Multiple sequence alignment - TraesCS3B01G209000

Loading Multiple Alignment...

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 TraesCS3B01G209000 chr3B 100.000 3146 0 0 1 3146 245008488 245011633 0.000000e+00 5810
1 TraesCS3B01G209000 chr3B 97.614 2305 51 2 843 3144 259399586 259397283 0.000000e+00 3949
2 TraesCS3B01G209000 chr3B 96.491 342 10 2 1 341 347896509 347896849 5.890000e-157 564
3 TraesCS3B01G209000 chr7A 98.254 2806 45 2 342 3144 299568844 299571648 0.000000e+00 4907
4 TraesCS3B01G209000 chr2A 97.933 2806 54 2 342 3144 57916518 57913714 0.000000e+00 4857
5 TraesCS3B01G209000 chr2A 97.897 2806 55 2 342 3144 678124286 678121482 0.000000e+00 4852
6 TraesCS3B01G209000 chr2A 95.545 2806 98 13 342 3144 672845011 672847792 0.000000e+00 4464
7 TraesCS3B01G209000 chr1D 97.577 2806 62 4 342 3144 283557064 283559866 0.000000e+00 4800
8 TraesCS3B01G209000 chr1D 95.614 342 13 2 1 341 411959224 411958884 5.930000e-152 547
9 TraesCS3B01G209000 chr1B 97.634 2789 62 2 339 3124 611146106 611148893 0.000000e+00 4782
10 TraesCS3B01G209000 chr1B 96.044 2806 77 13 342 3144 682092121 682089347 0.000000e+00 4536
11 TraesCS3B01G209000 chr4D 96.725 2809 63 12 341 3144 281202810 281200026 0.000000e+00 4650
12 TraesCS3B01G209000 chr4D 95.870 339 12 2 1 338 150050172 150050509 5.930000e-152 547
13 TraesCS3B01G209000 chr4D 95.870 339 12 2 1 338 314099269 314099606 5.930000e-152 547
14 TraesCS3B01G209000 chr4B 94.888 2817 122 13 332 3144 637596045 637598843 0.000000e+00 4385
15 TraesCS3B01G209000 chr6A 94.747 1066 51 3 344 1409 22479098 22480158 0.000000e+00 1653
16 TraesCS3B01G209000 chr2B 96.726 336 10 1 7 341 327742229 327742564 2.740000e-155 558
17 TraesCS3B01G209000 chr2B 95.906 342 12 2 1 341 132727796 132727456 1.280000e-153 553
18 TraesCS3B01G209000 chr2B 95.906 342 12 2 1 341 529552678 529552338 1.280000e-153 553
19 TraesCS3B01G209000 chr6D 95.870 339 12 2 1 338 87967853 87968190 5.930000e-152 547
20 TraesCS3B01G209000 chr5D 95.870 339 12 2 1 338 126351627 126351964 5.930000e-152 547


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 TraesCS3B01G209000 chr3B 245008488 245011633 3145 False 5810 5810 100.000 1 3146 1 chr3B.!!$F1 3145
1 TraesCS3B01G209000 chr3B 259397283 259399586 2303 True 3949 3949 97.614 843 3144 1 chr3B.!!$R1 2301
2 TraesCS3B01G209000 chr7A 299568844 299571648 2804 False 4907 4907 98.254 342 3144 1 chr7A.!!$F1 2802
3 TraesCS3B01G209000 chr2A 57913714 57916518 2804 True 4857 4857 97.933 342 3144 1 chr2A.!!$R1 2802
4 TraesCS3B01G209000 chr2A 678121482 678124286 2804 True 4852 4852 97.897 342 3144 1 chr2A.!!$R2 2802
5 TraesCS3B01G209000 chr2A 672845011 672847792 2781 False 4464 4464 95.545 342 3144 1 chr2A.!!$F1 2802
6 TraesCS3B01G209000 chr1D 283557064 283559866 2802 False 4800 4800 97.577 342 3144 1 chr1D.!!$F1 2802
7 TraesCS3B01G209000 chr1B 611146106 611148893 2787 False 4782 4782 97.634 339 3124 1 chr1B.!!$F1 2785
8 TraesCS3B01G209000 chr1B 682089347 682092121 2774 True 4536 4536 96.044 342 3144 1 chr1B.!!$R1 2802
9 TraesCS3B01G209000 chr4D 281200026 281202810 2784 True 4650 4650 96.725 341 3144 1 chr4D.!!$R1 2803
10 TraesCS3B01G209000 chr4B 637596045 637598843 2798 False 4385 4385 94.888 332 3144 1 chr4B.!!$F1 2812
11 TraesCS3B01G209000 chr6A 22479098 22480158 1060 False 1653 1653 94.747 344 1409 1 chr6A.!!$F1 1065

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
160 161 0.033601 TGGTTTGAGTGCTTGGGTGT 60.034 50.000 0.00 0.0 0.00 4.16 F
244 245 0.108138 AGAATTCCCGGAGTGCGAAG 60.108 55.000 5.27 0.0 0.00 3.79 F
296 297 0.111061 TGTCAGCCAGGCAAGTCATT 59.889 50.000 15.80 0.0 0.00 2.57 F
298 299 1.068055 GTCAGCCAGGCAAGTCATTTG 60.068 52.381 15.80 0.0 39.88 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1180 1182 0.612174 CCTCTCCTCGACCACCTCAA 60.612 60.000 0.0 0.0 0.00 3.02 R
1607 1609 3.897505 CCCCTTCAAAAACTTGAGGACAT 59.102 43.478 0.0 0.0 30.57 3.06 R
1860 1862 4.133078 CTCTGCCTTTGTTGTCTCTCTTT 58.867 43.478 0.0 0.0 0.00 2.52 R
2186 2190 6.428083 TGAGTCTAAAACCCAATCTACACA 57.572 37.500 0.0 0.0 0.00 3.72 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
25 26 8.268850 TGATGATTTTCCTTCTGTTAGTTAGC 57.731 34.615 0.00 0.00 0.00 3.09
26 27 7.882791 TGATGATTTTCCTTCTGTTAGTTAGCA 59.117 33.333 0.00 0.00 0.00 3.49
27 28 8.635765 ATGATTTTCCTTCTGTTAGTTAGCAA 57.364 30.769 0.00 0.00 0.00 3.91
28 29 8.458573 TGATTTTCCTTCTGTTAGTTAGCAAA 57.541 30.769 0.00 0.00 0.00 3.68
29 30 8.908903 TGATTTTCCTTCTGTTAGTTAGCAAAA 58.091 29.630 0.00 0.00 0.00 2.44
30 31 9.181805 GATTTTCCTTCTGTTAGTTAGCAAAAC 57.818 33.333 0.00 0.00 0.00 2.43
31 32 6.628919 TTCCTTCTGTTAGTTAGCAAAACC 57.371 37.500 0.00 0.00 0.00 3.27
32 33 5.067954 TCCTTCTGTTAGTTAGCAAAACCC 58.932 41.667 0.00 0.00 0.00 4.11
33 34 4.825085 CCTTCTGTTAGTTAGCAAAACCCA 59.175 41.667 0.00 0.00 0.00 4.51
34 35 5.476945 CCTTCTGTTAGTTAGCAAAACCCAT 59.523 40.000 0.00 0.00 0.00 4.00
35 36 5.957842 TCTGTTAGTTAGCAAAACCCATG 57.042 39.130 0.00 0.00 0.00 3.66
36 37 4.217550 TCTGTTAGTTAGCAAAACCCATGC 59.782 41.667 0.00 0.00 44.15 4.06
51 52 5.722021 ACCCATGCTTAGGTTTTGTTAAG 57.278 39.130 0.00 0.00 29.94 1.85
52 53 5.390387 ACCCATGCTTAGGTTTTGTTAAGA 58.610 37.500 0.00 0.00 29.94 2.10
53 54 5.836358 ACCCATGCTTAGGTTTTGTTAAGAA 59.164 36.000 0.00 0.00 29.94 2.52
54 55 6.325286 ACCCATGCTTAGGTTTTGTTAAGAAA 59.675 34.615 0.00 0.00 29.94 2.52
55 56 7.147637 ACCCATGCTTAGGTTTTGTTAAGAAAA 60.148 33.333 6.43 6.43 29.94 2.29
56 57 7.384932 CCCATGCTTAGGTTTTGTTAAGAAAAG 59.615 37.037 10.53 0.79 0.00 2.27
57 58 7.926018 CCATGCTTAGGTTTTGTTAAGAAAAGT 59.074 33.333 10.53 4.70 0.00 2.66
58 59 9.313118 CATGCTTAGGTTTTGTTAAGAAAAGTT 57.687 29.630 10.53 5.30 0.00 2.66
59 60 9.884636 ATGCTTAGGTTTTGTTAAGAAAAGTTT 57.115 25.926 10.53 3.16 0.00 2.66
60 61 9.713713 TGCTTAGGTTTTGTTAAGAAAAGTTTT 57.286 25.926 10.53 0.00 0.00 2.43
97 98 8.396272 ACTATTTCTTAGTTGTTGCTTGATGT 57.604 30.769 0.00 0.00 37.96 3.06
98 99 8.292448 ACTATTTCTTAGTTGTTGCTTGATGTG 58.708 33.333 0.00 0.00 37.96 3.21
99 100 5.437289 TTCTTAGTTGTTGCTTGATGTGG 57.563 39.130 0.00 0.00 0.00 4.17
100 101 4.460263 TCTTAGTTGTTGCTTGATGTGGT 58.540 39.130 0.00 0.00 0.00 4.16
101 102 4.275689 TCTTAGTTGTTGCTTGATGTGGTG 59.724 41.667 0.00 0.00 0.00 4.17
102 103 2.653726 AGTTGTTGCTTGATGTGGTGA 58.346 42.857 0.00 0.00 0.00 4.02
103 104 3.023119 AGTTGTTGCTTGATGTGGTGAA 58.977 40.909 0.00 0.00 0.00 3.18
104 105 3.446873 AGTTGTTGCTTGATGTGGTGAAA 59.553 39.130 0.00 0.00 0.00 2.69
105 106 4.081752 AGTTGTTGCTTGATGTGGTGAAAA 60.082 37.500 0.00 0.00 0.00 2.29
106 107 3.779759 TGTTGCTTGATGTGGTGAAAAC 58.220 40.909 0.00 0.00 0.00 2.43
107 108 3.123050 GTTGCTTGATGTGGTGAAAACC 58.877 45.455 0.00 0.00 0.00 3.27
108 109 2.665165 TGCTTGATGTGGTGAAAACCT 58.335 42.857 0.00 0.00 0.00 3.50
109 110 3.030291 TGCTTGATGTGGTGAAAACCTT 58.970 40.909 0.00 0.00 0.00 3.50
110 111 3.181477 TGCTTGATGTGGTGAAAACCTTG 60.181 43.478 0.00 0.00 0.00 3.61
111 112 3.068024 GCTTGATGTGGTGAAAACCTTGA 59.932 43.478 0.00 0.00 0.00 3.02
112 113 4.441356 GCTTGATGTGGTGAAAACCTTGAA 60.441 41.667 0.00 0.00 0.00 2.69
113 114 5.739935 GCTTGATGTGGTGAAAACCTTGAAT 60.740 40.000 0.00 0.00 0.00 2.57
114 115 5.867903 TGATGTGGTGAAAACCTTGAATT 57.132 34.783 0.00 0.00 0.00 2.17
115 116 5.599732 TGATGTGGTGAAAACCTTGAATTG 58.400 37.500 0.00 0.00 0.00 2.32
116 117 3.791245 TGTGGTGAAAACCTTGAATTGC 58.209 40.909 0.00 0.00 0.00 3.56
117 118 3.450457 TGTGGTGAAAACCTTGAATTGCT 59.550 39.130 0.00 0.00 0.00 3.91
118 119 4.081198 TGTGGTGAAAACCTTGAATTGCTT 60.081 37.500 0.00 0.00 0.00 3.91
119 120 4.875536 GTGGTGAAAACCTTGAATTGCTTT 59.124 37.500 0.00 0.00 0.00 3.51
120 121 5.006649 GTGGTGAAAACCTTGAATTGCTTTC 59.993 40.000 0.00 0.00 34.72 2.62
121 122 5.104982 TGGTGAAAACCTTGAATTGCTTTCT 60.105 36.000 0.00 0.00 35.23 2.52
122 123 5.463392 GGTGAAAACCTTGAATTGCTTTCTC 59.537 40.000 0.00 0.00 35.23 2.87
123 124 6.276091 GTGAAAACCTTGAATTGCTTTCTCT 58.724 36.000 0.00 0.00 35.23 3.10
124 125 6.199719 GTGAAAACCTTGAATTGCTTTCTCTG 59.800 38.462 0.00 0.00 35.23 3.35
125 126 6.096705 TGAAAACCTTGAATTGCTTTCTCTGA 59.903 34.615 0.00 0.00 35.23 3.27
126 127 5.702349 AACCTTGAATTGCTTTCTCTGAG 57.298 39.130 0.00 0.00 35.23 3.35
127 128 4.723309 ACCTTGAATTGCTTTCTCTGAGT 58.277 39.130 4.32 0.00 35.23 3.41
128 129 5.136105 ACCTTGAATTGCTTTCTCTGAGTT 58.864 37.500 4.32 0.00 35.23 3.01
129 130 5.595952 ACCTTGAATTGCTTTCTCTGAGTTT 59.404 36.000 4.32 0.00 35.23 2.66
130 131 6.097412 ACCTTGAATTGCTTTCTCTGAGTTTT 59.903 34.615 4.32 0.00 35.23 2.43
131 132 6.640092 CCTTGAATTGCTTTCTCTGAGTTTTC 59.360 38.462 4.32 0.76 35.23 2.29
132 133 6.949352 TGAATTGCTTTCTCTGAGTTTTCT 57.051 33.333 4.32 0.00 35.23 2.52
133 134 7.338800 TGAATTGCTTTCTCTGAGTTTTCTT 57.661 32.000 4.32 0.00 35.23 2.52
134 135 7.775120 TGAATTGCTTTCTCTGAGTTTTCTTT 58.225 30.769 4.32 0.00 35.23 2.52
135 136 7.703621 TGAATTGCTTTCTCTGAGTTTTCTTTG 59.296 33.333 4.32 0.00 35.23 2.77
136 137 5.505173 TGCTTTCTCTGAGTTTTCTTTGG 57.495 39.130 4.32 0.00 0.00 3.28
137 138 5.192927 TGCTTTCTCTGAGTTTTCTTTGGA 58.807 37.500 4.32 0.00 0.00 3.53
138 139 5.829924 TGCTTTCTCTGAGTTTTCTTTGGAT 59.170 36.000 4.32 0.00 0.00 3.41
139 140 6.322201 TGCTTTCTCTGAGTTTTCTTTGGATT 59.678 34.615 4.32 0.00 0.00 3.01
140 141 7.147846 TGCTTTCTCTGAGTTTTCTTTGGATTT 60.148 33.333 4.32 0.00 0.00 2.17
141 142 7.708322 GCTTTCTCTGAGTTTTCTTTGGATTTT 59.292 33.333 4.32 0.00 0.00 1.82
142 143 8.931385 TTTCTCTGAGTTTTCTTTGGATTTTG 57.069 30.769 4.32 0.00 0.00 2.44
143 144 7.042797 TCTCTGAGTTTTCTTTGGATTTTGG 57.957 36.000 4.32 0.00 0.00 3.28
144 145 6.607198 TCTCTGAGTTTTCTTTGGATTTTGGT 59.393 34.615 4.32 0.00 0.00 3.67
145 146 7.124147 TCTCTGAGTTTTCTTTGGATTTTGGTT 59.876 33.333 4.32 0.00 0.00 3.67
146 147 7.619965 TCTGAGTTTTCTTTGGATTTTGGTTT 58.380 30.769 0.00 0.00 0.00 3.27
147 148 7.548780 TCTGAGTTTTCTTTGGATTTTGGTTTG 59.451 33.333 0.00 0.00 0.00 2.93
148 149 7.390027 TGAGTTTTCTTTGGATTTTGGTTTGA 58.610 30.769 0.00 0.00 0.00 2.69
149 150 7.548780 TGAGTTTTCTTTGGATTTTGGTTTGAG 59.451 33.333 0.00 0.00 0.00 3.02
150 151 7.394016 AGTTTTCTTTGGATTTTGGTTTGAGT 58.606 30.769 0.00 0.00 0.00 3.41
151 152 7.334171 AGTTTTCTTTGGATTTTGGTTTGAGTG 59.666 33.333 0.00 0.00 0.00 3.51
152 153 4.692228 TCTTTGGATTTTGGTTTGAGTGC 58.308 39.130 0.00 0.00 0.00 4.40
153 154 4.405358 TCTTTGGATTTTGGTTTGAGTGCT 59.595 37.500 0.00 0.00 0.00 4.40
154 155 4.751767 TTGGATTTTGGTTTGAGTGCTT 57.248 36.364 0.00 0.00 0.00 3.91
155 156 4.057406 TGGATTTTGGTTTGAGTGCTTG 57.943 40.909 0.00 0.00 0.00 4.01
156 157 3.181467 TGGATTTTGGTTTGAGTGCTTGG 60.181 43.478 0.00 0.00 0.00 3.61
157 158 2.977772 TTTTGGTTTGAGTGCTTGGG 57.022 45.000 0.00 0.00 0.00 4.12
158 159 1.859302 TTTGGTTTGAGTGCTTGGGT 58.141 45.000 0.00 0.00 0.00 4.51
159 160 1.110442 TTGGTTTGAGTGCTTGGGTG 58.890 50.000 0.00 0.00 0.00 4.61
160 161 0.033601 TGGTTTGAGTGCTTGGGTGT 60.034 50.000 0.00 0.00 0.00 4.16
161 162 1.111277 GGTTTGAGTGCTTGGGTGTT 58.889 50.000 0.00 0.00 0.00 3.32
162 163 1.480545 GGTTTGAGTGCTTGGGTGTTT 59.519 47.619 0.00 0.00 0.00 2.83
163 164 2.093711 GGTTTGAGTGCTTGGGTGTTTT 60.094 45.455 0.00 0.00 0.00 2.43
164 165 3.131400 GGTTTGAGTGCTTGGGTGTTTTA 59.869 43.478 0.00 0.00 0.00 1.52
165 166 4.109766 GTTTGAGTGCTTGGGTGTTTTAC 58.890 43.478 0.00 0.00 0.00 2.01
166 167 3.290948 TGAGTGCTTGGGTGTTTTACT 57.709 42.857 0.00 0.00 0.00 2.24
167 168 3.626930 TGAGTGCTTGGGTGTTTTACTT 58.373 40.909 0.00 0.00 0.00 2.24
168 169 3.630312 TGAGTGCTTGGGTGTTTTACTTC 59.370 43.478 0.00 0.00 0.00 3.01
169 170 3.626930 AGTGCTTGGGTGTTTTACTTCA 58.373 40.909 0.00 0.00 0.00 3.02
170 171 4.020543 AGTGCTTGGGTGTTTTACTTCAA 58.979 39.130 0.00 0.00 0.00 2.69
171 172 4.109766 GTGCTTGGGTGTTTTACTTCAAC 58.890 43.478 0.00 0.00 0.00 3.18
172 173 4.020543 TGCTTGGGTGTTTTACTTCAACT 58.979 39.130 0.00 0.00 0.00 3.16
173 174 4.464597 TGCTTGGGTGTTTTACTTCAACTT 59.535 37.500 0.00 0.00 0.00 2.66
174 175 4.803613 GCTTGGGTGTTTTACTTCAACTTG 59.196 41.667 0.00 0.00 0.00 3.16
175 176 4.379339 TGGGTGTTTTACTTCAACTTGC 57.621 40.909 0.00 0.00 0.00 4.01
176 177 4.020543 TGGGTGTTTTACTTCAACTTGCT 58.979 39.130 0.00 0.00 0.00 3.91
177 178 4.142271 TGGGTGTTTTACTTCAACTTGCTG 60.142 41.667 0.00 0.00 0.00 4.41
178 179 4.142249 GGGTGTTTTACTTCAACTTGCTGT 60.142 41.667 0.00 0.00 0.00 4.40
179 180 5.407502 GGTGTTTTACTTCAACTTGCTGTT 58.592 37.500 0.00 0.00 39.92 3.16
180 181 6.404954 GGGTGTTTTACTTCAACTTGCTGTTA 60.405 38.462 0.00 0.00 37.07 2.41
181 182 7.200455 GGTGTTTTACTTCAACTTGCTGTTAT 58.800 34.615 0.00 0.00 37.07 1.89
182 183 7.167468 GGTGTTTTACTTCAACTTGCTGTTATG 59.833 37.037 0.00 0.00 37.07 1.90
183 184 7.700656 GTGTTTTACTTCAACTTGCTGTTATGT 59.299 33.333 0.00 0.00 37.07 2.29
184 185 8.247562 TGTTTTACTTCAACTTGCTGTTATGTT 58.752 29.630 0.00 0.00 37.07 2.71
185 186 9.724839 GTTTTACTTCAACTTGCTGTTATGTTA 57.275 29.630 0.00 0.00 37.07 2.41
192 193 9.838975 TTCAACTTGCTGTTATGTTATATTGTG 57.161 29.630 0.00 0.00 37.07 3.33
193 194 7.967854 TCAACTTGCTGTTATGTTATATTGTGC 59.032 33.333 0.00 0.00 37.07 4.57
194 195 7.630242 ACTTGCTGTTATGTTATATTGTGCT 57.370 32.000 0.00 0.00 0.00 4.40
195 196 8.731275 ACTTGCTGTTATGTTATATTGTGCTA 57.269 30.769 0.00 0.00 0.00 3.49
196 197 9.342308 ACTTGCTGTTATGTTATATTGTGCTAT 57.658 29.630 0.00 0.00 0.00 2.97
199 200 9.996554 TGCTGTTATGTTATATTGTGCTATACT 57.003 29.630 0.00 0.00 0.00 2.12
214 215 8.731275 TGTGCTATACTTATTTGTGCTATTGT 57.269 30.769 0.00 0.00 0.00 2.71
215 216 9.173021 TGTGCTATACTTATTTGTGCTATTGTT 57.827 29.630 0.00 0.00 0.00 2.83
222 223 8.165239 ACTTATTTGTGCTATTGTTTGACTCA 57.835 30.769 0.00 0.00 0.00 3.41
223 224 8.292448 ACTTATTTGTGCTATTGTTTGACTCAG 58.708 33.333 0.00 0.00 0.00 3.35
224 225 6.639632 ATTTGTGCTATTGTTTGACTCAGT 57.360 33.333 0.00 0.00 0.00 3.41
225 226 7.744087 ATTTGTGCTATTGTTTGACTCAGTA 57.256 32.000 0.00 0.00 0.00 2.74
226 227 6.785488 TTGTGCTATTGTTTGACTCAGTAG 57.215 37.500 0.00 0.00 0.00 2.57
227 228 6.096673 TGTGCTATTGTTTGACTCAGTAGA 57.903 37.500 0.00 0.00 30.27 2.59
228 229 6.521162 TGTGCTATTGTTTGACTCAGTAGAA 58.479 36.000 0.00 0.00 30.27 2.10
229 230 7.161404 TGTGCTATTGTTTGACTCAGTAGAAT 58.839 34.615 0.00 0.00 30.27 2.40
230 231 7.661437 TGTGCTATTGTTTGACTCAGTAGAATT 59.339 33.333 0.00 0.00 30.27 2.17
231 232 8.171840 GTGCTATTGTTTGACTCAGTAGAATTC 58.828 37.037 0.00 0.00 30.27 2.17
232 233 7.334421 TGCTATTGTTTGACTCAGTAGAATTCC 59.666 37.037 0.65 0.00 30.27 3.01
233 234 7.201652 GCTATTGTTTGACTCAGTAGAATTCCC 60.202 40.741 0.65 0.00 30.27 3.97
234 235 4.566004 TGTTTGACTCAGTAGAATTCCCG 58.434 43.478 0.65 0.00 0.00 5.14
235 236 3.887621 TTGACTCAGTAGAATTCCCGG 57.112 47.619 0.65 0.00 0.00 5.73
236 237 3.095912 TGACTCAGTAGAATTCCCGGA 57.904 47.619 0.73 0.00 0.00 5.14
237 238 3.024547 TGACTCAGTAGAATTCCCGGAG 58.975 50.000 0.73 16.22 0.00 4.63
238 239 3.025262 GACTCAGTAGAATTCCCGGAGT 58.975 50.000 20.67 20.67 36.89 3.85
239 240 2.761208 ACTCAGTAGAATTCCCGGAGTG 59.239 50.000 20.20 10.15 33.28 3.51
240 241 1.480954 TCAGTAGAATTCCCGGAGTGC 59.519 52.381 0.73 0.00 0.00 4.40
241 242 0.460311 AGTAGAATTCCCGGAGTGCG 59.540 55.000 0.73 0.00 0.00 5.34
242 243 0.458669 GTAGAATTCCCGGAGTGCGA 59.541 55.000 5.27 0.00 0.00 5.10
243 244 1.134907 GTAGAATTCCCGGAGTGCGAA 60.135 52.381 5.27 0.00 0.00 4.70
244 245 0.108138 AGAATTCCCGGAGTGCGAAG 60.108 55.000 5.27 0.00 0.00 3.79
259 260 2.493713 CGAAGCCTGCTATTACGAGT 57.506 50.000 0.00 0.00 0.00 4.18
260 261 2.386249 CGAAGCCTGCTATTACGAGTC 58.614 52.381 0.00 0.00 0.00 3.36
261 262 2.223502 CGAAGCCTGCTATTACGAGTCA 60.224 50.000 0.00 0.00 0.00 3.41
262 263 2.873133 AGCCTGCTATTACGAGTCAC 57.127 50.000 0.00 0.00 0.00 3.67
263 264 2.379972 AGCCTGCTATTACGAGTCACT 58.620 47.619 0.00 0.00 0.00 3.41
264 265 3.552875 AGCCTGCTATTACGAGTCACTA 58.447 45.455 0.00 0.00 0.00 2.74
265 266 3.566322 AGCCTGCTATTACGAGTCACTAG 59.434 47.826 0.00 0.00 0.00 2.57
266 267 3.854045 GCCTGCTATTACGAGTCACTAGC 60.854 52.174 0.00 0.00 36.26 3.42
267 268 3.566322 CCTGCTATTACGAGTCACTAGCT 59.434 47.826 0.00 0.00 36.59 3.32
268 269 4.036971 CCTGCTATTACGAGTCACTAGCTT 59.963 45.833 0.00 0.00 36.59 3.74
269 270 5.450688 CCTGCTATTACGAGTCACTAGCTTT 60.451 44.000 0.00 0.00 36.59 3.51
270 271 5.579718 TGCTATTACGAGTCACTAGCTTTC 58.420 41.667 0.00 0.00 36.59 2.62
271 272 4.671516 GCTATTACGAGTCACTAGCTTTCG 59.328 45.833 0.00 0.00 37.31 3.46
272 273 4.959596 ATTACGAGTCACTAGCTTTCGA 57.040 40.909 11.80 0.00 35.42 3.71
273 274 4.754372 TTACGAGTCACTAGCTTTCGAA 57.246 40.909 11.80 0.00 35.42 3.71
274 275 3.204597 ACGAGTCACTAGCTTTCGAAG 57.795 47.619 11.80 0.00 35.42 3.79
275 276 2.812591 ACGAGTCACTAGCTTTCGAAGA 59.187 45.455 11.80 0.00 35.42 2.87
276 277 3.165124 CGAGTCACTAGCTTTCGAAGAC 58.835 50.000 0.00 0.48 34.32 3.01
277 278 3.120130 CGAGTCACTAGCTTTCGAAGACT 60.120 47.826 12.22 12.22 37.55 3.24
278 279 4.162812 GAGTCACTAGCTTTCGAAGACTG 58.837 47.826 15.99 7.62 35.24 3.51
279 280 3.570550 AGTCACTAGCTTTCGAAGACTGT 59.429 43.478 11.75 6.16 34.32 3.55
280 281 3.915569 GTCACTAGCTTTCGAAGACTGTC 59.084 47.826 11.15 0.00 34.32 3.51
281 282 3.568430 TCACTAGCTTTCGAAGACTGTCA 59.432 43.478 10.88 0.00 34.32 3.58
282 283 3.917380 CACTAGCTTTCGAAGACTGTCAG 59.083 47.826 10.88 0.00 34.32 3.51
283 284 1.789506 AGCTTTCGAAGACTGTCAGC 58.210 50.000 10.88 8.84 34.32 4.26
284 285 0.793250 GCTTTCGAAGACTGTCAGCC 59.207 55.000 10.88 0.00 34.32 4.85
285 286 1.873903 GCTTTCGAAGACTGTCAGCCA 60.874 52.381 10.88 0.00 34.32 4.75
287 288 0.318441 TTCGAAGACTGTCAGCCAGG 59.682 55.000 10.88 0.00 46.06 4.45
292 293 3.244616 ACTGTCAGCCAGGCAAGT 58.755 55.556 15.80 8.71 46.06 3.16
293 294 1.072159 ACTGTCAGCCAGGCAAGTC 59.928 57.895 15.80 4.18 46.06 3.01
294 295 1.071987 CTGTCAGCCAGGCAAGTCA 59.928 57.895 15.80 8.82 37.54 3.41
295 296 0.322277 CTGTCAGCCAGGCAAGTCAT 60.322 55.000 15.80 0.00 37.54 3.06
296 297 0.111061 TGTCAGCCAGGCAAGTCATT 59.889 50.000 15.80 0.00 0.00 2.57
297 298 1.251251 GTCAGCCAGGCAAGTCATTT 58.749 50.000 15.80 0.00 0.00 2.32
298 299 1.068055 GTCAGCCAGGCAAGTCATTTG 60.068 52.381 15.80 0.00 39.88 2.32
299 300 1.202915 TCAGCCAGGCAAGTCATTTGA 60.203 47.619 15.80 2.56 39.21 2.69
300 301 1.822990 CAGCCAGGCAAGTCATTTGAT 59.177 47.619 15.80 0.00 39.21 2.57
301 302 2.097825 AGCCAGGCAAGTCATTTGATC 58.902 47.619 15.80 0.00 39.21 2.92
302 303 1.820519 GCCAGGCAAGTCATTTGATCA 59.179 47.619 6.55 0.00 39.21 2.92
303 304 2.429610 GCCAGGCAAGTCATTTGATCAT 59.570 45.455 6.55 0.00 39.21 2.45
304 305 3.737047 GCCAGGCAAGTCATTTGATCATG 60.737 47.826 6.55 0.00 39.21 3.07
305 306 3.446161 CCAGGCAAGTCATTTGATCATGT 59.554 43.478 0.00 0.00 39.21 3.21
306 307 4.081862 CCAGGCAAGTCATTTGATCATGTT 60.082 41.667 0.00 0.00 39.21 2.71
307 308 5.475719 CAGGCAAGTCATTTGATCATGTTT 58.524 37.500 0.00 0.00 39.21 2.83
308 309 5.929992 CAGGCAAGTCATTTGATCATGTTTT 59.070 36.000 0.00 0.00 39.21 2.43
309 310 6.425721 CAGGCAAGTCATTTGATCATGTTTTT 59.574 34.615 0.00 0.00 39.21 1.94
310 311 7.599621 CAGGCAAGTCATTTGATCATGTTTTTA 59.400 33.333 0.00 0.00 39.21 1.52
311 312 7.599998 AGGCAAGTCATTTGATCATGTTTTTAC 59.400 33.333 0.00 0.00 39.21 2.01
312 313 7.384660 GGCAAGTCATTTGATCATGTTTTTACA 59.615 33.333 0.00 0.00 39.21 2.41
313 314 8.763356 GCAAGTCATTTGATCATGTTTTTACAA 58.237 29.630 0.00 0.00 39.21 2.41
323 324 9.693739 TGATCATGTTTTTACAATACCTATGGT 57.306 29.630 0.00 0.00 40.16 3.55
439 440 1.352687 GGAGCTCCTCCTCCTTTGTTT 59.647 52.381 26.25 0.00 46.41 2.83
675 676 1.372683 GAGAGGAGGTTGCTGTGCA 59.627 57.895 0.00 0.00 36.47 4.57
862 863 1.758514 CCCCTTCTGCTCTCGGCTA 60.759 63.158 0.00 0.00 42.39 3.93
912 913 1.540267 GAGGTGACGAACTACTGCTGA 59.460 52.381 0.00 0.00 0.00 4.26
1104 1106 1.107114 CTACTGATGTGGGCTCGAGT 58.893 55.000 15.13 0.00 0.00 4.18
1180 1182 8.921205 TGAAGTTAGAAGGTGTAGAAAACTACT 58.079 33.333 0.00 0.00 0.00 2.57
1607 1609 1.668826 AAGTGGGTTGAGGATAGGCA 58.331 50.000 0.00 0.00 0.00 4.75
1705 1707 3.535561 CCGTCACTAAGAGATGCCATTT 58.464 45.455 0.00 0.00 0.00 2.32
1764 1766 1.600916 GCGGTCAAAGGTGGCTTCT 60.601 57.895 0.00 0.00 0.00 2.85
1860 1862 4.584518 CAGTGCACAGCCCCACCA 62.585 66.667 21.04 0.00 32.48 4.17
2133 2135 4.869861 GTGTTTGGTGACTTTGCTCATTTT 59.130 37.500 0.00 0.00 0.00 1.82
2186 2190 2.040278 TCTGTTGCTGTTCATAGGGCTT 59.960 45.455 0.00 0.00 0.00 4.35
2633 2637 3.443681 CCACCATTGTAGGTTTGGACATC 59.556 47.826 0.00 0.00 40.77 3.06
2824 2828 4.876107 ACATGTCCATCAACCTCGATAAAC 59.124 41.667 0.00 0.00 0.00 2.01
2935 2939 3.955771 TTCAAGGACTTTTGTGCGTAC 57.044 42.857 0.00 0.00 45.90 3.67
2938 2942 1.214367 AGGACTTTTGTGCGTACGTG 58.786 50.000 17.90 1.74 45.90 4.49
3029 3033 3.909732 CTGGGAGAGTTCCTATCAGACT 58.090 50.000 0.00 0.00 43.49 3.24
3144 3151 7.049754 TCAATCATGTACACTATGAATGTGCT 58.950 34.615 11.08 0.00 36.98 4.40
3145 3152 8.203485 TCAATCATGTACACTATGAATGTGCTA 58.797 33.333 11.08 0.00 36.98 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.882791 TGCTAACTAACAGAAGGAAAATCATCA 59.117 33.333 0.00 0.00 0.00 3.07
1 2 8.268850 TGCTAACTAACAGAAGGAAAATCATC 57.731 34.615 0.00 0.00 0.00 2.92
2 3 8.635765 TTGCTAACTAACAGAAGGAAAATCAT 57.364 30.769 0.00 0.00 0.00 2.45
4 5 9.181805 GTTTTGCTAACTAACAGAAGGAAAATC 57.818 33.333 12.08 6.51 40.04 2.17
5 6 8.141909 GGTTTTGCTAACTAACAGAAGGAAAAT 58.858 33.333 12.08 0.00 40.04 1.82
6 7 7.417003 GGGTTTTGCTAACTAACAGAAGGAAAA 60.417 37.037 0.00 0.00 37.07 2.29
7 8 6.040054 GGGTTTTGCTAACTAACAGAAGGAAA 59.960 38.462 3.00 0.00 0.00 3.13
8 9 5.533528 GGGTTTTGCTAACTAACAGAAGGAA 59.466 40.000 3.00 0.00 0.00 3.36
9 10 5.067954 GGGTTTTGCTAACTAACAGAAGGA 58.932 41.667 3.00 0.00 0.00 3.36
11 12 6.381801 CATGGGTTTTGCTAACTAACAGAAG 58.618 40.000 3.00 0.00 0.00 2.85
12 13 5.278758 GCATGGGTTTTGCTAACTAACAGAA 60.279 40.000 0.00 0.00 37.14 3.02
13 14 4.217550 GCATGGGTTTTGCTAACTAACAGA 59.782 41.667 0.00 0.00 37.14 3.41
14 15 4.485163 GCATGGGTTTTGCTAACTAACAG 58.515 43.478 0.00 0.00 37.14 3.16
15 16 4.513198 GCATGGGTTTTGCTAACTAACA 57.487 40.909 0.00 1.70 37.14 2.41
29 30 5.390387 TCTTAACAAAACCTAAGCATGGGT 58.610 37.500 0.00 0.00 43.25 4.51
30 31 5.975693 TCTTAACAAAACCTAAGCATGGG 57.024 39.130 0.00 0.00 0.00 4.00
31 32 7.926018 ACTTTTCTTAACAAAACCTAAGCATGG 59.074 33.333 0.00 0.00 0.00 3.66
32 33 8.871686 ACTTTTCTTAACAAAACCTAAGCATG 57.128 30.769 0.00 0.00 0.00 4.06
33 34 9.884636 AAACTTTTCTTAACAAAACCTAAGCAT 57.115 25.926 0.00 0.00 0.00 3.79
34 35 9.713713 AAAACTTTTCTTAACAAAACCTAAGCA 57.286 25.926 0.00 0.00 0.00 3.91
73 74 7.752239 CCACATCAAGCAACAACTAAGAAATAG 59.248 37.037 0.00 0.00 37.66 1.73
74 75 7.230510 ACCACATCAAGCAACAACTAAGAAATA 59.769 33.333 0.00 0.00 0.00 1.40
75 76 6.040842 ACCACATCAAGCAACAACTAAGAAAT 59.959 34.615 0.00 0.00 0.00 2.17
76 77 5.359576 ACCACATCAAGCAACAACTAAGAAA 59.640 36.000 0.00 0.00 0.00 2.52
77 78 4.887071 ACCACATCAAGCAACAACTAAGAA 59.113 37.500 0.00 0.00 0.00 2.52
78 79 4.275689 CACCACATCAAGCAACAACTAAGA 59.724 41.667 0.00 0.00 0.00 2.10
79 80 4.275689 TCACCACATCAAGCAACAACTAAG 59.724 41.667 0.00 0.00 0.00 2.18
80 81 4.203226 TCACCACATCAAGCAACAACTAA 58.797 39.130 0.00 0.00 0.00 2.24
81 82 3.814625 TCACCACATCAAGCAACAACTA 58.185 40.909 0.00 0.00 0.00 2.24
82 83 2.653726 TCACCACATCAAGCAACAACT 58.346 42.857 0.00 0.00 0.00 3.16
83 84 3.435105 TTCACCACATCAAGCAACAAC 57.565 42.857 0.00 0.00 0.00 3.32
84 85 4.180057 GTTTTCACCACATCAAGCAACAA 58.820 39.130 0.00 0.00 0.00 2.83
85 86 3.430098 GGTTTTCACCACATCAAGCAACA 60.430 43.478 0.00 0.00 43.61 3.33
86 87 3.123050 GGTTTTCACCACATCAAGCAAC 58.877 45.455 0.00 0.00 43.61 4.17
87 88 3.451141 GGTTTTCACCACATCAAGCAA 57.549 42.857 0.00 0.00 43.61 3.91
94 95 8.590445 GAAAGCAATTCAAGGTTTTCACCACAT 61.590 37.037 0.00 0.00 40.72 3.21
95 96 7.344222 GAAAGCAATTCAAGGTTTTCACCACA 61.344 38.462 0.00 0.00 40.72 4.17
96 97 5.006649 GAAAGCAATTCAAGGTTTTCACCAC 59.993 40.000 0.00 0.00 40.72 4.16
97 98 5.104982 AGAAAGCAATTCAAGGTTTTCACCA 60.105 36.000 5.24 0.00 42.27 4.17
98 99 5.359756 AGAAAGCAATTCAAGGTTTTCACC 58.640 37.500 5.24 0.00 41.07 4.02
99 100 6.199719 CAGAGAAAGCAATTCAAGGTTTTCAC 59.800 38.462 5.24 0.00 40.72 3.18
100 101 6.096705 TCAGAGAAAGCAATTCAAGGTTTTCA 59.903 34.615 5.24 0.00 40.72 2.69
101 102 6.507023 TCAGAGAAAGCAATTCAAGGTTTTC 58.493 36.000 5.24 0.00 40.72 2.29
102 103 6.097412 ACTCAGAGAAAGCAATTCAAGGTTTT 59.903 34.615 3.79 0.00 40.72 2.43
103 104 5.595952 ACTCAGAGAAAGCAATTCAAGGTTT 59.404 36.000 3.79 0.00 40.72 3.27
104 105 5.136105 ACTCAGAGAAAGCAATTCAAGGTT 58.864 37.500 3.79 0.00 40.72 3.50
105 106 4.723309 ACTCAGAGAAAGCAATTCAAGGT 58.277 39.130 3.79 0.00 40.72 3.50
106 107 5.702349 AACTCAGAGAAAGCAATTCAAGG 57.298 39.130 3.79 0.00 40.72 3.61
107 108 7.424001 AGAAAACTCAGAGAAAGCAATTCAAG 58.576 34.615 3.79 0.78 40.72 3.02
108 109 7.338800 AGAAAACTCAGAGAAAGCAATTCAA 57.661 32.000 3.79 0.00 40.72 2.69
109 110 6.949352 AGAAAACTCAGAGAAAGCAATTCA 57.051 33.333 3.79 0.00 40.72 2.57
110 111 7.168804 CCAAAGAAAACTCAGAGAAAGCAATTC 59.831 37.037 3.79 0.00 38.39 2.17
111 112 6.982724 CCAAAGAAAACTCAGAGAAAGCAATT 59.017 34.615 3.79 0.00 0.00 2.32
112 113 6.322201 TCCAAAGAAAACTCAGAGAAAGCAAT 59.678 34.615 3.79 0.00 0.00 3.56
113 114 5.652014 TCCAAAGAAAACTCAGAGAAAGCAA 59.348 36.000 3.79 0.00 0.00 3.91
114 115 5.192927 TCCAAAGAAAACTCAGAGAAAGCA 58.807 37.500 3.79 0.00 0.00 3.91
115 116 5.757850 TCCAAAGAAAACTCAGAGAAAGC 57.242 39.130 3.79 0.00 0.00 3.51
116 117 9.028185 CAAAATCCAAAGAAAACTCAGAGAAAG 57.972 33.333 3.79 0.00 0.00 2.62
117 118 7.981225 CCAAAATCCAAAGAAAACTCAGAGAAA 59.019 33.333 3.79 0.00 0.00 2.52
118 119 7.124147 ACCAAAATCCAAAGAAAACTCAGAGAA 59.876 33.333 3.79 0.00 0.00 2.87
119 120 6.607198 ACCAAAATCCAAAGAAAACTCAGAGA 59.393 34.615 3.79 0.00 0.00 3.10
120 121 6.809869 ACCAAAATCCAAAGAAAACTCAGAG 58.190 36.000 0.00 0.00 0.00 3.35
121 122 6.790232 ACCAAAATCCAAAGAAAACTCAGA 57.210 33.333 0.00 0.00 0.00 3.27
122 123 7.548780 TCAAACCAAAATCCAAAGAAAACTCAG 59.451 33.333 0.00 0.00 0.00 3.35
123 124 7.390027 TCAAACCAAAATCCAAAGAAAACTCA 58.610 30.769 0.00 0.00 0.00 3.41
124 125 7.549134 ACTCAAACCAAAATCCAAAGAAAACTC 59.451 33.333 0.00 0.00 0.00 3.01
125 126 7.334171 CACTCAAACCAAAATCCAAAGAAAACT 59.666 33.333 0.00 0.00 0.00 2.66
126 127 7.463544 CACTCAAACCAAAATCCAAAGAAAAC 58.536 34.615 0.00 0.00 0.00 2.43
127 128 6.093357 GCACTCAAACCAAAATCCAAAGAAAA 59.907 34.615 0.00 0.00 0.00 2.29
128 129 5.584251 GCACTCAAACCAAAATCCAAAGAAA 59.416 36.000 0.00 0.00 0.00 2.52
129 130 5.104982 AGCACTCAAACCAAAATCCAAAGAA 60.105 36.000 0.00 0.00 0.00 2.52
130 131 4.405358 AGCACTCAAACCAAAATCCAAAGA 59.595 37.500 0.00 0.00 0.00 2.52
131 132 4.696455 AGCACTCAAACCAAAATCCAAAG 58.304 39.130 0.00 0.00 0.00 2.77
132 133 4.751767 AGCACTCAAACCAAAATCCAAA 57.248 36.364 0.00 0.00 0.00 3.28
133 134 4.440880 CAAGCACTCAAACCAAAATCCAA 58.559 39.130 0.00 0.00 0.00 3.53
134 135 3.181467 CCAAGCACTCAAACCAAAATCCA 60.181 43.478 0.00 0.00 0.00 3.41
135 136 3.392882 CCAAGCACTCAAACCAAAATCC 58.607 45.455 0.00 0.00 0.00 3.01
136 137 3.181466 ACCCAAGCACTCAAACCAAAATC 60.181 43.478 0.00 0.00 0.00 2.17
137 138 2.771372 ACCCAAGCACTCAAACCAAAAT 59.229 40.909 0.00 0.00 0.00 1.82
138 139 2.093764 CACCCAAGCACTCAAACCAAAA 60.094 45.455 0.00 0.00 0.00 2.44
139 140 1.480137 CACCCAAGCACTCAAACCAAA 59.520 47.619 0.00 0.00 0.00 3.28
140 141 1.110442 CACCCAAGCACTCAAACCAA 58.890 50.000 0.00 0.00 0.00 3.67
141 142 0.033601 ACACCCAAGCACTCAAACCA 60.034 50.000 0.00 0.00 0.00 3.67
142 143 1.111277 AACACCCAAGCACTCAAACC 58.889 50.000 0.00 0.00 0.00 3.27
143 144 2.959507 AAACACCCAAGCACTCAAAC 57.040 45.000 0.00 0.00 0.00 2.93
144 145 4.020543 AGTAAAACACCCAAGCACTCAAA 58.979 39.130 0.00 0.00 0.00 2.69
145 146 3.626930 AGTAAAACACCCAAGCACTCAA 58.373 40.909 0.00 0.00 0.00 3.02
146 147 3.290948 AGTAAAACACCCAAGCACTCA 57.709 42.857 0.00 0.00 0.00 3.41
147 148 3.630312 TGAAGTAAAACACCCAAGCACTC 59.370 43.478 0.00 0.00 0.00 3.51
148 149 3.626930 TGAAGTAAAACACCCAAGCACT 58.373 40.909 0.00 0.00 0.00 4.40
149 150 4.109766 GTTGAAGTAAAACACCCAAGCAC 58.890 43.478 0.00 0.00 0.00 4.40
150 151 4.020543 AGTTGAAGTAAAACACCCAAGCA 58.979 39.130 0.00 0.00 0.00 3.91
151 152 4.649088 AGTTGAAGTAAAACACCCAAGC 57.351 40.909 0.00 0.00 0.00 4.01
152 153 4.803613 GCAAGTTGAAGTAAAACACCCAAG 59.196 41.667 7.16 0.00 0.00 3.61
153 154 4.464597 AGCAAGTTGAAGTAAAACACCCAA 59.535 37.500 7.16 0.00 0.00 4.12
154 155 4.020543 AGCAAGTTGAAGTAAAACACCCA 58.979 39.130 7.16 0.00 0.00 4.51
155 156 4.142249 ACAGCAAGTTGAAGTAAAACACCC 60.142 41.667 7.16 0.00 0.00 4.61
156 157 4.993905 ACAGCAAGTTGAAGTAAAACACC 58.006 39.130 7.16 0.00 0.00 4.16
157 158 7.700656 ACATAACAGCAAGTTGAAGTAAAACAC 59.299 33.333 7.16 0.00 41.50 3.32
158 159 7.767261 ACATAACAGCAAGTTGAAGTAAAACA 58.233 30.769 7.16 0.00 41.50 2.83
159 160 8.628882 AACATAACAGCAAGTTGAAGTAAAAC 57.371 30.769 7.16 0.00 41.50 2.43
166 167 9.838975 CACAATATAACATAACAGCAAGTTGAA 57.161 29.630 7.16 0.00 41.50 2.69
167 168 7.967854 GCACAATATAACATAACAGCAAGTTGA 59.032 33.333 7.16 0.00 41.50 3.18
168 169 7.970061 AGCACAATATAACATAACAGCAAGTTG 59.030 33.333 0.00 0.00 41.50 3.16
169 170 8.055279 AGCACAATATAACATAACAGCAAGTT 57.945 30.769 0.22 0.22 44.27 2.66
170 171 7.630242 AGCACAATATAACATAACAGCAAGT 57.370 32.000 0.00 0.00 0.00 3.16
173 174 9.996554 AGTATAGCACAATATAACATAACAGCA 57.003 29.630 0.00 0.00 0.00 4.41
188 189 9.173021 ACAATAGCACAAATAAGTATAGCACAA 57.827 29.630 0.00 0.00 0.00 3.33
189 190 8.731275 ACAATAGCACAAATAAGTATAGCACA 57.269 30.769 0.00 0.00 0.00 4.57
196 197 9.278978 TGAGTCAAACAATAGCACAAATAAGTA 57.721 29.630 0.00 0.00 0.00 2.24
197 198 8.165239 TGAGTCAAACAATAGCACAAATAAGT 57.835 30.769 0.00 0.00 0.00 2.24
198 199 8.292448 ACTGAGTCAAACAATAGCACAAATAAG 58.708 33.333 0.00 0.00 0.00 1.73
199 200 8.165239 ACTGAGTCAAACAATAGCACAAATAA 57.835 30.769 0.00 0.00 0.00 1.40
200 201 7.744087 ACTGAGTCAAACAATAGCACAAATA 57.256 32.000 0.00 0.00 0.00 1.40
201 202 6.639632 ACTGAGTCAAACAATAGCACAAAT 57.360 33.333 0.00 0.00 0.00 2.32
202 203 6.989759 TCTACTGAGTCAAACAATAGCACAAA 59.010 34.615 0.00 0.00 0.00 2.83
203 204 6.521162 TCTACTGAGTCAAACAATAGCACAA 58.479 36.000 0.00 0.00 0.00 3.33
204 205 6.096673 TCTACTGAGTCAAACAATAGCACA 57.903 37.500 0.00 0.00 0.00 4.57
205 206 7.602517 ATTCTACTGAGTCAAACAATAGCAC 57.397 36.000 0.00 0.00 0.00 4.40
206 207 7.334421 GGAATTCTACTGAGTCAAACAATAGCA 59.666 37.037 5.23 0.00 0.00 3.49
207 208 7.201652 GGGAATTCTACTGAGTCAAACAATAGC 60.202 40.741 5.23 0.00 0.00 2.97
208 209 7.010552 CGGGAATTCTACTGAGTCAAACAATAG 59.989 40.741 5.23 0.00 0.00 1.73
209 210 6.816640 CGGGAATTCTACTGAGTCAAACAATA 59.183 38.462 5.23 0.00 0.00 1.90
210 211 5.643777 CGGGAATTCTACTGAGTCAAACAAT 59.356 40.000 5.23 0.00 0.00 2.71
211 212 4.994852 CGGGAATTCTACTGAGTCAAACAA 59.005 41.667 5.23 0.00 0.00 2.83
212 213 4.562757 CCGGGAATTCTACTGAGTCAAACA 60.563 45.833 5.23 0.00 0.00 2.83
213 214 3.933332 CCGGGAATTCTACTGAGTCAAAC 59.067 47.826 5.23 0.00 0.00 2.93
214 215 3.835978 TCCGGGAATTCTACTGAGTCAAA 59.164 43.478 0.00 0.00 0.00 2.69
215 216 3.437213 TCCGGGAATTCTACTGAGTCAA 58.563 45.455 0.00 0.00 0.00 3.18
216 217 3.024547 CTCCGGGAATTCTACTGAGTCA 58.975 50.000 0.00 0.00 0.00 3.41
217 218 3.025262 ACTCCGGGAATTCTACTGAGTC 58.975 50.000 16.07 0.00 0.00 3.36
218 219 2.761208 CACTCCGGGAATTCTACTGAGT 59.239 50.000 16.07 16.07 0.00 3.41
219 220 2.482142 GCACTCCGGGAATTCTACTGAG 60.482 54.545 0.00 11.71 0.00 3.35
220 221 1.480954 GCACTCCGGGAATTCTACTGA 59.519 52.381 0.00 0.69 0.00 3.41
221 222 1.802880 CGCACTCCGGGAATTCTACTG 60.803 57.143 0.00 0.00 0.00 2.74
222 223 0.460311 CGCACTCCGGGAATTCTACT 59.540 55.000 0.00 0.00 0.00 2.57
223 224 0.458669 TCGCACTCCGGGAATTCTAC 59.541 55.000 0.00 0.00 37.59 2.59
224 225 1.136305 CTTCGCACTCCGGGAATTCTA 59.864 52.381 0.00 0.00 44.71 2.10
225 226 0.108138 CTTCGCACTCCGGGAATTCT 60.108 55.000 0.00 0.00 44.71 2.40
226 227 1.706287 GCTTCGCACTCCGGGAATTC 61.706 60.000 0.00 0.00 44.71 2.17
227 228 1.745489 GCTTCGCACTCCGGGAATT 60.745 57.895 0.00 0.00 44.71 2.17
228 229 2.125106 GCTTCGCACTCCGGGAAT 60.125 61.111 0.00 0.00 44.71 3.01
229 230 4.388499 GGCTTCGCACTCCGGGAA 62.388 66.667 0.00 0.00 43.72 3.97
233 234 2.635229 ATAGCAGGCTTCGCACTCCG 62.635 60.000 0.00 0.00 38.61 4.63
234 235 0.462759 AATAGCAGGCTTCGCACTCC 60.463 55.000 0.00 0.00 0.00 3.85
235 236 1.861575 GTAATAGCAGGCTTCGCACTC 59.138 52.381 0.00 0.00 0.00 3.51
236 237 1.802880 CGTAATAGCAGGCTTCGCACT 60.803 52.381 0.00 0.00 0.00 4.40
237 238 0.577269 CGTAATAGCAGGCTTCGCAC 59.423 55.000 0.00 0.00 0.00 5.34
238 239 0.458260 TCGTAATAGCAGGCTTCGCA 59.542 50.000 0.00 0.00 0.00 5.10
239 240 1.132588 CTCGTAATAGCAGGCTTCGC 58.867 55.000 0.00 0.00 0.00 4.70
240 241 2.223502 TGACTCGTAATAGCAGGCTTCG 60.224 50.000 0.00 0.78 0.00 3.79
241 242 3.117046 GTGACTCGTAATAGCAGGCTTC 58.883 50.000 0.00 0.00 0.00 3.86
242 243 2.761208 AGTGACTCGTAATAGCAGGCTT 59.239 45.455 0.00 0.00 0.00 4.35
243 244 2.379972 AGTGACTCGTAATAGCAGGCT 58.620 47.619 0.00 0.00 0.00 4.58
244 245 2.873133 AGTGACTCGTAATAGCAGGC 57.127 50.000 0.00 0.00 0.00 4.85
245 246 3.566322 AGCTAGTGACTCGTAATAGCAGG 59.434 47.826 5.68 0.00 41.01 4.85
246 247 4.822036 AGCTAGTGACTCGTAATAGCAG 57.178 45.455 5.68 0.00 41.01 4.24
247 248 5.578005 AAAGCTAGTGACTCGTAATAGCA 57.422 39.130 5.68 0.00 41.01 3.49
248 249 4.671516 CGAAAGCTAGTGACTCGTAATAGC 59.328 45.833 0.00 0.00 39.28 2.97
249 250 6.045698 TCGAAAGCTAGTGACTCGTAATAG 57.954 41.667 0.00 0.00 0.00 1.73
250 251 6.314648 TCTTCGAAAGCTAGTGACTCGTAATA 59.685 38.462 0.00 0.00 0.00 0.98
251 252 4.959596 TCGAAAGCTAGTGACTCGTAAT 57.040 40.909 0.00 0.00 0.00 1.89
252 253 4.453478 TCTTCGAAAGCTAGTGACTCGTAA 59.547 41.667 0.00 0.00 0.00 3.18
253 254 3.999001 TCTTCGAAAGCTAGTGACTCGTA 59.001 43.478 0.00 0.00 0.00 3.43
254 255 2.812591 TCTTCGAAAGCTAGTGACTCGT 59.187 45.455 0.00 0.00 0.00 4.18
255 256 3.120130 AGTCTTCGAAAGCTAGTGACTCG 60.120 47.826 7.84 0.00 0.00 4.18
256 257 4.162812 CAGTCTTCGAAAGCTAGTGACTC 58.837 47.826 10.10 0.00 31.93 3.36
257 258 3.570550 ACAGTCTTCGAAAGCTAGTGACT 59.429 43.478 7.84 7.84 34.18 3.41
258 259 3.903360 ACAGTCTTCGAAAGCTAGTGAC 58.097 45.455 0.00 1.19 0.00 3.67
259 260 3.568430 TGACAGTCTTCGAAAGCTAGTGA 59.432 43.478 0.00 0.00 0.00 3.41
260 261 3.902150 TGACAGTCTTCGAAAGCTAGTG 58.098 45.455 0.00 1.45 0.00 2.74
261 262 3.612955 GCTGACAGTCTTCGAAAGCTAGT 60.613 47.826 3.99 6.14 0.00 2.57
262 263 2.920490 GCTGACAGTCTTCGAAAGCTAG 59.080 50.000 3.99 1.94 0.00 3.42
263 264 2.352814 GGCTGACAGTCTTCGAAAGCTA 60.353 50.000 13.67 0.00 0.00 3.32
264 265 1.606737 GGCTGACAGTCTTCGAAAGCT 60.607 52.381 13.67 5.68 0.00 3.74
265 266 0.793250 GGCTGACAGTCTTCGAAAGC 59.207 55.000 3.99 7.12 0.00 3.51
266 267 2.064762 CTGGCTGACAGTCTTCGAAAG 58.935 52.381 8.81 0.00 42.42 2.62
267 268 1.270305 CCTGGCTGACAGTCTTCGAAA 60.270 52.381 10.12 0.00 46.06 3.46
268 269 0.318441 CCTGGCTGACAGTCTTCGAA 59.682 55.000 10.12 0.00 46.06 3.71
269 270 1.967535 CCTGGCTGACAGTCTTCGA 59.032 57.895 10.12 0.00 46.06 3.71
270 271 1.739562 GCCTGGCTGACAGTCTTCG 60.740 63.158 12.43 0.00 46.06 3.79
271 272 0.250467 TTGCCTGGCTGACAGTCTTC 60.250 55.000 21.03 0.00 46.06 2.87
272 273 0.250640 CTTGCCTGGCTGACAGTCTT 60.251 55.000 21.03 0.00 46.06 3.01
273 274 1.374190 CTTGCCTGGCTGACAGTCT 59.626 57.895 21.03 0.00 46.06 3.24
274 275 0.952984 GACTTGCCTGGCTGACAGTC 60.953 60.000 21.03 19.41 46.06 3.51
275 276 1.072159 GACTTGCCTGGCTGACAGT 59.928 57.895 21.03 15.46 46.06 3.55
277 278 0.111061 AATGACTTGCCTGGCTGACA 59.889 50.000 21.03 17.78 0.00 3.58
278 279 1.068055 CAAATGACTTGCCTGGCTGAC 60.068 52.381 21.03 12.98 0.00 3.51
279 280 1.202915 TCAAATGACTTGCCTGGCTGA 60.203 47.619 21.03 9.52 34.76 4.26
280 281 1.250328 TCAAATGACTTGCCTGGCTG 58.750 50.000 21.03 14.75 34.76 4.85
281 282 2.097825 GATCAAATGACTTGCCTGGCT 58.902 47.619 21.03 0.00 34.76 4.75
282 283 1.820519 TGATCAAATGACTTGCCTGGC 59.179 47.619 12.87 12.87 34.76 4.85
283 284 3.446161 ACATGATCAAATGACTTGCCTGG 59.554 43.478 0.00 0.00 34.76 4.45
284 285 4.713824 ACATGATCAAATGACTTGCCTG 57.286 40.909 0.00 0.00 34.76 4.85
285 286 5.733620 AAACATGATCAAATGACTTGCCT 57.266 34.783 0.00 0.00 34.76 4.75
286 287 6.790285 AAAAACATGATCAAATGACTTGCC 57.210 33.333 0.00 0.00 34.76 4.52
287 288 8.296799 TGTAAAAACATGATCAAATGACTTGC 57.703 30.769 0.00 0.00 34.76 4.01
297 298 9.693739 ACCATAGGTATTGTAAAAACATGATCA 57.306 29.630 0.00 0.00 32.11 2.92
320 321 9.770097 TCAACAAATTCTAATGCAATAAAACCA 57.230 25.926 0.00 0.00 0.00 3.67
324 325 8.920665 CGGTTCAACAAATTCTAATGCAATAAA 58.079 29.630 0.00 0.00 0.00 1.40
325 326 7.543868 CCGGTTCAACAAATTCTAATGCAATAA 59.456 33.333 0.00 0.00 0.00 1.40
326 327 7.032580 CCGGTTCAACAAATTCTAATGCAATA 58.967 34.615 0.00 0.00 0.00 1.90
327 328 5.868801 CCGGTTCAACAAATTCTAATGCAAT 59.131 36.000 0.00 0.00 0.00 3.56
328 329 5.221342 ACCGGTTCAACAAATTCTAATGCAA 60.221 36.000 0.00 0.00 0.00 4.08
329 330 4.279671 ACCGGTTCAACAAATTCTAATGCA 59.720 37.500 0.00 0.00 0.00 3.96
330 331 4.805219 ACCGGTTCAACAAATTCTAATGC 58.195 39.130 0.00 0.00 0.00 3.56
331 332 6.972328 CCATACCGGTTCAACAAATTCTAATG 59.028 38.462 15.04 4.68 0.00 1.90
332 333 6.096282 CCCATACCGGTTCAACAAATTCTAAT 59.904 38.462 15.04 0.00 0.00 1.73
333 334 5.416326 CCCATACCGGTTCAACAAATTCTAA 59.584 40.000 15.04 0.00 0.00 2.10
334 335 4.944930 CCCATACCGGTTCAACAAATTCTA 59.055 41.667 15.04 0.00 0.00 2.10
335 336 3.761752 CCCATACCGGTTCAACAAATTCT 59.238 43.478 15.04 0.00 0.00 2.40
336 337 3.674955 GCCCATACCGGTTCAACAAATTC 60.675 47.826 15.04 0.00 0.00 2.17
337 338 2.232696 GCCCATACCGGTTCAACAAATT 59.767 45.455 15.04 0.00 0.00 1.82
401 402 4.161377 AGCTCCTCTTCTAGGTCAACATTC 59.839 45.833 0.00 0.00 46.62 2.67
434 435 2.539338 GGCGGCTCACACGAAACAA 61.539 57.895 0.00 0.00 0.00 2.83
862 863 2.014010 ACCAACCCACAGCAATCAAT 57.986 45.000 0.00 0.00 0.00 2.57
912 913 4.711355 CACTCCTCTTCTCCTCTTCTCAAT 59.289 45.833 0.00 0.00 0.00 2.57
1087 1089 1.593787 CACTCGAGCCCACATCAGT 59.406 57.895 13.61 0.00 0.00 3.41
1180 1182 0.612174 CCTCTCCTCGACCACCTCAA 60.612 60.000 0.00 0.00 0.00 3.02
1607 1609 3.897505 CCCCTTCAAAAACTTGAGGACAT 59.102 43.478 0.00 0.00 30.57 3.06
1860 1862 4.133078 CTCTGCCTTTGTTGTCTCTCTTT 58.867 43.478 0.00 0.00 0.00 2.52
2133 2135 7.239763 TCATTACCTTCATCAGAGTACACAA 57.760 36.000 0.00 0.00 0.00 3.33
2186 2190 6.428083 TGAGTCTAAAACCCAATCTACACA 57.572 37.500 0.00 0.00 0.00 3.72
2824 2828 7.312154 TGAAGGTGACAAAATATTTCATTCCG 58.688 34.615 0.10 0.00 0.00 4.30
2935 2939 3.730715 GCACCTTGAATTGAGTTTTCACG 59.269 43.478 0.00 0.00 33.03 4.35
2938 2942 4.202151 ACCTGCACCTTGAATTGAGTTTTC 60.202 41.667 0.00 0.00 0.00 2.29
3029 3033 6.737720 AGATGTCTGATGCAGAATACCTTA 57.262 37.500 0.00 0.00 42.46 2.69


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

AutoCloner maintained by Alex Coulton.