Multiple sequence alignment - TraesCS4D01G225000

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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 TraesCS4D01G225000 chr4D 100.000 3953 0 0 1 3953 381901764 381897812 0.000000e+00 7300
1 TraesCS4D01G225000 chr4D 95.876 97 4 0 3783 3879 381897919 381897823 1.470000e-34 158
2 TraesCS4D01G225000 chr4D 95.876 97 4 0 3846 3942 381897982 381897886 1.470000e-34 158
3 TraesCS4D01G225000 chr4A 93.589 3697 135 47 252 3901 81762905 81766546 0.000000e+00 5421
4 TraesCS4D01G225000 chr4A 94.845 97 4 1 3846 3942 81766429 81766524 2.460000e-32 150
5 TraesCS4D01G225000 chr4B 95.299 3382 116 15 544 3901 469249452 469246090 0.000000e+00 5325
6 TraesCS4D01G225000 chr4B 92.568 148 10 1 248 394 469249860 469249713 1.110000e-50 211
7 TraesCS4D01G225000 chr4B 94.845 97 5 0 3846 3942 469246208 469246112 6.840000e-33 152
8 TraesCS4D01G225000 chr7A 93.074 231 13 2 1 230 206925410 206925638 6.330000e-88 335
9 TraesCS4D01G225000 chr7A 92.889 225 14 2 1 225 145390888 145391110 3.810000e-85 326
10 TraesCS4D01G225000 chr5D 93.074 231 13 2 1 230 520351204 520351432 6.330000e-88 335
11 TraesCS4D01G225000 chr3D 92.641 231 16 1 1 230 47752906 47753136 8.190000e-87 331
12 TraesCS4D01G225000 chr2B 92.609 230 16 1 1 230 704579018 704579246 2.940000e-86 329
13 TraesCS4D01G225000 chr7D 92.208 231 15 2 1 230 246148969 246149197 1.370000e-84 324
14 TraesCS4D01G225000 chr6D 90.323 248 18 3 1 248 335396105 335396346 1.770000e-83 320
15 TraesCS4D01G225000 chr6B 91.775 231 18 1 1 230 530575340 530575570 1.770000e-83 320
16 TraesCS4D01G225000 chr2A 92.105 228 16 2 1 228 680403974 680403749 1.770000e-83 320


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 TraesCS4D01G225000 chr4D 381897812 381901764 3952 True 2538.666667 7300 97.250667 1 3953 3 chr4D.!!$R1 3952
1 TraesCS4D01G225000 chr4A 81762905 81766546 3641 False 2785.500000 5421 94.217000 252 3942 2 chr4A.!!$F1 3690
2 TraesCS4D01G225000 chr4B 469246090 469249860 3770 True 1896.000000 5325 94.237333 248 3942 3 chr4B.!!$R1 3694

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
232 233 0.028242 CGATCCGATCCGATCCGATC 59.972 60.0 20.99 20.99 39.25 3.69 F
237 238 0.039437 CGATCCGATCCGATCCGTTT 60.039 55.0 15.61 0.00 36.13 3.60 F
275 276 0.375454 CGTTGTCGTGCAAAGTCCAA 59.625 50.0 0.00 0.00 39.03 3.53 F
1683 1837 0.322456 TCAGGGTATGTGTTGCTGCC 60.322 55.0 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1478 1632 0.765510 GGACTTGAAGTGGAGGTGGT 59.234 55.000 0.90 0.0 0.00 4.16 R
1683 1837 0.883833 CAGCCTTACAAACAGGGCAG 59.116 55.000 5.62 0.0 46.23 4.85 R
1734 1888 1.139095 CTTACCTCGTCCTGGCGAC 59.861 63.158 8.74 0.0 36.80 5.19 R
3602 3772 1.423541 ACACCAACCAGTCAGCCATAA 59.576 47.619 0.00 0.0 0.00 1.90 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
29 30 5.670149 ATTGCTCTTCTTTGCATAGATCG 57.330 39.130 7.73 3.14 39.07 3.69
30 31 4.128925 TGCTCTTCTTTGCATAGATCGT 57.871 40.909 7.73 0.00 33.94 3.73
31 32 3.867493 TGCTCTTCTTTGCATAGATCGTG 59.133 43.478 7.73 5.08 33.94 4.35
32 33 4.115516 GCTCTTCTTTGCATAGATCGTGA 58.884 43.478 7.73 4.22 0.00 4.35
33 34 4.749099 GCTCTTCTTTGCATAGATCGTGAT 59.251 41.667 7.73 0.00 0.00 3.06
34 35 5.923114 GCTCTTCTTTGCATAGATCGTGATA 59.077 40.000 7.73 0.00 0.00 2.15
35 36 6.089283 GCTCTTCTTTGCATAGATCGTGATAG 59.911 42.308 7.73 1.11 0.00 2.08
36 37 7.277174 TCTTCTTTGCATAGATCGTGATAGA 57.723 36.000 7.73 3.42 0.00 1.98
37 38 7.890515 TCTTCTTTGCATAGATCGTGATAGAT 58.109 34.615 7.73 0.00 0.00 1.98
38 39 9.014297 TCTTCTTTGCATAGATCGTGATAGATA 57.986 33.333 7.73 0.00 0.00 1.98
39 40 9.288124 CTTCTTTGCATAGATCGTGATAGATAG 57.712 37.037 7.73 0.00 0.00 2.08
40 41 8.341892 TCTTTGCATAGATCGTGATAGATAGT 57.658 34.615 2.39 0.00 0.00 2.12
41 42 9.449719 TCTTTGCATAGATCGTGATAGATAGTA 57.550 33.333 2.39 0.00 0.00 1.82
44 45 8.159344 TGCATAGATCGTGATAGATAGTATGG 57.841 38.462 5.47 0.00 33.04 2.74
45 46 7.993183 TGCATAGATCGTGATAGATAGTATGGA 59.007 37.037 5.47 5.57 33.04 3.41
46 47 8.841300 GCATAGATCGTGATAGATAGTATGGAA 58.159 37.037 5.47 0.00 33.04 3.53
50 51 9.521841 AGATCGTGATAGATAGTATGGAAAAGA 57.478 33.333 0.00 0.00 0.00 2.52
53 54 9.078990 TCGTGATAGATAGTATGGAAAAGATGT 57.921 33.333 0.00 0.00 0.00 3.06
90 91 0.094730 CGTTTTCGGTCCGAATCTGC 59.905 55.000 26.62 15.26 45.28 4.26
91 92 0.446616 GTTTTCGGTCCGAATCTGCC 59.553 55.000 26.62 9.76 45.28 4.85
92 93 0.675522 TTTTCGGTCCGAATCTGCCC 60.676 55.000 26.62 0.00 45.28 5.36
93 94 2.530958 TTTCGGTCCGAATCTGCCCC 62.531 60.000 26.62 0.00 45.28 5.80
94 95 4.891727 CGGTCCGAATCTGCCCCG 62.892 72.222 4.91 0.00 0.00 5.73
96 97 4.162690 GTCCGAATCTGCCCCGCT 62.163 66.667 0.00 0.00 0.00 5.52
97 98 3.399181 TCCGAATCTGCCCCGCTT 61.399 61.111 0.00 0.00 0.00 4.68
98 99 2.897350 CCGAATCTGCCCCGCTTC 60.897 66.667 0.00 0.00 0.00 3.86
99 100 2.897350 CGAATCTGCCCCGCTTCC 60.897 66.667 0.00 0.00 0.00 3.46
100 101 2.272146 GAATCTGCCCCGCTTCCA 59.728 61.111 0.00 0.00 0.00 3.53
101 102 2.044946 AATCTGCCCCGCTTCCAC 60.045 61.111 0.00 0.00 0.00 4.02
102 103 2.543067 GAATCTGCCCCGCTTCCACT 62.543 60.000 0.00 0.00 0.00 4.00
103 104 2.543067 AATCTGCCCCGCTTCCACTC 62.543 60.000 0.00 0.00 0.00 3.51
104 105 4.785453 CTGCCCCGCTTCCACTCC 62.785 72.222 0.00 0.00 0.00 3.85
107 108 3.702048 CCCCGCTTCCACTCCGAA 61.702 66.667 0.00 0.00 0.00 4.30
108 109 2.584608 CCCGCTTCCACTCCGAAT 59.415 61.111 0.00 0.00 0.00 3.34
109 110 1.521681 CCCGCTTCCACTCCGAATC 60.522 63.158 0.00 0.00 0.00 2.52
110 111 1.521681 CCGCTTCCACTCCGAATCC 60.522 63.158 0.00 0.00 0.00 3.01
111 112 1.878522 CGCTTCCACTCCGAATCCG 60.879 63.158 0.00 0.00 0.00 4.18
112 113 1.218316 GCTTCCACTCCGAATCCGT 59.782 57.895 0.00 0.00 0.00 4.69
113 114 0.458669 GCTTCCACTCCGAATCCGTA 59.541 55.000 0.00 0.00 0.00 4.02
114 115 1.536284 GCTTCCACTCCGAATCCGTAG 60.536 57.143 0.00 0.00 0.00 3.51
115 116 1.749634 CTTCCACTCCGAATCCGTAGT 59.250 52.381 0.00 0.00 35.27 2.73
116 117 1.386533 TCCACTCCGAATCCGTAGTC 58.613 55.000 0.00 0.00 32.49 2.59
117 118 0.384669 CCACTCCGAATCCGTAGTCC 59.615 60.000 0.00 0.00 32.49 3.85
118 119 1.100510 CACTCCGAATCCGTAGTCCA 58.899 55.000 0.00 0.00 32.49 4.02
119 120 1.475280 CACTCCGAATCCGTAGTCCAA 59.525 52.381 0.00 0.00 32.49 3.53
120 121 2.100916 CACTCCGAATCCGTAGTCCAAT 59.899 50.000 0.00 0.00 32.49 3.16
121 122 3.317149 CACTCCGAATCCGTAGTCCAATA 59.683 47.826 0.00 0.00 32.49 1.90
122 123 4.022242 CACTCCGAATCCGTAGTCCAATAT 60.022 45.833 0.00 0.00 32.49 1.28
123 124 5.182570 CACTCCGAATCCGTAGTCCAATATA 59.817 44.000 0.00 0.00 32.49 0.86
124 125 5.771666 ACTCCGAATCCGTAGTCCAATATAA 59.228 40.000 0.00 0.00 28.41 0.98
125 126 6.436532 ACTCCGAATCCGTAGTCCAATATAAT 59.563 38.462 0.00 0.00 28.41 1.28
126 127 6.860080 TCCGAATCCGTAGTCCAATATAATC 58.140 40.000 0.00 0.00 0.00 1.75
127 128 6.040878 CCGAATCCGTAGTCCAATATAATCC 58.959 44.000 0.00 0.00 0.00 3.01
128 129 5.742453 CGAATCCGTAGTCCAATATAATCCG 59.258 44.000 0.00 0.00 0.00 4.18
129 130 6.600882 AATCCGTAGTCCAATATAATCCGT 57.399 37.500 0.00 0.00 0.00 4.69
130 131 7.414429 CGAATCCGTAGTCCAATATAATCCGTA 60.414 40.741 0.00 0.00 0.00 4.02
131 132 7.893124 ATCCGTAGTCCAATATAATCCGTAT 57.107 36.000 0.00 0.00 0.00 3.06
132 133 7.707624 TCCGTAGTCCAATATAATCCGTATT 57.292 36.000 0.00 0.00 0.00 1.89
133 134 8.125978 TCCGTAGTCCAATATAATCCGTATTT 57.874 34.615 0.00 0.00 0.00 1.40
134 135 8.030692 TCCGTAGTCCAATATAATCCGTATTTG 58.969 37.037 0.00 0.00 0.00 2.32
135 136 8.030692 CCGTAGTCCAATATAATCCGTATTTGA 58.969 37.037 0.00 0.00 0.00 2.69
136 137 9.414295 CGTAGTCCAATATAATCCGTATTTGAA 57.586 33.333 0.00 0.00 0.00 2.69
139 140 9.449719 AGTCCAATATAATCCGTATTTGAATCC 57.550 33.333 0.00 0.00 0.00 3.01
140 141 8.388103 GTCCAATATAATCCGTATTTGAATCCG 58.612 37.037 0.00 0.00 0.00 4.18
141 142 7.065324 TCCAATATAATCCGTATTTGAATCCGC 59.935 37.037 0.00 0.00 0.00 5.54
142 143 7.148323 CCAATATAATCCGTATTTGAATCCGCA 60.148 37.037 0.00 0.00 0.00 5.69
143 144 8.397906 CAATATAATCCGTATTTGAATCCGCAT 58.602 33.333 0.00 0.00 0.00 4.73
144 145 4.749245 AATCCGTATTTGAATCCGCATC 57.251 40.909 0.00 0.00 0.00 3.91
145 146 2.489971 TCCGTATTTGAATCCGCATCC 58.510 47.619 0.00 0.00 0.00 3.51
146 147 1.194547 CCGTATTTGAATCCGCATCCG 59.805 52.381 0.00 0.00 0.00 4.18
161 162 3.865745 CGCATCCGGTCATTATCTAATCC 59.134 47.826 0.00 0.00 0.00 3.01
162 163 3.865745 GCATCCGGTCATTATCTAATCCG 59.134 47.826 0.00 0.00 34.62 4.18
163 164 4.381612 GCATCCGGTCATTATCTAATCCGA 60.382 45.833 0.00 0.98 36.00 4.55
164 165 5.682471 GCATCCGGTCATTATCTAATCCGAT 60.682 44.000 0.00 0.00 36.00 4.18
165 166 5.578005 TCCGGTCATTATCTAATCCGATC 57.422 43.478 0.00 0.00 36.00 3.69
166 167 4.401519 TCCGGTCATTATCTAATCCGATCC 59.598 45.833 0.00 0.00 36.00 3.36
167 168 4.352039 CGGTCATTATCTAATCCGATCCG 58.648 47.826 4.79 0.00 36.00 4.18
168 169 4.095932 CGGTCATTATCTAATCCGATCCGA 59.904 45.833 4.79 0.00 36.00 4.55
169 170 5.392703 CGGTCATTATCTAATCCGATCCGAA 60.393 44.000 4.79 0.00 36.00 4.30
170 171 6.574350 GGTCATTATCTAATCCGATCCGAAT 58.426 40.000 0.00 0.00 0.00 3.34
171 172 6.697892 GGTCATTATCTAATCCGATCCGAATC 59.302 42.308 0.00 0.00 0.00 2.52
172 173 6.697892 GTCATTATCTAATCCGATCCGAATCC 59.302 42.308 0.00 0.00 0.00 3.01
173 174 3.784701 ATCTAATCCGATCCGAATCCG 57.215 47.619 0.00 0.00 0.00 4.18
174 175 2.786777 TCTAATCCGATCCGAATCCGA 58.213 47.619 0.00 0.00 38.22 4.55
175 176 2.486982 TCTAATCCGATCCGAATCCGAC 59.513 50.000 0.00 0.00 38.22 4.79
176 177 1.037493 AATCCGATCCGAATCCGACA 58.963 50.000 0.00 0.00 38.22 4.35
177 178 1.037493 ATCCGATCCGAATCCGACAA 58.963 50.000 0.00 0.00 38.22 3.18
178 179 0.818938 TCCGATCCGAATCCGACAAA 59.181 50.000 0.00 0.00 38.22 2.83
179 180 1.205179 TCCGATCCGAATCCGACAAAA 59.795 47.619 0.00 0.00 38.22 2.44
180 181 2.004017 CCGATCCGAATCCGACAAAAA 58.996 47.619 0.00 0.00 38.22 1.94
205 206 8.533569 AAATGTGGTAAAGGATATGGTAAAGG 57.466 34.615 0.00 0.00 0.00 3.11
206 207 5.442391 TGTGGTAAAGGATATGGTAAAGGC 58.558 41.667 0.00 0.00 0.00 4.35
207 208 5.044772 TGTGGTAAAGGATATGGTAAAGGCA 60.045 40.000 0.00 0.00 0.00 4.75
208 209 6.068670 GTGGTAAAGGATATGGTAAAGGCAT 58.931 40.000 0.00 0.00 0.00 4.40
209 210 6.549736 GTGGTAAAGGATATGGTAAAGGCATT 59.450 38.462 0.00 0.00 0.00 3.56
210 211 7.722285 GTGGTAAAGGATATGGTAAAGGCATTA 59.278 37.037 0.00 0.00 0.00 1.90
211 212 8.452868 TGGTAAAGGATATGGTAAAGGCATTAT 58.547 33.333 0.00 0.00 0.00 1.28
212 213 8.957466 GGTAAAGGATATGGTAAAGGCATTATC 58.043 37.037 0.00 0.00 0.00 1.75
213 214 8.957466 GTAAAGGATATGGTAAAGGCATTATCC 58.043 37.037 0.99 0.99 34.11 2.59
214 215 5.745227 AGGATATGGTAAAGGCATTATCCG 58.255 41.667 3.40 0.00 37.78 4.18
215 216 5.487488 AGGATATGGTAAAGGCATTATCCGA 59.513 40.000 3.40 0.00 37.78 4.55
216 217 6.158695 AGGATATGGTAAAGGCATTATCCGAT 59.841 38.462 3.40 0.00 37.78 4.18
217 218 6.483640 GGATATGGTAAAGGCATTATCCGATC 59.516 42.308 0.00 0.00 0.00 3.69
218 219 4.015872 TGGTAAAGGCATTATCCGATCC 57.984 45.455 0.00 0.00 0.00 3.36
219 220 3.000727 GGTAAAGGCATTATCCGATCCG 58.999 50.000 0.00 0.00 0.00 4.18
220 221 3.306502 GGTAAAGGCATTATCCGATCCGA 60.307 47.826 0.00 0.00 0.00 4.55
221 222 3.703001 AAAGGCATTATCCGATCCGAT 57.297 42.857 2.11 2.11 0.00 4.18
222 223 2.969628 AGGCATTATCCGATCCGATC 57.030 50.000 0.00 0.00 0.00 3.69
223 224 1.482593 AGGCATTATCCGATCCGATCC 59.517 52.381 2.69 0.00 0.00 3.36
224 225 1.560923 GCATTATCCGATCCGATCCG 58.439 55.000 2.69 0.00 0.00 4.18
225 226 1.134367 GCATTATCCGATCCGATCCGA 59.866 52.381 2.69 2.56 0.00 4.55
226 227 2.223829 GCATTATCCGATCCGATCCGAT 60.224 50.000 14.26 14.26 33.08 4.18
227 228 3.633235 CATTATCCGATCCGATCCGATC 58.367 50.000 13.49 12.48 36.16 3.69
228 229 1.676746 TATCCGATCCGATCCGATCC 58.323 55.000 15.61 2.39 36.13 3.36
229 230 1.377366 ATCCGATCCGATCCGATCCG 61.377 60.000 15.61 10.81 36.13 4.18
230 231 2.038837 CCGATCCGATCCGATCCGA 61.039 63.158 15.61 2.56 36.13 4.55
231 232 1.377366 CCGATCCGATCCGATCCGAT 61.377 60.000 15.61 10.82 36.13 4.18
232 233 0.028242 CGATCCGATCCGATCCGATC 59.972 60.000 20.99 20.99 39.25 3.69
233 234 0.382515 GATCCGATCCGATCCGATCC 59.617 60.000 20.58 9.33 37.77 3.36
234 235 1.377366 ATCCGATCCGATCCGATCCG 61.377 60.000 15.61 10.81 36.13 4.18
235 236 2.333417 CCGATCCGATCCGATCCGT 61.333 63.158 15.61 0.00 36.13 4.69
236 237 1.579932 CGATCCGATCCGATCCGTT 59.420 57.895 15.61 0.00 36.13 4.44
237 238 0.039437 CGATCCGATCCGATCCGTTT 60.039 55.000 15.61 0.00 36.13 3.60
238 239 1.198408 CGATCCGATCCGATCCGTTTA 59.802 52.381 15.61 0.00 36.13 2.01
239 240 2.593257 GATCCGATCCGATCCGTTTAC 58.407 52.381 11.68 0.00 33.83 2.01
240 241 1.391577 TCCGATCCGATCCGTTTACA 58.608 50.000 2.69 0.00 0.00 2.41
241 242 1.066002 TCCGATCCGATCCGTTTACAC 59.934 52.381 2.69 0.00 0.00 2.90
242 243 1.484356 CGATCCGATCCGTTTACACC 58.516 55.000 2.69 0.00 0.00 4.16
243 244 1.861971 GATCCGATCCGTTTACACCC 58.138 55.000 0.00 0.00 0.00 4.61
244 245 0.466963 ATCCGATCCGTTTACACCCC 59.533 55.000 0.00 0.00 0.00 4.95
245 246 0.615544 TCCGATCCGTTTACACCCCT 60.616 55.000 0.00 0.00 0.00 4.79
246 247 1.113788 CCGATCCGTTTACACCCCTA 58.886 55.000 0.00 0.00 0.00 3.53
275 276 0.375454 CGTTGTCGTGCAAAGTCCAA 59.625 50.000 0.00 0.00 39.03 3.53
323 324 1.821753 CCAGAGACGATGGACTGAAGT 59.178 52.381 0.00 0.00 40.51 3.01
373 375 5.807520 CACGTGTGAAATTGAGATAGCTAGT 59.192 40.000 7.58 0.00 0.00 2.57
375 377 6.127591 ACGTGTGAAATTGAGATAGCTAGTCT 60.128 38.462 0.00 2.58 0.00 3.24
412 414 5.356882 TTTTTCGCTAGTCTGTGAAATGG 57.643 39.130 10.03 0.00 43.19 3.16
414 416 4.471904 TTCGCTAGTCTGTGAAATGGAT 57.528 40.909 0.00 0.00 34.10 3.41
415 417 4.471904 TCGCTAGTCTGTGAAATGGATT 57.528 40.909 0.00 0.00 0.00 3.01
416 418 4.832248 TCGCTAGTCTGTGAAATGGATTT 58.168 39.130 0.00 0.00 0.00 2.17
417 419 5.245531 TCGCTAGTCTGTGAAATGGATTTT 58.754 37.500 0.00 0.00 0.00 1.82
418 420 5.705441 TCGCTAGTCTGTGAAATGGATTTTT 59.295 36.000 0.00 0.00 0.00 1.94
455 457 4.672587 ATTTAGCATCGGAGCAAGTAGA 57.327 40.909 3.00 0.00 36.85 2.59
463 465 1.927174 CGGAGCAAGTAGATGTTTCGG 59.073 52.381 0.00 0.00 29.87 4.30
480 482 1.611491 TCGGTGCCCTGAAATTTTCAC 59.389 47.619 7.74 0.13 35.46 3.18
484 486 1.269517 TGCCCTGAAATTTTCACGTGC 60.270 47.619 11.67 10.64 35.46 5.34
532 547 2.275380 GCACCGATTTTGGCCCAGT 61.275 57.895 0.00 0.00 0.00 4.00
579 718 2.308570 ACTGGCACATGGGTTATGAGAA 59.691 45.455 0.00 0.00 39.21 2.87
665 805 1.411612 CTTCCATACCGGTAGACCACC 59.588 57.143 20.91 0.00 44.75 4.61
686 826 0.941542 GCGAGAGTAGAGAGACGCAT 59.058 55.000 0.00 0.00 44.29 4.73
712 852 4.335647 CCCGCCTGCAGTGTTCCT 62.336 66.667 13.81 0.00 0.00 3.36
721 861 3.389329 CCTGCAGTGTTCCTATGGTATCT 59.611 47.826 13.81 0.00 0.00 1.98
865 1005 4.030452 GCGGTGGCACAAGCTCAC 62.030 66.667 23.85 4.23 44.16 3.51
867 1007 2.610694 CGGTGGCACAAGCTCACAG 61.611 63.158 20.82 0.00 44.16 3.66
1629 1783 2.122729 AGGCAGGCCTGGACTGTA 59.877 61.111 33.46 0.00 46.22 2.74
1683 1837 0.322456 TCAGGGTATGTGTTGCTGCC 60.322 55.000 0.00 0.00 0.00 4.85
1734 1888 0.600557 AGCCCGATTCTGCTATCTCG 59.399 55.000 0.00 0.00 35.69 4.04
1794 1948 1.986757 AGAGACGCTGGATGTGCCT 60.987 57.895 0.00 0.00 37.63 4.75
1825 1979 4.742201 CACGCCGGCTACAGCAGT 62.742 66.667 26.68 10.27 44.36 4.40
1947 2101 2.438021 AGTGCCAACTTCAAGTAGTGGA 59.562 45.455 11.89 0.00 30.14 4.02
2148 2302 2.027625 GCTTTACGCCGTGCACTCT 61.028 57.895 16.19 0.00 0.00 3.24
2214 2368 0.623723 GGTTAGTTGGGCATCAGGGA 59.376 55.000 0.00 0.00 0.00 4.20
2226 2380 3.119352 GGCATCAGGGAACATTTGAGTTC 60.119 47.826 0.00 0.00 45.50 3.01
2235 2389 4.878397 GGAACATTTGAGTTCGATCCAGAT 59.122 41.667 0.00 0.00 46.81 2.90
2250 2404 8.763049 TCGATCCAGATATTTATGATGTCAAC 57.237 34.615 0.00 0.00 0.00 3.18
2340 2494 1.377725 CTTGCAGCAAGTCCGGGAT 60.378 57.895 24.89 0.00 36.79 3.85
2592 2746 3.394940 AGGAGGATGACATGCTTGATGAT 59.605 43.478 11.11 0.00 35.80 2.45
2658 2812 2.158842 GGATAGAATGGCAGCAGAGTGT 60.159 50.000 0.00 0.00 0.00 3.55
2817 2971 2.361119 GCCATTGATGCATGATGACACT 59.639 45.455 17.17 0.00 0.00 3.55
2829 2983 5.994054 GCATGATGACACTATGGTAACTGAT 59.006 40.000 0.00 0.00 37.61 2.90
3147 3305 5.406780 CGCTGTTGATTACTGTCTTCTTTCT 59.593 40.000 0.00 0.00 0.00 2.52
3248 3406 9.226345 GCATTAACTTAATCTATGTTCTTGTGC 57.774 33.333 0.00 0.00 0.00 4.57
3273 3432 1.072116 CATGTGTGGAATTTGGCGCG 61.072 55.000 0.00 0.00 0.00 6.86
3419 3581 6.430000 ACCATACTTAGTCGTTCATTTTTGCT 59.570 34.615 0.00 0.00 0.00 3.91
3536 3706 8.571336 CATACTGAAAATTCCAGAGTTCTTGTT 58.429 33.333 12.93 0.00 35.69 2.83
3562 3732 7.832769 TGGTTTAATTTATTGTAACCTCAGCC 58.167 34.615 15.90 0.00 37.03 4.85
3575 3745 1.610102 CCTCAGCCTTTCTGTGTGAGG 60.610 57.143 2.42 2.42 46.28 3.86
3592 3762 1.559682 GAGGTGGATGTTGCTTCCCTA 59.440 52.381 0.00 0.00 31.87 3.53
3602 3772 4.025360 TGTTGCTTCCCTATGCATTGATT 58.975 39.130 3.54 0.00 39.07 2.57
3608 3778 5.717119 CTTCCCTATGCATTGATTTATGGC 58.283 41.667 3.54 0.00 0.00 4.40
3635 3806 4.787551 TGGTTGGTGTTTACTGTGAGAAT 58.212 39.130 0.00 0.00 0.00 2.40
3638 3809 4.698201 TGGTGTTTACTGTGAGAATGGA 57.302 40.909 0.00 0.00 0.00 3.41
3679 3850 6.238842 GGTCACATAAGCATCATTACTTGCAT 60.239 38.462 0.00 0.00 41.35 3.96
3689 3860 9.439500 AGCATCATTACTTGCATAAACAAAATT 57.561 25.926 0.00 0.00 41.35 1.82
3864 4049 6.039717 GTCATAATTCTGGGCAGCTAAAATCA 59.960 38.462 0.00 0.00 0.00 2.57
3868 4053 3.966979 TCTGGGCAGCTAAAATCATTGA 58.033 40.909 0.00 0.00 0.00 2.57
3879 4064 6.016192 AGCTAAAATCATTGATCATGCTCAGG 60.016 38.462 0.00 0.00 32.13 3.86
3890 4075 8.473358 TTGATCATGCTCAGGAAAATGATTAT 57.527 30.769 0.00 0.00 39.31 1.28
3891 4076 8.473358 TGATCATGCTCAGGAAAATGATTATT 57.527 30.769 0.00 0.00 39.31 1.40
3915 4100 5.862845 AGTGCTAGATGTCATAATTCTGGG 58.137 41.667 0.00 0.00 0.00 4.45
3916 4101 4.453819 GTGCTAGATGTCATAATTCTGGGC 59.546 45.833 0.00 0.00 0.00 5.36
3917 4102 4.102996 TGCTAGATGTCATAATTCTGGGCA 59.897 41.667 0.00 0.00 31.85 5.36
3918 4103 4.694509 GCTAGATGTCATAATTCTGGGCAG 59.305 45.833 0.00 0.00 0.00 4.85
3919 4104 3.484407 AGATGTCATAATTCTGGGCAGC 58.516 45.455 0.00 0.00 0.00 5.25
3920 4105 3.137913 AGATGTCATAATTCTGGGCAGCT 59.862 43.478 0.00 0.00 0.00 4.24
3921 4106 4.349048 AGATGTCATAATTCTGGGCAGCTA 59.651 41.667 0.00 0.00 0.00 3.32
3922 4107 4.502105 TGTCATAATTCTGGGCAGCTAA 57.498 40.909 0.00 0.00 0.00 3.09
3923 4108 4.854173 TGTCATAATTCTGGGCAGCTAAA 58.146 39.130 0.00 0.00 0.00 1.85
3924 4109 5.260424 TGTCATAATTCTGGGCAGCTAAAA 58.740 37.500 0.00 0.00 0.00 1.52
3925 4110 5.893255 TGTCATAATTCTGGGCAGCTAAAAT 59.107 36.000 0.00 0.00 0.00 1.82
3926 4111 6.039717 TGTCATAATTCTGGGCAGCTAAAATC 59.960 38.462 0.00 0.00 0.00 2.17
3927 4112 5.239306 TCATAATTCTGGGCAGCTAAAATCG 59.761 40.000 0.00 0.00 0.00 3.34
3928 4113 2.489938 TTCTGGGCAGCTAAAATCGT 57.510 45.000 0.00 0.00 0.00 3.73
3929 4114 2.489938 TCTGGGCAGCTAAAATCGTT 57.510 45.000 0.00 0.00 0.00 3.85
3930 4115 2.083774 TCTGGGCAGCTAAAATCGTTG 58.916 47.619 0.00 0.00 0.00 4.10
3931 4116 1.812571 CTGGGCAGCTAAAATCGTTGT 59.187 47.619 0.00 0.00 0.00 3.32
3932 4117 2.228822 CTGGGCAGCTAAAATCGTTGTT 59.771 45.455 0.00 0.00 0.00 2.83
3933 4118 2.227865 TGGGCAGCTAAAATCGTTGTTC 59.772 45.455 0.00 0.00 0.00 3.18
3934 4119 2.227865 GGGCAGCTAAAATCGTTGTTCA 59.772 45.455 0.00 0.00 0.00 3.18
3935 4120 3.119495 GGGCAGCTAAAATCGTTGTTCAT 60.119 43.478 0.00 0.00 0.00 2.57
3936 4121 3.853671 GGCAGCTAAAATCGTTGTTCATG 59.146 43.478 0.00 0.00 0.00 3.07
3937 4122 3.301642 GCAGCTAAAATCGTTGTTCATGC 59.698 43.478 0.00 0.00 0.00 4.06
3938 4123 3.853671 CAGCTAAAATCGTTGTTCATGCC 59.146 43.478 0.00 0.00 0.00 4.40
3939 4124 3.119495 AGCTAAAATCGTTGTTCATGCCC 60.119 43.478 0.00 0.00 0.00 5.36
3940 4125 3.366883 GCTAAAATCGTTGTTCATGCCCA 60.367 43.478 0.00 0.00 0.00 5.36
3941 4126 3.302365 AAAATCGTTGTTCATGCCCAG 57.698 42.857 0.00 0.00 0.00 4.45
3942 4127 1.909700 AATCGTTGTTCATGCCCAGT 58.090 45.000 0.00 0.00 0.00 4.00
3943 4128 1.167851 ATCGTTGTTCATGCCCAGTG 58.832 50.000 0.00 0.00 0.00 3.66
3944 4129 0.107643 TCGTTGTTCATGCCCAGTGA 59.892 50.000 0.00 0.00 0.00 3.41
3945 4130 1.167851 CGTTGTTCATGCCCAGTGAT 58.832 50.000 0.00 0.00 0.00 3.06
3946 4131 1.541147 CGTTGTTCATGCCCAGTGATT 59.459 47.619 0.00 0.00 0.00 2.57
3947 4132 2.746904 CGTTGTTCATGCCCAGTGATTA 59.253 45.455 0.00 0.00 0.00 1.75
3948 4133 3.190327 CGTTGTTCATGCCCAGTGATTAA 59.810 43.478 0.00 0.00 0.00 1.40
3949 4134 4.485163 GTTGTTCATGCCCAGTGATTAAC 58.515 43.478 0.00 0.00 0.00 2.01
3950 4135 3.760738 TGTTCATGCCCAGTGATTAACA 58.239 40.909 0.00 0.00 0.00 2.41
3951 4136 3.758023 TGTTCATGCCCAGTGATTAACAG 59.242 43.478 0.00 0.00 0.00 3.16
3952 4137 3.719268 TCATGCCCAGTGATTAACAGT 57.281 42.857 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.096160 CGATCTATGCAAAGAAGAGCAATATAT 57.904 33.333 0.00 0.00 44.88 0.86
4 5 8.090831 ACGATCTATGCAAAGAAGAGCAATATA 58.909 33.333 0.00 0.00 44.88 0.86
5 6 6.933521 ACGATCTATGCAAAGAAGAGCAATAT 59.066 34.615 0.00 0.00 44.88 1.28
6 7 6.201615 CACGATCTATGCAAAGAAGAGCAATA 59.798 38.462 0.00 0.00 44.88 1.90
7 8 5.007430 CACGATCTATGCAAAGAAGAGCAAT 59.993 40.000 0.00 0.00 44.88 3.56
8 9 4.330894 CACGATCTATGCAAAGAAGAGCAA 59.669 41.667 0.00 0.00 44.88 3.91
9 10 3.867493 CACGATCTATGCAAAGAAGAGCA 59.133 43.478 0.00 0.00 45.92 4.26
10 11 4.115516 TCACGATCTATGCAAAGAAGAGC 58.884 43.478 0.00 0.00 0.00 4.09
11 12 7.366513 TCTATCACGATCTATGCAAAGAAGAG 58.633 38.462 0.00 0.00 0.00 2.85
12 13 7.277174 TCTATCACGATCTATGCAAAGAAGA 57.723 36.000 0.00 0.00 0.00 2.87
13 14 9.288124 CTATCTATCACGATCTATGCAAAGAAG 57.712 37.037 0.00 0.00 0.00 2.85
14 15 8.797438 ACTATCTATCACGATCTATGCAAAGAA 58.203 33.333 0.00 0.00 0.00 2.52
15 16 8.341892 ACTATCTATCACGATCTATGCAAAGA 57.658 34.615 0.00 0.00 0.00 2.52
18 19 8.624776 CCATACTATCTATCACGATCTATGCAA 58.375 37.037 0.00 0.00 0.00 4.08
19 20 7.993183 TCCATACTATCTATCACGATCTATGCA 59.007 37.037 0.00 0.00 0.00 3.96
20 21 8.384607 TCCATACTATCTATCACGATCTATGC 57.615 38.462 0.00 0.00 0.00 3.14
24 25 9.521841 TCTTTTCCATACTATCTATCACGATCT 57.478 33.333 0.00 0.00 0.00 2.75
27 28 9.078990 ACATCTTTTCCATACTATCTATCACGA 57.921 33.333 0.00 0.00 0.00 4.35
63 64 3.397482 TCGGACCGAAAACGGATAAAAA 58.603 40.909 15.79 0.00 31.06 1.94
64 65 3.037431 TCGGACCGAAAACGGATAAAA 57.963 42.857 15.79 0.00 31.06 1.52
65 66 2.739885 TCGGACCGAAAACGGATAAA 57.260 45.000 15.79 0.00 31.06 1.40
66 67 2.739885 TTCGGACCGAAAACGGATAA 57.260 45.000 26.62 0.39 43.00 1.75
76 77 3.467226 GGGGCAGATTCGGACCGA 61.467 66.667 13.88 13.88 0.00 4.69
77 78 4.891727 CGGGGCAGATTCGGACCG 62.892 72.222 7.84 7.84 35.01 4.79
79 80 3.682292 AAGCGGGGCAGATTCGGAC 62.682 63.158 0.00 0.00 0.00 4.79
80 81 3.385749 GAAGCGGGGCAGATTCGGA 62.386 63.158 0.00 0.00 0.00 4.55
81 82 2.897350 GAAGCGGGGCAGATTCGG 60.897 66.667 0.00 0.00 0.00 4.30
82 83 2.897350 GGAAGCGGGGCAGATTCG 60.897 66.667 4.58 0.00 37.40 3.34
83 84 2.115291 GTGGAAGCGGGGCAGATTC 61.115 63.158 2.27 2.27 35.95 2.52
84 85 2.044946 GTGGAAGCGGGGCAGATT 60.045 61.111 0.00 0.00 0.00 2.40
85 86 3.011517 AGTGGAAGCGGGGCAGAT 61.012 61.111 0.00 0.00 0.00 2.90
86 87 3.706373 GAGTGGAAGCGGGGCAGA 61.706 66.667 0.00 0.00 0.00 4.26
87 88 4.785453 GGAGTGGAAGCGGGGCAG 62.785 72.222 0.00 0.00 0.00 4.85
90 91 2.925162 GATTCGGAGTGGAAGCGGGG 62.925 65.000 0.00 0.00 0.00 5.73
91 92 1.521681 GATTCGGAGTGGAAGCGGG 60.522 63.158 0.00 0.00 0.00 6.13
92 93 1.521681 GGATTCGGAGTGGAAGCGG 60.522 63.158 0.00 0.00 33.27 5.52
93 94 1.878522 CGGATTCGGAGTGGAAGCG 60.879 63.158 0.00 0.00 33.27 4.68
94 95 0.458669 TACGGATTCGGAGTGGAAGC 59.541 55.000 0.00 0.00 41.39 3.86
95 96 2.493713 CTACGGATTCGGAGTGGAAG 57.506 55.000 0.00 0.00 42.18 3.46
102 103 6.127535 GGATTATATTGGACTACGGATTCGGA 60.128 42.308 0.00 0.00 41.39 4.55
103 104 6.040878 GGATTATATTGGACTACGGATTCGG 58.959 44.000 0.00 0.00 41.39 4.30
104 105 5.742453 CGGATTATATTGGACTACGGATTCG 59.258 44.000 0.00 0.00 43.02 3.34
105 106 6.628185 ACGGATTATATTGGACTACGGATTC 58.372 40.000 0.00 0.00 0.00 2.52
106 107 6.600882 ACGGATTATATTGGACTACGGATT 57.399 37.500 0.00 0.00 0.00 3.01
107 108 7.893124 ATACGGATTATATTGGACTACGGAT 57.107 36.000 0.00 0.00 0.00 4.18
108 109 7.707624 AATACGGATTATATTGGACTACGGA 57.292 36.000 0.00 0.00 0.00 4.69
109 110 8.030692 TCAAATACGGATTATATTGGACTACGG 58.969 37.037 0.00 0.00 0.00 4.02
110 111 8.975410 TCAAATACGGATTATATTGGACTACG 57.025 34.615 0.00 0.00 0.00 3.51
113 114 9.449719 GGATTCAAATACGGATTATATTGGACT 57.550 33.333 0.00 0.00 0.00 3.85
114 115 8.388103 CGGATTCAAATACGGATTATATTGGAC 58.612 37.037 0.00 0.00 39.06 4.02
115 116 7.065324 GCGGATTCAAATACGGATTATATTGGA 59.935 37.037 9.26 0.00 42.91 3.53
116 117 7.148323 TGCGGATTCAAATACGGATTATATTGG 60.148 37.037 9.26 0.00 42.91 3.16
117 118 7.747888 TGCGGATTCAAATACGGATTATATTG 58.252 34.615 9.26 0.00 42.91 1.90
118 119 7.915293 TGCGGATTCAAATACGGATTATATT 57.085 32.000 9.26 0.00 42.91 1.28
126 127 1.194547 CGGATGCGGATTCAAATACGG 59.805 52.381 9.26 0.00 42.91 4.02
127 128 1.194547 CCGGATGCGGATTCAAATACG 59.805 52.381 22.73 2.94 45.42 3.06
128 129 2.218603 ACCGGATGCGGATTCAAATAC 58.781 47.619 33.63 0.00 0.00 1.89
129 130 2.158885 TGACCGGATGCGGATTCAAATA 60.159 45.455 33.63 1.15 0.00 1.40
130 131 1.308998 GACCGGATGCGGATTCAAAT 58.691 50.000 33.63 7.65 0.00 2.32
131 132 0.035915 TGACCGGATGCGGATTCAAA 60.036 50.000 33.63 7.58 0.00 2.69
132 133 0.180171 ATGACCGGATGCGGATTCAA 59.820 50.000 33.63 12.37 0.00 2.69
133 134 0.180171 AATGACCGGATGCGGATTCA 59.820 50.000 33.63 25.41 0.00 2.57
134 135 2.163818 TAATGACCGGATGCGGATTC 57.836 50.000 33.63 20.39 0.00 2.52
135 136 2.303022 AGATAATGACCGGATGCGGATT 59.697 45.455 33.63 23.10 0.00 3.01
136 137 1.902508 AGATAATGACCGGATGCGGAT 59.097 47.619 33.63 14.90 0.00 4.18
137 138 1.338107 AGATAATGACCGGATGCGGA 58.662 50.000 33.63 11.63 0.00 5.54
138 139 3.313012 TTAGATAATGACCGGATGCGG 57.687 47.619 25.41 25.41 0.00 5.69
139 140 3.865745 GGATTAGATAATGACCGGATGCG 59.134 47.826 9.46 0.00 0.00 4.73
140 141 3.865745 CGGATTAGATAATGACCGGATGC 59.134 47.826 9.46 0.00 32.54 3.91
141 142 5.324784 TCGGATTAGATAATGACCGGATG 57.675 43.478 9.46 0.00 35.20 3.51
142 143 5.069251 GGATCGGATTAGATAATGACCGGAT 59.931 44.000 9.46 0.00 35.20 4.18
143 144 4.401519 GGATCGGATTAGATAATGACCGGA 59.598 45.833 9.46 0.00 35.20 5.14
144 145 4.683832 GGATCGGATTAGATAATGACCGG 58.316 47.826 0.00 0.00 35.20 5.28
145 146 4.095932 TCGGATCGGATTAGATAATGACCG 59.904 45.833 0.00 0.00 35.56 4.79
146 147 5.578005 TCGGATCGGATTAGATAATGACC 57.422 43.478 0.00 0.00 0.00 4.02
147 148 6.697892 GGATTCGGATCGGATTAGATAATGAC 59.302 42.308 3.55 0.00 32.84 3.06
148 149 6.459710 CGGATTCGGATCGGATTAGATAATGA 60.460 42.308 5.32 0.00 35.30 2.57
149 150 5.687730 CGGATTCGGATCGGATTAGATAATG 59.312 44.000 5.32 0.00 35.30 1.90
150 151 5.593095 TCGGATTCGGATCGGATTAGATAAT 59.407 40.000 9.76 0.00 36.89 1.28
151 152 4.945543 TCGGATTCGGATCGGATTAGATAA 59.054 41.667 9.76 0.00 36.89 1.75
152 153 4.334759 GTCGGATTCGGATCGGATTAGATA 59.665 45.833 16.18 0.00 41.71 1.98
153 154 3.128938 GTCGGATTCGGATCGGATTAGAT 59.871 47.826 16.18 0.00 41.71 1.98
154 155 2.486982 GTCGGATTCGGATCGGATTAGA 59.513 50.000 16.18 2.21 41.71 2.10
155 156 2.228103 TGTCGGATTCGGATCGGATTAG 59.772 50.000 16.18 0.06 41.71 1.73
156 157 2.232399 TGTCGGATTCGGATCGGATTA 58.768 47.619 16.18 7.06 41.71 1.75
157 158 1.037493 TGTCGGATTCGGATCGGATT 58.963 50.000 16.18 0.53 41.71 3.01
158 159 1.037493 TTGTCGGATTCGGATCGGAT 58.963 50.000 16.18 0.00 41.71 4.18
159 160 0.818938 TTTGTCGGATTCGGATCGGA 59.181 50.000 9.76 9.76 38.74 4.55
160 161 1.647346 TTTTGTCGGATTCGGATCGG 58.353 50.000 4.90 4.90 36.95 4.18
179 180 8.977412 CCTTTACCATATCCTTTACCACATTTT 58.023 33.333 0.00 0.00 0.00 1.82
180 181 7.069455 GCCTTTACCATATCCTTTACCACATTT 59.931 37.037 0.00 0.00 0.00 2.32
181 182 6.549736 GCCTTTACCATATCCTTTACCACATT 59.450 38.462 0.00 0.00 0.00 2.71
182 183 6.068670 GCCTTTACCATATCCTTTACCACAT 58.931 40.000 0.00 0.00 0.00 3.21
183 184 5.044772 TGCCTTTACCATATCCTTTACCACA 60.045 40.000 0.00 0.00 0.00 4.17
184 185 5.442391 TGCCTTTACCATATCCTTTACCAC 58.558 41.667 0.00 0.00 0.00 4.16
185 186 5.718801 TGCCTTTACCATATCCTTTACCA 57.281 39.130 0.00 0.00 0.00 3.25
186 187 8.879427 ATAATGCCTTTACCATATCCTTTACC 57.121 34.615 0.00 0.00 0.00 2.85
187 188 8.957466 GGATAATGCCTTTACCATATCCTTTAC 58.043 37.037 0.00 0.00 31.92 2.01
188 189 7.827236 CGGATAATGCCTTTACCATATCCTTTA 59.173 37.037 7.73 0.00 32.32 1.85
189 190 6.659242 CGGATAATGCCTTTACCATATCCTTT 59.341 38.462 7.73 0.00 32.32 3.11
190 191 6.012858 TCGGATAATGCCTTTACCATATCCTT 60.013 38.462 7.73 0.00 32.32 3.36
191 192 5.487488 TCGGATAATGCCTTTACCATATCCT 59.513 40.000 7.73 0.00 32.32 3.24
192 193 5.741011 TCGGATAATGCCTTTACCATATCC 58.259 41.667 0.00 0.00 0.00 2.59
193 194 6.483640 GGATCGGATAATGCCTTTACCATATC 59.516 42.308 0.00 0.00 0.00 1.63
194 195 6.357367 GGATCGGATAATGCCTTTACCATAT 58.643 40.000 0.00 0.00 0.00 1.78
195 196 5.625886 CGGATCGGATAATGCCTTTACCATA 60.626 44.000 0.00 0.00 0.00 2.74
196 197 4.589908 GGATCGGATAATGCCTTTACCAT 58.410 43.478 0.00 0.00 0.00 3.55
197 198 3.556213 CGGATCGGATAATGCCTTTACCA 60.556 47.826 0.00 0.00 0.00 3.25
198 199 3.000727 CGGATCGGATAATGCCTTTACC 58.999 50.000 0.00 0.00 0.00 2.85
199 200 3.921677 TCGGATCGGATAATGCCTTTAC 58.078 45.455 0.00 0.00 0.00 2.01
200 201 4.382685 GGATCGGATCGGATAATGCCTTTA 60.383 45.833 15.09 0.00 0.00 1.85
201 202 3.600388 GATCGGATCGGATAATGCCTTT 58.400 45.455 15.09 0.00 0.00 3.11
202 203 2.093447 GGATCGGATCGGATAATGCCTT 60.093 50.000 15.09 0.00 0.00 4.35
203 204 1.482593 GGATCGGATCGGATAATGCCT 59.517 52.381 15.09 0.00 0.00 4.75
204 205 1.802880 CGGATCGGATCGGATAATGCC 60.803 57.143 17.77 11.11 0.00 4.40
205 206 1.134367 TCGGATCGGATCGGATAATGC 59.866 52.381 20.36 3.86 34.26 3.56
206 207 3.551046 GGATCGGATCGGATCGGATAATG 60.551 52.174 29.64 8.63 45.65 1.90
207 208 2.623889 GGATCGGATCGGATCGGATAAT 59.376 50.000 29.64 16.64 45.65 1.28
208 209 2.022195 GGATCGGATCGGATCGGATAA 58.978 52.381 29.64 12.48 45.65 1.75
209 210 1.676746 GGATCGGATCGGATCGGATA 58.323 55.000 29.64 13.06 45.65 2.59
211 212 2.038837 CGGATCGGATCGGATCGGA 61.039 63.158 30.76 24.59 42.89 4.55
212 213 1.377366 ATCGGATCGGATCGGATCGG 61.377 60.000 29.59 29.59 43.26 4.18
213 214 2.099143 ATCGGATCGGATCGGATCG 58.901 57.895 26.28 23.09 43.26 3.69
216 217 2.038837 CGGATCGGATCGGATCGGA 61.039 63.158 30.76 24.59 42.89 4.55
217 218 1.863662 AACGGATCGGATCGGATCGG 61.864 60.000 31.69 31.69 43.00 4.18
218 219 0.039437 AAACGGATCGGATCGGATCG 60.039 55.000 27.38 24.29 43.00 3.69
219 220 2.030540 TGTAAACGGATCGGATCGGATC 60.031 50.000 26.93 26.93 41.67 3.36
220 221 1.958579 TGTAAACGGATCGGATCGGAT 59.041 47.619 26.28 15.03 34.17 4.18
221 222 1.066002 GTGTAAACGGATCGGATCGGA 59.934 52.381 26.28 5.34 34.17 4.55
222 223 1.484356 GTGTAAACGGATCGGATCGG 58.516 55.000 20.14 20.14 35.90 4.18
223 224 1.484356 GGTGTAAACGGATCGGATCG 58.516 55.000 11.62 9.49 0.00 3.69
224 225 1.539712 GGGGTGTAAACGGATCGGATC 60.540 57.143 9.54 9.54 0.00 3.36
225 226 0.466963 GGGGTGTAAACGGATCGGAT 59.533 55.000 7.35 0.00 0.00 4.18
226 227 0.615544 AGGGGTGTAAACGGATCGGA 60.616 55.000 7.35 0.00 0.00 4.55
227 228 1.068127 CTAGGGGTGTAAACGGATCGG 59.932 57.143 0.00 0.00 0.00 4.18
228 229 1.537562 GCTAGGGGTGTAAACGGATCG 60.538 57.143 0.00 0.00 0.00 3.69
229 230 1.761198 AGCTAGGGGTGTAAACGGATC 59.239 52.381 0.00 0.00 0.00 3.36
230 231 1.485066 CAGCTAGGGGTGTAAACGGAT 59.515 52.381 0.00 0.00 36.34 4.18
231 232 0.899720 CAGCTAGGGGTGTAAACGGA 59.100 55.000 0.00 0.00 36.34 4.69
232 233 0.743345 GCAGCTAGGGGTGTAAACGG 60.743 60.000 0.00 0.00 42.33 4.44
233 234 0.036765 TGCAGCTAGGGGTGTAAACG 60.037 55.000 0.00 0.00 42.33 3.60
234 235 1.271163 TGTGCAGCTAGGGGTGTAAAC 60.271 52.381 0.00 0.00 42.33 2.01
235 236 1.060729 TGTGCAGCTAGGGGTGTAAA 58.939 50.000 0.00 0.00 42.33 2.01
236 237 0.323629 GTGTGCAGCTAGGGGTGTAA 59.676 55.000 0.00 0.00 42.33 2.41
237 238 1.550130 GGTGTGCAGCTAGGGGTGTA 61.550 60.000 0.00 0.00 42.33 2.90
238 239 2.750350 GTGTGCAGCTAGGGGTGT 59.250 61.111 0.00 0.00 42.33 4.16
239 240 2.045926 GGTGTGCAGCTAGGGGTG 60.046 66.667 0.00 0.00 43.11 4.61
240 241 3.706373 CGGTGTGCAGCTAGGGGT 61.706 66.667 0.00 0.00 0.00 4.95
241 242 3.254024 AACGGTGTGCAGCTAGGGG 62.254 63.158 0.00 0.00 0.00 4.79
242 243 2.034879 CAACGGTGTGCAGCTAGGG 61.035 63.158 0.00 0.00 0.00 3.53
243 244 1.291877 GACAACGGTGTGCAGCTAGG 61.292 60.000 12.89 0.00 38.41 3.02
244 245 1.617755 CGACAACGGTGTGCAGCTAG 61.618 60.000 12.89 0.00 38.41 3.42
245 246 1.663388 CGACAACGGTGTGCAGCTA 60.663 57.895 12.89 0.00 38.41 3.32
246 247 2.967076 CGACAACGGTGTGCAGCT 60.967 61.111 12.89 0.00 38.41 4.24
323 324 5.887598 AGCAATAGCATGAATTGTACCTTCA 59.112 36.000 17.49 9.60 45.49 3.02
362 364 6.398234 TCCATTTCACAGACTAGCTATCTC 57.602 41.667 0.00 0.00 0.00 2.75
395 397 5.551760 AAAATCCATTTCACAGACTAGCG 57.448 39.130 0.00 0.00 0.00 4.26
419 421 8.826710 CCGATGCTAAATTCACTCAAGTAATAA 58.173 33.333 0.00 0.00 0.00 1.40
420 422 8.201464 TCCGATGCTAAATTCACTCAAGTAATA 58.799 33.333 0.00 0.00 0.00 0.98
429 431 3.266510 TGCTCCGATGCTAAATTCACT 57.733 42.857 0.00 0.00 0.00 3.41
463 465 2.393764 CACGTGAAAATTTCAGGGCAC 58.606 47.619 25.71 8.45 46.70 5.01
492 507 4.610945 CCAAATCCACTTTTGACACAGAC 58.389 43.478 0.00 0.00 38.58 3.51
539 554 7.765360 GTGCCAGTCTCTATCGTATACTACTAT 59.235 40.741 0.56 0.00 0.00 2.12
542 681 5.699915 TGTGCCAGTCTCTATCGTATACTAC 59.300 44.000 0.56 0.00 0.00 2.73
562 701 2.092429 TCCCTTCTCATAACCCATGTGC 60.092 50.000 0.00 0.00 35.96 4.57
579 718 1.229336 CTCTGGTCACTGGGTCCCT 60.229 63.158 10.00 0.00 0.00 4.20
665 805 0.303493 GCGTCTCTCTACTCTCGCTG 59.697 60.000 0.00 0.00 40.39 5.18
686 826 3.556306 GCAGGCGGGCCATACCTA 61.556 66.667 12.97 0.00 39.10 3.08
811 951 3.575351 GACGCGTGAACTGAGCCCT 62.575 63.158 20.70 0.00 0.00 5.19
812 952 3.112709 GACGCGTGAACTGAGCCC 61.113 66.667 20.70 0.00 0.00 5.19
1478 1632 0.765510 GGACTTGAAGTGGAGGTGGT 59.234 55.000 0.90 0.00 0.00 4.16
1629 1783 5.458215 GGGAATACCATAGAATTTGGCTCCT 60.458 44.000 9.33 0.00 37.81 3.69
1683 1837 0.883833 CAGCCTTACAAACAGGGCAG 59.116 55.000 5.62 0.00 46.23 4.85
1719 1873 1.322865 GCGACGAGATAGCAGAATCG 58.677 55.000 0.00 0.00 40.86 3.34
1734 1888 1.139095 CTTACCTCGTCCTGGCGAC 59.861 63.158 8.74 0.00 36.80 5.19
1776 1930 1.986757 AGGCACATCCAGCGTCTCT 60.987 57.895 0.00 0.00 37.29 3.10
1825 1979 2.500714 CCTTGTGCTTGGCAGCCAA 61.501 57.895 25.81 25.81 46.74 4.52
1947 2101 3.327757 TGGCTGAAGAGGACACAGTATTT 59.672 43.478 0.00 0.00 34.60 1.40
2214 2368 8.511604 AAATATCTGGATCGAACTCAAATGTT 57.488 30.769 0.00 0.00 0.00 2.71
2226 2380 7.542130 TCGTTGACATCATAAATATCTGGATCG 59.458 37.037 0.00 0.00 0.00 3.69
2235 2389 6.761242 CACCTTCCTCGTTGACATCATAAATA 59.239 38.462 0.00 0.00 0.00 1.40
2340 2494 0.407528 AGACCACCTCTGCTCTGAGA 59.592 55.000 9.28 0.00 36.23 3.27
2592 2746 6.127647 GGCTTGAACCAAAATCAGTATCATCA 60.128 38.462 0.00 0.00 0.00 3.07
2658 2812 3.135348 CCATTAGCATCTTCCTGTCCTCA 59.865 47.826 0.00 0.00 0.00 3.86
2817 2971 9.226606 CCTAACAAACTTGAATCAGTTACCATA 57.773 33.333 0.00 0.00 35.87 2.74
2829 2983 9.290988 TCTATTTGTATGCCTAACAAACTTGAA 57.709 29.630 9.64 0.00 46.40 2.69
2982 3136 7.987268 TCTAGCATACAGAATTTACAAGACG 57.013 36.000 0.00 0.00 0.00 4.18
3248 3406 2.052891 CAAATTCCACACATGTGCACG 58.947 47.619 25.68 13.92 44.34 5.34
3384 3546 6.127793 ACGACTAAGTATGGTAGGATCACTT 58.872 40.000 0.00 0.00 34.10 3.16
3396 3558 8.629986 CAAAGCAAAAATGAACGACTAAGTATG 58.370 33.333 0.00 0.00 0.00 2.39
3451 3613 7.550551 TCATATCAGGTTCAGTTTCTTTAGCTG 59.449 37.037 0.00 0.00 36.09 4.24
3536 3706 8.308207 GGCTGAGGTTACAATAAATTAAACCAA 58.692 33.333 15.89 7.52 37.41 3.67
3562 3732 3.131709 ACATCCACCTCACACAGAAAG 57.868 47.619 0.00 0.00 0.00 2.62
3575 3745 1.678101 GCATAGGGAAGCAACATCCAC 59.322 52.381 0.00 0.00 38.80 4.02
3592 3762 4.038763 CCAGTCAGCCATAAATCAATGCAT 59.961 41.667 0.00 0.00 0.00 3.96
3602 3772 1.423541 ACACCAACCAGTCAGCCATAA 59.576 47.619 0.00 0.00 0.00 1.90
3608 3778 3.312421 CACAGTAAACACCAACCAGTCAG 59.688 47.826 0.00 0.00 0.00 3.51
3635 3806 6.558394 TGTGACCATAAGATGAGGAATATCCA 59.442 38.462 0.00 0.00 39.61 3.41
3756 3927 9.460019 TGTTCCAAGAATTATGTGAATACATGA 57.540 29.630 0.00 0.00 46.63 3.07
3864 4049 6.978674 ATCATTTTCCTGAGCATGATCAAT 57.021 33.333 15.55 2.05 31.20 2.57
3868 4053 9.584008 ACTAATAATCATTTTCCTGAGCATGAT 57.416 29.630 0.00 0.00 31.20 2.45
3890 4075 7.445121 CCCAGAATTATGACATCTAGCACTAA 58.555 38.462 0.54 0.00 0.00 2.24
3891 4076 6.519043 GCCCAGAATTATGACATCTAGCACTA 60.519 42.308 0.54 0.00 0.00 2.74
3901 4086 4.502105 TTAGCTGCCCAGAATTATGACA 57.498 40.909 0.54 0.00 0.00 3.58
3902 4087 5.835113 TTTTAGCTGCCCAGAATTATGAC 57.165 39.130 0.54 0.00 0.00 3.06
3903 4088 5.239306 CGATTTTAGCTGCCCAGAATTATGA 59.761 40.000 0.54 0.00 0.00 2.15
3904 4089 5.009010 ACGATTTTAGCTGCCCAGAATTATG 59.991 40.000 0.00 0.00 0.00 1.90
3905 4090 5.133221 ACGATTTTAGCTGCCCAGAATTAT 58.867 37.500 0.00 0.00 0.00 1.28
3906 4091 4.523083 ACGATTTTAGCTGCCCAGAATTA 58.477 39.130 0.00 0.00 0.00 1.40
3907 4092 3.356290 ACGATTTTAGCTGCCCAGAATT 58.644 40.909 0.00 0.00 0.00 2.17
3908 4093 3.004752 ACGATTTTAGCTGCCCAGAAT 57.995 42.857 0.00 0.00 0.00 2.40
3909 4094 2.487762 CAACGATTTTAGCTGCCCAGAA 59.512 45.455 0.00 0.00 0.00 3.02
3910 4095 2.083774 CAACGATTTTAGCTGCCCAGA 58.916 47.619 0.00 0.00 0.00 3.86
3911 4096 1.812571 ACAACGATTTTAGCTGCCCAG 59.187 47.619 0.00 0.00 0.00 4.45
3912 4097 1.904287 ACAACGATTTTAGCTGCCCA 58.096 45.000 0.00 0.00 0.00 5.36
3913 4098 2.227865 TGAACAACGATTTTAGCTGCCC 59.772 45.455 0.00 0.00 0.00 5.36
3914 4099 3.552604 TGAACAACGATTTTAGCTGCC 57.447 42.857 0.00 0.00 0.00 4.85
3915 4100 3.301642 GCATGAACAACGATTTTAGCTGC 59.698 43.478 0.00 0.00 0.00 5.25
3916 4101 3.853671 GGCATGAACAACGATTTTAGCTG 59.146 43.478 0.00 0.00 0.00 4.24
3917 4102 3.119495 GGGCATGAACAACGATTTTAGCT 60.119 43.478 0.00 0.00 0.00 3.32
3918 4103 3.179048 GGGCATGAACAACGATTTTAGC 58.821 45.455 0.00 0.00 0.00 3.09
3919 4104 4.082787 ACTGGGCATGAACAACGATTTTAG 60.083 41.667 0.00 0.00 0.00 1.85
3920 4105 3.823873 ACTGGGCATGAACAACGATTTTA 59.176 39.130 0.00 0.00 0.00 1.52
3921 4106 2.627699 ACTGGGCATGAACAACGATTTT 59.372 40.909 0.00 0.00 0.00 1.82
3922 4107 2.030007 CACTGGGCATGAACAACGATTT 60.030 45.455 0.00 0.00 0.00 2.17
3923 4108 1.541147 CACTGGGCATGAACAACGATT 59.459 47.619 0.00 0.00 0.00 3.34
3924 4109 1.167851 CACTGGGCATGAACAACGAT 58.832 50.000 0.00 0.00 0.00 3.73
3925 4110 0.107643 TCACTGGGCATGAACAACGA 59.892 50.000 0.00 0.00 0.00 3.85
3926 4111 1.167851 ATCACTGGGCATGAACAACG 58.832 50.000 0.00 0.00 0.00 4.10
3927 4112 4.022416 TGTTAATCACTGGGCATGAACAAC 60.022 41.667 0.00 0.00 0.00 3.32
3928 4113 4.148079 TGTTAATCACTGGGCATGAACAA 58.852 39.130 0.00 0.00 0.00 2.83
3929 4114 3.758023 CTGTTAATCACTGGGCATGAACA 59.242 43.478 0.00 0.00 0.00 3.18
3930 4115 3.758554 ACTGTTAATCACTGGGCATGAAC 59.241 43.478 0.00 0.00 0.00 3.18
3931 4116 4.032960 ACTGTTAATCACTGGGCATGAA 57.967 40.909 0.00 0.00 0.00 2.57
3932 4117 3.719268 ACTGTTAATCACTGGGCATGA 57.281 42.857 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.