Multiple sequence alignment - TraesCS6D01G310700

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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 TraesCS6D01G310700 chr6D 100.000 3096 0 0 1 3096 420692815 420695910 0.000000e+00 5718.0
1 TraesCS6D01G310700 chr6D 86.382 492 39 12 923 1413 406620333 406619869 2.130000e-141 512.0
2 TraesCS6D01G310700 chr6D 80.337 178 29 5 2538 2712 430039842 430039668 2.510000e-26 130.0
3 TraesCS6D01G310700 chr6D 100.000 28 0 0 712 739 406620484 406620457 6.000000e-03 52.8
4 TraesCS6D01G310700 chr6B 91.703 1832 86 25 381 2205 633858063 633859835 0.000000e+00 2481.0
5 TraesCS6D01G310700 chr6B 86.928 306 31 4 2531 2834 633860461 633860759 4.950000e-88 335.0
6 TraesCS6D01G310700 chr6B 86.505 289 31 6 2246 2531 633860121 633860404 8.340000e-81 311.0
7 TraesCS6D01G310700 chr6A 93.450 1374 60 19 905 2266 563539305 563540660 0.000000e+00 2012.0
8 TraesCS6D01G310700 chr6A 96.890 836 21 3 2265 3096 563540821 563541655 0.000000e+00 1395.0
9 TraesCS6D01G310700 chr6A 89.835 423 17 10 502 923 563538024 563538421 1.270000e-143 520.0
10 TraesCS6D01G310700 chr6A 82.624 282 34 15 90 361 97610261 97609985 5.160000e-58 235.0
11 TraesCS6D01G310700 chr6A 94.118 68 4 0 404 471 563537670 563537737 1.520000e-18 104.0
12 TraesCS6D01G310700 chr5A 82.252 1110 153 26 1006 2095 677485993 677484908 0.000000e+00 918.0
13 TraesCS6D01G310700 chr5A 80.277 289 47 10 85 369 379090290 379090572 3.130000e-50 209.0
14 TraesCS6D01G310700 chr5A 80.488 287 42 13 90 367 138076228 138075947 1.130000e-49 207.0
15 TraesCS6D01G310700 chr4D 81.876 1109 161 22 1006 2096 497241121 497240035 0.000000e+00 898.0
16 TraesCS6D01G310700 chr4D 81.605 1109 170 19 1006 2096 497224396 497223304 0.000000e+00 887.0
17 TraesCS6D01G310700 chr4B 79.566 1106 156 41 1006 2096 638148324 638147274 0.000000e+00 726.0
18 TraesCS6D01G310700 chr4B 80.000 660 95 19 1456 2096 638175607 638174966 1.310000e-123 453.0
19 TraesCS6D01G310700 chr4B 89.206 315 31 3 1006 1319 638181317 638181005 1.040000e-104 390.0
20 TraesCS6D01G310700 chr5D 79.944 354 49 13 20 355 17478892 17479241 1.110000e-59 241.0
21 TraesCS6D01G310700 chr3D 84.047 257 26 14 106 357 349639955 349639709 1.860000e-57 233.0
22 TraesCS6D01G310700 chr4A 79.938 324 58 6 15 336 741433575 741433893 6.680000e-57 231.0
23 TraesCS6D01G310700 chr7B 81.973 294 31 19 84 369 354699808 354699529 2.400000e-56 230.0
24 TraesCS6D01G310700 chr7A 81.851 281 43 7 90 366 596327095 596327371 2.400000e-56 230.0
25 TraesCS6D01G310700 chr1A 80.851 282 38 12 90 368 483681438 483681706 1.130000e-49 207.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G310700 chr6D 420692815 420695910 3095 False 5718.000000 5718 100.000000 1 3096 1 chr6D.!!$F1 3095
1 TraesCS6D01G310700 chr6D 406619869 406620484 615 True 282.400000 512 93.191000 712 1413 2 chr6D.!!$R2 701
2 TraesCS6D01G310700 chr6B 633858063 633860759 2696 False 1042.333333 2481 88.378667 381 2834 3 chr6B.!!$F1 2453
3 TraesCS6D01G310700 chr6A 563537670 563541655 3985 False 1007.750000 2012 93.573250 404 3096 4 chr6A.!!$F1 2692
4 TraesCS6D01G310700 chr5A 677484908 677485993 1085 True 918.000000 918 82.252000 1006 2095 1 chr5A.!!$R2 1089
5 TraesCS6D01G310700 chr4D 497240035 497241121 1086 True 898.000000 898 81.876000 1006 2096 1 chr4D.!!$R2 1090
6 TraesCS6D01G310700 chr4D 497223304 497224396 1092 True 887.000000 887 81.605000 1006 2096 1 chr4D.!!$R1 1090
7 TraesCS6D01G310700 chr4B 638147274 638148324 1050 True 726.000000 726 79.566000 1006 2096 1 chr4B.!!$R1 1090
8 TraesCS6D01G310700 chr4B 638174966 638175607 641 True 453.000000 453 80.000000 1456 2096 1 chr4B.!!$R2 640

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
356 357 0.102481 CGCACGGACCTATTGCTAGT 59.898 55.0 7.70 0.0 33.9 2.57 F
1808 2994 0.036010 GAGGCAAGTGCTAGCTGGAA 60.036 55.0 17.23 0.0 41.7 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1834 3020 0.308993 GAAATAGCTGATGCCACGGC 59.691 55.0 0.00 0.0 40.8 5.68 R
2844 4531 0.533755 GCCGGCTTCATAGTGCTCAT 60.534 55.0 22.15 0.0 0.0 2.90 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
26 27 9.533253 AAATGTTCGAGAAATTCAGAAATTGTT 57.467 25.926 5.71 0.00 35.27 2.83
27 28 8.733857 ATGTTCGAGAAATTCAGAAATTGTTC 57.266 30.769 5.71 0.00 35.27 3.18
28 29 7.138736 TGTTCGAGAAATTCAGAAATTGTTCC 58.861 34.615 5.71 0.00 35.27 3.62
29 30 6.875948 TCGAGAAATTCAGAAATTGTTCCA 57.124 33.333 0.00 0.00 35.27 3.53
30 31 7.452880 TCGAGAAATTCAGAAATTGTTCCAT 57.547 32.000 0.00 0.00 35.27 3.41
31 32 7.530010 TCGAGAAATTCAGAAATTGTTCCATC 58.470 34.615 0.00 0.00 35.27 3.51
32 33 7.174772 TCGAGAAATTCAGAAATTGTTCCATCA 59.825 33.333 0.00 0.00 35.27 3.07
33 34 7.809331 CGAGAAATTCAGAAATTGTTCCATCAA 59.191 33.333 0.00 0.00 35.27 2.57
34 35 9.649167 GAGAAATTCAGAAATTGTTCCATCAAT 57.351 29.630 0.00 0.00 39.35 2.57
66 67 9.878599 AAAAAGTGTTCGACAATTATAGAAGTG 57.121 29.630 0.00 0.00 35.13 3.16
67 68 8.603242 AAAGTGTTCGACAATTATAGAAGTGT 57.397 30.769 2.37 2.37 46.09 3.55
68 69 8.603242 AAGTGTTCGACAATTATAGAAGTGTT 57.397 30.769 4.52 0.00 43.59 3.32
69 70 8.240883 AGTGTTCGACAATTATAGAAGTGTTC 57.759 34.615 4.52 0.00 43.59 3.18
70 71 7.061905 AGTGTTCGACAATTATAGAAGTGTTCG 59.938 37.037 4.52 9.65 43.59 3.95
71 72 5.944049 TCGACAATTATAGAAGTGTTCGC 57.056 39.130 4.52 0.00 43.59 4.70
72 73 5.404096 TCGACAATTATAGAAGTGTTCGCA 58.596 37.500 4.52 0.00 43.59 5.10
73 74 5.515270 TCGACAATTATAGAAGTGTTCGCAG 59.485 40.000 4.52 0.00 43.59 5.18
74 75 5.515270 CGACAATTATAGAAGTGTTCGCAGA 59.485 40.000 4.52 0.00 43.59 4.26
75 76 6.291322 CGACAATTATAGAAGTGTTCGCAGAG 60.291 42.308 4.52 0.00 43.59 3.35
76 77 6.398918 ACAATTATAGAAGTGTTCGCAGAGT 58.601 36.000 0.00 0.00 40.87 3.24
77 78 6.531948 ACAATTATAGAAGTGTTCGCAGAGTC 59.468 38.462 0.00 0.00 40.87 3.36
78 79 5.638596 TTATAGAAGTGTTCGCAGAGTCA 57.361 39.130 0.00 0.00 38.43 3.41
79 80 2.890808 AGAAGTGTTCGCAGAGTCAA 57.109 45.000 0.00 0.00 38.43 3.18
80 81 2.748605 AGAAGTGTTCGCAGAGTCAAG 58.251 47.619 0.00 0.00 38.43 3.02
81 82 2.362397 AGAAGTGTTCGCAGAGTCAAGA 59.638 45.455 0.00 0.00 38.43 3.02
82 83 2.890808 AGTGTTCGCAGAGTCAAGAA 57.109 45.000 0.00 0.00 38.43 2.52
83 84 3.179443 AGTGTTCGCAGAGTCAAGAAA 57.821 42.857 0.00 0.00 38.43 2.52
84 85 3.531538 AGTGTTCGCAGAGTCAAGAAAA 58.468 40.909 0.00 0.00 38.43 2.29
85 86 4.130118 AGTGTTCGCAGAGTCAAGAAAAT 58.870 39.130 0.00 0.00 38.43 1.82
86 87 4.576463 AGTGTTCGCAGAGTCAAGAAAATT 59.424 37.500 0.00 0.00 38.43 1.82
87 88 5.066505 AGTGTTCGCAGAGTCAAGAAAATTT 59.933 36.000 0.00 0.00 38.43 1.82
88 89 5.172053 GTGTTCGCAGAGTCAAGAAAATTTG 59.828 40.000 0.00 0.00 38.43 2.32
89 90 5.163663 TGTTCGCAGAGTCAAGAAAATTTGT 60.164 36.000 0.00 0.00 38.43 2.83
90 91 5.499139 TCGCAGAGTCAAGAAAATTTGTT 57.501 34.783 0.00 0.00 0.00 2.83
91 92 5.890334 TCGCAGAGTCAAGAAAATTTGTTT 58.110 33.333 0.00 0.00 0.00 2.83
92 93 7.022055 TCGCAGAGTCAAGAAAATTTGTTTA 57.978 32.000 0.00 0.00 0.00 2.01
93 94 7.476667 TCGCAGAGTCAAGAAAATTTGTTTAA 58.523 30.769 0.00 0.00 0.00 1.52
94 95 7.971168 TCGCAGAGTCAAGAAAATTTGTTTAAA 59.029 29.630 0.00 0.00 0.00 1.52
95 96 8.591312 CGCAGAGTCAAGAAAATTTGTTTAAAA 58.409 29.630 0.00 0.00 0.00 1.52
184 185 9.814899 ATTTCAAATTTGTACAAGTGTTCATGA 57.185 25.926 17.47 0.00 0.00 3.07
185 186 9.645059 TTTCAAATTTGTACAAGTGTTCATGAA 57.355 25.926 17.47 3.38 0.00 2.57
186 187 9.814899 TTCAAATTTGTACAAGTGTTCATGAAT 57.185 25.926 17.47 0.00 0.00 2.57
187 188 9.814899 TCAAATTTGTACAAGTGTTCATGAATT 57.185 25.926 17.47 0.00 0.00 2.17
190 191 9.814899 AATTTGTACAAGTGTTCATGAATTTGA 57.185 25.926 24.71 13.10 0.00 2.69
191 192 9.814899 ATTTGTACAAGTGTTCATGAATTTGAA 57.185 25.926 24.71 14.93 33.32 2.69
192 193 9.645059 TTTGTACAAGTGTTCATGAATTTGAAA 57.355 25.926 24.71 16.58 37.36 2.69
193 194 9.645059 TTGTACAAGTGTTCATGAATTTGAAAA 57.355 25.926 24.71 16.59 37.36 2.29
194 195 9.645059 TGTACAAGTGTTCATGAATTTGAAAAA 57.355 25.926 24.71 12.46 37.36 1.94
197 198 9.165035 ACAAGTGTTCATGAATTTGAAAAATGT 57.835 25.926 24.71 13.66 37.36 2.71
198 199 9.991388 CAAGTGTTCATGAATTTGAAAAATGTT 57.009 25.926 12.12 0.00 37.36 2.71
200 201 9.381033 AGTGTTCATGAATTTGAAAAATGTTCA 57.619 25.926 12.12 0.00 37.36 3.18
201 202 9.424659 GTGTTCATGAATTTGAAAAATGTTCAC 57.575 29.630 12.12 5.93 37.36 3.18
202 203 8.326713 TGTTCATGAATTTGAAAAATGTTCACG 58.673 29.630 12.12 0.00 37.36 4.35
203 204 8.538856 GTTCATGAATTTGAAAAATGTTCACGA 58.461 29.630 12.12 0.00 37.36 4.35
204 205 8.284557 TCATGAATTTGAAAAATGTTCACGAG 57.715 30.769 0.00 0.00 32.30 4.18
205 206 7.920151 TCATGAATTTGAAAAATGTTCACGAGT 59.080 29.630 0.00 0.00 32.30 4.18
206 207 8.542132 CATGAATTTGAAAAATGTTCACGAGTT 58.458 29.630 0.00 0.00 32.30 3.01
207 208 8.472683 TGAATTTGAAAAATGTTCACGAGTTT 57.527 26.923 0.00 0.00 0.00 2.66
208 209 9.574458 TGAATTTGAAAAATGTTCACGAGTTTA 57.426 25.926 0.00 0.00 0.00 2.01
211 212 8.744008 TTTGAAAAATGTTCACGAGTTTAACA 57.256 26.923 0.00 0.00 37.51 2.41
212 213 8.744008 TTGAAAAATGTTCACGAGTTTAACAA 57.256 26.923 0.00 0.00 36.75 2.83
213 214 8.744008 TGAAAAATGTTCACGAGTTTAACAAA 57.256 26.923 0.00 0.00 36.75 2.83
214 215 9.193133 TGAAAAATGTTCACGAGTTTAACAAAA 57.807 25.926 0.00 0.00 36.75 2.44
216 217 9.965748 AAAAATGTTCACGAGTTTAACAAAATG 57.034 25.926 0.00 0.00 36.75 2.32
217 218 8.696410 AAATGTTCACGAGTTTAACAAAATGT 57.304 26.923 0.00 0.00 36.75 2.71
218 219 7.678194 ATGTTCACGAGTTTAACAAAATGTG 57.322 32.000 0.00 0.00 36.75 3.21
219 220 5.513495 TGTTCACGAGTTTAACAAAATGTGC 59.487 36.000 0.00 0.00 30.54 4.57
220 221 5.236655 TCACGAGTTTAACAAAATGTGCA 57.763 34.783 0.00 0.00 0.00 4.57
221 222 5.826586 TCACGAGTTTAACAAAATGTGCAT 58.173 33.333 0.00 0.00 0.00 3.96
222 223 5.685068 TCACGAGTTTAACAAAATGTGCATG 59.315 36.000 0.00 0.00 0.00 4.06
223 224 5.685068 CACGAGTTTAACAAAATGTGCATGA 59.315 36.000 0.00 0.00 0.00 3.07
224 225 6.363088 CACGAGTTTAACAAAATGTGCATGAT 59.637 34.615 0.00 0.00 0.00 2.45
225 226 6.922957 ACGAGTTTAACAAAATGTGCATGATT 59.077 30.769 0.00 0.00 0.00 2.57
226 227 7.437862 ACGAGTTTAACAAAATGTGCATGATTT 59.562 29.630 0.00 0.00 0.00 2.17
227 228 7.946237 CGAGTTTAACAAAATGTGCATGATTTC 59.054 33.333 0.00 0.00 0.00 2.17
228 229 8.659925 AGTTTAACAAAATGTGCATGATTTCA 57.340 26.923 0.00 0.00 0.00 2.69
229 230 9.107177 AGTTTAACAAAATGTGCATGATTTCAA 57.893 25.926 0.00 0.00 0.00 2.69
230 231 9.713740 GTTTAACAAAATGTGCATGATTTCAAA 57.286 25.926 0.00 4.33 0.00 2.69
234 235 9.804758 AACAAAATGTGCATGATTTCAAAAATT 57.195 22.222 0.00 0.00 0.00 1.82
235 236 9.239002 ACAAAATGTGCATGATTTCAAAAATTG 57.761 25.926 0.00 3.82 0.00 2.32
236 237 9.239002 CAAAATGTGCATGATTTCAAAAATTGT 57.761 25.926 0.00 0.00 0.00 2.71
237 238 9.804758 AAAATGTGCATGATTTCAAAAATTGTT 57.195 22.222 0.00 0.00 0.00 2.83
238 239 9.453325 AAATGTGCATGATTTCAAAAATTGTTC 57.547 25.926 0.00 0.00 0.00 3.18
239 240 7.549615 TGTGCATGATTTCAAAAATTGTTCA 57.450 28.000 0.00 0.00 0.00 3.18
240 241 7.631822 TGTGCATGATTTCAAAAATTGTTCAG 58.368 30.769 0.00 0.00 0.00 3.02
241 242 7.073265 GTGCATGATTTCAAAAATTGTTCAGG 58.927 34.615 0.00 0.00 0.00 3.86
242 243 6.990939 TGCATGATTTCAAAAATTGTTCAGGA 59.009 30.769 0.00 0.00 0.00 3.86
243 244 7.662258 TGCATGATTTCAAAAATTGTTCAGGAT 59.338 29.630 0.00 0.00 0.00 3.24
244 245 8.508875 GCATGATTTCAAAAATTGTTCAGGATT 58.491 29.630 0.00 0.00 0.00 3.01
247 248 9.610705 TGATTTCAAAAATTGTTCAGGATTTGA 57.389 25.926 0.00 0.00 35.63 2.69
248 249 9.868389 GATTTCAAAAATTGTTCAGGATTTGAC 57.132 29.630 0.00 0.00 36.75 3.18
249 250 7.462109 TTCAAAAATTGTTCAGGATTTGACG 57.538 32.000 0.00 0.00 36.75 4.35
250 251 6.800543 TCAAAAATTGTTCAGGATTTGACGA 58.199 32.000 0.00 0.00 34.94 4.20
251 252 7.261325 TCAAAAATTGTTCAGGATTTGACGAA 58.739 30.769 0.00 0.00 34.94 3.85
252 253 7.221838 TCAAAAATTGTTCAGGATTTGACGAAC 59.778 33.333 0.00 0.00 38.55 3.95
253 254 5.766150 AATTGTTCAGGATTTGACGAACA 57.234 34.783 0.00 0.00 44.35 3.18
254 255 5.964958 ATTGTTCAGGATTTGACGAACAT 57.035 34.783 4.81 0.00 45.09 2.71
255 256 7.447374 AATTGTTCAGGATTTGACGAACATA 57.553 32.000 4.81 0.00 45.09 2.29
256 257 6.869315 TTGTTCAGGATTTGACGAACATAA 57.131 33.333 4.81 0.00 45.09 1.90
257 258 6.480524 TGTTCAGGATTTGACGAACATAAG 57.519 37.500 0.00 0.00 41.97 1.73
258 259 6.227522 TGTTCAGGATTTGACGAACATAAGA 58.772 36.000 0.00 0.00 41.97 2.10
259 260 6.368791 TGTTCAGGATTTGACGAACATAAGAG 59.631 38.462 0.00 0.00 41.97 2.85
260 261 6.037786 TCAGGATTTGACGAACATAAGAGT 57.962 37.500 0.00 0.00 0.00 3.24
261 262 5.869344 TCAGGATTTGACGAACATAAGAGTG 59.131 40.000 0.00 0.00 0.00 3.51
262 263 5.869344 CAGGATTTGACGAACATAAGAGTGA 59.131 40.000 0.00 0.00 0.00 3.41
263 264 6.536582 CAGGATTTGACGAACATAAGAGTGAT 59.463 38.462 0.00 0.00 0.00 3.06
264 265 7.706607 CAGGATTTGACGAACATAAGAGTGATA 59.293 37.037 0.00 0.00 0.00 2.15
265 266 7.923344 AGGATTTGACGAACATAAGAGTGATAG 59.077 37.037 0.00 0.00 0.00 2.08
266 267 7.707035 GGATTTGACGAACATAAGAGTGATAGT 59.293 37.037 0.00 0.00 0.00 2.12
267 268 7.812309 TTTGACGAACATAAGAGTGATAGTG 57.188 36.000 0.00 0.00 0.00 2.74
268 269 6.510879 TGACGAACATAAGAGTGATAGTGT 57.489 37.500 0.00 0.00 0.00 3.55
269 270 7.619964 TGACGAACATAAGAGTGATAGTGTA 57.380 36.000 0.00 0.00 0.00 2.90
270 271 7.694886 TGACGAACATAAGAGTGATAGTGTAG 58.305 38.462 0.00 0.00 0.00 2.74
271 272 6.496571 ACGAACATAAGAGTGATAGTGTAGC 58.503 40.000 0.00 0.00 0.00 3.58
272 273 6.319152 ACGAACATAAGAGTGATAGTGTAGCT 59.681 38.462 0.00 0.00 0.00 3.32
273 274 6.853872 CGAACATAAGAGTGATAGTGTAGCTC 59.146 42.308 0.00 0.00 0.00 4.09
274 275 7.467403 CGAACATAAGAGTGATAGTGTAGCTCA 60.467 40.741 0.00 0.00 0.00 4.26
275 276 7.270757 ACATAAGAGTGATAGTGTAGCTCAG 57.729 40.000 0.00 0.00 0.00 3.35
276 277 6.831353 ACATAAGAGTGATAGTGTAGCTCAGT 59.169 38.462 0.00 0.00 0.00 3.41
277 278 5.574891 AAGAGTGATAGTGTAGCTCAGTG 57.425 43.478 0.00 0.00 0.00 3.66
278 279 4.849518 AGAGTGATAGTGTAGCTCAGTGA 58.150 43.478 0.00 0.00 0.00 3.41
279 280 5.445069 AGAGTGATAGTGTAGCTCAGTGAT 58.555 41.667 0.00 0.00 0.00 3.06
280 281 5.299028 AGAGTGATAGTGTAGCTCAGTGATG 59.701 44.000 0.00 0.00 0.00 3.07
281 282 4.047822 GTGATAGTGTAGCTCAGTGATGC 58.952 47.826 0.00 0.00 0.00 3.91
282 283 3.701040 TGATAGTGTAGCTCAGTGATGCA 59.299 43.478 14.37 0.00 0.00 3.96
283 284 2.669300 AGTGTAGCTCAGTGATGCAG 57.331 50.000 14.37 0.00 0.00 4.41
284 285 1.005340 GTGTAGCTCAGTGATGCAGC 58.995 55.000 14.37 0.00 0.00 5.25
285 286 0.609662 TGTAGCTCAGTGATGCAGCA 59.390 50.000 0.00 0.00 35.46 4.41
286 287 1.002315 TGTAGCTCAGTGATGCAGCAA 59.998 47.619 6.05 0.00 35.46 3.91
287 288 2.079158 GTAGCTCAGTGATGCAGCAAA 58.921 47.619 6.05 0.00 35.46 3.68
288 289 1.612676 AGCTCAGTGATGCAGCAAAA 58.387 45.000 6.05 0.00 35.46 2.44
289 290 2.168496 AGCTCAGTGATGCAGCAAAAT 58.832 42.857 6.05 0.00 35.46 1.82
290 291 2.094700 AGCTCAGTGATGCAGCAAAATG 60.095 45.455 6.05 6.47 35.46 2.32
291 292 2.352421 GCTCAGTGATGCAGCAAAATGT 60.352 45.455 6.05 0.00 33.06 2.71
292 293 3.242518 CTCAGTGATGCAGCAAAATGTG 58.757 45.455 6.05 3.52 0.00 3.21
293 294 2.885894 TCAGTGATGCAGCAAAATGTGA 59.114 40.909 6.05 2.06 0.00 3.58
294 295 3.508402 TCAGTGATGCAGCAAAATGTGAT 59.492 39.130 6.05 0.00 0.00 3.06
295 296 3.857665 CAGTGATGCAGCAAAATGTGATC 59.142 43.478 6.05 0.00 0.00 2.92
296 297 3.508402 AGTGATGCAGCAAAATGTGATCA 59.492 39.130 6.05 0.00 0.00 2.92
297 298 4.159693 AGTGATGCAGCAAAATGTGATCAT 59.840 37.500 6.05 0.00 35.59 2.45
298 299 4.267690 GTGATGCAGCAAAATGTGATCATG 59.732 41.667 6.05 0.00 34.19 3.07
299 300 3.239587 TGCAGCAAAATGTGATCATGG 57.760 42.857 0.00 0.00 34.19 3.66
300 301 1.931172 GCAGCAAAATGTGATCATGGC 59.069 47.619 0.00 0.00 34.19 4.40
301 302 2.546778 CAGCAAAATGTGATCATGGCC 58.453 47.619 0.00 0.00 34.19 5.36
302 303 2.093921 CAGCAAAATGTGATCATGGCCA 60.094 45.455 8.56 8.56 34.19 5.36
303 304 2.769663 AGCAAAATGTGATCATGGCCAT 59.230 40.909 14.09 14.09 34.19 4.40
304 305 2.869801 GCAAAATGTGATCATGGCCATG 59.130 45.455 35.76 35.76 40.09 3.66
305 306 3.462982 CAAAATGTGATCATGGCCATGG 58.537 45.455 38.81 23.52 39.24 3.66
306 307 1.712056 AATGTGATCATGGCCATGGG 58.288 50.000 38.81 20.14 39.24 4.00
307 308 0.854908 ATGTGATCATGGCCATGGGA 59.145 50.000 38.81 25.10 39.24 4.37
308 309 0.106569 TGTGATCATGGCCATGGGAC 60.107 55.000 38.81 30.66 39.24 4.46
338 339 9.773328 ATGATATATATTTTTCCGTTGCAATCG 57.227 29.630 0.59 8.41 0.00 3.34
339 340 7.748683 TGATATATATTTTTCCGTTGCAATCGC 59.251 33.333 0.59 0.00 39.24 4.58
348 349 2.974717 TGCAATCGCACGGACCTA 59.025 55.556 0.00 0.00 45.36 3.08
349 350 1.520192 TGCAATCGCACGGACCTAT 59.480 52.632 0.00 0.00 45.36 2.57
350 351 0.107897 TGCAATCGCACGGACCTATT 60.108 50.000 0.00 0.00 45.36 1.73
351 352 0.304705 GCAATCGCACGGACCTATTG 59.695 55.000 0.00 0.00 38.36 1.90
352 353 0.304705 CAATCGCACGGACCTATTGC 59.695 55.000 0.00 0.00 0.00 3.56
353 354 0.178068 AATCGCACGGACCTATTGCT 59.822 50.000 7.70 0.00 33.90 3.91
354 355 1.037493 ATCGCACGGACCTATTGCTA 58.963 50.000 7.70 0.00 33.90 3.49
355 356 0.384309 TCGCACGGACCTATTGCTAG 59.616 55.000 7.70 0.00 33.90 3.42
356 357 0.102481 CGCACGGACCTATTGCTAGT 59.898 55.000 7.70 0.00 33.90 2.57
357 358 1.854227 GCACGGACCTATTGCTAGTC 58.146 55.000 3.06 0.00 33.26 2.59
358 359 1.136305 GCACGGACCTATTGCTAGTCA 59.864 52.381 3.06 0.00 33.26 3.41
359 360 2.224066 GCACGGACCTATTGCTAGTCAT 60.224 50.000 3.06 0.00 33.26 3.06
360 361 3.005472 GCACGGACCTATTGCTAGTCATA 59.995 47.826 3.06 0.00 33.26 2.15
361 362 4.322049 GCACGGACCTATTGCTAGTCATAT 60.322 45.833 3.06 0.00 33.26 1.78
362 363 5.105877 GCACGGACCTATTGCTAGTCATATA 60.106 44.000 3.06 0.00 33.26 0.86
363 364 6.571731 GCACGGACCTATTGCTAGTCATATAA 60.572 42.308 3.06 0.00 33.26 0.98
364 365 7.548097 CACGGACCTATTGCTAGTCATATAAT 58.452 38.462 0.00 0.00 0.00 1.28
365 366 8.683615 CACGGACCTATTGCTAGTCATATAATA 58.316 37.037 0.00 0.00 0.00 0.98
366 367 9.251440 ACGGACCTATTGCTAGTCATATAATAA 57.749 33.333 0.00 0.00 0.00 1.40
414 416 1.202302 TGGAAGACGATCGACTGCATC 60.202 52.381 23.85 16.00 0.00 3.91
473 475 1.137675 CACATCGCTCTCCTTCCATGA 59.862 52.381 0.00 0.00 0.00 3.07
482 484 0.918983 TCCTTCCATGACATCCACCC 59.081 55.000 0.00 0.00 0.00 4.61
592 859 4.935352 AGAAAAACTTGCCACATTGCTA 57.065 36.364 0.00 0.00 0.00 3.49
596 863 4.989279 AAACTTGCCACATTGCTATAGG 57.011 40.909 1.04 0.00 0.00 2.57
597 864 2.301346 ACTTGCCACATTGCTATAGGC 58.699 47.619 14.13 14.13 45.41 3.93
599 866 3.305709 GCCACATTGCTATAGGCGA 57.694 52.632 1.04 0.00 45.43 5.54
601 868 2.972625 GCCACATTGCTATAGGCGATA 58.027 47.619 1.04 0.00 42.75 2.92
657 924 0.460284 GACATGGACGGAACTGCGAT 60.460 55.000 0.00 0.00 0.00 4.58
689 956 1.513373 CGACGGCGACATCGAAGAA 60.513 57.895 16.62 0.00 40.86 2.52
690 957 1.464429 CGACGGCGACATCGAAGAAG 61.464 60.000 16.62 0.00 40.86 2.85
691 958 1.743855 GACGGCGACATCGAAGAAGC 61.744 60.000 16.62 0.00 43.58 3.86
692 959 1.805539 CGGCGACATCGAAGAAGCA 60.806 57.895 0.00 0.00 43.58 3.91
693 960 1.746727 CGGCGACATCGAAGAAGCAG 61.747 60.000 0.00 6.26 43.58 4.24
972 2151 0.822164 AGGTGCGTAAATACTCGGCT 59.178 50.000 0.00 0.00 0.00 5.52
1209 2389 1.077429 GTGGGGCATCTTCCAGGTC 60.077 63.158 0.00 0.00 33.13 3.85
1210 2390 1.541118 TGGGGCATCTTCCAGGTCA 60.541 57.895 0.00 0.00 0.00 4.02
1212 2392 1.077429 GGGCATCTTCCAGGTCACC 60.077 63.158 0.00 0.00 0.00 4.02
1800 2986 1.220206 CCAGATCGAGGCAAGTGCT 59.780 57.895 2.85 0.00 41.70 4.40
1801 2987 0.461548 CCAGATCGAGGCAAGTGCTA 59.538 55.000 2.85 0.00 41.70 3.49
1805 2991 0.179089 ATCGAGGCAAGTGCTAGCTG 60.179 55.000 17.23 7.21 41.70 4.24
1806 2992 1.812922 CGAGGCAAGTGCTAGCTGG 60.813 63.158 17.23 0.00 41.70 4.85
1808 2994 0.036010 GAGGCAAGTGCTAGCTGGAA 60.036 55.000 17.23 0.00 41.70 3.53
1809 2995 0.322008 AGGCAAGTGCTAGCTGGAAC 60.322 55.000 17.23 0.00 41.70 3.62
1810 2996 1.639298 GGCAAGTGCTAGCTGGAACG 61.639 60.000 17.23 0.80 41.70 3.95
1811 2997 0.951040 GCAAGTGCTAGCTGGAACGT 60.951 55.000 17.23 0.00 38.21 3.99
1812 2998 1.671850 GCAAGTGCTAGCTGGAACGTA 60.672 52.381 17.23 0.00 38.21 3.57
1813 2999 2.263077 CAAGTGCTAGCTGGAACGTAG 58.737 52.381 17.23 0.00 0.00 3.51
1815 3001 2.719739 AGTGCTAGCTGGAACGTAGTA 58.280 47.619 17.23 0.00 45.00 1.82
1816 3002 2.422832 AGTGCTAGCTGGAACGTAGTAC 59.577 50.000 17.23 0.57 45.00 2.73
1817 3003 1.399440 TGCTAGCTGGAACGTAGTACG 59.601 52.381 20.82 20.82 45.00 3.67
1834 3020 1.073216 ACGCTCTTGATCGACTTGCG 61.073 55.000 14.89 14.89 46.02 4.85
1846 3038 4.170062 CTTGCGCCGTGGCATCAG 62.170 66.667 12.06 0.00 43.52 2.90
1860 3059 2.423538 GGCATCAGCTATTTCACCGTTT 59.576 45.455 0.00 0.00 41.70 3.60
1861 3060 3.429085 GCATCAGCTATTTCACCGTTTG 58.571 45.455 0.00 0.00 37.91 2.93
1862 3061 3.126858 GCATCAGCTATTTCACCGTTTGA 59.873 43.478 0.00 0.00 37.91 2.69
1863 3062 4.651994 CATCAGCTATTTCACCGTTTGAC 58.348 43.478 0.00 0.00 32.26 3.18
1865 3064 4.323417 TCAGCTATTTCACCGTTTGACAT 58.677 39.130 0.00 0.00 32.26 3.06
1866 3065 4.154015 TCAGCTATTTCACCGTTTGACATG 59.846 41.667 0.00 0.00 32.26 3.21
1868 3067 3.438781 GCTATTTCACCGTTTGACATGGA 59.561 43.478 0.00 0.00 35.17 3.41
1869 3068 4.437390 GCTATTTCACCGTTTGACATGGAG 60.437 45.833 0.00 0.00 35.17 3.86
1870 3069 1.890876 TTCACCGTTTGACATGGAGG 58.109 50.000 0.00 0.00 35.17 4.30
1871 3070 0.762418 TCACCGTTTGACATGGAGGT 59.238 50.000 0.00 0.00 35.17 3.85
1873 3072 2.369203 TCACCGTTTGACATGGAGGTTA 59.631 45.455 0.00 0.00 35.17 2.85
1874 3073 3.142951 CACCGTTTGACATGGAGGTTAA 58.857 45.455 0.00 0.00 35.17 2.01
2170 3385 6.578944 ACTGTAATCCTACATTTCATGCGTA 58.421 36.000 0.00 0.00 37.41 4.42
2183 3398 4.880886 TCATGCGTATCTGTTTGGATTG 57.119 40.909 0.00 0.00 0.00 2.67
2189 3404 4.201822 GCGTATCTGTTTGGATTGTCTTCC 60.202 45.833 0.00 0.00 36.24 3.46
2232 3447 1.216678 TGTGCTTTTCTTGAAGGGGGA 59.783 47.619 0.00 0.00 0.00 4.81
2235 3450 3.324846 GTGCTTTTCTTGAAGGGGGATTT 59.675 43.478 0.00 0.00 0.00 2.17
2236 3451 3.973305 TGCTTTTCTTGAAGGGGGATTTT 59.027 39.130 0.00 0.00 0.00 1.82
2285 3907 3.134574 AGATAAAGCGACACCCAACAA 57.865 42.857 0.00 0.00 0.00 2.83
2313 3937 2.253758 CGCACCCACAGAACACCAG 61.254 63.158 0.00 0.00 0.00 4.00
2330 3956 2.083774 CCAGACAAACACACACACACT 58.916 47.619 0.00 0.00 0.00 3.55
2378 4004 2.127232 GGCCAGCAACCACAACACT 61.127 57.895 0.00 0.00 0.00 3.55
2462 4089 0.717224 GCGAAAGACACCGCGAATAA 59.283 50.000 8.23 0.00 42.02 1.40
2566 4251 5.416083 TCAATAAGGTAATGACGTCCACAG 58.584 41.667 14.12 0.00 0.00 3.66
2862 4549 1.224075 CATGAGCACTATGAAGCCGG 58.776 55.000 0.00 0.00 0.00 6.13
2928 4615 4.264217 TGAACCATGACCTCCTAGACAGTA 60.264 45.833 0.00 0.00 0.00 2.74
3027 4714 0.307760 GACAAGGAGCAACCACAACG 59.692 55.000 2.96 0.00 42.04 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.533253 AACAATTTCTGAATTTCTCGAACATTT 57.467 25.926 0.00 0.00 33.25 2.32
1 2 9.185192 GAACAATTTCTGAATTTCTCGAACATT 57.815 29.630 0.00 0.00 33.25 2.71
2 3 7.809806 GGAACAATTTCTGAATTTCTCGAACAT 59.190 33.333 0.00 0.00 33.25 2.71
3 4 7.138736 GGAACAATTTCTGAATTTCTCGAACA 58.861 34.615 0.00 0.00 33.25 3.18
5 6 7.270757 TGGAACAATTTCTGAATTTCTCGAA 57.729 32.000 0.00 0.00 33.25 3.71
6 7 6.875948 TGGAACAATTTCTGAATTTCTCGA 57.124 33.333 0.00 0.00 33.25 4.04
40 41 9.878599 CACTTCTATAATTGTCGAACACTTTTT 57.121 29.630 0.00 0.00 0.00 1.94
41 42 9.052759 ACACTTCTATAATTGTCGAACACTTTT 57.947 29.630 0.00 0.00 0.00 2.27
42 43 8.603242 ACACTTCTATAATTGTCGAACACTTT 57.397 30.769 0.00 0.00 0.00 2.66
43 44 8.603242 AACACTTCTATAATTGTCGAACACTT 57.397 30.769 0.00 0.00 29.06 3.16
44 45 7.061905 CGAACACTTCTATAATTGTCGAACACT 59.938 37.037 0.00 0.00 29.06 3.55
45 46 7.164858 CGAACACTTCTATAATTGTCGAACAC 58.835 38.462 0.00 0.00 29.06 3.32
46 47 6.183360 GCGAACACTTCTATAATTGTCGAACA 60.183 38.462 0.00 0.00 29.06 3.18
47 48 6.176453 GCGAACACTTCTATAATTGTCGAAC 58.824 40.000 0.00 0.00 29.06 3.95
48 49 5.865013 TGCGAACACTTCTATAATTGTCGAA 59.135 36.000 0.00 0.00 29.06 3.71
49 50 5.404096 TGCGAACACTTCTATAATTGTCGA 58.596 37.500 0.00 0.00 29.06 4.20
50 51 5.515270 TCTGCGAACACTTCTATAATTGTCG 59.485 40.000 0.00 0.00 29.06 4.35
51 52 6.531948 ACTCTGCGAACACTTCTATAATTGTC 59.468 38.462 0.00 0.00 29.06 3.18
52 53 6.398918 ACTCTGCGAACACTTCTATAATTGT 58.601 36.000 0.00 0.00 30.40 2.71
53 54 6.531594 TGACTCTGCGAACACTTCTATAATTG 59.468 38.462 0.00 0.00 0.00 2.32
54 55 6.631016 TGACTCTGCGAACACTTCTATAATT 58.369 36.000 0.00 0.00 0.00 1.40
55 56 6.208988 TGACTCTGCGAACACTTCTATAAT 57.791 37.500 0.00 0.00 0.00 1.28
56 57 5.638596 TGACTCTGCGAACACTTCTATAA 57.361 39.130 0.00 0.00 0.00 0.98
57 58 5.414765 TCTTGACTCTGCGAACACTTCTATA 59.585 40.000 0.00 0.00 0.00 1.31
58 59 4.218635 TCTTGACTCTGCGAACACTTCTAT 59.781 41.667 0.00 0.00 0.00 1.98
59 60 3.568430 TCTTGACTCTGCGAACACTTCTA 59.432 43.478 0.00 0.00 0.00 2.10
60 61 2.362397 TCTTGACTCTGCGAACACTTCT 59.638 45.455 0.00 0.00 0.00 2.85
61 62 2.743938 TCTTGACTCTGCGAACACTTC 58.256 47.619 0.00 0.00 0.00 3.01
62 63 2.890808 TCTTGACTCTGCGAACACTT 57.109 45.000 0.00 0.00 0.00 3.16
63 64 2.890808 TTCTTGACTCTGCGAACACT 57.109 45.000 0.00 0.00 0.00 3.55
64 65 3.944422 TTTTCTTGACTCTGCGAACAC 57.056 42.857 0.00 0.00 0.00 3.32
65 66 5.163663 ACAAATTTTCTTGACTCTGCGAACA 60.164 36.000 0.00 0.00 0.00 3.18
66 67 5.273944 ACAAATTTTCTTGACTCTGCGAAC 58.726 37.500 0.00 0.00 0.00 3.95
67 68 5.499139 ACAAATTTTCTTGACTCTGCGAA 57.501 34.783 0.00 0.00 0.00 4.70
68 69 5.499139 AACAAATTTTCTTGACTCTGCGA 57.501 34.783 0.00 0.00 0.00 5.10
69 70 7.678194 TTAAACAAATTTTCTTGACTCTGCG 57.322 32.000 0.00 0.00 0.00 5.18
158 159 9.814899 TCATGAACACTTGTACAAATTTGAAAT 57.185 25.926 24.64 5.12 0.00 2.17
159 160 9.645059 TTCATGAACACTTGTACAAATTTGAAA 57.355 25.926 24.64 13.65 0.00 2.69
160 161 9.814899 ATTCATGAACACTTGTACAAATTTGAA 57.185 25.926 24.64 11.41 0.00 2.69
161 162 9.814899 AATTCATGAACACTTGTACAAATTTGA 57.185 25.926 24.64 5.76 0.00 2.69
164 165 9.814899 TCAAATTCATGAACACTTGTACAAATT 57.185 25.926 11.07 4.55 0.00 1.82
165 166 9.814899 TTCAAATTCATGAACACTTGTACAAAT 57.185 25.926 11.07 0.00 34.50 2.32
166 167 9.645059 TTTCAAATTCATGAACACTTGTACAAA 57.355 25.926 11.07 8.55 38.95 2.83
167 168 9.645059 TTTTCAAATTCATGAACACTTGTACAA 57.355 25.926 11.07 8.28 38.95 2.41
168 169 9.645059 TTTTTCAAATTCATGAACACTTGTACA 57.355 25.926 11.07 0.00 38.95 2.90
171 172 9.165035 ACATTTTTCAAATTCATGAACACTTGT 57.835 25.926 11.07 3.00 38.95 3.16
172 173 9.991388 AACATTTTTCAAATTCATGAACACTTG 57.009 25.926 11.07 14.06 38.95 3.16
174 175 9.381033 TGAACATTTTTCAAATTCATGAACACT 57.619 25.926 11.07 0.00 38.95 3.55
175 176 9.424659 GTGAACATTTTTCAAATTCATGAACAC 57.575 29.630 11.07 5.39 38.95 3.32
176 177 8.326713 CGTGAACATTTTTCAAATTCATGAACA 58.673 29.630 11.07 0.00 38.95 3.18
177 178 8.538856 TCGTGAACATTTTTCAAATTCATGAAC 58.461 29.630 11.07 0.00 40.55 3.18
178 179 8.640091 TCGTGAACATTTTTCAAATTCATGAA 57.360 26.923 11.26 11.26 40.55 2.57
179 180 7.920151 ACTCGTGAACATTTTTCAAATTCATGA 59.080 29.630 6.13 6.13 40.98 3.07
180 181 8.064447 ACTCGTGAACATTTTTCAAATTCATG 57.936 30.769 0.00 0.00 37.55 3.07
181 182 8.647143 AACTCGTGAACATTTTTCAAATTCAT 57.353 26.923 0.00 0.00 32.30 2.57
182 183 8.472683 AAACTCGTGAACATTTTTCAAATTCA 57.527 26.923 0.00 0.00 0.00 2.57
185 186 9.360093 TGTTAAACTCGTGAACATTTTTCAAAT 57.640 25.926 0.00 0.00 0.00 2.32
186 187 8.744008 TGTTAAACTCGTGAACATTTTTCAAA 57.256 26.923 0.00 0.00 0.00 2.69
187 188 8.744008 TTGTTAAACTCGTGAACATTTTTCAA 57.256 26.923 0.00 0.00 33.33 2.69
188 189 8.744008 TTTGTTAAACTCGTGAACATTTTTCA 57.256 26.923 0.00 0.00 33.33 2.69
190 191 9.965748 CATTTTGTTAAACTCGTGAACATTTTT 57.034 25.926 0.00 0.00 33.33 1.94
191 192 9.145865 ACATTTTGTTAAACTCGTGAACATTTT 57.854 25.926 0.00 0.00 33.33 1.82
192 193 8.591312 CACATTTTGTTAAACTCGTGAACATTT 58.409 29.630 0.00 0.00 33.33 2.32
193 194 7.253950 GCACATTTTGTTAAACTCGTGAACATT 60.254 33.333 0.00 0.00 33.33 2.71
194 195 6.198216 GCACATTTTGTTAAACTCGTGAACAT 59.802 34.615 0.00 0.00 33.33 2.71
195 196 5.513495 GCACATTTTGTTAAACTCGTGAACA 59.487 36.000 0.00 0.00 0.00 3.18
196 197 5.513495 TGCACATTTTGTTAAACTCGTGAAC 59.487 36.000 0.00 0.00 0.00 3.18
197 198 5.641709 TGCACATTTTGTTAAACTCGTGAA 58.358 33.333 0.00 0.00 0.00 3.18
198 199 5.236655 TGCACATTTTGTTAAACTCGTGA 57.763 34.783 0.00 0.00 0.00 4.35
199 200 5.685068 TCATGCACATTTTGTTAAACTCGTG 59.315 36.000 0.00 0.00 0.00 4.35
200 201 5.826586 TCATGCACATTTTGTTAAACTCGT 58.173 33.333 0.00 0.00 0.00 4.18
201 202 6.932901 ATCATGCACATTTTGTTAAACTCG 57.067 33.333 0.00 0.00 0.00 4.18
202 203 8.763356 TGAAATCATGCACATTTTGTTAAACTC 58.237 29.630 6.85 0.00 0.00 3.01
203 204 8.659925 TGAAATCATGCACATTTTGTTAAACT 57.340 26.923 6.85 0.00 0.00 2.66
204 205 9.713740 TTTGAAATCATGCACATTTTGTTAAAC 57.286 25.926 6.85 0.00 0.00 2.01
208 209 9.804758 AATTTTTGAAATCATGCACATTTTGTT 57.195 22.222 6.85 0.00 0.00 2.83
209 210 9.239002 CAATTTTTGAAATCATGCACATTTTGT 57.761 25.926 6.85 0.00 0.00 2.83
210 211 9.239002 ACAATTTTTGAAATCATGCACATTTTG 57.761 25.926 6.85 3.21 0.00 2.44
211 212 9.804758 AACAATTTTTGAAATCATGCACATTTT 57.195 22.222 6.85 0.00 0.00 1.82
212 213 9.453325 GAACAATTTTTGAAATCATGCACATTT 57.547 25.926 5.35 5.35 0.00 2.32
213 214 8.622157 TGAACAATTTTTGAAATCATGCACATT 58.378 25.926 0.00 0.00 0.00 2.71
214 215 8.155821 TGAACAATTTTTGAAATCATGCACAT 57.844 26.923 0.00 0.00 0.00 3.21
215 216 7.254829 CCTGAACAATTTTTGAAATCATGCACA 60.255 33.333 0.00 0.00 0.00 4.57
216 217 7.041916 TCCTGAACAATTTTTGAAATCATGCAC 60.042 33.333 0.00 0.00 0.00 4.57
217 218 6.990939 TCCTGAACAATTTTTGAAATCATGCA 59.009 30.769 0.00 0.00 0.00 3.96
218 219 7.424227 TCCTGAACAATTTTTGAAATCATGC 57.576 32.000 0.00 0.00 0.00 4.06
221 222 9.610705 TCAAATCCTGAACAATTTTTGAAATCA 57.389 25.926 0.00 0.00 32.05 2.57
222 223 9.868389 GTCAAATCCTGAACAATTTTTGAAATC 57.132 29.630 0.00 0.00 35.55 2.17
223 224 8.550376 CGTCAAATCCTGAACAATTTTTGAAAT 58.450 29.630 0.00 0.00 35.55 2.17
224 225 7.761704 TCGTCAAATCCTGAACAATTTTTGAAA 59.238 29.630 0.00 0.00 35.55 2.69
225 226 7.261325 TCGTCAAATCCTGAACAATTTTTGAA 58.739 30.769 0.00 0.00 35.55 2.69
226 227 6.800543 TCGTCAAATCCTGAACAATTTTTGA 58.199 32.000 0.00 0.00 35.22 2.69
227 228 7.009999 TGTTCGTCAAATCCTGAACAATTTTTG 59.990 33.333 4.33 0.00 45.38 2.44
228 229 7.038659 TGTTCGTCAAATCCTGAACAATTTTT 58.961 30.769 4.33 0.00 45.38 1.94
229 230 6.568869 TGTTCGTCAAATCCTGAACAATTTT 58.431 32.000 4.33 0.00 45.38 1.82
230 231 6.142818 TGTTCGTCAAATCCTGAACAATTT 57.857 33.333 4.33 0.00 45.38 1.82
231 232 5.766150 TGTTCGTCAAATCCTGAACAATT 57.234 34.783 4.33 0.00 45.38 2.32
235 236 6.369065 ACTCTTATGTTCGTCAAATCCTGAAC 59.631 38.462 0.00 0.00 40.76 3.18
236 237 6.368791 CACTCTTATGTTCGTCAAATCCTGAA 59.631 38.462 0.00 0.00 35.22 3.02
237 238 5.869344 CACTCTTATGTTCGTCAAATCCTGA 59.131 40.000 0.00 0.00 0.00 3.86
238 239 5.869344 TCACTCTTATGTTCGTCAAATCCTG 59.131 40.000 0.00 0.00 0.00 3.86
239 240 6.037786 TCACTCTTATGTTCGTCAAATCCT 57.962 37.500 0.00 0.00 0.00 3.24
240 241 6.910536 ATCACTCTTATGTTCGTCAAATCC 57.089 37.500 0.00 0.00 0.00 3.01
241 242 8.535592 CACTATCACTCTTATGTTCGTCAAATC 58.464 37.037 0.00 0.00 0.00 2.17
242 243 8.035394 ACACTATCACTCTTATGTTCGTCAAAT 58.965 33.333 0.00 0.00 0.00 2.32
243 244 7.375834 ACACTATCACTCTTATGTTCGTCAAA 58.624 34.615 0.00 0.00 0.00 2.69
244 245 6.920817 ACACTATCACTCTTATGTTCGTCAA 58.079 36.000 0.00 0.00 0.00 3.18
245 246 6.510879 ACACTATCACTCTTATGTTCGTCA 57.489 37.500 0.00 0.00 0.00 4.35
246 247 6.633634 GCTACACTATCACTCTTATGTTCGTC 59.366 42.308 0.00 0.00 0.00 4.20
247 248 6.319152 AGCTACACTATCACTCTTATGTTCGT 59.681 38.462 0.00 0.00 0.00 3.85
248 249 6.730175 AGCTACACTATCACTCTTATGTTCG 58.270 40.000 0.00 0.00 0.00 3.95
249 250 7.708051 TGAGCTACACTATCACTCTTATGTTC 58.292 38.462 0.00 0.00 0.00 3.18
250 251 7.340743 ACTGAGCTACACTATCACTCTTATGTT 59.659 37.037 0.00 0.00 0.00 2.71
251 252 6.831353 ACTGAGCTACACTATCACTCTTATGT 59.169 38.462 0.00 0.00 0.00 2.29
252 253 7.012799 TCACTGAGCTACACTATCACTCTTATG 59.987 40.741 0.00 0.00 0.00 1.90
253 254 7.057264 TCACTGAGCTACACTATCACTCTTAT 58.943 38.462 0.00 0.00 0.00 1.73
254 255 6.415573 TCACTGAGCTACACTATCACTCTTA 58.584 40.000 0.00 0.00 0.00 2.10
255 256 5.257262 TCACTGAGCTACACTATCACTCTT 58.743 41.667 0.00 0.00 0.00 2.85
256 257 4.849518 TCACTGAGCTACACTATCACTCT 58.150 43.478 0.00 0.00 0.00 3.24
257 258 5.518812 CATCACTGAGCTACACTATCACTC 58.481 45.833 0.00 0.00 0.00 3.51
258 259 4.202101 GCATCACTGAGCTACACTATCACT 60.202 45.833 0.00 0.00 0.00 3.41
259 260 4.047822 GCATCACTGAGCTACACTATCAC 58.952 47.826 0.00 0.00 0.00 3.06
260 261 3.701040 TGCATCACTGAGCTACACTATCA 59.299 43.478 0.00 0.00 0.00 2.15
261 262 4.297510 CTGCATCACTGAGCTACACTATC 58.702 47.826 0.00 0.00 0.00 2.08
262 263 3.492309 GCTGCATCACTGAGCTACACTAT 60.492 47.826 0.00 0.00 0.00 2.12
263 264 2.159184 GCTGCATCACTGAGCTACACTA 60.159 50.000 0.00 0.00 0.00 2.74
264 265 1.405256 GCTGCATCACTGAGCTACACT 60.405 52.381 0.00 0.00 0.00 3.55
265 266 1.005340 GCTGCATCACTGAGCTACAC 58.995 55.000 0.00 0.00 0.00 2.90
266 267 0.609662 TGCTGCATCACTGAGCTACA 59.390 50.000 0.00 0.00 33.66 2.74
267 268 1.730501 TTGCTGCATCACTGAGCTAC 58.269 50.000 1.84 0.00 33.66 3.58
268 269 2.477845 TTTGCTGCATCACTGAGCTA 57.522 45.000 1.84 0.00 33.66 3.32
269 270 1.612676 TTTTGCTGCATCACTGAGCT 58.387 45.000 1.84 0.00 33.66 4.09
270 271 2.259618 CATTTTGCTGCATCACTGAGC 58.740 47.619 1.84 0.00 0.00 4.26
271 272 3.057806 TCACATTTTGCTGCATCACTGAG 60.058 43.478 1.84 0.00 0.00 3.35
272 273 2.885894 TCACATTTTGCTGCATCACTGA 59.114 40.909 1.84 0.00 0.00 3.41
273 274 3.291809 TCACATTTTGCTGCATCACTG 57.708 42.857 1.84 0.69 0.00 3.66
274 275 3.508402 TGATCACATTTTGCTGCATCACT 59.492 39.130 1.84 0.00 0.00 3.41
275 276 3.840468 TGATCACATTTTGCTGCATCAC 58.160 40.909 1.84 0.00 0.00 3.06
276 277 4.429108 CATGATCACATTTTGCTGCATCA 58.571 39.130 1.84 1.56 34.15 3.07
277 278 3.802139 CCATGATCACATTTTGCTGCATC 59.198 43.478 1.84 0.00 34.15 3.91
278 279 3.792401 CCATGATCACATTTTGCTGCAT 58.208 40.909 1.84 0.00 34.15 3.96
279 280 2.675603 GCCATGATCACATTTTGCTGCA 60.676 45.455 0.00 0.00 34.15 4.41
280 281 1.931172 GCCATGATCACATTTTGCTGC 59.069 47.619 0.00 0.00 34.15 5.25
281 282 2.093921 TGGCCATGATCACATTTTGCTG 60.094 45.455 0.00 0.00 34.15 4.41
282 283 2.181125 TGGCCATGATCACATTTTGCT 58.819 42.857 0.00 0.00 34.15 3.91
283 284 2.676632 TGGCCATGATCACATTTTGC 57.323 45.000 0.00 0.00 34.15 3.68
284 285 3.462982 CCATGGCCATGATCACATTTTG 58.537 45.455 41.32 19.92 41.20 2.44
285 286 2.436542 CCCATGGCCATGATCACATTTT 59.563 45.455 41.32 3.98 41.20 1.82
286 287 2.043992 CCCATGGCCATGATCACATTT 58.956 47.619 41.32 4.59 41.20 2.32
287 288 1.218450 TCCCATGGCCATGATCACATT 59.782 47.619 41.32 5.46 41.20 2.71
288 289 0.854908 TCCCATGGCCATGATCACAT 59.145 50.000 41.32 6.31 41.20 3.21
289 290 0.106569 GTCCCATGGCCATGATCACA 60.107 55.000 41.32 19.79 41.20 3.58
290 291 0.106569 TGTCCCATGGCCATGATCAC 60.107 55.000 41.32 31.47 41.20 3.06
291 292 0.854908 ATGTCCCATGGCCATGATCA 59.145 50.000 41.32 32.78 41.20 2.92
292 293 2.005370 AATGTCCCATGGCCATGATC 57.995 50.000 41.32 29.19 41.20 2.92
293 294 3.076333 TCATAATGTCCCATGGCCATGAT 59.924 43.478 41.32 26.07 41.20 2.45
294 295 2.446285 TCATAATGTCCCATGGCCATGA 59.554 45.455 41.32 25.04 41.20 3.07
295 296 2.879154 TCATAATGTCCCATGGCCATG 58.121 47.619 34.82 34.82 38.51 3.66
296 297 3.839323 ATCATAATGTCCCATGGCCAT 57.161 42.857 14.09 14.09 0.00 4.40
297 298 4.951873 ATATCATAATGTCCCATGGCCA 57.048 40.909 8.56 8.56 0.00 5.36
298 299 9.592196 AAATATATATCATAATGTCCCATGGCC 57.408 33.333 6.09 0.00 0.00 5.36
312 313 9.773328 CGATTGCAACGGAAAAATATATATCAT 57.227 29.630 0.00 0.00 0.00 2.45
313 314 7.748683 GCGATTGCAACGGAAAAATATATATCA 59.251 33.333 18.46 0.00 42.15 2.15
314 315 8.093063 GCGATTGCAACGGAAAAATATATATC 57.907 34.615 18.46 0.74 42.15 1.63
332 333 0.304705 CAATAGGTCCGTGCGATTGC 59.695 55.000 0.00 0.00 43.20 3.56
333 334 0.304705 GCAATAGGTCCGTGCGATTG 59.695 55.000 0.00 0.00 0.00 2.67
334 335 0.178068 AGCAATAGGTCCGTGCGATT 59.822 50.000 8.91 0.00 43.16 3.34
335 336 1.000163 CTAGCAATAGGTCCGTGCGAT 60.000 52.381 8.91 0.00 43.16 4.58
336 337 0.384309 CTAGCAATAGGTCCGTGCGA 59.616 55.000 8.91 4.38 43.16 5.10
337 338 0.102481 ACTAGCAATAGGTCCGTGCG 59.898 55.000 8.91 0.94 43.16 5.34
338 339 1.136305 TGACTAGCAATAGGTCCGTGC 59.864 52.381 7.04 7.04 38.59 5.34
339 340 3.735237 ATGACTAGCAATAGGTCCGTG 57.265 47.619 0.00 0.00 0.00 4.94
340 341 7.719871 ATTATATGACTAGCAATAGGTCCGT 57.280 36.000 0.00 0.00 0.00 4.69
359 360 9.969001 GGCAGGGGTTTTACATCTATTATTATA 57.031 33.333 0.00 0.00 0.00 0.98
360 361 7.893833 GGGCAGGGGTTTTACATCTATTATTAT 59.106 37.037 0.00 0.00 0.00 1.28
361 362 7.235804 GGGCAGGGGTTTTACATCTATTATTA 58.764 38.462 0.00 0.00 0.00 0.98
362 363 6.075315 GGGCAGGGGTTTTACATCTATTATT 58.925 40.000 0.00 0.00 0.00 1.40
363 364 5.641155 GGGCAGGGGTTTTACATCTATTAT 58.359 41.667 0.00 0.00 0.00 1.28
364 365 4.445162 CGGGCAGGGGTTTTACATCTATTA 60.445 45.833 0.00 0.00 0.00 0.98
365 366 3.687264 CGGGCAGGGGTTTTACATCTATT 60.687 47.826 0.00 0.00 0.00 1.73
366 367 2.158667 CGGGCAGGGGTTTTACATCTAT 60.159 50.000 0.00 0.00 0.00 1.98
367 368 1.210967 CGGGCAGGGGTTTTACATCTA 59.789 52.381 0.00 0.00 0.00 1.98
368 369 0.034477 CGGGCAGGGGTTTTACATCT 60.034 55.000 0.00 0.00 0.00 2.90
369 370 0.034863 TCGGGCAGGGGTTTTACATC 60.035 55.000 0.00 0.00 0.00 3.06
370 371 0.629058 ATCGGGCAGGGGTTTTACAT 59.371 50.000 0.00 0.00 0.00 2.29
371 372 0.034863 GATCGGGCAGGGGTTTTACA 60.035 55.000 0.00 0.00 0.00 2.41
372 373 0.255033 AGATCGGGCAGGGGTTTTAC 59.745 55.000 0.00 0.00 0.00 2.01
373 374 0.996583 AAGATCGGGCAGGGGTTTTA 59.003 50.000 0.00 0.00 0.00 1.52
374 375 0.323451 GAAGATCGGGCAGGGGTTTT 60.323 55.000 0.00 0.00 0.00 2.43
375 376 1.208165 AGAAGATCGGGCAGGGGTTT 61.208 55.000 0.00 0.00 0.00 3.27
376 377 1.616628 AGAAGATCGGGCAGGGGTT 60.617 57.895 0.00 0.00 0.00 4.11
377 378 2.041265 AGAAGATCGGGCAGGGGT 59.959 61.111 0.00 0.00 0.00 4.95
378 379 2.507944 CAGAAGATCGGGCAGGGG 59.492 66.667 0.00 0.00 0.00 4.79
379 380 1.626356 TTCCAGAAGATCGGGCAGGG 61.626 60.000 0.00 0.00 31.46 4.45
402 404 1.663074 GCGAGGGATGCAGTCGATC 60.663 63.158 11.62 0.00 35.70 3.69
473 475 1.075482 CAGCTGGTTGGGTGGATGT 59.925 57.895 5.57 0.00 0.00 3.06
482 484 2.334838 GGTCGTACTAACAGCTGGTTG 58.665 52.381 19.93 15.78 40.73 3.77
592 859 1.688735 TGTCAAGCAGCTATCGCCTAT 59.311 47.619 0.00 0.00 36.60 2.57
596 863 0.649475 CAGTGTCAAGCAGCTATCGC 59.351 55.000 0.00 0.00 0.00 4.58
597 864 2.284263 TCAGTGTCAAGCAGCTATCG 57.716 50.000 0.00 0.00 0.00 2.92
599 866 2.167281 ACGATCAGTGTCAAGCAGCTAT 59.833 45.455 0.00 0.00 0.00 2.97
601 868 0.319728 ACGATCAGTGTCAAGCAGCT 59.680 50.000 0.00 0.00 0.00 4.24
603 870 1.723542 GTGACGATCAGTGTCAAGCAG 59.276 52.381 3.82 0.00 46.99 4.24
605 872 1.783284 TGTGACGATCAGTGTCAAGC 58.217 50.000 3.82 0.00 46.99 4.01
606 873 2.156504 GCTTGTGACGATCAGTGTCAAG 59.843 50.000 16.84 16.84 46.99 3.02
607 874 2.135139 GCTTGTGACGATCAGTGTCAA 58.865 47.619 3.82 4.60 46.99 3.18
608 875 1.341209 AGCTTGTGACGATCAGTGTCA 59.659 47.619 0.00 0.00 43.68 3.58
609 876 1.989165 GAGCTTGTGACGATCAGTGTC 59.011 52.381 0.00 0.00 36.88 3.67
610 877 1.341209 TGAGCTTGTGACGATCAGTGT 59.659 47.619 0.00 0.00 0.00 3.55
611 878 2.070262 TGAGCTTGTGACGATCAGTG 57.930 50.000 0.00 0.00 0.00 3.66
657 924 3.467226 GTCGGGATCTTGGCGGGA 61.467 66.667 0.00 0.00 0.00 5.14
685 952 2.484889 GAACTCGGAACACTGCTTCTT 58.515 47.619 0.00 0.00 0.00 2.52
689 956 0.249911 GTGGAACTCGGAACACTGCT 60.250 55.000 0.00 0.00 0.00 4.24
690 957 1.228657 GGTGGAACTCGGAACACTGC 61.229 60.000 0.00 0.00 36.74 4.40
691 958 0.944311 CGGTGGAACTCGGAACACTG 60.944 60.000 0.00 0.00 36.74 3.66
692 959 1.366366 CGGTGGAACTCGGAACACT 59.634 57.895 0.00 0.00 36.74 3.55
693 960 2.315386 GCGGTGGAACTCGGAACAC 61.315 63.158 0.00 0.00 36.74 3.32
1386 2566 1.760613 ACGTTGTGGAAGAGGAAGTCA 59.239 47.619 0.00 0.00 0.00 3.41
1536 2716 4.748798 CCCTCCTCCAGCCCCAGT 62.749 72.222 0.00 0.00 0.00 4.00
1800 2986 1.667724 GAGCGTACTACGTTCCAGCTA 59.332 52.381 12.96 0.00 44.33 3.32
1801 2987 0.450983 GAGCGTACTACGTTCCAGCT 59.549 55.000 12.96 0.00 44.33 4.24
1808 2994 2.030213 GTCGATCAAGAGCGTACTACGT 59.970 50.000 10.23 0.00 44.73 3.57
1809 2995 2.284684 AGTCGATCAAGAGCGTACTACG 59.715 50.000 7.63 4.12 45.88 3.51
1810 2996 3.948196 AGTCGATCAAGAGCGTACTAC 57.052 47.619 7.63 0.00 41.48 2.73
1811 2997 3.487042 GCAAGTCGATCAAGAGCGTACTA 60.487 47.826 7.63 0.00 41.48 1.82
1812 2998 2.732597 GCAAGTCGATCAAGAGCGTACT 60.733 50.000 7.63 7.20 41.48 2.73
1813 2999 1.584308 GCAAGTCGATCAAGAGCGTAC 59.416 52.381 7.63 5.16 41.48 3.67
1814 3000 1.794076 CGCAAGTCGATCAAGAGCGTA 60.794 52.381 7.63 0.00 41.48 4.42
1815 3001 1.073216 CGCAAGTCGATCAAGAGCGT 61.073 55.000 7.63 0.00 41.48 5.07
1816 3002 1.627943 CGCAAGTCGATCAAGAGCG 59.372 57.895 0.65 0.65 41.67 5.03
1817 3003 1.346538 GCGCAAGTCGATCAAGAGC 59.653 57.895 0.30 0.00 41.67 4.09
1819 3005 4.185413 GGCGCAAGTCGATCAAGA 57.815 55.556 10.83 0.00 41.67 3.02
1834 3020 0.308993 GAAATAGCTGATGCCACGGC 59.691 55.000 0.00 0.00 40.80 5.68
1846 3038 3.438781 TCCATGTCAAACGGTGAAATAGC 59.561 43.478 0.00 0.00 38.23 2.97
1860 3059 6.806668 TCTATCACATTAACCTCCATGTCA 57.193 37.500 0.00 0.00 30.90 3.58
1861 3060 7.445121 TGATCTATCACATTAACCTCCATGTC 58.555 38.462 0.00 0.00 30.90 3.06
1862 3061 7.379059 TGATCTATCACATTAACCTCCATGT 57.621 36.000 0.00 0.00 33.72 3.21
1863 3062 8.098912 TCATGATCTATCACATTAACCTCCATG 58.901 37.037 0.00 0.00 40.03 3.66
1865 3064 7.616528 TCATGATCTATCACATTAACCTCCA 57.383 36.000 0.00 0.00 40.03 3.86
1866 3065 6.593382 GCTCATGATCTATCACATTAACCTCC 59.407 42.308 0.00 0.00 40.03 4.30
1868 3067 7.071069 TGCTCATGATCTATCACATTAACCT 57.929 36.000 0.00 0.00 40.03 3.50
1869 3068 7.570140 CGTTGCTCATGATCTATCACATTAACC 60.570 40.741 0.00 0.00 40.03 2.85
1870 3069 7.286508 CGTTGCTCATGATCTATCACATTAAC 58.713 38.462 0.00 0.00 40.03 2.01
1871 3070 6.424812 CCGTTGCTCATGATCTATCACATTAA 59.575 38.462 0.00 0.00 40.03 1.40
1873 3072 4.753610 CCGTTGCTCATGATCTATCACATT 59.246 41.667 0.00 0.00 40.03 2.71
1874 3073 4.313282 CCGTTGCTCATGATCTATCACAT 58.687 43.478 0.00 0.00 40.03 3.21
2023 3231 1.303317 CTTGTACTTGGCCGGGCTT 60.303 57.895 29.87 15.55 0.00 4.35
2025 3233 2.750237 CCTTGTACTTGGCCGGGC 60.750 66.667 23.42 23.42 0.00 6.13
2170 3385 4.768968 CCAAGGAAGACAATCCAAACAGAT 59.231 41.667 0.00 0.00 42.27 2.90
2183 3398 0.476771 TCCCAACCACCAAGGAAGAC 59.523 55.000 0.00 0.00 41.22 3.01
2189 3404 1.347378 CCCAAATTCCCAACCACCAAG 59.653 52.381 0.00 0.00 0.00 3.61
2232 3447 9.271828 CTATCCAAACAAAAGCCTTAACAAAAT 57.728 29.630 0.00 0.00 0.00 1.82
2235 3450 6.041523 AGCTATCCAAACAAAAGCCTTAACAA 59.958 34.615 0.00 0.00 33.63 2.83
2236 3451 5.538433 AGCTATCCAAACAAAAGCCTTAACA 59.462 36.000 0.00 0.00 33.63 2.41
2285 3907 0.816018 TGTGGGTGCGTCGAATTGTT 60.816 50.000 0.00 0.00 0.00 2.83
2313 3937 2.159572 GGTGAGTGTGTGTGTGTTTGTC 60.160 50.000 0.00 0.00 0.00 3.18
2330 3956 1.702401 TGTGTATCTTGCCTTGGGTGA 59.298 47.619 0.00 0.00 0.00 4.02
2378 4004 6.483385 TTTGTGTACTTTGAGTCGTTTGAA 57.517 33.333 0.00 0.00 0.00 2.69
2462 4089 3.261981 AGTCACGGTTTGTTCTTCACT 57.738 42.857 0.00 0.00 0.00 3.41
2837 4524 3.614092 CTTCATAGTGCTCATGGGTTGT 58.386 45.455 0.00 0.00 0.00 3.32
2838 4525 2.357009 GCTTCATAGTGCTCATGGGTTG 59.643 50.000 0.00 0.00 0.00 3.77
2840 4527 1.133976 GGCTTCATAGTGCTCATGGGT 60.134 52.381 0.00 0.00 0.00 4.51
2842 4529 1.224075 CGGCTTCATAGTGCTCATGG 58.776 55.000 0.00 0.00 0.00 3.66
2843 4530 1.224075 CCGGCTTCATAGTGCTCATG 58.776 55.000 0.00 0.00 0.00 3.07
2844 4531 0.533755 GCCGGCTTCATAGTGCTCAT 60.534 55.000 22.15 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.