Multiple sequence alignment - TraesCS2A01G111300

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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 TraesCS2A01G111300 chr2A 100.000 2354 0 0 1 2354 62396635 62398988 0.000000e+00 4348.0
1 TraesCS2A01G111300 chr2A 79.227 207 31 4 394 593 62391779 62391980 1.470000e-27 134.0
2 TraesCS2A01G111300 chr2D 94.281 1329 47 21 721 2044 62068746 62070050 0.000000e+00 2006.0
3 TraesCS2A01G111300 chr2D 95.012 421 15 4 306 726 62068151 62068565 0.000000e+00 656.0
4 TraesCS2A01G111300 chr2B 89.010 1647 109 35 722 2347 97441239 97442834 0.000000e+00 1973.0
5 TraesCS2A01G111300 chr2B 90.554 307 22 6 2 305 69558196 69557894 1.310000e-107 399.0
6 TraesCS2A01G111300 chr2B 80.400 250 28 13 306 546 97440694 97440931 1.120000e-38 171.0
7 TraesCS2A01G111300 chr2B 82.278 79 7 7 2109 2184 683060074 683060000 7.020000e-06 62.1
8 TraesCS2A01G111300 chr6A 95.177 311 7 2 1 305 524070848 524070540 3.520000e-133 484.0
9 TraesCS2A01G111300 chr6A 82.857 105 13 5 2043 2145 61043073 61042972 3.220000e-14 89.8
10 TraesCS2A01G111300 chr1A 94.569 313 7 2 1 307 559939509 559939817 2.120000e-130 475.0
11 TraesCS2A01G111300 chr1A 83.761 234 35 2 1 231 540633356 540633589 3.940000e-53 219.0
12 TraesCS2A01G111300 chr1A 86.826 167 21 1 1 167 581939981 581940146 4.000000e-43 185.0
13 TraesCS2A01G111300 chr1A 87.179 78 10 0 2084 2161 115976448 115976525 3.220000e-14 89.8
14 TraesCS2A01G111300 chr7B 92.079 303 14 5 1 303 446185475 446185767 3.620000e-113 418.0
15 TraesCS2A01G111300 chr5D 82.540 315 29 12 1 315 411163332 411163620 1.080000e-63 254.0
16 TraesCS2A01G111300 chr5D 92.063 63 4 1 2083 2145 101502148 101502087 1.160000e-13 87.9
17 TraesCS2A01G111300 chr5D 90.000 50 1 4 2113 2160 561578349 561578302 7.020000e-06 62.1
18 TraesCS2A01G111300 chr4D 87.745 204 21 4 1144 1345 293665346 293665145 3.910000e-58 235.0
19 TraesCS2A01G111300 chr4D 87.302 63 7 1 2083 2145 500684157 500684218 1.170000e-08 71.3
20 TraesCS2A01G111300 chr4B 86.207 203 26 2 1144 1345 290913478 290913277 3.940000e-53 219.0
21 TraesCS2A01G111300 chr3B 80.090 221 34 10 1 215 99994456 99994240 3.130000e-34 156.0
22 TraesCS2A01G111300 chr3B 80.090 221 34 10 1 215 696678084 696677868 3.130000e-34 156.0
23 TraesCS2A01G111300 chr3D 79.730 222 34 10 1 215 511682631 511682848 1.460000e-32 150.0
24 TraesCS2A01G111300 chr3D 89.552 67 6 1 2094 2160 174956722 174956657 1.500000e-12 84.2
25 TraesCS2A01G111300 chr1B 81.818 132 21 3 2043 2173 10185776 10185905 8.900000e-20 108.0
26 TraesCS2A01G111300 chr7D 94.000 50 3 0 2113 2162 397578581 397578630 2.510000e-10 76.8


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 TraesCS2A01G111300 chr2A 62396635 62398988 2353 False 4348 4348 100.0000 1 2354 1 chr2A.!!$F2 2353
1 TraesCS2A01G111300 chr2D 62068151 62070050 1899 False 1331 2006 94.6465 306 2044 2 chr2D.!!$F1 1738
2 TraesCS2A01G111300 chr2B 97440694 97442834 2140 False 1072 1973 84.7050 306 2347 2 chr2B.!!$F1 2041

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
60 61 0.039256 CGGACCGACGGTTTGAACTA 60.039 55.0 22.69 0.0 35.25 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1378 1618 0.179108 AGATACAAAGCGAGGCGACC 60.179 55.0 0.0 0.0 0.0 4.79 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.776072 CTCGTCGCGCCGAATTTT 59.224 55.556 14.89 0.00 37.72 1.82
18 19 1.131826 CTCGTCGCGCCGAATTTTT 59.868 52.632 14.89 0.00 37.72 1.94
46 47 5.740838 GAAAACAATTTTTCGATCGGACC 57.259 39.130 16.41 0.00 40.90 4.46
47 48 3.465122 AACAATTTTTCGATCGGACCG 57.535 42.857 16.41 7.84 0.00 4.79
48 49 2.690786 ACAATTTTTCGATCGGACCGA 58.309 42.857 20.85 20.85 41.13 4.69
49 50 2.414138 ACAATTTTTCGATCGGACCGAC 59.586 45.455 21.02 12.25 39.18 4.79
50 51 1.274596 ATTTTTCGATCGGACCGACG 58.725 50.000 21.02 22.86 39.18 5.12
51 52 0.733566 TTTTTCGATCGGACCGACGG 60.734 55.000 26.93 13.61 39.18 4.79
52 53 1.865788 TTTTCGATCGGACCGACGGT 61.866 55.000 21.93 21.93 39.18 4.83
53 54 1.865788 TTTCGATCGGACCGACGGTT 61.866 55.000 26.93 4.49 39.18 4.44
54 55 1.865788 TTCGATCGGACCGACGGTTT 61.866 55.000 26.93 11.81 39.18 3.27
55 56 2.156446 CGATCGGACCGACGGTTTG 61.156 63.158 22.69 16.46 39.18 2.93
56 57 1.213537 GATCGGACCGACGGTTTGA 59.786 57.895 22.69 21.15 39.18 2.69
57 58 0.388907 GATCGGACCGACGGTTTGAA 60.389 55.000 22.69 7.86 39.18 2.69
58 59 0.668401 ATCGGACCGACGGTTTGAAC 60.668 55.000 22.69 7.60 39.18 3.18
59 60 1.300388 CGGACCGACGGTTTGAACT 60.300 57.895 22.69 0.00 35.25 3.01
60 61 0.039256 CGGACCGACGGTTTGAACTA 60.039 55.000 22.69 0.00 35.25 2.24
61 62 1.422388 GGACCGACGGTTTGAACTAC 58.578 55.000 22.69 5.20 35.25 2.73
62 63 1.269726 GGACCGACGGTTTGAACTACA 60.270 52.381 22.69 0.00 35.25 2.74
63 64 2.472816 GACCGACGGTTTGAACTACAA 58.527 47.619 22.69 0.00 35.25 2.41
64 65 2.865551 GACCGACGGTTTGAACTACAAA 59.134 45.455 22.69 0.00 44.79 2.83
111 112 8.071177 TGAGAAAATCTAGAGTGATGTCATCA 57.929 34.615 11.62 11.62 36.84 3.07
112 113 8.534496 TGAGAAAATCTAGAGTGATGTCATCAA 58.466 33.333 17.11 1.11 41.69 2.57
113 114 9.545105 GAGAAAATCTAGAGTGATGTCATCAAT 57.455 33.333 17.11 16.20 41.69 2.57
114 115 9.902684 AGAAAATCTAGAGTGATGTCATCAATT 57.097 29.630 17.11 9.29 41.69 2.32
118 119 9.458727 AATCTAGAGTGATGTCATCAATTTTGT 57.541 29.630 17.11 5.57 41.69 2.83
119 120 8.484641 TCTAGAGTGATGTCATCAATTTTGTC 57.515 34.615 17.11 4.17 41.69 3.18
120 121 8.316946 TCTAGAGTGATGTCATCAATTTTGTCT 58.683 33.333 17.11 11.01 41.69 3.41
121 122 7.756395 AGAGTGATGTCATCAATTTTGTCTT 57.244 32.000 17.11 0.00 41.69 3.01
122 123 8.853077 AGAGTGATGTCATCAATTTTGTCTTA 57.147 30.769 17.11 0.00 41.69 2.10
123 124 8.725148 AGAGTGATGTCATCAATTTTGTCTTAC 58.275 33.333 17.11 1.43 41.69 2.34
124 125 8.394971 AGTGATGTCATCAATTTTGTCTTACA 57.605 30.769 17.11 0.00 41.69 2.41
125 126 9.017509 AGTGATGTCATCAATTTTGTCTTACAT 57.982 29.630 17.11 0.00 41.69 2.29
126 127 9.069078 GTGATGTCATCAATTTTGTCTTACATG 57.931 33.333 17.11 0.00 41.69 3.21
127 128 7.756272 TGATGTCATCAATTTTGTCTTACATGC 59.244 33.333 13.25 0.00 36.11 4.06
128 129 6.979465 TGTCATCAATTTTGTCTTACATGCA 58.021 32.000 0.00 0.00 0.00 3.96
129 130 7.604549 TGTCATCAATTTTGTCTTACATGCAT 58.395 30.769 0.00 0.00 0.00 3.96
130 131 7.542824 TGTCATCAATTTTGTCTTACATGCATG 59.457 33.333 25.09 25.09 0.00 4.06
131 132 6.532302 TCATCAATTTTGTCTTACATGCATGC 59.468 34.615 26.53 11.82 0.00 4.06
132 133 5.780984 TCAATTTTGTCTTACATGCATGCA 58.219 33.333 26.53 25.04 0.00 3.96
133 134 6.399743 TCAATTTTGTCTTACATGCATGCAT 58.600 32.000 27.46 27.46 37.08 3.96
134 135 7.545489 TCAATTTTGTCTTACATGCATGCATA 58.455 30.769 31.73 15.92 34.91 3.14
135 136 8.198778 TCAATTTTGTCTTACATGCATGCATAT 58.801 29.630 31.73 24.57 34.91 1.78
136 137 9.465985 CAATTTTGTCTTACATGCATGCATATA 57.534 29.630 31.73 23.38 34.91 0.86
142 143 8.949177 TGTCTTACATGCATGCATATAATTAGG 58.051 33.333 31.73 18.59 34.91 2.69
143 144 7.912250 GTCTTACATGCATGCATATAATTAGGC 59.088 37.037 31.73 17.43 35.70 3.93
144 145 5.239359 ACATGCATGCATATAATTAGGCG 57.761 39.130 31.73 17.62 37.94 5.52
145 146 4.701651 ACATGCATGCATATAATTAGGCGT 59.298 37.500 31.73 18.25 37.94 5.68
146 147 5.183713 ACATGCATGCATATAATTAGGCGTT 59.816 36.000 31.73 3.67 37.94 4.84
147 148 5.045668 TGCATGCATATAATTAGGCGTTG 57.954 39.130 18.46 0.00 37.94 4.10
148 149 4.518590 TGCATGCATATAATTAGGCGTTGT 59.481 37.500 18.46 0.00 37.94 3.32
149 150 5.703130 TGCATGCATATAATTAGGCGTTGTA 59.297 36.000 18.46 0.00 37.94 2.41
150 151 6.374053 TGCATGCATATAATTAGGCGTTGTAT 59.626 34.615 18.46 0.00 37.94 2.29
151 152 7.094420 TGCATGCATATAATTAGGCGTTGTATT 60.094 33.333 18.46 0.00 37.94 1.89
152 153 8.394877 GCATGCATATAATTAGGCGTTGTATTA 58.605 33.333 14.21 0.00 37.94 0.98
155 156 9.713713 TGCATATAATTAGGCGTTGTATTAAGA 57.286 29.630 0.00 0.00 37.94 2.10
160 161 9.998106 ATAATTAGGCGTTGTATTAAGAGTCAT 57.002 29.630 0.00 0.00 0.00 3.06
161 162 7.715265 ATTAGGCGTTGTATTAAGAGTCATG 57.285 36.000 0.00 0.00 0.00 3.07
162 163 5.339008 AGGCGTTGTATTAAGAGTCATGA 57.661 39.130 0.00 0.00 0.00 3.07
163 164 5.109903 AGGCGTTGTATTAAGAGTCATGAC 58.890 41.667 18.47 18.47 0.00 3.06
164 165 4.868171 GGCGTTGTATTAAGAGTCATGACA 59.132 41.667 27.02 6.95 0.00 3.58
165 166 5.523916 GGCGTTGTATTAAGAGTCATGACAT 59.476 40.000 27.02 13.80 0.00 3.06
166 167 6.414079 GCGTTGTATTAAGAGTCATGACATG 58.586 40.000 27.02 9.28 0.00 3.21
167 168 6.036083 GCGTTGTATTAAGAGTCATGACATGT 59.964 38.462 27.02 13.49 0.00 3.21
168 169 7.394099 CGTTGTATTAAGAGTCATGACATGTG 58.606 38.462 27.02 0.00 0.00 3.21
169 170 6.908870 TGTATTAAGAGTCATGACATGTGC 57.091 37.500 27.02 10.83 0.00 4.57
170 171 6.405538 TGTATTAAGAGTCATGACATGTGCA 58.594 36.000 27.02 12.84 0.00 4.57
171 172 7.049754 TGTATTAAGAGTCATGACATGTGCAT 58.950 34.615 27.02 13.51 0.00 3.96
172 173 5.806366 TTAAGAGTCATGACATGTGCATG 57.194 39.130 27.02 22.15 43.39 4.06
178 179 4.210724 TCATGACATGTGCATGAAGAGA 57.789 40.909 25.57 12.17 46.48 3.10
179 180 4.189231 TCATGACATGTGCATGAAGAGAG 58.811 43.478 25.57 9.29 46.48 3.20
180 181 3.967332 TGACATGTGCATGAAGAGAGA 57.033 42.857 17.85 0.00 41.20 3.10
181 182 3.858247 TGACATGTGCATGAAGAGAGAG 58.142 45.455 17.85 0.00 41.20 3.20
182 183 3.512724 TGACATGTGCATGAAGAGAGAGA 59.487 43.478 17.85 0.00 41.20 3.10
183 184 4.020839 TGACATGTGCATGAAGAGAGAGAA 60.021 41.667 17.85 0.00 41.20 2.87
184 185 4.903054 ACATGTGCATGAAGAGAGAGAAA 58.097 39.130 17.85 0.00 41.20 2.52
185 186 5.311265 ACATGTGCATGAAGAGAGAGAAAA 58.689 37.500 17.85 0.00 41.20 2.29
186 187 5.766670 ACATGTGCATGAAGAGAGAGAAAAA 59.233 36.000 17.85 0.00 41.20 1.94
187 188 5.679734 TGTGCATGAAGAGAGAGAAAAAC 57.320 39.130 0.00 0.00 0.00 2.43
188 189 5.371526 TGTGCATGAAGAGAGAGAAAAACT 58.628 37.500 0.00 0.00 0.00 2.66
189 190 6.524734 TGTGCATGAAGAGAGAGAAAAACTA 58.475 36.000 0.00 0.00 0.00 2.24
190 191 6.648310 TGTGCATGAAGAGAGAGAAAAACTAG 59.352 38.462 0.00 0.00 0.00 2.57
191 192 6.648725 GTGCATGAAGAGAGAGAAAAACTAGT 59.351 38.462 0.00 0.00 0.00 2.57
192 193 7.815068 GTGCATGAAGAGAGAGAAAAACTAGTA 59.185 37.037 0.00 0.00 0.00 1.82
193 194 8.367911 TGCATGAAGAGAGAGAAAAACTAGTAA 58.632 33.333 0.00 0.00 0.00 2.24
194 195 9.377312 GCATGAAGAGAGAGAAAAACTAGTAAT 57.623 33.333 0.00 0.00 0.00 1.89
197 198 9.915629 TGAAGAGAGAGAAAAACTAGTAATCAC 57.084 33.333 0.00 0.00 0.00 3.06
198 199 9.915629 GAAGAGAGAGAAAAACTAGTAATCACA 57.084 33.333 0.00 0.00 0.00 3.58
200 201 9.868277 AGAGAGAGAAAAACTAGTAATCACATG 57.132 33.333 0.00 0.00 0.00 3.21
201 202 8.485976 AGAGAGAAAAACTAGTAATCACATGC 57.514 34.615 0.00 0.00 0.00 4.06
202 203 8.097038 AGAGAGAAAAACTAGTAATCACATGCA 58.903 33.333 0.00 0.00 0.00 3.96
203 204 8.798859 AGAGAAAAACTAGTAATCACATGCAT 57.201 30.769 0.00 0.00 0.00 3.96
204 205 8.671921 AGAGAAAAACTAGTAATCACATGCATG 58.328 33.333 25.09 25.09 0.00 4.06
205 206 8.340618 AGAAAAACTAGTAATCACATGCATGT 57.659 30.769 26.61 26.61 42.84 3.21
218 219 3.998341 ACATGCATGTGAAGAAAAATGGC 59.002 39.130 30.92 0.00 40.03 4.40
219 220 4.250464 CATGCATGTGAAGAAAAATGGCT 58.750 39.130 18.91 0.00 0.00 4.75
220 221 3.655486 TGCATGTGAAGAAAAATGGCTG 58.345 40.909 0.00 0.00 0.00 4.85
221 222 2.414138 GCATGTGAAGAAAAATGGCTGC 59.586 45.455 0.00 0.00 0.00 5.25
222 223 3.655486 CATGTGAAGAAAAATGGCTGCA 58.345 40.909 0.50 0.00 0.00 4.41
223 224 4.250464 CATGTGAAGAAAAATGGCTGCAT 58.750 39.130 0.50 0.00 0.00 3.96
224 225 3.655486 TGTGAAGAAAAATGGCTGCATG 58.345 40.909 0.50 0.00 0.00 4.06
225 226 2.414138 GTGAAGAAAAATGGCTGCATGC 59.586 45.455 11.82 11.82 41.94 4.06
226 227 2.037381 TGAAGAAAAATGGCTGCATGCA 59.963 40.909 21.29 21.29 45.15 3.96
227 228 2.088950 AGAAAAATGGCTGCATGCAC 57.911 45.000 18.46 13.69 45.15 4.57
228 229 1.621814 AGAAAAATGGCTGCATGCACT 59.378 42.857 18.46 6.03 45.15 4.40
229 230 1.997606 GAAAAATGGCTGCATGCACTC 59.002 47.619 18.46 12.28 45.15 3.51
230 231 0.108992 AAAATGGCTGCATGCACTCG 60.109 50.000 18.46 8.85 45.15 4.18
231 232 2.552585 AAATGGCTGCATGCACTCGC 62.553 55.000 18.46 18.90 45.15 5.03
248 249 4.989588 CATGCATGCACGCACTAG 57.010 55.556 25.37 0.00 46.56 2.57
249 250 2.092374 CATGCATGCACGCACTAGT 58.908 52.632 25.37 0.38 46.56 2.57
250 251 0.448990 CATGCATGCACGCACTAGTT 59.551 50.000 25.37 0.00 46.56 2.24
251 252 1.665169 CATGCATGCACGCACTAGTTA 59.335 47.619 25.37 0.00 46.56 2.24
252 253 1.358877 TGCATGCACGCACTAGTTAG 58.641 50.000 18.46 0.00 36.86 2.34
253 254 0.652592 GCATGCACGCACTAGTTAGG 59.347 55.000 14.21 0.00 0.00 2.69
254 255 2.007049 GCATGCACGCACTAGTTAGGT 61.007 52.381 14.21 0.00 0.00 3.08
255 256 1.927174 CATGCACGCACTAGTTAGGTC 59.073 52.381 0.00 0.00 0.00 3.85
256 257 0.109458 TGCACGCACTAGTTAGGTCG 60.109 55.000 0.00 0.00 0.00 4.79
257 258 0.109412 GCACGCACTAGTTAGGTCGT 60.109 55.000 0.00 0.00 36.39 4.34
258 259 1.892468 CACGCACTAGTTAGGTCGTC 58.108 55.000 0.00 0.00 34.74 4.20
259 260 0.807496 ACGCACTAGTTAGGTCGTCC 59.193 55.000 0.00 0.00 32.73 4.79
261 262 2.283298 CGCACTAGTTAGGTCGTCCTA 58.717 52.381 4.16 4.16 44.58 2.94
275 276 7.571080 AGGTCGTCCTAATTTGTTGTTTAAA 57.429 32.000 0.00 0.00 43.12 1.52
276 277 7.998580 AGGTCGTCCTAATTTGTTGTTTAAAA 58.001 30.769 0.00 0.00 43.12 1.52
277 278 8.635328 AGGTCGTCCTAATTTGTTGTTTAAAAT 58.365 29.630 0.00 0.00 43.12 1.82
278 279 8.908678 GGTCGTCCTAATTTGTTGTTTAAAATC 58.091 33.333 0.00 0.00 0.00 2.17
279 280 8.908678 GTCGTCCTAATTTGTTGTTTAAAATCC 58.091 33.333 0.00 0.00 0.00 3.01
280 281 7.804129 TCGTCCTAATTTGTTGTTTAAAATCCG 59.196 33.333 0.00 0.00 0.00 4.18
281 282 7.804129 CGTCCTAATTTGTTGTTTAAAATCCGA 59.196 33.333 0.00 0.00 0.00 4.55
282 283 9.465985 GTCCTAATTTGTTGTTTAAAATCCGAA 57.534 29.630 0.00 0.00 0.00 4.30
283 284 9.465985 TCCTAATTTGTTGTTTAAAATCCGAAC 57.534 29.630 0.00 0.00 0.00 3.95
284 285 8.421701 CCTAATTTGTTGTTTAAAATCCGAACG 58.578 33.333 0.00 0.00 0.00 3.95
285 286 7.988904 AATTTGTTGTTTAAAATCCGAACGA 57.011 28.000 0.00 0.00 0.00 3.85
286 287 6.793479 TTTGTTGTTTAAAATCCGAACGAC 57.207 33.333 0.00 0.00 37.90 4.34
287 288 5.738118 TGTTGTTTAAAATCCGAACGACT 57.262 34.783 0.00 0.00 38.12 4.18
288 289 5.503498 TGTTGTTTAAAATCCGAACGACTG 58.497 37.500 0.00 0.00 38.12 3.51
289 290 4.136517 TGTTTAAAATCCGAACGACTGC 57.863 40.909 0.00 0.00 0.00 4.40
290 291 3.150731 GTTTAAAATCCGAACGACTGCG 58.849 45.455 0.00 0.00 44.79 5.18
291 292 0.717224 TAAAATCCGAACGACTGCGC 59.283 50.000 0.00 0.00 42.48 6.09
292 293 2.222953 AAAATCCGAACGACTGCGCG 62.223 55.000 0.00 0.00 42.48 6.86
299 300 4.447365 ACGACTGCGCGTTAGTAC 57.553 55.556 16.17 10.12 42.71 2.73
300 301 1.575922 ACGACTGCGCGTTAGTACA 59.424 52.632 16.17 0.16 42.71 2.90
301 302 0.453950 ACGACTGCGCGTTAGTACAG 60.454 55.000 16.17 11.94 42.71 2.74
302 303 0.453950 CGACTGCGCGTTAGTACAGT 60.454 55.000 16.17 14.85 45.66 3.55
303 304 3.396491 ACTGCGCGTTAGTACAGTC 57.604 52.632 14.93 0.00 39.04 3.51
304 305 0.109412 ACTGCGCGTTAGTACAGTCC 60.109 55.000 14.93 0.00 39.04 3.85
338 339 5.968254 CCCTCAAGGTTAGTCTAGTTTCTC 58.032 45.833 0.00 0.00 0.00 2.87
378 379 5.617751 GCAAATTCTACACGCAAAGTCTCAT 60.618 40.000 0.00 0.00 0.00 2.90
473 474 7.726033 TTTTAAGGGCATATCCTTTGCTTAA 57.274 32.000 1.28 0.00 44.14 1.85
585 592 7.812309 ATTTGCGCTTTATAAAAGGAAAGAC 57.188 32.000 9.73 0.73 35.12 3.01
589 596 5.220796 GCGCTTTATAAAAGGAAAGACGGAT 60.221 40.000 0.00 0.00 35.12 4.18
671 678 1.377725 GCCTCACACCCCATCACAG 60.378 63.158 0.00 0.00 0.00 3.66
672 679 1.300963 CCTCACACCCCATCACAGG 59.699 63.158 0.00 0.00 0.00 4.00
747 967 2.801077 ATTAACACGGAGAAAGGGGG 57.199 50.000 0.00 0.00 0.00 5.40
1373 1613 6.558014 ACCTGATCATCTTACTGGATTCTCAT 59.442 38.462 0.00 0.00 0.00 2.90
1378 1618 4.412796 TCTTACTGGATTCTCATGGCAG 57.587 45.455 0.00 0.00 0.00 4.85
1402 1642 1.789464 GCCTCGCTTTGTATCTCGATG 59.211 52.381 0.00 0.00 0.00 3.84
1508 1748 3.390135 TCTGGTTCGTCTGCTTAAACTG 58.610 45.455 0.00 0.00 0.00 3.16
1509 1749 3.131396 CTGGTTCGTCTGCTTAAACTGT 58.869 45.455 0.00 0.00 0.00 3.55
1536 1776 1.873591 CGGGCTGTATCCAGTAATTGC 59.126 52.381 0.00 0.00 41.02 3.56
1556 1796 5.250235 TGCATGTTTGTTTACTTCCGAAA 57.750 34.783 0.00 0.00 0.00 3.46
1569 1809 1.565067 TCCGAAACTACTTCCCCCTC 58.435 55.000 0.00 0.00 0.00 4.30
1599 1840 3.418068 GCAGCGTGTCTGGCAGTC 61.418 66.667 15.27 9.82 43.06 3.51
1626 1868 5.952347 AGGGAAAGGGAATGAAGATTACAAC 59.048 40.000 0.00 0.00 0.00 3.32
1629 1871 5.904362 AAGGGAATGAAGATTACAACAGC 57.096 39.130 0.00 0.00 0.00 4.40
1630 1872 3.941483 AGGGAATGAAGATTACAACAGCG 59.059 43.478 0.00 0.00 0.00 5.18
1631 1873 3.938963 GGGAATGAAGATTACAACAGCGA 59.061 43.478 0.00 0.00 0.00 4.93
1637 1879 3.963428 AGATTACAACAGCGAGGAGTT 57.037 42.857 0.00 0.00 0.00 3.01
1705 1947 2.091610 TCCTTTTTGATGTGTGGTGGGA 60.092 45.455 0.00 0.00 0.00 4.37
1706 1948 2.697751 CCTTTTTGATGTGTGGTGGGAA 59.302 45.455 0.00 0.00 0.00 3.97
1707 1949 3.492482 CCTTTTTGATGTGTGGTGGGAAC 60.492 47.826 0.00 0.00 0.00 3.62
1726 1968 6.127758 TGGGAACAATTATCGGTGAGAATTTG 60.128 38.462 0.00 0.00 32.20 2.32
1754 1996 5.512232 GGAACCTCTATCCAGCCTGAATTAG 60.512 48.000 0.00 0.00 36.92 1.73
1796 2038 2.351738 GCGTGGAAATTGACCTCTTTGG 60.352 50.000 4.05 0.00 42.93 3.28
1866 2108 5.258456 TGGATAACACGTCTTGTATCCTC 57.742 43.478 17.64 1.87 37.51 3.71
1867 2109 4.201980 TGGATAACACGTCTTGTATCCTCG 60.202 45.833 17.64 0.00 37.51 4.63
1868 2110 4.201990 GGATAACACGTCTTGTATCCTCGT 60.202 45.833 12.76 0.00 37.51 4.18
1902 2144 2.919666 ATCGCAAATTTCCTCCAACG 57.080 45.000 0.00 0.00 0.00 4.10
1904 2146 1.804151 TCGCAAATTTCCTCCAACGAG 59.196 47.619 0.00 0.00 35.72 4.18
2056 2299 3.897657 TTCATATACTCCCTCGGTCCT 57.102 47.619 0.00 0.00 0.00 3.85
2057 2300 5.531753 ATTCATATACTCCCTCGGTCCTA 57.468 43.478 0.00 0.00 0.00 2.94
2067 2310 4.355549 TCCCTCGGTCCTAAATTACTTGA 58.644 43.478 0.00 0.00 0.00 3.02
2071 2314 3.056678 TCGGTCCTAAATTACTTGACGCA 60.057 43.478 0.00 0.00 0.00 5.24
2072 2315 3.680937 CGGTCCTAAATTACTTGACGCAA 59.319 43.478 0.00 0.00 0.00 4.85
2082 2325 8.687824 AAATTACTTGACGCAAAAATGGATAG 57.312 30.769 0.00 0.00 0.00 2.08
2092 2335 8.647143 ACGCAAAAATGGATAGAAATTAATGG 57.353 30.769 0.00 0.00 0.00 3.16
2145 2388 9.466497 ACATCCATTTATGTGACAAGTAATTCT 57.534 29.630 0.00 0.00 38.65 2.40
2148 2391 9.613428 TCCATTTATGTGACAAGTAATTCTAGG 57.387 33.333 0.00 0.00 0.00 3.02
2149 2392 8.345565 CCATTTATGTGACAAGTAATTCTAGGC 58.654 37.037 0.00 0.00 0.00 3.93
2150 2393 7.534085 TTTATGTGACAAGTAATTCTAGGCG 57.466 36.000 0.00 0.00 0.00 5.52
2153 2396 5.168569 TGTGACAAGTAATTCTAGGCGAAG 58.831 41.667 0.00 0.00 34.56 3.79
2154 2397 4.567159 GTGACAAGTAATTCTAGGCGAAGG 59.433 45.833 0.00 0.00 34.56 3.46
2155 2398 4.120589 GACAAGTAATTCTAGGCGAAGGG 58.879 47.826 0.00 0.00 34.56 3.95
2162 2405 5.725325 AATTCTAGGCGAAGGGAGTATAC 57.275 43.478 0.00 0.00 34.56 1.47
2163 2406 3.870538 TCTAGGCGAAGGGAGTATACA 57.129 47.619 5.50 0.00 0.00 2.29
2212 2455 7.461182 TTCATATAAACCTGGTCAAACTTGG 57.539 36.000 0.00 0.00 0.00 3.61
2247 2490 8.747538 ACTTAGACAAAACCATAACTTCAACT 57.252 30.769 0.00 0.00 0.00 3.16
2337 2582 8.160521 TCCAATTTTTGATTCTTGTCTTACGA 57.839 30.769 0.00 0.00 0.00 3.43
2347 2592 3.483196 TCTTGTCTTACGAAACGAACGTG 59.517 43.478 13.85 0.00 43.73 4.49
2348 2593 2.796304 TGTCTTACGAAACGAACGTGT 58.204 42.857 13.85 0.00 43.73 4.49
2349 2594 2.783284 TGTCTTACGAAACGAACGTGTC 59.217 45.455 7.37 7.37 43.73 3.67
2350 2595 2.783284 GTCTTACGAAACGAACGTGTCA 59.217 45.455 16.00 0.00 43.73 3.58
2351 2596 3.038017 TCTTACGAAACGAACGTGTCAG 58.962 45.455 16.00 11.32 43.73 3.51
2352 2597 1.122849 TACGAAACGAACGTGTCAGC 58.877 50.000 16.00 0.00 43.73 4.26
2353 2598 1.155087 CGAAACGAACGTGTCAGCG 60.155 57.895 16.00 1.39 32.07 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.131826 AAAAATTCGGCGCGACGAG 59.868 52.632 37.36 9.26 44.47 4.18
24 25 4.319901 CGGTCCGATCGAAAAATTGTTTTC 59.680 41.667 18.66 2.51 46.17 2.29
25 26 4.023878 TCGGTCCGATCGAAAAATTGTTTT 60.024 37.500 18.66 0.00 39.70 2.43
26 27 3.499157 TCGGTCCGATCGAAAAATTGTTT 59.501 39.130 18.66 0.00 33.42 2.83
27 28 3.068560 TCGGTCCGATCGAAAAATTGTT 58.931 40.909 18.66 0.00 33.42 2.83
28 29 2.414138 GTCGGTCCGATCGAAAAATTGT 59.586 45.455 18.75 0.00 38.42 2.71
29 30 2.534150 CGTCGGTCCGATCGAAAAATTG 60.534 50.000 18.75 0.00 38.42 2.32
30 31 1.657094 CGTCGGTCCGATCGAAAAATT 59.343 47.619 18.75 0.00 38.42 1.82
31 32 1.274596 CGTCGGTCCGATCGAAAAAT 58.725 50.000 18.75 0.00 38.42 1.82
32 33 0.733566 CCGTCGGTCCGATCGAAAAA 60.734 55.000 26.93 0.00 38.42 1.94
33 34 1.153978 CCGTCGGTCCGATCGAAAA 60.154 57.895 26.93 0.00 38.42 2.29
34 35 1.865788 AACCGTCGGTCCGATCGAAA 61.866 55.000 26.93 0.63 38.42 3.46
35 36 1.865788 AAACCGTCGGTCCGATCGAA 61.866 55.000 26.93 0.00 38.42 3.71
36 37 2.334946 AAACCGTCGGTCCGATCGA 61.335 57.895 26.93 0.00 38.42 3.59
37 38 2.156446 CAAACCGTCGGTCCGATCG 61.156 63.158 19.16 20.61 38.42 3.69
38 39 0.388907 TTCAAACCGTCGGTCCGATC 60.389 55.000 19.16 10.27 38.42 3.69
39 40 0.668401 GTTCAAACCGTCGGTCCGAT 60.668 55.000 19.16 0.00 38.42 4.18
40 41 1.300080 GTTCAAACCGTCGGTCCGA 60.300 57.895 19.16 10.71 33.12 4.55
41 42 0.039256 TAGTTCAAACCGTCGGTCCG 60.039 55.000 19.16 11.98 33.12 4.79
42 43 1.269726 TGTAGTTCAAACCGTCGGTCC 60.270 52.381 19.16 3.75 33.12 4.46
43 44 2.138596 TGTAGTTCAAACCGTCGGTC 57.861 50.000 19.16 4.49 33.12 4.79
44 45 2.600470 TTGTAGTTCAAACCGTCGGT 57.400 45.000 12.23 12.23 37.65 4.69
45 46 3.063725 TGTTTTGTAGTTCAAACCGTCGG 59.936 43.478 10.48 10.48 44.39 4.79
46 47 4.261736 TGTTTTGTAGTTCAAACCGTCG 57.738 40.909 0.00 0.00 44.39 5.12
47 48 7.387945 CAAAATGTTTTGTAGTTCAAACCGTC 58.612 34.615 9.48 0.00 44.39 4.79
48 49 6.311690 CCAAAATGTTTTGTAGTTCAAACCGT 59.688 34.615 14.92 0.00 44.39 4.83
49 50 6.531948 TCCAAAATGTTTTGTAGTTCAAACCG 59.468 34.615 14.92 0.00 44.39 4.44
50 51 7.835634 TCCAAAATGTTTTGTAGTTCAAACC 57.164 32.000 14.92 0.00 44.39 3.27
54 55 9.658799 TGAATTTCCAAAATGTTTTGTAGTTCA 57.341 25.926 14.92 15.48 44.52 3.18
85 86 8.702819 TGATGACATCACTCTAGATTTTCTCAT 58.297 33.333 14.24 0.00 33.59 2.90
86 87 8.071177 TGATGACATCACTCTAGATTTTCTCA 57.929 34.615 14.24 0.00 33.59 3.27
87 88 8.939201 TTGATGACATCACTCTAGATTTTCTC 57.061 34.615 17.77 0.00 39.39 2.87
88 89 9.902684 AATTGATGACATCACTCTAGATTTTCT 57.097 29.630 17.77 0.00 39.39 2.52
92 93 9.458727 ACAAAATTGATGACATCACTCTAGATT 57.541 29.630 17.77 10.65 39.39 2.40
93 94 9.107177 GACAAAATTGATGACATCACTCTAGAT 57.893 33.333 17.77 5.02 39.39 1.98
94 95 8.316946 AGACAAAATTGATGACATCACTCTAGA 58.683 33.333 17.77 2.68 39.39 2.43
95 96 8.489990 AGACAAAATTGATGACATCACTCTAG 57.510 34.615 17.77 10.44 39.39 2.43
96 97 8.853077 AAGACAAAATTGATGACATCACTCTA 57.147 30.769 17.77 3.82 39.39 2.43
97 98 7.756395 AAGACAAAATTGATGACATCACTCT 57.244 32.000 17.77 8.00 39.39 3.24
98 99 8.506437 TGTAAGACAAAATTGATGACATCACTC 58.494 33.333 17.77 6.09 39.39 3.51
99 100 8.394971 TGTAAGACAAAATTGATGACATCACT 57.605 30.769 17.77 10.02 39.39 3.41
100 101 9.069078 CATGTAAGACAAAATTGATGACATCAC 57.931 33.333 17.77 4.87 39.39 3.06
101 102 7.756272 GCATGTAAGACAAAATTGATGACATCA 59.244 33.333 14.24 14.24 37.55 3.07
102 103 7.756272 TGCATGTAAGACAAAATTGATGACATC 59.244 33.333 8.59 8.59 0.00 3.06
103 104 7.604549 TGCATGTAAGACAAAATTGATGACAT 58.395 30.769 0.00 0.00 0.00 3.06
104 105 6.979465 TGCATGTAAGACAAAATTGATGACA 58.021 32.000 0.00 0.00 0.00 3.58
105 106 7.463648 GCATGCATGTAAGACAAAATTGATGAC 60.464 37.037 26.79 0.46 0.00 3.06
106 107 6.532302 GCATGCATGTAAGACAAAATTGATGA 59.468 34.615 26.79 0.00 0.00 2.92
107 108 6.311690 TGCATGCATGTAAGACAAAATTGATG 59.688 34.615 26.79 0.00 0.00 3.07
108 109 6.399743 TGCATGCATGTAAGACAAAATTGAT 58.600 32.000 26.79 0.00 0.00 2.57
109 110 5.780984 TGCATGCATGTAAGACAAAATTGA 58.219 33.333 26.79 0.00 0.00 2.57
110 111 6.656314 ATGCATGCATGTAAGACAAAATTG 57.344 33.333 31.74 0.00 35.03 2.32
116 117 8.949177 CCTAATTATATGCATGCATGTAAGACA 58.051 33.333 36.73 27.19 41.12 3.41
117 118 7.912250 GCCTAATTATATGCATGCATGTAAGAC 59.088 37.037 36.73 25.48 41.12 3.01
118 119 7.201635 CGCCTAATTATATGCATGCATGTAAGA 60.202 37.037 36.73 29.27 41.12 2.10
119 120 6.908820 CGCCTAATTATATGCATGCATGTAAG 59.091 38.462 36.73 28.39 41.12 2.34
120 121 6.374053 ACGCCTAATTATATGCATGCATGTAA 59.626 34.615 36.50 36.50 41.69 2.41
121 122 5.879777 ACGCCTAATTATATGCATGCATGTA 59.120 36.000 37.43 32.26 37.82 2.29
122 123 4.701651 ACGCCTAATTATATGCATGCATGT 59.298 37.500 37.43 33.30 37.82 3.21
123 124 5.239359 ACGCCTAATTATATGCATGCATG 57.761 39.130 37.43 22.70 37.82 4.06
124 125 5.183713 ACAACGCCTAATTATATGCATGCAT 59.816 36.000 33.92 33.92 40.19 3.96
125 126 4.518590 ACAACGCCTAATTATATGCATGCA 59.481 37.500 25.04 25.04 0.00 3.96
126 127 5.046910 ACAACGCCTAATTATATGCATGC 57.953 39.130 11.82 11.82 0.00 4.06
129 130 9.713713 TCTTAATACAACGCCTAATTATATGCA 57.286 29.630 0.00 0.00 0.00 3.96
134 135 9.998106 ATGACTCTTAATACAACGCCTAATTAT 57.002 29.630 0.00 0.00 0.00 1.28
135 136 9.256477 CATGACTCTTAATACAACGCCTAATTA 57.744 33.333 0.00 0.00 0.00 1.40
136 137 7.985184 TCATGACTCTTAATACAACGCCTAATT 59.015 33.333 0.00 0.00 0.00 1.40
137 138 7.438459 GTCATGACTCTTAATACAACGCCTAAT 59.562 37.037 18.83 0.00 0.00 1.73
138 139 6.755141 GTCATGACTCTTAATACAACGCCTAA 59.245 38.462 18.83 0.00 0.00 2.69
139 140 6.127563 TGTCATGACTCTTAATACAACGCCTA 60.128 38.462 25.55 0.00 0.00 3.93
140 141 5.109903 GTCATGACTCTTAATACAACGCCT 58.890 41.667 18.83 0.00 0.00 5.52
141 142 4.868171 TGTCATGACTCTTAATACAACGCC 59.132 41.667 25.55 0.00 0.00 5.68
142 143 6.036083 ACATGTCATGACTCTTAATACAACGC 59.964 38.462 25.55 0.00 0.00 4.84
143 144 7.394099 CACATGTCATGACTCTTAATACAACG 58.606 38.462 25.55 2.37 0.00 4.10
144 145 7.148423 TGCACATGTCATGACTCTTAATACAAC 60.148 37.037 25.55 5.35 0.00 3.32
145 146 6.878389 TGCACATGTCATGACTCTTAATACAA 59.122 34.615 25.55 2.57 0.00 2.41
146 147 6.405538 TGCACATGTCATGACTCTTAATACA 58.594 36.000 25.55 11.24 0.00 2.29
147 148 6.908870 TGCACATGTCATGACTCTTAATAC 57.091 37.500 25.55 9.01 0.00 1.89
148 149 7.274447 TCATGCACATGTCATGACTCTTAATA 58.726 34.615 25.55 4.83 43.63 0.98
149 150 6.117488 TCATGCACATGTCATGACTCTTAAT 58.883 36.000 25.55 8.50 43.63 1.40
150 151 5.490159 TCATGCACATGTCATGACTCTTAA 58.510 37.500 25.55 6.34 43.63 1.85
151 152 5.088680 TCATGCACATGTCATGACTCTTA 57.911 39.130 25.55 6.73 43.63 2.10
152 153 3.946606 TCATGCACATGTCATGACTCTT 58.053 40.909 25.55 8.82 43.63 2.85
153 154 3.622166 TCATGCACATGTCATGACTCT 57.378 42.857 25.55 11.11 43.63 3.24
154 155 3.937079 TCTTCATGCACATGTCATGACTC 59.063 43.478 26.68 10.58 46.84 3.36
155 156 3.939592 CTCTTCATGCACATGTCATGACT 59.060 43.478 26.68 9.43 46.84 3.41
156 157 3.937079 TCTCTTCATGCACATGTCATGAC 59.063 43.478 26.68 19.27 46.84 3.06
157 158 4.081309 TCTCTCTTCATGCACATGTCATGA 60.081 41.667 24.70 24.70 45.91 3.07
158 159 4.189231 TCTCTCTTCATGCACATGTCATG 58.811 43.478 22.15 22.15 41.87 3.07
159 160 4.161754 TCTCTCTCTTCATGCACATGTCAT 59.838 41.667 10.27 0.00 39.72 3.06
160 161 3.512724 TCTCTCTCTTCATGCACATGTCA 59.487 43.478 10.27 0.00 39.72 3.58
161 162 4.120792 TCTCTCTCTTCATGCACATGTC 57.879 45.455 10.27 0.00 39.72 3.06
162 163 4.548451 TTCTCTCTCTTCATGCACATGT 57.452 40.909 10.27 0.00 39.72 3.21
163 164 5.874895 TTTTCTCTCTCTTCATGCACATG 57.125 39.130 4.18 4.18 40.09 3.21
164 165 6.002704 AGTTTTTCTCTCTCTTCATGCACAT 58.997 36.000 0.00 0.00 0.00 3.21
165 166 5.371526 AGTTTTTCTCTCTCTTCATGCACA 58.628 37.500 0.00 0.00 0.00 4.57
166 167 5.938438 AGTTTTTCTCTCTCTTCATGCAC 57.062 39.130 0.00 0.00 0.00 4.57
167 168 6.763355 ACTAGTTTTTCTCTCTCTTCATGCA 58.237 36.000 0.00 0.00 0.00 3.96
168 169 8.764524 TTACTAGTTTTTCTCTCTCTTCATGC 57.235 34.615 0.00 0.00 0.00 4.06
171 172 9.915629 GTGATTACTAGTTTTTCTCTCTCTTCA 57.084 33.333 0.00 0.00 0.00 3.02
172 173 9.915629 TGTGATTACTAGTTTTTCTCTCTCTTC 57.084 33.333 0.00 0.00 0.00 2.87
174 175 9.868277 CATGTGATTACTAGTTTTTCTCTCTCT 57.132 33.333 0.00 0.00 0.00 3.10
175 176 8.599774 GCATGTGATTACTAGTTTTTCTCTCTC 58.400 37.037 0.00 0.00 0.00 3.20
176 177 8.097038 TGCATGTGATTACTAGTTTTTCTCTCT 58.903 33.333 0.00 0.00 0.00 3.10
177 178 8.256611 TGCATGTGATTACTAGTTTTTCTCTC 57.743 34.615 0.00 0.00 0.00 3.20
178 179 8.671921 CATGCATGTGATTACTAGTTTTTCTCT 58.328 33.333 18.91 0.00 0.00 3.10
179 180 8.454106 ACATGCATGTGATTACTAGTTTTTCTC 58.546 33.333 30.92 0.00 40.03 2.87
180 181 8.340618 ACATGCATGTGATTACTAGTTTTTCT 57.659 30.769 30.92 0.00 40.03 2.52
196 197 3.998341 GCCATTTTTCTTCACATGCATGT 59.002 39.130 26.61 26.61 42.84 3.21
197 198 4.092821 CAGCCATTTTTCTTCACATGCATG 59.907 41.667 25.09 25.09 0.00 4.06
198 199 4.250464 CAGCCATTTTTCTTCACATGCAT 58.750 39.130 0.00 0.00 0.00 3.96
199 200 3.655486 CAGCCATTTTTCTTCACATGCA 58.345 40.909 0.00 0.00 0.00 3.96
200 201 2.414138 GCAGCCATTTTTCTTCACATGC 59.586 45.455 0.00 0.00 0.00 4.06
201 202 3.655486 TGCAGCCATTTTTCTTCACATG 58.345 40.909 0.00 0.00 0.00 3.21
202 203 4.250464 CATGCAGCCATTTTTCTTCACAT 58.750 39.130 0.00 0.00 0.00 3.21
203 204 3.655486 CATGCAGCCATTTTTCTTCACA 58.345 40.909 0.00 0.00 0.00 3.58
204 205 2.414138 GCATGCAGCCATTTTTCTTCAC 59.586 45.455 14.21 0.00 37.23 3.18
205 206 2.037381 TGCATGCAGCCATTTTTCTTCA 59.963 40.909 18.46 0.00 44.83 3.02
206 207 2.414138 GTGCATGCAGCCATTTTTCTTC 59.586 45.455 23.41 0.00 44.83 2.87
207 208 2.038033 AGTGCATGCAGCCATTTTTCTT 59.962 40.909 23.41 0.00 44.83 2.52
208 209 1.621814 AGTGCATGCAGCCATTTTTCT 59.378 42.857 23.41 8.33 44.83 2.52
209 210 1.997606 GAGTGCATGCAGCCATTTTTC 59.002 47.619 23.41 5.77 44.83 2.29
210 211 1.670674 CGAGTGCATGCAGCCATTTTT 60.671 47.619 23.41 0.00 44.83 1.94
211 212 0.108992 CGAGTGCATGCAGCCATTTT 60.109 50.000 23.41 0.46 44.83 1.82
212 213 1.509463 CGAGTGCATGCAGCCATTT 59.491 52.632 23.41 2.39 44.83 2.32
213 214 3.060020 GCGAGTGCATGCAGCCATT 62.060 57.895 23.41 4.36 44.83 3.16
214 215 3.515286 GCGAGTGCATGCAGCCAT 61.515 61.111 23.41 7.55 44.83 4.40
233 234 1.358877 CTAACTAGTGCGTGCATGCA 58.641 50.000 29.30 29.30 43.95 3.96
234 235 0.652592 CCTAACTAGTGCGTGCATGC 59.347 55.000 24.20 24.20 0.00 4.06
235 236 1.927174 GACCTAACTAGTGCGTGCATG 59.073 52.381 0.09 0.09 0.00 4.06
236 237 1.469251 CGACCTAACTAGTGCGTGCAT 60.469 52.381 0.00 0.00 0.00 3.96
237 238 0.109458 CGACCTAACTAGTGCGTGCA 60.109 55.000 0.00 0.00 0.00 4.57
238 239 0.109412 ACGACCTAACTAGTGCGTGC 60.109 55.000 0.00 0.00 32.54 5.34
239 240 1.467035 GGACGACCTAACTAGTGCGTG 60.467 57.143 0.00 0.00 33.44 5.34
240 241 0.807496 GGACGACCTAACTAGTGCGT 59.193 55.000 0.00 1.87 35.10 5.24
241 242 1.093159 AGGACGACCTAACTAGTGCG 58.907 55.000 4.08 0.00 45.83 5.34
250 251 8.674263 TTTAAACAACAAATTAGGACGACCTA 57.326 30.769 9.70 9.70 45.83 3.08
252 253 8.806177 ATTTTAAACAACAAATTAGGACGACC 57.194 30.769 0.00 0.00 0.00 4.79
253 254 8.908678 GGATTTTAAACAACAAATTAGGACGAC 58.091 33.333 0.00 0.00 0.00 4.34
254 255 7.804129 CGGATTTTAAACAACAAATTAGGACGA 59.196 33.333 0.00 0.00 0.00 4.20
255 256 7.804129 TCGGATTTTAAACAACAAATTAGGACG 59.196 33.333 0.00 0.00 0.00 4.79
256 257 9.465985 TTCGGATTTTAAACAACAAATTAGGAC 57.534 29.630 0.00 0.00 0.00 3.85
257 258 9.465985 GTTCGGATTTTAAACAACAAATTAGGA 57.534 29.630 0.00 0.00 0.00 2.94
258 259 8.421701 CGTTCGGATTTTAAACAACAAATTAGG 58.578 33.333 0.00 0.00 0.00 2.69
259 260 9.171701 TCGTTCGGATTTTAAACAACAAATTAG 57.828 29.630 0.00 0.00 0.00 1.73
260 261 8.956014 GTCGTTCGGATTTTAAACAACAAATTA 58.044 29.630 0.00 0.00 0.00 1.40
261 262 7.703197 AGTCGTTCGGATTTTAAACAACAAATT 59.297 29.630 0.00 0.00 0.00 1.82
262 263 7.166804 CAGTCGTTCGGATTTTAAACAACAAAT 59.833 33.333 0.00 0.00 0.00 2.32
263 264 6.469595 CAGTCGTTCGGATTTTAAACAACAAA 59.530 34.615 0.00 0.00 0.00 2.83
264 265 5.966503 CAGTCGTTCGGATTTTAAACAACAA 59.033 36.000 0.00 0.00 0.00 2.83
265 266 5.503498 CAGTCGTTCGGATTTTAAACAACA 58.497 37.500 0.00 0.00 0.00 3.33
266 267 4.377738 GCAGTCGTTCGGATTTTAAACAAC 59.622 41.667 0.00 0.00 0.00 3.32
267 268 4.529446 GCAGTCGTTCGGATTTTAAACAA 58.471 39.130 0.00 0.00 0.00 2.83
268 269 3.363182 CGCAGTCGTTCGGATTTTAAACA 60.363 43.478 0.00 0.00 0.00 2.83
269 270 3.150731 CGCAGTCGTTCGGATTTTAAAC 58.849 45.455 0.00 0.00 0.00 2.01
270 271 2.411806 GCGCAGTCGTTCGGATTTTAAA 60.412 45.455 0.30 0.00 38.14 1.52
271 272 1.127213 GCGCAGTCGTTCGGATTTTAA 59.873 47.619 0.30 0.00 38.14 1.52
272 273 0.717224 GCGCAGTCGTTCGGATTTTA 59.283 50.000 0.30 0.00 38.14 1.52
273 274 1.495951 GCGCAGTCGTTCGGATTTT 59.504 52.632 0.30 0.00 38.14 1.82
274 275 2.726691 CGCGCAGTCGTTCGGATTT 61.727 57.895 8.75 0.00 38.14 2.17
275 276 3.179265 CGCGCAGTCGTTCGGATT 61.179 61.111 8.75 0.00 38.14 3.01
276 277 2.531927 TAACGCGCAGTCGTTCGGAT 62.532 55.000 5.73 0.00 43.94 4.18
277 278 3.252665 TAACGCGCAGTCGTTCGGA 62.253 57.895 5.73 0.00 43.94 4.55
278 279 2.774951 CTAACGCGCAGTCGTTCGG 61.775 63.158 5.73 0.00 43.94 4.30
279 280 0.790495 TACTAACGCGCAGTCGTTCG 60.790 55.000 16.32 1.89 43.94 3.95
280 281 0.632241 GTACTAACGCGCAGTCGTTC 59.368 55.000 16.32 2.59 43.94 3.95
282 283 0.453950 CTGTACTAACGCGCAGTCGT 60.454 55.000 16.32 9.80 41.35 4.34
283 284 0.453950 ACTGTACTAACGCGCAGTCG 60.454 55.000 16.32 9.59 37.62 4.18
284 285 1.257539 GACTGTACTAACGCGCAGTC 58.742 55.000 20.94 20.94 46.91 3.51
285 286 0.109412 GGACTGTACTAACGCGCAGT 60.109 55.000 16.92 16.92 43.85 4.40
286 287 0.109458 TGGACTGTACTAACGCGCAG 60.109 55.000 5.73 6.36 35.31 5.18
287 288 0.528924 ATGGACTGTACTAACGCGCA 59.471 50.000 5.73 0.00 0.00 6.09
288 289 1.197910 GATGGACTGTACTAACGCGC 58.802 55.000 5.73 0.00 0.00 6.86
289 290 2.846039 AGATGGACTGTACTAACGCG 57.154 50.000 3.53 3.53 0.00 6.01
290 291 4.491676 TGAAAGATGGACTGTACTAACGC 58.508 43.478 0.00 0.00 0.00 4.84
291 292 6.128634 GGTTTGAAAGATGGACTGTACTAACG 60.129 42.308 0.00 0.00 0.00 3.18
292 293 6.148976 GGGTTTGAAAGATGGACTGTACTAAC 59.851 42.308 0.00 0.00 0.00 2.34
293 294 6.043938 AGGGTTTGAAAGATGGACTGTACTAA 59.956 38.462 0.00 0.00 0.00 2.24
294 295 5.546499 AGGGTTTGAAAGATGGACTGTACTA 59.454 40.000 0.00 0.00 0.00 1.82
295 296 4.351111 AGGGTTTGAAAGATGGACTGTACT 59.649 41.667 0.00 0.00 0.00 2.73
296 297 4.652822 AGGGTTTGAAAGATGGACTGTAC 58.347 43.478 0.00 0.00 0.00 2.90
297 298 4.349636 TGAGGGTTTGAAAGATGGACTGTA 59.650 41.667 0.00 0.00 0.00 2.74
298 299 3.138283 TGAGGGTTTGAAAGATGGACTGT 59.862 43.478 0.00 0.00 0.00 3.55
299 300 3.754965 TGAGGGTTTGAAAGATGGACTG 58.245 45.455 0.00 0.00 0.00 3.51
300 301 4.401925 CTTGAGGGTTTGAAAGATGGACT 58.598 43.478 0.00 0.00 0.00 3.85
301 302 3.507622 CCTTGAGGGTTTGAAAGATGGAC 59.492 47.826 0.00 0.00 0.00 4.02
302 303 3.766545 CCTTGAGGGTTTGAAAGATGGA 58.233 45.455 0.00 0.00 0.00 3.41
338 339 7.388460 AGAATTTGCAAGAGACCAATTCTAG 57.612 36.000 15.33 0.00 33.22 2.43
378 379 3.443681 TGATGTCTACATGAAGAGACGCA 59.556 43.478 16.70 14.84 44.22 5.24
473 474 3.701241 ACGTGTGCATTTGATTCGTTTT 58.299 36.364 0.00 0.00 0.00 2.43
565 572 4.093850 TCCGTCTTTCCTTTTATAAAGCGC 59.906 41.667 0.00 0.00 34.21 5.92
585 592 2.272678 TGTGCGTACAATTACCATCCG 58.727 47.619 3.02 0.00 32.88 4.18
606 613 7.328737 GTCTCTTTGTGTGTCGACATAATAAGT 59.671 37.037 23.12 0.00 33.66 2.24
615 622 1.517276 CGTGTCTCTTTGTGTGTCGAC 59.483 52.381 9.11 9.11 0.00 4.20
671 678 6.276847 TCACAAAATTGGTGTGTTTACATCC 58.723 36.000 17.57 0.00 45.38 3.51
672 679 7.199766 TCTCACAAAATTGGTGTGTTTACATC 58.800 34.615 17.57 0.00 45.38 3.06
752 972 1.134401 GGTTCGGATCTGATTGGCTCA 60.134 52.381 4.74 0.00 0.00 4.26
753 973 1.587547 GGTTCGGATCTGATTGGCTC 58.412 55.000 4.74 0.00 0.00 4.70
754 974 0.179073 CGGTTCGGATCTGATTGGCT 60.179 55.000 4.74 0.00 0.00 4.75
1360 1600 2.435805 GACCTGCCATGAGAATCCAGTA 59.564 50.000 0.00 0.00 0.00 2.74
1361 1601 1.211457 GACCTGCCATGAGAATCCAGT 59.789 52.381 0.00 0.00 0.00 4.00
1378 1618 0.179108 AGATACAAAGCGAGGCGACC 60.179 55.000 0.00 0.00 0.00 4.79
1402 1642 6.524586 CCGAATAAAACACAGCAAAGAGATTC 59.475 38.462 0.00 0.00 0.00 2.52
1508 1748 1.429423 GATACAGCCCGCAAGCAAC 59.571 57.895 0.00 0.00 34.23 4.17
1509 1749 1.748879 GGATACAGCCCGCAAGCAA 60.749 57.895 0.00 0.00 34.23 3.91
1536 1776 7.636326 AGTAGTTTCGGAAGTAAACAAACATG 58.364 34.615 0.00 0.00 38.92 3.21
1556 1796 2.735259 TTTGGAGAGGGGGAAGTAGT 57.265 50.000 0.00 0.00 0.00 2.73
1599 1840 4.516652 ATCTTCATTCCCTTTCCCTCAG 57.483 45.455 0.00 0.00 0.00 3.35
1626 1868 2.750166 TCTCTAGACAAACTCCTCGCTG 59.250 50.000 0.00 0.00 0.00 5.18
1629 1871 6.540914 AGTCTAATCTCTAGACAAACTCCTCG 59.459 42.308 13.00 0.00 44.66 4.63
1630 1872 7.875327 AGTCTAATCTCTAGACAAACTCCTC 57.125 40.000 13.00 0.00 44.66 3.71
1631 1873 7.891183 TCAAGTCTAATCTCTAGACAAACTCCT 59.109 37.037 13.00 0.00 44.66 3.69
1705 1947 5.949354 TCCCAAATTCTCACCGATAATTGTT 59.051 36.000 0.00 0.00 0.00 2.83
1706 1948 5.505780 TCCCAAATTCTCACCGATAATTGT 58.494 37.500 0.00 0.00 0.00 2.71
1707 1949 5.009010 CCTCCCAAATTCTCACCGATAATTG 59.991 44.000 0.00 0.00 0.00 2.32
1726 1968 1.052617 GCTGGATAGAGGTTCCTCCC 58.947 60.000 14.40 9.75 36.75 4.30
1754 1996 0.983378 TCTCTTCCCTAGCCCCTTGC 60.983 60.000 0.00 0.00 41.71 4.01
1796 2038 1.282447 GGAGAGAAGGGGAAAGGGAAC 59.718 57.143 0.00 0.00 0.00 3.62
1904 2146 9.406828 GGATCAACCTAAAACTAAAATTGTGTC 57.593 33.333 0.00 0.00 35.41 3.67
1974 2216 8.936070 AATTTGATGGTGTGAATGTTGATATG 57.064 30.769 0.00 0.00 0.00 1.78
2045 2288 4.161001 GTCAAGTAATTTAGGACCGAGGGA 59.839 45.833 0.00 0.00 0.00 4.20
2047 2290 4.110482 CGTCAAGTAATTTAGGACCGAGG 58.890 47.826 0.00 0.00 0.00 4.63
2051 2294 5.616488 TTTGCGTCAAGTAATTTAGGACC 57.384 39.130 0.00 0.00 0.00 4.46
2056 2299 9.781834 CTATCCATTTTTGCGTCAAGTAATTTA 57.218 29.630 0.00 0.00 0.00 1.40
2057 2300 8.519526 TCTATCCATTTTTGCGTCAAGTAATTT 58.480 29.630 0.00 0.00 0.00 1.82
2067 2310 8.474025 TCCATTAATTTCTATCCATTTTTGCGT 58.526 29.630 0.00 0.00 0.00 5.24
2111 2354 9.764363 TTGTCACATAAATGGATGTATCTAGAC 57.236 33.333 0.00 0.00 37.99 2.59
2123 2366 8.345565 GCCTAGAATTACTTGTCACATAAATGG 58.654 37.037 0.00 0.00 0.00 3.16
2126 2369 7.324935 TCGCCTAGAATTACTTGTCACATAAA 58.675 34.615 0.00 0.00 0.00 1.40
2129 2372 5.339008 TCGCCTAGAATTACTTGTCACAT 57.661 39.130 0.00 0.00 0.00 3.21
2145 2388 4.079970 CAGATGTATACTCCCTTCGCCTA 58.920 47.826 4.17 0.00 0.00 3.93
2147 2390 2.891580 TCAGATGTATACTCCCTTCGCC 59.108 50.000 4.17 0.00 0.00 5.54
2148 2391 4.021894 ACATCAGATGTATACTCCCTTCGC 60.022 45.833 14.84 0.00 42.78 4.70
2149 2392 5.713792 ACATCAGATGTATACTCCCTTCG 57.286 43.478 14.84 0.00 42.78 3.79
2150 2393 6.821388 ACAACATCAGATGTATACTCCCTTC 58.179 40.000 16.71 0.00 44.07 3.46
2153 2396 7.526142 TCTACAACATCAGATGTATACTCCC 57.474 40.000 16.71 0.00 44.07 4.30
2185 2428 9.757227 CAAGTTTGACCAGGTTTATATGAAAAA 57.243 29.630 0.00 0.00 0.00 1.94
2190 2433 6.884295 TCTCCAAGTTTGACCAGGTTTATATG 59.116 38.462 0.00 0.00 0.00 1.78
2191 2434 7.027874 TCTCCAAGTTTGACCAGGTTTATAT 57.972 36.000 0.00 0.00 0.00 0.86
2192 2435 6.442541 TCTCCAAGTTTGACCAGGTTTATA 57.557 37.500 0.00 0.00 0.00 0.98
2193 2436 5.319043 TCTCCAAGTTTGACCAGGTTTAT 57.681 39.130 0.00 0.00 0.00 1.40
2194 2437 4.781775 TCTCCAAGTTTGACCAGGTTTA 57.218 40.909 0.00 0.00 0.00 2.01
2195 2438 3.662759 TCTCCAAGTTTGACCAGGTTT 57.337 42.857 0.00 0.00 0.00 3.27
2196 2439 3.053619 ACTTCTCCAAGTTTGACCAGGTT 60.054 43.478 0.00 0.00 40.16 3.50
2197 2440 2.509964 ACTTCTCCAAGTTTGACCAGGT 59.490 45.455 0.00 0.00 40.16 4.00
2198 2441 3.214696 ACTTCTCCAAGTTTGACCAGG 57.785 47.619 0.00 0.00 40.16 4.45
2212 2455 7.316544 TGGTTTTGTCTAAGTCAAACTTCTC 57.683 36.000 0.00 0.00 39.51 2.87
2247 2490 6.956102 TGGTACTACCTCCCTTTCAAATTA 57.044 37.500 6.79 0.00 39.58 1.40
2254 2497 2.910977 CTGGTTGGTACTACCTCCCTTT 59.089 50.000 15.55 0.00 39.58 3.11


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

AutoCloner maintained by Alex Coulton.