Multiple sequence alignment - TraesCS3D01G300800

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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 TraesCS3D01G300800 chr3D 100.000 3461 0 0 1 3461 415546544 415543084 0.000000e+00 6392
1 TraesCS3D01G300800 chr3D 98.291 117 1 1 1 116 161678952 161678836 1.630000e-48 204
2 TraesCS3D01G300800 chr3D 98.148 108 2 0 1 108 400479158 400479265 4.560000e-44 189
3 TraesCS3D01G300800 chr3A 94.552 2625 80 28 872 3461 534995478 534998074 0.000000e+00 3997
4 TraesCS3D01G300800 chr3A 99.123 114 1 0 1 114 331507909 331507796 4.530000e-49 206
5 TraesCS3D01G300800 chr3B 96.891 1994 41 3 884 2856 541528870 541526877 0.000000e+00 3319
6 TraesCS3D01G300800 chr3B 90.634 331 8 3 3131 3461 541524034 541523727 5.340000e-113 418
7 TraesCS3D01G300800 chr3B 91.459 281 15 3 2856 3135 541526698 541526426 9.070000e-101 377
8 TraesCS3D01G300800 chr2A 98.291 117 2 0 1 117 510119593 510119477 4.530000e-49 206
9 TraesCS3D01G300800 chr2A 95.200 125 4 2 1 125 182535030 182535152 2.730000e-46 196
10 TraesCS3D01G300800 chr1D 97.500 120 1 2 1 118 50366932 50366813 1.630000e-48 204
11 TraesCS3D01G300800 chr1D 97.500 120 1 2 1 118 50375201 50375082 1.630000e-48 204
12 TraesCS3D01G300800 chr2D 96.667 120 4 0 1 120 191334998 191335117 2.110000e-47 200
13 TraesCS3D01G300800 chr7D 95.935 123 3 1 1 123 573848440 573848320 7.580000e-47 198


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 TraesCS3D01G300800 chr3D 415543084 415546544 3460 True 6392.000000 6392 100.000000 1 3461 1 chr3D.!!$R2 3460
1 TraesCS3D01G300800 chr3A 534995478 534998074 2596 False 3997.000000 3997 94.552000 872 3461 1 chr3A.!!$F1 2589
2 TraesCS3D01G300800 chr3B 541523727 541528870 5143 True 1371.333333 3319 92.994667 884 3461 3 chr3B.!!$R1 2577

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
207 208 0.034089 ACATCTAGGCTGGCCAAACC 60.034 55.000 15.39 15.39 38.92 3.27 F
224 225 0.395312 ACCACTCATTTTCGTCCGGT 59.605 50.000 0.00 0.00 0.00 5.28 F
225 226 1.202722 ACCACTCATTTTCGTCCGGTT 60.203 47.619 0.00 0.00 0.00 4.44 F
438 439 1.731709 GCGGACATTTTCCAAATTGGC 59.268 47.619 7.24 0.00 46.29 4.52 F
439 440 2.869636 GCGGACATTTTCCAAATTGGCA 60.870 45.455 7.24 0.00 46.29 4.92 F
2401 2410 1.347707 TGTTAGGAGACAGGCTGTTGG 59.652 52.381 22.98 0.00 0.00 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1071 1080 2.317609 GCAGGTGTTGATCGCGTGT 61.318 57.895 5.77 0.0 42.24 4.49 R
1739 1748 4.706842 AATATAACGTCCAGCTCCCATT 57.293 40.909 0.00 0.0 0.00 3.16 R
1773 1782 5.190726 TCCACACTTCCCATACATATCAACA 59.809 40.000 0.00 0.0 0.00 3.33 R
2401 2410 2.334946 TGCTGCCAGATTTCGGTGC 61.335 57.895 0.00 0.0 0.00 5.01 R
2428 2437 3.268023 AGATCCTTGGATCGGAAACAC 57.732 47.619 20.14 0.0 36.73 3.32 R
3383 5993 2.076100 TCAAGATGCATCCGTCACAAC 58.924 47.619 23.06 0.0 0.00 3.32 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
36 37 8.484214 AGAGAGAATAGGCATAAGTATTGTGA 57.516 34.615 0.00 0.00 39.84 3.58
37 38 8.364142 AGAGAGAATAGGCATAAGTATTGTGAC 58.636 37.037 0.00 0.00 46.78 3.67
46 47 7.930217 GGCATAAGTATTGTGACATAATGTGT 58.070 34.615 7.62 0.00 45.57 3.72
47 48 9.051679 GGCATAAGTATTGTGACATAATGTGTA 57.948 33.333 7.62 0.00 45.57 2.90
56 57 7.315247 TGTGACATAATGTGTAATAACAGCC 57.685 36.000 0.00 0.00 42.36 4.85
57 58 6.317642 TGTGACATAATGTGTAATAACAGCCC 59.682 38.462 0.00 0.00 42.36 5.19
58 59 6.317642 GTGACATAATGTGTAATAACAGCCCA 59.682 38.462 0.00 0.00 42.36 5.36
59 60 7.013274 GTGACATAATGTGTAATAACAGCCCAT 59.987 37.037 0.00 0.00 42.36 4.00
60 61 8.214364 TGACATAATGTGTAATAACAGCCCATA 58.786 33.333 0.00 0.00 42.36 2.74
61 62 8.988546 ACATAATGTGTAATAACAGCCCATAA 57.011 30.769 0.00 0.00 39.91 1.90
62 63 9.586732 ACATAATGTGTAATAACAGCCCATAAT 57.413 29.630 0.00 0.00 39.91 1.28
63 64 9.844790 CATAATGTGTAATAACAGCCCATAATG 57.155 33.333 0.00 0.00 35.91 1.90
64 65 5.766150 TGTGTAATAACAGCCCATAATGC 57.234 39.130 0.00 0.00 35.91 3.56
65 66 5.196695 TGTGTAATAACAGCCCATAATGCA 58.803 37.500 0.00 0.00 35.91 3.96
66 67 5.654209 TGTGTAATAACAGCCCATAATGCAA 59.346 36.000 0.00 0.00 35.91 4.08
67 68 6.323482 TGTGTAATAACAGCCCATAATGCAAT 59.677 34.615 0.00 0.00 35.91 3.56
68 69 7.503902 TGTGTAATAACAGCCCATAATGCAATA 59.496 33.333 0.00 0.00 35.91 1.90
69 70 8.356657 GTGTAATAACAGCCCATAATGCAATAA 58.643 33.333 0.00 0.00 35.91 1.40
70 71 8.918116 TGTAATAACAGCCCATAATGCAATAAA 58.082 29.630 0.00 0.00 0.00 1.40
71 72 9.927668 GTAATAACAGCCCATAATGCAATAAAT 57.072 29.630 0.00 0.00 0.00 1.40
75 76 6.855836 ACAGCCCATAATGCAATAAATATCG 58.144 36.000 0.00 0.00 0.00 2.92
76 77 6.658816 ACAGCCCATAATGCAATAAATATCGA 59.341 34.615 0.00 0.00 0.00 3.59
77 78 7.340232 ACAGCCCATAATGCAATAAATATCGAT 59.660 33.333 2.16 2.16 0.00 3.59
78 79 8.839343 CAGCCCATAATGCAATAAATATCGATA 58.161 33.333 7.75 7.75 0.00 2.92
79 80 9.578576 AGCCCATAATGCAATAAATATCGATAT 57.421 29.630 12.25 12.25 0.00 1.63
102 103 2.640684 GCATGATGCAAAACGGACG 58.359 52.632 13.36 0.00 44.26 4.79
103 104 0.109781 GCATGATGCAAAACGGACGT 60.110 50.000 13.36 0.00 44.26 4.34
104 105 1.129624 GCATGATGCAAAACGGACGTA 59.870 47.619 13.36 0.00 44.26 3.57
105 106 2.223249 GCATGATGCAAAACGGACGTAT 60.223 45.455 13.36 0.00 44.26 3.06
106 107 3.607439 CATGATGCAAAACGGACGTATC 58.393 45.455 0.00 0.00 0.00 2.24
107 108 2.689646 TGATGCAAAACGGACGTATCA 58.310 42.857 0.00 0.47 0.00 2.15
108 109 2.413796 TGATGCAAAACGGACGTATCAC 59.586 45.455 0.00 0.00 0.00 3.06
109 110 1.149987 TGCAAAACGGACGTATCACC 58.850 50.000 0.00 0.00 0.00 4.02
114 115 3.829044 CGGACGTATCACCGGGCA 61.829 66.667 6.32 0.00 44.59 5.36
115 116 2.106332 GGACGTATCACCGGGCAG 59.894 66.667 6.32 0.00 0.00 4.85
116 117 2.585247 GACGTATCACCGGGCAGC 60.585 66.667 6.32 0.00 0.00 5.25
117 118 4.508128 ACGTATCACCGGGCAGCG 62.508 66.667 6.32 6.27 0.00 5.18
118 119 4.508128 CGTATCACCGGGCAGCGT 62.508 66.667 6.32 0.00 0.00 5.07
119 120 2.125269 GTATCACCGGGCAGCGTT 60.125 61.111 6.32 0.00 0.00 4.84
120 121 1.142314 GTATCACCGGGCAGCGTTA 59.858 57.895 6.32 0.00 0.00 3.18
121 122 0.249741 GTATCACCGGGCAGCGTTAT 60.250 55.000 6.32 0.00 0.00 1.89
122 123 0.249699 TATCACCGGGCAGCGTTATG 60.250 55.000 6.32 0.00 0.00 1.90
123 124 2.252072 ATCACCGGGCAGCGTTATGT 62.252 55.000 6.32 0.00 0.00 2.29
124 125 2.435938 ACCGGGCAGCGTTATGTG 60.436 61.111 6.32 0.00 0.00 3.21
125 126 3.202001 CCGGGCAGCGTTATGTGG 61.202 66.667 0.00 0.00 0.00 4.17
126 127 3.202001 CGGGCAGCGTTATGTGGG 61.202 66.667 0.00 0.00 0.00 4.61
127 128 2.270850 GGGCAGCGTTATGTGGGA 59.729 61.111 0.00 0.00 0.00 4.37
128 129 1.152963 GGGCAGCGTTATGTGGGAT 60.153 57.895 0.00 0.00 0.00 3.85
129 130 1.166531 GGGCAGCGTTATGTGGGATC 61.167 60.000 0.00 0.00 0.00 3.36
130 131 1.166531 GGCAGCGTTATGTGGGATCC 61.167 60.000 1.92 1.92 0.00 3.36
131 132 0.179045 GCAGCGTTATGTGGGATCCT 60.179 55.000 12.58 0.00 0.00 3.24
132 133 1.070134 GCAGCGTTATGTGGGATCCTA 59.930 52.381 12.58 1.47 0.00 2.94
133 134 2.289694 GCAGCGTTATGTGGGATCCTAT 60.290 50.000 12.58 6.80 0.00 2.57
134 135 3.807209 GCAGCGTTATGTGGGATCCTATT 60.807 47.826 12.58 0.00 0.00 1.73
135 136 4.389374 CAGCGTTATGTGGGATCCTATTT 58.611 43.478 12.58 0.00 0.00 1.40
136 137 4.214119 CAGCGTTATGTGGGATCCTATTTG 59.786 45.833 12.58 0.00 0.00 2.32
137 138 3.502211 GCGTTATGTGGGATCCTATTTGG 59.498 47.826 12.58 0.00 37.10 3.28
138 139 3.502211 CGTTATGTGGGATCCTATTTGGC 59.498 47.826 12.58 0.00 35.26 4.52
139 140 2.276732 ATGTGGGATCCTATTTGGCG 57.723 50.000 12.58 0.00 35.26 5.69
140 141 0.465460 TGTGGGATCCTATTTGGCGC 60.465 55.000 12.58 0.00 35.26 6.53
141 142 1.227823 TGGGATCCTATTTGGCGCG 60.228 57.895 12.58 0.00 35.26 6.86
142 143 1.227853 GGGATCCTATTTGGCGCGT 60.228 57.895 12.58 0.00 35.26 6.01
143 144 0.034337 GGGATCCTATTTGGCGCGTA 59.966 55.000 12.58 0.00 35.26 4.42
144 145 1.429463 GGATCCTATTTGGCGCGTAG 58.571 55.000 8.43 0.14 35.26 3.51
145 146 1.429463 GATCCTATTTGGCGCGTAGG 58.571 55.000 8.43 10.80 37.03 3.18
146 147 0.756903 ATCCTATTTGGCGCGTAGGT 59.243 50.000 16.59 4.88 37.01 3.08
147 148 0.103572 TCCTATTTGGCGCGTAGGTC 59.896 55.000 16.59 0.00 37.01 3.85
148 149 1.213094 CCTATTTGGCGCGTAGGTCG 61.213 60.000 8.43 0.00 43.12 4.79
157 158 2.254651 CGTAGGTCGCCCGATAGC 59.745 66.667 0.00 0.00 35.12 2.97
186 187 2.111878 CCCCCGCTTCCTGCTATG 59.888 66.667 0.00 0.00 40.11 2.23
187 188 2.592861 CCCCGCTTCCTGCTATGC 60.593 66.667 0.00 0.00 40.11 3.14
188 189 2.190313 CCCGCTTCCTGCTATGCA 59.810 61.111 0.00 0.00 40.11 3.96
189 190 2.182842 CCCGCTTCCTGCTATGCAC 61.183 63.158 0.00 0.00 40.11 4.57
190 191 1.450134 CCGCTTCCTGCTATGCACA 60.450 57.895 0.00 0.00 40.11 4.57
191 192 0.816825 CCGCTTCCTGCTATGCACAT 60.817 55.000 0.00 0.00 40.11 3.21
192 193 0.585357 CGCTTCCTGCTATGCACATC 59.415 55.000 0.00 0.00 40.11 3.06
193 194 1.809271 CGCTTCCTGCTATGCACATCT 60.809 52.381 0.00 0.00 40.11 2.90
194 195 2.546584 CGCTTCCTGCTATGCACATCTA 60.547 50.000 0.00 0.00 40.11 1.98
195 196 3.065655 GCTTCCTGCTATGCACATCTAG 58.934 50.000 0.00 0.00 38.95 2.43
196 197 3.661944 CTTCCTGCTATGCACATCTAGG 58.338 50.000 0.00 0.00 33.79 3.02
197 198 1.345741 TCCTGCTATGCACATCTAGGC 59.654 52.381 0.00 0.00 33.79 3.93
198 199 1.347050 CCTGCTATGCACATCTAGGCT 59.653 52.381 0.00 0.00 33.79 4.58
199 200 2.414806 CTGCTATGCACATCTAGGCTG 58.585 52.381 0.00 0.00 33.79 4.85
200 201 1.071228 TGCTATGCACATCTAGGCTGG 59.929 52.381 0.00 0.00 31.71 4.85
201 202 1.805869 CTATGCACATCTAGGCTGGC 58.194 55.000 0.00 0.00 0.00 4.85
202 203 0.397941 TATGCACATCTAGGCTGGCC 59.602 55.000 3.00 3.00 0.00 5.36
203 204 1.638679 ATGCACATCTAGGCTGGCCA 61.639 55.000 14.39 4.71 38.92 5.36
204 205 1.077501 GCACATCTAGGCTGGCCAA 60.078 57.895 7.01 0.00 38.92 4.52
205 206 0.680921 GCACATCTAGGCTGGCCAAA 60.681 55.000 7.01 0.66 38.92 3.28
206 207 1.098050 CACATCTAGGCTGGCCAAAC 58.902 55.000 7.01 1.82 38.92 2.93
207 208 0.034089 ACATCTAGGCTGGCCAAACC 60.034 55.000 15.39 15.39 38.92 3.27
209 210 0.034089 ATCTAGGCTGGCCAAACCAC 60.034 55.000 23.11 5.60 46.36 4.16
210 211 1.133809 TCTAGGCTGGCCAAACCACT 61.134 55.000 23.11 12.07 46.36 4.00
211 212 0.678048 CTAGGCTGGCCAAACCACTC 60.678 60.000 23.11 2.12 46.36 3.51
212 213 1.422977 TAGGCTGGCCAAACCACTCA 61.423 55.000 23.11 5.81 46.36 3.41
213 214 1.607467 GGCTGGCCAAACCACTCAT 60.607 57.895 17.75 0.00 46.36 2.90
214 215 1.187567 GGCTGGCCAAACCACTCATT 61.188 55.000 17.75 0.00 46.36 2.57
215 216 0.681175 GCTGGCCAAACCACTCATTT 59.319 50.000 7.01 0.00 46.36 2.32
216 217 1.070601 GCTGGCCAAACCACTCATTTT 59.929 47.619 7.01 0.00 46.36 1.82
217 218 2.867647 GCTGGCCAAACCACTCATTTTC 60.868 50.000 7.01 0.00 46.36 2.29
218 219 1.339610 TGGCCAAACCACTCATTTTCG 59.660 47.619 0.61 0.00 46.36 3.46
219 220 1.339929 GGCCAAACCACTCATTTTCGT 59.660 47.619 0.00 0.00 38.86 3.85
220 221 2.607038 GGCCAAACCACTCATTTTCGTC 60.607 50.000 0.00 0.00 38.86 4.20
221 222 2.607038 GCCAAACCACTCATTTTCGTCC 60.607 50.000 0.00 0.00 0.00 4.79
222 223 2.350388 CCAAACCACTCATTTTCGTCCG 60.350 50.000 0.00 0.00 0.00 4.79
223 224 1.519408 AACCACTCATTTTCGTCCGG 58.481 50.000 0.00 0.00 0.00 5.14
224 225 0.395312 ACCACTCATTTTCGTCCGGT 59.605 50.000 0.00 0.00 0.00 5.28
225 226 1.202722 ACCACTCATTTTCGTCCGGTT 60.203 47.619 0.00 0.00 0.00 4.44
226 227 1.877443 CCACTCATTTTCGTCCGGTTT 59.123 47.619 0.00 0.00 0.00 3.27
227 228 2.292292 CCACTCATTTTCGTCCGGTTTT 59.708 45.455 0.00 0.00 0.00 2.43
228 229 3.551551 CACTCATTTTCGTCCGGTTTTC 58.448 45.455 0.00 0.00 0.00 2.29
229 230 3.250040 CACTCATTTTCGTCCGGTTTTCT 59.750 43.478 0.00 0.00 0.00 2.52
230 231 3.881089 ACTCATTTTCGTCCGGTTTTCTT 59.119 39.130 0.00 0.00 0.00 2.52
231 232 4.337274 ACTCATTTTCGTCCGGTTTTCTTT 59.663 37.500 0.00 0.00 0.00 2.52
232 233 5.163591 ACTCATTTTCGTCCGGTTTTCTTTT 60.164 36.000 0.00 0.00 0.00 2.27
233 234 5.652518 TCATTTTCGTCCGGTTTTCTTTTT 58.347 33.333 0.00 0.00 0.00 1.94
345 346 9.717942 TCTTTGTTTTTCTTTCCAAATTCAAGA 57.282 25.926 0.00 0.00 0.00 3.02
346 347 9.977762 CTTTGTTTTTCTTTCCAAATTCAAGAG 57.022 29.630 0.00 0.00 0.00 2.85
347 348 9.717942 TTTGTTTTTCTTTCCAAATTCAAGAGA 57.282 25.926 0.00 0.00 0.00 3.10
348 349 9.717942 TTGTTTTTCTTTCCAAATTCAAGAGAA 57.282 25.926 0.00 0.00 38.31 2.87
349 350 9.889128 TGTTTTTCTTTCCAAATTCAAGAGAAT 57.111 25.926 0.00 0.00 46.20 2.40
364 365 6.985117 TCAAGAGAATTTTCTGAAATGTGGG 58.015 36.000 3.31 0.00 37.73 4.61
365 366 6.777091 TCAAGAGAATTTTCTGAAATGTGGGA 59.223 34.615 3.31 0.00 37.73 4.37
366 367 7.287466 TCAAGAGAATTTTCTGAAATGTGGGAA 59.713 33.333 3.31 0.00 37.73 3.97
367 368 6.986250 AGAGAATTTTCTGAAATGTGGGAAC 58.014 36.000 3.31 0.00 37.73 3.62
368 369 6.550854 AGAGAATTTTCTGAAATGTGGGAACA 59.449 34.615 3.31 0.00 37.73 3.18
369 370 7.234166 AGAGAATTTTCTGAAATGTGGGAACAT 59.766 33.333 3.31 0.00 39.51 2.71
370 371 7.738847 AGAATTTTCTGAAATGTGGGAACATT 58.261 30.769 3.31 0.00 37.28 2.71
372 373 8.750515 AATTTTCTGAAATGTGGGAACATTTT 57.249 26.923 15.73 3.16 46.56 1.82
373 374 8.750515 ATTTTCTGAAATGTGGGAACATTTTT 57.249 26.923 15.73 0.00 46.56 1.94
374 375 7.784633 TTTCTGAAATGTGGGAACATTTTTC 57.215 32.000 15.73 7.77 46.56 2.29
375 376 6.477053 TCTGAAATGTGGGAACATTTTTCA 57.523 33.333 15.73 11.13 46.56 2.69
376 377 6.882656 TCTGAAATGTGGGAACATTTTTCAA 58.117 32.000 15.73 4.80 46.56 2.69
377 378 7.334090 TCTGAAATGTGGGAACATTTTTCAAA 58.666 30.769 15.73 0.00 46.56 2.69
378 379 7.279758 TCTGAAATGTGGGAACATTTTTCAAAC 59.720 33.333 15.73 5.33 46.56 2.93
379 380 6.317391 TGAAATGTGGGAACATTTTTCAAACC 59.683 34.615 15.73 4.77 46.56 3.27
380 381 3.786635 TGTGGGAACATTTTTCAAACCG 58.213 40.909 0.00 0.00 46.14 4.44
381 382 3.127589 GTGGGAACATTTTTCAAACCGG 58.872 45.455 0.00 0.00 46.14 5.28
382 383 2.766828 TGGGAACATTTTTCAAACCGGT 59.233 40.909 0.00 0.00 33.40 5.28
383 384 3.127589 GGGAACATTTTTCAAACCGGTG 58.872 45.455 8.52 0.00 0.00 4.94
384 385 3.181474 GGGAACATTTTTCAAACCGGTGA 60.181 43.478 8.52 0.00 0.00 4.02
385 386 4.434520 GGAACATTTTTCAAACCGGTGAA 58.565 39.130 8.52 5.44 35.72 3.18
386 387 4.269123 GGAACATTTTTCAAACCGGTGAAC 59.731 41.667 8.52 0.00 37.24 3.18
387 388 4.457834 ACATTTTTCAAACCGGTGAACA 57.542 36.364 8.52 0.00 37.24 3.18
388 389 5.017294 ACATTTTTCAAACCGGTGAACAT 57.983 34.783 8.52 0.30 37.24 2.71
389 390 5.423886 ACATTTTTCAAACCGGTGAACATT 58.576 33.333 8.52 0.00 37.24 2.71
390 391 5.877564 ACATTTTTCAAACCGGTGAACATTT 59.122 32.000 8.52 0.00 37.24 2.32
391 392 6.372937 ACATTTTTCAAACCGGTGAACATTTT 59.627 30.769 8.52 0.00 37.24 1.82
392 393 6.803154 TTTTTCAAACCGGTGAACATTTTT 57.197 29.167 8.52 0.00 37.24 1.94
415 416 9.898152 TTTTTGAAATCTGGGAACACTTTTATT 57.102 25.926 0.00 0.00 35.60 1.40
416 417 9.541143 TTTTGAAATCTGGGAACACTTTTATTC 57.459 29.630 0.00 0.00 35.60 1.75
417 418 7.831691 TGAAATCTGGGAACACTTTTATTCA 57.168 32.000 0.00 0.00 35.60 2.57
418 419 7.885297 TGAAATCTGGGAACACTTTTATTCAG 58.115 34.615 0.00 0.00 35.60 3.02
419 420 5.904362 ATCTGGGAACACTTTTATTCAGC 57.096 39.130 0.00 0.00 35.60 4.26
420 421 3.751175 TCTGGGAACACTTTTATTCAGCG 59.249 43.478 0.00 0.00 35.60 5.18
421 422 2.817258 TGGGAACACTTTTATTCAGCGG 59.183 45.455 0.00 0.00 33.40 5.52
422 423 3.078837 GGGAACACTTTTATTCAGCGGA 58.921 45.455 0.00 0.00 0.00 5.54
423 424 3.119955 GGGAACACTTTTATTCAGCGGAC 60.120 47.826 0.00 0.00 0.00 4.79
424 425 3.500680 GGAACACTTTTATTCAGCGGACA 59.499 43.478 0.00 0.00 0.00 4.02
425 426 4.156008 GGAACACTTTTATTCAGCGGACAT 59.844 41.667 0.00 0.00 0.00 3.06
426 427 5.335661 GGAACACTTTTATTCAGCGGACATT 60.336 40.000 0.00 0.00 0.00 2.71
427 428 5.705609 ACACTTTTATTCAGCGGACATTT 57.294 34.783 0.00 0.00 0.00 2.32
428 429 6.084326 ACACTTTTATTCAGCGGACATTTT 57.916 33.333 0.00 0.00 0.00 1.82
429 430 6.149633 ACACTTTTATTCAGCGGACATTTTC 58.850 36.000 0.00 0.00 0.00 2.29
430 431 5.572896 CACTTTTATTCAGCGGACATTTTCC 59.427 40.000 0.00 0.00 41.75 3.13
431 432 5.242838 ACTTTTATTCAGCGGACATTTTCCA 59.757 36.000 0.00 0.00 46.29 3.53
432 433 5.713792 TTTATTCAGCGGACATTTTCCAA 57.286 34.783 0.00 0.00 46.29 3.53
433 434 5.713792 TTATTCAGCGGACATTTTCCAAA 57.286 34.783 0.00 0.00 46.29 3.28
434 435 4.806640 ATTCAGCGGACATTTTCCAAAT 57.193 36.364 0.00 0.00 46.29 2.32
435 436 4.599047 TTCAGCGGACATTTTCCAAATT 57.401 36.364 0.00 0.00 46.29 1.82
436 437 3.911868 TCAGCGGACATTTTCCAAATTG 58.088 40.909 0.00 0.00 46.29 2.32
437 438 2.995258 CAGCGGACATTTTCCAAATTGG 59.005 45.455 5.48 5.48 46.29 3.16
438 439 1.731709 GCGGACATTTTCCAAATTGGC 59.268 47.619 7.24 0.00 46.29 4.52
439 440 2.869636 GCGGACATTTTCCAAATTGGCA 60.870 45.455 7.24 0.00 46.29 4.92
440 441 3.397482 CGGACATTTTCCAAATTGGCAA 58.603 40.909 7.24 0.68 46.29 4.52
441 442 3.812053 CGGACATTTTCCAAATTGGCAAA 59.188 39.130 11.87 11.87 46.29 3.68
442 443 4.319405 CGGACATTTTCCAAATTGGCAAAC 60.319 41.667 11.74 0.57 46.29 2.93
443 444 4.578105 GGACATTTTCCAAATTGGCAAACA 59.422 37.500 11.74 0.00 45.10 2.83
444 445 5.241285 GGACATTTTCCAAATTGGCAAACAT 59.759 36.000 11.74 3.68 45.10 2.71
445 446 6.238981 GGACATTTTCCAAATTGGCAAACATT 60.239 34.615 11.74 0.12 45.10 2.71
446 447 7.110043 ACATTTTCCAAATTGGCAAACATTT 57.890 28.000 11.74 0.00 35.59 2.32
447 448 7.554211 ACATTTTCCAAATTGGCAAACATTTT 58.446 26.923 11.74 0.00 35.59 1.82
448 449 8.039538 ACATTTTCCAAATTGGCAAACATTTTT 58.960 25.926 11.74 0.00 35.59 1.94
480 481 8.945481 TGAAAATGTGTTCATTGAGTTCAATT 57.055 26.923 4.66 0.00 43.48 2.32
481 482 9.381033 TGAAAATGTGTTCATTGAGTTCAATTT 57.619 25.926 4.66 0.00 43.48 1.82
610 611 9.534565 TCCGTTGAATTTAAATTTTGTTCATCA 57.465 25.926 14.45 3.23 0.00 3.07
757 758 9.478768 TTTTAAACTTTTTCGAAAACCTGAACT 57.521 25.926 22.41 6.84 0.00 3.01
758 759 9.478768 TTTAAACTTTTTCGAAAACCTGAACTT 57.521 25.926 22.41 11.23 0.00 2.66
759 760 7.956420 AAACTTTTTCGAAAACCTGAACTTT 57.044 28.000 22.41 9.31 0.00 2.66
760 761 7.956420 AACTTTTTCGAAAACCTGAACTTTT 57.044 28.000 22.41 4.27 0.00 2.27
761 762 9.478768 AAACTTTTTCGAAAACCTGAACTTTTA 57.521 25.926 22.41 3.21 0.00 1.52
762 763 9.647797 AACTTTTTCGAAAACCTGAACTTTTAT 57.352 25.926 22.41 0.00 0.00 1.40
770 771 8.902735 CGAAAACCTGAACTTTTATAAAGAAGC 58.097 33.333 6.20 0.00 0.00 3.86
771 772 9.744468 GAAAACCTGAACTTTTATAAAGAAGCA 57.256 29.630 6.20 0.00 0.00 3.91
858 859 4.856801 CCAAGATCGCGGGTGGGG 62.857 72.222 6.13 0.00 0.00 4.96
859 860 3.781307 CAAGATCGCGGGTGGGGA 61.781 66.667 6.13 0.00 42.33 4.81
860 861 3.470888 AAGATCGCGGGTGGGGAG 61.471 66.667 6.13 0.00 41.34 4.30
870 871 4.394712 GTGGGGAGCGAGGGTGTG 62.395 72.222 0.00 0.00 0.00 3.82
1283 1292 3.610669 CATCCTCCGCTCCCTCCG 61.611 72.222 0.00 0.00 0.00 4.63
1581 1590 5.295292 CACCATGATCACCTCATACAAGAAC 59.705 44.000 0.00 0.00 42.91 3.01
1773 1782 4.766375 ACGTTATATTAGGCACTGCACTT 58.234 39.130 2.82 0.00 41.52 3.16
2401 2410 1.347707 TGTTAGGAGACAGGCTGTTGG 59.652 52.381 22.98 0.00 0.00 3.77
2533 2542 1.002069 TTGGAGGGTGGATTGATGCT 58.998 50.000 0.00 0.00 0.00 3.79
2873 3084 1.211949 GGCTGCAGGTTATGGTCCTTA 59.788 52.381 17.12 0.00 32.37 2.69
2876 3087 3.685550 GCTGCAGGTTATGGTCCTTACAT 60.686 47.826 17.12 0.00 32.37 2.29
2909 3120 3.554324 GCAGTACGAACTTTGAACTGTCA 59.446 43.478 0.00 0.00 39.74 3.58
2932 3143 4.771590 TCTGAATTGTGCAATGGACTTC 57.228 40.909 6.43 3.37 0.00 3.01
3003 3216 7.539034 AATATTGAGGTTTACAAGGCTGTTT 57.461 32.000 0.00 0.00 36.96 2.83
3180 5790 8.500773 TGAAAACCTGAAAAATCGTATCTACAC 58.499 33.333 0.00 0.00 0.00 2.90
3262 5872 7.339721 TGTGGAAATTAGTGGTCAAAGTTACAA 59.660 33.333 0.00 0.00 26.44 2.41
3282 5892 8.398665 GTTACAACTTGAAGACCATATGGATTC 58.601 37.037 28.77 26.50 38.94 2.52
3310 5920 7.954248 CGAAATGTCACTTATTCTGAACTGAAG 59.046 37.037 0.00 0.00 0.00 3.02
3350 5960 0.249868 TTGGTGCAGAAGGAGACACG 60.250 55.000 0.00 0.00 33.81 4.49
3383 5993 5.904362 ACTTAATTAAGGGCTTCTGCAAG 57.096 39.130 25.25 2.70 37.56 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.928448 TCACAATACTTATGCCTATTCTCTCTT 58.072 33.333 0.00 0.00 0.00 2.85
11 12 8.364142 GTCACAATACTTATGCCTATTCTCTCT 58.636 37.037 0.00 0.00 0.00 3.10
12 13 8.144478 TGTCACAATACTTATGCCTATTCTCTC 58.856 37.037 0.00 0.00 0.00 3.20
13 14 8.023021 TGTCACAATACTTATGCCTATTCTCT 57.977 34.615 0.00 0.00 0.00 3.10
14 15 8.839310 ATGTCACAATACTTATGCCTATTCTC 57.161 34.615 0.00 0.00 0.00 2.87
19 20 9.271828 CACATTATGTCACAATACTTATGCCTA 57.728 33.333 0.00 0.00 0.00 3.93
20 21 7.775093 ACACATTATGTCACAATACTTATGCCT 59.225 33.333 0.00 0.00 36.54 4.75
21 22 7.930217 ACACATTATGTCACAATACTTATGCC 58.070 34.615 0.00 0.00 36.54 4.40
30 31 8.405531 GGCTGTTATTACACATTATGTCACAAT 58.594 33.333 0.00 0.00 42.09 2.71
31 32 7.148154 GGGCTGTTATTACACATTATGTCACAA 60.148 37.037 0.00 0.00 42.09 3.33
32 33 6.317642 GGGCTGTTATTACACATTATGTCACA 59.682 38.462 0.00 0.00 42.09 3.58
33 34 6.317642 TGGGCTGTTATTACACATTATGTCAC 59.682 38.462 0.00 0.00 42.09 3.67
34 35 6.418946 TGGGCTGTTATTACACATTATGTCA 58.581 36.000 0.00 0.00 42.09 3.58
35 36 6.935741 TGGGCTGTTATTACACATTATGTC 57.064 37.500 0.00 0.00 42.09 3.06
36 37 8.988546 TTATGGGCTGTTATTACACATTATGT 57.011 30.769 0.00 0.00 46.06 2.29
37 38 9.844790 CATTATGGGCTGTTATTACACATTATG 57.155 33.333 0.00 0.00 28.27 1.90
38 39 8.522830 GCATTATGGGCTGTTATTACACATTAT 58.477 33.333 0.00 0.00 0.00 1.28
39 40 7.503902 TGCATTATGGGCTGTTATTACACATTA 59.496 33.333 0.00 0.00 0.00 1.90
40 41 6.323482 TGCATTATGGGCTGTTATTACACATT 59.677 34.615 0.00 0.00 0.00 2.71
41 42 5.832595 TGCATTATGGGCTGTTATTACACAT 59.167 36.000 0.00 0.00 0.00 3.21
42 43 5.196695 TGCATTATGGGCTGTTATTACACA 58.803 37.500 0.00 0.00 0.00 3.72
43 44 5.766150 TGCATTATGGGCTGTTATTACAC 57.234 39.130 0.00 0.00 0.00 2.90
44 45 6.975196 ATTGCATTATGGGCTGTTATTACA 57.025 33.333 0.00 0.00 0.00 2.41
45 46 9.927668 ATTTATTGCATTATGGGCTGTTATTAC 57.072 29.630 0.00 0.00 0.00 1.89
49 50 8.458052 CGATATTTATTGCATTATGGGCTGTTA 58.542 33.333 0.00 0.00 0.00 2.41
50 51 7.176515 TCGATATTTATTGCATTATGGGCTGTT 59.823 33.333 0.00 0.00 0.00 3.16
51 52 6.658816 TCGATATTTATTGCATTATGGGCTGT 59.341 34.615 0.00 0.00 0.00 4.40
52 53 7.087409 TCGATATTTATTGCATTATGGGCTG 57.913 36.000 0.00 0.00 0.00 4.85
53 54 7.886629 ATCGATATTTATTGCATTATGGGCT 57.113 32.000 0.00 0.00 0.00 5.19
71 72 9.611284 GTTTTGCATCATGCTTTTATATCGATA 57.389 29.630 11.84 7.75 45.31 2.92
72 73 7.324375 CGTTTTGCATCATGCTTTTATATCGAT 59.676 33.333 11.84 2.16 45.31 3.59
73 74 6.632434 CGTTTTGCATCATGCTTTTATATCGA 59.368 34.615 11.84 0.00 45.31 3.59
74 75 6.129378 CCGTTTTGCATCATGCTTTTATATCG 60.129 38.462 11.84 5.17 45.31 2.92
75 76 6.917477 TCCGTTTTGCATCATGCTTTTATATC 59.083 34.615 11.84 0.00 45.31 1.63
76 77 6.697019 GTCCGTTTTGCATCATGCTTTTATAT 59.303 34.615 11.84 0.00 45.31 0.86
77 78 6.033341 GTCCGTTTTGCATCATGCTTTTATA 58.967 36.000 11.84 0.00 45.31 0.98
78 79 4.864247 GTCCGTTTTGCATCATGCTTTTAT 59.136 37.500 11.84 0.00 45.31 1.40
79 80 4.233789 GTCCGTTTTGCATCATGCTTTTA 58.766 39.130 11.84 0.00 45.31 1.52
80 81 3.059166 GTCCGTTTTGCATCATGCTTTT 58.941 40.909 11.84 0.00 45.31 2.27
81 82 2.676076 GTCCGTTTTGCATCATGCTTT 58.324 42.857 11.84 0.00 45.31 3.51
82 83 1.401409 CGTCCGTTTTGCATCATGCTT 60.401 47.619 11.84 0.00 45.31 3.91
83 84 0.168788 CGTCCGTTTTGCATCATGCT 59.831 50.000 11.84 0.00 45.31 3.79
84 85 0.109781 ACGTCCGTTTTGCATCATGC 60.110 50.000 1.35 1.35 45.29 4.06
85 86 3.063316 TGATACGTCCGTTTTGCATCATG 59.937 43.478 0.00 0.00 0.00 3.07
86 87 3.063452 GTGATACGTCCGTTTTGCATCAT 59.937 43.478 0.00 0.00 0.00 2.45
87 88 2.413796 GTGATACGTCCGTTTTGCATCA 59.586 45.455 0.00 0.00 0.00 3.07
88 89 2.222953 GGTGATACGTCCGTTTTGCATC 60.223 50.000 0.00 0.00 0.00 3.91
89 90 1.735571 GGTGATACGTCCGTTTTGCAT 59.264 47.619 0.00 0.00 0.00 3.96
90 91 1.149987 GGTGATACGTCCGTTTTGCA 58.850 50.000 0.00 0.00 0.00 4.08
91 92 0.094046 CGGTGATACGTCCGTTTTGC 59.906 55.000 5.31 0.00 41.58 3.68
92 93 0.717224 CCGGTGATACGTCCGTTTTG 59.283 55.000 11.86 0.00 44.51 2.44
93 94 0.390209 CCCGGTGATACGTCCGTTTT 60.390 55.000 11.86 0.00 44.51 2.43
94 95 1.216178 CCCGGTGATACGTCCGTTT 59.784 57.895 11.86 0.00 44.51 3.60
95 96 2.887360 CCCGGTGATACGTCCGTT 59.113 61.111 11.86 0.00 44.51 4.44
96 97 3.830192 GCCCGGTGATACGTCCGT 61.830 66.667 11.86 0.00 44.51 4.69
97 98 3.768185 CTGCCCGGTGATACGTCCG 62.768 68.421 6.44 6.44 45.42 4.79
98 99 2.106332 CTGCCCGGTGATACGTCC 59.894 66.667 0.00 0.00 0.00 4.79
99 100 2.585247 GCTGCCCGGTGATACGTC 60.585 66.667 0.00 0.00 0.00 4.34
100 101 4.508128 CGCTGCCCGGTGATACGT 62.508 66.667 0.00 0.00 0.00 3.57
101 102 2.616786 TAACGCTGCCCGGTGATACG 62.617 60.000 0.00 0.00 42.52 3.06
102 103 0.249741 ATAACGCTGCCCGGTGATAC 60.250 55.000 0.00 0.00 42.52 2.24
103 104 0.249699 CATAACGCTGCCCGGTGATA 60.250 55.000 0.00 0.00 42.52 2.15
104 105 1.523711 CATAACGCTGCCCGGTGAT 60.524 57.895 0.00 0.00 42.52 3.06
105 106 2.125310 CATAACGCTGCCCGGTGA 60.125 61.111 0.00 0.00 42.52 4.02
106 107 2.435938 ACATAACGCTGCCCGGTG 60.436 61.111 0.00 0.00 42.52 4.94
107 108 2.435938 CACATAACGCTGCCCGGT 60.436 61.111 0.00 0.00 42.52 5.28
108 109 3.202001 CCACATAACGCTGCCCGG 61.202 66.667 0.00 0.00 42.52 5.73
109 110 2.940890 ATCCCACATAACGCTGCCCG 62.941 60.000 0.00 0.00 44.21 6.13
110 111 1.152963 ATCCCACATAACGCTGCCC 60.153 57.895 0.00 0.00 0.00 5.36
111 112 1.166531 GGATCCCACATAACGCTGCC 61.167 60.000 0.00 0.00 0.00 4.85
112 113 0.179045 AGGATCCCACATAACGCTGC 60.179 55.000 8.55 0.00 0.00 5.25
113 114 3.685139 ATAGGATCCCACATAACGCTG 57.315 47.619 8.55 0.00 0.00 5.18
114 115 4.389374 CAAATAGGATCCCACATAACGCT 58.611 43.478 8.55 0.00 0.00 5.07
115 116 3.502211 CCAAATAGGATCCCACATAACGC 59.498 47.826 8.55 0.00 41.22 4.84
116 117 3.502211 GCCAAATAGGATCCCACATAACG 59.498 47.826 8.55 0.00 41.22 3.18
117 118 3.502211 CGCCAAATAGGATCCCACATAAC 59.498 47.826 8.55 0.00 41.22 1.89
118 119 3.750371 CGCCAAATAGGATCCCACATAA 58.250 45.455 8.55 0.00 41.22 1.90
119 120 2.552155 GCGCCAAATAGGATCCCACATA 60.552 50.000 8.55 0.00 41.22 2.29
120 121 1.819305 GCGCCAAATAGGATCCCACAT 60.819 52.381 8.55 0.00 41.22 3.21
121 122 0.465460 GCGCCAAATAGGATCCCACA 60.465 55.000 8.55 0.00 41.22 4.17
122 123 1.507141 CGCGCCAAATAGGATCCCAC 61.507 60.000 8.55 0.00 41.22 4.61
123 124 1.227823 CGCGCCAAATAGGATCCCA 60.228 57.895 8.55 0.00 41.22 4.37
124 125 0.034337 TACGCGCCAAATAGGATCCC 59.966 55.000 8.55 0.00 41.22 3.85
125 126 1.429463 CTACGCGCCAAATAGGATCC 58.571 55.000 5.73 2.48 41.22 3.36
126 127 1.270147 ACCTACGCGCCAAATAGGATC 60.270 52.381 22.35 0.00 41.22 3.36
127 128 0.756903 ACCTACGCGCCAAATAGGAT 59.243 50.000 22.35 7.57 41.22 3.24
128 129 0.103572 GACCTACGCGCCAAATAGGA 59.896 55.000 22.35 0.00 41.22 2.94
129 130 1.213094 CGACCTACGCGCCAAATAGG 61.213 60.000 15.90 15.90 41.21 2.57
130 131 2.213483 CGACCTACGCGCCAAATAG 58.787 57.895 5.73 0.00 34.51 1.73
131 132 4.405762 CGACCTACGCGCCAAATA 57.594 55.556 5.73 0.00 34.51 1.40
174 175 1.964552 AGATGTGCATAGCAGGAAGC 58.035 50.000 0.43 0.00 40.08 3.86
175 176 3.661944 CCTAGATGTGCATAGCAGGAAG 58.338 50.000 10.25 0.00 40.08 3.46
176 177 2.224378 GCCTAGATGTGCATAGCAGGAA 60.224 50.000 16.99 0.00 40.08 3.36
177 178 1.345741 GCCTAGATGTGCATAGCAGGA 59.654 52.381 16.99 0.00 40.08 3.86
178 179 1.347050 AGCCTAGATGTGCATAGCAGG 59.653 52.381 0.43 7.10 40.08 4.85
179 180 2.414806 CAGCCTAGATGTGCATAGCAG 58.585 52.381 0.43 0.00 40.08 4.24
180 181 1.071228 CCAGCCTAGATGTGCATAGCA 59.929 52.381 0.43 0.00 35.60 3.49
181 182 1.805869 CCAGCCTAGATGTGCATAGC 58.194 55.000 0.00 0.00 0.00 2.97
182 183 1.610102 GGCCAGCCTAGATGTGCATAG 60.610 57.143 0.00 0.00 0.00 2.23
183 184 0.397941 GGCCAGCCTAGATGTGCATA 59.602 55.000 0.00 0.00 0.00 3.14
184 185 1.150081 GGCCAGCCTAGATGTGCAT 59.850 57.895 0.00 0.00 0.00 3.96
185 186 1.851065 TTGGCCAGCCTAGATGTGCA 61.851 55.000 5.11 0.00 36.94 4.57
186 187 0.680921 TTTGGCCAGCCTAGATGTGC 60.681 55.000 5.11 0.00 36.94 4.57
187 188 1.098050 GTTTGGCCAGCCTAGATGTG 58.902 55.000 5.11 0.00 36.94 3.21
188 189 0.034089 GGTTTGGCCAGCCTAGATGT 60.034 55.000 18.09 0.00 37.17 3.06
189 190 0.034186 TGGTTTGGCCAGCCTAGATG 60.034 55.000 23.48 0.00 43.61 2.90
190 191 2.397815 TGGTTTGGCCAGCCTAGAT 58.602 52.632 23.48 0.00 43.61 1.98
191 192 3.914645 TGGTTTGGCCAGCCTAGA 58.085 55.556 23.48 6.45 43.61 2.43
198 199 1.339610 CGAAAATGAGTGGTTTGGCCA 59.660 47.619 0.00 0.00 46.95 5.36
199 200 1.339929 ACGAAAATGAGTGGTTTGGCC 59.660 47.619 0.00 0.00 37.90 5.36
200 201 2.607038 GGACGAAAATGAGTGGTTTGGC 60.607 50.000 0.00 0.00 0.00 4.52
201 202 2.350388 CGGACGAAAATGAGTGGTTTGG 60.350 50.000 0.00 0.00 0.00 3.28
202 203 2.350388 CCGGACGAAAATGAGTGGTTTG 60.350 50.000 0.00 0.00 0.00 2.93
203 204 1.877443 CCGGACGAAAATGAGTGGTTT 59.123 47.619 0.00 0.00 0.00 3.27
204 205 1.202722 ACCGGACGAAAATGAGTGGTT 60.203 47.619 9.46 0.00 0.00 3.67
205 206 0.395312 ACCGGACGAAAATGAGTGGT 59.605 50.000 9.46 0.00 0.00 4.16
206 207 1.519408 AACCGGACGAAAATGAGTGG 58.481 50.000 9.46 0.00 0.00 4.00
207 208 3.250040 AGAAAACCGGACGAAAATGAGTG 59.750 43.478 9.46 0.00 0.00 3.51
208 209 3.473625 AGAAAACCGGACGAAAATGAGT 58.526 40.909 9.46 0.00 0.00 3.41
209 210 4.483476 AAGAAAACCGGACGAAAATGAG 57.517 40.909 9.46 0.00 0.00 2.90
210 211 4.904253 AAAGAAAACCGGACGAAAATGA 57.096 36.364 9.46 0.00 0.00 2.57
211 212 5.959652 AAAAAGAAAACCGGACGAAAATG 57.040 34.783 9.46 0.00 0.00 2.32
319 320 9.717942 TCTTGAATTTGGAAAGAAAAACAAAGA 57.282 25.926 0.00 0.00 36.41 2.52
320 321 9.977762 CTCTTGAATTTGGAAAGAAAAACAAAG 57.022 29.630 0.00 0.00 36.41 2.77
321 322 9.717942 TCTCTTGAATTTGGAAAGAAAAACAAA 57.282 25.926 0.00 0.00 37.25 2.83
322 323 9.717942 TTCTCTTGAATTTGGAAAGAAAAACAA 57.282 25.926 0.00 0.00 29.93 2.83
323 324 9.889128 ATTCTCTTGAATTTGGAAAGAAAAACA 57.111 25.926 0.00 0.00 39.68 2.83
338 339 8.092687 CCCACATTTCAGAAAATTCTCTTGAAT 58.907 33.333 0.00 0.00 44.08 2.57
339 340 7.287466 TCCCACATTTCAGAAAATTCTCTTGAA 59.713 33.333 0.00 0.00 34.74 2.69
340 341 6.777091 TCCCACATTTCAGAAAATTCTCTTGA 59.223 34.615 0.00 0.00 34.74 3.02
341 342 6.985117 TCCCACATTTCAGAAAATTCTCTTG 58.015 36.000 0.00 0.00 34.74 3.02
342 343 7.069826 TGTTCCCACATTTCAGAAAATTCTCTT 59.930 33.333 0.00 0.00 34.74 2.85
343 344 6.550854 TGTTCCCACATTTCAGAAAATTCTCT 59.449 34.615 0.00 0.00 34.74 3.10
344 345 6.748132 TGTTCCCACATTTCAGAAAATTCTC 58.252 36.000 0.00 0.00 34.74 2.87
345 346 6.729690 TGTTCCCACATTTCAGAAAATTCT 57.270 33.333 0.00 0.00 38.25 2.40
358 359 4.376146 CGGTTTGAAAAATGTTCCCACAT 58.624 39.130 0.00 0.00 46.34 3.21
359 360 3.430929 CCGGTTTGAAAAATGTTCCCACA 60.431 43.478 0.00 0.00 37.31 4.17
360 361 3.127589 CCGGTTTGAAAAATGTTCCCAC 58.872 45.455 0.00 0.00 0.00 4.61
361 362 2.766828 ACCGGTTTGAAAAATGTTCCCA 59.233 40.909 0.00 0.00 0.00 4.37
362 363 3.127589 CACCGGTTTGAAAAATGTTCCC 58.872 45.455 2.97 0.00 0.00 3.97
363 364 4.048241 TCACCGGTTTGAAAAATGTTCC 57.952 40.909 2.97 0.00 0.00 3.62
364 365 4.865365 TGTTCACCGGTTTGAAAAATGTTC 59.135 37.500 2.97 0.00 37.24 3.18
365 366 4.822026 TGTTCACCGGTTTGAAAAATGTT 58.178 34.783 2.97 0.00 37.24 2.71
366 367 4.457834 TGTTCACCGGTTTGAAAAATGT 57.542 36.364 2.97 0.00 37.24 2.71
367 368 5.982465 AATGTTCACCGGTTTGAAAAATG 57.018 34.783 2.97 0.00 37.24 2.32
368 369 6.993786 AAAATGTTCACCGGTTTGAAAAAT 57.006 29.167 2.97 1.41 37.24 1.82
369 370 6.803154 AAAAATGTTCACCGGTTTGAAAAA 57.197 29.167 2.97 0.00 37.24 1.94
389 390 9.898152 AATAAAAGTGTTCCCAGATTTCAAAAA 57.102 25.926 0.00 0.00 0.00 1.94
390 391 9.541143 GAATAAAAGTGTTCCCAGATTTCAAAA 57.459 29.630 0.00 0.00 0.00 2.44
391 392 8.700051 TGAATAAAAGTGTTCCCAGATTTCAAA 58.300 29.630 0.00 0.00 0.00 2.69
392 393 8.243961 TGAATAAAAGTGTTCCCAGATTTCAA 57.756 30.769 0.00 0.00 0.00 2.69
393 394 7.523709 GCTGAATAAAAGTGTTCCCAGATTTCA 60.524 37.037 0.00 0.00 0.00 2.69
394 395 6.808704 GCTGAATAAAAGTGTTCCCAGATTTC 59.191 38.462 0.00 0.00 0.00 2.17
395 396 6.570378 CGCTGAATAAAAGTGTTCCCAGATTT 60.570 38.462 0.00 0.00 0.00 2.17
396 397 5.106157 CGCTGAATAAAAGTGTTCCCAGATT 60.106 40.000 0.00 0.00 0.00 2.40
397 398 4.396166 CGCTGAATAAAAGTGTTCCCAGAT 59.604 41.667 0.00 0.00 0.00 2.90
398 399 3.751175 CGCTGAATAAAAGTGTTCCCAGA 59.249 43.478 0.00 0.00 0.00 3.86
399 400 3.119849 CCGCTGAATAAAAGTGTTCCCAG 60.120 47.826 0.00 0.00 0.00 4.45
400 401 2.817258 CCGCTGAATAAAAGTGTTCCCA 59.183 45.455 0.00 0.00 0.00 4.37
401 402 3.078837 TCCGCTGAATAAAAGTGTTCCC 58.921 45.455 0.00 0.00 0.00 3.97
402 403 3.500680 TGTCCGCTGAATAAAAGTGTTCC 59.499 43.478 0.00 0.00 0.00 3.62
403 404 4.742438 TGTCCGCTGAATAAAAGTGTTC 57.258 40.909 0.00 0.00 0.00 3.18
404 405 5.705609 AATGTCCGCTGAATAAAAGTGTT 57.294 34.783 0.00 0.00 0.00 3.32
405 406 5.705609 AAATGTCCGCTGAATAAAAGTGT 57.294 34.783 0.00 0.00 0.00 3.55
406 407 5.572896 GGAAAATGTCCGCTGAATAAAAGTG 59.427 40.000 0.00 0.00 36.40 3.16
407 408 5.709966 GGAAAATGTCCGCTGAATAAAAGT 58.290 37.500 0.00 0.00 36.40 2.66
418 419 7.754834 GTTTGCCAATTTGGAAAATGTCCGC 62.755 44.000 21.85 6.94 46.20 5.54
419 420 4.319405 GTTTGCCAATTTGGAAAATGTCCG 60.319 41.667 21.85 0.00 46.20 4.79
420 421 4.578105 TGTTTGCCAATTTGGAAAATGTCC 59.422 37.500 21.85 11.33 46.20 4.02
421 422 5.747951 TGTTTGCCAATTTGGAAAATGTC 57.252 34.783 21.85 11.63 46.20 3.06
422 423 6.712179 AATGTTTGCCAATTTGGAAAATGT 57.288 29.167 21.85 12.35 46.20 2.71
423 424 8.421673 AAAAATGTTTGCCAATTTGGAAAATG 57.578 26.923 21.85 0.00 46.20 2.32
454 455 9.550406 AATTGAACTCAATGAACACATTTTCAT 57.450 25.926 5.72 0.00 46.18 2.57
455 456 8.945481 AATTGAACTCAATGAACACATTTTCA 57.055 26.923 5.72 0.00 45.06 2.69
584 585 9.534565 TGATGAACAAAATTTAAATTCAACGGA 57.465 25.926 13.68 0.00 33.29 4.69
731 732 9.478768 AGTTCAGGTTTTCGAAAAAGTTTAAAA 57.521 25.926 24.04 10.02 0.00 1.52
732 733 9.478768 AAGTTCAGGTTTTCGAAAAAGTTTAAA 57.521 25.926 24.04 11.40 0.00 1.52
733 734 9.478768 AAAGTTCAGGTTTTCGAAAAAGTTTAA 57.521 25.926 24.04 12.33 0.00 1.52
734 735 9.478768 AAAAGTTCAGGTTTTCGAAAAAGTTTA 57.521 25.926 24.04 8.16 0.00 2.01
735 736 7.956420 AAAGTTCAGGTTTTCGAAAAAGTTT 57.044 28.000 24.04 18.53 0.00 2.66
736 737 7.956420 AAAAGTTCAGGTTTTCGAAAAAGTT 57.044 28.000 24.04 14.19 0.00 2.66
744 745 8.902735 GCTTCTTTATAAAAGTTCAGGTTTTCG 58.097 33.333 0.00 0.00 0.00 3.46
745 746 9.744468 TGCTTCTTTATAAAAGTTCAGGTTTTC 57.256 29.630 0.00 0.00 0.00 2.29
807 808 2.600470 GCGGGGCTCCCTGTTTTT 60.600 61.111 14.86 0.00 42.67 1.94
808 809 4.678743 GGCGGGGCTCCCTGTTTT 62.679 66.667 14.86 0.00 42.67 2.43
841 842 4.856801 CCCCACCCGCGATCTTGG 62.857 72.222 8.23 8.03 0.00 3.61
842 843 3.740128 CTCCCCACCCGCGATCTTG 62.740 68.421 8.23 0.00 0.00 3.02
843 844 3.470888 CTCCCCACCCGCGATCTT 61.471 66.667 8.23 0.00 0.00 2.40
853 854 4.394712 CACACCCTCGCTCCCCAC 62.395 72.222 0.00 0.00 0.00 4.61
872 873 4.722700 TGGGAAAGAGGGCAGCGC 62.723 66.667 0.00 0.00 0.00 5.92
873 874 2.437359 CTGGGAAAGAGGGCAGCG 60.437 66.667 0.00 0.00 0.00 5.18
874 875 2.753446 GCTGGGAAAGAGGGCAGC 60.753 66.667 0.00 0.00 0.00 5.25
875 876 2.437359 CGCTGGGAAAGAGGGCAG 60.437 66.667 0.00 0.00 0.00 4.85
876 877 4.722700 GCGCTGGGAAAGAGGGCA 62.723 66.667 0.00 0.00 45.99 5.36
880 881 3.494336 CTGCGCGCTGGGAAAGAG 61.494 66.667 33.29 14.75 0.00 2.85
951 952 1.337817 CTCGCACGTCCGAACTGAAG 61.338 60.000 1.99 0.00 36.72 3.02
1071 1080 2.317609 GCAGGTGTTGATCGCGTGT 61.318 57.895 5.77 0.00 42.24 4.49
1739 1748 4.706842 AATATAACGTCCAGCTCCCATT 57.293 40.909 0.00 0.00 0.00 3.16
1773 1782 5.190726 TCCACACTTCCCATACATATCAACA 59.809 40.000 0.00 0.00 0.00 3.33
2401 2410 2.334946 TGCTGCCAGATTTCGGTGC 61.335 57.895 0.00 0.00 0.00 5.01
2428 2437 3.268023 AGATCCTTGGATCGGAAACAC 57.732 47.619 20.14 0.00 36.73 3.32
2533 2542 6.246420 GCAAGTTCTTGCTTCTCTAAATGA 57.754 37.500 24.49 0.00 44.15 2.57
2775 2807 6.790319 AGTTAAAGGCTTATCTTCTTTCCCA 58.210 36.000 0.00 0.00 33.44 4.37
2813 2845 4.691216 CCGAGAAAACTCAGAACTAAAGGG 59.309 45.833 0.00 0.00 0.00 3.95
2891 3102 6.277605 TCAGATTGACAGTTCAAAGTTCGTA 58.722 36.000 0.00 0.00 45.01 3.43
2909 3120 5.479375 AGAAGTCCATTGCACAATTCAGATT 59.521 36.000 0.00 0.00 0.00 2.40
2932 3143 9.029243 TGTATTGTTTTTACAAATGAGCAACAG 57.971 29.630 0.00 0.00 32.94 3.16
3003 3216 6.882610 ATGCTCATTTTTGTTAGAGTGACA 57.117 33.333 0.00 0.00 0.00 3.58
3153 5763 9.058174 TGTAGATACGATTTTTCAGGTTTTCAA 57.942 29.630 0.00 0.00 0.00 2.69
3262 5872 4.444876 CGGGAATCCATATGGTCTTCAAGT 60.445 45.833 26.63 9.44 36.34 3.16
3275 5885 3.652057 AGTGACATTTCGGGAATCCAT 57.348 42.857 0.09 0.00 0.00 3.41
3282 5892 5.643777 AGTTCAGAATAAGTGACATTTCGGG 59.356 40.000 0.00 0.00 0.00 5.14
3310 5920 8.196103 CACCAAATCTAGTTTACTAGTACTCCC 58.804 40.741 14.73 0.00 44.74 4.30
3363 5973 5.538433 ACAACTTGCAGAAGCCCTTAATTAA 59.462 36.000 0.00 0.00 41.13 1.40
3383 5993 2.076100 TCAAGATGCATCCGTCACAAC 58.924 47.619 23.06 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.