Multiple sequence alignment - TraesCS5A01G148300

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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 TraesCS5A01G148300 chr5A 100.000 2938 0 0 1 2938 325997927 325994990 0.000000e+00 5426.0
1 TraesCS5A01G148300 chr5A 95.782 403 17 0 1 403 364204355 364204757 0.000000e+00 651.0
2 TraesCS5A01G148300 chr5A 95.297 404 19 0 1 404 457056082 457055679 2.470000e-180 641.0
3 TraesCS5A01G148300 chr5A 95.285 403 19 0 1 403 156206728 156207130 8.880000e-180 640.0
4 TraesCS5A01G148300 chr5B 90.954 2609 102 44 401 2938 275174502 275171957 0.000000e+00 3387.0
5 TraesCS5A01G148300 chr5D 92.595 1310 47 27 402 1689 231320932 231322213 0.000000e+00 1836.0
6 TraesCS5A01G148300 chr5D 93.016 1260 43 15 1710 2938 231322269 231323514 0.000000e+00 1797.0
7 TraesCS5A01G148300 chr4A 94.307 404 22 1 1 404 65803639 65803237 4.160000e-173 617.0
8 TraesCS5A01G148300 chr4A 94.045 403 24 0 1 403 684018429 684018831 1.940000e-171 612.0
9 TraesCS5A01G148300 chr4A 94.881 293 15 0 1380 1672 477834102 477833810 2.670000e-125 459.0
10 TraesCS5A01G148300 chr4A 89.286 112 12 0 1390 1501 477830667 477830556 1.100000e-29 141.0
11 TraesCS5A01G148300 chr2A 94.293 403 23 0 1 403 372739354 372739756 4.160000e-173 617.0
12 TraesCS5A01G148300 chr2A 94.264 401 23 0 1 401 491535147 491535547 5.380000e-172 614.0
13 TraesCS5A01G148300 chr7A 94.458 397 22 0 1 397 261085863 261085467 1.940000e-171 612.0
14 TraesCS5A01G148300 chr4B 93.187 411 26 2 1 410 361998783 361999192 1.160000e-168 603.0
15 TraesCS5A01G148300 chr4B 94.702 302 16 0 1371 1672 139769014 139769315 1.230000e-128 470.0
16 TraesCS5A01G148300 chr4D 94.371 302 17 0 1371 1672 98481761 98482062 5.740000e-127 464.0
17 TraesCS5A01G148300 chr1A 84.328 134 13 2 401 533 458410220 458410094 1.110000e-24 124.0
18 TraesCS5A01G148300 chr7B 79.104 134 20 2 401 533 490310719 490310593 5.220000e-13 86.1
19 TraesCS5A01G148300 chr7B 95.349 43 2 0 491 533 131372148 131372190 5.250000e-08 69.4


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 TraesCS5A01G148300 chr5A 325994990 325997927 2937 True 5426.0 5426 100.0000 1 2938 1 chr5A.!!$R1 2937
1 TraesCS5A01G148300 chr5B 275171957 275174502 2545 True 3387.0 3387 90.9540 401 2938 1 chr5B.!!$R1 2537
2 TraesCS5A01G148300 chr5D 231320932 231323514 2582 False 1816.5 1836 92.8055 402 2938 2 chr5D.!!$F1 2536
3 TraesCS5A01G148300 chr4A 477830556 477834102 3546 True 300.0 459 92.0835 1380 1672 2 chr4A.!!$R2 292

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
269 270 0.039618 GACAGGATGGGGCAAAAGGA 59.96 55.0 0.0 0.0 43.62 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2241 2385 1.748493 TGTTCTTTGCTGTGGTGAACC 59.252 47.619 0.0 0.0 36.98 3.62 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
18 19 2.009108 CCGTGAGATGCGTGATTGG 58.991 57.895 0.00 0.00 0.00 3.16
19 20 1.349627 CGTGAGATGCGTGATTGGC 59.650 57.895 0.00 0.00 0.00 4.52
20 21 1.360931 CGTGAGATGCGTGATTGGCA 61.361 55.000 0.00 0.00 45.71 4.92
21 22 0.097674 GTGAGATGCGTGATTGGCAC 59.902 55.000 0.00 0.00 44.23 5.01
34 35 5.063180 TGATTGGCACACTCATTTGAATC 57.937 39.130 0.00 0.00 43.06 2.52
35 36 3.940209 TTGGCACACTCATTTGAATCC 57.060 42.857 0.00 0.00 39.29 3.01
36 37 3.159213 TGGCACACTCATTTGAATCCT 57.841 42.857 0.00 0.00 0.00 3.24
37 38 3.084039 TGGCACACTCATTTGAATCCTC 58.916 45.455 0.00 0.00 0.00 3.71
38 39 3.084039 GGCACACTCATTTGAATCCTCA 58.916 45.455 0.00 0.00 0.00 3.86
39 40 3.507233 GGCACACTCATTTGAATCCTCAA 59.493 43.478 0.00 0.00 39.87 3.02
41 42 9.253295 TTGGCACACTCATTTGAATCCTCAAAA 62.253 37.037 4.54 0.00 46.55 2.44
50 51 6.729690 TTTGAATCCTCAAAATGACTTGGT 57.270 33.333 0.00 0.00 46.24 3.67
51 52 6.729690 TTGAATCCTCAAAATGACTTGGTT 57.270 33.333 0.00 0.00 38.65 3.67
52 53 6.088016 TGAATCCTCAAAATGACTTGGTTG 57.912 37.500 0.00 0.00 0.00 3.77
53 54 5.832595 TGAATCCTCAAAATGACTTGGTTGA 59.167 36.000 0.00 0.00 0.00 3.18
54 55 5.972107 ATCCTCAAAATGACTTGGTTGAG 57.028 39.130 5.48 5.48 44.25 3.02
55 56 3.569701 TCCTCAAAATGACTTGGTTGAGC 59.430 43.478 6.72 0.00 43.62 4.26
56 57 3.318839 CCTCAAAATGACTTGGTTGAGCA 59.681 43.478 6.72 0.00 43.62 4.26
57 58 4.293415 CTCAAAATGACTTGGTTGAGCAC 58.707 43.478 0.00 0.00 40.22 4.40
58 59 3.044986 CAAAATGACTTGGTTGAGCACG 58.955 45.455 0.00 0.00 0.00 5.34
59 60 1.967319 AATGACTTGGTTGAGCACGT 58.033 45.000 0.00 0.00 0.00 4.49
60 61 1.229428 ATGACTTGGTTGAGCACGTG 58.771 50.000 12.28 12.28 0.00 4.49
61 62 0.107897 TGACTTGGTTGAGCACGTGT 60.108 50.000 18.38 3.69 0.00 4.49
62 63 0.304705 GACTTGGTTGAGCACGTGTG 59.695 55.000 18.38 0.00 0.00 3.82
63 64 1.095228 ACTTGGTTGAGCACGTGTGG 61.095 55.000 18.38 0.00 0.00 4.17
64 65 1.785041 CTTGGTTGAGCACGTGTGGG 61.785 60.000 18.38 0.00 0.00 4.61
65 66 2.110213 GGTTGAGCACGTGTGGGA 59.890 61.111 18.38 0.00 0.00 4.37
66 67 1.302511 GGTTGAGCACGTGTGGGAT 60.303 57.895 18.38 0.00 0.00 3.85
67 68 1.298859 GGTTGAGCACGTGTGGGATC 61.299 60.000 18.38 8.42 0.00 3.36
68 69 0.602638 GTTGAGCACGTGTGGGATCA 60.603 55.000 18.38 10.83 0.00 2.92
69 70 0.602638 TTGAGCACGTGTGGGATCAC 60.603 55.000 18.38 0.00 43.87 3.06
79 80 0.532115 GTGGGATCACATTGGCAACC 59.468 55.000 0.00 0.00 43.13 3.77
80 81 0.113972 TGGGATCACATTGGCAACCA 59.886 50.000 0.00 0.00 0.00 3.67
81 82 3.667922 GTGGGATCACATTGGCAACCAA 61.668 50.000 0.00 0.77 43.13 3.67
112 113 9.521841 TGTATTGGTCCATTTTATGTTTAGTCA 57.478 29.630 0.00 0.00 0.00 3.41
115 116 8.698973 TTGGTCCATTTTATGTTTAGTCAAGA 57.301 30.769 0.00 0.00 0.00 3.02
116 117 8.106247 TGGTCCATTTTATGTTTAGTCAAGAC 57.894 34.615 0.00 0.00 0.00 3.01
117 118 7.721842 TGGTCCATTTTATGTTTAGTCAAGACA 59.278 33.333 2.72 0.00 0.00 3.41
118 119 8.573035 GGTCCATTTTATGTTTAGTCAAGACAA 58.427 33.333 2.72 0.00 0.00 3.18
128 129 8.781067 TGTTTAGTCAAGACAATTTCGATTTG 57.219 30.769 2.72 6.98 0.00 2.32
129 130 7.860373 TGTTTAGTCAAGACAATTTCGATTTGG 59.140 33.333 11.83 0.00 0.00 3.28
130 131 7.504924 TTAGTCAAGACAATTTCGATTTGGT 57.495 32.000 11.83 0.00 0.00 3.67
131 132 6.391227 AGTCAAGACAATTTCGATTTGGTT 57.609 33.333 11.83 4.09 0.00 3.67
132 133 6.208644 AGTCAAGACAATTTCGATTTGGTTG 58.791 36.000 11.83 13.00 0.00 3.77
133 134 5.977129 GTCAAGACAATTTCGATTTGGTTGT 59.023 36.000 16.73 10.87 35.87 3.32
134 135 7.012894 AGTCAAGACAATTTCGATTTGGTTGTA 59.987 33.333 16.73 8.34 33.55 2.41
135 136 7.646130 GTCAAGACAATTTCGATTTGGTTGTAA 59.354 33.333 16.73 0.00 33.55 2.41
136 137 8.191446 TCAAGACAATTTCGATTTGGTTGTAAA 58.809 29.630 16.73 0.00 33.55 2.01
137 138 8.812329 CAAGACAATTTCGATTTGGTTGTAAAA 58.188 29.630 11.83 0.00 33.55 1.52
138 139 8.347729 AGACAATTTCGATTTGGTTGTAAAAC 57.652 30.769 11.83 0.00 33.55 2.43
139 140 8.194769 AGACAATTTCGATTTGGTTGTAAAACT 58.805 29.630 11.83 0.44 32.01 2.66
140 141 9.453325 GACAATTTCGATTTGGTTGTAAAACTA 57.547 29.630 11.83 0.00 32.01 2.24
141 142 9.974980 ACAATTTCGATTTGGTTGTAAAACTAT 57.025 25.926 11.83 0.00 32.01 2.12
207 208 8.620116 AATTTTCAGACAAATATTTGGGTTGG 57.380 30.769 27.43 14.36 42.34 3.77
208 209 6.985653 TTTCAGACAAATATTTGGGTTGGA 57.014 33.333 27.43 16.09 42.34 3.53
209 210 6.985653 TTCAGACAAATATTTGGGTTGGAA 57.014 33.333 27.43 19.70 42.34 3.53
210 211 6.985653 TCAGACAAATATTTGGGTTGGAAA 57.014 33.333 27.43 8.25 42.34 3.13
211 212 6.754193 TCAGACAAATATTTGGGTTGGAAAC 58.246 36.000 27.43 10.22 42.94 2.78
212 213 6.553100 TCAGACAAATATTTGGGTTGGAAACT 59.447 34.615 27.43 6.71 43.10 2.66
213 214 7.726291 TCAGACAAATATTTGGGTTGGAAACTA 59.274 33.333 27.43 7.14 43.10 2.24
214 215 8.028938 CAGACAAATATTTGGGTTGGAAACTAG 58.971 37.037 27.43 2.64 43.10 2.57
215 216 7.728532 AGACAAATATTTGGGTTGGAAACTAGT 59.271 33.333 27.43 5.67 43.10 2.57
216 217 8.257602 ACAAATATTTGGGTTGGAAACTAGTT 57.742 30.769 27.43 1.12 43.10 2.24
217 218 8.710239 ACAAATATTTGGGTTGGAAACTAGTTT 58.290 29.630 27.43 20.67 43.10 2.66
231 232 9.323985 TGGAAACTAGTTTTGATGAAAATTTGG 57.676 29.630 21.40 0.00 33.63 3.28
232 233 8.773645 GGAAACTAGTTTTGATGAAAATTTGGG 58.226 33.333 21.40 0.00 33.63 4.12
233 234 7.728847 AACTAGTTTTGATGAAAATTTGGGC 57.271 32.000 1.12 0.00 33.63 5.36
234 235 6.825610 ACTAGTTTTGATGAAAATTTGGGCA 58.174 32.000 0.00 0.00 33.63 5.36
235 236 7.452562 ACTAGTTTTGATGAAAATTTGGGCAT 58.547 30.769 0.00 0.00 33.63 4.40
236 237 7.938490 ACTAGTTTTGATGAAAATTTGGGCATT 59.062 29.630 0.00 0.00 33.63 3.56
237 238 7.585579 AGTTTTGATGAAAATTTGGGCATTT 57.414 28.000 0.00 0.00 33.63 2.32
238 239 8.009622 AGTTTTGATGAAAATTTGGGCATTTT 57.990 26.923 0.00 0.00 38.75 1.82
239 240 8.476447 AGTTTTGATGAAAATTTGGGCATTTTT 58.524 25.926 0.00 0.00 36.64 1.94
240 241 8.541312 GTTTTGATGAAAATTTGGGCATTTTTG 58.459 29.630 0.00 0.00 36.64 2.44
241 242 6.328641 TGATGAAAATTTGGGCATTTTTGG 57.671 33.333 0.00 0.00 36.64 3.28
242 243 4.581077 TGAAAATTTGGGCATTTTTGGC 57.419 36.364 0.00 0.00 36.64 4.52
249 250 1.079888 GGCATTTTTGGCCCTGACG 60.080 57.895 0.00 0.00 45.87 4.35
250 251 1.079888 GCATTTTTGGCCCTGACGG 60.080 57.895 0.00 0.00 0.00 4.79
251 252 1.531739 GCATTTTTGGCCCTGACGGA 61.532 55.000 0.00 0.00 0.00 4.69
252 253 0.243636 CATTTTTGGCCCTGACGGAC 59.756 55.000 0.00 0.00 42.05 4.79
261 262 2.903357 CTGACGGACAGGATGGGG 59.097 66.667 0.00 0.00 43.62 4.96
262 263 3.391665 CTGACGGACAGGATGGGGC 62.392 68.421 0.00 0.00 43.62 5.80
263 264 3.399181 GACGGACAGGATGGGGCA 61.399 66.667 0.00 0.00 43.62 5.36
264 265 2.933287 ACGGACAGGATGGGGCAA 60.933 61.111 0.00 0.00 43.62 4.52
265 266 2.354729 CGGACAGGATGGGGCAAA 59.645 61.111 0.00 0.00 43.62 3.68
266 267 1.304052 CGGACAGGATGGGGCAAAA 60.304 57.895 0.00 0.00 43.62 2.44
267 268 1.315257 CGGACAGGATGGGGCAAAAG 61.315 60.000 0.00 0.00 43.62 2.27
268 269 0.972471 GGACAGGATGGGGCAAAAGG 60.972 60.000 0.00 0.00 43.62 3.11
269 270 0.039618 GACAGGATGGGGCAAAAGGA 59.960 55.000 0.00 0.00 43.62 3.36
270 271 0.712380 ACAGGATGGGGCAAAAGGAT 59.288 50.000 0.00 0.00 43.62 3.24
271 272 1.117150 CAGGATGGGGCAAAAGGATG 58.883 55.000 0.00 0.00 0.00 3.51
272 273 0.688749 AGGATGGGGCAAAAGGATGC 60.689 55.000 0.00 0.00 45.67 3.91
306 307 4.818863 CATGGCCACCGCATCCCA 62.819 66.667 8.16 0.00 36.38 4.37
307 308 4.511246 ATGGCCACCGCATCCCAG 62.511 66.667 8.16 0.00 36.38 4.45
311 312 3.716195 CCACCGCATCCCAGGACA 61.716 66.667 0.00 0.00 0.00 4.02
312 313 2.436646 CACCGCATCCCAGGACAC 60.437 66.667 0.00 0.00 0.00 3.67
313 314 4.082523 ACCGCATCCCAGGACACG 62.083 66.667 3.74 3.74 0.00 4.49
317 318 4.838152 CATCCCAGGACACGCCCG 62.838 72.222 0.00 0.00 37.37 6.13
331 332 3.943691 CCCGGACACGACCCCAAA 61.944 66.667 0.73 0.00 44.60 3.28
332 333 2.349755 CCGGACACGACCCCAAAT 59.650 61.111 0.00 0.00 44.60 2.32
333 334 1.743995 CCGGACACGACCCCAAATC 60.744 63.158 0.00 0.00 44.60 2.17
334 335 1.743995 CGGACACGACCCCAAATCC 60.744 63.158 0.00 0.00 44.60 3.01
335 336 1.378119 GGACACGACCCCAAATCCC 60.378 63.158 0.00 0.00 0.00 3.85
336 337 1.683441 GACACGACCCCAAATCCCT 59.317 57.895 0.00 0.00 0.00 4.20
337 338 0.906775 GACACGACCCCAAATCCCTA 59.093 55.000 0.00 0.00 0.00 3.53
338 339 1.489230 GACACGACCCCAAATCCCTAT 59.511 52.381 0.00 0.00 0.00 2.57
339 340 1.489230 ACACGACCCCAAATCCCTATC 59.511 52.381 0.00 0.00 0.00 2.08
340 341 1.137697 ACGACCCCAAATCCCTATCC 58.862 55.000 0.00 0.00 0.00 2.59
341 342 1.136828 CGACCCCAAATCCCTATCCA 58.863 55.000 0.00 0.00 0.00 3.41
342 343 1.493022 CGACCCCAAATCCCTATCCAA 59.507 52.381 0.00 0.00 0.00 3.53
343 344 2.092103 CGACCCCAAATCCCTATCCAAA 60.092 50.000 0.00 0.00 0.00 3.28
344 345 3.296854 GACCCCAAATCCCTATCCAAAC 58.703 50.000 0.00 0.00 0.00 2.93
345 346 2.306847 CCCCAAATCCCTATCCAAACG 58.693 52.381 0.00 0.00 0.00 3.60
346 347 2.306847 CCCAAATCCCTATCCAAACGG 58.693 52.381 0.00 0.00 0.00 4.44
347 348 2.092103 CCCAAATCCCTATCCAAACGGA 60.092 50.000 0.00 0.00 36.85 4.69
348 349 3.436470 CCCAAATCCCTATCCAAACGGAT 60.436 47.826 0.00 0.00 45.62 4.18
349 350 4.202524 CCCAAATCCCTATCCAAACGGATA 60.203 45.833 1.44 1.44 41.76 2.59
357 358 3.560636 ATCCAAACGGATAGAACCCAG 57.439 47.619 0.00 0.00 41.76 4.45
358 359 2.542550 TCCAAACGGATAGAACCCAGA 58.457 47.619 0.00 0.00 0.00 3.86
359 360 2.235402 TCCAAACGGATAGAACCCAGAC 59.765 50.000 0.00 0.00 0.00 3.51
360 361 2.027561 CCAAACGGATAGAACCCAGACA 60.028 50.000 0.00 0.00 0.00 3.41
361 362 3.558321 CCAAACGGATAGAACCCAGACAA 60.558 47.826 0.00 0.00 0.00 3.18
362 363 4.069304 CAAACGGATAGAACCCAGACAAA 58.931 43.478 0.00 0.00 0.00 2.83
363 364 4.360951 AACGGATAGAACCCAGACAAAA 57.639 40.909 0.00 0.00 0.00 2.44
364 365 3.671716 ACGGATAGAACCCAGACAAAAC 58.328 45.455 0.00 0.00 0.00 2.43
365 366 2.671396 CGGATAGAACCCAGACAAAACG 59.329 50.000 0.00 0.00 0.00 3.60
366 367 3.007635 GGATAGAACCCAGACAAAACGG 58.992 50.000 0.00 0.00 0.00 4.44
367 368 3.307199 GGATAGAACCCAGACAAAACGGA 60.307 47.826 0.00 0.00 0.00 4.69
368 369 1.963172 AGAACCCAGACAAAACGGAC 58.037 50.000 0.00 0.00 0.00 4.79
369 370 0.584876 GAACCCAGACAAAACGGACG 59.415 55.000 0.00 0.00 0.00 4.79
370 371 0.107557 AACCCAGACAAAACGGACGT 60.108 50.000 0.00 0.00 0.00 4.34
371 372 0.531311 ACCCAGACAAAACGGACGTC 60.531 55.000 7.13 7.13 0.00 4.34
372 373 1.226030 CCCAGACAAAACGGACGTCC 61.226 60.000 25.28 25.28 0.00 4.79
387 388 3.427425 TCCGTTTGGGATTGCGCG 61.427 61.111 0.00 0.00 40.94 6.86
388 389 4.474846 CCGTTTGGGATTGCGCGG 62.475 66.667 8.83 0.00 38.47 6.46
389 390 3.732892 CGTTTGGGATTGCGCGGT 61.733 61.111 8.83 0.00 0.00 5.68
390 391 2.126502 GTTTGGGATTGCGCGGTG 60.127 61.111 8.83 0.00 0.00 4.94
391 392 3.369400 TTTGGGATTGCGCGGTGG 61.369 61.111 8.83 0.00 0.00 4.61
392 393 3.851897 TTTGGGATTGCGCGGTGGA 62.852 57.895 8.83 0.00 0.00 4.02
393 394 4.776322 TGGGATTGCGCGGTGGAG 62.776 66.667 8.83 0.00 0.00 3.86
394 395 4.778143 GGGATTGCGCGGTGGAGT 62.778 66.667 8.83 0.00 0.00 3.85
395 396 2.746277 GGATTGCGCGGTGGAGTT 60.746 61.111 8.83 0.00 0.00 3.01
396 397 2.480555 GATTGCGCGGTGGAGTTG 59.519 61.111 8.83 0.00 0.00 3.16
397 398 3.039202 GATTGCGCGGTGGAGTTGG 62.039 63.158 8.83 0.00 0.00 3.77
414 415 5.012328 AGTTGGCCTAATTCTTCTAGTCG 57.988 43.478 3.32 0.00 0.00 4.18
416 417 5.655532 AGTTGGCCTAATTCTTCTAGTCGTA 59.344 40.000 3.32 0.00 0.00 3.43
444 446 3.555966 CAAACTTTGGAGGACTCAAGGT 58.444 45.455 1.32 0.00 36.26 3.50
487 489 5.183014 GTCAGGACCAAAGGTTGTTTTAG 57.817 43.478 0.00 0.00 35.25 1.85
488 490 4.885325 GTCAGGACCAAAGGTTGTTTTAGA 59.115 41.667 0.00 0.00 35.25 2.10
489 491 5.008712 GTCAGGACCAAAGGTTGTTTTAGAG 59.991 44.000 0.00 0.00 35.25 2.43
490 492 4.887655 CAGGACCAAAGGTTGTTTTAGAGT 59.112 41.667 0.00 0.00 35.25 3.24
491 493 5.359860 CAGGACCAAAGGTTGTTTTAGAGTT 59.640 40.000 0.00 0.00 35.25 3.01
492 494 5.955959 AGGACCAAAGGTTGTTTTAGAGTTT 59.044 36.000 0.00 0.00 35.25 2.66
493 495 7.067737 CAGGACCAAAGGTTGTTTTAGAGTTTA 59.932 37.037 0.00 0.00 35.25 2.01
558 560 8.736751 TCCTACAAGAATTAATTTCGCAAAAC 57.263 30.769 1.43 0.00 39.46 2.43
589 594 6.105333 GGCATGTGCATAAAAATCCTTACAA 58.895 36.000 7.36 0.00 44.36 2.41
804 824 1.269309 CGCTCCAAGATCCGACCTTAG 60.269 57.143 0.00 0.00 0.00 2.18
871 891 6.583427 TGTAATTTCGATACGATAATCGGTGG 59.417 38.462 15.62 0.00 46.81 4.61
948 968 0.173708 GCGACTAGCCAGTGTAGCTT 59.826 55.000 0.00 0.00 41.83 3.74
949 969 1.799548 GCGACTAGCCAGTGTAGCTTC 60.800 57.143 0.00 0.00 41.83 3.86
950 970 1.532090 CGACTAGCCAGTGTAGCTTCG 60.532 57.143 0.00 0.98 41.83 3.79
951 971 1.473278 GACTAGCCAGTGTAGCTTCGT 59.527 52.381 0.00 0.00 41.83 3.85
973 997 1.686052 GATCTTCCGCTCCTGTCATCT 59.314 52.381 0.00 0.00 0.00 2.90
976 1000 0.532573 TTCCGCTCCTGTCATCTGTC 59.467 55.000 0.00 0.00 0.00 3.51
982 1006 1.905215 CTCCTGTCATCTGTCCTTGGT 59.095 52.381 0.00 0.00 0.00 3.67
1271 1304 4.570663 GCAGTCGTCGCCCGCTAT 62.571 66.667 0.00 0.00 36.19 2.97
1284 1323 2.244651 CGCTATTAGCCCACCGTGC 61.245 63.158 10.04 0.00 38.18 5.34
1285 1324 2.244651 GCTATTAGCCCACCGTGCG 61.245 63.158 4.21 0.00 34.48 5.34
1286 1325 1.143183 CTATTAGCCCACCGTGCGT 59.857 57.895 0.00 0.00 0.00 5.24
1698 1742 5.350633 CCACATTGCTCTTTTGACTTTGAA 58.649 37.500 0.00 0.00 0.00 2.69
1703 1747 7.765360 ACATTGCTCTTTTGACTTTGAATTTGA 59.235 29.630 0.00 0.00 0.00 2.69
1706 1750 9.814899 TTGCTCTTTTGACTTTGAATTTGAATA 57.185 25.926 0.00 0.00 0.00 1.75
1707 1751 9.985730 TGCTCTTTTGACTTTGAATTTGAATAT 57.014 25.926 0.00 0.00 0.00 1.28
1739 1818 8.355169 TCTCTTGAGTTTGAATTTGAATTGAGG 58.645 33.333 0.00 0.00 0.00 3.86
1826 1907 2.501492 GCCAGCTTCATCAGGCAAT 58.499 52.632 5.66 0.00 46.26 3.56
1894 1990 6.627395 TGACCTACTAATTGGTTGTGTTTG 57.373 37.500 0.00 0.00 36.59 2.93
1904 2000 4.630894 TGGTTGTGTTTGTCTGATGTTC 57.369 40.909 0.00 0.00 0.00 3.18
1905 2001 4.269183 TGGTTGTGTTTGTCTGATGTTCT 58.731 39.130 0.00 0.00 0.00 3.01
1906 2002 5.432645 TGGTTGTGTTTGTCTGATGTTCTA 58.567 37.500 0.00 0.00 0.00 2.10
1953 2057 2.026641 CTTGATTGATGCCAACCGGAT 58.973 47.619 9.46 0.00 34.72 4.18
1965 2069 3.550974 CCGGATCGGGGATTCAGT 58.449 61.111 11.44 0.00 44.15 3.41
1968 2072 1.623811 CCGGATCGGGGATTCAGTTAT 59.376 52.381 11.44 0.00 44.15 1.89
2347 2513 8.870242 GTGAATGTAACACGATAAACTTTACC 57.130 34.615 0.00 0.00 0.00 2.85
2377 2543 5.353111 CCAAAATGAGCATATGCATGACAA 58.647 37.500 28.62 8.25 45.16 3.18
2608 3155 6.883756 TGTGGTAGATAACATCTTTTCATGCA 59.116 34.615 0.00 0.00 40.76 3.96
2870 4659 3.821033 CCTCTCGTGATGTTTTCCCTTTT 59.179 43.478 0.00 0.00 0.00 2.27
2871 4660 4.083271 CCTCTCGTGATGTTTTCCCTTTTC 60.083 45.833 0.00 0.00 0.00 2.29
2872 4661 4.714632 TCTCGTGATGTTTTCCCTTTTCT 58.285 39.130 0.00 0.00 0.00 2.52
2873 4662 5.130350 TCTCGTGATGTTTTCCCTTTTCTT 58.870 37.500 0.00 0.00 0.00 2.52
2874 4663 5.592688 TCTCGTGATGTTTTCCCTTTTCTTT 59.407 36.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.349627 GCCAATCACGCATCTCACG 59.650 57.895 0.00 0.00 0.00 4.35
2 3 0.097674 GTGCCAATCACGCATCTCAC 59.902 55.000 0.00 0.00 38.76 3.51
3 4 2.470156 GTGCCAATCACGCATCTCA 58.530 52.632 0.00 0.00 38.76 3.27
11 12 3.921119 TCAAATGAGTGTGCCAATCAC 57.079 42.857 7.35 0.00 41.15 3.06
12 13 4.082081 GGATTCAAATGAGTGTGCCAATCA 60.082 41.667 7.59 7.59 42.48 2.57
13 14 4.159135 AGGATTCAAATGAGTGTGCCAATC 59.841 41.667 0.00 0.00 0.00 2.67
14 15 4.091549 AGGATTCAAATGAGTGTGCCAAT 58.908 39.130 0.00 0.00 0.00 3.16
15 16 3.499338 AGGATTCAAATGAGTGTGCCAA 58.501 40.909 0.00 0.00 0.00 4.52
16 17 3.084039 GAGGATTCAAATGAGTGTGCCA 58.916 45.455 0.00 0.00 0.00 4.92
17 18 3.084039 TGAGGATTCAAATGAGTGTGCC 58.916 45.455 0.00 0.00 0.00 5.01
18 19 4.771590 TTGAGGATTCAAATGAGTGTGC 57.228 40.909 0.00 0.00 40.26 4.57
28 29 6.323482 TCAACCAAGTCATTTTGAGGATTCAA 59.677 34.615 0.00 0.00 41.44 2.69
29 30 5.832595 TCAACCAAGTCATTTTGAGGATTCA 59.167 36.000 0.00 0.00 0.00 2.57
30 31 6.331369 TCAACCAAGTCATTTTGAGGATTC 57.669 37.500 0.00 0.00 0.00 2.52
31 32 5.279156 GCTCAACCAAGTCATTTTGAGGATT 60.279 40.000 11.15 0.00 43.44 3.01
32 33 4.219288 GCTCAACCAAGTCATTTTGAGGAT 59.781 41.667 11.15 0.00 43.44 3.24
33 34 3.569701 GCTCAACCAAGTCATTTTGAGGA 59.430 43.478 11.15 0.00 43.44 3.71
34 35 3.318839 TGCTCAACCAAGTCATTTTGAGG 59.681 43.478 11.15 0.00 43.44 3.86
35 36 4.293415 GTGCTCAACCAAGTCATTTTGAG 58.707 43.478 5.93 5.93 45.19 3.02
36 37 3.243035 CGTGCTCAACCAAGTCATTTTGA 60.243 43.478 0.00 0.00 0.00 2.69
37 38 3.044986 CGTGCTCAACCAAGTCATTTTG 58.955 45.455 0.00 0.00 0.00 2.44
38 39 2.687935 ACGTGCTCAACCAAGTCATTTT 59.312 40.909 0.00 0.00 0.00 1.82
39 40 2.033299 CACGTGCTCAACCAAGTCATTT 59.967 45.455 0.82 0.00 0.00 2.32
40 41 1.603802 CACGTGCTCAACCAAGTCATT 59.396 47.619 0.82 0.00 0.00 2.57
41 42 1.229428 CACGTGCTCAACCAAGTCAT 58.771 50.000 0.82 0.00 0.00 3.06
42 43 0.107897 ACACGTGCTCAACCAAGTCA 60.108 50.000 17.22 0.00 0.00 3.41
43 44 0.304705 CACACGTGCTCAACCAAGTC 59.695 55.000 17.22 0.00 0.00 3.01
44 45 1.095228 CCACACGTGCTCAACCAAGT 61.095 55.000 17.22 0.00 0.00 3.16
45 46 1.648720 CCACACGTGCTCAACCAAG 59.351 57.895 17.22 0.00 0.00 3.61
46 47 1.821759 CCCACACGTGCTCAACCAA 60.822 57.895 17.22 0.00 0.00 3.67
47 48 2.050836 ATCCCACACGTGCTCAACCA 62.051 55.000 17.22 0.00 0.00 3.67
48 49 1.298859 GATCCCACACGTGCTCAACC 61.299 60.000 17.22 0.00 0.00 3.77
49 50 0.602638 TGATCCCACACGTGCTCAAC 60.603 55.000 17.22 3.93 0.00 3.18
50 51 0.602638 GTGATCCCACACGTGCTCAA 60.603 55.000 17.22 0.00 42.72 3.02
51 52 1.005037 GTGATCCCACACGTGCTCA 60.005 57.895 17.22 8.26 42.72 4.26
52 53 3.876300 GTGATCCCACACGTGCTC 58.124 61.111 17.22 5.64 42.72 4.26
60 61 0.532115 GGTTGCCAATGTGATCCCAC 59.468 55.000 0.00 0.00 43.46 4.61
61 62 0.113972 TGGTTGCCAATGTGATCCCA 59.886 50.000 0.00 0.00 0.00 4.37
62 63 1.265236 TTGGTTGCCAATGTGATCCC 58.735 50.000 0.00 0.00 38.75 3.85
86 87 9.521841 TGACTAAACATAAAATGGACCAATACA 57.478 29.630 0.00 0.00 33.60 2.29
89 90 9.308000 TCTTGACTAAACATAAAATGGACCAAT 57.692 29.630 0.00 0.00 33.60 3.16
90 91 8.573035 GTCTTGACTAAACATAAAATGGACCAA 58.427 33.333 0.00 0.00 33.60 3.67
91 92 7.721842 TGTCTTGACTAAACATAAAATGGACCA 59.278 33.333 0.00 0.00 33.60 4.02
92 93 8.106247 TGTCTTGACTAAACATAAAATGGACC 57.894 34.615 2.35 0.00 33.60 4.46
102 103 9.398170 CAAATCGAAATTGTCTTGACTAAACAT 57.602 29.630 6.23 0.00 0.00 2.71
103 104 7.860373 CCAAATCGAAATTGTCTTGACTAAACA 59.140 33.333 11.83 0.00 0.00 2.83
104 105 7.860872 ACCAAATCGAAATTGTCTTGACTAAAC 59.139 33.333 11.83 0.00 0.00 2.01
105 106 7.936584 ACCAAATCGAAATTGTCTTGACTAAA 58.063 30.769 11.83 0.00 0.00 1.85
106 107 7.504924 ACCAAATCGAAATTGTCTTGACTAA 57.495 32.000 11.83 0.00 0.00 2.24
107 108 7.012894 ACAACCAAATCGAAATTGTCTTGACTA 59.987 33.333 18.66 0.00 0.00 2.59
108 109 6.183360 ACAACCAAATCGAAATTGTCTTGACT 60.183 34.615 18.66 5.18 0.00 3.41
109 110 5.977129 ACAACCAAATCGAAATTGTCTTGAC 59.023 36.000 18.66 0.00 0.00 3.18
110 111 6.142818 ACAACCAAATCGAAATTGTCTTGA 57.857 33.333 18.66 0.00 0.00 3.02
111 112 7.922505 TTACAACCAAATCGAAATTGTCTTG 57.077 32.000 11.83 13.19 35.26 3.02
112 113 8.813282 GTTTTACAACCAAATCGAAATTGTCTT 58.187 29.630 11.83 2.61 35.26 3.01
113 114 8.194769 AGTTTTACAACCAAATCGAAATTGTCT 58.805 29.630 11.83 0.97 35.26 3.41
114 115 8.347729 AGTTTTACAACCAAATCGAAATTGTC 57.652 30.769 11.83 0.00 35.26 3.18
115 116 9.974980 ATAGTTTTACAACCAAATCGAAATTGT 57.025 25.926 11.83 9.75 37.30 2.71
181 182 9.717942 CCAACCCAAATATTTGTCTGAAAATTA 57.282 29.630 23.24 0.00 36.45 1.40
182 183 8.435982 TCCAACCCAAATATTTGTCTGAAAATT 58.564 29.630 23.24 6.19 36.45 1.82
183 184 7.972301 TCCAACCCAAATATTTGTCTGAAAAT 58.028 30.769 23.24 2.23 36.45 1.82
184 185 7.366847 TCCAACCCAAATATTTGTCTGAAAA 57.633 32.000 23.24 4.39 36.45 2.29
185 186 6.985653 TCCAACCCAAATATTTGTCTGAAA 57.014 33.333 23.24 5.66 36.45 2.69
186 187 6.985653 TTCCAACCCAAATATTTGTCTGAA 57.014 33.333 23.24 15.56 36.45 3.02
187 188 6.553100 AGTTTCCAACCCAAATATTTGTCTGA 59.447 34.615 23.24 11.50 36.45 3.27
188 189 6.758254 AGTTTCCAACCCAAATATTTGTCTG 58.242 36.000 23.24 16.79 36.45 3.51
189 190 6.994421 AGTTTCCAACCCAAATATTTGTCT 57.006 33.333 23.24 7.96 36.45 3.41
190 191 7.892609 ACTAGTTTCCAACCCAAATATTTGTC 58.107 34.615 23.24 5.79 36.45 3.18
191 192 7.849322 ACTAGTTTCCAACCCAAATATTTGT 57.151 32.000 23.24 6.48 36.45 2.83
192 193 9.554395 AAAACTAGTTTCCAACCCAAATATTTG 57.446 29.630 20.78 19.40 33.57 2.32
193 194 9.554395 CAAAACTAGTTTCCAACCCAAATATTT 57.446 29.630 20.78 0.00 31.45 1.40
194 195 8.929487 TCAAAACTAGTTTCCAACCCAAATATT 58.071 29.630 20.78 0.00 31.45 1.28
195 196 8.485578 TCAAAACTAGTTTCCAACCCAAATAT 57.514 30.769 20.78 0.00 31.45 1.28
196 197 7.899648 TCAAAACTAGTTTCCAACCCAAATA 57.100 32.000 20.78 0.00 31.45 1.40
197 198 6.800072 TCAAAACTAGTTTCCAACCCAAAT 57.200 33.333 20.78 0.00 31.45 2.32
198 199 6.381420 TCATCAAAACTAGTTTCCAACCCAAA 59.619 34.615 20.78 0.00 31.45 3.28
199 200 5.894393 TCATCAAAACTAGTTTCCAACCCAA 59.106 36.000 20.78 2.21 31.45 4.12
200 201 5.450453 TCATCAAAACTAGTTTCCAACCCA 58.550 37.500 20.78 0.56 31.45 4.51
201 202 6.399639 TTCATCAAAACTAGTTTCCAACCC 57.600 37.500 20.78 0.00 31.45 4.11
202 203 8.887036 ATTTTCATCAAAACTAGTTTCCAACC 57.113 30.769 20.78 0.00 34.24 3.77
205 206 9.323985 CCAAATTTTCATCAAAACTAGTTTCCA 57.676 29.630 20.78 10.93 34.24 3.53
206 207 8.773645 CCCAAATTTTCATCAAAACTAGTTTCC 58.226 33.333 20.78 0.00 34.24 3.13
207 208 8.282592 GCCCAAATTTTCATCAAAACTAGTTTC 58.717 33.333 20.78 0.00 34.24 2.78
208 209 7.772757 TGCCCAAATTTTCATCAAAACTAGTTT 59.227 29.630 15.22 15.22 34.24 2.66
209 210 7.278875 TGCCCAAATTTTCATCAAAACTAGTT 58.721 30.769 1.12 1.12 34.24 2.24
210 211 6.825610 TGCCCAAATTTTCATCAAAACTAGT 58.174 32.000 0.00 0.00 34.24 2.57
211 212 7.910441 ATGCCCAAATTTTCATCAAAACTAG 57.090 32.000 0.00 0.00 34.24 2.57
212 213 8.688747 AAATGCCCAAATTTTCATCAAAACTA 57.311 26.923 0.00 0.00 34.24 2.24
213 214 7.585579 AAATGCCCAAATTTTCATCAAAACT 57.414 28.000 0.00 0.00 34.24 2.66
214 215 8.541312 CAAAAATGCCCAAATTTTCATCAAAAC 58.459 29.630 0.00 0.00 38.49 2.43
215 216 7.709613 CCAAAAATGCCCAAATTTTCATCAAAA 59.290 29.630 0.00 0.00 38.49 2.44
216 217 7.208080 CCAAAAATGCCCAAATTTTCATCAAA 58.792 30.769 0.00 0.00 38.49 2.69
217 218 6.737899 GCCAAAAATGCCCAAATTTTCATCAA 60.738 34.615 0.00 0.00 38.49 2.57
218 219 5.278858 GCCAAAAATGCCCAAATTTTCATCA 60.279 36.000 0.00 0.00 38.49 3.07
219 220 5.162794 GCCAAAAATGCCCAAATTTTCATC 58.837 37.500 0.00 0.00 38.49 2.92
220 221 4.021280 GGCCAAAAATGCCCAAATTTTCAT 60.021 37.500 0.00 0.00 43.33 2.57
221 222 3.320256 GGCCAAAAATGCCCAAATTTTCA 59.680 39.130 0.00 0.00 43.33 2.69
222 223 3.911868 GGCCAAAAATGCCCAAATTTTC 58.088 40.909 0.00 0.00 43.33 2.29
232 233 1.079888 CCGTCAGGGCCAAAAATGC 60.080 57.895 6.18 0.00 0.00 3.56
233 234 0.243636 GTCCGTCAGGGCCAAAAATG 59.756 55.000 6.18 0.00 35.69 2.32
234 235 0.178975 TGTCCGTCAGGGCCAAAAAT 60.179 50.000 6.18 0.00 42.85 1.82
235 236 0.821711 CTGTCCGTCAGGGCCAAAAA 60.822 55.000 6.18 0.00 42.85 1.94
236 237 1.228124 CTGTCCGTCAGGGCCAAAA 60.228 57.895 6.18 0.00 42.85 2.44
237 238 2.429930 CTGTCCGTCAGGGCCAAA 59.570 61.111 6.18 0.00 42.85 3.28
244 245 2.903357 CCCCATCCTGTCCGTCAG 59.097 66.667 0.00 0.00 43.27 3.51
245 246 3.399181 GCCCCATCCTGTCCGTCA 61.399 66.667 0.00 0.00 0.00 4.35
246 247 2.478335 TTTGCCCCATCCTGTCCGTC 62.478 60.000 0.00 0.00 0.00 4.79
247 248 2.075355 TTTTGCCCCATCCTGTCCGT 62.075 55.000 0.00 0.00 0.00 4.69
248 249 1.304052 TTTTGCCCCATCCTGTCCG 60.304 57.895 0.00 0.00 0.00 4.79
249 250 0.972471 CCTTTTGCCCCATCCTGTCC 60.972 60.000 0.00 0.00 0.00 4.02
250 251 0.039618 TCCTTTTGCCCCATCCTGTC 59.960 55.000 0.00 0.00 0.00 3.51
251 252 0.712380 ATCCTTTTGCCCCATCCTGT 59.288 50.000 0.00 0.00 0.00 4.00
252 253 1.117150 CATCCTTTTGCCCCATCCTG 58.883 55.000 0.00 0.00 0.00 3.86
253 254 0.688749 GCATCCTTTTGCCCCATCCT 60.689 55.000 0.00 0.00 36.60 3.24
254 255 1.825341 GCATCCTTTTGCCCCATCC 59.175 57.895 0.00 0.00 36.60 3.51
255 256 1.322538 ACGCATCCTTTTGCCCCATC 61.323 55.000 0.00 0.00 39.52 3.51
256 257 1.305213 ACGCATCCTTTTGCCCCAT 60.305 52.632 0.00 0.00 39.52 4.00
257 258 1.976474 GACGCATCCTTTTGCCCCA 60.976 57.895 0.00 0.00 39.52 4.96
258 259 2.710902 GGACGCATCCTTTTGCCCC 61.711 63.158 0.00 0.00 42.45 5.80
259 260 2.885113 GGACGCATCCTTTTGCCC 59.115 61.111 0.00 0.00 42.45 5.36
260 261 2.485122 CGGACGCATCCTTTTGCC 59.515 61.111 0.00 0.00 43.73 4.52
261 262 2.202479 GCGGACGCATCCTTTTGC 60.202 61.111 12.31 0.00 43.73 3.68
289 290 4.818863 TGGGATGCGGTGGCCATG 62.819 66.667 9.72 6.07 38.85 3.66
290 291 4.511246 CTGGGATGCGGTGGCCAT 62.511 66.667 9.72 0.00 38.85 4.40
294 295 3.716195 TGTCCTGGGATGCGGTGG 61.716 66.667 0.00 0.00 0.00 4.61
295 296 2.436646 GTGTCCTGGGATGCGGTG 60.437 66.667 0.00 0.00 0.00 4.94
296 297 4.082523 CGTGTCCTGGGATGCGGT 62.083 66.667 0.00 0.00 0.00 5.68
300 301 4.838152 CGGGCGTGTCCTGGGATG 62.838 72.222 0.00 0.00 37.58 3.51
314 315 3.262448 ATTTGGGGTCGTGTCCGGG 62.262 63.158 0.00 0.00 33.95 5.73
315 316 1.743995 GATTTGGGGTCGTGTCCGG 60.744 63.158 0.00 0.00 33.95 5.14
316 317 1.743995 GGATTTGGGGTCGTGTCCG 60.744 63.158 0.00 0.00 0.00 4.79
317 318 1.378119 GGGATTTGGGGTCGTGTCC 60.378 63.158 0.00 0.00 0.00 4.02
318 319 0.906775 TAGGGATTTGGGGTCGTGTC 59.093 55.000 0.00 0.00 0.00 3.67
319 320 1.489230 GATAGGGATTTGGGGTCGTGT 59.511 52.381 0.00 0.00 0.00 4.49
320 321 1.202770 GGATAGGGATTTGGGGTCGTG 60.203 57.143 0.00 0.00 0.00 4.35
321 322 1.137697 GGATAGGGATTTGGGGTCGT 58.862 55.000 0.00 0.00 0.00 4.34
322 323 1.136828 TGGATAGGGATTTGGGGTCG 58.863 55.000 0.00 0.00 0.00 4.79
323 324 3.296854 GTTTGGATAGGGATTTGGGGTC 58.703 50.000 0.00 0.00 0.00 4.46
324 325 2.357777 CGTTTGGATAGGGATTTGGGGT 60.358 50.000 0.00 0.00 0.00 4.95
325 326 2.306847 CGTTTGGATAGGGATTTGGGG 58.693 52.381 0.00 0.00 0.00 4.96
326 327 2.092103 TCCGTTTGGATAGGGATTTGGG 60.092 50.000 0.00 0.00 40.17 4.12
327 328 3.290948 TCCGTTTGGATAGGGATTTGG 57.709 47.619 0.00 0.00 40.17 3.28
339 340 2.027561 TGTCTGGGTTCTATCCGTTTGG 60.028 50.000 0.00 0.00 0.00 3.28
340 341 3.328382 TGTCTGGGTTCTATCCGTTTG 57.672 47.619 0.00 0.00 0.00 2.93
341 342 4.360951 TTTGTCTGGGTTCTATCCGTTT 57.639 40.909 0.00 0.00 0.00 3.60
342 343 4.070009 GTTTTGTCTGGGTTCTATCCGTT 58.930 43.478 0.00 0.00 0.00 4.44
343 344 3.671716 GTTTTGTCTGGGTTCTATCCGT 58.328 45.455 0.00 0.00 0.00 4.69
344 345 2.671396 CGTTTTGTCTGGGTTCTATCCG 59.329 50.000 0.00 0.00 0.00 4.18
345 346 3.007635 CCGTTTTGTCTGGGTTCTATCC 58.992 50.000 0.00 0.00 0.00 2.59
346 347 3.683340 GTCCGTTTTGTCTGGGTTCTATC 59.317 47.826 0.00 0.00 0.00 2.08
347 348 3.671716 GTCCGTTTTGTCTGGGTTCTAT 58.328 45.455 0.00 0.00 0.00 1.98
348 349 2.546373 CGTCCGTTTTGTCTGGGTTCTA 60.546 50.000 0.00 0.00 0.00 2.10
349 350 1.808891 CGTCCGTTTTGTCTGGGTTCT 60.809 52.381 0.00 0.00 0.00 3.01
350 351 0.584876 CGTCCGTTTTGTCTGGGTTC 59.415 55.000 0.00 0.00 0.00 3.62
351 352 0.107557 ACGTCCGTTTTGTCTGGGTT 60.108 50.000 0.00 0.00 0.00 4.11
352 353 0.531311 GACGTCCGTTTTGTCTGGGT 60.531 55.000 3.51 0.00 0.00 4.51
353 354 1.226030 GGACGTCCGTTTTGTCTGGG 61.226 60.000 20.85 0.00 33.21 4.45
354 355 2.231820 GGACGTCCGTTTTGTCTGG 58.768 57.895 20.85 0.00 33.21 3.86
365 366 1.918868 GCAATCCCAAACGGACGTCC 61.919 60.000 25.28 25.28 46.09 4.79
366 367 1.500396 GCAATCCCAAACGGACGTC 59.500 57.895 7.13 7.13 46.09 4.34
367 368 2.322081 CGCAATCCCAAACGGACGT 61.322 57.895 0.00 0.00 46.09 4.34
368 369 2.478746 CGCAATCCCAAACGGACG 59.521 61.111 0.00 0.00 46.09 4.79
369 370 2.178273 GCGCAATCCCAAACGGAC 59.822 61.111 0.30 0.00 46.09 4.79
371 372 4.474846 CCGCGCAATCCCAAACGG 62.475 66.667 8.75 0.00 0.00 4.44
372 373 3.732892 ACCGCGCAATCCCAAACG 61.733 61.111 8.75 0.00 0.00 3.60
373 374 2.126502 CACCGCGCAATCCCAAAC 60.127 61.111 8.75 0.00 0.00 2.93
374 375 3.369400 CCACCGCGCAATCCCAAA 61.369 61.111 8.75 0.00 0.00 3.28
375 376 4.337177 TCCACCGCGCAATCCCAA 62.337 61.111 8.75 0.00 0.00 4.12
376 377 4.776322 CTCCACCGCGCAATCCCA 62.776 66.667 8.75 0.00 0.00 4.37
377 378 4.778143 ACTCCACCGCGCAATCCC 62.778 66.667 8.75 0.00 0.00 3.85
378 379 2.746277 AACTCCACCGCGCAATCC 60.746 61.111 8.75 0.00 0.00 3.01
379 380 2.480555 CAACTCCACCGCGCAATC 59.519 61.111 8.75 0.00 0.00 2.67
380 381 3.055719 CCAACTCCACCGCGCAAT 61.056 61.111 8.75 0.00 0.00 3.56
384 385 2.869503 ATTAGGCCAACTCCACCGCG 62.870 60.000 5.01 0.00 0.00 6.46
385 386 0.679960 AATTAGGCCAACTCCACCGC 60.680 55.000 5.01 0.00 0.00 5.68
386 387 1.065418 AGAATTAGGCCAACTCCACCG 60.065 52.381 5.01 0.00 0.00 4.94
387 388 2.808906 AGAATTAGGCCAACTCCACC 57.191 50.000 5.01 0.00 0.00 4.61
388 389 3.956744 AGAAGAATTAGGCCAACTCCAC 58.043 45.455 5.01 0.00 0.00 4.02
389 390 4.783227 ACTAGAAGAATTAGGCCAACTCCA 59.217 41.667 5.01 0.00 0.00 3.86
390 391 5.360649 ACTAGAAGAATTAGGCCAACTCC 57.639 43.478 5.01 0.00 0.00 3.85
391 392 5.044558 CGACTAGAAGAATTAGGCCAACTC 58.955 45.833 5.01 0.00 0.00 3.01
392 393 4.466726 ACGACTAGAAGAATTAGGCCAACT 59.533 41.667 5.01 0.00 0.00 3.16
393 394 4.756502 ACGACTAGAAGAATTAGGCCAAC 58.243 43.478 5.01 0.00 0.00 3.77
394 395 6.726490 ATACGACTAGAAGAATTAGGCCAA 57.274 37.500 5.01 0.00 0.00 4.52
395 396 6.726490 AATACGACTAGAAGAATTAGGCCA 57.274 37.500 5.01 0.00 0.00 5.36
396 397 7.041984 CCAAAATACGACTAGAAGAATTAGGCC 60.042 40.741 0.00 0.00 0.00 5.19
397 398 7.518529 GCCAAAATACGACTAGAAGAATTAGGC 60.519 40.741 0.00 5.31 0.00 3.93
398 399 7.494625 TGCCAAAATACGACTAGAAGAATTAGG 59.505 37.037 0.00 0.00 0.00 2.69
399 400 8.420374 TGCCAAAATACGACTAGAAGAATTAG 57.580 34.615 0.00 0.00 0.00 1.73
414 415 4.988540 GTCCTCCAAAGTTTGCCAAAATAC 59.011 41.667 10.25 0.00 0.00 1.89
416 417 3.711190 AGTCCTCCAAAGTTTGCCAAAAT 59.289 39.130 10.25 0.00 0.00 1.82
444 446 1.614051 CCAGGCCATACTGCAGTTTGA 60.614 52.381 31.27 14.02 37.16 2.69
475 477 6.018180 CAGCGTCTAAACTCTAAAACAACCTT 60.018 38.462 0.00 0.00 0.00 3.50
550 552 0.749649 ATGCCCACTTTGTTTTGCGA 59.250 45.000 0.00 0.00 0.00 5.10
558 560 3.316071 TTTATGCACATGCCCACTTTG 57.684 42.857 0.49 0.00 41.18 2.77
683 701 5.245531 TGTCATTGTGGAGTTAGGAACATC 58.754 41.667 0.00 0.00 0.00 3.06
804 824 1.889573 GCGGGGCATTGCTCTAGTC 60.890 63.158 8.71 0.00 0.00 2.59
871 891 5.333721 GCTTCTCGATTTATAGCTTGAAGCC 60.334 44.000 14.45 0.00 45.16 4.35
973 997 0.679505 CTTCTCGACCACCAAGGACA 59.320 55.000 0.00 0.00 41.22 4.02
976 1000 1.376037 GCCTTCTCGACCACCAAGG 60.376 63.158 0.00 0.00 45.67 3.61
982 1006 1.101635 ATCGATCGCCTTCTCGACCA 61.102 55.000 11.09 0.00 45.63 4.02
1263 1296 2.281553 GGTGGGCTAATAGCGGGC 60.282 66.667 6.15 0.00 43.62 6.13
1270 1303 2.125269 GACGCACGGTGGGCTAAT 60.125 61.111 23.15 5.47 33.10 1.73
1271 1304 3.583276 CTGACGCACGGTGGGCTAA 62.583 63.158 23.15 9.46 33.10 3.09
1641 1680 2.419851 GCAGATGAAGAGGACTTGAGGG 60.420 54.545 0.00 0.00 36.39 4.30
1739 1818 2.094390 TCCAGCTGCAAATCATTTGAGC 60.094 45.455 14.65 17.42 43.26 4.26
1884 1980 4.900635 AGAACATCAGACAAACACAACC 57.099 40.909 0.00 0.00 0.00 3.77
1894 1990 9.552114 CATGAAAAACAAGATAGAACATCAGAC 57.448 33.333 0.00 0.00 0.00 3.51
1904 2000 6.809689 TCAATGCTGCATGAAAAACAAGATAG 59.190 34.615 17.00 0.00 0.00 2.08
1905 2001 6.587226 GTCAATGCTGCATGAAAAACAAGATA 59.413 34.615 17.00 0.00 0.00 1.98
1906 2002 5.407387 GTCAATGCTGCATGAAAAACAAGAT 59.593 36.000 17.00 0.00 0.00 2.40
2049 2153 4.248859 CACAGGTGATGCAGCCTATATAC 58.751 47.826 0.00 0.00 33.07 1.47
2050 2154 3.306989 GCACAGGTGATGCAGCCTATATA 60.307 47.826 0.00 0.00 42.88 0.86
2195 2339 3.804325 TCTTCTCGTTGAAAGCTGAACAG 59.196 43.478 0.00 0.00 33.79 3.16
2241 2385 1.748493 TGTTCTTTGCTGTGGTGAACC 59.252 47.619 0.00 0.00 36.98 3.62
2242 2386 2.423538 AGTGTTCTTTGCTGTGGTGAAC 59.576 45.455 0.00 0.00 37.92 3.18
2249 2413 3.743521 TGCTGATAGTGTTCTTTGCTGT 58.256 40.909 0.00 0.00 0.00 4.40
2337 2503 2.257691 TGGCTGTGCGGTAAAGTTTA 57.742 45.000 0.00 0.00 0.00 2.01
2347 2513 0.108992 ATGCTCATTTTGGCTGTGCG 60.109 50.000 0.00 0.00 36.24 5.34
2377 2543 3.618594 GCATATATCATGTCGTCGCCAAT 59.381 43.478 0.00 0.00 0.00 3.16
2490 3037 9.983804 CAATGCATCAATATAGATGTCATGTAC 57.016 33.333 0.00 0.00 45.58 2.90
2622 3908 9.751542 CTTGTTGTTGGTTGGTATTGTAATAAA 57.248 29.630 0.00 0.00 0.00 1.40
2870 4659 2.290514 CCTCCACAAGGCATGAGAAAGA 60.291 50.000 0.00 0.00 38.67 2.52
2871 4660 2.089980 CCTCCACAAGGCATGAGAAAG 58.910 52.381 0.00 0.00 38.67 2.62
2872 4661 1.272092 CCCTCCACAAGGCATGAGAAA 60.272 52.381 0.00 0.00 44.71 2.52
2873 4662 0.329261 CCCTCCACAAGGCATGAGAA 59.671 55.000 0.00 0.00 44.71 2.87
2874 4663 0.547471 TCCCTCCACAAGGCATGAGA 60.547 55.000 0.00 0.00 44.71 3.27


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

AutoCloner maintained by Alex Coulton.