Multiple sequence alignment - TraesCS2D01G038500

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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 TraesCS2D01G038500 chr2D 100.000 2457 0 0 1 2457 14128216 14130672 0.000000e+00 4538.0
1 TraesCS2D01G038500 chr2D 79.701 335 54 10 2047 2376 549847977 549848302 1.900000e-56 230.0
2 TraesCS2D01G038500 chr2D 75.500 400 67 20 2047 2442 207246700 207246328 1.510000e-37 167.0
3 TraesCS2D01G038500 chr2D 77.833 203 37 6 1761 1959 470395485 470395287 4.290000e-23 119.0
4 TraesCS2D01G038500 chr2B 91.516 1886 124 17 582 2456 25847816 25849676 0.000000e+00 2564.0
5 TraesCS2D01G038500 chr2B 88.038 744 67 6 1730 2457 25932894 25933631 0.000000e+00 861.0
6 TraesCS2D01G038500 chr2B 78.481 395 74 11 2048 2437 656005717 656006105 5.250000e-62 248.0
7 TraesCS2D01G038500 chr2B 75.810 401 64 22 2047 2442 260649190 260649562 3.250000e-39 172.0
8 TraesCS2D01G038500 chr2A 92.790 1276 63 12 303 1573 16497439 16498690 0.000000e+00 1820.0
9 TraesCS2D01G038500 chr2A 87.500 632 71 6 1831 2456 16498707 16499336 0.000000e+00 723.0
10 TraesCS2D01G038500 chr5A 78.419 468 82 11 907 1360 643028872 643028410 1.110000e-73 287.0
11 TraesCS2D01G038500 chr7D 80.000 390 70 8 2049 2435 99960426 99960810 5.170000e-72 281.0
12 TraesCS2D01G038500 chr7D 78.694 291 53 9 2047 2334 571817390 571817674 4.170000e-43 185.0
13 TraesCS2D01G038500 chr3A 79.695 197 31 9 2236 2430 487442317 487442506 1.530000e-27 134.0
14 TraesCS2D01G038500 chr4B 88.889 45 4 1 120 164 497163765 497163722 1.000000e-03 54.7


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 TraesCS2D01G038500 chr2D 14128216 14130672 2456 False 4538.0 4538 100.000 1 2457 1 chr2D.!!$F1 2456
1 TraesCS2D01G038500 chr2B 25847816 25849676 1860 False 2564.0 2564 91.516 582 2456 1 chr2B.!!$F1 1874
2 TraesCS2D01G038500 chr2B 25932894 25933631 737 False 861.0 861 88.038 1730 2457 1 chr2B.!!$F2 727
3 TraesCS2D01G038500 chr2A 16497439 16499336 1897 False 1271.5 1820 90.145 303 2456 2 chr2A.!!$F1 2153

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
125 126 0.036164 TGGGTTGGTTCCATCACGAG 59.964 55.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2067 2081 0.956902 TGTCCTTGACGGATCGACGA 60.957 55.0 0.0 0.0 45.44 4.2 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
20 21 0.680061 AGTTGACTGGAACGTCCTCC 59.320 55.000 0.00 0.00 37.46 4.30
21 22 0.391597 GTTGACTGGAACGTCCTCCA 59.608 55.000 8.65 8.65 43.45 3.86
22 23 0.391597 TTGACTGGAACGTCCTCCAC 59.608 55.000 4.82 0.00 40.71 4.02
23 24 1.292541 GACTGGAACGTCCTCCACC 59.707 63.158 4.82 0.00 40.71 4.61
24 25 1.458777 ACTGGAACGTCCTCCACCA 60.459 57.895 4.82 0.55 40.71 4.17
25 26 1.004918 CTGGAACGTCCTCCACCAC 60.005 63.158 4.82 0.00 40.71 4.16
26 27 1.458777 TGGAACGTCCTCCACCACT 60.459 57.895 4.82 0.00 40.71 4.00
27 28 0.178955 TGGAACGTCCTCCACCACTA 60.179 55.000 4.82 0.00 40.71 2.74
28 29 0.971386 GGAACGTCCTCCACCACTAA 59.029 55.000 1.23 0.00 35.36 2.24
29 30 1.345415 GGAACGTCCTCCACCACTAAA 59.655 52.381 1.23 0.00 35.36 1.85
30 31 2.410939 GAACGTCCTCCACCACTAAAC 58.589 52.381 0.00 0.00 0.00 2.01
31 32 0.316204 ACGTCCTCCACCACTAAACG 59.684 55.000 0.00 0.00 35.00 3.60
32 33 0.599558 CGTCCTCCACCACTAAACGA 59.400 55.000 0.00 0.00 0.00 3.85
33 34 1.000060 CGTCCTCCACCACTAAACGAA 60.000 52.381 0.00 0.00 0.00 3.85
34 35 2.353406 CGTCCTCCACCACTAAACGAAT 60.353 50.000 0.00 0.00 0.00 3.34
35 36 3.119388 CGTCCTCCACCACTAAACGAATA 60.119 47.826 0.00 0.00 0.00 1.75
36 37 4.441079 CGTCCTCCACCACTAAACGAATAT 60.441 45.833 0.00 0.00 0.00 1.28
37 38 5.048507 GTCCTCCACCACTAAACGAATATC 58.951 45.833 0.00 0.00 0.00 1.63
38 39 4.712829 TCCTCCACCACTAAACGAATATCA 59.287 41.667 0.00 0.00 0.00 2.15
39 40 5.365605 TCCTCCACCACTAAACGAATATCAT 59.634 40.000 0.00 0.00 0.00 2.45
40 41 5.696724 CCTCCACCACTAAACGAATATCATC 59.303 44.000 0.00 0.00 0.00 2.92
41 42 6.228616 TCCACCACTAAACGAATATCATCA 57.771 37.500 0.00 0.00 0.00 3.07
42 43 6.280643 TCCACCACTAAACGAATATCATCAG 58.719 40.000 0.00 0.00 0.00 2.90
43 44 6.097696 TCCACCACTAAACGAATATCATCAGA 59.902 38.462 0.00 0.00 0.00 3.27
44 45 6.761242 CCACCACTAAACGAATATCATCAGAA 59.239 38.462 0.00 0.00 0.00 3.02
45 46 7.279981 CCACCACTAAACGAATATCATCAGAAA 59.720 37.037 0.00 0.00 0.00 2.52
46 47 8.664798 CACCACTAAACGAATATCATCAGAAAA 58.335 33.333 0.00 0.00 0.00 2.29
47 48 9.226606 ACCACTAAACGAATATCATCAGAAAAA 57.773 29.630 0.00 0.00 0.00 1.94
48 49 9.490663 CCACTAAACGAATATCATCAGAAAAAC 57.509 33.333 0.00 0.00 0.00 2.43
85 86 5.493133 AAAAATGCGAACAGTAGTGTCAA 57.507 34.783 3.07 0.00 35.08 3.18
86 87 4.732285 AAATGCGAACAGTAGTGTCAAG 57.268 40.909 3.07 0.00 35.08 3.02
87 88 2.882927 TGCGAACAGTAGTGTCAAGT 57.117 45.000 3.07 0.00 35.08 3.16
88 89 2.739292 TGCGAACAGTAGTGTCAAGTC 58.261 47.619 3.07 0.00 35.08 3.01
89 90 2.361119 TGCGAACAGTAGTGTCAAGTCT 59.639 45.455 3.07 0.00 35.08 3.24
90 91 3.566742 TGCGAACAGTAGTGTCAAGTCTA 59.433 43.478 3.07 0.00 35.08 2.59
91 92 4.159857 GCGAACAGTAGTGTCAAGTCTAG 58.840 47.826 3.07 0.00 35.08 2.43
92 93 4.724303 CGAACAGTAGTGTCAAGTCTAGG 58.276 47.826 3.07 0.00 35.08 3.02
93 94 4.454847 CGAACAGTAGTGTCAAGTCTAGGA 59.545 45.833 3.07 0.00 35.08 2.94
94 95 5.617308 CGAACAGTAGTGTCAAGTCTAGGAC 60.617 48.000 3.07 0.00 35.08 3.85
95 96 4.988029 ACAGTAGTGTCAAGTCTAGGACT 58.012 43.478 0.00 0.00 37.00 3.85
96 97 5.834204 AACAGTAGTGTCAAGTCTAGGACTT 59.166 40.000 3.07 7.06 44.11 3.01
97 98 7.002879 AACAGTAGTGTCAAGTCTAGGACTTA 58.997 38.462 11.80 0.00 42.63 2.24
98 99 7.175293 AACAGTAGTGTCAAGTCTAGGACTTAG 59.825 40.741 11.80 7.68 42.63 2.18
106 107 4.325084 AGTCTAGGACTTAGAGCTTGGT 57.675 45.455 0.00 0.00 40.28 3.67
107 108 4.020543 AGTCTAGGACTTAGAGCTTGGTG 58.979 47.826 0.00 0.00 40.28 4.17
108 109 3.131400 GTCTAGGACTTAGAGCTTGGTGG 59.869 52.174 0.00 0.00 39.05 4.61
109 110 1.280457 AGGACTTAGAGCTTGGTGGG 58.720 55.000 0.00 0.00 0.00 4.61
110 111 0.984995 GGACTTAGAGCTTGGTGGGT 59.015 55.000 0.00 0.00 0.00 4.51
111 112 1.351350 GGACTTAGAGCTTGGTGGGTT 59.649 52.381 0.00 0.00 0.00 4.11
112 113 2.427506 GACTTAGAGCTTGGTGGGTTG 58.572 52.381 0.00 0.00 0.00 3.77
113 114 1.073923 ACTTAGAGCTTGGTGGGTTGG 59.926 52.381 0.00 0.00 0.00 3.77
114 115 1.073923 CTTAGAGCTTGGTGGGTTGGT 59.926 52.381 0.00 0.00 0.00 3.67
115 116 1.145571 TAGAGCTTGGTGGGTTGGTT 58.854 50.000 0.00 0.00 0.00 3.67
116 117 0.178990 AGAGCTTGGTGGGTTGGTTC 60.179 55.000 0.00 0.00 0.00 3.62
117 118 1.152546 AGCTTGGTGGGTTGGTTCC 60.153 57.895 0.00 0.00 0.00 3.62
118 119 1.456705 GCTTGGTGGGTTGGTTCCA 60.457 57.895 0.00 0.00 0.00 3.53
119 120 0.831711 GCTTGGTGGGTTGGTTCCAT 60.832 55.000 0.00 0.00 36.58 3.41
120 121 1.256812 CTTGGTGGGTTGGTTCCATC 58.743 55.000 0.00 0.00 36.58 3.51
121 122 0.558220 TTGGTGGGTTGGTTCCATCA 59.442 50.000 0.00 0.00 43.04 3.07
122 123 0.178975 TGGTGGGTTGGTTCCATCAC 60.179 55.000 0.00 9.99 40.19 3.06
123 124 1.241315 GGTGGGTTGGTTCCATCACG 61.241 60.000 11.29 0.00 35.54 4.35
124 125 0.250553 GTGGGTTGGTTCCATCACGA 60.251 55.000 0.00 0.00 36.58 4.35
125 126 0.036164 TGGGTTGGTTCCATCACGAG 59.964 55.000 0.00 0.00 0.00 4.18
126 127 0.676782 GGGTTGGTTCCATCACGAGG 60.677 60.000 0.00 0.00 0.00 4.63
127 128 0.323629 GGTTGGTTCCATCACGAGGA 59.676 55.000 0.00 0.00 0.00 3.71
128 129 1.271163 GGTTGGTTCCATCACGAGGAA 60.271 52.381 0.00 0.00 42.62 3.36
133 134 1.639722 TTCCATCACGAGGAACCTGA 58.360 50.000 0.00 0.00 40.11 3.86
134 135 1.866015 TCCATCACGAGGAACCTGAT 58.134 50.000 0.00 0.00 30.71 2.90
135 136 1.757118 TCCATCACGAGGAACCTGATC 59.243 52.381 0.00 0.00 30.71 2.92
136 137 1.482182 CCATCACGAGGAACCTGATCA 59.518 52.381 0.00 0.00 0.00 2.92
137 138 2.103771 CCATCACGAGGAACCTGATCAT 59.896 50.000 0.00 0.00 0.00 2.45
138 139 3.388308 CATCACGAGGAACCTGATCATC 58.612 50.000 0.00 0.00 0.00 2.92
139 140 2.739943 TCACGAGGAACCTGATCATCT 58.260 47.619 0.00 0.00 0.00 2.90
140 141 2.428530 TCACGAGGAACCTGATCATCTG 59.571 50.000 0.00 0.00 0.00 2.90
141 142 2.428530 CACGAGGAACCTGATCATCTGA 59.571 50.000 0.00 0.00 0.00 3.27
142 143 2.692557 ACGAGGAACCTGATCATCTGAG 59.307 50.000 0.00 0.00 0.00 3.35
143 144 2.545532 CGAGGAACCTGATCATCTGAGC 60.546 54.545 0.00 0.00 0.00 4.26
144 145 2.699846 GAGGAACCTGATCATCTGAGCT 59.300 50.000 0.00 0.00 0.00 4.09
145 146 3.894427 GAGGAACCTGATCATCTGAGCTA 59.106 47.826 0.00 0.00 0.00 3.32
146 147 3.640967 AGGAACCTGATCATCTGAGCTAC 59.359 47.826 0.00 0.00 0.00 3.58
147 148 3.551863 GGAACCTGATCATCTGAGCTACG 60.552 52.174 0.00 0.00 0.00 3.51
148 149 1.339610 ACCTGATCATCTGAGCTACGC 59.660 52.381 0.00 0.00 0.00 4.42
149 150 1.612950 CCTGATCATCTGAGCTACGCT 59.387 52.381 0.00 0.00 43.88 5.07
159 160 3.498676 AGCTACGCTCAGTTCACAC 57.501 52.632 0.00 0.00 30.62 3.82
160 161 0.962489 AGCTACGCTCAGTTCACACT 59.038 50.000 0.00 0.00 30.62 3.55
161 162 1.341531 AGCTACGCTCAGTTCACACTT 59.658 47.619 0.00 0.00 30.62 3.16
162 163 1.457303 GCTACGCTCAGTTCACACTTG 59.543 52.381 0.00 0.00 0.00 3.16
163 164 1.457303 CTACGCTCAGTTCACACTTGC 59.543 52.381 0.00 0.00 0.00 4.01
164 165 0.461870 ACGCTCAGTTCACACTTGCA 60.462 50.000 0.00 0.00 32.21 4.08
165 166 0.041839 CGCTCAGTTCACACTTGCAC 60.042 55.000 0.00 0.00 32.21 4.57
166 167 1.016627 GCTCAGTTCACACTTGCACA 58.983 50.000 0.00 0.00 32.70 4.57
167 168 1.605710 GCTCAGTTCACACTTGCACAT 59.394 47.619 0.00 0.00 32.70 3.21
168 169 2.603892 GCTCAGTTCACACTTGCACATG 60.604 50.000 0.00 0.00 32.70 3.21
169 170 1.334556 TCAGTTCACACTTGCACATGC 59.665 47.619 0.00 0.00 42.50 4.06
184 185 5.756195 GCACATGCATCTTAGAACCATAA 57.244 39.130 0.00 0.00 41.59 1.90
185 186 5.514279 GCACATGCATCTTAGAACCATAAC 58.486 41.667 0.00 0.00 41.59 1.89
186 187 5.297776 GCACATGCATCTTAGAACCATAACT 59.702 40.000 0.00 0.00 41.59 2.24
187 188 6.512415 GCACATGCATCTTAGAACCATAACTC 60.512 42.308 0.00 0.00 41.59 3.01
188 189 6.539826 CACATGCATCTTAGAACCATAACTCA 59.460 38.462 0.00 0.00 0.00 3.41
189 190 6.765036 ACATGCATCTTAGAACCATAACTCAG 59.235 38.462 0.00 0.00 0.00 3.35
190 191 6.544928 TGCATCTTAGAACCATAACTCAGA 57.455 37.500 0.00 0.00 0.00 3.27
191 192 7.129457 TGCATCTTAGAACCATAACTCAGAT 57.871 36.000 0.00 0.00 30.36 2.90
192 193 6.988580 TGCATCTTAGAACCATAACTCAGATG 59.011 38.462 0.00 0.00 42.66 2.90
193 194 7.147672 TGCATCTTAGAACCATAACTCAGATGA 60.148 37.037 17.02 5.25 42.53 2.92
194 195 7.384660 GCATCTTAGAACCATAACTCAGATGAG 59.615 40.741 17.02 8.30 42.53 2.90
195 196 7.353414 TCTTAGAACCATAACTCAGATGAGG 57.647 40.000 14.09 0.00 46.13 3.86
196 197 7.126061 TCTTAGAACCATAACTCAGATGAGGA 58.874 38.462 14.09 2.39 46.13 3.71
197 198 7.786943 TCTTAGAACCATAACTCAGATGAGGAT 59.213 37.037 14.09 4.56 46.13 3.24
198 199 6.418057 AGAACCATAACTCAGATGAGGATC 57.582 41.667 14.09 1.80 46.13 3.36
199 200 6.142498 AGAACCATAACTCAGATGAGGATCT 58.858 40.000 14.09 3.91 46.13 2.75
200 201 7.301420 AGAACCATAACTCAGATGAGGATCTA 58.699 38.462 14.09 1.32 46.13 1.98
201 202 7.955185 AGAACCATAACTCAGATGAGGATCTAT 59.045 37.037 14.09 3.35 46.13 1.98
202 203 9.249053 GAACCATAACTCAGATGAGGATCTATA 57.751 37.037 14.09 0.00 46.13 1.31
203 204 9.607333 AACCATAACTCAGATGAGGATCTATAA 57.393 33.333 14.09 0.00 46.13 0.98
204 205 9.607333 ACCATAACTCAGATGAGGATCTATAAA 57.393 33.333 14.09 0.00 46.13 1.40
206 207 9.585099 CATAACTCAGATGAGGATCTATAAAGC 57.415 37.037 14.09 0.00 46.13 3.51
207 208 7.609097 AACTCAGATGAGGATCTATAAAGCA 57.391 36.000 14.09 0.00 46.13 3.91
208 209 7.609097 ACTCAGATGAGGATCTATAAAGCAA 57.391 36.000 14.09 0.00 46.13 3.91
209 210 8.204903 ACTCAGATGAGGATCTATAAAGCAAT 57.795 34.615 14.09 0.00 46.13 3.56
210 211 8.658619 ACTCAGATGAGGATCTATAAAGCAATT 58.341 33.333 14.09 0.00 46.13 2.32
211 212 9.153721 CTCAGATGAGGATCTATAAAGCAATTC 57.846 37.037 1.70 0.00 36.75 2.17
212 213 8.878211 TCAGATGAGGATCTATAAAGCAATTCT 58.122 33.333 0.00 0.00 36.75 2.40
213 214 9.504708 CAGATGAGGATCTATAAAGCAATTCTT 57.495 33.333 0.00 0.00 36.75 2.52
214 215 9.723601 AGATGAGGATCTATAAAGCAATTCTTC 57.276 33.333 0.00 0.00 37.15 2.87
215 216 9.723601 GATGAGGATCTATAAAGCAATTCTTCT 57.276 33.333 0.00 0.00 31.79 2.85
217 218 9.553064 TGAGGATCTATAAAGCAATTCTTCTTC 57.447 33.333 0.00 0.00 31.79 2.87
218 219 9.553064 GAGGATCTATAAAGCAATTCTTCTTCA 57.447 33.333 0.00 0.00 32.88 3.02
226 227 6.830873 AAGCAATTCTTCTTCATTAGCACT 57.169 33.333 0.00 0.00 0.00 4.40
227 228 6.192234 AGCAATTCTTCTTCATTAGCACTG 57.808 37.500 0.00 0.00 0.00 3.66
228 229 4.797349 GCAATTCTTCTTCATTAGCACTGC 59.203 41.667 0.00 0.00 0.00 4.40
229 230 5.392811 GCAATTCTTCTTCATTAGCACTGCT 60.393 40.000 8.95 8.95 43.41 4.24
230 231 6.183360 GCAATTCTTCTTCATTAGCACTGCTA 60.183 38.462 6.66 6.66 40.44 3.49
231 232 6.917217 ATTCTTCTTCATTAGCACTGCTAC 57.083 37.500 10.43 0.00 41.12 3.58
232 233 5.405935 TCTTCTTCATTAGCACTGCTACA 57.594 39.130 10.43 3.26 41.12 2.74
233 234 5.982356 TCTTCTTCATTAGCACTGCTACAT 58.018 37.500 10.43 5.32 41.12 2.29
234 235 5.814188 TCTTCTTCATTAGCACTGCTACATG 59.186 40.000 10.43 15.39 41.12 3.21
235 236 5.343307 TCTTCATTAGCACTGCTACATGA 57.657 39.130 20.52 20.52 41.12 3.07
236 237 5.922053 TCTTCATTAGCACTGCTACATGAT 58.078 37.500 22.75 10.21 41.12 2.45
237 238 5.756833 TCTTCATTAGCACTGCTACATGATG 59.243 40.000 22.75 22.93 41.12 3.07
238 239 5.280654 TCATTAGCACTGCTACATGATGA 57.719 39.130 20.52 18.03 41.12 2.92
239 240 5.673514 TCATTAGCACTGCTACATGATGAA 58.326 37.500 20.52 6.49 41.12 2.57
240 241 6.114767 TCATTAGCACTGCTACATGATGAAA 58.885 36.000 20.52 5.95 41.12 2.69
241 242 6.769341 TCATTAGCACTGCTACATGATGAAAT 59.231 34.615 20.52 7.52 41.12 2.17
242 243 4.895224 AGCACTGCTACATGATGAAATG 57.105 40.909 0.21 0.00 36.99 2.32
243 244 3.630769 AGCACTGCTACATGATGAAATGG 59.369 43.478 0.21 0.00 36.99 3.16
244 245 3.379372 GCACTGCTACATGATGAAATGGT 59.621 43.478 0.00 0.00 31.46 3.55
245 246 4.576053 GCACTGCTACATGATGAAATGGTA 59.424 41.667 0.00 0.00 31.46 3.25
246 247 5.240183 GCACTGCTACATGATGAAATGGTAT 59.760 40.000 0.00 0.00 31.46 2.73
247 248 6.427853 GCACTGCTACATGATGAAATGGTATA 59.572 38.462 0.00 0.00 31.46 1.47
248 249 7.041167 GCACTGCTACATGATGAAATGGTATAA 60.041 37.037 0.00 0.00 31.46 0.98
249 250 8.839343 CACTGCTACATGATGAAATGGTATAAA 58.161 33.333 0.00 0.00 31.46 1.40
250 251 9.578576 ACTGCTACATGATGAAATGGTATAAAT 57.421 29.630 0.00 0.00 31.46 1.40
251 252 9.836076 CTGCTACATGATGAAATGGTATAAATG 57.164 33.333 0.00 0.00 31.46 2.32
252 253 9.353431 TGCTACATGATGAAATGGTATAAATGT 57.647 29.630 0.00 0.00 31.46 2.71
253 254 9.831737 GCTACATGATGAAATGGTATAAATGTC 57.168 33.333 0.00 0.00 31.46 3.06
259 260 9.460019 TGATGAAATGGTATAAATGTCAACTGA 57.540 29.630 0.00 0.00 0.00 3.41
262 263 9.685276 TGAAATGGTATAAATGTCAACTGATCT 57.315 29.630 0.00 0.00 0.00 2.75
266 267 9.911788 ATGGTATAAATGTCAACTGATCTTTCT 57.088 29.630 0.00 0.00 0.00 2.52
267 268 9.739276 TGGTATAAATGTCAACTGATCTTTCTT 57.261 29.630 0.00 0.00 0.00 2.52
273 274 8.908786 AATGTCAACTGATCTTTCTTAAGTGA 57.091 30.769 1.63 0.63 32.98 3.41
274 275 7.953158 TGTCAACTGATCTTTCTTAAGTGAG 57.047 36.000 1.63 2.25 32.98 3.51
275 276 7.500992 TGTCAACTGATCTTTCTTAAGTGAGT 58.499 34.615 1.63 0.00 32.98 3.41
276 277 7.653713 TGTCAACTGATCTTTCTTAAGTGAGTC 59.346 37.037 1.63 3.85 32.98 3.36
277 278 7.870445 GTCAACTGATCTTTCTTAAGTGAGTCT 59.130 37.037 1.63 0.00 32.98 3.24
278 279 7.869937 TCAACTGATCTTTCTTAAGTGAGTCTG 59.130 37.037 1.63 8.27 32.98 3.51
279 280 7.296628 ACTGATCTTTCTTAAGTGAGTCTGT 57.703 36.000 1.63 8.74 32.98 3.41
280 281 8.410673 ACTGATCTTTCTTAAGTGAGTCTGTA 57.589 34.615 1.63 0.00 32.98 2.74
281 282 9.030452 ACTGATCTTTCTTAAGTGAGTCTGTAT 57.970 33.333 1.63 0.00 32.98 2.29
282 283 9.868277 CTGATCTTTCTTAAGTGAGTCTGTATT 57.132 33.333 1.63 0.00 32.98 1.89
286 287 9.832445 TCTTTCTTAAGTGAGTCTGTATTTTGT 57.168 29.630 1.63 0.00 32.98 2.83
289 290 8.603242 TCTTAAGTGAGTCTGTATTTTGTTCC 57.397 34.615 1.63 0.00 0.00 3.62
290 291 8.429641 TCTTAAGTGAGTCTGTATTTTGTTCCT 58.570 33.333 1.63 0.00 0.00 3.36
291 292 8.974060 TTAAGTGAGTCTGTATTTTGTTCCTT 57.026 30.769 0.00 0.00 0.00 3.36
299 300 8.947115 AGTCTGTATTTTGTTCCTTATAAGTGC 58.053 33.333 11.50 2.19 0.00 4.40
300 301 8.947115 GTCTGTATTTTGTTCCTTATAAGTGCT 58.053 33.333 11.50 0.00 0.00 4.40
301 302 9.162764 TCTGTATTTTGTTCCTTATAAGTGCTC 57.837 33.333 11.50 0.63 0.00 4.26
341 342 5.072741 ACTATGTGGCATATTTCACCATCC 58.927 41.667 0.94 0.00 35.53 3.51
343 344 3.706183 TGTGGCATATTTCACCATCCAA 58.294 40.909 0.00 0.00 35.53 3.53
443 445 8.995220 GTATAAAATTCTTATATGCACCCGACA 58.005 33.333 0.00 0.00 0.00 4.35
444 446 5.751243 AAATTCTTATATGCACCCGACAC 57.249 39.130 0.00 0.00 0.00 3.67
464 466 7.413657 CCGACACGTTATTCAAACTCCATTTAT 60.414 37.037 0.00 0.00 0.00 1.40
465 467 7.960738 CGACACGTTATTCAAACTCCATTTATT 59.039 33.333 0.00 0.00 0.00 1.40
527 529 1.481772 CAAATCATGGTTTCCGGCCAT 59.518 47.619 2.24 6.28 46.77 4.40
553 555 6.693545 CCTTTGTTAGCACGTTTTAAATGTCA 59.306 34.615 0.00 0.00 0.00 3.58
568 570 3.788227 ATGTCAACCTTAGCAACCTCA 57.212 42.857 0.00 0.00 0.00 3.86
579 581 5.869888 CCTTAGCAACCTCAGTGTACTAAAG 59.130 44.000 0.00 0.00 0.00 1.85
931 938 3.429822 CGCAAGCCATCAATTGAGGAATT 60.430 43.478 21.14 11.91 31.52 2.17
972 979 3.937814 TGTTCTTGTGATCTGCGGTAAT 58.062 40.909 0.00 0.00 0.00 1.89
987 994 3.672511 GCGGTAATGAGAACAAGTCGAGA 60.673 47.826 0.00 0.00 0.00 4.04
1033 1040 0.394352 CATGGTACCCACCCTTCTGC 60.394 60.000 10.07 0.00 45.11 4.26
1056 1063 2.751806 GCTGCTTCTGGCTATTTTCTGT 59.248 45.455 0.00 0.00 42.39 3.41
1092 1099 1.069022 CACAGCAAGGAATGGAACGTG 60.069 52.381 0.00 0.00 0.00 4.49
1167 1174 1.153647 CAAGGTCGGCGATGTGCTA 60.154 57.895 14.79 0.00 45.43 3.49
1180 1187 3.733380 CGATGTGCTAGGTGAGAACTCTG 60.733 52.174 3.51 0.00 34.27 3.35
1182 1189 3.230976 TGTGCTAGGTGAGAACTCTGAA 58.769 45.455 3.51 0.00 34.27 3.02
1183 1190 3.256879 TGTGCTAGGTGAGAACTCTGAAG 59.743 47.826 3.51 0.00 34.27 3.02
1203 1212 9.322773 TCTGAAGATCAAGTGATTAGCTATTTG 57.677 33.333 0.00 0.00 34.37 2.32
1205 1214 8.886719 TGAAGATCAAGTGATTAGCTATTTGTG 58.113 33.333 0.00 0.00 34.37 3.33
1229 1238 7.642978 GTGAATTCTGATATGCAATCTTGTGTC 59.357 37.037 7.05 0.00 0.00 3.67
1243 1254 7.627088 GCAATCTTGTGTCTAACTAATGCATGT 60.627 37.037 0.00 0.00 0.00 3.21
1244 1255 6.726258 TCTTGTGTCTAACTAATGCATGTG 57.274 37.500 0.00 0.00 0.00 3.21
1245 1256 6.230472 TCTTGTGTCTAACTAATGCATGTGT 58.770 36.000 0.00 0.00 0.00 3.72
1465 1476 6.872547 CCATCACTGTCCAATAGATAGACATG 59.127 42.308 0.00 0.00 39.64 3.21
1471 1482 5.485353 TGTCCAATAGATAGACATGATCCCC 59.515 44.000 0.00 0.00 35.67 4.81
1504 1515 4.796830 CGTACATATGCGTGTCTTTGTACT 59.203 41.667 1.58 0.00 38.04 2.73
1524 1535 5.401531 ACTAAGTCTTTAAGGTGCGATCA 57.598 39.130 0.00 0.00 0.00 2.92
1539 1550 3.558418 TGCGATCACATGACAGAATGATG 59.442 43.478 0.00 0.00 39.69 3.07
1574 1586 2.105006 TGATGCTTGGCTCAAGTCTC 57.895 50.000 14.04 11.58 42.77 3.36
1575 1587 1.339438 TGATGCTTGGCTCAAGTCTCC 60.339 52.381 14.04 1.80 42.77 3.71
1577 1589 1.644509 TGCTTGGCTCAAGTCTCCTA 58.355 50.000 14.04 0.00 42.77 2.94
1579 1591 1.552792 GCTTGGCTCAAGTCTCCTACT 59.447 52.381 14.04 0.00 42.77 2.57
1713 1725 1.842562 AGCCAGTGGAAGCATATCACT 59.157 47.619 15.20 0.00 41.81 3.41
2030 2044 9.778741 ACACTAGATACAAGTTTCTTTCATTCA 57.221 29.630 0.00 0.00 0.00 2.57
2035 2049 9.125026 AGATACAAGTTTCTTTCATTCAACTGT 57.875 29.630 0.00 0.00 29.78 3.55
2067 2081 5.680619 TGTGTTAGAATAATTCGAGGCCAT 58.319 37.500 5.01 0.00 34.02 4.40
2102 2116 0.041839 GACAAGCAGTCACACAAGCG 60.042 55.000 4.63 0.00 46.77 4.68
2106 2120 2.881266 GCAGTCACACAAGCGCGAA 61.881 57.895 12.10 0.00 0.00 4.70
2116 2130 1.054348 CAAGCGCGAACAATGACACG 61.054 55.000 12.10 0.00 0.00 4.49
2118 2132 2.202171 CGCGAACAATGACACGGC 60.202 61.111 0.00 0.00 0.00 5.68
2138 2152 4.260212 CGGCGATTTGTTAACGAGATTCAT 60.260 41.667 0.00 0.00 0.00 2.57
2150 2164 4.965814 ACGAGATTCATCAACATGGCTAT 58.034 39.130 0.00 0.00 0.00 2.97
2281 2303 2.366837 TCCGGTCATCCCTGCCAT 60.367 61.111 0.00 0.00 0.00 4.40
2311 2333 2.421670 GGACTGTCCCTCTCGTGATCTA 60.422 54.545 16.14 0.00 0.00 1.98
2319 2345 5.531659 GTCCCTCTCGTGATCTATGTCTTAA 59.468 44.000 0.00 0.00 0.00 1.85
2403 2432 2.209273 CACATGTCCGACTCAAACACA 58.791 47.619 0.00 0.00 0.00 3.72
2407 2436 5.122239 CACATGTCCGACTCAAACACATAAT 59.878 40.000 0.00 0.00 0.00 1.28
2408 2437 6.312672 CACATGTCCGACTCAAACACATAATA 59.687 38.462 0.00 0.00 0.00 0.98
2437 2473 6.037172 CGCTAATTACAAATCCAACTGTAGCT 59.963 38.462 0.00 0.00 30.06 3.32
2449 2485 5.661312 TCCAACTGTAGCTCAACCTATACAT 59.339 40.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.891150 GGAGGACGTTCCAGTCAACTA 59.109 52.381 1.23 0.00 42.62 2.24
1 2 0.680061 GGAGGACGTTCCAGTCAACT 59.320 55.000 1.23 0.00 42.62 3.16
2 3 0.391597 TGGAGGACGTTCCAGTCAAC 59.608 55.000 4.82 0.00 42.24 3.18
3 4 2.829094 TGGAGGACGTTCCAGTCAA 58.171 52.632 4.82 0.00 42.24 3.18
4 5 4.611119 TGGAGGACGTTCCAGTCA 57.389 55.556 4.82 0.00 42.24 3.41
8 9 0.178955 TAGTGGTGGAGGACGTTCCA 60.179 55.000 4.82 4.82 44.84 3.53
9 10 0.971386 TTAGTGGTGGAGGACGTTCC 59.029 55.000 0.00 0.00 37.77 3.62
10 11 2.410939 GTTTAGTGGTGGAGGACGTTC 58.589 52.381 0.00 0.00 0.00 3.95
11 12 1.269936 CGTTTAGTGGTGGAGGACGTT 60.270 52.381 0.00 0.00 0.00 3.99
12 13 0.316204 CGTTTAGTGGTGGAGGACGT 59.684 55.000 0.00 0.00 0.00 4.34
13 14 0.599558 TCGTTTAGTGGTGGAGGACG 59.400 55.000 0.00 0.00 0.00 4.79
14 15 2.825861 TTCGTTTAGTGGTGGAGGAC 57.174 50.000 0.00 0.00 0.00 3.85
15 16 4.712829 TGATATTCGTTTAGTGGTGGAGGA 59.287 41.667 0.00 0.00 0.00 3.71
16 17 5.018539 TGATATTCGTTTAGTGGTGGAGG 57.981 43.478 0.00 0.00 0.00 4.30
17 18 6.280643 TGATGATATTCGTTTAGTGGTGGAG 58.719 40.000 0.00 0.00 0.00 3.86
18 19 6.097696 TCTGATGATATTCGTTTAGTGGTGGA 59.902 38.462 0.00 0.00 0.00 4.02
19 20 6.280643 TCTGATGATATTCGTTTAGTGGTGG 58.719 40.000 0.00 0.00 0.00 4.61
20 21 7.770801 TTCTGATGATATTCGTTTAGTGGTG 57.229 36.000 0.00 0.00 0.00 4.17
21 22 8.786826 TTTTCTGATGATATTCGTTTAGTGGT 57.213 30.769 0.00 0.00 0.00 4.16
22 23 9.490663 GTTTTTCTGATGATATTCGTTTAGTGG 57.509 33.333 0.00 0.00 0.00 4.00
63 64 5.065988 ACTTGACACTACTGTTCGCATTTTT 59.934 36.000 0.00 0.00 0.00 1.94
64 65 4.574828 ACTTGACACTACTGTTCGCATTTT 59.425 37.500 0.00 0.00 0.00 1.82
65 66 4.127171 ACTTGACACTACTGTTCGCATTT 58.873 39.130 0.00 0.00 0.00 2.32
66 67 3.728845 ACTTGACACTACTGTTCGCATT 58.271 40.909 0.00 0.00 0.00 3.56
67 68 3.005897 AGACTTGACACTACTGTTCGCAT 59.994 43.478 0.00 0.00 0.00 4.73
68 69 2.361119 AGACTTGACACTACTGTTCGCA 59.639 45.455 0.00 0.00 0.00 5.10
69 70 3.014604 AGACTTGACACTACTGTTCGC 57.985 47.619 0.00 0.00 0.00 4.70
70 71 4.454847 TCCTAGACTTGACACTACTGTTCG 59.545 45.833 0.00 0.00 0.00 3.95
71 72 5.474189 AGTCCTAGACTTGACACTACTGTTC 59.526 44.000 0.00 0.00 40.28 3.18
72 73 5.386924 AGTCCTAGACTTGACACTACTGTT 58.613 41.667 0.00 0.00 40.28 3.16
73 74 4.988029 AGTCCTAGACTTGACACTACTGT 58.012 43.478 0.00 0.00 40.28 3.55
85 86 4.020543 CACCAAGCTCTAAGTCCTAGACT 58.979 47.826 0.00 0.00 45.64 3.24
86 87 3.131400 CCACCAAGCTCTAAGTCCTAGAC 59.869 52.174 0.00 0.00 32.91 2.59
87 88 3.366396 CCACCAAGCTCTAAGTCCTAGA 58.634 50.000 0.00 0.00 35.27 2.43
88 89 2.432510 CCCACCAAGCTCTAAGTCCTAG 59.567 54.545 0.00 0.00 0.00 3.02
89 90 2.225547 ACCCACCAAGCTCTAAGTCCTA 60.226 50.000 0.00 0.00 0.00 2.94
90 91 1.280457 CCCACCAAGCTCTAAGTCCT 58.720 55.000 0.00 0.00 0.00 3.85
91 92 0.984995 ACCCACCAAGCTCTAAGTCC 59.015 55.000 0.00 0.00 0.00 3.85
92 93 2.427506 CAACCCACCAAGCTCTAAGTC 58.572 52.381 0.00 0.00 0.00 3.01
93 94 1.073923 CCAACCCACCAAGCTCTAAGT 59.926 52.381 0.00 0.00 0.00 2.24
94 95 1.073923 ACCAACCCACCAAGCTCTAAG 59.926 52.381 0.00 0.00 0.00 2.18
95 96 1.145571 ACCAACCCACCAAGCTCTAA 58.854 50.000 0.00 0.00 0.00 2.10
96 97 1.073284 GAACCAACCCACCAAGCTCTA 59.927 52.381 0.00 0.00 0.00 2.43
97 98 0.178990 GAACCAACCCACCAAGCTCT 60.179 55.000 0.00 0.00 0.00 4.09
98 99 1.179174 GGAACCAACCCACCAAGCTC 61.179 60.000 0.00 0.00 0.00 4.09
99 100 1.152546 GGAACCAACCCACCAAGCT 60.153 57.895 0.00 0.00 0.00 3.74
100 101 0.831711 ATGGAACCAACCCACCAAGC 60.832 55.000 0.00 0.00 36.36 4.01
101 102 1.256812 GATGGAACCAACCCACCAAG 58.743 55.000 0.00 0.00 36.36 3.61
102 103 0.558220 TGATGGAACCAACCCACCAA 59.442 50.000 0.00 0.00 36.36 3.67
103 104 0.178975 GTGATGGAACCAACCCACCA 60.179 55.000 0.00 0.00 36.36 4.17
104 105 1.241315 CGTGATGGAACCAACCCACC 61.241 60.000 13.99 0.00 36.36 4.61
105 106 0.250553 TCGTGATGGAACCAACCCAC 60.251 55.000 0.00 6.08 36.36 4.61
106 107 0.036164 CTCGTGATGGAACCAACCCA 59.964 55.000 0.00 0.00 38.19 4.51
107 108 0.676782 CCTCGTGATGGAACCAACCC 60.677 60.000 0.00 0.00 0.00 4.11
108 109 0.323629 TCCTCGTGATGGAACCAACC 59.676 55.000 0.00 0.00 0.00 3.77
109 110 2.178912 TTCCTCGTGATGGAACCAAC 57.821 50.000 0.00 0.00 38.53 3.77
114 115 1.639722 TCAGGTTCCTCGTGATGGAA 58.360 50.000 0.00 0.00 40.85 3.53
115 116 1.866015 ATCAGGTTCCTCGTGATGGA 58.134 50.000 2.92 0.00 45.89 3.41
119 120 2.428530 CAGATGATCAGGTTCCTCGTGA 59.571 50.000 0.09 0.00 43.54 4.35
120 121 2.428530 TCAGATGATCAGGTTCCTCGTG 59.571 50.000 0.09 0.00 0.00 4.35
121 122 2.692557 CTCAGATGATCAGGTTCCTCGT 59.307 50.000 0.09 0.00 0.00 4.18
122 123 2.545532 GCTCAGATGATCAGGTTCCTCG 60.546 54.545 0.09 0.00 0.00 4.63
123 124 2.699846 AGCTCAGATGATCAGGTTCCTC 59.300 50.000 0.09 0.00 0.00 3.71
124 125 2.761809 AGCTCAGATGATCAGGTTCCT 58.238 47.619 0.09 0.00 0.00 3.36
125 126 3.551863 CGTAGCTCAGATGATCAGGTTCC 60.552 52.174 0.09 0.00 0.00 3.62
126 127 3.637432 CGTAGCTCAGATGATCAGGTTC 58.363 50.000 0.09 0.00 0.00 3.62
127 128 3.724508 CGTAGCTCAGATGATCAGGTT 57.275 47.619 0.09 0.00 0.00 3.50
143 144 1.457303 GCAAGTGTGAACTGAGCGTAG 59.543 52.381 0.00 0.00 0.00 3.51
144 145 1.202475 TGCAAGTGTGAACTGAGCGTA 60.202 47.619 0.00 0.00 0.00 4.42
145 146 0.461870 TGCAAGTGTGAACTGAGCGT 60.462 50.000 0.00 0.00 0.00 5.07
146 147 0.041839 GTGCAAGTGTGAACTGAGCG 60.042 55.000 0.00 0.00 29.47 5.03
147 148 1.016627 TGTGCAAGTGTGAACTGAGC 58.983 50.000 0.00 0.00 33.90 4.26
148 149 2.603892 GCATGTGCAAGTGTGAACTGAG 60.604 50.000 0.00 0.00 41.59 3.35
149 150 1.334556 GCATGTGCAAGTGTGAACTGA 59.665 47.619 0.00 0.00 41.59 3.41
150 151 1.762419 GCATGTGCAAGTGTGAACTG 58.238 50.000 0.00 0.00 41.59 3.16
162 163 5.297776 AGTTATGGTTCTAAGATGCATGTGC 59.702 40.000 2.46 0.00 42.50 4.57
163 164 6.539826 TGAGTTATGGTTCTAAGATGCATGTG 59.460 38.462 2.46 0.00 0.00 3.21
164 165 6.653020 TGAGTTATGGTTCTAAGATGCATGT 58.347 36.000 2.46 0.00 0.00 3.21
165 166 6.988580 TCTGAGTTATGGTTCTAAGATGCATG 59.011 38.462 2.46 0.00 0.00 4.06
166 167 7.129457 TCTGAGTTATGGTTCTAAGATGCAT 57.871 36.000 0.00 0.00 0.00 3.96
167 168 6.544928 TCTGAGTTATGGTTCTAAGATGCA 57.455 37.500 0.00 0.00 0.00 3.96
168 169 7.212976 TCATCTGAGTTATGGTTCTAAGATGC 58.787 38.462 12.25 0.00 43.81 3.91
169 170 7.871973 CCTCATCTGAGTTATGGTTCTAAGATG 59.128 40.741 11.30 11.30 44.72 2.90
170 171 7.786943 TCCTCATCTGAGTTATGGTTCTAAGAT 59.213 37.037 6.46 0.00 40.48 2.40
171 172 7.126061 TCCTCATCTGAGTTATGGTTCTAAGA 58.874 38.462 6.46 0.00 40.48 2.10
172 173 7.353414 TCCTCATCTGAGTTATGGTTCTAAG 57.647 40.000 6.46 0.00 40.48 2.18
173 174 7.786943 AGATCCTCATCTGAGTTATGGTTCTAA 59.213 37.037 6.46 0.00 38.03 2.10
174 175 7.301420 AGATCCTCATCTGAGTTATGGTTCTA 58.699 38.462 6.46 0.00 38.03 2.10
175 176 6.142498 AGATCCTCATCTGAGTTATGGTTCT 58.858 40.000 6.46 0.00 38.03 3.01
176 177 6.418057 AGATCCTCATCTGAGTTATGGTTC 57.582 41.667 6.46 0.00 38.03 3.62
177 178 9.607333 TTATAGATCCTCATCTGAGTTATGGTT 57.393 33.333 6.46 0.00 39.90 3.67
178 179 9.607333 TTTATAGATCCTCATCTGAGTTATGGT 57.393 33.333 6.46 0.00 39.90 3.55
180 181 9.585099 GCTTTATAGATCCTCATCTGAGTTATG 57.415 37.037 6.46 0.00 39.90 1.90
181 182 9.319060 TGCTTTATAGATCCTCATCTGAGTTAT 57.681 33.333 6.46 0.15 39.90 1.89
182 183 8.712228 TGCTTTATAGATCCTCATCTGAGTTA 57.288 34.615 6.46 0.00 39.90 2.24
183 184 7.609097 TGCTTTATAGATCCTCATCTGAGTT 57.391 36.000 6.46 0.00 39.90 3.01
184 185 7.609097 TTGCTTTATAGATCCTCATCTGAGT 57.391 36.000 6.46 0.00 39.90 3.41
185 186 9.153721 GAATTGCTTTATAGATCCTCATCTGAG 57.846 37.037 0.00 0.00 39.90 3.35
186 187 8.878211 AGAATTGCTTTATAGATCCTCATCTGA 58.122 33.333 0.00 0.00 39.90 3.27
187 188 9.504708 AAGAATTGCTTTATAGATCCTCATCTG 57.495 33.333 0.00 0.00 35.04 2.90
188 189 9.723601 GAAGAATTGCTTTATAGATCCTCATCT 57.276 33.333 0.00 0.00 38.84 2.90
189 190 9.723601 AGAAGAATTGCTTTATAGATCCTCATC 57.276 33.333 0.00 0.00 36.83 2.92
191 192 9.553064 GAAGAAGAATTGCTTTATAGATCCTCA 57.447 33.333 0.00 0.00 36.83 3.86
192 193 9.553064 TGAAGAAGAATTGCTTTATAGATCCTC 57.447 33.333 0.00 0.00 36.83 3.71
200 201 8.964772 AGTGCTAATGAAGAAGAATTGCTTTAT 58.035 29.630 0.00 0.00 36.83 1.40
201 202 8.239314 CAGTGCTAATGAAGAAGAATTGCTTTA 58.761 33.333 0.00 0.00 36.83 1.85
202 203 7.088905 CAGTGCTAATGAAGAAGAATTGCTTT 58.911 34.615 0.00 0.00 36.83 3.51
203 204 6.618811 CAGTGCTAATGAAGAAGAATTGCTT 58.381 36.000 0.00 0.00 40.25 3.91
204 205 5.392811 GCAGTGCTAATGAAGAAGAATTGCT 60.393 40.000 8.18 0.00 0.00 3.91
205 206 4.797349 GCAGTGCTAATGAAGAAGAATTGC 59.203 41.667 8.18 0.00 0.00 3.56
206 207 6.192234 AGCAGTGCTAATGAAGAAGAATTG 57.808 37.500 18.11 0.00 36.99 2.32
207 208 6.881065 TGTAGCAGTGCTAATGAAGAAGAATT 59.119 34.615 26.04 0.00 43.07 2.17
208 209 6.409704 TGTAGCAGTGCTAATGAAGAAGAAT 58.590 36.000 26.04 0.00 43.07 2.40
209 210 5.793817 TGTAGCAGTGCTAATGAAGAAGAA 58.206 37.500 26.04 0.00 43.07 2.52
210 211 5.405935 TGTAGCAGTGCTAATGAAGAAGA 57.594 39.130 26.04 0.00 43.07 2.87
211 212 5.814188 TCATGTAGCAGTGCTAATGAAGAAG 59.186 40.000 28.56 15.84 43.07 2.85
212 213 5.733676 TCATGTAGCAGTGCTAATGAAGAA 58.266 37.500 28.56 16.90 43.07 2.52
213 214 5.343307 TCATGTAGCAGTGCTAATGAAGA 57.657 39.130 28.56 19.93 43.07 2.87
214 215 5.756833 TCATCATGTAGCAGTGCTAATGAAG 59.243 40.000 31.23 28.59 43.07 3.02
215 216 5.673514 TCATCATGTAGCAGTGCTAATGAA 58.326 37.500 31.23 22.19 43.07 2.57
216 217 5.280654 TCATCATGTAGCAGTGCTAATGA 57.719 39.130 30.50 30.50 43.07 2.57
217 218 5.996669 TTCATCATGTAGCAGTGCTAATG 57.003 39.130 26.04 25.74 43.07 1.90
218 219 6.016527 CCATTTCATCATGTAGCAGTGCTAAT 60.017 38.462 26.04 17.56 43.07 1.73
219 220 5.297527 CCATTTCATCATGTAGCAGTGCTAA 59.702 40.000 26.04 16.18 43.07 3.09
220 221 4.818005 CCATTTCATCATGTAGCAGTGCTA 59.182 41.667 21.00 21.00 40.44 3.49
221 222 3.630769 CCATTTCATCATGTAGCAGTGCT 59.369 43.478 23.44 23.44 43.41 4.40
222 223 3.379372 ACCATTTCATCATGTAGCAGTGC 59.621 43.478 7.13 7.13 0.00 4.40
223 224 6.872628 ATACCATTTCATCATGTAGCAGTG 57.127 37.500 0.00 0.00 0.00 3.66
224 225 8.978874 TTTATACCATTTCATCATGTAGCAGT 57.021 30.769 0.00 0.00 0.00 4.40
225 226 9.836076 CATTTATACCATTTCATCATGTAGCAG 57.164 33.333 0.00 0.00 0.00 4.24
226 227 9.353431 ACATTTATACCATTTCATCATGTAGCA 57.647 29.630 0.00 0.00 0.00 3.49
227 228 9.831737 GACATTTATACCATTTCATCATGTAGC 57.168 33.333 0.00 0.00 0.00 3.58
233 234 9.460019 TCAGTTGACATTTATACCATTTCATCA 57.540 29.630 0.00 0.00 0.00 3.07
236 237 9.685276 AGATCAGTTGACATTTATACCATTTCA 57.315 29.630 0.00 0.00 0.00 2.69
240 241 9.911788 AGAAAGATCAGTTGACATTTATACCAT 57.088 29.630 0.00 0.00 0.00 3.55
241 242 9.739276 AAGAAAGATCAGTTGACATTTATACCA 57.261 29.630 0.00 0.00 0.00 3.25
247 248 9.342308 TCACTTAAGAAAGATCAGTTGACATTT 57.658 29.630 10.09 0.00 36.50 2.32
248 249 8.908786 TCACTTAAGAAAGATCAGTTGACATT 57.091 30.769 10.09 0.00 36.50 2.71
249 250 8.153550 ACTCACTTAAGAAAGATCAGTTGACAT 58.846 33.333 10.09 0.00 36.50 3.06
250 251 7.500992 ACTCACTTAAGAAAGATCAGTTGACA 58.499 34.615 10.09 0.00 36.50 3.58
251 252 7.870445 AGACTCACTTAAGAAAGATCAGTTGAC 59.130 37.037 10.09 0.00 36.50 3.18
252 253 7.869937 CAGACTCACTTAAGAAAGATCAGTTGA 59.130 37.037 10.09 0.00 36.50 3.18
253 254 7.655328 ACAGACTCACTTAAGAAAGATCAGTTG 59.345 37.037 10.09 0.00 36.50 3.16
254 255 7.731054 ACAGACTCACTTAAGAAAGATCAGTT 58.269 34.615 10.09 0.00 36.50 3.16
255 256 7.296628 ACAGACTCACTTAAGAAAGATCAGT 57.703 36.000 10.09 6.59 36.50 3.41
256 257 9.868277 AATACAGACTCACTTAAGAAAGATCAG 57.132 33.333 10.09 6.09 36.50 2.90
260 261 9.832445 ACAAAATACAGACTCACTTAAGAAAGA 57.168 29.630 10.09 3.37 36.50 2.52
263 264 9.052759 GGAACAAAATACAGACTCACTTAAGAA 57.947 33.333 10.09 0.00 0.00 2.52
264 265 8.429641 AGGAACAAAATACAGACTCACTTAAGA 58.570 33.333 10.09 0.00 0.00 2.10
265 266 8.608844 AGGAACAAAATACAGACTCACTTAAG 57.391 34.615 0.00 0.00 0.00 1.85
266 267 8.974060 AAGGAACAAAATACAGACTCACTTAA 57.026 30.769 0.00 0.00 0.00 1.85
273 274 8.947115 GCACTTATAAGGAACAAAATACAGACT 58.053 33.333 16.73 0.00 0.00 3.24
274 275 8.947115 AGCACTTATAAGGAACAAAATACAGAC 58.053 33.333 16.73 0.00 0.00 3.51
275 276 9.162764 GAGCACTTATAAGGAACAAAATACAGA 57.837 33.333 16.73 0.00 0.00 3.41
276 277 8.946085 TGAGCACTTATAAGGAACAAAATACAG 58.054 33.333 16.73 0.00 0.00 2.74
277 278 8.726988 GTGAGCACTTATAAGGAACAAAATACA 58.273 33.333 16.73 1.25 0.00 2.29
278 279 8.947115 AGTGAGCACTTATAAGGAACAAAATAC 58.053 33.333 16.73 4.47 38.83 1.89
279 280 8.946085 CAGTGAGCACTTATAAGGAACAAAATA 58.054 33.333 16.73 0.00 40.20 1.40
280 281 7.094205 CCAGTGAGCACTTATAAGGAACAAAAT 60.094 37.037 16.73 0.00 40.20 1.82
281 282 6.206634 CCAGTGAGCACTTATAAGGAACAAAA 59.793 38.462 16.73 0.00 40.20 2.44
282 283 5.705441 CCAGTGAGCACTTATAAGGAACAAA 59.295 40.000 16.73 0.00 40.20 2.83
283 284 5.221843 ACCAGTGAGCACTTATAAGGAACAA 60.222 40.000 16.73 0.00 40.20 2.83
284 285 4.286032 ACCAGTGAGCACTTATAAGGAACA 59.714 41.667 16.73 8.24 40.20 3.18
285 286 4.833390 ACCAGTGAGCACTTATAAGGAAC 58.167 43.478 16.73 5.62 40.20 3.62
286 287 5.012664 TCAACCAGTGAGCACTTATAAGGAA 59.987 40.000 16.73 0.00 40.20 3.36
287 288 4.530553 TCAACCAGTGAGCACTTATAAGGA 59.469 41.667 16.73 0.00 40.20 3.36
288 289 4.631813 GTCAACCAGTGAGCACTTATAAGG 59.368 45.833 16.73 6.96 40.20 2.69
289 290 4.327357 CGTCAACCAGTGAGCACTTATAAG 59.673 45.833 11.05 11.05 40.20 1.73
290 291 4.242475 CGTCAACCAGTGAGCACTTATAA 58.758 43.478 0.00 0.00 40.20 0.98
291 292 3.368013 CCGTCAACCAGTGAGCACTTATA 60.368 47.826 0.00 0.00 40.20 0.98
292 293 2.612972 CCGTCAACCAGTGAGCACTTAT 60.613 50.000 0.00 0.00 40.20 1.73
293 294 1.270094 CCGTCAACCAGTGAGCACTTA 60.270 52.381 0.00 0.00 40.20 2.24
294 295 0.532862 CCGTCAACCAGTGAGCACTT 60.533 55.000 0.00 0.00 40.20 3.16
295 296 1.069765 CCGTCAACCAGTGAGCACT 59.930 57.895 0.00 0.00 43.61 4.40
296 297 0.032952 TACCGTCAACCAGTGAGCAC 59.967 55.000 0.00 0.00 36.74 4.40
297 298 0.753867 TTACCGTCAACCAGTGAGCA 59.246 50.000 0.00 0.00 36.74 4.26
298 299 1.873698 TTTACCGTCAACCAGTGAGC 58.126 50.000 0.00 0.00 36.74 4.26
299 300 3.463944 AGTTTTACCGTCAACCAGTGAG 58.536 45.455 0.00 0.00 36.74 3.51
300 301 3.547054 AGTTTTACCGTCAACCAGTGA 57.453 42.857 0.00 0.00 0.00 3.41
301 302 4.753107 ACATAGTTTTACCGTCAACCAGTG 59.247 41.667 0.00 0.00 0.00 3.66
435 437 2.803956 AGTTTGAATAACGTGTCGGGTG 59.196 45.455 0.00 0.00 0.00 4.61
469 471 9.426837 CCAAATCAGTTGACATTGACATAAAAT 57.573 29.630 9.73 0.00 39.87 1.82
470 472 7.871973 CCCAAATCAGTTGACATTGACATAAAA 59.128 33.333 9.73 0.00 39.87 1.52
471 473 7.015098 ACCCAAATCAGTTGACATTGACATAAA 59.985 33.333 9.73 0.00 39.87 1.40
472 474 6.493115 ACCCAAATCAGTTGACATTGACATAA 59.507 34.615 9.73 0.00 39.87 1.90
473 475 6.009589 ACCCAAATCAGTTGACATTGACATA 58.990 36.000 9.73 0.00 39.87 2.29
474 476 4.834496 ACCCAAATCAGTTGACATTGACAT 59.166 37.500 9.73 0.00 39.87 3.06
475 477 4.214310 ACCCAAATCAGTTGACATTGACA 58.786 39.130 9.73 0.00 39.87 3.58
476 478 4.853924 ACCCAAATCAGTTGACATTGAC 57.146 40.909 9.73 0.00 39.87 3.18
477 479 5.240623 GTGTACCCAAATCAGTTGACATTGA 59.759 40.000 9.73 0.00 39.87 2.57
527 529 6.797454 ACATTTAAAACGTGCTAACAAAGGA 58.203 32.000 0.00 0.00 0.00 3.36
553 555 3.646637 AGTACACTGAGGTTGCTAAGGTT 59.353 43.478 0.00 0.00 0.00 3.50
568 570 9.331282 GGAATGCAGAAATATCTTTAGTACACT 57.669 33.333 0.00 0.00 32.03 3.55
691 696 8.202137 AGGATGCATGAATTTATTTCCTTCTTG 58.798 33.333 2.46 0.00 33.04 3.02
706 711 3.069016 GCAAATGGATGAGGATGCATGAA 59.931 43.478 2.46 0.00 39.57 2.57
707 712 2.626266 GCAAATGGATGAGGATGCATGA 59.374 45.455 2.46 0.00 39.57 3.07
708 713 2.364002 TGCAAATGGATGAGGATGCATG 59.636 45.455 2.46 0.00 39.57 4.06
889 896 2.163815 CGTTCGGTGAAGGACATCTACT 59.836 50.000 0.00 0.00 30.17 2.57
891 898 1.135199 GCGTTCGGTGAAGGACATCTA 60.135 52.381 3.64 0.00 30.17 1.98
895 902 0.878523 CTTGCGTTCGGTGAAGGACA 60.879 55.000 3.64 0.00 30.17 4.02
931 938 8.050778 AGAACAACAAAATGAAACAGTAGTCA 57.949 30.769 0.00 0.00 0.00 3.41
972 979 4.360563 GTGTTTCTCTCGACTTGTTCTCA 58.639 43.478 0.00 0.00 0.00 3.27
1092 1099 4.530857 CATCCGTCCTGGCGACCC 62.531 72.222 11.24 0.00 38.36 4.46
1167 1174 4.837860 ACTTGATCTTCAGAGTTCTCACCT 59.162 41.667 2.64 0.00 0.00 4.00
1180 1187 9.102757 TCACAAATAGCTAATCACTTGATCTTC 57.897 33.333 0.00 0.00 32.75 2.87
1182 1189 9.624373 ATTCACAAATAGCTAATCACTTGATCT 57.376 29.630 0.00 0.00 32.75 2.75
1203 1212 7.478322 ACACAAGATTGCATATCAGAATTCAC 58.522 34.615 8.44 0.00 0.00 3.18
1205 1214 7.928103 AGACACAAGATTGCATATCAGAATTC 58.072 34.615 0.00 0.00 0.00 2.17
1218 1227 7.695201 CACATGCATTAGTTAGACACAAGATTG 59.305 37.037 0.00 0.00 0.00 2.67
1229 1238 7.595311 TGAACACTACACATGCATTAGTTAG 57.405 36.000 6.78 3.97 0.00 2.34
1243 1254 4.409718 TGCCTTGTACTTGAACACTACA 57.590 40.909 0.00 0.00 0.00 2.74
1244 1255 5.941948 ATTGCCTTGTACTTGAACACTAC 57.058 39.130 0.00 0.00 0.00 2.73
1245 1256 5.278266 GCAATTGCCTTGTACTTGAACACTA 60.278 40.000 20.06 0.00 37.18 2.74
1465 1476 5.934402 ATGTACGTATCATAAGGGGGATC 57.066 43.478 0.00 0.00 0.00 3.36
1471 1482 6.090783 ACACGCATATGTACGTATCATAAGG 58.909 40.000 16.45 13.69 41.32 2.69
1504 1515 5.142061 TGTGATCGCACCTTAAAGACTTA 57.858 39.130 4.45 0.00 44.51 2.24
1524 1535 3.639672 TCTGCCATCATTCTGTCATGT 57.360 42.857 0.00 0.00 0.00 3.21
1539 1550 6.257193 CCAAGCATCAATTTATTTCTTCTGCC 59.743 38.462 0.00 0.00 0.00 4.85
1574 1586 9.436957 ACATGTTGAAGATACTAAACAAGTAGG 57.563 33.333 0.00 0.00 43.90 3.18
1585 1597 9.342308 TCTTGAAAGAAACATGTTGAAGATACT 57.658 29.630 12.82 0.00 30.73 2.12
1586 1598 9.387123 GTCTTGAAAGAAACATGTTGAAGATAC 57.613 33.333 12.82 2.16 36.68 2.24
1587 1599 9.342308 AGTCTTGAAAGAAACATGTTGAAGATA 57.658 29.630 12.82 0.00 36.68 1.98
1588 1600 8.133627 CAGTCTTGAAAGAAACATGTTGAAGAT 58.866 33.333 12.82 0.00 36.68 2.40
1589 1601 7.336679 TCAGTCTTGAAAGAAACATGTTGAAGA 59.663 33.333 12.82 9.85 36.68 2.87
1590 1602 7.475015 TCAGTCTTGAAAGAAACATGTTGAAG 58.525 34.615 12.82 7.86 36.68 3.02
1663 1675 6.072175 CGAACAGATATTGGTCCCTTCAAAAA 60.072 38.462 0.00 0.00 40.61 1.94
1670 1682 2.759355 TCCGAACAGATATTGGTCCCT 58.241 47.619 0.00 0.00 40.61 4.20
1713 1725 6.418101 ACCAACTAGTCGTATACTTCCACTA 58.582 40.000 0.00 1.90 39.80 2.74
1885 1898 4.749598 GCCGAAACATTCACCTGAAATTTT 59.250 37.500 0.00 0.00 37.61 1.82
1886 1899 4.306600 GCCGAAACATTCACCTGAAATTT 58.693 39.130 0.00 0.00 37.61 1.82
2030 2044 9.787435 TTATTCTAACACAAGGTATTGACAGTT 57.213 29.630 0.00 0.00 38.83 3.16
2035 2049 9.878667 TCGAATTATTCTAACACAAGGTATTGA 57.121 29.630 3.34 0.00 38.83 2.57
2067 2081 0.956902 TGTCCTTGACGGATCGACGA 60.957 55.000 0.00 0.00 45.44 4.20
2102 2116 1.966493 ATCGCCGTGTCATTGTTCGC 61.966 55.000 0.00 0.00 0.00 4.70
2106 2120 1.234821 ACAAATCGCCGTGTCATTGT 58.765 45.000 0.00 0.00 0.00 2.71
2116 2130 4.593597 TGAATCTCGTTAACAAATCGCC 57.406 40.909 6.39 0.00 0.00 5.54
2118 2132 7.233689 TGTTGATGAATCTCGTTAACAAATCG 58.766 34.615 6.39 0.00 38.42 3.34
2138 2152 3.901222 TCCCGAAGATATAGCCATGTTGA 59.099 43.478 0.00 0.00 0.00 3.18
2150 2164 3.889538 CCTGTAGTCATGTCCCGAAGATA 59.110 47.826 0.00 0.00 0.00 1.98
2225 2247 4.427661 GAGCGCTGTCTCGTGGCT 62.428 66.667 18.48 0.00 36.51 4.75
2407 2436 7.988599 ACAGTTGGATTTGTAATTAGCGGTATA 59.011 33.333 0.00 0.00 0.00 1.47
2408 2437 6.826741 ACAGTTGGATTTGTAATTAGCGGTAT 59.173 34.615 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.