Multiple sequence alignment - TraesCS7D01G400500

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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 TraesCS7D01G400500 chr7D 100.000 3245 0 0 1 3245 517553178 517556422 0.000000e+00 5993.0
1 TraesCS7D01G400500 chr7A 88.862 2864 157 62 447 3239 592261149 592263921 0.000000e+00 3373.0
2 TraesCS7D01G400500 chr7A 86.364 66 9 0 91 156 208136009 208136074 4.490000e-09 73.1
3 TraesCS7D01G400500 chr7B 94.210 1779 84 10 603 2368 550656476 550658248 0.000000e+00 2697.0
4 TraesCS7D01G400500 chr7B 89.780 499 24 11 2744 3239 550658544 550659018 5.950000e-172 614.0
5 TraesCS7D01G400500 chr7B 92.273 220 11 4 2440 2654 550658282 550658500 1.130000e-79 307.0
6 TraesCS7D01G400500 chr7B 87.629 97 11 1 61 156 709852545 709852641 9.520000e-21 111.0
7 TraesCS7D01G400500 chr1A 80.115 347 55 8 1643 1982 21675568 21675229 2.500000e-61 246.0
8 TraesCS7D01G400500 chr6D 77.470 253 33 14 1243 1492 472906086 472906317 2.630000e-26 130.0
9 TraesCS7D01G400500 chrUn 92.683 41 3 0 113 153 26773235 26773275 3.500000e-05 60.2


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 TraesCS7D01G400500 chr7D 517553178 517556422 3244 False 5993 5993 100.000000 1 3245 1 chr7D.!!$F1 3244
1 TraesCS7D01G400500 chr7A 592261149 592263921 2772 False 3373 3373 88.862000 447 3239 1 chr7A.!!$F2 2792
2 TraesCS7D01G400500 chr7B 550656476 550659018 2542 False 1206 2697 92.087667 603 3239 3 chr7B.!!$F2 2636

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
193 194 0.109458 CAGCATCAGCACACGCAAAT 60.109 50.0 0.0 0.0 45.49 2.32 F
440 441 0.112218 CCATTGTGTTCCACCCTCCA 59.888 55.0 0.0 0.0 32.73 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1984 2015 1.455217 CGGATCCCCAGTCGTAGGT 60.455 63.158 6.06 0.0 0.00 3.08 R
2382 2430 0.027716 TCGATTCTAGCGTCGTCTGC 59.972 55.000 13.74 0.0 38.85 4.26 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
110 111 7.883391 TTAACTCACAATAAAACACCAAGGA 57.117 32.000 0.00 0.00 0.00 3.36
111 112 6.976934 AACTCACAATAAAACACCAAGGAT 57.023 33.333 0.00 0.00 0.00 3.24
112 113 9.575868 TTAACTCACAATAAAACACCAAGGATA 57.424 29.630 0.00 0.00 0.00 2.59
113 114 8.650143 AACTCACAATAAAACACCAAGGATAT 57.350 30.769 0.00 0.00 0.00 1.63
114 115 9.747898 AACTCACAATAAAACACCAAGGATATA 57.252 29.630 0.00 0.00 0.00 0.86
115 116 9.174166 ACTCACAATAAAACACCAAGGATATAC 57.826 33.333 0.00 0.00 0.00 1.47
116 117 9.173021 CTCACAATAAAACACCAAGGATATACA 57.827 33.333 0.00 0.00 0.00 2.29
117 118 9.521841 TCACAATAAAACACCAAGGATATACAA 57.478 29.630 0.00 0.00 0.00 2.41
122 123 7.589958 AAAACACCAAGGATATACAAACACA 57.410 32.000 0.00 0.00 0.00 3.72
123 124 7.589958 AAACACCAAGGATATACAAACACAA 57.410 32.000 0.00 0.00 0.00 3.33
124 125 7.775053 AACACCAAGGATATACAAACACAAT 57.225 32.000 0.00 0.00 0.00 2.71
125 126 8.871629 AACACCAAGGATATACAAACACAATA 57.128 30.769 0.00 0.00 0.00 1.90
126 127 8.871629 ACACCAAGGATATACAAACACAATAA 57.128 30.769 0.00 0.00 0.00 1.40
127 128 8.956426 ACACCAAGGATATACAAACACAATAAG 58.044 33.333 0.00 0.00 0.00 1.73
128 129 7.915397 CACCAAGGATATACAAACACAATAAGC 59.085 37.037 0.00 0.00 0.00 3.09
129 130 7.613801 ACCAAGGATATACAAACACAATAAGCA 59.386 33.333 0.00 0.00 0.00 3.91
130 131 7.915397 CCAAGGATATACAAACACAATAAGCAC 59.085 37.037 0.00 0.00 0.00 4.40
131 132 8.458052 CAAGGATATACAAACACAATAAGCACA 58.542 33.333 0.00 0.00 0.00 4.57
132 133 7.985476 AGGATATACAAACACAATAAGCACAC 58.015 34.615 0.00 0.00 0.00 3.82
133 134 7.609918 AGGATATACAAACACAATAAGCACACA 59.390 33.333 0.00 0.00 0.00 3.72
134 135 8.405531 GGATATACAAACACAATAAGCACACAT 58.594 33.333 0.00 0.00 0.00 3.21
135 136 9.438291 GATATACAAACACAATAAGCACACATC 57.562 33.333 0.00 0.00 0.00 3.06
136 137 4.870363 ACAAACACAATAAGCACACATCC 58.130 39.130 0.00 0.00 0.00 3.51
137 138 3.829886 AACACAATAAGCACACATCCG 57.170 42.857 0.00 0.00 0.00 4.18
138 139 2.083774 ACACAATAAGCACACATCCGG 58.916 47.619 0.00 0.00 0.00 5.14
139 140 1.094785 ACAATAAGCACACATCCGGC 58.905 50.000 0.00 0.00 0.00 6.13
140 141 0.381801 CAATAAGCACACATCCGGCC 59.618 55.000 0.00 0.00 0.00 6.13
141 142 0.255890 AATAAGCACACATCCGGCCT 59.744 50.000 0.00 0.00 0.00 5.19
142 143 1.128200 ATAAGCACACATCCGGCCTA 58.872 50.000 0.00 0.00 0.00 3.93
143 144 1.128200 TAAGCACACATCCGGCCTAT 58.872 50.000 0.00 0.00 0.00 2.57
144 145 0.464373 AAGCACACATCCGGCCTATG 60.464 55.000 12.16 12.16 0.00 2.23
145 146 2.546494 GCACACATCCGGCCTATGC 61.546 63.158 13.35 0.00 0.00 3.14
146 147 1.153188 CACACATCCGGCCTATGCA 60.153 57.895 13.35 0.00 40.13 3.96
147 148 0.535780 CACACATCCGGCCTATGCAT 60.536 55.000 13.35 3.79 40.13 3.96
148 149 1.055849 ACACATCCGGCCTATGCATA 58.944 50.000 13.35 6.20 40.13 3.14
149 150 1.419762 ACACATCCGGCCTATGCATAA 59.580 47.619 8.00 0.00 40.13 1.90
150 151 1.806542 CACATCCGGCCTATGCATAAC 59.193 52.381 8.00 2.94 40.13 1.89
151 152 1.699634 ACATCCGGCCTATGCATAACT 59.300 47.619 8.00 0.00 40.13 2.24
152 153 2.903784 ACATCCGGCCTATGCATAACTA 59.096 45.455 8.00 0.00 40.13 2.24
153 154 3.055819 ACATCCGGCCTATGCATAACTAG 60.056 47.826 8.00 0.00 40.13 2.57
154 155 1.899814 TCCGGCCTATGCATAACTAGG 59.100 52.381 8.00 8.35 40.13 3.02
155 156 1.899814 CCGGCCTATGCATAACTAGGA 59.100 52.381 16.05 0.00 37.31 2.94
156 157 2.301870 CCGGCCTATGCATAACTAGGAA 59.698 50.000 16.05 0.00 37.31 3.36
157 158 3.055094 CCGGCCTATGCATAACTAGGAAT 60.055 47.826 16.05 0.00 37.31 3.01
158 159 4.184629 CGGCCTATGCATAACTAGGAATC 58.815 47.826 16.05 4.99 37.31 2.52
159 160 4.081420 CGGCCTATGCATAACTAGGAATCT 60.081 45.833 16.05 0.00 37.31 2.40
160 161 5.127194 CGGCCTATGCATAACTAGGAATCTA 59.873 44.000 16.05 0.00 37.31 1.98
161 162 6.578023 GGCCTATGCATAACTAGGAATCTAG 58.422 44.000 16.05 0.00 43.01 2.43
162 163 6.407525 GGCCTATGCATAACTAGGAATCTAGG 60.408 46.154 16.05 7.98 42.33 3.02
163 164 6.381420 GCCTATGCATAACTAGGAATCTAGGA 59.619 42.308 16.05 0.00 41.26 2.94
164 165 7.070571 GCCTATGCATAACTAGGAATCTAGGAT 59.929 40.741 16.05 0.00 41.26 3.24
165 166 8.420222 CCTATGCATAACTAGGAATCTAGGATG 58.580 40.741 8.00 8.50 45.50 3.51
173 174 7.595819 ACTAGGAATCTAGGATGCATATAGC 57.404 40.000 0.00 0.00 45.50 2.97
174 175 5.885449 AGGAATCTAGGATGCATATAGCC 57.115 43.478 0.00 0.00 44.83 3.93
175 176 5.283763 AGGAATCTAGGATGCATATAGCCA 58.716 41.667 0.00 0.00 44.83 4.75
176 177 5.366186 AGGAATCTAGGATGCATATAGCCAG 59.634 44.000 0.00 0.00 44.83 4.85
177 178 4.686191 ATCTAGGATGCATATAGCCAGC 57.314 45.455 0.00 0.00 44.83 4.85
178 179 3.444029 TCTAGGATGCATATAGCCAGCA 58.556 45.455 0.00 0.00 44.83 4.41
183 184 1.817357 TGCATATAGCCAGCATCAGC 58.183 50.000 0.00 0.00 44.83 4.26
184 185 1.072648 TGCATATAGCCAGCATCAGCA 59.927 47.619 0.00 0.00 43.29 4.41
185 186 1.467734 GCATATAGCCAGCATCAGCAC 59.532 52.381 0.00 0.00 39.64 4.40
186 187 2.774687 CATATAGCCAGCATCAGCACA 58.225 47.619 0.00 0.00 45.49 4.57
187 188 2.245159 TATAGCCAGCATCAGCACAC 57.755 50.000 0.00 0.00 45.49 3.82
188 189 0.812811 ATAGCCAGCATCAGCACACG 60.813 55.000 0.00 0.00 45.49 4.49
189 190 4.471726 GCCAGCATCAGCACACGC 62.472 66.667 0.00 0.00 45.49 5.34
190 191 3.051479 CCAGCATCAGCACACGCA 61.051 61.111 0.00 0.00 45.49 5.24
191 192 2.619165 CCAGCATCAGCACACGCAA 61.619 57.895 0.00 0.00 45.49 4.85
192 193 1.283487 CAGCATCAGCACACGCAAA 59.717 52.632 0.00 0.00 45.49 3.68
193 194 0.109458 CAGCATCAGCACACGCAAAT 60.109 50.000 0.00 0.00 45.49 2.32
194 195 1.130938 CAGCATCAGCACACGCAAATA 59.869 47.619 0.00 0.00 45.49 1.40
195 196 1.811965 AGCATCAGCACACGCAAATAA 59.188 42.857 0.00 0.00 45.49 1.40
196 197 2.228582 AGCATCAGCACACGCAAATAAA 59.771 40.909 0.00 0.00 45.49 1.40
197 198 2.342354 GCATCAGCACACGCAAATAAAC 59.658 45.455 0.00 0.00 42.27 2.01
198 199 3.563508 CATCAGCACACGCAAATAAACA 58.436 40.909 0.00 0.00 42.27 2.83
199 200 2.993545 TCAGCACACGCAAATAAACAC 58.006 42.857 0.00 0.00 42.27 3.32
200 201 2.356069 TCAGCACACGCAAATAAACACA 59.644 40.909 0.00 0.00 42.27 3.72
201 202 3.004210 TCAGCACACGCAAATAAACACAT 59.996 39.130 0.00 0.00 42.27 3.21
202 203 3.361644 CAGCACACGCAAATAAACACATC 59.638 43.478 0.00 0.00 42.27 3.06
203 204 2.661195 GCACACGCAAATAAACACATCC 59.339 45.455 0.00 0.00 38.36 3.51
204 205 3.855154 GCACACGCAAATAAACACATCCA 60.855 43.478 0.00 0.00 38.36 3.41
205 206 3.668191 CACACGCAAATAAACACATCCAC 59.332 43.478 0.00 0.00 0.00 4.02
206 207 3.568007 ACACGCAAATAAACACATCCACT 59.432 39.130 0.00 0.00 0.00 4.00
207 208 4.757657 ACACGCAAATAAACACATCCACTA 59.242 37.500 0.00 0.00 0.00 2.74
208 209 5.239744 ACACGCAAATAAACACATCCACTAA 59.760 36.000 0.00 0.00 0.00 2.24
209 210 6.072175 ACACGCAAATAAACACATCCACTAAT 60.072 34.615 0.00 0.00 0.00 1.73
210 211 7.119992 ACACGCAAATAAACACATCCACTAATA 59.880 33.333 0.00 0.00 0.00 0.98
211 212 7.965655 CACGCAAATAAACACATCCACTAATAA 59.034 33.333 0.00 0.00 0.00 1.40
212 213 8.181573 ACGCAAATAAACACATCCACTAATAAG 58.818 33.333 0.00 0.00 0.00 1.73
213 214 8.394877 CGCAAATAAACACATCCACTAATAAGA 58.605 33.333 0.00 0.00 0.00 2.10
220 221 9.520515 AAACACATCCACTAATAAGAATTGAGT 57.479 29.630 0.00 0.00 0.00 3.41
221 222 8.498054 ACACATCCACTAATAAGAATTGAGTG 57.502 34.615 0.00 0.00 37.78 3.51
314 315 9.527157 TGAACAAAAATATTCTTAGGATGGACA 57.473 29.630 0.00 0.00 0.00 4.02
324 325 8.814038 ATTCTTAGGATGGACATATATTTGCC 57.186 34.615 0.00 0.00 0.00 4.52
325 326 7.328404 TCTTAGGATGGACATATATTTGCCA 57.672 36.000 10.16 10.16 0.00 4.92
326 327 7.754624 TCTTAGGATGGACATATATTTGCCAA 58.245 34.615 11.25 0.00 31.53 4.52
327 328 8.224025 TCTTAGGATGGACATATATTTGCCAAA 58.776 33.333 11.25 0.00 31.53 3.28
328 329 6.906157 AGGATGGACATATATTTGCCAAAG 57.094 37.500 11.25 0.00 31.53 2.77
329 330 6.613699 AGGATGGACATATATTTGCCAAAGA 58.386 36.000 11.25 0.00 31.53 2.52
330 331 7.068702 AGGATGGACATATATTTGCCAAAGAA 58.931 34.615 11.25 0.00 31.53 2.52
331 332 7.232127 AGGATGGACATATATTTGCCAAAGAAG 59.768 37.037 11.25 0.00 31.53 2.85
332 333 6.147864 TGGACATATATTTGCCAAAGAAGC 57.852 37.500 0.00 0.00 0.00 3.86
333 334 5.655974 TGGACATATATTTGCCAAAGAAGCA 59.344 36.000 0.00 0.00 38.81 3.91
341 342 4.662468 TTGCCAAAGAAGCAATGTAACA 57.338 36.364 0.00 0.00 44.95 2.41
342 343 4.241590 TGCCAAAGAAGCAATGTAACAG 57.758 40.909 0.00 0.00 37.28 3.16
343 344 3.005684 TGCCAAAGAAGCAATGTAACAGG 59.994 43.478 0.00 0.00 37.28 4.00
344 345 3.005791 GCCAAAGAAGCAATGTAACAGGT 59.994 43.478 0.00 0.00 0.00 4.00
345 346 4.798574 CCAAAGAAGCAATGTAACAGGTC 58.201 43.478 0.00 0.00 0.00 3.85
346 347 4.466828 CAAAGAAGCAATGTAACAGGTCG 58.533 43.478 0.00 0.00 0.00 4.79
347 348 3.678056 AGAAGCAATGTAACAGGTCGA 57.322 42.857 0.00 0.00 0.00 4.20
348 349 3.589988 AGAAGCAATGTAACAGGTCGAG 58.410 45.455 0.00 0.00 0.00 4.04
349 350 3.258372 AGAAGCAATGTAACAGGTCGAGA 59.742 43.478 0.00 0.00 0.00 4.04
350 351 3.678056 AGCAATGTAACAGGTCGAGAA 57.322 42.857 0.00 0.00 0.00 2.87
351 352 3.326747 AGCAATGTAACAGGTCGAGAAC 58.673 45.455 0.00 0.00 0.00 3.01
352 353 2.092211 GCAATGTAACAGGTCGAGAACG 59.908 50.000 0.00 0.00 41.26 3.95
353 354 3.571571 CAATGTAACAGGTCGAGAACGA 58.428 45.455 0.00 0.00 46.56 3.85
394 395 8.319143 AGTAGTTTAAATTGCTTACGACATGT 57.681 30.769 0.00 0.00 0.00 3.21
395 396 8.227791 AGTAGTTTAAATTGCTTACGACATGTG 58.772 33.333 1.15 0.00 0.00 3.21
396 397 6.966021 AGTTTAAATTGCTTACGACATGTGT 58.034 32.000 1.15 4.54 0.00 3.72
397 398 7.075741 AGTTTAAATTGCTTACGACATGTGTC 58.924 34.615 1.15 3.07 41.47 3.67
398 399 6.546972 TTAAATTGCTTACGACATGTGTCA 57.453 33.333 1.15 0.00 44.99 3.58
399 400 4.404507 AATTGCTTACGACATGTGTCAC 57.595 40.909 1.15 0.00 44.99 3.67
400 401 2.517650 TGCTTACGACATGTGTCACA 57.482 45.000 8.40 8.40 44.99 3.58
401 402 2.403259 TGCTTACGACATGTGTCACAG 58.597 47.619 12.03 6.37 44.99 3.66
402 403 1.126846 GCTTACGACATGTGTCACAGC 59.873 52.381 12.03 11.66 44.99 4.40
403 404 2.403259 CTTACGACATGTGTCACAGCA 58.597 47.619 12.03 0.00 44.99 4.41
404 405 2.741759 TACGACATGTGTCACAGCAT 57.258 45.000 12.03 0.00 44.99 3.79
405 406 1.882912 ACGACATGTGTCACAGCATT 58.117 45.000 12.03 0.00 44.99 3.56
406 407 1.800586 ACGACATGTGTCACAGCATTC 59.199 47.619 12.03 4.19 44.99 2.67
407 408 1.129251 CGACATGTGTCACAGCATTCC 59.871 52.381 12.03 0.00 44.99 3.01
408 409 2.430465 GACATGTGTCACAGCATTCCT 58.570 47.619 12.03 0.00 44.18 3.36
409 410 2.161012 GACATGTGTCACAGCATTCCTG 59.839 50.000 12.03 5.45 44.18 3.86
410 411 2.224597 ACATGTGTCACAGCATTCCTGA 60.225 45.455 12.03 0.00 44.64 3.86
411 412 2.865119 TGTGTCACAGCATTCCTGAT 57.135 45.000 0.18 0.00 44.64 2.90
412 413 3.979101 TGTGTCACAGCATTCCTGATA 57.021 42.857 0.18 0.00 44.64 2.15
413 414 4.284829 TGTGTCACAGCATTCCTGATAA 57.715 40.909 0.18 0.00 44.64 1.75
414 415 4.650734 TGTGTCACAGCATTCCTGATAAA 58.349 39.130 0.18 0.00 44.64 1.40
415 416 4.455533 TGTGTCACAGCATTCCTGATAAAC 59.544 41.667 0.18 0.00 44.64 2.01
416 417 4.455533 GTGTCACAGCATTCCTGATAAACA 59.544 41.667 0.00 0.00 44.64 2.83
417 418 5.048782 GTGTCACAGCATTCCTGATAAACAA 60.049 40.000 0.00 0.00 44.64 2.83
418 419 5.534278 TGTCACAGCATTCCTGATAAACAAA 59.466 36.000 0.00 0.00 44.64 2.83
419 420 5.858581 GTCACAGCATTCCTGATAAACAAAC 59.141 40.000 0.00 0.00 44.64 2.93
420 421 5.534278 TCACAGCATTCCTGATAAACAAACA 59.466 36.000 0.00 0.00 44.64 2.83
421 422 5.630680 CACAGCATTCCTGATAAACAAACAC 59.369 40.000 0.00 0.00 44.64 3.32
422 423 5.163513 CAGCATTCCTGATAAACAAACACC 58.836 41.667 0.00 0.00 44.64 4.16
423 424 4.832266 AGCATTCCTGATAAACAAACACCA 59.168 37.500 0.00 0.00 0.00 4.17
424 425 5.481473 AGCATTCCTGATAAACAAACACCAT 59.519 36.000 0.00 0.00 0.00 3.55
425 426 6.014327 AGCATTCCTGATAAACAAACACCATT 60.014 34.615 0.00 0.00 0.00 3.16
426 427 6.091169 GCATTCCTGATAAACAAACACCATTG 59.909 38.462 0.00 0.00 36.37 2.82
427 428 6.723298 TTCCTGATAAACAAACACCATTGT 57.277 33.333 0.00 0.00 45.12 2.71
437 438 3.437642 CACCATTGTGTTCCACCCT 57.562 52.632 0.00 0.00 37.72 4.34
438 439 1.247567 CACCATTGTGTTCCACCCTC 58.752 55.000 0.00 0.00 37.72 4.30
439 440 0.112412 ACCATTGTGTTCCACCCTCC 59.888 55.000 0.00 0.00 32.73 4.30
440 441 0.112218 CCATTGTGTTCCACCCTCCA 59.888 55.000 0.00 0.00 32.73 3.86
441 442 1.480312 CCATTGTGTTCCACCCTCCAA 60.480 52.381 0.00 0.00 32.73 3.53
442 443 2.315176 CATTGTGTTCCACCCTCCAAA 58.685 47.619 0.00 0.00 32.73 3.28
443 444 2.765689 TTGTGTTCCACCCTCCAAAT 57.234 45.000 0.00 0.00 32.73 2.32
444 445 1.993956 TGTGTTCCACCCTCCAAATG 58.006 50.000 0.00 0.00 32.73 2.32
445 446 0.603065 GTGTTCCACCCTCCAAATGC 59.397 55.000 0.00 0.00 0.00 3.56
446 447 0.482446 TGTTCCACCCTCCAAATGCT 59.518 50.000 0.00 0.00 0.00 3.79
447 448 1.707989 TGTTCCACCCTCCAAATGCTA 59.292 47.619 0.00 0.00 0.00 3.49
448 449 2.092323 GTTCCACCCTCCAAATGCTAC 58.908 52.381 0.00 0.00 0.00 3.58
560 565 2.877582 CAGGCCGTGTACGTACGC 60.878 66.667 25.72 25.72 42.44 4.42
561 566 3.364441 AGGCCGTGTACGTACGCA 61.364 61.111 31.93 10.60 42.44 5.24
562 567 2.877582 GGCCGTGTACGTACGCAG 60.878 66.667 31.93 24.60 42.44 5.18
563 568 2.126734 GCCGTGTACGTACGCAGT 60.127 61.111 31.93 0.00 42.44 4.40
564 569 2.430942 GCCGTGTACGTACGCAGTG 61.431 63.158 31.93 22.17 42.44 3.66
565 570 1.081906 CCGTGTACGTACGCAGTGT 60.082 57.895 31.93 0.00 42.44 3.55
566 571 1.061799 CCGTGTACGTACGCAGTGTC 61.062 60.000 31.93 11.66 42.44 3.67
576 581 2.029666 GCAGTGTCGTCAGCCACT 59.970 61.111 0.00 0.00 42.47 4.00
593 598 1.432251 CTGCGTGGACCGTAGTAGG 59.568 63.158 0.00 0.00 43.34 3.18
595 600 1.750399 GCGTGGACCGTAGTAGGGA 60.750 63.158 15.76 0.00 39.32 4.20
596 601 1.722636 GCGTGGACCGTAGTAGGGAG 61.723 65.000 15.76 3.09 39.32 4.30
597 602 1.099879 CGTGGACCGTAGTAGGGAGG 61.100 65.000 15.76 0.00 35.02 4.30
598 603 0.257039 GTGGACCGTAGTAGGGAGGA 59.743 60.000 15.76 0.00 35.02 3.71
775 783 2.587322 TATACCACCGCACAGCAGCC 62.587 60.000 0.00 0.00 0.00 4.85
844 869 0.641601 ATCCCTCTTCCTCCTCTGCT 59.358 55.000 0.00 0.00 0.00 4.24
845 870 1.309876 TCCCTCTTCCTCCTCTGCTA 58.690 55.000 0.00 0.00 0.00 3.49
1059 1087 1.153469 CTCCTCCTCCGCTTCTTGC 60.153 63.158 0.00 0.00 38.57 4.01
1311 1342 1.805945 CTTGTCCCTGTACGCGCTC 60.806 63.158 5.73 0.00 0.00 5.03
1314 1345 3.138798 TCCCTGTACGCGCTCCTC 61.139 66.667 5.73 0.00 0.00 3.71
1434 1465 2.030562 CTCTGCCACCCGTCGTTT 59.969 61.111 0.00 0.00 0.00 3.60
1494 1525 4.103103 CAGCTCGTCCTCGTCGCA 62.103 66.667 0.00 0.00 37.17 5.10
1549 1580 3.796443 CGCTCGTCTTCGACCCGA 61.796 66.667 0.00 0.00 41.35 5.14
2013 2044 3.072468 GGATCCGACCGGTGGACA 61.072 66.667 22.82 8.93 38.60 4.02
2253 2297 1.381327 CCCCGAGTAGGCTTCCTCA 60.381 63.158 12.56 0.00 39.21 3.86
2254 2298 0.976073 CCCCGAGTAGGCTTCCTCAA 60.976 60.000 12.56 0.00 39.21 3.02
2255 2299 0.175989 CCCGAGTAGGCTTCCTCAAC 59.824 60.000 12.56 0.00 39.21 3.18
2281 2329 3.558418 CGCCACTGTACAAAGTACAAACT 59.442 43.478 10.77 0.00 37.65 2.66
2284 2332 6.073440 CGCCACTGTACAAAGTACAAACTTAT 60.073 38.462 10.77 0.00 45.37 1.73
2285 2333 7.116662 CGCCACTGTACAAAGTACAAACTTATA 59.883 37.037 10.77 0.00 45.37 0.98
2286 2334 8.440833 GCCACTGTACAAAGTACAAACTTATAG 58.559 37.037 10.77 0.79 45.37 1.31
2356 2404 3.124798 GAATCCGCATTGGCACCGG 62.125 63.158 12.64 12.64 43.21 5.28
2368 2416 3.797353 CACCGGCCTGGGCAGTAT 61.797 66.667 21.03 0.00 44.64 2.12
2369 2417 3.797353 ACCGGCCTGGGCAGTATG 61.797 66.667 21.03 3.03 44.64 2.39
2387 2435 0.181114 TGCAGTATGGATGGGCAGAC 59.819 55.000 0.00 0.00 35.86 3.51
2388 2436 0.882042 GCAGTATGGATGGGCAGACG 60.882 60.000 0.00 0.00 35.86 4.18
2393 2462 4.148825 GGATGGGCAGACGACGCT 62.149 66.667 0.00 0.00 0.00 5.07
2405 2474 3.178618 CAGACGACGCTAGAATCGATTTG 59.821 47.826 19.35 7.18 40.86 2.32
2407 2476 2.159282 ACGACGCTAGAATCGATTTGGT 60.159 45.455 19.35 6.19 40.86 3.67
2409 2478 3.061139 CGACGCTAGAATCGATTTGGTTC 60.061 47.826 12.81 0.00 40.86 3.62
2411 2480 2.544267 CGCTAGAATCGATTTGGTTCCC 59.456 50.000 12.81 0.00 0.00 3.97
2412 2481 2.544267 GCTAGAATCGATTTGGTTCCCG 59.456 50.000 12.81 0.00 0.00 5.14
2413 2482 2.781681 AGAATCGATTTGGTTCCCGT 57.218 45.000 12.81 0.00 0.00 5.28
2414 2483 2.356135 AGAATCGATTTGGTTCCCGTG 58.644 47.619 12.81 0.00 0.00 4.94
2415 2484 2.081462 GAATCGATTTGGTTCCCGTGT 58.919 47.619 12.81 0.00 0.00 4.49
2416 2485 1.448985 ATCGATTTGGTTCCCGTGTG 58.551 50.000 0.00 0.00 0.00 3.82
2424 2494 1.598130 GTTCCCGTGTGCTTCTGCT 60.598 57.895 0.00 0.00 40.48 4.24
2461 2531 6.810182 AGCTGGATTTCGAGATTTTGATTTTG 59.190 34.615 0.00 0.00 0.00 2.44
2466 2536 6.648879 TTTCGAGATTTTGATTTTGGAGGT 57.351 33.333 0.00 0.00 0.00 3.85
2510 2580 4.732285 TTGATTCTTGCGTTCTTCTGTC 57.268 40.909 0.00 0.00 0.00 3.51
2540 2610 5.517122 CCTCTGATCCTCTCTGTCCAGATAT 60.517 48.000 0.00 0.00 36.76 1.63
2615 2693 1.812571 CCAGCACATACACTTGGGAAC 59.187 52.381 0.00 0.00 0.00 3.62
2616 2694 2.553028 CCAGCACATACACTTGGGAACT 60.553 50.000 0.00 0.00 0.00 3.01
2620 2698 3.758554 GCACATACACTTGGGAACTGAAT 59.241 43.478 0.00 0.00 0.00 2.57
2621 2699 4.379813 GCACATACACTTGGGAACTGAATG 60.380 45.833 0.00 0.00 0.00 2.67
2622 2700 5.003160 CACATACACTTGGGAACTGAATGA 58.997 41.667 0.00 0.00 0.00 2.57
2638 2720 9.713740 GAACTGAATGAAATTAGACTGCTAATG 57.286 33.333 0.00 0.00 44.49 1.90
2653 2735 5.473504 ACTGCTAATGTTCTGTTAAACCCAG 59.526 40.000 0.00 0.00 0.00 4.45
2657 2739 2.841215 TGTTCTGTTAAACCCAGTCCG 58.159 47.619 0.00 0.00 0.00 4.79
2663 2745 4.336153 TCTGTTAAACCCAGTCCGTTTTTC 59.664 41.667 0.00 0.00 35.19 2.29
2670 2753 2.353803 CCCAGTCCGTTTTTCTCTCGAT 60.354 50.000 0.00 0.00 0.00 3.59
2682 2765 2.789213 TCTCTCGATGAGCAGGATAGG 58.211 52.381 6.93 0.00 42.38 2.57
2723 2806 3.793144 CCTGCGTCGCTTTGAGCC 61.793 66.667 19.50 0.00 38.18 4.70
2724 2807 4.139420 CTGCGTCGCTTTGAGCCG 62.139 66.667 19.50 0.00 38.18 5.52
2725 2808 4.961511 TGCGTCGCTTTGAGCCGT 62.962 61.111 19.50 0.00 38.18 5.68
2726 2809 4.135493 GCGTCGCTTTGAGCCGTC 62.135 66.667 10.68 0.00 38.18 4.79
2727 2810 3.827784 CGTCGCTTTGAGCCGTCG 61.828 66.667 0.00 0.00 38.18 5.12
2728 2811 4.135493 GTCGCTTTGAGCCGTCGC 62.135 66.667 0.00 0.00 38.18 5.19
2731 2814 3.843240 GCTTTGAGCCGTCGCGAG 61.843 66.667 10.24 0.00 41.18 5.03
2732 2815 2.430921 CTTTGAGCCGTCGCGAGT 60.431 61.111 10.24 0.00 41.18 4.18
2733 2816 2.430244 TTTGAGCCGTCGCGAGTC 60.430 61.111 10.24 4.79 41.18 3.36
2734 2817 4.753877 TTGAGCCGTCGCGAGTCG 62.754 66.667 10.24 11.16 41.18 4.18
2744 2827 4.838486 GCGAGTCGCGACCCTCAG 62.838 72.222 34.08 21.09 44.55 3.35
2745 2828 4.838486 CGAGTCGCGACCCTCAGC 62.838 72.222 34.08 15.91 44.57 4.26
2766 2850 4.771356 CGCTTTCTCGACGCCGGA 62.771 66.667 5.05 0.00 36.24 5.14
2893 2980 3.910914 TTGATTCCCCGGCCACACG 62.911 63.158 2.24 0.00 0.00 4.49
2979 3066 3.937079 CCGTTACCTCCTCAATTAACACC 59.063 47.826 0.00 0.00 0.00 4.16
2985 3072 0.446222 CCTCAATTAACACCCGTGCG 59.554 55.000 0.00 0.00 0.00 5.34
2986 3073 0.446222 CTCAATTAACACCCGTGCGG 59.554 55.000 3.25 3.25 37.81 5.69
3071 3158 1.810030 GCCGCGGACGATTCTTCTT 60.810 57.895 33.48 0.00 43.93 2.52
3072 3159 1.753468 GCCGCGGACGATTCTTCTTC 61.753 60.000 33.48 1.16 43.93 2.87
3074 3161 0.457853 CGCGGACGATTCTTCTTCCA 60.458 55.000 0.00 0.00 39.67 3.53
3104 3195 1.519455 CGCCCGCTAGTCTCCAAAG 60.519 63.158 0.00 0.00 0.00 2.77
3105 3196 1.898154 GCCCGCTAGTCTCCAAAGA 59.102 57.895 0.00 0.00 0.00 2.52
3170 3261 1.394266 GGTCCAATCAATGCGGGCAT 61.394 55.000 0.00 0.00 38.46 4.40
3211 3303 2.014033 TTTTCCCTCGGGGCCAAGTT 62.014 55.000 4.39 0.00 43.94 2.66
3233 3327 2.981350 GGCGCAAAAGGGTTCGGA 60.981 61.111 10.83 0.00 0.00 4.55
3234 3328 2.557372 GGCGCAAAAGGGTTCGGAA 61.557 57.895 10.83 0.00 0.00 4.30
3238 3332 2.124122 CGCAAAAGGGTTCGGAAAAAG 58.876 47.619 0.00 0.00 0.00 2.27
3239 3333 2.480587 CGCAAAAGGGTTCGGAAAAAGT 60.481 45.455 0.00 0.00 0.00 2.66
3240 3334 3.527533 GCAAAAGGGTTCGGAAAAAGTT 58.472 40.909 0.00 0.00 0.00 2.66
3241 3335 3.936453 GCAAAAGGGTTCGGAAAAAGTTT 59.064 39.130 0.00 0.00 0.00 2.66
3242 3336 4.201773 GCAAAAGGGTTCGGAAAAAGTTTG 60.202 41.667 11.10 11.10 0.00 2.93
3243 3337 2.882927 AGGGTTCGGAAAAAGTTTGC 57.117 45.000 0.00 0.00 0.00 3.68
3244 3338 1.411246 AGGGTTCGGAAAAAGTTTGCC 59.589 47.619 0.00 0.00 32.09 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 9.481340 GGTTACCCTAAAAATATCTTACGGTAG 57.519 37.037 0.00 0.00 0.00 3.18
24 25 8.428852 GGGTTACCCTAAAAATATCTTACGGTA 58.571 37.037 14.22 0.00 41.34 4.02
25 26 7.092489 TGGGTTACCCTAAAAATATCTTACGGT 60.092 37.037 22.29 0.00 45.70 4.83
26 27 7.227314 GTGGGTTACCCTAAAAATATCTTACGG 59.773 40.741 22.29 0.00 45.70 4.02
27 28 7.989170 AGTGGGTTACCCTAAAAATATCTTACG 59.011 37.037 22.29 0.00 45.70 3.18
84 85 9.575868 TCCTTGGTGTTTTATTGTGAGTTAATA 57.424 29.630 0.00 0.00 0.00 0.98
85 86 8.472007 TCCTTGGTGTTTTATTGTGAGTTAAT 57.528 30.769 0.00 0.00 0.00 1.40
86 87 7.883391 TCCTTGGTGTTTTATTGTGAGTTAA 57.117 32.000 0.00 0.00 0.00 2.01
87 88 9.747898 ATATCCTTGGTGTTTTATTGTGAGTTA 57.252 29.630 0.00 0.00 0.00 2.24
88 89 6.976934 ATCCTTGGTGTTTTATTGTGAGTT 57.023 33.333 0.00 0.00 0.00 3.01
89 90 9.174166 GTATATCCTTGGTGTTTTATTGTGAGT 57.826 33.333 0.00 0.00 0.00 3.41
90 91 9.173021 TGTATATCCTTGGTGTTTTATTGTGAG 57.827 33.333 0.00 0.00 0.00 3.51
91 92 9.521841 TTGTATATCCTTGGTGTTTTATTGTGA 57.478 29.630 0.00 0.00 0.00 3.58
96 97 9.303116 TGTGTTTGTATATCCTTGGTGTTTTAT 57.697 29.630 0.00 0.00 0.00 1.40
97 98 8.693120 TGTGTTTGTATATCCTTGGTGTTTTA 57.307 30.769 0.00 0.00 0.00 1.52
98 99 7.589958 TGTGTTTGTATATCCTTGGTGTTTT 57.410 32.000 0.00 0.00 0.00 2.43
99 100 7.589958 TTGTGTTTGTATATCCTTGGTGTTT 57.410 32.000 0.00 0.00 0.00 2.83
100 101 7.775053 ATTGTGTTTGTATATCCTTGGTGTT 57.225 32.000 0.00 0.00 0.00 3.32
101 102 8.871629 TTATTGTGTTTGTATATCCTTGGTGT 57.128 30.769 0.00 0.00 0.00 4.16
102 103 7.915397 GCTTATTGTGTTTGTATATCCTTGGTG 59.085 37.037 0.00 0.00 0.00 4.17
103 104 7.613801 TGCTTATTGTGTTTGTATATCCTTGGT 59.386 33.333 0.00 0.00 0.00 3.67
104 105 7.915397 GTGCTTATTGTGTTTGTATATCCTTGG 59.085 37.037 0.00 0.00 0.00 3.61
105 106 8.458052 TGTGCTTATTGTGTTTGTATATCCTTG 58.542 33.333 0.00 0.00 0.00 3.61
106 107 8.458843 GTGTGCTTATTGTGTTTGTATATCCTT 58.541 33.333 0.00 0.00 0.00 3.36
107 108 7.609918 TGTGTGCTTATTGTGTTTGTATATCCT 59.390 33.333 0.00 0.00 0.00 3.24
108 109 7.757526 TGTGTGCTTATTGTGTTTGTATATCC 58.242 34.615 0.00 0.00 0.00 2.59
109 110 9.438291 GATGTGTGCTTATTGTGTTTGTATATC 57.562 33.333 0.00 0.00 0.00 1.63
110 111 8.405531 GGATGTGTGCTTATTGTGTTTGTATAT 58.594 33.333 0.00 0.00 0.00 0.86
111 112 7.413548 CGGATGTGTGCTTATTGTGTTTGTATA 60.414 37.037 0.00 0.00 0.00 1.47
112 113 6.620678 GGATGTGTGCTTATTGTGTTTGTAT 58.379 36.000 0.00 0.00 0.00 2.29
113 114 5.334491 CGGATGTGTGCTTATTGTGTTTGTA 60.334 40.000 0.00 0.00 0.00 2.41
114 115 4.556501 CGGATGTGTGCTTATTGTGTTTGT 60.557 41.667 0.00 0.00 0.00 2.83
115 116 3.913763 CGGATGTGTGCTTATTGTGTTTG 59.086 43.478 0.00 0.00 0.00 2.93
116 117 3.057596 CCGGATGTGTGCTTATTGTGTTT 60.058 43.478 0.00 0.00 0.00 2.83
117 118 2.487762 CCGGATGTGTGCTTATTGTGTT 59.512 45.455 0.00 0.00 0.00 3.32
118 119 2.083774 CCGGATGTGTGCTTATTGTGT 58.916 47.619 0.00 0.00 0.00 3.72
119 120 1.202177 GCCGGATGTGTGCTTATTGTG 60.202 52.381 5.05 0.00 0.00 3.33
120 121 1.094785 GCCGGATGTGTGCTTATTGT 58.905 50.000 5.05 0.00 0.00 2.71
121 122 0.381801 GGCCGGATGTGTGCTTATTG 59.618 55.000 5.05 0.00 0.00 1.90
122 123 0.255890 AGGCCGGATGTGTGCTTATT 59.744 50.000 5.05 0.00 0.00 1.40
123 124 1.128200 TAGGCCGGATGTGTGCTTAT 58.872 50.000 5.05 0.00 0.00 1.73
124 125 1.128200 ATAGGCCGGATGTGTGCTTA 58.872 50.000 5.05 0.00 0.00 3.09
125 126 0.464373 CATAGGCCGGATGTGTGCTT 60.464 55.000 5.05 0.00 0.00 3.91
126 127 1.146930 CATAGGCCGGATGTGTGCT 59.853 57.895 5.05 0.00 0.00 4.40
127 128 2.546494 GCATAGGCCGGATGTGTGC 61.546 63.158 18.54 4.71 0.00 4.57
128 129 0.535780 ATGCATAGGCCGGATGTGTG 60.536 55.000 18.54 0.00 40.13 3.82
129 130 1.055849 TATGCATAGGCCGGATGTGT 58.944 50.000 18.54 11.66 40.13 3.72
130 131 1.806542 GTTATGCATAGGCCGGATGTG 59.193 52.381 18.54 1.96 40.13 3.21
131 132 1.699634 AGTTATGCATAGGCCGGATGT 59.300 47.619 18.54 5.97 40.13 3.06
132 133 2.479566 AGTTATGCATAGGCCGGATG 57.520 50.000 5.05 14.53 40.13 3.51
133 134 2.501723 CCTAGTTATGCATAGGCCGGAT 59.498 50.000 5.05 0.00 40.13 4.18
134 135 1.899814 CCTAGTTATGCATAGGCCGGA 59.100 52.381 5.05 0.00 40.13 5.14
135 136 1.899814 TCCTAGTTATGCATAGGCCGG 59.100 52.381 6.50 0.00 38.78 6.13
136 137 3.678056 TTCCTAGTTATGCATAGGCCG 57.322 47.619 6.50 0.00 38.78 6.13
137 138 5.428184 AGATTCCTAGTTATGCATAGGCC 57.572 43.478 6.50 0.00 38.78 5.19
138 139 6.381420 TCCTAGATTCCTAGTTATGCATAGGC 59.619 42.308 6.50 4.53 40.57 3.93
139 140 7.962995 TCCTAGATTCCTAGTTATGCATAGG 57.037 40.000 6.50 6.71 40.57 2.57
140 141 7.925483 GCATCCTAGATTCCTAGTTATGCATAG 59.075 40.741 20.31 0.00 46.49 2.23
141 142 7.786030 GCATCCTAGATTCCTAGTTATGCATA 58.214 38.462 20.31 1.16 46.49 3.14
142 143 6.648192 GCATCCTAGATTCCTAGTTATGCAT 58.352 40.000 20.31 3.79 46.49 3.96
143 144 6.042638 GCATCCTAGATTCCTAGTTATGCA 57.957 41.667 20.31 0.00 46.49 3.96
144 145 6.042638 TGCATCCTAGATTCCTAGTTATGC 57.957 41.667 19.35 19.35 46.87 3.14
147 148 9.137459 GCTATATGCATCCTAGATTCCTAGTTA 57.863 37.037 16.54 0.00 40.04 2.24
148 149 7.070571 GGCTATATGCATCCTAGATTCCTAGTT 59.929 40.741 16.54 0.00 45.15 2.24
149 150 6.553100 GGCTATATGCATCCTAGATTCCTAGT 59.447 42.308 16.54 0.00 45.15 2.57
150 151 6.552725 TGGCTATATGCATCCTAGATTCCTAG 59.447 42.308 16.54 0.00 45.15 3.02
151 152 6.443832 TGGCTATATGCATCCTAGATTCCTA 58.556 40.000 16.54 0.00 45.15 2.94
152 153 5.283763 TGGCTATATGCATCCTAGATTCCT 58.716 41.667 16.54 0.00 45.15 3.36
153 154 5.609423 CTGGCTATATGCATCCTAGATTCC 58.391 45.833 16.54 10.46 45.15 3.01
154 155 5.055812 GCTGGCTATATGCATCCTAGATTC 58.944 45.833 16.54 8.19 45.15 2.52
155 156 4.472470 TGCTGGCTATATGCATCCTAGATT 59.528 41.667 16.54 0.00 45.15 2.40
156 157 4.035814 TGCTGGCTATATGCATCCTAGAT 58.964 43.478 16.54 2.86 45.15 1.98
157 158 3.444029 TGCTGGCTATATGCATCCTAGA 58.556 45.455 16.54 0.00 45.15 2.43
158 159 3.900966 TGCTGGCTATATGCATCCTAG 57.099 47.619 0.19 7.16 45.15 3.02
164 165 1.072648 TGCTGATGCTGGCTATATGCA 59.927 47.619 0.00 0.00 41.10 3.96
165 166 1.467734 GTGCTGATGCTGGCTATATGC 59.532 52.381 0.00 0.00 40.48 3.14
166 167 2.483106 GTGTGCTGATGCTGGCTATATG 59.517 50.000 0.00 0.00 40.48 1.78
167 168 2.775890 GTGTGCTGATGCTGGCTATAT 58.224 47.619 0.00 0.00 40.48 0.86
168 169 1.538849 CGTGTGCTGATGCTGGCTATA 60.539 52.381 0.00 0.00 40.48 1.31
169 170 0.812811 CGTGTGCTGATGCTGGCTAT 60.813 55.000 0.00 0.00 40.48 2.97
170 171 1.448365 CGTGTGCTGATGCTGGCTA 60.448 57.895 0.00 0.00 40.48 3.93
171 172 2.745100 CGTGTGCTGATGCTGGCT 60.745 61.111 0.00 0.00 40.48 4.75
172 173 4.471726 GCGTGTGCTGATGCTGGC 62.472 66.667 0.00 0.00 40.48 4.85
173 174 2.132517 TTTGCGTGTGCTGATGCTGG 62.133 55.000 2.12 0.00 43.34 4.85
174 175 0.109458 ATTTGCGTGTGCTGATGCTG 60.109 50.000 2.12 0.00 43.34 4.41
175 176 1.452110 TATTTGCGTGTGCTGATGCT 58.548 45.000 2.12 0.00 43.34 3.79
176 177 2.261037 TTATTTGCGTGTGCTGATGC 57.739 45.000 0.00 0.00 43.34 3.91
177 178 3.361644 GTGTTTATTTGCGTGTGCTGATG 59.638 43.478 0.00 0.00 43.34 3.07
178 179 3.004210 TGTGTTTATTTGCGTGTGCTGAT 59.996 39.130 0.00 0.00 43.34 2.90
179 180 2.356069 TGTGTTTATTTGCGTGTGCTGA 59.644 40.909 0.00 0.00 43.34 4.26
180 181 2.725490 TGTGTTTATTTGCGTGTGCTG 58.275 42.857 0.00 0.00 43.34 4.41
181 182 3.564511 GATGTGTTTATTTGCGTGTGCT 58.435 40.909 0.00 0.00 43.34 4.40
182 183 2.661195 GGATGTGTTTATTTGCGTGTGC 59.339 45.455 0.00 0.00 43.20 4.57
183 184 3.668191 GTGGATGTGTTTATTTGCGTGTG 59.332 43.478 0.00 0.00 0.00 3.82
184 185 3.568007 AGTGGATGTGTTTATTTGCGTGT 59.432 39.130 0.00 0.00 0.00 4.49
185 186 4.159377 AGTGGATGTGTTTATTTGCGTG 57.841 40.909 0.00 0.00 0.00 5.34
186 187 5.950758 TTAGTGGATGTGTTTATTTGCGT 57.049 34.783 0.00 0.00 0.00 5.24
187 188 8.394877 TCTTATTAGTGGATGTGTTTATTTGCG 58.605 33.333 0.00 0.00 0.00 4.85
194 195 9.520515 ACTCAATTCTTATTAGTGGATGTGTTT 57.479 29.630 0.00 0.00 0.00 2.83
195 196 8.950210 CACTCAATTCTTATTAGTGGATGTGTT 58.050 33.333 0.00 0.00 35.12 3.32
196 197 8.498054 CACTCAATTCTTATTAGTGGATGTGT 57.502 34.615 0.00 0.00 35.12 3.72
288 289 9.527157 TGTCCATCCTAAGAATATTTTTGTTCA 57.473 29.630 1.59 0.00 0.00 3.18
298 299 9.905713 GGCAAATATATGTCCATCCTAAGAATA 57.094 33.333 0.00 0.00 0.00 1.75
299 300 8.393259 TGGCAAATATATGTCCATCCTAAGAAT 58.607 33.333 0.00 0.00 0.00 2.40
300 301 7.754624 TGGCAAATATATGTCCATCCTAAGAA 58.245 34.615 0.00 0.00 0.00 2.52
301 302 7.328404 TGGCAAATATATGTCCATCCTAAGA 57.672 36.000 0.00 0.00 0.00 2.10
302 303 8.408043 TTTGGCAAATATATGTCCATCCTAAG 57.592 34.615 8.93 0.00 0.00 2.18
303 304 8.224025 TCTTTGGCAAATATATGTCCATCCTAA 58.776 33.333 13.89 0.00 0.00 2.69
304 305 7.754624 TCTTTGGCAAATATATGTCCATCCTA 58.245 34.615 13.89 0.00 0.00 2.94
305 306 6.613699 TCTTTGGCAAATATATGTCCATCCT 58.386 36.000 13.89 0.00 0.00 3.24
306 307 6.899393 TCTTTGGCAAATATATGTCCATCC 57.101 37.500 13.89 0.00 0.00 3.51
307 308 6.865205 GCTTCTTTGGCAAATATATGTCCATC 59.135 38.462 13.89 0.00 0.00 3.51
308 309 6.324512 TGCTTCTTTGGCAAATATATGTCCAT 59.675 34.615 13.89 0.00 36.71 3.41
309 310 5.655974 TGCTTCTTTGGCAAATATATGTCCA 59.344 36.000 13.89 0.89 36.71 4.02
310 311 6.147864 TGCTTCTTTGGCAAATATATGTCC 57.852 37.500 13.89 0.00 36.71 4.02
321 322 3.005684 CCTGTTACATTGCTTCTTTGGCA 59.994 43.478 0.00 0.00 37.97 4.92
322 323 3.005791 ACCTGTTACATTGCTTCTTTGGC 59.994 43.478 0.00 0.00 0.00 4.52
323 324 4.613622 CGACCTGTTACATTGCTTCTTTGG 60.614 45.833 0.00 0.00 0.00 3.28
324 325 4.213270 TCGACCTGTTACATTGCTTCTTTG 59.787 41.667 0.00 0.00 0.00 2.77
325 326 4.385825 TCGACCTGTTACATTGCTTCTTT 58.614 39.130 0.00 0.00 0.00 2.52
326 327 3.997021 CTCGACCTGTTACATTGCTTCTT 59.003 43.478 0.00 0.00 0.00 2.52
327 328 3.258372 TCTCGACCTGTTACATTGCTTCT 59.742 43.478 0.00 0.00 0.00 2.85
328 329 3.585862 TCTCGACCTGTTACATTGCTTC 58.414 45.455 0.00 0.00 0.00 3.86
329 330 3.678056 TCTCGACCTGTTACATTGCTT 57.322 42.857 0.00 0.00 0.00 3.91
330 331 3.326747 GTTCTCGACCTGTTACATTGCT 58.673 45.455 0.00 0.00 0.00 3.91
331 332 2.092211 CGTTCTCGACCTGTTACATTGC 59.908 50.000 0.00 0.00 39.71 3.56
332 333 3.571571 TCGTTCTCGACCTGTTACATTG 58.428 45.455 0.00 0.00 41.35 2.82
333 334 3.928727 TCGTTCTCGACCTGTTACATT 57.071 42.857 0.00 0.00 41.35 2.71
334 335 3.834610 CTTCGTTCTCGACCTGTTACAT 58.165 45.455 0.00 0.00 46.03 2.29
335 336 2.606308 GCTTCGTTCTCGACCTGTTACA 60.606 50.000 0.00 0.00 46.03 2.41
336 337 1.984297 GCTTCGTTCTCGACCTGTTAC 59.016 52.381 0.00 0.00 46.03 2.50
337 338 1.884579 AGCTTCGTTCTCGACCTGTTA 59.115 47.619 0.00 0.00 46.03 2.41
338 339 0.674534 AGCTTCGTTCTCGACCTGTT 59.325 50.000 0.00 0.00 46.03 3.16
339 340 0.674534 AAGCTTCGTTCTCGACCTGT 59.325 50.000 0.00 0.00 46.03 4.00
340 341 1.784525 AAAGCTTCGTTCTCGACCTG 58.215 50.000 0.00 0.00 46.03 4.00
341 342 2.528041 AAAAGCTTCGTTCTCGACCT 57.472 45.000 0.00 0.00 46.03 3.85
342 343 4.923264 AATAAAAGCTTCGTTCTCGACC 57.077 40.909 0.00 0.00 46.03 4.79
368 369 9.426837 ACATGTCGTAAGCAATTTAAACTACTA 57.573 29.630 0.00 0.00 37.18 1.82
369 370 8.227791 CACATGTCGTAAGCAATTTAAACTACT 58.772 33.333 0.00 0.00 37.18 2.57
370 371 8.013378 ACACATGTCGTAAGCAATTTAAACTAC 58.987 33.333 0.00 0.00 37.18 2.73
371 372 8.090250 ACACATGTCGTAAGCAATTTAAACTA 57.910 30.769 0.00 0.00 37.18 2.24
372 373 6.966021 ACACATGTCGTAAGCAATTTAAACT 58.034 32.000 0.00 0.00 37.18 2.66
373 374 7.248381 GACACATGTCGTAAGCAATTTAAAC 57.752 36.000 0.00 0.00 35.12 2.01
388 389 2.161012 CAGGAATGCTGTGACACATGTC 59.839 50.000 9.11 5.02 44.97 3.06
389 390 2.156917 CAGGAATGCTGTGACACATGT 58.843 47.619 9.11 0.00 0.00 3.21
390 391 2.429478 TCAGGAATGCTGTGACACATG 58.571 47.619 9.11 2.71 0.00 3.21
391 392 2.865119 TCAGGAATGCTGTGACACAT 57.135 45.000 9.11 0.00 0.00 3.21
392 393 2.865119 ATCAGGAATGCTGTGACACA 57.135 45.000 8.26 8.26 0.00 3.72
393 394 4.455533 TGTTTATCAGGAATGCTGTGACAC 59.544 41.667 0.85 0.00 0.00 3.67
394 395 4.650734 TGTTTATCAGGAATGCTGTGACA 58.349 39.130 0.85 0.67 0.00 3.58
395 396 5.627499 TTGTTTATCAGGAATGCTGTGAC 57.373 39.130 0.85 0.00 0.00 3.67
396 397 5.534278 TGTTTGTTTATCAGGAATGCTGTGA 59.466 36.000 0.85 0.00 0.00 3.58
397 398 5.630680 GTGTTTGTTTATCAGGAATGCTGTG 59.369 40.000 0.85 0.00 0.00 3.66
398 399 5.278957 GGTGTTTGTTTATCAGGAATGCTGT 60.279 40.000 0.85 0.00 0.00 4.40
399 400 5.163513 GGTGTTTGTTTATCAGGAATGCTG 58.836 41.667 0.00 0.00 0.00 4.41
400 401 4.832266 TGGTGTTTGTTTATCAGGAATGCT 59.168 37.500 0.00 0.00 0.00 3.79
401 402 5.132897 TGGTGTTTGTTTATCAGGAATGC 57.867 39.130 0.00 0.00 0.00 3.56
402 403 7.116662 CACAATGGTGTTTGTTTATCAGGAATG 59.883 37.037 0.00 0.00 37.73 2.67
403 404 7.153985 CACAATGGTGTTTGTTTATCAGGAAT 58.846 34.615 0.00 0.00 37.73 3.01
404 405 6.511416 CACAATGGTGTTTGTTTATCAGGAA 58.489 36.000 0.00 0.00 37.73 3.36
405 406 6.083098 CACAATGGTGTTTGTTTATCAGGA 57.917 37.500 0.00 0.00 37.73 3.86
427 428 0.482446 AGCATTTGGAGGGTGGAACA 59.518 50.000 0.00 0.00 39.98 3.18
428 429 2.092323 GTAGCATTTGGAGGGTGGAAC 58.908 52.381 0.00 0.00 0.00 3.62
429 430 1.707989 TGTAGCATTTGGAGGGTGGAA 59.292 47.619 0.00 0.00 0.00 3.53
430 431 1.367346 TGTAGCATTTGGAGGGTGGA 58.633 50.000 0.00 0.00 0.00 4.02
431 432 2.214376 TTGTAGCATTTGGAGGGTGG 57.786 50.000 0.00 0.00 0.00 4.61
432 433 3.157087 AGTTTGTAGCATTTGGAGGGTG 58.843 45.455 0.00 0.00 0.00 4.61
433 434 3.525800 AGTTTGTAGCATTTGGAGGGT 57.474 42.857 0.00 0.00 0.00 4.34
434 435 3.119849 CGAAGTTTGTAGCATTTGGAGGG 60.120 47.826 0.00 0.00 0.00 4.30
435 436 3.502211 ACGAAGTTTGTAGCATTTGGAGG 59.498 43.478 0.00 0.00 37.78 4.30
436 437 4.749245 ACGAAGTTTGTAGCATTTGGAG 57.251 40.909 0.00 0.00 37.78 3.86
481 482 2.987149 CTGCGTCGGGATCATGTAATAC 59.013 50.000 0.00 0.00 0.00 1.89
482 483 2.609491 GCTGCGTCGGGATCATGTAATA 60.609 50.000 0.00 0.00 0.00 0.98
483 484 1.873903 GCTGCGTCGGGATCATGTAAT 60.874 52.381 0.00 0.00 0.00 1.89
528 529 2.102420 CGGCCTGTGATCCATGTAGTAA 59.898 50.000 0.00 0.00 0.00 2.24
544 549 3.332493 CTGCGTACGTACACGGCCT 62.332 63.158 24.50 0.00 44.95 5.19
563 568 3.911698 ACGCAGTGGCTGACGACA 61.912 61.111 15.55 0.00 42.51 4.35
590 595 1.546589 TTTTCGCGCCTTCCTCCCTA 61.547 55.000 0.00 0.00 0.00 3.53
591 596 2.804828 CTTTTCGCGCCTTCCTCCCT 62.805 60.000 0.00 0.00 0.00 4.20
592 597 2.359478 TTTTCGCGCCTTCCTCCC 60.359 61.111 0.00 0.00 0.00 4.30
593 598 2.399356 CCTTTTCGCGCCTTCCTCC 61.399 63.158 0.00 0.00 0.00 4.30
595 600 3.056328 GCCTTTTCGCGCCTTCCT 61.056 61.111 0.00 0.00 0.00 3.36
596 601 4.116328 GGCCTTTTCGCGCCTTCC 62.116 66.667 0.00 0.00 42.21 3.46
597 602 4.460873 CGGCCTTTTCGCGCCTTC 62.461 66.667 0.00 0.00 43.38 3.46
779 787 3.643978 GATGATGCCCGCTCGCAC 61.644 66.667 0.00 0.00 42.70 5.34
782 790 3.032609 GACGATGATGCCCGCTCG 61.033 66.667 0.00 0.00 37.17 5.03
783 791 2.663188 GGACGATGATGCCCGCTC 60.663 66.667 0.00 0.00 0.00 5.03
784 792 3.157217 GAGGACGATGATGCCCGCT 62.157 63.158 0.00 0.00 0.00 5.52
785 793 2.663188 GAGGACGATGATGCCCGC 60.663 66.667 0.00 0.00 0.00 6.13
786 794 2.029666 GGAGGACGATGATGCCCG 59.970 66.667 0.00 0.00 0.00 6.13
787 795 1.227674 GTGGAGGACGATGATGCCC 60.228 63.158 0.00 0.00 0.00 5.36
788 796 1.227674 GGTGGAGGACGATGATGCC 60.228 63.158 0.00 0.00 0.00 4.40
844 869 4.770874 GAAAGGCGCGGGGCAGTA 62.771 66.667 27.50 0.00 46.16 2.74
1416 1447 3.530910 AAACGACGGGTGGCAGAGG 62.531 63.158 0.00 0.00 0.00 3.69
1984 2015 1.455217 CGGATCCCCAGTCGTAGGT 60.455 63.158 6.06 0.00 0.00 3.08
2197 2237 4.314440 GTGCAGCGAGACCACCCA 62.314 66.667 0.00 0.00 0.00 4.51
2253 2297 0.470766 TTTGTACAGTGGCGGGAGTT 59.529 50.000 0.00 0.00 0.00 3.01
2254 2298 0.034896 CTTTGTACAGTGGCGGGAGT 59.965 55.000 0.00 0.00 0.00 3.85
2255 2299 0.034896 ACTTTGTACAGTGGCGGGAG 59.965 55.000 0.00 0.00 0.00 4.30
2281 2329 8.789762 GGAGAGCCTTTTGTTTTTGTACTATAA 58.210 33.333 0.00 0.00 0.00 0.98
2282 2330 7.392393 GGGAGAGCCTTTTGTTTTTGTACTATA 59.608 37.037 0.00 0.00 0.00 1.31
2284 2332 5.533528 GGGAGAGCCTTTTGTTTTTGTACTA 59.466 40.000 0.00 0.00 0.00 1.82
2285 2333 4.341235 GGGAGAGCCTTTTGTTTTTGTACT 59.659 41.667 0.00 0.00 0.00 2.73
2286 2334 4.341235 AGGGAGAGCCTTTTGTTTTTGTAC 59.659 41.667 0.00 0.00 0.00 2.90
2356 2404 0.109342 ATACTGCATACTGCCCAGGC 59.891 55.000 0.38 0.38 44.23 4.85
2358 2406 1.417517 TCCATACTGCATACTGCCCAG 59.582 52.381 0.00 0.00 44.23 4.45
2361 2409 2.430465 CCATCCATACTGCATACTGCC 58.570 52.381 0.00 0.00 44.23 4.85
2368 2416 0.181114 GTCTGCCCATCCATACTGCA 59.819 55.000 0.00 0.00 0.00 4.41
2369 2417 0.882042 CGTCTGCCCATCCATACTGC 60.882 60.000 0.00 0.00 0.00 4.40
2371 2419 0.753262 GTCGTCTGCCCATCCATACT 59.247 55.000 0.00 0.00 0.00 2.12
2372 2420 0.597637 CGTCGTCTGCCCATCCATAC 60.598 60.000 0.00 0.00 0.00 2.39
2373 2421 1.739667 CGTCGTCTGCCCATCCATA 59.260 57.895 0.00 0.00 0.00 2.74
2374 2422 2.501128 CGTCGTCTGCCCATCCAT 59.499 61.111 0.00 0.00 0.00 3.41
2375 2423 4.451150 GCGTCGTCTGCCCATCCA 62.451 66.667 0.00 0.00 0.00 3.41
2376 2424 2.685387 CTAGCGTCGTCTGCCCATCC 62.685 65.000 0.00 0.00 0.00 3.51
2377 2425 1.299468 CTAGCGTCGTCTGCCCATC 60.299 63.158 0.00 0.00 0.00 3.51
2378 2426 1.320344 TTCTAGCGTCGTCTGCCCAT 61.320 55.000 0.00 0.00 0.00 4.00
2380 2428 0.595310 GATTCTAGCGTCGTCTGCCC 60.595 60.000 0.00 0.00 0.00 5.36
2382 2430 0.027716 TCGATTCTAGCGTCGTCTGC 59.972 55.000 13.74 0.00 38.85 4.26
2383 2431 2.672188 ATCGATTCTAGCGTCGTCTG 57.328 50.000 13.74 0.00 38.85 3.51
2384 2432 3.364062 CAAATCGATTCTAGCGTCGTCT 58.636 45.455 11.83 0.00 38.85 4.18
2385 2433 2.468040 CCAAATCGATTCTAGCGTCGTC 59.532 50.000 11.83 0.00 38.85 4.20
2387 2435 2.460918 ACCAAATCGATTCTAGCGTCG 58.539 47.619 11.83 9.47 39.11 5.12
2388 2436 3.245519 GGAACCAAATCGATTCTAGCGTC 59.754 47.826 11.83 4.78 0.00 5.19
2405 2474 2.617274 GCAGAAGCACACGGGAACC 61.617 63.158 0.00 0.00 43.74 3.62
2407 2476 1.301716 GAGCAGAAGCACACGGGAA 60.302 57.895 0.00 0.00 45.49 3.97
2409 2478 1.597854 TTGAGCAGAAGCACACGGG 60.598 57.895 0.00 0.00 45.49 5.28
2411 2480 1.202568 CGTTGAGCAGAAGCACACG 59.797 57.895 0.00 0.00 45.49 4.49
2412 2481 1.571460 CCGTTGAGCAGAAGCACAC 59.429 57.895 0.00 0.00 45.49 3.82
2413 2482 2.253758 GCCGTTGAGCAGAAGCACA 61.254 57.895 0.00 0.00 45.49 4.57
2414 2483 0.670546 TAGCCGTTGAGCAGAAGCAC 60.671 55.000 0.00 0.00 45.49 4.40
2415 2484 0.670546 GTAGCCGTTGAGCAGAAGCA 60.671 55.000 0.00 0.00 45.49 3.91
2416 2485 1.362406 GGTAGCCGTTGAGCAGAAGC 61.362 60.000 0.00 0.00 42.56 3.86
2424 2494 1.264749 ATCCAGCTGGTAGCCGTTGA 61.265 55.000 31.58 10.14 43.77 3.18
2461 2531 3.243468 GGAAATCTAGCGTCTACACCTCC 60.243 52.174 0.00 0.00 0.00 4.30
2466 2536 5.401531 AAACTGGAAATCTAGCGTCTACA 57.598 39.130 0.00 0.00 0.00 2.74
2510 2580 1.133388 AGAGAGGATCAGAGGAGCAGG 60.133 57.143 0.00 0.00 37.82 4.85
2540 2610 5.964958 AAAATCTCGAATCCTGCTTTTGA 57.035 34.783 0.00 0.00 0.00 2.69
2566 2640 4.100279 TCTCTGAAAGAAAAGGAACCCC 57.900 45.455 0.00 0.00 46.34 4.95
2567 2641 6.477253 AGTATCTCTGAAAGAAAAGGAACCC 58.523 40.000 0.00 0.00 46.34 4.11
2615 2693 9.713740 GAACATTAGCAGTCTAATTTCATTCAG 57.286 33.333 0.00 0.00 42.10 3.02
2616 2694 9.453572 AGAACATTAGCAGTCTAATTTCATTCA 57.546 29.630 14.61 0.00 42.10 2.57
2620 2698 8.621532 AACAGAACATTAGCAGTCTAATTTCA 57.378 30.769 14.61 0.00 42.10 2.69
2638 2720 2.842457 ACGGACTGGGTTTAACAGAAC 58.158 47.619 0.00 0.00 39.24 3.01
2663 2745 4.674567 GGACCTATCCTGCTCATCGAGAG 61.675 56.522 7.32 7.32 43.70 3.20
2670 2753 2.447408 TAACGGACCTATCCTGCTCA 57.553 50.000 0.00 0.00 43.73 4.26
2682 2765 1.201414 CCAGCATTGGGTTTAACGGAC 59.799 52.381 0.00 0.00 41.05 4.79
2728 2811 4.838486 GCTGAGGGTCGCGACTCG 62.838 72.222 35.50 21.90 36.76 4.18
2729 2812 4.500116 GGCTGAGGGTCGCGACTC 62.500 72.222 35.50 33.66 0.00 3.36
2798 2882 7.652507 CGGAGAAAATATCTAGTACCAGGTTTC 59.347 40.741 0.00 0.00 38.96 2.78
2989 3076 1.475280 TGAGTGGTCTTCCGTTATCCG 59.525 52.381 0.00 0.00 36.30 4.18
2990 3077 3.194968 TCTTGAGTGGTCTTCCGTTATCC 59.805 47.826 0.00 0.00 36.30 2.59
2991 3078 4.451629 TCTTGAGTGGTCTTCCGTTATC 57.548 45.455 0.00 0.00 36.30 1.75
2992 3079 4.466370 TGATCTTGAGTGGTCTTCCGTTAT 59.534 41.667 0.00 0.00 36.30 1.89
2993 3080 3.830178 TGATCTTGAGTGGTCTTCCGTTA 59.170 43.478 0.00 0.00 36.30 3.18
2994 3081 2.632996 TGATCTTGAGTGGTCTTCCGTT 59.367 45.455 0.00 0.00 36.30 4.44
2995 3082 2.028930 GTGATCTTGAGTGGTCTTCCGT 60.029 50.000 0.00 0.00 36.30 4.69
2996 3083 2.029020 TGTGATCTTGAGTGGTCTTCCG 60.029 50.000 0.00 0.00 36.30 4.30
2997 3084 3.244215 TGTGTGATCTTGAGTGGTCTTCC 60.244 47.826 0.00 0.00 0.00 3.46
2998 3085 3.743396 GTGTGTGATCTTGAGTGGTCTTC 59.257 47.826 0.00 0.00 0.00 2.87
2999 3086 3.495100 GGTGTGTGATCTTGAGTGGTCTT 60.495 47.826 0.00 0.00 0.00 3.01
3000 3087 2.037772 GGTGTGTGATCTTGAGTGGTCT 59.962 50.000 0.00 0.00 0.00 3.85
3001 3088 2.417719 GGTGTGTGATCTTGAGTGGTC 58.582 52.381 0.00 0.00 0.00 4.02
3002 3089 1.270305 CGGTGTGTGATCTTGAGTGGT 60.270 52.381 0.00 0.00 0.00 4.16
3003 3090 1.432514 CGGTGTGTGATCTTGAGTGG 58.567 55.000 0.00 0.00 0.00 4.00
3004 3091 1.432514 CCGGTGTGTGATCTTGAGTG 58.567 55.000 0.00 0.00 0.00 3.51
3005 3092 0.320771 GCCGGTGTGTGATCTTGAGT 60.321 55.000 1.90 0.00 0.00 3.41
3006 3093 0.036952 AGCCGGTGTGTGATCTTGAG 60.037 55.000 1.90 0.00 0.00 3.02
3007 3094 0.396435 AAGCCGGTGTGTGATCTTGA 59.604 50.000 1.90 0.00 0.00 3.02
3088 3175 0.179097 GCTCTTTGGAGACTAGCGGG 60.179 60.000 0.00 0.00 41.86 6.13
3170 3261 1.439644 GCCAACAGCACCGGAAAAA 59.560 52.632 9.46 0.00 42.97 1.94
3211 3303 3.494736 AACCCTTTTGCGCCCGGTA 62.495 57.895 4.18 0.00 0.00 4.02
3218 3312 2.124122 CTTTTTCCGAACCCTTTTGCG 58.876 47.619 0.00 0.00 0.00 4.85
3219 3313 3.173668 ACTTTTTCCGAACCCTTTTGC 57.826 42.857 0.00 0.00 0.00 3.68
3220 3314 4.201773 GCAAACTTTTTCCGAACCCTTTTG 60.202 41.667 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.