Multiple sequence alignment - TraesCS7B01G136000

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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 TraesCS7B01G136000 chr7B 100.000 2948 0 0 1 2948 167688751 167685804 0.000000e+00 5445.0
1 TraesCS7B01G136000 chr7A 90.461 1866 100 32 252 2094 215881176 215879366 0.000000e+00 2388.0
2 TraesCS7B01G136000 chr7A 76.169 449 80 24 1512 1942 34722065 34722504 8.280000e-51 211.0
3 TraesCS7B01G136000 chr7A 92.208 77 6 0 105 181 122045136 122045060 3.110000e-20 110.0
4 TraesCS7B01G136000 chr7A 90.667 75 7 0 107 181 206036121 206036195 1.870000e-17 100.0
5 TraesCS7B01G136000 chr7A 88.000 75 9 0 107 181 5499925 5499999 4.050000e-14 89.8
6 TraesCS7B01G136000 chr7D 89.507 1868 81 41 252 2094 204088591 204086814 0.000000e+00 2257.0
7 TraesCS7B01G136000 chr7D 89.531 831 70 14 2097 2915 51419524 51420349 0.000000e+00 1037.0
8 TraesCS7B01G136000 chr7D 89.354 836 74 14 2095 2919 370973631 370974462 0.000000e+00 1037.0
9 TraesCS7B01G136000 chr7D 76.064 376 64 22 1585 1942 34337289 34337656 3.910000e-39 172.0
10 TraesCS7B01G136000 chr4D 89.218 844 77 12 2095 2928 329141719 329142558 0.000000e+00 1042.0
11 TraesCS7B01G136000 chr4D 77.257 576 109 19 1384 1942 508807751 508807181 4.740000e-83 318.0
12 TraesCS7B01G136000 chr3D 89.222 835 81 8 2095 2921 604796461 604795628 0.000000e+00 1035.0
13 TraesCS7B01G136000 chr3D 91.045 67 6 0 108 174 411046864 411046930 1.130000e-14 91.6
14 TraesCS7B01G136000 chr6D 89.141 838 75 14 2098 2927 306719147 306718318 0.000000e+00 1029.0
15 TraesCS7B01G136000 chr6B 89.036 830 81 9 2096 2919 223037025 223037850 0.000000e+00 1020.0
16 TraesCS7B01G136000 chr6B 92.308 78 5 1 105 181 62761655 62761732 3.110000e-20 110.0
17 TraesCS7B01G136000 chr5D 88.731 843 79 14 2097 2928 548190379 548191216 0.000000e+00 1016.0
18 TraesCS7B01G136000 chr1A 88.822 832 85 7 2093 2920 218120345 218121172 0.000000e+00 1014.0
19 TraesCS7B01G136000 chr1A 88.836 833 81 12 2093 2918 73810549 73811376 0.000000e+00 1013.0
20 TraesCS7B01G136000 chr3B 93.333 75 5 0 107 181 576051629 576051555 8.640000e-21 111.0
21 TraesCS7B01G136000 chr3B 90.667 75 7 0 107 181 73274880 73274954 1.870000e-17 100.0
22 TraesCS7B01G136000 chr4A 92.105 76 6 0 106 181 558220278 558220353 1.120000e-19 108.0
23 TraesCS7B01G136000 chr2B 88.158 76 8 1 106 181 1517247 1517173 4.050000e-14 89.8


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 TraesCS7B01G136000 chr7B 167685804 167688751 2947 True 5445 5445 100.000 1 2948 1 chr7B.!!$R1 2947
1 TraesCS7B01G136000 chr7A 215879366 215881176 1810 True 2388 2388 90.461 252 2094 1 chr7A.!!$R2 1842
2 TraesCS7B01G136000 chr7D 204086814 204088591 1777 True 2257 2257 89.507 252 2094 1 chr7D.!!$R1 1842
3 TraesCS7B01G136000 chr7D 51419524 51420349 825 False 1037 1037 89.531 2097 2915 1 chr7D.!!$F2 818
4 TraesCS7B01G136000 chr7D 370973631 370974462 831 False 1037 1037 89.354 2095 2919 1 chr7D.!!$F3 824
5 TraesCS7B01G136000 chr4D 329141719 329142558 839 False 1042 1042 89.218 2095 2928 1 chr4D.!!$F1 833
6 TraesCS7B01G136000 chr4D 508807181 508807751 570 True 318 318 77.257 1384 1942 1 chr4D.!!$R1 558
7 TraesCS7B01G136000 chr3D 604795628 604796461 833 True 1035 1035 89.222 2095 2921 1 chr3D.!!$R1 826
8 TraesCS7B01G136000 chr6D 306718318 306719147 829 True 1029 1029 89.141 2098 2927 1 chr6D.!!$R1 829
9 TraesCS7B01G136000 chr6B 223037025 223037850 825 False 1020 1020 89.036 2096 2919 1 chr6B.!!$F2 823
10 TraesCS7B01G136000 chr5D 548190379 548191216 837 False 1016 1016 88.731 2097 2928 1 chr5D.!!$F1 831
11 TraesCS7B01G136000 chr1A 218120345 218121172 827 False 1014 1014 88.822 2093 2920 1 chr1A.!!$F2 827
12 TraesCS7B01G136000 chr1A 73810549 73811376 827 False 1013 1013 88.836 2093 2918 1 chr1A.!!$F1 825

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
140 141 0.179081 GCCAGAATCCGACCACTACC 60.179 60.0 0.0 0.0 0.00 3.18 F
1114 1152 0.250295 CCAACCGTCACTCCATGTGT 60.250 55.0 0.0 0.0 46.27 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1339 1388 0.036671 GTCCCCAGTTAACTCACCGG 60.037 60.0 4.77 0.00 0.0 5.28 R
2720 2803 0.456995 CCTTCACGACGAGCTCTTCC 60.457 60.0 14.08 1.17 0.0 3.46 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
40 41 4.351874 AACTAGCAGAGTTTGTTAGCCA 57.648 40.909 4.69 0.00 46.79 4.75
41 42 4.559862 ACTAGCAGAGTTTGTTAGCCAT 57.440 40.909 4.69 0.00 42.48 4.40
42 43 5.677319 ACTAGCAGAGTTTGTTAGCCATA 57.323 39.130 4.69 0.00 42.48 2.74
43 44 6.240549 ACTAGCAGAGTTTGTTAGCCATAT 57.759 37.500 4.69 0.00 42.48 1.78
44 45 7.361457 ACTAGCAGAGTTTGTTAGCCATATA 57.639 36.000 4.69 0.00 42.48 0.86
45 46 7.210873 ACTAGCAGAGTTTGTTAGCCATATAC 58.789 38.462 4.69 0.00 42.48 1.47
46 47 6.240549 AGCAGAGTTTGTTAGCCATATACT 57.759 37.500 0.00 0.00 0.00 2.12
47 48 6.284459 AGCAGAGTTTGTTAGCCATATACTC 58.716 40.000 0.00 0.00 31.56 2.59
48 49 5.467063 GCAGAGTTTGTTAGCCATATACTCC 59.533 44.000 0.00 0.00 31.67 3.85
49 50 6.582636 CAGAGTTTGTTAGCCATATACTCCA 58.417 40.000 0.00 0.00 31.67 3.86
50 51 6.480320 CAGAGTTTGTTAGCCATATACTCCAC 59.520 42.308 0.00 0.00 31.67 4.02
51 52 6.156256 AGAGTTTGTTAGCCATATACTCCACA 59.844 38.462 0.00 0.00 31.67 4.17
52 53 6.900194 AGTTTGTTAGCCATATACTCCACAT 58.100 36.000 0.00 0.00 0.00 3.21
53 54 6.992715 AGTTTGTTAGCCATATACTCCACATC 59.007 38.462 0.00 0.00 0.00 3.06
54 55 6.493189 TTGTTAGCCATATACTCCACATCA 57.507 37.500 0.00 0.00 0.00 3.07
55 56 6.686484 TGTTAGCCATATACTCCACATCAT 57.314 37.500 0.00 0.00 0.00 2.45
56 57 7.078249 TGTTAGCCATATACTCCACATCATT 57.922 36.000 0.00 0.00 0.00 2.57
57 58 7.517320 TGTTAGCCATATACTCCACATCATTT 58.483 34.615 0.00 0.00 0.00 2.32
58 59 8.655901 TGTTAGCCATATACTCCACATCATTTA 58.344 33.333 0.00 0.00 0.00 1.40
59 60 9.672673 GTTAGCCATATACTCCACATCATTTAT 57.327 33.333 0.00 0.00 0.00 1.40
72 73 9.511272 TCCACATCATTTATATTGAGATTGAGG 57.489 33.333 0.00 0.00 0.00 3.86
73 74 8.737175 CCACATCATTTATATTGAGATTGAGGG 58.263 37.037 0.00 0.00 0.00 4.30
74 75 9.511272 CACATCATTTATATTGAGATTGAGGGA 57.489 33.333 0.00 0.00 0.00 4.20
75 76 9.736414 ACATCATTTATATTGAGATTGAGGGAG 57.264 33.333 0.00 0.00 0.00 4.30
76 77 9.736414 CATCATTTATATTGAGATTGAGGGAGT 57.264 33.333 0.00 0.00 0.00 3.85
88 89 9.206690 TGAGATTGAGGGAGTATTGATATATCC 57.793 37.037 10.25 0.00 0.00 2.59
89 90 9.432982 GAGATTGAGGGAGTATTGATATATCCT 57.567 37.037 10.25 0.00 0.00 3.24
90 91 9.796242 AGATTGAGGGAGTATTGATATATCCTT 57.204 33.333 10.25 0.51 0.00 3.36
93 94 8.972662 TGAGGGAGTATTGATATATCCTTTCA 57.027 34.615 10.25 3.84 0.00 2.69
94 95 9.392506 TGAGGGAGTATTGATATATCCTTTCAA 57.607 33.333 10.25 0.00 34.18 2.69
95 96 9.660180 GAGGGAGTATTGATATATCCTTTCAAC 57.340 37.037 10.25 1.05 32.61 3.18
96 97 9.398921 AGGGAGTATTGATATATCCTTTCAACT 57.601 33.333 10.25 5.39 32.61 3.16
97 98 9.660180 GGGAGTATTGATATATCCTTTCAACTC 57.340 37.037 10.25 12.45 32.61 3.01
98 99 9.660180 GGAGTATTGATATATCCTTTCAACTCC 57.340 37.037 19.76 19.76 38.89 3.85
109 110 5.557866 TCCTTTCAACTCCTAGTTTTAGGC 58.442 41.667 0.00 0.00 45.25 3.93
110 111 4.700692 CCTTTCAACTCCTAGTTTTAGGCC 59.299 45.833 0.00 0.00 45.25 5.19
111 112 3.994931 TCAACTCCTAGTTTTAGGCCC 57.005 47.619 0.00 0.00 45.25 5.80
112 113 3.253220 TCAACTCCTAGTTTTAGGCCCA 58.747 45.455 0.00 0.00 45.25 5.36
113 114 3.263425 TCAACTCCTAGTTTTAGGCCCAG 59.737 47.826 0.00 0.00 45.25 4.45
114 115 2.917205 ACTCCTAGTTTTAGGCCCAGT 58.083 47.619 0.00 0.00 45.25 4.00
115 116 3.257578 ACTCCTAGTTTTAGGCCCAGTT 58.742 45.455 0.00 0.00 45.25 3.16
116 117 3.263681 ACTCCTAGTTTTAGGCCCAGTTC 59.736 47.826 0.00 0.00 45.25 3.01
117 118 3.519913 CTCCTAGTTTTAGGCCCAGTTCT 59.480 47.826 0.00 0.00 45.25 3.01
118 119 3.914435 TCCTAGTTTTAGGCCCAGTTCTT 59.086 43.478 0.00 0.00 45.25 2.52
119 120 4.352893 TCCTAGTTTTAGGCCCAGTTCTTT 59.647 41.667 0.00 0.00 45.25 2.52
120 121 5.077564 CCTAGTTTTAGGCCCAGTTCTTTT 58.922 41.667 0.00 0.00 40.10 2.27
121 122 4.937201 AGTTTTAGGCCCAGTTCTTTTG 57.063 40.909 0.00 0.00 0.00 2.44
122 123 3.069586 AGTTTTAGGCCCAGTTCTTTTGC 59.930 43.478 0.00 0.00 0.00 3.68
123 124 1.627864 TTAGGCCCAGTTCTTTTGCC 58.372 50.000 0.00 0.00 42.48 4.52
124 125 0.480690 TAGGCCCAGTTCTTTTGCCA 59.519 50.000 0.00 0.00 44.60 4.92
125 126 0.829182 AGGCCCAGTTCTTTTGCCAG 60.829 55.000 0.00 0.00 44.60 4.85
126 127 0.827507 GGCCCAGTTCTTTTGCCAGA 60.828 55.000 0.00 0.00 41.76 3.86
127 128 1.039856 GCCCAGTTCTTTTGCCAGAA 58.960 50.000 0.00 0.00 0.00 3.02
128 129 1.620323 GCCCAGTTCTTTTGCCAGAAT 59.380 47.619 0.00 0.00 35.23 2.40
129 130 2.353109 GCCCAGTTCTTTTGCCAGAATC 60.353 50.000 0.00 0.00 35.23 2.52
130 131 2.232208 CCCAGTTCTTTTGCCAGAATCC 59.768 50.000 0.00 0.00 35.23 3.01
131 132 2.095059 CCAGTTCTTTTGCCAGAATCCG 60.095 50.000 0.00 0.00 35.23 4.18
132 133 2.813754 CAGTTCTTTTGCCAGAATCCGA 59.186 45.455 0.00 0.00 35.23 4.55
133 134 2.814336 AGTTCTTTTGCCAGAATCCGAC 59.186 45.455 0.00 0.00 35.23 4.79
134 135 1.821216 TCTTTTGCCAGAATCCGACC 58.179 50.000 0.00 0.00 0.00 4.79
135 136 1.073125 TCTTTTGCCAGAATCCGACCA 59.927 47.619 0.00 0.00 0.00 4.02
136 137 1.200020 CTTTTGCCAGAATCCGACCAC 59.800 52.381 0.00 0.00 0.00 4.16
137 138 0.400213 TTTGCCAGAATCCGACCACT 59.600 50.000 0.00 0.00 0.00 4.00
138 139 1.271856 TTGCCAGAATCCGACCACTA 58.728 50.000 0.00 0.00 0.00 2.74
139 140 0.535335 TGCCAGAATCCGACCACTAC 59.465 55.000 0.00 0.00 0.00 2.73
140 141 0.179081 GCCAGAATCCGACCACTACC 60.179 60.000 0.00 0.00 0.00 3.18
141 142 0.464452 CCAGAATCCGACCACTACCC 59.536 60.000 0.00 0.00 0.00 3.69
142 143 1.191535 CAGAATCCGACCACTACCCA 58.808 55.000 0.00 0.00 0.00 4.51
143 144 1.137086 CAGAATCCGACCACTACCCAG 59.863 57.143 0.00 0.00 0.00 4.45
144 145 0.179081 GAATCCGACCACTACCCAGC 60.179 60.000 0.00 0.00 0.00 4.85
145 146 0.617820 AATCCGACCACTACCCAGCT 60.618 55.000 0.00 0.00 0.00 4.24
146 147 0.617820 ATCCGACCACTACCCAGCTT 60.618 55.000 0.00 0.00 0.00 3.74
147 148 1.218316 CCGACCACTACCCAGCTTC 59.782 63.158 0.00 0.00 0.00 3.86
148 149 1.258445 CCGACCACTACCCAGCTTCT 61.258 60.000 0.00 0.00 0.00 2.85
149 150 0.608640 CGACCACTACCCAGCTTCTT 59.391 55.000 0.00 0.00 0.00 2.52
150 151 1.002087 CGACCACTACCCAGCTTCTTT 59.998 52.381 0.00 0.00 0.00 2.52
151 152 2.701107 GACCACTACCCAGCTTCTTTC 58.299 52.381 0.00 0.00 0.00 2.62
152 153 2.038557 GACCACTACCCAGCTTCTTTCA 59.961 50.000 0.00 0.00 0.00 2.69
153 154 2.039084 ACCACTACCCAGCTTCTTTCAG 59.961 50.000 0.00 0.00 0.00 3.02
154 155 2.303022 CCACTACCCAGCTTCTTTCAGA 59.697 50.000 0.00 0.00 0.00 3.27
155 156 3.244561 CCACTACCCAGCTTCTTTCAGAA 60.245 47.826 0.00 0.00 32.50 3.02
156 157 4.566488 CCACTACCCAGCTTCTTTCAGAAT 60.566 45.833 0.00 0.00 33.13 2.40
157 158 5.006386 CACTACCCAGCTTCTTTCAGAATT 58.994 41.667 0.00 0.00 33.13 2.17
158 159 5.474876 CACTACCCAGCTTCTTTCAGAATTT 59.525 40.000 0.00 0.00 33.13 1.82
159 160 6.015940 CACTACCCAGCTTCTTTCAGAATTTT 60.016 38.462 0.00 0.00 33.13 1.82
160 161 5.876651 ACCCAGCTTCTTTCAGAATTTTT 57.123 34.783 0.00 0.00 33.13 1.94
161 162 6.976934 ACCCAGCTTCTTTCAGAATTTTTA 57.023 33.333 0.00 0.00 33.13 1.52
162 163 7.360113 ACCCAGCTTCTTTCAGAATTTTTAA 57.640 32.000 0.00 0.00 33.13 1.52
163 164 7.436933 ACCCAGCTTCTTTCAGAATTTTTAAG 58.563 34.615 0.00 0.00 33.13 1.85
164 165 6.367149 CCCAGCTTCTTTCAGAATTTTTAAGC 59.633 38.462 0.00 0.00 38.64 3.09
165 166 6.367149 CCAGCTTCTTTCAGAATTTTTAAGCC 59.633 38.462 0.00 0.00 39.04 4.35
166 167 6.367149 CAGCTTCTTTCAGAATTTTTAAGCCC 59.633 38.462 0.00 0.00 39.04 5.19
167 168 5.639506 GCTTCTTTCAGAATTTTTAAGCCCC 59.360 40.000 0.00 0.00 33.13 5.80
168 169 6.739331 TTCTTTCAGAATTTTTAAGCCCCA 57.261 33.333 0.00 0.00 0.00 4.96
169 170 6.933514 TCTTTCAGAATTTTTAAGCCCCAT 57.066 33.333 0.00 0.00 0.00 4.00
170 171 7.315066 TCTTTCAGAATTTTTAAGCCCCATT 57.685 32.000 0.00 0.00 0.00 3.16
171 172 7.744733 TCTTTCAGAATTTTTAAGCCCCATTT 58.255 30.769 0.00 0.00 0.00 2.32
172 173 7.661027 TCTTTCAGAATTTTTAAGCCCCATTTG 59.339 33.333 0.00 0.00 0.00 2.32
173 174 6.432403 TCAGAATTTTTAAGCCCCATTTGT 57.568 33.333 0.00 0.00 0.00 2.83
174 175 6.836242 TCAGAATTTTTAAGCCCCATTTGTT 58.164 32.000 0.00 0.00 0.00 2.83
175 176 7.286313 TCAGAATTTTTAAGCCCCATTTGTTT 58.714 30.769 0.00 0.00 0.00 2.83
176 177 7.777440 TCAGAATTTTTAAGCCCCATTTGTTTT 59.223 29.630 0.00 0.00 0.00 2.43
177 178 9.061435 CAGAATTTTTAAGCCCCATTTGTTTTA 57.939 29.630 0.00 0.00 0.00 1.52
178 179 9.062524 AGAATTTTTAAGCCCCATTTGTTTTAC 57.937 29.630 0.00 0.00 0.00 2.01
179 180 8.753497 AATTTTTAAGCCCCATTTGTTTTACA 57.247 26.923 0.00 0.00 0.00 2.41
180 181 8.753497 ATTTTTAAGCCCCATTTGTTTTACAA 57.247 26.923 0.00 0.00 36.11 2.41
181 182 7.793927 TTTTAAGCCCCATTTGTTTTACAAG 57.206 32.000 0.00 0.00 39.53 3.16
182 183 6.732896 TTAAGCCCCATTTGTTTTACAAGA 57.267 33.333 0.00 0.00 39.53 3.02
183 184 5.823861 AAGCCCCATTTGTTTTACAAGAT 57.176 34.783 0.00 0.00 39.53 2.40
184 185 5.823861 AGCCCCATTTGTTTTACAAGATT 57.176 34.783 0.00 0.00 39.53 2.40
185 186 6.926630 AGCCCCATTTGTTTTACAAGATTA 57.073 33.333 0.00 0.00 39.53 1.75
186 187 7.494922 AGCCCCATTTGTTTTACAAGATTAT 57.505 32.000 0.00 0.00 39.53 1.28
187 188 7.330262 AGCCCCATTTGTTTTACAAGATTATG 58.670 34.615 0.00 0.00 39.53 1.90
188 189 6.538381 GCCCCATTTGTTTTACAAGATTATGG 59.462 38.462 11.42 11.42 40.15 2.74
189 190 7.580495 GCCCCATTTGTTTTACAAGATTATGGA 60.580 37.037 16.77 0.00 41.70 3.41
190 191 8.317679 CCCCATTTGTTTTACAAGATTATGGAA 58.682 33.333 16.77 0.00 41.70 3.53
191 192 9.150348 CCCATTTGTTTTACAAGATTATGGAAC 57.850 33.333 16.77 0.00 41.70 3.62
192 193 9.703892 CCATTTGTTTTACAAGATTATGGAACA 57.296 29.630 12.44 0.00 41.70 3.18
195 196 8.810652 TTGTTTTACAAGATTATGGAACAAGC 57.189 30.769 0.00 0.00 35.62 4.01
196 197 7.870445 TTGTTTTACAAGATTATGGAACAAGCC 59.130 33.333 0.00 0.00 35.62 4.35
204 205 2.074967 TGGAACAAGCCAGGTAGGG 58.925 57.895 0.00 0.00 33.58 3.53
205 206 0.474854 TGGAACAAGCCAGGTAGGGA 60.475 55.000 0.00 0.00 33.58 4.20
206 207 0.919710 GGAACAAGCCAGGTAGGGAT 59.080 55.000 0.00 0.00 38.09 3.85
207 208 1.134068 GGAACAAGCCAGGTAGGGATC 60.134 57.143 0.00 0.00 38.09 3.36
208 209 0.541863 AACAAGCCAGGTAGGGATCG 59.458 55.000 0.00 0.00 38.09 3.69
209 210 0.325296 ACAAGCCAGGTAGGGATCGA 60.325 55.000 0.00 0.00 38.09 3.59
210 211 0.830648 CAAGCCAGGTAGGGATCGAA 59.169 55.000 0.00 0.00 38.09 3.71
211 212 1.417890 CAAGCCAGGTAGGGATCGAAT 59.582 52.381 0.00 0.00 38.09 3.34
212 213 1.807814 AGCCAGGTAGGGATCGAATT 58.192 50.000 0.00 0.00 38.09 2.17
213 214 2.127708 AGCCAGGTAGGGATCGAATTT 58.872 47.619 0.00 0.00 38.09 1.82
214 215 2.509964 AGCCAGGTAGGGATCGAATTTT 59.490 45.455 0.00 0.00 38.09 1.82
215 216 2.618709 GCCAGGTAGGGATCGAATTTTG 59.381 50.000 0.00 0.00 38.09 2.44
216 217 3.684413 GCCAGGTAGGGATCGAATTTTGA 60.684 47.826 0.00 0.00 38.09 2.69
217 218 4.523083 CCAGGTAGGGATCGAATTTTGAA 58.477 43.478 0.00 0.00 0.00 2.69
218 219 4.947388 CCAGGTAGGGATCGAATTTTGAAA 59.053 41.667 0.00 0.00 0.00 2.69
219 220 5.066505 CCAGGTAGGGATCGAATTTTGAAAG 59.933 44.000 0.00 0.00 0.00 2.62
220 221 5.880332 CAGGTAGGGATCGAATTTTGAAAGA 59.120 40.000 0.00 0.00 0.00 2.52
221 222 6.374333 CAGGTAGGGATCGAATTTTGAAAGAA 59.626 38.462 0.00 0.00 0.00 2.52
222 223 7.067494 CAGGTAGGGATCGAATTTTGAAAGAAT 59.933 37.037 0.00 0.00 0.00 2.40
223 224 7.283354 AGGTAGGGATCGAATTTTGAAAGAATC 59.717 37.037 0.00 0.00 0.00 2.52
224 225 6.456795 AGGGATCGAATTTTGAAAGAATCC 57.543 37.500 0.00 0.00 0.00 3.01
225 226 5.360999 AGGGATCGAATTTTGAAAGAATCCC 59.639 40.000 11.94 11.94 43.16 3.85
226 227 5.360999 GGGATCGAATTTTGAAAGAATCCCT 59.639 40.000 12.38 0.00 40.50 4.20
227 228 6.546034 GGGATCGAATTTTGAAAGAATCCCTA 59.454 38.462 12.38 0.00 40.50 3.53
228 229 7.255277 GGGATCGAATTTTGAAAGAATCCCTAG 60.255 40.741 12.38 0.00 40.50 3.02
229 230 7.499232 GGATCGAATTTTGAAAGAATCCCTAGA 59.501 37.037 0.00 0.00 0.00 2.43
230 231 8.986929 ATCGAATTTTGAAAGAATCCCTAGAT 57.013 30.769 0.00 0.00 0.00 1.98
231 232 8.807948 TCGAATTTTGAAAGAATCCCTAGATT 57.192 30.769 0.00 0.00 45.63 2.40
268 269 5.250200 TGGGCCTTACACTGTTATTTACTG 58.750 41.667 4.53 0.00 0.00 2.74
348 350 2.593346 TGAGCCGCAAAATGTTGTTT 57.407 40.000 0.00 0.00 37.06 2.83
359 361 1.243902 ATGTTGTTTCGCCCGATTGT 58.756 45.000 0.00 0.00 0.00 2.71
369 371 3.283751 TCGCCCGATTGTAATTTGGATT 58.716 40.909 0.00 0.00 0.00 3.01
374 384 4.649218 CCCGATTGTAATTTGGATTTCCCT 59.351 41.667 0.00 0.00 35.38 4.20
409 419 2.296190 GGCACTTTTGGTAAACCTCCTG 59.704 50.000 0.02 0.00 36.82 3.86
410 420 2.296190 GCACTTTTGGTAAACCTCCTGG 59.704 50.000 0.02 0.00 36.82 4.45
411 421 2.296190 CACTTTTGGTAAACCTCCTGGC 59.704 50.000 0.02 0.00 36.63 4.85
539 552 0.825010 AAGGAACAGCAAGCACCAGG 60.825 55.000 0.00 0.00 0.00 4.45
570 583 0.764890 GCCATGTGGGTGAGGCTATA 59.235 55.000 0.54 0.00 43.70 1.31
571 584 1.271054 GCCATGTGGGTGAGGCTATAG 60.271 57.143 0.54 0.00 43.70 1.31
572 585 2.329267 CCATGTGGGTGAGGCTATAGA 58.671 52.381 3.21 0.00 0.00 1.98
573 586 2.909006 CCATGTGGGTGAGGCTATAGAT 59.091 50.000 3.21 0.00 0.00 1.98
574 587 3.055530 CCATGTGGGTGAGGCTATAGATC 60.056 52.174 3.21 1.13 0.00 2.75
605 618 4.528039 CCCATCCGGCAGGCCATT 62.528 66.667 5.01 0.00 37.47 3.16
606 619 2.908940 CCATCCGGCAGGCCATTC 60.909 66.667 5.01 0.00 37.47 2.67
607 620 2.908940 CATCCGGCAGGCCATTCC 60.909 66.667 5.01 0.97 37.47 3.01
608 621 4.569180 ATCCGGCAGGCCATTCCG 62.569 66.667 19.47 19.47 42.58 4.30
714 738 4.029186 CGCACACACGCTTGGCAT 62.029 61.111 0.00 0.00 0.00 4.40
717 741 2.985282 ACACACGCTTGGCATGGG 60.985 61.111 14.63 14.63 28.86 4.00
869 904 2.258591 CTCACCCTGGTCGTCACG 59.741 66.667 0.00 0.00 0.00 4.35
870 905 3.916392 CTCACCCTGGTCGTCACGC 62.916 68.421 0.00 0.00 0.00 5.34
874 909 4.337060 CCTGGTCGTCACGCGTCA 62.337 66.667 9.86 0.00 42.13 4.35
875 910 3.097728 CTGGTCGTCACGCGTCAC 61.098 66.667 9.86 5.73 42.13 3.67
888 923 4.643387 GTCACCCAAGCGCACCCT 62.643 66.667 11.47 0.00 0.00 4.34
1096 1134 1.349973 GACCTCTACGACGTACGCC 59.650 63.158 16.72 2.44 46.94 5.68
1114 1152 0.250295 CCAACCGTCACTCCATGTGT 60.250 55.000 0.00 0.00 46.27 3.72
1118 1156 1.000955 ACCGTCACTCCATGTGTCTTC 59.999 52.381 0.00 0.00 46.27 2.87
1120 1158 1.000843 CGTCACTCCATGTGTCTTCCA 59.999 52.381 0.00 0.00 46.27 3.53
1121 1159 2.417719 GTCACTCCATGTGTCTTCCAC 58.582 52.381 0.00 0.00 46.27 4.02
1151 1189 5.189180 GTCCCTGAATTTTATCTGCTGACT 58.811 41.667 0.00 0.00 0.00 3.41
1164 1209 1.566563 CTGACTGAGCGTGTGTTGC 59.433 57.895 0.00 0.00 0.00 4.17
1170 1215 0.461870 TGAGCGTGTGTTGCTTCTGT 60.462 50.000 0.00 0.00 44.18 3.41
1265 1314 1.625870 CGAGCACATCTTGTACGCG 59.374 57.895 3.53 3.53 31.30 6.01
1266 1315 1.742900 CGAGCACATCTTGTACGCGG 61.743 60.000 12.47 0.00 34.14 6.46
1283 1332 1.078356 GGTTCCGCTTCCTTCTCCC 60.078 63.158 0.00 0.00 0.00 4.30
1284 1333 1.078356 GTTCCGCTTCCTTCTCCCC 60.078 63.158 0.00 0.00 0.00 4.81
1304 1353 2.158842 CCTCCCTCGAGAATTGCAGATT 60.159 50.000 15.71 0.00 38.52 2.40
1314 1363 7.666623 TCGAGAATTGCAGATTATGGTATGTA 58.333 34.615 0.00 0.00 0.00 2.29
1315 1364 7.598869 TCGAGAATTGCAGATTATGGTATGTAC 59.401 37.037 0.00 0.00 0.00 2.90
1322 1371 7.094631 TGCAGATTATGGTATGTACGTATTCC 58.905 38.462 0.00 0.17 0.00 3.01
1328 1377 5.524971 TGGTATGTACGTATTCCAGAAGG 57.475 43.478 0.00 0.00 0.00 3.46
1338 1387 4.450419 CGTATTCCAGAAGGATTGCAGATC 59.550 45.833 0.00 0.00 45.26 2.75
1339 1388 3.287867 TTCCAGAAGGATTGCAGATCC 57.712 47.619 15.93 15.93 45.26 3.36
1340 1389 1.492176 TCCAGAAGGATTGCAGATCCC 59.508 52.381 18.57 9.00 39.61 3.85
1341 1390 1.590932 CAGAAGGATTGCAGATCCCG 58.409 55.000 18.57 6.91 38.98 5.14
1342 1391 0.471617 AGAAGGATTGCAGATCCCGG 59.528 55.000 18.57 0.00 38.98 5.73
1343 1392 0.181350 GAAGGATTGCAGATCCCGGT 59.819 55.000 18.57 9.01 38.98 5.28
1345 1394 0.982852 AGGATTGCAGATCCCGGTGA 60.983 55.000 18.57 0.00 38.98 4.02
1346 1395 0.533755 GGATTGCAGATCCCGGTGAG 60.534 60.000 13.81 0.00 32.09 3.51
1347 1396 0.179000 GATTGCAGATCCCGGTGAGT 59.821 55.000 0.00 0.00 0.00 3.41
1348 1397 0.620556 ATTGCAGATCCCGGTGAGTT 59.379 50.000 0.00 0.00 0.00 3.01
1349 1398 1.271856 TTGCAGATCCCGGTGAGTTA 58.728 50.000 0.00 0.00 0.00 2.24
1350 1399 1.271856 TGCAGATCCCGGTGAGTTAA 58.728 50.000 0.00 0.00 0.00 2.01
1351 1400 1.066430 TGCAGATCCCGGTGAGTTAAC 60.066 52.381 0.00 0.00 0.00 2.01
1358 1407 0.036671 CCGGTGAGTTAACTGGGGAC 60.037 60.000 14.14 4.16 42.12 4.46
1363 1412 2.546789 GTGAGTTAACTGGGGACGTTTG 59.453 50.000 14.14 0.00 0.00 2.93
1377 1426 2.596862 GACGTTTGTTTGTTCTGGTTGC 59.403 45.455 0.00 0.00 0.00 4.17
1422 1471 3.640407 GAGGGGCAGGTGCTGTCA 61.640 66.667 1.26 0.00 37.90 3.58
1692 1750 1.153823 CGACTTCGCCTTCGTGGAT 60.154 57.895 1.63 0.00 38.35 3.41
1961 2024 1.809684 GCTTGATTATAGGACCGGCC 58.190 55.000 0.00 3.58 0.00 6.13
1965 2028 3.584868 ATTATAGGACCGGCCGCGC 62.585 63.158 22.85 13.72 43.43 6.86
1993 2056 1.472276 CTGGTCGCGCGTCTTATGTC 61.472 60.000 30.98 10.62 0.00 3.06
2023 2086 8.167985 CGGAAATAAAATAAACTGGCATGTTTG 58.832 33.333 18.85 0.00 40.00 2.93
2143 2206 2.493035 TCTTGCACATCATTCACACGT 58.507 42.857 0.00 0.00 0.00 4.49
2152 2215 5.062683 CACATCATTCACACGTCTCCTTTAG 59.937 44.000 0.00 0.00 0.00 1.85
2155 2218 3.678056 TTCACACGTCTCCTTTAGCAT 57.322 42.857 0.00 0.00 0.00 3.79
2185 2248 3.940852 GCCACATGTGAACAGATGACATA 59.059 43.478 27.46 0.00 35.83 2.29
2187 2250 5.674569 GCCACATGTGAACAGATGACATAAC 60.675 44.000 27.46 0.00 35.83 1.89
2188 2251 5.412286 CCACATGTGAACAGATGACATAACA 59.588 40.000 27.46 0.00 35.83 2.41
2189 2252 6.094464 CCACATGTGAACAGATGACATAACAT 59.906 38.462 27.46 0.00 35.83 2.71
2191 2254 6.880529 ACATGTGAACAGATGACATAACATGA 59.119 34.615 16.65 0.00 43.94 3.07
2274 2338 4.041723 CCCGTTTTCATCATTAAATCCGC 58.958 43.478 0.00 0.00 0.00 5.54
2317 2381 6.122277 ACTAGACCCCATGTTGATATGTTTG 58.878 40.000 0.00 0.00 0.00 2.93
2320 2384 4.882559 ACCCCATGTTGATATGTTTGGAT 58.117 39.130 0.00 0.00 0.00 3.41
2412 2483 3.717400 TGCGGCAGTTTCAATTTGTAA 57.283 38.095 0.00 0.00 0.00 2.41
2665 2743 5.593502 TGGCAATTCATGTGCAATAGACATA 59.406 36.000 8.81 0.00 44.07 2.29
2671 2749 5.184711 TCATGTGCAATAGACATAGCAACA 58.815 37.500 0.00 0.00 38.91 3.33
2726 2809 7.265647 TGATACGAGATCTAGTTTGGAAGAG 57.734 40.000 13.99 0.00 0.00 2.85
2734 2817 0.674534 AGTTTGGAAGAGCTCGTCGT 59.325 50.000 21.08 2.94 0.00 4.34
2737 2820 0.671796 TTGGAAGAGCTCGTCGTGAA 59.328 50.000 21.08 12.02 0.00 3.18
2827 2910 8.837788 ATTGAAAATCCAAAAAGATTCTCACC 57.162 30.769 0.00 0.00 33.92 4.02
2928 3013 6.637365 CGTTAGCGTTGTCCTAATAGAAATG 58.363 40.000 0.00 0.00 0.00 2.32
2929 3014 6.255020 CGTTAGCGTTGTCCTAATAGAAATGT 59.745 38.462 0.00 0.00 0.00 2.71
2930 3015 7.201496 CGTTAGCGTTGTCCTAATAGAAATGTT 60.201 37.037 0.00 0.00 0.00 2.71
2931 3016 6.422776 AGCGTTGTCCTAATAGAAATGTTG 57.577 37.500 0.00 0.00 0.00 3.33
2932 3017 5.354234 AGCGTTGTCCTAATAGAAATGTTGG 59.646 40.000 0.00 0.00 0.00 3.77
2933 3018 5.353123 GCGTTGTCCTAATAGAAATGTTGGA 59.647 40.000 0.00 0.00 0.00 3.53
2934 3019 6.038271 GCGTTGTCCTAATAGAAATGTTGGAT 59.962 38.462 0.00 0.00 0.00 3.41
2935 3020 7.225931 GCGTTGTCCTAATAGAAATGTTGGATA 59.774 37.037 0.00 0.00 0.00 2.59
2936 3021 9.273016 CGTTGTCCTAATAGAAATGTTGGATAT 57.727 33.333 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.559862 ATGGCTAACAAACTCTGCTAGT 57.440 40.909 0.00 0.00 41.49 2.57
21 22 7.437748 AGTATATGGCTAACAAACTCTGCTAG 58.562 38.462 0.00 0.00 0.00 3.42
22 23 7.361457 AGTATATGGCTAACAAACTCTGCTA 57.639 36.000 0.00 0.00 0.00 3.49
23 24 6.240549 AGTATATGGCTAACAAACTCTGCT 57.759 37.500 0.00 0.00 0.00 4.24
24 25 5.467063 GGAGTATATGGCTAACAAACTCTGC 59.533 44.000 0.00 0.00 37.47 4.26
25 26 6.480320 GTGGAGTATATGGCTAACAAACTCTG 59.520 42.308 0.00 0.00 37.47 3.35
26 27 6.156256 TGTGGAGTATATGGCTAACAAACTCT 59.844 38.462 0.00 0.00 37.47 3.24
27 28 6.346096 TGTGGAGTATATGGCTAACAAACTC 58.654 40.000 0.00 0.00 37.00 3.01
28 29 6.308015 TGTGGAGTATATGGCTAACAAACT 57.692 37.500 0.00 0.00 0.00 2.66
29 30 6.765989 TGATGTGGAGTATATGGCTAACAAAC 59.234 38.462 0.00 0.00 0.00 2.93
30 31 6.894682 TGATGTGGAGTATATGGCTAACAAA 58.105 36.000 0.00 0.00 0.00 2.83
31 32 6.493189 TGATGTGGAGTATATGGCTAACAA 57.507 37.500 0.00 0.00 0.00 2.83
32 33 6.686484 ATGATGTGGAGTATATGGCTAACA 57.314 37.500 0.00 0.00 0.00 2.41
33 34 7.986085 AAATGATGTGGAGTATATGGCTAAC 57.014 36.000 0.00 0.00 0.00 2.34
46 47 9.511272 CCTCAATCTCAATATAAATGATGTGGA 57.489 33.333 6.38 0.00 0.00 4.02
47 48 8.737175 CCCTCAATCTCAATATAAATGATGTGG 58.263 37.037 0.00 0.00 0.00 4.17
48 49 9.511272 TCCCTCAATCTCAATATAAATGATGTG 57.489 33.333 0.00 0.00 0.00 3.21
49 50 9.736414 CTCCCTCAATCTCAATATAAATGATGT 57.264 33.333 0.00 0.00 0.00 3.06
50 51 9.736414 ACTCCCTCAATCTCAATATAAATGATG 57.264 33.333 0.00 0.00 0.00 3.07
62 63 9.206690 GGATATATCAATACTCCCTCAATCTCA 57.793 37.037 14.60 0.00 0.00 3.27
63 64 9.432982 AGGATATATCAATACTCCCTCAATCTC 57.567 37.037 14.60 0.00 0.00 2.75
64 65 9.796242 AAGGATATATCAATACTCCCTCAATCT 57.204 33.333 14.60 0.00 0.00 2.40
67 68 9.392506 TGAAAGGATATATCAATACTCCCTCAA 57.607 33.333 14.60 0.00 0.00 3.02
68 69 8.972662 TGAAAGGATATATCAATACTCCCTCA 57.027 34.615 14.60 0.92 0.00 3.86
69 70 9.660180 GTTGAAAGGATATATCAATACTCCCTC 57.340 37.037 14.60 0.00 35.70 4.30
70 71 9.398921 AGTTGAAAGGATATATCAATACTCCCT 57.601 33.333 14.60 0.00 35.70 4.20
71 72 9.660180 GAGTTGAAAGGATATATCAATACTCCC 57.340 37.037 14.60 0.00 35.70 4.30
72 73 9.660180 GGAGTTGAAAGGATATATCAATACTCC 57.340 37.037 20.52 20.52 40.82 3.85
83 84 7.993758 GCCTAAAACTAGGAGTTGAAAGGATAT 59.006 37.037 14.46 0.00 38.66 1.63
84 85 7.336396 GCCTAAAACTAGGAGTTGAAAGGATA 58.664 38.462 14.46 0.00 38.66 2.59
85 86 6.181190 GCCTAAAACTAGGAGTTGAAAGGAT 58.819 40.000 14.46 0.00 38.66 3.24
86 87 5.514310 GGCCTAAAACTAGGAGTTGAAAGGA 60.514 44.000 14.46 0.00 38.66 3.36
87 88 4.700692 GGCCTAAAACTAGGAGTTGAAAGG 59.299 45.833 0.00 9.13 38.66 3.11
88 89 4.700692 GGGCCTAAAACTAGGAGTTGAAAG 59.299 45.833 0.84 0.00 38.66 2.62
89 90 4.105057 TGGGCCTAAAACTAGGAGTTGAAA 59.895 41.667 4.53 0.00 38.66 2.69
90 91 3.653836 TGGGCCTAAAACTAGGAGTTGAA 59.346 43.478 4.53 0.00 38.66 2.69
91 92 3.253220 TGGGCCTAAAACTAGGAGTTGA 58.747 45.455 4.53 0.00 38.66 3.18
92 93 3.009143 ACTGGGCCTAAAACTAGGAGTTG 59.991 47.826 4.53 0.00 38.66 3.16
93 94 3.257578 ACTGGGCCTAAAACTAGGAGTT 58.742 45.455 4.53 0.00 40.80 3.01
94 95 2.917205 ACTGGGCCTAAAACTAGGAGT 58.083 47.619 4.53 0.00 39.60 3.85
95 96 3.519913 AGAACTGGGCCTAAAACTAGGAG 59.480 47.826 4.53 0.00 39.60 3.69
96 97 3.527937 AGAACTGGGCCTAAAACTAGGA 58.472 45.455 4.53 0.00 39.60 2.94
97 98 4.302559 AAGAACTGGGCCTAAAACTAGG 57.697 45.455 4.53 0.00 40.20 3.02
98 99 5.564848 GCAAAAGAACTGGGCCTAAAACTAG 60.565 44.000 4.53 0.00 0.00 2.57
99 100 4.279922 GCAAAAGAACTGGGCCTAAAACTA 59.720 41.667 4.53 0.00 0.00 2.24
100 101 3.069586 GCAAAAGAACTGGGCCTAAAACT 59.930 43.478 4.53 0.00 0.00 2.66
101 102 3.390135 GCAAAAGAACTGGGCCTAAAAC 58.610 45.455 4.53 0.00 0.00 2.43
102 103 2.367241 GGCAAAAGAACTGGGCCTAAAA 59.633 45.455 4.53 0.00 41.39 1.52
103 104 1.967779 GGCAAAAGAACTGGGCCTAAA 59.032 47.619 4.53 0.00 41.39 1.85
104 105 1.133325 TGGCAAAAGAACTGGGCCTAA 60.133 47.619 4.53 0.00 44.85 2.69
105 106 0.480690 TGGCAAAAGAACTGGGCCTA 59.519 50.000 4.53 0.00 44.85 3.93
106 107 0.829182 CTGGCAAAAGAACTGGGCCT 60.829 55.000 4.53 0.00 44.85 5.19
107 108 0.827507 TCTGGCAAAAGAACTGGGCC 60.828 55.000 0.00 0.00 44.82 5.80
108 109 1.039856 TTCTGGCAAAAGAACTGGGC 58.960 50.000 0.00 0.00 31.19 5.36
109 110 2.232208 GGATTCTGGCAAAAGAACTGGG 59.768 50.000 0.00 0.00 38.95 4.45
110 111 2.095059 CGGATTCTGGCAAAAGAACTGG 60.095 50.000 0.00 0.00 38.95 4.00
111 112 2.813754 TCGGATTCTGGCAAAAGAACTG 59.186 45.455 0.00 0.35 38.95 3.16
112 113 2.814336 GTCGGATTCTGGCAAAAGAACT 59.186 45.455 0.00 0.00 38.95 3.01
113 114 2.095212 GGTCGGATTCTGGCAAAAGAAC 60.095 50.000 0.00 0.00 38.95 3.01
114 115 2.159382 GGTCGGATTCTGGCAAAAGAA 58.841 47.619 0.00 0.00 40.36 2.52
115 116 1.073125 TGGTCGGATTCTGGCAAAAGA 59.927 47.619 0.00 0.00 0.00 2.52
116 117 1.200020 GTGGTCGGATTCTGGCAAAAG 59.800 52.381 0.00 0.00 0.00 2.27
117 118 1.202879 AGTGGTCGGATTCTGGCAAAA 60.203 47.619 0.00 0.00 0.00 2.44
118 119 0.400213 AGTGGTCGGATTCTGGCAAA 59.600 50.000 0.00 0.00 0.00 3.68
119 120 1.066430 GTAGTGGTCGGATTCTGGCAA 60.066 52.381 0.00 0.00 0.00 4.52
120 121 0.535335 GTAGTGGTCGGATTCTGGCA 59.465 55.000 0.00 0.00 0.00 4.92
121 122 0.179081 GGTAGTGGTCGGATTCTGGC 60.179 60.000 0.00 0.00 0.00 4.85
122 123 0.464452 GGGTAGTGGTCGGATTCTGG 59.536 60.000 0.00 0.00 0.00 3.86
123 124 1.137086 CTGGGTAGTGGTCGGATTCTG 59.863 57.143 0.00 0.00 0.00 3.02
124 125 1.486211 CTGGGTAGTGGTCGGATTCT 58.514 55.000 0.00 0.00 0.00 2.40
125 126 0.179081 GCTGGGTAGTGGTCGGATTC 60.179 60.000 0.00 0.00 0.00 2.52
126 127 0.617820 AGCTGGGTAGTGGTCGGATT 60.618 55.000 0.00 0.00 0.00 3.01
127 128 0.617820 AAGCTGGGTAGTGGTCGGAT 60.618 55.000 0.00 0.00 0.00 4.18
128 129 1.229082 AAGCTGGGTAGTGGTCGGA 60.229 57.895 0.00 0.00 0.00 4.55
129 130 1.218316 GAAGCTGGGTAGTGGTCGG 59.782 63.158 0.00 0.00 0.00 4.79
130 131 0.608640 AAGAAGCTGGGTAGTGGTCG 59.391 55.000 0.00 0.00 0.00 4.79
131 132 2.038557 TGAAAGAAGCTGGGTAGTGGTC 59.961 50.000 0.00 0.00 0.00 4.02
132 133 2.039084 CTGAAAGAAGCTGGGTAGTGGT 59.961 50.000 0.00 0.00 34.07 4.16
133 134 2.303022 TCTGAAAGAAGCTGGGTAGTGG 59.697 50.000 0.00 0.00 42.31 4.00
134 135 3.685139 TCTGAAAGAAGCTGGGTAGTG 57.315 47.619 0.00 0.00 42.31 2.74
146 147 6.933514 ATGGGGCTTAAAAATTCTGAAAGA 57.066 33.333 0.00 0.00 44.68 2.52
147 148 7.445096 ACAAATGGGGCTTAAAAATTCTGAAAG 59.555 33.333 0.00 0.00 0.00 2.62
148 149 7.286313 ACAAATGGGGCTTAAAAATTCTGAAA 58.714 30.769 0.00 0.00 0.00 2.69
149 150 6.836242 ACAAATGGGGCTTAAAAATTCTGAA 58.164 32.000 0.00 0.00 0.00 3.02
150 151 6.432403 ACAAATGGGGCTTAAAAATTCTGA 57.568 33.333 0.00 0.00 0.00 3.27
151 152 7.509141 AAACAAATGGGGCTTAAAAATTCTG 57.491 32.000 0.00 0.00 0.00 3.02
152 153 9.062524 GTAAAACAAATGGGGCTTAAAAATTCT 57.937 29.630 0.00 0.00 0.00 2.40
153 154 8.841300 TGTAAAACAAATGGGGCTTAAAAATTC 58.159 29.630 0.00 0.00 0.00 2.17
154 155 8.753497 TGTAAAACAAATGGGGCTTAAAAATT 57.247 26.923 0.00 0.00 0.00 1.82
155 156 8.753497 TTGTAAAACAAATGGGGCTTAAAAAT 57.247 26.923 0.00 0.00 34.76 1.82
156 157 8.047310 TCTTGTAAAACAAATGGGGCTTAAAAA 58.953 29.630 0.00 0.00 37.69 1.94
157 158 7.565680 TCTTGTAAAACAAATGGGGCTTAAAA 58.434 30.769 0.00 0.00 37.69 1.52
158 159 7.125792 TCTTGTAAAACAAATGGGGCTTAAA 57.874 32.000 0.00 0.00 37.69 1.52
159 160 6.732896 TCTTGTAAAACAAATGGGGCTTAA 57.267 33.333 0.00 0.00 37.69 1.85
160 161 6.926630 ATCTTGTAAAACAAATGGGGCTTA 57.073 33.333 0.00 0.00 37.69 3.09
161 162 5.823861 ATCTTGTAAAACAAATGGGGCTT 57.176 34.783 0.00 0.00 37.69 4.35
162 163 5.823861 AATCTTGTAAAACAAATGGGGCT 57.176 34.783 0.00 0.00 37.69 5.19
163 164 6.538381 CCATAATCTTGTAAAACAAATGGGGC 59.462 38.462 11.08 0.00 38.31 5.80
164 165 7.846066 TCCATAATCTTGTAAAACAAATGGGG 58.154 34.615 15.87 5.51 40.52 4.96
165 166 9.150348 GTTCCATAATCTTGTAAAACAAATGGG 57.850 33.333 15.87 4.75 40.52 4.00
166 167 9.703892 TGTTCCATAATCTTGTAAAACAAATGG 57.296 29.630 12.12 12.12 41.05 3.16
169 170 9.255304 GCTTGTTCCATAATCTTGTAAAACAAA 57.745 29.630 0.00 0.00 37.69 2.83
170 171 7.870445 GGCTTGTTCCATAATCTTGTAAAACAA 59.130 33.333 0.00 0.00 36.54 2.83
171 172 7.014711 TGGCTTGTTCCATAATCTTGTAAAACA 59.985 33.333 0.00 0.00 0.00 2.83
172 173 7.375053 TGGCTTGTTCCATAATCTTGTAAAAC 58.625 34.615 0.00 0.00 0.00 2.43
173 174 7.309744 CCTGGCTTGTTCCATAATCTTGTAAAA 60.310 37.037 0.00 0.00 35.22 1.52
174 175 6.152661 CCTGGCTTGTTCCATAATCTTGTAAA 59.847 38.462 0.00 0.00 35.22 2.01
175 176 5.652014 CCTGGCTTGTTCCATAATCTTGTAA 59.348 40.000 0.00 0.00 35.22 2.41
176 177 5.192927 CCTGGCTTGTTCCATAATCTTGTA 58.807 41.667 0.00 0.00 35.22 2.41
177 178 4.019174 CCTGGCTTGTTCCATAATCTTGT 58.981 43.478 0.00 0.00 35.22 3.16
178 179 4.019174 ACCTGGCTTGTTCCATAATCTTG 58.981 43.478 0.00 0.00 35.22 3.02
179 180 4.322057 ACCTGGCTTGTTCCATAATCTT 57.678 40.909 0.00 0.00 35.22 2.40
180 181 4.141390 CCTACCTGGCTTGTTCCATAATCT 60.141 45.833 0.00 0.00 35.22 2.40
181 182 4.137543 CCTACCTGGCTTGTTCCATAATC 58.862 47.826 0.00 0.00 35.22 1.75
182 183 3.117512 CCCTACCTGGCTTGTTCCATAAT 60.118 47.826 0.00 0.00 35.22 1.28
183 184 2.241176 CCCTACCTGGCTTGTTCCATAA 59.759 50.000 0.00 0.00 35.22 1.90
184 185 1.843851 CCCTACCTGGCTTGTTCCATA 59.156 52.381 0.00 0.00 35.22 2.74
185 186 0.625849 CCCTACCTGGCTTGTTCCAT 59.374 55.000 0.00 0.00 35.22 3.41
186 187 0.474854 TCCCTACCTGGCTTGTTCCA 60.475 55.000 0.00 0.00 34.42 3.53
187 188 0.919710 ATCCCTACCTGGCTTGTTCC 59.080 55.000 0.00 0.00 0.00 3.62
188 189 1.473434 CGATCCCTACCTGGCTTGTTC 60.473 57.143 0.00 0.00 0.00 3.18
189 190 0.541863 CGATCCCTACCTGGCTTGTT 59.458 55.000 0.00 0.00 0.00 2.83
190 191 0.325296 TCGATCCCTACCTGGCTTGT 60.325 55.000 0.00 0.00 0.00 3.16
191 192 0.830648 TTCGATCCCTACCTGGCTTG 59.169 55.000 0.00 0.00 0.00 4.01
192 193 1.807814 ATTCGATCCCTACCTGGCTT 58.192 50.000 0.00 0.00 0.00 4.35
193 194 1.807814 AATTCGATCCCTACCTGGCT 58.192 50.000 0.00 0.00 0.00 4.75
194 195 2.618709 CAAAATTCGATCCCTACCTGGC 59.381 50.000 0.00 0.00 0.00 4.85
195 196 4.150897 TCAAAATTCGATCCCTACCTGG 57.849 45.455 0.00 0.00 0.00 4.45
196 197 5.880332 TCTTTCAAAATTCGATCCCTACCTG 59.120 40.000 0.00 0.00 0.00 4.00
197 198 6.062258 TCTTTCAAAATTCGATCCCTACCT 57.938 37.500 0.00 0.00 0.00 3.08
198 199 6.753107 TTCTTTCAAAATTCGATCCCTACC 57.247 37.500 0.00 0.00 0.00 3.18
199 200 7.418408 GGATTCTTTCAAAATTCGATCCCTAC 58.582 38.462 0.00 0.00 0.00 3.18
200 201 6.546034 GGGATTCTTTCAAAATTCGATCCCTA 59.454 38.462 10.13 0.00 40.50 3.53
201 202 5.360999 GGGATTCTTTCAAAATTCGATCCCT 59.639 40.000 10.13 0.00 40.50 4.20
202 203 5.360999 AGGGATTCTTTCAAAATTCGATCCC 59.639 40.000 9.52 9.52 43.16 3.85
203 204 6.456795 AGGGATTCTTTCAAAATTCGATCC 57.543 37.500 0.00 0.00 0.00 3.36
204 205 8.438676 TCTAGGGATTCTTTCAAAATTCGATC 57.561 34.615 0.00 0.00 0.00 3.69
205 206 8.986929 ATCTAGGGATTCTTTCAAAATTCGAT 57.013 30.769 0.00 0.00 0.00 3.59
206 207 8.807948 AATCTAGGGATTCTTTCAAAATTCGA 57.192 30.769 0.00 0.00 37.61 3.71
239 240 3.026707 ACAGTGTAAGGCCCAGTTTTT 57.973 42.857 0.00 0.00 0.00 1.94
240 241 2.748209 ACAGTGTAAGGCCCAGTTTT 57.252 45.000 0.00 0.00 0.00 2.43
241 242 2.748209 AACAGTGTAAGGCCCAGTTT 57.252 45.000 0.00 0.00 0.00 2.66
242 243 4.382386 AATAACAGTGTAAGGCCCAGTT 57.618 40.909 0.00 0.00 0.00 3.16
243 244 4.382386 AAATAACAGTGTAAGGCCCAGT 57.618 40.909 0.00 0.00 0.00 4.00
244 245 5.354234 CAGTAAATAACAGTGTAAGGCCCAG 59.646 44.000 0.00 0.00 0.00 4.45
245 246 5.250200 CAGTAAATAACAGTGTAAGGCCCA 58.750 41.667 0.00 0.00 0.00 5.36
246 247 4.638865 CCAGTAAATAACAGTGTAAGGCCC 59.361 45.833 0.00 0.00 0.00 5.80
247 248 4.095932 GCCAGTAAATAACAGTGTAAGGCC 59.904 45.833 0.00 0.00 0.00 5.19
248 249 4.698304 TGCCAGTAAATAACAGTGTAAGGC 59.302 41.667 0.00 2.51 37.75 4.35
249 250 6.349033 GGTTGCCAGTAAATAACAGTGTAAGG 60.349 42.308 0.00 0.00 0.00 2.69
250 251 6.430000 AGGTTGCCAGTAAATAACAGTGTAAG 59.570 38.462 0.00 0.00 0.00 2.34
348 350 2.404923 TCCAAATTACAATCGGGCGA 57.595 45.000 0.00 0.00 0.00 5.54
369 371 2.268920 GCTCGCATGTGGAGGGAA 59.731 61.111 6.39 0.00 32.10 3.97
374 384 4.019312 TGCCTGCTCGCATGTGGA 62.019 61.111 6.39 0.00 32.62 4.02
409 419 0.887387 TGACCGGCTAACTTTGTGCC 60.887 55.000 0.00 0.00 42.94 5.01
410 420 0.948678 TTGACCGGCTAACTTTGTGC 59.051 50.000 0.00 0.00 0.00 4.57
411 421 1.069227 GCTTGACCGGCTAACTTTGTG 60.069 52.381 0.00 0.00 0.00 3.33
539 552 4.883354 CATGGCCGGGCTCCCTTC 62.883 72.222 29.87 0.88 0.00 3.46
570 583 1.227089 GCCGCGTGTGATCTGATCT 60.227 57.895 17.82 0.00 0.00 2.75
571 584 2.240500 GGCCGCGTGTGATCTGATC 61.241 63.158 10.72 10.72 0.00 2.92
572 585 2.202932 GGCCGCGTGTGATCTGAT 60.203 61.111 4.92 0.00 0.00 2.90
573 586 4.451150 GGGCCGCGTGTGATCTGA 62.451 66.667 4.92 0.00 0.00 3.27
574 587 4.758251 TGGGCCGCGTGTGATCTG 62.758 66.667 4.92 0.00 0.00 2.90
600 613 4.980805 TATCGGCGGCGGAATGGC 62.981 66.667 31.73 0.00 40.44 4.40
601 614 2.738521 CTATCGGCGGCGGAATGG 60.739 66.667 31.73 16.34 0.00 3.16
602 615 2.738521 CCTATCGGCGGCGGAATG 60.739 66.667 31.73 17.78 0.00 2.67
603 616 2.915659 TCCTATCGGCGGCGGAAT 60.916 61.111 31.73 20.39 0.00 3.01
604 617 3.602677 CTCCTATCGGCGGCGGAA 61.603 66.667 31.73 18.16 0.00 4.30
605 618 4.574271 TCTCCTATCGGCGGCGGA 62.574 66.667 31.73 18.88 0.00 5.54
606 619 4.344474 GTCTCCTATCGGCGGCGG 62.344 72.222 31.73 15.35 0.00 6.13
607 620 2.622903 TTTGTCTCCTATCGGCGGCG 62.623 60.000 27.15 27.15 0.00 6.46
608 621 0.249911 ATTTGTCTCCTATCGGCGGC 60.250 55.000 7.21 0.00 0.00 6.53
609 622 1.605712 GGATTTGTCTCCTATCGGCGG 60.606 57.143 7.21 0.00 32.18 6.13
610 623 1.068588 TGGATTTGTCTCCTATCGGCG 59.931 52.381 0.00 0.00 36.20 6.46
620 633 2.624838 CTGCAAACTGGTGGATTTGTCT 59.375 45.455 0.00 0.00 37.96 3.41
624 637 0.681175 GCCTGCAAACTGGTGGATTT 59.319 50.000 0.00 0.00 37.23 2.17
631 644 0.539438 TACTTGGGCCTGCAAACTGG 60.539 55.000 4.53 0.00 37.92 4.00
761 785 3.197790 GCGATGCGATGCAGTGGT 61.198 61.111 0.00 0.00 43.65 4.16
848 879 3.591254 GACGACCAGGGTGAGTGGC 62.591 68.421 0.00 0.00 38.83 5.01
849 880 2.207229 TGACGACCAGGGTGAGTGG 61.207 63.158 0.00 0.00 41.30 4.00
871 906 3.248446 TAGGGTGCGCTTGGGTGAC 62.248 63.158 9.73 0.00 0.00 3.67
872 907 2.925706 TAGGGTGCGCTTGGGTGA 60.926 61.111 9.73 0.00 0.00 4.02
873 908 2.436646 CTAGGGTGCGCTTGGGTG 60.437 66.667 9.73 0.00 0.00 4.61
874 909 4.410400 GCTAGGGTGCGCTTGGGT 62.410 66.667 9.73 0.00 0.00 4.51
875 910 2.324014 TATGCTAGGGTGCGCTTGGG 62.324 60.000 9.73 0.00 35.36 4.12
888 923 3.750371 AGCACGGCCATTATTTATGCTA 58.250 40.909 2.24 0.00 40.03 3.49
1121 1159 1.635663 AAAATTCAGGGACGAGCGCG 61.636 55.000 8.75 8.75 44.79 6.86
1122 1160 1.365699 TAAAATTCAGGGACGAGCGC 58.634 50.000 0.00 0.00 0.00 5.92
1151 1189 0.461870 ACAGAAGCAACACACGCTCA 60.462 50.000 0.00 0.00 39.29 4.26
1265 1314 1.078356 GGGAGAAGGAAGCGGAACC 60.078 63.158 0.00 0.00 0.00 3.62
1266 1315 1.078356 GGGGAGAAGGAAGCGGAAC 60.078 63.158 0.00 0.00 0.00 3.62
1274 1323 1.934341 TCGAGGGAGGGGAGAAGGA 60.934 63.158 0.00 0.00 0.00 3.36
1283 1332 0.826715 TCTGCAATTCTCGAGGGAGG 59.173 55.000 13.56 1.66 40.85 4.30
1284 1333 2.906691 ATCTGCAATTCTCGAGGGAG 57.093 50.000 13.56 7.09 41.89 4.30
1304 1353 7.005902 TCCTTCTGGAATACGTACATACCATA 58.994 38.462 0.00 0.00 39.87 2.74
1314 1363 3.197766 TCTGCAATCCTTCTGGAATACGT 59.802 43.478 0.00 0.00 46.80 3.57
1315 1364 3.797039 TCTGCAATCCTTCTGGAATACG 58.203 45.455 0.00 0.00 46.80 3.06
1322 1371 1.590932 CGGGATCTGCAATCCTTCTG 58.409 55.000 20.32 9.76 38.26 3.02
1328 1377 0.179000 ACTCACCGGGATCTGCAATC 59.821 55.000 6.32 0.00 0.00 2.67
1338 1387 1.196104 TCCCCAGTTAACTCACCGGG 61.196 60.000 17.98 17.98 0.00 5.73
1339 1388 0.036671 GTCCCCAGTTAACTCACCGG 60.037 60.000 4.77 0.00 0.00 5.28
1340 1389 0.389426 CGTCCCCAGTTAACTCACCG 60.389 60.000 4.77 0.54 0.00 4.94
1341 1390 0.683412 ACGTCCCCAGTTAACTCACC 59.317 55.000 4.77 0.00 0.00 4.02
1342 1391 2.538512 AACGTCCCCAGTTAACTCAC 57.461 50.000 4.77 0.00 0.00 3.51
1343 1392 2.171027 ACAAACGTCCCCAGTTAACTCA 59.829 45.455 4.77 0.00 0.00 3.41
1345 1394 3.286329 AACAAACGTCCCCAGTTAACT 57.714 42.857 1.12 1.12 0.00 2.24
1346 1395 3.129113 ACAAACAAACGTCCCCAGTTAAC 59.871 43.478 0.00 0.00 0.00 2.01
1347 1396 3.354467 ACAAACAAACGTCCCCAGTTAA 58.646 40.909 0.00 0.00 0.00 2.01
1348 1397 3.002038 ACAAACAAACGTCCCCAGTTA 57.998 42.857 0.00 0.00 0.00 2.24
1349 1398 1.842052 ACAAACAAACGTCCCCAGTT 58.158 45.000 0.00 0.00 0.00 3.16
1350 1399 1.746787 GAACAAACAAACGTCCCCAGT 59.253 47.619 0.00 0.00 0.00 4.00
1351 1400 2.021457 AGAACAAACAAACGTCCCCAG 58.979 47.619 0.00 0.00 0.00 4.45
1358 1407 2.598192 CTGCAACCAGAACAAACAAACG 59.402 45.455 0.00 0.00 41.77 3.60
1363 1412 0.594796 CCGCTGCAACCAGAACAAAC 60.595 55.000 0.00 0.00 41.77 2.93
1377 1426 2.444624 CGACGACATGAACCCGCTG 61.445 63.158 0.00 0.00 0.00 5.18
1422 1471 0.322277 CCATCACCTTGAGCAGCAGT 60.322 55.000 0.00 0.00 0.00 4.40
1542 1591 0.533032 GCTCGAAGTACTCCCTGCTT 59.467 55.000 0.00 0.00 0.00 3.91
1692 1750 1.336148 CCGTAGTTGTACTTGTCGGCA 60.336 52.381 0.00 0.00 32.61 5.69
1993 2056 6.616947 TGCCAGTTTATTTTATTTCCGTCAG 58.383 36.000 0.00 0.00 0.00 3.51
1998 2061 8.998377 ACAAACATGCCAGTTTATTTTATTTCC 58.002 29.630 3.65 0.00 39.55 3.13
2011 2074 1.163420 TCGCGAACAAACATGCCAGT 61.163 50.000 6.20 0.00 0.00 4.00
2023 2086 4.384846 TCACTAGAAGAAAATGTCGCGAAC 59.615 41.667 12.06 6.01 0.00 3.95
2113 2176 1.588824 ATGTGCAAGATGCCACACGG 61.589 55.000 8.87 0.00 44.23 4.94
2143 2206 4.771577 TGGCAAAATGAATGCTAAAGGAGA 59.228 37.500 0.00 0.00 43.34 3.71
2152 2215 3.327626 TCACATGTGGCAAAATGAATGC 58.672 40.909 25.16 0.00 43.08 3.56
2155 2218 4.099113 TCTGTTCACATGTGGCAAAATGAA 59.901 37.500 25.16 10.21 0.00 2.57
2201 2264 9.620259 AGATAAAACATTTTTAAGCCCAAAACA 57.380 25.926 0.00 0.00 0.00 2.83
2252 2315 4.041723 GCGGATTTAATGATGAAAACGGG 58.958 43.478 5.33 0.00 0.00 5.28
2262 2326 1.406180 TCGTCGAGGCGGATTTAATGA 59.594 47.619 0.00 0.00 0.00 2.57
2274 2338 3.839293 AGTTTTGAAGATCTCGTCGAGG 58.161 45.455 21.63 0.00 0.00 4.63
2355 2425 4.819105 AAGCACTATGGCAACTACAGTA 57.181 40.909 0.00 0.00 35.83 2.74
2443 2514 8.698973 TTTTCATGGTCAAATTACTGGAGTTA 57.301 30.769 0.00 0.00 0.00 2.24
2529 2601 8.854614 ATTAAGAAACTAGACTTGCATGAACT 57.145 30.769 6.60 7.73 0.00 3.01
2604 2681 7.663081 ACTGAAGTTGTCATGATATGTTTCAGT 59.337 33.333 24.61 24.61 44.16 3.41
2707 2790 4.606961 GAGCTCTTCCAAACTAGATCTCG 58.393 47.826 6.43 0.00 0.00 4.04
2720 2803 0.456995 CCTTCACGACGAGCTCTTCC 60.457 60.000 14.08 1.17 0.00 3.46
2726 2809 3.001330 CCATTAAATCCTTCACGACGAGC 59.999 47.826 0.00 0.00 0.00 5.03
2734 2817 5.770663 TCCGTTTTCACCATTAAATCCTTCA 59.229 36.000 0.00 0.00 0.00 3.02
2737 2820 6.187682 AGATCCGTTTTCACCATTAAATCCT 58.812 36.000 0.00 0.00 0.00 3.24
2839 2922 0.966179 ATAGACTGTGCCACGTCACA 59.034 50.000 17.58 9.45 43.93 3.58


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

AutoCloner maintained by Alex Coulton.