Multiple sequence alignment - TraesCS1D01G114500

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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 TraesCS1D01G114500 chr1D 100.000 2548 0 0 1 2548 110565504 110568051 0.000000e+00 4706.0
1 TraesCS1D01G114500 chr1A 92.276 1450 76 15 222 1662 115938999 115940421 0.000000e+00 2025.0
2 TraesCS1D01G114500 chr1A 88.750 400 16 8 1666 2058 115940475 115940852 1.790000e-126 462.0
3 TraesCS1D01G114500 chr1A 97.500 40 1 0 2064 2103 115941246 115941207 4.550000e-08 69.4
4 TraesCS1D01G114500 chr1B 93.079 1257 57 10 414 1662 168330029 168331263 0.000000e+00 1812.0
5 TraesCS1D01G114500 chr1B 93.776 482 21 3 2067 2548 168334209 168334681 0.000000e+00 715.0
6 TraesCS1D01G114500 chr1B 95.157 351 15 2 1731 2079 168331366 168331716 1.030000e-153 553.0
7 TraesCS1D01G114500 chr1B 89.062 192 20 1 1 192 168322208 168322398 1.180000e-58 237.0
8 TraesCS1D01G114500 chr1B 96.923 65 0 1 1664 1726 168331315 168331379 9.640000e-20 108.0


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 TraesCS1D01G114500 chr1D 110565504 110568051 2547 False 4706.0 4706 100.00000 1 2548 1 chr1D.!!$F1 2547
1 TraesCS1D01G114500 chr1A 115938999 115940852 1853 False 1243.5 2025 90.51300 222 2058 2 chr1A.!!$F1 1836
2 TraesCS1D01G114500 chr1B 168330029 168334681 4652 False 797.0 1812 94.73375 414 2548 4 chr1B.!!$F2 2134

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
182 183 0.033208 TGGAAATCCCCATCAGCCAC 60.033 55.0 0.0 0.0 34.29 5.01 F
183 184 0.033208 GGAAATCCCCATCAGCCACA 60.033 55.0 0.0 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1289 1305 1.065199 AGCGCCAGGATCATCAGAAAA 60.065 47.619 2.29 0.0 0.00 2.29 R
1596 1612 1.102809 TGAATTGCTAGCCCATGCCG 61.103 55.000 13.29 0.0 38.69 5.69 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 4.361253 GAGCCTGCACGAGTGAAA 57.639 55.556 7.50 0.00 0.00 2.69
18 19 2.616969 GAGCCTGCACGAGTGAAAA 58.383 52.632 7.50 0.00 0.00 2.29
19 20 0.235926 GAGCCTGCACGAGTGAAAAC 59.764 55.000 7.50 0.00 0.00 2.43
20 21 1.082756 GCCTGCACGAGTGAAAACG 60.083 57.895 7.50 0.00 0.00 3.60
21 22 1.495584 GCCTGCACGAGTGAAAACGA 61.496 55.000 7.50 0.00 0.00 3.85
22 23 0.508641 CCTGCACGAGTGAAAACGAG 59.491 55.000 7.50 0.00 0.00 4.18
23 24 0.508641 CTGCACGAGTGAAAACGAGG 59.491 55.000 7.50 0.00 0.00 4.63
24 25 0.103390 TGCACGAGTGAAAACGAGGA 59.897 50.000 7.50 0.00 0.00 3.71
25 26 1.270094 TGCACGAGTGAAAACGAGGAT 60.270 47.619 7.50 0.00 0.00 3.24
26 27 1.798813 GCACGAGTGAAAACGAGGATT 59.201 47.619 7.50 0.00 0.00 3.01
27 28 2.223377 GCACGAGTGAAAACGAGGATTT 59.777 45.455 7.50 0.00 0.00 2.17
28 29 3.799035 CACGAGTGAAAACGAGGATTTG 58.201 45.455 0.00 0.00 0.00 2.32
29 30 2.806244 ACGAGTGAAAACGAGGATTTGG 59.194 45.455 0.00 0.00 0.00 3.28
30 31 2.159627 CGAGTGAAAACGAGGATTTGGG 59.840 50.000 0.00 0.00 0.00 4.12
31 32 1.886542 AGTGAAAACGAGGATTTGGGC 59.113 47.619 0.00 0.00 0.00 5.36
32 33 1.067846 GTGAAAACGAGGATTTGGGCC 60.068 52.381 0.00 0.00 0.00 5.80
33 34 1.253100 GAAAACGAGGATTTGGGCCA 58.747 50.000 0.00 0.00 0.00 5.36
34 35 1.824852 GAAAACGAGGATTTGGGCCAT 59.175 47.619 7.26 0.00 0.00 4.40
35 36 1.937191 AAACGAGGATTTGGGCCATT 58.063 45.000 7.26 0.00 0.00 3.16
36 37 1.474330 AACGAGGATTTGGGCCATTC 58.526 50.000 7.26 7.83 0.00 2.67
37 38 0.395724 ACGAGGATTTGGGCCATTCC 60.396 55.000 22.39 22.39 0.00 3.01
38 39 0.106519 CGAGGATTTGGGCCATTCCT 60.107 55.000 29.14 29.14 41.29 3.36
39 40 1.697284 GAGGATTTGGGCCATTCCTC 58.303 55.000 33.19 33.19 45.37 3.71
40 41 0.262876 AGGATTTGGGCCATTCCTCC 59.737 55.000 25.38 19.41 33.22 4.30
41 42 0.760567 GGATTTGGGCCATTCCTCCC 60.761 60.000 22.53 9.58 42.93 4.30
45 46 3.100111 GGGCCATTCCTCCCAACT 58.900 61.111 4.39 0.00 42.18 3.16
46 47 2.317530 GGGCCATTCCTCCCAACTA 58.682 57.895 4.39 0.00 42.18 2.24
47 48 0.183731 GGGCCATTCCTCCCAACTAG 59.816 60.000 4.39 0.00 42.18 2.57
48 49 0.183731 GGCCATTCCTCCCAACTAGG 59.816 60.000 0.00 0.00 35.26 3.02
70 71 3.441496 CAATGTTGCTTGAAGTGGTGT 57.559 42.857 0.00 0.00 0.00 4.16
71 72 3.117794 CAATGTTGCTTGAAGTGGTGTG 58.882 45.455 0.00 0.00 0.00 3.82
72 73 0.455410 TGTTGCTTGAAGTGGTGTGC 59.545 50.000 0.00 0.00 0.00 4.57
73 74 0.592247 GTTGCTTGAAGTGGTGTGCG 60.592 55.000 0.00 0.00 0.00 5.34
74 75 1.723608 TTGCTTGAAGTGGTGTGCGG 61.724 55.000 0.00 0.00 0.00 5.69
75 76 2.639286 CTTGAAGTGGTGTGCGGC 59.361 61.111 0.00 0.00 0.00 6.53
76 77 3.240606 CTTGAAGTGGTGTGCGGCG 62.241 63.158 0.51 0.51 0.00 6.46
83 84 3.814268 GGTGTGCGGCGCATGAAT 61.814 61.111 38.43 0.00 41.91 2.57
84 85 2.179018 GTGTGCGGCGCATGAATT 59.821 55.556 38.43 0.00 41.91 2.17
85 86 1.869132 GTGTGCGGCGCATGAATTC 60.869 57.895 38.43 23.54 41.91 2.17
86 87 2.278142 GTGCGGCGCATGAATTCC 60.278 61.111 38.43 19.31 41.91 3.01
87 88 2.749441 TGCGGCGCATGAATTCCA 60.749 55.556 33.07 4.16 31.71 3.53
88 89 2.338785 TGCGGCGCATGAATTCCAA 61.339 52.632 33.07 3.24 31.71 3.53
89 90 1.587088 GCGGCGCATGAATTCCAAG 60.587 57.895 29.21 0.00 0.00 3.61
90 91 1.587088 CGGCGCATGAATTCCAAGC 60.587 57.895 10.83 3.52 36.23 4.01
91 92 1.811860 GGCGCATGAATTCCAAGCT 59.188 52.632 10.83 0.00 37.34 3.74
92 93 0.248784 GGCGCATGAATTCCAAGCTC 60.249 55.000 10.83 0.00 37.34 4.09
93 94 0.248784 GCGCATGAATTCCAAGCTCC 60.249 55.000 0.30 0.00 37.34 4.70
94 95 1.386533 CGCATGAATTCCAAGCTCCT 58.613 50.000 2.27 0.00 37.34 3.69
95 96 1.332997 CGCATGAATTCCAAGCTCCTC 59.667 52.381 2.27 0.00 37.34 3.71
96 97 2.372264 GCATGAATTCCAAGCTCCTCA 58.628 47.619 2.27 0.00 36.61 3.86
97 98 2.358267 GCATGAATTCCAAGCTCCTCAG 59.642 50.000 2.27 0.00 36.61 3.35
106 107 4.486503 GCTCCTCAGCCAGGCCAG 62.487 72.222 8.22 4.19 43.08 4.85
107 108 4.486503 CTCCTCAGCCAGGCCAGC 62.487 72.222 8.22 7.78 43.08 4.85
124 125 3.085010 CGCAAGCAAACACGACGC 61.085 61.111 0.00 0.00 0.00 5.19
125 126 3.085010 GCAAGCAAACACGACGCG 61.085 61.111 3.53 3.53 0.00 6.01
126 127 2.425124 CAAGCAAACACGACGCGG 60.425 61.111 12.47 0.00 0.00 6.46
127 128 2.586635 AAGCAAACACGACGCGGA 60.587 55.556 12.47 0.00 0.00 5.54
128 129 2.877974 AAGCAAACACGACGCGGAC 61.878 57.895 12.47 2.84 0.00 4.79
129 130 3.335534 GCAAACACGACGCGGACT 61.336 61.111 12.47 0.00 0.00 3.85
130 131 2.017783 GCAAACACGACGCGGACTA 61.018 57.895 12.47 0.00 0.00 2.59
131 132 1.349259 GCAAACACGACGCGGACTAT 61.349 55.000 12.47 0.00 0.00 2.12
132 133 1.898938 CAAACACGACGCGGACTATA 58.101 50.000 12.47 0.00 0.00 1.31
133 134 2.252747 CAAACACGACGCGGACTATAA 58.747 47.619 12.47 0.00 0.00 0.98
134 135 2.184385 AACACGACGCGGACTATAAG 57.816 50.000 12.47 0.00 0.00 1.73
135 136 1.372582 ACACGACGCGGACTATAAGA 58.627 50.000 12.47 0.00 0.00 2.10
136 137 1.739466 ACACGACGCGGACTATAAGAA 59.261 47.619 12.47 0.00 0.00 2.52
137 138 2.357009 ACACGACGCGGACTATAAGAAT 59.643 45.455 12.47 0.00 0.00 2.40
138 139 3.181493 ACACGACGCGGACTATAAGAATT 60.181 43.478 12.47 0.00 0.00 2.17
139 140 3.795101 CACGACGCGGACTATAAGAATTT 59.205 43.478 12.47 0.00 0.00 1.82
140 141 4.266976 CACGACGCGGACTATAAGAATTTT 59.733 41.667 12.47 0.00 0.00 1.82
141 142 5.456497 CACGACGCGGACTATAAGAATTTTA 59.544 40.000 12.47 0.00 0.00 1.52
142 143 5.456822 ACGACGCGGACTATAAGAATTTTAC 59.543 40.000 12.47 0.00 0.00 2.01
143 144 5.684626 CGACGCGGACTATAAGAATTTTACT 59.315 40.000 12.47 0.00 0.00 2.24
144 145 6.197842 CGACGCGGACTATAAGAATTTTACTT 59.802 38.462 12.47 0.00 0.00 2.24
145 146 7.460751 ACGCGGACTATAAGAATTTTACTTC 57.539 36.000 12.47 0.00 0.00 3.01
146 147 7.037438 ACGCGGACTATAAGAATTTTACTTCA 58.963 34.615 12.47 0.00 0.00 3.02
147 148 7.709613 ACGCGGACTATAAGAATTTTACTTCAT 59.290 33.333 12.47 0.00 0.00 2.57
148 149 8.004344 CGCGGACTATAAGAATTTTACTTCATG 58.996 37.037 0.00 0.00 0.00 3.07
149 150 7.798982 GCGGACTATAAGAATTTTACTTCATGC 59.201 37.037 0.00 0.00 0.00 4.06
150 151 8.826710 CGGACTATAAGAATTTTACTTCATGCA 58.173 33.333 0.00 0.00 0.00 3.96
152 153 9.657121 GACTATAAGAATTTTACTTCATGCAGC 57.343 33.333 0.00 0.00 0.00 5.25
153 154 8.624776 ACTATAAGAATTTTACTTCATGCAGCC 58.375 33.333 0.00 0.00 0.00 4.85
154 155 5.990120 AAGAATTTTACTTCATGCAGCCT 57.010 34.783 0.00 0.00 0.00 4.58
155 156 8.752005 ATAAGAATTTTACTTCATGCAGCCTA 57.248 30.769 0.00 0.00 0.00 3.93
156 157 7.651027 AAGAATTTTACTTCATGCAGCCTAT 57.349 32.000 0.00 0.00 0.00 2.57
157 158 7.035840 AGAATTTTACTTCATGCAGCCTATG 57.964 36.000 0.00 0.00 0.00 2.23
158 159 6.604795 AGAATTTTACTTCATGCAGCCTATGT 59.395 34.615 0.00 0.00 0.00 2.29
159 160 7.775093 AGAATTTTACTTCATGCAGCCTATGTA 59.225 33.333 0.00 0.00 0.00 2.29
160 161 6.677781 TTTTACTTCATGCAGCCTATGTAC 57.322 37.500 0.00 0.00 0.00 2.90
161 162 3.199880 ACTTCATGCAGCCTATGTACC 57.800 47.619 0.00 0.00 0.00 3.34
162 163 2.505407 ACTTCATGCAGCCTATGTACCA 59.495 45.455 0.00 0.00 0.00 3.25
163 164 3.137176 ACTTCATGCAGCCTATGTACCAT 59.863 43.478 0.00 0.00 0.00 3.55
164 165 3.130280 TCATGCAGCCTATGTACCATG 57.870 47.619 0.00 0.00 31.69 3.66
165 166 2.156917 CATGCAGCCTATGTACCATGG 58.843 52.381 11.19 11.19 0.00 3.66
166 167 1.506025 TGCAGCCTATGTACCATGGA 58.494 50.000 21.47 0.00 0.00 3.41
167 168 1.843206 TGCAGCCTATGTACCATGGAA 59.157 47.619 21.47 3.61 0.00 3.53
168 169 2.240921 TGCAGCCTATGTACCATGGAAA 59.759 45.455 21.47 2.58 0.00 3.13
169 170 3.117550 TGCAGCCTATGTACCATGGAAAT 60.118 43.478 21.47 11.04 0.00 2.17
170 171 3.503748 GCAGCCTATGTACCATGGAAATC 59.496 47.826 21.47 6.04 0.00 2.17
171 172 4.074970 CAGCCTATGTACCATGGAAATCC 58.925 47.826 21.47 1.30 0.00 3.01
172 173 3.074538 AGCCTATGTACCATGGAAATCCC 59.925 47.826 21.47 0.00 34.29 3.85
173 174 3.814316 GCCTATGTACCATGGAAATCCCC 60.814 52.174 21.47 0.00 34.29 4.81
174 175 3.397618 CCTATGTACCATGGAAATCCCCA 59.602 47.826 21.47 4.08 41.05 4.96
176 177 3.593442 TGTACCATGGAAATCCCCATC 57.407 47.619 21.47 0.00 44.69 3.51
177 178 2.855599 TGTACCATGGAAATCCCCATCA 59.144 45.455 21.47 0.00 44.69 3.07
178 179 2.761786 ACCATGGAAATCCCCATCAG 57.238 50.000 21.47 0.00 44.69 2.90
179 180 1.335145 CCATGGAAATCCCCATCAGC 58.665 55.000 5.56 0.00 44.69 4.26
180 181 1.335145 CATGGAAATCCCCATCAGCC 58.665 55.000 0.00 0.00 44.69 4.85
181 182 0.935942 ATGGAAATCCCCATCAGCCA 59.064 50.000 0.00 0.00 43.07 4.75
182 183 0.033208 TGGAAATCCCCATCAGCCAC 60.033 55.000 0.00 0.00 34.29 5.01
183 184 0.033208 GGAAATCCCCATCAGCCACA 60.033 55.000 0.00 0.00 0.00 4.17
184 185 1.412074 GGAAATCCCCATCAGCCACAT 60.412 52.381 0.00 0.00 0.00 3.21
185 186 1.684983 GAAATCCCCATCAGCCACATG 59.315 52.381 0.00 0.00 0.00 3.21
186 187 0.632835 AATCCCCATCAGCCACATGT 59.367 50.000 0.00 0.00 0.00 3.21
187 188 0.632835 ATCCCCATCAGCCACATGTT 59.367 50.000 0.00 0.00 0.00 2.71
188 189 0.323633 TCCCCATCAGCCACATGTTG 60.324 55.000 0.00 0.00 0.00 3.33
189 190 0.612732 CCCCATCAGCCACATGTTGT 60.613 55.000 0.00 0.00 0.00 3.32
201 202 3.307674 CACATGTTGTGGGAAAATGTCG 58.692 45.455 0.00 0.00 44.27 4.35
202 203 2.288152 ACATGTTGTGGGAAAATGTCGC 60.288 45.455 0.00 0.00 39.63 5.19
203 204 1.686355 TGTTGTGGGAAAATGTCGCT 58.314 45.000 0.00 0.00 39.89 4.93
204 205 1.336440 TGTTGTGGGAAAATGTCGCTG 59.664 47.619 0.00 0.00 39.89 5.18
205 206 0.313672 TTGTGGGAAAATGTCGCTGC 59.686 50.000 0.00 0.00 39.89 5.25
206 207 0.821301 TGTGGGAAAATGTCGCTGCA 60.821 50.000 0.00 0.00 39.89 4.41
207 208 0.313672 GTGGGAAAATGTCGCTGCAA 59.686 50.000 0.00 0.00 39.89 4.08
208 209 0.313672 TGGGAAAATGTCGCTGCAAC 59.686 50.000 0.00 0.00 39.89 4.17
209 210 0.729140 GGGAAAATGTCGCTGCAACG 60.729 55.000 2.36 2.36 36.28 4.10
210 211 1.337110 GGAAAATGTCGCTGCAACGC 61.337 55.000 4.23 0.77 0.00 4.84
211 212 0.660005 GAAAATGTCGCTGCAACGCA 60.660 50.000 4.23 6.85 36.92 5.24
212 213 0.934436 AAAATGTCGCTGCAACGCAC 60.934 50.000 4.23 5.02 33.79 5.34
213 214 2.057654 AAATGTCGCTGCAACGCACA 62.058 50.000 4.23 10.46 33.79 4.57
214 215 2.715864 AATGTCGCTGCAACGCACAC 62.716 55.000 14.05 5.21 33.79 3.82
218 219 4.666532 GCTGCAACGCACACGGAC 62.667 66.667 0.00 0.00 46.04 4.79
219 220 4.354212 CTGCAACGCACACGGACG 62.354 66.667 0.00 0.00 46.04 4.79
220 221 4.874977 TGCAACGCACACGGACGA 62.875 61.111 0.00 0.00 46.04 4.20
221 222 4.059459 GCAACGCACACGGACGAG 62.059 66.667 0.00 0.00 46.04 4.18
222 223 4.059459 CAACGCACACGGACGAGC 62.059 66.667 0.00 0.00 46.04 5.03
223 224 4.280494 AACGCACACGGACGAGCT 62.280 61.111 0.00 0.00 46.04 4.09
224 225 2.911484 AACGCACACGGACGAGCTA 61.911 57.895 0.00 0.00 46.04 3.32
225 226 2.577112 CGCACACGGACGAGCTAG 60.577 66.667 0.00 0.00 34.97 3.42
226 227 2.881352 GCACACGGACGAGCTAGC 60.881 66.667 6.62 6.62 0.00 3.42
241 242 1.589716 CTAGCAACCAAGTGGGCAGC 61.590 60.000 1.69 2.79 42.05 5.25
270 271 1.926108 AGTAAGCAGAGGGTTCTCGT 58.074 50.000 0.00 0.00 44.47 4.18
296 297 2.745884 TGCGAAGGTTCCATGCCG 60.746 61.111 0.00 0.00 0.00 5.69
297 298 2.746277 GCGAAGGTTCCATGCCGT 60.746 61.111 0.00 0.00 0.00 5.68
322 325 7.911362 TTTTTCGTAATTTTGGAAACCGTAG 57.089 32.000 0.00 0.00 30.06 3.51
337 340 6.798476 GGAAACCGTAGAAGATTTTTAAACCG 59.202 38.462 0.00 0.00 0.00 4.44
348 351 9.309516 GAAGATTTTTAAACCGGTTTTCTCTTT 57.690 29.630 35.69 20.62 34.23 2.52
360 363 5.220209 CGGTTTTCTCTTTGTTGTTGCTTTC 60.220 40.000 0.00 0.00 0.00 2.62
364 367 8.921670 GTTTTCTCTTTGTTGTTGCTTTCTTTA 58.078 29.630 0.00 0.00 0.00 1.85
365 368 8.460831 TTTCTCTTTGTTGTTGCTTTCTTTAC 57.539 30.769 0.00 0.00 0.00 2.01
373 379 4.542697 TGTTGCTTTCTTTACCCTTTCCT 58.457 39.130 0.00 0.00 0.00 3.36
381 387 5.397553 TCTTTACCCTTTCCTGGTCTTTT 57.602 39.130 0.00 0.00 37.31 2.27
383 389 7.098845 TCTTTACCCTTTCCTGGTCTTTTAT 57.901 36.000 0.00 0.00 37.31 1.40
463 470 9.710900 ACTCTTCAAAAACTGTTCAGAATTTTT 57.289 25.926 6.83 7.27 35.23 1.94
547 555 1.581934 TTGTCACAAGGAGCGTCTTG 58.418 50.000 16.75 16.75 46.86 3.02
573 581 0.036388 CTGCCATCTACCACCGTGTT 60.036 55.000 0.00 0.00 0.00 3.32
591 599 0.466555 TTGGCAACTAAACACGCCCT 60.467 50.000 0.00 0.00 44.22 5.19
607 615 3.694566 ACGCCCTAGTGATTTGATTTTCC 59.305 43.478 0.00 0.00 0.00 3.13
610 618 5.765182 CGCCCTAGTGATTTGATTTTCCTAT 59.235 40.000 0.00 0.00 0.00 2.57
707 721 0.931005 GTGAATCTGATTCGGCGTCC 59.069 55.000 21.70 1.76 42.15 4.79
832 846 6.656003 ACTGTAAAGACGGAAAAGAAATTCG 58.344 36.000 0.00 0.00 35.72 3.34
967 981 7.592885 ATCAATCAATTATCAAGGGAGGTTG 57.407 36.000 0.00 0.00 0.00 3.77
968 982 5.893255 TCAATCAATTATCAAGGGAGGTTGG 59.107 40.000 0.00 0.00 0.00 3.77
969 983 4.946160 TCAATTATCAAGGGAGGTTGGT 57.054 40.909 0.00 0.00 0.00 3.67
970 984 5.269554 TCAATTATCAAGGGAGGTTGGTT 57.730 39.130 0.00 0.00 0.00 3.67
1245 1261 5.765182 TCTGAATTTCCTCTCACTTGTTTCC 59.235 40.000 0.00 0.00 0.00 3.13
1246 1262 5.694995 TGAATTTCCTCTCACTTGTTTCCT 58.305 37.500 0.00 0.00 0.00 3.36
1424 1440 4.875544 TCTTCTTTCTGTTGTTCGTTGG 57.124 40.909 0.00 0.00 0.00 3.77
1475 1491 3.501828 TGGTTGTGTGAGATTCGATTTGG 59.498 43.478 0.00 0.00 0.00 3.28
1635 1651 6.925610 TTCATCAAGTGCATGAATAGTACC 57.074 37.500 0.00 0.00 35.71 3.34
1646 1662 4.295905 TGAATAGTACCCCCTCCAATCT 57.704 45.455 0.00 0.00 0.00 2.40
1662 1678 6.417191 TCCAATCTAAAATAAGTGTCGTGC 57.583 37.500 0.00 0.00 0.00 5.34
1799 1871 7.518188 AGTACTTATTCTGGTTATTCATGGGG 58.482 38.462 0.00 0.00 0.00 4.96
1860 1935 5.388599 AGGGGGTATTAAGTGAATTGGAG 57.611 43.478 0.00 0.00 0.00 3.86
2125 4706 7.609918 TGCAAGCCTGTAATTATCTTTTACTGA 59.390 33.333 0.00 0.00 33.05 3.41
2181 4762 8.864069 AATTACAGACATGAGAAATCTCGTAG 57.136 34.615 0.00 3.50 45.72 3.51
2184 4765 4.966970 CAGACATGAGAAATCTCGTAGACG 59.033 45.833 0.00 0.00 45.72 4.18
2191 4772 5.411977 TGAGAAATCTCGTAGACGTCTCTTT 59.588 40.000 23.89 12.58 45.72 2.52
2254 4835 6.403636 GGTCTATGCACTTTACCAAGACATTG 60.404 42.308 0.00 0.00 34.86 2.82
2255 4836 6.149474 GTCTATGCACTTTACCAAGACATTGT 59.851 38.462 0.00 0.00 34.37 2.71
2256 4837 5.789643 ATGCACTTTACCAAGACATTGTT 57.210 34.783 0.00 0.00 34.39 2.83
2257 4838 6.892658 ATGCACTTTACCAAGACATTGTTA 57.107 33.333 0.00 0.00 34.39 2.41
2258 4839 6.892658 TGCACTTTACCAAGACATTGTTAT 57.107 33.333 0.00 0.00 34.39 1.89
2259 4840 7.283625 TGCACTTTACCAAGACATTGTTATT 57.716 32.000 0.00 0.00 34.39 1.40
2260 4841 7.721402 TGCACTTTACCAAGACATTGTTATTT 58.279 30.769 0.00 0.00 34.39 1.40
2261 4842 8.200792 TGCACTTTACCAAGACATTGTTATTTT 58.799 29.630 0.00 0.00 34.39 1.82
2262 4843 9.685828 GCACTTTACCAAGACATTGTTATTTTA 57.314 29.630 0.00 0.00 34.39 1.52
2297 4878 2.561419 CTGGTAGACGTCTCTTTTGGGA 59.439 50.000 23.89 0.00 0.00 4.37
2306 4887 0.915364 CTCTTTTGGGAGAGAGGGGG 59.085 60.000 0.00 0.00 44.78 5.40
2327 4908 2.791004 GCGGCAAATGCAAGTATCATTC 59.209 45.455 7.80 0.00 44.36 2.67
2391 4972 2.489722 GTCTTGGAGTTCTGGATTTGCC 59.510 50.000 0.00 0.00 37.10 4.52
2404 4985 5.747951 TGGATTTGCCAAAACAAAACATC 57.252 34.783 0.00 0.00 45.87 3.06
2428 5009 3.557054 GCTTGATGACTAAGTGGTGGTGA 60.557 47.826 0.00 0.00 0.00 4.02
2432 5013 5.630121 TGATGACTAAGTGGTGGTGAAAAT 58.370 37.500 0.00 0.00 0.00 1.82
2493 5074 8.466798 CAAATCTAAGTATTTCCGGAACCAAAT 58.533 33.333 18.64 10.48 0.00 2.32
2494 5075 7.803279 ATCTAAGTATTTCCGGAACCAAATC 57.197 36.000 18.64 4.74 0.00 2.17
2500 5081 3.644966 TTCCGGAACCAAATCATAGCT 57.355 42.857 14.35 0.00 0.00 3.32
2504 5085 3.313526 CCGGAACCAAATCATAGCTTCAG 59.686 47.826 0.00 0.00 0.00 3.02
2542 5123 6.641169 AATGACTCTCCTTTCTGGAAAAAC 57.359 37.500 0.00 0.00 45.63 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.498865 CGTTTTCACTCGTGCAGGCT 61.499 55.000 0.35 0.00 0.00 4.58
2 3 1.082756 CGTTTTCACTCGTGCAGGC 60.083 57.895 0.35 0.00 0.00 4.85
3 4 0.508641 CTCGTTTTCACTCGTGCAGG 59.491 55.000 0.00 0.00 0.00 4.85
5 6 0.103390 TCCTCGTTTTCACTCGTGCA 59.897 50.000 0.00 0.00 0.00 4.57
6 7 1.429463 ATCCTCGTTTTCACTCGTGC 58.571 50.000 0.00 0.00 0.00 5.34
7 8 3.363970 CCAAATCCTCGTTTTCACTCGTG 60.364 47.826 0.00 0.00 0.00 4.35
8 9 2.806244 CCAAATCCTCGTTTTCACTCGT 59.194 45.455 0.00 0.00 0.00 4.18
9 10 2.159627 CCCAAATCCTCGTTTTCACTCG 59.840 50.000 0.00 0.00 0.00 4.18
10 11 2.095212 GCCCAAATCCTCGTTTTCACTC 60.095 50.000 0.00 0.00 0.00 3.51
11 12 1.886542 GCCCAAATCCTCGTTTTCACT 59.113 47.619 0.00 0.00 0.00 3.41
12 13 1.067846 GGCCCAAATCCTCGTTTTCAC 60.068 52.381 0.00 0.00 0.00 3.18
13 14 1.253100 GGCCCAAATCCTCGTTTTCA 58.747 50.000 0.00 0.00 0.00 2.69
14 15 1.253100 TGGCCCAAATCCTCGTTTTC 58.747 50.000 0.00 0.00 0.00 2.29
15 16 1.937191 ATGGCCCAAATCCTCGTTTT 58.063 45.000 0.00 0.00 0.00 2.43
16 17 1.824852 GAATGGCCCAAATCCTCGTTT 59.175 47.619 0.00 0.00 0.00 3.60
17 18 1.474330 GAATGGCCCAAATCCTCGTT 58.526 50.000 0.00 0.00 0.00 3.85
18 19 0.395724 GGAATGGCCCAAATCCTCGT 60.396 55.000 10.82 0.00 0.00 4.18
19 20 0.106519 AGGAATGGCCCAAATCCTCG 60.107 55.000 14.10 0.00 37.80 4.63
20 21 3.933206 AGGAATGGCCCAAATCCTC 57.067 52.632 14.10 0.00 37.80 3.71
21 22 0.262876 GGAGGAATGGCCCAAATCCT 59.737 55.000 18.56 18.56 44.85 3.24
22 23 0.760567 GGGAGGAATGGCCCAAATCC 60.761 60.000 10.23 10.23 44.07 3.01
23 24 2.826337 GGGAGGAATGGCCCAAATC 58.174 57.895 0.00 0.00 44.07 2.17
28 29 0.183731 CTAGTTGGGAGGAATGGCCC 59.816 60.000 0.00 0.00 44.93 5.80
29 30 0.183731 CCTAGTTGGGAGGAATGGCC 59.816 60.000 0.00 0.00 35.99 5.36
30 31 3.808984 CCTAGTTGGGAGGAATGGC 57.191 57.895 0.00 0.00 35.99 4.40
50 51 3.117794 CACACCACTTCAAGCAACATTG 58.882 45.455 0.00 0.00 0.00 2.82
51 52 2.481795 GCACACCACTTCAAGCAACATT 60.482 45.455 0.00 0.00 0.00 2.71
52 53 1.067516 GCACACCACTTCAAGCAACAT 59.932 47.619 0.00 0.00 0.00 2.71
53 54 0.455410 GCACACCACTTCAAGCAACA 59.545 50.000 0.00 0.00 0.00 3.33
54 55 0.592247 CGCACACCACTTCAAGCAAC 60.592 55.000 0.00 0.00 0.00 4.17
55 56 1.723608 CCGCACACCACTTCAAGCAA 61.724 55.000 0.00 0.00 0.00 3.91
56 57 2.186160 CCGCACACCACTTCAAGCA 61.186 57.895 0.00 0.00 0.00 3.91
57 58 2.639286 CCGCACACCACTTCAAGC 59.361 61.111 0.00 0.00 0.00 4.01
58 59 2.639286 GCCGCACACCACTTCAAG 59.361 61.111 0.00 0.00 0.00 3.02
59 60 3.276091 CGCCGCACACCACTTCAA 61.276 61.111 0.00 0.00 0.00 2.69
66 67 3.340953 AATTCATGCGCCGCACACC 62.341 57.895 16.70 0.00 43.04 4.16
67 68 1.869132 GAATTCATGCGCCGCACAC 60.869 57.895 16.70 0.00 43.04 3.82
68 69 2.484662 GAATTCATGCGCCGCACA 59.515 55.556 16.70 0.00 43.04 4.57
69 70 2.278142 GGAATTCATGCGCCGCAC 60.278 61.111 16.70 0.00 43.04 5.34
70 71 2.268988 CTTGGAATTCATGCGCCGCA 62.269 55.000 16.69 16.69 44.86 5.69
71 72 1.587088 CTTGGAATTCATGCGCCGC 60.587 57.895 4.18 0.00 0.00 6.53
72 73 1.587088 GCTTGGAATTCATGCGCCG 60.587 57.895 4.18 0.00 36.91 6.46
73 74 4.407551 GCTTGGAATTCATGCGCC 57.592 55.556 4.18 0.00 36.91 6.53
76 77 2.358267 CTGAGGAGCTTGGAATTCATGC 59.642 50.000 7.93 7.99 44.14 4.06
77 78 2.358267 GCTGAGGAGCTTGGAATTCATG 59.642 50.000 7.93 0.00 42.52 3.07
78 79 2.652590 GCTGAGGAGCTTGGAATTCAT 58.347 47.619 7.93 0.00 42.52 2.57
79 80 1.340405 GGCTGAGGAGCTTGGAATTCA 60.340 52.381 7.93 0.00 45.44 2.57
80 81 1.340405 TGGCTGAGGAGCTTGGAATTC 60.340 52.381 0.00 0.00 45.44 2.17
81 82 0.700564 TGGCTGAGGAGCTTGGAATT 59.299 50.000 0.00 0.00 45.44 2.17
82 83 0.255318 CTGGCTGAGGAGCTTGGAAT 59.745 55.000 0.00 0.00 45.44 3.01
83 84 1.681666 CTGGCTGAGGAGCTTGGAA 59.318 57.895 0.00 0.00 45.44 3.53
84 85 2.296365 CCTGGCTGAGGAGCTTGGA 61.296 63.158 0.00 0.00 46.33 3.53
85 86 2.271497 CCTGGCTGAGGAGCTTGG 59.729 66.667 0.00 0.00 46.33 3.61
86 87 2.438075 GCCTGGCTGAGGAGCTTG 60.438 66.667 12.43 0.00 46.33 4.01
87 88 3.726144 GGCCTGGCTGAGGAGCTT 61.726 66.667 19.68 0.00 46.33 3.74
89 90 4.486503 CTGGCCTGGCTGAGGAGC 62.487 72.222 19.68 0.00 46.33 4.70
90 91 4.486503 GCTGGCCTGGCTGAGGAG 62.487 72.222 19.68 8.05 46.33 3.69
99 100 3.980989 TTTGCTTGCGCTGGCCTG 61.981 61.111 18.94 4.26 38.85 4.85
100 101 3.982241 GTTTGCTTGCGCTGGCCT 61.982 61.111 18.94 0.00 38.85 5.19
101 102 4.283403 TGTTTGCTTGCGCTGGCC 62.283 61.111 18.94 0.00 38.85 5.36
102 103 3.032033 GTGTTTGCTTGCGCTGGC 61.032 61.111 9.73 13.61 40.52 4.85
103 104 2.726912 CGTGTTTGCTTGCGCTGG 60.727 61.111 9.73 1.88 36.97 4.85
104 105 2.005537 GTCGTGTTTGCTTGCGCTG 61.006 57.895 9.73 2.28 36.97 5.18
105 106 2.327940 GTCGTGTTTGCTTGCGCT 59.672 55.556 9.73 0.00 36.97 5.92
106 107 3.085010 CGTCGTGTTTGCTTGCGC 61.085 61.111 0.00 0.00 0.00 6.09
107 108 3.085010 GCGTCGTGTTTGCTTGCG 61.085 61.111 0.00 0.00 0.00 4.85
108 109 3.085010 CGCGTCGTGTTTGCTTGC 61.085 61.111 0.00 0.00 0.00 4.01
109 110 2.425124 CCGCGTCGTGTTTGCTTG 60.425 61.111 4.92 0.00 0.00 4.01
110 111 2.586635 TCCGCGTCGTGTTTGCTT 60.587 55.556 4.92 0.00 0.00 3.91
111 112 2.410638 TAGTCCGCGTCGTGTTTGCT 62.411 55.000 4.92 0.26 0.00 3.91
112 113 1.349259 ATAGTCCGCGTCGTGTTTGC 61.349 55.000 4.92 0.00 0.00 3.68
113 114 1.898938 TATAGTCCGCGTCGTGTTTG 58.101 50.000 4.92 0.00 0.00 2.93
114 115 2.162208 TCTTATAGTCCGCGTCGTGTTT 59.838 45.455 4.92 0.00 0.00 2.83
115 116 1.739466 TCTTATAGTCCGCGTCGTGTT 59.261 47.619 4.92 0.00 0.00 3.32
116 117 1.372582 TCTTATAGTCCGCGTCGTGT 58.627 50.000 4.92 0.00 0.00 4.49
117 118 2.463553 TTCTTATAGTCCGCGTCGTG 57.536 50.000 4.92 0.00 0.00 4.35
118 119 3.705043 AATTCTTATAGTCCGCGTCGT 57.295 42.857 4.92 0.00 0.00 4.34
119 120 5.684626 AGTAAAATTCTTATAGTCCGCGTCG 59.315 40.000 4.92 0.00 0.00 5.12
120 121 7.221452 TGAAGTAAAATTCTTATAGTCCGCGTC 59.779 37.037 4.92 0.00 0.00 5.19
121 122 7.037438 TGAAGTAAAATTCTTATAGTCCGCGT 58.963 34.615 4.92 0.00 0.00 6.01
122 123 7.459394 TGAAGTAAAATTCTTATAGTCCGCG 57.541 36.000 0.00 0.00 0.00 6.46
123 124 7.798982 GCATGAAGTAAAATTCTTATAGTCCGC 59.201 37.037 0.00 0.00 0.00 5.54
124 125 8.826710 TGCATGAAGTAAAATTCTTATAGTCCG 58.173 33.333 0.00 0.00 0.00 4.79
126 127 9.657121 GCTGCATGAAGTAAAATTCTTATAGTC 57.343 33.333 1.73 0.00 0.00 2.59
127 128 8.624776 GGCTGCATGAAGTAAAATTCTTATAGT 58.375 33.333 1.73 0.00 0.00 2.12
128 129 8.844244 AGGCTGCATGAAGTAAAATTCTTATAG 58.156 33.333 1.73 0.00 0.00 1.31
129 130 8.752005 AGGCTGCATGAAGTAAAATTCTTATA 57.248 30.769 1.73 0.00 0.00 0.98
130 131 7.651027 AGGCTGCATGAAGTAAAATTCTTAT 57.349 32.000 1.73 0.00 0.00 1.73
131 132 8.623903 CATAGGCTGCATGAAGTAAAATTCTTA 58.376 33.333 1.73 0.00 0.00 2.10
132 133 5.990120 AGGCTGCATGAAGTAAAATTCTT 57.010 34.783 1.73 0.00 0.00 2.52
133 134 6.604795 ACATAGGCTGCATGAAGTAAAATTCT 59.395 34.615 1.73 0.00 0.00 2.40
134 135 6.799512 ACATAGGCTGCATGAAGTAAAATTC 58.200 36.000 1.73 0.00 0.00 2.17
135 136 6.780457 ACATAGGCTGCATGAAGTAAAATT 57.220 33.333 1.73 0.00 0.00 1.82
136 137 6.263168 GGTACATAGGCTGCATGAAGTAAAAT 59.737 38.462 1.73 0.00 0.00 1.82
137 138 5.588648 GGTACATAGGCTGCATGAAGTAAAA 59.411 40.000 1.73 0.00 0.00 1.52
138 139 5.123227 GGTACATAGGCTGCATGAAGTAAA 58.877 41.667 1.73 0.00 0.00 2.01
139 140 4.163268 TGGTACATAGGCTGCATGAAGTAA 59.837 41.667 1.73 0.00 0.00 2.24
140 141 3.709141 TGGTACATAGGCTGCATGAAGTA 59.291 43.478 1.73 0.00 0.00 2.24
141 142 2.505407 TGGTACATAGGCTGCATGAAGT 59.495 45.455 1.73 0.00 0.00 3.01
142 143 3.198409 TGGTACATAGGCTGCATGAAG 57.802 47.619 0.50 0.00 0.00 3.02
152 153 5.807721 GATGGGGATTTCCATGGTACATAGG 60.808 48.000 12.58 0.00 46.67 2.57
153 154 5.222109 TGATGGGGATTTCCATGGTACATAG 60.222 44.000 12.58 0.00 46.67 2.23
154 155 4.667382 TGATGGGGATTTCCATGGTACATA 59.333 41.667 12.58 0.00 46.67 2.29
155 156 3.466723 TGATGGGGATTTCCATGGTACAT 59.533 43.478 12.58 1.21 46.67 2.29
156 157 2.855599 TGATGGGGATTTCCATGGTACA 59.144 45.455 12.58 0.00 46.67 2.90
157 158 3.490348 CTGATGGGGATTTCCATGGTAC 58.510 50.000 12.58 0.00 46.67 3.34
158 159 2.158475 GCTGATGGGGATTTCCATGGTA 60.158 50.000 12.58 0.00 46.67 3.25
159 160 1.412074 GCTGATGGGGATTTCCATGGT 60.412 52.381 12.58 0.00 46.67 3.55
160 161 1.335145 GCTGATGGGGATTTCCATGG 58.665 55.000 4.97 4.97 46.67 3.66
161 162 1.335145 GGCTGATGGGGATTTCCATG 58.665 55.000 0.64 0.00 46.67 3.66
163 164 0.033208 GTGGCTGATGGGGATTTCCA 60.033 55.000 0.00 0.00 41.60 3.53
164 165 0.033208 TGTGGCTGATGGGGATTTCC 60.033 55.000 0.00 0.00 0.00 3.13
165 166 1.684983 CATGTGGCTGATGGGGATTTC 59.315 52.381 0.00 0.00 0.00 2.17
166 167 1.007479 ACATGTGGCTGATGGGGATTT 59.993 47.619 0.00 0.00 0.00 2.17
167 168 0.632835 ACATGTGGCTGATGGGGATT 59.367 50.000 0.00 0.00 0.00 3.01
168 169 0.632835 AACATGTGGCTGATGGGGAT 59.367 50.000 0.00 0.00 0.00 3.85
169 170 0.323633 CAACATGTGGCTGATGGGGA 60.324 55.000 0.00 0.00 0.00 4.81
170 171 0.612732 ACAACATGTGGCTGATGGGG 60.613 55.000 0.00 0.00 0.00 4.96
171 172 0.528924 CACAACATGTGGCTGATGGG 59.471 55.000 0.00 0.00 44.27 4.00
181 182 2.288152 GCGACATTTTCCCACAACATGT 60.288 45.455 0.00 0.00 0.00 3.21
182 183 2.030007 AGCGACATTTTCCCACAACATG 60.030 45.455 0.00 0.00 0.00 3.21
183 184 2.030007 CAGCGACATTTTCCCACAACAT 60.030 45.455 0.00 0.00 0.00 2.71
184 185 1.336440 CAGCGACATTTTCCCACAACA 59.664 47.619 0.00 0.00 0.00 3.33
185 186 1.930371 GCAGCGACATTTTCCCACAAC 60.930 52.381 0.00 0.00 0.00 3.32
186 187 0.313672 GCAGCGACATTTTCCCACAA 59.686 50.000 0.00 0.00 0.00 3.33
187 188 0.821301 TGCAGCGACATTTTCCCACA 60.821 50.000 0.00 0.00 0.00 4.17
188 189 0.313672 TTGCAGCGACATTTTCCCAC 59.686 50.000 0.00 0.00 0.00 4.61
189 190 0.313672 GTTGCAGCGACATTTTCCCA 59.686 50.000 8.03 0.00 0.00 4.37
190 191 0.729140 CGTTGCAGCGACATTTTCCC 60.729 55.000 18.92 0.00 0.00 3.97
191 192 1.337110 GCGTTGCAGCGACATTTTCC 61.337 55.000 27.74 1.94 0.00 3.13
192 193 0.660005 TGCGTTGCAGCGACATTTTC 60.660 50.000 27.74 7.33 40.67 2.29
193 194 0.934436 GTGCGTTGCAGCGACATTTT 60.934 50.000 27.74 0.00 40.08 1.82
194 195 1.370414 GTGCGTTGCAGCGACATTT 60.370 52.632 27.74 0.00 40.08 2.32
195 196 2.252260 GTGCGTTGCAGCGACATT 59.748 55.556 27.74 0.00 40.08 2.71
196 197 2.971959 TGTGCGTTGCAGCGACAT 60.972 55.556 27.74 0.00 40.08 3.06
197 198 3.935872 GTGTGCGTTGCAGCGACA 61.936 61.111 27.74 22.27 40.08 4.35
198 199 4.993945 CGTGTGCGTTGCAGCGAC 62.994 66.667 27.74 20.12 40.08 5.19
201 202 4.666532 GTCCGTGTGCGTTGCAGC 62.667 66.667 0.00 0.00 40.08 5.25
202 203 4.354212 CGTCCGTGTGCGTTGCAG 62.354 66.667 0.00 0.00 40.08 4.41
203 204 4.874977 TCGTCCGTGTGCGTTGCA 62.875 61.111 0.00 0.00 35.60 4.08
204 205 4.059459 CTCGTCCGTGTGCGTTGC 62.059 66.667 0.00 0.00 36.15 4.17
205 206 4.059459 GCTCGTCCGTGTGCGTTG 62.059 66.667 0.00 0.00 36.15 4.10
206 207 2.797866 CTAGCTCGTCCGTGTGCGTT 62.798 60.000 0.00 0.00 36.15 4.84
207 208 3.324099 CTAGCTCGTCCGTGTGCGT 62.324 63.158 0.00 0.00 36.15 5.24
208 209 2.577112 CTAGCTCGTCCGTGTGCG 60.577 66.667 0.00 0.00 37.95 5.34
209 210 2.881352 GCTAGCTCGTCCGTGTGC 60.881 66.667 7.70 0.00 0.00 4.57
210 211 1.080772 TTGCTAGCTCGTCCGTGTG 60.081 57.895 17.23 0.00 0.00 3.82
211 212 1.080705 GTTGCTAGCTCGTCCGTGT 60.081 57.895 17.23 0.00 0.00 4.49
212 213 1.805945 GGTTGCTAGCTCGTCCGTG 60.806 63.158 17.23 0.00 0.00 4.94
213 214 1.812686 TTGGTTGCTAGCTCGTCCGT 61.813 55.000 17.23 0.00 0.00 4.69
214 215 1.078759 CTTGGTTGCTAGCTCGTCCG 61.079 60.000 17.23 0.00 0.00 4.79
215 216 0.037232 ACTTGGTTGCTAGCTCGTCC 60.037 55.000 17.23 12.68 0.00 4.79
216 217 1.071605 CACTTGGTTGCTAGCTCGTC 58.928 55.000 17.23 3.79 0.00 4.20
217 218 0.320771 CCACTTGGTTGCTAGCTCGT 60.321 55.000 17.23 1.11 0.00 4.18
218 219 1.021390 CCCACTTGGTTGCTAGCTCG 61.021 60.000 17.23 0.49 0.00 5.03
219 220 1.308783 GCCCACTTGGTTGCTAGCTC 61.309 60.000 17.23 9.00 36.04 4.09
220 221 1.303643 GCCCACTTGGTTGCTAGCT 60.304 57.895 17.23 0.00 36.04 3.32
221 222 1.589716 CTGCCCACTTGGTTGCTAGC 61.590 60.000 8.10 8.10 36.04 3.42
222 223 1.589716 GCTGCCCACTTGGTTGCTAG 61.590 60.000 0.00 0.00 36.04 3.42
223 224 1.603455 GCTGCCCACTTGGTTGCTA 60.603 57.895 0.00 0.00 36.04 3.49
224 225 2.914097 GCTGCCCACTTGGTTGCT 60.914 61.111 0.00 0.00 36.04 3.91
225 226 4.347453 CGCTGCCCACTTGGTTGC 62.347 66.667 0.00 0.00 36.04 4.17
226 227 3.673484 CCGCTGCCCACTTGGTTG 61.673 66.667 0.00 0.00 36.04 3.77
241 242 0.874390 TCTGCTTACTTTGCTTGCCG 59.126 50.000 0.00 0.00 0.00 5.69
244 245 2.508526 ACCCTCTGCTTACTTTGCTTG 58.491 47.619 0.00 0.00 0.00 4.01
270 271 1.153127 AACCTTCGCACAACCGGAA 60.153 52.632 9.46 0.00 0.00 4.30
303 304 6.470557 TCTTCTACGGTTTCCAAAATTACG 57.529 37.500 0.00 0.00 0.00 3.18
304 305 9.687210 AAAATCTTCTACGGTTTCCAAAATTAC 57.313 29.630 0.00 0.00 0.00 1.89
314 315 6.671190 CCGGTTTAAAAATCTTCTACGGTTT 58.329 36.000 0.00 0.00 33.48 3.27
319 320 9.390795 GAGAAAACCGGTTTAAAAATCTTCTAC 57.609 33.333 31.80 14.30 31.63 2.59
322 325 8.867112 AAGAGAAAACCGGTTTAAAAATCTTC 57.133 30.769 31.80 21.69 31.63 2.87
337 340 5.869344 AGAAAGCAACAACAAAGAGAAAACC 59.131 36.000 0.00 0.00 0.00 3.27
348 351 5.394773 GGAAAGGGTAAAGAAAGCAACAACA 60.395 40.000 0.00 0.00 0.00 3.33
360 363 7.776618 AATAAAAGACCAGGAAAGGGTAAAG 57.223 36.000 0.00 0.00 39.19 1.85
517 524 6.293190 CGCTCCTTGTGACAAAATTTGTACTA 60.293 38.462 11.71 6.83 45.52 1.82
518 525 5.505654 CGCTCCTTGTGACAAAATTTGTACT 60.506 40.000 11.71 0.00 45.52 2.73
519 526 4.675114 CGCTCCTTGTGACAAAATTTGTAC 59.325 41.667 11.71 10.49 45.52 2.90
607 615 4.402155 TGCAGCCTGGGAATACAAAAATAG 59.598 41.667 0.00 0.00 0.00 1.73
610 618 2.603021 TGCAGCCTGGGAATACAAAAA 58.397 42.857 0.00 0.00 0.00 1.94
707 721 1.970092 TTACTGGTTTGGTTGGACGG 58.030 50.000 0.00 0.00 0.00 4.79
967 981 4.154195 CGCCTCTTGTGCCATTATATAACC 59.846 45.833 0.00 0.00 0.00 2.85
968 982 4.154195 CCGCCTCTTGTGCCATTATATAAC 59.846 45.833 0.00 0.00 0.00 1.89
969 983 4.323417 CCGCCTCTTGTGCCATTATATAA 58.677 43.478 0.00 0.00 0.00 0.98
970 984 3.868369 GCCGCCTCTTGTGCCATTATATA 60.868 47.826 0.00 0.00 0.00 0.86
1179 1194 4.718774 AGGGAAGATGCTAGAGTTTGATGA 59.281 41.667 0.00 0.00 0.00 2.92
1190 1205 5.441718 ACAATTCAGAAGGGAAGATGCTA 57.558 39.130 0.00 0.00 0.00 3.49
1245 1261 3.113979 TGCTGCACGCATCGACAG 61.114 61.111 0.00 8.72 45.47 3.51
1289 1305 1.065199 AGCGCCAGGATCATCAGAAAA 60.065 47.619 2.29 0.00 0.00 2.29
1424 1440 5.833082 TCAAGAATCCACTAGCTTATCGAC 58.167 41.667 0.00 0.00 0.00 4.20
1475 1491 9.846248 AGTACAAGAGCAACAAATTAATGAATC 57.154 29.630 0.00 0.00 0.00 2.52
1596 1612 1.102809 TGAATTGCTAGCCCATGCCG 61.103 55.000 13.29 0.00 38.69 5.69
1597 1613 1.271656 GATGAATTGCTAGCCCATGCC 59.728 52.381 13.29 1.62 38.69 4.40
1598 1614 1.958579 TGATGAATTGCTAGCCCATGC 59.041 47.619 13.29 3.55 37.95 4.06
1599 1615 3.635373 ACTTGATGAATTGCTAGCCCATG 59.365 43.478 13.29 4.13 0.00 3.66
1600 1616 3.635373 CACTTGATGAATTGCTAGCCCAT 59.365 43.478 13.29 10.19 0.00 4.00
1601 1617 3.018856 CACTTGATGAATTGCTAGCCCA 58.981 45.455 13.29 5.49 0.00 5.36
1602 1618 2.223665 GCACTTGATGAATTGCTAGCCC 60.224 50.000 13.29 0.00 35.43 5.19
1603 1619 2.424601 TGCACTTGATGAATTGCTAGCC 59.575 45.455 13.29 0.00 38.31 3.93
1635 1651 5.527582 CGACACTTATTTTAGATTGGAGGGG 59.472 44.000 0.00 0.00 0.00 4.79
1646 1662 3.255725 CTCCCGCACGACACTTATTTTA 58.744 45.455 0.00 0.00 0.00 1.52
1822 1896 5.924769 ACCCCCTAATTAGAACCAATAGG 57.075 43.478 14.28 3.87 42.21 2.57
1860 1935 6.025749 TCATATGTCCTACATCGTCATTCC 57.974 41.667 1.90 0.00 39.88 3.01
1934 2010 7.212976 TGACCCATTCGAAAAATGAAAAATGA 58.787 30.769 0.00 0.00 0.00 2.57
2079 4660 7.306807 GCTTGCATCTAAACCTTTTCAAACTTC 60.307 37.037 0.00 0.00 0.00 3.01
2100 4681 7.910683 GTCAGTAAAAGATAATTACAGGCTTGC 59.089 37.037 0.00 0.00 36.04 4.01
2137 4718 7.276658 TGTAATTCTCTGTACAACCAAGTTCA 58.723 34.615 0.00 0.00 0.00 3.18
2278 4859 2.824341 TCTCCCAAAAGAGACGTCTACC 59.176 50.000 20.09 7.15 37.98 3.18
2297 4878 3.017581 ATTTGCCGCCCCCTCTCT 61.018 61.111 0.00 0.00 0.00 3.10
2306 4887 2.497107 ATGATACTTGCATTTGCCGC 57.503 45.000 0.00 0.00 41.18 6.53
2327 4908 5.458041 ACAAATGACCTTCCATTTCACTG 57.542 39.130 0.00 0.00 42.83 3.66
2373 4954 2.673775 TGGCAAATCCAGAACTCCAA 57.326 45.000 0.00 0.00 40.72 3.53
2404 4985 3.005554 CCACCACTTAGTCATCAAGCTG 58.994 50.000 0.00 0.00 0.00 4.24
2428 5009 8.585018 CATAACCCCTCTTGTGTTTCTAATTTT 58.415 33.333 0.00 0.00 0.00 1.82
2432 5013 5.566469 CCATAACCCCTCTTGTGTTTCTAA 58.434 41.667 0.00 0.00 0.00 2.10
2493 5074 5.755409 TCCAGGTTTAACTGAAGCTATGA 57.245 39.130 0.00 0.00 40.97 2.15
2494 5075 7.396540 AAATCCAGGTTTAACTGAAGCTATG 57.603 36.000 0.00 0.00 40.97 2.23
2500 5081 8.934023 AGTCATTAAATCCAGGTTTAACTGAA 57.066 30.769 0.00 0.00 40.97 3.02
2504 5085 7.829706 AGGAGAGTCATTAAATCCAGGTTTAAC 59.170 37.037 0.00 0.00 36.64 2.01


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

AutoCloner maintained by Alex Coulton.