Multiple sequence alignment - TraesCS4A01G198200

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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 TraesCS4A01G198200 chr4A 100.000 2987 0 0 1 2987 483384497 483381511 0.000000e+00 5517
1 TraesCS4A01G198200 chr4A 91.111 180 13 1 1270 1449 455302761 455302937 1.070000e-59 241
2 TraesCS4A01G198200 chr4D 93.012 2819 107 38 236 2987 95875805 95878600 0.000000e+00 4032
3 TraesCS4A01G198200 chr4D 87.500 240 28 2 1 239 508594502 508594264 2.930000e-70 276
4 TraesCS4A01G198200 chr4D 85.776 232 33 0 1 232 4086216 4086447 2.300000e-61 246
5 TraesCS4A01G198200 chr4B 95.423 1704 54 15 518 2213 135811734 135813421 0.000000e+00 2693
6 TraesCS4A01G198200 chr4B 94.483 725 24 7 2269 2987 135814342 135815056 0.000000e+00 1103
7 TraesCS4A01G198200 chr4B 87.352 253 28 4 259 510 135803260 135803509 1.350000e-73 287
8 TraesCS4A01G198200 chr4B 91.111 180 13 1 1270 1449 142710325 142710149 1.070000e-59 241
9 TraesCS4A01G198200 chr5A 76.981 934 164 31 1064 1987 280238921 280238029 1.240000e-133 486
10 TraesCS4A01G198200 chr5D 76.552 934 168 31 1064 1987 214360897 214360005 5.830000e-127 464
11 TraesCS4A01G198200 chr2A 88.085 235 26 2 1 234 445335512 445335745 8.150000e-71 278
12 TraesCS4A01G198200 chr3D 87.554 233 27 2 1 232 7858034 7858265 4.910000e-68 268
13 TraesCS4A01G198200 chr3D 87.179 234 30 0 1 234 7915708 7915941 1.770000e-67 267
14 TraesCS4A01G198200 chr1B 92.391 184 11 1 1270 1453 613023126 613022946 2.950000e-65 259
15 TraesCS4A01G198200 chr1B 92.308 169 12 1 1521 1688 613022925 613022757 3.850000e-59 239
16 TraesCS4A01G198200 chr6D 86.076 237 31 2 1 236 41946887 41946652 1.370000e-63 254
17 TraesCS4A01G198200 chr1D 86.325 234 29 1 1 234 457040854 457041084 4.940000e-63 252
18 TraesCS4A01G198200 chr3B 85.470 234 34 0 1 234 10152658 10152891 8.270000e-61 244
19 TraesCS4A01G198200 chr3B 85.470 234 33 1 1 234 813927272 813927040 2.970000e-60 243
20 TraesCS4A01G198200 chr1A 88.614 202 22 1 1486 1686 323262163 323262364 8.270000e-61 244
21 TraesCS4A01G198200 chr1A 89.894 188 16 1 1266 1453 323261978 323262162 3.850000e-59 239
22 TraesCS4A01G198200 chr5B 78.723 329 59 8 2651 2976 229086056 229085736 3.020000e-50 209
23 TraesCS4A01G198200 chr6A 93.333 135 8 1 1554 1687 591103881 591103747 6.530000e-47 198
24 TraesCS4A01G198200 chr6A 93.333 135 8 1 1554 1687 591127615 591127481 6.530000e-47 198
25 TraesCS4A01G198200 chr6A 93.333 135 8 1 1554 1687 591128942 591128808 6.530000e-47 198


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 TraesCS4A01G198200 chr4A 483381511 483384497 2986 True 5517 5517 100.000 1 2987 1 chr4A.!!$R1 2986
1 TraesCS4A01G198200 chr4D 95875805 95878600 2795 False 4032 4032 93.012 236 2987 1 chr4D.!!$F2 2751
2 TraesCS4A01G198200 chr4B 135811734 135815056 3322 False 1898 2693 94.953 518 2987 2 chr4B.!!$F2 2469
3 TraesCS4A01G198200 chr5A 280238029 280238921 892 True 486 486 76.981 1064 1987 1 chr5A.!!$R1 923
4 TraesCS4A01G198200 chr5D 214360005 214360897 892 True 464 464 76.552 1064 1987 1 chr5D.!!$R1 923

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
214 215 0.035176 TGGGTCGAGGGTTTTTACGG 59.965 55.0 0.0 0.0 0.0 4.02 F
216 217 0.321346 GGTCGAGGGTTTTTACGGGA 59.679 55.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1863 1899 2.391389 CGCGCTCTTCCCTTTCACC 61.391 63.158 5.56 0.00 0.00 4.02 R
1989 2025 2.697250 CTACTAGTCGATGCGCGCGT 62.697 60.000 32.35 28.54 40.61 6.01 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
18 19 3.283020 GGGTTGAAATGTCCCTCCC 57.717 57.895 0.00 0.00 38.29 4.30
19 20 0.679960 GGGTTGAAATGTCCCTCCCG 60.680 60.000 0.00 0.00 38.29 5.14
20 21 1.313091 GGTTGAAATGTCCCTCCCGC 61.313 60.000 0.00 0.00 0.00 6.13
21 22 1.001393 TTGAAATGTCCCTCCCGCC 60.001 57.895 0.00 0.00 0.00 6.13
22 23 1.784301 TTGAAATGTCCCTCCCGCCA 61.784 55.000 0.00 0.00 0.00 5.69
23 24 1.001393 GAAATGTCCCTCCCGCCAA 60.001 57.895 0.00 0.00 0.00 4.52
24 25 1.304134 AAATGTCCCTCCCGCCAAC 60.304 57.895 0.00 0.00 0.00 3.77
25 26 2.781431 AAATGTCCCTCCCGCCAACC 62.781 60.000 0.00 0.00 0.00 3.77
31 32 4.697756 CTCCCGCCAACCGCTTCA 62.698 66.667 0.00 0.00 35.03 3.02
34 35 2.047655 CCGCCAACCGCTTCACTA 60.048 61.111 0.00 0.00 35.03 2.74
35 36 1.449601 CCGCCAACCGCTTCACTAT 60.450 57.895 0.00 0.00 35.03 2.12
36 37 1.705337 CCGCCAACCGCTTCACTATG 61.705 60.000 0.00 0.00 35.03 2.23
37 38 0.739462 CGCCAACCGCTTCACTATGA 60.739 55.000 0.00 0.00 34.21 2.15
38 39 1.668419 GCCAACCGCTTCACTATGAT 58.332 50.000 0.00 0.00 0.00 2.45
39 40 2.801699 CGCCAACCGCTTCACTATGATA 60.802 50.000 0.00 0.00 34.21 2.15
40 41 2.544267 GCCAACCGCTTCACTATGATAC 59.456 50.000 0.00 0.00 0.00 2.24
41 42 2.794910 CCAACCGCTTCACTATGATACG 59.205 50.000 0.00 0.00 0.00 3.06
42 43 2.794910 CAACCGCTTCACTATGATACGG 59.205 50.000 14.87 14.87 45.23 4.02
43 44 1.340248 ACCGCTTCACTATGATACGGG 59.660 52.381 18.59 5.15 44.51 5.28
44 45 1.336887 CCGCTTCACTATGATACGGGG 60.337 57.143 10.59 3.32 39.84 5.73
45 46 1.797025 GCTTCACTATGATACGGGGC 58.203 55.000 0.00 0.00 0.00 5.80
46 47 1.070134 GCTTCACTATGATACGGGGCA 59.930 52.381 0.00 0.00 0.00 5.36
47 48 2.289694 GCTTCACTATGATACGGGGCAT 60.290 50.000 0.00 0.00 0.00 4.40
48 49 3.589988 CTTCACTATGATACGGGGCATC 58.410 50.000 0.00 0.00 0.00 3.91
49 50 1.544246 TCACTATGATACGGGGCATCG 59.456 52.381 0.00 0.00 0.00 3.84
50 51 1.272490 CACTATGATACGGGGCATCGT 59.728 52.381 9.80 9.80 45.88 3.73
52 53 2.753452 ACTATGATACGGGGCATCGTAG 59.247 50.000 15.30 12.20 46.65 3.51
53 54 0.895530 ATGATACGGGGCATCGTAGG 59.104 55.000 15.30 0.00 46.65 3.18
54 55 1.183030 TGATACGGGGCATCGTAGGG 61.183 60.000 15.30 0.00 46.65 3.53
55 56 1.885163 GATACGGGGCATCGTAGGGG 61.885 65.000 15.30 0.00 46.65 4.79
59 60 4.301027 GGGCATCGTAGGGGCGAG 62.301 72.222 0.00 0.00 44.43 5.03
60 61 4.301027 GGCATCGTAGGGGCGAGG 62.301 72.222 0.00 0.00 44.43 4.63
62 63 4.647615 CATCGTAGGGGCGAGGCG 62.648 72.222 0.00 0.00 44.43 5.52
66 67 3.777910 GTAGGGGCGAGGCGGAAA 61.778 66.667 0.00 0.00 0.00 3.13
67 68 3.777910 TAGGGGCGAGGCGGAAAC 61.778 66.667 0.00 0.00 0.00 2.78
74 75 2.263540 GAGGCGGAAACCTGCGTA 59.736 61.111 0.00 0.00 41.32 4.42
75 76 1.153429 GAGGCGGAAACCTGCGTAT 60.153 57.895 0.00 0.00 41.32 3.06
76 77 0.743345 GAGGCGGAAACCTGCGTATT 60.743 55.000 0.00 0.00 41.32 1.89
77 78 0.322187 AGGCGGAAACCTGCGTATTT 60.322 50.000 0.00 0.00 39.13 1.40
78 79 0.179174 GGCGGAAACCTGCGTATTTG 60.179 55.000 0.00 0.00 38.87 2.32
79 80 0.796870 GCGGAAACCTGCGTATTTGC 60.797 55.000 0.00 0.00 38.87 3.68
80 81 0.520412 CGGAAACCTGCGTATTTGCG 60.520 55.000 6.04 6.04 41.96 4.85
81 82 0.179174 GGAAACCTGCGTATTTGCGG 60.179 55.000 0.00 0.00 41.02 5.69
87 88 0.655733 CTGCGTATTTGCGGGTTAGG 59.344 55.000 0.00 0.00 37.59 2.69
88 89 0.745128 TGCGTATTTGCGGGTTAGGG 60.745 55.000 0.00 0.00 37.81 3.53
89 90 2.019337 CGTATTTGCGGGTTAGGGC 58.981 57.895 0.00 0.00 0.00 5.19
90 91 1.441732 CGTATTTGCGGGTTAGGGCC 61.442 60.000 0.00 0.00 0.00 5.80
91 92 1.153127 TATTTGCGGGTTAGGGCCG 60.153 57.895 0.00 0.00 0.00 6.13
92 93 1.624479 TATTTGCGGGTTAGGGCCGA 61.624 55.000 0.00 0.00 0.00 5.54
93 94 2.886730 ATTTGCGGGTTAGGGCCGAG 62.887 60.000 0.00 0.00 0.00 4.63
95 96 3.547513 GCGGGTTAGGGCCGAGAT 61.548 66.667 0.00 0.00 0.00 2.75
96 97 3.103091 GCGGGTTAGGGCCGAGATT 62.103 63.158 0.00 0.00 0.00 2.40
97 98 1.525442 CGGGTTAGGGCCGAGATTT 59.475 57.895 0.00 0.00 0.00 2.17
98 99 0.107361 CGGGTTAGGGCCGAGATTTT 60.107 55.000 0.00 0.00 0.00 1.82
99 100 1.389555 GGGTTAGGGCCGAGATTTTG 58.610 55.000 0.00 0.00 0.00 2.44
100 101 0.738975 GGTTAGGGCCGAGATTTTGC 59.261 55.000 0.00 0.00 0.00 3.68
101 102 0.738975 GTTAGGGCCGAGATTTTGCC 59.261 55.000 0.00 0.00 44.59 4.52
102 103 0.746563 TTAGGGCCGAGATTTTGCCG 60.747 55.000 0.00 0.00 46.31 5.69
103 104 4.193334 GGGCCGAGATTTTGCCGC 62.193 66.667 0.00 0.00 46.31 6.53
104 105 4.536687 GGCCGAGATTTTGCCGCG 62.537 66.667 0.00 0.00 35.08 6.46
106 107 3.499737 CCGAGATTTTGCCGCGCT 61.500 61.111 5.56 0.00 0.00 5.92
107 108 2.021931 CGAGATTTTGCCGCGCTC 59.978 61.111 5.56 0.00 0.00 5.03
108 109 2.405191 GAGATTTTGCCGCGCTCC 59.595 61.111 5.56 0.00 0.00 4.70
109 110 2.045926 AGATTTTGCCGCGCTCCT 60.046 55.556 5.56 0.00 0.00 3.69
110 111 2.041366 GAGATTTTGCCGCGCTCCTC 62.041 60.000 5.56 0.00 0.00 3.71
111 112 2.359850 ATTTTGCCGCGCTCCTCA 60.360 55.556 5.56 0.00 0.00 3.86
112 113 1.922135 GATTTTGCCGCGCTCCTCAA 61.922 55.000 5.56 0.89 0.00 3.02
113 114 1.523154 ATTTTGCCGCGCTCCTCAAA 61.523 50.000 5.56 7.43 0.00 2.69
114 115 1.729470 TTTTGCCGCGCTCCTCAAAA 61.729 50.000 5.56 12.88 36.45 2.44
115 116 1.729470 TTTGCCGCGCTCCTCAAAAA 61.729 50.000 5.56 0.00 0.00 1.94
131 132 2.465860 AAAAATTTTACGGGCTGGCC 57.534 45.000 10.75 10.75 0.00 5.36
132 133 0.245266 AAAATTTTACGGGCTGGCCG 59.755 50.000 36.80 36.80 36.85 6.13
133 134 2.220615 AAATTTTACGGGCTGGCCGC 62.221 55.000 38.05 10.60 36.85 6.53
144 145 4.652131 TGGCCGCGTTTGTGGGAT 62.652 61.111 4.92 0.00 46.30 3.85
145 146 3.810896 GGCCGCGTTTGTGGGATC 61.811 66.667 4.92 0.00 46.30 3.36
146 147 2.746277 GCCGCGTTTGTGGGATCT 60.746 61.111 4.92 0.00 46.30 2.75
147 148 3.039202 GCCGCGTTTGTGGGATCTG 62.039 63.158 4.92 0.00 46.30 2.90
148 149 1.671054 CCGCGTTTGTGGGATCTGT 60.671 57.895 4.92 0.00 42.32 3.41
149 150 1.234615 CCGCGTTTGTGGGATCTGTT 61.235 55.000 4.92 0.00 42.32 3.16
150 151 0.165944 CGCGTTTGTGGGATCTGTTC 59.834 55.000 0.00 0.00 0.00 3.18
151 152 0.165944 GCGTTTGTGGGATCTGTTCG 59.834 55.000 0.00 0.00 0.00 3.95
152 153 0.796312 CGTTTGTGGGATCTGTTCGG 59.204 55.000 0.00 0.00 0.00 4.30
153 154 1.606994 CGTTTGTGGGATCTGTTCGGA 60.607 52.381 0.00 0.00 0.00 4.55
154 155 1.804748 GTTTGTGGGATCTGTTCGGAC 59.195 52.381 0.00 0.00 0.00 4.79
155 156 0.037697 TTGTGGGATCTGTTCGGACG 60.038 55.000 0.00 0.00 0.00 4.79
156 157 1.153628 GTGGGATCTGTTCGGACGG 60.154 63.158 0.00 0.00 0.00 4.79
157 158 2.355986 TGGGATCTGTTCGGACGGG 61.356 63.158 1.96 0.00 32.78 5.28
158 159 2.056223 GGGATCTGTTCGGACGGGA 61.056 63.158 1.96 0.00 32.78 5.14
159 160 1.400530 GGGATCTGTTCGGACGGGAT 61.401 60.000 1.96 2.18 32.78 3.85
160 161 0.464452 GGATCTGTTCGGACGGGATT 59.536 55.000 1.96 0.00 32.78 3.01
161 162 1.134491 GGATCTGTTCGGACGGGATTT 60.134 52.381 1.96 0.00 32.78 2.17
162 163 2.629051 GATCTGTTCGGACGGGATTTT 58.371 47.619 1.96 0.00 32.78 1.82
163 164 2.088950 TCTGTTCGGACGGGATTTTC 57.911 50.000 1.96 0.00 32.78 2.29
164 165 1.084289 CTGTTCGGACGGGATTTTCC 58.916 55.000 0.00 0.00 35.23 3.13
165 166 0.397187 TGTTCGGACGGGATTTTCCA 59.603 50.000 0.00 0.00 38.64 3.53
166 167 1.003812 TGTTCGGACGGGATTTTCCAT 59.996 47.619 0.00 0.00 38.64 3.41
167 168 1.400494 GTTCGGACGGGATTTTCCATG 59.600 52.381 0.00 0.00 38.64 3.66
168 169 0.616371 TCGGACGGGATTTTCCATGT 59.384 50.000 0.00 0.00 38.64 3.21
169 170 1.014352 CGGACGGGATTTTCCATGTC 58.986 55.000 8.75 8.75 40.56 3.06
170 171 1.677518 CGGACGGGATTTTCCATGTCA 60.678 52.381 15.61 0.00 42.04 3.58
171 172 2.442413 GGACGGGATTTTCCATGTCAA 58.558 47.619 15.61 0.00 42.04 3.18
172 173 3.023832 GGACGGGATTTTCCATGTCAAT 58.976 45.455 15.61 0.00 42.04 2.57
173 174 3.066760 GGACGGGATTTTCCATGTCAATC 59.933 47.826 15.61 0.00 42.04 2.67
174 175 3.023832 ACGGGATTTTCCATGTCAATCC 58.976 45.455 15.05 15.05 43.72 3.01
175 176 2.033299 CGGGATTTTCCATGTCAATCCG 59.967 50.000 16.13 10.72 44.90 4.18
176 177 2.223805 GGGATTTTCCATGTCAATCCGC 60.224 50.000 16.13 9.36 44.90 5.54
177 178 2.426738 GGATTTTCCATGTCAATCCGCA 59.573 45.455 10.47 0.00 37.34 5.69
178 179 3.068590 GGATTTTCCATGTCAATCCGCAT 59.931 43.478 10.47 0.00 37.34 4.73
179 180 3.507103 TTTTCCATGTCAATCCGCATG 57.493 42.857 0.00 0.00 41.37 4.06
180 181 2.127271 TTCCATGTCAATCCGCATGT 57.873 45.000 0.00 0.00 40.42 3.21
181 182 2.127271 TCCATGTCAATCCGCATGTT 57.873 45.000 0.00 0.00 40.42 2.71
182 183 1.744522 TCCATGTCAATCCGCATGTTG 59.255 47.619 0.00 0.00 40.42 3.33
183 184 1.744522 CCATGTCAATCCGCATGTTGA 59.255 47.619 0.00 0.00 40.42 3.18
185 186 3.586039 GTCAATCCGCATGTTGACG 57.414 52.632 10.17 0.00 43.08 4.35
186 187 1.075542 GTCAATCCGCATGTTGACGA 58.924 50.000 10.17 0.00 43.08 4.20
187 188 1.665679 GTCAATCCGCATGTTGACGAT 59.334 47.619 10.17 0.00 43.08 3.73
188 189 2.095853 GTCAATCCGCATGTTGACGATT 59.904 45.455 10.17 1.58 43.08 3.34
189 190 3.308595 GTCAATCCGCATGTTGACGATTA 59.691 43.478 10.17 0.00 43.08 1.75
190 191 4.024893 GTCAATCCGCATGTTGACGATTAT 60.025 41.667 10.17 0.00 43.08 1.28
191 192 4.574421 TCAATCCGCATGTTGACGATTATT 59.426 37.500 0.00 0.00 29.93 1.40
192 193 5.065859 TCAATCCGCATGTTGACGATTATTT 59.934 36.000 0.00 0.00 29.93 1.40
193 194 4.955925 TCCGCATGTTGACGATTATTTT 57.044 36.364 0.00 0.00 0.00 1.82
194 195 4.657055 TCCGCATGTTGACGATTATTTTG 58.343 39.130 0.00 0.00 0.00 2.44
195 196 4.155099 TCCGCATGTTGACGATTATTTTGT 59.845 37.500 0.00 0.00 0.00 2.83
196 197 4.262743 CCGCATGTTGACGATTATTTTGTG 59.737 41.667 0.00 0.00 0.00 3.33
197 198 4.262743 CGCATGTTGACGATTATTTTGTGG 59.737 41.667 0.00 0.00 0.00 4.17
198 199 4.562394 GCATGTTGACGATTATTTTGTGGG 59.438 41.667 0.00 0.00 0.00 4.61
199 200 5.708948 CATGTTGACGATTATTTTGTGGGT 58.291 37.500 0.00 0.00 0.00 4.51
200 201 5.365403 TGTTGACGATTATTTTGTGGGTC 57.635 39.130 0.00 0.00 0.00 4.46
201 202 4.083749 TGTTGACGATTATTTTGTGGGTCG 60.084 41.667 0.00 0.00 35.42 4.79
202 203 3.927854 TGACGATTATTTTGTGGGTCGA 58.072 40.909 0.00 0.00 33.68 4.20
203 204 3.930229 TGACGATTATTTTGTGGGTCGAG 59.070 43.478 0.00 0.00 33.68 4.04
204 205 3.267483 ACGATTATTTTGTGGGTCGAGG 58.733 45.455 0.00 0.00 33.68 4.63
205 206 2.612212 CGATTATTTTGTGGGTCGAGGG 59.388 50.000 0.00 0.00 0.00 4.30
206 207 3.617284 GATTATTTTGTGGGTCGAGGGT 58.383 45.455 0.00 0.00 0.00 4.34
207 208 3.512219 TTATTTTGTGGGTCGAGGGTT 57.488 42.857 0.00 0.00 0.00 4.11
208 209 2.375014 ATTTTGTGGGTCGAGGGTTT 57.625 45.000 0.00 0.00 0.00 3.27
209 210 2.146920 TTTTGTGGGTCGAGGGTTTT 57.853 45.000 0.00 0.00 0.00 2.43
210 211 2.146920 TTTGTGGGTCGAGGGTTTTT 57.853 45.000 0.00 0.00 0.00 1.94
211 212 3.294038 TTTGTGGGTCGAGGGTTTTTA 57.706 42.857 0.00 0.00 0.00 1.52
212 213 2.259266 TGTGGGTCGAGGGTTTTTAC 57.741 50.000 0.00 0.00 0.00 2.01
213 214 1.150827 GTGGGTCGAGGGTTTTTACG 58.849 55.000 0.00 0.00 0.00 3.18
214 215 0.035176 TGGGTCGAGGGTTTTTACGG 59.965 55.000 0.00 0.00 0.00 4.02
215 216 0.674581 GGGTCGAGGGTTTTTACGGG 60.675 60.000 0.00 0.00 0.00 5.28
216 217 0.321346 GGTCGAGGGTTTTTACGGGA 59.679 55.000 0.00 0.00 0.00 5.14
217 218 1.065926 GGTCGAGGGTTTTTACGGGAT 60.066 52.381 0.00 0.00 0.00 3.85
218 219 2.274437 GTCGAGGGTTTTTACGGGATC 58.726 52.381 0.00 0.00 0.00 3.36
219 220 2.093816 GTCGAGGGTTTTTACGGGATCT 60.094 50.000 0.00 0.00 0.00 2.75
220 221 2.093869 TCGAGGGTTTTTACGGGATCTG 60.094 50.000 0.00 0.00 0.00 2.90
221 222 2.014857 GAGGGTTTTTACGGGATCTGC 58.985 52.381 0.00 0.00 0.00 4.26
222 223 1.633945 AGGGTTTTTACGGGATCTGCT 59.366 47.619 0.00 0.00 0.00 4.24
223 224 2.841881 AGGGTTTTTACGGGATCTGCTA 59.158 45.455 0.00 0.00 0.00 3.49
224 225 3.118371 AGGGTTTTTACGGGATCTGCTAG 60.118 47.826 0.00 0.00 0.00 3.42
225 226 3.118519 GGGTTTTTACGGGATCTGCTAGA 60.119 47.826 0.00 0.00 0.00 2.43
226 227 4.120589 GGTTTTTACGGGATCTGCTAGAG 58.879 47.826 0.00 0.00 0.00 2.43
227 228 4.382793 GGTTTTTACGGGATCTGCTAGAGT 60.383 45.833 0.00 0.00 0.00 3.24
228 229 5.176592 GTTTTTACGGGATCTGCTAGAGTT 58.823 41.667 0.00 0.00 0.00 3.01
229 230 4.386867 TTTACGGGATCTGCTAGAGTTG 57.613 45.455 0.00 0.00 0.00 3.16
230 231 0.461961 ACGGGATCTGCTAGAGTTGC 59.538 55.000 0.00 0.00 0.00 4.17
231 232 0.749649 CGGGATCTGCTAGAGTTGCT 59.250 55.000 0.00 0.00 0.00 3.91
232 233 1.269517 CGGGATCTGCTAGAGTTGCTC 60.270 57.143 0.00 0.00 0.00 4.26
233 234 2.038659 GGGATCTGCTAGAGTTGCTCT 58.961 52.381 4.02 4.02 43.83 4.09
234 235 3.226777 GGGATCTGCTAGAGTTGCTCTA 58.773 50.000 0.00 5.84 41.50 2.43
235 236 3.639094 GGGATCTGCTAGAGTTGCTCTAA 59.361 47.826 7.22 0.00 41.74 2.10
236 237 4.500716 GGGATCTGCTAGAGTTGCTCTAAC 60.501 50.000 7.22 4.03 41.74 2.34
237 238 4.098654 GGATCTGCTAGAGTTGCTCTAACA 59.901 45.833 7.22 7.86 41.74 2.41
238 239 5.394663 GGATCTGCTAGAGTTGCTCTAACAA 60.395 44.000 9.59 3.76 41.74 2.83
239 240 5.065704 TCTGCTAGAGTTGCTCTAACAAG 57.934 43.478 9.59 6.81 41.74 3.16
240 241 4.524714 TCTGCTAGAGTTGCTCTAACAAGT 59.475 41.667 9.59 0.00 41.74 3.16
261 262 8.166367 CAAGTTAGTTGTAGACACCGTTATAC 57.834 38.462 0.00 0.00 0.00 1.47
262 263 7.452880 AGTTAGTTGTAGACACCGTTATACA 57.547 36.000 0.00 0.00 0.00 2.29
263 264 7.308435 AGTTAGTTGTAGACACCGTTATACAC 58.692 38.462 0.00 0.00 0.00 2.90
297 309 9.202273 CAAGAAAATACTCCTATCAGCTATCAC 57.798 37.037 0.00 0.00 0.00 3.06
309 321 4.242475 TCAGCTATCACGGTGTTAGTTTG 58.758 43.478 21.22 19.11 34.23 2.93
312 324 4.929808 AGCTATCACGGTGTTAGTTTGAAG 59.070 41.667 21.22 4.11 0.00 3.02
340 352 1.609783 CAGAGGCGGGGAAGGAAAT 59.390 57.895 0.00 0.00 0.00 2.17
347 359 3.093814 GGCGGGGAAGGAAATTTTTCTA 58.906 45.455 3.28 0.00 37.35 2.10
367 379 1.150536 AACCCTGGAACACGCATGT 59.849 52.632 0.00 0.00 42.46 3.21
392 404 1.282248 GCGAAACAGACAGCGCTACA 61.282 55.000 10.99 0.00 45.41 2.74
393 405 0.435008 CGAAACAGACAGCGCTACAC 59.565 55.000 10.99 4.38 0.00 2.90
448 460 3.317608 TCGCTCCGTACGATTTCAC 57.682 52.632 18.76 0.00 33.96 3.18
449 461 0.522626 TCGCTCCGTACGATTTCACA 59.477 50.000 18.76 0.00 33.96 3.58
454 466 4.668177 CGCTCCGTACGATTTCACATTTTT 60.668 41.667 18.76 0.00 0.00 1.94
526 546 4.790962 TCCGTCTCCCCGAGTCCG 62.791 72.222 0.00 0.00 0.00 4.79
549 569 0.526211 GTGCCGGTTTGATTTCTCCC 59.474 55.000 1.90 0.00 0.00 4.30
553 573 2.299013 GCCGGTTTGATTTCTCCCTTTT 59.701 45.455 1.90 0.00 0.00 2.27
615 635 3.046374 ACCCACAAGACTAGAAACACCT 58.954 45.455 0.00 0.00 0.00 4.00
620 640 4.335315 CACAAGACTAGAAACACCTTTGCA 59.665 41.667 0.00 0.00 0.00 4.08
640 660 2.888834 TTGAGCAACTTGGCCTTTTC 57.111 45.000 3.32 0.00 0.00 2.29
740 762 7.382218 GTGATAAAACAAACCCAGAAACATCAG 59.618 37.037 0.00 0.00 0.00 2.90
749 771 3.367703 CCCAGAAACATCAGGACATTTGC 60.368 47.826 0.00 0.00 0.00 3.68
781 803 8.606602 CATTTATTTTATTCTGGCCTTTGCTTC 58.393 33.333 3.32 0.00 37.74 3.86
872 898 9.862149 TGATCACTCACCTTACTCACTATATAA 57.138 33.333 0.00 0.00 0.00 0.98
874 900 9.869667 ATCACTCACCTTACTCACTATATAAGT 57.130 33.333 0.00 0.00 39.81 2.24
877 903 9.796180 ACTCACCTTACTCACTATATAAGTAGG 57.204 37.037 0.00 0.00 35.76 3.18
991 1021 3.767230 CGGTGCGAGCTTCGTGTG 61.767 66.667 7.27 0.00 42.81 3.82
1323 1356 3.235481 TTCCCGTTCCCAGCGACA 61.235 61.111 0.00 0.00 0.00 4.35
1324 1357 3.234630 TTCCCGTTCCCAGCGACAG 62.235 63.158 0.00 0.00 0.00 3.51
1416 1449 1.212688 CACAAGGGGGTCTGCATCATA 59.787 52.381 0.00 0.00 0.00 2.15
1506 1539 3.393970 CAGGAGGGCTTCTCGGCA 61.394 66.667 0.00 0.00 43.34 5.69
1863 1899 2.125673 CGGCAGTACGGGGAGTTG 60.126 66.667 0.00 0.00 0.00 3.16
1869 1905 1.071071 CAGTACGGGGAGTTGGTGAAA 59.929 52.381 0.00 0.00 0.00 2.69
2005 2041 3.672397 CACGCGCGCATCGACTAG 61.672 66.667 32.58 14.51 41.67 2.57
2087 2123 4.803426 GACAGAGGGTCGCTGCCG 62.803 72.222 0.00 0.00 36.65 5.69
2128 2164 2.293170 GCAGGGCCAAGAGTTATCTTC 58.707 52.381 6.18 0.00 44.15 2.87
2152 2188 7.160726 TCTTTGCATTAATTTTCAGAAAGGGG 58.839 34.615 0.00 0.00 0.00 4.79
2185 2221 1.675552 ACCGTTGAAAGTTGGGAGTG 58.324 50.000 0.00 0.00 0.00 3.51
2208 2244 6.655425 GTGTAGGACTCCTAATTTTGAAGCTT 59.345 38.462 6.37 0.00 37.91 3.74
2213 2249 7.391833 AGGACTCCTAATTTTGAAGCTTAGTTG 59.608 37.037 0.00 0.00 28.47 3.16
2214 2250 7.362142 GGACTCCTAATTTTGAAGCTTAGTTGG 60.362 40.741 0.00 0.00 0.00 3.77
2215 2251 7.004691 ACTCCTAATTTTGAAGCTTAGTTGGT 58.995 34.615 0.00 0.00 0.00 3.67
2216 2252 7.040409 ACTCCTAATTTTGAAGCTTAGTTGGTG 60.040 37.037 0.00 0.00 0.00 4.17
2217 2253 7.001674 TCCTAATTTTGAAGCTTAGTTGGTGA 58.998 34.615 0.00 0.00 0.00 4.02
2226 2276 7.051623 TGAAGCTTAGTTGGTGAAACTCTTAA 58.948 34.615 0.00 0.00 46.60 1.85
2233 2283 7.096884 AGTTGGTGAAACTCTTAAAAAGGTC 57.903 36.000 0.00 0.00 46.60 3.85
2244 2294 5.690865 TCTTAAAAAGGTCTCTGGAGCAAA 58.309 37.500 0.00 0.00 41.89 3.68
2246 2296 2.575805 AAAGGTCTCTGGAGCAAAGG 57.424 50.000 0.00 0.00 41.89 3.11
2250 2300 2.175715 AGGTCTCTGGAGCAAAGGTTTT 59.824 45.455 0.00 0.00 41.89 2.43
2251 2301 2.294512 GGTCTCTGGAGCAAAGGTTTTG 59.705 50.000 0.00 0.00 39.51 2.44
2274 3201 7.466746 TGCCAAGCTTCAATAGAACTTAAAT 57.533 32.000 0.00 0.00 0.00 1.40
2276 3203 7.814107 TGCCAAGCTTCAATAGAACTTAAATTG 59.186 33.333 0.00 0.00 32.96 2.32
2373 3301 0.904865 AACCCTGATGCTGACCGAGA 60.905 55.000 0.00 0.00 0.00 4.04
2505 3433 6.672657 ACAAGGAAGACCATAAGTACTACCAT 59.327 38.462 0.00 0.00 38.94 3.55
2510 3438 7.453752 GGAAGACCATAAGTACTACCATCCATA 59.546 40.741 0.00 0.00 35.97 2.74
2711 3645 2.224079 CACTCTGTTGGGAAACATGACG 59.776 50.000 0.00 0.00 31.47 4.35
2713 3647 0.240945 CTGTTGGGAAACATGACGCC 59.759 55.000 0.00 0.00 31.47 5.68
2728 3662 1.929836 GACGCCAGAGTTAGAAGCATG 59.070 52.381 0.00 0.00 0.00 4.06
2864 3798 1.899437 GCGAAGGATGGAGGTGGTGA 61.899 60.000 0.00 0.00 0.00 4.02
2894 3828 0.992695 AAAGGTTGGAGTAGAGGGGC 59.007 55.000 0.00 0.00 0.00 5.80
2949 3883 3.149196 TGAAGTTGAATGAAGAGGTGGC 58.851 45.455 0.00 0.00 0.00 5.01
2955 3889 0.674895 AATGAAGAGGTGGCGCTGTC 60.675 55.000 7.64 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.313091 GCGGGAGGGACATTTCAACC 61.313 60.000 0.00 0.00 0.00 3.77
3 4 1.001393 GGCGGGAGGGACATTTCAA 60.001 57.895 0.00 0.00 0.00 2.69
4 5 1.784301 TTGGCGGGAGGGACATTTCA 61.784 55.000 0.00 0.00 0.00 2.69
5 6 1.001393 TTGGCGGGAGGGACATTTC 60.001 57.895 0.00 0.00 0.00 2.17
6 7 1.304134 GTTGGCGGGAGGGACATTT 60.304 57.895 0.00 0.00 0.00 2.32
7 8 2.355115 GTTGGCGGGAGGGACATT 59.645 61.111 0.00 0.00 0.00 2.71
8 9 3.728373 GGTTGGCGGGAGGGACAT 61.728 66.667 0.00 0.00 0.00 3.06
19 20 1.668419 ATCATAGTGAAGCGGTTGGC 58.332 50.000 3.70 0.00 44.05 4.52
20 21 2.794910 CGTATCATAGTGAAGCGGTTGG 59.205 50.000 3.70 0.00 0.00 3.77
21 22 2.794910 CCGTATCATAGTGAAGCGGTTG 59.205 50.000 3.70 0.00 40.39 3.77
22 23 2.223971 CCCGTATCATAGTGAAGCGGTT 60.224 50.000 17.66 0.00 42.22 4.44
23 24 1.340248 CCCGTATCATAGTGAAGCGGT 59.660 52.381 17.66 0.00 42.22 5.68
24 25 1.336887 CCCCGTATCATAGTGAAGCGG 60.337 57.143 14.41 14.41 42.87 5.52
25 26 1.935300 GCCCCGTATCATAGTGAAGCG 60.935 57.143 0.00 0.00 0.00 4.68
26 27 1.070134 TGCCCCGTATCATAGTGAAGC 59.930 52.381 0.00 0.00 0.00 3.86
27 28 3.589988 GATGCCCCGTATCATAGTGAAG 58.410 50.000 0.00 0.00 0.00 3.02
28 29 2.029380 CGATGCCCCGTATCATAGTGAA 60.029 50.000 0.00 0.00 0.00 3.18
29 30 1.544246 CGATGCCCCGTATCATAGTGA 59.456 52.381 0.00 0.00 0.00 3.41
30 31 1.272490 ACGATGCCCCGTATCATAGTG 59.728 52.381 0.00 0.00 41.44 2.74
31 32 1.629043 ACGATGCCCCGTATCATAGT 58.371 50.000 0.00 0.00 41.44 2.12
32 33 2.099263 CCTACGATGCCCCGTATCATAG 59.901 54.545 7.91 0.00 43.05 2.23
33 34 2.097036 CCTACGATGCCCCGTATCATA 58.903 52.381 7.91 0.00 43.05 2.15
34 35 0.895530 CCTACGATGCCCCGTATCAT 59.104 55.000 7.91 0.00 43.05 2.45
35 36 1.183030 CCCTACGATGCCCCGTATCA 61.183 60.000 7.91 0.00 43.05 2.15
36 37 1.590147 CCCTACGATGCCCCGTATC 59.410 63.158 7.91 0.00 43.05 2.24
37 38 1.911766 CCCCTACGATGCCCCGTAT 60.912 63.158 7.91 0.00 43.05 3.06
38 39 2.522436 CCCCTACGATGCCCCGTA 60.522 66.667 7.35 7.35 43.20 4.02
42 43 4.301027 CTCGCCCCTACGATGCCC 62.301 72.222 0.00 0.00 42.02 5.36
43 44 4.301027 CCTCGCCCCTACGATGCC 62.301 72.222 0.00 0.00 42.02 4.40
44 45 4.971125 GCCTCGCCCCTACGATGC 62.971 72.222 0.00 0.00 44.26 3.91
45 46 4.647615 CGCCTCGCCCCTACGATG 62.648 72.222 0.00 0.00 42.02 3.84
49 50 3.777910 TTTCCGCCTCGCCCCTAC 61.778 66.667 0.00 0.00 0.00 3.18
50 51 3.777910 GTTTCCGCCTCGCCCCTA 61.778 66.667 0.00 0.00 0.00 3.53
56 57 2.901051 ATACGCAGGTTTCCGCCTCG 62.901 60.000 0.00 0.00 36.58 4.63
57 58 0.743345 AATACGCAGGTTTCCGCCTC 60.743 55.000 0.00 0.00 36.58 4.70
58 59 0.322187 AAATACGCAGGTTTCCGCCT 60.322 50.000 0.00 0.00 39.99 5.52
59 60 0.179174 CAAATACGCAGGTTTCCGCC 60.179 55.000 0.00 0.00 0.00 6.13
60 61 0.796870 GCAAATACGCAGGTTTCCGC 60.797 55.000 0.00 0.00 0.00 5.54
61 62 0.520412 CGCAAATACGCAGGTTTCCG 60.520 55.000 0.00 0.00 0.00 4.30
62 63 0.179174 CCGCAAATACGCAGGTTTCC 60.179 55.000 0.00 0.00 0.00 3.13
63 64 0.179174 CCCGCAAATACGCAGGTTTC 60.179 55.000 0.00 0.00 0.00 2.78
64 65 0.891904 ACCCGCAAATACGCAGGTTT 60.892 50.000 0.00 0.00 39.75 3.27
65 66 0.891904 AACCCGCAAATACGCAGGTT 60.892 50.000 0.00 0.00 45.73 3.50
66 67 0.036199 TAACCCGCAAATACGCAGGT 60.036 50.000 0.00 0.00 44.72 4.00
67 68 0.655733 CTAACCCGCAAATACGCAGG 59.344 55.000 0.00 0.00 35.44 4.85
68 69 0.655733 CCTAACCCGCAAATACGCAG 59.344 55.000 0.00 0.00 0.00 5.18
69 70 0.745128 CCCTAACCCGCAAATACGCA 60.745 55.000 0.00 0.00 0.00 5.24
70 71 2.019337 CCCTAACCCGCAAATACGC 58.981 57.895 0.00 0.00 0.00 4.42
71 72 1.441732 GGCCCTAACCCGCAAATACG 61.442 60.000 0.00 0.00 0.00 3.06
72 73 1.441732 CGGCCCTAACCCGCAAATAC 61.442 60.000 0.00 0.00 39.22 1.89
73 74 1.153127 CGGCCCTAACCCGCAAATA 60.153 57.895 0.00 0.00 39.22 1.40
74 75 2.439519 CGGCCCTAACCCGCAAAT 60.440 61.111 0.00 0.00 39.22 2.32
75 76 3.615509 CTCGGCCCTAACCCGCAAA 62.616 63.158 0.00 0.00 45.19 3.68
76 77 4.090588 CTCGGCCCTAACCCGCAA 62.091 66.667 0.00 0.00 45.19 4.85
78 79 2.604299 AAATCTCGGCCCTAACCCGC 62.604 60.000 0.00 0.00 45.19 6.13
79 80 0.107361 AAAATCTCGGCCCTAACCCG 60.107 55.000 0.00 0.00 46.88 5.28
80 81 1.389555 CAAAATCTCGGCCCTAACCC 58.610 55.000 0.00 0.00 0.00 4.11
81 82 0.738975 GCAAAATCTCGGCCCTAACC 59.261 55.000 0.00 0.00 0.00 2.85
82 83 0.738975 GGCAAAATCTCGGCCCTAAC 59.261 55.000 0.00 0.00 41.90 2.34
83 84 0.746563 CGGCAAAATCTCGGCCCTAA 60.747 55.000 0.00 0.00 44.90 2.69
84 85 1.153249 CGGCAAAATCTCGGCCCTA 60.153 57.895 0.00 0.00 44.90 3.53
85 86 2.438434 CGGCAAAATCTCGGCCCT 60.438 61.111 0.00 0.00 44.90 5.19
86 87 4.193334 GCGGCAAAATCTCGGCCC 62.193 66.667 0.00 0.00 44.90 5.80
87 88 4.536687 CGCGGCAAAATCTCGGCC 62.537 66.667 0.00 0.00 44.27 6.13
89 90 3.440356 GAGCGCGGCAAAATCTCGG 62.440 63.158 8.83 0.00 0.00 4.63
90 91 2.021931 GAGCGCGGCAAAATCTCG 59.978 61.111 8.83 0.00 0.00 4.04
91 92 2.041366 GAGGAGCGCGGCAAAATCTC 62.041 60.000 8.83 3.40 0.00 2.75
92 93 2.045926 AGGAGCGCGGCAAAATCT 60.046 55.556 8.83 0.00 0.00 2.40
93 94 1.922135 TTGAGGAGCGCGGCAAAATC 61.922 55.000 8.83 0.00 0.00 2.17
94 95 1.523154 TTTGAGGAGCGCGGCAAAAT 61.523 50.000 8.83 0.00 0.00 1.82
95 96 1.729470 TTTTGAGGAGCGCGGCAAAA 61.729 50.000 20.42 20.42 37.74 2.44
96 97 1.729470 TTTTTGAGGAGCGCGGCAAA 61.729 50.000 8.83 8.74 0.00 3.68
97 98 2.190170 TTTTTGAGGAGCGCGGCAA 61.190 52.632 8.83 2.22 0.00 4.52
98 99 2.593148 TTTTTGAGGAGCGCGGCA 60.593 55.556 8.83 0.00 0.00 5.69
112 113 2.465860 GGCCAGCCCGTAAAATTTTT 57.534 45.000 9.06 0.00 0.00 1.94
127 128 4.652131 ATCCCACAAACGCGGCCA 62.652 61.111 12.47 0.00 0.00 5.36
128 129 3.810896 GATCCCACAAACGCGGCC 61.811 66.667 12.47 0.00 0.00 6.13
129 130 2.746277 AGATCCCACAAACGCGGC 60.746 61.111 12.47 0.00 0.00 6.53
130 131 1.234615 AACAGATCCCACAAACGCGG 61.235 55.000 12.47 0.00 0.00 6.46
131 132 0.165944 GAACAGATCCCACAAACGCG 59.834 55.000 3.53 3.53 0.00 6.01
132 133 0.165944 CGAACAGATCCCACAAACGC 59.834 55.000 0.00 0.00 0.00 4.84
133 134 0.796312 CCGAACAGATCCCACAAACG 59.204 55.000 0.00 0.00 0.00 3.60
134 135 1.804748 GTCCGAACAGATCCCACAAAC 59.195 52.381 0.00 0.00 0.00 2.93
135 136 1.606994 CGTCCGAACAGATCCCACAAA 60.607 52.381 0.00 0.00 0.00 2.83
136 137 0.037697 CGTCCGAACAGATCCCACAA 60.038 55.000 0.00 0.00 0.00 3.33
137 138 1.589630 CGTCCGAACAGATCCCACA 59.410 57.895 0.00 0.00 0.00 4.17
138 139 1.153628 CCGTCCGAACAGATCCCAC 60.154 63.158 0.00 0.00 0.00 4.61
139 140 2.355986 CCCGTCCGAACAGATCCCA 61.356 63.158 0.00 0.00 0.00 4.37
140 141 1.400530 ATCCCGTCCGAACAGATCCC 61.401 60.000 0.00 0.00 0.00 3.85
141 142 0.464452 AATCCCGTCCGAACAGATCC 59.536 55.000 0.00 0.00 0.00 3.36
142 143 2.311124 AAATCCCGTCCGAACAGATC 57.689 50.000 0.00 0.00 0.00 2.75
143 144 2.629051 GAAAATCCCGTCCGAACAGAT 58.371 47.619 0.00 0.00 0.00 2.90
144 145 1.338389 GGAAAATCCCGTCCGAACAGA 60.338 52.381 0.00 0.00 0.00 3.41
145 146 1.084289 GGAAAATCCCGTCCGAACAG 58.916 55.000 0.00 0.00 0.00 3.16
146 147 0.397187 TGGAAAATCCCGTCCGAACA 59.603 50.000 0.00 0.00 36.65 3.18
147 148 1.400494 CATGGAAAATCCCGTCCGAAC 59.600 52.381 0.00 0.00 36.65 3.95
148 149 1.003812 ACATGGAAAATCCCGTCCGAA 59.996 47.619 0.00 0.00 36.65 4.30
149 150 0.616371 ACATGGAAAATCCCGTCCGA 59.384 50.000 0.00 0.00 36.65 4.55
150 151 1.014352 GACATGGAAAATCCCGTCCG 58.986 55.000 0.00 0.00 36.65 4.79
151 152 2.122783 TGACATGGAAAATCCCGTCC 57.877 50.000 0.00 0.00 37.23 4.79
152 153 3.066760 GGATTGACATGGAAAATCCCGTC 59.933 47.826 18.61 8.40 42.33 4.79
153 154 3.023832 GGATTGACATGGAAAATCCCGT 58.976 45.455 18.61 0.00 42.33 5.28
154 155 2.033299 CGGATTGACATGGAAAATCCCG 59.967 50.000 21.34 15.66 44.33 5.14
155 156 2.223805 GCGGATTGACATGGAAAATCCC 60.224 50.000 21.34 14.43 44.33 3.85
156 157 2.426738 TGCGGATTGACATGGAAAATCC 59.573 45.455 19.08 19.08 43.93 3.01
157 158 3.781079 TGCGGATTGACATGGAAAATC 57.219 42.857 0.00 3.35 0.00 2.17
158 159 3.448301 ACATGCGGATTGACATGGAAAAT 59.552 39.130 7.78 0.00 46.35 1.82
159 160 2.824936 ACATGCGGATTGACATGGAAAA 59.175 40.909 7.78 0.00 46.35 2.29
160 161 2.445427 ACATGCGGATTGACATGGAAA 58.555 42.857 7.78 0.00 46.35 3.13
161 162 2.127271 ACATGCGGATTGACATGGAA 57.873 45.000 7.78 0.00 46.35 3.53
162 163 1.744522 CAACATGCGGATTGACATGGA 59.255 47.619 7.78 0.00 46.35 3.41
163 164 1.744522 TCAACATGCGGATTGACATGG 59.255 47.619 7.78 0.00 46.35 3.66
168 169 2.022764 ATCGTCAACATGCGGATTGA 57.977 45.000 0.00 0.00 32.44 2.57
169 170 2.830772 AATCGTCAACATGCGGATTG 57.169 45.000 0.00 0.00 0.00 2.67
170 171 5.499139 AAATAATCGTCAACATGCGGATT 57.501 34.783 0.00 0.00 0.00 3.01
171 172 5.163663 ACAAAATAATCGTCAACATGCGGAT 60.164 36.000 0.00 0.00 0.00 4.18
172 173 4.155099 ACAAAATAATCGTCAACATGCGGA 59.845 37.500 0.00 0.00 0.00 5.54
173 174 4.262743 CACAAAATAATCGTCAACATGCGG 59.737 41.667 0.00 0.00 0.00 5.69
174 175 4.262743 CCACAAAATAATCGTCAACATGCG 59.737 41.667 0.00 0.00 0.00 4.73
175 176 4.562394 CCCACAAAATAATCGTCAACATGC 59.438 41.667 0.00 0.00 0.00 4.06
176 177 5.708948 ACCCACAAAATAATCGTCAACATG 58.291 37.500 0.00 0.00 0.00 3.21
177 178 5.391523 CGACCCACAAAATAATCGTCAACAT 60.392 40.000 0.00 0.00 0.00 2.71
178 179 4.083749 CGACCCACAAAATAATCGTCAACA 60.084 41.667 0.00 0.00 0.00 3.33
179 180 4.152759 TCGACCCACAAAATAATCGTCAAC 59.847 41.667 0.00 0.00 0.00 3.18
180 181 4.316645 TCGACCCACAAAATAATCGTCAA 58.683 39.130 0.00 0.00 0.00 3.18
181 182 3.927854 TCGACCCACAAAATAATCGTCA 58.072 40.909 0.00 0.00 0.00 4.35
182 183 3.308866 CCTCGACCCACAAAATAATCGTC 59.691 47.826 0.00 0.00 0.00 4.20
183 184 3.267483 CCTCGACCCACAAAATAATCGT 58.733 45.455 0.00 0.00 0.00 3.73
184 185 2.612212 CCCTCGACCCACAAAATAATCG 59.388 50.000 0.00 0.00 0.00 3.34
185 186 3.617284 ACCCTCGACCCACAAAATAATC 58.383 45.455 0.00 0.00 0.00 1.75
186 187 3.732048 ACCCTCGACCCACAAAATAAT 57.268 42.857 0.00 0.00 0.00 1.28
187 188 3.512219 AACCCTCGACCCACAAAATAA 57.488 42.857 0.00 0.00 0.00 1.40
188 189 3.512219 AAACCCTCGACCCACAAAATA 57.488 42.857 0.00 0.00 0.00 1.40
189 190 2.375014 AAACCCTCGACCCACAAAAT 57.625 45.000 0.00 0.00 0.00 1.82
190 191 2.146920 AAAACCCTCGACCCACAAAA 57.853 45.000 0.00 0.00 0.00 2.44
191 192 2.146920 AAAAACCCTCGACCCACAAA 57.853 45.000 0.00 0.00 0.00 2.83
192 193 2.574450 GTAAAAACCCTCGACCCACAA 58.426 47.619 0.00 0.00 0.00 3.33
193 194 1.540797 CGTAAAAACCCTCGACCCACA 60.541 52.381 0.00 0.00 0.00 4.17
194 195 1.150827 CGTAAAAACCCTCGACCCAC 58.849 55.000 0.00 0.00 0.00 4.61
195 196 0.035176 CCGTAAAAACCCTCGACCCA 59.965 55.000 0.00 0.00 0.00 4.51
196 197 0.674581 CCCGTAAAAACCCTCGACCC 60.675 60.000 0.00 0.00 0.00 4.46
197 198 0.321346 TCCCGTAAAAACCCTCGACC 59.679 55.000 0.00 0.00 0.00 4.79
198 199 2.093816 AGATCCCGTAAAAACCCTCGAC 60.094 50.000 0.00 0.00 0.00 4.20
199 200 2.093869 CAGATCCCGTAAAAACCCTCGA 60.094 50.000 0.00 0.00 0.00 4.04
200 201 2.277084 CAGATCCCGTAAAAACCCTCG 58.723 52.381 0.00 0.00 0.00 4.63
201 202 2.014857 GCAGATCCCGTAAAAACCCTC 58.985 52.381 0.00 0.00 0.00 4.30
202 203 1.633945 AGCAGATCCCGTAAAAACCCT 59.366 47.619 0.00 0.00 0.00 4.34
203 204 2.124277 AGCAGATCCCGTAAAAACCC 57.876 50.000 0.00 0.00 0.00 4.11
204 205 4.120589 CTCTAGCAGATCCCGTAAAAACC 58.879 47.826 0.00 0.00 0.00 3.27
205 206 4.756502 ACTCTAGCAGATCCCGTAAAAAC 58.243 43.478 0.00 0.00 0.00 2.43
206 207 5.175859 CAACTCTAGCAGATCCCGTAAAAA 58.824 41.667 0.00 0.00 0.00 1.94
207 208 4.755411 CAACTCTAGCAGATCCCGTAAAA 58.245 43.478 0.00 0.00 0.00 1.52
208 209 3.430374 GCAACTCTAGCAGATCCCGTAAA 60.430 47.826 0.00 0.00 0.00 2.01
209 210 2.100916 GCAACTCTAGCAGATCCCGTAA 59.899 50.000 0.00 0.00 0.00 3.18
210 211 1.681793 GCAACTCTAGCAGATCCCGTA 59.318 52.381 0.00 0.00 0.00 4.02
211 212 0.461961 GCAACTCTAGCAGATCCCGT 59.538 55.000 0.00 0.00 0.00 5.28
212 213 0.749649 AGCAACTCTAGCAGATCCCG 59.250 55.000 0.00 0.00 0.00 5.14
213 214 2.038659 AGAGCAACTCTAGCAGATCCC 58.961 52.381 0.00 0.00 39.28 3.85
214 215 4.098654 TGTTAGAGCAACTCTAGCAGATCC 59.901 45.833 14.73 0.00 44.88 3.36
215 216 5.255710 TGTTAGAGCAACTCTAGCAGATC 57.744 43.478 14.73 0.00 44.88 2.75
219 220 4.873746 ACTTGTTAGAGCAACTCTAGCA 57.126 40.909 14.73 14.73 46.86 3.49
220 221 6.391537 ACTAACTTGTTAGAGCAACTCTAGC 58.608 40.000 22.59 10.50 42.92 3.42
221 222 7.868415 ACAACTAACTTGTTAGAGCAACTCTAG 59.132 37.037 22.59 0.00 40.45 2.43
222 223 7.723324 ACAACTAACTTGTTAGAGCAACTCTA 58.277 34.615 22.59 0.16 40.45 2.43
223 224 6.583562 ACAACTAACTTGTTAGAGCAACTCT 58.416 36.000 22.59 2.23 40.45 3.24
224 225 6.846325 ACAACTAACTTGTTAGAGCAACTC 57.154 37.500 22.59 0.00 40.45 3.01
225 226 7.652507 GTCTACAACTAACTTGTTAGAGCAACT 59.347 37.037 22.59 1.48 40.45 3.16
226 227 7.437267 TGTCTACAACTAACTTGTTAGAGCAAC 59.563 37.037 22.59 13.86 40.45 4.17
227 228 7.437267 GTGTCTACAACTAACTTGTTAGAGCAA 59.563 37.037 22.59 8.19 40.45 3.91
228 229 6.921857 GTGTCTACAACTAACTTGTTAGAGCA 59.078 38.462 22.59 11.19 40.45 4.26
229 230 6.365518 GGTGTCTACAACTAACTTGTTAGAGC 59.634 42.308 22.59 7.48 40.45 4.09
230 231 6.581542 CGGTGTCTACAACTAACTTGTTAGAG 59.418 42.308 22.59 16.89 40.45 2.43
231 232 6.039717 ACGGTGTCTACAACTAACTTGTTAGA 59.960 38.462 22.59 3.08 40.45 2.10
232 233 6.211515 ACGGTGTCTACAACTAACTTGTTAG 58.788 40.000 16.31 16.31 40.45 2.34
233 234 6.147864 ACGGTGTCTACAACTAACTTGTTA 57.852 37.500 0.00 0.00 40.45 2.41
234 235 5.014808 ACGGTGTCTACAACTAACTTGTT 57.985 39.130 0.00 0.00 40.45 2.83
235 236 4.660789 ACGGTGTCTACAACTAACTTGT 57.339 40.909 0.00 0.00 45.57 3.16
236 237 7.809331 TGTATAACGGTGTCTACAACTAACTTG 59.191 37.037 0.00 0.00 35.77 3.16
237 238 7.809806 GTGTATAACGGTGTCTACAACTAACTT 59.190 37.037 0.00 0.00 0.00 2.66
238 239 7.308435 GTGTATAACGGTGTCTACAACTAACT 58.692 38.462 0.00 0.00 0.00 2.24
239 240 6.528072 GGTGTATAACGGTGTCTACAACTAAC 59.472 42.308 0.00 0.00 30.80 2.34
240 241 6.350110 GGGTGTATAACGGTGTCTACAACTAA 60.350 42.308 10.80 0.00 33.35 2.24
259 260 1.717038 TTTTCTTGGCCGGGGGTGTA 61.717 55.000 2.18 0.00 0.00 2.90
260 261 2.380571 ATTTTCTTGGCCGGGGGTGT 62.381 55.000 2.18 0.00 0.00 4.16
261 262 0.323908 TATTTTCTTGGCCGGGGGTG 60.324 55.000 2.18 0.00 0.00 4.61
262 263 0.323999 GTATTTTCTTGGCCGGGGGT 60.324 55.000 2.18 0.00 0.00 4.95
263 264 0.033503 AGTATTTTCTTGGCCGGGGG 60.034 55.000 2.18 0.00 0.00 5.40
324 336 1.557099 AAAATTTCCTTCCCCGCCTC 58.443 50.000 0.00 0.00 0.00 4.70
340 352 3.628487 CGTGTTCCAGGGTTGTAGAAAAA 59.372 43.478 0.00 0.00 0.00 1.94
347 359 1.150536 ATGCGTGTTCCAGGGTTGT 59.849 52.632 0.00 0.00 0.00 3.32
367 379 1.003972 CGCTGTCTGTTTCGCTGAAAA 60.004 47.619 5.51 0.00 33.14 2.29
401 413 2.047655 GTGTCGGGATGGCAACGA 60.048 61.111 7.98 7.98 42.51 3.85
447 459 5.293569 GCACCTGTAGCTCGTATAAAAATGT 59.706 40.000 0.00 0.00 0.00 2.71
448 460 5.556382 CGCACCTGTAGCTCGTATAAAAATG 60.556 44.000 0.00 0.00 0.00 2.32
449 461 4.506654 CGCACCTGTAGCTCGTATAAAAAT 59.493 41.667 0.00 0.00 0.00 1.82
454 466 1.957668 TCGCACCTGTAGCTCGTATA 58.042 50.000 0.00 0.00 0.00 1.47
476 491 1.342082 CCGTGCGTTACAGAACTCGG 61.342 60.000 0.00 0.00 36.47 4.63
526 546 1.000274 AGAAATCAAACCGGCACAAGC 60.000 47.619 0.00 0.00 41.10 4.01
549 569 3.896238 CGTCACGCGTACATCTTAAAAG 58.104 45.455 13.44 0.00 35.54 2.27
620 640 2.967887 AGAAAAGGCCAAGTTGCTCAAT 59.032 40.909 5.01 0.00 0.00 2.57
769 791 2.601367 GCCCAGAAGCAAAGGCCA 60.601 61.111 5.01 0.00 42.56 5.36
781 803 2.049802 CTTGCTTGCGTTGCCCAG 60.050 61.111 0.00 0.00 0.00 4.45
1416 1449 4.796231 GTCTCCACCACGCGCGAT 62.796 66.667 39.36 18.46 0.00 4.58
1863 1899 2.391389 CGCGCTCTTCCCTTTCACC 61.391 63.158 5.56 0.00 0.00 4.02
1989 2025 2.697250 CTACTAGTCGATGCGCGCGT 62.697 60.000 32.35 28.54 40.61 6.01
2003 2039 5.221303 ACGTGTGAGCAAACCTTTACTACTA 60.221 40.000 0.00 0.00 0.00 1.82
2004 2040 4.056050 CGTGTGAGCAAACCTTTACTACT 58.944 43.478 0.00 0.00 0.00 2.57
2005 2041 3.805971 ACGTGTGAGCAAACCTTTACTAC 59.194 43.478 0.00 0.00 0.00 2.73
2087 2123 4.201773 TGCGCTACAGTACATTTACATTGC 60.202 41.667 9.73 0.00 0.00 3.56
2128 2164 7.160726 TCCCCTTTCTGAAAATTAATGCAAAG 58.839 34.615 4.18 0.00 0.00 2.77
2152 2188 6.424207 ACTTTCAACGGTATCTTCTCAAGTTC 59.576 38.462 0.00 0.00 0.00 3.01
2185 2221 8.041919 ACTAAGCTTCAAAATTAGGAGTCCTAC 58.958 37.037 18.97 4.10 35.63 3.18
2194 2230 8.968242 GTTTCACCAACTAAGCTTCAAAATTAG 58.032 33.333 0.00 0.00 33.63 1.73
2196 2232 7.555965 AGTTTCACCAACTAAGCTTCAAAATT 58.444 30.769 0.00 0.00 44.56 1.82
2197 2233 7.068716 AGAGTTTCACCAACTAAGCTTCAAAAT 59.931 33.333 0.00 0.00 46.53 1.82
2208 2244 8.050930 AGACCTTTTTAAGAGTTTCACCAACTA 58.949 33.333 0.00 0.00 46.53 2.24
2213 2249 6.017026 CCAGAGACCTTTTTAAGAGTTTCACC 60.017 42.308 0.00 0.00 0.00 4.02
2214 2250 6.766467 TCCAGAGACCTTTTTAAGAGTTTCAC 59.234 38.462 0.00 0.00 0.00 3.18
2215 2251 6.895782 TCCAGAGACCTTTTTAAGAGTTTCA 58.104 36.000 0.00 0.00 0.00 2.69
2216 2252 6.072948 GCTCCAGAGACCTTTTTAAGAGTTTC 60.073 42.308 0.00 0.00 0.00 2.78
2217 2253 5.765677 GCTCCAGAGACCTTTTTAAGAGTTT 59.234 40.000 0.00 0.00 0.00 2.66
2226 2276 2.175715 ACCTTTGCTCCAGAGACCTTTT 59.824 45.455 0.00 0.00 0.00 2.27
2233 2283 1.000171 GGCAAAACCTTTGCTCCAGAG 60.000 52.381 20.13 0.00 44.36 3.35
2244 2294 4.151883 TCTATTGAAGCTTGGCAAAACCT 58.848 39.130 2.10 0.00 40.22 3.50
2246 2296 5.532557 AGTTCTATTGAAGCTTGGCAAAAC 58.467 37.500 2.10 4.90 32.15 2.43
2250 2300 6.892658 TTTAAGTTCTATTGAAGCTTGGCA 57.107 33.333 2.10 0.00 32.15 4.92
2251 2301 7.276438 CCAATTTAAGTTCTATTGAAGCTTGGC 59.724 37.037 2.10 0.00 32.36 4.52
2373 3301 4.754618 TCGTGTGTTTTACTGAGCAATCAT 59.245 37.500 0.00 0.00 0.00 2.45
2711 3645 5.643777 TCTTTTACATGCTTCTAACTCTGGC 59.356 40.000 0.00 0.00 0.00 4.85
2713 3647 8.087982 TGTTCTTTTACATGCTTCTAACTCTG 57.912 34.615 0.00 0.00 0.00 3.35
2760 3694 5.011329 ACTTGTTCAGGTATGTTCCTCGTTA 59.989 40.000 0.00 0.00 35.37 3.18
2763 3697 3.926616 ACTTGTTCAGGTATGTTCCTCG 58.073 45.455 0.00 0.00 35.37 4.63
2766 3700 4.894784 TGAGACTTGTTCAGGTATGTTCC 58.105 43.478 0.00 0.00 0.00 3.62
2864 3798 1.289530 TCCAACCTTTTCCACCACCTT 59.710 47.619 0.00 0.00 0.00 3.50
2894 3828 2.586079 CTCAGTACGGGCATGGCG 60.586 66.667 13.76 11.05 0.00 5.69
2949 3883 3.879619 TTCATCAATGATGCCGACAGCG 61.880 50.000 17.81 0.00 39.63 5.18
2955 3889 2.919387 GCCGATTTCATCAATGATGCCG 60.919 50.000 17.81 16.00 39.63 5.69


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

AutoCloner maintained by Alex Coulton.