Multiple sequence alignment - TraesCS5B01G127100

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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 TraesCS5B01G127100 chr5B 100.000 2850 0 0 1 2850 232292788 232295637 0.000000e+00 5264.0
1 TraesCS5B01G127100 chr5A 95.130 2033 67 10 829 2850 285395511 285397522 0.000000e+00 3177.0
2 TraesCS5B01G127100 chr5A 94.558 147 8 0 1 147 78755891 78756037 7.940000e-56 228.0
3 TraesCS5B01G127100 chr5D 96.615 1861 37 4 991 2850 216154079 216155914 0.000000e+00 3064.0
4 TraesCS5B01G127100 chr5D 94.393 214 9 2 587 799 421982577 421982366 2.740000e-85 326.0
5 TraesCS5B01G127100 chr5D 95.906 171 6 1 834 1004 216153878 216154047 2.800000e-70 276.0
6 TraesCS5B01G127100 chr5D 91.667 180 13 2 416 593 216152569 216152748 6.100000e-62 248.0
7 TraesCS5B01G127100 chr5D 95.614 114 5 0 305 418 216152293 216152406 1.740000e-42 183.0
8 TraesCS5B01G127100 chr5D 98.765 81 1 0 226 306 216151885 216151965 8.230000e-31 145.0
9 TraesCS5B01G127100 chr5D 97.297 37 1 0 803 839 216152735 216152771 2.370000e-06 63.9
10 TraesCS5B01G127100 chr6D 83.956 1097 111 35 853 1912 24219409 24220477 0.000000e+00 990.0
11 TraesCS5B01G127100 chr6D 94.860 214 8 2 587 799 385659340 385659129 5.890000e-87 331.0
12 TraesCS5B01G127100 chr6A 83.051 1062 104 34 854 1876 22684328 22685352 0.000000e+00 894.0
13 TraesCS5B01G127100 chr6B 82.482 1096 101 44 871 1900 39180405 39181475 0.000000e+00 876.0
14 TraesCS5B01G127100 chr2D 94.144 222 11 2 587 807 608483167 608482947 1.260000e-88 337.0
15 TraesCS5B01G127100 chr2D 94.393 214 9 2 587 799 284560167 284559956 2.740000e-85 326.0
16 TraesCS5B01G127100 chr1D 95.305 213 8 2 587 798 494935159 494935370 1.260000e-88 337.0
17 TraesCS5B01G127100 chr1D 94.860 214 7 3 587 799 46331027 46330817 5.890000e-87 331.0
18 TraesCS5B01G127100 chr3D 95.305 213 7 2 587 798 108291053 108290843 4.550000e-88 335.0
19 TraesCS5B01G127100 chr3D 94.595 148 7 1 1 147 404431267 404431120 7.940000e-56 228.0
20 TraesCS5B01G127100 chr7D 94.836 213 8 2 587 798 326052755 326052545 2.120000e-86 329.0
21 TraesCS5B01G127100 chr4D 94.836 213 8 2 587 798 67339725 67339935 2.120000e-86 329.0
22 TraesCS5B01G127100 chr4B 95.238 147 7 0 1 147 633957799 633957945 1.710000e-57 233.0
23 TraesCS5B01G127100 chr4B 93.919 148 8 1 1 147 90455094 90455241 3.700000e-54 222.0
24 TraesCS5B01G127100 chr7B 94.595 148 7 1 1 147 702326173 702326026 7.940000e-56 228.0
25 TraesCS5B01G127100 chr2B 94.595 148 7 1 1 147 717480211 717480358 7.940000e-56 228.0
26 TraesCS5B01G127100 chr2B 90.698 43 3 1 2143 2185 131182289 131182248 3.970000e-04 56.5
27 TraesCS5B01G127100 chr2A 94.558 147 8 0 1 147 176657402 176657548 7.940000e-56 228.0
28 TraesCS5B01G127100 chr2A 96.403 139 4 1 1 138 765573572 765573710 7.940000e-56 228.0
29 TraesCS5B01G127100 chr3A 93.377 151 9 1 1 150 662832119 662831969 3.700000e-54 222.0


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 TraesCS5B01G127100 chr5B 232292788 232295637 2849 False 5264.000000 5264 100.000000 1 2850 1 chr5B.!!$F1 2849
1 TraesCS5B01G127100 chr5A 285395511 285397522 2011 False 3177.000000 3177 95.130000 829 2850 1 chr5A.!!$F2 2021
2 TraesCS5B01G127100 chr5D 216151885 216155914 4029 False 663.316667 3064 95.977333 226 2850 6 chr5D.!!$F1 2624
3 TraesCS5B01G127100 chr6D 24219409 24220477 1068 False 990.000000 990 83.956000 853 1912 1 chr6D.!!$F1 1059
4 TraesCS5B01G127100 chr6A 22684328 22685352 1024 False 894.000000 894 83.051000 854 1876 1 chr6A.!!$F1 1022
5 TraesCS5B01G127100 chr6B 39180405 39181475 1070 False 876.000000 876 82.482000 871 1900 1 chr6B.!!$F1 1029

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
134 135 0.114364 TCCATATAGCTCGGCCTCCA 59.886 55.0 0.00 0.0 0.0 3.86 F
191 192 0.250901 TCAGTTCCCTTCCAGCAAGC 60.251 55.0 0.00 0.0 0.0 4.01 F
608 1104 0.320421 TCTCAGTTTACAGGGCGTGC 60.320 55.0 7.17 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1479 3179 0.176680 ATGAGAGCCACCATGTCGTC 59.823 55.0 0.0 0.0 0.00 4.20 R
1505 3226 0.602372 GCTGCTGATCTTCCGATCCC 60.602 60.0 0.0 0.0 44.40 3.85 R
2246 3997 0.768221 TCCACTGAGAGCCAAAGGGT 60.768 55.0 0.0 0.0 36.17 4.34 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
27 28 9.761504 TTTCATCATGAATTTTTACACACATGT 57.238 25.926 0.00 0.00 38.32 3.21
28 29 9.194271 TTCATCATGAATTTTTACACACATGTG 57.806 29.630 24.25 24.25 40.52 3.21
49 50 7.234661 TGTGAGTTACATCCTTACATACACA 57.765 36.000 0.00 0.00 33.42 3.72
50 51 7.094631 TGTGAGTTACATCCTTACATACACAC 58.905 38.462 0.00 0.00 33.42 3.82
51 52 7.094631 GTGAGTTACATCCTTACATACACACA 58.905 38.462 0.00 0.00 0.00 3.72
52 53 7.764443 GTGAGTTACATCCTTACATACACACAT 59.236 37.037 0.00 0.00 0.00 3.21
53 54 8.973182 TGAGTTACATCCTTACATACACACATA 58.027 33.333 0.00 0.00 0.00 2.29
54 55 9.982651 GAGTTACATCCTTACATACACACATAT 57.017 33.333 0.00 0.00 0.00 1.78
97 98 9.883142 TGAACCATAAAAGTTTGAATTTGAACT 57.117 25.926 0.00 2.56 37.69 3.01
117 118 8.432110 TGAACTTTTCAAAAATAAAAGCCTCC 57.568 30.769 7.93 0.00 44.25 4.30
118 119 8.043710 TGAACTTTTCAAAAATAAAAGCCTCCA 58.956 29.630 7.93 0.58 44.25 3.86
119 120 8.978874 AACTTTTCAAAAATAAAAGCCTCCAT 57.021 26.923 7.93 0.00 44.25 3.41
124 125 9.816354 TTTCAAAAATAAAAGCCTCCATATAGC 57.184 29.630 0.00 0.00 0.00 2.97
125 126 8.766994 TCAAAAATAAAAGCCTCCATATAGCT 57.233 30.769 0.00 0.00 38.88 3.32
126 127 8.850156 TCAAAAATAAAAGCCTCCATATAGCTC 58.150 33.333 0.00 0.00 35.30 4.09
127 128 7.440523 AAAATAAAAGCCTCCATATAGCTCG 57.559 36.000 0.00 0.00 35.30 5.03
128 129 3.409026 AAAAGCCTCCATATAGCTCGG 57.591 47.619 0.00 0.00 35.30 4.63
129 130 0.610687 AAGCCTCCATATAGCTCGGC 59.389 55.000 0.00 0.00 35.30 5.54
130 131 1.219393 GCCTCCATATAGCTCGGCC 59.781 63.158 0.00 0.00 0.00 6.13
131 132 1.261238 GCCTCCATATAGCTCGGCCT 61.261 60.000 0.00 0.00 0.00 5.19
132 133 0.820871 CCTCCATATAGCTCGGCCTC 59.179 60.000 0.00 0.00 0.00 4.70
133 134 0.820871 CTCCATATAGCTCGGCCTCC 59.179 60.000 0.00 0.00 0.00 4.30
134 135 0.114364 TCCATATAGCTCGGCCTCCA 59.886 55.000 0.00 0.00 0.00 3.86
135 136 0.976641 CCATATAGCTCGGCCTCCAA 59.023 55.000 0.00 0.00 0.00 3.53
136 137 1.347707 CCATATAGCTCGGCCTCCAAA 59.652 52.381 0.00 0.00 0.00 3.28
137 138 2.224523 CCATATAGCTCGGCCTCCAAAA 60.225 50.000 0.00 0.00 0.00 2.44
138 139 2.614829 TATAGCTCGGCCTCCAAAAC 57.385 50.000 0.00 0.00 0.00 2.43
139 140 0.462047 ATAGCTCGGCCTCCAAAACG 60.462 55.000 0.00 0.00 0.00 3.60
140 141 2.515996 TAGCTCGGCCTCCAAAACGG 62.516 60.000 0.00 0.00 0.00 4.44
141 142 3.431725 CTCGGCCTCCAAAACGGC 61.432 66.667 0.00 0.00 45.55 5.68
142 143 3.901797 CTCGGCCTCCAAAACGGCT 62.902 63.158 0.00 0.00 45.57 5.52
143 144 3.431725 CGGCCTCCAAAACGGCTC 61.432 66.667 0.00 0.00 45.57 4.70
144 145 2.034221 GGCCTCCAAAACGGCTCT 59.966 61.111 0.00 0.00 45.57 4.09
145 146 2.041115 GGCCTCCAAAACGGCTCTC 61.041 63.158 0.00 0.00 45.57 3.20
146 147 1.003233 GCCTCCAAAACGGCTCTCT 60.003 57.895 0.00 0.00 42.98 3.10
147 148 0.606673 GCCTCCAAAACGGCTCTCTT 60.607 55.000 0.00 0.00 42.98 2.85
148 149 1.160137 CCTCCAAAACGGCTCTCTTG 58.840 55.000 0.00 0.00 33.14 3.02
149 150 1.160137 CTCCAAAACGGCTCTCTTGG 58.840 55.000 0.00 0.00 39.80 3.61
150 151 0.472471 TCCAAAACGGCTCTCTTGGT 59.528 50.000 7.67 0.00 39.51 3.67
151 152 1.695242 TCCAAAACGGCTCTCTTGGTA 59.305 47.619 7.67 0.00 39.51 3.25
152 153 2.076863 CCAAAACGGCTCTCTTGGTAG 58.923 52.381 0.00 0.00 34.77 3.18
153 154 2.076863 CAAAACGGCTCTCTTGGTAGG 58.923 52.381 0.00 0.00 0.00 3.18
154 155 1.349067 AAACGGCTCTCTTGGTAGGT 58.651 50.000 0.00 0.00 0.00 3.08
155 156 1.349067 AACGGCTCTCTTGGTAGGTT 58.651 50.000 0.00 0.00 0.00 3.50
156 157 0.608640 ACGGCTCTCTTGGTAGGTTG 59.391 55.000 0.00 0.00 0.00 3.77
157 158 0.608640 CGGCTCTCTTGGTAGGTTGT 59.391 55.000 0.00 0.00 0.00 3.32
158 159 1.002087 CGGCTCTCTTGGTAGGTTGTT 59.998 52.381 0.00 0.00 0.00 2.83
159 160 2.427506 GGCTCTCTTGGTAGGTTGTTG 58.572 52.381 0.00 0.00 0.00 3.33
160 161 2.224548 GGCTCTCTTGGTAGGTTGTTGT 60.225 50.000 0.00 0.00 0.00 3.32
161 162 3.477530 GCTCTCTTGGTAGGTTGTTGTT 58.522 45.455 0.00 0.00 0.00 2.83
162 163 4.504340 GGCTCTCTTGGTAGGTTGTTGTTA 60.504 45.833 0.00 0.00 0.00 2.41
163 164 5.246307 GCTCTCTTGGTAGGTTGTTGTTAT 58.754 41.667 0.00 0.00 0.00 1.89
164 165 5.351740 GCTCTCTTGGTAGGTTGTTGTTATC 59.648 44.000 0.00 0.00 0.00 1.75
165 166 5.475719 TCTCTTGGTAGGTTGTTGTTATCG 58.524 41.667 0.00 0.00 0.00 2.92
166 167 3.998341 TCTTGGTAGGTTGTTGTTATCGC 59.002 43.478 0.00 0.00 0.00 4.58
167 168 2.702261 TGGTAGGTTGTTGTTATCGCC 58.298 47.619 0.00 0.00 0.00 5.54
168 169 1.662122 GGTAGGTTGTTGTTATCGCCG 59.338 52.381 0.00 0.00 0.00 6.46
169 170 2.609350 GTAGGTTGTTGTTATCGCCGA 58.391 47.619 0.00 0.00 0.00 5.54
170 171 1.435577 AGGTTGTTGTTATCGCCGAC 58.564 50.000 0.00 0.00 0.00 4.79
171 172 1.001633 AGGTTGTTGTTATCGCCGACT 59.998 47.619 0.00 0.00 0.00 4.18
172 173 1.802365 GGTTGTTGTTATCGCCGACTT 59.198 47.619 0.00 0.00 0.00 3.01
173 174 2.159747 GGTTGTTGTTATCGCCGACTTC 60.160 50.000 0.00 0.00 0.00 3.01
174 175 2.442212 TGTTGTTATCGCCGACTTCA 57.558 45.000 0.00 0.00 0.00 3.02
175 176 2.333926 TGTTGTTATCGCCGACTTCAG 58.666 47.619 0.00 0.00 0.00 3.02
176 177 2.288579 TGTTGTTATCGCCGACTTCAGT 60.289 45.455 0.00 0.00 0.00 3.41
177 178 2.735134 GTTGTTATCGCCGACTTCAGTT 59.265 45.455 0.00 0.00 0.00 3.16
178 179 2.602878 TGTTATCGCCGACTTCAGTTC 58.397 47.619 0.00 0.00 0.00 3.01
179 180 1.925185 GTTATCGCCGACTTCAGTTCC 59.075 52.381 0.00 0.00 0.00 3.62
180 181 0.458669 TATCGCCGACTTCAGTTCCC 59.541 55.000 0.00 0.00 0.00 3.97
181 182 1.258445 ATCGCCGACTTCAGTTCCCT 61.258 55.000 0.00 0.00 0.00 4.20
182 183 1.004918 CGCCGACTTCAGTTCCCTT 60.005 57.895 0.00 0.00 0.00 3.95
183 184 1.014564 CGCCGACTTCAGTTCCCTTC 61.015 60.000 0.00 0.00 0.00 3.46
184 185 0.673956 GCCGACTTCAGTTCCCTTCC 60.674 60.000 0.00 0.00 0.00 3.46
185 186 0.685097 CCGACTTCAGTTCCCTTCCA 59.315 55.000 0.00 0.00 0.00 3.53
186 187 1.338200 CCGACTTCAGTTCCCTTCCAG 60.338 57.143 0.00 0.00 0.00 3.86
187 188 1.814793 GACTTCAGTTCCCTTCCAGC 58.185 55.000 0.00 0.00 0.00 4.85
188 189 1.072331 GACTTCAGTTCCCTTCCAGCA 59.928 52.381 0.00 0.00 0.00 4.41
189 190 1.494721 ACTTCAGTTCCCTTCCAGCAA 59.505 47.619 0.00 0.00 0.00 3.91
190 191 2.157738 CTTCAGTTCCCTTCCAGCAAG 58.842 52.381 0.00 0.00 0.00 4.01
191 192 0.250901 TCAGTTCCCTTCCAGCAAGC 60.251 55.000 0.00 0.00 0.00 4.01
192 193 0.538057 CAGTTCCCTTCCAGCAAGCA 60.538 55.000 0.00 0.00 0.00 3.91
193 194 0.407139 AGTTCCCTTCCAGCAAGCAT 59.593 50.000 0.00 0.00 0.00 3.79
194 195 1.203100 AGTTCCCTTCCAGCAAGCATT 60.203 47.619 0.00 0.00 0.00 3.56
195 196 1.620323 GTTCCCTTCCAGCAAGCATTT 59.380 47.619 0.00 0.00 0.00 2.32
196 197 2.825532 GTTCCCTTCCAGCAAGCATTTA 59.174 45.455 0.00 0.00 0.00 1.40
197 198 2.726821 TCCCTTCCAGCAAGCATTTAG 58.273 47.619 0.00 0.00 0.00 1.85
198 199 2.308570 TCCCTTCCAGCAAGCATTTAGA 59.691 45.455 0.00 0.00 0.00 2.10
199 200 3.091545 CCCTTCCAGCAAGCATTTAGAA 58.908 45.455 0.00 0.00 0.00 2.10
200 201 3.119352 CCCTTCCAGCAAGCATTTAGAAC 60.119 47.826 0.00 0.00 0.00 3.01
201 202 3.119352 CCTTCCAGCAAGCATTTAGAACC 60.119 47.826 0.00 0.00 0.00 3.62
202 203 2.446435 TCCAGCAAGCATTTAGAACCC 58.554 47.619 0.00 0.00 0.00 4.11
203 204 1.478105 CCAGCAAGCATTTAGAACCCC 59.522 52.381 0.00 0.00 0.00 4.95
204 205 2.170166 CAGCAAGCATTTAGAACCCCA 58.830 47.619 0.00 0.00 0.00 4.96
205 206 2.762327 CAGCAAGCATTTAGAACCCCAT 59.238 45.455 0.00 0.00 0.00 4.00
206 207 3.196254 CAGCAAGCATTTAGAACCCCATT 59.804 43.478 0.00 0.00 0.00 3.16
207 208 3.840078 AGCAAGCATTTAGAACCCCATTT 59.160 39.130 0.00 0.00 0.00 2.32
208 209 3.934579 GCAAGCATTTAGAACCCCATTTG 59.065 43.478 0.00 0.00 0.00 2.32
209 210 4.563374 GCAAGCATTTAGAACCCCATTTGT 60.563 41.667 0.00 0.00 0.00 2.83
210 211 5.170748 CAAGCATTTAGAACCCCATTTGTC 58.829 41.667 0.00 0.00 0.00 3.18
211 212 3.769300 AGCATTTAGAACCCCATTTGTCC 59.231 43.478 0.00 0.00 0.00 4.02
212 213 3.118775 GCATTTAGAACCCCATTTGTCCC 60.119 47.826 0.00 0.00 0.00 4.46
213 214 3.905493 TTTAGAACCCCATTTGTCCCA 57.095 42.857 0.00 0.00 0.00 4.37
214 215 3.449746 TTAGAACCCCATTTGTCCCAG 57.550 47.619 0.00 0.00 0.00 4.45
215 216 1.455822 AGAACCCCATTTGTCCCAGA 58.544 50.000 0.00 0.00 0.00 3.86
216 217 1.786441 AGAACCCCATTTGTCCCAGAA 59.214 47.619 0.00 0.00 0.00 3.02
217 218 2.178984 AGAACCCCATTTGTCCCAGAAA 59.821 45.455 0.00 0.00 0.00 2.52
218 219 3.173151 GAACCCCATTTGTCCCAGAAAT 58.827 45.455 0.00 0.00 0.00 2.17
219 220 4.045334 AGAACCCCATTTGTCCCAGAAATA 59.955 41.667 0.00 0.00 0.00 1.40
220 221 4.625225 ACCCCATTTGTCCCAGAAATAT 57.375 40.909 0.00 0.00 0.00 1.28
221 222 4.289245 ACCCCATTTGTCCCAGAAATATG 58.711 43.478 0.00 0.00 0.00 1.78
222 223 4.264804 ACCCCATTTGTCCCAGAAATATGT 60.265 41.667 0.00 0.00 0.00 2.29
223 224 5.043732 ACCCCATTTGTCCCAGAAATATGTA 60.044 40.000 0.00 0.00 0.00 2.29
224 225 6.077322 CCCCATTTGTCCCAGAAATATGTAT 58.923 40.000 0.00 0.00 0.00 2.29
306 307 5.163854 GCGTATGATTATGATACAGGGCAAC 60.164 44.000 3.04 0.00 0.00 4.17
323 653 1.935873 CAACTACCATCATGTCCAGCG 59.064 52.381 0.00 0.00 0.00 5.18
334 664 0.596577 TGTCCAGCGTGTAGTCACTC 59.403 55.000 0.00 0.00 41.89 3.51
350 680 6.019656 AGTCACTCTAGGTATCCATGAAGA 57.980 41.667 0.00 0.00 0.00 2.87
391 721 0.946221 AGCGAACAGTTCAAGGCTCG 60.946 55.000 13.82 0.00 0.00 5.03
424 919 6.170506 TGAGACTGACTGTGTTACAAAGTTT 58.829 36.000 9.79 0.00 31.26 2.66
436 931 9.843334 TGTGTTACAAAGTTTAACTGTTTAAGG 57.157 29.630 0.00 0.00 31.74 2.69
494 990 1.153628 GACCCCGTGACTTCCATCG 60.154 63.158 0.00 0.00 0.00 3.84
502 998 2.044946 ACTTCCATCGGGCCAAGC 60.045 61.111 4.39 0.00 0.00 4.01
534 1030 5.619981 GCCACATCTGTCCATAAACTTCAAC 60.620 44.000 0.00 0.00 0.00 3.18
575 1071 7.561021 TTGTTTGTAACTGTAGCATTTCTCA 57.439 32.000 0.00 0.00 0.00 3.27
580 1076 7.977789 TGTAACTGTAGCATTTCTCATGAAA 57.022 32.000 0.00 0.00 44.99 2.69
581 1077 8.032952 TGTAACTGTAGCATTTCTCATGAAAG 57.967 34.615 0.00 0.00 44.25 2.62
582 1078 7.661437 TGTAACTGTAGCATTTCTCATGAAAGT 59.339 33.333 0.00 0.00 44.25 2.66
583 1079 6.492007 ACTGTAGCATTTCTCATGAAAGTG 57.508 37.500 0.00 3.25 44.25 3.16
584 1080 5.106396 ACTGTAGCATTTCTCATGAAAGTGC 60.106 40.000 20.22 20.22 44.25 4.40
585 1081 3.482722 AGCATTTCTCATGAAAGTGCG 57.517 42.857 20.92 2.88 44.25 5.34
586 1082 1.916000 GCATTTCTCATGAAAGTGCGC 59.084 47.619 16.25 0.00 44.25 6.09
587 1083 2.415090 GCATTTCTCATGAAAGTGCGCT 60.415 45.455 9.73 0.00 44.25 5.92
588 1084 3.423571 CATTTCTCATGAAAGTGCGCTC 58.576 45.455 9.73 4.74 44.25 5.03
589 1085 2.462456 TTCTCATGAAAGTGCGCTCT 57.538 45.000 9.73 7.80 0.00 4.09
590 1086 2.001812 TCTCATGAAAGTGCGCTCTC 57.998 50.000 13.07 0.00 0.00 3.20
591 1087 1.547820 TCTCATGAAAGTGCGCTCTCT 59.452 47.619 13.07 0.00 0.00 3.10
592 1088 1.925847 CTCATGAAAGTGCGCTCTCTC 59.074 52.381 13.07 9.27 0.00 3.20
593 1089 1.273327 TCATGAAAGTGCGCTCTCTCA 59.727 47.619 16.97 16.97 0.00 3.27
594 1090 1.659601 CATGAAAGTGCGCTCTCTCAG 59.340 52.381 19.07 9.04 0.00 3.35
595 1091 0.676184 TGAAAGTGCGCTCTCTCAGT 59.324 50.000 11.25 0.00 0.00 3.41
596 1092 1.069204 TGAAAGTGCGCTCTCTCAGTT 59.931 47.619 11.25 2.35 0.00 3.16
597 1093 2.139118 GAAAGTGCGCTCTCTCAGTTT 58.861 47.619 13.07 4.01 38.22 2.66
598 1094 3.243737 TGAAAGTGCGCTCTCTCAGTTTA 60.244 43.478 11.25 0.00 36.35 2.01
599 1095 2.355717 AGTGCGCTCTCTCAGTTTAC 57.644 50.000 9.73 0.00 0.00 2.01
600 1096 1.613925 AGTGCGCTCTCTCAGTTTACA 59.386 47.619 9.73 0.00 0.00 2.41
601 1097 1.989165 GTGCGCTCTCTCAGTTTACAG 59.011 52.381 9.73 0.00 0.00 2.74
602 1098 1.067565 TGCGCTCTCTCAGTTTACAGG 60.068 52.381 9.73 0.00 0.00 4.00
603 1099 1.737363 GCGCTCTCTCAGTTTACAGGG 60.737 57.143 0.00 0.00 0.00 4.45
604 1100 1.737363 CGCTCTCTCAGTTTACAGGGC 60.737 57.143 0.00 0.00 0.00 5.19
605 1101 1.737363 GCTCTCTCAGTTTACAGGGCG 60.737 57.143 0.00 0.00 0.00 6.13
606 1102 1.546476 CTCTCTCAGTTTACAGGGCGT 59.454 52.381 0.00 0.00 0.00 5.68
607 1103 1.272490 TCTCTCAGTTTACAGGGCGTG 59.728 52.381 5.50 5.50 0.00 5.34
608 1104 0.320421 TCTCAGTTTACAGGGCGTGC 60.320 55.000 7.17 0.00 0.00 5.34
609 1105 1.626654 CTCAGTTTACAGGGCGTGCG 61.627 60.000 7.17 0.00 0.00 5.34
610 1106 3.047877 AGTTTACAGGGCGTGCGC 61.048 61.111 7.17 8.17 41.06 6.09
611 1107 4.439472 GTTTACAGGGCGTGCGCG 62.439 66.667 16.86 16.86 43.06 6.86
612 1108 4.973055 TTTACAGGGCGTGCGCGT 62.973 61.111 22.18 2.94 43.06 6.01
613 1109 3.570621 TTTACAGGGCGTGCGCGTA 62.571 57.895 22.18 0.00 43.06 4.42
614 1110 4.781959 TACAGGGCGTGCGCGTAC 62.782 66.667 22.18 17.94 43.06 3.67
621 1117 4.564116 CGTGCGCGTACCCCTAGG 62.564 72.222 21.71 0.06 40.04 3.02
623 1119 3.142838 TGCGCGTACCCCTAGGTC 61.143 66.667 8.43 0.00 46.45 3.85
624 1120 4.261781 GCGCGTACCCCTAGGTCG 62.262 72.222 8.43 8.12 46.45 4.79
625 1121 2.825836 CGCGTACCCCTAGGTCGT 60.826 66.667 8.29 6.00 46.45 4.34
626 1122 2.409870 CGCGTACCCCTAGGTCGTT 61.410 63.158 8.29 0.00 46.45 3.85
627 1123 1.095228 CGCGTACCCCTAGGTCGTTA 61.095 60.000 8.29 0.00 46.45 3.18
628 1124 1.102978 GCGTACCCCTAGGTCGTTAA 58.897 55.000 8.29 0.00 46.45 2.01
629 1125 1.683385 GCGTACCCCTAGGTCGTTAAT 59.317 52.381 8.29 0.00 46.45 1.40
630 1126 2.101415 GCGTACCCCTAGGTCGTTAATT 59.899 50.000 8.29 0.00 46.45 1.40
631 1127 3.430790 GCGTACCCCTAGGTCGTTAATTT 60.431 47.826 8.29 0.00 46.45 1.82
632 1128 4.114794 CGTACCCCTAGGTCGTTAATTTG 58.885 47.826 8.29 0.00 46.45 2.32
633 1129 4.142182 CGTACCCCTAGGTCGTTAATTTGA 60.142 45.833 8.29 0.00 46.45 2.69
634 1130 4.212143 ACCCCTAGGTCGTTAATTTGAC 57.788 45.455 8.29 0.00 46.45 3.18
635 1131 3.054875 ACCCCTAGGTCGTTAATTTGACC 60.055 47.826 8.29 13.65 46.45 4.02
646 1142 8.031848 GTCGTTAATTTGACCAACCTAATACA 57.968 34.615 0.00 0.00 0.00 2.29
647 1143 8.505625 GTCGTTAATTTGACCAACCTAATACAA 58.494 33.333 0.00 0.00 0.00 2.41
648 1144 8.723311 TCGTTAATTTGACCAACCTAATACAAG 58.277 33.333 0.00 0.00 0.00 3.16
649 1145 8.508875 CGTTAATTTGACCAACCTAATACAAGT 58.491 33.333 0.00 0.00 0.00 3.16
650 1146 9.836076 GTTAATTTGACCAACCTAATACAAGTC 57.164 33.333 0.00 0.00 0.00 3.01
651 1147 9.575868 TTAATTTGACCAACCTAATACAAGTCA 57.424 29.630 0.00 0.00 0.00 3.41
652 1148 8.650143 AATTTGACCAACCTAATACAAGTCAT 57.350 30.769 0.00 0.00 33.21 3.06
653 1149 9.747898 AATTTGACCAACCTAATACAAGTCATA 57.252 29.630 0.00 0.00 33.21 2.15
654 1150 9.920946 ATTTGACCAACCTAATACAAGTCATAT 57.079 29.630 0.00 0.00 33.21 1.78
705 1201 9.450807 AAACTTCAGATGTTCTATTTTCAAACG 57.549 29.630 2.28 0.00 0.00 3.60
706 1202 7.078228 ACTTCAGATGTTCTATTTTCAAACGC 58.922 34.615 0.00 0.00 0.00 4.84
707 1203 6.801539 TCAGATGTTCTATTTTCAAACGCT 57.198 33.333 0.00 0.00 0.00 5.07
708 1204 7.899178 TCAGATGTTCTATTTTCAAACGCTA 57.101 32.000 0.00 0.00 0.00 4.26
709 1205 8.492673 TCAGATGTTCTATTTTCAAACGCTAT 57.507 30.769 0.00 0.00 0.00 2.97
710 1206 9.594478 TCAGATGTTCTATTTTCAAACGCTATA 57.406 29.630 0.00 0.00 0.00 1.31
770 1266 9.745880 AAATTGACAACCTAGATATACACGTAG 57.254 33.333 0.00 0.00 0.00 3.51
771 1267 6.872628 TGACAACCTAGATATACACGTAGG 57.127 41.667 0.00 0.00 38.45 3.18
772 1268 6.594744 TGACAACCTAGATATACACGTAGGA 58.405 40.000 3.81 0.00 36.34 2.94
773 1269 6.484643 TGACAACCTAGATATACACGTAGGAC 59.515 42.308 3.81 0.00 36.34 3.85
774 1270 6.599445 ACAACCTAGATATACACGTAGGACT 58.401 40.000 3.81 0.00 36.34 3.85
775 1271 7.059156 ACAACCTAGATATACACGTAGGACTT 58.941 38.462 3.81 0.00 36.34 3.01
776 1272 7.013083 ACAACCTAGATATACACGTAGGACTTG 59.987 40.741 3.81 2.11 36.34 3.16
777 1273 6.599445 ACCTAGATATACACGTAGGACTTGT 58.401 40.000 3.81 0.00 36.34 3.16
778 1274 7.739825 ACCTAGATATACACGTAGGACTTGTA 58.260 38.462 3.81 0.00 37.27 2.41
779 1275 8.213679 ACCTAGATATACACGTAGGACTTGTAA 58.786 37.037 3.81 0.00 36.60 2.41
780 1276 9.060347 CCTAGATATACACGTAGGACTTGTAAA 57.940 37.037 0.00 0.00 36.60 2.01
781 1277 9.875675 CTAGATATACACGTAGGACTTGTAAAC 57.124 37.037 0.00 0.00 36.60 2.01
782 1278 8.517062 AGATATACACGTAGGACTTGTAAACT 57.483 34.615 0.00 0.00 36.60 2.66
783 1279 8.404000 AGATATACACGTAGGACTTGTAAACTG 58.596 37.037 0.00 0.00 36.60 3.16
784 1280 4.924305 ACACGTAGGACTTGTAAACTGA 57.076 40.909 0.00 0.00 28.16 3.41
785 1281 5.266733 ACACGTAGGACTTGTAAACTGAA 57.733 39.130 0.00 0.00 28.16 3.02
786 1282 5.663456 ACACGTAGGACTTGTAAACTGAAA 58.337 37.500 0.00 0.00 28.16 2.69
787 1283 5.521372 ACACGTAGGACTTGTAAACTGAAAC 59.479 40.000 0.00 0.00 28.16 2.78
788 1284 4.741676 ACGTAGGACTTGTAAACTGAAACG 59.258 41.667 0.00 0.00 0.00 3.60
789 1285 4.149396 CGTAGGACTTGTAAACTGAAACGG 59.851 45.833 0.00 0.00 0.00 4.44
790 1286 4.411256 AGGACTTGTAAACTGAAACGGA 57.589 40.909 0.00 0.00 0.00 4.69
791 1287 4.377897 AGGACTTGTAAACTGAAACGGAG 58.622 43.478 0.00 0.00 0.00 4.63
792 1288 3.497262 GGACTTGTAAACTGAAACGGAGG 59.503 47.826 0.00 0.00 0.00 4.30
793 1289 4.374399 GACTTGTAAACTGAAACGGAGGA 58.626 43.478 0.00 0.00 0.00 3.71
794 1290 4.773013 ACTTGTAAACTGAAACGGAGGAA 58.227 39.130 0.00 0.00 0.00 3.36
795 1291 4.814771 ACTTGTAAACTGAAACGGAGGAAG 59.185 41.667 0.00 0.00 0.00 3.46
796 1292 4.411256 TGTAAACTGAAACGGAGGAAGT 57.589 40.909 0.00 0.00 0.00 3.01
797 1293 5.534207 TGTAAACTGAAACGGAGGAAGTA 57.466 39.130 0.00 0.00 0.00 2.24
798 1294 5.535333 TGTAAACTGAAACGGAGGAAGTAG 58.465 41.667 0.00 0.00 0.00 2.57
799 1295 3.679824 AACTGAAACGGAGGAAGTAGG 57.320 47.619 0.00 0.00 0.00 3.18
800 1296 1.900486 ACTGAAACGGAGGAAGTAGGG 59.100 52.381 0.00 0.00 0.00 3.53
801 1297 0.611714 TGAAACGGAGGAAGTAGGGC 59.388 55.000 0.00 0.00 0.00 5.19
844 2452 6.753107 ATGGTTATAGCTTGTTGTTGTACC 57.247 37.500 0.00 0.00 0.00 3.34
1222 2910 1.668101 GACGGCGAGATCCTCAAGGT 61.668 60.000 16.62 0.00 36.34 3.50
1321 3015 0.528901 CAACACCTCAACGACGTCCA 60.529 55.000 10.58 0.00 0.00 4.02
1365 3059 1.070105 CGTTTGTTCCCCTCCGACA 59.930 57.895 0.00 0.00 0.00 4.35
1459 3159 4.802051 GCGGATGCTGGGCAAGGA 62.802 66.667 0.00 0.00 43.62 3.36
1460 3160 2.825836 CGGATGCTGGGCAAGGAC 60.826 66.667 0.00 0.00 43.62 3.85
1461 3161 2.825836 GGATGCTGGGCAAGGACG 60.826 66.667 0.00 0.00 43.62 4.79
1462 3162 2.268920 GATGCTGGGCAAGGACGA 59.731 61.111 0.00 0.00 43.62 4.20
1463 3163 2.045926 ATGCTGGGCAAGGACGAC 60.046 61.111 0.00 0.00 43.62 4.34
1464 3164 3.628646 ATGCTGGGCAAGGACGACC 62.629 63.158 0.00 0.00 43.62 4.79
1465 3165 4.329545 GCTGGGCAAGGACGACCA 62.330 66.667 6.71 0.00 38.94 4.02
1466 3166 2.046892 CTGGGCAAGGACGACCAG 60.047 66.667 6.71 0.00 43.87 4.00
1467 3167 3.612247 CTGGGCAAGGACGACCAGG 62.612 68.421 6.71 0.00 45.21 4.45
1505 3226 1.817099 GGTGGCTCTCATGCGAAGG 60.817 63.158 0.00 0.00 0.00 3.46
1612 3337 9.429359 CGGTGATTTATTCTATTAGCAGAAGAT 57.571 33.333 0.00 0.00 37.93 2.40
1652 3377 1.965643 AGCTTGCTGGAGAAAATGCAA 59.034 42.857 0.00 0.00 42.16 4.08
1668 3394 9.321562 AGAAAATGCAAATTGGATAATAAGCAG 57.678 29.630 0.00 0.00 38.63 4.24
1968 3719 2.125106 ACCCTTCTTGGCGATCGC 60.125 61.111 31.52 31.52 41.06 4.58
2018 3769 6.714810 TGGGCATGTATAATGGTTGATAAGTC 59.285 38.462 0.00 0.00 0.00 3.01
2220 3971 5.472478 CCACCTCATCATTTATCTCACATGG 59.528 44.000 0.00 0.00 0.00 3.66
2246 3997 5.901276 ACTTCCTAGGATAACACGGGAAATA 59.099 40.000 13.57 0.00 33.31 1.40
2263 4014 3.356529 AATACCCTTTGGCTCTCAGTG 57.643 47.619 0.00 0.00 33.59 3.66
2308 4059 6.706055 TCGCAGAAGTAGTTTCAAACATAG 57.294 37.500 2.41 0.00 38.31 2.23
2350 4101 4.037208 CAGGAAAATTGACTTGCACAGAGT 59.963 41.667 0.00 0.00 0.00 3.24
2537 4288 8.157476 AGTCAAACAGATATCCAACAACTTAGT 58.843 33.333 0.00 0.00 0.00 2.24
2589 4340 5.572211 CATATAACACACACACTTCCATGC 58.428 41.667 0.00 0.00 0.00 4.06
2594 4345 0.662619 CACACACTTCCATGCGTTGT 59.337 50.000 0.00 0.00 0.00 3.32
2609 4360 3.940221 TGCGTTGTTAGTGGTGTTTAGTT 59.060 39.130 0.00 0.00 0.00 2.24
2764 4516 4.540824 GAACACTCTGCCATTTCAAAGAC 58.459 43.478 0.00 0.00 0.00 3.01
2775 4527 1.229428 TTCAAAGACGCTGAAGGCAG 58.771 50.000 0.00 0.00 45.13 4.85
2788 4540 4.318332 CTGAAGGCAGAACAGTGAACATA 58.682 43.478 0.00 0.00 45.17 2.29
2834 4586 7.576287 GCATTCTTGTTCTGATGATTCTTTGGA 60.576 37.037 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.761504 ACATGTGTGTAAAAATTCATGATGAAA 57.238 25.926 12.36 0.00 37.02 2.69
2 3 9.194271 CACATGTGTGTAAAAATTCATGATGAA 57.806 29.630 18.03 10.65 39.72 2.57
3 4 8.574737 TCACATGTGTGTAAAAATTCATGATGA 58.425 29.630 24.63 0.00 45.76 2.92
4 5 8.745464 TCACATGTGTGTAAAAATTCATGATG 57.255 30.769 24.63 0.00 45.76 3.07
5 6 8.579006 ACTCACATGTGTGTAAAAATTCATGAT 58.421 29.630 27.36 2.52 45.76 2.45
6 7 7.939782 ACTCACATGTGTGTAAAAATTCATGA 58.060 30.769 27.36 2.56 45.76 3.07
7 8 8.578308 AACTCACATGTGTGTAAAAATTCATG 57.422 30.769 28.35 0.00 45.76 3.07
8 9 9.677567 GTAACTCACATGTGTGTAAAAATTCAT 57.322 29.630 28.35 14.99 45.76 2.57
9 10 8.678199 TGTAACTCACATGTGTGTAAAAATTCA 58.322 29.630 28.35 16.00 45.76 2.57
10 11 9.677567 ATGTAACTCACATGTGTGTAAAAATTC 57.322 29.630 28.35 14.03 46.41 2.17
25 26 7.094631 GTGTGTATGTAAGGATGTAACTCACA 58.905 38.462 0.00 0.00 42.69 3.58
26 27 7.094631 TGTGTGTATGTAAGGATGTAACTCAC 58.905 38.462 0.00 0.00 33.07 3.51
27 28 7.234661 TGTGTGTATGTAAGGATGTAACTCA 57.765 36.000 0.00 0.00 0.00 3.41
28 29 9.982651 ATATGTGTGTATGTAAGGATGTAACTC 57.017 33.333 0.00 0.00 0.00 3.01
71 72 9.883142 AGTTCAAATTCAAACTTTTATGGTTCA 57.117 25.926 0.75 0.00 31.81 3.18
92 93 8.043710 TGGAGGCTTTTATTTTTGAAAAGTTCA 58.956 29.630 9.03 0.00 43.06 3.18
93 94 8.432110 TGGAGGCTTTTATTTTTGAAAAGTTC 57.568 30.769 9.03 7.45 43.06 3.01
94 95 8.978874 ATGGAGGCTTTTATTTTTGAAAAGTT 57.021 26.923 9.03 0.19 43.06 2.66
98 99 9.816354 GCTATATGGAGGCTTTTATTTTTGAAA 57.184 29.630 0.00 0.00 0.00 2.69
99 100 9.200817 AGCTATATGGAGGCTTTTATTTTTGAA 57.799 29.630 0.00 0.00 31.81 2.69
100 101 8.766994 AGCTATATGGAGGCTTTTATTTTTGA 57.233 30.769 0.00 0.00 31.81 2.69
101 102 7.805071 CGAGCTATATGGAGGCTTTTATTTTTG 59.195 37.037 0.00 0.00 36.37 2.44
102 103 7.040409 CCGAGCTATATGGAGGCTTTTATTTTT 60.040 37.037 0.00 0.00 36.37 1.94
103 104 6.431234 CCGAGCTATATGGAGGCTTTTATTTT 59.569 38.462 0.00 0.00 36.37 1.82
104 105 5.940470 CCGAGCTATATGGAGGCTTTTATTT 59.060 40.000 0.00 0.00 36.37 1.40
105 106 5.491982 CCGAGCTATATGGAGGCTTTTATT 58.508 41.667 0.00 0.00 36.37 1.40
106 107 4.624125 GCCGAGCTATATGGAGGCTTTTAT 60.624 45.833 11.48 0.00 41.21 1.40
107 108 3.306780 GCCGAGCTATATGGAGGCTTTTA 60.307 47.826 11.48 0.00 41.21 1.52
108 109 2.551071 GCCGAGCTATATGGAGGCTTTT 60.551 50.000 11.48 0.00 41.21 2.27
109 110 1.002544 GCCGAGCTATATGGAGGCTTT 59.997 52.381 11.48 0.00 41.21 3.51
110 111 0.610687 GCCGAGCTATATGGAGGCTT 59.389 55.000 11.48 0.00 41.21 4.35
111 112 1.261238 GGCCGAGCTATATGGAGGCT 61.261 60.000 16.02 0.00 43.68 4.58
112 113 1.219393 GGCCGAGCTATATGGAGGC 59.781 63.158 10.65 10.65 43.47 4.70
113 114 0.820871 GAGGCCGAGCTATATGGAGG 59.179 60.000 0.00 0.00 0.00 4.30
114 115 0.820871 GGAGGCCGAGCTATATGGAG 59.179 60.000 0.00 0.00 0.00 3.86
115 116 0.114364 TGGAGGCCGAGCTATATGGA 59.886 55.000 0.00 0.00 0.00 3.41
116 117 0.976641 TTGGAGGCCGAGCTATATGG 59.023 55.000 0.00 0.00 0.00 2.74
117 118 2.808543 GTTTTGGAGGCCGAGCTATATG 59.191 50.000 0.00 0.00 0.00 1.78
118 119 2.548067 CGTTTTGGAGGCCGAGCTATAT 60.548 50.000 0.00 0.00 0.00 0.86
119 120 1.202486 CGTTTTGGAGGCCGAGCTATA 60.202 52.381 0.00 0.00 0.00 1.31
120 121 0.462047 CGTTTTGGAGGCCGAGCTAT 60.462 55.000 0.00 0.00 0.00 2.97
121 122 1.079405 CGTTTTGGAGGCCGAGCTA 60.079 57.895 0.00 0.00 0.00 3.32
122 123 2.358737 CGTTTTGGAGGCCGAGCT 60.359 61.111 0.00 0.00 0.00 4.09
123 124 3.431725 CCGTTTTGGAGGCCGAGC 61.432 66.667 0.00 0.00 42.00 5.03
129 130 1.160137 CAAGAGAGCCGTTTTGGAGG 58.840 55.000 0.00 0.00 42.00 4.30
130 131 1.160137 CCAAGAGAGCCGTTTTGGAG 58.840 55.000 0.01 0.00 42.05 3.86
131 132 0.472471 ACCAAGAGAGCCGTTTTGGA 59.528 50.000 11.12 0.00 42.05 3.53
132 133 2.076863 CTACCAAGAGAGCCGTTTTGG 58.923 52.381 4.18 4.18 44.38 3.28
133 134 2.076863 CCTACCAAGAGAGCCGTTTTG 58.923 52.381 0.00 0.00 0.00 2.44
134 135 1.697982 ACCTACCAAGAGAGCCGTTTT 59.302 47.619 0.00 0.00 0.00 2.43
135 136 1.349067 ACCTACCAAGAGAGCCGTTT 58.651 50.000 0.00 0.00 0.00 3.60
136 137 1.002087 CAACCTACCAAGAGAGCCGTT 59.998 52.381 0.00 0.00 0.00 4.44
137 138 0.608640 CAACCTACCAAGAGAGCCGT 59.391 55.000 0.00 0.00 0.00 5.68
138 139 0.608640 ACAACCTACCAAGAGAGCCG 59.391 55.000 0.00 0.00 0.00 5.52
139 140 2.224548 ACAACAACCTACCAAGAGAGCC 60.225 50.000 0.00 0.00 0.00 4.70
140 141 3.127425 ACAACAACCTACCAAGAGAGC 57.873 47.619 0.00 0.00 0.00 4.09
141 142 5.577164 CGATAACAACAACCTACCAAGAGAG 59.423 44.000 0.00 0.00 0.00 3.20
142 143 5.475719 CGATAACAACAACCTACCAAGAGA 58.524 41.667 0.00 0.00 0.00 3.10
143 144 4.092968 GCGATAACAACAACCTACCAAGAG 59.907 45.833 0.00 0.00 0.00 2.85
144 145 3.998341 GCGATAACAACAACCTACCAAGA 59.002 43.478 0.00 0.00 0.00 3.02
145 146 3.126343 GGCGATAACAACAACCTACCAAG 59.874 47.826 0.00 0.00 0.00 3.61
146 147 3.075884 GGCGATAACAACAACCTACCAA 58.924 45.455 0.00 0.00 0.00 3.67
147 148 2.702261 GGCGATAACAACAACCTACCA 58.298 47.619 0.00 0.00 0.00 3.25
148 149 1.662122 CGGCGATAACAACAACCTACC 59.338 52.381 0.00 0.00 0.00 3.18
149 150 2.346545 GTCGGCGATAACAACAACCTAC 59.653 50.000 14.79 0.00 0.00 3.18
150 151 2.231964 AGTCGGCGATAACAACAACCTA 59.768 45.455 14.79 0.00 0.00 3.08
151 152 1.001633 AGTCGGCGATAACAACAACCT 59.998 47.619 14.79 0.00 0.00 3.50
152 153 1.435577 AGTCGGCGATAACAACAACC 58.564 50.000 14.79 0.00 0.00 3.77
153 154 2.477375 TGAAGTCGGCGATAACAACAAC 59.523 45.455 14.79 0.00 0.00 3.32
154 155 2.734606 CTGAAGTCGGCGATAACAACAA 59.265 45.455 14.79 0.00 0.00 2.83
155 156 2.288579 ACTGAAGTCGGCGATAACAACA 60.289 45.455 14.79 7.36 0.00 3.33
156 157 2.334838 ACTGAAGTCGGCGATAACAAC 58.665 47.619 14.79 0.00 0.00 3.32
157 158 2.736144 ACTGAAGTCGGCGATAACAA 57.264 45.000 14.79 0.00 0.00 2.83
158 159 2.602878 GAACTGAAGTCGGCGATAACA 58.397 47.619 14.79 12.34 0.00 2.41
159 160 1.925185 GGAACTGAAGTCGGCGATAAC 59.075 52.381 14.79 8.03 0.00 1.89
160 161 1.134907 GGGAACTGAAGTCGGCGATAA 60.135 52.381 14.79 0.00 0.00 1.75
161 162 0.458669 GGGAACTGAAGTCGGCGATA 59.541 55.000 14.79 0.00 0.00 2.92
162 163 1.218316 GGGAACTGAAGTCGGCGAT 59.782 57.895 14.79 0.00 0.00 4.58
163 164 1.469335 AAGGGAACTGAAGTCGGCGA 61.469 55.000 4.99 4.99 42.68 5.54
164 165 1.004918 AAGGGAACTGAAGTCGGCG 60.005 57.895 0.00 0.00 42.68 6.46
165 166 0.673956 GGAAGGGAACTGAAGTCGGC 60.674 60.000 0.00 0.00 42.68 5.54
166 167 0.685097 TGGAAGGGAACTGAAGTCGG 59.315 55.000 0.00 0.00 42.68 4.79
167 168 1.941668 GCTGGAAGGGAACTGAAGTCG 60.942 57.143 0.00 0.00 42.68 4.18
168 169 1.072331 TGCTGGAAGGGAACTGAAGTC 59.928 52.381 0.00 0.00 42.68 3.01
169 170 1.140312 TGCTGGAAGGGAACTGAAGT 58.860 50.000 0.00 0.00 42.68 3.01
170 171 2.157738 CTTGCTGGAAGGGAACTGAAG 58.842 52.381 0.37 0.00 42.68 3.02
171 172 1.819305 GCTTGCTGGAAGGGAACTGAA 60.819 52.381 10.99 0.00 42.68 3.02
172 173 0.250901 GCTTGCTGGAAGGGAACTGA 60.251 55.000 10.99 0.00 42.68 3.41
173 174 0.538057 TGCTTGCTGGAAGGGAACTG 60.538 55.000 10.99 0.00 42.68 3.16
175 176 1.260544 AATGCTTGCTGGAAGGGAAC 58.739 50.000 10.99 0.00 31.56 3.62
176 177 2.014010 AAATGCTTGCTGGAAGGGAA 57.986 45.000 10.99 0.00 31.56 3.97
177 178 2.308570 TCTAAATGCTTGCTGGAAGGGA 59.691 45.455 10.99 0.00 31.56 4.20
178 179 2.726821 TCTAAATGCTTGCTGGAAGGG 58.273 47.619 10.99 0.00 31.56 3.95
179 180 3.119352 GGTTCTAAATGCTTGCTGGAAGG 60.119 47.826 10.99 0.00 31.56 3.46
180 181 3.119352 GGGTTCTAAATGCTTGCTGGAAG 60.119 47.826 4.37 4.37 34.41 3.46
181 182 2.825532 GGGTTCTAAATGCTTGCTGGAA 59.174 45.455 0.00 0.00 0.00 3.53
182 183 2.446435 GGGTTCTAAATGCTTGCTGGA 58.554 47.619 0.00 0.00 0.00 3.86
183 184 1.478105 GGGGTTCTAAATGCTTGCTGG 59.522 52.381 0.00 0.00 0.00 4.85
184 185 2.170166 TGGGGTTCTAAATGCTTGCTG 58.830 47.619 0.00 0.00 0.00 4.41
185 186 2.603075 TGGGGTTCTAAATGCTTGCT 57.397 45.000 0.00 0.00 0.00 3.91
186 187 3.893326 AATGGGGTTCTAAATGCTTGC 57.107 42.857 0.00 0.00 0.00 4.01
187 188 5.151297 ACAAATGGGGTTCTAAATGCTTG 57.849 39.130 0.00 0.00 0.00 4.01
188 189 4.222810 GGACAAATGGGGTTCTAAATGCTT 59.777 41.667 0.00 0.00 0.00 3.91
189 190 3.769300 GGACAAATGGGGTTCTAAATGCT 59.231 43.478 0.00 0.00 0.00 3.79
190 191 3.118775 GGGACAAATGGGGTTCTAAATGC 60.119 47.826 0.00 0.00 0.00 3.56
191 192 4.093011 TGGGACAAATGGGGTTCTAAATG 58.907 43.478 0.00 0.00 31.92 2.32
192 193 4.045334 TCTGGGACAAATGGGGTTCTAAAT 59.955 41.667 0.00 0.00 38.70 1.40
193 194 3.399644 TCTGGGACAAATGGGGTTCTAAA 59.600 43.478 0.00 0.00 38.70 1.85
194 195 2.990284 TCTGGGACAAATGGGGTTCTAA 59.010 45.455 0.00 0.00 38.70 2.10
195 196 2.638325 TCTGGGACAAATGGGGTTCTA 58.362 47.619 0.00 0.00 38.70 2.10
196 197 1.455822 TCTGGGACAAATGGGGTTCT 58.544 50.000 0.00 0.00 38.70 3.01
197 198 2.302587 TTCTGGGACAAATGGGGTTC 57.697 50.000 0.00 0.00 38.70 3.62
198 199 2.785357 TTTCTGGGACAAATGGGGTT 57.215 45.000 0.00 0.00 38.70 4.11
199 200 4.264804 ACATATTTCTGGGACAAATGGGGT 60.265 41.667 0.00 0.00 38.70 4.95
200 201 4.289245 ACATATTTCTGGGACAAATGGGG 58.711 43.478 0.00 0.00 38.70 4.96
201 202 7.255942 GGAATACATATTTCTGGGACAAATGGG 60.256 40.741 0.00 0.00 38.70 4.00
202 203 7.255942 GGGAATACATATTTCTGGGACAAATGG 60.256 40.741 0.00 0.00 38.70 3.16
203 204 7.287466 TGGGAATACATATTTCTGGGACAAATG 59.713 37.037 0.00 0.00 38.70 2.32
204 205 7.361438 TGGGAATACATATTTCTGGGACAAAT 58.639 34.615 0.00 0.00 38.70 2.32
205 206 6.736581 TGGGAATACATATTTCTGGGACAAA 58.263 36.000 0.00 0.00 38.70 2.83
206 207 6.334378 TGGGAATACATATTTCTGGGACAA 57.666 37.500 0.00 0.00 38.70 3.18
207 208 5.985175 TGGGAATACATATTTCTGGGACA 57.015 39.130 0.00 0.00 0.00 4.02
208 209 6.601332 TCTTGGGAATACATATTTCTGGGAC 58.399 40.000 0.00 0.00 0.00 4.46
209 210 6.840090 TCTTGGGAATACATATTTCTGGGA 57.160 37.500 0.00 0.00 0.00 4.37
210 211 7.896383 TTTCTTGGGAATACATATTTCTGGG 57.104 36.000 0.00 0.00 0.00 4.45
220 221 9.967451 TGTACAGAATAATTTCTTGGGAATACA 57.033 29.630 0.00 0.00 40.28 2.29
249 250 8.568794 TCGATTGTTAACACCAAATTATCACAA 58.431 29.630 8.07 0.00 0.00 3.33
306 307 1.134699 ACACGCTGGACATGATGGTAG 60.135 52.381 0.00 0.00 0.00 3.18
323 653 6.062749 TCATGGATACCTAGAGTGACTACAC 58.937 44.000 0.00 0.00 46.24 2.90
334 664 5.004361 TCCCTCTCTTCATGGATACCTAG 57.996 47.826 0.00 0.00 0.00 3.02
350 680 6.183347 GCTAATTTATGTGGCATATCCCTCT 58.817 40.000 0.00 0.00 0.00 3.69
391 721 9.813080 GTAACACAGTCAGTCTCAATTTAAATC 57.187 33.333 0.10 0.00 0.00 2.17
457 952 6.326583 CGGGGTCCCACATAATATATAGACAT 59.673 42.308 10.98 0.00 35.37 3.06
458 953 5.659525 CGGGGTCCCACATAATATATAGACA 59.340 44.000 10.98 0.00 35.37 3.41
459 954 5.659971 ACGGGGTCCCACATAATATATAGAC 59.340 44.000 10.98 0.00 35.37 2.59
460 955 5.659525 CACGGGGTCCCACATAATATATAGA 59.340 44.000 10.98 0.00 35.37 1.98
509 1005 2.632377 AGTTTATGGACAGATGTGGCG 58.368 47.619 0.00 0.00 28.79 5.69
556 1052 7.661437 ACTTTCATGAGAAATGCTACAGTTACA 59.339 33.333 0.00 0.00 42.49 2.41
557 1053 7.959651 CACTTTCATGAGAAATGCTACAGTTAC 59.040 37.037 0.00 0.00 42.49 2.50
575 1071 1.274728 ACTGAGAGAGCGCACTTTCAT 59.725 47.619 24.21 13.88 32.18 2.57
580 1076 1.613925 TGTAAACTGAGAGAGCGCACT 59.386 47.619 11.47 9.28 0.00 4.40
581 1077 1.989165 CTGTAAACTGAGAGAGCGCAC 59.011 52.381 11.47 2.25 0.00 5.34
582 1078 1.067565 CCTGTAAACTGAGAGAGCGCA 60.068 52.381 11.47 0.00 0.00 6.09
583 1079 1.634702 CCTGTAAACTGAGAGAGCGC 58.365 55.000 0.00 0.00 0.00 5.92
584 1080 1.737363 GCCCTGTAAACTGAGAGAGCG 60.737 57.143 0.00 0.00 0.00 5.03
585 1081 1.737363 CGCCCTGTAAACTGAGAGAGC 60.737 57.143 0.00 0.00 0.00 4.09
586 1082 1.546476 ACGCCCTGTAAACTGAGAGAG 59.454 52.381 0.00 0.00 0.00 3.20
587 1083 1.272490 CACGCCCTGTAAACTGAGAGA 59.728 52.381 0.00 0.00 0.00 3.10
588 1084 1.714794 CACGCCCTGTAAACTGAGAG 58.285 55.000 0.00 0.00 0.00 3.20
589 1085 0.320421 GCACGCCCTGTAAACTGAGA 60.320 55.000 0.00 0.00 0.00 3.27
590 1086 1.626654 CGCACGCCCTGTAAACTGAG 61.627 60.000 0.00 0.00 0.00 3.35
591 1087 1.666553 CGCACGCCCTGTAAACTGA 60.667 57.895 0.00 0.00 0.00 3.41
592 1088 2.860293 CGCACGCCCTGTAAACTG 59.140 61.111 0.00 0.00 0.00 3.16
593 1089 3.047877 GCGCACGCCCTGTAAACT 61.048 61.111 0.30 0.00 34.56 2.66
594 1090 4.439472 CGCGCACGCCCTGTAAAC 62.439 66.667 8.75 0.00 37.98 2.01
595 1091 3.570621 TACGCGCACGCCCTGTAAA 62.571 57.895 5.73 0.00 45.53 2.01
596 1092 4.053526 TACGCGCACGCCCTGTAA 62.054 61.111 5.73 0.00 45.53 2.41
597 1093 4.781959 GTACGCGCACGCCCTGTA 62.782 66.667 5.73 3.39 45.53 2.74
614 1110 3.538591 GGTCAAATTAACGACCTAGGGG 58.461 50.000 14.81 7.16 46.83 4.79
621 1117 8.031848 TGTATTAGGTTGGTCAAATTAACGAC 57.968 34.615 0.00 0.00 0.00 4.34
622 1118 8.618702 TTGTATTAGGTTGGTCAAATTAACGA 57.381 30.769 0.00 0.00 0.00 3.85
623 1119 8.508875 ACTTGTATTAGGTTGGTCAAATTAACG 58.491 33.333 0.00 0.00 0.00 3.18
624 1120 9.836076 GACTTGTATTAGGTTGGTCAAATTAAC 57.164 33.333 0.00 0.00 0.00 2.01
625 1121 9.575868 TGACTTGTATTAGGTTGGTCAAATTAA 57.424 29.630 0.00 0.00 30.81 1.40
626 1122 9.747898 ATGACTTGTATTAGGTTGGTCAAATTA 57.252 29.630 0.00 0.00 36.16 1.40
627 1123 8.650143 ATGACTTGTATTAGGTTGGTCAAATT 57.350 30.769 0.00 0.00 36.16 1.82
628 1124 9.920946 ATATGACTTGTATTAGGTTGGTCAAAT 57.079 29.630 0.00 0.00 36.16 2.32
679 1175 9.450807 CGTTTGAAAATAGAACATCTGAAGTTT 57.549 29.630 0.00 0.00 0.00 2.66
680 1176 7.591426 GCGTTTGAAAATAGAACATCTGAAGTT 59.409 33.333 0.00 0.00 0.00 2.66
681 1177 7.041098 AGCGTTTGAAAATAGAACATCTGAAGT 60.041 33.333 0.00 0.00 0.00 3.01
682 1178 7.301054 AGCGTTTGAAAATAGAACATCTGAAG 58.699 34.615 0.00 0.00 0.00 3.02
683 1179 7.202016 AGCGTTTGAAAATAGAACATCTGAA 57.798 32.000 0.00 0.00 0.00 3.02
684 1180 6.801539 AGCGTTTGAAAATAGAACATCTGA 57.198 33.333 0.00 0.00 0.00 3.27
744 1240 9.745880 CTACGTGTATATCTAGGTTGTCAATTT 57.254 33.333 0.00 0.00 0.00 1.82
745 1241 8.358148 CCTACGTGTATATCTAGGTTGTCAATT 58.642 37.037 0.00 0.00 0.00 2.32
746 1242 7.722728 TCCTACGTGTATATCTAGGTTGTCAAT 59.277 37.037 0.00 0.00 0.00 2.57
747 1243 7.012704 GTCCTACGTGTATATCTAGGTTGTCAA 59.987 40.741 0.00 0.00 0.00 3.18
748 1244 6.484643 GTCCTACGTGTATATCTAGGTTGTCA 59.515 42.308 0.00 0.00 0.00 3.58
749 1245 6.709846 AGTCCTACGTGTATATCTAGGTTGTC 59.290 42.308 0.00 0.00 0.00 3.18
750 1246 6.599445 AGTCCTACGTGTATATCTAGGTTGT 58.401 40.000 0.00 0.00 0.00 3.32
751 1247 7.013083 ACAAGTCCTACGTGTATATCTAGGTTG 59.987 40.741 0.00 0.00 38.97 3.77
752 1248 7.059156 ACAAGTCCTACGTGTATATCTAGGTT 58.941 38.462 0.00 0.00 38.97 3.50
753 1249 6.599445 ACAAGTCCTACGTGTATATCTAGGT 58.401 40.000 0.00 0.00 38.97 3.08
754 1250 8.613060 TTACAAGTCCTACGTGTATATCTAGG 57.387 38.462 0.00 0.00 41.34 3.02
755 1251 9.875675 GTTTACAAGTCCTACGTGTATATCTAG 57.124 37.037 0.00 0.00 41.34 2.43
756 1252 9.618890 AGTTTACAAGTCCTACGTGTATATCTA 57.381 33.333 0.00 0.00 41.34 1.98
757 1253 8.404000 CAGTTTACAAGTCCTACGTGTATATCT 58.596 37.037 0.00 4.14 41.34 1.98
758 1254 8.400947 TCAGTTTACAAGTCCTACGTGTATATC 58.599 37.037 0.00 2.43 41.34 1.63
759 1255 8.284945 TCAGTTTACAAGTCCTACGTGTATAT 57.715 34.615 0.00 0.00 41.34 0.86
760 1256 7.686438 TCAGTTTACAAGTCCTACGTGTATA 57.314 36.000 0.00 0.77 41.34 1.47
761 1257 6.579666 TCAGTTTACAAGTCCTACGTGTAT 57.420 37.500 0.00 0.00 41.34 2.29
762 1258 6.389830 TTCAGTTTACAAGTCCTACGTGTA 57.610 37.500 0.00 2.37 40.98 2.90
763 1259 4.924305 TCAGTTTACAAGTCCTACGTGT 57.076 40.909 0.00 4.18 43.02 4.49
764 1260 5.332055 CGTTTCAGTTTACAAGTCCTACGTG 60.332 44.000 0.00 0.00 33.76 4.49
765 1261 4.741676 CGTTTCAGTTTACAAGTCCTACGT 59.258 41.667 0.00 0.00 0.00 3.57
766 1262 4.149396 CCGTTTCAGTTTACAAGTCCTACG 59.851 45.833 0.00 0.00 0.00 3.51
767 1263 5.291971 TCCGTTTCAGTTTACAAGTCCTAC 58.708 41.667 0.00 0.00 0.00 3.18
768 1264 5.510179 CCTCCGTTTCAGTTTACAAGTCCTA 60.510 44.000 0.00 0.00 0.00 2.94
769 1265 4.377897 CTCCGTTTCAGTTTACAAGTCCT 58.622 43.478 0.00 0.00 0.00 3.85
770 1266 3.497262 CCTCCGTTTCAGTTTACAAGTCC 59.503 47.826 0.00 0.00 0.00 3.85
771 1267 4.374399 TCCTCCGTTTCAGTTTACAAGTC 58.626 43.478 0.00 0.00 0.00 3.01
772 1268 4.411256 TCCTCCGTTTCAGTTTACAAGT 57.589 40.909 0.00 0.00 0.00 3.16
773 1269 4.814771 ACTTCCTCCGTTTCAGTTTACAAG 59.185 41.667 0.00 0.00 0.00 3.16
774 1270 4.773013 ACTTCCTCCGTTTCAGTTTACAA 58.227 39.130 0.00 0.00 0.00 2.41
775 1271 4.411256 ACTTCCTCCGTTTCAGTTTACA 57.589 40.909 0.00 0.00 0.00 2.41
776 1272 4.928020 CCTACTTCCTCCGTTTCAGTTTAC 59.072 45.833 0.00 0.00 0.00 2.01
777 1273 4.020839 CCCTACTTCCTCCGTTTCAGTTTA 60.021 45.833 0.00 0.00 0.00 2.01
778 1274 3.244457 CCCTACTTCCTCCGTTTCAGTTT 60.244 47.826 0.00 0.00 0.00 2.66
779 1275 2.302157 CCCTACTTCCTCCGTTTCAGTT 59.698 50.000 0.00 0.00 0.00 3.16
780 1276 1.900486 CCCTACTTCCTCCGTTTCAGT 59.100 52.381 0.00 0.00 0.00 3.41
781 1277 1.405661 GCCCTACTTCCTCCGTTTCAG 60.406 57.143 0.00 0.00 0.00 3.02
782 1278 0.611714 GCCCTACTTCCTCCGTTTCA 59.388 55.000 0.00 0.00 0.00 2.69
783 1279 0.611714 TGCCCTACTTCCTCCGTTTC 59.388 55.000 0.00 0.00 0.00 2.78
784 1280 1.003233 CTTGCCCTACTTCCTCCGTTT 59.997 52.381 0.00 0.00 0.00 3.60
785 1281 0.613777 CTTGCCCTACTTCCTCCGTT 59.386 55.000 0.00 0.00 0.00 4.44
786 1282 0.544595 ACTTGCCCTACTTCCTCCGT 60.545 55.000 0.00 0.00 0.00 4.69
787 1283 0.108138 CACTTGCCCTACTTCCTCCG 60.108 60.000 0.00 0.00 0.00 4.63
788 1284 0.393132 GCACTTGCCCTACTTCCTCC 60.393 60.000 0.00 0.00 34.31 4.30
789 1285 0.741221 CGCACTTGCCCTACTTCCTC 60.741 60.000 0.00 0.00 37.91 3.71
790 1286 1.296715 CGCACTTGCCCTACTTCCT 59.703 57.895 0.00 0.00 37.91 3.36
791 1287 2.399356 GCGCACTTGCCCTACTTCC 61.399 63.158 0.30 0.00 37.91 3.46
792 1288 1.362406 GAGCGCACTTGCCCTACTTC 61.362 60.000 11.47 0.00 37.91 3.01
793 1289 1.376037 GAGCGCACTTGCCCTACTT 60.376 57.895 11.47 0.00 37.91 2.24
794 1290 2.266055 GAGCGCACTTGCCCTACT 59.734 61.111 11.47 0.00 37.91 2.57
795 1291 3.188786 CGAGCGCACTTGCCCTAC 61.189 66.667 11.47 0.00 37.91 3.18
844 2452 0.390472 GGAGTGAAGTTGCCTCCTCG 60.390 60.000 9.29 0.00 41.31 4.63
862 2470 2.041216 ACCTTGGCCTACCTTTAAGTGG 59.959 50.000 3.32 0.00 36.63 4.00
868 2476 1.075536 CTTGGACCTTGGCCTACCTTT 59.924 52.381 3.32 0.00 36.63 3.11
989 2647 7.885399 AGTGCTCTATTTAAAGAAGTGATGGTT 59.115 33.333 0.00 0.00 0.00 3.67
1095 2774 1.511768 GTGGTGAGCTACGAGGGAC 59.488 63.158 0.00 0.00 0.00 4.46
1461 3161 3.775654 CAGGGAGACGGCCTGGTC 61.776 72.222 0.00 1.11 37.19 4.02
1464 3164 3.775654 GTCCAGGGAGACGGCCTG 61.776 72.222 0.00 0.00 0.00 4.85
1475 3175 2.436646 GCCACCATGTCGTCCAGG 60.437 66.667 0.00 0.00 0.00 4.45
1476 3176 1.448540 GAGCCACCATGTCGTCCAG 60.449 63.158 0.00 0.00 0.00 3.86
1477 3177 1.888436 GAGAGCCACCATGTCGTCCA 61.888 60.000 0.00 0.00 0.00 4.02
1478 3178 1.153549 GAGAGCCACCATGTCGTCC 60.154 63.158 0.00 0.00 0.00 4.79
1479 3179 0.176680 ATGAGAGCCACCATGTCGTC 59.823 55.000 0.00 0.00 0.00 4.20
1505 3226 0.602372 GCTGCTGATCTTCCGATCCC 60.602 60.000 0.00 0.00 44.40 3.85
1612 3337 3.630312 GCTCCCAAAATCGCCAGTTAATA 59.370 43.478 0.00 0.00 0.00 0.98
2220 3971 2.483188 CCCGTGTTATCCTAGGAAGTGC 60.483 54.545 17.30 7.27 0.00 4.40
2246 3997 0.768221 TCCACTGAGAGCCAAAGGGT 60.768 55.000 0.00 0.00 36.17 4.34
2350 4101 4.141824 TGCCTACATCGTGGATCATTGTTA 60.142 41.667 0.00 0.00 0.00 2.41
2531 4282 9.270640 CCGTATACAGTTCAGTATCTACTAAGT 57.729 37.037 3.32 0.00 36.23 2.24
2537 4288 7.447545 AGCAATCCGTATACAGTTCAGTATCTA 59.552 37.037 3.32 0.00 36.23 1.98
2589 4340 5.473796 ACAACTAAACACCACTAACAACG 57.526 39.130 0.00 0.00 0.00 4.10
2594 4345 6.526526 TCAGCATACAACTAAACACCACTAA 58.473 36.000 0.00 0.00 0.00 2.24
2609 4360 1.078497 CCCACCGCTTCAGCATACA 60.078 57.895 0.00 0.00 42.21 2.29
2775 4527 5.504665 GCATGCCAGTATATGTTCACTGTTC 60.505 44.000 6.36 0.00 40.47 3.18
2788 4540 2.826428 CTACACGAAGCATGCCAGTAT 58.174 47.619 15.66 3.84 0.00 2.12


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

AutoCloner maintained by Alex Coulton.