Multiple sequence alignment - TraesCS3D01G411600

Loading Multiple Alignment...

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 TraesCS3D01G411600 chr3D 100.000 2975 0 0 1 2975 524200764 524203738 0.000000e+00 5494
1 TraesCS3D01G411600 chr3B 90.250 2759 126 50 252 2974 691459867 691457216 0.000000e+00 3472
2 TraesCS3D01G411600 chr3A 90.302 2052 91 38 987 2974 658843558 658841551 0.000000e+00 2588
3 TraesCS3D01G411600 chr3A 77.778 567 43 32 241 783 658844632 658844125 3.780000e-69 272
4 TraesCS3D01G411600 chr7D 95.417 240 11 0 3 242 602283260 602283499 1.670000e-102 383
5 TraesCS3D01G411600 chr4D 94.262 244 13 1 1 244 484449355 484449597 3.620000e-99 372
6 TraesCS3D01G411600 chr2D 94.215 242 14 0 1 242 370188013 370187772 1.300000e-98 370
7 TraesCS3D01G411600 chr2D 94.239 243 13 1 1 242 484900795 484901037 1.300000e-98 370
8 TraesCS3D01G411600 chr1A 94.215 242 13 1 1 242 68301338 68301098 4.680000e-98 368
9 TraesCS3D01G411600 chr2A 93.827 243 15 0 1 243 114327670 114327912 1.680000e-97 366
10 TraesCS3D01G411600 chr1D 93.802 242 14 1 1 242 61780804 61780564 2.180000e-96 363
11 TraesCS3D01G411600 chr5D 93.416 243 16 0 1 243 221002180 221001938 7.840000e-96 361
12 TraesCS3D01G411600 chr5D 93.416 243 15 1 1 242 485933345 485933587 2.820000e-95 359


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 TraesCS3D01G411600 chr3D 524200764 524203738 2974 False 5494 5494 100.00 1 2975 1 chr3D.!!$F1 2974
1 TraesCS3D01G411600 chr3B 691457216 691459867 2651 True 3472 3472 90.25 252 2974 1 chr3B.!!$R1 2722
2 TraesCS3D01G411600 chr3A 658841551 658844632 3081 True 1430 2588 84.04 241 2974 2 chr3A.!!$R1 2733

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
459 487 0.179043 TGGTGAAAGTTGGCAGCGTA 60.179 50.0 0.0 0.0 35.41 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2225 2673 0.029681 ACTATCCTGTGCCCCTCCAT 60.03 55.0 0.0 0.0 0.0 3.41 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
46 47 9.844257 AACAAATTGAACCAATAAAAGGAATCA 57.156 25.926 0.00 0.00 32.43 2.57
47 48 9.844257 ACAAATTGAACCAATAAAAGGAATCAA 57.156 25.926 0.00 0.00 38.67 2.57
56 57 8.949177 ACCAATAAAAGGAATCAATTGATTTGC 58.051 29.630 29.44 19.43 44.14 3.68
57 58 8.948145 CCAATAAAAGGAATCAATTGATTTGCA 58.052 29.630 29.44 14.97 44.14 4.08
79 80 8.378172 TGCATAATTTAAGGAAGTTAGATCCG 57.622 34.615 0.00 0.00 42.03 4.18
80 81 7.990886 TGCATAATTTAAGGAAGTTAGATCCGT 59.009 33.333 0.00 0.00 42.03 4.69
81 82 8.283291 GCATAATTTAAGGAAGTTAGATCCGTG 58.717 37.037 0.00 0.00 42.03 4.94
82 83 9.542462 CATAATTTAAGGAAGTTAGATCCGTGA 57.458 33.333 0.00 0.00 42.03 4.35
85 86 9.462606 AATTTAAGGAAGTTAGATCCGTGATTT 57.537 29.630 0.00 0.00 42.03 2.17
86 87 7.843490 TTAAGGAAGTTAGATCCGTGATTTG 57.157 36.000 0.00 0.00 42.03 2.32
87 88 5.422214 AGGAAGTTAGATCCGTGATTTGT 57.578 39.130 0.00 0.00 42.03 2.83
88 89 5.805728 AGGAAGTTAGATCCGTGATTTGTT 58.194 37.500 0.00 0.00 42.03 2.83
89 90 6.942976 AGGAAGTTAGATCCGTGATTTGTTA 58.057 36.000 0.00 0.00 42.03 2.41
90 91 7.565680 AGGAAGTTAGATCCGTGATTTGTTAT 58.434 34.615 0.00 0.00 42.03 1.89
91 92 8.701895 AGGAAGTTAGATCCGTGATTTGTTATA 58.298 33.333 0.00 0.00 42.03 0.98
92 93 8.979574 GGAAGTTAGATCCGTGATTTGTTATAG 58.020 37.037 0.00 0.00 0.00 1.31
93 94 8.888579 AAGTTAGATCCGTGATTTGTTATAGG 57.111 34.615 0.00 0.00 0.00 2.57
94 95 8.019656 AGTTAGATCCGTGATTTGTTATAGGT 57.980 34.615 0.00 0.00 0.00 3.08
95 96 8.483758 AGTTAGATCCGTGATTTGTTATAGGTT 58.516 33.333 0.00 0.00 0.00 3.50
96 97 9.754382 GTTAGATCCGTGATTTGTTATAGGTTA 57.246 33.333 0.00 0.00 0.00 2.85
97 98 9.976511 TTAGATCCGTGATTTGTTATAGGTTAG 57.023 33.333 0.00 0.00 0.00 2.34
98 99 7.442656 AGATCCGTGATTTGTTATAGGTTAGG 58.557 38.462 0.00 0.00 0.00 2.69
99 100 6.795144 TCCGTGATTTGTTATAGGTTAGGA 57.205 37.500 0.00 0.00 0.00 2.94
100 101 7.185318 TCCGTGATTTGTTATAGGTTAGGAA 57.815 36.000 0.00 0.00 0.00 3.36
101 102 7.622713 TCCGTGATTTGTTATAGGTTAGGAAA 58.377 34.615 0.00 0.00 0.00 3.13
102 103 7.767198 TCCGTGATTTGTTATAGGTTAGGAAAG 59.233 37.037 0.00 0.00 0.00 2.62
103 104 7.551617 CCGTGATTTGTTATAGGTTAGGAAAGT 59.448 37.037 0.00 0.00 0.00 2.66
104 105 8.943002 CGTGATTTGTTATAGGTTAGGAAAGTT 58.057 33.333 0.00 0.00 0.00 2.66
108 109 8.857694 TTTGTTATAGGTTAGGAAAGTTCTGG 57.142 34.615 0.00 0.00 0.00 3.86
109 110 7.563724 TGTTATAGGTTAGGAAAGTTCTGGT 57.436 36.000 0.00 0.00 0.00 4.00
110 111 7.981142 TGTTATAGGTTAGGAAAGTTCTGGTT 58.019 34.615 0.00 0.00 0.00 3.67
111 112 7.881232 TGTTATAGGTTAGGAAAGTTCTGGTTG 59.119 37.037 0.00 0.00 0.00 3.77
112 113 4.790718 AGGTTAGGAAAGTTCTGGTTGT 57.209 40.909 0.00 0.00 0.00 3.32
113 114 5.899631 AGGTTAGGAAAGTTCTGGTTGTA 57.100 39.130 0.00 0.00 0.00 2.41
114 115 6.256643 AGGTTAGGAAAGTTCTGGTTGTAA 57.743 37.500 0.00 0.00 0.00 2.41
115 116 6.849151 AGGTTAGGAAAGTTCTGGTTGTAAT 58.151 36.000 0.00 0.00 0.00 1.89
116 117 7.981142 AGGTTAGGAAAGTTCTGGTTGTAATA 58.019 34.615 0.00 0.00 0.00 0.98
117 118 8.442374 AGGTTAGGAAAGTTCTGGTTGTAATAA 58.558 33.333 0.00 0.00 0.00 1.40
118 119 9.070179 GGTTAGGAAAGTTCTGGTTGTAATAAA 57.930 33.333 0.00 0.00 0.00 1.40
121 122 8.622948 AGGAAAGTTCTGGTTGTAATAAAGAG 57.377 34.615 0.00 0.00 0.00 2.85
122 123 8.218488 AGGAAAGTTCTGGTTGTAATAAAGAGT 58.782 33.333 0.00 0.00 0.00 3.24
123 124 8.290325 GGAAAGTTCTGGTTGTAATAAAGAGTG 58.710 37.037 0.00 0.00 0.00 3.51
124 125 8.974060 AAAGTTCTGGTTGTAATAAAGAGTGA 57.026 30.769 0.00 0.00 0.00 3.41
125 126 8.974060 AAGTTCTGGTTGTAATAAAGAGTGAA 57.026 30.769 0.00 0.00 0.00 3.18
126 127 8.608844 AGTTCTGGTTGTAATAAAGAGTGAAG 57.391 34.615 0.00 0.00 0.00 3.02
127 128 8.429641 AGTTCTGGTTGTAATAAAGAGTGAAGA 58.570 33.333 0.00 0.00 0.00 2.87
128 129 8.713271 GTTCTGGTTGTAATAAAGAGTGAAGAG 58.287 37.037 0.00 0.00 0.00 2.85
129 130 8.190326 TCTGGTTGTAATAAAGAGTGAAGAGA 57.810 34.615 0.00 0.00 0.00 3.10
130 131 8.647796 TCTGGTTGTAATAAAGAGTGAAGAGAA 58.352 33.333 0.00 0.00 0.00 2.87
131 132 9.273016 CTGGTTGTAATAAAGAGTGAAGAGAAA 57.727 33.333 0.00 0.00 0.00 2.52
132 133 9.621629 TGGTTGTAATAAAGAGTGAAGAGAAAA 57.378 29.630 0.00 0.00 0.00 2.29
141 142 8.446599 AAAGAGTGAAGAGAAAAATAAACCGA 57.553 30.769 0.00 0.00 0.00 4.69
142 143 8.622948 AAGAGTGAAGAGAAAAATAAACCGAT 57.377 30.769 0.00 0.00 0.00 4.18
143 144 8.034058 AGAGTGAAGAGAAAAATAAACCGATG 57.966 34.615 0.00 0.00 0.00 3.84
144 145 7.878127 AGAGTGAAGAGAAAAATAAACCGATGA 59.122 33.333 0.00 0.00 0.00 2.92
145 146 8.391075 AGTGAAGAGAAAAATAAACCGATGAA 57.609 30.769 0.00 0.00 0.00 2.57
146 147 8.290325 AGTGAAGAGAAAAATAAACCGATGAAC 58.710 33.333 0.00 0.00 0.00 3.18
147 148 7.537649 GTGAAGAGAAAAATAAACCGATGAACC 59.462 37.037 0.00 0.00 0.00 3.62
148 149 7.229707 TGAAGAGAAAAATAAACCGATGAACCA 59.770 33.333 0.00 0.00 0.00 3.67
149 150 7.145932 AGAGAAAAATAAACCGATGAACCAG 57.854 36.000 0.00 0.00 0.00 4.00
150 151 6.151144 AGAGAAAAATAAACCGATGAACCAGG 59.849 38.462 0.00 0.00 0.00 4.45
151 152 6.007703 AGAAAAATAAACCGATGAACCAGGA 58.992 36.000 0.00 0.00 0.00 3.86
152 153 6.663523 AGAAAAATAAACCGATGAACCAGGAT 59.336 34.615 0.00 0.00 0.00 3.24
153 154 5.835113 AAATAAACCGATGAACCAGGATG 57.165 39.130 0.00 0.00 0.00 3.51
164 165 3.099170 CAGGATGGGAGGGGGTGG 61.099 72.222 0.00 0.00 0.00 4.61
165 166 3.637544 AGGATGGGAGGGGGTGGT 61.638 66.667 0.00 0.00 0.00 4.16
166 167 3.420482 GGATGGGAGGGGGTGGTG 61.420 72.222 0.00 0.00 0.00 4.17
167 168 3.420482 GATGGGAGGGGGTGGTGG 61.420 72.222 0.00 0.00 0.00 4.61
171 172 4.348495 GGAGGGGGTGGTGGGAGA 62.348 72.222 0.00 0.00 0.00 3.71
172 173 2.204090 GAGGGGGTGGTGGGAGAA 60.204 66.667 0.00 0.00 0.00 2.87
173 174 2.204151 AGGGGGTGGTGGGAGAAG 60.204 66.667 0.00 0.00 0.00 2.85
174 175 2.204090 GGGGGTGGTGGGAGAAGA 60.204 66.667 0.00 0.00 0.00 2.87
175 176 2.301738 GGGGGTGGTGGGAGAAGAG 61.302 68.421 0.00 0.00 0.00 2.85
176 177 1.229529 GGGGTGGTGGGAGAAGAGA 60.230 63.158 0.00 0.00 0.00 3.10
177 178 1.554583 GGGGTGGTGGGAGAAGAGAC 61.555 65.000 0.00 0.00 0.00 3.36
178 179 1.592223 GGTGGTGGGAGAAGAGACG 59.408 63.158 0.00 0.00 0.00 4.18
179 180 0.898789 GGTGGTGGGAGAAGAGACGA 60.899 60.000 0.00 0.00 0.00 4.20
180 181 0.966920 GTGGTGGGAGAAGAGACGAA 59.033 55.000 0.00 0.00 0.00 3.85
181 182 1.343465 GTGGTGGGAGAAGAGACGAAA 59.657 52.381 0.00 0.00 0.00 3.46
182 183 2.043992 TGGTGGGAGAAGAGACGAAAA 58.956 47.619 0.00 0.00 0.00 2.29
183 184 2.436542 TGGTGGGAGAAGAGACGAAAAA 59.563 45.455 0.00 0.00 0.00 1.94
203 204 5.977171 AAAAACCAGCGAAAATAAACCAC 57.023 34.783 0.00 0.00 0.00 4.16
204 205 2.981400 ACCAGCGAAAATAAACCACG 57.019 45.000 0.00 0.00 0.00 4.94
205 206 1.538075 ACCAGCGAAAATAAACCACGG 59.462 47.619 0.00 0.00 0.00 4.94
206 207 1.807742 CCAGCGAAAATAAACCACGGA 59.192 47.619 0.00 0.00 0.00 4.69
207 208 2.159572 CCAGCGAAAATAAACCACGGAG 60.160 50.000 0.00 0.00 0.00 4.63
208 209 2.739913 CAGCGAAAATAAACCACGGAGA 59.260 45.455 0.00 0.00 0.00 3.71
209 210 2.740447 AGCGAAAATAAACCACGGAGAC 59.260 45.455 0.00 0.00 0.00 3.36
223 224 1.630148 GGAGACGATTCACCAACTCG 58.370 55.000 0.00 0.00 38.34 4.18
225 226 2.609737 GGAGACGATTCACCAACTCGTT 60.610 50.000 0.00 0.00 44.89 3.85
226 227 2.662156 GAGACGATTCACCAACTCGTTC 59.338 50.000 0.00 0.00 44.89 3.95
227 228 2.035449 AGACGATTCACCAACTCGTTCA 59.965 45.455 0.00 0.00 44.89 3.18
228 229 2.993899 GACGATTCACCAACTCGTTCAT 59.006 45.455 0.00 0.00 44.89 2.57
229 230 3.399330 ACGATTCACCAACTCGTTCATT 58.601 40.909 0.00 0.00 42.52 2.57
230 231 4.562082 ACGATTCACCAACTCGTTCATTA 58.438 39.130 0.00 0.00 42.52 1.90
231 232 4.992319 ACGATTCACCAACTCGTTCATTAA 59.008 37.500 0.00 0.00 42.52 1.40
232 233 5.467399 ACGATTCACCAACTCGTTCATTAAA 59.533 36.000 0.00 0.00 42.52 1.52
233 234 6.017770 ACGATTCACCAACTCGTTCATTAAAA 60.018 34.615 0.00 0.00 42.52 1.52
234 235 6.519761 CGATTCACCAACTCGTTCATTAAAAG 59.480 38.462 0.00 0.00 0.00 2.27
235 236 6.687081 TTCACCAACTCGTTCATTAAAAGT 57.313 33.333 0.00 0.00 0.00 2.66
236 237 7.789273 TTCACCAACTCGTTCATTAAAAGTA 57.211 32.000 0.00 0.00 0.00 2.24
237 238 7.416154 TCACCAACTCGTTCATTAAAAGTAG 57.584 36.000 0.00 0.00 0.00 2.57
238 239 7.211573 TCACCAACTCGTTCATTAAAAGTAGA 58.788 34.615 0.00 0.00 0.00 2.59
239 240 7.384115 TCACCAACTCGTTCATTAAAAGTAGAG 59.616 37.037 0.00 0.00 0.00 2.43
240 241 7.384115 CACCAACTCGTTCATTAAAAGTAGAGA 59.616 37.037 7.36 0.00 0.00 3.10
241 242 8.095169 ACCAACTCGTTCATTAAAAGTAGAGAT 58.905 33.333 7.36 0.00 0.00 2.75
242 243 8.596380 CCAACTCGTTCATTAAAAGTAGAGATC 58.404 37.037 7.36 0.00 0.00 2.75
243 244 8.596380 CAACTCGTTCATTAAAAGTAGAGATCC 58.404 37.037 7.36 0.00 0.00 3.36
244 245 7.266400 ACTCGTTCATTAAAAGTAGAGATCCC 58.734 38.462 7.36 0.00 0.00 3.85
245 246 6.579865 TCGTTCATTAAAAGTAGAGATCCCC 58.420 40.000 0.00 0.00 0.00 4.81
246 247 6.155565 TCGTTCATTAAAAGTAGAGATCCCCA 59.844 38.462 0.00 0.00 0.00 4.96
247 248 6.480320 CGTTCATTAAAAGTAGAGATCCCCAG 59.520 42.308 0.00 0.00 0.00 4.45
248 249 7.565680 GTTCATTAAAAGTAGAGATCCCCAGA 58.434 38.462 0.00 0.00 0.00 3.86
249 250 7.366847 TCATTAAAAGTAGAGATCCCCAGAG 57.633 40.000 0.00 0.00 0.00 3.35
250 251 6.327626 TCATTAAAAGTAGAGATCCCCAGAGG 59.672 42.308 0.00 0.00 0.00 3.69
292 297 2.240918 ACACATCCCCACATGCCCT 61.241 57.895 0.00 0.00 0.00 5.19
302 307 4.021559 CATGCCCTTCCATGTGCA 57.978 55.556 0.00 0.00 38.19 4.57
303 308 2.511818 CATGCCCTTCCATGTGCAT 58.488 52.632 0.00 0.00 44.79 3.96
304 309 2.511818 ATGCCCTTCCATGTGCATG 58.488 52.632 5.26 5.26 42.48 4.06
376 392 2.666098 CCCCAGACAGTAACCCCGG 61.666 68.421 0.00 0.00 0.00 5.73
385 401 2.203877 TAACCCCGGGCTCACTGT 60.204 61.111 17.73 2.78 0.00 3.55
391 407 1.079819 CCGGGCTCACTGTACACTG 60.080 63.158 0.00 0.00 0.00 3.66
395 411 0.671781 GGCTCACTGTACACTGCCTG 60.672 60.000 13.30 0.00 37.58 4.85
396 412 0.318441 GCTCACTGTACACTGCCTGA 59.682 55.000 0.00 0.00 0.00 3.86
397 413 1.671261 GCTCACTGTACACTGCCTGAG 60.671 57.143 0.00 0.00 0.00 3.35
398 414 1.889170 CTCACTGTACACTGCCTGAGA 59.111 52.381 0.00 0.00 0.00 3.27
401 417 0.894141 CTGTACACTGCCTGAGAGCT 59.106 55.000 0.00 0.00 0.00 4.09
402 418 2.095461 CTGTACACTGCCTGAGAGCTA 58.905 52.381 0.00 0.00 0.00 3.32
403 419 2.692557 CTGTACACTGCCTGAGAGCTAT 59.307 50.000 0.00 0.00 0.00 2.97
404 420 2.690497 TGTACACTGCCTGAGAGCTATC 59.310 50.000 0.08 0.08 0.00 2.08
406 422 1.480137 ACACTGCCTGAGAGCTATCAC 59.520 52.381 7.02 0.00 0.00 3.06
407 423 0.743688 ACTGCCTGAGAGCTATCACG 59.256 55.000 7.02 4.89 0.00 4.35
434 462 2.762234 ATGGCCTCTCGTCGTCGAC 61.762 63.158 15.51 15.51 41.35 4.20
457 485 0.387622 CATGGTGAAAGTTGGCAGCG 60.388 55.000 0.00 0.00 35.41 5.18
458 486 0.823356 ATGGTGAAAGTTGGCAGCGT 60.823 50.000 0.00 0.00 35.41 5.07
459 487 0.179043 TGGTGAAAGTTGGCAGCGTA 60.179 50.000 0.00 0.00 35.41 4.42
460 488 0.948678 GGTGAAAGTTGGCAGCGTAA 59.051 50.000 0.00 0.00 0.00 3.18
461 489 1.069227 GGTGAAAGTTGGCAGCGTAAG 60.069 52.381 0.00 0.00 43.44 2.34
480 508 7.707919 CGTAAGCTTAGTATATAGTGAAGCG 57.292 40.000 6.38 0.00 45.63 4.68
481 509 7.296660 CGTAAGCTTAGTATATAGTGAAGCGT 58.703 38.462 6.38 16.72 45.63 5.07
482 510 7.268659 CGTAAGCTTAGTATATAGTGAAGCGTG 59.731 40.741 6.38 11.22 45.63 5.34
624 677 2.098117 GCATTTACTCGCTCCAAGCAAT 59.902 45.455 0.00 0.00 42.58 3.56
625 678 3.312421 GCATTTACTCGCTCCAAGCAATA 59.688 43.478 0.00 0.00 42.58 1.90
628 681 0.250234 ACTCGCTCCAAGCAATAGCA 59.750 50.000 0.00 0.00 42.58 3.49
630 683 1.945394 CTCGCTCCAAGCAATAGCAAT 59.055 47.619 0.00 0.00 42.58 3.56
631 684 3.133691 CTCGCTCCAAGCAATAGCAATA 58.866 45.455 0.00 0.00 42.58 1.90
633 686 2.350197 CGCTCCAAGCAATAGCAATAGC 60.350 50.000 0.00 0.00 42.58 2.97
634 687 2.620115 GCTCCAAGCAATAGCAATAGCA 59.380 45.455 0.00 0.00 45.49 3.49
635 688 3.067180 GCTCCAAGCAATAGCAATAGCAA 59.933 43.478 0.00 0.00 45.49 3.91
636 689 4.261909 GCTCCAAGCAATAGCAATAGCAAT 60.262 41.667 0.00 0.00 45.49 3.56
637 690 5.048504 GCTCCAAGCAATAGCAATAGCAATA 60.049 40.000 0.00 0.00 45.49 1.90
638 691 6.564709 TCCAAGCAATAGCAATAGCAATAG 57.435 37.500 0.00 0.00 45.49 1.73
639 692 5.048504 TCCAAGCAATAGCAATAGCAATAGC 60.049 40.000 0.00 0.00 45.49 2.97
640 693 5.278610 CCAAGCAATAGCAATAGCAATAGCA 60.279 40.000 0.00 0.00 43.66 3.49
641 694 6.210796 CAAGCAATAGCAATAGCAATAGCAA 58.789 36.000 0.00 0.00 43.66 3.91
642 695 6.585695 AGCAATAGCAATAGCAATAGCAAT 57.414 33.333 0.00 0.00 43.66 3.56
643 696 7.692460 AGCAATAGCAATAGCAATAGCAATA 57.308 32.000 0.00 0.00 43.66 1.90
644 697 8.114331 AGCAATAGCAATAGCAATAGCAATAA 57.886 30.769 0.00 0.00 43.66 1.40
645 698 8.025445 AGCAATAGCAATAGCAATAGCAATAAC 58.975 33.333 0.00 0.00 43.66 1.89
646 699 7.809331 GCAATAGCAATAGCAATAGCAATAACA 59.191 33.333 0.00 0.00 45.49 2.41
647 700 9.681692 CAATAGCAATAGCAATAGCAATAACAA 57.318 29.630 0.00 0.00 45.49 2.83
651 704 8.025445 AGCAATAGCAATAGCAATAACAATAGC 58.975 33.333 0.00 0.00 45.49 2.97
652 705 7.809331 GCAATAGCAATAGCAATAACAATAGCA 59.191 33.333 0.00 0.00 45.49 3.49
653 706 9.681692 CAATAGCAATAGCAATAACAATAGCAA 57.318 29.630 0.00 0.00 45.49 3.91
665 718 3.480470 ACAATAGCAATAGCAAGCGGAT 58.520 40.909 0.00 0.00 45.49 4.18
677 730 2.426522 CAAGCGGATGAAGAAGGTTCA 58.573 47.619 0.00 0.00 0.00 3.18
694 747 3.491104 GGTTCATGGTTTAAAACGCCACA 60.491 43.478 0.00 0.00 34.84 4.17
697 750 1.765230 TGGTTTAAAACGCCACACCT 58.235 45.000 0.00 0.00 0.00 4.00
852 1236 1.067084 CGAGCTCCGTCATCATGCT 59.933 57.895 8.47 0.00 36.63 3.79
939 1323 0.767375 TCCTTGCTAGCCCATCATCC 59.233 55.000 13.29 0.00 0.00 3.51
946 1330 2.683152 GCTAGCCCATCATCCATCCATC 60.683 54.545 2.29 0.00 0.00 3.51
977 1361 1.531578 CTCGTGTCTCTCAGTTCGTCA 59.468 52.381 0.00 0.00 0.00 4.35
985 1411 3.562141 TCTCTCAGTTCGTCATAGCTAGC 59.438 47.826 6.62 6.62 0.00 3.42
1896 2334 4.195334 CCCTCCCCCTCGCCATTG 62.195 72.222 0.00 0.00 0.00 2.82
1978 2416 2.479656 GCATGGAAGATCGAATGAGCTC 59.520 50.000 6.82 6.82 40.73 4.09
1979 2417 2.898729 TGGAAGATCGAATGAGCTCC 57.101 50.000 12.15 0.00 40.73 4.70
1980 2418 1.414181 TGGAAGATCGAATGAGCTCCC 59.586 52.381 12.15 1.09 40.73 4.30
1981 2419 1.691434 GGAAGATCGAATGAGCTCCCT 59.309 52.381 12.15 0.00 40.73 4.20
2085 2523 5.957798 ACATTTCACCATGTTATGAGCAAG 58.042 37.500 0.00 0.00 33.29 4.01
2106 2544 8.144478 AGCAAGATACTACTACCATGTAATGTG 58.856 37.037 0.00 0.00 44.81 3.21
2109 2547 8.762481 AGATACTACTACCATGTAATGTGACA 57.238 34.615 0.00 0.00 44.81 3.58
2115 2553 6.237901 ACTACCATGTAATGTGACAATGTGT 58.762 36.000 0.00 0.00 44.81 3.72
2158 2606 3.007398 GTCTGTCTGATTGAGGTTGAGGT 59.993 47.826 0.00 0.00 0.00 3.85
2164 2612 2.040278 TGATTGAGGTTGAGGTTGAGGG 59.960 50.000 0.00 0.00 0.00 4.30
2166 2614 1.002011 GAGGTTGAGGTTGAGGGCC 60.002 63.158 0.00 0.00 0.00 5.80
2168 2616 1.303643 GGTTGAGGTTGAGGGCCTG 60.304 63.158 12.95 0.00 36.29 4.85
2169 2617 1.761174 GTTGAGGTTGAGGGCCTGA 59.239 57.895 12.95 0.00 36.29 3.86
2170 2618 0.322008 GTTGAGGTTGAGGGCCTGAG 60.322 60.000 12.95 0.00 36.29 3.35
2225 2673 1.986632 ATGCACATGGAGGATCGGCA 61.987 55.000 0.00 0.00 34.37 5.69
2277 2725 0.842030 AACAGCCTGGTCCTGATGGA 60.842 55.000 8.13 0.00 40.69 3.41
2289 2737 4.454678 GTCCTGATGGAGAAACATGCATA 58.545 43.478 0.00 0.00 44.16 3.14
2290 2738 5.068636 GTCCTGATGGAGAAACATGCATAT 58.931 41.667 0.00 0.00 44.16 1.78
2291 2739 5.048921 GTCCTGATGGAGAAACATGCATATG 60.049 44.000 0.00 0.00 44.16 1.78
2292 2740 4.321008 CCTGATGGAGAAACATGCATATGC 60.321 45.833 21.09 21.09 34.85 3.14
2293 2741 6.724290 CCTGATGGAGAAACATGCATATGCA 61.724 44.000 31.29 31.29 45.84 3.96
2321 2769 1.639298 GGCGACATGACAGGCAGAAC 61.639 60.000 0.00 0.00 0.00 3.01
2394 2850 2.112190 CTAAGAGAACTGGTCCCTCCC 58.888 57.143 0.00 0.00 34.77 4.30
2496 2960 2.740447 GACCGGCCTAACTAACAAACTG 59.260 50.000 0.00 0.00 0.00 3.16
2557 3035 4.271696 TGGACAAGGACACAAGATACTG 57.728 45.455 0.00 0.00 0.00 2.74
2643 3124 4.180817 GTTTTTCACCCAGGTTTTCAGTG 58.819 43.478 0.00 0.00 0.00 3.66
2676 3157 1.202348 GGACCATGCAGCTTTGGTAAC 59.798 52.381 17.55 11.55 46.14 2.50
2705 3186 2.093235 CCCAAGTTGAGATCTCAGGGAC 60.093 54.545 30.94 23.62 41.39 4.46
2709 3190 2.096248 GTTGAGATCTCAGGGACGTCT 58.904 52.381 23.92 0.00 41.13 4.18
2731 3213 3.697166 ACTGGGCCAGTTTTAATAGTGG 58.303 45.455 33.18 13.76 42.59 4.00
2938 3437 0.682209 CCTTCCCCATTGGCTGACAG 60.682 60.000 0.00 0.00 0.00 3.51
2939 3438 1.304381 TTCCCCATTGGCTGACAGC 60.304 57.895 19.55 19.55 41.46 4.40
2974 3473 5.789575 ACCAGGAATGCCATAGAATCTAGAT 59.210 40.000 0.00 0.00 36.29 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.844257 TGATTCCTTTTATTGGTTCAATTTGTT 57.156 25.926 0.00 0.00 35.54 2.83
21 22 9.844257 TTGATTCCTTTTATTGGTTCAATTTGT 57.156 25.926 0.00 0.00 35.54 2.83
30 31 8.949177 GCAAATCAATTGATTCCTTTTATTGGT 58.051 29.630 29.08 10.23 43.41 3.67
31 32 8.948145 TGCAAATCAATTGATTCCTTTTATTGG 58.052 29.630 29.08 8.13 43.41 3.16
53 54 8.836413 CGGATCTAACTTCCTTAAATTATGCAA 58.164 33.333 0.00 0.00 0.00 4.08
54 55 7.990886 ACGGATCTAACTTCCTTAAATTATGCA 59.009 33.333 0.00 0.00 0.00 3.96
55 56 8.283291 CACGGATCTAACTTCCTTAAATTATGC 58.717 37.037 0.00 0.00 0.00 3.14
56 57 9.542462 TCACGGATCTAACTTCCTTAAATTATG 57.458 33.333 0.00 0.00 0.00 1.90
59 60 9.462606 AAATCACGGATCTAACTTCCTTAAATT 57.537 29.630 0.00 0.00 0.00 1.82
60 61 8.893727 CAAATCACGGATCTAACTTCCTTAAAT 58.106 33.333 0.00 0.00 0.00 1.40
61 62 7.881232 ACAAATCACGGATCTAACTTCCTTAAA 59.119 33.333 0.00 0.00 0.00 1.52
62 63 7.391620 ACAAATCACGGATCTAACTTCCTTAA 58.608 34.615 0.00 0.00 0.00 1.85
63 64 6.942976 ACAAATCACGGATCTAACTTCCTTA 58.057 36.000 0.00 0.00 0.00 2.69
64 65 5.805728 ACAAATCACGGATCTAACTTCCTT 58.194 37.500 0.00 0.00 0.00 3.36
65 66 5.422214 ACAAATCACGGATCTAACTTCCT 57.578 39.130 0.00 0.00 0.00 3.36
66 67 7.787725 ATAACAAATCACGGATCTAACTTCC 57.212 36.000 0.00 0.00 0.00 3.46
67 68 8.979574 CCTATAACAAATCACGGATCTAACTTC 58.020 37.037 0.00 0.00 0.00 3.01
68 69 8.483758 ACCTATAACAAATCACGGATCTAACTT 58.516 33.333 0.00 0.00 0.00 2.66
69 70 8.019656 ACCTATAACAAATCACGGATCTAACT 57.980 34.615 0.00 0.00 0.00 2.24
70 71 8.658499 AACCTATAACAAATCACGGATCTAAC 57.342 34.615 0.00 0.00 0.00 2.34
71 72 9.976511 CTAACCTATAACAAATCACGGATCTAA 57.023 33.333 0.00 0.00 0.00 2.10
72 73 8.582437 CCTAACCTATAACAAATCACGGATCTA 58.418 37.037 0.00 0.00 0.00 1.98
73 74 7.289317 TCCTAACCTATAACAAATCACGGATCT 59.711 37.037 0.00 0.00 0.00 2.75
74 75 7.439381 TCCTAACCTATAACAAATCACGGATC 58.561 38.462 0.00 0.00 0.00 3.36
75 76 7.369551 TCCTAACCTATAACAAATCACGGAT 57.630 36.000 0.00 0.00 0.00 4.18
76 77 6.795144 TCCTAACCTATAACAAATCACGGA 57.205 37.500 0.00 0.00 0.00 4.69
77 78 7.551617 ACTTTCCTAACCTATAACAAATCACGG 59.448 37.037 0.00 0.00 0.00 4.94
78 79 8.488651 ACTTTCCTAACCTATAACAAATCACG 57.511 34.615 0.00 0.00 0.00 4.35
82 83 9.462606 CCAGAACTTTCCTAACCTATAACAAAT 57.537 33.333 0.00 0.00 0.00 2.32
83 84 8.442374 ACCAGAACTTTCCTAACCTATAACAAA 58.558 33.333 0.00 0.00 0.00 2.83
84 85 7.981142 ACCAGAACTTTCCTAACCTATAACAA 58.019 34.615 0.00 0.00 0.00 2.83
85 86 7.563724 ACCAGAACTTTCCTAACCTATAACA 57.436 36.000 0.00 0.00 0.00 2.41
86 87 7.881751 ACAACCAGAACTTTCCTAACCTATAAC 59.118 37.037 0.00 0.00 0.00 1.89
87 88 7.981142 ACAACCAGAACTTTCCTAACCTATAA 58.019 34.615 0.00 0.00 0.00 0.98
88 89 7.563724 ACAACCAGAACTTTCCTAACCTATA 57.436 36.000 0.00 0.00 0.00 1.31
89 90 6.449830 ACAACCAGAACTTTCCTAACCTAT 57.550 37.500 0.00 0.00 0.00 2.57
90 91 5.899631 ACAACCAGAACTTTCCTAACCTA 57.100 39.130 0.00 0.00 0.00 3.08
91 92 4.790718 ACAACCAGAACTTTCCTAACCT 57.209 40.909 0.00 0.00 0.00 3.50
92 93 8.625786 TTATTACAACCAGAACTTTCCTAACC 57.374 34.615 0.00 0.00 0.00 2.85
95 96 9.720769 CTCTTTATTACAACCAGAACTTTCCTA 57.279 33.333 0.00 0.00 0.00 2.94
96 97 8.218488 ACTCTTTATTACAACCAGAACTTTCCT 58.782 33.333 0.00 0.00 0.00 3.36
97 98 8.290325 CACTCTTTATTACAACCAGAACTTTCC 58.710 37.037 0.00 0.00 0.00 3.13
98 99 9.052759 TCACTCTTTATTACAACCAGAACTTTC 57.947 33.333 0.00 0.00 0.00 2.62
99 100 8.974060 TCACTCTTTATTACAACCAGAACTTT 57.026 30.769 0.00 0.00 0.00 2.66
100 101 8.974060 TTCACTCTTTATTACAACCAGAACTT 57.026 30.769 0.00 0.00 0.00 2.66
101 102 8.429641 TCTTCACTCTTTATTACAACCAGAACT 58.570 33.333 0.00 0.00 0.00 3.01
102 103 8.603242 TCTTCACTCTTTATTACAACCAGAAC 57.397 34.615 0.00 0.00 0.00 3.01
103 104 8.647796 TCTCTTCACTCTTTATTACAACCAGAA 58.352 33.333 0.00 0.00 0.00 3.02
104 105 8.190326 TCTCTTCACTCTTTATTACAACCAGA 57.810 34.615 0.00 0.00 0.00 3.86
105 106 8.833231 TTCTCTTCACTCTTTATTACAACCAG 57.167 34.615 0.00 0.00 0.00 4.00
106 107 9.621629 TTTTCTCTTCACTCTTTATTACAACCA 57.378 29.630 0.00 0.00 0.00 3.67
115 116 9.550406 TCGGTTTATTTTTCTCTTCACTCTTTA 57.450 29.630 0.00 0.00 0.00 1.85
116 117 8.446599 TCGGTTTATTTTTCTCTTCACTCTTT 57.553 30.769 0.00 0.00 0.00 2.52
117 118 8.507249 CATCGGTTTATTTTTCTCTTCACTCTT 58.493 33.333 0.00 0.00 0.00 2.85
118 119 7.878127 TCATCGGTTTATTTTTCTCTTCACTCT 59.122 33.333 0.00 0.00 0.00 3.24
119 120 8.029642 TCATCGGTTTATTTTTCTCTTCACTC 57.970 34.615 0.00 0.00 0.00 3.51
120 121 7.979444 TCATCGGTTTATTTTTCTCTTCACT 57.021 32.000 0.00 0.00 0.00 3.41
121 122 7.537649 GGTTCATCGGTTTATTTTTCTCTTCAC 59.462 37.037 0.00 0.00 0.00 3.18
122 123 7.229707 TGGTTCATCGGTTTATTTTTCTCTTCA 59.770 33.333 0.00 0.00 0.00 3.02
123 124 7.590279 TGGTTCATCGGTTTATTTTTCTCTTC 58.410 34.615 0.00 0.00 0.00 2.87
124 125 7.309194 CCTGGTTCATCGGTTTATTTTTCTCTT 60.309 37.037 0.00 0.00 0.00 2.85
125 126 6.151144 CCTGGTTCATCGGTTTATTTTTCTCT 59.849 38.462 0.00 0.00 0.00 3.10
126 127 6.150474 TCCTGGTTCATCGGTTTATTTTTCTC 59.850 38.462 0.00 0.00 0.00 2.87
127 128 6.007703 TCCTGGTTCATCGGTTTATTTTTCT 58.992 36.000 0.00 0.00 0.00 2.52
128 129 6.262193 TCCTGGTTCATCGGTTTATTTTTC 57.738 37.500 0.00 0.00 0.00 2.29
129 130 6.350949 CCATCCTGGTTCATCGGTTTATTTTT 60.351 38.462 0.00 0.00 31.35 1.94
130 131 5.127031 CCATCCTGGTTCATCGGTTTATTTT 59.873 40.000 0.00 0.00 31.35 1.82
131 132 4.644685 CCATCCTGGTTCATCGGTTTATTT 59.355 41.667 0.00 0.00 31.35 1.40
132 133 4.207165 CCATCCTGGTTCATCGGTTTATT 58.793 43.478 0.00 0.00 31.35 1.40
133 134 3.435026 CCCATCCTGGTTCATCGGTTTAT 60.435 47.826 0.00 0.00 35.17 1.40
134 135 2.092646 CCCATCCTGGTTCATCGGTTTA 60.093 50.000 0.00 0.00 35.17 2.01
135 136 1.340991 CCCATCCTGGTTCATCGGTTT 60.341 52.381 0.00 0.00 35.17 3.27
136 137 0.255890 CCCATCCTGGTTCATCGGTT 59.744 55.000 0.00 0.00 35.17 4.44
137 138 0.620410 TCCCATCCTGGTTCATCGGT 60.620 55.000 0.00 0.00 35.17 4.69
138 139 0.107456 CTCCCATCCTGGTTCATCGG 59.893 60.000 0.00 0.00 35.17 4.18
139 140 0.107456 CCTCCCATCCTGGTTCATCG 59.893 60.000 0.00 0.00 35.17 3.84
140 141 0.475906 CCCTCCCATCCTGGTTCATC 59.524 60.000 0.00 0.00 35.17 2.92
141 142 0.995675 CCCCTCCCATCCTGGTTCAT 60.996 60.000 0.00 0.00 35.17 2.57
142 143 1.619363 CCCCTCCCATCCTGGTTCA 60.619 63.158 0.00 0.00 35.17 3.18
143 144 2.386935 CCCCCTCCCATCCTGGTTC 61.387 68.421 0.00 0.00 35.17 3.62
144 145 2.287194 CCCCCTCCCATCCTGGTT 60.287 66.667 0.00 0.00 35.17 3.67
145 146 3.637544 ACCCCCTCCCATCCTGGT 61.638 66.667 0.00 0.00 35.17 4.00
146 147 3.099170 CACCCCCTCCCATCCTGG 61.099 72.222 0.00 0.00 37.25 4.45
147 148 3.099170 CCACCCCCTCCCATCCTG 61.099 72.222 0.00 0.00 0.00 3.86
148 149 3.637544 ACCACCCCCTCCCATCCT 61.638 66.667 0.00 0.00 0.00 3.24
149 150 3.420482 CACCACCCCCTCCCATCC 61.420 72.222 0.00 0.00 0.00 3.51
150 151 3.420482 CCACCACCCCCTCCCATC 61.420 72.222 0.00 0.00 0.00 3.51
154 155 3.883822 TTCTCCCACCACCCCCTCC 62.884 68.421 0.00 0.00 0.00 4.30
155 156 2.204090 TTCTCCCACCACCCCCTC 60.204 66.667 0.00 0.00 0.00 4.30
156 157 2.204151 CTTCTCCCACCACCCCCT 60.204 66.667 0.00 0.00 0.00 4.79
157 158 2.204090 TCTTCTCCCACCACCCCC 60.204 66.667 0.00 0.00 0.00 5.40
158 159 1.229529 TCTCTTCTCCCACCACCCC 60.230 63.158 0.00 0.00 0.00 4.95
159 160 1.889530 CGTCTCTTCTCCCACCACCC 61.890 65.000 0.00 0.00 0.00 4.61
160 161 0.898789 TCGTCTCTTCTCCCACCACC 60.899 60.000 0.00 0.00 0.00 4.61
161 162 0.966920 TTCGTCTCTTCTCCCACCAC 59.033 55.000 0.00 0.00 0.00 4.16
162 163 1.712056 TTTCGTCTCTTCTCCCACCA 58.288 50.000 0.00 0.00 0.00 4.17
163 164 2.833631 TTTTCGTCTCTTCTCCCACC 57.166 50.000 0.00 0.00 0.00 4.61
181 182 4.504826 CGTGGTTTATTTTCGCTGGTTTTT 59.495 37.500 0.00 0.00 0.00 1.94
182 183 4.045783 CGTGGTTTATTTTCGCTGGTTTT 58.954 39.130 0.00 0.00 0.00 2.43
183 184 3.551250 CCGTGGTTTATTTTCGCTGGTTT 60.551 43.478 0.00 0.00 0.00 3.27
184 185 2.030628 CCGTGGTTTATTTTCGCTGGTT 60.031 45.455 0.00 0.00 0.00 3.67
185 186 1.538075 CCGTGGTTTATTTTCGCTGGT 59.462 47.619 0.00 0.00 0.00 4.00
186 187 1.807742 TCCGTGGTTTATTTTCGCTGG 59.192 47.619 0.00 0.00 0.00 4.85
187 188 2.739913 TCTCCGTGGTTTATTTTCGCTG 59.260 45.455 0.00 0.00 0.00 5.18
188 189 2.740447 GTCTCCGTGGTTTATTTTCGCT 59.260 45.455 0.00 0.00 0.00 4.93
189 190 2.473376 CGTCTCCGTGGTTTATTTTCGC 60.473 50.000 0.00 0.00 0.00 4.70
190 191 2.988493 TCGTCTCCGTGGTTTATTTTCG 59.012 45.455 0.00 0.00 35.01 3.46
191 192 5.121142 TGAATCGTCTCCGTGGTTTATTTTC 59.879 40.000 0.00 0.00 35.01 2.29
192 193 4.998672 TGAATCGTCTCCGTGGTTTATTTT 59.001 37.500 0.00 0.00 35.01 1.82
193 194 4.390909 GTGAATCGTCTCCGTGGTTTATTT 59.609 41.667 0.00 0.00 35.01 1.40
194 195 3.930848 GTGAATCGTCTCCGTGGTTTATT 59.069 43.478 0.00 0.00 35.01 1.40
195 196 3.518590 GTGAATCGTCTCCGTGGTTTAT 58.481 45.455 0.00 0.00 35.01 1.40
196 197 2.353011 GGTGAATCGTCTCCGTGGTTTA 60.353 50.000 0.00 0.00 35.01 2.01
197 198 1.607251 GGTGAATCGTCTCCGTGGTTT 60.607 52.381 0.00 0.00 35.01 3.27
198 199 0.037605 GGTGAATCGTCTCCGTGGTT 60.038 55.000 0.00 0.00 35.01 3.67
199 200 1.183030 TGGTGAATCGTCTCCGTGGT 61.183 55.000 0.00 0.00 39.83 4.16
200 201 0.037697 TTGGTGAATCGTCTCCGTGG 60.038 55.000 0.00 0.00 39.83 4.94
201 202 1.068474 GTTGGTGAATCGTCTCCGTG 58.932 55.000 0.00 0.00 39.83 4.94
202 203 0.966920 AGTTGGTGAATCGTCTCCGT 59.033 50.000 0.00 0.00 39.83 4.69
203 204 1.630148 GAGTTGGTGAATCGTCTCCG 58.370 55.000 0.00 0.00 39.83 4.63
204 205 1.067776 ACGAGTTGGTGAATCGTCTCC 60.068 52.381 0.00 0.00 45.92 3.71
205 206 2.349297 ACGAGTTGGTGAATCGTCTC 57.651 50.000 0.00 0.00 45.92 3.36
209 210 5.524511 TTAATGAACGAGTTGGTGAATCG 57.475 39.130 0.00 0.00 42.04 3.34
210 211 7.360361 ACTTTTAATGAACGAGTTGGTGAATC 58.640 34.615 0.00 0.00 0.00 2.52
211 212 7.272037 ACTTTTAATGAACGAGTTGGTGAAT 57.728 32.000 0.00 0.00 0.00 2.57
212 213 6.687081 ACTTTTAATGAACGAGTTGGTGAA 57.313 33.333 0.00 0.00 0.00 3.18
213 214 7.211573 TCTACTTTTAATGAACGAGTTGGTGA 58.788 34.615 0.00 0.00 0.00 4.02
214 215 7.384115 TCTCTACTTTTAATGAACGAGTTGGTG 59.616 37.037 0.00 0.00 0.00 4.17
215 216 7.439381 TCTCTACTTTTAATGAACGAGTTGGT 58.561 34.615 0.00 0.00 0.00 3.67
216 217 7.884816 TCTCTACTTTTAATGAACGAGTTGG 57.115 36.000 0.00 0.00 0.00 3.77
217 218 8.596380 GGATCTCTACTTTTAATGAACGAGTTG 58.404 37.037 0.00 0.00 0.00 3.16
218 219 7.764901 GGGATCTCTACTTTTAATGAACGAGTT 59.235 37.037 0.00 0.00 0.00 3.01
219 220 7.266400 GGGATCTCTACTTTTAATGAACGAGT 58.734 38.462 0.00 0.00 0.00 4.18
220 221 6.702282 GGGGATCTCTACTTTTAATGAACGAG 59.298 42.308 0.00 0.00 0.00 4.18
221 222 6.155565 TGGGGATCTCTACTTTTAATGAACGA 59.844 38.462 0.00 0.00 0.00 3.85
222 223 6.346096 TGGGGATCTCTACTTTTAATGAACG 58.654 40.000 0.00 0.00 0.00 3.95
223 224 7.565680 TCTGGGGATCTCTACTTTTAATGAAC 58.434 38.462 0.00 0.00 0.00 3.18
224 225 7.147479 CCTCTGGGGATCTCTACTTTTAATGAA 60.147 40.741 0.00 0.00 37.23 2.57
225 226 6.327626 CCTCTGGGGATCTCTACTTTTAATGA 59.672 42.308 0.00 0.00 37.23 2.57
226 227 6.529220 CCTCTGGGGATCTCTACTTTTAATG 58.471 44.000 0.00 0.00 37.23 1.90
227 228 5.072464 GCCTCTGGGGATCTCTACTTTTAAT 59.928 44.000 0.00 0.00 37.23 1.40
228 229 4.409247 GCCTCTGGGGATCTCTACTTTTAA 59.591 45.833 0.00 0.00 37.23 1.52
229 230 3.967987 GCCTCTGGGGATCTCTACTTTTA 59.032 47.826 0.00 0.00 37.23 1.52
230 231 2.774809 GCCTCTGGGGATCTCTACTTTT 59.225 50.000 0.00 0.00 37.23 2.27
231 232 2.403561 GCCTCTGGGGATCTCTACTTT 58.596 52.381 0.00 0.00 37.23 2.66
232 233 1.413808 GGCCTCTGGGGATCTCTACTT 60.414 57.143 0.00 0.00 37.23 2.24
233 234 0.189822 GGCCTCTGGGGATCTCTACT 59.810 60.000 0.00 0.00 37.23 2.57
234 235 0.105453 TGGCCTCTGGGGATCTCTAC 60.105 60.000 3.32 0.00 37.23 2.59
235 236 0.189574 CTGGCCTCTGGGGATCTCTA 59.810 60.000 3.32 0.00 37.23 2.43
236 237 1.074623 CTGGCCTCTGGGGATCTCT 60.075 63.158 3.32 0.00 37.23 3.10
237 238 1.074926 TCTGGCCTCTGGGGATCTC 60.075 63.158 3.32 0.00 37.23 2.75
238 239 1.074623 CTCTGGCCTCTGGGGATCT 60.075 63.158 3.32 0.00 37.23 2.75
239 240 2.146061 CCTCTGGCCTCTGGGGATC 61.146 68.421 3.32 0.00 34.72 3.36
240 241 2.040043 CCTCTGGCCTCTGGGGAT 60.040 66.667 3.32 0.00 34.72 3.85
292 297 4.515718 TGGCACATGCACATGGAA 57.484 50.000 14.73 0.00 42.91 3.53
304 309 0.952280 CATGCTGGAGATCATGGCAC 59.048 55.000 0.00 0.00 37.13 5.01
356 372 1.540617 GGGGTTACTGTCTGGGGGT 60.541 63.158 0.00 0.00 0.00 4.95
361 377 2.240162 GAGCCCGGGGTTACTGTCTG 62.240 65.000 29.16 0.00 0.00 3.51
376 392 0.671781 CAGGCAGTGTACAGTGAGCC 60.672 60.000 30.56 24.79 42.31 4.70
385 401 2.690497 GTGATAGCTCTCAGGCAGTGTA 59.310 50.000 1.37 0.00 34.17 2.90
391 407 4.334837 GCGTGATAGCTCTCAGGC 57.665 61.111 24.84 24.84 46.05 4.85
395 411 1.417372 GCTGATGCGTGATAGCTCTC 58.583 55.000 0.00 0.00 38.13 3.20
396 412 0.033228 GGCTGATGCGTGATAGCTCT 59.967 55.000 0.00 0.00 40.82 4.09
397 413 0.249615 TGGCTGATGCGTGATAGCTC 60.250 55.000 0.00 0.00 40.82 4.09
398 414 0.395686 ATGGCTGATGCGTGATAGCT 59.604 50.000 0.00 0.00 40.82 3.32
401 417 0.886043 GCCATGGCTGATGCGTGATA 60.886 55.000 29.98 0.00 40.82 2.15
402 418 2.191513 GCCATGGCTGATGCGTGAT 61.192 57.895 29.98 0.00 40.82 3.06
403 419 2.825387 GCCATGGCTGATGCGTGA 60.825 61.111 29.98 0.00 40.82 4.35
404 420 3.896133 GGCCATGGCTGATGCGTG 61.896 66.667 34.70 0.00 41.60 5.34
406 422 3.285215 GAGGCCATGGCTGATGCG 61.285 66.667 34.70 0.00 38.98 4.73
407 423 1.897615 GAGAGGCCATGGCTGATGC 60.898 63.158 34.70 18.64 38.98 3.91
457 485 7.537991 CCACGCTTCACTATATACTAAGCTTAC 59.462 40.741 0.86 0.00 40.25 2.34
458 486 7.230108 ACCACGCTTCACTATATACTAAGCTTA 59.770 37.037 5.94 5.94 40.25 3.09
459 487 6.040616 ACCACGCTTCACTATATACTAAGCTT 59.959 38.462 3.48 3.48 40.25 3.74
460 488 5.535406 ACCACGCTTCACTATATACTAAGCT 59.465 40.000 13.21 0.00 40.25 3.74
461 489 5.770417 ACCACGCTTCACTATATACTAAGC 58.230 41.667 0.00 0.00 39.28 3.09
462 490 8.097078 ACTACCACGCTTCACTATATACTAAG 57.903 38.462 0.00 0.00 0.00 2.18
463 491 9.212641 CTACTACCACGCTTCACTATATACTAA 57.787 37.037 0.00 0.00 0.00 2.24
464 492 8.588472 TCTACTACCACGCTTCACTATATACTA 58.412 37.037 0.00 0.00 0.00 1.82
465 493 7.448420 TCTACTACCACGCTTCACTATATACT 58.552 38.462 0.00 0.00 0.00 2.12
466 494 7.664082 TCTACTACCACGCTTCACTATATAC 57.336 40.000 0.00 0.00 0.00 1.47
467 495 8.681486 TTTCTACTACCACGCTTCACTATATA 57.319 34.615 0.00 0.00 0.00 0.86
468 496 7.578310 TTTCTACTACCACGCTTCACTATAT 57.422 36.000 0.00 0.00 0.00 0.86
469 497 7.395190 TTTTCTACTACCACGCTTCACTATA 57.605 36.000 0.00 0.00 0.00 1.31
470 498 5.909621 TTTCTACTACCACGCTTCACTAT 57.090 39.130 0.00 0.00 0.00 2.12
471 499 5.710513 TTTTCTACTACCACGCTTCACTA 57.289 39.130 0.00 0.00 0.00 2.74
472 500 4.595762 TTTTCTACTACCACGCTTCACT 57.404 40.909 0.00 0.00 0.00 3.41
473 501 5.390567 CCATTTTTCTACTACCACGCTTCAC 60.391 44.000 0.00 0.00 0.00 3.18
474 502 4.693566 CCATTTTTCTACTACCACGCTTCA 59.306 41.667 0.00 0.00 0.00 3.02
475 503 4.933400 TCCATTTTTCTACTACCACGCTTC 59.067 41.667 0.00 0.00 0.00 3.86
476 504 4.901868 TCCATTTTTCTACTACCACGCTT 58.098 39.130 0.00 0.00 0.00 4.68
477 505 4.546829 TCCATTTTTCTACTACCACGCT 57.453 40.909 0.00 0.00 0.00 5.07
478 506 5.616488 TTTCCATTTTTCTACTACCACGC 57.384 39.130 0.00 0.00 0.00 5.34
625 678 8.025445 GCTATTGTTATTGCTATTGCTATTGCT 58.975 33.333 14.39 0.00 40.48 3.91
631 684 8.025445 GCTATTGCTATTGTTATTGCTATTGCT 58.975 33.333 0.00 0.00 40.07 3.91
633 686 9.681692 TTGCTATTGCTATTGTTATTGCTATTG 57.318 29.630 0.00 0.00 40.48 1.90
634 687 9.903682 CTTGCTATTGCTATTGTTATTGCTATT 57.096 29.630 0.00 0.00 40.48 1.73
635 688 8.025445 GCTTGCTATTGCTATTGTTATTGCTAT 58.975 33.333 0.00 0.00 40.48 2.97
636 689 7.362662 GCTTGCTATTGCTATTGTTATTGCTA 58.637 34.615 0.00 0.00 40.48 3.49
637 690 6.211515 GCTTGCTATTGCTATTGTTATTGCT 58.788 36.000 0.00 0.00 40.48 3.91
638 691 5.116074 CGCTTGCTATTGCTATTGTTATTGC 59.884 40.000 0.00 0.00 40.48 3.56
639 692 5.626543 CCGCTTGCTATTGCTATTGTTATTG 59.373 40.000 0.00 0.00 40.48 1.90
640 693 5.530915 TCCGCTTGCTATTGCTATTGTTATT 59.469 36.000 0.00 0.00 40.48 1.40
641 694 5.063204 TCCGCTTGCTATTGCTATTGTTAT 58.937 37.500 0.00 0.00 40.48 1.89
642 695 4.447290 TCCGCTTGCTATTGCTATTGTTA 58.553 39.130 0.00 0.00 40.48 2.41
643 696 3.278574 TCCGCTTGCTATTGCTATTGTT 58.721 40.909 0.00 0.00 40.48 2.83
644 697 2.917933 TCCGCTTGCTATTGCTATTGT 58.082 42.857 0.00 0.00 40.48 2.71
645 698 3.499537 TCATCCGCTTGCTATTGCTATTG 59.500 43.478 0.00 0.00 40.48 1.90
646 699 3.743521 TCATCCGCTTGCTATTGCTATT 58.256 40.909 0.00 0.00 40.48 1.73
647 700 3.407424 TCATCCGCTTGCTATTGCTAT 57.593 42.857 0.00 0.00 40.48 2.97
648 701 2.908688 TCATCCGCTTGCTATTGCTA 57.091 45.000 0.00 0.00 40.48 3.49
649 702 1.945394 CTTCATCCGCTTGCTATTGCT 59.055 47.619 0.00 0.00 40.48 3.91
650 703 1.942657 TCTTCATCCGCTTGCTATTGC 59.057 47.619 0.00 0.00 40.20 3.56
651 704 3.003068 CCTTCTTCATCCGCTTGCTATTG 59.997 47.826 0.00 0.00 0.00 1.90
652 705 3.209410 CCTTCTTCATCCGCTTGCTATT 58.791 45.455 0.00 0.00 0.00 1.73
653 706 2.171448 ACCTTCTTCATCCGCTTGCTAT 59.829 45.455 0.00 0.00 0.00 2.97
654 707 1.555075 ACCTTCTTCATCCGCTTGCTA 59.445 47.619 0.00 0.00 0.00 3.49
655 708 0.326264 ACCTTCTTCATCCGCTTGCT 59.674 50.000 0.00 0.00 0.00 3.91
665 718 6.500041 CGTTTTAAACCATGAACCTTCTTCA 58.500 36.000 1.97 0.00 0.00 3.02
677 730 2.295070 GAGGTGTGGCGTTTTAAACCAT 59.705 45.455 1.97 0.00 35.53 3.55
939 1323 2.093606 CGAGAGGATGGATGGATGGATG 60.094 54.545 0.00 0.00 0.00 3.51
946 1330 1.339610 GAGACACGAGAGGATGGATGG 59.660 57.143 0.00 0.00 0.00 3.51
977 1361 1.153989 TCTGCCCCTCGCTAGCTAT 59.846 57.895 13.93 0.00 38.78 2.97
985 1411 2.503061 CATCCTGTCTGCCCCTCG 59.497 66.667 0.00 0.00 0.00 4.63
1083 1509 4.087892 CTCTGCCCCGACCTGGTG 62.088 72.222 2.82 0.00 35.15 4.17
1125 1551 2.415010 CTCTGCCCGGAGATCACG 59.585 66.667 0.73 0.00 35.52 4.35
1286 1718 2.897350 AGCTCTTATTGGCGCCGC 60.897 61.111 23.90 17.18 0.00 6.53
1288 1720 2.056481 CTGCAGCTCTTATTGGCGCC 62.056 60.000 22.73 22.73 0.00 6.53
1289 1721 1.354506 CTGCAGCTCTTATTGGCGC 59.645 57.895 0.00 0.00 0.00 6.53
1290 1722 1.354506 GCTGCAGCTCTTATTGGCG 59.645 57.895 31.33 0.00 38.21 5.69
1291 1723 1.354506 CGCTGCAGCTCTTATTGGC 59.645 57.895 34.22 7.17 39.32 4.52
1617 2049 1.376037 GCCCTTCTCGTGGAACCTG 60.376 63.158 0.00 0.00 0.00 4.00
1890 2328 4.179579 GCGAAGTCGGGCAATGGC 62.180 66.667 0.00 0.00 40.23 4.40
1891 2329 3.508840 GGCGAAGTCGGGCAATGG 61.509 66.667 2.47 0.00 40.23 3.16
2004 2442 4.689345 ACAAACGAATGTAGGTAAGAGCAC 59.311 41.667 0.00 0.00 0.00 4.40
2085 2523 9.982651 ATTGTCACATTACATGGTAGTAGTATC 57.017 33.333 0.00 0.00 33.60 2.24
2106 2544 3.074412 CCCCTCTTACACACACATTGTC 58.926 50.000 0.00 0.00 35.67 3.18
2109 2547 2.305927 CTCCCCCTCTTACACACACATT 59.694 50.000 0.00 0.00 0.00 2.71
2115 2553 2.409064 TTCACTCCCCCTCTTACACA 57.591 50.000 0.00 0.00 0.00 3.72
2166 2614 3.269178 GAACAGAGAAGAATGGCCTCAG 58.731 50.000 3.32 0.00 0.00 3.35
2168 2616 2.026822 TGGAACAGAGAAGAATGGCCTC 60.027 50.000 3.32 0.00 0.00 4.70
2169 2617 1.988107 TGGAACAGAGAAGAATGGCCT 59.012 47.619 3.32 0.00 0.00 5.19
2170 2618 2.496899 TGGAACAGAGAAGAATGGCC 57.503 50.000 0.00 0.00 0.00 5.36
2225 2673 0.029681 ACTATCCTGTGCCCCTCCAT 60.030 55.000 0.00 0.00 0.00 3.41
2289 2737 3.410628 TCGCCACCCTCCATGCAT 61.411 61.111 0.00 0.00 0.00 3.96
2290 2738 4.408821 GTCGCCACCCTCCATGCA 62.409 66.667 0.00 0.00 0.00 3.96
2291 2739 3.704231 ATGTCGCCACCCTCCATGC 62.704 63.158 0.00 0.00 0.00 4.06
2292 2740 1.820906 CATGTCGCCACCCTCCATG 60.821 63.158 0.00 0.00 0.00 3.66
2293 2741 1.995066 TCATGTCGCCACCCTCCAT 60.995 57.895 0.00 0.00 0.00 3.41
2294 2742 2.606213 TCATGTCGCCACCCTCCA 60.606 61.111 0.00 0.00 0.00 3.86
2394 2850 6.325919 CTGCTAGATAGGAGTTAGGAGTTG 57.674 45.833 0.00 0.00 37.05 3.16
2496 2960 1.003233 AACGGAGGAAAGCAGAGGC 60.003 57.895 0.00 0.00 41.61 4.70
2676 3157 1.683365 CTCAACTTGGGCATGGGGG 60.683 63.158 0.00 0.00 0.00 5.40
2705 3186 2.754946 TAAAACTGGCCCAGTAGACG 57.245 50.000 18.61 0.00 44.62 4.18
2709 3190 4.850680 CCACTATTAAAACTGGCCCAGTA 58.149 43.478 18.61 0.77 44.62 2.74
2731 3213 3.243002 GCCTTTCATCTGCATCTGTTAGC 60.243 47.826 0.00 0.00 0.00 3.09
2787 3282 4.777896 AGCCCTGTATACCCTATGTATGTG 59.222 45.833 0.00 0.00 40.42 3.21
2791 3287 4.752621 TGAGCCCTGTATACCCTATGTA 57.247 45.455 0.00 0.00 0.00 2.29
2793 3289 4.160329 TCTTGAGCCCTGTATACCCTATG 58.840 47.826 0.00 0.00 0.00 2.23
2826 3322 1.205893 GTTCTCCAGGGAGCTACTGTG 59.794 57.143 10.55 4.80 41.71 3.66
2938 3437 3.684305 GCATTCCTGGTTTAAACAATGGC 59.316 43.478 19.57 11.93 0.00 4.40
2939 3438 4.252878 GGCATTCCTGGTTTAAACAATGG 58.747 43.478 19.57 16.25 0.00 3.16


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

AutoCloner maintained by Alex Coulton.