Multiple sequence alignment - TraesCS1A01G197400

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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 TraesCS1A01G197400 chr1A 100.000 3519 0 0 1 3519 355341906 355345424 0.000000e+00 6499.0
1 TraesCS1A01G197400 chr1A 93.478 46 2 1 2541 2586 143815893 143815849 2.270000e-07 67.6
2 TraesCS1A01G197400 chr1A 93.478 46 2 1 2548 2593 481924462 481924418 2.270000e-07 67.6
3 TraesCS1A01G197400 chr1D 92.743 3307 137 47 276 3518 283616275 283619542 0.000000e+00 4682.0
4 TraesCS1A01G197400 chr1D 86.691 278 23 12 1 277 436207810 436208074 2.660000e-76 296.0
5 TraesCS1A01G197400 chr1B 91.114 3320 150 54 282 3519 385295231 385298487 0.000000e+00 4362.0
6 TraesCS1A01G197400 chr1B 89.091 55 4 2 2533 2586 6423509 6423562 2.270000e-07 67.6
7 TraesCS1A01G197400 chr4D 90.614 277 21 3 1 277 471214525 471214796 2.580000e-96 363.0
8 TraesCS1A01G197400 chr6A 89.892 277 25 1 1 277 203766929 203767202 1.550000e-93 353.0
9 TraesCS1A01G197400 chr3B 89.170 277 27 1 1 277 780875833 780876106 3.360000e-90 342.0
10 TraesCS1A01G197400 chr3B 91.870 123 10 0 1821 1943 525242493 525242371 4.670000e-39 172.0
11 TraesCS1A01G197400 chr7D 88.809 277 27 2 1 277 3606145 3605873 1.560000e-88 337.0
12 TraesCS1A01G197400 chr7D 81.690 213 32 6 1759 1966 428952595 428952805 1.680000e-38 171.0
13 TraesCS1A01G197400 chr3A 89.338 272 24 2 1 272 498233015 498233281 1.560000e-88 337.0
14 TraesCS1A01G197400 chr6D 88.448 277 29 1 1 277 115814760 115814487 7.280000e-87 331.0
15 TraesCS1A01G197400 chr6D 89.655 58 3 3 2532 2586 264679088 264679145 1.750000e-08 71.3
16 TraesCS1A01G197400 chr3D 89.098 266 26 1 1 266 20344323 20344585 9.420000e-86 327.0
17 TraesCS1A01G197400 chr3D 91.870 123 10 0 1821 1943 399380486 399380364 4.670000e-39 172.0
18 TraesCS1A01G197400 chr3D 89.655 58 3 2 2532 2586 403700731 403700674 1.750000e-08 71.3
19 TraesCS1A01G197400 chr3D 85.075 67 10 0 1757 1823 390041932 390041998 6.300000e-08 69.4
20 TraesCS1A01G197400 chr5B 87.726 277 29 3 1 277 692376709 692376438 5.670000e-83 318.0
21 TraesCS1A01G197400 chr2D 87.582 153 18 1 1823 1975 553729964 553729813 3.610000e-40 176.0
22 TraesCS1A01G197400 chr2B 87.582 153 18 1 1823 1975 659533300 659533149 3.610000e-40 176.0
23 TraesCS1A01G197400 chr2B 95.455 44 1 1 2548 2591 40453235 40453277 6.300000e-08 69.4
24 TraesCS1A01G197400 chr7B 81.690 213 32 6 1759 1966 446665448 446665658 1.680000e-38 171.0
25 TraesCS1A01G197400 chr7A 81.905 210 31 6 1762 1966 503052302 503052095 1.680000e-38 171.0
26 TraesCS1A01G197400 chr7A 97.436 39 1 0 2548 2586 562274960 562274922 2.270000e-07 67.6
27 TraesCS1A01G197400 chr5A 97.222 36 1 0 2551 2586 401142986 401142951 1.050000e-05 62.1


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 TraesCS1A01G197400 chr1A 355341906 355345424 3518 False 6499 6499 100.000 1 3519 1 chr1A.!!$F1 3518
1 TraesCS1A01G197400 chr1D 283616275 283619542 3267 False 4682 4682 92.743 276 3518 1 chr1D.!!$F1 3242
2 TraesCS1A01G197400 chr1B 385295231 385298487 3256 False 4362 4362 91.114 282 3519 1 chr1B.!!$F2 3237

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
40 41 0.031585 CAGGAAGGTCACGACGTCAA 59.968 55.0 17.16 0.00 0.0 3.18 F
44 45 0.031721 AAGGTCACGACGTCAAGGAC 59.968 55.0 17.16 17.63 0.0 3.85 F
435 440 0.038251 GGCCAGTTTAACAAGCTGCC 60.038 55.0 0.00 4.14 0.0 4.85 F
636 650 0.538977 GATGACCGTCGATAGGGGGA 60.539 60.0 13.38 0.00 34.8 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1219 1277 0.255318 TGTACTCGTCCTCCTCCTCC 59.745 60.000 0.0 0.0 0.00 4.30 R
1611 1678 0.454600 ACACGTAGTAGTGCCATCGG 59.545 55.000 0.0 0.0 45.45 4.18 R
2256 2332 0.179124 CTTCAGCGGTAGAGGCAGAC 60.179 60.000 0.0 0.0 0.00 3.51 R
2560 2638 1.129811 CCGTCCCAAAATAAGTGTCGC 59.870 52.381 0.0 0.0 0.00 5.19 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
36 37 3.108521 CTTCAGGAAGGTCACGACG 57.891 57.895 1.01 0.00 34.87 5.12
37 38 0.314302 CTTCAGGAAGGTCACGACGT 59.686 55.000 0.00 0.00 34.87 4.34
38 39 0.313043 TTCAGGAAGGTCACGACGTC 59.687 55.000 5.18 5.18 0.00 4.34
39 40 0.820482 TCAGGAAGGTCACGACGTCA 60.820 55.000 17.16 0.00 0.00 4.35
40 41 0.031585 CAGGAAGGTCACGACGTCAA 59.968 55.000 17.16 0.00 0.00 3.18
41 42 0.314302 AGGAAGGTCACGACGTCAAG 59.686 55.000 17.16 7.15 0.00 3.02
42 43 0.666577 GGAAGGTCACGACGTCAAGG 60.667 60.000 17.16 4.01 0.00 3.61
43 44 0.313043 GAAGGTCACGACGTCAAGGA 59.687 55.000 17.16 6.54 0.00 3.36
44 45 0.031721 AAGGTCACGACGTCAAGGAC 59.968 55.000 17.16 17.63 0.00 3.85
73 74 2.494918 CGCTCACCGGAGTTAGGG 59.505 66.667 9.46 4.06 43.37 3.53
74 75 2.348888 CGCTCACCGGAGTTAGGGT 61.349 63.158 9.46 0.00 43.37 4.34
75 76 1.885163 CGCTCACCGGAGTTAGGGTT 61.885 60.000 9.46 0.00 43.37 4.11
76 77 0.323957 GCTCACCGGAGTTAGGGTTT 59.676 55.000 9.46 0.00 43.37 3.27
77 78 1.271217 GCTCACCGGAGTTAGGGTTTT 60.271 52.381 9.46 0.00 43.37 2.43
78 79 2.696506 CTCACCGGAGTTAGGGTTTTC 58.303 52.381 9.46 0.00 36.36 2.29
79 80 2.038033 CTCACCGGAGTTAGGGTTTTCA 59.962 50.000 9.46 0.00 36.36 2.69
80 81 2.148768 CACCGGAGTTAGGGTTTTCAC 58.851 52.381 9.46 0.00 33.23 3.18
81 82 1.072806 ACCGGAGTTAGGGTTTTCACC 59.927 52.381 9.46 0.00 43.37 4.02
99 100 4.517934 CGAGAGGCGGGTAGGGGA 62.518 72.222 0.00 0.00 36.03 4.81
100 101 2.522193 GAGAGGCGGGTAGGGGAG 60.522 72.222 0.00 0.00 0.00 4.30
101 102 3.028098 AGAGGCGGGTAGGGGAGA 61.028 66.667 0.00 0.00 0.00 3.71
102 103 2.042230 GAGGCGGGTAGGGGAGAA 60.042 66.667 0.00 0.00 0.00 2.87
103 104 2.041819 AGGCGGGTAGGGGAGAAG 60.042 66.667 0.00 0.00 0.00 2.85
104 105 2.365237 GGCGGGTAGGGGAGAAGT 60.365 66.667 0.00 0.00 0.00 3.01
105 106 1.075748 GGCGGGTAGGGGAGAAGTA 60.076 63.158 0.00 0.00 0.00 2.24
106 107 1.114119 GGCGGGTAGGGGAGAAGTAG 61.114 65.000 0.00 0.00 0.00 2.57
107 108 0.106318 GCGGGTAGGGGAGAAGTAGA 60.106 60.000 0.00 0.00 0.00 2.59
108 109 1.984066 CGGGTAGGGGAGAAGTAGAG 58.016 60.000 0.00 0.00 0.00 2.43
109 110 1.479021 CGGGTAGGGGAGAAGTAGAGG 60.479 61.905 0.00 0.00 0.00 3.69
110 111 1.858246 GGGTAGGGGAGAAGTAGAGGA 59.142 57.143 0.00 0.00 0.00 3.71
111 112 2.158430 GGGTAGGGGAGAAGTAGAGGAG 60.158 59.091 0.00 0.00 0.00 3.69
112 113 2.589720 GTAGGGGAGAAGTAGAGGAGC 58.410 57.143 0.00 0.00 0.00 4.70
113 114 1.011595 AGGGGAGAAGTAGAGGAGCA 58.988 55.000 0.00 0.00 0.00 4.26
114 115 1.063266 AGGGGAGAAGTAGAGGAGCAG 60.063 57.143 0.00 0.00 0.00 4.24
115 116 1.063567 GGGGAGAAGTAGAGGAGCAGA 60.064 57.143 0.00 0.00 0.00 4.26
116 117 2.425683 GGGGAGAAGTAGAGGAGCAGAT 60.426 54.545 0.00 0.00 0.00 2.90
117 118 3.181427 GGGGAGAAGTAGAGGAGCAGATA 60.181 52.174 0.00 0.00 0.00 1.98
118 119 4.510205 GGGGAGAAGTAGAGGAGCAGATAT 60.510 50.000 0.00 0.00 0.00 1.63
119 120 5.281297 GGGGAGAAGTAGAGGAGCAGATATA 60.281 48.000 0.00 0.00 0.00 0.86
120 121 5.885912 GGGAGAAGTAGAGGAGCAGATATAG 59.114 48.000 0.00 0.00 0.00 1.31
121 122 6.296778 GGGAGAAGTAGAGGAGCAGATATAGA 60.297 46.154 0.00 0.00 0.00 1.98
122 123 6.598064 GGAGAAGTAGAGGAGCAGATATAGAC 59.402 46.154 0.00 0.00 0.00 2.59
123 124 6.481643 AGAAGTAGAGGAGCAGATATAGACC 58.518 44.000 0.00 0.00 0.00 3.85
124 125 4.839121 AGTAGAGGAGCAGATATAGACCG 58.161 47.826 0.00 0.00 0.00 4.79
125 126 4.532916 AGTAGAGGAGCAGATATAGACCGA 59.467 45.833 0.00 0.00 0.00 4.69
126 127 3.681593 AGAGGAGCAGATATAGACCGAC 58.318 50.000 0.00 0.00 0.00 4.79
127 128 2.417239 GAGGAGCAGATATAGACCGACG 59.583 54.545 0.00 0.00 0.00 5.12
128 129 2.152830 GGAGCAGATATAGACCGACGT 58.847 52.381 0.00 0.00 0.00 4.34
129 130 2.160022 GGAGCAGATATAGACCGACGTC 59.840 54.545 5.18 5.18 39.50 4.34
131 132 3.068560 AGCAGATATAGACCGACGTCTC 58.931 50.000 14.70 5.28 46.90 3.36
132 133 3.068560 GCAGATATAGACCGACGTCTCT 58.931 50.000 14.70 12.92 46.90 3.10
133 134 4.021280 AGCAGATATAGACCGACGTCTCTA 60.021 45.833 14.70 14.71 46.90 2.43
134 135 4.689812 GCAGATATAGACCGACGTCTCTAA 59.310 45.833 15.93 8.21 46.90 2.10
135 136 5.163933 GCAGATATAGACCGACGTCTCTAAG 60.164 48.000 15.93 0.10 46.90 2.18
136 137 6.157904 CAGATATAGACCGACGTCTCTAAGA 58.842 44.000 15.93 9.37 46.90 2.10
137 138 6.645827 CAGATATAGACCGACGTCTCTAAGAA 59.354 42.308 15.93 7.60 46.90 2.52
138 139 6.869913 AGATATAGACCGACGTCTCTAAGAAG 59.130 42.308 15.93 0.00 46.90 2.85
139 140 3.331478 AGACCGACGTCTCTAAGAAGA 57.669 47.619 14.70 0.00 46.90 2.87
140 141 3.672808 AGACCGACGTCTCTAAGAAGAA 58.327 45.455 14.70 0.00 46.90 2.52
141 142 4.070716 AGACCGACGTCTCTAAGAAGAAA 58.929 43.478 14.70 0.00 46.90 2.52
142 143 4.518211 AGACCGACGTCTCTAAGAAGAAAA 59.482 41.667 14.70 0.00 46.90 2.29
143 144 4.796369 ACCGACGTCTCTAAGAAGAAAAG 58.204 43.478 14.70 0.00 0.00 2.27
144 145 3.608939 CCGACGTCTCTAAGAAGAAAAGC 59.391 47.826 14.70 0.00 0.00 3.51
145 146 3.298499 CGACGTCTCTAAGAAGAAAAGCG 59.702 47.826 14.70 0.00 0.00 4.68
146 147 3.576648 ACGTCTCTAAGAAGAAAAGCGG 58.423 45.455 0.00 0.00 0.00 5.52
147 148 2.345942 CGTCTCTAAGAAGAAAAGCGGC 59.654 50.000 0.00 0.00 0.00 6.53
148 149 2.345942 GTCTCTAAGAAGAAAAGCGGCG 59.654 50.000 0.51 0.51 0.00 6.46
149 150 1.061276 CTCTAAGAAGAAAAGCGGCGC 59.939 52.381 26.86 26.86 0.00 6.53
150 151 0.097150 CTAAGAAGAAAAGCGGCGCC 59.903 55.000 30.40 19.07 0.00 6.53
151 152 1.303091 TAAGAAGAAAAGCGGCGCCC 61.303 55.000 30.40 14.23 0.00 6.13
152 153 3.056328 GAAGAAAAGCGGCGCCCT 61.056 61.111 30.40 16.55 0.00 5.19
153 154 2.597510 AAGAAAAGCGGCGCCCTT 60.598 55.556 30.40 21.93 0.00 3.95
154 155 2.802740 GAAGAAAAGCGGCGCCCTTG 62.803 60.000 30.40 12.53 0.00 3.61
155 156 3.361977 GAAAAGCGGCGCCCTTGA 61.362 61.111 30.40 0.00 0.00 3.02
156 157 3.328288 GAAAAGCGGCGCCCTTGAG 62.328 63.158 30.40 11.82 0.00 3.02
161 162 4.183686 CGGCGCCCTTGAGCATTG 62.184 66.667 23.46 0.00 39.30 2.82
162 163 3.064324 GGCGCCCTTGAGCATTGT 61.064 61.111 18.11 0.00 39.30 2.71
163 164 2.486966 GCGCCCTTGAGCATTGTC 59.513 61.111 0.00 0.00 37.24 3.18
164 165 2.787249 CGCCCTTGAGCATTGTCG 59.213 61.111 0.00 0.00 0.00 4.35
165 166 2.034879 CGCCCTTGAGCATTGTCGT 61.035 57.895 0.00 0.00 0.00 4.34
166 167 1.796796 GCCCTTGAGCATTGTCGTC 59.203 57.895 0.00 0.00 0.00 4.20
167 168 1.970917 GCCCTTGAGCATTGTCGTCG 61.971 60.000 0.00 0.00 0.00 5.12
168 169 1.361668 CCCTTGAGCATTGTCGTCGG 61.362 60.000 0.00 0.00 0.00 4.79
169 170 0.670546 CCTTGAGCATTGTCGTCGGT 60.671 55.000 0.00 0.00 0.00 4.69
170 171 0.439985 CTTGAGCATTGTCGTCGGTG 59.560 55.000 0.00 0.00 0.00 4.94
171 172 1.565156 TTGAGCATTGTCGTCGGTGC 61.565 55.000 0.00 0.00 37.84 5.01
172 173 3.071459 GAGCATTGTCGTCGGTGCG 62.071 63.158 0.00 0.00 42.18 5.34
173 174 4.147322 GCATTGTCGTCGGTGCGG 62.147 66.667 0.00 0.00 0.00 5.69
174 175 4.147322 CATTGTCGTCGGTGCGGC 62.147 66.667 0.00 0.00 36.96 6.53
205 206 2.203567 CCAAGGGGTTTCCGCCAA 60.204 61.111 0.00 0.00 45.93 4.52
206 207 1.609210 CCAAGGGGTTTCCGCCAAT 60.609 57.895 0.00 0.00 45.93 3.16
207 208 1.604147 CCAAGGGGTTTCCGCCAATC 61.604 60.000 0.00 0.00 45.93 2.67
208 209 0.611896 CAAGGGGTTTCCGCCAATCT 60.612 55.000 0.00 0.00 45.93 2.40
209 210 0.611896 AAGGGGTTTCCGCCAATCTG 60.612 55.000 0.00 0.00 45.93 2.90
210 211 2.052104 GGGGTTTCCGCCAATCTGG 61.052 63.158 0.00 0.00 43.08 3.86
211 212 1.001393 GGGTTTCCGCCAATCTGGA 60.001 57.895 0.00 0.00 40.96 3.86
212 213 0.395724 GGGTTTCCGCCAATCTGGAT 60.396 55.000 0.00 0.00 40.96 3.41
213 214 1.025041 GGTTTCCGCCAATCTGGATC 58.975 55.000 0.00 0.00 40.96 3.36
214 215 1.408822 GGTTTCCGCCAATCTGGATCT 60.409 52.381 0.00 0.00 40.96 2.75
215 216 2.369394 GTTTCCGCCAATCTGGATCTT 58.631 47.619 0.00 0.00 40.96 2.40
216 217 2.332063 TTCCGCCAATCTGGATCTTC 57.668 50.000 0.00 0.00 40.96 2.87
217 218 1.500474 TCCGCCAATCTGGATCTTCT 58.500 50.000 0.00 0.00 40.96 2.85
218 219 1.414181 TCCGCCAATCTGGATCTTCTC 59.586 52.381 0.00 0.00 40.96 2.87
219 220 1.542108 CCGCCAATCTGGATCTTCTCC 60.542 57.143 0.00 0.00 40.96 3.71
228 229 2.323968 GGATCTTCTCCACCAGCTTC 57.676 55.000 0.00 0.00 44.26 3.86
229 230 1.556911 GGATCTTCTCCACCAGCTTCA 59.443 52.381 0.00 0.00 44.26 3.02
230 231 2.172293 GGATCTTCTCCACCAGCTTCAT 59.828 50.000 0.00 0.00 44.26 2.57
231 232 3.465871 GATCTTCTCCACCAGCTTCATC 58.534 50.000 0.00 0.00 0.00 2.92
232 233 1.205655 TCTTCTCCACCAGCTTCATCG 59.794 52.381 0.00 0.00 0.00 3.84
233 234 0.250234 TTCTCCACCAGCTTCATCGG 59.750 55.000 0.00 0.00 0.00 4.18
234 235 1.817099 CTCCACCAGCTTCATCGGC 60.817 63.158 0.00 0.00 0.00 5.54
235 236 3.197790 CCACCAGCTTCATCGGCG 61.198 66.667 0.00 0.00 34.52 6.46
236 237 3.197790 CACCAGCTTCATCGGCGG 61.198 66.667 7.21 0.00 34.52 6.13
259 260 4.410400 GGCCAGGGTCCCGACAAG 62.410 72.222 0.99 0.00 0.00 3.16
261 262 4.410400 CCAGGGTCCCGACAAGCC 62.410 72.222 0.99 0.00 34.42 4.35
262 263 3.636231 CAGGGTCCCGACAAGCCA 61.636 66.667 0.99 0.00 36.73 4.75
263 264 3.637273 AGGGTCCCGACAAGCCAC 61.637 66.667 0.99 0.00 36.73 5.01
377 382 0.467844 TTCAGAAAGCTGCTGCCCAA 60.468 50.000 12.44 0.17 42.01 4.12
386 391 1.881498 GCTGCTGCCCAAGATAGATCC 60.881 57.143 3.85 0.00 0.00 3.36
405 410 4.090761 TCCATGCATCTCATTTCTACCC 57.909 45.455 0.00 0.00 31.79 3.69
407 412 2.620251 TGCATCTCATTTCTACCCCG 57.380 50.000 0.00 0.00 0.00 5.73
408 413 1.140852 TGCATCTCATTTCTACCCCGG 59.859 52.381 0.00 0.00 0.00 5.73
435 440 0.038251 GGCCAGTTTAACAAGCTGCC 60.038 55.000 0.00 4.14 0.00 4.85
636 650 0.538977 GATGACCGTCGATAGGGGGA 60.539 60.000 13.38 0.00 34.80 4.81
642 656 1.446366 GTCGATAGGGGGAGTTGCC 59.554 63.158 0.00 0.00 0.00 4.52
652 666 0.608035 GGGAGTTGCCGATTTGGACA 60.608 55.000 0.00 0.00 42.00 4.02
668 682 0.861837 GACAGTGCAAGACAAGACCG 59.138 55.000 0.00 0.00 0.00 4.79
736 750 6.310960 CCGTTCGTTCAAATATTGTGATCAA 58.689 36.000 0.00 0.00 37.98 2.57
737 751 6.248420 CCGTTCGTTCAAATATTGTGATCAAC 59.752 38.462 0.00 0.00 36.33 3.18
758 777 6.476706 TCAACTGATTAGATGTAGTTCATGCG 59.523 38.462 0.00 0.00 36.83 4.73
766 787 1.090052 GTAGTTCATGCGTGCTCCCC 61.090 60.000 0.00 0.00 0.00 4.81
794 815 7.424452 GCGAACTAGTTACCGTGAATTTTATTG 59.576 37.037 8.42 0.00 0.00 1.90
800 824 7.985476 AGTTACCGTGAATTTTATTGGATCTG 58.015 34.615 0.00 0.00 0.00 2.90
802 826 8.885722 GTTACCGTGAATTTTATTGGATCTGTA 58.114 33.333 0.00 0.00 0.00 2.74
803 827 9.621629 TTACCGTGAATTTTATTGGATCTGTAT 57.378 29.630 0.00 0.00 0.00 2.29
1020 1070 1.399440 CGATATGCATGCATGGTAGGC 59.601 52.381 37.43 20.08 37.82 3.93
1115 1170 2.658593 CCGTCGGGTCGATCATGC 60.659 66.667 2.34 0.00 38.42 4.06
1231 1289 1.820481 CGACGAGGAGGAGGAGGAC 60.820 68.421 0.00 0.00 0.00 3.85
1336 1400 1.183030 CCATGATGATGGGCGGCAAT 61.183 55.000 12.47 4.32 45.11 3.56
1338 1402 1.887854 CATGATGATGGGCGGCAATAA 59.112 47.619 12.47 0.00 0.00 1.40
1341 1405 3.346315 TGATGATGGGCGGCAATAATAG 58.654 45.455 12.47 0.00 0.00 1.73
1342 1406 2.949177 TGATGGGCGGCAATAATAGT 57.051 45.000 12.47 0.00 0.00 2.12
1343 1407 4.019771 TGATGATGGGCGGCAATAATAGTA 60.020 41.667 12.47 0.00 0.00 1.82
1344 1408 3.937814 TGATGGGCGGCAATAATAGTAG 58.062 45.455 12.47 0.00 0.00 2.57
1527 1594 2.322422 GCAGCACATGTCGATCGC 59.678 61.111 11.09 6.41 0.00 4.58
1543 1610 2.436646 GCCCATCACCCTCGTGTG 60.437 66.667 0.00 0.00 41.09 3.82
1547 1614 1.613317 CCATCACCCTCGTGTGCCTA 61.613 60.000 0.00 0.00 41.09 3.93
1549 1616 1.614241 ATCACCCTCGTGTGCCTACC 61.614 60.000 0.00 0.00 41.09 3.18
1609 1676 3.682696 TCTACTCCTAGCTTTCACACGA 58.317 45.455 0.00 0.00 0.00 4.35
1611 1678 3.027974 ACTCCTAGCTTTCACACGAAC 57.972 47.619 0.00 0.00 0.00 3.95
1696 1772 0.798776 CGAAGAAGGTGGTGTGCATC 59.201 55.000 0.00 0.00 0.00 3.91
1981 2057 4.090588 GGATCAACCCGCCCGTCA 62.091 66.667 0.00 0.00 0.00 4.35
2151 2227 2.187946 GGACATGGACGCCCTCAG 59.812 66.667 0.00 0.00 0.00 3.35
2256 2332 7.272299 CGACTACATCTAATCCAGAATTCATCG 59.728 40.741 8.44 0.00 36.67 3.84
2303 2380 2.401195 GAGCAAGCAATCGACGCC 59.599 61.111 5.09 0.00 0.00 5.68
2320 2397 1.469940 CGCCTACACAGTCCTGATGAC 60.470 57.143 0.40 0.00 44.82 3.06
2356 2433 5.836821 TGTGTCAGTAGTAGCTTCTATGG 57.163 43.478 3.17 0.00 0.00 2.74
2503 2581 9.726438 CAGCTTAAGGTATATAGCTTACCAATT 57.274 33.333 26.47 12.74 43.50 2.32
2509 2587 7.922382 AGGTATATAGCTTACCAATTCATGCT 58.078 34.615 14.19 0.00 41.37 3.79
2534 2612 2.560504 TCACTCGCTTCTTGAAGCAAA 58.439 42.857 27.77 17.34 45.75 3.68
2535 2613 2.942376 TCACTCGCTTCTTGAAGCAAAA 59.058 40.909 27.77 15.38 45.75 2.44
2539 2617 5.566774 CACTCGCTTCTTGAAGCAAAATAAG 59.433 40.000 27.77 18.08 45.75 1.73
2540 2618 5.239525 ACTCGCTTCTTGAAGCAAAATAAGT 59.760 36.000 27.77 18.54 45.75 2.24
2541 2619 5.451908 TCGCTTCTTGAAGCAAAATAAGTG 58.548 37.500 27.77 13.02 45.75 3.16
2544 2622 6.208644 GCTTCTTGAAGCAAAATAAGTGTCA 58.791 36.000 25.03 0.00 44.85 3.58
2545 2623 6.865205 GCTTCTTGAAGCAAAATAAGTGTCAT 59.135 34.615 25.03 0.00 44.85 3.06
2546 2624 7.061557 GCTTCTTGAAGCAAAATAAGTGTCATC 59.938 37.037 25.03 0.00 44.85 2.92
2547 2625 7.750229 TCTTGAAGCAAAATAAGTGTCATCT 57.250 32.000 0.00 0.00 0.00 2.90
2548 2626 8.169977 TCTTGAAGCAAAATAAGTGTCATCTT 57.830 30.769 0.00 0.00 0.00 2.40
2551 2629 8.389779 TGAAGCAAAATAAGTGTCATCTTGTA 57.610 30.769 0.00 0.00 0.00 2.41
2553 2631 7.986085 AGCAAAATAAGTGTCATCTTGTACT 57.014 32.000 0.00 0.00 0.00 2.73
2561 2639 7.602517 AAGTGTCATCTTGTACTAAATCAGC 57.397 36.000 0.00 0.00 0.00 4.26
2562 2640 5.807520 AGTGTCATCTTGTACTAAATCAGCG 59.192 40.000 0.00 0.00 0.00 5.18
2778 2867 0.112412 AAAACCTGAGGCCCGAATGT 59.888 50.000 0.00 0.00 0.00 2.71
2924 3013 2.372837 ACCAATTGCAGCCCAAAAAGAT 59.627 40.909 0.00 0.00 36.92 2.40
2949 3038 6.313744 ACTTTCTATATGGCCAATAAACGC 57.686 37.500 10.96 0.00 0.00 4.84
2970 3059 3.458189 CTGCTCTTTATCCTTGGGTACG 58.542 50.000 0.00 0.00 0.00 3.67
2990 3079 5.725110 ACGCATTCATACTCAGATTCAAC 57.275 39.130 0.00 0.00 0.00 3.18
3111 3207 4.250464 TCTCCGAATCACAACCACAATAC 58.750 43.478 0.00 0.00 0.00 1.89
3119 3215 7.305935 CGAATCACAACCACAATACAAACAAAG 60.306 37.037 0.00 0.00 0.00 2.77
3154 3250 3.814842 TGATTCGAGAAAACACAGCACAT 59.185 39.130 0.00 0.00 0.00 3.21
3156 3252 5.468409 TGATTCGAGAAAACACAGCACATAA 59.532 36.000 0.00 0.00 0.00 1.90
3157 3253 4.990543 TCGAGAAAACACAGCACATAAG 57.009 40.909 0.00 0.00 0.00 1.73
3158 3254 4.627058 TCGAGAAAACACAGCACATAAGA 58.373 39.130 0.00 0.00 0.00 2.10
3159 3255 4.447724 TCGAGAAAACACAGCACATAAGAC 59.552 41.667 0.00 0.00 0.00 3.01
3160 3256 4.211164 CGAGAAAACACAGCACATAAGACA 59.789 41.667 0.00 0.00 0.00 3.41
3161 3257 5.613360 CGAGAAAACACAGCACATAAGACAG 60.613 44.000 0.00 0.00 0.00 3.51
3162 3258 4.516698 AGAAAACACAGCACATAAGACAGG 59.483 41.667 0.00 0.00 0.00 4.00
3242 3338 4.681744 CTCACTGAATCTGAAGCTAGGAC 58.318 47.826 0.00 0.00 0.00 3.85
3439 3535 4.746535 ATCTGATGGCAATGCATCAAAA 57.253 36.364 7.79 6.29 37.37 2.44
3451 3547 6.401367 GCAATGCATCAAAAGGACAAATGTAC 60.401 38.462 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.314302 ACGTCGTGACCTTCCTGAAG 59.686 55.000 0.00 0.00 38.14 3.02
19 20 0.313043 GACGTCGTGACCTTCCTGAA 59.687 55.000 0.63 0.00 0.00 3.02
20 21 0.820482 TGACGTCGTGACCTTCCTGA 60.820 55.000 11.62 0.00 0.00 3.86
21 22 0.031585 TTGACGTCGTGACCTTCCTG 59.968 55.000 11.62 0.00 0.00 3.86
22 23 0.314302 CTTGACGTCGTGACCTTCCT 59.686 55.000 11.62 0.00 0.00 3.36
23 24 0.666577 CCTTGACGTCGTGACCTTCC 60.667 60.000 11.62 0.00 0.00 3.46
24 25 0.313043 TCCTTGACGTCGTGACCTTC 59.687 55.000 11.62 0.00 0.00 3.46
25 26 0.031721 GTCCTTGACGTCGTGACCTT 59.968 55.000 11.62 0.00 0.00 3.50
26 27 1.658673 GTCCTTGACGTCGTGACCT 59.341 57.895 11.62 0.00 0.00 3.85
27 28 4.240049 GTCCTTGACGTCGTGACC 57.760 61.111 11.62 0.00 0.00 4.02
53 54 4.124351 TAACTCCGGTGAGCGGCG 62.124 66.667 19.57 15.62 42.74 6.46
54 55 2.202756 CTAACTCCGGTGAGCGGC 60.203 66.667 19.57 0.00 42.74 6.53
55 56 2.494918 CCTAACTCCGGTGAGCGG 59.505 66.667 18.22 18.22 42.74 5.52
56 57 1.885163 AACCCTAACTCCGGTGAGCG 61.885 60.000 11.17 0.00 42.74 5.03
57 58 0.323957 AAACCCTAACTCCGGTGAGC 59.676 55.000 11.17 0.00 42.74 4.26
58 59 2.038033 TGAAAACCCTAACTCCGGTGAG 59.962 50.000 11.17 0.00 44.62 3.51
59 60 2.048601 TGAAAACCCTAACTCCGGTGA 58.951 47.619 11.17 0.00 30.96 4.02
60 61 2.148768 GTGAAAACCCTAACTCCGGTG 58.851 52.381 0.00 0.00 30.96 4.94
61 62 1.072806 GGTGAAAACCCTAACTCCGGT 59.927 52.381 0.00 0.00 0.00 5.28
62 63 1.612462 GGGTGAAAACCCTAACTCCGG 60.612 57.143 6.68 0.00 46.39 5.14
63 64 1.817357 GGGTGAAAACCCTAACTCCG 58.183 55.000 6.68 0.00 46.39 4.63
71 72 1.674651 GCCTCTCGGGTGAAAACCC 60.675 63.158 3.69 3.69 46.43 4.11
72 73 3.982829 GCCTCTCGGGTGAAAACC 58.017 61.111 0.00 0.00 37.43 3.27
82 83 4.517934 TCCCCTACCCGCCTCTCG 62.518 72.222 0.00 0.00 38.08 4.04
83 84 2.522193 CTCCCCTACCCGCCTCTC 60.522 72.222 0.00 0.00 0.00 3.20
84 85 2.591193 CTTCTCCCCTACCCGCCTCT 62.591 65.000 0.00 0.00 0.00 3.69
85 86 2.042230 TTCTCCCCTACCCGCCTC 60.042 66.667 0.00 0.00 0.00 4.70
86 87 1.587522 TACTTCTCCCCTACCCGCCT 61.588 60.000 0.00 0.00 0.00 5.52
87 88 1.075748 TACTTCTCCCCTACCCGCC 60.076 63.158 0.00 0.00 0.00 6.13
88 89 0.106318 TCTACTTCTCCCCTACCCGC 60.106 60.000 0.00 0.00 0.00 6.13
89 90 1.479021 CCTCTACTTCTCCCCTACCCG 60.479 61.905 0.00 0.00 0.00 5.28
90 91 1.858246 TCCTCTACTTCTCCCCTACCC 59.142 57.143 0.00 0.00 0.00 3.69
91 92 2.753846 GCTCCTCTACTTCTCCCCTACC 60.754 59.091 0.00 0.00 0.00 3.18
92 93 2.091775 TGCTCCTCTACTTCTCCCCTAC 60.092 54.545 0.00 0.00 0.00 3.18
93 94 2.175931 CTGCTCCTCTACTTCTCCCCTA 59.824 54.545 0.00 0.00 0.00 3.53
94 95 1.011595 TGCTCCTCTACTTCTCCCCT 58.988 55.000 0.00 0.00 0.00 4.79
95 96 1.063567 TCTGCTCCTCTACTTCTCCCC 60.064 57.143 0.00 0.00 0.00 4.81
96 97 2.445682 TCTGCTCCTCTACTTCTCCC 57.554 55.000 0.00 0.00 0.00 4.30
97 98 6.598064 GTCTATATCTGCTCCTCTACTTCTCC 59.402 46.154 0.00 0.00 0.00 3.71
98 99 6.598064 GGTCTATATCTGCTCCTCTACTTCTC 59.402 46.154 0.00 0.00 0.00 2.87
99 100 6.481643 GGTCTATATCTGCTCCTCTACTTCT 58.518 44.000 0.00 0.00 0.00 2.85
100 101 5.353123 CGGTCTATATCTGCTCCTCTACTTC 59.647 48.000 0.00 0.00 0.00 3.01
101 102 5.013287 TCGGTCTATATCTGCTCCTCTACTT 59.987 44.000 0.00 0.00 0.00 2.24
102 103 4.532916 TCGGTCTATATCTGCTCCTCTACT 59.467 45.833 0.00 0.00 0.00 2.57
103 104 4.632688 GTCGGTCTATATCTGCTCCTCTAC 59.367 50.000 0.00 0.00 0.00 2.59
104 105 4.621038 CGTCGGTCTATATCTGCTCCTCTA 60.621 50.000 0.00 0.00 0.00 2.43
105 106 3.681593 GTCGGTCTATATCTGCTCCTCT 58.318 50.000 0.00 0.00 0.00 3.69
106 107 2.417239 CGTCGGTCTATATCTGCTCCTC 59.583 54.545 0.00 0.00 0.00 3.71
107 108 2.224572 ACGTCGGTCTATATCTGCTCCT 60.225 50.000 0.00 0.00 0.00 3.69
108 109 2.152830 ACGTCGGTCTATATCTGCTCC 58.847 52.381 0.00 0.00 0.00 4.70
109 110 3.458779 GACGTCGGTCTATATCTGCTC 57.541 52.381 0.00 0.00 40.15 4.26
120 121 4.416505 TTTCTTCTTAGAGACGTCGGTC 57.583 45.455 10.46 3.03 43.76 4.79
121 122 4.796369 CTTTTCTTCTTAGAGACGTCGGT 58.204 43.478 10.46 3.79 0.00 4.69
122 123 3.608939 GCTTTTCTTCTTAGAGACGTCGG 59.391 47.826 10.46 0.00 0.00 4.79
123 124 3.298499 CGCTTTTCTTCTTAGAGACGTCG 59.702 47.826 10.46 0.00 0.00 5.12
124 125 3.608939 CCGCTTTTCTTCTTAGAGACGTC 59.391 47.826 7.70 7.70 0.00 4.34
125 126 3.576648 CCGCTTTTCTTCTTAGAGACGT 58.423 45.455 0.00 0.00 0.00 4.34
126 127 2.345942 GCCGCTTTTCTTCTTAGAGACG 59.654 50.000 0.00 0.00 0.00 4.18
127 128 2.345942 CGCCGCTTTTCTTCTTAGAGAC 59.654 50.000 0.00 0.00 0.00 3.36
128 129 2.607187 CGCCGCTTTTCTTCTTAGAGA 58.393 47.619 0.00 0.00 0.00 3.10
129 130 1.061276 GCGCCGCTTTTCTTCTTAGAG 59.939 52.381 0.00 0.00 0.00 2.43
130 131 1.076332 GCGCCGCTTTTCTTCTTAGA 58.924 50.000 0.00 0.00 0.00 2.10
131 132 0.097150 GGCGCCGCTTTTCTTCTTAG 59.903 55.000 12.58 0.00 0.00 2.18
132 133 1.303091 GGGCGCCGCTTTTCTTCTTA 61.303 55.000 22.54 0.00 0.00 2.10
133 134 2.626780 GGGCGCCGCTTTTCTTCTT 61.627 57.895 22.54 0.00 0.00 2.52
134 135 3.056328 GGGCGCCGCTTTTCTTCT 61.056 61.111 22.54 0.00 0.00 2.85
135 136 2.626780 AAGGGCGCCGCTTTTCTTC 61.627 57.895 22.54 2.36 32.78 2.87
136 137 2.597510 AAGGGCGCCGCTTTTCTT 60.598 55.556 22.54 14.08 32.78 2.52
137 138 3.365265 CAAGGGCGCCGCTTTTCT 61.365 61.111 22.54 7.71 34.44 2.52
138 139 3.328288 CTCAAGGGCGCCGCTTTTC 62.328 63.158 22.54 4.96 34.44 2.29
139 140 3.365265 CTCAAGGGCGCCGCTTTT 61.365 61.111 22.54 9.36 34.44 2.27
144 145 4.183686 CAATGCTCAAGGGCGCCG 62.184 66.667 22.54 6.96 34.52 6.46
145 146 3.056313 GACAATGCTCAAGGGCGCC 62.056 63.158 21.18 21.18 34.52 6.53
146 147 2.486966 GACAATGCTCAAGGGCGC 59.513 61.111 0.00 0.00 34.52 6.53
147 148 1.970917 GACGACAATGCTCAAGGGCG 61.971 60.000 0.00 0.00 34.52 6.13
148 149 1.796796 GACGACAATGCTCAAGGGC 59.203 57.895 0.00 0.00 0.00 5.19
149 150 1.361668 CCGACGACAATGCTCAAGGG 61.362 60.000 0.00 0.00 0.00 3.95
150 151 0.670546 ACCGACGACAATGCTCAAGG 60.671 55.000 0.00 0.00 0.00 3.61
151 152 0.439985 CACCGACGACAATGCTCAAG 59.560 55.000 0.00 0.00 0.00 3.02
152 153 1.565156 GCACCGACGACAATGCTCAA 61.565 55.000 0.00 0.00 35.16 3.02
153 154 2.027073 GCACCGACGACAATGCTCA 61.027 57.895 0.00 0.00 35.16 4.26
154 155 2.778679 GCACCGACGACAATGCTC 59.221 61.111 0.00 0.00 35.16 4.26
155 156 3.112075 CGCACCGACGACAATGCT 61.112 61.111 0.00 0.00 35.88 3.79
156 157 4.147322 CCGCACCGACGACAATGC 62.147 66.667 0.00 0.00 34.06 3.56
157 158 4.147322 GCCGCACCGACGACAATG 62.147 66.667 0.00 0.00 34.06 2.82
188 189 1.604147 GATTGGCGGAAACCCCTTGG 61.604 60.000 0.00 0.00 37.80 3.61
189 190 0.611896 AGATTGGCGGAAACCCCTTG 60.612 55.000 0.00 0.00 0.00 3.61
190 191 0.611896 CAGATTGGCGGAAACCCCTT 60.612 55.000 0.00 0.00 0.00 3.95
191 192 1.000896 CAGATTGGCGGAAACCCCT 60.001 57.895 0.00 0.00 0.00 4.79
192 193 2.052104 CCAGATTGGCGGAAACCCC 61.052 63.158 0.00 0.00 0.00 4.95
193 194 0.395724 ATCCAGATTGGCGGAAACCC 60.396 55.000 0.00 0.00 37.47 4.11
194 195 1.025041 GATCCAGATTGGCGGAAACC 58.975 55.000 0.00 0.00 37.47 3.27
195 196 2.044123 AGATCCAGATTGGCGGAAAC 57.956 50.000 0.00 0.00 37.47 2.78
196 197 2.239654 AGAAGATCCAGATTGGCGGAAA 59.760 45.455 0.00 0.00 37.47 3.13
197 198 1.839994 AGAAGATCCAGATTGGCGGAA 59.160 47.619 0.00 0.00 37.47 4.30
198 199 1.414181 GAGAAGATCCAGATTGGCGGA 59.586 52.381 0.00 0.00 37.47 5.54
199 200 1.876322 GAGAAGATCCAGATTGGCGG 58.124 55.000 0.00 0.00 37.47 6.13
210 211 3.465871 GATGAAGCTGGTGGAGAAGATC 58.534 50.000 0.00 0.00 0.00 2.75
211 212 2.158986 CGATGAAGCTGGTGGAGAAGAT 60.159 50.000 0.00 0.00 0.00 2.40
212 213 1.205655 CGATGAAGCTGGTGGAGAAGA 59.794 52.381 0.00 0.00 0.00 2.87
213 214 1.649664 CGATGAAGCTGGTGGAGAAG 58.350 55.000 0.00 0.00 0.00 2.85
214 215 0.250234 CCGATGAAGCTGGTGGAGAA 59.750 55.000 0.00 0.00 0.00 2.87
215 216 1.900351 CCGATGAAGCTGGTGGAGA 59.100 57.895 0.00 0.00 0.00 3.71
216 217 1.817099 GCCGATGAAGCTGGTGGAG 60.817 63.158 0.00 0.00 0.00 3.86
217 218 2.268920 GCCGATGAAGCTGGTGGA 59.731 61.111 0.00 0.00 0.00 4.02
218 219 3.197790 CGCCGATGAAGCTGGTGG 61.198 66.667 0.00 0.00 0.00 4.61
219 220 3.197790 CCGCCGATGAAGCTGGTG 61.198 66.667 0.00 0.00 0.00 4.17
242 243 4.410400 CTTGTCGGGACCCTGGCC 62.410 72.222 9.41 0.00 0.00 5.36
244 245 4.410400 GGCTTGTCGGGACCCTGG 62.410 72.222 9.41 0.00 0.00 4.45
245 246 3.636231 TGGCTTGTCGGGACCCTG 61.636 66.667 9.41 2.25 0.00 4.45
246 247 3.637273 GTGGCTTGTCGGGACCCT 61.637 66.667 9.41 0.00 0.00 4.34
264 265 4.408821 TGACATGGAGGTGCCGGC 62.409 66.667 22.73 22.73 40.66 6.13
265 266 2.124983 CTGACATGGAGGTGCCGG 60.125 66.667 0.00 0.00 40.66 6.13
266 267 2.821366 GCTGACATGGAGGTGCCG 60.821 66.667 0.00 0.00 40.66 5.69
267 268 2.439156 GGCTGACATGGAGGTGCC 60.439 66.667 0.00 0.00 37.10 5.01
268 269 2.439156 GGGCTGACATGGAGGTGC 60.439 66.667 0.00 0.00 0.00 5.01
269 270 0.911769 TAAGGGCTGACATGGAGGTG 59.088 55.000 0.00 0.00 0.00 4.00
270 271 1.898863 ATAAGGGCTGACATGGAGGT 58.101 50.000 0.00 0.00 0.00 3.85
271 272 4.137543 GTTTATAAGGGCTGACATGGAGG 58.862 47.826 0.00 0.00 0.00 4.30
272 273 4.137543 GGTTTATAAGGGCTGACATGGAG 58.862 47.826 0.00 0.00 0.00 3.86
273 274 3.117663 GGGTTTATAAGGGCTGACATGGA 60.118 47.826 0.00 0.00 0.00 3.41
274 275 3.117512 AGGGTTTATAAGGGCTGACATGG 60.118 47.826 0.00 0.00 0.00 3.66
280 281 2.561569 CGACAGGGTTTATAAGGGCTG 58.438 52.381 0.00 0.00 0.00 4.85
331 332 0.594602 CCACATATGCATGCCCTTCG 59.405 55.000 16.68 2.34 35.39 3.79
333 334 0.397394 TGCCACATATGCATGCCCTT 60.397 50.000 16.68 2.45 35.39 3.95
377 382 7.260387 AGAAATGAGATGCATGGATCTATCT 57.740 36.000 27.40 22.64 37.28 1.98
386 391 2.810274 CGGGGTAGAAATGAGATGCATG 59.190 50.000 2.46 0.00 37.28 4.06
407 412 0.891904 TTAAACTGGCCGGCAAGACC 60.892 55.000 37.65 15.71 0.00 3.85
408 413 0.240145 GTTAAACTGGCCGGCAAGAC 59.760 55.000 37.65 20.78 0.00 3.01
435 440 3.423154 GGGTTTCGGCGAGCACTG 61.423 66.667 10.46 0.00 0.00 3.66
469 474 4.473520 CCGCCGATTCCAGCCACT 62.474 66.667 0.00 0.00 0.00 4.00
622 636 1.740285 CAACTCCCCCTATCGACGG 59.260 63.158 0.00 0.00 0.00 4.79
631 645 2.052104 CCAAATCGGCAACTCCCCC 61.052 63.158 0.00 0.00 0.00 5.40
636 650 1.238439 CACTGTCCAAATCGGCAACT 58.762 50.000 0.00 0.00 33.14 3.16
642 656 1.872952 TGTCTTGCACTGTCCAAATCG 59.127 47.619 0.00 0.00 0.00 3.34
652 666 1.598130 GGCGGTCTTGTCTTGCACT 60.598 57.895 0.00 0.00 0.00 4.40
698 712 0.868406 GAACGGGCTACTGCATATGC 59.132 55.000 21.09 21.09 41.91 3.14
736 750 5.750547 CACGCATGAACTACATCTAATCAGT 59.249 40.000 0.00 0.00 37.07 3.41
737 751 5.332883 GCACGCATGAACTACATCTAATCAG 60.333 44.000 0.00 0.00 37.07 2.90
747 761 1.090052 GGGGAGCACGCATGAACTAC 61.090 60.000 0.00 0.00 0.00 2.73
758 777 3.718210 CTAGTTCGCCGGGGAGCAC 62.718 68.421 31.64 23.06 0.00 4.40
766 787 0.168788 TCACGGTAACTAGTTCGCCG 59.831 55.000 32.29 32.29 42.67 6.46
800 824 7.169476 GGCGAGAAAGGAGACAACTTATTATAC 59.831 40.741 0.00 0.00 0.00 1.47
802 826 6.049790 GGCGAGAAAGGAGACAACTTATTAT 58.950 40.000 0.00 0.00 0.00 1.28
803 827 5.187186 AGGCGAGAAAGGAGACAACTTATTA 59.813 40.000 0.00 0.00 0.00 0.98
804 828 4.020128 AGGCGAGAAAGGAGACAACTTATT 60.020 41.667 0.00 0.00 0.00 1.40
1044 1094 3.249091 GTGCAGCTTATGATCGATCGAT 58.751 45.455 29.76 29.76 37.59 3.59
1045 1095 2.608016 GGTGCAGCTTATGATCGATCGA 60.608 50.000 21.86 21.86 0.00 3.59
1046 1096 1.723542 GGTGCAGCTTATGATCGATCG 59.276 52.381 20.03 9.36 0.00 3.69
1059 1109 0.953727 TGTTGATTCACTGGTGCAGC 59.046 50.000 9.47 9.47 34.37 5.25
1115 1170 0.307760 GACAGCCAAAACAGGTCACG 59.692 55.000 0.00 0.00 0.00 4.35
1217 1275 0.838608 TACTCGTCCTCCTCCTCCTC 59.161 60.000 0.00 0.00 0.00 3.71
1218 1276 0.547553 GTACTCGTCCTCCTCCTCCT 59.452 60.000 0.00 0.00 0.00 3.69
1219 1277 0.255318 TGTACTCGTCCTCCTCCTCC 59.745 60.000 0.00 0.00 0.00 4.30
1336 1400 2.245582 GAAGGAGGCCGGCTACTATTA 58.754 52.381 28.56 0.00 0.00 0.98
1338 1402 1.179814 CGAAGGAGGCCGGCTACTAT 61.180 60.000 28.56 10.53 0.00 2.12
1341 1405 3.427598 GACGAAGGAGGCCGGCTAC 62.428 68.421 28.56 19.78 0.00 3.58
1342 1406 3.145551 GACGAAGGAGGCCGGCTA 61.146 66.667 28.56 0.00 0.00 3.93
1344 1408 4.821589 CAGACGAAGGAGGCCGGC 62.822 72.222 21.18 21.18 0.00 6.13
1453 1520 1.183030 TGTCGCCTTCCCTCTCGAAA 61.183 55.000 0.00 0.00 32.49 3.46
1454 1521 0.970937 ATGTCGCCTTCCCTCTCGAA 60.971 55.000 0.00 0.00 32.49 3.71
1543 1610 1.312371 TTGGCTTCATTGCGGTAGGC 61.312 55.000 0.00 0.00 43.96 3.93
1547 1614 0.827507 AACCTTGGCTTCATTGCGGT 60.828 50.000 0.00 0.00 0.00 5.68
1549 1616 2.030363 TGTTAACCTTGGCTTCATTGCG 60.030 45.455 2.48 0.00 0.00 4.85
1592 1659 2.338500 GGTTCGTGTGAAAGCTAGGAG 58.662 52.381 0.00 0.00 35.46 3.69
1593 1660 1.336517 CGGTTCGTGTGAAAGCTAGGA 60.337 52.381 0.00 0.00 35.46 2.94
1594 1661 1.068474 CGGTTCGTGTGAAAGCTAGG 58.932 55.000 0.00 0.00 35.46 3.02
1595 1662 2.060326 TCGGTTCGTGTGAAAGCTAG 57.940 50.000 0.00 0.00 35.46 3.42
1596 1663 2.333926 CATCGGTTCGTGTGAAAGCTA 58.666 47.619 0.00 0.00 35.46 3.32
1597 1664 1.148310 CATCGGTTCGTGTGAAAGCT 58.852 50.000 0.00 0.00 35.46 3.74
1602 1669 1.666553 GTGCCATCGGTTCGTGTGA 60.667 57.895 0.00 0.00 0.00 3.58
1609 1676 1.135199 CACGTAGTAGTGCCATCGGTT 60.135 52.381 0.00 0.00 41.61 4.44
1611 1678 0.454600 ACACGTAGTAGTGCCATCGG 59.545 55.000 0.00 0.00 45.45 4.18
1978 2054 4.593864 GCGGCGGAGGAGGATGAC 62.594 72.222 9.78 0.00 0.00 3.06
2151 2227 0.248702 GTCGATGGAGGAGAAGACGC 60.249 60.000 0.00 0.00 0.00 5.19
2256 2332 0.179124 CTTCAGCGGTAGAGGCAGAC 60.179 60.000 0.00 0.00 0.00 3.51
2303 2380 3.010420 TCTCGTCATCAGGACTGTGTAG 58.990 50.000 0.00 0.00 44.68 2.74
2320 2397 5.968387 ACTGACACAAGTAAAAAGTCTCG 57.032 39.130 0.00 0.00 0.00 4.04
2503 2581 1.882912 AGCGAGTGAAAACAGCATGA 58.117 45.000 0.00 0.00 39.69 3.07
2509 2587 4.536364 CTTCAAGAAGCGAGTGAAAACA 57.464 40.909 0.00 0.00 31.21 2.83
2535 2613 9.319143 GCTGATTTAGTACAAGATGACACTTAT 57.681 33.333 0.00 0.00 0.00 1.73
2539 2617 5.805486 TCGCTGATTTAGTACAAGATGACAC 59.195 40.000 0.00 0.00 0.00 3.67
2540 2618 5.805486 GTCGCTGATTTAGTACAAGATGACA 59.195 40.000 0.00 0.00 0.00 3.58
2541 2619 5.805486 TGTCGCTGATTTAGTACAAGATGAC 59.195 40.000 0.00 0.00 0.00 3.06
2544 2622 5.967088 AGTGTCGCTGATTTAGTACAAGAT 58.033 37.500 0.00 0.00 0.00 2.40
2545 2623 5.386958 AGTGTCGCTGATTTAGTACAAGA 57.613 39.130 0.00 0.00 0.00 3.02
2546 2624 7.757097 ATAAGTGTCGCTGATTTAGTACAAG 57.243 36.000 0.00 0.00 0.00 3.16
2547 2625 8.542497 AAATAAGTGTCGCTGATTTAGTACAA 57.458 30.769 6.91 0.00 36.68 2.41
2548 2626 8.440059 CAAAATAAGTGTCGCTGATTTAGTACA 58.560 33.333 8.84 0.00 37.29 2.90
2551 2629 6.128007 CCCAAAATAAGTGTCGCTGATTTAGT 60.128 38.462 8.84 0.00 37.29 2.24
2553 2631 5.941058 TCCCAAAATAAGTGTCGCTGATTTA 59.059 36.000 8.84 0.00 37.29 1.40
2557 2635 3.071479 GTCCCAAAATAAGTGTCGCTGA 58.929 45.455 0.00 0.00 0.00 4.26
2558 2636 2.159707 CGTCCCAAAATAAGTGTCGCTG 60.160 50.000 0.00 0.00 0.00 5.18
2560 2638 1.129811 CCGTCCCAAAATAAGTGTCGC 59.870 52.381 0.00 0.00 0.00 5.19
2561 2639 2.690786 TCCGTCCCAAAATAAGTGTCG 58.309 47.619 0.00 0.00 0.00 4.35
2562 2640 3.377172 CCATCCGTCCCAAAATAAGTGTC 59.623 47.826 0.00 0.00 0.00 3.67
2778 2867 3.254060 GTCGTCTGAGCTTTTATCTGCA 58.746 45.455 0.00 0.00 0.00 4.41
2924 3013 7.717875 AGCGTTTATTGGCCATATAGAAAGTTA 59.282 33.333 6.09 0.00 0.00 2.24
2949 3038 3.458189 CGTACCCAAGGATAAAGAGCAG 58.542 50.000 0.00 0.00 0.00 4.24
2970 3059 5.505324 GCAGGTTGAATCTGAGTATGAATGC 60.505 44.000 10.11 0.00 34.36 3.56
3111 3207 3.974401 CACATAGTTCACCGCTTTGTTTG 59.026 43.478 0.00 0.00 0.00 2.93
3119 3215 2.535984 CTCGAATCACATAGTTCACCGC 59.464 50.000 0.00 0.00 0.00 5.68
3162 3258 7.672983 TTGTAGAAATTCAGAGGACATTGTC 57.327 36.000 8.34 8.34 0.00 3.18
3242 3338 6.109359 CAGTAAGGAAACTCTATGTCCCTTG 58.891 44.000 0.00 0.00 42.68 3.61
3439 3535 6.659242 CCAACTTATCTTGGTACATTTGTCCT 59.341 38.462 0.00 0.00 39.30 3.85
3451 3547 6.949352 ATACTGATTGCCAACTTATCTTGG 57.051 37.500 0.00 0.00 43.36 3.61


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

AutoCloner maintained by Alex Coulton.