Multiple sequence alignment - TraesCS5D01G510400

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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 TraesCS5D01G510400 chr5D 100.000 3422 0 0 1 3422 535497720 535494299 0.000000e+00 6320.0
1 TraesCS5D01G510400 chr5D 92.617 1964 94 17 587 2519 57819449 57821392 0.000000e+00 2776.0
2 TraesCS5D01G510400 chr5D 87.500 64 7 1 3205 3267 535494455 535494392 4.740000e-09 73.1
3 TraesCS5D01G510400 chr5D 87.500 64 7 1 3266 3329 535494516 535494454 4.740000e-09 73.1
4 TraesCS5D01G510400 chr7B 86.309 2739 244 76 587 3267 591461549 591464214 0.000000e+00 2859.0
5 TraesCS5D01G510400 chr5B 92.261 1964 101 18 587 2519 60826075 60824132 0.000000e+00 2737.0
6 TraesCS5D01G510400 chr1B 91.808 1892 97 21 670 2519 70232782 70234657 0.000000e+00 2582.0
7 TraesCS5D01G510400 chr1B 89.293 1980 151 28 587 2519 4954559 4952594 0.000000e+00 2425.0
8 TraesCS5D01G510400 chr1B 87.260 2190 195 40 379 2520 4109882 4112035 0.000000e+00 2422.0
9 TraesCS5D01G510400 chr1B 87.954 2067 191 31 587 2622 4144649 4146688 0.000000e+00 2385.0
10 TraesCS5D01G510400 chr1B 89.036 1961 164 24 587 2520 4519078 4517142 0.000000e+00 2383.0
11 TraesCS5D01G510400 chr1B 89.720 1751 133 19 719 2433 46691980 46693719 0.000000e+00 2193.0
12 TraesCS5D01G510400 chr1B 92.009 876 42 8 2520 3393 70234709 70235558 0.000000e+00 1205.0
13 TraesCS5D01G510400 chr1B 90.733 723 57 5 1806 2518 4798955 4798233 0.000000e+00 955.0
14 TraesCS5D01G510400 chr1B 83.471 363 36 14 442 794 4519753 4519405 1.980000e-82 316.0
15 TraesCS5D01G510400 chr1B 80.663 362 36 15 444 794 538505172 538505510 2.040000e-62 250.0
16 TraesCS5D01G510400 chr1B 83.696 184 14 8 442 621 4955090 4954919 3.530000e-35 159.0
17 TraesCS5D01G510400 chr1B 84.314 153 9 8 447 594 4597744 4597602 5.960000e-28 135.0
18 TraesCS5D01G510400 chr1B 89.062 64 6 1 3205 3267 70235434 70235497 1.020000e-10 78.7
19 TraesCS5D01G510400 chr1D 92.998 1728 95 11 812 2517 49764492 49766215 0.000000e+00 2497.0
20 TraesCS5D01G510400 chr1D 90.143 771 58 6 2628 3393 49766616 49767373 0.000000e+00 987.0
21 TraesCS5D01G510400 chr1D 97.309 223 6 0 1 223 62223733 62223511 2.490000e-101 379.0
22 TraesCS5D01G510400 chr1D 96.861 223 7 0 1 223 62233618 62233396 1.160000e-99 374.0
23 TraesCS5D01G510400 chr1D 96.413 223 7 1 1 223 62226582 62226361 1.940000e-97 366.0
24 TraesCS5D01G510400 chr1D 95.495 222 10 0 1 222 217009461 217009682 4.200000e-94 355.0
25 TraesCS5D01G510400 chr1D 89.062 64 6 1 3205 3267 49767250 49767313 1.020000e-10 78.7
26 TraesCS5D01G510400 chr1A 88.347 2111 156 37 447 2517 32545364 32547424 0.000000e+00 2453.0
27 TraesCS5D01G510400 chr1A 93.519 108 5 2 2515 2622 3014920 3015025 3.530000e-35 159.0
28 TraesCS5D01G510400 chr1A 77.824 239 25 13 334 560 2942918 2943140 4.640000e-24 122.0
29 TraesCS5D01G510400 chr6A 88.624 1969 162 31 587 2520 613493540 613495481 0.000000e+00 2338.0
30 TraesCS5D01G510400 chr6A 85.621 765 78 18 2523 3274 64165973 64165228 0.000000e+00 774.0
31 TraesCS5D01G510400 chr6B 86.551 2186 194 44 379 2520 120595712 120593583 0.000000e+00 2316.0
32 TraesCS5D01G510400 chr6B 86.556 2172 201 51 379 2518 120355375 120353263 0.000000e+00 2309.0
33 TraesCS5D01G510400 chr6B 82.745 765 93 22 2516 3267 120315590 120314852 0.000000e+00 645.0
34 TraesCS5D01G510400 chr6B 87.674 430 38 5 2516 2934 120353213 120352788 1.430000e-133 486.0
35 TraesCS5D01G510400 chr6D 87.971 1962 170 32 587 2520 51068117 51070040 0.000000e+00 2255.0
36 TraesCS5D01G510400 chr6D 89.295 1831 151 20 717 2520 51342952 51344764 0.000000e+00 2254.0
37 TraesCS5D01G510400 chr6D 83.879 763 86 16 2516 3267 53174134 53173398 0.000000e+00 693.0
38 TraesCS5D01G510400 chr6D 88.605 430 33 10 2516 2934 51344812 51345236 3.050000e-140 508.0
39 TraesCS5D01G510400 chr6D 87.907 430 36 10 2516 2934 51070088 51070512 3.070000e-135 492.0
40 TraesCS5D01G510400 chr6D 88.022 359 36 3 2816 3171 50958572 50958926 5.280000e-113 418.0
41 TraesCS5D01G510400 chr6D 96.347 219 8 0 3 221 41205852 41205634 9.030000e-96 361.0
42 TraesCS5D01G510400 chr6D 95.946 222 7 1 1 222 418628186 418627967 3.250000e-95 359.0
43 TraesCS5D01G510400 chr7D 96.847 222 7 0 1 222 114489007 114488786 4.170000e-99 372.0
44 TraesCS5D01G510400 chr2D 96.833 221 6 1 1 221 595122561 595122780 5.400000e-98 368.0
45 TraesCS5D01G510400 chr4D 96.380 221 8 0 1 221 349014821 349014601 6.980000e-97 364.0
46 TraesCS5D01G510400 chr3D 83.288 365 36 10 442 801 560025665 560025321 2.560000e-81 313.0
47 TraesCS5D01G510400 chr2B 81.471 367 34 16 439 794 741895706 741896049 1.570000e-68 270.0
48 TraesCS5D01G510400 chrUn 77.824 239 25 13 334 560 361631323 361631545 4.640000e-24 122.0
49 TraesCS5D01G510400 chr4A 80.357 112 10 7 448 558 666694196 666694096 1.320000e-09 75.0


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 TraesCS5D01G510400 chr5D 535494299 535497720 3421 True 2155.400000 6320 91.666667 1 3422 3 chr5D.!!$R1 3421
1 TraesCS5D01G510400 chr5D 57819449 57821392 1943 False 2776.000000 2776 92.617000 587 2519 1 chr5D.!!$F1 1932
2 TraesCS5D01G510400 chr7B 591461549 591464214 2665 False 2859.000000 2859 86.309000 587 3267 1 chr7B.!!$F1 2680
3 TraesCS5D01G510400 chr5B 60824132 60826075 1943 True 2737.000000 2737 92.261000 587 2519 1 chr5B.!!$R1 1932
4 TraesCS5D01G510400 chr1B 4109882 4112035 2153 False 2422.000000 2422 87.260000 379 2520 1 chr1B.!!$F1 2141
5 TraesCS5D01G510400 chr1B 4144649 4146688 2039 False 2385.000000 2385 87.954000 587 2622 1 chr1B.!!$F2 2035
6 TraesCS5D01G510400 chr1B 46691980 46693719 1739 False 2193.000000 2193 89.720000 719 2433 1 chr1B.!!$F3 1714
7 TraesCS5D01G510400 chr1B 4517142 4519753 2611 True 1349.500000 2383 86.253500 442 2520 2 chr1B.!!$R3 2078
8 TraesCS5D01G510400 chr1B 4952594 4955090 2496 True 1292.000000 2425 86.494500 442 2519 2 chr1B.!!$R4 2077
9 TraesCS5D01G510400 chr1B 70232782 70235558 2776 False 1288.566667 2582 90.959667 670 3393 3 chr1B.!!$F5 2723
10 TraesCS5D01G510400 chr1B 4798233 4798955 722 True 955.000000 955 90.733000 1806 2518 1 chr1B.!!$R2 712
11 TraesCS5D01G510400 chr1D 49764492 49767373 2881 False 1187.566667 2497 90.734333 812 3393 3 chr1D.!!$F2 2581
12 TraesCS5D01G510400 chr1D 62223511 62226582 3071 True 372.500000 379 96.861000 1 223 2 chr1D.!!$R2 222
13 TraesCS5D01G510400 chr1A 32545364 32547424 2060 False 2453.000000 2453 88.347000 447 2517 1 chr1A.!!$F3 2070
14 TraesCS5D01G510400 chr6A 613493540 613495481 1941 False 2338.000000 2338 88.624000 587 2520 1 chr6A.!!$F1 1933
15 TraesCS5D01G510400 chr6A 64165228 64165973 745 True 774.000000 774 85.621000 2523 3274 1 chr6A.!!$R1 751
16 TraesCS5D01G510400 chr6B 120593583 120595712 2129 True 2316.000000 2316 86.551000 379 2520 1 chr6B.!!$R2 2141
17 TraesCS5D01G510400 chr6B 120352788 120355375 2587 True 1397.500000 2309 87.115000 379 2934 2 chr6B.!!$R3 2555
18 TraesCS5D01G510400 chr6B 120314852 120315590 738 True 645.000000 645 82.745000 2516 3267 1 chr6B.!!$R1 751
19 TraesCS5D01G510400 chr6D 51342952 51345236 2284 False 1381.000000 2254 88.950000 717 2934 2 chr6D.!!$F3 2217
20 TraesCS5D01G510400 chr6D 51068117 51070512 2395 False 1373.500000 2255 87.939000 587 2934 2 chr6D.!!$F2 2347
21 TraesCS5D01G510400 chr6D 53173398 53174134 736 True 693.000000 693 83.879000 2516 3267 1 chr6D.!!$R2 751

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
365 366 0.461693 TTTTTGCCTGGTGTTGCAGC 60.462 50.0 0.00 0.0 38.95 5.25 F
370 371 0.602562 GCCTGGTGTTGCAGCAAATA 59.397 50.0 10.11 0.0 41.37 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2310 4206 0.536233 ACAACTTATGTGCACGCCCA 60.536 50.000 13.13 0.0 41.93 5.36 R
2520 4448 5.615925 ACCATAGCAGTAAAGGTAGAAGG 57.384 43.478 0.00 0.0 0.00 3.46 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
93 94 1.490693 CTCTCACACGCCACACACAC 61.491 60.000 0.00 0.00 0.00 3.82
120 121 3.805422 TGTCCTACGTGACACACAAATTC 59.195 43.478 6.37 0.00 40.22 2.17
132 133 8.128582 GTGACACACAAATTCAGTCTTTTCATA 58.871 33.333 0.00 0.00 34.08 2.15
145 146 5.122396 AGTCTTTTCATACCAAGATTCGTGC 59.878 40.000 0.00 0.00 31.71 5.34
147 148 5.471797 TCTTTTCATACCAAGATTCGTGCAA 59.528 36.000 0.00 0.00 0.00 4.08
148 149 5.697473 TTTCATACCAAGATTCGTGCAAA 57.303 34.783 0.00 0.00 0.00 3.68
150 151 5.697473 TCATACCAAGATTCGTGCAAAAA 57.303 34.783 0.00 0.00 0.00 1.94
151 152 5.698832 TCATACCAAGATTCGTGCAAAAAG 58.301 37.500 0.00 0.00 0.00 2.27
152 153 2.742774 ACCAAGATTCGTGCAAAAAGC 58.257 42.857 0.00 0.00 45.96 3.51
161 162 2.429069 GCAAAAAGCGCTGGACGG 60.429 61.111 12.58 0.65 43.93 4.79
171 172 4.899239 CTGGACGGCGATGGAGGC 62.899 72.222 16.62 0.00 0.00 4.70
189 190 2.345991 GTGTGGGCGAGTTGGCTA 59.654 61.111 3.60 0.00 44.11 3.93
190 191 1.302192 GTGTGGGCGAGTTGGCTAA 60.302 57.895 3.60 0.00 44.11 3.09
191 192 1.302192 TGTGGGCGAGTTGGCTAAC 60.302 57.895 4.51 4.51 44.11 2.34
212 213 3.240203 CACACGTGTGGGCGTTAG 58.760 61.111 35.65 12.08 43.83 2.34
214 215 1.593209 ACACGTGTGGGCGTTAGTG 60.593 57.895 22.71 0.00 43.83 2.74
215 216 1.593209 CACGTGTGGGCGTTAGTGT 60.593 57.895 7.58 0.00 43.83 3.55
218 219 0.658897 CGTGTGGGCGTTAGTGTTTT 59.341 50.000 0.00 0.00 0.00 2.43
219 220 1.333435 CGTGTGGGCGTTAGTGTTTTC 60.333 52.381 0.00 0.00 0.00 2.29
220 221 0.938713 TGTGGGCGTTAGTGTTTTCG 59.061 50.000 0.00 0.00 0.00 3.46
222 223 2.134346 GTGGGCGTTAGTGTTTTCGTA 58.866 47.619 0.00 0.00 0.00 3.43
223 224 2.156310 GTGGGCGTTAGTGTTTTCGTAG 59.844 50.000 0.00 0.00 0.00 3.51
224 225 1.728425 GGGCGTTAGTGTTTTCGTAGG 59.272 52.381 0.00 0.00 0.00 3.18
225 226 1.728425 GGCGTTAGTGTTTTCGTAGGG 59.272 52.381 0.00 0.00 0.00 3.53
227 228 2.610232 GCGTTAGTGTTTTCGTAGGGGA 60.610 50.000 0.00 0.00 0.00 4.81
228 229 3.652274 CGTTAGTGTTTTCGTAGGGGAA 58.348 45.455 0.00 0.00 0.00 3.97
229 230 4.057432 CGTTAGTGTTTTCGTAGGGGAAA 58.943 43.478 0.00 0.00 34.28 3.13
230 231 4.084380 CGTTAGTGTTTTCGTAGGGGAAAC 60.084 45.833 7.79 7.79 35.75 2.78
249 250 7.652300 GGAAACCAATCTCATGTTTTAAACC 57.348 36.000 5.32 0.00 32.67 3.27
250 251 6.364976 GGAAACCAATCTCATGTTTTAAACCG 59.635 38.462 5.32 0.00 32.67 4.44
251 252 5.385509 ACCAATCTCATGTTTTAAACCGG 57.614 39.130 0.00 0.00 0.00 5.28
252 253 4.830600 ACCAATCTCATGTTTTAAACCGGT 59.169 37.500 0.00 0.00 0.00 5.28
255 256 6.150474 CCAATCTCATGTTTTAAACCGGTAGT 59.850 38.462 8.00 0.62 0.00 2.73
256 257 7.334921 CCAATCTCATGTTTTAAACCGGTAGTA 59.665 37.037 8.00 0.00 0.00 1.82
257 258 8.889717 CAATCTCATGTTTTAAACCGGTAGTAT 58.110 33.333 8.00 0.00 0.00 2.12
263 264 9.111613 CATGTTTTAAACCGGTAGTATAATCCA 57.888 33.333 8.00 5.88 0.00 3.41
264 265 9.856162 ATGTTTTAAACCGGTAGTATAATCCAT 57.144 29.630 8.00 7.71 0.00 3.41
302 303 7.552050 AATGTTCTAGATCCATTCTCCTAGG 57.448 40.000 0.82 0.82 35.79 3.02
303 304 6.031964 TGTTCTAGATCCATTCTCCTAGGT 57.968 41.667 9.08 0.00 35.79 3.08
304 305 7.162973 TGTTCTAGATCCATTCTCCTAGGTA 57.837 40.000 9.08 0.00 35.79 3.08
305 306 7.005296 TGTTCTAGATCCATTCTCCTAGGTAC 58.995 42.308 9.08 0.00 35.79 3.34
306 307 7.147105 TGTTCTAGATCCATTCTCCTAGGTACT 60.147 40.741 9.08 0.00 38.06 2.73
307 308 8.384718 GTTCTAGATCCATTCTCCTAGGTACTA 58.615 40.741 9.08 0.00 36.36 1.82
308 309 8.521519 TCTAGATCCATTCTCCTAGGTACTAA 57.478 38.462 9.08 0.00 36.78 2.24
309 310 8.956860 TCTAGATCCATTCTCCTAGGTACTAAA 58.043 37.037 9.08 0.00 36.78 1.85
310 311 9.238368 CTAGATCCATTCTCCTAGGTACTAAAG 57.762 40.741 9.08 0.00 36.78 1.85
311 312 7.597327 AGATCCATTCTCCTAGGTACTAAAGT 58.403 38.462 9.08 0.00 42.17 2.66
312 313 8.734763 AGATCCATTCTCCTAGGTACTAAAGTA 58.265 37.037 9.08 0.00 42.17 2.24
313 314 9.364653 GATCCATTCTCCTAGGTACTAAAGTAA 57.635 37.037 9.08 0.00 42.17 2.24
314 315 8.763984 TCCATTCTCCTAGGTACTAAAGTAAG 57.236 38.462 9.08 0.00 42.17 2.34
315 316 7.287235 TCCATTCTCCTAGGTACTAAAGTAAGC 59.713 40.741 9.08 0.00 42.17 3.09
316 317 7.288158 CCATTCTCCTAGGTACTAAAGTAAGCT 59.712 40.741 9.08 0.00 42.17 3.74
317 318 8.697292 CATTCTCCTAGGTACTAAAGTAAGCTT 58.303 37.037 9.08 3.48 42.17 3.74
318 319 9.933240 ATTCTCCTAGGTACTAAAGTAAGCTTA 57.067 33.333 9.08 0.86 42.17 3.09
319 320 9.933240 TTCTCCTAGGTACTAAAGTAAGCTTAT 57.067 33.333 9.88 0.00 42.17 1.73
320 321 9.352191 TCTCCTAGGTACTAAAGTAAGCTTATG 57.648 37.037 9.88 1.29 42.17 1.90
321 322 8.474710 TCCTAGGTACTAAAGTAAGCTTATGG 57.525 38.462 9.88 0.00 42.17 2.74
322 323 8.284435 TCCTAGGTACTAAAGTAAGCTTATGGA 58.716 37.037 9.88 0.00 42.17 3.41
323 324 8.921205 CCTAGGTACTAAAGTAAGCTTATGGAA 58.079 37.037 9.88 0.00 42.17 3.53
333 334 8.617290 AAGTAAGCTTATGGAATATTAACCGG 57.383 34.615 9.88 0.00 32.27 5.28
334 335 7.742767 AGTAAGCTTATGGAATATTAACCGGT 58.257 34.615 9.88 0.00 0.00 5.28
335 336 8.873144 AGTAAGCTTATGGAATATTAACCGGTA 58.127 33.333 8.00 0.00 0.00 4.02
336 337 9.148104 GTAAGCTTATGGAATATTAACCGGTAG 57.852 37.037 8.00 0.00 0.00 3.18
337 338 7.312415 AGCTTATGGAATATTAACCGGTAGT 57.688 36.000 8.00 0.00 0.00 2.73
338 339 8.426569 AGCTTATGGAATATTAACCGGTAGTA 57.573 34.615 8.00 1.12 0.00 1.82
339 340 8.873144 AGCTTATGGAATATTAACCGGTAGTAA 58.127 33.333 8.00 3.93 0.00 2.24
340 341 9.148104 GCTTATGGAATATTAACCGGTAGTAAG 57.852 37.037 8.00 5.88 0.00 2.34
341 342 9.148104 CTTATGGAATATTAACCGGTAGTAAGC 57.852 37.037 8.00 0.00 0.00 3.09
342 343 6.736110 TGGAATATTAACCGGTAGTAAGCT 57.264 37.500 8.00 0.00 0.00 3.74
343 344 7.128234 TGGAATATTAACCGGTAGTAAGCTT 57.872 36.000 8.00 3.48 0.00 3.74
344 345 8.248904 TGGAATATTAACCGGTAGTAAGCTTA 57.751 34.615 8.00 0.86 0.00 3.09
345 346 8.143835 TGGAATATTAACCGGTAGTAAGCTTAC 58.856 37.037 26.04 26.04 0.00 2.34
346 347 8.363390 GGAATATTAACCGGTAGTAAGCTTACT 58.637 37.037 34.85 34.85 45.39 2.24
347 348 9.755804 GAATATTAACCGGTAGTAAGCTTACTT 57.244 33.333 36.91 23.23 40.96 2.24
350 351 8.853077 ATTAACCGGTAGTAAGCTTACTTTTT 57.147 30.769 36.91 24.57 40.96 1.94
351 352 6.549912 AACCGGTAGTAAGCTTACTTTTTG 57.450 37.500 36.91 25.78 40.96 2.44
352 353 4.453478 ACCGGTAGTAAGCTTACTTTTTGC 59.547 41.667 36.91 22.78 40.96 3.68
353 354 4.142752 CCGGTAGTAAGCTTACTTTTTGCC 60.143 45.833 36.91 27.45 40.96 4.52
354 355 4.694037 CGGTAGTAAGCTTACTTTTTGCCT 59.306 41.667 36.91 17.69 40.96 4.75
355 356 5.390567 CGGTAGTAAGCTTACTTTTTGCCTG 60.391 44.000 36.91 22.23 40.96 4.85
356 357 5.106277 GGTAGTAAGCTTACTTTTTGCCTGG 60.106 44.000 36.91 0.00 40.96 4.45
357 358 4.470602 AGTAAGCTTACTTTTTGCCTGGT 58.529 39.130 29.48 7.00 40.96 4.00
358 359 3.733443 AAGCTTACTTTTTGCCTGGTG 57.267 42.857 0.00 0.00 29.41 4.17
359 360 2.666317 AGCTTACTTTTTGCCTGGTGT 58.334 42.857 0.00 0.00 0.00 4.16
360 361 3.031013 AGCTTACTTTTTGCCTGGTGTT 58.969 40.909 0.00 0.00 0.00 3.32
361 362 3.123050 GCTTACTTTTTGCCTGGTGTTG 58.877 45.455 0.00 0.00 0.00 3.33
362 363 2.880963 TACTTTTTGCCTGGTGTTGC 57.119 45.000 0.00 0.00 0.00 4.17
363 364 0.901124 ACTTTTTGCCTGGTGTTGCA 59.099 45.000 0.00 0.00 35.27 4.08
364 365 1.134729 ACTTTTTGCCTGGTGTTGCAG 60.135 47.619 0.00 0.00 38.95 4.41
365 366 0.461693 TTTTTGCCTGGTGTTGCAGC 60.462 50.000 0.00 0.00 38.95 5.25
366 367 1.611474 TTTTGCCTGGTGTTGCAGCA 61.611 50.000 0.00 0.00 39.63 4.41
367 368 1.611474 TTTGCCTGGTGTTGCAGCAA 61.611 50.000 4.25 2.83 41.37 3.91
368 369 1.611474 TTGCCTGGTGTTGCAGCAAA 61.611 50.000 10.11 0.00 41.37 3.68
369 370 1.368579 GCCTGGTGTTGCAGCAAAT 59.631 52.632 10.11 0.00 41.37 2.32
370 371 0.602562 GCCTGGTGTTGCAGCAAATA 59.397 50.000 10.11 0.00 41.37 1.40
371 372 1.669795 GCCTGGTGTTGCAGCAAATAC 60.670 52.381 10.11 11.96 41.37 1.89
372 373 1.888512 CCTGGTGTTGCAGCAAATACT 59.111 47.619 10.11 0.00 41.37 2.12
373 374 3.081061 CCTGGTGTTGCAGCAAATACTA 58.919 45.455 10.11 9.29 41.37 1.82
374 375 3.127548 CCTGGTGTTGCAGCAAATACTAG 59.872 47.826 21.15 21.15 41.37 2.57
375 376 3.750371 TGGTGTTGCAGCAAATACTAGT 58.250 40.909 10.11 0.00 38.96 2.57
376 377 3.751175 TGGTGTTGCAGCAAATACTAGTC 59.249 43.478 10.11 0.00 38.96 2.59
377 378 3.181520 GGTGTTGCAGCAAATACTAGTCG 60.182 47.826 10.11 0.00 0.00 4.18
413 415 8.718102 TCTAGTTGAACAGATATTAGTTTGGC 57.282 34.615 0.00 0.00 0.00 4.52
414 416 6.422776 AGTTGAACAGATATTAGTTTGGCG 57.577 37.500 0.00 0.00 0.00 5.69
417 419 7.604927 AGTTGAACAGATATTAGTTTGGCGTTA 59.395 33.333 0.00 0.00 0.00 3.18
419 421 9.602568 TTGAACAGATATTAGTTTGGCGTTATA 57.397 29.630 0.00 0.00 0.00 0.98
436 438 8.188799 TGGCGTTATATATCTACTAATGACTGC 58.811 37.037 0.00 0.00 0.00 4.40
437 439 8.407064 GGCGTTATATATCTACTAATGACTGCT 58.593 37.037 0.00 0.00 0.00 4.24
439 441 9.938670 CGTTATATATCTACTAATGACTGCTCC 57.061 37.037 0.00 0.00 0.00 4.70
443 445 7.789202 ATATCTACTAATGACTGCTCCATGT 57.211 36.000 0.00 0.00 0.00 3.21
444 446 5.268118 TCTACTAATGACTGCTCCATGTG 57.732 43.478 0.00 0.00 0.00 3.21
445 447 3.272574 ACTAATGACTGCTCCATGTGG 57.727 47.619 0.00 0.00 0.00 4.17
458 677 1.153289 ATGTGGACTCATCGGCTGC 60.153 57.895 0.00 0.00 0.00 5.25
466 685 2.504681 CATCGGCTGCGGCAAAAC 60.505 61.111 21.31 0.00 40.87 2.43
476 695 2.730928 CTGCGGCAAAACGATTGATTTT 59.269 40.909 3.44 0.00 35.47 1.82
477 696 2.728839 TGCGGCAAAACGATTGATTTTC 59.271 40.909 0.00 0.00 35.47 2.29
478 697 2.092055 GCGGCAAAACGATTGATTTTCC 59.908 45.455 9.35 0.00 35.47 3.13
479 698 2.666022 CGGCAAAACGATTGATTTTCCC 59.334 45.455 9.35 0.00 35.47 3.97
481 700 4.380023 CGGCAAAACGATTGATTTTCCCTA 60.380 41.667 9.35 0.00 35.47 3.53
485 704 6.645003 GCAAAACGATTGATTTTCCCTACTTT 59.355 34.615 9.35 0.00 0.00 2.66
490 709 8.857694 ACGATTGATTTTCCCTACTTTCTTTA 57.142 30.769 0.00 0.00 0.00 1.85
524 743 3.829948 GCAAGAGCTACAAGTACGTACA 58.170 45.455 26.55 5.91 37.91 2.90
525 744 3.607209 GCAAGAGCTACAAGTACGTACAC 59.393 47.826 26.55 4.23 37.91 2.90
526 745 4.615452 GCAAGAGCTACAAGTACGTACACT 60.615 45.833 26.55 11.19 37.91 3.55
577 853 6.394809 TCGTGTTCAGATTCAGCAATTAGTA 58.605 36.000 0.00 0.00 0.00 1.82
578 854 6.310467 TCGTGTTCAGATTCAGCAATTAGTAC 59.690 38.462 0.00 0.00 0.00 2.73
622 970 1.590238 CTTGCGTCAATTCTAGCTCGG 59.410 52.381 0.00 0.00 0.00 4.63
630 978 4.929808 GTCAATTCTAGCTCGGTTCTTTGA 59.070 41.667 0.00 0.00 0.00 2.69
631 979 5.582665 GTCAATTCTAGCTCGGTTCTTTGAT 59.417 40.000 0.00 0.00 0.00 2.57
634 982 6.716934 ATTCTAGCTCGGTTCTTTGATCTA 57.283 37.500 0.00 0.00 0.00 1.98
638 989 3.131400 AGCTCGGTTCTTTGATCTACTCC 59.869 47.826 0.00 0.00 0.00 3.85
664 1018 5.130145 AGCTAGTTCATTATTCAGGCTCTGT 59.870 40.000 0.00 0.00 32.61 3.41
687 1059 9.257651 CTGTTACTTAATTATGGTGGTAGCTAC 57.742 37.037 15.88 15.88 0.00 3.58
712 1084 9.754382 ACTTTAATTTAATGATGATGATGTGGC 57.246 29.630 8.56 0.00 0.00 5.01
713 1085 9.199982 CTTTAATTTAATGATGATGATGTGGCC 57.800 33.333 0.00 0.00 0.00 5.36
714 1086 5.733620 ATTTAATGATGATGATGTGGCCC 57.266 39.130 0.00 0.00 0.00 5.80
715 1087 4.458256 TTAATGATGATGATGTGGCCCT 57.542 40.909 0.00 0.00 0.00 5.19
765 1143 5.939764 AATCTAGACACAGATAAGGTGCA 57.060 39.130 0.00 0.00 39.87 4.57
808 1204 5.663456 TCTCCATGCTTATGAAATTTTGGC 58.337 37.500 0.00 0.00 0.00 4.52
810 1206 3.878699 CCATGCTTATGAAATTTTGGCCC 59.121 43.478 0.00 0.00 0.00 5.80
841 1241 7.749570 CAGAAAATGCTCAAAGTTCATCAGTAG 59.250 37.037 0.00 0.00 0.00 2.57
870 1275 2.657184 TCGTAATGTGAGTGTGTGTCG 58.343 47.619 0.00 0.00 0.00 4.35
872 1277 1.459592 GTAATGTGAGTGTGTGTCGCC 59.540 52.381 0.00 0.00 0.00 5.54
877 1282 3.785189 GAGTGTGTGTCGCCGGTGT 62.785 63.158 16.01 0.00 0.00 4.16
1003 1694 5.241285 TGCTACAGCTGAATTTGTTCAATGA 59.759 36.000 23.35 0.00 42.66 2.57
1017 1708 1.829222 TCAATGAAGGACCTACCGGAC 59.171 52.381 9.46 0.00 44.74 4.79
1203 1986 0.811281 GGTTCCCAAATCTGCGGAAG 59.189 55.000 0.00 0.00 34.49 3.46
1210 1993 1.470098 CAAATCTGCGGAAGGTGGAAG 59.530 52.381 0.00 0.00 0.00 3.46
1286 2069 5.561725 GCCTTTCTGTGTTTTCATCTCACTC 60.562 44.000 0.00 0.00 33.82 3.51
1515 2310 2.504175 GTGGCTGGAATACCTTGGTAGA 59.496 50.000 5.71 0.00 37.04 2.59
1548 2343 4.632153 TGGAAGAGCTTGTAGTGAAGAAC 58.368 43.478 0.00 0.00 0.00 3.01
1638 2434 7.100458 TGAGTTTGAAAGGAAAAGAGAAAGG 57.900 36.000 0.00 0.00 0.00 3.11
1691 2496 1.132453 CTCCTCGTACGATGCTCACAA 59.868 52.381 19.87 0.00 0.00 3.33
1699 2504 2.283298 ACGATGCTCACAACATGGATC 58.717 47.619 0.00 0.00 0.00 3.36
1866 2671 6.127925 ACAATGACATTATTGCATTGTCTCGT 60.128 34.615 21.46 9.98 46.09 4.18
1980 2785 4.184629 CTGATAACAGCCTTTACGCTCTT 58.815 43.478 0.00 0.00 36.82 2.85
1989 2794 2.359900 CTTTACGCTCTTGCCCTCAAT 58.640 47.619 0.00 0.00 35.36 2.57
2310 4206 2.158623 TGATGTTGGAGTGGCTGAACTT 60.159 45.455 0.00 0.00 0.00 2.66
2520 4448 1.270274 TGTTCAGTGTGCATCATTGGC 59.730 47.619 10.32 0.00 35.03 4.52
2622 4878 1.738099 GCAGGCACCACTCGTGTAG 60.738 63.158 0.00 0.00 44.97 2.74
2640 4896 3.493129 TGTAGTGTGATTCTTGTTGCGTC 59.507 43.478 0.00 0.00 0.00 5.19
2661 4924 8.622157 TGCGTCATTTCTACTCTATATATAGCC 58.378 37.037 14.03 0.00 0.00 3.93
2707 5100 2.289631 CCCAAGATTCCCTGTTTTTGCC 60.290 50.000 0.00 0.00 0.00 4.52
2713 5106 3.990959 TTCCCTGTTTTTGCCTGTTTT 57.009 38.095 0.00 0.00 0.00 2.43
2738 5136 7.861630 TGTAGTGTTGTTTCTCTAAGAAATGC 58.138 34.615 5.50 1.27 44.94 3.56
2848 5364 5.219633 GTGGTAATGGTCAATGTTTCACAC 58.780 41.667 0.00 0.00 0.00 3.82
2957 5527 5.809719 AGTTACGAGTAGTTACTAGCACC 57.190 43.478 0.00 0.00 40.50 5.01
2991 5561 8.909708 TTTTAGATTCCAAGATTACAAATGCG 57.090 30.769 0.00 0.00 0.00 4.73
3011 5581 3.448686 CGGTGTAGTCATCTCATGGAAC 58.551 50.000 0.00 0.00 0.00 3.62
3026 5596 1.002659 TGGAACCTGATGTACAACCGG 59.997 52.381 11.32 11.32 0.00 5.28
3087 5673 9.502091 TCGCTAATTACAGGCTTGATATTAAAT 57.498 29.630 1.40 0.00 0.00 1.40
3171 5759 6.114187 AGTACACACCATTTGAGAAGATCA 57.886 37.500 0.00 0.00 35.62 2.92
3211 5799 0.594796 CAGCACCGAACTTTGGTTGC 60.595 55.000 11.76 11.76 37.72 4.17
3259 5848 7.969536 TCTGGATGAAAAACTGAACTCTAAG 57.030 36.000 0.00 0.00 0.00 2.18
3275 5864 7.872993 TGAACTCTAAGAAGTATTGGTTGTGAG 59.127 37.037 0.00 0.00 0.00 3.51
3279 5868 7.506114 TCTAAGAAGTATTGGTTGTGAGTGTT 58.494 34.615 0.00 0.00 0.00 3.32
3280 5869 6.377327 AAGAAGTATTGGTTGTGAGTGTTG 57.623 37.500 0.00 0.00 0.00 3.33
3390 5979 9.675464 TTTTTGAGGGAATATATGTAGAACGTT 57.325 29.630 0.00 0.00 0.00 3.99
3391 5980 9.675464 TTTTGAGGGAATATATGTAGAACGTTT 57.325 29.630 0.46 0.00 0.00 3.60
3420 6009 9.550406 TTAGGGAATATATGTAGAACGTTTTGG 57.450 33.333 0.46 0.00 0.00 3.28
3421 6010 7.571025 AGGGAATATATGTAGAACGTTTTGGT 58.429 34.615 0.46 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 1.520564 GTGTGTGTGGCGTGTGAGA 60.521 57.895 0.00 0.00 0.00 3.27
109 110 7.068103 TGGTATGAAAAGACTGAATTTGTGTGT 59.932 33.333 0.00 0.00 0.00 3.72
120 121 6.537566 CACGAATCTTGGTATGAAAAGACTG 58.462 40.000 0.00 0.00 35.34 3.51
132 133 2.742774 GCTTTTTGCACGAATCTTGGT 58.257 42.857 0.00 0.00 42.31 3.67
145 146 2.429069 GCCGTCCAGCGCTTTTTG 60.429 61.111 7.50 0.00 39.71 2.44
154 155 4.899239 GCCTCCATCGCCGTCCAG 62.899 72.222 0.00 0.00 0.00 3.86
167 168 4.681978 AACTCGCCCACACGCCTC 62.682 66.667 0.00 0.00 0.00 4.70
168 169 4.988598 CAACTCGCCCACACGCCT 62.989 66.667 0.00 0.00 0.00 5.52
171 172 3.583276 TAGCCAACTCGCCCACACG 62.583 63.158 0.00 0.00 0.00 4.49
172 173 1.302192 TTAGCCAACTCGCCCACAC 60.302 57.895 0.00 0.00 0.00 3.82
173 174 1.302192 GTTAGCCAACTCGCCCACA 60.302 57.895 0.00 0.00 0.00 4.17
174 175 2.388232 CGTTAGCCAACTCGCCCAC 61.388 63.158 0.00 0.00 32.09 4.61
186 187 2.663852 ACACGTGTGGGCGTTAGC 60.664 61.111 22.71 0.00 43.83 3.09
187 188 3.240203 CACACGTGTGGGCGTTAG 58.760 61.111 35.65 12.08 43.83 2.34
199 200 0.658897 AAAACACTAACGCCCACACG 59.341 50.000 0.00 0.00 39.50 4.49
200 201 1.333435 CGAAAACACTAACGCCCACAC 60.333 52.381 0.00 0.00 0.00 3.82
202 203 0.939419 ACGAAAACACTAACGCCCAC 59.061 50.000 0.00 0.00 0.00 4.61
205 206 1.728425 CCCTACGAAAACACTAACGCC 59.272 52.381 0.00 0.00 0.00 5.68
206 207 1.728425 CCCCTACGAAAACACTAACGC 59.272 52.381 0.00 0.00 0.00 4.84
207 208 3.302365 TCCCCTACGAAAACACTAACG 57.698 47.619 0.00 0.00 0.00 3.18
208 209 4.214119 GGTTTCCCCTACGAAAACACTAAC 59.786 45.833 0.00 0.00 38.95 2.34
209 210 4.141528 TGGTTTCCCCTACGAAAACACTAA 60.142 41.667 0.00 0.00 42.94 2.24
211 212 2.173143 TGGTTTCCCCTACGAAAACACT 59.827 45.455 0.00 0.00 42.94 3.55
212 213 2.574450 TGGTTTCCCCTACGAAAACAC 58.426 47.619 0.00 0.00 42.94 3.32
214 215 4.077108 AGATTGGTTTCCCCTACGAAAAC 58.923 43.478 0.00 0.00 39.45 2.43
215 216 4.202482 TGAGATTGGTTTCCCCTACGAAAA 60.202 41.667 0.00 0.00 33.68 2.29
218 219 2.542550 TGAGATTGGTTTCCCCTACGA 58.457 47.619 0.00 0.00 0.00 3.43
219 220 3.206150 CATGAGATTGGTTTCCCCTACG 58.794 50.000 0.00 0.00 0.00 3.51
220 221 4.236527 ACATGAGATTGGTTTCCCCTAC 57.763 45.455 0.00 0.00 0.00 3.18
222 223 3.833559 AACATGAGATTGGTTTCCCCT 57.166 42.857 0.00 0.00 0.00 4.79
223 224 4.890158 AAAACATGAGATTGGTTTCCCC 57.110 40.909 0.00 0.00 30.83 4.81
224 225 6.649141 GGTTTAAAACATGAGATTGGTTTCCC 59.351 38.462 0.00 0.00 37.65 3.97
225 226 6.364976 CGGTTTAAAACATGAGATTGGTTTCC 59.635 38.462 3.76 0.00 37.65 3.13
227 228 6.183360 ACCGGTTTAAAACATGAGATTGGTTT 60.183 34.615 0.00 0.00 39.70 3.27
228 229 5.303333 ACCGGTTTAAAACATGAGATTGGTT 59.697 36.000 0.00 0.00 0.00 3.67
229 230 4.830600 ACCGGTTTAAAACATGAGATTGGT 59.169 37.500 0.00 0.00 0.00 3.67
230 231 5.385509 ACCGGTTTAAAACATGAGATTGG 57.614 39.130 0.00 0.00 0.00 3.16
231 232 7.141100 ACTACCGGTTTAAAACATGAGATTG 57.859 36.000 15.04 0.00 0.00 2.67
237 238 9.111613 TGGATTATACTACCGGTTTAAAACATG 57.888 33.333 15.04 0.00 0.00 3.21
238 239 9.856162 ATGGATTATACTACCGGTTTAAAACAT 57.144 29.630 15.04 11.42 0.00 2.71
247 248 9.372189 ACTAAGTTTATGGATTATACTACCGGT 57.628 33.333 13.98 13.98 0.00 5.28
277 278 8.235230 ACCTAGGAGAATGGATCTAGAACATTA 58.765 37.037 17.98 8.48 38.96 1.90
279 280 6.629156 ACCTAGGAGAATGGATCTAGAACAT 58.371 40.000 17.98 1.74 38.96 2.71
280 281 6.031964 ACCTAGGAGAATGGATCTAGAACA 57.968 41.667 17.98 0.00 38.96 3.18
281 282 7.235804 AGTACCTAGGAGAATGGATCTAGAAC 58.764 42.308 17.98 0.00 38.96 3.01
282 283 7.409408 AGTACCTAGGAGAATGGATCTAGAA 57.591 40.000 17.98 0.00 38.96 2.10
283 284 8.521519 TTAGTACCTAGGAGAATGGATCTAGA 57.478 38.462 17.98 0.00 38.96 2.43
284 285 9.238368 CTTTAGTACCTAGGAGAATGGATCTAG 57.762 40.741 17.98 0.00 38.96 2.43
285 286 8.734763 ACTTTAGTACCTAGGAGAATGGATCTA 58.265 37.037 17.98 1.89 38.96 1.98
286 287 7.597327 ACTTTAGTACCTAGGAGAATGGATCT 58.403 38.462 17.98 2.77 42.61 2.75
287 288 7.842887 ACTTTAGTACCTAGGAGAATGGATC 57.157 40.000 17.98 0.00 0.00 3.36
288 289 9.369672 CTTACTTTAGTACCTAGGAGAATGGAT 57.630 37.037 17.98 0.00 0.00 3.41
289 290 7.287235 GCTTACTTTAGTACCTAGGAGAATGGA 59.713 40.741 17.98 0.08 0.00 3.41
290 291 7.288158 AGCTTACTTTAGTACCTAGGAGAATGG 59.712 40.741 17.98 2.45 0.00 3.16
291 292 8.240267 AGCTTACTTTAGTACCTAGGAGAATG 57.760 38.462 17.98 8.13 0.00 2.67
292 293 8.841754 AAGCTTACTTTAGTACCTAGGAGAAT 57.158 34.615 17.98 4.63 29.41 2.40
293 294 9.933240 ATAAGCTTACTTTAGTACCTAGGAGAA 57.067 33.333 17.98 0.37 37.33 2.87
294 295 9.352191 CATAAGCTTACTTTAGTACCTAGGAGA 57.648 37.037 17.98 0.00 37.33 3.71
295 296 8.578151 CCATAAGCTTACTTTAGTACCTAGGAG 58.422 40.741 17.98 3.24 37.33 3.69
296 297 8.284435 TCCATAAGCTTACTTTAGTACCTAGGA 58.716 37.037 17.98 0.00 37.33 2.94
297 298 8.474710 TCCATAAGCTTACTTTAGTACCTAGG 57.525 38.462 8.70 7.41 37.33 3.02
307 308 9.063615 CCGGTTAATATTCCATAAGCTTACTTT 57.936 33.333 8.70 0.00 37.33 2.66
308 309 8.215736 ACCGGTTAATATTCCATAAGCTTACTT 58.784 33.333 8.70 0.00 40.07 2.24
309 310 7.742767 ACCGGTTAATATTCCATAAGCTTACT 58.257 34.615 8.70 0.00 0.00 2.24
310 311 7.974482 ACCGGTTAATATTCCATAAGCTTAC 57.026 36.000 8.70 0.00 0.00 2.34
311 312 8.873144 ACTACCGGTTAATATTCCATAAGCTTA 58.127 33.333 15.04 8.99 0.00 3.09
312 313 7.742767 ACTACCGGTTAATATTCCATAAGCTT 58.257 34.615 15.04 3.48 0.00 3.74
313 314 7.312415 ACTACCGGTTAATATTCCATAAGCT 57.688 36.000 15.04 0.00 0.00 3.74
314 315 9.148104 CTTACTACCGGTTAATATTCCATAAGC 57.852 37.037 15.04 0.00 0.00 3.09
315 316 9.148104 GCTTACTACCGGTTAATATTCCATAAG 57.852 37.037 15.04 0.59 0.00 1.73
316 317 8.873144 AGCTTACTACCGGTTAATATTCCATAA 58.127 33.333 15.04 0.00 0.00 1.90
317 318 8.426569 AGCTTACTACCGGTTAATATTCCATA 57.573 34.615 15.04 0.00 0.00 2.74
318 319 7.312415 AGCTTACTACCGGTTAATATTCCAT 57.688 36.000 15.04 0.00 0.00 3.41
319 320 6.736110 AGCTTACTACCGGTTAATATTCCA 57.264 37.500 15.04 0.00 0.00 3.53
320 321 8.363390 AGTAAGCTTACTACCGGTTAATATTCC 58.637 37.037 32.78 3.90 41.92 3.01
321 322 9.755804 AAGTAAGCTTACTACCGGTTAATATTC 57.244 33.333 33.60 5.27 42.86 1.75
324 325 9.942850 AAAAAGTAAGCTTACTACCGGTTAATA 57.057 29.630 33.60 0.00 42.86 0.98
325 326 8.724229 CAAAAAGTAAGCTTACTACCGGTTAAT 58.276 33.333 33.60 15.90 42.86 1.40
326 327 7.307930 GCAAAAAGTAAGCTTACTACCGGTTAA 60.308 37.037 33.60 5.33 42.86 2.01
327 328 6.147656 GCAAAAAGTAAGCTTACTACCGGTTA 59.852 38.462 33.60 0.00 42.86 2.85
328 329 5.049198 GCAAAAAGTAAGCTTACTACCGGTT 60.049 40.000 33.60 22.63 42.86 4.44
329 330 4.453478 GCAAAAAGTAAGCTTACTACCGGT 59.547 41.667 33.60 18.56 42.86 5.28
330 331 4.142752 GGCAAAAAGTAAGCTTACTACCGG 60.143 45.833 33.60 24.32 42.86 5.28
331 332 4.694037 AGGCAAAAAGTAAGCTTACTACCG 59.306 41.667 33.60 23.43 42.86 4.02
332 333 5.106277 CCAGGCAAAAAGTAAGCTTACTACC 60.106 44.000 33.60 27.02 42.86 3.18
333 334 5.472478 ACCAGGCAAAAAGTAAGCTTACTAC 59.528 40.000 33.60 21.31 42.86 2.73
334 335 5.472137 CACCAGGCAAAAAGTAAGCTTACTA 59.528 40.000 33.60 0.85 42.86 1.82
335 336 4.278419 CACCAGGCAAAAAGTAAGCTTACT 59.722 41.667 29.48 29.48 45.43 2.24
336 337 4.037565 ACACCAGGCAAAAAGTAAGCTTAC 59.962 41.667 26.04 26.04 33.95 2.34
337 338 4.211920 ACACCAGGCAAAAAGTAAGCTTA 58.788 39.130 0.86 0.86 33.95 3.09
338 339 3.031013 ACACCAGGCAAAAAGTAAGCTT 58.969 40.909 3.48 3.48 36.30 3.74
339 340 2.666317 ACACCAGGCAAAAAGTAAGCT 58.334 42.857 0.00 0.00 0.00 3.74
340 341 3.123050 CAACACCAGGCAAAAAGTAAGC 58.877 45.455 0.00 0.00 0.00 3.09
341 342 3.123050 GCAACACCAGGCAAAAAGTAAG 58.877 45.455 0.00 0.00 0.00 2.34
342 343 2.497675 TGCAACACCAGGCAAAAAGTAA 59.502 40.909 0.00 0.00 37.03 2.24
343 344 2.100584 CTGCAACACCAGGCAAAAAGTA 59.899 45.455 0.00 0.00 39.93 2.24
344 345 0.901124 TGCAACACCAGGCAAAAAGT 59.099 45.000 0.00 0.00 37.03 2.66
345 346 1.574134 CTGCAACACCAGGCAAAAAG 58.426 50.000 0.00 0.00 39.93 2.27
346 347 0.461693 GCTGCAACACCAGGCAAAAA 60.462 50.000 0.00 0.00 39.93 1.94
347 348 1.143620 GCTGCAACACCAGGCAAAA 59.856 52.632 0.00 0.00 39.93 2.44
348 349 1.611474 TTGCTGCAACACCAGGCAAA 61.611 50.000 11.69 0.00 39.93 3.68
349 350 1.611474 TTTGCTGCAACACCAGGCAA 61.611 50.000 15.72 3.42 39.93 4.52
350 351 1.401318 ATTTGCTGCAACACCAGGCA 61.401 50.000 15.72 0.00 38.52 4.75
351 352 0.602562 TATTTGCTGCAACACCAGGC 59.397 50.000 15.72 0.00 33.44 4.85
352 353 1.888512 AGTATTTGCTGCAACACCAGG 59.111 47.619 15.72 0.00 33.44 4.45
353 354 3.753272 ACTAGTATTTGCTGCAACACCAG 59.247 43.478 15.72 15.50 35.93 4.00
354 355 3.750371 ACTAGTATTTGCTGCAACACCA 58.250 40.909 15.72 0.01 0.00 4.17
355 356 3.181520 CGACTAGTATTTGCTGCAACACC 60.182 47.826 15.72 5.46 0.00 4.16
356 357 3.432252 ACGACTAGTATTTGCTGCAACAC 59.568 43.478 15.72 15.34 0.00 3.32
357 358 3.659786 ACGACTAGTATTTGCTGCAACA 58.340 40.909 15.72 7.12 0.00 3.33
358 359 4.863131 ACTACGACTAGTATTTGCTGCAAC 59.137 41.667 15.72 4.55 34.34 4.17
359 360 5.068234 ACTACGACTAGTATTTGCTGCAA 57.932 39.130 11.69 11.69 34.34 4.08
360 361 4.713824 ACTACGACTAGTATTTGCTGCA 57.286 40.909 0.00 0.00 34.34 4.41
361 362 5.819059 ACTACTACGACTAGTATTTGCTGC 58.181 41.667 0.00 0.00 35.34 5.25
362 363 9.947669 AAATACTACTACGACTAGTATTTGCTG 57.052 33.333 22.11 5.42 46.35 4.41
373 374 9.224267 TGTTCAACTAGAAATACTACTACGACT 57.776 33.333 0.00 0.00 38.13 4.18
374 375 9.488124 CTGTTCAACTAGAAATACTACTACGAC 57.512 37.037 0.00 0.00 38.13 4.34
375 376 9.440773 TCTGTTCAACTAGAAATACTACTACGA 57.559 33.333 0.00 0.00 38.13 3.43
410 412 8.188799 GCAGTCATTAGTAGATATATAACGCCA 58.811 37.037 0.00 0.00 0.00 5.69
411 413 8.407064 AGCAGTCATTAGTAGATATATAACGCC 58.593 37.037 0.00 0.00 0.00 5.68
412 414 9.440784 GAGCAGTCATTAGTAGATATATAACGC 57.559 37.037 0.00 0.00 0.00 4.84
413 415 9.938670 GGAGCAGTCATTAGTAGATATATAACG 57.061 37.037 0.00 0.00 0.00 3.18
417 419 9.486123 ACATGGAGCAGTCATTAGTAGATATAT 57.514 33.333 0.00 0.00 0.00 0.86
419 421 7.310299 CCACATGGAGCAGTCATTAGTAGATAT 60.310 40.741 0.00 0.00 37.39 1.63
421 423 5.221601 CCACATGGAGCAGTCATTAGTAGAT 60.222 44.000 0.00 0.00 37.39 1.98
423 425 4.100035 TCCACATGGAGCAGTCATTAGTAG 59.900 45.833 0.00 0.00 39.78 2.57
424 426 4.030216 TCCACATGGAGCAGTCATTAGTA 58.970 43.478 0.00 0.00 39.78 1.82
425 427 2.840038 TCCACATGGAGCAGTCATTAGT 59.160 45.455 0.00 0.00 39.78 2.24
426 428 3.118482 AGTCCACATGGAGCAGTCATTAG 60.118 47.826 0.00 0.00 46.49 1.73
427 429 2.840038 AGTCCACATGGAGCAGTCATTA 59.160 45.455 0.00 0.00 46.49 1.90
429 431 1.209019 GAGTCCACATGGAGCAGTCAT 59.791 52.381 0.00 0.00 46.49 3.06
430 432 0.610174 GAGTCCACATGGAGCAGTCA 59.390 55.000 0.00 0.00 46.49 3.41
431 433 0.610174 TGAGTCCACATGGAGCAGTC 59.390 55.000 0.00 0.00 46.49 3.51
432 434 1.209019 GATGAGTCCACATGGAGCAGT 59.791 52.381 0.00 0.00 46.49 4.40
434 436 0.176449 CGATGAGTCCACATGGAGCA 59.824 55.000 0.00 3.41 46.49 4.26
435 437 0.531532 CCGATGAGTCCACATGGAGC 60.532 60.000 0.00 0.00 46.49 4.70
436 438 0.531532 GCCGATGAGTCCACATGGAG 60.532 60.000 0.00 0.00 46.49 3.86
437 439 0.977627 AGCCGATGAGTCCACATGGA 60.978 55.000 0.00 0.00 43.08 3.41
439 441 1.434622 GCAGCCGATGAGTCCACATG 61.435 60.000 0.00 0.00 0.00 3.21
440 442 1.153289 GCAGCCGATGAGTCCACAT 60.153 57.895 0.00 0.00 0.00 3.21
441 443 2.265739 GCAGCCGATGAGTCCACA 59.734 61.111 0.00 0.00 0.00 4.17
442 444 2.887568 CGCAGCCGATGAGTCCAC 60.888 66.667 0.00 0.00 36.29 4.02
443 445 4.147449 CCGCAGCCGATGAGTCCA 62.147 66.667 0.00 0.00 36.29 4.02
445 447 4.819761 TGCCGCAGCCGATGAGTC 62.820 66.667 0.00 0.00 38.69 3.36
458 677 2.666022 GGGAAAATCAATCGTTTTGCCG 59.334 45.455 6.20 0.00 43.73 5.69
476 695 7.415086 TGGGCAATTAATAAAGAAAGTAGGGA 58.585 34.615 0.00 0.00 0.00 4.20
477 696 7.654022 TGGGCAATTAATAAAGAAAGTAGGG 57.346 36.000 0.00 0.00 0.00 3.53
478 697 7.706607 GCTTGGGCAATTAATAAAGAAAGTAGG 59.293 37.037 0.00 0.00 38.54 3.18
479 698 8.250332 TGCTTGGGCAATTAATAAAGAAAGTAG 58.750 33.333 0.00 0.00 46.36 2.57
481 700 7.003402 TGCTTGGGCAATTAATAAAGAAAGT 57.997 32.000 0.00 0.00 46.36 2.66
555 781 7.602517 AGTACTAATTGCTGAATCTGAACAC 57.397 36.000 0.00 0.00 0.00 3.32
577 853 7.885399 AGCAATTCCACAAGAAGAATTACTAGT 59.115 33.333 0.00 0.00 39.97 2.57
578 854 8.273780 AGCAATTCCACAAGAAGAATTACTAG 57.726 34.615 0.00 0.00 39.97 2.57
622 970 7.576861 ACTAGCTAGGAGTAGATCAAAGAAC 57.423 40.000 24.35 0.00 0.00 3.01
630 978 9.815306 TGAATAATGAACTAGCTAGGAGTAGAT 57.185 33.333 24.35 8.37 0.00 1.98
631 979 9.290988 CTGAATAATGAACTAGCTAGGAGTAGA 57.709 37.037 24.35 6.41 0.00 2.59
634 982 6.239458 GCCTGAATAATGAACTAGCTAGGAGT 60.239 42.308 24.35 9.46 0.00 3.85
638 989 6.867816 CAGAGCCTGAATAATGAACTAGCTAG 59.132 42.308 19.44 19.44 32.44 3.42
687 1059 9.199982 GGCCACATCATCATCATTAAATTAAAG 57.800 33.333 0.00 0.00 0.00 1.85
703 1075 1.135094 CTACAGGAGGGCCACATCAT 58.865 55.000 6.18 0.00 36.29 2.45
706 1078 2.735772 CGCTACAGGAGGGCCACAT 61.736 63.158 6.18 0.00 36.29 3.21
707 1079 3.390521 CGCTACAGGAGGGCCACA 61.391 66.667 6.18 0.00 36.29 4.17
708 1080 3.372554 GACGCTACAGGAGGGCCAC 62.373 68.421 6.18 0.00 41.86 5.01
709 1081 3.075005 GACGCTACAGGAGGGCCA 61.075 66.667 6.18 0.00 41.86 5.36
710 1082 4.208686 CGACGCTACAGGAGGGCC 62.209 72.222 0.00 0.00 41.86 5.80
711 1083 2.502692 AAACGACGCTACAGGAGGGC 62.503 60.000 0.00 0.00 41.86 5.19
712 1084 0.037605 AAAACGACGCTACAGGAGGG 60.038 55.000 0.00 0.00 43.73 4.30
713 1085 1.792006 AAAAACGACGCTACAGGAGG 58.208 50.000 0.00 0.00 0.00 4.30
740 1118 6.818644 TGCACCTTATCTGTGTCTAGATTTTC 59.181 38.462 0.00 0.00 38.35 2.29
742 1120 6.299805 TGCACCTTATCTGTGTCTAGATTT 57.700 37.500 0.00 0.00 38.35 2.17
801 1183 4.680440 GCATTTTCTGTATCGGGCCAAAAT 60.680 41.667 4.39 2.50 0.00 1.82
808 1204 4.396166 ACTTTGAGCATTTTCTGTATCGGG 59.604 41.667 0.00 0.00 0.00 5.14
810 1206 6.602179 TGAACTTTGAGCATTTTCTGTATCG 58.398 36.000 0.00 0.00 0.00 2.92
848 1253 3.673338 CGACACACACTCACATTACGAAT 59.327 43.478 0.00 0.00 0.00 3.34
860 1265 1.812686 ATACACCGGCGACACACACT 61.813 55.000 9.30 0.00 0.00 3.55
867 1272 0.104304 AATGGAGATACACCGGCGAC 59.896 55.000 9.30 0.00 0.00 5.19
870 1275 4.273148 AGATAAATGGAGATACACCGGC 57.727 45.455 0.00 0.00 0.00 6.13
872 1277 6.280643 TGTGAAGATAAATGGAGATACACCG 58.719 40.000 0.00 0.00 0.00 4.94
877 1282 8.929260 AATGCATGTGAAGATAAATGGAGATA 57.071 30.769 0.00 0.00 0.00 1.98
992 1682 4.069304 CGGTAGGTCCTTCATTGAACAAA 58.931 43.478 0.00 0.00 0.00 2.83
1003 1694 2.036890 AGCGTCCGGTAGGTCCTT 59.963 61.111 0.00 0.00 39.05 3.36
1121 1904 1.369625 GGAACCAACACGGATAGCAG 58.630 55.000 0.00 0.00 38.63 4.24
1172 1955 3.597728 GGAACCGGGCGCAAAACA 61.598 61.111 10.83 0.00 0.00 2.83
1203 1986 2.496470 ACCAGAGTAATCGACTTCCACC 59.504 50.000 0.00 0.00 39.06 4.61
1286 2069 1.205655 TGAGGTCAATCAGCGAGGAAG 59.794 52.381 0.00 0.00 0.00 3.46
1491 2286 1.408822 CCAAGGTATTCCAGCCACTCC 60.409 57.143 0.00 0.00 35.89 3.85
1515 2310 2.114616 AGCTCTTCCAACGATCCATCT 58.885 47.619 0.00 0.00 0.00 2.90
1548 2343 4.583073 TCATGATGATTGATTCCTTGGCAG 59.417 41.667 0.00 0.00 0.00 4.85
1638 2434 5.295292 CACATCACCTGGAAGACAATCATAC 59.705 44.000 0.00 0.00 34.07 2.39
1691 2496 9.281371 CACAACAGAAATCATATAGATCCATGT 57.719 33.333 0.00 0.00 35.39 3.21
1866 2671 2.228822 GCTTTTAAGGTTGCTGCAGCTA 59.771 45.455 36.61 28.48 42.66 3.32
1980 2785 1.065491 AGCATACGACAATTGAGGGCA 60.065 47.619 13.59 0.00 0.00 5.36
1989 2794 3.610040 ACCATCTGAAGCATACGACAA 57.390 42.857 0.00 0.00 0.00 3.18
2310 4206 0.536233 ACAACTTATGTGCACGCCCA 60.536 50.000 13.13 0.00 41.93 5.36
2520 4448 5.615925 ACCATAGCAGTAAAGGTAGAAGG 57.384 43.478 0.00 0.00 0.00 3.46
2622 4878 3.542712 ATGACGCAACAAGAATCACAC 57.457 42.857 0.00 0.00 0.00 3.82
2626 4882 6.091441 AGAGTAGAAATGACGCAACAAGAATC 59.909 38.462 0.00 0.00 0.00 2.52
2657 4920 1.733360 GTGCGGATTACAAAACGGCTA 59.267 47.619 0.00 0.00 0.00 3.93
2658 4921 0.519961 GTGCGGATTACAAAACGGCT 59.480 50.000 0.00 0.00 0.00 5.52
2660 4923 2.690173 TTGTGCGGATTACAAAACGG 57.310 45.000 0.00 0.00 35.29 4.44
2707 5100 8.879759 TCTTAGAGAAACAACACTACAAAACAG 58.120 33.333 0.00 0.00 0.00 3.16
2713 5106 7.041372 GGCATTTCTTAGAGAAACAACACTACA 60.041 37.037 5.34 0.00 45.83 2.74
2738 5136 2.158254 GCGTACTAAAAAGGGTTCACGG 59.842 50.000 0.00 0.00 0.00 4.94
2848 5364 1.734707 CGCCTTTGTACTACAGGTCCG 60.735 57.143 0.00 0.00 0.00 4.79
2991 5561 3.452627 AGGTTCCATGAGATGACTACACC 59.547 47.826 0.00 0.00 0.00 4.16
3011 5581 2.742053 CAAGTTCCGGTTGTACATCAGG 59.258 50.000 14.83 14.83 0.00 3.86
3026 5596 2.297701 TGCCTTCAGTGGTTCAAGTTC 58.702 47.619 0.00 0.00 0.00 3.01
3061 5635 8.896320 TTTAATATCAAGCCTGTAATTAGCGA 57.104 30.769 0.00 0.00 0.00 4.93
3087 5673 1.040339 AAACAGAAACGCAAGCCCCA 61.040 50.000 0.00 0.00 45.62 4.96
3171 5759 6.835488 TGCTGGCTTCTCCAATTTTAAGATAT 59.165 34.615 0.00 0.00 46.01 1.63
3196 5784 1.001815 CAATCGCAACCAAAGTTCGGT 60.002 47.619 0.00 0.00 38.85 4.69
3211 5799 6.442487 TTTGAACTTAGTACACGACAATCG 57.558 37.500 0.00 0.00 46.93 3.34
3259 5848 4.036262 TGCAACACTCACAACCAATACTTC 59.964 41.667 0.00 0.00 0.00 3.01
3275 5864 7.023575 CCAGATTTGAACTTAGTATGCAACAC 58.976 38.462 0.00 0.00 0.00 3.32
3279 5868 7.337938 TCATCCAGATTTGAACTTAGTATGCA 58.662 34.615 0.00 0.00 0.00 3.96
3280 5869 7.792374 TCATCCAGATTTGAACTTAGTATGC 57.208 36.000 0.00 0.00 0.00 3.14
3333 5922 8.765219 CGTTCTACATATATTTTGGAACAGAGG 58.235 37.037 15.32 2.37 42.39 3.69
3364 5953 9.675464 AACGTTCTACATATATTCCCTCAAAAA 57.325 29.630 0.00 0.00 0.00 1.94
3365 5954 9.675464 AAACGTTCTACATATATTCCCTCAAAA 57.325 29.630 0.00 0.00 0.00 2.44
3366 5955 9.675464 AAAACGTTCTACATATATTCCCTCAAA 57.325 29.630 0.00 0.00 0.00 2.69
3367 5956 9.675464 AAAAACGTTCTACATATATTCCCTCAA 57.325 29.630 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.