Multiple sequence alignment - TraesCS4D01G020600

Loading Multiple Alignment...

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 TraesCS4D01G020600 chr4D 100.000 2492 0 0 1 2492 8931253 8928762 0.000000e+00 4602.0
1 TraesCS4D01G020600 chr4A 91.483 1315 86 16 520 1820 594427178 594428480 0.000000e+00 1784.0
2 TraesCS4D01G020600 chr4A 92.412 514 23 9 1870 2370 594428498 594429008 0.000000e+00 719.0
3 TraesCS4D01G020600 chr4B 85.786 1597 131 47 259 1827 16872526 16870998 0.000000e+00 1604.0
4 TraesCS4D01G020600 chr4B 93.766 385 15 6 1994 2370 16870849 16870466 1.000000e-158 569.0
5 TraesCS4D01G020600 chr4B 83.883 273 33 6 1 262 16872665 16872393 1.480000e-62 250.0
6 TraesCS4D01G020600 chr4B 80.240 167 27 6 268 430 393363437 393363601 1.210000e-23 121.0
7 TraesCS4D01G020600 chr7A 81.884 276 34 9 1 262 567345539 567345266 4.170000e-53 219.0
8 TraesCS4D01G020600 chr7A 92.683 41 2 1 2452 2492 696848631 696848670 9.630000e-05 58.4
9 TraesCS4D01G020600 chr6B 81.181 271 39 7 1 259 347225566 347225296 9.030000e-50 207.0
10 TraesCS4D01G020600 chr6B 79.641 167 26 8 259 421 354318442 354318280 2.030000e-21 113.0
11 TraesCS4D01G020600 chr6B 79.755 163 26 7 268 425 413643263 413643423 7.290000e-21 111.0
12 TraesCS4D01G020600 chr1A 80.153 262 34 13 5 251 105308219 105308477 1.970000e-41 180.0
13 TraesCS4D01G020600 chr7D 78.682 258 40 12 18 262 514087856 514087601 9.230000e-35 158.0
14 TraesCS4D01G020600 chr7B 81.218 197 31 6 70 262 544962206 544962012 1.190000e-33 154.0
15 TraesCS4D01G020600 chr6A 81.159 207 26 10 62 262 15805240 15805041 1.190000e-33 154.0
16 TraesCS4D01G020600 chr1B 81.026 195 31 6 62 253 121558476 121558285 1.540000e-32 150.0
17 TraesCS4D01G020600 chr1B 81.026 195 31 6 62 253 121708204 121708013 1.540000e-32 150.0
18 TraesCS4D01G020600 chr3A 79.885 174 25 9 260 429 181108121 181107954 4.350000e-23 119.0
19 TraesCS4D01G020600 chr3A 97.436 39 1 0 2452 2490 540652848 540652886 1.600000e-07 67.6
20 TraesCS4D01G020600 chr5A 84.746 118 15 2 1143 1257 7487483 7487600 5.630000e-22 115.0
21 TraesCS4D01G020600 chr3D 78.889 180 29 8 259 432 319844029 319843853 2.030000e-21 113.0
22 TraesCS4D01G020600 chr2B 80.137 146 26 3 276 419 246438188 246438332 3.390000e-19 106.0
23 TraesCS4D01G020600 chr3B 78.235 170 32 5 259 425 400321700 400321867 1.220000e-18 104.0
24 TraesCS4D01G020600 chr1D 78.161 174 30 8 268 435 19454423 19454252 1.220000e-18 104.0
25 TraesCS4D01G020600 chr1D 92.157 51 4 0 2435 2485 260587547 260587597 3.440000e-09 73.1
26 TraesCS4D01G020600 chr2D 78.182 165 32 4 260 421 639924569 639924732 4.380000e-18 102.0


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 TraesCS4D01G020600 chr4D 8928762 8931253 2491 True 4602.000000 4602 100.000000 1 2492 1 chr4D.!!$R1 2491
1 TraesCS4D01G020600 chr4A 594427178 594429008 1830 False 1251.500000 1784 91.947500 520 2370 2 chr4A.!!$F1 1850
2 TraesCS4D01G020600 chr4B 16870466 16872665 2199 True 807.666667 1604 87.811667 1 2370 3 chr4B.!!$R1 2369

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
271 283 0.033796 CCCTGATGCACCCTGTTCAT 60.034 55.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1859 1910 0.026803 GGTGCTACGTACGTACTCGG 59.973 60.0 23.6 14.94 41.85 4.63 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
57 69 2.030562 CGGTTTGTGCTCTCGGGT 59.969 61.111 0.00 0.00 0.00 5.28
60 72 1.966451 GTTTGTGCTCTCGGGTGGG 60.966 63.158 0.00 0.00 0.00 4.61
65 77 3.319198 GCTCTCGGGTGGGTTGGA 61.319 66.667 0.00 0.00 0.00 3.53
76 88 4.506255 GGTTGGATGGGGCCTCCG 62.506 72.222 0.00 0.00 38.76 4.63
77 89 3.407967 GTTGGATGGGGCCTCCGA 61.408 66.667 0.00 0.00 38.76 4.55
89 101 1.405463 GGCCTCCGATTTTGATGTTCC 59.595 52.381 0.00 0.00 0.00 3.62
90 102 1.064060 GCCTCCGATTTTGATGTTCCG 59.936 52.381 0.00 0.00 0.00 4.30
91 103 2.356135 CCTCCGATTTTGATGTTCCGT 58.644 47.619 0.00 0.00 0.00 4.69
92 104 2.095853 CCTCCGATTTTGATGTTCCGTG 59.904 50.000 0.00 0.00 0.00 4.94
105 117 0.253610 TTCCGTGTTGGTGTGAGGTT 59.746 50.000 0.00 0.00 39.52 3.50
161 173 5.289595 TCATCATTTGATAGGTGTAGCGAC 58.710 41.667 0.00 0.00 32.63 5.19
163 175 4.682787 TCATTTGATAGGTGTAGCGACTG 58.317 43.478 0.00 0.00 0.00 3.51
164 176 2.579207 TTGATAGGTGTAGCGACTGC 57.421 50.000 0.00 0.00 43.24 4.40
178 190 1.334419 CGACTGCTGTTGCCAAAGAAG 60.334 52.381 0.00 0.00 38.71 2.85
179 191 1.000938 GACTGCTGTTGCCAAAGAAGG 60.001 52.381 0.00 0.00 38.71 3.46
181 193 1.410153 CTGCTGTTGCCAAAGAAGGTT 59.590 47.619 0.00 0.00 38.71 3.50
187 199 1.774110 TGCCAAAGAAGGTTGCTTCA 58.226 45.000 0.00 0.00 35.91 3.02
190 202 2.287849 GCCAAAGAAGGTTGCTTCAGAC 60.288 50.000 0.00 0.00 35.91 3.51
193 205 4.498682 CCAAAGAAGGTTGCTTCAGACTTG 60.499 45.833 0.00 0.00 35.91 3.16
205 217 6.671190 TGCTTCAGACTTGTTGATGTATTTG 58.329 36.000 0.00 0.00 0.00 2.32
211 223 9.114952 TCAGACTTGTTGATGTATTTGTTTGTA 57.885 29.630 0.00 0.00 0.00 2.41
216 228 9.180678 CTTGTTGATGTATTTGTTTGTAAGGTC 57.819 33.333 0.00 0.00 0.00 3.85
220 232 8.458573 TGATGTATTTGTTTGTAAGGTCTTGT 57.541 30.769 0.00 0.00 0.00 3.16
221 233 8.564574 TGATGTATTTGTTTGTAAGGTCTTGTC 58.435 33.333 0.00 0.00 0.00 3.18
222 234 7.867305 TGTATTTGTTTGTAAGGTCTTGTCA 57.133 32.000 0.00 0.00 0.00 3.58
255 267 0.183492 ATGGTTGTATGCATCGCCCT 59.817 50.000 0.19 0.00 0.00 5.19
256 268 0.747644 TGGTTGTATGCATCGCCCTG 60.748 55.000 0.19 0.00 0.00 4.45
257 269 0.463654 GGTTGTATGCATCGCCCTGA 60.464 55.000 0.19 0.00 0.00 3.86
258 270 1.597742 GTTGTATGCATCGCCCTGAT 58.402 50.000 0.19 0.00 38.01 2.90
265 277 3.092511 ATCGCCCTGATGCACCCT 61.093 61.111 0.00 0.00 35.45 4.34
266 278 3.411114 ATCGCCCTGATGCACCCTG 62.411 63.158 0.00 0.00 35.45 4.45
267 279 4.415150 CGCCCTGATGCACCCTGT 62.415 66.667 0.00 0.00 0.00 4.00
268 280 2.036256 GCCCTGATGCACCCTGTT 59.964 61.111 0.00 0.00 0.00 3.16
269 281 2.048603 GCCCTGATGCACCCTGTTC 61.049 63.158 0.00 0.00 0.00 3.18
270 282 1.379916 CCCTGATGCACCCTGTTCA 59.620 57.895 0.00 0.00 0.00 3.18
271 283 0.033796 CCCTGATGCACCCTGTTCAT 60.034 55.000 0.00 0.00 0.00 2.57
272 284 1.386533 CCTGATGCACCCTGTTCATC 58.613 55.000 0.00 0.76 36.88 2.92
273 285 1.340308 CCTGATGCACCCTGTTCATCA 60.340 52.381 8.78 8.78 42.01 3.07
274 286 2.651455 CTGATGCACCCTGTTCATCAT 58.349 47.619 9.40 0.00 42.89 2.45
275 287 3.021695 CTGATGCACCCTGTTCATCATT 58.978 45.455 9.40 0.00 42.89 2.57
276 288 3.433343 TGATGCACCCTGTTCATCATTT 58.567 40.909 5.62 0.00 40.14 2.32
277 289 3.193903 TGATGCACCCTGTTCATCATTTG 59.806 43.478 5.62 0.00 40.14 2.32
278 290 2.874014 TGCACCCTGTTCATCATTTGA 58.126 42.857 0.00 0.00 0.00 2.69
279 291 3.433343 TGCACCCTGTTCATCATTTGAT 58.567 40.909 0.00 0.00 33.34 2.57
280 292 4.598022 TGCACCCTGTTCATCATTTGATA 58.402 39.130 0.00 0.00 33.34 2.15
281 293 4.641541 TGCACCCTGTTCATCATTTGATAG 59.358 41.667 0.00 0.00 33.34 2.08
282 294 4.037208 GCACCCTGTTCATCATTTGATAGG 59.963 45.833 0.00 0.00 38.16 2.57
283 295 5.195940 CACCCTGTTCATCATTTGATAGGT 58.804 41.667 6.42 0.00 37.36 3.08
284 296 5.066893 CACCCTGTTCATCATTTGATAGGTG 59.933 44.000 6.42 0.00 37.36 4.00
285 297 5.195940 CCCTGTTCATCATTTGATAGGTGT 58.804 41.667 6.42 0.00 37.36 4.16
286 298 6.069673 ACCCTGTTCATCATTTGATAGGTGTA 60.070 38.462 6.42 0.00 37.36 2.90
287 299 6.484643 CCCTGTTCATCATTTGATAGGTGTAG 59.515 42.308 6.42 0.00 37.36 2.74
288 300 6.017605 CCTGTTCATCATTTGATAGGTGTAGC 60.018 42.308 0.00 0.00 35.70 3.58
289 301 5.523552 TGTTCATCATTTGATAGGTGTAGCG 59.476 40.000 0.00 0.00 33.34 4.26
290 302 5.529581 TCATCATTTGATAGGTGTAGCGA 57.470 39.130 0.00 0.00 32.63 4.93
291 303 5.289595 TCATCATTTGATAGGTGTAGCGAC 58.710 41.667 0.00 0.00 32.63 5.19
292 304 5.069119 TCATCATTTGATAGGTGTAGCGACT 59.931 40.000 0.00 0.00 32.63 4.18
293 305 6.264518 TCATCATTTGATAGGTGTAGCGACTA 59.735 38.462 0.00 0.00 32.63 2.59
294 306 5.828747 TCATTTGATAGGTGTAGCGACTAC 58.171 41.667 9.27 9.27 37.46 2.73
295 307 5.593095 TCATTTGATAGGTGTAGCGACTACT 59.407 40.000 15.00 0.00 37.78 2.57
296 308 4.895224 TTGATAGGTGTAGCGACTACTG 57.105 45.455 15.00 0.00 37.78 2.74
297 309 3.882444 TGATAGGTGTAGCGACTACTGT 58.118 45.455 15.00 0.00 37.78 3.55
298 310 4.267536 TGATAGGTGTAGCGACTACTGTT 58.732 43.478 15.00 6.06 37.78 3.16
299 311 5.430886 TGATAGGTGTAGCGACTACTGTTA 58.569 41.667 15.00 7.49 37.78 2.41
300 312 5.295292 TGATAGGTGTAGCGACTACTGTTAC 59.705 44.000 15.00 7.30 37.78 2.50
301 313 2.751806 AGGTGTAGCGACTACTGTTACC 59.248 50.000 15.00 13.55 37.78 2.85
302 314 2.489329 GGTGTAGCGACTACTGTTACCA 59.511 50.000 15.00 0.00 37.78 3.25
303 315 3.057315 GGTGTAGCGACTACTGTTACCAA 60.057 47.826 15.00 0.00 37.78 3.67
304 316 4.549458 GTGTAGCGACTACTGTTACCAAA 58.451 43.478 15.00 0.00 37.78 3.28
305 317 4.620184 GTGTAGCGACTACTGTTACCAAAG 59.380 45.833 15.00 0.00 37.78 2.77
306 318 4.520111 TGTAGCGACTACTGTTACCAAAGA 59.480 41.667 15.00 0.00 37.78 2.52
307 319 4.175787 AGCGACTACTGTTACCAAAGAG 57.824 45.455 0.00 0.00 32.33 2.85
308 320 3.056749 AGCGACTACTGTTACCAAAGAGG 60.057 47.826 0.00 0.00 45.67 3.69
309 321 3.846360 CGACTACTGTTACCAAAGAGGG 58.154 50.000 0.00 0.00 43.89 4.30
310 322 3.257624 CGACTACTGTTACCAAAGAGGGT 59.742 47.826 0.00 0.00 43.89 4.34
311 323 4.262335 CGACTACTGTTACCAAAGAGGGTT 60.262 45.833 0.00 0.00 43.89 4.11
312 324 4.969484 ACTACTGTTACCAAAGAGGGTTG 58.031 43.478 0.00 0.00 43.89 3.77
313 325 2.583143 ACTGTTACCAAAGAGGGTTGC 58.417 47.619 0.00 0.00 43.89 4.17
314 326 2.174854 ACTGTTACCAAAGAGGGTTGCT 59.825 45.455 0.00 0.00 43.89 3.91
315 327 3.222603 CTGTTACCAAAGAGGGTTGCTT 58.777 45.455 0.00 0.00 43.89 3.91
316 328 2.955660 TGTTACCAAAGAGGGTTGCTTG 59.044 45.455 0.00 0.00 43.89 4.01
317 329 3.219281 GTTACCAAAGAGGGTTGCTTGA 58.781 45.455 0.00 0.00 43.89 3.02
318 330 1.986882 ACCAAAGAGGGTTGCTTGAG 58.013 50.000 0.00 0.00 43.89 3.02
319 331 1.494721 ACCAAAGAGGGTTGCTTGAGA 59.505 47.619 0.00 0.00 43.89 3.27
320 332 1.882623 CCAAAGAGGGTTGCTTGAGAC 59.117 52.381 0.00 0.00 0.00 3.36
321 333 2.487986 CCAAAGAGGGTTGCTTGAGACT 60.488 50.000 0.00 0.00 0.00 3.24
322 334 3.217626 CAAAGAGGGTTGCTTGAGACTT 58.782 45.455 0.00 0.00 0.00 3.01
323 335 2.557920 AGAGGGTTGCTTGAGACTTG 57.442 50.000 0.00 0.00 0.00 3.16
324 336 1.771255 AGAGGGTTGCTTGAGACTTGT 59.229 47.619 0.00 0.00 0.00 3.16
325 337 2.173569 AGAGGGTTGCTTGAGACTTGTT 59.826 45.455 0.00 0.00 0.00 2.83
326 338 2.291741 GAGGGTTGCTTGAGACTTGTTG 59.708 50.000 0.00 0.00 0.00 3.33
327 339 2.092429 AGGGTTGCTTGAGACTTGTTGA 60.092 45.455 0.00 0.00 0.00 3.18
328 340 2.887152 GGGTTGCTTGAGACTTGTTGAT 59.113 45.455 0.00 0.00 0.00 2.57
329 341 4.072131 GGGTTGCTTGAGACTTGTTGATA 58.928 43.478 0.00 0.00 0.00 2.15
330 342 4.702131 GGGTTGCTTGAGACTTGTTGATAT 59.298 41.667 0.00 0.00 0.00 1.63
331 343 5.880332 GGGTTGCTTGAGACTTGTTGATATA 59.120 40.000 0.00 0.00 0.00 0.86
332 344 6.543831 GGGTTGCTTGAGACTTGTTGATATAT 59.456 38.462 0.00 0.00 0.00 0.86
333 345 7.067494 GGGTTGCTTGAGACTTGTTGATATATT 59.933 37.037 0.00 0.00 0.00 1.28
334 346 8.462016 GGTTGCTTGAGACTTGTTGATATATTT 58.538 33.333 0.00 0.00 0.00 1.40
335 347 9.282247 GTTGCTTGAGACTTGTTGATATATTTG 57.718 33.333 0.00 0.00 0.00 2.32
336 348 8.565896 TGCTTGAGACTTGTTGATATATTTGT 57.434 30.769 0.00 0.00 0.00 2.83
337 349 9.013229 TGCTTGAGACTTGTTGATATATTTGTT 57.987 29.630 0.00 0.00 0.00 2.83
338 350 9.495754 GCTTGAGACTTGTTGATATATTTGTTC 57.504 33.333 0.00 0.00 0.00 3.18
339 351 9.694520 CTTGAGACTTGTTGATATATTTGTTCG 57.305 33.333 0.00 0.00 0.00 3.95
340 352 8.771920 TGAGACTTGTTGATATATTTGTTCGT 57.228 30.769 0.00 0.00 0.00 3.85
341 353 9.863845 TGAGACTTGTTGATATATTTGTTCGTA 57.136 29.630 0.00 0.00 0.00 3.43
351 363 9.878667 TGATATATTTGTTCGTAAAGTCTTGGA 57.121 29.630 0.00 0.00 0.00 3.53
396 408 1.153309 CGTCATGATGCAGAGGCCA 60.153 57.895 5.01 0.00 40.13 5.36
403 415 4.980592 TGCAGAGGCCAGGGGTCA 62.981 66.667 5.01 0.00 40.13 4.02
413 425 1.002857 CCAGGGGTCATCCTCCTTTT 58.997 55.000 0.00 0.00 33.94 2.27
414 426 1.064389 CCAGGGGTCATCCTCCTTTTC 60.064 57.143 0.00 0.00 33.94 2.29
421 433 4.082733 GGGTCATCCTCCTTTTCGAAAAAG 60.083 45.833 22.67 17.41 0.00 2.27
422 434 4.760204 GGTCATCCTCCTTTTCGAAAAAGA 59.240 41.667 22.67 20.39 0.00 2.52
425 443 6.637254 GTCATCCTCCTTTTCGAAAAAGAAAC 59.363 38.462 22.67 14.61 39.53 2.78
427 445 7.717875 TCATCCTCCTTTTCGAAAAAGAAACTA 59.282 33.333 22.67 9.11 39.53 2.24
479 497 1.778591 CAAATGTTGTCCAAACGTCGC 59.221 47.619 0.00 0.00 0.00 5.19
492 510 1.509787 CGTCGCAAACTCGCAATGG 60.510 57.895 0.00 0.00 0.00 3.16
498 516 1.701704 CAAACTCGCAATGGGAAAGC 58.298 50.000 0.81 0.00 0.00 3.51
514 532 0.602905 AAGCGGTGTCAAGTGGCTAC 60.603 55.000 0.00 0.00 32.82 3.58
523 541 0.323629 CAAGTGGCTACGGGAGGAAA 59.676 55.000 0.00 0.00 0.00 3.13
560 578 1.671261 CCTTGTGAAGGTCGAGCTCAG 60.671 57.143 18.90 8.83 43.95 3.35
587 605 4.593634 GGACATACCTAGGGCTGAACTATT 59.406 45.833 14.81 0.00 35.41 1.73
588 606 5.511545 GGACATACCTAGGGCTGAACTATTG 60.512 48.000 14.81 0.00 35.41 1.90
589 607 4.969359 ACATACCTAGGGCTGAACTATTGT 59.031 41.667 14.81 0.00 0.00 2.71
590 608 3.914426 ACCTAGGGCTGAACTATTGTG 57.086 47.619 14.81 0.00 0.00 3.33
591 609 3.182152 ACCTAGGGCTGAACTATTGTGT 58.818 45.455 14.81 0.00 0.00 3.72
592 610 3.055094 ACCTAGGGCTGAACTATTGTGTG 60.055 47.826 14.81 0.00 0.00 3.82
593 611 3.055094 CCTAGGGCTGAACTATTGTGTGT 60.055 47.826 0.00 0.00 0.00 3.72
630 648 1.544691 GGCAGAGAGGAACTACGACAA 59.455 52.381 0.00 0.00 41.55 3.18
634 652 4.327627 GCAGAGAGGAACTACGACAAATTC 59.672 45.833 0.00 0.00 41.55 2.17
636 654 6.625300 GCAGAGAGGAACTACGACAAATTCTA 60.625 42.308 0.00 0.00 41.55 2.10
637 655 7.484975 CAGAGAGGAACTACGACAAATTCTAT 58.515 38.462 0.00 0.00 41.55 1.98
638 656 8.622157 CAGAGAGGAACTACGACAAATTCTATA 58.378 37.037 0.00 0.00 41.55 1.31
639 657 9.357161 AGAGAGGAACTACGACAAATTCTATAT 57.643 33.333 0.00 0.00 41.55 0.86
640 658 9.968870 GAGAGGAACTACGACAAATTCTATATT 57.031 33.333 0.00 0.00 41.55 1.28
641 659 9.751542 AGAGGAACTACGACAAATTCTATATTG 57.248 33.333 0.00 0.00 41.55 1.90
642 660 8.366671 AGGAACTACGACAAATTCTATATTGC 57.633 34.615 0.00 0.00 36.02 3.56
643 661 8.204836 AGGAACTACGACAAATTCTATATTGCT 58.795 33.333 0.00 0.00 36.02 3.91
688 706 6.925610 TGATGAATGAAATCCTCTTTACCG 57.074 37.500 0.00 0.00 0.00 4.02
691 709 6.302535 TGAATGAAATCCTCTTTACCGGTA 57.697 37.500 11.16 11.16 0.00 4.02
735 754 8.816640 TTCAAAAGATTATCTGCAACTTTTCC 57.183 30.769 0.00 0.00 38.26 3.13
736 755 7.950512 TCAAAAGATTATCTGCAACTTTTCCA 58.049 30.769 0.00 0.00 38.26 3.53
737 756 8.420222 TCAAAAGATTATCTGCAACTTTTCCAA 58.580 29.630 0.00 0.00 38.26 3.53
738 757 8.490355 CAAAAGATTATCTGCAACTTTTCCAAC 58.510 33.333 0.00 0.00 38.26 3.77
778 797 1.411041 ACTTGGACGGTCTATAGGCC 58.589 55.000 13.79 13.79 35.66 5.19
907 930 0.401395 ATCCCGGAAATGCCCCTCTA 60.401 55.000 0.73 0.00 0.00 2.43
924 947 7.017254 TGCCCCTCTAAAACCCTCTATAAATAG 59.983 40.741 0.00 0.00 0.00 1.73
956 979 2.992847 TTTCTTCCCTCCCTTTTCCC 57.007 50.000 0.00 0.00 0.00 3.97
987 1010 7.110155 TCCTTCCTAAATCACTGAATTACCAC 58.890 38.462 0.00 0.00 0.00 4.16
1007 1030 2.628657 ACTCTACCCTTATCATGCCGTC 59.371 50.000 0.00 0.00 0.00 4.79
1017 1040 0.036388 TCATGCCGTCCTCAAGTTCC 60.036 55.000 0.00 0.00 0.00 3.62
1024 1047 1.014564 GTCCTCAAGTTCCGCTTCCG 61.015 60.000 0.00 0.00 34.69 4.30
1026 1049 0.602905 CCTCAAGTTCCGCTTCCGTT 60.603 55.000 0.00 0.00 34.69 4.44
1030 1053 1.069906 CAAGTTCCGCTTCCGTTCAAG 60.070 52.381 0.00 0.00 34.69 3.02
1047 1070 2.677573 AAGCCTTCGCGCCACAAAAC 62.678 55.000 0.00 0.00 41.18 2.43
1048 1071 2.050442 CCTTCGCGCCACAAAACC 60.050 61.111 0.00 0.00 0.00 3.27
1127 1153 4.397348 GGTGACGGATGCCTTTGT 57.603 55.556 0.00 0.00 0.00 2.83
1493 1519 0.964700 CTGATCGCCTGGAGCTGATA 59.035 55.000 0.00 0.00 40.39 2.15
1809 1860 4.048470 GGTTCCCCCTGTCCTGCC 62.048 72.222 0.00 0.00 0.00 4.85
1820 1871 0.471022 TGTCCTGCCGGCTCCATATA 60.471 55.000 29.70 3.67 0.00 0.86
1822 1873 2.108168 GTCCTGCCGGCTCCATATATA 58.892 52.381 29.70 1.91 0.00 0.86
1825 1876 3.780294 TCCTGCCGGCTCCATATATATTT 59.220 43.478 29.70 0.00 0.00 1.40
1827 1878 4.576463 CCTGCCGGCTCCATATATATTTTC 59.424 45.833 29.70 0.00 0.00 2.29
1828 1879 5.431765 CTGCCGGCTCCATATATATTTTCT 58.568 41.667 29.70 0.00 0.00 2.52
1829 1880 5.428253 TGCCGGCTCCATATATATTTTCTC 58.572 41.667 29.70 0.00 0.00 2.87
1830 1881 5.189736 TGCCGGCTCCATATATATTTTCTCT 59.810 40.000 29.70 0.00 0.00 3.10
1832 1883 6.258947 GCCGGCTCCATATATATTTTCTCTTC 59.741 42.308 22.15 0.00 0.00 2.87
1833 1884 7.560368 CCGGCTCCATATATATTTTCTCTTCT 58.440 38.462 0.00 0.00 0.00 2.85
1834 1885 7.493971 CCGGCTCCATATATATTTTCTCTTCTG 59.506 40.741 0.00 0.00 0.00 3.02
1849 1900 6.992063 TCTCTTCTGAATTCTTGGTTATGC 57.008 37.500 7.05 0.00 0.00 3.14
1851 1902 7.114754 TCTCTTCTGAATTCTTGGTTATGCAT 58.885 34.615 3.79 3.79 0.00 3.96
1853 1904 7.541162 TCTTCTGAATTCTTGGTTATGCATTG 58.459 34.615 3.54 0.00 0.00 2.82
1854 1905 5.653507 TCTGAATTCTTGGTTATGCATTGC 58.346 37.500 3.54 0.46 0.00 3.56
1855 1906 5.185442 TCTGAATTCTTGGTTATGCATTGCA 59.815 36.000 14.72 14.72 44.86 4.08
1856 1907 5.170021 TGAATTCTTGGTTATGCATTGCAC 58.830 37.500 14.66 1.46 43.04 4.57
1857 1908 2.917701 TCTTGGTTATGCATTGCACG 57.082 45.000 14.66 0.00 43.04 5.34
1858 1909 2.431454 TCTTGGTTATGCATTGCACGA 58.569 42.857 14.66 1.87 43.04 4.35
1859 1910 2.161410 TCTTGGTTATGCATTGCACGAC 59.839 45.455 14.66 14.61 43.04 4.34
1860 1911 0.808125 TGGTTATGCATTGCACGACC 59.192 50.000 26.60 26.60 43.04 4.79
1861 1912 0.248054 GGTTATGCATTGCACGACCG 60.248 55.000 22.19 0.00 43.04 4.79
1862 1913 0.724549 GTTATGCATTGCACGACCGA 59.275 50.000 14.66 0.00 43.04 4.69
1863 1914 1.006086 TTATGCATTGCACGACCGAG 58.994 50.000 14.66 0.00 43.04 4.63
1864 1915 0.108377 TATGCATTGCACGACCGAGT 60.108 50.000 14.66 0.00 43.04 4.18
1865 1916 0.108377 ATGCATTGCACGACCGAGTA 60.108 50.000 14.66 0.00 43.04 2.59
1866 1917 1.011968 TGCATTGCACGACCGAGTAC 61.012 55.000 7.38 0.00 31.71 2.73
1867 1918 1.988409 CATTGCACGACCGAGTACG 59.012 57.895 0.00 0.00 39.43 3.67
1868 1919 0.731514 CATTGCACGACCGAGTACGT 60.732 55.000 0.00 0.00 43.50 3.57
1869 1920 0.804364 ATTGCACGACCGAGTACGTA 59.196 50.000 0.00 0.00 40.76 3.57
1870 1921 0.110238 TTGCACGACCGAGTACGTAC 60.110 55.000 18.10 18.10 40.76 3.67
1871 1922 1.578618 GCACGACCGAGTACGTACG 60.579 63.158 19.49 15.01 40.76 3.67
1872 1923 1.781555 CACGACCGAGTACGTACGT 59.218 57.895 25.98 25.98 44.29 3.57
1873 1924 0.989164 CACGACCGAGTACGTACGTA 59.011 55.000 23.60 23.60 42.84 3.57
1874 1925 1.007011 CACGACCGAGTACGTACGTAG 60.007 57.143 27.48 17.89 42.84 3.51
1875 1926 0.043822 CGACCGAGTACGTACGTAGC 60.044 60.000 27.48 20.26 37.88 3.58
1876 1927 0.999406 GACCGAGTACGTACGTAGCA 59.001 55.000 27.48 6.83 37.88 3.49
1877 1928 0.721718 ACCGAGTACGTACGTAGCAC 59.278 55.000 27.48 18.84 37.88 4.40
2064 2136 4.461431 GTCCTTGTTTAATTAGTGGTGGGG 59.539 45.833 0.00 0.00 0.00 4.96
2215 2297 1.968704 TGTATTTTGTGCGGGTGTCA 58.031 45.000 0.00 0.00 0.00 3.58
2216 2298 2.509569 TGTATTTTGTGCGGGTGTCAT 58.490 42.857 0.00 0.00 0.00 3.06
2352 2435 4.962362 TGCATACCTTAATCTCTCACCTCA 59.038 41.667 0.00 0.00 0.00 3.86
2365 2448 1.806542 TCACCTCATCGCAAAGAAAGC 59.193 47.619 0.00 0.00 0.00 3.51
2370 2453 4.050553 CCTCATCGCAAAGAAAGCAAAAA 58.949 39.130 0.00 0.00 0.00 1.94
2390 2473 2.464157 AAAGAGGAGAGAAGCCAACG 57.536 50.000 0.00 0.00 0.00 4.10
2391 2474 1.343069 AAGAGGAGAGAAGCCAACGT 58.657 50.000 0.00 0.00 0.00 3.99
2392 2475 2.217510 AGAGGAGAGAAGCCAACGTA 57.782 50.000 0.00 0.00 0.00 3.57
2393 2476 2.526432 AGAGGAGAGAAGCCAACGTAA 58.474 47.619 0.00 0.00 0.00 3.18
2394 2477 3.100671 AGAGGAGAGAAGCCAACGTAAT 58.899 45.455 0.00 0.00 0.00 1.89
2395 2478 3.131400 AGAGGAGAGAAGCCAACGTAATC 59.869 47.826 0.00 0.00 0.00 1.75
2396 2479 3.100671 AGGAGAGAAGCCAACGTAATCT 58.899 45.455 0.00 0.00 0.00 2.40
2397 2480 3.131400 AGGAGAGAAGCCAACGTAATCTC 59.869 47.826 0.00 0.00 37.40 2.75
2398 2481 3.109619 GAGAGAAGCCAACGTAATCTCG 58.890 50.000 0.00 0.00 41.04 4.04
2399 2482 2.159226 AGAGAAGCCAACGTAATCTCGG 60.159 50.000 0.00 0.00 41.04 4.63
2400 2483 0.651031 GAAGCCAACGTAATCTCGGC 59.349 55.000 0.00 0.00 43.31 5.54
2401 2484 0.743345 AAGCCAACGTAATCTCGGCC 60.743 55.000 0.00 0.00 44.06 6.13
2402 2485 1.153429 GCCAACGTAATCTCGGCCT 60.153 57.895 0.00 0.00 36.73 5.19
2403 2486 1.429148 GCCAACGTAATCTCGGCCTG 61.429 60.000 0.00 0.00 36.73 4.85
2404 2487 0.810031 CCAACGTAATCTCGGCCTGG 60.810 60.000 0.00 0.00 34.94 4.45
2405 2488 0.108329 CAACGTAATCTCGGCCTGGT 60.108 55.000 0.00 0.00 34.94 4.00
2406 2489 0.108329 AACGTAATCTCGGCCTGGTG 60.108 55.000 0.00 0.00 34.94 4.17
2407 2490 1.883084 CGTAATCTCGGCCTGGTGC 60.883 63.158 0.00 0.00 40.16 5.01
2408 2491 1.220749 GTAATCTCGGCCTGGTGCA 59.779 57.895 0.00 0.00 43.89 4.57
2409 2492 0.179045 GTAATCTCGGCCTGGTGCAT 60.179 55.000 0.00 0.00 43.89 3.96
2410 2493 0.106708 TAATCTCGGCCTGGTGCATC 59.893 55.000 0.00 0.00 43.89 3.91
2411 2494 2.930385 AATCTCGGCCTGGTGCATCG 62.930 60.000 0.00 0.00 43.89 3.84
2412 2495 4.457496 CTCGGCCTGGTGCATCGT 62.457 66.667 0.00 0.00 43.89 3.73
2413 2496 3.958147 CTCGGCCTGGTGCATCGTT 62.958 63.158 0.00 0.00 43.89 3.85
2414 2497 3.055719 CGGCCTGGTGCATCGTTT 61.056 61.111 0.00 0.00 43.89 3.60
2415 2498 2.625823 CGGCCTGGTGCATCGTTTT 61.626 57.895 0.00 0.00 43.89 2.43
2416 2499 1.665442 GGCCTGGTGCATCGTTTTT 59.335 52.632 0.00 0.00 43.89 1.94
2448 2531 4.618965 CGTAGCTAAGATGGTTAGGTTCC 58.381 47.826 0.00 0.00 34.86 3.62
2449 2532 4.341520 CGTAGCTAAGATGGTTAGGTTCCT 59.658 45.833 0.00 0.00 34.86 3.36
2450 2533 5.507650 CGTAGCTAAGATGGTTAGGTTCCTC 60.508 48.000 0.00 0.00 34.86 3.71
2451 2534 3.385111 AGCTAAGATGGTTAGGTTCCTCG 59.615 47.826 0.00 0.00 29.36 4.63
2452 2535 3.132467 GCTAAGATGGTTAGGTTCCTCGT 59.868 47.826 0.00 0.00 0.00 4.18
2453 2536 3.611766 AAGATGGTTAGGTTCCTCGTG 57.388 47.619 0.00 0.00 0.00 4.35
2454 2537 2.816411 AGATGGTTAGGTTCCTCGTGA 58.184 47.619 0.00 0.00 0.00 4.35
2455 2538 3.375699 AGATGGTTAGGTTCCTCGTGAT 58.624 45.455 0.00 0.00 0.00 3.06
2456 2539 3.133003 AGATGGTTAGGTTCCTCGTGATG 59.867 47.826 0.00 0.00 0.00 3.07
2457 2540 1.553248 TGGTTAGGTTCCTCGTGATGG 59.447 52.381 0.00 0.00 0.00 3.51
2458 2541 1.829222 GGTTAGGTTCCTCGTGATGGA 59.171 52.381 0.00 0.00 0.00 3.41
2459 2542 2.235402 GGTTAGGTTCCTCGTGATGGAA 59.765 50.000 0.00 0.00 40.85 3.53
2464 2547 2.178912 TTCCTCGTGATGGAACCAAC 57.821 50.000 0.00 0.00 38.53 3.77
2465 2548 0.323629 TCCTCGTGATGGAACCAACC 59.676 55.000 0.00 0.00 0.00 3.77
2466 2549 0.676782 CCTCGTGATGGAACCAACCC 60.677 60.000 0.00 0.00 0.00 4.11
2467 2550 0.036164 CTCGTGATGGAACCAACCCA 59.964 55.000 0.00 0.00 38.19 4.51
2468 2551 0.695924 TCGTGATGGAACCAACCCAT 59.304 50.000 0.00 0.00 46.40 4.00
2487 2570 5.012328 CCATCAGGGTTCAAGTACTAGAC 57.988 47.826 0.00 0.00 0.00 2.59
2488 2571 4.712337 CCATCAGGGTTCAAGTACTAGACT 59.288 45.833 0.00 0.00 41.56 3.24
2490 2573 6.295916 CCATCAGGGTTCAAGTACTAGACTTT 60.296 42.308 0.00 0.00 46.79 2.66
2491 2574 6.097915 TCAGGGTTCAAGTACTAGACTTTG 57.902 41.667 0.00 0.00 46.79 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.338620 CGGTCCAACGTGCTCTCA 59.661 61.111 0.00 0.00 0.00 3.27
32 33 2.113131 GAGCACAAACCGGTCCAACG 62.113 60.000 8.04 0.00 0.00 4.10
57 69 3.346734 GAGGCCCCATCCAACCCA 61.347 66.667 0.00 0.00 0.00 4.51
60 72 2.284515 AATCGGAGGCCCCATCCAAC 62.285 60.000 9.99 0.00 36.57 3.77
65 77 0.557729 ATCAAAATCGGAGGCCCCAT 59.442 50.000 0.00 0.00 34.14 4.00
76 88 3.980775 CACCAACACGGAACATCAAAATC 59.019 43.478 0.00 0.00 38.63 2.17
77 89 3.383185 ACACCAACACGGAACATCAAAAT 59.617 39.130 0.00 0.00 38.63 1.82
89 101 1.508632 CCTAACCTCACACCAACACG 58.491 55.000 0.00 0.00 0.00 4.49
90 102 1.892209 CCCTAACCTCACACCAACAC 58.108 55.000 0.00 0.00 0.00 3.32
91 103 0.109723 GCCCTAACCTCACACCAACA 59.890 55.000 0.00 0.00 0.00 3.33
92 104 0.109723 TGCCCTAACCTCACACCAAC 59.890 55.000 0.00 0.00 0.00 3.77
135 147 5.985530 CGCTACACCTATCAAATGATGAAGA 59.014 40.000 6.17 0.00 42.54 2.87
164 176 4.042189 GAAGCAACCTTCTTTGGCAACAG 61.042 47.826 0.00 1.11 45.59 3.16
166 178 2.159114 TGAAGCAACCTTCTTTGGCAAC 60.159 45.455 0.00 0.00 46.13 4.17
178 190 3.316308 ACATCAACAAGTCTGAAGCAACC 59.684 43.478 0.00 0.00 0.00 3.77
179 191 4.558538 ACATCAACAAGTCTGAAGCAAC 57.441 40.909 0.00 0.00 0.00 4.17
181 193 6.262944 ACAAATACATCAACAAGTCTGAAGCA 59.737 34.615 0.00 0.00 0.00 3.91
187 199 9.950680 CTTACAAACAAATACATCAACAAGTCT 57.049 29.630 0.00 0.00 0.00 3.24
190 202 9.180678 GACCTTACAAACAAATACATCAACAAG 57.819 33.333 0.00 0.00 0.00 3.16
193 205 9.180678 CAAGACCTTACAAACAAATACATCAAC 57.819 33.333 0.00 0.00 0.00 3.18
238 250 0.463654 TCAGGGCGATGCATACAACC 60.464 55.000 0.00 0.00 0.00 3.77
256 268 3.444742 TCAAATGATGAACAGGGTGCATC 59.555 43.478 9.88 9.88 45.99 3.91
257 269 3.433343 TCAAATGATGAACAGGGTGCAT 58.567 40.909 0.00 0.00 33.96 3.96
258 270 2.874014 TCAAATGATGAACAGGGTGCA 58.126 42.857 0.00 0.00 34.30 4.57
259 271 4.037208 CCTATCAAATGATGAACAGGGTGC 59.963 45.833 6.17 0.00 42.54 5.01
260 272 5.066893 CACCTATCAAATGATGAACAGGGTG 59.933 44.000 12.37 12.01 43.64 4.61
261 273 5.195940 CACCTATCAAATGATGAACAGGGT 58.804 41.667 12.37 6.23 43.64 4.34
262 274 5.195940 ACACCTATCAAATGATGAACAGGG 58.804 41.667 12.37 6.14 43.64 4.45
263 275 6.017605 GCTACACCTATCAAATGATGAACAGG 60.018 42.308 6.17 7.18 44.34 4.00
264 276 6.292542 CGCTACACCTATCAAATGATGAACAG 60.293 42.308 6.17 0.00 42.54 3.16
265 277 5.523552 CGCTACACCTATCAAATGATGAACA 59.476 40.000 6.17 0.00 42.54 3.18
266 278 5.753438 TCGCTACACCTATCAAATGATGAAC 59.247 40.000 6.17 0.00 42.54 3.18
267 279 5.753438 GTCGCTACACCTATCAAATGATGAA 59.247 40.000 6.17 0.00 42.54 2.57
268 280 5.069119 AGTCGCTACACCTATCAAATGATGA 59.931 40.000 6.17 0.00 43.67 2.92
269 281 5.292765 AGTCGCTACACCTATCAAATGATG 58.707 41.667 6.17 0.00 36.05 3.07
270 282 5.537300 AGTCGCTACACCTATCAAATGAT 57.463 39.130 1.01 1.01 38.51 2.45
271 283 5.593095 AGTAGTCGCTACACCTATCAAATGA 59.407 40.000 15.98 0.00 39.22 2.57
272 284 5.687730 CAGTAGTCGCTACACCTATCAAATG 59.312 44.000 15.98 2.31 39.22 2.32
273 285 5.360144 ACAGTAGTCGCTACACCTATCAAAT 59.640 40.000 15.98 0.00 39.22 2.32
274 286 4.703575 ACAGTAGTCGCTACACCTATCAAA 59.296 41.667 15.98 0.00 39.22 2.69
275 287 4.267536 ACAGTAGTCGCTACACCTATCAA 58.732 43.478 15.98 0.00 39.22 2.57
276 288 3.882444 ACAGTAGTCGCTACACCTATCA 58.118 45.455 15.98 0.00 39.22 2.15
277 289 4.897025 AACAGTAGTCGCTACACCTATC 57.103 45.455 15.98 0.00 39.22 2.08
278 290 4.578105 GGTAACAGTAGTCGCTACACCTAT 59.422 45.833 15.98 4.16 39.22 2.57
279 291 3.941483 GGTAACAGTAGTCGCTACACCTA 59.059 47.826 15.98 4.74 39.22 3.08
280 292 2.751806 GGTAACAGTAGTCGCTACACCT 59.248 50.000 15.98 5.44 39.22 4.00
281 293 2.489329 TGGTAACAGTAGTCGCTACACC 59.511 50.000 15.98 14.28 46.17 4.16
282 294 3.837213 TGGTAACAGTAGTCGCTACAC 57.163 47.619 15.98 7.72 46.17 2.90
296 308 3.219281 TCAAGCAACCCTCTTTGGTAAC 58.781 45.455 0.00 0.00 37.76 2.50
297 309 3.137544 TCTCAAGCAACCCTCTTTGGTAA 59.862 43.478 0.00 0.00 37.76 2.85
298 310 2.708861 TCTCAAGCAACCCTCTTTGGTA 59.291 45.455 0.00 0.00 37.76 3.25
299 311 1.494721 TCTCAAGCAACCCTCTTTGGT 59.505 47.619 0.00 0.00 41.55 3.67
300 312 1.882623 GTCTCAAGCAACCCTCTTTGG 59.117 52.381 0.00 0.00 0.00 3.28
301 313 2.856222 AGTCTCAAGCAACCCTCTTTG 58.144 47.619 0.00 0.00 0.00 2.77
302 314 3.217626 CAAGTCTCAAGCAACCCTCTTT 58.782 45.455 0.00 0.00 0.00 2.52
303 315 2.173569 ACAAGTCTCAAGCAACCCTCTT 59.826 45.455 0.00 0.00 0.00 2.85
304 316 1.771255 ACAAGTCTCAAGCAACCCTCT 59.229 47.619 0.00 0.00 0.00 3.69
305 317 2.262423 ACAAGTCTCAAGCAACCCTC 57.738 50.000 0.00 0.00 0.00 4.30
306 318 2.092429 TCAACAAGTCTCAAGCAACCCT 60.092 45.455 0.00 0.00 0.00 4.34
307 319 2.297701 TCAACAAGTCTCAAGCAACCC 58.702 47.619 0.00 0.00 0.00 4.11
308 320 5.886960 ATATCAACAAGTCTCAAGCAACC 57.113 39.130 0.00 0.00 0.00 3.77
309 321 9.282247 CAAATATATCAACAAGTCTCAAGCAAC 57.718 33.333 0.00 0.00 0.00 4.17
310 322 9.013229 ACAAATATATCAACAAGTCTCAAGCAA 57.987 29.630 0.00 0.00 0.00 3.91
311 323 8.565896 ACAAATATATCAACAAGTCTCAAGCA 57.434 30.769 0.00 0.00 0.00 3.91
312 324 9.495754 GAACAAATATATCAACAAGTCTCAAGC 57.504 33.333 0.00 0.00 0.00 4.01
313 325 9.694520 CGAACAAATATATCAACAAGTCTCAAG 57.305 33.333 0.00 0.00 0.00 3.02
314 326 9.214957 ACGAACAAATATATCAACAAGTCTCAA 57.785 29.630 0.00 0.00 0.00 3.02
315 327 8.771920 ACGAACAAATATATCAACAAGTCTCA 57.228 30.769 0.00 0.00 0.00 3.27
325 337 9.878667 TCCAAGACTTTACGAACAAATATATCA 57.121 29.630 0.00 0.00 0.00 2.15
362 374 8.503196 GCATCATGACGATTATACAACCATTTA 58.497 33.333 0.00 0.00 29.21 1.40
363 375 7.013178 TGCATCATGACGATTATACAACCATTT 59.987 33.333 0.00 0.00 29.21 2.32
364 376 6.486320 TGCATCATGACGATTATACAACCATT 59.514 34.615 0.00 0.00 29.21 3.16
365 377 5.997129 TGCATCATGACGATTATACAACCAT 59.003 36.000 0.00 0.00 29.21 3.55
366 378 5.363939 TGCATCATGACGATTATACAACCA 58.636 37.500 0.00 0.00 29.21 3.67
367 379 5.696270 TCTGCATCATGACGATTATACAACC 59.304 40.000 0.00 0.00 29.21 3.77
368 380 6.128715 CCTCTGCATCATGACGATTATACAAC 60.129 42.308 0.00 0.00 29.21 3.32
369 381 5.928264 CCTCTGCATCATGACGATTATACAA 59.072 40.000 0.00 0.00 29.21 2.41
370 382 5.473039 CCTCTGCATCATGACGATTATACA 58.527 41.667 0.00 0.00 29.21 2.29
371 383 4.328440 GCCTCTGCATCATGACGATTATAC 59.672 45.833 0.00 0.00 37.47 1.47
372 384 4.498241 GCCTCTGCATCATGACGATTATA 58.502 43.478 0.00 0.00 37.47 0.98
373 385 3.332919 GCCTCTGCATCATGACGATTAT 58.667 45.455 0.00 0.00 37.47 1.28
374 386 2.548707 GGCCTCTGCATCATGACGATTA 60.549 50.000 0.00 0.00 40.13 1.75
375 387 1.590932 GCCTCTGCATCATGACGATT 58.409 50.000 0.00 0.00 37.47 3.34
376 388 0.250209 GGCCTCTGCATCATGACGAT 60.250 55.000 0.00 0.00 40.13 3.73
377 389 1.144716 GGCCTCTGCATCATGACGA 59.855 57.895 0.00 0.00 40.13 4.20
378 390 1.153309 TGGCCTCTGCATCATGACG 60.153 57.895 3.32 0.00 40.13 4.35
379 391 0.818445 CCTGGCCTCTGCATCATGAC 60.818 60.000 3.32 0.00 40.13 3.06
380 392 1.530283 CCTGGCCTCTGCATCATGA 59.470 57.895 3.32 0.00 40.13 3.07
381 393 1.528542 CCCTGGCCTCTGCATCATG 60.529 63.158 3.32 0.00 40.13 3.07
382 394 2.764737 CCCCTGGCCTCTGCATCAT 61.765 63.158 3.32 0.00 40.13 2.45
383 395 3.414193 CCCCTGGCCTCTGCATCA 61.414 66.667 3.32 0.00 40.13 3.07
396 408 0.912486 CGAAAAGGAGGATGACCCCT 59.088 55.000 0.00 0.00 38.08 4.79
403 415 6.961360 AGTTTCTTTTTCGAAAAGGAGGAT 57.039 33.333 27.48 17.68 35.76 3.24
413 425 8.788806 TGCAATATTCCTTAGTTTCTTTTTCGA 58.211 29.630 0.00 0.00 0.00 3.71
414 426 8.964420 TGCAATATTCCTTAGTTTCTTTTTCG 57.036 30.769 0.00 0.00 0.00 3.46
459 477 1.778591 GCGACGTTTGGACAACATTTG 59.221 47.619 0.00 0.00 0.00 2.32
474 492 1.509787 CCATTGCGAGTTTGCGACG 60.510 57.895 0.00 0.00 37.81 5.12
479 497 1.701704 GCTTTCCCATTGCGAGTTTG 58.298 50.000 0.00 0.00 0.00 2.93
492 510 1.949257 CCACTTGACACCGCTTTCC 59.051 57.895 0.00 0.00 0.00 3.13
498 516 1.736645 CCGTAGCCACTTGACACCG 60.737 63.158 0.00 0.00 0.00 4.94
514 532 1.068741 CGGTTCTCCTATTTCCTCCCG 59.931 57.143 0.00 0.00 0.00 5.14
523 541 2.959707 CAAGGTAGCTCGGTTCTCCTAT 59.040 50.000 0.00 0.00 0.00 2.57
551 569 1.400846 GTATGTCCGAACTGAGCTCGA 59.599 52.381 6.86 0.00 38.61 4.04
560 578 1.068741 CAGCCCTAGGTATGTCCGAAC 59.931 57.143 8.29 0.00 41.99 3.95
587 605 0.478072 AGATCCTGGCCAAACACACA 59.522 50.000 7.01 0.00 0.00 3.72
588 606 2.359900 CTAGATCCTGGCCAAACACAC 58.640 52.381 7.01 0.00 0.00 3.82
589 607 1.340017 GCTAGATCCTGGCCAAACACA 60.340 52.381 7.01 0.00 31.69 3.72
590 608 1.383523 GCTAGATCCTGGCCAAACAC 58.616 55.000 7.01 0.00 31.69 3.32
591 609 0.107703 CGCTAGATCCTGGCCAAACA 60.108 55.000 7.01 0.00 34.43 2.83
592 610 0.815615 CCGCTAGATCCTGGCCAAAC 60.816 60.000 7.01 0.00 34.43 2.93
593 611 1.526887 CCGCTAGATCCTGGCCAAA 59.473 57.895 7.01 0.00 34.43 3.28
634 652 9.746711 GCATCGTTACAATCTTTAGCAATATAG 57.253 33.333 0.00 0.00 0.00 1.31
636 654 8.383318 AGCATCGTTACAATCTTTAGCAATAT 57.617 30.769 0.00 0.00 0.00 1.28
637 655 7.786178 AGCATCGTTACAATCTTTAGCAATA 57.214 32.000 0.00 0.00 0.00 1.90
638 656 6.683974 AGCATCGTTACAATCTTTAGCAAT 57.316 33.333 0.00 0.00 0.00 3.56
639 657 7.786178 ATAGCATCGTTACAATCTTTAGCAA 57.214 32.000 0.00 0.00 0.00 3.91
640 658 7.786178 AATAGCATCGTTACAATCTTTAGCA 57.214 32.000 0.00 0.00 0.00 3.49
641 659 8.335356 TCAAATAGCATCGTTACAATCTTTAGC 58.665 33.333 0.00 0.00 0.00 3.09
706 725 7.823149 AGTTGCAGATAATCTTTTGAATTGC 57.177 32.000 0.00 0.00 0.00 3.56
735 754 8.869897 AGTTCATTAGTGTACATCGTATTGTTG 58.130 33.333 0.00 0.00 0.00 3.33
736 755 8.997621 AGTTCATTAGTGTACATCGTATTGTT 57.002 30.769 0.00 0.00 0.00 2.83
737 756 8.869897 CAAGTTCATTAGTGTACATCGTATTGT 58.130 33.333 0.00 0.00 0.00 2.71
738 757 8.328146 CCAAGTTCATTAGTGTACATCGTATTG 58.672 37.037 0.00 0.00 0.00 1.90
893 916 2.108168 GGGTTTTAGAGGGGCATTTCC 58.892 52.381 0.00 0.00 0.00 3.13
907 930 4.820173 GCCGTGCTATTTATAGAGGGTTTT 59.180 41.667 0.97 0.00 32.05 2.43
924 947 1.131315 GGAAGAAATGAAGAGCCGTGC 59.869 52.381 0.00 0.00 0.00 5.34
956 979 4.471386 TCAGTGATTTAGGAAGGAGAAGGG 59.529 45.833 0.00 0.00 0.00 3.95
987 1010 2.028930 GGACGGCATGATAAGGGTAGAG 60.029 54.545 0.00 0.00 0.00 2.43
1007 1030 0.602905 AACGGAAGCGGAACTTGAGG 60.603 55.000 0.00 0.00 39.29 3.86
1024 1047 3.353836 TGGCGCGAAGGCTTGAAC 61.354 61.111 12.10 0.00 46.88 3.18
1026 1049 4.617520 TGTGGCGCGAAGGCTTGA 62.618 61.111 12.10 0.00 46.88 3.02
1030 1053 2.729491 GTTTTGTGGCGCGAAGGC 60.729 61.111 12.10 0.00 46.95 4.35
1047 1070 2.029369 TTCGTTCCGAACCCGTGG 59.971 61.111 5.67 0.00 41.05 4.94
1073 1096 1.193203 CCGCATCTTCGATCGGAATTG 59.807 52.381 16.41 8.04 44.23 2.32
1111 1137 0.889186 ACCACAAAGGCATCCGTCAC 60.889 55.000 0.00 0.00 43.14 3.67
1227 1253 4.477975 CGGAGGTCGTCGAGGTGC 62.478 72.222 4.85 0.00 0.00 5.01
1305 1331 1.944676 GATAGTGACGCGGCTTCGG 60.945 63.158 15.80 0.00 0.00 4.30
1445 1471 4.796231 CCTGCTCGAACGTCCCGG 62.796 72.222 9.85 0.00 0.00 5.73
1482 1508 2.030262 GGCGCCTATCAGCTCCAG 59.970 66.667 22.15 0.00 37.58 3.86
1640 1671 3.244700 CCCAATCACAAGACTTCAGGACT 60.245 47.826 0.00 0.00 0.00 3.85
1754 1795 9.411189 ACAAGGTTTAGATGTTGGTTTAGTAAA 57.589 29.630 0.00 0.00 0.00 2.01
1809 1860 8.253810 TCAGAAGAGAAAATATATATGGAGCCG 58.746 37.037 0.00 0.00 0.00 5.52
1825 1876 6.942005 TGCATAACCAAGAATTCAGAAGAGAA 59.058 34.615 8.44 0.00 0.00 2.87
1827 1878 6.748333 TGCATAACCAAGAATTCAGAAGAG 57.252 37.500 8.44 0.00 0.00 2.85
1828 1879 7.541162 CAATGCATAACCAAGAATTCAGAAGA 58.459 34.615 8.44 0.00 0.00 2.87
1829 1880 6.255020 GCAATGCATAACCAAGAATTCAGAAG 59.745 38.462 8.44 0.00 0.00 2.85
1830 1881 6.101332 GCAATGCATAACCAAGAATTCAGAA 58.899 36.000 8.44 0.00 0.00 3.02
1832 1883 5.290158 GTGCAATGCATAACCAAGAATTCAG 59.710 40.000 12.38 0.00 41.91 3.02
1833 1884 5.170021 GTGCAATGCATAACCAAGAATTCA 58.830 37.500 12.38 0.00 41.91 2.57
1834 1885 4.266029 CGTGCAATGCATAACCAAGAATTC 59.734 41.667 12.38 0.00 41.91 2.17
1837 1888 2.816672 TCGTGCAATGCATAACCAAGAA 59.183 40.909 12.38 0.00 41.91 2.52
1838 1889 2.161410 GTCGTGCAATGCATAACCAAGA 59.839 45.455 12.38 2.76 41.91 3.02
1839 1890 2.518949 GTCGTGCAATGCATAACCAAG 58.481 47.619 12.38 0.22 41.91 3.61
1843 1894 0.724549 TCGGTCGTGCAATGCATAAC 59.275 50.000 12.38 12.50 41.91 1.89
1844 1895 1.006086 CTCGGTCGTGCAATGCATAA 58.994 50.000 12.38 0.00 41.91 1.90
1845 1896 0.108377 ACTCGGTCGTGCAATGCATA 60.108 50.000 12.38 0.00 41.91 3.14
1846 1897 0.108377 TACTCGGTCGTGCAATGCAT 60.108 50.000 12.38 0.00 41.91 3.96
1848 1899 1.708027 GTACTCGGTCGTGCAATGC 59.292 57.895 0.00 0.00 0.00 3.56
1849 1900 0.731514 ACGTACTCGGTCGTGCAATG 60.732 55.000 0.00 0.00 41.85 2.82
1851 1902 0.110238 GTACGTACTCGGTCGTGCAA 60.110 55.000 18.47 0.00 40.96 4.08
1853 1904 1.578618 CGTACGTACTCGGTCGTGC 60.579 63.158 22.55 0.00 40.50 5.34
1854 1905 0.989164 TACGTACGTACTCGGTCGTG 59.011 55.000 23.60 7.67 44.24 4.35
1855 1906 1.269166 CTACGTACGTACTCGGTCGT 58.731 55.000 23.60 16.27 45.40 4.34
1856 1907 0.043822 GCTACGTACGTACTCGGTCG 60.044 60.000 23.60 13.21 41.85 4.79
1857 1908 0.999406 TGCTACGTACGTACTCGGTC 59.001 55.000 23.60 10.75 41.85 4.79
1858 1909 0.721718 GTGCTACGTACGTACTCGGT 59.278 55.000 23.60 15.43 41.85 4.69
1859 1910 0.026803 GGTGCTACGTACGTACTCGG 59.973 60.000 23.60 14.94 41.85 4.63
1860 1911 0.721154 TGGTGCTACGTACGTACTCG 59.279 55.000 23.60 15.29 43.34 4.18
1861 1912 3.181507 TGAATGGTGCTACGTACGTACTC 60.182 47.826 23.60 17.57 0.00 2.59
1862 1913 2.749076 TGAATGGTGCTACGTACGTACT 59.251 45.455 23.60 12.43 0.00 2.73
1863 1914 3.103738 CTGAATGGTGCTACGTACGTAC 58.896 50.000 23.60 16.71 0.00 3.67
1864 1915 2.749076 ACTGAATGGTGCTACGTACGTA 59.251 45.455 25.41 25.41 0.00 3.57
1865 1916 1.542915 ACTGAATGGTGCTACGTACGT 59.457 47.619 25.98 25.98 0.00 3.57
1866 1917 1.917955 CACTGAATGGTGCTACGTACG 59.082 52.381 15.01 15.01 0.00 3.67
1867 1918 2.268298 CCACTGAATGGTGCTACGTAC 58.732 52.381 0.00 0.00 44.46 3.67
1868 1919 2.665649 CCACTGAATGGTGCTACGTA 57.334 50.000 0.00 0.00 44.46 3.57
1869 1920 3.532896 CCACTGAATGGTGCTACGT 57.467 52.632 0.00 0.00 44.46 3.57
1975 2026 5.572126 GTCGATCGCCTCCACTAATATTAAC 59.428 44.000 11.09 0.00 0.00 2.01
2064 2136 4.852962 GAGCATCTGGCCTGTCTC 57.147 61.111 3.32 8.69 46.50 3.36
2370 2453 2.104963 ACGTTGGCTTCTCTCCTCTTTT 59.895 45.455 0.00 0.00 0.00 2.27
2371 2454 1.694696 ACGTTGGCTTCTCTCCTCTTT 59.305 47.619 0.00 0.00 0.00 2.52
2372 2455 1.343069 ACGTTGGCTTCTCTCCTCTT 58.657 50.000 0.00 0.00 0.00 2.85
2373 2456 2.217510 TACGTTGGCTTCTCTCCTCT 57.782 50.000 0.00 0.00 0.00 3.69
2374 2457 3.131400 AGATTACGTTGGCTTCTCTCCTC 59.869 47.826 0.00 0.00 0.00 3.71
2375 2458 3.100671 AGATTACGTTGGCTTCTCTCCT 58.899 45.455 0.00 0.00 0.00 3.69
2376 2459 3.449632 GAGATTACGTTGGCTTCTCTCC 58.550 50.000 0.00 0.00 32.07 3.71
2377 2460 3.109619 CGAGATTACGTTGGCTTCTCTC 58.890 50.000 0.00 0.00 32.50 3.20
2378 2461 2.159226 CCGAGATTACGTTGGCTTCTCT 60.159 50.000 0.00 0.00 32.50 3.10
2379 2462 2.194271 CCGAGATTACGTTGGCTTCTC 58.806 52.381 0.00 0.00 0.00 2.87
2380 2463 1.739371 GCCGAGATTACGTTGGCTTCT 60.739 52.381 0.00 0.00 42.44 2.85
2381 2464 0.651031 GCCGAGATTACGTTGGCTTC 59.349 55.000 0.00 0.00 42.44 3.86
2382 2465 0.743345 GGCCGAGATTACGTTGGCTT 60.743 55.000 0.00 0.00 45.06 4.35
2383 2466 1.153429 GGCCGAGATTACGTTGGCT 60.153 57.895 0.00 0.00 45.06 4.75
2384 2467 1.153429 AGGCCGAGATTACGTTGGC 60.153 57.895 0.00 0.00 44.98 4.52
2385 2468 0.810031 CCAGGCCGAGATTACGTTGG 60.810 60.000 0.00 0.00 0.00 3.77
2386 2469 0.108329 ACCAGGCCGAGATTACGTTG 60.108 55.000 0.00 0.00 0.00 4.10
2387 2470 0.108329 CACCAGGCCGAGATTACGTT 60.108 55.000 0.00 0.00 0.00 3.99
2388 2471 1.515954 CACCAGGCCGAGATTACGT 59.484 57.895 0.00 0.00 0.00 3.57
2389 2472 1.883084 GCACCAGGCCGAGATTACG 60.883 63.158 0.00 0.00 36.11 3.18
2390 2473 0.179045 ATGCACCAGGCCGAGATTAC 60.179 55.000 0.00 0.00 43.89 1.89
2391 2474 0.106708 GATGCACCAGGCCGAGATTA 59.893 55.000 0.00 0.00 43.89 1.75
2392 2475 1.153086 GATGCACCAGGCCGAGATT 60.153 57.895 0.00 0.00 43.89 2.40
2393 2476 2.507944 GATGCACCAGGCCGAGAT 59.492 61.111 0.00 0.00 43.89 2.75
2394 2477 4.147449 CGATGCACCAGGCCGAGA 62.147 66.667 0.00 0.00 43.89 4.04
2395 2478 3.958147 AACGATGCACCAGGCCGAG 62.958 63.158 0.00 0.00 43.89 4.63
2396 2479 3.545124 AAACGATGCACCAGGCCGA 62.545 57.895 0.00 0.00 43.89 5.54
2397 2480 2.141122 AAAAACGATGCACCAGGCCG 62.141 55.000 0.00 0.00 43.89 6.13
2398 2481 1.665442 AAAAACGATGCACCAGGCC 59.335 52.632 0.00 0.00 43.89 5.19
2419 2502 2.131183 CCATCTTAGCTACGCTTCAGC 58.869 52.381 0.00 0.00 40.44 4.26
2420 2503 3.444703 ACCATCTTAGCTACGCTTCAG 57.555 47.619 0.00 0.00 40.44 3.02
2421 2504 3.887621 AACCATCTTAGCTACGCTTCA 57.112 42.857 0.00 0.00 40.44 3.02
2422 2505 4.202131 ACCTAACCATCTTAGCTACGCTTC 60.202 45.833 0.00 0.00 40.44 3.86
2423 2506 3.705072 ACCTAACCATCTTAGCTACGCTT 59.295 43.478 0.00 0.00 40.44 4.68
2424 2507 3.297736 ACCTAACCATCTTAGCTACGCT 58.702 45.455 0.00 0.00 43.41 5.07
2425 2508 3.729862 ACCTAACCATCTTAGCTACGC 57.270 47.619 0.00 0.00 0.00 4.42
2426 2509 4.341520 AGGAACCTAACCATCTTAGCTACG 59.658 45.833 0.00 0.00 0.00 3.51
2427 2510 5.507650 CGAGGAACCTAACCATCTTAGCTAC 60.508 48.000 0.00 0.00 0.00 3.58
2428 2511 4.583489 CGAGGAACCTAACCATCTTAGCTA 59.417 45.833 0.00 0.00 0.00 3.32
2429 2512 3.385111 CGAGGAACCTAACCATCTTAGCT 59.615 47.826 0.00 0.00 0.00 3.32
2430 2513 3.132467 ACGAGGAACCTAACCATCTTAGC 59.868 47.826 0.00 0.00 0.00 3.09
2431 2514 4.401519 TCACGAGGAACCTAACCATCTTAG 59.598 45.833 0.00 0.00 0.00 2.18
2432 2515 4.346730 TCACGAGGAACCTAACCATCTTA 58.653 43.478 0.00 0.00 0.00 2.10
2433 2516 3.170717 TCACGAGGAACCTAACCATCTT 58.829 45.455 0.00 0.00 0.00 2.40
2434 2517 2.816411 TCACGAGGAACCTAACCATCT 58.184 47.619 0.00 0.00 0.00 2.90
2435 2518 3.458189 CATCACGAGGAACCTAACCATC 58.542 50.000 0.00 0.00 0.00 3.51
2436 2519 2.170607 CCATCACGAGGAACCTAACCAT 59.829 50.000 0.00 0.00 0.00 3.55
2437 2520 1.553248 CCATCACGAGGAACCTAACCA 59.447 52.381 0.00 0.00 0.00 3.67
2438 2521 1.829222 TCCATCACGAGGAACCTAACC 59.171 52.381 0.00 0.00 30.71 2.85
2439 2522 3.604875 TTCCATCACGAGGAACCTAAC 57.395 47.619 0.00 0.00 40.11 2.34
2445 2528 1.271163 GGTTGGTTCCATCACGAGGAA 60.271 52.381 0.00 0.00 42.62 3.36
2446 2529 0.323629 GGTTGGTTCCATCACGAGGA 59.676 55.000 0.00 0.00 0.00 3.71
2447 2530 0.676782 GGGTTGGTTCCATCACGAGG 60.677 60.000 0.00 0.00 0.00 4.63
2448 2531 0.036164 TGGGTTGGTTCCATCACGAG 59.964 55.000 0.00 0.00 0.00 4.18
2449 2532 0.695924 ATGGGTTGGTTCCATCACGA 59.304 50.000 0.00 0.00 40.74 4.35
2450 2533 3.264574 ATGGGTTGGTTCCATCACG 57.735 52.632 0.00 0.00 40.74 4.35
2465 2548 4.712337 AGTCTAGTACTTGAACCCTGATGG 59.288 45.833 8.65 0.00 33.35 3.51
2466 2549 5.923733 AGTCTAGTACTTGAACCCTGATG 57.076 43.478 8.65 0.00 33.35 3.07


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

AutoCloner maintained by Alex Coulton.