Multiple sequence alignment - TraesCS5B01G072200

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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 TraesCS5B01G072200 chr5B 100.000 2366 0 0 1 2366 83906897 83904532 0.000000e+00 4370.0
1 TraesCS5B01G072200 chr5D 95.423 1879 37 15 526 2366 75419789 75417922 0.000000e+00 2948.0
2 TraesCS5B01G072200 chr5D 95.870 339 14 0 1 339 8611846 8612184 1.240000e-152 549.0
3 TraesCS5B01G072200 chr5A 93.851 1480 50 14 337 1797 70677185 70675728 0.000000e+00 2191.0
4 TraesCS5B01G072200 chr5A 88.745 462 24 8 1800 2247 70665454 70665007 7.440000e-150 540.0
5 TraesCS5B01G072200 chr7B 96.755 339 11 0 1 339 703728429 703728767 1.230000e-157 566.0
6 TraesCS5B01G072200 chr7B 96.165 339 13 0 1 339 350527244 350526906 2.660000e-154 555.0
7 TraesCS5B01G072200 chr2B 96.450 338 12 0 1 338 610602222 610602559 2.050000e-155 558.0
8 TraesCS5B01G072200 chr2B 95.562 338 15 0 1 338 766017848 766018185 2.070000e-150 542.0
9 TraesCS5B01G072200 chr2B 91.935 62 4 1 354 414 449935697 449935758 4.190000e-13 86.1
10 TraesCS5B01G072200 chr6B 96.154 338 13 0 1 338 561282995 561283332 9.560000e-154 553.0
11 TraesCS5B01G072200 chr2D 95.575 339 15 0 1 339 570983987 570984325 5.750000e-151 544.0
12 TraesCS5B01G072200 chr2D 88.710 62 6 1 358 418 11594501 11594440 9.070000e-10 75.0
13 TraesCS5B01G072200 chr3B 95.294 340 16 0 1 340 693648828 693649167 7.440000e-150 540.0
14 TraesCS5B01G072200 chr1D 95.280 339 16 0 2 340 11317710 11317372 2.680000e-149 538.0
15 TraesCS5B01G072200 chr3D 94.118 51 2 1 352 401 452582961 452582911 2.520000e-10 76.8
16 TraesCS5B01G072200 chrUn 93.617 47 3 0 372 418 101289583 101289537 1.170000e-08 71.3
17 TraesCS5B01G072200 chr4B 86.667 60 6 2 358 416 426146223 426146281 5.460000e-07 65.8
18 TraesCS5B01G072200 chr1B 96.970 33 1 0 386 418 316776371 316776403 3.290000e-04 56.5


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 TraesCS5B01G072200 chr5B 83904532 83906897 2365 True 4370 4370 100.000 1 2366 1 chr5B.!!$R1 2365
1 TraesCS5B01G072200 chr5D 75417922 75419789 1867 True 2948 2948 95.423 526 2366 1 chr5D.!!$R1 1840
2 TraesCS5B01G072200 chr5A 70675728 70677185 1457 True 2191 2191 93.851 337 1797 1 chr5A.!!$R2 1460

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
44 45 0.031043 TTTCTTGAAGGCGTCGTCGA 59.969 50.0 6.17 0.0 39.71 4.20 F
99 100 0.034616 CTCTGATCCTTGGATCGGGC 59.965 60.0 28.36 8.4 38.24 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1050 1066 1.292223 GCGGTACTTGGTGCTCTCA 59.708 57.895 0.0 0.0 0.0 3.27 R
1830 1855 2.940147 TGGCATCAACAAATACGTTGC 58.060 42.857 0.0 0.0 44.8 4.17 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
23 24 2.278336 CGGCGGCGAAGATCGTTA 60.278 61.111 29.19 0.00 42.81 3.18
24 25 2.574222 CGGCGGCGAAGATCGTTAC 61.574 63.158 29.19 0.00 42.81 2.50
25 26 1.226888 GGCGGCGAAGATCGTTACT 60.227 57.895 12.98 0.00 42.81 2.24
26 27 0.804933 GGCGGCGAAGATCGTTACTT 60.805 55.000 12.98 0.00 42.81 2.24
27 28 0.997196 GCGGCGAAGATCGTTACTTT 59.003 50.000 12.98 0.00 42.81 2.66
28 29 1.006287 GCGGCGAAGATCGTTACTTTC 60.006 52.381 12.98 0.00 42.81 2.62
29 30 2.527100 CGGCGAAGATCGTTACTTTCT 58.473 47.619 0.00 0.00 42.81 2.52
30 31 2.921754 CGGCGAAGATCGTTACTTTCTT 59.078 45.455 0.00 0.00 42.81 2.52
31 32 3.241678 CGGCGAAGATCGTTACTTTCTTG 60.242 47.826 0.00 0.00 42.81 3.02
32 33 3.924686 GGCGAAGATCGTTACTTTCTTGA 59.075 43.478 1.45 0.00 42.81 3.02
33 34 4.387862 GGCGAAGATCGTTACTTTCTTGAA 59.612 41.667 1.45 0.00 42.81 2.69
34 35 5.444745 GGCGAAGATCGTTACTTTCTTGAAG 60.445 44.000 1.45 0.00 42.81 3.02
35 36 5.444745 GCGAAGATCGTTACTTTCTTGAAGG 60.445 44.000 1.45 0.00 42.81 3.46
36 37 5.444745 CGAAGATCGTTACTTTCTTGAAGGC 60.445 44.000 0.00 0.00 35.98 4.35
37 38 3.927142 AGATCGTTACTTTCTTGAAGGCG 59.073 43.478 0.00 0.00 39.79 5.52
38 39 3.102052 TCGTTACTTTCTTGAAGGCGT 57.898 42.857 0.00 0.00 39.79 5.68
39 40 3.054878 TCGTTACTTTCTTGAAGGCGTC 58.945 45.455 0.00 0.00 39.79 5.19
40 41 2.160013 CGTTACTTTCTTGAAGGCGTCG 60.160 50.000 0.00 0.00 39.79 5.12
41 42 2.798847 GTTACTTTCTTGAAGGCGTCGT 59.201 45.455 0.00 0.00 39.79 4.34
42 43 1.499049 ACTTTCTTGAAGGCGTCGTC 58.501 50.000 0.00 0.00 39.79 4.20
43 44 0.435008 CTTTCTTGAAGGCGTCGTCG 59.565 55.000 0.00 0.00 40.37 5.12
44 45 0.031043 TTTCTTGAAGGCGTCGTCGA 59.969 50.000 6.17 0.00 39.71 4.20
45 46 0.386858 TTCTTGAAGGCGTCGTCGAG 60.387 55.000 13.37 13.37 39.71 4.04
46 47 1.801913 CTTGAAGGCGTCGTCGAGG 60.802 63.158 11.91 10.51 39.71 4.63
47 48 3.909258 TTGAAGGCGTCGTCGAGGC 62.909 63.158 27.22 27.22 41.88 4.70
48 49 4.117661 GAAGGCGTCGTCGAGGCT 62.118 66.667 31.65 22.01 45.54 4.58
49 50 4.117661 AAGGCGTCGTCGAGGCTC 62.118 66.667 31.65 23.34 42.68 4.70
51 52 4.539881 GGCGTCGTCGAGGCTCTC 62.540 72.222 31.65 16.72 42.20 3.20
52 53 3.800863 GCGTCGTCGAGGCTCTCA 61.801 66.667 27.69 0.00 39.86 3.27
53 54 3.102985 CGTCGTCGAGGCTCTCAT 58.897 61.111 13.50 0.00 39.71 2.90
54 55 1.429825 CGTCGTCGAGGCTCTCATT 59.570 57.895 13.50 0.00 39.71 2.57
55 56 0.863538 CGTCGTCGAGGCTCTCATTG 60.864 60.000 13.50 0.00 39.71 2.82
56 57 1.139734 TCGTCGAGGCTCTCATTGC 59.860 57.895 13.50 0.00 0.00 3.56
62 63 2.268920 GGCTCTCATTGCCCGTCA 59.731 61.111 0.00 0.00 44.32 4.35
63 64 1.153086 GGCTCTCATTGCCCGTCAT 60.153 57.895 0.00 0.00 44.32 3.06
64 65 1.442526 GGCTCTCATTGCCCGTCATG 61.443 60.000 0.00 0.00 44.32 3.07
65 66 2.020131 CTCTCATTGCCCGTCATGC 58.980 57.895 0.00 0.00 0.00 4.06
66 67 1.769098 CTCTCATTGCCCGTCATGCG 61.769 60.000 3.02 3.02 40.95 4.73
93 94 2.649742 AGGGAACTCTGATCCTTGGA 57.350 50.000 0.00 0.00 32.90 3.53
94 95 3.142579 AGGGAACTCTGATCCTTGGAT 57.857 47.619 1.18 1.18 32.90 3.41
95 96 3.044894 AGGGAACTCTGATCCTTGGATC 58.955 50.000 19.70 19.70 32.90 3.36
96 97 2.224161 GGGAACTCTGATCCTTGGATCG 60.224 54.545 20.69 16.06 37.14 3.69
97 98 2.224161 GGAACTCTGATCCTTGGATCGG 60.224 54.545 25.14 25.14 38.86 4.18
98 99 1.418334 ACTCTGATCCTTGGATCGGG 58.582 55.000 28.36 22.56 38.24 5.14
99 100 0.034616 CTCTGATCCTTGGATCGGGC 59.965 60.000 28.36 8.40 38.24 6.13
100 101 1.301244 CTGATCCTTGGATCGGGCG 60.301 63.158 23.98 10.55 35.02 6.13
101 102 2.031163 GATCCTTGGATCGGGCGG 59.969 66.667 13.16 0.00 0.00 6.13
102 103 2.768344 ATCCTTGGATCGGGCGGT 60.768 61.111 0.00 0.00 0.00 5.68
103 104 2.996168 GATCCTTGGATCGGGCGGTG 62.996 65.000 13.16 0.00 0.00 4.94
104 105 4.856801 CCTTGGATCGGGCGGTGG 62.857 72.222 0.00 0.00 0.00 4.61
126 127 3.593794 GCTCCGGCGTCGTATCCT 61.594 66.667 9.28 0.00 33.95 3.24
127 128 3.117372 CTCCGGCGTCGTATCCTT 58.883 61.111 9.28 0.00 33.95 3.36
128 129 1.008767 CTCCGGCGTCGTATCCTTC 60.009 63.158 9.28 0.00 33.95 3.46
129 130 2.027169 CCGGCGTCGTATCCTTCC 59.973 66.667 9.28 0.00 33.95 3.46
130 131 2.487532 CCGGCGTCGTATCCTTCCT 61.488 63.158 9.28 0.00 33.95 3.36
131 132 1.299165 CGGCGTCGTATCCTTCCTG 60.299 63.158 0.00 0.00 0.00 3.86
132 133 1.721664 CGGCGTCGTATCCTTCCTGA 61.722 60.000 0.00 0.00 0.00 3.86
133 134 0.458669 GGCGTCGTATCCTTCCTGAA 59.541 55.000 0.00 0.00 0.00 3.02
134 135 1.536284 GGCGTCGTATCCTTCCTGAAG 60.536 57.143 0.00 0.00 38.14 3.02
142 143 2.815647 CTTCCTGAAGGCGCCGTC 60.816 66.667 32.12 32.12 34.87 4.79
143 144 3.302347 CTTCCTGAAGGCGCCGTCT 62.302 63.158 36.30 19.98 34.87 4.18
144 145 2.788191 CTTCCTGAAGGCGCCGTCTT 62.788 60.000 36.30 20.68 34.87 3.01
145 146 3.121030 CCTGAAGGCGCCGTCTTG 61.121 66.667 36.30 28.20 0.00 3.02
146 147 3.121030 CTGAAGGCGCCGTCTTGG 61.121 66.667 36.30 24.03 42.50 3.61
147 148 3.589654 CTGAAGGCGCCGTCTTGGA 62.590 63.158 36.30 19.63 42.00 3.53
148 149 2.815647 GAAGGCGCCGTCTTGGAG 60.816 66.667 31.62 0.00 42.00 3.86
154 155 3.869272 GCCGTCTTGGAGCGCATG 61.869 66.667 11.47 0.00 42.00 4.06
155 156 3.197790 CCGTCTTGGAGCGCATGG 61.198 66.667 11.47 0.00 42.00 3.66
156 157 2.434884 CGTCTTGGAGCGCATGGT 60.435 61.111 11.47 0.00 0.00 3.55
157 158 2.034879 CGTCTTGGAGCGCATGGTT 61.035 57.895 11.47 0.00 0.00 3.67
158 159 1.796796 GTCTTGGAGCGCATGGTTC 59.203 57.895 11.47 0.00 0.00 3.62
159 160 1.741401 TCTTGGAGCGCATGGTTCG 60.741 57.895 11.47 0.00 0.00 3.95
160 161 2.031919 TTGGAGCGCATGGTTCGT 59.968 55.556 11.47 0.00 0.00 3.85
161 162 1.970917 CTTGGAGCGCATGGTTCGTC 61.971 60.000 11.47 0.00 0.00 4.20
162 163 2.434185 GGAGCGCATGGTTCGTCA 60.434 61.111 11.47 0.00 0.00 4.35
163 164 1.815421 GGAGCGCATGGTTCGTCAT 60.815 57.895 11.47 0.00 0.00 3.06
164 165 0.529773 GGAGCGCATGGTTCGTCATA 60.530 55.000 11.47 0.00 0.00 2.15
165 166 1.502231 GAGCGCATGGTTCGTCATAT 58.498 50.000 11.47 0.00 0.00 1.78
166 167 1.193203 GAGCGCATGGTTCGTCATATG 59.807 52.381 11.47 0.00 0.00 1.78
167 168 0.937304 GCGCATGGTTCGTCATATGT 59.063 50.000 0.30 0.00 0.00 2.29
168 169 2.131972 GCGCATGGTTCGTCATATGTA 58.868 47.619 0.30 0.00 0.00 2.29
169 170 2.155732 GCGCATGGTTCGTCATATGTAG 59.844 50.000 0.30 0.00 0.00 2.74
170 171 2.155732 CGCATGGTTCGTCATATGTAGC 59.844 50.000 1.90 0.00 0.00 3.58
171 172 3.393800 GCATGGTTCGTCATATGTAGCT 58.606 45.455 1.90 0.00 0.00 3.32
172 173 3.809832 GCATGGTTCGTCATATGTAGCTT 59.190 43.478 1.90 0.00 0.00 3.74
173 174 4.084328 GCATGGTTCGTCATATGTAGCTTC 60.084 45.833 1.90 0.00 0.00 3.86
174 175 4.729227 TGGTTCGTCATATGTAGCTTCA 57.271 40.909 1.90 0.00 0.00 3.02
175 176 5.276461 TGGTTCGTCATATGTAGCTTCAT 57.724 39.130 10.88 10.88 0.00 2.57
176 177 5.670485 TGGTTCGTCATATGTAGCTTCATT 58.330 37.500 11.36 0.00 0.00 2.57
177 178 6.112734 TGGTTCGTCATATGTAGCTTCATTT 58.887 36.000 11.36 0.63 0.00 2.32
178 179 6.257849 TGGTTCGTCATATGTAGCTTCATTTC 59.742 38.462 11.36 0.16 0.00 2.17
179 180 6.480320 GGTTCGTCATATGTAGCTTCATTTCT 59.520 38.462 11.36 0.00 0.00 2.52
180 181 7.011482 GGTTCGTCATATGTAGCTTCATTTCTT 59.989 37.037 11.36 0.00 0.00 2.52
181 182 7.700322 TCGTCATATGTAGCTTCATTTCTTC 57.300 36.000 11.36 0.00 0.00 2.87
182 183 6.417930 TCGTCATATGTAGCTTCATTTCTTCG 59.582 38.462 11.36 10.12 0.00 3.79
183 184 6.346120 CGTCATATGTAGCTTCATTTCTTCGG 60.346 42.308 11.36 0.00 0.00 4.30
184 185 5.991606 TCATATGTAGCTTCATTTCTTCGGG 59.008 40.000 11.36 0.00 0.00 5.14
185 186 2.985896 TGTAGCTTCATTTCTTCGGGG 58.014 47.619 0.00 0.00 0.00 5.73
186 187 1.671328 GTAGCTTCATTTCTTCGGGGC 59.329 52.381 0.00 0.00 0.00 5.80
187 188 1.026718 AGCTTCATTTCTTCGGGGCG 61.027 55.000 0.00 0.00 0.00 6.13
188 189 1.993369 GCTTCATTTCTTCGGGGCGG 61.993 60.000 0.00 0.00 0.00 6.13
189 190 0.676782 CTTCATTTCTTCGGGGCGGT 60.677 55.000 0.00 0.00 0.00 5.68
190 191 0.614294 TTCATTTCTTCGGGGCGGTA 59.386 50.000 0.00 0.00 0.00 4.02
191 192 0.177141 TCATTTCTTCGGGGCGGTAG 59.823 55.000 0.00 0.00 0.00 3.18
192 193 0.107848 CATTTCTTCGGGGCGGTAGT 60.108 55.000 0.00 0.00 0.00 2.73
193 194 0.107848 ATTTCTTCGGGGCGGTAGTG 60.108 55.000 0.00 0.00 0.00 2.74
194 195 2.791501 TTTCTTCGGGGCGGTAGTGC 62.792 60.000 0.00 0.00 0.00 4.40
195 196 3.771160 CTTCGGGGCGGTAGTGCT 61.771 66.667 0.00 0.00 34.52 4.40
196 197 2.362760 TTCGGGGCGGTAGTGCTA 60.363 61.111 0.00 0.00 34.52 3.49
197 198 2.351336 CTTCGGGGCGGTAGTGCTAG 62.351 65.000 0.00 0.00 34.52 3.42
198 199 3.912907 CGGGGCGGTAGTGCTAGG 61.913 72.222 0.00 0.00 34.52 3.02
199 200 2.443390 GGGGCGGTAGTGCTAGGA 60.443 66.667 0.00 0.00 34.52 2.94
200 201 2.499827 GGGGCGGTAGTGCTAGGAG 61.500 68.421 0.00 0.00 34.52 3.69
201 202 1.757340 GGGCGGTAGTGCTAGGAGT 60.757 63.158 0.00 0.00 34.52 3.85
202 203 1.437986 GGCGGTAGTGCTAGGAGTG 59.562 63.158 1.14 0.00 34.52 3.51
203 204 1.437986 GCGGTAGTGCTAGGAGTGG 59.562 63.158 1.14 0.00 0.00 4.00
204 205 1.321074 GCGGTAGTGCTAGGAGTGGT 61.321 60.000 1.14 0.00 0.00 4.16
205 206 0.456221 CGGTAGTGCTAGGAGTGGTG 59.544 60.000 1.14 0.00 0.00 4.17
206 207 0.824759 GGTAGTGCTAGGAGTGGTGG 59.175 60.000 1.14 0.00 0.00 4.61
207 208 1.558233 GTAGTGCTAGGAGTGGTGGT 58.442 55.000 1.14 0.00 0.00 4.16
208 209 1.204941 GTAGTGCTAGGAGTGGTGGTG 59.795 57.143 1.14 0.00 0.00 4.17
209 210 0.471971 AGTGCTAGGAGTGGTGGTGT 60.472 55.000 0.00 0.00 0.00 4.16
210 211 0.396811 GTGCTAGGAGTGGTGGTGTT 59.603 55.000 0.00 0.00 0.00 3.32
211 212 0.396435 TGCTAGGAGTGGTGGTGTTG 59.604 55.000 0.00 0.00 0.00 3.33
212 213 0.955919 GCTAGGAGTGGTGGTGTTGC 60.956 60.000 0.00 0.00 0.00 4.17
213 214 0.670546 CTAGGAGTGGTGGTGTTGCG 60.671 60.000 0.00 0.00 0.00 4.85
214 215 2.725203 TAGGAGTGGTGGTGTTGCGC 62.725 60.000 0.00 0.00 0.00 6.09
215 216 2.591715 GAGTGGTGGTGTTGCGCT 60.592 61.111 9.73 0.00 0.00 5.92
216 217 2.591715 AGTGGTGGTGTTGCGCTC 60.592 61.111 9.73 2.14 0.00 5.03
217 218 2.899838 GTGGTGGTGTTGCGCTCA 60.900 61.111 9.73 5.24 0.00 4.26
218 219 2.591429 TGGTGGTGTTGCGCTCAG 60.591 61.111 9.73 0.00 0.00 3.35
231 232 3.129792 GCTCAGCGCCTATGTATCC 57.870 57.895 2.29 0.00 0.00 2.59
232 233 0.605589 GCTCAGCGCCTATGTATCCT 59.394 55.000 2.29 0.00 0.00 3.24
233 234 1.671261 GCTCAGCGCCTATGTATCCTG 60.671 57.143 2.29 0.00 0.00 3.86
234 235 1.615883 CTCAGCGCCTATGTATCCTGT 59.384 52.381 2.29 0.00 0.00 4.00
235 236 1.613925 TCAGCGCCTATGTATCCTGTC 59.386 52.381 2.29 0.00 0.00 3.51
236 237 1.615883 CAGCGCCTATGTATCCTGTCT 59.384 52.381 2.29 0.00 0.00 3.41
237 238 2.036475 CAGCGCCTATGTATCCTGTCTT 59.964 50.000 2.29 0.00 0.00 3.01
238 239 2.036475 AGCGCCTATGTATCCTGTCTTG 59.964 50.000 2.29 0.00 0.00 3.02
239 240 2.868044 GCGCCTATGTATCCTGTCTTGG 60.868 54.545 0.00 0.00 0.00 3.61
240 241 2.289072 CGCCTATGTATCCTGTCTTGGG 60.289 54.545 0.00 0.00 0.00 4.12
241 242 2.706190 GCCTATGTATCCTGTCTTGGGT 59.294 50.000 0.00 0.00 0.00 4.51
242 243 3.495100 GCCTATGTATCCTGTCTTGGGTG 60.495 52.174 0.00 0.00 0.00 4.61
243 244 3.711704 CCTATGTATCCTGTCTTGGGTGT 59.288 47.826 0.00 0.00 0.00 4.16
244 245 3.634397 ATGTATCCTGTCTTGGGTGTG 57.366 47.619 0.00 0.00 0.00 3.82
245 246 2.334977 TGTATCCTGTCTTGGGTGTGT 58.665 47.619 0.00 0.00 0.00 3.72
246 247 2.038426 TGTATCCTGTCTTGGGTGTGTG 59.962 50.000 0.00 0.00 0.00 3.82
247 248 0.250901 ATCCTGTCTTGGGTGTGTGC 60.251 55.000 0.00 0.00 0.00 4.57
248 249 2.253758 CCTGTCTTGGGTGTGTGCG 61.254 63.158 0.00 0.00 0.00 5.34
249 250 1.523711 CTGTCTTGGGTGTGTGCGT 60.524 57.895 0.00 0.00 0.00 5.24
250 251 1.775039 CTGTCTTGGGTGTGTGCGTG 61.775 60.000 0.00 0.00 0.00 5.34
251 252 1.817941 GTCTTGGGTGTGTGCGTGT 60.818 57.895 0.00 0.00 0.00 4.49
252 253 1.817520 TCTTGGGTGTGTGCGTGTG 60.818 57.895 0.00 0.00 0.00 3.82
253 254 2.045829 TTGGGTGTGTGCGTGTGT 60.046 55.556 0.00 0.00 0.00 3.72
254 255 1.653094 CTTGGGTGTGTGCGTGTGTT 61.653 55.000 0.00 0.00 0.00 3.32
255 256 1.927608 TTGGGTGTGTGCGTGTGTTG 61.928 55.000 0.00 0.00 0.00 3.33
256 257 2.277884 GGTGTGTGCGTGTGTTGC 60.278 61.111 0.00 0.00 0.00 4.17
257 258 2.647481 GTGTGTGCGTGTGTTGCG 60.647 61.111 0.00 0.00 34.24 4.85
258 259 3.870422 TGTGTGCGTGTGTTGCGG 61.870 61.111 0.00 0.00 34.24 5.69
259 260 3.871574 GTGTGCGTGTGTTGCGGT 61.872 61.111 0.00 0.00 34.24 5.68
260 261 3.870422 TGTGCGTGTGTTGCGGTG 61.870 61.111 0.00 0.00 34.24 4.94
261 262 4.605967 GTGCGTGTGTTGCGGTGG 62.606 66.667 0.00 0.00 34.24 4.61
265 266 4.605967 GTGTGTTGCGGTGGCGTG 62.606 66.667 0.00 0.00 44.10 5.34
275 276 3.294493 GTGGCGTGGCATGTGGTT 61.294 61.111 8.75 0.00 0.00 3.67
276 277 3.293714 TGGCGTGGCATGTGGTTG 61.294 61.111 8.75 0.00 0.00 3.77
277 278 3.294493 GGCGTGGCATGTGGTTGT 61.294 61.111 8.75 0.00 0.00 3.32
278 279 1.969064 GGCGTGGCATGTGGTTGTA 60.969 57.895 8.75 0.00 0.00 2.41
279 280 1.209127 GCGTGGCATGTGGTTGTAC 59.791 57.895 8.75 0.00 0.00 2.90
280 281 1.234615 GCGTGGCATGTGGTTGTACT 61.235 55.000 8.75 0.00 0.00 2.73
281 282 0.516877 CGTGGCATGTGGTTGTACTG 59.483 55.000 0.00 0.00 0.00 2.74
282 283 0.881118 GTGGCATGTGGTTGTACTGG 59.119 55.000 0.00 0.00 0.00 4.00
283 284 0.767998 TGGCATGTGGTTGTACTGGA 59.232 50.000 0.00 0.00 0.00 3.86
284 285 1.354031 TGGCATGTGGTTGTACTGGAT 59.646 47.619 0.00 0.00 0.00 3.41
285 286 1.745087 GGCATGTGGTTGTACTGGATG 59.255 52.381 0.00 0.00 0.00 3.51
286 287 1.133025 GCATGTGGTTGTACTGGATGC 59.867 52.381 0.00 0.00 0.00 3.91
287 288 2.715046 CATGTGGTTGTACTGGATGCT 58.285 47.619 0.00 0.00 0.00 3.79
288 289 2.949177 TGTGGTTGTACTGGATGCTT 57.051 45.000 0.00 0.00 0.00 3.91
289 290 2.503331 TGTGGTTGTACTGGATGCTTG 58.497 47.619 0.00 0.00 0.00 4.01
290 291 2.158682 TGTGGTTGTACTGGATGCTTGT 60.159 45.455 0.00 0.00 0.00 3.16
291 292 2.226437 GTGGTTGTACTGGATGCTTGTG 59.774 50.000 0.00 0.00 0.00 3.33
292 293 1.812571 GGTTGTACTGGATGCTTGTGG 59.187 52.381 0.00 0.00 0.00 4.17
293 294 2.504367 GTTGTACTGGATGCTTGTGGT 58.496 47.619 0.00 0.00 0.00 4.16
294 295 2.884639 GTTGTACTGGATGCTTGTGGTT 59.115 45.455 0.00 0.00 0.00 3.67
295 296 3.222173 TGTACTGGATGCTTGTGGTTT 57.778 42.857 0.00 0.00 0.00 3.27
296 297 2.884012 TGTACTGGATGCTTGTGGTTTG 59.116 45.455 0.00 0.00 0.00 2.93
297 298 1.331214 ACTGGATGCTTGTGGTTTGG 58.669 50.000 0.00 0.00 0.00 3.28
298 299 1.331214 CTGGATGCTTGTGGTTTGGT 58.669 50.000 0.00 0.00 0.00 3.67
299 300 1.000060 CTGGATGCTTGTGGTTTGGTG 60.000 52.381 0.00 0.00 0.00 4.17
300 301 0.319813 GGATGCTTGTGGTTTGGTGC 60.320 55.000 0.00 0.00 0.00 5.01
301 302 0.675633 GATGCTTGTGGTTTGGTGCT 59.324 50.000 0.00 0.00 0.00 4.40
302 303 1.069049 GATGCTTGTGGTTTGGTGCTT 59.931 47.619 0.00 0.00 0.00 3.91
303 304 0.901124 TGCTTGTGGTTTGGTGCTTT 59.099 45.000 0.00 0.00 0.00 3.51
304 305 2.103373 TGCTTGTGGTTTGGTGCTTTA 58.897 42.857 0.00 0.00 0.00 1.85
305 306 2.697751 TGCTTGTGGTTTGGTGCTTTAT 59.302 40.909 0.00 0.00 0.00 1.40
306 307 3.891977 TGCTTGTGGTTTGGTGCTTTATA 59.108 39.130 0.00 0.00 0.00 0.98
307 308 4.526262 TGCTTGTGGTTTGGTGCTTTATAT 59.474 37.500 0.00 0.00 0.00 0.86
308 309 5.712446 TGCTTGTGGTTTGGTGCTTTATATA 59.288 36.000 0.00 0.00 0.00 0.86
309 310 6.379703 TGCTTGTGGTTTGGTGCTTTATATAT 59.620 34.615 0.00 0.00 0.00 0.86
310 311 7.558081 TGCTTGTGGTTTGGTGCTTTATATATA 59.442 33.333 0.00 0.00 0.00 0.86
311 312 8.410141 GCTTGTGGTTTGGTGCTTTATATATAA 58.590 33.333 0.81 0.81 0.00 0.98
323 324 6.730960 CTTTATATATAAAGCGGGGCGAAA 57.269 37.500 25.10 1.66 41.69 3.46
324 325 6.730960 TTTATATATAAAGCGGGGCGAAAG 57.269 37.500 12.90 0.00 0.00 2.62
347 348 6.089920 GCCTTTTTCGGTAAAAATGCATAC 57.910 37.500 0.00 0.00 46.65 2.39
397 398 1.456705 GGGCTGGTTCCACCACAAA 60.457 57.895 10.75 0.00 44.79 2.83
398 399 1.045911 GGGCTGGTTCCACCACAAAA 61.046 55.000 10.75 0.00 44.79 2.44
465 466 8.704234 GTTGTTGTTTAATCAATAAAATGCCGA 58.296 29.630 9.26 0.00 35.33 5.54
472 473 9.868277 TTTAATCAATAAAATGCCGACATTCTT 57.132 25.926 0.00 0.00 45.90 2.52
862 878 8.824756 ATTAAATACCACACTCTCACTCTCTA 57.175 34.615 0.00 0.00 0.00 2.43
930 946 5.187186 ACACAAAGCCTAACTAGCTAGCTTA 59.813 40.000 24.88 15.63 40.49 3.09
954 970 3.133183 GCTTCTGCTTACTAGGGTTAGCT 59.867 47.826 8.26 0.00 45.11 3.32
955 971 4.341520 GCTTCTGCTTACTAGGGTTAGCTA 59.658 45.833 8.26 0.00 45.11 3.32
956 972 5.163437 GCTTCTGCTTACTAGGGTTAGCTAA 60.163 44.000 0.86 0.86 45.11 3.09
957 973 6.463190 GCTTCTGCTTACTAGGGTTAGCTAAT 60.463 42.308 9.88 0.00 45.11 1.73
1050 1066 3.090532 GGGAAGGATGGCGGAGGT 61.091 66.667 0.00 0.00 0.00 3.85
1867 1892 4.167554 TGCCAACGAAATTACAACATCC 57.832 40.909 0.00 0.00 0.00 3.51
1869 1894 3.120130 GCCAACGAAATTACAACATCCGA 60.120 43.478 0.00 0.00 0.00 4.55
1903 1928 3.000041 TGATTGGTTCGTATGCACACTC 59.000 45.455 0.00 0.00 0.00 3.51
1979 2004 5.278907 CCAAGGTACAAATGCTCAAATGTGA 60.279 40.000 0.00 0.00 0.00 3.58
1980 2005 5.376854 AGGTACAAATGCTCAAATGTGAC 57.623 39.130 0.00 0.00 0.00 3.67
1981 2006 4.826733 AGGTACAAATGCTCAAATGTGACA 59.173 37.500 0.00 0.00 0.00 3.58
1982 2007 4.917415 GGTACAAATGCTCAAATGTGACAC 59.083 41.667 0.00 0.00 0.00 3.67
1984 2009 5.204409 ACAAATGCTCAAATGTGACACAT 57.796 34.783 15.48 15.48 41.31 3.21
2038 2063 7.044183 GCCAGCAAAAATTGTTTTACAAATGTG 60.044 33.333 0.00 0.00 41.96 3.21
2047 2072 8.931385 ATTGTTTTACAAATGTGCATATCCTC 57.069 30.769 0.00 0.00 41.96 3.71
2066 2091 2.018515 TCACGTACCGATGCATGAGTA 58.981 47.619 2.46 2.19 0.00 2.59
2114 2139 4.093408 CGTGCTAGAAAGAATTTAGCTGCA 59.907 41.667 1.02 0.00 39.70 4.41
2157 2184 4.943705 TCCTCATATGGAAAGTTGTTGCTC 59.056 41.667 2.13 0.00 32.39 4.26
2281 2308 8.213518 TGGAATAGAATTCAAGTATGTTCTGC 57.786 34.615 8.44 0.00 33.36 4.26
2286 2313 7.516198 AGAATTCAAGTATGTTCTGCAAGTT 57.484 32.000 8.44 0.00 33.76 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.278336 TAACGATCTTCGCCGCCG 60.278 61.111 0.00 0.00 45.12 6.46
7 8 0.804933 AAGTAACGATCTTCGCCGCC 60.805 55.000 0.00 0.00 45.12 6.13
8 9 0.997196 AAAGTAACGATCTTCGCCGC 59.003 50.000 0.00 0.00 45.12 6.53
9 10 2.527100 AGAAAGTAACGATCTTCGCCG 58.473 47.619 0.00 0.00 45.12 6.46
10 11 3.924686 TCAAGAAAGTAACGATCTTCGCC 59.075 43.478 0.00 0.00 45.12 5.54
11 12 5.444745 CCTTCAAGAAAGTAACGATCTTCGC 60.445 44.000 0.00 0.00 36.98 4.70
12 13 5.444745 GCCTTCAAGAAAGTAACGATCTTCG 60.445 44.000 0.00 0.00 38.42 3.79
13 14 5.444745 CGCCTTCAAGAAAGTAACGATCTTC 60.445 44.000 0.00 0.00 31.26 2.87
14 15 4.389077 CGCCTTCAAGAAAGTAACGATCTT 59.611 41.667 0.00 0.00 33.83 2.40
15 16 3.927142 CGCCTTCAAGAAAGTAACGATCT 59.073 43.478 0.00 0.00 32.69 2.75
16 17 3.678548 ACGCCTTCAAGAAAGTAACGATC 59.321 43.478 0.00 0.00 32.69 3.69
17 18 3.660865 ACGCCTTCAAGAAAGTAACGAT 58.339 40.909 0.00 0.00 32.69 3.73
18 19 3.054878 GACGCCTTCAAGAAAGTAACGA 58.945 45.455 0.00 0.00 32.69 3.85
19 20 2.160013 CGACGCCTTCAAGAAAGTAACG 60.160 50.000 0.00 0.00 32.69 3.18
20 21 2.798847 ACGACGCCTTCAAGAAAGTAAC 59.201 45.455 0.00 0.00 32.69 2.50
21 22 3.054878 GACGACGCCTTCAAGAAAGTAA 58.945 45.455 0.00 0.00 32.69 2.24
22 23 2.669364 GACGACGCCTTCAAGAAAGTA 58.331 47.619 0.00 0.00 32.69 2.24
23 24 1.499049 GACGACGCCTTCAAGAAAGT 58.501 50.000 0.00 0.00 32.69 2.66
24 25 0.435008 CGACGACGCCTTCAAGAAAG 59.565 55.000 0.00 0.00 34.52 2.62
25 26 0.031043 TCGACGACGCCTTCAAGAAA 59.969 50.000 1.48 0.00 39.58 2.52
26 27 0.386858 CTCGACGACGCCTTCAAGAA 60.387 55.000 1.48 0.00 39.58 2.52
27 28 1.209383 CTCGACGACGCCTTCAAGA 59.791 57.895 1.48 0.00 39.58 3.02
28 29 1.801913 CCTCGACGACGCCTTCAAG 60.802 63.158 1.48 0.00 39.58 3.02
29 30 2.257371 CCTCGACGACGCCTTCAA 59.743 61.111 1.48 0.00 39.58 2.69
30 31 4.415332 GCCTCGACGACGCCTTCA 62.415 66.667 7.50 0.00 39.58 3.02
31 32 4.117661 AGCCTCGACGACGCCTTC 62.118 66.667 14.05 0.00 39.58 3.46
32 33 4.117661 GAGCCTCGACGACGCCTT 62.118 66.667 14.05 0.00 39.58 4.35
34 35 4.539881 GAGAGCCTCGACGACGCC 62.540 72.222 14.05 7.08 39.58 5.68
35 36 2.600122 AATGAGAGCCTCGACGACGC 62.600 60.000 10.37 10.37 39.58 5.19
36 37 0.863538 CAATGAGAGCCTCGACGACG 60.864 60.000 0.00 0.00 41.26 5.12
37 38 1.142778 GCAATGAGAGCCTCGACGAC 61.143 60.000 0.00 0.00 32.35 4.34
38 39 1.139734 GCAATGAGAGCCTCGACGA 59.860 57.895 0.00 0.00 32.35 4.20
39 40 3.698382 GCAATGAGAGCCTCGACG 58.302 61.111 0.00 0.00 32.35 5.12
46 47 2.020131 CATGACGGGCAATGAGAGC 58.980 57.895 0.00 0.00 0.00 4.09
47 48 1.769098 CGCATGACGGGCAATGAGAG 61.769 60.000 0.00 0.00 38.44 3.20
48 49 1.815003 CGCATGACGGGCAATGAGA 60.815 57.895 0.00 0.00 38.44 3.27
49 50 2.711311 CGCATGACGGGCAATGAG 59.289 61.111 0.00 0.00 38.44 2.90
59 60 4.899239 CCTCCGGAGCCGCATGAC 62.899 72.222 26.87 0.00 38.24 3.06
65 66 3.839432 GAGTTCCCTCCGGAGCCG 61.839 72.222 26.87 17.50 40.16 5.52
66 67 2.364448 AGAGTTCCCTCCGGAGCC 60.364 66.667 26.87 12.70 40.16 4.70
67 68 1.045911 ATCAGAGTTCCCTCCGGAGC 61.046 60.000 26.87 12.38 40.10 4.70
68 69 1.036707 GATCAGAGTTCCCTCCGGAG 58.963 60.000 25.36 25.36 40.10 4.63
69 70 0.397254 GGATCAGAGTTCCCTCCGGA 60.397 60.000 2.93 2.93 38.58 5.14
70 71 0.397816 AGGATCAGAGTTCCCTCCGG 60.398 60.000 0.00 0.00 38.58 5.14
71 72 1.137872 CAAGGATCAGAGTTCCCTCCG 59.862 57.143 0.00 0.00 38.58 4.63
72 73 1.488393 CCAAGGATCAGAGTTCCCTCC 59.512 57.143 0.00 0.00 38.58 4.30
73 74 2.472029 TCCAAGGATCAGAGTTCCCTC 58.528 52.381 0.00 0.00 38.04 4.30
74 75 2.649742 TCCAAGGATCAGAGTTCCCT 57.350 50.000 0.00 0.00 33.45 4.20
84 85 2.031163 CCGCCCGATCCAAGGATC 59.969 66.667 17.30 17.30 45.42 3.36
85 86 2.768344 ACCGCCCGATCCAAGGAT 60.768 61.111 0.16 0.16 37.59 3.24
86 87 3.781307 CACCGCCCGATCCAAGGA 61.781 66.667 0.00 0.00 0.00 3.36
87 88 4.856801 CCACCGCCCGATCCAAGG 62.857 72.222 0.00 0.00 0.00 3.61
109 110 3.135056 AAGGATACGACGCCGGAGC 62.135 63.158 5.05 0.00 46.39 4.70
110 111 1.008767 GAAGGATACGACGCCGGAG 60.009 63.158 5.05 3.72 46.39 4.63
111 112 2.484062 GGAAGGATACGACGCCGGA 61.484 63.158 5.05 0.00 46.39 5.14
112 113 2.027169 GGAAGGATACGACGCCGG 59.973 66.667 0.00 0.00 46.39 6.13
113 114 1.299165 CAGGAAGGATACGACGCCG 60.299 63.158 0.00 0.00 46.39 6.46
114 115 0.458669 TTCAGGAAGGATACGACGCC 59.541 55.000 0.00 0.00 46.39 5.68
115 116 1.841450 CTTCAGGAAGGATACGACGC 58.159 55.000 0.00 0.00 46.39 5.19
125 126 2.788191 AAGACGGCGCCTTCAGGAAG 62.788 60.000 31.78 13.60 37.39 3.46
126 127 2.879233 AAGACGGCGCCTTCAGGAA 61.879 57.895 31.78 0.00 37.39 3.36
127 128 3.311110 AAGACGGCGCCTTCAGGA 61.311 61.111 31.78 0.00 37.39 3.86
128 129 3.121030 CAAGACGGCGCCTTCAGG 61.121 66.667 31.78 20.13 38.53 3.86
129 130 3.121030 CCAAGACGGCGCCTTCAG 61.121 66.667 31.78 23.13 0.00 3.02
130 131 3.589654 CTCCAAGACGGCGCCTTCA 62.590 63.158 31.78 12.59 33.14 3.02
131 132 2.815647 CTCCAAGACGGCGCCTTC 60.816 66.667 24.53 24.53 33.14 3.46
137 138 3.869272 CATGCGCTCCAAGACGGC 61.869 66.667 9.73 0.00 33.14 5.68
138 139 3.197790 CCATGCGCTCCAAGACGG 61.198 66.667 9.73 0.00 0.00 4.79
139 140 1.970917 GAACCATGCGCTCCAAGACG 61.971 60.000 9.73 0.00 0.00 4.18
140 141 1.796796 GAACCATGCGCTCCAAGAC 59.203 57.895 9.73 0.00 0.00 3.01
141 142 1.741401 CGAACCATGCGCTCCAAGA 60.741 57.895 9.73 0.00 0.00 3.02
142 143 1.970917 GACGAACCATGCGCTCCAAG 61.971 60.000 9.73 0.00 0.00 3.61
143 144 2.031919 ACGAACCATGCGCTCCAA 59.968 55.556 9.73 0.00 0.00 3.53
144 145 2.434185 GACGAACCATGCGCTCCA 60.434 61.111 9.73 0.00 0.00 3.86
145 146 0.529773 TATGACGAACCATGCGCTCC 60.530 55.000 9.73 0.00 0.00 4.70
146 147 1.193203 CATATGACGAACCATGCGCTC 59.807 52.381 9.73 0.00 0.00 5.03
147 148 1.220529 CATATGACGAACCATGCGCT 58.779 50.000 9.73 0.00 0.00 5.92
148 149 0.937304 ACATATGACGAACCATGCGC 59.063 50.000 10.38 0.00 0.00 6.09
149 150 2.155732 GCTACATATGACGAACCATGCG 59.844 50.000 10.38 0.00 0.00 4.73
150 151 3.393800 AGCTACATATGACGAACCATGC 58.606 45.455 10.38 0.53 0.00 4.06
151 152 5.049828 TGAAGCTACATATGACGAACCATG 58.950 41.667 10.38 0.00 0.00 3.66
152 153 5.276461 TGAAGCTACATATGACGAACCAT 57.724 39.130 10.38 0.00 0.00 3.55
153 154 4.729227 TGAAGCTACATATGACGAACCA 57.271 40.909 10.38 0.00 0.00 3.67
154 155 6.480320 AGAAATGAAGCTACATATGACGAACC 59.520 38.462 10.38 0.00 0.00 3.62
155 156 7.470289 AGAAATGAAGCTACATATGACGAAC 57.530 36.000 10.38 0.00 0.00 3.95
156 157 7.043391 CGAAGAAATGAAGCTACATATGACGAA 60.043 37.037 10.38 0.00 0.00 3.85
157 158 6.417930 CGAAGAAATGAAGCTACATATGACGA 59.582 38.462 10.38 0.00 0.00 4.20
158 159 6.346120 CCGAAGAAATGAAGCTACATATGACG 60.346 42.308 10.38 0.60 0.00 4.35
159 160 6.073548 CCCGAAGAAATGAAGCTACATATGAC 60.074 42.308 10.38 0.00 0.00 3.06
160 161 5.991606 CCCGAAGAAATGAAGCTACATATGA 59.008 40.000 10.38 0.00 0.00 2.15
161 162 5.180117 CCCCGAAGAAATGAAGCTACATATG 59.820 44.000 0.00 0.00 0.00 1.78
162 163 5.308825 CCCCGAAGAAATGAAGCTACATAT 58.691 41.667 0.00 0.00 0.00 1.78
163 164 4.703897 CCCCGAAGAAATGAAGCTACATA 58.296 43.478 0.00 0.00 0.00 2.29
164 165 3.545703 CCCCGAAGAAATGAAGCTACAT 58.454 45.455 0.00 0.00 0.00 2.29
165 166 2.939640 GCCCCGAAGAAATGAAGCTACA 60.940 50.000 0.00 0.00 0.00 2.74
166 167 1.671328 GCCCCGAAGAAATGAAGCTAC 59.329 52.381 0.00 0.00 0.00 3.58
167 168 1.742411 CGCCCCGAAGAAATGAAGCTA 60.742 52.381 0.00 0.00 0.00 3.32
168 169 1.026718 CGCCCCGAAGAAATGAAGCT 61.027 55.000 0.00 0.00 0.00 3.74
169 170 1.429423 CGCCCCGAAGAAATGAAGC 59.571 57.895 0.00 0.00 0.00 3.86
170 171 0.676782 ACCGCCCCGAAGAAATGAAG 60.677 55.000 0.00 0.00 0.00 3.02
171 172 0.614294 TACCGCCCCGAAGAAATGAA 59.386 50.000 0.00 0.00 0.00 2.57
172 173 0.177141 CTACCGCCCCGAAGAAATGA 59.823 55.000 0.00 0.00 0.00 2.57
173 174 0.107848 ACTACCGCCCCGAAGAAATG 60.108 55.000 0.00 0.00 0.00 2.32
174 175 0.107848 CACTACCGCCCCGAAGAAAT 60.108 55.000 0.00 0.00 0.00 2.17
175 176 1.294138 CACTACCGCCCCGAAGAAA 59.706 57.895 0.00 0.00 0.00 2.52
176 177 2.975536 CACTACCGCCCCGAAGAA 59.024 61.111 0.00 0.00 0.00 2.52
177 178 2.842188 TAGCACTACCGCCCCGAAGA 62.842 60.000 0.00 0.00 0.00 2.87
178 179 2.351336 CTAGCACTACCGCCCCGAAG 62.351 65.000 0.00 0.00 0.00 3.79
179 180 2.362760 TAGCACTACCGCCCCGAA 60.363 61.111 0.00 0.00 0.00 4.30
180 181 2.831742 CTAGCACTACCGCCCCGA 60.832 66.667 0.00 0.00 0.00 5.14
181 182 3.912907 CCTAGCACTACCGCCCCG 61.913 72.222 0.00 0.00 0.00 5.73
182 183 2.443390 TCCTAGCACTACCGCCCC 60.443 66.667 0.00 0.00 0.00 5.80
183 184 1.757340 ACTCCTAGCACTACCGCCC 60.757 63.158 0.00 0.00 0.00 6.13
184 185 1.437986 CACTCCTAGCACTACCGCC 59.562 63.158 0.00 0.00 0.00 6.13
185 186 1.321074 ACCACTCCTAGCACTACCGC 61.321 60.000 0.00 0.00 0.00 5.68
186 187 0.456221 CACCACTCCTAGCACTACCG 59.544 60.000 0.00 0.00 0.00 4.02
187 188 0.824759 CCACCACTCCTAGCACTACC 59.175 60.000 0.00 0.00 0.00 3.18
188 189 1.204941 CACCACCACTCCTAGCACTAC 59.795 57.143 0.00 0.00 0.00 2.73
189 190 1.203137 ACACCACCACTCCTAGCACTA 60.203 52.381 0.00 0.00 0.00 2.74
190 191 0.471971 ACACCACCACTCCTAGCACT 60.472 55.000 0.00 0.00 0.00 4.40
191 192 0.396811 AACACCACCACTCCTAGCAC 59.603 55.000 0.00 0.00 0.00 4.40
192 193 0.396435 CAACACCACCACTCCTAGCA 59.604 55.000 0.00 0.00 0.00 3.49
193 194 0.955919 GCAACACCACCACTCCTAGC 60.956 60.000 0.00 0.00 0.00 3.42
194 195 0.670546 CGCAACACCACCACTCCTAG 60.671 60.000 0.00 0.00 0.00 3.02
195 196 1.369692 CGCAACACCACCACTCCTA 59.630 57.895 0.00 0.00 0.00 2.94
196 197 2.111043 CGCAACACCACCACTCCT 59.889 61.111 0.00 0.00 0.00 3.69
197 198 3.660111 GCGCAACACCACCACTCC 61.660 66.667 0.30 0.00 0.00 3.85
198 199 2.591715 AGCGCAACACCACCACTC 60.592 61.111 11.47 0.00 0.00 3.51
199 200 2.591715 GAGCGCAACACCACCACT 60.592 61.111 11.47 0.00 0.00 4.00
200 201 2.896801 CTGAGCGCAACACCACCAC 61.897 63.158 11.47 0.00 0.00 4.16
201 202 2.591429 CTGAGCGCAACACCACCA 60.591 61.111 11.47 0.00 0.00 4.17
202 203 4.030452 GCTGAGCGCAACACCACC 62.030 66.667 11.47 0.00 38.92 4.61
213 214 0.605589 AGGATACATAGGCGCTGAGC 59.394 55.000 7.64 0.00 43.13 4.26
214 215 1.615883 ACAGGATACATAGGCGCTGAG 59.384 52.381 7.64 0.00 41.41 3.35
215 216 1.613925 GACAGGATACATAGGCGCTGA 59.386 52.381 7.64 0.00 41.41 4.26
216 217 1.615883 AGACAGGATACATAGGCGCTG 59.384 52.381 7.64 0.00 41.41 5.18
217 218 2.002505 AGACAGGATACATAGGCGCT 57.997 50.000 7.64 0.00 41.41 5.92
218 219 2.408050 CAAGACAGGATACATAGGCGC 58.592 52.381 0.00 0.00 41.41 6.53
219 220 2.289072 CCCAAGACAGGATACATAGGCG 60.289 54.545 0.00 0.00 41.41 5.52
220 221 2.706190 ACCCAAGACAGGATACATAGGC 59.294 50.000 0.00 0.00 41.41 3.93
221 222 3.711704 ACACCCAAGACAGGATACATAGG 59.288 47.826 0.00 0.00 41.41 2.57
222 223 4.162320 ACACACCCAAGACAGGATACATAG 59.838 45.833 0.00 0.00 41.41 2.23
223 224 4.081142 CACACACCCAAGACAGGATACATA 60.081 45.833 0.00 0.00 41.41 2.29
224 225 2.912956 ACACACCCAAGACAGGATACAT 59.087 45.455 0.00 0.00 41.41 2.29
225 226 2.038426 CACACACCCAAGACAGGATACA 59.962 50.000 0.00 0.00 41.41 2.29
226 227 2.699954 CACACACCCAAGACAGGATAC 58.300 52.381 0.00 0.00 0.00 2.24
227 228 1.003118 GCACACACCCAAGACAGGATA 59.997 52.381 0.00 0.00 0.00 2.59
228 229 0.250901 GCACACACCCAAGACAGGAT 60.251 55.000 0.00 0.00 0.00 3.24
229 230 1.148273 GCACACACCCAAGACAGGA 59.852 57.895 0.00 0.00 0.00 3.86
230 231 2.253758 CGCACACACCCAAGACAGG 61.254 63.158 0.00 0.00 0.00 4.00
231 232 1.523711 ACGCACACACCCAAGACAG 60.524 57.895 0.00 0.00 0.00 3.51
232 233 1.817520 CACGCACACACCCAAGACA 60.818 57.895 0.00 0.00 0.00 3.41
233 234 1.817941 ACACGCACACACCCAAGAC 60.818 57.895 0.00 0.00 0.00 3.01
234 235 1.817520 CACACGCACACACCCAAGA 60.818 57.895 0.00 0.00 0.00 3.02
235 236 1.653094 AACACACGCACACACCCAAG 61.653 55.000 0.00 0.00 0.00 3.61
236 237 1.675972 AACACACGCACACACCCAA 60.676 52.632 0.00 0.00 0.00 4.12
237 238 2.045829 AACACACGCACACACCCA 60.046 55.556 0.00 0.00 0.00 4.51
238 239 2.407210 CAACACACGCACACACCC 59.593 61.111 0.00 0.00 0.00 4.61
239 240 2.277884 GCAACACACGCACACACC 60.278 61.111 0.00 0.00 0.00 4.16
240 241 2.647481 CGCAACACACGCACACAC 60.647 61.111 0.00 0.00 0.00 3.82
241 242 3.870422 CCGCAACACACGCACACA 61.870 61.111 0.00 0.00 0.00 3.72
242 243 3.871574 ACCGCAACACACGCACAC 61.872 61.111 0.00 0.00 0.00 3.82
243 244 3.870422 CACCGCAACACACGCACA 61.870 61.111 0.00 0.00 0.00 4.57
244 245 4.605967 CCACCGCAACACACGCAC 62.606 66.667 0.00 0.00 0.00 5.34
248 249 4.605967 CACGCCACCGCAACACAC 62.606 66.667 0.00 0.00 38.22 3.82
258 259 3.294493 AACCACATGCCACGCCAC 61.294 61.111 0.00 0.00 0.00 5.01
259 260 2.682582 TACAACCACATGCCACGCCA 62.683 55.000 0.00 0.00 0.00 5.69
260 261 1.969064 TACAACCACATGCCACGCC 60.969 57.895 0.00 0.00 0.00 5.68
261 262 1.209127 GTACAACCACATGCCACGC 59.791 57.895 0.00 0.00 0.00 5.34
262 263 0.516877 CAGTACAACCACATGCCACG 59.483 55.000 0.00 0.00 0.00 4.94
263 264 0.881118 CCAGTACAACCACATGCCAC 59.119 55.000 0.00 0.00 0.00 5.01
264 265 0.767998 TCCAGTACAACCACATGCCA 59.232 50.000 0.00 0.00 0.00 4.92
265 266 1.745087 CATCCAGTACAACCACATGCC 59.255 52.381 0.00 0.00 0.00 4.40
266 267 1.133025 GCATCCAGTACAACCACATGC 59.867 52.381 0.00 0.00 0.00 4.06
267 268 2.715046 AGCATCCAGTACAACCACATG 58.285 47.619 0.00 0.00 0.00 3.21
268 269 3.084039 CAAGCATCCAGTACAACCACAT 58.916 45.455 0.00 0.00 0.00 3.21
269 270 2.158682 ACAAGCATCCAGTACAACCACA 60.159 45.455 0.00 0.00 0.00 4.17
270 271 2.226437 CACAAGCATCCAGTACAACCAC 59.774 50.000 0.00 0.00 0.00 4.16
271 272 2.503331 CACAAGCATCCAGTACAACCA 58.497 47.619 0.00 0.00 0.00 3.67
272 273 1.812571 CCACAAGCATCCAGTACAACC 59.187 52.381 0.00 0.00 0.00 3.77
273 274 2.504367 ACCACAAGCATCCAGTACAAC 58.496 47.619 0.00 0.00 0.00 3.32
274 275 2.949177 ACCACAAGCATCCAGTACAA 57.051 45.000 0.00 0.00 0.00 2.41
275 276 2.884012 CAAACCACAAGCATCCAGTACA 59.116 45.455 0.00 0.00 0.00 2.90
276 277 2.228822 CCAAACCACAAGCATCCAGTAC 59.771 50.000 0.00 0.00 0.00 2.73
277 278 2.158534 ACCAAACCACAAGCATCCAGTA 60.159 45.455 0.00 0.00 0.00 2.74
278 279 1.331214 CCAAACCACAAGCATCCAGT 58.669 50.000 0.00 0.00 0.00 4.00
279 280 1.000060 CACCAAACCACAAGCATCCAG 60.000 52.381 0.00 0.00 0.00 3.86
280 281 1.039068 CACCAAACCACAAGCATCCA 58.961 50.000 0.00 0.00 0.00 3.41
281 282 0.319813 GCACCAAACCACAAGCATCC 60.320 55.000 0.00 0.00 0.00 3.51
282 283 0.675633 AGCACCAAACCACAAGCATC 59.324 50.000 0.00 0.00 0.00 3.91
283 284 1.122227 AAGCACCAAACCACAAGCAT 58.878 45.000 0.00 0.00 0.00 3.79
284 285 0.901124 AAAGCACCAAACCACAAGCA 59.099 45.000 0.00 0.00 0.00 3.91
285 286 2.880963 TAAAGCACCAAACCACAAGC 57.119 45.000 0.00 0.00 0.00 4.01
301 302 5.122711 GCTTTCGCCCCGCTTTATATATAAA 59.877 40.000 15.47 15.47 0.00 1.40
302 303 4.632688 GCTTTCGCCCCGCTTTATATATAA 59.367 41.667 0.81 0.81 0.00 0.98
303 304 4.186159 GCTTTCGCCCCGCTTTATATATA 58.814 43.478 0.00 0.00 0.00 0.86
304 305 3.007635 GCTTTCGCCCCGCTTTATATAT 58.992 45.455 0.00 0.00 0.00 0.86
305 306 2.419667 GCTTTCGCCCCGCTTTATATA 58.580 47.619 0.00 0.00 0.00 0.86
306 307 1.235724 GCTTTCGCCCCGCTTTATAT 58.764 50.000 0.00 0.00 0.00 0.86
307 308 2.697819 GCTTTCGCCCCGCTTTATA 58.302 52.632 0.00 0.00 0.00 0.98
308 309 3.509659 GCTTTCGCCCCGCTTTAT 58.490 55.556 0.00 0.00 0.00 1.40
316 317 6.807607 TTTTACCGAAAAAGGCTTTCGCCC 62.808 45.833 13.76 2.28 46.89 6.13
317 318 3.796165 TTTTACCGAAAAAGGCTTTCGCC 60.796 43.478 13.76 0.00 46.89 5.54
318 319 2.691984 TTACCGAAAAAGGCTTTCGC 57.308 45.000 13.76 7.41 46.89 4.70
319 320 5.900413 CATTTTTACCGAAAAAGGCTTTCG 58.100 37.500 13.76 13.37 45.33 3.46
325 326 5.220135 GCGTATGCATTTTTACCGAAAAAGG 60.220 40.000 3.54 3.81 45.33 3.11
326 327 5.571357 AGCGTATGCATTTTTACCGAAAAAG 59.429 36.000 3.54 0.00 46.23 2.27
327 328 5.462405 AGCGTATGCATTTTTACCGAAAAA 58.538 33.333 3.54 0.00 46.23 1.94
328 329 5.049398 AGCGTATGCATTTTTACCGAAAA 57.951 34.783 3.54 0.00 46.23 2.29
329 330 4.688511 AGCGTATGCATTTTTACCGAAA 57.311 36.364 3.54 0.00 46.23 3.46
330 331 4.871557 ACTAGCGTATGCATTTTTACCGAA 59.128 37.500 3.54 0.00 46.23 4.30
331 332 4.269123 CACTAGCGTATGCATTTTTACCGA 59.731 41.667 3.54 0.00 46.23 4.69
332 333 4.033587 ACACTAGCGTATGCATTTTTACCG 59.966 41.667 3.54 0.00 46.23 4.02
333 334 5.064198 TGACACTAGCGTATGCATTTTTACC 59.936 40.000 3.54 0.00 46.23 2.85
334 335 6.102006 TGACACTAGCGTATGCATTTTTAC 57.898 37.500 3.54 0.00 46.23 2.01
335 336 6.370442 ACTTGACACTAGCGTATGCATTTTTA 59.630 34.615 3.54 0.00 46.23 1.52
347 348 2.488545 AGTCCTACACTTGACACTAGCG 59.511 50.000 0.00 0.00 33.89 4.26
397 398 5.499004 TGTAGCTCAGATGGTTAGGTTTT 57.501 39.130 0.00 0.00 0.00 2.43
398 399 5.700402 ATGTAGCTCAGATGGTTAGGTTT 57.300 39.130 0.00 0.00 0.00 3.27
404 405 6.382570 AGAGAAAGTATGTAGCTCAGATGGTT 59.617 38.462 0.00 0.00 0.00 3.67
405 406 5.896678 AGAGAAAGTATGTAGCTCAGATGGT 59.103 40.000 0.00 0.00 0.00 3.55
444 445 8.994429 AATGTCGGCATTTTATTGATTAAACA 57.006 26.923 10.00 0.00 42.19 2.83
490 491 7.330946 TCCTTAGTGTCGAATGAAATAACTGTG 59.669 37.037 0.00 0.00 0.00 3.66
493 494 7.837863 TCTCCTTAGTGTCGAATGAAATAACT 58.162 34.615 0.00 0.00 0.00 2.24
494 495 8.475331 TTCTCCTTAGTGTCGAATGAAATAAC 57.525 34.615 0.00 0.00 0.00 1.89
598 599 3.687698 CCTGGACGGTCGTCAATATTTTT 59.312 43.478 22.35 0.00 46.20 1.94
791 794 5.016173 CCCTAATGGATCGATTCTCTCTCT 58.984 45.833 6.19 0.00 35.39 3.10
862 878 0.107703 ACGATGGCGATGTGAATGGT 60.108 50.000 0.00 0.00 41.64 3.55
934 950 7.433537 AATTAGCTAACCCTAGTAAGCAGAA 57.566 36.000 8.70 0.00 37.44 3.02
954 970 6.549912 TCGATCCGAGATCGTTCTTAATTA 57.450 37.500 25.27 9.10 41.77 1.40
955 971 5.434352 TCGATCCGAGATCGTTCTTAATT 57.566 39.130 25.27 0.00 41.77 1.40
956 972 5.630661 ATCGATCCGAGATCGTTCTTAAT 57.369 39.130 25.27 13.98 39.91 1.40
957 973 5.032100 GATCGATCCGAGATCGTTCTTAA 57.968 43.478 25.27 12.76 39.91 1.85
1050 1066 1.292223 GCGGTACTTGGTGCTCTCA 59.708 57.895 0.00 0.00 0.00 3.27
1498 1514 9.034800 ACTGGAAATCCAACATTAACATACATT 57.965 29.630 3.35 0.00 46.97 2.71
1643 1664 4.220382 TGATTAATCCAACAAGCAACCCAG 59.780 41.667 12.90 0.00 0.00 4.45
1751 1773 9.533253 ACATTAATCATATAGGCTTGCAAAAAC 57.467 29.630 0.00 0.00 0.00 2.43
1792 1814 6.056884 AGTTTATGGTAAACTCGTGACCAAA 58.943 36.000 8.81 3.23 46.03 3.28
1830 1855 2.940147 TGGCATCAACAAATACGTTGC 58.060 42.857 0.00 0.00 44.80 4.17
1867 1892 5.556355 ACCAATCATATATTGCATGCTCG 57.444 39.130 20.33 0.00 0.00 5.03
1869 1894 5.474532 ACGAACCAATCATATATTGCATGCT 59.525 36.000 20.33 1.26 0.00 3.79
1903 1928 6.774170 TGGATGATCTCATTTTATGTTCCAGG 59.226 38.462 0.00 0.00 36.57 4.45
1979 2004 5.178797 GCCACTACTGATTACTCAATGTGT 58.821 41.667 0.00 0.00 30.50 3.72
1980 2005 5.178061 TGCCACTACTGATTACTCAATGTG 58.822 41.667 0.00 0.00 0.00 3.21
1981 2006 5.187772 TCTGCCACTACTGATTACTCAATGT 59.812 40.000 0.00 0.00 0.00 2.71
1982 2007 5.664457 TCTGCCACTACTGATTACTCAATG 58.336 41.667 0.00 0.00 0.00 2.82
1984 2009 5.939764 ATCTGCCACTACTGATTACTCAA 57.060 39.130 0.00 0.00 0.00 3.02
2066 2091 4.023193 ACCGTCAAAAGCAATTCTTCGATT 60.023 37.500 0.00 0.00 32.88 3.34
2114 2139 4.472833 AGGATGCTCTTTAGTTCAGGTCAT 59.527 41.667 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.