Multiple sequence alignment - TraesCS1B01G063100

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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 TraesCS1B01G063100 chr1B 100.000 3161 0 0 1 3161 48063345 48060185 0.000000e+00 5838
1 TraesCS1B01G063100 chr1B 80.248 1048 138 38 801 1800 48102637 48101611 0.000000e+00 725
2 TraesCS1B01G063100 chr1B 95.018 281 9 4 2880 3158 383399170 383399447 1.350000e-118 436
3 TraesCS1B01G063100 chr6D 88.298 2162 221 15 1010 3161 15344826 15342687 0.000000e+00 2562
4 TraesCS1B01G063100 chr6D 86.030 1582 164 34 895 2455 14503253 14504798 0.000000e+00 1644
5 TraesCS1B01G063100 chr6D 86.862 1332 166 8 952 2278 14727372 14726045 0.000000e+00 1482
6 TraesCS1B01G063100 chr6D 83.281 1591 218 26 972 2554 14732959 14731409 0.000000e+00 1421
7 TraesCS1B01G063100 chr6D 90.695 892 76 6 1827 2716 14441376 14442262 0.000000e+00 1181
8 TraesCS1B01G063100 chr6D 85.579 423 54 6 2553 2971 15347599 15347180 1.350000e-118 436
9 TraesCS1B01G063100 chr6A 86.569 1988 236 19 973 2948 15694585 15696553 0.000000e+00 2163
10 TraesCS1B01G063100 chr6A 84.254 1448 189 29 972 2396 15684833 15686264 0.000000e+00 1375
11 TraesCS1B01G063100 chr6B 85.255 1587 202 22 972 2556 27065982 27064426 0.000000e+00 1605
12 TraesCS1B01G063100 chr6B 84.591 1603 205 28 974 2556 26688254 26686674 0.000000e+00 1554
13 TraesCS1B01G063100 chr6B 85.615 1446 172 27 973 2396 26488580 26490011 0.000000e+00 1485
14 TraesCS1B01G063100 chr6B 81.761 1431 235 20 983 2405 26500510 26501922 0.000000e+00 1173
15 TraesCS1B01G063100 chr7B 92.014 576 28 6 2197 2758 731306880 731307451 0.000000e+00 793
16 TraesCS1B01G063100 chr7B 91.319 576 32 6 2197 2758 744822400 744822971 0.000000e+00 771
17 TraesCS1B01G063100 chr7B 95.374 281 8 4 2880 3158 744822967 744823244 2.890000e-120 442
18 TraesCS1B01G063100 chrUn 95.018 281 9 4 2880 3158 49478400 49478677 1.350000e-118 436
19 TraesCS1B01G063100 chrUn 95.636 275 7 4 2886 3158 275173231 275172960 1.350000e-118 436
20 TraesCS1B01G063100 chrUn 95.018 281 9 4 2880 3158 388080357 388080634 1.350000e-118 436
21 TraesCS1B01G063100 chrUn 95.636 275 7 4 2886 3158 417831584 417831313 1.350000e-118 436
22 TraesCS1B01G063100 chrUn 98.013 151 3 0 2608 2758 49478254 49478404 2.420000e-66 263
23 TraesCS1B01G063100 chrUn 98.013 151 3 0 2608 2758 65539754 65539604 2.420000e-66 263
24 TraesCS1B01G063100 chrUn 98.013 151 3 0 2608 2758 275173383 275173233 2.420000e-66 263
25 TraesCS1B01G063100 chr5B 95.018 281 9 4 2880 3158 260121054 260121331 1.350000e-118 436
26 TraesCS1B01G063100 chr5B 95.636 275 7 4 2886 3158 345288599 345288328 1.350000e-118 436


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 TraesCS1B01G063100 chr1B 48060185 48063345 3160 True 5838.0 5838 100.0000 1 3161 1 chr1B.!!$R1 3160
1 TraesCS1B01G063100 chr1B 48101611 48102637 1026 True 725.0 725 80.2480 801 1800 1 chr1B.!!$R2 999
2 TraesCS1B01G063100 chr6D 14503253 14504798 1545 False 1644.0 1644 86.0300 895 2455 1 chr6D.!!$F2 1560
3 TraesCS1B01G063100 chr6D 15342687 15347599 4912 True 1499.0 2562 86.9385 1010 3161 2 chr6D.!!$R3 2151
4 TraesCS1B01G063100 chr6D 14726045 14727372 1327 True 1482.0 1482 86.8620 952 2278 1 chr6D.!!$R1 1326
5 TraesCS1B01G063100 chr6D 14731409 14732959 1550 True 1421.0 1421 83.2810 972 2554 1 chr6D.!!$R2 1582
6 TraesCS1B01G063100 chr6D 14441376 14442262 886 False 1181.0 1181 90.6950 1827 2716 1 chr6D.!!$F1 889
7 TraesCS1B01G063100 chr6A 15694585 15696553 1968 False 2163.0 2163 86.5690 973 2948 1 chr6A.!!$F2 1975
8 TraesCS1B01G063100 chr6A 15684833 15686264 1431 False 1375.0 1375 84.2540 972 2396 1 chr6A.!!$F1 1424
9 TraesCS1B01G063100 chr6B 27064426 27065982 1556 True 1605.0 1605 85.2550 972 2556 1 chr6B.!!$R2 1584
10 TraesCS1B01G063100 chr6B 26686674 26688254 1580 True 1554.0 1554 84.5910 974 2556 1 chr6B.!!$R1 1582
11 TraesCS1B01G063100 chr6B 26488580 26490011 1431 False 1485.0 1485 85.6150 973 2396 1 chr6B.!!$F1 1423
12 TraesCS1B01G063100 chr6B 26500510 26501922 1412 False 1173.0 1173 81.7610 983 2405 1 chr6B.!!$F2 1422
13 TraesCS1B01G063100 chr7B 731306880 731307451 571 False 793.0 793 92.0140 2197 2758 1 chr7B.!!$F1 561
14 TraesCS1B01G063100 chr7B 744822400 744823244 844 False 606.5 771 93.3465 2197 3158 2 chr7B.!!$F2 961

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
950 990 0.027324 GAGCAAGCGCAGTAGCAATC 59.973 55.0 11.47 0.0 42.27 2.67 F
1047 2812 0.257616 CCCGTCTCCTCTCTTCTCCT 59.742 60.0 0.00 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 3600 0.036010 AATTCCTCAGCACACTCGGG 60.036 55.000 0.00 0.0 0.0 5.14 R
2801 4638 1.142262 CCCATCTGCAGTCATCCATCA 59.858 52.381 14.67 0.0 0.0 3.07 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
24 25 6.655078 AGTTTCCATTAGATGCAAGTTTGT 57.345 33.333 0.00 0.00 0.00 2.83
25 26 7.054491 AGTTTCCATTAGATGCAAGTTTGTT 57.946 32.000 0.00 0.00 0.00 2.83
26 27 7.500141 AGTTTCCATTAGATGCAAGTTTGTTT 58.500 30.769 0.00 0.00 0.00 2.83
27 28 7.653311 AGTTTCCATTAGATGCAAGTTTGTTTC 59.347 33.333 0.00 0.00 0.00 2.78
28 29 6.024552 TCCATTAGATGCAAGTTTGTTTCC 57.975 37.500 0.00 0.00 0.00 3.13
29 30 5.538053 TCCATTAGATGCAAGTTTGTTTCCA 59.462 36.000 0.00 0.00 0.00 3.53
31 32 6.875195 CCATTAGATGCAAGTTTGTTTCCATT 59.125 34.615 0.00 0.00 0.00 3.16
33 34 9.421806 CATTAGATGCAAGTTTGTTTCCATTTA 57.578 29.630 0.00 0.00 0.00 1.40
37 38 9.643693 AGATGCAAGTTTGTTTCCATTTATAAG 57.356 29.630 0.00 0.00 0.00 1.73
38 39 7.650834 TGCAAGTTTGTTTCCATTTATAAGC 57.349 32.000 0.00 0.00 0.00 3.09
39 40 7.441017 TGCAAGTTTGTTTCCATTTATAAGCT 58.559 30.769 0.00 0.00 0.00 3.74
41 42 7.622048 GCAAGTTTGTTTCCATTTATAAGCTGC 60.622 37.037 0.00 0.00 0.00 5.25
42 43 6.092748 AGTTTGTTTCCATTTATAAGCTGCG 58.907 36.000 0.00 0.00 0.00 5.18
46 47 7.147143 TGTTTCCATTTATAAGCTGCGTTAA 57.853 32.000 0.00 0.00 0.00 2.01
47 48 7.594714 TGTTTCCATTTATAAGCTGCGTTAAA 58.405 30.769 0.00 0.59 0.00 1.52
48 49 7.753132 TGTTTCCATTTATAAGCTGCGTTAAAG 59.247 33.333 0.00 0.00 0.00 1.85
51 52 6.600032 TCCATTTATAAGCTGCGTTAAAGGAA 59.400 34.615 13.91 0.00 0.00 3.36
52 53 7.121463 TCCATTTATAAGCTGCGTTAAAGGAAA 59.879 33.333 13.91 2.45 0.00 3.13
54 55 9.134734 CATTTATAAGCTGCGTTAAAGGAAAAA 57.865 29.630 9.45 0.00 0.00 1.94
78 79 9.777575 AAAATATAGTACCGCACATTTGTTTAC 57.222 29.630 0.00 0.00 0.00 2.01
79 80 8.495361 AATATAGTACCGCACATTTGTTTACA 57.505 30.769 0.00 0.00 0.00 2.41
80 81 6.804770 ATAGTACCGCACATTTGTTTACAA 57.195 33.333 0.00 0.00 0.00 2.41
82 83 5.457140 AGTACCGCACATTTGTTTACAATG 58.543 37.500 0.00 0.97 35.55 2.82
83 84 4.576216 ACCGCACATTTGTTTACAATGA 57.424 36.364 0.00 0.00 35.55 2.57
84 85 4.938080 ACCGCACATTTGTTTACAATGAA 58.062 34.783 0.00 0.00 35.55 2.57
85 86 5.352284 ACCGCACATTTGTTTACAATGAAA 58.648 33.333 0.00 0.00 35.55 2.69
87 88 6.481644 ACCGCACATTTGTTTACAATGAAAAT 59.518 30.769 0.00 0.00 35.55 1.82
89 90 7.530190 CCGCACATTTGTTTACAATGAAAATTC 59.470 33.333 0.00 0.00 35.55 2.17
90 91 7.530190 CGCACATTTGTTTACAATGAAAATTCC 59.470 33.333 0.00 0.00 35.55 3.01
91 92 8.341173 GCACATTTGTTTACAATGAAAATTCCA 58.659 29.630 0.00 0.00 35.55 3.53
98 99 9.618890 TGTTTACAATGAAAATTCCAAAATGGA 57.381 25.926 0.00 0.00 46.61 3.41
166 167 6.739331 AAATGTGTAACCATGAAAAGGGAA 57.261 33.333 0.00 0.00 34.36 3.97
168 169 5.055265 TGTGTAACCATGAAAAGGGAAGA 57.945 39.130 0.00 0.00 34.36 2.87
173 174 7.384932 GTGTAACCATGAAAAGGGAAGAAAATG 59.615 37.037 0.00 0.00 0.00 2.32
174 175 5.488262 ACCATGAAAAGGGAAGAAAATGG 57.512 39.130 0.00 0.00 39.38 3.16
175 176 5.154418 ACCATGAAAAGGGAAGAAAATGGA 58.846 37.500 5.41 0.00 37.38 3.41
176 177 5.786975 ACCATGAAAAGGGAAGAAAATGGAT 59.213 36.000 5.41 0.00 37.38 3.41
178 179 7.170277 CCATGAAAAGGGAAGAAAATGGATTT 58.830 34.615 0.00 0.00 36.27 2.17
179 180 7.666804 CCATGAAAAGGGAAGAAAATGGATTTT 59.333 33.333 0.00 0.00 42.24 1.82
193 194 9.208022 GAAAATGGATTTTTCTTAGAACAAGGG 57.792 33.333 0.00 0.00 46.42 3.95
194 195 6.857437 ATGGATTTTTCTTAGAACAAGGGG 57.143 37.500 0.00 0.00 0.00 4.79
195 196 5.959512 TGGATTTTTCTTAGAACAAGGGGA 58.040 37.500 0.00 0.00 0.00 4.81
196 197 6.010219 TGGATTTTTCTTAGAACAAGGGGAG 58.990 40.000 0.00 0.00 0.00 4.30
197 198 5.419155 GGATTTTTCTTAGAACAAGGGGAGG 59.581 44.000 0.00 0.00 0.00 4.30
198 199 5.656549 TTTTTCTTAGAACAAGGGGAGGA 57.343 39.130 0.00 0.00 0.00 3.71
199 200 5.860648 TTTTCTTAGAACAAGGGGAGGAT 57.139 39.130 0.00 0.00 0.00 3.24
201 202 5.860648 TTCTTAGAACAAGGGGAGGATTT 57.139 39.130 0.00 0.00 0.00 2.17
202 203 5.860648 TCTTAGAACAAGGGGAGGATTTT 57.139 39.130 0.00 0.00 0.00 1.82
229 230 7.461182 TTTGAGACAAAGAACAAGGAAAGAA 57.539 32.000 0.00 0.00 0.00 2.52
230 231 7.461182 TTGAGACAAAGAACAAGGAAAGAAA 57.539 32.000 0.00 0.00 0.00 2.52
234 235 7.267857 AGACAAAGAACAAGGAAAGAAAATGG 58.732 34.615 0.00 0.00 0.00 3.16
235 236 7.124147 AGACAAAGAACAAGGAAAGAAAATGGA 59.876 33.333 0.00 0.00 0.00 3.41
237 238 7.712205 ACAAAGAACAAGGAAAGAAAATGGATG 59.288 33.333 0.00 0.00 0.00 3.51
238 239 7.601705 AAGAACAAGGAAAGAAAATGGATGA 57.398 32.000 0.00 0.00 0.00 2.92
239 240 7.601705 AGAACAAGGAAAGAAAATGGATGAA 57.398 32.000 0.00 0.00 0.00 2.57
240 241 8.021898 AGAACAAGGAAAGAAAATGGATGAAA 57.978 30.769 0.00 0.00 0.00 2.69
241 242 8.485392 AGAACAAGGAAAGAAAATGGATGAAAA 58.515 29.630 0.00 0.00 0.00 2.29
264 265 5.638596 AAATGAACGTCTATCAAAACCCC 57.361 39.130 0.00 0.00 0.00 4.95
265 266 2.690786 TGAACGTCTATCAAAACCCCG 58.309 47.619 0.00 0.00 0.00 5.73
267 268 0.392060 ACGTCTATCAAAACCCCGGC 60.392 55.000 0.00 0.00 0.00 6.13
268 269 1.426041 CGTCTATCAAAACCCCGGCG 61.426 60.000 0.00 0.00 0.00 6.46
269 270 1.450669 TCTATCAAAACCCCGGCGC 60.451 57.895 0.00 0.00 0.00 6.53
270 271 1.747367 CTATCAAAACCCCGGCGCA 60.747 57.895 10.83 0.00 0.00 6.09
271 272 1.714899 CTATCAAAACCCCGGCGCAG 61.715 60.000 10.83 4.65 0.00 5.18
273 274 2.472414 ATCAAAACCCCGGCGCAGTA 62.472 55.000 10.83 0.00 0.00 2.74
274 275 2.359478 AAAACCCCGGCGCAGTAG 60.359 61.111 10.83 0.34 0.00 2.57
275 276 2.886134 AAAACCCCGGCGCAGTAGA 61.886 57.895 10.83 0.00 0.00 2.59
284 285 4.435436 CGCAGTAGAGCCCACGCA 62.435 66.667 0.00 0.00 37.52 5.24
285 286 2.815647 GCAGTAGAGCCCACGCAC 60.816 66.667 0.00 0.00 37.52 5.34
286 287 2.656646 CAGTAGAGCCCACGCACA 59.343 61.111 0.00 0.00 37.52 4.57
287 288 1.738099 CAGTAGAGCCCACGCACAC 60.738 63.158 0.00 0.00 37.52 3.82
288 289 2.207229 AGTAGAGCCCACGCACACA 61.207 57.895 0.00 0.00 37.52 3.72
289 290 1.738099 GTAGAGCCCACGCACACAG 60.738 63.158 0.00 0.00 37.52 3.66
290 291 1.906333 TAGAGCCCACGCACACAGA 60.906 57.895 0.00 0.00 37.52 3.41
291 292 1.877576 TAGAGCCCACGCACACAGAG 61.878 60.000 0.00 0.00 37.52 3.35
292 293 3.226429 GAGCCCACGCACACAGAGA 62.226 63.158 0.00 0.00 37.52 3.10
293 294 2.280797 GCCCACGCACACAGAGAA 60.281 61.111 0.00 0.00 34.03 2.87
294 295 1.891919 GCCCACGCACACAGAGAAA 60.892 57.895 0.00 0.00 34.03 2.52
295 296 1.444119 GCCCACGCACACAGAGAAAA 61.444 55.000 0.00 0.00 34.03 2.29
312 313 0.661020 AAAAAGAAGGCCACGACACG 59.339 50.000 5.01 0.00 0.00 4.49
313 314 1.782028 AAAAGAAGGCCACGACACGC 61.782 55.000 5.01 0.00 0.00 5.34
314 315 2.933878 AAAGAAGGCCACGACACGCA 62.934 55.000 5.01 0.00 0.00 5.24
315 316 3.414700 GAAGGCCACGACACGCAG 61.415 66.667 5.01 0.00 0.00 5.18
316 317 3.858868 GAAGGCCACGACACGCAGA 62.859 63.158 5.01 0.00 0.00 4.26
317 318 3.865929 AAGGCCACGACACGCAGAG 62.866 63.158 5.01 0.00 0.00 3.35
345 346 2.129823 GCAATTGCAATCCATCGGAG 57.870 50.000 25.36 0.00 41.59 4.63
346 347 1.677576 GCAATTGCAATCCATCGGAGA 59.322 47.619 25.36 0.00 40.94 3.71
348 349 3.503363 GCAATTGCAATCCATCGGAGATA 59.497 43.478 25.36 0.00 41.00 1.98
349 350 4.157289 GCAATTGCAATCCATCGGAGATAT 59.843 41.667 25.36 0.00 41.00 1.63
350 351 5.675575 GCAATTGCAATCCATCGGAGATATC 60.676 44.000 25.36 0.00 41.00 1.63
351 352 4.897509 TTGCAATCCATCGGAGATATCT 57.102 40.909 4.47 4.47 45.12 1.98
353 354 5.233083 TGCAATCCATCGGAGATATCTTT 57.767 39.130 6.70 0.00 45.12 2.52
354 355 4.999311 TGCAATCCATCGGAGATATCTTTG 59.001 41.667 6.70 5.98 45.12 2.77
355 356 4.999950 GCAATCCATCGGAGATATCTTTGT 59.000 41.667 6.70 0.00 45.12 2.83
356 357 5.121454 GCAATCCATCGGAGATATCTTTGTC 59.879 44.000 6.70 0.00 45.12 3.18
357 358 4.505313 TCCATCGGAGATATCTTTGTCG 57.495 45.455 6.70 9.09 45.12 4.35
358 359 3.889538 TCCATCGGAGATATCTTTGTCGT 59.110 43.478 6.70 0.00 45.12 4.34
359 360 4.023107 TCCATCGGAGATATCTTTGTCGTC 60.023 45.833 6.70 0.00 45.12 4.20
361 362 2.044860 CGGAGATATCTTTGTCGTCGC 58.955 52.381 6.70 0.00 0.00 5.19
362 363 2.395654 GGAGATATCTTTGTCGTCGCC 58.604 52.381 6.70 0.00 0.00 5.54
363 364 2.044860 GAGATATCTTTGTCGTCGCCG 58.955 52.381 6.70 0.00 0.00 6.46
364 365 0.503117 GATATCTTTGTCGTCGCCGC 59.497 55.000 0.00 0.00 0.00 6.53
365 366 0.874607 ATATCTTTGTCGTCGCCGCC 60.875 55.000 0.00 0.00 0.00 6.13
367 368 4.072088 CTTTGTCGTCGCCGCCAC 62.072 66.667 0.00 0.00 0.00 5.01
386 387 3.774702 GCCGCCGTCGTTGTTCTC 61.775 66.667 0.00 0.00 0.00 2.87
387 388 3.467119 CCGCCGTCGTTGTTCTCG 61.467 66.667 0.00 0.00 0.00 4.04
388 389 4.117372 CGCCGTCGTTGTTCTCGC 62.117 66.667 0.00 0.00 0.00 5.03
389 390 3.774702 GCCGTCGTTGTTCTCGCC 61.775 66.667 0.00 0.00 0.00 5.54
390 391 3.467119 CCGTCGTTGTTCTCGCCG 61.467 66.667 0.00 0.00 0.00 6.46
391 392 2.427905 CGTCGTTGTTCTCGCCGA 60.428 61.111 0.00 0.00 31.56 5.54
392 393 2.012414 CGTCGTTGTTCTCGCCGAA 61.012 57.895 0.00 0.00 31.56 4.30
394 395 0.578211 GTCGTTGTTCTCGCCGAAAA 59.422 50.000 0.00 0.00 32.41 2.29
395 396 1.193874 GTCGTTGTTCTCGCCGAAAAT 59.806 47.619 0.00 0.00 32.41 1.82
396 397 1.193650 TCGTTGTTCTCGCCGAAAATG 59.806 47.619 0.00 0.00 32.41 2.32
397 398 1.193650 CGTTGTTCTCGCCGAAAATGA 59.806 47.619 0.00 0.00 32.41 2.57
399 400 3.417185 GTTGTTCTCGCCGAAAATGATC 58.583 45.455 0.00 0.00 32.41 2.92
400 401 2.694213 TGTTCTCGCCGAAAATGATCA 58.306 42.857 0.00 0.00 32.41 2.92
401 402 3.270027 TGTTCTCGCCGAAAATGATCAT 58.730 40.909 1.18 1.18 32.41 2.45
402 403 3.063861 TGTTCTCGCCGAAAATGATCATG 59.936 43.478 9.46 0.00 32.41 3.07
403 404 1.599071 TCTCGCCGAAAATGATCATGC 59.401 47.619 9.46 6.93 0.00 4.06
404 405 1.331447 CTCGCCGAAAATGATCATGCA 59.669 47.619 9.46 0.00 0.00 3.96
405 406 1.948834 TCGCCGAAAATGATCATGCAT 59.051 42.857 9.46 0.00 0.00 3.96
406 407 2.048498 CGCCGAAAATGATCATGCATG 58.952 47.619 21.07 21.07 0.00 4.06
407 408 2.542205 CGCCGAAAATGATCATGCATGT 60.542 45.455 25.43 13.42 0.00 3.21
408 409 3.047796 GCCGAAAATGATCATGCATGTC 58.952 45.455 25.43 20.69 0.00 3.06
409 410 3.489568 GCCGAAAATGATCATGCATGTCA 60.490 43.478 25.43 24.84 0.00 3.58
411 412 5.103687 CCGAAAATGATCATGCATGTCAAA 58.896 37.500 25.43 7.44 0.00 2.69
412 413 5.751509 CCGAAAATGATCATGCATGTCAAAT 59.248 36.000 25.43 12.20 0.00 2.32
414 415 7.435784 CCGAAAATGATCATGCATGTCAAATAA 59.564 33.333 25.43 6.11 0.00 1.40
415 416 8.809478 CGAAAATGATCATGCATGTCAAATAAA 58.191 29.630 25.43 4.73 0.00 1.40
418 419 8.642908 AATGATCATGCATGTCAAATAAAGTG 57.357 30.769 25.43 0.00 0.00 3.16
419 420 7.160547 TGATCATGCATGTCAAATAAAGTGT 57.839 32.000 25.43 0.00 0.00 3.55
420 421 7.604549 TGATCATGCATGTCAAATAAAGTGTT 58.395 30.769 25.43 0.00 0.00 3.32
422 423 9.740239 GATCATGCATGTCAAATAAAGTGTTAT 57.260 29.630 25.43 6.35 0.00 1.89
423 424 9.740239 ATCATGCATGTCAAATAAAGTGTTATC 57.260 29.630 25.43 0.00 0.00 1.75
424 425 8.190122 TCATGCATGTCAAATAAAGTGTTATCC 58.810 33.333 25.43 0.00 0.00 2.59
426 427 8.065473 TGCATGTCAAATAAAGTGTTATCCAT 57.935 30.769 0.00 0.00 0.00 3.41
427 428 8.530311 TGCATGTCAAATAAAGTGTTATCCATT 58.470 29.630 0.00 0.00 0.00 3.16
428 429 9.369904 GCATGTCAAATAAAGTGTTATCCATTT 57.630 29.630 0.00 0.00 0.00 2.32
641 642 7.873739 AAATTCTGCATTTGTTAAGTAGTGC 57.126 32.000 0.00 0.00 33.47 4.40
644 645 4.824537 TCTGCATTTGTTAAGTAGTGCCAA 59.175 37.500 0.00 0.00 0.00 4.52
645 646 5.300539 TCTGCATTTGTTAAGTAGTGCCAAA 59.699 36.000 0.00 0.00 0.00 3.28
646 647 5.527951 TGCATTTGTTAAGTAGTGCCAAAG 58.472 37.500 0.00 0.00 0.00 2.77
647 648 4.923281 GCATTTGTTAAGTAGTGCCAAAGG 59.077 41.667 0.00 0.00 31.94 3.11
693 694 9.967346 TTAATATATAGGAGTATCTCATTGCGC 57.033 33.333 0.00 0.00 33.73 6.09
694 695 5.921962 ATATAGGAGTATCTCATTGCGCA 57.078 39.130 5.66 5.66 33.73 6.09
696 697 2.763933 AGGAGTATCTCATTGCGCATG 58.236 47.619 12.75 12.25 33.73 4.06
697 698 1.802960 GGAGTATCTCATTGCGCATGG 59.197 52.381 12.75 6.72 33.07 3.66
698 699 2.548707 GGAGTATCTCATTGCGCATGGA 60.549 50.000 12.75 11.39 33.07 3.41
699 700 3.133691 GAGTATCTCATTGCGCATGGAA 58.866 45.455 12.75 0.00 33.07 3.53
702 703 4.581824 AGTATCTCATTGCGCATGGAATTT 59.418 37.500 12.75 2.34 33.38 1.82
703 704 3.425577 TCTCATTGCGCATGGAATTTC 57.574 42.857 12.75 0.00 33.38 2.17
705 706 2.100252 CTCATTGCGCATGGAATTTCCT 59.900 45.455 12.75 0.00 37.46 3.36
706 707 2.496871 TCATTGCGCATGGAATTTCCTT 59.503 40.909 12.75 7.47 37.46 3.36
707 708 3.698539 TCATTGCGCATGGAATTTCCTTA 59.301 39.130 12.75 0.00 37.46 2.69
709 710 4.527509 TTGCGCATGGAATTTCCTTAAA 57.472 36.364 12.75 0.00 37.46 1.52
710 711 4.527509 TGCGCATGGAATTTCCTTAAAA 57.472 36.364 5.66 0.00 37.46 1.52
711 712 5.083533 TGCGCATGGAATTTCCTTAAAAT 57.916 34.783 5.66 0.00 39.30 1.82
712 713 4.869297 TGCGCATGGAATTTCCTTAAAATG 59.131 37.500 5.66 11.56 37.64 2.32
717 718 7.201461 CGCATGGAATTTCCTTAAAATGTTCAG 60.201 37.037 16.25 2.58 37.64 3.02
718 719 7.603784 GCATGGAATTTCCTTAAAATGTTCAGT 59.396 33.333 16.25 0.00 37.64 3.41
719 720 8.928733 CATGGAATTTCCTTAAAATGTTCAGTG 58.071 33.333 16.25 0.00 37.64 3.66
721 722 7.925483 TGGAATTTCCTTAAAATGTTCAGTGTG 59.075 33.333 16.25 0.00 37.64 3.82
722 723 7.095649 GGAATTTCCTTAAAATGTTCAGTGTGC 60.096 37.037 8.25 0.00 37.64 4.57
723 724 6.463995 TTTCCTTAAAATGTTCAGTGTGCT 57.536 33.333 0.00 0.00 0.00 4.40
726 727 7.759489 TCCTTAAAATGTTCAGTGTGCTTAT 57.241 32.000 0.00 0.00 0.00 1.73
727 728 8.856153 TCCTTAAAATGTTCAGTGTGCTTATA 57.144 30.769 0.00 0.00 0.00 0.98
728 729 9.290988 TCCTTAAAATGTTCAGTGTGCTTATAA 57.709 29.630 0.00 0.00 0.00 0.98
741 742 9.722056 CAGTGTGCTTATAAAAATTATCTCACC 57.278 33.333 0.00 0.00 0.00 4.02
742 743 9.461312 AGTGTGCTTATAAAAATTATCTCACCA 57.539 29.630 0.00 0.00 0.00 4.17
743 744 9.722056 GTGTGCTTATAAAAATTATCTCACCAG 57.278 33.333 0.00 0.00 0.00 4.00
744 745 9.679661 TGTGCTTATAAAAATTATCTCACCAGA 57.320 29.630 0.00 0.00 0.00 3.86
779 780 8.125978 TCCATATGAATGAGCAAATTATTCCC 57.874 34.615 3.65 0.00 34.84 3.97
780 781 7.951806 TCCATATGAATGAGCAAATTATTCCCT 59.048 33.333 3.65 0.00 34.84 4.20
781 782 8.033038 CCATATGAATGAGCAAATTATTCCCTG 58.967 37.037 3.65 0.00 34.84 4.45
783 784 9.812347 ATATGAATGAGCAAATTATTCCCTGTA 57.188 29.630 0.00 0.00 31.47 2.74
784 785 7.953005 TGAATGAGCAAATTATTCCCTGTAA 57.047 32.000 0.00 0.00 31.47 2.41
785 786 7.771183 TGAATGAGCAAATTATTCCCTGTAAC 58.229 34.615 0.00 0.00 31.47 2.50
786 787 6.715347 ATGAGCAAATTATTCCCTGTAACC 57.285 37.500 0.00 0.00 0.00 2.85
787 788 5.826643 TGAGCAAATTATTCCCTGTAACCT 58.173 37.500 0.00 0.00 0.00 3.50
788 789 6.964464 TGAGCAAATTATTCCCTGTAACCTA 58.036 36.000 0.00 0.00 0.00 3.08
789 790 7.582719 TGAGCAAATTATTCCCTGTAACCTAT 58.417 34.615 0.00 0.00 0.00 2.57
790 791 8.058847 TGAGCAAATTATTCCCTGTAACCTATT 58.941 33.333 0.00 0.00 0.00 1.73
791 792 8.838649 AGCAAATTATTCCCTGTAACCTATTT 57.161 30.769 0.00 0.00 0.00 1.40
792 793 9.267071 AGCAAATTATTCCCTGTAACCTATTTT 57.733 29.630 0.00 0.00 0.00 1.82
793 794 9.529325 GCAAATTATTCCCTGTAACCTATTTTC 57.471 33.333 0.00 0.00 0.00 2.29
796 797 7.533923 TTATTCCCTGTAACCTATTTTCCCT 57.466 36.000 0.00 0.00 0.00 4.20
797 798 5.446260 TTCCCTGTAACCTATTTTCCCTC 57.554 43.478 0.00 0.00 0.00 4.30
798 799 4.440808 TCCCTGTAACCTATTTTCCCTCA 58.559 43.478 0.00 0.00 0.00 3.86
799 800 4.853276 TCCCTGTAACCTATTTTCCCTCAA 59.147 41.667 0.00 0.00 0.00 3.02
893 927 3.286353 TGGATGGCAAATAAAGATGCGA 58.714 40.909 0.00 0.00 43.47 5.10
912 946 4.060038 CGAAGCCCATATTGACTACAGT 57.940 45.455 0.00 0.00 0.00 3.55
914 948 5.223382 CGAAGCCCATATTGACTACAGTAG 58.777 45.833 6.00 6.00 0.00 2.57
950 990 0.027324 GAGCAAGCGCAGTAGCAATC 59.973 55.000 11.47 0.00 42.27 2.67
969 1009 5.163764 GCAATCGCAATCCATCGGAAATATA 60.164 40.000 0.00 0.00 38.36 0.86
1047 2812 0.257616 CCCGTCTCCTCTCTTCTCCT 59.742 60.000 0.00 0.00 0.00 3.69
1048 2813 1.675552 CCGTCTCCTCTCTTCTCCTC 58.324 60.000 0.00 0.00 0.00 3.71
1068 2839 1.440893 CACCTCTCCCATCTGCTCG 59.559 63.158 0.00 0.00 0.00 5.03
1143 2918 1.392710 CCTTCGCCGTGGAGGAGTAT 61.393 60.000 0.00 0.00 45.00 2.12
1252 3027 1.380650 GTCCTCGCCTTCCTCTCCT 60.381 63.158 0.00 0.00 0.00 3.69
1311 3086 3.246880 AAGGACCCGCGGTTCCTT 61.247 61.111 41.68 41.68 37.92 3.36
1353 3128 2.668632 GCTCCGGTGGTTGATGGA 59.331 61.111 0.00 0.00 0.00 3.41
1495 3270 1.071471 CACAACTTCCTCCGGCTGT 59.929 57.895 0.00 0.00 0.00 4.40
1515 3290 0.615331 TCAAGCACTCATCCCACCTC 59.385 55.000 0.00 0.00 0.00 3.85
1516 3291 0.617413 CAAGCACTCATCCCACCTCT 59.383 55.000 0.00 0.00 0.00 3.69
1520 3295 1.271597 GCACTCATCCCACCTCTTGTT 60.272 52.381 0.00 0.00 0.00 2.83
1521 3296 2.815589 GCACTCATCCCACCTCTTGTTT 60.816 50.000 0.00 0.00 0.00 2.83
1572 3348 4.438346 GTGTTCCTGCACGAGTGT 57.562 55.556 5.07 0.00 0.00 3.55
1638 3414 1.380302 GATGCTGACCACCAACCCT 59.620 57.895 0.00 0.00 0.00 4.34
1848 3624 3.438087 CGAGTGTGCTGAGGAATTCAAAT 59.562 43.478 7.93 0.00 34.81 2.32
1863 3639 6.404074 GGAATTCAAATGAATCTCTGAAGCGT 60.404 38.462 7.93 0.00 43.41 5.07
2293 4086 5.871834 TGGTTGTTTACTGTAGTATGCCTT 58.128 37.500 0.00 0.00 0.00 4.35
2298 4091 8.776470 GTTGTTTACTGTAGTATGCCTTTTACA 58.224 33.333 0.00 0.00 0.00 2.41
2302 4095 5.745227 ACTGTAGTATGCCTTTTACATGCT 58.255 37.500 0.00 0.00 42.21 3.79
2307 4100 8.479689 TGTAGTATGCCTTTTACATGCTAGTTA 58.520 33.333 0.00 0.00 41.44 2.24
2326 4137 8.279103 GCTAGTTAGTCATTGCTAAATGCTAAG 58.721 37.037 11.86 6.07 42.55 2.18
2356 4172 5.119125 GCGAAACTGAAAATTTGATTCCTGG 59.881 40.000 0.00 0.00 0.00 4.45
2518 4339 3.007182 CACCCATGAAACCAGAAAGCAAT 59.993 43.478 0.00 0.00 0.00 3.56
2566 4387 3.440173 CGAAATGTATCACCCTGCTGTTT 59.560 43.478 0.00 0.00 0.00 2.83
2577 4398 4.403432 CACCCTGCTGTTTGGATTCATAAT 59.597 41.667 0.00 0.00 0.00 1.28
2766 4603 3.874392 ATTGCAAGGCTGAATTACCAC 57.126 42.857 4.94 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.681777 ACAAACTTGCATCTAATGGAAACTC 58.318 36.000 0.00 0.00 40.14 3.01
1 2 6.655078 ACAAACTTGCATCTAATGGAAACT 57.345 33.333 0.00 0.00 40.14 2.66
2 3 7.095649 GGAAACAAACTTGCATCTAATGGAAAC 60.096 37.037 0.00 0.00 40.14 2.78
3 4 6.928492 GGAAACAAACTTGCATCTAATGGAAA 59.072 34.615 0.00 0.00 40.14 3.13
4 5 6.041409 TGGAAACAAACTTGCATCTAATGGAA 59.959 34.615 0.00 0.00 36.24 3.53
5 6 5.538053 TGGAAACAAACTTGCATCTAATGGA 59.462 36.000 0.00 0.00 37.44 3.41
6 7 5.782047 TGGAAACAAACTTGCATCTAATGG 58.218 37.500 0.00 0.00 37.44 3.16
23 24 7.220108 CCTTTAACGCAGCTTATAAATGGAAAC 59.780 37.037 0.00 0.00 0.00 2.78
24 25 7.121463 TCCTTTAACGCAGCTTATAAATGGAAA 59.879 33.333 0.00 0.00 0.00 3.13
25 26 6.600032 TCCTTTAACGCAGCTTATAAATGGAA 59.400 34.615 0.00 0.00 0.00 3.53
26 27 6.116806 TCCTTTAACGCAGCTTATAAATGGA 58.883 36.000 0.00 1.16 0.00 3.41
27 28 6.371809 TCCTTTAACGCAGCTTATAAATGG 57.628 37.500 0.00 0.00 0.00 3.16
28 29 8.682128 TTTTCCTTTAACGCAGCTTATAAATG 57.318 30.769 0.00 0.00 0.00 2.32
52 53 9.777575 GTAAACAAATGTGCGGTACTATATTTT 57.222 29.630 0.00 0.00 0.00 1.82
54 55 8.495361 TGTAAACAAATGTGCGGTACTATATT 57.505 30.769 0.00 0.00 0.00 1.28
56 57 7.902387 TTGTAAACAAATGTGCGGTACTATA 57.098 32.000 0.00 0.00 32.11 1.31
57 58 6.804770 TTGTAAACAAATGTGCGGTACTAT 57.195 33.333 0.00 0.00 32.11 2.12
60 61 5.453648 TCATTGTAAACAAATGTGCGGTAC 58.546 37.500 0.00 0.00 39.55 3.34
62 63 4.576216 TCATTGTAAACAAATGTGCGGT 57.424 36.364 0.00 0.00 39.55 5.68
63 64 5.896922 TTTCATTGTAAACAAATGTGCGG 57.103 34.783 0.00 0.00 39.55 5.69
64 65 7.530190 GGAATTTTCATTGTAAACAAATGTGCG 59.470 33.333 0.00 0.00 39.55 5.34
65 66 8.341173 TGGAATTTTCATTGTAAACAAATGTGC 58.659 29.630 0.00 0.00 39.55 4.57
72 73 9.618890 TCCATTTTGGAATTTTCATTGTAAACA 57.381 25.926 0.00 0.00 45.00 2.83
143 144 6.553100 TCTTCCCTTTTCATGGTTACACATTT 59.447 34.615 0.00 0.00 0.00 2.32
146 147 5.055265 TCTTCCCTTTTCATGGTTACACA 57.945 39.130 0.00 0.00 0.00 3.72
147 148 6.399639 TTTCTTCCCTTTTCATGGTTACAC 57.600 37.500 0.00 0.00 0.00 2.90
149 150 6.873605 CCATTTTCTTCCCTTTTCATGGTTAC 59.126 38.462 0.00 0.00 0.00 2.50
150 151 6.784969 TCCATTTTCTTCCCTTTTCATGGTTA 59.215 34.615 0.00 0.00 33.10 2.85
152 153 5.154418 TCCATTTTCTTCCCTTTTCATGGT 58.846 37.500 0.00 0.00 33.10 3.55
154 155 8.625786 AAAATCCATTTTCTTCCCTTTTCATG 57.374 30.769 0.00 0.00 35.18 3.07
168 169 8.156820 CCCCTTGTTCTAAGAAAAATCCATTTT 58.843 33.333 0.00 0.00 43.85 1.82
173 174 5.419155 CCTCCCCTTGTTCTAAGAAAAATCC 59.581 44.000 0.00 0.00 0.00 3.01
174 175 6.246163 TCCTCCCCTTGTTCTAAGAAAAATC 58.754 40.000 0.00 0.00 0.00 2.17
175 176 6.214177 TCCTCCCCTTGTTCTAAGAAAAAT 57.786 37.500 0.00 0.00 0.00 1.82
176 177 5.656549 TCCTCCCCTTGTTCTAAGAAAAA 57.343 39.130 0.00 0.00 0.00 1.94
178 179 5.860648 AATCCTCCCCTTGTTCTAAGAAA 57.139 39.130 0.00 0.00 0.00 2.52
179 180 5.860648 AAATCCTCCCCTTGTTCTAAGAA 57.139 39.130 0.00 0.00 0.00 2.52
204 205 7.461182 TCTTTCCTTGTTCTTTGTCTCAAAA 57.539 32.000 0.00 0.00 0.00 2.44
205 206 7.461182 TTCTTTCCTTGTTCTTTGTCTCAAA 57.539 32.000 0.00 0.00 0.00 2.69
207 208 7.461182 TTTTCTTTCCTTGTTCTTTGTCTCA 57.539 32.000 0.00 0.00 0.00 3.27
208 209 7.436376 CCATTTTCTTTCCTTGTTCTTTGTCTC 59.564 37.037 0.00 0.00 0.00 3.36
210 211 7.264947 TCCATTTTCTTTCCTTGTTCTTTGTC 58.735 34.615 0.00 0.00 0.00 3.18
211 212 7.181569 TCCATTTTCTTTCCTTGTTCTTTGT 57.818 32.000 0.00 0.00 0.00 2.83
212 213 7.927629 TCATCCATTTTCTTTCCTTGTTCTTTG 59.072 33.333 0.00 0.00 0.00 2.77
213 214 8.021898 TCATCCATTTTCTTTCCTTGTTCTTT 57.978 30.769 0.00 0.00 0.00 2.52
214 215 7.601705 TCATCCATTTTCTTTCCTTGTTCTT 57.398 32.000 0.00 0.00 0.00 2.52
216 217 8.661352 TTTTCATCCATTTTCTTTCCTTGTTC 57.339 30.769 0.00 0.00 0.00 3.18
240 241 6.452242 GGGGTTTTGATAGACGTTCATTTTT 58.548 36.000 0.00 0.00 0.00 1.94
241 242 5.335348 CGGGGTTTTGATAGACGTTCATTTT 60.335 40.000 0.00 0.00 0.00 1.82
243 244 3.687698 CGGGGTTTTGATAGACGTTCATT 59.312 43.478 0.00 0.00 0.00 2.57
244 245 3.267483 CGGGGTTTTGATAGACGTTCAT 58.733 45.455 0.00 0.00 0.00 2.57
245 246 2.613474 CCGGGGTTTTGATAGACGTTCA 60.613 50.000 0.00 0.00 0.00 3.18
246 247 2.004733 CCGGGGTTTTGATAGACGTTC 58.995 52.381 0.00 0.00 0.00 3.95
247 248 1.947212 GCCGGGGTTTTGATAGACGTT 60.947 52.381 2.18 0.00 0.00 3.99
249 250 1.426041 CGCCGGGGTTTTGATAGACG 61.426 60.000 11.01 0.00 0.00 4.18
250 251 1.712018 GCGCCGGGGTTTTGATAGAC 61.712 60.000 20.83 0.00 0.00 2.59
251 252 1.450669 GCGCCGGGGTTTTGATAGA 60.451 57.895 20.83 0.00 0.00 1.98
252 253 1.714899 CTGCGCCGGGGTTTTGATAG 61.715 60.000 20.83 4.00 0.00 2.08
253 254 1.747367 CTGCGCCGGGGTTTTGATA 60.747 57.895 20.83 0.00 0.00 2.15
254 255 2.472414 TACTGCGCCGGGGTTTTGAT 62.472 55.000 20.83 3.00 0.00 2.57
255 256 3.179888 TACTGCGCCGGGGTTTTGA 62.180 57.895 20.83 0.00 0.00 2.69
256 257 2.670251 TACTGCGCCGGGGTTTTG 60.670 61.111 20.83 10.04 0.00 2.44
258 259 3.310860 CTCTACTGCGCCGGGGTTT 62.311 63.158 20.83 7.11 0.00 3.27
259 260 3.771160 CTCTACTGCGCCGGGGTT 61.771 66.667 20.83 7.48 0.00 4.11
267 268 4.435436 TGCGTGGGCTCTACTGCG 62.435 66.667 0.00 0.00 40.82 5.18
268 269 2.815647 GTGCGTGGGCTCTACTGC 60.816 66.667 0.00 0.00 40.82 4.40
269 270 1.738099 GTGTGCGTGGGCTCTACTG 60.738 63.158 0.00 0.00 40.82 2.74
270 271 2.159819 CTGTGTGCGTGGGCTCTACT 62.160 60.000 0.00 0.00 40.82 2.57
271 272 1.738099 CTGTGTGCGTGGGCTCTAC 60.738 63.158 0.00 0.00 40.82 2.59
273 274 3.231889 CTCTGTGTGCGTGGGCTCT 62.232 63.158 0.00 0.00 40.82 4.09
274 275 2.715532 TTCTCTGTGTGCGTGGGCTC 62.716 60.000 0.00 0.00 40.82 4.70
275 276 2.324014 TTTCTCTGTGTGCGTGGGCT 62.324 55.000 0.00 0.00 40.82 5.19
277 278 1.021202 TTTTTCTCTGTGTGCGTGGG 58.979 50.000 0.00 0.00 0.00 4.61
293 294 0.661020 CGTGTCGTGGCCTTCTTTTT 59.339 50.000 3.32 0.00 0.00 1.94
294 295 1.782028 GCGTGTCGTGGCCTTCTTTT 61.782 55.000 3.32 0.00 0.00 2.27
295 296 2.251642 GCGTGTCGTGGCCTTCTTT 61.252 57.895 3.32 0.00 0.00 2.52
297 298 3.865929 CTGCGTGTCGTGGCCTTCT 62.866 63.158 3.32 0.00 0.00 2.85
298 299 3.414700 CTGCGTGTCGTGGCCTTC 61.415 66.667 3.32 0.00 0.00 3.46
300 301 4.363990 CTCTGCGTGTCGTGGCCT 62.364 66.667 3.32 0.00 0.00 5.19
313 314 1.748122 AATTGCAGCTCCGCCTCTG 60.748 57.895 0.00 0.00 0.00 3.35
314 315 1.748122 CAATTGCAGCTCCGCCTCT 60.748 57.895 0.00 0.00 0.00 3.69
315 316 2.796651 CAATTGCAGCTCCGCCTC 59.203 61.111 0.00 0.00 0.00 4.70
316 317 3.446570 GCAATTGCAGCTCCGCCT 61.447 61.111 25.36 0.00 41.59 5.52
327 328 5.646793 AGATATCTCCGATGGATTGCAATTG 59.353 40.000 14.33 0.00 0.00 2.32
328 329 5.813383 AGATATCTCCGATGGATTGCAATT 58.187 37.500 14.33 0.00 0.00 2.32
329 330 5.432680 AGATATCTCCGATGGATTGCAAT 57.567 39.130 12.83 12.83 0.00 3.56
330 331 4.897509 AGATATCTCCGATGGATTGCAA 57.102 40.909 0.00 0.00 0.00 4.08
333 334 5.347093 CGACAAAGATATCTCCGATGGATTG 59.653 44.000 5.51 6.82 0.00 2.67
334 335 5.011125 ACGACAAAGATATCTCCGATGGATT 59.989 40.000 5.51 0.00 0.00 3.01
335 336 4.524714 ACGACAAAGATATCTCCGATGGAT 59.475 41.667 5.51 0.00 0.00 3.41
336 337 3.889538 ACGACAAAGATATCTCCGATGGA 59.110 43.478 5.51 0.00 0.00 3.41
337 338 4.230657 GACGACAAAGATATCTCCGATGG 58.769 47.826 5.51 0.00 0.00 3.51
338 339 3.908978 CGACGACAAAGATATCTCCGATG 59.091 47.826 5.51 6.04 0.00 3.84
339 340 3.609644 GCGACGACAAAGATATCTCCGAT 60.610 47.826 5.51 0.00 0.00 4.18
340 341 2.286831 GCGACGACAAAGATATCTCCGA 60.287 50.000 5.51 0.00 0.00 4.55
341 342 2.044860 GCGACGACAAAGATATCTCCG 58.955 52.381 5.51 9.89 0.00 4.63
342 343 2.395654 GGCGACGACAAAGATATCTCC 58.604 52.381 5.51 0.00 0.00 3.71
369 370 3.774702 GAGAACAACGACGGCGGC 61.775 66.667 18.49 7.52 43.17 6.53
370 371 3.467119 CGAGAACAACGACGGCGG 61.467 66.667 18.49 0.00 43.17 6.13
371 372 4.117372 GCGAGAACAACGACGGCG 62.117 66.667 10.39 10.39 44.79 6.46
372 373 3.774702 GGCGAGAACAACGACGGC 61.775 66.667 0.00 0.00 39.73 5.68
376 377 1.193650 CATTTTCGGCGAGAACAACGA 59.806 47.619 15.41 0.00 38.83 3.85
377 378 1.193650 TCATTTTCGGCGAGAACAACG 59.806 47.619 15.41 4.91 38.83 4.10
378 379 2.961522 TCATTTTCGGCGAGAACAAC 57.038 45.000 15.41 0.00 38.83 3.32
379 380 3.070748 TGATCATTTTCGGCGAGAACAA 58.929 40.909 15.41 6.88 38.83 2.83
382 383 2.032054 GCATGATCATTTTCGGCGAGAA 59.968 45.455 15.44 15.44 37.01 2.87
384 385 1.331447 TGCATGATCATTTTCGGCGAG 59.669 47.619 10.46 0.00 0.00 5.03
386 387 2.048498 CATGCATGATCATTTTCGGCG 58.952 47.619 22.59 0.00 0.00 6.46
387 388 3.047796 GACATGCATGATCATTTTCGGC 58.952 45.455 32.75 6.74 0.00 5.54
388 389 4.295857 TGACATGCATGATCATTTTCGG 57.704 40.909 32.75 1.99 0.00 4.30
389 390 6.822073 ATTTGACATGCATGATCATTTTCG 57.178 33.333 32.75 2.55 0.00 3.46
391 392 9.661563 ACTTTATTTGACATGCATGATCATTTT 57.338 25.926 32.75 18.48 0.00 1.82
392 393 9.093970 CACTTTATTTGACATGCATGATCATTT 57.906 29.630 32.75 20.39 0.00 2.32
394 395 7.778083 ACACTTTATTTGACATGCATGATCAT 58.222 30.769 32.75 18.94 0.00 2.45
395 396 7.160547 ACACTTTATTTGACATGCATGATCA 57.839 32.000 32.75 25.70 0.00 2.92
396 397 9.740239 ATAACACTTTATTTGACATGCATGATC 57.260 29.630 32.75 23.67 0.00 2.92
397 398 9.740239 GATAACACTTTATTTGACATGCATGAT 57.260 29.630 32.75 17.57 0.00 2.45
399 400 7.975058 TGGATAACACTTTATTTGACATGCATG 59.025 33.333 25.09 25.09 0.00 4.06
400 401 8.065473 TGGATAACACTTTATTTGACATGCAT 57.935 30.769 0.00 0.00 0.00 3.96
401 402 7.459795 TGGATAACACTTTATTTGACATGCA 57.540 32.000 0.00 0.00 0.00 3.96
402 403 8.931385 AATGGATAACACTTTATTTGACATGC 57.069 30.769 0.00 0.00 0.00 4.06
615 616 8.764287 GCACTACTTAACAAATGCAGAATTTTT 58.236 29.630 0.00 0.00 36.28 1.94
616 617 7.384932 GGCACTACTTAACAAATGCAGAATTTT 59.615 33.333 0.00 0.00 36.28 1.82
617 618 6.868339 GGCACTACTTAACAAATGCAGAATTT 59.132 34.615 0.00 0.00 39.13 1.82
618 619 6.015519 TGGCACTACTTAACAAATGCAGAATT 60.016 34.615 0.00 0.00 34.73 2.17
620 621 4.824537 TGGCACTACTTAACAAATGCAGAA 59.175 37.500 0.00 0.00 34.73 3.02
621 622 4.393834 TGGCACTACTTAACAAATGCAGA 58.606 39.130 0.00 0.00 34.73 4.26
622 623 4.764679 TGGCACTACTTAACAAATGCAG 57.235 40.909 0.00 0.00 34.73 4.41
623 624 5.508825 CCTTTGGCACTACTTAACAAATGCA 60.509 40.000 0.00 0.00 34.73 3.96
624 625 4.923281 CCTTTGGCACTACTTAACAAATGC 59.077 41.667 0.00 0.00 31.51 3.56
640 641 9.986833 CAAAATAAAAGTATTTATGCCTTTGGC 57.013 29.630 1.01 1.01 43.99 4.52
667 668 9.967346 GCGCAATGAGATACTCCTATATATTAA 57.033 33.333 0.30 0.00 0.00 1.40
668 669 9.131791 TGCGCAATGAGATACTCCTATATATTA 57.868 33.333 8.16 0.00 0.00 0.98
669 670 8.011844 TGCGCAATGAGATACTCCTATATATT 57.988 34.615 8.16 0.00 0.00 1.28
670 671 7.588497 TGCGCAATGAGATACTCCTATATAT 57.412 36.000 8.16 0.00 0.00 0.86
672 673 5.921962 TGCGCAATGAGATACTCCTATAT 57.078 39.130 8.16 0.00 0.00 0.86
673 674 5.394553 CCATGCGCAATGAGATACTCCTATA 60.395 44.000 17.11 0.00 38.72 1.31
674 675 4.502016 CATGCGCAATGAGATACTCCTAT 58.498 43.478 17.11 0.00 38.72 2.57
677 678 1.802960 CCATGCGCAATGAGATACTCC 59.197 52.381 17.11 0.00 38.72 3.85
678 679 2.759191 TCCATGCGCAATGAGATACTC 58.241 47.619 17.11 0.00 38.72 2.59
679 680 2.916702 TCCATGCGCAATGAGATACT 57.083 45.000 17.11 0.00 38.72 2.12
681 682 4.022935 GGAAATTCCATGCGCAATGAGATA 60.023 41.667 17.11 0.00 38.72 1.98
682 683 3.243636 GGAAATTCCATGCGCAATGAGAT 60.244 43.478 17.11 7.64 38.72 2.75
683 684 2.099592 GGAAATTCCATGCGCAATGAGA 59.900 45.455 17.11 6.00 38.72 3.27
684 685 2.100252 AGGAAATTCCATGCGCAATGAG 59.900 45.455 17.11 4.69 39.61 2.90
685 686 2.101783 AGGAAATTCCATGCGCAATGA 58.898 42.857 17.11 11.66 39.61 2.57
688 689 4.527509 TTTAAGGAAATTCCATGCGCAA 57.472 36.364 17.11 0.00 39.61 4.85
689 690 4.527509 TTTTAAGGAAATTCCATGCGCA 57.472 36.364 14.96 14.96 39.61 6.09
690 691 4.869861 ACATTTTAAGGAAATTCCATGCGC 59.130 37.500 15.21 0.00 39.61 6.09
691 692 6.589523 TGAACATTTTAAGGAAATTCCATGCG 59.410 34.615 15.21 0.00 39.61 4.73
692 693 7.603784 ACTGAACATTTTAAGGAAATTCCATGC 59.396 33.333 15.21 0.00 39.61 4.06
693 694 8.928733 CACTGAACATTTTAAGGAAATTCCATG 58.071 33.333 15.21 10.77 39.61 3.66
694 695 8.650490 ACACTGAACATTTTAAGGAAATTCCAT 58.350 29.630 15.21 4.72 39.61 3.41
696 697 7.095649 GCACACTGAACATTTTAAGGAAATTCC 60.096 37.037 3.29 3.29 35.79 3.01
697 698 7.653311 AGCACACTGAACATTTTAAGGAAATTC 59.347 33.333 0.00 0.00 35.79 2.17
698 699 7.500141 AGCACACTGAACATTTTAAGGAAATT 58.500 30.769 0.00 0.00 35.79 1.82
699 700 7.054491 AGCACACTGAACATTTTAAGGAAAT 57.946 32.000 0.00 0.00 38.49 2.17
702 703 7.759489 ATAAGCACACTGAACATTTTAAGGA 57.241 32.000 0.00 0.00 0.00 3.36
703 704 9.906660 TTTATAAGCACACTGAACATTTTAAGG 57.093 29.630 0.00 0.00 0.00 2.69
717 718 9.722056 CTGGTGAGATAATTTTTATAAGCACAC 57.278 33.333 0.00 0.00 0.00 3.82
718 719 9.679661 TCTGGTGAGATAATTTTTATAAGCACA 57.320 29.630 0.00 0.00 0.00 4.57
753 754 8.755977 GGGAATAATTTGCTCATTCATATGGAT 58.244 33.333 2.13 0.00 31.61 3.41
755 756 8.033038 CAGGGAATAATTTGCTCATTCATATGG 58.967 37.037 2.13 0.00 31.61 2.74
756 757 8.582437 ACAGGGAATAATTTGCTCATTCATATG 58.418 33.333 0.00 0.00 31.61 1.78
758 759 9.639563 TTACAGGGAATAATTTGCTCATTCATA 57.360 29.630 1.45 0.00 31.61 2.15
759 760 8.416329 GTTACAGGGAATAATTTGCTCATTCAT 58.584 33.333 1.45 0.00 31.61 2.57
761 762 7.068716 AGGTTACAGGGAATAATTTGCTCATTC 59.931 37.037 0.00 0.00 0.00 2.67
762 763 6.897413 AGGTTACAGGGAATAATTTGCTCATT 59.103 34.615 0.00 0.00 0.00 2.57
765 766 8.465273 AATAGGTTACAGGGAATAATTTGCTC 57.535 34.615 0.00 0.00 0.00 4.26
766 767 8.838649 AAATAGGTTACAGGGAATAATTTGCT 57.161 30.769 0.00 0.00 0.00 3.91
767 768 9.529325 GAAAATAGGTTACAGGGAATAATTTGC 57.471 33.333 0.00 0.00 0.00 3.68
769 770 9.209048 GGGAAAATAGGTTACAGGGAATAATTT 57.791 33.333 0.00 0.00 0.00 1.82
770 771 8.574853 AGGGAAAATAGGTTACAGGGAATAATT 58.425 33.333 0.00 0.00 0.00 1.40
771 772 8.126241 AGGGAAAATAGGTTACAGGGAATAAT 57.874 34.615 0.00 0.00 0.00 1.28
772 773 7.184936 TGAGGGAAAATAGGTTACAGGGAATAA 59.815 37.037 0.00 0.00 0.00 1.40
773 774 6.679303 TGAGGGAAAATAGGTTACAGGGAATA 59.321 38.462 0.00 0.00 0.00 1.75
774 775 5.494706 TGAGGGAAAATAGGTTACAGGGAAT 59.505 40.000 0.00 0.00 0.00 3.01
777 778 4.855298 TGAGGGAAAATAGGTTACAGGG 57.145 45.455 0.00 0.00 0.00 4.45
778 779 7.718334 AATTTGAGGGAAAATAGGTTACAGG 57.282 36.000 0.00 0.00 0.00 4.00
828 829 8.630054 AAGTACAGTAACATATTTGCCTCAAA 57.370 30.769 0.00 0.00 37.75 2.69
830 831 7.549134 CAGAAGTACAGTAACATATTTGCCTCA 59.451 37.037 0.00 0.00 0.00 3.86
871 872 3.890756 TCGCATCTTTATTTGCCATCCAT 59.109 39.130 0.00 0.00 35.41 3.41
883 884 4.515191 GTCAATATGGGCTTCGCATCTTTA 59.485 41.667 0.00 0.00 38.05 1.85
884 885 3.316308 GTCAATATGGGCTTCGCATCTTT 59.684 43.478 0.00 0.00 38.05 2.52
887 888 2.498167 AGTCAATATGGGCTTCGCATC 58.502 47.619 0.00 0.00 38.05 3.91
889 890 2.169561 TGTAGTCAATATGGGCTTCGCA 59.830 45.455 0.00 0.00 0.00 5.10
890 891 2.802816 CTGTAGTCAATATGGGCTTCGC 59.197 50.000 0.00 0.00 0.00 4.70
893 927 4.969359 ACCTACTGTAGTCAATATGGGCTT 59.031 41.667 13.42 0.00 0.00 4.35
910 944 1.731720 GTCCGTCGTAGTGACCTACT 58.268 55.000 0.00 0.00 45.23 2.57
911 945 0.371645 CGTCCGTCGTAGTGACCTAC 59.628 60.000 0.00 0.00 45.23 3.18
912 946 0.740868 CCGTCCGTCGTAGTGACCTA 60.741 60.000 0.00 0.00 45.23 3.08
914 948 1.975363 CTCCGTCCGTCGTAGTGACC 61.975 65.000 0.00 0.00 45.23 4.02
943 983 1.069978 TCCGATGGATTGCGATTGCTA 59.930 47.619 6.47 0.00 43.34 3.49
950 990 5.409643 GGATATATTTCCGATGGATTGCG 57.590 43.478 0.00 0.00 0.00 4.85
1047 2812 1.690633 GCAGATGGGAGAGGTGGGA 60.691 63.158 0.00 0.00 0.00 4.37
1048 2813 1.692042 AGCAGATGGGAGAGGTGGG 60.692 63.158 0.00 0.00 0.00 4.61
1311 3086 1.107114 TTTTCTCCACTTTGGCGCAA 58.893 45.000 10.83 0.00 37.47 4.85
1347 3122 2.284625 AGGCCGGTGAGTCCATCA 60.285 61.111 1.90 0.00 35.57 3.07
1495 3270 1.003580 GAGGTGGGATGAGTGCTTGAA 59.996 52.381 0.00 0.00 0.00 2.69
1542 3317 1.349688 AGGAACACGACATTGGGCTTA 59.650 47.619 0.00 0.00 0.00 3.09
1572 3348 4.717877 CAATATCACAATCACCTAGCCCA 58.282 43.478 0.00 0.00 0.00 5.36
1649 3425 2.182284 CACATGCCACCATTGCGG 59.818 61.111 0.00 0.00 42.50 5.69
1823 3599 0.904865 ATTCCTCAGCACACTCGGGA 60.905 55.000 0.00 0.00 0.00 5.14
1824 3600 0.036010 AATTCCTCAGCACACTCGGG 60.036 55.000 0.00 0.00 0.00 5.14
1848 3624 2.427453 GGACCTACGCTTCAGAGATTCA 59.573 50.000 0.00 0.00 0.00 2.57
1863 3639 2.512896 AGATACCAGGAACTCGGACCTA 59.487 50.000 0.00 0.00 34.60 3.08
2049 3825 8.383175 GGGGATATGAGTTTCTCCATAAATACA 58.617 37.037 0.00 0.00 32.36 2.29
2164 3940 3.903467 ACCAATTTCCATAGCCCTTCTC 58.097 45.455 0.00 0.00 0.00 2.87
2293 4086 9.443323 TTTAGCAATGACTAACTAGCATGTAAA 57.557 29.630 0.00 0.00 31.94 2.01
2298 4091 6.963796 GCATTTAGCAATGACTAACTAGCAT 58.036 36.000 1.12 0.00 42.35 3.79
2326 4137 5.040635 TCAAATTTTCAGTTTCGCAAGGAC 58.959 37.500 0.00 0.00 38.47 3.85
2356 4172 3.631250 ACAACATCAACATATGGGGGTC 58.369 45.455 7.80 0.00 0.00 4.46
2801 4638 1.142262 CCCATCTGCAGTCATCCATCA 59.858 52.381 14.67 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.