Multiple sequence alignment - TraesCS5B01G438500

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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 TraesCS5B01G438500 chr5B 100.000 3068 0 0 1 3068 611322118 611325185 0.000000e+00 5666
1 TraesCS5B01G438500 chr5B 83.358 1358 189 21 785 2133 610922763 610924092 0.000000e+00 1221
2 TraesCS5B01G438500 chr5B 84.201 1076 153 11 985 2053 610965571 610966636 0.000000e+00 1029
3 TraesCS5B01G438500 chr5B 79.834 1329 234 23 790 2106 610873883 610875189 0.000000e+00 939
4 TraesCS5B01G438500 chr5B 80.152 1184 190 31 585 1761 610957974 610959119 0.000000e+00 843
5 TraesCS5B01G438500 chr5B 92.830 265 14 3 258 518 231782597 231782860 2.230000e-101 379
6 TraesCS5B01G438500 chr5B 90.809 272 23 1 258 527 528970227 528970498 2.250000e-96 363
7 TraesCS5B01G438500 chr5D 95.031 1630 55 7 587 2211 494761396 494763004 0.000000e+00 2538
8 TraesCS5B01G438500 chr5D 82.196 1539 216 35 586 2085 494684356 494685875 0.000000e+00 1271
9 TraesCS5B01G438500 chr5D 88.511 853 63 19 2234 3068 529544976 529545811 0.000000e+00 1000
10 TraesCS5B01G438500 chr5D 82.246 1104 179 14 984 2077 494654379 494655475 0.000000e+00 937
11 TraesCS5B01G438500 chr5D 93.562 233 15 0 1 233 494761033 494761265 6.300000e-92 348
12 TraesCS5B01G438500 chr5D 88.043 184 18 4 585 768 494713378 494713557 6.660000e-52 215
13 TraesCS5B01G438500 chr5D 94.203 69 4 0 515 583 494761279 494761347 4.180000e-19 106
14 TraesCS5B01G438500 chr5A 94.413 1611 61 5 607 2211 618602350 618603937 0.000000e+00 2449
15 TraesCS5B01G438500 chr5A 83.861 1295 183 14 855 2132 618270423 618271708 0.000000e+00 1210
16 TraesCS5B01G438500 chr5A 85.746 891 122 4 1158 2044 618430316 618431205 0.000000e+00 937
17 TraesCS5B01G438500 chr5A 81.170 1094 191 11 984 2077 618273220 618274298 0.000000e+00 865
18 TraesCS5B01G438500 chr5A 94.595 259 13 1 1 259 618601968 618602225 1.710000e-107 399
19 TraesCS5B01G438500 chr5A 87.500 184 19 4 585 768 618486018 618486197 3.100000e-50 209
20 TraesCS5B01G438500 chr5A 94.203 69 4 0 515 583 618602222 618602290 4.180000e-19 106
21 TraesCS5B01G438500 chr1D 88.201 856 63 17 2237 3068 54200811 54199970 0.000000e+00 987
22 TraesCS5B01G438500 chr1D 87.135 855 74 19 2236 3068 474125983 474126823 0.000000e+00 937
23 TraesCS5B01G438500 chr1D 85.470 234 16 7 2237 2456 54201368 54201139 8.560000e-56 228
24 TraesCS5B01G438500 chr7A 87.296 858 70 19 2236 3068 59604075 59604918 0.000000e+00 944
25 TraesCS5B01G438500 chr7A 91.635 263 20 1 258 518 718593703 718593965 2.250000e-96 363
26 TraesCS5B01G438500 chr7A 87.379 103 11 2 2235 2335 50075336 50075234 1.930000e-22 117
27 TraesCS5B01G438500 chr2D 87.048 857 62 22 2236 3068 396182007 396182838 0.000000e+00 922
28 TraesCS5B01G438500 chr2D 91.200 500 40 3 2572 3068 101981680 101982178 0.000000e+00 676
29 TraesCS5B01G438500 chrUn 86.166 853 82 22 2239 3068 112535292 112534453 0.000000e+00 889
30 TraesCS5B01G438500 chr4D 85.648 857 64 23 2236 3068 92205385 92204564 0.000000e+00 846
31 TraesCS5B01G438500 chr2A 87.215 657 67 12 2421 3068 4709983 4709335 0.000000e+00 732
32 TraesCS5B01G438500 chr1A 89.376 593 46 11 2484 3068 4261822 4262405 0.000000e+00 730
33 TraesCS5B01G438500 chr1A 87.681 138 11 4 2235 2368 4261680 4261815 4.100000e-34 156
34 TraesCS5B01G438500 chr1B 93.156 263 14 3 258 518 294242338 294242598 1.730000e-102 383
35 TraesCS5B01G438500 chr1B 90.706 269 22 2 253 518 266379161 266379429 3.760000e-94 355
36 TraesCS5B01G438500 chr1B 87.037 108 8 5 2228 2330 660000975 660000869 1.930000e-22 117
37 TraesCS5B01G438500 chr6D 91.481 270 21 1 258 525 434030797 434030528 1.340000e-98 370
38 TraesCS5B01G438500 chr4B 91.635 263 20 1 258 518 654841125 654840863 2.250000e-96 363
39 TraesCS5B01G438500 chr3D 90.323 279 24 2 258 533 346851821 346852099 2.250000e-96 363
40 TraesCS5B01G438500 chr2B 86.970 330 31 9 2747 3068 88613815 88614140 8.090000e-96 361
41 TraesCS5B01G438500 chr7B 90.775 271 22 2 258 525 636708468 636708738 2.910000e-95 359
42 TraesCS5B01G438500 chr7B 86.111 252 34 1 1 252 41648699 41648949 1.400000e-68 270
43 TraesCS5B01G438500 chr7D 92.308 130 8 2 2235 2362 556175154 556175283 1.880000e-42 183


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 TraesCS5B01G438500 chr5B 611322118 611325185 3067 False 5666.000000 5666 100.000000 1 3068 1 chr5B.!!$F7 3067
1 TraesCS5B01G438500 chr5B 610922763 610924092 1329 False 1221.000000 1221 83.358000 785 2133 1 chr5B.!!$F4 1348
2 TraesCS5B01G438500 chr5B 610965571 610966636 1065 False 1029.000000 1029 84.201000 985 2053 1 chr5B.!!$F6 1068
3 TraesCS5B01G438500 chr5B 610873883 610875189 1306 False 939.000000 939 79.834000 790 2106 1 chr5B.!!$F3 1316
4 TraesCS5B01G438500 chr5B 610957974 610959119 1145 False 843.000000 843 80.152000 585 1761 1 chr5B.!!$F5 1176
5 TraesCS5B01G438500 chr5D 494684356 494685875 1519 False 1271.000000 1271 82.196000 586 2085 1 chr5D.!!$F2 1499
6 TraesCS5B01G438500 chr5D 529544976 529545811 835 False 1000.000000 1000 88.511000 2234 3068 1 chr5D.!!$F4 834
7 TraesCS5B01G438500 chr5D 494761033 494763004 1971 False 997.333333 2538 94.265333 1 2211 3 chr5D.!!$F5 2210
8 TraesCS5B01G438500 chr5D 494654379 494655475 1096 False 937.000000 937 82.246000 984 2077 1 chr5D.!!$F1 1093
9 TraesCS5B01G438500 chr5A 618270423 618274298 3875 False 1037.500000 1210 82.515500 855 2132 2 chr5A.!!$F3 1277
10 TraesCS5B01G438500 chr5A 618601968 618603937 1969 False 984.666667 2449 94.403667 1 2211 3 chr5A.!!$F4 2210
11 TraesCS5B01G438500 chr5A 618430316 618431205 889 False 937.000000 937 85.746000 1158 2044 1 chr5A.!!$F1 886
12 TraesCS5B01G438500 chr1D 474125983 474126823 840 False 937.000000 937 87.135000 2236 3068 1 chr1D.!!$F1 832
13 TraesCS5B01G438500 chr1D 54199970 54201368 1398 True 607.500000 987 86.835500 2237 3068 2 chr1D.!!$R1 831
14 TraesCS5B01G438500 chr7A 59604075 59604918 843 False 944.000000 944 87.296000 2236 3068 1 chr7A.!!$F1 832
15 TraesCS5B01G438500 chr2D 396182007 396182838 831 False 922.000000 922 87.048000 2236 3068 1 chr2D.!!$F2 832
16 TraesCS5B01G438500 chrUn 112534453 112535292 839 True 889.000000 889 86.166000 2239 3068 1 chrUn.!!$R1 829
17 TraesCS5B01G438500 chr4D 92204564 92205385 821 True 846.000000 846 85.648000 2236 3068 1 chr4D.!!$R1 832
18 TraesCS5B01G438500 chr2A 4709335 4709983 648 True 732.000000 732 87.215000 2421 3068 1 chr2A.!!$R1 647
19 TraesCS5B01G438500 chr1A 4261680 4262405 725 False 443.000000 730 88.528500 2235 3068 2 chr1A.!!$F1 833

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
754 805 0.035458 CCTTCTCCCTTGCGTGTCTT 59.965 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2472 3189 0.402861 TGAACTGGAGGGGGAGGTTT 60.403 55.0 0.0 0.0 0.0 3.27 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
47 48 2.359107 TCTCTCCACCGTACGCGT 60.359 61.111 19.17 19.17 36.15 6.01
102 103 3.368116 CCCTAACGTGAAATCTCGGAACT 60.368 47.826 9.35 0.00 37.19 3.01
103 104 3.612860 CCTAACGTGAAATCTCGGAACTG 59.387 47.826 9.35 0.00 37.19 3.16
213 214 2.167398 GACAGTAGCGGCCCACAGAA 62.167 60.000 0.00 0.00 0.00 3.02
220 221 1.212935 AGCGGCCCACAGAATAAAGAT 59.787 47.619 0.00 0.00 0.00 2.40
255 256 7.335673 TCAGCCAGATACGACATAAATTCAAAA 59.664 33.333 0.00 0.00 0.00 2.44
256 257 7.641411 CAGCCAGATACGACATAAATTCAAAAG 59.359 37.037 0.00 0.00 0.00 2.27
257 258 7.336931 AGCCAGATACGACATAAATTCAAAAGT 59.663 33.333 0.00 0.00 0.00 2.66
258 259 8.609176 GCCAGATACGACATAAATTCAAAAGTA 58.391 33.333 0.00 0.00 0.00 2.24
259 260 9.916397 CCAGATACGACATAAATTCAAAAGTAC 57.084 33.333 0.00 0.00 0.00 2.73
264 265 8.617290 ACGACATAAATTCAAAAGTACTTCCT 57.383 30.769 8.95 0.00 0.00 3.36
265 266 8.718734 ACGACATAAATTCAAAAGTACTTCCTC 58.281 33.333 8.95 0.00 0.00 3.71
266 267 8.175716 CGACATAAATTCAAAAGTACTTCCTCC 58.824 37.037 8.95 0.00 0.00 4.30
267 268 8.934023 ACATAAATTCAAAAGTACTTCCTCCA 57.066 30.769 8.95 0.00 0.00 3.86
268 269 9.533831 ACATAAATTCAAAAGTACTTCCTCCAT 57.466 29.630 8.95 0.00 0.00 3.41
271 272 7.468141 AATTCAAAAGTACTTCCTCCATTCC 57.532 36.000 8.95 0.00 0.00 3.01
272 273 5.843019 TCAAAAGTACTTCCTCCATTCCT 57.157 39.130 8.95 0.00 0.00 3.36
273 274 6.200878 TCAAAAGTACTTCCTCCATTCCTT 57.799 37.500 8.95 0.00 0.00 3.36
274 275 6.003950 TCAAAAGTACTTCCTCCATTCCTTG 58.996 40.000 8.95 5.86 0.00 3.61
275 276 5.843019 AAAGTACTTCCTCCATTCCTTGA 57.157 39.130 8.95 0.00 0.00 3.02
276 277 6.394345 AAAGTACTTCCTCCATTCCTTGAT 57.606 37.500 8.95 0.00 0.00 2.57
277 278 7.510675 AAAGTACTTCCTCCATTCCTTGATA 57.489 36.000 8.95 0.00 0.00 2.15
278 279 7.698163 AAGTACTTCCTCCATTCCTTGATAT 57.302 36.000 1.12 0.00 0.00 1.63
279 280 8.798975 AAGTACTTCCTCCATTCCTTGATATA 57.201 34.615 1.12 0.00 0.00 0.86
280 281 8.798975 AGTACTTCCTCCATTCCTTGATATAA 57.201 34.615 0.00 0.00 0.00 0.98
281 282 8.875168 AGTACTTCCTCCATTCCTTGATATAAG 58.125 37.037 0.00 0.00 0.00 1.73
282 283 7.084268 ACTTCCTCCATTCCTTGATATAAGG 57.916 40.000 0.00 0.00 38.78 2.69
283 284 6.621514 ACTTCCTCCATTCCTTGATATAAGGT 59.378 38.462 5.67 0.00 38.55 3.50
284 285 6.439636 TCCTCCATTCCTTGATATAAGGTG 57.560 41.667 5.67 0.00 38.55 4.00
285 286 5.911178 TCCTCCATTCCTTGATATAAGGTGT 59.089 40.000 5.67 0.00 38.55 4.16
286 287 7.079700 TCCTCCATTCCTTGATATAAGGTGTA 58.920 38.462 5.67 0.00 38.55 2.90
287 288 7.739444 TCCTCCATTCCTTGATATAAGGTGTAT 59.261 37.037 5.67 0.00 38.55 2.29
288 289 9.046846 CCTCCATTCCTTGATATAAGGTGTATA 57.953 37.037 5.67 0.00 38.55 1.47
290 291 9.837681 TCCATTCCTTGATATAAGGTGTATAGA 57.162 33.333 5.67 0.00 38.55 1.98
328 329 9.816354 AAATCCAAAATATAAGGTGTATTGTGC 57.184 29.630 0.00 0.00 29.30 4.57
329 330 8.766994 ATCCAAAATATAAGGTGTATTGTGCT 57.233 30.769 0.00 0.00 29.30 4.40
330 331 7.995289 TCCAAAATATAAGGTGTATTGTGCTG 58.005 34.615 0.00 0.00 29.30 4.41
331 332 6.697019 CCAAAATATAAGGTGTATTGTGCTGC 59.303 38.462 0.00 0.00 29.30 5.25
332 333 7.257003 CAAAATATAAGGTGTATTGTGCTGCA 58.743 34.615 0.00 0.00 0.00 4.41
333 334 6.377327 AATATAAGGTGTATTGTGCTGCAC 57.623 37.500 25.15 25.15 34.56 4.57
338 339 2.867429 GTGTATTGTGCTGCACCATTC 58.133 47.619 28.17 20.38 32.73 2.67
339 340 1.468127 TGTATTGTGCTGCACCATTCG 59.532 47.619 28.17 0.00 32.73 3.34
340 341 0.451383 TATTGTGCTGCACCATTCGC 59.549 50.000 28.17 3.75 32.73 4.70
341 342 1.246056 ATTGTGCTGCACCATTCGCT 61.246 50.000 28.17 0.64 32.73 4.93
342 343 1.454572 TTGTGCTGCACCATTCGCTT 61.455 50.000 28.17 0.00 32.73 4.68
343 344 1.443194 GTGCTGCACCATTCGCTTG 60.443 57.895 21.78 0.00 0.00 4.01
344 345 2.180017 GCTGCACCATTCGCTTGG 59.820 61.111 0.00 2.29 42.82 3.61
345 346 2.334946 GCTGCACCATTCGCTTGGA 61.335 57.895 10.05 0.00 39.25 3.53
346 347 1.660560 GCTGCACCATTCGCTTGGAT 61.661 55.000 10.05 0.00 39.25 3.41
347 348 1.667236 CTGCACCATTCGCTTGGATA 58.333 50.000 10.05 0.00 39.25 2.59
348 349 2.016318 CTGCACCATTCGCTTGGATAA 58.984 47.619 10.05 0.00 39.25 1.75
349 350 2.620115 CTGCACCATTCGCTTGGATAAT 59.380 45.455 10.05 0.00 39.25 1.28
350 351 3.023119 TGCACCATTCGCTTGGATAATT 58.977 40.909 10.05 0.00 39.25 1.40
351 352 3.446873 TGCACCATTCGCTTGGATAATTT 59.553 39.130 10.05 0.00 39.25 1.82
352 353 4.081752 TGCACCATTCGCTTGGATAATTTT 60.082 37.500 10.05 0.00 39.25 1.82
353 354 4.869861 GCACCATTCGCTTGGATAATTTTT 59.130 37.500 10.05 0.00 39.25 1.94
392 393 9.569122 TTACATTTCCTTATATTAGTCAAGCCC 57.431 33.333 0.00 0.00 0.00 5.19
393 394 7.004691 ACATTTCCTTATATTAGTCAAGCCCC 58.995 38.462 0.00 0.00 0.00 5.80
394 395 6.841781 TTTCCTTATATTAGTCAAGCCCCT 57.158 37.500 0.00 0.00 0.00 4.79
395 396 6.435292 TTCCTTATATTAGTCAAGCCCCTC 57.565 41.667 0.00 0.00 0.00 4.30
396 397 5.727630 TCCTTATATTAGTCAAGCCCCTCT 58.272 41.667 0.00 0.00 0.00 3.69
397 398 6.871035 TCCTTATATTAGTCAAGCCCCTCTA 58.129 40.000 0.00 0.00 0.00 2.43
398 399 7.488205 TCCTTATATTAGTCAAGCCCCTCTAT 58.512 38.462 0.00 0.00 0.00 1.98
399 400 7.962003 TCCTTATATTAGTCAAGCCCCTCTATT 59.038 37.037 0.00 0.00 0.00 1.73
400 401 8.606830 CCTTATATTAGTCAAGCCCCTCTATTT 58.393 37.037 0.00 0.00 0.00 1.40
403 404 6.582929 ATTAGTCAAGCCCCTCTATTTTCT 57.417 37.500 0.00 0.00 0.00 2.52
404 405 4.495690 AGTCAAGCCCCTCTATTTTCTC 57.504 45.455 0.00 0.00 0.00 2.87
405 406 3.846588 AGTCAAGCCCCTCTATTTTCTCA 59.153 43.478 0.00 0.00 0.00 3.27
406 407 4.476479 AGTCAAGCCCCTCTATTTTCTCAT 59.524 41.667 0.00 0.00 0.00 2.90
407 408 4.578105 GTCAAGCCCCTCTATTTTCTCATG 59.422 45.833 0.00 0.00 0.00 3.07
408 409 4.228210 TCAAGCCCCTCTATTTTCTCATGT 59.772 41.667 0.00 0.00 0.00 3.21
409 410 4.429854 AGCCCCTCTATTTTCTCATGTC 57.570 45.455 0.00 0.00 0.00 3.06
410 411 3.782523 AGCCCCTCTATTTTCTCATGTCA 59.217 43.478 0.00 0.00 0.00 3.58
411 412 4.228210 AGCCCCTCTATTTTCTCATGTCAA 59.772 41.667 0.00 0.00 0.00 3.18
412 413 5.103771 AGCCCCTCTATTTTCTCATGTCAAT 60.104 40.000 0.00 0.00 0.00 2.57
413 414 5.595952 GCCCCTCTATTTTCTCATGTCAATT 59.404 40.000 0.00 0.00 0.00 2.32
414 415 6.772716 GCCCCTCTATTTTCTCATGTCAATTA 59.227 38.462 0.00 0.00 0.00 1.40
415 416 7.040823 GCCCCTCTATTTTCTCATGTCAATTAG 60.041 40.741 0.00 0.00 0.00 1.73
416 417 7.995488 CCCCTCTATTTTCTCATGTCAATTAGT 59.005 37.037 0.00 0.00 0.00 2.24
417 418 9.050601 CCCTCTATTTTCTCATGTCAATTAGTC 57.949 37.037 0.00 0.00 0.00 2.59
418 419 9.605275 CCTCTATTTTCTCATGTCAATTAGTCA 57.395 33.333 0.00 0.00 0.00 3.41
420 421 9.605275 TCTATTTTCTCATGTCAATTAGTCAGG 57.395 33.333 0.00 0.00 0.00 3.86
421 422 9.388506 CTATTTTCTCATGTCAATTAGTCAGGT 57.611 33.333 0.00 0.00 0.00 4.00
422 423 7.439157 TTTTCTCATGTCAATTAGTCAGGTG 57.561 36.000 0.00 0.00 0.00 4.00
423 424 5.745312 TCTCATGTCAATTAGTCAGGTGT 57.255 39.130 0.00 0.00 0.00 4.16
424 425 6.850752 TCTCATGTCAATTAGTCAGGTGTA 57.149 37.500 0.00 0.00 0.00 2.90
425 426 7.239763 TCTCATGTCAATTAGTCAGGTGTAA 57.760 36.000 0.00 0.00 0.00 2.41
426 427 7.851228 TCTCATGTCAATTAGTCAGGTGTAAT 58.149 34.615 0.00 0.00 0.00 1.89
427 428 7.981789 TCTCATGTCAATTAGTCAGGTGTAATC 59.018 37.037 0.00 0.00 0.00 1.75
428 429 7.047891 TCATGTCAATTAGTCAGGTGTAATCC 58.952 38.462 0.00 0.00 0.00 3.01
429 430 5.741011 TGTCAATTAGTCAGGTGTAATCCC 58.259 41.667 0.00 0.00 0.00 3.85
430 431 4.809426 GTCAATTAGTCAGGTGTAATCCCG 59.191 45.833 0.00 0.00 0.00 5.14
431 432 2.973694 TTAGTCAGGTGTAATCCCGC 57.026 50.000 0.00 0.00 0.00 6.13
432 433 1.117150 TAGTCAGGTGTAATCCCGCC 58.883 55.000 0.00 0.00 35.13 6.13
433 434 1.153229 GTCAGGTGTAATCCCGCCC 60.153 63.158 0.00 0.00 35.52 6.13
434 435 1.613928 TCAGGTGTAATCCCGCCCA 60.614 57.895 0.00 0.00 35.52 5.36
435 436 1.202099 TCAGGTGTAATCCCGCCCAA 61.202 55.000 0.00 0.00 35.52 4.12
436 437 0.322997 CAGGTGTAATCCCGCCCAAA 60.323 55.000 0.00 0.00 35.52 3.28
437 438 0.406361 AGGTGTAATCCCGCCCAAAA 59.594 50.000 0.00 0.00 35.52 2.44
438 439 0.528924 GGTGTAATCCCGCCCAAAAC 59.471 55.000 0.00 0.00 0.00 2.43
439 440 1.541379 GTGTAATCCCGCCCAAAACT 58.459 50.000 0.00 0.00 0.00 2.66
440 441 1.890489 GTGTAATCCCGCCCAAAACTT 59.110 47.619 0.00 0.00 0.00 2.66
441 442 1.889829 TGTAATCCCGCCCAAAACTTG 59.110 47.619 0.00 0.00 0.00 3.16
442 443 2.164338 GTAATCCCGCCCAAAACTTGA 58.836 47.619 0.00 0.00 0.00 3.02
443 444 1.710816 AATCCCGCCCAAAACTTGAA 58.289 45.000 0.00 0.00 0.00 2.69
444 445 1.937191 ATCCCGCCCAAAACTTGAAT 58.063 45.000 0.00 0.00 0.00 2.57
445 446 1.710816 TCCCGCCCAAAACTTGAATT 58.289 45.000 0.00 0.00 0.00 2.17
446 447 2.043227 TCCCGCCCAAAACTTGAATTT 58.957 42.857 0.00 0.00 0.00 1.82
447 448 2.436173 TCCCGCCCAAAACTTGAATTTT 59.564 40.909 0.00 0.00 31.87 1.82
448 449 3.118223 TCCCGCCCAAAACTTGAATTTTT 60.118 39.130 0.00 0.00 29.17 1.94
467 468 4.647424 TTTTTCTCCACATGCGTTCTTT 57.353 36.364 0.00 0.00 0.00 2.52
468 469 5.759506 TTTTTCTCCACATGCGTTCTTTA 57.240 34.783 0.00 0.00 0.00 1.85
469 470 5.759506 TTTTCTCCACATGCGTTCTTTAA 57.240 34.783 0.00 0.00 0.00 1.52
470 471 5.957842 TTTCTCCACATGCGTTCTTTAAT 57.042 34.783 0.00 0.00 0.00 1.40
471 472 5.957842 TTCTCCACATGCGTTCTTTAATT 57.042 34.783 0.00 0.00 0.00 1.40
472 473 5.957842 TCTCCACATGCGTTCTTTAATTT 57.042 34.783 0.00 0.00 0.00 1.82
473 474 5.938322 TCTCCACATGCGTTCTTTAATTTC 58.062 37.500 0.00 0.00 0.00 2.17
474 475 5.054390 TCCACATGCGTTCTTTAATTTCC 57.946 39.130 0.00 0.00 0.00 3.13
475 476 3.851403 CCACATGCGTTCTTTAATTTCCG 59.149 43.478 0.00 0.00 0.00 4.30
476 477 4.472286 CACATGCGTTCTTTAATTTCCGT 58.528 39.130 0.00 0.00 0.00 4.69
477 478 4.320690 CACATGCGTTCTTTAATTTCCGTG 59.679 41.667 0.00 0.00 0.00 4.94
478 479 2.923643 TGCGTTCTTTAATTTCCGTGC 58.076 42.857 0.00 0.00 0.00 5.34
479 480 2.247637 GCGTTCTTTAATTTCCGTGCC 58.752 47.619 0.00 0.00 0.00 5.01
480 481 2.350964 GCGTTCTTTAATTTCCGTGCCA 60.351 45.455 0.00 0.00 0.00 4.92
481 482 3.854045 GCGTTCTTTAATTTCCGTGCCAA 60.854 43.478 0.00 0.00 0.00 4.52
482 483 4.291783 CGTTCTTTAATTTCCGTGCCAAA 58.708 39.130 0.00 0.00 0.00 3.28
483 484 4.740695 CGTTCTTTAATTTCCGTGCCAAAA 59.259 37.500 0.00 0.00 0.00 2.44
484 485 5.232414 CGTTCTTTAATTTCCGTGCCAAAAA 59.768 36.000 0.00 0.00 0.00 1.94
485 486 6.415702 GTTCTTTAATTTCCGTGCCAAAAAC 58.584 36.000 0.00 0.00 0.00 2.43
486 487 5.908341 TCTTTAATTTCCGTGCCAAAAACT 58.092 33.333 0.00 0.00 0.00 2.66
487 488 7.040473 TCTTTAATTTCCGTGCCAAAAACTA 57.960 32.000 0.00 0.00 0.00 2.24
488 489 7.662897 TCTTTAATTTCCGTGCCAAAAACTAT 58.337 30.769 0.00 0.00 0.00 2.12
489 490 8.794553 TCTTTAATTTCCGTGCCAAAAACTATA 58.205 29.630 0.00 0.00 0.00 1.31
490 491 9.581099 CTTTAATTTCCGTGCCAAAAACTATAT 57.419 29.630 0.00 0.00 0.00 0.86
493 494 6.439675 TTTCCGTGCCAAAAACTATATACC 57.560 37.500 0.00 0.00 0.00 2.73
494 495 4.453751 TCCGTGCCAAAAACTATATACCC 58.546 43.478 0.00 0.00 0.00 3.69
495 496 4.164604 TCCGTGCCAAAAACTATATACCCT 59.835 41.667 0.00 0.00 0.00 4.34
496 497 5.366186 TCCGTGCCAAAAACTATATACCCTA 59.634 40.000 0.00 0.00 0.00 3.53
497 498 6.043474 TCCGTGCCAAAAACTATATACCCTAT 59.957 38.462 0.00 0.00 0.00 2.57
498 499 7.235193 TCCGTGCCAAAAACTATATACCCTATA 59.765 37.037 0.00 0.00 0.00 1.31
499 500 8.044908 CCGTGCCAAAAACTATATACCCTATAT 58.955 37.037 0.00 0.00 35.62 0.86
500 501 9.444600 CGTGCCAAAAACTATATACCCTATATT 57.555 33.333 0.00 0.00 33.60 1.28
508 509 8.466617 AACTATATACCCTATATTGAGGAGCG 57.533 38.462 0.00 0.00 39.15 5.03
509 510 7.005296 ACTATATACCCTATATTGAGGAGCGG 58.995 42.308 0.00 0.00 39.15 5.52
510 511 2.696526 ACCCTATATTGAGGAGCGGA 57.303 50.000 0.00 0.00 39.15 5.54
511 512 2.530701 ACCCTATATTGAGGAGCGGAG 58.469 52.381 0.00 0.00 39.15 4.63
512 513 1.827969 CCCTATATTGAGGAGCGGAGG 59.172 57.143 0.00 0.00 39.15 4.30
513 514 1.827969 CCTATATTGAGGAGCGGAGGG 59.172 57.143 0.00 0.00 39.15 4.30
546 547 9.525409 AAATAAGAAGCACTATTCATTGATTGC 57.475 29.630 0.00 0.00 0.00 3.56
583 584 2.825836 CGGCCAGGATTGCTCCAC 60.826 66.667 2.24 0.00 44.79 4.02
625 671 1.950973 GCCGTCCAGTCTCCTTCCTC 61.951 65.000 0.00 0.00 0.00 3.71
626 672 1.324005 CCGTCCAGTCTCCTTCCTCC 61.324 65.000 0.00 0.00 0.00 4.30
627 673 0.323908 CGTCCAGTCTCCTTCCTCCT 60.324 60.000 0.00 0.00 0.00 3.69
628 674 1.064611 CGTCCAGTCTCCTTCCTCCTA 60.065 57.143 0.00 0.00 0.00 2.94
690 736 0.106419 AACCAGCCCGAAGAAAACCA 60.106 50.000 0.00 0.00 0.00 3.67
693 739 1.000274 CCAGCCCGAAGAAAACCAAAG 60.000 52.381 0.00 0.00 0.00 2.77
709 760 0.605589 AAAGTCGCCAGTCCTCTCTG 59.394 55.000 0.00 0.00 35.45 3.35
749 800 2.750350 CACCCTTCTCCCTTGCGT 59.250 61.111 0.00 0.00 0.00 5.24
754 805 0.035458 CCTTCTCCCTTGCGTGTCTT 59.965 55.000 0.00 0.00 0.00 3.01
755 806 1.433534 CTTCTCCCTTGCGTGTCTTC 58.566 55.000 0.00 0.00 0.00 2.87
760 811 1.550130 CCCTTGCGTGTCTTCCCCTA 61.550 60.000 0.00 0.00 0.00 3.53
777 828 2.978298 CTACCGATCCCCTCCGCTGA 62.978 65.000 0.00 0.00 0.00 4.26
879 957 2.443394 CCTCCAATCCCTAGCGCCA 61.443 63.158 2.29 0.00 0.00 5.69
907 988 1.645034 CGTTCTTCTGGCGACATCAT 58.355 50.000 0.00 0.00 41.51 2.45
1037 1146 4.712051 AGATTTCTGCTGCCATGGTATA 57.288 40.909 14.67 0.00 0.00 1.47
1153 1268 0.771127 CCCTTTCAGTGTTGGAGGGA 59.229 55.000 13.91 0.00 44.42 4.20
1528 1653 3.070159 CCTCCTCGAGAATAAGGATGCAA 59.930 47.826 15.71 0.00 40.83 4.08
1539 1664 8.034313 AGAATAAGGATGCAACAGACCTAATA 57.966 34.615 0.00 0.00 32.06 0.98
1557 1682 5.296780 CCTAATATTTCAAGTCGGTGCACAT 59.703 40.000 20.43 2.33 0.00 3.21
1732 1859 1.524863 CGACTCCGTTCCTCCAGTGT 61.525 60.000 0.00 0.00 0.00 3.55
2211 2348 9.561069 TTTTCTTGCTAGAGAGTCTTGTTTTAT 57.439 29.630 0.00 0.00 0.00 1.40
2322 2459 5.796424 AATAAAGGGCATGATGGTCATTC 57.204 39.130 0.00 0.00 34.28 2.67
2428 3142 3.861263 GCGCGCGGGAGGTAAAAG 61.861 66.667 33.06 0.00 0.00 2.27
2470 3187 0.035152 TAGCACGAGGGGTCGAACTA 60.035 55.000 0.00 0.35 36.85 2.24
2472 3189 0.037975 GCACGAGGGGTCGAACTAAA 60.038 55.000 0.00 0.00 36.85 1.85
2479 3196 2.039480 AGGGGTCGAACTAAAAACCTCC 59.961 50.000 0.00 0.00 32.33 4.30
2480 3197 2.430465 GGGTCGAACTAAAAACCTCCC 58.570 52.381 0.00 0.00 32.22 4.30
2523 3244 1.063811 GACTACGCCACCGCTACTC 59.936 63.158 0.00 0.00 38.22 2.59
2524 3245 2.024305 CTACGCCACCGCTACTCG 59.976 66.667 0.00 0.00 38.22 4.18
2528 3249 1.735198 CGCCACCGCTACTCGAAAA 60.735 57.895 0.00 0.00 41.67 2.29
2529 3250 1.286354 CGCCACCGCTACTCGAAAAA 61.286 55.000 0.00 0.00 41.67 1.94
2593 3328 9.717892 CTTTGTACTACTCAAGTTTCTTTTTCC 57.282 33.333 0.00 0.00 39.80 3.13
2594 3329 9.457436 TTTGTACTACTCAAGTTTCTTTTTCCT 57.543 29.630 0.00 0.00 39.80 3.36
2620 3357 7.872993 TGAGAATCTTTGTACTACTCAAGTTGG 59.127 37.037 2.34 0.00 36.26 3.77
2663 3400 9.438228 TGTATATTTATTTTGTGTCGAGGAACA 57.562 29.630 0.00 0.00 0.00 3.18
2755 3493 0.588233 CGCGCATGTCATTTCTGCTC 60.588 55.000 8.75 0.00 33.75 4.26
2783 3521 5.464389 TCTTCGTGATAGATTCATGCATGTG 59.536 40.000 25.43 3.46 40.58 3.21
2827 3565 5.822519 GTCTCCAAACAGCCATTGTATCATA 59.177 40.000 0.00 0.00 39.73 2.15
2938 3802 7.750458 CGTAGTATGCAATTTGTCTTCAACATT 59.250 33.333 0.00 0.00 37.82 2.71
3046 5940 6.605594 TGACAAAATTTCAGGAAGTGGTTACT 59.394 34.615 0.00 0.00 39.32 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 2.396955 CGCGTACGGTGGAGAGAGT 61.397 63.158 18.39 0.00 34.97 3.24
47 48 3.479203 CCGTGGATGGCTGGGCTA 61.479 66.667 0.00 0.00 0.00 3.93
181 182 3.127721 CGCTACTGTCATTGACTCTGAGA 59.872 47.826 17.26 0.00 33.15 3.27
213 214 2.173569 GGCTGACAGGTGGGATCTTTAT 59.826 50.000 4.26 0.00 0.00 1.40
255 256 8.798975 TTATATCAAGGAATGGAGGAAGTACT 57.201 34.615 0.00 0.00 0.00 2.73
256 257 8.097662 CCTTATATCAAGGAATGGAGGAAGTAC 58.902 40.741 0.00 0.00 39.81 2.73
257 258 7.794683 ACCTTATATCAAGGAATGGAGGAAGTA 59.205 37.037 9.96 0.00 39.81 2.24
258 259 6.621514 ACCTTATATCAAGGAATGGAGGAAGT 59.378 38.462 9.96 0.00 39.81 3.01
259 260 6.939163 CACCTTATATCAAGGAATGGAGGAAG 59.061 42.308 9.96 0.00 39.81 3.46
260 261 6.389869 ACACCTTATATCAAGGAATGGAGGAA 59.610 38.462 9.96 0.00 39.81 3.36
261 262 5.911178 ACACCTTATATCAAGGAATGGAGGA 59.089 40.000 9.96 0.00 39.81 3.71
262 263 6.192970 ACACCTTATATCAAGGAATGGAGG 57.807 41.667 9.96 0.00 39.81 4.30
264 265 9.837681 TCTATACACCTTATATCAAGGAATGGA 57.162 33.333 9.96 5.31 39.81 3.41
302 303 9.816354 GCACAATACACCTTATATTTTGGATTT 57.184 29.630 0.00 0.00 0.00 2.17
303 304 9.200817 AGCACAATACACCTTATATTTTGGATT 57.799 29.630 0.00 0.00 0.00 3.01
304 305 8.632679 CAGCACAATACACCTTATATTTTGGAT 58.367 33.333 0.00 0.00 0.00 3.41
305 306 7.416213 GCAGCACAATACACCTTATATTTTGGA 60.416 37.037 0.00 0.00 0.00 3.53
306 307 6.697019 GCAGCACAATACACCTTATATTTTGG 59.303 38.462 0.00 0.00 0.00 3.28
307 308 7.220683 GTGCAGCACAATACACCTTATATTTTG 59.779 37.037 21.22 0.00 34.08 2.44
308 309 7.257722 GTGCAGCACAATACACCTTATATTTT 58.742 34.615 21.22 0.00 34.08 1.82
309 310 6.795399 GTGCAGCACAATACACCTTATATTT 58.205 36.000 21.22 0.00 34.08 1.40
310 311 6.377327 GTGCAGCACAATACACCTTATATT 57.623 37.500 21.22 0.00 34.08 1.28
318 319 2.728846 CGAATGGTGCAGCACAATACAC 60.729 50.000 26.78 14.37 35.86 2.90
319 320 1.468127 CGAATGGTGCAGCACAATACA 59.532 47.619 26.78 15.50 35.86 2.29
320 321 1.795162 GCGAATGGTGCAGCACAATAC 60.795 52.381 26.78 10.79 35.86 1.89
321 322 0.451383 GCGAATGGTGCAGCACAATA 59.549 50.000 26.78 12.82 35.86 1.90
322 323 1.213537 GCGAATGGTGCAGCACAAT 59.786 52.632 26.78 18.99 35.86 2.71
323 324 1.454572 AAGCGAATGGTGCAGCACAA 61.455 50.000 26.78 17.31 35.86 3.33
324 325 1.898094 AAGCGAATGGTGCAGCACA 60.898 52.632 26.78 13.36 35.86 4.57
325 326 1.443194 CAAGCGAATGGTGCAGCAC 60.443 57.895 22.79 17.97 33.85 4.40
326 327 2.628696 CCAAGCGAATGGTGCAGCA 61.629 57.895 22.56 22.56 35.65 4.41
327 328 1.660560 ATCCAAGCGAATGGTGCAGC 61.661 55.000 9.47 9.47 41.46 5.25
328 329 1.667236 TATCCAAGCGAATGGTGCAG 58.333 50.000 6.78 0.00 41.46 4.41
329 330 2.121291 TTATCCAAGCGAATGGTGCA 57.879 45.000 6.78 0.00 41.46 4.57
330 331 3.715628 AATTATCCAAGCGAATGGTGC 57.284 42.857 6.78 0.00 41.46 5.01
366 367 9.569122 GGGCTTGACTAATATAAGGAAATGTAA 57.431 33.333 0.00 0.00 0.00 2.41
367 368 8.161425 GGGGCTTGACTAATATAAGGAAATGTA 58.839 37.037 0.00 0.00 0.00 2.29
368 369 7.004691 GGGGCTTGACTAATATAAGGAAATGT 58.995 38.462 0.00 0.00 0.00 2.71
369 370 7.234355 AGGGGCTTGACTAATATAAGGAAATG 58.766 38.462 0.00 0.00 0.00 2.32
370 371 7.295911 AGAGGGGCTTGACTAATATAAGGAAAT 59.704 37.037 0.00 0.00 0.00 2.17
371 372 6.619852 AGAGGGGCTTGACTAATATAAGGAAA 59.380 38.462 0.00 0.00 0.00 3.13
372 373 6.151049 AGAGGGGCTTGACTAATATAAGGAA 58.849 40.000 0.00 0.00 0.00 3.36
373 374 5.727630 AGAGGGGCTTGACTAATATAAGGA 58.272 41.667 0.00 0.00 0.00 3.36
374 375 7.741554 ATAGAGGGGCTTGACTAATATAAGG 57.258 40.000 0.00 0.00 0.00 2.69
377 378 9.393786 AGAAAATAGAGGGGCTTGACTAATATA 57.606 33.333 0.00 0.00 0.00 0.86
378 379 8.281529 AGAAAATAGAGGGGCTTGACTAATAT 57.718 34.615 0.00 0.00 0.00 1.28
379 380 7.347222 TGAGAAAATAGAGGGGCTTGACTAATA 59.653 37.037 0.00 0.00 0.00 0.98
380 381 6.158695 TGAGAAAATAGAGGGGCTTGACTAAT 59.841 38.462 0.00 0.00 0.00 1.73
381 382 5.487488 TGAGAAAATAGAGGGGCTTGACTAA 59.513 40.000 0.00 0.00 0.00 2.24
382 383 5.030147 TGAGAAAATAGAGGGGCTTGACTA 58.970 41.667 0.00 0.00 0.00 2.59
383 384 3.846588 TGAGAAAATAGAGGGGCTTGACT 59.153 43.478 0.00 0.00 0.00 3.41
384 385 4.222124 TGAGAAAATAGAGGGGCTTGAC 57.778 45.455 0.00 0.00 0.00 3.18
385 386 4.228210 ACATGAGAAAATAGAGGGGCTTGA 59.772 41.667 0.00 0.00 0.00 3.02
386 387 4.530875 ACATGAGAAAATAGAGGGGCTTG 58.469 43.478 0.00 0.00 0.00 4.01
387 388 4.228210 TGACATGAGAAAATAGAGGGGCTT 59.772 41.667 0.00 0.00 0.00 4.35
388 389 3.782523 TGACATGAGAAAATAGAGGGGCT 59.217 43.478 0.00 0.00 0.00 5.19
389 390 4.156455 TGACATGAGAAAATAGAGGGGC 57.844 45.455 0.00 0.00 0.00 5.80
390 391 7.995488 ACTAATTGACATGAGAAAATAGAGGGG 59.005 37.037 0.00 0.00 0.00 4.79
391 392 8.970859 ACTAATTGACATGAGAAAATAGAGGG 57.029 34.615 0.00 0.00 0.00 4.30
392 393 9.605275 TGACTAATTGACATGAGAAAATAGAGG 57.395 33.333 0.00 0.00 0.00 3.69
394 395 9.605275 CCTGACTAATTGACATGAGAAAATAGA 57.395 33.333 0.00 0.00 0.00 1.98
395 396 9.388506 ACCTGACTAATTGACATGAGAAAATAG 57.611 33.333 0.00 0.49 0.00 1.73
396 397 9.166173 CACCTGACTAATTGACATGAGAAAATA 57.834 33.333 0.00 0.00 0.00 1.40
397 398 7.667219 ACACCTGACTAATTGACATGAGAAAAT 59.333 33.333 0.00 0.00 0.00 1.82
398 399 6.998074 ACACCTGACTAATTGACATGAGAAAA 59.002 34.615 0.00 0.00 0.00 2.29
399 400 6.533730 ACACCTGACTAATTGACATGAGAAA 58.466 36.000 0.00 0.00 0.00 2.52
400 401 6.114187 ACACCTGACTAATTGACATGAGAA 57.886 37.500 0.00 0.00 0.00 2.87
401 402 5.745312 ACACCTGACTAATTGACATGAGA 57.255 39.130 0.00 0.00 0.00 3.27
402 403 7.225538 GGATTACACCTGACTAATTGACATGAG 59.774 40.741 0.00 0.00 0.00 2.90
403 404 7.047891 GGATTACACCTGACTAATTGACATGA 58.952 38.462 0.00 0.00 0.00 3.07
404 405 6.260936 GGGATTACACCTGACTAATTGACATG 59.739 42.308 0.00 0.00 0.00 3.21
405 406 6.357367 GGGATTACACCTGACTAATTGACAT 58.643 40.000 0.00 0.00 0.00 3.06
406 407 5.625886 CGGGATTACACCTGACTAATTGACA 60.626 44.000 0.00 0.00 38.49 3.58
407 408 4.809426 CGGGATTACACCTGACTAATTGAC 59.191 45.833 0.00 0.00 38.49 3.18
408 409 4.682320 GCGGGATTACACCTGACTAATTGA 60.682 45.833 0.00 0.00 38.49 2.57
409 410 3.560068 GCGGGATTACACCTGACTAATTG 59.440 47.826 0.00 0.00 38.49 2.32
410 411 3.433173 GGCGGGATTACACCTGACTAATT 60.433 47.826 0.00 0.00 40.93 1.40
411 412 2.104281 GGCGGGATTACACCTGACTAAT 59.896 50.000 0.00 0.00 40.93 1.73
412 413 1.483415 GGCGGGATTACACCTGACTAA 59.517 52.381 0.00 0.00 40.93 2.24
413 414 1.117150 GGCGGGATTACACCTGACTA 58.883 55.000 0.00 0.00 40.93 2.59
414 415 1.623542 GGGCGGGATTACACCTGACT 61.624 60.000 0.00 0.00 43.47 3.41
415 416 1.153229 GGGCGGGATTACACCTGAC 60.153 63.158 0.00 0.00 43.24 3.51
416 417 1.202099 TTGGGCGGGATTACACCTGA 61.202 55.000 0.00 0.00 38.49 3.86
417 418 0.322997 TTTGGGCGGGATTACACCTG 60.323 55.000 0.00 0.00 39.16 4.00
418 419 0.406361 TTTTGGGCGGGATTACACCT 59.594 50.000 0.00 0.00 0.00 4.00
419 420 0.528924 GTTTTGGGCGGGATTACACC 59.471 55.000 0.00 0.00 0.00 4.16
420 421 1.541379 AGTTTTGGGCGGGATTACAC 58.459 50.000 0.00 0.00 0.00 2.90
421 422 1.889829 CAAGTTTTGGGCGGGATTACA 59.110 47.619 0.00 0.00 0.00 2.41
422 423 2.164338 TCAAGTTTTGGGCGGGATTAC 58.836 47.619 0.00 0.00 0.00 1.89
423 424 2.588464 TCAAGTTTTGGGCGGGATTA 57.412 45.000 0.00 0.00 0.00 1.75
424 425 1.710816 TTCAAGTTTTGGGCGGGATT 58.289 45.000 0.00 0.00 0.00 3.01
425 426 1.937191 ATTCAAGTTTTGGGCGGGAT 58.063 45.000 0.00 0.00 0.00 3.85
426 427 1.710816 AATTCAAGTTTTGGGCGGGA 58.289 45.000 0.00 0.00 0.00 5.14
427 428 2.542020 AAATTCAAGTTTTGGGCGGG 57.458 45.000 0.00 0.00 0.00 6.13
446 447 4.647424 AAAGAACGCATGTGGAGAAAAA 57.353 36.364 11.65 0.00 0.00 1.94
447 448 5.759506 TTAAAGAACGCATGTGGAGAAAA 57.240 34.783 11.65 0.00 0.00 2.29
448 449 5.957842 ATTAAAGAACGCATGTGGAGAAA 57.042 34.783 11.65 0.00 0.00 2.52
449 450 5.957842 AATTAAAGAACGCATGTGGAGAA 57.042 34.783 11.65 0.00 0.00 2.87
450 451 5.106317 GGAAATTAAAGAACGCATGTGGAGA 60.106 40.000 11.65 0.00 0.00 3.71
451 452 5.095490 GGAAATTAAAGAACGCATGTGGAG 58.905 41.667 11.65 0.00 0.00 3.86
452 453 4.378978 CGGAAATTAAAGAACGCATGTGGA 60.379 41.667 11.65 0.00 0.00 4.02
453 454 3.851403 CGGAAATTAAAGAACGCATGTGG 59.149 43.478 11.65 0.00 0.00 4.17
454 455 4.320690 CACGGAAATTAAAGAACGCATGTG 59.679 41.667 4.30 4.30 0.00 3.21
455 456 4.472286 CACGGAAATTAAAGAACGCATGT 58.528 39.130 0.00 0.00 0.00 3.21
456 457 3.300590 GCACGGAAATTAAAGAACGCATG 59.699 43.478 0.00 0.00 0.00 4.06
457 458 3.498082 GCACGGAAATTAAAGAACGCAT 58.502 40.909 0.00 0.00 0.00 4.73
458 459 2.350964 GGCACGGAAATTAAAGAACGCA 60.351 45.455 0.00 0.00 0.00 5.24
459 460 2.247637 GGCACGGAAATTAAAGAACGC 58.752 47.619 0.00 0.00 0.00 4.84
460 461 3.546002 TGGCACGGAAATTAAAGAACG 57.454 42.857 0.00 0.00 0.00 3.95
461 462 6.256975 AGTTTTTGGCACGGAAATTAAAGAAC 59.743 34.615 0.00 0.00 0.00 3.01
462 463 6.342111 AGTTTTTGGCACGGAAATTAAAGAA 58.658 32.000 0.00 0.00 0.00 2.52
463 464 5.908341 AGTTTTTGGCACGGAAATTAAAGA 58.092 33.333 0.00 0.00 0.00 2.52
464 465 7.883229 ATAGTTTTTGGCACGGAAATTAAAG 57.117 32.000 0.00 0.00 0.00 1.85
467 468 8.623030 GGTATATAGTTTTTGGCACGGAAATTA 58.377 33.333 0.00 0.00 0.00 1.40
468 469 7.417003 GGGTATATAGTTTTTGGCACGGAAATT 60.417 37.037 0.00 0.00 0.00 1.82
469 470 6.040054 GGGTATATAGTTTTTGGCACGGAAAT 59.960 38.462 0.00 0.00 0.00 2.17
470 471 5.357596 GGGTATATAGTTTTTGGCACGGAAA 59.642 40.000 0.00 0.00 0.00 3.13
471 472 4.883006 GGGTATATAGTTTTTGGCACGGAA 59.117 41.667 0.00 0.00 0.00 4.30
472 473 4.164604 AGGGTATATAGTTTTTGGCACGGA 59.835 41.667 0.00 0.00 0.00 4.69
473 474 4.457466 AGGGTATATAGTTTTTGGCACGG 58.543 43.478 0.00 0.00 0.00 4.94
474 475 9.444600 AATATAGGGTATATAGTTTTTGGCACG 57.555 33.333 0.00 0.00 31.37 5.34
482 483 8.915036 CGCTCCTCAATATAGGGTATATAGTTT 58.085 37.037 0.00 0.00 37.24 2.66
483 484 7.506261 CCGCTCCTCAATATAGGGTATATAGTT 59.494 40.741 0.00 0.00 37.24 2.24
484 485 7.005296 CCGCTCCTCAATATAGGGTATATAGT 58.995 42.308 0.00 0.00 37.24 2.12
485 486 7.232188 TCCGCTCCTCAATATAGGGTATATAG 58.768 42.308 0.00 0.00 37.24 1.31
486 487 7.157947 TCCGCTCCTCAATATAGGGTATATA 57.842 40.000 0.00 0.00 37.24 0.86
487 488 6.027025 TCCGCTCCTCAATATAGGGTATAT 57.973 41.667 0.00 0.00 37.24 0.86
488 489 5.446860 CTCCGCTCCTCAATATAGGGTATA 58.553 45.833 0.00 0.00 37.24 1.47
489 490 4.282496 CTCCGCTCCTCAATATAGGGTAT 58.718 47.826 0.00 0.00 37.24 2.73
490 491 3.563697 CCTCCGCTCCTCAATATAGGGTA 60.564 52.174 0.00 0.00 37.24 3.69
491 492 2.530701 CTCCGCTCCTCAATATAGGGT 58.469 52.381 0.00 0.00 37.24 4.34
492 493 1.827969 CCTCCGCTCCTCAATATAGGG 59.172 57.143 0.00 0.00 37.24 3.53
493 494 1.827969 CCCTCCGCTCCTCAATATAGG 59.172 57.143 0.00 0.00 38.06 2.57
494 495 2.757868 CTCCCTCCGCTCCTCAATATAG 59.242 54.545 0.00 0.00 0.00 1.31
495 496 2.110188 ACTCCCTCCGCTCCTCAATATA 59.890 50.000 0.00 0.00 0.00 0.86
496 497 1.133009 ACTCCCTCCGCTCCTCAATAT 60.133 52.381 0.00 0.00 0.00 1.28
497 498 0.261991 ACTCCCTCCGCTCCTCAATA 59.738 55.000 0.00 0.00 0.00 1.90
498 499 0.261991 TACTCCCTCCGCTCCTCAAT 59.738 55.000 0.00 0.00 0.00 2.57
499 500 0.040646 TTACTCCCTCCGCTCCTCAA 59.959 55.000 0.00 0.00 0.00 3.02
500 501 0.395862 CTTACTCCCTCCGCTCCTCA 60.396 60.000 0.00 0.00 0.00 3.86
501 502 0.106619 TCTTACTCCCTCCGCTCCTC 60.107 60.000 0.00 0.00 0.00 3.71
502 503 0.335361 TTCTTACTCCCTCCGCTCCT 59.665 55.000 0.00 0.00 0.00 3.69
503 504 1.192428 TTTCTTACTCCCTCCGCTCC 58.808 55.000 0.00 0.00 0.00 4.70
504 505 4.341520 TCTTATTTCTTACTCCCTCCGCTC 59.658 45.833 0.00 0.00 0.00 5.03
505 506 4.287552 TCTTATTTCTTACTCCCTCCGCT 58.712 43.478 0.00 0.00 0.00 5.52
506 507 4.667519 TCTTATTTCTTACTCCCTCCGC 57.332 45.455 0.00 0.00 0.00 5.54
507 508 5.051153 GCTTCTTATTTCTTACTCCCTCCG 58.949 45.833 0.00 0.00 0.00 4.63
508 509 5.818336 GTGCTTCTTATTTCTTACTCCCTCC 59.182 44.000 0.00 0.00 0.00 4.30
509 510 6.645306 AGTGCTTCTTATTTCTTACTCCCTC 58.355 40.000 0.00 0.00 0.00 4.30
510 511 6.628644 AGTGCTTCTTATTTCTTACTCCCT 57.371 37.500 0.00 0.00 0.00 4.20
511 512 8.966069 AATAGTGCTTCTTATTTCTTACTCCC 57.034 34.615 0.00 0.00 0.00 4.30
512 513 9.601217 TGAATAGTGCTTCTTATTTCTTACTCC 57.399 33.333 0.00 0.00 0.00 3.85
542 543 2.684881 GGATCAACTTCGATGTGGCAAT 59.315 45.455 4.52 0.00 0.00 3.56
546 547 1.927174 GTCGGATCAACTTCGATGTGG 59.073 52.381 4.52 1.81 35.35 4.17
583 584 0.379669 GACTGCATTCGCCCTGATTG 59.620 55.000 0.00 0.00 37.32 2.67
679 725 1.332375 TGGCGACTTTGGTTTTCTTCG 59.668 47.619 0.00 0.00 0.00 3.79
690 736 0.605589 CAGAGAGGACTGGCGACTTT 59.394 55.000 0.00 0.00 34.64 2.66
693 739 1.509004 GACAGAGAGGACTGGCGAC 59.491 63.158 0.00 0.00 41.59 5.19
709 760 1.817209 CGGGAGCAGTAGAAGGGAC 59.183 63.158 0.00 0.00 0.00 4.46
749 800 0.398098 GGGATCGGTAGGGGAAGACA 60.398 60.000 0.00 0.00 0.00 3.41
754 805 2.786899 GGAGGGGATCGGTAGGGGA 61.787 68.421 0.00 0.00 0.00 4.81
755 806 2.203803 GGAGGGGATCGGTAGGGG 60.204 72.222 0.00 0.00 0.00 4.79
760 811 4.458829 TCAGCGGAGGGGATCGGT 62.459 66.667 0.00 0.00 37.61 4.69
857 935 1.149401 GCTAGGGATTGGAGGTGGC 59.851 63.158 0.00 0.00 0.00 5.01
885 963 2.048127 GTCGCCAGAAGAACGGCT 60.048 61.111 0.00 0.00 46.62 5.52
896 977 1.026182 GCTGTCCAATGATGTCGCCA 61.026 55.000 0.00 0.00 0.00 5.69
907 988 1.741401 CATTCTCGCCGCTGTCCAA 60.741 57.895 0.00 0.00 0.00 3.53
1037 1146 2.498167 GCGCATATGACCTTTCCTCAT 58.502 47.619 6.97 0.00 32.91 2.90
1153 1268 0.320421 CATTCCACGGTCCAGTCGTT 60.320 55.000 0.00 0.00 38.94 3.85
1528 1653 6.106673 CACCGACTTGAAATATTAGGTCTGT 58.893 40.000 0.00 0.00 0.00 3.41
1539 1664 3.674997 ACTATGTGCACCGACTTGAAAT 58.325 40.909 15.69 0.00 0.00 2.17
1557 1682 1.347707 CACCTGTGGGCTGAGAAACTA 59.652 52.381 0.00 0.00 35.63 2.24
1732 1859 0.827089 CTGGCCATGACCACACCAAA 60.827 55.000 5.51 0.00 35.33 3.28
1736 1863 3.064324 GGCTGGCCATGACCACAC 61.064 66.667 5.51 0.00 35.33 3.82
2135 2268 4.327898 CCACAACATTCATGCATAAACAGC 59.672 41.667 0.00 0.00 0.00 4.40
2217 2354 7.333269 CAGAAGTGATCGATAAAAAGTGATCG 58.667 38.462 0.00 0.00 44.97 3.69
2218 2355 7.010923 AGCAGAAGTGATCGATAAAAAGTGATC 59.989 37.037 0.00 0.00 38.14 2.92
2219 2356 6.820656 AGCAGAAGTGATCGATAAAAAGTGAT 59.179 34.615 0.00 0.00 0.00 3.06
2220 2357 6.166279 AGCAGAAGTGATCGATAAAAAGTGA 58.834 36.000 0.00 0.00 0.00 3.41
2221 2358 6.414408 AGCAGAAGTGATCGATAAAAAGTG 57.586 37.500 0.00 0.00 0.00 3.16
2222 2359 6.183360 CGAAGCAGAAGTGATCGATAAAAAGT 60.183 38.462 0.00 0.00 36.95 2.66
2223 2360 6.181255 CGAAGCAGAAGTGATCGATAAAAAG 58.819 40.000 0.00 0.00 36.95 2.27
2224 2361 5.063438 CCGAAGCAGAAGTGATCGATAAAAA 59.937 40.000 0.00 0.00 36.95 1.94
2225 2362 4.566759 CCGAAGCAGAAGTGATCGATAAAA 59.433 41.667 0.00 0.00 36.95 1.52
2226 2363 4.112634 CCGAAGCAGAAGTGATCGATAAA 58.887 43.478 0.00 0.00 36.95 1.40
2227 2364 3.130516 ACCGAAGCAGAAGTGATCGATAA 59.869 43.478 0.00 0.00 36.95 1.75
2228 2365 2.688446 ACCGAAGCAGAAGTGATCGATA 59.312 45.455 0.00 0.00 36.95 2.92
2229 2366 1.478510 ACCGAAGCAGAAGTGATCGAT 59.521 47.619 0.00 0.00 36.95 3.59
2230 2367 0.888619 ACCGAAGCAGAAGTGATCGA 59.111 50.000 0.00 0.00 36.95 3.59
2231 2368 2.097629 TCTACCGAAGCAGAAGTGATCG 59.902 50.000 0.00 0.00 35.48 3.69
2232 2369 3.440228 GTCTACCGAAGCAGAAGTGATC 58.560 50.000 0.00 0.00 0.00 2.92
2418 3132 4.929819 TTTTCCAGCAACTTTTACCTCC 57.070 40.909 0.00 0.00 0.00 4.30
2428 3142 8.487970 GCTAGTTTTCTTAATTTTTCCAGCAAC 58.512 33.333 0.00 0.00 0.00 4.17
2470 3187 1.147191 GAACTGGAGGGGGAGGTTTTT 59.853 52.381 0.00 0.00 0.00 1.94
2472 3189 0.402861 TGAACTGGAGGGGGAGGTTT 60.403 55.000 0.00 0.00 0.00 3.27
2529 3250 8.594687 GCAAATAATAGTGAATTGCGTGAATTT 58.405 29.630 0.00 0.00 37.27 1.82
2538 3260 7.338800 ACAGGGAGCAAATAATAGTGAATTG 57.661 36.000 0.00 0.00 0.00 2.32
2592 3327 7.607250 ACTTGAGTAGTACAAAGATTCTCAGG 58.393 38.462 17.83 7.35 34.56 3.86
2593 3328 8.920665 CAACTTGAGTAGTACAAAGATTCTCAG 58.079 37.037 17.83 4.10 35.54 3.35
2594 3329 7.872993 CCAACTTGAGTAGTACAAAGATTCTCA 59.127 37.037 17.83 2.58 35.54 3.27
2620 3357 2.038387 ACACACACAGAACCCTTGAC 57.962 50.000 0.00 0.00 0.00 3.18
2655 3392 3.611113 CGTGGTAATTACTGTGTTCCTCG 59.389 47.826 15.05 5.96 0.00 4.63
2663 3400 3.267483 GCATCCACGTGGTAATTACTGT 58.733 45.455 32.74 8.79 36.34 3.55
2664 3401 3.266636 TGCATCCACGTGGTAATTACTG 58.733 45.455 32.74 19.04 36.34 2.74
2670 3408 1.447945 CACATGCATCCACGTGGTAA 58.552 50.000 32.74 16.65 31.86 2.85
2696 3434 8.360756 AAGTATAGCTTGCACAAATCGATTTGC 61.361 37.037 38.19 30.36 42.09 3.68
2730 3468 3.649896 AATGACATGCGCGCACACG 62.650 57.895 39.05 28.69 44.07 4.49
2755 3493 6.951643 TGCATGAATCTATCACGAAGAAATG 58.048 36.000 0.00 0.00 41.93 2.32
2783 3521 6.452494 AGACACATACACATACACTAGACC 57.548 41.667 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.