Multiple sequence alignment - TraesCS7B01G179600

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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 TraesCS7B01G179600 chr7B 100.000 4772 0 0 1 4772 265429270 265434041 0.000000e+00 8813.0
1 TraesCS7B01G179600 chr7D 95.910 4059 93 27 425 4433 272602383 272598348 0.000000e+00 6508.0
2 TraesCS7B01G179600 chr7D 90.094 212 19 2 1 211 383981241 383981451 1.690000e-69 274.0
3 TraesCS7B01G179600 chr7D 97.468 158 4 0 252 409 272602525 272602368 2.190000e-68 270.0
4 TraesCS7B01G179600 chr7D 88.732 213 20 4 1 211 551502322 551502532 1.700000e-64 257.0
5 TraesCS7B01G179600 chr7D 96.739 92 3 0 4457 4548 272598356 272598265 2.300000e-33 154.0
6 TraesCS7B01G179600 chr7A 95.925 3828 87 19 647 4433 306348637 306344838 0.000000e+00 6141.0
7 TraesCS7B01G179600 chr7A 86.944 360 11 7 252 607 306349229 306348902 5.830000e-99 372.0
8 TraesCS7B01G179600 chr7A 98.913 92 1 0 4457 4548 306344846 306344755 1.060000e-36 165.0
9 TraesCS7B01G179600 chr3B 89.623 212 18 4 1 211 738122777 738122985 2.830000e-67 267.0
10 TraesCS7B01G179600 chr3B 88.525 183 2 2 4590 4772 592301099 592300936 2.250000e-48 204.0
11 TraesCS7B01G179600 chr1D 89.623 212 19 3 1 211 36605929 36606138 2.830000e-67 267.0
12 TraesCS7B01G179600 chr1D 87.907 215 24 2 4 217 480814408 480814195 7.930000e-63 252.0
13 TraesCS7B01G179600 chr3A 89.151 212 21 2 1 211 531911607 531911817 3.660000e-66 263.0
14 TraesCS7B01G179600 chr3A 89.100 211 21 2 1 210 673589336 673589127 1.320000e-65 261.0
15 TraesCS7B01G179600 chr2B 88.584 219 20 4 1 217 672317292 672317077 1.320000e-65 261.0
16 TraesCS7B01G179600 chr2B 84.615 78 12 0 1327 1404 17040286 17040363 1.420000e-10 78.7
17 TraesCS7B01G179600 chr2B 100.000 38 0 0 4735 4772 679702531 679702568 2.380000e-08 71.3
18 TraesCS7B01G179600 chr5B 88.095 210 22 3 1 209 586854742 586854949 3.690000e-61 246.0
19 TraesCS7B01G179600 chr4B 84.810 79 12 0 1330 1408 23822195 23822117 3.960000e-11 80.5
20 TraesCS7B01G179600 chr4A 84.146 82 13 0 1327 1408 589108502 589108583 3.960000e-11 80.5
21 TraesCS7B01G179600 chr4D 83.951 81 13 0 1330 1410 13200255 13200175 1.420000e-10 78.7


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 TraesCS7B01G179600 chr7B 265429270 265434041 4771 False 8813.000000 8813 100.000000 1 4772 1 chr7B.!!$F1 4771
1 TraesCS7B01G179600 chr7D 272598265 272602525 4260 True 2310.666667 6508 96.705667 252 4548 3 chr7D.!!$R1 4296
2 TraesCS7B01G179600 chr7A 306344755 306349229 4474 True 2226.000000 6141 93.927333 252 4548 3 chr7A.!!$R1 4296

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
19 20 0.030235 GCGTCTTTGGTTTGTGGGTC 59.970 55.000 0.0 0.0 0.00 4.46 F
206 207 0.036388 TTTTGCGGGGTCTGCTAGAG 60.036 55.000 0.0 0.0 0.00 2.43 F
255 256 0.671781 CTTCTTGCGGTGGAGAGTGG 60.672 60.000 0.0 0.0 0.00 4.00 F
1800 2111 1.008424 CTCGTCATCGTCATCCCCG 60.008 63.158 0.0 0.0 38.33 5.73 F
1994 2311 3.270877 ACGTTCCATTATCAGAGGCAAC 58.729 45.455 0.0 0.0 0.00 4.17 F
3429 3748 1.342374 GGAACAGCATTCTCCCCCAAT 60.342 52.381 1.3 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1440 1739 0.323725 GGATCAGCCCAGCCAAAGAA 60.324 55.000 0.00 0.00 0.00 2.52 R
1692 2003 0.394762 TGCTAAGGCCATTCTGCTGG 60.395 55.000 5.01 0.00 39.45 4.85 R
2096 2413 2.590007 GGATTCCTGCAGCGCGAT 60.590 61.111 12.10 0.00 0.00 4.58 R
2692 3009 0.747644 TGGTGCCAACATGATAGCCG 60.748 55.000 0.00 0.00 0.00 5.52 R
3480 3799 1.815003 CCTCTTGATGAACCAAGTGGC 59.185 52.381 10.52 0.00 45.15 5.01 R
4641 4964 0.037139 TGTTAATACGGTGCGCAGGT 60.037 50.000 12.22 15.34 0.00 4.00 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.112029 GCGTCTTTGGTTTGTGGGT 58.888 52.632 0.00 0.00 0.00 4.51
19 20 0.030235 GCGTCTTTGGTTTGTGGGTC 59.970 55.000 0.00 0.00 0.00 4.46
20 21 0.306533 CGTCTTTGGTTTGTGGGTCG 59.693 55.000 0.00 0.00 0.00 4.79
21 22 1.670791 GTCTTTGGTTTGTGGGTCGA 58.329 50.000 0.00 0.00 0.00 4.20
22 23 1.332686 GTCTTTGGTTTGTGGGTCGAC 59.667 52.381 7.13 7.13 0.00 4.20
23 24 0.306533 CTTTGGTTTGTGGGTCGACG 59.693 55.000 9.92 0.00 0.00 5.12
24 25 1.716826 TTTGGTTTGTGGGTCGACGC 61.717 55.000 24.41 24.41 0.00 5.19
25 26 3.708734 GGTTTGTGGGTCGACGCG 61.709 66.667 25.18 3.53 0.00 6.01
26 27 3.708734 GTTTGTGGGTCGACGCGG 61.709 66.667 25.18 0.00 0.00 6.46
50 51 3.066190 CCGAGCAGACCCCGTGTA 61.066 66.667 0.00 0.00 0.00 2.90
51 52 2.490217 CGAGCAGACCCCGTGTAG 59.510 66.667 0.00 0.00 0.00 2.74
52 53 2.184579 GAGCAGACCCCGTGTAGC 59.815 66.667 0.00 0.00 0.00 3.58
53 54 3.372554 GAGCAGACCCCGTGTAGCC 62.373 68.421 0.00 0.00 0.00 3.93
54 55 4.814294 GCAGACCCCGTGTAGCCG 62.814 72.222 0.00 0.00 0.00 5.52
55 56 3.066190 CAGACCCCGTGTAGCCGA 61.066 66.667 0.00 0.00 0.00 5.54
56 57 3.066814 AGACCCCGTGTAGCCGAC 61.067 66.667 0.00 0.00 0.00 4.79
57 58 4.139234 GACCCCGTGTAGCCGACC 62.139 72.222 0.00 0.00 0.00 4.79
61 62 3.133464 CCGTGTAGCCGACCCGTA 61.133 66.667 0.00 0.00 0.00 4.02
62 63 2.699768 CCGTGTAGCCGACCCGTAA 61.700 63.158 0.00 0.00 0.00 3.18
63 64 1.212490 CGTGTAGCCGACCCGTAAA 59.788 57.895 0.00 0.00 0.00 2.01
64 65 0.388391 CGTGTAGCCGACCCGTAAAA 60.388 55.000 0.00 0.00 0.00 1.52
65 66 1.794512 GTGTAGCCGACCCGTAAAAA 58.205 50.000 0.00 0.00 0.00 1.94
117 118 3.253955 CGTTTTGCGGGGTCTGAG 58.746 61.111 0.00 0.00 36.85 3.35
118 119 1.597027 CGTTTTGCGGGGTCTGAGT 60.597 57.895 0.00 0.00 36.85 3.41
119 120 1.566018 CGTTTTGCGGGGTCTGAGTC 61.566 60.000 0.00 0.00 36.85 3.36
120 121 0.250338 GTTTTGCGGGGTCTGAGTCT 60.250 55.000 0.00 0.00 0.00 3.24
121 122 0.250295 TTTTGCGGGGTCTGAGTCTG 60.250 55.000 0.00 0.00 0.00 3.51
122 123 1.118965 TTTGCGGGGTCTGAGTCTGA 61.119 55.000 0.00 0.00 0.00 3.27
123 124 1.816863 TTGCGGGGTCTGAGTCTGAC 61.817 60.000 19.02 19.02 0.00 3.51
124 125 3.007973 GCGGGGTCTGAGTCTGACC 62.008 68.421 31.21 31.21 46.94 4.02
125 126 1.304547 CGGGGTCTGAGTCTGACCT 60.305 63.158 34.77 0.00 46.87 3.85
126 127 1.316706 CGGGGTCTGAGTCTGACCTC 61.317 65.000 34.77 32.56 46.87 3.85
127 128 1.316706 GGGGTCTGAGTCTGACCTCG 61.317 65.000 34.77 1.86 46.87 4.63
128 129 1.509004 GGTCTGAGTCTGACCTCGC 59.491 63.158 31.52 13.12 45.14 5.03
129 130 1.509004 GTCTGAGTCTGACCTCGCC 59.491 63.158 17.02 0.00 34.04 5.54
130 131 1.679305 TCTGAGTCTGACCTCGCCC 60.679 63.158 3.76 0.00 34.04 6.13
131 132 3.057547 CTGAGTCTGACCTCGCCCG 62.058 68.421 3.76 0.00 34.04 6.13
132 133 3.063084 GAGTCTGACCTCGCCCGT 61.063 66.667 3.76 0.00 0.00 5.28
133 134 3.343788 GAGTCTGACCTCGCCCGTG 62.344 68.421 3.76 0.00 0.00 4.94
145 146 2.584064 CCCGTGCTGACCTGCATA 59.416 61.111 4.94 0.00 45.23 3.14
146 147 1.146930 CCCGTGCTGACCTGCATAT 59.853 57.895 4.94 0.00 45.23 1.78
147 148 0.392706 CCCGTGCTGACCTGCATATA 59.607 55.000 4.94 0.00 45.23 0.86
148 149 1.502231 CCGTGCTGACCTGCATATAC 58.498 55.000 4.94 0.00 45.23 1.47
149 150 1.202521 CCGTGCTGACCTGCATATACA 60.203 52.381 4.94 0.00 45.23 2.29
150 151 2.548707 CCGTGCTGACCTGCATATACAT 60.549 50.000 4.94 0.00 45.23 2.29
151 152 3.133691 CGTGCTGACCTGCATATACATT 58.866 45.455 4.94 0.00 45.23 2.71
152 153 3.561310 CGTGCTGACCTGCATATACATTT 59.439 43.478 4.94 0.00 45.23 2.32
153 154 4.035558 CGTGCTGACCTGCATATACATTTT 59.964 41.667 4.94 0.00 45.23 1.82
154 155 5.514279 GTGCTGACCTGCATATACATTTTC 58.486 41.667 4.94 0.00 45.23 2.29
155 156 4.580167 TGCTGACCTGCATATACATTTTCC 59.420 41.667 0.00 0.00 38.12 3.13
156 157 4.319766 GCTGACCTGCATATACATTTTCCG 60.320 45.833 0.00 0.00 0.00 4.30
157 158 3.563808 TGACCTGCATATACATTTTCCGC 59.436 43.478 0.00 0.00 0.00 5.54
158 159 2.548057 ACCTGCATATACATTTTCCGCG 59.452 45.455 0.00 0.00 0.00 6.46
159 160 2.805671 CCTGCATATACATTTTCCGCGA 59.194 45.455 8.23 0.00 0.00 5.87
160 161 3.249799 CCTGCATATACATTTTCCGCGAA 59.750 43.478 8.23 0.00 0.00 4.70
161 162 4.083324 CCTGCATATACATTTTCCGCGAAT 60.083 41.667 8.23 0.00 0.00 3.34
162 163 5.431420 TGCATATACATTTTCCGCGAATT 57.569 34.783 8.23 0.00 0.00 2.17
163 164 5.211454 TGCATATACATTTTCCGCGAATTG 58.789 37.500 8.23 4.20 0.00 2.32
164 165 5.008118 TGCATATACATTTTCCGCGAATTGA 59.992 36.000 8.23 0.00 0.00 2.57
165 166 5.912396 GCATATACATTTTCCGCGAATTGAA 59.088 36.000 8.23 0.00 0.00 2.69
166 167 6.416455 GCATATACATTTTCCGCGAATTGAAA 59.584 34.615 8.23 5.85 0.00 2.69
167 168 7.043722 GCATATACATTTTCCGCGAATTGAAAA 60.044 33.333 18.70 18.70 42.67 2.29
168 169 8.802856 CATATACATTTTCCGCGAATTGAAAAA 58.197 29.630 19.78 11.44 42.02 1.94
169 170 5.574815 ACATTTTCCGCGAATTGAAAAAG 57.425 34.783 19.78 18.04 42.02 2.27
170 171 5.285651 ACATTTTCCGCGAATTGAAAAAGA 58.714 33.333 21.64 5.96 42.02 2.52
171 172 5.174943 ACATTTTCCGCGAATTGAAAAAGAC 59.825 36.000 21.64 0.00 42.02 3.01
172 173 4.561735 TTTCCGCGAATTGAAAAAGACT 57.438 36.364 8.23 0.00 0.00 3.24
173 174 4.561735 TTCCGCGAATTGAAAAAGACTT 57.438 36.364 8.23 0.00 0.00 3.01
174 175 5.676532 TTCCGCGAATTGAAAAAGACTTA 57.323 34.783 8.23 0.00 0.00 2.24
175 176 5.873179 TCCGCGAATTGAAAAAGACTTAT 57.127 34.783 8.23 0.00 0.00 1.73
176 177 6.971527 TCCGCGAATTGAAAAAGACTTATA 57.028 33.333 8.23 0.00 0.00 0.98
177 178 6.768078 TCCGCGAATTGAAAAAGACTTATAC 58.232 36.000 8.23 0.00 0.00 1.47
178 179 5.671140 CCGCGAATTGAAAAAGACTTATACG 59.329 40.000 8.23 0.00 0.00 3.06
179 180 5.671140 CGCGAATTGAAAAAGACTTATACGG 59.329 40.000 0.00 0.00 0.00 4.02
180 181 5.963586 GCGAATTGAAAAAGACTTATACGGG 59.036 40.000 0.00 0.00 0.00 5.28
181 182 6.402875 GCGAATTGAAAAAGACTTATACGGGT 60.403 38.462 0.00 0.00 0.00 5.28
182 183 7.524065 CGAATTGAAAAAGACTTATACGGGTT 58.476 34.615 0.00 0.00 0.00 4.11
183 184 7.480542 CGAATTGAAAAAGACTTATACGGGTTG 59.519 37.037 0.00 0.00 0.00 3.77
184 185 6.563222 TTGAAAAAGACTTATACGGGTTGG 57.437 37.500 0.00 0.00 0.00 3.77
185 186 5.867330 TGAAAAAGACTTATACGGGTTGGA 58.133 37.500 0.00 0.00 0.00 3.53
186 187 6.297582 TGAAAAAGACTTATACGGGTTGGAA 58.702 36.000 0.00 0.00 0.00 3.53
187 188 6.943718 TGAAAAAGACTTATACGGGTTGGAAT 59.056 34.615 0.00 0.00 0.00 3.01
188 189 7.449086 TGAAAAAGACTTATACGGGTTGGAATT 59.551 33.333 0.00 0.00 0.00 2.17
189 190 7.770366 AAAAGACTTATACGGGTTGGAATTT 57.230 32.000 0.00 0.00 0.00 1.82
190 191 7.770366 AAAGACTTATACGGGTTGGAATTTT 57.230 32.000 0.00 0.00 0.00 1.82
191 192 6.753107 AGACTTATACGGGTTGGAATTTTG 57.247 37.500 0.00 0.00 0.00 2.44
192 193 5.124936 AGACTTATACGGGTTGGAATTTTGC 59.875 40.000 0.00 0.00 0.00 3.68
193 194 2.931512 ATACGGGTTGGAATTTTGCG 57.068 45.000 0.00 0.00 0.00 4.85
194 195 0.882474 TACGGGTTGGAATTTTGCGG 59.118 50.000 0.00 0.00 0.00 5.69
195 196 1.080161 CGGGTTGGAATTTTGCGGG 60.080 57.895 0.00 0.00 0.00 6.13
196 197 1.295101 GGGTTGGAATTTTGCGGGG 59.705 57.895 0.00 0.00 0.00 5.73
197 198 1.476845 GGGTTGGAATTTTGCGGGGT 61.477 55.000 0.00 0.00 0.00 4.95
198 199 0.037697 GGTTGGAATTTTGCGGGGTC 60.038 55.000 0.00 0.00 0.00 4.46
199 200 0.966179 GTTGGAATTTTGCGGGGTCT 59.034 50.000 0.00 0.00 0.00 3.85
200 201 0.965439 TTGGAATTTTGCGGGGTCTG 59.035 50.000 0.00 0.00 0.00 3.51
201 202 1.215382 GGAATTTTGCGGGGTCTGC 59.785 57.895 0.00 0.00 0.00 4.26
202 203 1.250840 GGAATTTTGCGGGGTCTGCT 61.251 55.000 0.30 0.00 0.00 4.24
203 204 1.459450 GAATTTTGCGGGGTCTGCTA 58.541 50.000 0.30 0.00 0.00 3.49
204 205 1.401905 GAATTTTGCGGGGTCTGCTAG 59.598 52.381 0.30 0.00 0.00 3.42
205 206 0.618458 ATTTTGCGGGGTCTGCTAGA 59.382 50.000 0.00 0.00 0.00 2.43
206 207 0.036388 TTTTGCGGGGTCTGCTAGAG 60.036 55.000 0.00 0.00 0.00 2.43
207 208 0.902984 TTTGCGGGGTCTGCTAGAGA 60.903 55.000 0.00 0.00 0.00 3.10
208 209 0.687757 TTGCGGGGTCTGCTAGAGAT 60.688 55.000 0.00 0.00 31.63 2.75
209 210 1.365633 GCGGGGTCTGCTAGAGATG 59.634 63.158 0.00 0.00 31.63 2.90
210 211 1.365633 CGGGGTCTGCTAGAGATGC 59.634 63.158 0.00 0.00 31.63 3.91
211 212 1.751563 GGGGTCTGCTAGAGATGCC 59.248 63.158 0.00 0.00 31.63 4.40
212 213 1.365633 GGGTCTGCTAGAGATGCCG 59.634 63.158 0.00 0.00 31.63 5.69
213 214 1.395826 GGGTCTGCTAGAGATGCCGT 61.396 60.000 0.00 0.00 31.63 5.68
214 215 1.319541 GGTCTGCTAGAGATGCCGTA 58.680 55.000 0.00 0.00 31.63 4.02
215 216 1.681793 GGTCTGCTAGAGATGCCGTAA 59.318 52.381 0.00 0.00 31.63 3.18
216 217 2.287909 GGTCTGCTAGAGATGCCGTAAG 60.288 54.545 0.00 0.00 31.63 2.34
234 235 6.526566 CGTAAGGCTGGTAGAATGAATAAC 57.473 41.667 0.00 0.00 0.00 1.89
235 236 6.281405 CGTAAGGCTGGTAGAATGAATAACT 58.719 40.000 0.00 0.00 0.00 2.24
236 237 6.421202 CGTAAGGCTGGTAGAATGAATAACTC 59.579 42.308 0.00 0.00 0.00 3.01
237 238 6.567602 AAGGCTGGTAGAATGAATAACTCT 57.432 37.500 0.00 0.00 0.00 3.24
238 239 6.567602 AGGCTGGTAGAATGAATAACTCTT 57.432 37.500 0.00 0.00 0.00 2.85
239 240 6.587273 AGGCTGGTAGAATGAATAACTCTTC 58.413 40.000 0.00 0.00 0.00 2.87
240 241 6.385467 AGGCTGGTAGAATGAATAACTCTTCT 59.615 38.462 0.00 0.00 0.00 2.85
241 242 7.051000 GGCTGGTAGAATGAATAACTCTTCTT 58.949 38.462 0.00 0.00 0.00 2.52
242 243 7.011857 GGCTGGTAGAATGAATAACTCTTCTTG 59.988 40.741 0.00 0.00 0.00 3.02
243 244 7.466590 GCTGGTAGAATGAATAACTCTTCTTGC 60.467 40.741 0.00 0.00 0.00 4.01
244 245 6.535150 TGGTAGAATGAATAACTCTTCTTGCG 59.465 38.462 0.00 0.00 0.00 4.85
245 246 6.018669 GGTAGAATGAATAACTCTTCTTGCGG 60.019 42.308 0.00 0.00 0.00 5.69
246 247 5.491982 AGAATGAATAACTCTTCTTGCGGT 58.508 37.500 0.00 0.00 0.00 5.68
247 248 5.352569 AGAATGAATAACTCTTCTTGCGGTG 59.647 40.000 0.00 0.00 0.00 4.94
248 249 3.334691 TGAATAACTCTTCTTGCGGTGG 58.665 45.455 0.00 0.00 0.00 4.61
249 250 3.007506 TGAATAACTCTTCTTGCGGTGGA 59.992 43.478 0.00 0.00 0.00 4.02
250 251 2.743636 TAACTCTTCTTGCGGTGGAG 57.256 50.000 0.00 0.00 0.00 3.86
255 256 0.671781 CTTCTTGCGGTGGAGAGTGG 60.672 60.000 0.00 0.00 0.00 4.00
414 415 9.796120 CCTGAAACCTAATAAATAAATTTCGCA 57.204 29.630 0.00 0.00 0.00 5.10
469 478 4.382457 CACAAGTTCATGGTAATTTGCGTG 59.618 41.667 0.00 0.00 31.34 5.34
1007 1276 1.195115 CGACAAGGAAGGATGGAGGA 58.805 55.000 0.00 0.00 0.00 3.71
1146 1436 3.081409 GCAGCGGGGAAGAGGGTA 61.081 66.667 0.00 0.00 0.00 3.69
1419 1718 3.010584 AGAGGTACACCCATTGATTGCTT 59.989 43.478 0.00 0.00 36.42 3.91
1440 1739 3.553828 TTGTCGAGGGTTCAACTTTCT 57.446 42.857 0.00 0.00 0.00 2.52
1678 1989 3.907474 TGTCCATTCTCCTTGACCTTGTA 59.093 43.478 0.00 0.00 0.00 2.41
1692 2003 4.391830 TGACCTTGTATTGTTTCAGATCGC 59.608 41.667 0.00 0.00 0.00 4.58
1800 2111 1.008424 CTCGTCATCGTCATCCCCG 60.008 63.158 0.00 0.00 38.33 5.73
1941 2258 3.462021 GACTACACATTCTGGCTCATCC 58.538 50.000 0.00 0.00 0.00 3.51
1994 2311 3.270877 ACGTTCCATTATCAGAGGCAAC 58.729 45.455 0.00 0.00 0.00 4.17
2334 2651 9.357161 GTACTAGAGGAAGAAAATCTCTATGGA 57.643 37.037 0.00 0.00 38.81 3.41
2412 2729 4.141528 GGGTCCATCTCTGTGAAAGATCAT 60.142 45.833 0.00 0.00 38.01 2.45
2583 2900 8.094548 TCAGAGCATTTAAGTAGTGAAAGCTTA 58.905 33.333 0.00 0.00 0.00 3.09
2727 3044 2.019249 CACCATGGACTTCGATGCATT 58.981 47.619 21.47 0.00 31.78 3.56
2745 3062 5.359756 TGCATTATTGTCTTGATAGCGAGT 58.640 37.500 0.00 0.00 0.00 4.18
2778 3095 2.598565 TGCTTATCGGATAGCTGAGGT 58.401 47.619 15.51 0.00 31.75 3.85
2881 3200 9.166173 TGTGTCTCAATATATTGAAAAGACTGG 57.834 33.333 28.54 17.52 45.26 4.00
2952 3271 2.109126 CAGGGCGCTGAGGTTTAGC 61.109 63.158 25.55 0.00 37.80 3.09
2965 3284 1.369625 GTTTAGCGGACATCCCACTG 58.630 55.000 0.00 0.00 34.14 3.66
3171 3490 5.823045 CCTAACTACCTAGAAATTGGCAAGG 59.177 44.000 5.96 2.20 0.00 3.61
3226 3545 6.640518 TGCTATACAGTACCTTCCTTGAAAG 58.359 40.000 0.00 0.00 0.00 2.62
3342 3661 1.855599 AGGGATATGGAAAGCTTGGCT 59.144 47.619 0.00 0.00 42.56 4.75
3429 3748 1.342374 GGAACAGCATTCTCCCCCAAT 60.342 52.381 1.30 0.00 0.00 3.16
3440 3759 3.125656 TCTCCCCCAATTCTGATGTCAT 58.874 45.455 0.00 0.00 0.00 3.06
3480 3799 3.204526 AGAACGTAGTACTGGATCCTCG 58.795 50.000 14.23 6.69 45.00 4.63
3546 3865 7.891183 CCCACTAGGTAAATTATCTTCATCG 57.109 40.000 0.00 0.00 0.00 3.84
3550 3869 8.577296 CACTAGGTAAATTATCTTCATCGAGGA 58.423 37.037 0.00 0.00 0.00 3.71
3751 4070 5.063204 CACCCTTGTGTGAAGAAAGTGATA 58.937 41.667 0.00 0.00 38.55 2.15
3759 4078 5.007626 GTGTGAAGAAAGTGATAACAGCACA 59.992 40.000 0.00 0.00 38.70 4.57
3828 4147 4.099881 TCTTTGGAATTTGCTGCTTGTCTT 59.900 37.500 0.00 0.00 0.00 3.01
3838 4157 3.181497 TGCTGCTTGTCTTGAAGTTGTTC 60.181 43.478 0.00 0.00 0.00 3.18
3864 4183 6.237915 GGTTGAAAGTGCAGTTTGATTCTTTG 60.238 38.462 23.88 0.00 0.00 2.77
3868 4187 7.387397 TGAAAGTGCAGTTTGATTCTTTGTTTT 59.613 29.630 23.88 0.00 0.00 2.43
4154 4477 7.111865 CAGTCCACTGTAAATGCTAAATGCAC 61.112 42.308 0.00 0.00 45.62 4.57
4331 4654 2.159824 GCCTCGAGTTAGCTTTTGTTCC 59.840 50.000 12.31 0.00 0.00 3.62
4431 4754 1.964552 TGCAAATTTGGCCTGTTTGG 58.035 45.000 19.47 6.28 34.34 3.28
4452 4775 1.330234 GGAACGGTAGAGGATCCTCC 58.670 60.000 33.81 20.98 43.70 4.30
4460 4783 4.796408 AGGATCCTCCTCGCTGTT 57.204 55.556 9.02 0.00 45.66 3.16
4461 4784 2.998493 AGGATCCTCCTCGCTGTTT 58.002 52.632 9.02 0.00 45.66 2.83
4462 4785 0.539051 AGGATCCTCCTCGCTGTTTG 59.461 55.000 9.02 0.00 45.66 2.93
4543 4866 3.792401 TGATGTATGGACGTGGTGATTC 58.208 45.455 0.00 0.00 0.00 2.52
4548 4871 2.649531 TGGACGTGGTGATTCCTTTT 57.350 45.000 0.00 0.00 37.07 2.27
4549 4872 2.226330 TGGACGTGGTGATTCCTTTTG 58.774 47.619 0.00 0.00 37.07 2.44
4550 4873 1.068541 GGACGTGGTGATTCCTTTTGC 60.069 52.381 0.00 0.00 37.07 3.68
4551 4874 1.880027 GACGTGGTGATTCCTTTTGCT 59.120 47.619 0.00 0.00 37.07 3.91
4552 4875 3.071479 GACGTGGTGATTCCTTTTGCTA 58.929 45.455 0.00 0.00 37.07 3.49
4553 4876 3.074412 ACGTGGTGATTCCTTTTGCTAG 58.926 45.455 0.00 0.00 37.07 3.42
4554 4877 2.420022 CGTGGTGATTCCTTTTGCTAGG 59.580 50.000 0.00 0.00 37.07 3.02
4555 4878 3.686016 GTGGTGATTCCTTTTGCTAGGA 58.314 45.455 0.00 0.00 42.56 2.94
4574 4897 3.543680 GAATGAGATTCCCTGTCCGAA 57.456 47.619 0.00 0.00 33.17 4.30
4575 4898 2.990066 ATGAGATTCCCTGTCCGAAC 57.010 50.000 0.00 0.00 0.00 3.95
4576 4899 0.530744 TGAGATTCCCTGTCCGAACG 59.469 55.000 0.00 0.00 0.00 3.95
4577 4900 0.531200 GAGATTCCCTGTCCGAACGT 59.469 55.000 0.00 0.00 0.00 3.99
4578 4901 1.747355 GAGATTCCCTGTCCGAACGTA 59.253 52.381 0.00 0.00 0.00 3.57
4579 4902 1.475682 AGATTCCCTGTCCGAACGTAC 59.524 52.381 0.00 0.00 0.00 3.67
4580 4903 0.533951 ATTCCCTGTCCGAACGTACC 59.466 55.000 0.00 0.00 0.00 3.34
4581 4904 1.535204 TTCCCTGTCCGAACGTACCC 61.535 60.000 0.00 0.00 0.00 3.69
4582 4905 2.277591 CCCTGTCCGAACGTACCCA 61.278 63.158 0.00 0.00 0.00 4.51
4583 4906 1.214589 CCTGTCCGAACGTACCCAG 59.785 63.158 0.00 0.00 0.00 4.45
4584 4907 1.246056 CCTGTCCGAACGTACCCAGA 61.246 60.000 0.00 0.00 0.00 3.86
4585 4908 0.109412 CTGTCCGAACGTACCCAGAC 60.109 60.000 0.00 0.00 0.00 3.51
4586 4909 1.213799 GTCCGAACGTACCCAGACC 59.786 63.158 0.00 0.00 0.00 3.85
4587 4910 1.228521 TCCGAACGTACCCAGACCA 60.229 57.895 0.00 0.00 0.00 4.02
4588 4911 1.080298 CCGAACGTACCCAGACCAC 60.080 63.158 0.00 0.00 0.00 4.16
4589 4912 1.443194 CGAACGTACCCAGACCACG 60.443 63.158 0.00 0.00 41.32 4.94
4590 4913 1.855213 CGAACGTACCCAGACCACGA 61.855 60.000 0.00 0.00 38.96 4.35
4591 4914 0.529378 GAACGTACCCAGACCACGAT 59.471 55.000 0.00 0.00 38.96 3.73
4592 4915 0.971386 AACGTACCCAGACCACGATT 59.029 50.000 0.00 0.00 38.96 3.34
4593 4916 0.971386 ACGTACCCAGACCACGATTT 59.029 50.000 0.00 0.00 38.96 2.17
4594 4917 1.345415 ACGTACCCAGACCACGATTTT 59.655 47.619 0.00 0.00 38.96 1.82
4595 4918 2.224354 ACGTACCCAGACCACGATTTTT 60.224 45.455 0.00 0.00 38.96 1.94
4626 4949 7.696992 AAAAAGACCACATACGGTTTCATAT 57.303 32.000 0.00 0.00 40.22 1.78
4627 4950 7.696992 AAAAGACCACATACGGTTTCATATT 57.303 32.000 0.00 0.00 40.22 1.28
4628 4951 6.677781 AAGACCACATACGGTTTCATATTG 57.322 37.500 0.00 0.00 40.22 1.90
4629 4952 5.984725 AGACCACATACGGTTTCATATTGA 58.015 37.500 0.00 0.00 40.22 2.57
4630 4953 5.815740 AGACCACATACGGTTTCATATTGAC 59.184 40.000 0.00 0.00 40.22 3.18
4631 4954 5.492895 ACCACATACGGTTTCATATTGACA 58.507 37.500 0.00 0.00 34.91 3.58
4632 4955 5.941058 ACCACATACGGTTTCATATTGACAA 59.059 36.000 0.00 0.00 34.91 3.18
4633 4956 6.431543 ACCACATACGGTTTCATATTGACAAA 59.568 34.615 0.00 0.00 34.91 2.83
4634 4957 7.040340 ACCACATACGGTTTCATATTGACAAAA 60.040 33.333 0.00 0.00 34.91 2.44
4635 4958 7.810282 CCACATACGGTTTCATATTGACAAAAA 59.190 33.333 0.00 0.00 0.00 1.94
4649 4972 4.251246 AAAAAGACCACCTGCGCA 57.749 50.000 10.98 10.98 0.00 6.09
4650 4973 1.733526 AAAAAGACCACCTGCGCAC 59.266 52.632 5.66 0.00 0.00 5.34
4651 4974 1.734388 AAAAAGACCACCTGCGCACC 61.734 55.000 5.66 0.00 0.00 5.01
4652 4975 4.988598 AAGACCACCTGCGCACCG 62.989 66.667 5.66 1.12 0.00 4.94
4654 4977 4.367023 GACCACCTGCGCACCGTA 62.367 66.667 5.66 0.00 0.00 4.02
4655 4978 3.659089 GACCACCTGCGCACCGTAT 62.659 63.158 5.66 0.00 0.00 3.06
4656 4979 2.435938 CCACCTGCGCACCGTATT 60.436 61.111 5.66 0.00 0.00 1.89
4657 4980 1.153529 CCACCTGCGCACCGTATTA 60.154 57.895 5.66 0.00 0.00 0.98
4658 4981 0.741574 CCACCTGCGCACCGTATTAA 60.742 55.000 5.66 0.00 0.00 1.40
4659 4982 0.372334 CACCTGCGCACCGTATTAAC 59.628 55.000 5.66 0.00 0.00 2.01
4660 4983 0.037139 ACCTGCGCACCGTATTAACA 60.037 50.000 5.66 0.00 0.00 2.41
4661 4984 1.080298 CCTGCGCACCGTATTAACAA 58.920 50.000 5.66 0.00 0.00 2.83
4662 4985 1.465387 CCTGCGCACCGTATTAACAAA 59.535 47.619 5.66 0.00 0.00 2.83
4663 4986 2.095668 CCTGCGCACCGTATTAACAAAA 60.096 45.455 5.66 0.00 0.00 2.44
4664 4987 3.556513 CTGCGCACCGTATTAACAAAAA 58.443 40.909 5.66 0.00 0.00 1.94
4683 5006 2.024176 AAGACCACATACGTCATGGC 57.976 50.000 11.50 0.00 39.13 4.40
4684 5007 0.179111 AGACCACATACGTCATGGCG 60.179 55.000 19.93 19.93 39.13 5.69
4685 5008 1.151777 GACCACATACGTCATGGCGG 61.152 60.000 25.37 8.87 39.13 6.13
4686 5009 2.534019 CCACATACGTCATGGCGGC 61.534 63.158 25.37 0.00 39.13 6.53
4687 5010 1.813337 CACATACGTCATGGCGGCA 60.813 57.895 25.37 16.34 39.13 5.69
4688 5011 1.521457 ACATACGTCATGGCGGCAG 60.521 57.895 25.37 14.75 39.13 4.85
4689 5012 2.108976 ATACGTCATGGCGGCAGG 59.891 61.111 25.37 18.43 35.98 4.85
4690 5013 3.460672 ATACGTCATGGCGGCAGGG 62.461 63.158 25.37 15.06 35.98 4.45
4715 5038 4.012895 CCGACACGTGGCACTTGC 62.013 66.667 23.63 14.35 41.14 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.030235 GACCCACAAACCAAAGACGC 59.970 55.000 0.00 0.00 0.00 5.19
1 2 0.306533 CGACCCACAAACCAAAGACG 59.693 55.000 0.00 0.00 0.00 4.18
2 3 1.332686 GTCGACCCACAAACCAAAGAC 59.667 52.381 3.51 0.00 0.00 3.01
3 4 1.670791 GTCGACCCACAAACCAAAGA 58.329 50.000 3.51 0.00 0.00 2.52
4 5 0.306533 CGTCGACCCACAAACCAAAG 59.693 55.000 10.58 0.00 0.00 2.77
5 6 1.716826 GCGTCGACCCACAAACCAAA 61.717 55.000 10.58 0.00 0.00 3.28
6 7 2.181521 GCGTCGACCCACAAACCAA 61.182 57.895 10.58 0.00 0.00 3.67
7 8 2.589442 GCGTCGACCCACAAACCA 60.589 61.111 10.58 0.00 0.00 3.67
8 9 3.708734 CGCGTCGACCCACAAACC 61.709 66.667 10.58 0.00 0.00 3.27
9 10 3.708734 CCGCGTCGACCCACAAAC 61.709 66.667 10.58 0.00 0.00 2.93
33 34 3.064987 CTACACGGGGTCTGCTCGG 62.065 68.421 0.00 0.00 0.00 4.63
34 35 2.490217 CTACACGGGGTCTGCTCG 59.510 66.667 0.00 0.00 0.00 5.03
35 36 2.184579 GCTACACGGGGTCTGCTC 59.815 66.667 0.00 0.00 0.00 4.26
36 37 3.391382 GGCTACACGGGGTCTGCT 61.391 66.667 7.94 0.00 32.05 4.24
37 38 4.814294 CGGCTACACGGGGTCTGC 62.814 72.222 0.00 0.00 0.00 4.26
38 39 3.066190 TCGGCTACACGGGGTCTG 61.066 66.667 0.00 0.00 0.00 3.51
39 40 3.066814 GTCGGCTACACGGGGTCT 61.067 66.667 0.00 0.00 0.00 3.85
40 41 4.139234 GGTCGGCTACACGGGGTC 62.139 72.222 0.00 0.00 0.00 4.46
46 47 1.794512 TTTTTACGGGTCGGCTACAC 58.205 50.000 0.00 0.00 0.00 2.90
100 101 1.566018 GACTCAGACCCCGCAAAACG 61.566 60.000 0.00 0.00 43.15 3.60
101 102 0.250338 AGACTCAGACCCCGCAAAAC 60.250 55.000 0.00 0.00 0.00 2.43
102 103 0.250295 CAGACTCAGACCCCGCAAAA 60.250 55.000 0.00 0.00 0.00 2.44
103 104 1.118965 TCAGACTCAGACCCCGCAAA 61.119 55.000 0.00 0.00 0.00 3.68
104 105 1.533033 TCAGACTCAGACCCCGCAA 60.533 57.895 0.00 0.00 0.00 4.85
105 106 2.117423 TCAGACTCAGACCCCGCA 59.883 61.111 0.00 0.00 0.00 5.69
106 107 2.574399 GTCAGACTCAGACCCCGC 59.426 66.667 0.00 0.00 0.00 6.13
111 112 1.509004 GGCGAGGTCAGACTCAGAC 59.491 63.158 0.00 0.00 37.34 3.51
112 113 1.679305 GGGCGAGGTCAGACTCAGA 60.679 63.158 0.00 0.00 37.34 3.27
113 114 2.888863 GGGCGAGGTCAGACTCAG 59.111 66.667 0.00 0.00 37.34 3.35
114 115 3.062466 CGGGCGAGGTCAGACTCA 61.062 66.667 0.00 0.00 37.34 3.41
115 116 3.063084 ACGGGCGAGGTCAGACTC 61.063 66.667 0.00 0.00 0.00 3.36
116 117 3.374402 CACGGGCGAGGTCAGACT 61.374 66.667 0.00 0.00 0.00 3.24
133 134 4.319766 CGGAAAATGTATATGCAGGTCAGC 60.320 45.833 0.00 0.00 0.00 4.26
134 135 4.319766 GCGGAAAATGTATATGCAGGTCAG 60.320 45.833 0.00 0.00 0.00 3.51
135 136 3.563808 GCGGAAAATGTATATGCAGGTCA 59.436 43.478 0.00 0.00 0.00 4.02
136 137 3.363970 CGCGGAAAATGTATATGCAGGTC 60.364 47.826 0.00 0.00 0.00 3.85
137 138 2.548057 CGCGGAAAATGTATATGCAGGT 59.452 45.455 0.00 0.00 0.00 4.00
138 139 2.805671 TCGCGGAAAATGTATATGCAGG 59.194 45.455 6.13 0.00 0.00 4.85
139 140 4.466567 TTCGCGGAAAATGTATATGCAG 57.533 40.909 6.13 0.00 0.00 4.41
140 141 5.008118 TCAATTCGCGGAAAATGTATATGCA 59.992 36.000 6.13 0.00 0.00 3.96
141 142 5.448438 TCAATTCGCGGAAAATGTATATGC 58.552 37.500 6.13 0.00 0.00 3.14
142 143 7.906611 TTTCAATTCGCGGAAAATGTATATG 57.093 32.000 6.13 0.00 30.59 1.78
143 144 8.918961 TTTTTCAATTCGCGGAAAATGTATAT 57.081 26.923 17.60 0.00 41.20 0.86
144 145 8.237949 TCTTTTTCAATTCGCGGAAAATGTATA 58.762 29.630 21.69 9.79 41.20 1.47
145 146 7.061789 GTCTTTTTCAATTCGCGGAAAATGTAT 59.938 33.333 21.69 0.00 41.20 2.29
146 147 6.361214 GTCTTTTTCAATTCGCGGAAAATGTA 59.639 34.615 21.69 10.28 41.20 2.29
147 148 5.174943 GTCTTTTTCAATTCGCGGAAAATGT 59.825 36.000 21.69 0.00 41.20 2.71
148 149 5.402270 AGTCTTTTTCAATTCGCGGAAAATG 59.598 36.000 17.60 18.39 41.20 2.32
149 150 5.528870 AGTCTTTTTCAATTCGCGGAAAAT 58.471 33.333 17.60 4.08 41.20 1.82
150 151 4.927422 AGTCTTTTTCAATTCGCGGAAAA 58.073 34.783 14.35 14.35 40.23 2.29
151 152 4.561735 AGTCTTTTTCAATTCGCGGAAA 57.438 36.364 6.13 5.10 0.00 3.13
152 153 4.561735 AAGTCTTTTTCAATTCGCGGAA 57.438 36.364 6.13 0.00 0.00 4.30
153 154 5.873179 ATAAGTCTTTTTCAATTCGCGGA 57.127 34.783 6.13 0.00 0.00 5.54
154 155 5.671140 CGTATAAGTCTTTTTCAATTCGCGG 59.329 40.000 6.13 0.00 0.00 6.46
155 156 5.671140 CCGTATAAGTCTTTTTCAATTCGCG 59.329 40.000 0.00 0.00 0.00 5.87
156 157 5.963586 CCCGTATAAGTCTTTTTCAATTCGC 59.036 40.000 0.00 0.00 0.00 4.70
157 158 7.068692 ACCCGTATAAGTCTTTTTCAATTCG 57.931 36.000 0.00 0.00 0.00 3.34
158 159 7.753580 CCAACCCGTATAAGTCTTTTTCAATTC 59.246 37.037 0.00 0.00 0.00 2.17
159 160 7.449086 TCCAACCCGTATAAGTCTTTTTCAATT 59.551 33.333 0.00 0.00 0.00 2.32
160 161 6.943718 TCCAACCCGTATAAGTCTTTTTCAAT 59.056 34.615 0.00 0.00 0.00 2.57
161 162 6.297582 TCCAACCCGTATAAGTCTTTTTCAA 58.702 36.000 0.00 0.00 0.00 2.69
162 163 5.867330 TCCAACCCGTATAAGTCTTTTTCA 58.133 37.500 0.00 0.00 0.00 2.69
163 164 6.806388 TTCCAACCCGTATAAGTCTTTTTC 57.194 37.500 0.00 0.00 0.00 2.29
164 165 7.770366 AATTCCAACCCGTATAAGTCTTTTT 57.230 32.000 0.00 0.00 0.00 1.94
165 166 7.770366 AAATTCCAACCCGTATAAGTCTTTT 57.230 32.000 0.00 0.00 0.00 2.27
166 167 7.599171 CAAAATTCCAACCCGTATAAGTCTTT 58.401 34.615 0.00 0.00 0.00 2.52
167 168 6.349860 GCAAAATTCCAACCCGTATAAGTCTT 60.350 38.462 0.00 0.00 0.00 3.01
168 169 5.124936 GCAAAATTCCAACCCGTATAAGTCT 59.875 40.000 0.00 0.00 0.00 3.24
169 170 5.337554 GCAAAATTCCAACCCGTATAAGTC 58.662 41.667 0.00 0.00 0.00 3.01
170 171 4.142556 CGCAAAATTCCAACCCGTATAAGT 60.143 41.667 0.00 0.00 0.00 2.24
171 172 4.347813 CGCAAAATTCCAACCCGTATAAG 58.652 43.478 0.00 0.00 0.00 1.73
172 173 3.128938 CCGCAAAATTCCAACCCGTATAA 59.871 43.478 0.00 0.00 0.00 0.98
173 174 2.683867 CCGCAAAATTCCAACCCGTATA 59.316 45.455 0.00 0.00 0.00 1.47
174 175 1.474879 CCGCAAAATTCCAACCCGTAT 59.525 47.619 0.00 0.00 0.00 3.06
175 176 0.882474 CCGCAAAATTCCAACCCGTA 59.118 50.000 0.00 0.00 0.00 4.02
176 177 1.663173 CCGCAAAATTCCAACCCGT 59.337 52.632 0.00 0.00 0.00 5.28
177 178 1.080161 CCCGCAAAATTCCAACCCG 60.080 57.895 0.00 0.00 0.00 5.28
178 179 1.295101 CCCCGCAAAATTCCAACCC 59.705 57.895 0.00 0.00 0.00 4.11
179 180 0.037697 GACCCCGCAAAATTCCAACC 60.038 55.000 0.00 0.00 0.00 3.77
180 181 0.966179 AGACCCCGCAAAATTCCAAC 59.034 50.000 0.00 0.00 0.00 3.77
181 182 0.965439 CAGACCCCGCAAAATTCCAA 59.035 50.000 0.00 0.00 0.00 3.53
182 183 1.531739 GCAGACCCCGCAAAATTCCA 61.532 55.000 0.00 0.00 0.00 3.53
183 184 1.215382 GCAGACCCCGCAAAATTCC 59.785 57.895 0.00 0.00 0.00 3.01
184 185 1.401905 CTAGCAGACCCCGCAAAATTC 59.598 52.381 0.00 0.00 0.00 2.17
185 186 1.004277 TCTAGCAGACCCCGCAAAATT 59.996 47.619 0.00 0.00 0.00 1.82
186 187 0.618458 TCTAGCAGACCCCGCAAAAT 59.382 50.000 0.00 0.00 0.00 1.82
187 188 0.036388 CTCTAGCAGACCCCGCAAAA 60.036 55.000 0.00 0.00 0.00 2.44
188 189 0.902984 TCTCTAGCAGACCCCGCAAA 60.903 55.000 0.00 0.00 0.00 3.68
189 190 0.687757 ATCTCTAGCAGACCCCGCAA 60.688 55.000 0.00 0.00 32.26 4.85
190 191 1.075970 ATCTCTAGCAGACCCCGCA 60.076 57.895 0.00 0.00 32.26 5.69
191 192 1.365633 CATCTCTAGCAGACCCCGC 59.634 63.158 0.00 0.00 32.26 6.13
192 193 1.365633 GCATCTCTAGCAGACCCCG 59.634 63.158 0.00 0.00 32.26 5.73
193 194 1.751563 GGCATCTCTAGCAGACCCC 59.248 63.158 0.00 0.00 32.26 4.95
194 195 1.365633 CGGCATCTCTAGCAGACCC 59.634 63.158 0.00 0.00 32.26 4.46
195 196 1.319541 TACGGCATCTCTAGCAGACC 58.680 55.000 0.00 0.00 32.26 3.85
196 197 2.287909 CCTTACGGCATCTCTAGCAGAC 60.288 54.545 0.00 0.00 32.26 3.51
197 198 1.957177 CCTTACGGCATCTCTAGCAGA 59.043 52.381 0.00 0.00 34.78 4.26
198 199 2.430546 CCTTACGGCATCTCTAGCAG 57.569 55.000 0.00 0.00 0.00 4.24
210 211 3.536956 TTCATTCTACCAGCCTTACGG 57.463 47.619 0.00 0.00 0.00 4.02
211 212 6.281405 AGTTATTCATTCTACCAGCCTTACG 58.719 40.000 0.00 0.00 0.00 3.18
212 213 7.501844 AGAGTTATTCATTCTACCAGCCTTAC 58.498 38.462 0.00 0.00 0.00 2.34
213 214 7.676683 AGAGTTATTCATTCTACCAGCCTTA 57.323 36.000 0.00 0.00 0.00 2.69
214 215 6.567602 AGAGTTATTCATTCTACCAGCCTT 57.432 37.500 0.00 0.00 0.00 4.35
215 216 6.385467 AGAAGAGTTATTCATTCTACCAGCCT 59.615 38.462 0.00 0.00 30.41 4.58
216 217 6.587273 AGAAGAGTTATTCATTCTACCAGCC 58.413 40.000 0.00 0.00 30.41 4.85
217 218 7.466590 GCAAGAAGAGTTATTCATTCTACCAGC 60.467 40.741 0.00 0.00 31.90 4.85
218 219 7.254252 CGCAAGAAGAGTTATTCATTCTACCAG 60.254 40.741 0.00 0.00 43.02 4.00
219 220 6.535150 CGCAAGAAGAGTTATTCATTCTACCA 59.465 38.462 0.00 0.00 43.02 3.25
220 221 6.018669 CCGCAAGAAGAGTTATTCATTCTACC 60.019 42.308 0.00 0.00 43.02 3.18
221 222 6.535508 ACCGCAAGAAGAGTTATTCATTCTAC 59.464 38.462 0.00 0.00 43.02 2.59
222 223 6.535150 CACCGCAAGAAGAGTTATTCATTCTA 59.465 38.462 0.00 0.00 43.02 2.10
223 224 5.352569 CACCGCAAGAAGAGTTATTCATTCT 59.647 40.000 0.00 0.00 43.02 2.40
224 225 5.447818 CCACCGCAAGAAGAGTTATTCATTC 60.448 44.000 0.00 0.00 43.02 2.67
225 226 4.396166 CCACCGCAAGAAGAGTTATTCATT 59.604 41.667 0.00 0.00 43.02 2.57
226 227 3.941483 CCACCGCAAGAAGAGTTATTCAT 59.059 43.478 0.00 0.00 43.02 2.57
227 228 3.007506 TCCACCGCAAGAAGAGTTATTCA 59.992 43.478 0.00 0.00 43.02 2.57
228 229 3.596214 TCCACCGCAAGAAGAGTTATTC 58.404 45.455 0.00 0.00 43.02 1.75
229 230 3.260884 TCTCCACCGCAAGAAGAGTTATT 59.739 43.478 0.00 0.00 43.02 1.40
230 231 2.832129 TCTCCACCGCAAGAAGAGTTAT 59.168 45.455 0.00 0.00 43.02 1.89
231 232 2.231478 CTCTCCACCGCAAGAAGAGTTA 59.769 50.000 0.00 0.00 43.02 2.24
232 233 1.001406 CTCTCCACCGCAAGAAGAGTT 59.999 52.381 0.00 0.00 43.02 3.01
233 234 0.605589 CTCTCCACCGCAAGAAGAGT 59.394 55.000 0.00 0.00 43.02 3.24
234 235 0.605589 ACTCTCCACCGCAAGAAGAG 59.394 55.000 0.00 0.00 43.02 2.85
235 236 0.318441 CACTCTCCACCGCAAGAAGA 59.682 55.000 0.00 0.00 43.02 2.87
236 237 0.671781 CCACTCTCCACCGCAAGAAG 60.672 60.000 0.00 0.00 43.02 2.85
237 238 1.371183 CCACTCTCCACCGCAAGAA 59.629 57.895 0.00 0.00 43.02 2.52
238 239 2.583441 CCCACTCTCCACCGCAAGA 61.583 63.158 0.00 0.00 43.02 3.02
239 240 2.046892 CCCACTCTCCACCGCAAG 60.047 66.667 0.00 0.00 0.00 4.01
240 241 2.525629 TCCCACTCTCCACCGCAA 60.526 61.111 0.00 0.00 0.00 4.85
241 242 2.997315 CTCCCACTCTCCACCGCA 60.997 66.667 0.00 0.00 0.00 5.69
242 243 4.459089 GCTCCCACTCTCCACCGC 62.459 72.222 0.00 0.00 0.00 5.68
243 244 2.513026 CTTGCTCCCACTCTCCACCG 62.513 65.000 0.00 0.00 0.00 4.94
244 245 1.298014 CTTGCTCCCACTCTCCACC 59.702 63.158 0.00 0.00 0.00 4.61
245 246 1.298014 CCTTGCTCCCACTCTCCAC 59.702 63.158 0.00 0.00 0.00 4.02
246 247 0.116342 TACCTTGCTCCCACTCTCCA 59.884 55.000 0.00 0.00 0.00 3.86
247 248 0.827368 CTACCTTGCTCCCACTCTCC 59.173 60.000 0.00 0.00 0.00 3.71
248 249 0.827368 CCTACCTTGCTCCCACTCTC 59.173 60.000 0.00 0.00 0.00 3.20
249 250 0.618968 CCCTACCTTGCTCCCACTCT 60.619 60.000 0.00 0.00 0.00 3.24
250 251 1.908483 CCCTACCTTGCTCCCACTC 59.092 63.158 0.00 0.00 0.00 3.51
255 256 3.081409 TCCGCCCTACCTTGCTCC 61.081 66.667 0.00 0.00 0.00 4.70
432 433 9.927668 CCATGAACTTGTGAGGTTTATTTATTT 57.072 29.630 0.00 0.00 0.00 1.40
433 434 9.088987 ACCATGAACTTGTGAGGTTTATTTATT 57.911 29.630 0.00 0.00 0.00 1.40
434 435 8.650143 ACCATGAACTTGTGAGGTTTATTTAT 57.350 30.769 0.00 0.00 0.00 1.40
435 436 9.575868 TTACCATGAACTTGTGAGGTTTATTTA 57.424 29.630 0.00 0.00 0.00 1.40
436 437 6.976934 ACCATGAACTTGTGAGGTTTATTT 57.023 33.333 0.00 0.00 0.00 1.40
437 438 8.650143 ATTACCATGAACTTGTGAGGTTTATT 57.350 30.769 0.00 0.00 0.00 1.40
438 439 8.650143 AATTACCATGAACTTGTGAGGTTTAT 57.350 30.769 0.00 0.00 0.00 1.40
439 440 8.356657 CAAATTACCATGAACTTGTGAGGTTTA 58.643 33.333 0.00 0.00 0.00 2.01
469 478 1.867233 CGCATATTAGCCTGGACACAC 59.133 52.381 0.00 0.00 0.00 3.82
543 552 4.374828 CGCCGAAAACGAAAAGTTCTAAAG 59.625 41.667 0.00 0.00 43.37 1.85
552 561 2.095532 TCTTTGACGCCGAAAACGAAAA 59.904 40.909 0.00 0.00 0.00 2.29
553 562 1.664659 TCTTTGACGCCGAAAACGAAA 59.335 42.857 0.00 0.00 0.00 3.46
554 563 1.288350 TCTTTGACGCCGAAAACGAA 58.712 45.000 0.00 0.00 0.00 3.85
555 564 1.193650 CATCTTTGACGCCGAAAACGA 59.806 47.619 0.00 0.00 0.00 3.85
556 565 1.591248 CATCTTTGACGCCGAAAACG 58.409 50.000 0.00 0.00 0.00 3.60
557 566 1.069227 AGCATCTTTGACGCCGAAAAC 60.069 47.619 0.00 0.00 0.00 2.43
619 632 9.503399 AATGATTAATCCCTTCTTCCGTATTAC 57.497 33.333 12.90 0.00 0.00 1.89
620 633 9.502091 CAATGATTAATCCCTTCTTCCGTATTA 57.498 33.333 12.90 0.00 0.00 0.98
621 634 8.217799 TCAATGATTAATCCCTTCTTCCGTATT 58.782 33.333 12.90 0.00 0.00 1.89
622 635 7.745717 TCAATGATTAATCCCTTCTTCCGTAT 58.254 34.615 12.90 0.00 0.00 3.06
1131 1421 2.764547 GCTACCCTCTTCCCCGCT 60.765 66.667 0.00 0.00 0.00 5.52
1146 1436 0.540923 AGAGGTAGTAGACGACCGCT 59.459 55.000 11.44 11.44 44.15 5.52
1419 1718 3.881220 AGAAAGTTGAACCCTCGACAAA 58.119 40.909 0.00 0.00 38.31 2.83
1440 1739 0.323725 GGATCAGCCCAGCCAAAGAA 60.324 55.000 0.00 0.00 0.00 2.52
1678 1989 1.741706 CTGCTGGCGATCTGAAACAAT 59.258 47.619 0.00 0.00 0.00 2.71
1692 2003 0.394762 TGCTAAGGCCATTCTGCTGG 60.395 55.000 5.01 0.00 39.45 4.85
1800 2111 2.680339 GGCCTCTTTGATAACAGCAGAC 59.320 50.000 0.00 0.00 0.00 3.51
1994 2311 3.083997 CGGAAGGTCCAGGGGAGG 61.084 72.222 0.00 0.00 35.91 4.30
2096 2413 2.590007 GGATTCCTGCAGCGCGAT 60.590 61.111 12.10 0.00 0.00 4.58
2323 2640 3.788142 ACACCCATTGGTCCATAGAGATT 59.212 43.478 1.20 0.00 45.57 2.40
2412 2729 0.036388 GGATGAGTCCAAAGCCACGA 60.036 55.000 0.00 0.00 44.42 4.35
2583 2900 1.282447 TCCTGCTTACTCTCCTCGACT 59.718 52.381 0.00 0.00 0.00 4.18
2692 3009 0.747644 TGGTGCCAACATGATAGCCG 60.748 55.000 0.00 0.00 0.00 5.52
2757 3074 2.965831 ACCTCAGCTATCCGATAAGCAA 59.034 45.455 10.53 1.56 0.00 3.91
2765 3082 2.868583 CAATGTGAACCTCAGCTATCCG 59.131 50.000 0.00 0.00 0.00 4.18
2778 3095 2.839975 TGTGCGACTAACCAATGTGAA 58.160 42.857 0.00 0.00 0.00 3.18
2952 3271 2.630098 AGATCATACAGTGGGATGTCCG 59.370 50.000 0.00 0.00 38.76 4.79
3171 3490 9.922305 GACATAGCAACTAAAAACATGATAGTC 57.078 33.333 0.00 0.00 0.00 2.59
3342 3661 3.162666 ACATCTGAAACTACCCGACTCA 58.837 45.455 0.00 0.00 0.00 3.41
3429 3748 5.654209 ACTAGAGCTGTACATGACATCAGAA 59.346 40.000 0.00 0.00 37.45 3.02
3440 3759 5.529791 GTTCTTGTTGACTAGAGCTGTACA 58.470 41.667 0.00 0.00 0.00 2.90
3480 3799 1.815003 CCTCTTGATGAACCAAGTGGC 59.185 52.381 10.52 0.00 45.15 5.01
3626 3945 3.838317 ACAGATAGACAACTAGGCCAACA 59.162 43.478 5.01 0.00 31.78 3.33
3759 4078 3.394606 ACACAACCCCTTACAGTGATTCT 59.605 43.478 0.00 0.00 34.47 2.40
3828 4147 3.426963 GCACTTTCAACCGAACAACTTCA 60.427 43.478 0.00 0.00 0.00 3.02
3838 4157 2.842208 TCAAACTGCACTTTCAACCG 57.158 45.000 0.00 0.00 0.00 4.44
3868 4187 9.598517 ACAAAATGAATCAAACTCAGCTAAAAA 57.401 25.926 0.00 0.00 0.00 1.94
3872 4191 8.296713 GGTTACAAAATGAATCAAACTCAGCTA 58.703 33.333 0.00 0.00 0.00 3.32
3969 4288 7.918562 GGAGACAAACTGATCAGAGTAAGATAC 59.081 40.741 29.27 11.39 0.00 2.24
4154 4477 4.326826 TGAAGAAACAAGCTATCCAGTGG 58.673 43.478 1.40 1.40 0.00 4.00
4331 4654 4.550076 AGCAGGCTCAGGCTTTATATAG 57.450 45.455 0.00 0.00 36.92 1.31
4431 4754 1.108132 AGGATCCTCTACCGTTCCGC 61.108 60.000 9.02 0.00 0.00 5.54
4432 4755 0.953003 GAGGATCCTCTACCGTTCCG 59.047 60.000 31.11 0.00 39.80 4.30
4445 4768 1.092345 GCCAAACAGCGAGGAGGATC 61.092 60.000 0.00 0.00 0.00 3.36
4446 4769 1.078143 GCCAAACAGCGAGGAGGAT 60.078 57.895 0.00 0.00 0.00 3.24
4447 4770 2.347490 GCCAAACAGCGAGGAGGA 59.653 61.111 0.00 0.00 0.00 3.71
4448 4771 2.032528 TGCCAAACAGCGAGGAGG 59.967 61.111 0.00 0.00 34.65 4.30
4449 4772 3.571119 CTGCCAAACAGCGAGGAG 58.429 61.111 0.00 0.00 40.19 3.69
4457 4780 0.459489 GCAAACCAGACTGCCAAACA 59.541 50.000 0.00 0.00 32.18 2.83
4458 4781 0.594796 CGCAAACCAGACTGCCAAAC 60.595 55.000 0.00 0.00 35.01 2.93
4459 4782 1.732917 CGCAAACCAGACTGCCAAA 59.267 52.632 0.00 0.00 35.01 3.28
4460 4783 2.844451 GCGCAAACCAGACTGCCAA 61.844 57.895 0.30 0.00 35.01 4.52
4461 4784 3.286751 GCGCAAACCAGACTGCCA 61.287 61.111 0.30 0.00 35.01 4.92
4462 4785 2.980233 AGCGCAAACCAGACTGCC 60.980 61.111 11.47 0.00 35.01 4.85
4554 4877 3.198872 GTTCGGACAGGGAATCTCATTC 58.801 50.000 0.00 0.00 38.55 2.67
4555 4878 2.418746 CGTTCGGACAGGGAATCTCATT 60.419 50.000 0.00 0.00 0.00 2.57
4556 4879 1.137086 CGTTCGGACAGGGAATCTCAT 59.863 52.381 0.00 0.00 0.00 2.90
4557 4880 0.530744 CGTTCGGACAGGGAATCTCA 59.469 55.000 0.00 0.00 0.00 3.27
4558 4881 0.531200 ACGTTCGGACAGGGAATCTC 59.469 55.000 0.00 0.00 0.00 2.75
4559 4882 1.475682 GTACGTTCGGACAGGGAATCT 59.524 52.381 0.00 0.00 0.00 2.40
4560 4883 1.470458 GGTACGTTCGGACAGGGAATC 60.470 57.143 9.76 0.00 0.00 2.52
4561 4884 0.533951 GGTACGTTCGGACAGGGAAT 59.466 55.000 9.76 0.00 0.00 3.01
4562 4885 1.535204 GGGTACGTTCGGACAGGGAA 61.535 60.000 9.76 0.00 0.00 3.97
4563 4886 1.978617 GGGTACGTTCGGACAGGGA 60.979 63.158 9.76 0.00 0.00 4.20
4564 4887 2.221906 CTGGGTACGTTCGGACAGGG 62.222 65.000 9.76 0.00 0.00 4.45
4565 4888 1.214589 CTGGGTACGTTCGGACAGG 59.785 63.158 9.76 0.00 0.00 4.00
4566 4889 0.109412 GTCTGGGTACGTTCGGACAG 60.109 60.000 9.76 10.41 38.69 3.51
4567 4890 1.526575 GGTCTGGGTACGTTCGGACA 61.527 60.000 19.57 5.51 40.13 4.02
4568 4891 1.213799 GGTCTGGGTACGTTCGGAC 59.786 63.158 13.42 13.42 38.26 4.79
4569 4892 1.228521 TGGTCTGGGTACGTTCGGA 60.229 57.895 0.00 0.00 0.00 4.55
4570 4893 1.080298 GTGGTCTGGGTACGTTCGG 60.080 63.158 0.00 0.00 0.00 4.30
4571 4894 1.443194 CGTGGTCTGGGTACGTTCG 60.443 63.158 0.00 0.00 33.48 3.95
4572 4895 0.529378 ATCGTGGTCTGGGTACGTTC 59.471 55.000 0.00 0.00 38.80 3.95
4573 4896 0.971386 AATCGTGGTCTGGGTACGTT 59.029 50.000 0.00 0.00 38.80 3.99
4574 4897 0.971386 AAATCGTGGTCTGGGTACGT 59.029 50.000 0.00 0.00 38.80 3.57
4575 4898 2.088950 AAAATCGTGGTCTGGGTACG 57.911 50.000 0.00 0.00 39.04 3.67
4602 4925 7.696992 ATATGAAACCGTATGTGGTCTTTTT 57.303 32.000 0.00 0.00 42.89 1.94
4603 4926 7.392113 TCAATATGAAACCGTATGTGGTCTTTT 59.608 33.333 0.00 0.00 42.89 2.27
4604 4927 6.882140 TCAATATGAAACCGTATGTGGTCTTT 59.118 34.615 0.00 0.00 42.89 2.52
4605 4928 6.315393 GTCAATATGAAACCGTATGTGGTCTT 59.685 38.462 0.00 0.00 42.89 3.01
4606 4929 5.815740 GTCAATATGAAACCGTATGTGGTCT 59.184 40.000 0.00 0.00 42.89 3.85
4607 4930 5.583061 TGTCAATATGAAACCGTATGTGGTC 59.417 40.000 0.00 0.00 42.89 4.02
4608 4931 5.492895 TGTCAATATGAAACCGTATGTGGT 58.507 37.500 0.00 0.00 46.67 4.16
4609 4932 6.429791 TTGTCAATATGAAACCGTATGTGG 57.570 37.500 0.00 0.00 0.00 4.17
4610 4933 8.735303 TTTTTGTCAATATGAAACCGTATGTG 57.265 30.769 0.00 0.00 0.00 3.21
4632 4955 1.733526 GTGCGCAGGTGGTCTTTTT 59.266 52.632 12.22 0.00 0.00 1.94
4633 4956 2.193536 GGTGCGCAGGTGGTCTTTT 61.194 57.895 12.22 0.00 0.00 2.27
4634 4957 2.594592 GGTGCGCAGGTGGTCTTT 60.595 61.111 12.22 0.00 0.00 2.52
4635 4958 4.988598 CGGTGCGCAGGTGGTCTT 62.989 66.667 12.22 0.00 0.00 3.01
4637 4960 3.659089 ATACGGTGCGCAGGTGGTC 62.659 63.158 12.22 0.00 0.00 4.02
4638 4961 1.890625 TAATACGGTGCGCAGGTGGT 61.891 55.000 12.22 9.17 0.00 4.16
4639 4962 0.741574 TTAATACGGTGCGCAGGTGG 60.742 55.000 12.22 2.34 0.00 4.61
4640 4963 0.372334 GTTAATACGGTGCGCAGGTG 59.628 55.000 12.22 6.05 0.00 4.00
4641 4964 0.037139 TGTTAATACGGTGCGCAGGT 60.037 50.000 12.22 15.34 0.00 4.00
4642 4965 1.080298 TTGTTAATACGGTGCGCAGG 58.920 50.000 12.22 8.92 0.00 4.85
4643 4966 2.884663 TTTGTTAATACGGTGCGCAG 57.115 45.000 12.22 1.57 0.00 5.18
4644 4967 3.620929 TTTTTGTTAATACGGTGCGCA 57.379 38.095 5.66 5.66 0.00 6.09
4661 4984 3.190535 GCCATGACGTATGTGGTCTTTTT 59.809 43.478 13.05 0.00 34.87 1.94
4662 4985 2.747446 GCCATGACGTATGTGGTCTTTT 59.253 45.455 13.05 0.00 34.87 2.27
4663 4986 2.356135 GCCATGACGTATGTGGTCTTT 58.644 47.619 13.05 0.00 34.87 2.52
4664 4987 1.739035 CGCCATGACGTATGTGGTCTT 60.739 52.381 13.05 0.00 34.87 3.01
4665 4988 0.179111 CGCCATGACGTATGTGGTCT 60.179 55.000 13.05 0.00 34.87 3.85
4666 4989 1.151777 CCGCCATGACGTATGTGGTC 61.152 60.000 13.05 6.50 34.87 4.02
4667 4990 1.153449 CCGCCATGACGTATGTGGT 60.153 57.895 13.05 0.00 34.87 4.16
4668 4991 2.534019 GCCGCCATGACGTATGTGG 61.534 63.158 0.00 8.54 34.87 4.17
4669 4992 1.765161 CTGCCGCCATGACGTATGTG 61.765 60.000 0.00 0.00 34.87 3.21
4670 4993 1.521457 CTGCCGCCATGACGTATGT 60.521 57.895 0.00 0.00 34.87 2.29
4671 4994 2.246739 CCTGCCGCCATGACGTATG 61.247 63.158 0.00 0.00 36.50 2.39
4672 4995 2.108976 CCTGCCGCCATGACGTAT 59.891 61.111 0.00 0.00 0.00 3.06
4673 4996 4.155733 CCCTGCCGCCATGACGTA 62.156 66.667 0.00 0.00 0.00 3.57
4698 5021 4.012895 GCAAGTGCCACGTGTCGG 62.013 66.667 15.65 0.00 34.31 4.79


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

AutoCloner maintained by Alex Coulton.