Multiple sequence alignment - TraesCS7A01G169300

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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 TraesCS7A01G169300 chr7A 100.000 2738 0 0 1 2738 126036291 126033554 0.000000e+00 5057.0
1 TraesCS7A01G169300 chr7A 88.860 386 35 3 1 386 730559209 730558832 4.130000e-128 468.0
2 TraesCS7A01G169300 chr7A 87.671 365 25 8 1 365 585337855 585338199 9.130000e-110 407.0
3 TraesCS7A01G169300 chr7A 100.000 29 0 0 2672 2700 699259462 699259434 1.000000e-03 54.7
4 TraesCS7A01G169300 chr7B 90.418 1868 93 26 386 2229 84219962 84221767 0.000000e+00 2379.0
5 TraesCS7A01G169300 chr7B 89.950 199 15 5 2541 2738 84246224 84246418 4.530000e-63 252.0
6 TraesCS7A01G169300 chr7B 96.491 114 4 0 2257 2370 84221757 84221870 3.600000e-44 189.0
7 TraesCS7A01G169300 chr7D 90.471 1847 85 28 386 2228 123145642 123147401 0.000000e+00 2351.0
8 TraesCS7A01G169300 chr7D 90.299 402 25 4 1 390 40617612 40617213 5.230000e-142 514.0
9 TraesCS7A01G169300 chr7D 90.411 146 6 3 2257 2394 123147392 123147537 4.660000e-43 185.0
10 TraesCS7A01G169300 chr6A 91.284 436 26 4 1120 1552 53455245 53455671 3.930000e-163 584.0
11 TraesCS7A01G169300 chr6A 92.537 67 4 1 1884 1950 563027256 563027321 8.070000e-16 95.3
12 TraesCS7A01G169300 chr1A 91.495 388 29 4 1 387 38876675 38877059 5.190000e-147 531.0
13 TraesCS7A01G169300 chr1A 90.793 391 31 3 1 390 112032756 112032370 4.040000e-143 518.0
14 TraesCS7A01G169300 chr1A 90.000 210 15 2 1368 1577 374684415 374684212 1.620000e-67 267.0
15 TraesCS7A01G169300 chr1A 96.250 80 3 0 1120 1199 374684474 374684395 6.150000e-27 132.0
16 TraesCS7A01G169300 chr3D 91.026 390 31 2 1 390 409028553 409028938 8.690000e-145 523.0
17 TraesCS7A01G169300 chr3D 90.201 398 26 7 1 387 465508183 465508578 8.750000e-140 507.0
18 TraesCS7A01G169300 chr3D 100.000 28 0 0 2672 2699 515809558 515809585 5.000000e-03 52.8
19 TraesCS7A01G169300 chr5D 90.025 401 25 4 1 389 467608439 467608042 3.150000e-139 505.0
20 TraesCS7A01G169300 chr1D 88.776 392 24 9 4 391 350902769 350902394 1.920000e-126 462.0
21 TraesCS7A01G169300 chr3A 86.480 392 45 5 1 389 536630348 536629962 9.060000e-115 424.0
22 TraesCS7A01G169300 chr6B 86.260 393 37 10 1 392 613311458 613311082 7.060000e-111 411.0
23 TraesCS7A01G169300 chr6B 89.855 69 5 2 1884 1952 632955819 632955885 1.350000e-13 87.9
24 TraesCS7A01G169300 chr4D 87.805 205 20 3 190 390 19400570 19400367 4.560000e-58 235.0
25 TraesCS7A01G169300 chr6D 89.855 69 5 2 1884 1952 420004954 420005020 1.350000e-13 87.9


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 TraesCS7A01G169300 chr7A 126033554 126036291 2737 True 5057 5057 100.0000 1 2738 1 chr7A.!!$R1 2737
1 TraesCS7A01G169300 chr7B 84219962 84221870 1908 False 1284 2379 93.4545 386 2370 2 chr7B.!!$F2 1984
2 TraesCS7A01G169300 chr7D 123145642 123147537 1895 False 1268 2351 90.4410 386 2394 2 chr7D.!!$F1 2008

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
434 435 0.179018 GGTTGACACTTGAGGCCACT 60.179 55.0 5.01 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2023 2057 0.10412 CACCCACACAGTTGACGAGA 59.896 55.0 0.0 0.0 0.0 4.04 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
20 21 3.559238 GACATGCGTGATTGGAAAACT 57.441 42.857 14.17 0.00 0.00 2.66
21 22 3.492313 GACATGCGTGATTGGAAAACTC 58.508 45.455 14.17 0.00 0.00 3.01
22 23 2.884012 ACATGCGTGATTGGAAAACTCA 59.116 40.909 14.17 0.00 0.00 3.41
23 24 3.236816 CATGCGTGATTGGAAAACTCAC 58.763 45.455 0.00 0.00 36.72 3.51
24 25 2.571212 TGCGTGATTGGAAAACTCACT 58.429 42.857 0.00 0.00 37.68 3.41
25 26 2.948979 TGCGTGATTGGAAAACTCACTT 59.051 40.909 0.00 0.00 37.68 3.16
26 27 3.243035 TGCGTGATTGGAAAACTCACTTG 60.243 43.478 0.00 0.00 37.68 3.16
27 28 3.300009 CGTGATTGGAAAACTCACTTGC 58.700 45.455 0.00 0.00 37.68 4.01
28 29 3.243035 CGTGATTGGAAAACTCACTTGCA 60.243 43.478 0.00 0.00 37.68 4.08
29 30 4.681744 GTGATTGGAAAACTCACTTGCAA 58.318 39.130 0.00 0.00 38.29 4.08
30 31 5.291971 GTGATTGGAAAACTCACTTGCAAT 58.708 37.500 0.00 2.48 44.47 3.56
31 32 5.754890 GTGATTGGAAAACTCACTTGCAATT 59.245 36.000 0.00 0.00 42.64 2.32
32 33 5.754406 TGATTGGAAAACTCACTTGCAATTG 59.246 36.000 10.37 10.37 42.64 2.32
33 34 3.456280 TGGAAAACTCACTTGCAATTGC 58.544 40.909 23.69 23.69 42.50 3.56
48 49 4.965062 GCAATTGCAGAATGATTTGGTTG 58.035 39.130 25.36 0.00 39.69 3.77
49 50 4.691685 GCAATTGCAGAATGATTTGGTTGA 59.308 37.500 25.36 0.00 39.69 3.18
50 51 5.163893 GCAATTGCAGAATGATTTGGTTGAG 60.164 40.000 25.36 0.00 39.69 3.02
51 52 3.581024 TGCAGAATGATTTGGTTGAGC 57.419 42.857 0.00 0.00 39.69 4.26
52 53 2.892215 TGCAGAATGATTTGGTTGAGCA 59.108 40.909 0.00 0.00 39.69 4.26
53 54 3.512329 TGCAGAATGATTTGGTTGAGCAT 59.488 39.130 0.00 0.00 39.69 3.79
54 55 4.705991 TGCAGAATGATTTGGTTGAGCATA 59.294 37.500 0.00 0.00 39.69 3.14
55 56 5.361571 TGCAGAATGATTTGGTTGAGCATAT 59.638 36.000 0.00 0.00 39.69 1.78
56 57 5.690409 GCAGAATGATTTGGTTGAGCATATG 59.310 40.000 0.00 0.00 39.69 1.78
57 58 6.682113 GCAGAATGATTTGGTTGAGCATATGT 60.682 38.462 4.29 0.00 39.69 2.29
58 59 6.695713 CAGAATGATTTGGTTGAGCATATGTG 59.304 38.462 4.29 0.00 39.69 3.21
59 60 4.987408 TGATTTGGTTGAGCATATGTGG 57.013 40.909 4.29 0.00 0.00 4.17
60 61 4.598022 TGATTTGGTTGAGCATATGTGGA 58.402 39.130 4.29 0.00 0.00 4.02
61 62 4.398988 TGATTTGGTTGAGCATATGTGGAC 59.601 41.667 4.29 0.00 0.00 4.02
62 63 3.719268 TTGGTTGAGCATATGTGGACT 57.281 42.857 4.29 0.00 0.00 3.85
63 64 3.266510 TGGTTGAGCATATGTGGACTC 57.733 47.619 4.29 3.05 0.00 3.36
64 65 2.571202 TGGTTGAGCATATGTGGACTCA 59.429 45.455 4.29 5.68 37.38 3.41
65 66 3.200605 TGGTTGAGCATATGTGGACTCAT 59.799 43.478 10.41 0.00 38.84 2.90
66 67 4.408596 TGGTTGAGCATATGTGGACTCATA 59.591 41.667 10.41 0.00 38.84 2.15
67 68 5.072193 TGGTTGAGCATATGTGGACTCATAT 59.928 40.000 10.41 2.06 40.35 1.78
68 69 6.000219 GGTTGAGCATATGTGGACTCATATT 59.000 40.000 10.41 0.00 38.47 1.28
69 70 6.072838 GGTTGAGCATATGTGGACTCATATTG 60.073 42.308 10.41 3.33 38.47 1.90
70 71 5.554070 TGAGCATATGTGGACTCATATTGG 58.446 41.667 4.29 0.00 38.47 3.16
71 72 4.330250 AGCATATGTGGACTCATATTGGC 58.670 43.478 4.29 6.44 38.47 4.52
72 73 4.074259 GCATATGTGGACTCATATTGGCA 58.926 43.478 4.29 0.00 38.47 4.92
73 74 4.520111 GCATATGTGGACTCATATTGGCAA 59.480 41.667 0.68 0.68 38.47 4.52
74 75 5.563475 GCATATGTGGACTCATATTGGCAAC 60.563 44.000 0.00 0.00 38.47 4.17
75 76 2.722094 TGTGGACTCATATTGGCAACC 58.278 47.619 0.00 0.00 0.00 3.77
76 77 2.040947 TGTGGACTCATATTGGCAACCA 59.959 45.455 0.00 0.00 0.00 3.67
116 117 8.858003 TTTTATTCGTTTGCAAAACTATGTGA 57.142 26.923 14.67 0.94 0.00 3.58
117 118 8.858003 TTTATTCGTTTGCAAAACTATGTGAA 57.142 26.923 14.67 9.56 0.00 3.18
118 119 8.858003 TTATTCGTTTGCAAAACTATGTGAAA 57.142 26.923 14.67 0.00 0.00 2.69
119 120 6.561945 TTCGTTTGCAAAACTATGTGAAAC 57.438 33.333 14.67 0.00 37.35 2.78
168 169 6.812879 AACTATACTATTTATTTGGGCGGC 57.187 37.500 0.00 0.00 0.00 6.53
169 170 5.250982 ACTATACTATTTATTTGGGCGGCC 58.749 41.667 23.42 23.42 0.00 6.13
170 171 1.314730 ACTATTTATTTGGGCGGCCG 58.685 50.000 24.05 24.05 0.00 6.13
171 172 1.134037 ACTATTTATTTGGGCGGCCGA 60.134 47.619 33.48 20.16 0.00 5.54
172 173 1.950909 CTATTTATTTGGGCGGCCGAA 59.049 47.619 33.48 30.90 0.00 4.30
173 174 0.458260 ATTTATTTGGGCGGCCGAAC 59.542 50.000 31.34 21.30 0.00 3.95
174 175 0.609681 TTTATTTGGGCGGCCGAACT 60.610 50.000 31.34 21.45 0.00 3.01
175 176 0.252479 TTATTTGGGCGGCCGAACTA 59.748 50.000 31.34 20.53 0.00 2.24
176 177 0.470766 TATTTGGGCGGCCGAACTAT 59.529 50.000 31.34 18.90 0.00 2.12
177 178 0.395173 ATTTGGGCGGCCGAACTATT 60.395 50.000 31.34 14.17 0.00 1.73
178 179 0.609681 TTTGGGCGGCCGAACTATTT 60.610 50.000 33.48 0.00 0.00 1.40
179 180 1.309499 TTGGGCGGCCGAACTATTTG 61.309 55.000 33.48 0.00 0.00 2.32
180 181 2.478033 GGGCGGCCGAACTATTTGG 61.478 63.158 33.48 0.00 37.26 3.28
192 193 7.100829 CCGAACTATTTGGCTTGTTTTAAAC 57.899 36.000 0.20 0.20 0.00 2.01
193 194 6.697892 CCGAACTATTTGGCTTGTTTTAAACA 59.302 34.615 6.41 6.41 40.21 2.83
194 195 7.383843 CCGAACTATTTGGCTTGTTTTAAACAT 59.616 33.333 11.50 0.00 41.79 2.71
195 196 8.760569 CGAACTATTTGGCTTGTTTTAAACATT 58.239 29.630 11.50 0.00 41.79 2.71
203 204 9.780413 TTGGCTTGTTTTAAACATTTTCATTTC 57.220 25.926 11.50 0.00 41.79 2.17
204 205 8.950210 TGGCTTGTTTTAAACATTTTCATTTCA 58.050 25.926 11.50 0.00 41.79 2.69
205 206 9.220635 GGCTTGTTTTAAACATTTTCATTTCAC 57.779 29.630 11.50 0.00 41.79 3.18
206 207 9.766277 GCTTGTTTTAAACATTTTCATTTCACA 57.234 25.926 11.50 0.00 41.79 3.58
243 244 8.472683 TGAAAAATCAATGTAAAATTAGGCGG 57.527 30.769 0.00 0.00 0.00 6.13
244 245 6.902224 AAAATCAATGTAAAATTAGGCGGC 57.098 33.333 0.00 0.00 0.00 6.53
245 246 4.584327 ATCAATGTAAAATTAGGCGGCC 57.416 40.909 12.11 12.11 0.00 6.13
246 247 3.357203 TCAATGTAAAATTAGGCGGCCA 58.643 40.909 23.09 0.60 0.00 5.36
247 248 3.380004 TCAATGTAAAATTAGGCGGCCAG 59.620 43.478 23.09 0.00 0.00 4.85
267 268 2.516930 GGCCACGCCTGCACATAT 60.517 61.111 0.00 0.00 46.69 1.78
268 269 2.717485 GCCACGCCTGCACATATG 59.283 61.111 0.00 0.00 0.00 1.78
269 270 2.837883 GCCACGCCTGCACATATGG 61.838 63.158 7.80 0.00 0.00 2.74
270 271 1.153188 CCACGCCTGCACATATGGA 60.153 57.895 7.80 0.00 0.00 3.41
271 272 0.535780 CCACGCCTGCACATATGGAT 60.536 55.000 7.80 0.00 0.00 3.41
272 273 1.311859 CACGCCTGCACATATGGATT 58.688 50.000 7.80 0.00 0.00 3.01
273 274 1.002142 CACGCCTGCACATATGGATTG 60.002 52.381 7.80 0.00 0.00 2.67
274 275 1.134128 ACGCCTGCACATATGGATTGA 60.134 47.619 7.80 0.00 0.00 2.57
275 276 1.265095 CGCCTGCACATATGGATTGAC 59.735 52.381 7.80 0.00 0.00 3.18
276 277 1.265095 GCCTGCACATATGGATTGACG 59.735 52.381 7.80 0.00 0.00 4.35
277 278 1.265095 CCTGCACATATGGATTGACGC 59.735 52.381 7.80 0.00 0.00 5.19
278 279 0.936600 TGCACATATGGATTGACGCG 59.063 50.000 3.53 3.53 0.00 6.01
279 280 0.937304 GCACATATGGATTGACGCGT 59.063 50.000 13.85 13.85 0.00 6.01
280 281 1.330521 GCACATATGGATTGACGCGTT 59.669 47.619 15.53 0.00 0.00 4.84
281 282 2.850631 GCACATATGGATTGACGCGTTG 60.851 50.000 15.53 6.73 0.00 4.10
282 283 1.939934 ACATATGGATTGACGCGTTGG 59.060 47.619 15.53 0.00 0.00 3.77
283 284 1.264020 CATATGGATTGACGCGTTGGG 59.736 52.381 15.53 0.00 0.00 4.12
284 285 1.092921 TATGGATTGACGCGTTGGGC 61.093 55.000 15.53 0.00 38.69 5.36
301 302 4.969196 CGCGCTGCCGACCCATAT 62.969 66.667 5.56 0.00 36.29 1.78
302 303 3.044305 GCGCTGCCGACCCATATC 61.044 66.667 0.00 0.00 36.29 1.63
303 304 2.421314 CGCTGCCGACCCATATCA 59.579 61.111 0.00 0.00 36.29 2.15
304 305 1.227527 CGCTGCCGACCCATATCAA 60.228 57.895 0.00 0.00 36.29 2.57
305 306 0.813610 CGCTGCCGACCCATATCAAA 60.814 55.000 0.00 0.00 36.29 2.69
306 307 1.388547 GCTGCCGACCCATATCAAAA 58.611 50.000 0.00 0.00 0.00 2.44
307 308 1.748493 GCTGCCGACCCATATCAAAAA 59.252 47.619 0.00 0.00 0.00 1.94
308 309 2.479560 GCTGCCGACCCATATCAAAAAC 60.480 50.000 0.00 0.00 0.00 2.43
309 310 2.752354 CTGCCGACCCATATCAAAAACA 59.248 45.455 0.00 0.00 0.00 2.83
310 311 2.752354 TGCCGACCCATATCAAAAACAG 59.248 45.455 0.00 0.00 0.00 3.16
311 312 2.099098 GCCGACCCATATCAAAAACAGG 59.901 50.000 0.00 0.00 0.00 4.00
312 313 2.687935 CCGACCCATATCAAAAACAGGG 59.312 50.000 0.00 0.00 42.07 4.45
313 314 2.099098 CGACCCATATCAAAAACAGGGC 59.901 50.000 0.00 0.00 39.97 5.19
314 315 2.099098 GACCCATATCAAAAACAGGGCG 59.901 50.000 0.00 0.00 39.97 6.13
315 316 1.408702 CCCATATCAAAAACAGGGCGG 59.591 52.381 0.00 0.00 0.00 6.13
316 317 2.374184 CCATATCAAAAACAGGGCGGA 58.626 47.619 0.00 0.00 0.00 5.54
317 318 2.099098 CCATATCAAAAACAGGGCGGAC 59.901 50.000 0.00 0.00 0.00 4.79
318 319 1.444836 TATCAAAAACAGGGCGGACG 58.555 50.000 0.00 0.00 0.00 4.79
319 320 1.241315 ATCAAAAACAGGGCGGACGG 61.241 55.000 0.00 0.00 0.00 4.79
320 321 3.292159 AAAAACAGGGCGGACGGC 61.292 61.111 9.97 9.97 42.51 5.68
331 332 2.046700 GGACGGCCGATCCAAACA 60.047 61.111 35.90 0.00 36.15 2.83
332 333 1.673009 GGACGGCCGATCCAAACAA 60.673 57.895 35.90 0.00 36.15 2.83
333 334 1.238625 GGACGGCCGATCCAAACAAA 61.239 55.000 35.90 0.00 36.15 2.83
334 335 0.808755 GACGGCCGATCCAAACAAAT 59.191 50.000 35.90 3.54 34.01 2.32
335 336 2.011222 GACGGCCGATCCAAACAAATA 58.989 47.619 35.90 0.00 34.01 1.40
336 337 2.420722 GACGGCCGATCCAAACAAATAA 59.579 45.455 35.90 0.00 34.01 1.40
337 338 2.820787 ACGGCCGATCCAAACAAATAAA 59.179 40.909 35.90 0.00 34.01 1.40
338 339 3.256136 ACGGCCGATCCAAACAAATAAAA 59.744 39.130 35.90 0.00 34.01 1.52
339 340 4.238514 CGGCCGATCCAAACAAATAAAAA 58.761 39.130 24.07 0.00 34.01 1.94
340 341 4.326009 CGGCCGATCCAAACAAATAAAAAG 59.674 41.667 24.07 0.00 34.01 2.27
341 342 4.092821 GGCCGATCCAAACAAATAAAAAGC 59.907 41.667 0.00 0.00 34.01 3.51
342 343 4.201580 GCCGATCCAAACAAATAAAAAGCG 60.202 41.667 0.00 0.00 0.00 4.68
343 344 4.326009 CCGATCCAAACAAATAAAAAGCGG 59.674 41.667 0.00 0.00 0.00 5.52
344 345 5.157781 CGATCCAAACAAATAAAAAGCGGA 58.842 37.500 0.00 0.00 0.00 5.54
345 346 5.060446 CGATCCAAACAAATAAAAAGCGGAC 59.940 40.000 0.00 0.00 0.00 4.79
346 347 4.291783 TCCAAACAAATAAAAAGCGGACG 58.708 39.130 0.00 0.00 0.00 4.79
347 348 4.036498 TCCAAACAAATAAAAAGCGGACGA 59.964 37.500 0.00 0.00 0.00 4.20
348 349 4.740695 CCAAACAAATAAAAAGCGGACGAA 59.259 37.500 0.00 0.00 0.00 3.85
349 350 5.232414 CCAAACAAATAAAAAGCGGACGAAA 59.768 36.000 0.00 0.00 0.00 3.46
350 351 6.074034 CCAAACAAATAAAAAGCGGACGAAAT 60.074 34.615 0.00 0.00 0.00 2.17
351 352 6.684609 AACAAATAAAAAGCGGACGAAATC 57.315 33.333 0.00 0.00 0.00 2.17
352 353 4.849383 ACAAATAAAAAGCGGACGAAATCG 59.151 37.500 0.48 0.48 46.33 3.34
361 362 2.048877 ACGAAATCGCCGTCCGTT 60.049 55.556 2.15 0.00 44.43 4.44
362 363 1.665599 ACGAAATCGCCGTCCGTTT 60.666 52.632 2.15 0.00 44.43 3.60
363 364 1.225637 CGAAATCGCCGTCCGTTTG 60.226 57.895 0.00 0.00 38.35 2.93
364 365 1.133869 GAAATCGCCGTCCGTTTGG 59.866 57.895 0.00 0.00 38.35 3.28
365 366 2.248274 GAAATCGCCGTCCGTTTGGG 62.248 60.000 0.00 0.00 38.35 4.12
366 367 3.540367 AATCGCCGTCCGTTTGGGT 62.540 57.895 0.00 0.00 38.35 4.51
367 368 3.945304 ATCGCCGTCCGTTTGGGTC 62.945 63.158 0.00 0.00 38.35 4.46
381 382 2.355115 GGTCGGCCCATTGGAGTT 59.645 61.111 3.62 0.00 0.00 3.01
382 383 2.046285 GGTCGGCCCATTGGAGTTG 61.046 63.158 3.62 0.00 0.00 3.16
383 384 2.361104 TCGGCCCATTGGAGTTGC 60.361 61.111 3.62 0.00 0.00 4.17
384 385 2.361610 CGGCCCATTGGAGTTGCT 60.362 61.111 3.62 0.00 0.00 3.91
431 432 2.331265 GTGGTTGACACTTGAGGCC 58.669 57.895 0.00 0.00 46.72 5.19
432 433 0.465460 GTGGTTGACACTTGAGGCCA 60.465 55.000 5.01 0.00 46.72 5.36
433 434 0.465460 TGGTTGACACTTGAGGCCAC 60.465 55.000 5.01 0.00 0.00 5.01
434 435 0.179018 GGTTGACACTTGAGGCCACT 60.179 55.000 5.01 0.00 0.00 4.00
502 504 1.067416 CATCATGCATGCCACAGCC 59.933 57.895 22.25 0.00 38.69 4.85
503 505 2.131709 ATCATGCATGCCACAGCCC 61.132 57.895 22.25 0.00 38.69 5.19
504 506 2.864770 ATCATGCATGCCACAGCCCA 62.865 55.000 22.25 1.33 38.69 5.36
505 507 3.072468 ATGCATGCCACAGCCCAC 61.072 61.111 16.68 0.00 38.69 4.61
506 508 3.890250 ATGCATGCCACAGCCCACA 62.890 57.895 16.68 0.00 38.69 4.17
507 509 3.755628 GCATGCCACAGCCCACAG 61.756 66.667 6.36 0.00 38.69 3.66
508 510 3.755628 CATGCCACAGCCCACAGC 61.756 66.667 0.00 0.00 44.25 4.40
513 515 4.584518 CACAGCCCACAGCCCACA 62.585 66.667 0.00 0.00 45.47 4.17
514 516 4.275508 ACAGCCCACAGCCCACAG 62.276 66.667 0.00 0.00 45.47 3.66
582 584 8.980481 AGGCACTATTATTTTATGCTAACACT 57.020 30.769 0.00 0.00 36.02 3.55
589 591 4.932268 TTTTATGCTAACACTGTACGCC 57.068 40.909 0.00 0.00 0.00 5.68
616 618 4.440987 GACGCAGCGTCGAGTCGA 62.441 66.667 30.89 12.09 46.56 4.20
668 679 5.164233 GCTTCCTTGCTTGGATTTTCTTAC 58.836 41.667 0.00 0.00 35.83 2.34
684 695 5.900339 TTCTTACGCTATTATTTGCTCCG 57.100 39.130 0.00 0.00 0.00 4.63
766 778 2.774007 GCTGTGATGTGAACGTAATGC 58.226 47.619 0.00 0.00 0.00 3.56
806 818 3.756434 ACCAGTAAACAAATCCATGGACG 59.244 43.478 18.99 11.38 0.00 4.79
817 829 1.004560 CATGGACGAGGCACACACT 60.005 57.895 0.00 0.00 0.00 3.55
837 849 1.145819 TTTTGGGCTGTGGCTTTGC 59.854 52.632 0.00 0.00 38.73 3.68
909 921 1.077123 GCACACAGATCAGCACTCAG 58.923 55.000 0.00 0.00 0.00 3.35
929 946 4.961511 ACAAGCCTCGCGTCGCAA 62.962 61.111 18.75 0.00 0.00 4.85
930 947 3.711842 CAAGCCTCGCGTCGCAAA 61.712 61.111 18.75 3.42 0.00 3.68
931 948 3.712881 AAGCCTCGCGTCGCAAAC 61.713 61.111 18.75 3.18 0.00 2.93
964 981 0.741915 GGAGGAACCGACTGAGCTAG 59.258 60.000 0.00 0.00 0.00 3.42
975 992 1.643811 ACTGAGCTAGGAGGAGGTTCT 59.356 52.381 0.00 0.00 0.00 3.01
977 994 1.314730 GAGCTAGGAGGAGGTTCTCG 58.685 60.000 0.00 0.00 34.74 4.04
992 1009 0.179702 TCTCGGAGAAGCTAGCCGTA 59.820 55.000 12.13 8.06 45.02 4.02
1011 1028 0.889186 ACGTGGCAATGGTGAAGACC 60.889 55.000 0.00 0.00 43.48 3.85
1377 1397 3.774702 GCGTTCGACTTCACCGCC 61.775 66.667 0.00 0.00 38.52 6.13
1379 1399 3.110178 GTTCGACTTCACCGCCGG 61.110 66.667 0.00 0.00 0.00 6.13
1380 1400 4.367023 TTCGACTTCACCGCCGGG 62.367 66.667 8.57 0.00 40.11 5.73
1402 1422 4.363990 ACGACAGTCCCAGCGCTG 62.364 66.667 30.52 30.52 38.58 5.18
1602 1622 1.482593 GAGATCGAGGCCTTCTTCCAA 59.517 52.381 6.77 0.00 0.00 3.53
1712 1732 0.462759 GAGGAAGGAGGCGACATTGG 60.463 60.000 0.00 0.00 0.00 3.16
1793 1820 1.527311 GACAACTCAAGCGAAGACCAC 59.473 52.381 0.00 0.00 0.00 4.16
1828 1855 8.607441 TGCATGGTGATAACTATACTTGATTC 57.393 34.615 0.00 0.00 0.00 2.52
1973 2007 8.649841 CAATTGCTTGTTACATCCATGTTAAAG 58.350 33.333 0.00 1.86 41.97 1.85
1976 2010 7.367285 TGCTTGTTACATCCATGTTAAAGAAC 58.633 34.615 0.00 0.00 41.97 3.01
2010 2044 7.853929 GCAATTGCAAGCATATATTTCTTTTGG 59.146 33.333 25.36 0.00 41.59 3.28
2039 2073 0.319900 CCCTCTCGTCAACTGTGTGG 60.320 60.000 0.00 0.00 0.00 4.17
2083 2122 7.217200 TCGAATGATAAGGGATTTCAGTAAGG 58.783 38.462 0.00 0.00 0.00 2.69
2112 2151 2.544685 CTTATCCAGAAGAGTGCACCG 58.455 52.381 14.63 0.00 0.00 4.94
2119 2158 1.276421 AGAAGAGTGCACCGCTACAAT 59.724 47.619 14.63 0.00 0.00 2.71
2194 2233 8.038944 GGACATTTAGGGGGTTAATTCTTTTTC 58.961 37.037 0.00 0.00 0.00 2.29
2204 2243 7.812669 GGGGTTAATTCTTTTTCACACTACATG 59.187 37.037 0.00 0.00 0.00 3.21
2228 2267 4.140924 GGAGGAGGGGGTCAATTTAATCAT 60.141 45.833 0.00 0.00 0.00 2.45
2229 2268 4.808042 AGGAGGGGGTCAATTTAATCATG 58.192 43.478 0.00 0.00 0.00 3.07
2230 2269 3.321968 GGAGGGGGTCAATTTAATCATGC 59.678 47.826 0.00 0.00 0.00 4.06
2231 2270 3.308401 AGGGGGTCAATTTAATCATGCC 58.692 45.455 0.00 0.00 0.00 4.40
2232 2271 2.368548 GGGGGTCAATTTAATCATGCCC 59.631 50.000 0.00 0.00 32.81 5.36
2233 2272 2.368548 GGGGTCAATTTAATCATGCCCC 59.631 50.000 10.29 10.29 40.71 5.80
2234 2273 2.368548 GGGTCAATTTAATCATGCCCCC 59.631 50.000 0.00 0.00 0.00 5.40
2235 2274 2.035832 GGTCAATTTAATCATGCCCCCG 59.964 50.000 0.00 0.00 0.00 5.73
2236 2275 2.693074 GTCAATTTAATCATGCCCCCGT 59.307 45.455 0.00 0.00 0.00 5.28
2237 2276 3.886505 GTCAATTTAATCATGCCCCCGTA 59.113 43.478 0.00 0.00 0.00 4.02
2238 2277 4.339814 GTCAATTTAATCATGCCCCCGTAA 59.660 41.667 0.00 0.00 0.00 3.18
2239 2278 4.956700 TCAATTTAATCATGCCCCCGTAAA 59.043 37.500 0.00 0.00 0.00 2.01
2240 2279 5.422331 TCAATTTAATCATGCCCCCGTAAAA 59.578 36.000 0.00 0.00 0.00 1.52
2241 2280 6.098982 TCAATTTAATCATGCCCCCGTAAAAT 59.901 34.615 0.00 0.00 0.00 1.82
2242 2281 7.287927 TCAATTTAATCATGCCCCCGTAAAATA 59.712 33.333 0.00 0.00 0.00 1.40
2243 2282 7.604657 ATTTAATCATGCCCCCGTAAAATAA 57.395 32.000 0.00 0.00 0.00 1.40
2244 2283 7.419711 TTTAATCATGCCCCCGTAAAATAAA 57.580 32.000 0.00 0.00 0.00 1.40
2245 2284 5.941555 AATCATGCCCCCGTAAAATAAAA 57.058 34.783 0.00 0.00 0.00 1.52
2246 2285 5.941555 ATCATGCCCCCGTAAAATAAAAA 57.058 34.783 0.00 0.00 0.00 1.94
2247 2286 5.941555 TCATGCCCCCGTAAAATAAAAAT 57.058 34.783 0.00 0.00 0.00 1.82
2248 2287 7.604657 ATCATGCCCCCGTAAAATAAAAATA 57.395 32.000 0.00 0.00 0.00 1.40
2249 2288 7.419711 TCATGCCCCCGTAAAATAAAAATAA 57.580 32.000 0.00 0.00 0.00 1.40
2250 2289 7.848128 TCATGCCCCCGTAAAATAAAAATAAA 58.152 30.769 0.00 0.00 0.00 1.40
2251 2290 8.319146 TCATGCCCCCGTAAAATAAAAATAAAA 58.681 29.630 0.00 0.00 0.00 1.52
2252 2291 8.947115 CATGCCCCCGTAAAATAAAAATAAAAA 58.053 29.630 0.00 0.00 0.00 1.94
2253 2292 9.688091 ATGCCCCCGTAAAATAAAAATAAAAAT 57.312 25.926 0.00 0.00 0.00 1.82
2395 2442 3.726291 CCACAACGGTCATTTTCCTTT 57.274 42.857 0.00 0.00 0.00 3.11
2396 2443 4.053469 CCACAACGGTCATTTTCCTTTT 57.947 40.909 0.00 0.00 0.00 2.27
2397 2444 4.048504 CCACAACGGTCATTTTCCTTTTC 58.951 43.478 0.00 0.00 0.00 2.29
2398 2445 4.202111 CCACAACGGTCATTTTCCTTTTCT 60.202 41.667 0.00 0.00 0.00 2.52
2399 2446 5.348164 CACAACGGTCATTTTCCTTTTCTT 58.652 37.500 0.00 0.00 0.00 2.52
2400 2447 5.458779 CACAACGGTCATTTTCCTTTTCTTC 59.541 40.000 0.00 0.00 0.00 2.87
2401 2448 5.126384 ACAACGGTCATTTTCCTTTTCTTCA 59.874 36.000 0.00 0.00 0.00 3.02
2402 2449 5.438761 ACGGTCATTTTCCTTTTCTTCAG 57.561 39.130 0.00 0.00 0.00 3.02
2403 2450 4.887655 ACGGTCATTTTCCTTTTCTTCAGT 59.112 37.500 0.00 0.00 0.00 3.41
2404 2451 5.359860 ACGGTCATTTTCCTTTTCTTCAGTT 59.640 36.000 0.00 0.00 0.00 3.16
2405 2452 6.544564 ACGGTCATTTTCCTTTTCTTCAGTTA 59.455 34.615 0.00 0.00 0.00 2.24
2406 2453 7.230712 ACGGTCATTTTCCTTTTCTTCAGTTAT 59.769 33.333 0.00 0.00 0.00 1.89
2407 2454 8.082242 CGGTCATTTTCCTTTTCTTCAGTTATT 58.918 33.333 0.00 0.00 0.00 1.40
2408 2455 9.764363 GGTCATTTTCCTTTTCTTCAGTTATTT 57.236 29.630 0.00 0.00 0.00 1.40
2410 2457 9.981114 TCATTTTCCTTTTCTTCAGTTATTTCC 57.019 29.630 0.00 0.00 0.00 3.13
2411 2458 9.208022 CATTTTCCTTTTCTTCAGTTATTTCCC 57.792 33.333 0.00 0.00 0.00 3.97
2412 2459 8.547481 TTTTCCTTTTCTTCAGTTATTTCCCT 57.453 30.769 0.00 0.00 0.00 4.20
2413 2460 8.547481 TTTCCTTTTCTTCAGTTATTTCCCTT 57.453 30.769 0.00 0.00 0.00 3.95
2414 2461 8.547481 TTCCTTTTCTTCAGTTATTTCCCTTT 57.453 30.769 0.00 0.00 0.00 3.11
2415 2462 8.547481 TCCTTTTCTTCAGTTATTTCCCTTTT 57.453 30.769 0.00 0.00 0.00 2.27
2416 2463 9.649316 TCCTTTTCTTCAGTTATTTCCCTTTTA 57.351 29.630 0.00 0.00 0.00 1.52
2593 2640 9.814899 TGTTTGATTTTCTTTCATACACATTGT 57.185 25.926 0.00 0.00 32.49 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.058293 TGAGTTTTCCAATCACGCATGTC 60.058 43.478 0.00 0.00 0.00 3.06
1 2 2.884012 TGAGTTTTCCAATCACGCATGT 59.116 40.909 0.00 0.00 0.00 3.21
2 3 3.058016 AGTGAGTTTTCCAATCACGCATG 60.058 43.478 0.00 0.00 46.25 4.06
3 4 3.149196 AGTGAGTTTTCCAATCACGCAT 58.851 40.909 0.00 0.00 46.25 4.73
4 5 2.571212 AGTGAGTTTTCCAATCACGCA 58.429 42.857 0.00 0.00 46.25 5.24
5 6 3.300009 CAAGTGAGTTTTCCAATCACGC 58.700 45.455 0.00 0.00 46.25 5.34
6 7 3.243035 TGCAAGTGAGTTTTCCAATCACG 60.243 43.478 0.00 0.00 46.25 4.35
7 8 4.305989 TGCAAGTGAGTTTTCCAATCAC 57.694 40.909 0.00 0.00 42.91 3.06
8 9 4.998671 TTGCAAGTGAGTTTTCCAATCA 57.001 36.364 0.00 0.00 0.00 2.57
9 10 5.333568 GCAATTGCAAGTGAGTTTTCCAATC 60.334 40.000 29.48 4.16 41.59 2.67
10 11 4.512571 GCAATTGCAAGTGAGTTTTCCAAT 59.487 37.500 29.48 0.00 41.59 3.16
11 12 3.870419 GCAATTGCAAGTGAGTTTTCCAA 59.130 39.130 29.48 0.00 41.59 3.53
12 13 3.456280 GCAATTGCAAGTGAGTTTTCCA 58.544 40.909 29.48 0.00 41.59 3.53
26 27 4.691685 TCAACCAAATCATTCTGCAATTGC 59.308 37.500 23.69 23.69 42.50 3.56
27 28 5.163893 GCTCAACCAAATCATTCTGCAATTG 60.164 40.000 0.00 0.00 0.00 2.32
28 29 4.933400 GCTCAACCAAATCATTCTGCAATT 59.067 37.500 0.00 0.00 0.00 2.32
29 30 4.020928 TGCTCAACCAAATCATTCTGCAAT 60.021 37.500 0.00 0.00 0.00 3.56
30 31 3.321396 TGCTCAACCAAATCATTCTGCAA 59.679 39.130 0.00 0.00 0.00 4.08
31 32 2.892215 TGCTCAACCAAATCATTCTGCA 59.108 40.909 0.00 0.00 0.00 4.41
32 33 3.581024 TGCTCAACCAAATCATTCTGC 57.419 42.857 0.00 0.00 0.00 4.26
33 34 6.695713 CACATATGCTCAACCAAATCATTCTG 59.304 38.462 1.58 0.00 0.00 3.02
34 35 6.183360 CCACATATGCTCAACCAAATCATTCT 60.183 38.462 1.58 0.00 0.00 2.40
35 36 5.981315 CCACATATGCTCAACCAAATCATTC 59.019 40.000 1.58 0.00 0.00 2.67
36 37 5.657745 TCCACATATGCTCAACCAAATCATT 59.342 36.000 1.58 0.00 0.00 2.57
37 38 5.068198 GTCCACATATGCTCAACCAAATCAT 59.932 40.000 1.58 0.00 0.00 2.45
38 39 4.398988 GTCCACATATGCTCAACCAAATCA 59.601 41.667 1.58 0.00 0.00 2.57
39 40 4.641989 AGTCCACATATGCTCAACCAAATC 59.358 41.667 1.58 0.00 0.00 2.17
40 41 4.603131 AGTCCACATATGCTCAACCAAAT 58.397 39.130 1.58 0.00 0.00 2.32
41 42 4.009675 GAGTCCACATATGCTCAACCAAA 58.990 43.478 1.58 0.00 0.00 3.28
42 43 3.008923 TGAGTCCACATATGCTCAACCAA 59.991 43.478 1.58 0.00 35.36 3.67
43 44 2.571202 TGAGTCCACATATGCTCAACCA 59.429 45.455 1.58 0.00 35.36 3.67
44 45 3.266510 TGAGTCCACATATGCTCAACC 57.733 47.619 1.58 0.00 35.36 3.77
45 46 6.072838 CCAATATGAGTCCACATATGCTCAAC 60.073 42.308 12.80 3.29 40.97 3.18
46 47 5.999600 CCAATATGAGTCCACATATGCTCAA 59.000 40.000 12.80 5.61 40.97 3.02
47 48 5.554070 CCAATATGAGTCCACATATGCTCA 58.446 41.667 11.62 11.62 40.97 4.26
48 49 4.394300 GCCAATATGAGTCCACATATGCTC 59.606 45.833 1.58 1.94 40.97 4.26
49 50 4.202493 TGCCAATATGAGTCCACATATGCT 60.202 41.667 1.58 0.00 40.97 3.79
50 51 4.074259 TGCCAATATGAGTCCACATATGC 58.926 43.478 1.58 0.00 40.97 3.14
51 52 5.048504 GGTTGCCAATATGAGTCCACATATG 60.049 44.000 0.00 0.00 40.97 1.78
52 53 5.072741 GGTTGCCAATATGAGTCCACATAT 58.927 41.667 0.00 0.00 42.82 1.78
53 54 4.080072 TGGTTGCCAATATGAGTCCACATA 60.080 41.667 0.00 0.00 37.20 2.29
54 55 3.290710 GGTTGCCAATATGAGTCCACAT 58.709 45.455 0.00 0.00 0.00 3.21
55 56 2.040947 TGGTTGCCAATATGAGTCCACA 59.959 45.455 0.00 0.00 0.00 4.17
56 57 2.722094 TGGTTGCCAATATGAGTCCAC 58.278 47.619 0.00 0.00 0.00 4.02
57 58 3.448093 TTGGTTGCCAATATGAGTCCA 57.552 42.857 0.00 0.00 38.75 4.02
90 91 9.302345 TCACATAGTTTTGCAAACGAATAAAAA 57.698 25.926 12.39 0.00 0.00 1.94
91 92 8.858003 TCACATAGTTTTGCAAACGAATAAAA 57.142 26.923 12.39 0.00 0.00 1.52
92 93 8.858003 TTCACATAGTTTTGCAAACGAATAAA 57.142 26.923 12.39 0.00 0.00 1.40
93 94 8.747666 GTTTCACATAGTTTTGCAAACGAATAA 58.252 29.630 12.39 0.00 0.00 1.40
94 95 7.915923 TGTTTCACATAGTTTTGCAAACGAATA 59.084 29.630 12.39 2.21 0.00 1.75
95 96 6.754209 TGTTTCACATAGTTTTGCAAACGAAT 59.246 30.769 12.39 0.00 0.00 3.34
96 97 6.093404 TGTTTCACATAGTTTTGCAAACGAA 58.907 32.000 12.39 0.00 0.00 3.85
97 98 5.641709 TGTTTCACATAGTTTTGCAAACGA 58.358 33.333 12.39 4.34 0.00 3.85
98 99 5.940603 TGTTTCACATAGTTTTGCAAACG 57.059 34.783 12.39 0.96 0.00 3.60
99 100 9.553418 AAAAATGTTTCACATAGTTTTGCAAAC 57.447 25.926 12.39 7.48 37.97 2.93
142 143 8.785946 GCCGCCCAAATAAATAGTATAGTTTTA 58.214 33.333 0.00 0.00 28.73 1.52
143 144 7.255695 GGCCGCCCAAATAAATAGTATAGTTTT 60.256 37.037 0.00 0.00 28.73 2.43
144 145 6.208007 GGCCGCCCAAATAAATAGTATAGTTT 59.792 38.462 0.00 0.00 28.73 2.66
145 146 5.708697 GGCCGCCCAAATAAATAGTATAGTT 59.291 40.000 0.00 0.00 31.73 2.24
146 147 5.250982 GGCCGCCCAAATAAATAGTATAGT 58.749 41.667 0.00 0.00 0.00 2.12
147 148 4.331717 CGGCCGCCCAAATAAATAGTATAG 59.668 45.833 14.67 0.00 0.00 1.31
148 149 4.020396 TCGGCCGCCCAAATAAATAGTATA 60.020 41.667 23.51 0.00 0.00 1.47
149 150 3.078837 CGGCCGCCCAAATAAATAGTAT 58.921 45.455 14.67 0.00 0.00 2.12
150 151 2.104451 TCGGCCGCCCAAATAAATAGTA 59.896 45.455 23.51 0.00 0.00 1.82
151 152 1.134037 TCGGCCGCCCAAATAAATAGT 60.134 47.619 23.51 0.00 0.00 2.12
152 153 1.600023 TCGGCCGCCCAAATAAATAG 58.400 50.000 23.51 0.00 0.00 1.73
153 154 1.677052 GTTCGGCCGCCCAAATAAATA 59.323 47.619 23.51 0.00 0.00 1.40
154 155 0.458260 GTTCGGCCGCCCAAATAAAT 59.542 50.000 23.51 0.00 0.00 1.40
155 156 0.609681 AGTTCGGCCGCCCAAATAAA 60.610 50.000 23.51 3.41 0.00 1.40
156 157 0.252479 TAGTTCGGCCGCCCAAATAA 59.748 50.000 23.51 4.32 0.00 1.40
157 158 0.470766 ATAGTTCGGCCGCCCAAATA 59.529 50.000 23.51 14.11 0.00 1.40
158 159 0.395173 AATAGTTCGGCCGCCCAAAT 60.395 50.000 23.51 12.08 0.00 2.32
159 160 0.609681 AAATAGTTCGGCCGCCCAAA 60.610 50.000 23.51 6.58 0.00 3.28
160 161 1.001887 AAATAGTTCGGCCGCCCAA 60.002 52.632 23.51 7.04 0.00 4.12
161 162 1.747367 CAAATAGTTCGGCCGCCCA 60.747 57.895 23.51 3.33 0.00 5.36
162 163 2.478033 CCAAATAGTTCGGCCGCCC 61.478 63.158 23.51 13.46 0.00 6.13
163 164 3.107447 CCAAATAGTTCGGCCGCC 58.893 61.111 23.51 13.88 0.00 6.13
164 165 2.407616 GCCAAATAGTTCGGCCGC 59.592 61.111 23.51 7.63 40.07 6.53
167 168 3.297830 AAACAAGCCAAATAGTTCGGC 57.702 42.857 7.90 7.90 46.62 5.54
168 169 6.697892 TGTTTAAAACAAGCCAAATAGTTCGG 59.302 34.615 0.00 0.00 38.72 4.30
169 170 7.687005 TGTTTAAAACAAGCCAAATAGTTCG 57.313 32.000 0.00 0.00 38.72 3.95
177 178 9.780413 GAAATGAAAATGTTTAAAACAAGCCAA 57.220 25.926 0.00 0.00 45.86 4.52
178 179 8.950210 TGAAATGAAAATGTTTAAAACAAGCCA 58.050 25.926 0.00 0.00 45.86 4.75
179 180 9.220635 GTGAAATGAAAATGTTTAAAACAAGCC 57.779 29.630 0.00 0.00 45.86 4.35
180 181 9.766277 TGTGAAATGAAAATGTTTAAAACAAGC 57.234 25.926 0.00 0.00 45.86 4.01
217 218 9.097257 CCGCCTAATTTTACATTGATTTTTCAT 57.903 29.630 0.00 0.00 0.00 2.57
218 219 7.064016 GCCGCCTAATTTTACATTGATTTTTCA 59.936 33.333 0.00 0.00 0.00 2.69
219 220 7.398746 GCCGCCTAATTTTACATTGATTTTTC 58.601 34.615 0.00 0.00 0.00 2.29
220 221 6.315144 GGCCGCCTAATTTTACATTGATTTTT 59.685 34.615 0.71 0.00 0.00 1.94
221 222 5.815222 GGCCGCCTAATTTTACATTGATTTT 59.185 36.000 0.71 0.00 0.00 1.82
222 223 5.105146 TGGCCGCCTAATTTTACATTGATTT 60.105 36.000 11.61 0.00 0.00 2.17
223 224 4.404073 TGGCCGCCTAATTTTACATTGATT 59.596 37.500 11.61 0.00 0.00 2.57
224 225 3.957497 TGGCCGCCTAATTTTACATTGAT 59.043 39.130 11.61 0.00 0.00 2.57
225 226 3.357203 TGGCCGCCTAATTTTACATTGA 58.643 40.909 11.61 0.00 0.00 2.57
226 227 3.705604 CTGGCCGCCTAATTTTACATTG 58.294 45.455 11.61 0.00 0.00 2.82
227 228 2.100749 GCTGGCCGCCTAATTTTACATT 59.899 45.455 11.61 0.00 0.00 2.71
228 229 1.681264 GCTGGCCGCCTAATTTTACAT 59.319 47.619 11.61 0.00 0.00 2.29
229 230 1.099689 GCTGGCCGCCTAATTTTACA 58.900 50.000 11.61 0.00 0.00 2.41
230 231 3.938653 GCTGGCCGCCTAATTTTAC 57.061 52.632 11.61 0.00 0.00 2.01
251 252 2.717485 CATATGTGCAGGCGTGGC 59.283 61.111 8.72 1.33 0.00 5.01
252 253 0.535780 ATCCATATGTGCAGGCGTGG 60.536 55.000 8.72 0.00 0.00 4.94
253 254 1.002142 CAATCCATATGTGCAGGCGTG 60.002 52.381 1.01 1.01 0.00 5.34
254 255 1.134128 TCAATCCATATGTGCAGGCGT 60.134 47.619 1.24 0.00 0.00 5.68
255 256 1.265095 GTCAATCCATATGTGCAGGCG 59.735 52.381 1.24 0.00 0.00 5.52
256 257 1.265095 CGTCAATCCATATGTGCAGGC 59.735 52.381 1.24 0.00 0.00 4.85
257 258 1.265095 GCGTCAATCCATATGTGCAGG 59.735 52.381 1.24 0.00 0.00 4.85
258 259 1.070376 CGCGTCAATCCATATGTGCAG 60.070 52.381 0.00 0.00 0.00 4.41
259 260 0.936600 CGCGTCAATCCATATGTGCA 59.063 50.000 0.00 0.00 0.00 4.57
260 261 0.937304 ACGCGTCAATCCATATGTGC 59.063 50.000 5.58 0.00 0.00 4.57
261 262 2.286359 CCAACGCGTCAATCCATATGTG 60.286 50.000 14.44 1.55 0.00 3.21
262 263 1.939934 CCAACGCGTCAATCCATATGT 59.060 47.619 14.44 0.00 0.00 2.29
263 264 1.264020 CCCAACGCGTCAATCCATATG 59.736 52.381 14.44 3.04 0.00 1.78
264 265 1.593196 CCCAACGCGTCAATCCATAT 58.407 50.000 14.44 0.00 0.00 1.78
265 266 1.092921 GCCCAACGCGTCAATCCATA 61.093 55.000 14.44 0.00 0.00 2.74
266 267 2.406616 GCCCAACGCGTCAATCCAT 61.407 57.895 14.44 0.00 0.00 3.41
267 268 3.053291 GCCCAACGCGTCAATCCA 61.053 61.111 14.44 0.00 0.00 3.41
284 285 4.969196 ATATGGGTCGGCAGCGCG 62.969 66.667 0.00 0.00 0.00 6.86
285 286 3.044305 GATATGGGTCGGCAGCGC 61.044 66.667 0.00 0.00 0.00 5.92
286 287 0.813610 TTTGATATGGGTCGGCAGCG 60.814 55.000 0.00 0.00 0.00 5.18
287 288 1.388547 TTTTGATATGGGTCGGCAGC 58.611 50.000 0.00 0.00 0.00 5.25
288 289 2.752354 TGTTTTTGATATGGGTCGGCAG 59.248 45.455 0.00 0.00 0.00 4.85
289 290 2.752354 CTGTTTTTGATATGGGTCGGCA 59.248 45.455 0.00 0.00 0.00 5.69
290 291 2.099098 CCTGTTTTTGATATGGGTCGGC 59.901 50.000 0.00 0.00 0.00 5.54
291 292 2.687935 CCCTGTTTTTGATATGGGTCGG 59.312 50.000 0.00 0.00 0.00 4.79
292 293 2.099098 GCCCTGTTTTTGATATGGGTCG 59.901 50.000 0.00 0.00 37.09 4.79
293 294 2.099098 CGCCCTGTTTTTGATATGGGTC 59.901 50.000 0.00 0.00 37.09 4.46
294 295 2.099405 CGCCCTGTTTTTGATATGGGT 58.901 47.619 0.00 0.00 37.09 4.51
295 296 1.408702 CCGCCCTGTTTTTGATATGGG 59.591 52.381 0.00 0.00 37.76 4.00
296 297 2.099098 GTCCGCCCTGTTTTTGATATGG 59.901 50.000 0.00 0.00 0.00 2.74
297 298 2.223249 CGTCCGCCCTGTTTTTGATATG 60.223 50.000 0.00 0.00 0.00 1.78
298 299 2.014128 CGTCCGCCCTGTTTTTGATAT 58.986 47.619 0.00 0.00 0.00 1.63
299 300 1.444836 CGTCCGCCCTGTTTTTGATA 58.555 50.000 0.00 0.00 0.00 2.15
300 301 1.241315 CCGTCCGCCCTGTTTTTGAT 61.241 55.000 0.00 0.00 0.00 2.57
301 302 1.894756 CCGTCCGCCCTGTTTTTGA 60.895 57.895 0.00 0.00 0.00 2.69
302 303 2.642700 CCGTCCGCCCTGTTTTTG 59.357 61.111 0.00 0.00 0.00 2.44
303 304 3.292159 GCCGTCCGCCCTGTTTTT 61.292 61.111 0.00 0.00 0.00 1.94
314 315 1.238625 TTTGTTTGGATCGGCCGTCC 61.239 55.000 28.99 28.99 40.66 4.79
315 316 0.808755 ATTTGTTTGGATCGGCCGTC 59.191 50.000 27.15 20.82 40.66 4.79
316 317 2.116827 TATTTGTTTGGATCGGCCGT 57.883 45.000 27.15 12.96 40.66 5.68
317 318 3.495670 TTTATTTGTTTGGATCGGCCG 57.504 42.857 22.12 22.12 40.66 6.13
318 319 4.092821 GCTTTTTATTTGTTTGGATCGGCC 59.907 41.667 0.00 0.00 37.10 6.13
319 320 4.201580 CGCTTTTTATTTGTTTGGATCGGC 60.202 41.667 0.00 0.00 0.00 5.54
320 321 4.326009 CCGCTTTTTATTTGTTTGGATCGG 59.674 41.667 0.00 0.00 0.00 4.18
321 322 5.060446 GTCCGCTTTTTATTTGTTTGGATCG 59.940 40.000 0.00 0.00 0.00 3.69
322 323 5.060446 CGTCCGCTTTTTATTTGTTTGGATC 59.940 40.000 0.00 0.00 0.00 3.36
323 324 4.920927 CGTCCGCTTTTTATTTGTTTGGAT 59.079 37.500 0.00 0.00 0.00 3.41
324 325 4.036498 TCGTCCGCTTTTTATTTGTTTGGA 59.964 37.500 0.00 0.00 0.00 3.53
325 326 4.291783 TCGTCCGCTTTTTATTTGTTTGG 58.708 39.130 0.00 0.00 0.00 3.28
326 327 5.874892 TTCGTCCGCTTTTTATTTGTTTG 57.125 34.783 0.00 0.00 0.00 2.93
327 328 6.129300 CGATTTCGTCCGCTTTTTATTTGTTT 60.129 34.615 0.00 0.00 34.11 2.83
328 329 5.341196 CGATTTCGTCCGCTTTTTATTTGTT 59.659 36.000 0.00 0.00 34.11 2.83
329 330 4.849383 CGATTTCGTCCGCTTTTTATTTGT 59.151 37.500 0.00 0.00 34.11 2.83
330 331 4.258860 GCGATTTCGTCCGCTTTTTATTTG 60.259 41.667 0.00 0.00 46.96 2.32
331 332 3.849708 GCGATTTCGTCCGCTTTTTATTT 59.150 39.130 0.00 0.00 46.96 1.40
332 333 3.422655 GCGATTTCGTCCGCTTTTTATT 58.577 40.909 0.00 0.00 46.96 1.40
333 334 3.047613 GCGATTTCGTCCGCTTTTTAT 57.952 42.857 0.00 0.00 46.96 1.40
334 335 2.513964 GCGATTTCGTCCGCTTTTTA 57.486 45.000 0.00 0.00 46.96 1.52
335 336 3.378013 GCGATTTCGTCCGCTTTTT 57.622 47.368 0.00 0.00 46.96 1.94
344 345 1.665599 AAACGGACGGCGATTTCGT 60.666 52.632 16.62 14.37 44.03 3.85
345 346 1.225637 CAAACGGACGGCGATTTCG 60.226 57.895 16.62 13.70 43.27 3.46
346 347 1.133869 CCAAACGGACGGCGATTTC 59.866 57.895 16.62 0.00 0.00 2.17
347 348 2.329614 CCCAAACGGACGGCGATTT 61.330 57.895 16.62 5.62 0.00 2.17
348 349 2.744709 CCCAAACGGACGGCGATT 60.745 61.111 16.62 0.00 0.00 3.34
349 350 3.945304 GACCCAAACGGACGGCGAT 62.945 63.158 16.62 0.00 34.64 4.58
350 351 4.668118 GACCCAAACGGACGGCGA 62.668 66.667 16.62 0.00 34.64 5.54
364 365 2.046285 CAACTCCAATGGGCCGACC 61.046 63.158 0.00 0.00 40.81 4.79
365 366 2.700773 GCAACTCCAATGGGCCGAC 61.701 63.158 0.00 0.00 0.00 4.79
366 367 2.361104 GCAACTCCAATGGGCCGA 60.361 61.111 0.00 0.00 0.00 5.54
367 368 2.361610 AGCAACTCCAATGGGCCG 60.362 61.111 0.00 0.00 0.00 6.13
368 369 0.613012 AAGAGCAACTCCAATGGGCC 60.613 55.000 0.00 0.00 0.00 5.80
369 370 2.019984 CTAAGAGCAACTCCAATGGGC 58.980 52.381 0.00 0.00 0.00 5.36
370 371 2.019984 GCTAAGAGCAACTCCAATGGG 58.980 52.381 0.00 0.00 41.89 4.00
381 382 3.076621 CTTGGAACATGTGCTAAGAGCA 58.923 45.455 22.36 0.00 45.05 4.26
382 383 3.126000 GTCTTGGAACATGTGCTAAGAGC 59.874 47.826 27.97 19.60 39.49 4.09
383 384 4.318332 TGTCTTGGAACATGTGCTAAGAG 58.682 43.478 27.97 7.63 39.30 2.85
384 385 4.318332 CTGTCTTGGAACATGTGCTAAGA 58.682 43.478 24.70 24.70 39.30 2.10
425 426 0.321919 GAGTGCATCAAGTGGCCTCA 60.322 55.000 3.32 0.00 31.72 3.86
426 427 0.035630 AGAGTGCATCAAGTGGCCTC 60.036 55.000 3.32 0.00 0.00 4.70
427 428 0.322277 CAGAGTGCATCAAGTGGCCT 60.322 55.000 3.32 0.00 0.00 5.19
428 429 1.930908 GCAGAGTGCATCAAGTGGCC 61.931 60.000 0.00 0.00 44.26 5.36
429 430 1.505353 GCAGAGTGCATCAAGTGGC 59.495 57.895 0.00 0.00 44.26 5.01
507 509 1.815421 CGGACATACAGCTGTGGGC 60.815 63.158 29.57 21.99 42.19 5.36
508 510 0.179100 CTCGGACATACAGCTGTGGG 60.179 60.000 29.57 21.70 0.00 4.61
509 511 0.807667 GCTCGGACATACAGCTGTGG 60.808 60.000 29.57 22.06 0.00 4.17
510 512 0.807667 GGCTCGGACATACAGCTGTG 60.808 60.000 29.57 16.03 33.38 3.66
511 513 1.517832 GGCTCGGACATACAGCTGT 59.482 57.895 25.12 25.12 33.38 4.40
512 514 1.589993 CGGCTCGGACATACAGCTG 60.590 63.158 13.48 13.48 33.38 4.24
513 515 2.052690 ACGGCTCGGACATACAGCT 61.053 57.895 0.00 0.00 33.38 4.24
514 516 1.878522 CACGGCTCGGACATACAGC 60.879 63.158 0.00 0.00 0.00 4.40
515 517 1.878522 GCACGGCTCGGACATACAG 60.879 63.158 0.00 0.00 0.00 2.74
589 591 2.256461 GCTGCGTCTTTGCCTTGG 59.744 61.111 0.00 0.00 0.00 3.61
612 614 4.749598 GCTACTCCTACTAAGGTAGTCGAC 59.250 50.000 7.70 7.70 44.09 4.20
613 615 4.406972 TGCTACTCCTACTAAGGTAGTCGA 59.593 45.833 0.00 0.00 44.09 4.20
614 616 4.511082 GTGCTACTCCTACTAAGGTAGTCG 59.489 50.000 0.00 0.00 44.09 4.18
615 617 5.296531 GTGTGCTACTCCTACTAAGGTAGTC 59.703 48.000 0.00 0.00 44.09 2.59
616 618 5.192176 GTGTGCTACTCCTACTAAGGTAGT 58.808 45.833 0.00 0.00 44.09 2.73
625 627 2.482142 GCATCCTGTGTGCTACTCCTAC 60.482 54.545 0.00 0.00 39.45 3.18
652 663 7.801716 ATAATAGCGTAAGAAAATCCAAGCA 57.198 32.000 0.00 0.00 43.02 3.91
653 664 8.958043 CAAATAATAGCGTAAGAAAATCCAAGC 58.042 33.333 0.00 0.00 43.02 4.01
668 679 3.431912 TGCATACGGAGCAAATAATAGCG 59.568 43.478 0.00 0.00 39.39 4.26
702 713 0.317269 ATACAATCCGCGGTCGTACG 60.317 55.000 27.15 9.53 0.00 3.67
806 818 0.385390 CCCAAAACAGTGTGTGCCTC 59.615 55.000 0.00 0.00 0.00 4.70
817 829 0.177604 CAAAGCCACAGCCCAAAACA 59.822 50.000 0.00 0.00 41.25 2.83
837 849 4.153835 CGGGCTACTTCTACTTATAGGACG 59.846 50.000 0.00 0.00 0.00 4.79
909 921 4.430423 CGACGCGAGGCTTGTTGC 62.430 66.667 15.93 0.00 36.51 4.17
920 932 2.724358 GGTTTGGTTTGCGACGCG 60.724 61.111 16.14 3.53 0.00 6.01
929 946 0.321298 CTCCGGTCGATGGTTTGGTT 60.321 55.000 0.00 0.00 0.00 3.67
930 947 1.295423 CTCCGGTCGATGGTTTGGT 59.705 57.895 0.00 0.00 0.00 3.67
931 948 1.449601 CCTCCGGTCGATGGTTTGG 60.450 63.158 0.00 4.75 0.00 3.28
932 949 0.036765 TTCCTCCGGTCGATGGTTTG 60.037 55.000 0.00 0.22 0.00 2.93
933 950 0.036671 GTTCCTCCGGTCGATGGTTT 60.037 55.000 0.00 0.00 0.00 3.27
964 981 1.107945 CTTCTCCGAGAACCTCCTCC 58.892 60.000 6.75 0.00 29.89 4.30
975 992 1.434622 CGTACGGCTAGCTTCTCCGA 61.435 60.000 22.24 7.97 45.53 4.55
977 994 0.248539 CACGTACGGCTAGCTTCTCC 60.249 60.000 21.06 0.00 0.00 3.71
992 1009 0.889186 GGTCTTCACCATTGCCACGT 60.889 55.000 0.00 0.00 43.17 4.49
1020 1037 4.431131 CCACCGCCATTGCTCCCT 62.431 66.667 0.00 0.00 34.43 4.20
1077 1094 2.159085 CCCCTTGTACGTCCTCATCTTC 60.159 54.545 0.00 0.00 0.00 2.87
1146 1163 2.100879 ATATCCGCGTCTTCTGCCCC 62.101 60.000 4.92 0.00 0.00 5.80
1361 1381 3.467119 CGGCGGTGAAGTCGAACG 61.467 66.667 0.00 0.00 42.53 3.95
1380 1400 4.436998 CTGGGACTGTCGTCGGCC 62.437 72.222 1.07 0.00 41.16 6.13
1446 1466 2.882876 CAGTACTCCGGGGTGACG 59.117 66.667 20.02 0.00 0.00 4.35
1477 1497 0.532862 CTCACCGGCGAGGCATTATT 60.533 55.000 11.86 0.00 46.52 1.40
1478 1498 1.069765 CTCACCGGCGAGGCATTAT 59.930 57.895 11.86 0.00 46.52 1.28
1479 1499 2.499205 CTCACCGGCGAGGCATTA 59.501 61.111 11.86 0.00 46.52 1.90
1584 1604 2.488952 GATTGGAAGAAGGCCTCGATC 58.511 52.381 5.23 4.10 0.00 3.69
1602 1622 1.452651 CTCCATGCACTTGGGCGAT 60.453 57.895 6.50 0.00 37.37 4.58
1671 1691 1.812922 GCTGCACTCGTCCTCCATG 60.813 63.158 0.00 0.00 0.00 3.66
1793 1820 1.536940 TCACCATGCATGACCAGTTG 58.463 50.000 28.31 11.52 0.00 3.16
1834 1861 9.814899 TGTGTACAAAGAATCACATCAATTTTT 57.185 25.926 0.00 0.00 36.17 1.94
1835 1862 9.467258 CTGTGTACAAAGAATCACATCAATTTT 57.533 29.630 7.32 0.00 39.51 1.82
1900 1934 3.756434 TGCCTTAAAACATGTAGCTCCAC 59.244 43.478 0.00 0.00 0.00 4.02
2010 2044 2.434359 CGAGAGGGCCCGTTGTTC 60.434 66.667 18.44 8.20 0.00 3.18
2023 2057 0.104120 CACCCACACAGTTGACGAGA 59.896 55.000 0.00 0.00 0.00 4.04
2024 2058 0.179084 ACACCCACACAGTTGACGAG 60.179 55.000 0.00 0.00 0.00 4.18
2039 2073 3.192844 TCGAAGTGAATAGTCCAGACACC 59.807 47.826 0.00 0.00 32.76 4.16
2083 2122 6.549952 CACTCTTCTGGATAAGCATGAAAAC 58.450 40.000 0.00 0.00 0.00 2.43
2112 2151 5.590104 AAAATCCGCACAAAAATTGTAGC 57.410 34.783 0.00 2.35 43.23 3.58
2119 2158 4.187694 AGCTTCAAAAATCCGCACAAAAA 58.812 34.783 0.00 0.00 0.00 1.94
2194 2233 0.833287 CCCTCCTCCCATGTAGTGTG 59.167 60.000 0.00 0.00 0.00 3.82
2204 2243 1.603634 TAAATTGACCCCCTCCTCCC 58.396 55.000 0.00 0.00 0.00 4.30
2255 2294 9.357652 CGACATCAAAGGTGAATGATTAATTTT 57.642 29.630 0.00 0.00 37.30 1.82
2256 2295 7.489113 GCGACATCAAAGGTGAATGATTAATTT 59.511 33.333 0.00 0.00 37.30 1.82
2257 2296 6.974622 GCGACATCAAAGGTGAATGATTAATT 59.025 34.615 0.00 0.00 37.30 1.40
2258 2297 6.460123 GGCGACATCAAAGGTGAATGATTAAT 60.460 38.462 0.00 0.00 37.30 1.40
2259 2298 5.163663 GGCGACATCAAAGGTGAATGATTAA 60.164 40.000 0.00 0.00 37.30 1.40
2260 2299 4.335315 GGCGACATCAAAGGTGAATGATTA 59.665 41.667 0.00 0.00 37.30 1.75
2261 2300 3.129287 GGCGACATCAAAGGTGAATGATT 59.871 43.478 0.00 0.00 37.30 2.57
2262 2301 2.684881 GGCGACATCAAAGGTGAATGAT 59.315 45.455 0.00 0.00 37.30 2.45
2263 2302 2.083774 GGCGACATCAAAGGTGAATGA 58.916 47.619 0.00 0.00 37.30 2.57
2264 2303 2.086869 AGGCGACATCAAAGGTGAATG 58.913 47.619 0.00 0.00 37.30 2.67
2265 2304 2.086869 CAGGCGACATCAAAGGTGAAT 58.913 47.619 0.00 0.00 37.30 2.57
2380 2427 4.887655 ACTGAAGAAAAGGAAAATGACCGT 59.112 37.500 0.00 0.00 0.00 4.83
2390 2437 8.547481 AAAAGGGAAATAACTGAAGAAAAGGA 57.453 30.769 0.00 0.00 0.00 3.36
2567 2614 9.814899 ACAATGTGTATGAAAGAAAATCAAACA 57.185 25.926 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.