Multiple sequence alignment - TraesCS1D01G221600

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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 TraesCS1D01G221600 chr1D 100.000 4005 0 0 983 4987 309460103 309456099 0.000000e+00 7396
1 TraesCS1D01G221600 chr1D 100.000 696 0 0 1 696 309461085 309460390 0.000000e+00 1286
2 TraesCS1D01G221600 chr1A 95.608 4053 128 15 983 4987 388944892 388940842 0.000000e+00 6453
3 TraesCS1D01G221600 chr1A 93.991 233 13 1 346 578 388945335 388945104 7.940000e-93 351
4 TraesCS1D01G221600 chr1A 96.667 120 2 1 577 696 388945075 388944958 1.100000e-46 198
5 TraesCS1D01G221600 chr1B 94.141 4045 159 34 985 4987 419198803 419194795 0.000000e+00 6085
6 TraesCS1D01G221600 chr1B 84.866 337 18 7 389 696 419199198 419198866 4.850000e-80 309
7 TraesCS1D01G221600 chr2A 95.044 343 15 2 1 343 61666413 61666073 5.680000e-149 538
8 TraesCS1D01G221600 chr3B 94.925 335 17 0 2 336 568933697 568933363 4.420000e-145 525
9 TraesCS1D01G221600 chr3B 86.047 172 24 0 2583 2754 322218735 322218906 8.530000e-43 185
10 TraesCS1D01G221600 chr7D 93.895 344 21 0 1 344 638600498 638600841 2.060000e-143 520
11 TraesCS1D01G221600 chr3A 88.439 173 20 0 2583 2755 205702235 205702063 5.060000e-50 209
12 TraesCS1D01G221600 chr3A 87.931 174 21 0 2583 2756 205699749 205699576 6.540000e-49 206
13 TraesCS1D01G221600 chr4B 86.047 172 24 0 2583 2754 346196626 346196797 8.530000e-43 185
14 TraesCS1D01G221600 chr4B 84.302 172 25 1 2583 2754 349455051 349454882 3.090000e-37 167
15 TraesCS1D01G221600 chr4A 85.965 171 24 0 2577 2747 570578642 570578812 3.070000e-42 183
16 TraesCS1D01G221600 chr6B 84.302 172 27 0 2583 2754 169140788 169140959 8.590000e-38 169


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 TraesCS1D01G221600 chr1D 309456099 309461085 4986 True 4341.0 7396 100.0000 1 4987 2 chr1D.!!$R1 4986
1 TraesCS1D01G221600 chr1A 388940842 388945335 4493 True 2334.0 6453 95.4220 346 4987 3 chr1A.!!$R1 4641
2 TraesCS1D01G221600 chr1B 419194795 419199198 4403 True 3197.0 6085 89.5035 389 4987 2 chr1B.!!$R1 4598
3 TraesCS1D01G221600 chr3A 205699576 205702235 2659 True 207.5 209 88.1850 2583 2756 2 chr3A.!!$R1 173

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
45 46 0.038159 CCAAGTCTTCCTCGCGAAGT 60.038 55.000 11.33 0.00 46.97 3.01 F
49 50 0.038526 GTCTTCCTCGCGAAGTCCAA 60.039 55.000 11.33 0.00 46.97 3.53 F
103 104 0.040204 ATTTCCTCCAGGCACCCTTG 59.960 55.000 0.00 0.00 34.44 3.61 F
138 139 0.107703 CCGCTGCCATAACTCTGGAA 60.108 55.000 0.00 0.00 38.69 3.53 F
149 150 0.115745 ACTCTGGAACCCTAACCCGA 59.884 55.000 0.00 0.00 0.00 5.14 F
151 152 0.115745 TCTGGAACCCTAACCCGACT 59.884 55.000 0.00 0.00 0.00 4.18 F
207 208 0.172352 CTTCTCACGGCTGAGGAGTC 59.828 60.000 15.30 0.00 43.19 3.36 F
218 219 0.255318 TGAGGAGTCGACCTAGGTCC 59.745 60.000 31.78 20.34 41.76 4.46 F
288 289 0.326618 GTGATCAGGGGAGGGAAGGA 60.327 60.000 0.00 0.00 0.00 3.36 F
294 295 0.409876 AGGGGAGGGAAGGAAAAAGC 59.590 55.000 0.00 0.00 0.00 3.51 F
295 296 0.409876 GGGGAGGGAAGGAAAAAGCT 59.590 55.000 0.00 0.00 0.00 3.74 F
304 305 0.666577 AGGAAAAAGCTCGACGACGG 60.667 55.000 7.55 0.00 40.21 4.79 F
334 335 1.001269 CCCCGGGAGAAGAAAACCC 60.001 63.158 26.32 0.00 40.17 4.11 F
337 338 1.209747 CCCGGGAGAAGAAAACCCTAG 59.790 57.143 18.48 0.00 41.28 3.02 F
3398 3492 0.324943 TGTTGCTAAGGGCTGAGACC 59.675 55.000 0.00 0.00 42.39 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1725 1756 1.133598 ACATTCCGATGCAGCAATGTG 59.866 47.619 16.97 6.40 37.92 3.21 R
2248 2279 5.940192 TCACTAACGCAATTCACATTTCT 57.060 34.783 0.00 0.00 0.00 2.52 R
2520 2551 4.343239 ACCTGTCCGGGTAATAGTAACATC 59.657 45.833 0.00 0.00 37.90 3.06 R
2567 2604 8.515414 GTTTTATTGAAACTCCTGAATAGCAGT 58.485 33.333 0.00 0.00 43.44 4.40 R
2568 2605 8.902040 GTTTTATTGAAACTCCTGAATAGCAG 57.098 34.615 0.00 0.00 43.44 4.24 R
2619 2665 4.275810 ACAGCAAATGGACATTAGCTCAT 58.724 39.130 0.00 0.00 0.00 2.90 R
2658 2704 5.278957 CCCAAAACTTCCAATACCTGAACAG 60.279 44.000 0.00 0.00 0.00 3.16 R
2695 2741 5.007682 TCAACTTTGTAGATAAGCCCCAAC 58.992 41.667 0.00 0.00 0.00 3.77 R
3080 3128 1.006102 GTAGGCCCCGTCATCATCG 60.006 63.158 0.00 0.00 0.00 3.84 R
3236 3284 7.819415 TCAGTAGGTGATCACTAACAATCTTTG 59.181 37.037 24.50 14.56 0.00 2.77 R
3259 3307 5.406175 CCAGTAATGTTGTTTGCCAAATCAG 59.594 40.000 0.00 0.00 34.07 2.90 R
3298 3346 8.049117 TGACAGGAGCAGAATTAATAATCAACT 58.951 33.333 0.00 0.00 0.00 3.16 R
3398 3492 4.935205 TCACCTGGTAAATGTTGAATCTCG 59.065 41.667 0.00 0.00 0.00 4.04 R
3409 3503 4.169059 TGCATAGCATCACCTGGTAAAT 57.831 40.909 0.00 0.00 40.97 1.40 R
4842 4956 0.990374 GGCCCAGATGGAGCAGATAT 59.010 55.000 0.00 0.00 37.39 1.63 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
35 36 2.709631 CGACGTCGTCCAAGTCTTC 58.290 57.895 29.08 0.00 33.10 2.87
36 37 0.728466 CGACGTCGTCCAAGTCTTCC 60.728 60.000 29.08 0.00 33.10 3.46
37 38 0.597072 GACGTCGTCCAAGTCTTCCT 59.403 55.000 14.60 0.00 32.58 3.36
38 39 0.597072 ACGTCGTCCAAGTCTTCCTC 59.403 55.000 0.00 0.00 0.00 3.71
40 41 0.733223 GTCGTCCAAGTCTTCCTCGC 60.733 60.000 0.00 0.00 0.00 5.03
41 42 1.801913 CGTCCAAGTCTTCCTCGCG 60.802 63.158 0.00 0.00 0.00 5.87
42 43 1.585006 GTCCAAGTCTTCCTCGCGA 59.415 57.895 9.26 9.26 0.00 5.87
43 44 0.038526 GTCCAAGTCTTCCTCGCGAA 60.039 55.000 11.33 0.00 0.00 4.70
45 46 0.038159 CCAAGTCTTCCTCGCGAAGT 60.038 55.000 11.33 0.00 46.97 3.01
46 47 1.341606 CAAGTCTTCCTCGCGAAGTC 58.658 55.000 11.33 2.60 46.97 3.01
47 48 0.244178 AAGTCTTCCTCGCGAAGTCC 59.756 55.000 11.33 0.67 46.97 3.85
48 49 0.894184 AGTCTTCCTCGCGAAGTCCA 60.894 55.000 11.33 0.00 46.97 4.02
49 50 0.038526 GTCTTCCTCGCGAAGTCCAA 60.039 55.000 11.33 0.00 46.97 3.53
50 51 0.243907 TCTTCCTCGCGAAGTCCAAG 59.756 55.000 11.33 4.24 46.97 3.61
51 52 1.355066 CTTCCTCGCGAAGTCCAAGC 61.355 60.000 11.33 0.00 42.74 4.01
53 54 1.807573 CCTCGCGAAGTCCAAGCTC 60.808 63.158 11.33 0.00 0.00 4.09
54 55 1.807573 CTCGCGAAGTCCAAGCTCC 60.808 63.158 11.33 0.00 0.00 4.70
57 58 2.815647 CGAAGTCCAAGCTCCGCC 60.816 66.667 0.00 0.00 0.00 6.13
60 61 1.078143 AAGTCCAAGCTCCGCCATC 60.078 57.895 0.00 0.00 0.00 3.51
61 62 1.841302 AAGTCCAAGCTCCGCCATCA 61.841 55.000 0.00 0.00 0.00 3.07
63 64 1.146930 TCCAAGCTCCGCCATCATC 59.853 57.895 0.00 0.00 0.00 2.92
64 65 1.147824 CCAAGCTCCGCCATCATCT 59.852 57.895 0.00 0.00 0.00 2.90
66 67 1.386533 CAAGCTCCGCCATCATCTTT 58.613 50.000 0.00 0.00 0.00 2.52
67 68 1.065102 CAAGCTCCGCCATCATCTTTG 59.935 52.381 0.00 0.00 0.00 2.77
68 69 1.099879 AGCTCCGCCATCATCTTTGC 61.100 55.000 0.00 0.00 0.00 3.68
69 70 1.099879 GCTCCGCCATCATCTTTGCT 61.100 55.000 0.00 0.00 0.00 3.91
70 71 1.811558 GCTCCGCCATCATCTTTGCTA 60.812 52.381 0.00 0.00 0.00 3.49
72 73 2.740981 CTCCGCCATCATCTTTGCTATC 59.259 50.000 0.00 0.00 0.00 2.08
73 74 2.369860 TCCGCCATCATCTTTGCTATCT 59.630 45.455 0.00 0.00 0.00 1.98
74 75 2.740981 CCGCCATCATCTTTGCTATCTC 59.259 50.000 0.00 0.00 0.00 2.75
75 76 2.411069 CGCCATCATCTTTGCTATCTCG 59.589 50.000 0.00 0.00 0.00 4.04
76 77 2.159234 GCCATCATCTTTGCTATCTCGC 59.841 50.000 0.00 0.00 0.00 5.03
77 78 2.740981 CCATCATCTTTGCTATCTCGCC 59.259 50.000 0.00 0.00 0.00 5.54
78 79 3.396560 CATCATCTTTGCTATCTCGCCA 58.603 45.455 0.00 0.00 0.00 5.69
79 80 3.103447 TCATCTTTGCTATCTCGCCAG 57.897 47.619 0.00 0.00 0.00 4.85
81 82 0.528466 TCTTTGCTATCTCGCCAGCG 60.528 55.000 5.50 5.50 40.79 5.18
82 83 1.493950 CTTTGCTATCTCGCCAGCGG 61.494 60.000 12.71 3.22 40.79 5.52
88 89 2.186903 TCTCGCCAGCGGGATTTC 59.813 61.111 11.21 0.00 44.69 2.17
89 90 2.897350 CTCGCCAGCGGGATTTCC 60.897 66.667 5.89 0.00 43.62 3.13
90 91 3.391665 CTCGCCAGCGGGATTTCCT 62.392 63.158 5.89 0.00 43.62 3.36
91 92 2.897350 CGCCAGCGGGATTTCCTC 60.897 66.667 7.23 0.00 35.59 3.71
92 93 2.517166 GCCAGCGGGATTTCCTCC 60.517 66.667 7.23 0.00 44.11 4.30
93 94 2.998097 CCAGCGGGATTTCCTCCA 59.002 61.111 0.00 0.00 46.98 3.86
94 95 1.153086 CCAGCGGGATTTCCTCCAG 60.153 63.158 0.00 0.00 46.98 3.86
95 96 1.153086 CAGCGGGATTTCCTCCAGG 60.153 63.158 0.00 0.00 46.98 4.45
96 97 2.517166 GCGGGATTTCCTCCAGGC 60.517 66.667 0.00 0.00 46.98 4.85
97 98 2.998097 CGGGATTTCCTCCAGGCA 59.002 61.111 0.00 0.00 46.98 4.75
98 99 1.452108 CGGGATTTCCTCCAGGCAC 60.452 63.158 0.00 0.00 46.98 5.01
99 100 1.076705 GGGATTTCCTCCAGGCACC 60.077 63.158 0.00 0.00 46.98 5.01
100 101 1.076705 GGATTTCCTCCAGGCACCC 60.077 63.158 0.00 0.00 44.26 4.61
103 104 0.040204 ATTTCCTCCAGGCACCCTTG 59.960 55.000 0.00 0.00 34.44 3.61
114 115 3.382832 ACCCTTGCCGTCGAGGAG 61.383 66.667 6.70 0.00 45.22 3.69
115 116 4.821589 CCCTTGCCGTCGAGGAGC 62.822 72.222 6.70 8.97 45.22 4.70
116 117 3.764466 CCTTGCCGTCGAGGAGCT 61.764 66.667 6.70 0.00 45.22 4.09
119 120 3.282745 TTGCCGTCGAGGAGCTGTC 62.283 63.158 6.70 0.00 45.00 3.51
131 132 3.102097 GCTGTCCGCTGCCATAAC 58.898 61.111 0.00 0.00 34.09 1.89
132 133 1.450312 GCTGTCCGCTGCCATAACT 60.450 57.895 0.00 0.00 34.09 2.24
133 134 1.432270 GCTGTCCGCTGCCATAACTC 61.432 60.000 0.00 0.00 34.09 3.01
136 137 0.811616 GTCCGCTGCCATAACTCTGG 60.812 60.000 0.00 0.00 39.45 3.86
137 138 0.975556 TCCGCTGCCATAACTCTGGA 60.976 55.000 0.00 0.00 38.69 3.86
138 139 0.107703 CCGCTGCCATAACTCTGGAA 60.108 55.000 0.00 0.00 38.69 3.53
139 140 1.009829 CGCTGCCATAACTCTGGAAC 58.990 55.000 0.00 0.00 38.69 3.62
140 141 1.383523 GCTGCCATAACTCTGGAACC 58.616 55.000 0.00 0.00 38.69 3.62
141 142 2.019156 GCTGCCATAACTCTGGAACCC 61.019 57.143 0.00 0.00 38.69 4.11
142 143 1.561542 CTGCCATAACTCTGGAACCCT 59.438 52.381 0.00 0.00 38.69 4.34
143 144 2.771943 CTGCCATAACTCTGGAACCCTA 59.228 50.000 0.00 0.00 38.69 3.53
144 145 3.186283 TGCCATAACTCTGGAACCCTAA 58.814 45.455 0.00 0.00 38.69 2.69
145 146 3.054655 TGCCATAACTCTGGAACCCTAAC 60.055 47.826 0.00 0.00 38.69 2.34
146 147 3.684697 GCCATAACTCTGGAACCCTAACC 60.685 52.174 0.00 0.00 38.69 2.85
148 149 0.981943 AACTCTGGAACCCTAACCCG 59.018 55.000 0.00 0.00 0.00 5.28
149 150 0.115745 ACTCTGGAACCCTAACCCGA 59.884 55.000 0.00 0.00 0.00 5.14
150 151 0.535797 CTCTGGAACCCTAACCCGAC 59.464 60.000 0.00 0.00 0.00 4.79
151 152 0.115745 TCTGGAACCCTAACCCGACT 59.884 55.000 0.00 0.00 0.00 4.18
153 154 1.350019 CTGGAACCCTAACCCGACTTT 59.650 52.381 0.00 0.00 0.00 2.66
154 155 2.568509 CTGGAACCCTAACCCGACTTTA 59.431 50.000 0.00 0.00 0.00 1.85
155 156 2.568509 TGGAACCCTAACCCGACTTTAG 59.431 50.000 0.00 0.00 0.00 1.85
156 157 2.833943 GGAACCCTAACCCGACTTTAGA 59.166 50.000 0.00 0.00 0.00 2.10
158 159 4.442612 GGAACCCTAACCCGACTTTAGATC 60.443 50.000 0.00 0.00 0.00 2.75
159 160 3.036819 ACCCTAACCCGACTTTAGATCC 58.963 50.000 0.00 0.00 0.00 3.36
160 161 3.036091 CCCTAACCCGACTTTAGATCCA 58.964 50.000 0.00 0.00 0.00 3.41
161 162 3.453353 CCCTAACCCGACTTTAGATCCAA 59.547 47.826 0.00 0.00 0.00 3.53
162 163 4.102681 CCCTAACCCGACTTTAGATCCAAT 59.897 45.833 0.00 0.00 0.00 3.16
163 164 5.298347 CCTAACCCGACTTTAGATCCAATC 58.702 45.833 0.00 0.00 0.00 2.67
164 165 3.454371 ACCCGACTTTAGATCCAATCG 57.546 47.619 0.00 0.00 0.00 3.34
165 166 2.102588 ACCCGACTTTAGATCCAATCGG 59.897 50.000 8.44 8.44 46.77 4.18
166 167 2.755650 CCGACTTTAGATCCAATCGGG 58.244 52.381 7.73 0.00 44.18 5.14
168 169 3.123804 CGACTTTAGATCCAATCGGGTG 58.876 50.000 0.00 0.00 38.11 4.61
169 170 3.430374 CGACTTTAGATCCAATCGGGTGT 60.430 47.826 0.00 0.00 38.11 4.16
170 171 4.514401 GACTTTAGATCCAATCGGGTGTT 58.486 43.478 0.00 0.00 38.11 3.32
171 172 4.261801 ACTTTAGATCCAATCGGGTGTTG 58.738 43.478 0.00 0.00 38.11 3.33
173 174 0.327924 AGATCCAATCGGGTGTTGCA 59.672 50.000 0.00 0.00 38.11 4.08
174 175 0.734889 GATCCAATCGGGTGTTGCAG 59.265 55.000 0.00 0.00 38.11 4.41
175 176 0.680921 ATCCAATCGGGTGTTGCAGG 60.681 55.000 0.00 0.00 38.11 4.85
176 177 2.342650 CCAATCGGGTGTTGCAGGG 61.343 63.158 0.00 0.00 0.00 4.45
177 178 2.035626 AATCGGGTGTTGCAGGGG 59.964 61.111 0.00 0.00 0.00 4.79
178 179 4.740822 ATCGGGTGTTGCAGGGGC 62.741 66.667 0.00 0.00 41.68 5.80
182 183 3.657350 GGTGTTGCAGGGGCCCTA 61.657 66.667 28.28 8.18 40.13 3.53
183 184 2.438795 GTGTTGCAGGGGCCCTAA 59.561 61.111 28.28 15.13 40.13 2.69
184 185 1.977009 GTGTTGCAGGGGCCCTAAC 60.977 63.158 28.28 26.45 40.13 2.34
185 186 2.160171 TGTTGCAGGGGCCCTAACT 61.160 57.895 29.53 7.63 40.13 2.24
186 187 1.378646 GTTGCAGGGGCCCTAACTC 60.379 63.158 28.28 15.12 40.13 3.01
187 188 2.612493 TTGCAGGGGCCCTAACTCC 61.612 63.158 28.28 11.83 40.13 3.85
188 189 3.810188 GCAGGGGCCCTAACTCCC 61.810 72.222 28.28 2.05 41.87 4.30
193 194 1.346479 GGGGCCCTAACTCCCTTCTC 61.346 65.000 24.38 0.00 42.25 2.87
194 195 0.620700 GGGCCCTAACTCCCTTCTCA 60.621 60.000 17.04 0.00 39.46 3.27
195 196 0.542333 GGCCCTAACTCCCTTCTCAC 59.458 60.000 0.00 0.00 0.00 3.51
196 197 0.175989 GCCCTAACTCCCTTCTCACG 59.824 60.000 0.00 0.00 0.00 4.35
198 199 0.175989 CCTAACTCCCTTCTCACGGC 59.824 60.000 0.00 0.00 0.00 5.68
201 202 0.832135 AACTCCCTTCTCACGGCTGA 60.832 55.000 0.00 0.00 0.00 4.26
202 203 1.254284 ACTCCCTTCTCACGGCTGAG 61.254 60.000 0.00 0.00 44.94 3.35
203 204 1.954362 CTCCCTTCTCACGGCTGAGG 61.954 65.000 0.00 0.00 43.87 3.86
204 205 1.984570 CCCTTCTCACGGCTGAGGA 60.985 63.158 0.00 0.00 43.87 3.71
205 206 1.515020 CCTTCTCACGGCTGAGGAG 59.485 63.158 12.65 12.65 46.58 3.69
207 208 0.172352 CTTCTCACGGCTGAGGAGTC 59.828 60.000 15.30 0.00 43.19 3.36
213 214 4.659986 GGCTGAGGAGTCGACCTA 57.340 61.111 13.01 0.00 40.73 3.08
214 215 2.410466 GGCTGAGGAGTCGACCTAG 58.590 63.158 13.01 4.95 40.73 3.02
215 216 1.104577 GGCTGAGGAGTCGACCTAGG 61.105 65.000 13.01 7.41 40.73 3.02
216 217 0.394625 GCTGAGGAGTCGACCTAGGT 60.395 60.000 16.26 16.26 40.73 3.08
217 218 1.670791 CTGAGGAGTCGACCTAGGTC 58.329 60.000 29.18 29.18 40.73 3.85
218 219 0.255318 TGAGGAGTCGACCTAGGTCC 59.745 60.000 31.78 20.34 41.76 4.46
219 220 0.466007 GAGGAGTCGACCTAGGTCCC 60.466 65.000 31.78 26.19 41.76 4.46
221 222 2.439883 AGTCGACCTAGGTCCCGC 60.440 66.667 31.78 22.09 41.76 6.13
222 223 3.885521 GTCGACCTAGGTCCCGCG 61.886 72.222 31.78 22.45 41.76 6.46
226 227 4.371417 ACCTAGGTCCCGCGGTGA 62.371 66.667 26.12 18.17 0.00 4.02
227 228 3.834799 CCTAGGTCCCGCGGTGAC 61.835 72.222 28.27 28.27 0.00 3.67
258 259 3.467226 GAGATCGGCCCGGGTCAA 61.467 66.667 27.89 7.24 0.00 3.18
260 261 3.467226 GATCGGCCCGGGTCAAGA 61.467 66.667 27.89 16.21 0.00 3.02
261 262 3.735037 GATCGGCCCGGGTCAAGAC 62.735 68.421 27.89 9.42 0.00 3.01
274 275 2.966050 GTCAAGACCAGAGGTGTGATC 58.034 52.381 0.00 0.00 35.25 2.92
276 277 2.564504 TCAAGACCAGAGGTGTGATCAG 59.435 50.000 0.00 0.00 35.25 2.90
277 278 1.566211 AGACCAGAGGTGTGATCAGG 58.434 55.000 0.00 0.00 35.25 3.86
278 279 0.539051 GACCAGAGGTGTGATCAGGG 59.461 60.000 0.00 0.00 35.25 4.45
279 280 0.911525 ACCAGAGGTGTGATCAGGGG 60.912 60.000 0.00 0.00 32.98 4.79
280 281 0.618680 CCAGAGGTGTGATCAGGGGA 60.619 60.000 0.00 0.00 0.00 4.81
281 282 0.829333 CAGAGGTGTGATCAGGGGAG 59.171 60.000 0.00 0.00 0.00 4.30
283 284 1.307343 AGGTGTGATCAGGGGAGGG 60.307 63.158 0.00 0.00 0.00 4.30
284 285 1.306997 GGTGTGATCAGGGGAGGGA 60.307 63.158 0.00 0.00 0.00 4.20
286 287 0.543749 GTGTGATCAGGGGAGGGAAG 59.456 60.000 0.00 0.00 0.00 3.46
288 289 0.326618 GTGATCAGGGGAGGGAAGGA 60.327 60.000 0.00 0.00 0.00 3.36
289 290 0.421495 TGATCAGGGGAGGGAAGGAA 59.579 55.000 0.00 0.00 0.00 3.36
290 291 1.203557 TGATCAGGGGAGGGAAGGAAA 60.204 52.381 0.00 0.00 0.00 3.13
292 293 1.841334 TCAGGGGAGGGAAGGAAAAA 58.159 50.000 0.00 0.00 0.00 1.94
293 294 1.710809 TCAGGGGAGGGAAGGAAAAAG 59.289 52.381 0.00 0.00 0.00 2.27
294 295 0.409876 AGGGGAGGGAAGGAAAAAGC 59.590 55.000 0.00 0.00 0.00 3.51
295 296 0.409876 GGGGAGGGAAGGAAAAAGCT 59.590 55.000 0.00 0.00 0.00 3.74
296 297 1.617263 GGGGAGGGAAGGAAAAAGCTC 60.617 57.143 0.00 0.00 0.00 4.09
297 298 1.454201 GGAGGGAAGGAAAAAGCTCG 58.546 55.000 0.00 0.00 0.00 5.03
298 299 1.003233 GGAGGGAAGGAAAAAGCTCGA 59.997 52.381 0.00 0.00 0.00 4.04
299 300 2.077627 GAGGGAAGGAAAAAGCTCGAC 58.922 52.381 0.00 0.00 0.00 4.20
300 301 0.796927 GGGAAGGAAAAAGCTCGACG 59.203 55.000 0.00 0.00 0.00 5.12
301 302 1.607251 GGGAAGGAAAAAGCTCGACGA 60.607 52.381 0.00 0.00 0.00 4.20
302 303 1.459975 GGAAGGAAAAAGCTCGACGAC 59.540 52.381 0.00 0.00 0.00 4.34
303 304 1.124477 GAAGGAAAAAGCTCGACGACG 59.876 52.381 0.00 0.00 41.26 5.12
304 305 0.666577 AGGAAAAAGCTCGACGACGG 60.667 55.000 7.55 0.00 40.21 4.79
305 306 1.130009 GAAAAAGCTCGACGACGGC 59.870 57.895 7.55 9.77 40.21 5.68
306 307 2.530001 GAAAAAGCTCGACGACGGCG 62.530 60.000 19.07 19.07 44.79 6.46
307 308 3.547249 AAAAGCTCGACGACGGCGA 62.547 57.895 26.26 26.26 41.64 5.54
308 309 4.755614 AAGCTCGACGACGGCGAC 62.756 66.667 24.20 18.65 41.64 5.19
311 312 3.785499 CTCGACGACGGCGACAGA 61.785 66.667 24.20 12.78 41.64 3.41
312 313 3.304764 CTCGACGACGGCGACAGAA 62.305 63.158 24.20 0.46 41.64 3.02
313 314 2.202440 CGACGACGGCGACAGAAT 60.202 61.111 22.49 0.00 41.64 2.40
314 315 2.215604 CGACGACGGCGACAGAATC 61.216 63.158 22.49 0.86 41.64 2.52
322 323 4.891727 CGACAGAATCGCCCCGGG 62.892 72.222 15.80 15.80 45.52 5.73
323 324 3.467226 GACAGAATCGCCCCGGGA 61.467 66.667 26.32 0.92 0.00 5.14
324 325 3.447025 GACAGAATCGCCCCGGGAG 62.447 68.421 26.32 16.47 0.00 4.30
325 326 3.154473 CAGAATCGCCCCGGGAGA 61.154 66.667 26.32 21.75 35.71 3.71
326 327 2.365105 AGAATCGCCCCGGGAGAA 60.365 61.111 26.32 6.59 34.75 2.87
328 329 2.365105 AATCGCCCCGGGAGAAGA 60.365 61.111 26.32 15.76 34.75 2.87
329 330 1.968050 GAATCGCCCCGGGAGAAGAA 61.968 60.000 26.32 0.56 34.75 2.52
330 331 1.559065 AATCGCCCCGGGAGAAGAAA 61.559 55.000 26.32 0.00 34.75 2.52
331 332 1.559065 ATCGCCCCGGGAGAAGAAAA 61.559 55.000 26.32 0.00 34.75 2.29
334 335 1.001269 CCCCGGGAGAAGAAAACCC 60.001 63.158 26.32 0.00 40.17 4.11
335 336 1.498176 CCCCGGGAGAAGAAAACCCT 61.498 60.000 26.32 0.00 41.28 4.34
337 338 1.209747 CCCGGGAGAAGAAAACCCTAG 59.790 57.143 18.48 0.00 41.28 3.02
338 339 1.407025 CCGGGAGAAGAAAACCCTAGC 60.407 57.143 0.00 0.00 41.28 3.42
340 341 2.764572 CGGGAGAAGAAAACCCTAGCTA 59.235 50.000 0.00 0.00 41.28 3.32
341 342 3.181474 CGGGAGAAGAAAACCCTAGCTAG 60.181 52.174 14.20 14.20 41.28 3.42
342 343 4.031611 GGGAGAAGAAAACCCTAGCTAGA 58.968 47.826 22.70 0.00 40.39 2.43
343 344 4.100344 GGGAGAAGAAAACCCTAGCTAGAG 59.900 50.000 22.70 11.93 40.39 2.43
344 345 4.100344 GGAGAAGAAAACCCTAGCTAGAGG 59.900 50.000 22.70 21.44 36.23 3.69
356 357 3.248495 AGCTAGAGGGAACTAAAACGC 57.752 47.619 0.00 0.00 44.43 4.84
364 365 1.325210 GAACTAAAACGCGCGTTGGC 61.325 55.000 44.28 25.94 38.47 4.52
387 388 1.956620 GCGCGTTGGAGTTGCTCTAC 61.957 60.000 8.43 0.00 0.00 2.59
684 715 1.340114 GCCCCGTTTCAAATCCTCTCT 60.340 52.381 0.00 0.00 0.00 3.10
685 716 2.633488 CCCCGTTTCAAATCCTCTCTC 58.367 52.381 0.00 0.00 0.00 3.20
1338 1369 2.357034 GCTCGCTTCACGTTCCCA 60.357 61.111 0.00 0.00 44.19 4.37
2156 2187 5.533903 GGGATGCAGATATCAAGAACATTGT 59.466 40.000 5.32 0.00 0.00 2.71
2567 2604 7.598493 GGTCTGAATTTTGCTAAATGTGCTAAA 59.402 33.333 6.89 0.00 38.83 1.85
2568 2605 8.427774 GTCTGAATTTTGCTAAATGTGCTAAAC 58.572 33.333 6.89 0.00 37.78 2.01
2570 2607 8.296799 TGAATTTTGCTAAATGTGCTAAACTG 57.703 30.769 6.89 0.00 37.78 3.16
2571 2608 6.710692 ATTTTGCTAAATGTGCTAAACTGC 57.289 33.333 5.29 0.00 37.78 4.40
2572 2609 5.452078 TTTGCTAAATGTGCTAAACTGCT 57.548 34.783 0.00 0.00 0.00 4.24
2573 2610 6.567687 TTTGCTAAATGTGCTAAACTGCTA 57.432 33.333 0.00 0.00 0.00 3.49
2575 2612 6.757897 TGCTAAATGTGCTAAACTGCTATT 57.242 33.333 0.00 0.00 0.00 1.73
2658 2704 2.029606 GCTGTTTTGCTGCTGTTTTGAC 59.970 45.455 0.00 0.00 38.75 3.18
2695 2741 2.890945 AGTTTTGGGTTCCTCGGAATTG 59.109 45.455 1.13 0.00 36.45 2.32
3113 3161 1.807142 GCCTACAACTTGCTTCAGGTC 59.193 52.381 0.00 0.00 0.00 3.85
3123 3171 7.716998 ACAACTTGCTTCAGGTCCATATATTAG 59.283 37.037 0.00 0.00 0.00 1.73
3126 3174 8.368668 ACTTGCTTCAGGTCCATATATTAGTAC 58.631 37.037 0.00 0.00 0.00 2.73
3236 3284 4.338118 TGAAAACTCTCCACATGTTGAACC 59.662 41.667 0.00 0.00 0.00 3.62
3259 3307 6.879458 ACCAAAGATTGTTAGTGATCACCTAC 59.121 38.462 22.21 19.12 0.00 3.18
3298 3346 9.764363 CAACATTACTGGCTCTGTTATTCTATA 57.236 33.333 0.00 0.00 31.01 1.31
3398 3492 0.324943 TGTTGCTAAGGGCTGAGACC 59.675 55.000 0.00 0.00 42.39 3.85
3409 3503 1.066858 GGCTGAGACCGAGATTCAACA 60.067 52.381 0.00 0.00 0.00 3.33
3430 3524 3.643199 TTTACCAGGTGATGCTATGCA 57.357 42.857 0.76 0.00 44.86 3.96
3621 3715 5.292101 GCTGATATGAAATATAGCGGTGACC 59.708 44.000 0.00 0.00 40.26 4.02
3698 3792 7.090173 TGATATGTTTTTCAGCTTGGCTTAAC 58.910 34.615 0.00 0.00 36.40 2.01
3758 3852 0.680921 CGACAGGCCCAACCATCATT 60.681 55.000 0.00 0.00 43.14 2.57
3854 3948 4.560743 TTGCTCACTGTGGCGGCA 62.561 61.111 7.97 7.97 0.00 5.69
3880 3974 2.092753 GGATCCTGCAGTTCATGAGGAA 60.093 50.000 13.81 0.00 38.16 3.36
3929 4023 3.233507 TCTTGCATCCAAAAAGCTCCTT 58.766 40.909 0.00 0.00 0.00 3.36
3990 4084 6.208204 AGCAAAGAATATGTTGTCTTGAGCTT 59.792 34.615 8.30 0.00 40.37 3.74
4069 4163 5.661312 TGCCTTGAGTAGAGGTGTTACATAT 59.339 40.000 0.00 0.00 36.63 1.78
4117 4211 3.923017 AACTGAAGGAAATTTCGGCAG 57.077 42.857 21.81 21.81 37.02 4.85
4124 4218 1.202076 GGAAATTTCGGCAGCTCTTCG 60.202 52.381 11.95 0.00 0.00 3.79
4135 4229 3.038710 GCAGCTCTTCGAAACTTGTTTG 58.961 45.455 0.00 0.00 0.00 2.93
4136 4230 3.038710 CAGCTCTTCGAAACTTGTTTGC 58.961 45.455 0.00 0.40 0.00 3.68
4251 4346 1.484240 TGGTGCAAGGAAAGTTTTGGG 59.516 47.619 0.00 0.00 0.00 4.12
4290 4390 5.157940 ACATTCCTGGAATCTGGATATCG 57.842 43.478 18.87 7.40 40.09 2.92
4313 4413 8.437360 TCGCATTTTCAGAGATATTGTAATGT 57.563 30.769 0.00 0.00 0.00 2.71
4356 4456 6.604735 TGTTTTTCTAGCAGAGAAGTTGAC 57.395 37.500 1.86 1.87 45.05 3.18
4458 4568 1.544825 GGTGAGGGTGCTCTGTGCTA 61.545 60.000 3.20 0.00 43.37 3.49
4560 4670 0.039074 AGCTTCCGTTCTCGTGTCAG 60.039 55.000 0.00 0.00 35.01 3.51
4649 4762 9.936759 TTCTTGAAACCACTTAAATTTTCAACT 57.063 25.926 0.00 0.00 41.01 3.16
4650 4763 9.364989 TCTTGAAACCACTTAAATTTTCAACTG 57.635 29.630 0.00 0.00 41.01 3.16
4687 4800 5.957910 TTTGTTTTTAACGCAGTGAATGG 57.042 34.783 0.00 0.00 45.00 3.16
4842 4956 2.296190 CTGTAGCCGTATGTGCATAGGA 59.704 50.000 11.95 0.00 32.53 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.597072 AGGAAGACTTGGACGACGTC 59.403 55.000 19.70 19.70 0.00 4.34
19 20 0.597072 GAGGAAGACTTGGACGACGT 59.403 55.000 0.00 0.00 0.00 4.34
20 21 0.454620 CGAGGAAGACTTGGACGACG 60.455 60.000 0.00 0.00 0.00 5.12
21 22 0.733223 GCGAGGAAGACTTGGACGAC 60.733 60.000 0.00 0.00 0.00 4.34
22 23 1.585006 GCGAGGAAGACTTGGACGA 59.415 57.895 0.00 0.00 0.00 4.20
23 24 1.801913 CGCGAGGAAGACTTGGACG 60.802 63.158 0.00 0.00 0.00 4.79
24 25 0.038526 TTCGCGAGGAAGACTTGGAC 60.039 55.000 9.59 0.00 0.00 4.02
25 26 2.347630 TTCGCGAGGAAGACTTGGA 58.652 52.632 9.59 0.00 0.00 3.53
35 36 1.807573 GAGCTTGGACTTCGCGAGG 60.808 63.158 17.51 17.51 0.00 4.63
36 37 1.807573 GGAGCTTGGACTTCGCGAG 60.808 63.158 9.59 6.46 0.00 5.03
37 38 2.261671 GGAGCTTGGACTTCGCGA 59.738 61.111 3.71 3.71 0.00 5.87
38 39 3.181967 CGGAGCTTGGACTTCGCG 61.182 66.667 0.00 0.00 30.59 5.87
51 52 2.245159 TAGCAAAGATGATGGCGGAG 57.755 50.000 0.00 0.00 0.00 4.63
53 54 2.740981 GAGATAGCAAAGATGATGGCGG 59.259 50.000 0.00 0.00 0.00 6.13
54 55 2.411069 CGAGATAGCAAAGATGATGGCG 59.589 50.000 0.00 0.00 0.00 5.69
57 58 3.396560 TGGCGAGATAGCAAAGATGATG 58.603 45.455 0.00 0.00 39.27 3.07
60 61 1.530293 GCTGGCGAGATAGCAAAGATG 59.470 52.381 0.00 0.00 39.67 2.90
61 62 1.871408 CGCTGGCGAGATAGCAAAGAT 60.871 52.381 9.51 0.00 42.83 2.40
63 64 1.493950 CCGCTGGCGAGATAGCAAAG 61.494 60.000 16.79 0.00 42.83 2.77
64 65 1.521457 CCGCTGGCGAGATAGCAAA 60.521 57.895 16.79 0.00 42.83 3.68
66 67 3.916544 CCCGCTGGCGAGATAGCA 61.917 66.667 16.79 0.00 42.83 3.49
67 68 2.441822 AATCCCGCTGGCGAGATAGC 62.442 60.000 16.79 0.00 35.91 2.97
68 69 0.034059 AAATCCCGCTGGCGAGATAG 59.966 55.000 16.79 0.00 35.91 2.08
69 70 0.033504 GAAATCCCGCTGGCGAGATA 59.966 55.000 16.79 0.00 35.91 1.98
70 71 1.227674 GAAATCCCGCTGGCGAGAT 60.228 57.895 16.79 11.32 38.50 2.75
72 73 2.897350 GGAAATCCCGCTGGCGAG 60.897 66.667 16.79 2.98 42.83 5.03
73 74 3.385749 GAGGAAATCCCGCTGGCGA 62.386 63.158 16.79 0.00 42.83 5.54
74 75 2.897350 GAGGAAATCCCGCTGGCG 60.897 66.667 8.08 8.08 40.87 5.69
75 76 2.517166 GGAGGAAATCCCGCTGGC 60.517 66.667 0.00 0.00 43.01 4.85
84 85 0.040204 CAAGGGTGCCTGGAGGAAAT 59.960 55.000 0.00 0.00 37.39 2.17
86 87 3.170362 CAAGGGTGCCTGGAGGAA 58.830 61.111 0.00 0.00 37.39 3.36
96 97 3.649277 CTCCTCGACGGCAAGGGTG 62.649 68.421 0.00 0.00 33.21 4.61
97 98 3.382832 CTCCTCGACGGCAAGGGT 61.383 66.667 0.00 0.00 33.21 4.34
98 99 4.821589 GCTCCTCGACGGCAAGGG 62.822 72.222 0.00 0.00 33.21 3.95
99 100 3.764466 AGCTCCTCGACGGCAAGG 61.764 66.667 0.00 0.00 0.00 3.61
100 101 2.507992 CAGCTCCTCGACGGCAAG 60.508 66.667 0.00 0.00 0.00 4.01
103 104 4.500116 GGACAGCTCCTCGACGGC 62.500 72.222 0.00 0.00 33.07 5.68
105 106 4.838486 GCGGACAGCTCCTCGACG 62.838 72.222 3.66 0.00 44.04 5.12
115 116 0.176680 AGAGTTATGGCAGCGGACAG 59.823 55.000 0.00 0.00 33.72 3.51
116 117 0.108186 CAGAGTTATGGCAGCGGACA 60.108 55.000 0.00 0.00 35.65 4.02
119 120 0.107703 TTCCAGAGTTATGGCAGCGG 60.108 55.000 0.00 0.00 40.41 5.52
121 122 1.383523 GGTTCCAGAGTTATGGCAGC 58.616 55.000 0.00 0.00 40.41 5.25
122 123 1.561542 AGGGTTCCAGAGTTATGGCAG 59.438 52.381 0.00 0.00 40.41 4.85
123 124 1.668826 AGGGTTCCAGAGTTATGGCA 58.331 50.000 0.00 0.00 40.41 4.92
124 125 3.542648 GTTAGGGTTCCAGAGTTATGGC 58.457 50.000 0.00 0.00 40.41 4.40
126 127 3.431766 CGGGTTAGGGTTCCAGAGTTATG 60.432 52.174 0.00 0.00 0.00 1.90
128 129 2.181975 CGGGTTAGGGTTCCAGAGTTA 58.818 52.381 0.00 0.00 0.00 2.24
131 132 0.535797 GTCGGGTTAGGGTTCCAGAG 59.464 60.000 0.00 0.00 0.00 3.35
132 133 0.115745 AGTCGGGTTAGGGTTCCAGA 59.884 55.000 0.00 0.00 0.00 3.86
133 134 0.981943 AAGTCGGGTTAGGGTTCCAG 59.018 55.000 0.00 0.00 0.00 3.86
136 137 4.442612 GGATCTAAAGTCGGGTTAGGGTTC 60.443 50.000 0.00 0.00 0.00 3.62
137 138 3.453717 GGATCTAAAGTCGGGTTAGGGTT 59.546 47.826 0.00 0.00 0.00 4.11
138 139 3.036819 GGATCTAAAGTCGGGTTAGGGT 58.963 50.000 0.00 0.00 0.00 4.34
139 140 3.036091 TGGATCTAAAGTCGGGTTAGGG 58.964 50.000 0.00 0.00 0.00 3.53
140 141 4.748277 TTGGATCTAAAGTCGGGTTAGG 57.252 45.455 0.00 0.00 0.00 2.69
141 142 4.982916 CGATTGGATCTAAAGTCGGGTTAG 59.017 45.833 6.86 0.00 0.00 2.34
142 143 4.202182 CCGATTGGATCTAAAGTCGGGTTA 60.202 45.833 20.34 0.00 43.47 2.85
143 144 3.431766 CCGATTGGATCTAAAGTCGGGTT 60.432 47.826 20.34 0.00 43.47 4.11
144 145 2.102588 CCGATTGGATCTAAAGTCGGGT 59.897 50.000 20.34 0.00 43.47 5.28
145 146 2.755650 CCGATTGGATCTAAAGTCGGG 58.244 52.381 20.34 7.19 43.47 5.14
146 147 2.102588 ACCCGATTGGATCTAAAGTCGG 59.897 50.000 20.87 20.87 45.93 4.79
148 149 4.138487 ACACCCGATTGGATCTAAAGTC 57.862 45.455 0.00 0.00 37.49 3.01
149 150 4.261801 CAACACCCGATTGGATCTAAAGT 58.738 43.478 0.00 0.00 37.49 2.66
150 151 3.065371 GCAACACCCGATTGGATCTAAAG 59.935 47.826 0.00 0.00 37.49 1.85
151 152 3.013921 GCAACACCCGATTGGATCTAAA 58.986 45.455 0.00 0.00 37.49 1.85
153 154 1.557371 TGCAACACCCGATTGGATCTA 59.443 47.619 0.00 0.00 37.49 1.98
154 155 0.327924 TGCAACACCCGATTGGATCT 59.672 50.000 0.00 0.00 37.49 2.75
155 156 0.734889 CTGCAACACCCGATTGGATC 59.265 55.000 0.00 0.00 37.49 3.36
156 157 0.680921 CCTGCAACACCCGATTGGAT 60.681 55.000 0.00 0.00 37.49 3.41
158 159 2.342650 CCCTGCAACACCCGATTGG 61.343 63.158 0.00 0.00 41.37 3.16
159 160 2.342650 CCCCTGCAACACCCGATTG 61.343 63.158 0.00 0.00 0.00 2.67
160 161 2.035626 CCCCTGCAACACCCGATT 59.964 61.111 0.00 0.00 0.00 3.34
161 162 4.740822 GCCCCTGCAACACCCGAT 62.741 66.667 0.00 0.00 37.47 4.18
165 166 3.218386 TTAGGGCCCCTGCAACACC 62.218 63.158 21.43 0.00 40.13 4.16
166 167 1.977009 GTTAGGGCCCCTGCAACAC 60.977 63.158 21.43 0.52 40.13 3.32
168 169 1.378646 GAGTTAGGGCCCCTGCAAC 60.379 63.158 21.43 17.43 40.13 4.17
169 170 2.612493 GGAGTTAGGGCCCCTGCAA 61.612 63.158 21.43 4.69 40.13 4.08
170 171 3.015145 GGAGTTAGGGCCCCTGCA 61.015 66.667 21.43 0.00 40.13 4.41
171 172 3.810188 GGGAGTTAGGGCCCCTGC 61.810 72.222 21.43 14.26 38.45 4.85
174 175 1.307953 AGAAGGGAGTTAGGGCCCC 60.308 63.158 21.43 2.42 45.89 5.80
175 176 0.620700 TGAGAAGGGAGTTAGGGCCC 60.621 60.000 16.46 16.46 45.04 5.80
176 177 0.542333 GTGAGAAGGGAGTTAGGGCC 59.458 60.000 0.00 0.00 0.00 5.80
177 178 0.175989 CGTGAGAAGGGAGTTAGGGC 59.824 60.000 0.00 0.00 0.00 5.19
178 179 0.824759 CCGTGAGAAGGGAGTTAGGG 59.175 60.000 0.00 0.00 0.00 3.53
179 180 0.175989 GCCGTGAGAAGGGAGTTAGG 59.824 60.000 0.00 0.00 0.00 2.69
180 181 1.134965 CAGCCGTGAGAAGGGAGTTAG 60.135 57.143 0.00 0.00 0.00 2.34
181 182 0.895530 CAGCCGTGAGAAGGGAGTTA 59.104 55.000 0.00 0.00 0.00 2.24
182 183 0.832135 TCAGCCGTGAGAAGGGAGTT 60.832 55.000 0.00 0.00 0.00 3.01
183 184 1.228894 TCAGCCGTGAGAAGGGAGT 60.229 57.895 0.00 0.00 0.00 3.85
184 185 3.700109 TCAGCCGTGAGAAGGGAG 58.300 61.111 0.00 0.00 0.00 4.30
193 194 2.179517 GTCGACTCCTCAGCCGTG 59.820 66.667 8.70 0.00 0.00 4.94
194 195 2.194388 TAGGTCGACTCCTCAGCCGT 62.194 60.000 16.46 0.00 38.86 5.68
195 196 1.440938 CTAGGTCGACTCCTCAGCCG 61.441 65.000 16.46 0.00 38.86 5.52
196 197 1.104577 CCTAGGTCGACTCCTCAGCC 61.105 65.000 16.46 0.00 38.86 4.85
198 199 1.670791 GACCTAGGTCGACTCCTCAG 58.329 60.000 25.83 5.60 38.86 3.35
201 202 1.614160 GGGACCTAGGTCGACTCCT 59.386 63.158 31.00 7.73 45.41 3.69
202 203 1.823041 CGGGACCTAGGTCGACTCC 60.823 68.421 31.00 24.99 45.41 3.85
203 204 2.479750 GCGGGACCTAGGTCGACTC 61.480 68.421 31.00 19.41 45.41 3.36
204 205 2.439883 GCGGGACCTAGGTCGACT 60.440 66.667 31.00 1.74 45.41 4.18
205 206 3.885521 CGCGGGACCTAGGTCGAC 61.886 72.222 31.00 25.03 45.41 4.20
208 209 3.834799 CACCGCGGGACCTAGGTC 61.835 72.222 30.72 30.72 43.87 3.85
209 210 4.371417 TCACCGCGGGACCTAGGT 62.371 66.667 31.76 16.26 37.49 3.08
241 242 3.447025 CTTGACCCGGGCCGATCTC 62.447 68.421 30.79 18.18 0.00 2.75
242 243 3.470888 CTTGACCCGGGCCGATCT 61.471 66.667 30.79 8.82 0.00 2.75
243 244 3.467226 TCTTGACCCGGGCCGATC 61.467 66.667 30.79 24.05 0.00 3.69
247 248 4.410400 CTGGTCTTGACCCGGGCC 62.410 72.222 24.08 11.40 0.00 5.80
248 249 3.316573 CTCTGGTCTTGACCCGGGC 62.317 68.421 24.08 14.70 0.00 6.13
249 250 2.660064 CCTCTGGTCTTGACCCGGG 61.660 68.421 22.25 22.25 0.00 5.73
251 252 1.293498 CACCTCTGGTCTTGACCCG 59.707 63.158 16.23 10.63 31.02 5.28
252 253 0.035458 CACACCTCTGGTCTTGACCC 59.965 60.000 16.23 0.65 31.02 4.46
254 255 2.300152 TGATCACACCTCTGGTCTTGAC 59.700 50.000 0.00 0.00 31.02 3.18
256 257 2.354503 CCTGATCACACCTCTGGTCTTG 60.355 54.545 0.00 0.00 31.02 3.02
258 259 1.566211 CCTGATCACACCTCTGGTCT 58.434 55.000 0.00 0.00 31.02 3.85
260 261 0.911525 CCCCTGATCACACCTCTGGT 60.912 60.000 0.00 0.00 35.62 4.00
261 262 0.618680 TCCCCTGATCACACCTCTGG 60.619 60.000 0.00 0.00 0.00 3.86
262 263 0.829333 CTCCCCTGATCACACCTCTG 59.171 60.000 0.00 0.00 0.00 3.35
263 264 0.326048 CCTCCCCTGATCACACCTCT 60.326 60.000 0.00 0.00 0.00 3.69
264 265 1.341156 CCCTCCCCTGATCACACCTC 61.341 65.000 0.00 0.00 0.00 3.85
265 266 1.307343 CCCTCCCCTGATCACACCT 60.307 63.158 0.00 0.00 0.00 4.00
266 267 0.914417 TTCCCTCCCCTGATCACACC 60.914 60.000 0.00 0.00 0.00 4.16
267 268 0.543749 CTTCCCTCCCCTGATCACAC 59.456 60.000 0.00 0.00 0.00 3.82
269 270 0.326618 TCCTTCCCTCCCCTGATCAC 60.327 60.000 0.00 0.00 0.00 3.06
270 271 0.421495 TTCCTTCCCTCCCCTGATCA 59.579 55.000 0.00 0.00 0.00 2.92
271 272 1.596496 TTTCCTTCCCTCCCCTGATC 58.404 55.000 0.00 0.00 0.00 2.92
272 273 2.074922 TTTTCCTTCCCTCCCCTGAT 57.925 50.000 0.00 0.00 0.00 2.90
273 274 1.710809 CTTTTTCCTTCCCTCCCCTGA 59.289 52.381 0.00 0.00 0.00 3.86
274 275 1.892769 GCTTTTTCCTTCCCTCCCCTG 60.893 57.143 0.00 0.00 0.00 4.45
276 277 0.409876 AGCTTTTTCCTTCCCTCCCC 59.590 55.000 0.00 0.00 0.00 4.81
277 278 1.840737 GAGCTTTTTCCTTCCCTCCC 58.159 55.000 0.00 0.00 0.00 4.30
278 279 1.003233 TCGAGCTTTTTCCTTCCCTCC 59.997 52.381 0.00 0.00 0.00 4.30
279 280 2.077627 GTCGAGCTTTTTCCTTCCCTC 58.922 52.381 0.00 0.00 0.00 4.30
280 281 1.608283 CGTCGAGCTTTTTCCTTCCCT 60.608 52.381 0.00 0.00 0.00 4.20
281 282 0.796927 CGTCGAGCTTTTTCCTTCCC 59.203 55.000 0.00 0.00 0.00 3.97
283 284 1.124477 CGTCGTCGAGCTTTTTCCTTC 59.876 52.381 0.00 0.00 39.71 3.46
284 285 1.137513 CGTCGTCGAGCTTTTTCCTT 58.862 50.000 0.00 0.00 39.71 3.36
286 287 1.779683 CCGTCGTCGAGCTTTTTCC 59.220 57.895 2.98 0.00 39.71 3.13
288 289 2.654912 CGCCGTCGTCGAGCTTTTT 61.655 57.895 2.98 0.00 39.71 1.94
289 290 3.103911 CGCCGTCGTCGAGCTTTT 61.104 61.111 2.98 0.00 39.71 2.27
290 291 4.034258 TCGCCGTCGTCGAGCTTT 62.034 61.111 2.98 0.00 39.71 3.51
294 295 2.579241 ATTCTGTCGCCGTCGTCGAG 62.579 60.000 0.00 0.00 39.71 4.04
295 296 2.573341 GATTCTGTCGCCGTCGTCGA 62.573 60.000 2.98 0.00 39.71 4.20
296 297 2.202440 ATTCTGTCGCCGTCGTCG 60.202 61.111 0.00 0.00 36.96 5.12
297 298 2.215604 CGATTCTGTCGCCGTCGTC 61.216 63.158 0.00 0.00 44.33 4.20
298 299 2.202440 CGATTCTGTCGCCGTCGT 60.202 61.111 0.00 0.00 44.33 4.34
306 307 3.447025 CTCCCGGGGCGATTCTGTC 62.447 68.421 23.50 0.00 0.00 3.51
307 308 3.470888 CTCCCGGGGCGATTCTGT 61.471 66.667 23.50 0.00 0.00 3.41
308 309 2.650813 CTTCTCCCGGGGCGATTCTG 62.651 65.000 23.50 5.14 0.00 3.02
309 310 2.365105 TTCTCCCGGGGCGATTCT 60.365 61.111 23.50 0.00 0.00 2.40
311 312 1.559065 TTTCTTCTCCCGGGGCGATT 61.559 55.000 23.50 0.00 0.00 3.34
312 313 1.559065 TTTTCTTCTCCCGGGGCGAT 61.559 55.000 23.50 0.00 0.00 4.58
313 314 2.218454 TTTTCTTCTCCCGGGGCGA 61.218 57.895 23.50 15.25 0.00 5.54
314 315 2.038837 GTTTTCTTCTCCCGGGGCG 61.039 63.158 23.50 12.84 0.00 6.13
315 316 1.677966 GGTTTTCTTCTCCCGGGGC 60.678 63.158 23.50 0.00 0.00 5.80
316 317 1.001269 GGGTTTTCTTCTCCCGGGG 60.001 63.158 23.50 12.05 0.00 5.73
317 318 1.209747 CTAGGGTTTTCTTCTCCCGGG 59.790 57.143 16.85 16.85 45.27 5.73
318 319 1.407025 GCTAGGGTTTTCTTCTCCCGG 60.407 57.143 0.00 0.00 45.27 5.73
319 320 1.555533 AGCTAGGGTTTTCTTCTCCCG 59.444 52.381 0.00 0.00 45.27 5.14
320 321 4.031611 TCTAGCTAGGGTTTTCTTCTCCC 58.968 47.826 20.58 0.00 41.36 4.30
321 322 4.100344 CCTCTAGCTAGGGTTTTCTTCTCC 59.900 50.000 19.37 0.00 32.55 3.71
322 323 5.270893 CCTCTAGCTAGGGTTTTCTTCTC 57.729 47.826 19.37 0.00 32.55 2.87
334 335 4.361420 GCGTTTTAGTTCCCTCTAGCTAG 58.639 47.826 15.01 15.01 0.00 3.42
335 336 3.181493 CGCGTTTTAGTTCCCTCTAGCTA 60.181 47.826 0.00 0.00 0.00 3.32
337 338 1.925185 CGCGTTTTAGTTCCCTCTAGC 59.075 52.381 0.00 0.00 0.00 3.42
338 339 1.925185 GCGCGTTTTAGTTCCCTCTAG 59.075 52.381 8.43 0.00 0.00 2.43
340 341 1.012486 CGCGCGTTTTAGTTCCCTCT 61.012 55.000 24.19 0.00 0.00 3.69
341 342 1.287041 ACGCGCGTTTTAGTTCCCTC 61.287 55.000 32.73 0.00 0.00 4.30
342 343 0.881600 AACGCGCGTTTTAGTTCCCT 60.882 50.000 39.88 16.68 34.22 4.20
343 344 0.723459 CAACGCGCGTTTTAGTTCCC 60.723 55.000 42.41 0.00 36.00 3.97
344 345 0.723459 CCAACGCGCGTTTTAGTTCC 60.723 55.000 42.41 0.00 36.00 3.62
345 346 1.325210 GCCAACGCGCGTTTTAGTTC 61.325 55.000 42.41 23.35 36.00 3.01
346 347 1.369568 GCCAACGCGCGTTTTAGTT 60.370 52.632 42.41 21.46 36.00 2.24
347 348 2.166584 GAGCCAACGCGCGTTTTAGT 62.167 55.000 42.41 27.34 41.18 2.24
348 349 1.509162 GAGCCAACGCGCGTTTTAG 60.509 57.895 42.41 32.42 41.18 1.85
364 365 3.777925 CAACTCCAACGCGCCGAG 61.778 66.667 5.73 11.23 0.00 4.63
369 370 1.352156 GGTAGAGCAACTCCAACGCG 61.352 60.000 3.53 3.53 0.00 6.01
375 376 1.222113 GCCAGGGTAGAGCAACTCC 59.778 63.158 0.00 0.00 0.00 3.85
416 417 0.040067 CTTGAAAAGGACGCTGTGGC 60.040 55.000 0.00 0.00 41.27 5.01
584 615 1.079543 CACGCTCTCTCCCACTTGG 60.080 63.158 0.00 0.00 0.00 3.61
586 617 1.228894 TCCACGCTCTCTCCCACTT 60.229 57.895 0.00 0.00 0.00 3.16
1722 1753 2.277692 CGATGCAGCAATGTGCCG 60.278 61.111 1.53 0.00 46.52 5.69
1725 1756 1.133598 ACATTCCGATGCAGCAATGTG 59.866 47.619 16.97 6.40 37.92 3.21
2248 2279 5.940192 TCACTAACGCAATTCACATTTCT 57.060 34.783 0.00 0.00 0.00 2.52
2520 2551 4.343239 ACCTGTCCGGGTAATAGTAACATC 59.657 45.833 0.00 0.00 37.90 3.06
2567 2604 8.515414 GTTTTATTGAAACTCCTGAATAGCAGT 58.485 33.333 0.00 0.00 43.44 4.40
2568 2605 8.902040 GTTTTATTGAAACTCCTGAATAGCAG 57.098 34.615 0.00 0.00 43.44 4.24
2618 2664 5.439721 ACAGCAAATGGACATTAGCTCATA 58.560 37.500 0.00 0.00 0.00 2.15
2619 2665 4.275810 ACAGCAAATGGACATTAGCTCAT 58.724 39.130 0.00 0.00 0.00 2.90
2658 2704 5.278957 CCCAAAACTTCCAATACCTGAACAG 60.279 44.000 0.00 0.00 0.00 3.16
2695 2741 5.007682 TCAACTTTGTAGATAAGCCCCAAC 58.992 41.667 0.00 0.00 0.00 3.77
3080 3128 1.006102 GTAGGCCCCGTCATCATCG 60.006 63.158 0.00 0.00 0.00 3.84
3236 3284 7.819415 TCAGTAGGTGATCACTAACAATCTTTG 59.181 37.037 24.50 14.56 0.00 2.77
3259 3307 5.406175 CCAGTAATGTTGTTTGCCAAATCAG 59.594 40.000 0.00 0.00 34.07 2.90
3298 3346 8.049117 TGACAGGAGCAGAATTAATAATCAACT 58.951 33.333 0.00 0.00 0.00 3.16
3398 3492 4.935205 TCACCTGGTAAATGTTGAATCTCG 59.065 41.667 0.00 0.00 0.00 4.04
3409 3503 4.169059 TGCATAGCATCACCTGGTAAAT 57.831 40.909 0.00 0.00 40.97 1.40
3621 3715 0.533755 GAGATGGGCCTCAACATCCG 60.534 60.000 14.09 0.00 43.42 4.18
3758 3852 6.374053 TGCTTGGTTCATTTTGATCGATCTTA 59.626 34.615 25.02 11.30 0.00 2.10
3854 3948 2.885135 TGAACTGCAGGATCCATTGT 57.115 45.000 19.93 4.21 0.00 2.71
3880 3974 6.385176 TCTGAGATTGATCCTAATCTTGTGGT 59.615 38.462 9.09 0.00 45.00 4.16
3881 3975 6.824553 TCTGAGATTGATCCTAATCTTGTGG 58.175 40.000 9.09 2.72 45.00 4.17
4016 4110 2.484264 AGGTTTGAGCAATTACTCGCAC 59.516 45.455 1.27 0.73 39.68 5.34
4069 4163 6.445357 TCTCGTATGATTTACTGTACAGCA 57.555 37.500 22.90 12.29 0.00 4.41
4101 4195 2.087646 AGAGCTGCCGAAATTTCCTTC 58.912 47.619 12.54 2.81 0.00 3.46
4117 4211 3.340337 AGCAAACAAGTTTCGAAGAGC 57.660 42.857 0.00 0.00 38.43 4.09
4124 4218 6.343226 TGCACAAAATAGCAAACAAGTTTC 57.657 33.333 0.00 0.00 37.90 2.78
4135 4229 5.180117 ACCTCGATGATATGCACAAAATAGC 59.820 40.000 0.00 0.00 0.00 2.97
4136 4230 6.128445 GGACCTCGATGATATGCACAAAATAG 60.128 42.308 0.00 0.00 0.00 1.73
4266 4361 6.000219 CGATATCCAGATTCCAGGAATGTTT 59.000 40.000 20.21 5.55 37.48 2.83
4290 4390 8.844244 AGGACATTACAATATCTCTGAAAATGC 58.156 33.333 0.00 0.00 30.61 3.56
4313 4413 9.739276 AAAAACAATTGACAGATCATAGTAGGA 57.261 29.630 13.59 0.00 33.85 2.94
4356 4456 3.871594 GGAAAGGAACCAGATGATGTACG 59.128 47.826 0.00 0.00 0.00 3.67
4458 4568 2.226962 AACATTCTCCAGCCTGCAAT 57.773 45.000 0.00 0.00 0.00 3.56
4560 4670 8.910351 AGAGTCATACCTATTTTGATTTAGCC 57.090 34.615 0.00 0.00 0.00 3.93
4623 4734 9.936759 AGTTGAAAATTTAAGTGGTTTCAAGAA 57.063 25.926 9.90 0.00 45.59 2.52
4649 4762 9.823647 TTAAAAACAAAATGAGAATACCTTGCA 57.176 25.926 0.00 0.00 0.00 4.08
4687 4800 7.573627 AGTTCAAGCAATTTAACTACTCGAAC 58.426 34.615 0.00 0.00 30.62 3.95
4842 4956 0.990374 GGCCCAGATGGAGCAGATAT 59.010 55.000 0.00 0.00 37.39 1.63


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

AutoCloner maintained by Alex Coulton.