Multiple sequence alignment - TraesCS2A01G283400

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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 TraesCS2A01G283400 chr2A 100.000 2311 0 0 1 2311 474797967 474795657 0.000000e+00 4268.0
1 TraesCS2A01G283400 chr2A 86.751 317 28 6 14 316 68540056 68540372 7.910000e-90 340.0
2 TraesCS2A01G283400 chr2A 82.609 115 17 2 316 428 775020139 775020026 5.250000e-17 99.0
3 TraesCS2A01G283400 chr2D 97.357 681 16 2 1631 2311 354968203 354967525 0.000000e+00 1157.0
4 TraesCS2A01G283400 chr2D 96.104 539 21 0 316 854 354983359 354982821 0.000000e+00 880.0
5 TraesCS2A01G283400 chr2D 92.549 510 30 4 969 1474 354968706 354968201 0.000000e+00 725.0
6 TraesCS2A01G283400 chr2D 86.349 315 31 3 14 316 378278940 378279254 1.320000e-87 333.0
7 TraesCS2A01G283400 chr2D 96.386 83 3 0 894 976 354968813 354968731 1.110000e-28 137.0
8 TraesCS2A01G283400 chr2D 86.667 75 8 2 316 388 649813948 649814022 5.290000e-12 82.4
9 TraesCS2A01G283400 chr2B 93.274 669 34 6 1649 2311 422509293 422508630 0.000000e+00 976.0
10 TraesCS2A01G283400 chr2B 92.157 561 33 5 316 875 422510565 422510015 0.000000e+00 782.0
11 TraesCS2A01G283400 chr2B 89.605 481 23 15 1170 1650 422509796 422509343 9.200000e-164 586.0
12 TraesCS2A01G283400 chr2B 86.239 327 25 7 1 319 52118206 52118520 1.020000e-88 337.0
13 TraesCS2A01G283400 chr2B 91.736 242 13 2 888 1122 422510035 422509794 1.710000e-86 329.0
14 TraesCS2A01G283400 chr7D 92.945 326 13 1 1 316 370161945 370162270 1.250000e-127 466.0
15 TraesCS2A01G283400 chr7D 89.508 305 30 2 14 316 99194032 99193728 3.600000e-103 385.0
16 TraesCS2A01G283400 chr7D 85.580 319 35 5 14 321 541276894 541277212 7.960000e-85 324.0
17 TraesCS2A01G283400 chr6D 90.879 307 24 4 14 318 300294643 300294947 2.140000e-110 409.0
18 TraesCS2A01G283400 chr4A 87.025 316 26 6 14 316 95193657 95193970 2.200000e-90 342.0
19 TraesCS2A01G283400 chr7A 86.799 303 29 2 25 316 641983604 641983906 6.160000e-86 327.0
20 TraesCS2A01G283400 chr3A 85.161 310 36 9 14 318 143545625 143545321 2.230000e-80 309.0
21 TraesCS2A01G283400 chr3A 77.586 116 18 8 360 472 431130634 431130524 1.920000e-06 63.9
22 TraesCS2A01G283400 chr5B 78.363 171 27 5 315 481 45224085 45224249 4.060000e-18 102.0
23 TraesCS2A01G283400 chr3D 78.571 140 23 6 346 481 571508046 571507910 4.090000e-13 86.1
24 TraesCS2A01G283400 chr6A 84.375 64 10 0 325 388 106898518 106898581 1.920000e-06 63.9


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 TraesCS2A01G283400 chr2A 474795657 474797967 2310 True 4268.00 4268 100.000000 1 2311 1 chr2A.!!$R1 2310
1 TraesCS2A01G283400 chr2D 354982821 354983359 538 True 880.00 880 96.104000 316 854 1 chr2D.!!$R1 538
2 TraesCS2A01G283400 chr2D 354967525 354968813 1288 True 673.00 1157 95.430667 894 2311 3 chr2D.!!$R2 1417
3 TraesCS2A01G283400 chr2B 422508630 422510565 1935 True 668.25 976 91.693000 316 2311 4 chr2B.!!$R1 1995

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
291 292 0.028374 CGTTTTGCGGGTCGAGTTTT 59.972 50.0 0.0 0.0 36.85 2.43 F
294 295 0.248702 TTTGCGGGTCGAGTTTTTGC 60.249 50.0 0.0 0.0 0.00 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1166 1254 0.035317 TCACCTGCACAGTGATCACC 59.965 55.0 22.21 7.53 0.0 4.02 R
1910 2064 0.318360 TGTCGTACAACAGTGCTCGG 60.318 55.0 0.00 0.00 0.0 4.63 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
19 20 0.827368 ATTGAGCGTCCTTCTCCTCC 59.173 55.000 0.00 0.00 0.00 4.30
20 21 0.541998 TTGAGCGTCCTTCTCCTCCA 60.542 55.000 0.00 0.00 0.00 3.86
21 22 1.251527 TGAGCGTCCTTCTCCTCCAC 61.252 60.000 0.00 0.00 0.00 4.02
22 23 2.182030 GCGTCCTTCTCCTCCACG 59.818 66.667 0.00 0.00 0.00 4.94
23 24 2.885861 CGTCCTTCTCCTCCACGG 59.114 66.667 0.00 0.00 0.00 4.94
24 25 2.579738 GTCCTTCTCCTCCACGGC 59.420 66.667 0.00 0.00 0.00 5.68
25 26 3.068691 TCCTTCTCCTCCACGGCG 61.069 66.667 4.80 4.80 0.00 6.46
26 27 3.382832 CCTTCTCCTCCACGGCGT 61.383 66.667 6.77 6.77 0.00 5.68
27 28 2.182030 CTTCTCCTCCACGGCGTC 59.818 66.667 10.85 0.00 0.00 5.19
28 29 3.685214 CTTCTCCTCCACGGCGTCG 62.685 68.421 10.85 8.42 43.02 5.12
45 46 3.890674 GTCCATGGACGCAACCTC 58.109 61.111 28.52 3.94 35.30 3.85
46 47 2.100631 GTCCATGGACGCAACCTCG 61.101 63.158 28.52 0.00 35.30 4.63
47 48 3.499737 CCATGGACGCAACCTCGC 61.500 66.667 5.56 0.00 0.00 5.03
48 49 3.499737 CATGGACGCAACCTCGCC 61.500 66.667 0.00 0.00 0.00 5.54
59 60 4.933064 CCTCGCCGCCGTCAGATC 62.933 72.222 0.00 0.00 35.54 2.75
60 61 4.933064 CTCGCCGCCGTCAGATCC 62.933 72.222 0.00 0.00 35.54 3.36
64 65 4.530857 CCGCCGTCAGATCCCCAC 62.531 72.222 0.00 0.00 0.00 4.61
65 66 4.530857 CGCCGTCAGATCCCCACC 62.531 72.222 0.00 0.00 0.00 4.61
66 67 4.176752 GCCGTCAGATCCCCACCC 62.177 72.222 0.00 0.00 0.00 4.61
67 68 3.480133 CCGTCAGATCCCCACCCC 61.480 72.222 0.00 0.00 0.00 4.95
68 69 2.365635 CGTCAGATCCCCACCCCT 60.366 66.667 0.00 0.00 0.00 4.79
69 70 2.435693 CGTCAGATCCCCACCCCTC 61.436 68.421 0.00 0.00 0.00 4.30
70 71 1.003573 GTCAGATCCCCACCCCTCT 59.996 63.158 0.00 0.00 0.00 3.69
71 72 0.264955 GTCAGATCCCCACCCCTCTA 59.735 60.000 0.00 0.00 0.00 2.43
72 73 0.563173 TCAGATCCCCACCCCTCTAG 59.437 60.000 0.00 0.00 0.00 2.43
73 74 0.266152 CAGATCCCCACCCCTCTAGT 59.734 60.000 0.00 0.00 0.00 2.57
74 75 1.503784 CAGATCCCCACCCCTCTAGTA 59.496 57.143 0.00 0.00 0.00 1.82
75 76 1.504221 AGATCCCCACCCCTCTAGTAC 59.496 57.143 0.00 0.00 0.00 2.73
76 77 1.504221 GATCCCCACCCCTCTAGTACT 59.496 57.143 0.00 0.00 0.00 2.73
77 78 2.308722 TCCCCACCCCTCTAGTACTA 57.691 55.000 1.89 1.89 0.00 1.82
78 79 2.141911 TCCCCACCCCTCTAGTACTAG 58.858 57.143 21.87 21.87 34.56 2.57
79 80 1.858246 CCCCACCCCTCTAGTACTAGT 59.142 57.143 25.58 7.73 34.84 2.57
80 81 3.059097 CCCCACCCCTCTAGTACTAGTA 58.941 54.545 25.58 13.72 34.84 1.82
81 82 3.661654 CCCCACCCCTCTAGTACTAGTAT 59.338 52.174 25.58 8.53 34.84 2.12
82 83 4.107636 CCCCACCCCTCTAGTACTAGTATT 59.892 50.000 25.58 4.37 34.84 1.89
83 84 5.314306 CCCCACCCCTCTAGTACTAGTATTA 59.686 48.000 25.58 5.41 34.84 0.98
84 85 6.183361 CCCCACCCCTCTAGTACTAGTATTAA 60.183 46.154 25.58 8.61 34.84 1.40
85 86 6.718912 CCCACCCCTCTAGTACTAGTATTAAC 59.281 46.154 25.58 0.00 34.84 2.01
86 87 6.429385 CCACCCCTCTAGTACTAGTATTAACG 59.571 46.154 25.58 12.27 34.84 3.18
87 88 6.995091 CACCCCTCTAGTACTAGTATTAACGT 59.005 42.308 25.58 12.92 34.84 3.99
88 89 8.150945 CACCCCTCTAGTACTAGTATTAACGTA 58.849 40.741 25.58 6.00 34.84 3.57
89 90 8.371699 ACCCCTCTAGTACTAGTATTAACGTAG 58.628 40.741 25.58 13.97 34.84 3.51
90 91 8.371699 CCCCTCTAGTACTAGTATTAACGTAGT 58.628 40.741 25.58 0.00 37.01 2.73
121 122 9.772973 AGTATGAACTATGTTTGTAGTGTTTGA 57.227 29.630 0.00 0.00 35.20 2.69
124 125 8.902540 TGAACTATGTTTGTAGTGTTTGATCT 57.097 30.769 0.00 0.00 35.20 2.75
125 126 9.990360 TGAACTATGTTTGTAGTGTTTGATCTA 57.010 29.630 0.00 0.00 35.20 1.98
128 129 9.944376 ACTATGTTTGTAGTGTTTGATCTATGT 57.056 29.630 0.00 0.00 33.78 2.29
131 132 9.944376 ATGTTTGTAGTGTTTGATCTATGTAGT 57.056 29.630 0.00 0.00 0.00 2.73
139 140 9.755804 AGTGTTTGATCTATGTAGTATGTGATG 57.244 33.333 0.00 0.00 0.00 3.07
140 141 9.750125 GTGTTTGATCTATGTAGTATGTGATGA 57.250 33.333 0.00 0.00 0.00 2.92
148 149 8.989980 TCTATGTAGTATGTGATGAACTACTCG 58.010 37.037 11.78 2.91 43.81 4.18
149 150 6.997239 TGTAGTATGTGATGAACTACTCGT 57.003 37.500 11.78 0.00 43.81 4.18
150 151 6.782150 TGTAGTATGTGATGAACTACTCGTG 58.218 40.000 11.78 0.00 43.81 4.35
151 152 5.899120 AGTATGTGATGAACTACTCGTGT 57.101 39.130 0.00 0.00 0.00 4.49
152 153 5.881447 AGTATGTGATGAACTACTCGTGTC 58.119 41.667 0.00 0.00 0.00 3.67
153 154 4.783764 ATGTGATGAACTACTCGTGTCA 57.216 40.909 0.00 0.00 0.00 3.58
154 155 4.577834 TGTGATGAACTACTCGTGTCAA 57.422 40.909 0.00 0.00 0.00 3.18
155 156 4.295870 TGTGATGAACTACTCGTGTCAAC 58.704 43.478 0.00 0.00 0.00 3.18
171 172 6.149504 GTGTCAACGAGGTACAATTTCTAC 57.850 41.667 0.00 0.00 0.00 2.59
172 173 5.119743 GTGTCAACGAGGTACAATTTCTACC 59.880 44.000 0.00 1.98 34.81 3.18
173 174 4.325472 GTCAACGAGGTACAATTTCTACCG 59.675 45.833 0.00 0.00 39.03 4.02
174 175 2.884827 ACGAGGTACAATTTCTACCGC 58.115 47.619 0.00 3.97 39.03 5.68
175 176 1.850441 CGAGGTACAATTTCTACCGCG 59.150 52.381 16.13 16.13 46.48 6.46
176 177 3.155093 GAGGTACAATTTCTACCGCGA 57.845 47.619 8.23 0.00 39.03 5.87
177 178 3.514645 GAGGTACAATTTCTACCGCGAA 58.485 45.455 8.23 0.00 39.03 4.70
178 179 3.928375 GAGGTACAATTTCTACCGCGAAA 59.072 43.478 8.23 0.00 39.03 3.46
179 180 3.930848 AGGTACAATTTCTACCGCGAAAG 59.069 43.478 8.23 4.18 39.03 2.62
180 181 3.681417 GGTACAATTTCTACCGCGAAAGT 59.319 43.478 8.23 0.00 36.44 2.66
182 183 3.806316 CAATTTCTACCGCGAAAGTGT 57.194 42.857 8.23 0.00 41.46 3.55
183 184 4.141855 CAATTTCTACCGCGAAAGTGTT 57.858 40.909 8.23 0.00 41.46 3.32
184 185 4.533222 CAATTTCTACCGCGAAAGTGTTT 58.467 39.130 8.23 0.00 41.46 2.83
185 186 4.823790 ATTTCTACCGCGAAAGTGTTTT 57.176 36.364 8.23 0.00 40.80 2.43
186 187 4.619437 TTTCTACCGCGAAAGTGTTTTT 57.381 36.364 8.23 0.00 40.80 1.94
211 212 9.781834 TTTCAAATTATGCAGTTTTAGATACGG 57.218 29.630 0.00 0.00 0.00 4.02
212 213 8.500753 TCAAATTATGCAGTTTTAGATACGGT 57.499 30.769 0.00 0.00 0.00 4.83
213 214 8.952278 TCAAATTATGCAGTTTTAGATACGGTT 58.048 29.630 0.00 0.00 0.00 4.44
214 215 9.567848 CAAATTATGCAGTTTTAGATACGGTTT 57.432 29.630 0.00 0.00 0.00 3.27
215 216 9.783256 AAATTATGCAGTTTTAGATACGGTTTC 57.217 29.630 0.00 0.00 0.00 2.78
216 217 8.732746 ATTATGCAGTTTTAGATACGGTTTCT 57.267 30.769 6.36 6.36 0.00 2.52
217 218 5.856126 TGCAGTTTTAGATACGGTTTCTG 57.144 39.130 10.80 0.00 0.00 3.02
218 219 5.302360 TGCAGTTTTAGATACGGTTTCTGT 58.698 37.500 10.80 0.00 0.00 3.41
219 220 5.761234 TGCAGTTTTAGATACGGTTTCTGTT 59.239 36.000 10.80 0.00 0.00 3.16
220 221 6.073440 TGCAGTTTTAGATACGGTTTCTGTTC 60.073 38.462 10.80 0.86 0.00 3.18
221 222 6.522761 CAGTTTTAGATACGGTTTCTGTTCG 58.477 40.000 10.80 0.00 0.00 3.95
222 223 5.636543 AGTTTTAGATACGGTTTCTGTTCGG 59.363 40.000 10.80 0.00 0.00 4.30
223 224 2.005971 AGATACGGTTTCTGTTCGGC 57.994 50.000 0.07 0.00 0.00 5.54
224 225 1.004595 GATACGGTTTCTGTTCGGCC 58.995 55.000 0.00 0.00 0.00 6.13
225 226 0.738412 ATACGGTTTCTGTTCGGCCG 60.738 55.000 22.12 22.12 46.83 6.13
226 227 4.084888 CGGTTTCTGTTCGGCCGC 62.085 66.667 23.51 8.29 35.90 6.53
227 228 4.084888 GGTTTCTGTTCGGCCGCG 62.085 66.667 23.51 8.82 0.00 6.46
228 229 4.736631 GTTTCTGTTCGGCCGCGC 62.737 66.667 23.51 16.17 0.00 6.86
229 230 4.980805 TTTCTGTTCGGCCGCGCT 62.981 61.111 23.51 0.00 0.00 5.92
230 231 3.576932 TTTCTGTTCGGCCGCGCTA 62.577 57.895 23.51 0.00 0.00 4.26
231 232 3.982372 TTCTGTTCGGCCGCGCTAG 62.982 63.158 23.51 15.68 0.00 3.42
232 233 4.796231 CTGTTCGGCCGCGCTAGT 62.796 66.667 23.51 0.00 0.00 2.57
233 234 4.367023 TGTTCGGCCGCGCTAGTT 62.367 61.111 23.51 0.00 0.00 2.24
234 235 3.116531 GTTCGGCCGCGCTAGTTT 61.117 61.111 23.51 0.00 0.00 2.66
235 236 2.357760 TTCGGCCGCGCTAGTTTT 60.358 55.556 23.51 0.00 0.00 2.43
236 237 2.385091 TTCGGCCGCGCTAGTTTTC 61.385 57.895 23.51 0.00 0.00 2.29
237 238 4.204891 CGGCCGCGCTAGTTTTCG 62.205 66.667 14.67 0.00 0.00 3.46
238 239 2.812178 GGCCGCGCTAGTTTTCGA 60.812 61.111 5.56 0.00 0.00 3.71
239 240 2.394524 GCCGCGCTAGTTTTCGAC 59.605 61.111 5.56 0.00 0.00 4.20
240 241 3.078560 CCGCGCTAGTTTTCGACC 58.921 61.111 5.56 0.00 0.00 4.79
241 242 2.450345 CCGCGCTAGTTTTCGACCC 61.450 63.158 5.56 0.00 0.00 4.46
242 243 2.785105 CGCGCTAGTTTTCGACCCG 61.785 63.158 5.56 0.00 0.00 5.28
243 244 3.078560 CGCTAGTTTTCGACCCGC 58.921 61.111 0.00 0.00 0.00 6.13
244 245 1.735198 CGCTAGTTTTCGACCCGCA 60.735 57.895 0.00 0.00 0.00 5.69
245 246 1.286354 CGCTAGTTTTCGACCCGCAA 61.286 55.000 0.00 0.00 0.00 4.85
246 247 0.869730 GCTAGTTTTCGACCCGCAAA 59.130 50.000 0.00 0.00 0.00 3.68
247 248 1.467342 GCTAGTTTTCGACCCGCAAAT 59.533 47.619 0.00 0.00 0.00 2.32
248 249 2.727916 GCTAGTTTTCGACCCGCAAATG 60.728 50.000 0.00 0.00 0.00 2.32
249 250 1.600023 AGTTTTCGACCCGCAAATGA 58.400 45.000 0.00 0.00 0.00 2.57
250 251 1.535462 AGTTTTCGACCCGCAAATGAG 59.465 47.619 0.00 0.00 0.00 2.90
251 252 1.533731 GTTTTCGACCCGCAAATGAGA 59.466 47.619 0.00 0.00 0.00 3.27
252 253 2.107950 TTTCGACCCGCAAATGAGAT 57.892 45.000 0.00 0.00 0.00 2.75
253 254 1.651987 TTCGACCCGCAAATGAGATC 58.348 50.000 0.00 0.00 0.00 2.75
254 255 0.824109 TCGACCCGCAAATGAGATCT 59.176 50.000 0.00 0.00 0.00 2.75
255 256 1.207089 TCGACCCGCAAATGAGATCTT 59.793 47.619 0.00 0.00 0.00 2.40
256 257 1.594862 CGACCCGCAAATGAGATCTTC 59.405 52.381 0.00 0.00 0.00 2.87
257 258 2.632377 GACCCGCAAATGAGATCTTCA 58.368 47.619 0.00 0.00 40.85 3.02
259 260 2.947652 ACCCGCAAATGAGATCTTCATG 59.052 45.455 0.00 0.00 45.82 3.07
260 261 3.208594 CCCGCAAATGAGATCTTCATGA 58.791 45.455 0.00 0.00 45.82 3.07
261 262 3.628942 CCCGCAAATGAGATCTTCATGAA 59.371 43.478 8.12 8.12 45.82 2.57
262 263 4.096833 CCCGCAAATGAGATCTTCATGAAA 59.903 41.667 9.88 1.39 45.82 2.69
263 264 5.032863 CCGCAAATGAGATCTTCATGAAAC 58.967 41.667 9.88 4.43 45.82 2.78
264 265 5.163683 CCGCAAATGAGATCTTCATGAAACT 60.164 40.000 9.88 9.08 45.82 2.66
265 266 5.737757 CGCAAATGAGATCTTCATGAAACTG 59.262 40.000 9.88 0.00 45.82 3.16
266 267 5.515626 GCAAATGAGATCTTCATGAAACTGC 59.484 40.000 9.88 3.21 45.82 4.40
267 268 6.617879 CAAATGAGATCTTCATGAAACTGCA 58.382 36.000 9.88 5.06 45.82 4.41
268 269 6.829229 AATGAGATCTTCATGAAACTGCAA 57.171 33.333 9.88 0.00 45.82 4.08
269 270 6.829229 ATGAGATCTTCATGAAACTGCAAA 57.171 33.333 9.88 0.00 44.84 3.68
270 271 6.005583 TGAGATCTTCATGAAACTGCAAAC 57.994 37.500 9.88 0.00 0.00 2.93
271 272 5.039480 AGATCTTCATGAAACTGCAAACG 57.961 39.130 9.88 0.00 0.00 3.60
272 273 2.998772 TCTTCATGAAACTGCAAACGC 58.001 42.857 9.88 0.00 0.00 4.84
273 274 1.710249 CTTCATGAAACTGCAAACGCG 59.290 47.619 9.88 3.53 0.00 6.01
274 275 0.660488 TCATGAAACTGCAAACGCGT 59.340 45.000 5.58 5.58 0.00 6.01
275 276 1.064803 TCATGAAACTGCAAACGCGTT 59.935 42.857 20.79 20.79 0.00 4.84
276 277 1.851666 CATGAAACTGCAAACGCGTTT 59.148 42.857 30.36 30.36 38.17 3.60
277 278 1.983972 TGAAACTGCAAACGCGTTTT 58.016 40.000 33.05 18.69 36.75 2.43
278 279 1.651138 TGAAACTGCAAACGCGTTTTG 59.349 42.857 33.05 26.38 46.57 2.44
288 289 3.343421 GCGTTTTGCGGGTCGAGT 61.343 61.111 0.00 0.00 41.69 4.18
289 290 2.888998 GCGTTTTGCGGGTCGAGTT 61.889 57.895 0.00 0.00 41.69 3.01
290 291 1.644913 CGTTTTGCGGGTCGAGTTT 59.355 52.632 0.00 0.00 36.85 2.66
291 292 0.028374 CGTTTTGCGGGTCGAGTTTT 59.972 50.000 0.00 0.00 36.85 2.43
292 293 1.532298 CGTTTTGCGGGTCGAGTTTTT 60.532 47.619 0.00 0.00 36.85 1.94
293 294 1.849829 GTTTTGCGGGTCGAGTTTTTG 59.150 47.619 0.00 0.00 0.00 2.44
294 295 0.248702 TTTGCGGGTCGAGTTTTTGC 60.249 50.000 0.00 0.00 0.00 3.68
295 296 1.377366 TTGCGGGTCGAGTTTTTGCA 61.377 50.000 0.00 0.00 0.00 4.08
296 297 1.082104 GCGGGTCGAGTTTTTGCAG 60.082 57.895 0.00 0.00 0.00 4.41
297 298 1.574428 CGGGTCGAGTTTTTGCAGG 59.426 57.895 0.00 0.00 0.00 4.85
298 299 1.852067 CGGGTCGAGTTTTTGCAGGG 61.852 60.000 0.00 0.00 0.00 4.45
299 300 0.822121 GGGTCGAGTTTTTGCAGGGT 60.822 55.000 0.00 0.00 0.00 4.34
300 301 0.591659 GGTCGAGTTTTTGCAGGGTC 59.408 55.000 0.00 0.00 0.00 4.46
301 302 1.594331 GTCGAGTTTTTGCAGGGTCT 58.406 50.000 0.00 0.00 0.00 3.85
302 303 1.264288 GTCGAGTTTTTGCAGGGTCTG 59.736 52.381 0.00 0.00 34.12 3.51
312 313 3.450028 CAGGGTCTGCTAGAGTTGC 57.550 57.895 0.00 0.00 0.00 4.17
313 314 0.901124 CAGGGTCTGCTAGAGTTGCT 59.099 55.000 0.00 0.00 0.00 3.91
314 315 1.134848 CAGGGTCTGCTAGAGTTGCTC 60.135 57.143 0.00 0.00 0.00 4.26
332 333 2.628657 GCTCTAAGGATATCACGGGTGT 59.371 50.000 4.83 0.00 0.00 4.16
343 344 1.140052 TCACGGGTGTCACTGTTTCAT 59.860 47.619 2.35 0.00 0.00 2.57
535 537 5.526479 TCAGATCTTATCACATTTGAGCTGC 59.474 40.000 0.00 0.00 39.90 5.25
593 595 6.812656 TCGCTATTTCGGTTATTGTTTACTGA 59.187 34.615 0.00 0.00 0.00 3.41
613 615 0.587768 TGTGAACTGAGCAATGCACG 59.412 50.000 8.35 0.45 0.00 5.34
662 664 7.934855 AAGTGCATATCTCAGAAAAGAATGT 57.065 32.000 0.00 0.00 0.00 2.71
691 693 4.982241 ATTCCATCCAAGGACACGATAT 57.018 40.909 0.00 0.00 37.42 1.63
767 769 8.882736 TGTAGTGCAAATCAAATGTGTCTATAG 58.117 33.333 0.00 0.00 0.00 1.31
854 856 9.157104 TCGTCATGAAGTGCACTAATTTATTTA 57.843 29.630 22.01 0.00 0.00 1.40
855 857 9.767684 CGTCATGAAGTGCACTAATTTATTTAA 57.232 29.630 22.01 0.00 0.00 1.52
884 886 3.846955 GAAGGATTCCCCGTTTCGA 57.153 52.632 0.00 0.00 39.83 3.71
885 887 2.103537 GAAGGATTCCCCGTTTCGAA 57.896 50.000 0.00 0.00 39.83 3.71
886 888 2.429478 GAAGGATTCCCCGTTTCGAAA 58.571 47.619 6.47 6.47 39.83 3.46
971 973 1.260561 CACACCGCACAAGTACAGAAC 59.739 52.381 0.00 0.00 0.00 3.01
1045 1079 1.302033 AGAGCAACGAGGCACAAGG 60.302 57.895 5.91 0.00 35.83 3.61
1118 1152 2.115910 CCAGGCAGGCAACAAGGA 59.884 61.111 0.00 0.00 41.41 3.36
1122 1210 0.323178 AGGCAGGCAACAAGGAGATG 60.323 55.000 0.00 0.00 41.41 2.90
1123 1211 1.509923 GCAGGCAACAAGGAGATGC 59.490 57.895 0.00 0.00 44.52 3.91
1126 1214 3.608432 GCAACAAGGAGATGCCCC 58.392 61.111 0.00 0.00 39.87 5.80
1127 1215 2.054453 GCAACAAGGAGATGCCCCC 61.054 63.158 0.00 0.00 39.87 5.40
1267 1355 1.343142 TGCCGCCTTGTACATATCGAT 59.657 47.619 2.16 2.16 0.00 3.59
1285 1373 4.704833 GGTGCAGGAGCGGCTCAA 62.705 66.667 29.33 10.59 46.23 3.02
1298 1398 3.570638 CTCAAGCGCGAGGGCATG 61.571 66.667 12.10 12.32 39.92 4.06
1342 1442 6.299805 AGGAATAAGTACACTGCTGATTCA 57.700 37.500 0.00 0.00 0.00 2.57
1354 1454 2.868583 TGCTGATTCATAGCGAGCTTTC 59.131 45.455 1.86 0.00 44.01 2.62
1392 1492 0.863144 GTGATGCCGTACGTGTGTTT 59.137 50.000 15.21 0.00 0.00 2.83
1404 1504 5.958372 CGTACGTGTGTTTTGTAAAATCACA 59.042 36.000 7.22 16.90 37.46 3.58
1463 1563 9.539825 TTAACATACAAAGTTACCAACGTCTAA 57.460 29.630 0.00 0.00 36.23 2.10
1464 1564 7.647907 ACATACAAAGTTACCAACGTCTAAG 57.352 36.000 0.00 0.00 36.23 2.18
1465 1565 7.436118 ACATACAAAGTTACCAACGTCTAAGA 58.564 34.615 0.00 0.00 36.23 2.10
1466 1566 8.092687 ACATACAAAGTTACCAACGTCTAAGAT 58.907 33.333 0.00 0.00 36.23 2.40
1467 1567 8.592998 CATACAAAGTTACCAACGTCTAAGATC 58.407 37.037 0.00 0.00 36.23 2.75
1468 1568 6.518493 ACAAAGTTACCAACGTCTAAGATCA 58.482 36.000 0.00 0.00 36.23 2.92
1469 1569 6.423001 ACAAAGTTACCAACGTCTAAGATCAC 59.577 38.462 0.00 0.00 36.23 3.06
1470 1570 4.730657 AGTTACCAACGTCTAAGATCACG 58.269 43.478 0.00 0.00 41.90 4.35
1471 1571 4.456911 AGTTACCAACGTCTAAGATCACGA 59.543 41.667 9.96 0.00 39.38 4.35
1479 1579 4.142116 ACGTCTAAGATCACGAGAGAGAGA 60.142 45.833 9.96 0.00 39.38 3.10
1494 1594 2.159128 AGAGAGACAGTCCATGCATTCG 60.159 50.000 0.00 0.00 0.00 3.34
1495 1595 1.134580 AGAGACAGTCCATGCATTCGG 60.135 52.381 0.00 0.00 0.00 4.30
1508 1608 2.355444 TGCATTCGGTAGCAATGTGATG 59.645 45.455 14.33 0.00 37.90 3.07
1509 1609 2.355756 GCATTCGGTAGCAATGTGATGT 59.644 45.455 14.33 0.00 34.27 3.06
1510 1610 3.789791 GCATTCGGTAGCAATGTGATGTG 60.790 47.826 14.33 0.00 34.27 3.21
1511 1611 3.326836 TTCGGTAGCAATGTGATGTGA 57.673 42.857 0.00 0.00 0.00 3.58
1512 1612 3.541996 TCGGTAGCAATGTGATGTGAT 57.458 42.857 0.00 0.00 0.00 3.06
1513 1613 3.457234 TCGGTAGCAATGTGATGTGATC 58.543 45.455 0.00 0.00 0.00 2.92
1514 1614 3.118811 TCGGTAGCAATGTGATGTGATCA 60.119 43.478 0.00 0.00 36.84 2.92
1519 1619 5.306532 AGCAATGTGATGTGATCAAAGAC 57.693 39.130 0.00 0.00 41.69 3.01
1555 1655 0.749454 CAGTGCCCTTAGTCATGCCC 60.749 60.000 0.00 0.00 0.00 5.36
1559 1659 0.837272 GCCCTTAGTCATGCCCAGTA 59.163 55.000 0.00 0.00 0.00 2.74
1560 1660 1.211949 GCCCTTAGTCATGCCCAGTAA 59.788 52.381 0.00 0.00 0.00 2.24
1571 1671 5.877012 GTCATGCCCAGTAATATGATGTAGG 59.123 44.000 0.00 0.00 32.76 3.18
1595 1695 4.974645 TGTCCTGAACCTCAGTAACAAT 57.025 40.909 3.15 0.00 42.80 2.71
1599 1699 6.605594 TGTCCTGAACCTCAGTAACAATTTTT 59.394 34.615 3.15 0.00 42.80 1.94
1788 1942 4.678509 TGAAATGAAGAACATGCGTACC 57.321 40.909 0.00 0.00 39.39 3.34
1910 2064 7.223582 TCAATCTCTATTCGCTCTCATTTTGAC 59.776 37.037 0.00 0.00 0.00 3.18
1915 2069 0.371645 CGCTCTCATTTTGACCGAGC 59.628 55.000 8.08 8.08 39.73 5.03
2081 2235 2.840038 TGATCTCCATGTACTGGCAACT 59.160 45.455 6.51 0.00 45.52 3.16
2156 2310 5.163754 GGGACAGAAAATAAGACACGGAATG 60.164 44.000 0.00 0.00 0.00 2.67
2163 2317 6.727824 AAATAAGACACGGAATGAGTTCTG 57.272 37.500 0.00 0.00 44.64 3.02
2292 2449 6.308766 GTGTTATGCAAGAAACCAACATGATC 59.691 38.462 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.827368 GGAGGAGAAGGACGCTCAAT 59.173 55.000 0.00 0.00 34.07 2.57
1 2 0.541998 TGGAGGAGAAGGACGCTCAA 60.542 55.000 0.00 0.00 34.07 3.02
2 3 1.076727 TGGAGGAGAAGGACGCTCA 59.923 57.895 0.00 0.00 34.07 4.26
3 4 1.513622 GTGGAGGAGAAGGACGCTC 59.486 63.158 0.00 0.00 0.00 5.03
4 5 2.344203 CGTGGAGGAGAAGGACGCT 61.344 63.158 0.00 0.00 0.00 5.07
5 6 2.182030 CGTGGAGGAGAAGGACGC 59.818 66.667 0.00 0.00 0.00 5.19
6 7 2.885861 CCGTGGAGGAGAAGGACG 59.114 66.667 0.00 0.00 45.00 4.79
7 8 2.579738 GCCGTGGAGGAGAAGGAC 59.420 66.667 0.00 0.00 45.00 3.85
8 9 3.068691 CGCCGTGGAGGAGAAGGA 61.069 66.667 0.00 0.00 43.02 3.36
9 10 3.358076 GACGCCGTGGAGGAGAAGG 62.358 68.421 0.00 0.00 43.02 3.46
10 11 2.182030 GACGCCGTGGAGGAGAAG 59.818 66.667 0.00 0.00 43.02 2.85
11 12 3.744719 CGACGCCGTGGAGGAGAA 61.745 66.667 0.00 0.00 43.02 2.87
28 29 2.100631 CGAGGTTGCGTCCATGGAC 61.101 63.158 31.59 31.59 41.40 4.02
29 30 2.264480 CGAGGTTGCGTCCATGGA 59.736 61.111 11.44 11.44 0.00 3.41
30 31 3.499737 GCGAGGTTGCGTCCATGG 61.500 66.667 4.97 4.97 0.00 3.66
31 32 3.499737 GGCGAGGTTGCGTCCATG 61.500 66.667 0.00 0.00 35.06 3.66
42 43 4.933064 GATCTGACGGCGGCGAGG 62.933 72.222 38.93 24.39 0.00 4.63
43 44 4.933064 GGATCTGACGGCGGCGAG 62.933 72.222 38.93 25.22 0.00 5.03
47 48 4.530857 GTGGGGATCTGACGGCGG 62.531 72.222 13.24 0.00 0.00 6.13
48 49 4.530857 GGTGGGGATCTGACGGCG 62.531 72.222 4.80 4.80 0.00 6.46
49 50 4.176752 GGGTGGGGATCTGACGGC 62.177 72.222 0.00 0.00 0.00 5.68
50 51 3.480133 GGGGTGGGGATCTGACGG 61.480 72.222 0.00 0.00 0.00 4.79
51 52 2.365635 AGGGGTGGGGATCTGACG 60.366 66.667 0.00 0.00 0.00 4.35
52 53 0.264955 TAGAGGGGTGGGGATCTGAC 59.735 60.000 0.00 0.00 0.00 3.51
53 54 0.563173 CTAGAGGGGTGGGGATCTGA 59.437 60.000 0.00 0.00 0.00 3.27
54 55 0.266152 ACTAGAGGGGTGGGGATCTG 59.734 60.000 0.00 0.00 0.00 2.90
55 56 1.504221 GTACTAGAGGGGTGGGGATCT 59.496 57.143 0.00 0.00 0.00 2.75
56 57 1.504221 AGTACTAGAGGGGTGGGGATC 59.496 57.143 0.00 0.00 0.00 3.36
57 58 1.634003 AGTACTAGAGGGGTGGGGAT 58.366 55.000 0.00 0.00 0.00 3.85
58 59 2.141911 CTAGTACTAGAGGGGTGGGGA 58.858 57.143 23.20 0.00 35.21 4.81
59 60 1.858246 ACTAGTACTAGAGGGGTGGGG 59.142 57.143 31.93 6.88 36.97 4.96
60 61 5.336491 AATACTAGTACTAGAGGGGTGGG 57.664 47.826 31.93 7.57 36.97 4.61
61 62 6.429385 CGTTAATACTAGTACTAGAGGGGTGG 59.571 46.154 31.93 14.37 36.97 4.61
62 63 6.995091 ACGTTAATACTAGTACTAGAGGGGTG 59.005 42.308 31.93 18.40 36.97 4.61
63 64 7.142995 ACGTTAATACTAGTACTAGAGGGGT 57.857 40.000 31.93 15.31 36.97 4.95
64 65 8.371699 ACTACGTTAATACTAGTACTAGAGGGG 58.628 40.741 31.93 17.03 36.97 4.79
95 96 9.772973 TCAAACACTACAAACATAGTTCATACT 57.227 29.630 0.00 0.00 32.92 2.12
98 99 9.507329 AGATCAAACACTACAAACATAGTTCAT 57.493 29.630 0.00 0.00 32.92 2.57
99 100 8.902540 AGATCAAACACTACAAACATAGTTCA 57.097 30.769 0.00 0.00 32.92 3.18
102 103 9.944376 ACATAGATCAAACACTACAAACATAGT 57.056 29.630 0.00 0.00 35.72 2.12
105 106 9.944376 ACTACATAGATCAAACACTACAAACAT 57.056 29.630 0.00 0.00 0.00 2.71
113 114 9.755804 CATCACATACTACATAGATCAAACACT 57.244 33.333 0.00 0.00 0.00 3.55
114 115 9.750125 TCATCACATACTACATAGATCAAACAC 57.250 33.333 0.00 0.00 0.00 3.32
122 123 8.989980 CGAGTAGTTCATCACATACTACATAGA 58.010 37.037 12.52 0.00 44.14 1.98
123 124 8.775527 ACGAGTAGTTCATCACATACTACATAG 58.224 37.037 12.52 6.83 44.14 2.23
124 125 8.557029 CACGAGTAGTTCATCACATACTACATA 58.443 37.037 12.52 0.00 44.14 2.29
125 126 7.067129 ACACGAGTAGTTCATCACATACTACAT 59.933 37.037 12.52 0.78 44.14 2.29
126 127 6.373495 ACACGAGTAGTTCATCACATACTACA 59.627 38.462 12.52 0.00 44.14 2.74
127 128 6.783162 ACACGAGTAGTTCATCACATACTAC 58.217 40.000 0.00 0.00 42.78 2.73
128 129 6.596497 TGACACGAGTAGTTCATCACATACTA 59.404 38.462 0.00 0.00 0.00 1.82
129 130 5.414765 TGACACGAGTAGTTCATCACATACT 59.585 40.000 0.00 0.00 0.00 2.12
130 131 5.637809 TGACACGAGTAGTTCATCACATAC 58.362 41.667 0.00 0.00 0.00 2.39
131 132 5.890424 TGACACGAGTAGTTCATCACATA 57.110 39.130 0.00 0.00 0.00 2.29
132 133 4.783764 TGACACGAGTAGTTCATCACAT 57.216 40.909 0.00 0.00 0.00 3.21
133 134 4.295870 GTTGACACGAGTAGTTCATCACA 58.704 43.478 0.00 0.00 0.00 3.58
134 135 4.887763 GTTGACACGAGTAGTTCATCAC 57.112 45.455 0.00 0.00 0.00 3.06
147 148 8.024681 GGTAGAAATTGTACCTCGTTGACACG 62.025 46.154 11.59 0.00 38.01 4.49
148 149 5.119743 GGTAGAAATTGTACCTCGTTGACAC 59.880 44.000 11.59 0.00 37.54 3.67
149 150 5.232463 GGTAGAAATTGTACCTCGTTGACA 58.768 41.667 11.59 0.00 37.54 3.58
150 151 4.325472 CGGTAGAAATTGTACCTCGTTGAC 59.675 45.833 15.91 0.00 38.27 3.18
151 152 4.487948 CGGTAGAAATTGTACCTCGTTGA 58.512 43.478 15.91 0.00 38.27 3.18
152 153 3.061697 GCGGTAGAAATTGTACCTCGTTG 59.938 47.826 15.91 2.98 38.27 4.10
153 154 3.256558 GCGGTAGAAATTGTACCTCGTT 58.743 45.455 15.91 0.00 38.27 3.85
154 155 2.733227 CGCGGTAGAAATTGTACCTCGT 60.733 50.000 19.35 0.00 41.66 4.18
155 156 1.850441 CGCGGTAGAAATTGTACCTCG 59.150 52.381 15.40 15.40 41.05 4.63
156 157 3.155093 TCGCGGTAGAAATTGTACCTC 57.845 47.619 15.91 8.27 38.27 3.85
157 158 3.598019 TTCGCGGTAGAAATTGTACCT 57.402 42.857 15.91 0.00 38.27 3.08
158 159 3.681417 ACTTTCGCGGTAGAAATTGTACC 59.319 43.478 6.13 9.08 39.13 3.34
159 160 4.151157 ACACTTTCGCGGTAGAAATTGTAC 59.849 41.667 6.13 0.00 45.64 2.90
160 161 4.309099 ACACTTTCGCGGTAGAAATTGTA 58.691 39.130 6.13 0.00 45.64 2.41
161 162 3.135994 ACACTTTCGCGGTAGAAATTGT 58.864 40.909 6.13 7.21 44.00 2.71
162 163 3.806316 ACACTTTCGCGGTAGAAATTG 57.194 42.857 6.13 6.54 42.63 2.32
163 164 4.823790 AAACACTTTCGCGGTAGAAATT 57.176 36.364 6.13 0.00 39.13 1.82
164 165 4.823790 AAAACACTTTCGCGGTAGAAAT 57.176 36.364 6.13 0.00 39.13 2.17
165 166 4.619437 AAAAACACTTTCGCGGTAGAAA 57.381 36.364 6.13 0.00 37.74 2.52
185 186 9.781834 CCGTATCTAAAACTGCATAATTTGAAA 57.218 29.630 0.00 0.00 0.00 2.69
186 187 8.952278 ACCGTATCTAAAACTGCATAATTTGAA 58.048 29.630 0.00 0.00 0.00 2.69
187 188 8.500753 ACCGTATCTAAAACTGCATAATTTGA 57.499 30.769 0.00 0.00 0.00 2.69
188 189 9.567848 AAACCGTATCTAAAACTGCATAATTTG 57.432 29.630 0.00 0.00 0.00 2.32
189 190 9.783256 GAAACCGTATCTAAAACTGCATAATTT 57.217 29.630 0.00 0.00 0.00 1.82
190 191 9.174166 AGAAACCGTATCTAAAACTGCATAATT 57.826 29.630 0.00 0.00 0.00 1.40
191 192 8.612619 CAGAAACCGTATCTAAAACTGCATAAT 58.387 33.333 0.00 0.00 0.00 1.28
192 193 7.604927 ACAGAAACCGTATCTAAAACTGCATAA 59.395 33.333 0.00 0.00 0.00 1.90
193 194 7.101054 ACAGAAACCGTATCTAAAACTGCATA 58.899 34.615 0.00 0.00 0.00 3.14
194 195 5.938125 ACAGAAACCGTATCTAAAACTGCAT 59.062 36.000 0.00 0.00 0.00 3.96
195 196 5.302360 ACAGAAACCGTATCTAAAACTGCA 58.698 37.500 0.00 0.00 0.00 4.41
196 197 5.857822 ACAGAAACCGTATCTAAAACTGC 57.142 39.130 0.00 0.00 0.00 4.40
197 198 6.400727 CCGAACAGAAACCGTATCTAAAACTG 60.401 42.308 0.00 0.00 0.00 3.16
198 199 5.636543 CCGAACAGAAACCGTATCTAAAACT 59.363 40.000 0.00 0.00 0.00 2.66
199 200 5.669602 GCCGAACAGAAACCGTATCTAAAAC 60.670 44.000 0.00 0.00 0.00 2.43
200 201 4.389687 GCCGAACAGAAACCGTATCTAAAA 59.610 41.667 0.00 0.00 0.00 1.52
201 202 3.928375 GCCGAACAGAAACCGTATCTAAA 59.072 43.478 0.00 0.00 0.00 1.85
202 203 3.514645 GCCGAACAGAAACCGTATCTAA 58.485 45.455 0.00 0.00 0.00 2.10
203 204 2.159198 GGCCGAACAGAAACCGTATCTA 60.159 50.000 0.00 0.00 0.00 1.98
204 205 1.405121 GGCCGAACAGAAACCGTATCT 60.405 52.381 0.00 0.00 0.00 1.98
205 206 1.004595 GGCCGAACAGAAACCGTATC 58.995 55.000 0.00 0.00 0.00 2.24
206 207 0.738412 CGGCCGAACAGAAACCGTAT 60.738 55.000 24.07 0.00 39.05 3.06
207 208 1.373246 CGGCCGAACAGAAACCGTA 60.373 57.895 24.07 0.00 39.05 4.02
208 209 2.663852 CGGCCGAACAGAAACCGT 60.664 61.111 24.07 0.00 39.05 4.83
209 210 4.084888 GCGGCCGAACAGAAACCG 62.085 66.667 33.48 0.00 46.50 4.44
210 211 4.084888 CGCGGCCGAACAGAAACC 62.085 66.667 33.48 6.41 36.29 3.27
211 212 4.736631 GCGCGGCCGAACAGAAAC 62.737 66.667 33.48 7.28 36.29 2.78
212 213 3.576932 TAGCGCGGCCGAACAGAAA 62.577 57.895 33.48 3.24 36.29 2.52
213 214 3.982372 CTAGCGCGGCCGAACAGAA 62.982 63.158 33.48 7.29 36.29 3.02
214 215 4.492160 CTAGCGCGGCCGAACAGA 62.492 66.667 33.48 10.65 36.29 3.41
215 216 4.796231 ACTAGCGCGGCCGAACAG 62.796 66.667 33.48 21.04 36.29 3.16
216 217 3.869473 AAACTAGCGCGGCCGAACA 62.869 57.895 33.48 9.33 36.29 3.18
217 218 2.558717 GAAAACTAGCGCGGCCGAAC 62.559 60.000 33.48 20.34 36.29 3.95
218 219 2.357760 AAAACTAGCGCGGCCGAA 60.358 55.556 33.48 9.73 36.29 4.30
219 220 2.812178 GAAAACTAGCGCGGCCGA 60.812 61.111 33.48 6.73 36.29 5.54
220 221 4.204891 CGAAAACTAGCGCGGCCG 62.205 66.667 24.05 24.05 37.57 6.13
221 222 2.812178 TCGAAAACTAGCGCGGCC 60.812 61.111 8.83 0.00 0.00 6.13
222 223 2.394524 GTCGAAAACTAGCGCGGC 59.605 61.111 8.83 0.00 0.00 6.53
223 224 2.450345 GGGTCGAAAACTAGCGCGG 61.450 63.158 8.83 1.05 0.00 6.46
224 225 2.785105 CGGGTCGAAAACTAGCGCG 61.785 63.158 0.00 0.00 0.00 6.86
225 226 3.078560 CGGGTCGAAAACTAGCGC 58.921 61.111 0.00 0.00 0.00 5.92
226 227 1.286354 TTGCGGGTCGAAAACTAGCG 61.286 55.000 0.00 0.00 34.51 4.26
227 228 0.869730 TTTGCGGGTCGAAAACTAGC 59.130 50.000 0.00 0.00 28.61 3.42
228 229 2.739913 TCATTTGCGGGTCGAAAACTAG 59.260 45.455 0.00 0.00 37.20 2.57
229 230 2.739913 CTCATTTGCGGGTCGAAAACTA 59.260 45.455 0.00 0.00 37.20 2.24
230 231 1.535462 CTCATTTGCGGGTCGAAAACT 59.465 47.619 0.00 0.00 37.20 2.66
231 232 1.533731 TCTCATTTGCGGGTCGAAAAC 59.466 47.619 0.00 0.00 37.20 2.43
232 233 1.885560 TCTCATTTGCGGGTCGAAAA 58.114 45.000 0.00 0.00 38.81 2.29
233 234 2.006888 GATCTCATTTGCGGGTCGAAA 58.993 47.619 0.00 0.00 0.00 3.46
234 235 1.207089 AGATCTCATTTGCGGGTCGAA 59.793 47.619 0.00 0.00 0.00 3.71
235 236 0.824109 AGATCTCATTTGCGGGTCGA 59.176 50.000 0.00 0.00 0.00 4.20
236 237 1.594862 GAAGATCTCATTTGCGGGTCG 59.405 52.381 0.00 0.00 0.00 4.79
237 238 2.632377 TGAAGATCTCATTTGCGGGTC 58.368 47.619 0.00 0.00 0.00 4.46
238 239 2.787473 TGAAGATCTCATTTGCGGGT 57.213 45.000 0.00 0.00 0.00 5.28
239 240 3.208594 TCATGAAGATCTCATTTGCGGG 58.791 45.455 0.00 0.00 42.46 6.13
240 241 4.888038 TTCATGAAGATCTCATTTGCGG 57.112 40.909 3.38 0.00 42.46 5.69
241 242 5.737757 CAGTTTCATGAAGATCTCATTTGCG 59.262 40.000 8.41 0.00 42.46 4.85
242 243 5.515626 GCAGTTTCATGAAGATCTCATTTGC 59.484 40.000 8.41 4.24 42.46 3.68
243 244 6.617879 TGCAGTTTCATGAAGATCTCATTTG 58.382 36.000 8.41 0.00 42.46 2.32
244 245 6.829229 TGCAGTTTCATGAAGATCTCATTT 57.171 33.333 8.41 0.00 42.46 2.32
245 246 6.829229 TTGCAGTTTCATGAAGATCTCATT 57.171 33.333 8.41 0.00 42.46 2.57
246 247 6.618811 GTTTGCAGTTTCATGAAGATCTCAT 58.381 36.000 8.41 0.00 46.25 2.90
247 248 5.334337 CGTTTGCAGTTTCATGAAGATCTCA 60.334 40.000 8.41 2.32 38.81 3.27
248 249 5.084722 CGTTTGCAGTTTCATGAAGATCTC 58.915 41.667 8.41 0.00 0.00 2.75
249 250 4.614535 GCGTTTGCAGTTTCATGAAGATCT 60.615 41.667 8.41 6.20 42.15 2.75
250 251 3.605486 GCGTTTGCAGTTTCATGAAGATC 59.395 43.478 8.41 4.03 42.15 2.75
251 252 3.568538 GCGTTTGCAGTTTCATGAAGAT 58.431 40.909 8.41 0.00 42.15 2.40
252 253 2.601979 CGCGTTTGCAGTTTCATGAAGA 60.602 45.455 8.41 0.00 42.97 2.87
253 254 1.710249 CGCGTTTGCAGTTTCATGAAG 59.290 47.619 8.41 0.00 42.97 3.02
254 255 1.064803 ACGCGTTTGCAGTTTCATGAA 59.935 42.857 5.58 3.38 42.97 2.57
255 256 0.660488 ACGCGTTTGCAGTTTCATGA 59.340 45.000 5.58 0.00 42.97 3.07
256 257 1.476074 AACGCGTTTGCAGTTTCATG 58.524 45.000 20.79 0.00 42.97 3.07
257 258 2.202295 AAACGCGTTTGCAGTTTCAT 57.798 40.000 34.36 8.10 40.90 2.57
258 259 1.651138 CAAAACGCGTTTGCAGTTTCA 59.349 42.857 35.31 0.00 42.57 2.69
259 260 2.330034 CAAAACGCGTTTGCAGTTTC 57.670 45.000 35.31 0.00 42.57 2.78
271 272 2.383027 AAACTCGACCCGCAAAACGC 62.383 55.000 0.00 0.00 41.76 4.84
272 273 0.028374 AAAACTCGACCCGCAAAACG 59.972 50.000 0.00 0.00 43.15 3.60
273 274 1.849829 CAAAAACTCGACCCGCAAAAC 59.150 47.619 0.00 0.00 0.00 2.43
274 275 1.799548 GCAAAAACTCGACCCGCAAAA 60.800 47.619 0.00 0.00 0.00 2.44
275 276 0.248702 GCAAAAACTCGACCCGCAAA 60.249 50.000 0.00 0.00 0.00 3.68
276 277 1.357334 GCAAAAACTCGACCCGCAA 59.643 52.632 0.00 0.00 0.00 4.85
277 278 1.781025 CTGCAAAAACTCGACCCGCA 61.781 55.000 0.00 0.00 0.00 5.69
278 279 1.082104 CTGCAAAAACTCGACCCGC 60.082 57.895 0.00 0.00 0.00 6.13
279 280 1.574428 CCTGCAAAAACTCGACCCG 59.426 57.895 0.00 0.00 0.00 5.28
280 281 0.822121 ACCCTGCAAAAACTCGACCC 60.822 55.000 0.00 0.00 0.00 4.46
281 282 0.591659 GACCCTGCAAAAACTCGACC 59.408 55.000 0.00 0.00 0.00 4.79
282 283 1.264288 CAGACCCTGCAAAAACTCGAC 59.736 52.381 0.00 0.00 0.00 4.20
283 284 1.593196 CAGACCCTGCAAAAACTCGA 58.407 50.000 0.00 0.00 0.00 4.04
294 295 0.901124 AGCAACTCTAGCAGACCCTG 59.099 55.000 0.00 0.00 34.12 4.45
295 296 1.190643 GAGCAACTCTAGCAGACCCT 58.809 55.000 0.00 0.00 0.00 4.34
296 297 1.190643 AGAGCAACTCTAGCAGACCC 58.809 55.000 0.00 0.00 39.28 4.46
297 298 3.181480 CCTTAGAGCAACTCTAGCAGACC 60.181 52.174 4.64 0.00 42.92 3.85
298 299 3.697045 TCCTTAGAGCAACTCTAGCAGAC 59.303 47.826 4.64 0.00 42.92 3.51
299 300 3.969553 TCCTTAGAGCAACTCTAGCAGA 58.030 45.455 4.64 1.65 42.92 4.26
300 301 4.935352 ATCCTTAGAGCAACTCTAGCAG 57.065 45.455 4.64 1.45 42.92 4.24
301 302 6.015856 GTGATATCCTTAGAGCAACTCTAGCA 60.016 42.308 0.00 0.00 42.92 3.49
302 303 6.386654 GTGATATCCTTAGAGCAACTCTAGC 58.613 44.000 0.00 0.00 42.92 3.42
303 304 6.348950 CCGTGATATCCTTAGAGCAACTCTAG 60.349 46.154 0.00 0.00 42.92 2.43
304 305 5.473846 CCGTGATATCCTTAGAGCAACTCTA 59.526 44.000 0.00 0.16 41.50 2.43
305 306 4.279671 CCGTGATATCCTTAGAGCAACTCT 59.720 45.833 0.00 2.23 43.83 3.24
306 307 4.551388 CCGTGATATCCTTAGAGCAACTC 58.449 47.826 0.00 0.00 0.00 3.01
307 308 3.322254 CCCGTGATATCCTTAGAGCAACT 59.678 47.826 0.00 0.00 0.00 3.16
308 309 3.069729 ACCCGTGATATCCTTAGAGCAAC 59.930 47.826 0.00 0.00 0.00 4.17
309 310 3.069586 CACCCGTGATATCCTTAGAGCAA 59.930 47.826 0.00 0.00 0.00 3.91
310 311 2.628178 CACCCGTGATATCCTTAGAGCA 59.372 50.000 0.00 0.00 0.00 4.26
311 312 2.628657 ACACCCGTGATATCCTTAGAGC 59.371 50.000 0.96 0.00 0.00 4.09
312 313 3.889538 TGACACCCGTGATATCCTTAGAG 59.110 47.826 0.96 0.00 0.00 2.43
313 314 3.635373 GTGACACCCGTGATATCCTTAGA 59.365 47.826 0.96 0.00 0.00 2.10
314 315 3.637229 AGTGACACCCGTGATATCCTTAG 59.363 47.826 0.84 0.00 0.00 2.18
343 344 4.642445 TCTACTCACGTGTCAAGTTTCA 57.358 40.909 16.51 0.00 0.00 2.69
535 537 5.048224 ACTTTGCATTCCATCAGACTTCAAG 60.048 40.000 0.00 0.00 0.00 3.02
593 595 1.198408 CGTGCATTGCTCAGTTCACAT 59.802 47.619 10.49 0.00 0.00 3.21
678 680 4.408182 AAGAGGGAATATCGTGTCCTTG 57.592 45.455 0.00 0.00 34.10 3.61
679 681 4.717280 AGAAAGAGGGAATATCGTGTCCTT 59.283 41.667 0.00 0.00 34.10 3.36
854 856 5.652452 CGGGGAATCCTTCTTTCTAAATGTT 59.348 40.000 0.00 0.00 0.00 2.71
855 857 5.193679 CGGGGAATCCTTCTTTCTAAATGT 58.806 41.667 0.00 0.00 0.00 2.71
856 858 5.193679 ACGGGGAATCCTTCTTTCTAAATG 58.806 41.667 0.00 0.00 0.00 2.32
857 859 5.452341 ACGGGGAATCCTTCTTTCTAAAT 57.548 39.130 0.00 0.00 0.00 1.40
858 860 4.921644 ACGGGGAATCCTTCTTTCTAAA 57.078 40.909 0.00 0.00 0.00 1.85
859 861 4.921644 AACGGGGAATCCTTCTTTCTAA 57.078 40.909 0.00 0.00 0.00 2.10
860 862 4.622220 CGAAACGGGGAATCCTTCTTTCTA 60.622 45.833 0.00 0.00 0.00 2.10
861 863 3.687125 GAAACGGGGAATCCTTCTTTCT 58.313 45.455 0.00 0.00 0.00 2.52
862 864 2.418976 CGAAACGGGGAATCCTTCTTTC 59.581 50.000 0.00 3.09 0.00 2.62
863 865 2.039348 TCGAAACGGGGAATCCTTCTTT 59.961 45.455 0.00 0.00 0.00 2.52
864 866 1.626825 TCGAAACGGGGAATCCTTCTT 59.373 47.619 0.00 0.00 0.00 2.52
865 867 1.272807 TCGAAACGGGGAATCCTTCT 58.727 50.000 0.00 0.00 0.00 2.85
866 868 2.103537 TTCGAAACGGGGAATCCTTC 57.896 50.000 0.00 0.00 0.00 3.46
867 869 2.572209 TTTCGAAACGGGGAATCCTT 57.428 45.000 6.47 0.00 0.00 3.36
868 870 2.555325 GTTTTTCGAAACGGGGAATCCT 59.445 45.455 10.79 0.00 0.00 3.24
869 871 2.293955 TGTTTTTCGAAACGGGGAATCC 59.706 45.455 10.79 0.00 35.50 3.01
870 872 3.629438 TGTTTTTCGAAACGGGGAATC 57.371 42.857 10.79 0.00 35.50 2.52
871 873 4.594123 AATGTTTTTCGAAACGGGGAAT 57.406 36.364 10.79 0.00 35.50 3.01
872 874 4.388378 AAATGTTTTTCGAAACGGGGAA 57.612 36.364 10.79 0.00 35.50 3.97
873 875 4.820716 TCTAAATGTTTTTCGAAACGGGGA 59.179 37.500 10.79 0.00 35.50 4.81
874 876 5.110940 TCTAAATGTTTTTCGAAACGGGG 57.889 39.130 10.79 0.00 35.50 5.73
875 877 6.913673 TCTTTCTAAATGTTTTTCGAAACGGG 59.086 34.615 10.79 0.00 33.84 5.28
876 878 7.901874 TCTTTCTAAATGTTTTTCGAAACGG 57.098 32.000 10.79 0.00 33.84 4.44
877 879 8.469125 CCTTCTTTCTAAATGTTTTTCGAAACG 58.531 33.333 10.79 0.00 33.84 3.60
878 880 9.511144 TCCTTCTTTCTAAATGTTTTTCGAAAC 57.489 29.630 10.79 0.99 33.84 2.78
881 883 9.893305 GAATCCTTCTTTCTAAATGTTTTTCGA 57.107 29.630 0.00 0.00 0.00 3.71
882 884 9.677567 TGAATCCTTCTTTCTAAATGTTTTTCG 57.322 29.630 0.00 0.00 0.00 3.46
926 928 2.481449 GCTCGAGGTATTCCGTTCATGT 60.481 50.000 15.58 0.00 39.05 3.21
971 973 3.059188 GGTGAGGTGTCGTTGTATGTTTG 60.059 47.826 0.00 0.00 0.00 2.93
1056 1090 3.159347 GGCGACCGGGGGTAGAAT 61.159 66.667 6.32 0.00 35.25 2.40
1159 1247 4.838152 CAGTGATCACCCCCGGCG 62.838 72.222 22.21 0.00 0.00 6.46
1160 1248 3.717294 ACAGTGATCACCCCCGGC 61.717 66.667 22.21 0.00 0.00 6.13
1161 1249 2.268920 CACAGTGATCACCCCCGG 59.731 66.667 22.21 9.46 0.00 5.73
1162 1250 2.436646 GCACAGTGATCACCCCCG 60.437 66.667 22.21 10.91 0.00 5.73
1163 1251 1.377725 CTGCACAGTGATCACCCCC 60.378 63.158 22.21 9.03 0.00 5.40
1164 1252 1.377725 CCTGCACAGTGATCACCCC 60.378 63.158 22.21 8.70 0.00 4.95
1165 1253 0.957395 CACCTGCACAGTGATCACCC 60.957 60.000 22.21 9.04 0.00 4.61
1166 1254 0.035317 TCACCTGCACAGTGATCACC 59.965 55.000 22.21 7.53 0.00 4.02
1167 1255 1.736126 CATCACCTGCACAGTGATCAC 59.264 52.381 18.47 18.47 35.87 3.06
1168 1256 1.339342 CCATCACCTGCACAGTGATCA 60.339 52.381 19.91 0.00 35.87 2.92
1169 1257 1.376543 CCATCACCTGCACAGTGATC 58.623 55.000 19.91 0.00 35.87 2.92
1170 1258 0.679002 GCCATCACCTGCACAGTGAT 60.679 55.000 17.90 17.90 38.23 3.06
1171 1259 1.302752 GCCATCACCTGCACAGTGA 60.303 57.895 15.28 15.28 0.00 3.41
1212 1300 3.692406 GTCGCCTCCTGGTCCGTT 61.692 66.667 0.00 0.00 35.27 4.44
1292 1392 4.789075 CAGCGCTTGTGCATGCCC 62.789 66.667 16.68 3.59 39.64 5.36
1293 1393 3.740397 TCAGCGCTTGTGCATGCC 61.740 61.111 16.68 7.25 39.64 4.40
1294 1394 2.503375 GTCAGCGCTTGTGCATGC 60.503 61.111 7.50 11.82 39.64 4.06
1295 1395 2.202260 CGTCAGCGCTTGTGCATG 60.202 61.111 7.50 0.00 39.64 4.06
1313 1413 1.407979 AGTGTACTTATTCCTCCGGCG 59.592 52.381 0.00 0.00 0.00 6.46
1324 1424 5.067283 TCGCTATGAATCAGCAGTGTACTTA 59.933 40.000 7.70 0.00 39.04 2.24
1331 1431 1.411977 AGCTCGCTATGAATCAGCAGT 59.588 47.619 0.00 0.00 39.04 4.40
1342 1442 2.101582 ACAAGATCGGAAAGCTCGCTAT 59.898 45.455 0.00 0.00 0.00 2.97
1354 1454 3.250762 TCACTCAAGCAAAACAAGATCGG 59.749 43.478 0.00 0.00 0.00 4.18
1392 1492 9.247126 CAACTCAAACATCATGTGATTTTACAA 57.753 29.630 0.00 0.00 33.69 2.41
1463 1563 3.531538 GACTGTCTCTCTCTCGTGATCT 58.468 50.000 0.00 0.00 0.00 2.75
1464 1564 2.612212 GGACTGTCTCTCTCTCGTGATC 59.388 54.545 7.85 0.00 0.00 2.92
1465 1565 2.026729 TGGACTGTCTCTCTCTCGTGAT 60.027 50.000 7.85 0.00 0.00 3.06
1466 1566 1.348036 TGGACTGTCTCTCTCTCGTGA 59.652 52.381 7.85 0.00 0.00 4.35
1467 1567 1.814793 TGGACTGTCTCTCTCTCGTG 58.185 55.000 7.85 0.00 0.00 4.35
1468 1568 2.364632 CATGGACTGTCTCTCTCTCGT 58.635 52.381 7.85 0.00 0.00 4.18
1469 1569 1.065401 GCATGGACTGTCTCTCTCTCG 59.935 57.143 7.85 0.00 0.00 4.04
1470 1570 2.098614 TGCATGGACTGTCTCTCTCTC 58.901 52.381 7.85 0.00 0.00 3.20
1471 1571 2.228545 TGCATGGACTGTCTCTCTCT 57.771 50.000 7.85 0.00 0.00 3.10
1479 1579 1.743772 GCTACCGAATGCATGGACTGT 60.744 52.381 9.94 5.77 0.00 3.55
1494 1594 5.355071 TCTTTGATCACATCACATTGCTACC 59.645 40.000 0.00 0.00 39.39 3.18
1495 1595 6.253746 GTCTTTGATCACATCACATTGCTAC 58.746 40.000 0.00 0.00 39.39 3.58
1508 1608 6.140737 GTCAATCAAACAACGTCTTTGATCAC 59.859 38.462 23.96 20.34 44.15 3.06
1509 1609 6.038161 AGTCAATCAAACAACGTCTTTGATCA 59.962 34.615 23.96 15.76 44.15 2.92
1510 1610 6.430451 AGTCAATCAAACAACGTCTTTGATC 58.570 36.000 23.96 16.22 44.15 2.92
1511 1611 6.377327 AGTCAATCAAACAACGTCTTTGAT 57.623 33.333 20.58 20.58 45.96 2.57
1512 1612 5.811399 AGTCAATCAAACAACGTCTTTGA 57.189 34.783 18.55 18.55 40.89 2.69
1513 1613 6.027131 TGAAGTCAATCAAACAACGTCTTTG 58.973 36.000 10.89 10.89 41.49 2.77
1514 1614 6.128007 ACTGAAGTCAATCAAACAACGTCTTT 60.128 34.615 0.00 0.00 0.00 2.52
1519 1619 3.725740 GCACTGAAGTCAATCAAACAACG 59.274 43.478 0.00 0.00 0.00 4.10
1531 1631 3.265791 CATGACTAAGGGCACTGAAGTC 58.734 50.000 19.99 19.99 39.35 3.01
1788 1942 8.657387 TCTTGGAGAGGAATATTATGGAGTAG 57.343 38.462 0.00 0.00 0.00 2.57
1910 2064 0.318360 TGTCGTACAACAGTGCTCGG 60.318 55.000 0.00 0.00 0.00 4.63
1915 2069 8.462143 ACTTAATCTATTGTCGTACAACAGTG 57.538 34.615 0.00 0.00 41.40 3.66
2081 2235 1.024271 GAGTGGTGCTTGACTGCAAA 58.976 50.000 0.00 0.00 45.12 3.68
2156 2310 4.575645 ACTAGGTATGCTACGACAGAACTC 59.424 45.833 0.00 0.00 30.02 3.01
2163 2317 6.616774 AAGAGTAACTAGGTATGCTACGAC 57.383 41.667 0.00 0.00 0.00 4.34
2165 2319 6.793349 ACAAAGAGTAACTAGGTATGCTACG 58.207 40.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.