Multiple sequence alignment - TraesCS1D01G178200

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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 TraesCS1D01G178200 chr1D 100.000 2648 0 0 1 2648 253191296 253193943 0.000000e+00 4891.0
1 TraesCS1D01G178200 chr1D 96.875 32 1 0 281 312 10162205 10162174 1.000000e-03 54.7
2 TraesCS1D01G178200 chr1D 100.000 28 0 0 281 308 10147629 10147602 5.000000e-03 52.8
3 TraesCS1D01G178200 chr1B 89.941 2018 117 45 665 2648 359225952 359223987 0.000000e+00 2523.0
4 TraesCS1D01G178200 chr1B 92.473 279 12 5 357 631 359226299 359226026 8.890000e-105 390.0
5 TraesCS1D01G178200 chr1B 94.286 35 2 0 239 273 667268122 667268088 1.000000e-03 54.7
6 TraesCS1D01G178200 chr1A 92.051 1711 61 28 322 2005 325031752 325033414 0.000000e+00 2337.0
7 TraesCS1D01G178200 chr1A 91.875 320 16 8 2248 2563 325034441 325034754 3.130000e-119 438.0
8 TraesCS1D01G178200 chr1A 94.413 179 10 0 2053 2231 325034193 325034371 2.600000e-70 276.0
9 TraesCS1D01G178200 chr1A 91.000 200 15 2 37 236 84272799 84272603 1.560000e-67 267.0
10 TraesCS1D01G178200 chr1A 97.368 38 1 0 281 318 84272599 84272562 6.120000e-07 65.8
11 TraesCS1D01G178200 chr1A 100.000 28 0 0 2224 2251 325034359 325034332 5.000000e-03 52.8
12 TraesCS1D01G178200 chr6D 93.017 358 19 2 1361 1718 267689453 267689804 3.910000e-143 518.0
13 TraesCS1D01G178200 chr6D 90.141 142 9 3 1225 1366 267549341 267549477 2.090000e-41 180.0
14 TraesCS1D01G178200 chr6D 92.308 39 3 0 239 277 28268122 28268084 3.680000e-04 56.5
15 TraesCS1D01G178200 chr6B 87.429 350 22 10 962 1307 33632242 33632573 1.490000e-102 383.0
16 TraesCS1D01G178200 chr6B 93.467 199 11 1 38 236 26089504 26089308 7.170000e-76 294.0
17 TraesCS1D01G178200 chr6B 89.340 197 19 2 38 234 37261448 37261254 2.040000e-61 246.0
18 TraesCS1D01G178200 chr6B 92.857 126 8 1 1321 1445 33632554 33632679 5.820000e-42 182.0
19 TraesCS1D01G178200 chr3D 92.965 199 12 1 38 236 82744906 82744710 3.330000e-74 289.0
20 TraesCS1D01G178200 chr2D 91.960 199 14 1 38 236 595156303 595156107 7.220000e-71 278.0
21 TraesCS1D01G178200 chr5B 91.457 199 15 1 38 236 599794437 599794633 3.360000e-69 272.0
22 TraesCS1D01G178200 chr2A 91.457 199 15 1 38 236 450578792 450578596 3.360000e-69 272.0
23 TraesCS1D01G178200 chr2A 88.442 199 21 1 38 236 700027775 700027579 3.410000e-59 239.0
24 TraesCS1D01G178200 chr5A 90.291 206 18 1 32 237 607718734 607718937 4.340000e-68 268.0
25 TraesCS1D01G178200 chr4D 100.000 35 0 0 239 273 78834361 78834327 6.120000e-07 65.8


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 TraesCS1D01G178200 chr1D 253191296 253193943 2647 False 4891.0 4891 100.000000 1 2648 1 chr1D.!!$F1 2647
1 TraesCS1D01G178200 chr1B 359223987 359226299 2312 True 1456.5 2523 91.207000 357 2648 2 chr1B.!!$R2 2291
2 TraesCS1D01G178200 chr1A 325031752 325034754 3002 False 1017.0 2337 92.779667 322 2563 3 chr1A.!!$F1 2241

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
274 275 0.037590 TAGGAGCCAAAACACCGCAT 59.962 50.0 0.00 0.00 0.00 4.73 F
304 305 0.374758 TTGCAATCGATTCTCGCAGC 59.625 50.0 17.73 13.34 40.21 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1118 1181 1.664649 CACGCCTTGACGAAGCTCA 60.665 57.895 0.00 0.0 36.7 4.26 R
1678 1746 2.851195 AGAAAAAGGAGAAGAAGCGCA 58.149 42.857 11.47 0.0 0.0 6.09 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 1.595357 CAAGTACTCCCACCGTCCC 59.405 63.158 0.00 0.00 0.00 4.46
19 20 1.156803 AAGTACTCCCACCGTCCCA 59.843 57.895 0.00 0.00 0.00 4.37
20 21 0.472352 AAGTACTCCCACCGTCCCAA 60.472 55.000 0.00 0.00 0.00 4.12
21 22 0.472352 AGTACTCCCACCGTCCCAAA 60.472 55.000 0.00 0.00 0.00 3.28
22 23 0.397564 GTACTCCCACCGTCCCAAAA 59.602 55.000 0.00 0.00 0.00 2.44
23 24 1.003928 GTACTCCCACCGTCCCAAAAT 59.996 52.381 0.00 0.00 0.00 1.82
24 25 1.364269 ACTCCCACCGTCCCAAAATA 58.636 50.000 0.00 0.00 0.00 1.40
25 26 1.706305 ACTCCCACCGTCCCAAAATAA 59.294 47.619 0.00 0.00 0.00 1.40
26 27 2.108601 ACTCCCACCGTCCCAAAATAAA 59.891 45.455 0.00 0.00 0.00 1.40
27 28 3.245479 ACTCCCACCGTCCCAAAATAAAT 60.245 43.478 0.00 0.00 0.00 1.40
28 29 3.093057 TCCCACCGTCCCAAAATAAATG 58.907 45.455 0.00 0.00 0.00 2.32
29 30 2.418060 CCCACCGTCCCAAAATAAATGC 60.418 50.000 0.00 0.00 0.00 3.56
30 31 2.418060 CCACCGTCCCAAAATAAATGCC 60.418 50.000 0.00 0.00 0.00 4.40
31 32 2.495669 CACCGTCCCAAAATAAATGCCT 59.504 45.455 0.00 0.00 0.00 4.75
32 33 2.758423 ACCGTCCCAAAATAAATGCCTC 59.242 45.455 0.00 0.00 0.00 4.70
33 34 2.757868 CCGTCCCAAAATAAATGCCTCA 59.242 45.455 0.00 0.00 0.00 3.86
34 35 3.194542 CCGTCCCAAAATAAATGCCTCAA 59.805 43.478 0.00 0.00 0.00 3.02
35 36 4.173256 CGTCCCAAAATAAATGCCTCAAC 58.827 43.478 0.00 0.00 0.00 3.18
36 37 4.082245 CGTCCCAAAATAAATGCCTCAACT 60.082 41.667 0.00 0.00 0.00 3.16
37 38 5.410924 GTCCCAAAATAAATGCCTCAACTC 58.589 41.667 0.00 0.00 0.00 3.01
38 39 5.047377 GTCCCAAAATAAATGCCTCAACTCA 60.047 40.000 0.00 0.00 0.00 3.41
39 40 5.541868 TCCCAAAATAAATGCCTCAACTCAA 59.458 36.000 0.00 0.00 0.00 3.02
40 41 6.042552 TCCCAAAATAAATGCCTCAACTCAAA 59.957 34.615 0.00 0.00 0.00 2.69
41 42 6.709846 CCCAAAATAAATGCCTCAACTCAAAA 59.290 34.615 0.00 0.00 0.00 2.44
42 43 7.391275 CCCAAAATAAATGCCTCAACTCAAAAT 59.609 33.333 0.00 0.00 0.00 1.82
43 44 9.434420 CCAAAATAAATGCCTCAACTCAAAATA 57.566 29.630 0.00 0.00 0.00 1.40
47 48 9.643693 AATAAATGCCTCAACTCAAAATAAGTG 57.356 29.630 0.00 0.00 0.00 3.16
48 49 6.655078 AATGCCTCAACTCAAAATAAGTGT 57.345 33.333 0.00 0.00 0.00 3.55
49 50 5.689383 TGCCTCAACTCAAAATAAGTGTC 57.311 39.130 0.00 0.00 0.00 3.67
50 51 5.376625 TGCCTCAACTCAAAATAAGTGTCT 58.623 37.500 0.00 0.00 0.00 3.41
51 52 5.470098 TGCCTCAACTCAAAATAAGTGTCTC 59.530 40.000 0.00 0.00 0.00 3.36
52 53 5.470098 GCCTCAACTCAAAATAAGTGTCTCA 59.530 40.000 0.00 0.00 0.00 3.27
53 54 6.017109 GCCTCAACTCAAAATAAGTGTCTCAA 60.017 38.462 0.00 0.00 0.00 3.02
54 55 7.355778 CCTCAACTCAAAATAAGTGTCTCAAC 58.644 38.462 0.00 0.00 0.00 3.18
55 56 7.227512 CCTCAACTCAAAATAAGTGTCTCAACT 59.772 37.037 0.00 0.00 0.00 3.16
56 57 8.506168 TCAACTCAAAATAAGTGTCTCAACTT 57.494 30.769 0.00 0.00 42.89 2.66
57 58 8.956426 TCAACTCAAAATAAGTGTCTCAACTTT 58.044 29.630 0.00 0.00 40.77 2.66
102 103 9.686683 AATAAGTGTCTTAATCCTAATGCAACT 57.313 29.630 0.00 0.00 0.00 3.16
105 106 9.686683 AAGTGTCTTAATCCTAATGCAACTAAT 57.313 29.630 0.00 0.00 0.00 1.73
106 107 9.686683 AGTGTCTTAATCCTAATGCAACTAATT 57.313 29.630 0.00 0.00 0.00 1.40
107 108 9.722056 GTGTCTTAATCCTAATGCAACTAATTG 57.278 33.333 0.00 0.00 38.99 2.32
108 109 9.461312 TGTCTTAATCCTAATGCAACTAATTGT 57.539 29.630 0.00 0.00 38.17 2.71
116 117 9.953565 TCCTAATGCAACTAATTGTACTAAAGT 57.046 29.630 0.00 0.00 38.17 2.66
120 121 7.718272 TGCAACTAATTGTACTAAAGTTCGT 57.282 32.000 0.00 0.00 38.17 3.85
121 122 8.815141 TGCAACTAATTGTACTAAAGTTCGTA 57.185 30.769 0.00 0.00 38.17 3.43
122 123 9.426837 TGCAACTAATTGTACTAAAGTTCGTAT 57.573 29.630 0.00 0.00 38.17 3.06
132 133 9.630098 TGTACTAAAGTTCGTATAAAGTTGAGG 57.370 33.333 0.00 0.00 27.97 3.86
133 134 7.592439 ACTAAAGTTCGTATAAAGTTGAGGC 57.408 36.000 0.00 0.00 27.97 4.70
134 135 7.156673 ACTAAAGTTCGTATAAAGTTGAGGCA 58.843 34.615 0.00 0.00 27.97 4.75
135 136 5.857822 AAGTTCGTATAAAGTTGAGGCAC 57.142 39.130 0.00 0.00 0.00 5.01
137 138 5.548406 AGTTCGTATAAAGTTGAGGCACTT 58.452 37.500 0.00 0.00 41.55 3.16
138 139 6.694447 AGTTCGTATAAAGTTGAGGCACTTA 58.306 36.000 0.00 0.00 41.55 2.24
139 140 7.328737 AGTTCGTATAAAGTTGAGGCACTTAT 58.671 34.615 0.00 0.00 41.55 1.73
140 141 7.822822 AGTTCGTATAAAGTTGAGGCACTTATT 59.177 33.333 0.00 0.00 41.55 1.40
141 142 8.448615 GTTCGTATAAAGTTGAGGCACTTATTT 58.551 33.333 0.00 0.00 41.55 1.40
142 143 8.556213 TCGTATAAAGTTGAGGCACTTATTTT 57.444 30.769 0.00 0.00 41.55 1.82
143 144 8.447833 TCGTATAAAGTTGAGGCACTTATTTTG 58.552 33.333 0.00 0.00 41.55 2.44
144 145 8.447833 CGTATAAAGTTGAGGCACTTATTTTGA 58.552 33.333 0.00 0.00 41.55 2.69
145 146 9.774742 GTATAAAGTTGAGGCACTTATTTTGAG 57.225 33.333 0.00 0.00 41.55 3.02
146 147 6.959639 AAAGTTGAGGCACTTATTTTGAGA 57.040 33.333 0.00 0.00 41.55 3.27
147 148 5.948992 AGTTGAGGCACTTATTTTGAGAC 57.051 39.130 0.00 0.00 41.55 3.36
148 149 4.452455 AGTTGAGGCACTTATTTTGAGACG 59.548 41.667 0.00 0.00 41.55 4.18
149 150 4.265904 TGAGGCACTTATTTTGAGACGA 57.734 40.909 0.00 0.00 41.55 4.20
150 151 4.637276 TGAGGCACTTATTTTGAGACGAA 58.363 39.130 0.00 0.00 41.55 3.85
151 152 4.690748 TGAGGCACTTATTTTGAGACGAAG 59.309 41.667 0.00 0.00 41.55 3.79
152 153 4.003648 AGGCACTTATTTTGAGACGAAGG 58.996 43.478 0.00 0.00 27.25 3.46
153 154 3.127030 GGCACTTATTTTGAGACGAAGGG 59.873 47.826 0.00 0.00 0.00 3.95
154 155 3.426292 GCACTTATTTTGAGACGAAGGGC 60.426 47.826 0.00 0.00 39.18 5.19
171 172 7.591006 CGAAGGGCGTACAATATACAATATT 57.409 36.000 0.00 0.00 34.64 1.28
172 173 8.025243 CGAAGGGCGTACAATATACAATATTT 57.975 34.615 0.00 0.00 34.64 1.40
173 174 9.142515 CGAAGGGCGTACAATATACAATATTTA 57.857 33.333 0.00 0.00 34.64 1.40
228 229 9.513906 TTCAACTATGGAAACTTCATACAATCA 57.486 29.630 0.00 0.00 0.00 2.57
229 230 9.513906 TCAACTATGGAAACTTCATACAATCAA 57.486 29.630 0.00 0.00 0.00 2.57
235 236 8.408043 TGGAAACTTCATACAATCAAATCACT 57.592 30.769 0.00 0.00 0.00 3.41
236 237 9.513906 TGGAAACTTCATACAATCAAATCACTA 57.486 29.630 0.00 0.00 0.00 2.74
245 246 9.999009 CATACAATCAAATCACTATATGGATGC 57.001 33.333 0.00 0.00 0.00 3.91
246 247 9.743581 ATACAATCAAATCACTATATGGATGCA 57.256 29.630 0.00 0.00 0.00 3.96
247 248 8.645814 ACAATCAAATCACTATATGGATGCAT 57.354 30.769 4.68 4.68 0.00 3.96
248 249 9.743581 ACAATCAAATCACTATATGGATGCATA 57.256 29.630 9.55 9.55 0.00 3.14
251 252 8.217131 TCAAATCACTATATGGATGCATATGC 57.783 34.615 25.18 21.09 42.50 3.14
263 264 2.775911 GCATATGCATCTAGGAGCCA 57.224 50.000 22.84 0.00 41.59 4.75
264 265 3.063510 GCATATGCATCTAGGAGCCAA 57.936 47.619 22.84 0.00 41.59 4.52
265 266 3.415212 GCATATGCATCTAGGAGCCAAA 58.585 45.455 22.84 0.00 41.59 3.28
266 267 3.822735 GCATATGCATCTAGGAGCCAAAA 59.177 43.478 22.84 0.00 41.59 2.44
267 268 4.320788 GCATATGCATCTAGGAGCCAAAAC 60.321 45.833 22.84 0.00 41.59 2.43
268 269 2.877097 TGCATCTAGGAGCCAAAACA 57.123 45.000 5.13 0.00 0.00 2.83
269 270 2.436417 TGCATCTAGGAGCCAAAACAC 58.564 47.619 5.13 0.00 0.00 3.32
270 271 1.745653 GCATCTAGGAGCCAAAACACC 59.254 52.381 0.00 0.00 0.00 4.16
271 272 2.009774 CATCTAGGAGCCAAAACACCG 58.990 52.381 0.00 0.00 0.00 4.94
272 273 0.321298 TCTAGGAGCCAAAACACCGC 60.321 55.000 0.00 0.00 0.00 5.68
273 274 0.605319 CTAGGAGCCAAAACACCGCA 60.605 55.000 0.00 0.00 0.00 5.69
274 275 0.037590 TAGGAGCCAAAACACCGCAT 59.962 50.000 0.00 0.00 0.00 4.73
275 276 1.212751 GGAGCCAAAACACCGCATC 59.787 57.895 0.00 0.00 0.00 3.91
276 277 1.212751 GAGCCAAAACACCGCATCC 59.787 57.895 0.00 0.00 0.00 3.51
277 278 1.228552 AGCCAAAACACCGCATCCT 60.229 52.632 0.00 0.00 0.00 3.24
278 279 0.037590 AGCCAAAACACCGCATCCTA 59.962 50.000 0.00 0.00 0.00 2.94
279 280 1.102978 GCCAAAACACCGCATCCTAT 58.897 50.000 0.00 0.00 0.00 2.57
280 281 2.092646 AGCCAAAACACCGCATCCTATA 60.093 45.455 0.00 0.00 0.00 1.31
281 282 2.884639 GCCAAAACACCGCATCCTATAT 59.115 45.455 0.00 0.00 0.00 0.86
282 283 4.069304 GCCAAAACACCGCATCCTATATA 58.931 43.478 0.00 0.00 0.00 0.86
283 284 4.700213 GCCAAAACACCGCATCCTATATAT 59.300 41.667 0.00 0.00 0.00 0.86
284 285 5.878116 GCCAAAACACCGCATCCTATATATA 59.122 40.000 0.00 0.00 0.00 0.86
285 286 6.542370 GCCAAAACACCGCATCCTATATATAT 59.458 38.462 0.00 0.00 0.00 0.86
286 287 7.067008 GCCAAAACACCGCATCCTATATATATT 59.933 37.037 0.00 0.00 0.00 1.28
287 288 8.397906 CCAAAACACCGCATCCTATATATATTG 58.602 37.037 0.00 0.00 0.00 1.90
288 289 7.553881 AAACACCGCATCCTATATATATTGC 57.446 36.000 0.00 3.98 0.00 3.56
289 290 6.233905 ACACCGCATCCTATATATATTGCA 57.766 37.500 14.47 0.00 0.00 4.08
290 291 6.649155 ACACCGCATCCTATATATATTGCAA 58.351 36.000 14.47 0.00 0.00 4.08
291 292 7.282585 ACACCGCATCCTATATATATTGCAAT 58.717 34.615 17.56 17.56 0.00 3.56
292 293 7.442364 ACACCGCATCCTATATATATTGCAATC 59.558 37.037 16.86 0.00 0.00 2.67
293 294 6.646653 ACCGCATCCTATATATATTGCAATCG 59.353 38.462 16.86 8.19 0.00 3.34
294 295 6.868339 CCGCATCCTATATATATTGCAATCGA 59.132 38.462 16.86 5.36 0.00 3.59
295 296 7.547019 CCGCATCCTATATATATTGCAATCGAT 59.453 37.037 16.86 12.67 0.00 3.59
296 297 8.929746 CGCATCCTATATATATTGCAATCGATT 58.070 33.333 16.86 4.39 0.00 3.34
300 301 9.899226 TCCTATATATATTGCAATCGATTCTCG 57.101 33.333 16.86 0.00 42.10 4.04
301 302 8.642885 CCTATATATATTGCAATCGATTCTCGC 58.357 37.037 16.86 9.78 40.21 5.03
302 303 9.185192 CTATATATATTGCAATCGATTCTCGCA 57.815 33.333 16.86 15.39 40.21 5.10
303 304 4.658713 ATATTGCAATCGATTCTCGCAG 57.341 40.909 16.86 4.53 40.21 5.18
304 305 0.374758 TTGCAATCGATTCTCGCAGC 59.625 50.000 17.73 13.34 40.21 5.25
305 306 0.740516 TGCAATCGATTCTCGCAGCA 60.741 50.000 15.39 14.13 40.21 4.41
306 307 0.374758 GCAATCGATTCTCGCAGCAA 59.625 50.000 7.92 0.00 40.21 3.91
307 308 1.853646 GCAATCGATTCTCGCAGCAAC 60.854 52.381 7.92 0.00 40.21 4.17
308 309 0.647410 AATCGATTCTCGCAGCAACG 59.353 50.000 4.39 0.00 40.21 4.10
309 310 1.756375 ATCGATTCTCGCAGCAACGC 61.756 55.000 0.00 0.00 40.21 4.84
325 326 2.262292 GCGCGGGGTAGTGTAACA 59.738 61.111 8.83 0.00 41.43 2.41
332 333 2.145536 GGGGTAGTGTAACAACGGTTG 58.854 52.381 18.81 18.81 41.43 3.77
399 400 0.597637 CGAAGCTGTCGTCAACCAGT 60.598 55.000 9.30 0.00 45.09 4.00
458 459 2.510238 GCTAGACAGGCACAGGCG 60.510 66.667 0.00 0.00 42.47 5.52
711 757 1.081556 CCATTTGGATCGCGACGTCA 61.082 55.000 12.93 7.43 37.39 4.35
800 850 4.505217 CATGTGAACCGCGAGCGC 62.505 66.667 8.23 0.00 38.24 5.92
1028 1088 4.760047 CGTTGGCTGCCCGCTACT 62.760 66.667 17.53 0.00 39.13 2.57
1029 1089 2.820037 GTTGGCTGCCCGCTACTC 60.820 66.667 17.53 0.00 39.13 2.59
1030 1090 3.003173 TTGGCTGCCCGCTACTCT 61.003 61.111 17.53 0.00 39.13 3.24
1031 1091 3.019003 TTGGCTGCCCGCTACTCTC 62.019 63.158 17.53 0.00 39.13 3.20
1032 1092 4.228567 GGCTGCCCGCTACTCTCC 62.229 72.222 7.66 0.00 39.13 3.71
1033 1093 4.577246 GCTGCCCGCTACTCTCCG 62.577 72.222 0.00 0.00 35.14 4.63
1034 1094 4.577246 CTGCCCGCTACTCTCCGC 62.577 72.222 0.00 0.00 0.00 5.54
1453 1519 0.898789 GAGGACGGTGAGGTTCCAGA 60.899 60.000 0.00 0.00 0.00 3.86
1678 1746 5.125417 GGAAATATACATGCCTTGTGTGTGT 59.875 40.000 0.00 0.00 39.48 3.72
1679 1747 5.565592 AATATACATGCCTTGTGTGTGTG 57.434 39.130 0.00 0.00 39.48 3.82
1680 1748 0.950836 TACATGCCTTGTGTGTGTGC 59.049 50.000 0.00 0.00 39.48 4.57
1681 1749 1.370778 CATGCCTTGTGTGTGTGCG 60.371 57.895 0.00 0.00 0.00 5.34
1697 1765 2.290641 TGTGCGCTTCTTCTCCTTTTTC 59.709 45.455 9.73 0.00 0.00 2.29
1720 1789 4.333913 TTTGCAATTGCCATGTGTTAGT 57.666 36.364 26.94 0.00 41.18 2.24
1742 1811 4.992381 AGCTCGAAGTGTAACATGTTTC 57.008 40.909 17.78 12.52 41.43 2.78
1743 1812 3.428870 AGCTCGAAGTGTAACATGTTTCG 59.571 43.478 17.78 18.47 41.43 3.46
1744 1813 3.423123 GCTCGAAGTGTAACATGTTTCGG 60.423 47.826 22.59 16.33 41.43 4.30
1745 1814 3.719924 TCGAAGTGTAACATGTTTCGGT 58.280 40.909 22.59 6.55 41.43 4.69
1748 1817 5.064962 TCGAAGTGTAACATGTTTCGGTTTT 59.935 36.000 22.59 9.87 41.43 2.43
1749 1818 5.394322 CGAAGTGTAACATGTTTCGGTTTTC 59.606 40.000 17.78 11.90 41.43 2.29
1750 1819 5.177725 AGTGTAACATGTTTCGGTTTTCC 57.822 39.130 17.78 0.00 41.43 3.13
1751 1820 4.037089 AGTGTAACATGTTTCGGTTTTCCC 59.963 41.667 17.78 0.00 41.43 3.97
1752 1821 4.037089 GTGTAACATGTTTCGGTTTTCCCT 59.963 41.667 17.78 0.00 36.32 4.20
1753 1822 4.645588 TGTAACATGTTTCGGTTTTCCCTT 59.354 37.500 17.78 0.00 36.42 3.95
1754 1823 3.726291 ACATGTTTCGGTTTTCCCTTG 57.274 42.857 0.00 0.00 36.42 3.61
1755 1824 3.028130 ACATGTTTCGGTTTTCCCTTGT 58.972 40.909 0.00 0.00 36.42 3.16
1756 1825 4.208746 ACATGTTTCGGTTTTCCCTTGTA 58.791 39.130 0.00 0.00 36.42 2.41
1757 1826 4.830600 ACATGTTTCGGTTTTCCCTTGTAT 59.169 37.500 0.00 0.00 36.42 2.29
1758 1827 6.005198 ACATGTTTCGGTTTTCCCTTGTATA 58.995 36.000 0.00 0.00 36.42 1.47
1759 1828 5.945466 TGTTTCGGTTTTCCCTTGTATAC 57.055 39.130 0.00 0.00 36.42 1.47
1760 1829 5.623169 TGTTTCGGTTTTCCCTTGTATACT 58.377 37.500 4.17 0.00 36.42 2.12
1761 1830 5.702209 TGTTTCGGTTTTCCCTTGTATACTC 59.298 40.000 4.17 0.00 36.42 2.59
1762 1831 4.476628 TCGGTTTTCCCTTGTATACTCC 57.523 45.455 4.17 0.00 36.42 3.85
1803 1872 0.029700 CGTGTACGTGTGACCTGTCA 59.970 55.000 0.00 0.00 34.13 3.58
1981 2058 5.920193 TGGGAGATGATTTTTGGAATCAC 57.080 39.130 3.79 0.18 39.22 3.06
1986 2063 6.263168 GGAGATGATTTTTGGAATCACGGTAT 59.737 38.462 3.79 0.00 39.22 2.73
1988 2065 8.924511 AGATGATTTTTGGAATCACGGTATAT 57.075 30.769 3.79 0.00 39.22 0.86
2000 2077 7.384387 GGAATCACGGTATATTGGAACTTACTC 59.616 40.741 0.00 0.00 0.00 2.59
2240 3049 8.567285 AAGTGAAGACTTAAAACTATCCCATG 57.433 34.615 0.00 0.00 40.85 3.66
2242 3051 8.822805 AGTGAAGACTTAAAACTATCCCATGTA 58.177 33.333 0.00 0.00 0.00 2.29
2243 3052 9.444600 GTGAAGACTTAAAACTATCCCATGTAA 57.555 33.333 0.00 0.00 0.00 2.41
2244 3053 9.667107 TGAAGACTTAAAACTATCCCATGTAAG 57.333 33.333 0.00 0.00 0.00 2.34
2260 3122 4.921470 TGTAAGTTTTCATACAGCTCGC 57.079 40.909 0.00 0.00 31.63 5.03
2274 3136 7.983484 TCATACAGCTCGCAATCATCATATTAT 59.017 33.333 0.00 0.00 0.00 1.28
2283 3145 9.667989 TCGCAATCATCATATTATTTTTGTGAG 57.332 29.630 0.00 0.00 31.16 3.51
2390 3253 5.250200 ACATCGGTTAAGAAATAACTGGCA 58.750 37.500 7.19 0.00 46.58 4.92
2589 3455 9.866655 TTTCCTATGCCTCTTATATGACAAAAT 57.133 29.630 0.00 0.00 0.00 1.82
2592 3458 9.071276 CCTATGCCTCTTATATGACAAAATTGT 57.929 33.333 0.00 0.00 45.65 2.71
2622 3488 8.053355 AGACCAAACCTAAATAAGATGGGTTAG 58.947 37.037 0.00 0.00 39.05 2.34
2623 3489 7.705700 ACCAAACCTAAATAAGATGGGTTAGT 58.294 34.615 0.00 0.00 39.05 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.189524 TGGGACGGTGGGAGTACTTG 61.190 60.000 0.00 0.00 0.00 3.16
1 2 0.472352 TTGGGACGGTGGGAGTACTT 60.472 55.000 0.00 0.00 0.00 2.24
2 3 0.472352 TTTGGGACGGTGGGAGTACT 60.472 55.000 0.00 0.00 0.00 2.73
3 4 0.397564 TTTTGGGACGGTGGGAGTAC 59.602 55.000 0.00 0.00 0.00 2.73
4 5 1.364269 ATTTTGGGACGGTGGGAGTA 58.636 50.000 0.00 0.00 0.00 2.59
5 6 1.364269 TATTTTGGGACGGTGGGAGT 58.636 50.000 0.00 0.00 0.00 3.85
6 7 2.500392 TTATTTTGGGACGGTGGGAG 57.500 50.000 0.00 0.00 0.00 4.30
7 8 2.973983 TTTATTTTGGGACGGTGGGA 57.026 45.000 0.00 0.00 0.00 4.37
8 9 2.418060 GCATTTATTTTGGGACGGTGGG 60.418 50.000 0.00 0.00 0.00 4.61
9 10 2.418060 GGCATTTATTTTGGGACGGTGG 60.418 50.000 0.00 0.00 0.00 4.61
10 11 2.495669 AGGCATTTATTTTGGGACGGTG 59.504 45.455 0.00 0.00 0.00 4.94
11 12 2.758423 GAGGCATTTATTTTGGGACGGT 59.242 45.455 0.00 0.00 0.00 4.83
12 13 2.757868 TGAGGCATTTATTTTGGGACGG 59.242 45.455 0.00 0.00 0.00 4.79
13 14 4.082245 AGTTGAGGCATTTATTTTGGGACG 60.082 41.667 0.00 0.00 0.00 4.79
14 15 5.047377 TGAGTTGAGGCATTTATTTTGGGAC 60.047 40.000 0.00 0.00 0.00 4.46
15 16 5.083122 TGAGTTGAGGCATTTATTTTGGGA 58.917 37.500 0.00 0.00 0.00 4.37
16 17 5.404466 TGAGTTGAGGCATTTATTTTGGG 57.596 39.130 0.00 0.00 0.00 4.12
17 18 7.727331 TTTTGAGTTGAGGCATTTATTTTGG 57.273 32.000 0.00 0.00 0.00 3.28
21 22 9.643693 CACTTATTTTGAGTTGAGGCATTTATT 57.356 29.630 0.00 0.00 0.00 1.40
22 23 8.806146 ACACTTATTTTGAGTTGAGGCATTTAT 58.194 29.630 0.00 0.00 0.00 1.40
23 24 8.177119 ACACTTATTTTGAGTTGAGGCATTTA 57.823 30.769 0.00 0.00 0.00 1.40
24 25 7.014615 AGACACTTATTTTGAGTTGAGGCATTT 59.985 33.333 0.00 0.00 0.00 2.32
25 26 6.491403 AGACACTTATTTTGAGTTGAGGCATT 59.509 34.615 0.00 0.00 0.00 3.56
26 27 6.006449 AGACACTTATTTTGAGTTGAGGCAT 58.994 36.000 0.00 0.00 0.00 4.40
27 28 5.376625 AGACACTTATTTTGAGTTGAGGCA 58.623 37.500 0.00 0.00 0.00 4.75
28 29 5.470098 TGAGACACTTATTTTGAGTTGAGGC 59.530 40.000 0.00 0.00 0.00 4.70
29 30 7.227512 AGTTGAGACACTTATTTTGAGTTGAGG 59.772 37.037 0.00 0.00 0.00 3.86
30 31 8.147642 AGTTGAGACACTTATTTTGAGTTGAG 57.852 34.615 0.00 0.00 0.00 3.02
31 32 8.506168 AAGTTGAGACACTTATTTTGAGTTGA 57.494 30.769 0.00 0.00 35.10 3.18
76 77 9.686683 AGTTGCATTAGGATTAAGACACTTATT 57.313 29.630 0.00 0.00 0.00 1.40
79 80 9.686683 ATTAGTTGCATTAGGATTAAGACACTT 57.313 29.630 0.00 0.00 0.00 3.16
80 81 9.686683 AATTAGTTGCATTAGGATTAAGACACT 57.313 29.630 0.00 0.00 0.00 3.55
81 82 9.722056 CAATTAGTTGCATTAGGATTAAGACAC 57.278 33.333 0.00 0.00 0.00 3.67
82 83 9.461312 ACAATTAGTTGCATTAGGATTAAGACA 57.539 29.630 0.00 0.00 38.96 3.41
90 91 9.953565 ACTTTAGTACAATTAGTTGCATTAGGA 57.046 29.630 0.00 0.00 38.96 2.94
94 95 8.780249 ACGAACTTTAGTACAATTAGTTGCATT 58.220 29.630 0.00 0.00 38.96 3.56
95 96 8.319143 ACGAACTTTAGTACAATTAGTTGCAT 57.681 30.769 0.00 0.00 38.96 3.96
96 97 7.718272 ACGAACTTTAGTACAATTAGTTGCA 57.282 32.000 0.00 0.00 38.96 4.08
106 107 9.630098 CCTCAACTTTATACGAACTTTAGTACA 57.370 33.333 0.00 0.00 0.00 2.90
107 108 8.590470 GCCTCAACTTTATACGAACTTTAGTAC 58.410 37.037 0.00 0.00 0.00 2.73
108 109 8.306038 TGCCTCAACTTTATACGAACTTTAGTA 58.694 33.333 0.00 0.00 0.00 1.82
109 110 7.117379 GTGCCTCAACTTTATACGAACTTTAGT 59.883 37.037 0.00 0.00 0.00 2.24
110 111 7.331193 AGTGCCTCAACTTTATACGAACTTTAG 59.669 37.037 0.00 0.00 0.00 1.85
111 112 7.156673 AGTGCCTCAACTTTATACGAACTTTA 58.843 34.615 0.00 0.00 0.00 1.85
112 113 5.995897 AGTGCCTCAACTTTATACGAACTTT 59.004 36.000 0.00 0.00 0.00 2.66
113 114 5.548406 AGTGCCTCAACTTTATACGAACTT 58.452 37.500 0.00 0.00 0.00 2.66
114 115 5.148651 AGTGCCTCAACTTTATACGAACT 57.851 39.130 0.00 0.00 0.00 3.01
115 116 5.857822 AAGTGCCTCAACTTTATACGAAC 57.142 39.130 0.00 0.00 37.05 3.95
116 117 8.556213 AAATAAGTGCCTCAACTTTATACGAA 57.444 30.769 0.00 0.00 40.77 3.85
117 118 8.447833 CAAAATAAGTGCCTCAACTTTATACGA 58.552 33.333 0.00 0.00 40.77 3.43
118 119 8.447833 TCAAAATAAGTGCCTCAACTTTATACG 58.552 33.333 0.00 0.00 40.77 3.06
119 120 9.774742 CTCAAAATAAGTGCCTCAACTTTATAC 57.225 33.333 0.00 0.00 40.77 1.47
120 121 9.733556 TCTCAAAATAAGTGCCTCAACTTTATA 57.266 29.630 0.00 0.00 40.77 0.98
121 122 8.515414 GTCTCAAAATAAGTGCCTCAACTTTAT 58.485 33.333 0.00 0.00 40.77 1.40
122 123 7.307751 CGTCTCAAAATAAGTGCCTCAACTTTA 60.308 37.037 0.00 0.00 40.77 1.85
123 124 6.513393 CGTCTCAAAATAAGTGCCTCAACTTT 60.513 38.462 0.00 0.00 40.77 2.66
124 125 5.049405 CGTCTCAAAATAAGTGCCTCAACTT 60.049 40.000 0.00 0.00 42.89 2.66
125 126 4.452455 CGTCTCAAAATAAGTGCCTCAACT 59.548 41.667 0.00 0.00 0.00 3.16
126 127 4.451096 TCGTCTCAAAATAAGTGCCTCAAC 59.549 41.667 0.00 0.00 0.00 3.18
127 128 4.637276 TCGTCTCAAAATAAGTGCCTCAA 58.363 39.130 0.00 0.00 0.00 3.02
128 129 4.265904 TCGTCTCAAAATAAGTGCCTCA 57.734 40.909 0.00 0.00 0.00 3.86
129 130 4.093556 CCTTCGTCTCAAAATAAGTGCCTC 59.906 45.833 0.00 0.00 0.00 4.70
130 131 4.003648 CCTTCGTCTCAAAATAAGTGCCT 58.996 43.478 0.00 0.00 0.00 4.75
131 132 3.127030 CCCTTCGTCTCAAAATAAGTGCC 59.873 47.826 0.00 0.00 0.00 5.01
132 133 3.426292 GCCCTTCGTCTCAAAATAAGTGC 60.426 47.826 0.00 0.00 0.00 4.40
133 134 3.181520 CGCCCTTCGTCTCAAAATAAGTG 60.182 47.826 0.00 0.00 0.00 3.16
134 135 3.000727 CGCCCTTCGTCTCAAAATAAGT 58.999 45.455 0.00 0.00 0.00 2.24
135 136 3.658351 CGCCCTTCGTCTCAAAATAAG 57.342 47.619 0.00 0.00 0.00 1.73
147 148 7.591006 AATATTGTATATTGTACGCCCTTCG 57.409 36.000 0.00 0.00 45.38 3.79
202 203 9.513906 TGATTGTATGAAGTTTCCATAGTTGAA 57.486 29.630 0.00 0.00 0.00 2.69
203 204 9.513906 TTGATTGTATGAAGTTTCCATAGTTGA 57.486 29.630 0.00 0.00 0.00 3.18
209 210 9.028284 AGTGATTTGATTGTATGAAGTTTCCAT 57.972 29.630 0.00 0.00 0.00 3.41
210 211 8.408043 AGTGATTTGATTGTATGAAGTTTCCA 57.592 30.769 0.00 0.00 0.00 3.53
219 220 9.999009 GCATCCATATAGTGATTTGATTGTATG 57.001 33.333 0.00 0.00 0.00 2.39
220 221 9.743581 TGCATCCATATAGTGATTTGATTGTAT 57.256 29.630 0.00 0.00 0.00 2.29
221 222 9.743581 ATGCATCCATATAGTGATTTGATTGTA 57.256 29.630 0.00 0.00 0.00 2.41
222 223 8.645814 ATGCATCCATATAGTGATTTGATTGT 57.354 30.769 0.00 0.00 0.00 2.71
225 226 8.847196 GCATATGCATCCATATAGTGATTTGAT 58.153 33.333 22.84 0.00 41.55 2.57
226 227 8.217131 GCATATGCATCCATATAGTGATTTGA 57.783 34.615 22.84 0.00 41.55 2.69
244 245 2.775911 TGGCTCCTAGATGCATATGC 57.224 50.000 21.09 21.09 42.50 3.14
245 246 4.823442 TGTTTTGGCTCCTAGATGCATATG 59.177 41.667 3.54 0.00 0.00 1.78
246 247 4.823989 GTGTTTTGGCTCCTAGATGCATAT 59.176 41.667 0.00 0.00 0.00 1.78
247 248 4.199310 GTGTTTTGGCTCCTAGATGCATA 58.801 43.478 0.00 0.00 0.00 3.14
248 249 3.019564 GTGTTTTGGCTCCTAGATGCAT 58.980 45.455 0.00 0.00 0.00 3.96
249 250 2.436417 GTGTTTTGGCTCCTAGATGCA 58.564 47.619 8.71 0.00 0.00 3.96
250 251 1.745653 GGTGTTTTGGCTCCTAGATGC 59.254 52.381 0.00 0.00 0.00 3.91
251 252 2.009774 CGGTGTTTTGGCTCCTAGATG 58.990 52.381 0.00 0.00 0.00 2.90
252 253 1.679032 GCGGTGTTTTGGCTCCTAGAT 60.679 52.381 0.00 0.00 0.00 1.98
253 254 0.321298 GCGGTGTTTTGGCTCCTAGA 60.321 55.000 0.00 0.00 0.00 2.43
254 255 0.605319 TGCGGTGTTTTGGCTCCTAG 60.605 55.000 0.00 0.00 0.00 3.02
255 256 0.037590 ATGCGGTGTTTTGGCTCCTA 59.962 50.000 0.00 0.00 0.00 2.94
256 257 1.228552 ATGCGGTGTTTTGGCTCCT 60.229 52.632 0.00 0.00 0.00 3.69
257 258 1.212751 GATGCGGTGTTTTGGCTCC 59.787 57.895 0.00 0.00 0.00 4.70
258 259 1.212751 GGATGCGGTGTTTTGGCTC 59.787 57.895 0.00 0.00 0.00 4.70
259 260 0.037590 TAGGATGCGGTGTTTTGGCT 59.962 50.000 0.00 0.00 0.00 4.75
260 261 1.102978 ATAGGATGCGGTGTTTTGGC 58.897 50.000 0.00 0.00 0.00 4.52
261 262 8.397906 CAATATATATAGGATGCGGTGTTTTGG 58.602 37.037 0.00 0.00 0.00 3.28
262 263 7.910162 GCAATATATATAGGATGCGGTGTTTTG 59.090 37.037 10.43 2.50 0.00 2.44
263 264 7.609918 TGCAATATATATAGGATGCGGTGTTTT 59.390 33.333 16.71 0.00 36.62 2.43
264 265 7.109501 TGCAATATATATAGGATGCGGTGTTT 58.890 34.615 16.71 0.00 36.62 2.83
265 266 6.649155 TGCAATATATATAGGATGCGGTGTT 58.351 36.000 16.71 0.00 36.62 3.32
266 267 6.233905 TGCAATATATATAGGATGCGGTGT 57.766 37.500 16.71 0.00 36.62 4.16
267 268 7.359514 CGATTGCAATATATATAGGATGCGGTG 60.360 40.741 12.97 8.11 36.62 4.94
268 269 6.646653 CGATTGCAATATATATAGGATGCGGT 59.353 38.462 12.97 11.05 36.62 5.68
269 270 6.868339 TCGATTGCAATATATATAGGATGCGG 59.132 38.462 12.97 10.03 36.62 5.69
270 271 7.873739 TCGATTGCAATATATATAGGATGCG 57.126 36.000 12.97 6.94 36.62 4.73
304 305 3.629883 TACACTACCCCGCGCGTTG 62.630 63.158 29.95 21.02 0.00 4.10
305 306 2.929903 TTACACTACCCCGCGCGTT 61.930 57.895 29.95 14.98 0.00 4.84
306 307 3.372730 TTACACTACCCCGCGCGT 61.373 61.111 29.95 13.36 0.00 6.01
307 308 2.882301 GTTACACTACCCCGCGCG 60.882 66.667 25.67 25.67 0.00 6.86
308 309 1.374505 TTGTTACACTACCCCGCGC 60.375 57.895 0.00 0.00 0.00 6.86
309 310 1.346378 CGTTGTTACACTACCCCGCG 61.346 60.000 0.00 0.00 0.00 6.46
310 311 1.015607 CCGTTGTTACACTACCCCGC 61.016 60.000 0.00 0.00 0.00 6.13
311 312 0.318120 ACCGTTGTTACACTACCCCG 59.682 55.000 0.00 0.00 0.00 5.73
312 313 2.145536 CAACCGTTGTTACACTACCCC 58.854 52.381 2.87 0.00 32.09 4.95
313 314 2.802247 GACAACCGTTGTTACACTACCC 59.198 50.000 17.81 0.00 45.52 3.69
314 315 2.802247 GGACAACCGTTGTTACACTACC 59.198 50.000 17.81 8.97 45.52 3.18
315 316 2.802247 GGGACAACCGTTGTTACACTAC 59.198 50.000 17.81 3.71 45.52 2.73
316 317 2.224257 GGGGACAACCGTTGTTACACTA 60.224 50.000 17.81 0.00 45.52 2.74
317 318 1.475571 GGGGACAACCGTTGTTACACT 60.476 52.381 17.81 0.00 45.52 3.55
318 319 0.946528 GGGGACAACCGTTGTTACAC 59.053 55.000 17.81 11.57 45.52 2.90
319 320 3.400439 GGGGACAACCGTTGTTACA 57.600 52.632 17.81 0.00 45.52 2.41
399 400 2.355837 GTGACCGTGAGCAGCGAA 60.356 61.111 0.00 0.00 0.00 4.70
458 459 3.165875 TCCTACTACATGATGGCTAGCC 58.834 50.000 27.71 27.71 0.00 3.93
608 614 1.515952 CGTCTCTTCAGGCGCAGAG 60.516 63.158 10.83 13.15 41.78 3.35
711 757 0.881118 CATGCACGTAACCCAAGCTT 59.119 50.000 0.00 0.00 0.00 3.74
781 831 2.379634 CGCTCGCGGTTCACATGAA 61.380 57.895 6.13 0.00 35.56 2.57
805 855 3.156740 GAAAAGATCGCCGGCTCGC 62.157 63.158 26.68 13.07 0.00 5.03
852 902 3.379865 GATAAGGGCACGGTCGGCA 62.380 63.158 0.00 0.00 0.00 5.69
853 903 2.588034 GATAAGGGCACGGTCGGC 60.588 66.667 0.00 0.00 0.00 5.54
854 904 2.108362 GGATAAGGGCACGGTCGG 59.892 66.667 0.00 0.00 0.00 4.79
855 905 2.108362 GGGATAAGGGCACGGTCG 59.892 66.667 0.00 0.00 0.00 4.79
856 906 2.041206 GAGGGGATAAGGGCACGGTC 62.041 65.000 0.00 0.00 0.00 4.79
857 907 2.042261 AGGGGATAAGGGCACGGT 59.958 61.111 0.00 0.00 0.00 4.83
927 979 2.350498 GTGTGTTGCAGTTTGTACGAGT 59.650 45.455 0.00 0.00 0.00 4.18
936 988 1.136565 GCGTGTGTGTGTTGCAGTT 59.863 52.632 0.00 0.00 0.00 3.16
939 991 3.089729 GACGCGTGTGTGTGTTGCA 62.090 57.895 20.70 0.00 39.39 4.08
943 995 2.952783 GTCGACGCGTGTGTGTGT 60.953 61.111 20.70 0.00 39.39 3.72
1024 1084 2.409651 GAGCACGGCGGAGAGTAG 59.590 66.667 13.24 0.00 0.00 2.57
1025 1085 3.138798 GGAGCACGGCGGAGAGTA 61.139 66.667 13.24 0.00 0.00 2.59
1028 1088 4.742649 AGAGGAGCACGGCGGAGA 62.743 66.667 13.24 0.00 0.00 3.71
1029 1089 4.200283 GAGAGGAGCACGGCGGAG 62.200 72.222 13.24 4.25 0.00 4.63
1034 1094 3.753434 AGCACGAGAGGAGCACGG 61.753 66.667 0.00 0.00 38.48 4.94
1035 1095 2.505777 CAGCACGAGAGGAGCACG 60.506 66.667 0.00 0.00 38.48 5.34
1036 1096 2.125753 CCAGCACGAGAGGAGCAC 60.126 66.667 0.00 0.00 38.48 4.40
1117 1180 1.664965 ACGCCTTGACGAAGCTCAC 60.665 57.895 0.00 0.00 36.70 3.51
1118 1181 1.664649 CACGCCTTGACGAAGCTCA 60.665 57.895 0.00 0.00 36.70 4.26
1678 1746 2.851195 AGAAAAAGGAGAAGAAGCGCA 58.149 42.857 11.47 0.00 0.00 6.09
1679 1747 3.906014 AAGAAAAAGGAGAAGAAGCGC 57.094 42.857 0.00 0.00 0.00 5.92
1680 1748 4.442403 GCAAAAGAAAAAGGAGAAGAAGCG 59.558 41.667 0.00 0.00 0.00 4.68
1681 1749 5.351458 TGCAAAAGAAAAAGGAGAAGAAGC 58.649 37.500 0.00 0.00 0.00 3.86
1697 1765 4.751098 ACTAACACATGGCAATTGCAAAAG 59.249 37.500 30.32 18.85 44.36 2.27
1720 1789 4.619760 CGAAACATGTTACACTTCGAGCTA 59.380 41.667 19.86 0.00 40.94 3.32
1742 1811 3.937079 GTGGAGTATACAAGGGAAAACCG 59.063 47.826 5.50 0.00 46.96 4.44
1743 1812 4.698780 GTGTGGAGTATACAAGGGAAAACC 59.301 45.833 5.50 0.00 40.67 3.27
1744 1813 5.310451 TGTGTGGAGTATACAAGGGAAAAC 58.690 41.667 5.50 0.00 0.00 2.43
1745 1814 5.072600 ACTGTGTGGAGTATACAAGGGAAAA 59.927 40.000 5.50 0.00 29.49 2.29
1748 1817 3.786553 ACTGTGTGGAGTATACAAGGGA 58.213 45.455 5.50 0.00 29.49 4.20
1749 1818 4.439700 CGTACTGTGTGGAGTATACAAGGG 60.440 50.000 5.50 0.00 31.14 3.95
1750 1819 4.157289 ACGTACTGTGTGGAGTATACAAGG 59.843 45.833 5.50 0.00 31.14 3.61
1751 1820 5.093457 CACGTACTGTGTGGAGTATACAAG 58.907 45.833 5.50 0.00 43.88 3.16
1752 1821 5.050644 CACGTACTGTGTGGAGTATACAA 57.949 43.478 5.50 0.00 43.88 2.41
1753 1822 4.690184 CACGTACTGTGTGGAGTATACA 57.310 45.455 5.50 0.00 43.88 2.29
2145 2954 7.872163 TTGCAACATGTATGAAAATGACTTC 57.128 32.000 0.00 0.00 0.00 3.01
2231 3040 7.716998 AGCTGTATGAAAACTTACATGGGATAG 59.283 37.037 0.00 0.00 0.00 2.08
2232 3041 7.573710 AGCTGTATGAAAACTTACATGGGATA 58.426 34.615 0.00 0.00 0.00 2.59
2233 3042 6.426587 AGCTGTATGAAAACTTACATGGGAT 58.573 36.000 0.00 0.00 0.00 3.85
2234 3043 5.815581 AGCTGTATGAAAACTTACATGGGA 58.184 37.500 0.00 0.00 0.00 4.37
2235 3044 5.220662 CGAGCTGTATGAAAACTTACATGGG 60.221 44.000 0.00 0.00 0.00 4.00
2236 3045 5.727791 GCGAGCTGTATGAAAACTTACATGG 60.728 44.000 0.00 0.00 0.00 3.66
2237 3046 5.163864 TGCGAGCTGTATGAAAACTTACATG 60.164 40.000 0.00 0.00 0.00 3.21
2238 3047 4.935205 TGCGAGCTGTATGAAAACTTACAT 59.065 37.500 0.00 0.00 0.00 2.29
2240 3049 4.921470 TGCGAGCTGTATGAAAACTTAC 57.079 40.909 0.00 0.00 0.00 2.34
2242 3051 4.455533 TGATTGCGAGCTGTATGAAAACTT 59.544 37.500 0.00 0.00 0.00 2.66
2243 3052 4.002982 TGATTGCGAGCTGTATGAAAACT 58.997 39.130 0.00 0.00 0.00 2.66
2244 3053 4.340894 TGATTGCGAGCTGTATGAAAAC 57.659 40.909 0.00 0.00 0.00 2.43
2246 3055 4.190772 TGATGATTGCGAGCTGTATGAAA 58.809 39.130 0.00 0.00 0.00 2.69
2283 3145 9.103048 CGAGTCAAAACTTACACATGTAAATTC 57.897 33.333 0.00 0.00 39.70 2.17
2421 3284 3.074538 ACTTGGCAAAAGACATACTCCCT 59.925 43.478 0.00 0.00 0.00 4.20
2566 3432 9.071276 ACAATTTTGTCATATAAGAGGCATAGG 57.929 33.333 0.00 0.00 36.50 2.57
2569 3435 9.851686 TCTACAATTTTGTCATATAAGAGGCAT 57.148 29.630 0.00 0.00 42.35 4.40
2580 3446 7.287696 AGGTTTGGTCTTCTACAATTTTGTCAT 59.712 33.333 0.00 0.00 42.35 3.06
2581 3447 6.605594 AGGTTTGGTCTTCTACAATTTTGTCA 59.394 34.615 0.00 0.00 42.35 3.58
2592 3458 8.272173 CCCATCTTATTTAGGTTTGGTCTTCTA 58.728 37.037 0.00 0.00 0.00 2.10
2622 3488 5.121768 TGCGCCTCTTTAAAAACTATGAGAC 59.878 40.000 4.18 0.00 0.00 3.36
2623 3489 5.242434 TGCGCCTCTTTAAAAACTATGAGA 58.758 37.500 4.18 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.