Multiple sequence alignment - TraesCS4D01G302800

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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 TraesCS4D01G302800 chr4D 100.000 2360 0 0 1 2360 470857810 470855451 0.000000e+00 4359.0
1 TraesCS4D01G302800 chr4D 83.697 595 48 26 784 1363 471229494 471228934 1.250000e-142 516.0
2 TraesCS4D01G302800 chr4D 91.525 354 25 5 5 354 139307866 139307514 1.270000e-132 483.0
3 TraesCS4D01G302800 chr4D 80.922 629 76 24 756 1363 471212892 471212287 7.690000e-125 457.0
4 TraesCS4D01G302800 chr4D 79.079 717 79 32 684 1363 471217114 471216432 6.030000e-116 427.0
5 TraesCS4D01G302800 chr4D 84.921 378 33 7 1000 1365 471265412 471265047 6.200000e-96 361.0
6 TraesCS4D01G302800 chr4B 90.021 1874 100 37 347 2184 593117354 593115532 0.000000e+00 2344.0
7 TraesCS4D01G302800 chr4B 91.223 376 33 0 997 1372 593135972 593135597 1.620000e-141 512.0
8 TraesCS4D01G302800 chr4B 80.791 708 86 27 684 1363 593198000 593197315 2.090000e-140 508.0
9 TraesCS4D01G302800 chr4B 87.644 348 35 7 6 349 12847971 12848314 4.730000e-107 398.0
10 TraesCS4D01G302800 chr4B 79.734 602 78 24 784 1363 593200537 593199958 1.700000e-106 396.0
11 TraesCS4D01G302800 chr4B 87.941 340 29 5 1038 1365 593347917 593347578 7.910000e-105 390.0
12 TraesCS4D01G302800 chr4A 88.150 1595 112 34 504 2055 678341440 678339880 0.000000e+00 1827.0
13 TraesCS4D01G302800 chr4A 81.592 603 64 23 788 1363 678405134 678404552 2.760000e-124 455.0
14 TraesCS4D01G302800 chr4A 81.135 599 62 22 784 1363 678376781 678376215 1.300000e-117 433.0
15 TraesCS4D01G302800 chr4A 88.690 168 17 2 347 512 678341790 678341623 1.110000e-48 204.0
16 TraesCS4D01G302800 chr4A 93.846 65 1 2 2191 2255 678339798 678339737 6.940000e-16 95.3
17 TraesCS4D01G302800 chr3A 91.714 350 20 6 6 349 492326288 492325942 5.900000e-131 477.0
18 TraesCS4D01G302800 chr1D 90.730 356 27 6 1 352 5530227 5529874 9.870000e-129 470.0
19 TraesCS4D01G302800 chr7D 90.395 354 25 6 1 349 191572342 191571993 7.690000e-125 457.0
20 TraesCS4D01G302800 chr7D 89.577 355 30 7 1 351 6578047 6578398 5.990000e-121 444.0
21 TraesCS4D01G302800 chr7D 95.455 44 2 0 2262 2305 166662262 166662219 1.170000e-08 71.3
22 TraesCS4D01G302800 chr2D 89.256 363 32 7 1 358 640638121 640637761 4.630000e-122 448.0
23 TraesCS4D01G302800 chr7A 89.607 356 25 8 1 351 441586082 441586430 2.150000e-120 442.0
24 TraesCS4D01G302800 chr2A 90.520 327 26 5 1 324 543764367 543764043 6.030000e-116 427.0


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 TraesCS4D01G302800 chr4D 470855451 470857810 2359 True 4359.000000 4359 100.000000 1 2360 1 chr4D.!!$R2 2359
1 TraesCS4D01G302800 chr4D 471228934 471229494 560 True 516.000000 516 83.697000 784 1363 1 chr4D.!!$R3 579
2 TraesCS4D01G302800 chr4D 471212287 471217114 4827 True 442.000000 457 80.000500 684 1363 2 chr4D.!!$R5 679
3 TraesCS4D01G302800 chr4B 593115532 593117354 1822 True 2344.000000 2344 90.021000 347 2184 1 chr4B.!!$R1 1837
4 TraesCS4D01G302800 chr4B 593197315 593200537 3222 True 452.000000 508 80.262500 684 1363 2 chr4B.!!$R4 679
5 TraesCS4D01G302800 chr4A 678339737 678341790 2053 True 708.766667 1827 90.228667 347 2255 3 chr4A.!!$R3 1908
6 TraesCS4D01G302800 chr4A 678404552 678405134 582 True 455.000000 455 81.592000 788 1363 1 chr4A.!!$R2 575
7 TraesCS4D01G302800 chr4A 678376215 678376781 566 True 433.000000 433 81.135000 784 1363 1 chr4A.!!$R1 579

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
470 472 0.029567 GTATGGGCGACGAGTCTGAG 59.97 60.0 0.0 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2165 9262 0.039978 TGCCGCAACAAATTACACCG 60.04 50.0 0.0 0.0 0.0 4.94 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
25 26 8.900511 CGATGTGTGATGAAATATGAGTTTTT 57.099 30.769 0.00 0.00 0.00 1.94
26 27 9.986833 CGATGTGTGATGAAATATGAGTTTTTA 57.013 29.630 0.00 0.00 0.00 1.52
68 69 7.922505 TGTGTATTGAACTATTTGTTGTTGC 57.077 32.000 0.00 0.00 39.30 4.17
69 70 7.484140 TGTGTATTGAACTATTTGTTGTTGCA 58.516 30.769 0.00 0.00 39.30 4.08
70 71 7.433719 TGTGTATTGAACTATTTGTTGTTGCAC 59.566 33.333 0.00 0.00 39.30 4.57
71 72 7.647715 GTGTATTGAACTATTTGTTGTTGCACT 59.352 33.333 0.00 0.00 39.30 4.40
72 73 8.841300 TGTATTGAACTATTTGTTGTTGCACTA 58.159 29.630 0.00 0.00 39.30 2.74
73 74 9.840427 GTATTGAACTATTTGTTGTTGCACTAT 57.160 29.630 0.00 0.00 39.30 2.12
75 76 9.762933 ATTGAACTATTTGTTGTTGCACTATTT 57.237 25.926 0.00 0.00 39.30 1.40
76 77 9.593134 TTGAACTATTTGTTGTTGCACTATTTT 57.407 25.926 0.00 0.00 39.30 1.82
77 78 9.029243 TGAACTATTTGTTGTTGCACTATTTTG 57.971 29.630 0.00 0.00 39.30 2.44
78 79 8.940768 AACTATTTGTTGTTGCACTATTTTGT 57.059 26.923 0.00 0.00 37.52 2.83
79 80 8.940768 ACTATTTGTTGTTGCACTATTTTGTT 57.059 26.923 0.00 0.00 0.00 2.83
80 81 8.816144 ACTATTTGTTGTTGCACTATTTTGTTG 58.184 29.630 0.00 0.00 0.00 3.33
81 82 7.840342 ATTTGTTGTTGCACTATTTTGTTGA 57.160 28.000 0.00 0.00 0.00 3.18
82 83 7.658179 TTTGTTGTTGCACTATTTTGTTGAA 57.342 28.000 0.00 0.00 0.00 2.69
83 84 7.840342 TTGTTGTTGCACTATTTTGTTGAAT 57.160 28.000 0.00 0.00 0.00 2.57
84 85 7.840342 TGTTGTTGCACTATTTTGTTGAATT 57.160 28.000 0.00 0.00 0.00 2.17
85 86 8.932945 TGTTGTTGCACTATTTTGTTGAATTA 57.067 26.923 0.00 0.00 0.00 1.40
86 87 9.539825 TGTTGTTGCACTATTTTGTTGAATTAT 57.460 25.926 0.00 0.00 0.00 1.28
113 114 9.984190 TTGATTTTGATTGATTTTCTGTGATGA 57.016 25.926 0.00 0.00 0.00 2.92
114 115 9.984190 TGATTTTGATTGATTTTCTGTGATGAA 57.016 25.926 0.00 0.00 0.00 2.57
116 117 9.991906 ATTTTGATTGATTTTCTGTGATGAACT 57.008 25.926 0.00 0.00 0.00 3.01
118 119 9.897744 TTTGATTGATTTTCTGTGATGAACTAC 57.102 29.630 0.00 0.00 0.00 2.73
119 120 7.742151 TGATTGATTTTCTGTGATGAACTACG 58.258 34.615 0.00 0.00 0.00 3.51
120 121 7.387673 TGATTGATTTTCTGTGATGAACTACGT 59.612 33.333 0.00 0.00 0.00 3.57
121 122 6.706055 TGATTTTCTGTGATGAACTACGTC 57.294 37.500 0.00 0.00 35.29 4.34
122 123 5.637810 TGATTTTCTGTGATGAACTACGTCC 59.362 40.000 0.00 0.00 33.92 4.79
123 124 4.866508 TTTCTGTGATGAACTACGTCCT 57.133 40.909 0.00 0.00 33.92 3.85
124 125 5.970317 TTTCTGTGATGAACTACGTCCTA 57.030 39.130 0.00 0.00 33.92 2.94
125 126 5.970317 TTCTGTGATGAACTACGTCCTAA 57.030 39.130 0.00 0.00 33.92 2.69
126 127 5.970317 TCTGTGATGAACTACGTCCTAAA 57.030 39.130 0.00 0.00 33.92 1.85
127 128 6.335471 TCTGTGATGAACTACGTCCTAAAA 57.665 37.500 0.00 0.00 33.92 1.52
128 129 6.751157 TCTGTGATGAACTACGTCCTAAAAA 58.249 36.000 0.00 0.00 33.92 1.94
154 155 8.856490 AATTATTTATGTTGAGAATTCACGCC 57.144 30.769 8.44 0.00 31.71 5.68
155 156 4.335082 TTTATGTTGAGAATTCACGCCG 57.665 40.909 8.44 0.00 31.71 6.46
156 157 2.093306 ATGTTGAGAATTCACGCCGA 57.907 45.000 8.44 0.00 31.71 5.54
157 158 1.872388 TGTTGAGAATTCACGCCGAA 58.128 45.000 8.44 0.00 38.22 4.30
158 159 1.529438 TGTTGAGAATTCACGCCGAAC 59.471 47.619 8.44 2.91 36.12 3.95
159 160 1.136057 GTTGAGAATTCACGCCGAACC 60.136 52.381 8.44 0.00 36.12 3.62
160 161 0.034198 TGAGAATTCACGCCGAACCA 59.966 50.000 8.44 0.00 36.12 3.67
161 162 0.442699 GAGAATTCACGCCGAACCAC 59.557 55.000 8.44 0.00 36.12 4.16
162 163 1.131826 GAATTCACGCCGAACCACG 59.868 57.895 0.00 0.00 36.12 4.94
163 164 1.562575 GAATTCACGCCGAACCACGT 61.563 55.000 0.00 0.00 44.75 4.49
164 165 1.562575 AATTCACGCCGAACCACGTC 61.563 55.000 0.00 0.00 41.32 4.34
166 167 4.986587 CACGCCGAACCACGTCGA 62.987 66.667 0.00 0.00 46.15 4.20
167 168 4.268939 ACGCCGAACCACGTCGAA 62.269 61.111 0.00 0.00 46.15 3.71
168 169 2.807895 CGCCGAACCACGTCGAAT 60.808 61.111 0.00 0.00 46.15 3.34
169 170 1.514657 CGCCGAACCACGTCGAATA 60.515 57.895 0.00 0.00 46.15 1.75
170 171 0.868602 CGCCGAACCACGTCGAATAT 60.869 55.000 0.00 0.00 46.15 1.28
171 172 0.575390 GCCGAACCACGTCGAATATG 59.425 55.000 0.00 0.00 43.86 1.78
172 173 1.205657 CCGAACCACGTCGAATATGG 58.794 55.000 0.00 8.86 43.86 2.74
173 174 1.205657 CGAACCACGTCGAATATGGG 58.794 55.000 13.72 2.77 43.86 4.00
174 175 0.935196 GAACCACGTCGAATATGGGC 59.065 55.000 13.72 3.89 37.86 5.36
175 176 0.463116 AACCACGTCGAATATGGGCC 60.463 55.000 13.72 0.00 37.86 5.80
176 177 1.954146 CCACGTCGAATATGGGCCG 60.954 63.158 0.00 0.00 0.00 6.13
177 178 1.066752 CACGTCGAATATGGGCCGA 59.933 57.895 0.00 0.00 0.00 5.54
178 179 0.319555 CACGTCGAATATGGGCCGAT 60.320 55.000 5.29 5.29 34.71 4.18
179 180 0.391597 ACGTCGAATATGGGCCGATT 59.608 50.000 5.24 0.02 34.71 3.34
180 181 1.068474 CGTCGAATATGGGCCGATTC 58.932 55.000 17.03 17.03 34.71 2.52
181 182 1.336887 CGTCGAATATGGGCCGATTCT 60.337 52.381 21.82 0.00 34.71 2.40
182 183 2.338500 GTCGAATATGGGCCGATTCTC 58.662 52.381 21.82 14.08 34.71 2.87
183 184 1.067846 TCGAATATGGGCCGATTCTCG 60.068 52.381 21.82 18.95 40.07 4.04
184 185 1.079503 GAATATGGGCCGATTCTCGC 58.920 55.000 18.85 0.00 38.82 5.03
185 186 0.321653 AATATGGGCCGATTCTCGCC 60.322 55.000 5.24 3.62 38.82 5.54
186 187 2.507110 ATATGGGCCGATTCTCGCCG 62.507 60.000 5.24 0.00 38.82 6.46
188 189 4.301027 GGGCCGATTCTCGCCGAT 62.301 66.667 0.00 0.00 38.82 4.18
189 190 2.649034 GGCCGATTCTCGCCGATA 59.351 61.111 0.00 0.00 38.82 2.92
190 191 1.215647 GGCCGATTCTCGCCGATAT 59.784 57.895 0.00 0.00 38.82 1.63
191 192 0.802607 GGCCGATTCTCGCCGATATC 60.803 60.000 0.00 0.00 38.82 1.63
192 193 1.134530 GCCGATTCTCGCCGATATCG 61.135 60.000 18.31 18.31 38.82 2.92
205 206 1.986378 CGATATCGGGTCATTTCTCGC 59.014 52.381 17.51 0.00 35.37 5.03
206 207 2.338500 GATATCGGGTCATTTCTCGCC 58.662 52.381 0.00 0.00 0.00 5.54
207 208 0.031585 TATCGGGTCATTTCTCGCCG 59.968 55.000 0.00 0.00 0.00 6.46
208 209 1.672854 ATCGGGTCATTTCTCGCCGA 61.673 55.000 0.00 0.00 33.61 5.54
209 210 1.447140 CGGGTCATTTCTCGCCGAA 60.447 57.895 0.00 0.00 0.00 4.30
210 211 1.017177 CGGGTCATTTCTCGCCGAAA 61.017 55.000 0.00 2.88 45.08 3.46
211 212 0.727398 GGGTCATTTCTCGCCGAAAG 59.273 55.000 0.00 0.00 44.29 2.62
212 213 1.439679 GGTCATTTCTCGCCGAAAGT 58.560 50.000 0.00 0.00 44.29 2.66
213 214 1.128692 GGTCATTTCTCGCCGAAAGTG 59.871 52.381 0.00 0.00 44.29 3.16
214 215 1.128692 GTCATTTCTCGCCGAAAGTGG 59.871 52.381 0.00 0.00 44.29 4.00
215 216 0.447801 CATTTCTCGCCGAAAGTGGG 59.552 55.000 0.00 0.00 44.29 4.61
216 217 1.305930 ATTTCTCGCCGAAAGTGGGC 61.306 55.000 0.00 0.00 44.29 5.36
221 222 2.981350 GCCGAAAGTGGGCCGAAA 60.981 61.111 0.00 0.00 44.97 3.46
222 223 2.557372 GCCGAAAGTGGGCCGAAAA 61.557 57.895 0.00 0.00 44.97 2.29
223 224 1.284715 CCGAAAGTGGGCCGAAAAC 59.715 57.895 0.00 0.00 0.00 2.43
224 225 1.170290 CCGAAAGTGGGCCGAAAACT 61.170 55.000 0.00 0.00 0.00 2.66
225 226 0.040425 CGAAAGTGGGCCGAAAACTG 60.040 55.000 0.00 0.00 0.00 3.16
226 227 0.313987 GAAAGTGGGCCGAAAACTGG 59.686 55.000 0.00 0.00 0.00 4.00
233 234 3.981308 CCGAAAACTGGCCGACAT 58.019 55.556 0.00 0.00 0.00 3.06
234 235 1.794222 CCGAAAACTGGCCGACATC 59.206 57.895 0.00 0.00 0.00 3.06
235 236 1.419922 CGAAAACTGGCCGACATCG 59.580 57.895 0.00 0.31 39.44 3.84
236 237 1.011968 CGAAAACTGGCCGACATCGA 61.012 55.000 11.00 0.00 43.02 3.59
237 238 0.442699 GAAAACTGGCCGACATCGAC 59.557 55.000 2.09 0.00 43.02 4.20
238 239 1.289109 AAAACTGGCCGACATCGACG 61.289 55.000 2.09 0.00 43.02 5.12
239 240 4.796231 ACTGGCCGACATCGACGC 62.796 66.667 2.09 0.00 43.02 5.19
244 245 4.873129 CCGACATCGACGCCTGGG 62.873 72.222 2.09 0.00 43.02 4.45
245 246 4.873129 CGACATCGACGCCTGGGG 62.873 72.222 9.49 9.49 43.02 4.96
281 282 3.546543 CCGCCCCAGAGCCGATTA 61.547 66.667 0.00 0.00 0.00 1.75
282 283 2.743718 CGCCCCAGAGCCGATTAT 59.256 61.111 0.00 0.00 0.00 1.28
283 284 1.541310 CCGCCCCAGAGCCGATTATA 61.541 60.000 0.00 0.00 0.00 0.98
284 285 0.389948 CGCCCCAGAGCCGATTATAC 60.390 60.000 0.00 0.00 0.00 1.47
285 286 0.036294 GCCCCAGAGCCGATTATACC 60.036 60.000 0.00 0.00 0.00 2.73
286 287 0.246635 CCCCAGAGCCGATTATACCG 59.753 60.000 0.00 0.00 0.00 4.02
287 288 0.389948 CCCAGAGCCGATTATACCGC 60.390 60.000 0.00 0.00 0.00 5.68
288 289 0.389948 CCAGAGCCGATTATACCGCC 60.390 60.000 0.00 0.00 0.00 6.13
289 290 0.732880 CAGAGCCGATTATACCGCCG 60.733 60.000 0.00 0.00 0.00 6.46
290 291 1.445582 GAGCCGATTATACCGCCGG 60.446 63.158 0.00 0.00 44.34 6.13
292 293 2.654877 CCGATTATACCGCCGGCT 59.345 61.111 26.68 9.55 35.29 5.52
293 294 1.445582 CCGATTATACCGCCGGCTC 60.446 63.158 26.68 12.39 35.29 4.70
294 295 1.800315 CGATTATACCGCCGGCTCG 60.800 63.158 26.68 20.74 0.00 5.03
295 296 2.048503 ATTATACCGCCGGCTCGC 60.049 61.111 26.68 0.00 0.00 5.03
296 297 3.584868 ATTATACCGCCGGCTCGCC 62.585 63.158 26.68 0.00 0.00 5.54
312 313 2.438434 CCTCCAGGCGGCGATTTT 60.438 61.111 12.98 0.00 0.00 1.82
313 314 2.046285 CCTCCAGGCGGCGATTTTT 61.046 57.895 12.98 0.00 0.00 1.94
314 315 0.746563 CCTCCAGGCGGCGATTTTTA 60.747 55.000 12.98 0.00 0.00 1.52
315 316 1.308998 CTCCAGGCGGCGATTTTTAT 58.691 50.000 12.98 0.00 0.00 1.40
316 317 1.002468 CTCCAGGCGGCGATTTTTATG 60.002 52.381 12.98 0.00 0.00 1.90
317 318 0.594796 CCAGGCGGCGATTTTTATGC 60.595 55.000 12.98 0.00 0.00 3.14
318 319 0.594796 CAGGCGGCGATTTTTATGCC 60.595 55.000 12.98 0.00 45.39 4.40
324 325 2.208326 GCGATTTTTATGCCACCTGG 57.792 50.000 0.00 0.00 38.53 4.45
325 326 1.202405 GCGATTTTTATGCCACCTGGG 60.202 52.381 0.00 0.00 40.85 4.45
326 327 2.374184 CGATTTTTATGCCACCTGGGA 58.626 47.619 0.00 0.00 40.01 4.37
327 328 2.358898 CGATTTTTATGCCACCTGGGAG 59.641 50.000 0.00 0.00 39.50 4.30
328 329 2.230130 TTTTTATGCCACCTGGGAGG 57.770 50.000 0.00 0.22 39.50 4.30
334 335 4.722700 CCACCTGGGAGGCCAACG 62.723 72.222 5.01 0.00 39.63 4.10
335 336 3.636231 CACCTGGGAGGCCAACGA 61.636 66.667 5.01 0.00 39.63 3.85
336 337 3.637273 ACCTGGGAGGCCAACGAC 61.637 66.667 5.01 0.00 39.63 4.34
337 338 3.322466 CCTGGGAGGCCAACGACT 61.322 66.667 5.01 0.00 0.00 4.18
338 339 2.046892 CTGGGAGGCCAACGACTG 60.047 66.667 5.01 0.00 0.00 3.51
390 391 4.982295 TGATCAAAACCATATAGCGACTCG 59.018 41.667 0.00 0.00 0.00 4.18
411 413 5.470368 TCGGTCAGAGTTACTCAATCAAAG 58.530 41.667 15.23 0.29 32.06 2.77
417 419 6.648310 TCAGAGTTACTCAATCAAAGCAGAAG 59.352 38.462 15.23 0.00 32.06 2.85
470 472 0.029567 GTATGGGCGACGAGTCTGAG 59.970 60.000 0.00 0.00 0.00 3.35
479 482 2.055100 GACGAGTCTGAGCAAACTGAC 58.945 52.381 0.00 0.00 38.43 3.51
485 488 2.030185 GTCTGAGCAAACTGACCGACTA 60.030 50.000 0.00 0.00 34.32 2.59
555 749 4.154375 GCAAAGCCAAACTTCTACTACTCC 59.846 45.833 0.00 0.00 37.75 3.85
579 773 2.039818 TCTGCTAGACCACCGACTAG 57.960 55.000 0.00 0.00 39.05 2.57
594 788 2.352421 CGACTAGGAACCACACGTGATT 60.352 50.000 25.01 13.21 0.00 2.57
603 797 1.071299 ACACGTGATTCAGCAGCCA 59.929 52.632 25.01 0.00 0.00 4.75
624 818 4.380655 CCAACTCGAAGTCTCGGTAGAAAT 60.381 45.833 0.00 0.00 45.49 2.17
634 828 4.325472 GTCTCGGTAGAAATTTGTACACGG 59.675 45.833 22.64 16.62 32.16 4.94
661 859 5.935945 TCCAATCTTCACCTTCTACACAAA 58.064 37.500 0.00 0.00 0.00 2.83
676 874 2.803956 ACACAAAGTGTCCCGATTAACG 59.196 45.455 0.00 0.00 43.92 3.18
862 1088 3.587797 TCGCCTTCCCGCTATAAATAG 57.412 47.619 0.00 0.00 0.00 1.73
937 1198 2.125673 GAGCCCAAGCGTTCGCTA 60.126 61.111 19.67 0.00 46.67 4.26
938 1199 1.521681 GAGCCCAAGCGTTCGCTAT 60.522 57.895 19.67 7.90 46.67 2.97
939 1200 0.249322 GAGCCCAAGCGTTCGCTATA 60.249 55.000 19.67 0.00 46.67 1.31
1384 8442 1.357334 GGAGGATCGTCGAGCTGAC 59.643 63.158 10.72 0.00 44.53 3.51
1423 8481 2.029020 CGTGGATCTTTGAGTCTGTCCA 60.029 50.000 0.00 0.00 33.63 4.02
1496 8554 5.524971 TGGGGAGTGAGTTATATGTAACG 57.475 43.478 6.70 0.00 43.92 3.18
1531 8589 0.308684 ACGCATGCGCCAGATTATTG 59.691 50.000 38.15 9.62 44.19 1.90
1579 8637 2.630580 ACCTTATTGATCTCCGCTCCTC 59.369 50.000 0.00 0.00 0.00 3.71
1589 8647 1.730902 CCGCTCCTCGATGTATGCG 60.731 63.158 14.13 14.13 41.67 4.73
1607 8665 4.002906 TGCGTCTGTTCTCCATTAACTT 57.997 40.909 0.00 0.00 0.00 2.66
1609 8667 3.746492 GCGTCTGTTCTCCATTAACTTGT 59.254 43.478 0.00 0.00 0.00 3.16
1612 8670 5.696724 CGTCTGTTCTCCATTAACTTGTTCT 59.303 40.000 0.00 0.00 0.00 3.01
1620 8686 9.567776 TTCTCCATTAACTTGTTCTGATTAACA 57.432 29.630 0.00 0.00 37.58 2.41
1627 8693 6.767524 ACTTGTTCTGATTAACAACAACCA 57.232 33.333 0.00 0.00 42.78 3.67
1633 8700 8.037758 TGTTCTGATTAACAACAACCACAAAAT 58.962 29.630 0.00 0.00 36.45 1.82
1651 8718 5.997129 ACAAAATTGGCAAGAAACCCTAATG 59.003 36.000 5.96 0.00 0.00 1.90
1653 8720 5.405935 AATTGGCAAGAAACCCTAATGTC 57.594 39.130 5.96 0.00 0.00 3.06
1656 8723 3.245586 TGGCAAGAAACCCTAATGTCCAT 60.246 43.478 0.00 0.00 0.00 3.41
1657 8724 3.769300 GGCAAGAAACCCTAATGTCCATT 59.231 43.478 0.00 0.00 34.93 3.16
1711 8778 2.280524 CGGCCGTGTGGAACTTGA 60.281 61.111 19.50 0.00 38.04 3.02
1712 8779 2.604174 CGGCCGTGTGGAACTTGAC 61.604 63.158 19.50 0.00 38.04 3.18
1716 8783 0.859232 CCGTGTGGAACTTGACGAAG 59.141 55.000 0.00 0.00 38.04 3.79
1839 8911 1.796796 GATGAGAGTTGCCGTTGCC 59.203 57.895 0.00 0.00 36.33 4.52
1962 9039 3.313249 GCCTGCTTGCTTTTGTTTTTCAT 59.687 39.130 0.00 0.00 0.00 2.57
1963 9040 4.553351 GCCTGCTTGCTTTTGTTTTTCATC 60.553 41.667 0.00 0.00 0.00 2.92
2072 9154 3.526931 TTTCTGGACTCCAATAGCGAG 57.473 47.619 0.00 0.00 30.80 5.03
2075 9157 3.300388 TCTGGACTCCAATAGCGAGAAT 58.700 45.455 0.00 0.00 30.80 2.40
2087 9171 5.818136 ATAGCGAGAATGCTTTTGCTTTA 57.182 34.783 11.14 0.00 44.46 1.85
2136 9233 1.375908 CACGCTTCTGCTTAGGCCA 60.376 57.895 5.01 0.00 37.74 5.36
2137 9234 1.376037 ACGCTTCTGCTTAGGCCAC 60.376 57.895 5.01 0.00 37.74 5.01
2143 9240 4.752879 TGCTTAGGCCACCGACGC 62.753 66.667 5.01 0.00 37.74 5.19
2165 9262 0.097674 ATTGATTTCTGCGCGTCTGC 59.902 50.000 8.43 0.00 37.91 4.26
2184 9281 0.039978 CGGTGTAATTTGTTGCGGCA 60.040 50.000 0.00 0.00 0.00 5.69
2185 9282 1.600663 CGGTGTAATTTGTTGCGGCAA 60.601 47.619 12.11 12.11 0.00 4.52
2186 9283 2.058057 GGTGTAATTTGTTGCGGCAAG 58.942 47.619 16.97 0.00 0.00 4.01
2187 9284 2.058057 GTGTAATTTGTTGCGGCAAGG 58.942 47.619 16.97 0.00 0.00 3.61
2188 9285 1.000283 TGTAATTTGTTGCGGCAAGGG 60.000 47.619 16.97 0.00 0.00 3.95
2189 9286 1.000394 GTAATTTGTTGCGGCAAGGGT 60.000 47.619 16.97 2.80 0.00 4.34
2255 9352 1.344763 GGAGGATGGAGGAATACCACG 59.655 57.143 0.00 0.00 40.36 4.94
2256 9353 2.317040 GAGGATGGAGGAATACCACGA 58.683 52.381 0.00 0.00 40.36 4.35
2257 9354 2.297597 GAGGATGGAGGAATACCACGAG 59.702 54.545 0.00 0.00 40.36 4.18
2258 9355 2.040178 GGATGGAGGAATACCACGAGT 58.960 52.381 0.00 0.00 40.36 4.18
2259 9356 2.224066 GGATGGAGGAATACCACGAGTG 60.224 54.545 0.00 0.00 40.36 3.51
2268 9365 2.593436 CCACGAGTGGGGCGTTTT 60.593 61.111 14.19 0.00 46.81 2.43
2269 9366 2.637025 CACGAGTGGGGCGTTTTG 59.363 61.111 0.00 0.00 40.44 2.44
2270 9367 2.593436 ACGAGTGGGGCGTTTTGG 60.593 61.111 0.00 0.00 39.18 3.28
2271 9368 2.593436 CGAGTGGGGCGTTTTGGT 60.593 61.111 0.00 0.00 0.00 3.67
2272 9369 2.903547 CGAGTGGGGCGTTTTGGTG 61.904 63.158 0.00 0.00 0.00 4.17
2273 9370 3.207547 GAGTGGGGCGTTTTGGTGC 62.208 63.158 0.00 0.00 0.00 5.01
2279 9376 3.605664 GCGTTTTGGTGCCAGGCT 61.606 61.111 14.15 0.00 0.00 4.58
2280 9377 2.644992 CGTTTTGGTGCCAGGCTC 59.355 61.111 14.15 9.31 0.00 4.70
2281 9378 2.192861 CGTTTTGGTGCCAGGCTCA 61.193 57.895 14.15 8.50 0.00 4.26
2282 9379 1.526575 CGTTTTGGTGCCAGGCTCAT 61.527 55.000 14.15 0.00 0.00 2.90
2283 9380 0.244721 GTTTTGGTGCCAGGCTCATC 59.755 55.000 14.15 0.00 0.00 2.92
2284 9381 0.112995 TTTTGGTGCCAGGCTCATCT 59.887 50.000 14.15 0.00 0.00 2.90
2285 9382 0.609957 TTTGGTGCCAGGCTCATCTG 60.610 55.000 14.15 0.00 34.70 2.90
2286 9383 2.827642 GGTGCCAGGCTCATCTGC 60.828 66.667 14.15 0.00 33.64 4.26
2287 9384 2.045634 GTGCCAGGCTCATCTGCA 60.046 61.111 14.15 0.00 33.64 4.41
2288 9385 2.045634 TGCCAGGCTCATCTGCAC 60.046 61.111 14.15 0.00 33.64 4.57
2289 9386 2.827642 GCCAGGCTCATCTGCACC 60.828 66.667 3.29 0.00 33.64 5.01
2290 9387 2.124403 CCAGGCTCATCTGCACCC 60.124 66.667 0.00 0.00 33.64 4.61
2291 9388 2.513204 CAGGCTCATCTGCACCCG 60.513 66.667 0.00 0.00 34.04 5.28
2292 9389 3.790437 AGGCTCATCTGCACCCGG 61.790 66.667 0.00 0.00 34.04 5.73
2293 9390 4.101448 GGCTCATCTGCACCCGGT 62.101 66.667 0.00 0.00 34.04 5.28
2294 9391 2.045926 GCTCATCTGCACCCGGTT 60.046 61.111 0.00 0.00 0.00 4.44
2295 9392 1.220749 GCTCATCTGCACCCGGTTA 59.779 57.895 0.00 0.00 0.00 2.85
2296 9393 0.811616 GCTCATCTGCACCCGGTTAG 60.812 60.000 0.00 0.00 0.00 2.34
2297 9394 0.824109 CTCATCTGCACCCGGTTAGA 59.176 55.000 0.00 4.22 0.00 2.10
2298 9395 1.207089 CTCATCTGCACCCGGTTAGAA 59.793 52.381 0.00 0.00 0.00 2.10
2299 9396 1.626321 TCATCTGCACCCGGTTAGAAA 59.374 47.619 0.00 0.00 0.00 2.52
2300 9397 2.039216 TCATCTGCACCCGGTTAGAAAA 59.961 45.455 0.00 0.00 0.00 2.29
2301 9398 2.642154 TCTGCACCCGGTTAGAAAAA 57.358 45.000 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.900511 AAAAACTCATATTTCATCACACATCG 57.099 30.769 0.00 0.00 0.00 3.84
42 43 8.977505 GCAACAACAAATAGTTCAATACACATT 58.022 29.630 0.00 0.00 38.74 2.71
43 44 8.140628 TGCAACAACAAATAGTTCAATACACAT 58.859 29.630 0.00 0.00 38.74 3.21
44 45 7.433719 GTGCAACAACAAATAGTTCAATACACA 59.566 33.333 0.00 0.00 38.74 3.72
45 46 7.647715 AGTGCAACAACAAATAGTTCAATACAC 59.352 33.333 0.00 0.00 41.43 2.90
46 47 7.711846 AGTGCAACAACAAATAGTTCAATACA 58.288 30.769 0.00 0.00 41.43 2.29
47 48 9.840427 ATAGTGCAACAACAAATAGTTCAATAC 57.160 29.630 0.00 0.00 41.43 1.89
49 50 9.762933 AAATAGTGCAACAACAAATAGTTCAAT 57.237 25.926 0.00 0.00 41.43 2.57
50 51 9.593134 AAAATAGTGCAACAACAAATAGTTCAA 57.407 25.926 0.00 0.00 41.43 2.69
51 52 9.029243 CAAAATAGTGCAACAACAAATAGTTCA 57.971 29.630 0.00 0.00 41.43 3.18
52 53 9.030301 ACAAAATAGTGCAACAACAAATAGTTC 57.970 29.630 0.00 0.00 41.43 3.01
53 54 8.940768 ACAAAATAGTGCAACAACAAATAGTT 57.059 26.923 0.00 0.00 41.43 2.24
54 55 8.816144 CAACAAAATAGTGCAACAACAAATAGT 58.184 29.630 0.00 0.00 41.43 2.12
55 56 9.029243 TCAACAAAATAGTGCAACAACAAATAG 57.971 29.630 0.00 0.00 41.43 1.73
56 57 8.932945 TCAACAAAATAGTGCAACAACAAATA 57.067 26.923 0.00 0.00 41.43 1.40
57 58 7.840342 TCAACAAAATAGTGCAACAACAAAT 57.160 28.000 0.00 0.00 41.43 2.32
58 59 7.658179 TTCAACAAAATAGTGCAACAACAAA 57.342 28.000 0.00 0.00 41.43 2.83
59 60 7.840342 ATTCAACAAAATAGTGCAACAACAA 57.160 28.000 0.00 0.00 41.43 2.83
60 61 7.840342 AATTCAACAAAATAGTGCAACAACA 57.160 28.000 0.00 0.00 41.43 3.33
87 88 9.984190 TCATCACAGAAAATCAATCAAAATCAA 57.016 25.926 0.00 0.00 0.00 2.57
88 89 9.984190 TTCATCACAGAAAATCAATCAAAATCA 57.016 25.926 0.00 0.00 0.00 2.57
90 91 9.991906 AGTTCATCACAGAAAATCAATCAAAAT 57.008 25.926 0.00 0.00 0.00 1.82
92 93 9.897744 GTAGTTCATCACAGAAAATCAATCAAA 57.102 29.630 0.00 0.00 0.00 2.69
93 94 8.229811 CGTAGTTCATCACAGAAAATCAATCAA 58.770 33.333 0.00 0.00 0.00 2.57
94 95 7.387673 ACGTAGTTCATCACAGAAAATCAATCA 59.612 33.333 0.00 0.00 37.78 2.57
95 96 7.743104 ACGTAGTTCATCACAGAAAATCAATC 58.257 34.615 0.00 0.00 37.78 2.67
96 97 7.672983 ACGTAGTTCATCACAGAAAATCAAT 57.327 32.000 0.00 0.00 37.78 2.57
128 129 9.301153 GGCGTGAATTCTCAACATAAATAATTT 57.699 29.630 7.05 0.00 31.88 1.82
129 130 7.643764 CGGCGTGAATTCTCAACATAAATAATT 59.356 33.333 7.05 0.00 31.88 1.40
130 131 7.011950 TCGGCGTGAATTCTCAACATAAATAAT 59.988 33.333 6.85 0.00 31.88 1.28
131 132 6.314152 TCGGCGTGAATTCTCAACATAAATAA 59.686 34.615 6.85 0.00 31.88 1.40
132 133 5.813157 TCGGCGTGAATTCTCAACATAAATA 59.187 36.000 6.85 0.00 31.88 1.40
133 134 4.634004 TCGGCGTGAATTCTCAACATAAAT 59.366 37.500 6.85 0.00 31.88 1.40
134 135 3.997681 TCGGCGTGAATTCTCAACATAAA 59.002 39.130 6.85 0.00 31.88 1.40
135 136 3.591023 TCGGCGTGAATTCTCAACATAA 58.409 40.909 6.85 0.00 31.88 1.90
136 137 3.239587 TCGGCGTGAATTCTCAACATA 57.760 42.857 6.85 0.00 31.88 2.29
137 138 2.093306 TCGGCGTGAATTCTCAACAT 57.907 45.000 6.85 0.00 31.88 2.71
138 139 1.529438 GTTCGGCGTGAATTCTCAACA 59.471 47.619 6.85 0.00 39.21 3.33
139 140 1.136057 GGTTCGGCGTGAATTCTCAAC 60.136 52.381 6.85 0.00 39.21 3.18
140 141 1.153353 GGTTCGGCGTGAATTCTCAA 58.847 50.000 6.85 0.00 39.21 3.02
141 142 0.034198 TGGTTCGGCGTGAATTCTCA 59.966 50.000 6.85 0.00 39.21 3.27
142 143 0.442699 GTGGTTCGGCGTGAATTCTC 59.557 55.000 6.85 1.90 39.21 2.87
143 144 1.289109 CGTGGTTCGGCGTGAATTCT 61.289 55.000 6.85 0.00 39.21 2.40
144 145 1.131826 CGTGGTTCGGCGTGAATTC 59.868 57.895 6.85 0.00 39.21 2.17
145 146 1.562575 GACGTGGTTCGGCGTGAATT 61.563 55.000 6.85 0.00 44.69 2.17
146 147 2.025418 GACGTGGTTCGGCGTGAAT 61.025 57.895 6.85 0.00 44.69 2.57
147 148 2.659244 GACGTGGTTCGGCGTGAA 60.659 61.111 6.85 0.00 44.69 3.18
152 153 0.575390 CATATTCGACGTGGTTCGGC 59.425 55.000 0.00 0.00 45.27 5.54
153 154 1.205657 CCATATTCGACGTGGTTCGG 58.794 55.000 0.00 0.00 44.69 4.30
154 155 1.205657 CCCATATTCGACGTGGTTCG 58.794 55.000 0.00 0.00 46.00 3.95
155 156 0.935196 GCCCATATTCGACGTGGTTC 59.065 55.000 0.00 0.00 0.00 3.62
156 157 0.463116 GGCCCATATTCGACGTGGTT 60.463 55.000 0.00 0.00 0.00 3.67
157 158 1.145377 GGCCCATATTCGACGTGGT 59.855 57.895 0.00 0.00 0.00 4.16
158 159 1.954146 CGGCCCATATTCGACGTGG 60.954 63.158 0.00 0.00 0.00 4.94
159 160 0.319555 ATCGGCCCATATTCGACGTG 60.320 55.000 0.00 0.00 35.70 4.49
160 161 0.391597 AATCGGCCCATATTCGACGT 59.608 50.000 0.00 0.00 35.70 4.34
161 162 1.068474 GAATCGGCCCATATTCGACG 58.932 55.000 0.00 0.00 35.70 5.12
162 163 2.338500 GAGAATCGGCCCATATTCGAC 58.662 52.381 12.18 8.52 37.22 4.20
163 164 2.743636 GAGAATCGGCCCATATTCGA 57.256 50.000 12.18 0.00 37.22 3.71
185 186 1.986378 GCGAGAAATGACCCGATATCG 59.014 52.381 18.31 18.31 39.44 2.92
186 187 2.338500 GGCGAGAAATGACCCGATATC 58.662 52.381 0.00 0.00 0.00 1.63
187 188 1.336887 CGGCGAGAAATGACCCGATAT 60.337 52.381 0.00 0.00 41.34 1.63
188 189 0.031585 CGGCGAGAAATGACCCGATA 59.968 55.000 0.00 0.00 41.34 2.92
189 190 1.227263 CGGCGAGAAATGACCCGAT 60.227 57.895 0.00 0.00 41.34 4.18
190 191 1.879737 TTCGGCGAGAAATGACCCGA 61.880 55.000 10.46 0.00 45.31 5.14
191 192 1.017177 TTTCGGCGAGAAATGACCCG 61.017 55.000 10.46 0.00 43.35 5.28
192 193 0.727398 CTTTCGGCGAGAAATGACCC 59.273 55.000 10.46 0.00 46.60 4.46
193 194 1.128692 CACTTTCGGCGAGAAATGACC 59.871 52.381 10.46 0.00 46.60 4.02
194 195 1.128692 CCACTTTCGGCGAGAAATGAC 59.871 52.381 10.46 0.00 46.60 3.06
195 196 1.438651 CCACTTTCGGCGAGAAATGA 58.561 50.000 10.46 0.00 46.60 2.57
196 197 0.447801 CCCACTTTCGGCGAGAAATG 59.552 55.000 10.46 7.02 46.60 2.32
197 198 1.305930 GCCCACTTTCGGCGAGAAAT 61.306 55.000 10.46 0.00 46.60 2.17
198 199 1.964373 GCCCACTTTCGGCGAGAAA 60.964 57.895 10.46 1.10 45.76 2.52
199 200 2.358247 GCCCACTTTCGGCGAGAA 60.358 61.111 10.46 7.00 36.47 2.87
204 205 2.557372 TTTTCGGCCCACTTTCGGC 61.557 57.895 0.00 0.00 46.29 5.54
205 206 1.170290 AGTTTTCGGCCCACTTTCGG 61.170 55.000 0.00 0.00 0.00 4.30
206 207 0.040425 CAGTTTTCGGCCCACTTTCG 60.040 55.000 0.00 0.00 0.00 3.46
207 208 0.313987 CCAGTTTTCGGCCCACTTTC 59.686 55.000 0.00 0.00 0.00 2.62
208 209 1.744320 GCCAGTTTTCGGCCCACTTT 61.744 55.000 0.00 0.00 44.22 2.66
209 210 2.200337 GCCAGTTTTCGGCCCACTT 61.200 57.895 0.00 0.00 44.22 3.16
210 211 2.597510 GCCAGTTTTCGGCCCACT 60.598 61.111 0.00 0.00 44.22 4.00
216 217 1.794222 GATGTCGGCCAGTTTTCGG 59.206 57.895 2.24 0.00 0.00 4.30
217 218 1.011968 TCGATGTCGGCCAGTTTTCG 61.012 55.000 2.24 4.59 40.29 3.46
218 219 0.442699 GTCGATGTCGGCCAGTTTTC 59.557 55.000 2.24 0.00 38.15 2.29
219 220 1.289109 CGTCGATGTCGGCCAGTTTT 61.289 55.000 2.24 0.00 41.58 2.43
220 221 1.736645 CGTCGATGTCGGCCAGTTT 60.737 57.895 2.24 0.00 41.58 2.66
221 222 2.126071 CGTCGATGTCGGCCAGTT 60.126 61.111 2.24 0.00 41.58 3.16
222 223 4.796231 GCGTCGATGTCGGCCAGT 62.796 66.667 2.24 0.00 41.58 4.00
227 228 4.873129 CCCAGGCGTCGATGTCGG 62.873 72.222 6.48 9.52 40.29 4.79
228 229 4.873129 CCCCAGGCGTCGATGTCG 62.873 72.222 6.48 0.00 41.45 4.35
266 267 0.036294 GGTATAATCGGCTCTGGGGC 60.036 60.000 0.00 0.00 37.12 5.80
267 268 0.246635 CGGTATAATCGGCTCTGGGG 59.753 60.000 0.00 0.00 0.00 4.96
268 269 0.389948 GCGGTATAATCGGCTCTGGG 60.390 60.000 0.00 0.00 0.00 4.45
269 270 3.123674 GCGGTATAATCGGCTCTGG 57.876 57.895 0.00 0.00 0.00 3.86
275 276 1.445582 GAGCCGGCGGTATAATCGG 60.446 63.158 28.82 0.00 44.70 4.18
276 277 1.800315 CGAGCCGGCGGTATAATCG 60.800 63.158 28.82 22.84 0.00 3.34
277 278 2.092882 GCGAGCCGGCGGTATAATC 61.093 63.158 28.82 15.99 0.00 1.75
278 279 2.048503 GCGAGCCGGCGGTATAAT 60.049 61.111 28.82 8.64 0.00 1.28
279 280 4.289245 GGCGAGCCGGCGGTATAA 62.289 66.667 28.82 0.00 43.33 0.98
295 296 0.746563 TAAAAATCGCCGCCTGGAGG 60.747 55.000 12.67 12.67 37.49 4.30
296 297 1.002468 CATAAAAATCGCCGCCTGGAG 60.002 52.381 0.00 0.00 37.49 3.86
297 298 1.021202 CATAAAAATCGCCGCCTGGA 58.979 50.000 0.00 0.00 37.49 3.86
298 299 0.594796 GCATAAAAATCGCCGCCTGG 60.595 55.000 0.00 0.00 38.77 4.45
299 300 0.594796 GGCATAAAAATCGCCGCCTG 60.595 55.000 0.00 0.00 35.79 4.85
300 301 1.733526 GGCATAAAAATCGCCGCCT 59.266 52.632 0.00 0.00 35.79 5.52
301 302 4.319249 GGCATAAAAATCGCCGCC 57.681 55.556 0.00 0.00 35.79 6.13
304 305 1.202405 CCAGGTGGCATAAAAATCGCC 60.202 52.381 0.00 0.00 46.43 5.54
305 306 1.202405 CCCAGGTGGCATAAAAATCGC 60.202 52.381 0.00 0.00 0.00 4.58
306 307 2.358898 CTCCCAGGTGGCATAAAAATCG 59.641 50.000 0.00 0.00 0.00 3.34
307 308 2.695147 CCTCCCAGGTGGCATAAAAATC 59.305 50.000 0.00 0.00 0.00 2.17
308 309 2.750814 CCTCCCAGGTGGCATAAAAAT 58.249 47.619 0.00 0.00 0.00 1.82
309 310 2.230130 CCTCCCAGGTGGCATAAAAA 57.770 50.000 0.00 0.00 0.00 1.94
310 311 3.998560 CCTCCCAGGTGGCATAAAA 57.001 52.632 0.00 0.00 0.00 1.52
317 318 4.722700 CGTTGGCCTCCCAGGTGG 62.723 72.222 3.32 0.15 43.37 4.61
318 319 3.636231 TCGTTGGCCTCCCAGGTG 61.636 66.667 3.32 0.00 43.37 4.00
319 320 3.637273 GTCGTTGGCCTCCCAGGT 61.637 66.667 3.32 0.00 43.37 4.00
320 321 3.322466 AGTCGTTGGCCTCCCAGG 61.322 66.667 3.32 0.00 43.37 4.45
321 322 2.046892 CAGTCGTTGGCCTCCCAG 60.047 66.667 3.32 0.00 43.37 4.45
322 323 3.636231 CCAGTCGTTGGCCTCCCA 61.636 66.667 3.32 0.00 40.87 4.37
341 342 9.236006 ACCATAATAACCATTGATAAGAGCATC 57.764 33.333 0.00 0.00 0.00 3.91
342 343 9.017509 CACCATAATAACCATTGATAAGAGCAT 57.982 33.333 0.00 0.00 0.00 3.79
343 344 8.217111 TCACCATAATAACCATTGATAAGAGCA 58.783 33.333 0.00 0.00 0.00 4.26
344 345 8.621532 TCACCATAATAACCATTGATAAGAGC 57.378 34.615 0.00 0.00 0.00 4.09
374 375 2.293677 CTGACCGAGTCGCTATATGGTT 59.706 50.000 7.12 0.00 34.95 3.67
390 391 4.997395 TGCTTTGATTGAGTAACTCTGACC 59.003 41.667 0.00 0.00 0.00 4.02
411 413 3.248171 CCGACGCGCTACTTCTGC 61.248 66.667 5.73 0.00 0.00 4.26
417 419 1.297745 CTCTTCTCCGACGCGCTAC 60.298 63.158 5.73 0.00 0.00 3.58
470 472 3.326747 ACTCATTAGTCGGTCAGTTTGC 58.673 45.455 0.00 0.00 0.00 3.68
485 488 0.320374 TTTGACTCCGCCGACTCATT 59.680 50.000 0.00 0.00 0.00 2.57
495 498 6.599437 AGAAAACGTAAATGATTTGACTCCG 58.401 36.000 0.00 0.00 0.00 4.63
551 745 1.273838 TGGTCTAGCAGATTGGGGAGT 60.274 52.381 0.00 0.00 0.00 3.85
555 749 0.179073 CGGTGGTCTAGCAGATTGGG 60.179 60.000 0.00 0.00 0.00 4.12
594 788 0.319900 GACTTCGAGTTGGCTGCTGA 60.320 55.000 0.00 0.00 0.00 4.26
624 818 2.004017 GATTGGATCGCCGTGTACAAA 58.996 47.619 0.00 0.00 36.79 2.83
634 828 2.911484 AGAAGGTGAAGATTGGATCGC 58.089 47.619 0.00 0.00 0.00 4.58
661 859 0.171903 CGGTCGTTAATCGGGACACT 59.828 55.000 0.00 0.00 40.32 3.55
732 930 1.210413 GAGCAGTCTGTCTTCGCGA 59.790 57.895 3.71 3.71 0.00 5.87
937 1198 1.150135 AGGAGATGGGACGATGGGTAT 59.850 52.381 0.00 0.00 0.00 2.73
938 1199 0.561184 AGGAGATGGGACGATGGGTA 59.439 55.000 0.00 0.00 0.00 3.69
939 1200 0.760945 GAGGAGATGGGACGATGGGT 60.761 60.000 0.00 0.00 0.00 4.51
1407 8465 2.368875 ACGGTTGGACAGACTCAAAGAT 59.631 45.455 0.00 0.00 0.00 2.40
1408 8466 1.760613 ACGGTTGGACAGACTCAAAGA 59.239 47.619 0.00 0.00 0.00 2.52
1411 8469 1.208535 ACAACGGTTGGACAGACTCAA 59.791 47.619 23.51 0.00 34.12 3.02
1423 8481 3.057596 TCGTCGGAGTATAAACAACGGTT 60.058 43.478 0.00 0.00 39.43 4.44
1511 8569 0.308684 AATAATCTGGCGCATGCGTG 59.691 50.000 37.54 27.13 44.10 5.34
1514 8572 1.334556 TGACAATAATCTGGCGCATGC 59.665 47.619 10.83 7.91 41.71 4.06
1579 8637 2.120232 GGAGAACAGACGCATACATCG 58.880 52.381 0.00 0.00 0.00 3.84
1589 8647 6.706270 TCAGAACAAGTTAATGGAGAACAGAC 59.294 38.462 0.00 0.00 0.00 3.51
1607 8665 6.516739 TTGTGGTTGTTGTTAATCAGAACA 57.483 33.333 0.00 0.00 37.54 3.18
1609 8667 8.877779 CAATTTTGTGGTTGTTGTTAATCAGAA 58.122 29.630 0.00 0.00 0.00 3.02
1612 8670 6.037610 GCCAATTTTGTGGTTGTTGTTAATCA 59.962 34.615 0.00 0.00 41.12 2.57
1620 8686 4.213564 TCTTGCCAATTTTGTGGTTGTT 57.786 36.364 0.00 0.00 41.12 2.83
1627 8693 5.622346 TTAGGGTTTCTTGCCAATTTTGT 57.378 34.783 0.00 0.00 0.00 2.83
1633 8700 3.161866 GGACATTAGGGTTTCTTGCCAA 58.838 45.455 0.00 0.00 0.00 4.52
1651 8718 3.850273 CACGTAGTCGAGTAACAATGGAC 59.150 47.826 0.44 0.00 41.61 4.02
1653 8720 2.597305 GCACGTAGTCGAGTAACAATGG 59.403 50.000 0.44 0.00 41.61 3.16
1656 8723 2.810274 AGAGCACGTAGTCGAGTAACAA 59.190 45.455 0.44 0.00 41.61 2.83
1657 8724 2.159037 CAGAGCACGTAGTCGAGTAACA 59.841 50.000 0.44 0.00 41.61 2.41
1691 8758 3.530910 AAGTTCCACACGGCCGAGG 62.531 63.158 35.90 28.38 0.00 4.63
1695 8762 2.604174 CGTCAAGTTCCACACGGCC 61.604 63.158 0.00 0.00 0.00 6.13
1711 8778 3.564644 CCGTATGATAGGTGAGACTTCGT 59.435 47.826 0.00 0.00 0.00 3.85
1712 8779 3.813724 TCCGTATGATAGGTGAGACTTCG 59.186 47.826 0.00 0.00 0.00 3.79
1716 8783 4.156922 CCTGATCCGTATGATAGGTGAGAC 59.843 50.000 0.00 0.00 32.41 3.36
1724 8791 1.078823 AGGCCCCTGATCCGTATGATA 59.921 52.381 0.00 0.00 32.41 2.15
1778 8850 3.312697 GCTTAGCTTTTTGATCCCCGTAG 59.687 47.826 0.00 0.00 0.00 3.51
1839 8911 1.419922 CCAATCGAGAACGCAACGG 59.580 57.895 0.00 0.00 39.58 4.44
1962 9039 5.730296 AAGAAAAGAAGAGACGATGGAGA 57.270 39.130 0.00 0.00 0.00 3.71
1963 9040 5.390356 GCAAAGAAAAGAAGAGACGATGGAG 60.390 44.000 0.00 0.00 0.00 3.86
2072 9154 3.317603 TGGGCTAAAGCAAAAGCATTC 57.682 42.857 4.07 0.00 44.36 2.67
2075 9157 3.767902 AAATGGGCTAAAGCAAAAGCA 57.232 38.095 4.07 0.00 44.36 3.91
2087 9171 6.867723 AGATTATATCTTCCCAAAATGGGCT 58.132 36.000 10.68 0.00 43.91 5.19
2136 9233 2.668279 GCAGAAATCAATTTGCGTCGGT 60.668 45.455 0.00 0.00 0.00 4.69
2137 9234 1.913403 GCAGAAATCAATTTGCGTCGG 59.087 47.619 0.00 0.00 0.00 4.79
2143 9240 2.591148 CAGACGCGCAGAAATCAATTTG 59.409 45.455 5.73 0.00 0.00 2.32
2165 9262 0.039978 TGCCGCAACAAATTACACCG 60.040 50.000 0.00 0.00 0.00 4.94
2167 9264 2.058057 CCTTGCCGCAACAAATTACAC 58.942 47.619 0.38 0.00 0.00 2.90
2255 9352 3.039134 CACCAAAACGCCCCACTC 58.961 61.111 0.00 0.00 0.00 3.51
2256 9353 3.223589 GCACCAAAACGCCCCACT 61.224 61.111 0.00 0.00 0.00 4.00
2257 9354 4.293648 GGCACCAAAACGCCCCAC 62.294 66.667 0.00 0.00 42.82 4.61
2262 9359 3.558099 GAGCCTGGCACCAAAACGC 62.558 63.158 22.65 0.00 0.00 4.84
2263 9360 1.526575 ATGAGCCTGGCACCAAAACG 61.527 55.000 22.65 0.00 0.00 3.60
2264 9361 0.244721 GATGAGCCTGGCACCAAAAC 59.755 55.000 22.65 10.11 0.00 2.43
2265 9362 0.112995 AGATGAGCCTGGCACCAAAA 59.887 50.000 22.65 0.00 0.00 2.44
2266 9363 0.609957 CAGATGAGCCTGGCACCAAA 60.610 55.000 22.65 0.00 0.00 3.28
2267 9364 1.001764 CAGATGAGCCTGGCACCAA 60.002 57.895 22.65 3.11 0.00 3.67
2268 9365 2.672908 CAGATGAGCCTGGCACCA 59.327 61.111 22.65 18.06 0.00 4.17
2269 9366 2.827642 GCAGATGAGCCTGGCACC 60.828 66.667 22.65 12.64 34.82 5.01
2270 9367 2.045634 TGCAGATGAGCCTGGCAC 60.046 61.111 22.65 15.93 34.82 5.01
2271 9368 2.045634 GTGCAGATGAGCCTGGCA 60.046 61.111 22.65 0.22 34.82 4.92
2272 9369 2.827642 GGTGCAGATGAGCCTGGC 60.828 66.667 11.65 11.65 34.82 4.85
2273 9370 2.124403 GGGTGCAGATGAGCCTGG 60.124 66.667 0.00 0.00 34.82 4.45
2274 9371 2.513204 CGGGTGCAGATGAGCCTG 60.513 66.667 0.00 0.00 37.23 4.85
2275 9372 3.790437 CCGGGTGCAGATGAGCCT 61.790 66.667 0.00 0.00 0.00 4.58
2276 9373 2.252072 TAACCGGGTGCAGATGAGCC 62.252 60.000 0.00 0.00 0.00 4.70
2277 9374 0.811616 CTAACCGGGTGCAGATGAGC 60.812 60.000 0.00 0.00 0.00 4.26
2278 9375 0.824109 TCTAACCGGGTGCAGATGAG 59.176 55.000 0.00 0.00 0.00 2.90
2279 9376 1.271856 TTCTAACCGGGTGCAGATGA 58.728 50.000 0.00 0.00 0.00 2.92
2280 9377 2.107950 TTTCTAACCGGGTGCAGATG 57.892 50.000 0.00 0.00 0.00 2.90
2281 9378 2.871096 TTTTCTAACCGGGTGCAGAT 57.129 45.000 0.00 0.00 0.00 2.90
2282 9379 2.642154 TTTTTCTAACCGGGTGCAGA 57.358 45.000 0.00 3.87 0.00 4.26


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

AutoCloner maintained by Alex Coulton.