Multiple sequence alignment - TraesCS2A01G145300

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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 TraesCS2A01G145300 chr2A 100.000 3596 0 0 1 3596 90415561 90419156 0.000000e+00 6641.0
1 TraesCS2A01G145300 chr2D 95.305 3365 119 13 243 3596 90500172 90503508 0.000000e+00 5302.0
2 TraesCS2A01G145300 chr2B 96.246 3117 111 5 485 3596 143272650 143275765 0.000000e+00 5103.0
3 TraesCS2A01G145300 chr2B 89.091 55 6 0 1 55 421665186 421665132 6.440000e-08 69.4
4 TraesCS2A01G145300 chr1D 91.082 2153 191 1 543 2694 476255828 476253676 0.000000e+00 2911.0
5 TraesCS2A01G145300 chr1B 90.989 2153 193 1 543 2694 662555084 662552932 0.000000e+00 2900.0
6 TraesCS2A01G145300 chr1A 90.711 2153 199 1 543 2694 572019135 572016983 0.000000e+00 2867.0
7 TraesCS2A01G145300 chr3D 96.875 32 1 0 76 107 533413788 533413819 2.000000e-03 54.7


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 TraesCS2A01G145300 chr2A 90415561 90419156 3595 False 6641 6641 100.000 1 3596 1 chr2A.!!$F1 3595
1 TraesCS2A01G145300 chr2D 90500172 90503508 3336 False 5302 5302 95.305 243 3596 1 chr2D.!!$F1 3353
2 TraesCS2A01G145300 chr2B 143272650 143275765 3115 False 5103 5103 96.246 485 3596 1 chr2B.!!$F1 3111
3 TraesCS2A01G145300 chr1D 476253676 476255828 2152 True 2911 2911 91.082 543 2694 1 chr1D.!!$R1 2151
4 TraesCS2A01G145300 chr1B 662552932 662555084 2152 True 2900 2900 90.989 543 2694 1 chr1B.!!$R1 2151
5 TraesCS2A01G145300 chr1A 572016983 572019135 2152 True 2867 2867 90.711 543 2694 1 chr1A.!!$R1 2151

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
172 173 0.027586 GCTAAAATAGCGCCACCGTG 59.972 55.0 2.29 0.00 42.62 4.94 F
180 181 0.107897 AGCGCCACCGTGAAATATCA 60.108 50.0 2.29 0.00 36.67 2.15 F
1672 1675 0.179076 CTCTATGCCATGGCGTGACA 60.179 55.0 36.66 19.32 45.51 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1337 1340 0.383860 CAAAACCTCGAACGCGGAAC 60.384 55.0 12.47 0.0 38.28 3.62 R
1899 1902 0.390124 ACAGCAAACCAACCATGCAG 59.610 50.0 0.00 0.0 42.45 4.41 R
3053 3058 0.972983 ACCTGGATCTGCTACAGCGT 60.973 55.0 0.00 0.0 45.83 5.07 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
29 30 8.855279 TCTGTTTTTATTTCATATTTTTCGGCG 58.145 29.630 0.00 0.00 0.00 6.46
30 31 8.744008 TGTTTTTATTTCATATTTTTCGGCGA 57.256 26.923 4.99 4.99 0.00 5.54
31 32 9.360093 TGTTTTTATTTCATATTTTTCGGCGAT 57.640 25.926 11.76 0.00 0.00 4.58
32 33 9.618410 GTTTTTATTTCATATTTTTCGGCGATG 57.382 29.630 11.76 4.79 0.00 3.84
33 34 8.918961 TTTTATTTCATATTTTTCGGCGATGT 57.081 26.923 11.76 0.00 0.00 3.06
34 35 8.918961 TTTATTTCATATTTTTCGGCGATGTT 57.081 26.923 11.76 0.00 0.00 2.71
35 36 8.555166 TTATTTCATATTTTTCGGCGATGTTC 57.445 30.769 11.76 0.00 0.00 3.18
36 37 4.190304 TCATATTTTTCGGCGATGTTCG 57.810 40.909 11.76 0.00 43.89 3.95
37 38 3.619483 TCATATTTTTCGGCGATGTTCGT 59.381 39.130 11.76 0.00 42.81 3.85
38 39 2.981400 ATTTTTCGGCGATGTTCGTT 57.019 40.000 11.76 0.00 42.81 3.85
39 40 2.759538 TTTTTCGGCGATGTTCGTTT 57.240 40.000 11.76 0.00 42.81 3.60
40 41 2.025544 TTTTCGGCGATGTTCGTTTG 57.974 45.000 11.76 0.00 42.81 2.93
41 42 1.218763 TTTCGGCGATGTTCGTTTGA 58.781 45.000 11.76 0.00 42.81 2.69
42 43 1.434555 TTCGGCGATGTTCGTTTGAT 58.565 45.000 11.76 0.00 42.81 2.57
43 44 0.718904 TCGGCGATGTTCGTTTGATG 59.281 50.000 4.99 0.00 42.81 3.07
44 45 0.247655 CGGCGATGTTCGTTTGATGG 60.248 55.000 0.00 0.00 42.81 3.51
45 46 0.098728 GGCGATGTTCGTTTGATGGG 59.901 55.000 0.00 0.00 42.81 4.00
46 47 1.083489 GCGATGTTCGTTTGATGGGA 58.917 50.000 0.00 0.00 42.81 4.37
47 48 1.062587 GCGATGTTCGTTTGATGGGAG 59.937 52.381 0.00 0.00 42.81 4.30
48 49 1.665679 CGATGTTCGTTTGATGGGAGG 59.334 52.381 0.00 0.00 34.72 4.30
49 50 2.676750 CGATGTTCGTTTGATGGGAGGA 60.677 50.000 0.00 0.00 34.72 3.71
50 51 2.940994 TGTTCGTTTGATGGGAGGAA 57.059 45.000 0.00 0.00 0.00 3.36
51 52 3.216187 TGTTCGTTTGATGGGAGGAAA 57.784 42.857 0.00 0.00 0.00 3.13
52 53 2.882137 TGTTCGTTTGATGGGAGGAAAC 59.118 45.455 0.00 0.00 0.00 2.78
54 55 1.519408 CGTTTGATGGGAGGAAACGT 58.481 50.000 0.00 0.00 44.27 3.99
55 56 1.877443 CGTTTGATGGGAGGAAACGTT 59.123 47.619 0.00 0.00 44.27 3.99
56 57 2.292292 CGTTTGATGGGAGGAAACGTTT 59.708 45.455 14.57 14.57 44.27 3.60
57 58 3.608474 CGTTTGATGGGAGGAAACGTTTC 60.608 47.826 28.83 28.83 44.27 2.78
71 72 6.592348 GAAACGTTTCCATCAAATACGAAC 57.408 37.500 27.01 0.00 36.21 3.95
72 73 4.673534 ACGTTTCCATCAAATACGAACC 57.326 40.909 0.00 0.00 36.21 3.62
73 74 4.066490 ACGTTTCCATCAAATACGAACCA 58.934 39.130 0.00 0.00 36.21 3.67
74 75 4.698304 ACGTTTCCATCAAATACGAACCAT 59.302 37.500 0.00 0.00 36.21 3.55
75 76 5.027737 CGTTTCCATCAAATACGAACCATG 58.972 41.667 0.00 0.00 34.36 3.66
76 77 5.391523 CGTTTCCATCAAATACGAACCATGT 60.392 40.000 0.00 0.00 34.36 3.21
77 78 5.559427 TTCCATCAAATACGAACCATGTG 57.441 39.130 0.00 0.00 0.00 3.21
78 79 4.584874 TCCATCAAATACGAACCATGTGT 58.415 39.130 0.00 0.00 0.00 3.72
79 80 5.735766 TCCATCAAATACGAACCATGTGTA 58.264 37.500 0.00 0.00 0.00 2.90
80 81 6.353323 TCCATCAAATACGAACCATGTGTAT 58.647 36.000 0.00 0.00 0.00 2.29
81 82 6.259829 TCCATCAAATACGAACCATGTGTATG 59.740 38.462 0.00 0.00 0.00 2.39
82 83 6.038161 CCATCAAATACGAACCATGTGTATGT 59.962 38.462 0.00 0.00 32.21 2.29
83 84 6.415798 TCAAATACGAACCATGTGTATGTG 57.584 37.500 0.00 7.80 35.87 3.21
84 85 5.352846 TCAAATACGAACCATGTGTATGTGG 59.647 40.000 11.66 0.00 35.46 4.17
85 86 2.107950 ACGAACCATGTGTATGTGGG 57.892 50.000 0.00 0.00 39.86 4.61
86 87 0.732571 CGAACCATGTGTATGTGGGC 59.267 55.000 0.00 0.00 39.86 5.36
87 88 1.832883 GAACCATGTGTATGTGGGCA 58.167 50.000 0.00 0.00 39.86 5.36
88 89 2.378038 GAACCATGTGTATGTGGGCAT 58.622 47.619 0.00 0.00 39.86 4.40
89 90 2.057137 ACCATGTGTATGTGGGCATC 57.943 50.000 0.00 0.00 39.86 3.91
90 91 1.565759 ACCATGTGTATGTGGGCATCT 59.434 47.619 0.00 0.00 39.86 2.90
91 92 2.777114 ACCATGTGTATGTGGGCATCTA 59.223 45.455 0.00 0.00 39.86 1.98
92 93 3.141398 CCATGTGTATGTGGGCATCTAC 58.859 50.000 0.00 0.00 36.58 2.59
93 94 2.595124 TGTGTATGTGGGCATCTACG 57.405 50.000 0.00 0.00 36.58 3.51
94 95 2.104170 TGTGTATGTGGGCATCTACGA 58.896 47.619 0.00 0.00 36.58 3.43
95 96 2.698274 TGTGTATGTGGGCATCTACGAT 59.302 45.455 0.00 0.00 36.58 3.73
96 97 3.133901 TGTGTATGTGGGCATCTACGATT 59.866 43.478 0.00 0.00 36.58 3.34
97 98 4.342665 TGTGTATGTGGGCATCTACGATTA 59.657 41.667 0.00 0.00 36.58 1.75
98 99 5.011635 TGTGTATGTGGGCATCTACGATTAT 59.988 40.000 0.00 0.00 36.58 1.28
99 100 6.209788 TGTGTATGTGGGCATCTACGATTATA 59.790 38.462 0.00 0.00 36.58 0.98
100 101 6.530534 GTGTATGTGGGCATCTACGATTATAC 59.469 42.308 0.00 0.00 36.58 1.47
101 102 6.436218 TGTATGTGGGCATCTACGATTATACT 59.564 38.462 0.00 0.00 36.58 2.12
102 103 5.134202 TGTGGGCATCTACGATTATACTG 57.866 43.478 0.00 0.00 0.00 2.74
103 104 4.587262 TGTGGGCATCTACGATTATACTGT 59.413 41.667 0.00 0.00 0.00 3.55
104 105 4.923871 GTGGGCATCTACGATTATACTGTG 59.076 45.833 0.00 0.00 0.00 3.66
105 106 4.587262 TGGGCATCTACGATTATACTGTGT 59.413 41.667 0.00 0.00 0.00 3.72
106 107 5.069914 TGGGCATCTACGATTATACTGTGTT 59.930 40.000 0.00 0.00 0.00 3.32
107 108 5.989777 GGGCATCTACGATTATACTGTGTTT 59.010 40.000 0.00 0.00 0.00 2.83
108 109 6.145696 GGGCATCTACGATTATACTGTGTTTC 59.854 42.308 0.00 0.00 0.00 2.78
109 110 6.700081 GGCATCTACGATTATACTGTGTTTCA 59.300 38.462 0.00 0.00 0.00 2.69
110 111 7.385205 GGCATCTACGATTATACTGTGTTTCAT 59.615 37.037 0.00 0.00 0.00 2.57
111 112 9.406828 GCATCTACGATTATACTGTGTTTCATA 57.593 33.333 0.00 0.00 0.00 2.15
133 134 9.342308 TCATAAAACAAAAATGCCAAAATACCA 57.658 25.926 0.00 0.00 0.00 3.25
136 137 8.868635 AAAACAAAAATGCCAAAATACCATTG 57.131 26.923 0.00 0.00 30.26 2.82
137 138 6.011476 ACAAAAATGCCAAAATACCATTGC 57.989 33.333 0.00 0.00 30.26 3.56
138 139 5.769162 ACAAAAATGCCAAAATACCATTGCT 59.231 32.000 0.00 0.00 30.26 3.91
139 140 6.939163 ACAAAAATGCCAAAATACCATTGCTA 59.061 30.769 0.00 0.00 30.26 3.49
140 141 7.611079 ACAAAAATGCCAAAATACCATTGCTAT 59.389 29.630 0.00 0.00 30.26 2.97
141 142 8.460428 CAAAAATGCCAAAATACCATTGCTATT 58.540 29.630 0.00 0.00 30.26 1.73
142 143 8.578448 AAAATGCCAAAATACCATTGCTATTT 57.422 26.923 0.00 0.00 30.26 1.40
143 144 8.578448 AAATGCCAAAATACCATTGCTATTTT 57.422 26.923 4.54 4.54 35.21 1.82
144 145 6.981762 TGCCAAAATACCATTGCTATTTTG 57.018 33.333 20.59 20.59 44.30 2.44
154 155 7.376435 ACCATTGCTATTTTGGTTTTTATGC 57.624 32.000 0.00 0.00 40.87 3.14
155 156 7.167535 ACCATTGCTATTTTGGTTTTTATGCT 58.832 30.769 0.00 0.00 40.87 3.79
156 157 8.317679 ACCATTGCTATTTTGGTTTTTATGCTA 58.682 29.630 0.00 0.00 40.87 3.49
157 158 9.160496 CCATTGCTATTTTGGTTTTTATGCTAA 57.840 29.630 0.00 0.00 0.00 3.09
171 172 2.390427 GCTAAAATAGCGCCACCGT 58.610 52.632 2.29 0.00 42.62 4.83
172 173 0.027586 GCTAAAATAGCGCCACCGTG 59.972 55.000 2.29 0.00 42.62 4.94
173 174 1.647346 CTAAAATAGCGCCACCGTGA 58.353 50.000 2.29 0.00 36.67 4.35
174 175 2.004017 CTAAAATAGCGCCACCGTGAA 58.996 47.619 2.29 0.00 36.67 3.18
175 176 1.240256 AAAATAGCGCCACCGTGAAA 58.760 45.000 2.29 0.00 36.67 2.69
176 177 1.459450 AAATAGCGCCACCGTGAAAT 58.541 45.000 2.29 0.00 36.67 2.17
177 178 2.319136 AATAGCGCCACCGTGAAATA 57.681 45.000 2.29 0.00 36.67 1.40
178 179 2.543777 ATAGCGCCACCGTGAAATAT 57.456 45.000 2.29 0.00 36.67 1.28
179 180 1.860676 TAGCGCCACCGTGAAATATC 58.139 50.000 2.29 0.00 36.67 1.63
180 181 0.107897 AGCGCCACCGTGAAATATCA 60.108 50.000 2.29 0.00 36.67 2.15
181 182 0.730265 GCGCCACCGTGAAATATCAA 59.270 50.000 0.00 0.00 37.30 2.57
182 183 1.531058 GCGCCACCGTGAAATATCAAC 60.531 52.381 0.00 0.00 37.30 3.18
183 184 1.735018 CGCCACCGTGAAATATCAACA 59.265 47.619 0.00 0.00 37.30 3.33
184 185 2.354510 CGCCACCGTGAAATATCAACAT 59.645 45.455 0.00 0.00 37.30 2.71
185 186 3.558006 CGCCACCGTGAAATATCAACATA 59.442 43.478 0.00 0.00 37.30 2.29
186 187 4.213270 CGCCACCGTGAAATATCAACATAT 59.787 41.667 0.00 0.00 37.30 1.78
187 188 5.614668 CGCCACCGTGAAATATCAACATATC 60.615 44.000 0.00 0.00 37.30 1.63
188 189 5.238432 GCCACCGTGAAATATCAACATATCA 59.762 40.000 0.00 0.00 37.30 2.15
189 190 6.072508 GCCACCGTGAAATATCAACATATCAT 60.073 38.462 0.00 0.00 37.30 2.45
190 191 7.300320 CCACCGTGAAATATCAACATATCATG 58.700 38.462 0.00 0.00 37.30 3.07
205 206 7.643569 ACATATCATGTTAGCCAAATTGTGA 57.356 32.000 0.00 0.00 41.63 3.58
206 207 8.065473 ACATATCATGTTAGCCAAATTGTGAA 57.935 30.769 0.00 0.00 41.63 3.18
207 208 8.698210 ACATATCATGTTAGCCAAATTGTGAAT 58.302 29.630 0.00 0.00 41.63 2.57
210 211 6.563422 TCATGTTAGCCAAATTGTGAATAGC 58.437 36.000 0.00 0.00 0.00 2.97
211 212 4.980590 TGTTAGCCAAATTGTGAATAGCG 58.019 39.130 0.00 0.00 0.00 4.26
212 213 4.457603 TGTTAGCCAAATTGTGAATAGCGT 59.542 37.500 0.00 0.00 0.00 5.07
213 214 5.048364 TGTTAGCCAAATTGTGAATAGCGTT 60.048 36.000 0.00 0.00 0.00 4.84
214 215 4.519540 AGCCAAATTGTGAATAGCGTTT 57.480 36.364 0.00 0.00 0.00 3.60
215 216 4.881920 AGCCAAATTGTGAATAGCGTTTT 58.118 34.783 0.00 0.00 0.00 2.43
216 217 4.923281 AGCCAAATTGTGAATAGCGTTTTC 59.077 37.500 0.00 0.00 0.00 2.29
217 218 4.923281 GCCAAATTGTGAATAGCGTTTTCT 59.077 37.500 0.00 0.00 0.00 2.52
218 219 5.405269 GCCAAATTGTGAATAGCGTTTTCTT 59.595 36.000 0.00 0.00 0.00 2.52
219 220 6.399986 GCCAAATTGTGAATAGCGTTTTCTTC 60.400 38.462 0.00 0.00 0.00 2.87
220 221 6.863126 CCAAATTGTGAATAGCGTTTTCTTCT 59.137 34.615 0.00 0.00 0.00 2.85
221 222 7.382218 CCAAATTGTGAATAGCGTTTTCTTCTT 59.618 33.333 0.00 0.00 0.00 2.52
222 223 8.420189 CAAATTGTGAATAGCGTTTTCTTCTTC 58.580 33.333 0.00 0.00 0.00 2.87
223 224 6.861065 TTGTGAATAGCGTTTTCTTCTTCT 57.139 33.333 0.00 0.00 0.00 2.85
224 225 6.861065 TGTGAATAGCGTTTTCTTCTTCTT 57.139 33.333 0.00 0.00 0.00 2.52
225 226 7.259290 TGTGAATAGCGTTTTCTTCTTCTTT 57.741 32.000 0.00 0.00 0.00 2.52
226 227 7.703328 TGTGAATAGCGTTTTCTTCTTCTTTT 58.297 30.769 0.00 0.00 0.00 2.27
227 228 7.643764 TGTGAATAGCGTTTTCTTCTTCTTTTG 59.356 33.333 0.00 0.00 0.00 2.44
228 229 7.855904 GTGAATAGCGTTTTCTTCTTCTTTTGA 59.144 33.333 0.00 0.00 0.00 2.69
229 230 7.855904 TGAATAGCGTTTTCTTCTTCTTTTGAC 59.144 33.333 0.00 0.00 0.00 3.18
230 231 5.819825 AGCGTTTTCTTCTTCTTTTGACT 57.180 34.783 0.00 0.00 0.00 3.41
231 232 6.920569 AGCGTTTTCTTCTTCTTTTGACTA 57.079 33.333 0.00 0.00 0.00 2.59
232 233 6.716438 AGCGTTTTCTTCTTCTTTTGACTAC 58.284 36.000 0.00 0.00 0.00 2.73
233 234 6.315393 AGCGTTTTCTTCTTCTTTTGACTACA 59.685 34.615 0.00 0.00 0.00 2.74
234 235 6.629252 GCGTTTTCTTCTTCTTTTGACTACAG 59.371 38.462 0.00 0.00 0.00 2.74
235 236 7.676572 GCGTTTTCTTCTTCTTTTGACTACAGT 60.677 37.037 0.00 0.00 0.00 3.55
236 237 7.846592 CGTTTTCTTCTTCTTTTGACTACAGTC 59.153 37.037 2.29 2.29 44.97 3.51
266 267 5.713025 TGAATAGCTTGTCAGATTTTTGGC 58.287 37.500 0.00 0.00 0.00 4.52
270 271 4.312443 AGCTTGTCAGATTTTTGGCATTG 58.688 39.130 0.00 0.00 31.87 2.82
283 284 1.006998 TGGCATTGCAAGATTACCCCT 59.993 47.619 11.39 0.00 0.00 4.79
284 285 1.410153 GGCATTGCAAGATTACCCCTG 59.590 52.381 11.39 0.00 0.00 4.45
285 286 2.102578 GCATTGCAAGATTACCCCTGT 58.897 47.619 4.94 0.00 0.00 4.00
286 287 2.099756 GCATTGCAAGATTACCCCTGTC 59.900 50.000 4.94 0.00 0.00 3.51
287 288 3.355378 CATTGCAAGATTACCCCTGTCA 58.645 45.455 4.94 0.00 0.00 3.58
290 291 4.046286 TGCAAGATTACCCCTGTCAAAT 57.954 40.909 0.00 0.00 0.00 2.32
291 292 4.016444 TGCAAGATTACCCCTGTCAAATC 58.984 43.478 0.00 0.00 0.00 2.17
292 293 4.263905 TGCAAGATTACCCCTGTCAAATCT 60.264 41.667 0.00 0.00 39.70 2.40
293 294 4.706962 GCAAGATTACCCCTGTCAAATCTT 59.293 41.667 4.33 4.33 45.13 2.40
294 295 5.163612 GCAAGATTACCCCTGTCAAATCTTC 60.164 44.000 6.51 1.23 43.39 2.87
295 296 6.183347 CAAGATTACCCCTGTCAAATCTTCT 58.817 40.000 6.51 0.00 43.39 2.85
296 297 7.338710 CAAGATTACCCCTGTCAAATCTTCTA 58.661 38.462 6.51 0.00 43.39 2.10
297 298 7.698163 AGATTACCCCTGTCAAATCTTCTAT 57.302 36.000 0.00 0.00 35.65 1.98
298 299 7.740805 AGATTACCCCTGTCAAATCTTCTATC 58.259 38.462 0.00 0.00 35.65 2.08
423 424 4.222847 CTAGTTCCGCCGCCCTCC 62.223 72.222 0.00 0.00 0.00 4.30
433 434 2.757077 CGCCCTCCCTTGGTTCTT 59.243 61.111 0.00 0.00 0.00 2.52
492 493 0.321564 TGCTAGTCACTGCGCCATTT 60.322 50.000 4.18 0.00 0.00 2.32
501 502 1.097232 CTGCGCCATTTCCATTCTCA 58.903 50.000 4.18 0.00 0.00 3.27
540 541 4.008330 TCTCTACTTGTTAGCTACTGCGT 58.992 43.478 0.00 0.00 45.42 5.24
551 552 0.940126 CTACTGCGTCATTCCCATGC 59.060 55.000 0.00 0.00 0.00 4.06
650 651 4.641645 CGGGCAAGGCAGTCCACA 62.642 66.667 1.58 0.00 33.74 4.17
659 660 2.335011 CAGTCCACACGCAGACGA 59.665 61.111 0.00 0.00 43.93 4.20
668 669 2.343426 ACGCAGACGATCAGAGCCA 61.343 57.895 0.00 0.00 43.93 4.75
818 819 2.132352 GGATACGCTTCCTCCGGGT 61.132 63.158 0.00 0.00 32.68 5.28
911 913 4.602259 CCGCGACGGCCCATGTAT 62.602 66.667 8.23 0.00 41.17 2.29
914 916 2.504032 CGACGGCCCATGTATGGT 59.496 61.111 9.87 0.00 46.65 3.55
932 934 0.839946 GTGCTATGACATGGGGAGGT 59.160 55.000 0.00 0.00 0.00 3.85
940 942 1.224592 CATGGGGAGGTAGTGCCAC 59.775 63.158 0.00 0.00 38.84 5.01
1005 1008 2.032894 GCAACGCGTTCTGCATATGTAT 60.033 45.455 26.42 0.00 46.97 2.29
1189 1192 0.448593 TCATGTGTCGTATGTCGCGA 59.551 50.000 3.71 3.71 39.67 5.87
1328 1331 3.431673 TGGGAAATGTGAGTGTGCATA 57.568 42.857 0.00 0.00 0.00 3.14
1358 1361 2.604174 CCGCGTTCGAGGTTTTGCT 61.604 57.895 4.92 0.00 38.10 3.91
1437 1440 3.888323 TGTTTGAAGAGGCATTGCAGTTA 59.112 39.130 11.39 0.00 0.00 2.24
1533 1536 1.345415 CTTGCAGCCCTGAAAAATGGT 59.655 47.619 0.00 0.00 0.00 3.55
1672 1675 0.179076 CTCTATGCCATGGCGTGACA 60.179 55.000 36.66 19.32 45.51 3.58
1768 1771 7.884257 TCATGATATGTTGTTTGCTGAAGAAA 58.116 30.769 0.00 0.00 0.00 2.52
1899 1902 4.287766 ACCTGGAAGAGAACATTACACC 57.712 45.455 0.00 0.00 34.07 4.16
1960 1963 4.264253 TGAGGCAGAACACTTCATATTGG 58.736 43.478 0.00 0.00 0.00 3.16
2120 2123 8.183536 TGTTATGCTTTCTAACATGTATGCAAG 58.816 33.333 0.00 2.54 34.90 4.01
2165 2168 0.984230 AAGGTCCGGAAGCTGATGAA 59.016 50.000 5.23 0.00 35.40 2.57
2188 2191 0.903236 GAGGGGCGTTAGGAAAGAGT 59.097 55.000 0.00 0.00 0.00 3.24
2309 2312 6.098124 AGAGAGTTGATAGACCAGATCAAAGG 59.902 42.308 0.00 0.00 43.18 3.11
2614 2617 4.324254 GGTGATCCATACCTTGGTTCTCAA 60.324 45.833 0.00 0.00 46.52 3.02
2615 2618 5.440610 GTGATCCATACCTTGGTTCTCAAT 58.559 41.667 0.00 0.00 46.52 2.57
2991 2996 5.390461 CGGCGATATTTTCTTCTTTGACACA 60.390 40.000 0.00 0.00 0.00 3.72
3053 3058 3.320541 CCAGCAGGAACAAACAATGGTAA 59.679 43.478 0.00 0.00 36.89 2.85
3181 3187 4.776349 TGAGAACAAAGGAACTAGCACAA 58.224 39.130 0.00 0.00 38.49 3.33
3230 3236 2.068519 TGACAAGATAACAGCACAGCG 58.931 47.619 0.00 0.00 0.00 5.18
3244 3250 0.532573 ACAGCGACAACATCCTCGAT 59.467 50.000 0.00 0.00 31.24 3.59
3279 3285 4.101585 TGGATCCTCTTATCAGCGAATGTT 59.898 41.667 14.23 0.00 0.00 2.71
3293 3299 3.941483 GCGAATGTTATCCATCCCATAGG 59.059 47.826 0.00 0.00 31.75 2.57
3295 3301 5.338056 GCGAATGTTATCCATCCCATAGGTA 60.338 44.000 0.00 0.00 31.75 3.08
3337 3343 0.951558 GCCTGCTTGAAAGTTTCCGA 59.048 50.000 13.01 1.32 0.00 4.55
3399 3412 3.394719 TGTGTGCAGTTTGCTTACGATA 58.605 40.909 2.48 0.00 45.31 2.92
3494 3507 6.748198 TGGCGGCTAAACTAATAAAATTTTCG 59.252 34.615 11.43 1.55 0.00 3.46
3496 3509 7.044510 GGCGGCTAAACTAATAAAATTTTCGTC 60.045 37.037 6.72 0.00 0.00 4.20
3510 3523 8.970691 AAAATTTTCGTCAAGTATCAATGAGG 57.029 30.769 0.00 0.00 33.83 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 8.855279 CGCCGAAAAATATGAAATAAAAACAGA 58.145 29.630 0.00 0.00 29.06 3.41
4 5 8.855279 TCGCCGAAAAATATGAAATAAAAACAG 58.145 29.630 0.00 0.00 29.06 3.16
5 6 8.744008 TCGCCGAAAAATATGAAATAAAAACA 57.256 26.923 0.00 0.00 29.06 2.83
6 7 9.618410 CATCGCCGAAAAATATGAAATAAAAAC 57.382 29.630 0.00 0.00 29.06 2.43
7 8 9.360093 ACATCGCCGAAAAATATGAAATAAAAA 57.640 25.926 0.00 0.00 29.06 1.94
8 9 8.918961 ACATCGCCGAAAAATATGAAATAAAA 57.081 26.923 0.00 0.00 29.06 1.52
9 10 8.918961 AACATCGCCGAAAAATATGAAATAAA 57.081 26.923 0.00 0.00 29.06 1.40
10 11 7.374754 CGAACATCGCCGAAAAATATGAAATAA 59.625 33.333 0.00 0.00 31.14 1.40
11 12 6.848800 CGAACATCGCCGAAAAATATGAAATA 59.151 34.615 0.00 0.00 31.14 1.40
12 13 5.681105 CGAACATCGCCGAAAAATATGAAAT 59.319 36.000 0.00 0.00 31.14 2.17
13 14 5.025190 CGAACATCGCCGAAAAATATGAAA 58.975 37.500 0.00 0.00 31.14 2.69
14 15 4.093703 ACGAACATCGCCGAAAAATATGAA 59.906 37.500 0.00 0.00 45.12 2.57
15 16 3.619483 ACGAACATCGCCGAAAAATATGA 59.381 39.130 0.00 0.00 45.12 2.15
16 17 3.935450 ACGAACATCGCCGAAAAATATG 58.065 40.909 0.00 0.00 45.12 1.78
17 18 4.609691 AACGAACATCGCCGAAAAATAT 57.390 36.364 0.00 0.00 45.12 1.28
18 19 4.083961 TCAAACGAACATCGCCGAAAAATA 60.084 37.500 0.00 0.00 45.12 1.40
19 20 2.977169 CAAACGAACATCGCCGAAAAAT 59.023 40.909 0.00 0.00 45.12 1.82
20 21 2.031807 TCAAACGAACATCGCCGAAAAA 59.968 40.909 0.00 0.00 45.12 1.94
21 22 1.598132 TCAAACGAACATCGCCGAAAA 59.402 42.857 0.00 0.00 45.12 2.29
22 23 1.218763 TCAAACGAACATCGCCGAAA 58.781 45.000 0.00 0.00 45.12 3.46
23 24 1.127766 CATCAAACGAACATCGCCGAA 59.872 47.619 0.00 0.00 45.12 4.30
24 25 0.718904 CATCAAACGAACATCGCCGA 59.281 50.000 0.00 0.00 45.12 5.54
25 26 0.247655 CCATCAAACGAACATCGCCG 60.248 55.000 0.00 0.00 45.12 6.46
26 27 0.098728 CCCATCAAACGAACATCGCC 59.901 55.000 0.00 0.00 45.12 5.54
27 28 1.062587 CTCCCATCAAACGAACATCGC 59.937 52.381 0.00 0.00 45.12 4.58
28 29 1.665679 CCTCCCATCAAACGAACATCG 59.334 52.381 0.00 0.00 46.93 3.84
29 30 2.985896 TCCTCCCATCAAACGAACATC 58.014 47.619 0.00 0.00 0.00 3.06
30 31 3.433306 TTCCTCCCATCAAACGAACAT 57.567 42.857 0.00 0.00 0.00 2.71
31 32 2.882137 GTTTCCTCCCATCAAACGAACA 59.118 45.455 0.00 0.00 0.00 3.18
32 33 3.554259 GTTTCCTCCCATCAAACGAAC 57.446 47.619 0.00 0.00 0.00 3.95
36 37 3.897325 GAAACGTTTCCTCCCATCAAAC 58.103 45.455 27.01 1.00 0.00 2.93
48 49 5.566395 GGTTCGTATTTGATGGAAACGTTTC 59.434 40.000 28.83 28.83 35.21 2.78
49 50 5.008811 TGGTTCGTATTTGATGGAAACGTTT 59.991 36.000 14.57 14.57 35.21 3.60
50 51 4.515944 TGGTTCGTATTTGATGGAAACGTT 59.484 37.500 0.00 0.00 35.21 3.99
51 52 4.066490 TGGTTCGTATTTGATGGAAACGT 58.934 39.130 0.00 0.00 35.21 3.99
52 53 4.671880 TGGTTCGTATTTGATGGAAACG 57.328 40.909 0.00 0.00 34.99 3.60
53 54 5.799936 CACATGGTTCGTATTTGATGGAAAC 59.200 40.000 0.00 0.00 0.00 2.78
54 55 5.475220 ACACATGGTTCGTATTTGATGGAAA 59.525 36.000 0.00 0.00 0.00 3.13
55 56 5.007034 ACACATGGTTCGTATTTGATGGAA 58.993 37.500 0.00 0.00 0.00 3.53
56 57 4.584874 ACACATGGTTCGTATTTGATGGA 58.415 39.130 0.00 0.00 0.00 3.41
57 58 4.963276 ACACATGGTTCGTATTTGATGG 57.037 40.909 0.00 0.00 0.00 3.51
58 59 6.906678 CACATACACATGGTTCGTATTTGATG 59.093 38.462 0.00 0.00 36.39 3.07
59 60 6.038161 CCACATACACATGGTTCGTATTTGAT 59.962 38.462 0.00 0.00 36.39 2.57
60 61 5.352846 CCACATACACATGGTTCGTATTTGA 59.647 40.000 0.00 0.00 36.39 2.69
61 62 5.448496 CCCACATACACATGGTTCGTATTTG 60.448 44.000 0.00 2.49 36.39 2.32
62 63 4.638421 CCCACATACACATGGTTCGTATTT 59.362 41.667 0.00 0.00 36.39 1.40
63 64 4.196193 CCCACATACACATGGTTCGTATT 58.804 43.478 0.00 0.00 36.39 1.89
64 65 3.804036 CCCACATACACATGGTTCGTAT 58.196 45.455 0.00 0.00 36.39 3.06
65 66 2.678479 GCCCACATACACATGGTTCGTA 60.678 50.000 0.00 0.00 36.39 3.43
66 67 1.948611 GCCCACATACACATGGTTCGT 60.949 52.381 0.00 0.00 36.39 3.85
67 68 0.732571 GCCCACATACACATGGTTCG 59.267 55.000 0.00 0.00 36.39 3.95
68 69 1.832883 TGCCCACATACACATGGTTC 58.167 50.000 0.00 0.00 36.39 3.62
69 70 2.025037 AGATGCCCACATACACATGGTT 60.025 45.455 0.00 0.00 36.35 3.67
70 71 1.565759 AGATGCCCACATACACATGGT 59.434 47.619 0.00 0.00 36.35 3.55
71 72 2.353357 AGATGCCCACATACACATGG 57.647 50.000 0.00 0.00 36.35 3.66
72 73 2.802247 CGTAGATGCCCACATACACATG 59.198 50.000 0.00 0.00 36.35 3.21
73 74 2.698274 TCGTAGATGCCCACATACACAT 59.302 45.455 0.00 0.00 36.35 3.21
74 75 2.104170 TCGTAGATGCCCACATACACA 58.896 47.619 0.00 0.00 36.35 3.72
75 76 2.882927 TCGTAGATGCCCACATACAC 57.117 50.000 0.00 0.00 36.35 2.90
76 77 5.738619 ATAATCGTAGATGCCCACATACA 57.261 39.130 0.00 0.00 45.12 2.29
77 78 6.752351 CAGTATAATCGTAGATGCCCACATAC 59.248 42.308 0.00 0.00 45.12 2.39
78 79 6.436218 ACAGTATAATCGTAGATGCCCACATA 59.564 38.462 0.00 0.00 45.12 2.29
79 80 5.246203 ACAGTATAATCGTAGATGCCCACAT 59.754 40.000 0.00 0.00 45.12 3.21
80 81 4.587262 ACAGTATAATCGTAGATGCCCACA 59.413 41.667 0.00 0.00 45.12 4.17
81 82 4.923871 CACAGTATAATCGTAGATGCCCAC 59.076 45.833 0.00 0.00 45.12 4.61
82 83 4.587262 ACACAGTATAATCGTAGATGCCCA 59.413 41.667 0.00 0.00 45.12 5.36
83 84 5.135508 ACACAGTATAATCGTAGATGCCC 57.864 43.478 0.00 0.00 45.12 5.36
84 85 6.700081 TGAAACACAGTATAATCGTAGATGCC 59.300 38.462 0.00 0.00 45.12 4.40
85 86 7.694388 TGAAACACAGTATAATCGTAGATGC 57.306 36.000 0.00 0.00 45.12 3.91
107 108 9.342308 TGGTATTTTGGCATTTTTGTTTTATGA 57.658 25.926 0.00 0.00 0.00 2.15
110 111 9.956720 CAATGGTATTTTGGCATTTTTGTTTTA 57.043 25.926 0.00 0.00 0.00 1.52
111 112 7.437565 GCAATGGTATTTTGGCATTTTTGTTTT 59.562 29.630 0.00 0.00 0.00 2.43
112 113 6.922407 GCAATGGTATTTTGGCATTTTTGTTT 59.078 30.769 0.00 0.00 0.00 2.83
113 114 6.264970 AGCAATGGTATTTTGGCATTTTTGTT 59.735 30.769 0.00 0.00 0.00 2.83
114 115 5.769162 AGCAATGGTATTTTGGCATTTTTGT 59.231 32.000 0.00 0.00 0.00 2.83
115 116 6.256912 AGCAATGGTATTTTGGCATTTTTG 57.743 33.333 0.00 0.00 0.00 2.44
116 117 8.578448 AATAGCAATGGTATTTTGGCATTTTT 57.422 26.923 11.46 0.00 33.22 1.94
117 118 8.578448 AAATAGCAATGGTATTTTGGCATTTT 57.422 26.923 20.70 1.33 41.45 1.82
118 119 8.578448 AAAATAGCAATGGTATTTTGGCATTT 57.422 26.923 30.42 13.60 46.96 2.32
128 129 9.108284 GCATAAAAACCAAAATAGCAATGGTAT 57.892 29.630 0.00 0.00 46.46 2.73
129 130 8.317679 AGCATAAAAACCAAAATAGCAATGGTA 58.682 29.630 0.00 0.00 46.46 3.25
131 132 7.614124 AGCATAAAAACCAAAATAGCAATGG 57.386 32.000 0.00 0.00 40.16 3.16
154 155 1.647346 TCACGGTGGCGCTATTTTAG 58.353 50.000 7.64 0.00 0.00 1.85
155 156 2.096220 TTCACGGTGGCGCTATTTTA 57.904 45.000 7.64 0.00 0.00 1.52
156 157 1.240256 TTTCACGGTGGCGCTATTTT 58.760 45.000 7.64 0.00 0.00 1.82
157 158 1.459450 ATTTCACGGTGGCGCTATTT 58.541 45.000 7.64 0.00 0.00 1.40
158 159 2.319136 TATTTCACGGTGGCGCTATT 57.681 45.000 7.64 0.00 0.00 1.73
159 160 2.224185 TGATATTTCACGGTGGCGCTAT 60.224 45.455 7.64 1.35 0.00 2.97
160 161 1.137282 TGATATTTCACGGTGGCGCTA 59.863 47.619 7.64 0.00 0.00 4.26
161 162 0.107897 TGATATTTCACGGTGGCGCT 60.108 50.000 7.64 0.00 0.00 5.92
162 163 0.730265 TTGATATTTCACGGTGGCGC 59.270 50.000 8.50 0.00 0.00 6.53
163 164 1.735018 TGTTGATATTTCACGGTGGCG 59.265 47.619 8.50 0.00 0.00 5.69
164 165 5.238432 TGATATGTTGATATTTCACGGTGGC 59.762 40.000 8.50 0.00 0.00 5.01
165 166 6.859420 TGATATGTTGATATTTCACGGTGG 57.141 37.500 8.50 0.00 0.00 4.61
166 167 7.864686 ACATGATATGTTGATATTTCACGGTG 58.135 34.615 0.00 0.56 41.63 4.94
184 185 8.352201 GCTATTCACAATTTGGCTAACATGATA 58.648 33.333 0.00 0.00 0.00 2.15
185 186 7.205297 GCTATTCACAATTTGGCTAACATGAT 58.795 34.615 0.00 0.00 0.00 2.45
186 187 6.563422 GCTATTCACAATTTGGCTAACATGA 58.437 36.000 0.00 0.00 0.00 3.07
187 188 5.456497 CGCTATTCACAATTTGGCTAACATG 59.544 40.000 0.78 0.00 0.00 3.21
188 189 5.125417 ACGCTATTCACAATTTGGCTAACAT 59.875 36.000 0.78 0.00 0.00 2.71
189 190 4.457603 ACGCTATTCACAATTTGGCTAACA 59.542 37.500 0.78 0.00 0.00 2.41
190 191 4.981794 ACGCTATTCACAATTTGGCTAAC 58.018 39.130 0.78 0.00 0.00 2.34
191 192 5.637006 AACGCTATTCACAATTTGGCTAA 57.363 34.783 0.78 0.00 0.00 3.09
192 193 5.637006 AAACGCTATTCACAATTTGGCTA 57.363 34.783 0.78 0.00 0.00 3.93
193 194 4.519540 AAACGCTATTCACAATTTGGCT 57.480 36.364 0.78 0.00 0.00 4.75
194 195 4.923281 AGAAAACGCTATTCACAATTTGGC 59.077 37.500 0.78 0.00 0.00 4.52
195 196 6.863126 AGAAGAAAACGCTATTCACAATTTGG 59.137 34.615 0.78 0.00 0.00 3.28
196 197 7.858052 AGAAGAAAACGCTATTCACAATTTG 57.142 32.000 0.00 0.00 0.00 2.32
197 198 8.352942 AGAAGAAGAAAACGCTATTCACAATTT 58.647 29.630 0.00 0.00 0.00 1.82
198 199 7.875971 AGAAGAAGAAAACGCTATTCACAATT 58.124 30.769 0.00 0.00 0.00 2.32
199 200 7.440523 AGAAGAAGAAAACGCTATTCACAAT 57.559 32.000 0.00 0.00 0.00 2.71
200 201 6.861065 AGAAGAAGAAAACGCTATTCACAA 57.139 33.333 0.00 0.00 0.00 3.33
201 202 6.861065 AAGAAGAAGAAAACGCTATTCACA 57.139 33.333 0.00 0.00 0.00 3.58
202 203 7.855904 TCAAAAGAAGAAGAAAACGCTATTCAC 59.144 33.333 0.00 0.00 0.00 3.18
203 204 7.855904 GTCAAAAGAAGAAGAAAACGCTATTCA 59.144 33.333 0.00 0.00 0.00 2.57
204 205 8.070769 AGTCAAAAGAAGAAGAAAACGCTATTC 58.929 33.333 0.00 0.00 0.00 1.75
205 206 7.931275 AGTCAAAAGAAGAAGAAAACGCTATT 58.069 30.769 0.00 0.00 0.00 1.73
206 207 7.497925 AGTCAAAAGAAGAAGAAAACGCTAT 57.502 32.000 0.00 0.00 0.00 2.97
207 208 6.920569 AGTCAAAAGAAGAAGAAAACGCTA 57.079 33.333 0.00 0.00 0.00 4.26
208 209 5.819825 AGTCAAAAGAAGAAGAAAACGCT 57.180 34.783 0.00 0.00 0.00 5.07
209 210 6.483687 TGTAGTCAAAAGAAGAAGAAAACGC 58.516 36.000 0.00 0.00 0.00 4.84
210 211 7.685594 ACTGTAGTCAAAAGAAGAAGAAAACG 58.314 34.615 0.00 0.00 0.00 3.60
211 212 7.846592 CGACTGTAGTCAAAAGAAGAAGAAAAC 59.153 37.037 12.11 0.00 44.99 2.43
212 213 7.762615 TCGACTGTAGTCAAAAGAAGAAGAAAA 59.237 33.333 12.11 0.00 44.99 2.29
213 214 7.262772 TCGACTGTAGTCAAAAGAAGAAGAAA 58.737 34.615 12.11 0.00 44.99 2.52
214 215 6.802608 TCGACTGTAGTCAAAAGAAGAAGAA 58.197 36.000 12.11 0.00 44.99 2.52
215 216 6.387041 TCGACTGTAGTCAAAAGAAGAAGA 57.613 37.500 12.11 0.00 44.99 2.87
216 217 5.117897 GCTCGACTGTAGTCAAAAGAAGAAG 59.882 44.000 12.11 0.00 44.99 2.85
217 218 4.982916 GCTCGACTGTAGTCAAAAGAAGAA 59.017 41.667 12.11 0.00 44.99 2.52
218 219 4.278669 AGCTCGACTGTAGTCAAAAGAAGA 59.721 41.667 12.11 0.00 44.99 2.87
219 220 4.551388 AGCTCGACTGTAGTCAAAAGAAG 58.449 43.478 12.11 1.54 44.99 2.85
220 221 4.585955 AGCTCGACTGTAGTCAAAAGAA 57.414 40.909 12.11 0.00 44.99 2.52
221 222 5.414765 TCATAGCTCGACTGTAGTCAAAAGA 59.585 40.000 12.11 1.02 44.99 2.52
222 223 5.641709 TCATAGCTCGACTGTAGTCAAAAG 58.358 41.667 12.11 7.13 44.99 2.27
223 224 5.638596 TCATAGCTCGACTGTAGTCAAAA 57.361 39.130 12.11 0.00 44.99 2.44
224 225 5.638596 TTCATAGCTCGACTGTAGTCAAA 57.361 39.130 12.11 0.00 44.99 2.69
225 226 5.836821 ATTCATAGCTCGACTGTAGTCAA 57.163 39.130 12.11 0.00 44.99 3.18
226 227 6.546972 CTATTCATAGCTCGACTGTAGTCA 57.453 41.667 12.11 0.00 44.99 3.41
240 241 7.646922 GCCAAAAATCTGACAAGCTATTCATAG 59.353 37.037 0.00 0.00 0.00 2.23
241 242 7.122501 TGCCAAAAATCTGACAAGCTATTCATA 59.877 33.333 0.00 0.00 0.00 2.15
257 258 5.065090 GGGTAATCTTGCAATGCCAAAAATC 59.935 40.000 1.53 0.00 0.00 2.17
266 267 3.355378 TGACAGGGGTAATCTTGCAATG 58.645 45.455 0.00 0.00 0.00 2.82
270 271 4.273318 AGATTTGACAGGGGTAATCTTGC 58.727 43.478 0.00 0.00 31.37 4.01
283 284 6.884472 TGGTTAGGGATAGAAGATTTGACA 57.116 37.500 0.00 0.00 0.00 3.58
284 285 8.575649 TTTTGGTTAGGGATAGAAGATTTGAC 57.424 34.615 0.00 0.00 0.00 3.18
382 383 2.771762 AGGATGGCCAGGAGGAGC 60.772 66.667 13.05 0.00 36.89 4.70
390 391 0.189574 CTAGAGAGGGAGGATGGCCA 59.810 60.000 8.56 8.56 36.29 5.36
423 424 1.377333 GCGGGAGGAAGAACCAAGG 60.377 63.158 0.00 0.00 42.04 3.61
471 472 1.607801 ATGGCGCAGTGACTAGCAGA 61.608 55.000 10.83 1.39 0.00 4.26
492 493 4.322499 GGAAAACTACGACCTGAGAATGGA 60.322 45.833 0.00 0.00 0.00 3.41
501 502 5.715753 AGTAGAGAATGGAAAACTACGACCT 59.284 40.000 0.00 0.00 38.55 3.85
540 541 1.140312 GGGACTAGGCATGGGAATGA 58.860 55.000 0.00 0.00 0.00 2.57
568 569 4.828925 GCGTGCCTCTGGAGAGCC 62.829 72.222 0.00 0.00 40.75 4.70
619 620 4.776322 CCCGCGGACAGATTGCCA 62.776 66.667 30.73 0.00 0.00 4.92
650 651 2.343426 TGGCTCTGATCGTCTGCGT 61.343 57.895 0.00 0.00 39.49 5.24
659 660 0.911769 TCGAAATGGGTGGCTCTGAT 59.088 50.000 0.00 0.00 0.00 2.90
668 669 1.080298 GGACGACGTCGAAATGGGT 60.080 57.895 41.52 19.68 43.02 4.51
818 819 4.424566 GAGCGCGTCCCCGTGTTA 62.425 66.667 8.43 0.00 46.08 2.41
910 912 1.422781 CTCCCCATGTCATAGCACCAT 59.577 52.381 0.00 0.00 0.00 3.55
911 913 0.839277 CTCCCCATGTCATAGCACCA 59.161 55.000 0.00 0.00 0.00 4.17
914 916 2.329267 CTACCTCCCCATGTCATAGCA 58.671 52.381 0.00 0.00 0.00 3.49
940 942 1.376424 AGACTTGACAGCATGCCCG 60.376 57.895 15.66 8.79 42.53 6.13
1005 1008 1.174078 CCACATGAGCACACTGGCAA 61.174 55.000 0.00 0.00 35.83 4.52
1189 1192 1.753073 GCTAGCACAATGCCCAAGAAT 59.247 47.619 10.63 0.00 46.52 2.40
1328 1331 1.571919 GAACGCGGAACTAGCATCAT 58.428 50.000 12.47 0.00 34.19 2.45
1336 1339 0.531311 AAAACCTCGAACGCGGAACT 60.531 50.000 12.47 0.00 38.28 3.01
1337 1340 0.383860 CAAAACCTCGAACGCGGAAC 60.384 55.000 12.47 0.00 38.28 3.62
1358 1361 8.287439 TGTCCAAGAAACAACATTCTTTTCTA 57.713 30.769 0.00 0.00 45.05 2.10
1437 1440 6.077322 TCCTTCCATTTTCAAGTCCAAGAAT 58.923 36.000 0.00 0.00 0.00 2.40
1672 1675 4.760530 TGATCGAATTCCAAGAGACCAT 57.239 40.909 0.00 0.00 0.00 3.55
1768 1771 2.242196 CAAAGGTCACATAGGATGGGGT 59.758 50.000 0.00 0.00 33.47 4.95
1899 1902 0.390124 ACAGCAAACCAACCATGCAG 59.610 50.000 0.00 0.00 42.45 4.41
1960 1963 3.315191 ACGTCTGTGCCAATATAATTGCC 59.685 43.478 0.00 0.00 0.00 4.52
2120 2123 0.394352 ACCATCCCATCGGTTTGCTC 60.394 55.000 0.00 0.00 28.43 4.26
2165 2168 1.555533 CTTTCCTAACGCCCCTCTCTT 59.444 52.381 0.00 0.00 0.00 2.85
2188 2191 5.304686 ACTTGAATCCAACTAACACCAGA 57.695 39.130 0.00 0.00 0.00 3.86
2273 2276 7.309499 GGTCTATCAACTCTCTCAGTTTTCTCA 60.309 40.741 0.00 0.00 43.38 3.27
2369 2372 6.510536 TCACTGTGATACATAAGATGCTCTG 58.489 40.000 6.36 0.00 0.00 3.35
2409 2412 2.947448 GGCTGTGAATAAGGCCAAAG 57.053 50.000 5.01 0.00 43.59 2.77
2677 2680 5.310451 TGCGGAAACAGAGTATAACCTTTT 58.690 37.500 0.00 0.00 0.00 2.27
2955 2960 2.622903 TATCGCCGCTGGTGTAGTGC 62.623 60.000 7.78 0.00 35.54 4.40
3053 3058 0.972983 ACCTGGATCTGCTACAGCGT 60.973 55.000 0.00 0.00 45.83 5.07
3097 3102 4.211374 GTGTTGCGTGTTAAGATCTGTCTT 59.789 41.667 0.00 0.00 46.22 3.01
3150 3156 2.108075 TCCTTTGTTCTCAGCAATGGGA 59.892 45.455 9.16 4.11 39.88 4.37
3181 3187 5.486526 CTTCTGTACTGGCTCATCTTTTCT 58.513 41.667 0.00 0.00 0.00 2.52
3244 3250 1.556911 GAGGATCCAGCAAGAAGTCCA 59.443 52.381 15.82 0.00 0.00 4.02
3279 3285 7.430007 TCAATGAGATACCTATGGGATGGATA 58.570 38.462 0.25 0.00 36.25 2.59
3293 3299 9.070149 GCAATGAACTTCTTTTCAATGAGATAC 57.930 33.333 5.32 0.00 38.26 2.24
3295 3301 7.039223 AGGCAATGAACTTCTTTTCAATGAGAT 60.039 33.333 5.32 0.00 38.26 2.75
3337 3343 7.406104 AGAATAAATGGCTAGAAAGTCACCTT 58.594 34.615 0.00 0.00 40.98 3.50
3521 3534 9.474313 TGGTAATTTAGGAAGCATAACTGAATT 57.526 29.630 0.00 0.00 35.49 2.17
3522 3535 9.646522 ATGGTAATTTAGGAAGCATAACTGAAT 57.353 29.630 0.00 0.00 30.03 2.57
3563 3576 6.310149 GGATTCCCAACATGGATAGAAGATT 58.690 40.000 0.00 0.00 40.96 2.40
3568 3581 3.313791 TCGGATTCCCAACATGGATAGA 58.686 45.455 0.00 0.00 40.96 1.98


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

AutoCloner maintained by Alex Coulton.