Multiple sequence alignment - TraesCS5D01G504200

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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 TraesCS5D01G504200 chr5D 100.000 2644 0 0 1 2644 530776950 530774307 0.000000e+00 4883.0
1 TraesCS5D01G504200 chr5D 90.741 108 9 1 1876 1982 510161885 510161778 2.740000e-30 143.0
2 TraesCS5D01G504200 chr5D 90.654 107 9 1 1876 1981 6979586 6979480 9.870000e-30 141.0
3 TraesCS5D01G504200 chr5B 87.181 1334 62 27 214 1505 670021057 670019791 0.000000e+00 1415.0
4 TraesCS5D01G504200 chr5B 87.097 651 45 24 1998 2640 670016894 670016275 0.000000e+00 701.0
5 TraesCS5D01G504200 chr5B 85.600 375 22 17 1507 1871 670019477 670019125 5.380000e-97 364.0
6 TraesCS5D01G504200 chr5B 85.484 186 18 6 2459 2640 670013992 670013812 4.490000e-43 185.0
7 TraesCS5D01G504200 chr5B 87.356 87 11 0 1158 1244 670099097 670099011 1.670000e-17 100.0
8 TraesCS5D01G504200 chr5B 85.057 87 13 0 1158 1244 670081190 670081104 3.620000e-14 89.8
9 TraesCS5D01G504200 chr4A 88.750 880 49 26 1158 2017 641480883 641481732 0.000000e+00 1031.0
10 TraesCS5D01G504200 chr4A 93.053 547 27 9 2101 2644 641482465 641483003 0.000000e+00 789.0
11 TraesCS5D01G504200 chr4A 80.377 530 50 31 594 1105 641480376 641480869 1.160000e-93 353.0
12 TraesCS5D01G504200 chr4A 95.082 61 3 0 2006 2066 641482405 641482465 2.170000e-16 97.1
13 TraesCS5D01G504200 chr6A 91.071 112 10 0 1876 1987 422776145 422776256 4.560000e-33 152.0
14 TraesCS5D01G504200 chr7D 92.381 105 8 0 1876 1980 13691397 13691293 1.640000e-32 150.0
15 TraesCS5D01G504200 chr3D 91.589 107 9 0 1876 1982 525540379 525540273 5.900000e-32 148.0
16 TraesCS5D01G504200 chr1D 91.509 106 8 1 1882 1986 7178240 7178135 7.630000e-31 145.0
17 TraesCS5D01G504200 chr2B 90.566 106 10 0 1876 1981 96231096 96231201 9.870000e-30 141.0
18 TraesCS5D01G504200 chr1B 92.000 100 8 0 1882 1981 484457654 484457555 9.870000e-30 141.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G504200 chr5D 530774307 530776950 2643 True 4883.000 4883 100.0000 1 2644 1 chr5D.!!$R3 2643
1 TraesCS5D01G504200 chr5B 670013812 670021057 7245 True 666.250 1415 86.3405 214 2640 4 chr5B.!!$R3 2426
2 TraesCS5D01G504200 chr4A 641480376 641483003 2627 False 567.525 1031 89.3155 594 2644 4 chr4A.!!$F1 2050

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
115 116 0.039074 AGACAGCCTGAAAGTCGTCG 60.039 55.0 0.0 0.0 37.36 5.12 F
149 150 0.041238 TGAACCCACCCACCAAAACA 59.959 50.0 0.0 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1145 1178 0.508641 CGAGCTGCTTACACACACAC 59.491 55.0 2.53 0.0 0.0 3.82 R
1682 2056 0.534877 ATTGTTCCAGCAGCGTGACA 60.535 50.0 0.00 0.0 0.0 3.58 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
17 18 4.509737 GGACCACCTAGCGACGGC 62.510 72.222 0.00 0.00 40.37 5.68
27 28 4.732106 GCGACGGCTATAAGCACT 57.268 55.556 0.00 0.00 44.75 4.40
28 29 3.859650 GCGACGGCTATAAGCACTA 57.140 52.632 0.00 0.00 44.75 2.74
29 30 2.129823 GCGACGGCTATAAGCACTAA 57.870 50.000 0.00 0.00 44.75 2.24
30 31 2.466846 GCGACGGCTATAAGCACTAAA 58.533 47.619 0.00 0.00 44.75 1.85
31 32 2.471743 GCGACGGCTATAAGCACTAAAG 59.528 50.000 0.00 0.00 44.75 1.85
32 33 2.471743 CGACGGCTATAAGCACTAAAGC 59.528 50.000 0.78 0.00 44.75 3.51
33 34 2.470821 ACGGCTATAAGCACTAAAGCG 58.529 47.619 0.78 0.00 44.75 4.68
34 35 2.100252 ACGGCTATAAGCACTAAAGCGA 59.900 45.455 0.78 0.00 44.75 4.93
35 36 2.726760 CGGCTATAAGCACTAAAGCGAG 59.273 50.000 0.78 0.00 44.75 5.03
36 37 2.476997 GGCTATAAGCACTAAAGCGAGC 59.523 50.000 0.78 0.00 44.75 5.03
37 38 2.476997 GCTATAAGCACTAAAGCGAGCC 59.523 50.000 0.00 0.00 41.89 4.70
38 39 1.571919 ATAAGCACTAAAGCGAGCCG 58.428 50.000 0.00 0.00 40.15 5.52
39 40 0.528924 TAAGCACTAAAGCGAGCCGA 59.471 50.000 0.00 0.00 40.15 5.54
40 41 0.320421 AAGCACTAAAGCGAGCCGAA 60.320 50.000 0.00 0.00 40.15 4.30
41 42 0.320421 AGCACTAAAGCGAGCCGAAA 60.320 50.000 0.00 0.00 40.15 3.46
42 43 0.515564 GCACTAAAGCGAGCCGAAAA 59.484 50.000 0.00 0.00 0.00 2.29
43 44 1.724973 GCACTAAAGCGAGCCGAAAAC 60.725 52.381 0.00 0.00 0.00 2.43
44 45 1.798813 CACTAAAGCGAGCCGAAAACT 59.201 47.619 0.00 0.00 0.00 2.66
45 46 2.067013 ACTAAAGCGAGCCGAAAACTC 58.933 47.619 0.00 0.00 0.00 3.01
50 51 4.148645 GAGCCGAAAACTCGCCGC 62.149 66.667 0.00 0.00 0.00 6.53
51 52 4.681978 AGCCGAAAACTCGCCGCT 62.682 61.111 0.00 0.00 0.00 5.52
52 53 4.445545 GCCGAAAACTCGCCGCTG 62.446 66.667 0.00 0.00 0.00 5.18
53 54 3.041940 CCGAAAACTCGCCGCTGT 61.042 61.111 0.00 0.00 0.00 4.40
54 55 2.470286 CGAAAACTCGCCGCTGTC 59.530 61.111 0.00 0.00 0.00 3.51
55 56 2.307309 CGAAAACTCGCCGCTGTCA 61.307 57.895 0.00 0.00 0.00 3.58
56 57 1.626654 CGAAAACTCGCCGCTGTCAT 61.627 55.000 0.00 0.00 0.00 3.06
57 58 0.095417 GAAAACTCGCCGCTGTCATC 59.905 55.000 0.00 0.00 0.00 2.92
58 59 1.626654 AAAACTCGCCGCTGTCATCG 61.627 55.000 0.00 0.00 0.00 3.84
67 68 3.770040 CTGTCATCGCCCCCGTCA 61.770 66.667 0.00 0.00 35.54 4.35
68 69 3.080765 TGTCATCGCCCCCGTCAT 61.081 61.111 0.00 0.00 35.54 3.06
69 70 2.280186 GTCATCGCCCCCGTCATC 60.280 66.667 0.00 0.00 35.54 2.92
70 71 2.762043 TCATCGCCCCCGTCATCA 60.762 61.111 0.00 0.00 35.54 3.07
71 72 2.189257 CATCGCCCCCGTCATCAA 59.811 61.111 0.00 0.00 35.54 2.57
72 73 1.451207 CATCGCCCCCGTCATCAAA 60.451 57.895 0.00 0.00 35.54 2.69
73 74 1.029408 CATCGCCCCCGTCATCAAAA 61.029 55.000 0.00 0.00 35.54 2.44
74 75 0.748005 ATCGCCCCCGTCATCAAAAG 60.748 55.000 0.00 0.00 35.54 2.27
75 76 1.376683 CGCCCCCGTCATCAAAAGA 60.377 57.895 0.00 0.00 0.00 2.52
76 77 1.644786 CGCCCCCGTCATCAAAAGAC 61.645 60.000 0.00 0.00 0.00 3.01
87 88 5.970879 GTCATCAAAAGACGAGTAAACGTT 58.029 37.500 0.00 0.00 46.52 3.99
88 89 5.839239 GTCATCAAAAGACGAGTAAACGTTG 59.161 40.000 0.00 0.00 46.52 4.10
89 90 5.521010 TCATCAAAAGACGAGTAAACGTTGT 59.479 36.000 0.00 0.00 46.52 3.32
90 91 5.783100 TCAAAAGACGAGTAAACGTTGTT 57.217 34.783 0.00 0.00 46.52 2.83
91 92 5.552807 TCAAAAGACGAGTAAACGTTGTTG 58.447 37.500 0.00 0.00 46.52 3.33
92 93 5.120519 TCAAAAGACGAGTAAACGTTGTTGT 59.879 36.000 0.00 0.00 46.52 3.32
93 94 6.309980 TCAAAAGACGAGTAAACGTTGTTGTA 59.690 34.615 0.00 0.00 46.52 2.41
94 95 6.645700 AAAGACGAGTAAACGTTGTTGTAA 57.354 33.333 0.00 0.00 46.52 2.41
95 96 6.833342 AAGACGAGTAAACGTTGTTGTAAT 57.167 33.333 0.00 0.00 46.52 1.89
96 97 7.928908 AAGACGAGTAAACGTTGTTGTAATA 57.071 32.000 0.00 0.00 46.52 0.98
97 98 7.558435 AGACGAGTAAACGTTGTTGTAATAG 57.442 36.000 0.00 0.00 46.52 1.73
98 99 7.362662 AGACGAGTAAACGTTGTTGTAATAGA 58.637 34.615 0.00 0.00 46.52 1.98
99 100 7.324616 AGACGAGTAAACGTTGTTGTAATAGAC 59.675 37.037 0.00 0.00 46.52 2.59
100 101 6.917477 ACGAGTAAACGTTGTTGTAATAGACA 59.083 34.615 0.00 0.00 44.14 3.41
101 102 7.113965 ACGAGTAAACGTTGTTGTAATAGACAG 59.886 37.037 0.00 0.00 44.14 3.51
102 103 7.113704 AGTAAACGTTGTTGTAATAGACAGC 57.886 36.000 0.00 0.00 39.88 4.40
103 104 5.352643 AAACGTTGTTGTAATAGACAGCC 57.647 39.130 0.00 0.00 39.88 4.85
104 105 4.267349 ACGTTGTTGTAATAGACAGCCT 57.733 40.909 0.00 0.00 39.88 4.58
105 106 3.994392 ACGTTGTTGTAATAGACAGCCTG 59.006 43.478 0.00 0.00 39.88 4.85
106 107 4.242475 CGTTGTTGTAATAGACAGCCTGA 58.758 43.478 0.00 0.00 39.88 3.86
107 108 4.688879 CGTTGTTGTAATAGACAGCCTGAA 59.311 41.667 0.00 0.00 39.88 3.02
108 109 5.178623 CGTTGTTGTAATAGACAGCCTGAAA 59.821 40.000 0.00 0.00 39.88 2.69
109 110 6.603095 GTTGTTGTAATAGACAGCCTGAAAG 58.397 40.000 0.00 0.00 39.88 2.62
110 111 5.865085 TGTTGTAATAGACAGCCTGAAAGT 58.135 37.500 0.00 0.00 39.88 2.66
111 112 5.932303 TGTTGTAATAGACAGCCTGAAAGTC 59.068 40.000 0.00 0.00 39.88 3.01
112 113 4.744570 TGTAATAGACAGCCTGAAAGTCG 58.255 43.478 0.00 0.00 37.36 4.18
113 114 3.963428 AATAGACAGCCTGAAAGTCGT 57.037 42.857 0.00 0.00 37.36 4.34
114 115 3.512033 ATAGACAGCCTGAAAGTCGTC 57.488 47.619 0.00 0.00 37.36 4.20
115 116 0.039074 AGACAGCCTGAAAGTCGTCG 60.039 55.000 0.00 0.00 37.36 5.12
116 117 0.318784 GACAGCCTGAAAGTCGTCGT 60.319 55.000 0.00 0.00 0.00 4.34
117 118 0.597637 ACAGCCTGAAAGTCGTCGTG 60.598 55.000 0.00 0.00 0.00 4.35
118 119 1.664965 AGCCTGAAAGTCGTCGTGC 60.665 57.895 0.00 0.00 0.00 5.34
119 120 1.664965 GCCTGAAAGTCGTCGTGCT 60.665 57.895 0.00 0.00 0.00 4.40
120 121 0.388134 GCCTGAAAGTCGTCGTGCTA 60.388 55.000 0.00 0.00 0.00 3.49
121 122 1.933500 GCCTGAAAGTCGTCGTGCTAA 60.934 52.381 0.00 0.00 0.00 3.09
122 123 1.986378 CCTGAAAGTCGTCGTGCTAAG 59.014 52.381 0.00 0.00 0.00 2.18
123 124 1.986378 CTGAAAGTCGTCGTGCTAAGG 59.014 52.381 0.00 0.00 0.00 2.69
124 125 0.714439 GAAAGTCGTCGTGCTAAGGC 59.286 55.000 0.00 0.00 39.26 4.35
125 126 0.669625 AAAGTCGTCGTGCTAAGGCC 60.670 55.000 0.00 0.00 37.74 5.19
126 127 1.533469 AAGTCGTCGTGCTAAGGCCT 61.533 55.000 0.00 0.00 37.74 5.19
127 128 1.516603 GTCGTCGTGCTAAGGCCTC 60.517 63.158 5.23 0.00 37.74 4.70
128 129 1.974875 TCGTCGTGCTAAGGCCTCA 60.975 57.895 5.23 0.00 37.74 3.86
129 130 1.080093 CGTCGTGCTAAGGCCTCAA 60.080 57.895 5.23 0.00 37.74 3.02
130 131 0.460284 CGTCGTGCTAAGGCCTCAAT 60.460 55.000 5.23 0.00 37.74 2.57
131 132 1.009829 GTCGTGCTAAGGCCTCAATG 58.990 55.000 5.23 0.00 37.74 2.82
132 133 0.901827 TCGTGCTAAGGCCTCAATGA 59.098 50.000 5.23 0.00 37.74 2.57
133 134 1.277842 TCGTGCTAAGGCCTCAATGAA 59.722 47.619 5.23 0.00 37.74 2.57
134 135 1.398390 CGTGCTAAGGCCTCAATGAAC 59.602 52.381 5.23 0.11 37.74 3.18
135 136 1.745653 GTGCTAAGGCCTCAATGAACC 59.254 52.381 5.23 0.00 37.74 3.62
136 137 1.340991 TGCTAAGGCCTCAATGAACCC 60.341 52.381 5.23 0.00 37.74 4.11
137 138 1.340991 GCTAAGGCCTCAATGAACCCA 60.341 52.381 5.23 0.00 0.00 4.51
138 139 2.369394 CTAAGGCCTCAATGAACCCAC 58.631 52.381 5.23 0.00 0.00 4.61
139 140 0.251787 AAGGCCTCAATGAACCCACC 60.252 55.000 5.23 0.00 0.00 4.61
140 141 1.682344 GGCCTCAATGAACCCACCC 60.682 63.158 0.00 0.00 0.00 4.61
141 142 1.076549 GCCTCAATGAACCCACCCA 59.923 57.895 0.00 0.00 0.00 4.51
142 143 1.250840 GCCTCAATGAACCCACCCAC 61.251 60.000 0.00 0.00 0.00 4.61
143 144 0.611896 CCTCAATGAACCCACCCACC 60.612 60.000 0.00 0.00 0.00 4.61
144 145 0.112218 CTCAATGAACCCACCCACCA 59.888 55.000 0.00 0.00 0.00 4.17
145 146 0.558220 TCAATGAACCCACCCACCAA 59.442 50.000 0.00 0.00 0.00 3.67
146 147 1.062886 TCAATGAACCCACCCACCAAA 60.063 47.619 0.00 0.00 0.00 3.28
147 148 1.765314 CAATGAACCCACCCACCAAAA 59.235 47.619 0.00 0.00 0.00 2.44
148 149 1.419381 ATGAACCCACCCACCAAAAC 58.581 50.000 0.00 0.00 0.00 2.43
149 150 0.041238 TGAACCCACCCACCAAAACA 59.959 50.000 0.00 0.00 0.00 2.83
150 151 1.343478 TGAACCCACCCACCAAAACAT 60.343 47.619 0.00 0.00 0.00 2.71
151 152 1.343142 GAACCCACCCACCAAAACATC 59.657 52.381 0.00 0.00 0.00 3.06
152 153 0.263172 ACCCACCCACCAAAACATCA 59.737 50.000 0.00 0.00 0.00 3.07
153 154 1.343478 ACCCACCCACCAAAACATCAA 60.343 47.619 0.00 0.00 0.00 2.57
154 155 1.069978 CCCACCCACCAAAACATCAAC 59.930 52.381 0.00 0.00 0.00 3.18
155 156 1.269517 CCACCCACCAAAACATCAACG 60.270 52.381 0.00 0.00 0.00 4.10
156 157 1.036707 ACCCACCAAAACATCAACGG 58.963 50.000 0.00 0.00 0.00 4.44
157 158 0.319469 CCCACCAAAACATCAACGGC 60.319 55.000 0.00 0.00 0.00 5.68
158 159 0.387202 CCACCAAAACATCAACGGCA 59.613 50.000 0.00 0.00 0.00 5.69
159 160 1.486439 CACCAAAACATCAACGGCAC 58.514 50.000 0.00 0.00 0.00 5.01
160 161 0.387565 ACCAAAACATCAACGGCACC 59.612 50.000 0.00 0.00 0.00 5.01
161 162 0.319469 CCAAAACATCAACGGCACCC 60.319 55.000 0.00 0.00 0.00 4.61
172 173 2.047179 GGCACCCGACCAAGAGAC 60.047 66.667 0.00 0.00 0.00 3.36
173 174 2.432628 GCACCCGACCAAGAGACG 60.433 66.667 0.00 0.00 0.00 4.18
174 175 2.432628 CACCCGACCAAGAGACGC 60.433 66.667 0.00 0.00 0.00 5.19
175 176 4.052229 ACCCGACCAAGAGACGCG 62.052 66.667 3.53 3.53 0.00 6.01
192 193 4.235762 GCGCGATGGGCCCTTCTA 62.236 66.667 29.57 9.10 38.94 2.10
193 194 2.743718 CGCGATGGGCCCTTCTAT 59.256 61.111 29.57 13.77 38.94 1.98
194 195 1.071471 CGCGATGGGCCCTTCTATT 59.929 57.895 29.57 6.84 38.94 1.73
195 196 1.230635 CGCGATGGGCCCTTCTATTG 61.231 60.000 29.57 17.28 38.94 1.90
196 197 1.518903 GCGATGGGCCCTTCTATTGC 61.519 60.000 29.57 22.33 34.80 3.56
197 198 0.109342 CGATGGGCCCTTCTATTGCT 59.891 55.000 29.57 2.64 0.00 3.91
198 199 1.879796 CGATGGGCCCTTCTATTGCTC 60.880 57.143 29.57 7.28 0.00 4.26
199 200 0.109342 ATGGGCCCTTCTATTGCTCG 59.891 55.000 25.70 0.00 0.00 5.03
200 201 1.894282 GGGCCCTTCTATTGCTCGC 60.894 63.158 17.04 0.00 0.00 5.03
201 202 2.247437 GGCCCTTCTATTGCTCGCG 61.247 63.158 0.00 0.00 0.00 5.87
202 203 1.227263 GCCCTTCTATTGCTCGCGA 60.227 57.895 9.26 9.26 0.00 5.87
203 204 0.810031 GCCCTTCTATTGCTCGCGAA 60.810 55.000 11.33 0.00 0.00 4.70
204 205 0.931005 CCCTTCTATTGCTCGCGAAC 59.069 55.000 11.33 6.37 0.00 3.95
205 206 1.640428 CCTTCTATTGCTCGCGAACA 58.360 50.000 11.33 9.78 0.00 3.18
206 207 1.590238 CCTTCTATTGCTCGCGAACAG 59.410 52.381 11.33 0.00 0.00 3.16
207 208 2.263077 CTTCTATTGCTCGCGAACAGT 58.737 47.619 11.33 11.87 0.00 3.55
208 209 1.629013 TCTATTGCTCGCGAACAGTG 58.371 50.000 16.58 9.33 0.00 3.66
209 210 1.201414 TCTATTGCTCGCGAACAGTGA 59.799 47.619 16.58 11.25 37.83 3.41
217 218 1.284297 CGCGAACAGTGAGTGATGCA 61.284 55.000 0.00 0.00 0.00 3.96
229 230 1.378911 TGATGCATGCACCTGGGAC 60.379 57.895 25.37 9.00 0.00 4.46
232 233 3.127533 GCATGCACCTGGGACGAC 61.128 66.667 14.21 0.00 0.00 4.34
240 241 1.001268 CACCTGGGACGACGATGATAG 60.001 57.143 0.00 0.00 0.00 2.08
252 253 4.800993 CGACGATGATAGGATAAGAATGGC 59.199 45.833 0.00 0.00 0.00 4.40
254 255 4.780021 ACGATGATAGGATAAGAATGGCCT 59.220 41.667 3.32 0.00 34.56 5.19
258 259 7.418368 CGATGATAGGATAAGAATGGCCTACAT 60.418 40.741 3.32 0.00 43.07 2.29
266 267 3.733337 AGAATGGCCTACATCGAATGTC 58.267 45.455 3.32 0.00 43.67 3.06
269 270 3.179443 TGGCCTACATCGAATGTCTTC 57.821 47.619 3.32 0.00 43.67 2.87
368 369 2.184322 CATACGCACTGACGGCCT 59.816 61.111 0.00 0.00 37.37 5.19
458 459 0.804989 CCAGCACCGAACCAGATTTC 59.195 55.000 0.00 0.00 0.00 2.17
468 469 2.682155 ACCAGATTTCTTCCGAGCTC 57.318 50.000 2.73 2.73 0.00 4.09
503 514 5.163437 ACGTTTCTATCTATCGGGAAGCTTT 60.163 40.000 0.00 0.00 0.00 3.51
504 515 5.753921 CGTTTCTATCTATCGGGAAGCTTTT 59.246 40.000 0.00 0.00 0.00 2.27
557 568 6.196724 CCGATCTTGTGAGTACGTTTCTATTC 59.803 42.308 0.00 0.00 0.00 1.75
596 613 6.015010 GGAACATGGTAGTATCAGATGCTACT 60.015 42.308 28.00 14.73 44.62 2.57
609 626 5.470437 TCAGATGCTACTGAAGTACCGATAG 59.530 44.000 10.09 0.00 42.79 2.08
728 748 0.250038 CAGTGCCACTCCGGATATGG 60.250 60.000 24.44 24.44 36.56 2.74
764 785 4.403113 TGTGCTAATCCGGTATCTGTTGTA 59.597 41.667 0.00 0.00 0.00 2.41
766 787 3.988517 GCTAATCCGGTATCTGTTGTAGC 59.011 47.826 0.00 0.00 0.00 3.58
769 790 2.453521 TCCGGTATCTGTTGTAGCAGT 58.546 47.619 0.00 0.00 37.70 4.40
771 792 3.379372 TCCGGTATCTGTTGTAGCAGTAC 59.621 47.826 0.00 0.00 37.70 2.73
855 879 9.517609 GACATATATAAATACGACCAGATCCAC 57.482 37.037 0.00 0.00 0.00 4.02
875 899 4.449068 CCACCGATGATGCTTATCAGTTAC 59.551 45.833 0.00 0.00 33.59 2.50
929 954 7.147897 ACACATTCTTGTCTATTCGATCCTACA 60.148 37.037 0.00 0.00 32.34 2.74
930 955 7.706607 CACATTCTTGTCTATTCGATCCTACAA 59.293 37.037 0.00 0.00 32.34 2.41
932 957 7.406031 TTCTTGTCTATTCGATCCTACAAGT 57.594 36.000 20.96 0.00 42.64 3.16
935 960 8.784994 TCTTGTCTATTCGATCCTACAAGTATC 58.215 37.037 20.96 0.00 42.64 2.24
1109 1142 5.407995 GCTTGCAGCCATGTTTATGTTTTTA 59.592 36.000 0.00 0.00 34.48 1.52
1111 1144 7.361116 GCTTGCAGCCATGTTTATGTTTTTATT 60.361 33.333 0.00 0.00 34.48 1.40
1112 1145 9.149225 CTTGCAGCCATGTTTATGTTTTTATTA 57.851 29.630 0.00 0.00 32.21 0.98
1113 1146 9.664332 TTGCAGCCATGTTTATGTTTTTATTAT 57.336 25.926 0.00 0.00 32.21 1.28
1134 1167 2.031769 TGTTGCTTGCTTTGATCGTCAG 60.032 45.455 0.00 0.00 0.00 3.51
1138 1171 3.058708 TGCTTGCTTTGATCGTCAGAAAG 60.059 43.478 3.04 3.04 0.00 2.62
1142 1175 4.928661 GCTTTGATCGTCAGAAAGCTAA 57.071 40.909 16.26 0.00 45.31 3.09
1143 1176 4.642953 GCTTTGATCGTCAGAAAGCTAAC 58.357 43.478 16.26 0.00 45.31 2.34
1144 1177 4.390297 GCTTTGATCGTCAGAAAGCTAACT 59.610 41.667 16.26 0.00 45.31 2.24
1145 1178 5.669848 GCTTTGATCGTCAGAAAGCTAACTG 60.670 44.000 16.26 12.14 45.31 3.16
1214 1259 1.613630 GAGGTGGAGGCCTTCTGGA 60.614 63.158 13.68 0.00 39.34 3.86
1266 1311 4.003788 CGGTGAGACCCTTGCCGT 62.004 66.667 0.00 0.00 37.87 5.68
1279 1324 4.773117 GCCGTCGACGTCACCTCC 62.773 72.222 33.49 10.94 37.74 4.30
1281 1326 3.054503 CGTCGACGTCACCTCCCT 61.055 66.667 29.08 0.00 34.11 4.20
1283 1328 2.114625 TCGACGTCACCTCCCTGT 59.885 61.111 17.16 0.00 0.00 4.00
1287 1332 2.432628 CGTCACCTCCCTGTTCGC 60.433 66.667 0.00 0.00 0.00 4.70
1384 1435 4.593864 GCCGGCCACGAGGAGATC 62.594 72.222 18.11 0.00 44.60 2.75
1393 1444 3.115556 GAGGAGATCGACGCAGCT 58.884 61.111 0.00 0.00 0.00 4.24
1466 1519 1.148157 CCGCCGATGATGACACTGTC 61.148 60.000 1.86 1.86 0.00 3.51
1497 1550 1.614903 ACGTGGTCAGTTCGTTGGATA 59.385 47.619 0.00 0.00 34.07 2.59
1682 2056 5.826737 AGAGTGTACGCAATACTAGTACCAT 59.173 40.000 4.31 0.00 39.77 3.55
1696 2070 1.540435 TACCATGTCACGCTGCTGGA 61.540 55.000 9.95 0.00 0.00 3.86
1697 2071 1.672030 CCATGTCACGCTGCTGGAA 60.672 57.895 0.00 0.00 0.00 3.53
1698 2072 1.499056 CATGTCACGCTGCTGGAAC 59.501 57.895 0.00 0.00 0.00 3.62
1732 2112 4.742201 CTACTGCCTGCACCGCGT 62.742 66.667 4.92 0.00 0.00 6.01
1903 2292 1.343069 GAGGTGCTCATAGGGGTAGG 58.657 60.000 0.00 0.00 0.00 3.18
1904 2293 0.941963 AGGTGCTCATAGGGGTAGGA 59.058 55.000 0.00 0.00 0.00 2.94
1918 2307 3.243636 GGGGTAGGATGTGTATGTGTACG 60.244 52.174 0.00 0.00 33.36 3.67
1928 2317 4.463539 TGTGTATGTGTACGTTCATAGGGT 59.536 41.667 0.00 0.00 33.36 4.34
1948 2337 1.835121 TGAGTGTATGCGCGTATGTC 58.165 50.000 20.45 12.76 0.00 3.06
2091 5018 8.732413 TCTTCATTTTTCAGTCAATTTCATCG 57.268 30.769 0.00 0.00 0.00 3.84
2092 5019 6.932901 TCATTTTTCAGTCAATTTCATCGC 57.067 33.333 0.00 0.00 0.00 4.58
2093 5020 5.568677 TCATTTTTCAGTCAATTTCATCGCG 59.431 36.000 0.00 0.00 0.00 5.87
2412 5342 8.581253 AATATTTTCTTAAGACCCAAGACTGG 57.419 34.615 4.18 0.00 43.10 4.00
2430 5360 5.351189 AGACTGGTTTTTGCAAATTTGTGAC 59.649 36.000 19.03 10.39 0.00 3.67
2436 5366 7.592903 TGGTTTTTGCAAATTTGTGACTTTTTC 59.407 29.630 19.03 0.40 0.00 2.29
2516 5448 1.529226 TGTCCCTTTTACATGGCACG 58.471 50.000 0.00 0.00 0.00 5.34
2569 5501 8.881743 CATAAAATTGACCAATAAACACATGGG 58.118 33.333 0.00 0.00 38.58 4.00
2641 5573 9.944663 GTAGTTTCCGATGATATAATTTTTGCA 57.055 29.630 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.509737 GCCGTCGCTAGGTGGTCC 62.510 72.222 0.00 0.00 0.00 4.46
1 2 2.117156 TAGCCGTCGCTAGGTGGTC 61.117 63.158 0.00 0.00 46.08 4.02
2 3 2.044650 TAGCCGTCGCTAGGTGGT 60.045 61.111 0.00 0.00 46.08 4.16
10 11 2.129823 TTAGTGCTTATAGCCGTCGC 57.870 50.000 0.00 0.00 41.51 5.19
11 12 2.471743 GCTTTAGTGCTTATAGCCGTCG 59.528 50.000 0.00 0.00 41.51 5.12
12 13 2.471743 CGCTTTAGTGCTTATAGCCGTC 59.528 50.000 0.00 0.00 41.51 4.79
13 14 2.100252 TCGCTTTAGTGCTTATAGCCGT 59.900 45.455 0.00 0.00 41.51 5.68
14 15 2.726760 CTCGCTTTAGTGCTTATAGCCG 59.273 50.000 0.00 0.00 41.51 5.52
15 16 2.476997 GCTCGCTTTAGTGCTTATAGCC 59.523 50.000 0.00 0.00 41.51 3.93
16 17 2.476997 GGCTCGCTTTAGTGCTTATAGC 59.523 50.000 0.00 0.00 42.82 2.97
17 18 2.726760 CGGCTCGCTTTAGTGCTTATAG 59.273 50.000 0.00 0.00 0.00 1.31
18 19 2.359848 TCGGCTCGCTTTAGTGCTTATA 59.640 45.455 0.00 0.00 0.00 0.98
19 20 1.136305 TCGGCTCGCTTTAGTGCTTAT 59.864 47.619 0.00 0.00 0.00 1.73
20 21 0.528924 TCGGCTCGCTTTAGTGCTTA 59.471 50.000 0.00 0.00 0.00 3.09
21 22 0.320421 TTCGGCTCGCTTTAGTGCTT 60.320 50.000 0.00 0.00 0.00 3.91
22 23 0.320421 TTTCGGCTCGCTTTAGTGCT 60.320 50.000 0.00 0.00 0.00 4.40
23 24 0.515564 TTTTCGGCTCGCTTTAGTGC 59.484 50.000 0.00 0.00 0.00 4.40
24 25 1.798813 AGTTTTCGGCTCGCTTTAGTG 59.201 47.619 0.00 0.00 0.00 2.74
25 26 2.067013 GAGTTTTCGGCTCGCTTTAGT 58.933 47.619 0.00 0.00 0.00 2.24
26 27 2.789569 GAGTTTTCGGCTCGCTTTAG 57.210 50.000 0.00 0.00 0.00 1.85
36 37 3.011760 GACAGCGGCGAGTTTTCGG 62.012 63.158 12.98 0.00 46.76 4.30
38 39 0.095417 GATGACAGCGGCGAGTTTTC 59.905 55.000 12.98 5.76 0.00 2.29
39 40 1.626654 CGATGACAGCGGCGAGTTTT 61.627 55.000 12.98 0.00 0.00 2.43
40 41 2.094659 CGATGACAGCGGCGAGTTT 61.095 57.895 12.98 0.00 0.00 2.66
41 42 2.507102 CGATGACAGCGGCGAGTT 60.507 61.111 12.98 0.00 0.00 3.01
50 51 2.978452 GATGACGGGGGCGATGACAG 62.978 65.000 0.00 0.00 0.00 3.51
51 52 3.080765 ATGACGGGGGCGATGACA 61.081 61.111 0.00 0.00 0.00 3.58
52 53 2.280186 GATGACGGGGGCGATGAC 60.280 66.667 0.00 0.00 0.00 3.06
53 54 1.904990 TTTGATGACGGGGGCGATGA 61.905 55.000 0.00 0.00 0.00 2.92
54 55 1.029408 TTTTGATGACGGGGGCGATG 61.029 55.000 0.00 0.00 0.00 3.84
55 56 0.748005 CTTTTGATGACGGGGGCGAT 60.748 55.000 0.00 0.00 0.00 4.58
56 57 1.376683 CTTTTGATGACGGGGGCGA 60.377 57.895 0.00 0.00 0.00 5.54
57 58 1.376683 TCTTTTGATGACGGGGGCG 60.377 57.895 0.00 0.00 0.00 6.13
58 59 2.180674 GTCTTTTGATGACGGGGGC 58.819 57.895 0.00 0.00 0.00 5.80
64 65 5.571778 ACGTTTACTCGTCTTTTGATGAC 57.428 39.130 0.00 0.00 40.04 3.06
65 66 5.521010 ACAACGTTTACTCGTCTTTTGATGA 59.479 36.000 0.00 0.00 43.38 2.92
66 67 5.734311 ACAACGTTTACTCGTCTTTTGATG 58.266 37.500 0.00 0.00 43.38 3.07
67 68 5.978934 ACAACGTTTACTCGTCTTTTGAT 57.021 34.783 0.00 0.00 43.38 2.57
68 69 5.120519 ACAACAACGTTTACTCGTCTTTTGA 59.879 36.000 0.00 0.00 43.38 2.69
69 70 5.318349 ACAACAACGTTTACTCGTCTTTTG 58.682 37.500 0.00 0.00 43.38 2.44
70 71 5.535043 ACAACAACGTTTACTCGTCTTTT 57.465 34.783 0.00 0.00 43.38 2.27
71 72 6.645700 TTACAACAACGTTTACTCGTCTTT 57.354 33.333 0.00 0.00 43.38 2.52
72 73 6.833342 ATTACAACAACGTTTACTCGTCTT 57.167 33.333 0.00 0.00 43.38 3.01
73 74 7.324616 GTCTATTACAACAACGTTTACTCGTCT 59.675 37.037 0.00 0.00 43.38 4.18
74 75 7.113404 TGTCTATTACAACAACGTTTACTCGTC 59.887 37.037 0.00 0.00 37.91 4.20
75 76 6.917477 TGTCTATTACAACAACGTTTACTCGT 59.083 34.615 0.00 0.00 39.46 4.18
76 77 7.324322 TGTCTATTACAACAACGTTTACTCG 57.676 36.000 0.00 0.00 34.29 4.18
77 78 7.225397 GCTGTCTATTACAACAACGTTTACTC 58.775 38.462 0.00 0.00 37.74 2.59
78 79 6.146673 GGCTGTCTATTACAACAACGTTTACT 59.853 38.462 0.00 0.00 37.74 2.24
79 80 6.146673 AGGCTGTCTATTACAACAACGTTTAC 59.853 38.462 0.00 0.00 37.74 2.01
80 81 6.146510 CAGGCTGTCTATTACAACAACGTTTA 59.853 38.462 6.28 0.00 37.74 2.01
81 82 5.049680 CAGGCTGTCTATTACAACAACGTTT 60.050 40.000 6.28 0.00 37.74 3.60
82 83 4.451096 CAGGCTGTCTATTACAACAACGTT 59.549 41.667 6.28 0.00 37.74 3.99
83 84 3.994392 CAGGCTGTCTATTACAACAACGT 59.006 43.478 6.28 0.00 37.74 3.99
84 85 4.242475 TCAGGCTGTCTATTACAACAACG 58.758 43.478 15.27 0.00 37.74 4.10
85 86 6.204882 ACTTTCAGGCTGTCTATTACAACAAC 59.795 38.462 15.27 0.00 37.74 3.32
86 87 6.296026 ACTTTCAGGCTGTCTATTACAACAA 58.704 36.000 15.27 0.00 37.74 2.83
87 88 5.865085 ACTTTCAGGCTGTCTATTACAACA 58.135 37.500 15.27 0.00 37.74 3.33
88 89 5.062308 CGACTTTCAGGCTGTCTATTACAAC 59.938 44.000 15.27 0.00 37.74 3.32
89 90 5.168569 CGACTTTCAGGCTGTCTATTACAA 58.831 41.667 15.27 0.00 37.74 2.41
90 91 4.219944 ACGACTTTCAGGCTGTCTATTACA 59.780 41.667 15.27 0.00 36.42 2.41
91 92 4.745649 ACGACTTTCAGGCTGTCTATTAC 58.254 43.478 15.27 1.22 0.00 1.89
92 93 4.438336 CGACGACTTTCAGGCTGTCTATTA 60.438 45.833 15.27 0.00 28.99 0.98
93 94 3.673594 CGACGACTTTCAGGCTGTCTATT 60.674 47.826 15.27 0.00 28.99 1.73
94 95 2.159366 CGACGACTTTCAGGCTGTCTAT 60.159 50.000 15.27 0.00 28.99 1.98
95 96 1.199327 CGACGACTTTCAGGCTGTCTA 59.801 52.381 15.27 0.00 28.99 2.59
96 97 0.039074 CGACGACTTTCAGGCTGTCT 60.039 55.000 15.27 0.00 28.99 3.41
97 98 0.318784 ACGACGACTTTCAGGCTGTC 60.319 55.000 15.27 3.46 0.00 3.51
98 99 0.597637 CACGACGACTTTCAGGCTGT 60.598 55.000 15.27 0.00 0.00 4.40
99 100 1.891060 GCACGACGACTTTCAGGCTG 61.891 60.000 8.58 8.58 0.00 4.85
100 101 1.664965 GCACGACGACTTTCAGGCT 60.665 57.895 0.00 0.00 0.00 4.58
101 102 0.388134 TAGCACGACGACTTTCAGGC 60.388 55.000 0.00 0.00 0.00 4.85
102 103 1.986378 CTTAGCACGACGACTTTCAGG 59.014 52.381 0.00 0.00 0.00 3.86
103 104 1.986378 CCTTAGCACGACGACTTTCAG 59.014 52.381 0.00 0.00 0.00 3.02
104 105 1.933500 GCCTTAGCACGACGACTTTCA 60.934 52.381 0.00 0.00 39.53 2.69
105 106 0.714439 GCCTTAGCACGACGACTTTC 59.286 55.000 0.00 0.00 39.53 2.62
106 107 0.669625 GGCCTTAGCACGACGACTTT 60.670 55.000 0.00 0.00 42.56 2.66
107 108 1.080025 GGCCTTAGCACGACGACTT 60.080 57.895 0.00 0.00 42.56 3.01
108 109 1.935327 GAGGCCTTAGCACGACGACT 61.935 60.000 6.77 0.59 42.56 4.18
109 110 1.516603 GAGGCCTTAGCACGACGAC 60.517 63.158 6.77 0.00 42.56 4.34
110 111 1.529152 TTGAGGCCTTAGCACGACGA 61.529 55.000 6.77 0.00 42.56 4.20
111 112 0.460284 ATTGAGGCCTTAGCACGACG 60.460 55.000 6.77 0.00 42.56 5.12
112 113 1.009829 CATTGAGGCCTTAGCACGAC 58.990 55.000 6.77 0.00 42.56 4.34
113 114 0.901827 TCATTGAGGCCTTAGCACGA 59.098 50.000 6.77 0.00 42.56 4.35
114 115 1.398390 GTTCATTGAGGCCTTAGCACG 59.602 52.381 6.77 0.00 42.56 5.34
115 116 1.745653 GGTTCATTGAGGCCTTAGCAC 59.254 52.381 6.77 0.00 42.56 4.40
116 117 1.340991 GGGTTCATTGAGGCCTTAGCA 60.341 52.381 6.77 0.00 42.56 3.49
117 118 1.340991 TGGGTTCATTGAGGCCTTAGC 60.341 52.381 6.77 0.00 38.76 3.09
118 119 2.369394 GTGGGTTCATTGAGGCCTTAG 58.631 52.381 6.77 0.00 0.00 2.18
119 120 1.005450 GGTGGGTTCATTGAGGCCTTA 59.995 52.381 6.77 0.00 0.00 2.69
120 121 0.251787 GGTGGGTTCATTGAGGCCTT 60.252 55.000 6.77 0.00 0.00 4.35
121 122 1.384191 GGTGGGTTCATTGAGGCCT 59.616 57.895 3.86 3.86 0.00 5.19
122 123 1.682344 GGGTGGGTTCATTGAGGCC 60.682 63.158 0.00 0.00 0.00 5.19
123 124 1.076549 TGGGTGGGTTCATTGAGGC 59.923 57.895 0.00 0.00 0.00 4.70
124 125 0.611896 GGTGGGTGGGTTCATTGAGG 60.612 60.000 0.00 0.00 0.00 3.86
125 126 0.112218 TGGTGGGTGGGTTCATTGAG 59.888 55.000 0.00 0.00 0.00 3.02
126 127 0.558220 TTGGTGGGTGGGTTCATTGA 59.442 50.000 0.00 0.00 0.00 2.57
127 128 1.418334 TTTGGTGGGTGGGTTCATTG 58.582 50.000 0.00 0.00 0.00 2.82
128 129 1.765904 GTTTTGGTGGGTGGGTTCATT 59.234 47.619 0.00 0.00 0.00 2.57
129 130 1.343478 TGTTTTGGTGGGTGGGTTCAT 60.343 47.619 0.00 0.00 0.00 2.57
130 131 0.041238 TGTTTTGGTGGGTGGGTTCA 59.959 50.000 0.00 0.00 0.00 3.18
131 132 1.343142 GATGTTTTGGTGGGTGGGTTC 59.657 52.381 0.00 0.00 0.00 3.62
132 133 1.343478 TGATGTTTTGGTGGGTGGGTT 60.343 47.619 0.00 0.00 0.00 4.11
133 134 0.263172 TGATGTTTTGGTGGGTGGGT 59.737 50.000 0.00 0.00 0.00 4.51
134 135 1.069978 GTTGATGTTTTGGTGGGTGGG 59.930 52.381 0.00 0.00 0.00 4.61
135 136 1.269517 CGTTGATGTTTTGGTGGGTGG 60.270 52.381 0.00 0.00 0.00 4.61
136 137 1.269517 CCGTTGATGTTTTGGTGGGTG 60.270 52.381 0.00 0.00 0.00 4.61
137 138 1.036707 CCGTTGATGTTTTGGTGGGT 58.963 50.000 0.00 0.00 0.00 4.51
138 139 0.319469 GCCGTTGATGTTTTGGTGGG 60.319 55.000 0.00 0.00 0.00 4.61
139 140 0.387202 TGCCGTTGATGTTTTGGTGG 59.613 50.000 0.00 0.00 0.00 4.61
140 141 1.486439 GTGCCGTTGATGTTTTGGTG 58.514 50.000 0.00 0.00 0.00 4.17
141 142 0.387565 GGTGCCGTTGATGTTTTGGT 59.612 50.000 0.00 0.00 0.00 3.67
142 143 0.319469 GGGTGCCGTTGATGTTTTGG 60.319 55.000 0.00 0.00 0.00 3.28
143 144 0.662970 CGGGTGCCGTTGATGTTTTG 60.663 55.000 0.00 0.00 42.73 2.44
144 145 1.657556 CGGGTGCCGTTGATGTTTT 59.342 52.632 0.00 0.00 42.73 2.43
145 146 3.350377 CGGGTGCCGTTGATGTTT 58.650 55.556 0.00 0.00 42.73 2.83
155 156 2.047179 GTCTCTTGGTCGGGTGCC 60.047 66.667 0.00 0.00 0.00 5.01
156 157 2.432628 CGTCTCTTGGTCGGGTGC 60.433 66.667 0.00 0.00 0.00 5.01
157 158 2.432628 GCGTCTCTTGGTCGGGTG 60.433 66.667 0.00 0.00 0.00 4.61
158 159 4.052229 CGCGTCTCTTGGTCGGGT 62.052 66.667 0.00 0.00 33.96 5.28
165 166 4.257376 CATCGCGCGCGTCTCTTG 62.257 66.667 46.54 31.84 40.74 3.02
176 177 1.071471 AATAGAAGGGCCCATCGCG 59.929 57.895 27.56 0.00 38.94 5.87
177 178 1.518903 GCAATAGAAGGGCCCATCGC 61.519 60.000 27.56 16.63 0.00 4.58
178 179 0.109342 AGCAATAGAAGGGCCCATCG 59.891 55.000 27.56 10.05 0.00 3.84
179 180 1.879796 CGAGCAATAGAAGGGCCCATC 60.880 57.143 27.56 23.47 0.00 3.51
180 181 0.109342 CGAGCAATAGAAGGGCCCAT 59.891 55.000 27.56 13.79 0.00 4.00
181 182 1.526887 CGAGCAATAGAAGGGCCCA 59.473 57.895 27.56 2.25 0.00 5.36
182 183 1.894282 GCGAGCAATAGAAGGGCCC 60.894 63.158 16.46 16.46 0.00 5.80
183 184 2.247437 CGCGAGCAATAGAAGGGCC 61.247 63.158 0.00 0.00 0.00 5.80
184 185 0.810031 TTCGCGAGCAATAGAAGGGC 60.810 55.000 9.59 0.00 0.00 5.19
185 186 0.931005 GTTCGCGAGCAATAGAAGGG 59.069 55.000 18.62 0.00 0.00 3.95
186 187 1.590238 CTGTTCGCGAGCAATAGAAGG 59.410 52.381 25.68 9.23 0.00 3.46
187 188 2.028523 CACTGTTCGCGAGCAATAGAAG 59.971 50.000 25.68 15.38 0.00 2.85
188 189 1.992667 CACTGTTCGCGAGCAATAGAA 59.007 47.619 25.68 2.64 0.00 2.10
189 190 1.201414 TCACTGTTCGCGAGCAATAGA 59.799 47.619 25.68 19.33 0.00 1.98
190 191 1.585668 CTCACTGTTCGCGAGCAATAG 59.414 52.381 25.68 18.03 0.00 1.73
191 192 1.067846 ACTCACTGTTCGCGAGCAATA 60.068 47.619 25.68 13.10 0.00 1.90
192 193 0.319900 ACTCACTGTTCGCGAGCAAT 60.320 50.000 25.68 14.61 0.00 3.56
193 194 1.067416 ACTCACTGTTCGCGAGCAA 59.933 52.632 25.68 11.12 0.00 3.91
194 195 1.661509 CACTCACTGTTCGCGAGCA 60.662 57.895 24.32 24.32 0.00 4.26
195 196 0.734253 ATCACTCACTGTTCGCGAGC 60.734 55.000 16.69 16.69 0.00 5.03
196 197 0.987715 CATCACTCACTGTTCGCGAG 59.012 55.000 9.59 0.00 0.00 5.03
197 198 1.008875 GCATCACTCACTGTTCGCGA 61.009 55.000 3.71 3.71 0.00 5.87
198 199 1.284297 TGCATCACTCACTGTTCGCG 61.284 55.000 0.00 0.00 0.00 5.87
199 200 1.081892 ATGCATCACTCACTGTTCGC 58.918 50.000 0.00 0.00 0.00 4.70
200 201 1.201998 GCATGCATCACTCACTGTTCG 60.202 52.381 14.21 0.00 0.00 3.95
201 202 1.808343 TGCATGCATCACTCACTGTTC 59.192 47.619 18.46 0.00 0.00 3.18
202 203 1.538512 GTGCATGCATCACTCACTGTT 59.461 47.619 25.64 0.00 0.00 3.16
203 204 1.162698 GTGCATGCATCACTCACTGT 58.837 50.000 25.64 0.00 0.00 3.55
204 205 0.450583 GGTGCATGCATCACTCACTG 59.549 55.000 26.02 2.95 34.97 3.66
205 206 0.327259 AGGTGCATGCATCACTCACT 59.673 50.000 31.54 14.30 34.97 3.41
206 207 0.450583 CAGGTGCATGCATCACTCAC 59.549 55.000 31.54 13.34 34.97 3.51
207 208 0.678684 CCAGGTGCATGCATCACTCA 60.679 55.000 31.54 0.00 34.97 3.41
208 209 1.381928 CCCAGGTGCATGCATCACTC 61.382 60.000 31.54 14.83 34.97 3.51
209 210 1.379443 CCCAGGTGCATGCATCACT 60.379 57.895 31.54 22.21 34.97 3.41
210 211 1.378911 TCCCAGGTGCATGCATCAC 60.379 57.895 31.54 20.43 0.00 3.06
211 212 1.378911 GTCCCAGGTGCATGCATCA 60.379 57.895 31.54 9.26 0.00 3.07
212 213 2.475466 CGTCCCAGGTGCATGCATC 61.475 63.158 25.64 24.66 0.00 3.91
217 218 2.359169 ATCGTCGTCCCAGGTGCAT 61.359 57.895 0.00 0.00 0.00 3.96
229 230 4.800993 GCCATTCTTATCCTATCATCGTCG 59.199 45.833 0.00 0.00 0.00 5.12
232 233 5.350504 AGGCCATTCTTATCCTATCATCG 57.649 43.478 5.01 0.00 0.00 3.84
240 241 4.537135 TCGATGTAGGCCATTCTTATCC 57.463 45.455 5.01 0.00 32.56 2.59
284 285 2.104928 GCCGCCAAAGCCATTAGC 59.895 61.111 0.00 0.00 44.25 3.09
285 286 1.139520 GTGCCGCCAAAGCCATTAG 59.860 57.895 0.00 0.00 34.57 1.73
286 287 2.695759 CGTGCCGCCAAAGCCATTA 61.696 57.895 0.00 0.00 34.57 1.90
316 317 2.668279 CGTTCCATTCCTTTCGCCAAAG 60.668 50.000 0.00 0.00 39.11 2.77
347 348 1.080093 CCGTCAGTGCGTATGTGGT 60.080 57.895 6.29 0.00 0.00 4.16
350 351 2.125673 GGCCGTCAGTGCGTATGT 60.126 61.111 0.00 0.00 0.00 2.29
387 388 2.661866 ATCGTTATCCAGCGGCGC 60.662 61.111 26.86 26.86 0.00 6.53
446 447 1.661112 GCTCGGAAGAAATCTGGTTCG 59.339 52.381 0.00 0.00 41.32 3.95
450 451 1.135139 TCGAGCTCGGAAGAAATCTGG 59.865 52.381 33.98 3.12 41.32 3.86
458 459 2.492090 CAGGGTCGAGCTCGGAAG 59.508 66.667 33.98 16.62 40.29 3.46
468 469 1.504359 TAGAAACGTTTGCAGGGTCG 58.496 50.000 20.10 0.00 0.00 4.79
503 514 7.254829 GCATCGAAGACAGAGTCTACATACTAA 60.255 40.741 0.00 0.00 42.59 2.24
504 515 6.203145 GCATCGAAGACAGAGTCTACATACTA 59.797 42.308 0.00 0.00 42.59 1.82
596 613 0.028505 GCGTCGCTATCGGTACTTCA 59.971 55.000 10.68 0.00 36.13 3.02
599 616 0.532417 AGAGCGTCGCTATCGGTACT 60.532 55.000 21.77 8.19 39.88 2.73
609 626 2.456119 CCATTGGTCAGAGCGTCGC 61.456 63.158 9.80 9.80 0.00 5.19
701 721 3.689002 GAGTGGCACTGGGGCTAGC 62.689 68.421 27.45 6.04 43.83 3.42
728 748 0.108992 TAGCACACGGGATTGTCGAC 60.109 55.000 9.11 9.11 0.00 4.20
769 790 5.251468 TGGACACTGGAAGGTACTAGTAGTA 59.749 44.000 5.90 5.90 38.49 1.82
771 792 4.597004 TGGACACTGGAAGGTACTAGTAG 58.403 47.826 1.87 0.00 38.49 2.57
855 879 4.449068 GTGGTAACTGATAAGCATCATCGG 59.551 45.833 0.00 0.00 40.40 4.18
875 899 3.488721 CGAATGGTACCGAAGAGTAGTGG 60.489 52.174 7.57 0.00 0.00 4.00
929 954 8.524487 GGATGTGGTAGAATCGAATAGATACTT 58.476 37.037 0.00 0.00 38.98 2.24
930 955 7.670140 TGGATGTGGTAGAATCGAATAGATACT 59.330 37.037 0.00 0.00 38.98 2.12
932 957 8.595362 ATGGATGTGGTAGAATCGAATAGATA 57.405 34.615 0.00 0.00 38.98 1.98
935 960 6.929625 AGATGGATGTGGTAGAATCGAATAG 58.070 40.000 0.00 0.00 0.00 1.73
1109 1142 5.106197 TGACGATCAAAGCAAGCAACATAAT 60.106 36.000 0.00 0.00 0.00 1.28
1111 1144 3.750652 TGACGATCAAAGCAAGCAACATA 59.249 39.130 0.00 0.00 0.00 2.29
1112 1145 2.553602 TGACGATCAAAGCAAGCAACAT 59.446 40.909 0.00 0.00 0.00 2.71
1113 1146 1.946081 TGACGATCAAAGCAAGCAACA 59.054 42.857 0.00 0.00 0.00 3.33
1134 1167 5.728351 TTACACACACACAGTTAGCTTTC 57.272 39.130 0.00 0.00 0.00 2.62
1138 1171 2.869801 TGCTTACACACACACAGTTAGC 59.130 45.455 0.00 0.00 38.13 3.09
1139 1172 3.059597 GCTGCTTACACACACACAGTTAG 60.060 47.826 0.00 0.00 0.00 2.34
1140 1173 2.869801 GCTGCTTACACACACACAGTTA 59.130 45.455 0.00 0.00 0.00 2.24
1142 1175 1.134401 AGCTGCTTACACACACACAGT 60.134 47.619 0.00 0.00 0.00 3.55
1143 1176 1.528586 GAGCTGCTTACACACACACAG 59.471 52.381 2.53 0.00 0.00 3.66
1144 1177 1.581934 GAGCTGCTTACACACACACA 58.418 50.000 2.53 0.00 0.00 3.72
1145 1178 0.508641 CGAGCTGCTTACACACACAC 59.491 55.000 2.53 0.00 0.00 3.82
1250 1295 2.047179 GACGGCAAGGGTCTCACC 60.047 66.667 0.00 0.00 37.60 4.02
1251 1296 2.432628 CGACGGCAAGGGTCTCAC 60.433 66.667 0.00 0.00 32.24 3.51
1252 1297 2.599281 TCGACGGCAAGGGTCTCA 60.599 61.111 0.00 0.00 32.24 3.27
1253 1298 2.126031 GTCGACGGCAAGGGTCTC 60.126 66.667 0.00 0.00 32.24 3.36
1254 1299 4.052229 CGTCGACGGCAAGGGTCT 62.052 66.667 29.70 0.00 35.37 3.85
1255 1300 4.353437 ACGTCGACGGCAAGGGTC 62.353 66.667 37.89 0.00 44.95 4.46
1263 1308 4.112341 GGGAGGTGACGTCGACGG 62.112 72.222 37.89 21.83 44.95 4.79
1264 1309 3.054503 AGGGAGGTGACGTCGACG 61.055 66.667 34.58 34.58 46.33 5.12
1265 1310 1.803366 AACAGGGAGGTGACGTCGAC 61.803 60.000 11.62 5.18 0.00 4.20
1266 1311 1.521450 GAACAGGGAGGTGACGTCGA 61.521 60.000 11.62 0.00 0.00 4.20
1279 1324 4.101448 CCAGGGGAGGCGAACAGG 62.101 72.222 0.00 0.00 0.00 4.00
1281 1326 3.319198 GACCAGGGGAGGCGAACA 61.319 66.667 0.00 0.00 0.00 3.18
1283 1328 4.689549 TCGACCAGGGGAGGCGAA 62.690 66.667 0.00 0.00 35.41 4.70
1287 1332 1.115930 CATAGGTCGACCAGGGGAGG 61.116 65.000 35.00 13.15 38.89 4.30
1368 1419 4.271816 CGATCTCCTCGTGGCCGG 62.272 72.222 0.00 0.00 42.56 6.13
1466 1519 2.878406 ACTGACCACGTCAAATCAAAGG 59.122 45.455 0.00 0.00 42.26 3.11
1497 1550 7.388500 CCCAAAACAAACAATTAGCAGATCAAT 59.612 33.333 0.00 0.00 0.00 2.57
1682 2056 0.534877 ATTGTTCCAGCAGCGTGACA 60.535 50.000 0.00 0.00 0.00 3.58
1732 2112 2.126057 TGGACATATGGTGCATCTCCA 58.874 47.619 7.80 6.28 43.49 3.86
1903 2292 5.690409 CCCTATGAACGTACACATACACATC 59.310 44.000 0.00 0.00 0.00 3.06
1904 2293 5.128171 ACCCTATGAACGTACACATACACAT 59.872 40.000 0.00 0.00 0.00 3.21
1918 2307 3.555956 CGCATACACTCAACCCTATGAAC 59.444 47.826 0.00 0.00 0.00 3.18
1928 2317 2.159296 AGACATACGCGCATACACTCAA 60.159 45.455 5.73 0.00 0.00 3.02
1948 2337 1.444383 TACAGACGCAAGCGCTCAG 60.444 57.895 12.06 8.10 44.19 3.35
2073 5000 4.213270 AGTCGCGATGAAATTGACTGAAAA 59.787 37.500 14.06 0.00 38.41 2.29
2074 5001 3.745975 AGTCGCGATGAAATTGACTGAAA 59.254 39.130 14.06 0.00 38.41 2.69
2075 5002 3.325870 AGTCGCGATGAAATTGACTGAA 58.674 40.909 14.06 0.00 38.41 3.02
2076 5003 2.923655 GAGTCGCGATGAAATTGACTGA 59.076 45.455 14.06 0.00 39.83 3.41
2077 5004 2.284684 CGAGTCGCGATGAAATTGACTG 60.285 50.000 14.06 0.00 44.57 3.51
2078 5005 1.920574 CGAGTCGCGATGAAATTGACT 59.079 47.619 14.06 0.47 44.57 3.41
2079 5006 1.589968 GCGAGTCGCGATGAAATTGAC 60.590 52.381 23.39 0.00 44.55 3.18
2080 5007 0.645355 GCGAGTCGCGATGAAATTGA 59.355 50.000 23.39 0.00 44.55 2.57
2081 5008 3.118996 GCGAGTCGCGATGAAATTG 57.881 52.632 23.39 1.61 44.55 2.32
2092 5019 2.033550 AGCATAAACCTAGAGCGAGTCG 59.966 50.000 8.54 8.54 0.00 4.18
2093 5020 3.719173 AGCATAAACCTAGAGCGAGTC 57.281 47.619 0.00 0.00 0.00 3.36
2412 5342 8.499514 TGAAAAAGTCACAAATTTGCAAAAAC 57.500 26.923 17.19 9.01 0.00 2.43
2475 5406 3.232720 AGGGTGTACGTCCCAAATTTT 57.767 42.857 22.44 3.79 46.82 1.82


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

AutoCloner maintained by Alex Coulton.