Multiple sequence alignment - TraesCS3B01G467900

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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 TraesCS3B01G467900 chr3B 100.000 3827 0 0 1 3827 711642833 711639007 0.000000e+00 7068.0
1 TraesCS3B01G467900 chr3B 87.826 1651 114 45 815 2457 711885118 711883547 0.000000e+00 1855.0
2 TraesCS3B01G467900 chr3B 78.747 367 30 22 350 682 712187657 712187305 6.480000e-48 202.0
3 TraesCS3B01G467900 chr3B 83.158 190 5 7 354 525 711946262 711946082 8.570000e-32 148.0
4 TraesCS3B01G467900 chr3B 92.857 56 4 0 727 782 712186051 712185996 8.810000e-12 82.4
5 TraesCS3B01G467900 chr3D 90.848 3562 164 69 348 3827 537559070 537555589 0.000000e+00 4623.0
6 TraesCS3B01G467900 chr3D 91.346 104 3 2 345 448 537680831 537680734 1.850000e-28 137.0
7 TraesCS3B01G467900 chr3A 87.927 2725 186 66 350 3029 672870757 672868131 0.000000e+00 3077.0
8 TraesCS3B01G467900 chr3A 89.113 496 34 13 3337 3826 672865677 672865196 1.970000e-167 599.0
9 TraesCS3B01G467900 chr3A 85.841 339 12 15 3026 3345 672867972 672867651 1.030000e-85 327.0
10 TraesCS3B01G467900 chr3A 91.919 99 2 2 350 448 673192416 673192324 2.400000e-27 134.0
11 TraesCS3B01G467900 chr5B 94.767 344 18 0 1 344 571108391 571108048 1.560000e-148 536.0
12 TraesCS3B01G467900 chr5B 94.444 342 19 0 1 342 427216023 427215682 9.420000e-146 527.0
13 TraesCS3B01G467900 chr5B 94.186 344 20 0 1 344 341523507 341523164 3.390000e-145 525.0
14 TraesCS3B01G467900 chr5B 94.186 344 18 2 1 344 59719238 59719579 1.220000e-144 523.0
15 TraesCS3B01G467900 chr5B 93.714 350 21 1 1 350 634073437 634073089 1.220000e-144 523.0
16 TraesCS3B01G467900 chr2B 94.540 348 18 1 1 348 763844626 763844280 1.560000e-148 536.0
17 TraesCS3B01G467900 chr2B 94.444 342 19 0 3 344 736107483 736107142 9.420000e-146 527.0
18 TraesCS3B01G467900 chr2B 94.152 342 20 0 1 342 723437689 723438030 4.380000e-144 521.0
19 TraesCS3B01G467900 chr2B 83.062 307 42 8 1756 2057 420203435 420203736 1.750000e-68 270.0
20 TraesCS3B01G467900 chr4A 94.203 345 20 0 1 345 721376380 721376036 9.420000e-146 527.0


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 TraesCS3B01G467900 chr3B 711639007 711642833 3826 True 7068.000000 7068 100.000 1 3827 1 chr3B.!!$R1 3826
1 TraesCS3B01G467900 chr3B 711883547 711885118 1571 True 1855.000000 1855 87.826 815 2457 1 chr3B.!!$R2 1642
2 TraesCS3B01G467900 chr3D 537555589 537559070 3481 True 4623.000000 4623 90.848 348 3827 1 chr3D.!!$R1 3479
3 TraesCS3B01G467900 chr3A 672865196 672870757 5561 True 1334.333333 3077 87.627 350 3826 3 chr3A.!!$R2 3476

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
325 326 0.027586 GCGGCACTAGTTTAATGCGG 59.972 55.0 0.0 0.0 40.37 5.69 F
338 339 0.390209 AATGCGGCTGTTGGAAATGC 60.390 50.0 0.0 0.0 0.00 3.56 F
1732 1806 0.460987 CGGAGTGTCAGGGATCAAGC 60.461 60.0 0.0 0.0 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2155 2229 0.107606 CGAAGTCGGAGAGGAGAGGA 60.108 60.000 0.00 0.0 36.95 3.71 R
2254 2331 1.741770 GTCGGTCTTCTTGGCGCAT 60.742 57.895 10.83 0.0 0.00 4.73 R
2886 2983 0.249489 AAGCGACAGAAGCAACGTCT 60.249 50.000 0.00 0.0 37.01 4.18 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
17 18 2.910994 CCGGCGGTACTAGGAGGG 60.911 72.222 19.97 0.00 0.00 4.30
18 19 2.910994 CGGCGGTACTAGGAGGGG 60.911 72.222 0.00 0.00 0.00 4.79
19 20 2.605299 GGCGGTACTAGGAGGGGA 59.395 66.667 0.00 0.00 0.00 4.81
20 21 1.155624 GGCGGTACTAGGAGGGGAT 59.844 63.158 0.00 0.00 0.00 3.85
21 22 1.186267 GGCGGTACTAGGAGGGGATG 61.186 65.000 0.00 0.00 0.00 3.51
22 23 1.186267 GCGGTACTAGGAGGGGATGG 61.186 65.000 0.00 0.00 0.00 3.51
23 24 0.542232 CGGTACTAGGAGGGGATGGG 60.542 65.000 0.00 0.00 0.00 4.00
24 25 0.836830 GGTACTAGGAGGGGATGGGC 60.837 65.000 0.00 0.00 0.00 5.36
25 26 1.155390 TACTAGGAGGGGATGGGCG 59.845 63.158 0.00 0.00 0.00 6.13
26 27 2.382023 TACTAGGAGGGGATGGGCGG 62.382 65.000 0.00 0.00 0.00 6.13
27 28 3.444417 TAGGAGGGGATGGGCGGA 61.444 66.667 0.00 0.00 0.00 5.54
28 29 2.965226 CTAGGAGGGGATGGGCGGAA 62.965 65.000 0.00 0.00 0.00 4.30
29 30 2.965226 TAGGAGGGGATGGGCGGAAG 62.965 65.000 0.00 0.00 0.00 3.46
58 59 3.249961 GGGGATAGGCCGGGGAAG 61.250 72.222 2.18 0.00 37.63 3.46
59 60 3.955044 GGGATAGGCCGGGGAAGC 61.955 72.222 2.18 0.00 37.63 3.86
70 71 4.410400 GGGAAGCCTGGGACGGTG 62.410 72.222 0.00 0.00 0.00 4.94
71 72 4.410400 GGAAGCCTGGGACGGTGG 62.410 72.222 0.00 0.00 0.00 4.61
127 128 4.821589 GGGGTGGAAGCGCGAGAG 62.822 72.222 12.10 0.00 37.58 3.20
128 129 4.821589 GGGTGGAAGCGCGAGAGG 62.822 72.222 12.10 0.00 33.03 3.69
129 130 3.760035 GGTGGAAGCGCGAGAGGA 61.760 66.667 12.10 0.00 0.00 3.71
130 131 2.261671 GTGGAAGCGCGAGAGGAA 59.738 61.111 12.10 0.00 0.00 3.36
131 132 1.807573 GTGGAAGCGCGAGAGGAAG 60.808 63.158 12.10 0.00 0.00 3.46
132 133 1.977009 TGGAAGCGCGAGAGGAAGA 60.977 57.895 12.10 0.00 0.00 2.87
133 134 1.226831 GGAAGCGCGAGAGGAAGAG 60.227 63.158 12.10 0.00 0.00 2.85
134 135 1.876263 GAAGCGCGAGAGGAAGAGC 60.876 63.158 12.10 0.00 0.00 4.09
138 139 4.882396 GCGAGAGGAAGAGCGGGC 62.882 72.222 0.00 0.00 0.00 6.13
139 140 4.560856 CGAGAGGAAGAGCGGGCG 62.561 72.222 0.00 0.00 0.00 6.13
140 141 4.882396 GAGAGGAAGAGCGGGCGC 62.882 72.222 0.00 0.00 42.33 6.53
167 168 3.626680 GAGTGTGCCGCTCGCTGTA 62.627 63.158 12.97 0.00 38.78 2.74
168 169 3.181967 GTGTGCCGCTCGCTGTAG 61.182 66.667 0.00 0.00 38.78 2.74
169 170 3.680786 TGTGCCGCTCGCTGTAGT 61.681 61.111 0.00 0.00 38.78 2.73
170 171 3.181967 GTGCCGCTCGCTGTAGTG 61.182 66.667 0.00 0.00 38.78 2.74
179 180 4.065281 GCTGTAGTGGGCGTCCGT 62.065 66.667 0.00 0.00 35.24 4.69
180 181 2.703798 GCTGTAGTGGGCGTCCGTA 61.704 63.158 0.00 0.00 35.24 4.02
181 182 1.885157 CTGTAGTGGGCGTCCGTAA 59.115 57.895 0.00 0.00 35.24 3.18
182 183 0.458669 CTGTAGTGGGCGTCCGTAAT 59.541 55.000 0.00 0.00 35.24 1.89
183 184 1.677576 CTGTAGTGGGCGTCCGTAATA 59.322 52.381 0.00 0.00 35.24 0.98
184 185 1.405105 TGTAGTGGGCGTCCGTAATAC 59.595 52.381 0.00 0.00 35.24 1.89
185 186 0.662619 TAGTGGGCGTCCGTAATACG 59.337 55.000 5.74 5.74 43.12 3.06
190 191 3.592369 CGTCCGTAATACGCCACG 58.408 61.111 16.86 16.86 40.91 4.94
191 192 2.570678 CGTCCGTAATACGCCACGC 61.571 63.158 17.88 2.74 40.91 5.34
202 203 2.667199 GCCACGCGGGTAAGTGTT 60.667 61.111 12.47 0.00 39.65 3.32
203 204 2.255881 GCCACGCGGGTAAGTGTTT 61.256 57.895 12.47 0.00 39.65 2.83
204 205 1.788067 GCCACGCGGGTAAGTGTTTT 61.788 55.000 12.47 0.00 39.65 2.43
205 206 0.664224 CCACGCGGGTAAGTGTTTTT 59.336 50.000 12.47 0.00 36.69 1.94
206 207 1.334329 CCACGCGGGTAAGTGTTTTTC 60.334 52.381 12.47 0.00 36.69 2.29
207 208 1.331138 CACGCGGGTAAGTGTTTTTCA 59.669 47.619 12.47 0.00 33.97 2.69
208 209 1.331447 ACGCGGGTAAGTGTTTTTCAC 59.669 47.619 12.47 0.00 46.46 3.18
215 216 2.023601 GTGTTTTTCACCGCGCGT 59.976 55.556 29.95 14.24 40.84 6.01
216 217 2.001880 GTGTTTTTCACCGCGCGTC 61.002 57.895 29.95 8.54 40.84 5.19
217 218 2.426261 GTTTTTCACCGCGCGTCC 60.426 61.111 29.95 2.83 0.00 4.79
218 219 2.895865 TTTTTCACCGCGCGTCCA 60.896 55.556 29.95 8.53 0.00 4.02
219 220 2.470362 TTTTTCACCGCGCGTCCAA 61.470 52.632 29.95 14.58 0.00 3.53
220 221 2.649843 TTTTTCACCGCGCGTCCAAC 62.650 55.000 29.95 0.00 0.00 3.77
227 228 3.956317 GCGCGTCCAACCCGTTTT 61.956 61.111 8.43 0.00 0.00 2.43
228 229 2.606030 GCGCGTCCAACCCGTTTTA 61.606 57.895 8.43 0.00 0.00 1.52
229 230 1.494189 CGCGTCCAACCCGTTTTAG 59.506 57.895 0.00 0.00 0.00 1.85
230 231 1.208358 GCGTCCAACCCGTTTTAGC 59.792 57.895 0.00 0.00 0.00 3.09
231 232 1.494189 CGTCCAACCCGTTTTAGCG 59.506 57.895 0.00 0.00 0.00 4.26
232 233 1.208358 GTCCAACCCGTTTTAGCGC 59.792 57.895 0.00 0.00 0.00 5.92
233 234 2.174835 CCAACCCGTTTTAGCGCG 59.825 61.111 0.00 0.00 0.00 6.86
234 235 2.501008 CAACCCGTTTTAGCGCGC 60.501 61.111 26.66 26.66 0.00 6.86
235 236 4.079748 AACCCGTTTTAGCGCGCG 62.080 61.111 28.44 28.44 0.00 6.86
254 255 4.940593 GCTGTTTTTGCGCGCCCA 62.941 61.111 30.77 13.07 0.00 5.36
255 256 3.029735 CTGTTTTTGCGCGCCCAC 61.030 61.111 30.77 19.25 0.00 4.61
256 257 3.483235 CTGTTTTTGCGCGCCCACT 62.483 57.895 30.77 0.00 0.00 4.00
257 258 3.029735 GTTTTTGCGCGCCCACTG 61.030 61.111 30.77 0.00 0.00 3.66
258 259 4.277593 TTTTTGCGCGCCCACTGG 62.278 61.111 30.77 0.00 0.00 4.00
269 270 4.767255 CCACTGGAGCGCCCTGAC 62.767 72.222 22.28 3.64 37.33 3.51
288 289 4.711193 CGTTGCGCGCGTGCTAAA 62.711 61.111 40.02 26.85 39.65 1.85
289 290 2.426098 GTTGCGCGCGTGCTAAAA 60.426 55.556 40.02 26.14 39.65 1.52
290 291 2.426098 TTGCGCGCGTGCTAAAAC 60.426 55.556 40.02 15.40 39.65 2.43
291 292 4.711193 TGCGCGCGTGCTAAAACG 62.711 61.111 40.02 19.10 46.30 3.60
292 293 4.418470 GCGCGCGTGCTAAAACGA 62.418 61.111 35.43 0.00 46.49 3.85
293 294 2.567270 CGCGCGTGCTAAAACGAC 60.567 61.111 24.19 0.00 46.49 4.34
294 295 2.202133 GCGCGTGCTAAAACGACC 60.202 61.111 15.02 0.00 46.49 4.79
295 296 2.664436 GCGCGTGCTAAAACGACCT 61.664 57.895 15.02 0.00 46.49 3.85
296 297 1.346378 GCGCGTGCTAAAACGACCTA 61.346 55.000 15.02 0.00 46.49 3.08
297 298 1.274596 CGCGTGCTAAAACGACCTAT 58.725 50.000 0.00 0.00 46.49 2.57
298 299 1.657094 CGCGTGCTAAAACGACCTATT 59.343 47.619 0.00 0.00 46.49 1.73
299 300 2.093152 CGCGTGCTAAAACGACCTATTT 59.907 45.455 0.00 0.00 46.49 1.40
300 301 3.423907 CGCGTGCTAAAACGACCTATTTT 60.424 43.478 0.00 0.00 46.49 1.82
301 302 3.844099 GCGTGCTAAAACGACCTATTTTG 59.156 43.478 0.17 0.00 46.49 2.44
302 303 3.844099 CGTGCTAAAACGACCTATTTTGC 59.156 43.478 0.00 0.00 46.49 3.68
303 304 3.844099 GTGCTAAAACGACCTATTTTGCG 59.156 43.478 0.00 0.00 31.47 4.85
304 305 3.747010 TGCTAAAACGACCTATTTTGCGA 59.253 39.130 0.00 0.00 31.47 5.10
305 306 4.086574 GCTAAAACGACCTATTTTGCGAC 58.913 43.478 0.00 0.00 31.79 5.19
306 307 2.867456 AAACGACCTATTTTGCGACG 57.133 45.000 0.00 0.00 0.00 5.12
307 308 0.441145 AACGACCTATTTTGCGACGC 59.559 50.000 14.19 14.19 0.00 5.19
308 309 1.013755 CGACCTATTTTGCGACGCG 60.014 57.895 16.14 3.53 0.00 6.01
309 310 1.347221 GACCTATTTTGCGACGCGG 59.653 57.895 16.14 11.38 0.00 6.46
310 311 2.022762 CCTATTTTGCGACGCGGC 59.977 61.111 16.14 6.41 0.00 6.53
311 312 2.745785 CCTATTTTGCGACGCGGCA 61.746 57.895 14.85 9.83 42.12 5.69
312 313 1.580132 CTATTTTGCGACGCGGCAC 60.580 57.895 14.85 1.22 43.82 5.01
313 314 1.966493 CTATTTTGCGACGCGGCACT 61.966 55.000 14.85 2.26 43.82 4.40
314 315 0.736672 TATTTTGCGACGCGGCACTA 60.737 50.000 14.85 0.00 43.82 2.74
315 316 1.966493 ATTTTGCGACGCGGCACTAG 61.966 55.000 14.85 0.00 43.82 2.57
316 317 3.851845 TTTGCGACGCGGCACTAGT 62.852 57.895 14.85 0.00 43.82 2.57
317 318 3.851845 TTGCGACGCGGCACTAGTT 62.852 57.895 14.85 0.00 43.82 2.24
318 319 3.110178 GCGACGCGGCACTAGTTT 61.110 61.111 14.85 0.00 0.00 2.66
319 320 1.802715 GCGACGCGGCACTAGTTTA 60.803 57.895 14.85 0.00 0.00 2.01
320 321 1.346378 GCGACGCGGCACTAGTTTAA 61.346 55.000 14.85 0.00 0.00 1.52
321 322 1.274596 CGACGCGGCACTAGTTTAAT 58.725 50.000 14.85 0.00 0.00 1.40
322 323 1.006391 CGACGCGGCACTAGTTTAATG 60.006 52.381 14.85 0.00 0.00 1.90
323 324 0.725117 ACGCGGCACTAGTTTAATGC 59.275 50.000 12.47 0.00 38.68 3.56
324 325 0.315059 CGCGGCACTAGTTTAATGCG 60.315 55.000 0.00 9.40 40.37 4.73
325 326 0.027586 GCGGCACTAGTTTAATGCGG 59.972 55.000 0.00 0.00 40.37 5.69
326 327 0.027586 CGGCACTAGTTTAATGCGGC 59.972 55.000 0.00 0.00 40.37 6.53
327 328 1.379527 GGCACTAGTTTAATGCGGCT 58.620 50.000 0.00 0.00 40.37 5.52
328 329 1.064060 GGCACTAGTTTAATGCGGCTG 59.936 52.381 0.00 0.00 40.37 4.85
329 330 1.737793 GCACTAGTTTAATGCGGCTGT 59.262 47.619 0.00 0.00 0.00 4.40
330 331 2.161609 GCACTAGTTTAATGCGGCTGTT 59.838 45.455 0.00 0.00 0.00 3.16
331 332 3.747193 CACTAGTTTAATGCGGCTGTTG 58.253 45.455 0.00 0.00 0.00 3.33
332 333 2.747446 ACTAGTTTAATGCGGCTGTTGG 59.253 45.455 0.00 0.00 0.00 3.77
333 334 1.904287 AGTTTAATGCGGCTGTTGGA 58.096 45.000 0.00 0.00 0.00 3.53
334 335 2.235016 AGTTTAATGCGGCTGTTGGAA 58.765 42.857 0.00 0.00 0.00 3.53
335 336 2.625790 AGTTTAATGCGGCTGTTGGAAA 59.374 40.909 0.00 0.00 0.00 3.13
336 337 3.258123 AGTTTAATGCGGCTGTTGGAAAT 59.742 39.130 0.00 0.00 0.00 2.17
337 338 2.937469 TAATGCGGCTGTTGGAAATG 57.063 45.000 0.00 0.00 0.00 2.32
338 339 0.390209 AATGCGGCTGTTGGAAATGC 60.390 50.000 0.00 0.00 0.00 3.56
339 340 1.252904 ATGCGGCTGTTGGAAATGCT 61.253 50.000 0.00 0.00 0.00 3.79
340 341 1.153958 GCGGCTGTTGGAAATGCTC 60.154 57.895 0.00 0.00 0.00 4.26
341 342 1.589716 GCGGCTGTTGGAAATGCTCT 61.590 55.000 0.00 0.00 0.00 4.09
342 343 0.883833 CGGCTGTTGGAAATGCTCTT 59.116 50.000 0.00 0.00 0.00 2.85
343 344 2.083774 CGGCTGTTGGAAATGCTCTTA 58.916 47.619 0.00 0.00 0.00 2.10
344 345 2.487762 CGGCTGTTGGAAATGCTCTTAA 59.512 45.455 0.00 0.00 0.00 1.85
345 346 3.426695 CGGCTGTTGGAAATGCTCTTAAG 60.427 47.826 0.00 0.00 0.00 1.85
357 358 1.486726 GCTCTTAAGCCTAAGCCTGGA 59.513 52.381 0.00 0.00 43.10 3.86
486 503 1.247567 GTCCAACACTCCACCCATTG 58.752 55.000 0.00 0.00 0.00 2.82
508 525 1.202794 CCGTACTCTACCCTCCTCCTC 60.203 61.905 0.00 0.00 0.00 3.71
519 539 2.559931 CCCTCCTCCTCCAAGTAGAACA 60.560 54.545 0.00 0.00 0.00 3.18
534 554 1.267806 AGAACACGTACGGTACTGGTG 59.732 52.381 21.06 18.64 0.00 4.17
618 642 1.855213 GCACACGCAATGAAGGAGCA 61.855 55.000 0.00 0.00 38.36 4.26
627 651 4.617959 GCAATGAAGGAGCACTACGTATA 58.382 43.478 0.00 0.00 0.00 1.47
633 657 2.743126 AGGAGCACTACGTATAGCGATC 59.257 50.000 12.05 6.83 44.77 3.69
666 690 3.181511 GGCGTCGTGAATGAATGAATGAA 60.182 43.478 0.00 0.00 0.00 2.57
667 691 4.496341 GGCGTCGTGAATGAATGAATGAAT 60.496 41.667 0.00 0.00 0.00 2.57
668 692 4.435554 GCGTCGTGAATGAATGAATGAATG 59.564 41.667 0.00 0.00 0.00 2.67
669 693 5.727515 GCGTCGTGAATGAATGAATGAATGA 60.728 40.000 0.00 0.00 0.00 2.57
674 698 6.742264 CGTGAATGAATGAATGAATGAACGAA 59.258 34.615 0.00 0.00 0.00 3.85
688 712 4.433186 TGAACGAACAATAATGCCCTTG 57.567 40.909 0.00 0.00 0.00 3.61
710 734 0.742281 TCTCGCAGCAAAGATGGCTC 60.742 55.000 0.00 0.00 40.23 4.70
794 818 4.457496 TACGCCTGCAGCCTGCTC 62.457 66.667 18.96 6.20 45.31 4.26
896 927 4.087892 CCAGGACCCGGCTGACAG 62.088 72.222 8.95 0.00 0.00 3.51
1014 1076 4.200092 GCTATCCCTTTTCCGAAACATCT 58.800 43.478 0.00 0.00 0.00 2.90
1080 1148 2.612251 CTCTCCTCCCTCCCTCCC 59.388 72.222 0.00 0.00 0.00 4.30
1081 1149 2.018086 CTCTCCTCCCTCCCTCCCT 61.018 68.421 0.00 0.00 0.00 4.20
1082 1150 2.015726 TCTCCTCCCTCCCTCCCTC 61.016 68.421 0.00 0.00 0.00 4.30
1083 1151 3.036959 TCCTCCCTCCCTCCCTCC 61.037 72.222 0.00 0.00 0.00 4.30
1207 1277 2.124942 CCGGCCAGAAGAGGAAGC 60.125 66.667 2.24 0.00 0.00 3.86
1209 1279 2.821810 GGCCAGAAGAGGAAGCGC 60.822 66.667 0.00 0.00 0.00 5.92
1687 1761 6.590357 ACAAATCTTGTTGACTTATCGTTCG 58.410 36.000 0.00 0.00 42.22 3.95
1719 1793 3.896133 GCATGCATGGCCGGAGTG 61.896 66.667 27.34 0.28 0.00 3.51
1728 1802 2.501610 GCCGGAGTGTCAGGGATC 59.498 66.667 5.05 0.00 32.07 3.36
1732 1806 0.460987 CGGAGTGTCAGGGATCAAGC 60.461 60.000 0.00 0.00 0.00 4.01
1864 1938 3.664025 CTCGCTGGCCGTCATCCAA 62.664 63.158 0.00 0.00 38.35 3.53
1882 1956 2.406002 AATTCAACGGGAGCGGTGGT 62.406 55.000 0.00 0.00 0.00 4.16
1903 1977 3.745803 AAGTCGGACCGCGACCTC 61.746 66.667 8.23 6.93 37.10 3.85
2069 2143 4.813235 AGCTCTCCCTCGCGCTCT 62.813 66.667 5.56 0.00 0.00 4.09
2158 2232 3.386237 GGCGTCACCAGCTCTCCT 61.386 66.667 0.00 0.00 38.86 3.69
2273 2350 2.357034 GCGCCAAGAAGACCGACA 60.357 61.111 0.00 0.00 0.00 4.35
2404 2481 2.663196 GCCAACTACTGCTCCCGT 59.337 61.111 0.00 0.00 0.00 5.28
2555 2642 1.966451 AACAAGTAGCAGCACCGGC 60.966 57.895 0.00 0.00 41.61 6.13
2734 2828 2.862674 GATTCTACCGCGGCCACCAA 62.863 60.000 28.58 11.67 0.00 3.67
2754 2848 5.656859 ACCAAAACTCTAGCCTTGTTTTCTT 59.343 36.000 10.50 2.59 40.51 2.52
2755 2849 6.831868 ACCAAAACTCTAGCCTTGTTTTCTTA 59.168 34.615 10.50 0.00 40.51 2.10
2762 2856 9.438228 ACTCTAGCCTTGTTTTCTTAATTAGTC 57.562 33.333 0.00 0.00 0.00 2.59
2764 2858 6.835819 AGCCTTGTTTTCTTAATTAGTCCC 57.164 37.500 0.00 0.00 0.00 4.46
2767 2861 8.336987 AGCCTTGTTTTCTTAATTAGTCCCTAT 58.663 33.333 0.00 0.00 0.00 2.57
2848 2945 6.476378 CGTAATATGAAAATCCTGGATCCCT 58.524 40.000 10.14 0.00 0.00 4.20
2852 2949 4.953781 TGAAAATCCTGGATCCCTCTTT 57.046 40.909 10.14 6.33 0.00 2.52
2858 2955 4.074799 TCCTGGATCCCTCTTTGAACTA 57.925 45.455 9.90 0.00 0.00 2.24
2867 2964 8.894731 GGATCCCTCTTTGAACTAATTTTCTAC 58.105 37.037 0.00 0.00 0.00 2.59
2868 2965 9.674068 GATCCCTCTTTGAACTAATTTTCTACT 57.326 33.333 0.00 0.00 0.00 2.57
2886 2983 9.578576 TTTTCTACTAGAGTTCTACCAAGTGTA 57.421 33.333 0.00 0.00 0.00 2.90
2910 3007 0.029300 TTGCTTCTGTCGCTTTGTGC 59.971 50.000 0.00 0.00 38.57 4.57
2980 3077 0.246360 TCCAGCACTCCATGTACGTG 59.754 55.000 8.18 8.18 0.00 4.49
3012 3109 1.374343 CTCCTACGCTACGTGCCTCA 61.374 60.000 0.00 0.00 41.39 3.86
3035 3298 3.426426 CGTAGCTTATCGGATGAGTAGGC 60.426 52.174 10.94 0.00 0.00 3.93
3146 3421 2.113139 CCGCTGGTGTTGGACCTT 59.887 61.111 0.00 0.00 46.32 3.50
3242 3526 3.908103 ACTTTTCTGTTACCTAGGCAGGA 59.092 43.478 9.30 0.00 45.91 3.86
3295 3579 4.036380 ACAAGATGATGACGATGCTACGTA 59.964 41.667 8.49 0.00 46.52 3.57
3296 3580 4.411993 AGATGATGACGATGCTACGTAG 57.588 45.455 18.47 18.47 46.52 3.51
3327 3612 2.527951 CTAGCCAGCCCGCTCTGTTT 62.528 60.000 0.00 0.00 40.39 2.83
3389 5654 2.164422 TGCACACGAGTAGATTCTCAGG 59.836 50.000 0.00 0.00 34.46 3.86
3425 5692 8.696374 AGTTCGATTTCTCTGGTATTCTATTCA 58.304 33.333 0.00 0.00 0.00 2.57
3533 5802 4.863707 ACAGGTGTGTGCTCACTG 57.136 55.556 18.85 11.76 44.14 3.66
3535 5804 1.598962 CAGGTGTGTGCTCACTGGG 60.599 63.158 18.85 3.79 44.14 4.45
3536 5805 2.281761 GGTGTGTGCTCACTGGGG 60.282 66.667 18.85 0.00 44.14 4.96
3537 5806 2.818169 GGTGTGTGCTCACTGGGGA 61.818 63.158 18.85 0.00 44.14 4.81
3539 5808 1.459348 TGTGTGCTCACTGGGGAGA 60.459 57.895 18.85 0.00 44.14 3.71
3540 5809 1.294780 GTGTGCTCACTGGGGAGAG 59.705 63.158 11.58 0.00 40.98 3.20
3542 5811 3.005539 TGCTCACTGGGGAGAGGC 61.006 66.667 3.80 0.00 37.05 4.70
3544 5819 2.373707 GCTCACTGGGGAGAGGCAT 61.374 63.158 3.80 0.00 37.05 4.40
3552 5827 1.963338 GGGAGAGGCATGCATACGC 60.963 63.158 21.36 14.28 39.24 4.42
3559 5834 2.484062 GCATGCATACGCCAAGGCT 61.484 57.895 14.21 0.00 39.32 4.58
3562 5837 3.272334 GCATACGCCAAGGCTCCG 61.272 66.667 9.73 0.00 39.32 4.63
3563 5838 2.588877 CATACGCCAAGGCTCCGG 60.589 66.667 9.73 0.00 39.32 5.14
3806 6083 0.413037 TCCAAACTAGACCGGGGGTA 59.587 55.000 6.32 0.00 35.25 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.910994 CCCTCCTAGTACCGCCGG 60.911 72.222 0.00 0.00 0.00 6.13
1 2 2.710237 ATCCCCTCCTAGTACCGCCG 62.710 65.000 0.00 0.00 0.00 6.46
2 3 1.155624 ATCCCCTCCTAGTACCGCC 59.844 63.158 0.00 0.00 0.00 6.13
3 4 1.186267 CCATCCCCTCCTAGTACCGC 61.186 65.000 0.00 0.00 0.00 5.68
4 5 0.542232 CCCATCCCCTCCTAGTACCG 60.542 65.000 0.00 0.00 0.00 4.02
5 6 0.836830 GCCCATCCCCTCCTAGTACC 60.837 65.000 0.00 0.00 0.00 3.34
6 7 1.186267 CGCCCATCCCCTCCTAGTAC 61.186 65.000 0.00 0.00 0.00 2.73
7 8 1.155390 CGCCCATCCCCTCCTAGTA 59.845 63.158 0.00 0.00 0.00 1.82
8 9 2.122813 CGCCCATCCCCTCCTAGT 60.123 66.667 0.00 0.00 0.00 2.57
9 10 2.925170 CCGCCCATCCCCTCCTAG 60.925 72.222 0.00 0.00 0.00 3.02
10 11 2.965226 CTTCCGCCCATCCCCTCCTA 62.965 65.000 0.00 0.00 0.00 2.94
11 12 4.431524 TTCCGCCCATCCCCTCCT 62.432 66.667 0.00 0.00 0.00 3.69
12 13 3.878667 CTTCCGCCCATCCCCTCC 61.879 72.222 0.00 0.00 0.00 4.30
13 14 4.570874 GCTTCCGCCCATCCCCTC 62.571 72.222 0.00 0.00 0.00 4.30
41 42 3.249961 CTTCCCCGGCCTATCCCC 61.250 72.222 0.00 0.00 0.00 4.81
42 43 3.955044 GCTTCCCCGGCCTATCCC 61.955 72.222 0.00 0.00 0.00 3.85
43 44 3.955044 GGCTTCCCCGGCCTATCC 61.955 72.222 0.00 0.00 45.57 2.59
53 54 4.410400 CACCGTCCCAGGCTTCCC 62.410 72.222 0.00 0.00 33.69 3.97
54 55 4.410400 CCACCGTCCCAGGCTTCC 62.410 72.222 0.00 0.00 33.69 3.46
110 111 4.821589 CTCTCGCGCTTCCACCCC 62.822 72.222 5.56 0.00 0.00 4.95
111 112 4.821589 CCTCTCGCGCTTCCACCC 62.822 72.222 5.56 0.00 0.00 4.61
112 113 3.296709 TTCCTCTCGCGCTTCCACC 62.297 63.158 5.56 0.00 0.00 4.61
113 114 1.807573 CTTCCTCTCGCGCTTCCAC 60.808 63.158 5.56 0.00 0.00 4.02
114 115 1.938657 CTCTTCCTCTCGCGCTTCCA 61.939 60.000 5.56 0.00 0.00 3.53
115 116 1.226831 CTCTTCCTCTCGCGCTTCC 60.227 63.158 5.56 0.00 0.00 3.46
116 117 1.876263 GCTCTTCCTCTCGCGCTTC 60.876 63.158 5.56 0.00 0.00 3.86
117 118 2.183046 GCTCTTCCTCTCGCGCTT 59.817 61.111 5.56 0.00 0.00 4.68
118 119 4.186433 CGCTCTTCCTCTCGCGCT 62.186 66.667 5.56 0.00 39.11 5.92
120 121 4.560856 CCCGCTCTTCCTCTCGCG 62.561 72.222 0.00 0.00 44.69 5.87
121 122 4.882396 GCCCGCTCTTCCTCTCGC 62.882 72.222 0.00 0.00 0.00 5.03
122 123 4.560856 CGCCCGCTCTTCCTCTCG 62.561 72.222 0.00 0.00 0.00 4.04
123 124 4.882396 GCGCCCGCTCTTCCTCTC 62.882 72.222 5.27 0.00 38.26 3.20
162 163 2.216750 TTACGGACGCCCACTACAGC 62.217 60.000 0.00 0.00 0.00 4.40
163 164 0.458669 ATTACGGACGCCCACTACAG 59.541 55.000 0.00 0.00 0.00 2.74
164 165 1.405105 GTATTACGGACGCCCACTACA 59.595 52.381 0.00 0.00 0.00 2.74
165 166 1.597937 CGTATTACGGACGCCCACTAC 60.598 57.143 8.36 0.00 38.08 2.73
166 167 0.662619 CGTATTACGGACGCCCACTA 59.337 55.000 8.36 0.00 38.08 2.74
167 168 1.434696 CGTATTACGGACGCCCACT 59.565 57.895 8.36 0.00 38.08 4.00
168 169 4.002037 CGTATTACGGACGCCCAC 57.998 61.111 8.36 0.00 38.08 4.61
173 174 2.570678 GCGTGGCGTATTACGGACG 61.571 63.158 17.26 6.86 42.82 4.79
174 175 3.302597 GCGTGGCGTATTACGGAC 58.697 61.111 17.26 2.20 42.82 4.79
185 186 1.788067 AAAACACTTACCCGCGTGGC 61.788 55.000 10.27 0.00 37.83 5.01
186 187 0.664224 AAAAACACTTACCCGCGTGG 59.336 50.000 8.42 8.42 41.37 4.94
187 188 1.331138 TGAAAAACACTTACCCGCGTG 59.669 47.619 4.92 0.00 37.18 5.34
188 189 1.331447 GTGAAAAACACTTACCCGCGT 59.669 47.619 4.92 0.00 45.13 6.01
189 190 2.026915 GTGAAAAACACTTACCCGCG 57.973 50.000 0.00 0.00 45.13 6.46
199 200 2.325166 GACGCGCGGTGAAAAACA 59.675 55.556 35.22 0.00 0.00 2.83
200 201 2.426261 GGACGCGCGGTGAAAAAC 60.426 61.111 35.22 13.33 0.00 2.43
201 202 2.470362 TTGGACGCGCGGTGAAAAA 61.470 52.632 35.22 15.84 0.00 1.94
202 203 2.895865 TTGGACGCGCGGTGAAAA 60.896 55.556 35.22 17.29 0.00 2.29
203 204 3.641986 GTTGGACGCGCGGTGAAA 61.642 61.111 35.22 19.14 0.00 2.69
212 213 1.208358 GCTAAAACGGGTTGGACGC 59.792 57.895 0.00 0.00 34.00 5.19
213 214 1.494189 CGCTAAAACGGGTTGGACG 59.506 57.895 0.00 0.00 37.36 4.79
214 215 1.208358 GCGCTAAAACGGGTTGGAC 59.792 57.895 0.00 0.00 0.00 4.02
215 216 2.319096 CGCGCTAAAACGGGTTGGA 61.319 57.895 5.56 0.00 40.69 3.53
216 217 2.174835 CGCGCTAAAACGGGTTGG 59.825 61.111 5.56 0.00 40.69 3.77
217 218 2.501008 GCGCGCTAAAACGGGTTG 60.501 61.111 26.67 0.00 46.53 3.77
218 219 4.079748 CGCGCGCTAAAACGGGTT 62.080 61.111 30.48 0.00 46.53 4.11
237 238 4.940593 TGGGCGCGCAAAAACAGC 62.941 61.111 34.42 12.59 0.00 4.40
238 239 3.029735 GTGGGCGCGCAAAAACAG 61.030 61.111 34.42 0.00 0.00 3.16
239 240 3.522731 AGTGGGCGCGCAAAAACA 61.523 55.556 34.42 19.39 0.00 2.83
240 241 3.029735 CAGTGGGCGCGCAAAAAC 61.030 61.111 34.42 22.97 0.00 2.43
241 242 4.277593 CCAGTGGGCGCGCAAAAA 62.278 61.111 34.42 12.03 0.00 1.94
252 253 4.767255 GTCAGGGCGCTCCAGTGG 62.767 72.222 2.00 1.40 38.24 4.00
271 272 4.711193 TTTAGCACGCGCGCAACG 62.711 61.111 32.58 19.17 45.49 4.10
272 273 2.426098 TTTTAGCACGCGCGCAAC 60.426 55.556 32.58 19.71 45.49 4.17
273 274 2.426098 GTTTTAGCACGCGCGCAA 60.426 55.556 32.58 14.81 45.49 4.85
274 275 4.711193 CGTTTTAGCACGCGCGCA 62.711 61.111 32.58 8.18 45.49 6.09
275 276 4.418470 TCGTTTTAGCACGCGCGC 62.418 61.111 32.58 23.91 45.49 6.86
276 277 2.567270 GTCGTTTTAGCACGCGCG 60.567 61.111 30.96 30.96 45.49 6.86
277 278 1.346378 TAGGTCGTTTTAGCACGCGC 61.346 55.000 5.73 0.00 40.14 6.86
278 279 1.274596 ATAGGTCGTTTTAGCACGCG 58.725 50.000 3.53 3.53 40.14 6.01
279 280 3.734776 AAATAGGTCGTTTTAGCACGC 57.265 42.857 0.00 0.00 40.14 5.34
280 281 3.844099 GCAAAATAGGTCGTTTTAGCACG 59.156 43.478 0.00 0.00 41.78 5.34
281 282 3.844099 CGCAAAATAGGTCGTTTTAGCAC 59.156 43.478 0.00 0.00 0.00 4.40
282 283 3.747010 TCGCAAAATAGGTCGTTTTAGCA 59.253 39.130 0.00 0.00 0.00 3.49
283 284 4.086574 GTCGCAAAATAGGTCGTTTTAGC 58.913 43.478 0.00 0.00 0.00 3.09
284 285 4.320491 CGTCGCAAAATAGGTCGTTTTAG 58.680 43.478 0.00 0.00 0.00 1.85
285 286 3.423384 GCGTCGCAAAATAGGTCGTTTTA 60.423 43.478 13.44 0.00 0.00 1.52
286 287 2.663606 GCGTCGCAAAATAGGTCGTTTT 60.664 45.455 13.44 0.00 0.00 2.43
287 288 1.136169 GCGTCGCAAAATAGGTCGTTT 60.136 47.619 13.44 0.00 0.00 3.60
288 289 0.441145 GCGTCGCAAAATAGGTCGTT 59.559 50.000 13.44 0.00 0.00 3.85
289 290 1.680105 CGCGTCGCAAAATAGGTCGT 61.680 55.000 18.75 0.00 0.00 4.34
290 291 1.013755 CGCGTCGCAAAATAGGTCG 60.014 57.895 18.75 0.00 0.00 4.79
291 292 1.347221 CCGCGTCGCAAAATAGGTC 59.653 57.895 18.75 0.00 0.00 3.85
292 293 2.746803 GCCGCGTCGCAAAATAGGT 61.747 57.895 18.75 0.00 0.00 3.08
293 294 2.022762 GCCGCGTCGCAAAATAGG 59.977 61.111 18.75 10.06 0.00 2.57
294 295 1.580132 GTGCCGCGTCGCAAAATAG 60.580 57.895 18.75 0.00 41.30 1.73
295 296 0.736672 TAGTGCCGCGTCGCAAAATA 60.737 50.000 18.75 2.52 41.30 1.40
296 297 1.966493 CTAGTGCCGCGTCGCAAAAT 61.966 55.000 18.75 3.53 41.30 1.82
297 298 2.662196 TAGTGCCGCGTCGCAAAA 60.662 55.556 18.75 0.63 41.30 2.44
298 299 3.109547 CTAGTGCCGCGTCGCAAA 61.110 61.111 18.75 3.00 41.30 3.68
299 300 3.851845 AACTAGTGCCGCGTCGCAA 62.852 57.895 18.75 0.00 41.30 4.85
300 301 2.475098 TAAACTAGTGCCGCGTCGCA 62.475 55.000 18.75 5.48 36.08 5.10
301 302 1.346378 TTAAACTAGTGCCGCGTCGC 61.346 55.000 7.29 7.29 0.00 5.19
302 303 1.006391 CATTAAACTAGTGCCGCGTCG 60.006 52.381 4.92 0.00 0.00 5.12
303 304 1.267383 GCATTAAACTAGTGCCGCGTC 60.267 52.381 4.92 0.00 35.63 5.19
304 305 0.725117 GCATTAAACTAGTGCCGCGT 59.275 50.000 4.92 0.00 35.63 6.01
305 306 0.315059 CGCATTAAACTAGTGCCGCG 60.315 55.000 0.00 0.00 38.06 6.46
306 307 0.027586 CCGCATTAAACTAGTGCCGC 59.972 55.000 0.00 0.00 38.06 6.53
307 308 0.027586 GCCGCATTAAACTAGTGCCG 59.972 55.000 0.00 0.00 38.06 5.69
308 309 1.064060 CAGCCGCATTAAACTAGTGCC 59.936 52.381 0.00 0.00 38.06 5.01
309 310 1.737793 ACAGCCGCATTAAACTAGTGC 59.262 47.619 0.00 0.00 37.96 4.40
310 311 3.426159 CCAACAGCCGCATTAAACTAGTG 60.426 47.826 0.00 0.00 0.00 2.74
311 312 2.747446 CCAACAGCCGCATTAAACTAGT 59.253 45.455 0.00 0.00 0.00 2.57
312 313 3.006940 TCCAACAGCCGCATTAAACTAG 58.993 45.455 0.00 0.00 0.00 2.57
313 314 3.060736 TCCAACAGCCGCATTAAACTA 57.939 42.857 0.00 0.00 0.00 2.24
314 315 1.904287 TCCAACAGCCGCATTAAACT 58.096 45.000 0.00 0.00 0.00 2.66
315 316 2.715737 TTCCAACAGCCGCATTAAAC 57.284 45.000 0.00 0.00 0.00 2.01
316 317 3.583806 CATTTCCAACAGCCGCATTAAA 58.416 40.909 0.00 0.00 0.00 1.52
317 318 2.673610 GCATTTCCAACAGCCGCATTAA 60.674 45.455 0.00 0.00 0.00 1.40
318 319 1.135141 GCATTTCCAACAGCCGCATTA 60.135 47.619 0.00 0.00 0.00 1.90
319 320 0.390209 GCATTTCCAACAGCCGCATT 60.390 50.000 0.00 0.00 0.00 3.56
320 321 1.216178 GCATTTCCAACAGCCGCAT 59.784 52.632 0.00 0.00 0.00 4.73
321 322 1.865788 GAGCATTTCCAACAGCCGCA 61.866 55.000 0.00 0.00 0.00 5.69
322 323 1.153958 GAGCATTTCCAACAGCCGC 60.154 57.895 0.00 0.00 0.00 6.53
323 324 0.883833 AAGAGCATTTCCAACAGCCG 59.116 50.000 0.00 0.00 0.00 5.52
324 325 4.102035 CTTAAGAGCATTTCCAACAGCC 57.898 45.455 0.00 0.00 0.00 4.85
338 339 2.158885 GGTCCAGGCTTAGGCTTAAGAG 60.159 54.545 18.99 7.75 38.88 2.85
339 340 1.838077 GGTCCAGGCTTAGGCTTAAGA 59.162 52.381 18.99 0.51 38.88 2.10
340 341 1.473434 CGGTCCAGGCTTAGGCTTAAG 60.473 57.143 5.28 11.09 39.44 1.85
341 342 0.539986 CGGTCCAGGCTTAGGCTTAA 59.460 55.000 5.28 0.00 35.88 1.85
342 343 0.324923 TCGGTCCAGGCTTAGGCTTA 60.325 55.000 5.28 0.00 35.88 3.09
343 344 1.198759 TTCGGTCCAGGCTTAGGCTT 61.199 55.000 5.28 0.00 35.88 4.35
344 345 1.198759 TTTCGGTCCAGGCTTAGGCT 61.199 55.000 1.28 1.28 39.66 4.58
345 346 0.744771 CTTTCGGTCCAGGCTTAGGC 60.745 60.000 0.00 0.00 37.82 3.93
346 347 0.744771 GCTTTCGGTCCAGGCTTAGG 60.745 60.000 0.00 0.00 0.00 2.69
357 358 1.458064 CACGACATAAACGCTTTCGGT 59.542 47.619 0.00 0.00 40.69 4.69
486 503 0.822944 GAGGAGGGTAGAGTACGGGC 60.823 65.000 0.00 0.00 0.00 6.13
508 525 2.712057 ACCGTACGTGTTCTACTTGG 57.288 50.000 15.21 0.00 0.00 3.61
519 539 2.164219 CCATAACACCAGTACCGTACGT 59.836 50.000 15.21 5.08 0.00 3.57
534 554 1.803998 GCGTTACCGGGAGTCCATAAC 60.804 57.143 12.30 14.29 33.88 1.89
627 651 1.448540 CCAGGCAGTTTCGATCGCT 60.449 57.895 11.09 0.00 0.00 4.93
633 657 3.777925 CGACGCCAGGCAGTTTCG 61.778 66.667 13.30 9.68 0.00 3.46
666 690 4.462483 ACAAGGGCATTATTGTTCGTTCAT 59.538 37.500 0.00 0.00 36.23 2.57
667 691 3.823873 ACAAGGGCATTATTGTTCGTTCA 59.176 39.130 0.00 0.00 36.23 3.18
668 692 4.434713 ACAAGGGCATTATTGTTCGTTC 57.565 40.909 0.00 0.00 36.23 3.95
669 693 4.864704 AACAAGGGCATTATTGTTCGTT 57.135 36.364 0.00 0.00 44.20 3.85
674 698 3.119495 GCGAGAAACAAGGGCATTATTGT 60.119 43.478 0.00 0.00 41.28 2.71
688 712 1.730446 GCCATCTTTGCTGCGAGAAAC 60.730 52.381 9.17 0.35 0.00 2.78
710 734 2.068519 GAATGCCGGGCTTTCAAAAAG 58.931 47.619 31.46 0.00 40.73 2.27
794 818 0.036952 AGTCTTGATGGCGTGTGAGG 60.037 55.000 0.00 0.00 0.00 3.86
847 876 1.726248 CCGCTTTTAACTTTGCATGCC 59.274 47.619 16.68 0.00 0.00 4.40
848 877 1.726248 CCCGCTTTTAACTTTGCATGC 59.274 47.619 11.82 11.82 0.00 4.06
849 878 2.986479 GTCCCGCTTTTAACTTTGCATG 59.014 45.455 0.00 0.00 0.00 4.06
852 881 1.664874 CCGTCCCGCTTTTAACTTTGC 60.665 52.381 0.00 0.00 0.00 3.68
853 882 1.874872 TCCGTCCCGCTTTTAACTTTG 59.125 47.619 0.00 0.00 0.00 2.77
1014 1076 1.930204 TGGTGGAGTGGAGAGGAGATA 59.070 52.381 0.00 0.00 0.00 1.98
1060 1128 2.015726 GAGGGAGGGAGGAGAGGGA 61.016 68.421 0.00 0.00 0.00 4.20
1064 1132 2.015726 GAGGGAGGGAGGGAGGAGA 61.016 68.421 0.00 0.00 0.00 3.71
1110 1180 2.609984 CCTCATCTTATCTCTGGCTGCG 60.610 54.545 0.00 0.00 0.00 5.18
1194 1264 1.518133 CGAGCGCTTCCTCTTCTGG 60.518 63.158 13.26 0.00 0.00 3.86
1341 1411 3.681835 GACAGCAGGTCGGACGGT 61.682 66.667 1.43 0.00 36.65 4.83
1442 1512 1.066908 CGTTCAGGCAACCAAACACAT 59.933 47.619 0.00 0.00 37.17 3.21
1624 1694 2.748605 CCTAGAATGTAGCAAGCCTCG 58.251 52.381 0.00 0.00 0.00 4.63
1680 1754 1.002659 TGGATGTCAAACCCGAACGAT 59.997 47.619 0.00 0.00 0.00 3.73
1681 1755 0.393448 TGGATGTCAAACCCGAACGA 59.607 50.000 0.00 0.00 0.00 3.85
1682 1756 1.130373 CATGGATGTCAAACCCGAACG 59.870 52.381 0.00 0.00 0.00 3.95
1683 1757 1.135402 GCATGGATGTCAAACCCGAAC 60.135 52.381 0.00 0.00 0.00 3.95
1684 1758 1.173043 GCATGGATGTCAAACCCGAA 58.827 50.000 0.00 0.00 0.00 4.30
1686 1760 1.105457 ATGCATGGATGTCAAACCCG 58.895 50.000 0.00 0.00 0.00 5.28
1687 1761 1.472026 GCATGCATGGATGTCAAACCC 60.472 52.381 27.34 6.08 0.00 4.11
1719 1793 1.086634 GTCAGCGCTTGATCCCTGAC 61.087 60.000 7.50 6.81 44.84 3.51
1728 1802 0.861837 AAGAAACTCGTCAGCGCTTG 59.138 50.000 7.50 3.43 38.14 4.01
1732 1806 1.682982 ACGTAAGAAACTCGTCAGCG 58.317 50.000 0.00 0.00 43.62 5.18
1864 1938 2.046314 CCACCGCTCCCGTTGAAT 60.046 61.111 0.00 0.00 0.00 2.57
2096 2170 4.798682 GGGGAGGGAGGCGAAGGA 62.799 72.222 0.00 0.00 0.00 3.36
2153 2227 1.210967 GAAGTCGGAGAGGAGAGGAGA 59.789 57.143 0.00 0.00 36.95 3.71
2154 2228 1.675552 GAAGTCGGAGAGGAGAGGAG 58.324 60.000 0.00 0.00 36.95 3.69
2155 2229 0.107606 CGAAGTCGGAGAGGAGAGGA 60.108 60.000 0.00 0.00 36.95 3.71
2254 2331 1.741770 GTCGGTCTTCTTGGCGCAT 60.742 57.895 10.83 0.00 0.00 4.73
2528 2611 1.081442 GCTACTTGTTGCCGTTGCC 60.081 57.895 0.00 0.00 36.33 4.52
2600 2687 0.659957 GCTTCCTCATTCATCACCGC 59.340 55.000 0.00 0.00 0.00 5.68
2819 2913 7.606135 TCCAGGATTTTCATATTACGGAGTA 57.394 36.000 0.00 0.00 45.11 2.59
2821 2915 6.595716 GGATCCAGGATTTTCATATTACGGAG 59.404 42.308 6.95 0.00 0.00 4.63
2822 2916 6.472887 GGATCCAGGATTTTCATATTACGGA 58.527 40.000 6.95 0.00 0.00 4.69
2823 2917 5.648092 GGGATCCAGGATTTTCATATTACGG 59.352 44.000 15.23 0.00 0.00 4.02
2824 2918 6.476378 AGGGATCCAGGATTTTCATATTACG 58.524 40.000 15.23 0.00 0.00 3.18
2825 2919 7.694093 AGAGGGATCCAGGATTTTCATATTAC 58.306 38.462 15.23 0.00 0.00 1.89
2826 2920 7.895144 AGAGGGATCCAGGATTTTCATATTA 57.105 36.000 15.23 0.00 0.00 0.98
2827 2921 6.793518 AGAGGGATCCAGGATTTTCATATT 57.206 37.500 15.23 0.00 0.00 1.28
2830 2924 5.043881 TCAAAGAGGGATCCAGGATTTTCAT 60.044 40.000 15.23 0.00 0.00 2.57
2831 2925 4.292041 TCAAAGAGGGATCCAGGATTTTCA 59.708 41.667 15.23 0.00 0.00 2.69
2832 2926 4.860022 TCAAAGAGGGATCCAGGATTTTC 58.140 43.478 15.23 2.27 0.00 2.29
2837 2934 2.921221 AGTTCAAAGAGGGATCCAGGA 58.079 47.619 15.23 0.00 0.00 3.86
2858 2955 9.930693 CACTTGGTAGAACTCTAGTAGAAAATT 57.069 33.333 0.64 0.00 0.00 1.82
2876 2973 3.319972 AGAAGCAACGTCTACACTTGGTA 59.680 43.478 0.00 0.00 0.00 3.25
2877 2974 2.102588 AGAAGCAACGTCTACACTTGGT 59.897 45.455 0.00 0.00 0.00 3.67
2878 2975 2.476619 CAGAAGCAACGTCTACACTTGG 59.523 50.000 0.00 0.00 0.00 3.61
2879 2976 3.123804 ACAGAAGCAACGTCTACACTTG 58.876 45.455 0.00 0.00 0.00 3.16
2880 2977 3.381949 GACAGAAGCAACGTCTACACTT 58.618 45.455 0.00 0.00 0.00 3.16
2883 2980 1.929038 GCGACAGAAGCAACGTCTACA 60.929 52.381 0.00 0.00 34.19 2.74
2886 2983 0.249489 AAGCGACAGAAGCAACGTCT 60.249 50.000 0.00 0.00 37.01 4.18
2889 2986 0.304705 ACAAAGCGACAGAAGCAACG 59.695 50.000 0.00 0.00 37.01 4.10
2910 3007 3.747529 GCATCCATCCAAAACACCAAAAG 59.252 43.478 0.00 0.00 0.00 2.27
3012 3109 3.752222 CCTACTCATCCGATAAGCTACGT 59.248 47.826 0.00 0.00 0.00 3.57
3070 3343 2.857104 GCAAAACCAAAGCCTACACGAC 60.857 50.000 0.00 0.00 0.00 4.34
3144 3419 1.285962 ACATGGATTCCACCTCCCAAG 59.714 52.381 7.76 0.00 35.80 3.61
3146 3421 2.126882 CTACATGGATTCCACCTCCCA 58.873 52.381 7.76 0.00 35.80 4.37
3294 3578 3.801698 CTGGCTAGTCGTGGTAGTACTA 58.198 50.000 0.00 0.00 0.00 1.82
3295 3579 2.641305 CTGGCTAGTCGTGGTAGTACT 58.359 52.381 0.00 0.00 0.00 2.73
3296 3580 1.065251 GCTGGCTAGTCGTGGTAGTAC 59.935 57.143 0.00 0.00 0.00 2.73
3327 3612 2.286833 GCGTGCTCGAGCCATATAAAAA 59.713 45.455 33.23 9.65 41.18 1.94
3380 5645 5.220892 CGAACTGTACTCTACCCTGAGAATC 60.221 48.000 0.00 0.00 37.50 2.52
3385 5650 3.708403 TCGAACTGTACTCTACCCTGA 57.292 47.619 0.00 0.00 0.00 3.86
3389 5654 6.259638 CAGAGAAATCGAACTGTACTCTACC 58.740 44.000 0.00 0.00 33.00 3.18
3425 5692 5.291128 GTCCGTTCAATGATTCATACGTTCT 59.709 40.000 15.54 0.00 0.00 3.01
3527 5796 1.525923 CATGCCTCTCCCCAGTGAG 59.474 63.158 0.00 0.00 34.12 3.51
3528 5797 2.673200 GCATGCCTCTCCCCAGTGA 61.673 63.158 6.36 0.00 0.00 3.41
3529 5798 2.124403 GCATGCCTCTCCCCAGTG 60.124 66.667 6.36 0.00 0.00 3.66
3530 5799 0.695462 TATGCATGCCTCTCCCCAGT 60.695 55.000 16.68 0.00 0.00 4.00
3531 5800 0.250640 GTATGCATGCCTCTCCCCAG 60.251 60.000 16.68 0.00 0.00 4.45
3532 5801 1.839191 GTATGCATGCCTCTCCCCA 59.161 57.895 16.68 0.00 0.00 4.96
3533 5802 1.302033 CGTATGCATGCCTCTCCCC 60.302 63.158 16.68 0.00 0.00 4.81
3535 5804 3.647824 GCGTATGCATGCCTCTCC 58.352 61.111 16.68 0.00 42.15 3.71
3542 5811 1.650912 GAGCCTTGGCGTATGCATG 59.349 57.895 10.16 0.00 45.35 4.06
3544 5819 2.124736 GGAGCCTTGGCGTATGCA 60.125 61.111 9.59 0.00 45.35 3.96
3562 5837 2.106683 GTACTCGTGTGCCATGCCC 61.107 63.158 0.00 0.00 0.00 5.36
3563 5838 0.744414 ATGTACTCGTGTGCCATGCC 60.744 55.000 0.00 0.00 0.00 4.40
3569 5844 2.915463 GTGTAGTCATGTACTCGTGTGC 59.085 50.000 0.00 0.00 39.80 4.57
3570 5845 3.161306 CGTGTAGTCATGTACTCGTGTG 58.839 50.000 0.00 0.00 39.80 3.82
3571 5846 2.161012 CCGTGTAGTCATGTACTCGTGT 59.839 50.000 13.50 0.00 39.80 4.49
3572 5847 2.417586 TCCGTGTAGTCATGTACTCGTG 59.582 50.000 13.50 7.87 39.80 4.35
3573 5848 2.417933 GTCCGTGTAGTCATGTACTCGT 59.582 50.000 13.50 0.00 39.80 4.18
3574 5849 2.536329 CGTCCGTGTAGTCATGTACTCG 60.536 54.545 9.67 9.67 39.80 4.18
3575 5850 2.790468 GCGTCCGTGTAGTCATGTACTC 60.790 54.545 0.00 0.00 39.80 2.59
3576 5851 1.131883 GCGTCCGTGTAGTCATGTACT 59.868 52.381 0.00 0.00 42.62 2.73
3582 5857 3.376078 GGGGCGTCCGTGTAGTCA 61.376 66.667 0.00 0.00 0.00 3.41
3610 5887 2.175811 GCCACGCACATTCGAACC 59.824 61.111 0.00 0.00 0.00 3.62
3768 6045 4.003788 ACCGGCCGTCAGTTCAGG 62.004 66.667 26.12 7.62 0.00 3.86


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

AutoCloner maintained by Alex Coulton.