Multiple sequence alignment - TraesCS4D01G144300

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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 TraesCS4D01G144300 chr4D 100.000 3241 0 0 1 3241 132293523 132290283 0.000000e+00 5986
1 TraesCS4D01G144300 chr4D 93.191 235 16 0 1 235 360461570 360461336 2.390000e-91 346
2 TraesCS4D01G144300 chr4A 94.164 2296 71 17 223 2476 429979264 429981538 0.000000e+00 3439
3 TraesCS4D01G144300 chr4A 93.382 136 8 1 2895 3030 429982222 429982356 1.970000e-47 200
4 TraesCS4D01G144300 chr4A 84.422 199 6 4 2542 2715 429982034 429982232 4.300000e-39 172
5 TraesCS4D01G144300 chr4B 94.111 1800 55 19 641 2409 164917909 164919688 0.000000e+00 2689
6 TraesCS4D01G144300 chr4B 86.018 329 36 4 2908 3228 164922416 164922742 8.610000e-91 344
7 TraesCS4D01G144300 chr4B 91.089 202 9 1 237 429 164916757 164916958 6.890000e-67 265
8 TraesCS4D01G144300 chr4B 89.474 171 15 2 3026 3195 665401249 665401417 2.530000e-51 213
9 TraesCS4D01G144300 chr4B 85.492 193 17 10 2712 2898 159604569 159604382 1.190000e-44 191
10 TraesCS4D01G144300 chr4B 83.978 181 14 8 447 626 164917345 164917511 3.350000e-35 159
11 TraesCS4D01G144300 chr3D 94.043 235 14 0 1 235 548395323 548395557 1.110000e-94 357
12 TraesCS4D01G144300 chr3D 93.617 235 15 0 1 235 586210140 586210374 5.140000e-93 351
13 TraesCS4D01G144300 chr5D 93.617 235 14 1 1 235 475353716 475353949 1.850000e-92 350
14 TraesCS4D01G144300 chr5D 92.827 237 17 0 1 237 275166132 275165896 8.610000e-91 344
15 TraesCS4D01G144300 chr5D 91.124 169 15 0 3025 3193 230416827 230416995 2.520000e-56 230
16 TraesCS4D01G144300 chr5D 75.497 302 47 18 1098 1395 114600165 114599887 4.390000e-24 122
17 TraesCS4D01G144300 chr1D 93.277 238 15 1 4 241 66325998 66326234 1.850000e-92 350
18 TraesCS4D01G144300 chr1D 86.782 174 17 6 2726 2895 7993413 7993242 4.270000e-44 189
19 TraesCS4D01G144300 chrUn 92.917 240 15 2 1 239 47932830 47933068 6.660000e-92 348
20 TraesCS4D01G144300 chr5A 92.116 241 18 1 1 241 99426785 99426546 4.010000e-89 339
21 TraesCS4D01G144300 chr5A 75.497 302 47 18 1098 1395 119862342 119862064 4.390000e-24 122
22 TraesCS4D01G144300 chr7D 91.429 245 21 0 1 245 55574600 55574356 1.440000e-88 337
23 TraesCS4D01G144300 chr7D 90.854 164 15 0 3027 3190 47121287 47121450 1.510000e-53 220
24 TraesCS4D01G144300 chr7D 87.432 183 18 4 2716 2895 161459242 161459062 4.240000e-49 206
25 TraesCS4D01G144300 chr2D 93.923 181 7 2 3014 3194 111572289 111572465 1.480000e-68 270
26 TraesCS4D01G144300 chr2D 84.574 188 19 7 2726 2905 609579799 609579614 9.240000e-41 178
27 TraesCS4D01G144300 chr2D 84.409 186 20 7 2713 2895 618333128 618333307 1.200000e-39 174
28 TraesCS4D01G144300 chr6D 95.758 165 7 0 3029 3193 457260031 457260195 1.920000e-67 267
29 TraesCS4D01G144300 chr6D 89.326 178 17 2 3028 3203 467084181 467084004 4.210000e-54 222
30 TraesCS4D01G144300 chr6D 83.684 190 26 5 2715 2901 167226492 167226305 1.200000e-39 174
31 TraesCS4D01G144300 chr1B 90.751 173 16 0 3025 3197 53070120 53070292 6.990000e-57 231
32 TraesCS4D01G144300 chr6B 88.824 170 19 0 3023 3192 40457225 40457394 3.280000e-50 209
33 TraesCS4D01G144300 chr1A 86.957 184 18 5 2714 2895 71725814 71725635 5.480000e-48 202
34 TraesCS4D01G144300 chr3B 86.559 186 20 4 2716 2898 52435354 52435171 1.970000e-47 200
35 TraesCS4D01G144300 chr3A 83.168 202 23 11 2708 2905 447565594 447565400 1.200000e-39 174


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 TraesCS4D01G144300 chr4D 132290283 132293523 3240 True 5986.000000 5986 100.000 1 3241 1 chr4D.!!$R1 3240
1 TraesCS4D01G144300 chr4A 429979264 429982356 3092 False 1270.333333 3439 90.656 223 3030 3 chr4A.!!$F1 2807
2 TraesCS4D01G144300 chr4B 164916757 164922742 5985 False 864.250000 2689 88.799 237 3228 4 chr4B.!!$F2 2991

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
675 1448 0.108585 CAGGCAGGGCGTGGTAATAT 59.891 55.0 9.49 0.0 40.2 1.28 F
1784 2565 0.319383 CCATCTCCTTCTCCATCGCG 60.319 60.0 0.00 0.0 0.0 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2057 2844 0.176219 CTCCAGCTCCAGCAGAGAAG 59.824 60.0 11.40 0.0 46.5 2.85 R
2640 6139 0.179018 AAGGGAAAACAGCTGCTCGT 60.179 50.0 15.27 0.0 0.0 4.18 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.873812 GGGCGGGTGGGAGGTATG 61.874 72.222 0.00 0.00 0.00 2.39
18 19 3.087906 GGCGGGTGGGAGGTATGT 61.088 66.667 0.00 0.00 0.00 2.29
19 20 2.189521 GCGGGTGGGAGGTATGTG 59.810 66.667 0.00 0.00 0.00 3.21
20 21 2.908015 CGGGTGGGAGGTATGTGG 59.092 66.667 0.00 0.00 0.00 4.17
21 22 2.595655 GGGTGGGAGGTATGTGGC 59.404 66.667 0.00 0.00 0.00 5.01
22 23 2.595655 GGTGGGAGGTATGTGGCC 59.404 66.667 0.00 0.00 0.00 5.36
23 24 2.189521 GTGGGAGGTATGTGGCCG 59.810 66.667 0.00 0.00 0.00 6.13
24 25 3.792736 TGGGAGGTATGTGGCCGC 61.793 66.667 10.11 10.11 0.00 6.53
25 26 4.564110 GGGAGGTATGTGGCCGCC 62.564 72.222 15.15 1.04 43.94 6.13
26 27 3.480133 GGAGGTATGTGGCCGCCT 61.480 66.667 15.15 6.58 41.84 5.52
27 28 2.203070 GAGGTATGTGGCCGCCTG 60.203 66.667 15.15 0.00 0.00 4.85
28 29 4.489771 AGGTATGTGGCCGCCTGC 62.490 66.667 15.15 7.56 40.16 4.85
71 72 4.364409 GCGCGTCCGTTTGGTGTC 62.364 66.667 8.43 0.00 36.67 3.67
72 73 3.708734 CGCGTCCGTTTGGTGTCC 61.709 66.667 0.00 0.00 36.30 4.02
73 74 3.708734 GCGTCCGTTTGGTGTCCG 61.709 66.667 0.00 0.00 36.30 4.79
74 75 3.708734 CGTCCGTTTGGTGTCCGC 61.709 66.667 0.00 0.00 36.30 5.54
75 76 3.351416 GTCCGTTTGGTGTCCGCC 61.351 66.667 0.00 0.00 36.30 6.13
76 77 4.973055 TCCGTTTGGTGTCCGCCG 62.973 66.667 0.00 0.00 36.30 6.46
98 99 3.601685 CCAAACCCGGCGCAAGTT 61.602 61.111 10.83 6.41 41.68 2.66
99 100 2.415426 CAAACCCGGCGCAAGTTT 59.585 55.556 10.83 12.71 41.68 2.66
100 101 1.948635 CAAACCCGGCGCAAGTTTG 60.949 57.895 24.85 24.85 42.93 2.93
109 110 4.607024 GCAAGTTTGCGCTCGAAA 57.393 50.000 9.73 0.00 45.11 3.46
110 111 3.092081 GCAAGTTTGCGCTCGAAAT 57.908 47.368 9.73 0.00 45.11 2.17
111 112 0.704551 GCAAGTTTGCGCTCGAAATG 59.295 50.000 9.73 1.98 45.11 2.32
112 113 1.330306 CAAGTTTGCGCTCGAAATGG 58.670 50.000 9.73 0.00 0.00 3.16
113 114 0.240945 AAGTTTGCGCTCGAAATGGG 59.759 50.000 9.73 0.00 0.00 4.00
114 115 0.889186 AGTTTGCGCTCGAAATGGGT 60.889 50.000 9.73 0.00 0.00 4.51
115 116 0.454452 GTTTGCGCTCGAAATGGGTC 60.454 55.000 9.73 0.00 0.00 4.46
116 117 1.906994 TTTGCGCTCGAAATGGGTCG 61.907 55.000 9.73 0.00 42.48 4.79
117 118 3.564027 GCGCTCGAAATGGGTCGG 61.564 66.667 0.00 0.00 41.43 4.79
118 119 3.564027 CGCTCGAAATGGGTCGGC 61.564 66.667 0.00 0.00 41.43 5.54
119 120 3.202706 GCTCGAAATGGGTCGGCC 61.203 66.667 0.00 0.00 41.43 6.13
129 130 4.629523 GGTCGGCCCGGACACAAA 62.630 66.667 0.73 0.00 38.70 2.83
130 131 2.592287 GTCGGCCCGGACACAAAA 60.592 61.111 0.73 0.00 36.91 2.44
131 132 2.592287 TCGGCCCGGACACAAAAC 60.592 61.111 0.73 0.00 0.00 2.43
132 133 4.020378 CGGCCCGGACACAAAACG 62.020 66.667 0.73 0.00 0.00 3.60
133 134 2.592287 GGCCCGGACACAAAACGA 60.592 61.111 0.73 0.00 0.00 3.85
134 135 2.188161 GGCCCGGACACAAAACGAA 61.188 57.895 0.73 0.00 0.00 3.85
135 136 1.009335 GCCCGGACACAAAACGAAC 60.009 57.895 0.73 0.00 0.00 3.95
136 137 1.716826 GCCCGGACACAAAACGAACA 61.717 55.000 0.73 0.00 0.00 3.18
137 138 0.733729 CCCGGACACAAAACGAACAA 59.266 50.000 0.73 0.00 0.00 2.83
138 139 1.268335 CCCGGACACAAAACGAACAAG 60.268 52.381 0.73 0.00 0.00 3.16
139 140 1.666700 CCGGACACAAAACGAACAAGA 59.333 47.619 0.00 0.00 0.00 3.02
140 141 2.289547 CCGGACACAAAACGAACAAGAT 59.710 45.455 0.00 0.00 0.00 2.40
141 142 3.288242 CGGACACAAAACGAACAAGATG 58.712 45.455 0.00 0.00 0.00 2.90
142 143 3.628017 GGACACAAAACGAACAAGATGG 58.372 45.455 0.00 0.00 0.00 3.51
143 144 3.550030 GGACACAAAACGAACAAGATGGG 60.550 47.826 0.00 0.00 0.00 4.00
144 145 3.020984 ACACAAAACGAACAAGATGGGT 58.979 40.909 0.00 0.00 0.00 4.51
145 146 3.066203 ACACAAAACGAACAAGATGGGTC 59.934 43.478 0.00 0.00 0.00 4.46
146 147 2.621526 ACAAAACGAACAAGATGGGTCC 59.378 45.455 0.00 0.00 0.00 4.46
147 148 2.884639 CAAAACGAACAAGATGGGTCCT 59.115 45.455 0.00 0.00 0.00 3.85
148 149 2.185004 AACGAACAAGATGGGTCCTG 57.815 50.000 0.00 0.00 0.00 3.86
149 150 0.324943 ACGAACAAGATGGGTCCTGG 59.675 55.000 0.00 0.00 0.00 4.45
150 151 1.026718 CGAACAAGATGGGTCCTGGC 61.027 60.000 0.00 0.00 0.00 4.85
151 152 0.681243 GAACAAGATGGGTCCTGGCC 60.681 60.000 0.00 0.00 0.00 5.36
152 153 2.124570 CAAGATGGGTCCTGGCCG 60.125 66.667 0.00 0.00 0.00 6.13
153 154 2.610859 AAGATGGGTCCTGGCCGT 60.611 61.111 0.00 0.00 0.00 5.68
154 155 2.670148 AAGATGGGTCCTGGCCGTC 61.670 63.158 0.00 4.82 0.00 4.79
155 156 4.530857 GATGGGTCCTGGCCGTCG 62.531 72.222 0.00 0.00 0.00 5.12
176 177 3.423154 GCTGGACCGCCTCGTTTG 61.423 66.667 0.00 0.00 34.31 2.93
177 178 2.030562 CTGGACCGCCTCGTTTGT 59.969 61.111 0.00 0.00 34.31 2.83
178 179 2.027625 CTGGACCGCCTCGTTTGTC 61.028 63.158 0.00 0.00 34.31 3.18
179 180 2.342648 GGACCGCCTCGTTTGTCT 59.657 61.111 0.00 0.00 0.00 3.41
180 181 1.301479 GGACCGCCTCGTTTGTCTT 60.301 57.895 0.00 0.00 0.00 3.01
181 182 0.883370 GGACCGCCTCGTTTGTCTTT 60.883 55.000 0.00 0.00 0.00 2.52
182 183 0.942252 GACCGCCTCGTTTGTCTTTT 59.058 50.000 0.00 0.00 0.00 2.27
183 184 1.332686 GACCGCCTCGTTTGTCTTTTT 59.667 47.619 0.00 0.00 0.00 1.94
200 201 3.967203 TTTTTACCTCAAACGAACGGG 57.033 42.857 0.00 0.00 0.00 5.28
201 202 1.881591 TTTACCTCAAACGAACGGGG 58.118 50.000 0.00 0.00 0.00 5.73
202 203 0.758123 TTACCTCAAACGAACGGGGT 59.242 50.000 0.00 0.00 0.00 4.95
203 204 0.318120 TACCTCAAACGAACGGGGTC 59.682 55.000 0.00 0.00 0.00 4.46
204 205 2.025418 CCTCAAACGAACGGGGTCG 61.025 63.158 4.31 4.31 46.54 4.79
205 206 2.025418 CTCAAACGAACGGGGTCGG 61.025 63.158 11.18 0.00 45.40 4.79
206 207 2.029369 CAAACGAACGGGGTCGGA 59.971 61.111 11.18 0.00 45.40 4.55
207 208 2.029518 AAACGAACGGGGTCGGAC 59.970 61.111 11.18 0.00 45.40 4.79
208 209 2.795110 AAACGAACGGGGTCGGACA 61.795 57.895 11.18 0.00 45.40 4.02
209 210 2.704342 AAACGAACGGGGTCGGACAG 62.704 60.000 11.18 3.39 45.40 3.51
210 211 4.430765 CGAACGGGGTCGGACAGG 62.431 72.222 10.76 0.80 41.39 4.00
211 212 2.993264 GAACGGGGTCGGACAGGA 60.993 66.667 10.76 0.00 41.39 3.86
212 213 2.284405 AACGGGGTCGGACAGGAT 60.284 61.111 10.76 0.00 41.39 3.24
213 214 2.573609 GAACGGGGTCGGACAGGATG 62.574 65.000 10.76 0.00 41.34 3.51
214 215 3.849951 CGGGGTCGGACAGGATGG 61.850 72.222 10.76 0.00 43.62 3.51
215 216 3.480133 GGGGTCGGACAGGATGGG 61.480 72.222 10.76 0.00 43.62 4.00
216 217 3.480133 GGGTCGGACAGGATGGGG 61.480 72.222 10.76 0.00 43.62 4.96
217 218 2.687566 GGTCGGACAGGATGGGGT 60.688 66.667 10.76 0.00 43.62 4.95
218 219 2.732619 GGTCGGACAGGATGGGGTC 61.733 68.421 10.76 0.00 43.62 4.46
219 220 2.758327 TCGGACAGGATGGGGTCG 60.758 66.667 0.00 0.00 43.62 4.79
220 221 4.530857 CGGACAGGATGGGGTCGC 62.531 72.222 0.00 0.00 43.62 5.19
221 222 4.530857 GGACAGGATGGGGTCGCG 62.531 72.222 0.00 0.00 43.62 5.87
227 228 4.944372 GATGGGGTCGCGCGGTAG 62.944 72.222 31.69 0.71 0.00 3.18
231 232 4.125695 GGGTCGCGCGGTAGAGTT 62.126 66.667 31.69 0.00 0.00 3.01
232 233 2.879462 GGTCGCGCGGTAGAGTTG 60.879 66.667 31.69 0.00 0.00 3.16
233 234 2.879462 GTCGCGCGGTAGAGTTGG 60.879 66.667 31.69 0.00 0.00 3.77
234 235 4.789075 TCGCGCGGTAGAGTTGGC 62.789 66.667 31.69 0.00 0.00 4.52
235 236 4.796231 CGCGCGGTAGAGTTGGCT 62.796 66.667 24.84 0.00 0.00 4.75
242 243 1.743772 CGGTAGAGTTGGCTTGATGGG 60.744 57.143 0.00 0.00 0.00 4.00
272 273 4.636435 CACCGGCCGTGGGAAGTT 62.636 66.667 26.12 0.00 38.96 2.66
326 336 0.890542 TACGTACGCACCTCACCTGT 60.891 55.000 16.72 0.00 0.00 4.00
333 343 1.961277 CACCTCACCTGTCGCCAAC 60.961 63.158 0.00 0.00 0.00 3.77
579 969 8.504815 CAAGAATCTGCCAAACTCATATATCAG 58.495 37.037 0.00 0.00 0.00 2.90
592 982 5.439721 TCATATATCAGCAGTGGCAACTTT 58.560 37.500 0.00 0.00 44.61 2.66
621 1011 0.522180 TTTGCAAAACCGTGTCGTGT 59.478 45.000 10.02 0.00 0.00 4.49
672 1445 2.925706 TCAGGCAGGGCGTGGTAA 60.926 61.111 9.49 0.00 43.44 2.85
673 1446 2.272146 CAGGCAGGGCGTGGTAAT 59.728 61.111 9.49 0.00 40.20 1.89
674 1447 0.978667 TCAGGCAGGGCGTGGTAATA 60.979 55.000 9.49 0.00 43.44 0.98
675 1448 0.108585 CAGGCAGGGCGTGGTAATAT 59.891 55.000 9.49 0.00 40.20 1.28
676 1449 1.346395 CAGGCAGGGCGTGGTAATATA 59.654 52.381 9.49 0.00 40.20 0.86
720 1493 3.244700 GCCGGACCCATCTACTACTACTA 60.245 52.174 5.05 0.00 0.00 1.82
835 1609 7.436080 TCCCATCGTATCAAGAAAACGTAATAC 59.564 37.037 0.00 0.00 37.83 1.89
865 1645 2.045926 CTCCCACAAAGCCCCTCG 60.046 66.667 0.00 0.00 0.00 4.63
866 1646 3.628646 CTCCCACAAAGCCCCTCGG 62.629 68.421 0.00 0.00 0.00 4.63
1524 2305 4.742201 CGTGCCCACTGGAGGTCG 62.742 72.222 0.00 0.00 0.00 4.79
1531 2312 3.063084 ACTGGAGGTCGCCGTCTC 61.063 66.667 2.59 2.59 0.00 3.36
1698 2479 2.651361 CGGAGCAAGTCAGACGGT 59.349 61.111 0.00 0.00 0.00 4.83
1784 2565 0.319383 CCATCTCCTTCTCCATCGCG 60.319 60.000 0.00 0.00 0.00 5.87
2063 2850 2.496817 GGACGCATCCGCTTCTCT 59.503 61.111 0.00 0.00 36.66 3.10
2096 2885 2.440627 AGCTGGATGGATGCTGATGTTA 59.559 45.455 0.00 0.00 35.54 2.41
2098 2887 4.287845 AGCTGGATGGATGCTGATGTTATA 59.712 41.667 0.00 0.00 35.54 0.98
2102 2891 7.256494 TGGATGGATGCTGATGTTATATGTA 57.744 36.000 0.00 0.00 0.00 2.29
2103 2892 7.688343 TGGATGGATGCTGATGTTATATGTAA 58.312 34.615 0.00 0.00 0.00 2.41
2123 2923 1.331756 ACAGCGTGAAGAAGTGCAAAG 59.668 47.619 0.00 0.00 0.00 2.77
2274 3082 8.817092 AGTCTACTACTTGCTTCTCTTATCTT 57.183 34.615 0.00 0.00 33.35 2.40
2299 3108 2.072298 GTGATGTGTGCAAGAGACCTC 58.928 52.381 0.00 0.00 0.00 3.85
2409 3223 4.100035 TGATTGTTTGGTTTGGCATGTGTA 59.900 37.500 0.00 0.00 0.00 2.90
2420 3234 1.407437 GGCATGTGTACTTCCTCCTGG 60.407 57.143 0.00 0.00 0.00 4.45
2444 3260 6.086871 GGGAAAGTAGAAATCTTTTCTTGCG 58.913 40.000 7.72 0.00 35.62 4.85
2532 6031 3.498661 GGAACTGGAACTCTGGAAATGGT 60.499 47.826 0.00 0.00 0.00 3.55
2555 6054 6.693113 GGTTGCTACTTCTGTTTCTTTTCTTG 59.307 38.462 0.00 0.00 0.00 3.02
2617 6116 3.064931 CCAAACTCTCCTTCAACGGTAC 58.935 50.000 0.00 0.00 0.00 3.34
2623 6122 4.641094 ACTCTCCTTCAACGGTACTATCAG 59.359 45.833 0.00 0.00 0.00 2.90
2639 6138 8.798402 GGTACTATCAGTCTAATTATCTGCAGT 58.202 37.037 14.67 17.72 32.92 4.40
2661 6185 1.068954 CGAGCAGCTGTTTTCCCTTTC 60.069 52.381 16.64 0.00 0.00 2.62
2732 6256 8.429237 AAATAAATGGGTATTTCAAGGACACA 57.571 30.769 0.00 0.00 37.64 3.72
2733 6257 8.608185 AATAAATGGGTATTTCAAGGACACAT 57.392 30.769 0.00 0.00 38.87 3.21
2734 6258 6.530019 AAATGGGTATTTCAAGGACACATC 57.470 37.500 0.00 0.00 36.18 3.06
2735 6259 4.927267 TGGGTATTTCAAGGACACATCT 57.073 40.909 0.00 0.00 0.00 2.90
2736 6260 6.575244 ATGGGTATTTCAAGGACACATCTA 57.425 37.500 0.00 0.00 31.51 1.98
2737 6261 5.989477 TGGGTATTTCAAGGACACATCTAG 58.011 41.667 0.00 0.00 0.00 2.43
2738 6262 5.724370 TGGGTATTTCAAGGACACATCTAGA 59.276 40.000 0.00 0.00 0.00 2.43
2739 6263 6.386927 TGGGTATTTCAAGGACACATCTAGAT 59.613 38.462 0.00 0.00 0.00 1.98
2740 6264 6.708054 GGGTATTTCAAGGACACATCTAGATG 59.292 42.308 27.63 27.63 44.15 2.90
2756 6280 8.171164 CATCTAGATGTGTCCTAGTTATGTCA 57.829 38.462 22.42 0.00 36.06 3.58
2757 6281 7.569639 TCTAGATGTGTCCTAGTTATGTCAC 57.430 40.000 0.00 0.00 36.06 3.67
2758 6282 7.116736 TCTAGATGTGTCCTAGTTATGTCACA 58.883 38.462 0.00 0.00 39.49 3.58
2759 6283 6.798427 AGATGTGTCCTAGTTATGTCACAT 57.202 37.500 8.06 8.06 45.14 3.21
2761 6285 6.798427 ATGTGTCCTAGTTATGTCACATCT 57.202 37.500 0.00 0.00 40.81 2.90
2762 6286 7.898014 ATGTGTCCTAGTTATGTCACATCTA 57.102 36.000 0.00 0.00 40.81 1.98
2763 6287 7.712204 TGTGTCCTAGTTATGTCACATCTAA 57.288 36.000 0.00 0.00 32.19 2.10
2764 6288 7.544622 TGTGTCCTAGTTATGTCACATCTAAC 58.455 38.462 0.00 0.00 32.19 2.34
2765 6289 6.979238 GTGTCCTAGTTATGTCACATCTAACC 59.021 42.308 0.00 0.00 0.00 2.85
2766 6290 6.895756 TGTCCTAGTTATGTCACATCTAACCT 59.104 38.462 0.00 0.00 0.00 3.50
2767 6291 7.147897 TGTCCTAGTTATGTCACATCTAACCTG 60.148 40.741 0.00 0.00 0.00 4.00
2768 6292 7.068348 GTCCTAGTTATGTCACATCTAACCTGA 59.932 40.741 0.00 0.00 0.00 3.86
2769 6293 7.785028 TCCTAGTTATGTCACATCTAACCTGAT 59.215 37.037 0.00 0.00 0.00 2.90
2770 6294 7.869937 CCTAGTTATGTCACATCTAACCTGATG 59.130 40.741 0.00 0.00 46.61 3.07
2771 6295 6.051717 AGTTATGTCACATCTAACCTGATGC 58.948 40.000 0.00 0.00 45.51 3.91
2772 6296 3.266510 TGTCACATCTAACCTGATGCC 57.733 47.619 4.63 0.00 45.51 4.40
2773 6297 2.092968 TGTCACATCTAACCTGATGCCC 60.093 50.000 4.63 0.00 45.51 5.36
2774 6298 2.092968 GTCACATCTAACCTGATGCCCA 60.093 50.000 4.63 0.00 45.51 5.36
2775 6299 2.779430 TCACATCTAACCTGATGCCCAT 59.221 45.455 4.63 0.00 45.51 4.00
2776 6300 3.202818 TCACATCTAACCTGATGCCCATT 59.797 43.478 4.63 0.00 45.51 3.16
2777 6301 4.411869 TCACATCTAACCTGATGCCCATTA 59.588 41.667 4.63 0.00 45.51 1.90
2778 6302 5.073554 TCACATCTAACCTGATGCCCATTAT 59.926 40.000 4.63 0.00 45.51 1.28
2779 6303 6.272090 TCACATCTAACCTGATGCCCATTATA 59.728 38.462 4.63 0.00 45.51 0.98
2780 6304 7.037370 TCACATCTAACCTGATGCCCATTATAT 60.037 37.037 4.63 0.00 45.51 0.86
2781 6305 8.267183 CACATCTAACCTGATGCCCATTATATA 58.733 37.037 4.63 0.00 45.51 0.86
2782 6306 9.007494 ACATCTAACCTGATGCCCATTATATAT 57.993 33.333 4.63 0.00 45.51 0.86
2783 6307 9.857656 CATCTAACCTGATGCCCATTATATATT 57.142 33.333 0.00 0.00 37.59 1.28
2784 6308 9.857656 ATCTAACCTGATGCCCATTATATATTG 57.142 33.333 0.00 0.00 0.00 1.90
2785 6309 8.274322 TCTAACCTGATGCCCATTATATATTGG 58.726 37.037 14.34 14.34 0.00 3.16
2820 6344 9.744468 TTTTGTCCTAGCTATTTTTCTTTGTTC 57.256 29.630 0.00 0.00 0.00 3.18
2821 6345 8.691661 TTGTCCTAGCTATTTTTCTTTGTTCT 57.308 30.769 0.00 0.00 0.00 3.01
2822 6346 8.691661 TGTCCTAGCTATTTTTCTTTGTTCTT 57.308 30.769 0.00 0.00 0.00 2.52
2823 6347 9.131791 TGTCCTAGCTATTTTTCTTTGTTCTTT 57.868 29.630 0.00 0.00 0.00 2.52
2824 6348 9.399403 GTCCTAGCTATTTTTCTTTGTTCTTTG 57.601 33.333 0.00 0.00 0.00 2.77
2825 6349 9.131791 TCCTAGCTATTTTTCTTTGTTCTTTGT 57.868 29.630 0.00 0.00 0.00 2.83
2826 6350 9.750125 CCTAGCTATTTTTCTTTGTTCTTTGTT 57.250 29.630 0.00 0.00 0.00 2.83
2828 6352 7.909267 AGCTATTTTTCTTTGTTCTTTGTTGC 58.091 30.769 0.00 0.00 0.00 4.17
2829 6353 7.765819 AGCTATTTTTCTTTGTTCTTTGTTGCT 59.234 29.630 0.00 0.00 0.00 3.91
2830 6354 7.847564 GCTATTTTTCTTTGTTCTTTGTTGCTG 59.152 33.333 0.00 0.00 0.00 4.41
2831 6355 7.671495 ATTTTTCTTTGTTCTTTGTTGCTGT 57.329 28.000 0.00 0.00 0.00 4.40
2832 6356 6.704512 TTTTCTTTGTTCTTTGTTGCTGTC 57.295 33.333 0.00 0.00 0.00 3.51
2833 6357 5.643379 TTCTTTGTTCTTTGTTGCTGTCT 57.357 34.783 0.00 0.00 0.00 3.41
2834 6358 5.643379 TCTTTGTTCTTTGTTGCTGTCTT 57.357 34.783 0.00 0.00 0.00 3.01
2835 6359 6.751514 TCTTTGTTCTTTGTTGCTGTCTTA 57.248 33.333 0.00 0.00 0.00 2.10
2836 6360 7.333528 TCTTTGTTCTTTGTTGCTGTCTTAT 57.666 32.000 0.00 0.00 0.00 1.73
2837 6361 7.771183 TCTTTGTTCTTTGTTGCTGTCTTATT 58.229 30.769 0.00 0.00 0.00 1.40
2838 6362 8.250332 TCTTTGTTCTTTGTTGCTGTCTTATTT 58.750 29.630 0.00 0.00 0.00 1.40
2839 6363 7.754069 TTGTTCTTTGTTGCTGTCTTATTTG 57.246 32.000 0.00 0.00 0.00 2.32
2840 6364 6.862209 TGTTCTTTGTTGCTGTCTTATTTGT 58.138 32.000 0.00 0.00 0.00 2.83
2841 6365 6.751425 TGTTCTTTGTTGCTGTCTTATTTGTG 59.249 34.615 0.00 0.00 0.00 3.33
2842 6366 5.830912 TCTTTGTTGCTGTCTTATTTGTGG 58.169 37.500 0.00 0.00 0.00 4.17
2843 6367 4.582701 TTGTTGCTGTCTTATTTGTGGG 57.417 40.909 0.00 0.00 0.00 4.61
2844 6368 3.826524 TGTTGCTGTCTTATTTGTGGGA 58.173 40.909 0.00 0.00 0.00 4.37
2845 6369 3.820467 TGTTGCTGTCTTATTTGTGGGAG 59.180 43.478 0.00 0.00 0.00 4.30
2846 6370 4.072131 GTTGCTGTCTTATTTGTGGGAGA 58.928 43.478 0.00 0.00 0.00 3.71
2847 6371 4.574674 TGCTGTCTTATTTGTGGGAGAT 57.425 40.909 0.00 0.00 0.00 2.75
2848 6372 4.922206 TGCTGTCTTATTTGTGGGAGATT 58.078 39.130 0.00 0.00 0.00 2.40
2849 6373 6.061022 TGCTGTCTTATTTGTGGGAGATTA 57.939 37.500 0.00 0.00 0.00 1.75
2850 6374 6.115446 TGCTGTCTTATTTGTGGGAGATTAG 58.885 40.000 0.00 0.00 0.00 1.73
2851 6375 6.070251 TGCTGTCTTATTTGTGGGAGATTAGA 60.070 38.462 0.00 0.00 0.00 2.10
2852 6376 6.995091 GCTGTCTTATTTGTGGGAGATTAGAT 59.005 38.462 0.00 0.00 0.00 1.98
2853 6377 7.041508 GCTGTCTTATTTGTGGGAGATTAGATG 60.042 40.741 0.00 0.00 0.00 2.90
2854 6378 7.861629 TGTCTTATTTGTGGGAGATTAGATGT 58.138 34.615 0.00 0.00 0.00 3.06
2855 6379 7.770433 TGTCTTATTTGTGGGAGATTAGATGTG 59.230 37.037 0.00 0.00 0.00 3.21
2856 6380 7.987458 GTCTTATTTGTGGGAGATTAGATGTGA 59.013 37.037 0.00 0.00 0.00 3.58
2857 6381 8.717717 TCTTATTTGTGGGAGATTAGATGTGAT 58.282 33.333 0.00 0.00 0.00 3.06
2861 6385 6.611613 TGTGGGAGATTAGATGTGATATCC 57.388 41.667 0.00 0.04 33.83 2.59
2862 6386 6.326161 TGTGGGAGATTAGATGTGATATCCT 58.674 40.000 8.00 0.00 34.76 3.24
2863 6387 6.789457 TGTGGGAGATTAGATGTGATATCCTT 59.211 38.462 8.00 0.00 34.76 3.36
2864 6388 7.955750 TGTGGGAGATTAGATGTGATATCCTTA 59.044 37.037 8.00 0.00 34.76 2.69
2865 6389 8.816894 GTGGGAGATTAGATGTGATATCCTTAA 58.183 37.037 8.00 0.00 34.76 1.85
2866 6390 9.392506 TGGGAGATTAGATGTGATATCCTTAAA 57.607 33.333 8.00 0.00 34.76 1.52
2933 6700 4.336889 AGAAAGACGGACAGATTTGTGA 57.663 40.909 0.00 0.00 37.76 3.58
2948 6715 4.671880 TTTGTGACCCGAAAATCATACG 57.328 40.909 0.00 0.00 0.00 3.06
2950 6717 1.329599 GTGACCCGAAAATCATACGGC 59.670 52.381 0.00 0.00 44.45 5.68
3015 6788 1.458445 GTTAGCGTCCGTCACCTTTTC 59.542 52.381 0.00 0.00 0.00 2.29
3108 6883 7.927048 ACAAAGTAAAATGAGTGAACCTACAC 58.073 34.615 0.00 0.00 40.60 2.90
3150 6925 4.455533 ACGTCCGTATGTAGTTTGTAGTGA 59.544 41.667 0.00 0.00 0.00 3.41
3156 6931 7.972277 TCCGTATGTAGTTTGTAGTGAAATCTC 59.028 37.037 0.00 0.00 0.00 2.75
3157 6932 7.974501 CCGTATGTAGTTTGTAGTGAAATCTCT 59.025 37.037 0.00 0.00 0.00 3.10
3165 6940 8.417884 AGTTTGTAGTGAAATCTCTATAGAGGC 58.582 37.037 26.02 14.98 42.30 4.70
3166 6941 8.417884 GTTTGTAGTGAAATCTCTATAGAGGCT 58.582 37.037 26.02 13.41 42.30 4.58
3185 6960 4.286291 AGGCTTATATTTAGGAACGGAGGG 59.714 45.833 0.00 0.00 0.00 4.30
3190 6965 7.093421 GCTTATATTTAGGAACGGAGGGAGTAT 60.093 40.741 0.00 0.00 0.00 2.12
3195 6970 2.091222 AGGAACGGAGGGAGTATAAGCT 60.091 50.000 0.00 0.00 0.00 3.74
3233 7008 2.924903 GTTAACAGTAACGCCTTTGCC 58.075 47.619 0.00 0.00 30.76 4.52
3234 7009 1.525941 TAACAGTAACGCCTTTGCCC 58.474 50.000 0.00 0.00 0.00 5.36
3235 7010 1.176619 AACAGTAACGCCTTTGCCCC 61.177 55.000 0.00 0.00 0.00 5.80
3236 7011 2.035155 AGTAACGCCTTTGCCCCC 59.965 61.111 0.00 0.00 0.00 5.40
3237 7012 2.035155 GTAACGCCTTTGCCCCCT 59.965 61.111 0.00 0.00 0.00 4.79
3238 7013 1.605451 GTAACGCCTTTGCCCCCTT 60.605 57.895 0.00 0.00 0.00 3.95
3239 7014 1.303806 TAACGCCTTTGCCCCCTTC 60.304 57.895 0.00 0.00 0.00 3.46
3240 7015 1.785353 TAACGCCTTTGCCCCCTTCT 61.785 55.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.873812 CATACCTCCCACCCGCCC 61.874 72.222 0.00 0.00 0.00 6.13
3 4 2.908015 CCACATACCTCCCACCCG 59.092 66.667 0.00 0.00 0.00 5.28
4 5 2.595655 GCCACATACCTCCCACCC 59.404 66.667 0.00 0.00 0.00 4.61
6 7 2.189521 CGGCCACATACCTCCCAC 59.810 66.667 2.24 0.00 0.00 4.61
7 8 3.792736 GCGGCCACATACCTCCCA 61.793 66.667 2.24 0.00 0.00 4.37
9 10 3.480133 AGGCGGCCACATACCTCC 61.480 66.667 23.09 0.00 31.80 4.30
10 11 2.203070 CAGGCGGCCACATACCTC 60.203 66.667 23.09 0.00 0.00 3.85
11 12 4.489771 GCAGGCGGCCACATACCT 62.490 66.667 23.09 0.00 36.11 3.08
54 55 4.364409 GACACCAAACGGACGCGC 62.364 66.667 5.73 0.00 0.00 6.86
55 56 3.708734 GGACACCAAACGGACGCG 61.709 66.667 3.53 3.53 0.00 6.01
56 57 3.708734 CGGACACCAAACGGACGC 61.709 66.667 0.00 0.00 0.00 5.19
57 58 3.708734 GCGGACACCAAACGGACG 61.709 66.667 0.00 0.00 0.00 4.79
58 59 3.351416 GGCGGACACCAAACGGAC 61.351 66.667 0.00 0.00 0.00 4.79
59 60 4.973055 CGGCGGACACCAAACGGA 62.973 66.667 0.00 0.00 0.00 4.69
81 82 3.145422 AAACTTGCGCCGGGTTTGG 62.145 57.895 17.28 0.00 32.84 3.28
82 83 1.948635 CAAACTTGCGCCGGGTTTG 60.949 57.895 24.29 24.29 42.01 2.93
83 84 2.415426 CAAACTTGCGCCGGGTTT 59.585 55.556 4.18 10.66 34.10 3.27
84 85 4.279043 GCAAACTTGCGCCGGGTT 62.279 61.111 4.18 4.28 45.11 4.11
93 94 1.330306 CCATTTCGAGCGCAAACTTG 58.670 50.000 11.47 0.00 0.00 3.16
94 95 0.240945 CCCATTTCGAGCGCAAACTT 59.759 50.000 11.47 0.00 0.00 2.66
95 96 0.889186 ACCCATTTCGAGCGCAAACT 60.889 50.000 11.47 0.00 0.00 2.66
96 97 0.454452 GACCCATTTCGAGCGCAAAC 60.454 55.000 11.47 0.00 0.00 2.93
97 98 1.873165 GACCCATTTCGAGCGCAAA 59.127 52.632 11.47 1.09 0.00 3.68
98 99 2.387445 CGACCCATTTCGAGCGCAA 61.387 57.895 11.47 0.00 41.78 4.85
99 100 2.813474 CGACCCATTTCGAGCGCA 60.813 61.111 11.47 0.00 41.78 6.09
100 101 3.564027 CCGACCCATTTCGAGCGC 61.564 66.667 0.00 0.00 41.78 5.92
101 102 3.564027 GCCGACCCATTTCGAGCG 61.564 66.667 0.00 0.00 41.78 5.03
102 103 3.202706 GGCCGACCCATTTCGAGC 61.203 66.667 0.00 0.00 41.78 5.03
112 113 4.629523 TTTGTGTCCGGGCCGACC 62.630 66.667 30.79 17.72 31.35 4.79
113 114 2.592287 TTTTGTGTCCGGGCCGAC 60.592 61.111 30.79 22.88 0.00 4.79
114 115 2.592287 GTTTTGTGTCCGGGCCGA 60.592 61.111 30.79 11.12 0.00 5.54
115 116 4.020378 CGTTTTGTGTCCGGGCCG 62.020 66.667 21.46 21.46 0.00 6.13
116 117 2.188161 TTCGTTTTGTGTCCGGGCC 61.188 57.895 2.12 0.00 0.00 5.80
117 118 1.009335 GTTCGTTTTGTGTCCGGGC 60.009 57.895 0.00 0.00 0.00 6.13
118 119 0.733729 TTGTTCGTTTTGTGTCCGGG 59.266 50.000 0.00 0.00 0.00 5.73
119 120 1.666700 TCTTGTTCGTTTTGTGTCCGG 59.333 47.619 0.00 0.00 0.00 5.14
120 121 3.288242 CATCTTGTTCGTTTTGTGTCCG 58.712 45.455 0.00 0.00 0.00 4.79
121 122 3.550030 CCCATCTTGTTCGTTTTGTGTCC 60.550 47.826 0.00 0.00 0.00 4.02
122 123 3.066203 ACCCATCTTGTTCGTTTTGTGTC 59.934 43.478 0.00 0.00 0.00 3.67
123 124 3.020984 ACCCATCTTGTTCGTTTTGTGT 58.979 40.909 0.00 0.00 0.00 3.72
124 125 3.550030 GGACCCATCTTGTTCGTTTTGTG 60.550 47.826 0.00 0.00 0.00 3.33
125 126 2.621526 GGACCCATCTTGTTCGTTTTGT 59.378 45.455 0.00 0.00 0.00 2.83
126 127 2.884639 AGGACCCATCTTGTTCGTTTTG 59.115 45.455 0.00 0.00 0.00 2.44
127 128 2.884639 CAGGACCCATCTTGTTCGTTTT 59.115 45.455 0.00 0.00 0.00 2.43
128 129 2.504367 CAGGACCCATCTTGTTCGTTT 58.496 47.619 0.00 0.00 0.00 3.60
129 130 1.271379 CCAGGACCCATCTTGTTCGTT 60.271 52.381 0.00 0.00 29.93 3.85
130 131 0.324943 CCAGGACCCATCTTGTTCGT 59.675 55.000 0.00 0.00 29.93 3.85
131 132 1.026718 GCCAGGACCCATCTTGTTCG 61.027 60.000 0.00 0.00 29.93 3.95
132 133 0.681243 GGCCAGGACCCATCTTGTTC 60.681 60.000 0.00 0.00 29.93 3.18
133 134 1.384191 GGCCAGGACCCATCTTGTT 59.616 57.895 0.00 0.00 29.93 2.83
134 135 2.971598 CGGCCAGGACCCATCTTGT 61.972 63.158 2.24 0.00 29.93 3.16
135 136 2.124570 CGGCCAGGACCCATCTTG 60.125 66.667 2.24 0.00 0.00 3.02
136 137 2.610859 ACGGCCAGGACCCATCTT 60.611 61.111 2.24 0.00 0.00 2.40
137 138 3.083997 GACGGCCAGGACCCATCT 61.084 66.667 2.24 0.00 0.00 2.90
138 139 4.530857 CGACGGCCAGGACCCATC 62.531 72.222 2.24 0.00 0.00 3.51
159 160 3.423154 CAAACGAGGCGGTCCAGC 61.423 66.667 0.00 0.00 33.74 4.85
160 161 2.027625 GACAAACGAGGCGGTCCAG 61.028 63.158 0.00 0.00 33.74 3.86
161 162 2.029964 GACAAACGAGGCGGTCCA 59.970 61.111 0.00 0.00 33.74 4.02
162 163 0.883370 AAAGACAAACGAGGCGGTCC 60.883 55.000 0.00 0.00 0.00 4.46
163 164 0.942252 AAAAGACAAACGAGGCGGTC 59.058 50.000 0.00 0.00 0.00 4.79
164 165 1.385528 AAAAAGACAAACGAGGCGGT 58.614 45.000 0.00 0.00 0.00 5.68
180 181 2.617774 CCCCGTTCGTTTGAGGTAAAAA 59.382 45.455 0.00 0.00 0.00 1.94
181 182 2.220313 CCCCGTTCGTTTGAGGTAAAA 58.780 47.619 0.00 0.00 0.00 1.52
182 183 1.140652 ACCCCGTTCGTTTGAGGTAAA 59.859 47.619 0.00 0.00 0.00 2.01
183 184 0.758123 ACCCCGTTCGTTTGAGGTAA 59.242 50.000 0.00 0.00 0.00 2.85
184 185 0.318120 GACCCCGTTCGTTTGAGGTA 59.682 55.000 0.00 0.00 0.00 3.08
185 186 1.070275 GACCCCGTTCGTTTGAGGT 59.930 57.895 0.00 0.00 0.00 3.85
186 187 2.025418 CGACCCCGTTCGTTTGAGG 61.025 63.158 0.00 0.00 34.16 3.86
187 188 2.025418 CCGACCCCGTTCGTTTGAG 61.025 63.158 0.00 0.00 37.29 3.02
188 189 2.029369 CCGACCCCGTTCGTTTGA 59.971 61.111 0.00 0.00 37.29 2.69
189 190 2.029369 TCCGACCCCGTTCGTTTG 59.971 61.111 0.00 0.00 37.29 2.93
190 191 2.029518 GTCCGACCCCGTTCGTTT 59.970 61.111 0.00 0.00 37.29 3.60
191 192 3.216944 CTGTCCGACCCCGTTCGTT 62.217 63.158 0.00 0.00 37.29 3.85
192 193 3.677648 CTGTCCGACCCCGTTCGT 61.678 66.667 0.00 0.00 37.29 3.85
193 194 4.430765 CCTGTCCGACCCCGTTCG 62.431 72.222 0.00 0.00 38.80 3.95
194 195 2.356780 ATCCTGTCCGACCCCGTTC 61.357 63.158 0.00 0.00 0.00 3.95
195 196 2.284405 ATCCTGTCCGACCCCGTT 60.284 61.111 0.00 0.00 0.00 4.44
196 197 3.075005 CATCCTGTCCGACCCCGT 61.075 66.667 0.00 0.00 0.00 5.28
197 198 3.849951 CCATCCTGTCCGACCCCG 61.850 72.222 0.00 0.00 0.00 5.73
198 199 3.480133 CCCATCCTGTCCGACCCC 61.480 72.222 0.00 0.00 0.00 4.95
199 200 3.480133 CCCCATCCTGTCCGACCC 61.480 72.222 0.00 0.00 0.00 4.46
200 201 2.687566 ACCCCATCCTGTCCGACC 60.688 66.667 0.00 0.00 0.00 4.79
201 202 2.901042 GACCCCATCCTGTCCGAC 59.099 66.667 0.00 0.00 0.00 4.79
202 203 2.758327 CGACCCCATCCTGTCCGA 60.758 66.667 0.00 0.00 0.00 4.55
203 204 4.530857 GCGACCCCATCCTGTCCG 62.531 72.222 0.00 0.00 0.00 4.79
204 205 4.530857 CGCGACCCCATCCTGTCC 62.531 72.222 0.00 0.00 0.00 4.02
210 211 4.944372 CTACCGCGCGACCCCATC 62.944 72.222 34.63 0.00 0.00 3.51
214 215 4.125695 AACTCTACCGCGCGACCC 62.126 66.667 34.63 0.00 0.00 4.46
215 216 2.879462 CAACTCTACCGCGCGACC 60.879 66.667 34.63 0.00 0.00 4.79
216 217 2.879462 CCAACTCTACCGCGCGAC 60.879 66.667 34.63 0.00 0.00 5.19
217 218 4.789075 GCCAACTCTACCGCGCGA 62.789 66.667 34.63 11.99 0.00 5.87
218 219 4.796231 AGCCAACTCTACCGCGCG 62.796 66.667 25.67 25.67 0.00 6.86
219 220 2.434359 AAGCCAACTCTACCGCGC 60.434 61.111 0.00 0.00 0.00 6.86
220 221 0.460284 ATCAAGCCAACTCTACCGCG 60.460 55.000 0.00 0.00 0.00 6.46
221 222 1.009829 CATCAAGCCAACTCTACCGC 58.990 55.000 0.00 0.00 0.00 5.68
222 223 1.656652 CCATCAAGCCAACTCTACCG 58.343 55.000 0.00 0.00 0.00 4.02
223 224 1.559682 TCCCATCAAGCCAACTCTACC 59.440 52.381 0.00 0.00 0.00 3.18
224 225 2.027192 TGTCCCATCAAGCCAACTCTAC 60.027 50.000 0.00 0.00 0.00 2.59
225 226 2.265367 TGTCCCATCAAGCCAACTCTA 58.735 47.619 0.00 0.00 0.00 2.43
226 227 1.067295 TGTCCCATCAAGCCAACTCT 58.933 50.000 0.00 0.00 0.00 3.24
227 228 1.909700 TTGTCCCATCAAGCCAACTC 58.090 50.000 0.00 0.00 0.00 3.01
228 229 2.610438 ATTGTCCCATCAAGCCAACT 57.390 45.000 0.00 0.00 0.00 3.16
229 230 6.127479 TGTTTATATTGTCCCATCAAGCCAAC 60.127 38.462 0.00 0.00 0.00 3.77
230 231 5.954752 TGTTTATATTGTCCCATCAAGCCAA 59.045 36.000 0.00 0.00 0.00 4.52
231 232 5.359576 GTGTTTATATTGTCCCATCAAGCCA 59.640 40.000 0.00 0.00 0.00 4.75
232 233 5.359576 TGTGTTTATATTGTCCCATCAAGCC 59.640 40.000 0.00 0.00 0.00 4.35
233 234 6.265577 GTGTGTTTATATTGTCCCATCAAGC 58.734 40.000 0.00 0.00 0.00 4.01
234 235 6.458206 CGGTGTGTTTATATTGTCCCATCAAG 60.458 42.308 0.00 0.00 0.00 3.02
235 236 5.355630 CGGTGTGTTTATATTGTCCCATCAA 59.644 40.000 0.00 0.00 0.00 2.57
242 243 2.031191 CGGCCGGTGTGTTTATATTGTC 59.969 50.000 20.10 0.00 0.00 3.18
270 271 3.907894 TCATGACAACGCCCTTTTAAC 57.092 42.857 0.00 0.00 0.00 2.01
272 273 4.075682 TCATTCATGACAACGCCCTTTTA 58.924 39.130 0.00 0.00 0.00 1.52
579 969 5.049828 ACAAAATTAGAAAGTTGCCACTGC 58.950 37.500 0.00 0.00 31.60 4.40
621 1011 8.308931 GGAGTACGTATAATCCAACCAATCATA 58.691 37.037 15.64 0.00 43.74 2.15
655 1428 0.978667 TATTACCACGCCCTGCCTGA 60.979 55.000 0.00 0.00 0.00 3.86
674 1447 7.989170 GGCAGAATCCAAGAAAATTTCCATTAT 59.011 33.333 1.57 0.00 0.00 1.28
675 1448 7.330262 GGCAGAATCCAAGAAAATTTCCATTA 58.670 34.615 1.57 0.00 0.00 1.90
676 1449 6.175471 GGCAGAATCCAAGAAAATTTCCATT 58.825 36.000 1.57 0.00 0.00 3.16
720 1493 3.395941 GGGGAAACATGGTCCTCATCTAT 59.604 47.826 15.19 0.00 35.50 1.98
835 1609 5.335191 GCTTTGTGGGAGAAGACAAATACTG 60.335 44.000 0.00 0.00 40.38 2.74
840 1614 2.306847 GGCTTTGTGGGAGAAGACAAA 58.693 47.619 0.00 0.00 39.24 2.83
842 1616 0.110486 GGGCTTTGTGGGAGAAGACA 59.890 55.000 0.00 0.00 32.40 3.41
843 1617 0.609406 GGGGCTTTGTGGGAGAAGAC 60.609 60.000 0.00 0.00 0.00 3.01
865 1645 4.700213 TGTGAAGCTAATAACAAGGAAGCC 59.300 41.667 0.00 0.00 33.63 4.35
866 1646 5.412904 AGTGTGAAGCTAATAACAAGGAAGC 59.587 40.000 0.00 0.00 0.00 3.86
993 1774 2.224159 TGGGAGGAGTGTGGGAAGC 61.224 63.158 0.00 0.00 0.00 3.86
1826 2607 4.819761 GCCTCTCATGCGCCGACA 62.820 66.667 4.18 0.00 0.00 4.35
1921 2702 1.819632 GGCCGATGCAACCGAAGAT 60.820 57.895 12.59 0.00 40.13 2.40
2056 2843 1.449956 CCAGCTCCAGCAGAGAAGC 60.450 63.158 7.89 0.00 46.50 3.86
2057 2844 0.176219 CTCCAGCTCCAGCAGAGAAG 59.824 60.000 11.40 0.00 46.50 2.85
2058 2845 1.897225 GCTCCAGCTCCAGCAGAGAA 61.897 60.000 18.12 0.00 46.50 2.87
2059 2846 2.357575 GCTCCAGCTCCAGCAGAGA 61.358 63.158 18.12 4.50 46.50 3.10
2060 2847 2.187424 GCTCCAGCTCCAGCAGAG 59.813 66.667 8.33 12.18 46.29 3.35
2096 2885 4.330074 GCACTTCTTCACGCTGTTACATAT 59.670 41.667 0.00 0.00 0.00 1.78
2098 2887 2.480419 GCACTTCTTCACGCTGTTACAT 59.520 45.455 0.00 0.00 0.00 2.29
2102 2891 1.378531 TTGCACTTCTTCACGCTGTT 58.621 45.000 0.00 0.00 0.00 3.16
2103 2892 1.331756 CTTTGCACTTCTTCACGCTGT 59.668 47.619 0.00 0.00 0.00 4.40
2123 2923 7.934120 ACTACTGGTATCTTCTATGCAATTTCC 59.066 37.037 0.00 0.00 0.00 3.13
2274 3082 4.455533 GGTCTCTTGCACACATCACAATAA 59.544 41.667 0.00 0.00 0.00 1.40
2276 3084 2.816087 GGTCTCTTGCACACATCACAAT 59.184 45.455 0.00 0.00 0.00 2.71
2299 3108 8.922058 AATATAGCTGCAAATTTTCAGTCTTG 57.078 30.769 17.35 0.00 33.09 3.02
2409 3223 2.113777 TCTACTTTCCCCAGGAGGAAGT 59.886 50.000 0.00 0.00 46.44 3.01
2420 3234 6.086871 CGCAAGAAAAGATTTCTACTTTCCC 58.913 40.000 5.83 0.00 36.71 3.97
2499 5998 3.073062 AGTTCCAGTTCCAGCAATGTAGT 59.927 43.478 0.00 0.00 0.00 2.73
2500 5999 3.679389 AGTTCCAGTTCCAGCAATGTAG 58.321 45.455 0.00 0.00 0.00 2.74
2508 6007 3.492102 TTTCCAGAGTTCCAGTTCCAG 57.508 47.619 0.00 0.00 0.00 3.86
2532 6031 6.183360 CCCAAGAAAAGAAACAGAAGTAGCAA 60.183 38.462 0.00 0.00 0.00 3.91
2555 6054 1.465794 TAGCCGCCATTTTGTTACCC 58.534 50.000 0.00 0.00 0.00 3.69
2617 6116 8.722394 TCGTACTGCAGATAATTAGACTGATAG 58.278 37.037 23.35 17.75 34.07 2.08
2623 6122 5.520632 TGCTCGTACTGCAGATAATTAGAC 58.479 41.667 23.35 4.01 35.31 2.59
2639 6138 0.685097 AGGGAAAACAGCTGCTCGTA 59.315 50.000 15.27 0.00 0.00 3.43
2640 6139 0.179018 AAGGGAAAACAGCTGCTCGT 60.179 50.000 15.27 0.00 0.00 4.18
2706 6230 9.535170 TGTGTCCTTGAAATACCCATTTATTTA 57.465 29.630 0.00 0.00 34.44 1.40
2707 6231 8.429237 TGTGTCCTTGAAATACCCATTTATTT 57.571 30.769 0.00 0.00 34.44 1.40
2708 6232 8.608185 ATGTGTCCTTGAAATACCCATTTATT 57.392 30.769 0.00 0.00 34.44 1.40
2709 6233 8.061304 AGATGTGTCCTTGAAATACCCATTTAT 58.939 33.333 0.00 0.00 34.44 1.40
2710 6234 7.410174 AGATGTGTCCTTGAAATACCCATTTA 58.590 34.615 0.00 0.00 34.44 1.40
2711 6235 6.256053 AGATGTGTCCTTGAAATACCCATTT 58.744 36.000 0.00 0.00 37.06 2.32
2712 6236 5.831103 AGATGTGTCCTTGAAATACCCATT 58.169 37.500 0.00 0.00 0.00 3.16
2713 6237 5.456921 AGATGTGTCCTTGAAATACCCAT 57.543 39.130 0.00 0.00 0.00 4.00
2714 6238 4.927267 AGATGTGTCCTTGAAATACCCA 57.073 40.909 0.00 0.00 0.00 4.51
2715 6239 6.235231 TCTAGATGTGTCCTTGAAATACCC 57.765 41.667 0.00 0.00 0.00 3.69
2716 6240 7.721286 CATCTAGATGTGTCCTTGAAATACC 57.279 40.000 22.42 0.00 34.23 2.73
2731 6255 8.079203 GTGACATAACTAGGACACATCTAGATG 58.921 40.741 27.63 27.63 44.15 2.90
2732 6256 7.780271 TGTGACATAACTAGGACACATCTAGAT 59.220 37.037 0.00 0.00 37.63 1.98
2733 6257 7.116736 TGTGACATAACTAGGACACATCTAGA 58.883 38.462 0.00 0.00 37.63 2.43
2734 6258 7.334844 TGTGACATAACTAGGACACATCTAG 57.665 40.000 3.26 0.00 37.63 2.43
2735 6259 7.898014 ATGTGACATAACTAGGACACATCTA 57.102 36.000 11.73 0.00 44.99 1.98
2736 6260 6.798427 ATGTGACATAACTAGGACACATCT 57.202 37.500 11.73 0.00 44.99 2.90
2739 6263 7.363530 GGTTAGATGTGACATAACTAGGACACA 60.364 40.741 10.13 8.62 43.79 3.72
2740 6264 6.979238 GGTTAGATGTGACATAACTAGGACAC 59.021 42.308 10.13 0.00 34.33 3.67
2741 6265 6.895756 AGGTTAGATGTGACATAACTAGGACA 59.104 38.462 10.13 0.00 31.53 4.02
2742 6266 7.068348 TCAGGTTAGATGTGACATAACTAGGAC 59.932 40.741 10.13 1.19 31.53 3.85
2743 6267 7.123383 TCAGGTTAGATGTGACATAACTAGGA 58.877 38.462 10.13 4.48 31.53 2.94
2744 6268 7.348080 TCAGGTTAGATGTGACATAACTAGG 57.652 40.000 10.13 2.70 31.53 3.02
2745 6269 7.383572 GCATCAGGTTAGATGTGACATAACTAG 59.616 40.741 10.13 4.86 45.58 2.57
2746 6270 7.210174 GCATCAGGTTAGATGTGACATAACTA 58.790 38.462 10.13 1.46 45.58 2.24
2747 6271 6.051717 GCATCAGGTTAGATGTGACATAACT 58.948 40.000 10.13 2.33 45.58 2.24
2748 6272 5.237344 GGCATCAGGTTAGATGTGACATAAC 59.763 44.000 0.00 0.00 45.58 1.89
2749 6273 5.368145 GGCATCAGGTTAGATGTGACATAA 58.632 41.667 0.00 0.00 45.58 1.90
2750 6274 4.202357 GGGCATCAGGTTAGATGTGACATA 60.202 45.833 0.00 0.00 45.58 2.29
2751 6275 3.434167 GGGCATCAGGTTAGATGTGACAT 60.434 47.826 0.00 0.00 45.58 3.06
2752 6276 2.092968 GGGCATCAGGTTAGATGTGACA 60.093 50.000 5.90 0.00 45.58 3.58
2753 6277 2.092968 TGGGCATCAGGTTAGATGTGAC 60.093 50.000 5.90 0.00 45.58 3.67
2754 6278 2.195727 TGGGCATCAGGTTAGATGTGA 58.804 47.619 5.90 0.00 45.58 3.58
2755 6279 2.715749 TGGGCATCAGGTTAGATGTG 57.284 50.000 5.90 0.00 45.58 3.21
2756 6280 3.959495 AATGGGCATCAGGTTAGATGT 57.041 42.857 5.90 0.00 45.58 3.06
2757 6281 9.857656 AATATATAATGGGCATCAGGTTAGATG 57.142 33.333 0.00 0.00 46.36 2.90
2758 6282 9.857656 CAATATATAATGGGCATCAGGTTAGAT 57.142 33.333 0.00 0.00 0.00 1.98
2759 6283 8.274322 CCAATATATAATGGGCATCAGGTTAGA 58.726 37.037 8.77 0.00 32.87 2.10
2760 6284 8.455903 CCAATATATAATGGGCATCAGGTTAG 57.544 38.462 8.77 0.00 32.87 2.34
2794 6318 9.744468 GAACAAAGAAAAATAGCTAGGACAAAA 57.256 29.630 0.00 0.00 0.00 2.44
2795 6319 9.131791 AGAACAAAGAAAAATAGCTAGGACAAA 57.868 29.630 0.00 0.00 0.00 2.83
2796 6320 8.691661 AGAACAAAGAAAAATAGCTAGGACAA 57.308 30.769 0.00 0.00 0.00 3.18
2797 6321 8.691661 AAGAACAAAGAAAAATAGCTAGGACA 57.308 30.769 0.00 0.00 0.00 4.02
2798 6322 9.399403 CAAAGAACAAAGAAAAATAGCTAGGAC 57.601 33.333 0.00 0.00 0.00 3.85
2799 6323 9.131791 ACAAAGAACAAAGAAAAATAGCTAGGA 57.868 29.630 0.00 0.00 0.00 2.94
2800 6324 9.750125 AACAAAGAACAAAGAAAAATAGCTAGG 57.250 29.630 0.00 0.00 0.00 3.02
2802 6326 9.030301 GCAACAAAGAACAAAGAAAAATAGCTA 57.970 29.630 0.00 0.00 0.00 3.32
2803 6327 7.765819 AGCAACAAAGAACAAAGAAAAATAGCT 59.234 29.630 0.00 0.00 0.00 3.32
2804 6328 7.847564 CAGCAACAAAGAACAAAGAAAAATAGC 59.152 33.333 0.00 0.00 0.00 2.97
2805 6329 8.872845 ACAGCAACAAAGAACAAAGAAAAATAG 58.127 29.630 0.00 0.00 0.00 1.73
2806 6330 8.770438 ACAGCAACAAAGAACAAAGAAAAATA 57.230 26.923 0.00 0.00 0.00 1.40
2807 6331 7.603784 AGACAGCAACAAAGAACAAAGAAAAAT 59.396 29.630 0.00 0.00 0.00 1.82
2808 6332 6.928492 AGACAGCAACAAAGAACAAAGAAAAA 59.072 30.769 0.00 0.00 0.00 1.94
2809 6333 6.454795 AGACAGCAACAAAGAACAAAGAAAA 58.545 32.000 0.00 0.00 0.00 2.29
2810 6334 6.024552 AGACAGCAACAAAGAACAAAGAAA 57.975 33.333 0.00 0.00 0.00 2.52
2811 6335 5.643379 AGACAGCAACAAAGAACAAAGAA 57.357 34.783 0.00 0.00 0.00 2.52
2812 6336 5.643379 AAGACAGCAACAAAGAACAAAGA 57.357 34.783 0.00 0.00 0.00 2.52
2813 6337 7.992180 AATAAGACAGCAACAAAGAACAAAG 57.008 32.000 0.00 0.00 0.00 2.77
2814 6338 7.816995 ACAAATAAGACAGCAACAAAGAACAAA 59.183 29.630 0.00 0.00 0.00 2.83
2815 6339 7.275341 CACAAATAAGACAGCAACAAAGAACAA 59.725 33.333 0.00 0.00 0.00 2.83
2816 6340 6.751425 CACAAATAAGACAGCAACAAAGAACA 59.249 34.615 0.00 0.00 0.00 3.18
2817 6341 6.198966 CCACAAATAAGACAGCAACAAAGAAC 59.801 38.462 0.00 0.00 0.00 3.01
2818 6342 6.272318 CCACAAATAAGACAGCAACAAAGAA 58.728 36.000 0.00 0.00 0.00 2.52
2819 6343 5.221224 CCCACAAATAAGACAGCAACAAAGA 60.221 40.000 0.00 0.00 0.00 2.52
2820 6344 4.984161 CCCACAAATAAGACAGCAACAAAG 59.016 41.667 0.00 0.00 0.00 2.77
2821 6345 4.646945 TCCCACAAATAAGACAGCAACAAA 59.353 37.500 0.00 0.00 0.00 2.83
2822 6346 4.211125 TCCCACAAATAAGACAGCAACAA 58.789 39.130 0.00 0.00 0.00 2.83
2823 6347 3.820467 CTCCCACAAATAAGACAGCAACA 59.180 43.478 0.00 0.00 0.00 3.33
2824 6348 4.072131 TCTCCCACAAATAAGACAGCAAC 58.928 43.478 0.00 0.00 0.00 4.17
2825 6349 4.365514 TCTCCCACAAATAAGACAGCAA 57.634 40.909 0.00 0.00 0.00 3.91
2826 6350 4.574674 ATCTCCCACAAATAAGACAGCA 57.425 40.909 0.00 0.00 0.00 4.41
2827 6351 6.349300 TCTAATCTCCCACAAATAAGACAGC 58.651 40.000 0.00 0.00 0.00 4.40
2828 6352 7.989741 ACATCTAATCTCCCACAAATAAGACAG 59.010 37.037 0.00 0.00 0.00 3.51
2829 6353 7.770433 CACATCTAATCTCCCACAAATAAGACA 59.230 37.037 0.00 0.00 0.00 3.41
2830 6354 7.987458 TCACATCTAATCTCCCACAAATAAGAC 59.013 37.037 0.00 0.00 0.00 3.01
2831 6355 8.089625 TCACATCTAATCTCCCACAAATAAGA 57.910 34.615 0.00 0.00 0.00 2.10
2832 6356 8.915057 ATCACATCTAATCTCCCACAAATAAG 57.085 34.615 0.00 0.00 0.00 1.73
2835 6359 8.105829 GGATATCACATCTAATCTCCCACAAAT 58.894 37.037 4.83 0.00 0.00 2.32
2836 6360 7.293299 AGGATATCACATCTAATCTCCCACAAA 59.707 37.037 4.83 0.00 0.00 2.83
2837 6361 6.789457 AGGATATCACATCTAATCTCCCACAA 59.211 38.462 4.83 0.00 0.00 3.33
2838 6362 6.326161 AGGATATCACATCTAATCTCCCACA 58.674 40.000 4.83 0.00 0.00 4.17
2839 6363 6.865834 AGGATATCACATCTAATCTCCCAC 57.134 41.667 4.83 0.00 0.00 4.61
2840 6364 8.972662 TTAAGGATATCACATCTAATCTCCCA 57.027 34.615 4.83 0.00 0.00 4.37
2933 6700 1.663695 CTGCCGTATGATTTTCGGGT 58.336 50.000 5.06 0.00 43.77 5.28
2950 6717 2.158856 TGATGATCCTTGTAGGCAGCTG 60.159 50.000 10.11 10.11 34.61 4.24
3085 6860 8.747538 AAGTGTAGGTTCACTCATTTTACTTT 57.252 30.769 0.00 0.00 46.25 2.66
3086 6861 8.747538 AAAGTGTAGGTTCACTCATTTTACTT 57.252 30.769 0.00 0.00 46.25 2.24
3128 6903 4.973396 TCACTACAAACTACATACGGACG 58.027 43.478 0.00 0.00 0.00 4.79
3129 6904 7.758528 AGATTTCACTACAAACTACATACGGAC 59.241 37.037 0.00 0.00 0.00 4.79
3132 6907 8.912787 AGAGATTTCACTACAAACTACATACG 57.087 34.615 0.00 0.00 0.00 3.06
3156 6931 9.186837 TCCGTTCCTAAATATAAGCCTCTATAG 57.813 37.037 0.00 0.00 0.00 1.31
3157 6932 9.186837 CTCCGTTCCTAAATATAAGCCTCTATA 57.813 37.037 0.00 0.00 0.00 1.31
3159 6934 6.436532 CCTCCGTTCCTAAATATAAGCCTCTA 59.563 42.308 0.00 0.00 0.00 2.43
3161 6936 5.480205 CCTCCGTTCCTAAATATAAGCCTC 58.520 45.833 0.00 0.00 0.00 4.70
3163 6938 4.285260 TCCCTCCGTTCCTAAATATAAGCC 59.715 45.833 0.00 0.00 0.00 4.35
3164 6939 5.011840 ACTCCCTCCGTTCCTAAATATAAGC 59.988 44.000 0.00 0.00 0.00 3.09
3165 6940 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3166 6941 9.827198 TTATACTCCCTCCGTTCCTAAATATAA 57.173 33.333 0.00 0.00 0.00 0.98
3179 6954 3.488363 ACAGTAGCTTATACTCCCTCCG 58.512 50.000 0.00 0.00 0.00 4.63
3185 6960 9.915629 AAAGCATACATACAGTAGCTTATACTC 57.084 33.333 0.00 0.00 41.74 2.59
3190 6965 6.802608 ACGAAAGCATACATACAGTAGCTTA 58.197 36.000 0.00 0.00 41.74 3.09
3195 6970 8.030692 ACTGTTAACGAAAGCATACATACAGTA 58.969 33.333 0.00 0.00 40.24 2.74


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

AutoCloner maintained by Alex Coulton.