Multiple sequence alignment - TraesCS3B01G284000

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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 TraesCS3B01G284000 chr3B 100.000 2189 0 0 1 2189 454877790 454875602 0.000000e+00 4043
1 TraesCS3B01G284000 chr3A 90.845 1835 78 26 396 2189 472906942 472905157 0.000000e+00 2375
2 TraesCS3B01G284000 chr3A 98.276 58 1 0 288 345 472907421 472907364 3.840000e-18 102
3 TraesCS3B01G284000 chr3D 88.610 1115 61 28 445 1520 354275514 354274427 0.000000e+00 1295
4 TraesCS3B01G284000 chr3D 92.857 672 23 13 1521 2189 354274388 354273739 0.000000e+00 952
5 TraesCS3B01G284000 chr3D 92.500 80 6 0 288 367 354277236 354277157 4.940000e-22 115
6 TraesCS3B01G284000 chr1B 92.334 287 22 0 1 287 633868129 633868415 2.020000e-110 409
7 TraesCS3B01G284000 chr4A 92.042 289 23 0 1 289 675810961 675811249 7.280000e-110 407
8 TraesCS3B01G284000 chr6B 89.583 288 28 2 1 287 26868641 26868355 4.440000e-97 364
9 TraesCS3B01G284000 chr2D 89.199 287 31 0 1 287 645415825 645415539 2.070000e-95 359
10 TraesCS3B01G284000 chr2B 89.199 287 31 0 1 287 639238132 639238418 2.070000e-95 359
11 TraesCS3B01G284000 chr2A 88.850 287 32 0 1 287 770945960 770945674 9.610000e-94 353
12 TraesCS3B01G284000 chr6D 88.542 288 31 2 1 287 35503480 35503766 4.470000e-92 348
13 TraesCS3B01G284000 chr1D 88.693 283 32 0 1 283 65084995 65085277 1.610000e-91 346
14 TraesCS3B01G284000 chr5D 88.153 287 34 0 1 287 421378299 421378013 2.080000e-90 342


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 TraesCS3B01G284000 chr3B 454875602 454877790 2188 True 4043.000000 4043 100.000000 1 2189 1 chr3B.!!$R1 2188
1 TraesCS3B01G284000 chr3A 472905157 472907421 2264 True 1238.500000 2375 94.560500 288 2189 2 chr3A.!!$R1 1901
2 TraesCS3B01G284000 chr3D 354273739 354277236 3497 True 787.333333 1295 91.322333 288 2189 3 chr3D.!!$R1 1901

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
193 194 0.03438 TCCTACTGTCCGAGGGTCTG 60.034 60.0 0.0 0.0 33.27 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1596 3692 0.596082 CGCCCGATGAAAAACTGGTT 59.404 50.0 0.0 0.0 0.0 3.67 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
24 25 5.856126 TCAAAGTAGTTAAGTTCATGCGG 57.144 39.130 0.00 0.00 0.00 5.69
25 26 5.543714 TCAAAGTAGTTAAGTTCATGCGGA 58.456 37.500 0.00 0.00 0.00 5.54
26 27 5.407387 TCAAAGTAGTTAAGTTCATGCGGAC 59.593 40.000 0.00 0.00 0.00 4.79
27 28 4.803098 AGTAGTTAAGTTCATGCGGACT 57.197 40.909 0.00 0.00 0.00 3.85
28 29 5.909621 AGTAGTTAAGTTCATGCGGACTA 57.090 39.130 0.00 0.00 0.00 2.59
29 30 6.466885 AGTAGTTAAGTTCATGCGGACTAT 57.533 37.500 0.00 0.00 0.00 2.12
30 31 6.273825 AGTAGTTAAGTTCATGCGGACTATG 58.726 40.000 0.00 0.00 0.00 2.23
31 32 5.339008 AGTTAAGTTCATGCGGACTATGA 57.661 39.130 0.00 0.00 33.00 2.15
32 33 5.918608 AGTTAAGTTCATGCGGACTATGAT 58.081 37.500 0.00 0.00 34.76 2.45
33 34 7.050970 AGTTAAGTTCATGCGGACTATGATA 57.949 36.000 0.00 0.00 34.76 2.15
34 35 7.497595 AGTTAAGTTCATGCGGACTATGATAA 58.502 34.615 0.00 0.00 34.76 1.75
35 36 7.438459 AGTTAAGTTCATGCGGACTATGATAAC 59.562 37.037 0.00 0.00 34.76 1.89
36 37 4.632153 AGTTCATGCGGACTATGATAACC 58.368 43.478 0.00 0.00 34.76 2.85
37 38 4.345257 AGTTCATGCGGACTATGATAACCT 59.655 41.667 0.00 0.00 34.76 3.50
38 39 5.538813 AGTTCATGCGGACTATGATAACCTA 59.461 40.000 0.00 0.00 34.76 3.08
39 40 5.386958 TCATGCGGACTATGATAACCTAC 57.613 43.478 0.00 0.00 30.03 3.18
40 41 4.219944 TCATGCGGACTATGATAACCTACC 59.780 45.833 0.00 0.00 30.03 3.18
41 42 2.555325 TGCGGACTATGATAACCTACCG 59.445 50.000 0.00 0.00 41.63 4.02
42 43 3.213249 CGGACTATGATAACCTACCGC 57.787 52.381 0.00 0.00 33.24 5.68
43 44 2.094854 CGGACTATGATAACCTACCGCC 60.095 54.545 0.00 0.00 33.24 6.13
44 45 2.895404 GGACTATGATAACCTACCGCCA 59.105 50.000 0.00 0.00 0.00 5.69
45 46 3.056749 GGACTATGATAACCTACCGCCAG 60.057 52.174 0.00 0.00 0.00 4.85
46 47 2.897969 ACTATGATAACCTACCGCCAGG 59.102 50.000 0.00 0.00 45.13 4.45
47 48 1.056660 ATGATAACCTACCGCCAGGG 58.943 55.000 5.62 0.00 43.47 4.45
48 49 1.070957 GATAACCTACCGCCAGGGC 59.929 63.158 0.00 0.00 43.47 5.19
49 50 1.691337 ATAACCTACCGCCAGGGCA 60.691 57.895 11.42 0.00 43.47 5.36
50 51 1.060163 ATAACCTACCGCCAGGGCAT 61.060 55.000 11.42 0.00 43.47 4.40
51 52 1.276140 TAACCTACCGCCAGGGCATT 61.276 55.000 11.42 0.00 43.47 3.56
52 53 2.203209 CCTACCGCCAGGGCATTC 60.203 66.667 11.42 0.00 43.47 2.67
53 54 2.588877 CTACCGCCAGGGCATTCG 60.589 66.667 11.42 0.00 43.47 3.34
54 55 4.169696 TACCGCCAGGGCATTCGG 62.170 66.667 11.42 7.88 46.61 4.30
59 60 4.169696 CCAGGGCATTCGGCGGTA 62.170 66.667 7.21 0.00 46.16 4.02
60 61 2.588877 CAGGGCATTCGGCGGTAG 60.589 66.667 7.21 0.00 46.16 3.18
61 62 3.861797 AGGGCATTCGGCGGTAGG 61.862 66.667 7.21 0.00 46.16 3.18
62 63 4.171103 GGGCATTCGGCGGTAGGT 62.171 66.667 7.21 0.00 46.16 3.08
63 64 2.124860 GGCATTCGGCGGTAGGTT 60.125 61.111 7.21 0.00 46.16 3.50
64 65 1.747745 GGCATTCGGCGGTAGGTTT 60.748 57.895 7.21 0.00 46.16 3.27
65 66 0.462403 GGCATTCGGCGGTAGGTTTA 60.462 55.000 7.21 0.00 46.16 2.01
66 67 1.589803 GCATTCGGCGGTAGGTTTAT 58.410 50.000 7.21 0.00 0.00 1.40
67 68 1.263217 GCATTCGGCGGTAGGTTTATG 59.737 52.381 7.21 0.05 0.00 1.90
68 69 2.557317 CATTCGGCGGTAGGTTTATGT 58.443 47.619 7.21 0.00 0.00 2.29
69 70 2.012937 TTCGGCGGTAGGTTTATGTG 57.987 50.000 7.21 0.00 0.00 3.21
70 71 0.176219 TCGGCGGTAGGTTTATGTGG 59.824 55.000 7.21 0.00 0.00 4.17
71 72 0.812412 CGGCGGTAGGTTTATGTGGG 60.812 60.000 0.00 0.00 0.00 4.61
72 73 1.099295 GGCGGTAGGTTTATGTGGGC 61.099 60.000 0.00 0.00 0.00 5.36
73 74 0.107361 GCGGTAGGTTTATGTGGGCT 60.107 55.000 0.00 0.00 0.00 5.19
74 75 1.139455 GCGGTAGGTTTATGTGGGCTA 59.861 52.381 0.00 0.00 0.00 3.93
75 76 2.830104 CGGTAGGTTTATGTGGGCTAC 58.170 52.381 0.00 0.00 0.00 3.58
76 77 2.484241 CGGTAGGTTTATGTGGGCTACC 60.484 54.545 0.00 0.00 33.89 3.18
77 78 2.484241 GGTAGGTTTATGTGGGCTACCG 60.484 54.545 0.00 0.00 40.75 4.02
88 89 2.047560 GCTACCGCCGTGGACTTT 60.048 61.111 4.58 0.00 42.00 2.66
89 90 2.388232 GCTACCGCCGTGGACTTTG 61.388 63.158 4.58 0.00 42.00 2.77
90 91 1.740296 CTACCGCCGTGGACTTTGG 60.740 63.158 4.58 0.00 42.00 3.28
91 92 3.887335 TACCGCCGTGGACTTTGGC 62.887 63.158 4.58 0.00 45.39 4.52
95 96 2.344500 CCGTGGACTTTGGCGGTA 59.656 61.111 0.00 0.00 39.41 4.02
96 97 1.740296 CCGTGGACTTTGGCGGTAG 60.740 63.158 0.00 0.00 39.41 3.18
97 98 1.740296 CGTGGACTTTGGCGGTAGG 60.740 63.158 0.00 0.00 0.00 3.18
98 99 1.373812 GTGGACTTTGGCGGTAGGT 59.626 57.895 0.00 0.00 0.00 3.08
99 100 0.609662 GTGGACTTTGGCGGTAGGTA 59.390 55.000 0.00 0.00 0.00 3.08
100 101 0.609662 TGGACTTTGGCGGTAGGTAC 59.390 55.000 0.00 0.00 0.00 3.34
101 102 0.459063 GGACTTTGGCGGTAGGTACG 60.459 60.000 0.00 0.00 0.00 3.67
102 103 0.244721 GACTTTGGCGGTAGGTACGT 59.755 55.000 0.00 0.00 0.00 3.57
103 104 1.472480 GACTTTGGCGGTAGGTACGTA 59.528 52.381 0.00 0.00 0.00 3.57
104 105 1.892474 ACTTTGGCGGTAGGTACGTAA 59.108 47.619 0.00 0.00 0.00 3.18
106 107 0.173255 TTGGCGGTAGGTACGTAAGC 59.827 55.000 12.95 12.95 45.62 3.09
107 108 0.964860 TGGCGGTAGGTACGTAAGCA 60.965 55.000 19.27 8.42 45.62 3.91
108 109 0.248784 GGCGGTAGGTACGTAAGCAG 60.249 60.000 19.27 3.83 45.62 4.24
109 110 0.869028 GCGGTAGGTACGTAAGCAGC 60.869 60.000 15.21 6.16 45.62 5.25
110 111 0.248784 CGGTAGGTACGTAAGCAGCC 60.249 60.000 0.00 0.00 45.62 4.85
111 112 0.248784 GGTAGGTACGTAAGCAGCCG 60.249 60.000 0.00 0.00 45.62 5.52
112 113 0.453390 GTAGGTACGTAAGCAGCCGT 59.547 55.000 0.00 0.78 45.62 5.68
113 114 1.135286 GTAGGTACGTAAGCAGCCGTT 60.135 52.381 0.00 0.00 45.62 4.44
114 115 1.176527 AGGTACGTAAGCAGCCGTTA 58.823 50.000 0.00 0.00 45.62 3.18
115 116 1.545582 AGGTACGTAAGCAGCCGTTAA 59.454 47.619 0.00 0.00 45.62 2.01
116 117 1.655597 GGTACGTAAGCAGCCGTTAAC 59.344 52.381 0.00 0.00 45.62 2.01
117 118 1.655597 GTACGTAAGCAGCCGTTAACC 59.344 52.381 0.00 0.00 45.62 2.85
118 119 1.010419 ACGTAAGCAGCCGTTAACCG 61.010 55.000 0.00 0.00 45.62 4.44
119 120 1.010419 CGTAAGCAGCCGTTAACCGT 61.010 55.000 0.00 0.00 33.66 4.83
120 121 1.150827 GTAAGCAGCCGTTAACCGTT 58.849 50.000 0.00 0.00 33.66 4.44
121 122 1.532437 GTAAGCAGCCGTTAACCGTTT 59.468 47.619 0.00 0.00 33.66 3.60
122 123 0.309612 AAGCAGCCGTTAACCGTTTG 59.690 50.000 0.00 0.00 33.66 2.93
123 124 0.533308 AGCAGCCGTTAACCGTTTGA 60.533 50.000 0.00 0.00 33.66 2.69
124 125 0.385098 GCAGCCGTTAACCGTTTGAC 60.385 55.000 0.00 0.00 33.66 3.18
125 126 0.111001 CAGCCGTTAACCGTTTGACG 60.111 55.000 2.97 2.97 42.71 4.35
151 152 4.382320 GCACACCTACCGCCGGAA 62.382 66.667 11.71 0.00 0.00 4.30
152 153 2.433664 CACACCTACCGCCGGAAC 60.434 66.667 11.71 0.00 0.00 3.62
153 154 3.698820 ACACCTACCGCCGGAACC 61.699 66.667 11.71 0.00 0.00 3.62
154 155 3.387947 CACCTACCGCCGGAACCT 61.388 66.667 11.71 0.00 0.00 3.50
155 156 3.387947 ACCTACCGCCGGAACCTG 61.388 66.667 11.71 0.00 0.00 4.00
156 157 3.387947 CCTACCGCCGGAACCTGT 61.388 66.667 11.71 0.00 0.00 4.00
157 158 2.125673 CTACCGCCGGAACCTGTG 60.126 66.667 11.71 0.00 0.00 3.66
158 159 3.659089 CTACCGCCGGAACCTGTGG 62.659 68.421 11.71 12.11 36.96 4.17
163 164 3.697747 CCGGAACCTGTGGCGGTA 61.698 66.667 0.00 0.00 35.89 4.02
164 165 2.125673 CGGAACCTGTGGCGGTAG 60.126 66.667 0.00 0.00 35.89 3.18
165 166 2.642254 CGGAACCTGTGGCGGTAGA 61.642 63.158 0.00 0.00 35.89 2.59
166 167 1.079336 GGAACCTGTGGCGGTAGAC 60.079 63.158 0.00 0.00 35.89 2.59
167 168 1.542187 GGAACCTGTGGCGGTAGACT 61.542 60.000 0.00 0.00 35.89 3.24
168 169 0.389948 GAACCTGTGGCGGTAGACTG 60.390 60.000 0.00 0.00 35.89 3.51
169 170 1.119574 AACCTGTGGCGGTAGACTGT 61.120 55.000 0.00 0.00 35.89 3.55
170 171 1.079819 CCTGTGGCGGTAGACTGTG 60.080 63.158 0.00 0.00 0.00 3.66
171 172 1.738099 CTGTGGCGGTAGACTGTGC 60.738 63.158 0.00 0.00 0.00 4.57
172 173 2.342279 GTGGCGGTAGACTGTGCA 59.658 61.111 0.00 0.00 0.00 4.57
173 174 1.301401 GTGGCGGTAGACTGTGCAA 60.301 57.895 0.00 0.00 0.00 4.08
174 175 0.673644 GTGGCGGTAGACTGTGCAAT 60.674 55.000 0.00 0.00 0.00 3.56
175 176 0.391130 TGGCGGTAGACTGTGCAATC 60.391 55.000 0.00 0.00 0.00 2.67
176 177 1.090052 GGCGGTAGACTGTGCAATCC 61.090 60.000 0.00 0.00 0.00 3.01
177 178 0.108138 GCGGTAGACTGTGCAATCCT 60.108 55.000 0.00 0.00 0.00 3.24
178 179 1.136305 GCGGTAGACTGTGCAATCCTA 59.864 52.381 0.00 0.00 0.00 2.94
179 180 2.810650 CGGTAGACTGTGCAATCCTAC 58.189 52.381 0.00 0.00 0.00 3.18
180 181 2.427453 CGGTAGACTGTGCAATCCTACT 59.573 50.000 13.12 2.26 32.56 2.57
181 182 3.735208 CGGTAGACTGTGCAATCCTACTG 60.735 52.174 13.12 11.43 32.56 2.74
182 183 3.195825 GGTAGACTGTGCAATCCTACTGT 59.804 47.826 13.12 0.00 32.56 3.55
183 184 3.601443 AGACTGTGCAATCCTACTGTC 57.399 47.619 0.00 0.00 42.51 3.51
184 185 2.234908 AGACTGTGCAATCCTACTGTCC 59.765 50.000 0.00 0.00 42.91 4.02
185 186 1.066858 ACTGTGCAATCCTACTGTCCG 60.067 52.381 0.00 0.00 0.00 4.79
186 187 1.204704 CTGTGCAATCCTACTGTCCGA 59.795 52.381 0.00 0.00 0.00 4.55
187 188 1.204704 TGTGCAATCCTACTGTCCGAG 59.795 52.381 0.00 0.00 0.00 4.63
188 189 0.824109 TGCAATCCTACTGTCCGAGG 59.176 55.000 0.00 0.00 0.00 4.63
189 190 0.105039 GCAATCCTACTGTCCGAGGG 59.895 60.000 0.00 0.00 33.27 4.30
190 191 1.486211 CAATCCTACTGTCCGAGGGT 58.514 55.000 0.00 0.00 33.27 4.34
191 192 1.409427 CAATCCTACTGTCCGAGGGTC 59.591 57.143 0.00 0.00 33.27 4.46
192 193 0.927767 ATCCTACTGTCCGAGGGTCT 59.072 55.000 0.00 0.00 33.27 3.85
193 194 0.034380 TCCTACTGTCCGAGGGTCTG 60.034 60.000 0.00 0.00 33.27 3.51
194 195 1.038130 CCTACTGTCCGAGGGTCTGG 61.038 65.000 0.00 0.00 0.00 3.86
195 196 1.668101 CTACTGTCCGAGGGTCTGGC 61.668 65.000 0.00 0.00 0.00 4.85
196 197 4.135153 CTGTCCGAGGGTCTGGCG 62.135 72.222 0.00 0.00 0.00 5.69
197 198 4.671590 TGTCCGAGGGTCTGGCGA 62.672 66.667 0.00 0.00 0.00 5.54
198 199 3.148279 GTCCGAGGGTCTGGCGAT 61.148 66.667 0.00 0.00 0.00 4.58
199 200 1.826921 GTCCGAGGGTCTGGCGATA 60.827 63.158 0.00 0.00 0.00 2.92
200 201 1.528542 TCCGAGGGTCTGGCGATAG 60.529 63.158 0.00 0.00 0.00 2.08
201 202 1.828660 CCGAGGGTCTGGCGATAGT 60.829 63.158 0.00 0.00 39.35 2.12
202 203 0.536687 CCGAGGGTCTGGCGATAGTA 60.537 60.000 0.00 0.00 39.35 1.82
203 204 1.315690 CGAGGGTCTGGCGATAGTAA 58.684 55.000 0.00 0.00 39.35 2.24
204 205 1.679680 CGAGGGTCTGGCGATAGTAAA 59.320 52.381 0.00 0.00 39.35 2.01
205 206 2.100252 CGAGGGTCTGGCGATAGTAAAA 59.900 50.000 0.00 0.00 39.35 1.52
206 207 3.718815 GAGGGTCTGGCGATAGTAAAAG 58.281 50.000 0.00 0.00 39.35 2.27
207 208 2.434702 AGGGTCTGGCGATAGTAAAAGG 59.565 50.000 0.00 0.00 39.35 3.11
208 209 2.484947 GGGTCTGGCGATAGTAAAAGGG 60.485 54.545 0.00 0.00 39.35 3.95
209 210 2.169978 GGTCTGGCGATAGTAAAAGGGT 59.830 50.000 0.00 0.00 39.35 4.34
210 211 3.455327 GTCTGGCGATAGTAAAAGGGTC 58.545 50.000 0.00 0.00 39.35 4.46
211 212 3.101437 TCTGGCGATAGTAAAAGGGTCA 58.899 45.455 0.00 0.00 39.35 4.02
212 213 3.516300 TCTGGCGATAGTAAAAGGGTCAA 59.484 43.478 0.00 0.00 39.35 3.18
213 214 4.020039 TCTGGCGATAGTAAAAGGGTCAAA 60.020 41.667 0.00 0.00 39.35 2.69
214 215 4.850680 TGGCGATAGTAAAAGGGTCAAAT 58.149 39.130 0.00 0.00 39.35 2.32
215 216 4.879545 TGGCGATAGTAAAAGGGTCAAATC 59.120 41.667 0.00 0.00 39.35 2.17
216 217 5.123936 GGCGATAGTAAAAGGGTCAAATCT 58.876 41.667 0.00 0.00 39.35 2.40
217 218 5.589050 GGCGATAGTAAAAGGGTCAAATCTT 59.411 40.000 0.00 0.00 39.35 2.40
218 219 6.458342 GGCGATAGTAAAAGGGTCAAATCTTG 60.458 42.308 0.00 0.00 39.35 3.02
219 220 6.315393 GCGATAGTAAAAGGGTCAAATCTTGA 59.685 38.462 0.00 0.00 36.20 3.02
220 221 7.148306 GCGATAGTAAAAGGGTCAAATCTTGAA 60.148 37.037 0.00 0.00 39.19 2.69
221 222 8.726988 CGATAGTAAAAGGGTCAAATCTTGAAA 58.273 33.333 0.00 0.00 42.15 2.69
224 225 8.250143 AGTAAAAGGGTCAAATCTTGAAATGT 57.750 30.769 0.00 0.00 42.15 2.71
225 226 8.704668 AGTAAAAGGGTCAAATCTTGAAATGTT 58.295 29.630 0.00 0.00 42.15 2.71
226 227 9.325198 GTAAAAGGGTCAAATCTTGAAATGTTT 57.675 29.630 0.00 0.00 42.15 2.83
227 228 8.806429 AAAAGGGTCAAATCTTGAAATGTTTT 57.194 26.923 0.00 0.00 42.15 2.43
228 229 8.437360 AAAGGGTCAAATCTTGAAATGTTTTC 57.563 30.769 0.00 0.00 42.15 2.29
229 230 7.123355 AGGGTCAAATCTTGAAATGTTTTCA 57.877 32.000 0.00 0.00 42.15 2.69
230 231 7.563906 AGGGTCAAATCTTGAAATGTTTTCAA 58.436 30.769 13.15 13.15 42.15 2.69
231 232 8.046107 AGGGTCAAATCTTGAAATGTTTTCAAA 58.954 29.630 14.33 7.88 42.15 2.69
232 233 8.122330 GGGTCAAATCTTGAAATGTTTTCAAAC 58.878 33.333 14.33 9.42 42.15 2.93
233 234 8.882736 GGTCAAATCTTGAAATGTTTTCAAACT 58.117 29.630 14.33 4.60 42.15 2.66
234 235 9.693157 GTCAAATCTTGAAATGTTTTCAAACTG 57.307 29.630 14.33 9.94 42.15 3.16
235 236 9.650539 TCAAATCTTGAAATGTTTTCAAACTGA 57.349 25.926 14.33 9.88 37.89 3.41
240 241 9.650539 TCTTGAAATGTTTTCAAACTGAAATCA 57.349 25.926 14.33 12.74 44.75 2.57
241 242 9.910511 CTTGAAATGTTTTCAAACTGAAATCAG 57.089 29.630 14.33 8.84 44.75 2.90
242 243 9.650539 TTGAAATGTTTTCAAACTGAAATCAGA 57.349 25.926 16.93 0.00 44.75 3.27
243 244 9.820725 TGAAATGTTTTCAAACTGAAATCAGAT 57.179 25.926 16.93 2.26 44.75 2.90
246 247 9.688592 AATGTTTTCAAACTGAAATCAGATCTC 57.311 29.630 16.93 0.99 44.75 2.75
247 248 7.355017 TGTTTTCAAACTGAAATCAGATCTCG 58.645 34.615 16.93 1.60 44.75 4.04
248 249 7.226523 TGTTTTCAAACTGAAATCAGATCTCGA 59.773 33.333 16.93 0.00 44.75 4.04
249 250 7.728847 TTTCAAACTGAAATCAGATCTCGAA 57.271 32.000 16.93 8.74 46.59 3.71
250 251 7.912056 TTCAAACTGAAATCAGATCTCGAAT 57.088 32.000 16.93 0.00 46.59 3.34
251 252 7.912056 TCAAACTGAAATCAGATCTCGAATT 57.088 32.000 16.93 0.00 46.59 2.17
252 253 8.327941 TCAAACTGAAATCAGATCTCGAATTT 57.672 30.769 16.93 0.00 46.59 1.82
253 254 8.232513 TCAAACTGAAATCAGATCTCGAATTTG 58.767 33.333 16.93 12.93 46.59 2.32
254 255 7.678947 AACTGAAATCAGATCTCGAATTTGT 57.321 32.000 16.93 3.44 46.59 2.83
255 256 7.678947 ACTGAAATCAGATCTCGAATTTGTT 57.321 32.000 16.93 0.00 46.59 2.83
256 257 8.103948 ACTGAAATCAGATCTCGAATTTGTTT 57.896 30.769 16.93 2.81 46.59 2.83
257 258 8.019669 ACTGAAATCAGATCTCGAATTTGTTTG 58.980 33.333 16.93 3.55 46.59 2.93
258 259 8.098220 TGAAATCAGATCTCGAATTTGTTTGA 57.902 30.769 10.48 0.00 0.00 2.69
259 260 8.017373 TGAAATCAGATCTCGAATTTGTTTGAC 58.983 33.333 10.48 0.05 0.00 3.18
260 261 7.439157 AATCAGATCTCGAATTTGTTTGACA 57.561 32.000 0.00 0.00 0.00 3.58
261 262 6.859420 TCAGATCTCGAATTTGTTTGACAA 57.141 33.333 0.00 0.00 36.11 3.18
276 277 3.495670 TGACAAAAGGGTCAAAACACG 57.504 42.857 0.00 0.00 44.34 4.49
277 278 2.164624 TGACAAAAGGGTCAAAACACGG 59.835 45.455 0.00 0.00 44.34 4.94
278 279 2.424246 GACAAAAGGGTCAAAACACGGA 59.576 45.455 0.00 0.00 37.73 4.69
279 280 2.826725 ACAAAAGGGTCAAAACACGGAA 59.173 40.909 0.00 0.00 32.44 4.30
280 281 3.449377 ACAAAAGGGTCAAAACACGGAAT 59.551 39.130 0.00 0.00 32.44 3.01
281 282 4.081365 ACAAAAGGGTCAAAACACGGAATT 60.081 37.500 0.00 0.00 32.44 2.17
282 283 4.746535 AAAGGGTCAAAACACGGAATTT 57.253 36.364 0.00 0.00 32.44 1.82
283 284 3.726291 AGGGTCAAAACACGGAATTTG 57.274 42.857 3.53 3.53 37.77 2.32
284 285 2.364002 AGGGTCAAAACACGGAATTTGG 59.636 45.455 8.54 0.00 37.19 3.28
285 286 2.131972 GGTCAAAACACGGAATTTGGC 58.868 47.619 8.54 7.04 39.72 4.52
286 287 2.131972 GTCAAAACACGGAATTTGGCC 58.868 47.619 0.00 0.00 35.62 5.36
353 742 1.599071 GCAGCAGCTATATTGCGAACA 59.401 47.619 0.00 0.00 45.98 3.18
358 747 3.496130 GCAGCTATATTGCGAACAGATGT 59.504 43.478 3.46 0.00 38.13 3.06
369 758 3.617669 CGAACAGATGTTTGGTCACAAC 58.382 45.455 5.21 0.00 38.56 3.32
371 760 4.552767 CGAACAGATGTTTGGTCACAACTC 60.553 45.833 5.21 0.00 38.56 3.01
373 762 3.627577 ACAGATGTTTGGTCACAACTCAC 59.372 43.478 0.00 0.00 36.06 3.51
374 763 3.627123 CAGATGTTTGGTCACAACTCACA 59.373 43.478 0.00 0.00 36.06 3.58
375 764 4.096231 CAGATGTTTGGTCACAACTCACAA 59.904 41.667 0.00 0.00 36.06 3.33
376 765 4.336433 AGATGTTTGGTCACAACTCACAAG 59.664 41.667 0.00 0.00 36.06 3.16
377 766 3.417101 TGTTTGGTCACAACTCACAAGT 58.583 40.909 0.00 0.00 36.06 3.16
378 767 4.580868 TGTTTGGTCACAACTCACAAGTA 58.419 39.130 0.00 0.00 36.06 2.24
379 768 4.634004 TGTTTGGTCACAACTCACAAGTAG 59.366 41.667 0.00 0.00 36.06 2.57
380 769 4.746535 TTGGTCACAACTCACAAGTAGA 57.253 40.909 0.00 0.00 33.48 2.59
381 770 4.054780 TGGTCACAACTCACAAGTAGAC 57.945 45.455 0.00 0.00 33.48 2.59
382 771 3.704566 TGGTCACAACTCACAAGTAGACT 59.295 43.478 0.00 0.00 34.70 3.24
383 772 4.891168 TGGTCACAACTCACAAGTAGACTA 59.109 41.667 0.00 0.00 34.70 2.59
384 773 5.361571 TGGTCACAACTCACAAGTAGACTAA 59.638 40.000 0.00 0.00 34.70 2.24
385 774 6.127281 TGGTCACAACTCACAAGTAGACTAAA 60.127 38.462 0.00 0.00 34.70 1.85
386 775 6.421202 GGTCACAACTCACAAGTAGACTAAAG 59.579 42.308 0.00 0.00 34.70 1.85
387 776 7.201145 GTCACAACTCACAAGTAGACTAAAGA 58.799 38.462 0.00 0.00 33.48 2.52
388 777 7.380065 GTCACAACTCACAAGTAGACTAAAGAG 59.620 40.741 0.00 0.00 33.48 2.85
389 778 7.284716 TCACAACTCACAAGTAGACTAAAGAGA 59.715 37.037 10.39 0.00 33.48 3.10
390 779 7.921214 CACAACTCACAAGTAGACTAAAGAGAA 59.079 37.037 10.39 0.00 33.48 2.87
391 780 8.475639 ACAACTCACAAGTAGACTAAAGAGAAA 58.524 33.333 10.39 0.00 33.48 2.52
392 781 8.973378 CAACTCACAAGTAGACTAAAGAGAAAG 58.027 37.037 10.39 0.00 33.48 2.62
393 782 7.149307 ACTCACAAGTAGACTAAAGAGAAAGC 58.851 38.462 10.39 0.00 32.59 3.51
394 783 6.150318 TCACAAGTAGACTAAAGAGAAAGCG 58.850 40.000 0.00 0.00 0.00 4.68
413 802 2.073816 CGACCGTGGCTTCAAGTAAAT 58.926 47.619 0.00 0.00 0.00 1.40
453 842 4.744570 CTTGTAAGCTGACGTCCTGATAA 58.255 43.478 14.12 0.90 0.00 1.75
491 2487 4.529769 TCTTTCTGATGCTTCTCCTTCTCA 59.470 41.667 0.88 0.00 0.00 3.27
495 2491 4.654724 TCTGATGCTTCTCCTTCTCATGAT 59.345 41.667 0.00 0.00 0.00 2.45
504 2500 1.434622 CTTCTCATGATGCGGCGCTT 61.435 55.000 33.26 27.17 0.00 4.68
509 2505 1.746615 ATGATGCGGCGCTTGTTCT 60.747 52.632 33.26 10.23 0.00 3.01
518 2514 0.811616 GCGCTTGTTCTGGGATCGAT 60.812 55.000 0.00 0.00 0.00 3.59
525 2521 4.694760 TGTTCTGGGATCGATGAATGAT 57.305 40.909 0.54 0.00 0.00 2.45
550 2546 4.087892 GGCTGCTCGCTTCCAGGA 62.088 66.667 0.00 0.00 39.13 3.86
574 2570 0.980423 TCACCCGATCAACACATCCA 59.020 50.000 0.00 0.00 0.00 3.41
577 2573 2.754552 CACCCGATCAACACATCCAATT 59.245 45.455 0.00 0.00 0.00 2.32
716 2723 0.663568 CAGAGTGCTTTGCTTGCAGC 60.664 55.000 0.00 1.70 41.41 5.25
743 2750 2.747855 CGGGAGGAGCAAAGGCAC 60.748 66.667 0.00 0.00 44.61 5.01
746 2753 0.613012 GGGAGGAGCAAAGGCACATT 60.613 55.000 0.00 0.00 44.61 2.71
833 2840 1.474077 GCCAGACTGTAAAATGCAGGG 59.526 52.381 0.93 0.00 38.22 4.45
856 2866 0.257039 CCCATTCCCCAACTCCTCTG 59.743 60.000 0.00 0.00 0.00 3.35
871 2881 6.798427 ACTCCTCTGTTCATCAGCTATAAA 57.202 37.500 0.00 0.00 43.32 1.40
878 2888 4.201773 TGTTCATCAGCTATAAAAACGCGG 60.202 41.667 12.47 0.00 0.00 6.46
910 2920 1.056660 TTCCCTCCGGCATTATCTCC 58.943 55.000 0.00 0.00 0.00 3.71
939 2949 3.997064 CTCGCCTCCTCCGCAGTTG 62.997 68.421 0.00 0.00 0.00 3.16
1131 3158 1.974343 AGCTGTCTCCTCGTCGCTT 60.974 57.895 0.00 0.00 0.00 4.68
1201 3230 1.541310 CCACTGAGTTGGCCGAGGTA 61.541 60.000 0.00 0.00 0.00 3.08
1371 3429 2.037251 AGTCGATGCTGTTAGTGTTGGT 59.963 45.455 0.00 0.00 0.00 3.67
1443 3501 9.107177 AGATATTTGTCAGAATTTGCTCTACTG 57.893 33.333 0.00 0.00 0.00 2.74
1576 3672 2.433868 TCGACACCTTCTTTTCTCGG 57.566 50.000 0.00 0.00 0.00 4.63
1596 3692 3.616821 CGGATCATTTCTGCACGAAGTTA 59.383 43.478 0.00 0.00 41.61 2.24
1995 4094 1.803366 GCCTCGTTCCGTATCCCGAT 61.803 60.000 0.00 0.00 39.56 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.653320 TCCGCATGAACTTAACTACTTTGATT 59.347 34.615 0.00 0.00 0.00 2.57
1 2 6.092259 GTCCGCATGAACTTAACTACTTTGAT 59.908 38.462 0.00 0.00 0.00 2.57
2 3 5.407387 GTCCGCATGAACTTAACTACTTTGA 59.593 40.000 0.00 0.00 0.00 2.69
3 4 5.408604 AGTCCGCATGAACTTAACTACTTTG 59.591 40.000 0.00 0.00 0.00 2.77
4 5 5.548406 AGTCCGCATGAACTTAACTACTTT 58.452 37.500 0.00 0.00 0.00 2.66
5 6 5.148651 AGTCCGCATGAACTTAACTACTT 57.851 39.130 0.00 0.00 0.00 2.24
6 7 4.803098 AGTCCGCATGAACTTAACTACT 57.197 40.909 0.00 0.00 0.00 2.57
7 8 6.270815 TCATAGTCCGCATGAACTTAACTAC 58.729 40.000 0.00 0.00 29.55 2.73
8 9 6.459670 TCATAGTCCGCATGAACTTAACTA 57.540 37.500 0.00 0.00 29.55 2.24
9 10 5.339008 TCATAGTCCGCATGAACTTAACT 57.661 39.130 0.00 0.00 29.55 2.24
10 11 7.307219 GGTTATCATAGTCCGCATGAACTTAAC 60.307 40.741 0.00 2.72 36.08 2.01
11 12 6.704493 GGTTATCATAGTCCGCATGAACTTAA 59.296 38.462 0.00 0.00 36.08 1.85
12 13 6.041637 AGGTTATCATAGTCCGCATGAACTTA 59.958 38.462 0.00 0.00 36.08 2.24
13 14 5.057149 GGTTATCATAGTCCGCATGAACTT 58.943 41.667 0.00 0.00 36.08 2.66
14 15 4.345257 AGGTTATCATAGTCCGCATGAACT 59.655 41.667 0.00 0.00 36.08 3.01
15 16 4.632153 AGGTTATCATAGTCCGCATGAAC 58.368 43.478 0.00 0.00 36.08 3.18
16 17 4.955811 AGGTTATCATAGTCCGCATGAA 57.044 40.909 0.00 0.00 36.08 2.57
17 18 4.219944 GGTAGGTTATCATAGTCCGCATGA 59.780 45.833 0.00 0.00 36.86 3.07
18 19 4.495422 GGTAGGTTATCATAGTCCGCATG 58.505 47.826 0.00 0.00 0.00 4.06
19 20 3.192844 CGGTAGGTTATCATAGTCCGCAT 59.807 47.826 0.00 0.00 0.00 4.73
20 21 2.555325 CGGTAGGTTATCATAGTCCGCA 59.445 50.000 0.00 0.00 0.00 5.69
21 22 3.213249 CGGTAGGTTATCATAGTCCGC 57.787 52.381 0.00 0.00 0.00 5.54
22 23 2.094854 GGCGGTAGGTTATCATAGTCCG 60.095 54.545 0.00 0.00 39.71 4.79
23 24 2.895404 TGGCGGTAGGTTATCATAGTCC 59.105 50.000 0.00 0.00 0.00 3.85
24 25 3.056749 CCTGGCGGTAGGTTATCATAGTC 60.057 52.174 0.00 0.00 32.99 2.59
25 26 2.897969 CCTGGCGGTAGGTTATCATAGT 59.102 50.000 0.00 0.00 32.99 2.12
26 27 2.233922 CCCTGGCGGTAGGTTATCATAG 59.766 54.545 0.00 0.00 36.02 2.23
27 28 2.253610 CCCTGGCGGTAGGTTATCATA 58.746 52.381 0.00 0.00 36.02 2.15
28 29 1.056660 CCCTGGCGGTAGGTTATCAT 58.943 55.000 0.00 0.00 36.02 2.45
29 30 1.692173 GCCCTGGCGGTAGGTTATCA 61.692 60.000 0.00 0.00 36.02 2.15
30 31 1.070957 GCCCTGGCGGTAGGTTATC 59.929 63.158 0.00 0.00 36.02 1.75
31 32 1.060163 ATGCCCTGGCGGTAGGTTAT 61.060 55.000 3.32 0.00 45.51 1.89
32 33 1.276140 AATGCCCTGGCGGTAGGTTA 61.276 55.000 3.32 0.00 45.51 2.85
33 34 2.552231 GAATGCCCTGGCGGTAGGTT 62.552 60.000 3.32 0.00 45.51 3.50
34 35 3.015145 AATGCCCTGGCGGTAGGT 61.015 61.111 3.32 0.00 45.51 3.08
35 36 2.203209 GAATGCCCTGGCGGTAGG 60.203 66.667 3.32 0.00 45.51 3.18
36 37 2.588877 CGAATGCCCTGGCGGTAG 60.589 66.667 3.32 0.00 45.51 3.18
37 38 4.169696 CCGAATGCCCTGGCGGTA 62.170 66.667 3.32 0.00 45.51 4.02
42 43 4.169696 TACCGCCGAATGCCCTGG 62.170 66.667 0.00 0.00 36.24 4.45
43 44 2.588877 CTACCGCCGAATGCCCTG 60.589 66.667 0.00 0.00 36.24 4.45
44 45 3.861797 CCTACCGCCGAATGCCCT 61.862 66.667 0.00 0.00 36.24 5.19
45 46 3.692370 AACCTACCGCCGAATGCCC 62.692 63.158 0.00 0.00 36.24 5.36
46 47 0.462403 TAAACCTACCGCCGAATGCC 60.462 55.000 0.00 0.00 36.24 4.40
47 48 1.263217 CATAAACCTACCGCCGAATGC 59.737 52.381 0.00 0.00 0.00 3.56
48 49 2.286833 CACATAAACCTACCGCCGAATG 59.713 50.000 0.00 0.00 0.00 2.67
49 50 2.557317 CACATAAACCTACCGCCGAAT 58.443 47.619 0.00 0.00 0.00 3.34
50 51 1.405797 CCACATAAACCTACCGCCGAA 60.406 52.381 0.00 0.00 0.00 4.30
51 52 0.176219 CCACATAAACCTACCGCCGA 59.824 55.000 0.00 0.00 0.00 5.54
52 53 0.812412 CCCACATAAACCTACCGCCG 60.812 60.000 0.00 0.00 0.00 6.46
53 54 1.099295 GCCCACATAAACCTACCGCC 61.099 60.000 0.00 0.00 0.00 6.13
54 55 0.107361 AGCCCACATAAACCTACCGC 60.107 55.000 0.00 0.00 0.00 5.68
55 56 2.484241 GGTAGCCCACATAAACCTACCG 60.484 54.545 0.00 0.00 38.82 4.02
56 57 2.484241 CGGTAGCCCACATAAACCTACC 60.484 54.545 0.00 0.00 42.80 3.18
57 58 2.830104 CGGTAGCCCACATAAACCTAC 58.170 52.381 0.00 0.00 0.00 3.18
58 59 1.139455 GCGGTAGCCCACATAAACCTA 59.861 52.381 0.00 0.00 37.42 3.08
59 60 0.107361 GCGGTAGCCCACATAAACCT 60.107 55.000 0.00 0.00 37.42 3.50
60 61 2.400911 GCGGTAGCCCACATAAACC 58.599 57.895 0.00 0.00 37.42 3.27
71 72 2.047560 AAAGTCCACGGCGGTAGC 60.048 61.111 13.24 0.00 44.18 3.58
72 73 1.740296 CCAAAGTCCACGGCGGTAG 60.740 63.158 13.24 0.00 35.57 3.18
73 74 2.344500 CCAAAGTCCACGGCGGTA 59.656 61.111 13.24 0.00 35.57 4.02
79 80 1.740296 CCTACCGCCAAAGTCCACG 60.740 63.158 0.00 0.00 0.00 4.94
80 81 0.609662 TACCTACCGCCAAAGTCCAC 59.390 55.000 0.00 0.00 0.00 4.02
81 82 0.609662 GTACCTACCGCCAAAGTCCA 59.390 55.000 0.00 0.00 0.00 4.02
82 83 0.459063 CGTACCTACCGCCAAAGTCC 60.459 60.000 0.00 0.00 0.00 3.85
83 84 0.244721 ACGTACCTACCGCCAAAGTC 59.755 55.000 0.00 0.00 0.00 3.01
84 85 1.544724 TACGTACCTACCGCCAAAGT 58.455 50.000 0.00 0.00 0.00 2.66
85 86 2.533266 CTTACGTACCTACCGCCAAAG 58.467 52.381 0.00 0.00 0.00 2.77
86 87 1.404047 GCTTACGTACCTACCGCCAAA 60.404 52.381 0.00 0.00 0.00 3.28
87 88 0.173255 GCTTACGTACCTACCGCCAA 59.827 55.000 0.00 0.00 0.00 4.52
88 89 0.964860 TGCTTACGTACCTACCGCCA 60.965 55.000 0.00 0.00 0.00 5.69
89 90 0.248784 CTGCTTACGTACCTACCGCC 60.249 60.000 0.00 0.00 0.00 6.13
90 91 0.869028 GCTGCTTACGTACCTACCGC 60.869 60.000 0.00 0.00 0.00 5.68
91 92 0.248784 GGCTGCTTACGTACCTACCG 60.249 60.000 0.00 0.00 0.00 4.02
92 93 0.248784 CGGCTGCTTACGTACCTACC 60.249 60.000 0.00 0.00 0.00 3.18
93 94 0.453390 ACGGCTGCTTACGTACCTAC 59.547 55.000 0.00 0.00 42.15 3.18
94 95 1.176527 AACGGCTGCTTACGTACCTA 58.823 50.000 0.00 0.00 43.31 3.08
95 96 1.176527 TAACGGCTGCTTACGTACCT 58.823 50.000 0.00 0.00 43.31 3.08
96 97 1.655597 GTTAACGGCTGCTTACGTACC 59.344 52.381 0.00 0.00 43.31 3.34
97 98 1.655597 GGTTAACGGCTGCTTACGTAC 59.344 52.381 0.00 0.00 43.31 3.67
98 99 1.732077 CGGTTAACGGCTGCTTACGTA 60.732 52.381 0.00 0.00 43.31 3.57
99 100 1.010419 CGGTTAACGGCTGCTTACGT 61.010 55.000 0.00 0.00 46.48 3.57
100 101 1.705727 CGGTTAACGGCTGCTTACG 59.294 57.895 0.00 0.00 39.42 3.18
127 128 2.264794 GGTAGGTGTGCCTGACGG 59.735 66.667 0.00 0.00 46.47 4.79
128 129 2.126071 CGGTAGGTGTGCCTGACG 60.126 66.667 0.00 0.00 46.47 4.35
129 130 2.434359 GCGGTAGGTGTGCCTGAC 60.434 66.667 0.00 0.00 46.47 3.51
130 131 3.702048 GGCGGTAGGTGTGCCTGA 61.702 66.667 0.00 0.00 46.47 3.86
134 135 4.382320 TTCCGGCGGTAGGTGTGC 62.382 66.667 27.32 0.00 0.00 4.57
135 136 2.433664 GTTCCGGCGGTAGGTGTG 60.434 66.667 27.32 0.00 0.00 3.82
136 137 3.698820 GGTTCCGGCGGTAGGTGT 61.699 66.667 27.32 0.00 0.00 4.16
137 138 3.387947 AGGTTCCGGCGGTAGGTG 61.388 66.667 27.32 0.00 0.00 4.00
138 139 3.387947 CAGGTTCCGGCGGTAGGT 61.388 66.667 27.32 6.82 0.00 3.08
139 140 3.387947 ACAGGTTCCGGCGGTAGG 61.388 66.667 27.32 14.25 0.00 3.18
140 141 2.125673 CACAGGTTCCGGCGGTAG 60.126 66.667 27.32 14.21 0.00 3.18
141 142 3.697747 CCACAGGTTCCGGCGGTA 61.698 66.667 27.32 14.78 0.00 4.02
146 147 3.659089 CTACCGCCACAGGTTCCGG 62.659 68.421 0.00 0.00 43.00 5.14
147 148 2.125673 CTACCGCCACAGGTTCCG 60.126 66.667 0.00 0.00 43.00 4.30
148 149 1.079336 GTCTACCGCCACAGGTTCC 60.079 63.158 0.00 0.00 43.00 3.62
149 150 0.389948 CAGTCTACCGCCACAGGTTC 60.390 60.000 0.00 0.00 43.00 3.62
150 151 1.119574 ACAGTCTACCGCCACAGGTT 61.120 55.000 0.00 0.00 43.00 3.50
152 153 1.079819 CACAGTCTACCGCCACAGG 60.080 63.158 0.00 0.00 37.30 4.00
153 154 1.738099 GCACAGTCTACCGCCACAG 60.738 63.158 0.00 0.00 0.00 3.66
154 155 2.034048 TTGCACAGTCTACCGCCACA 62.034 55.000 0.00 0.00 0.00 4.17
155 156 0.673644 ATTGCACAGTCTACCGCCAC 60.674 55.000 0.00 0.00 0.00 5.01
156 157 0.391130 GATTGCACAGTCTACCGCCA 60.391 55.000 0.00 0.00 0.00 5.69
157 158 1.090052 GGATTGCACAGTCTACCGCC 61.090 60.000 0.00 0.00 0.00 6.13
158 159 0.108138 AGGATTGCACAGTCTACCGC 60.108 55.000 0.00 0.00 0.00 5.68
159 160 2.427453 AGTAGGATTGCACAGTCTACCG 59.573 50.000 10.30 0.00 32.95 4.02
160 161 3.195825 ACAGTAGGATTGCACAGTCTACC 59.804 47.826 10.30 0.00 32.95 3.18
161 162 4.425520 GACAGTAGGATTGCACAGTCTAC 58.574 47.826 0.00 0.00 30.87 2.59
162 163 3.447586 GGACAGTAGGATTGCACAGTCTA 59.552 47.826 0.00 0.00 33.23 2.59
163 164 2.234908 GGACAGTAGGATTGCACAGTCT 59.765 50.000 0.00 0.00 33.23 3.24
164 165 2.622436 GGACAGTAGGATTGCACAGTC 58.378 52.381 0.00 0.00 32.24 3.51
165 166 1.066858 CGGACAGTAGGATTGCACAGT 60.067 52.381 0.00 0.00 0.00 3.55
166 167 1.204704 TCGGACAGTAGGATTGCACAG 59.795 52.381 0.00 0.00 0.00 3.66
167 168 1.204704 CTCGGACAGTAGGATTGCACA 59.795 52.381 0.00 0.00 0.00 4.57
168 169 1.471676 CCTCGGACAGTAGGATTGCAC 60.472 57.143 0.00 0.00 34.58 4.57
169 170 0.824109 CCTCGGACAGTAGGATTGCA 59.176 55.000 0.00 0.00 34.58 4.08
170 171 0.105039 CCCTCGGACAGTAGGATTGC 59.895 60.000 0.00 0.00 34.58 3.56
171 172 1.409427 GACCCTCGGACAGTAGGATTG 59.591 57.143 0.00 0.00 34.58 2.67
172 173 1.288335 AGACCCTCGGACAGTAGGATT 59.712 52.381 0.00 0.00 34.58 3.01
173 174 0.927767 AGACCCTCGGACAGTAGGAT 59.072 55.000 0.00 0.00 34.58 3.24
174 175 0.034380 CAGACCCTCGGACAGTAGGA 60.034 60.000 0.00 0.00 34.58 2.94
175 176 1.038130 CCAGACCCTCGGACAGTAGG 61.038 65.000 0.00 0.00 0.00 3.18
176 177 1.668101 GCCAGACCCTCGGACAGTAG 61.668 65.000 0.00 0.00 0.00 2.57
177 178 1.681327 GCCAGACCCTCGGACAGTA 60.681 63.158 0.00 0.00 0.00 2.74
178 179 2.997897 GCCAGACCCTCGGACAGT 60.998 66.667 0.00 0.00 0.00 3.55
179 180 4.135153 CGCCAGACCCTCGGACAG 62.135 72.222 0.00 0.00 0.00 3.51
180 181 2.561467 TATCGCCAGACCCTCGGACA 62.561 60.000 0.00 0.00 0.00 4.02
181 182 1.797211 CTATCGCCAGACCCTCGGAC 61.797 65.000 0.00 0.00 0.00 4.79
182 183 1.528542 CTATCGCCAGACCCTCGGA 60.529 63.158 0.00 0.00 0.00 4.55
183 184 0.536687 TACTATCGCCAGACCCTCGG 60.537 60.000 0.00 0.00 0.00 4.63
184 185 1.315690 TTACTATCGCCAGACCCTCG 58.684 55.000 0.00 0.00 0.00 4.63
185 186 3.492829 CCTTTTACTATCGCCAGACCCTC 60.493 52.174 0.00 0.00 0.00 4.30
186 187 2.434702 CCTTTTACTATCGCCAGACCCT 59.565 50.000 0.00 0.00 0.00 4.34
187 188 2.484947 CCCTTTTACTATCGCCAGACCC 60.485 54.545 0.00 0.00 0.00 4.46
188 189 2.169978 ACCCTTTTACTATCGCCAGACC 59.830 50.000 0.00 0.00 0.00 3.85
189 190 3.118884 TGACCCTTTTACTATCGCCAGAC 60.119 47.826 0.00 0.00 0.00 3.51
190 191 3.101437 TGACCCTTTTACTATCGCCAGA 58.899 45.455 0.00 0.00 0.00 3.86
191 192 3.536956 TGACCCTTTTACTATCGCCAG 57.463 47.619 0.00 0.00 0.00 4.85
192 193 3.985019 TTGACCCTTTTACTATCGCCA 57.015 42.857 0.00 0.00 0.00 5.69
193 194 5.123936 AGATTTGACCCTTTTACTATCGCC 58.876 41.667 0.00 0.00 0.00 5.54
194 195 6.315393 TCAAGATTTGACCCTTTTACTATCGC 59.685 38.462 0.00 0.00 34.08 4.58
195 196 7.843490 TCAAGATTTGACCCTTTTACTATCG 57.157 36.000 0.00 0.00 34.08 2.92
198 199 9.362151 ACATTTCAAGATTTGACCCTTTTACTA 57.638 29.630 0.00 0.00 39.87 1.82
199 200 8.250143 ACATTTCAAGATTTGACCCTTTTACT 57.750 30.769 0.00 0.00 39.87 2.24
200 201 8.887036 AACATTTCAAGATTTGACCCTTTTAC 57.113 30.769 0.00 0.00 39.87 2.01
201 202 9.898152 AAAACATTTCAAGATTTGACCCTTTTA 57.102 25.926 0.00 0.00 39.87 1.52
202 203 8.806429 AAAACATTTCAAGATTTGACCCTTTT 57.194 26.923 0.00 0.00 39.87 2.27
203 204 8.046107 TGAAAACATTTCAAGATTTGACCCTTT 58.954 29.630 3.18 0.00 39.87 3.11
204 205 7.563906 TGAAAACATTTCAAGATTTGACCCTT 58.436 30.769 3.18 0.00 39.87 3.95
205 206 7.123355 TGAAAACATTTCAAGATTTGACCCT 57.877 32.000 3.18 0.00 39.87 4.34
206 207 7.784633 TTGAAAACATTTCAAGATTTGACCC 57.215 32.000 12.80 0.00 39.87 4.46
207 208 8.882736 AGTTTGAAAACATTTCAAGATTTGACC 58.117 29.630 15.41 2.53 41.30 4.02
208 209 9.693157 CAGTTTGAAAACATTTCAAGATTTGAC 57.307 29.630 15.41 11.07 41.30 3.18
209 210 9.650539 TCAGTTTGAAAACATTTCAAGATTTGA 57.349 25.926 15.41 14.15 41.30 2.69
226 227 7.912056 ATTCGAGATCTGATTTCAGTTTGAA 57.088 32.000 0.00 9.73 44.12 2.69
227 228 7.912056 AATTCGAGATCTGATTTCAGTTTGA 57.088 32.000 0.00 2.57 44.12 2.69
228 229 8.019669 ACAAATTCGAGATCTGATTTCAGTTTG 58.980 33.333 18.03 18.03 44.12 2.93
229 230 8.103948 ACAAATTCGAGATCTGATTTCAGTTT 57.896 30.769 0.00 3.76 44.12 2.66
230 231 7.678947 ACAAATTCGAGATCTGATTTCAGTT 57.321 32.000 0.00 0.00 44.12 3.16
231 232 7.678947 AACAAATTCGAGATCTGATTTCAGT 57.321 32.000 0.00 0.00 44.12 3.41
232 233 8.232513 TCAAACAAATTCGAGATCTGATTTCAG 58.767 33.333 0.00 0.97 45.08 3.02
233 234 8.017373 GTCAAACAAATTCGAGATCTGATTTCA 58.983 33.333 0.00 0.00 0.00 2.69
234 235 8.017373 TGTCAAACAAATTCGAGATCTGATTTC 58.983 33.333 0.00 0.00 0.00 2.17
235 236 7.874940 TGTCAAACAAATTCGAGATCTGATTT 58.125 30.769 0.00 1.24 0.00 2.17
236 237 7.439157 TGTCAAACAAATTCGAGATCTGATT 57.561 32.000 0.00 0.00 0.00 2.57
237 238 7.439157 TTGTCAAACAAATTCGAGATCTGAT 57.561 32.000 0.00 0.00 34.76 2.90
238 239 6.859420 TTGTCAAACAAATTCGAGATCTGA 57.141 33.333 0.00 0.00 34.76 3.27
239 240 7.113965 CCTTTTGTCAAACAAATTCGAGATCTG 59.886 37.037 0.00 0.00 46.17 2.90
240 241 7.141363 CCTTTTGTCAAACAAATTCGAGATCT 58.859 34.615 6.12 0.00 46.17 2.75
241 242 6.363357 CCCTTTTGTCAAACAAATTCGAGATC 59.637 38.462 6.12 0.00 46.17 2.75
242 243 6.183360 ACCCTTTTGTCAAACAAATTCGAGAT 60.183 34.615 6.12 0.00 46.17 2.75
243 244 5.126384 ACCCTTTTGTCAAACAAATTCGAGA 59.874 36.000 6.12 0.00 46.17 4.04
244 245 5.348164 ACCCTTTTGTCAAACAAATTCGAG 58.652 37.500 6.12 1.60 46.17 4.04
245 246 5.105716 TGACCCTTTTGTCAAACAAATTCGA 60.106 36.000 6.12 0.00 46.17 3.71
246 247 5.105752 TGACCCTTTTGTCAAACAAATTCG 58.894 37.500 6.12 0.51 46.17 3.34
256 257 2.164624 CCGTGTTTTGACCCTTTTGTCA 59.835 45.455 0.00 0.00 43.26 3.58
257 258 2.424246 TCCGTGTTTTGACCCTTTTGTC 59.576 45.455 0.00 0.00 35.77 3.18
258 259 2.448453 TCCGTGTTTTGACCCTTTTGT 58.552 42.857 0.00 0.00 0.00 2.83
259 260 3.512033 TTCCGTGTTTTGACCCTTTTG 57.488 42.857 0.00 0.00 0.00 2.44
260 261 4.746535 AATTCCGTGTTTTGACCCTTTT 57.253 36.364 0.00 0.00 0.00 2.27
261 262 4.438148 CAAATTCCGTGTTTTGACCCTTT 58.562 39.130 0.00 0.00 35.34 3.11
262 263 3.181470 CCAAATTCCGTGTTTTGACCCTT 60.181 43.478 0.00 0.00 35.34 3.95
263 264 2.364002 CCAAATTCCGTGTTTTGACCCT 59.636 45.455 0.00 0.00 35.34 4.34
264 265 2.749776 CCAAATTCCGTGTTTTGACCC 58.250 47.619 0.00 0.00 35.34 4.46
265 266 2.131972 GCCAAATTCCGTGTTTTGACC 58.868 47.619 0.00 0.00 35.34 4.02
266 267 2.131972 GGCCAAATTCCGTGTTTTGAC 58.868 47.619 0.00 0.00 35.34 3.18
267 268 2.035321 GAGGCCAAATTCCGTGTTTTGA 59.965 45.455 5.01 0.00 35.34 2.69
268 269 2.035832 AGAGGCCAAATTCCGTGTTTTG 59.964 45.455 5.01 0.00 33.58 2.44
269 270 2.316108 AGAGGCCAAATTCCGTGTTTT 58.684 42.857 5.01 0.00 0.00 2.43
270 271 1.995376 AGAGGCCAAATTCCGTGTTT 58.005 45.000 5.01 0.00 0.00 2.83
271 272 1.886542 GAAGAGGCCAAATTCCGTGTT 59.113 47.619 5.01 0.00 0.00 3.32
272 273 1.534729 GAAGAGGCCAAATTCCGTGT 58.465 50.000 5.01 0.00 0.00 4.49
273 274 0.811281 GGAAGAGGCCAAATTCCGTG 59.189 55.000 15.40 0.00 33.67 4.94
274 275 3.266240 GGAAGAGGCCAAATTCCGT 57.734 52.632 15.40 0.00 33.67 4.69
276 277 2.493547 CCGGAAGAGGCCAAATTCC 58.506 57.895 18.86 18.86 39.31 3.01
285 286 1.153349 GCCTAACAGCCGGAAGAGG 60.153 63.158 5.05 4.65 0.00 3.69
286 287 0.179000 ATGCCTAACAGCCGGAAGAG 59.821 55.000 5.05 0.00 0.00 2.85
348 737 3.312421 AGTTGTGACCAAACATCTGTTCG 59.688 43.478 0.00 0.00 37.25 3.95
350 739 4.096382 GTGAGTTGTGACCAAACATCTGTT 59.904 41.667 0.00 0.00 40.50 3.16
353 742 3.884895 TGTGAGTTGTGACCAAACATCT 58.115 40.909 0.00 0.00 33.74 2.90
358 747 4.873827 GTCTACTTGTGAGTTGTGACCAAA 59.126 41.667 0.00 0.00 37.33 3.28
369 758 6.306837 CGCTTTCTCTTTAGTCTACTTGTGAG 59.693 42.308 0.00 0.00 0.00 3.51
371 760 6.088350 GTCGCTTTCTCTTTAGTCTACTTGTG 59.912 42.308 0.00 0.00 0.00 3.33
373 762 5.573669 GGTCGCTTTCTCTTTAGTCTACTTG 59.426 44.000 0.00 0.00 0.00 3.16
374 763 5.619533 CGGTCGCTTTCTCTTTAGTCTACTT 60.620 44.000 0.00 0.00 0.00 2.24
375 764 4.142643 CGGTCGCTTTCTCTTTAGTCTACT 60.143 45.833 0.00 0.00 0.00 2.57
376 765 4.097012 CGGTCGCTTTCTCTTTAGTCTAC 58.903 47.826 0.00 0.00 0.00 2.59
377 766 3.755378 ACGGTCGCTTTCTCTTTAGTCTA 59.245 43.478 0.00 0.00 0.00 2.59
378 767 2.557490 ACGGTCGCTTTCTCTTTAGTCT 59.443 45.455 0.00 0.00 0.00 3.24
379 768 2.662156 CACGGTCGCTTTCTCTTTAGTC 59.338 50.000 0.00 0.00 0.00 2.59
380 769 2.609737 CCACGGTCGCTTTCTCTTTAGT 60.610 50.000 0.00 0.00 0.00 2.24
381 770 1.993370 CCACGGTCGCTTTCTCTTTAG 59.007 52.381 0.00 0.00 0.00 1.85
382 771 1.938016 GCCACGGTCGCTTTCTCTTTA 60.938 52.381 0.00 0.00 0.00 1.85
383 772 1.228657 GCCACGGTCGCTTTCTCTTT 61.229 55.000 0.00 0.00 0.00 2.52
384 773 1.668151 GCCACGGTCGCTTTCTCTT 60.668 57.895 0.00 0.00 0.00 2.85
385 774 2.048127 GCCACGGTCGCTTTCTCT 60.048 61.111 0.00 0.00 0.00 3.10
386 775 1.627550 GAAGCCACGGTCGCTTTCTC 61.628 60.000 14.08 0.00 46.37 2.87
387 776 1.668151 GAAGCCACGGTCGCTTTCT 60.668 57.895 14.08 0.00 46.37 2.52
388 777 1.503818 TTGAAGCCACGGTCGCTTTC 61.504 55.000 14.08 8.30 46.37 2.62
389 778 1.507141 CTTGAAGCCACGGTCGCTTT 61.507 55.000 14.08 0.00 46.37 3.51
391 780 1.812686 TACTTGAAGCCACGGTCGCT 61.813 55.000 0.00 0.00 38.53 4.93
392 781 0.947180 TTACTTGAAGCCACGGTCGC 60.947 55.000 0.00 0.00 0.00 5.19
393 782 1.504359 TTTACTTGAAGCCACGGTCG 58.496 50.000 0.00 0.00 0.00 4.79
394 783 3.335579 AGATTTACTTGAAGCCACGGTC 58.664 45.455 0.00 0.00 0.00 4.79
453 842 6.805016 TCAGAAAGAAAGAGGAGCATATCT 57.195 37.500 0.00 0.00 0.00 1.98
491 2487 1.746615 AGAACAAGCGCCGCATCAT 60.747 52.632 13.36 0.00 0.00 2.45
504 2500 4.694760 ATCATTCATCGATCCCAGAACA 57.305 40.909 0.00 0.00 0.00 3.18
509 2505 2.549329 CGCAAATCATTCATCGATCCCA 59.451 45.455 0.00 0.00 0.00 4.37
518 2514 0.171679 CAGCCAGCGCAAATCATTCA 59.828 50.000 11.47 0.00 37.52 2.57
550 2546 2.244695 TGTGTTGATCGGGTGACTAGT 58.755 47.619 0.00 0.00 0.00 2.57
574 2570 2.960129 GTCGCGCGGATCGGAATT 60.960 61.111 31.69 0.00 38.94 2.17
577 2573 4.201679 AATGTCGCGCGGATCGGA 62.202 61.111 31.69 6.17 38.94 4.55
670 2677 3.353557 TGCGACTAGTGAGTTGGAGTAT 58.646 45.455 0.00 0.00 37.53 2.12
743 2750 3.197766 TGTAGGAGTAGGACCAGCAAATG 59.802 47.826 0.00 0.00 0.00 2.32
746 2753 2.176889 GTGTAGGAGTAGGACCAGCAA 58.823 52.381 0.00 0.00 0.00 3.91
833 2840 1.682344 GAGTTGGGGAATGGGGTGC 60.682 63.158 0.00 0.00 0.00 5.01
856 2866 4.271687 CCGCGTTTTTATAGCTGATGAAC 58.728 43.478 4.92 0.00 0.00 3.18
878 2888 2.034048 GAGGGAATCAGGACGAGGCC 62.034 65.000 0.00 0.00 0.00 5.19
910 2920 1.373497 GAGGCGAGTGAGTGTGTGG 60.373 63.158 0.00 0.00 0.00 4.17
952 2962 1.020861 CAGATGCGGCTGTGCTACAA 61.021 55.000 0.00 0.00 35.36 2.41
1371 3429 7.093354 TGTAGCACATGAAAAGAAAAACACAA 58.907 30.769 0.00 0.00 0.00 3.33
1443 3501 5.059833 GGGACCAATACAGAGAACATGATC 58.940 45.833 0.00 0.00 0.00 2.92
1576 3672 5.106712 TGGTTAACTTCGTGCAGAAATGATC 60.107 40.000 5.42 0.00 38.57 2.92
1596 3692 0.596082 CGCCCGATGAAAAACTGGTT 59.404 50.000 0.00 0.00 0.00 3.67
1659 3755 3.831323 TGGGATGCAGAAAAACAGAGAA 58.169 40.909 0.00 0.00 0.00 2.87
1660 3756 3.507162 TGGGATGCAGAAAAACAGAGA 57.493 42.857 0.00 0.00 0.00 3.10
1661 3757 3.318839 TGTTGGGATGCAGAAAAACAGAG 59.681 43.478 0.00 0.00 0.00 3.35
1662 3758 3.295093 TGTTGGGATGCAGAAAAACAGA 58.705 40.909 0.00 0.00 0.00 3.41
1663 3759 3.318839 TCTGTTGGGATGCAGAAAAACAG 59.681 43.478 20.64 20.64 43.62 3.16
1711 3808 4.101790 AAGTTGCCGCGGCGATTG 62.102 61.111 40.71 8.56 45.51 2.67
1995 4094 1.276622 GGGCTCCCACTTCTACTTCA 58.723 55.000 0.00 0.00 35.81 3.02
2131 4230 3.628646 GACCATCAACAGCCCCGCT 62.629 63.158 0.00 0.00 40.77 5.52


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

AutoCloner maintained by Alex Coulton.