Multiple sequence alignment - TraesCS5B01G331900

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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 TraesCS5B01G331900 chr5B 100.000 3482 0 0 1596 5077 516043713 516040232 0.000000e+00 6431.0
1 TraesCS5B01G331900 chr5B 100.000 1125 0 0 1 1125 516045308 516044184 0.000000e+00 2078.0
2 TraesCS5B01G331900 chr5B 84.028 144 14 2 290 433 659822702 659822568 4.130000e-26 130.0
3 TraesCS5B01G331900 chr5B 85.484 124 8 3 291 413 380312576 380312690 2.480000e-23 121.0
4 TraesCS5B01G331900 chr5B 85.484 124 7 6 303 424 447071593 447071707 8.930000e-23 119.0
5 TraesCS5B01G331900 chr5A 90.643 2875 169 38 1626 4461 540372010 540369197 0.000000e+00 3727.0
6 TraesCS5B01G331900 chr5A 90.126 557 19 20 574 1125 540372574 540372049 0.000000e+00 691.0
7 TraesCS5B01G331900 chr5A 91.413 361 21 6 4718 5075 540369103 540368750 2.120000e-133 486.0
8 TraesCS5B01G331900 chr5A 90.455 220 13 3 2371 2583 599410338 599410556 2.990000e-72 283.0
9 TraesCS5B01G331900 chr5A 87.234 141 12 4 434 570 540372756 540372618 6.810000e-34 156.0
10 TraesCS5B01G331900 chr5A 84.286 140 13 2 290 429 598356837 598356707 1.480000e-25 128.0
11 TraesCS5B01G331900 chr5D 92.516 1991 89 20 1618 3571 426170651 426168684 0.000000e+00 2796.0
12 TraesCS5B01G331900 chr5D 89.305 907 45 15 3608 4495 426168686 426167813 0.000000e+00 1090.0
13 TraesCS5B01G331900 chr5D 90.385 520 17 19 573 1091 426171201 426170714 0.000000e+00 652.0
14 TraesCS5B01G331900 chr5D 86.170 470 29 14 4631 5075 426167668 426167210 4.600000e-130 475.0
15 TraesCS5B01G331900 chr5D 94.182 275 13 1 1 275 426171682 426171411 2.830000e-112 416.0
16 TraesCS5B01G331900 chr5D 84.659 176 8 4 415 571 426171412 426171237 1.890000e-34 158.0
17 TraesCS5B01G331900 chr5D 93.103 87 5 1 290 376 411155782 411155867 5.340000e-25 126.0
18 TraesCS5B01G331900 chr6D 90.065 463 29 7 2132 2583 133888397 133887941 7.320000e-163 584.0
19 TraesCS5B01G331900 chr6D 84.672 137 9 5 290 423 238479517 238479390 5.340000e-25 126.0
20 TraesCS5B01G331900 chr4B 89.518 477 24 9 2132 2582 604275759 604276235 9.480000e-162 580.0
21 TraesCS5B01G331900 chr4B 92.035 113 6 2 2263 2372 14933969 14934081 6.810000e-34 156.0
22 TraesCS5B01G331900 chr4B 92.035 113 6 2 2263 2372 553681548 553681436 6.810000e-34 156.0
23 TraesCS5B01G331900 chr4B 92.941 85 5 1 292 376 471776923 471776840 6.900000e-24 122.0
24 TraesCS5B01G331900 chr3D 89.121 478 26 8 2132 2583 30772615 30773092 5.700000e-159 571.0
25 TraesCS5B01G331900 chr7B 86.902 481 34 12 2132 2583 452911414 452911894 3.510000e-141 512.0
26 TraesCS5B01G331900 chr2B 91.324 219 12 2 2371 2583 393752806 393753023 4.970000e-75 292.0
27 TraesCS5B01G331900 chr2B 93.258 89 5 1 2130 2217 625470261 625470173 4.130000e-26 130.0
28 TraesCS5B01G331900 chr7A 90.909 220 12 3 2371 2583 435337024 435337242 6.430000e-74 289.0
29 TraesCS5B01G331900 chr6B 91.549 213 11 2 2378 2583 715035158 715035370 2.310000e-73 287.0
30 TraesCS5B01G331900 chr6B 86.290 124 8 2 290 413 659257030 659257144 5.340000e-25 126.0
31 TraesCS5B01G331900 chr6B 95.775 71 2 1 2129 2199 715035053 715035122 4.150000e-21 113.0
32 TraesCS5B01G331900 chr6B 80.795 151 18 3 290 438 200306579 200306720 1.930000e-19 108.0
33 TraesCS5B01G331900 chr2A 90.455 220 13 3 2371 2583 689216545 689216327 2.990000e-72 283.0
34 TraesCS5B01G331900 chr2A 90.455 220 13 3 2371 2583 689304508 689304290 2.990000e-72 283.0
35 TraesCS5B01G331900 chr4A 92.035 113 6 2 2263 2372 651556446 651556334 6.810000e-34 156.0
36 TraesCS5B01G331900 chr1A 86.232 138 8 4 290 425 250488351 250488479 6.850000e-29 139.0
37 TraesCS5B01G331900 chr7D 85.612 139 10 7 290 428 552278025 552277897 2.470000e-28 137.0
38 TraesCS5B01G331900 chr3B 87.097 124 8 1 290 413 47794019 47794134 3.190000e-27 134.0
39 TraesCS5B01G331900 chr1B 85.401 137 10 6 290 425 593826171 593826298 3.190000e-27 134.0
40 TraesCS5B01G331900 chr1B 78.082 146 17 6 290 434 585549266 585549397 1.520000e-10 78.7
41 TraesCS5B01G331900 chr3A 84.559 136 10 7 290 425 686828424 686828300 1.920000e-24 124.0
42 TraesCS5B01G331900 chr3A 95.588 68 3 0 2132 2199 90106873 90106806 5.370000e-20 110.0
43 TraesCS5B01G331900 chr4D 83.212 137 13 6 291 426 61608334 61608461 3.210000e-22 117.0
44 TraesCS5B01G331900 chr2D 90.909 88 5 3 290 376 82093913 82093828 1.160000e-21 115.0


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 TraesCS5B01G331900 chr5B 516040232 516045308 5076 True 4254.500000 6431 100.000000 1 5077 2 chr5B.!!$R2 5076
1 TraesCS5B01G331900 chr5A 540368750 540372756 4006 True 1265.000000 3727 89.854000 434 5075 4 chr5A.!!$R2 4641
2 TraesCS5B01G331900 chr5D 426167210 426171682 4472 True 931.166667 2796 89.536167 1 5075 6 chr5D.!!$R1 5074

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
752 810 0.030638 GGCATCGAGACTCTCTCTGC 59.969 60.0 16.07 16.07 41.32 4.26 F
753 811 0.737804 GCATCGAGACTCTCTCTGCA 59.262 55.0 18.10 0.00 41.53 4.41 F
1732 1795 0.652071 GGTCGAAACGTCCGTGTTTT 59.348 50.0 9.58 0.00 41.89 2.43 F
2122 2189 0.030369 GCTTCATGGTAGCATGCTGC 59.970 55.0 30.42 28.01 45.46 5.25 F
2747 2837 0.684535 TCAATGCCAACTCGGTCTCA 59.315 50.0 0.00 0.00 36.97 3.27 F
3806 3932 0.463833 ATTTTCATCCGTCGGAGCCC 60.464 55.0 20.50 0.00 34.05 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1612 1675 0.174845 TAATCTCAGGAACACCGCCG 59.825 55.000 0.00 0.00 0.00 6.46 R
1772 1835 0.297820 GCGCGAAATTCAGTCCTACG 59.702 55.000 12.10 0.00 0.00 3.51 R
2709 2799 1.261619 GATTGCCTGTAAATCGCCGAG 59.738 52.381 0.00 0.00 0.00 4.63 R
3792 3918 0.676782 AAAAAGGGCTCCGACGGATG 60.677 55.000 18.71 12.59 0.00 3.51 R
3989 4115 0.904865 ACTCCTCCACGCTGATTCCA 60.905 55.000 0.00 0.00 0.00 3.53 R
4935 5085 0.094730 GATGCCGCACAAACGAGTAC 59.905 55.000 0.00 0.00 34.06 2.73 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 1.134226 GAAAAGGCGAACGAACGAGA 58.866 50.000 9.67 0.00 35.09 4.04
71 72 3.346315 CAGAACCATTCATAGTGTGGCA 58.654 45.455 0.00 0.00 36.47 4.92
104 105 1.197430 AGTGGGGCTCTCTGGTTCAG 61.197 60.000 0.00 0.00 0.00 3.02
147 148 3.403936 GTGGCATCCCGCTTTATCT 57.596 52.632 0.00 0.00 41.91 1.98
198 199 5.447683 GCTCGTATGAACATTTTGCTCATCA 60.448 40.000 0.00 0.00 35.16 3.07
199 200 5.868257 TCGTATGAACATTTTGCTCATCAC 58.132 37.500 0.00 0.00 35.16 3.06
259 260 0.035152 CCGTTTTGTACCCTACCCCC 60.035 60.000 0.00 0.00 0.00 5.40
269 270 0.468771 CCCTACCCCCGACTCGTATT 60.469 60.000 0.00 0.00 0.00 1.89
272 273 2.958355 CCTACCCCCGACTCGTATTTAA 59.042 50.000 0.00 0.00 0.00 1.52
275 276 1.758862 CCCCCGACTCGTATTTAACCT 59.241 52.381 0.00 0.00 0.00 3.50
276 277 2.223900 CCCCCGACTCGTATTTAACCTC 60.224 54.545 0.00 0.00 0.00 3.85
277 278 2.692041 CCCCGACTCGTATTTAACCTCT 59.308 50.000 0.00 0.00 0.00 3.69
278 279 3.885297 CCCCGACTCGTATTTAACCTCTA 59.115 47.826 0.00 0.00 0.00 2.43
279 280 4.522022 CCCCGACTCGTATTTAACCTCTAT 59.478 45.833 0.00 0.00 0.00 1.98
280 281 5.335504 CCCCGACTCGTATTTAACCTCTATC 60.336 48.000 0.00 0.00 0.00 2.08
281 282 5.240183 CCCGACTCGTATTTAACCTCTATCA 59.760 44.000 0.00 0.00 0.00 2.15
282 283 6.238842 CCCGACTCGTATTTAACCTCTATCAA 60.239 42.308 0.00 0.00 0.00 2.57
283 284 6.636044 CCGACTCGTATTTAACCTCTATCAAC 59.364 42.308 0.00 0.00 0.00 3.18
284 285 7.191551 CGACTCGTATTTAACCTCTATCAACA 58.808 38.462 0.00 0.00 0.00 3.33
285 286 7.861372 CGACTCGTATTTAACCTCTATCAACAT 59.139 37.037 0.00 0.00 0.00 2.71
286 287 9.530633 GACTCGTATTTAACCTCTATCAACATT 57.469 33.333 0.00 0.00 0.00 2.71
287 288 9.886132 ACTCGTATTTAACCTCTATCAACATTT 57.114 29.630 0.00 0.00 0.00 2.32
290 291 9.221775 CGTATTTAACCTCTATCAACATTTTGC 57.778 33.333 0.00 0.00 32.17 3.68
293 294 5.551760 AACCTCTATCAACATTTTGCTCG 57.448 39.130 0.00 0.00 32.17 5.03
294 295 3.375299 ACCTCTATCAACATTTTGCTCGC 59.625 43.478 0.00 0.00 32.17 5.03
295 296 3.624861 CCTCTATCAACATTTTGCTCGCT 59.375 43.478 0.00 0.00 32.17 4.93
296 297 4.095483 CCTCTATCAACATTTTGCTCGCTT 59.905 41.667 0.00 0.00 32.17 4.68
297 298 5.221891 TCTATCAACATTTTGCTCGCTTC 57.778 39.130 0.00 0.00 32.17 3.86
298 299 3.921119 ATCAACATTTTGCTCGCTTCA 57.079 38.095 0.00 0.00 32.17 3.02
299 300 3.272439 TCAACATTTTGCTCGCTTCAG 57.728 42.857 0.00 0.00 32.17 3.02
300 301 2.618241 TCAACATTTTGCTCGCTTCAGT 59.382 40.909 0.00 0.00 32.17 3.41
301 302 2.693797 ACATTTTGCTCGCTTCAGTG 57.306 45.000 0.00 0.00 0.00 3.66
302 303 1.949525 ACATTTTGCTCGCTTCAGTGT 59.050 42.857 0.00 0.00 0.00 3.55
303 304 2.358898 ACATTTTGCTCGCTTCAGTGTT 59.641 40.909 0.00 0.00 0.00 3.32
304 305 3.181487 ACATTTTGCTCGCTTCAGTGTTT 60.181 39.130 0.00 0.00 0.00 2.83
305 306 4.036262 ACATTTTGCTCGCTTCAGTGTTTA 59.964 37.500 0.00 0.00 0.00 2.01
306 307 4.829064 TTTTGCTCGCTTCAGTGTTTAT 57.171 36.364 0.00 0.00 0.00 1.40
307 308 5.933187 TTTTGCTCGCTTCAGTGTTTATA 57.067 34.783 0.00 0.00 0.00 0.98
308 309 5.530519 TTTGCTCGCTTCAGTGTTTATAG 57.469 39.130 0.00 0.00 0.00 1.31
309 310 4.188247 TGCTCGCTTCAGTGTTTATAGT 57.812 40.909 0.00 0.00 0.00 2.12
310 311 4.174009 TGCTCGCTTCAGTGTTTATAGTC 58.826 43.478 0.00 0.00 0.00 2.59
311 312 3.240861 GCTCGCTTCAGTGTTTATAGTCG 59.759 47.826 0.00 0.00 0.00 4.18
312 313 4.413087 CTCGCTTCAGTGTTTATAGTCGT 58.587 43.478 0.00 0.00 0.00 4.34
313 314 4.409570 TCGCTTCAGTGTTTATAGTCGTC 58.590 43.478 0.00 0.00 0.00 4.20
314 315 3.237660 CGCTTCAGTGTTTATAGTCGTCG 59.762 47.826 0.00 0.00 0.00 5.12
315 316 4.164294 GCTTCAGTGTTTATAGTCGTCGT 58.836 43.478 0.00 0.00 0.00 4.34
316 317 4.620184 GCTTCAGTGTTTATAGTCGTCGTT 59.380 41.667 0.00 0.00 0.00 3.85
317 318 5.796935 GCTTCAGTGTTTATAGTCGTCGTTA 59.203 40.000 0.00 0.00 0.00 3.18
318 319 6.021626 GCTTCAGTGTTTATAGTCGTCGTTAG 60.022 42.308 0.00 0.00 0.00 2.34
319 320 5.872635 TCAGTGTTTATAGTCGTCGTTAGG 58.127 41.667 0.00 0.00 0.00 2.69
320 321 5.412594 TCAGTGTTTATAGTCGTCGTTAGGT 59.587 40.000 0.00 0.00 0.00 3.08
321 322 5.510674 CAGTGTTTATAGTCGTCGTTAGGTG 59.489 44.000 0.00 0.00 0.00 4.00
322 323 4.795278 GTGTTTATAGTCGTCGTTAGGTGG 59.205 45.833 0.00 0.00 0.00 4.61
323 324 4.458989 TGTTTATAGTCGTCGTTAGGTGGT 59.541 41.667 0.00 0.00 0.00 4.16
324 325 4.882671 TTATAGTCGTCGTTAGGTGGTC 57.117 45.455 0.00 0.00 0.00 4.02
325 326 2.479566 TAGTCGTCGTTAGGTGGTCT 57.520 50.000 0.00 0.00 0.00 3.85
326 327 2.479566 AGTCGTCGTTAGGTGGTCTA 57.520 50.000 0.00 0.00 0.00 2.59
327 328 2.079925 AGTCGTCGTTAGGTGGTCTAC 58.920 52.381 0.00 0.00 0.00 2.59
328 329 1.078709 TCGTCGTTAGGTGGTCTACG 58.921 55.000 0.00 0.00 0.00 3.51
329 330 0.097674 CGTCGTTAGGTGGTCTACGG 59.902 60.000 0.00 0.00 0.00 4.02
330 331 1.453155 GTCGTTAGGTGGTCTACGGA 58.547 55.000 0.00 0.00 0.00 4.69
331 332 2.019984 GTCGTTAGGTGGTCTACGGAT 58.980 52.381 0.00 0.00 0.00 4.18
332 333 2.424956 GTCGTTAGGTGGTCTACGGATT 59.575 50.000 0.00 0.00 0.00 3.01
333 334 3.091545 TCGTTAGGTGGTCTACGGATTT 58.908 45.455 0.00 0.00 0.00 2.17
334 335 3.119388 TCGTTAGGTGGTCTACGGATTTG 60.119 47.826 0.00 0.00 0.00 2.32
335 336 3.528532 GTTAGGTGGTCTACGGATTTGG 58.471 50.000 0.00 0.00 0.00 3.28
336 337 1.946984 AGGTGGTCTACGGATTTGGA 58.053 50.000 0.00 0.00 0.00 3.53
337 338 2.478292 AGGTGGTCTACGGATTTGGAT 58.522 47.619 0.00 0.00 0.00 3.41
338 339 2.170607 AGGTGGTCTACGGATTTGGATG 59.829 50.000 0.00 0.00 0.00 3.51
339 340 1.940613 GTGGTCTACGGATTTGGATGC 59.059 52.381 0.00 0.00 0.00 3.91
340 341 1.557371 TGGTCTACGGATTTGGATGCA 59.443 47.619 0.00 0.00 0.00 3.96
341 342 2.026729 TGGTCTACGGATTTGGATGCAA 60.027 45.455 0.00 0.00 0.00 4.08
342 343 3.214328 GGTCTACGGATTTGGATGCAAT 58.786 45.455 0.00 0.00 0.00 3.56
343 344 3.632145 GGTCTACGGATTTGGATGCAATT 59.368 43.478 0.00 0.00 0.00 2.32
344 345 4.097892 GGTCTACGGATTTGGATGCAATTT 59.902 41.667 0.00 0.00 0.00 1.82
345 346 5.394115 GGTCTACGGATTTGGATGCAATTTT 60.394 40.000 0.00 0.00 0.00 1.82
346 347 6.099341 GTCTACGGATTTGGATGCAATTTTT 58.901 36.000 0.00 0.00 0.00 1.94
379 380 9.701098 TTTTAGTGTTCGTTGTACTATCAATCT 57.299 29.630 0.00 0.00 0.00 2.40
381 382 9.778993 TTAGTGTTCGTTGTACTATCAATCTAC 57.221 33.333 0.00 0.00 0.00 2.59
382 383 7.256286 AGTGTTCGTTGTACTATCAATCTACC 58.744 38.462 0.00 0.00 0.00 3.18
383 384 7.031372 GTGTTCGTTGTACTATCAATCTACCA 58.969 38.462 0.00 0.00 0.00 3.25
384 385 7.705325 GTGTTCGTTGTACTATCAATCTACCAT 59.295 37.037 0.00 0.00 0.00 3.55
385 386 7.704899 TGTTCGTTGTACTATCAATCTACCATG 59.295 37.037 0.00 0.00 0.00 3.66
386 387 7.576861 TCGTTGTACTATCAATCTACCATGA 57.423 36.000 0.00 0.00 0.00 3.07
387 388 8.178313 TCGTTGTACTATCAATCTACCATGAT 57.822 34.615 0.00 0.00 39.50 2.45
388 389 8.638873 TCGTTGTACTATCAATCTACCATGATT 58.361 33.333 0.00 0.00 37.46 2.57
482 483 0.179084 CGTGCCATCTTCCGTGGTAT 60.179 55.000 0.00 0.00 39.01 2.73
483 484 1.067974 CGTGCCATCTTCCGTGGTATA 59.932 52.381 0.00 0.00 39.01 1.47
528 546 0.677731 TACCTCACTCACCCGTACCG 60.678 60.000 0.00 0.00 0.00 4.02
568 591 0.852777 CTCAACCACACGAGAACACG 59.147 55.000 0.00 0.00 39.31 4.49
571 594 0.742505 AACCACACGAGAACACGAGA 59.257 50.000 0.00 0.00 37.03 4.04
580 637 0.317603 AGAACACGAGAACACGTCCG 60.318 55.000 0.00 0.00 44.76 4.79
620 677 3.775654 ACGAGCCAGCCTAGCACC 61.776 66.667 0.00 0.00 0.00 5.01
621 678 3.774528 CGAGCCAGCCTAGCACCA 61.775 66.667 0.00 0.00 0.00 4.17
622 679 2.188994 GAGCCAGCCTAGCACCAG 59.811 66.667 0.00 0.00 0.00 4.00
623 680 4.106925 AGCCAGCCTAGCACCAGC 62.107 66.667 0.00 0.00 42.56 4.85
624 681 4.415150 GCCAGCCTAGCACCAGCA 62.415 66.667 0.00 0.00 45.49 4.41
625 682 2.437359 CCAGCCTAGCACCAGCAC 60.437 66.667 0.00 0.00 45.49 4.40
648 705 2.433436 CACCGGGTTTTCCTTCCTAAG 58.567 52.381 6.32 0.00 40.46 2.18
672 729 2.476051 GACGCAGCACCGTTGATG 59.524 61.111 0.00 0.00 42.24 3.07
673 730 2.027073 GACGCAGCACCGTTGATGA 61.027 57.895 1.11 0.00 42.05 2.92
674 731 1.361668 GACGCAGCACCGTTGATGAT 61.362 55.000 1.11 0.00 42.05 2.45
675 732 1.061411 CGCAGCACCGTTGATGATG 59.939 57.895 1.11 0.00 42.05 3.07
741 799 3.917760 GGGGACGGAGGCATCGAG 61.918 72.222 6.51 0.00 0.00 4.04
742 800 2.833582 GGGACGGAGGCATCGAGA 60.834 66.667 6.51 0.00 0.00 4.04
743 801 2.413765 GGACGGAGGCATCGAGAC 59.586 66.667 6.51 0.00 0.00 3.36
744 802 2.122167 GGACGGAGGCATCGAGACT 61.122 63.158 6.51 0.00 39.48 3.24
751 809 1.679139 AGGCATCGAGACTCTCTCTG 58.321 55.000 4.52 3.08 41.26 3.35
752 810 0.030638 GGCATCGAGACTCTCTCTGC 59.969 60.000 16.07 16.07 41.32 4.26
753 811 0.737804 GCATCGAGACTCTCTCTGCA 59.262 55.000 18.10 0.00 41.53 4.41
825 883 3.986006 TCGATACGCCCGATGCCC 61.986 66.667 0.00 0.00 36.24 5.36
880 938 1.749258 GGCCCCGCTAACTTCCTTG 60.749 63.158 0.00 0.00 0.00 3.61
1009 1072 1.383803 GTCTCCCTCATGGCCTCCT 60.384 63.158 3.32 0.00 0.00 3.69
1612 1675 4.230603 GGTAGGGTTTAAGCGCCC 57.769 61.111 2.29 0.00 45.16 6.13
1671 1734 2.111878 CCTGCCGTGGATGGGATC 59.888 66.667 0.00 0.00 0.00 3.36
1730 1793 4.017092 GGTCGAAACGTCCGTGTT 57.983 55.556 9.58 0.00 0.00 3.32
1731 1794 2.300533 GGTCGAAACGTCCGTGTTT 58.699 52.632 9.58 0.00 44.36 2.83
1732 1795 0.652071 GGTCGAAACGTCCGTGTTTT 59.348 50.000 9.58 0.00 41.89 2.43
1733 1796 1.062440 GGTCGAAACGTCCGTGTTTTT 59.938 47.619 9.58 0.00 41.89 1.94
1771 1834 0.248784 GATCTGGCACCGTACCGTAC 60.249 60.000 0.00 0.00 0.00 3.67
1772 1835 1.669999 ATCTGGCACCGTACCGTACC 61.670 60.000 3.04 0.00 0.00 3.34
1773 1836 3.688475 CTGGCACCGTACCGTACCG 62.688 68.421 3.04 0.00 0.00 4.02
1774 1837 3.747976 GGCACCGTACCGTACCGT 61.748 66.667 3.04 0.19 0.00 4.83
1775 1838 2.403378 GGCACCGTACCGTACCGTA 61.403 63.158 3.04 0.00 0.00 4.02
1803 1866 2.221906 TTTCGCGCTCCCTGTCCTAC 62.222 60.000 5.56 0.00 0.00 3.18
1815 1878 0.387929 TGTCCTACGCCAATCGATCC 59.612 55.000 0.00 0.00 41.67 3.36
1818 1881 2.022129 CTACGCCAATCGATCCGGC 61.022 63.158 22.81 22.81 41.67 6.13
1850 1917 9.702494 CTACCGCATTCATCATGATACATATAT 57.298 33.333 8.15 0.00 34.31 0.86
1863 1930 5.422012 TGATACATATATCCGCATGTGACCT 59.578 40.000 8.11 0.00 37.04 3.85
1893 1960 2.093921 TGCTCGTTGGATCGGATGTTTA 60.094 45.455 0.00 0.00 0.00 2.01
1903 1970 4.214332 GGATCGGATGTTTAGGAATTCTGC 59.786 45.833 5.23 0.00 0.00 4.26
1932 1999 3.446873 TGTTCACTGGATTTTGTTGTGCT 59.553 39.130 0.00 0.00 0.00 4.40
1942 2009 6.096987 TGGATTTTGTTGTGCTTGTAACCTTA 59.903 34.615 0.00 0.00 0.00 2.69
1982 2049 0.940126 GCCATGATCGTGCTTACAGG 59.060 55.000 9.58 0.00 0.00 4.00
2120 2187 3.888424 TGCTTCATGGTAGCATGCT 57.112 47.368 26.47 25.99 43.30 3.79
2121 2188 1.385528 TGCTTCATGGTAGCATGCTG 58.614 50.000 30.42 21.08 43.30 4.41
2122 2189 0.030369 GCTTCATGGTAGCATGCTGC 59.970 55.000 30.42 28.01 45.46 5.25
2219 2286 2.682856 GGTTGCTTCACACTCAACTTGA 59.317 45.455 0.00 0.00 39.79 3.02
2238 2305 4.146745 TGAATGCATGATGTGTAGCTCT 57.853 40.909 0.00 0.00 0.00 4.09
2281 2348 0.947244 CCGCCTTTAAGCTATGCAGG 59.053 55.000 0.00 0.00 0.00 4.85
2328 2396 4.244862 CATGGGGTTGTTGATTAAACTGC 58.755 43.478 0.00 0.00 39.70 4.40
2344 2412 2.300433 ACTGCTGCTGTGTTCAATGAA 58.700 42.857 11.54 0.00 0.00 2.57
2345 2413 2.689471 ACTGCTGCTGTGTTCAATGAAA 59.311 40.909 11.54 0.00 0.00 2.69
2346 2414 3.130869 ACTGCTGCTGTGTTCAATGAAAA 59.869 39.130 11.54 0.00 0.00 2.29
2373 2441 9.581099 AAAAAGTGTAGTTAATTCAGGTTGTTG 57.419 29.630 0.00 0.00 0.00 3.33
2374 2442 7.875327 AAGTGTAGTTAATTCAGGTTGTTGT 57.125 32.000 0.00 0.00 0.00 3.32
2375 2443 7.259290 AGTGTAGTTAATTCAGGTTGTTGTG 57.741 36.000 0.00 0.00 0.00 3.33
2376 2444 6.826741 AGTGTAGTTAATTCAGGTTGTTGTGT 59.173 34.615 0.00 0.00 0.00 3.72
2379 2447 9.175312 TGTAGTTAATTCAGGTTGTTGTGTTTA 57.825 29.630 0.00 0.00 0.00 2.01
2680 2770 5.191722 TCTGGTTTGCTATTCCCTAGTTCAT 59.808 40.000 0.00 0.00 0.00 2.57
2709 2799 6.431198 TTTCCCTTACTTACGAAATCATGC 57.569 37.500 0.00 0.00 0.00 4.06
2747 2837 0.684535 TCAATGCCAACTCGGTCTCA 59.315 50.000 0.00 0.00 36.97 3.27
2792 2882 1.757699 GTATCCTTCCGTCTTCAGCCT 59.242 52.381 0.00 0.00 0.00 4.58
2796 2886 1.543429 CCTTCCGTCTTCAGCCTGTTT 60.543 52.381 0.00 0.00 0.00 2.83
2832 2922 2.188837 TCGCTGTGCTGTAAGTATCG 57.811 50.000 0.00 0.00 35.30 2.92
2942 3047 2.699846 TGCAGGCAACATCCTTTCTTTT 59.300 40.909 0.00 0.00 41.41 2.27
3102 3207 6.349300 TGTCTCTTGCTCTCTTACAAAAGTT 58.651 36.000 0.00 0.00 34.13 2.66
3128 3233 4.209538 TGGAGATAATTCCAGCAATGGTG 58.790 43.478 5.31 5.31 42.24 4.17
3141 3246 2.493035 CAATGGTGGTTCCTTTTTGGC 58.507 47.619 0.00 0.00 37.07 4.52
3284 3390 8.851541 AAATTACCATGCAATGTTTCTGAAAT 57.148 26.923 6.06 0.00 44.81 2.17
3589 3695 7.711846 TGTTAAGTTTGTAACAGTGCATCATT 58.288 30.769 0.00 0.00 38.70 2.57
3598 3704 8.334263 TGTAACAGTGCATCATTCATCTAAAA 57.666 30.769 0.00 0.00 0.00 1.52
3599 3705 8.791675 TGTAACAGTGCATCATTCATCTAAAAA 58.208 29.630 0.00 0.00 0.00 1.94
3606 3712 6.044682 GCATCATTCATCTAAAAACCCCTTG 58.955 40.000 0.00 0.00 0.00 3.61
3667 3783 8.442384 AGCAACAACAAATAGTTTCTGTTTTTG 58.558 29.630 8.11 8.11 40.86 2.44
3711 3833 9.307623 GACTCACTAGTAAGTTGGAACCCAAGT 62.308 44.444 0.00 0.00 41.51 3.16
3740 3862 6.073003 GGAATGTGTAGGTCTGTTCTCTTTTG 60.073 42.308 0.00 0.00 0.00 2.44
3777 3903 1.197721 CTGCGAGAACCATGTTGTTCC 59.802 52.381 10.21 3.48 44.55 3.62
3792 3918 7.042523 CCATGTTGTTCCACTTTCTTCATTTTC 60.043 37.037 0.00 0.00 0.00 2.29
3797 3923 5.627499 TCCACTTTCTTCATTTTCATCCG 57.373 39.130 0.00 0.00 0.00 4.18
3806 3932 0.463833 ATTTTCATCCGTCGGAGCCC 60.464 55.000 20.50 0.00 34.05 5.19
3872 3998 3.713858 TCAACACTCTTTTGTGCATGG 57.286 42.857 0.00 0.00 41.30 3.66
3891 4017 5.105997 GCATGGAAATAAGCACTCTGAAAGT 60.106 40.000 0.00 0.00 39.44 2.66
3915 4041 6.634436 GTGTAGTTTTCAGTTTGAGATTGCAG 59.366 38.462 0.00 0.00 0.00 4.41
3928 4054 4.402793 TGAGATTGCAGAGGTCCTAACTAC 59.597 45.833 0.00 0.00 0.00 2.73
3992 4118 1.983224 CCTCGAGGAGGCTTTTGGA 59.017 57.895 28.21 0.00 43.29 3.53
4040 4166 2.767536 CATCGCAACGGTGGAAGAT 58.232 52.632 0.90 0.00 34.00 2.40
4055 4181 0.323725 AAGATGCCGCCAACCTCATT 60.324 50.000 0.00 0.00 0.00 2.57
4113 4239 1.247567 AATGTGCTACCCACTGCAAC 58.752 50.000 0.00 0.00 44.92 4.17
4306 4432 3.126514 GTCTGAACATGATGTGCTGGAAG 59.873 47.826 10.13 0.00 0.00 3.46
4317 4443 2.565834 TGTGCTGGAAGTAACTACTCCC 59.434 50.000 0.00 0.00 34.99 4.30
4444 4576 3.005684 AGAATTTCAGCATTTTGACCGCA 59.994 39.130 0.00 0.00 0.00 5.69
4459 4599 4.368315 TGACCGCAGCAAGTACTATTATG 58.632 43.478 0.00 0.00 0.00 1.90
4461 4601 4.119862 ACCGCAGCAAGTACTATTATGTG 58.880 43.478 0.00 0.01 0.00 3.21
4464 4604 4.025730 CGCAGCAAGTACTATTATGTGTGG 60.026 45.833 0.00 0.00 0.00 4.17
4470 4610 5.932619 AGTACTATTATGTGTGGTGCTCA 57.067 39.130 0.00 0.00 0.00 4.26
4471 4611 5.907207 AGTACTATTATGTGTGGTGCTCAG 58.093 41.667 0.00 0.00 0.00 3.35
4491 4631 4.488879 CAGGCAAACTTTCCTGCTATTTC 58.511 43.478 0.00 0.00 42.79 2.17
4497 4637 6.806739 GCAAACTTTCCTGCTATTTCGTATTT 59.193 34.615 0.00 0.00 35.62 1.40
4502 4642 9.391006 ACTTTCCTGCTATTTCGTATTTCAATA 57.609 29.630 0.00 0.00 0.00 1.90
4505 4645 9.554395 TTCCTGCTATTTCGTATTTCAATATGA 57.446 29.630 0.00 0.00 35.64 2.15
4506 4646 9.554395 TCCTGCTATTTCGTATTTCAATATGAA 57.446 29.630 9.30 9.30 42.24 2.57
4539 4679 9.924650 ACGAAGTAAAATGATGAGTACTACTTT 57.075 29.630 0.00 0.00 41.94 2.66
4579 4719 7.956328 AATTCTGTATGTAGTCTGTAGTCCA 57.044 36.000 0.00 0.00 0.00 4.02
4585 4725 8.584063 TGTATGTAGTCTGTAGTCCACATTAA 57.416 34.615 0.00 0.00 36.29 1.40
4586 4726 9.027202 TGTATGTAGTCTGTAGTCCACATTAAA 57.973 33.333 0.00 0.00 36.29 1.52
4589 4729 8.997621 TGTAGTCTGTAGTCCACATTAAAATC 57.002 34.615 0.00 0.00 36.29 2.17
4590 4730 8.812972 TGTAGTCTGTAGTCCACATTAAAATCT 58.187 33.333 0.00 0.00 36.29 2.40
4592 4732 8.140112 AGTCTGTAGTCCACATTAAAATCTCT 57.860 34.615 0.00 0.00 36.29 3.10
4593 4733 9.256228 AGTCTGTAGTCCACATTAAAATCTCTA 57.744 33.333 0.00 0.00 36.29 2.43
4601 4741 9.832445 GTCCACATTAAAATCTCTAATAGGACA 57.168 33.333 14.92 0.00 39.71 4.02
4610 4750 9.454859 AAAATCTCTAATAGGACAAAGGACTTG 57.545 33.333 0.00 0.00 41.19 3.16
4622 4762 6.796705 ACAAAGGACTTGTATTTAGGAACG 57.203 37.500 0.00 0.00 46.75 3.95
4623 4763 5.704053 ACAAAGGACTTGTATTTAGGAACGG 59.296 40.000 0.00 0.00 46.75 4.44
4624 4764 5.750352 AAGGACTTGTATTTAGGAACGGA 57.250 39.130 0.00 0.00 0.00 4.69
4625 4765 5.340439 AGGACTTGTATTTAGGAACGGAG 57.660 43.478 0.00 0.00 0.00 4.63
4626 4766 4.161754 AGGACTTGTATTTAGGAACGGAGG 59.838 45.833 0.00 0.00 0.00 4.30
4627 4767 4.161001 GGACTTGTATTTAGGAACGGAGGA 59.839 45.833 0.00 0.00 0.00 3.71
4641 4790 2.289565 CGGAGGAGGGTATTTGCTTTC 58.710 52.381 0.00 0.00 0.00 2.62
4648 4797 4.007659 GAGGGTATTTGCTTTCGGAAAGA 58.992 43.478 29.49 12.71 41.02 2.52
4654 4803 4.404507 TTTGCTTTCGGAAAGATTCTCG 57.595 40.909 29.49 6.92 41.02 4.04
4659 4808 1.182667 TCGGAAAGATTCTCGCCTCA 58.817 50.000 4.00 0.00 0.00 3.86
4663 4812 2.933260 GGAAAGATTCTCGCCTCAGTTC 59.067 50.000 0.00 0.00 0.00 3.01
4668 4817 1.919240 TTCTCGCCTCAGTTCCACTA 58.081 50.000 0.00 0.00 0.00 2.74
4691 4840 5.012893 AGAACCAGGAGGCTAAGAAATTTG 58.987 41.667 0.00 0.00 39.06 2.32
4694 4844 6.327386 ACCAGGAGGCTAAGAAATTTGATA 57.673 37.500 0.00 0.00 39.06 2.15
4741 4891 6.037720 TGCATTTGGTTACCGTATGAATGTAG 59.962 38.462 16.35 0.00 0.00 2.74
4777 4927 4.737054 TCGAACCTAATCTCGTGGTTAAC 58.263 43.478 0.00 0.00 43.28 2.01
4812 4962 3.706594 ACAGTCATCGACTCATTATGGGT 59.293 43.478 0.00 0.00 41.37 4.51
4879 5029 1.916181 AGCAGCCTGGTTAGTGGTTAT 59.084 47.619 0.00 0.00 0.00 1.89
4882 5032 3.118371 GCAGCCTGGTTAGTGGTTATACT 60.118 47.826 0.00 0.00 34.71 2.12
4935 5085 9.630098 TGAGTGGTAGTAGTTTTAAATTCTACG 57.370 33.333 17.48 0.00 38.99 3.51
4936 5086 9.631452 GAGTGGTAGTAGTTTTAAATTCTACGT 57.369 33.333 17.48 0.00 38.99 3.57
4970 5124 3.303857 CGGCATCGTTCTAGGTAGTACAG 60.304 52.174 2.06 0.00 0.00 2.74
4971 5125 3.004524 GGCATCGTTCTAGGTAGTACAGG 59.995 52.174 2.06 0.00 0.00 4.00
5071 5245 2.123640 GCGTCCCTAGCCTCTCCT 60.124 66.667 0.00 0.00 0.00 3.69
5075 5249 0.178973 GTCCCTAGCCTCTCCTCTCC 60.179 65.000 0.00 0.00 0.00 3.71
5076 5250 0.329039 TCCCTAGCCTCTCCTCTCCT 60.329 60.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 3.308402 CCACACTATGAATGGTTCTGGGT 60.308 47.826 0.00 0.00 0.00 4.51
71 72 2.972505 CACTTCGGCGCCTGTTGT 60.973 61.111 26.68 14.73 0.00 3.32
121 122 0.392461 GCGGGATGCCACTTAGTCAA 60.392 55.000 3.39 0.00 37.76 3.18
165 166 9.988350 CAAAATGTTCATACGAGCTAGTAAATT 57.012 29.630 10.89 4.22 0.00 1.82
169 170 6.338146 AGCAAAATGTTCATACGAGCTAGTA 58.662 36.000 9.24 9.24 0.00 1.82
170 171 5.178797 AGCAAAATGTTCATACGAGCTAGT 58.821 37.500 4.47 4.47 0.00 2.57
171 172 5.291858 TGAGCAAAATGTTCATACGAGCTAG 59.708 40.000 0.00 0.00 32.63 3.42
176 177 5.163764 GGTGATGAGCAAAATGTTCATACGA 60.164 40.000 9.26 0.00 46.08 3.43
198 199 6.610075 ATTCAATGTTGATTTTAGCCAGGT 57.390 33.333 0.00 0.00 37.00 4.00
199 200 7.910441 AAATTCAATGTTGATTTTAGCCAGG 57.090 32.000 11.70 0.00 38.34 4.45
259 260 7.191551 TGTTGATAGAGGTTAAATACGAGTCG 58.808 38.462 11.85 11.85 0.00 4.18
269 270 6.403200 GCGAGCAAAATGTTGATAGAGGTTAA 60.403 38.462 0.00 0.00 36.83 2.01
272 273 3.375299 GCGAGCAAAATGTTGATAGAGGT 59.625 43.478 0.00 0.00 36.83 3.85
275 276 4.694982 TGAAGCGAGCAAAATGTTGATAGA 59.305 37.500 0.00 0.00 36.83 1.98
276 277 4.973396 TGAAGCGAGCAAAATGTTGATAG 58.027 39.130 0.00 0.00 36.83 2.08
277 278 4.455533 ACTGAAGCGAGCAAAATGTTGATA 59.544 37.500 0.00 0.00 36.83 2.15
278 279 3.254166 ACTGAAGCGAGCAAAATGTTGAT 59.746 39.130 0.00 0.00 36.83 2.57
279 280 2.618241 ACTGAAGCGAGCAAAATGTTGA 59.382 40.909 0.00 0.00 36.83 3.18
280 281 2.722629 CACTGAAGCGAGCAAAATGTTG 59.277 45.455 0.00 0.00 37.83 3.33
281 282 2.358898 ACACTGAAGCGAGCAAAATGTT 59.641 40.909 0.00 0.00 0.00 2.71
282 283 1.949525 ACACTGAAGCGAGCAAAATGT 59.050 42.857 0.00 0.00 0.00 2.71
283 284 2.693797 ACACTGAAGCGAGCAAAATG 57.306 45.000 0.00 0.00 0.00 2.32
284 285 3.715628 AAACACTGAAGCGAGCAAAAT 57.284 38.095 0.00 0.00 0.00 1.82
285 286 4.829064 ATAAACACTGAAGCGAGCAAAA 57.171 36.364 0.00 0.00 0.00 2.44
286 287 4.994852 ACTATAAACACTGAAGCGAGCAAA 59.005 37.500 0.00 0.00 0.00 3.68
287 288 4.566004 ACTATAAACACTGAAGCGAGCAA 58.434 39.130 0.00 0.00 0.00 3.91
288 289 4.174009 GACTATAAACACTGAAGCGAGCA 58.826 43.478 0.00 0.00 0.00 4.26
289 290 3.240861 CGACTATAAACACTGAAGCGAGC 59.759 47.826 0.00 0.00 0.00 5.03
290 291 4.413087 ACGACTATAAACACTGAAGCGAG 58.587 43.478 0.00 0.00 0.00 5.03
291 292 4.409570 GACGACTATAAACACTGAAGCGA 58.590 43.478 0.00 0.00 0.00 4.93
292 293 3.237660 CGACGACTATAAACACTGAAGCG 59.762 47.826 0.00 0.00 0.00 4.68
293 294 4.164294 ACGACGACTATAAACACTGAAGC 58.836 43.478 0.00 0.00 0.00 3.86
294 295 6.468319 CCTAACGACGACTATAAACACTGAAG 59.532 42.308 0.00 0.00 0.00 3.02
295 296 6.072508 ACCTAACGACGACTATAAACACTGAA 60.073 38.462 0.00 0.00 0.00 3.02
296 297 5.412594 ACCTAACGACGACTATAAACACTGA 59.587 40.000 0.00 0.00 0.00 3.41
297 298 5.510674 CACCTAACGACGACTATAAACACTG 59.489 44.000 0.00 0.00 0.00 3.66
298 299 5.392380 CCACCTAACGACGACTATAAACACT 60.392 44.000 0.00 0.00 0.00 3.55
299 300 4.795278 CCACCTAACGACGACTATAAACAC 59.205 45.833 0.00 0.00 0.00 3.32
300 301 4.458989 ACCACCTAACGACGACTATAAACA 59.541 41.667 0.00 0.00 0.00 2.83
301 302 4.986622 ACCACCTAACGACGACTATAAAC 58.013 43.478 0.00 0.00 0.00 2.01
302 303 4.943705 AGACCACCTAACGACGACTATAAA 59.056 41.667 0.00 0.00 0.00 1.40
303 304 4.517285 AGACCACCTAACGACGACTATAA 58.483 43.478 0.00 0.00 0.00 0.98
304 305 4.142609 AGACCACCTAACGACGACTATA 57.857 45.455 0.00 0.00 0.00 1.31
305 306 2.996631 AGACCACCTAACGACGACTAT 58.003 47.619 0.00 0.00 0.00 2.12
306 307 2.479566 AGACCACCTAACGACGACTA 57.520 50.000 0.00 0.00 0.00 2.59
307 308 2.079925 GTAGACCACCTAACGACGACT 58.920 52.381 0.00 0.00 0.00 4.18
308 309 1.201965 CGTAGACCACCTAACGACGAC 60.202 57.143 0.00 0.00 35.43 4.34
309 310 1.078709 CGTAGACCACCTAACGACGA 58.921 55.000 0.00 0.00 35.43 4.20
310 311 0.097674 CCGTAGACCACCTAACGACG 59.902 60.000 0.00 0.00 33.84 5.12
311 312 1.453155 TCCGTAGACCACCTAACGAC 58.547 55.000 0.00 0.00 0.00 4.34
312 313 2.425143 ATCCGTAGACCACCTAACGA 57.575 50.000 0.00 0.00 0.00 3.85
313 314 3.184541 CAAATCCGTAGACCACCTAACG 58.815 50.000 0.00 0.00 0.00 3.18
314 315 3.196254 TCCAAATCCGTAGACCACCTAAC 59.804 47.826 0.00 0.00 0.00 2.34
315 316 3.443052 TCCAAATCCGTAGACCACCTAA 58.557 45.455 0.00 0.00 0.00 2.69
316 317 3.104519 TCCAAATCCGTAGACCACCTA 57.895 47.619 0.00 0.00 0.00 3.08
317 318 1.946984 TCCAAATCCGTAGACCACCT 58.053 50.000 0.00 0.00 0.00 4.00
318 319 2.561569 CATCCAAATCCGTAGACCACC 58.438 52.381 0.00 0.00 0.00 4.61
319 320 1.940613 GCATCCAAATCCGTAGACCAC 59.059 52.381 0.00 0.00 0.00 4.16
320 321 1.557371 TGCATCCAAATCCGTAGACCA 59.443 47.619 0.00 0.00 0.00 4.02
321 322 2.325583 TGCATCCAAATCCGTAGACC 57.674 50.000 0.00 0.00 0.00 3.85
322 323 4.900635 AATTGCATCCAAATCCGTAGAC 57.099 40.909 0.00 0.00 34.05 2.59
323 324 5.913137 AAAATTGCATCCAAATCCGTAGA 57.087 34.783 0.00 0.00 34.05 2.59
353 354 9.701098 AGATTGATAGTACAACGAACACTAAAA 57.299 29.630 0.00 0.00 32.50 1.52
355 356 9.778993 GTAGATTGATAGTACAACGAACACTAA 57.221 33.333 0.00 0.00 32.50 2.24
356 357 8.400947 GGTAGATTGATAGTACAACGAACACTA 58.599 37.037 0.00 0.00 32.50 2.74
357 358 7.094075 TGGTAGATTGATAGTACAACGAACACT 60.094 37.037 0.00 0.00 32.50 3.55
358 359 7.031372 TGGTAGATTGATAGTACAACGAACAC 58.969 38.462 0.00 0.00 32.50 3.32
359 360 7.160547 TGGTAGATTGATAGTACAACGAACA 57.839 36.000 0.00 0.00 32.50 3.18
360 361 7.919091 TCATGGTAGATTGATAGTACAACGAAC 59.081 37.037 0.00 0.00 32.50 3.95
361 362 8.002984 TCATGGTAGATTGATAGTACAACGAA 57.997 34.615 0.00 0.00 32.50 3.85
362 363 7.576861 TCATGGTAGATTGATAGTACAACGA 57.423 36.000 0.00 0.00 32.50 3.85
363 364 8.818141 AATCATGGTAGATTGATAGTACAACG 57.182 34.615 0.00 0.00 36.88 4.10
437 438 8.312669 ACCAGCTCTCAATAACTAAGAATACT 57.687 34.615 0.00 0.00 0.00 2.12
442 443 4.705507 ACGACCAGCTCTCAATAACTAAGA 59.294 41.667 0.00 0.00 0.00 2.10
482 483 0.524862 GTTGGAGAGCGAGGAACGTA 59.475 55.000 0.00 0.00 44.60 3.57
483 484 1.289380 GTTGGAGAGCGAGGAACGT 59.711 57.895 0.00 0.00 44.60 3.99
568 591 1.161563 TTTTGGCCGGACGTGTTCTC 61.162 55.000 5.05 0.00 0.00 2.87
571 594 1.313812 TGTTTTTGGCCGGACGTGTT 61.314 50.000 5.05 0.00 0.00 3.32
621 678 4.887190 AAAACCCGGTGGCGTGCT 62.887 61.111 0.00 0.00 33.59 4.40
622 679 4.337060 GAAAACCCGGTGGCGTGC 62.337 66.667 0.00 0.00 33.59 5.34
623 680 3.666253 GGAAAACCCGGTGGCGTG 61.666 66.667 0.00 0.00 33.59 5.34
624 681 3.424780 AAGGAAAACCCGGTGGCGT 62.425 57.895 0.00 0.00 40.87 5.68
625 682 2.596338 AAGGAAAACCCGGTGGCG 60.596 61.111 0.00 0.00 40.87 5.69
634 691 5.557703 CGTCGTTTGTCTTAGGAAGGAAAAC 60.558 44.000 7.22 7.22 34.10 2.43
637 694 3.645884 CGTCGTTTGTCTTAGGAAGGAA 58.354 45.455 0.00 0.00 0.00 3.36
648 705 2.248431 GGTGCTGCGTCGTTTGTC 59.752 61.111 0.00 0.00 0.00 3.18
672 729 1.302832 CCCGGCTGGCCTATTCATC 60.303 63.158 5.85 0.00 0.00 2.92
673 730 2.839098 CCCGGCTGGCCTATTCAT 59.161 61.111 5.85 0.00 0.00 2.57
747 805 1.269673 CCCATGACGATCTCTGCAGAG 60.270 57.143 33.73 33.73 43.36 3.35
748 806 0.749049 CCCATGACGATCTCTGCAGA 59.251 55.000 17.19 17.19 0.00 4.26
749 807 0.879400 GCCCATGACGATCTCTGCAG 60.879 60.000 7.63 7.63 0.00 4.41
750 808 1.144716 GCCCATGACGATCTCTGCA 59.855 57.895 0.00 0.00 0.00 4.41
751 809 1.596477 GGCCCATGACGATCTCTGC 60.596 63.158 0.00 0.00 0.00 4.26
752 810 1.300465 CGGCCCATGACGATCTCTG 60.300 63.158 0.00 0.00 0.00 3.35
753 811 2.502492 CCGGCCCATGACGATCTCT 61.502 63.158 0.00 0.00 0.00 3.10
880 938 4.778143 AGGGTTGGATGCGCGTCC 62.778 66.667 36.66 36.66 38.81 4.79
1595 1658 1.816679 CGGGCGCTTAAACCCTACC 60.817 63.158 7.64 0.00 44.63 3.18
1596 1659 1.816679 CCGGGCGCTTAAACCCTAC 60.817 63.158 7.64 0.00 44.63 3.18
1597 1660 2.585698 CCGGGCGCTTAAACCCTA 59.414 61.111 7.64 0.00 44.63 3.53
1610 1673 4.760047 CTCAGGAACACCGCCGGG 62.760 72.222 8.57 0.00 40.11 5.73
1611 1674 2.521958 AATCTCAGGAACACCGCCGG 62.522 60.000 0.00 0.00 0.00 6.13
1612 1675 0.174845 TAATCTCAGGAACACCGCCG 59.825 55.000 0.00 0.00 0.00 6.46
1613 1676 1.473434 CCTAATCTCAGGAACACCGCC 60.473 57.143 0.00 0.00 38.00 6.13
1614 1677 1.207329 ACCTAATCTCAGGAACACCGC 59.793 52.381 0.00 0.00 39.18 5.68
1615 1678 2.893637 CACCTAATCTCAGGAACACCG 58.106 52.381 0.00 0.00 39.18 4.94
1616 1679 2.633488 GCACCTAATCTCAGGAACACC 58.367 52.381 0.00 0.00 39.18 4.16
1617 1680 2.271800 CGCACCTAATCTCAGGAACAC 58.728 52.381 0.00 0.00 39.18 3.32
1618 1681 1.207089 CCGCACCTAATCTCAGGAACA 59.793 52.381 0.00 0.00 39.18 3.18
1619 1682 1.480954 TCCGCACCTAATCTCAGGAAC 59.519 52.381 0.00 0.00 39.18 3.62
1620 1683 1.860641 TCCGCACCTAATCTCAGGAA 58.139 50.000 0.00 0.00 39.18 3.36
1621 1684 1.964223 GATCCGCACCTAATCTCAGGA 59.036 52.381 0.00 0.00 39.18 3.86
1622 1685 1.001406 GGATCCGCACCTAATCTCAGG 59.999 57.143 0.00 0.00 41.87 3.86
1623 1686 1.336332 CGGATCCGCACCTAATCTCAG 60.336 57.143 23.37 0.00 0.00 3.35
1624 1687 0.673985 CGGATCCGCACCTAATCTCA 59.326 55.000 23.37 0.00 0.00 3.27
1664 1727 2.451294 GGCCTCCAGGGATCCCAT 60.451 66.667 32.69 14.92 38.92 4.00
1671 1734 2.770048 CACCTAGGGCCTCCAGGG 60.770 72.222 23.34 17.20 36.37 4.45
1672 1735 3.483869 GCACCTAGGGCCTCCAGG 61.484 72.222 19.04 19.04 37.36 4.45
1771 1834 0.921347 CGCGAAATTCAGTCCTACGG 59.079 55.000 0.00 0.00 0.00 4.02
1772 1835 0.297820 GCGCGAAATTCAGTCCTACG 59.702 55.000 12.10 0.00 0.00 3.51
1773 1836 1.588861 GAGCGCGAAATTCAGTCCTAC 59.411 52.381 12.10 0.00 0.00 3.18
1774 1837 1.470979 GGAGCGCGAAATTCAGTCCTA 60.471 52.381 12.10 0.00 0.00 2.94
1775 1838 0.741221 GGAGCGCGAAATTCAGTCCT 60.741 55.000 12.10 0.00 0.00 3.85
1778 1841 1.021390 CAGGGAGCGCGAAATTCAGT 61.021 55.000 12.10 0.00 0.00 3.41
1783 1846 1.327690 TAGGACAGGGAGCGCGAAAT 61.328 55.000 12.10 0.00 0.00 2.17
1850 1917 2.011548 GCACATAAGGTCACATGCGGA 61.012 52.381 0.00 0.00 0.00 5.54
1863 1930 0.319986 TCCAACGAGCACGCACATAA 60.320 50.000 2.62 0.00 43.96 1.90
1893 1960 0.392998 ACAATCCGCGCAGAATTCCT 60.393 50.000 8.75 0.00 0.00 3.36
1903 1970 1.086696 AATCCAGTGAACAATCCGCG 58.913 50.000 0.00 0.00 0.00 6.46
1942 2009 7.172868 TGGCATCACATCACATAAAGAAAAT 57.827 32.000 0.00 0.00 0.00 1.82
2122 2189 1.826385 CCTTTAGTGGGCAGTCCTTG 58.174 55.000 0.00 0.00 36.20 3.61
2219 2286 4.127907 CTCAGAGCTACACATCATGCATT 58.872 43.478 0.00 0.00 0.00 3.56
2281 2348 8.883731 TGCTTTACTATAGAATGTTTCTTCTGC 58.116 33.333 6.78 0.00 41.14 4.26
2374 2442 6.484977 TGTGAAGCATGTATGTGTCTTAAACA 59.515 34.615 0.00 0.00 34.78 2.83
2375 2443 6.898041 TGTGAAGCATGTATGTGTCTTAAAC 58.102 36.000 0.00 0.00 0.00 2.01
2376 2444 6.348458 GCTGTGAAGCATGTATGTGTCTTAAA 60.348 38.462 0.00 0.00 34.41 1.52
2379 2447 3.438087 GCTGTGAAGCATGTATGTGTCTT 59.562 43.478 0.00 0.00 34.41 3.01
2605 2695 8.925161 TTGCATAAAATTATCAACTAGGTTGC 57.075 30.769 5.63 0.00 42.55 4.17
2689 2779 4.209288 CGAGCATGATTTCGTAAGTAAGGG 59.791 45.833 0.00 0.00 39.48 3.95
2709 2799 1.261619 GATTGCCTGTAAATCGCCGAG 59.738 52.381 0.00 0.00 0.00 4.63
2747 2837 3.328931 TGTCTTTCCTTGGAGCAGAGAAT 59.671 43.478 2.07 0.00 0.00 2.40
2832 2922 4.156008 ACGATTGCAATACCAGAAAAGGAC 59.844 41.667 12.97 0.00 0.00 3.85
2911 3016 5.475909 AGGATGTTGCCTGCATATATGAAAG 59.524 40.000 17.10 11.97 36.76 2.62
2923 3028 4.589216 TCAAAAGAAAGGATGTTGCCTG 57.411 40.909 0.00 0.00 38.58 4.85
3102 3207 7.014518 CACCATTGCTGGAATTATCTCCAAATA 59.985 37.037 0.00 0.00 44.97 1.40
3128 3233 1.934849 GCACGATGCCAAAAAGGAACC 60.935 52.381 0.00 0.00 41.22 3.62
3132 3237 2.083167 AATGCACGATGCCAAAAAGG 57.917 45.000 7.38 0.00 44.23 3.11
3284 3390 4.974933 AGCCCTATGATGGATAGTAGGA 57.025 45.455 0.00 0.00 36.62 2.94
3589 3695 5.163034 TGTCCTTCAAGGGGTTTTTAGATGA 60.163 40.000 2.75 0.00 35.59 2.92
3598 3704 2.608623 CCAAATGTCCTTCAAGGGGTT 58.391 47.619 2.75 0.00 35.59 4.11
3599 3705 1.827245 GCCAAATGTCCTTCAAGGGGT 60.827 52.381 2.75 0.00 35.59 4.95
3606 3712 4.762251 AGAAACTACTGCCAAATGTCCTTC 59.238 41.667 0.00 0.00 0.00 3.46
3667 3783 7.035542 GTGAGTCGTAGTCACAAAATACTTC 57.964 40.000 14.22 0.00 45.49 3.01
3711 3833 2.902608 ACAGACCTACACATTCCCAGA 58.097 47.619 0.00 0.00 0.00 3.86
3740 3862 1.269257 GCAGACACTGGAACTTTTGCC 60.269 52.381 0.00 0.00 31.21 4.52
3777 3903 5.082059 CGACGGATGAAAATGAAGAAAGTG 58.918 41.667 0.00 0.00 0.00 3.16
3792 3918 0.676782 AAAAAGGGCTCCGACGGATG 60.677 55.000 18.71 12.59 0.00 3.51
3806 3932 4.045636 ACAAAGTACTGCTGCCAAAAAG 57.954 40.909 0.00 0.00 0.00 2.27
3886 4012 9.226345 CAATCTCAAACTGAAAACTACACTTTC 57.774 33.333 0.00 0.00 34.09 2.62
3891 4017 6.542005 TCTGCAATCTCAAACTGAAAACTACA 59.458 34.615 0.00 0.00 0.00 2.74
3892 4018 6.959361 TCTGCAATCTCAAACTGAAAACTAC 58.041 36.000 0.00 0.00 0.00 2.73
3915 4041 6.424207 CACAAAGTTTCAGTAGTTAGGACCTC 59.576 42.308 0.00 0.00 0.00 3.85
3928 4054 2.684881 ACAGAGCCACACAAAGTTTCAG 59.315 45.455 0.00 0.00 0.00 3.02
3989 4115 0.904865 ACTCCTCCACGCTGATTCCA 60.905 55.000 0.00 0.00 0.00 3.53
3992 4118 0.965866 TCGACTCCTCCACGCTGATT 60.966 55.000 0.00 0.00 0.00 2.57
4040 4166 1.971167 GTCAATGAGGTTGGCGGCA 60.971 57.895 7.97 7.97 38.39 5.69
4055 4181 1.473258 AGTTTGCAACAAGGCTGTCA 58.527 45.000 0.00 0.00 33.45 3.58
4113 4239 2.110967 CCATCTCCAGCAGCAACGG 61.111 63.158 0.00 0.00 0.00 4.44
4397 4529 5.060077 CACATCGCAAAGCATAAACTGAAAG 59.940 40.000 0.00 0.00 42.29 2.62
4444 4576 4.876107 GCACCACACATAATAGTACTTGCT 59.124 41.667 0.00 0.00 0.00 3.91
4470 4610 3.191371 CGAAATAGCAGGAAAGTTTGCCT 59.809 43.478 3.17 2.46 41.17 4.75
4471 4611 3.057526 ACGAAATAGCAGGAAAGTTTGCC 60.058 43.478 3.17 0.11 41.17 4.52
4481 4621 9.599322 GTTCATATTGAAATACGAAATAGCAGG 57.401 33.333 0.00 0.00 38.22 4.85
4503 4643 9.863845 TCATCATTTTACTTCGTACATAGTTCA 57.136 29.630 2.58 0.00 0.00 3.18
4505 4645 9.871238 ACTCATCATTTTACTTCGTACATAGTT 57.129 29.630 2.58 0.00 0.00 2.24
4510 4650 9.778993 GTAGTACTCATCATTTTACTTCGTACA 57.221 33.333 0.00 0.00 0.00 2.90
4553 4693 9.642343 TGGACTACAGACTACATACAGAATTAT 57.358 33.333 0.00 0.00 0.00 1.28
4554 4694 8.900781 GTGGACTACAGACTACATACAGAATTA 58.099 37.037 0.00 0.00 0.00 1.40
4556 4696 6.890268 TGTGGACTACAGACTACATACAGAAT 59.110 38.462 0.00 0.00 33.42 2.40
4558 4698 5.812286 TGTGGACTACAGACTACATACAGA 58.188 41.667 0.00 0.00 33.42 3.41
4559 4699 6.701145 ATGTGGACTACAGACTACATACAG 57.299 41.667 8.46 0.00 43.80 2.74
4561 4701 9.865321 TTTTAATGTGGACTACAGACTACATAC 57.135 33.333 10.11 0.00 43.80 2.39
4564 4704 8.812972 AGATTTTAATGTGGACTACAGACTACA 58.187 33.333 0.00 1.04 43.80 2.74
4565 4705 9.303537 GAGATTTTAATGTGGACTACAGACTAC 57.696 37.037 0.00 0.00 43.80 2.73
4566 4706 9.256228 AGAGATTTTAATGTGGACTACAGACTA 57.744 33.333 0.00 0.00 43.80 2.59
4567 4707 8.140112 AGAGATTTTAATGTGGACTACAGACT 57.860 34.615 0.00 0.00 43.80 3.24
4575 4715 9.832445 TGTCCTATTAGAGATTTTAATGTGGAC 57.168 33.333 16.32 16.32 40.69 4.02
4600 4740 5.935789 TCCGTTCCTAAATACAAGTCCTTTG 59.064 40.000 0.00 0.00 42.68 2.77
4601 4741 6.117975 TCCGTTCCTAAATACAAGTCCTTT 57.882 37.500 0.00 0.00 0.00 3.11
4602 4742 5.338137 CCTCCGTTCCTAAATACAAGTCCTT 60.338 44.000 0.00 0.00 0.00 3.36
4603 4743 4.161754 CCTCCGTTCCTAAATACAAGTCCT 59.838 45.833 0.00 0.00 0.00 3.85
4604 4744 4.161001 TCCTCCGTTCCTAAATACAAGTCC 59.839 45.833 0.00 0.00 0.00 3.85
4605 4745 5.334724 TCCTCCGTTCCTAAATACAAGTC 57.665 43.478 0.00 0.00 0.00 3.01
4606 4746 4.161754 CCTCCTCCGTTCCTAAATACAAGT 59.838 45.833 0.00 0.00 0.00 3.16
4607 4747 4.443034 CCCTCCTCCGTTCCTAAATACAAG 60.443 50.000 0.00 0.00 0.00 3.16
4608 4748 3.453353 CCCTCCTCCGTTCCTAAATACAA 59.547 47.826 0.00 0.00 0.00 2.41
4609 4749 3.036091 CCCTCCTCCGTTCCTAAATACA 58.964 50.000 0.00 0.00 0.00 2.29
4610 4750 3.036819 ACCCTCCTCCGTTCCTAAATAC 58.963 50.000 0.00 0.00 0.00 1.89
4611 4751 3.409804 ACCCTCCTCCGTTCCTAAATA 57.590 47.619 0.00 0.00 0.00 1.40
4612 4752 2.265526 ACCCTCCTCCGTTCCTAAAT 57.734 50.000 0.00 0.00 0.00 1.40
4613 4753 2.925966 TACCCTCCTCCGTTCCTAAA 57.074 50.000 0.00 0.00 0.00 1.85
4614 4754 3.409804 AATACCCTCCTCCGTTCCTAA 57.590 47.619 0.00 0.00 0.00 2.69
4615 4755 3.036091 CAAATACCCTCCTCCGTTCCTA 58.964 50.000 0.00 0.00 0.00 2.94
4616 4756 1.838077 CAAATACCCTCCTCCGTTCCT 59.162 52.381 0.00 0.00 0.00 3.36
4617 4757 1.746171 GCAAATACCCTCCTCCGTTCC 60.746 57.143 0.00 0.00 0.00 3.62
4618 4758 1.209747 AGCAAATACCCTCCTCCGTTC 59.790 52.381 0.00 0.00 0.00 3.95
4619 4759 1.286248 AGCAAATACCCTCCTCCGTT 58.714 50.000 0.00 0.00 0.00 4.44
4620 4760 1.286248 AAGCAAATACCCTCCTCCGT 58.714 50.000 0.00 0.00 0.00 4.69
4621 4761 2.289565 GAAAGCAAATACCCTCCTCCG 58.710 52.381 0.00 0.00 0.00 4.63
4622 4762 2.289565 CGAAAGCAAATACCCTCCTCC 58.710 52.381 0.00 0.00 0.00 4.30
4623 4763 2.093128 TCCGAAAGCAAATACCCTCCTC 60.093 50.000 0.00 0.00 0.00 3.71
4624 4764 1.913419 TCCGAAAGCAAATACCCTCCT 59.087 47.619 0.00 0.00 0.00 3.69
4625 4765 2.413310 TCCGAAAGCAAATACCCTCC 57.587 50.000 0.00 0.00 0.00 4.30
4626 4766 4.007659 TCTTTCCGAAAGCAAATACCCTC 58.992 43.478 14.99 0.00 38.39 4.30
4627 4767 4.028993 TCTTTCCGAAAGCAAATACCCT 57.971 40.909 14.99 0.00 38.39 4.34
4641 4790 1.134965 ACTGAGGCGAGAATCTTTCCG 60.135 52.381 0.00 0.00 0.00 4.30
4648 4797 3.842869 GTGGAACTGAGGCGAGAAT 57.157 52.632 0.00 0.00 0.00 2.40
4663 4812 2.160721 TAGCCTCCTGGTTCTAGTGG 57.839 55.000 0.00 0.00 35.27 4.00
4668 4817 4.936685 AATTTCTTAGCCTCCTGGTTCT 57.063 40.909 0.00 0.00 35.27 3.01
4675 4824 8.348507 CACAGAATATCAAATTTCTTAGCCTCC 58.651 37.037 0.00 0.00 29.85 4.30
4691 4840 8.554528 CACTGGAACATCATAACACAGAATATC 58.445 37.037 0.00 0.00 38.20 1.63
4694 4844 5.124457 GCACTGGAACATCATAACACAGAAT 59.876 40.000 0.00 0.00 38.20 2.40
4713 4863 3.687212 TCATACGGTAACCAAATGCACTG 59.313 43.478 0.00 0.00 0.00 3.66
4741 4891 2.171079 TTCGAATGCGCGTCCATCC 61.171 57.895 8.43 0.00 37.46 3.51
4934 5084 1.623081 ATGCCGCACAAACGAGTACG 61.623 55.000 0.00 0.00 45.75 3.67
4935 5085 0.094730 GATGCCGCACAAACGAGTAC 59.905 55.000 0.00 0.00 34.06 2.73
4936 5086 1.348538 CGATGCCGCACAAACGAGTA 61.349 55.000 0.00 0.00 35.24 2.59
4937 5087 2.667318 CGATGCCGCACAAACGAGT 61.667 57.895 0.00 0.00 35.24 4.18
4940 5090 1.792057 GAACGATGCCGCACAAACG 60.792 57.895 0.00 2.42 39.95 3.60
4946 5096 0.384309 CTACCTAGAACGATGCCGCA 59.616 55.000 0.00 0.00 39.95 5.69
4970 5124 0.248289 TTTCTTCATCGGGTCGGACC 59.752 55.000 19.06 19.06 37.60 4.46
4971 5125 2.000447 CTTTTCTTCATCGGGTCGGAC 59.000 52.381 0.00 0.00 0.00 4.79
5057 5231 0.329039 AGGAGAGGAGAGGCTAGGGA 60.329 60.000 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.