Multiple sequence alignment - TraesCS3D01G431900

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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 TraesCS3D01G431900 chr3D 100.000 3219 0 0 1 3219 545912025 545915243 0.000000e+00 5945
1 TraesCS3D01G431900 chr3A 90.157 1148 69 18 475 1601 682324263 682325387 0.000000e+00 1454
2 TraesCS3D01G431900 chr3A 89.863 947 63 8 2296 3219 682326161 682327097 0.000000e+00 1186
3 TraesCS3D01G431900 chr3A 93.228 694 40 5 1538 2227 682325456 682326146 0.000000e+00 1014
4 TraesCS3D01G431900 chr3B 92.779 914 50 11 2307 3212 722359127 722360032 0.000000e+00 1308
5 TraesCS3D01G431900 chr3B 91.815 843 43 10 1384 2222 722358302 722359122 0.000000e+00 1151
6 TraesCS3D01G431900 chr3B 90.796 641 35 5 799 1419 722357671 722358307 0.000000e+00 835
7 TraesCS3D01G431900 chr3B 90.402 323 24 4 475 791 722357001 722357322 4.970000e-113 418
8 TraesCS3D01G431900 chr3B 91.200 125 8 2 4 127 722356437 722356559 1.990000e-37 167
9 TraesCS3D01G431900 chr4D 99.398 166 1 0 145 310 457481051 457481216 5.220000e-78 302
10 TraesCS3D01G431900 chr4D 98.235 170 3 0 141 310 243613268 243613437 6.750000e-77 298
11 TraesCS3D01G431900 chr4D 98.795 166 2 0 144 309 423909747 423909582 2.430000e-76 296
12 TraesCS3D01G431900 chr2B 96.089 179 7 0 132 310 72616576 72616754 3.140000e-75 292
13 TraesCS3D01G431900 chr7D 98.193 166 3 0 145 310 312574128 312574293 1.130000e-74 291
14 TraesCS3D01G431900 chr7D 98.193 166 3 0 144 309 363148832 363148997 1.130000e-74 291
15 TraesCS3D01G431900 chr1D 97.093 172 5 0 139 310 1590358 1590529 1.130000e-74 291
16 TraesCS3D01G431900 chr6D 97.076 171 5 0 143 313 431000182 431000012 4.060000e-74 289
17 TraesCS3D01G431900 chr4A 97.619 168 4 0 142 309 141122664 141122831 4.060000e-74 289


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 TraesCS3D01G431900 chr3D 545912025 545915243 3218 False 5945.0 5945 100.000000 1 3219 1 chr3D.!!$F1 3218
1 TraesCS3D01G431900 chr3A 682324263 682327097 2834 False 1218.0 1454 91.082667 475 3219 3 chr3A.!!$F1 2744
2 TraesCS3D01G431900 chr3B 722356437 722360032 3595 False 775.8 1308 91.398400 4 3212 5 chr3B.!!$F1 3208

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
891 1548 0.035458 CAGCCCAGAAACTCGAAGGT 59.965 55.0 0.0 0.0 0.0 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2575 3444 1.898574 CATAGGTGCATTCCGGCCC 60.899 63.158 0.0 0.0 0.0 5.8 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
29 30 7.528996 TTCACACCATCTTGATTCTCAAAAT 57.471 32.000 0.00 0.00 35.73 1.82
30 31 7.528996 TCACACCATCTTGATTCTCAAAATT 57.471 32.000 0.00 0.00 35.73 1.82
31 32 7.596494 TCACACCATCTTGATTCTCAAAATTC 58.404 34.615 0.00 0.00 35.73 2.17
77 78 2.529744 GGAAGCACTCCACCTGGGT 61.530 63.158 0.00 0.00 44.67 4.51
78 79 1.456287 GAAGCACTCCACCTGGGTT 59.544 57.895 0.00 0.00 38.11 4.11
109 110 1.133407 GCTGGACTCCGTACTCTTGAG 59.867 57.143 0.00 0.00 0.00 3.02
122 123 5.473162 CGTACTCTTGAGATCCTCATCATCT 59.527 44.000 4.49 0.00 40.39 2.90
126 127 7.472741 ACTCTTGAGATCCTCATCATCTAGAT 58.527 38.462 0.00 0.00 40.39 1.98
127 128 7.951806 ACTCTTGAGATCCTCATCATCTAGATT 59.048 37.037 1.33 0.00 40.39 2.40
128 129 8.124808 TCTTGAGATCCTCATCATCTAGATTG 57.875 38.462 1.33 0.00 40.39 2.67
129 130 7.729431 TCTTGAGATCCTCATCATCTAGATTGT 59.271 37.037 1.33 0.00 40.39 2.71
130 131 8.946797 TTGAGATCCTCATCATCTAGATTGTA 57.053 34.615 1.33 0.00 40.39 2.41
131 132 9.544579 TTGAGATCCTCATCATCTAGATTGTAT 57.455 33.333 1.33 0.00 40.39 2.29
132 133 9.544579 TGAGATCCTCATCATCTAGATTGTATT 57.455 33.333 1.33 0.00 35.39 1.89
134 135 8.980596 AGATCCTCATCATCTAGATTGTATTCC 58.019 37.037 1.33 0.00 33.72 3.01
135 136 7.487822 TCCTCATCATCTAGATTGTATTCCC 57.512 40.000 1.33 0.00 33.72 3.97
136 137 7.251936 TCCTCATCATCTAGATTGTATTCCCT 58.748 38.462 1.33 0.00 33.72 4.20
137 138 7.736691 TCCTCATCATCTAGATTGTATTCCCTT 59.263 37.037 1.33 0.00 33.72 3.95
138 139 7.823310 CCTCATCATCTAGATTGTATTCCCTTG 59.177 40.741 1.33 0.00 33.72 3.61
139 140 7.683578 TCATCATCTAGATTGTATTCCCTTGG 58.316 38.462 1.33 0.00 33.72 3.61
140 141 5.869579 TCATCTAGATTGTATTCCCTTGGC 58.130 41.667 1.33 0.00 0.00 4.52
141 142 5.369404 TCATCTAGATTGTATTCCCTTGGCA 59.631 40.000 1.33 0.00 0.00 4.92
142 143 5.912149 TCTAGATTGTATTCCCTTGGCAT 57.088 39.130 0.00 0.00 0.00 4.40
143 144 5.624159 TCTAGATTGTATTCCCTTGGCATG 58.376 41.667 0.00 0.00 0.00 4.06
144 145 4.255510 AGATTGTATTCCCTTGGCATGT 57.744 40.909 0.00 0.00 0.00 3.21
145 146 5.387113 AGATTGTATTCCCTTGGCATGTA 57.613 39.130 0.00 0.00 0.00 2.29
146 147 5.133221 AGATTGTATTCCCTTGGCATGTAC 58.867 41.667 0.00 0.00 0.00 2.90
147 148 4.584638 TTGTATTCCCTTGGCATGTACT 57.415 40.909 0.00 0.00 0.00 2.73
148 149 4.150897 TGTATTCCCTTGGCATGTACTC 57.849 45.455 0.00 0.00 0.00 2.59
149 150 2.736670 ATTCCCTTGGCATGTACTCC 57.263 50.000 0.00 0.00 0.00 3.85
150 151 0.623723 TTCCCTTGGCATGTACTCCC 59.376 55.000 0.00 0.00 0.00 4.30
151 152 0.253160 TCCCTTGGCATGTACTCCCT 60.253 55.000 0.00 0.00 0.00 4.20
152 153 0.181350 CCCTTGGCATGTACTCCCTC 59.819 60.000 0.00 0.00 0.00 4.30
153 154 0.181350 CCTTGGCATGTACTCCCTCC 59.819 60.000 0.00 0.00 0.00 4.30
154 155 0.179073 CTTGGCATGTACTCCCTCCG 60.179 60.000 0.00 0.00 0.00 4.63
155 156 0.907704 TTGGCATGTACTCCCTCCGT 60.908 55.000 0.00 0.00 0.00 4.69
156 157 0.907704 TGGCATGTACTCCCTCCGTT 60.908 55.000 0.00 0.00 0.00 4.44
157 158 0.179081 GGCATGTACTCCCTCCGTTC 60.179 60.000 0.00 0.00 0.00 3.95
158 159 0.179081 GCATGTACTCCCTCCGTTCC 60.179 60.000 0.00 0.00 0.00 3.62
159 160 1.486211 CATGTACTCCCTCCGTTCCT 58.514 55.000 0.00 0.00 0.00 3.36
160 161 2.662866 CATGTACTCCCTCCGTTCCTA 58.337 52.381 0.00 0.00 0.00 2.94
161 162 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
162 163 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
163 164 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
164 165 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
165 166 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
166 167 6.613699 TGTACTCCCTCCGTTCCTAAATATA 58.386 40.000 0.00 0.00 0.00 0.86
167 168 7.068702 TGTACTCCCTCCGTTCCTAAATATAA 58.931 38.462 0.00 0.00 0.00 0.98
168 169 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
169 170 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
170 171 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
171 172 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
172 173 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
173 174 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
174 175 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
175 176 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
203 204 8.948853 ACATTTCAAATGAACTACAACATACG 57.051 30.769 17.30 0.00 33.13 3.06
204 205 8.020819 ACATTTCAAATGAACTACAACATACGG 58.979 33.333 17.30 0.00 33.13 4.02
205 206 7.731882 TTTCAAATGAACTACAACATACGGA 57.268 32.000 0.00 0.00 33.13 4.69
206 207 7.915293 TTCAAATGAACTACAACATACGGAT 57.085 32.000 0.00 0.00 0.00 4.18
207 208 7.302350 TCAAATGAACTACAACATACGGATG 57.698 36.000 5.94 5.94 39.16 3.51
209 210 8.035984 TCAAATGAACTACAACATACGGATGTA 58.964 33.333 15.10 0.00 45.93 2.29
210 211 8.826710 CAAATGAACTACAACATACGGATGTAT 58.173 33.333 15.10 8.21 45.93 2.29
249 250 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
250 251 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
251 252 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
252 253 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
253 254 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
254 255 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
255 256 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
256 257 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
257 258 3.684305 TCACTCATTTTGCTCCGTATGTG 59.316 43.478 0.00 0.00 0.00 3.21
258 259 3.009723 ACTCATTTTGCTCCGTATGTGG 58.990 45.455 0.00 0.00 0.00 4.17
259 260 3.009723 CTCATTTTGCTCCGTATGTGGT 58.990 45.455 0.00 0.00 0.00 4.16
260 261 3.006940 TCATTTTGCTCCGTATGTGGTC 58.993 45.455 0.00 0.00 0.00 4.02
261 262 2.552599 TTTTGCTCCGTATGTGGTCA 57.447 45.000 0.00 0.00 0.00 4.02
262 263 1.803334 TTTGCTCCGTATGTGGTCAC 58.197 50.000 0.00 0.00 0.00 3.67
263 264 0.973632 TTGCTCCGTATGTGGTCACT 59.026 50.000 2.66 0.00 0.00 3.41
264 265 0.973632 TGCTCCGTATGTGGTCACTT 59.026 50.000 2.66 0.00 0.00 3.16
265 266 1.337728 TGCTCCGTATGTGGTCACTTG 60.338 52.381 2.66 0.00 0.00 3.16
266 267 1.337823 GCTCCGTATGTGGTCACTTGT 60.338 52.381 2.66 0.00 0.00 3.16
267 268 2.870435 GCTCCGTATGTGGTCACTTGTT 60.870 50.000 2.66 0.00 0.00 2.83
268 269 2.736721 CTCCGTATGTGGTCACTTGTTG 59.263 50.000 2.66 0.00 0.00 3.33
269 270 1.804151 CCGTATGTGGTCACTTGTTGG 59.196 52.381 2.66 0.00 0.00 3.77
270 271 2.549134 CCGTATGTGGTCACTTGTTGGA 60.549 50.000 2.66 0.00 0.00 3.53
271 272 3.135225 CGTATGTGGTCACTTGTTGGAA 58.865 45.455 2.66 0.00 0.00 3.53
272 273 3.751175 CGTATGTGGTCACTTGTTGGAAT 59.249 43.478 2.66 0.00 0.00 3.01
273 274 4.142902 CGTATGTGGTCACTTGTTGGAATC 60.143 45.833 2.66 0.00 0.00 2.52
274 275 3.576078 TGTGGTCACTTGTTGGAATCT 57.424 42.857 2.66 0.00 0.00 2.40
275 276 3.476552 TGTGGTCACTTGTTGGAATCTC 58.523 45.455 2.66 0.00 0.00 2.75
276 277 3.136443 TGTGGTCACTTGTTGGAATCTCT 59.864 43.478 2.66 0.00 0.00 3.10
277 278 4.346709 TGTGGTCACTTGTTGGAATCTCTA 59.653 41.667 2.66 0.00 0.00 2.43
278 279 5.163248 TGTGGTCACTTGTTGGAATCTCTAA 60.163 40.000 2.66 0.00 0.00 2.10
279 280 5.763204 GTGGTCACTTGTTGGAATCTCTAAA 59.237 40.000 0.00 0.00 0.00 1.85
280 281 6.262273 GTGGTCACTTGTTGGAATCTCTAAAA 59.738 38.462 0.00 0.00 0.00 1.52
281 282 6.831353 TGGTCACTTGTTGGAATCTCTAAAAA 59.169 34.615 0.00 0.00 0.00 1.94
282 283 7.013274 TGGTCACTTGTTGGAATCTCTAAAAAG 59.987 37.037 2.17 2.17 37.94 2.27
283 284 7.228706 GGTCACTTGTTGGAATCTCTAAAAAGA 59.771 37.037 9.03 0.00 35.06 2.52
284 285 8.070769 GTCACTTGTTGGAATCTCTAAAAAGAC 58.929 37.037 9.03 0.00 35.06 3.01
285 286 7.993183 TCACTTGTTGGAATCTCTAAAAAGACT 59.007 33.333 9.03 0.00 35.06 3.24
286 287 8.624776 CACTTGTTGGAATCTCTAAAAAGACTT 58.375 33.333 9.03 0.00 35.06 3.01
287 288 9.847224 ACTTGTTGGAATCTCTAAAAAGACTTA 57.153 29.630 9.03 0.00 35.06 2.24
300 301 9.169592 TCTAAAAAGACTTATATTTGGGAACGG 57.830 33.333 0.00 0.00 0.00 4.44
301 302 9.169592 CTAAAAAGACTTATATTTGGGAACGGA 57.830 33.333 0.00 0.00 0.00 4.69
302 303 7.625828 AAAAGACTTATATTTGGGAACGGAG 57.374 36.000 0.00 0.00 0.00 4.63
303 304 5.291905 AGACTTATATTTGGGAACGGAGG 57.708 43.478 0.00 0.00 0.00 4.30
304 305 4.102681 AGACTTATATTTGGGAACGGAGGG 59.897 45.833 0.00 0.00 0.00 4.30
305 306 4.042174 ACTTATATTTGGGAACGGAGGGA 58.958 43.478 0.00 0.00 0.00 4.20
306 307 4.102681 ACTTATATTTGGGAACGGAGGGAG 59.897 45.833 0.00 0.00 0.00 4.30
307 308 1.961133 TATTTGGGAACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
308 309 1.961133 ATTTGGGAACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
309 310 1.272807 TTTGGGAACGGAGGGAGTAG 58.727 55.000 0.00 0.00 0.00 2.57
310 311 0.616679 TTGGGAACGGAGGGAGTAGG 60.617 60.000 0.00 0.00 0.00 3.18
316 317 0.706433 ACGGAGGGAGTAGGTACCAA 59.294 55.000 15.94 0.00 0.00 3.67
325 326 2.901839 GAGTAGGTACCAAGGTCACCAA 59.098 50.000 15.94 0.00 34.62 3.67
341 342 1.303888 CAACATCTGTGCCCCTGCT 60.304 57.895 0.00 0.00 38.71 4.24
344 345 4.790962 ATCTGTGCCCCTGCTGCG 62.791 66.667 0.00 0.00 38.71 5.18
404 703 2.040012 AGTACTCTTCCCGTGACTCTCA 59.960 50.000 0.00 0.00 0.00 3.27
412 711 3.527186 GTGACTCTCACACACGCG 58.473 61.111 3.53 3.53 46.22 6.01
413 712 2.354656 TGACTCTCACACACGCGC 60.355 61.111 5.73 0.00 0.00 6.86
422 721 3.913573 CACACGCGCGCCTGATAC 61.914 66.667 31.76 2.19 0.00 2.24
433 732 3.403038 GCGCCTGATACATGAATACCTT 58.597 45.455 0.00 0.00 0.00 3.50
434 733 3.815401 GCGCCTGATACATGAATACCTTT 59.185 43.478 0.00 0.00 0.00 3.11
435 734 4.319766 GCGCCTGATACATGAATACCTTTG 60.320 45.833 0.00 0.00 0.00 2.77
436 735 4.816385 CGCCTGATACATGAATACCTTTGT 59.184 41.667 0.00 0.00 0.00 2.83
437 736 5.989168 CGCCTGATACATGAATACCTTTGTA 59.011 40.000 0.00 0.00 0.00 2.41
438 737 6.481976 CGCCTGATACATGAATACCTTTGTAA 59.518 38.462 0.00 0.00 0.00 2.41
439 738 7.173218 CGCCTGATACATGAATACCTTTGTAAT 59.827 37.037 0.00 0.00 0.00 1.89
440 739 8.850156 GCCTGATACATGAATACCTTTGTAATT 58.150 33.333 0.00 0.00 0.00 1.40
456 755 8.739039 CCTTTGTAATTTGTATCATCCTGTTCA 58.261 33.333 0.00 0.00 0.00 3.18
458 757 7.864108 TGTAATTTGTATCATCCTGTTCAGG 57.136 36.000 12.20 12.20 0.00 3.86
466 765 0.706433 ATCCTGTTCAGGCCAACCAT 59.294 50.000 5.01 0.00 39.06 3.55
467 766 0.038166 TCCTGTTCAGGCCAACCATC 59.962 55.000 5.01 0.00 39.06 3.51
468 767 0.251297 CCTGTTCAGGCCAACCATCA 60.251 55.000 5.01 0.00 39.06 3.07
469 768 1.617804 CCTGTTCAGGCCAACCATCAT 60.618 52.381 5.01 0.00 39.06 2.45
470 769 2.357050 CCTGTTCAGGCCAACCATCATA 60.357 50.000 5.01 0.00 39.06 2.15
471 770 2.947652 CTGTTCAGGCCAACCATCATAG 59.052 50.000 5.01 0.00 39.06 2.23
472 771 2.575735 TGTTCAGGCCAACCATCATAGA 59.424 45.455 5.01 0.00 39.06 1.98
473 772 3.202818 TGTTCAGGCCAACCATCATAGAT 59.797 43.478 5.01 0.00 39.06 1.98
497 796 1.314730 AGTTAGCCAACAAACACCGG 58.685 50.000 0.00 0.00 37.10 5.28
503 802 1.671901 CCAACAAACACCGGGCAGTT 61.672 55.000 6.32 4.72 0.00 3.16
539 838 1.086067 CCATCTCGCATCACACGCTT 61.086 55.000 0.00 0.00 0.00 4.68
546 845 0.950555 GCATCACACGCTTCCAGTCA 60.951 55.000 0.00 0.00 0.00 3.41
642 941 3.163594 GTTTGCATGCTTGATCGTACAC 58.836 45.455 20.33 0.00 0.00 2.90
643 942 2.091852 TGCATGCTTGATCGTACACA 57.908 45.000 20.33 0.00 0.00 3.72
650 949 4.430007 TGCTTGATCGTACACAGGAATAC 58.570 43.478 0.00 0.00 0.00 1.89
728 1030 6.094464 TCCTATGAATCAAAAGAGCACATGTG 59.906 38.462 21.83 21.83 0.00 3.21
819 1466 2.592102 TCAATCAAAGAGGCCTGCTT 57.408 45.000 12.00 11.06 0.00 3.91
820 1467 3.719268 TCAATCAAAGAGGCCTGCTTA 57.281 42.857 12.00 0.00 0.00 3.09
821 1468 3.347216 TCAATCAAAGAGGCCTGCTTAC 58.653 45.455 12.00 0.00 0.00 2.34
822 1469 2.424956 CAATCAAAGAGGCCTGCTTACC 59.575 50.000 12.00 0.00 0.00 2.85
860 1508 7.509546 CCCATCTTCACTAAAGGCTCTTATAA 58.490 38.462 0.00 0.00 35.54 0.98
865 1522 9.823647 TCTTCACTAAAGGCTCTTATAAGATTG 57.176 33.333 15.47 6.51 35.54 2.67
884 1541 0.605589 GTTACCGCAGCCCAGAAACT 60.606 55.000 0.00 0.00 0.00 2.66
891 1548 0.035458 CAGCCCAGAAACTCGAAGGT 59.965 55.000 0.00 0.00 0.00 3.50
963 1638 4.509756 CTGTCATCAGCCACCTCG 57.490 61.111 0.00 0.00 34.79 4.63
1230 1906 3.036429 GCAGGATCCTTCGGTGCCT 62.036 63.158 13.00 0.00 30.13 4.75
1233 1909 2.514824 GATCCTTCGGTGCCTGCC 60.515 66.667 0.00 0.00 0.00 4.85
1434 2140 0.246635 ACGAATTCGCCAGTGCTACT 59.753 50.000 27.03 0.92 44.43 2.57
1459 2165 2.097036 GTAATTTGTTCCCCTTCCCCG 58.903 52.381 0.00 0.00 0.00 5.73
1501 2207 1.516161 TGCTCTGCATCACACAAGTC 58.484 50.000 0.00 0.00 31.71 3.01
1536 2242 0.512952 GCGCTGACACTTTGAATCGT 59.487 50.000 0.00 0.00 0.00 3.73
1539 2376 2.143122 GCTGACACTTTGAATCGTCCA 58.857 47.619 0.00 0.00 0.00 4.02
1542 2379 4.572389 GCTGACACTTTGAATCGTCCATAT 59.428 41.667 0.00 0.00 0.00 1.78
1570 2407 2.214181 GACACGACTCTGGCGGTCAT 62.214 60.000 0.00 0.00 33.73 3.06
1702 2539 2.094545 GCAGTTGCCCAAATGTAAGGAG 60.095 50.000 9.75 0.00 38.50 3.69
1776 2613 1.597742 GCCTGTCACAGCAAGAGAAA 58.402 50.000 0.00 0.00 0.00 2.52
1807 2647 1.306397 TCCTCATCCTCCTGCTGCA 60.306 57.895 0.88 0.88 0.00 4.41
1945 2785 2.166459 TGATTCAGTCACCTCCGATGAC 59.834 50.000 0.00 0.00 45.70 3.06
2020 2860 1.945394 CCTGCATATGAGCAACTGGTC 59.055 52.381 6.97 1.92 45.13 4.02
2024 2864 1.863454 CATATGAGCAACTGGTCTCGC 59.137 52.381 10.05 0.00 42.60 5.03
2107 2947 6.798482 TGCAGAAAAATGGATAAGCATACTG 58.202 36.000 0.00 0.00 0.00 2.74
2142 2983 2.303890 TCATGCAAGCCTTCTCTTCTGA 59.696 45.455 0.00 0.00 0.00 3.27
2143 2984 2.936919 TGCAAGCCTTCTCTTCTGAA 57.063 45.000 0.00 0.00 0.00 3.02
2147 2988 4.217118 TGCAAGCCTTCTCTTCTGAAAATC 59.783 41.667 0.00 0.00 0.00 2.17
2222 3064 5.121380 AGACCATTTCCAGTTATCTGCAT 57.879 39.130 0.00 0.00 40.09 3.96
2227 3069 5.450965 CCATTTCCAGTTATCTGCATTGTCC 60.451 44.000 0.00 0.00 40.09 4.02
2228 3070 3.998913 TCCAGTTATCTGCATTGTCCA 57.001 42.857 0.00 0.00 40.09 4.02
2229 3071 4.508551 TCCAGTTATCTGCATTGTCCAT 57.491 40.909 0.00 0.00 40.09 3.41
2231 3073 5.263599 TCCAGTTATCTGCATTGTCCATTT 58.736 37.500 0.00 0.00 40.09 2.32
2234 3076 6.532657 CCAGTTATCTGCATTGTCCATTTTTC 59.467 38.462 0.00 0.00 40.09 2.29
2235 3077 7.092079 CAGTTATCTGCATTGTCCATTTTTCA 58.908 34.615 0.00 0.00 34.79 2.69
2236 3078 7.062605 CAGTTATCTGCATTGTCCATTTTTCAC 59.937 37.037 0.00 0.00 34.79 3.18
2237 3079 4.255833 TCTGCATTGTCCATTTTTCACC 57.744 40.909 0.00 0.00 0.00 4.02
2238 3080 3.896888 TCTGCATTGTCCATTTTTCACCT 59.103 39.130 0.00 0.00 0.00 4.00
2239 3081 4.344679 TCTGCATTGTCCATTTTTCACCTT 59.655 37.500 0.00 0.00 0.00 3.50
2241 3083 5.435291 TGCATTGTCCATTTTTCACCTTTT 58.565 33.333 0.00 0.00 0.00 2.27
2242 3084 5.526846 TGCATTGTCCATTTTTCACCTTTTC 59.473 36.000 0.00 0.00 0.00 2.29
2243 3085 5.049474 GCATTGTCCATTTTTCACCTTTTCC 60.049 40.000 0.00 0.00 0.00 3.13
2244 3086 5.948742 TTGTCCATTTTTCACCTTTTCCT 57.051 34.783 0.00 0.00 0.00 3.36
2245 3087 5.529581 TGTCCATTTTTCACCTTTTCCTC 57.470 39.130 0.00 0.00 0.00 3.71
2246 3088 5.208121 TGTCCATTTTTCACCTTTTCCTCT 58.792 37.500 0.00 0.00 0.00 3.69
2247 3089 6.369629 TGTCCATTTTTCACCTTTTCCTCTA 58.630 36.000 0.00 0.00 0.00 2.43
2248 3090 6.836527 TGTCCATTTTTCACCTTTTCCTCTAA 59.163 34.615 0.00 0.00 0.00 2.10
2249 3091 7.508977 TGTCCATTTTTCACCTTTTCCTCTAAT 59.491 33.333 0.00 0.00 0.00 1.73
2250 3092 8.367911 GTCCATTTTTCACCTTTTCCTCTAATT 58.632 33.333 0.00 0.00 0.00 1.40
2251 3093 8.933653 TCCATTTTTCACCTTTTCCTCTAATTT 58.066 29.630 0.00 0.00 0.00 1.82
2252 3094 8.992073 CCATTTTTCACCTTTTCCTCTAATTTG 58.008 33.333 0.00 0.00 0.00 2.32
2253 3095 8.498358 CATTTTTCACCTTTTCCTCTAATTTGC 58.502 33.333 0.00 0.00 0.00 3.68
2254 3096 6.723298 TTTCACCTTTTCCTCTAATTTGCA 57.277 33.333 0.00 0.00 0.00 4.08
2255 3097 6.916360 TTCACCTTTTCCTCTAATTTGCAT 57.084 33.333 0.00 0.00 0.00 3.96
2256 3098 8.415950 TTTCACCTTTTCCTCTAATTTGCATA 57.584 30.769 0.00 0.00 0.00 3.14
2257 3099 8.593945 TTCACCTTTTCCTCTAATTTGCATAT 57.406 30.769 0.00 0.00 0.00 1.78
2258 3100 9.693739 TTCACCTTTTCCTCTAATTTGCATATA 57.306 29.630 0.00 0.00 0.00 0.86
2259 3101 9.866655 TCACCTTTTCCTCTAATTTGCATATAT 57.133 29.630 0.00 0.00 0.00 0.86
2284 3126 5.990408 GTGAGAAGTCACCTACACAATTTG 58.010 41.667 0.00 0.00 46.58 2.32
2285 3127 4.515191 TGAGAAGTCACCTACACAATTTGC 59.485 41.667 0.00 0.00 0.00 3.68
2286 3128 4.460263 AGAAGTCACCTACACAATTTGCA 58.540 39.130 0.00 0.00 0.00 4.08
2287 3129 5.072741 AGAAGTCACCTACACAATTTGCAT 58.927 37.500 0.00 0.00 0.00 3.96
2288 3130 6.237901 AGAAGTCACCTACACAATTTGCATA 58.762 36.000 0.00 0.00 0.00 3.14
2289 3131 6.886459 AGAAGTCACCTACACAATTTGCATAT 59.114 34.615 0.00 0.00 0.00 1.78
2290 3132 8.046708 AGAAGTCACCTACACAATTTGCATATA 58.953 33.333 0.00 0.00 0.00 0.86
2291 3133 8.752005 AAGTCACCTACACAATTTGCATATAT 57.248 30.769 0.00 0.00 0.00 0.86
2292 3134 8.158169 AGTCACCTACACAATTTGCATATATG 57.842 34.615 8.45 8.45 0.00 1.78
2293 3135 7.229306 AGTCACCTACACAATTTGCATATATGG 59.771 37.037 14.51 0.00 0.00 2.74
2294 3136 6.016360 TCACCTACACAATTTGCATATATGGC 60.016 38.462 14.51 7.40 0.00 4.40
2303 3145 2.989909 TGCATATATGGCCTGAATCCG 58.010 47.619 14.51 0.00 0.00 4.18
2305 3147 3.244875 TGCATATATGGCCTGAATCCGTT 60.245 43.478 14.51 0.00 0.00 4.44
2442 3306 3.010138 TGACCAGGGGATGTAAGAAAAGG 59.990 47.826 0.00 0.00 0.00 3.11
2506 3375 6.428083 TGTCATTTGACTAAACCTACTGGA 57.572 37.500 11.67 0.00 44.99 3.86
2508 3377 7.458397 TGTCATTTGACTAAACCTACTGGAAT 58.542 34.615 11.67 0.00 44.99 3.01
2575 3444 1.592669 CGGATGGCCAAGCGAGTAG 60.593 63.158 10.96 0.00 0.00 2.57
2614 3483 3.860930 AACCGTGGAAGGCGCCATT 62.861 57.895 31.54 19.82 40.68 3.16
2662 3531 0.321671 CCTTCTTCGGGCTGTTCAGA 59.678 55.000 3.84 0.00 0.00 3.27
2707 3576 3.073274 AGGCTCGGCATTTTCTTTAGT 57.927 42.857 0.00 0.00 0.00 2.24
2934 3803 8.864069 TTTGATAAAAAGCGTCAATTGAAGAA 57.136 26.923 23.23 4.29 0.00 2.52
2948 3817 8.064814 GTCAATTGAAGAAGACACAAGAAGTAC 58.935 37.037 10.35 0.00 0.00 2.73
2951 3820 8.682936 ATTGAAGAAGACACAAGAAGTACAAT 57.317 30.769 0.00 0.00 0.00 2.71
2953 3822 9.607988 TTGAAGAAGACACAAGAAGTACAATTA 57.392 29.630 0.00 0.00 0.00 1.40
2954 3823 9.607988 TGAAGAAGACACAAGAAGTACAATTAA 57.392 29.630 0.00 0.00 0.00 1.40
2957 3826 8.548721 AGAAGACACAAGAAGTACAATTAAACG 58.451 33.333 0.00 0.00 0.00 3.60
2959 3828 7.627340 AGACACAAGAAGTACAATTAAACGTG 58.373 34.615 0.00 0.00 0.00 4.49
2960 3829 7.493320 AGACACAAGAAGTACAATTAAACGTGA 59.507 33.333 0.00 0.00 0.00 4.35
2989 3858 9.537192 TTTTAGTGGTATTTCGGTATCATACAG 57.463 33.333 0.00 0.00 0.00 2.74
2990 3859 6.726490 AGTGGTATTTCGGTATCATACAGT 57.274 37.500 0.00 0.00 0.00 3.55
2992 3861 7.208080 AGTGGTATTTCGGTATCATACAGTTC 58.792 38.462 0.00 0.00 0.00 3.01
2994 3863 6.982141 TGGTATTTCGGTATCATACAGTTCAC 59.018 38.462 0.00 0.00 0.00 3.18
2995 3864 6.982141 GGTATTTCGGTATCATACAGTTCACA 59.018 38.462 0.00 0.00 0.00 3.58
2996 3865 7.656137 GGTATTTCGGTATCATACAGTTCACAT 59.344 37.037 0.00 0.00 0.00 3.21
2997 3866 9.042008 GTATTTCGGTATCATACAGTTCACATT 57.958 33.333 0.00 0.00 0.00 2.71
2998 3867 7.915293 TTTCGGTATCATACAGTTCACATTT 57.085 32.000 0.00 0.00 0.00 2.32
2999 3868 7.534085 TTCGGTATCATACAGTTCACATTTC 57.466 36.000 0.00 0.00 0.00 2.17
3065 3934 0.321346 CTTTGGGTTTCCATGTGGCC 59.679 55.000 0.00 0.00 43.63 5.36
3076 3945 3.738982 TCCATGTGGCCTATTATTGACG 58.261 45.455 3.32 0.00 34.44 4.35
3130 3999 1.425066 TGTGAGATGGGCTTTCTGGTT 59.575 47.619 0.00 0.00 0.00 3.67
3131 4000 1.815003 GTGAGATGGGCTTTCTGGTTG 59.185 52.381 0.00 0.00 0.00 3.77
3139 4008 2.297701 GGCTTTCTGGTTGTTGTCTGA 58.702 47.619 0.00 0.00 0.00 3.27
3148 4017 3.131577 TGGTTGTTGTCTGACGTTCTACT 59.868 43.478 2.98 0.00 0.00 2.57
3151 4020 4.224715 TGTTGTCTGACGTTCTACTGAG 57.775 45.455 2.98 0.00 0.00 3.35
3215 4084 4.398988 TGTTGAAGCTTCTTGTGACACAAT 59.601 37.500 26.09 5.53 37.48 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.261603 TGAGAATCAAGATGGTGTGAATATGC 59.738 38.462 0.00 0.00 45.97 3.14
1 2 7.797038 TGAGAATCAAGATGGTGTGAATATG 57.203 36.000 0.00 0.00 45.97 1.78
90 91 2.712709 TCTCAAGAGTACGGAGTCCAG 58.287 52.381 10.49 4.72 43.93 3.86
109 110 8.203485 GGGAATACAATCTAGATGATGAGGATC 58.797 40.741 5.86 1.99 35.21 3.36
122 123 5.387113 ACATGCCAAGGGAATACAATCTA 57.613 39.130 0.00 0.00 0.00 1.98
126 127 4.523083 GAGTACATGCCAAGGGAATACAA 58.477 43.478 0.00 0.00 0.00 2.41
127 128 3.118038 GGAGTACATGCCAAGGGAATACA 60.118 47.826 0.00 0.00 0.00 2.29
128 129 3.477530 GGAGTACATGCCAAGGGAATAC 58.522 50.000 0.00 0.00 0.00 1.89
129 130 2.441750 GGGAGTACATGCCAAGGGAATA 59.558 50.000 0.00 0.00 39.77 1.75
130 131 1.215423 GGGAGTACATGCCAAGGGAAT 59.785 52.381 0.00 0.00 39.77 3.01
131 132 0.623723 GGGAGTACATGCCAAGGGAA 59.376 55.000 0.00 0.00 39.77 3.97
132 133 0.253160 AGGGAGTACATGCCAAGGGA 60.253 55.000 0.00 0.00 43.31 4.20
133 134 0.181350 GAGGGAGTACATGCCAAGGG 59.819 60.000 0.00 0.00 43.31 3.95
134 135 0.181350 GGAGGGAGTACATGCCAAGG 59.819 60.000 0.00 0.00 43.31 3.61
135 136 0.179073 CGGAGGGAGTACATGCCAAG 60.179 60.000 0.00 0.00 43.31 3.61
136 137 0.907704 ACGGAGGGAGTACATGCCAA 60.908 55.000 0.00 0.00 43.31 4.52
137 138 0.907704 AACGGAGGGAGTACATGCCA 60.908 55.000 0.00 0.00 43.31 4.92
138 139 0.179081 GAACGGAGGGAGTACATGCC 60.179 60.000 0.00 0.00 40.48 4.40
139 140 0.179081 GGAACGGAGGGAGTACATGC 60.179 60.000 0.00 0.00 0.00 4.06
140 141 1.486211 AGGAACGGAGGGAGTACATG 58.514 55.000 0.00 0.00 0.00 3.21
141 142 3.393426 TTAGGAACGGAGGGAGTACAT 57.607 47.619 0.00 0.00 0.00 2.29
142 143 2.905415 TTAGGAACGGAGGGAGTACA 57.095 50.000 0.00 0.00 0.00 2.90
143 144 7.232330 ACTTATATTTAGGAACGGAGGGAGTAC 59.768 40.741 0.00 0.00 0.00 2.73
144 145 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
145 146 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
146 147 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
147 148 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
148 149 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
149 150 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
177 178 9.051027 CGTATGTTGTAGTTCATTTGAAATGTC 57.949 33.333 16.62 11.39 35.58 3.06
178 179 8.020819 CCGTATGTTGTAGTTCATTTGAAATGT 58.979 33.333 16.62 1.69 35.58 2.71
179 180 8.233868 TCCGTATGTTGTAGTTCATTTGAAATG 58.766 33.333 11.54 11.54 35.58 2.32
180 181 8.330466 TCCGTATGTTGTAGTTCATTTGAAAT 57.670 30.769 0.00 0.00 35.58 2.17
181 182 7.731882 TCCGTATGTTGTAGTTCATTTGAAA 57.268 32.000 0.00 0.00 35.58 2.69
182 183 7.389330 ACATCCGTATGTTGTAGTTCATTTGAA 59.611 33.333 0.00 0.00 44.07 2.69
183 184 6.876789 ACATCCGTATGTTGTAGTTCATTTGA 59.123 34.615 0.00 0.00 44.07 2.69
184 185 7.072177 ACATCCGTATGTTGTAGTTCATTTG 57.928 36.000 0.00 0.00 44.07 2.32
185 186 8.826710 CATACATCCGTATGTTGTAGTTCATTT 58.173 33.333 0.00 0.00 46.70 2.32
186 187 8.365399 CATACATCCGTATGTTGTAGTTCATT 57.635 34.615 0.00 0.00 46.70 2.57
187 188 7.946655 CATACATCCGTATGTTGTAGTTCAT 57.053 36.000 0.00 0.00 46.70 2.57
227 228 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
228 229 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
229 230 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
230 231 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
231 232 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
232 233 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
233 234 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
234 235 4.154015 CACATACGGAGCAAAATGAGTGAA 59.846 41.667 0.00 0.00 0.00 3.18
235 236 3.684305 CACATACGGAGCAAAATGAGTGA 59.316 43.478 0.00 0.00 0.00 3.41
236 237 3.181507 CCACATACGGAGCAAAATGAGTG 60.182 47.826 0.00 0.00 0.00 3.51
237 238 3.009723 CCACATACGGAGCAAAATGAGT 58.990 45.455 0.00 0.00 0.00 3.41
238 239 3.009723 ACCACATACGGAGCAAAATGAG 58.990 45.455 0.00 0.00 0.00 2.90
239 240 3.006940 GACCACATACGGAGCAAAATGA 58.993 45.455 0.00 0.00 0.00 2.57
240 241 2.746904 TGACCACATACGGAGCAAAATG 59.253 45.455 0.00 0.00 0.00 2.32
241 242 2.747446 GTGACCACATACGGAGCAAAAT 59.253 45.455 0.00 0.00 0.00 1.82
242 243 2.147958 GTGACCACATACGGAGCAAAA 58.852 47.619 0.00 0.00 0.00 2.44
243 244 1.346395 AGTGACCACATACGGAGCAAA 59.654 47.619 2.78 0.00 0.00 3.68
244 245 0.973632 AGTGACCACATACGGAGCAA 59.026 50.000 2.78 0.00 0.00 3.91
245 246 0.973632 AAGTGACCACATACGGAGCA 59.026 50.000 2.78 0.00 0.00 4.26
246 247 1.337823 ACAAGTGACCACATACGGAGC 60.338 52.381 2.78 0.00 0.00 4.70
247 248 2.736721 CAACAAGTGACCACATACGGAG 59.263 50.000 2.78 0.00 0.00 4.63
248 249 2.549134 CCAACAAGTGACCACATACGGA 60.549 50.000 2.78 0.00 0.00 4.69
249 250 1.804151 CCAACAAGTGACCACATACGG 59.196 52.381 2.78 0.00 0.00 4.02
250 251 2.761559 TCCAACAAGTGACCACATACG 58.238 47.619 2.78 0.00 0.00 3.06
251 252 5.003804 AGATTCCAACAAGTGACCACATAC 58.996 41.667 2.78 0.00 0.00 2.39
252 253 5.013079 AGAGATTCCAACAAGTGACCACATA 59.987 40.000 2.78 0.00 0.00 2.29
253 254 4.074970 GAGATTCCAACAAGTGACCACAT 58.925 43.478 2.78 0.00 0.00 3.21
254 255 3.136443 AGAGATTCCAACAAGTGACCACA 59.864 43.478 2.78 0.00 0.00 4.17
255 256 3.744660 AGAGATTCCAACAAGTGACCAC 58.255 45.455 0.00 0.00 0.00 4.16
256 257 5.560722 TTAGAGATTCCAACAAGTGACCA 57.439 39.130 0.00 0.00 0.00 4.02
257 258 6.877611 TTTTAGAGATTCCAACAAGTGACC 57.122 37.500 0.00 0.00 0.00 4.02
258 259 8.070769 GTCTTTTTAGAGATTCCAACAAGTGAC 58.929 37.037 0.00 0.00 0.00 3.67
259 260 7.993183 AGTCTTTTTAGAGATTCCAACAAGTGA 59.007 33.333 0.00 0.00 0.00 3.41
260 261 8.159344 AGTCTTTTTAGAGATTCCAACAAGTG 57.841 34.615 0.00 0.00 0.00 3.16
261 262 8.753497 AAGTCTTTTTAGAGATTCCAACAAGT 57.247 30.769 0.00 0.00 0.00 3.16
274 275 9.169592 CCGTTCCCAAATATAAGTCTTTTTAGA 57.830 33.333 0.00 0.00 0.00 2.10
275 276 9.169592 TCCGTTCCCAAATATAAGTCTTTTTAG 57.830 33.333 0.00 0.00 0.00 1.85
276 277 9.169592 CTCCGTTCCCAAATATAAGTCTTTTTA 57.830 33.333 0.00 0.00 0.00 1.52
277 278 7.122204 CCTCCGTTCCCAAATATAAGTCTTTTT 59.878 37.037 0.00 0.00 0.00 1.94
278 279 6.602009 CCTCCGTTCCCAAATATAAGTCTTTT 59.398 38.462 0.00 0.00 0.00 2.27
279 280 6.120220 CCTCCGTTCCCAAATATAAGTCTTT 58.880 40.000 0.00 0.00 0.00 2.52
280 281 5.397559 CCCTCCGTTCCCAAATATAAGTCTT 60.398 44.000 0.00 0.00 0.00 3.01
281 282 4.102681 CCCTCCGTTCCCAAATATAAGTCT 59.897 45.833 0.00 0.00 0.00 3.24
282 283 4.102054 TCCCTCCGTTCCCAAATATAAGTC 59.898 45.833 0.00 0.00 0.00 3.01
283 284 4.042174 TCCCTCCGTTCCCAAATATAAGT 58.958 43.478 0.00 0.00 0.00 2.24
284 285 4.102681 ACTCCCTCCGTTCCCAAATATAAG 59.897 45.833 0.00 0.00 0.00 1.73
285 286 4.042174 ACTCCCTCCGTTCCCAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
286 287 3.660959 ACTCCCTCCGTTCCCAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
287 288 2.488836 ACTCCCTCCGTTCCCAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
288 289 1.961133 ACTCCCTCCGTTCCCAAATA 58.039 50.000 0.00 0.00 0.00 1.40
289 290 1.838077 CTACTCCCTCCGTTCCCAAAT 59.162 52.381 0.00 0.00 0.00 2.32
290 291 1.272807 CTACTCCCTCCGTTCCCAAA 58.727 55.000 0.00 0.00 0.00 3.28
291 292 0.616679 CCTACTCCCTCCGTTCCCAA 60.617 60.000 0.00 0.00 0.00 4.12
292 293 1.001248 CCTACTCCCTCCGTTCCCA 59.999 63.158 0.00 0.00 0.00 4.37
293 294 0.259938 TACCTACTCCCTCCGTTCCC 59.740 60.000 0.00 0.00 0.00 3.97
294 295 1.397672 GTACCTACTCCCTCCGTTCC 58.602 60.000 0.00 0.00 0.00 3.62
295 296 1.341383 TGGTACCTACTCCCTCCGTTC 60.341 57.143 14.36 0.00 0.00 3.95
296 297 0.706433 TGGTACCTACTCCCTCCGTT 59.294 55.000 14.36 0.00 0.00 4.44
297 298 0.706433 TTGGTACCTACTCCCTCCGT 59.294 55.000 14.36 0.00 0.00 4.69
298 299 1.400737 CTTGGTACCTACTCCCTCCG 58.599 60.000 14.36 0.00 0.00 4.63
299 300 1.008084 ACCTTGGTACCTACTCCCTCC 59.992 57.143 14.36 0.00 0.00 4.30
300 301 2.292061 TGACCTTGGTACCTACTCCCTC 60.292 54.545 14.36 0.00 0.00 4.30
301 302 1.720533 TGACCTTGGTACCTACTCCCT 59.279 52.381 14.36 0.00 0.00 4.20
302 303 1.829849 GTGACCTTGGTACCTACTCCC 59.170 57.143 14.36 0.00 0.00 4.30
303 304 1.829849 GGTGACCTTGGTACCTACTCC 59.170 57.143 14.36 6.59 0.00 3.85
304 305 2.532843 TGGTGACCTTGGTACCTACTC 58.467 52.381 14.36 3.19 35.51 2.59
305 306 2.636403 GTTGGTGACCTTGGTACCTACT 59.364 50.000 14.36 0.00 37.29 2.57
306 307 2.369532 TGTTGGTGACCTTGGTACCTAC 59.630 50.000 14.36 17.01 39.56 3.18
307 308 2.692024 TGTTGGTGACCTTGGTACCTA 58.308 47.619 14.36 4.36 35.51 3.08
308 309 1.513858 TGTTGGTGACCTTGGTACCT 58.486 50.000 14.36 0.00 35.51 3.08
309 310 2.039879 AGATGTTGGTGACCTTGGTACC 59.960 50.000 4.43 4.43 35.05 3.34
310 311 3.074412 CAGATGTTGGTGACCTTGGTAC 58.926 50.000 2.11 0.00 0.00 3.34
316 317 0.250901 GGCACAGATGTTGGTGACCT 60.251 55.000 2.11 0.00 37.05 3.85
325 326 2.353958 CAGCAGGGGCACAGATGT 59.646 61.111 0.00 0.00 44.61 3.06
344 345 2.533266 TAGAGGAAGCCATGCGAATC 57.467 50.000 0.00 0.00 0.00 2.52
356 357 3.168773 GGCAACGGCAATAGAGGAA 57.831 52.632 0.00 0.00 43.71 3.36
369 370 0.669625 AGTACTTTCCGAGCGGCAAC 60.670 55.000 1.45 0.00 34.68 4.17
370 371 0.389426 GAGTACTTTCCGAGCGGCAA 60.389 55.000 1.45 0.00 34.68 4.52
404 703 4.429212 TATCAGGCGCGCGTGTGT 62.429 61.111 41.50 33.62 33.97 3.72
409 708 1.560004 ATTCATGTATCAGGCGCGCG 61.560 55.000 28.44 28.44 0.00 6.86
410 709 1.126846 GTATTCATGTATCAGGCGCGC 59.873 52.381 25.94 25.94 0.00 6.86
411 710 1.726791 GGTATTCATGTATCAGGCGCG 59.273 52.381 0.00 0.00 0.00 6.86
412 711 3.045601 AGGTATTCATGTATCAGGCGC 57.954 47.619 0.00 0.00 0.00 6.53
413 712 4.816385 ACAAAGGTATTCATGTATCAGGCG 59.184 41.667 0.00 0.00 0.00 5.52
451 750 2.575735 TCTATGATGGTTGGCCTGAACA 59.424 45.455 3.32 1.26 35.27 3.18
456 755 4.736611 ATGAATCTATGATGGTTGGCCT 57.263 40.909 3.32 0.00 35.27 5.19
458 757 7.148340 GCTAACTATGAATCTATGATGGTTGGC 60.148 40.741 0.00 0.00 33.31 4.52
466 765 9.109393 GTTTGTTGGCTAACTATGAATCTATGA 57.891 33.333 14.47 0.00 37.68 2.15
467 766 8.892723 TGTTTGTTGGCTAACTATGAATCTATG 58.107 33.333 14.47 0.00 37.68 2.23
468 767 8.893727 GTGTTTGTTGGCTAACTATGAATCTAT 58.106 33.333 14.47 0.00 37.68 1.98
469 768 7.335924 GGTGTTTGTTGGCTAACTATGAATCTA 59.664 37.037 14.47 0.00 37.68 1.98
470 769 6.151144 GGTGTTTGTTGGCTAACTATGAATCT 59.849 38.462 14.47 0.00 37.68 2.40
471 770 6.322491 GGTGTTTGTTGGCTAACTATGAATC 58.678 40.000 14.47 0.53 37.68 2.52
472 771 5.106317 CGGTGTTTGTTGGCTAACTATGAAT 60.106 40.000 14.47 0.00 37.68 2.57
473 772 4.214545 CGGTGTTTGTTGGCTAACTATGAA 59.785 41.667 14.47 0.00 37.68 2.57
497 796 0.170339 GTGGTTATTCCGCAACTGCC 59.830 55.000 0.00 0.00 45.32 4.85
503 802 1.078988 GGTCCGTGGTTATTCCGCA 60.079 57.895 0.00 0.00 46.24 5.69
539 838 1.999648 AAATTGCTTGGCTGACTGGA 58.000 45.000 0.00 0.00 0.00 3.86
642 941 6.881065 TGGAGAGAATTCTTTGTGTATTCCTG 59.119 38.462 9.87 0.00 34.33 3.86
643 942 7.020827 TGGAGAGAATTCTTTGTGTATTCCT 57.979 36.000 9.87 0.00 34.33 3.36
794 1100 4.628766 GCAGGCCTCTTTGATTGAAAATTC 59.371 41.667 0.00 0.00 0.00 2.17
795 1101 4.285260 AGCAGGCCTCTTTGATTGAAAATT 59.715 37.500 0.00 0.00 0.00 1.82
796 1102 3.836562 AGCAGGCCTCTTTGATTGAAAAT 59.163 39.130 0.00 0.00 0.00 1.82
801 1448 2.424956 GGTAAGCAGGCCTCTTTGATTG 59.575 50.000 18.63 1.80 0.00 2.67
819 1466 0.040942 TGGGCCGTTAGTGGTAGGTA 59.959 55.000 0.00 0.00 0.00 3.08
820 1467 0.619543 ATGGGCCGTTAGTGGTAGGT 60.620 55.000 0.00 0.00 0.00 3.08
821 1468 0.106149 GATGGGCCGTTAGTGGTAGG 59.894 60.000 0.00 0.00 0.00 3.18
822 1469 1.120530 AGATGGGCCGTTAGTGGTAG 58.879 55.000 0.00 0.00 0.00 3.18
860 1508 0.392998 CTGGGCTGCGGTAACAATCT 60.393 55.000 0.00 0.00 0.00 2.40
865 1522 0.605589 AGTTTCTGGGCTGCGGTAAC 60.606 55.000 0.00 0.00 0.00 2.50
884 1541 1.816224 GCTGGCCATTTTAACCTTCGA 59.184 47.619 5.51 0.00 0.00 3.71
963 1638 4.777854 ATTTGGCGGGGAAGGGGC 62.778 66.667 0.00 0.00 0.00 5.80
1290 1966 4.493747 GCCGTCTCTTCCCCGTCG 62.494 72.222 0.00 0.00 0.00 5.12
1323 1999 0.760945 AGTAGATCCGGAAGCTGGGG 60.761 60.000 9.01 0.00 0.00 4.96
1358 2034 2.651361 CCACCAGAGCGTCGACTT 59.349 61.111 14.70 1.06 0.00 3.01
1359 2035 4.057428 GCCACCAGAGCGTCGACT 62.057 66.667 14.70 0.00 0.00 4.18
1385 2061 2.377310 CCGTCCGCGTTTTCATCGT 61.377 57.895 4.92 0.00 36.15 3.73
1459 2165 1.869767 CAAGCAACAGTGACAGGAGAC 59.130 52.381 0.00 0.00 0.00 3.36
1501 2207 4.704007 GCAATGCGCCTGAATGAG 57.296 55.556 4.18 0.00 32.94 2.90
1536 2242 2.499693 TCGTGTCTGCAAGGAATATGGA 59.500 45.455 0.00 0.00 0.00 3.41
1539 2376 3.449018 AGAGTCGTGTCTGCAAGGAATAT 59.551 43.478 0.00 0.00 0.00 1.28
1542 2379 1.040646 AGAGTCGTGTCTGCAAGGAA 58.959 50.000 0.00 0.00 0.00 3.36
1570 2407 3.599343 CATTGTGGAGGATCGTTCTTCA 58.401 45.455 7.77 0.00 34.37 3.02
1702 2539 2.190488 CTCTGACCTTCAGCCACCCC 62.190 65.000 0.00 0.00 43.95 4.95
1745 2582 2.232696 TGTGACAGGCGATAAAGCTGTA 59.767 45.455 0.00 0.00 37.29 2.74
1758 2595 3.817084 TGAATTTCTCTTGCTGTGACAGG 59.183 43.478 15.24 0.00 31.21 4.00
1776 2613 2.328319 GATGAGGAGGAGGAGCTGAAT 58.672 52.381 0.00 0.00 0.00 2.57
1807 2647 2.281970 GGACGGCGGGGAGTTTTT 60.282 61.111 13.24 0.00 0.00 1.94
1908 2748 6.567050 ACTGAATCATCCACATTTTACATGC 58.433 36.000 0.00 0.00 0.00 4.06
2039 2879 3.904136 AATGAACAAAAGGAGCACTCG 57.096 42.857 0.00 0.00 0.00 4.18
2107 2947 3.451141 TGCATGAACAGTTTCCAAACC 57.549 42.857 0.00 0.00 39.71 3.27
2147 2988 7.226325 CCCTCTAGCATTCAAGAACAGATAAAG 59.774 40.741 0.00 0.00 0.00 1.85
2222 3064 5.660864 AGAGGAAAAGGTGAAAAATGGACAA 59.339 36.000 0.00 0.00 0.00 3.18
2227 3069 8.498358 GCAAATTAGAGGAAAAGGTGAAAAATG 58.502 33.333 0.00 0.00 0.00 2.32
2228 3070 8.210265 TGCAAATTAGAGGAAAAGGTGAAAAAT 58.790 29.630 0.00 0.00 0.00 1.82
2229 3071 7.560368 TGCAAATTAGAGGAAAAGGTGAAAAA 58.440 30.769 0.00 0.00 0.00 1.94
2231 3073 6.723298 TGCAAATTAGAGGAAAAGGTGAAA 57.277 33.333 0.00 0.00 0.00 2.69
2261 3103 5.560953 GCAAATTGTGTAGGTGACTTCTCAC 60.561 44.000 0.00 0.00 45.54 3.51
2262 3104 4.515191 GCAAATTGTGTAGGTGACTTCTCA 59.485 41.667 0.00 0.00 43.67 3.27
2263 3105 4.515191 TGCAAATTGTGTAGGTGACTTCTC 59.485 41.667 0.00 0.00 43.67 2.87
2264 3106 4.460263 TGCAAATTGTGTAGGTGACTTCT 58.540 39.130 0.00 0.00 43.67 2.85
2265 3107 4.829064 TGCAAATTGTGTAGGTGACTTC 57.171 40.909 0.00 0.00 43.67 3.01
2266 3108 8.623903 CATATATGCAAATTGTGTAGGTGACTT 58.376 33.333 0.00 0.00 43.67 3.01
2268 3110 7.362662 CCATATATGCAAATTGTGTAGGTGAC 58.637 38.462 7.24 0.00 0.00 3.67
2269 3111 6.016360 GCCATATATGCAAATTGTGTAGGTGA 60.016 38.462 7.24 0.00 0.00 4.02
2270 3112 6.151691 GCCATATATGCAAATTGTGTAGGTG 58.848 40.000 7.24 0.00 0.00 4.00
2271 3113 5.243730 GGCCATATATGCAAATTGTGTAGGT 59.756 40.000 7.24 0.00 0.00 3.08
2272 3114 5.477984 AGGCCATATATGCAAATTGTGTAGG 59.522 40.000 5.01 0.00 0.00 3.18
2273 3115 6.207221 TCAGGCCATATATGCAAATTGTGTAG 59.793 38.462 5.01 0.00 0.00 2.74
2274 3116 6.067350 TCAGGCCATATATGCAAATTGTGTA 58.933 36.000 5.01 0.00 0.00 2.90
2275 3117 4.894705 TCAGGCCATATATGCAAATTGTGT 59.105 37.500 5.01 0.00 0.00 3.72
2276 3118 5.456548 TCAGGCCATATATGCAAATTGTG 57.543 39.130 5.01 0.00 0.00 3.33
2277 3119 6.295462 GGATTCAGGCCATATATGCAAATTGT 60.295 38.462 5.01 0.00 0.00 2.71
2278 3120 6.103997 GGATTCAGGCCATATATGCAAATTG 58.896 40.000 5.01 1.79 0.00 2.32
2279 3121 5.105635 CGGATTCAGGCCATATATGCAAATT 60.106 40.000 5.01 0.00 0.00 1.82
2280 3122 4.400251 CGGATTCAGGCCATATATGCAAAT 59.600 41.667 5.01 2.42 0.00 2.32
2281 3123 3.758023 CGGATTCAGGCCATATATGCAAA 59.242 43.478 5.01 0.00 0.00 3.68
2282 3124 3.244875 ACGGATTCAGGCCATATATGCAA 60.245 43.478 5.01 0.00 0.00 4.08
2283 3125 2.305635 ACGGATTCAGGCCATATATGCA 59.694 45.455 5.01 0.00 0.00 3.96
2284 3126 2.991250 ACGGATTCAGGCCATATATGC 58.009 47.619 5.01 3.21 0.00 3.14
2285 3127 5.003160 TGAAACGGATTCAGGCCATATATG 58.997 41.667 5.01 5.68 43.08 1.78
2286 3128 5.241403 TGAAACGGATTCAGGCCATATAT 57.759 39.130 5.01 0.00 43.08 0.86
2287 3129 4.698201 TGAAACGGATTCAGGCCATATA 57.302 40.909 5.01 0.00 43.08 0.86
2288 3130 3.576078 TGAAACGGATTCAGGCCATAT 57.424 42.857 5.01 0.00 43.08 1.78
2290 3132 3.976704 TGAAACGGATTCAGGCCAT 57.023 47.368 5.01 0.00 43.08 4.40
2305 3147 7.619965 TGTACATATGAGATTTCACCAGTGAA 58.380 34.615 10.38 9.12 46.72 3.18
2392 3234 8.847196 AGTAGCTGTTCATCTTAATACACGATA 58.153 33.333 0.00 0.00 0.00 2.92
2506 3375 3.899980 AGCTCAGAGCCAAAGGAAAAATT 59.100 39.130 19.40 0.00 43.77 1.82
2508 3377 2.624838 CAGCTCAGAGCCAAAGGAAAAA 59.375 45.455 19.40 0.00 43.77 1.94
2575 3444 1.898574 CATAGGTGCATTCCGGCCC 60.899 63.158 0.00 0.00 0.00 5.80
2662 3531 9.314321 CTACTATTTGGTCACGTGAAATCTTAT 57.686 33.333 21.95 11.38 0.00 1.73
2707 3576 3.260632 TCTTCTCATCATCGGTTGTGGAA 59.739 43.478 0.00 0.00 0.00 3.53
2934 3803 7.493320 TCACGTTTAATTGTACTTCTTGTGTCT 59.507 33.333 0.00 0.00 0.00 3.41
2967 3836 6.726490 ACTGTATGATACCGAAATACCACT 57.274 37.500 0.00 0.00 0.00 4.00
2968 3837 6.982141 TGAACTGTATGATACCGAAATACCAC 59.018 38.462 0.00 0.00 0.00 4.16
2969 3838 6.982141 GTGAACTGTATGATACCGAAATACCA 59.018 38.462 0.00 0.00 0.00 3.25
2972 3841 9.607988 AAATGTGAACTGTATGATACCGAAATA 57.392 29.630 0.00 0.00 0.00 1.40
2975 3844 7.064134 GTGAAATGTGAACTGTATGATACCGAA 59.936 37.037 0.00 0.00 0.00 4.30
2976 3845 6.533723 GTGAAATGTGAACTGTATGATACCGA 59.466 38.462 0.00 0.00 0.00 4.69
2977 3846 6.312672 TGTGAAATGTGAACTGTATGATACCG 59.687 38.462 0.00 0.00 0.00 4.02
2982 3851 6.765512 TCAACTGTGAAATGTGAACTGTATGA 59.234 34.615 0.00 0.00 0.00 2.15
2984 3853 6.992123 TCTCAACTGTGAAATGTGAACTGTAT 59.008 34.615 0.00 0.00 31.88 2.29
2986 3855 5.065218 GTCTCAACTGTGAAATGTGAACTGT 59.935 40.000 0.00 0.00 31.88 3.55
2989 3858 5.484173 TGTCTCAACTGTGAAATGTGAAC 57.516 39.130 0.00 0.00 31.88 3.18
2990 3859 6.507958 TTTGTCTCAACTGTGAAATGTGAA 57.492 33.333 0.00 0.00 31.88 3.18
2992 3861 7.703621 AGAATTTTGTCTCAACTGTGAAATGTG 59.296 33.333 0.00 0.00 31.88 3.21
2994 3863 8.537223 CAAGAATTTTGTCTCAACTGTGAAATG 58.463 33.333 0.00 0.00 31.88 2.32
2995 3864 7.223387 GCAAGAATTTTGTCTCAACTGTGAAAT 59.777 33.333 0.00 0.00 31.88 2.17
2996 3865 6.531240 GCAAGAATTTTGTCTCAACTGTGAAA 59.469 34.615 0.00 0.00 31.88 2.69
2997 3866 6.035843 GCAAGAATTTTGTCTCAACTGTGAA 58.964 36.000 0.00 0.00 31.88 3.18
2998 3867 5.125257 TGCAAGAATTTTGTCTCAACTGTGA 59.875 36.000 0.00 0.00 0.00 3.58
2999 3868 5.342433 TGCAAGAATTTTGTCTCAACTGTG 58.658 37.500 0.00 0.00 0.00 3.66
3097 3966 3.691118 CCATCTCACAAAATCATGGTCGT 59.309 43.478 0.00 0.00 31.01 4.34
3130 3999 3.550233 GCTCAGTAGAACGTCAGACAACA 60.550 47.826 0.41 0.00 0.00 3.33
3131 4000 2.981140 GCTCAGTAGAACGTCAGACAAC 59.019 50.000 0.41 0.00 0.00 3.32
3139 4008 1.736032 GCGAATGGCTCAGTAGAACGT 60.736 52.381 0.00 0.00 39.11 3.99
3151 4020 1.478105 AGAAAATTGAGGGCGAATGGC 59.522 47.619 0.00 0.00 42.51 4.40
3188 4057 3.565482 GTCACAAGAAGCTTCAACATCCA 59.435 43.478 27.57 3.09 0.00 3.41


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

AutoCloner maintained by Alex Coulton.