Multiple sequence alignment - TraesCS7D01G025400

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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 TraesCS7D01G025400 chr7D 100.000 2612 0 0 1 2612 12069376 12071987 0.000000e+00 4824.0
1 TraesCS7D01G025400 chr7D 98.807 1090 13 0 655 1744 49271224 49270135 0.000000e+00 1941.0
2 TraesCS7D01G025400 chr7D 98.393 871 13 1 1742 2612 478781378 478782247 0.000000e+00 1530.0
3 TraesCS7D01G025400 chr7D 93.502 831 54 0 1782 2612 33648223 33647393 0.000000e+00 1236.0
4 TraesCS7D01G025400 chr7D 92.396 868 63 2 1745 2612 109615939 109616803 0.000000e+00 1234.0
5 TraesCS7D01G025400 chr7D 90.371 862 83 0 1751 2612 604397710 604398571 0.000000e+00 1133.0
6 TraesCS7D01G025400 chr7D 81.371 1342 202 32 297 1624 12336164 12334857 0.000000e+00 1050.0
7 TraesCS7D01G025400 chr6D 98.487 859 13 0 1754 2612 45662602 45661744 0.000000e+00 1515.0
8 TraesCS7D01G025400 chr1D 92.857 868 62 0 1745 2612 4228578 4227711 0.000000e+00 1260.0
9 TraesCS7D01G025400 chr3D 88.331 857 96 4 1753 2607 564143925 564143071 0.000000e+00 1026.0
10 TraesCS7D01G025400 chr2D 88.331 857 96 4 1753 2607 602228496 602229350 0.000000e+00 1026.0
11 TraesCS7D01G025400 chr7A 81.804 1264 184 30 297 1545 11907030 11905798 0.000000e+00 1018.0
12 TraesCS7D01G025400 chr7A 81.725 1264 185 30 297 1545 11861123 11859891 0.000000e+00 1013.0
13 TraesCS7D01G025400 chr7A 82.942 469 78 2 1078 1545 11976623 11976156 3.110000e-114 422.0
14 TraesCS7D01G025400 chr7A 80.258 542 101 5 1078 1616 11814588 11814050 1.130000e-108 403.0
15 TraesCS7D01G025400 chr7A 80.074 542 102 5 1078 1616 11780482 11779944 5.240000e-107 398.0
16 TraesCS7D01G025400 chr7B 80.984 1341 197 38 300 1625 717054009 717055306 0.000000e+00 1011.0
17 TraesCS7D01G025400 chr5D 87.981 857 98 5 1753 2607 247327082 247326229 0.000000e+00 1007.0
18 TraesCS7D01G025400 chr4A 81.842 1129 163 28 505 1624 725856634 725857729 0.000000e+00 911.0
19 TraesCS7D01G025400 chr4A 76.413 407 87 8 1026 1429 715558837 715559237 7.320000e-51 211.0
20 TraesCS7D01G025400 chr4A 76.238 404 87 8 1029 1429 715945493 715945096 3.410000e-49 206.0
21 TraesCS7D01G025400 chrUn 76.953 256 33 19 5 239 35852925 35852675 3.530000e-24 122.0
22 TraesCS7D01G025400 chrUn 76.834 259 34 19 2 239 299962513 299962766 3.530000e-24 122.0
23 TraesCS7D01G025400 chr3A 89.474 76 4 2 206 277 685337440 685337515 2.770000e-15 93.5
24 TraesCS7D01G025400 chr4B 74.667 225 39 15 34 243 612256336 612256557 1.670000e-12 84.2


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 TraesCS7D01G025400 chr7D 12069376 12071987 2611 False 4824 4824 100.000 1 2612 1 chr7D.!!$F1 2611
1 TraesCS7D01G025400 chr7D 49270135 49271224 1089 True 1941 1941 98.807 655 1744 1 chr7D.!!$R3 1089
2 TraesCS7D01G025400 chr7D 478781378 478782247 869 False 1530 1530 98.393 1742 2612 1 chr7D.!!$F3 870
3 TraesCS7D01G025400 chr7D 33647393 33648223 830 True 1236 1236 93.502 1782 2612 1 chr7D.!!$R2 830
4 TraesCS7D01G025400 chr7D 109615939 109616803 864 False 1234 1234 92.396 1745 2612 1 chr7D.!!$F2 867
5 TraesCS7D01G025400 chr7D 604397710 604398571 861 False 1133 1133 90.371 1751 2612 1 chr7D.!!$F4 861
6 TraesCS7D01G025400 chr7D 12334857 12336164 1307 True 1050 1050 81.371 297 1624 1 chr7D.!!$R1 1327
7 TraesCS7D01G025400 chr6D 45661744 45662602 858 True 1515 1515 98.487 1754 2612 1 chr6D.!!$R1 858
8 TraesCS7D01G025400 chr1D 4227711 4228578 867 True 1260 1260 92.857 1745 2612 1 chr1D.!!$R1 867
9 TraesCS7D01G025400 chr3D 564143071 564143925 854 True 1026 1026 88.331 1753 2607 1 chr3D.!!$R1 854
10 TraesCS7D01G025400 chr2D 602228496 602229350 854 False 1026 1026 88.331 1753 2607 1 chr2D.!!$F1 854
11 TraesCS7D01G025400 chr7A 11905798 11907030 1232 True 1018 1018 81.804 297 1545 1 chr7A.!!$R4 1248
12 TraesCS7D01G025400 chr7A 11859891 11861123 1232 True 1013 1013 81.725 297 1545 1 chr7A.!!$R3 1248
13 TraesCS7D01G025400 chr7A 11814050 11814588 538 True 403 403 80.258 1078 1616 1 chr7A.!!$R2 538
14 TraesCS7D01G025400 chr7A 11779944 11780482 538 True 398 398 80.074 1078 1616 1 chr7A.!!$R1 538
15 TraesCS7D01G025400 chr7B 717054009 717055306 1297 False 1011 1011 80.984 300 1625 1 chr7B.!!$F1 1325
16 TraesCS7D01G025400 chr5D 247326229 247327082 853 True 1007 1007 87.981 1753 2607 1 chr5D.!!$R1 854
17 TraesCS7D01G025400 chr4A 725856634 725857729 1095 False 911 911 81.842 505 1624 1 chr4A.!!$F2 1119

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
232 233 0.038744 AGCAATGTTGGAGGGGTGAG 59.961 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1738 1751 2.89735 CGCCCCGCTCATTCCTTC 60.897 66.667 0.0 0.0 0.0 3.46 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 7.754625 AGGATTTGTTCATGCATTTTAAATGC 58.245 30.769 29.24 29.24 44.76 3.56
29 30 7.608761 AGGATTTGTTCATGCATTTTAAATGCT 59.391 29.630 33.22 20.74 44.79 3.79
30 31 8.238631 GGATTTGTTCATGCATTTTAAATGCTT 58.761 29.630 33.22 27.02 44.79 3.91
79 80 9.503427 GTCTCATTTTGTATACTTATGTTTGGC 57.497 33.333 4.17 0.33 0.00 4.52
80 81 8.682710 TCTCATTTTGTATACTTATGTTTGGCC 58.317 33.333 4.17 0.00 0.00 5.36
81 82 8.354711 TCATTTTGTATACTTATGTTTGGCCA 57.645 30.769 0.00 0.00 0.00 5.36
82 83 8.807118 TCATTTTGTATACTTATGTTTGGCCAA 58.193 29.630 16.05 16.05 0.00 4.52
83 84 9.429359 CATTTTGTATACTTATGTTTGGCCAAA 57.571 29.630 27.13 27.13 0.00 3.28
85 86 9.832445 TTTTGTATACTTATGTTTGGCCAAAAA 57.168 25.926 31.92 27.66 31.33 1.94
109 110 4.753233 TGTGGAAGGTTTTTCACACATTG 58.247 39.130 0.00 0.00 45.68 2.82
110 111 4.464244 TGTGGAAGGTTTTTCACACATTGA 59.536 37.500 0.00 0.00 45.68 2.57
111 112 5.128499 TGTGGAAGGTTTTTCACACATTGAT 59.872 36.000 0.00 0.00 45.68 2.57
112 113 5.463061 GTGGAAGGTTTTTCACACATTGATG 59.537 40.000 0.00 0.00 41.62 3.07
113 114 5.128499 TGGAAGGTTTTTCACACATTGATGT 59.872 36.000 0.00 0.00 42.84 3.06
114 115 6.048509 GGAAGGTTTTTCACACATTGATGTT 58.951 36.000 0.00 0.00 39.39 2.71
115 116 6.200854 GGAAGGTTTTTCACACATTGATGTTC 59.799 38.462 0.00 0.00 39.39 3.18
116 117 6.469782 AGGTTTTTCACACATTGATGTTCT 57.530 33.333 0.00 0.00 39.39 3.01
117 118 7.581213 AGGTTTTTCACACATTGATGTTCTA 57.419 32.000 0.00 0.00 39.39 2.10
118 119 8.006298 AGGTTTTTCACACATTGATGTTCTAA 57.994 30.769 0.00 0.00 39.39 2.10
119 120 8.474025 AGGTTTTTCACACATTGATGTTCTAAA 58.526 29.630 0.00 0.00 39.39 1.85
120 121 8.755018 GGTTTTTCACACATTGATGTTCTAAAG 58.245 33.333 0.00 0.00 39.39 1.85
121 122 9.301153 GTTTTTCACACATTGATGTTCTAAAGT 57.699 29.630 0.00 0.00 39.39 2.66
122 123 9.868277 TTTTTCACACATTGATGTTCTAAAGTT 57.132 25.926 0.00 0.00 39.39 2.66
123 124 9.868277 TTTTCACACATTGATGTTCTAAAGTTT 57.132 25.926 0.00 0.00 39.39 2.66
124 125 8.854979 TTCACACATTGATGTTCTAAAGTTTG 57.145 30.769 0.00 0.00 39.39 2.93
125 126 7.995289 TCACACATTGATGTTCTAAAGTTTGT 58.005 30.769 0.00 0.00 39.39 2.83
126 127 8.465999 TCACACATTGATGTTCTAAAGTTTGTT 58.534 29.630 0.00 0.00 39.39 2.83
127 128 9.086336 CACACATTGATGTTCTAAAGTTTGTTT 57.914 29.630 0.00 0.00 39.39 2.83
128 129 9.651913 ACACATTGATGTTCTAAAGTTTGTTTT 57.348 25.926 0.00 0.00 39.39 2.43
133 134 8.810652 TGATGTTCTAAAGTTTGTTTTATGCC 57.189 30.769 0.00 0.00 0.00 4.40
134 135 8.417106 TGATGTTCTAAAGTTTGTTTTATGCCA 58.583 29.630 0.00 0.00 0.00 4.92
135 136 9.255304 GATGTTCTAAAGTTTGTTTTATGCCAA 57.745 29.630 0.00 0.00 0.00 4.52
136 137 8.641499 TGTTCTAAAGTTTGTTTTATGCCAAG 57.359 30.769 0.00 0.00 0.00 3.61
137 138 8.254508 TGTTCTAAAGTTTGTTTTATGCCAAGT 58.745 29.630 0.00 0.00 0.00 3.16
138 139 9.093970 GTTCTAAAGTTTGTTTTATGCCAAGTT 57.906 29.630 0.00 0.00 0.00 2.66
139 140 9.660180 TTCTAAAGTTTGTTTTATGCCAAGTTT 57.340 25.926 0.00 0.00 0.00 2.66
140 141 9.092876 TCTAAAGTTTGTTTTATGCCAAGTTTG 57.907 29.630 0.00 0.00 0.00 2.93
141 142 7.913674 AAAGTTTGTTTTATGCCAAGTTTGA 57.086 28.000 0.00 0.00 0.00 2.69
142 143 7.913674 AAGTTTGTTTTATGCCAAGTTTGAA 57.086 28.000 0.00 0.00 0.00 2.69
143 144 7.538303 AGTTTGTTTTATGCCAAGTTTGAAG 57.462 32.000 0.00 0.00 0.00 3.02
144 145 7.102993 AGTTTGTTTTATGCCAAGTTTGAAGT 58.897 30.769 0.00 0.00 0.00 3.01
145 146 7.277760 AGTTTGTTTTATGCCAAGTTTGAAGTC 59.722 33.333 0.00 0.00 0.00 3.01
146 147 5.596845 TGTTTTATGCCAAGTTTGAAGTCC 58.403 37.500 0.00 0.00 0.00 3.85
147 148 5.127845 TGTTTTATGCCAAGTTTGAAGTCCA 59.872 36.000 0.00 0.00 0.00 4.02
148 149 6.183360 TGTTTTATGCCAAGTTTGAAGTCCAT 60.183 34.615 0.00 0.00 0.00 3.41
149 150 7.014711 TGTTTTATGCCAAGTTTGAAGTCCATA 59.985 33.333 0.00 0.00 0.00 2.74
150 151 7.716799 TTTATGCCAAGTTTGAAGTCCATAT 57.283 32.000 0.00 0.00 0.00 1.78
151 152 5.587388 ATGCCAAGTTTGAAGTCCATATG 57.413 39.130 0.00 0.00 0.00 1.78
152 153 3.193267 TGCCAAGTTTGAAGTCCATATGC 59.807 43.478 0.00 0.00 0.00 3.14
153 154 3.445096 GCCAAGTTTGAAGTCCATATGCT 59.555 43.478 0.00 0.00 0.00 3.79
154 155 4.676196 GCCAAGTTTGAAGTCCATATGCTG 60.676 45.833 0.00 0.00 0.00 4.41
155 156 4.460382 CCAAGTTTGAAGTCCATATGCTGT 59.540 41.667 0.00 0.00 0.00 4.40
156 157 5.047802 CCAAGTTTGAAGTCCATATGCTGTT 60.048 40.000 0.00 0.00 0.00 3.16
157 158 6.449698 CAAGTTTGAAGTCCATATGCTGTTT 58.550 36.000 0.00 0.00 0.00 2.83
158 159 6.259550 AGTTTGAAGTCCATATGCTGTTTC 57.740 37.500 0.00 0.00 0.00 2.78
159 160 5.769662 AGTTTGAAGTCCATATGCTGTTTCA 59.230 36.000 0.00 2.15 0.00 2.69
160 161 6.435277 AGTTTGAAGTCCATATGCTGTTTCAT 59.565 34.615 0.00 0.00 0.00 2.57
161 162 6.839124 TTGAAGTCCATATGCTGTTTCATT 57.161 33.333 0.00 0.00 0.00 2.57
162 163 6.441093 TGAAGTCCATATGCTGTTTCATTC 57.559 37.500 0.00 0.00 0.00 2.67
163 164 5.065090 TGAAGTCCATATGCTGTTTCATTCG 59.935 40.000 0.00 0.00 0.00 3.34
164 165 4.769688 AGTCCATATGCTGTTTCATTCGA 58.230 39.130 0.00 0.00 0.00 3.71
165 166 4.813161 AGTCCATATGCTGTTTCATTCGAG 59.187 41.667 0.00 0.00 0.00 4.04
166 167 4.811024 GTCCATATGCTGTTTCATTCGAGA 59.189 41.667 0.00 0.00 0.00 4.04
167 168 5.050499 GTCCATATGCTGTTTCATTCGAGAG 60.050 44.000 0.00 0.00 0.00 3.20
168 169 5.052481 CCATATGCTGTTTCATTCGAGAGA 58.948 41.667 0.00 0.00 39.20 3.10
204 205 9.448438 AAATTCATGTATTAGTTGTAGAGCACA 57.552 29.630 0.00 0.00 34.51 4.57
205 206 9.448438 AATTCATGTATTAGTTGTAGAGCACAA 57.552 29.630 0.00 0.00 44.97 3.33
215 216 2.819608 TGTAGAGCACAAATCCCAAAGC 59.180 45.455 0.00 0.00 32.95 3.51
216 217 1.999648 AGAGCACAAATCCCAAAGCA 58.000 45.000 0.00 0.00 0.00 3.91
217 218 2.318908 AGAGCACAAATCCCAAAGCAA 58.681 42.857 0.00 0.00 0.00 3.91
218 219 2.901839 AGAGCACAAATCCCAAAGCAAT 59.098 40.909 0.00 0.00 0.00 3.56
219 220 2.997986 GAGCACAAATCCCAAAGCAATG 59.002 45.455 0.00 0.00 0.00 2.82
220 221 2.369532 AGCACAAATCCCAAAGCAATGT 59.630 40.909 0.00 0.00 0.00 2.71
221 222 3.140623 GCACAAATCCCAAAGCAATGTT 58.859 40.909 0.00 0.00 0.00 2.71
222 223 3.058777 GCACAAATCCCAAAGCAATGTTG 60.059 43.478 0.00 0.00 0.00 3.33
223 224 3.499157 CACAAATCCCAAAGCAATGTTGG 59.501 43.478 0.00 0.00 44.42 3.77
229 230 1.341080 CAAAGCAATGTTGGAGGGGT 58.659 50.000 0.00 0.00 0.00 4.95
230 231 1.001181 CAAAGCAATGTTGGAGGGGTG 59.999 52.381 0.00 0.00 0.00 4.61
231 232 0.482446 AAGCAATGTTGGAGGGGTGA 59.518 50.000 0.00 0.00 0.00 4.02
232 233 0.038744 AGCAATGTTGGAGGGGTGAG 59.961 55.000 0.00 0.00 0.00 3.51
233 234 0.967380 GCAATGTTGGAGGGGTGAGG 60.967 60.000 0.00 0.00 0.00 3.86
234 235 0.405585 CAATGTTGGAGGGGTGAGGT 59.594 55.000 0.00 0.00 0.00 3.85
235 236 1.158007 AATGTTGGAGGGGTGAGGTT 58.842 50.000 0.00 0.00 0.00 3.50
236 237 2.041081 CAATGTTGGAGGGGTGAGGTTA 59.959 50.000 0.00 0.00 0.00 2.85
237 238 1.822425 TGTTGGAGGGGTGAGGTTAA 58.178 50.000 0.00 0.00 0.00 2.01
238 239 1.702957 TGTTGGAGGGGTGAGGTTAAG 59.297 52.381 0.00 0.00 0.00 1.85
239 240 1.004394 GTTGGAGGGGTGAGGTTAAGG 59.996 57.143 0.00 0.00 0.00 2.69
240 241 0.549169 TGGAGGGGTGAGGTTAAGGG 60.549 60.000 0.00 0.00 0.00 3.95
241 242 1.279749 GGAGGGGTGAGGTTAAGGGG 61.280 65.000 0.00 0.00 0.00 4.79
242 243 0.549413 GAGGGGTGAGGTTAAGGGGT 60.549 60.000 0.00 0.00 0.00 4.95
243 244 0.103554 AGGGGTGAGGTTAAGGGGTT 60.104 55.000 0.00 0.00 0.00 4.11
244 245 0.330604 GGGGTGAGGTTAAGGGGTTC 59.669 60.000 0.00 0.00 0.00 3.62
245 246 1.069775 GGGTGAGGTTAAGGGGTTCA 58.930 55.000 0.00 0.00 0.00 3.18
246 247 1.426215 GGGTGAGGTTAAGGGGTTCAA 59.574 52.381 0.00 0.00 0.00 2.69
247 248 2.042569 GGGTGAGGTTAAGGGGTTCAAT 59.957 50.000 0.00 0.00 0.00 2.57
248 249 3.089284 GGTGAGGTTAAGGGGTTCAATG 58.911 50.000 0.00 0.00 0.00 2.82
249 250 3.499745 GGTGAGGTTAAGGGGTTCAATGT 60.500 47.826 0.00 0.00 0.00 2.71
250 251 4.263594 GGTGAGGTTAAGGGGTTCAATGTA 60.264 45.833 0.00 0.00 0.00 2.29
251 252 4.941873 GTGAGGTTAAGGGGTTCAATGTAG 59.058 45.833 0.00 0.00 0.00 2.74
252 253 3.945921 GAGGTTAAGGGGTTCAATGTAGC 59.054 47.826 0.00 0.00 0.00 3.58
253 254 3.591977 AGGTTAAGGGGTTCAATGTAGCT 59.408 43.478 0.00 0.00 0.00 3.32
254 255 3.945921 GGTTAAGGGGTTCAATGTAGCTC 59.054 47.826 0.00 0.00 0.00 4.09
255 256 4.566907 GGTTAAGGGGTTCAATGTAGCTCA 60.567 45.833 0.00 0.00 0.00 4.26
256 257 3.806949 AAGGGGTTCAATGTAGCTCAA 57.193 42.857 0.00 0.00 0.00 3.02
257 258 3.073274 AGGGGTTCAATGTAGCTCAAC 57.927 47.619 0.00 0.00 0.00 3.18
258 259 2.092323 GGGGTTCAATGTAGCTCAACC 58.908 52.381 0.00 0.00 0.00 3.77
259 260 2.290960 GGGGTTCAATGTAGCTCAACCT 60.291 50.000 0.00 0.00 0.00 3.50
260 261 3.010420 GGGTTCAATGTAGCTCAACCTC 58.990 50.000 0.00 0.00 0.00 3.85
261 262 3.010420 GGTTCAATGTAGCTCAACCTCC 58.990 50.000 0.00 0.00 0.00 4.30
262 263 3.559171 GGTTCAATGTAGCTCAACCTCCA 60.559 47.826 0.00 0.00 0.00 3.86
263 264 4.265073 GTTCAATGTAGCTCAACCTCCAT 58.735 43.478 0.00 0.00 0.00 3.41
264 265 5.428253 GTTCAATGTAGCTCAACCTCCATA 58.572 41.667 0.00 0.00 0.00 2.74
265 266 5.282055 TCAATGTAGCTCAACCTCCATAG 57.718 43.478 0.00 0.00 0.00 2.23
266 267 4.962362 TCAATGTAGCTCAACCTCCATAGA 59.038 41.667 0.00 0.00 0.00 1.98
267 268 5.425217 TCAATGTAGCTCAACCTCCATAGAA 59.575 40.000 0.00 0.00 0.00 2.10
268 269 5.957771 ATGTAGCTCAACCTCCATAGAAA 57.042 39.130 0.00 0.00 0.00 2.52
269 270 5.086104 TGTAGCTCAACCTCCATAGAAAC 57.914 43.478 0.00 0.00 0.00 2.78
270 271 4.777896 TGTAGCTCAACCTCCATAGAAACT 59.222 41.667 0.00 0.00 0.00 2.66
271 272 4.917906 AGCTCAACCTCCATAGAAACTT 57.082 40.909 0.00 0.00 0.00 2.66
272 273 5.248380 AGCTCAACCTCCATAGAAACTTT 57.752 39.130 0.00 0.00 0.00 2.66
273 274 5.249420 AGCTCAACCTCCATAGAAACTTTC 58.751 41.667 0.00 0.00 0.00 2.62
274 275 5.013599 AGCTCAACCTCCATAGAAACTTTCT 59.986 40.000 9.04 9.04 43.72 2.52
275 276 5.123027 GCTCAACCTCCATAGAAACTTTCTG 59.877 44.000 13.44 0.00 40.94 3.02
276 277 5.560724 TCAACCTCCATAGAAACTTTCTGG 58.439 41.667 13.44 8.49 40.94 3.86
277 278 5.073144 TCAACCTCCATAGAAACTTTCTGGT 59.927 40.000 13.44 8.94 40.94 4.00
278 279 5.167303 ACCTCCATAGAAACTTTCTGGTC 57.833 43.478 13.44 0.00 40.94 4.02
279 280 4.597507 ACCTCCATAGAAACTTTCTGGTCA 59.402 41.667 13.44 0.00 40.94 4.02
280 281 5.251700 ACCTCCATAGAAACTTTCTGGTCAT 59.748 40.000 13.44 0.00 40.94 3.06
281 282 6.183347 CCTCCATAGAAACTTTCTGGTCATT 58.817 40.000 13.44 0.00 40.94 2.57
282 283 6.660949 CCTCCATAGAAACTTTCTGGTCATTT 59.339 38.462 13.44 0.00 40.94 2.32
283 284 7.829211 CCTCCATAGAAACTTTCTGGTCATTTA 59.171 37.037 13.44 0.00 40.94 1.40
284 285 9.231297 CTCCATAGAAACTTTCTGGTCATTTAA 57.769 33.333 13.44 0.00 40.94 1.52
285 286 9.753674 TCCATAGAAACTTTCTGGTCATTTAAT 57.246 29.630 13.44 0.00 40.94 1.40
288 289 7.468141 AGAAACTTTCTGGTCATTTAATCCC 57.532 36.000 3.07 0.00 38.91 3.85
289 290 7.241628 AGAAACTTTCTGGTCATTTAATCCCT 58.758 34.615 3.07 0.00 38.91 4.20
290 291 8.390921 AGAAACTTTCTGGTCATTTAATCCCTA 58.609 33.333 3.07 0.00 38.91 3.53
291 292 8.950007 AAACTTTCTGGTCATTTAATCCCTAA 57.050 30.769 0.00 0.00 0.00 2.69
292 293 8.950007 AACTTTCTGGTCATTTAATCCCTAAA 57.050 30.769 0.00 0.00 34.00 1.85
293 294 8.950007 ACTTTCTGGTCATTTAATCCCTAAAA 57.050 30.769 0.00 0.00 33.20 1.52
294 295 8.803235 ACTTTCTGGTCATTTAATCCCTAAAAC 58.197 33.333 0.00 0.00 33.20 2.43
295 296 6.995511 TCTGGTCATTTAATCCCTAAAACG 57.004 37.500 0.00 0.00 33.20 3.60
296 297 6.713276 TCTGGTCATTTAATCCCTAAAACGA 58.287 36.000 0.00 0.00 33.20 3.85
297 298 6.596497 TCTGGTCATTTAATCCCTAAAACGAC 59.404 38.462 0.00 0.00 36.33 4.34
298 299 6.478129 TGGTCATTTAATCCCTAAAACGACT 58.522 36.000 0.00 0.00 36.80 4.18
299 300 6.943718 TGGTCATTTAATCCCTAAAACGACTT 59.056 34.615 0.00 0.00 36.80 3.01
300 301 7.449086 TGGTCATTTAATCCCTAAAACGACTTT 59.551 33.333 0.00 0.00 36.80 2.66
301 302 7.753580 GGTCATTTAATCCCTAAAACGACTTTG 59.246 37.037 0.00 0.00 36.80 2.77
302 303 8.508875 GTCATTTAATCCCTAAAACGACTTTGA 58.491 33.333 0.00 0.00 35.30 2.69
303 304 9.069082 TCATTTAATCCCTAAAACGACTTTGAA 57.931 29.630 0.00 0.00 33.20 2.69
325 327 4.841443 AAGTTAACCCATCGGACAAAAC 57.159 40.909 0.88 0.00 0.00 2.43
327 329 2.885894 GTTAACCCATCGGACAAAACCA 59.114 45.455 0.00 0.00 0.00 3.67
332 334 2.364002 CCCATCGGACAAAACCAACTTT 59.636 45.455 0.00 0.00 0.00 2.66
343 347 8.888716 GGACAAAACCAACTTTGAAATACAAAT 58.111 29.630 3.23 0.00 45.63 2.32
411 417 3.813166 GACAAGTTAACTAAGTGGCTGCA 59.187 43.478 15.86 0.00 0.00 4.41
421 427 1.228245 GTGGCTGCACCCTGAGAAA 60.228 57.895 0.50 0.00 37.83 2.52
438 444 9.892130 CCCTGAGAAATTATTTGTAACTACTCT 57.108 33.333 0.00 0.00 0.00 3.24
451 457 5.693104 TGTAACTACTCTAAAGTTGCAACGG 59.307 40.000 23.21 14.52 43.56 4.44
464 470 2.468831 TGCAACGGAAAATTGAGCAAC 58.531 42.857 0.00 0.00 0.00 4.17
470 476 4.079253 ACGGAAAATTGAGCAACCATAGT 58.921 39.130 0.00 0.00 0.00 2.12
471 477 4.082787 ACGGAAAATTGAGCAACCATAGTG 60.083 41.667 0.00 0.00 0.00 2.74
485 491 4.589908 ACCATAGTGTTGATGAGGGAAAC 58.410 43.478 0.00 0.00 0.00 2.78
486 492 4.042809 ACCATAGTGTTGATGAGGGAAACA 59.957 41.667 0.00 0.00 0.00 2.83
488 494 5.106157 CCATAGTGTTGATGAGGGAAACAAC 60.106 44.000 0.00 0.00 41.64 3.32
489 495 2.878406 AGTGTTGATGAGGGAAACAACG 59.122 45.455 0.00 0.00 43.39 4.10
490 496 1.606668 TGTTGATGAGGGAAACAACGC 59.393 47.619 0.00 0.00 43.39 4.84
491 497 1.068541 GTTGATGAGGGAAACAACGCC 60.069 52.381 0.00 0.00 34.46 5.68
493 499 1.304134 ATGAGGGAAACAACGCCCC 60.304 57.895 0.00 0.00 45.89 5.80
494 500 2.675423 GAGGGAAACAACGCCCCC 60.675 66.667 0.00 0.00 45.89 5.40
495 501 3.501040 GAGGGAAACAACGCCCCCA 62.501 63.158 0.00 0.00 45.89 4.96
511 517 2.433664 CACCCCCGCACGAAGTAC 60.434 66.667 0.00 0.00 41.61 2.73
577 583 7.688478 AAAAAGCAAATAAGACGTACCAAAC 57.312 32.000 0.00 0.00 0.00 2.93
604 610 8.212995 TGAGCATCAACATATATATGTATGGGG 58.787 37.037 25.95 20.17 45.97 4.96
613 619 8.717717 ACATATATATGTATGGGGATTCAGTGG 58.282 37.037 23.90 0.00 44.54 4.00
634 640 7.503566 CAGTGGACACTAATCATTTGGGATATT 59.496 37.037 4.41 0.00 40.20 1.28
636 642 7.502226 GTGGACACTAATCATTTGGGATATTCA 59.498 37.037 0.00 0.00 0.00 2.57
646 652 6.375174 TCATTTGGGATATTCATGATTAGGCG 59.625 38.462 0.00 0.00 0.00 5.52
647 653 4.220693 TGGGATATTCATGATTAGGCGG 57.779 45.455 0.00 0.00 0.00 6.13
648 654 3.587061 TGGGATATTCATGATTAGGCGGT 59.413 43.478 0.00 0.00 0.00 5.68
724 731 1.656095 GTGAGCAGCTGTGTATTCGTC 59.344 52.381 16.64 0.00 0.00 4.20
728 735 1.724623 GCAGCTGTGTATTCGTCGAAA 59.275 47.619 16.64 0.00 0.00 3.46
957 970 6.982160 ATCTCTCATATCTCTCAGCACTTT 57.018 37.500 0.00 0.00 0.00 2.66
1675 1688 4.330620 GGCATCCATTTGCACTGTTATTTG 59.669 41.667 0.00 0.00 44.59 2.32
2474 2487 2.945984 CGCATGCACCAGTCGTTT 59.054 55.556 19.57 0.00 0.00 3.60
2521 2534 2.622903 TAGGTTTCTCCATCGCCGCG 62.623 60.000 6.39 6.39 39.02 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.608761 AGCATTTAAAATGCATGAACAAATCCT 59.391 29.630 18.49 0.00 46.77 3.24
4 5 7.754625 AGCATTTAAAATGCATGAACAAATCC 58.245 30.769 18.49 0.00 46.77 3.01
53 54 9.503427 GCCAAACATAAGTATACAAAATGAGAC 57.497 33.333 15.12 2.03 0.00 3.36
54 55 8.682710 GGCCAAACATAAGTATACAAAATGAGA 58.317 33.333 15.12 0.00 0.00 3.27
55 56 8.465999 TGGCCAAACATAAGTATACAAAATGAG 58.534 33.333 0.61 7.49 0.00 2.90
56 57 8.354711 TGGCCAAACATAAGTATACAAAATGA 57.645 30.769 0.61 0.00 0.00 2.57
57 58 8.994429 TTGGCCAAACATAAGTATACAAAATG 57.006 30.769 17.98 7.90 0.00 2.32
59 60 9.832445 TTTTTGGCCAAACATAAGTATACAAAA 57.168 25.926 30.43 13.59 33.79 2.44
82 83 6.234177 TGTGTGAAAAACCTTCCACATTTTT 58.766 32.000 0.00 0.00 40.94 1.94
83 84 5.799213 TGTGTGAAAAACCTTCCACATTTT 58.201 33.333 0.00 0.00 40.94 1.82
84 85 5.413309 TGTGTGAAAAACCTTCCACATTT 57.587 34.783 0.00 0.00 40.94 2.32
85 86 5.612725 ATGTGTGAAAAACCTTCCACATT 57.387 34.783 12.12 0.00 40.94 2.71
86 87 5.128499 TCAATGTGTGAAAAACCTTCCACAT 59.872 36.000 12.12 12.12 40.94 3.21
87 88 4.464244 TCAATGTGTGAAAAACCTTCCACA 59.536 37.500 9.61 9.61 37.21 4.17
88 89 5.004922 TCAATGTGTGAAAAACCTTCCAC 57.995 39.130 0.00 0.00 31.51 4.02
89 90 5.128499 ACATCAATGTGTGAAAAACCTTCCA 59.872 36.000 0.00 0.00 40.50 3.53
90 91 5.600696 ACATCAATGTGTGAAAAACCTTCC 58.399 37.500 0.00 0.00 40.50 3.46
91 92 6.980397 AGAACATCAATGTGTGAAAAACCTTC 59.020 34.615 0.00 0.00 41.61 3.46
92 93 6.877236 AGAACATCAATGTGTGAAAAACCTT 58.123 32.000 0.00 0.00 41.61 3.50
93 94 6.469782 AGAACATCAATGTGTGAAAAACCT 57.530 33.333 0.00 0.00 41.61 3.50
94 95 8.641499 TTTAGAACATCAATGTGTGAAAAACC 57.359 30.769 0.00 0.00 41.61 3.27
95 96 9.301153 ACTTTAGAACATCAATGTGTGAAAAAC 57.699 29.630 0.00 0.00 41.61 2.43
96 97 9.868277 AACTTTAGAACATCAATGTGTGAAAAA 57.132 25.926 0.00 0.00 41.61 1.94
97 98 9.868277 AAACTTTAGAACATCAATGTGTGAAAA 57.132 25.926 0.00 0.00 41.61 2.29
98 99 9.299963 CAAACTTTAGAACATCAATGTGTGAAA 57.700 29.630 0.00 0.00 41.61 2.69
99 100 8.465999 ACAAACTTTAGAACATCAATGTGTGAA 58.534 29.630 0.00 0.00 41.61 3.18
100 101 7.995289 ACAAACTTTAGAACATCAATGTGTGA 58.005 30.769 0.00 0.00 41.61 3.58
101 102 8.633075 AACAAACTTTAGAACATCAATGTGTG 57.367 30.769 0.00 0.00 41.61 3.82
102 103 9.651913 AAAACAAACTTTAGAACATCAATGTGT 57.348 25.926 0.00 0.00 41.61 3.72
107 108 9.255304 GGCATAAAACAAACTTTAGAACATCAA 57.745 29.630 0.00 0.00 0.00 2.57
108 109 8.417106 TGGCATAAAACAAACTTTAGAACATCA 58.583 29.630 0.00 0.00 0.00 3.07
109 110 8.810652 TGGCATAAAACAAACTTTAGAACATC 57.189 30.769 0.00 0.00 0.00 3.06
110 111 9.260002 CTTGGCATAAAACAAACTTTAGAACAT 57.740 29.630 0.00 0.00 0.00 2.71
111 112 8.254508 ACTTGGCATAAAACAAACTTTAGAACA 58.745 29.630 0.00 0.00 0.00 3.18
112 113 8.642908 ACTTGGCATAAAACAAACTTTAGAAC 57.357 30.769 0.00 0.00 0.00 3.01
113 114 9.660180 AAACTTGGCATAAAACAAACTTTAGAA 57.340 25.926 0.00 0.00 0.00 2.10
114 115 9.092876 CAAACTTGGCATAAAACAAACTTTAGA 57.907 29.630 0.00 0.00 0.00 2.10
115 116 9.092876 TCAAACTTGGCATAAAACAAACTTTAG 57.907 29.630 0.00 0.00 0.00 1.85
116 117 9.436957 TTCAAACTTGGCATAAAACAAACTTTA 57.563 25.926 0.00 0.00 0.00 1.85
117 118 7.913674 TCAAACTTGGCATAAAACAAACTTT 57.086 28.000 0.00 0.00 0.00 2.66
118 119 7.606073 ACTTCAAACTTGGCATAAAACAAACTT 59.394 29.630 0.00 0.00 0.00 2.66
119 120 7.102993 ACTTCAAACTTGGCATAAAACAAACT 58.897 30.769 0.00 0.00 0.00 2.66
120 121 7.302350 ACTTCAAACTTGGCATAAAACAAAC 57.698 32.000 0.00 0.00 0.00 2.93
121 122 6.536941 GGACTTCAAACTTGGCATAAAACAAA 59.463 34.615 0.00 0.00 0.00 2.83
122 123 6.045955 GGACTTCAAACTTGGCATAAAACAA 58.954 36.000 0.00 0.00 0.00 2.83
123 124 5.127845 TGGACTTCAAACTTGGCATAAAACA 59.872 36.000 0.00 0.00 0.00 2.83
124 125 5.596845 TGGACTTCAAACTTGGCATAAAAC 58.403 37.500 0.00 0.00 0.00 2.43
125 126 5.860941 TGGACTTCAAACTTGGCATAAAA 57.139 34.783 0.00 0.00 0.00 1.52
126 127 7.546358 CATATGGACTTCAAACTTGGCATAAA 58.454 34.615 0.00 0.00 0.00 1.40
127 128 6.405731 GCATATGGACTTCAAACTTGGCATAA 60.406 38.462 4.56 0.00 0.00 1.90
128 129 5.067674 GCATATGGACTTCAAACTTGGCATA 59.932 40.000 4.56 0.00 0.00 3.14
129 130 4.142093 GCATATGGACTTCAAACTTGGCAT 60.142 41.667 4.56 0.00 0.00 4.40
130 131 3.193267 GCATATGGACTTCAAACTTGGCA 59.807 43.478 4.56 0.00 0.00 4.92
131 132 3.445096 AGCATATGGACTTCAAACTTGGC 59.555 43.478 4.56 0.00 0.00 4.52
132 133 4.460382 ACAGCATATGGACTTCAAACTTGG 59.540 41.667 4.56 0.00 0.00 3.61
133 134 5.633830 ACAGCATATGGACTTCAAACTTG 57.366 39.130 4.56 0.00 0.00 3.16
134 135 6.265196 TGAAACAGCATATGGACTTCAAACTT 59.735 34.615 4.56 0.00 0.00 2.66
135 136 5.769662 TGAAACAGCATATGGACTTCAAACT 59.230 36.000 4.56 0.00 0.00 2.66
136 137 6.012658 TGAAACAGCATATGGACTTCAAAC 57.987 37.500 4.56 0.00 0.00 2.93
137 138 6.839124 ATGAAACAGCATATGGACTTCAAA 57.161 33.333 4.56 0.00 32.94 2.69
138 139 6.403527 CGAATGAAACAGCATATGGACTTCAA 60.404 38.462 4.56 0.00 32.94 2.69
139 140 5.065090 CGAATGAAACAGCATATGGACTTCA 59.935 40.000 4.56 4.75 33.41 3.02
140 141 5.294306 TCGAATGAAACAGCATATGGACTTC 59.706 40.000 4.56 0.00 0.00 3.01
141 142 5.185454 TCGAATGAAACAGCATATGGACTT 58.815 37.500 4.56 0.00 0.00 3.01
142 143 4.769688 TCGAATGAAACAGCATATGGACT 58.230 39.130 4.56 0.00 0.00 3.85
143 144 4.811024 TCTCGAATGAAACAGCATATGGAC 59.189 41.667 4.56 0.00 0.00 4.02
144 145 5.022282 TCTCGAATGAAACAGCATATGGA 57.978 39.130 4.56 0.00 0.00 3.41
145 146 5.052481 TCTCTCGAATGAAACAGCATATGG 58.948 41.667 4.56 0.00 0.00 2.74
146 147 6.594284 TTCTCTCGAATGAAACAGCATATG 57.406 37.500 0.00 0.00 0.00 1.78
147 148 7.009568 GTTTCTCTCGAATGAAACAGCATAT 57.990 36.000 25.26 0.00 46.45 1.78
148 149 6.408858 GTTTCTCTCGAATGAAACAGCATA 57.591 37.500 25.26 1.60 46.45 3.14
149 150 5.288543 GTTTCTCTCGAATGAAACAGCAT 57.711 39.130 25.26 0.00 46.45 3.79
150 151 4.732285 GTTTCTCTCGAATGAAACAGCA 57.268 40.909 25.26 2.68 46.45 4.41
178 179 9.448438 TGTGCTCTACAACTAATACATGAATTT 57.552 29.630 0.00 0.00 36.06 1.82
179 180 9.448438 TTGTGCTCTACAACTAATACATGAATT 57.552 29.630 0.00 0.00 44.07 2.17
194 195 2.819608 GCTTTGGGATTTGTGCTCTACA 59.180 45.455 0.00 0.00 37.56 2.74
195 196 2.819608 TGCTTTGGGATTTGTGCTCTAC 59.180 45.455 0.00 0.00 0.00 2.59
196 197 3.153369 TGCTTTGGGATTTGTGCTCTA 57.847 42.857 0.00 0.00 0.00 2.43
197 198 1.999648 TGCTTTGGGATTTGTGCTCT 58.000 45.000 0.00 0.00 0.00 4.09
198 199 2.818130 TTGCTTTGGGATTTGTGCTC 57.182 45.000 0.00 0.00 0.00 4.26
199 200 2.369532 ACATTGCTTTGGGATTTGTGCT 59.630 40.909 0.00 0.00 0.00 4.40
200 201 2.769893 ACATTGCTTTGGGATTTGTGC 58.230 42.857 0.00 0.00 0.00 4.57
201 202 3.499157 CCAACATTGCTTTGGGATTTGTG 59.501 43.478 0.00 0.00 40.03 3.33
202 203 3.390639 TCCAACATTGCTTTGGGATTTGT 59.609 39.130 6.28 0.00 43.38 2.83
203 204 3.998341 CTCCAACATTGCTTTGGGATTTG 59.002 43.478 6.28 0.00 43.38 2.32
204 205 3.008266 CCTCCAACATTGCTTTGGGATTT 59.992 43.478 6.28 0.00 43.38 2.17
205 206 2.568509 CCTCCAACATTGCTTTGGGATT 59.431 45.455 6.28 0.00 43.38 3.01
206 207 2.181975 CCTCCAACATTGCTTTGGGAT 58.818 47.619 6.28 0.00 43.38 3.85
207 208 1.631405 CCTCCAACATTGCTTTGGGA 58.369 50.000 6.28 0.00 43.38 4.37
208 209 0.609662 CCCTCCAACATTGCTTTGGG 59.390 55.000 6.28 0.00 43.38 4.12
209 210 0.609662 CCCCTCCAACATTGCTTTGG 59.390 55.000 0.63 0.63 44.39 3.28
210 211 1.001181 CACCCCTCCAACATTGCTTTG 59.999 52.381 0.00 0.00 0.00 2.77
211 212 1.133199 TCACCCCTCCAACATTGCTTT 60.133 47.619 0.00 0.00 0.00 3.51
212 213 0.482446 TCACCCCTCCAACATTGCTT 59.518 50.000 0.00 0.00 0.00 3.91
213 214 0.038744 CTCACCCCTCCAACATTGCT 59.961 55.000 0.00 0.00 0.00 3.91
214 215 0.967380 CCTCACCCCTCCAACATTGC 60.967 60.000 0.00 0.00 0.00 3.56
215 216 0.405585 ACCTCACCCCTCCAACATTG 59.594 55.000 0.00 0.00 0.00 2.82
216 217 1.158007 AACCTCACCCCTCCAACATT 58.842 50.000 0.00 0.00 0.00 2.71
217 218 2.053747 TAACCTCACCCCTCCAACAT 57.946 50.000 0.00 0.00 0.00 2.71
218 219 1.702957 CTTAACCTCACCCCTCCAACA 59.297 52.381 0.00 0.00 0.00 3.33
219 220 1.004394 CCTTAACCTCACCCCTCCAAC 59.996 57.143 0.00 0.00 0.00 3.77
220 221 1.368374 CCTTAACCTCACCCCTCCAA 58.632 55.000 0.00 0.00 0.00 3.53
221 222 0.549169 CCCTTAACCTCACCCCTCCA 60.549 60.000 0.00 0.00 0.00 3.86
222 223 1.279749 CCCCTTAACCTCACCCCTCC 61.280 65.000 0.00 0.00 0.00 4.30
223 224 0.549413 ACCCCTTAACCTCACCCCTC 60.549 60.000 0.00 0.00 0.00 4.30
224 225 0.103554 AACCCCTTAACCTCACCCCT 60.104 55.000 0.00 0.00 0.00 4.79
225 226 0.330604 GAACCCCTTAACCTCACCCC 59.669 60.000 0.00 0.00 0.00 4.95
226 227 1.069775 TGAACCCCTTAACCTCACCC 58.930 55.000 0.00 0.00 0.00 4.61
227 228 2.963599 TTGAACCCCTTAACCTCACC 57.036 50.000 0.00 0.00 0.00 4.02
228 229 3.763057 ACATTGAACCCCTTAACCTCAC 58.237 45.455 0.00 0.00 0.00 3.51
229 230 4.566907 GCTACATTGAACCCCTTAACCTCA 60.567 45.833 0.00 0.00 0.00 3.86
230 231 3.945921 GCTACATTGAACCCCTTAACCTC 59.054 47.826 0.00 0.00 0.00 3.85
231 232 3.591977 AGCTACATTGAACCCCTTAACCT 59.408 43.478 0.00 0.00 0.00 3.50
232 233 3.945921 GAGCTACATTGAACCCCTTAACC 59.054 47.826 0.00 0.00 0.00 2.85
233 234 4.585879 TGAGCTACATTGAACCCCTTAAC 58.414 43.478 0.00 0.00 0.00 2.01
234 235 4.919774 TGAGCTACATTGAACCCCTTAA 57.080 40.909 0.00 0.00 0.00 1.85
235 236 4.566907 GGTTGAGCTACATTGAACCCCTTA 60.567 45.833 0.00 0.00 0.00 2.69
236 237 3.421844 GTTGAGCTACATTGAACCCCTT 58.578 45.455 0.00 0.00 0.00 3.95
237 238 2.290960 GGTTGAGCTACATTGAACCCCT 60.291 50.000 0.00 0.00 0.00 4.79
238 239 2.092323 GGTTGAGCTACATTGAACCCC 58.908 52.381 0.00 0.00 0.00 4.95
239 240 3.010420 GAGGTTGAGCTACATTGAACCC 58.990 50.000 0.00 0.00 0.00 4.11
240 241 3.010420 GGAGGTTGAGCTACATTGAACC 58.990 50.000 0.00 0.00 0.00 3.62
241 242 3.674997 TGGAGGTTGAGCTACATTGAAC 58.325 45.455 0.00 0.00 0.00 3.18
242 243 4.574674 ATGGAGGTTGAGCTACATTGAA 57.425 40.909 2.12 0.00 0.00 2.69
243 244 4.962362 TCTATGGAGGTTGAGCTACATTGA 59.038 41.667 12.69 12.95 0.00 2.57
244 245 5.282055 TCTATGGAGGTTGAGCTACATTG 57.718 43.478 12.69 11.00 0.00 2.82
245 246 5.957771 TTCTATGGAGGTTGAGCTACATT 57.042 39.130 12.69 0.00 0.00 2.71
246 247 5.426833 AGTTTCTATGGAGGTTGAGCTACAT 59.573 40.000 12.17 12.17 0.00 2.29
247 248 4.777896 AGTTTCTATGGAGGTTGAGCTACA 59.222 41.667 0.00 0.00 0.00 2.74
248 249 5.346181 AGTTTCTATGGAGGTTGAGCTAC 57.654 43.478 0.00 0.00 0.00 3.58
249 250 6.213600 AGAAAGTTTCTATGGAGGTTGAGCTA 59.786 38.462 16.60 0.00 38.49 3.32
250 251 4.917906 AAGTTTCTATGGAGGTTGAGCT 57.082 40.909 0.00 0.00 0.00 4.09
251 252 5.123027 CAGAAAGTTTCTATGGAGGTTGAGC 59.877 44.000 17.62 0.00 38.11 4.26
252 253 5.645497 CCAGAAAGTTTCTATGGAGGTTGAG 59.355 44.000 17.62 1.55 38.11 3.02
253 254 5.073144 ACCAGAAAGTTTCTATGGAGGTTGA 59.927 40.000 23.73 0.00 38.11 3.18
254 255 5.316987 ACCAGAAAGTTTCTATGGAGGTTG 58.683 41.667 23.73 9.05 38.11 3.77
255 256 5.073144 TGACCAGAAAGTTTCTATGGAGGTT 59.927 40.000 23.73 10.52 38.11 3.50
256 257 4.597507 TGACCAGAAAGTTTCTATGGAGGT 59.402 41.667 23.73 21.56 38.11 3.85
257 258 5.165961 TGACCAGAAAGTTTCTATGGAGG 57.834 43.478 23.73 19.13 38.11 4.30
258 259 7.693969 AAATGACCAGAAAGTTTCTATGGAG 57.306 36.000 23.73 10.70 38.11 3.86
259 260 9.753674 ATTAAATGACCAGAAAGTTTCTATGGA 57.246 29.630 23.73 8.62 38.11 3.41
262 263 9.190317 GGGATTAAATGACCAGAAAGTTTCTAT 57.810 33.333 17.62 9.29 38.11 1.98
263 264 8.390921 AGGGATTAAATGACCAGAAAGTTTCTA 58.609 33.333 17.62 3.08 38.11 2.10
264 265 7.241628 AGGGATTAAATGACCAGAAAGTTTCT 58.758 34.615 12.50 12.50 41.70 2.52
265 266 7.468141 AGGGATTAAATGACCAGAAAGTTTC 57.532 36.000 7.57 7.57 0.00 2.78
266 267 8.950007 TTAGGGATTAAATGACCAGAAAGTTT 57.050 30.769 0.00 0.00 0.00 2.66
267 268 8.950007 TTTAGGGATTAAATGACCAGAAAGTT 57.050 30.769 0.00 0.00 0.00 2.66
268 269 8.803235 GTTTTAGGGATTAAATGACCAGAAAGT 58.197 33.333 0.00 0.00 31.57 2.66
269 270 7.968405 CGTTTTAGGGATTAAATGACCAGAAAG 59.032 37.037 0.00 0.00 31.57 2.62
270 271 7.666388 TCGTTTTAGGGATTAAATGACCAGAAA 59.334 33.333 0.00 0.00 31.57 2.52
271 272 7.120138 GTCGTTTTAGGGATTAAATGACCAGAA 59.880 37.037 0.00 0.00 41.26 3.02
272 273 6.596497 GTCGTTTTAGGGATTAAATGACCAGA 59.404 38.462 0.00 0.00 41.26 3.86
273 274 6.598064 AGTCGTTTTAGGGATTAAATGACCAG 59.402 38.462 13.38 0.00 45.09 4.00
274 275 6.478129 AGTCGTTTTAGGGATTAAATGACCA 58.522 36.000 13.38 0.00 45.09 4.02
275 276 6.997239 AGTCGTTTTAGGGATTAAATGACC 57.003 37.500 13.38 0.00 45.09 4.02
276 277 8.508875 TCAAAGTCGTTTTAGGGATTAAATGAC 58.491 33.333 10.41 10.41 44.67 3.06
277 278 8.624367 TCAAAGTCGTTTTAGGGATTAAATGA 57.376 30.769 0.00 0.00 31.57 2.57
278 279 9.685828 TTTCAAAGTCGTTTTAGGGATTAAATG 57.314 29.630 0.00 0.00 31.57 2.32
280 281 9.738832 CTTTTCAAAGTCGTTTTAGGGATTAAA 57.261 29.630 0.00 0.00 0.00 1.52
281 282 8.905850 ACTTTTCAAAGTCGTTTTAGGGATTAA 58.094 29.630 0.00 0.00 45.65 1.40
282 283 8.454570 ACTTTTCAAAGTCGTTTTAGGGATTA 57.545 30.769 0.00 0.00 45.65 1.75
283 284 7.342769 ACTTTTCAAAGTCGTTTTAGGGATT 57.657 32.000 0.00 0.00 45.65 3.01
284 285 6.954487 ACTTTTCAAAGTCGTTTTAGGGAT 57.046 33.333 0.00 0.00 45.65 3.85
294 295 7.943246 TCCGATGGGTTAACTTTTCAAAGTCG 61.943 42.308 5.42 2.91 40.40 4.18
295 296 5.239963 TCCGATGGGTTAACTTTTCAAAGTC 59.760 40.000 5.42 0.00 40.40 3.01
296 297 5.009310 GTCCGATGGGTTAACTTTTCAAAGT 59.991 40.000 5.42 0.00 41.83 2.66
297 298 5.009210 TGTCCGATGGGTTAACTTTTCAAAG 59.991 40.000 5.42 0.00 37.01 2.77
298 299 4.888239 TGTCCGATGGGTTAACTTTTCAAA 59.112 37.500 5.42 0.00 33.83 2.69
299 300 4.462133 TGTCCGATGGGTTAACTTTTCAA 58.538 39.130 5.42 0.00 33.83 2.69
300 301 4.088056 TGTCCGATGGGTTAACTTTTCA 57.912 40.909 5.42 0.31 33.83 2.69
301 302 5.441709 TTTGTCCGATGGGTTAACTTTTC 57.558 39.130 5.42 0.00 33.83 2.29
302 303 5.452216 GGTTTTGTCCGATGGGTTAACTTTT 60.452 40.000 5.42 0.00 33.83 2.27
303 304 4.038282 GGTTTTGTCCGATGGGTTAACTTT 59.962 41.667 5.42 0.00 33.83 2.66
308 309 2.885894 GTTGGTTTTGTCCGATGGGTTA 59.114 45.455 0.00 0.00 33.83 2.85
317 318 7.835634 TTGTATTTCAAAGTTGGTTTTGTCC 57.164 32.000 0.00 0.00 38.77 4.02
383 387 6.378848 AGCCACTTAGTTAACTTGTCCAAAAA 59.621 34.615 14.49 0.00 0.00 1.94
386 390 4.819630 CAGCCACTTAGTTAACTTGTCCAA 59.180 41.667 14.49 0.30 0.00 3.53
389 393 3.813166 TGCAGCCACTTAGTTAACTTGTC 59.187 43.478 14.49 0.00 0.00 3.18
390 394 3.564225 GTGCAGCCACTTAGTTAACTTGT 59.436 43.478 14.49 10.46 38.93 3.16
406 412 4.082026 ACAAATAATTTCTCAGGGTGCAGC 60.082 41.667 7.55 7.55 0.00 5.25
411 417 9.668497 GAGTAGTTACAAATAATTTCTCAGGGT 57.332 33.333 0.00 0.00 0.00 4.34
438 444 4.742659 GCTCAATTTTCCGTTGCAACTTTA 59.257 37.500 26.09 9.40 0.00 1.85
442 448 2.468831 TGCTCAATTTTCCGTTGCAAC 58.531 42.857 19.89 19.89 0.00 4.17
449 455 4.082787 ACACTATGGTTGCTCAATTTTCCG 60.083 41.667 0.00 0.00 0.00 4.30
451 457 6.446318 TCAACACTATGGTTGCTCAATTTTC 58.554 36.000 0.00 0.00 45.98 2.29
464 470 4.588899 TGTTTCCCTCATCAACACTATGG 58.411 43.478 0.00 0.00 0.00 2.74
470 476 1.606668 GCGTTGTTTCCCTCATCAACA 59.393 47.619 0.00 0.00 39.72 3.33
471 477 1.068541 GGCGTTGTTTCCCTCATCAAC 60.069 52.381 0.00 0.00 37.42 3.18
493 499 3.697747 TACTTCGTGCGGGGGTGG 61.698 66.667 0.00 0.00 0.00 4.61
494 500 2.433664 GTACTTCGTGCGGGGGTG 60.434 66.667 0.00 0.00 0.00 4.61
495 501 2.444700 CTTGTACTTCGTGCGGGGGT 62.445 60.000 0.00 0.00 0.00 4.95
500 506 4.440851 TTTGTTACTTGTACTTCGTGCG 57.559 40.909 0.00 0.00 0.00 5.34
501 507 5.981174 TGATTTGTTACTTGTACTTCGTGC 58.019 37.500 0.00 0.00 0.00 5.34
502 508 7.173863 ACTGATTTGTTACTTGTACTTCGTG 57.826 36.000 0.00 0.00 0.00 4.35
503 509 7.781548 AACTGATTTGTTACTTGTACTTCGT 57.218 32.000 0.00 0.00 0.00 3.85
553 559 7.434013 CAGTTTGGTACGTCTTATTTGCTTTTT 59.566 33.333 0.00 0.00 0.00 1.94
554 560 6.915843 CAGTTTGGTACGTCTTATTTGCTTTT 59.084 34.615 0.00 0.00 0.00 2.27
557 563 5.302360 TCAGTTTGGTACGTCTTATTTGCT 58.698 37.500 0.00 0.00 0.00 3.91
577 583 9.269453 CCCATACATATATATGTTGATGCTCAG 57.731 37.037 28.62 15.36 43.99 3.35
593 599 4.913355 TGTCCACTGAATCCCCATACATAT 59.087 41.667 0.00 0.00 0.00 1.78
594 600 4.102524 GTGTCCACTGAATCCCCATACATA 59.897 45.833 0.00 0.00 0.00 2.29
595 601 3.117888 GTGTCCACTGAATCCCCATACAT 60.118 47.826 0.00 0.00 0.00 2.29
596 602 2.238646 GTGTCCACTGAATCCCCATACA 59.761 50.000 0.00 0.00 0.00 2.29
604 610 6.183360 CCCAAATGATTAGTGTCCACTGAATC 60.183 42.308 10.15 13.47 42.52 2.52
613 619 9.288576 TCATGAATATCCCAAATGATTAGTGTC 57.711 33.333 0.00 0.00 0.00 3.67
634 640 1.339535 TGCAACACCGCCTAATCATGA 60.340 47.619 0.00 0.00 0.00 3.07
636 642 2.057137 ATGCAACACCGCCTAATCAT 57.943 45.000 0.00 0.00 0.00 2.45
641 647 1.276705 TCAGTAATGCAACACCGCCTA 59.723 47.619 0.00 0.00 0.00 3.93
643 649 0.878416 TTCAGTAATGCAACACCGCC 59.122 50.000 0.00 0.00 0.00 6.13
646 652 5.104374 CCATGAATTCAGTAATGCAACACC 58.896 41.667 14.54 0.00 34.19 4.16
647 653 5.953183 TCCATGAATTCAGTAATGCAACAC 58.047 37.500 14.54 0.00 34.19 3.32
648 654 6.209192 ACTTCCATGAATTCAGTAATGCAACA 59.791 34.615 14.54 0.00 34.19 3.33
957 970 8.162746 GGGATAGCTAGAAACCTAGAAGTACTA 58.837 40.741 0.00 0.00 36.58 1.82
1738 1751 2.897350 CGCCCCGCTCATTCCTTC 60.897 66.667 0.00 0.00 0.00 3.46
1791 1804 3.062466 CCTCTGACTCGCCGGTCA 61.062 66.667 1.90 7.90 42.96 4.02


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

AutoCloner maintained by Alex Coulton.