Multiple sequence alignment - TraesCS3B01G006300

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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 TraesCS3B01G006300 chr3B 100.000 3243 0 0 1 3243 3309513 3306271 0.000000e+00 5989.0
1 TraesCS3B01G006300 chr3B 89.137 2108 125 51 1154 3196 5408086 5410154 0.000000e+00 2529.0
2 TraesCS3B01G006300 chr3B 82.529 601 42 31 554 1113 5407507 5408085 1.360000e-128 470.0
3 TraesCS3B01G006300 chr3B 85.714 210 20 5 5 210 5407052 5407255 2.530000e-51 213.0
4 TraesCS3B01G006300 chr3B 94.505 91 1 3 3157 3243 5411167 5411257 1.570000e-28 137.0
5 TraesCS3B01G006300 chr3D 84.425 2549 143 117 809 3243 1316351 1313943 0.000000e+00 2274.0
6 TraesCS3B01G006300 chr3D 81.714 175 16 8 144 312 1316957 1316793 7.300000e-27 132.0
7 TraesCS3B01G006300 chr3A 84.378 2202 133 81 809 2981 7655143 7657162 0.000000e+00 1965.0
8 TraesCS3B01G006300 chr3A 83.688 141 13 8 3020 3154 7657170 7657306 1.220000e-24 124.0
9 TraesCS3B01G006300 chr3A 87.059 85 8 1 575 659 7654860 7654941 3.450000e-15 93.5
10 TraesCS3B01G006300 chr7A 82.759 116 5 7 1008 1112 498035687 498035576 4.460000e-14 89.8
11 TraesCS3B01G006300 chr2A 81.034 116 7 7 1008 1112 603379975 603380086 9.650000e-11 78.7
12 TraesCS3B01G006300 chr7D 100.000 29 0 0 1259 1287 38795009 38795037 2.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G006300 chr3B 3306271 3309513 3242 True 5989.00 5989 100.000000 1 3243 1 chr3B.!!$R1 3242
1 TraesCS3B01G006300 chr3B 5407052 5411257 4205 False 837.25 2529 87.971250 5 3243 4 chr3B.!!$F1 3238
2 TraesCS3B01G006300 chr3D 1313943 1316957 3014 True 1203.00 2274 83.069500 144 3243 2 chr3D.!!$R1 3099
3 TraesCS3B01G006300 chr3A 7654860 7657306 2446 False 727.50 1965 85.041667 575 3154 3 chr3A.!!$F1 2579

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
450 460 0.032678 ATATTCAGCGTCAGGCCTCG 59.967 55.0 0.0 5.72 45.17 4.63 F
1149 1332 0.105964 TACACCCACACACACTCAGC 59.894 55.0 0.0 0.00 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2114 2341 0.179163 GCGCTTCAAGGTTACCATGC 60.179 55.0 3.51 0.00 0.00 4.06 R
3136 3498 0.108424 CCCTACTCTGTGCAGCTCAC 60.108 60.0 8.75 8.75 45.82 3.51 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
69 70 6.886459 TCAATACTGAACCTACGGTTACTAGT 59.114 38.462 0.00 0.00 46.95 2.57
71 72 7.793927 ATACTGAACCTACGGTTACTAGTAC 57.206 40.000 0.91 0.00 46.95 2.73
72 73 5.810095 ACTGAACCTACGGTTACTAGTACT 58.190 41.667 0.91 0.00 46.95 2.73
74 75 7.394816 ACTGAACCTACGGTTACTAGTACTAA 58.605 38.462 0.91 0.00 46.95 2.24
75 76 7.334671 ACTGAACCTACGGTTACTAGTACTAAC 59.665 40.741 0.91 0.00 46.95 2.34
76 77 7.394816 TGAACCTACGGTTACTAGTACTAACT 58.605 38.462 0.91 0.00 46.95 2.24
77 78 7.334421 TGAACCTACGGTTACTAGTACTAACTG 59.666 40.741 12.39 12.39 46.95 3.16
97 98 1.741732 GCCTGTGAATCAGATCGCACT 60.742 52.381 14.25 0.00 46.27 4.40
100 101 3.181482 CCTGTGAATCAGATCGCACTACT 60.181 47.826 14.25 0.00 46.27 2.57
102 103 2.537625 GTGAATCAGATCGCACTACTGC 59.462 50.000 8.44 0.00 40.38 4.40
108 109 0.926846 GATCGCACTACTGCTTCAGC 59.073 55.000 0.00 0.00 41.77 4.26
112 113 1.800805 GCACTACTGCTTCAGCTTCA 58.199 50.000 0.00 0.00 40.63 3.02
131 136 7.485277 CAGCTTCAGAAGAAACATGAATGAATC 59.515 37.037 14.86 0.00 32.82 2.52
141 146 6.459670 AACATGAATGAATCAATGCAGCTA 57.540 33.333 0.00 0.00 42.54 3.32
158 163 4.213059 GCAGCTAGAAATGAATAGGAGCAC 59.787 45.833 0.00 0.00 0.00 4.40
160 165 6.739843 GCAGCTAGAAATGAATAGGAGCACTA 60.740 42.308 0.00 0.00 35.80 2.74
162 167 5.631512 GCTAGAAATGAATAGGAGCACTACG 59.368 44.000 0.00 0.00 33.70 3.51
163 168 5.854010 AGAAATGAATAGGAGCACTACGA 57.146 39.130 0.00 0.00 33.70 3.43
166 171 7.275920 AGAAATGAATAGGAGCACTACGAAAT 58.724 34.615 0.00 0.00 33.70 2.17
168 173 8.594881 AAATGAATAGGAGCACTACGAAATAG 57.405 34.615 0.00 0.00 33.70 1.73
169 174 6.710597 TGAATAGGAGCACTACGAAATAGT 57.289 37.500 0.00 0.00 45.61 2.12
171 176 7.646314 TGAATAGGAGCACTACGAAATAGTAC 58.354 38.462 0.00 0.00 42.62 2.73
172 177 4.915158 AGGAGCACTACGAAATAGTACC 57.085 45.455 0.00 0.00 42.62 3.34
210 215 2.232208 GGTGCCCCATCAAGAAAGAAAG 59.768 50.000 0.00 0.00 0.00 2.62
211 216 3.157087 GTGCCCCATCAAGAAAGAAAGA 58.843 45.455 0.00 0.00 0.00 2.52
212 217 3.573967 GTGCCCCATCAAGAAAGAAAGAA 59.426 43.478 0.00 0.00 0.00 2.52
213 218 4.039124 GTGCCCCATCAAGAAAGAAAGAAA 59.961 41.667 0.00 0.00 0.00 2.52
233 238 0.318360 GAAACCTTTCCGTTTGGCCG 60.318 55.000 0.00 0.00 36.10 6.13
241 246 4.160635 CGTTTGGCCGGCGTCATC 62.161 66.667 22.54 6.51 0.00 2.92
242 247 3.053291 GTTTGGCCGGCGTCATCA 61.053 61.111 22.54 9.62 0.00 3.07
243 248 3.053291 TTTGGCCGGCGTCATCAC 61.053 61.111 22.54 4.79 0.00 3.06
250 255 3.554692 GGCGTCATCACCGAAGCG 61.555 66.667 0.00 0.00 40.75 4.68
251 256 2.809601 GCGTCATCACCGAAGCGT 60.810 61.111 0.00 0.00 30.88 5.07
252 257 2.789203 GCGTCATCACCGAAGCGTC 61.789 63.158 0.00 0.00 30.88 5.19
253 258 1.443702 CGTCATCACCGAAGCGTCA 60.444 57.895 0.00 0.00 0.00 4.35
254 259 1.006825 CGTCATCACCGAAGCGTCAA 61.007 55.000 0.00 0.00 0.00 3.18
255 260 0.716108 GTCATCACCGAAGCGTCAAG 59.284 55.000 0.00 0.00 0.00 3.02
256 261 0.389817 TCATCACCGAAGCGTCAAGG 60.390 55.000 0.00 0.00 0.00 3.61
257 262 1.741770 ATCACCGAAGCGTCAAGGC 60.742 57.895 0.00 0.00 0.00 4.35
258 263 3.423154 CACCGAAGCGTCAAGGCC 61.423 66.667 0.00 0.00 0.00 5.19
259 264 3.626924 ACCGAAGCGTCAAGGCCT 61.627 61.111 0.00 0.00 0.00 5.19
260 265 2.815647 CCGAAGCGTCAAGGCCTC 60.816 66.667 5.23 0.00 0.00 4.70
261 266 2.048222 CGAAGCGTCAAGGCCTCA 60.048 61.111 5.23 0.00 0.00 3.86
262 267 1.667830 CGAAGCGTCAAGGCCTCAA 60.668 57.895 5.23 0.00 0.00 3.02
263 268 1.869690 GAAGCGTCAAGGCCTCAAC 59.130 57.895 5.23 6.56 0.00 3.18
264 269 1.578206 GAAGCGTCAAGGCCTCAACC 61.578 60.000 5.23 1.95 0.00 3.77
265 270 2.281484 GCGTCAAGGCCTCAACCA 60.281 61.111 5.23 0.00 0.00 3.67
266 271 1.896660 GCGTCAAGGCCTCAACCAA 60.897 57.895 5.23 0.00 0.00 3.67
267 272 1.452145 GCGTCAAGGCCTCAACCAAA 61.452 55.000 5.23 0.00 0.00 3.28
268 273 1.247567 CGTCAAGGCCTCAACCAAAT 58.752 50.000 5.23 0.00 0.00 2.32
269 274 1.200020 CGTCAAGGCCTCAACCAAATC 59.800 52.381 5.23 0.00 0.00 2.17
270 275 2.519013 GTCAAGGCCTCAACCAAATCT 58.481 47.619 5.23 0.00 0.00 2.40
271 276 2.489722 GTCAAGGCCTCAACCAAATCTC 59.510 50.000 5.23 0.00 0.00 2.75
272 277 2.376518 TCAAGGCCTCAACCAAATCTCT 59.623 45.455 5.23 0.00 0.00 3.10
273 278 2.751806 CAAGGCCTCAACCAAATCTCTC 59.248 50.000 5.23 0.00 0.00 3.20
274 279 1.065854 AGGCCTCAACCAAATCTCTCG 60.066 52.381 0.00 0.00 0.00 4.04
275 280 0.729690 GCCTCAACCAAATCTCTCGC 59.270 55.000 0.00 0.00 0.00 5.03
276 281 1.373570 CCTCAACCAAATCTCTCGCC 58.626 55.000 0.00 0.00 0.00 5.54
277 282 1.339055 CCTCAACCAAATCTCTCGCCA 60.339 52.381 0.00 0.00 0.00 5.69
278 283 2.636830 CTCAACCAAATCTCTCGCCAT 58.363 47.619 0.00 0.00 0.00 4.40
279 284 2.611292 CTCAACCAAATCTCTCGCCATC 59.389 50.000 0.00 0.00 0.00 3.51
280 285 2.027285 TCAACCAAATCTCTCGCCATCA 60.027 45.455 0.00 0.00 0.00 3.07
281 286 2.029838 ACCAAATCTCTCGCCATCAC 57.970 50.000 0.00 0.00 0.00 3.06
282 287 1.303309 CCAAATCTCTCGCCATCACC 58.697 55.000 0.00 0.00 0.00 4.02
283 288 1.407299 CCAAATCTCTCGCCATCACCA 60.407 52.381 0.00 0.00 0.00 4.17
284 289 2.358957 CAAATCTCTCGCCATCACCAA 58.641 47.619 0.00 0.00 0.00 3.67
285 290 2.322355 AATCTCTCGCCATCACCAAG 57.678 50.000 0.00 0.00 0.00 3.61
286 291 0.467384 ATCTCTCGCCATCACCAAGG 59.533 55.000 0.00 0.00 0.00 3.61
287 292 0.614697 TCTCTCGCCATCACCAAGGA 60.615 55.000 0.00 0.00 0.00 3.36
288 293 0.250234 CTCTCGCCATCACCAAGGAA 59.750 55.000 0.00 0.00 0.00 3.36
289 294 0.911769 TCTCGCCATCACCAAGGAAT 59.088 50.000 0.00 0.00 0.00 3.01
290 295 1.281867 TCTCGCCATCACCAAGGAATT 59.718 47.619 0.00 0.00 0.00 2.17
291 296 2.503765 TCTCGCCATCACCAAGGAATTA 59.496 45.455 0.00 0.00 0.00 1.40
292 297 2.614057 CTCGCCATCACCAAGGAATTAC 59.386 50.000 0.00 0.00 0.00 1.89
293 298 1.676006 CGCCATCACCAAGGAATTACC 59.324 52.381 0.00 0.00 39.35 2.85
294 299 2.031870 GCCATCACCAAGGAATTACCC 58.968 52.381 0.00 0.00 40.05 3.69
295 300 2.297701 CCATCACCAAGGAATTACCCG 58.702 52.381 0.00 0.00 40.05 5.28
296 301 2.297701 CATCACCAAGGAATTACCCGG 58.702 52.381 0.00 0.00 40.05 5.73
297 302 0.034863 TCACCAAGGAATTACCCGGC 60.035 55.000 0.00 0.00 40.05 6.13
298 303 0.322997 CACCAAGGAATTACCCGGCA 60.323 55.000 0.00 0.00 40.05 5.69
299 304 0.034477 ACCAAGGAATTACCCGGCAG 60.034 55.000 0.00 0.00 40.05 4.85
300 305 0.254747 CCAAGGAATTACCCGGCAGA 59.745 55.000 0.00 0.00 40.05 4.26
301 306 1.340600 CCAAGGAATTACCCGGCAGAA 60.341 52.381 0.00 0.00 40.05 3.02
302 307 2.017049 CAAGGAATTACCCGGCAGAAG 58.983 52.381 0.00 0.00 40.05 2.85
303 308 1.580059 AGGAATTACCCGGCAGAAGA 58.420 50.000 0.00 0.00 40.05 2.87
304 309 2.127708 AGGAATTACCCGGCAGAAGAT 58.872 47.619 0.00 0.00 40.05 2.40
305 310 2.158755 AGGAATTACCCGGCAGAAGATG 60.159 50.000 0.00 0.00 40.05 2.90
306 311 2.158813 GGAATTACCCGGCAGAAGATGA 60.159 50.000 0.00 0.00 0.00 2.92
307 312 3.541632 GAATTACCCGGCAGAAGATGAA 58.458 45.455 0.00 0.00 0.00 2.57
308 313 2.691409 TTACCCGGCAGAAGATGAAG 57.309 50.000 0.00 0.00 0.00 3.02
309 314 1.860641 TACCCGGCAGAAGATGAAGA 58.139 50.000 0.00 0.00 0.00 2.87
310 315 1.207791 ACCCGGCAGAAGATGAAGAT 58.792 50.000 0.00 0.00 0.00 2.40
311 316 1.134280 ACCCGGCAGAAGATGAAGATG 60.134 52.381 0.00 0.00 0.00 2.90
312 317 1.590932 CCGGCAGAAGATGAAGATGG 58.409 55.000 0.00 0.00 0.00 3.51
313 318 1.134280 CCGGCAGAAGATGAAGATGGT 60.134 52.381 0.00 0.00 0.00 3.55
314 319 2.103094 CCGGCAGAAGATGAAGATGGTA 59.897 50.000 0.00 0.00 0.00 3.25
315 320 3.432186 CCGGCAGAAGATGAAGATGGTAA 60.432 47.826 0.00 0.00 0.00 2.85
316 321 3.806521 CGGCAGAAGATGAAGATGGTAAG 59.193 47.826 0.00 0.00 0.00 2.34
317 322 3.563390 GGCAGAAGATGAAGATGGTAAGC 59.437 47.826 0.00 0.00 0.00 3.09
318 323 3.247173 GCAGAAGATGAAGATGGTAAGCG 59.753 47.826 0.00 0.00 0.00 4.68
319 324 3.806521 CAGAAGATGAAGATGGTAAGCGG 59.193 47.826 0.00 0.00 0.00 5.52
320 325 3.706594 AGAAGATGAAGATGGTAAGCGGA 59.293 43.478 0.00 0.00 0.00 5.54
321 326 3.460857 AGATGAAGATGGTAAGCGGAC 57.539 47.619 0.00 0.00 0.00 4.79
322 327 2.128035 GATGAAGATGGTAAGCGGACG 58.872 52.381 0.00 0.00 0.00 4.79
323 328 0.174845 TGAAGATGGTAAGCGGACGG 59.825 55.000 0.00 0.00 0.00 4.79
324 329 0.529992 GAAGATGGTAAGCGGACGGG 60.530 60.000 0.00 0.00 0.00 5.28
325 330 1.262640 AAGATGGTAAGCGGACGGGT 61.263 55.000 0.00 0.00 0.00 5.28
326 331 1.227176 GATGGTAAGCGGACGGGTC 60.227 63.158 0.00 0.00 0.00 4.46
327 332 1.673808 GATGGTAAGCGGACGGGTCT 61.674 60.000 0.00 0.00 0.00 3.85
328 333 0.396139 ATGGTAAGCGGACGGGTCTA 60.396 55.000 0.00 0.00 0.00 2.59
329 334 1.315257 TGGTAAGCGGACGGGTCTAC 61.315 60.000 0.00 0.00 0.00 2.59
330 335 1.435105 GTAAGCGGACGGGTCTACC 59.565 63.158 0.00 0.00 0.00 3.18
362 367 3.423154 GCGTCAAGGCCTCAACCG 61.423 66.667 5.23 7.77 33.69 4.44
380 390 1.536922 CCGATTCTCTCACCATCACCG 60.537 57.143 0.00 0.00 0.00 4.94
385 395 0.743688 CTCTCACCATCACCGAGGAG 59.256 60.000 0.00 0.00 0.00 3.69
406 416 1.470098 CAAACCGGCAGAAGATGAAGG 59.530 52.381 0.00 0.00 34.35 3.46
413 423 3.806521 CGGCAGAAGATGAAGGTGATTAG 59.193 47.826 0.00 0.00 0.00 1.73
415 425 5.451937 CGGCAGAAGATGAAGGTGATTAGTA 60.452 44.000 0.00 0.00 0.00 1.82
417 427 5.755861 GCAGAAGATGAAGGTGATTAGTACC 59.244 44.000 0.00 0.00 38.52 3.34
419 429 5.892119 AGAAGATGAAGGTGATTAGTACCGA 59.108 40.000 0.00 0.00 43.06 4.69
422 432 3.972133 TGAAGGTGATTAGTACCGAGGA 58.028 45.455 0.00 0.00 43.06 3.71
423 433 4.346730 TGAAGGTGATTAGTACCGAGGAA 58.653 43.478 0.00 0.00 43.06 3.36
428 438 7.613551 AGGTGATTAGTACCGAGGAATAAAT 57.386 36.000 0.00 0.00 43.06 1.40
430 440 9.151177 AGGTGATTAGTACCGAGGAATAAATAA 57.849 33.333 0.00 0.00 43.06 1.40
440 450 8.029642 ACCGAGGAATAAATAAATATTCAGCG 57.970 34.615 8.74 9.94 41.84 5.18
443 453 8.708742 CGAGGAATAAATAAATATTCAGCGTCA 58.291 33.333 8.74 0.00 41.84 4.35
445 455 9.003658 AGGAATAAATAAATATTCAGCGTCAGG 57.996 33.333 8.74 0.00 41.84 3.86
446 456 7.750903 GGAATAAATAAATATTCAGCGTCAGGC 59.249 37.037 8.74 0.00 41.84 4.85
447 457 5.438761 AAATAAATATTCAGCGTCAGGCC 57.561 39.130 0.00 0.00 45.17 5.19
450 460 0.032678 ATATTCAGCGTCAGGCCTCG 59.967 55.000 0.00 5.72 45.17 4.63
451 461 1.035385 TATTCAGCGTCAGGCCTCGA 61.035 55.000 17.43 9.23 45.17 4.04
452 462 2.564553 ATTCAGCGTCAGGCCTCGAC 62.565 60.000 17.43 18.67 45.17 4.20
453 463 4.803426 CAGCGTCAGGCCTCGACC 62.803 72.222 17.43 14.04 45.17 4.79
455 465 4.373116 GCGTCAGGCCTCGACCAA 62.373 66.667 17.43 0.00 34.80 3.67
456 466 2.579201 CGTCAGGCCTCGACCAAT 59.421 61.111 22.03 0.00 0.00 3.16
457 467 1.079127 CGTCAGGCCTCGACCAATT 60.079 57.895 22.03 0.00 0.00 2.32
458 468 1.361668 CGTCAGGCCTCGACCAATTG 61.362 60.000 22.03 0.00 0.00 2.32
466 476 0.592637 CTCGACCAATTGCTGCACAA 59.407 50.000 0.00 4.56 44.01 3.33
477 487 3.354948 TGCTGCACAATAATCCTCTGT 57.645 42.857 0.00 0.00 0.00 3.41
478 488 4.486125 TGCTGCACAATAATCCTCTGTA 57.514 40.909 0.00 0.00 0.00 2.74
479 489 4.842574 TGCTGCACAATAATCCTCTGTAA 58.157 39.130 0.00 0.00 0.00 2.41
480 490 5.252547 TGCTGCACAATAATCCTCTGTAAA 58.747 37.500 0.00 0.00 0.00 2.01
481 491 5.709631 TGCTGCACAATAATCCTCTGTAAAA 59.290 36.000 0.00 0.00 0.00 1.52
482 492 6.127925 TGCTGCACAATAATCCTCTGTAAAAG 60.128 38.462 0.00 0.00 0.00 2.27
484 494 5.652014 TGCACAATAATCCTCTGTAAAAGGG 59.348 40.000 0.00 0.00 34.46 3.95
486 496 6.038714 GCACAATAATCCTCTGTAAAAGGGAG 59.961 42.308 0.00 0.00 34.46 4.30
487 497 6.038714 CACAATAATCCTCTGTAAAAGGGAGC 59.961 42.308 0.00 0.00 34.46 4.70
488 498 5.975988 ATAATCCTCTGTAAAAGGGAGCA 57.024 39.130 0.00 0.00 34.46 4.26
489 499 3.922171 ATCCTCTGTAAAAGGGAGCAG 57.078 47.619 0.00 0.00 34.46 4.24
492 502 3.261897 TCCTCTGTAAAAGGGAGCAGAAG 59.738 47.826 0.00 0.00 37.50 2.85
493 503 3.006247 CTCTGTAAAAGGGAGCAGAAGC 58.994 50.000 0.00 0.00 37.50 3.86
494 504 2.371841 TCTGTAAAAGGGAGCAGAAGCA 59.628 45.455 0.00 0.00 45.49 3.91
496 506 3.760684 CTGTAAAAGGGAGCAGAAGCAAT 59.239 43.478 0.00 0.00 45.49 3.56
497 507 3.507233 TGTAAAAGGGAGCAGAAGCAATG 59.493 43.478 0.00 0.00 45.49 2.82
499 509 3.439857 AAAGGGAGCAGAAGCAATGTA 57.560 42.857 0.00 0.00 45.49 2.29
500 510 2.409948 AGGGAGCAGAAGCAATGTAC 57.590 50.000 0.00 0.00 45.49 2.90
501 511 1.912043 AGGGAGCAGAAGCAATGTACT 59.088 47.619 0.00 0.00 45.49 2.73
502 512 2.307098 AGGGAGCAGAAGCAATGTACTT 59.693 45.455 0.00 0.00 45.49 2.24
529 601 3.886505 TCGTTAAGAAACTGCCATTTGGT 59.113 39.130 0.00 0.00 33.72 3.67
535 607 4.684623 CTGCCATTTGGTAGGGGG 57.315 61.111 6.79 0.00 43.16 5.40
536 608 1.697297 CTGCCATTTGGTAGGGGGT 59.303 57.895 6.79 0.00 43.16 4.95
547 626 1.767088 GGTAGGGGGTTACTCATCACC 59.233 57.143 0.00 0.00 0.00 4.02
552 631 2.884894 GGGTTACTCATCACCCGTAG 57.115 55.000 0.00 0.00 43.54 3.51
582 661 3.626680 TTTCAGAGCGGAGGCGTCG 62.627 63.158 0.00 0.00 46.35 5.12
625 704 2.736719 CGACCAAATCTCTCGCTGTCAT 60.737 50.000 0.00 0.00 0.00 3.06
659 738 1.339151 ACAAGGGCGGAAGATGAAGAC 60.339 52.381 0.00 0.00 0.00 3.01
712 806 7.241376 CCGACATGACCTTTGATTAAGTTAAC 58.759 38.462 0.00 0.00 31.56 2.01
727 821 4.357918 AGTTAACTCTGCACCATGAACT 57.642 40.909 1.12 0.00 0.00 3.01
728 822 5.483685 AGTTAACTCTGCACCATGAACTA 57.516 39.130 1.12 0.00 0.00 2.24
729 823 5.482908 AGTTAACTCTGCACCATGAACTAG 58.517 41.667 1.12 0.00 0.00 2.57
800 907 7.878127 AGTCTCGATTCCAAGAAGAATAACAAA 59.122 33.333 0.00 0.00 36.60 2.83
801 908 8.669243 GTCTCGATTCCAAGAAGAATAACAAAT 58.331 33.333 0.00 0.00 36.60 2.32
803 910 9.495754 CTCGATTCCAAGAAGAATAACAAATTC 57.504 33.333 0.00 0.00 36.60 2.17
806 913 8.992835 ATTCCAAGAAGAATAACAAATTCTGC 57.007 30.769 1.23 0.00 38.29 4.26
807 914 7.765695 TCCAAGAAGAATAACAAATTCTGCT 57.234 32.000 2.89 2.89 43.94 4.24
846 992 3.980646 TGAAAAACATTCCGGTCACTG 57.019 42.857 0.00 0.00 0.00 3.66
891 1041 1.198637 GGTGCAGAGAAAGATGTGTGC 59.801 52.381 0.00 0.00 39.29 4.57
915 1072 0.182537 TCTTTCCAGTGGTGGTGGTG 59.817 55.000 9.54 0.00 45.28 4.17
917 1074 1.576368 TTTCCAGTGGTGGTGGTGGT 61.576 55.000 9.54 0.00 45.28 4.16
918 1075 2.203337 CCAGTGGTGGTGGTGGTG 60.203 66.667 0.00 0.00 39.30 4.17
919 1076 2.203337 CAGTGGTGGTGGTGGTGG 60.203 66.667 0.00 0.00 0.00 4.61
920 1077 2.694616 AGTGGTGGTGGTGGTGGT 60.695 61.111 0.00 0.00 0.00 4.16
921 1078 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.00 0.00 4.17
922 1079 4.514585 TGGTGGTGGTGGTGGTGC 62.515 66.667 0.00 0.00 0.00 5.01
933 1090 0.620410 TGGTGGTGCTAGGGCTGTAT 60.620 55.000 0.00 0.00 39.59 2.29
968 1129 5.118642 TCGACTGAGATAATCATGCAGAG 57.881 43.478 0.00 0.00 37.28 3.35
1007 1170 4.347813 CGTTTGAATCACGTCACCTTTTT 58.652 39.130 0.00 0.00 32.80 1.94
1058 1235 6.538742 CCACGATATGATTAGTCCAAAGTTGT 59.461 38.462 0.00 0.00 0.00 3.32
1059 1236 7.709182 CCACGATATGATTAGTCCAAAGTTGTA 59.291 37.037 0.00 0.00 0.00 2.41
1060 1237 8.540492 CACGATATGATTAGTCCAAAGTTGTAC 58.460 37.037 0.00 0.00 0.00 2.90
1095 1278 1.909700 CTTAGCTTGGCCACCAGAAA 58.090 50.000 3.88 0.00 33.81 2.52
1139 1322 1.837439 CCCTGCTAGAATACACCCACA 59.163 52.381 0.00 0.00 0.00 4.17
1143 1326 2.635427 TGCTAGAATACACCCACACACA 59.365 45.455 0.00 0.00 0.00 3.72
1145 1328 3.306780 GCTAGAATACACCCACACACACT 60.307 47.826 0.00 0.00 0.00 3.55
1148 1331 2.839486 ATACACCCACACACACTCAG 57.161 50.000 0.00 0.00 0.00 3.35
1149 1332 0.105964 TACACCCACACACACTCAGC 59.894 55.000 0.00 0.00 0.00 4.26
1150 1333 2.108976 ACCCACACACACTCAGCG 59.891 61.111 0.00 0.00 0.00 5.18
1151 1334 2.666190 CCCACACACACTCAGCGG 60.666 66.667 0.00 0.00 0.00 5.52
1152 1335 2.421314 CCACACACACTCAGCGGA 59.579 61.111 0.00 0.00 0.00 5.54
1156 1339 0.464036 ACACACACTCAGCGGAAGAA 59.536 50.000 0.00 0.00 0.00 2.52
1157 1340 1.143305 CACACACTCAGCGGAAGAAG 58.857 55.000 0.00 0.00 0.00 2.85
1159 1342 1.620819 ACACACTCAGCGGAAGAAGAT 59.379 47.619 0.00 0.00 0.00 2.40
1160 1343 1.998315 CACACTCAGCGGAAGAAGATG 59.002 52.381 0.00 0.00 0.00 2.90
1161 1344 1.895798 ACACTCAGCGGAAGAAGATGA 59.104 47.619 0.00 0.00 0.00 2.92
1164 1347 3.748048 CACTCAGCGGAAGAAGATGAAAA 59.252 43.478 0.00 0.00 0.00 2.29
1179 1362 5.241662 AGATGAAAAGAAAAGGAGACGAGG 58.758 41.667 0.00 0.00 0.00 4.63
1293 1486 1.354368 ACACAAATTCCCCACCGAGAT 59.646 47.619 0.00 0.00 0.00 2.75
1410 1621 2.799562 GCGAGCTTTTCTTGCTTTTGGT 60.800 45.455 0.00 0.00 46.54 3.67
2067 2284 4.415150 GGGCTAGCAGCTGCACCA 62.415 66.667 38.24 22.20 45.16 4.17
2076 2299 3.499737 GCTGCACCATTCGACCGG 61.500 66.667 0.00 0.00 0.00 5.28
2094 2317 2.123468 TCGATCCATGGAGCCGGA 60.123 61.111 28.18 18.01 35.27 5.14
2095 2318 2.029666 CGATCCATGGAGCCGGAC 59.970 66.667 23.90 7.86 33.05 4.79
2096 2319 2.029666 GATCCATGGAGCCGGACG 59.970 66.667 19.66 0.00 33.05 4.79
2097 2320 2.764128 ATCCATGGAGCCGGACGT 60.764 61.111 21.33 0.00 33.05 4.34
2114 2341 4.680237 TTGAGCCGCCGTGGTGAG 62.680 66.667 0.00 0.00 41.21 3.51
2231 2470 0.755686 AAGCAGGTCGATCCATCTCC 59.244 55.000 0.00 0.00 39.02 3.71
2337 2584 0.516877 TGTACGTACGTTGGGTCTCG 59.483 55.000 27.92 0.00 34.06 4.04
2338 2585 0.517316 GTACGTACGTTGGGTCTCGT 59.483 55.000 27.92 0.00 42.82 4.18
2339 2586 1.069227 GTACGTACGTTGGGTCTCGTT 60.069 52.381 27.92 0.00 40.70 3.85
2493 2753 6.166984 TCCATGTCTCATCTTCTTGGTATC 57.833 41.667 0.00 0.00 0.00 2.24
2494 2754 5.901853 TCCATGTCTCATCTTCTTGGTATCT 59.098 40.000 0.00 0.00 0.00 1.98
2495 2755 7.069344 TCCATGTCTCATCTTCTTGGTATCTA 58.931 38.462 0.00 0.00 0.00 1.98
2496 2756 7.732140 TCCATGTCTCATCTTCTTGGTATCTAT 59.268 37.037 0.00 0.00 0.00 1.98
2581 2873 3.181507 CCGATCAATGTGTGCAACCTAAG 60.182 47.826 0.00 0.00 34.36 2.18
2607 2899 6.930068 ACCTCTGTGTTAGGTACATTAACT 57.070 37.500 15.99 0.00 45.69 2.24
2617 2909 7.645058 TTAGGTACATTAACTAACTAGCCGT 57.355 36.000 0.00 0.00 33.25 5.68
2618 2910 6.141560 AGGTACATTAACTAACTAGCCGTC 57.858 41.667 0.00 0.00 0.00 4.79
2631 2937 2.228138 AGCCGTCGTTAACACTTTGA 57.772 45.000 6.39 0.00 0.00 2.69
2632 2938 2.132762 AGCCGTCGTTAACACTTTGAG 58.867 47.619 6.39 0.00 0.00 3.02
2633 2939 1.398071 GCCGTCGTTAACACTTTGAGC 60.398 52.381 6.39 0.00 0.00 4.26
2634 2940 2.132762 CCGTCGTTAACACTTTGAGCT 58.867 47.619 6.39 0.00 0.00 4.09
2681 2999 1.227999 GGTACATGCACACACACGCT 61.228 55.000 0.00 0.00 0.00 5.07
2738 3056 4.955811 TCCATCCACGAACAAGCTATAT 57.044 40.909 0.00 0.00 0.00 0.86
2739 3057 6.605471 ATCCATCCACGAACAAGCTATATA 57.395 37.500 0.00 0.00 0.00 0.86
2740 3058 6.605471 TCCATCCACGAACAAGCTATATAT 57.395 37.500 0.00 0.00 0.00 0.86
2741 3059 6.398095 TCCATCCACGAACAAGCTATATATG 58.602 40.000 0.00 0.00 0.00 1.78
3006 3354 1.709147 GCTGGTGGATGATCACGCAC 61.709 60.000 0.00 3.52 38.46 5.34
3047 3399 0.925466 GGCAAATCATTGATGCGTGC 59.075 50.000 16.32 16.32 40.94 5.34
3067 3424 2.447250 CGCAGGTATGTACAGTGTACG 58.553 52.381 24.61 12.66 0.00 3.67
3068 3425 2.096335 CGCAGGTATGTACAGTGTACGA 59.904 50.000 24.61 14.61 0.00 3.43
3074 3432 7.254898 GCAGGTATGTACAGTGTACGAGTATAA 60.255 40.741 24.61 8.99 0.00 0.98
3107 3465 1.405526 GGAGTGACGGAAGCTTGCATA 60.406 52.381 18.65 0.19 0.00 3.14
3111 3473 2.484264 GTGACGGAAGCTTGCATAACTT 59.516 45.455 18.65 0.00 0.00 2.66
3113 3475 2.742053 GACGGAAGCTTGCATAACTTCA 59.258 45.455 18.65 0.00 41.26 3.02
3117 3479 4.676546 GGAAGCTTGCATAACTTCAATCC 58.323 43.478 13.73 0.00 41.26 3.01
3119 3481 5.163478 GGAAGCTTGCATAACTTCAATCCAT 60.163 40.000 13.73 0.00 41.26 3.41
3134 3496 1.452651 CCATCTGCCACGCTGGATT 60.453 57.895 8.04 0.00 40.96 3.01
3136 3498 1.452651 ATCTGCCACGCTGGATTGG 60.453 57.895 8.04 0.00 40.96 3.16
3154 3516 3.432517 GTGAGCTGCACAGAGTAGG 57.567 57.895 1.02 0.00 46.91 3.18
3155 3517 0.108424 GTGAGCTGCACAGAGTAGGG 60.108 60.000 1.02 0.00 46.91 3.53
3157 3519 1.118838 GAGCTGCACAGAGTAGGGAT 58.881 55.000 1.02 0.00 0.00 3.85
3160 3522 2.307098 AGCTGCACAGAGTAGGGATTTT 59.693 45.455 1.02 0.00 0.00 1.82
3163 3525 4.074970 CTGCACAGAGTAGGGATTTTGTT 58.925 43.478 0.00 0.00 0.00 2.83
3164 3526 4.072131 TGCACAGAGTAGGGATTTTGTTC 58.928 43.478 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.876789 ACTTTTGTTTTTGTTAAGACCCCAAG 59.123 34.615 0.00 0.00 0.00 3.61
1 2 6.770542 ACTTTTGTTTTTGTTAAGACCCCAA 58.229 32.000 0.00 0.00 0.00 4.12
2 3 6.361768 ACTTTTGTTTTTGTTAAGACCCCA 57.638 33.333 0.00 0.00 0.00 4.96
3 4 8.036575 AGTTACTTTTGTTTTTGTTAAGACCCC 58.963 33.333 0.00 0.00 0.00 4.95
57 58 5.586243 CAGGCAGTTAGTACTAGTAACCGTA 59.414 44.000 3.61 0.00 35.19 4.02
69 70 5.450550 CGATCTGATTCACAGGCAGTTAGTA 60.451 44.000 0.00 0.00 45.76 1.82
71 72 3.801050 CGATCTGATTCACAGGCAGTTAG 59.199 47.826 0.00 0.00 45.76 2.34
72 73 3.785486 CGATCTGATTCACAGGCAGTTA 58.215 45.455 0.00 0.00 45.76 2.24
74 75 1.741732 GCGATCTGATTCACAGGCAGT 60.742 52.381 0.00 0.00 45.76 4.40
75 76 0.935898 GCGATCTGATTCACAGGCAG 59.064 55.000 0.00 0.00 45.76 4.85
76 77 0.249955 TGCGATCTGATTCACAGGCA 59.750 50.000 0.00 0.00 45.76 4.75
77 78 0.654683 GTGCGATCTGATTCACAGGC 59.345 55.000 14.85 0.00 45.76 4.85
97 98 4.607293 TTCTTCTGAAGCTGAAGCAGTA 57.393 40.909 12.54 0.00 45.16 2.74
100 101 3.544684 TGTTTCTTCTGAAGCTGAAGCA 58.455 40.909 12.54 7.72 45.16 3.91
102 103 5.936686 TCATGTTTCTTCTGAAGCTGAAG 57.063 39.130 12.54 6.04 39.62 3.02
108 109 9.856488 ATTGATTCATTCATGTTTCTTCTGAAG 57.144 29.630 11.18 11.18 33.34 3.02
112 113 7.608153 TGCATTGATTCATTCATGTTTCTTCT 58.392 30.769 0.00 0.00 33.34 2.85
131 136 6.568081 GCTCCTATTCATTTCTAGCTGCATTG 60.568 42.308 1.02 0.00 0.00 2.82
141 146 5.854010 TCGTAGTGCTCCTATTCATTTCT 57.146 39.130 0.00 0.00 0.00 2.52
158 163 5.465724 GCTTTGATGGGGTACTATTTCGTAG 59.534 44.000 0.00 0.00 36.44 3.51
160 165 4.196971 GCTTTGATGGGGTACTATTTCGT 58.803 43.478 0.00 0.00 0.00 3.85
162 167 6.524101 TTTGCTTTGATGGGGTACTATTTC 57.476 37.500 0.00 0.00 0.00 2.17
163 168 7.494922 AATTTGCTTTGATGGGGTACTATTT 57.505 32.000 0.00 0.00 0.00 1.40
166 171 6.126409 CCTAATTTGCTTTGATGGGGTACTA 58.874 40.000 0.00 0.00 0.00 1.82
168 173 4.709886 ACCTAATTTGCTTTGATGGGGTAC 59.290 41.667 0.00 0.00 0.00 3.34
169 174 4.709397 CACCTAATTTGCTTTGATGGGGTA 59.291 41.667 0.00 0.00 0.00 3.69
171 176 3.679639 GCACCTAATTTGCTTTGATGGGG 60.680 47.826 0.00 0.00 37.00 4.96
172 177 3.524541 GCACCTAATTTGCTTTGATGGG 58.475 45.455 0.00 0.00 37.00 4.00
211 216 2.159014 GGCCAAACGGAAAGGTTTCTTT 60.159 45.455 0.00 0.00 45.09 2.52
212 217 1.411246 GGCCAAACGGAAAGGTTTCTT 59.589 47.619 0.00 0.00 38.01 2.52
213 218 1.037493 GGCCAAACGGAAAGGTTTCT 58.963 50.000 0.00 0.00 38.01 2.52
233 238 3.554692 CGCTTCGGTGATGACGCC 61.555 66.667 0.00 0.00 42.65 5.68
235 240 1.006825 TTGACGCTTCGGTGATGACG 61.007 55.000 0.00 0.00 0.00 4.35
236 241 0.716108 CTTGACGCTTCGGTGATGAC 59.284 55.000 0.00 0.00 0.00 3.06
237 242 0.389817 CCTTGACGCTTCGGTGATGA 60.390 55.000 0.00 0.00 0.00 2.92
238 243 1.970917 GCCTTGACGCTTCGGTGATG 61.971 60.000 0.00 0.00 0.00 3.07
239 244 1.741770 GCCTTGACGCTTCGGTGAT 60.742 57.895 0.00 0.00 0.00 3.06
240 245 2.357034 GCCTTGACGCTTCGGTGA 60.357 61.111 0.00 0.00 0.00 4.02
241 246 3.423154 GGCCTTGACGCTTCGGTG 61.423 66.667 0.00 0.00 0.00 4.94
242 247 3.591254 GAGGCCTTGACGCTTCGGT 62.591 63.158 6.77 0.00 0.00 4.69
243 248 2.815647 GAGGCCTTGACGCTTCGG 60.816 66.667 6.77 0.00 0.00 4.30
244 249 1.667830 TTGAGGCCTTGACGCTTCG 60.668 57.895 6.77 0.00 37.66 3.79
245 250 1.578206 GGTTGAGGCCTTGACGCTTC 61.578 60.000 6.77 0.00 35.53 3.86
246 251 1.600916 GGTTGAGGCCTTGACGCTT 60.601 57.895 6.77 0.00 0.00 4.68
247 252 2.032681 GGTTGAGGCCTTGACGCT 59.967 61.111 6.77 0.00 0.00 5.07
248 253 1.452145 TTTGGTTGAGGCCTTGACGC 61.452 55.000 6.77 4.07 0.00 5.19
249 254 1.200020 GATTTGGTTGAGGCCTTGACG 59.800 52.381 6.77 0.00 0.00 4.35
250 255 2.489722 GAGATTTGGTTGAGGCCTTGAC 59.510 50.000 6.77 8.97 0.00 3.18
251 256 2.376518 AGAGATTTGGTTGAGGCCTTGA 59.623 45.455 6.77 0.00 0.00 3.02
252 257 2.751806 GAGAGATTTGGTTGAGGCCTTG 59.248 50.000 6.77 0.00 0.00 3.61
253 258 2.616510 CGAGAGATTTGGTTGAGGCCTT 60.617 50.000 6.77 0.00 0.00 4.35
254 259 1.065854 CGAGAGATTTGGTTGAGGCCT 60.066 52.381 3.86 3.86 0.00 5.19
255 260 1.373570 CGAGAGATTTGGTTGAGGCC 58.626 55.000 0.00 0.00 0.00 5.19
256 261 0.729690 GCGAGAGATTTGGTTGAGGC 59.270 55.000 0.00 0.00 0.00 4.70
257 262 1.339055 TGGCGAGAGATTTGGTTGAGG 60.339 52.381 0.00 0.00 0.00 3.86
258 263 2.099141 TGGCGAGAGATTTGGTTGAG 57.901 50.000 0.00 0.00 0.00 3.02
259 264 2.027285 TGATGGCGAGAGATTTGGTTGA 60.027 45.455 0.00 0.00 0.00 3.18
260 265 2.096496 GTGATGGCGAGAGATTTGGTTG 59.904 50.000 0.00 0.00 0.00 3.77
261 266 2.359900 GTGATGGCGAGAGATTTGGTT 58.640 47.619 0.00 0.00 0.00 3.67
262 267 1.407437 GGTGATGGCGAGAGATTTGGT 60.407 52.381 0.00 0.00 0.00 3.67
263 268 1.303309 GGTGATGGCGAGAGATTTGG 58.697 55.000 0.00 0.00 0.00 3.28
264 269 2.028420 TGGTGATGGCGAGAGATTTG 57.972 50.000 0.00 0.00 0.00 2.32
265 270 2.636830 CTTGGTGATGGCGAGAGATTT 58.363 47.619 0.00 0.00 0.00 2.17
266 271 1.134280 CCTTGGTGATGGCGAGAGATT 60.134 52.381 0.00 0.00 0.00 2.40
267 272 0.467384 CCTTGGTGATGGCGAGAGAT 59.533 55.000 0.00 0.00 0.00 2.75
268 273 0.614697 TCCTTGGTGATGGCGAGAGA 60.615 55.000 0.00 0.00 0.00 3.10
269 274 0.250234 TTCCTTGGTGATGGCGAGAG 59.750 55.000 0.00 0.00 0.00 3.20
270 275 0.911769 ATTCCTTGGTGATGGCGAGA 59.088 50.000 0.00 0.00 0.00 4.04
271 276 1.755179 AATTCCTTGGTGATGGCGAG 58.245 50.000 0.00 0.00 0.00 5.03
272 277 2.639065 GTAATTCCTTGGTGATGGCGA 58.361 47.619 0.00 0.00 0.00 5.54
273 278 1.676006 GGTAATTCCTTGGTGATGGCG 59.324 52.381 0.00 0.00 0.00 5.69
274 279 2.031870 GGGTAATTCCTTGGTGATGGC 58.968 52.381 0.00 0.00 36.25 4.40
275 280 2.297701 CGGGTAATTCCTTGGTGATGG 58.702 52.381 0.00 0.00 36.25 3.51
276 281 2.297701 CCGGGTAATTCCTTGGTGATG 58.702 52.381 0.00 0.00 36.25 3.07
277 282 1.409661 GCCGGGTAATTCCTTGGTGAT 60.410 52.381 2.18 0.00 35.29 3.06
278 283 0.034863 GCCGGGTAATTCCTTGGTGA 60.035 55.000 2.18 0.00 35.29 4.02
279 284 0.322997 TGCCGGGTAATTCCTTGGTG 60.323 55.000 2.18 0.00 35.29 4.17
280 285 0.034477 CTGCCGGGTAATTCCTTGGT 60.034 55.000 2.18 0.00 35.29 3.67
281 286 0.254747 TCTGCCGGGTAATTCCTTGG 59.745 55.000 2.18 0.00 36.25 3.61
282 287 2.017049 CTTCTGCCGGGTAATTCCTTG 58.983 52.381 2.18 0.00 36.25 3.61
283 288 1.913419 TCTTCTGCCGGGTAATTCCTT 59.087 47.619 2.18 0.00 36.25 3.36
284 289 1.580059 TCTTCTGCCGGGTAATTCCT 58.420 50.000 2.18 0.00 36.25 3.36
285 290 2.158813 TCATCTTCTGCCGGGTAATTCC 60.159 50.000 2.18 0.00 0.00 3.01
286 291 3.194005 TCATCTTCTGCCGGGTAATTC 57.806 47.619 2.18 0.00 0.00 2.17
287 292 3.199946 TCTTCATCTTCTGCCGGGTAATT 59.800 43.478 2.18 0.00 0.00 1.40
288 293 2.771943 TCTTCATCTTCTGCCGGGTAAT 59.228 45.455 2.18 0.00 0.00 1.89
289 294 2.184533 TCTTCATCTTCTGCCGGGTAA 58.815 47.619 2.18 0.00 0.00 2.85
290 295 1.860641 TCTTCATCTTCTGCCGGGTA 58.139 50.000 2.18 0.00 0.00 3.69
291 296 1.134280 CATCTTCATCTTCTGCCGGGT 60.134 52.381 2.18 0.00 0.00 5.28
292 297 1.590932 CATCTTCATCTTCTGCCGGG 58.409 55.000 2.18 0.00 0.00 5.73
293 298 1.134280 ACCATCTTCATCTTCTGCCGG 60.134 52.381 0.00 0.00 0.00 6.13
294 299 2.322355 ACCATCTTCATCTTCTGCCG 57.678 50.000 0.00 0.00 0.00 5.69
295 300 3.563390 GCTTACCATCTTCATCTTCTGCC 59.437 47.826 0.00 0.00 0.00 4.85
296 301 3.247173 CGCTTACCATCTTCATCTTCTGC 59.753 47.826 0.00 0.00 0.00 4.26
297 302 3.806521 CCGCTTACCATCTTCATCTTCTG 59.193 47.826 0.00 0.00 0.00 3.02
298 303 3.706594 TCCGCTTACCATCTTCATCTTCT 59.293 43.478 0.00 0.00 0.00 2.85
299 304 3.804873 GTCCGCTTACCATCTTCATCTTC 59.195 47.826 0.00 0.00 0.00 2.87
300 305 3.738281 CGTCCGCTTACCATCTTCATCTT 60.738 47.826 0.00 0.00 0.00 2.40
301 306 2.223829 CGTCCGCTTACCATCTTCATCT 60.224 50.000 0.00 0.00 0.00 2.90
302 307 2.128035 CGTCCGCTTACCATCTTCATC 58.872 52.381 0.00 0.00 0.00 2.92
303 308 1.202533 CCGTCCGCTTACCATCTTCAT 60.203 52.381 0.00 0.00 0.00 2.57
304 309 0.174845 CCGTCCGCTTACCATCTTCA 59.825 55.000 0.00 0.00 0.00 3.02
305 310 0.529992 CCCGTCCGCTTACCATCTTC 60.530 60.000 0.00 0.00 0.00 2.87
306 311 1.262640 ACCCGTCCGCTTACCATCTT 61.263 55.000 0.00 0.00 0.00 2.40
307 312 1.673808 GACCCGTCCGCTTACCATCT 61.674 60.000 0.00 0.00 0.00 2.90
308 313 1.227176 GACCCGTCCGCTTACCATC 60.227 63.158 0.00 0.00 0.00 3.51
309 314 0.396139 TAGACCCGTCCGCTTACCAT 60.396 55.000 0.00 0.00 0.00 3.55
310 315 1.001020 TAGACCCGTCCGCTTACCA 60.001 57.895 0.00 0.00 0.00 3.25
311 316 1.435105 GTAGACCCGTCCGCTTACC 59.565 63.158 0.00 0.00 0.00 2.85
312 317 1.435105 GGTAGACCCGTCCGCTTAC 59.565 63.158 0.00 0.00 0.00 2.34
313 318 3.924507 GGTAGACCCGTCCGCTTA 58.075 61.111 0.00 0.00 0.00 3.09
322 327 1.226888 GTGATGACGCGGTAGACCC 60.227 63.158 12.47 0.00 0.00 4.46
323 328 0.525668 CAGTGATGACGCGGTAGACC 60.526 60.000 12.47 0.00 0.00 3.85
324 329 0.450583 TCAGTGATGACGCGGTAGAC 59.549 55.000 12.47 0.00 0.00 2.59
325 330 1.132453 CTTCAGTGATGACGCGGTAGA 59.868 52.381 12.47 0.00 0.00 2.59
326 331 1.550065 CTTCAGTGATGACGCGGTAG 58.450 55.000 12.47 0.00 0.00 3.18
327 332 0.457853 GCTTCAGTGATGACGCGGTA 60.458 55.000 12.47 0.00 0.00 4.02
328 333 1.738099 GCTTCAGTGATGACGCGGT 60.738 57.895 12.47 0.00 0.00 5.68
329 334 3.084579 GCTTCAGTGATGACGCGG 58.915 61.111 12.47 0.00 0.00 6.46
330 335 2.691522 CGCTTCAGTGATGACGCG 59.308 61.111 13.42 13.42 46.67 6.01
331 336 1.008875 TGACGCTTCAGTGATGACGC 61.009 55.000 10.08 9.12 0.00 5.19
332 337 1.388093 CTTGACGCTTCAGTGATGACG 59.612 52.381 10.08 13.59 31.71 4.35
333 338 1.728971 CCTTGACGCTTCAGTGATGAC 59.271 52.381 10.08 1.21 31.71 3.06
334 339 1.941209 GCCTTGACGCTTCAGTGATGA 60.941 52.381 10.08 0.00 31.71 2.92
335 340 0.445436 GCCTTGACGCTTCAGTGATG 59.555 55.000 0.00 0.00 31.71 3.07
362 367 2.223923 CCTCGGTGATGGTGAGAGAATC 60.224 54.545 0.00 0.00 31.31 2.52
380 390 1.301677 CTTCTGCCGGTTTGCTCCTC 61.302 60.000 1.90 0.00 0.00 3.71
385 395 0.881118 TTCATCTTCTGCCGGTTTGC 59.119 50.000 1.90 0.00 0.00 3.68
415 425 7.660208 ACGCTGAATATTTATTTATTCCTCGGT 59.340 33.333 14.04 3.09 37.65 4.69
417 427 8.708742 TGACGCTGAATATTTATTTATTCCTCG 58.291 33.333 0.00 10.69 37.65 4.63
419 429 9.003658 CCTGACGCTGAATATTTATTTATTCCT 57.996 33.333 0.00 0.00 37.65 3.36
422 432 7.448469 AGGCCTGACGCTGAATATTTATTTATT 59.552 33.333 3.11 0.00 37.74 1.40
423 433 6.942576 AGGCCTGACGCTGAATATTTATTTAT 59.057 34.615 3.11 0.00 37.74 1.40
428 438 3.728845 GAGGCCTGACGCTGAATATTTA 58.271 45.455 12.00 0.00 37.74 1.40
430 440 1.539065 CGAGGCCTGACGCTGAATATT 60.539 52.381 12.00 0.00 37.74 1.28
432 442 1.035385 TCGAGGCCTGACGCTGAATA 61.035 55.000 12.00 0.00 37.74 1.75
433 443 2.185350 CGAGGCCTGACGCTGAAT 59.815 61.111 12.00 0.00 37.74 2.57
434 444 2.989253 TCGAGGCCTGACGCTGAA 60.989 61.111 12.00 0.00 37.74 3.02
435 445 3.749064 GTCGAGGCCTGACGCTGA 61.749 66.667 12.00 0.00 37.74 4.26
436 446 4.803426 GGTCGAGGCCTGACGCTG 62.803 72.222 12.00 0.00 37.22 5.18
438 448 3.665675 ATTGGTCGAGGCCTGACGC 62.666 63.158 12.00 12.38 37.22 5.19
439 449 1.079127 AATTGGTCGAGGCCTGACG 60.079 57.895 12.00 9.25 37.22 4.35
440 450 1.648467 GCAATTGGTCGAGGCCTGAC 61.648 60.000 12.00 18.06 35.60 3.51
443 453 1.377725 CAGCAATTGGTCGAGGCCT 60.378 57.895 3.86 3.86 0.00 5.19
444 454 3.056313 GCAGCAATTGGTCGAGGCC 62.056 63.158 7.29 0.00 0.00 5.19
445 455 2.334946 TGCAGCAATTGGTCGAGGC 61.335 57.895 7.29 8.87 0.00 4.70
446 456 1.236616 TGTGCAGCAATTGGTCGAGG 61.237 55.000 7.29 0.00 0.00 4.63
447 457 0.592637 TTGTGCAGCAATTGGTCGAG 59.407 50.000 7.29 0.00 31.07 4.04
450 460 4.114794 GGATTATTGTGCAGCAATTGGTC 58.885 43.478 7.29 3.83 44.82 4.02
451 461 3.770933 AGGATTATTGTGCAGCAATTGGT 59.229 39.130 16.19 3.82 44.82 3.67
452 462 4.098960 AGAGGATTATTGTGCAGCAATTGG 59.901 41.667 16.19 0.00 44.82 3.16
453 463 5.041287 CAGAGGATTATTGTGCAGCAATTG 58.959 41.667 16.19 0.00 44.82 2.32
456 466 3.689347 ACAGAGGATTATTGTGCAGCAA 58.311 40.909 0.00 4.56 41.89 3.91
457 467 3.354948 ACAGAGGATTATTGTGCAGCA 57.645 42.857 0.00 0.00 0.00 4.41
458 468 5.818136 TTTACAGAGGATTATTGTGCAGC 57.182 39.130 0.00 0.00 0.00 5.25
466 476 5.667626 TCTGCTCCCTTTTACAGAGGATTAT 59.332 40.000 0.00 0.00 36.33 1.28
471 481 3.604582 CTTCTGCTCCCTTTTACAGAGG 58.395 50.000 0.00 0.00 40.08 3.69
472 482 3.006247 GCTTCTGCTCCCTTTTACAGAG 58.994 50.000 0.00 0.00 40.08 3.35
476 486 3.507622 ACATTGCTTCTGCTCCCTTTTAC 59.492 43.478 0.00 0.00 40.48 2.01
477 487 3.766545 ACATTGCTTCTGCTCCCTTTTA 58.233 40.909 0.00 0.00 40.48 1.52
478 488 2.601905 ACATTGCTTCTGCTCCCTTTT 58.398 42.857 0.00 0.00 40.48 2.27
479 489 2.299326 ACATTGCTTCTGCTCCCTTT 57.701 45.000 0.00 0.00 40.48 3.11
480 490 2.307098 AGTACATTGCTTCTGCTCCCTT 59.693 45.455 0.00 0.00 40.48 3.95
481 491 1.912043 AGTACATTGCTTCTGCTCCCT 59.088 47.619 0.00 0.00 40.48 4.20
482 492 2.409948 AGTACATTGCTTCTGCTCCC 57.590 50.000 0.00 0.00 40.48 4.30
489 499 7.754027 TCTTAACGAGTAGAAGTACATTGCTTC 59.246 37.037 0.00 0.00 41.78 3.86
492 502 7.807687 TTCTTAACGAGTAGAAGTACATTGC 57.192 36.000 0.00 0.00 0.00 3.56
493 503 9.408069 AGTTTCTTAACGAGTAGAAGTACATTG 57.592 33.333 0.00 0.00 39.31 2.82
494 504 9.408069 CAGTTTCTTAACGAGTAGAAGTACATT 57.592 33.333 0.00 0.00 39.31 2.71
496 506 6.860023 GCAGTTTCTTAACGAGTAGAAGTACA 59.140 38.462 0.00 0.00 39.31 2.90
497 507 6.307558 GGCAGTTTCTTAACGAGTAGAAGTAC 59.692 42.308 0.00 0.00 39.31 2.73
499 509 5.221382 TGGCAGTTTCTTAACGAGTAGAAGT 60.221 40.000 0.00 0.00 39.31 3.01
500 510 5.227908 TGGCAGTTTCTTAACGAGTAGAAG 58.772 41.667 0.00 0.00 39.31 2.85
501 511 5.204409 TGGCAGTTTCTTAACGAGTAGAA 57.796 39.130 0.00 0.00 39.31 2.10
502 512 4.859304 TGGCAGTTTCTTAACGAGTAGA 57.141 40.909 0.00 0.00 39.31 2.59
506 516 4.023193 ACCAAATGGCAGTTTCTTAACGAG 60.023 41.667 0.00 0.00 37.80 4.18
507 517 3.886505 ACCAAATGGCAGTTTCTTAACGA 59.113 39.130 0.00 0.00 37.80 3.85
509 519 5.336451 CCCTACCAAATGGCAGTTTCTTAAC 60.336 44.000 0.00 0.00 39.32 2.01
535 607 2.361438 CTCCCTACGGGTGATGAGTAAC 59.639 54.545 0.00 0.00 44.74 2.50
536 608 2.662866 CTCCCTACGGGTGATGAGTAA 58.337 52.381 0.00 0.00 44.74 2.24
547 626 0.109132 AAAACGTACGCTCCCTACGG 60.109 55.000 16.72 0.00 41.08 4.02
552 631 1.347320 CTCTGAAAACGTACGCTCCC 58.653 55.000 16.72 3.24 0.00 4.30
560 639 1.668151 GCCTCCGCTCTGAAAACGT 60.668 57.895 0.00 0.00 0.00 3.99
582 661 3.414700 CTTGACGCGTCAGTGGGC 61.415 66.667 37.06 13.33 41.13 5.36
625 704 1.301423 CCTTGTTTTTCCGTCGGTGA 58.699 50.000 11.88 0.00 0.00 4.02
659 738 1.219522 GGGTGTTGAGGACGTTGTCG 61.220 60.000 0.00 0.00 43.34 4.35
668 762 1.818674 GGCAATTAGTGGGTGTTGAGG 59.181 52.381 0.00 0.00 0.00 3.86
674 768 1.401552 CATGTCGGCAATTAGTGGGTG 59.598 52.381 0.00 0.00 0.00 4.61
712 806 2.687700 AGCTAGTTCATGGTGCAGAG 57.312 50.000 0.00 0.00 0.00 3.35
727 821 1.153107 TACGTGGCGCCTCTAGCTA 60.153 57.895 29.70 1.01 40.39 3.32
728 822 2.439701 TACGTGGCGCCTCTAGCT 60.440 61.111 29.70 8.86 40.39 3.32
729 823 2.026301 CTACGTGGCGCCTCTAGC 59.974 66.667 29.70 11.37 38.52 3.42
800 907 3.851458 TGGTGCATCTATCAGCAGAAT 57.149 42.857 0.00 0.00 42.14 2.40
801 908 3.198417 TCTTGGTGCATCTATCAGCAGAA 59.802 43.478 0.00 0.00 42.14 3.02
803 910 3.189618 TCTTGGTGCATCTATCAGCAG 57.810 47.619 0.00 0.00 42.14 4.24
806 913 6.688637 TTCATTTCTTGGTGCATCTATCAG 57.311 37.500 0.00 0.00 0.00 2.90
807 914 7.465353 TTTTCATTTCTTGGTGCATCTATCA 57.535 32.000 0.00 0.00 0.00 2.15
815 960 5.333263 CGGAATGTTTTTCATTTCTTGGTGC 60.333 40.000 0.00 0.00 45.49 5.01
846 992 2.342910 TTTTCTAGTCGACCGCTGAC 57.657 50.000 13.01 0.00 36.60 3.51
891 1041 2.880890 CACCACCACTGGAAAGAAAGAG 59.119 50.000 0.71 0.00 40.55 2.85
915 1072 0.179045 CATACAGCCCTAGCACCACC 60.179 60.000 0.00 0.00 43.56 4.61
917 1074 0.620410 ACCATACAGCCCTAGCACCA 60.620 55.000 0.00 0.00 43.56 4.17
918 1075 1.344763 CTACCATACAGCCCTAGCACC 59.655 57.143 0.00 0.00 43.56 5.01
919 1076 1.344763 CCTACCATACAGCCCTAGCAC 59.655 57.143 0.00 0.00 43.56 4.40
920 1077 1.219469 TCCTACCATACAGCCCTAGCA 59.781 52.381 0.00 0.00 43.56 3.49
921 1078 2.011122 TCCTACCATACAGCCCTAGC 57.989 55.000 0.00 0.00 40.32 3.42
922 1079 2.755655 CGATCCTACCATACAGCCCTAG 59.244 54.545 0.00 0.00 0.00 3.02
933 1090 1.208776 TCAGTCGAGTCGATCCTACCA 59.791 52.381 19.75 0.00 38.42 3.25
968 1129 1.739067 ACGGCTCCAACTTCTTATGC 58.261 50.000 0.00 0.00 0.00 3.14
971 1132 3.478857 TCAAACGGCTCCAACTTCTTA 57.521 42.857 0.00 0.00 0.00 2.10
978 1141 0.871722 CGTGATTCAAACGGCTCCAA 59.128 50.000 0.00 0.00 37.39 3.53
1007 1170 2.499289 ACCAATGTTTGTGTCCTTGCAA 59.501 40.909 0.00 0.00 0.00 4.08
1095 1278 4.065789 GCTACCTAAGCGGCAGAATATTT 58.934 43.478 1.45 0.00 42.53 1.40
1139 1322 1.040646 TCTTCTTCCGCTGAGTGTGT 58.959 50.000 0.00 0.00 0.00 3.72
1143 1326 3.685139 TTTCATCTTCTTCCGCTGAGT 57.315 42.857 0.00 0.00 0.00 3.41
1145 1328 4.271696 TCTTTTCATCTTCTTCCGCTGA 57.728 40.909 0.00 0.00 0.00 4.26
1148 1331 5.048713 TCCTTTTCTTTTCATCTTCTTCCGC 60.049 40.000 0.00 0.00 0.00 5.54
1149 1332 6.428159 TCTCCTTTTCTTTTCATCTTCTTCCG 59.572 38.462 0.00 0.00 0.00 4.30
1150 1333 7.572168 CGTCTCCTTTTCTTTTCATCTTCTTCC 60.572 40.741 0.00 0.00 0.00 3.46
1151 1334 7.171678 TCGTCTCCTTTTCTTTTCATCTTCTTC 59.828 37.037 0.00 0.00 0.00 2.87
1152 1335 6.992715 TCGTCTCCTTTTCTTTTCATCTTCTT 59.007 34.615 0.00 0.00 0.00 2.52
1156 1339 5.241662 CCTCGTCTCCTTTTCTTTTCATCT 58.758 41.667 0.00 0.00 0.00 2.90
1157 1340 4.142795 GCCTCGTCTCCTTTTCTTTTCATC 60.143 45.833 0.00 0.00 0.00 2.92
1159 1342 3.139077 GCCTCGTCTCCTTTTCTTTTCA 58.861 45.455 0.00 0.00 0.00 2.69
1160 1343 2.157863 CGCCTCGTCTCCTTTTCTTTTC 59.842 50.000 0.00 0.00 0.00 2.29
1161 1344 2.143925 CGCCTCGTCTCCTTTTCTTTT 58.856 47.619 0.00 0.00 0.00 2.27
1164 1347 0.244178 GTCGCCTCGTCTCCTTTTCT 59.756 55.000 0.00 0.00 0.00 2.52
1293 1486 2.718073 GGCTCGGGGTTCGCTTCTA 61.718 63.158 0.00 0.00 39.05 2.10
1326 1524 3.078305 TCTTCCTTCTCCTCCTCTCCTTT 59.922 47.826 0.00 0.00 0.00 3.11
1327 1525 2.657459 TCTTCCTTCTCCTCCTCTCCTT 59.343 50.000 0.00 0.00 0.00 3.36
1328 1526 2.293246 TCTTCCTTCTCCTCCTCTCCT 58.707 52.381 0.00 0.00 0.00 3.69
1407 1618 4.720902 CACCTCGCCATGGCACCA 62.721 66.667 34.93 17.71 42.06 4.17
1410 1621 4.408821 GTCCACCTCGCCATGGCA 62.409 66.667 34.93 20.95 42.06 4.92
2076 2299 2.029666 CCGGCTCCATGGATCGAC 59.970 66.667 28.37 15.92 0.00 4.20
2096 2319 4.980805 TCACCACGGCGGCTCAAC 62.981 66.667 13.24 0.00 39.03 3.18
2097 2320 4.680237 CTCACCACGGCGGCTCAA 62.680 66.667 13.24 0.00 39.03 3.02
2114 2341 0.179163 GCGCTTCAAGGTTACCATGC 60.179 55.000 3.51 0.00 0.00 4.06
2337 2584 5.465935 TGACTGACCAAAGTGAAAAACAAC 58.534 37.500 0.00 0.00 0.00 3.32
2338 2585 5.713792 TGACTGACCAAAGTGAAAAACAA 57.286 34.783 0.00 0.00 0.00 2.83
2339 2586 5.713792 TTGACTGACCAAAGTGAAAAACA 57.286 34.783 0.00 0.00 0.00 2.83
2496 2756 4.460034 CATGAGTTGGTGATCATGGAAACA 59.540 41.667 0.00 0.00 45.87 2.83
2581 2873 8.309656 AGTTAATGTACCTAACACAGAGGTTAC 58.690 37.037 14.18 0.00 45.40 2.50
2607 2899 4.503741 AAGTGTTAACGACGGCTAGTTA 57.496 40.909 0.00 0.00 0.00 2.24
2615 2907 3.181543 GCTAGCTCAAAGTGTTAACGACG 60.182 47.826 7.70 0.00 0.00 5.12
2617 2909 3.985008 TGCTAGCTCAAAGTGTTAACGA 58.015 40.909 17.23 0.00 0.00 3.85
2618 2910 4.201724 GGATGCTAGCTCAAAGTGTTAACG 60.202 45.833 17.23 0.00 0.00 3.18
2631 2937 1.890979 GCATGTGCGGATGCTAGCT 60.891 57.895 17.23 0.83 44.57 3.32
2632 2938 2.635899 GCATGTGCGGATGCTAGC 59.364 61.111 8.10 8.10 44.57 3.42
2725 3043 3.684788 GGCCACCATATATAGCTTGTTCG 59.315 47.826 0.00 0.00 0.00 3.95
2738 3056 2.363276 ACCTCGTCGGCCACCATA 60.363 61.111 2.24 0.00 35.61 2.74
2739 3057 3.771160 GACCTCGTCGGCCACCAT 61.771 66.667 2.24 0.00 35.61 3.55
2949 3282 0.962356 ACGCCTGGAGCAATTGAAGG 60.962 55.000 10.34 10.63 44.04 3.46
3006 3354 1.229428 GGGTGCGTACATGATGATGG 58.771 55.000 5.86 0.00 33.39 3.51
3047 3399 2.096335 TCGTACACTGTACATACCTGCG 59.904 50.000 17.59 3.36 0.00 5.18
3067 3424 6.255887 CACTCCGAAGTTCCAATGTTATACTC 59.744 42.308 0.00 0.00 31.71 2.59
3068 3425 6.070995 TCACTCCGAAGTTCCAATGTTATACT 60.071 38.462 0.00 0.00 31.71 2.12
3074 3432 2.767505 GTCACTCCGAAGTTCCAATGT 58.232 47.619 0.00 0.00 31.71 2.71
3107 3465 2.086869 CGTGGCAGATGGATTGAAGTT 58.913 47.619 0.00 0.00 0.00 2.66
3111 3473 0.745486 CAGCGTGGCAGATGGATTGA 60.745 55.000 0.00 0.00 0.00 2.57
3113 3475 4.230603 CAGCGTGGCAGATGGATT 57.769 55.556 0.00 0.00 0.00 3.01
3117 3479 1.721664 CCAATCCAGCGTGGCAGATG 61.722 60.000 0.00 0.00 37.47 2.90
3119 3481 2.046023 CCAATCCAGCGTGGCAGA 60.046 61.111 0.00 0.00 37.47 4.26
3134 3496 0.605083 CTACTCTGTGCAGCTCACCA 59.395 55.000 11.99 0.00 45.03 4.17
3136 3498 0.108424 CCCTACTCTGTGCAGCTCAC 60.108 60.000 8.75 8.75 45.82 3.51
3210 4639 7.027161 CCTGTCCGTTTCACCTTTTATTATTG 58.973 38.462 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.