Multiple sequence alignment - TraesCS1A01G436400

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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 TraesCS1A01G436400 chr1A 100.000 2570 0 0 1 2570 586607068 586604499 0.000000e+00 4747.0
1 TraesCS1A01G436400 chr1A 89.123 616 60 3 983 1591 586599121 586598506 0.000000e+00 760.0
2 TraesCS1A01G436400 chr1A 99.016 305 3 0 1 305 586615139 586614835 4.830000e-152 547.0
3 TraesCS1A01G436400 chr1A 91.429 140 10 2 1762 1899 586598220 586598081 9.390000e-45 191.0
4 TraesCS1A01G436400 chr1A 87.248 149 9 6 1601 1744 586598462 586598319 7.360000e-36 161.0
5 TraesCS1A01G436400 chr1A 79.042 167 26 8 814 975 586599320 586599158 3.500000e-19 106.0
6 TraesCS1A01G436400 chr1A 85.714 63 4 4 1968 2026 586495716 586495655 7.680000e-06 62.1
7 TraesCS1A01G436400 chr1D 85.138 942 70 26 859 1748 487865175 487864252 0.000000e+00 900.0
8 TraesCS1A01G436400 chr1D 88.950 724 35 19 1782 2463 487864082 487863362 0.000000e+00 852.0
9 TraesCS1A01G436400 chr1D 94.549 477 18 7 305 777 487867486 487867014 0.000000e+00 730.0
10 TraesCS1A01G436400 chr1D 85.377 677 60 22 931 1589 487883634 487884289 0.000000e+00 665.0
11 TraesCS1A01G436400 chr1D 89.308 318 31 1 1246 1563 487858982 487858668 1.850000e-106 396.0
12 TraesCS1A01G436400 chr1D 86.857 350 26 10 2068 2406 487880084 487880424 8.680000e-100 374.0
13 TraesCS1A01G436400 chr1D 81.236 437 37 25 859 1251 487859919 487859484 6.910000e-81 311.0
14 TraesCS1A01G436400 chr1D 88.148 135 12 2 1618 1748 487884436 487884570 9.520000e-35 158.0
15 TraesCS1A01G436400 chr1D 92.523 107 6 1 1611 1717 487858563 487858459 4.430000e-33 152.0
16 TraesCS1A01G436400 chr1D 96.296 81 3 0 1809 1889 487884750 487884830 1.600000e-27 134.0
17 TraesCS1A01G436400 chr1D 95.238 42 2 0 816 857 487865249 487865208 1.650000e-07 67.6
18 TraesCS1A01G436400 chr1D 100.000 34 0 0 814 847 487883560 487883593 2.130000e-06 63.9
19 TraesCS1A01G436400 chr1D 86.441 59 4 3 1968 2023 487875125 487875068 7.680000e-06 62.1
20 TraesCS1A01G436400 chr1B 86.071 761 70 16 1000 1743 679674181 679673440 0.000000e+00 785.0
21 TraesCS1A01G436400 chr1B 84.795 684 43 20 1820 2463 679672893 679672231 4.670000e-177 630.0
22 TraesCS1A01G436400 chr1B 82.249 507 44 21 859 1345 679668706 679668226 1.850000e-106 396.0
23 TraesCS1A01G436400 chr1B 88.449 303 27 6 305 601 679675420 679675120 2.430000e-95 359.0
24 TraesCS1A01G436400 chr1B 87.600 250 27 3 1342 1591 679667799 679667554 1.160000e-73 287.0
25 TraesCS1A01G436400 chr1B 89.899 198 18 2 369 565 679660243 679660047 1.180000e-63 254.0
26 TraesCS1A01G436400 chr1B 86.869 99 8 4 1968 2063 679681478 679681382 3.500000e-19 106.0
27 TraesCS1A01G436400 chr2D 84.670 698 80 17 895 1580 313714894 313714212 0.000000e+00 671.0
28 TraesCS1A01G436400 chr2B 82.764 702 96 17 896 1586 381317251 381316564 1.020000e-168 603.0
29 TraesCS1A01G436400 chr2A 82.879 660 86 14 942 1586 423176329 423176976 3.710000e-158 568.0
30 TraesCS1A01G436400 chr2A 97.727 308 7 0 1 308 248592029 248591722 4.870000e-147 531.0
31 TraesCS1A01G436400 chr2A 96.845 317 8 2 1 317 313997370 313997056 1.750000e-146 529.0
32 TraesCS1A01G436400 chr2A 97.125 313 9 0 1 313 770596182 770595870 1.750000e-146 529.0
33 TraesCS1A01G436400 chr4A 98.039 306 6 0 1 306 695961725 695962030 1.350000e-147 532.0
34 TraesCS1A01G436400 chr4A 98.033 305 6 0 1 305 695953715 695954019 4.870000e-147 531.0
35 TraesCS1A01G436400 chr5A 98.033 305 6 0 1 305 695653847 695654151 4.870000e-147 531.0
36 TraesCS1A01G436400 chr7B 97.125 313 7 2 1 312 671855717 671855406 6.300000e-146 527.0
37 TraesCS1A01G436400 chr7B 91.818 110 8 1 1783 1891 744645638 744645529 4.430000e-33 152.0
38 TraesCS1A01G436400 chr7B 85.185 108 10 4 1782 1889 746380693 746380592 3.500000e-19 106.0
39 TraesCS1A01G436400 chr4B 96.552 319 10 1 1 318 341595021 341594703 6.300000e-146 527.0
40 TraesCS1A01G436400 chr5B 96.296 108 4 0 2463 2570 575061155 575061262 7.310000e-41 178.0
41 TraesCS1A01G436400 chr6A 96.190 105 4 0 2466 2570 531329220 531329324 3.400000e-39 172.0
42 TraesCS1A01G436400 chr4D 96.190 105 4 0 2466 2570 330859843 330859739 3.400000e-39 172.0
43 TraesCS1A01G436400 chr3A 94.595 111 6 0 2460 2570 585605632 585605742 3.400000e-39 172.0
44 TraesCS1A01G436400 chr7D 95.283 106 5 0 2465 2570 568976418 568976523 4.400000e-38 169.0
45 TraesCS1A01G436400 chr7D 91.057 123 6 4 2452 2570 562409510 562409389 7.360000e-36 161.0
46 TraesCS1A01G436400 chr5D 93.750 112 7 0 2459 2570 517310477 517310588 4.400000e-38 169.0
47 TraesCS1A01G436400 chr3B 95.283 106 5 0 2465 2570 235888515 235888620 4.400000e-38 169.0
48 TraesCS1A01G436400 chr3D 92.920 113 8 0 2458 2570 327121796 327121908 5.690000e-37 165.0
49 TraesCS1A01G436400 chr6B 92.593 54 4 0 585 638 471098866 471098813 7.620000e-11 78.7


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 TraesCS1A01G436400 chr1A 586604499 586607068 2569 True 4747.000000 4747 100.000000 1 2570 1 chr1A.!!$R2 2569
1 TraesCS1A01G436400 chr1A 586598081 586599320 1239 True 304.500000 760 86.710500 814 1899 4 chr1A.!!$R4 1085
2 TraesCS1A01G436400 chr1D 487858459 487867486 9027 True 486.942857 900 89.563143 305 2463 7 chr1D.!!$R2 2158
3 TraesCS1A01G436400 chr1D 487880084 487884830 4746 False 278.980000 665 91.335600 814 2406 5 chr1D.!!$F1 1592
4 TraesCS1A01G436400 chr1B 679667554 679675420 7866 True 491.400000 785 85.832800 305 2463 5 chr1B.!!$R3 2158
5 TraesCS1A01G436400 chr2D 313714212 313714894 682 True 671.000000 671 84.670000 895 1580 1 chr2D.!!$R1 685
6 TraesCS1A01G436400 chr2B 381316564 381317251 687 True 603.000000 603 82.764000 896 1586 1 chr2B.!!$R1 690
7 TraesCS1A01G436400 chr2A 423176329 423176976 647 False 568.000000 568 82.879000 942 1586 1 chr2A.!!$F1 644

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
865 3529 0.188342 TTTGAGGAAAAGGCTGCCCT 59.812 50.0 16.57 4.34 45.77 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2057 11293 0.108138 GGTAATCCTCTGCACTGCGT 60.108 55.0 0.0 0.0 0.0 5.24 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
67 68 8.011844 AGCTAATGAATTAAATCCAAAGTCCC 57.988 34.615 0.00 0.00 0.00 4.46
68 69 7.619302 AGCTAATGAATTAAATCCAAAGTCCCA 59.381 33.333 0.00 0.00 0.00 4.37
80 81 7.813087 ATCCAAAGTCCCAAAAATAAATCCT 57.187 32.000 0.00 0.00 0.00 3.24
81 82 7.625498 TCCAAAGTCCCAAAAATAAATCCTT 57.375 32.000 0.00 0.00 0.00 3.36
82 83 8.728596 TCCAAAGTCCCAAAAATAAATCCTTA 57.271 30.769 0.00 0.00 0.00 2.69
83 84 9.160412 TCCAAAGTCCCAAAAATAAATCCTTAA 57.840 29.630 0.00 0.00 0.00 1.85
118 119 1.851267 GGTTGGGACCAGAACCCTT 59.149 57.895 11.95 0.00 46.82 3.95
119 120 1.069775 GGTTGGGACCAGAACCCTTA 58.930 55.000 11.95 0.00 46.82 2.69
120 121 1.271762 GGTTGGGACCAGAACCCTTAC 60.272 57.143 11.95 0.00 46.82 2.34
121 122 1.069775 TTGGGACCAGAACCCTTACC 58.930 55.000 0.00 0.00 46.82 2.85
123 124 1.069775 GGGACCAGAACCCTTACCAA 58.930 55.000 0.00 0.00 43.65 3.67
125 126 2.158430 GGGACCAGAACCCTTACCAAAA 60.158 50.000 0.00 0.00 43.65 2.44
126 127 3.568443 GGACCAGAACCCTTACCAAAAA 58.432 45.455 0.00 0.00 0.00 1.94
127 128 4.157246 GGACCAGAACCCTTACCAAAAAT 58.843 43.478 0.00 0.00 0.00 1.82
128 129 4.591498 GGACCAGAACCCTTACCAAAAATT 59.409 41.667 0.00 0.00 0.00 1.82
130 131 6.439375 GGACCAGAACCCTTACCAAAAATTAT 59.561 38.462 0.00 0.00 0.00 1.28
131 132 7.363530 GGACCAGAACCCTTACCAAAAATTATC 60.364 40.741 0.00 0.00 0.00 1.75
132 133 7.013834 ACCAGAACCCTTACCAAAAATTATCA 58.986 34.615 0.00 0.00 0.00 2.15
133 134 7.511028 ACCAGAACCCTTACCAAAAATTATCAA 59.489 33.333 0.00 0.00 0.00 2.57
135 136 9.203421 CAGAACCCTTACCAAAAATTATCAAAC 57.797 33.333 0.00 0.00 0.00 2.93
155 156 8.592105 TCAAACATTTAAGAAGAGCATTTTGG 57.408 30.769 0.00 0.00 0.00 3.28
156 157 8.420222 TCAAACATTTAAGAAGAGCATTTTGGA 58.580 29.630 0.00 0.00 0.00 3.53
157 158 8.706035 CAAACATTTAAGAAGAGCATTTTGGAG 58.294 33.333 0.00 0.00 0.00 3.86
158 159 6.393171 ACATTTAAGAAGAGCATTTTGGAGC 58.607 36.000 0.00 0.00 0.00 4.70
159 160 6.015180 ACATTTAAGAAGAGCATTTTGGAGCA 60.015 34.615 0.00 0.00 0.00 4.26
161 162 6.594788 TTAAGAAGAGCATTTTGGAGCAAT 57.405 33.333 0.00 0.00 0.00 3.56
162 163 4.451629 AGAAGAGCATTTTGGAGCAATG 57.548 40.909 0.00 0.00 35.12 2.82
163 164 4.084287 AGAAGAGCATTTTGGAGCAATGA 58.916 39.130 0.00 0.00 34.05 2.57
164 165 4.525487 AGAAGAGCATTTTGGAGCAATGAA 59.475 37.500 0.00 0.00 34.05 2.57
165 166 5.187186 AGAAGAGCATTTTGGAGCAATGAAT 59.813 36.000 0.00 0.00 34.05 2.57
166 167 4.755411 AGAGCATTTTGGAGCAATGAATG 58.245 39.130 0.00 0.00 34.05 2.67
168 169 4.755411 AGCATTTTGGAGCAATGAATGAG 58.245 39.130 0.00 0.00 34.05 2.90
169 170 4.464951 AGCATTTTGGAGCAATGAATGAGA 59.535 37.500 0.00 0.00 34.05 3.27
170 171 5.128827 AGCATTTTGGAGCAATGAATGAGAT 59.871 36.000 0.00 0.00 34.05 2.75
171 172 5.815740 GCATTTTGGAGCAATGAATGAGATT 59.184 36.000 0.00 0.00 34.05 2.40
172 173 6.315393 GCATTTTGGAGCAATGAATGAGATTT 59.685 34.615 0.00 0.00 34.05 2.17
173 174 7.465513 GCATTTTGGAGCAATGAATGAGATTTC 60.466 37.037 0.00 0.00 34.05 2.17
174 175 6.845758 TTTGGAGCAATGAATGAGATTTCT 57.154 33.333 0.00 0.00 0.00 2.52
176 177 7.563888 TTGGAGCAATGAATGAGATTTCTAG 57.436 36.000 0.00 0.00 0.00 2.43
177 178 6.060136 TGGAGCAATGAATGAGATTTCTAGG 58.940 40.000 0.00 0.00 0.00 3.02
179 180 6.011122 AGCAATGAATGAGATTTCTAGGGT 57.989 37.500 0.00 0.00 0.00 4.34
180 181 6.430007 AGCAATGAATGAGATTTCTAGGGTT 58.570 36.000 0.00 0.00 0.00 4.11
182 183 7.398332 AGCAATGAATGAGATTTCTAGGGTTTT 59.602 33.333 0.00 0.00 0.00 2.43
184 185 9.362539 CAATGAATGAGATTTCTAGGGTTTTTG 57.637 33.333 0.00 0.00 0.00 2.44
185 186 6.924111 TGAATGAGATTTCTAGGGTTTTTGC 58.076 36.000 0.00 0.00 0.00 3.68
186 187 5.921962 ATGAGATTTCTAGGGTTTTTGCC 57.078 39.130 0.00 0.00 0.00 4.52
197 198 4.634012 GGGTTTTTGCCCCTCTTTTATT 57.366 40.909 0.00 0.00 42.89 1.40
198 199 4.980573 GGGTTTTTGCCCCTCTTTTATTT 58.019 39.130 0.00 0.00 42.89 1.40
200 201 6.170506 GGGTTTTTGCCCCTCTTTTATTTAG 58.829 40.000 0.00 0.00 42.89 1.85
210 211 7.170393 CCCTCTTTTATTTAGGGTTTTCAGG 57.830 40.000 0.00 0.00 44.34 3.86
211 212 6.351033 CCCTCTTTTATTTAGGGTTTTCAGGC 60.351 42.308 0.00 0.00 44.34 4.85
212 213 6.437477 CCTCTTTTATTTAGGGTTTTCAGGCT 59.563 38.462 0.00 0.00 0.00 4.58
213 214 7.039011 CCTCTTTTATTTAGGGTTTTCAGGCTT 60.039 37.037 0.00 0.00 0.00 4.35
214 215 7.892609 TCTTTTATTTAGGGTTTTCAGGCTTC 58.107 34.615 0.00 0.00 0.00 3.86
215 216 6.599356 TTTATTTAGGGTTTTCAGGCTTCC 57.401 37.500 0.00 0.00 0.00 3.46
216 217 3.603965 TTTAGGGTTTTCAGGCTTCCA 57.396 42.857 0.00 0.00 0.00 3.53
218 219 2.702270 AGGGTTTTCAGGCTTCCAAT 57.298 45.000 0.00 0.00 0.00 3.16
219 220 3.825908 AGGGTTTTCAGGCTTCCAATA 57.174 42.857 0.00 0.00 0.00 1.90
220 221 4.337264 AGGGTTTTCAGGCTTCCAATAT 57.663 40.909 0.00 0.00 0.00 1.28
221 222 4.687976 AGGGTTTTCAGGCTTCCAATATT 58.312 39.130 0.00 0.00 0.00 1.28
222 223 4.711846 AGGGTTTTCAGGCTTCCAATATTC 59.288 41.667 0.00 0.00 0.00 1.75
223 224 4.141937 GGGTTTTCAGGCTTCCAATATTCC 60.142 45.833 0.00 0.00 0.00 3.01
224 225 4.711846 GGTTTTCAGGCTTCCAATATTCCT 59.288 41.667 0.00 0.00 0.00 3.36
225 226 5.163509 GGTTTTCAGGCTTCCAATATTCCTC 60.164 44.000 0.00 0.00 0.00 3.71
226 227 4.860802 TTCAGGCTTCCAATATTCCTCA 57.139 40.909 0.00 0.00 0.00 3.86
227 228 4.860802 TCAGGCTTCCAATATTCCTCAA 57.139 40.909 0.00 0.00 0.00 3.02
228 229 4.526970 TCAGGCTTCCAATATTCCTCAAC 58.473 43.478 0.00 0.00 0.00 3.18
230 231 4.578105 CAGGCTTCCAATATTCCTCAACTC 59.422 45.833 0.00 0.00 0.00 3.01
231 232 4.228210 AGGCTTCCAATATTCCTCAACTCA 59.772 41.667 0.00 0.00 0.00 3.41
232 233 4.949856 GGCTTCCAATATTCCTCAACTCAA 59.050 41.667 0.00 0.00 0.00 3.02
233 234 5.067023 GGCTTCCAATATTCCTCAACTCAAG 59.933 44.000 0.00 0.00 0.00 3.02
234 235 5.649831 GCTTCCAATATTCCTCAACTCAAGT 59.350 40.000 0.00 0.00 0.00 3.16
235 236 6.151817 GCTTCCAATATTCCTCAACTCAAGTT 59.848 38.462 0.00 0.00 39.12 2.66
236 237 7.309438 GCTTCCAATATTCCTCAACTCAAGTTT 60.309 37.037 0.00 0.00 35.83 2.66
237 238 7.687941 TCCAATATTCCTCAACTCAAGTTTC 57.312 36.000 0.00 0.00 35.83 2.78
238 239 7.230747 TCCAATATTCCTCAACTCAAGTTTCA 58.769 34.615 0.00 0.00 35.83 2.69
240 241 8.359642 CCAATATTCCTCAACTCAAGTTTCAAA 58.640 33.333 0.00 0.00 35.83 2.69
241 242 9.748708 CAATATTCCTCAACTCAAGTTTCAAAA 57.251 29.630 0.00 0.00 35.83 2.44
258 259 9.793252 AGTTTCAAAAATATAGACATGATGCAC 57.207 29.630 0.00 0.00 0.00 4.57
259 260 9.571810 GTTTCAAAAATATAGACATGATGCACA 57.428 29.630 0.00 0.00 0.00 4.57
262 263 8.905850 TCAAAAATATAGACATGATGCACACAT 58.094 29.630 0.00 0.00 39.98 3.21
263 264 8.964150 CAAAAATATAGACATGATGCACACATG 58.036 33.333 24.68 24.68 46.96 3.21
264 265 8.454570 AAAATATAGACATGATGCACACATGA 57.545 30.769 29.78 15.86 45.22 3.07
266 267 7.668525 ATATAGACATGATGCACACATGAAG 57.331 36.000 29.78 13.29 45.22 3.02
269 270 3.613030 ACATGATGCACACATGAAGCTA 58.387 40.909 29.78 0.00 45.22 3.32
271 272 2.635714 TGATGCACACATGAAGCTAGG 58.364 47.619 0.00 0.00 36.35 3.02
272 273 1.332997 GATGCACACATGAAGCTAGGC 59.667 52.381 0.00 0.00 36.35 3.93
273 274 0.325933 TGCACACATGAAGCTAGGCT 59.674 50.000 0.00 0.00 42.56 4.58
274 275 1.554617 TGCACACATGAAGCTAGGCTA 59.445 47.619 0.00 0.00 38.25 3.93
275 276 2.208431 GCACACATGAAGCTAGGCTAG 58.792 52.381 17.33 17.33 38.25 3.42
277 278 3.715495 CACACATGAAGCTAGGCTAGAG 58.285 50.000 25.37 2.37 38.25 2.43
278 279 2.102252 ACACATGAAGCTAGGCTAGAGC 59.898 50.000 25.37 13.57 38.25 4.09
279 280 2.102084 CACATGAAGCTAGGCTAGAGCA 59.898 50.000 25.37 17.59 42.69 4.26
280 281 2.768527 ACATGAAGCTAGGCTAGAGCAA 59.231 45.455 25.37 7.71 42.69 3.91
282 283 3.465742 TGAAGCTAGGCTAGAGCAATG 57.534 47.619 25.37 0.00 42.69 2.82
283 284 2.142319 GAAGCTAGGCTAGAGCAATGC 58.858 52.381 25.37 8.60 42.69 3.56
284 285 0.396060 AGCTAGGCTAGAGCAATGCC 59.604 55.000 25.37 4.65 46.42 4.40
288 289 3.483954 GGCTAGAGCAATGCCAGAA 57.516 52.632 0.00 0.00 45.46 3.02
289 290 1.307097 GGCTAGAGCAATGCCAGAAG 58.693 55.000 0.00 0.00 45.46 2.85
290 291 0.662085 GCTAGAGCAATGCCAGAAGC 59.338 55.000 0.00 2.53 41.59 3.86
291 292 1.746516 GCTAGAGCAATGCCAGAAGCT 60.747 52.381 0.00 0.00 41.16 3.74
293 294 1.720301 GAGCAATGCCAGAAGCTCG 59.280 57.895 0.00 0.00 43.27 5.03
294 295 1.712977 GAGCAATGCCAGAAGCTCGG 61.713 60.000 0.00 0.00 43.27 4.63
295 296 2.768492 GCAATGCCAGAAGCTCGGG 61.768 63.158 0.00 0.00 44.23 5.14
296 297 1.078214 CAATGCCAGAAGCTCGGGA 60.078 57.895 6.54 0.64 44.23 5.14
297 298 0.465097 CAATGCCAGAAGCTCGGGAT 60.465 55.000 6.54 2.87 44.23 3.85
298 299 0.465097 AATGCCAGAAGCTCGGGATG 60.465 55.000 4.82 0.00 44.23 3.51
300 301 1.817099 GCCAGAAGCTCGGGATGTG 60.817 63.158 6.54 0.00 38.99 3.21
301 302 1.900351 CCAGAAGCTCGGGATGTGA 59.100 57.895 0.00 0.00 33.29 3.58
302 303 0.460987 CCAGAAGCTCGGGATGTGAC 60.461 60.000 0.00 0.00 33.29 3.67
303 304 0.247460 CAGAAGCTCGGGATGTGACA 59.753 55.000 0.00 0.00 0.00 3.58
533 540 6.547141 TCGTCCGTTATTTCTTTCCTCCTATA 59.453 38.462 0.00 0.00 0.00 1.31
565 572 4.809958 TCACATCGTCTGTTTTCGGTTTTA 59.190 37.500 0.00 0.00 35.29 1.52
568 575 5.467399 ACATCGTCTGTTTTCGGTTTTATCA 59.533 36.000 0.00 0.00 32.90 2.15
597 606 4.620589 TCAACCGGTGTTTCCAATAGTA 57.379 40.909 8.52 0.00 35.57 1.82
599 608 2.963432 ACCGGTGTTTCCAATAGTACG 58.037 47.619 6.12 0.00 35.57 3.67
607 616 5.820947 GTGTTTCCAATAGTACGGAATGGAT 59.179 40.000 11.70 0.00 40.89 3.41
613 622 7.969004 TCCAATAGTACGGAATGGATCATTTA 58.031 34.615 8.15 0.00 35.33 1.40
773 782 7.681939 ATCACATTAACAGTAAAATGACCGT 57.318 32.000 13.15 0.00 36.73 4.83
774 783 8.780846 ATCACATTAACAGTAAAATGACCGTA 57.219 30.769 13.15 0.00 36.73 4.02
781 790 9.881529 TTAACAGTAAAATGACCGTAAAATCAC 57.118 29.630 0.00 0.00 0.00 3.06
782 791 7.499321 ACAGTAAAATGACCGTAAAATCACA 57.501 32.000 0.00 0.00 0.00 3.58
783 792 7.581476 ACAGTAAAATGACCGTAAAATCACAG 58.419 34.615 0.00 0.00 0.00 3.66
789 798 7.915293 AATGACCGTAAAATCACAGTGATTA 57.085 32.000 25.93 11.33 45.57 1.75
790 799 6.715344 TGACCGTAAAATCACAGTGATTAC 57.285 37.500 25.93 20.06 45.57 1.89
791 800 5.346551 TGACCGTAAAATCACAGTGATTACG 59.653 40.000 29.21 29.21 45.57 3.18
793 802 6.389091 ACCGTAAAATCACAGTGATTACGTA 58.611 36.000 31.29 21.06 45.57 3.57
794 803 6.308766 ACCGTAAAATCACAGTGATTACGTAC 59.691 38.462 31.29 26.34 45.57 3.67
795 804 6.308524 CCGTAAAATCACAGTGATTACGTACA 59.691 38.462 31.29 14.44 45.57 2.90
796 805 7.148771 CCGTAAAATCACAGTGATTACGTACAA 60.149 37.037 31.29 13.68 45.57 2.41
797 806 7.891220 CGTAAAATCACAGTGATTACGTACAAG 59.109 37.037 28.45 16.62 45.57 3.16
800 809 7.956420 AATCACAGTGATTACGTACAAGAAA 57.044 32.000 24.76 0.00 44.57 2.52
802 811 7.956420 TCACAGTGATTACGTACAAGAAAAT 57.044 32.000 0.00 0.00 0.00 1.82
850 3514 0.547075 TCCACTCCCAAACGGTTTGA 59.453 50.000 29.82 13.60 43.26 2.69
859 3523 2.469826 CAAACGGTTTGAGGAAAAGGC 58.530 47.619 25.43 0.00 43.26 4.35
863 3527 0.318441 GGTTTGAGGAAAAGGCTGCC 59.682 55.000 11.65 11.65 0.00 4.85
864 3528 0.318441 GTTTGAGGAAAAGGCTGCCC 59.682 55.000 16.57 0.00 0.00 5.36
865 3529 0.188342 TTTGAGGAAAAGGCTGCCCT 59.812 50.000 16.57 4.34 45.77 5.19
866 3530 0.540365 TTGAGGAAAAGGCTGCCCTG 60.540 55.000 16.57 0.00 41.90 4.45
867 3531 1.680314 GAGGAAAAGGCTGCCCTGG 60.680 63.158 16.57 0.00 41.90 4.45
868 3532 3.385384 GGAAAAGGCTGCCCTGGC 61.385 66.667 16.57 0.00 41.90 4.85
940 3644 4.292178 GCCTCCTCCTCCATCGCG 62.292 72.222 0.00 0.00 0.00 5.87
957 3661 2.893398 GATCGCCGTCTCCCAACT 59.107 61.111 0.00 0.00 0.00 3.16
993 3704 1.523758 AAAAGATCACCACAGACGCC 58.476 50.000 0.00 0.00 0.00 5.68
995 3706 0.396435 AAGATCACCACAGACGCCAA 59.604 50.000 0.00 0.00 0.00 4.52
1200 9580 1.513373 CGACGAGATGCCGTTCGAA 60.513 57.895 0.00 0.00 43.49 3.71
1258 9638 1.645710 CCCGGGGCAGATATACTTCT 58.354 55.000 14.71 0.00 0.00 2.85
1263 9643 3.406764 GGGGCAGATATACTTCTTGCTG 58.593 50.000 0.00 0.00 0.00 4.41
1510 10320 2.433491 TGGCGCGTGCGAATAGTT 60.433 55.556 19.66 0.00 44.10 2.24
1591 10516 0.319469 CAACACAATGGCGTTTCCCC 60.319 55.000 0.00 0.00 0.00 4.81
1608 10567 3.314331 CGGCAGACAGGGAGGTGT 61.314 66.667 0.00 0.00 0.00 4.16
1739 10704 5.363580 TGATTTTGCCAAAACTTCTCCTCTT 59.636 36.000 4.45 0.00 32.37 2.85
1748 10713 6.017026 CCAAAACTTCTCCTCTTGTTTCTACC 60.017 42.308 0.00 0.00 32.35 3.18
1749 10714 4.522722 ACTTCTCCTCTTGTTTCTACCG 57.477 45.455 0.00 0.00 0.00 4.02
1751 10716 5.075493 ACTTCTCCTCTTGTTTCTACCGTA 58.925 41.667 0.00 0.00 0.00 4.02
1752 10717 5.715753 ACTTCTCCTCTTGTTTCTACCGTAT 59.284 40.000 0.00 0.00 0.00 3.06
1754 10719 7.560626 ACTTCTCCTCTTGTTTCTACCGTATAT 59.439 37.037 0.00 0.00 0.00 0.86
1760 10919 8.077386 CCTCTTGTTTCTACCGTATATTCTCTC 58.923 40.741 0.00 0.00 0.00 3.20
1799 11014 2.759783 CGGGAGCTCATGTCAGTTG 58.240 57.895 17.19 0.00 0.00 3.16
1942 11164 9.549078 TTATTTTTCCAATTTTACTGTTGACCC 57.451 29.630 0.00 0.00 0.00 4.46
1943 11165 4.839668 TTCCAATTTTACTGTTGACCCG 57.160 40.909 0.00 0.00 0.00 5.28
1944 11166 4.088056 TCCAATTTTACTGTTGACCCGA 57.912 40.909 0.00 0.00 0.00 5.14
1945 11167 4.069304 TCCAATTTTACTGTTGACCCGAG 58.931 43.478 0.00 0.00 0.00 4.63
1946 11168 3.365969 CCAATTTTACTGTTGACCCGAGC 60.366 47.826 0.00 0.00 0.00 5.03
1947 11169 2.922740 TTTTACTGTTGACCCGAGCT 57.077 45.000 0.00 0.00 0.00 4.09
1948 11170 2.450609 TTTACTGTTGACCCGAGCTC 57.549 50.000 2.73 2.73 0.00 4.09
1949 11171 1.334160 TTACTGTTGACCCGAGCTCA 58.666 50.000 15.40 0.00 0.00 4.26
1961 11195 2.432510 CCCGAGCTCATAAGAAACTCCT 59.567 50.000 15.40 0.00 0.00 3.69
1968 11202 4.565652 GCTCATAAGAAACTCCTTGTCCCA 60.566 45.833 0.00 0.00 0.00 4.37
2039 11275 9.525409 GTGCTGAAATAAGATATTTGCATCTTT 57.475 29.630 5.65 0.00 41.46 2.52
2064 11300 2.173669 CGGGCCTATCAACGCAGTG 61.174 63.158 0.84 0.00 45.00 3.66
2065 11301 2.472909 GGGCCTATCAACGCAGTGC 61.473 63.158 4.58 4.58 45.00 4.40
2066 11302 1.745115 GGCCTATCAACGCAGTGCA 60.745 57.895 16.83 0.00 45.00 4.57
2085 11322 5.001232 GTGCAGAGGATTACCAAAGTACAA 58.999 41.667 0.00 0.00 38.94 2.41
2093 11330 8.260270 AGGATTACCAAAGTACAACGAAATAC 57.740 34.615 0.00 0.00 38.94 1.89
2120 11357 8.867935 CAACAAGATATAGCTGACTATACATGC 58.132 37.037 0.00 0.00 42.71 4.06
2130 11367 5.406780 GCTGACTATACATGCCACTATCAAC 59.593 44.000 0.00 0.00 0.00 3.18
2133 11370 6.761242 TGACTATACATGCCACTATCAACAAC 59.239 38.462 0.00 0.00 0.00 3.32
2138 11375 5.531634 ACATGCCACTATCAACAACAAAAG 58.468 37.500 0.00 0.00 0.00 2.27
2139 11376 5.301551 ACATGCCACTATCAACAACAAAAGA 59.698 36.000 0.00 0.00 0.00 2.52
2173 11410 0.875908 CCGACGTGATGCATGGGTAG 60.876 60.000 2.46 0.00 0.00 3.18
2234 11485 2.485426 ACTGATGACACCAATCGCAAAG 59.515 45.455 0.00 0.00 0.00 2.77
2239 11490 4.377839 TGACACCAATCGCAAAGAAAAA 57.622 36.364 0.00 0.00 0.00 1.94
2280 11535 3.548745 TGGCCAATGTGAGTGATAGAG 57.451 47.619 0.61 0.00 0.00 2.43
2333 11590 4.159693 ACTGGAAGGAAAAGTCAAACAACC 59.840 41.667 0.00 0.00 39.30 3.77
2335 11592 3.181469 GGAAGGAAAAGTCAAACAACCCC 60.181 47.826 0.00 0.00 0.00 4.95
2423 11680 6.826741 TCAAACTGTTAAAGGGCAGATATACC 59.173 38.462 0.00 0.00 36.62 2.73
2424 11681 5.968676 ACTGTTAAAGGGCAGATATACCA 57.031 39.130 0.00 0.00 36.62 3.25
2463 11720 7.486407 AACCCTGCTCTGAATCATTTAAAAT 57.514 32.000 0.00 0.00 0.00 1.82
2464 11721 7.486407 ACCCTGCTCTGAATCATTTAAAATT 57.514 32.000 0.00 0.00 0.00 1.82
2467 11724 9.305925 CCCTGCTCTGAATCATTTAAAATTTAC 57.694 33.333 0.00 0.00 0.00 2.01
2471 11728 9.521503 GCTCTGAATCATTTAAAATTTACTCCC 57.478 33.333 0.00 0.00 0.00 4.30
2475 11732 8.682710 TGAATCATTTAAAATTTACTCCCTCCG 58.317 33.333 0.00 0.00 0.00 4.63
2478 11735 8.047413 TCATTTAAAATTTACTCCCTCCGTTC 57.953 34.615 0.00 0.00 0.00 3.95
2479 11736 6.822667 TTTAAAATTTACTCCCTCCGTTCC 57.177 37.500 0.00 0.00 0.00 3.62
2480 11737 4.652679 AAAATTTACTCCCTCCGTTCCT 57.347 40.909 0.00 0.00 0.00 3.36
2481 11738 5.767277 AAAATTTACTCCCTCCGTTCCTA 57.233 39.130 0.00 0.00 0.00 2.94
2482 11739 5.970501 AAATTTACTCCCTCCGTTCCTAT 57.029 39.130 0.00 0.00 0.00 2.57
2484 11741 7.628501 AAATTTACTCCCTCCGTTCCTATAT 57.371 36.000 0.00 0.00 0.00 0.86
2485 11742 7.628501 AATTTACTCCCTCCGTTCCTATATT 57.371 36.000 0.00 0.00 0.00 1.28
2486 11743 7.628501 ATTTACTCCCTCCGTTCCTATATTT 57.371 36.000 0.00 0.00 0.00 1.40
2488 11745 5.970501 ACTCCCTCCGTTCCTATATTTTT 57.029 39.130 0.00 0.00 0.00 1.94
2489 11746 5.681639 ACTCCCTCCGTTCCTATATTTTTG 58.318 41.667 0.00 0.00 0.00 2.44
2491 11748 5.677567 TCCCTCCGTTCCTATATTTTTGTC 58.322 41.667 0.00 0.00 0.00 3.18
2492 11749 5.427481 TCCCTCCGTTCCTATATTTTTGTCT 59.573 40.000 0.00 0.00 0.00 3.41
2493 11750 6.069847 TCCCTCCGTTCCTATATTTTTGTCTT 60.070 38.462 0.00 0.00 0.00 3.01
2495 11752 7.122204 CCCTCCGTTCCTATATTTTTGTCTTTT 59.878 37.037 0.00 0.00 0.00 2.27
2496 11753 8.520351 CCTCCGTTCCTATATTTTTGTCTTTTT 58.480 33.333 0.00 0.00 0.00 1.94
2513 11770 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
2514 11771 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 7.619302 TGGGACTTTGGATTTAATTCATTAGCT 59.381 33.333 0.00 0.00 0.00 3.32
43 44 7.781056 TGGGACTTTGGATTTAATTCATTAGC 58.219 34.615 0.20 0.00 0.00 3.09
53 54 9.952030 GGATTTATTTTTGGGACTTTGGATTTA 57.048 29.630 0.00 0.00 0.00 1.40
54 55 8.668653 AGGATTTATTTTTGGGACTTTGGATTT 58.331 29.630 0.00 0.00 0.00 2.17
56 57 7.813087 AGGATTTATTTTTGGGACTTTGGAT 57.187 32.000 0.00 0.00 0.00 3.41
58 59 9.785982 TTTAAGGATTTATTTTTGGGACTTTGG 57.214 29.630 0.00 0.00 0.00 3.28
83 84 9.290988 GGTCCCAACCAAAATATTAAACATTTT 57.709 29.630 5.67 5.67 45.68 1.82
101 102 1.271762 GGTAAGGGTTCTGGTCCCAAC 60.272 57.143 3.79 1.66 46.82 3.77
102 103 1.069775 GGTAAGGGTTCTGGTCCCAA 58.930 55.000 3.79 0.00 46.82 4.12
103 104 0.104356 TGGTAAGGGTTCTGGTCCCA 60.104 55.000 3.79 0.00 46.82 4.37
104 105 1.069775 TTGGTAAGGGTTCTGGTCCC 58.930 55.000 0.00 0.00 44.90 4.46
105 106 2.963599 TTTGGTAAGGGTTCTGGTCC 57.036 50.000 0.00 0.00 0.00 4.46
106 107 5.801531 AATTTTTGGTAAGGGTTCTGGTC 57.198 39.130 0.00 0.00 0.00 4.02
108 109 7.475137 TGATAATTTTTGGTAAGGGTTCTGG 57.525 36.000 0.00 0.00 0.00 3.86
110 111 8.929487 TGTTTGATAATTTTTGGTAAGGGTTCT 58.071 29.630 0.00 0.00 0.00 3.01
130 131 8.420222 TCCAAAATGCTCTTCTTAAATGTTTGA 58.580 29.630 0.00 0.00 0.00 2.69
131 132 8.592105 TCCAAAATGCTCTTCTTAAATGTTTG 57.408 30.769 0.00 0.00 0.00 2.93
132 133 7.386025 GCTCCAAAATGCTCTTCTTAAATGTTT 59.614 33.333 0.00 0.00 0.00 2.83
133 134 6.870439 GCTCCAAAATGCTCTTCTTAAATGTT 59.130 34.615 0.00 0.00 0.00 2.71
135 136 6.392354 TGCTCCAAAATGCTCTTCTTAAATG 58.608 36.000 0.00 0.00 0.00 2.32
138 139 6.209192 TCATTGCTCCAAAATGCTCTTCTTAA 59.791 34.615 0.00 0.00 35.43 1.85
139 140 5.711506 TCATTGCTCCAAAATGCTCTTCTTA 59.288 36.000 0.00 0.00 35.43 2.10
141 142 4.084287 TCATTGCTCCAAAATGCTCTTCT 58.916 39.130 0.00 0.00 35.43 2.85
142 143 4.445452 TCATTGCTCCAAAATGCTCTTC 57.555 40.909 0.00 0.00 35.43 2.87
144 145 4.464951 TCATTCATTGCTCCAAAATGCTCT 59.535 37.500 0.00 0.00 35.43 4.09
145 146 4.751060 TCATTCATTGCTCCAAAATGCTC 58.249 39.130 0.00 0.00 35.43 4.26
146 147 4.464951 TCTCATTCATTGCTCCAAAATGCT 59.535 37.500 0.00 0.00 35.43 3.79
147 148 4.751060 TCTCATTCATTGCTCCAAAATGC 58.249 39.130 0.00 0.00 35.43 3.56
152 153 6.544931 CCTAGAAATCTCATTCATTGCTCCAA 59.455 38.462 0.00 0.00 0.00 3.53
153 154 6.060136 CCTAGAAATCTCATTCATTGCTCCA 58.940 40.000 0.00 0.00 0.00 3.86
155 156 6.060788 ACCCTAGAAATCTCATTCATTGCTC 58.939 40.000 0.00 0.00 0.00 4.26
156 157 6.011122 ACCCTAGAAATCTCATTCATTGCT 57.989 37.500 0.00 0.00 0.00 3.91
157 158 6.705863 AACCCTAGAAATCTCATTCATTGC 57.294 37.500 0.00 0.00 0.00 3.56
158 159 9.362539 CAAAAACCCTAGAAATCTCATTCATTG 57.637 33.333 0.00 0.00 0.00 2.82
159 160 8.037166 GCAAAAACCCTAGAAATCTCATTCATT 58.963 33.333 0.00 0.00 0.00 2.57
161 162 6.071391 GGCAAAAACCCTAGAAATCTCATTCA 60.071 38.462 0.00 0.00 0.00 2.57
162 163 6.333416 GGCAAAAACCCTAGAAATCTCATTC 58.667 40.000 0.00 0.00 0.00 2.67
163 164 6.286240 GGCAAAAACCCTAGAAATCTCATT 57.714 37.500 0.00 0.00 0.00 2.57
164 165 5.921962 GGCAAAAACCCTAGAAATCTCAT 57.078 39.130 0.00 0.00 0.00 2.90
177 178 6.170506 CCTAAATAAAAGAGGGGCAAAAACC 58.829 40.000 0.00 0.00 0.00 3.27
179 180 6.367374 CCCTAAATAAAAGAGGGGCAAAAA 57.633 37.500 0.00 0.00 45.53 1.94
187 188 6.437477 AGCCTGAAAACCCTAAATAAAAGAGG 59.563 38.462 0.00 0.00 0.00 3.69
188 189 7.468141 AGCCTGAAAACCCTAAATAAAAGAG 57.532 36.000 0.00 0.00 0.00 2.85
189 190 7.039293 GGAAGCCTGAAAACCCTAAATAAAAGA 60.039 37.037 0.00 0.00 0.00 2.52
190 191 7.097192 GGAAGCCTGAAAACCCTAAATAAAAG 58.903 38.462 0.00 0.00 0.00 2.27
191 192 6.555360 TGGAAGCCTGAAAACCCTAAATAAAA 59.445 34.615 0.00 0.00 0.00 1.52
194 195 5.263872 TGGAAGCCTGAAAACCCTAAATA 57.736 39.130 0.00 0.00 0.00 1.40
195 196 4.126520 TGGAAGCCTGAAAACCCTAAAT 57.873 40.909 0.00 0.00 0.00 1.40
196 197 3.603965 TGGAAGCCTGAAAACCCTAAA 57.396 42.857 0.00 0.00 0.00 1.85
197 198 3.603965 TTGGAAGCCTGAAAACCCTAA 57.396 42.857 0.00 0.00 0.00 2.69
198 199 3.825908 ATTGGAAGCCTGAAAACCCTA 57.174 42.857 0.00 0.00 0.00 3.53
200 201 4.141937 GGAATATTGGAAGCCTGAAAACCC 60.142 45.833 0.00 0.00 0.00 4.11
202 203 5.418840 TGAGGAATATTGGAAGCCTGAAAAC 59.581 40.000 0.00 0.00 0.00 2.43
203 204 5.579047 TGAGGAATATTGGAAGCCTGAAAA 58.421 37.500 0.00 0.00 0.00 2.29
204 205 5.191727 TGAGGAATATTGGAAGCCTGAAA 57.808 39.130 0.00 0.00 0.00 2.69
205 206 4.860802 TGAGGAATATTGGAAGCCTGAA 57.139 40.909 0.00 0.00 0.00 3.02
207 208 4.530875 AGTTGAGGAATATTGGAAGCCTG 58.469 43.478 0.00 0.00 0.00 4.85
209 210 4.526970 TGAGTTGAGGAATATTGGAAGCC 58.473 43.478 0.00 0.00 0.00 4.35
210 211 5.649831 ACTTGAGTTGAGGAATATTGGAAGC 59.350 40.000 0.00 0.00 0.00 3.86
211 212 7.693969 AACTTGAGTTGAGGAATATTGGAAG 57.306 36.000 0.00 0.00 36.80 3.46
212 213 7.723616 TGAAACTTGAGTTGAGGAATATTGGAA 59.276 33.333 0.00 0.00 38.44 3.53
213 214 7.230747 TGAAACTTGAGTTGAGGAATATTGGA 58.769 34.615 0.00 0.00 38.44 3.53
214 215 7.452880 TGAAACTTGAGTTGAGGAATATTGG 57.547 36.000 0.00 0.00 38.44 3.16
215 216 9.748708 TTTTGAAACTTGAGTTGAGGAATATTG 57.251 29.630 0.00 0.00 38.44 1.90
232 233 9.793252 GTGCATCATGTCTATATTTTTGAAACT 57.207 29.630 0.00 0.00 0.00 2.66
233 234 9.571810 TGTGCATCATGTCTATATTTTTGAAAC 57.428 29.630 0.00 0.00 0.00 2.78
234 235 9.571810 GTGTGCATCATGTCTATATTTTTGAAA 57.428 29.630 0.00 0.00 0.00 2.69
235 236 8.738106 TGTGTGCATCATGTCTATATTTTTGAA 58.262 29.630 0.00 0.00 0.00 2.69
236 237 8.278729 TGTGTGCATCATGTCTATATTTTTGA 57.721 30.769 0.00 0.00 0.00 2.69
237 238 8.964150 CATGTGTGCATCATGTCTATATTTTTG 58.036 33.333 19.74 0.24 38.17 2.44
238 239 8.905850 TCATGTGTGCATCATGTCTATATTTTT 58.094 29.630 23.97 0.00 42.03 1.94
240 241 8.454570 TTCATGTGTGCATCATGTCTATATTT 57.545 30.769 23.97 0.00 42.03 1.40
241 242 7.308408 GCTTCATGTGTGCATCATGTCTATATT 60.308 37.037 23.97 0.00 42.03 1.28
242 243 6.148976 GCTTCATGTGTGCATCATGTCTATAT 59.851 38.462 23.97 0.00 42.03 0.86
244 245 4.275196 GCTTCATGTGTGCATCATGTCTAT 59.725 41.667 23.97 0.00 42.03 1.98
245 246 3.624410 GCTTCATGTGTGCATCATGTCTA 59.376 43.478 23.97 14.81 42.03 2.59
246 247 2.422479 GCTTCATGTGTGCATCATGTCT 59.578 45.455 23.97 0.00 42.03 3.41
247 248 2.422479 AGCTTCATGTGTGCATCATGTC 59.578 45.455 23.97 17.33 42.03 3.06
248 249 2.443416 AGCTTCATGTGTGCATCATGT 58.557 42.857 23.97 10.38 42.03 3.21
249 250 3.003378 CCTAGCTTCATGTGTGCATCATG 59.997 47.826 21.12 21.12 42.53 3.07
251 252 2.635714 CCTAGCTTCATGTGTGCATCA 58.364 47.619 0.00 0.00 31.99 3.07
253 254 1.064906 AGCCTAGCTTCATGTGTGCAT 60.065 47.619 0.00 0.00 33.89 3.96
254 255 0.325933 AGCCTAGCTTCATGTGTGCA 59.674 50.000 0.00 0.00 33.89 4.57
255 256 2.159043 TCTAGCCTAGCTTCATGTGTGC 60.159 50.000 0.00 0.00 40.44 4.57
256 257 3.715495 CTCTAGCCTAGCTTCATGTGTG 58.285 50.000 0.00 0.00 40.44 3.82
258 259 2.102084 TGCTCTAGCCTAGCTTCATGTG 59.898 50.000 0.00 0.00 40.44 3.21
259 260 2.392662 TGCTCTAGCCTAGCTTCATGT 58.607 47.619 0.00 0.00 40.44 3.21
262 263 2.484417 GCATTGCTCTAGCCTAGCTTCA 60.484 50.000 0.16 0.00 40.44 3.02
263 264 2.142319 GCATTGCTCTAGCCTAGCTTC 58.858 52.381 0.16 0.00 40.44 3.86
264 265 1.202746 GGCATTGCTCTAGCCTAGCTT 60.203 52.381 8.82 0.00 44.92 3.74
266 267 2.925594 GGCATTGCTCTAGCCTAGC 58.074 57.895 8.82 0.66 44.92 3.42
271 272 0.662085 GCTTCTGGCATTGCTCTAGC 59.338 55.000 8.82 8.82 41.35 3.42
272 273 2.211806 GAGCTTCTGGCATTGCTCTAG 58.788 52.381 21.24 5.33 45.78 2.43
273 274 1.472201 CGAGCTTCTGGCATTGCTCTA 60.472 52.381 23.79 0.00 46.70 2.43
274 275 0.743701 CGAGCTTCTGGCATTGCTCT 60.744 55.000 23.79 5.79 46.70 4.09
275 276 1.712977 CCGAGCTTCTGGCATTGCTC 61.713 60.000 19.64 19.64 45.79 4.26
277 278 2.768492 CCCGAGCTTCTGGCATTGC 61.768 63.158 0.00 0.00 44.79 3.56
278 279 0.465097 ATCCCGAGCTTCTGGCATTG 60.465 55.000 0.00 0.00 44.79 2.82
279 280 0.465097 CATCCCGAGCTTCTGGCATT 60.465 55.000 0.00 0.00 44.79 3.56
280 281 1.147824 CATCCCGAGCTTCTGGCAT 59.852 57.895 0.00 0.00 44.79 4.40
282 283 1.817099 CACATCCCGAGCTTCTGGC 60.817 63.158 0.00 0.00 42.19 4.85
283 284 0.460987 GTCACATCCCGAGCTTCTGG 60.461 60.000 0.00 0.00 0.00 3.86
284 285 0.247460 TGTCACATCCCGAGCTTCTG 59.753 55.000 0.00 0.00 0.00 3.02
285 286 0.976641 TTGTCACATCCCGAGCTTCT 59.023 50.000 0.00 0.00 0.00 2.85
286 287 2.029838 ATTGTCACATCCCGAGCTTC 57.970 50.000 0.00 0.00 0.00 3.86
288 289 4.774726 AGATATATTGTCACATCCCGAGCT 59.225 41.667 0.00 0.00 0.00 4.09
289 290 4.867047 CAGATATATTGTCACATCCCGAGC 59.133 45.833 0.00 0.00 0.00 5.03
290 291 6.030548 ACAGATATATTGTCACATCCCGAG 57.969 41.667 0.00 0.00 0.00 4.63
291 292 7.533289 TTACAGATATATTGTCACATCCCGA 57.467 36.000 4.48 0.00 0.00 5.14
292 293 8.659491 CATTTACAGATATATTGTCACATCCCG 58.341 37.037 4.48 0.00 0.00 5.14
293 294 9.725019 TCATTTACAGATATATTGTCACATCCC 57.275 33.333 4.48 0.00 0.00 3.85
364 367 5.751509 CACGTGGGATATAAGTGAAAATCGA 59.248 40.000 7.95 0.00 35.03 3.59
533 540 0.251832 AGACGATGTGAGGTGGAGGT 60.252 55.000 0.00 0.00 0.00 3.85
575 584 3.822940 ACTATTGGAAACACCGGTTGAA 58.177 40.909 2.97 0.00 42.67 2.69
597 606 5.253330 ACTGTTGTAAATGATCCATTCCGT 58.747 37.500 0.00 0.00 32.43 4.69
599 608 7.396540 AGAACTGTTGTAAATGATCCATTCC 57.603 36.000 0.00 0.00 32.43 3.01
607 616 5.472137 GGCCTACAAGAACTGTTGTAAATGA 59.528 40.000 0.00 0.00 41.31 2.57
613 622 3.508845 ATGGCCTACAAGAACTGTTGT 57.491 42.857 3.32 0.00 43.22 3.32
761 770 7.577979 TCACTGTGATTTTACGGTCATTTTAC 58.422 34.615 6.36 0.00 38.07 2.01
767 776 5.346551 CGTAATCACTGTGATTTTACGGTCA 59.653 40.000 31.68 17.35 44.03 4.02
769 778 5.232463 ACGTAATCACTGTGATTTTACGGT 58.768 37.500 36.50 27.14 45.62 4.83
770 779 5.773239 ACGTAATCACTGTGATTTTACGG 57.227 39.130 36.50 26.74 45.62 4.02
772 781 8.918658 TCTTGTACGTAATCACTGTGATTTTAC 58.081 33.333 33.40 28.21 44.03 2.01
773 782 9.478768 TTCTTGTACGTAATCACTGTGATTTTA 57.521 29.630 33.40 21.47 44.03 1.52
774 783 7.956420 TCTTGTACGTAATCACTGTGATTTT 57.044 32.000 33.40 22.29 44.03 1.82
779 788 8.067784 ACAATTTTCTTGTACGTAATCACTGTG 58.932 33.333 0.17 0.17 0.00 3.66
780 789 8.149973 ACAATTTTCTTGTACGTAATCACTGT 57.850 30.769 0.00 0.00 0.00 3.55
781 790 9.525007 GTACAATTTTCTTGTACGTAATCACTG 57.475 33.333 11.25 0.00 43.30 3.66
791 800 8.497554 TGGTGAATACGTACAATTTTCTTGTAC 58.502 33.333 15.06 15.06 46.73 2.90
793 802 7.357303 GTGGTGAATACGTACAATTTTCTTGT 58.643 34.615 0.00 0.00 36.49 3.16
794 803 6.518395 CGTGGTGAATACGTACAATTTTCTTG 59.482 38.462 0.00 0.00 36.83 3.02
795 804 6.595794 CGTGGTGAATACGTACAATTTTCTT 58.404 36.000 0.00 0.00 36.83 2.52
796 805 6.160664 CGTGGTGAATACGTACAATTTTCT 57.839 37.500 0.00 0.00 36.83 2.52
850 3514 2.442413 CCAGGGCAGCCTTTTCCT 59.558 61.111 12.43 0.00 0.00 3.36
863 3527 2.438434 CGTTTAGCAGGGGCCAGG 60.438 66.667 4.39 0.00 42.56 4.45
875 3571 3.936453 GGAATATGACACAGTGGCGTTTA 59.064 43.478 6.39 0.00 0.00 2.01
940 3644 1.227002 GAGTTGGGAGACGGCGATC 60.227 63.158 16.62 11.34 0.00 3.69
957 3661 5.384063 TCTTTTTGTTGTGTGAGCTTTGA 57.616 34.783 0.00 0.00 0.00 2.69
993 3704 1.259609 TGCAGAGCCCCATTTTCTTG 58.740 50.000 0.00 0.00 0.00 3.02
995 3706 1.272872 ACATGCAGAGCCCCATTTTCT 60.273 47.619 0.00 0.00 0.00 2.52
1329 9709 0.676736 CCTTTTTAACAAGGGCCGCA 59.323 50.000 11.93 0.00 39.95 5.69
1335 9715 3.462982 GGTGTTGGCCTTTTTAACAAGG 58.537 45.455 14.93 14.93 45.70 3.61
1338 9718 1.202428 GCGGTGTTGGCCTTTTTAACA 60.202 47.619 3.32 2.31 32.39 2.41
1506 10316 1.686325 GCTGCATCCTCCCGGAACTA 61.686 60.000 0.73 0.00 44.02 2.24
1591 10516 2.397413 AAACACCTCCCTGTCTGCCG 62.397 60.000 0.00 0.00 0.00 5.69
1598 10534 3.325135 ACAGAGTCTAAAACACCTCCCTG 59.675 47.826 0.00 0.00 0.00 4.45
1599 10535 3.588569 ACAGAGTCTAAAACACCTCCCT 58.411 45.455 0.00 0.00 0.00 4.20
1645 10606 3.635373 AGACACAAACTCGACTAACAGGA 59.365 43.478 0.00 0.00 0.00 3.86
1739 10704 7.893124 AAGGAGAGAATATACGGTAGAAACA 57.107 36.000 0.00 0.00 0.00 2.83
1748 10713 3.243771 ACCGGCAAAGGAGAGAATATACG 60.244 47.826 0.00 0.00 34.73 3.06
1749 10714 4.338379 ACCGGCAAAGGAGAGAATATAC 57.662 45.455 0.00 0.00 34.73 1.47
1751 10716 3.933861 AACCGGCAAAGGAGAGAATAT 57.066 42.857 0.00 0.00 34.73 1.28
1752 10717 3.343617 CAAACCGGCAAAGGAGAGAATA 58.656 45.455 0.00 0.00 34.73 1.75
1754 10719 1.604604 CAAACCGGCAAAGGAGAGAA 58.395 50.000 0.00 0.00 34.73 2.87
1760 10919 1.743321 TTCCAGCAAACCGGCAAAGG 61.743 55.000 0.00 0.00 35.83 3.11
1799 11014 1.739466 TGTGGCTGAAAAGATGATCGC 59.261 47.619 0.00 0.00 0.00 4.58
1925 11147 3.502211 AGCTCGGGTCAACAGTAAAATTG 59.498 43.478 0.00 0.00 0.00 2.32
1938 11160 3.449632 GAGTTTCTTATGAGCTCGGGTC 58.550 50.000 9.64 0.00 0.00 4.46
1940 11162 2.432510 AGGAGTTTCTTATGAGCTCGGG 59.567 50.000 9.64 0.00 31.46 5.14
1941 11163 3.810310 AGGAGTTTCTTATGAGCTCGG 57.190 47.619 9.64 0.00 31.46 4.63
1942 11164 4.499183 ACAAGGAGTTTCTTATGAGCTCG 58.501 43.478 9.64 0.00 31.46 5.03
1943 11165 4.873259 GGACAAGGAGTTTCTTATGAGCTC 59.127 45.833 6.82 6.82 0.00 4.09
1944 11166 4.323868 GGGACAAGGAGTTTCTTATGAGCT 60.324 45.833 0.00 0.00 0.00 4.09
1945 11167 3.942115 GGGACAAGGAGTTTCTTATGAGC 59.058 47.826 0.00 0.00 0.00 4.26
1946 11168 5.165961 TGGGACAAGGAGTTTCTTATGAG 57.834 43.478 0.00 0.00 31.92 2.90
1961 11195 6.633500 CTCACAAAGAGTTATTTGGGACAA 57.367 37.500 0.34 0.00 45.33 3.18
2039 11275 1.406341 CGTTGATAGGCCCGAGGAAAA 60.406 52.381 0.00 0.00 0.00 2.29
2048 11284 1.709147 CTGCACTGCGTTGATAGGCC 61.709 60.000 0.00 0.00 34.30 5.19
2057 11293 0.108138 GGTAATCCTCTGCACTGCGT 60.108 55.000 0.00 0.00 0.00 5.24
2063 11299 4.901197 TGTACTTTGGTAATCCTCTGCA 57.099 40.909 0.00 0.00 34.23 4.41
2064 11300 4.092968 CGTTGTACTTTGGTAATCCTCTGC 59.907 45.833 0.00 0.00 34.23 4.26
2065 11301 5.475719 TCGTTGTACTTTGGTAATCCTCTG 58.524 41.667 0.00 0.00 34.23 3.35
2066 11302 5.733620 TCGTTGTACTTTGGTAATCCTCT 57.266 39.130 0.00 0.00 34.23 3.69
2085 11322 7.438459 GTCAGCTATATCTTGTTGGTATTTCGT 59.562 37.037 0.00 0.00 0.00 3.85
2093 11330 9.363763 CATGTATAGTCAGCTATATCTTGTTGG 57.636 37.037 0.00 0.00 40.90 3.77
2130 11367 9.708222 CGGTGAGATATTATTCTTCTTTTGTTG 57.292 33.333 0.00 0.00 0.00 3.33
2133 11370 8.269424 CGTCGGTGAGATATTATTCTTCTTTTG 58.731 37.037 0.00 0.00 0.00 2.44
2190 11428 6.716628 AGTGGATATGGTTTTGCCTATATGTG 59.283 38.462 0.00 0.00 38.35 3.21
2244 11495 8.963725 CACATTGGCCAACATATATGATATTCT 58.036 33.333 23.27 0.00 0.00 2.40
2328 11585 3.368739 CCTTAACGATTCGTAGGGGTTGT 60.369 47.826 16.87 1.40 39.99 3.32
2333 11590 4.382345 AGTTCCTTAACGATTCGTAGGG 57.618 45.455 21.91 18.18 39.99 3.53
2361 11618 4.170468 AGCCCTTCAGAAAAAGAGAACA 57.830 40.909 0.00 0.00 0.00 3.18
2405 11662 5.063880 CCTGTGGTATATCTGCCCTTTAAC 58.936 45.833 0.00 0.00 0.00 2.01
2407 11664 4.562767 TCCTGTGGTATATCTGCCCTTTA 58.437 43.478 0.00 0.00 0.00 1.85
2423 11680 6.773638 AGCAGGGTTAATATATTCTCCTGTG 58.226 40.000 25.82 18.99 41.49 3.66
2424 11681 6.789959 AGAGCAGGGTTAATATATTCTCCTGT 59.210 38.462 25.82 18.68 41.49 4.00
2458 11715 5.767277 AGGAACGGAGGGAGTAAATTTTA 57.233 39.130 0.00 0.00 0.00 1.52
2463 11720 7.441903 AAAATATAGGAACGGAGGGAGTAAA 57.558 36.000 0.00 0.00 0.00 2.01
2464 11721 7.092757 ACAAAAATATAGGAACGGAGGGAGTAA 60.093 37.037 0.00 0.00 0.00 2.24
2467 11724 5.681639 ACAAAAATATAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2468 11725 5.427481 AGACAAAAATATAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2469 11726 5.681639 AGACAAAAATATAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2470 11727 7.625828 AAAGACAAAAATATAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
2488 11745 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
2492 11749 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
2493 11750 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
2495 11752 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
2496 11753 7.252612 TGTGGTAGTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
2497 11754 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
2499 11756 7.402054 TGTATGTGGTAGTCCATTTGAAATCT 58.598 34.615 0.00 0.00 46.20 2.40
2500 11757 7.552687 TCTGTATGTGGTAGTCCATTTGAAATC 59.447 37.037 0.00 0.00 46.20 2.17
2501 11758 7.402054 TCTGTATGTGGTAGTCCATTTGAAAT 58.598 34.615 0.00 0.00 46.20 2.17
2502 11759 6.774673 TCTGTATGTGGTAGTCCATTTGAAA 58.225 36.000 0.00 0.00 46.20 2.69
2504 11761 6.070251 ACATCTGTATGTGGTAGTCCATTTGA 60.070 38.462 0.00 0.00 44.79 2.69
2505 11762 6.115446 ACATCTGTATGTGGTAGTCCATTTG 58.885 40.000 0.00 0.00 44.79 2.32
2506 11763 6.313519 ACATCTGTATGTGGTAGTCCATTT 57.686 37.500 0.00 0.00 44.79 2.32
2507 11764 5.957771 ACATCTGTATGTGGTAGTCCATT 57.042 39.130 0.00 0.00 44.79 3.16


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

AutoCloner maintained by Alex Coulton.