Multiple sequence alignment - TraesCS5D01G310200

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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 TraesCS5D01G310200 chr5D 100.000 3233 0 0 1 3233 406958391 406961623 0.000000e+00 5971
1 TraesCS5D01G310200 chr5D 86.806 1243 150 9 993 2231 429980178 429978946 0.000000e+00 1375
2 TraesCS5D01G310200 chr5D 84.392 551 65 12 1643 2187 402726149 402726684 3.700000e-144 521
3 TraesCS5D01G310200 chr5D 96.498 257 8 1 1 256 406955532 406955276 1.070000e-114 424
4 TraesCS5D01G310200 chr5D 86.207 174 17 6 2310 2476 402727836 402728009 7.130000e-42 182
5 TraesCS5D01G310200 chr5B 92.599 2324 110 25 352 2661 488192020 488189745 0.000000e+00 3282
6 TraesCS5D01G310200 chr5B 90.140 2221 157 30 723 2907 488127150 488124956 0.000000e+00 2832
7 TraesCS5D01G310200 chr5B 86.484 1243 154 10 993 2231 519232646 519231414 0.000000e+00 1352
8 TraesCS5D01G310200 chr5B 87.097 341 41 3 2896 3233 488124902 488124562 1.820000e-102 383
9 TraesCS5D01G310200 chr5B 86.977 215 19 7 2653 2864 488189571 488189363 1.940000e-57 233
10 TraesCS5D01G310200 chr5B 89.928 139 14 0 120 258 380957491 380957353 2.560000e-41 180
11 TraesCS5D01G310200 chr5B 83.217 143 18 5 2334 2476 482190722 482190858 3.390000e-25 126
12 TraesCS5D01G310200 chr5A 93.766 1989 82 23 277 2242 512643391 512641422 0.000000e+00 2948
13 TraesCS5D01G310200 chr5A 87.138 1244 144 11 993 2231 545832552 545831320 0.000000e+00 1397
14 TraesCS5D01G310200 chr5A 88.055 653 65 9 2585 3232 512634169 512633525 0.000000e+00 761
15 TraesCS5D01G310200 chr5A 90.816 196 14 2 2285 2479 512634394 512634202 3.200000e-65 259
16 TraesCS5D01G310200 chr7D 83.082 1259 170 32 998 2233 104740557 104741795 0.000000e+00 1105
17 TraesCS5D01G310200 chr7D 78.906 256 45 9 5 254 403272650 403272398 7.180000e-37 165
18 TraesCS5D01G310200 chr7A 82.456 1254 178 31 998 2233 109236820 109238049 0.000000e+00 1059
19 TraesCS5D01G310200 chr7A 76.923 442 31 34 842 1263 232061617 232062007 5.510000e-43 185
20 TraesCS5D01G310200 chr7B 81.344 1265 184 31 998 2233 63542865 63541624 0.000000e+00 981
21 TraesCS5D01G310200 chr7B 86.914 405 45 3 1828 2225 58245252 58245655 6.360000e-122 448
22 TraesCS5D01G310200 chr7B 91.453 234 18 2 24 255 628346150 628346383 1.450000e-83 320
23 TraesCS5D01G310200 chr7B 82.492 297 35 11 2336 2616 58246971 58247266 8.960000e-61 244
24 TraesCS5D01G310200 chr2A 90.551 254 22 2 1 254 14929270 14929521 5.170000e-88 335
25 TraesCS5D01G310200 chr3A 83.696 184 25 5 76 256 38994051 38993870 5.550000e-38 169
26 TraesCS5D01G310200 chr2B 86.093 151 15 5 107 254 24696786 24696639 1.200000e-34 158
27 TraesCS5D01G310200 chr2B 83.133 166 26 2 90 254 504317561 504317725 2.010000e-32 150
28 TraesCS5D01G310200 chr1D 81.395 172 26 5 90 259 2490967 2491134 5.630000e-28 135


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 TraesCS5D01G310200 chr5D 406958391 406961623 3232 False 5971.0 5971 100.0000 1 3233 1 chr5D.!!$F1 3232
1 TraesCS5D01G310200 chr5D 429978946 429980178 1232 True 1375.0 1375 86.8060 993 2231 1 chr5D.!!$R2 1238
2 TraesCS5D01G310200 chr5D 402726149 402728009 1860 False 351.5 521 85.2995 1643 2476 2 chr5D.!!$F2 833
3 TraesCS5D01G310200 chr5B 488189363 488192020 2657 True 1757.5 3282 89.7880 352 2864 2 chr5B.!!$R4 2512
4 TraesCS5D01G310200 chr5B 488124562 488127150 2588 True 1607.5 2832 88.6185 723 3233 2 chr5B.!!$R3 2510
5 TraesCS5D01G310200 chr5B 519231414 519232646 1232 True 1352.0 1352 86.4840 993 2231 1 chr5B.!!$R2 1238
6 TraesCS5D01G310200 chr5A 512641422 512643391 1969 True 2948.0 2948 93.7660 277 2242 1 chr5A.!!$R1 1965
7 TraesCS5D01G310200 chr5A 545831320 545832552 1232 True 1397.0 1397 87.1380 993 2231 1 chr5A.!!$R2 1238
8 TraesCS5D01G310200 chr5A 512633525 512634394 869 True 510.0 761 89.4355 2285 3232 2 chr5A.!!$R3 947
9 TraesCS5D01G310200 chr7D 104740557 104741795 1238 False 1105.0 1105 83.0820 998 2233 1 chr7D.!!$F1 1235
10 TraesCS5D01G310200 chr7A 109236820 109238049 1229 False 1059.0 1059 82.4560 998 2233 1 chr7A.!!$F1 1235
11 TraesCS5D01G310200 chr7B 63541624 63542865 1241 True 981.0 981 81.3440 998 2233 1 chr7B.!!$R1 1235
12 TraesCS5D01G310200 chr7B 58245252 58247266 2014 False 346.0 448 84.7030 1828 2616 2 chr7B.!!$F2 788

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
172 173 0.104671 TGCTCAAGCCAAGTTTTGCC 59.895 50.0 0.00 0.0 41.18 4.52 F
195 196 0.179200 GGTTCAACGTATGCCGCAAG 60.179 55.0 0.00 0.0 41.42 4.01 F
1006 1043 0.445043 CGTACTCGTCGACATGGTCA 59.555 55.0 17.16 0.0 32.09 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1352 1398 1.739929 TTGGCGTACACGATGCTGG 60.740 57.895 5.84 0.00 43.02 4.85 R
1804 1854 2.665185 GAAGTGCTCCGCCAACGT 60.665 61.111 0.00 0.00 37.70 3.99 R
2282 4643 0.383949 AAAACATGTGTGGCACGTCC 59.616 50.000 13.77 3.98 37.14 4.79 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
33 34 9.495572 AAAATAAAATTCCAAAGTATTTCCGCA 57.504 25.926 0.00 0.00 35.03 5.69
34 35 9.495572 AAATAAAATTCCAAAGTATTTCCGCAA 57.504 25.926 0.00 0.00 35.03 4.85
35 36 9.495572 AATAAAATTCCAAAGTATTTCCGCAAA 57.504 25.926 0.00 0.00 35.03 3.68
36 37 7.793927 AAAATTCCAAAGTATTTCCGCAAAA 57.206 28.000 0.00 0.00 35.03 2.44
37 38 7.793927 AAATTCCAAAGTATTTCCGCAAAAA 57.206 28.000 0.00 0.00 35.03 1.94
59 60 4.626081 GCACACGCCCTCACCTGT 62.626 66.667 0.00 0.00 0.00 4.00
60 61 2.666190 CACACGCCCTCACCTGTG 60.666 66.667 0.00 0.00 38.28 3.66
61 62 4.626081 ACACGCCCTCACCTGTGC 62.626 66.667 0.00 0.00 35.79 4.57
66 67 4.394712 CCCTCACCTGTGCCGTCC 62.395 72.222 0.00 0.00 0.00 4.79
67 68 3.625897 CCTCACCTGTGCCGTCCA 61.626 66.667 0.00 0.00 0.00 4.02
68 69 2.047844 CTCACCTGTGCCGTCCAG 60.048 66.667 0.00 0.00 0.00 3.86
69 70 4.314440 TCACCTGTGCCGTCCAGC 62.314 66.667 0.00 0.00 0.00 4.85
75 76 4.947147 GTGCCGTCCAGCCACCAA 62.947 66.667 0.00 0.00 0.00 3.67
76 77 4.947147 TGCCGTCCAGCCACCAAC 62.947 66.667 0.00 0.00 0.00 3.77
77 78 4.947147 GCCGTCCAGCCACCAACA 62.947 66.667 0.00 0.00 0.00 3.33
78 79 2.669569 CCGTCCAGCCACCAACAG 60.670 66.667 0.00 0.00 0.00 3.16
79 80 2.111043 CGTCCAGCCACCAACAGT 59.889 61.111 0.00 0.00 0.00 3.55
80 81 2.253758 CGTCCAGCCACCAACAGTG 61.254 63.158 0.00 0.00 46.83 3.66
89 90 2.738521 CCAACAGTGGGTCTCGCG 60.739 66.667 0.00 0.00 41.77 5.87
90 91 3.414700 CAACAGTGGGTCTCGCGC 61.415 66.667 0.00 0.00 0.00 6.86
91 92 4.681978 AACAGTGGGTCTCGCGCC 62.682 66.667 0.00 0.00 0.00 6.53
93 94 4.457496 CAGTGGGTCTCGCGCCAT 62.457 66.667 0.00 0.00 0.00 4.40
94 95 4.457496 AGTGGGTCTCGCGCCATG 62.457 66.667 0.00 0.00 0.00 3.66
107 108 3.129502 CCATGCTGGCACACTCCG 61.130 66.667 0.00 0.00 0.00 4.63
108 109 2.359107 CATGCTGGCACACTCCGT 60.359 61.111 0.00 0.00 0.00 4.69
109 110 1.968017 CATGCTGGCACACTCCGTT 60.968 57.895 0.00 0.00 0.00 4.44
110 111 0.673333 CATGCTGGCACACTCCGTTA 60.673 55.000 0.00 0.00 0.00 3.18
111 112 0.391661 ATGCTGGCACACTCCGTTAG 60.392 55.000 0.00 0.00 0.00 2.34
112 113 2.391389 GCTGGCACACTCCGTTAGC 61.391 63.158 0.00 0.00 0.00 3.09
113 114 1.005037 CTGGCACACTCCGTTAGCA 60.005 57.895 0.00 0.00 0.00 3.49
114 115 0.391661 CTGGCACACTCCGTTAGCAT 60.392 55.000 0.00 0.00 0.00 3.79
115 116 0.391130 TGGCACACTCCGTTAGCATC 60.391 55.000 0.00 0.00 0.00 3.91
116 117 0.108138 GGCACACTCCGTTAGCATCT 60.108 55.000 0.00 0.00 0.00 2.90
117 118 1.676014 GGCACACTCCGTTAGCATCTT 60.676 52.381 0.00 0.00 0.00 2.40
118 119 1.394917 GCACACTCCGTTAGCATCTTG 59.605 52.381 0.00 0.00 0.00 3.02
119 120 2.688507 CACACTCCGTTAGCATCTTGT 58.311 47.619 0.00 0.00 0.00 3.16
120 121 2.413112 CACACTCCGTTAGCATCTTGTG 59.587 50.000 0.00 0.00 0.00 3.33
135 136 6.887368 GCATCTTGTGCGTATACAAATATGA 58.113 36.000 17.87 8.59 45.23 2.15
136 137 7.521529 GCATCTTGTGCGTATACAAATATGAT 58.478 34.615 17.87 9.81 45.23 2.45
137 138 8.017373 GCATCTTGTGCGTATACAAATATGATT 58.983 33.333 17.87 0.00 45.23 2.57
140 141 8.708742 TCTTGTGCGTATACAAATATGATTAGC 58.291 33.333 3.32 0.00 39.81 3.09
141 142 7.954788 TGTGCGTATACAAATATGATTAGCA 57.045 32.000 3.32 0.00 0.00 3.49
142 143 7.792925 TGTGCGTATACAAATATGATTAGCAC 58.207 34.615 13.65 13.65 46.82 4.40
143 144 7.655732 TGTGCGTATACAAATATGATTAGCACT 59.344 33.333 18.33 0.00 46.78 4.40
144 145 7.952101 GTGCGTATACAAATATGATTAGCACTG 59.048 37.037 13.40 0.00 44.33 3.66
145 146 7.655732 TGCGTATACAAATATGATTAGCACTGT 59.344 33.333 3.32 0.00 0.00 3.55
146 147 9.135843 GCGTATACAAATATGATTAGCACTGTA 57.864 33.333 3.32 0.00 0.00 2.74
151 152 8.425577 ACAAATATGATTAGCACTGTAGACAC 57.574 34.615 0.00 0.00 0.00 3.67
152 153 8.040727 ACAAATATGATTAGCACTGTAGACACA 58.959 33.333 0.00 0.00 0.00 3.72
153 154 9.049523 CAAATATGATTAGCACTGTAGACACAT 57.950 33.333 0.00 0.00 33.14 3.21
154 155 8.599055 AATATGATTAGCACTGTAGACACATG 57.401 34.615 0.00 0.00 33.14 3.21
155 156 4.183865 TGATTAGCACTGTAGACACATGC 58.816 43.478 0.00 6.17 38.44 4.06
156 157 3.961480 TTAGCACTGTAGACACATGCT 57.039 42.857 16.77 16.77 44.45 3.79
157 158 2.376808 AGCACTGTAGACACATGCTC 57.623 50.000 9.78 0.00 41.53 4.26
158 159 1.620323 AGCACTGTAGACACATGCTCA 59.380 47.619 9.78 0.00 41.53 4.26
159 160 2.037641 AGCACTGTAGACACATGCTCAA 59.962 45.455 9.78 0.00 41.53 3.02
160 161 2.414481 GCACTGTAGACACATGCTCAAG 59.586 50.000 0.00 0.00 36.79 3.02
161 162 2.414481 CACTGTAGACACATGCTCAAGC 59.586 50.000 0.00 0.00 42.50 4.01
162 163 2.005451 CTGTAGACACATGCTCAAGCC 58.995 52.381 0.00 0.00 41.18 4.35
163 164 1.347378 TGTAGACACATGCTCAAGCCA 59.653 47.619 0.00 0.00 41.18 4.75
164 165 2.224499 TGTAGACACATGCTCAAGCCAA 60.224 45.455 0.00 0.00 41.18 4.52
165 166 1.531423 AGACACATGCTCAAGCCAAG 58.469 50.000 0.00 0.00 41.18 3.61
166 167 1.202855 AGACACATGCTCAAGCCAAGT 60.203 47.619 0.00 0.00 41.18 3.16
167 168 1.610522 GACACATGCTCAAGCCAAGTT 59.389 47.619 0.00 0.00 41.18 2.66
168 169 2.034124 ACACATGCTCAAGCCAAGTTT 58.966 42.857 0.00 0.00 41.18 2.66
169 170 2.431782 ACACATGCTCAAGCCAAGTTTT 59.568 40.909 0.00 0.00 41.18 2.43
170 171 2.798283 CACATGCTCAAGCCAAGTTTTG 59.202 45.455 0.00 0.00 41.18 2.44
171 172 1.796459 CATGCTCAAGCCAAGTTTTGC 59.204 47.619 0.00 0.00 41.18 3.68
172 173 0.104671 TGCTCAAGCCAAGTTTTGCC 59.895 50.000 0.00 0.00 41.18 4.52
173 174 0.104671 GCTCAAGCCAAGTTTTGCCA 59.895 50.000 0.00 0.00 34.31 4.92
174 175 1.270465 GCTCAAGCCAAGTTTTGCCAT 60.270 47.619 0.00 0.00 34.31 4.40
175 176 2.807837 GCTCAAGCCAAGTTTTGCCATT 60.808 45.455 0.00 0.00 34.31 3.16
176 177 2.803956 CTCAAGCCAAGTTTTGCCATTG 59.196 45.455 0.00 0.00 0.00 2.82
177 178 1.874872 CAAGCCAAGTTTTGCCATTGG 59.125 47.619 0.00 0.00 45.16 3.16
178 179 1.130777 AGCCAAGTTTTGCCATTGGT 58.869 45.000 4.26 0.00 44.38 3.67
179 180 1.490069 AGCCAAGTTTTGCCATTGGTT 59.510 42.857 4.26 0.00 44.38 3.67
180 181 1.872952 GCCAAGTTTTGCCATTGGTTC 59.127 47.619 4.26 0.00 44.38 3.62
181 182 2.744494 GCCAAGTTTTGCCATTGGTTCA 60.744 45.455 4.26 0.00 44.38 3.18
182 183 3.539604 CCAAGTTTTGCCATTGGTTCAA 58.460 40.909 4.26 0.00 38.92 2.69
183 184 3.312146 CCAAGTTTTGCCATTGGTTCAAC 59.688 43.478 4.26 4.95 38.92 3.18
184 185 2.820330 AGTTTTGCCATTGGTTCAACG 58.180 42.857 4.26 0.00 0.00 4.10
185 186 2.167487 AGTTTTGCCATTGGTTCAACGT 59.833 40.909 4.26 0.00 0.00 3.99
186 187 3.381908 AGTTTTGCCATTGGTTCAACGTA 59.618 39.130 4.26 0.00 0.00 3.57
187 188 4.038642 AGTTTTGCCATTGGTTCAACGTAT 59.961 37.500 4.26 0.00 0.00 3.06
188 189 3.567576 TTGCCATTGGTTCAACGTATG 57.432 42.857 4.26 0.00 0.00 2.39
189 190 1.201181 TGCCATTGGTTCAACGTATGC 59.799 47.619 4.26 0.00 0.00 3.14
190 191 1.469079 GCCATTGGTTCAACGTATGCC 60.469 52.381 4.26 0.00 0.00 4.40
191 192 1.202132 CCATTGGTTCAACGTATGCCG 60.202 52.381 0.00 0.00 44.03 5.69
192 193 0.450184 ATTGGTTCAACGTATGCCGC 59.550 50.000 0.00 0.00 41.42 6.53
193 194 0.885150 TTGGTTCAACGTATGCCGCA 60.885 50.000 0.00 0.00 41.42 5.69
194 195 0.885150 TGGTTCAACGTATGCCGCAA 60.885 50.000 0.00 0.00 41.42 4.85
195 196 0.179200 GGTTCAACGTATGCCGCAAG 60.179 55.000 0.00 0.00 41.42 4.01
196 197 0.515564 GTTCAACGTATGCCGCAAGT 59.484 50.000 0.00 0.00 41.42 3.16
197 198 1.069500 GTTCAACGTATGCCGCAAGTT 60.069 47.619 0.00 1.71 41.42 2.66
198 199 1.231221 TCAACGTATGCCGCAAGTTT 58.769 45.000 0.00 0.00 41.42 2.66
199 200 1.604755 TCAACGTATGCCGCAAGTTTT 59.395 42.857 0.00 0.00 41.42 2.43
200 201 2.806818 TCAACGTATGCCGCAAGTTTTA 59.193 40.909 0.00 0.00 41.42 1.52
201 202 3.120477 TCAACGTATGCCGCAAGTTTTAG 60.120 43.478 0.00 0.00 41.42 1.85
202 203 1.129811 ACGTATGCCGCAAGTTTTAGC 59.870 47.619 0.00 0.00 41.42 3.09
203 204 1.129624 CGTATGCCGCAAGTTTTAGCA 59.870 47.619 0.00 0.00 37.94 3.49
204 205 2.223249 CGTATGCCGCAAGTTTTAGCAT 60.223 45.455 0.00 8.01 45.58 3.79
205 206 2.566952 ATGCCGCAAGTTTTAGCATC 57.433 45.000 0.00 0.00 39.95 3.91
206 207 1.242989 TGCCGCAAGTTTTAGCATCA 58.757 45.000 0.00 0.00 0.00 3.07
207 208 1.611006 TGCCGCAAGTTTTAGCATCAA 59.389 42.857 0.00 0.00 0.00 2.57
208 209 2.035193 TGCCGCAAGTTTTAGCATCAAA 59.965 40.909 0.00 0.00 0.00 2.69
209 210 2.408368 GCCGCAAGTTTTAGCATCAAAC 59.592 45.455 0.00 0.00 34.80 2.93
210 211 3.857010 GCCGCAAGTTTTAGCATCAAACT 60.857 43.478 2.91 2.91 44.67 2.66
211 212 3.670055 CCGCAAGTTTTAGCATCAAACTG 59.330 43.478 8.26 5.25 42.47 3.16
212 213 4.536065 CGCAAGTTTTAGCATCAAACTGA 58.464 39.130 8.26 0.00 42.47 3.41
213 214 4.379793 CGCAAGTTTTAGCATCAAACTGAC 59.620 41.667 8.26 4.28 42.47 3.51
214 215 5.523369 GCAAGTTTTAGCATCAAACTGACT 58.477 37.500 8.26 0.00 42.47 3.41
215 216 5.979517 GCAAGTTTTAGCATCAAACTGACTT 59.020 36.000 8.26 0.53 42.47 3.01
216 217 6.476706 GCAAGTTTTAGCATCAAACTGACTTT 59.523 34.615 8.26 0.00 42.47 2.66
217 218 7.010460 GCAAGTTTTAGCATCAAACTGACTTTT 59.990 33.333 8.26 0.00 42.47 2.27
218 219 8.534778 CAAGTTTTAGCATCAAACTGACTTTTC 58.465 33.333 8.26 0.00 42.47 2.29
219 220 8.000780 AGTTTTAGCATCAAACTGACTTTTCT 57.999 30.769 7.03 0.00 41.86 2.52
220 221 8.131731 AGTTTTAGCATCAAACTGACTTTTCTC 58.868 33.333 7.03 0.00 41.86 2.87
221 222 4.739046 AGCATCAAACTGACTTTTCTCG 57.261 40.909 0.00 0.00 0.00 4.04
222 223 3.058639 AGCATCAAACTGACTTTTCTCGC 60.059 43.478 0.00 0.00 0.00 5.03
223 224 3.814945 CATCAAACTGACTTTTCTCGCC 58.185 45.455 0.00 0.00 0.00 5.54
224 225 2.912771 TCAAACTGACTTTTCTCGCCA 58.087 42.857 0.00 0.00 0.00 5.69
225 226 3.275143 TCAAACTGACTTTTCTCGCCAA 58.725 40.909 0.00 0.00 0.00 4.52
226 227 3.312421 TCAAACTGACTTTTCTCGCCAAG 59.688 43.478 0.00 0.00 0.00 3.61
227 228 2.622064 ACTGACTTTTCTCGCCAAGT 57.378 45.000 0.00 0.00 35.88 3.16
228 229 2.919228 ACTGACTTTTCTCGCCAAGTT 58.081 42.857 0.00 0.00 33.22 2.66
229 230 2.872858 ACTGACTTTTCTCGCCAAGTTC 59.127 45.455 0.00 0.00 33.22 3.01
230 231 2.872245 CTGACTTTTCTCGCCAAGTTCA 59.128 45.455 0.00 0.00 33.22 3.18
231 232 3.275143 TGACTTTTCTCGCCAAGTTCAA 58.725 40.909 0.00 0.00 33.22 2.69
232 233 3.882888 TGACTTTTCTCGCCAAGTTCAAT 59.117 39.130 0.00 0.00 33.22 2.57
233 234 4.024048 TGACTTTTCTCGCCAAGTTCAATC 60.024 41.667 0.00 0.00 33.22 2.67
234 235 3.882888 ACTTTTCTCGCCAAGTTCAATCA 59.117 39.130 0.00 0.00 28.27 2.57
235 236 3.896648 TTTCTCGCCAAGTTCAATCAC 57.103 42.857 0.00 0.00 0.00 3.06
236 237 1.808411 TCTCGCCAAGTTCAATCACC 58.192 50.000 0.00 0.00 0.00 4.02
237 238 1.347707 TCTCGCCAAGTTCAATCACCT 59.652 47.619 0.00 0.00 0.00 4.00
238 239 1.466167 CTCGCCAAGTTCAATCACCTG 59.534 52.381 0.00 0.00 0.00 4.00
239 240 1.202758 TCGCCAAGTTCAATCACCTGT 60.203 47.619 0.00 0.00 0.00 4.00
240 241 1.069022 CGCCAAGTTCAATCACCTGTG 60.069 52.381 0.00 0.00 0.00 3.66
241 242 1.270550 GCCAAGTTCAATCACCTGTGG 59.729 52.381 0.00 0.00 0.00 4.17
242 243 2.586425 CCAAGTTCAATCACCTGTGGT 58.414 47.619 0.00 0.00 35.62 4.16
257 258 6.374417 ACCTGTGGTGTAATTGACTCTATT 57.626 37.500 0.00 0.00 32.98 1.73
258 259 6.407202 ACCTGTGGTGTAATTGACTCTATTC 58.593 40.000 0.00 0.00 32.98 1.75
259 260 5.520288 CCTGTGGTGTAATTGACTCTATTCG 59.480 44.000 0.00 0.00 0.00 3.34
260 261 6.275494 TGTGGTGTAATTGACTCTATTCGA 57.725 37.500 0.00 0.00 0.00 3.71
261 262 6.693466 TGTGGTGTAATTGACTCTATTCGAA 58.307 36.000 0.00 0.00 0.00 3.71
262 263 7.156000 TGTGGTGTAATTGACTCTATTCGAAA 58.844 34.615 0.00 0.00 0.00 3.46
263 264 7.658167 TGTGGTGTAATTGACTCTATTCGAAAA 59.342 33.333 0.00 0.00 0.00 2.29
264 265 8.169268 GTGGTGTAATTGACTCTATTCGAAAAG 58.831 37.037 0.00 2.90 0.00 2.27
265 266 7.333423 TGGTGTAATTGACTCTATTCGAAAAGG 59.667 37.037 0.00 0.00 0.00 3.11
266 267 7.548075 GGTGTAATTGACTCTATTCGAAAAGGA 59.452 37.037 0.00 0.00 0.00 3.36
267 268 8.596380 GTGTAATTGACTCTATTCGAAAAGGAG 58.404 37.037 17.71 17.71 0.00 3.69
268 269 7.764443 TGTAATTGACTCTATTCGAAAAGGAGG 59.236 37.037 21.01 7.24 0.00 4.30
269 270 5.995565 TTGACTCTATTCGAAAAGGAGGA 57.004 39.130 21.01 10.46 0.00 3.71
270 271 5.584253 TGACTCTATTCGAAAAGGAGGAG 57.416 43.478 21.01 15.23 0.00 3.69
271 272 5.017490 TGACTCTATTCGAAAAGGAGGAGT 58.983 41.667 21.01 17.33 35.83 3.85
272 273 6.185511 TGACTCTATTCGAAAAGGAGGAGTA 58.814 40.000 21.01 8.47 33.72 2.59
273 274 6.834451 TGACTCTATTCGAAAAGGAGGAGTAT 59.166 38.462 21.01 7.36 33.72 2.12
274 275 7.997223 TGACTCTATTCGAAAAGGAGGAGTATA 59.003 37.037 21.01 10.93 33.72 1.47
275 276 8.168790 ACTCTATTCGAAAAGGAGGAGTATAC 57.831 38.462 21.01 0.00 32.12 1.47
276 277 7.231115 ACTCTATTCGAAAAGGAGGAGTATACC 59.769 40.741 21.01 0.00 32.12 2.73
277 278 5.548181 ATTCGAAAAGGAGGAGTATACCC 57.452 43.478 0.00 0.73 0.00 3.69
278 279 3.985127 TCGAAAAGGAGGAGTATACCCA 58.015 45.455 11.53 0.00 0.00 4.51
279 280 3.703052 TCGAAAAGGAGGAGTATACCCAC 59.297 47.826 11.53 6.31 0.00 4.61
280 281 3.449737 CGAAAAGGAGGAGTATACCCACA 59.550 47.826 11.53 0.00 0.00 4.17
281 282 4.081309 CGAAAAGGAGGAGTATACCCACAA 60.081 45.833 11.53 0.00 0.00 3.33
282 283 5.570034 CGAAAAGGAGGAGTATACCCACAAA 60.570 44.000 11.53 0.00 0.00 2.83
283 284 5.853572 AAAGGAGGAGTATACCCACAAAA 57.146 39.130 11.53 0.00 0.00 2.44
284 285 6.402981 AAAGGAGGAGTATACCCACAAAAT 57.597 37.500 11.53 0.00 0.00 1.82
301 302 9.632807 CCCACAAAATCATTTATTAACGAGAAA 57.367 29.630 0.00 0.00 0.00 2.52
325 326 7.989416 ACGAGTATCCAAGTTCCAAATAAAA 57.011 32.000 0.00 0.00 0.00 1.52
337 338 7.602753 AGTTCCAAATAAAAGATCCGGAAAAG 58.397 34.615 9.01 0.00 33.13 2.27
338 339 6.524101 TCCAAATAAAAGATCCGGAAAAGG 57.476 37.500 9.01 0.00 0.00 3.11
341 342 7.338449 TCCAAATAAAAGATCCGGAAAAGGTAG 59.662 37.037 9.01 0.00 0.00 3.18
460 479 3.055819 TGGAAAAGACGAGATGCTAGCTT 60.056 43.478 17.23 9.95 0.00 3.74
489 508 9.581099 GTGTTTTTATAGTGGTTGGAATTATGG 57.419 33.333 0.00 0.00 0.00 2.74
490 509 9.315363 TGTTTTTATAGTGGTTGGAATTATGGT 57.685 29.630 0.00 0.00 0.00 3.55
491 510 9.581099 GTTTTTATAGTGGTTGGAATTATGGTG 57.419 33.333 0.00 0.00 0.00 4.17
492 511 6.952773 TTATAGTGGTTGGAATTATGGTGC 57.047 37.500 0.00 0.00 0.00 5.01
493 512 3.168035 AGTGGTTGGAATTATGGTGCA 57.832 42.857 0.00 0.00 0.00 4.57
494 513 3.711863 AGTGGTTGGAATTATGGTGCAT 58.288 40.909 0.00 0.00 0.00 3.96
495 514 3.448301 AGTGGTTGGAATTATGGTGCATG 59.552 43.478 0.00 0.00 0.00 4.06
496 515 3.195396 GTGGTTGGAATTATGGTGCATGT 59.805 43.478 0.00 0.00 0.00 3.21
497 516 4.400884 GTGGTTGGAATTATGGTGCATGTA 59.599 41.667 0.00 0.00 0.00 2.29
498 517 4.400884 TGGTTGGAATTATGGTGCATGTAC 59.599 41.667 5.22 5.22 0.00 2.90
499 518 4.497340 GGTTGGAATTATGGTGCATGTACG 60.497 45.833 7.89 0.00 0.00 3.67
500 519 3.210227 TGGAATTATGGTGCATGTACGG 58.790 45.455 7.89 0.00 0.00 4.02
520 539 1.001597 GATGTACCTACTCCCGCTTCG 60.002 57.143 0.00 0.00 0.00 3.79
613 637 4.457466 CTCTCTCTGTTCTCTACCTACCC 58.543 52.174 0.00 0.00 0.00 3.69
801 829 4.095483 AGGCAACAGAATTAAGCATTCGAG 59.905 41.667 0.00 0.00 45.53 4.04
834 863 1.202463 CGACCTCCTCGATCTGCATTT 60.202 52.381 0.00 0.00 46.14 2.32
849 878 1.331756 GCATTTGGCATCGGTAGTCAG 59.668 52.381 0.00 0.00 43.97 3.51
873 902 4.787293 TTGCTCGATCGCGCCGAA 62.787 61.111 25.71 12.64 39.99 4.30
911 940 5.975282 ACCTTAAGTTAGCAAGCTAGGTAC 58.025 41.667 9.57 2.89 0.00 3.34
990 1027 2.317689 GATCGCGTCGTCGTCGTA 59.682 61.111 5.77 3.11 39.49 3.43
991 1028 1.990598 GATCGCGTCGTCGTCGTAC 60.991 63.158 5.77 0.00 39.49 3.67
1006 1043 0.445043 CGTACTCGTCGACATGGTCA 59.555 55.000 17.16 0.00 32.09 4.02
1329 1372 2.042843 AGGGAGATCGAGGCCGTT 60.043 61.111 0.00 0.00 37.05 4.44
1663 1709 2.048877 CCCGCACCGACGTTTACT 60.049 61.111 0.00 0.00 0.00 2.24
2468 4867 8.081517 AGGAAATGGCATGATCTGAATAAAAA 57.918 30.769 0.00 0.00 0.00 1.94
2500 4900 4.428209 CTGACCAAGCTCAGTGTATACAG 58.572 47.826 5.62 0.00 34.10 2.74
2518 4918 9.725019 TGTATACAGAAATCCATATAGCTTTGG 57.275 33.333 0.08 0.00 0.00 3.28
2593 4997 4.417437 ACCCAACTAAGAGCAAGTAGAGA 58.583 43.478 0.00 0.00 0.00 3.10
2632 5037 4.776322 TCATCCGGTGCAAGCCCG 62.776 66.667 7.24 7.24 45.07 6.13
2647 5052 4.084589 GCAAGCCCGTTGAAAGTTAAATTG 60.085 41.667 0.00 0.00 38.60 2.32
2713 5303 6.363577 ACCAAGCTCATTGTCAATAATACG 57.636 37.500 0.00 0.00 37.17 3.06
2721 5311 7.386299 GCTCATTGTCAATAATACGAAGATCCT 59.614 37.037 0.00 0.00 0.00 3.24
2729 5320 8.572185 TCAATAATACGAAGATCCTTCTCTCAG 58.428 37.037 5.34 0.00 0.00 3.35
2740 5331 3.072915 TCCTTCTCTCAGAACATGGCAAA 59.927 43.478 0.00 0.00 29.89 3.68
2757 5348 3.264104 GCAAATTGGCAAGTGCACATAT 58.736 40.909 25.44 1.26 44.36 1.78
2758 5349 4.431809 GCAAATTGGCAAGTGCACATATA 58.568 39.130 25.44 0.00 44.36 0.86
2759 5350 5.051816 GCAAATTGGCAAGTGCACATATAT 58.948 37.500 25.44 1.54 44.36 0.86
2760 5351 6.215121 GCAAATTGGCAAGTGCACATATATA 58.785 36.000 25.44 0.04 44.36 0.86
2761 5352 6.364165 GCAAATTGGCAAGTGCACATATATAG 59.636 38.462 25.44 1.36 44.36 1.31
2795 5386 5.830912 TGAATAATTAAGCTGGAAATGGCG 58.169 37.500 0.00 0.00 0.00 5.69
2800 5391 1.098050 AAGCTGGAAATGGCGTGATC 58.902 50.000 0.00 0.00 0.00 2.92
2810 5401 1.948104 TGGCGTGATCCGGATAAAAG 58.052 50.000 19.15 12.24 36.94 2.27
2823 5414 7.540474 TCCGGATAAAAGTAGCATCTAAGAT 57.460 36.000 0.00 0.00 0.00 2.40
2824 5415 8.645814 TCCGGATAAAAGTAGCATCTAAGATA 57.354 34.615 0.00 0.00 0.00 1.98
2839 5431 6.753913 TCTAAGATATGGACCAAGCTCATT 57.246 37.500 0.00 0.00 0.00 2.57
2852 5444 4.701651 CCAAGCTCATTGTCAATAGGTCAA 59.298 41.667 0.00 0.00 37.17 3.18
2873 5465 7.955864 GGTCAAACATAAAACTAGCTAAGAACG 59.044 37.037 0.00 0.00 0.00 3.95
2882 5474 7.492352 AAACTAGCTAAGAACGTCACAAAAT 57.508 32.000 0.00 0.00 0.00 1.82
2891 5483 6.202516 AGAACGTCACAAAATTGGAAAGAA 57.797 33.333 0.00 0.00 0.00 2.52
2996 5656 2.758423 GTTGATATGTTGGGTTGGGTCC 59.242 50.000 0.00 0.00 0.00 4.46
2999 5659 0.039035 TATGTTGGGTTGGGTCCAGC 59.961 55.000 0.00 0.00 35.48 4.85
3008 5668 2.040606 GGGTCCAGCCTACCAGGA 59.959 66.667 0.00 0.00 37.67 3.86
3013 5673 1.762460 CCAGCCTACCAGGACCGAT 60.762 63.158 0.00 0.00 37.67 4.18
3020 5680 3.028850 CCTACCAGGACCGATGAGTTTA 58.971 50.000 0.00 0.00 37.67 2.01
3068 5729 9.277783 GTATAGTAGTCTAAACGATTACCTCCA 57.722 37.037 0.00 0.00 35.95 3.86
3073 5734 9.623350 GTAGTCTAAACGATTACCTCCATTATC 57.377 37.037 0.00 0.00 30.86 1.75
3098 5759 2.827755 TCAGTAGTATGGTTGGCAGGA 58.172 47.619 0.00 0.00 0.00 3.86
3112 5773 1.708993 GCAGGACCATCCAGGCCATA 61.709 60.000 5.01 0.00 43.14 2.74
3162 5823 4.015872 TCTTAATGTGGCTTTTCCTCGT 57.984 40.909 0.00 0.00 35.26 4.18
3163 5824 4.394729 TCTTAATGTGGCTTTTCCTCGTT 58.605 39.130 0.00 0.00 39.91 3.85
3181 5842 4.806330 TCGTTCTTGGTCTACTTGATGTC 58.194 43.478 0.00 0.00 0.00 3.06
3182 5843 4.279922 TCGTTCTTGGTCTACTTGATGTCA 59.720 41.667 0.00 0.00 0.00 3.58
3204 5865 1.061579 AGGGGAGGTGGGGTAACTATC 60.062 57.143 0.00 0.00 0.00 2.08
3211 5872 4.015084 AGGTGGGGTAACTATCGATATCG 58.985 47.826 19.14 19.14 41.45 2.92
3212 5873 3.129988 GGTGGGGTAACTATCGATATCGG 59.870 52.174 24.12 11.37 40.29 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 9.495572 TTGCGGAAATACTTTGGAATTTTATTT 57.504 25.926 0.00 0.00 0.00 1.40
10 11 9.495572 TTTTGCGGAAATACTTTGGAATTTTAT 57.504 25.926 1.94 0.00 0.00 1.40
11 12 8.888579 TTTTGCGGAAATACTTTGGAATTTTA 57.111 26.923 1.94 0.00 0.00 1.52
12 13 7.793927 TTTTGCGGAAATACTTTGGAATTTT 57.206 28.000 1.94 0.00 0.00 1.82
13 14 7.793927 TTTTTGCGGAAATACTTTGGAATTT 57.206 28.000 1.94 0.00 0.00 1.82
42 43 4.626081 ACAGGTGAGGGCGTGTGC 62.626 66.667 0.00 0.00 36.32 4.57
43 44 2.666190 CACAGGTGAGGGCGTGTG 60.666 66.667 4.85 4.85 44.84 3.82
44 45 4.626081 GCACAGGTGAGGGCGTGT 62.626 66.667 3.10 0.00 37.89 4.49
49 50 4.394712 GGACGGCACAGGTGAGGG 62.395 72.222 3.10 0.00 0.00 4.30
50 51 3.596066 CTGGACGGCACAGGTGAGG 62.596 68.421 3.10 0.00 32.38 3.86
51 52 2.047844 CTGGACGGCACAGGTGAG 60.048 66.667 3.10 0.00 32.38 3.51
52 53 4.314440 GCTGGACGGCACAGGTGA 62.314 66.667 3.10 0.00 36.48 4.02
60 61 4.947147 TGTTGGTGGCTGGACGGC 62.947 66.667 0.00 0.00 38.97 5.68
61 62 2.669569 CTGTTGGTGGCTGGACGG 60.670 66.667 0.00 0.00 0.00 4.79
62 63 2.111043 ACTGTTGGTGGCTGGACG 59.889 61.111 0.00 0.00 0.00 4.79
63 64 3.749981 CACTGTTGGTGGCTGGAC 58.250 61.111 0.00 0.00 41.90 4.02
70 71 1.961277 GCGAGACCCACTGTTGGTG 60.961 63.158 8.47 0.00 42.10 4.17
71 72 2.426023 GCGAGACCCACTGTTGGT 59.574 61.111 2.77 2.77 42.10 3.67
72 73 2.738521 CGCGAGACCCACTGTTGG 60.739 66.667 0.00 0.00 43.50 3.77
73 74 3.414700 GCGCGAGACCCACTGTTG 61.415 66.667 12.10 0.00 0.00 3.33
74 75 4.681978 GGCGCGAGACCCACTGTT 62.682 66.667 12.10 0.00 0.00 3.16
76 77 4.457496 ATGGCGCGAGACCCACTG 62.457 66.667 12.10 0.00 39.67 3.66
77 78 4.457496 CATGGCGCGAGACCCACT 62.457 66.667 12.10 0.00 39.67 4.00
91 92 0.673333 TAACGGAGTGTGCCAGCATG 60.673 55.000 0.00 0.00 45.00 4.06
92 93 0.391661 CTAACGGAGTGTGCCAGCAT 60.392 55.000 0.00 0.00 45.00 3.79
93 94 1.005037 CTAACGGAGTGTGCCAGCA 60.005 57.895 0.00 0.00 45.00 4.41
94 95 2.391389 GCTAACGGAGTGTGCCAGC 61.391 63.158 0.00 0.00 45.00 4.85
95 96 0.391661 ATGCTAACGGAGTGTGCCAG 60.392 55.000 0.00 0.00 45.00 4.85
96 97 0.391130 GATGCTAACGGAGTGTGCCA 60.391 55.000 0.00 0.00 45.00 4.92
97 98 0.108138 AGATGCTAACGGAGTGTGCC 60.108 55.000 0.00 0.00 45.00 5.01
98 99 1.394917 CAAGATGCTAACGGAGTGTGC 59.605 52.381 0.00 0.00 45.00 4.57
99 100 2.413112 CACAAGATGCTAACGGAGTGTG 59.587 50.000 0.00 0.00 45.00 3.82
100 101 2.688507 CACAAGATGCTAACGGAGTGT 58.311 47.619 0.00 0.00 45.00 3.55
114 115 8.708742 GCTAATCATATTTGTATACGCACAAGA 58.291 33.333 0.00 0.00 39.46 3.02
115 116 8.495148 TGCTAATCATATTTGTATACGCACAAG 58.505 33.333 0.00 0.00 39.46 3.16
116 117 8.279800 GTGCTAATCATATTTGTATACGCACAA 58.720 33.333 14.91 0.00 41.57 3.33
117 118 7.655732 AGTGCTAATCATATTTGTATACGCACA 59.344 33.333 19.23 0.00 43.61 4.57
118 119 7.952101 CAGTGCTAATCATATTTGTATACGCAC 59.048 37.037 13.01 13.01 42.07 5.34
119 120 7.655732 ACAGTGCTAATCATATTTGTATACGCA 59.344 33.333 0.00 0.00 0.00 5.24
120 121 8.018677 ACAGTGCTAATCATATTTGTATACGC 57.981 34.615 0.00 0.00 0.00 4.42
125 126 9.529325 GTGTCTACAGTGCTAATCATATTTGTA 57.471 33.333 0.00 0.00 0.00 2.41
126 127 8.040727 TGTGTCTACAGTGCTAATCATATTTGT 58.959 33.333 0.00 0.00 31.91 2.83
127 128 8.424274 TGTGTCTACAGTGCTAATCATATTTG 57.576 34.615 0.00 0.00 31.91 2.32
128 129 9.049523 CATGTGTCTACAGTGCTAATCATATTT 57.950 33.333 0.00 0.00 40.79 1.40
129 130 7.172190 GCATGTGTCTACAGTGCTAATCATATT 59.828 37.037 11.25 0.00 40.79 1.28
130 131 6.648310 GCATGTGTCTACAGTGCTAATCATAT 59.352 38.462 11.25 0.00 40.79 1.78
131 132 5.985530 GCATGTGTCTACAGTGCTAATCATA 59.014 40.000 11.25 0.00 40.79 2.15
132 133 4.813161 GCATGTGTCTACAGTGCTAATCAT 59.187 41.667 11.25 0.00 40.79 2.45
133 134 4.081476 AGCATGTGTCTACAGTGCTAATCA 60.081 41.667 16.86 0.00 43.40 2.57
134 135 4.437239 AGCATGTGTCTACAGTGCTAATC 58.563 43.478 16.86 0.00 43.40 1.75
135 136 4.081476 TGAGCATGTGTCTACAGTGCTAAT 60.081 41.667 17.85 2.95 44.28 1.73
136 137 3.258123 TGAGCATGTGTCTACAGTGCTAA 59.742 43.478 17.85 11.28 44.28 3.09
137 138 2.825532 TGAGCATGTGTCTACAGTGCTA 59.174 45.455 17.85 8.25 44.28 3.49
138 139 1.620323 TGAGCATGTGTCTACAGTGCT 59.380 47.619 17.86 17.86 45.55 4.40
139 140 2.084610 TGAGCATGTGTCTACAGTGC 57.915 50.000 10.76 10.76 40.79 4.40
140 141 2.414481 GCTTGAGCATGTGTCTACAGTG 59.586 50.000 0.00 0.00 40.79 3.66
141 142 2.613977 GGCTTGAGCATGTGTCTACAGT 60.614 50.000 5.24 0.00 44.36 3.55
142 143 2.005451 GGCTTGAGCATGTGTCTACAG 58.995 52.381 5.24 0.00 44.36 2.74
143 144 1.347378 TGGCTTGAGCATGTGTCTACA 59.653 47.619 5.24 0.00 44.36 2.74
144 145 2.099141 TGGCTTGAGCATGTGTCTAC 57.901 50.000 5.24 0.00 44.36 2.59
145 146 2.038952 ACTTGGCTTGAGCATGTGTCTA 59.961 45.455 5.24 0.00 44.36 2.59
146 147 1.202855 ACTTGGCTTGAGCATGTGTCT 60.203 47.619 5.24 0.00 44.36 3.41
147 148 1.242076 ACTTGGCTTGAGCATGTGTC 58.758 50.000 5.24 0.00 44.36 3.67
148 149 1.696063 AACTTGGCTTGAGCATGTGT 58.304 45.000 5.24 0.00 44.36 3.72
149 150 2.798283 CAAAACTTGGCTTGAGCATGTG 59.202 45.455 5.24 0.00 44.36 3.21
150 151 2.804212 GCAAAACTTGGCTTGAGCATGT 60.804 45.455 5.24 0.00 44.36 3.21
151 152 1.796459 GCAAAACTTGGCTTGAGCATG 59.204 47.619 5.24 0.00 44.36 4.06
152 153 2.159327 GCAAAACTTGGCTTGAGCAT 57.841 45.000 5.24 0.00 44.36 3.79
153 154 3.665544 GCAAAACTTGGCTTGAGCA 57.334 47.368 5.24 0.00 44.36 4.26
161 162 3.191078 TGAACCAATGGCAAAACTTGG 57.809 42.857 14.48 14.48 44.06 3.61
162 163 3.001127 CGTTGAACCAATGGCAAAACTTG 59.999 43.478 0.00 0.00 0.00 3.16
163 164 3.194062 CGTTGAACCAATGGCAAAACTT 58.806 40.909 0.00 0.00 0.00 2.66
164 165 2.167487 ACGTTGAACCAATGGCAAAACT 59.833 40.909 0.00 0.00 34.96 2.66
165 166 2.545731 ACGTTGAACCAATGGCAAAAC 58.454 42.857 0.00 0.17 34.96 2.43
166 167 2.969628 ACGTTGAACCAATGGCAAAA 57.030 40.000 0.00 0.00 34.96 2.44
167 168 3.858877 GCATACGTTGAACCAATGGCAAA 60.859 43.478 0.00 0.00 34.96 3.68
168 169 2.352225 GCATACGTTGAACCAATGGCAA 60.352 45.455 0.00 0.00 34.96 4.52
169 170 1.201181 GCATACGTTGAACCAATGGCA 59.799 47.619 0.00 0.00 34.96 4.92
170 171 1.469079 GGCATACGTTGAACCAATGGC 60.469 52.381 12.90 12.90 34.96 4.40
171 172 1.202132 CGGCATACGTTGAACCAATGG 60.202 52.381 0.00 0.00 34.96 3.16
172 173 1.793714 GCGGCATACGTTGAACCAATG 60.794 52.381 0.00 0.00 46.52 2.82
173 174 0.450184 GCGGCATACGTTGAACCAAT 59.550 50.000 0.00 0.00 46.52 3.16
174 175 0.885150 TGCGGCATACGTTGAACCAA 60.885 50.000 0.00 0.00 46.52 3.67
175 176 0.885150 TTGCGGCATACGTTGAACCA 60.885 50.000 2.28 0.00 46.52 3.67
176 177 0.179200 CTTGCGGCATACGTTGAACC 60.179 55.000 2.28 0.00 46.52 3.62
177 178 0.515564 ACTTGCGGCATACGTTGAAC 59.484 50.000 2.28 0.00 46.52 3.18
178 179 1.231221 AACTTGCGGCATACGTTGAA 58.769 45.000 2.28 0.00 46.52 2.69
179 180 1.231221 AAACTTGCGGCATACGTTGA 58.769 45.000 2.28 0.00 46.52 3.18
180 181 2.044888 AAAACTTGCGGCATACGTTG 57.955 45.000 2.28 0.00 46.52 4.10
181 182 2.413634 GCTAAAACTTGCGGCATACGTT 60.414 45.455 2.28 5.27 46.52 3.99
182 183 1.129811 GCTAAAACTTGCGGCATACGT 59.870 47.619 2.28 0.00 46.52 3.57
183 184 4.085366 GATGCTAAAACTTGCGGCATACG 61.085 47.826 2.28 0.00 42.57 3.06
184 185 2.911819 TGCTAAAACTTGCGGCATAC 57.088 45.000 2.28 0.00 0.00 2.39
185 186 3.013219 TGATGCTAAAACTTGCGGCATA 58.987 40.909 2.28 0.00 42.57 3.14
186 187 1.818060 TGATGCTAAAACTTGCGGCAT 59.182 42.857 2.28 0.00 44.73 4.40
187 188 1.242989 TGATGCTAAAACTTGCGGCA 58.757 45.000 0.00 0.00 37.32 5.69
188 189 2.346099 TTGATGCTAAAACTTGCGGC 57.654 45.000 0.00 0.00 0.00 6.53
189 190 3.670055 CAGTTTGATGCTAAAACTTGCGG 59.330 43.478 8.61 0.00 43.60 5.69
190 191 4.379793 GTCAGTTTGATGCTAAAACTTGCG 59.620 41.667 8.61 1.26 43.60 4.85
191 192 5.523369 AGTCAGTTTGATGCTAAAACTTGC 58.477 37.500 8.61 5.93 43.60 4.01
192 193 7.992180 AAAGTCAGTTTGATGCTAAAACTTG 57.008 32.000 8.61 6.16 43.60 3.16
193 194 8.470002 AGAAAAGTCAGTTTGATGCTAAAACTT 58.530 29.630 8.61 2.17 43.60 2.66
194 195 8.000780 AGAAAAGTCAGTTTGATGCTAAAACT 57.999 30.769 6.27 6.27 46.25 2.66
195 196 7.112148 CGAGAAAAGTCAGTTTGATGCTAAAAC 59.888 37.037 2.47 2.47 37.71 2.43
196 197 7.132213 CGAGAAAAGTCAGTTTGATGCTAAAA 58.868 34.615 0.00 0.00 0.00 1.52
197 198 6.658831 CGAGAAAAGTCAGTTTGATGCTAAA 58.341 36.000 0.00 0.00 0.00 1.85
198 199 5.334105 GCGAGAAAAGTCAGTTTGATGCTAA 60.334 40.000 0.00 0.00 0.00 3.09
199 200 4.152402 GCGAGAAAAGTCAGTTTGATGCTA 59.848 41.667 0.00 0.00 0.00 3.49
200 201 3.058639 GCGAGAAAAGTCAGTTTGATGCT 60.059 43.478 0.00 0.00 0.00 3.79
201 202 3.229552 GCGAGAAAAGTCAGTTTGATGC 58.770 45.455 0.00 0.00 0.00 3.91
202 203 3.250762 TGGCGAGAAAAGTCAGTTTGATG 59.749 43.478 0.00 0.00 0.00 3.07
203 204 3.476552 TGGCGAGAAAAGTCAGTTTGAT 58.523 40.909 0.00 0.00 0.00 2.57
204 205 2.912771 TGGCGAGAAAAGTCAGTTTGA 58.087 42.857 0.00 0.00 0.00 2.69
205 206 3.065371 ACTTGGCGAGAAAAGTCAGTTTG 59.935 43.478 9.20 0.00 30.87 2.93
206 207 3.279434 ACTTGGCGAGAAAAGTCAGTTT 58.721 40.909 9.20 0.00 30.87 2.66
207 208 2.919228 ACTTGGCGAGAAAAGTCAGTT 58.081 42.857 9.20 0.00 30.87 3.16
208 209 2.622064 ACTTGGCGAGAAAAGTCAGT 57.378 45.000 9.20 0.00 30.87 3.41
209 210 2.872245 TGAACTTGGCGAGAAAAGTCAG 59.128 45.455 9.20 0.00 35.60 3.51
210 211 2.912771 TGAACTTGGCGAGAAAAGTCA 58.087 42.857 9.20 1.26 35.60 3.41
211 212 3.963383 TTGAACTTGGCGAGAAAAGTC 57.037 42.857 9.20 0.00 35.60 3.01
212 213 3.882888 TGATTGAACTTGGCGAGAAAAGT 59.117 39.130 9.20 0.00 38.25 2.66
213 214 4.222114 GTGATTGAACTTGGCGAGAAAAG 58.778 43.478 9.20 0.00 0.00 2.27
214 215 3.004315 GGTGATTGAACTTGGCGAGAAAA 59.996 43.478 9.20 0.00 0.00 2.29
215 216 2.552315 GGTGATTGAACTTGGCGAGAAA 59.448 45.455 9.20 0.35 0.00 2.52
216 217 2.151202 GGTGATTGAACTTGGCGAGAA 58.849 47.619 9.20 0.00 0.00 2.87
217 218 1.347707 AGGTGATTGAACTTGGCGAGA 59.652 47.619 9.20 0.00 0.00 4.04
218 219 1.466167 CAGGTGATTGAACTTGGCGAG 59.534 52.381 0.00 0.00 0.00 5.03
219 220 1.202758 ACAGGTGATTGAACTTGGCGA 60.203 47.619 0.00 0.00 31.76 5.54
220 221 1.069022 CACAGGTGATTGAACTTGGCG 60.069 52.381 0.00 0.00 31.76 5.69
221 222 1.270550 CCACAGGTGATTGAACTTGGC 59.729 52.381 0.00 0.00 31.76 4.52
222 223 2.586425 ACCACAGGTGATTGAACTTGG 58.414 47.619 0.00 0.00 32.98 3.61
234 235 6.374417 AATAGAGTCAATTACACCACAGGT 57.626 37.500 0.00 0.00 35.62 4.00
235 236 5.520288 CGAATAGAGTCAATTACACCACAGG 59.480 44.000 0.00 0.00 0.00 4.00
236 237 6.330278 TCGAATAGAGTCAATTACACCACAG 58.670 40.000 0.00 0.00 0.00 3.66
237 238 6.275494 TCGAATAGAGTCAATTACACCACA 57.725 37.500 0.00 0.00 0.00 4.17
238 239 7.591006 TTTCGAATAGAGTCAATTACACCAC 57.409 36.000 0.00 0.00 0.00 4.16
239 240 7.333423 CCTTTTCGAATAGAGTCAATTACACCA 59.667 37.037 16.09 0.00 0.00 4.17
240 241 7.548075 TCCTTTTCGAATAGAGTCAATTACACC 59.452 37.037 16.09 0.00 0.00 4.16
241 242 8.475331 TCCTTTTCGAATAGAGTCAATTACAC 57.525 34.615 16.09 0.00 0.00 2.90
242 243 7.764443 CCTCCTTTTCGAATAGAGTCAATTACA 59.236 37.037 16.09 0.00 0.00 2.41
243 244 7.980099 TCCTCCTTTTCGAATAGAGTCAATTAC 59.020 37.037 16.09 0.00 0.00 1.89
244 245 8.074613 TCCTCCTTTTCGAATAGAGTCAATTA 57.925 34.615 16.09 0.00 0.00 1.40
245 246 6.947464 TCCTCCTTTTCGAATAGAGTCAATT 58.053 36.000 16.09 0.00 0.00 2.32
246 247 6.155393 ACTCCTCCTTTTCGAATAGAGTCAAT 59.845 38.462 16.09 0.00 0.00 2.57
247 248 5.480772 ACTCCTCCTTTTCGAATAGAGTCAA 59.519 40.000 16.09 0.00 0.00 3.18
248 249 5.017490 ACTCCTCCTTTTCGAATAGAGTCA 58.983 41.667 16.09 3.68 0.00 3.41
249 250 5.585820 ACTCCTCCTTTTCGAATAGAGTC 57.414 43.478 16.09 0.00 0.00 3.36
250 251 7.231115 GGTATACTCCTCCTTTTCGAATAGAGT 59.769 40.741 16.09 13.25 37.18 3.24
251 252 7.309316 GGGTATACTCCTCCTTTTCGAATAGAG 60.309 44.444 16.09 13.21 0.00 2.43
252 253 6.492772 GGGTATACTCCTCCTTTTCGAATAGA 59.507 42.308 16.09 4.89 0.00 1.98
253 254 6.267014 TGGGTATACTCCTCCTTTTCGAATAG 59.733 42.308 8.48 8.48 0.00 1.73
254 255 6.041296 GTGGGTATACTCCTCCTTTTCGAATA 59.959 42.308 0.00 0.00 0.00 1.75
255 256 4.966805 TGGGTATACTCCTCCTTTTCGAAT 59.033 41.667 0.00 0.00 0.00 3.34
256 257 4.161001 GTGGGTATACTCCTCCTTTTCGAA 59.839 45.833 0.00 0.00 0.00 3.71
257 258 3.703052 GTGGGTATACTCCTCCTTTTCGA 59.297 47.826 0.00 0.00 0.00 3.71
258 259 3.449737 TGTGGGTATACTCCTCCTTTTCG 59.550 47.826 0.00 0.00 0.00 3.46
259 260 5.431179 TTGTGGGTATACTCCTCCTTTTC 57.569 43.478 0.00 0.00 0.00 2.29
260 261 5.853572 TTTGTGGGTATACTCCTCCTTTT 57.146 39.130 0.00 0.00 0.00 2.27
261 262 5.853572 TTTTGTGGGTATACTCCTCCTTT 57.146 39.130 0.00 0.00 0.00 3.11
262 263 5.491078 TGATTTTGTGGGTATACTCCTCCTT 59.509 40.000 0.00 0.00 0.00 3.36
263 264 5.036916 TGATTTTGTGGGTATACTCCTCCT 58.963 41.667 0.00 0.00 0.00 3.69
264 265 5.367945 TGATTTTGTGGGTATACTCCTCC 57.632 43.478 0.00 0.00 0.00 4.30
265 266 7.881775 AAATGATTTTGTGGGTATACTCCTC 57.118 36.000 0.00 3.30 0.00 3.71
266 267 9.936329 AATAAATGATTTTGTGGGTATACTCCT 57.064 29.630 0.00 0.00 0.00 3.69
273 274 9.451002 TCTCGTTAATAAATGATTTTGTGGGTA 57.549 29.630 0.00 0.00 30.29 3.69
274 275 8.343168 TCTCGTTAATAAATGATTTTGTGGGT 57.657 30.769 0.00 0.00 30.29 4.51
275 276 9.632807 TTTCTCGTTAATAAATGATTTTGTGGG 57.367 29.630 0.00 0.00 30.29 4.61
284 285 9.241317 GGATACTCGTTTCTCGTTAATAAATGA 57.759 33.333 0.00 0.00 40.80 2.57
295 296 3.858238 GGAACTTGGATACTCGTTTCTCG 59.142 47.826 0.00 0.00 41.41 4.04
297 298 4.884668 TGGAACTTGGATACTCGTTTCT 57.115 40.909 0.00 0.00 37.61 2.52
301 302 7.881232 TCTTTTATTTGGAACTTGGATACTCGT 59.119 33.333 0.00 0.00 37.61 4.18
306 307 7.284489 CCGGATCTTTTATTTGGAACTTGGATA 59.716 37.037 0.00 0.00 0.00 2.59
325 326 6.616237 TTTACTTCTACCTTTTCCGGATCT 57.384 37.500 4.15 0.00 0.00 2.75
411 430 6.031471 GCTGTTCCTTTCGTCTTTTAACAAA 58.969 36.000 0.00 0.00 0.00 2.83
417 436 3.065371 CACTGCTGTTCCTTTCGTCTTTT 59.935 43.478 0.00 0.00 0.00 2.27
421 440 0.868406 CCACTGCTGTTCCTTTCGTC 59.132 55.000 0.00 0.00 0.00 4.20
485 504 3.985008 GTACATCCGTACATGCACCATA 58.015 45.455 0.00 0.00 46.18 2.74
486 505 2.833794 GTACATCCGTACATGCACCAT 58.166 47.619 0.00 0.00 46.18 3.55
487 506 2.303163 GTACATCCGTACATGCACCA 57.697 50.000 0.00 0.00 46.18 4.17
495 514 1.876156 CGGGAGTAGGTACATCCGTAC 59.124 57.143 10.94 0.00 46.18 3.67
496 515 1.815408 GCGGGAGTAGGTACATCCGTA 60.815 57.143 16.89 0.00 42.10 4.02
497 516 1.105759 GCGGGAGTAGGTACATCCGT 61.106 60.000 16.89 0.00 42.10 4.69
498 517 0.822532 AGCGGGAGTAGGTACATCCG 60.823 60.000 13.47 13.47 42.58 4.18
499 518 1.340568 GAAGCGGGAGTAGGTACATCC 59.659 57.143 0.00 0.00 0.00 3.51
500 519 1.001597 CGAAGCGGGAGTAGGTACATC 60.002 57.143 0.00 0.00 0.00 3.06
520 539 5.826208 TCTGGTCCTTTTCTTACTTCAAACC 59.174 40.000 0.00 0.00 0.00 3.27
531 550 2.972713 TGCTACAGTCTGGTCCTTTTCT 59.027 45.455 4.53 0.00 0.00 2.52
613 637 1.516386 CCAGCACGCACGTACCTAG 60.516 63.158 0.00 0.00 0.00 3.02
676 700 0.248907 TAGACAAGCTATGCGACGCC 60.249 55.000 18.69 0.92 0.00 5.68
686 710 6.058183 GTCAAATGGACCATATAGACAAGCT 58.942 40.000 20.51 0.00 40.83 3.74
801 829 1.218230 GAGGTCGATCGATGGCTTGC 61.218 60.000 22.50 6.07 0.00 4.01
834 863 0.108186 CAAGCTGACTACCGATGCCA 60.108 55.000 0.00 0.00 0.00 4.92
849 878 1.653533 GCGATCGAGCAATGCAAGC 60.654 57.895 21.57 6.40 37.05 4.01
873 902 1.551452 AAGGTTGCTCGAGCTAGACT 58.449 50.000 35.27 24.93 42.66 3.24
911 940 4.130286 AGCCCTAGAAGATTTCTCAACG 57.870 45.455 0.00 0.00 41.14 4.10
977 1014 2.639856 CGAGTACGACGACGACGC 60.640 66.667 18.98 8.60 43.96 5.19
990 1027 1.200252 CTTCTGACCATGTCGACGAGT 59.800 52.381 11.62 7.87 34.95 4.18
991 1028 1.901538 CTTCTGACCATGTCGACGAG 58.098 55.000 11.62 5.55 34.95 4.18
1006 1043 2.044252 CTGCATGGGGCTGCTTCT 60.044 61.111 0.00 0.00 45.15 2.85
1352 1398 1.739929 TTGGCGTACACGATGCTGG 60.740 57.895 5.84 0.00 43.02 4.85
1659 1705 3.078196 TCGATGGCCCCGCAGTAA 61.078 61.111 0.00 0.00 0.00 2.24
1804 1854 2.665185 GAAGTGCTCCGCCAACGT 60.665 61.111 0.00 0.00 37.70 3.99
2280 4641 3.055719 CATGTGTGGCACGTCCCC 61.056 66.667 13.77 0.00 37.14 4.81
2281 4642 1.452145 AAACATGTGTGGCACGTCCC 61.452 55.000 13.77 0.00 37.14 4.46
2282 4643 0.383949 AAAACATGTGTGGCACGTCC 59.616 50.000 13.77 3.98 37.14 4.79
2283 4644 2.202295 AAAAACATGTGTGGCACGTC 57.798 45.000 13.77 9.29 37.14 4.34
2468 4867 5.482908 CTGAGCTTGGTCAGTGTTAGTTAT 58.517 41.667 18.38 0.00 39.39 1.89
2518 4918 8.451908 ACTATGCCAGTTTCACCTTAATAATC 57.548 34.615 0.00 0.00 31.59 1.75
2566 4966 3.883489 ACTTGCTCTTAGTTGGGTTTGTC 59.117 43.478 0.00 0.00 0.00 3.18
2593 4997 9.183368 GATGAAAGTGAGGGAAAGAGAAATATT 57.817 33.333 0.00 0.00 0.00 1.28
2613 5018 1.976474 GGGCTTGCACCGGATGAAA 60.976 57.895 9.46 2.49 0.00 2.69
2647 5052 7.913821 ACAAGTTGACGGTTTCTTTTTATCTTC 59.086 33.333 10.54 0.00 0.00 2.87
2713 5303 5.358922 CCATGTTCTGAGAGAAGGATCTTC 58.641 45.833 0.00 0.00 34.42 2.87
2721 5311 4.219070 CCAATTTGCCATGTTCTGAGAGAA 59.781 41.667 0.00 0.00 0.00 2.87
2729 5320 2.481185 CACTTGCCAATTTGCCATGTTC 59.519 45.455 0.00 0.00 0.00 3.18
2740 5331 7.884877 ACATACTATATATGTGCACTTGCCAAT 59.115 33.333 19.41 4.28 41.18 3.16
2784 5375 1.439353 CCGGATCACGCCATTTCCAG 61.439 60.000 0.00 0.00 42.52 3.86
2795 5386 5.542779 AGATGCTACTTTTATCCGGATCAC 58.457 41.667 23.08 5.30 0.00 3.06
2800 5391 9.307121 CATATCTTAGATGCTACTTTTATCCGG 57.693 37.037 4.78 0.00 0.00 5.14
2810 5401 5.872070 GCTTGGTCCATATCTTAGATGCTAC 59.128 44.000 4.78 0.00 0.00 3.58
2823 5414 3.998913 TGACAATGAGCTTGGTCCATA 57.001 42.857 0.00 0.00 39.30 2.74
2824 5415 2.885135 TGACAATGAGCTTGGTCCAT 57.115 45.000 0.00 0.00 39.30 3.41
2839 5431 8.726988 GCTAGTTTTATGTTTGACCTATTGACA 58.273 33.333 0.00 0.00 0.00 3.58
2852 5444 7.654520 TGTGACGTTCTTAGCTAGTTTTATGTT 59.345 33.333 0.00 0.00 0.00 2.71
2873 5465 8.641499 TTATGTGTTCTTTCCAATTTTGTGAC 57.359 30.769 0.00 0.00 0.00 3.67
2916 5575 2.881513 TGCCGACTGAACATTTGCTAAA 59.118 40.909 0.00 0.00 0.00 1.85
2950 5610 3.283751 CCTAACAACCACACCTTTCACA 58.716 45.455 0.00 0.00 0.00 3.58
2996 5656 1.043116 TCATCGGTCCTGGTAGGCTG 61.043 60.000 0.00 0.00 34.61 4.85
2999 5659 1.486211 AACTCATCGGTCCTGGTAGG 58.514 55.000 0.00 0.00 36.46 3.18
3008 5668 6.749036 ATTCCCTAATCTAAACTCATCGGT 57.251 37.500 0.00 0.00 0.00 4.69
3066 5727 8.830580 CAACCATACTACTGAAACTGATAATGG 58.169 37.037 0.00 0.00 36.93 3.16
3068 5729 7.499232 GCCAACCATACTACTGAAACTGATAAT 59.501 37.037 0.00 0.00 0.00 1.28
3073 5734 4.323417 TGCCAACCATACTACTGAAACTG 58.677 43.478 0.00 0.00 0.00 3.16
3098 5759 1.842007 CTGCTATGGCCTGGATGGT 59.158 57.895 3.32 0.00 38.35 3.55
3112 5773 1.510480 GAGAAGGTGTTTGCGCTGCT 61.510 55.000 9.73 0.00 0.00 4.24
3162 5823 6.127054 CCCTATGACATCAAGTAGACCAAGAA 60.127 42.308 0.00 0.00 0.00 2.52
3163 5824 5.363868 CCCTATGACATCAAGTAGACCAAGA 59.636 44.000 0.00 0.00 0.00 3.02
3181 5842 1.137697 GTTACCCCACCTCCCCTATG 58.862 60.000 0.00 0.00 0.00 2.23
3182 5843 1.032768 AGTTACCCCACCTCCCCTAT 58.967 55.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.