Multiple sequence alignment - TraesCS2A01G179500

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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 TraesCS2A01G179500 chr2A 100.000 2438 0 0 1 2438 138135089 138132652 0.000000e+00 4503
1 TraesCS2A01G179500 chr2A 92.727 275 16 3 1 275 530244444 530244714 6.320000e-106 394
2 TraesCS2A01G179500 chr2A 90.385 260 24 1 3 262 57971435 57971693 8.350000e-90 340
3 TraesCS2A01G179500 chr1A 98.206 1059 19 0 1380 2438 103711898 103710840 0.000000e+00 1851
4 TraesCS2A01G179500 chr1A 98.017 1059 20 1 1380 2438 573174495 573175552 0.000000e+00 1838
5 TraesCS2A01G179500 chr1A 97.923 1059 21 1 1380 2438 403418353 403417296 0.000000e+00 1832
6 TraesCS2A01G179500 chr1A 97.832 1061 23 0 1378 2438 562797946 562796886 0.000000e+00 1832
7 TraesCS2A01G179500 chr1A 88.446 251 28 1 6 255 291671313 291671063 3.940000e-78 302
8 TraesCS2A01G179500 chr6A 98.111 1059 20 0 1380 2438 471898833 471897775 0.000000e+00 1845
9 TraesCS2A01G179500 chr6A 97.926 1061 21 1 1379 2438 472389668 472388608 0.000000e+00 1836
10 TraesCS2A01G179500 chr6A 97.923 1059 21 1 1380 2438 472382662 472381605 0.000000e+00 1832
11 TraesCS2A01G179500 chr4A 98.017 1059 21 0 1380 2438 521839025 521840083 0.000000e+00 1840
12 TraesCS2A01G179500 chr5A 97.923 1059 22 0 1380 2438 598026565 598027623 0.000000e+00 1834
13 TraesCS2A01G179500 chr2D 88.462 624 46 5 760 1381 131382855 131382256 0.000000e+00 730
14 TraesCS2A01G179500 chr2D 94.834 271 14 0 477 747 131383290 131383020 8.060000e-115 424
15 TraesCS2A01G179500 chr3A 95.367 259 11 1 4 262 80493494 80493237 6.270000e-111 411
16 TraesCS2A01G179500 chr3A 89.734 263 27 0 3 265 6677725 6677987 1.080000e-88 337
17 TraesCS2A01G179500 chrUn 91.418 268 20 3 6 273 101224992 101224728 4.950000e-97 364
18 TraesCS2A01G179500 chr6D 91.506 259 21 1 3 261 291664531 291664788 2.980000e-94 355
19 TraesCS2A01G179500 chr7B 85.603 257 34 2 9 262 197702749 197703005 1.440000e-67 267
20 TraesCS2A01G179500 chr1B 83.942 274 39 5 9 278 606364455 606364183 8.650000e-65 257


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 TraesCS2A01G179500 chr2A 138132652 138135089 2437 True 4503 4503 100.000 1 2438 1 chr2A.!!$R1 2437
1 TraesCS2A01G179500 chr1A 103710840 103711898 1058 True 1851 1851 98.206 1380 2438 1 chr1A.!!$R1 1058
2 TraesCS2A01G179500 chr1A 573174495 573175552 1057 False 1838 1838 98.017 1380 2438 1 chr1A.!!$F1 1058
3 TraesCS2A01G179500 chr1A 403417296 403418353 1057 True 1832 1832 97.923 1380 2438 1 chr1A.!!$R3 1058
4 TraesCS2A01G179500 chr1A 562796886 562797946 1060 True 1832 1832 97.832 1378 2438 1 chr1A.!!$R4 1060
5 TraesCS2A01G179500 chr6A 471897775 471898833 1058 True 1845 1845 98.111 1380 2438 1 chr6A.!!$R1 1058
6 TraesCS2A01G179500 chr6A 472388608 472389668 1060 True 1836 1836 97.926 1379 2438 1 chr6A.!!$R3 1059
7 TraesCS2A01G179500 chr6A 472381605 472382662 1057 True 1832 1832 97.923 1380 2438 1 chr6A.!!$R2 1058
8 TraesCS2A01G179500 chr4A 521839025 521840083 1058 False 1840 1840 98.017 1380 2438 1 chr4A.!!$F1 1058
9 TraesCS2A01G179500 chr5A 598026565 598027623 1058 False 1834 1834 97.923 1380 2438 1 chr5A.!!$F1 1058
10 TraesCS2A01G179500 chr2D 131382256 131383290 1034 True 577 730 91.648 477 1381 2 chr2D.!!$R1 904

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
962 1116 0.028505 CGAAGATGCCTGAATTGCCG 59.971 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2021 2175 0.174845 TTGCCCGAGATTCGATCGTT 59.825 50.0 15.94 3.86 43.74 3.85 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
21 22 4.989279 AAGACTCTTTGCAAGAAAAGCA 57.011 36.364 0.00 0.00 40.85 3.91
22 23 5.526506 AAGACTCTTTGCAAGAAAAGCAT 57.473 34.783 0.00 0.00 42.33 3.79
23 24 5.118642 AGACTCTTTGCAAGAAAAGCATC 57.881 39.130 0.00 0.00 42.33 3.91
24 25 4.826183 AGACTCTTTGCAAGAAAAGCATCT 59.174 37.500 0.00 0.00 42.33 2.90
25 26 4.868067 ACTCTTTGCAAGAAAAGCATCTG 58.132 39.130 0.00 0.00 42.33 2.90
26 27 4.340381 ACTCTTTGCAAGAAAAGCATCTGT 59.660 37.500 0.00 0.00 42.33 3.41
27 28 5.163478 ACTCTTTGCAAGAAAAGCATCTGTT 60.163 36.000 0.00 0.00 42.33 3.16
28 29 5.284079 TCTTTGCAAGAAAAGCATCTGTTC 58.716 37.500 0.00 0.00 42.33 3.18
29 30 3.272439 TGCAAGAAAAGCATCTGTTCG 57.728 42.857 0.00 0.00 37.02 3.95
30 31 2.877786 TGCAAGAAAAGCATCTGTTCGA 59.122 40.909 0.00 0.00 37.02 3.71
31 32 3.314913 TGCAAGAAAAGCATCTGTTCGAA 59.685 39.130 0.00 0.00 37.02 3.71
32 33 4.202000 TGCAAGAAAAGCATCTGTTCGAAA 60.202 37.500 0.00 0.00 37.02 3.46
33 34 4.739716 GCAAGAAAAGCATCTGTTCGAAAA 59.260 37.500 0.00 0.00 33.28 2.29
34 35 5.231991 GCAAGAAAAGCATCTGTTCGAAAAA 59.768 36.000 0.00 0.00 33.28 1.94
35 36 6.074142 GCAAGAAAAGCATCTGTTCGAAAAAT 60.074 34.615 0.00 0.00 33.28 1.82
36 37 6.998258 AGAAAAGCATCTGTTCGAAAAATG 57.002 33.333 0.00 5.40 33.28 2.32
37 38 6.738114 AGAAAAGCATCTGTTCGAAAAATGA 58.262 32.000 15.86 6.51 33.28 2.57
38 39 7.373493 AGAAAAGCATCTGTTCGAAAAATGAT 58.627 30.769 15.86 9.31 33.28 2.45
39 40 7.540055 AGAAAAGCATCTGTTCGAAAAATGATC 59.460 33.333 15.86 9.57 33.28 2.92
40 41 6.506500 AAGCATCTGTTCGAAAAATGATCT 57.493 33.333 15.86 5.45 0.00 2.75
41 42 6.506500 AGCATCTGTTCGAAAAATGATCTT 57.493 33.333 15.86 0.00 0.00 2.40
42 43 6.917533 AGCATCTGTTCGAAAAATGATCTTT 58.082 32.000 15.86 0.00 0.00 2.52
43 44 7.373493 AGCATCTGTTCGAAAAATGATCTTTT 58.627 30.769 15.86 0.88 0.00 2.27
44 45 7.869429 AGCATCTGTTCGAAAAATGATCTTTTT 59.131 29.630 12.28 12.28 34.64 1.94
45 46 8.158445 GCATCTGTTCGAAAAATGATCTTTTTC 58.842 33.333 21.11 21.11 42.10 2.29
46 47 9.184062 CATCTGTTCGAAAAATGATCTTTTTCA 57.816 29.630 25.62 16.74 44.37 2.69
47 48 8.786937 TCTGTTCGAAAAATGATCTTTTTCAG 57.213 30.769 25.62 21.78 44.37 3.02
48 49 8.620416 TCTGTTCGAAAAATGATCTTTTTCAGA 58.380 29.630 25.62 22.91 44.37 3.27
49 50 9.236691 CTGTTCGAAAAATGATCTTTTTCAGAA 57.763 29.630 25.62 24.28 44.37 3.02
50 51 9.579768 TGTTCGAAAAATGATCTTTTTCAGAAA 57.420 25.926 25.62 18.76 44.37 2.52
202 203 8.830201 TTGAATATAAAATGGTGCATAATGGC 57.170 30.769 0.00 0.00 0.00 4.40
203 204 7.960262 TGAATATAAAATGGTGCATAATGGCA 58.040 30.769 0.00 0.00 42.53 4.92
209 210 4.557554 TGCATAATGGCACCGGAG 57.442 55.556 9.46 0.00 39.25 4.63
230 231 0.039165 CAGGTTCTGCCCTTTTTCGC 60.039 55.000 0.00 0.00 38.26 4.70
231 232 1.179174 AGGTTCTGCCCTTTTTCGCC 61.179 55.000 0.00 0.00 38.26 5.54
232 233 1.289066 GTTCTGCCCTTTTTCGCCC 59.711 57.895 0.00 0.00 0.00 6.13
233 234 2.265182 TTCTGCCCTTTTTCGCCCG 61.265 57.895 0.00 0.00 0.00 6.13
234 235 3.747976 CTGCCCTTTTTCGCCCGG 61.748 66.667 0.00 0.00 0.00 5.73
235 236 4.589675 TGCCCTTTTTCGCCCGGT 62.590 61.111 0.00 0.00 0.00 5.28
236 237 4.050934 GCCCTTTTTCGCCCGGTG 62.051 66.667 0.00 0.00 0.00 4.94
237 238 4.050934 CCCTTTTTCGCCCGGTGC 62.051 66.667 0.00 2.24 0.00 5.01
238 239 3.291383 CCTTTTTCGCCCGGTGCA 61.291 61.111 14.17 0.00 41.33 4.57
239 240 2.725008 CTTTTTCGCCCGGTGCAA 59.275 55.556 14.17 5.92 41.33 4.08
240 241 1.660264 CTTTTTCGCCCGGTGCAAC 60.660 57.895 14.17 0.00 41.33 4.17
241 242 3.471244 TTTTTCGCCCGGTGCAACG 62.471 57.895 19.45 19.45 41.33 4.10
254 255 3.659092 CAACGCACGGGCATGTGT 61.659 61.111 11.77 0.00 45.12 3.72
255 256 2.031314 AACGCACGGGCATGTGTA 59.969 55.556 11.77 0.00 42.42 2.90
256 257 2.322081 AACGCACGGGCATGTGTAC 61.322 57.895 11.77 0.00 42.42 2.90
257 258 2.434185 CGCACGGGCATGTGTACT 60.434 61.111 11.77 0.00 41.94 2.73
258 259 1.153726 CGCACGGGCATGTGTACTA 60.154 57.895 11.77 0.00 41.94 1.82
259 260 1.145759 CGCACGGGCATGTGTACTAG 61.146 60.000 11.77 0.00 41.94 2.57
260 261 0.108329 GCACGGGCATGTGTACTAGT 60.108 55.000 3.77 0.00 41.94 2.57
261 262 1.135527 GCACGGGCATGTGTACTAGTA 59.864 52.381 3.77 0.00 41.94 1.82
262 263 2.223971 GCACGGGCATGTGTACTAGTAT 60.224 50.000 3.77 0.00 41.94 2.12
263 264 3.005050 GCACGGGCATGTGTACTAGTATA 59.995 47.826 3.77 0.00 41.94 1.47
264 265 4.321750 GCACGGGCATGTGTACTAGTATAT 60.322 45.833 3.77 0.00 41.94 0.86
265 266 5.106038 GCACGGGCATGTGTACTAGTATATA 60.106 44.000 3.77 1.93 41.94 0.86
266 267 6.405508 GCACGGGCATGTGTACTAGTATATAT 60.406 42.308 3.77 4.46 41.94 0.86
267 268 7.201758 GCACGGGCATGTGTACTAGTATATATA 60.202 40.741 3.77 0.00 41.94 0.86
268 269 8.847196 CACGGGCATGTGTACTAGTATATATAT 58.153 37.037 5.75 0.00 35.12 0.86
292 293 8.958119 ATATAGGTTTACATGACGATTGTTGT 57.042 30.769 0.00 0.00 0.00 3.32
293 294 7.681939 ATAGGTTTACATGACGATTGTTGTT 57.318 32.000 0.00 0.00 0.00 2.83
294 295 6.385649 AGGTTTACATGACGATTGTTGTTT 57.614 33.333 0.00 0.00 0.00 2.83
295 296 7.499321 AGGTTTACATGACGATTGTTGTTTA 57.501 32.000 0.00 0.00 0.00 2.01
296 297 7.581476 AGGTTTACATGACGATTGTTGTTTAG 58.419 34.615 0.00 0.00 0.00 1.85
297 298 7.227910 AGGTTTACATGACGATTGTTGTTTAGT 59.772 33.333 0.00 0.00 0.00 2.24
298 299 7.532884 GGTTTACATGACGATTGTTGTTTAGTC 59.467 37.037 0.00 0.00 0.00 2.59
299 300 7.716768 TTACATGACGATTGTTGTTTAGTCA 57.283 32.000 0.00 0.00 41.85 3.41
300 301 5.985781 ACATGACGATTGTTGTTTAGTCAC 58.014 37.500 0.00 0.00 40.70 3.67
301 302 5.758296 ACATGACGATTGTTGTTTAGTCACT 59.242 36.000 0.00 0.00 40.70 3.41
302 303 5.900339 TGACGATTGTTGTTTAGTCACTC 57.100 39.130 0.00 0.00 34.24 3.51
303 304 5.353111 TGACGATTGTTGTTTAGTCACTCA 58.647 37.500 0.00 0.00 34.24 3.41
304 305 5.813157 TGACGATTGTTGTTTAGTCACTCAA 59.187 36.000 0.00 0.00 34.24 3.02
305 306 6.314152 TGACGATTGTTGTTTAGTCACTCAAA 59.686 34.615 0.00 0.00 34.24 2.69
306 307 7.011950 TGACGATTGTTGTTTAGTCACTCAAAT 59.988 33.333 0.00 0.00 34.24 2.32
307 308 8.373048 ACGATTGTTGTTTAGTCACTCAAATA 57.627 30.769 0.00 0.00 0.00 1.40
308 309 8.999431 ACGATTGTTGTTTAGTCACTCAAATAT 58.001 29.630 0.00 0.00 0.00 1.28
333 334 3.830744 ATATTGTAGCCCGCAGTAACA 57.169 42.857 0.00 0.00 0.00 2.41
334 335 1.734163 ATTGTAGCCCGCAGTAACAC 58.266 50.000 0.00 0.00 0.00 3.32
335 336 0.393448 TTGTAGCCCGCAGTAACACA 59.607 50.000 0.00 0.00 0.00 3.72
336 337 0.320073 TGTAGCCCGCAGTAACACAC 60.320 55.000 0.00 0.00 0.00 3.82
337 338 1.080366 TAGCCCGCAGTAACACACG 60.080 57.895 0.00 0.00 0.00 4.49
338 339 2.495366 TAGCCCGCAGTAACACACGG 62.495 60.000 0.00 0.00 45.21 4.94
341 342 4.329619 CGCAGTAACACACGGACA 57.670 55.556 0.00 0.00 0.00 4.02
342 343 2.822306 CGCAGTAACACACGGACAT 58.178 52.632 0.00 0.00 0.00 3.06
343 344 1.144969 CGCAGTAACACACGGACATT 58.855 50.000 0.00 0.00 0.00 2.71
344 345 1.126113 CGCAGTAACACACGGACATTC 59.874 52.381 0.00 0.00 0.00 2.67
345 346 2.413837 GCAGTAACACACGGACATTCT 58.586 47.619 0.00 0.00 0.00 2.40
346 347 3.581755 GCAGTAACACACGGACATTCTA 58.418 45.455 0.00 0.00 0.00 2.10
347 348 3.991773 GCAGTAACACACGGACATTCTAA 59.008 43.478 0.00 0.00 0.00 2.10
348 349 4.630069 GCAGTAACACACGGACATTCTAAT 59.370 41.667 0.00 0.00 0.00 1.73
349 350 5.121768 GCAGTAACACACGGACATTCTAATT 59.878 40.000 0.00 0.00 0.00 1.40
350 351 6.672357 GCAGTAACACACGGACATTCTAATTC 60.672 42.308 0.00 0.00 0.00 2.17
351 352 6.590292 CAGTAACACACGGACATTCTAATTCT 59.410 38.462 0.00 0.00 0.00 2.40
352 353 7.758076 CAGTAACACACGGACATTCTAATTCTA 59.242 37.037 0.00 0.00 0.00 2.10
353 354 6.963049 AACACACGGACATTCTAATTCTAC 57.037 37.500 0.00 0.00 0.00 2.59
354 355 6.282199 ACACACGGACATTCTAATTCTACT 57.718 37.500 0.00 0.00 0.00 2.57
355 356 7.400599 ACACACGGACATTCTAATTCTACTA 57.599 36.000 0.00 0.00 0.00 1.82
356 357 7.481642 ACACACGGACATTCTAATTCTACTAG 58.518 38.462 0.00 0.00 0.00 2.57
357 358 7.122353 ACACACGGACATTCTAATTCTACTAGT 59.878 37.037 0.00 0.00 0.00 2.57
358 359 7.432545 CACACGGACATTCTAATTCTACTAGTG 59.567 40.741 5.39 0.00 0.00 2.74
359 360 6.418226 CACGGACATTCTAATTCTACTAGTGC 59.582 42.308 5.39 0.00 0.00 4.40
360 361 6.321690 ACGGACATTCTAATTCTACTAGTGCT 59.678 38.462 5.39 0.00 0.00 4.40
361 362 7.147880 ACGGACATTCTAATTCTACTAGTGCTT 60.148 37.037 5.39 0.00 0.00 3.91
362 363 8.350722 CGGACATTCTAATTCTACTAGTGCTTA 58.649 37.037 5.39 0.00 0.00 3.09
363 364 9.685828 GGACATTCTAATTCTACTAGTGCTTAG 57.314 37.037 5.39 7.31 35.39 2.18
378 379 8.792633 ACTAGTGCTTAGTAATTTTGAAATGCA 58.207 29.630 0.00 0.00 40.85 3.96
379 380 9.793252 CTAGTGCTTAGTAATTTTGAAATGCAT 57.207 29.630 0.00 0.00 0.00 3.96
380 381 8.693542 AGTGCTTAGTAATTTTGAAATGCATC 57.306 30.769 0.00 0.00 0.00 3.91
381 382 8.306038 AGTGCTTAGTAATTTTGAAATGCATCA 58.694 29.630 0.00 0.00 0.00 3.07
382 383 8.375465 GTGCTTAGTAATTTTGAAATGCATCAC 58.625 33.333 0.00 0.00 0.00 3.06
383 384 7.545265 TGCTTAGTAATTTTGAAATGCATCACC 59.455 33.333 0.00 0.00 0.00 4.02
384 385 7.545265 GCTTAGTAATTTTGAAATGCATCACCA 59.455 33.333 0.00 0.00 0.00 4.17
385 386 9.421806 CTTAGTAATTTTGAAATGCATCACCAA 57.578 29.630 0.00 1.85 0.00 3.67
386 387 9.770097 TTAGTAATTTTGAAATGCATCACCAAA 57.230 25.926 0.00 8.21 0.00 3.28
387 388 8.086851 AGTAATTTTGAAATGCATCACCAAAC 57.913 30.769 15.93 9.02 0.00 2.93
388 389 5.945466 ATTTTGAAATGCATCACCAAACC 57.055 34.783 15.93 0.00 0.00 3.27
389 390 4.686191 TTTGAAATGCATCACCAAACCT 57.314 36.364 0.00 0.00 0.00 3.50
390 391 3.663995 TGAAATGCATCACCAAACCTG 57.336 42.857 0.00 0.00 0.00 4.00
391 392 2.288948 TGAAATGCATCACCAAACCTGC 60.289 45.455 0.00 0.00 35.21 4.85
392 393 4.595031 TGCATCACCAAACCTGCA 57.405 50.000 0.00 0.00 41.98 4.41
393 394 0.892755 ATGCATCACCAAACCTGCAG 59.107 50.000 6.78 6.78 46.67 4.41
394 395 0.467844 TGCATCACCAAACCTGCAGT 60.468 50.000 13.81 0.00 39.54 4.40
395 396 0.242017 GCATCACCAAACCTGCAGTC 59.758 55.000 13.81 0.00 34.77 3.51
396 397 1.901591 CATCACCAAACCTGCAGTCT 58.098 50.000 13.81 0.00 0.00 3.24
397 398 1.808945 CATCACCAAACCTGCAGTCTC 59.191 52.381 13.81 0.00 0.00 3.36
398 399 0.836606 TCACCAAACCTGCAGTCTCA 59.163 50.000 13.81 0.00 0.00 3.27
399 400 1.421268 TCACCAAACCTGCAGTCTCAT 59.579 47.619 13.81 0.00 0.00 2.90
400 401 2.637382 TCACCAAACCTGCAGTCTCATA 59.363 45.455 13.81 0.00 0.00 2.15
401 402 3.072330 TCACCAAACCTGCAGTCTCATAA 59.928 43.478 13.81 0.00 0.00 1.90
402 403 3.820467 CACCAAACCTGCAGTCTCATAAA 59.180 43.478 13.81 0.00 0.00 1.40
403 404 4.460382 CACCAAACCTGCAGTCTCATAAAT 59.540 41.667 13.81 0.00 0.00 1.40
404 405 5.647658 CACCAAACCTGCAGTCTCATAAATA 59.352 40.000 13.81 0.00 0.00 1.40
405 406 6.319658 CACCAAACCTGCAGTCTCATAAATAT 59.680 38.462 13.81 0.00 0.00 1.28
406 407 7.498900 CACCAAACCTGCAGTCTCATAAATATA 59.501 37.037 13.81 0.00 0.00 0.86
407 408 7.716998 ACCAAACCTGCAGTCTCATAAATATAG 59.283 37.037 13.81 0.00 0.00 1.31
408 409 7.716998 CCAAACCTGCAGTCTCATAAATATAGT 59.283 37.037 13.81 0.00 0.00 2.12
409 410 9.113838 CAAACCTGCAGTCTCATAAATATAGTT 57.886 33.333 13.81 1.21 0.00 2.24
410 411 9.686683 AAACCTGCAGTCTCATAAATATAGTTT 57.313 29.630 13.81 7.46 0.00 2.66
411 412 8.894768 ACCTGCAGTCTCATAAATATAGTTTC 57.105 34.615 13.81 0.00 0.00 2.78
412 413 7.934120 ACCTGCAGTCTCATAAATATAGTTTCC 59.066 37.037 13.81 0.00 0.00 3.13
413 414 7.389053 CCTGCAGTCTCATAAATATAGTTTCCC 59.611 40.741 13.81 0.00 0.00 3.97
414 415 7.801104 TGCAGTCTCATAAATATAGTTTCCCA 58.199 34.615 0.00 0.00 0.00 4.37
415 416 8.271458 TGCAGTCTCATAAATATAGTTTCCCAA 58.729 33.333 0.00 0.00 0.00 4.12
416 417 9.120538 GCAGTCTCATAAATATAGTTTCCCAAA 57.879 33.333 0.00 0.00 0.00 3.28
426 427 3.391506 AGTTTCCCAAAATTGCTCTGC 57.608 42.857 0.00 0.00 0.00 4.26
427 428 2.037641 AGTTTCCCAAAATTGCTCTGCC 59.962 45.455 0.00 0.00 0.00 4.85
428 429 2.014010 TTCCCAAAATTGCTCTGCCT 57.986 45.000 0.00 0.00 0.00 4.75
429 430 1.549203 TCCCAAAATTGCTCTGCCTC 58.451 50.000 0.00 0.00 0.00 4.70
430 431 1.076024 TCCCAAAATTGCTCTGCCTCT 59.924 47.619 0.00 0.00 0.00 3.69
431 432 1.475682 CCCAAAATTGCTCTGCCTCTC 59.524 52.381 0.00 0.00 0.00 3.20
432 433 1.131883 CCAAAATTGCTCTGCCTCTCG 59.868 52.381 0.00 0.00 0.00 4.04
433 434 0.807496 AAAATTGCTCTGCCTCTCGC 59.193 50.000 0.00 0.00 38.31 5.03
434 435 1.028868 AAATTGCTCTGCCTCTCGCC 61.029 55.000 0.00 0.00 36.24 5.54
435 436 1.908340 AATTGCTCTGCCTCTCGCCT 61.908 55.000 0.00 0.00 36.24 5.52
436 437 1.908340 ATTGCTCTGCCTCTCGCCTT 61.908 55.000 0.00 0.00 36.24 4.35
437 438 2.116983 TTGCTCTGCCTCTCGCCTTT 62.117 55.000 0.00 0.00 36.24 3.11
438 439 1.376553 GCTCTGCCTCTCGCCTTTT 60.377 57.895 0.00 0.00 36.24 2.27
439 440 0.957888 GCTCTGCCTCTCGCCTTTTT 60.958 55.000 0.00 0.00 36.24 1.94
440 441 0.801251 CTCTGCCTCTCGCCTTTTTG 59.199 55.000 0.00 0.00 36.24 2.44
441 442 0.108585 TCTGCCTCTCGCCTTTTTGT 59.891 50.000 0.00 0.00 36.24 2.83
442 443 0.954452 CTGCCTCTCGCCTTTTTGTT 59.046 50.000 0.00 0.00 36.24 2.83
443 444 0.667993 TGCCTCTCGCCTTTTTGTTG 59.332 50.000 0.00 0.00 36.24 3.33
444 445 0.951558 GCCTCTCGCCTTTTTGTTGA 59.048 50.000 0.00 0.00 0.00 3.18
445 446 1.336755 GCCTCTCGCCTTTTTGTTGAA 59.663 47.619 0.00 0.00 0.00 2.69
446 447 2.858646 GCCTCTCGCCTTTTTGTTGAAC 60.859 50.000 0.00 0.00 0.00 3.18
447 448 2.357637 CCTCTCGCCTTTTTGTTGAACA 59.642 45.455 0.00 0.00 0.00 3.18
448 449 3.181491 CCTCTCGCCTTTTTGTTGAACAA 60.181 43.478 6.66 6.66 36.11 2.83
449 450 4.499696 CCTCTCGCCTTTTTGTTGAACAAT 60.500 41.667 11.97 0.00 38.00 2.71
450 451 4.606961 TCTCGCCTTTTTGTTGAACAATC 58.393 39.130 11.97 0.00 38.00 2.67
451 452 4.338118 TCTCGCCTTTTTGTTGAACAATCT 59.662 37.500 11.97 0.00 38.00 2.40
452 453 5.004922 TCGCCTTTTTGTTGAACAATCTT 57.995 34.783 11.97 0.00 38.00 2.40
453 454 6.038825 TCTCGCCTTTTTGTTGAACAATCTTA 59.961 34.615 11.97 0.00 38.00 2.10
454 455 6.565234 TCGCCTTTTTGTTGAACAATCTTAA 58.435 32.000 11.97 0.09 38.00 1.85
455 456 7.206687 TCGCCTTTTTGTTGAACAATCTTAAT 58.793 30.769 11.97 0.00 38.00 1.40
456 457 7.381139 TCGCCTTTTTGTTGAACAATCTTAATC 59.619 33.333 11.97 0.00 38.00 1.75
457 458 7.359181 CGCCTTTTTGTTGAACAATCTTAATCC 60.359 37.037 11.97 0.00 38.00 3.01
458 459 7.440856 GCCTTTTTGTTGAACAATCTTAATCCA 59.559 33.333 11.97 0.00 38.00 3.41
459 460 9.492973 CCTTTTTGTTGAACAATCTTAATCCAT 57.507 29.630 11.97 0.00 38.00 3.41
472 473 8.975439 CAATCTTAATCCATATTTTTCAGCTGC 58.025 33.333 9.47 0.00 0.00 5.25
473 474 7.042797 TCTTAATCCATATTTTTCAGCTGCC 57.957 36.000 9.47 0.00 0.00 4.85
474 475 4.677673 AATCCATATTTTTCAGCTGCCC 57.322 40.909 9.47 0.00 0.00 5.36
475 476 3.098774 TCCATATTTTTCAGCTGCCCA 57.901 42.857 9.47 0.00 0.00 5.36
507 508 5.810587 GGACACGTGTATTCATGATACTTGT 59.189 40.000 23.44 4.23 41.05 3.16
513 514 7.169813 ACGTGTATTCATGATACTTGTGCATAG 59.830 37.037 0.00 0.00 41.05 2.23
515 516 9.212641 GTGTATTCATGATACTTGTGCATAGAT 57.787 33.333 0.00 0.00 41.05 1.98
573 574 6.116806 ACTAATTAAACCACACACAGACACA 58.883 36.000 0.00 0.00 0.00 3.72
581 582 0.390340 CACACAGACACAGATCGGGG 60.390 60.000 0.00 0.00 0.00 5.73
582 583 1.219124 CACAGACACAGATCGGGGG 59.781 63.158 0.00 0.00 0.00 5.40
589 590 0.179073 CACAGATCGGGGGATCACAC 60.179 60.000 0.00 0.00 34.19 3.82
591 592 1.076265 AGATCGGGGGATCACACGA 60.076 57.895 26.97 26.97 39.85 4.35
605 606 3.374402 ACGAGGCGACCAGACTGG 61.374 66.667 20.45 20.45 39.26 4.00
648 649 3.485394 TGAGCTGCCACTGACAAAAATA 58.515 40.909 0.00 0.00 0.00 1.40
659 660 6.925165 CCACTGACAAAAATAAACATGAAGCT 59.075 34.615 0.00 0.00 0.00 3.74
676 677 3.391506 AGCTTGATTTCACTTTTGGGC 57.608 42.857 0.00 0.00 0.00 5.36
694 695 5.194473 TGGGCCAGGTGTTATAAATACAA 57.806 39.130 0.00 0.00 0.00 2.41
721 722 6.828273 CCTTCTCATCTCTCGTATGGATATCT 59.172 42.308 2.05 0.00 0.00 1.98
756 757 6.679843 ACTAGCTTAGTTCTAGTTCACACAC 58.320 40.000 0.00 0.00 42.85 3.82
757 758 5.531122 AGCTTAGTTCTAGTTCACACACA 57.469 39.130 0.00 0.00 0.00 3.72
766 919 2.710377 AGTTCACACACACACACACAT 58.290 42.857 0.00 0.00 0.00 3.21
799 952 0.524816 CGCAGACAATTCAGCATGGC 60.525 55.000 0.00 0.00 33.93 4.40
823 977 2.048503 GAAGACCACCGTCCCACG 60.049 66.667 0.00 0.00 40.12 4.94
875 1029 2.515523 ACTGGCATGATCAGCGCC 60.516 61.111 25.23 25.23 46.43 6.53
888 1042 4.799824 GCGCCGCACGGTACCTTA 62.800 66.667 10.90 0.00 43.93 2.69
903 1057 2.426842 CCTTAAAGAGAAGGGGCCAG 57.573 55.000 4.39 0.00 42.12 4.85
929 1083 2.183555 CACCTTCCGCGTCCTACC 59.816 66.667 4.92 0.00 0.00 3.18
931 1085 3.446570 CCTTCCGCGTCCTACCGT 61.447 66.667 4.92 0.00 0.00 4.83
942 1096 2.125512 CTACCGTGCCTGAGGTGC 60.126 66.667 0.00 0.00 41.51 5.01
957 1111 0.749454 GGTGCCGAAGATGCCTGAAT 60.749 55.000 0.00 0.00 0.00 2.57
962 1116 0.028505 CGAAGATGCCTGAATTGCCG 59.971 55.000 0.00 0.00 0.00 5.69
967 1121 0.754217 ATGCCTGAATTGCCGCATCT 60.754 50.000 0.00 0.00 37.38 2.90
975 1129 2.113860 ATTGCCGCATCTAGTTGTGT 57.886 45.000 12.22 0.00 0.00 3.72
976 1130 1.438651 TTGCCGCATCTAGTTGTGTC 58.561 50.000 12.22 1.62 0.00 3.67
977 1131 0.391130 TGCCGCATCTAGTTGTGTCC 60.391 55.000 12.22 4.99 0.00 4.02
986 1140 1.823169 TAGTTGTGTCCGAGGTGCCC 61.823 60.000 0.00 0.00 0.00 5.36
990 1144 3.636231 TGTCCGAGGTGCCCAAGG 61.636 66.667 0.00 0.00 0.00 3.61
997 1151 1.774217 AGGTGCCCAAGGTTCCAGA 60.774 57.895 0.00 0.00 0.00 3.86
1006 1160 0.603065 AAGGTTCCAGAAAATGCCGC 59.397 50.000 0.00 0.00 0.00 6.53
1013 1167 1.305213 AGAAAATGCCGCACCCCAT 60.305 52.632 0.00 0.00 0.00 4.00
1038 1192 0.963856 CAAAGATGCCAGAGCTGCCA 60.964 55.000 0.00 0.00 40.80 4.92
1047 1201 2.269241 GAGCTGCCACACCCTACC 59.731 66.667 0.00 0.00 0.00 3.18
1076 1230 3.510388 GCTACCAAAGCCTGAATTTCC 57.490 47.619 0.00 0.00 46.25 3.13
1077 1231 2.166459 GCTACCAAAGCCTGAATTTCCC 59.834 50.000 0.00 0.00 46.25 3.97
1078 1232 2.397044 ACCAAAGCCTGAATTTCCCA 57.603 45.000 0.00 0.00 0.00 4.37
1079 1233 1.970640 ACCAAAGCCTGAATTTCCCAC 59.029 47.619 0.00 0.00 0.00 4.61
1080 1234 1.969923 CCAAAGCCTGAATTTCCCACA 59.030 47.619 0.00 0.00 0.00 4.17
1081 1235 2.028748 CCAAAGCCTGAATTTCCCACAG 60.029 50.000 0.00 0.00 0.00 3.66
1084 1238 2.183409 CCTGAATTTCCCACAGGCG 58.817 57.895 0.00 0.00 43.32 5.52
1085 1239 0.609131 CCTGAATTTCCCACAGGCGT 60.609 55.000 0.00 0.00 43.32 5.68
1086 1240 0.523072 CTGAATTTCCCACAGGCGTG 59.477 55.000 4.53 4.53 43.21 5.34
1087 1241 1.212751 GAATTTCCCACAGGCGTGC 59.787 57.895 6.26 0.00 42.17 5.34
1088 1242 2.212900 GAATTTCCCACAGGCGTGCC 62.213 60.000 6.26 1.67 42.17 5.01
1089 1243 2.992817 AATTTCCCACAGGCGTGCCA 62.993 55.000 14.29 0.00 42.17 4.92
1129 1283 3.645975 CGTCGCAACCCACCACAC 61.646 66.667 0.00 0.00 0.00 3.82
1130 1284 3.284449 GTCGCAACCCACCACACC 61.284 66.667 0.00 0.00 0.00 4.16
1140 1294 3.484806 ACCACACCGGAGCAACCA 61.485 61.111 9.46 0.00 38.63 3.67
1146 1300 2.597217 CCGGAGCAACCAAAGCCA 60.597 61.111 0.00 0.00 38.90 4.75
1174 1328 2.346803 CACATACCGTTGTTCCTGAGG 58.653 52.381 0.00 0.00 0.00 3.86
1187 1341 1.302033 CTGAGGTGCCAAAGACGCT 60.302 57.895 0.00 0.00 0.00 5.07
1202 1356 2.908073 CGCTTGAAGTGCCACACCC 61.908 63.158 0.00 0.00 34.49 4.61
1213 1367 2.665089 CCACACCCTACCATGCCGA 61.665 63.158 0.00 0.00 0.00 5.54
1242 1396 0.251354 AGATGCTCGAACTGCCACAT 59.749 50.000 0.00 0.00 0.00 3.21
1262 1416 3.281727 TCCAATTGTATCAGAGGTGCC 57.718 47.619 4.43 0.00 0.00 5.01
1286 1440 1.244019 ATGCCCGAAGTGCCAAAGAC 61.244 55.000 0.00 0.00 0.00 3.01
1291 1445 0.588252 CGAAGTGCCAAAGACACCTG 59.412 55.000 0.00 0.00 38.87 4.00
1349 1503 0.326927 CCCGAACTACCACACCCAAT 59.673 55.000 0.00 0.00 0.00 3.16
1350 1504 1.271707 CCCGAACTACCACACCCAATT 60.272 52.381 0.00 0.00 0.00 2.32
1356 1510 2.289819 ACTACCACACCCAATTGTACCG 60.290 50.000 4.43 0.00 0.00 4.02
1375 1529 4.431131 AGGTGCCCAAGATGCCCG 62.431 66.667 0.00 0.00 0.00 6.13
1746 1900 2.975799 GCAACTCCCGTTTGCCGA 60.976 61.111 0.00 0.00 39.56 5.54
1887 2041 3.992260 CGATTGTCGGAGAGGTATCTT 57.008 47.619 0.00 0.00 36.95 2.40
1913 2067 2.477825 CCTCTCGGTAATGCACATCAG 58.522 52.381 0.00 0.00 0.00 2.90
1919 2073 5.069119 TCTCGGTAATGCACATCAGATAAGT 59.931 40.000 0.00 0.00 0.00 2.24
1963 2117 8.939201 AATGAGTTAGTTGTGAGATGATGTAG 57.061 34.615 0.00 0.00 0.00 2.74
1988 2142 3.915536 GGAACGAGTAAAGAGACTTGCT 58.084 45.455 0.00 0.00 34.59 3.91
2106 2260 5.661458 GGTCTGACCGATAAAGATCTTCAA 58.339 41.667 11.71 0.35 0.00 2.69
2372 2527 7.437713 AGCCTATATTTGGATATCGGAATCA 57.562 36.000 5.70 0.00 34.52 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.043750 CGAACAGATGCTTTTCTTGCAAA 58.956 39.130 0.00 0.00 44.01 3.68
8 9 3.314913 TCGAACAGATGCTTTTCTTGCAA 59.685 39.130 0.00 0.00 44.01 4.08
9 10 2.877786 TCGAACAGATGCTTTTCTTGCA 59.122 40.909 0.00 0.00 44.95 4.08
10 11 3.542712 TCGAACAGATGCTTTTCTTGC 57.457 42.857 0.00 0.00 0.00 4.01
11 12 6.810888 TTTTTCGAACAGATGCTTTTCTTG 57.189 33.333 0.00 0.00 0.00 3.02
12 13 7.202526 TCATTTTTCGAACAGATGCTTTTCTT 58.797 30.769 0.00 0.00 0.00 2.52
13 14 6.738114 TCATTTTTCGAACAGATGCTTTTCT 58.262 32.000 0.00 0.00 0.00 2.52
14 15 6.991485 TCATTTTTCGAACAGATGCTTTTC 57.009 33.333 0.00 0.00 0.00 2.29
15 16 7.373493 AGATCATTTTTCGAACAGATGCTTTT 58.627 30.769 0.00 0.00 0.00 2.27
16 17 6.917533 AGATCATTTTTCGAACAGATGCTTT 58.082 32.000 0.00 0.00 0.00 3.51
17 18 6.506500 AGATCATTTTTCGAACAGATGCTT 57.493 33.333 0.00 0.00 0.00 3.91
18 19 6.506500 AAGATCATTTTTCGAACAGATGCT 57.493 33.333 0.00 0.00 0.00 3.79
19 20 7.572502 AAAAGATCATTTTTCGAACAGATGC 57.427 32.000 0.00 0.00 0.00 3.91
20 21 9.184062 TGAAAAAGATCATTTTTCGAACAGATG 57.816 29.630 23.23 2.82 46.06 2.90
21 22 9.403110 CTGAAAAAGATCATTTTTCGAACAGAT 57.597 29.630 23.23 0.00 46.06 2.90
22 23 8.620416 TCTGAAAAAGATCATTTTTCGAACAGA 58.380 29.630 23.23 19.52 46.06 3.41
23 24 8.786937 TCTGAAAAAGATCATTTTTCGAACAG 57.213 30.769 23.23 18.27 46.06 3.16
24 25 9.579768 TTTCTGAAAAAGATCATTTTTCGAACA 57.420 25.926 24.56 19.36 46.06 3.18
176 177 9.439500 GCCATTATGCACCATTTTATATTCAAT 57.561 29.630 0.00 0.00 0.00 2.57
177 178 8.427276 TGCCATTATGCACCATTTTATATTCAA 58.573 29.630 0.00 0.00 36.04 2.69
178 179 7.960262 TGCCATTATGCACCATTTTATATTCA 58.040 30.769 0.00 0.00 36.04 2.57
192 193 1.152984 CCTCCGGTGCCATTATGCA 60.153 57.895 0.00 0.00 39.37 3.96
193 194 2.555547 GCCTCCGGTGCCATTATGC 61.556 63.158 0.00 0.00 0.00 3.14
194 195 1.152984 TGCCTCCGGTGCCATTATG 60.153 57.895 14.59 0.00 0.00 1.90
195 196 1.149174 CTGCCTCCGGTGCCATTAT 59.851 57.895 14.59 0.00 0.00 1.28
196 197 2.589540 CTGCCTCCGGTGCCATTA 59.410 61.111 14.59 0.00 0.00 1.90
197 198 4.431131 CCTGCCTCCGGTGCCATT 62.431 66.667 14.59 0.00 0.00 3.16
201 202 4.021925 AGAACCTGCCTCCGGTGC 62.022 66.667 0.00 6.56 34.33 5.01
202 203 2.046892 CAGAACCTGCCTCCGGTG 60.047 66.667 0.00 0.00 34.33 4.94
211 212 0.039165 GCGAAAAAGGGCAGAACCTG 60.039 55.000 0.00 0.00 40.87 4.00
212 213 1.179174 GGCGAAAAAGGGCAGAACCT 61.179 55.000 0.00 0.00 44.56 3.50
213 214 1.289066 GGCGAAAAAGGGCAGAACC 59.711 57.895 0.00 0.00 37.93 3.62
214 215 1.289066 GGGCGAAAAAGGGCAGAAC 59.711 57.895 0.00 0.00 0.00 3.01
215 216 2.265182 CGGGCGAAAAAGGGCAGAA 61.265 57.895 0.00 0.00 0.00 3.02
216 217 2.671619 CGGGCGAAAAAGGGCAGA 60.672 61.111 0.00 0.00 0.00 4.26
217 218 3.747976 CCGGGCGAAAAAGGGCAG 61.748 66.667 0.00 0.00 0.00 4.85
218 219 4.589675 ACCGGGCGAAAAAGGGCA 62.590 61.111 6.32 0.00 0.00 5.36
219 220 4.050934 CACCGGGCGAAAAAGGGC 62.051 66.667 6.32 0.00 0.00 5.19
220 221 4.050934 GCACCGGGCGAAAAAGGG 62.051 66.667 6.32 0.00 0.00 3.95
237 238 2.321333 TACACATGCCCGTGCGTTG 61.321 57.895 2.69 0.00 40.73 4.10
238 239 2.031314 TACACATGCCCGTGCGTT 59.969 55.556 2.69 0.00 40.73 4.84
239 240 1.879737 TAGTACACATGCCCGTGCGT 61.880 55.000 0.00 0.00 40.73 5.24
240 241 1.145759 CTAGTACACATGCCCGTGCG 61.146 60.000 0.00 0.00 40.73 5.34
241 242 0.108329 ACTAGTACACATGCCCGTGC 60.108 55.000 0.00 0.00 40.73 5.34
242 243 3.728076 ATACTAGTACACATGCCCGTG 57.272 47.619 4.31 1.29 42.81 4.94
243 244 8.991783 ATATATATACTAGTACACATGCCCGT 57.008 34.615 4.31 0.00 0.00 5.28
267 268 8.958119 ACAACAATCGTCATGTAAACCTATAT 57.042 30.769 0.00 0.00 0.00 0.86
268 269 8.780846 AACAACAATCGTCATGTAAACCTATA 57.219 30.769 0.00 0.00 0.00 1.31
269 270 7.681939 AACAACAATCGTCATGTAAACCTAT 57.318 32.000 0.00 0.00 0.00 2.57
270 271 7.499321 AAACAACAATCGTCATGTAAACCTA 57.501 32.000 0.00 0.00 0.00 3.08
271 272 6.385649 AAACAACAATCGTCATGTAAACCT 57.614 33.333 0.00 0.00 0.00 3.50
272 273 7.357303 ACTAAACAACAATCGTCATGTAAACC 58.643 34.615 0.00 0.00 0.00 3.27
273 274 8.065407 TGACTAAACAACAATCGTCATGTAAAC 58.935 33.333 0.00 0.00 0.00 2.01
274 275 8.065407 GTGACTAAACAACAATCGTCATGTAAA 58.935 33.333 0.00 0.00 34.41 2.01
275 276 7.439955 AGTGACTAAACAACAATCGTCATGTAA 59.560 33.333 0.00 0.00 34.41 2.41
276 277 6.926826 AGTGACTAAACAACAATCGTCATGTA 59.073 34.615 0.00 0.00 34.41 2.29
277 278 5.758296 AGTGACTAAACAACAATCGTCATGT 59.242 36.000 0.00 0.00 34.41 3.21
278 279 6.073819 TGAGTGACTAAACAACAATCGTCATG 60.074 38.462 0.00 0.00 34.41 3.07
279 280 5.989168 TGAGTGACTAAACAACAATCGTCAT 59.011 36.000 0.00 0.00 34.41 3.06
280 281 5.353111 TGAGTGACTAAACAACAATCGTCA 58.647 37.500 0.00 0.00 32.50 4.35
281 282 5.900339 TGAGTGACTAAACAACAATCGTC 57.100 39.130 0.00 0.00 32.50 4.20
282 283 6.671614 TTTGAGTGACTAAACAACAATCGT 57.328 33.333 0.00 0.00 32.50 3.73
307 308 8.920174 TGTTACTGCGGGCTACAATATATATAT 58.080 33.333 0.00 0.00 0.00 0.86
308 309 8.192774 GTGTTACTGCGGGCTACAATATATATA 58.807 37.037 0.00 0.00 0.00 0.86
309 310 7.039882 GTGTTACTGCGGGCTACAATATATAT 58.960 38.462 0.00 0.00 0.00 0.86
310 311 6.015265 TGTGTTACTGCGGGCTACAATATATA 60.015 38.462 0.00 0.00 0.00 0.86
311 312 5.221561 TGTGTTACTGCGGGCTACAATATAT 60.222 40.000 0.00 0.00 0.00 0.86
312 313 4.099727 TGTGTTACTGCGGGCTACAATATA 59.900 41.667 0.00 0.00 0.00 0.86
313 314 3.118555 TGTGTTACTGCGGGCTACAATAT 60.119 43.478 0.00 0.00 0.00 1.28
314 315 2.234168 TGTGTTACTGCGGGCTACAATA 59.766 45.455 0.00 0.00 0.00 1.90
315 316 1.002659 TGTGTTACTGCGGGCTACAAT 59.997 47.619 0.00 0.00 0.00 2.71
316 317 0.393448 TGTGTTACTGCGGGCTACAA 59.607 50.000 0.00 0.00 0.00 2.41
317 318 0.320073 GTGTGTTACTGCGGGCTACA 60.320 55.000 0.00 0.00 0.00 2.74
318 319 1.349259 CGTGTGTTACTGCGGGCTAC 61.349 60.000 0.00 0.00 0.00 3.58
319 320 1.080366 CGTGTGTTACTGCGGGCTA 60.080 57.895 0.00 0.00 0.00 3.93
320 321 2.357034 CGTGTGTTACTGCGGGCT 60.357 61.111 0.00 0.00 0.00 5.19
321 322 3.419759 CCGTGTGTTACTGCGGGC 61.420 66.667 0.00 0.00 40.45 6.13
322 323 2.025418 GTCCGTGTGTTACTGCGGG 61.025 63.158 0.00 0.00 43.87 6.13
323 324 0.669318 ATGTCCGTGTGTTACTGCGG 60.669 55.000 0.00 0.00 44.95 5.69
324 325 1.126113 GAATGTCCGTGTGTTACTGCG 59.874 52.381 0.00 0.00 0.00 5.18
325 326 2.413837 AGAATGTCCGTGTGTTACTGC 58.586 47.619 0.00 0.00 0.00 4.40
326 327 6.590292 AGAATTAGAATGTCCGTGTGTTACTG 59.410 38.462 0.00 0.00 0.00 2.74
327 328 6.698380 AGAATTAGAATGTCCGTGTGTTACT 58.302 36.000 0.00 0.00 0.00 2.24
328 329 6.963049 AGAATTAGAATGTCCGTGTGTTAC 57.037 37.500 0.00 0.00 0.00 2.50
329 330 7.833786 AGTAGAATTAGAATGTCCGTGTGTTA 58.166 34.615 0.00 0.00 0.00 2.41
330 331 6.698380 AGTAGAATTAGAATGTCCGTGTGTT 58.302 36.000 0.00 0.00 0.00 3.32
331 332 6.282199 AGTAGAATTAGAATGTCCGTGTGT 57.718 37.500 0.00 0.00 0.00 3.72
332 333 7.432545 CACTAGTAGAATTAGAATGTCCGTGTG 59.567 40.741 3.59 0.00 0.00 3.82
333 334 7.481642 CACTAGTAGAATTAGAATGTCCGTGT 58.518 38.462 3.59 0.00 0.00 4.49
334 335 6.418226 GCACTAGTAGAATTAGAATGTCCGTG 59.582 42.308 3.59 0.00 0.00 4.94
335 336 6.321690 AGCACTAGTAGAATTAGAATGTCCGT 59.678 38.462 3.59 0.00 0.00 4.69
336 337 6.740110 AGCACTAGTAGAATTAGAATGTCCG 58.260 40.000 3.59 0.00 0.00 4.79
337 338 9.685828 CTAAGCACTAGTAGAATTAGAATGTCC 57.314 37.037 3.59 0.00 0.00 4.02
352 353 8.792633 TGCATTTCAAAATTACTAAGCACTAGT 58.207 29.630 0.00 0.00 43.58 2.57
353 354 9.793252 ATGCATTTCAAAATTACTAAGCACTAG 57.207 29.630 0.00 0.00 0.00 2.57
354 355 9.787532 GATGCATTTCAAAATTACTAAGCACTA 57.212 29.630 0.00 0.00 0.00 2.74
355 356 8.306038 TGATGCATTTCAAAATTACTAAGCACT 58.694 29.630 0.00 0.00 0.00 4.40
356 357 8.375465 GTGATGCATTTCAAAATTACTAAGCAC 58.625 33.333 0.00 0.00 0.00 4.40
357 358 7.545265 GGTGATGCATTTCAAAATTACTAAGCA 59.455 33.333 0.00 0.00 0.00 3.91
358 359 7.545265 TGGTGATGCATTTCAAAATTACTAAGC 59.455 33.333 0.00 0.00 0.00 3.09
359 360 8.984891 TGGTGATGCATTTCAAAATTACTAAG 57.015 30.769 0.00 0.00 0.00 2.18
360 361 9.770097 TTTGGTGATGCATTTCAAAATTACTAA 57.230 25.926 15.69 0.00 0.00 2.24
361 362 9.202273 GTTTGGTGATGCATTTCAAAATTACTA 57.798 29.630 18.11 0.79 0.00 1.82
362 363 7.173047 GGTTTGGTGATGCATTTCAAAATTACT 59.827 33.333 18.11 0.00 0.00 2.24
363 364 7.173047 AGGTTTGGTGATGCATTTCAAAATTAC 59.827 33.333 18.11 10.64 0.00 1.89
364 365 7.172875 CAGGTTTGGTGATGCATTTCAAAATTA 59.827 33.333 18.11 2.09 0.00 1.40
365 366 6.016943 CAGGTTTGGTGATGCATTTCAAAATT 60.017 34.615 18.11 10.66 0.00 1.82
366 367 5.470777 CAGGTTTGGTGATGCATTTCAAAAT 59.529 36.000 18.11 11.15 0.00 1.82
367 368 4.815308 CAGGTTTGGTGATGCATTTCAAAA 59.185 37.500 18.11 10.74 0.00 2.44
368 369 4.378774 CAGGTTTGGTGATGCATTTCAAA 58.621 39.130 0.00 9.49 0.00 2.69
369 370 3.803021 GCAGGTTTGGTGATGCATTTCAA 60.803 43.478 0.00 3.46 38.54 2.69
370 371 2.288948 GCAGGTTTGGTGATGCATTTCA 60.289 45.455 0.00 0.00 38.54 2.69
371 372 2.288948 TGCAGGTTTGGTGATGCATTTC 60.289 45.455 0.00 0.00 43.34 2.17
372 373 1.693062 TGCAGGTTTGGTGATGCATTT 59.307 42.857 0.00 0.00 43.34 2.32
373 374 1.274167 CTGCAGGTTTGGTGATGCATT 59.726 47.619 5.57 0.00 46.67 3.56
374 375 0.892755 CTGCAGGTTTGGTGATGCAT 59.107 50.000 5.57 0.00 46.67 3.96
375 376 0.467844 ACTGCAGGTTTGGTGATGCA 60.468 50.000 19.93 0.00 45.82 3.96
376 377 0.242017 GACTGCAGGTTTGGTGATGC 59.758 55.000 19.93 0.00 39.14 3.91
377 378 1.808945 GAGACTGCAGGTTTGGTGATG 59.191 52.381 19.93 0.00 0.00 3.07
378 379 1.421268 TGAGACTGCAGGTTTGGTGAT 59.579 47.619 19.93 0.00 0.00 3.06
379 380 0.836606 TGAGACTGCAGGTTTGGTGA 59.163 50.000 19.93 0.00 0.00 4.02
380 381 1.901591 ATGAGACTGCAGGTTTGGTG 58.098 50.000 19.93 0.00 0.00 4.17
381 382 3.788227 TTATGAGACTGCAGGTTTGGT 57.212 42.857 19.93 0.00 0.00 3.67
382 383 6.949352 ATATTTATGAGACTGCAGGTTTGG 57.051 37.500 19.93 0.00 0.00 3.28
383 384 8.668510 ACTATATTTATGAGACTGCAGGTTTG 57.331 34.615 19.93 0.00 0.00 2.93
384 385 9.686683 AAACTATATTTATGAGACTGCAGGTTT 57.313 29.630 19.93 10.02 0.00 3.27
385 386 9.331282 GAAACTATATTTATGAGACTGCAGGTT 57.669 33.333 19.93 5.16 0.00 3.50
386 387 7.934120 GGAAACTATATTTATGAGACTGCAGGT 59.066 37.037 19.93 4.31 0.00 4.00
387 388 7.389053 GGGAAACTATATTTATGAGACTGCAGG 59.611 40.741 19.93 0.00 0.00 4.85
388 389 7.933577 TGGGAAACTATATTTATGAGACTGCAG 59.066 37.037 13.48 13.48 0.00 4.41
389 390 7.801104 TGGGAAACTATATTTATGAGACTGCA 58.199 34.615 0.00 0.00 0.00 4.41
390 391 8.677148 TTGGGAAACTATATTTATGAGACTGC 57.323 34.615 0.00 0.00 0.00 4.40
400 401 7.765819 GCAGAGCAATTTTGGGAAACTATATTT 59.234 33.333 0.00 0.00 0.00 1.40
401 402 7.267857 GCAGAGCAATTTTGGGAAACTATATT 58.732 34.615 0.00 0.00 0.00 1.28
402 403 6.183360 GGCAGAGCAATTTTGGGAAACTATAT 60.183 38.462 0.00 0.00 0.00 0.86
403 404 5.127031 GGCAGAGCAATTTTGGGAAACTATA 59.873 40.000 0.00 0.00 0.00 1.31
404 405 4.081476 GGCAGAGCAATTTTGGGAAACTAT 60.081 41.667 0.00 0.00 0.00 2.12
405 406 3.258123 GGCAGAGCAATTTTGGGAAACTA 59.742 43.478 0.00 0.00 0.00 2.24
406 407 2.037641 GGCAGAGCAATTTTGGGAAACT 59.962 45.455 0.00 0.00 0.00 2.66
407 408 2.037641 AGGCAGAGCAATTTTGGGAAAC 59.962 45.455 0.00 0.00 0.00 2.78
408 409 2.299867 GAGGCAGAGCAATTTTGGGAAA 59.700 45.455 0.00 0.00 0.00 3.13
409 410 1.895131 GAGGCAGAGCAATTTTGGGAA 59.105 47.619 0.00 0.00 0.00 3.97
410 411 1.076024 AGAGGCAGAGCAATTTTGGGA 59.924 47.619 0.00 0.00 0.00 4.37
411 412 1.475682 GAGAGGCAGAGCAATTTTGGG 59.524 52.381 0.00 0.00 0.00 4.12
412 413 1.131883 CGAGAGGCAGAGCAATTTTGG 59.868 52.381 0.00 0.00 0.00 3.28
413 414 1.467035 GCGAGAGGCAGAGCAATTTTG 60.467 52.381 0.00 0.00 42.87 2.44
414 415 0.807496 GCGAGAGGCAGAGCAATTTT 59.193 50.000 0.00 0.00 42.87 1.82
415 416 2.475666 GCGAGAGGCAGAGCAATTT 58.524 52.632 0.00 0.00 42.87 1.82
416 417 4.215349 GCGAGAGGCAGAGCAATT 57.785 55.556 0.00 0.00 42.87 2.32
425 426 6.743837 TTGTTCAACAAAAAGGCGAGAGGC 62.744 45.833 0.00 0.00 46.01 4.70
426 427 2.357637 TGTTCAACAAAAAGGCGAGAGG 59.642 45.455 0.00 0.00 0.00 3.69
427 428 3.691049 TGTTCAACAAAAAGGCGAGAG 57.309 42.857 0.00 0.00 0.00 3.20
428 429 4.338118 AGATTGTTCAACAAAAAGGCGAGA 59.662 37.500 7.14 0.00 41.96 4.04
429 430 4.610945 AGATTGTTCAACAAAAAGGCGAG 58.389 39.130 7.14 0.00 41.96 5.03
430 431 4.647424 AGATTGTTCAACAAAAAGGCGA 57.353 36.364 7.14 0.00 41.96 5.54
431 432 6.820470 TTAAGATTGTTCAACAAAAAGGCG 57.180 33.333 7.14 0.00 41.96 5.52
432 433 7.440856 TGGATTAAGATTGTTCAACAAAAAGGC 59.559 33.333 7.14 0.00 41.96 4.35
433 434 8.885494 TGGATTAAGATTGTTCAACAAAAAGG 57.115 30.769 7.14 0.00 41.96 3.11
446 447 8.975439 GCAGCTGAAAAATATGGATTAAGATTG 58.025 33.333 20.43 0.00 0.00 2.67
447 448 8.146412 GGCAGCTGAAAAATATGGATTAAGATT 58.854 33.333 20.43 0.00 0.00 2.40
448 449 7.256083 GGGCAGCTGAAAAATATGGATTAAGAT 60.256 37.037 20.43 0.00 0.00 2.40
449 450 6.040842 GGGCAGCTGAAAAATATGGATTAAGA 59.959 38.462 20.43 0.00 0.00 2.10
450 451 6.183360 TGGGCAGCTGAAAAATATGGATTAAG 60.183 38.462 20.43 0.00 0.00 1.85
451 452 5.660417 TGGGCAGCTGAAAAATATGGATTAA 59.340 36.000 20.43 0.00 0.00 1.40
452 453 5.207354 TGGGCAGCTGAAAAATATGGATTA 58.793 37.500 20.43 0.00 0.00 1.75
453 454 4.032310 TGGGCAGCTGAAAAATATGGATT 58.968 39.130 20.43 0.00 0.00 3.01
454 455 3.640029 CTGGGCAGCTGAAAAATATGGAT 59.360 43.478 20.43 0.00 0.00 3.41
455 456 3.025978 CTGGGCAGCTGAAAAATATGGA 58.974 45.455 20.43 0.00 0.00 3.41
456 457 3.447918 CTGGGCAGCTGAAAAATATGG 57.552 47.619 20.43 0.00 0.00 2.74
471 472 0.393077 ACGTGTCCATATAGCTGGGC 59.607 55.000 0.00 0.00 41.49 5.36
472 473 1.412710 ACACGTGTCCATATAGCTGGG 59.587 52.381 17.22 0.00 36.89 4.45
473 474 2.890808 ACACGTGTCCATATAGCTGG 57.109 50.000 17.22 0.00 37.66 4.85
474 475 5.528870 TGAATACACGTGTCCATATAGCTG 58.471 41.667 27.16 0.00 0.00 4.24
475 476 5.784578 TGAATACACGTGTCCATATAGCT 57.215 39.130 27.16 0.00 0.00 3.32
573 574 1.076265 TCGTGTGATCCCCCGATCT 60.076 57.895 2.11 0.00 44.61 2.75
581 582 2.202756 GGTCGCCTCGTGTGATCC 60.203 66.667 0.00 0.00 35.57 3.36
582 583 1.517257 CTGGTCGCCTCGTGTGATC 60.517 63.158 0.00 0.00 35.57 2.92
589 590 4.135153 CCCAGTCTGGTCGCCTCG 62.135 72.222 17.85 0.00 35.17 4.63
605 606 3.499737 CATCTCGCGGTGGTTGCC 61.500 66.667 6.13 0.00 0.00 4.52
648 649 7.011669 CCAAAAGTGAAATCAAGCTTCATGTTT 59.988 33.333 0.00 0.00 35.36 2.83
659 660 2.368221 CCTGGCCCAAAAGTGAAATCAA 59.632 45.455 0.00 0.00 0.00 2.57
676 677 6.828785 AGAAGGCTTGTATTTATAACACCTGG 59.171 38.462 3.46 0.00 0.00 4.45
694 695 2.890311 CCATACGAGAGATGAGAAGGCT 59.110 50.000 0.00 0.00 0.00 4.58
747 748 3.372514 TGTATGTGTGTGTGTGTGTGAAC 59.627 43.478 0.00 0.00 0.00 3.18
749 750 2.933260 GTGTATGTGTGTGTGTGTGTGA 59.067 45.455 0.00 0.00 0.00 3.58
751 752 1.930503 CGTGTATGTGTGTGTGTGTGT 59.069 47.619 0.00 0.00 0.00 3.72
752 753 2.197577 TCGTGTATGTGTGTGTGTGTG 58.802 47.619 0.00 0.00 0.00 3.82
753 754 2.469826 CTCGTGTATGTGTGTGTGTGT 58.530 47.619 0.00 0.00 0.00 3.72
754 755 1.192312 GCTCGTGTATGTGTGTGTGTG 59.808 52.381 0.00 0.00 0.00 3.82
756 757 1.192312 GTGCTCGTGTATGTGTGTGTG 59.808 52.381 0.00 0.00 0.00 3.82
757 758 1.202475 TGTGCTCGTGTATGTGTGTGT 60.202 47.619 0.00 0.00 0.00 3.72
766 919 2.021584 CTGCGCTTGTGCTCGTGTA 61.022 57.895 9.73 0.00 36.97 2.90
799 952 1.608283 GGACGGTGGTCTTCTTGGAAG 60.608 57.143 1.28 1.28 42.97 3.46
875 1029 2.642139 TCTCTTTAAGGTACCGTGCG 57.358 50.000 10.95 0.00 0.00 5.34
888 1042 0.178861 TCCTCTGGCCCCTTCTCTTT 60.179 55.000 0.00 0.00 0.00 2.52
898 1052 3.791586 GGTGCTCCTCCTCTGGCC 61.792 72.222 0.00 0.00 0.00 5.36
903 1057 2.896443 CGGAAGGTGCTCCTCCTC 59.104 66.667 7.99 2.80 44.35 3.71
921 1075 2.490217 CTCAGGCACGGTAGGACG 59.510 66.667 0.00 0.00 40.31 4.79
929 1083 4.680237 TTCGGCACCTCAGGCACG 62.680 66.667 0.00 0.00 0.00 5.34
931 1085 2.293318 ATCTTCGGCACCTCAGGCA 61.293 57.895 0.00 0.00 0.00 4.75
942 1096 0.383231 GGCAATTCAGGCATCTTCGG 59.617 55.000 0.00 0.00 0.00 4.30
957 1111 1.438651 GACACAACTAGATGCGGCAA 58.561 50.000 6.82 0.00 0.00 4.52
962 1116 1.204941 ACCTCGGACACAACTAGATGC 59.795 52.381 0.00 0.00 0.00 3.91
967 1121 1.669440 GGCACCTCGGACACAACTA 59.331 57.895 0.00 0.00 0.00 2.24
986 1140 1.669795 GCGGCATTTTCTGGAACCTTG 60.670 52.381 0.00 0.00 0.00 3.61
990 1144 0.388520 GGTGCGGCATTTTCTGGAAC 60.389 55.000 5.72 0.00 0.00 3.62
997 1151 0.977108 ATGATGGGGTGCGGCATTTT 60.977 50.000 5.72 0.00 0.00 1.82
1006 1160 2.101917 GCATCTTTGGAATGATGGGGTG 59.898 50.000 13.99 0.00 39.58 4.61
1013 1167 2.025605 AGCTCTGGCATCTTTGGAATGA 60.026 45.455 0.00 0.00 41.70 2.57
1038 1192 1.542187 GCTCTGGAACGGTAGGGTGT 61.542 60.000 0.00 0.00 35.30 4.16
1047 1201 1.079503 GCTTTGGTAGCTCTGGAACG 58.920 55.000 0.00 0.00 46.77 3.95
1069 1223 1.212751 GCACGCCTGTGGGAAATTC 59.787 57.895 0.00 0.00 46.51 2.17
1070 1224 2.275380 GGCACGCCTGTGGGAAATT 61.275 57.895 0.00 0.00 46.51 1.82
1071 1225 2.676471 GGCACGCCTGTGGGAAAT 60.676 61.111 0.00 0.00 46.51 2.17
1072 1226 4.196778 TGGCACGCCTGTGGGAAA 62.197 61.111 9.92 0.00 46.51 3.13
1073 1227 4.641645 CTGGCACGCCTGTGGGAA 62.642 66.667 9.92 0.00 46.51 3.97
1078 1232 4.320456 CACCTCTGGCACGCCTGT 62.320 66.667 9.92 0.00 36.57 4.00
1086 1240 1.941999 GCATCTTTGGCACCTCTGGC 61.942 60.000 0.00 0.00 43.44 4.85
1087 1241 2.187073 GCATCTTTGGCACCTCTGG 58.813 57.895 0.00 0.00 0.00 3.86
1129 1283 2.597217 TGGCTTTGGTTGCTCCGG 60.597 61.111 0.00 0.00 39.52 5.14
1130 1284 1.172180 TTCTGGCTTTGGTTGCTCCG 61.172 55.000 0.00 0.00 39.52 4.63
1140 1294 3.365472 GGTATGTGGGATTTCTGGCTTT 58.635 45.455 0.00 0.00 0.00 3.51
1146 1300 3.713826 ACAACGGTATGTGGGATTTCT 57.286 42.857 0.00 0.00 30.82 2.52
1174 1328 0.663153 ACTTCAAGCGTCTTTGGCAC 59.337 50.000 0.00 0.00 0.00 5.01
1187 1341 0.109723 GGTAGGGTGTGGCACTTCAA 59.890 55.000 19.83 0.00 34.40 2.69
1202 1356 1.691976 TCCATACCTTCGGCATGGTAG 59.308 52.381 11.02 0.81 41.46 3.18
1213 1367 3.452627 AGTTCGAGCATCTTCCATACCTT 59.547 43.478 1.01 0.00 0.00 3.50
1220 1374 0.391661 TGGCAGTTCGAGCATCTTCC 60.392 55.000 1.01 0.00 0.00 3.46
1229 1383 1.811965 CAATTGGATGTGGCAGTTCGA 59.188 47.619 0.00 0.00 0.00 3.71
1242 1396 2.419990 CGGCACCTCTGATACAATTGGA 60.420 50.000 10.83 0.10 0.00 3.53
1262 1416 2.464459 GGCACTTCGGGCATCTTCG 61.464 63.158 0.00 0.00 0.00 3.79
1309 1463 3.741476 CTTTGGCACCTCTGGCGC 61.741 66.667 0.00 0.00 46.17 6.53
1310 1464 1.377725 ATCTTTGGCACCTCTGGCG 60.378 57.895 0.00 0.00 46.17 5.69
1375 1529 5.930135 TCTAGGGCATATTTCCTTCACTTC 58.070 41.667 0.00 0.00 34.75 3.01
1746 1900 2.949644 GGTAGCACACAAAGTGTTCCTT 59.050 45.455 0.00 0.00 45.08 3.36
1963 2117 4.676849 AGTCTCTTTACTCGTTCCGTAC 57.323 45.455 0.00 0.00 0.00 3.67
1988 2142 7.123098 TCAATACCTAGTTCAATCTCGTTACCA 59.877 37.037 0.00 0.00 0.00 3.25
2021 2175 0.174845 TTGCCCGAGATTCGATCGTT 59.825 50.000 15.94 3.86 43.74 3.85
2106 2260 8.439971 TGCTCATATTGGTTCCTACATATTCTT 58.560 33.333 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.