Multiple sequence alignment - TraesCS3B01G429500

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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 TraesCS3B01G429500 chr3B 100.000 3456 0 0 1 3456 668143873 668147328 0.000000e+00 6383.0
1 TraesCS3B01G429500 chr3B 91.608 143 8 3 2848 2986 668146643 668146785 9.790000e-46 195.0
2 TraesCS3B01G429500 chr3B 91.608 143 8 3 2771 2913 668146720 668146858 9.790000e-46 195.0
3 TraesCS3B01G429500 chr3D 96.163 2606 50 13 399 2986 506200686 506203259 0.000000e+00 4213.0
4 TraesCS3B01G429500 chr3D 93.886 687 36 5 2771 3456 506203122 506203803 0.000000e+00 1031.0
5 TraesCS3B01G429500 chr3D 89.757 371 28 6 1 369 20707021 20707383 1.880000e-127 466.0
6 TraesCS3B01G429500 chr3D 90.909 143 9 3 2848 2986 506203045 506203187 4.550000e-44 189.0
7 TraesCS3B01G429500 chr3D 89.510 143 10 4 2771 2913 506203195 506203332 3.540000e-40 176.0
8 TraesCS3B01G429500 chr3D 78.261 138 12 13 278 406 238592611 238592483 4.780000e-09 73.1
9 TraesCS3B01G429500 chr2B 88.943 407 39 3 1 402 605013278 605012873 6.660000e-137 497.0
10 TraesCS3B01G429500 chr2B 90.054 372 26 9 1 369 693858731 693858368 4.040000e-129 472.0
11 TraesCS3B01G429500 chr2D 90.984 366 33 0 2 367 188896147 188895782 8.620000e-136 494.0
12 TraesCS3B01G429500 chr4D 90.710 366 30 2 2 367 47691326 47690965 5.190000e-133 484.0
13 TraesCS3B01G429500 chr4D 87.302 63 5 2 348 407 469601489 469601427 6.190000e-08 69.4
14 TraesCS3B01G429500 chr5D 89.918 367 33 2 1 367 294225681 294225319 1.450000e-128 470.0
15 TraesCS3B01G429500 chr5D 89.946 368 31 4 1 367 338496083 338496445 1.450000e-128 470.0
16 TraesCS3B01G429500 chr6B 87.871 404 41 7 2 400 124626741 124627141 5.220000e-128 468.0
17 TraesCS3B01G429500 chr5B 86.881 404 46 5 1 400 212629088 212629488 2.450000e-121 446.0
18 TraesCS3B01G429500 chr4A 90.000 60 3 3 350 406 100671535 100671594 1.330000e-09 75.0
19 TraesCS3B01G429500 chr7A 89.655 58 3 3 346 400 696010696 696010753 1.720000e-08 71.3
20 TraesCS3B01G429500 chr5A 89.655 58 3 2 348 402 53188870 53188813 1.720000e-08 71.3
21 TraesCS3B01G429500 chr4B 87.097 62 5 2 348 406 427358824 427358885 2.230000e-07 67.6


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 TraesCS3B01G429500 chr3B 668143873 668147328 3455 False 2257.666667 6383 94.405333 1 3456 3 chr3B.!!$F1 3455
1 TraesCS3B01G429500 chr3D 506200686 506203803 3117 False 1402.250000 4213 92.617000 399 3456 4 chr3D.!!$F2 3057

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
289 290 0.030235 GCCGTTAAAATGGATCGGGC 59.970 55.000 5.11 0.0 41.24 6.13 F
290 291 0.306533 CCGTTAAAATGGATCGGGCG 59.693 55.000 0.00 0.0 37.24 6.13 F
294 295 0.878523 TAAAATGGATCGGGCGAGCG 60.879 55.000 0.00 0.0 0.00 5.03 F
1100 1119 1.005037 TGATCGCGGATATGGTGGC 60.005 57.895 6.13 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1781 1800 0.397254 GGACGAGGAAGATGAGGGGA 60.397 60.000 0.0 0.0 0.00 4.81 R
1782 1801 0.687757 TGGACGAGGAAGATGAGGGG 60.688 60.000 0.0 0.0 0.00 4.79 R
1810 1829 1.153349 GTCCCTGAGGATGTTCGGC 60.153 63.158 0.0 0.0 46.41 5.54 R
2491 2510 0.108615 AAGAGTGAGAACCGATGCCG 60.109 55.000 0.0 0.0 0.00 5.69 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
23 24 3.941836 GGCTTACATCGCCGCTGC 61.942 66.667 0.00 0.00 37.87 5.25
24 25 3.195002 GCTTACATCGCCGCTGCA 61.195 61.111 0.00 0.00 37.32 4.41
25 26 2.537560 GCTTACATCGCCGCTGCAT 61.538 57.895 0.00 0.00 37.32 3.96
26 27 1.277739 CTTACATCGCCGCTGCATG 59.722 57.895 0.00 6.03 37.32 4.06
27 28 2.109538 CTTACATCGCCGCTGCATGG 62.110 60.000 13.79 0.79 37.32 3.66
28 29 2.585791 TTACATCGCCGCTGCATGGA 62.586 55.000 9.21 5.73 37.32 3.41
29 30 2.585791 TACATCGCCGCTGCATGGAA 62.586 55.000 9.21 0.00 37.32 3.53
30 31 3.204827 ATCGCCGCTGCATGGAAC 61.205 61.111 9.21 0.00 37.32 3.62
45 46 4.571243 AACACAACGTTCCCCTGG 57.429 55.556 0.00 0.00 29.27 4.45
46 47 1.152839 AACACAACGTTCCCCTGGG 60.153 57.895 5.50 5.50 29.27 4.45
47 48 2.983592 CACAACGTTCCCCTGGGC 60.984 66.667 7.39 0.00 34.68 5.36
48 49 4.280019 ACAACGTTCCCCTGGGCC 62.280 66.667 7.39 0.00 34.68 5.80
73 74 3.554692 CGCCGACGCTCATCAACC 61.555 66.667 0.00 0.00 0.00 3.77
74 75 2.125512 GCCGACGCTCATCAACCT 60.126 61.111 0.00 0.00 0.00 3.50
75 76 2.167861 GCCGACGCTCATCAACCTC 61.168 63.158 0.00 0.00 0.00 3.85
76 77 1.215382 CCGACGCTCATCAACCTCA 59.785 57.895 0.00 0.00 0.00 3.86
77 78 1.078759 CCGACGCTCATCAACCTCAC 61.079 60.000 0.00 0.00 0.00 3.51
78 79 1.078759 CGACGCTCATCAACCTCACC 61.079 60.000 0.00 0.00 0.00 4.02
79 80 1.078759 GACGCTCATCAACCTCACCG 61.079 60.000 0.00 0.00 0.00 4.94
80 81 1.215382 CGCTCATCAACCTCACCGA 59.785 57.895 0.00 0.00 0.00 4.69
81 82 1.078759 CGCTCATCAACCTCACCGAC 61.079 60.000 0.00 0.00 0.00 4.79
82 83 0.741221 GCTCATCAACCTCACCGACC 60.741 60.000 0.00 0.00 0.00 4.79
83 84 0.108138 CTCATCAACCTCACCGACCC 60.108 60.000 0.00 0.00 0.00 4.46
84 85 1.078426 CATCAACCTCACCGACCCC 60.078 63.158 0.00 0.00 0.00 4.95
85 86 2.656069 ATCAACCTCACCGACCCCG 61.656 63.158 0.00 0.00 0.00 5.73
86 87 3.307906 CAACCTCACCGACCCCGA 61.308 66.667 0.00 0.00 38.22 5.14
87 88 2.995574 AACCTCACCGACCCCGAG 60.996 66.667 0.00 0.00 38.22 4.63
90 91 3.450115 CTCACCGACCCCGAGGAC 61.450 72.222 0.00 0.00 38.22 3.85
96 97 3.295800 GACCCCGAGGACGACAAT 58.704 61.111 0.00 0.00 42.66 2.71
97 98 1.153628 GACCCCGAGGACGACAATG 60.154 63.158 0.00 0.00 42.66 2.82
98 99 1.601419 GACCCCGAGGACGACAATGA 61.601 60.000 0.00 0.00 42.66 2.57
99 100 1.153628 CCCCGAGGACGACAATGAC 60.154 63.158 0.00 0.00 42.66 3.06
100 101 1.516386 CCCGAGGACGACAATGACG 60.516 63.158 3.29 3.29 42.66 4.35
101 102 1.504900 CCGAGGACGACAATGACGA 59.495 57.895 12.41 0.00 42.66 4.20
102 103 0.797249 CCGAGGACGACAATGACGAC 60.797 60.000 12.41 5.57 42.66 4.34
103 104 0.109919 CGAGGACGACAATGACGACA 60.110 55.000 12.41 0.00 42.66 4.35
104 105 1.664874 CGAGGACGACAATGACGACAA 60.665 52.381 12.41 0.00 42.66 3.18
105 106 1.719780 GAGGACGACAATGACGACAAC 59.280 52.381 12.41 0.61 34.70 3.32
106 107 0.433492 GGACGACAATGACGACAACG 59.567 55.000 12.41 0.00 45.75 4.10
107 108 0.179282 GACGACAATGACGACAACGC 60.179 55.000 12.41 0.00 43.96 4.84
108 109 1.129809 CGACAATGACGACAACGCC 59.870 57.895 0.00 0.00 43.96 5.68
109 110 1.282248 CGACAATGACGACAACGCCT 61.282 55.000 0.00 0.00 43.96 5.52
110 111 1.705256 GACAATGACGACAACGCCTA 58.295 50.000 0.00 0.00 43.96 3.93
111 112 2.063266 GACAATGACGACAACGCCTAA 58.937 47.619 0.00 0.00 43.96 2.69
112 113 2.066262 ACAATGACGACAACGCCTAAG 58.934 47.619 0.00 0.00 43.96 2.18
113 114 1.393539 CAATGACGACAACGCCTAAGG 59.606 52.381 0.00 0.00 43.96 2.69
114 115 0.739813 ATGACGACAACGCCTAAGGC 60.740 55.000 0.00 0.00 46.75 4.35
139 140 4.865761 GCATCGCGTCGCCTGGTA 62.866 66.667 12.44 0.00 0.00 3.25
140 141 2.655364 CATCGCGTCGCCTGGTAG 60.655 66.667 12.44 0.00 0.00 3.18
141 142 3.138798 ATCGCGTCGCCTGGTAGT 61.139 61.111 12.44 0.00 0.00 2.73
142 143 2.707849 ATCGCGTCGCCTGGTAGTT 61.708 57.895 12.44 0.00 0.00 2.24
143 144 1.378882 ATCGCGTCGCCTGGTAGTTA 61.379 55.000 12.44 0.00 0.00 2.24
144 145 1.585521 CGCGTCGCCTGGTAGTTAG 60.586 63.158 12.44 0.00 0.00 2.34
145 146 1.226888 GCGTCGCCTGGTAGTTAGG 60.227 63.158 5.75 0.00 38.39 2.69
146 147 1.941999 GCGTCGCCTGGTAGTTAGGT 61.942 60.000 5.75 0.00 37.64 3.08
147 148 0.529378 CGTCGCCTGGTAGTTAGGTT 59.471 55.000 0.00 0.00 37.64 3.50
148 149 1.734707 CGTCGCCTGGTAGTTAGGTTG 60.735 57.143 0.00 0.00 37.64 3.77
149 150 1.274447 GTCGCCTGGTAGTTAGGTTGT 59.726 52.381 0.00 0.00 37.64 3.32
150 151 1.972795 TCGCCTGGTAGTTAGGTTGTT 59.027 47.619 0.00 0.00 37.64 2.83
151 152 2.369532 TCGCCTGGTAGTTAGGTTGTTT 59.630 45.455 0.00 0.00 37.64 2.83
152 153 3.143728 CGCCTGGTAGTTAGGTTGTTTT 58.856 45.455 0.00 0.00 37.64 2.43
153 154 3.566742 CGCCTGGTAGTTAGGTTGTTTTT 59.433 43.478 0.00 0.00 37.64 1.94
154 155 4.756135 CGCCTGGTAGTTAGGTTGTTTTTA 59.244 41.667 0.00 0.00 37.64 1.52
155 156 5.239087 CGCCTGGTAGTTAGGTTGTTTTTAA 59.761 40.000 0.00 0.00 37.64 1.52
156 157 6.072342 CGCCTGGTAGTTAGGTTGTTTTTAAT 60.072 38.462 0.00 0.00 37.64 1.40
157 158 7.522562 CGCCTGGTAGTTAGGTTGTTTTTAATT 60.523 37.037 0.00 0.00 37.64 1.40
158 159 8.145767 GCCTGGTAGTTAGGTTGTTTTTAATTT 58.854 33.333 0.00 0.00 37.64 1.82
159 160 9.687210 CCTGGTAGTTAGGTTGTTTTTAATTTC 57.313 33.333 0.00 0.00 0.00 2.17
179 180 8.980143 AATTTCTTTTAATGGTAATGTGGACG 57.020 30.769 0.00 0.00 0.00 4.79
180 181 5.554822 TCTTTTAATGGTAATGTGGACGC 57.445 39.130 0.00 0.00 0.00 5.19
181 182 4.093703 TCTTTTAATGGTAATGTGGACGCG 59.906 41.667 3.53 3.53 0.00 6.01
182 183 2.676632 TAATGGTAATGTGGACGCGT 57.323 45.000 13.85 13.85 0.00 6.01
183 184 1.083489 AATGGTAATGTGGACGCGTG 58.917 50.000 20.70 0.00 0.00 5.34
184 185 0.742990 ATGGTAATGTGGACGCGTGG 60.743 55.000 20.70 0.00 0.00 4.94
185 186 1.079681 GGTAATGTGGACGCGTGGA 60.080 57.895 20.70 0.00 0.00 4.02
186 187 1.356527 GGTAATGTGGACGCGTGGAC 61.357 60.000 20.70 13.83 0.00 4.02
187 188 0.389426 GTAATGTGGACGCGTGGACT 60.389 55.000 20.70 0.02 0.00 3.85
188 189 0.108992 TAATGTGGACGCGTGGACTC 60.109 55.000 20.70 8.41 0.00 3.36
189 190 1.816863 AATGTGGACGCGTGGACTCT 61.817 55.000 20.70 1.77 0.00 3.24
190 191 2.126424 GTGGACGCGTGGACTCTC 60.126 66.667 20.70 0.00 0.00 3.20
191 192 3.733960 TGGACGCGTGGACTCTCG 61.734 66.667 20.70 0.00 0.00 4.04
200 201 4.516195 GGACTCTCGCCGGCCTTC 62.516 72.222 23.46 9.81 0.00 3.46
201 202 4.516195 GACTCTCGCCGGCCTTCC 62.516 72.222 23.46 1.23 0.00 3.46
203 204 4.521062 CTCTCGCCGGCCTTCCTG 62.521 72.222 23.46 5.48 0.00 3.86
213 214 2.674754 CCTTCCTGGCCGGCTTTA 59.325 61.111 28.56 12.39 0.00 1.85
214 215 1.001393 CCTTCCTGGCCGGCTTTAA 60.001 57.895 28.56 14.43 0.00 1.52
215 216 0.395724 CCTTCCTGGCCGGCTTTAAT 60.396 55.000 28.56 0.00 0.00 1.40
216 217 0.740737 CTTCCTGGCCGGCTTTAATG 59.259 55.000 28.56 9.45 0.00 1.90
217 218 0.039035 TTCCTGGCCGGCTTTAATGT 59.961 50.000 28.56 0.00 0.00 2.71
218 219 0.039035 TCCTGGCCGGCTTTAATGTT 59.961 50.000 28.56 0.00 0.00 2.71
219 220 0.894835 CCTGGCCGGCTTTAATGTTT 59.105 50.000 28.56 0.00 0.00 2.83
220 221 2.096248 CCTGGCCGGCTTTAATGTTTA 58.904 47.619 28.56 0.00 0.00 2.01
221 222 2.494073 CCTGGCCGGCTTTAATGTTTAA 59.506 45.455 28.56 0.00 0.00 1.52
222 223 3.132111 CCTGGCCGGCTTTAATGTTTAAT 59.868 43.478 28.56 0.00 0.00 1.40
223 224 4.382577 CCTGGCCGGCTTTAATGTTTAATT 60.383 41.667 28.56 0.00 0.00 1.40
224 225 5.163499 CCTGGCCGGCTTTAATGTTTAATTA 60.163 40.000 28.56 0.00 0.00 1.40
225 226 6.282199 TGGCCGGCTTTAATGTTTAATTAA 57.718 33.333 28.56 0.00 0.00 1.40
226 227 6.334202 TGGCCGGCTTTAATGTTTAATTAAG 58.666 36.000 28.56 0.00 0.00 1.85
227 228 6.071278 TGGCCGGCTTTAATGTTTAATTAAGT 60.071 34.615 28.56 0.00 0.00 2.24
228 229 6.814644 GGCCGGCTTTAATGTTTAATTAAGTT 59.185 34.615 28.56 0.00 0.00 2.66
229 230 7.201487 GGCCGGCTTTAATGTTTAATTAAGTTG 60.201 37.037 28.56 0.00 0.00 3.16
230 231 7.329962 GCCGGCTTTAATGTTTAATTAAGTTGT 59.670 33.333 22.15 0.00 0.00 3.32
231 232 9.198837 CCGGCTTTAATGTTTAATTAAGTTGTT 57.801 29.630 0.00 0.00 0.00 2.83
252 253 9.823098 GTTGTTTTCATTTTAAATATGCATGCA 57.177 25.926 25.04 25.04 0.00 3.96
253 254 9.823098 TTGTTTTCATTTTAAATATGCATGCAC 57.177 25.926 25.37 4.19 0.00 4.57
254 255 8.996271 TGTTTTCATTTTAAATATGCATGCACA 58.004 25.926 25.37 13.37 0.00 4.57
255 256 9.480538 GTTTTCATTTTAAATATGCATGCACAG 57.519 29.630 25.37 0.00 0.00 3.66
256 257 8.774890 TTTCATTTTAAATATGCATGCACAGT 57.225 26.923 25.37 8.19 0.00 3.55
257 258 8.774890 TTCATTTTAAATATGCATGCACAGTT 57.225 26.923 25.37 20.49 0.00 3.16
258 259 8.774890 TCATTTTAAATATGCATGCACAGTTT 57.225 26.923 25.37 23.43 0.00 2.66
259 260 9.217278 TCATTTTAAATATGCATGCACAGTTTT 57.783 25.926 25.37 20.28 0.00 2.43
260 261 9.828852 CATTTTAAATATGCATGCACAGTTTTT 57.171 25.926 25.37 18.65 0.00 1.94
276 277 3.728474 TTTTTGTCGGCGCCGTTA 58.272 50.000 44.16 31.76 40.74 3.18
277 278 2.020131 TTTTTGTCGGCGCCGTTAA 58.980 47.368 44.16 34.85 40.74 2.01
278 279 0.379669 TTTTTGTCGGCGCCGTTAAA 59.620 45.000 44.16 37.50 40.74 1.52
279 280 0.379669 TTTTGTCGGCGCCGTTAAAA 59.620 45.000 44.16 39.80 40.74 1.52
280 281 0.592148 TTTGTCGGCGCCGTTAAAAT 59.408 45.000 44.16 0.00 40.74 1.82
281 282 0.110147 TTGTCGGCGCCGTTAAAATG 60.110 50.000 44.16 18.00 40.74 2.32
282 283 1.226184 GTCGGCGCCGTTAAAATGG 60.226 57.895 44.16 17.22 40.74 3.16
283 284 1.375652 TCGGCGCCGTTAAAATGGA 60.376 52.632 44.16 22.53 40.74 3.41
284 285 0.745128 TCGGCGCCGTTAAAATGGAT 60.745 50.000 44.16 0.00 40.74 3.41
285 286 0.316689 CGGCGCCGTTAAAATGGATC 60.317 55.000 39.71 0.00 37.24 3.36
286 287 0.316689 GGCGCCGTTAAAATGGATCG 60.317 55.000 12.58 1.50 37.24 3.69
287 288 0.316689 GCGCCGTTAAAATGGATCGG 60.317 55.000 5.11 0.00 43.37 4.18
288 289 0.306533 CGCCGTTAAAATGGATCGGG 59.693 55.000 5.11 0.00 41.24 5.14
289 290 0.030235 GCCGTTAAAATGGATCGGGC 59.970 55.000 5.11 0.00 41.24 6.13
290 291 0.306533 CCGTTAAAATGGATCGGGCG 59.693 55.000 0.00 0.00 37.24 6.13
291 292 1.292061 CGTTAAAATGGATCGGGCGA 58.708 50.000 0.00 0.00 0.00 5.54
292 293 1.260561 CGTTAAAATGGATCGGGCGAG 59.739 52.381 0.00 0.00 0.00 5.03
293 294 1.002792 GTTAAAATGGATCGGGCGAGC 60.003 52.381 0.00 0.00 0.00 5.03
294 295 0.878523 TAAAATGGATCGGGCGAGCG 60.879 55.000 0.00 0.00 0.00 5.03
295 296 2.869503 AAAATGGATCGGGCGAGCGT 62.870 55.000 0.00 0.00 0.00 5.07
296 297 2.869503 AAATGGATCGGGCGAGCGTT 62.870 55.000 0.00 0.00 0.00 4.84
297 298 4.812476 TGGATCGGGCGAGCGTTG 62.812 66.667 0.00 0.00 0.00 4.10
315 316 4.501714 GGCGCATACGTCGACCCA 62.502 66.667 10.83 0.00 42.83 4.51
316 317 2.507547 GCGCATACGTCGACCCAA 60.508 61.111 10.58 0.00 42.83 4.12
317 318 2.095847 GCGCATACGTCGACCCAAA 61.096 57.895 10.58 0.00 42.83 3.28
318 319 1.705727 CGCATACGTCGACCCAAAC 59.294 57.895 10.58 0.00 33.53 2.93
319 320 1.705727 GCATACGTCGACCCAAACG 59.294 57.895 10.58 0.00 44.22 3.60
320 321 1.705727 CATACGTCGACCCAAACGC 59.294 57.895 10.58 0.00 42.47 4.84
321 322 1.802715 ATACGTCGACCCAAACGCG 60.803 57.895 10.58 3.53 42.47 6.01
322 323 2.198906 ATACGTCGACCCAAACGCGA 62.199 55.000 15.93 0.00 42.47 5.87
323 324 2.399511 TACGTCGACCCAAACGCGAA 62.400 55.000 15.93 0.00 42.47 4.70
324 325 2.587679 CGTCGACCCAAACGCGAAA 61.588 57.895 15.93 0.00 35.66 3.46
325 326 1.203313 GTCGACCCAAACGCGAAAG 59.797 57.895 15.93 0.46 35.66 2.62
338 339 3.621520 GAAAGCGGACGTTCGTGT 58.378 55.556 19.12 2.35 0.00 4.49
339 340 1.485943 GAAAGCGGACGTTCGTGTC 59.514 57.895 19.12 9.03 38.17 3.67
345 346 3.103911 GACGTTCGTGTCCGCCTG 61.104 66.667 1.74 0.00 32.61 4.85
346 347 3.547249 GACGTTCGTGTCCGCCTGA 62.547 63.158 1.74 0.00 32.61 3.86
347 348 3.103911 CGTTCGTGTCCGCCTGAC 61.104 66.667 0.00 0.00 44.72 3.51
348 349 2.737376 GTTCGTGTCCGCCTGACC 60.737 66.667 0.00 0.00 43.78 4.02
349 350 4.351938 TTCGTGTCCGCCTGACCG 62.352 66.667 0.00 3.07 43.78 4.79
351 352 4.129737 CGTGTCCGCCTGACCGAT 62.130 66.667 0.00 0.00 43.78 4.18
352 353 2.202756 GTGTCCGCCTGACCGATC 60.203 66.667 0.00 0.00 43.78 3.69
353 354 3.458163 TGTCCGCCTGACCGATCC 61.458 66.667 0.00 0.00 43.78 3.36
354 355 3.148279 GTCCGCCTGACCGATCCT 61.148 66.667 0.00 0.00 38.09 3.24
355 356 1.826921 GTCCGCCTGACCGATCCTA 60.827 63.158 0.00 0.00 38.09 2.94
356 357 1.076559 TCCGCCTGACCGATCCTAA 60.077 57.895 0.00 0.00 0.00 2.69
357 358 1.067582 CCGCCTGACCGATCCTAAC 59.932 63.158 0.00 0.00 0.00 2.34
358 359 1.299165 CGCCTGACCGATCCTAACG 60.299 63.158 0.00 0.00 0.00 3.18
383 384 1.449726 AAAACTCCGTTTGGGTCGGC 61.450 55.000 0.00 0.00 46.49 5.54
384 385 3.837570 AACTCCGTTTGGGTCGGCC 62.838 63.158 0.00 0.00 46.49 6.13
394 395 4.324991 GGTCGGCCCGTTGGAGTT 62.325 66.667 1.63 0.00 0.00 3.01
395 396 3.047877 GTCGGCCCGTTGGAGTTG 61.048 66.667 1.63 0.00 0.00 3.16
502 506 6.349611 CCACAAACATATGGAGAAAGGAAGTG 60.350 42.308 7.80 0.00 38.34 3.16
503 507 5.711976 ACAAACATATGGAGAAAGGAAGTGG 59.288 40.000 7.80 0.00 0.00 4.00
504 508 5.779241 AACATATGGAGAAAGGAAGTGGA 57.221 39.130 7.80 0.00 0.00 4.02
505 509 5.104259 ACATATGGAGAAAGGAAGTGGAC 57.896 43.478 7.80 0.00 0.00 4.02
506 510 4.785376 ACATATGGAGAAAGGAAGTGGACT 59.215 41.667 7.80 0.00 0.00 3.85
507 511 3.990959 ATGGAGAAAGGAAGTGGACTC 57.009 47.619 0.00 0.00 0.00 3.36
508 512 1.978580 TGGAGAAAGGAAGTGGACTCC 59.021 52.381 0.00 0.00 42.64 3.85
509 513 1.978580 GGAGAAAGGAAGTGGACTCCA 59.021 52.381 0.00 0.00 42.11 3.86
635 640 3.787001 CCCCGCCCTCTGTTCTCC 61.787 72.222 0.00 0.00 0.00 3.71
673 687 2.572284 CCGTCTTCGTCCCCACTC 59.428 66.667 0.00 0.00 35.01 3.51
1100 1119 1.005037 TGATCGCGGATATGGTGGC 60.005 57.895 6.13 0.00 0.00 5.01
1154 1173 1.538204 GCGATTGATGAAGGCGTCCTA 60.538 52.381 0.00 0.00 31.13 2.94
1408 1427 1.645710 CACCTACCTCTCTTGGGTGT 58.354 55.000 0.00 0.00 41.52 4.16
1448 1467 3.157881 CCTCCGCTAGATACCTCATTCA 58.842 50.000 0.00 0.00 0.00 2.57
1458 1477 4.349342 AGATACCTCATTCATCAGGAACCC 59.651 45.833 0.00 0.00 38.60 4.11
1517 1536 1.337703 CGATCCTGAGAAGAGGCAGAG 59.662 57.143 0.00 0.00 34.06 3.35
1572 1591 3.112709 GCTCAACGTGCCGAGGAC 61.113 66.667 10.78 0.00 0.00 3.85
1612 1631 2.970974 GCGGACAAGGAAGCACTGC 61.971 63.158 0.00 0.00 0.00 4.40
1634 1653 2.956132 TCTATTAGCAGAGGCAGCTCT 58.044 47.619 2.37 0.00 42.32 4.09
1713 1732 1.400629 CGAGCTTGGATGTTGCTGTTG 60.401 52.381 0.00 0.00 37.16 3.33
1731 1750 4.966787 GGGTGGCGCAACAAGGGA 62.967 66.667 18.47 0.00 0.00 4.20
1744 1763 1.988846 ACAAGGGAAAGGAGAAGGAGG 59.011 52.381 0.00 0.00 0.00 4.30
1750 1769 2.448453 GAAAGGAGAAGGAGGACGAGA 58.552 52.381 0.00 0.00 0.00 4.04
1810 1829 2.047844 CCTCGTCCACAGGCACAG 60.048 66.667 0.00 0.00 0.00 3.66
1823 1842 1.375908 GCACAGCCGAACATCCTCA 60.376 57.895 0.00 0.00 0.00 3.86
1824 1843 1.364626 GCACAGCCGAACATCCTCAG 61.365 60.000 0.00 0.00 0.00 3.35
1825 1844 0.742281 CACAGCCGAACATCCTCAGG 60.742 60.000 0.00 0.00 0.00 3.86
1826 1845 1.153289 CAGCCGAACATCCTCAGGG 60.153 63.158 0.00 0.00 0.00 4.45
1827 1846 1.306141 AGCCGAACATCCTCAGGGA 60.306 57.895 0.00 0.00 46.81 4.20
1828 1847 1.153349 GCCGAACATCCTCAGGGAC 60.153 63.158 0.00 0.00 45.43 4.46
1829 1848 1.522569 CCGAACATCCTCAGGGACC 59.477 63.158 0.00 0.00 45.43 4.46
1830 1849 0.978146 CCGAACATCCTCAGGGACCT 60.978 60.000 0.00 0.00 45.43 3.85
1831 1850 0.461961 CGAACATCCTCAGGGACCTC 59.538 60.000 0.00 0.00 45.43 3.85
1852 1871 2.890766 CGGCCACCCAAGGTACACT 61.891 63.158 2.24 0.00 32.11 3.55
1853 1872 1.002502 GGCCACCCAAGGTACACTC 60.003 63.158 0.00 0.00 32.11 3.51
1874 1893 2.784356 CGCAGCTCCCTCCTCTCAG 61.784 68.421 0.00 0.00 0.00 3.35
1875 1894 1.685421 GCAGCTCCCTCCTCTCAGT 60.685 63.158 0.00 0.00 0.00 3.41
1883 1902 1.412079 CCTCCTCTCAGTCTCCCATG 58.588 60.000 0.00 0.00 0.00 3.66
2178 2197 4.410743 GCTTGGCTTGCTGACCGC 62.411 66.667 0.00 0.00 39.77 5.68
2249 2268 1.123928 ATAGCACCAGAGGCCACTAC 58.876 55.000 5.01 0.00 0.00 2.73
2491 2510 3.181506 CGAACCTCTTTGCAAGAATAGCC 60.182 47.826 0.00 0.00 37.02 3.93
2543 2562 3.982829 GAACCGCCCTTGTTCCTC 58.017 61.111 0.00 0.00 36.87 3.71
2562 2581 4.082125 CCTCACAGTTCCTAAGGCATTTT 58.918 43.478 0.00 0.00 0.00 1.82
2574 2593 0.521735 GGCATTTTCCTCACCACGAC 59.478 55.000 0.00 0.00 0.00 4.34
2659 2678 4.431416 AGAGTGTGACCATACAAAACCA 57.569 40.909 0.03 0.00 31.36 3.67
2698 2717 3.424962 GCCTCGCAAGTGTTGATTCTAAC 60.425 47.826 0.00 0.00 39.48 2.34
2818 2837 9.659830 GTTGTTGTATGTAGTTTTAAGTTCTGG 57.340 33.333 0.00 0.00 0.00 3.86
2889 2908 5.299949 TCGGTCCTTGTAGTTTTAAGTTCC 58.700 41.667 0.00 0.00 0.00 3.62
3054 3145 7.398829 TGCAGTGTTGTTATCCTTCCTAATTA 58.601 34.615 0.00 0.00 0.00 1.40
3066 3157 5.306160 TCCTTCCTAATTAATACAGGGTCCG 59.694 44.000 13.49 3.26 0.00 4.79
3077 3168 1.305887 AGGGTCCGACTAAGTGGGG 60.306 63.158 0.00 0.00 32.22 4.96
3081 3172 1.690527 GGTCCGACTAAGTGGGGGTAT 60.691 57.143 0.00 0.00 32.22 2.73
3164 3255 3.056607 AGTTGTGCTGAACTGCAAAAACT 60.057 39.130 19.67 19.67 45.12 2.66
3213 3304 6.314648 GCATTGTTGAAGATACTGATGTCTCA 59.685 38.462 0.00 0.00 0.00 3.27
3276 3367 1.538512 GAAGTGTCACTGTGCATGCAT 59.461 47.619 25.64 4.77 0.00 3.96
3294 3385 2.806818 GCATATGAGACCATCAGCACAG 59.193 50.000 6.97 0.00 42.53 3.66
3297 3388 0.322648 TGAGACCATCAGCACAGTGG 59.677 55.000 1.84 0.00 38.96 4.00
3306 3397 1.893808 AGCACAGTGGGCTTTCGTG 60.894 57.895 15.99 0.00 38.81 4.35
3329 3420 6.638873 GTGACGTCTTACTAGATCATTGATGG 59.361 42.308 17.92 0.00 31.86 3.51
3404 3496 5.357878 ACAAATATTTGGACGCATGATGAGT 59.642 36.000 27.43 0.27 42.34 3.41
3435 3527 7.392418 GGTCTAAACCAAGTAATAGTTCTGGT 58.608 38.462 0.00 0.00 45.68 4.00
3442 3534 5.235516 CAAGTAATAGTTCTGGTGGTTCGT 58.764 41.667 0.00 0.00 0.00 3.85
3447 3539 3.594603 AGTTCTGGTGGTTCGTATCAG 57.405 47.619 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.537560 ATGCAGCGGCGATGTAAGC 61.538 57.895 26.78 12.75 45.35 3.09
8 9 1.277739 CATGCAGCGGCGATGTAAG 59.722 57.895 26.78 15.80 45.35 2.34
9 10 2.179547 CCATGCAGCGGCGATGTAA 61.180 57.895 26.78 15.68 45.35 2.41
10 11 2.585791 TTCCATGCAGCGGCGATGTA 62.586 55.000 26.78 23.34 45.35 2.29
11 12 3.974835 TTCCATGCAGCGGCGATGT 62.975 57.895 26.78 4.47 45.35 3.06
12 13 3.204119 TTCCATGCAGCGGCGATG 61.204 61.111 22.35 22.35 45.35 3.84
13 14 3.204827 GTTCCATGCAGCGGCGAT 61.205 61.111 12.98 0.00 45.35 4.58
14 15 4.695993 TGTTCCATGCAGCGGCGA 62.696 61.111 12.98 0.00 45.35 5.54
15 16 4.465512 GTGTTCCATGCAGCGGCG 62.466 66.667 0.51 0.51 45.35 6.46
16 17 2.918345 TTGTGTTCCATGCAGCGGC 61.918 57.895 0.31 0.31 41.68 6.53
17 18 1.081242 GTTGTGTTCCATGCAGCGG 60.081 57.895 0.00 0.00 0.00 5.52
18 19 1.440850 CGTTGTGTTCCATGCAGCG 60.441 57.895 0.00 0.00 0.00 5.18
19 20 0.030638 AACGTTGTGTTCCATGCAGC 59.969 50.000 0.00 0.00 35.27 5.25
28 29 1.152839 CCCAGGGGAACGTTGTGTT 60.153 57.895 5.00 0.00 45.61 3.32
29 30 2.513895 CCCAGGGGAACGTTGTGT 59.486 61.111 5.00 0.00 37.50 3.72
30 31 2.983592 GCCCAGGGGAACGTTGTG 60.984 66.667 5.00 0.00 37.50 3.33
31 32 4.280019 GGCCCAGGGGAACGTTGT 62.280 66.667 5.00 0.00 37.50 3.32
56 57 3.554692 GGTTGATGAGCGTCGGCG 61.555 66.667 4.29 4.29 46.35 6.46
57 58 2.125512 AGGTTGATGAGCGTCGGC 60.126 61.111 0.00 0.00 40.37 5.54
58 59 1.078759 GTGAGGTTGATGAGCGTCGG 61.079 60.000 0.00 0.00 0.00 4.79
59 60 1.078759 GGTGAGGTTGATGAGCGTCG 61.079 60.000 0.00 0.00 0.00 5.12
60 61 1.078759 CGGTGAGGTTGATGAGCGTC 61.079 60.000 0.00 0.00 0.00 5.19
61 62 1.079819 CGGTGAGGTTGATGAGCGT 60.080 57.895 0.00 0.00 0.00 5.07
62 63 1.078759 GTCGGTGAGGTTGATGAGCG 61.079 60.000 0.00 0.00 0.00 5.03
63 64 0.741221 GGTCGGTGAGGTTGATGAGC 60.741 60.000 0.00 0.00 0.00 4.26
64 65 0.108138 GGGTCGGTGAGGTTGATGAG 60.108 60.000 0.00 0.00 0.00 2.90
65 66 1.550130 GGGGTCGGTGAGGTTGATGA 61.550 60.000 0.00 0.00 0.00 2.92
66 67 1.078426 GGGGTCGGTGAGGTTGATG 60.078 63.158 0.00 0.00 0.00 3.07
67 68 2.656069 CGGGGTCGGTGAGGTTGAT 61.656 63.158 0.00 0.00 0.00 2.57
68 69 3.307906 CGGGGTCGGTGAGGTTGA 61.308 66.667 0.00 0.00 0.00 3.18
69 70 3.296709 CTCGGGGTCGGTGAGGTTG 62.297 68.421 0.00 0.00 36.95 3.77
70 71 2.995574 CTCGGGGTCGGTGAGGTT 60.996 66.667 0.00 0.00 36.95 3.50
73 74 3.450115 GTCCTCGGGGTCGGTGAG 61.450 72.222 0.00 0.00 36.95 3.51
78 79 2.707849 ATTGTCGTCCTCGGGGTCG 61.708 63.158 15.22 15.22 43.50 4.79
79 80 1.153628 CATTGTCGTCCTCGGGGTC 60.154 63.158 0.00 0.00 37.69 4.46
80 81 1.608336 TCATTGTCGTCCTCGGGGT 60.608 57.895 0.00 0.00 37.69 4.95
81 82 1.153628 GTCATTGTCGTCCTCGGGG 60.154 63.158 0.00 0.00 37.69 5.73
82 83 1.516386 CGTCATTGTCGTCCTCGGG 60.516 63.158 0.00 0.00 37.69 5.14
83 84 0.797249 GTCGTCATTGTCGTCCTCGG 60.797 60.000 3.38 0.00 37.69 4.63
84 85 0.109919 TGTCGTCATTGTCGTCCTCG 60.110 55.000 3.38 0.00 38.55 4.63
85 86 1.719780 GTTGTCGTCATTGTCGTCCTC 59.280 52.381 3.38 0.00 0.00 3.71
86 87 1.779569 GTTGTCGTCATTGTCGTCCT 58.220 50.000 3.38 0.00 0.00 3.85
87 88 0.433492 CGTTGTCGTCATTGTCGTCC 59.567 55.000 3.38 0.00 0.00 4.79
88 89 0.179282 GCGTTGTCGTCATTGTCGTC 60.179 55.000 3.38 0.00 39.49 4.20
89 90 1.554042 GGCGTTGTCGTCATTGTCGT 61.554 55.000 3.38 0.00 41.67 4.34
90 91 1.129809 GGCGTTGTCGTCATTGTCG 59.870 57.895 0.00 0.00 41.67 4.35
91 92 1.705256 TAGGCGTTGTCGTCATTGTC 58.295 50.000 0.00 0.00 44.74 3.18
92 93 2.066262 CTTAGGCGTTGTCGTCATTGT 58.934 47.619 0.00 0.00 44.74 2.71
93 94 1.393539 CCTTAGGCGTTGTCGTCATTG 59.606 52.381 0.00 0.00 44.74 2.82
94 95 1.722011 CCTTAGGCGTTGTCGTCATT 58.278 50.000 0.00 0.00 44.74 2.57
95 96 0.739813 GCCTTAGGCGTTGTCGTCAT 60.740 55.000 7.77 0.00 44.74 3.06
96 97 1.373748 GCCTTAGGCGTTGTCGTCA 60.374 57.895 7.77 0.00 44.74 4.35
97 98 3.471399 GCCTTAGGCGTTGTCGTC 58.529 61.111 7.77 0.00 39.62 4.20
122 123 4.865761 TACCAGGCGACGCGATGC 62.866 66.667 15.93 16.48 0.00 3.91
123 124 2.655364 CTACCAGGCGACGCGATG 60.655 66.667 15.93 14.66 0.00 3.84
124 125 1.378882 TAACTACCAGGCGACGCGAT 61.379 55.000 15.93 1.48 0.00 4.58
125 126 1.985447 CTAACTACCAGGCGACGCGA 61.985 60.000 15.93 0.00 0.00 5.87
126 127 1.585521 CTAACTACCAGGCGACGCG 60.586 63.158 14.61 3.53 0.00 6.01
127 128 1.226888 CCTAACTACCAGGCGACGC 60.227 63.158 12.43 12.43 0.00 5.19
128 129 0.529378 AACCTAACTACCAGGCGACG 59.471 55.000 0.00 0.00 36.57 5.12
129 130 1.274447 ACAACCTAACTACCAGGCGAC 59.726 52.381 0.00 0.00 36.57 5.19
130 131 1.636148 ACAACCTAACTACCAGGCGA 58.364 50.000 0.00 0.00 36.57 5.54
131 132 2.467566 AACAACCTAACTACCAGGCG 57.532 50.000 0.00 0.00 36.57 5.52
132 133 6.638096 TTAAAAACAACCTAACTACCAGGC 57.362 37.500 0.00 0.00 36.57 4.85
133 134 9.687210 GAAATTAAAAACAACCTAACTACCAGG 57.313 33.333 0.00 0.00 39.25 4.45
154 155 7.544217 GCGTCCACATTACCATTAAAAGAAATT 59.456 33.333 0.00 0.00 0.00 1.82
155 156 7.033185 GCGTCCACATTACCATTAAAAGAAAT 58.967 34.615 0.00 0.00 0.00 2.17
156 157 6.383415 GCGTCCACATTACCATTAAAAGAAA 58.617 36.000 0.00 0.00 0.00 2.52
157 158 5.391097 CGCGTCCACATTACCATTAAAAGAA 60.391 40.000 0.00 0.00 0.00 2.52
158 159 4.093703 CGCGTCCACATTACCATTAAAAGA 59.906 41.667 0.00 0.00 0.00 2.52
159 160 4.142773 ACGCGTCCACATTACCATTAAAAG 60.143 41.667 5.58 0.00 0.00 2.27
160 161 3.752222 ACGCGTCCACATTACCATTAAAA 59.248 39.130 5.58 0.00 0.00 1.52
161 162 3.125487 CACGCGTCCACATTACCATTAAA 59.875 43.478 9.86 0.00 0.00 1.52
162 163 2.673862 CACGCGTCCACATTACCATTAA 59.326 45.455 9.86 0.00 0.00 1.40
163 164 2.272678 CACGCGTCCACATTACCATTA 58.727 47.619 9.86 0.00 0.00 1.90
164 165 1.083489 CACGCGTCCACATTACCATT 58.917 50.000 9.86 0.00 0.00 3.16
165 166 0.742990 CCACGCGTCCACATTACCAT 60.743 55.000 9.86 0.00 0.00 3.55
166 167 1.374885 CCACGCGTCCACATTACCA 60.375 57.895 9.86 0.00 0.00 3.25
167 168 1.079681 TCCACGCGTCCACATTACC 60.080 57.895 9.86 0.00 0.00 2.85
168 169 0.389426 AGTCCACGCGTCCACATTAC 60.389 55.000 9.86 0.00 0.00 1.89
169 170 0.108992 GAGTCCACGCGTCCACATTA 60.109 55.000 9.86 0.00 0.00 1.90
170 171 1.374252 GAGTCCACGCGTCCACATT 60.374 57.895 9.86 0.00 0.00 2.71
171 172 2.214181 GAGAGTCCACGCGTCCACAT 62.214 60.000 9.86 1.40 0.00 3.21
172 173 2.910479 AGAGTCCACGCGTCCACA 60.910 61.111 9.86 0.00 0.00 4.17
173 174 2.126424 GAGAGTCCACGCGTCCAC 60.126 66.667 9.86 9.15 0.00 4.02
174 175 3.733960 CGAGAGTCCACGCGTCCA 61.734 66.667 9.86 0.00 0.00 4.02
183 184 4.516195 GAAGGCCGGCGAGAGTCC 62.516 72.222 22.54 4.09 0.00 3.85
184 185 4.516195 GGAAGGCCGGCGAGAGTC 62.516 72.222 22.54 12.33 0.00 3.36
186 187 4.521062 CAGGAAGGCCGGCGAGAG 62.521 72.222 22.54 3.92 39.96 3.20
196 197 0.395724 ATTAAAGCCGGCCAGGAAGG 60.396 55.000 26.15 3.49 45.00 3.46
197 198 0.740737 CATTAAAGCCGGCCAGGAAG 59.259 55.000 26.15 5.89 45.00 3.46
198 199 0.039035 ACATTAAAGCCGGCCAGGAA 59.961 50.000 26.15 13.16 45.00 3.36
199 200 0.039035 AACATTAAAGCCGGCCAGGA 59.961 50.000 26.15 7.86 45.00 3.86
200 201 0.894835 AAACATTAAAGCCGGCCAGG 59.105 50.000 26.15 9.36 44.97 4.45
201 202 3.859411 TTAAACATTAAAGCCGGCCAG 57.141 42.857 26.15 9.37 0.00 4.85
202 203 4.810191 AATTAAACATTAAAGCCGGCCA 57.190 36.364 26.15 5.71 0.00 5.36
203 204 6.334989 ACTTAATTAAACATTAAAGCCGGCC 58.665 36.000 26.15 5.07 0.00 6.13
204 205 7.329962 ACAACTTAATTAAACATTAAAGCCGGC 59.670 33.333 21.89 21.89 0.00 6.13
205 206 8.751302 ACAACTTAATTAAACATTAAAGCCGG 57.249 30.769 0.00 0.00 0.00 6.13
226 227 9.823098 TGCATGCATATTTAAAATGAAAACAAC 57.177 25.926 18.46 0.00 0.00 3.32
227 228 9.823098 GTGCATGCATATTTAAAATGAAAACAA 57.177 25.926 25.64 0.00 0.00 2.83
228 229 8.996271 TGTGCATGCATATTTAAAATGAAAACA 58.004 25.926 25.64 7.63 0.00 2.83
229 230 9.480538 CTGTGCATGCATATTTAAAATGAAAAC 57.519 29.630 25.64 4.82 0.00 2.43
230 231 9.217278 ACTGTGCATGCATATTTAAAATGAAAA 57.783 25.926 25.64 0.00 0.00 2.29
231 232 8.774890 ACTGTGCATGCATATTTAAAATGAAA 57.225 26.923 25.64 0.00 0.00 2.69
232 233 8.774890 AACTGTGCATGCATATTTAAAATGAA 57.225 26.923 25.64 0.00 0.00 2.57
233 234 8.774890 AAACTGTGCATGCATATTTAAAATGA 57.225 26.923 25.64 0.00 0.00 2.57
234 235 9.828852 AAAAACTGTGCATGCATATTTAAAATG 57.171 25.926 25.64 9.01 0.00 2.32
266 267 0.316689 GATCCATTTTAACGGCGCCG 60.317 55.000 44.88 44.88 46.03 6.46
267 268 0.316689 CGATCCATTTTAACGGCGCC 60.317 55.000 19.07 19.07 0.00 6.53
268 269 0.316689 CCGATCCATTTTAACGGCGC 60.317 55.000 6.90 0.00 37.32 6.53
269 270 0.306533 CCCGATCCATTTTAACGGCG 59.693 55.000 4.80 4.80 41.86 6.46
270 271 0.030235 GCCCGATCCATTTTAACGGC 59.970 55.000 0.00 0.00 41.86 5.68
271 272 0.306533 CGCCCGATCCATTTTAACGG 59.693 55.000 0.00 0.00 42.67 4.44
272 273 1.260561 CTCGCCCGATCCATTTTAACG 59.739 52.381 0.00 0.00 0.00 3.18
273 274 1.002792 GCTCGCCCGATCCATTTTAAC 60.003 52.381 0.00 0.00 0.00 2.01
274 275 1.305201 GCTCGCCCGATCCATTTTAA 58.695 50.000 0.00 0.00 0.00 1.52
275 276 0.878523 CGCTCGCCCGATCCATTTTA 60.879 55.000 0.00 0.00 0.00 1.52
276 277 2.180204 CGCTCGCCCGATCCATTTT 61.180 57.895 0.00 0.00 0.00 1.82
277 278 2.588877 CGCTCGCCCGATCCATTT 60.589 61.111 0.00 0.00 0.00 2.32
278 279 3.385749 AACGCTCGCCCGATCCATT 62.386 57.895 1.63 0.00 0.00 3.16
279 280 3.849951 AACGCTCGCCCGATCCAT 61.850 61.111 1.63 0.00 0.00 3.41
280 281 4.812476 CAACGCTCGCCCGATCCA 62.812 66.667 1.63 0.00 0.00 3.41
294 295 2.507547 TCGACGTATGCGCCCAAC 60.508 61.111 4.18 0.00 42.83 3.77
295 296 2.507547 GTCGACGTATGCGCCCAA 60.508 61.111 4.18 0.00 42.83 4.12
296 297 4.501714 GGTCGACGTATGCGCCCA 62.502 66.667 9.92 0.00 42.83 5.36
298 299 3.993376 TTGGGTCGACGTATGCGCC 62.993 63.158 9.92 3.56 42.83 6.53
299 300 2.095847 TTTGGGTCGACGTATGCGC 61.096 57.895 9.92 0.00 42.83 6.09
300 301 1.705727 GTTTGGGTCGACGTATGCG 59.294 57.895 9.92 0.19 44.93 4.73
301 302 1.705727 CGTTTGGGTCGACGTATGC 59.294 57.895 9.92 0.00 34.75 3.14
302 303 1.705727 GCGTTTGGGTCGACGTATG 59.294 57.895 9.92 1.44 41.10 2.39
303 304 1.802715 CGCGTTTGGGTCGACGTAT 60.803 57.895 9.92 0.00 41.10 3.06
304 305 2.399511 TTCGCGTTTGGGTCGACGTA 62.400 55.000 9.92 0.00 41.10 3.57
305 306 3.771568 TTCGCGTTTGGGTCGACGT 62.772 57.895 9.92 0.00 41.10 4.34
306 307 2.474842 CTTTCGCGTTTGGGTCGACG 62.475 60.000 9.92 0.00 41.89 5.12
307 308 1.203313 CTTTCGCGTTTGGGTCGAC 59.797 57.895 7.13 7.13 31.48 4.20
308 309 2.600475 GCTTTCGCGTTTGGGTCGA 61.600 57.895 5.77 0.00 0.00 4.20
309 310 2.127383 GCTTTCGCGTTTGGGTCG 60.127 61.111 5.77 0.00 0.00 4.79
319 320 3.400590 ACGAACGTCCGCTTTCGC 61.401 61.111 0.00 0.00 46.10 4.70
321 322 1.485943 GACACGAACGTCCGCTTTC 59.514 57.895 0.00 0.00 0.00 2.62
322 323 1.952635 GGACACGAACGTCCGCTTT 60.953 57.895 0.00 0.00 45.77 3.51
323 324 2.355481 GGACACGAACGTCCGCTT 60.355 61.111 0.00 0.00 45.77 4.68
328 329 3.103911 CAGGCGGACACGAACGTC 61.104 66.667 0.00 0.00 44.60 4.34
329 330 3.598715 TCAGGCGGACACGAACGT 61.599 61.111 0.00 0.00 44.60 3.99
330 331 3.103911 GTCAGGCGGACACGAACG 61.104 66.667 13.03 0.00 46.19 3.95
337 338 1.389609 TTAGGATCGGTCAGGCGGAC 61.390 60.000 9.42 9.42 46.20 4.79
338 339 1.076559 TTAGGATCGGTCAGGCGGA 60.077 57.895 0.00 0.00 0.00 5.54
339 340 1.067582 GTTAGGATCGGTCAGGCGG 59.932 63.158 0.00 0.00 0.00 6.13
340 341 1.299165 CGTTAGGATCGGTCAGGCG 60.299 63.158 0.00 0.00 0.00 5.52
341 342 1.067582 CCGTTAGGATCGGTCAGGC 59.932 63.158 0.00 0.00 42.62 4.85
342 343 2.803203 TCCGTTAGGATCGGTCAGG 58.197 57.895 0.00 0.00 46.86 3.86
377 378 4.324991 AACTCCAACGGGCCGACC 62.325 66.667 35.78 0.00 0.00 4.79
378 379 3.047877 CAACTCCAACGGGCCGAC 61.048 66.667 35.78 0.00 0.00 4.79
381 382 3.056328 GAGCAACTCCAACGGGCC 61.056 66.667 0.00 0.00 0.00 5.80
382 383 0.321298 TAAGAGCAACTCCAACGGGC 60.321 55.000 0.00 0.00 0.00 6.13
383 384 1.270625 TGTAAGAGCAACTCCAACGGG 60.271 52.381 0.00 0.00 0.00 5.28
384 385 2.163818 TGTAAGAGCAACTCCAACGG 57.836 50.000 0.00 0.00 0.00 4.44
385 386 3.589988 AGATGTAAGAGCAACTCCAACG 58.410 45.455 0.00 0.00 0.00 4.10
386 387 4.568760 GCTAGATGTAAGAGCAACTCCAAC 59.431 45.833 0.00 0.00 36.20 3.77
387 388 4.383118 GGCTAGATGTAAGAGCAACTCCAA 60.383 45.833 0.00 0.00 37.98 3.53
388 389 3.133003 GGCTAGATGTAAGAGCAACTCCA 59.867 47.826 0.00 0.00 37.98 3.86
389 390 3.133003 TGGCTAGATGTAAGAGCAACTCC 59.867 47.826 0.00 0.00 37.98 3.85
390 391 4.392921 TGGCTAGATGTAAGAGCAACTC 57.607 45.455 0.00 0.00 37.98 3.01
391 392 5.365021 AATGGCTAGATGTAAGAGCAACT 57.635 39.130 0.00 0.00 37.98 3.16
392 393 5.586243 TGAAATGGCTAGATGTAAGAGCAAC 59.414 40.000 0.00 0.00 37.98 4.17
393 394 5.744171 TGAAATGGCTAGATGTAAGAGCAA 58.256 37.500 0.00 0.00 37.98 3.91
394 395 5.357742 TGAAATGGCTAGATGTAAGAGCA 57.642 39.130 0.00 0.00 37.98 4.26
395 396 6.709846 AGAATGAAATGGCTAGATGTAAGAGC 59.290 38.462 0.00 0.00 35.39 4.09
396 397 8.674263 AAGAATGAAATGGCTAGATGTAAGAG 57.326 34.615 0.00 0.00 0.00 2.85
397 398 9.466497 AAAAGAATGAAATGGCTAGATGTAAGA 57.534 29.630 0.00 0.00 0.00 2.10
513 517 2.887568 GATCAGCGTGGCAGTCCG 60.888 66.667 0.00 0.00 34.14 4.79
635 640 2.622436 CAAAGGAGAGCGGAAGGTTAG 58.378 52.381 0.00 0.00 45.11 2.34
673 687 4.675303 TGGAGAGGTGGGTGGGGG 62.675 72.222 0.00 0.00 0.00 5.40
977 996 1.548269 CTCTCCTTCTTGAGTCGCCTT 59.452 52.381 0.00 0.00 33.93 4.35
1057 1076 2.809601 CTTCTTGGCGTCGACGGG 60.810 66.667 36.13 13.02 40.23 5.28
1154 1173 3.181436 GGGTTCACATCCCATCAGATGAT 60.181 47.826 12.41 0.00 45.43 2.45
1408 1427 1.529948 CGTAGGCCACCCTATCCGA 60.530 63.158 5.01 0.00 45.22 4.55
1448 1467 1.486726 GGAGTGATTCGGGTTCCTGAT 59.513 52.381 0.89 0.00 0.00 2.90
1458 1477 1.961180 AAGCCTCCCGGAGTGATTCG 61.961 60.000 13.62 0.00 0.00 3.34
1484 1503 1.903890 GGATCGGATGAGGCGAGGA 60.904 63.158 0.00 0.00 0.00 3.71
1612 1631 3.321682 AGAGCTGCCTCTGCTAATAGAAG 59.678 47.826 0.00 0.00 46.51 2.85
1652 1671 2.418083 GCCTCCCCGAATTGCTTGG 61.418 63.158 0.00 0.00 0.00 3.61
1731 1750 2.452505 CTCTCGTCCTCCTTCTCCTTT 58.547 52.381 0.00 0.00 0.00 3.11
1750 1769 4.845580 CTCATTGAGGCCGCCGCT 62.846 66.667 14.72 0.00 34.44 5.52
1781 1800 0.397254 GGACGAGGAAGATGAGGGGA 60.397 60.000 0.00 0.00 0.00 4.81
1782 1801 0.687757 TGGACGAGGAAGATGAGGGG 60.688 60.000 0.00 0.00 0.00 4.79
1810 1829 1.153349 GTCCCTGAGGATGTTCGGC 60.153 63.158 0.00 0.00 46.41 5.54
1818 1837 2.363018 CGCTGAGGTCCCTGAGGA 60.363 66.667 0.00 0.00 41.08 3.71
1831 1850 4.028490 TACCTTGGGTGGCCGCTG 62.028 66.667 17.49 4.33 36.19 5.18
1838 1857 1.375523 GCGGAGTGTACCTTGGGTG 60.376 63.158 0.00 0.00 36.19 4.61
1841 1860 2.813908 GCGCGGAGTGTACCTTGG 60.814 66.667 8.83 0.00 41.96 3.61
1894 1913 1.281577 CCAAATTTGGGGTGGATTGGG 59.718 52.381 26.87 0.00 44.70 4.12
1921 1940 2.632377 TCCTCATTTCAATCAGGCGAC 58.368 47.619 0.00 0.00 0.00 5.19
2284 2303 7.287810 ACCAAAATGGAAGACCCTATATGTAC 58.712 38.462 2.85 0.00 40.96 2.90
2350 2369 5.935945 TCAATTACCAAGAGACCAGAACAA 58.064 37.500 0.00 0.00 0.00 2.83
2443 2462 0.681733 TGTCAACTCACTGCCTCCTC 59.318 55.000 0.00 0.00 0.00 3.71
2491 2510 0.108615 AAGAGTGAGAACCGATGCCG 60.109 55.000 0.00 0.00 0.00 5.69
2543 2562 4.082125 AGGAAAATGCCTTAGGAACTGTG 58.918 43.478 0.69 0.00 41.52 3.66
2795 2814 8.387190 ACCCAGAACTTAAAACTACATACAAC 57.613 34.615 0.00 0.00 0.00 3.32
2971 3062 9.681692 CTCATGAACTTTTGTAACATTCAATCA 57.318 29.630 0.00 0.00 33.29 2.57
2974 3065 8.006298 ACCTCATGAACTTTTGTAACATTCAA 57.994 30.769 0.00 0.00 33.29 2.69
3008 3099 4.261867 GCAAACCGACAAGGATAAAAAGGT 60.262 41.667 0.00 0.00 45.00 3.50
3054 3145 2.764572 CCACTTAGTCGGACCCTGTATT 59.235 50.000 4.14 0.00 0.00 1.89
3057 3148 0.903454 CCCACTTAGTCGGACCCTGT 60.903 60.000 4.14 0.00 0.00 4.00
3066 3157 5.899631 TTCCAATATACCCCCACTTAGTC 57.100 43.478 0.00 0.00 0.00 2.59
3077 3168 7.817418 TGGTAAAAGAGCATTCCAATATACC 57.183 36.000 0.00 0.00 0.00 2.73
3081 3172 7.716799 AACATGGTAAAAGAGCATTCCAATA 57.283 32.000 0.00 0.00 43.93 1.90
3213 3304 7.675962 TTACAATTATTTGTACAACGGCTCT 57.324 32.000 8.07 0.00 45.60 4.09
3248 3339 1.417890 ACAGTGACACTTCTTCCCCTG 59.582 52.381 5.04 0.00 0.00 4.45
3259 3350 2.679336 TCATATGCATGCACAGTGACAC 59.321 45.455 25.37 0.00 31.73 3.67
3276 3367 2.169144 CCACTGTGCTGATGGTCTCATA 59.831 50.000 1.29 0.00 32.98 2.15
3294 3385 0.878961 AAGACGTCACGAAAGCCCAC 60.879 55.000 19.50 0.00 0.00 4.61
3297 3388 2.061740 AGTAAGACGTCACGAAAGCC 57.938 50.000 19.50 0.00 0.00 4.35
3306 3397 5.631512 GCCATCAATGATCTAGTAAGACGTC 59.368 44.000 7.70 7.70 33.57 4.34
3371 3463 8.050778 TGCGTCCAAATATTTGTAGAAATTCT 57.949 30.769 23.24 0.00 36.45 2.40
3377 3469 6.765512 TCATCATGCGTCCAAATATTTGTAGA 59.234 34.615 23.24 13.50 36.45 2.59
3404 3496 6.961721 ACTATTACTTGGTTTAGACCTGGGTA 59.038 38.462 3.79 2.12 46.66 3.69
3428 3520 3.587797 TCTGATACGAACCACCAGAAC 57.412 47.619 0.00 0.00 31.72 3.01
3429 3521 3.322541 TGTTCTGATACGAACCACCAGAA 59.677 43.478 0.00 0.00 41.95 3.02


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

AutoCloner maintained by Alex Coulton.