Multiple sequence alignment - TraesCS1B01G168200

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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 TraesCS1B01G168200 chr1B 100.000 3558 0 0 940 4497 297723972 297727529 0.000000e+00 6571.0
1 TraesCS1B01G168200 chr1B 100.000 679 0 0 1 679 297723033 297723711 0.000000e+00 1254.0
2 TraesCS1B01G168200 chr1D 95.597 3611 89 16 940 4490 203745654 203749254 0.000000e+00 5723.0
3 TraesCS1B01G168200 chr1D 81.752 274 20 6 407 679 203745344 203745588 7.630000e-48 202.0
4 TraesCS1B01G168200 chr1A 93.543 3345 123 42 940 4195 258738346 258741686 0.000000e+00 4894.0
5 TraesCS1B01G168200 chr1A 82.843 204 16 13 4299 4487 258741941 258742140 1.000000e-36 165.0
6 TraesCS1B01G168200 chr1A 81.675 191 9 12 512 679 258738117 258738304 7.850000e-28 135.0
7 TraesCS1B01G168200 chr5D 90.411 73 4 3 4193 4263 298964162 298964091 4.790000e-15 93.5
8 TraesCS1B01G168200 chr6D 86.905 84 7 4 4191 4270 294774922 294774839 1.720000e-14 91.6
9 TraesCS1B01G168200 chr6B 88.158 76 5 4 4193 4265 502301274 502301348 2.230000e-13 87.9
10 TraesCS1B01G168200 chr5A 88.158 76 5 4 4193 4265 706502473 706502399 2.230000e-13 87.9
11 TraesCS1B01G168200 chr2B 88.889 72 6 1 4192 4263 766079403 766079472 2.230000e-13 87.9
12 TraesCS1B01G168200 chr2A 89.041 73 4 2 4191 4263 73540726 73540658 2.230000e-13 87.9
13 TraesCS1B01G168200 chr7A 88.000 75 5 4 4193 4264 716394702 716394629 8.020000e-13 86.1
14 TraesCS1B01G168200 chr2D 88.732 71 7 1 4191 4261 487492531 487492462 8.020000e-13 86.1


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 TraesCS1B01G168200 chr1B 297723033 297727529 4496 False 3912.500000 6571 100.000000 1 4497 2 chr1B.!!$F1 4496
1 TraesCS1B01G168200 chr1D 203745344 203749254 3910 False 2962.500000 5723 88.674500 407 4490 2 chr1D.!!$F1 4083
2 TraesCS1B01G168200 chr1A 258738117 258742140 4023 False 1731.333333 4894 86.020333 512 4487 3 chr1A.!!$F1 3975

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
558 562 0.106015 ACAAGAACAGCCAAAGCCCT 60.106 50.000 0.0 0.0 41.25 5.19 F
978 1005 1.007849 GCGAGAGAATCCGAGGAGC 60.008 63.158 0.0 0.0 33.66 4.70 F
2524 2583 1.406205 GGTTGCTCAGTAGAAGAGGCC 60.406 57.143 0.0 0.0 33.72 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2108 2167 0.552848 CCCCAGTGCCATAACCAGAT 59.447 55.0 0.0 0.0 0.00 2.90 R
2611 2670 0.916086 TAACCGGCAGAATGGATGGT 59.084 50.0 0.0 0.0 35.86 3.55 R
4187 4320 0.614134 GGGACGGAGGGAGTAGTGTT 60.614 60.0 0.0 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
37 38 9.393512 TCTTTAAGTACTAGAGATTCTTAGCGT 57.606 33.333 0.00 0.00 0.00 5.07
38 39 9.654417 CTTTAAGTACTAGAGATTCTTAGCGTC 57.346 37.037 0.00 0.00 0.00 5.19
39 40 6.622833 AAGTACTAGAGATTCTTAGCGTCC 57.377 41.667 0.00 0.00 0.00 4.79
40 41 5.932455 AGTACTAGAGATTCTTAGCGTCCT 58.068 41.667 0.00 0.00 0.00 3.85
41 42 5.993441 AGTACTAGAGATTCTTAGCGTCCTC 59.007 44.000 0.00 0.00 0.00 3.71
42 43 5.043737 ACTAGAGATTCTTAGCGTCCTCT 57.956 43.478 0.00 0.00 35.46 3.69
43 44 5.442391 ACTAGAGATTCTTAGCGTCCTCTT 58.558 41.667 0.00 0.00 33.58 2.85
44 45 6.593807 ACTAGAGATTCTTAGCGTCCTCTTA 58.406 40.000 0.00 0.00 33.58 2.10
45 46 7.055378 ACTAGAGATTCTTAGCGTCCTCTTAA 58.945 38.462 0.00 0.00 33.58 1.85
46 47 6.969993 AGAGATTCTTAGCGTCCTCTTAAT 57.030 37.500 0.00 0.00 0.00 1.40
47 48 6.744112 AGAGATTCTTAGCGTCCTCTTAATG 58.256 40.000 0.00 0.00 0.00 1.90
48 49 6.547880 AGAGATTCTTAGCGTCCTCTTAATGA 59.452 38.462 0.00 0.00 0.00 2.57
49 50 7.068839 AGAGATTCTTAGCGTCCTCTTAATGAA 59.931 37.037 0.00 0.00 0.00 2.57
50 51 7.206687 AGATTCTTAGCGTCCTCTTAATGAAG 58.793 38.462 0.00 0.00 0.00 3.02
51 52 5.263968 TCTTAGCGTCCTCTTAATGAAGG 57.736 43.478 0.00 0.00 33.09 3.46
52 53 2.317530 AGCGTCCTCTTAATGAAGGC 57.682 50.000 0.00 0.00 33.09 4.35
53 54 1.555075 AGCGTCCTCTTAATGAAGGCA 59.445 47.619 0.00 0.00 33.09 4.75
54 55 2.171448 AGCGTCCTCTTAATGAAGGCAT 59.829 45.455 0.00 0.00 35.92 4.40
55 56 2.945668 GCGTCCTCTTAATGAAGGCATT 59.054 45.455 0.00 0.00 46.11 3.56
56 57 3.378427 GCGTCCTCTTAATGAAGGCATTT 59.622 43.478 0.00 0.00 41.87 2.32
57 58 4.142381 GCGTCCTCTTAATGAAGGCATTTT 60.142 41.667 0.00 0.00 41.87 1.82
58 59 5.622233 GCGTCCTCTTAATGAAGGCATTTTT 60.622 40.000 0.00 0.00 41.87 1.94
81 82 6.998968 TTTACGGGTTACAGTTCAAAAAGA 57.001 33.333 0.00 0.00 0.00 2.52
82 83 6.998968 TTACGGGTTACAGTTCAAAAAGAA 57.001 33.333 0.00 0.00 0.00 2.52
83 84 5.900865 ACGGGTTACAGTTCAAAAAGAAA 57.099 34.783 0.00 0.00 38.13 2.52
84 85 5.643664 ACGGGTTACAGTTCAAAAAGAAAC 58.356 37.500 0.00 0.00 38.13 2.78
85 86 5.183522 ACGGGTTACAGTTCAAAAAGAAACA 59.816 36.000 0.00 0.00 38.13 2.83
86 87 5.513849 CGGGTTACAGTTCAAAAAGAAACAC 59.486 40.000 0.00 0.00 38.13 3.32
87 88 6.624204 CGGGTTACAGTTCAAAAAGAAACACT 60.624 38.462 0.00 0.00 38.13 3.55
88 89 7.414319 CGGGTTACAGTTCAAAAAGAAACACTA 60.414 37.037 0.00 0.00 38.13 2.74
89 90 8.410912 GGGTTACAGTTCAAAAAGAAACACTAT 58.589 33.333 0.00 0.00 38.13 2.12
90 91 9.447040 GGTTACAGTTCAAAAAGAAACACTATC 57.553 33.333 0.00 0.00 38.13 2.08
95 96 9.334693 CAGTTCAAAAAGAAACACTATCTATGC 57.665 33.333 0.00 0.00 38.13 3.14
96 97 9.066892 AGTTCAAAAAGAAACACTATCTATGCA 57.933 29.630 0.00 0.00 38.13 3.96
97 98 9.846248 GTTCAAAAAGAAACACTATCTATGCAT 57.154 29.630 3.79 3.79 38.13 3.96
99 100 8.677300 TCAAAAAGAAACACTATCTATGCATCC 58.323 33.333 0.19 0.00 0.00 3.51
100 101 8.461222 CAAAAAGAAACACTATCTATGCATCCA 58.539 33.333 0.19 0.00 0.00 3.41
101 102 8.757982 AAAAGAAACACTATCTATGCATCCAT 57.242 30.769 0.19 0.00 35.44 3.41
102 103 7.741027 AAGAAACACTATCTATGCATCCATG 57.259 36.000 0.19 0.00 32.85 3.66
103 104 6.835174 AGAAACACTATCTATGCATCCATGT 58.165 36.000 0.19 0.00 32.85 3.21
104 105 7.285566 AGAAACACTATCTATGCATCCATGTT 58.714 34.615 0.19 4.26 32.85 2.71
105 106 7.776969 AGAAACACTATCTATGCATCCATGTTT 59.223 33.333 0.19 12.45 32.85 2.83
106 107 7.886629 AACACTATCTATGCATCCATGTTTT 57.113 32.000 0.19 0.00 32.85 2.43
107 108 7.886629 ACACTATCTATGCATCCATGTTTTT 57.113 32.000 0.19 0.00 32.85 1.94
129 130 7.778470 TTTTTAACGTCCATGCTTGAATTTT 57.222 28.000 0.22 0.00 0.00 1.82
130 131 7.401484 TTTTAACGTCCATGCTTGAATTTTC 57.599 32.000 0.22 0.00 0.00 2.29
131 132 4.853924 AACGTCCATGCTTGAATTTTCT 57.146 36.364 0.22 0.00 0.00 2.52
132 133 5.957842 AACGTCCATGCTTGAATTTTCTA 57.042 34.783 0.22 0.00 0.00 2.10
133 134 5.551760 ACGTCCATGCTTGAATTTTCTAG 57.448 39.130 0.22 0.00 33.97 2.43
134 135 4.396166 ACGTCCATGCTTGAATTTTCTAGG 59.604 41.667 0.22 0.00 31.95 3.02
135 136 4.396166 CGTCCATGCTTGAATTTTCTAGGT 59.604 41.667 0.22 0.00 31.95 3.08
136 137 5.644644 GTCCATGCTTGAATTTTCTAGGTG 58.355 41.667 0.22 0.00 31.95 4.00
137 138 4.158394 TCCATGCTTGAATTTTCTAGGTGC 59.842 41.667 0.22 0.00 31.95 5.01
138 139 4.159135 CCATGCTTGAATTTTCTAGGTGCT 59.841 41.667 0.22 0.00 31.95 4.40
139 140 5.337009 CCATGCTTGAATTTTCTAGGTGCTT 60.337 40.000 0.22 0.00 31.95 3.91
140 141 5.125100 TGCTTGAATTTTCTAGGTGCTTG 57.875 39.130 4.38 0.00 31.95 4.01
141 142 4.584325 TGCTTGAATTTTCTAGGTGCTTGT 59.416 37.500 4.38 0.00 31.95 3.16
142 143 5.767665 TGCTTGAATTTTCTAGGTGCTTGTA 59.232 36.000 4.38 0.00 31.95 2.41
143 144 6.264292 TGCTTGAATTTTCTAGGTGCTTGTAA 59.736 34.615 4.38 0.00 31.95 2.41
144 145 6.582672 GCTTGAATTTTCTAGGTGCTTGTAAC 59.417 38.462 4.38 0.00 31.95 2.50
145 146 7.522236 GCTTGAATTTTCTAGGTGCTTGTAACT 60.522 37.037 4.38 0.00 31.95 2.24
146 147 7.817418 TGAATTTTCTAGGTGCTTGTAACTT 57.183 32.000 0.00 0.00 0.00 2.66
147 148 8.232913 TGAATTTTCTAGGTGCTTGTAACTTT 57.767 30.769 0.00 0.00 0.00 2.66
148 149 8.691797 TGAATTTTCTAGGTGCTTGTAACTTTT 58.308 29.630 0.00 0.00 0.00 2.27
149 150 9.529325 GAATTTTCTAGGTGCTTGTAACTTTTT 57.471 29.630 0.00 0.00 0.00 1.94
171 172 6.704289 TTTTTGCCAAGATCATATCTGGAG 57.296 37.500 0.00 0.00 40.13 3.86
172 173 4.362470 TTGCCAAGATCATATCTGGAGG 57.638 45.455 0.00 4.98 40.13 4.30
173 174 3.590714 TGCCAAGATCATATCTGGAGGA 58.409 45.455 0.00 0.00 40.13 3.71
174 175 3.581770 TGCCAAGATCATATCTGGAGGAG 59.418 47.826 0.00 0.00 40.13 3.69
175 176 3.619487 GCCAAGATCATATCTGGAGGAGC 60.619 52.174 0.00 0.00 40.13 4.70
176 177 3.839490 CCAAGATCATATCTGGAGGAGCT 59.161 47.826 0.00 0.00 40.13 4.09
177 178 4.081531 CCAAGATCATATCTGGAGGAGCTC 60.082 50.000 4.71 4.71 40.13 4.09
178 179 4.401048 AGATCATATCTGGAGGAGCTCA 57.599 45.455 17.19 0.00 38.44 4.26
179 180 4.346730 AGATCATATCTGGAGGAGCTCAG 58.653 47.826 17.19 4.81 38.44 3.35
180 181 3.609256 TCATATCTGGAGGAGCTCAGT 57.391 47.619 17.19 0.97 31.08 3.41
181 182 3.495331 TCATATCTGGAGGAGCTCAGTC 58.505 50.000 17.19 11.32 31.08 3.51
182 183 3.117360 TCATATCTGGAGGAGCTCAGTCA 60.117 47.826 17.19 8.84 31.08 3.41
183 184 2.244486 ATCTGGAGGAGCTCAGTCAA 57.756 50.000 17.19 4.09 31.08 3.18
184 185 2.015456 TCTGGAGGAGCTCAGTCAAA 57.985 50.000 17.19 3.30 31.08 2.69
185 186 2.329267 TCTGGAGGAGCTCAGTCAAAA 58.671 47.619 17.19 0.95 31.08 2.44
186 187 2.705658 TCTGGAGGAGCTCAGTCAAAAA 59.294 45.455 17.19 0.00 31.08 1.94
217 218 9.889128 AAAAGAAAAATGAAAATCAGAGTTCCA 57.111 25.926 0.00 0.00 0.00 3.53
218 219 9.889128 AAAGAAAAATGAAAATCAGAGTTCCAA 57.111 25.926 0.00 0.00 0.00 3.53
219 220 9.889128 AAGAAAAATGAAAATCAGAGTTCCAAA 57.111 25.926 0.00 0.00 0.00 3.28
220 221 9.889128 AGAAAAATGAAAATCAGAGTTCCAAAA 57.111 25.926 0.00 0.00 0.00 2.44
223 224 9.617523 AAAATGAAAATCAGAGTTCCAAAATGT 57.382 25.926 0.00 0.00 0.00 2.71
224 225 8.822652 AATGAAAATCAGAGTTCCAAAATGTC 57.177 30.769 0.00 0.00 0.00 3.06
225 226 6.748132 TGAAAATCAGAGTTCCAAAATGTCC 58.252 36.000 0.00 0.00 0.00 4.02
226 227 6.323482 TGAAAATCAGAGTTCCAAAATGTCCA 59.677 34.615 0.00 0.00 0.00 4.02
227 228 6.729690 AAATCAGAGTTCCAAAATGTCCAA 57.270 33.333 0.00 0.00 0.00 3.53
228 229 6.729690 AATCAGAGTTCCAAAATGTCCAAA 57.270 33.333 0.00 0.00 0.00 3.28
229 230 5.772825 TCAGAGTTCCAAAATGTCCAAAG 57.227 39.130 0.00 0.00 0.00 2.77
230 231 5.200483 TCAGAGTTCCAAAATGTCCAAAGT 58.800 37.500 0.00 0.00 0.00 2.66
231 232 5.656416 TCAGAGTTCCAAAATGTCCAAAGTT 59.344 36.000 0.00 0.00 0.00 2.66
232 233 5.750067 CAGAGTTCCAAAATGTCCAAAGTTG 59.250 40.000 0.00 0.00 0.00 3.16
233 234 4.441792 AGTTCCAAAATGTCCAAAGTTGC 58.558 39.130 0.00 0.00 0.00 4.17
234 235 4.162131 AGTTCCAAAATGTCCAAAGTTGCT 59.838 37.500 0.00 0.00 0.00 3.91
235 236 4.320608 TCCAAAATGTCCAAAGTTGCTC 57.679 40.909 0.00 0.00 0.00 4.26
236 237 3.052036 CCAAAATGTCCAAAGTTGCTCG 58.948 45.455 0.00 0.00 0.00 5.03
237 238 2.422276 AAATGTCCAAAGTTGCTCGC 57.578 45.000 0.00 0.00 0.00 5.03
238 239 1.609208 AATGTCCAAAGTTGCTCGCT 58.391 45.000 0.00 0.00 0.00 4.93
239 240 1.609208 ATGTCCAAAGTTGCTCGCTT 58.391 45.000 0.00 0.00 0.00 4.68
240 241 1.388547 TGTCCAAAGTTGCTCGCTTT 58.611 45.000 0.00 0.00 36.70 3.51
241 242 1.748493 TGTCCAAAGTTGCTCGCTTTT 59.252 42.857 0.00 0.00 34.32 2.27
242 243 2.223479 TGTCCAAAGTTGCTCGCTTTTC 60.223 45.455 0.00 0.00 34.32 2.29
243 244 1.336755 TCCAAAGTTGCTCGCTTTTCC 59.663 47.619 0.00 0.00 34.32 3.13
244 245 1.398595 CAAAGTTGCTCGCTTTTCCG 58.601 50.000 0.00 0.00 34.32 4.30
245 246 1.002900 CAAAGTTGCTCGCTTTTCCGA 60.003 47.619 0.00 0.00 34.32 4.55
250 251 4.900154 CTCGCTTTTCCGAGCTCT 57.100 55.556 12.85 0.00 46.69 4.09
251 252 2.659740 CTCGCTTTTCCGAGCTCTC 58.340 57.895 12.85 0.00 46.69 3.20
252 253 0.109086 CTCGCTTTTCCGAGCTCTCA 60.109 55.000 12.85 0.00 46.69 3.27
253 254 0.317160 TCGCTTTTCCGAGCTCTCAA 59.683 50.000 12.85 0.81 40.52 3.02
254 255 1.066858 TCGCTTTTCCGAGCTCTCAAT 60.067 47.619 12.85 0.00 40.52 2.57
255 256 1.061711 CGCTTTTCCGAGCTCTCAATG 59.938 52.381 12.85 5.25 40.52 2.82
256 257 2.079925 GCTTTTCCGAGCTCTCAATGT 58.920 47.619 12.85 0.00 39.57 2.71
257 258 2.485814 GCTTTTCCGAGCTCTCAATGTT 59.514 45.455 12.85 0.00 39.57 2.71
258 259 3.057946 GCTTTTCCGAGCTCTCAATGTTT 60.058 43.478 12.85 0.00 39.57 2.83
259 260 4.557496 GCTTTTCCGAGCTCTCAATGTTTT 60.557 41.667 12.85 0.00 39.57 2.43
260 261 4.749245 TTTCCGAGCTCTCAATGTTTTC 57.251 40.909 12.85 0.00 0.00 2.29
261 262 3.685139 TCCGAGCTCTCAATGTTTTCT 57.315 42.857 12.85 0.00 0.00 2.52
262 263 4.008074 TCCGAGCTCTCAATGTTTTCTT 57.992 40.909 12.85 0.00 0.00 2.52
263 264 4.389374 TCCGAGCTCTCAATGTTTTCTTT 58.611 39.130 12.85 0.00 0.00 2.52
264 265 5.547465 TCCGAGCTCTCAATGTTTTCTTTA 58.453 37.500 12.85 0.00 0.00 1.85
265 266 5.408604 TCCGAGCTCTCAATGTTTTCTTTAC 59.591 40.000 12.85 0.00 0.00 2.01
266 267 5.390991 CCGAGCTCTCAATGTTTTCTTTACC 60.391 44.000 12.85 0.00 0.00 2.85
267 268 5.409826 CGAGCTCTCAATGTTTTCTTTACCT 59.590 40.000 12.85 0.00 0.00 3.08
268 269 6.590292 CGAGCTCTCAATGTTTTCTTTACCTA 59.410 38.462 12.85 0.00 0.00 3.08
269 270 7.201478 CGAGCTCTCAATGTTTTCTTTACCTAG 60.201 40.741 12.85 0.00 0.00 3.02
270 271 6.372937 AGCTCTCAATGTTTTCTTTACCTAGC 59.627 38.462 0.00 0.00 0.00 3.42
271 272 6.372937 GCTCTCAATGTTTTCTTTACCTAGCT 59.627 38.462 0.00 0.00 0.00 3.32
272 273 7.413548 GCTCTCAATGTTTTCTTTACCTAGCTC 60.414 40.741 0.00 0.00 0.00 4.09
273 274 6.879458 TCTCAATGTTTTCTTTACCTAGCTCC 59.121 38.462 0.00 0.00 0.00 4.70
274 275 6.779860 TCAATGTTTTCTTTACCTAGCTCCT 58.220 36.000 0.00 0.00 0.00 3.69
275 276 6.879458 TCAATGTTTTCTTTACCTAGCTCCTC 59.121 38.462 0.00 0.00 0.00 3.71
276 277 5.161943 TGTTTTCTTTACCTAGCTCCTCC 57.838 43.478 0.00 0.00 0.00 4.30
277 278 4.182339 GTTTTCTTTACCTAGCTCCTCCG 58.818 47.826 0.00 0.00 0.00 4.63
278 279 3.377253 TTCTTTACCTAGCTCCTCCGA 57.623 47.619 0.00 0.00 0.00 4.55
279 280 3.596940 TCTTTACCTAGCTCCTCCGAT 57.403 47.619 0.00 0.00 0.00 4.18
280 281 3.223435 TCTTTACCTAGCTCCTCCGATG 58.777 50.000 0.00 0.00 0.00 3.84
281 282 2.750141 TTACCTAGCTCCTCCGATGT 57.250 50.000 0.00 0.00 0.00 3.06
282 283 2.273538 TACCTAGCTCCTCCGATGTC 57.726 55.000 0.00 0.00 0.00 3.06
283 284 0.259065 ACCTAGCTCCTCCGATGTCA 59.741 55.000 0.00 0.00 0.00 3.58
284 285 1.133325 ACCTAGCTCCTCCGATGTCAT 60.133 52.381 0.00 0.00 0.00 3.06
285 286 1.543802 CCTAGCTCCTCCGATGTCATC 59.456 57.143 2.43 2.43 0.00 2.92
286 287 2.513753 CTAGCTCCTCCGATGTCATCT 58.486 52.381 11.04 0.00 0.00 2.90
287 288 1.327303 AGCTCCTCCGATGTCATCTC 58.673 55.000 11.04 0.00 0.00 2.75
288 289 1.035923 GCTCCTCCGATGTCATCTCA 58.964 55.000 11.04 0.00 0.00 3.27
289 290 1.269517 GCTCCTCCGATGTCATCTCAC 60.270 57.143 11.04 0.00 0.00 3.51
290 291 1.339610 CTCCTCCGATGTCATCTCACC 59.660 57.143 11.04 0.00 0.00 4.02
291 292 1.114627 CCTCCGATGTCATCTCACCA 58.885 55.000 11.04 0.00 0.00 4.17
292 293 1.690893 CCTCCGATGTCATCTCACCAT 59.309 52.381 11.04 0.00 0.00 3.55
293 294 2.547430 CCTCCGATGTCATCTCACCATG 60.547 54.545 11.04 0.00 0.00 3.66
294 295 2.363359 CTCCGATGTCATCTCACCATGA 59.637 50.000 11.04 0.00 0.00 3.07
295 296 2.765699 TCCGATGTCATCTCACCATGAA 59.234 45.455 11.04 0.00 34.50 2.57
296 297 3.197549 TCCGATGTCATCTCACCATGAAA 59.802 43.478 11.04 0.00 34.50 2.69
297 298 3.940852 CCGATGTCATCTCACCATGAAAA 59.059 43.478 11.04 0.00 34.50 2.29
298 299 4.577693 CCGATGTCATCTCACCATGAAAAT 59.422 41.667 11.04 0.00 34.50 1.82
299 300 5.277683 CCGATGTCATCTCACCATGAAAATC 60.278 44.000 11.04 0.00 34.50 2.17
300 301 5.277683 CGATGTCATCTCACCATGAAAATCC 60.278 44.000 11.04 0.00 34.50 3.01
301 302 4.920999 TGTCATCTCACCATGAAAATCCA 58.079 39.130 0.00 0.00 34.50 3.41
302 303 4.701651 TGTCATCTCACCATGAAAATCCAC 59.298 41.667 0.00 0.00 34.50 4.02
303 304 4.701651 GTCATCTCACCATGAAAATCCACA 59.298 41.667 0.00 0.00 34.50 4.17
304 305 5.359009 GTCATCTCACCATGAAAATCCACAT 59.641 40.000 0.00 0.00 34.50 3.21
305 306 5.358725 TCATCTCACCATGAAAATCCACATG 59.641 40.000 0.00 0.00 42.12 3.21
306 307 3.444742 TCTCACCATGAAAATCCACATGC 59.555 43.478 0.00 0.00 41.43 4.06
307 308 3.163467 TCACCATGAAAATCCACATGCA 58.837 40.909 0.00 0.00 41.43 3.96
308 309 3.056678 TCACCATGAAAATCCACATGCAC 60.057 43.478 0.00 0.00 41.43 4.57
309 310 2.234414 ACCATGAAAATCCACATGCACC 59.766 45.455 0.00 0.00 41.43 5.01
310 311 2.498481 CCATGAAAATCCACATGCACCT 59.502 45.455 0.00 0.00 41.43 4.00
311 312 3.700539 CCATGAAAATCCACATGCACCTA 59.299 43.478 0.00 0.00 41.43 3.08
312 313 4.202080 CCATGAAAATCCACATGCACCTAG 60.202 45.833 0.00 0.00 41.43 3.02
313 314 4.299586 TGAAAATCCACATGCACCTAGA 57.700 40.909 0.00 0.00 0.00 2.43
314 315 4.661222 TGAAAATCCACATGCACCTAGAA 58.339 39.130 0.00 0.00 0.00 2.10
315 316 5.076182 TGAAAATCCACATGCACCTAGAAA 58.924 37.500 0.00 0.00 0.00 2.52
316 317 5.538053 TGAAAATCCACATGCACCTAGAAAA 59.462 36.000 0.00 0.00 0.00 2.29
317 318 6.211184 TGAAAATCCACATGCACCTAGAAAAT 59.789 34.615 0.00 0.00 0.00 1.82
318 319 6.610075 AAATCCACATGCACCTAGAAAATT 57.390 33.333 0.00 0.00 0.00 1.82
319 320 6.610075 AATCCACATGCACCTAGAAAATTT 57.390 33.333 0.00 0.00 0.00 1.82
320 321 7.716799 AATCCACATGCACCTAGAAAATTTA 57.283 32.000 0.00 0.00 0.00 1.40
321 322 7.716799 ATCCACATGCACCTAGAAAATTTAA 57.283 32.000 0.00 0.00 0.00 1.52
322 323 7.156876 TCCACATGCACCTAGAAAATTTAAG 57.843 36.000 0.00 0.00 0.00 1.85
323 324 5.807011 CCACATGCACCTAGAAAATTTAAGC 59.193 40.000 0.00 0.00 0.00 3.09
324 325 6.389091 CACATGCACCTAGAAAATTTAAGCA 58.611 36.000 0.00 0.00 0.00 3.91
325 326 7.037438 CACATGCACCTAGAAAATTTAAGCAT 58.963 34.615 0.00 0.00 40.43 3.79
326 327 7.221452 CACATGCACCTAGAAAATTTAAGCATC 59.779 37.037 0.00 0.00 38.03 3.91
327 328 7.123247 ACATGCACCTAGAAAATTTAAGCATCT 59.877 33.333 0.00 0.00 38.03 2.90
328 329 7.466746 TGCACCTAGAAAATTTAAGCATCTT 57.533 32.000 0.00 0.00 0.00 2.40
329 330 7.895759 TGCACCTAGAAAATTTAAGCATCTTT 58.104 30.769 0.00 0.00 0.00 2.52
330 331 7.814107 TGCACCTAGAAAATTTAAGCATCTTTG 59.186 33.333 0.00 0.00 0.00 2.77
407 408 8.871686 AAAAATTGCGAGACAGTTTTCTAATT 57.128 26.923 0.00 0.00 44.62 1.40
408 409 8.871686 AAAATTGCGAGACAGTTTTCTAATTT 57.128 26.923 0.00 0.00 42.58 1.82
409 410 8.871686 AAATTGCGAGACAGTTTTCTAATTTT 57.128 26.923 0.00 0.00 34.83 1.82
410 411 8.871686 AATTGCGAGACAGTTTTCTAATTTTT 57.128 26.923 0.00 0.00 0.00 1.94
490 494 1.474077 ACCTGGATGCAGAAATTTCGC 59.526 47.619 16.85 20.70 0.00 4.70
508 512 1.408683 CGCCCTCCAGATCCATTTCAA 60.409 52.381 0.00 0.00 0.00 2.69
510 514 2.941480 CCCTCCAGATCCATTTCAAGG 58.059 52.381 0.00 0.00 0.00 3.61
514 518 5.206587 CCTCCAGATCCATTTCAAGGAAAT 58.793 41.667 0.00 0.00 42.14 2.17
554 558 5.066505 AGAGTAACAACAAGAACAGCCAAAG 59.933 40.000 0.00 0.00 0.00 2.77
555 559 2.584492 ACAACAAGAACAGCCAAAGC 57.416 45.000 0.00 0.00 40.32 3.51
558 562 0.106015 ACAAGAACAGCCAAAGCCCT 60.106 50.000 0.00 0.00 41.25 5.19
571 582 3.638627 CCAAAGCCCTGAGAAAAAGAACT 59.361 43.478 0.00 0.00 0.00 3.01
575 586 2.550208 GCCCTGAGAAAAAGAACTCCGA 60.550 50.000 0.00 0.00 32.84 4.55
978 1005 1.007849 GCGAGAGAATCCGAGGAGC 60.008 63.158 0.00 0.00 33.66 4.70
1206 1234 2.528818 CCTCCAAGAGCCCCACACA 61.529 63.158 0.00 0.00 0.00 3.72
1382 1435 5.679638 GCTTGTGATTTTGTTGTCTCAGGTT 60.680 40.000 0.00 0.00 0.00 3.50
1475 1534 4.677151 GGAGGTGGAGGGGGTGGT 62.677 72.222 0.00 0.00 0.00 4.16
1814 1873 5.949952 GGGTTTTCATAGTAACAATGGACCT 59.050 40.000 0.00 0.00 0.00 3.85
2524 2583 1.406205 GGTTGCTCAGTAGAAGAGGCC 60.406 57.143 0.00 0.00 33.72 5.19
2611 2670 1.911057 TGCTCTCGTCTTCCTGAAGA 58.089 50.000 5.50 5.50 44.47 2.87
2774 2833 1.197721 CCTTCGGTGTGCTTTGTCATC 59.802 52.381 0.00 0.00 0.00 2.92
3074 3144 3.369471 GCACTGATAGAAGCTTGGTACCA 60.369 47.826 11.60 11.60 0.00 3.25
3092 3162 2.292267 CCATAGCTGCTTCAAACGGAT 58.708 47.619 7.79 0.00 0.00 4.18
3106 3176 2.743636 ACGGATGGTCAAGTGTAGTG 57.256 50.000 0.00 0.00 0.00 2.74
3288 3361 5.163353 CCCTTCAAGCCTTTTGGTCTTAAAA 60.163 40.000 0.00 0.00 42.99 1.52
3292 3365 8.800370 TTCAAGCCTTTTGGTCTTAAAATTTT 57.200 26.923 8.75 8.75 42.99 1.82
3429 3502 6.422333 GGTAGAAACCCTAGAGTACAGTAGT 58.578 44.000 0.00 0.00 40.21 2.73
3699 3772 6.360681 CGTGGAAACAAAGATTCATTGTCTTC 59.639 38.462 7.65 11.93 46.06 2.87
3764 3837 3.421394 TGGAGATGATACCCTGGTTCT 57.579 47.619 0.00 0.00 0.00 3.01
3852 3935 0.396060 GCCTTGTCAATTTTGGCCCA 59.604 50.000 0.00 0.00 37.81 5.36
3929 4036 9.226606 TGTAGATTTTGGTAGTAATTTCCACAG 57.773 33.333 0.00 0.00 0.00 3.66
4139 4264 9.855361 CTTACACAGAAGATTTAGCATTATTCG 57.145 33.333 0.00 0.00 0.00 3.34
4145 4270 8.397906 CAGAAGATTTAGCATTATTCGTTCCAA 58.602 33.333 0.00 0.00 0.00 3.53
4148 4273 8.050778 AGATTTAGCATTATTCGTTCCAAACA 57.949 30.769 0.00 0.00 0.00 2.83
4204 4337 3.256631 TGTTAAACACTACTCCCTCCGTC 59.743 47.826 0.00 0.00 0.00 4.79
4230 4363 6.183360 CCACAATATAAGACGTAGCTTGCAAA 60.183 38.462 0.00 0.00 0.00 3.68
4233 4366 8.458843 ACAATATAAGACGTAGCTTGCAAAAAT 58.541 29.630 0.00 0.00 0.00 1.82
4295 4428 6.204688 TGGTTATGCGTTTGATAGATTCCATC 59.795 38.462 0.00 0.00 0.00 3.51
4304 4649 5.233083 TGATAGATTCCATCGCCTGAAAT 57.767 39.130 0.00 0.00 0.00 2.17
4423 4782 8.420222 TGAAGATGGAAAGCAGAAAATTTGTTA 58.580 29.630 0.00 0.00 0.00 2.41
4424 4783 8.822652 AAGATGGAAAGCAGAAAATTTGTTAG 57.177 30.769 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.393512 ACGCTAAGAATCTCTAGTACTTAAAGA 57.606 33.333 0.00 2.27 0.00 2.52
12 13 9.654417 GACGCTAAGAATCTCTAGTACTTAAAG 57.346 37.037 0.00 0.00 0.00 1.85
13 14 8.619546 GGACGCTAAGAATCTCTAGTACTTAAA 58.380 37.037 0.00 0.00 0.00 1.52
14 15 7.992033 AGGACGCTAAGAATCTCTAGTACTTAA 59.008 37.037 0.00 0.00 0.00 1.85
15 16 7.507829 AGGACGCTAAGAATCTCTAGTACTTA 58.492 38.462 0.00 0.00 0.00 2.24
16 17 6.358991 AGGACGCTAAGAATCTCTAGTACTT 58.641 40.000 0.00 0.00 0.00 2.24
17 18 5.932455 AGGACGCTAAGAATCTCTAGTACT 58.068 41.667 0.00 0.00 0.00 2.73
18 19 5.993441 AGAGGACGCTAAGAATCTCTAGTAC 59.007 44.000 0.00 0.00 30.81 2.73
19 20 6.177310 AGAGGACGCTAAGAATCTCTAGTA 57.823 41.667 0.00 0.00 30.81 1.82
20 21 5.043737 AGAGGACGCTAAGAATCTCTAGT 57.956 43.478 0.00 0.00 30.81 2.57
21 22 7.499321 TTAAGAGGACGCTAAGAATCTCTAG 57.501 40.000 0.00 0.00 32.12 2.43
22 23 7.720074 TCATTAAGAGGACGCTAAGAATCTCTA 59.280 37.037 0.00 0.00 32.12 2.43
23 24 6.547880 TCATTAAGAGGACGCTAAGAATCTCT 59.452 38.462 0.00 0.00 33.58 3.10
24 25 6.740110 TCATTAAGAGGACGCTAAGAATCTC 58.260 40.000 0.00 0.00 0.00 2.75
25 26 6.716934 TCATTAAGAGGACGCTAAGAATCT 57.283 37.500 0.00 0.00 0.00 2.40
26 27 6.422400 CCTTCATTAAGAGGACGCTAAGAATC 59.578 42.308 0.00 0.00 34.37 2.52
27 28 6.284459 CCTTCATTAAGAGGACGCTAAGAAT 58.716 40.000 0.00 0.00 34.37 2.40
28 29 5.661458 CCTTCATTAAGAGGACGCTAAGAA 58.339 41.667 0.00 0.00 34.37 2.52
29 30 4.441634 GCCTTCATTAAGAGGACGCTAAGA 60.442 45.833 6.52 0.00 34.37 2.10
30 31 3.804873 GCCTTCATTAAGAGGACGCTAAG 59.195 47.826 6.52 0.00 34.37 2.18
31 32 3.196901 TGCCTTCATTAAGAGGACGCTAA 59.803 43.478 6.52 0.00 34.37 3.09
32 33 2.764010 TGCCTTCATTAAGAGGACGCTA 59.236 45.455 6.52 0.00 34.37 4.26
33 34 1.555075 TGCCTTCATTAAGAGGACGCT 59.445 47.619 6.52 0.00 34.37 5.07
34 35 2.024176 TGCCTTCATTAAGAGGACGC 57.976 50.000 6.52 0.00 34.37 5.19
35 36 5.567138 AAAATGCCTTCATTAAGAGGACG 57.433 39.130 6.52 0.00 41.77 4.79
56 57 7.824672 TCTTTTTGAACTGTAACCCGTAAAAA 58.175 30.769 0.00 0.00 0.00 1.94
57 58 7.388460 TCTTTTTGAACTGTAACCCGTAAAA 57.612 32.000 0.00 0.00 0.00 1.52
58 59 6.998968 TCTTTTTGAACTGTAACCCGTAAA 57.001 33.333 0.00 0.00 0.00 2.01
59 60 6.998968 TTCTTTTTGAACTGTAACCCGTAA 57.001 33.333 0.00 0.00 0.00 3.18
60 61 6.373774 TGTTTCTTTTTGAACTGTAACCCGTA 59.626 34.615 0.00 0.00 33.88 4.02
61 62 5.183522 TGTTTCTTTTTGAACTGTAACCCGT 59.816 36.000 0.00 0.00 33.88 5.28
62 63 5.513849 GTGTTTCTTTTTGAACTGTAACCCG 59.486 40.000 0.00 0.00 33.88 5.28
63 64 6.627243 AGTGTTTCTTTTTGAACTGTAACCC 58.373 36.000 0.00 0.00 33.88 4.11
64 65 9.447040 GATAGTGTTTCTTTTTGAACTGTAACC 57.553 33.333 0.00 0.00 33.88 2.85
69 70 9.334693 GCATAGATAGTGTTTCTTTTTGAACTG 57.665 33.333 0.00 0.00 33.88 3.16
70 71 9.066892 TGCATAGATAGTGTTTCTTTTTGAACT 57.933 29.630 0.00 0.00 33.88 3.01
71 72 9.846248 ATGCATAGATAGTGTTTCTTTTTGAAC 57.154 29.630 0.00 0.00 33.88 3.18
73 74 8.677300 GGATGCATAGATAGTGTTTCTTTTTGA 58.323 33.333 0.00 0.00 0.00 2.69
74 75 8.461222 TGGATGCATAGATAGTGTTTCTTTTTG 58.539 33.333 0.00 0.00 0.00 2.44
75 76 8.579850 TGGATGCATAGATAGTGTTTCTTTTT 57.420 30.769 0.00 0.00 0.00 1.94
76 77 8.627403 CATGGATGCATAGATAGTGTTTCTTTT 58.373 33.333 0.00 0.00 0.00 2.27
77 78 7.776969 ACATGGATGCATAGATAGTGTTTCTTT 59.223 33.333 0.00 0.00 0.00 2.52
78 79 7.285566 ACATGGATGCATAGATAGTGTTTCTT 58.714 34.615 0.00 0.00 0.00 2.52
79 80 6.835174 ACATGGATGCATAGATAGTGTTTCT 58.165 36.000 0.00 0.00 0.00 2.52
80 81 7.502120 AACATGGATGCATAGATAGTGTTTC 57.498 36.000 0.00 0.00 0.00 2.78
81 82 7.886629 AAACATGGATGCATAGATAGTGTTT 57.113 32.000 0.00 8.88 33.80 2.83
82 83 7.886629 AAAACATGGATGCATAGATAGTGTT 57.113 32.000 0.00 3.06 0.00 3.32
83 84 7.886629 AAAAACATGGATGCATAGATAGTGT 57.113 32.000 0.00 0.00 0.00 3.55
105 106 7.708752 AGAAAATTCAAGCATGGACGTTAAAAA 59.291 29.630 0.00 0.00 0.00 1.94
106 107 7.206687 AGAAAATTCAAGCATGGACGTTAAAA 58.793 30.769 0.00 0.00 0.00 1.52
107 108 6.744112 AGAAAATTCAAGCATGGACGTTAAA 58.256 32.000 0.00 0.00 0.00 1.52
108 109 6.325919 AGAAAATTCAAGCATGGACGTTAA 57.674 33.333 0.00 0.00 0.00 2.01
109 110 5.957842 AGAAAATTCAAGCATGGACGTTA 57.042 34.783 0.00 0.00 0.00 3.18
110 111 4.853924 AGAAAATTCAAGCATGGACGTT 57.146 36.364 0.00 0.00 0.00 3.99
111 112 4.396166 CCTAGAAAATTCAAGCATGGACGT 59.604 41.667 0.00 0.00 0.00 4.34
112 113 4.396166 ACCTAGAAAATTCAAGCATGGACG 59.604 41.667 0.00 0.00 0.00 4.79
113 114 5.644644 CACCTAGAAAATTCAAGCATGGAC 58.355 41.667 0.00 0.00 0.00 4.02
114 115 4.158394 GCACCTAGAAAATTCAAGCATGGA 59.842 41.667 0.00 0.00 0.00 3.41
115 116 4.159135 AGCACCTAGAAAATTCAAGCATGG 59.841 41.667 0.00 0.00 0.00 3.66
116 117 5.320549 AGCACCTAGAAAATTCAAGCATG 57.679 39.130 0.00 0.00 0.00 4.06
117 118 5.244626 ACAAGCACCTAGAAAATTCAAGCAT 59.755 36.000 0.00 0.00 0.00 3.79
118 119 4.584325 ACAAGCACCTAGAAAATTCAAGCA 59.416 37.500 0.00 0.00 0.00 3.91
119 120 5.126396 ACAAGCACCTAGAAAATTCAAGC 57.874 39.130 0.00 0.00 0.00 4.01
120 121 7.875971 AGTTACAAGCACCTAGAAAATTCAAG 58.124 34.615 0.00 0.00 0.00 3.02
121 122 7.817418 AGTTACAAGCACCTAGAAAATTCAA 57.183 32.000 0.00 0.00 0.00 2.69
122 123 7.817418 AAGTTACAAGCACCTAGAAAATTCA 57.183 32.000 0.00 0.00 0.00 2.57
123 124 9.529325 AAAAAGTTACAAGCACCTAGAAAATTC 57.471 29.630 0.00 0.00 0.00 2.17
148 149 5.595542 CCTCCAGATATGATCTTGGCAAAAA 59.404 40.000 0.00 0.00 37.58 1.94
149 150 5.103982 TCCTCCAGATATGATCTTGGCAAAA 60.104 40.000 0.00 0.00 37.58 2.44
150 151 4.413189 TCCTCCAGATATGATCTTGGCAAA 59.587 41.667 0.00 0.00 37.58 3.68
151 152 3.975982 TCCTCCAGATATGATCTTGGCAA 59.024 43.478 0.00 0.00 37.58 4.52
152 153 3.581770 CTCCTCCAGATATGATCTTGGCA 59.418 47.826 0.00 0.00 37.58 4.92
153 154 3.619487 GCTCCTCCAGATATGATCTTGGC 60.619 52.174 0.00 0.00 37.58 4.52
154 155 3.839490 AGCTCCTCCAGATATGATCTTGG 59.161 47.826 0.00 0.00 37.58 3.61
155 156 4.527427 TGAGCTCCTCCAGATATGATCTTG 59.473 45.833 12.15 0.00 37.58 3.02
156 157 4.749820 TGAGCTCCTCCAGATATGATCTT 58.250 43.478 12.15 0.00 37.58 2.40
157 158 4.202706 ACTGAGCTCCTCCAGATATGATCT 60.203 45.833 12.15 0.00 41.15 2.75
158 159 4.088634 ACTGAGCTCCTCCAGATATGATC 58.911 47.826 12.15 0.00 0.00 2.92
159 160 4.088634 GACTGAGCTCCTCCAGATATGAT 58.911 47.826 12.15 0.00 0.00 2.45
160 161 3.117360 TGACTGAGCTCCTCCAGATATGA 60.117 47.826 12.15 0.00 0.00 2.15
161 162 3.229293 TGACTGAGCTCCTCCAGATATG 58.771 50.000 12.15 0.00 0.00 1.78
162 163 3.609256 TGACTGAGCTCCTCCAGATAT 57.391 47.619 12.15 0.00 0.00 1.63
163 164 3.388552 TTGACTGAGCTCCTCCAGATA 57.611 47.619 12.15 0.00 0.00 1.98
164 165 2.244486 TTGACTGAGCTCCTCCAGAT 57.756 50.000 12.15 0.00 0.00 2.90
165 166 2.015456 TTTGACTGAGCTCCTCCAGA 57.985 50.000 12.15 0.00 0.00 3.86
166 167 2.847327 TTTTGACTGAGCTCCTCCAG 57.153 50.000 12.15 4.81 0.00 3.86
191 192 9.889128 TGGAACTCTGATTTTCATTTTTCTTTT 57.111 25.926 2.66 0.00 0.00 2.27
192 193 9.889128 TTGGAACTCTGATTTTCATTTTTCTTT 57.111 25.926 0.00 0.00 0.00 2.52
193 194 9.889128 TTTGGAACTCTGATTTTCATTTTTCTT 57.111 25.926 0.00 0.00 0.00 2.52
194 195 9.889128 TTTTGGAACTCTGATTTTCATTTTTCT 57.111 25.926 0.00 0.00 0.00 2.52
197 198 9.617523 ACATTTTGGAACTCTGATTTTCATTTT 57.382 25.926 0.00 0.00 0.00 1.82
198 199 9.264719 GACATTTTGGAACTCTGATTTTCATTT 57.735 29.630 0.00 0.00 0.00 2.32
199 200 7.874528 GGACATTTTGGAACTCTGATTTTCATT 59.125 33.333 0.00 0.00 0.00 2.57
200 201 7.015487 TGGACATTTTGGAACTCTGATTTTCAT 59.985 33.333 0.00 0.00 0.00 2.57
201 202 6.323482 TGGACATTTTGGAACTCTGATTTTCA 59.677 34.615 2.66 0.00 0.00 2.69
202 203 6.748132 TGGACATTTTGGAACTCTGATTTTC 58.252 36.000 0.00 0.00 0.00 2.29
203 204 6.729690 TGGACATTTTGGAACTCTGATTTT 57.270 33.333 0.00 0.00 0.00 1.82
204 205 6.729690 TTGGACATTTTGGAACTCTGATTT 57.270 33.333 0.00 0.00 0.00 2.17
205 206 6.324770 ACTTTGGACATTTTGGAACTCTGATT 59.675 34.615 0.00 0.00 0.00 2.57
206 207 5.835280 ACTTTGGACATTTTGGAACTCTGAT 59.165 36.000 0.00 0.00 0.00 2.90
207 208 5.200483 ACTTTGGACATTTTGGAACTCTGA 58.800 37.500 0.00 0.00 0.00 3.27
208 209 5.520376 ACTTTGGACATTTTGGAACTCTG 57.480 39.130 0.00 0.00 0.00 3.35
209 210 5.682212 GCAACTTTGGACATTTTGGAACTCT 60.682 40.000 0.00 0.00 0.00 3.24
210 211 4.507756 GCAACTTTGGACATTTTGGAACTC 59.492 41.667 0.00 0.00 0.00 3.01
211 212 4.162131 AGCAACTTTGGACATTTTGGAACT 59.838 37.500 0.00 0.00 0.00 3.01
212 213 4.441792 AGCAACTTTGGACATTTTGGAAC 58.558 39.130 0.00 0.00 0.00 3.62
213 214 4.692228 GAGCAACTTTGGACATTTTGGAA 58.308 39.130 0.00 0.00 0.00 3.53
214 215 3.243367 CGAGCAACTTTGGACATTTTGGA 60.243 43.478 0.00 0.00 0.00 3.53
215 216 3.052036 CGAGCAACTTTGGACATTTTGG 58.948 45.455 0.00 0.00 0.00 3.28
216 217 2.472488 GCGAGCAACTTTGGACATTTTG 59.528 45.455 0.00 0.00 0.00 2.44
217 218 2.362077 AGCGAGCAACTTTGGACATTTT 59.638 40.909 0.00 0.00 0.00 1.82
218 219 1.956477 AGCGAGCAACTTTGGACATTT 59.044 42.857 0.00 0.00 0.00 2.32
219 220 1.609208 AGCGAGCAACTTTGGACATT 58.391 45.000 0.00 0.00 0.00 2.71
220 221 1.609208 AAGCGAGCAACTTTGGACAT 58.391 45.000 0.00 0.00 0.00 3.06
221 222 1.388547 AAAGCGAGCAACTTTGGACA 58.611 45.000 0.00 0.00 36.04 4.02
222 223 2.385315 GAAAAGCGAGCAACTTTGGAC 58.615 47.619 0.00 0.00 37.42 4.02
223 224 1.336755 GGAAAAGCGAGCAACTTTGGA 59.663 47.619 0.00 0.00 37.42 3.53
224 225 1.770957 GGAAAAGCGAGCAACTTTGG 58.229 50.000 0.00 0.00 37.42 3.28
225 226 1.002900 TCGGAAAAGCGAGCAACTTTG 60.003 47.619 0.00 0.00 37.42 2.77
226 227 1.264288 CTCGGAAAAGCGAGCAACTTT 59.736 47.619 0.00 0.00 38.98 2.66
227 228 0.868406 CTCGGAAAAGCGAGCAACTT 59.132 50.000 0.00 0.00 0.00 2.66
228 229 2.533318 CTCGGAAAAGCGAGCAACT 58.467 52.632 0.00 0.00 0.00 3.16
236 237 2.079925 ACATTGAGAGCTCGGAAAAGC 58.920 47.619 8.37 0.00 42.82 3.51
237 238 4.756084 AAACATTGAGAGCTCGGAAAAG 57.244 40.909 8.37 4.12 0.00 2.27
238 239 4.821805 AGAAAACATTGAGAGCTCGGAAAA 59.178 37.500 8.37 2.02 0.00 2.29
239 240 4.389374 AGAAAACATTGAGAGCTCGGAAA 58.611 39.130 8.37 4.65 0.00 3.13
240 241 4.008074 AGAAAACATTGAGAGCTCGGAA 57.992 40.909 8.37 5.47 0.00 4.30
241 242 3.685139 AGAAAACATTGAGAGCTCGGA 57.315 42.857 8.37 0.00 0.00 4.55
242 243 4.756084 AAAGAAAACATTGAGAGCTCGG 57.244 40.909 8.37 0.00 0.00 4.63
243 244 5.409826 AGGTAAAGAAAACATTGAGAGCTCG 59.590 40.000 8.37 0.00 0.00 5.03
244 245 6.809630 AGGTAAAGAAAACATTGAGAGCTC 57.190 37.500 5.27 5.27 0.00 4.09
245 246 6.372937 GCTAGGTAAAGAAAACATTGAGAGCT 59.627 38.462 0.00 0.00 0.00 4.09
246 247 6.372937 AGCTAGGTAAAGAAAACATTGAGAGC 59.627 38.462 0.00 0.00 0.00 4.09
247 248 7.065204 GGAGCTAGGTAAAGAAAACATTGAGAG 59.935 40.741 0.00 0.00 0.00 3.20
248 249 6.879458 GGAGCTAGGTAAAGAAAACATTGAGA 59.121 38.462 0.00 0.00 0.00 3.27
249 250 6.881602 AGGAGCTAGGTAAAGAAAACATTGAG 59.118 38.462 0.00 0.00 0.00 3.02
250 251 6.779860 AGGAGCTAGGTAAAGAAAACATTGA 58.220 36.000 0.00 0.00 0.00 2.57
251 252 6.094186 GGAGGAGCTAGGTAAAGAAAACATTG 59.906 42.308 0.00 0.00 0.00 2.82
252 253 6.181190 GGAGGAGCTAGGTAAAGAAAACATT 58.819 40.000 0.00 0.00 0.00 2.71
253 254 5.627040 CGGAGGAGCTAGGTAAAGAAAACAT 60.627 44.000 0.00 0.00 0.00 2.71
254 255 4.322499 CGGAGGAGCTAGGTAAAGAAAACA 60.322 45.833 0.00 0.00 0.00 2.83
255 256 4.081807 TCGGAGGAGCTAGGTAAAGAAAAC 60.082 45.833 0.00 0.00 0.00 2.43
256 257 4.091549 TCGGAGGAGCTAGGTAAAGAAAA 58.908 43.478 0.00 0.00 0.00 2.29
257 258 3.705051 TCGGAGGAGCTAGGTAAAGAAA 58.295 45.455 0.00 0.00 0.00 2.52
258 259 3.377253 TCGGAGGAGCTAGGTAAAGAA 57.623 47.619 0.00 0.00 0.00 2.52
259 260 3.223435 CATCGGAGGAGCTAGGTAAAGA 58.777 50.000 0.00 0.00 0.00 2.52
260 261 2.959707 ACATCGGAGGAGCTAGGTAAAG 59.040 50.000 0.00 0.00 0.00 1.85
261 262 2.957006 GACATCGGAGGAGCTAGGTAAA 59.043 50.000 0.00 0.00 0.00 2.01
262 263 2.092049 TGACATCGGAGGAGCTAGGTAA 60.092 50.000 0.00 0.00 0.00 2.85
263 264 1.493446 TGACATCGGAGGAGCTAGGTA 59.507 52.381 0.00 0.00 0.00 3.08
264 265 0.259065 TGACATCGGAGGAGCTAGGT 59.741 55.000 0.00 0.00 0.00 3.08
265 266 1.543802 GATGACATCGGAGGAGCTAGG 59.456 57.143 0.00 0.00 0.00 3.02
266 267 2.487762 GAGATGACATCGGAGGAGCTAG 59.512 54.545 9.77 0.00 0.00 3.42
267 268 2.158608 TGAGATGACATCGGAGGAGCTA 60.159 50.000 9.77 0.00 0.00 3.32
268 269 1.327303 GAGATGACATCGGAGGAGCT 58.673 55.000 9.77 0.00 0.00 4.09
269 270 1.035923 TGAGATGACATCGGAGGAGC 58.964 55.000 9.77 0.00 0.00 4.70
270 271 1.339610 GGTGAGATGACATCGGAGGAG 59.660 57.143 9.77 0.00 0.00 3.69
271 272 1.341976 TGGTGAGATGACATCGGAGGA 60.342 52.381 9.77 0.00 0.00 3.71
272 273 1.114627 TGGTGAGATGACATCGGAGG 58.885 55.000 9.77 0.00 0.00 4.30
273 274 2.363359 TCATGGTGAGATGACATCGGAG 59.637 50.000 9.77 0.00 0.00 4.63
274 275 2.387757 TCATGGTGAGATGACATCGGA 58.612 47.619 9.77 0.00 0.00 4.55
275 276 2.896745 TCATGGTGAGATGACATCGG 57.103 50.000 9.77 0.00 0.00 4.18
276 277 5.277683 GGATTTTCATGGTGAGATGACATCG 60.278 44.000 9.77 0.00 31.92 3.84
277 278 5.591472 TGGATTTTCATGGTGAGATGACATC 59.409 40.000 7.39 7.39 31.92 3.06
278 279 5.359009 GTGGATTTTCATGGTGAGATGACAT 59.641 40.000 0.00 0.00 31.92 3.06
279 280 4.701651 GTGGATTTTCATGGTGAGATGACA 59.298 41.667 0.00 0.00 31.92 3.58
280 281 4.701651 TGTGGATTTTCATGGTGAGATGAC 59.298 41.667 0.00 0.00 31.92 3.06
281 282 4.920999 TGTGGATTTTCATGGTGAGATGA 58.079 39.130 0.00 0.00 0.00 2.92
282 283 5.588240 CATGTGGATTTTCATGGTGAGATG 58.412 41.667 0.00 0.00 38.10 2.90
283 284 4.098960 GCATGTGGATTTTCATGGTGAGAT 59.901 41.667 7.15 0.00 40.91 2.75
284 285 3.444742 GCATGTGGATTTTCATGGTGAGA 59.555 43.478 7.15 0.00 40.91 3.27
285 286 3.193903 TGCATGTGGATTTTCATGGTGAG 59.806 43.478 7.15 0.00 40.91 3.51
286 287 3.056678 GTGCATGTGGATTTTCATGGTGA 60.057 43.478 0.00 0.00 40.91 4.02
287 288 3.255725 GTGCATGTGGATTTTCATGGTG 58.744 45.455 0.00 0.00 40.91 4.17
288 289 2.234414 GGTGCATGTGGATTTTCATGGT 59.766 45.455 0.00 0.00 40.91 3.55
289 290 2.498481 AGGTGCATGTGGATTTTCATGG 59.502 45.455 0.00 0.00 40.91 3.66
290 291 3.880047 AGGTGCATGTGGATTTTCATG 57.120 42.857 0.00 0.00 42.71 3.07
291 292 4.858850 TCTAGGTGCATGTGGATTTTCAT 58.141 39.130 0.00 0.00 0.00 2.57
292 293 4.299586 TCTAGGTGCATGTGGATTTTCA 57.700 40.909 0.00 0.00 0.00 2.69
293 294 5.643379 TTTCTAGGTGCATGTGGATTTTC 57.357 39.130 0.00 0.00 0.00 2.29
294 295 6.610075 ATTTTCTAGGTGCATGTGGATTTT 57.390 33.333 0.00 0.00 0.00 1.82
295 296 6.610075 AATTTTCTAGGTGCATGTGGATTT 57.390 33.333 0.00 0.00 0.00 2.17
296 297 6.610075 AAATTTTCTAGGTGCATGTGGATT 57.390 33.333 0.00 0.00 0.00 3.01
297 298 7.631377 GCTTAAATTTTCTAGGTGCATGTGGAT 60.631 37.037 0.00 0.00 0.00 3.41
298 299 6.350110 GCTTAAATTTTCTAGGTGCATGTGGA 60.350 38.462 0.00 0.00 0.00 4.02
299 300 5.807011 GCTTAAATTTTCTAGGTGCATGTGG 59.193 40.000 0.00 0.00 0.00 4.17
300 301 6.389091 TGCTTAAATTTTCTAGGTGCATGTG 58.611 36.000 0.00 0.00 0.00 3.21
301 302 6.588719 TGCTTAAATTTTCTAGGTGCATGT 57.411 33.333 0.00 0.00 0.00 3.21
302 303 7.486647 AGATGCTTAAATTTTCTAGGTGCATG 58.513 34.615 0.00 0.00 38.50 4.06
303 304 7.651027 AGATGCTTAAATTTTCTAGGTGCAT 57.349 32.000 0.00 0.00 40.63 3.96
304 305 7.466746 AAGATGCTTAAATTTTCTAGGTGCA 57.533 32.000 0.00 0.00 0.00 4.57
305 306 8.177980 CAAAGATGCTTAAATTTTCTAGGTGC 57.822 34.615 0.00 0.00 0.00 5.01
382 383 8.871686 AATTAGAAAACTGTCTCGCAATTTTT 57.128 26.923 0.00 0.00 36.75 1.94
383 384 8.871686 AAATTAGAAAACTGTCTCGCAATTTT 57.128 26.923 9.68 0.00 38.94 1.82
384 385 8.871686 AAAATTAGAAAACTGTCTCGCAATTT 57.128 26.923 9.68 9.68 0.00 1.82
385 386 8.871686 AAAAATTAGAAAACTGTCTCGCAATT 57.128 26.923 0.00 0.00 0.00 2.32
427 428 6.018588 TCCCGTGCGTGAACAATAAATAATAG 60.019 38.462 0.00 0.00 0.00 1.73
430 431 4.001652 TCCCGTGCGTGAACAATAAATAA 58.998 39.130 0.00 0.00 0.00 1.40
466 470 4.990426 CGAAATTTCTGCATCCAGGTTTTT 59.010 37.500 15.92 0.00 39.61 1.94
467 471 4.559153 CGAAATTTCTGCATCCAGGTTTT 58.441 39.130 15.92 0.00 39.61 2.43
468 472 3.614870 GCGAAATTTCTGCATCCAGGTTT 60.615 43.478 21.83 0.00 39.61 3.27
470 474 1.474077 GCGAAATTTCTGCATCCAGGT 59.526 47.619 21.83 0.00 39.61 4.00
472 476 1.202336 GGGCGAAATTTCTGCATCCAG 60.202 52.381 25.38 8.53 40.54 3.86
473 477 0.817013 GGGCGAAATTTCTGCATCCA 59.183 50.000 25.38 0.00 0.00 3.41
474 478 1.066152 GAGGGCGAAATTTCTGCATCC 59.934 52.381 25.38 20.29 0.00 3.51
485 489 0.918983 AATGGATCTGGAGGGCGAAA 59.081 50.000 0.00 0.00 0.00 3.46
486 490 0.918983 AAATGGATCTGGAGGGCGAA 59.081 50.000 0.00 0.00 0.00 4.70
490 494 2.511218 TCCTTGAAATGGATCTGGAGGG 59.489 50.000 0.00 0.00 34.87 4.30
508 512 4.724279 ACTATATGGGCCGAAATTTCCT 57.276 40.909 12.54 0.00 0.00 3.36
510 514 6.465084 ACTCTACTATATGGGCCGAAATTTC 58.535 40.000 8.20 8.20 0.00 2.17
514 518 5.834742 TGTTACTCTACTATATGGGCCGAAA 59.165 40.000 0.00 0.00 0.00 3.46
554 558 1.807142 CGGAGTTCTTTTTCTCAGGGC 59.193 52.381 0.00 0.00 32.93 5.19
555 559 3.402628 TCGGAGTTCTTTTTCTCAGGG 57.597 47.619 0.00 0.00 32.93 4.45
558 562 4.036380 GGCTTTTCGGAGTTCTTTTTCTCA 59.964 41.667 0.00 0.00 32.93 3.27
571 582 1.220749 CTCATCGGGGCTTTTCGGA 59.779 57.895 0.00 0.00 0.00 4.55
575 586 4.654262 TCTTACTATCTCATCGGGGCTTTT 59.346 41.667 0.00 0.00 0.00 2.27
1194 1222 2.203640 TCGAGTGTGTGGGGCTCT 60.204 61.111 0.00 0.00 0.00 4.09
1303 1332 1.067582 CAGCGGGGTAGATCGGAAC 59.932 63.158 0.00 0.00 0.00 3.62
1352 1381 1.032014 ACAAAATCACAAGCCACGCT 58.968 45.000 0.00 0.00 42.56 5.07
1365 1415 5.593909 TCACATCAACCTGAGACAACAAAAT 59.406 36.000 0.00 0.00 0.00 1.82
1814 1873 4.344968 TCATAGCTGCTAGCATTGGAGTTA 59.655 41.667 19.72 8.84 45.56 2.24
2051 2110 3.261677 GGGCCACCCTGGTAACCA 61.262 66.667 4.39 0.00 41.34 3.67
2108 2167 0.552848 CCCCAGTGCCATAACCAGAT 59.447 55.000 0.00 0.00 0.00 2.90
2611 2670 0.916086 TAACCGGCAGAATGGATGGT 59.084 50.000 0.00 0.00 35.86 3.55
2774 2833 1.972872 AGCAACCTGAAACTCCACTG 58.027 50.000 0.00 0.00 0.00 3.66
2935 3004 1.133823 AGATGAACACAACCACCAGCA 60.134 47.619 0.00 0.00 0.00 4.41
3004 3073 5.287035 GCAAGCCGTCAAATTTGAAGAATAG 59.713 40.000 28.59 18.30 38.67 1.73
3074 3144 2.292267 CCATCCGTTTGAAGCAGCTAT 58.708 47.619 0.00 0.00 0.00 2.97
3092 3162 0.105964 AAGCGCACTACACTTGACCA 59.894 50.000 11.47 0.00 0.00 4.02
3106 3176 4.939509 TTCCAGTTACATAAAGAAGCGC 57.060 40.909 0.00 0.00 0.00 5.92
3292 3365 8.237811 TCTCTATCACTGCAAACATACTATCA 57.762 34.615 0.00 0.00 0.00 2.15
3300 3373 3.969287 AGCTCTCTATCACTGCAAACA 57.031 42.857 0.00 0.00 0.00 2.83
3383 3456 7.365497 ACCTGTACATCATTCATCATGTAGA 57.635 36.000 0.00 0.00 36.40 2.59
3429 3502 4.888326 ATTTTACTTGCCAAATGCCTCA 57.112 36.364 0.00 0.00 40.16 3.86
3583 3656 1.885233 TGTGCCAATGCTTCAAATCGA 59.115 42.857 0.00 0.00 38.71 3.59
3699 3772 6.415798 AAACGATTTTCCAAACAAAACTGG 57.584 33.333 0.00 0.00 0.00 4.00
3764 3837 5.189736 AGGACATACCAAATCTACAGAGCAA 59.810 40.000 0.00 0.00 42.04 3.91
3915 4022 6.368779 AGTGTAAGCCTGTGGAAATTACTA 57.631 37.500 0.00 0.00 0.00 1.82
4005 4119 1.068610 GCTATCGCTGGTGTTTTTGCA 60.069 47.619 0.00 0.00 0.00 4.08
4048 4173 2.080693 AGAGCAGTGACGTCAGTAGAG 58.919 52.381 24.83 14.28 0.00 2.43
4185 4318 2.450476 GGACGGAGGGAGTAGTGTTTA 58.550 52.381 0.00 0.00 0.00 2.01
4187 4320 0.614134 GGGACGGAGGGAGTAGTGTT 60.614 60.000 0.00 0.00 0.00 3.32
4204 4337 4.211374 GCAAGCTACGTCTTATATTGTGGG 59.789 45.833 0.00 0.00 0.00 4.61
4230 4363 7.394816 CCTCCGTCCCATAATATAAGACATTT 58.605 38.462 0.00 0.00 0.00 2.32
4233 4366 4.775780 CCCTCCGTCCCATAATATAAGACA 59.224 45.833 0.00 0.00 0.00 3.41
4249 4382 3.393426 TTTAGGATGTACTCCCTCCGT 57.607 47.619 9.41 0.00 46.27 4.69
4326 4671 9.899661 ACTGGTTTTTATGTCAGCATATAGTAA 57.100 29.630 0.00 0.00 37.42 2.24
4441 4800 6.919662 CCGGTAACTCAGCTAAAATATCGTTA 59.080 38.462 0.00 0.00 0.00 3.18
4442 4801 5.751990 CCGGTAACTCAGCTAAAATATCGTT 59.248 40.000 0.00 0.00 0.00 3.85
4443 4802 5.163478 ACCGGTAACTCAGCTAAAATATCGT 60.163 40.000 4.49 0.00 0.00 3.73
4444 4803 5.287226 ACCGGTAACTCAGCTAAAATATCG 58.713 41.667 4.49 0.00 0.00 2.92
4457 4816 9.591792 AATAAACTACAGATTAACCGGTAACTC 57.408 33.333 8.00 4.65 0.00 3.01


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

AutoCloner maintained by Alex Coulton.