Multiple sequence alignment - TraesCS5A01G203600

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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 TraesCS5A01G203600 chr5A 100.000 3561 0 0 1 3561 413053011 413049451 0.000000e+00 6577.0
1 TraesCS5A01G203600 chr5A 95.539 964 36 5 529 1491 413063742 413062785 0.000000e+00 1535.0
2 TraesCS5A01G203600 chr5A 81.532 222 32 6 72 287 608422653 608422435 1.310000e-39 174.0
3 TraesCS5A01G203600 chr5D 93.723 3298 145 24 281 3559 318463259 318460005 0.000000e+00 4887.0
4 TraesCS5A01G203600 chr5D 79.344 305 41 5 1 283 464612040 464612344 1.010000e-45 195.0
5 TraesCS5A01G203600 chr5B 93.110 2206 99 21 1152 3335 368505376 368503202 0.000000e+00 3182.0
6 TraesCS5A01G203600 chr5B 91.065 873 56 8 289 1151 368506346 368505486 0.000000e+00 1160.0
7 TraesCS5A01G203600 chr5B 81.279 219 36 2 72 285 674273651 674273433 4.730000e-39 172.0
8 TraesCS5A01G203600 chr2D 83.920 199 30 2 95 292 127942150 127941953 4.690000e-44 189.0
9 TraesCS5A01G203600 chr6D 84.127 189 28 2 95 283 368734478 368734664 7.850000e-42 182.0
10 TraesCS5A01G203600 chr6D 81.776 214 35 1 76 285 458391526 458391313 3.650000e-40 176.0
11 TraesCS5A01G203600 chr6D 81.567 217 34 6 74 285 427237814 427237599 1.310000e-39 174.0
12 TraesCS5A01G203600 chr2B 82.192 219 32 5 72 286 687245520 687245305 7.850000e-42 182.0
13 TraesCS5A01G203600 chr2B 80.930 215 38 3 75 286 256447648 256447862 2.200000e-37 167.0
14 TraesCS5A01G203600 chr3A 81.395 215 37 2 72 285 725414743 725414955 4.730000e-39 172.0
15 TraesCS5A01G203600 chr7B 81.951 205 30 5 87 286 126170487 126170285 2.200000e-37 167.0
16 TraesCS5A01G203600 chr7B 76.959 217 47 2 72 285 333966269 333966485 1.740000e-23 121.0
17 TraesCS5A01G203600 chr4A 85.897 78 5 4 1 73 713370351 713370427 1.060000e-10 78.7
18 TraesCS5A01G203600 chr3B 83.544 79 9 3 1 76 765554279 765554202 1.770000e-08 71.3


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 TraesCS5A01G203600 chr5A 413049451 413053011 3560 True 6577 6577 100.0000 1 3561 1 chr5A.!!$R1 3560
1 TraesCS5A01G203600 chr5A 413062785 413063742 957 True 1535 1535 95.5390 529 1491 1 chr5A.!!$R2 962
2 TraesCS5A01G203600 chr5D 318460005 318463259 3254 True 4887 4887 93.7230 281 3559 1 chr5D.!!$R1 3278
3 TraesCS5A01G203600 chr5B 368503202 368506346 3144 True 2171 3182 92.0875 289 3335 2 chr5B.!!$R2 3046

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
240 241 0.035343 TGTCAACACCGACCCAAACA 60.035 50.0 0.00 0.0 34.88 2.83 F
279 280 0.442699 GATCGTCCCGTTGAAGTTGC 59.557 55.0 0.00 0.0 0.00 4.17 F
833 843 0.526096 GCGCGTTGCAATTGGATGAT 60.526 50.0 8.43 0.0 45.45 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1054 1073 2.731976 GCACAACGAGGAGAACTAACAG 59.268 50.00 0.0 0.0 0.0 3.16 R
1546 1675 3.320541 TCATTCGACAAGCCCACATTTTT 59.679 39.13 0.0 0.0 0.0 1.94 R
2780 2920 0.684535 TCCGCATCTGGTCTGAAACA 59.315 50.00 0.0 0.0 0.0 2.83 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 3.790437 CGTCCTCCATGGCTGGCT 61.790 66.667 6.96 0.00 42.80 4.75
19 20 2.124403 GTCCTCCATGGCTGGCTG 60.124 66.667 6.96 0.00 42.80 4.85
20 21 3.414193 TCCTCCATGGCTGGCTGG 61.414 66.667 6.96 11.63 42.80 4.85
21 22 4.517934 CCTCCATGGCTGGCTGGG 62.518 72.222 6.96 11.20 42.80 4.45
22 23 4.517934 CTCCATGGCTGGCTGGGG 62.518 72.222 6.96 11.03 42.80 4.96
51 52 2.593436 CGTGGGCGGGAGTGTTTT 60.593 61.111 0.00 0.00 0.00 2.43
52 53 2.190841 CGTGGGCGGGAGTGTTTTT 61.191 57.895 0.00 0.00 0.00 1.94
53 54 1.362355 GTGGGCGGGAGTGTTTTTG 59.638 57.895 0.00 0.00 0.00 2.44
54 55 1.830408 TGGGCGGGAGTGTTTTTGG 60.830 57.895 0.00 0.00 0.00 3.28
55 56 2.570284 GGGCGGGAGTGTTTTTGGG 61.570 63.158 0.00 0.00 0.00 4.12
56 57 2.570284 GGCGGGAGTGTTTTTGGGG 61.570 63.158 0.00 0.00 0.00 4.96
57 58 1.529713 GCGGGAGTGTTTTTGGGGA 60.530 57.895 0.00 0.00 0.00 4.81
58 59 1.110518 GCGGGAGTGTTTTTGGGGAA 61.111 55.000 0.00 0.00 0.00 3.97
59 60 1.404843 CGGGAGTGTTTTTGGGGAAA 58.595 50.000 0.00 0.00 0.00 3.13
60 61 1.757699 CGGGAGTGTTTTTGGGGAAAA 59.242 47.619 0.00 0.00 34.93 2.29
61 62 2.367241 CGGGAGTGTTTTTGGGGAAAAT 59.633 45.455 0.00 0.00 39.29 1.82
62 63 3.738982 GGGAGTGTTTTTGGGGAAAATG 58.261 45.455 0.00 0.00 39.29 2.32
63 64 3.495983 GGGAGTGTTTTTGGGGAAAATGG 60.496 47.826 0.00 0.00 39.29 3.16
64 65 3.389656 GGAGTGTTTTTGGGGAAAATGGA 59.610 43.478 0.00 0.00 39.29 3.41
65 66 4.503123 GGAGTGTTTTTGGGGAAAATGGAG 60.503 45.833 0.00 0.00 39.29 3.86
66 67 4.294347 AGTGTTTTTGGGGAAAATGGAGA 58.706 39.130 0.00 0.00 39.29 3.71
67 68 4.719273 AGTGTTTTTGGGGAAAATGGAGAA 59.281 37.500 0.00 0.00 39.29 2.87
68 69 5.190726 AGTGTTTTTGGGGAAAATGGAGAAA 59.809 36.000 0.00 0.00 39.29 2.52
69 70 5.883115 GTGTTTTTGGGGAAAATGGAGAAAA 59.117 36.000 0.00 0.00 39.29 2.29
70 71 6.545666 GTGTTTTTGGGGAAAATGGAGAAAAT 59.454 34.615 0.00 0.00 39.29 1.82
71 72 6.545298 TGTTTTTGGGGAAAATGGAGAAAATG 59.455 34.615 0.00 0.00 39.29 2.32
72 73 4.906747 TTGGGGAAAATGGAGAAAATGG 57.093 40.909 0.00 0.00 0.00 3.16
73 74 2.571202 TGGGGAAAATGGAGAAAATGGC 59.429 45.455 0.00 0.00 0.00 4.40
74 75 2.418609 GGGGAAAATGGAGAAAATGGCG 60.419 50.000 0.00 0.00 0.00 5.69
75 76 2.418609 GGGAAAATGGAGAAAATGGCGG 60.419 50.000 0.00 0.00 0.00 6.13
76 77 2.418609 GGAAAATGGAGAAAATGGCGGG 60.419 50.000 0.00 0.00 0.00 6.13
77 78 0.536724 AAATGGAGAAAATGGCGGGC 59.463 50.000 0.00 0.00 0.00 6.13
78 79 1.329913 AATGGAGAAAATGGCGGGCC 61.330 55.000 1.86 1.86 0.00 5.80
79 80 3.147595 GGAGAAAATGGCGGGCCC 61.148 66.667 13.57 13.57 34.56 5.80
80 81 3.518068 GAGAAAATGGCGGGCCCG 61.518 66.667 40.26 40.26 43.09 6.13
92 93 2.042230 GGCCCGGGAAGAGGAGTA 60.042 66.667 29.31 0.00 0.00 2.59
93 94 2.134933 GGCCCGGGAAGAGGAGTAG 61.135 68.421 29.31 0.00 0.00 2.57
94 95 2.134933 GCCCGGGAAGAGGAGTAGG 61.135 68.421 29.31 0.00 0.00 3.18
95 96 2.134933 CCCGGGAAGAGGAGTAGGC 61.135 68.421 18.48 0.00 0.00 3.93
96 97 2.491022 CCGGGAAGAGGAGTAGGCG 61.491 68.421 0.00 0.00 0.00 5.52
97 98 1.753463 CGGGAAGAGGAGTAGGCGT 60.753 63.158 0.00 0.00 0.00 5.68
98 99 1.817209 GGGAAGAGGAGTAGGCGTG 59.183 63.158 0.00 0.00 0.00 5.34
99 100 1.142097 GGAAGAGGAGTAGGCGTGC 59.858 63.158 0.00 0.00 0.00 5.34
100 101 1.226717 GAAGAGGAGTAGGCGTGCG 60.227 63.158 0.00 0.00 0.00 5.34
101 102 3.358076 AAGAGGAGTAGGCGTGCGC 62.358 63.158 8.17 8.17 41.06 6.09
116 117 4.344109 CGCGCGTCCGTTTCGTTT 62.344 61.111 24.19 0.00 36.67 3.60
117 118 2.052854 GCGCGTCCGTTTCGTTTT 60.053 55.556 8.43 0.00 36.67 2.43
118 119 2.065368 GCGCGTCCGTTTCGTTTTC 61.065 57.895 8.43 0.00 36.67 2.29
119 120 1.781760 CGCGTCCGTTTCGTTTTCG 60.782 57.895 0.00 0.00 45.64 3.46
120 121 2.065368 GCGTCCGTTTCGTTTTCGC 61.065 57.895 0.00 0.00 43.73 4.70
121 122 1.781760 CGTCCGTTTCGTTTTCGCG 60.782 57.895 0.00 0.00 43.73 5.87
122 123 2.065368 GTCCGTTTCGTTTTCGCGC 61.065 57.895 0.00 0.00 43.73 6.86
123 124 2.793759 CCGTTTCGTTTTCGCGCC 60.794 61.111 0.00 0.00 43.73 6.53
124 125 3.147951 CGTTTCGTTTTCGCGCCG 61.148 61.111 0.00 0.00 43.73 6.46
125 126 2.246108 GTTTCGTTTTCGCGCCGA 59.754 55.556 0.00 0.66 43.73 5.54
126 127 2.065368 GTTTCGTTTTCGCGCCGAC 61.065 57.895 0.00 0.00 43.73 4.79
127 128 3.546256 TTTCGTTTTCGCGCCGACG 62.546 57.895 17.60 17.60 43.73 5.12
139 140 3.124921 CCGACGCAAATCCGGCTT 61.125 61.111 0.00 0.00 36.62 4.35
140 141 1.812093 CCGACGCAAATCCGGCTTA 60.812 57.895 0.00 0.00 36.62 3.09
141 142 1.363145 CCGACGCAAATCCGGCTTAA 61.363 55.000 0.00 0.00 36.62 1.85
142 143 0.444651 CGACGCAAATCCGGCTTAAA 59.555 50.000 0.00 0.00 33.03 1.52
143 144 1.135916 CGACGCAAATCCGGCTTAAAA 60.136 47.619 0.00 0.00 33.03 1.52
144 145 2.666069 CGACGCAAATCCGGCTTAAAAA 60.666 45.455 0.00 0.00 33.03 1.94
145 146 3.507786 GACGCAAATCCGGCTTAAAAAT 58.492 40.909 0.00 0.00 32.31 1.82
146 147 4.664188 GACGCAAATCCGGCTTAAAAATA 58.336 39.130 0.00 0.00 32.31 1.40
147 148 4.668289 ACGCAAATCCGGCTTAAAAATAG 58.332 39.130 0.00 0.00 0.00 1.73
148 149 4.041723 CGCAAATCCGGCTTAAAAATAGG 58.958 43.478 0.00 0.00 0.00 2.57
149 150 4.439563 CGCAAATCCGGCTTAAAAATAGGT 60.440 41.667 0.00 0.00 0.00 3.08
150 151 5.416083 GCAAATCCGGCTTAAAAATAGGTT 58.584 37.500 0.00 0.00 0.00 3.50
151 152 5.290885 GCAAATCCGGCTTAAAAATAGGTTG 59.709 40.000 0.00 0.00 0.00 3.77
152 153 5.592104 AATCCGGCTTAAAAATAGGTTGG 57.408 39.130 0.00 0.00 0.00 3.77
153 154 3.358118 TCCGGCTTAAAAATAGGTTGGG 58.642 45.455 0.00 0.00 0.00 4.12
154 155 3.010361 TCCGGCTTAAAAATAGGTTGGGA 59.990 43.478 0.00 0.00 0.00 4.37
155 156 3.764972 CCGGCTTAAAAATAGGTTGGGAA 59.235 43.478 0.00 0.00 0.00 3.97
156 157 4.404394 CCGGCTTAAAAATAGGTTGGGAAT 59.596 41.667 0.00 0.00 0.00 3.01
157 158 5.348164 CGGCTTAAAAATAGGTTGGGAATG 58.652 41.667 0.00 0.00 0.00 2.67
158 159 5.670485 GGCTTAAAAATAGGTTGGGAATGG 58.330 41.667 0.00 0.00 0.00 3.16
159 160 5.423931 GGCTTAAAAATAGGTTGGGAATGGA 59.576 40.000 0.00 0.00 0.00 3.41
160 161 6.099701 GGCTTAAAAATAGGTTGGGAATGGAT 59.900 38.462 0.00 0.00 0.00 3.41
161 162 7.210174 GCTTAAAAATAGGTTGGGAATGGATC 58.790 38.462 0.00 0.00 0.00 3.36
162 163 5.852282 AAAAATAGGTTGGGAATGGATCG 57.148 39.130 0.00 0.00 0.00 3.69
163 164 2.568623 ATAGGTTGGGAATGGATCGC 57.431 50.000 0.00 0.00 41.21 4.58
164 165 0.472471 TAGGTTGGGAATGGATCGCC 59.528 55.000 0.00 0.00 40.15 5.54
165 166 1.227383 GGTTGGGAATGGATCGCCT 59.773 57.895 0.00 0.00 40.15 5.52
166 167 1.103398 GGTTGGGAATGGATCGCCTG 61.103 60.000 0.00 0.00 40.15 4.85
167 168 1.453745 TTGGGAATGGATCGCCTGC 60.454 57.895 0.00 0.00 40.15 4.85
168 169 2.192979 GGGAATGGATCGCCTGCA 59.807 61.111 0.00 0.00 35.03 4.41
169 170 1.453745 GGGAATGGATCGCCTGCAA 60.454 57.895 0.00 0.00 35.03 4.08
170 171 1.037030 GGGAATGGATCGCCTGCAAA 61.037 55.000 0.00 0.00 35.03 3.68
171 172 0.101219 GGAATGGATCGCCTGCAAAC 59.899 55.000 0.00 0.00 34.31 2.93
172 173 0.248215 GAATGGATCGCCTGCAAACG 60.248 55.000 1.73 1.73 34.31 3.60
173 174 0.676466 AATGGATCGCCTGCAAACGA 60.676 50.000 12.51 12.51 43.33 3.85
174 175 0.676466 ATGGATCGCCTGCAAACGAA 60.676 50.000 13.91 0.00 42.31 3.85
175 176 0.886938 TGGATCGCCTGCAAACGAAA 60.887 50.000 13.91 2.02 42.31 3.46
176 177 0.239879 GGATCGCCTGCAAACGAAAA 59.760 50.000 13.91 0.00 42.31 2.29
177 178 1.335506 GGATCGCCTGCAAACGAAAAA 60.336 47.619 13.91 0.00 42.31 1.94
178 179 1.713932 GATCGCCTGCAAACGAAAAAC 59.286 47.619 13.91 4.22 42.31 2.43
188 189 3.227667 CGAAAAACGGACGCGTCT 58.772 55.556 35.50 17.48 38.46 4.18
189 190 1.127225 CGAAAAACGGACGCGTCTC 59.873 57.895 35.50 24.63 38.46 3.36
190 191 1.490258 GAAAAACGGACGCGTCTCC 59.510 57.895 35.50 21.95 0.00 3.71
199 200 4.477975 CGCGTCTCCGTCTGGGTC 62.478 72.222 0.00 0.00 37.00 4.46
200 201 4.477975 GCGTCTCCGTCTGGGTCG 62.478 72.222 0.00 0.00 37.00 4.79
202 203 2.675772 GTCTCCGTCTGGGTCGGT 60.676 66.667 4.36 0.00 46.86 4.69
203 204 2.675423 TCTCCGTCTGGGTCGGTG 60.675 66.667 4.36 2.56 46.86 4.94
204 205 4.436998 CTCCGTCTGGGTCGGTGC 62.437 72.222 4.36 0.00 46.86 5.01
207 208 4.657824 CGTCTGGGTCGGTGCGTT 62.658 66.667 0.00 0.00 0.00 4.84
208 209 3.041940 GTCTGGGTCGGTGCGTTG 61.042 66.667 0.00 0.00 0.00 4.10
209 210 4.308458 TCTGGGTCGGTGCGTTGG 62.308 66.667 0.00 0.00 0.00 3.77
218 219 3.284449 GTGCGTTGGGCCGACTTT 61.284 61.111 21.44 0.00 42.61 2.66
219 220 2.517402 TGCGTTGGGCCGACTTTT 60.517 55.556 21.44 0.00 42.61 2.27
220 221 2.254350 GCGTTGGGCCGACTTTTC 59.746 61.111 21.44 4.69 34.80 2.29
221 222 2.258726 GCGTTGGGCCGACTTTTCT 61.259 57.895 21.44 0.00 34.80 2.52
222 223 1.574428 CGTTGGGCCGACTTTTCTG 59.426 57.895 21.44 1.08 0.00 3.02
223 224 1.164041 CGTTGGGCCGACTTTTCTGT 61.164 55.000 21.44 0.00 0.00 3.41
224 225 0.591659 GTTGGGCCGACTTTTCTGTC 59.408 55.000 17.07 0.00 0.00 3.51
225 226 0.181587 TTGGGCCGACTTTTCTGTCA 59.818 50.000 0.00 0.00 36.82 3.58
226 227 0.181587 TGGGCCGACTTTTCTGTCAA 59.818 50.000 0.00 0.00 36.82 3.18
227 228 0.591659 GGGCCGACTTTTCTGTCAAC 59.408 55.000 0.00 0.00 36.82 3.18
228 229 1.305201 GGCCGACTTTTCTGTCAACA 58.695 50.000 0.00 0.00 36.82 3.33
229 230 1.002792 GGCCGACTTTTCTGTCAACAC 60.003 52.381 0.00 0.00 36.82 3.32
230 231 1.002792 GCCGACTTTTCTGTCAACACC 60.003 52.381 0.00 0.00 36.82 4.16
231 232 1.260561 CCGACTTTTCTGTCAACACCG 59.739 52.381 0.00 0.00 36.82 4.94
232 233 2.198406 CGACTTTTCTGTCAACACCGA 58.802 47.619 0.00 0.00 36.82 4.69
233 234 2.034001 CGACTTTTCTGTCAACACCGAC 60.034 50.000 0.00 0.00 36.82 4.79
234 235 2.285977 ACTTTTCTGTCAACACCGACC 58.714 47.619 0.00 0.00 34.88 4.79
235 236 1.602377 CTTTTCTGTCAACACCGACCC 59.398 52.381 0.00 0.00 34.88 4.46
236 237 0.542333 TTTCTGTCAACACCGACCCA 59.458 50.000 0.00 0.00 34.88 4.51
237 238 0.542333 TTCTGTCAACACCGACCCAA 59.458 50.000 0.00 0.00 34.88 4.12
238 239 0.542333 TCTGTCAACACCGACCCAAA 59.458 50.000 0.00 0.00 34.88 3.28
239 240 0.661020 CTGTCAACACCGACCCAAAC 59.339 55.000 0.00 0.00 34.88 2.93
240 241 0.035343 TGTCAACACCGACCCAAACA 60.035 50.000 0.00 0.00 34.88 2.83
241 242 1.096416 GTCAACACCGACCCAAACAA 58.904 50.000 0.00 0.00 0.00 2.83
242 243 1.473278 GTCAACACCGACCCAAACAAA 59.527 47.619 0.00 0.00 0.00 2.83
243 244 1.473278 TCAACACCGACCCAAACAAAC 59.527 47.619 0.00 0.00 0.00 2.93
244 245 0.452585 AACACCGACCCAAACAAACG 59.547 50.000 0.00 0.00 0.00 3.60
246 247 2.333581 CCGACCCAAACAAACGGC 59.666 61.111 0.00 0.00 37.32 5.68
247 248 2.051703 CGACCCAAACAAACGGCG 60.052 61.111 4.80 4.80 0.00 6.46
248 249 2.333581 GACCCAAACAAACGGCGG 59.666 61.111 13.24 0.00 0.00 6.13
249 250 3.834447 GACCCAAACAAACGGCGGC 62.834 63.158 13.24 0.00 0.00 6.53
250 251 4.992294 CCCAAACAAACGGCGGCG 62.992 66.667 31.06 31.06 0.00 6.46
251 252 4.992294 CCAAACAAACGGCGGCGG 62.992 66.667 35.05 19.88 0.00 6.13
252 253 3.955101 CAAACAAACGGCGGCGGA 61.955 61.111 35.05 0.00 0.00 5.54
253 254 3.956317 AAACAAACGGCGGCGGAC 61.956 61.111 35.05 0.00 0.00 4.79
270 271 4.827481 CGAAATGGATCGTCCCGT 57.173 55.556 2.23 0.00 38.01 5.28
271 272 3.059603 CGAAATGGATCGTCCCGTT 57.940 52.632 2.23 0.53 38.01 4.44
272 273 0.650512 CGAAATGGATCGTCCCGTTG 59.349 55.000 4.54 0.00 38.01 4.10
273 274 1.737696 CGAAATGGATCGTCCCGTTGA 60.738 52.381 4.54 0.00 38.01 3.18
274 275 2.352388 GAAATGGATCGTCCCGTTGAA 58.648 47.619 4.54 0.00 35.70 2.69
275 276 2.024176 AATGGATCGTCCCGTTGAAG 57.976 50.000 3.22 0.00 35.03 3.02
276 277 0.902531 ATGGATCGTCCCGTTGAAGT 59.097 50.000 2.23 0.00 35.03 3.01
277 278 0.682852 TGGATCGTCCCGTTGAAGTT 59.317 50.000 2.23 0.00 35.03 2.66
278 279 1.076332 GGATCGTCCCGTTGAAGTTG 58.924 55.000 0.00 0.00 0.00 3.16
279 280 0.442699 GATCGTCCCGTTGAAGTTGC 59.557 55.000 0.00 0.00 0.00 4.17
284 285 2.762745 GTCCCGTTGAAGTTGCTCTTA 58.237 47.619 0.00 0.00 36.40 2.10
334 336 2.567049 CGGTCTCGTCTCCACCAC 59.433 66.667 0.00 0.00 0.00 4.16
413 416 4.862823 CTCTCCCGGGTCCCCTCC 62.863 77.778 22.86 0.00 0.00 4.30
467 470 2.681778 CTCCCAGTCCCAGTCGCT 60.682 66.667 0.00 0.00 0.00 4.93
554 563 2.242401 CCCAATACCCACCCCACCA 61.242 63.158 0.00 0.00 0.00 4.17
621 631 1.403647 CCAGTTCAACCTCATCGCGTA 60.404 52.381 5.77 0.00 0.00 4.42
680 690 3.499918 GGATTCCGAGGTATGAGCATTTG 59.500 47.826 0.00 0.00 0.00 2.32
682 692 0.947244 CCGAGGTATGAGCATTTGGC 59.053 55.000 0.00 0.00 45.30 4.52
709 719 1.153229 GCTAGCTAAACCCCACCCG 60.153 63.158 7.70 0.00 0.00 5.28
728 738 1.135916 CGCGCGAGAAATTTTTGGGTA 60.136 47.619 28.94 0.00 0.00 3.69
832 842 1.154054 GCGCGTTGCAATTGGATGA 60.154 52.632 8.43 0.00 45.45 2.92
833 843 0.526096 GCGCGTTGCAATTGGATGAT 60.526 50.000 8.43 0.00 45.45 2.45
920 938 1.670087 CCGTTCTCGTGTGCAGAGATT 60.670 52.381 5.10 0.00 43.39 2.40
922 940 2.408050 GTTCTCGTGTGCAGAGATTGT 58.592 47.619 5.10 0.00 43.39 2.71
1054 1073 4.995594 AGCTATGCTTGGGCCTTC 57.004 55.556 4.53 0.00 33.89 3.46
1449 1578 5.887214 TTCTTATGCCTAATAGAGTGCCA 57.113 39.130 0.00 0.00 0.00 4.92
1483 1612 4.399303 GCAGATTGTAACTATGCAAAGGGT 59.601 41.667 0.00 0.00 34.73 4.34
1579 1708 0.853224 GTCGAATGATGCAACGCACG 60.853 55.000 0.00 0.00 43.04 5.34
1686 1815 5.176407 TGTGCTATTTTTAACTGTGCGTT 57.824 34.783 0.00 0.00 39.64 4.84
1811 1940 5.585844 CAGTCCATCATGTGTATAGCAACAA 59.414 40.000 0.00 0.00 0.00 2.83
1984 2113 5.215252 TGGAACCTTTGAACACAACAAAA 57.785 34.783 0.00 0.00 36.91 2.44
1990 2119 7.164230 ACCTTTGAACACAACAAAATCAGTA 57.836 32.000 0.00 0.00 36.91 2.74
2020 2149 1.091771 CGTTGCATCTTGATCGGCCT 61.092 55.000 0.00 0.00 0.00 5.19
2113 2242 6.071165 ACAGAGGGAAATTCAATGGAAATCAC 60.071 38.462 0.00 0.00 36.43 3.06
2382 2511 0.471617 AGTGACTTGCCTGCAGAGTT 59.528 50.000 17.39 0.00 0.00 3.01
2452 2581 1.414181 CAACTACGAGATGAGGGGCAT 59.586 52.381 0.00 0.00 40.77 4.40
2566 2695 5.940470 CCTCTTTGCACAGATTTAGTACCTT 59.060 40.000 2.40 0.00 0.00 3.50
2615 2749 4.263243 CCCAGAGGCCCAAGAATCTATTAG 60.263 50.000 0.00 0.00 0.00 1.73
2714 2848 1.779221 TTTGGTCATCCATCCATGCC 58.221 50.000 0.00 0.00 43.91 4.40
2726 2860 3.372566 CCATCCATGCCTAGGTGGTTAAA 60.373 47.826 16.12 0.12 38.35 1.52
2764 2898 8.814038 ATAGCATTCTTTCCAGTGTATTTCTT 57.186 30.769 0.00 0.00 0.00 2.52
2769 2903 9.403110 CATTCTTTCCAGTGTATTTCTTTTCAG 57.597 33.333 0.00 0.00 0.00 3.02
2780 2920 7.554476 GTGTATTTCTTTTCAGATCTTAGCCCT 59.446 37.037 0.00 0.00 0.00 5.19
2837 2979 1.059913 ATATGTAGTGCTCCCCAGCC 58.940 55.000 0.00 0.00 46.26 4.85
2838 2980 1.054406 TATGTAGTGCTCCCCAGCCC 61.054 60.000 0.00 0.00 46.26 5.19
2839 2981 3.798511 GTAGTGCTCCCCAGCCCC 61.799 72.222 0.00 0.00 46.26 5.80
2840 2982 4.346889 TAGTGCTCCCCAGCCCCA 62.347 66.667 0.00 0.00 46.26 4.96
2841 2983 3.881926 TAGTGCTCCCCAGCCCCAA 62.882 63.158 0.00 0.00 46.26 4.12
2842 2984 4.748144 GTGCTCCCCAGCCCCAAG 62.748 72.222 0.00 0.00 46.26 3.61
2855 3000 1.528309 CCCAAGGCACGTCAAACCT 60.528 57.895 0.00 0.00 34.45 3.50
2942 3087 8.419076 AAAATGTTCATACAAGTTGACCAAAC 57.581 30.769 10.54 8.99 37.91 2.93
2999 3149 6.438763 GTGGAACTTTTGGTTGAGTCTTATG 58.561 40.000 0.00 0.00 38.41 1.90
3018 3168 3.713826 TGTCCCCAAACCTCTTATCAC 57.286 47.619 0.00 0.00 0.00 3.06
3105 3255 5.006649 TGTTCTCGAATAATCAAATGGCTCG 59.993 40.000 0.00 0.00 0.00 5.03
3160 3310 5.471116 TGAGAAATACCATATGCAGTGATGC 59.529 40.000 0.00 0.00 0.00 3.91
3169 3319 2.512485 TGCAGTGATGCCAGTTTTTG 57.488 45.000 0.00 0.00 0.00 2.44
3174 3325 3.057736 CAGTGATGCCAGTTTTTGAGGAG 60.058 47.826 0.00 0.00 0.00 3.69
3323 3478 5.932303 GTGTGGAACTAGCTGAGTAAAATCA 59.068 40.000 0.00 0.00 37.44 2.57
3346 3501 8.114359 TCAACGTTGAAGCTTTTATTTTTCTG 57.886 30.769 27.94 0.00 33.55 3.02
3369 3524 8.921205 TCTGTACTATAAAAATGGTACTCCCTC 58.079 37.037 11.64 0.00 38.70 4.30
3371 3526 6.170846 ACTATAAAAATGGTACTCCCTCGG 57.829 41.667 0.00 0.00 0.00 4.63
3372 3527 5.901276 ACTATAAAAATGGTACTCCCTCGGA 59.099 40.000 0.00 0.00 0.00 4.55
3373 3528 5.906772 ATAAAAATGGTACTCCCTCGGAT 57.093 39.130 0.00 0.00 0.00 4.18
3374 3529 7.731688 ACTATAAAAATGGTACTCCCTCGGATA 59.268 37.037 0.00 0.00 0.00 2.59
3428 3583 4.405116 AAATGGACAGTTTTGCATGTGT 57.595 36.364 0.00 0.00 0.00 3.72
3433 3588 4.023279 TGGACAGTTTTGCATGTGTATCAC 60.023 41.667 0.00 0.00 34.56 3.06
3495 3650 7.792374 TTGACCAAAGTGCTATATGATCTTC 57.208 36.000 0.00 0.00 0.00 2.87
3527 3687 5.289595 GTGGATCCTTCTTTTTGTGAAACC 58.710 41.667 14.23 0.00 34.36 3.27
3559 3719 5.649782 AGTGGAGCTTTTGGTTGATATTG 57.350 39.130 0.00 0.00 0.00 1.90
3560 3720 5.079643 AGTGGAGCTTTTGGTTGATATTGT 58.920 37.500 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.190841 AAAAACACTCCCGCCCACG 61.191 57.895 0.00 0.00 39.67 4.94
35 36 1.362355 CAAAAACACTCCCGCCCAC 59.638 57.895 0.00 0.00 0.00 4.61
36 37 1.830408 CCAAAAACACTCCCGCCCA 60.830 57.895 0.00 0.00 0.00 5.36
37 38 2.570284 CCCAAAAACACTCCCGCCC 61.570 63.158 0.00 0.00 0.00 6.13
38 39 2.570284 CCCCAAAAACACTCCCGCC 61.570 63.158 0.00 0.00 0.00 6.13
39 40 1.110518 TTCCCCAAAAACACTCCCGC 61.111 55.000 0.00 0.00 0.00 6.13
40 41 1.404843 TTTCCCCAAAAACACTCCCG 58.595 50.000 0.00 0.00 0.00 5.14
41 42 3.495983 CCATTTTCCCCAAAAACACTCCC 60.496 47.826 0.00 0.00 39.59 4.30
42 43 3.389656 TCCATTTTCCCCAAAAACACTCC 59.610 43.478 0.00 0.00 39.59 3.85
43 44 4.343814 TCTCCATTTTCCCCAAAAACACTC 59.656 41.667 0.00 0.00 39.59 3.51
44 45 4.294347 TCTCCATTTTCCCCAAAAACACT 58.706 39.130 0.00 0.00 39.59 3.55
45 46 4.681074 TCTCCATTTTCCCCAAAAACAC 57.319 40.909 0.00 0.00 39.59 3.32
46 47 5.700402 TTTCTCCATTTTCCCCAAAAACA 57.300 34.783 0.00 0.00 39.59 2.83
47 48 6.016360 CCATTTTCTCCATTTTCCCCAAAAAC 60.016 38.462 0.00 0.00 39.59 2.43
48 49 6.067350 CCATTTTCTCCATTTTCCCCAAAAA 58.933 36.000 0.00 0.00 40.98 1.94
49 50 5.629125 CCATTTTCTCCATTTTCCCCAAAA 58.371 37.500 0.00 0.00 35.92 2.44
50 51 4.506448 GCCATTTTCTCCATTTTCCCCAAA 60.506 41.667 0.00 0.00 0.00 3.28
51 52 3.008923 GCCATTTTCTCCATTTTCCCCAA 59.991 43.478 0.00 0.00 0.00 4.12
52 53 2.571202 GCCATTTTCTCCATTTTCCCCA 59.429 45.455 0.00 0.00 0.00 4.96
53 54 2.418609 CGCCATTTTCTCCATTTTCCCC 60.419 50.000 0.00 0.00 0.00 4.81
54 55 2.418609 CCGCCATTTTCTCCATTTTCCC 60.419 50.000 0.00 0.00 0.00 3.97
55 56 2.418609 CCCGCCATTTTCTCCATTTTCC 60.419 50.000 0.00 0.00 0.00 3.13
56 57 2.892374 CCCGCCATTTTCTCCATTTTC 58.108 47.619 0.00 0.00 0.00 2.29
57 58 1.066215 GCCCGCCATTTTCTCCATTTT 60.066 47.619 0.00 0.00 0.00 1.82
58 59 0.536724 GCCCGCCATTTTCTCCATTT 59.463 50.000 0.00 0.00 0.00 2.32
59 60 1.329913 GGCCCGCCATTTTCTCCATT 61.330 55.000 0.00 0.00 35.81 3.16
60 61 1.758122 GGCCCGCCATTTTCTCCAT 60.758 57.895 0.00 0.00 35.81 3.41
61 62 2.362375 GGCCCGCCATTTTCTCCA 60.362 61.111 0.00 0.00 35.81 3.86
62 63 3.147595 GGGCCCGCCATTTTCTCC 61.148 66.667 5.69 0.00 37.98 3.71
63 64 3.518068 CGGGCCCGCCATTTTCTC 61.518 66.667 34.96 0.00 37.98 2.87
74 75 3.691297 TACTCCTCTTCCCGGGCCC 62.691 68.421 18.49 13.57 0.00 5.80
75 76 2.042230 TACTCCTCTTCCCGGGCC 60.042 66.667 18.49 0.00 0.00 5.80
76 77 2.134933 CCTACTCCTCTTCCCGGGC 61.135 68.421 18.49 0.00 0.00 6.13
77 78 2.134933 GCCTACTCCTCTTCCCGGG 61.135 68.421 16.85 16.85 0.00 5.73
78 79 2.491022 CGCCTACTCCTCTTCCCGG 61.491 68.421 0.00 0.00 0.00 5.73
79 80 1.753463 ACGCCTACTCCTCTTCCCG 60.753 63.158 0.00 0.00 0.00 5.14
80 81 1.817209 CACGCCTACTCCTCTTCCC 59.183 63.158 0.00 0.00 0.00 3.97
81 82 1.142097 GCACGCCTACTCCTCTTCC 59.858 63.158 0.00 0.00 0.00 3.46
82 83 1.226717 CGCACGCCTACTCCTCTTC 60.227 63.158 0.00 0.00 0.00 2.87
83 84 2.885861 CGCACGCCTACTCCTCTT 59.114 61.111 0.00 0.00 0.00 2.85
84 85 3.827898 GCGCACGCCTACTCCTCT 61.828 66.667 0.30 0.00 34.56 3.69
99 100 3.826470 AAAACGAAACGGACGCGCG 62.826 57.895 30.96 30.96 0.00 6.86
100 101 2.052854 AAAACGAAACGGACGCGC 60.053 55.556 5.73 0.00 0.00 6.86
101 102 1.781760 CGAAAACGAAACGGACGCG 60.782 57.895 3.53 3.53 0.00 6.01
102 103 2.065368 GCGAAAACGAAACGGACGC 61.065 57.895 0.00 0.00 38.03 5.19
103 104 1.781760 CGCGAAAACGAAACGGACG 60.782 57.895 0.00 0.00 34.06 4.79
104 105 2.065368 GCGCGAAAACGAAACGGAC 61.065 57.895 12.10 0.00 34.06 4.79
105 106 2.246108 GCGCGAAAACGAAACGGA 59.754 55.556 12.10 0.00 34.06 4.69
106 107 2.793759 GGCGCGAAAACGAAACGG 60.794 61.111 12.10 0.00 34.06 4.44
107 108 3.147951 CGGCGCGAAAACGAAACG 61.148 61.111 12.10 0.00 34.06 3.60
108 109 2.065368 GTCGGCGCGAAAACGAAAC 61.065 57.895 12.10 0.00 37.72 2.78
109 110 2.246108 GTCGGCGCGAAAACGAAA 59.754 55.556 12.10 0.00 37.72 3.46
110 111 4.049477 CGTCGGCGCGAAAACGAA 62.049 61.111 12.10 0.00 37.72 3.85
122 123 1.363145 TTAAGCCGGATTTGCGTCGG 61.363 55.000 11.69 0.00 45.84 4.79
123 124 0.444651 TTTAAGCCGGATTTGCGTCG 59.555 50.000 11.69 0.00 0.00 5.12
124 125 2.622546 TTTTAAGCCGGATTTGCGTC 57.377 45.000 11.69 0.00 0.00 5.19
125 126 3.586100 ATTTTTAAGCCGGATTTGCGT 57.414 38.095 11.69 0.00 0.00 5.24
126 127 4.041723 CCTATTTTTAAGCCGGATTTGCG 58.958 43.478 11.69 0.00 0.00 4.85
127 128 5.006153 ACCTATTTTTAAGCCGGATTTGC 57.994 39.130 11.69 0.00 0.00 3.68
128 129 5.810074 CCAACCTATTTTTAAGCCGGATTTG 59.190 40.000 11.69 0.00 0.00 2.32
129 130 5.105106 CCCAACCTATTTTTAAGCCGGATTT 60.105 40.000 11.69 3.16 0.00 2.17
130 131 4.404394 CCCAACCTATTTTTAAGCCGGATT 59.596 41.667 11.03 11.03 0.00 3.01
131 132 3.958147 CCCAACCTATTTTTAAGCCGGAT 59.042 43.478 5.05 0.00 0.00 4.18
132 133 3.010361 TCCCAACCTATTTTTAAGCCGGA 59.990 43.478 5.05 0.00 0.00 5.14
133 134 3.358118 TCCCAACCTATTTTTAAGCCGG 58.642 45.455 0.00 0.00 0.00 6.13
134 135 5.348164 CATTCCCAACCTATTTTTAAGCCG 58.652 41.667 0.00 0.00 0.00 5.52
135 136 5.423931 TCCATTCCCAACCTATTTTTAAGCC 59.576 40.000 0.00 0.00 0.00 4.35
136 137 6.538945 TCCATTCCCAACCTATTTTTAAGC 57.461 37.500 0.00 0.00 0.00 3.09
137 138 7.425606 CGATCCATTCCCAACCTATTTTTAAG 58.574 38.462 0.00 0.00 0.00 1.85
138 139 6.183360 GCGATCCATTCCCAACCTATTTTTAA 60.183 38.462 0.00 0.00 0.00 1.52
139 140 5.300792 GCGATCCATTCCCAACCTATTTTTA 59.699 40.000 0.00 0.00 0.00 1.52
140 141 4.099419 GCGATCCATTCCCAACCTATTTTT 59.901 41.667 0.00 0.00 0.00 1.94
141 142 3.636764 GCGATCCATTCCCAACCTATTTT 59.363 43.478 0.00 0.00 0.00 1.82
142 143 3.222603 GCGATCCATTCCCAACCTATTT 58.777 45.455 0.00 0.00 0.00 1.40
143 144 2.489073 GGCGATCCATTCCCAACCTATT 60.489 50.000 0.00 0.00 0.00 1.73
144 145 1.073923 GGCGATCCATTCCCAACCTAT 59.926 52.381 0.00 0.00 0.00 2.57
145 146 0.472471 GGCGATCCATTCCCAACCTA 59.528 55.000 0.00 0.00 0.00 3.08
146 147 1.227383 GGCGATCCATTCCCAACCT 59.773 57.895 0.00 0.00 0.00 3.50
147 148 1.103398 CAGGCGATCCATTCCCAACC 61.103 60.000 0.00 0.00 33.74 3.77
148 149 1.728490 GCAGGCGATCCATTCCCAAC 61.728 60.000 0.00 0.00 33.74 3.77
149 150 1.453745 GCAGGCGATCCATTCCCAA 60.454 57.895 0.00 0.00 33.74 4.12
150 151 2.192979 GCAGGCGATCCATTCCCA 59.807 61.111 0.00 0.00 33.74 4.37
151 152 1.037030 TTTGCAGGCGATCCATTCCC 61.037 55.000 0.00 0.00 33.74 3.97
152 153 0.101219 GTTTGCAGGCGATCCATTCC 59.899 55.000 0.00 0.00 33.74 3.01
153 154 0.248215 CGTTTGCAGGCGATCCATTC 60.248 55.000 6.17 0.00 33.74 2.67
154 155 0.676466 TCGTTTGCAGGCGATCCATT 60.676 50.000 10.02 0.00 33.74 3.16
155 156 0.676466 TTCGTTTGCAGGCGATCCAT 60.676 50.000 13.90 0.00 36.97 3.41
156 157 0.886938 TTTCGTTTGCAGGCGATCCA 60.887 50.000 13.90 0.00 36.97 3.41
157 158 0.239879 TTTTCGTTTGCAGGCGATCC 59.760 50.000 13.90 0.00 36.97 3.36
158 159 1.713932 GTTTTTCGTTTGCAGGCGATC 59.286 47.619 13.90 4.32 36.97 3.69
159 160 1.766069 GTTTTTCGTTTGCAGGCGAT 58.234 45.000 13.90 0.00 36.97 4.58
160 161 0.590230 CGTTTTTCGTTTGCAGGCGA 60.590 50.000 10.02 10.02 35.17 5.54
161 162 1.536462 CCGTTTTTCGTTTGCAGGCG 61.536 55.000 5.76 5.76 37.94 5.52
162 163 0.248702 TCCGTTTTTCGTTTGCAGGC 60.249 50.000 0.00 0.00 37.94 4.85
163 164 1.472990 GTCCGTTTTTCGTTTGCAGG 58.527 50.000 0.00 0.00 37.94 4.85
164 165 1.109296 CGTCCGTTTTTCGTTTGCAG 58.891 50.000 0.00 0.00 37.94 4.41
165 166 0.862283 GCGTCCGTTTTTCGTTTGCA 60.862 50.000 0.00 0.00 37.94 4.08
166 167 1.834852 GCGTCCGTTTTTCGTTTGC 59.165 52.632 0.00 0.00 37.94 3.68
167 168 2.109934 CGCGTCCGTTTTTCGTTTG 58.890 52.632 0.00 0.00 37.94 2.93
168 169 4.574978 CGCGTCCGTTTTTCGTTT 57.425 50.000 0.00 0.00 37.94 3.60
190 191 4.657824 AACGCACCGACCCAGACG 62.658 66.667 0.00 0.00 0.00 4.18
191 192 3.041940 CAACGCACCGACCCAGAC 61.042 66.667 0.00 0.00 0.00 3.51
192 193 4.308458 CCAACGCACCGACCCAGA 62.308 66.667 0.00 0.00 0.00 3.86
201 202 2.726850 GAAAAGTCGGCCCAACGCAC 62.727 60.000 0.00 0.00 40.31 5.34
202 203 2.517402 AAAAGTCGGCCCAACGCA 60.517 55.556 0.00 0.00 40.31 5.24
203 204 2.254350 GAAAAGTCGGCCCAACGC 59.746 61.111 0.00 0.00 0.00 4.84
204 205 1.164041 ACAGAAAAGTCGGCCCAACG 61.164 55.000 0.00 0.00 0.00 4.10
205 206 0.591659 GACAGAAAAGTCGGCCCAAC 59.408 55.000 0.00 0.00 0.00 3.77
206 207 0.181587 TGACAGAAAAGTCGGCCCAA 59.818 50.000 0.00 0.00 41.41 4.12
207 208 0.181587 TTGACAGAAAAGTCGGCCCA 59.818 50.000 0.00 0.00 41.41 5.36
208 209 0.591659 GTTGACAGAAAAGTCGGCCC 59.408 55.000 0.00 0.00 41.41 5.80
209 210 1.002792 GTGTTGACAGAAAAGTCGGCC 60.003 52.381 0.00 0.00 41.41 6.13
210 211 1.002792 GGTGTTGACAGAAAAGTCGGC 60.003 52.381 0.00 0.00 41.41 5.54
211 212 1.260561 CGGTGTTGACAGAAAAGTCGG 59.739 52.381 0.00 0.00 41.41 4.79
212 213 2.034001 GTCGGTGTTGACAGAAAAGTCG 60.034 50.000 0.00 0.00 41.41 4.18
213 214 2.287103 GGTCGGTGTTGACAGAAAAGTC 59.713 50.000 0.00 0.00 40.72 3.01
214 215 2.285977 GGTCGGTGTTGACAGAAAAGT 58.714 47.619 0.00 0.00 40.72 2.66
215 216 1.602377 GGGTCGGTGTTGACAGAAAAG 59.398 52.381 0.00 0.00 40.72 2.27
216 217 1.065345 TGGGTCGGTGTTGACAGAAAA 60.065 47.619 0.00 0.00 40.72 2.29
217 218 0.542333 TGGGTCGGTGTTGACAGAAA 59.458 50.000 0.00 0.00 40.72 2.52
218 219 0.542333 TTGGGTCGGTGTTGACAGAA 59.458 50.000 0.00 0.00 40.72 3.02
219 220 0.542333 TTTGGGTCGGTGTTGACAGA 59.458 50.000 0.00 0.00 40.72 3.41
220 221 0.661020 GTTTGGGTCGGTGTTGACAG 59.339 55.000 0.00 0.00 40.72 3.51
221 222 0.035343 TGTTTGGGTCGGTGTTGACA 60.035 50.000 0.00 0.00 40.72 3.58
222 223 1.096416 TTGTTTGGGTCGGTGTTGAC 58.904 50.000 0.00 0.00 38.17 3.18
223 224 1.473278 GTTTGTTTGGGTCGGTGTTGA 59.527 47.619 0.00 0.00 0.00 3.18
224 225 1.795889 CGTTTGTTTGGGTCGGTGTTG 60.796 52.381 0.00 0.00 0.00 3.33
225 226 0.452585 CGTTTGTTTGGGTCGGTGTT 59.547 50.000 0.00 0.00 0.00 3.32
226 227 1.378124 CCGTTTGTTTGGGTCGGTGT 61.378 55.000 0.00 0.00 36.99 4.16
227 228 1.357334 CCGTTTGTTTGGGTCGGTG 59.643 57.895 0.00 0.00 36.99 4.94
228 229 2.483197 GCCGTTTGTTTGGGTCGGT 61.483 57.895 0.00 0.00 42.62 4.69
229 230 2.333581 GCCGTTTGTTTGGGTCGG 59.666 61.111 0.00 0.00 43.37 4.79
230 231 2.051703 CGCCGTTTGTTTGGGTCG 60.052 61.111 0.00 0.00 0.00 4.79
231 232 2.333581 CCGCCGTTTGTTTGGGTC 59.666 61.111 0.00 0.00 0.00 4.46
232 233 3.906879 GCCGCCGTTTGTTTGGGT 61.907 61.111 0.00 0.00 0.00 4.51
233 234 4.992294 CGCCGCCGTTTGTTTGGG 62.992 66.667 0.00 0.00 0.00 4.12
234 235 4.992294 CCGCCGCCGTTTGTTTGG 62.992 66.667 0.00 0.00 0.00 3.28
235 236 3.955101 TCCGCCGCCGTTTGTTTG 61.955 61.111 0.00 0.00 0.00 2.93
236 237 3.956317 GTCCGCCGCCGTTTGTTT 61.956 61.111 0.00 0.00 0.00 2.83
245 246 2.882366 GATCCATTTCGTCCGCCGC 61.882 63.158 0.00 0.00 36.19 6.53
246 247 2.585869 CGATCCATTTCGTCCGCCG 61.586 63.158 0.00 0.00 34.46 6.46
247 248 3.319904 CGATCCATTTCGTCCGCC 58.680 61.111 0.00 0.00 34.46 6.13
261 262 5.674607 AAGAGCAACTTCAACGGGACGAT 62.675 47.826 0.00 0.00 46.18 3.73
262 263 4.430058 AAGAGCAACTTCAACGGGACGA 62.430 50.000 0.00 0.00 46.18 4.20
264 265 1.594331 AAGAGCAACTTCAACGGGAC 58.406 50.000 0.00 0.00 32.91 4.46
265 266 3.695830 ATAAGAGCAACTTCAACGGGA 57.304 42.857 0.00 0.00 39.72 5.14
266 267 7.576236 CATAATATAAGAGCAACTTCAACGGG 58.424 38.462 0.00 0.00 39.72 5.28
267 268 7.072030 GCATAATATAAGAGCAACTTCAACGG 58.928 38.462 0.00 0.00 39.72 4.44
268 269 7.072030 GGCATAATATAAGAGCAACTTCAACG 58.928 38.462 0.00 0.00 39.72 4.10
269 270 7.229506 AGGGCATAATATAAGAGCAACTTCAAC 59.770 37.037 0.00 0.00 39.72 3.18
270 271 7.290061 AGGGCATAATATAAGAGCAACTTCAA 58.710 34.615 0.00 0.00 39.72 2.69
271 272 6.841601 AGGGCATAATATAAGAGCAACTTCA 58.158 36.000 0.00 0.00 39.72 3.02
272 273 6.091441 CGAGGGCATAATATAAGAGCAACTTC 59.909 42.308 0.00 0.00 39.72 3.01
273 274 5.934625 CGAGGGCATAATATAAGAGCAACTT 59.065 40.000 2.10 2.10 42.04 2.66
274 275 5.482908 CGAGGGCATAATATAAGAGCAACT 58.517 41.667 0.00 0.00 0.00 3.16
275 276 4.631813 CCGAGGGCATAATATAAGAGCAAC 59.368 45.833 0.00 0.00 0.00 4.17
276 277 4.530553 TCCGAGGGCATAATATAAGAGCAA 59.469 41.667 0.00 0.00 0.00 3.91
277 278 4.093743 TCCGAGGGCATAATATAAGAGCA 58.906 43.478 0.00 0.00 0.00 4.26
278 279 4.160626 ACTCCGAGGGCATAATATAAGAGC 59.839 45.833 0.00 0.00 0.00 4.09
279 280 5.419155 TGACTCCGAGGGCATAATATAAGAG 59.581 44.000 0.00 0.00 0.00 2.85
284 285 4.974645 TTTGACTCCGAGGGCATAATAT 57.025 40.909 0.00 0.00 0.00 1.28
321 323 2.675423 TCCGGTGGTGGAGACGAG 60.675 66.667 0.00 0.00 33.05 4.18
334 336 3.537874 GGAGATGGGACGGTCCGG 61.538 72.222 20.35 0.00 37.43 5.14
406 409 2.696893 GCAGGGTAGAGGAGGGGA 59.303 66.667 0.00 0.00 0.00 4.81
413 416 4.514577 CACGGCGGCAGGGTAGAG 62.515 72.222 13.24 0.00 0.00 2.43
483 486 1.448540 CTTACTGGGAGCCGCTGTG 60.449 63.158 0.00 0.00 31.85 3.66
526 535 2.764010 GTGGGTATTGGGATTTGGGAAC 59.236 50.000 0.00 0.00 0.00 3.62
527 536 2.292587 GGTGGGTATTGGGATTTGGGAA 60.293 50.000 0.00 0.00 0.00 3.97
554 563 0.970427 GGGATGCGGATGGGTTTGTT 60.970 55.000 0.00 0.00 0.00 2.83
631 641 2.195123 GAAATTGTGGACGGGGTGCG 62.195 60.000 0.00 0.00 0.00 5.34
692 702 1.153229 GCGGGTGGGGTTTAGCTAG 60.153 63.158 0.00 0.00 0.00 3.42
709 719 2.247637 GTACCCAAAAATTTCTCGCGC 58.752 47.619 0.00 0.00 0.00 6.86
749 759 1.542108 GCAGATCTAGATGGTGTGCCC 60.542 57.143 10.74 0.00 0.00 5.36
920 938 0.589223 GATCGACCGCACCAAAAACA 59.411 50.000 0.00 0.00 0.00 2.83
922 940 0.600518 TCGATCGACCGCACCAAAAA 60.601 50.000 15.15 0.00 0.00 1.94
1054 1073 2.731976 GCACAACGAGGAGAACTAACAG 59.268 50.000 0.00 0.00 0.00 3.16
1449 1578 5.846203 AGTTACAATCTGCAAAGCAACAAT 58.154 33.333 0.00 0.00 38.41 2.71
1483 1612 4.381612 CGTTTCTCATCTGCTACCCACTTA 60.382 45.833 0.00 0.00 0.00 2.24
1546 1675 3.320541 TCATTCGACAAGCCCACATTTTT 59.679 39.130 0.00 0.00 0.00 1.94
1579 1708 6.183360 ACCGGTAACTCTCATAGAAGAAATCC 60.183 42.308 4.49 0.00 0.00 3.01
1811 1940 3.523564 ACATCTGGGCTGTATTTACCACT 59.476 43.478 0.00 0.00 0.00 4.00
1984 2113 4.051922 GCAACGCATAGCTAGTTACTGAT 58.948 43.478 0.00 0.00 0.00 2.90
2020 2149 8.160765 TGGAAATACTTCTTCAGGAATGTTACA 58.839 33.333 0.00 0.00 33.01 2.41
2382 2511 4.098914 ACCTGAGTTCCATTTACAGCAA 57.901 40.909 0.00 0.00 0.00 3.91
2452 2581 7.101652 AGCTCTGAAAGTACGATTTGAGATA 57.898 36.000 15.42 0.00 32.98 1.98
2566 2695 6.889722 AGAAAAATGCCCTTACTGCAGTATAA 59.110 34.615 26.54 14.20 42.92 0.98
2615 2749 0.886490 CAGACCACCAGCAGGAACAC 60.886 60.000 0.35 0.00 38.69 3.32
2714 2848 5.223449 TCTTGACACCTTTAACCACCTAG 57.777 43.478 0.00 0.00 0.00 3.02
2726 2860 5.627182 AGAATGCTATCATCTTGACACCT 57.373 39.130 0.00 0.00 31.27 4.00
2764 2898 5.013079 TCTGAAACAGGGCTAAGATCTGAAA 59.987 40.000 0.00 0.00 33.19 2.69
2769 2903 3.055094 TGGTCTGAAACAGGGCTAAGATC 60.055 47.826 0.00 0.00 31.51 2.75
2780 2920 0.684535 TCCGCATCTGGTCTGAAACA 59.315 50.000 0.00 0.00 0.00 2.83
2836 2978 2.561037 GGTTTGACGTGCCTTGGGG 61.561 63.158 0.00 0.00 0.00 4.96
2837 2979 1.106944 AAGGTTTGACGTGCCTTGGG 61.107 55.000 0.00 0.00 40.71 4.12
2838 2980 0.744281 AAAGGTTTGACGTGCCTTGG 59.256 50.000 0.00 0.00 41.31 3.61
2839 2981 2.577449 AAAAGGTTTGACGTGCCTTG 57.423 45.000 0.00 0.00 41.31 3.61
2840 2982 2.758423 AGAAAAAGGTTTGACGTGCCTT 59.242 40.909 0.00 0.00 43.75 4.35
2841 2983 2.375146 AGAAAAAGGTTTGACGTGCCT 58.625 42.857 0.00 0.00 0.00 4.75
2842 2984 2.863401 AGAAAAAGGTTTGACGTGCC 57.137 45.000 0.00 0.00 0.00 5.01
2883 3028 3.573538 TGCTGCACATTGTAAACTGGAAT 59.426 39.130 0.00 0.00 0.00 3.01
2997 3147 3.852578 AGTGATAAGAGGTTTGGGGACAT 59.147 43.478 0.00 0.00 42.32 3.06
2999 3149 3.009143 ACAGTGATAAGAGGTTTGGGGAC 59.991 47.826 0.00 0.00 0.00 4.46
3105 3255 1.133668 ACCTATGATTGGAGCAAGCCC 60.134 52.381 0.00 0.00 0.00 5.19
3160 3310 4.655963 TCATCCTTCTCCTCAAAAACTGG 58.344 43.478 0.00 0.00 0.00 4.00
3169 3319 7.334858 ACTATGTTCTTTTCATCCTTCTCCTC 58.665 38.462 0.00 0.00 0.00 3.71
3262 3413 1.869767 GCAATCTGAACCGAGCTATGG 59.130 52.381 2.94 2.94 0.00 2.74
3323 3478 9.016623 GTACAGAAAAATAAAAGCTTCAACGTT 57.983 29.630 0.00 0.00 0.00 3.99
3346 3501 7.014615 TCCGAGGGAGTACCATTTTTATAGTAC 59.985 40.741 0.00 0.00 43.89 2.73
3467 3622 6.741992 TCATATAGCACTTTGGTCAAACTG 57.258 37.500 0.00 0.00 0.00 3.16
3495 3650 9.326413 ACAAAAAGAAGGATCCACGTTATATAG 57.674 33.333 15.82 0.00 0.00 1.31
3527 3687 3.575965 AAAGCTCCACTTTTTATGCGG 57.424 42.857 0.00 0.00 46.73 5.69


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

AutoCloner maintained by Alex Coulton.