.00 0.00 0.00 2.27
2084 4533 0.378962 CGAGTAAGGAGAGTGGAGCG 59.621 60.000 0.00 0.00 0.00 5.03
2126 4575 1.565305 CCTACTCTTCAGCGACATGC 58.435 55.000 0.00 0.00 46.98 4.06
2142 4591 1.330521 CATGCGCACCAACCACTATAC 59.669 52.381 14.90 0.00 0.00 1.47
2144 4593 1.270893 TGCGCACCAACCACTATACAA 60.271 47.619 5.66 0.00 0.00 2.41
2162 4611 1.024271 AAGATGGTGTGTGTGTGTGC 58.976 50.000 0.00 0.00 0.00 4.57
2163 4612 1.159713 AGATGGTGTGTGTGTGTGCG 61.160 55.000 0.00 0.00 0.00 5.34
2164 4613 2.715864 GATGGTGTGTGTGTGTGCGC 62.716 60.000 0.00 0.00 0.00 6.09
2165 4614 4.589700 GGTGTGTGTGTGTGCGCG 62.590 66.667 0.00 0.00 0.00 6.86
2175 4624 4.444024 TGTGCGCGCGATTTGAGC 62.444 61.111 37.18 14.77 40.38 4.26
2183 4632 3.056313 GCGATTTGAGCAGGTGGCC 62.056 63.158 0.00 0.00 46.50 5.36
2275 4724 0.249031 GCTTGGTCCAAAGTGTGCAC 60.249 55.000 10.75 10.75 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.057851 CCGGCCCCCACCTCTTTATA 61.058 60.000 0.00 0.00 0.00 0.98
48 49 3.884704 TAGGTGGGGTGTACGGCGT 62.885 63.158 19.64 19.64 0.00 5.68
50 51 1.619807 ATGTAGGTGGGGTGTACGGC 61.620 60.000 0.00 0.00 0.00 5.68
51 52 0.462789 GATGTAGGTGGGGTGTACGG 59.537 60.000 0.00 0.00 0.00 4.02
53 54 0.835276 GGGATGTAGGTGGGGTGTAC 59.165 60.000 0.00 0.00 0.00 2.90
54 55 0.326808 GGGGATGTAGGTGGGGTGTA 60.327 60.000 0.00 0.00 0.00 2.90
55 56 1.618447 GGGGATGTAGGTGGGGTGT 60.618 63.158 0.00 0.00 0.00 4.16
57 58 0.030399 GTAGGGGATGTAGGTGGGGT 60.030 60.000 0.00 0.00 0.00 4.95
60 61 0.105862 TCGGTAGGGGATGTAGGTGG 60.106 60.000 0.00 0.00 0.00 4.61
61 62 1.893801 GATCGGTAGGGGATGTAGGTG 59.106 57.143 0.00 0.00 0.00 4.00
62 63 1.787676 AGATCGGTAGGGGATGTAGGT 59.212 52.381 0.00 0.00 0.00 3.08
63 64 2.606751 AGATCGGTAGGGGATGTAGG 57.393 55.000 0.00 0.00 0.00 3.18
66 67 2.717515 ACTCTAGATCGGTAGGGGATGT 59.282 50.000 0.00 0.00 0.00 3.06
68 69 4.602732 ACTAACTCTAGATCGGTAGGGGAT 59.397 45.833 8.49 0.00 0.00 3.85
69 70 3.979347 ACTAACTCTAGATCGGTAGGGGA 59.021 47.826 8.49 0.00 0.00 4.81
70 71 4.073549 CACTAACTCTAGATCGGTAGGGG 58.926 52.174 8.49 0.00 0.00 4.79
71 72 3.502979 GCACTAACTCTAGATCGGTAGGG 59.497 52.174 8.49 5.69 0.00 3.53
72 73 4.135306 TGCACTAACTCTAGATCGGTAGG 58.865 47.826 8.49 0.73 0.00 3.18
74 75 4.575236 CACTGCACTAACTCTAGATCGGTA 59.425 45.833 0.00 0.00 0.00 4.02
75 76 3.378742 CACTGCACTAACTCTAGATCGGT 59.621 47.826 0.00 0.00 0.00 4.69
77 78 3.066064 AGCACTGCACTAACTCTAGATCG 59.934 47.826 3.30 0.00 0.00 3.69
78 79 4.097135 TCAGCACTGCACTAACTCTAGATC 59.903 45.833 3.30 0.00 0.00 2.75
79 80 4.019858 TCAGCACTGCACTAACTCTAGAT 58.980 43.478 3.30 0.00 0.00 1.98
80 81 3.191581 GTCAGCACTGCACTAACTCTAGA 59.808 47.826 3.30 0.00 0.00 2.43
81 82 3.506810 GTCAGCACTGCACTAACTCTAG 58.493 50.000 3.30 0.00 0.00 2.43
85 86 0.319900 CCGTCAGCACTGCACTAACT 60.320 55.000 3.30 0.00 0.00 2.24
87 88 1.005037 CCCGTCAGCACTGCACTAA 60.005 57.895 3.30 0.00 0.00 2.24
88 89 1.468506 TTCCCGTCAGCACTGCACTA 61.469 55.000 3.30 0.00 0.00 2.74
89 90 2.721971 CTTCCCGTCAGCACTGCACT 62.722 60.000 3.30 0.00 0.00 4.40
91 92 2.031012 CTTCCCGTCAGCACTGCA 59.969 61.111 3.30 0.00 0.00 4.41
92 93 3.426568 GCTTCCCGTCAGCACTGC 61.427 66.667 0.00 0.00 37.22 4.40
93 94 2.031012 TGCTTCCCGTCAGCACTG 59.969 61.111 0.00 0.00 42.49 3.66
96 97 4.680237 CGGTGCTTCCCGTCAGCA 62.680 66.667 2.44 0.00 45.21 4.41
110 111 3.760035 CAGAGTAGCGGTGGCGGT 61.760 66.667 0.00 0.00 46.35 5.68
113 114 2.876368 AATGGCAGAGTAGCGGTGGC 62.876 60.000 0.00 0.00 40.37 5.01
114 115 0.464036 TAATGGCAGAGTAGCGGTGG 59.536 55.000 0.00 0.00 34.64 4.61
115 116 1.571919 GTAATGGCAGAGTAGCGGTG 58.428 55.000 0.00 0.00 34.64 4.94
116 117 0.464452 GGTAATGGCAGAGTAGCGGT 59.536 55.000 0.00 0.00 34.64 5.68
117 118 0.597637 CGGTAATGGCAGAGTAGCGG 60.598 60.000 15.34 2.65 41.24 5.52
119 120 3.290776 CCGGTAATGGCAGAGTAGC 57.709 57.895 0.00 0.00 0.00 3.58
144 145 4.854924 CGATGCCGGCCATGGTGA 62.855 66.667 26.77 2.60 33.29 4.02
155 156 4.292178 CGAGGAGCTCCCGATGCC 62.292 72.222 29.54 10.47 40.87 4.40
156 157 3.206211 CTCGAGGAGCTCCCGATGC 62.206 68.421 32.65 17.63 40.87 3.91
167 168 1.273606 CTTCTTCTTGTGGCTCGAGGA 59.726 52.381 15.58 0.00 0.00 3.71
169 170 1.001406 ACCTTCTTCTTGTGGCTCGAG 59.999 52.381 8.45 8.45 0.00 4.04
170 171 1.048601 ACCTTCTTCTTGTGGCTCGA 58.951 50.000 0.00 0.00 0.00 4.04
171 172 2.743636 TACCTTCTTCTTGTGGCTCG 57.256 50.000 0.00 0.00 0.00 5.03
173 174 4.844884 GGTATTACCTTCTTCTTGTGGCT 58.155 43.478 5.56 0.00 34.73 4.75
188 189 3.937079 GCAACAGTGGTGGTAGGTATTAC 59.063 47.826 10.86 0.00 0.00 1.89
189 190 3.054948 GGCAACAGTGGTGGTAGGTATTA 60.055 47.826 10.86 0.00 0.00 0.98
190 191 2.290705 GGCAACAGTGGTGGTAGGTATT 60.291 50.000 10.86 0.00 0.00 1.89
193 194 1.454539 GGCAACAGTGGTGGTAGGT 59.545 57.895 10.86 0.00 0.00 3.08
194 195 1.671054 CGGCAACAGTGGTGGTAGG 60.671 63.158 10.86 0.00 0.00 3.18
197 198 2.351924 ATTCCGGCAACAGTGGTGGT 62.352 55.000 10.86 0.00 0.00 4.16
200 201 1.303317 GGATTCCGGCAACAGTGGT 60.303 57.895 0.00 0.00 0.00 4.16
201 202 0.251916 TAGGATTCCGGCAACAGTGG 59.748 55.000 0.00 0.00 0.00 4.00
202 203 1.656652 CTAGGATTCCGGCAACAGTG 58.343 55.000 0.00 0.00 0.00 3.66
203 204 0.107654 GCTAGGATTCCGGCAACAGT 60.108 55.000 15.45 0.00 0.00 3.55
204 205 0.815615 GGCTAGGATTCCGGCAACAG 60.816 60.000 19.78 5.14 0.00 3.16
205 206 1.223487 GGCTAGGATTCCGGCAACA 59.777 57.895 19.78 0.00 0.00 3.33
206 207 0.756903 TAGGCTAGGATTCCGGCAAC 59.243 55.000 19.78 8.23 0.00 4.17
208 209 0.756903 GTTAGGCTAGGATTCCGGCA 59.243 55.000 19.78 0.00 0.00 5.69
211 212 1.325355 TCGGTTAGGCTAGGATTCCG 58.675 55.000 13.64 13.64 38.16 4.30
212 213 2.234168 GGATCGGTTAGGCTAGGATTCC 59.766 54.545 0.00 0.00 0.00 3.01
214 215 2.633481 GTGGATCGGTTAGGCTAGGATT 59.367 50.000 0.00 0.00 0.00 3.01
215 216 2.249139 GTGGATCGGTTAGGCTAGGAT 58.751 52.381 0.00 0.00 0.00 3.24
216 217 1.063492 TGTGGATCGGTTAGGCTAGGA 60.063 52.381 0.00 0.00 0.00 2.94
217 218 1.341531 CTGTGGATCGGTTAGGCTAGG 59.658 57.143 0.00 0.00 0.00 3.02
218 219 2.307768 TCTGTGGATCGGTTAGGCTAG 58.692 52.381 0.00 0.00 0.00 3.42
219 220 2.447408 TCTGTGGATCGGTTAGGCTA 57.553 50.000 0.00 0.00 0.00 3.93
220 221 1.568504 TTCTGTGGATCGGTTAGGCT 58.431 50.000 0.00 0.00 0.00 4.58
222 223 5.243954 TGATAGATTCTGTGGATCGGTTAGG 59.756 44.000 0.00 0.00 0.00 2.69
224 225 5.010719 GGTGATAGATTCTGTGGATCGGTTA 59.989 44.000 0.00 0.00 0.00 2.85
225 226 4.202264 GGTGATAGATTCTGTGGATCGGTT 60.202 45.833 0.00 0.00 0.00 4.44
226 227 3.322254 GGTGATAGATTCTGTGGATCGGT 59.678 47.826 0.00 0.00 0.00 4.69
227 228 3.576118 AGGTGATAGATTCTGTGGATCGG 59.424 47.826 0.00 0.00 0.00 4.18
228 229 4.862902 AGGTGATAGATTCTGTGGATCG 57.137 45.455 0.00 0.00 0.00 3.69
229 230 6.166984 TGAAGGTGATAGATTCTGTGGATC 57.833 41.667 0.00 0.00 0.00 3.36
230 231 6.070021 TGTTGAAGGTGATAGATTCTGTGGAT 60.070 38.462 0.00 0.00 0.00 3.41
231 232 5.248248 TGTTGAAGGTGATAGATTCTGTGGA 59.752 40.000 0.00 0.00 0.00 4.02
232 233 5.491070 TGTTGAAGGTGATAGATTCTGTGG 58.509 41.667 0.00 0.00 0.00 4.17
233 234 7.046652 AGATGTTGAAGGTGATAGATTCTGTG 58.953 38.462 0.00 0.00 0.00 3.66
236 237 7.930865 GCTAAGATGTTGAAGGTGATAGATTCT 59.069 37.037 0.00 0.00 0.00 2.40
237 238 7.172361 GGCTAAGATGTTGAAGGTGATAGATTC 59.828 40.741 0.00 0.00 0.00 2.52
239 240 6.465035 GGGCTAAGATGTTGAAGGTGATAGAT 60.465 42.308 0.00 0.00 0.00 1.98
240 241 5.163301 GGGCTAAGATGTTGAAGGTGATAGA 60.163 44.000 0.00 0.00 0.00 1.98
242 243 4.473196 TGGGCTAAGATGTTGAAGGTGATA 59.527 41.667 0.00 0.00 0.00 2.15
243 244 3.266772 TGGGCTAAGATGTTGAAGGTGAT 59.733 43.478 0.00 0.00 0.00 3.06
244 245 2.642311 TGGGCTAAGATGTTGAAGGTGA 59.358 45.455 0.00 0.00 0.00 4.02
245 246 3.071874 TGGGCTAAGATGTTGAAGGTG 57.928 47.619 0.00 0.00 0.00 4.00
246 247 3.074538 AGTTGGGCTAAGATGTTGAAGGT 59.925 43.478 0.00 0.00 0.00 3.50
247 248 3.441572 CAGTTGGGCTAAGATGTTGAAGG 59.558 47.826 0.00 0.00 0.00 3.46
248 249 4.074970 ACAGTTGGGCTAAGATGTTGAAG 58.925 43.478 0.00 0.00 0.00 3.02
249 250 4.098914 ACAGTTGGGCTAAGATGTTGAA 57.901 40.909 0.00 0.00 0.00 2.69
250 251 3.788227 ACAGTTGGGCTAAGATGTTGA 57.212 42.857 0.00 0.00 0.00 3.18
257 258 3.055819 TCAGAGCTAACAGTTGGGCTAAG 60.056 47.826 13.35 10.02 35.01 2.18
258 259 2.903784 TCAGAGCTAACAGTTGGGCTAA 59.096 45.455 13.35 3.29 35.01 3.09
261 262 2.185004 TTCAGAGCTAACAGTTGGGC 57.815 50.000 0.00 0.50 0.00 5.36
263 264 5.163683 CCATTCATTCAGAGCTAACAGTTGG 60.164 44.000 0.00 0.00 0.00 3.77
264 265 5.645067 TCCATTCATTCAGAGCTAACAGTTG 59.355 40.000 0.00 0.00 0.00 3.16
266 267 5.426689 TCCATTCATTCAGAGCTAACAGT 57.573 39.130 0.00 0.00 0.00 3.55
268 269 4.577693 GCATCCATTCATTCAGAGCTAACA 59.422 41.667 0.00 0.00 0.00 2.41
269 270 4.577693 TGCATCCATTCATTCAGAGCTAAC 59.422 41.667 0.00 0.00 0.00 2.34
270 271 4.784177 TGCATCCATTCATTCAGAGCTAA 58.216 39.130 0.00 0.00 0.00 3.09
271 272 4.386711 CTGCATCCATTCATTCAGAGCTA 58.613 43.478 0.00 0.00 0.00 3.32
272 273 3.215151 CTGCATCCATTCATTCAGAGCT 58.785 45.455 0.00 0.00 0.00 4.09
274 275 2.293677 GCCTGCATCCATTCATTCAGAG 59.706 50.000 0.00 0.00 0.00 3.35
275 276 2.304092 GCCTGCATCCATTCATTCAGA 58.696 47.619 0.00 0.00 0.00 3.27
276 277 2.028876 TGCCTGCATCCATTCATTCAG 58.971 47.619 0.00 0.00 0.00 3.02
279 280 1.691976 CCATGCCTGCATCCATTCATT 59.308 47.619 0.70 0.00 33.90 2.57
280 281 1.338107 CCATGCCTGCATCCATTCAT 58.662 50.000 0.70 0.00 33.90 2.57
281 282 0.032912 ACCATGCCTGCATCCATTCA 60.033 50.000 0.70 0.00 33.90 2.57
282 283 1.117150 AACCATGCCTGCATCCATTC 58.883 50.000 0.70 0.00 33.90 2.67
283 284 2.431782 GTTAACCATGCCTGCATCCATT 59.568 45.455 0.70 0.09 33.90 3.16
284 285 2.034124 GTTAACCATGCCTGCATCCAT 58.966 47.619 0.70 0.00 33.90 3.41
285 286 1.473258 GTTAACCATGCCTGCATCCA 58.527 50.000 0.70 0.00 33.90 3.41
286 287 0.746659 GGTTAACCATGCCTGCATCC 59.253 55.000 20.12 0.00 33.90 3.51
287 288 0.746659 GGGTTAACCATGCCTGCATC 59.253 55.000 25.71 0.78 39.85 3.91
288 289 0.336048 AGGGTTAACCATGCCTGCAT 59.664 50.000 25.71 0.00 43.89 3.96
289 290 0.611618 CAGGGTTAACCATGCCTGCA 60.612 55.000 24.94 0.00 41.16 4.41
296 297 6.322201 CAGAGAAAATATGCAGGGTTAACCAT 59.678 38.462 25.71 17.07 43.89 3.55
297 298 5.652014 CAGAGAAAATATGCAGGGTTAACCA 59.348 40.000 25.71 5.89 43.89 3.67
298 299 5.885912 TCAGAGAAAATATGCAGGGTTAACC 59.114 40.000 16.85 16.85 40.67 2.85
301 302 6.560003 TCTCAGAGAAAATATGCAGGGTTA 57.440 37.500 0.00 0.00 0.00 2.85
305 306 7.563888 TCATTTCTCAGAGAAAATATGCAGG 57.436 36.000 26.01 6.85 46.08 4.85
306 307 8.675504 ACTTCATTTCTCAGAGAAAATATGCAG 58.324 33.333 26.01 20.65 46.08 4.41
307 308 8.571461 ACTTCATTTCTCAGAGAAAATATGCA 57.429 30.769 26.01 11.97 46.08 3.96
308 309 9.286946 CAACTTCATTTCTCAGAGAAAATATGC 57.713 33.333 26.01 0.00 46.08 3.14
310 311 9.525826 ACCAACTTCATTTCTCAGAGAAAATAT 57.474 29.630 26.01 10.18 46.08 1.28
312 313 7.830099 ACCAACTTCATTTCTCAGAGAAAAT 57.170 32.000 26.01 13.74 46.08 1.82
313 314 8.621286 GTTACCAACTTCATTTCTCAGAGAAAA 58.379 33.333 26.01 10.86 46.08 2.29
314 315 7.773224 TGTTACCAACTTCATTTCTCAGAGAAA 59.227 33.333 24.78 24.78 46.89 2.52
315 316 7.279615 TGTTACCAACTTCATTTCTCAGAGAA 58.720 34.615 8.95 8.95 31.28 2.87
316 317 6.826668 TGTTACCAACTTCATTTCTCAGAGA 58.173 36.000 0.00 0.00 0.00 3.10
319 320 7.435192 GGTTTTGTTACCAACTTCATTTCTCAG 59.565 37.037 0.00 0.00 38.12 3.35
320 321 7.093727 TGGTTTTGTTACCAACTTCATTTCTCA 60.094 33.333 0.00 0.00 44.97 3.27
321 322 7.262048 TGGTTTTGTTACCAACTTCATTTCTC 58.738 34.615 0.00 0.00 44.97 2.87
322 323 7.176589 TGGTTTTGTTACCAACTTCATTTCT 57.823 32.000 0.00 0.00 44.97 2.52
334 335 3.554129 GGTTCTGCCATGGTTTTGTTACC 60.554 47.826 14.67 8.44 36.58 2.85
335 336 3.068873 TGGTTCTGCCATGGTTTTGTTAC 59.931 43.478 14.67 3.07 43.61 2.50
336 337 3.300388 TGGTTCTGCCATGGTTTTGTTA 58.700 40.909 14.67 0.00 43.61 2.41
337 338 2.114616 TGGTTCTGCCATGGTTTTGTT 58.885 42.857 14.67 0.00 43.61 2.83
349 350 3.859386 CCGCTTATTTGATTTGGTTCTGC 59.141 43.478 0.00 0.00 0.00 4.26
350 351 5.059404 ACCGCTTATTTGATTTGGTTCTG 57.941 39.130 0.00 0.00 0.00 3.02
352 353 5.120053 CCAAACCGCTTATTTGATTTGGTTC 59.880 40.000 5.56 0.00 40.67 3.62
353 354 4.994217 CCAAACCGCTTATTTGATTTGGTT 59.006 37.500 5.56 0.00 40.67 3.67
354 355 4.565022 CCAAACCGCTTATTTGATTTGGT 58.435 39.130 5.56 0.00 40.67 3.67
355 356 3.370672 GCCAAACCGCTTATTTGATTTGG 59.629 43.478 8.80 8.80 45.76 3.28
356 357 3.993081 TGCCAAACCGCTTATTTGATTTG 59.007 39.130 5.93 0.00 39.01 2.32
357 358 4.244862 CTGCCAAACCGCTTATTTGATTT 58.755 39.130 5.93 0.00 39.01 2.17
358 359 3.368323 CCTGCCAAACCGCTTATTTGATT 60.368 43.478 5.93 0.00 39.01 2.57
359 360 2.166254 CCTGCCAAACCGCTTATTTGAT 59.834 45.455 5.93 0.00 39.01 2.57
361 362 1.272212 ACCTGCCAAACCGCTTATTTG 59.728 47.619 0.00 0.00 36.90 2.32
362 363 1.627864 ACCTGCCAAACCGCTTATTT 58.372 45.000 0.00 0.00 0.00 1.40
363 364 1.272212 CAACCTGCCAAACCGCTTATT 59.728 47.619 0.00 0.00 0.00 1.40
365 366 1.175983 CCAACCTGCCAAACCGCTTA 61.176 55.000 0.00 0.00 0.00 3.09
366 367 2.498056 CCAACCTGCCAAACCGCTT 61.498 57.895 0.00 0.00 0.00 4.68
368 369 4.662961 GCCAACCTGCCAAACCGC 62.663 66.667 0.00 0.00 0.00 5.68
369 370 2.098426 AATGCCAACCTGCCAAACCG 62.098 55.000 0.00 0.00 0.00 4.44
370 371 0.320683 GAATGCCAACCTGCCAAACC 60.321 55.000 0.00 0.00 0.00 3.27
371 372 0.681175 AGAATGCCAACCTGCCAAAC 59.319 50.000 0.00 0.00 0.00 2.93
372 373 1.070445 CAAGAATGCCAACCTGCCAAA 59.930 47.619 0.00 0.00 0.00 3.28
374 375 0.178967 TCAAGAATGCCAACCTGCCA 60.179 50.000 0.00 0.00 0.00 4.92
375 376 0.529378 CTCAAGAATGCCAACCTGCC 59.471 55.000 0.00 0.00 0.00 4.85
378 379 1.075601 TCCCTCAAGAATGCCAACCT 58.924 50.000 0.00 0.00 0.00 3.50
379 380 1.821136 CTTCCCTCAAGAATGCCAACC 59.179 52.381 0.00 0.00 33.29 3.77
380 381 2.795329 TCTTCCCTCAAGAATGCCAAC 58.205 47.619 0.00 0.00 38.26 3.77
388 389 3.136443 TGCTGAAAGTTCTTCCCTCAAGA 59.864 43.478 0.00 0.00 39.56 3.02
390 391 3.576078 TGCTGAAAGTTCTTCCCTCAA 57.424 42.857 0.00 0.00 35.30 3.02
391 392 3.795688 ATGCTGAAAGTTCTTCCCTCA 57.204 42.857 0.00 0.00 35.30 3.86
392 393 4.331108 AGAATGCTGAAAGTTCTTCCCTC 58.669 43.478 0.00 0.00 35.30 4.30
393 394 4.379302 AGAATGCTGAAAGTTCTTCCCT 57.621 40.909 0.00 0.00 35.30 4.20
395 396 4.321527 CCCAAGAATGCTGAAAGTTCTTCC 60.322 45.833 0.00 0.00 39.46 3.46
396 397 4.802999 CCCAAGAATGCTGAAAGTTCTTC 58.197 43.478 0.00 0.00 39.46 2.87
397 398 3.006217 GCCCAAGAATGCTGAAAGTTCTT 59.994 43.478 0.00 0.00 41.48 2.52
399 400 2.297033 TGCCCAAGAATGCTGAAAGTTC 59.703 45.455 0.00 0.00 35.30 3.01
400 401 2.318908 TGCCCAAGAATGCTGAAAGTT 58.681 42.857 0.00 0.00 35.30 2.66
401 402 1.999648 TGCCCAAGAATGCTGAAAGT 58.000 45.000 0.00 0.00 35.30 2.66
402 403 2.298163 AGTTGCCCAAGAATGCTGAAAG 59.702 45.455 0.00 0.00 0.00 2.62
404 405 1.999648 AGTTGCCCAAGAATGCTGAA 58.000 45.000 0.00 0.00 0.00 3.02
405 406 2.436417 GTAGTTGCCCAAGAATGCTGA 58.564 47.619 0.00 0.00 0.00 4.26
406 407 1.131126 CGTAGTTGCCCAAGAATGCTG 59.869 52.381 0.00 0.00 0.00 4.41
407 408 1.453155 CGTAGTTGCCCAAGAATGCT 58.547 50.000 0.00 0.00 0.00 3.79
409 410 1.821216 ACCGTAGTTGCCCAAGAATG 58.179 50.000 0.00 0.00 0.00 2.67
410 411 2.835764 TCTACCGTAGTTGCCCAAGAAT 59.164 45.455 5.46 0.00 0.00 2.40
412 413 1.927487 TCTACCGTAGTTGCCCAAGA 58.073 50.000 5.46 0.00 0.00 3.02
413 414 2.754946 TTCTACCGTAGTTGCCCAAG 57.245 50.000 5.46 0.00 0.00 3.61
414 415 2.835764 AGATTCTACCGTAGTTGCCCAA 59.164 45.455 5.46 0.00 0.00 4.12
415 416 2.429610 GAGATTCTACCGTAGTTGCCCA 59.570 50.000 5.46 0.00 0.00 5.36
416 417 2.543238 CGAGATTCTACCGTAGTTGCCC 60.543 54.545 5.46 0.00 0.00 5.36
418 419 3.361414 GACGAGATTCTACCGTAGTTGC 58.639 50.000 5.46 0.00 36.60 4.17
419 420 3.243002 GGGACGAGATTCTACCGTAGTTG 60.243 52.174 5.46 0.00 36.60 3.16
422 423 2.848691 AGGGACGAGATTCTACCGTAG 58.151 52.381 0.00 0.00 36.60 3.51
424 425 2.140839 AAGGGACGAGATTCTACCGT 57.859 50.000 0.50 0.50 39.41 4.83
425 426 3.521947 AAAAGGGACGAGATTCTACCG 57.478 47.619 0.00 0.00 0.00 4.02
553 554 7.159322 ACTACTACTGCCAGATTATATTCCG 57.841 40.000 0.00 0.00 0.00 4.30
581 585 4.067192 AGGTGTGTGGTTATTTTCGTACC 58.933 43.478 0.00 0.00 0.00 3.34
583 587 4.922692 CGTAGGTGTGTGGTTATTTTCGTA 59.077 41.667 0.00 0.00 0.00 3.43
584 588 3.742369 CGTAGGTGTGTGGTTATTTTCGT 59.258 43.478 0.00 0.00 0.00 3.85
585 589 3.423907 GCGTAGGTGTGTGGTTATTTTCG 60.424 47.826 0.00 0.00 0.00 3.46
586 590 3.423907 CGCGTAGGTGTGTGGTTATTTTC 60.424 47.826 0.00 0.00 0.00 2.29
587 591 2.481185 CGCGTAGGTGTGTGGTTATTTT 59.519 45.455 0.00 0.00 0.00 1.82
639 643 9.622004 CTGACATTTCCTAATAAATCATGCATC 57.378 33.333 0.00 0.00 0.00 3.91
654 659 3.515602 AGTCTTTGCCTGACATTTCCT 57.484 42.857 0.00 0.00 36.94 3.36
666 671 5.509622 GCATTGTTCGATTCTTAGTCTTTGC 59.490 40.000 0.00 0.00 0.00 3.68
690 695 6.355928 CGATTTCTTTCTCGAGAGACTTATCG 59.644 42.308 23.80 23.80 39.31 2.92
695 700 3.191581 TGCGATTTCTTTCTCGAGAGACT 59.808 43.478 15.94 0.83 37.14 3.24
710 715 5.446741 GGTTATGTGTATCACGTTGCGATTT 60.447 40.000 0.00 0.00 37.14 2.17
814 2991 4.388469 GGCGCTGATCTGAATCTTATCTTC 59.612 45.833 7.64 0.00 32.75 2.87
815 2992 4.314121 GGCGCTGATCTGAATCTTATCTT 58.686 43.478 7.64 0.00 32.75 2.40
886 3065 5.416326 CCTCCTTTTATAGTCGATCCGATCT 59.584 44.000 6.81 0.00 38.42 2.75
930 3109 3.384168 AGCTAAGGTGATGGATGGTGTA 58.616 45.455 0.00 0.00 0.00 2.90
1314 3511 1.676529 TCAGTAGGTCGAGCATAGCAC 59.323 52.381 18.15 6.33 0.00 4.40
1326 3523 7.736893 ACTTGAGTAGTTTTCATTCAGTAGGT 58.263 34.615 0.00 0.00 31.29 3.08
1374 3822 1.337071 ACCATATCACACGACGCTAGG 59.663 52.381 0.00 0.00 0.00 3.02
1398 3847 1.200948 GGAGAAGTTGGCATGTCAAGC 59.799 52.381 14.22 8.64 0.00 4.01
1444 3893 4.696899 AGTGGCGAACCTTTAATTAAGC 57.303 40.909 0.00 0.00 36.63 3.09
1452 3901 1.271379 ACTGCATAGTGGCGAACCTTT 60.271 47.619 0.00 0.00 35.34 3.11
1497 3946 2.354003 GGGGCACAACATCAAATTCCAG 60.354 50.000 0.00 0.00 0.00 3.86
1537 3986 1.263356 AGAATTCGGACAGAACGGGA 58.737 50.000 0.00 0.00 42.39 5.14
1544 3993 4.430007 TCAAACGGATAGAATTCGGACAG 58.570 43.478 0.00 0.00 0.00 3.51
1549 3998 4.026475 GCTGACTCAAACGGATAGAATTCG 60.026 45.833 0.00 0.00 0.00 3.34
1551 4000 4.192317 GGCTGACTCAAACGGATAGAATT 58.808 43.478 0.00 0.00 0.00 2.17
1559 4008 1.001378 CCTTTTGGCTGACTCAAACGG 60.001 52.381 0.00 0.00 37.24 4.44
1560 4009 1.001378 CCCTTTTGGCTGACTCAAACG 60.001 52.381 0.00 0.00 38.58 3.60
1562 4011 2.306847 GTCCCTTTTGGCTGACTCAAA 58.693 47.619 0.00 0.00 38.58 2.69
1563 4012 1.813862 CGTCCCTTTTGGCTGACTCAA 60.814 52.381 0.00 0.00 38.58 3.02
1565 4014 1.578206 GCGTCCCTTTTGGCTGACTC 61.578 60.000 0.00 0.00 38.58 3.36
1568 4017 2.282180 GGCGTCCCTTTTGGCTGA 60.282 61.111 0.00 0.00 38.58 4.26
1570 4019 4.265056 ACGGCGTCCCTTTTGGCT 62.265 61.111 6.77 0.00 38.58 4.75
1571 4020 3.733960 GACGGCGTCCCTTTTGGC 61.734 66.667 28.72 0.73 38.58 4.52
1572 4021 3.053896 GGACGGCGTCCCTTTTGG 61.054 66.667 41.63 0.00 46.19 3.28
1581 4030 3.745803 GAAGAGGTCGGACGGCGT 61.746 66.667 14.65 14.65 0.00 5.68
1602 4051 2.554272 CGCACTACCCACGCAAAC 59.446 61.111 0.00 0.00 0.00 2.93
1619 4068 2.862674 TACATTTGGTCCGCTCGGCC 62.863 60.000 2.96 8.87 34.68 6.13
1804 4253 1.074775 GACTCACCATGGCCACCAA 59.925 57.895 8.16 0.00 36.95 3.67
1805 4254 2.756400 GACTCACCATGGCCACCA 59.244 61.111 8.16 0.00 38.19 4.17
1884 4333 8.515414 GGGCAATTATGTTATCTTTGGTAGATC 58.485 37.037 0.00 0.00 42.69 2.75
1890 4339 6.469782 ACAGGGCAATTATGTTATCTTTGG 57.530 37.500 0.00 0.00 0.00 3.28
1920 4369 6.183360 CGCTCGATTTTTACCTGATATAGCTG 60.183 42.308 0.00 0.00 0.00 4.24
1996 4445 2.356535 CCCTCTGATCCCAGGACAAAAG 60.357 54.545 8.37 0.00 40.76 2.27
2000 4449 0.417437 TTCCCTCTGATCCCAGGACA 59.583 55.000 8.37 0.00 40.76 4.02
2065 4514 0.378962 CGCTCCACTCTCCTTACTCG 59.621 60.000 0.00 0.00 0.00 4.18
2084 4533 7.459234 AGGCCACTAACACTAATATATTTCCC 58.541 38.462 5.01 0.00 0.00 3.97
2126 4575 2.967362 TCTTGTATAGTGGTTGGTGCG 58.033 47.619 0.00 0.00 0.00 5.34
2142 4591 1.268692 GCACACACACACACCATCTTG 60.269 52.381 0.00 0.00 0.00 3.02
2144 4593 1.159713 CGCACACACACACACCATCT 61.160 55.000 0.00 0.00 0.00 2.90
2162 4611 3.490759 ACCTGCTCAAATCGCGCG 61.491 61.111 26.76 26.76 0.00 6.86
2163 4612 2.099062 CACCTGCTCAAATCGCGC 59.901 61.111 0.00 0.00 0.00 6.86
2164 4613 2.787249 CCACCTGCTCAAATCGCG 59.213 61.111 0.00 0.00 0.00 5.87
2165 4614 2.486966 GCCACCTGCTCAAATCGC 59.513 61.111 0.00 0.00 36.87 4.58
2166 4615 1.243342 TTGGCCACCTGCTCAAATCG 61.243 55.000 3.88 0.00 40.92 3.34
2167 4616 0.968405 TTTGGCCACCTGCTCAAATC 59.032 50.000 3.88 0.00 40.92 2.17
2175 4624 3.967332 AAAATCATCTTTGGCCACCTG 57.033 42.857 3.88 0.05 0.00 4.00
2242 4691 1.610522 ACCAAGCAACAAGAGCATGTC 59.389 47.619 0.00 0.00 31.81 3.06


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

AutoCloner maintained by Alex Coulton.