Multiple sequence alignment - TraesCS2D01G320100

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 TraesCS2D01G320100 chr2D 100.000 3856 0 0 1 3856 411412216 411416071 0.000000e+00 7121.0
1 TraesCS2D01G320100 chr2D 97.033 3236 70 6 325 3543 411698505 411701731 0.000000e+00 5421.0
2 TraesCS2D01G320100 chr2D 96.845 317 10 0 3540 3856 411701843 411702159 7.340000e-147 531.0
3 TraesCS2D01G320100 chr2D 85.748 421 55 2 1512 1932 411965340 411965755 1.270000e-119 440.0
4 TraesCS2D01G320100 chr2D 91.131 327 25 4 1 324 555385762 555386087 1.270000e-119 440.0
5 TraesCS2D01G320100 chr2D 89.602 327 30 4 1 324 589511740 589512065 2.770000e-111 412.0
6 TraesCS2D01G320100 chr2D 97.059 34 1 0 1113 1146 411694144 411694177 1.500000e-04 58.4
7 TraesCS2D01G320100 chr2A 95.336 3173 96 19 325 3449 579073756 579076924 0.000000e+00 4992.0
8 TraesCS2D01G320100 chr2A 87.323 1412 170 7 1512 2920 579461019 579462424 0.000000e+00 1607.0
9 TraesCS2D01G320100 chr2A 90.780 423 28 6 3445 3856 579142051 579142473 4.350000e-154 555.0
10 TraesCS2D01G320100 chr2A 90.214 327 28 4 1 324 487378243 487378568 1.280000e-114 424.0
11 TraesCS2D01G320100 chr2A 79.412 136 16 7 910 1038 579460707 579460837 6.860000e-13 86.1
12 TraesCS2D01G320100 chr6D 91.265 332 26 3 1 329 46919018 46919349 2.110000e-122 449.0
13 TraesCS2D01G320100 chr6D 89.394 330 31 4 1 327 127393179 127392851 2.770000e-111 412.0
14 TraesCS2D01G320100 chr7B 90.214 327 29 3 4 327 211785282 211784956 1.280000e-114 424.0
15 TraesCS2D01G320100 chr7A 89.908 327 30 3 1 324 223134295 223134621 5.960000e-113 418.0
16 TraesCS2D01G320100 chr4A 89.666 329 31 3 1 326 30803181 30803509 2.140000e-112 416.0
17 TraesCS2D01G320100 chr2B 89.877 326 30 3 4 326 799449933 799449608 2.140000e-112 416.0
18 TraesCS2D01G320100 chr5A 96.774 31 1 0 3508 3538 143033989 143033959 7.000000e-03 52.8


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 TraesCS2D01G320100 chr2D 411412216 411416071 3855 False 7121.00 7121 100.0000 1 3856 1 chr2D.!!$F1 3855
1 TraesCS2D01G320100 chr2D 411698505 411702159 3654 False 2976.00 5421 96.9390 325 3856 2 chr2D.!!$F6 3531
2 TraesCS2D01G320100 chr2A 579073756 579076924 3168 False 4992.00 4992 95.3360 325 3449 1 chr2A.!!$F2 3124
3 TraesCS2D01G320100 chr2A 579460707 579462424 1717 False 846.55 1607 83.3675 910 2920 2 chr2A.!!$F4 2010

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
135 136 0.034059 AAATCTCGCTGCGGATAGGG 59.966 55.0 23.03 6.04 0.0 3.53 F
275 276 0.169009 GCCTCGACCTGCATTTTGAC 59.831 55.0 0.00 0.00 0.0 3.18 F
1882 1914 0.034059 AGTTGAACACCTGGAGCTCG 59.966 55.0 7.83 0.00 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 1869 0.185175 GTGGTCCAAACCCCTGAGTT 59.815 55.000 0.00 0.00 45.83 3.01 R
2246 2279 1.671054 TTAGCTGGCAGAACACGGC 60.671 57.895 20.86 0.74 39.25 5.68 R
3259 3342 0.475044 ACCGAACAAGGGCCTTACAA 59.525 50.000 20.44 0.00 35.02 2.41 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 2.203056 TCATCCATGGCGGCGAAG 60.203 61.111 12.98 0.00 33.14 3.79
18 19 3.282157 CATCCATGGCGGCGAAGG 61.282 66.667 12.98 6.00 33.14 3.46
19 20 3.479203 ATCCATGGCGGCGAAGGA 61.479 61.111 12.98 11.29 33.14 3.36
20 21 3.757248 ATCCATGGCGGCGAAGGAC 62.757 63.158 12.98 0.00 33.14 3.85
31 32 4.468689 GAAGGACGGCCGGGGAAG 62.469 72.222 31.76 0.00 39.96 3.46
33 34 4.798682 AGGACGGCCGGGGAAGAT 62.799 66.667 31.76 5.85 39.96 2.40
34 35 4.547367 GGACGGCCGGGGAAGATG 62.547 72.222 31.76 0.00 0.00 2.90
41 42 3.781307 CGGGGAAGATGCACCGGA 61.781 66.667 9.46 0.00 42.48 5.14
42 43 2.190578 GGGGAAGATGCACCGGAG 59.809 66.667 9.46 0.00 0.00 4.63
43 44 2.514824 GGGAAGATGCACCGGAGC 60.515 66.667 17.78 17.78 0.00 4.70
44 45 2.892425 GGAAGATGCACCGGAGCG 60.892 66.667 19.24 2.57 37.31 5.03
45 46 2.125512 GAAGATGCACCGGAGCGT 60.126 61.111 19.09 19.09 37.31 5.07
46 47 2.434884 AAGATGCACCGGAGCGTG 60.435 61.111 23.89 4.10 37.31 5.34
74 75 4.740822 GCAATGGTGGCGGAGGGT 62.741 66.667 0.00 0.00 0.00 4.34
75 76 2.751436 CAATGGTGGCGGAGGGTG 60.751 66.667 0.00 0.00 0.00 4.61
76 77 4.047125 AATGGTGGCGGAGGGTGG 62.047 66.667 0.00 0.00 0.00 4.61
110 111 3.564027 CGCGCGGAAATGTCCCTC 61.564 66.667 24.84 0.00 41.44 4.30
111 112 3.202706 GCGCGGAAATGTCCCTCC 61.203 66.667 8.83 0.00 41.44 4.30
112 113 2.513897 CGCGGAAATGTCCCTCCC 60.514 66.667 0.00 0.00 41.44 4.30
113 114 2.513897 GCGGAAATGTCCCTCCCG 60.514 66.667 0.00 0.00 41.44 5.14
114 115 2.987125 CGGAAATGTCCCTCCCGT 59.013 61.111 0.00 0.00 41.44 5.28
115 116 1.153429 CGGAAATGTCCCTCCCGTC 60.153 63.158 0.00 0.00 41.44 4.79
116 117 1.895020 CGGAAATGTCCCTCCCGTCA 61.895 60.000 0.00 0.00 41.44 4.35
117 118 0.326927 GGAAATGTCCCTCCCGTCAA 59.673 55.000 0.00 0.00 38.08 3.18
118 119 1.271707 GGAAATGTCCCTCCCGTCAAA 60.272 52.381 0.00 0.00 38.08 2.69
119 120 2.620627 GGAAATGTCCCTCCCGTCAAAT 60.621 50.000 0.00 0.00 38.08 2.32
120 121 2.420058 AATGTCCCTCCCGTCAAATC 57.580 50.000 0.00 0.00 0.00 2.17
121 122 1.584724 ATGTCCCTCCCGTCAAATCT 58.415 50.000 0.00 0.00 0.00 2.40
122 123 0.902531 TGTCCCTCCCGTCAAATCTC 59.097 55.000 0.00 0.00 0.00 2.75
123 124 0.179108 GTCCCTCCCGTCAAATCTCG 60.179 60.000 0.00 0.00 0.00 4.04
124 125 1.521681 CCCTCCCGTCAAATCTCGC 60.522 63.158 0.00 0.00 0.00 5.03
125 126 1.517832 CCTCCCGTCAAATCTCGCT 59.482 57.895 0.00 0.00 0.00 4.93
126 127 0.807667 CCTCCCGTCAAATCTCGCTG 60.808 60.000 0.00 0.00 0.00 5.18
127 128 1.424493 CTCCCGTCAAATCTCGCTGC 61.424 60.000 0.00 0.00 0.00 5.25
128 129 2.697425 CCGTCAAATCTCGCTGCG 59.303 61.111 17.25 17.25 0.00 5.18
129 130 2.697425 CGTCAAATCTCGCTGCGG 59.303 61.111 23.03 12.92 0.00 5.69
130 131 1.805539 CGTCAAATCTCGCTGCGGA 60.806 57.895 23.03 17.84 0.00 5.54
131 132 1.148157 CGTCAAATCTCGCTGCGGAT 61.148 55.000 23.03 19.24 0.00 4.18
132 133 1.852942 GTCAAATCTCGCTGCGGATA 58.147 50.000 23.03 8.25 0.00 2.59
133 134 1.789464 GTCAAATCTCGCTGCGGATAG 59.211 52.381 23.03 12.49 0.00 2.08
134 135 1.143305 CAAATCTCGCTGCGGATAGG 58.857 55.000 23.03 13.87 0.00 2.57
135 136 0.034059 AAATCTCGCTGCGGATAGGG 59.966 55.000 23.03 6.04 0.00 3.53
136 137 1.821061 AATCTCGCTGCGGATAGGGG 61.821 60.000 23.03 4.37 0.00 4.79
137 138 4.671569 CTCGCTGCGGATAGGGGC 62.672 72.222 23.03 0.00 0.00 5.80
139 140 4.976925 CGCTGCGGATAGGGGCTG 62.977 72.222 15.40 0.00 0.00 4.85
140 141 3.550431 GCTGCGGATAGGGGCTGA 61.550 66.667 0.00 0.00 0.00 4.26
141 142 2.739784 CTGCGGATAGGGGCTGAG 59.260 66.667 0.00 0.00 0.00 3.35
142 143 3.527775 CTGCGGATAGGGGCTGAGC 62.528 68.421 0.00 0.00 0.00 4.26
143 144 3.237741 GCGGATAGGGGCTGAGCT 61.238 66.667 3.72 0.00 0.00 4.09
144 145 3.055580 CGGATAGGGGCTGAGCTC 58.944 66.667 6.82 6.82 0.00 4.09
145 146 2.925262 CGGATAGGGGCTGAGCTCG 61.925 68.421 9.64 5.21 0.00 5.03
146 147 2.578714 GGATAGGGGCTGAGCTCGG 61.579 68.421 18.77 18.77 0.00 4.63
147 148 2.525381 ATAGGGGCTGAGCTCGGG 60.525 66.667 23.87 12.90 0.00 5.14
148 149 3.396822 ATAGGGGCTGAGCTCGGGT 62.397 63.158 23.87 0.60 0.00 5.28
152 153 4.500116 GGCTGAGCTCGGGTCGTC 62.500 72.222 23.87 6.62 32.15 4.20
153 154 4.500116 GCTGAGCTCGGGTCGTCC 62.500 72.222 23.87 2.22 32.15 4.79
154 155 2.752238 CTGAGCTCGGGTCGTCCT 60.752 66.667 15.27 0.00 32.15 3.85
155 156 2.750637 TGAGCTCGGGTCGTCCTC 60.751 66.667 9.64 0.00 32.15 3.71
156 157 3.519930 GAGCTCGGGTCGTCCTCC 61.520 72.222 0.00 0.00 0.00 4.30
157 158 3.999297 GAGCTCGGGTCGTCCTCCT 62.999 68.421 0.00 0.00 0.00 3.69
158 159 2.124403 GCTCGGGTCGTCCTCCTA 60.124 66.667 0.00 0.00 0.00 2.94
159 160 2.188161 GCTCGGGTCGTCCTCCTAG 61.188 68.421 0.00 0.00 0.00 3.02
160 161 2.124403 TCGGGTCGTCCTCCTAGC 60.124 66.667 0.00 0.00 0.00 3.42
161 162 3.217743 CGGGTCGTCCTCCTAGCC 61.218 72.222 0.00 0.00 0.00 3.93
162 163 2.838693 GGGTCGTCCTCCTAGCCC 60.839 72.222 0.00 0.00 0.00 5.19
163 164 3.217743 GGTCGTCCTCCTAGCCCG 61.218 72.222 0.00 0.00 0.00 6.13
164 165 2.439883 GTCGTCCTCCTAGCCCGT 60.440 66.667 0.00 0.00 0.00 5.28
165 166 2.439701 TCGTCCTCCTAGCCCGTG 60.440 66.667 0.00 0.00 0.00 4.94
166 167 2.439701 CGTCCTCCTAGCCCGTGA 60.440 66.667 0.00 0.00 0.00 4.35
167 168 2.050350 CGTCCTCCTAGCCCGTGAA 61.050 63.158 0.00 0.00 0.00 3.18
168 169 1.392710 CGTCCTCCTAGCCCGTGAAT 61.393 60.000 0.00 0.00 0.00 2.57
169 170 0.389757 GTCCTCCTAGCCCGTGAATC 59.610 60.000 0.00 0.00 0.00 2.52
170 171 0.261991 TCCTCCTAGCCCGTGAATCT 59.738 55.000 0.00 0.00 0.00 2.40
171 172 1.497716 TCCTCCTAGCCCGTGAATCTA 59.502 52.381 0.00 0.00 0.00 1.98
172 173 1.889829 CCTCCTAGCCCGTGAATCTAG 59.110 57.143 0.00 0.00 0.00 2.43
173 174 2.489255 CCTCCTAGCCCGTGAATCTAGA 60.489 54.545 0.00 0.00 33.44 2.43
174 175 2.817258 CTCCTAGCCCGTGAATCTAGAG 59.183 54.545 0.00 0.00 33.44 2.43
175 176 1.889829 CCTAGCCCGTGAATCTAGAGG 59.110 57.143 0.00 0.00 33.44 3.69
176 177 2.588620 CTAGCCCGTGAATCTAGAGGT 58.411 52.381 0.00 0.00 33.44 3.85
177 178 1.867363 AGCCCGTGAATCTAGAGGTT 58.133 50.000 0.00 0.00 0.00 3.50
178 179 1.482593 AGCCCGTGAATCTAGAGGTTG 59.517 52.381 0.00 0.00 0.00 3.77
179 180 1.473434 GCCCGTGAATCTAGAGGTTGG 60.473 57.143 0.00 0.00 0.00 3.77
180 181 1.139058 CCCGTGAATCTAGAGGTTGGG 59.861 57.143 0.00 2.10 0.00 4.12
181 182 1.139058 CCGTGAATCTAGAGGTTGGGG 59.861 57.143 0.00 0.00 0.00 4.96
182 183 2.108168 CGTGAATCTAGAGGTTGGGGA 58.892 52.381 0.00 0.00 0.00 4.81
183 184 2.101582 CGTGAATCTAGAGGTTGGGGAG 59.898 54.545 0.00 0.00 0.00 4.30
184 185 3.375699 GTGAATCTAGAGGTTGGGGAGA 58.624 50.000 0.00 0.00 0.00 3.71
185 186 3.970640 GTGAATCTAGAGGTTGGGGAGAT 59.029 47.826 0.00 0.00 0.00 2.75
186 187 3.969976 TGAATCTAGAGGTTGGGGAGATG 59.030 47.826 0.00 0.00 0.00 2.90
187 188 3.715648 ATCTAGAGGTTGGGGAGATGT 57.284 47.619 0.00 0.00 0.00 3.06
188 189 3.491766 TCTAGAGGTTGGGGAGATGTT 57.508 47.619 0.00 0.00 0.00 2.71
189 190 3.803340 TCTAGAGGTTGGGGAGATGTTT 58.197 45.455 0.00 0.00 0.00 2.83
190 191 4.175962 TCTAGAGGTTGGGGAGATGTTTT 58.824 43.478 0.00 0.00 0.00 2.43
191 192 3.160679 AGAGGTTGGGGAGATGTTTTG 57.839 47.619 0.00 0.00 0.00 2.44
192 193 1.546029 GAGGTTGGGGAGATGTTTTGC 59.454 52.381 0.00 0.00 0.00 3.68
193 194 0.608130 GGTTGGGGAGATGTTTTGCC 59.392 55.000 0.00 0.00 0.00 4.52
194 195 0.243636 GTTGGGGAGATGTTTTGCCG 59.756 55.000 0.00 0.00 0.00 5.69
195 196 1.531739 TTGGGGAGATGTTTTGCCGC 61.532 55.000 0.00 0.00 0.00 6.53
196 197 2.710902 GGGGAGATGTTTTGCCGCC 61.711 63.158 0.00 0.00 0.00 6.13
197 198 2.710902 GGGAGATGTTTTGCCGCCC 61.711 63.158 0.00 0.00 32.96 6.13
198 199 2.710902 GGAGATGTTTTGCCGCCCC 61.711 63.158 0.00 0.00 0.00 5.80
199 200 2.679996 AGATGTTTTGCCGCCCCC 60.680 61.111 0.00 0.00 0.00 5.40
200 201 4.128388 GATGTTTTGCCGCCCCCG 62.128 66.667 0.00 0.00 0.00 5.73
208 209 3.453679 GCCGCCCCCGCAAAAATA 61.454 61.111 0.00 0.00 34.03 1.40
209 210 2.791868 GCCGCCCCCGCAAAAATAT 61.792 57.895 0.00 0.00 34.03 1.28
210 211 1.819905 CCGCCCCCGCAAAAATATT 59.180 52.632 0.00 0.00 34.03 1.28
211 212 0.176910 CCGCCCCCGCAAAAATATTT 59.823 50.000 0.00 0.00 34.03 1.40
212 213 1.409427 CCGCCCCCGCAAAAATATTTA 59.591 47.619 0.01 0.00 34.03 1.40
213 214 2.465855 CGCCCCCGCAAAAATATTTAC 58.534 47.619 0.01 0.00 34.03 2.01
214 215 2.465855 GCCCCCGCAAAAATATTTACG 58.534 47.619 0.01 6.21 35.53 3.18
218 219 2.465855 CCGCAAAAATATTTACGGGCC 58.534 47.619 21.03 0.00 46.93 5.80
219 220 2.113289 CGCAAAAATATTTACGGGCCG 58.887 47.619 27.06 27.06 32.80 6.13
220 221 2.465855 GCAAAAATATTTACGGGCCGG 58.534 47.619 31.78 12.53 0.00 6.13
221 222 2.800273 GCAAAAATATTTACGGGCCGGG 60.800 50.000 31.78 3.37 0.00 5.73
222 223 1.694844 AAAATATTTACGGGCCGGGG 58.305 50.000 31.78 2.48 0.00 5.73
223 224 0.824595 AAATATTTACGGGCCGGGGC 60.825 55.000 31.78 13.01 41.06 5.80
224 225 3.540367 ATATTTACGGGCCGGGGCG 62.540 63.158 31.78 12.18 43.06 6.13
240 241 3.550431 CGGGATGCGGGGTCTGAT 61.550 66.667 0.00 0.00 0.00 2.90
241 242 2.427753 GGGATGCGGGGTCTGATC 59.572 66.667 0.00 0.00 0.00 2.92
242 243 2.443394 GGGATGCGGGGTCTGATCA 61.443 63.158 0.00 0.00 0.00 2.92
243 244 1.757306 GGATGCGGGGTCTGATCAT 59.243 57.895 0.00 0.00 0.00 2.45
244 245 0.976641 GGATGCGGGGTCTGATCATA 59.023 55.000 0.00 0.00 0.00 2.15
245 246 1.347707 GGATGCGGGGTCTGATCATAA 59.652 52.381 0.00 0.00 0.00 1.90
246 247 2.026822 GGATGCGGGGTCTGATCATAAT 60.027 50.000 0.00 0.00 0.00 1.28
247 248 2.549064 TGCGGGGTCTGATCATAATG 57.451 50.000 0.00 0.00 0.00 1.90
248 249 2.046292 TGCGGGGTCTGATCATAATGA 58.954 47.619 0.00 0.00 0.00 2.57
249 250 2.639347 TGCGGGGTCTGATCATAATGAT 59.361 45.455 0.00 0.00 40.34 2.45
250 251 3.072915 TGCGGGGTCTGATCATAATGATT 59.927 43.478 0.00 0.00 37.20 2.57
251 252 4.074970 GCGGGGTCTGATCATAATGATTT 58.925 43.478 0.00 0.00 37.20 2.17
252 253 4.520492 GCGGGGTCTGATCATAATGATTTT 59.480 41.667 0.00 0.00 37.20 1.82
253 254 5.335191 GCGGGGTCTGATCATAATGATTTTC 60.335 44.000 0.00 0.00 37.20 2.29
254 255 5.182001 CGGGGTCTGATCATAATGATTTTCC 59.818 44.000 0.00 0.00 37.20 3.13
255 256 5.478332 GGGGTCTGATCATAATGATTTTCCC 59.522 44.000 0.00 0.00 37.20 3.97
256 257 5.182001 GGGTCTGATCATAATGATTTTCCCG 59.818 44.000 0.00 0.00 37.20 5.14
257 258 5.335191 GGTCTGATCATAATGATTTTCCCGC 60.335 44.000 0.00 0.00 37.20 6.13
258 259 4.761739 TCTGATCATAATGATTTTCCCGCC 59.238 41.667 0.00 0.00 37.20 6.13
259 260 4.728772 TGATCATAATGATTTTCCCGCCT 58.271 39.130 0.00 0.00 37.20 5.52
260 261 4.761739 TGATCATAATGATTTTCCCGCCTC 59.238 41.667 0.00 0.00 37.20 4.70
261 262 3.138304 TCATAATGATTTTCCCGCCTCG 58.862 45.455 0.00 0.00 0.00 4.63
262 263 2.992124 TAATGATTTTCCCGCCTCGA 57.008 45.000 0.00 0.00 0.00 4.04
263 264 1.379527 AATGATTTTCCCGCCTCGAC 58.620 50.000 0.00 0.00 0.00 4.20
264 265 0.463833 ATGATTTTCCCGCCTCGACC 60.464 55.000 0.00 0.00 0.00 4.79
265 266 1.221021 GATTTTCCCGCCTCGACCT 59.779 57.895 0.00 0.00 0.00 3.85
266 267 1.078426 ATTTTCCCGCCTCGACCTG 60.078 57.895 0.00 0.00 0.00 4.00
267 268 3.894547 TTTTCCCGCCTCGACCTGC 62.895 63.158 0.00 0.00 0.00 4.85
270 271 4.473520 CCCGCCTCGACCTGCATT 62.474 66.667 0.00 0.00 0.00 3.56
271 272 2.436646 CCGCCTCGACCTGCATTT 60.437 61.111 0.00 0.00 0.00 2.32
272 273 2.040544 CCGCCTCGACCTGCATTTT 61.041 57.895 0.00 0.00 0.00 1.82
273 274 1.135315 CGCCTCGACCTGCATTTTG 59.865 57.895 0.00 0.00 0.00 2.44
274 275 1.298157 CGCCTCGACCTGCATTTTGA 61.298 55.000 0.00 0.00 0.00 2.69
275 276 0.169009 GCCTCGACCTGCATTTTGAC 59.831 55.000 0.00 0.00 0.00 3.18
276 277 0.443869 CCTCGACCTGCATTTTGACG 59.556 55.000 0.00 0.00 0.00 4.35
277 278 0.443869 CTCGACCTGCATTTTGACGG 59.556 55.000 0.00 0.00 0.00 4.79
278 279 0.250124 TCGACCTGCATTTTGACGGT 60.250 50.000 0.00 0.00 0.00 4.83
279 280 0.591170 CGACCTGCATTTTGACGGTT 59.409 50.000 0.00 0.00 0.00 4.44
280 281 1.801771 CGACCTGCATTTTGACGGTTA 59.198 47.619 0.00 0.00 0.00 2.85
281 282 2.418628 CGACCTGCATTTTGACGGTTAT 59.581 45.455 0.00 0.00 0.00 1.89
282 283 3.119990 CGACCTGCATTTTGACGGTTATT 60.120 43.478 0.00 0.00 0.00 1.40
283 284 4.614993 CGACCTGCATTTTGACGGTTATTT 60.615 41.667 0.00 0.00 0.00 1.40
284 285 5.208463 ACCTGCATTTTGACGGTTATTTT 57.792 34.783 0.00 0.00 0.00 1.82
285 286 4.987912 ACCTGCATTTTGACGGTTATTTTG 59.012 37.500 0.00 0.00 0.00 2.44
286 287 4.143137 CCTGCATTTTGACGGTTATTTTGC 60.143 41.667 0.00 0.00 0.00 3.68
287 288 3.426859 TGCATTTTGACGGTTATTTTGCG 59.573 39.130 0.00 0.00 0.00 4.85
288 289 3.181535 GCATTTTGACGGTTATTTTGCGG 60.182 43.478 0.00 0.00 0.00 5.69
289 290 2.708386 TTTGACGGTTATTTTGCGGG 57.292 45.000 0.00 0.00 0.00 6.13
290 291 0.241481 TTGACGGTTATTTTGCGGGC 59.759 50.000 0.00 0.00 0.00 6.13
291 292 1.138036 GACGGTTATTTTGCGGGCC 59.862 57.895 0.00 0.00 0.00 5.80
292 293 2.101380 CGGTTATTTTGCGGGCCG 59.899 61.111 24.35 24.35 0.00 6.13
293 294 2.492560 GGTTATTTTGCGGGCCGG 59.507 61.111 29.48 9.71 0.00 6.13
294 295 2.492560 GTTATTTTGCGGGCCGGG 59.507 61.111 29.48 0.00 0.00 5.73
295 296 3.453679 TTATTTTGCGGGCCGGGC 61.454 61.111 29.48 22.00 0.00 6.13
296 297 4.742649 TATTTTGCGGGCCGGGCA 62.743 61.111 30.95 15.65 38.93 5.36
320 321 1.871077 CGGGGTCCGTTAAAGTTGC 59.129 57.895 0.00 0.00 42.73 4.17
321 322 0.604511 CGGGGTCCGTTAAAGTTGCT 60.605 55.000 0.00 0.00 42.73 3.91
322 323 1.162698 GGGGTCCGTTAAAGTTGCTC 58.837 55.000 0.00 0.00 0.00 4.26
323 324 1.271217 GGGGTCCGTTAAAGTTGCTCT 60.271 52.381 0.00 0.00 0.00 4.09
324 325 2.501261 GGGTCCGTTAAAGTTGCTCTT 58.499 47.619 0.00 0.00 38.10 2.85
325 326 3.557686 GGGGTCCGTTAAAGTTGCTCTTA 60.558 47.826 0.00 0.00 35.02 2.10
326 327 3.683340 GGGTCCGTTAAAGTTGCTCTTAG 59.317 47.826 0.00 0.00 35.02 2.18
327 328 4.313282 GGTCCGTTAAAGTTGCTCTTAGT 58.687 43.478 0.00 0.00 35.02 2.24
328 329 4.388165 GGTCCGTTAAAGTTGCTCTTAGTC 59.612 45.833 0.00 0.00 35.02 2.59
329 330 4.089636 GTCCGTTAAAGTTGCTCTTAGTCG 59.910 45.833 0.00 0.00 35.02 4.18
330 331 3.985925 CCGTTAAAGTTGCTCTTAGTCGT 59.014 43.478 0.00 0.00 35.02 4.34
331 332 4.089636 CCGTTAAAGTTGCTCTTAGTCGTC 59.910 45.833 0.00 0.00 35.02 4.20
362 363 0.546747 TCCGAACTCCATCCCAACCT 60.547 55.000 0.00 0.00 0.00 3.50
409 410 5.682234 TTCCATACAGAGAGAGAAATGCA 57.318 39.130 0.00 0.00 0.00 3.96
615 616 2.478539 GGCTTCCTAATTTGCTCTTGCG 60.479 50.000 0.00 0.00 43.34 4.85
619 620 1.098050 CTAATTTGCTCTTGCGGGCT 58.902 50.000 0.00 0.00 43.34 5.19
626 627 2.922503 TCTTGCGGGCTGTCTGGA 60.923 61.111 0.00 0.00 0.00 3.86
717 718 2.309528 TCGAGCTGCATACCGAAATT 57.690 45.000 1.02 0.00 0.00 1.82
792 793 0.631212 ACCCCCAGCAGAATTAAGGG 59.369 55.000 0.00 0.00 39.29 3.95
853 856 1.801178 CTCCGAAGTTGGAAGCTTGAC 59.199 52.381 2.10 0.00 37.64 3.18
885 888 0.399949 ATATCCCCTCCAAGCGGTCA 60.400 55.000 0.00 0.00 0.00 4.02
1062 1090 7.338196 TCCTTCACAATATTCTCGGCAAAAATA 59.662 33.333 0.00 0.00 0.00 1.40
1063 1091 7.973388 CCTTCACAATATTCTCGGCAAAAATAA 59.027 33.333 0.00 0.00 0.00 1.40
1261 1291 3.633235 CAGGATGGTAATCGAGAAGACG 58.367 50.000 0.00 0.00 33.18 4.18
1319 1349 1.071542 TCTTGACCGGCTCAATGTTCA 59.928 47.619 16.44 1.97 38.26 3.18
1390 1420 6.054295 CCTGCTATGCTCTCTCAAATTAAGT 58.946 40.000 0.00 0.00 0.00 2.24
1435 1465 0.447801 GGGAACAACTGCATGCTACG 59.552 55.000 20.33 9.80 0.00 3.51
1837 1869 2.095314 CACCTACGCATGTTCAATTGCA 60.095 45.455 0.00 0.00 38.80 4.08
1882 1914 0.034059 AGTTGAACACCTGGAGCTCG 59.966 55.000 7.83 0.00 0.00 5.03
2246 2279 1.445754 CTGACGAGACAGCTGGCAG 60.446 63.158 24.55 17.94 0.00 4.85
2425 2458 7.490725 TGCAATATTGATAAACCGTTTCCATTG 59.509 33.333 19.73 4.03 0.00 2.82
2429 2462 4.399219 TGATAAACCGTTTCCATTGACCA 58.601 39.130 0.00 0.00 0.00 4.02
2436 2469 2.218603 GTTTCCATTGACCAGTGTCGT 58.781 47.619 0.00 0.00 44.86 4.34
2452 2485 0.107066 TCGTCCTATGGTACGCAGGA 60.107 55.000 4.98 4.98 38.38 3.86
2479 2512 6.099341 GGGATCATTTGTGTACAATGGAAAC 58.901 40.000 0.00 0.00 35.55 2.78
2526 2559 4.765856 TCTCGTATAGCATAAGGAAGGGTC 59.234 45.833 0.00 0.00 0.00 4.46
2688 2721 1.953559 ATACAATAGGCTGGCGTGTG 58.046 50.000 15.03 8.43 0.00 3.82
2805 2838 2.787994 CTGCCTCAATTCACTTCCTGT 58.212 47.619 0.00 0.00 0.00 4.00
2885 2918 6.607689 TCAGTTCAAGTTTGTGTTGTAACTG 58.392 36.000 12.18 12.18 40.19 3.16
2996 3029 6.365789 GCAGCATTTTGTTTTATCAGTAAGCA 59.634 34.615 0.00 0.00 0.00 3.91
3256 3339 1.172812 AGCTGGCAGGTTTCGGTTTC 61.173 55.000 14.51 0.00 0.00 2.78
3257 3340 1.574428 CTGGCAGGTTTCGGTTTCG 59.426 57.895 6.61 0.00 37.82 3.46
3258 3341 1.852067 CTGGCAGGTTTCGGTTTCGG 61.852 60.000 6.61 0.00 36.95 4.30
3259 3342 1.895231 GGCAGGTTTCGGTTTCGGT 60.895 57.895 0.00 0.00 36.95 4.69
3260 3343 1.449726 GGCAGGTTTCGGTTTCGGTT 61.450 55.000 0.00 0.00 36.95 4.44
3261 3344 0.317519 GCAGGTTTCGGTTTCGGTTG 60.318 55.000 0.00 0.00 36.95 3.77
3325 3408 1.619654 TGGGTGATCCTTTGTTGCTG 58.380 50.000 0.00 0.00 36.20 4.41
3488 3571 5.066505 TGAAAAGTTCTCAGTTCCTTCAAGC 59.933 40.000 0.00 0.00 0.00 4.01
3512 3595 5.130292 AGAGTCGGACGTTTTCAGAAATA 57.870 39.130 1.89 0.00 29.34 1.40
3519 3602 4.630505 GGACGTTTTCAGAAATACTCCCTC 59.369 45.833 0.00 0.00 0.00 4.30
3581 3779 8.967664 AGAGGTAGTAGTGTTTAGTATCTCTG 57.032 38.462 9.81 0.00 38.70 3.35
3691 3889 8.225603 AGTTGTCATGAAGAACTGTAAATGTT 57.774 30.769 16.85 0.00 0.00 2.71
3760 3958 6.699575 TTCAAGGGAAGAAAAGTTGAAGAG 57.300 37.500 0.00 0.00 33.33 2.85
3780 3978 9.241317 TGAAGAGTCGTTTTAGTAGTTAAGTTG 57.759 33.333 0.00 0.00 0.00 3.16
3790 3988 8.534333 TTTAGTAGTTAAGTTGCAGAGTGATG 57.466 34.615 0.00 0.00 0.00 3.07
3845 4043 2.672874 CGCAGCAAGCAGAGTGTATTAA 59.327 45.455 0.00 0.00 46.13 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.282157 CCTTCGCCGCCATGGATG 61.282 66.667 18.40 6.69 42.00 3.51
2 3 3.479203 TCCTTCGCCGCCATGGAT 61.479 61.111 18.40 0.00 42.00 3.41
14 15 4.468689 CTTCCCCGGCCGTCCTTC 62.469 72.222 26.12 0.00 0.00 3.46
16 17 4.798682 ATCTTCCCCGGCCGTCCT 62.799 66.667 26.12 0.00 0.00 3.85
17 18 4.547367 CATCTTCCCCGGCCGTCC 62.547 72.222 26.12 0.00 0.00 4.79
24 25 3.740128 CTCCGGTGCATCTTCCCCG 62.740 68.421 0.00 4.30 40.12 5.73
25 26 2.190578 CTCCGGTGCATCTTCCCC 59.809 66.667 0.00 0.00 0.00 4.81
26 27 2.514824 GCTCCGGTGCATCTTCCC 60.515 66.667 23.09 0.00 0.00 3.97
27 28 2.892425 CGCTCCGGTGCATCTTCC 60.892 66.667 26.64 0.00 0.00 3.46
28 29 2.125512 ACGCTCCGGTGCATCTTC 60.126 61.111 26.64 0.00 0.00 2.87
29 30 2.434884 CACGCTCCGGTGCATCTT 60.435 61.111 26.64 6.23 0.00 2.40
57 58 4.740822 ACCCTCCGCCACCATTGC 62.741 66.667 0.00 0.00 0.00 3.56
58 59 2.751436 CACCCTCCGCCACCATTG 60.751 66.667 0.00 0.00 0.00 2.82
59 60 4.047125 CCACCCTCCGCCACCATT 62.047 66.667 0.00 0.00 0.00 3.16
93 94 3.564027 GAGGGACATTTCCGCGCG 61.564 66.667 25.67 25.67 43.94 6.86
94 95 3.202706 GGAGGGACATTTCCGCGC 61.203 66.667 0.00 0.00 43.94 6.86
95 96 2.513897 GGGAGGGACATTTCCGCG 60.514 66.667 0.00 0.00 43.94 6.46
96 97 2.513897 CGGGAGGGACATTTCCGC 60.514 66.667 0.00 0.00 43.94 5.54
97 98 1.153429 GACGGGAGGGACATTTCCG 60.153 63.158 0.00 0.00 43.94 4.30
98 99 0.326927 TTGACGGGAGGGACATTTCC 59.673 55.000 0.00 0.00 41.95 3.13
99 100 2.194201 TTTGACGGGAGGGACATTTC 57.806 50.000 0.00 0.00 0.00 2.17
100 101 2.308866 AGATTTGACGGGAGGGACATTT 59.691 45.455 0.00 0.00 0.00 2.32
101 102 1.916181 AGATTTGACGGGAGGGACATT 59.084 47.619 0.00 0.00 0.00 2.71
102 103 1.486726 GAGATTTGACGGGAGGGACAT 59.513 52.381 0.00 0.00 0.00 3.06
103 104 0.902531 GAGATTTGACGGGAGGGACA 59.097 55.000 0.00 0.00 0.00 4.02
104 105 0.179108 CGAGATTTGACGGGAGGGAC 60.179 60.000 0.00 0.00 0.00 4.46
105 106 1.956629 GCGAGATTTGACGGGAGGGA 61.957 60.000 0.00 0.00 0.00 4.20
106 107 1.521681 GCGAGATTTGACGGGAGGG 60.522 63.158 0.00 0.00 0.00 4.30
107 108 0.807667 CAGCGAGATTTGACGGGAGG 60.808 60.000 0.00 0.00 0.00 4.30
108 109 1.424493 GCAGCGAGATTTGACGGGAG 61.424 60.000 0.00 0.00 0.00 4.30
109 110 1.447838 GCAGCGAGATTTGACGGGA 60.448 57.895 0.00 0.00 0.00 5.14
110 111 2.802667 CGCAGCGAGATTTGACGGG 61.803 63.158 9.98 0.00 0.00 5.28
111 112 2.697425 CGCAGCGAGATTTGACGG 59.303 61.111 9.98 0.00 0.00 4.79
112 113 1.148157 ATCCGCAGCGAGATTTGACG 61.148 55.000 18.75 0.00 0.00 4.35
113 114 1.789464 CTATCCGCAGCGAGATTTGAC 59.211 52.381 18.75 0.00 0.00 3.18
114 115 1.269778 CCTATCCGCAGCGAGATTTGA 60.270 52.381 18.75 3.67 0.00 2.69
115 116 1.143305 CCTATCCGCAGCGAGATTTG 58.857 55.000 18.75 12.54 0.00 2.32
116 117 0.034059 CCCTATCCGCAGCGAGATTT 59.966 55.000 18.75 0.57 0.00 2.17
117 118 1.668294 CCCTATCCGCAGCGAGATT 59.332 57.895 18.75 0.00 0.00 2.40
118 119 2.279069 CCCCTATCCGCAGCGAGAT 61.279 63.158 18.75 18.76 0.00 2.75
119 120 2.912542 CCCCTATCCGCAGCGAGA 60.913 66.667 18.75 12.55 0.00 4.04
120 121 4.671569 GCCCCTATCCGCAGCGAG 62.672 72.222 18.75 5.59 0.00 5.03
122 123 4.976925 CAGCCCCTATCCGCAGCG 62.977 72.222 8.18 8.18 0.00 5.18
123 124 3.527775 CTCAGCCCCTATCCGCAGC 62.528 68.421 0.00 0.00 0.00 5.25
124 125 2.739784 CTCAGCCCCTATCCGCAG 59.260 66.667 0.00 0.00 0.00 5.18
125 126 3.550431 GCTCAGCCCCTATCCGCA 61.550 66.667 0.00 0.00 0.00 5.69
126 127 3.233259 GAGCTCAGCCCCTATCCGC 62.233 68.421 9.40 0.00 0.00 5.54
127 128 2.925262 CGAGCTCAGCCCCTATCCG 61.925 68.421 15.40 0.00 0.00 4.18
128 129 2.578714 CCGAGCTCAGCCCCTATCC 61.579 68.421 15.40 0.00 0.00 2.59
129 130 2.578714 CCCGAGCTCAGCCCCTATC 61.579 68.421 15.40 0.00 0.00 2.08
130 131 2.525381 CCCGAGCTCAGCCCCTAT 60.525 66.667 15.40 0.00 0.00 2.57
131 132 4.075793 ACCCGAGCTCAGCCCCTA 62.076 66.667 15.40 0.00 0.00 3.53
135 136 4.500116 GACGACCCGAGCTCAGCC 62.500 72.222 15.40 0.00 0.00 4.85
136 137 4.500116 GGACGACCCGAGCTCAGC 62.500 72.222 15.40 0.00 0.00 4.26
137 138 2.752238 AGGACGACCCGAGCTCAG 60.752 66.667 15.40 6.88 40.87 3.35
138 139 2.750637 GAGGACGACCCGAGCTCA 60.751 66.667 15.40 0.00 40.87 4.26
139 140 2.605854 TAGGAGGACGACCCGAGCTC 62.606 65.000 2.73 2.73 40.87 4.09
140 141 2.612095 CTAGGAGGACGACCCGAGCT 62.612 65.000 0.00 0.00 40.87 4.09
141 142 2.124403 TAGGAGGACGACCCGAGC 60.124 66.667 0.00 0.00 40.87 5.03
142 143 2.188161 GCTAGGAGGACGACCCGAG 61.188 68.421 0.00 0.00 40.87 4.63
143 144 2.124403 GCTAGGAGGACGACCCGA 60.124 66.667 0.00 0.00 40.87 5.14
144 145 3.217743 GGCTAGGAGGACGACCCG 61.218 72.222 0.00 0.00 40.87 5.28
145 146 2.838693 GGGCTAGGAGGACGACCC 60.839 72.222 0.00 0.00 36.73 4.46
146 147 3.217743 CGGGCTAGGAGGACGACC 61.218 72.222 0.00 0.00 0.00 4.79
147 148 2.439883 ACGGGCTAGGAGGACGAC 60.440 66.667 0.00 0.00 0.00 4.34
148 149 2.439701 CACGGGCTAGGAGGACGA 60.440 66.667 0.00 0.00 0.00 4.20
149 150 1.392710 ATTCACGGGCTAGGAGGACG 61.393 60.000 0.00 0.00 0.00 4.79
150 151 0.389757 GATTCACGGGCTAGGAGGAC 59.610 60.000 0.00 0.00 0.00 3.85
151 152 0.261991 AGATTCACGGGCTAGGAGGA 59.738 55.000 0.00 0.00 0.00 3.71
152 153 1.889829 CTAGATTCACGGGCTAGGAGG 59.110 57.143 0.00 0.00 0.00 4.30
153 154 2.817258 CTCTAGATTCACGGGCTAGGAG 59.183 54.545 0.00 0.00 33.97 3.69
154 155 2.489255 CCTCTAGATTCACGGGCTAGGA 60.489 54.545 0.00 0.00 33.97 2.94
155 156 1.889829 CCTCTAGATTCACGGGCTAGG 59.110 57.143 0.00 0.00 33.97 3.02
156 157 2.588620 ACCTCTAGATTCACGGGCTAG 58.411 52.381 0.00 0.00 34.37 3.42
157 158 2.693591 CAACCTCTAGATTCACGGGCTA 59.306 50.000 0.00 0.00 0.00 3.93
158 159 1.482593 CAACCTCTAGATTCACGGGCT 59.517 52.381 0.00 0.00 0.00 5.19
159 160 1.473434 CCAACCTCTAGATTCACGGGC 60.473 57.143 0.00 0.00 0.00 6.13
160 161 1.139058 CCCAACCTCTAGATTCACGGG 59.861 57.143 0.00 0.00 0.00 5.28
161 162 1.139058 CCCCAACCTCTAGATTCACGG 59.861 57.143 0.00 0.00 0.00 4.94
162 163 2.101582 CTCCCCAACCTCTAGATTCACG 59.898 54.545 0.00 0.00 0.00 4.35
163 164 3.375699 TCTCCCCAACCTCTAGATTCAC 58.624 50.000 0.00 0.00 0.00 3.18
164 165 3.776731 TCTCCCCAACCTCTAGATTCA 57.223 47.619 0.00 0.00 0.00 2.57
165 166 3.970640 ACATCTCCCCAACCTCTAGATTC 59.029 47.826 0.00 0.00 0.00 2.52
166 167 4.014273 ACATCTCCCCAACCTCTAGATT 57.986 45.455 0.00 0.00 0.00 2.40
167 168 3.715648 ACATCTCCCCAACCTCTAGAT 57.284 47.619 0.00 0.00 0.00 1.98
168 169 3.491766 AACATCTCCCCAACCTCTAGA 57.508 47.619 0.00 0.00 0.00 2.43
169 170 4.265073 CAAAACATCTCCCCAACCTCTAG 58.735 47.826 0.00 0.00 0.00 2.43
170 171 3.561313 GCAAAACATCTCCCCAACCTCTA 60.561 47.826 0.00 0.00 0.00 2.43
171 172 2.819348 GCAAAACATCTCCCCAACCTCT 60.819 50.000 0.00 0.00 0.00 3.69
172 173 1.546029 GCAAAACATCTCCCCAACCTC 59.454 52.381 0.00 0.00 0.00 3.85
173 174 1.632589 GCAAAACATCTCCCCAACCT 58.367 50.000 0.00 0.00 0.00 3.50
174 175 0.608130 GGCAAAACATCTCCCCAACC 59.392 55.000 0.00 0.00 0.00 3.77
175 176 0.243636 CGGCAAAACATCTCCCCAAC 59.756 55.000 0.00 0.00 0.00 3.77
176 177 1.531739 GCGGCAAAACATCTCCCCAA 61.532 55.000 0.00 0.00 0.00 4.12
177 178 1.976474 GCGGCAAAACATCTCCCCA 60.976 57.895 0.00 0.00 0.00 4.96
178 179 2.710902 GGCGGCAAAACATCTCCCC 61.711 63.158 3.07 0.00 0.00 4.81
179 180 2.710902 GGGCGGCAAAACATCTCCC 61.711 63.158 12.47 0.00 0.00 4.30
180 181 2.710902 GGGGCGGCAAAACATCTCC 61.711 63.158 12.47 0.00 0.00 3.71
181 182 2.710902 GGGGGCGGCAAAACATCTC 61.711 63.158 12.47 0.00 0.00 2.75
182 183 2.679996 GGGGGCGGCAAAACATCT 60.680 61.111 12.47 0.00 0.00 2.90
183 184 4.128388 CGGGGGCGGCAAAACATC 62.128 66.667 12.47 0.00 0.00 3.06
191 192 2.304901 AATATTTTTGCGGGGGCGGC 62.305 55.000 0.00 0.00 0.00 6.53
192 193 0.176910 AAATATTTTTGCGGGGGCGG 59.823 50.000 0.00 0.00 0.00 6.13
193 194 2.465855 GTAAATATTTTTGCGGGGGCG 58.534 47.619 5.91 0.00 0.00 6.13
194 195 2.465855 CGTAAATATTTTTGCGGGGGC 58.534 47.619 5.91 0.00 44.14 5.80
199 200 2.113289 CGGCCCGTAAATATTTTTGCG 58.887 47.619 5.91 11.10 46.40 4.85
200 201 2.465855 CCGGCCCGTAAATATTTTTGC 58.534 47.619 5.91 4.50 0.00 3.68
201 202 2.223852 CCCCGGCCCGTAAATATTTTTG 60.224 50.000 5.91 0.00 0.00 2.44
202 203 2.033372 CCCCGGCCCGTAAATATTTTT 58.967 47.619 5.91 0.00 0.00 1.94
203 204 1.694844 CCCCGGCCCGTAAATATTTT 58.305 50.000 5.91 0.00 0.00 1.82
204 205 0.824595 GCCCCGGCCCGTAAATATTT 60.825 55.000 0.85 5.89 34.56 1.40
205 206 1.228337 GCCCCGGCCCGTAAATATT 60.228 57.895 0.85 0.00 34.56 1.28
206 207 2.433004 GCCCCGGCCCGTAAATAT 59.567 61.111 0.85 0.00 34.56 1.28
207 208 4.238654 CGCCCCGGCCCGTAAATA 62.239 66.667 0.85 0.00 37.98 1.40
223 224 3.521529 GATCAGACCCCGCATCCCG 62.522 68.421 0.00 0.00 0.00 5.14
224 225 1.772819 ATGATCAGACCCCGCATCCC 61.773 60.000 0.09 0.00 0.00 3.85
225 226 0.976641 TATGATCAGACCCCGCATCC 59.023 55.000 0.09 0.00 0.00 3.51
226 227 2.839486 TTATGATCAGACCCCGCATC 57.161 50.000 0.09 0.00 0.00 3.91
227 228 2.639347 TCATTATGATCAGACCCCGCAT 59.361 45.455 0.09 0.00 0.00 4.73
228 229 2.046292 TCATTATGATCAGACCCCGCA 58.954 47.619 0.09 0.00 0.00 5.69
229 230 2.839486 TCATTATGATCAGACCCCGC 57.161 50.000 0.09 0.00 0.00 6.13
230 231 5.182001 GGAAAATCATTATGATCAGACCCCG 59.818 44.000 8.26 0.00 35.76 5.73
231 232 5.478332 GGGAAAATCATTATGATCAGACCCC 59.522 44.000 19.14 15.70 35.76 4.95
232 233 5.182001 CGGGAAAATCATTATGATCAGACCC 59.818 44.000 19.54 19.54 35.76 4.46
233 234 5.335191 GCGGGAAAATCATTATGATCAGACC 60.335 44.000 8.26 9.39 35.76 3.85
234 235 5.335191 GGCGGGAAAATCATTATGATCAGAC 60.335 44.000 8.26 0.00 35.76 3.51
235 236 4.761739 GGCGGGAAAATCATTATGATCAGA 59.238 41.667 8.26 0.00 35.76 3.27
236 237 4.763793 AGGCGGGAAAATCATTATGATCAG 59.236 41.667 8.26 0.00 35.76 2.90
237 238 4.728772 AGGCGGGAAAATCATTATGATCA 58.271 39.130 8.26 0.00 35.76 2.92
238 239 4.142816 CGAGGCGGGAAAATCATTATGATC 60.143 45.833 8.26 0.00 35.76 2.92
239 240 3.753272 CGAGGCGGGAAAATCATTATGAT 59.247 43.478 1.25 1.25 39.09 2.45
240 241 3.138304 CGAGGCGGGAAAATCATTATGA 58.862 45.455 0.00 0.00 0.00 2.15
241 242 3.058914 GTCGAGGCGGGAAAATCATTATG 60.059 47.826 0.00 0.00 0.00 1.90
242 243 3.139077 GTCGAGGCGGGAAAATCATTAT 58.861 45.455 0.00 0.00 0.00 1.28
243 244 2.557317 GTCGAGGCGGGAAAATCATTA 58.443 47.619 0.00 0.00 0.00 1.90
244 245 1.379527 GTCGAGGCGGGAAAATCATT 58.620 50.000 0.00 0.00 0.00 2.57
245 246 0.463833 GGTCGAGGCGGGAAAATCAT 60.464 55.000 0.00 0.00 0.00 2.45
246 247 1.078708 GGTCGAGGCGGGAAAATCA 60.079 57.895 0.00 0.00 0.00 2.57
247 248 1.090052 CAGGTCGAGGCGGGAAAATC 61.090 60.000 0.00 0.00 0.00 2.17
248 249 1.078426 CAGGTCGAGGCGGGAAAAT 60.078 57.895 0.00 0.00 0.00 1.82
249 250 2.345991 CAGGTCGAGGCGGGAAAA 59.654 61.111 0.00 0.00 0.00 2.29
250 251 4.388499 GCAGGTCGAGGCGGGAAA 62.388 66.667 0.00 0.00 0.00 3.13
253 254 3.976701 AAATGCAGGTCGAGGCGGG 62.977 63.158 0.00 0.00 0.00 6.13
254 255 2.040544 AAAATGCAGGTCGAGGCGG 61.041 57.895 0.00 0.00 0.00 6.13
255 256 1.135315 CAAAATGCAGGTCGAGGCG 59.865 57.895 0.00 0.00 0.00 5.52
256 257 0.169009 GTCAAAATGCAGGTCGAGGC 59.831 55.000 0.00 0.00 0.00 4.70
257 258 0.443869 CGTCAAAATGCAGGTCGAGG 59.556 55.000 0.00 0.00 0.00 4.63
258 259 0.443869 CCGTCAAAATGCAGGTCGAG 59.556 55.000 0.00 0.00 0.00 4.04
259 260 0.250124 ACCGTCAAAATGCAGGTCGA 60.250 50.000 0.00 0.00 0.00 4.20
260 261 0.591170 AACCGTCAAAATGCAGGTCG 59.409 50.000 0.00 0.00 33.50 4.79
261 262 4.434713 AATAACCGTCAAAATGCAGGTC 57.565 40.909 0.00 0.00 33.50 3.85
262 263 4.864704 AAATAACCGTCAAAATGCAGGT 57.135 36.364 0.00 0.00 36.66 4.00
263 264 4.143137 GCAAAATAACCGTCAAAATGCAGG 60.143 41.667 0.00 0.00 0.00 4.85
264 265 4.432762 CGCAAAATAACCGTCAAAATGCAG 60.433 41.667 0.00 0.00 0.00 4.41
265 266 3.426859 CGCAAAATAACCGTCAAAATGCA 59.573 39.130 0.00 0.00 0.00 3.96
266 267 3.181535 CCGCAAAATAACCGTCAAAATGC 60.182 43.478 0.00 0.00 0.00 3.56
267 268 3.366422 CCCGCAAAATAACCGTCAAAATG 59.634 43.478 0.00 0.00 0.00 2.32
268 269 3.580731 CCCGCAAAATAACCGTCAAAAT 58.419 40.909 0.00 0.00 0.00 1.82
269 270 2.862921 GCCCGCAAAATAACCGTCAAAA 60.863 45.455 0.00 0.00 0.00 2.44
270 271 1.336056 GCCCGCAAAATAACCGTCAAA 60.336 47.619 0.00 0.00 0.00 2.69
271 272 0.241481 GCCCGCAAAATAACCGTCAA 59.759 50.000 0.00 0.00 0.00 3.18
272 273 1.587933 GGCCCGCAAAATAACCGTCA 61.588 55.000 0.00 0.00 0.00 4.35
273 274 1.138036 GGCCCGCAAAATAACCGTC 59.862 57.895 0.00 0.00 0.00 4.79
274 275 2.692766 CGGCCCGCAAAATAACCGT 61.693 57.895 0.00 0.00 35.99 4.83
275 276 2.101380 CGGCCCGCAAAATAACCG 59.899 61.111 0.00 0.00 0.00 4.44
276 277 2.492560 CCGGCCCGCAAAATAACC 59.507 61.111 0.00 0.00 0.00 2.85
277 278 2.492560 CCCGGCCCGCAAAATAAC 59.507 61.111 0.00 0.00 0.00 1.89
278 279 3.453679 GCCCGGCCCGCAAAATAA 61.454 61.111 0.00 0.00 0.00 1.40
279 280 4.742649 TGCCCGGCCCGCAAAATA 62.743 61.111 9.67 0.00 32.05 1.40
302 303 6.883135 TAAGAGCAACTTTAACGGACCCCG 62.883 50.000 3.58 3.58 44.90 5.73
303 304 1.162698 GAGCAACTTTAACGGACCCC 58.837 55.000 0.00 0.00 0.00 4.95
304 305 2.180432 AGAGCAACTTTAACGGACCC 57.820 50.000 0.00 0.00 0.00 4.46
305 306 4.313282 ACTAAGAGCAACTTTAACGGACC 58.687 43.478 1.81 0.00 39.72 4.46
306 307 4.089636 CGACTAAGAGCAACTTTAACGGAC 59.910 45.833 1.81 0.00 39.72 4.79
307 308 4.232221 CGACTAAGAGCAACTTTAACGGA 58.768 43.478 1.81 0.00 39.72 4.69
308 309 3.985925 ACGACTAAGAGCAACTTTAACGG 59.014 43.478 0.00 0.00 39.72 4.44
309 310 4.089636 GGACGACTAAGAGCAACTTTAACG 59.910 45.833 0.00 0.00 39.72 3.18
310 311 4.388165 GGGACGACTAAGAGCAACTTTAAC 59.612 45.833 0.00 0.00 39.72 2.01
311 312 4.562143 GGGGACGACTAAGAGCAACTTTAA 60.562 45.833 0.00 0.00 39.72 1.52
312 313 3.056322 GGGGACGACTAAGAGCAACTTTA 60.056 47.826 0.00 0.00 39.72 1.85
313 314 2.289506 GGGGACGACTAAGAGCAACTTT 60.290 50.000 0.00 0.00 39.72 2.66
314 315 1.275573 GGGGACGACTAAGAGCAACTT 59.724 52.381 0.00 2.10 42.04 2.66
315 316 0.896226 GGGGACGACTAAGAGCAACT 59.104 55.000 0.00 0.00 0.00 3.16
316 317 0.108281 GGGGGACGACTAAGAGCAAC 60.108 60.000 0.00 0.00 0.00 4.17
317 318 0.252103 AGGGGGACGACTAAGAGCAA 60.252 55.000 0.00 0.00 0.00 3.91
318 319 0.683504 GAGGGGGACGACTAAGAGCA 60.684 60.000 0.00 0.00 0.00 4.26
319 320 1.393487 GGAGGGGGACGACTAAGAGC 61.393 65.000 0.00 0.00 0.00 4.09
320 321 0.033405 TGGAGGGGGACGACTAAGAG 60.033 60.000 0.00 0.00 0.00 2.85
321 322 0.410663 TTGGAGGGGGACGACTAAGA 59.589 55.000 0.00 0.00 0.00 2.10
322 323 1.207329 CTTTGGAGGGGGACGACTAAG 59.793 57.143 0.00 0.00 0.00 2.18
323 324 1.272807 CTTTGGAGGGGGACGACTAA 58.727 55.000 0.00 0.00 0.00 2.24
324 325 0.115745 ACTTTGGAGGGGGACGACTA 59.884 55.000 0.00 0.00 0.00 2.59
325 326 1.152096 ACTTTGGAGGGGGACGACT 60.152 57.895 0.00 0.00 0.00 4.18
326 327 1.295746 GACTTTGGAGGGGGACGAC 59.704 63.158 0.00 0.00 0.00 4.34
327 328 1.916777 GGACTTTGGAGGGGGACGA 60.917 63.158 0.00 0.00 0.00 4.20
328 329 2.669240 GGACTTTGGAGGGGGACG 59.331 66.667 0.00 0.00 0.00 4.79
329 330 1.486145 TTCGGACTTTGGAGGGGGAC 61.486 60.000 0.00 0.00 0.00 4.46
330 331 1.151987 TTCGGACTTTGGAGGGGGA 60.152 57.895 0.00 0.00 0.00 4.81
331 332 1.002502 GTTCGGACTTTGGAGGGGG 60.003 63.158 0.00 0.00 0.00 5.40
362 363 1.025113 AGATCTGAGACGAACCGCGA 61.025 55.000 8.23 0.00 44.57 5.87
371 372 5.598830 TGTATGGAAACCCTAGATCTGAGAC 59.401 44.000 5.18 0.00 0.00 3.36
409 410 2.370189 CTCGCCTCCAATTAATCTCCCT 59.630 50.000 0.00 0.00 0.00 4.20
490 491 2.547430 GGGAGAAAAGAAAGACGACGGT 60.547 50.000 0.00 0.00 0.00 4.83
619 620 4.357947 GCAGTCGCCGTCCAGACA 62.358 66.667 0.00 0.00 39.67 3.41
717 718 5.448438 CGAAATGAAAACAGAAACGGATCA 58.552 37.500 0.00 0.00 0.00 2.92
792 793 0.663153 CGAAATTGGAAGGCGATCCC 59.337 55.000 9.46 0.00 38.82 3.85
853 856 3.456277 GAGGGGATATATAGTGGCTTGGG 59.544 52.174 0.00 0.00 0.00 4.12
885 888 4.845580 CCTGATGGCTTCGGCGCT 62.846 66.667 7.64 0.00 42.91 5.92
1261 1291 1.238439 TCAGGCAAGTTGCTAAGCAC 58.762 50.000 26.16 9.43 44.28 4.40
1319 1349 0.880278 ACATGTTCTTGCAGCGTCGT 60.880 50.000 0.00 0.00 0.00 4.34
1616 1648 2.412770 GTCAAAATTGCGAATTGGGCTG 59.587 45.455 0.00 0.00 0.00 4.85
1837 1869 0.185175 GTGGTCCAAACCCCTGAGTT 59.815 55.000 0.00 0.00 45.83 3.01
1882 1914 4.631813 ACAATTAACGATCTCAAGCTCACC 59.368 41.667 0.00 0.00 0.00 4.02
2246 2279 1.671054 TTAGCTGGCAGAACACGGC 60.671 57.895 20.86 0.74 39.25 5.68
2425 2458 1.183549 ACCATAGGACGACACTGGTC 58.816 55.000 0.00 0.00 35.29 4.02
2429 2462 0.737219 GCGTACCATAGGACGACACT 59.263 55.000 0.00 0.00 41.60 3.55
2436 2469 1.399714 CACTCCTGCGTACCATAGGA 58.600 55.000 7.08 7.08 38.25 2.94
2452 2485 4.706476 CCATTGTACACAAATGATCCCACT 59.294 41.667 7.46 0.00 39.55 4.00
2479 2512 1.040339 CCTCCTCTTCTCCCTGTCCG 61.040 65.000 0.00 0.00 0.00 4.79
2526 2559 3.565764 TGCAGATGATTCCCACCTTAG 57.434 47.619 0.00 0.00 0.00 2.18
2688 2721 2.740714 GGTTGTCGCGGCACATCTC 61.741 63.158 15.66 1.38 0.00 2.75
2805 2838 1.972198 CCCATATAGCTTCGCCGGA 59.028 57.895 5.05 0.00 0.00 5.14
2885 2918 2.664825 TGGCACAAAGGGCATTACC 58.335 52.632 0.00 0.00 38.55 2.85
2996 3029 4.463891 CACAAAAAGGAGCATATGTTCCCT 59.536 41.667 29.04 17.79 45.27 4.20
3239 3322 1.574428 CGAAACCGAAACCTGCCAG 59.426 57.895 0.00 0.00 0.00 4.85
3256 3339 0.879090 GAACAAGGGCCTTACAACCG 59.121 55.000 20.44 8.04 0.00 4.44
3257 3340 0.879090 CGAACAAGGGCCTTACAACC 59.121 55.000 20.44 5.91 0.00 3.77
3258 3341 0.879090 CCGAACAAGGGCCTTACAAC 59.121 55.000 20.44 9.83 0.00 3.32
3259 3342 0.475044 ACCGAACAAGGGCCTTACAA 59.525 50.000 20.44 0.00 35.02 2.41
3260 3343 0.475044 AACCGAACAAGGGCCTTACA 59.525 50.000 20.44 0.00 35.02 2.41
3261 3344 1.162698 GAACCGAACAAGGGCCTTAC 58.837 55.000 20.44 12.32 35.02 2.34
3325 3408 6.371809 TTGGATCTTGTTTGTGTTACTGTC 57.628 37.500 0.00 0.00 0.00 3.51
3488 3571 3.826236 TCTGAAAACGTCCGACTCTAG 57.174 47.619 0.00 0.00 0.00 2.43
3536 3619 5.182760 CCTCTAGTGACCTAAAACGTACAGT 59.817 44.000 0.00 0.00 0.00 3.55
3538 3621 5.072741 ACCTCTAGTGACCTAAAACGTACA 58.927 41.667 0.00 0.00 0.00 2.90
3581 3779 2.798976 TTTGTCCATGTGAAGCTTGC 57.201 45.000 2.10 0.00 0.00 4.01
3609 3807 3.330267 GCGGGAAGGTCTCATATTGATC 58.670 50.000 0.00 0.00 0.00 2.92
3691 3889 6.247229 TGCATAAGAAACAGGGCTATCTTA 57.753 37.500 0.00 0.00 38.38 2.10
3698 3896 6.162777 TGTTTAATTGCATAAGAAACAGGGC 58.837 36.000 10.79 0.00 33.83 5.19
3743 3941 5.736486 AACGACTCTTCAACTTTTCTTCC 57.264 39.130 0.00 0.00 0.00 3.46
3760 3958 7.168804 ACTCTGCAACTTAACTACTAAAACGAC 59.831 37.037 0.00 0.00 0.00 4.34
3780 3978 1.572085 AAGCGTGCACATCACTCTGC 61.572 55.000 18.64 9.31 39.64 4.26
3821 4019 1.957695 CACTCTGCTTGCTGCGTCA 60.958 57.895 0.00 0.00 46.63 4.35


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

AutoCloner maintained by Alex Coulton.