Multiple sequence alignment - TraesCS3D01G178600

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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 TraesCS3D01G178600 chr3D 100.000 3019 0 0 1 3019 160563227 160560209 0.000000e+00 5576.0
1 TraesCS3D01G178600 chr3D 100.000 43 0 0 2025 2067 160561162 160561120 2.490000e-11 80.5
2 TraesCS3D01G178600 chr3D 100.000 43 0 0 2066 2108 160561203 160561161 2.490000e-11 80.5
3 TraesCS3D01G178600 chr3B 92.279 2176 71 42 927 3019 237112095 237109934 0.000000e+00 2998.0
4 TraesCS3D01G178600 chr3B 91.770 644 22 13 254 874 237112734 237112099 0.000000e+00 867.0
5 TraesCS3D01G178600 chr3A 96.673 1683 30 15 378 2040 186752119 186750443 0.000000e+00 2774.0
6 TraesCS3D01G178600 chr3A 95.879 922 10 5 2100 3019 186750451 186749556 0.000000e+00 1467.0
7 TraesCS3D01G178600 chr3A 95.373 389 11 2 1 382 186757891 186757503 1.990000e-171 612.0


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 TraesCS3D01G178600 chr3D 160560209 160563227 3018 True 1912.333333 5576 100.0000 1 3019 3 chr3D.!!$R1 3018
1 TraesCS3D01G178600 chr3B 237109934 237112734 2800 True 1932.500000 2998 92.0245 254 3019 2 chr3B.!!$R1 2765
2 TraesCS3D01G178600 chr3A 186749556 186752119 2563 True 2120.500000 2774 96.2760 378 3019 2 chr3A.!!$R2 2641

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
481 496 0.027324 GCTACAAAGCGCAGATGCTC 59.973 55.0 11.47 0.0 46.6 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2163 1.916651 CATCGTCTCTGCACTTCTTCG 59.083 52.381 0.0 0.0 0.0 3.79 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.587520 AGTGGCCCAAGATGAGGA 57.412 55.556 0.00 0.00 0.00 3.71
18 19 2.305095 AGTGGCCCAAGATGAGGAG 58.695 57.895 0.00 0.00 0.00 3.69
19 20 1.452833 GTGGCCCAAGATGAGGAGC 60.453 63.158 0.00 0.00 0.00 4.70
20 21 1.924939 TGGCCCAAGATGAGGAGCA 60.925 57.895 0.00 0.00 0.00 4.26
21 22 1.304282 GGCCCAAGATGAGGAGCAA 59.696 57.895 0.00 0.00 0.00 3.91
22 23 0.750911 GGCCCAAGATGAGGAGCAAG 60.751 60.000 0.00 0.00 0.00 4.01
23 24 0.254178 GCCCAAGATGAGGAGCAAGA 59.746 55.000 0.00 0.00 0.00 3.02
24 25 1.340405 GCCCAAGATGAGGAGCAAGAA 60.340 52.381 0.00 0.00 0.00 2.52
25 26 2.363683 CCCAAGATGAGGAGCAAGAAC 58.636 52.381 0.00 0.00 0.00 3.01
26 27 2.290514 CCCAAGATGAGGAGCAAGAACA 60.291 50.000 0.00 0.00 0.00 3.18
27 28 2.746362 CCAAGATGAGGAGCAAGAACAC 59.254 50.000 0.00 0.00 0.00 3.32
28 29 3.405831 CAAGATGAGGAGCAAGAACACA 58.594 45.455 0.00 0.00 0.00 3.72
29 30 3.777106 AGATGAGGAGCAAGAACACAA 57.223 42.857 0.00 0.00 0.00 3.33
30 31 4.298103 AGATGAGGAGCAAGAACACAAT 57.702 40.909 0.00 0.00 0.00 2.71
31 32 4.008330 AGATGAGGAGCAAGAACACAATG 58.992 43.478 0.00 0.00 0.00 2.82
32 33 3.213206 TGAGGAGCAAGAACACAATGT 57.787 42.857 0.00 0.00 0.00 2.71
33 34 3.554934 TGAGGAGCAAGAACACAATGTT 58.445 40.909 0.00 0.00 44.37 2.71
34 35 3.953612 TGAGGAGCAAGAACACAATGTTT 59.046 39.130 0.00 0.00 41.28 2.83
35 36 4.202040 TGAGGAGCAAGAACACAATGTTTG 60.202 41.667 0.00 0.00 41.28 2.93
36 37 3.701040 AGGAGCAAGAACACAATGTTTGT 59.299 39.130 0.00 0.00 41.28 2.83
47 48 3.993920 ACAATGTTTGTGGAATTGAGCC 58.006 40.909 1.89 0.00 43.48 4.70
48 49 3.387374 ACAATGTTTGTGGAATTGAGCCA 59.613 39.130 1.89 0.00 43.48 4.75
49 50 4.141756 ACAATGTTTGTGGAATTGAGCCAA 60.142 37.500 1.89 0.00 43.48 4.52
50 51 4.895668 ATGTTTGTGGAATTGAGCCAAT 57.104 36.364 0.00 0.00 37.12 3.16
51 52 5.999205 ATGTTTGTGGAATTGAGCCAATA 57.001 34.783 1.52 0.00 37.12 1.90
52 53 5.389859 TGTTTGTGGAATTGAGCCAATAG 57.610 39.130 1.52 0.00 37.12 1.73
53 54 5.076182 TGTTTGTGGAATTGAGCCAATAGA 58.924 37.500 1.52 0.00 37.12 1.98
54 55 5.538053 TGTTTGTGGAATTGAGCCAATAGAA 59.462 36.000 1.52 0.00 37.12 2.10
55 56 5.902613 TTGTGGAATTGAGCCAATAGAAG 57.097 39.130 1.52 0.00 37.12 2.85
56 57 4.922206 TGTGGAATTGAGCCAATAGAAGT 58.078 39.130 1.52 0.00 37.12 3.01
57 58 5.324409 TGTGGAATTGAGCCAATAGAAGTT 58.676 37.500 1.52 0.00 37.12 2.66
58 59 5.774690 TGTGGAATTGAGCCAATAGAAGTTT 59.225 36.000 1.52 0.00 37.12 2.66
59 60 6.095377 GTGGAATTGAGCCAATAGAAGTTTG 58.905 40.000 1.52 0.00 37.12 2.93
60 61 5.774690 TGGAATTGAGCCAATAGAAGTTTGT 59.225 36.000 1.52 0.00 32.43 2.83
61 62 6.071952 TGGAATTGAGCCAATAGAAGTTTGTC 60.072 38.462 1.52 0.00 32.43 3.18
62 63 6.151817 GGAATTGAGCCAATAGAAGTTTGTCT 59.848 38.462 1.52 0.00 32.43 3.41
63 64 6.749923 ATTGAGCCAATAGAAGTTTGTCTC 57.250 37.500 0.00 0.00 31.77 3.36
64 65 5.227569 TGAGCCAATAGAAGTTTGTCTCA 57.772 39.130 0.00 0.00 36.90 3.27
65 66 5.809001 TGAGCCAATAGAAGTTTGTCTCAT 58.191 37.500 0.00 0.00 35.01 2.90
66 67 6.240894 TGAGCCAATAGAAGTTTGTCTCATT 58.759 36.000 0.00 0.00 35.01 2.57
67 68 7.394016 TGAGCCAATAGAAGTTTGTCTCATTA 58.606 34.615 0.00 0.00 35.01 1.90
68 69 7.882791 TGAGCCAATAGAAGTTTGTCTCATTAA 59.117 33.333 0.00 0.00 35.01 1.40
69 70 8.814038 AGCCAATAGAAGTTTGTCTCATTAAT 57.186 30.769 0.00 0.00 0.00 1.40
70 71 8.680903 AGCCAATAGAAGTTTGTCTCATTAATG 58.319 33.333 9.29 9.29 0.00 1.90
71 72 7.433425 GCCAATAGAAGTTTGTCTCATTAATGC 59.567 37.037 10.76 0.00 0.00 3.56
72 73 8.680903 CCAATAGAAGTTTGTCTCATTAATGCT 58.319 33.333 10.76 0.96 0.00 3.79
75 76 7.992754 AGAAGTTTGTCTCATTAATGCTTCT 57.007 32.000 18.66 18.66 36.38 2.85
76 77 7.814642 AGAAGTTTGTCTCATTAATGCTTCTG 58.185 34.615 21.45 7.97 38.74 3.02
77 78 7.663081 AGAAGTTTGTCTCATTAATGCTTCTGA 59.337 33.333 21.45 9.56 38.74 3.27
78 79 7.750229 AGTTTGTCTCATTAATGCTTCTGAA 57.250 32.000 10.76 0.00 0.00 3.02
79 80 8.169977 AGTTTGTCTCATTAATGCTTCTGAAA 57.830 30.769 10.76 2.66 0.00 2.69
80 81 8.632679 AGTTTGTCTCATTAATGCTTCTGAAAA 58.367 29.630 10.76 3.05 0.00 2.29
81 82 8.909671 GTTTGTCTCATTAATGCTTCTGAAAAG 58.090 33.333 10.76 0.05 0.00 2.27
82 83 7.984422 TGTCTCATTAATGCTTCTGAAAAGA 57.016 32.000 10.76 2.45 0.00 2.52
83 84 8.571461 TGTCTCATTAATGCTTCTGAAAAGAT 57.429 30.769 10.76 0.00 0.00 2.40
84 85 9.017509 TGTCTCATTAATGCTTCTGAAAAGATT 57.982 29.630 10.76 0.00 0.00 2.40
85 86 9.286946 GTCTCATTAATGCTTCTGAAAAGATTG 57.713 33.333 10.76 0.00 0.00 2.67
86 87 9.234827 TCTCATTAATGCTTCTGAAAAGATTGA 57.765 29.630 10.76 0.00 0.00 2.57
88 89 9.797556 TCATTAATGCTTCTGAAAAGATTGATG 57.202 29.630 10.76 10.81 0.00 3.07
89 90 9.797556 CATTAATGCTTCTGAAAAGATTGATGA 57.202 29.630 1.74 0.00 0.00 2.92
90 91 9.798994 ATTAATGCTTCTGAAAAGATTGATGAC 57.201 29.630 0.00 0.00 0.00 3.06
91 92 7.463961 AATGCTTCTGAAAAGATTGATGACT 57.536 32.000 0.00 0.00 0.00 3.41
92 93 6.889301 TGCTTCTGAAAAGATTGATGACTT 57.111 33.333 0.00 0.00 0.00 3.01
93 94 6.675026 TGCTTCTGAAAAGATTGATGACTTG 58.325 36.000 0.00 0.00 0.00 3.16
94 95 5.572126 GCTTCTGAAAAGATTGATGACTTGC 59.428 40.000 0.00 0.00 0.00 4.01
95 96 6.638096 TTCTGAAAAGATTGATGACTTGCA 57.362 33.333 0.00 0.00 0.00 4.08
96 97 6.829229 TCTGAAAAGATTGATGACTTGCAT 57.171 33.333 0.00 0.00 40.77 3.96
97 98 6.617879 TCTGAAAAGATTGATGACTTGCATG 58.382 36.000 0.00 0.00 37.34 4.06
98 99 6.431852 TCTGAAAAGATTGATGACTTGCATGA 59.568 34.615 6.60 0.00 37.34 3.07
99 100 6.617879 TGAAAAGATTGATGACTTGCATGAG 58.382 36.000 6.60 0.00 37.34 2.90
100 101 6.431852 TGAAAAGATTGATGACTTGCATGAGA 59.568 34.615 6.60 0.00 37.34 3.27
101 102 5.814764 AAGATTGATGACTTGCATGAGAC 57.185 39.130 6.60 0.00 37.34 3.36
102 103 4.197750 AGATTGATGACTTGCATGAGACC 58.802 43.478 6.60 0.00 37.34 3.85
103 104 3.708403 TTGATGACTTGCATGAGACCT 57.292 42.857 6.60 0.00 37.34 3.85
104 105 4.824479 TTGATGACTTGCATGAGACCTA 57.176 40.909 6.60 0.00 37.34 3.08
105 106 4.824479 TGATGACTTGCATGAGACCTAA 57.176 40.909 6.60 0.00 37.34 2.69
106 107 5.363562 TGATGACTTGCATGAGACCTAAT 57.636 39.130 6.60 0.00 37.34 1.73
107 108 5.121105 TGATGACTTGCATGAGACCTAATG 58.879 41.667 6.60 0.00 37.34 1.90
108 109 3.877559 TGACTTGCATGAGACCTAATGG 58.122 45.455 6.60 0.00 39.83 3.16
109 110 4.080129 ATGACTTGCATGAGACCTAATGGT 60.080 41.667 6.60 0.00 42.19 3.55
110 111 5.574326 ATGACTTGCATGAGACCTAATGGTT 60.574 40.000 6.60 0.00 40.58 3.67
111 112 7.030244 ATGACTTGCATGAGACCTAATGGTTT 61.030 38.462 6.60 0.00 40.58 3.27
112 113 8.760541 ATGACTTGCATGAGACCTAATGGTTTC 61.761 40.741 6.60 0.00 44.90 2.78
121 122 4.675063 ACCTAATGGTTTCCCAACATCT 57.325 40.909 0.00 0.00 46.05 2.90
122 123 5.789574 ACCTAATGGTTTCCCAACATCTA 57.210 39.130 0.00 0.00 46.05 1.98
123 124 6.341408 ACCTAATGGTTTCCCAACATCTAT 57.659 37.500 0.00 0.00 46.05 1.98
124 125 6.741724 ACCTAATGGTTTCCCAACATCTATT 58.258 36.000 0.00 0.00 46.05 1.73
125 126 7.189087 ACCTAATGGTTTCCCAACATCTATTT 58.811 34.615 0.00 0.00 46.05 1.40
126 127 7.124147 ACCTAATGGTTTCCCAACATCTATTTG 59.876 37.037 0.00 0.00 46.05 2.32
127 128 7.341769 CCTAATGGTTTCCCAACATCTATTTGA 59.658 37.037 0.00 0.00 46.04 2.69
128 129 7.552050 AATGGTTTCCCAACATCTATTTGAA 57.448 32.000 0.00 0.00 46.04 2.69
129 130 6.985653 TGGTTTCCCAACATCTATTTGAAA 57.014 33.333 0.00 0.00 37.98 2.69
130 131 7.366847 TGGTTTCCCAACATCTATTTGAAAA 57.633 32.000 0.00 0.00 37.98 2.29
131 132 7.796054 TGGTTTCCCAACATCTATTTGAAAAA 58.204 30.769 0.00 0.00 37.98 1.94
132 133 8.435982 TGGTTTCCCAACATCTATTTGAAAAAT 58.564 29.630 0.00 0.00 37.98 1.82
133 134 9.936759 GGTTTCCCAACATCTATTTGAAAAATA 57.063 29.630 0.00 0.00 34.15 1.40
138 139 9.248291 CCCAACATCTATTTGAAAAATAATCCG 57.752 33.333 0.00 0.00 0.00 4.18
139 140 9.248291 CCAACATCTATTTGAAAAATAATCCGG 57.752 33.333 0.00 0.00 0.00 5.14
140 141 9.801873 CAACATCTATTTGAAAAATAATCCGGT 57.198 29.630 0.00 0.00 0.00 5.28
141 142 9.801873 AACATCTATTTGAAAAATAATCCGGTG 57.198 29.630 0.00 0.00 0.00 4.94
142 143 9.184523 ACATCTATTTGAAAAATAATCCGGTGA 57.815 29.630 0.00 0.00 0.00 4.02
146 147 9.463443 CTATTTGAAAAATAATCCGGTGAATCC 57.537 33.333 0.00 0.00 0.00 3.01
147 148 6.842437 TTGAAAAATAATCCGGTGAATCCA 57.158 33.333 0.00 0.00 35.57 3.41
148 149 7.416964 TTGAAAAATAATCCGGTGAATCCAT 57.583 32.000 0.00 0.00 35.57 3.41
149 150 7.038154 TGAAAAATAATCCGGTGAATCCATC 57.962 36.000 0.00 0.00 35.57 3.51
150 151 6.040391 TGAAAAATAATCCGGTGAATCCATCC 59.960 38.462 0.00 0.00 35.57 3.51
151 152 2.831685 TAATCCGGTGAATCCATCCG 57.168 50.000 0.00 0.00 43.30 4.18
152 153 1.128200 AATCCGGTGAATCCATCCGA 58.872 50.000 0.00 0.00 46.05 4.55
153 154 0.393077 ATCCGGTGAATCCATCCGAC 59.607 55.000 0.00 0.00 46.05 4.79
154 155 1.591594 CCGGTGAATCCATCCGACG 60.592 63.158 9.42 0.00 46.05 5.12
155 156 2.237751 CGGTGAATCCATCCGACGC 61.238 63.158 0.00 0.00 46.05 5.19
156 157 2.237751 GGTGAATCCATCCGACGCG 61.238 63.158 3.53 3.53 35.97 6.01
174 175 3.161450 GGGGGATGTCGCTAGGCA 61.161 66.667 0.00 0.00 35.88 4.75
175 176 2.520536 GGGGGATGTCGCTAGGCAT 61.521 63.158 0.00 0.00 46.86 4.40
176 177 1.451936 GGGGATGTCGCTAGGCATT 59.548 57.895 0.00 0.00 43.74 3.56
177 178 0.179018 GGGGATGTCGCTAGGCATTT 60.179 55.000 0.00 0.00 43.74 2.32
178 179 0.947244 GGGATGTCGCTAGGCATTTG 59.053 55.000 0.00 0.00 43.74 2.32
179 180 1.475034 GGGATGTCGCTAGGCATTTGA 60.475 52.381 0.00 0.00 43.74 2.69
180 181 2.498167 GGATGTCGCTAGGCATTTGAT 58.502 47.619 0.00 0.00 43.74 2.57
181 182 2.880890 GGATGTCGCTAGGCATTTGATT 59.119 45.455 0.00 0.00 43.74 2.57
182 183 3.304257 GGATGTCGCTAGGCATTTGATTG 60.304 47.826 0.00 0.00 43.74 2.67
183 184 2.984562 TGTCGCTAGGCATTTGATTGA 58.015 42.857 0.00 0.00 0.00 2.57
184 185 3.544684 TGTCGCTAGGCATTTGATTGAT 58.455 40.909 0.00 0.00 0.00 2.57
185 186 4.702831 TGTCGCTAGGCATTTGATTGATA 58.297 39.130 0.00 0.00 0.00 2.15
186 187 4.751600 TGTCGCTAGGCATTTGATTGATAG 59.248 41.667 0.00 0.00 0.00 2.08
187 188 3.748048 TCGCTAGGCATTTGATTGATAGC 59.252 43.478 0.00 0.00 33.52 2.97
188 189 3.424039 CGCTAGGCATTTGATTGATAGCG 60.424 47.826 8.99 8.99 43.68 4.26
189 190 3.499918 GCTAGGCATTTGATTGATAGCGT 59.500 43.478 0.00 0.00 0.00 5.07
190 191 4.377841 GCTAGGCATTTGATTGATAGCGTC 60.378 45.833 0.00 0.00 0.00 5.19
191 192 3.544684 AGGCATTTGATTGATAGCGTCA 58.455 40.909 0.00 0.00 34.25 4.35
192 193 3.313526 AGGCATTTGATTGATAGCGTCAC 59.686 43.478 0.00 0.00 36.32 3.67
193 194 3.313526 GGCATTTGATTGATAGCGTCACT 59.686 43.478 0.00 0.00 36.32 3.41
194 195 4.201950 GGCATTTGATTGATAGCGTCACTT 60.202 41.667 0.00 0.00 36.32 3.16
195 196 5.007626 GGCATTTGATTGATAGCGTCACTTA 59.992 40.000 0.00 0.00 36.32 2.24
196 197 5.904080 GCATTTGATTGATAGCGTCACTTAC 59.096 40.000 0.00 0.00 36.32 2.34
197 198 6.238211 GCATTTGATTGATAGCGTCACTTACT 60.238 38.462 0.00 0.00 36.32 2.24
198 199 7.677276 GCATTTGATTGATAGCGTCACTTACTT 60.677 37.037 0.00 0.00 36.32 2.24
199 200 6.887376 TTGATTGATAGCGTCACTTACTTC 57.113 37.500 0.00 0.00 36.32 3.01
200 201 5.348986 TGATTGATAGCGTCACTTACTTCC 58.651 41.667 0.00 0.00 36.32 3.46
201 202 5.127194 TGATTGATAGCGTCACTTACTTCCT 59.873 40.000 0.00 0.00 36.32 3.36
202 203 4.634184 TGATAGCGTCACTTACTTCCTC 57.366 45.455 0.00 0.00 0.00 3.71
203 204 3.380637 TGATAGCGTCACTTACTTCCTCC 59.619 47.826 0.00 0.00 0.00 4.30
204 205 1.926108 AGCGTCACTTACTTCCTCCT 58.074 50.000 0.00 0.00 0.00 3.69
205 206 2.249139 AGCGTCACTTACTTCCTCCTT 58.751 47.619 0.00 0.00 0.00 3.36
206 207 2.028930 AGCGTCACTTACTTCCTCCTTG 60.029 50.000 0.00 0.00 0.00 3.61
207 208 2.931320 GCGTCACTTACTTCCTCCTTGG 60.931 54.545 0.00 0.00 37.10 3.61
208 209 2.561419 CGTCACTTACTTCCTCCTTGGA 59.439 50.000 0.00 0.00 44.51 3.53
218 219 3.827008 TCCTCCTTGGAGAAATGATCG 57.173 47.619 17.55 0.00 40.56 3.69
219 220 2.435805 TCCTCCTTGGAGAAATGATCGG 59.564 50.000 17.55 0.00 40.56 4.18
220 221 2.216898 CTCCTTGGAGAAATGATCGGC 58.783 52.381 11.02 0.00 0.00 5.54
221 222 1.559219 TCCTTGGAGAAATGATCGGCA 59.441 47.619 0.00 0.00 0.00 5.69
222 223 2.173356 TCCTTGGAGAAATGATCGGCAT 59.827 45.455 0.00 0.00 39.43 4.40
223 224 2.292569 CCTTGGAGAAATGATCGGCATG 59.707 50.000 0.00 0.00 37.28 4.06
224 225 1.311859 TGGAGAAATGATCGGCATGC 58.688 50.000 9.90 9.90 37.28 4.06
225 226 0.595095 GGAGAAATGATCGGCATGCC 59.405 55.000 27.67 27.67 37.28 4.40
226 227 0.595095 GAGAAATGATCGGCATGCCC 59.405 55.000 30.79 17.44 37.28 5.36
227 228 0.106569 AGAAATGATCGGCATGCCCA 60.107 50.000 30.79 22.60 37.28 5.36
228 229 0.746063 GAAATGATCGGCATGCCCAA 59.254 50.000 30.79 19.55 37.28 4.12
229 230 0.748450 AAATGATCGGCATGCCCAAG 59.252 50.000 30.79 17.20 37.28 3.61
230 231 0.396139 AATGATCGGCATGCCCAAGT 60.396 50.000 30.79 14.01 37.28 3.16
231 232 0.473755 ATGATCGGCATGCCCAAGTA 59.526 50.000 30.79 13.92 35.42 2.24
232 233 0.463654 TGATCGGCATGCCCAAGTAC 60.464 55.000 30.79 15.84 0.00 2.73
233 234 1.152963 ATCGGCATGCCCAAGTACC 60.153 57.895 30.79 3.55 0.00 3.34
234 235 1.920734 ATCGGCATGCCCAAGTACCA 61.921 55.000 30.79 5.04 0.00 3.25
235 236 1.677300 CGGCATGCCCAAGTACCAA 60.677 57.895 30.79 0.00 0.00 3.67
236 237 1.037030 CGGCATGCCCAAGTACCAAT 61.037 55.000 30.79 0.00 0.00 3.16
237 238 0.461135 GGCATGCCCAAGTACCAATG 59.539 55.000 27.24 0.00 0.00 2.82
238 239 0.461135 GCATGCCCAAGTACCAATGG 59.539 55.000 6.36 0.00 36.42 3.16
239 240 1.851304 CATGCCCAAGTACCAATGGT 58.149 50.000 10.81 10.81 40.16 3.55
240 241 1.750778 CATGCCCAAGTACCAATGGTC 59.249 52.381 8.82 0.49 37.09 4.02
241 242 0.322098 TGCCCAAGTACCAATGGTCG 60.322 55.000 8.82 0.00 37.09 4.79
242 243 0.322187 GCCCAAGTACCAATGGTCGT 60.322 55.000 8.82 0.00 37.09 4.34
243 244 1.734163 CCCAAGTACCAATGGTCGTC 58.266 55.000 8.82 0.81 37.09 4.20
244 245 1.677820 CCCAAGTACCAATGGTCGTCC 60.678 57.143 8.82 0.00 37.09 4.79
245 246 1.278127 CCAAGTACCAATGGTCGTCCT 59.722 52.381 8.82 0.00 37.09 3.85
246 247 2.498481 CCAAGTACCAATGGTCGTCCTA 59.502 50.000 8.82 0.00 37.09 2.94
247 248 3.134081 CCAAGTACCAATGGTCGTCCTAT 59.866 47.826 8.82 0.00 37.09 2.57
248 249 4.342951 CCAAGTACCAATGGTCGTCCTATA 59.657 45.833 8.82 0.00 37.09 1.31
249 250 5.011738 CCAAGTACCAATGGTCGTCCTATAT 59.988 44.000 8.82 0.00 37.09 0.86
250 251 5.979288 AGTACCAATGGTCGTCCTATATC 57.021 43.478 8.82 0.00 37.09 1.63
251 252 4.771054 AGTACCAATGGTCGTCCTATATCC 59.229 45.833 8.82 0.00 37.09 2.59
252 253 3.583228 ACCAATGGTCGTCCTATATCCA 58.417 45.455 0.00 0.00 34.23 3.41
277 278 9.204570 CATATTATTAAGGTAAACAGGAGTCGG 57.795 37.037 0.00 0.00 0.00 4.79
285 286 4.141779 GGTAAACAGGAGTCGGGATAATGT 60.142 45.833 0.00 0.00 0.00 2.71
289 290 3.517901 ACAGGAGTCGGGATAATGTTCAA 59.482 43.478 0.00 0.00 0.00 2.69
294 295 4.269183 AGTCGGGATAATGTTCAAATGCA 58.731 39.130 0.00 0.00 0.00 3.96
302 303 6.318648 GGATAATGTTCAAATGCACTCCACTA 59.681 38.462 0.00 0.00 0.00 2.74
358 365 3.119245 GCAAGCTGATTCATCACCAATGT 60.119 43.478 0.00 0.00 36.68 2.71
360 367 5.393352 GCAAGCTGATTCATCACCAATGTAA 60.393 40.000 0.00 0.00 36.68 2.41
365 372 4.894705 TGATTCATCACCAATGTAATGGGG 59.105 41.667 0.00 0.00 43.97 4.96
410 417 3.250762 CGACCTTGCATCTGTTTTCTTCA 59.749 43.478 0.00 0.00 0.00 3.02
481 496 0.027324 GCTACAAAGCGCAGATGCTC 59.973 55.000 11.47 0.00 46.60 4.26
555 570 2.685380 AAGGTGCCCTCCTCTCCG 60.685 66.667 0.00 0.00 36.74 4.63
819 856 2.579787 CCTTGACGGCTAGACGCG 60.580 66.667 20.33 3.53 40.44 6.01
888 925 1.686455 TATCCGGCCGTGGAAAGGA 60.686 57.895 26.12 12.70 42.46 3.36
1198 1243 4.868116 ACCAACCAACACGCGGCT 62.868 61.111 12.47 0.00 0.00 5.52
1230 1302 2.361992 TGATGCTGCCTGGGCTTG 60.362 61.111 13.05 6.95 42.51 4.01
1231 1303 3.145551 GATGCTGCCTGGGCTTGG 61.146 66.667 13.05 4.64 42.51 3.61
2031 2148 1.250328 TGTTTGAATGCCTGAGCCTG 58.750 50.000 0.00 0.00 38.69 4.85
2033 2150 1.200948 GTTTGAATGCCTGAGCCTGAC 59.799 52.381 0.00 0.00 38.69 3.51
2034 2151 0.401356 TTGAATGCCTGAGCCTGACA 59.599 50.000 0.00 0.00 38.69 3.58
2046 2163 2.421424 GAGCCTGACACAATGAATGGTC 59.579 50.000 0.00 0.00 32.82 4.02
2047 2164 1.131126 GCCTGACACAATGAATGGTCG 59.869 52.381 0.00 0.00 34.09 4.79
2063 2180 1.332178 GTCGAAGAAGTGCAGAGACG 58.668 55.000 0.00 0.00 39.69 4.18
2075 2192 0.813821 CAGAGACGATGAGCCTGACA 59.186 55.000 0.00 0.00 0.00 3.58
2091 2208 3.125829 CCTGACACAATGAATGGTCGAAG 59.874 47.826 0.00 0.00 34.09 3.79
2095 2212 4.389374 ACACAATGAATGGTCGAAGAAGT 58.611 39.130 0.00 0.00 39.69 3.01
2311 2439 7.124347 ACATGCAAATCAAAATTGATCACAC 57.876 32.000 8.96 1.54 46.60 3.82
2520 2651 4.764308 TGCACACCATACTAAAGATGCAAA 59.236 37.500 0.00 0.00 38.78 3.68
2820 2951 5.004821 GCTACCATATCGAGCAAATATGACG 59.995 44.000 12.14 0.00 38.73 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.919600 GCTCCTCATCTTGGGCCACT 61.920 60.000 5.23 0.00 0.00 4.00
1 2 1.452833 GCTCCTCATCTTGGGCCAC 60.453 63.158 5.23 0.00 0.00 5.01
2 3 1.499913 TTGCTCCTCATCTTGGGCCA 61.500 55.000 0.00 0.00 0.00 5.36
3 4 0.750911 CTTGCTCCTCATCTTGGGCC 60.751 60.000 0.00 0.00 0.00 5.80
4 5 0.254178 TCTTGCTCCTCATCTTGGGC 59.746 55.000 0.00 0.00 0.00 5.36
5 6 2.290514 TGTTCTTGCTCCTCATCTTGGG 60.291 50.000 0.00 0.00 0.00 4.12
6 7 2.746362 GTGTTCTTGCTCCTCATCTTGG 59.254 50.000 0.00 0.00 0.00 3.61
7 8 3.405831 TGTGTTCTTGCTCCTCATCTTG 58.594 45.455 0.00 0.00 0.00 3.02
8 9 3.777106 TGTGTTCTTGCTCCTCATCTT 57.223 42.857 0.00 0.00 0.00 2.40
9 10 3.777106 TTGTGTTCTTGCTCCTCATCT 57.223 42.857 0.00 0.00 0.00 2.90
10 11 3.755378 ACATTGTGTTCTTGCTCCTCATC 59.245 43.478 0.00 0.00 0.00 2.92
11 12 3.759581 ACATTGTGTTCTTGCTCCTCAT 58.240 40.909 0.00 0.00 0.00 2.90
12 13 3.213206 ACATTGTGTTCTTGCTCCTCA 57.787 42.857 0.00 0.00 0.00 3.86
13 14 4.202050 ACAAACATTGTGTTCTTGCTCCTC 60.202 41.667 0.00 0.00 40.14 3.71
14 15 3.701040 ACAAACATTGTGTTCTTGCTCCT 59.299 39.130 0.00 0.00 40.14 3.69
15 16 4.045636 ACAAACATTGTGTTCTTGCTCC 57.954 40.909 0.00 0.00 40.14 4.70
24 25 9.737911 ATTGGCTCAATTCCACAAACATTGTGT 62.738 37.037 18.73 0.00 43.93 3.72
25 26 7.457740 ATTGGCTCAATTCCACAAACATTGTG 61.458 38.462 14.65 14.65 44.46 3.33
26 27 3.387374 TGGCTCAATTCCACAAACATTGT 59.613 39.130 0.00 0.00 46.75 2.71
27 28 3.992643 TGGCTCAATTCCACAAACATTG 58.007 40.909 0.00 0.00 0.00 2.82
28 29 4.686191 TTGGCTCAATTCCACAAACATT 57.314 36.364 0.00 0.00 32.45 2.71
29 30 4.895668 ATTGGCTCAATTCCACAAACAT 57.104 36.364 0.00 0.00 28.76 2.71
30 31 5.076182 TCTATTGGCTCAATTCCACAAACA 58.924 37.500 5.85 0.00 35.54 2.83
31 32 5.643379 TCTATTGGCTCAATTCCACAAAC 57.357 39.130 5.85 0.00 35.54 2.93
32 33 5.774690 ACTTCTATTGGCTCAATTCCACAAA 59.225 36.000 5.85 0.00 35.54 2.83
33 34 5.324409 ACTTCTATTGGCTCAATTCCACAA 58.676 37.500 5.85 0.00 35.54 3.33
34 35 4.922206 ACTTCTATTGGCTCAATTCCACA 58.078 39.130 5.85 0.00 35.54 4.17
35 36 5.904362 AACTTCTATTGGCTCAATTCCAC 57.096 39.130 5.85 0.00 35.54 4.02
36 37 5.774690 ACAAACTTCTATTGGCTCAATTCCA 59.225 36.000 5.85 0.00 35.54 3.53
37 38 6.151817 AGACAAACTTCTATTGGCTCAATTCC 59.848 38.462 5.85 0.00 42.47 3.01
38 39 7.150783 AGACAAACTTCTATTGGCTCAATTC 57.849 36.000 5.85 0.00 42.47 2.17
45 46 7.433425 GCATTAATGAGACAAACTTCTATTGGC 59.567 37.037 19.73 0.00 35.99 4.52
46 47 8.680903 AGCATTAATGAGACAAACTTCTATTGG 58.319 33.333 19.73 0.00 32.02 3.16
49 50 9.678260 AGAAGCATTAATGAGACAAACTTCTAT 57.322 29.630 19.73 3.41 39.49 1.98
50 51 8.939929 CAGAAGCATTAATGAGACAAACTTCTA 58.060 33.333 19.73 0.00 39.31 2.10
51 52 7.663081 TCAGAAGCATTAATGAGACAAACTTCT 59.337 33.333 19.73 19.07 41.35 2.85
52 53 7.810658 TCAGAAGCATTAATGAGACAAACTTC 58.189 34.615 19.73 17.41 33.01 3.01
53 54 7.750229 TCAGAAGCATTAATGAGACAAACTT 57.250 32.000 19.73 10.29 0.00 2.66
54 55 7.750229 TTCAGAAGCATTAATGAGACAAACT 57.250 32.000 19.73 1.81 0.00 2.66
55 56 8.801715 TTTTCAGAAGCATTAATGAGACAAAC 57.198 30.769 19.73 0.00 0.00 2.93
56 57 8.849168 TCTTTTCAGAAGCATTAATGAGACAAA 58.151 29.630 19.73 6.63 0.00 2.83
57 58 8.394971 TCTTTTCAGAAGCATTAATGAGACAA 57.605 30.769 19.73 6.65 0.00 3.18
58 59 7.984422 TCTTTTCAGAAGCATTAATGAGACA 57.016 32.000 19.73 0.00 0.00 3.41
59 60 9.286946 CAATCTTTTCAGAAGCATTAATGAGAC 57.713 33.333 19.73 8.54 30.76 3.36
60 61 9.234827 TCAATCTTTTCAGAAGCATTAATGAGA 57.765 29.630 19.73 9.50 30.76 3.27
62 63 9.797556 CATCAATCTTTTCAGAAGCATTAATGA 57.202 29.630 19.73 0.00 30.76 2.57
63 64 9.797556 TCATCAATCTTTTCAGAAGCATTAATG 57.202 29.630 11.27 11.27 30.76 1.90
64 65 9.798994 GTCATCAATCTTTTCAGAAGCATTAAT 57.201 29.630 0.00 0.00 30.76 1.40
65 66 9.017509 AGTCATCAATCTTTTCAGAAGCATTAA 57.982 29.630 0.00 0.00 30.76 1.40
66 67 8.571461 AGTCATCAATCTTTTCAGAAGCATTA 57.429 30.769 0.00 0.00 30.76 1.90
67 68 7.463961 AGTCATCAATCTTTTCAGAAGCATT 57.536 32.000 0.00 0.00 30.76 3.56
68 69 7.313646 CAAGTCATCAATCTTTTCAGAAGCAT 58.686 34.615 0.00 0.00 30.76 3.79
69 70 6.675026 CAAGTCATCAATCTTTTCAGAAGCA 58.325 36.000 0.00 0.00 30.76 3.91
70 71 5.572126 GCAAGTCATCAATCTTTTCAGAAGC 59.428 40.000 0.00 0.00 30.76 3.86
71 72 6.675026 TGCAAGTCATCAATCTTTTCAGAAG 58.325 36.000 0.00 0.00 30.76 2.85
72 73 6.638096 TGCAAGTCATCAATCTTTTCAGAA 57.362 33.333 0.00 0.00 30.76 3.02
73 74 6.431852 TCATGCAAGTCATCAATCTTTTCAGA 59.568 34.615 0.00 0.00 31.79 3.27
74 75 6.617879 TCATGCAAGTCATCAATCTTTTCAG 58.382 36.000 0.00 0.00 31.79 3.02
75 76 6.431852 TCTCATGCAAGTCATCAATCTTTTCA 59.568 34.615 0.00 0.00 31.79 2.69
76 77 6.746364 GTCTCATGCAAGTCATCAATCTTTTC 59.254 38.462 0.00 0.00 31.79 2.29
77 78 6.349944 GGTCTCATGCAAGTCATCAATCTTTT 60.350 38.462 0.00 0.00 31.79 2.27
78 79 5.125097 GGTCTCATGCAAGTCATCAATCTTT 59.875 40.000 0.00 0.00 31.79 2.52
79 80 4.639310 GGTCTCATGCAAGTCATCAATCTT 59.361 41.667 0.00 0.00 31.79 2.40
80 81 4.080469 AGGTCTCATGCAAGTCATCAATCT 60.080 41.667 0.00 0.00 31.79 2.40
81 82 4.197750 AGGTCTCATGCAAGTCATCAATC 58.802 43.478 0.00 0.00 31.79 2.67
82 83 4.232188 AGGTCTCATGCAAGTCATCAAT 57.768 40.909 0.00 0.00 31.79 2.57
83 84 3.708403 AGGTCTCATGCAAGTCATCAA 57.292 42.857 0.00 0.00 31.79 2.57
84 85 4.824479 TTAGGTCTCATGCAAGTCATCA 57.176 40.909 0.00 0.00 31.79 3.07
85 86 4.514441 CCATTAGGTCTCATGCAAGTCATC 59.486 45.833 0.00 0.00 31.79 2.92
86 87 4.458397 CCATTAGGTCTCATGCAAGTCAT 58.542 43.478 0.00 0.00 35.31 3.06
87 88 3.877559 CCATTAGGTCTCATGCAAGTCA 58.122 45.455 0.00 0.00 0.00 3.41
112 113 9.248291 CGGATTATTTTTCAAATAGATGTTGGG 57.752 33.333 0.00 0.00 0.00 4.12
113 114 9.248291 CCGGATTATTTTTCAAATAGATGTTGG 57.752 33.333 0.00 0.00 0.00 3.77
114 115 9.801873 ACCGGATTATTTTTCAAATAGATGTTG 57.198 29.630 9.46 0.00 0.00 3.33
115 116 9.801873 CACCGGATTATTTTTCAAATAGATGTT 57.198 29.630 9.46 0.00 0.00 2.71
116 117 9.184523 TCACCGGATTATTTTTCAAATAGATGT 57.815 29.630 9.46 0.00 0.00 3.06
120 121 9.463443 GGATTCACCGGATTATTTTTCAAATAG 57.537 33.333 9.46 0.00 0.00 1.73
121 122 8.972127 TGGATTCACCGGATTATTTTTCAAATA 58.028 29.630 9.46 0.00 42.61 1.40
122 123 7.846066 TGGATTCACCGGATTATTTTTCAAAT 58.154 30.769 9.46 0.00 42.61 2.32
123 124 7.233389 TGGATTCACCGGATTATTTTTCAAA 57.767 32.000 9.46 0.00 42.61 2.69
124 125 6.842437 TGGATTCACCGGATTATTTTTCAA 57.158 33.333 9.46 0.00 42.61 2.69
125 126 6.040391 GGATGGATTCACCGGATTATTTTTCA 59.960 38.462 9.46 0.00 42.61 2.69
126 127 6.447162 GGATGGATTCACCGGATTATTTTTC 58.553 40.000 9.46 0.00 42.61 2.29
127 128 5.009610 CGGATGGATTCACCGGATTATTTTT 59.990 40.000 9.46 0.00 42.48 1.94
128 129 4.518970 CGGATGGATTCACCGGATTATTTT 59.481 41.667 9.46 0.00 42.48 1.82
129 130 4.072131 CGGATGGATTCACCGGATTATTT 58.928 43.478 9.46 0.00 42.48 1.40
130 131 3.326588 TCGGATGGATTCACCGGATTATT 59.673 43.478 9.46 0.00 45.61 1.40
131 132 2.903784 TCGGATGGATTCACCGGATTAT 59.096 45.455 9.46 0.00 45.61 1.28
132 133 2.036733 GTCGGATGGATTCACCGGATTA 59.963 50.000 9.46 0.00 45.61 1.75
133 134 1.128200 TCGGATGGATTCACCGGATT 58.872 50.000 9.46 0.00 45.61 3.01
134 135 0.393077 GTCGGATGGATTCACCGGAT 59.607 55.000 9.46 0.00 45.61 4.18
135 136 1.820581 GTCGGATGGATTCACCGGA 59.179 57.895 9.46 0.00 45.61 5.14
136 137 1.591594 CGTCGGATGGATTCACCGG 60.592 63.158 13.05 0.00 45.61 5.28
137 138 2.237751 GCGTCGGATGGATTCACCG 61.238 63.158 8.28 8.28 46.71 4.94
138 139 2.237751 CGCGTCGGATGGATTCACC 61.238 63.158 0.00 0.00 39.54 4.02
139 140 3.309675 CGCGTCGGATGGATTCAC 58.690 61.111 0.00 0.00 0.00 3.18
157 158 2.056906 AATGCCTAGCGACATCCCCC 62.057 60.000 0.00 0.00 0.00 5.40
158 159 0.179018 AAATGCCTAGCGACATCCCC 60.179 55.000 0.00 0.00 0.00 4.81
159 160 0.947244 CAAATGCCTAGCGACATCCC 59.053 55.000 0.00 0.00 0.00 3.85
160 161 1.953559 TCAAATGCCTAGCGACATCC 58.046 50.000 0.00 0.00 0.00 3.51
161 162 3.561310 TCAATCAAATGCCTAGCGACATC 59.439 43.478 0.00 0.00 0.00 3.06
162 163 3.544684 TCAATCAAATGCCTAGCGACAT 58.455 40.909 0.00 0.00 0.00 3.06
163 164 2.984562 TCAATCAAATGCCTAGCGACA 58.015 42.857 0.00 0.00 0.00 4.35
164 165 4.377841 GCTATCAATCAAATGCCTAGCGAC 60.378 45.833 0.00 0.00 0.00 5.19
165 166 3.748048 GCTATCAATCAAATGCCTAGCGA 59.252 43.478 0.00 0.00 0.00 4.93
166 167 3.424039 CGCTATCAATCAAATGCCTAGCG 60.424 47.826 6.66 6.66 42.53 4.26
167 168 3.499918 ACGCTATCAATCAAATGCCTAGC 59.500 43.478 0.00 0.00 32.51 3.42
168 169 4.751600 TGACGCTATCAATCAAATGCCTAG 59.248 41.667 0.00 0.00 33.02 3.02
169 170 4.511454 GTGACGCTATCAATCAAATGCCTA 59.489 41.667 0.00 0.00 39.72 3.93
170 171 3.313526 GTGACGCTATCAATCAAATGCCT 59.686 43.478 0.00 0.00 39.72 4.75
171 172 3.313526 AGTGACGCTATCAATCAAATGCC 59.686 43.478 0.00 0.00 39.72 4.40
172 173 4.542662 AGTGACGCTATCAATCAAATGC 57.457 40.909 0.00 0.00 39.72 3.56
173 174 7.239166 AGTAAGTGACGCTATCAATCAAATG 57.761 36.000 0.00 0.00 39.72 2.32
174 175 7.011482 GGAAGTAAGTGACGCTATCAATCAAAT 59.989 37.037 0.00 0.00 39.72 2.32
175 176 6.312918 GGAAGTAAGTGACGCTATCAATCAAA 59.687 38.462 0.00 0.00 39.72 2.69
176 177 5.810587 GGAAGTAAGTGACGCTATCAATCAA 59.189 40.000 0.00 0.00 39.72 2.57
177 178 5.127194 AGGAAGTAAGTGACGCTATCAATCA 59.873 40.000 0.00 0.00 39.72 2.57
178 179 5.593010 AGGAAGTAAGTGACGCTATCAATC 58.407 41.667 0.00 0.00 39.72 2.67
179 180 5.452077 GGAGGAAGTAAGTGACGCTATCAAT 60.452 44.000 0.00 0.00 39.72 2.57
180 181 4.142227 GGAGGAAGTAAGTGACGCTATCAA 60.142 45.833 0.00 0.00 39.72 2.57
181 182 3.380637 GGAGGAAGTAAGTGACGCTATCA 59.619 47.826 0.00 0.00 33.79 2.15
182 183 3.633065 AGGAGGAAGTAAGTGACGCTATC 59.367 47.826 0.00 0.00 0.00 2.08
183 184 3.633418 AGGAGGAAGTAAGTGACGCTAT 58.367 45.455 0.00 0.00 0.00 2.97
184 185 3.083122 AGGAGGAAGTAAGTGACGCTA 57.917 47.619 0.00 0.00 0.00 4.26
185 186 1.926108 AGGAGGAAGTAAGTGACGCT 58.074 50.000 0.00 0.00 0.00 5.07
186 187 2.338500 CAAGGAGGAAGTAAGTGACGC 58.662 52.381 0.00 0.00 0.00 5.19
187 188 2.561419 TCCAAGGAGGAAGTAAGTGACG 59.439 50.000 0.00 0.00 45.65 4.35
198 199 2.435805 CCGATCATTTCTCCAAGGAGGA 59.564 50.000 15.74 4.46 46.75 3.71
199 200 2.843701 CCGATCATTTCTCCAAGGAGG 58.156 52.381 15.74 0.38 42.20 4.30
200 201 2.216898 GCCGATCATTTCTCCAAGGAG 58.783 52.381 9.90 9.90 43.21 3.69
201 202 1.559219 TGCCGATCATTTCTCCAAGGA 59.441 47.619 0.00 0.00 0.00 3.36
202 203 2.042686 TGCCGATCATTTCTCCAAGG 57.957 50.000 0.00 0.00 0.00 3.61
203 204 2.287427 GCATGCCGATCATTTCTCCAAG 60.287 50.000 6.36 0.00 31.79 3.61
204 205 1.677576 GCATGCCGATCATTTCTCCAA 59.322 47.619 6.36 0.00 31.79 3.53
205 206 1.311859 GCATGCCGATCATTTCTCCA 58.688 50.000 6.36 0.00 31.79 3.86
206 207 0.595095 GGCATGCCGATCATTTCTCC 59.405 55.000 23.48 0.00 31.79 3.71
207 208 0.595095 GGGCATGCCGATCATTTCTC 59.405 55.000 29.90 8.58 36.85 2.87
208 209 0.106569 TGGGCATGCCGATCATTTCT 60.107 50.000 29.90 0.00 36.85 2.52
209 210 0.746063 TTGGGCATGCCGATCATTTC 59.254 50.000 29.90 14.10 36.85 2.17
210 211 0.748450 CTTGGGCATGCCGATCATTT 59.252 50.000 29.90 0.00 36.85 2.32
211 212 0.396139 ACTTGGGCATGCCGATCATT 60.396 50.000 29.90 9.40 36.85 2.57
212 213 0.473755 TACTTGGGCATGCCGATCAT 59.526 50.000 29.90 16.38 36.85 2.45
213 214 0.463654 GTACTTGGGCATGCCGATCA 60.464 55.000 29.90 19.62 36.85 2.92
214 215 1.166531 GGTACTTGGGCATGCCGATC 61.167 60.000 29.90 17.11 36.85 3.69
215 216 1.152963 GGTACTTGGGCATGCCGAT 60.153 57.895 29.90 15.08 36.85 4.18
216 217 2.130821 TTGGTACTTGGGCATGCCGA 62.131 55.000 29.90 24.63 36.85 5.54
217 218 1.037030 ATTGGTACTTGGGCATGCCG 61.037 55.000 29.90 18.88 36.85 5.69
218 219 0.461135 CATTGGTACTTGGGCATGCC 59.539 55.000 29.47 29.47 0.00 4.40
219 220 0.461135 CCATTGGTACTTGGGCATGC 59.539 55.000 9.90 9.90 0.00 4.06
220 221 1.750778 GACCATTGGTACTTGGGCATG 59.249 52.381 8.70 0.00 39.59 4.06
221 222 1.681780 CGACCATTGGTACTTGGGCAT 60.682 52.381 8.70 0.00 39.75 4.40
222 223 0.322098 CGACCATTGGTACTTGGGCA 60.322 55.000 8.70 0.00 39.75 5.36
223 224 0.322187 ACGACCATTGGTACTTGGGC 60.322 55.000 8.70 9.45 35.25 5.36
224 225 1.677820 GGACGACCATTGGTACTTGGG 60.678 57.143 8.70 0.00 35.25 4.12
225 226 1.278127 AGGACGACCATTGGTACTTGG 59.722 52.381 8.70 8.04 35.25 3.61
226 227 2.762535 AGGACGACCATTGGTACTTG 57.237 50.000 8.70 1.96 35.25 3.16
227 228 5.245526 GGATATAGGACGACCATTGGTACTT 59.754 44.000 8.70 3.01 35.25 2.24
228 229 4.771054 GGATATAGGACGACCATTGGTACT 59.229 45.833 8.70 7.58 35.25 2.73
229 230 4.525487 TGGATATAGGACGACCATTGGTAC 59.475 45.833 8.70 3.62 35.25 3.34
230 231 4.743124 TGGATATAGGACGACCATTGGTA 58.257 43.478 8.70 0.00 35.25 3.25
231 232 3.583228 TGGATATAGGACGACCATTGGT 58.417 45.455 8.42 8.42 39.44 3.67
232 233 4.826274 ATGGATATAGGACGACCATTGG 57.174 45.455 6.71 0.00 38.01 3.16
250 251 9.204570 CGACTCCTGTTTACCTTAATAATATGG 57.795 37.037 0.00 0.00 33.56 2.74
251 252 9.204570 CCGACTCCTGTTTACCTTAATAATATG 57.795 37.037 0.00 0.00 0.00 1.78
252 253 8.373220 CCCGACTCCTGTTTACCTTAATAATAT 58.627 37.037 0.00 0.00 0.00 1.28
262 263 4.141779 ACATTATCCCGACTCCTGTTTACC 60.142 45.833 0.00 0.00 0.00 2.85
263 264 5.019785 ACATTATCCCGACTCCTGTTTAC 57.980 43.478 0.00 0.00 0.00 2.01
277 278 5.126061 AGTGGAGTGCATTTGAACATTATCC 59.874 40.000 0.00 0.00 0.00 2.59
285 286 4.156556 GCTGAATAGTGGAGTGCATTTGAA 59.843 41.667 0.00 0.00 0.00 2.69
289 290 3.539604 GAGCTGAATAGTGGAGTGCATT 58.460 45.455 0.00 0.00 0.00 3.56
294 295 2.234908 GTGTGGAGCTGAATAGTGGAGT 59.765 50.000 0.00 0.00 0.00 3.85
302 303 1.242076 GCACTTGTGTGGAGCTGAAT 58.758 50.000 0.00 0.00 43.97 2.57
555 570 3.149196 TCTTTTTCACCAGTGATGAGGC 58.851 45.455 0.48 0.00 39.64 4.70
819 856 2.493501 GCCGGTCGGTCTCTAACC 59.506 66.667 11.25 0.00 45.45 2.85
821 858 2.757099 GGGCCGGTCGGTCTCTAA 60.757 66.667 13.85 0.00 40.34 2.10
888 925 0.461961 CGCAGTTAGGCTAGGCTTCT 59.538 55.000 25.37 18.99 0.00 2.85
902 939 2.336478 CGACCTCACTCCTCGCAGT 61.336 63.158 0.00 0.00 0.00 4.40
1177 1222 3.656045 GCGTGTTGGTTGGTCGGG 61.656 66.667 0.00 0.00 0.00 5.14
1179 1224 4.007940 CCGCGTGTTGGTTGGTCG 62.008 66.667 4.92 0.00 0.00 4.79
1180 1225 4.322385 GCCGCGTGTTGGTTGGTC 62.322 66.667 4.92 0.00 0.00 4.02
1184 1229 2.411290 CAAAGCCGCGTGTTGGTT 59.589 55.556 4.92 0.00 0.00 3.67
1230 1302 2.359230 GGACACCTGCAGAGTGCC 60.359 66.667 25.86 23.17 44.23 5.01
1231 1303 1.227943 TTGGACACCTGCAGAGTGC 60.228 57.895 25.86 22.51 45.29 4.40
1232 1304 0.107456 AGTTGGACACCTGCAGAGTG 59.893 55.000 24.89 24.89 41.15 3.51
1233 1305 1.344763 GTAGTTGGACACCTGCAGAGT 59.655 52.381 17.39 13.63 0.00 3.24
1234 1306 1.338200 GGTAGTTGGACACCTGCAGAG 60.338 57.143 17.39 10.07 0.00 3.35
1235 1307 0.685097 GGTAGTTGGACACCTGCAGA 59.315 55.000 17.39 0.00 0.00 4.26
2031 2148 4.452455 ACTTCTTCGACCATTCATTGTGTC 59.548 41.667 0.00 0.00 0.00 3.67
2033 2150 4.715896 CACTTCTTCGACCATTCATTGTG 58.284 43.478 0.00 0.00 0.00 3.33
2034 2151 3.189287 GCACTTCTTCGACCATTCATTGT 59.811 43.478 0.00 0.00 0.00 2.71
2046 2163 1.916651 CATCGTCTCTGCACTTCTTCG 59.083 52.381 0.00 0.00 0.00 3.79
2047 2164 3.178267 CTCATCGTCTCTGCACTTCTTC 58.822 50.000 0.00 0.00 0.00 2.87
2063 2180 3.066342 CCATTCATTGTGTCAGGCTCATC 59.934 47.826 0.00 0.00 0.00 2.92
2075 2192 3.189287 GCACTTCTTCGACCATTCATTGT 59.811 43.478 0.00 0.00 0.00 2.71
2091 2208 3.128259 TGCATCGTCTCTGCACTTC 57.872 52.632 0.00 0.00 44.30 3.01
2311 2439 2.845967 GTGTCGTTGCTCAGTTTTGTTG 59.154 45.455 0.00 0.00 0.00 3.33
2361 2489 2.979813 GTTTGTCCGAACATGTCAATGC 59.020 45.455 0.00 0.00 37.29 3.56
2520 2651 3.925261 ATCAGGCTACTATGTAGGGGT 57.075 47.619 6.83 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.