Multiple sequence alignment - TraesCS6D01G281800

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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 TraesCS6D01G281800 chr6D 100.000 4480 0 0 1 4480 389587734 389583255 0.000000e+00 8274.0
1 TraesCS6D01G281800 chr6D 87.243 486 58 3 226 711 337846805 337847286 6.550000e-153 551.0
2 TraesCS6D01G281800 chr6B 90.852 4285 202 78 324 4480 582828894 582824672 0.000000e+00 5566.0
3 TraesCS6D01G281800 chr6B 84.725 491 73 2 226 716 482469883 482469395 1.450000e-134 490.0
4 TraesCS6D01G281800 chr6A 92.084 3891 168 53 661 4480 535980421 535976600 0.000000e+00 5350.0
5 TraesCS6D01G281800 chr6A 92.414 145 11 0 85 229 384087777 384087921 1.630000e-49 207.0
6 TraesCS6D01G281800 chr6A 88.312 77 9 0 1865 1941 424798817 424798893 4.770000e-15 93.5
7 TraesCS6D01G281800 chr2D 87.474 479 57 3 226 703 617956778 617956302 2.360000e-152 549.0
8 TraesCS6D01G281800 chr4D 85.859 495 64 6 226 717 58273851 58274342 5.140000e-144 521.0
9 TraesCS6D01G281800 chr7D 84.979 486 67 5 226 711 602074370 602073891 5.210000e-134 488.0
10 TraesCS6D01G281800 chr7D 83.778 487 75 4 226 711 99187549 99187066 4.080000e-125 459.0
11 TraesCS6D01G281800 chr7D 79.526 591 86 30 2106 2668 136471337 136470754 5.430000e-104 388.0
12 TraesCS6D01G281800 chr3D 84.458 489 71 5 226 712 426881439 426880954 1.130000e-130 477.0
13 TraesCS6D01G281800 chr3D 74.286 210 34 14 2388 2583 71495604 71495401 2.240000e-08 71.3
14 TraesCS6D01G281800 chr3A 84.189 487 64 9 235 713 721342602 721343083 1.140000e-125 460.0
15 TraesCS6D01G281800 chr1D 83.436 489 77 4 226 711 347407886 347408373 6.830000e-123 451.0
16 TraesCS6D01G281800 chr1D 89.506 162 16 1 69 229 100462004 100461843 2.110000e-48 204.0
17 TraesCS6D01G281800 chr1D 90.260 154 14 1 77 229 348665001 348665154 2.730000e-47 200.0
18 TraesCS6D01G281800 chr7B 77.632 836 119 54 1867 2668 99629945 99630746 3.180000e-121 446.0
19 TraesCS6D01G281800 chr7A 77.377 831 127 48 1867 2668 136173147 136172349 1.910000e-118 436.0
20 TraesCS6D01G281800 chr7A 90.783 217 16 1 13 229 672533206 672532994 2.040000e-73 287.0
21 TraesCS6D01G281800 chr7A 88.679 212 21 2 19 229 672655190 672654981 5.750000e-64 255.0
22 TraesCS6D01G281800 chr5D 89.571 163 16 1 67 229 482583883 482584044 5.870000e-49 206.0
23 TraesCS6D01G281800 chr3B 86.082 194 23 4 37 229 5104243 5104433 5.870000e-49 206.0
24 TraesCS6D01G281800 chr3B 85.641 195 23 4 37 229 4232735 4232926 2.730000e-47 200.0
25 TraesCS6D01G281800 chr3B 88.889 45 5 0 2388 2432 117553110 117553066 6.260000e-04 56.5
26 TraesCS6D01G281800 chr2B 88.435 147 16 1 86 232 194639850 194639705 4.610000e-40 176.0
27 TraesCS6D01G281800 chrUn 85.246 61 8 1 2374 2433 9982666 9982726 1.350000e-05 62.1


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 TraesCS6D01G281800 chr6D 389583255 389587734 4479 True 8274 8274 100.000 1 4480 1 chr6D.!!$R1 4479
1 TraesCS6D01G281800 chr6B 582824672 582828894 4222 True 5566 5566 90.852 324 4480 1 chr6B.!!$R2 4156
2 TraesCS6D01G281800 chr6A 535976600 535980421 3821 True 5350 5350 92.084 661 4480 1 chr6A.!!$R1 3819
3 TraesCS6D01G281800 chr7D 136470754 136471337 583 True 388 388 79.526 2106 2668 1 chr7D.!!$R2 562
4 TraesCS6D01G281800 chr7B 99629945 99630746 801 False 446 446 77.632 1867 2668 1 chr7B.!!$F1 801
5 TraesCS6D01G281800 chr7A 136172349 136173147 798 True 436 436 77.377 1867 2668 1 chr7A.!!$R1 801

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
743 754 0.108851 GGCGCCCGTTCATTCATTTT 60.109 50.0 18.11 0.0 0.0 1.82 F
1229 1250 0.179004 TTCCCTTGCTCGCCTTTTGA 60.179 50.0 0.00 0.0 0.0 2.69 F
1837 1882 0.313672 GACGCTGCACATTTTTCCCA 59.686 50.0 0.00 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 1861 0.729140 GGAAAAATGTGCAGCGTCGG 60.729 55.0 0.0 0.0 0.00 4.79 R
2964 3089 0.108585 TTGGTCACCCAGCAGAGTTC 59.891 55.0 0.0 0.0 43.15 3.01 R
3800 3941 0.035458 CTGAACACTCCCTTTCCGCT 59.965 55.0 0.0 0.0 0.00 5.52 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
189 190 7.463961 AAAGTAGAGATACTTTGACTTCGGA 57.536 36.000 11.52 0.00 45.44 4.55
190 191 6.439675 AGTAGAGATACTTTGACTTCGGAC 57.560 41.667 0.00 0.00 0.00 4.79
191 192 5.944599 AGTAGAGATACTTTGACTTCGGACA 59.055 40.000 0.00 0.00 0.00 4.02
192 193 5.723672 AGAGATACTTTGACTTCGGACAA 57.276 39.130 0.00 0.00 0.00 3.18
193 194 6.097915 AGAGATACTTTGACTTCGGACAAA 57.902 37.500 0.00 0.00 37.29 2.83
194 195 6.522054 AGAGATACTTTGACTTCGGACAAAA 58.478 36.000 0.00 0.00 38.59 2.44
195 196 6.424207 AGAGATACTTTGACTTCGGACAAAAC 59.576 38.462 0.00 0.00 38.59 2.43
196 197 6.289064 AGATACTTTGACTTCGGACAAAACT 58.711 36.000 0.00 0.00 38.59 2.66
197 198 6.766467 AGATACTTTGACTTCGGACAAAACTT 59.234 34.615 0.00 0.00 38.59 2.66
198 199 7.929785 AGATACTTTGACTTCGGACAAAACTTA 59.070 33.333 0.00 0.00 38.59 2.24
199 200 6.937436 ACTTTGACTTCGGACAAAACTTAT 57.063 33.333 0.00 0.00 38.59 1.73
200 201 9.715121 ATACTTTGACTTCGGACAAAACTTATA 57.285 29.630 0.00 0.00 38.59 0.98
201 202 8.617290 ACTTTGACTTCGGACAAAACTTATAT 57.383 30.769 0.00 0.00 38.59 0.86
202 203 8.504005 ACTTTGACTTCGGACAAAACTTATATG 58.496 33.333 0.00 0.00 38.59 1.78
203 204 6.417191 TGACTTCGGACAAAACTTATATGC 57.583 37.500 0.00 0.00 0.00 3.14
204 205 5.935206 TGACTTCGGACAAAACTTATATGCA 59.065 36.000 0.00 0.00 0.00 3.96
205 206 6.092122 TGACTTCGGACAAAACTTATATGCAG 59.908 38.462 0.00 0.00 0.00 4.41
206 207 6.170506 ACTTCGGACAAAACTTATATGCAGA 58.829 36.000 0.00 0.00 0.00 4.26
207 208 6.092259 ACTTCGGACAAAACTTATATGCAGAC 59.908 38.462 0.00 0.00 0.00 3.51
208 209 5.730550 TCGGACAAAACTTATATGCAGACT 58.269 37.500 0.00 0.00 0.00 3.24
209 210 6.869695 TCGGACAAAACTTATATGCAGACTA 58.130 36.000 0.00 0.00 0.00 2.59
210 211 7.324935 TCGGACAAAACTTATATGCAGACTAA 58.675 34.615 0.00 0.00 0.00 2.24
211 212 7.820386 TCGGACAAAACTTATATGCAGACTAAA 59.180 33.333 0.00 0.00 0.00 1.85
212 213 8.447833 CGGACAAAACTTATATGCAGACTAAAA 58.552 33.333 0.00 0.00 0.00 1.52
219 220 8.142994 ACTTATATGCAGACTAAAAATGACCG 57.857 34.615 0.00 0.00 0.00 4.79
220 221 7.226720 ACTTATATGCAGACTAAAAATGACCGG 59.773 37.037 0.00 0.00 0.00 5.28
221 222 3.410631 TGCAGACTAAAAATGACCGGA 57.589 42.857 9.46 0.00 0.00 5.14
222 223 3.334691 TGCAGACTAAAAATGACCGGAG 58.665 45.455 9.46 0.00 0.00 4.63
236 237 3.284711 CGGAGGGAGTAGTTCAGGT 57.715 57.895 0.00 0.00 0.00 4.00
237 238 1.558233 CGGAGGGAGTAGTTCAGGTT 58.442 55.000 0.00 0.00 0.00 3.50
238 239 2.731572 CGGAGGGAGTAGTTCAGGTTA 58.268 52.381 0.00 0.00 0.00 2.85
239 240 2.688958 CGGAGGGAGTAGTTCAGGTTAG 59.311 54.545 0.00 0.00 0.00 2.34
240 241 3.032459 GGAGGGAGTAGTTCAGGTTAGG 58.968 54.545 0.00 0.00 0.00 2.69
241 242 3.032459 GAGGGAGTAGTTCAGGTTAGGG 58.968 54.545 0.00 0.00 0.00 3.53
242 243 2.386113 AGGGAGTAGTTCAGGTTAGGGT 59.614 50.000 0.00 0.00 0.00 4.34
243 244 3.179685 GGGAGTAGTTCAGGTTAGGGTT 58.820 50.000 0.00 0.00 0.00 4.11
244 245 3.586174 GGGAGTAGTTCAGGTTAGGGTTT 59.414 47.826 0.00 0.00 0.00 3.27
245 246 4.042560 GGGAGTAGTTCAGGTTAGGGTTTT 59.957 45.833 0.00 0.00 0.00 2.43
246 247 5.457197 GGGAGTAGTTCAGGTTAGGGTTTTT 60.457 44.000 0.00 0.00 0.00 1.94
264 265 2.068837 TTTAGTCGTTGTAGGTGCGG 57.931 50.000 0.00 0.00 0.00 5.69
265 266 0.961019 TTAGTCGTTGTAGGTGCGGT 59.039 50.000 0.00 0.00 0.00 5.68
266 267 0.241749 TAGTCGTTGTAGGTGCGGTG 59.758 55.000 0.00 0.00 0.00 4.94
267 268 2.356553 TCGTTGTAGGTGCGGTGC 60.357 61.111 0.00 0.00 0.00 5.01
268 269 2.357034 CGTTGTAGGTGCGGTGCT 60.357 61.111 0.00 0.00 0.00 4.40
269 270 1.959226 CGTTGTAGGTGCGGTGCTT 60.959 57.895 0.00 0.00 0.00 3.91
270 271 1.574428 GTTGTAGGTGCGGTGCTTG 59.426 57.895 0.00 0.00 0.00 4.01
271 272 1.599518 TTGTAGGTGCGGTGCTTGG 60.600 57.895 0.00 0.00 0.00 3.61
272 273 2.746277 GTAGGTGCGGTGCTTGGG 60.746 66.667 0.00 0.00 0.00 4.12
273 274 4.715523 TAGGTGCGGTGCTTGGGC 62.716 66.667 0.00 0.00 39.26 5.36
290 291 2.104331 CGGATGGCGACGCTACTT 59.896 61.111 20.77 0.00 0.00 2.24
291 292 1.944676 CGGATGGCGACGCTACTTC 60.945 63.158 20.77 9.04 0.00 3.01
292 293 1.437986 GGATGGCGACGCTACTTCT 59.562 57.895 20.77 0.00 0.00 2.85
293 294 0.179108 GGATGGCGACGCTACTTCTT 60.179 55.000 20.77 0.00 0.00 2.52
294 295 1.201343 GATGGCGACGCTACTTCTTC 58.799 55.000 20.77 3.75 0.00 2.87
295 296 0.525668 ATGGCGACGCTACTTCTTCG 60.526 55.000 20.77 0.00 34.56 3.79
296 297 1.136147 GGCGACGCTACTTCTTCGA 59.864 57.895 20.77 0.00 33.20 3.71
297 298 0.862283 GGCGACGCTACTTCTTCGAG 60.862 60.000 20.77 0.00 33.20 4.04
298 299 0.179194 GCGACGCTACTTCTTCGAGT 60.179 55.000 13.73 0.00 33.20 4.18
299 300 1.728502 GCGACGCTACTTCTTCGAGTT 60.729 52.381 13.73 0.00 33.20 3.01
300 301 2.582687 CGACGCTACTTCTTCGAGTTT 58.417 47.619 0.00 0.00 33.20 2.66
301 302 2.338813 CGACGCTACTTCTTCGAGTTTG 59.661 50.000 0.00 0.00 33.20 2.93
302 303 3.306818 GACGCTACTTCTTCGAGTTTGT 58.693 45.455 0.00 0.00 0.00 2.83
303 304 3.306818 ACGCTACTTCTTCGAGTTTGTC 58.693 45.455 0.00 0.00 0.00 3.18
304 305 3.004524 ACGCTACTTCTTCGAGTTTGTCT 59.995 43.478 0.00 0.00 0.00 3.41
305 306 3.982058 CGCTACTTCTTCGAGTTTGTCTT 59.018 43.478 0.00 0.00 0.00 3.01
306 307 4.088781 CGCTACTTCTTCGAGTTTGTCTTC 59.911 45.833 0.00 0.00 0.00 2.87
307 308 4.386350 GCTACTTCTTCGAGTTTGTCTTCC 59.614 45.833 0.00 0.00 0.00 3.46
308 309 3.381949 ACTTCTTCGAGTTTGTCTTCCG 58.618 45.455 0.00 0.00 0.00 4.30
309 310 2.433868 TCTTCGAGTTTGTCTTCCGG 57.566 50.000 0.00 0.00 0.00 5.14
310 311 1.000506 TCTTCGAGTTTGTCTTCCGGG 59.999 52.381 0.00 0.00 0.00 5.73
311 312 0.601841 TTCGAGTTTGTCTTCCGGGC 60.602 55.000 0.00 0.00 0.00 6.13
312 313 1.004918 CGAGTTTGTCTTCCGGGCT 60.005 57.895 0.00 0.00 0.00 5.19
313 314 1.014564 CGAGTTTGTCTTCCGGGCTC 61.015 60.000 0.00 0.00 0.00 4.70
314 315 0.673956 GAGTTTGTCTTCCGGGCTCC 60.674 60.000 0.00 0.00 0.00 4.70
325 326 3.299190 GGGCTCCGATCCTCCTCG 61.299 72.222 0.00 0.00 38.37 4.63
326 327 2.203365 GGCTCCGATCCTCCTCGA 60.203 66.667 0.00 0.00 41.12 4.04
327 328 2.265182 GGCTCCGATCCTCCTCGAG 61.265 68.421 5.13 5.13 41.12 4.04
328 329 1.527380 GCTCCGATCCTCCTCGAGT 60.527 63.158 12.31 0.00 41.12 4.18
329 330 1.104577 GCTCCGATCCTCCTCGAGTT 61.105 60.000 12.31 0.00 41.12 3.01
330 331 1.394618 CTCCGATCCTCCTCGAGTTT 58.605 55.000 12.31 0.00 41.12 2.66
331 332 1.066303 CTCCGATCCTCCTCGAGTTTG 59.934 57.143 12.31 0.64 41.12 2.93
332 333 0.818296 CCGATCCTCCTCGAGTTTGT 59.182 55.000 12.31 0.00 41.12 2.83
333 334 1.202313 CCGATCCTCCTCGAGTTTGTC 60.202 57.143 12.31 2.18 41.12 3.18
334 335 1.746220 CGATCCTCCTCGAGTTTGTCT 59.254 52.381 12.31 0.00 41.12 3.41
335 336 2.478709 CGATCCTCCTCGAGTTTGTCTG 60.479 54.545 12.31 0.00 41.12 3.51
336 337 1.996798 TCCTCCTCGAGTTTGTCTGT 58.003 50.000 12.31 0.00 0.00 3.41
375 376 1.436983 CTCCGGCGTAAATTCCTGCC 61.437 60.000 6.01 5.04 44.09 4.85
379 380 1.680338 GGCGTAAATTCCTGCCATCT 58.320 50.000 9.25 0.00 46.76 2.90
384 385 4.142381 GCGTAAATTCCTGCCATCTCTTTT 60.142 41.667 0.00 0.00 0.00 2.27
387 388 2.220653 TTCCTGCCATCTCTTTTGGG 57.779 50.000 0.00 0.00 34.66 4.12
388 389 0.332632 TCCTGCCATCTCTTTTGGGG 59.667 55.000 0.00 0.00 34.66 4.96
408 409 2.608268 GCGGTGAGGTTAGAGTTTCTC 58.392 52.381 0.00 0.00 0.00 2.87
429 430 2.224549 CGTCTTGTGGCGAAATTTGGTA 59.775 45.455 0.00 0.00 0.00 3.25
430 431 3.119990 CGTCTTGTGGCGAAATTTGGTAT 60.120 43.478 0.00 0.00 0.00 2.73
434 435 3.680490 TGTGGCGAAATTTGGTATCAGA 58.320 40.909 0.00 0.00 0.00 3.27
439 440 4.202050 GGCGAAATTTGGTATCAGATGCTT 60.202 41.667 0.00 0.00 0.00 3.91
451 452 4.268797 TCAGATGCTTCAGATCTATGCC 57.731 45.455 0.00 0.00 0.00 4.40
462 463 2.846206 AGATCTATGCCAGGGTTCAACA 59.154 45.455 0.00 0.00 0.00 3.33
469 470 1.300620 CAGGGTTCAACAGCGACGA 60.301 57.895 0.00 0.00 0.00 4.20
470 471 0.670546 CAGGGTTCAACAGCGACGAT 60.671 55.000 0.00 0.00 0.00 3.73
486 487 1.675641 GATTGTGGCTCAAGGGCGT 60.676 57.895 8.09 0.00 44.11 5.68
502 503 0.751643 GCGTTGGTCCTTATGGGCAT 60.752 55.000 1.21 0.00 40.42 4.40
508 509 1.027357 GTCCTTATGGGCATGTGCAG 58.973 55.000 7.36 0.00 44.36 4.41
512 513 2.101783 CTTATGGGCATGTGCAGGAAA 58.898 47.619 7.36 0.00 44.36 3.13
517 518 1.337167 GGGCATGTGCAGGAAAACTTC 60.337 52.381 7.36 0.00 44.36 3.01
532 533 1.519455 CTTCCCGGCTGTCATCGAC 60.519 63.158 0.00 0.00 0.00 4.20
544 545 0.684535 TCATCGACAAGGTCAAGCCA 59.315 50.000 0.00 0.00 40.61 4.75
552 553 0.250338 AAGGTCAAGCCAACTCCGAC 60.250 55.000 0.00 0.00 40.61 4.79
555 556 0.951040 GTCAAGCCAACTCCGACAGG 60.951 60.000 0.00 0.00 39.46 4.00
559 560 2.890766 GCCAACTCCGACAGGGGAA 61.891 63.158 0.00 0.00 41.93 3.97
562 563 1.532316 AACTCCGACAGGGGAACGA 60.532 57.895 0.00 0.00 41.93 3.85
565 566 4.430765 CCGACAGGGGAACGACGG 62.431 72.222 0.00 0.00 34.77 4.79
592 593 4.415332 GTCGGCGGCTCGTTCTGA 62.415 66.667 3.23 0.00 0.00 3.27
593 594 3.449227 TCGGCGGCTCGTTCTGAT 61.449 61.111 7.21 0.00 0.00 2.90
594 595 3.257561 CGGCGGCTCGTTCTGATG 61.258 66.667 7.61 0.00 0.00 3.07
595 596 2.892425 GGCGGCTCGTTCTGATGG 60.892 66.667 0.00 0.00 0.00 3.51
596 597 3.567797 GCGGCTCGTTCTGATGGC 61.568 66.667 0.00 0.00 0.00 4.40
597 598 2.125552 CGGCTCGTTCTGATGGCA 60.126 61.111 0.00 0.00 0.00 4.92
598 599 2.169789 CGGCTCGTTCTGATGGCAG 61.170 63.158 0.00 0.00 43.67 4.85
599 600 1.078848 GGCTCGTTCTGATGGCAGT 60.079 57.895 0.00 0.00 42.84 4.40
600 601 0.175760 GGCTCGTTCTGATGGCAGTA 59.824 55.000 0.00 0.00 42.84 2.74
601 602 1.281899 GCTCGTTCTGATGGCAGTAC 58.718 55.000 0.00 0.00 42.84 2.73
606 607 2.612972 CGTTCTGATGGCAGTACTGGTT 60.613 50.000 23.95 0.00 42.84 3.67
621 622 0.631753 TGGTTGTTTGGGGGTCTTGA 59.368 50.000 0.00 0.00 0.00 3.02
667 678 3.953712 TCGAGATGCTTTGTACTTCCA 57.046 42.857 0.00 0.00 0.00 3.53
676 687 4.574828 TGCTTTGTACTTCCACTGAACTTC 59.425 41.667 0.00 0.00 0.00 3.01
691 702 7.443575 CCACTGAACTTCAATAATAGATCTGGG 59.556 40.741 5.18 0.00 0.00 4.45
696 707 9.213799 GAACTTCAATAATAGATCTGGGTCATC 57.786 37.037 5.18 0.00 0.00 2.92
705 716 2.099141 TCTGGGTCATCTTCGCAAAG 57.901 50.000 0.00 0.00 0.00 2.77
706 717 1.623311 TCTGGGTCATCTTCGCAAAGA 59.377 47.619 0.00 0.00 45.36 2.52
707 718 2.038426 TCTGGGTCATCTTCGCAAAGAA 59.962 45.455 0.00 0.00 44.49 2.52
743 754 0.108851 GGCGCCCGTTCATTCATTTT 60.109 50.000 18.11 0.00 0.00 1.82
744 755 1.268265 GCGCCCGTTCATTCATTTTC 58.732 50.000 0.00 0.00 0.00 2.29
745 756 1.402194 GCGCCCGTTCATTCATTTTCA 60.402 47.619 0.00 0.00 0.00 2.69
746 757 2.735126 GCGCCCGTTCATTCATTTTCAT 60.735 45.455 0.00 0.00 0.00 2.57
747 758 3.510719 CGCCCGTTCATTCATTTTCATT 58.489 40.909 0.00 0.00 0.00 2.57
748 759 3.925913 CGCCCGTTCATTCATTTTCATTT 59.074 39.130 0.00 0.00 0.00 2.32
880 900 4.075793 CCGTGGGGAGGGGAGAGA 62.076 72.222 0.00 0.00 34.06 3.10
885 905 1.073098 TGGGGAGGGGAGAGAAAAAC 58.927 55.000 0.00 0.00 0.00 2.43
1227 1248 1.515521 CGTTCCCTTGCTCGCCTTTT 61.516 55.000 0.00 0.00 0.00 2.27
1229 1250 0.179004 TTCCCTTGCTCGCCTTTTGA 60.179 50.000 0.00 0.00 0.00 2.69
1231 1252 1.207593 CCTTGCTCGCCTTTTGACG 59.792 57.895 0.00 0.00 0.00 4.35
1466 1503 3.975035 GGATCACACTGCGTTTCTTTTTC 59.025 43.478 0.00 0.00 0.00 2.29
1467 1504 4.261197 GGATCACACTGCGTTTCTTTTTCT 60.261 41.667 0.00 0.00 0.00 2.52
1468 1505 4.695217 TCACACTGCGTTTCTTTTTCTT 57.305 36.364 0.00 0.00 0.00 2.52
1471 1508 5.344665 TCACACTGCGTTTCTTTTTCTTTTG 59.655 36.000 0.00 0.00 0.00 2.44
1479 1522 5.343860 CGTTTCTTTTTCTTTTGGTGTCGTT 59.656 36.000 0.00 0.00 0.00 3.85
1480 1523 6.129035 CGTTTCTTTTTCTTTTGGTGTCGTTT 60.129 34.615 0.00 0.00 0.00 3.60
1617 1660 7.757526 TCTTCAATTTTCGTCTGAACTTTTGA 58.242 30.769 0.00 0.00 32.71 2.69
1621 1664 8.405531 TCAATTTTCGTCTGAACTTTTGATCTT 58.594 29.630 0.00 0.00 32.71 2.40
1622 1665 9.023967 CAATTTTCGTCTGAACTTTTGATCTTT 57.976 29.630 0.00 0.00 32.71 2.52
1623 1666 7.969387 TTTTCGTCTGAACTTTTGATCTTTG 57.031 32.000 0.00 0.00 32.71 2.77
1625 1668 6.287107 TCGTCTGAACTTTTGATCTTTGAC 57.713 37.500 0.00 0.00 0.00 3.18
1627 1670 5.904080 CGTCTGAACTTTTGATCTTTGACAC 59.096 40.000 0.00 0.00 0.00 3.67
1628 1671 6.456853 CGTCTGAACTTTTGATCTTTGACACA 60.457 38.462 0.00 0.00 0.00 3.72
1629 1672 6.909357 GTCTGAACTTTTGATCTTTGACACAG 59.091 38.462 0.00 0.00 0.00 3.66
1631 1674 4.574599 ACTTTTGATCTTTGACACAGGC 57.425 40.909 0.00 0.00 0.00 4.85
1632 1675 4.210331 ACTTTTGATCTTTGACACAGGCT 58.790 39.130 0.00 0.00 0.00 4.58
1633 1676 4.037208 ACTTTTGATCTTTGACACAGGCTG 59.963 41.667 14.16 14.16 0.00 4.85
1634 1677 3.490439 TTGATCTTTGACACAGGCTGA 57.510 42.857 23.66 0.00 0.00 4.26
1635 1678 3.708403 TGATCTTTGACACAGGCTGAT 57.292 42.857 23.66 8.79 0.00 2.90
1636 1679 3.603532 TGATCTTTGACACAGGCTGATC 58.396 45.455 23.66 17.89 0.00 2.92
1662 1707 3.384146 TCAAGTTGATGGCATTGTGTTGT 59.616 39.130 0.00 0.00 0.00 3.32
1803 1848 3.019564 AGGATCTCCCTGCAATTTTTCG 58.980 45.455 0.00 0.00 45.61 3.46
1811 1856 5.410067 TCCCTGCAATTTTTCGATGAAATC 58.590 37.500 7.48 0.00 40.89 2.17
1816 1861 7.280730 TGCAATTTTTCGATGAAATCATGAC 57.719 32.000 0.00 0.00 45.97 3.06
1820 1865 4.857871 TTTCGATGAAATCATGACCGAC 57.142 40.909 0.00 0.00 45.97 4.79
1836 1881 0.729140 CGACGCTGCACATTTTTCCC 60.729 55.000 0.00 0.00 0.00 3.97
1837 1882 0.313672 GACGCTGCACATTTTTCCCA 59.686 50.000 0.00 0.00 0.00 4.37
1838 1883 0.968405 ACGCTGCACATTTTTCCCAT 59.032 45.000 0.00 0.00 0.00 4.00
1839 1884 1.337074 ACGCTGCACATTTTTCCCATG 60.337 47.619 0.00 0.00 0.00 3.66
1840 1885 1.067706 CGCTGCACATTTTTCCCATGA 60.068 47.619 0.00 0.00 0.00 3.07
1848 1893 6.598457 TGCACATTTTTCCCATGAAATTATGG 59.402 34.615 0.00 0.76 45.83 2.74
2709 2817 2.872557 TCGACCACGAGTAAGCCG 59.127 61.111 0.00 0.00 43.81 5.52
2726 2836 2.927056 GATCCCATCACCCACCCC 59.073 66.667 0.00 0.00 0.00 4.95
2727 2837 2.006415 GATCCCATCACCCACCCCA 61.006 63.158 0.00 0.00 0.00 4.96
2758 2880 1.864862 CTCTGTTTGTGCTCGCTGG 59.135 57.895 0.00 0.00 0.00 4.85
2775 2897 3.058016 CGCTGGTGTTGATTTCATCTGTT 60.058 43.478 0.00 0.00 0.00 3.16
2821 2943 1.153881 GGACCTGAACTACCGCGTC 60.154 63.158 4.92 0.00 0.00 5.19
2842 2964 1.794864 GCTGAGCTACGACGAGACA 59.205 57.895 0.00 0.00 0.00 3.41
2950 3072 1.143305 GATATGCTACAGTGGCAGCG 58.857 55.000 17.46 0.00 43.15 5.18
2951 3073 0.752658 ATATGCTACAGTGGCAGCGA 59.247 50.000 17.46 5.64 43.15 4.93
2952 3074 0.534873 TATGCTACAGTGGCAGCGAA 59.465 50.000 17.46 0.22 43.15 4.70
2964 3089 1.539776 GCAGCGAACAAAACCAAGCG 61.540 55.000 0.00 0.00 0.00 4.68
2967 3093 0.843872 GCGAACAAAACCAAGCGAAC 59.156 50.000 0.00 0.00 0.00 3.95
2976 3102 2.037136 CCAAGCGAACTCTGCTGGG 61.037 63.158 0.00 0.00 46.66 4.45
3081 3207 1.010350 CTACTTCGCGCCGACGTAT 60.010 57.895 15.02 0.00 39.22 3.06
3177 3304 3.431233 GGTAGTTACCAGCAGAAAACGAC 59.569 47.826 3.45 0.00 45.73 4.34
3179 3306 2.158871 AGTTACCAGCAGAAAACGACCA 60.159 45.455 0.00 0.00 0.00 4.02
3183 3310 1.581934 CAGCAGAAAACGACCAGTCA 58.418 50.000 0.00 0.00 0.00 3.41
3212 3339 6.729690 TCTGAACCATGAAATTTTCAGGTT 57.270 33.333 27.61 27.61 45.36 3.50
3215 3342 7.710475 TCTGAACCATGAAATTTTCAGGTTTTC 59.290 33.333 27.75 23.49 44.08 2.29
3221 3348 4.568760 TGAAATTTTCAGGTTTTCGCCAAC 59.431 37.500 7.74 0.00 34.08 3.77
3222 3349 4.400529 AATTTTCAGGTTTTCGCCAACT 57.599 36.364 0.00 0.00 0.00 3.16
3223 3350 2.861462 TTTCAGGTTTTCGCCAACTG 57.139 45.000 0.00 0.00 0.00 3.16
3224 3351 2.045561 TTCAGGTTTTCGCCAACTGA 57.954 45.000 0.00 0.00 0.00 3.41
3225 3352 1.305201 TCAGGTTTTCGCCAACTGAC 58.695 50.000 0.00 0.00 0.00 3.51
3227 3354 1.370051 GGTTTTCGCCAACTGACGC 60.370 57.895 0.00 0.00 0.00 5.19
3228 3355 1.353804 GTTTTCGCCAACTGACGCA 59.646 52.632 0.00 0.00 0.00 5.24
3229 3356 0.928451 GTTTTCGCCAACTGACGCAC 60.928 55.000 0.00 0.00 0.00 5.34
3231 3358 1.771073 TTTCGCCAACTGACGCACTG 61.771 55.000 0.00 0.00 0.00 3.66
3232 3359 2.916502 TTCGCCAACTGACGCACTGT 62.917 55.000 0.00 0.00 0.00 3.55
3233 3360 2.534019 CGCCAACTGACGCACTGTT 61.534 57.895 0.00 0.00 40.37 3.16
3234 3361 1.218875 CGCCAACTGACGCACTGTTA 61.219 55.000 5.49 0.00 38.31 2.41
3235 3362 0.234884 GCCAACTGACGCACTGTTAC 59.765 55.000 5.49 0.00 38.31 2.50
3248 3384 1.027357 CTGTTACCTCCATGCCATGC 58.973 55.000 0.00 0.00 0.00 4.06
3250 3386 0.395586 GTTACCTCCATGCCATGCCA 60.396 55.000 0.00 0.00 0.00 4.92
3492 3628 8.258007 TCTATGACTTTTGACCTGTTATAGTGG 58.742 37.037 0.00 0.00 34.22 4.00
3494 3630 6.597562 TGACTTTTGACCTGTTATAGTGGTT 58.402 36.000 0.00 0.00 33.74 3.67
3547 3684 7.397476 ACACAAGGATCAGAAATGTCTCTAGTA 59.603 37.037 0.00 0.00 28.78 1.82
3584 3721 4.326504 AGTTTTTCAACTTCCATGCCTG 57.673 40.909 0.00 0.00 40.66 4.85
3633 3770 4.989875 AATGGTGGCTTCTAGCAGATAT 57.010 40.909 0.00 0.00 44.75 1.63
3681 3819 4.794246 GCTTTGACACTAGCTTAGTACTCG 59.206 45.833 0.00 0.00 37.23 4.18
3810 3951 6.510879 AAAGTTAAGAAATAGCGGAAAGGG 57.489 37.500 0.00 0.00 0.00 3.95
3811 3952 5.431179 AGTTAAGAAATAGCGGAAAGGGA 57.569 39.130 0.00 0.00 0.00 4.20
3812 3953 5.429130 AGTTAAGAAATAGCGGAAAGGGAG 58.571 41.667 0.00 0.00 0.00 4.30
3814 3955 3.268023 AGAAATAGCGGAAAGGGAGTG 57.732 47.619 0.00 0.00 0.00 3.51
4026 4167 4.160626 CACTTCCCCCTTGTGTGTTAAAAA 59.839 41.667 0.00 0.00 0.00 1.94
4173 4314 2.687914 GCTGATGCAATACCTTCCCCTT 60.688 50.000 0.00 0.00 39.41 3.95
4245 4416 5.909477 TCTTTTCAGAAACGGTCTCAGTTA 58.091 37.500 0.00 0.00 32.70 2.24
4246 4417 6.342906 TCTTTTCAGAAACGGTCTCAGTTAA 58.657 36.000 0.00 0.00 32.70 2.01
4271 4442 2.854777 CTCCTTTACAGATTCAGTCGCG 59.145 50.000 0.00 0.00 0.00 5.87
4289 4460 0.035343 CGTTTTCTCCCCTCTTCCCC 60.035 60.000 0.00 0.00 0.00 4.81
4343 4514 1.808133 GCAGCCTCGGTATCTTCCTTG 60.808 57.143 0.00 0.00 0.00 3.61
4385 4556 1.471684 CCACTCTTTTCAGATGCAGCC 59.528 52.381 0.00 0.00 0.00 4.85
4402 4573 1.177401 GCCTCTGTTTCCCCAATCAC 58.823 55.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
167 168 5.944599 TGTCCGAAGTCAAAGTATCTCTACT 59.055 40.000 0.00 0.00 39.97 2.57
168 169 6.192234 TGTCCGAAGTCAAAGTATCTCTAC 57.808 41.667 0.00 0.00 0.00 2.59
169 170 6.829229 TTGTCCGAAGTCAAAGTATCTCTA 57.171 37.500 0.00 0.00 0.00 2.43
170 171 5.723672 TTGTCCGAAGTCAAAGTATCTCT 57.276 39.130 0.00 0.00 0.00 3.10
171 172 6.424207 AGTTTTGTCCGAAGTCAAAGTATCTC 59.576 38.462 0.00 0.00 35.47 2.75
172 173 6.289064 AGTTTTGTCCGAAGTCAAAGTATCT 58.711 36.000 0.00 0.00 35.47 1.98
173 174 6.541111 AGTTTTGTCCGAAGTCAAAGTATC 57.459 37.500 0.00 0.00 35.47 2.24
174 175 6.937436 AAGTTTTGTCCGAAGTCAAAGTAT 57.063 33.333 0.00 0.00 35.47 2.12
175 176 9.715121 ATATAAGTTTTGTCCGAAGTCAAAGTA 57.285 29.630 0.00 0.00 35.47 2.24
176 177 6.937436 ATAAGTTTTGTCCGAAGTCAAAGT 57.063 33.333 0.00 0.00 35.47 2.66
177 178 7.481798 GCATATAAGTTTTGTCCGAAGTCAAAG 59.518 37.037 0.00 0.00 35.47 2.77
178 179 7.041030 TGCATATAAGTTTTGTCCGAAGTCAAA 60.041 33.333 0.00 0.00 32.75 2.69
179 180 6.428465 TGCATATAAGTTTTGTCCGAAGTCAA 59.572 34.615 0.00 0.00 0.00 3.18
180 181 5.935206 TGCATATAAGTTTTGTCCGAAGTCA 59.065 36.000 0.00 0.00 0.00 3.41
181 182 6.312918 TCTGCATATAAGTTTTGTCCGAAGTC 59.687 38.462 0.00 0.00 0.00 3.01
182 183 6.092259 GTCTGCATATAAGTTTTGTCCGAAGT 59.908 38.462 0.00 0.00 0.00 3.01
183 184 6.313905 AGTCTGCATATAAGTTTTGTCCGAAG 59.686 38.462 0.00 0.00 0.00 3.79
184 185 6.170506 AGTCTGCATATAAGTTTTGTCCGAA 58.829 36.000 0.00 0.00 0.00 4.30
185 186 5.730550 AGTCTGCATATAAGTTTTGTCCGA 58.269 37.500 0.00 0.00 0.00 4.55
186 187 7.534085 TTAGTCTGCATATAAGTTTTGTCCG 57.466 36.000 0.00 0.00 0.00 4.79
193 194 8.612619 CGGTCATTTTTAGTCTGCATATAAGTT 58.387 33.333 0.00 0.00 0.00 2.66
194 195 7.226720 CCGGTCATTTTTAGTCTGCATATAAGT 59.773 37.037 0.00 0.00 0.00 2.24
195 196 7.441157 TCCGGTCATTTTTAGTCTGCATATAAG 59.559 37.037 0.00 0.00 0.00 1.73
196 197 7.276658 TCCGGTCATTTTTAGTCTGCATATAA 58.723 34.615 0.00 0.00 0.00 0.98
197 198 6.822442 TCCGGTCATTTTTAGTCTGCATATA 58.178 36.000 0.00 0.00 0.00 0.86
198 199 5.680619 TCCGGTCATTTTTAGTCTGCATAT 58.319 37.500 0.00 0.00 0.00 1.78
199 200 5.092554 TCCGGTCATTTTTAGTCTGCATA 57.907 39.130 0.00 0.00 0.00 3.14
200 201 3.941483 CTCCGGTCATTTTTAGTCTGCAT 59.059 43.478 0.00 0.00 0.00 3.96
201 202 3.334691 CTCCGGTCATTTTTAGTCTGCA 58.665 45.455 0.00 0.00 0.00 4.41
202 203 2.678336 CCTCCGGTCATTTTTAGTCTGC 59.322 50.000 0.00 0.00 0.00 4.26
203 204 3.055385 TCCCTCCGGTCATTTTTAGTCTG 60.055 47.826 0.00 0.00 0.00 3.51
204 205 3.178865 TCCCTCCGGTCATTTTTAGTCT 58.821 45.455 0.00 0.00 0.00 3.24
205 206 3.055312 ACTCCCTCCGGTCATTTTTAGTC 60.055 47.826 0.00 0.00 0.00 2.59
206 207 2.910977 ACTCCCTCCGGTCATTTTTAGT 59.089 45.455 0.00 0.00 0.00 2.24
207 208 3.629142 ACTCCCTCCGGTCATTTTTAG 57.371 47.619 0.00 0.00 0.00 1.85
208 209 4.098894 ACTACTCCCTCCGGTCATTTTTA 58.901 43.478 0.00 0.00 0.00 1.52
209 210 2.910977 ACTACTCCCTCCGGTCATTTTT 59.089 45.455 0.00 0.00 0.00 1.94
210 211 2.547990 ACTACTCCCTCCGGTCATTTT 58.452 47.619 0.00 0.00 0.00 1.82
211 212 2.249309 ACTACTCCCTCCGGTCATTT 57.751 50.000 0.00 0.00 0.00 2.32
212 213 2.108970 GAACTACTCCCTCCGGTCATT 58.891 52.381 0.00 0.00 0.00 2.57
213 214 1.006758 TGAACTACTCCCTCCGGTCAT 59.993 52.381 0.00 0.00 0.00 3.06
214 215 0.406750 TGAACTACTCCCTCCGGTCA 59.593 55.000 0.00 0.00 0.00 4.02
215 216 1.104630 CTGAACTACTCCCTCCGGTC 58.895 60.000 0.00 0.00 0.00 4.79
216 217 0.324460 CCTGAACTACTCCCTCCGGT 60.324 60.000 0.00 0.00 0.00 5.28
217 218 0.324460 ACCTGAACTACTCCCTCCGG 60.324 60.000 0.00 0.00 0.00 5.14
218 219 1.558233 AACCTGAACTACTCCCTCCG 58.442 55.000 0.00 0.00 0.00 4.63
219 220 3.032459 CCTAACCTGAACTACTCCCTCC 58.968 54.545 0.00 0.00 0.00 4.30
220 221 3.032459 CCCTAACCTGAACTACTCCCTC 58.968 54.545 0.00 0.00 0.00 4.30
221 222 2.386113 ACCCTAACCTGAACTACTCCCT 59.614 50.000 0.00 0.00 0.00 4.20
222 223 2.830293 ACCCTAACCTGAACTACTCCC 58.170 52.381 0.00 0.00 0.00 4.30
223 224 4.904895 AAACCCTAACCTGAACTACTCC 57.095 45.455 0.00 0.00 0.00 3.85
243 244 2.801679 CCGCACCTACAACGACTAAAAA 59.198 45.455 0.00 0.00 0.00 1.94
244 245 2.224018 ACCGCACCTACAACGACTAAAA 60.224 45.455 0.00 0.00 0.00 1.52
245 246 1.340889 ACCGCACCTACAACGACTAAA 59.659 47.619 0.00 0.00 0.00 1.85
246 247 0.961019 ACCGCACCTACAACGACTAA 59.039 50.000 0.00 0.00 0.00 2.24
247 248 0.241749 CACCGCACCTACAACGACTA 59.758 55.000 0.00 0.00 0.00 2.59
248 249 1.006571 CACCGCACCTACAACGACT 60.007 57.895 0.00 0.00 0.00 4.18
249 250 2.664436 GCACCGCACCTACAACGAC 61.664 63.158 0.00 0.00 0.00 4.34
250 251 2.356553 GCACCGCACCTACAACGA 60.357 61.111 0.00 0.00 0.00 3.85
251 252 1.959226 AAGCACCGCACCTACAACG 60.959 57.895 0.00 0.00 0.00 4.10
252 253 1.574428 CAAGCACCGCACCTACAAC 59.426 57.895 0.00 0.00 0.00 3.32
253 254 1.599518 CCAAGCACCGCACCTACAA 60.600 57.895 0.00 0.00 0.00 2.41
254 255 2.031919 CCAAGCACCGCACCTACA 59.968 61.111 0.00 0.00 0.00 2.74
255 256 2.746277 CCCAAGCACCGCACCTAC 60.746 66.667 0.00 0.00 0.00 3.18
256 257 4.715523 GCCCAAGCACCGCACCTA 62.716 66.667 0.00 0.00 39.53 3.08
273 274 1.944676 GAAGTAGCGTCGCCATCCG 60.945 63.158 14.86 0.00 38.61 4.18
274 275 0.179108 AAGAAGTAGCGTCGCCATCC 60.179 55.000 14.86 0.00 0.00 3.51
275 276 1.201343 GAAGAAGTAGCGTCGCCATC 58.799 55.000 14.86 7.30 0.00 3.51
276 277 0.525668 CGAAGAAGTAGCGTCGCCAT 60.526 55.000 14.86 0.00 33.49 4.40
277 278 1.154093 CGAAGAAGTAGCGTCGCCA 60.154 57.895 14.86 0.00 33.49 5.69
278 279 0.862283 CTCGAAGAAGTAGCGTCGCC 60.862 60.000 14.86 0.00 39.15 5.54
279 280 0.179194 ACTCGAAGAAGTAGCGTCGC 60.179 55.000 9.80 9.80 39.15 5.19
280 281 2.244281 AACTCGAAGAAGTAGCGTCG 57.756 50.000 0.00 0.00 40.33 5.12
281 282 3.306818 ACAAACTCGAAGAAGTAGCGTC 58.693 45.455 0.00 0.00 34.09 5.19
282 283 3.004524 AGACAAACTCGAAGAAGTAGCGT 59.995 43.478 0.00 0.00 34.09 5.07
283 284 3.566523 AGACAAACTCGAAGAAGTAGCG 58.433 45.455 0.00 0.00 34.09 4.26
284 285 4.386350 GGAAGACAAACTCGAAGAAGTAGC 59.614 45.833 0.00 0.00 34.09 3.58
285 286 4.617645 CGGAAGACAAACTCGAAGAAGTAG 59.382 45.833 0.00 0.00 34.09 2.57
286 287 4.543692 CGGAAGACAAACTCGAAGAAGTA 58.456 43.478 0.00 0.00 34.09 2.24
287 288 3.381949 CGGAAGACAAACTCGAAGAAGT 58.618 45.455 0.00 0.00 34.09 3.01
288 289 2.731976 CCGGAAGACAAACTCGAAGAAG 59.268 50.000 0.00 0.00 34.09 2.85
289 290 2.547218 CCCGGAAGACAAACTCGAAGAA 60.547 50.000 0.73 0.00 34.09 2.52
290 291 1.000506 CCCGGAAGACAAACTCGAAGA 59.999 52.381 0.73 0.00 0.00 2.87
291 292 1.429463 CCCGGAAGACAAACTCGAAG 58.571 55.000 0.73 0.00 0.00 3.79
292 293 0.601841 GCCCGGAAGACAAACTCGAA 60.602 55.000 0.73 0.00 0.00 3.71
293 294 1.005394 GCCCGGAAGACAAACTCGA 60.005 57.895 0.73 0.00 0.00 4.04
294 295 1.004918 AGCCCGGAAGACAAACTCG 60.005 57.895 0.73 0.00 0.00 4.18
295 296 0.673956 GGAGCCCGGAAGACAAACTC 60.674 60.000 0.73 0.00 0.00 3.01
296 297 1.375326 GGAGCCCGGAAGACAAACT 59.625 57.895 0.73 0.00 0.00 2.66
297 298 2.033194 CGGAGCCCGGAAGACAAAC 61.033 63.158 0.73 0.00 44.15 2.93
298 299 2.345991 CGGAGCCCGGAAGACAAA 59.654 61.111 0.73 0.00 44.15 2.83
308 309 3.299190 CGAGGAGGATCGGAGCCC 61.299 72.222 9.01 0.28 39.04 5.19
309 310 2.203365 TCGAGGAGGATCGGAGCC 60.203 66.667 3.56 3.56 42.93 4.70
310 311 1.104577 AACTCGAGGAGGATCGGAGC 61.105 60.000 18.41 0.00 42.93 4.70
311 312 1.066303 CAAACTCGAGGAGGATCGGAG 59.934 57.143 18.41 0.00 42.93 4.63
312 313 1.103803 CAAACTCGAGGAGGATCGGA 58.896 55.000 18.41 0.00 42.93 4.55
313 314 0.818296 ACAAACTCGAGGAGGATCGG 59.182 55.000 18.41 0.00 42.93 4.18
314 315 1.746220 AGACAAACTCGAGGAGGATCG 59.254 52.381 18.41 0.20 44.07 3.69
315 316 2.494073 ACAGACAAACTCGAGGAGGATC 59.506 50.000 18.41 7.55 33.35 3.36
316 317 2.494073 GACAGACAAACTCGAGGAGGAT 59.506 50.000 18.41 0.00 33.35 3.24
317 318 1.887198 GACAGACAAACTCGAGGAGGA 59.113 52.381 18.41 0.00 33.35 3.71
318 319 1.889829 AGACAGACAAACTCGAGGAGG 59.110 52.381 18.41 7.64 33.35 4.30
319 320 2.352225 CCAGACAGACAAACTCGAGGAG 60.352 54.545 18.41 8.40 35.52 3.69
320 321 1.613925 CCAGACAGACAAACTCGAGGA 59.386 52.381 18.41 0.00 0.00 3.71
321 322 1.613925 TCCAGACAGACAAACTCGAGG 59.386 52.381 18.41 1.00 0.00 4.63
322 323 2.667137 GTCCAGACAGACAAACTCGAG 58.333 52.381 11.84 11.84 36.73 4.04
323 324 1.001706 CGTCCAGACAGACAAACTCGA 60.002 52.381 0.00 0.00 36.52 4.04
324 325 1.269102 ACGTCCAGACAGACAAACTCG 60.269 52.381 0.00 0.00 36.52 4.18
325 326 2.510768 ACGTCCAGACAGACAAACTC 57.489 50.000 0.00 0.00 36.52 3.01
326 327 2.957006 ACTACGTCCAGACAGACAAACT 59.043 45.455 0.00 0.00 36.52 2.66
327 328 3.306818 GACTACGTCCAGACAGACAAAC 58.693 50.000 0.00 0.00 36.52 2.93
328 329 2.031420 CGACTACGTCCAGACAGACAAA 60.031 50.000 0.00 0.00 36.52 2.83
329 330 1.534163 CGACTACGTCCAGACAGACAA 59.466 52.381 0.00 0.00 36.52 3.18
330 331 1.154197 CGACTACGTCCAGACAGACA 58.846 55.000 0.00 0.00 36.52 3.41
331 332 1.128321 GTCGACTACGTCCAGACAGAC 59.872 57.143 8.70 0.00 40.69 3.51
332 333 1.436600 GTCGACTACGTCCAGACAGA 58.563 55.000 8.70 0.00 40.69 3.41
333 334 0.094901 CGTCGACTACGTCCAGACAG 59.905 60.000 14.70 0.00 46.72 3.51
334 335 2.156542 CGTCGACTACGTCCAGACA 58.843 57.895 14.70 0.00 46.72 3.41
358 359 3.107447 GGCAGGAATTTACGCCGG 58.893 61.111 0.00 0.00 34.26 6.13
375 376 0.322456 TCACCGCCCCAAAAGAGATG 60.322 55.000 0.00 0.00 0.00 2.90
376 377 0.035056 CTCACCGCCCCAAAAGAGAT 60.035 55.000 0.00 0.00 0.00 2.75
379 380 2.002018 AACCTCACCGCCCCAAAAGA 62.002 55.000 0.00 0.00 0.00 2.52
384 385 1.987855 CTCTAACCTCACCGCCCCA 60.988 63.158 0.00 0.00 0.00 4.96
387 388 1.275573 AGAAACTCTAACCTCACCGCC 59.724 52.381 0.00 0.00 0.00 6.13
388 389 2.608268 GAGAAACTCTAACCTCACCGC 58.392 52.381 0.00 0.00 0.00 5.68
408 409 1.001815 ACCAAATTTCGCCACAAGACG 60.002 47.619 0.00 0.00 0.00 4.18
429 430 4.286291 TGGCATAGATCTGAAGCATCTGAT 59.714 41.667 10.61 10.61 44.21 2.90
430 431 3.644738 TGGCATAGATCTGAAGCATCTGA 59.355 43.478 5.18 0.85 37.83 3.27
434 435 2.040012 CCCTGGCATAGATCTGAAGCAT 59.960 50.000 5.18 0.00 0.00 3.79
439 440 2.763039 TGAACCCTGGCATAGATCTGA 58.237 47.619 5.18 0.00 0.00 3.27
451 452 0.670546 ATCGTCGCTGTTGAACCCTG 60.671 55.000 0.00 0.00 0.00 4.45
462 463 1.005037 TTGAGCCACAATCGTCGCT 60.005 52.632 0.00 0.00 42.81 4.93
469 470 1.228552 AACGCCCTTGAGCCACAAT 60.229 52.632 0.00 0.00 37.88 2.71
470 471 2.192861 CAACGCCCTTGAGCCACAA 61.193 57.895 0.00 0.00 36.97 3.33
479 480 0.034477 CCATAAGGACCAACGCCCTT 60.034 55.000 0.00 0.00 44.37 3.95
486 487 1.959508 GCACATGCCCATAAGGACCAA 60.960 52.381 0.00 0.00 38.24 3.67
512 513 1.079127 CGATGACAGCCGGGAAGTT 60.079 57.895 2.18 0.00 0.00 2.66
517 518 1.811266 CTTGTCGATGACAGCCGGG 60.811 63.158 2.18 0.00 43.69 5.73
532 533 0.250295 TCGGAGTTGGCTTGACCTTG 60.250 55.000 0.00 0.00 40.22 3.61
544 545 1.532316 TCGTTCCCCTGTCGGAGTT 60.532 57.895 0.00 0.00 32.13 3.01
552 553 4.003788 ACTGCCGTCGTTCCCCTG 62.004 66.667 0.00 0.00 0.00 4.45
577 578 3.257561 CATCAGAACGAGCCGCCG 61.258 66.667 0.00 0.44 0.00 6.46
578 579 2.892425 CCATCAGAACGAGCCGCC 60.892 66.667 0.00 0.00 0.00 6.13
579 580 3.567797 GCCATCAGAACGAGCCGC 61.568 66.667 0.00 0.00 0.00 6.53
580 581 2.125552 TGCCATCAGAACGAGCCG 60.126 61.111 0.00 0.00 0.00 5.52
582 583 1.134965 AGTACTGCCATCAGAACGAGC 60.135 52.381 0.00 0.00 42.95 5.03
583 584 2.534298 CAGTACTGCCATCAGAACGAG 58.466 52.381 10.54 0.00 42.95 4.18
584 585 1.204704 CCAGTACTGCCATCAGAACGA 59.795 52.381 17.86 0.00 42.95 3.85
586 587 2.744202 CAACCAGTACTGCCATCAGAAC 59.256 50.000 17.86 0.00 42.95 3.01
587 588 2.371841 ACAACCAGTACTGCCATCAGAA 59.628 45.455 17.86 0.00 42.95 3.02
589 590 2.479566 ACAACCAGTACTGCCATCAG 57.520 50.000 17.86 5.22 45.71 2.90
590 591 2.884012 CAAACAACCAGTACTGCCATCA 59.116 45.455 17.86 0.00 0.00 3.07
591 592 2.228822 CCAAACAACCAGTACTGCCATC 59.771 50.000 17.86 0.00 0.00 3.51
592 593 2.238521 CCAAACAACCAGTACTGCCAT 58.761 47.619 17.86 1.99 0.00 4.40
593 594 1.686355 CCAAACAACCAGTACTGCCA 58.314 50.000 17.86 0.00 0.00 4.92
594 595 0.958822 CCCAAACAACCAGTACTGCC 59.041 55.000 17.86 0.00 0.00 4.85
595 596 0.958822 CCCCAAACAACCAGTACTGC 59.041 55.000 17.86 0.00 0.00 4.40
596 597 1.133606 ACCCCCAAACAACCAGTACTG 60.134 52.381 16.34 16.34 0.00 2.74
597 598 1.144298 GACCCCCAAACAACCAGTACT 59.856 52.381 0.00 0.00 0.00 2.73
598 599 1.144298 AGACCCCCAAACAACCAGTAC 59.856 52.381 0.00 0.00 0.00 2.73
599 600 1.525175 AGACCCCCAAACAACCAGTA 58.475 50.000 0.00 0.00 0.00 2.74
600 601 0.634465 AAGACCCCCAAACAACCAGT 59.366 50.000 0.00 0.00 0.00 4.00
601 602 1.039856 CAAGACCCCCAAACAACCAG 58.960 55.000 0.00 0.00 0.00 4.00
606 607 3.117322 TGAGATTTCAAGACCCCCAAACA 60.117 43.478 0.00 0.00 0.00 2.83
642 643 4.895224 AGTACAAAGCATCTCGATCGTA 57.105 40.909 15.94 5.15 0.00 3.43
644 645 3.487574 GGAAGTACAAAGCATCTCGATCG 59.512 47.826 9.36 9.36 0.00 3.69
645 646 4.268884 GTGGAAGTACAAAGCATCTCGATC 59.731 45.833 0.00 0.00 0.00 3.69
646 647 4.081420 AGTGGAAGTACAAAGCATCTCGAT 60.081 41.667 0.00 0.00 0.00 3.59
648 649 3.369147 CAGTGGAAGTACAAAGCATCTCG 59.631 47.826 0.00 0.00 0.00 4.04
649 650 4.569943 TCAGTGGAAGTACAAAGCATCTC 58.430 43.478 0.00 0.00 0.00 2.75
667 678 8.095452 ACCCAGATCTATTATTGAAGTTCAGT 57.905 34.615 5.56 5.86 0.00 3.41
676 687 6.312426 GCGAAGATGACCCAGATCTATTATTG 59.688 42.308 0.00 0.00 29.67 1.90
743 754 1.540435 GCCCGGGGCTTCAAAAATGA 61.540 55.000 30.86 0.00 46.69 2.57
744 755 1.079197 GCCCGGGGCTTCAAAAATG 60.079 57.895 30.86 0.00 46.69 2.32
745 756 3.387716 GCCCGGGGCTTCAAAAAT 58.612 55.556 30.86 0.00 46.69 1.82
1185 1206 1.898885 GAAGAGGAAGTCCCGGTCC 59.101 63.158 0.00 0.00 40.87 4.46
1223 1244 1.078426 ATCCTCCGGCCGTCAAAAG 60.078 57.895 26.12 12.54 0.00 2.27
1452 1489 4.625311 ACACCAAAAGAAAAAGAAACGCAG 59.375 37.500 0.00 0.00 0.00 5.18
1466 1503 3.363970 CCGATCTGAAACGACACCAAAAG 60.364 47.826 8.69 0.00 0.00 2.27
1467 1504 2.546368 CCGATCTGAAACGACACCAAAA 59.454 45.455 8.69 0.00 0.00 2.44
1468 1505 2.139917 CCGATCTGAAACGACACCAAA 58.860 47.619 8.69 0.00 0.00 3.28
1471 1508 0.669318 TGCCGATCTGAAACGACACC 60.669 55.000 8.69 0.00 0.00 4.16
1479 1522 2.812122 CGCGCAATGCCGATCTGAA 61.812 57.895 8.75 0.00 42.08 3.02
1480 1523 3.264159 CGCGCAATGCCGATCTGA 61.264 61.111 8.75 0.00 42.08 3.27
1543 1586 3.095278 CCGTGTGTCGACGTTCCG 61.095 66.667 11.62 10.07 42.86 4.30
1598 1641 8.405531 TCAAAGATCAAAAGTTCAGACGAAAAT 58.594 29.630 0.00 0.00 31.43 1.82
1617 1660 3.996921 AGATCAGCCTGTGTCAAAGAT 57.003 42.857 0.00 0.00 0.00 2.40
1621 1664 2.104622 TGACAAGATCAGCCTGTGTCAA 59.895 45.455 12.02 0.00 44.06 3.18
1622 1665 1.693606 TGACAAGATCAGCCTGTGTCA 59.306 47.619 10.75 10.75 44.64 3.58
1623 1666 2.462456 TGACAAGATCAGCCTGTGTC 57.538 50.000 6.30 6.30 39.22 3.67
1625 1668 2.775890 ACTTGACAAGATCAGCCTGTG 58.224 47.619 21.95 0.00 38.99 3.66
1627 1670 3.405831 TCAACTTGACAAGATCAGCCTG 58.594 45.455 21.95 7.00 38.99 4.85
1628 1671 3.777106 TCAACTTGACAAGATCAGCCT 57.223 42.857 21.95 0.00 38.99 4.58
1629 1672 3.128242 CCATCAACTTGACAAGATCAGCC 59.872 47.826 21.95 0.00 38.99 4.85
1631 1674 3.754850 TGCCATCAACTTGACAAGATCAG 59.245 43.478 21.95 8.12 38.99 2.90
1632 1675 3.753815 TGCCATCAACTTGACAAGATCA 58.246 40.909 21.95 0.00 34.65 2.92
1633 1676 4.978083 ATGCCATCAACTTGACAAGATC 57.022 40.909 21.95 0.00 0.00 2.75
1634 1677 4.525487 ACAATGCCATCAACTTGACAAGAT 59.475 37.500 21.95 7.21 0.00 2.40
1635 1678 3.890756 ACAATGCCATCAACTTGACAAGA 59.109 39.130 21.95 0.00 0.00 3.02
1636 1679 3.985279 CACAATGCCATCAACTTGACAAG 59.015 43.478 13.77 13.77 0.00 3.16
1662 1707 2.745037 GTGCCCACGAACACCCTA 59.255 61.111 0.00 0.00 0.00 3.53
1803 1848 2.033407 CAGCGTCGGTCATGATTTCATC 60.033 50.000 0.00 0.00 33.61 2.92
1811 1856 1.638388 AATGTGCAGCGTCGGTCATG 61.638 55.000 0.00 0.00 0.00 3.07
1816 1861 0.729140 GGAAAAATGTGCAGCGTCGG 60.729 55.000 0.00 0.00 0.00 4.79
1820 1865 1.067706 TCATGGGAAAAATGTGCAGCG 60.068 47.619 0.00 0.00 0.00 5.18
1836 1881 6.458751 GCGCCCATATAGACCATAATTTCATG 60.459 42.308 0.00 0.00 0.00 3.07
1837 1882 5.590259 GCGCCCATATAGACCATAATTTCAT 59.410 40.000 0.00 0.00 0.00 2.57
1838 1883 4.941263 GCGCCCATATAGACCATAATTTCA 59.059 41.667 0.00 0.00 0.00 2.69
1839 1884 4.941263 TGCGCCCATATAGACCATAATTTC 59.059 41.667 4.18 0.00 0.00 2.17
1840 1885 4.917385 TGCGCCCATATAGACCATAATTT 58.083 39.130 4.18 0.00 0.00 1.82
1848 1893 1.081892 CTGCATGCGCCCATATAGAC 58.918 55.000 14.09 0.00 37.32 2.59
2081 2138 2.124695 GACTTGGGGATGGACGGC 60.125 66.667 0.00 0.00 0.00 5.68
2709 2817 1.580066 TTGGGGTGGGTGATGGGATC 61.580 60.000 0.00 0.00 0.00 3.36
2736 2858 1.864862 CGAGCACAAACAGAGCCTG 59.135 57.895 1.16 1.16 37.52 4.85
2821 2943 4.516135 TCGTCGTAGCTCAGCGCG 62.516 66.667 0.00 0.00 45.59 6.86
2950 3072 3.363178 CAGAGTTCGCTTGGTTTTGTTC 58.637 45.455 0.00 0.00 0.00 3.18
2951 3073 2.479560 GCAGAGTTCGCTTGGTTTTGTT 60.480 45.455 0.00 0.00 0.00 2.83
2952 3074 1.065551 GCAGAGTTCGCTTGGTTTTGT 59.934 47.619 0.00 0.00 0.00 2.83
2964 3089 0.108585 TTGGTCACCCAGCAGAGTTC 59.891 55.000 0.00 0.00 43.15 3.01
2967 3093 0.397941 TTCTTGGTCACCCAGCAGAG 59.602 55.000 0.00 0.00 43.15 3.35
2976 3102 4.825085 TGGATAAACAGGTTTCTTGGTCAC 59.175 41.667 0.00 0.00 34.23 3.67
3081 3207 3.570975 TGTCGGAGTTGAGCTTGTACTTA 59.429 43.478 0.00 0.00 0.00 2.24
3179 3306 3.176411 TCATGGTTCAGATCCAGTGACT 58.824 45.455 6.38 0.00 38.42 3.41
3183 3310 6.494491 TGAAAATTTCATGGTTCAGATCCAGT 59.506 34.615 4.03 0.00 38.42 4.00
3221 3348 0.317160 TGGAGGTAACAGTGCGTCAG 59.683 55.000 0.00 0.00 41.41 3.51
3222 3349 0.973632 ATGGAGGTAACAGTGCGTCA 59.026 50.000 0.00 0.00 41.41 4.35
3223 3350 1.359848 CATGGAGGTAACAGTGCGTC 58.640 55.000 0.00 0.00 41.41 5.19
3224 3351 0.673644 GCATGGAGGTAACAGTGCGT 60.674 55.000 0.00 0.00 41.41 5.24
3225 3352 1.369091 GGCATGGAGGTAACAGTGCG 61.369 60.000 0.00 0.00 41.41 5.34
3227 3354 2.019249 CATGGCATGGAGGTAACAGTG 58.981 52.381 19.80 0.00 41.41 3.66
3228 3355 1.683011 GCATGGCATGGAGGTAACAGT 60.683 52.381 27.48 0.00 41.41 3.55
3229 3356 1.027357 GCATGGCATGGAGGTAACAG 58.973 55.000 27.48 0.00 41.41 3.16
3231 3358 0.395586 TGGCATGGCATGGAGGTAAC 60.396 55.000 27.48 9.74 0.00 2.50
3232 3359 0.334335 TTGGCATGGCATGGAGGTAA 59.666 50.000 27.48 1.89 0.00 2.85
3233 3360 0.557238 ATTGGCATGGCATGGAGGTA 59.443 50.000 27.48 6.39 0.00 3.08
3234 3361 1.046472 CATTGGCATGGCATGGAGGT 61.046 55.000 27.48 2.61 0.00 3.85
3235 3362 1.745890 CATTGGCATGGCATGGAGG 59.254 57.895 27.48 6.22 0.00 4.30
3248 3384 3.803082 CGGTCGCACCTGCATTGG 61.803 66.667 0.00 0.00 42.21 3.16
3250 3386 1.966901 TATCCGGTCGCACCTGCATT 61.967 55.000 0.00 0.00 42.21 3.56
3510 3646 7.825331 TCTGATCCTTGTGTAACCTATAGAG 57.175 40.000 0.00 0.00 34.36 2.43
3547 3684 1.450360 AACTTTCAGCCCCTCCTCTT 58.550 50.000 0.00 0.00 0.00 2.85
3584 3721 2.358898 TCAGTCAGCAAGAAAAAGTGCC 59.641 45.455 0.00 0.00 41.88 5.01
3673 3811 8.565896 TGTTATTTACTCCTCAACGAGTACTA 57.434 34.615 0.00 0.00 43.40 1.82
3800 3941 0.035458 CTGAACACTCCCTTTCCGCT 59.965 55.000 0.00 0.00 0.00 5.52
4108 4249 0.894835 TCCGTGAAGCTATCAGCACA 59.105 50.000 0.38 0.00 45.56 4.57
4173 4314 2.409012 TGTAAAATCGACAAGCTCGCA 58.591 42.857 0.00 0.00 42.62 5.10
4245 4416 6.109359 CGACTGAATCTGTAAAGGAGGAATT 58.891 40.000 0.00 0.00 0.00 2.17
4246 4417 5.665459 CGACTGAATCTGTAAAGGAGGAAT 58.335 41.667 0.00 0.00 0.00 3.01
4271 4442 0.035343 CGGGGAAGAGGGGAGAAAAC 60.035 60.000 0.00 0.00 0.00 2.43
4289 4460 2.223386 GGAAGAGACCGAGACTTCATCG 60.223 54.545 0.00 0.00 40.89 3.84
4343 4514 1.461127 GAAACAGACACTGCATCGGAC 59.539 52.381 0.00 0.00 34.37 4.79
4385 4556 2.076863 GACGTGATTGGGGAAACAGAG 58.923 52.381 0.00 0.00 0.00 3.35
4402 4573 2.094803 ACTGAAGAGACTGCATCTGACG 60.095 50.000 3.76 0.00 38.00 4.35


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

AutoCloner maintained by Alex Coulton.