Multiple sequence alignment - TraesCS6A01G312600

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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 TraesCS6A01G312600 chr6A 100.000 2580 0 0 1 2580 549320880 549323459 0.000000e+00 4765
1 TraesCS6A01G312600 chr6A 100.000 480 0 0 2889 3368 549323768 549324247 0.000000e+00 887
2 TraesCS6A01G312600 chr6D 93.750 2352 100 26 256 2580 402879116 402881447 0.000000e+00 3485
3 TraesCS6A01G312600 chr6D 91.630 454 22 8 2889 3332 402881494 402881941 6.180000e-172 614
4 TraesCS6A01G312600 chr6B 92.284 2242 115 25 356 2580 603770905 603773105 0.000000e+00 3129
5 TraesCS6A01G312600 chr7B 75.549 1276 252 46 1126 2368 121883823 121885071 1.050000e-159 573
6 TraesCS6A01G312600 chr7D 75.157 1276 257 45 1126 2368 160629078 160630326 2.290000e-151 545
7 TraesCS6A01G312600 chr7A 95.000 200 10 0 1 200 730857378 730857577 7.010000e-82 315
8 TraesCS6A01G312600 chr7A 94.059 202 11 1 1 201 721097367 721097166 4.220000e-79 305
9 TraesCS6A01G312600 chrUn 94.924 197 10 0 1 197 48038166 48037970 3.260000e-80 309
10 TraesCS6A01G312600 chr4B 94.924 197 10 0 1 197 3438446 3438642 3.260000e-80 309
11 TraesCS6A01G312600 chr2A 94.500 200 11 0 1 200 43530519 43530718 3.260000e-80 309
12 TraesCS6A01G312600 chr2A 94.924 197 10 0 1 197 355453478 355453674 3.260000e-80 309
13 TraesCS6A01G312600 chr2A 94.924 197 10 0 1 197 706553122 706552926 3.260000e-80 309
14 TraesCS6A01G312600 chr1D 93.301 209 11 2 4 211 309072158 309071952 4.220000e-79 305
15 TraesCS6A01G312600 chr1B 92.417 211 14 2 1 210 580156355 580156564 1.960000e-77 300


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 TraesCS6A01G312600 chr6A 549320880 549324247 3367 False 2826.0 4765 100.000 1 3368 2 chr6A.!!$F1 3367
1 TraesCS6A01G312600 chr6D 402879116 402881941 2825 False 2049.5 3485 92.690 256 3332 2 chr6D.!!$F1 3076
2 TraesCS6A01G312600 chr6B 603770905 603773105 2200 False 3129.0 3129 92.284 356 2580 1 chr6B.!!$F1 2224
3 TraesCS6A01G312600 chr7B 121883823 121885071 1248 False 573.0 573 75.549 1126 2368 1 chr7B.!!$F1 1242
4 TraesCS6A01G312600 chr7D 160629078 160630326 1248 False 545.0 545 75.157 1126 2368 1 chr7D.!!$F1 1242

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
818 842 0.787787 TCTCGCCGTTCAAACAATCG 59.212 50.0 0.0 0.0 0.0 3.34 F
819 843 0.789383 CTCGCCGTTCAAACAATCGC 60.789 55.0 0.0 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2295 2344 0.107456 CGTCCCTGGATCCATTGAGG 59.893 60.000 16.63 15.6 39.47 3.86 R
2408 2457 3.766545 ACCTAATTGTGTCTGCATGGTT 58.233 40.909 0.00 0.0 0.00 3.67 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
35 36 8.746052 CCTAGGTGGTTATTTATTGATTGTGA 57.254 34.615 0.00 0.00 0.00 3.58
36 37 8.840321 CCTAGGTGGTTATTTATTGATTGTGAG 58.160 37.037 0.00 0.00 0.00 3.51
37 38 9.613428 CTAGGTGGTTATTTATTGATTGTGAGA 57.387 33.333 0.00 0.00 0.00 3.27
39 40 8.906867 AGGTGGTTATTTATTGATTGTGAGATG 58.093 33.333 0.00 0.00 0.00 2.90
40 41 8.137437 GGTGGTTATTTATTGATTGTGAGATGG 58.863 37.037 0.00 0.00 0.00 3.51
41 42 8.137437 GTGGTTATTTATTGATTGTGAGATGGG 58.863 37.037 0.00 0.00 0.00 4.00
42 43 7.147976 GGTTATTTATTGATTGTGAGATGGGC 58.852 38.462 0.00 0.00 0.00 5.36
43 44 7.014615 GGTTATTTATTGATTGTGAGATGGGCT 59.985 37.037 0.00 0.00 0.00 5.19
44 45 9.066892 GTTATTTATTGATTGTGAGATGGGCTA 57.933 33.333 0.00 0.00 0.00 3.93
45 46 9.639563 TTATTTATTGATTGTGAGATGGGCTAA 57.360 29.630 0.00 0.00 0.00 3.09
46 47 7.953005 TTTATTGATTGTGAGATGGGCTAAA 57.047 32.000 0.00 0.00 0.00 1.85
47 48 7.953005 TTATTGATTGTGAGATGGGCTAAAA 57.047 32.000 0.00 0.00 0.00 1.52
48 49 6.855763 ATTGATTGTGAGATGGGCTAAAAA 57.144 33.333 0.00 0.00 0.00 1.94
70 71 5.907197 AATAGTATTCACACTACGCATGC 57.093 39.130 7.91 7.91 33.94 4.06
71 72 3.245518 AGTATTCACACTACGCATGCA 57.754 42.857 19.57 0.00 0.00 3.96
72 73 3.797039 AGTATTCACACTACGCATGCAT 58.203 40.909 19.57 4.54 0.00 3.96
73 74 4.944048 AGTATTCACACTACGCATGCATA 58.056 39.130 19.57 5.77 0.00 3.14
74 75 5.541845 AGTATTCACACTACGCATGCATAT 58.458 37.500 19.57 4.84 0.00 1.78
75 76 6.687604 AGTATTCACACTACGCATGCATATA 58.312 36.000 19.57 5.83 0.00 0.86
76 77 6.808704 AGTATTCACACTACGCATGCATATAG 59.191 38.462 19.57 17.15 0.00 1.31
77 78 4.846779 TCACACTACGCATGCATATAGA 57.153 40.909 19.57 3.38 0.00 1.98
78 79 5.195001 TCACACTACGCATGCATATAGAA 57.805 39.130 19.57 2.99 0.00 2.10
79 80 5.596845 TCACACTACGCATGCATATAGAAA 58.403 37.500 19.57 0.00 0.00 2.52
80 81 6.223120 TCACACTACGCATGCATATAGAAAT 58.777 36.000 19.57 4.78 0.00 2.17
81 82 7.375053 TCACACTACGCATGCATATAGAAATA 58.625 34.615 19.57 3.27 0.00 1.40
82 83 7.542130 TCACACTACGCATGCATATAGAAATAG 59.458 37.037 19.57 6.89 0.00 1.73
83 84 7.329471 CACACTACGCATGCATATAGAAATAGT 59.671 37.037 19.57 5.11 0.00 2.12
84 85 8.520351 ACACTACGCATGCATATAGAAATAGTA 58.480 33.333 19.57 6.04 0.00 1.82
85 86 9.521503 CACTACGCATGCATATAGAAATAGTAT 57.478 33.333 19.57 0.00 0.00 2.12
89 90 9.399403 ACGCATGCATATAGAAATAGTATATCG 57.601 33.333 19.57 0.00 0.00 2.92
90 91 8.854312 CGCATGCATATAGAAATAGTATATCGG 58.146 37.037 19.57 0.00 0.00 4.18
91 92 9.914131 GCATGCATATAGAAATAGTATATCGGA 57.086 33.333 14.21 0.00 0.00 4.55
112 113 9.790344 ATCGGAGTACTAATTAGCTACTAGAAA 57.210 33.333 19.17 11.04 0.00 2.52
113 114 9.790344 TCGGAGTACTAATTAGCTACTAGAAAT 57.210 33.333 19.17 0.00 0.00 2.17
125 126 6.662616 AGCTACTAGAAATAAATGCAATGCG 58.337 36.000 0.00 0.00 0.00 4.73
126 127 5.340667 GCTACTAGAAATAAATGCAATGCGC 59.659 40.000 0.00 0.00 42.89 6.09
127 128 4.610945 ACTAGAAATAAATGCAATGCGCC 58.389 39.130 4.18 0.00 41.33 6.53
128 129 2.825205 AGAAATAAATGCAATGCGCCC 58.175 42.857 4.18 0.00 41.33 6.13
129 130 2.431782 AGAAATAAATGCAATGCGCCCT 59.568 40.909 4.18 0.00 41.33 5.19
130 131 3.636300 AGAAATAAATGCAATGCGCCCTA 59.364 39.130 4.18 0.00 41.33 3.53
131 132 4.099266 AGAAATAAATGCAATGCGCCCTAA 59.901 37.500 4.18 0.00 41.33 2.69
132 133 4.399004 AATAAATGCAATGCGCCCTAAA 57.601 36.364 4.18 0.00 41.33 1.85
133 134 2.985957 AAATGCAATGCGCCCTAAAT 57.014 40.000 4.18 0.00 41.33 1.40
134 135 2.514205 AATGCAATGCGCCCTAAATC 57.486 45.000 4.18 0.00 41.33 2.17
135 136 1.696063 ATGCAATGCGCCCTAAATCT 58.304 45.000 4.18 0.00 41.33 2.40
136 137 1.473258 TGCAATGCGCCCTAAATCTT 58.527 45.000 4.18 0.00 41.33 2.40
137 138 1.134753 TGCAATGCGCCCTAAATCTTG 59.865 47.619 4.18 0.00 41.33 3.02
138 139 1.134946 GCAATGCGCCCTAAATCTTGT 59.865 47.619 4.18 0.00 32.94 3.16
139 140 2.796032 GCAATGCGCCCTAAATCTTGTC 60.796 50.000 4.18 0.00 32.94 3.18
140 141 2.684881 CAATGCGCCCTAAATCTTGTCT 59.315 45.455 4.18 0.00 0.00 3.41
141 142 3.838244 ATGCGCCCTAAATCTTGTCTA 57.162 42.857 4.18 0.00 0.00 2.59
142 143 3.838244 TGCGCCCTAAATCTTGTCTAT 57.162 42.857 4.18 0.00 0.00 1.98
143 144 4.150897 TGCGCCCTAAATCTTGTCTATT 57.849 40.909 4.18 0.00 0.00 1.73
144 145 3.876914 TGCGCCCTAAATCTTGTCTATTG 59.123 43.478 4.18 0.00 0.00 1.90
145 146 3.877508 GCGCCCTAAATCTTGTCTATTGT 59.122 43.478 0.00 0.00 0.00 2.71
146 147 4.260784 GCGCCCTAAATCTTGTCTATTGTG 60.261 45.833 0.00 0.00 0.00 3.33
147 148 5.116180 CGCCCTAAATCTTGTCTATTGTGA 58.884 41.667 0.00 0.00 0.00 3.58
148 149 5.584649 CGCCCTAAATCTTGTCTATTGTGAA 59.415 40.000 0.00 0.00 0.00 3.18
149 150 6.093495 CGCCCTAAATCTTGTCTATTGTGAAA 59.907 38.462 0.00 0.00 0.00 2.69
150 151 7.361713 CGCCCTAAATCTTGTCTATTGTGAAAA 60.362 37.037 0.00 0.00 0.00 2.29
151 152 7.755373 GCCCTAAATCTTGTCTATTGTGAAAAC 59.245 37.037 0.00 0.00 0.00 2.43
152 153 8.792633 CCCTAAATCTTGTCTATTGTGAAAACA 58.207 33.333 0.00 0.00 0.00 2.83
153 154 9.612620 CCTAAATCTTGTCTATTGTGAAAACAC 57.387 33.333 0.00 0.00 0.00 3.32
155 156 8.856490 AAATCTTGTCTATTGTGAAAACACAC 57.144 30.769 2.48 0.00 40.68 3.82
156 157 6.043327 TCTTGTCTATTGTGAAAACACACG 57.957 37.500 2.48 0.00 42.86 4.49
157 158 4.203950 TGTCTATTGTGAAAACACACGC 57.796 40.909 2.48 0.00 42.86 5.34
158 159 3.623510 TGTCTATTGTGAAAACACACGCA 59.376 39.130 2.48 0.00 42.86 5.24
159 160 4.095036 TGTCTATTGTGAAAACACACGCAA 59.905 37.500 2.48 0.00 42.86 4.85
160 161 5.031578 GTCTATTGTGAAAACACACGCAAA 58.968 37.500 2.48 0.00 42.86 3.68
161 162 5.685511 GTCTATTGTGAAAACACACGCAAAT 59.314 36.000 2.48 0.00 42.86 2.32
162 163 6.198216 GTCTATTGTGAAAACACACGCAAATT 59.802 34.615 2.48 0.00 42.86 1.82
163 164 5.793026 ATTGTGAAAACACACGCAAATTT 57.207 30.435 2.48 0.00 42.86 1.82
164 165 6.893958 ATTGTGAAAACACACGCAAATTTA 57.106 29.167 2.48 0.00 42.86 1.40
165 166 6.706055 TTGTGAAAACACACGCAAATTTAA 57.294 29.167 2.48 0.00 42.86 1.52
166 167 6.083925 TGTGAAAACACACGCAAATTTAAC 57.916 33.333 0.00 0.00 42.86 2.01
167 168 5.177556 GTGAAAACACACGCAAATTTAACG 58.822 37.500 10.32 10.32 0.00 3.18
168 169 4.265556 TGAAAACACACGCAAATTTAACGG 59.734 37.500 14.90 8.08 0.00 4.44
169 170 3.423996 AACACACGCAAATTTAACGGT 57.576 38.095 14.90 8.57 0.00 4.83
170 171 2.722071 ACACACGCAAATTTAACGGTG 58.278 42.857 20.25 20.25 35.52 4.94
171 172 2.097791 ACACACGCAAATTTAACGGTGT 59.902 40.909 21.02 21.02 36.82 4.16
172 173 2.717011 CACACGCAAATTTAACGGTGTC 59.283 45.455 14.90 0.00 0.00 3.67
173 174 2.614983 ACACGCAAATTTAACGGTGTCT 59.385 40.909 14.90 0.00 0.00 3.41
174 175 3.065648 ACACGCAAATTTAACGGTGTCTT 59.934 39.130 14.90 0.00 0.00 3.01
175 176 3.662186 CACGCAAATTTAACGGTGTCTTC 59.338 43.478 14.90 0.00 0.00 2.87
176 177 3.562557 ACGCAAATTTAACGGTGTCTTCT 59.437 39.130 14.90 0.00 0.00 2.85
177 178 4.751098 ACGCAAATTTAACGGTGTCTTCTA 59.249 37.500 14.90 0.00 0.00 2.10
178 179 5.236911 ACGCAAATTTAACGGTGTCTTCTAA 59.763 36.000 14.90 0.00 0.00 2.10
179 180 6.137415 CGCAAATTTAACGGTGTCTTCTAAA 58.863 36.000 5.17 0.00 0.00 1.85
180 181 6.085849 CGCAAATTTAACGGTGTCTTCTAAAC 59.914 38.462 5.17 0.00 0.00 2.01
181 182 6.361481 GCAAATTTAACGGTGTCTTCTAAACC 59.639 38.462 0.00 0.00 0.00 3.27
187 188 2.056577 GGTGTCTTCTAAACCGTGACG 58.943 52.381 0.00 0.00 0.00 4.35
198 199 3.991999 CGTGACGGAGGGAGTACA 58.008 61.111 0.00 0.00 0.00 2.90
199 200 2.260247 CGTGACGGAGGGAGTACAA 58.740 57.895 0.00 0.00 0.00 2.41
200 201 0.815734 CGTGACGGAGGGAGTACAAT 59.184 55.000 0.00 0.00 0.00 2.71
201 202 2.019249 CGTGACGGAGGGAGTACAATA 58.981 52.381 0.00 0.00 0.00 1.90
202 203 2.424601 CGTGACGGAGGGAGTACAATAA 59.575 50.000 0.00 0.00 0.00 1.40
203 204 3.067742 CGTGACGGAGGGAGTACAATAAT 59.932 47.826 0.00 0.00 0.00 1.28
204 205 4.441079 CGTGACGGAGGGAGTACAATAATT 60.441 45.833 0.00 0.00 0.00 1.40
205 206 5.425630 GTGACGGAGGGAGTACAATAATTT 58.574 41.667 0.00 0.00 0.00 1.82
206 207 6.576185 GTGACGGAGGGAGTACAATAATTTA 58.424 40.000 0.00 0.00 0.00 1.40
207 208 7.215085 GTGACGGAGGGAGTACAATAATTTAT 58.785 38.462 0.00 0.00 0.00 1.40
208 209 7.713942 GTGACGGAGGGAGTACAATAATTTATT 59.286 37.037 0.00 0.00 0.00 1.40
209 210 8.269317 TGACGGAGGGAGTACAATAATTTATTT 58.731 33.333 0.00 0.00 0.00 1.40
210 211 9.768662 GACGGAGGGAGTACAATAATTTATTTA 57.231 33.333 0.00 0.00 0.00 1.40
215 216 9.734984 AGGGAGTACAATAATTTATTTATCCGG 57.265 33.333 0.00 0.00 29.96 5.14
216 217 9.729281 GGGAGTACAATAATTTATTTATCCGGA 57.271 33.333 6.61 6.61 29.96 5.14
222 223 8.303876 ACAATAATTTATTTATCCGGACATGCC 58.696 33.333 6.12 0.00 29.96 4.40
223 224 8.522830 CAATAATTTATTTATCCGGACATGCCT 58.477 33.333 6.12 0.00 29.96 4.75
224 225 9.747898 AATAATTTATTTATCCGGACATGCCTA 57.252 29.630 6.12 0.00 29.96 3.93
225 226 9.747898 ATAATTTATTTATCCGGACATGCCTAA 57.252 29.630 6.12 0.00 0.00 2.69
226 227 8.650143 AATTTATTTATCCGGACATGCCTAAT 57.350 30.769 6.12 0.00 0.00 1.73
227 228 9.747898 AATTTATTTATCCGGACATGCCTAATA 57.252 29.630 6.12 0.00 0.00 0.98
228 229 9.747898 ATTTATTTATCCGGACATGCCTAATAA 57.252 29.630 6.12 0.00 0.00 1.40
229 230 9.575868 TTTATTTATCCGGACATGCCTAATAAA 57.424 29.630 6.12 5.73 36.23 1.40
230 231 9.747898 TTATTTATCCGGACATGCCTAATAAAT 57.252 29.630 6.12 21.80 40.58 1.40
232 233 9.920946 ATTTATCCGGACATGCCTAATAAATAT 57.079 29.630 6.12 0.00 38.39 1.28
233 234 9.747898 TTTATCCGGACATGCCTAATAAATATT 57.252 29.630 6.12 0.00 31.33 1.28
234 235 7.630242 ATCCGGACATGCCTAATAAATATTG 57.370 36.000 6.12 0.00 0.00 1.90
235 236 6.539173 TCCGGACATGCCTAATAAATATTGT 58.461 36.000 0.00 0.00 0.00 2.71
236 237 7.001674 TCCGGACATGCCTAATAAATATTGTT 58.998 34.615 0.00 0.00 0.00 2.83
237 238 7.040755 TCCGGACATGCCTAATAAATATTGTTG 60.041 37.037 0.00 0.00 0.00 3.33
238 239 7.040755 CCGGACATGCCTAATAAATATTGTTGA 60.041 37.037 0.00 0.00 0.00 3.18
239 240 7.803189 CGGACATGCCTAATAAATATTGTTGAC 59.197 37.037 0.00 0.00 0.00 3.18
240 241 8.629158 GGACATGCCTAATAAATATTGTTGACA 58.371 33.333 0.00 0.00 0.00 3.58
241 242 9.450807 GACATGCCTAATAAATATTGTTGACAC 57.549 33.333 0.00 0.00 0.00 3.67
242 243 8.965819 ACATGCCTAATAAATATTGTTGACACA 58.034 29.630 0.00 0.00 0.00 3.72
270 271 2.525368 GACAATGTTTGGCCCTAGGTT 58.475 47.619 8.29 0.00 30.38 3.50
272 273 2.158385 ACAATGTTTGGCCCTAGGTTGA 60.158 45.455 8.29 0.00 34.12 3.18
273 274 2.215942 ATGTTTGGCCCTAGGTTGAC 57.784 50.000 8.29 0.00 0.00 3.18
274 275 0.847373 TGTTTGGCCCTAGGTTGACA 59.153 50.000 8.29 0.00 0.00 3.58
276 277 2.158385 TGTTTGGCCCTAGGTTGACATT 60.158 45.455 8.29 0.00 0.00 2.71
277 278 3.074687 TGTTTGGCCCTAGGTTGACATTA 59.925 43.478 8.29 0.00 0.00 1.90
279 280 2.557869 TGGCCCTAGGTTGACATTACT 58.442 47.619 8.29 0.00 0.00 2.24
283 286 3.136626 GCCCTAGGTTGACATTACTCCAT 59.863 47.826 8.29 0.00 0.00 3.41
285 288 4.130118 CCTAGGTTGACATTACTCCATGC 58.870 47.826 0.00 0.00 0.00 4.06
301 304 1.111277 ATGCTTGTAAAATCCGCCCC 58.889 50.000 0.00 0.00 0.00 5.80
302 305 1.309499 TGCTTGTAAAATCCGCCCCG 61.309 55.000 0.00 0.00 0.00 5.73
324 327 3.982058 GGAGAACGATGTTTATAGGCGAG 59.018 47.826 0.00 0.00 0.00 5.03
327 330 3.644884 ACGATGTTTATAGGCGAGGAG 57.355 47.619 0.00 0.00 0.00 3.69
336 339 6.984474 TGTTTATAGGCGAGGAGATGTTTAAG 59.016 38.462 0.00 0.00 0.00 1.85
338 341 3.252974 AGGCGAGGAGATGTTTAAGTG 57.747 47.619 0.00 0.00 0.00 3.16
339 342 2.567615 AGGCGAGGAGATGTTTAAGTGT 59.432 45.455 0.00 0.00 0.00 3.55
343 346 5.383130 GCGAGGAGATGTTTAAGTGTTTTC 58.617 41.667 0.00 0.00 0.00 2.29
344 347 5.049680 GCGAGGAGATGTTTAAGTGTTTTCA 60.050 40.000 0.00 0.00 0.00 2.69
345 348 6.348540 GCGAGGAGATGTTTAAGTGTTTTCAT 60.349 38.462 0.00 0.00 0.00 2.57
347 350 7.746475 CGAGGAGATGTTTAAGTGTTTTCATTC 59.254 37.037 0.00 0.00 0.00 2.67
349 352 6.801862 GGAGATGTTTAAGTGTTTTCATTCCG 59.198 38.462 0.00 0.00 0.00 4.30
350 353 7.272037 AGATGTTTAAGTGTTTTCATTCCGT 57.728 32.000 0.00 0.00 0.00 4.69
352 355 6.438259 TGTTTAAGTGTTTTCATTCCGTCA 57.562 33.333 0.00 0.00 0.00 4.35
354 357 7.313646 TGTTTAAGTGTTTTCATTCCGTCAAA 58.686 30.769 0.00 0.00 0.00 2.69
355 358 7.813148 TGTTTAAGTGTTTTCATTCCGTCAAAA 59.187 29.630 0.00 0.00 0.00 2.44
379 382 9.868160 AAATTTTAAATTAAATCCCACAACCCA 57.132 25.926 3.17 0.00 0.00 4.51
380 383 8.856153 ATTTTAAATTAAATCCCACAACCCAC 57.144 30.769 0.00 0.00 0.00 4.61
397 400 4.129380 ACCCACCGAAACACTAAAGTTAC 58.871 43.478 0.00 0.00 0.00 2.50
400 403 3.499537 CACCGAAACACTAAAGTTACCCC 59.500 47.826 0.00 0.00 0.00 4.95
402 405 3.244665 CCGAAACACTAAAGTTACCCCCT 60.245 47.826 0.00 0.00 0.00 4.79
411 414 4.923516 AAAGTTACCCCCTAGGAACTTC 57.076 45.455 20.72 4.79 41.33 3.01
416 419 3.739401 ACCCCCTAGGAACTTCAATTG 57.261 47.619 11.48 0.00 41.75 2.32
422 425 6.127338 CCCCCTAGGAACTTCAATTGAAATTC 60.127 42.308 26.50 26.50 38.95 2.17
474 477 7.621428 ATTCAGATAGTTTGTTCACCATCTG 57.379 36.000 3.65 3.65 40.34 2.90
494 497 2.087646 GGTCTTCTCAATCCAAGCCAC 58.912 52.381 0.00 0.00 0.00 5.01
495 498 1.734465 GTCTTCTCAATCCAAGCCACG 59.266 52.381 0.00 0.00 0.00 4.94
567 570 4.929211 TCAGTTTACATGTGGACGATGAAG 59.071 41.667 9.11 0.00 0.00 3.02
759 783 4.135153 CAGTCAGTCTCCGCCCCG 62.135 72.222 0.00 0.00 0.00 5.73
797 821 2.378886 TCCTTTCTTTTTCCCTCCCTCC 59.621 50.000 0.00 0.00 0.00 4.30
816 840 1.156736 CCTCTCGCCGTTCAAACAAT 58.843 50.000 0.00 0.00 0.00 2.71
817 841 1.128692 CCTCTCGCCGTTCAAACAATC 59.871 52.381 0.00 0.00 0.00 2.67
818 842 0.787787 TCTCGCCGTTCAAACAATCG 59.212 50.000 0.00 0.00 0.00 3.34
819 843 0.789383 CTCGCCGTTCAAACAATCGC 60.789 55.000 0.00 0.00 0.00 4.58
887 911 1.154225 GCACGCCATTTTCACCTCG 60.154 57.895 0.00 0.00 0.00 4.63
889 913 2.332654 ACGCCATTTTCACCTCGCC 61.333 57.895 0.00 0.00 0.00 5.54
890 914 2.485122 GCCATTTTCACCTCGCCG 59.515 61.111 0.00 0.00 0.00 6.46
999 1033 1.411493 GCCGCTTTCTTCTACCGTCG 61.411 60.000 0.00 0.00 0.00 5.12
1170 1204 2.158900 CCACTTCTTGTGCCCGATATCT 60.159 50.000 0.34 0.00 44.92 1.98
1173 1207 3.452627 ACTTCTTGTGCCCGATATCTCTT 59.547 43.478 0.34 0.00 0.00 2.85
1176 1210 3.643320 TCTTGTGCCCGATATCTCTTGAT 59.357 43.478 0.34 0.00 36.74 2.57
1383 1417 3.432051 GATAGAGCGCGTGCCCACT 62.432 63.158 19.02 16.56 44.31 4.00
1572 1606 2.323790 GCGCTCTCGTCGACGTAT 59.676 61.111 34.40 0.00 40.80 3.06
2041 2090 3.240134 GACGGCCTGCTCCTCACAA 62.240 63.158 0.00 0.00 0.00 3.33
2115 2164 1.010935 AGAAGATGCAGCACGTGTCG 61.011 55.000 18.38 9.68 0.00 4.35
2388 2437 2.493278 AGTGTGCATATTGGAACTTGGC 59.507 45.455 0.00 0.00 0.00 4.52
2408 2457 3.190744 GGCTACGATCGATGTGGATAGAA 59.809 47.826 24.34 0.00 0.00 2.10
2449 2498 9.936329 ATTAGGTTTAGATTCTCTCTCTCTCTT 57.064 33.333 0.00 0.00 35.28 2.85
2464 2515 7.507616 TCTCTCTCTCTTTTTGGAAGAACTACT 59.492 37.037 0.00 0.00 0.00 2.57
2500 2551 4.081142 GGGTATTTTTGGAACCTGGGAATG 60.081 45.833 0.00 0.00 33.59 2.67
2517 2568 4.007659 GGAATGTACGGTTCCACTCAAAT 58.992 43.478 19.50 0.00 43.67 2.32
2947 3004 8.868916 CAAACTGTGCAGTAAAATACAAAAAGT 58.131 29.630 5.18 0.00 41.58 2.66
2963 3020 2.022764 AAGTGCAAAACCCTTTGTGC 57.977 45.000 0.00 0.00 43.34 4.57
2964 3021 1.194218 AGTGCAAAACCCTTTGTGCT 58.806 45.000 0.00 0.00 43.34 4.40
2965 3022 1.554617 AGTGCAAAACCCTTTGTGCTT 59.445 42.857 0.00 0.00 43.34 3.91
2966 3023 2.763448 AGTGCAAAACCCTTTGTGCTTA 59.237 40.909 0.00 0.00 43.34 3.09
2967 3024 3.387699 AGTGCAAAACCCTTTGTGCTTAT 59.612 39.130 0.00 0.00 43.34 1.73
2968 3025 4.586841 AGTGCAAAACCCTTTGTGCTTATA 59.413 37.500 0.00 0.00 43.34 0.98
3055 3113 9.919416 TCATATTTCTAGAAATTTCCATGGACA 57.081 29.630 30.39 8.93 40.99 4.02
3077 3135 9.921637 GGACATGTTTCAATTTATTTTCCTGTA 57.078 29.630 0.00 0.00 0.00 2.74
3192 3258 7.989826 ACTGAAAATACAATGTCCTTGCTATC 58.010 34.615 0.00 0.00 38.50 2.08
3234 3300 5.896678 AGCCAAACCAAATTACAGGCATATA 59.103 36.000 0.00 0.00 42.90 0.86
3286 3352 3.247006 AGGCTCACCACTAAACATACG 57.753 47.619 0.00 0.00 39.06 3.06
3295 3361 3.865745 CCACTAAACATACGCTTGAGGAG 59.134 47.826 0.00 0.00 0.00 3.69
3326 3392 1.613925 GCCAACAAAGTTCTCCTTCCC 59.386 52.381 0.00 0.00 31.27 3.97
3329 3395 2.545537 ACAAAGTTCTCCTTCCCGTC 57.454 50.000 0.00 0.00 31.27 4.79
3330 3396 2.047830 ACAAAGTTCTCCTTCCCGTCT 58.952 47.619 0.00 0.00 31.27 4.18
3331 3397 2.037381 ACAAAGTTCTCCTTCCCGTCTC 59.963 50.000 0.00 0.00 31.27 3.36
3332 3398 2.011122 AAGTTCTCCTTCCCGTCTCA 57.989 50.000 0.00 0.00 0.00 3.27
3333 3399 2.011122 AGTTCTCCTTCCCGTCTCAA 57.989 50.000 0.00 0.00 0.00 3.02
3334 3400 2.326428 AGTTCTCCTTCCCGTCTCAAA 58.674 47.619 0.00 0.00 0.00 2.69
3335 3401 2.704065 AGTTCTCCTTCCCGTCTCAAAA 59.296 45.455 0.00 0.00 0.00 2.44
3336 3402 3.135895 AGTTCTCCTTCCCGTCTCAAAAA 59.864 43.478 0.00 0.00 0.00 1.94
3360 3426 5.638530 AAAAGTTCTCCTTCCTGTTCTCT 57.361 39.130 0.00 0.00 31.27 3.10
3361 3427 5.638530 AAAGTTCTCCTTCCTGTTCTCTT 57.361 39.130 0.00 0.00 31.27 2.85
3362 3428 4.615588 AGTTCTCCTTCCTGTTCTCTTG 57.384 45.455 0.00 0.00 0.00 3.02
3363 3429 4.227197 AGTTCTCCTTCCTGTTCTCTTGA 58.773 43.478 0.00 0.00 0.00 3.02
3364 3430 4.039852 AGTTCTCCTTCCTGTTCTCTTGAC 59.960 45.833 0.00 0.00 0.00 3.18
3365 3431 3.850752 TCTCCTTCCTGTTCTCTTGACT 58.149 45.455 0.00 0.00 0.00 3.41
3366 3432 4.227197 TCTCCTTCCTGTTCTCTTGACTT 58.773 43.478 0.00 0.00 0.00 3.01
3367 3433 5.394738 TCTCCTTCCTGTTCTCTTGACTTA 58.605 41.667 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.746052 TCACAATCAATAAATAACCACCTAGG 57.254 34.615 7.41 7.41 45.67 3.02
11 12 9.613428 TCTCACAATCAATAAATAACCACCTAG 57.387 33.333 0.00 0.00 0.00 3.02
13 14 8.906867 CATCTCACAATCAATAAATAACCACCT 58.093 33.333 0.00 0.00 0.00 4.00
14 15 8.137437 CCATCTCACAATCAATAAATAACCACC 58.863 37.037 0.00 0.00 0.00 4.61
15 16 8.137437 CCCATCTCACAATCAATAAATAACCAC 58.863 37.037 0.00 0.00 0.00 4.16
16 17 7.201902 GCCCATCTCACAATCAATAAATAACCA 60.202 37.037 0.00 0.00 0.00 3.67
17 18 7.014615 AGCCCATCTCACAATCAATAAATAACC 59.985 37.037 0.00 0.00 0.00 2.85
18 19 7.945134 AGCCCATCTCACAATCAATAAATAAC 58.055 34.615 0.00 0.00 0.00 1.89
19 20 9.639563 TTAGCCCATCTCACAATCAATAAATAA 57.360 29.630 0.00 0.00 0.00 1.40
20 21 9.639563 TTTAGCCCATCTCACAATCAATAAATA 57.360 29.630 0.00 0.00 0.00 1.40
21 22 8.537728 TTTAGCCCATCTCACAATCAATAAAT 57.462 30.769 0.00 0.00 0.00 1.40
22 23 7.953005 TTTAGCCCATCTCACAATCAATAAA 57.047 32.000 0.00 0.00 0.00 1.40
23 24 7.953005 TTTTAGCCCATCTCACAATCAATAA 57.047 32.000 0.00 0.00 0.00 1.40
24 25 7.953005 TTTTTAGCCCATCTCACAATCAATA 57.047 32.000 0.00 0.00 0.00 1.90
25 26 6.855763 TTTTTAGCCCATCTCACAATCAAT 57.144 33.333 0.00 0.00 0.00 2.57
45 46 7.148323 TGCATGCGTAGTGTGAATACTATTTTT 60.148 33.333 14.09 0.00 35.75 1.94
46 47 6.315144 TGCATGCGTAGTGTGAATACTATTTT 59.685 34.615 14.09 0.00 35.75 1.82
47 48 5.815222 TGCATGCGTAGTGTGAATACTATTT 59.185 36.000 14.09 0.00 35.75 1.40
48 49 5.356426 TGCATGCGTAGTGTGAATACTATT 58.644 37.500 14.09 0.00 35.75 1.73
49 50 4.944048 TGCATGCGTAGTGTGAATACTAT 58.056 39.130 14.09 0.00 35.75 2.12
50 51 4.379339 TGCATGCGTAGTGTGAATACTA 57.621 40.909 14.09 0.00 32.19 1.82
51 52 3.245518 TGCATGCGTAGTGTGAATACT 57.754 42.857 14.09 0.00 34.71 2.12
52 53 5.845985 ATATGCATGCGTAGTGTGAATAC 57.154 39.130 23.20 0.00 0.00 1.89
53 54 6.919721 TCTATATGCATGCGTAGTGTGAATA 58.080 36.000 23.20 10.20 0.00 1.75
54 55 5.783111 TCTATATGCATGCGTAGTGTGAAT 58.217 37.500 23.20 9.61 0.00 2.57
55 56 5.195001 TCTATATGCATGCGTAGTGTGAA 57.805 39.130 23.20 2.26 0.00 3.18
56 57 4.846779 TCTATATGCATGCGTAGTGTGA 57.153 40.909 23.20 15.02 0.00 3.58
57 58 5.905480 TTTCTATATGCATGCGTAGTGTG 57.095 39.130 23.20 13.27 0.00 3.82
58 59 7.378966 ACTATTTCTATATGCATGCGTAGTGT 58.621 34.615 23.20 10.69 0.00 3.55
59 60 7.818493 ACTATTTCTATATGCATGCGTAGTG 57.182 36.000 23.20 17.51 0.00 2.74
63 64 9.399403 CGATATACTATTTCTATATGCATGCGT 57.601 33.333 18.07 18.07 0.00 5.24
64 65 8.854312 CCGATATACTATTTCTATATGCATGCG 58.146 37.037 14.09 0.00 0.00 4.73
65 66 9.914131 TCCGATATACTATTTCTATATGCATGC 57.086 33.333 11.82 11.82 0.00 4.06
86 87 9.790344 TTTCTAGTAGCTAATTAGTACTCCGAT 57.210 33.333 21.10 8.68 0.00 4.18
87 88 9.790344 ATTTCTAGTAGCTAATTAGTACTCCGA 57.210 33.333 21.10 17.46 0.00 4.55
99 100 8.282592 CGCATTGCATTTATTTCTAGTAGCTAA 58.717 33.333 9.69 0.00 0.00 3.09
100 101 7.571244 GCGCATTGCATTTATTTCTAGTAGCTA 60.571 37.037 9.69 0.00 45.45 3.32
101 102 6.662616 CGCATTGCATTTATTTCTAGTAGCT 58.337 36.000 9.69 0.00 0.00 3.32
102 103 5.340667 GCGCATTGCATTTATTTCTAGTAGC 59.659 40.000 9.69 0.00 45.45 3.58
103 104 6.901699 GCGCATTGCATTTATTTCTAGTAG 57.098 37.500 9.69 0.00 45.45 2.57
118 119 1.134946 ACAAGATTTAGGGCGCATTGC 59.865 47.619 10.83 0.00 45.38 3.56
119 120 2.684881 AGACAAGATTTAGGGCGCATTG 59.315 45.455 10.83 3.20 0.00 2.82
120 121 3.004752 AGACAAGATTTAGGGCGCATT 57.995 42.857 10.83 0.00 0.00 3.56
121 122 2.717639 AGACAAGATTTAGGGCGCAT 57.282 45.000 10.83 0.00 0.00 4.73
122 123 3.838244 ATAGACAAGATTTAGGGCGCA 57.162 42.857 10.83 0.00 0.00 6.09
123 124 3.877508 ACAATAGACAAGATTTAGGGCGC 59.122 43.478 0.00 0.00 0.00 6.53
124 125 5.116180 TCACAATAGACAAGATTTAGGGCG 58.884 41.667 0.00 0.00 0.00 6.13
125 126 7.391148 TTTCACAATAGACAAGATTTAGGGC 57.609 36.000 0.00 0.00 0.00 5.19
126 127 8.792633 TGTTTTCACAATAGACAAGATTTAGGG 58.207 33.333 0.00 0.00 0.00 3.53
145 146 4.265556 CCGTTAAATTTGCGTGTGTTTTCA 59.734 37.500 0.00 0.00 0.00 2.69
146 147 4.265792 ACCGTTAAATTTGCGTGTGTTTTC 59.734 37.500 0.00 0.00 0.00 2.29
147 148 4.031878 CACCGTTAAATTTGCGTGTGTTTT 59.968 37.500 18.49 0.00 0.00 2.43
148 149 3.548268 CACCGTTAAATTTGCGTGTGTTT 59.452 39.130 18.49 0.00 0.00 2.83
149 150 3.109619 CACCGTTAAATTTGCGTGTGTT 58.890 40.909 18.49 0.00 0.00 3.32
150 151 2.097791 ACACCGTTAAATTTGCGTGTGT 59.902 40.909 22.27 22.27 36.24 3.72
151 152 2.717011 GACACCGTTAAATTTGCGTGTG 59.283 45.455 21.54 21.54 35.02 3.82
152 153 2.614983 AGACACCGTTAAATTTGCGTGT 59.385 40.909 16.40 16.40 0.00 4.49
153 154 3.262135 AGACACCGTTAAATTTGCGTG 57.738 42.857 0.00 8.77 0.00 5.34
154 155 3.562557 AGAAGACACCGTTAAATTTGCGT 59.437 39.130 0.00 0.00 0.00 5.24
155 156 4.141855 AGAAGACACCGTTAAATTTGCG 57.858 40.909 0.00 5.54 0.00 4.85
156 157 6.361481 GGTTTAGAAGACACCGTTAAATTTGC 59.639 38.462 0.00 0.00 0.00 3.68
157 158 6.575942 CGGTTTAGAAGACACCGTTAAATTTG 59.424 38.462 0.00 0.00 46.90 2.32
158 159 6.661669 CGGTTTAGAAGACACCGTTAAATTT 58.338 36.000 1.74 0.00 46.90 1.82
159 160 6.232139 CGGTTTAGAAGACACCGTTAAATT 57.768 37.500 1.74 0.00 46.90 1.82
160 161 5.851047 CGGTTTAGAAGACACCGTTAAAT 57.149 39.130 1.74 0.00 46.90 1.40
167 168 2.056577 CGTCACGGTTTAGAAGACACC 58.943 52.381 0.00 0.00 0.00 4.16
168 169 2.056577 CCGTCACGGTTTAGAAGACAC 58.943 52.381 8.54 0.00 42.73 3.67
169 170 2.427232 CCGTCACGGTTTAGAAGACA 57.573 50.000 8.54 0.00 42.73 3.41
181 182 0.815734 ATTGTACTCCCTCCGTCACG 59.184 55.000 0.00 0.00 0.00 4.35
182 183 4.667519 ATTATTGTACTCCCTCCGTCAC 57.332 45.455 0.00 0.00 0.00 3.67
183 184 5.687166 AAATTATTGTACTCCCTCCGTCA 57.313 39.130 0.00 0.00 0.00 4.35
184 185 8.672823 AAATAAATTATTGTACTCCCTCCGTC 57.327 34.615 0.00 0.00 0.00 4.79
189 190 9.734984 CCGGATAAATAAATTATTGTACTCCCT 57.265 33.333 0.00 0.00 34.30 4.20
190 191 9.729281 TCCGGATAAATAAATTATTGTACTCCC 57.271 33.333 0.00 0.00 34.30 4.30
196 197 8.303876 GGCATGTCCGGATAAATAAATTATTGT 58.696 33.333 7.81 0.00 34.30 2.71
197 198 8.522830 AGGCATGTCCGGATAAATAAATTATTG 58.477 33.333 7.81 0.00 40.77 1.90
198 199 8.650143 AGGCATGTCCGGATAAATAAATTATT 57.350 30.769 7.81 0.00 40.77 1.40
199 200 9.747898 TTAGGCATGTCCGGATAAATAAATTAT 57.252 29.630 7.81 0.00 40.77 1.28
200 201 9.747898 ATTAGGCATGTCCGGATAAATAAATTA 57.252 29.630 7.81 0.00 40.77 1.40
201 202 8.650143 ATTAGGCATGTCCGGATAAATAAATT 57.350 30.769 7.81 0.00 40.77 1.82
202 203 9.747898 TTATTAGGCATGTCCGGATAAATAAAT 57.252 29.630 7.81 5.97 40.77 1.40
203 204 9.575868 TTTATTAGGCATGTCCGGATAAATAAA 57.424 29.630 17.13 17.13 40.77 1.40
204 205 9.747898 ATTTATTAGGCATGTCCGGATAAATAA 57.252 29.630 22.56 9.04 40.83 1.40
206 207 9.920946 ATATTTATTAGGCATGTCCGGATAAAT 57.079 29.630 24.46 24.46 42.69 1.40
207 208 9.747898 AATATTTATTAGGCATGTCCGGATAAA 57.252 29.630 7.81 19.30 39.01 1.40
208 209 9.173021 CAATATTTATTAGGCATGTCCGGATAA 57.827 33.333 7.81 0.56 40.77 1.75
209 210 8.325787 ACAATATTTATTAGGCATGTCCGGATA 58.674 33.333 7.81 4.93 40.77 2.59
210 211 7.175104 ACAATATTTATTAGGCATGTCCGGAT 58.825 34.615 7.81 0.00 40.77 4.18
211 212 6.539173 ACAATATTTATTAGGCATGTCCGGA 58.461 36.000 0.00 0.00 40.77 5.14
212 213 6.817765 ACAATATTTATTAGGCATGTCCGG 57.182 37.500 0.00 0.00 40.77 5.14
213 214 7.803189 GTCAACAATATTTATTAGGCATGTCCG 59.197 37.037 0.00 0.00 40.77 4.79
214 215 8.629158 TGTCAACAATATTTATTAGGCATGTCC 58.371 33.333 0.00 0.00 0.00 4.02
215 216 9.450807 GTGTCAACAATATTTATTAGGCATGTC 57.549 33.333 0.00 0.00 0.00 3.06
216 217 8.965819 TGTGTCAACAATATTTATTAGGCATGT 58.034 29.630 0.00 0.00 31.82 3.21
217 218 9.800433 TTGTGTCAACAATATTTATTAGGCATG 57.200 29.630 0.00 0.00 41.41 4.06
244 245 2.777114 AGGGCCAAACATTGTCCTTTTT 59.223 40.909 6.18 0.00 31.25 1.94
245 246 2.407562 AGGGCCAAACATTGTCCTTTT 58.592 42.857 6.18 0.00 31.25 2.27
246 247 2.101640 AGGGCCAAACATTGTCCTTT 57.898 45.000 6.18 0.00 31.25 3.11
247 248 2.557452 CCTAGGGCCAAACATTGTCCTT 60.557 50.000 6.18 0.00 35.20 3.36
248 249 1.005924 CCTAGGGCCAAACATTGTCCT 59.994 52.381 6.18 0.00 36.69 3.85
249 250 1.272480 ACCTAGGGCCAAACATTGTCC 60.272 52.381 14.81 0.00 0.00 4.02
250 251 2.215942 ACCTAGGGCCAAACATTGTC 57.784 50.000 14.81 0.00 0.00 3.18
251 252 2.158385 TCAACCTAGGGCCAAACATTGT 60.158 45.455 14.81 0.00 0.00 2.71
252 253 2.231235 GTCAACCTAGGGCCAAACATTG 59.769 50.000 14.81 5.95 0.00 2.82
253 254 2.158385 TGTCAACCTAGGGCCAAACATT 60.158 45.455 14.81 0.00 0.00 2.71
254 255 1.427368 TGTCAACCTAGGGCCAAACAT 59.573 47.619 14.81 0.00 0.00 2.71
265 266 5.185454 CAAGCATGGAGTAATGTCAACCTA 58.815 41.667 0.00 0.00 0.00 3.08
266 267 4.012374 CAAGCATGGAGTAATGTCAACCT 58.988 43.478 0.00 0.00 0.00 3.50
267 268 3.758554 ACAAGCATGGAGTAATGTCAACC 59.241 43.478 0.00 0.00 0.00 3.77
268 269 6.494893 TTACAAGCATGGAGTAATGTCAAC 57.505 37.500 0.00 0.00 0.00 3.18
270 271 7.148086 GGATTTTACAAGCATGGAGTAATGTCA 60.148 37.037 0.00 0.00 0.00 3.58
272 273 6.183360 CGGATTTTACAAGCATGGAGTAATGT 60.183 38.462 0.00 0.00 0.00 2.71
273 274 6.201517 CGGATTTTACAAGCATGGAGTAATG 58.798 40.000 0.00 0.00 0.00 1.90
274 275 5.221048 GCGGATTTTACAAGCATGGAGTAAT 60.221 40.000 0.00 0.00 0.00 1.89
276 277 3.625764 GCGGATTTTACAAGCATGGAGTA 59.374 43.478 0.00 0.00 0.00 2.59
277 278 2.423538 GCGGATTTTACAAGCATGGAGT 59.576 45.455 0.00 0.00 0.00 3.85
279 280 1.748493 GGCGGATTTTACAAGCATGGA 59.252 47.619 0.00 0.00 0.00 3.41
283 286 1.309499 CGGGGCGGATTTTACAAGCA 61.309 55.000 0.00 0.00 0.00 3.91
301 304 2.724690 CGCCTATAAACATCGTTCTCCG 59.275 50.000 0.00 0.00 38.13 4.63
302 305 3.973657 TCGCCTATAAACATCGTTCTCC 58.026 45.455 0.00 0.00 0.00 3.71
303 306 3.982058 CCTCGCCTATAAACATCGTTCTC 59.018 47.826 0.00 0.00 0.00 2.87
309 312 5.140747 ACATCTCCTCGCCTATAAACATC 57.859 43.478 0.00 0.00 0.00 3.06
318 321 2.567615 ACACTTAAACATCTCCTCGCCT 59.432 45.455 0.00 0.00 0.00 5.52
324 327 6.801862 CGGAATGAAAACACTTAAACATCTCC 59.198 38.462 0.00 0.00 0.00 3.71
327 330 7.136119 TGACGGAATGAAAACACTTAAACATC 58.864 34.615 0.00 0.00 0.00 3.06
336 339 9.974750 TTTAAAATTTTGACGGAATGAAAACAC 57.025 25.926 13.76 0.00 0.00 3.32
354 357 9.290988 GTGGGTTGTGGGATTTAATTTAAAATT 57.709 29.630 5.73 0.00 0.00 1.82
355 358 7.885922 GGTGGGTTGTGGGATTTAATTTAAAAT 59.114 33.333 5.73 0.00 0.00 1.82
364 367 1.065647 TCGGTGGGTTGTGGGATTTA 58.934 50.000 0.00 0.00 0.00 1.40
374 377 3.286329 ACTTTAGTGTTTCGGTGGGTT 57.714 42.857 0.00 0.00 0.00 4.11
379 382 3.496692 GGGGGTAACTTTAGTGTTTCGGT 60.497 47.826 0.00 0.00 0.00 4.69
380 383 3.076621 GGGGGTAACTTTAGTGTTTCGG 58.923 50.000 0.00 0.00 0.00 4.30
397 400 4.316025 TTCAATTGAAGTTCCTAGGGGG 57.684 45.455 16.91 0.00 0.00 5.40
443 446 9.076596 GGTGAACAAACTATCTGAATTAAATGC 57.923 33.333 0.00 0.00 0.00 3.56
474 477 2.087646 GTGGCTTGGATTGAGAAGACC 58.912 52.381 0.00 0.00 0.00 3.85
477 480 1.089920 CCGTGGCTTGGATTGAGAAG 58.910 55.000 0.00 0.00 0.00 2.85
512 515 1.098050 GCATCTTGGCTGGTTAGTGG 58.902 55.000 0.00 0.00 0.00 4.00
521 524 2.182842 GCGAATCGGCATCTTGGCT 61.183 57.895 4.35 0.00 41.25 4.75
547 550 3.435327 TGCTTCATCGTCCACATGTAAAC 59.565 43.478 0.00 0.00 0.00 2.01
567 570 2.262211 GGAAGACGGCATTTGAAATGC 58.738 47.619 29.37 29.37 43.85 3.56
631 644 0.255890 ATGGTATTTGGCTCCGTGCT 59.744 50.000 0.00 0.00 42.39 4.40
797 821 1.128692 GATTGTTTGAACGGCGAGAGG 59.871 52.381 16.62 0.00 0.00 3.69
895 919 2.406616 CCGATGACCGCCTTTTGGG 61.407 63.158 0.00 0.00 40.82 4.12
905 929 2.202756 GGCTGACGACCGATGACC 60.203 66.667 0.00 0.00 0.00 4.02
1069 1103 4.849329 CCTGACGGCGAGCGGTAC 62.849 72.222 16.62 3.91 0.00 3.34
1170 1204 1.347707 GGGTCCCGCATCATATCAAGA 59.652 52.381 0.00 0.00 0.00 3.02
1173 1207 2.066340 GGGGTCCCGCATCATATCA 58.934 57.895 0.48 0.00 0.00 2.15
1366 1400 3.432051 GAGTGGGCACGCGCTCTAT 62.432 63.158 17.94 0.00 40.38 1.98
1697 1746 2.481185 GAGAGGATAGACACGACGGATC 59.519 54.545 0.00 0.00 0.00 3.36
1890 1939 1.349973 GACGAGGTAGTACGCGGTC 59.650 63.158 12.47 2.33 0.00 4.79
2026 2075 2.749441 GCTTGTGAGGAGCAGGCC 60.749 66.667 0.00 0.00 39.89 5.19
2115 2164 1.810030 GAACTCCGTCGCCATGTCC 60.810 63.158 0.00 0.00 0.00 4.02
2295 2344 0.107456 CGTCCCTGGATCCATTGAGG 59.893 60.000 16.63 15.60 39.47 3.86
2388 2437 5.154932 GGTTTCTATCCACATCGATCGTAG 58.845 45.833 15.94 11.24 0.00 3.51
2408 2457 3.766545 ACCTAATTGTGTCTGCATGGTT 58.233 40.909 0.00 0.00 0.00 3.67
2449 2498 4.776349 TGAGCACAGTAGTTCTTCCAAAA 58.224 39.130 0.00 0.00 0.00 2.44
2478 2529 4.530553 ACATTCCCAGGTTCCAAAAATACC 59.469 41.667 0.00 0.00 0.00 2.73
2500 2551 4.453136 TGCTAAATTTGAGTGGAACCGTAC 59.547 41.667 0.00 0.00 37.80 3.67
2555 2610 5.472148 TGTTGCATGGATGATTCTTTTCAC 58.528 37.500 0.00 0.00 0.00 3.18
2932 2989 8.203937 AGGGTTTTGCACTTTTTGTATTTTAC 57.796 30.769 0.00 0.00 0.00 2.01
2947 3004 5.736951 ATATAAGCACAAAGGGTTTTGCA 57.263 34.783 0.98 0.00 46.05 4.08
3047 3104 8.667463 GGAAAATAAATTGAAACATGTCCATGG 58.333 33.333 4.97 4.97 42.91 3.66
3086 3144 9.688592 AAAATTGCATGTTTCAAGTTTCAAAAA 57.311 22.222 4.75 0.00 37.19 1.94
3180 3246 4.343814 TGATAATGGACGATAGCAAGGACA 59.656 41.667 0.00 0.00 42.67 4.02
3181 3247 4.883083 TGATAATGGACGATAGCAAGGAC 58.117 43.478 0.00 0.00 42.67 3.85
3192 3258 3.070018 GGCTGGAAGATGATAATGGACG 58.930 50.000 0.00 0.00 34.07 4.79
3234 3300 5.408079 ACCCCATTTACATCCATGATCTT 57.592 39.130 0.00 0.00 0.00 2.40
3262 3328 5.815740 CGTATGTTTAGTGGTGAGCCTAAAT 59.184 40.000 8.00 0.00 36.04 1.40
3303 3369 1.692411 AGGAGAACTTTGTTGGCACC 58.308 50.000 0.00 0.00 0.00 5.01
3337 3403 6.007485 AGAGAACAGGAAGGAGAACTTTTT 57.993 37.500 0.00 0.00 40.21 1.94
3338 3404 5.638530 AGAGAACAGGAAGGAGAACTTTT 57.361 39.130 0.00 0.00 40.21 2.27
3339 3405 5.131142 TCAAGAGAACAGGAAGGAGAACTTT 59.869 40.000 0.00 0.00 40.21 2.66
3340 3406 4.656112 TCAAGAGAACAGGAAGGAGAACTT 59.344 41.667 0.00 0.00 43.65 2.66
3341 3407 4.039852 GTCAAGAGAACAGGAAGGAGAACT 59.960 45.833 0.00 0.00 0.00 3.01
3342 3408 4.039852 AGTCAAGAGAACAGGAAGGAGAAC 59.960 45.833 0.00 0.00 0.00 3.01
3343 3409 4.227197 AGTCAAGAGAACAGGAAGGAGAA 58.773 43.478 0.00 0.00 0.00 2.87
3344 3410 3.850752 AGTCAAGAGAACAGGAAGGAGA 58.149 45.455 0.00 0.00 0.00 3.71
3345 3411 4.615588 AAGTCAAGAGAACAGGAAGGAG 57.384 45.455 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.