Multiple sequence alignment - TraesCS3B01G127000

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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 TraesCS3B01G127000 chr3B 100.000 2162 0 0 927 3088 104324958 104327119 0.000000e+00 3993.0
1 TraesCS3B01G127000 chr3B 100.000 544 0 0 1 544 104324032 104324575 0.000000e+00 1005.0
2 TraesCS3B01G127000 chr3B 93.243 148 9 1 55 202 600913034 600912888 1.860000e-52 217.0
3 TraesCS3B01G127000 chr3B 81.592 201 35 2 2624 2823 788737230 788737429 6.850000e-37 165.0
4 TraesCS3B01G127000 chr3B 82.514 183 30 2 2642 2823 788389783 788389602 3.190000e-35 159.0
5 TraesCS3B01G127000 chr3B 93.069 101 7 0 293 393 744600870 744600770 6.900000e-32 148.0
6 TraesCS3B01G127000 chr3B 92.727 55 4 0 2 56 828779641 828779587 2.550000e-11 80.5
7 TraesCS3B01G127000 chr2B 97.498 2118 42 8 972 3088 794920849 794922956 0.000000e+00 3607.0
8 TraesCS3B01G127000 chr2B 97.402 2117 44 5 972 3088 794926828 794928933 0.000000e+00 3594.0
9 TraesCS3B01G127000 chr2B 97.355 2117 45 7 972 3088 794914872 794916977 0.000000e+00 3589.0
10 TraesCS3B01G127000 chr2B 93.789 161 10 0 384 544 794920564 794920724 3.080000e-60 243.0
11 TraesCS3B01G127000 chr2B 93.789 161 10 0 384 544 794926543 794926703 3.080000e-60 243.0
12 TraesCS3B01G127000 chr2B 93.168 161 11 0 384 544 794914587 794914747 1.430000e-58 237.0
13 TraesCS3B01G127000 chr2B 91.275 149 12 1 293 440 601432111 601432259 5.220000e-48 202.0
14 TraesCS3B01G127000 chr2B 95.876 97 4 0 293 389 794920197 794920293 1.150000e-34 158.0
15 TraesCS3B01G127000 chr2B 100.000 45 0 0 927 971 794926759 794926803 1.970000e-12 84.2
16 TraesCS3B01G127000 chr2B 97.778 45 1 0 927 971 794920780 794920824 9.180000e-11 78.7
17 TraesCS3B01G127000 chr2B 100.000 39 0 0 927 965 794914803 794914841 4.270000e-09 73.1
18 TraesCS3B01G127000 chr4A 82.107 1291 188 22 1800 3088 375778943 375777694 0.000000e+00 1064.0
19 TraesCS3B01G127000 chr2D 80.680 1294 217 25 1583 2857 147771246 147772525 0.000000e+00 974.0
20 TraesCS3B01G127000 chr2D 82.906 117 20 0 2680 2796 137028262 137028378 4.210000e-19 106.0
21 TraesCS3B01G127000 chr2D 100.000 28 0 0 294 321 2314132 2314159 6.000000e-03 52.8
22 TraesCS3B01G127000 chr5A 85.045 662 92 6 1945 2604 437055446 437054790 0.000000e+00 667.0
23 TraesCS3B01G127000 chr5B 90.132 152 13 2 293 443 543285347 543285497 2.430000e-46 196.0
24 TraesCS3B01G127000 chr4B 89.542 153 15 1 292 443 95456171 95456019 3.140000e-45 193.0
25 TraesCS3B01G127000 chrUn 81.592 201 35 2 2624 2823 233630030 233630229 6.850000e-37 165.0
26 TraesCS3B01G127000 chr6B 84.800 125 15 3 2681 2801 2044891 2045015 4.180000e-24 122.0
27 TraesCS3B01G127000 chr3A 98.182 55 1 0 2 56 745502944 745502998 2.530000e-16 97.1
28 TraesCS3B01G127000 chr3A 84.058 69 9 2 294 361 64324673 64324606 7.150000e-07 65.8
29 TraesCS3B01G127000 chr7B 84.286 70 9 2 293 361 616430952 616430884 1.990000e-07 67.6
30 TraesCS3B01G127000 chr1D 82.857 70 10 2 293 361 31233796 31233864 9.250000e-06 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G127000 chr3B 104324032 104327119 3087 False 2499.0 3993 100.0000 1 3088 2 chr3B.!!$F2 3087
1 TraesCS3B01G127000 chr2B 794914587 794928933 14346 False 1190.7 3607 96.6655 293 3088 10 chr2B.!!$F2 2795
2 TraesCS3B01G127000 chr4A 375777694 375778943 1249 True 1064.0 1064 82.1070 1800 3088 1 chr4A.!!$R1 1288
3 TraesCS3B01G127000 chr2D 147771246 147772525 1279 False 974.0 974 80.6800 1583 2857 1 chr2D.!!$F3 1274
4 TraesCS3B01G127000 chr5A 437054790 437055446 656 True 667.0 667 85.0450 1945 2604 1 chr5A.!!$R1 659

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
181 182 0.113190 AAAGCTCAGGGGGAACTTGG 59.887 55.0 0.00 0.0 32.40 3.61 F
293 294 0.325484 TTAAGCCCCGCTACTACCCA 60.325 55.0 0.00 0.0 38.25 4.51 F
357 5676 0.467474 TCCGGCCATATCAGTCTCGT 60.467 55.0 2.24 0.0 0.00 4.18 F
393 5988 0.817013 CCCACGCTGGCATTACAAAT 59.183 50.0 0.00 0.0 35.79 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1268 6887 0.107410 AAAACTCTCGCACACACCCA 60.107 50.0 0.0 0.0 0.00 4.51 R
1271 6890 0.317020 GCCAAAACTCTCGCACACAC 60.317 55.0 0.0 0.0 0.00 3.82 R
1280 6899 0.465460 TCCTTGCGTGCCAAAACTCT 60.465 50.0 0.0 0.0 31.94 3.24 R
2262 7890 0.584876 GGTGGTTGTGAACTGTACGC 59.415 55.0 0.0 0.0 0.00 4.42 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
21 22 4.880886 GCATGACATTGTATGTACAGCA 57.119 40.909 0.33 0.00 45.03 4.41
22 23 5.233957 GCATGACATTGTATGTACAGCAA 57.766 39.130 15.13 15.13 45.03 3.91
23 24 5.030295 GCATGACATTGTATGTACAGCAAC 58.970 41.667 15.10 7.97 45.03 4.17
24 25 5.391843 GCATGACATTGTATGTACAGCAACA 60.392 40.000 15.10 10.14 45.03 3.33
26 27 6.421377 TGACATTGTATGTACAGCAACATC 57.579 37.500 15.10 14.86 45.03 3.06
27 28 5.353956 TGACATTGTATGTACAGCAACATCC 59.646 40.000 15.10 7.94 45.03 3.51
28 29 4.332543 ACATTGTATGTACAGCAACATCCG 59.667 41.667 15.10 7.50 42.78 4.18
29 30 3.603158 TGTATGTACAGCAACATCCGT 57.397 42.857 0.33 0.00 40.52 4.69
30 31 3.932822 TGTATGTACAGCAACATCCGTT 58.067 40.909 0.33 0.00 40.52 4.44
31 32 3.930229 TGTATGTACAGCAACATCCGTTC 59.070 43.478 0.33 0.00 40.52 3.95
33 34 1.070914 TGTACAGCAACATCCGTTCCA 59.929 47.619 0.00 0.00 31.13 3.53
34 35 2.290008 TGTACAGCAACATCCGTTCCAT 60.290 45.455 0.00 0.00 31.13 3.41
35 36 2.779755 ACAGCAACATCCGTTCCATA 57.220 45.000 0.00 0.00 31.13 2.74
36 37 3.281727 ACAGCAACATCCGTTCCATAT 57.718 42.857 0.00 0.00 31.13 1.78
37 38 3.620488 ACAGCAACATCCGTTCCATATT 58.380 40.909 0.00 0.00 31.13 1.28
39 40 5.189928 ACAGCAACATCCGTTCCATATTAA 58.810 37.500 0.00 0.00 31.13 1.40
41 42 5.296780 CAGCAACATCCGTTCCATATTAAGT 59.703 40.000 0.00 0.00 31.13 2.24
42 43 6.481976 CAGCAACATCCGTTCCATATTAAGTA 59.518 38.462 0.00 0.00 31.13 2.24
43 44 7.173218 CAGCAACATCCGTTCCATATTAAGTAT 59.827 37.037 0.00 0.00 31.13 2.12
44 45 7.387948 AGCAACATCCGTTCCATATTAAGTATC 59.612 37.037 0.00 0.00 31.13 2.24
45 46 7.621426 GCAACATCCGTTCCATATTAAGTATCG 60.621 40.741 0.00 0.00 31.13 2.92
46 47 5.867716 ACATCCGTTCCATATTAAGTATCGC 59.132 40.000 0.00 0.00 0.00 4.58
47 48 5.717078 TCCGTTCCATATTAAGTATCGCT 57.283 39.130 0.00 0.00 0.00 4.93
48 49 5.466819 TCCGTTCCATATTAAGTATCGCTG 58.533 41.667 0.00 0.00 0.00 5.18
49 50 4.625742 CCGTTCCATATTAAGTATCGCTGG 59.374 45.833 0.00 0.00 0.00 4.85
50 51 5.227908 CGTTCCATATTAAGTATCGCTGGT 58.772 41.667 0.00 0.00 0.00 4.00
51 52 6.384224 CGTTCCATATTAAGTATCGCTGGTA 58.616 40.000 0.00 0.00 0.00 3.25
52 53 6.307318 CGTTCCATATTAAGTATCGCTGGTAC 59.693 42.308 0.00 0.00 0.00 3.34
54 55 8.517878 GTTCCATATTAAGTATCGCTGGTACTA 58.482 37.037 2.62 0.00 32.34 1.82
55 56 8.640063 TCCATATTAAGTATCGCTGGTACTAA 57.360 34.615 2.62 0.32 32.34 2.24
56 57 8.737175 TCCATATTAAGTATCGCTGGTACTAAG 58.263 37.037 2.62 0.00 32.34 2.18
60 61 7.636150 TTAAGTATCGCTGGTACTAAGAGTT 57.364 36.000 2.62 0.00 32.34 3.01
61 62 6.527057 AAGTATCGCTGGTACTAAGAGTTT 57.473 37.500 2.62 0.00 32.34 2.66
62 63 6.134040 AGTATCGCTGGTACTAAGAGTTTC 57.866 41.667 0.50 0.00 30.91 2.78
63 64 5.887035 AGTATCGCTGGTACTAAGAGTTTCT 59.113 40.000 0.50 0.00 30.91 2.52
64 65 4.436242 TCGCTGGTACTAAGAGTTTCTG 57.564 45.455 0.00 0.00 0.00 3.02
65 66 2.924290 CGCTGGTACTAAGAGTTTCTGC 59.076 50.000 0.00 0.00 0.00 4.26
67 68 3.306780 GCTGGTACTAAGAGTTTCTGCCA 60.307 47.826 0.00 0.00 0.00 4.92
68 69 4.802918 GCTGGTACTAAGAGTTTCTGCCAA 60.803 45.833 0.00 0.00 0.00 4.52
70 71 4.591498 TGGTACTAAGAGTTTCTGCCAAGA 59.409 41.667 0.00 0.00 0.00 3.02
71 72 5.172205 GGTACTAAGAGTTTCTGCCAAGAG 58.828 45.833 0.00 0.00 32.79 2.85
73 74 2.947127 AAGAGTTTCTGCCAAGAGCT 57.053 45.000 0.00 0.00 44.23 4.09
74 75 2.181954 AGAGTTTCTGCCAAGAGCTG 57.818 50.000 0.00 0.00 44.23 4.24
75 76 1.696336 AGAGTTTCTGCCAAGAGCTGA 59.304 47.619 0.00 0.00 46.55 4.26
79 80 3.923354 TCTGCCAAGAGCTGAGTTC 57.077 52.632 0.00 0.00 43.74 3.01
80 81 1.051008 TCTGCCAAGAGCTGAGTTCA 58.949 50.000 0.00 0.00 43.74 3.18
81 82 1.155042 CTGCCAAGAGCTGAGTTCAC 58.845 55.000 0.00 0.00 42.76 3.18
83 84 1.970640 TGCCAAGAGCTGAGTTCACTA 59.029 47.619 0.00 0.00 44.23 2.74
84 85 2.368548 TGCCAAGAGCTGAGTTCACTAA 59.631 45.455 0.00 0.00 44.23 2.24
85 86 3.008375 TGCCAAGAGCTGAGTTCACTAAT 59.992 43.478 0.00 0.00 44.23 1.73
86 87 3.373439 GCCAAGAGCTGAGTTCACTAATG 59.627 47.826 0.00 0.00 38.99 1.90
87 88 3.937706 CCAAGAGCTGAGTTCACTAATGG 59.062 47.826 0.00 0.00 0.00 3.16
88 89 3.902881 AGAGCTGAGTTCACTAATGGG 57.097 47.619 0.00 0.00 0.00 4.00
89 90 2.093235 AGAGCTGAGTTCACTAATGGGC 60.093 50.000 0.00 0.00 0.00 5.36
90 91 1.630369 AGCTGAGTTCACTAATGGGCA 59.370 47.619 0.00 0.00 0.00 5.36
91 92 1.740025 GCTGAGTTCACTAATGGGCAC 59.260 52.381 0.00 0.00 0.00 5.01
115 116 3.706373 GTGGAGCCAGCCGGAGAA 61.706 66.667 5.05 0.00 0.00 2.87
116 117 3.393970 TGGAGCCAGCCGGAGAAG 61.394 66.667 5.05 0.00 0.00 2.85
117 118 4.168291 GGAGCCAGCCGGAGAAGG 62.168 72.222 5.05 0.74 0.00 3.46
121 122 1.303317 GCCAGCCGGAGAAGGAAAA 60.303 57.895 5.05 0.00 0.00 2.29
122 123 1.587043 GCCAGCCGGAGAAGGAAAAC 61.587 60.000 5.05 0.00 0.00 2.43
123 124 0.250727 CCAGCCGGAGAAGGAAAACA 60.251 55.000 5.05 0.00 0.00 2.83
124 125 0.875059 CAGCCGGAGAAGGAAAACAC 59.125 55.000 5.05 0.00 0.00 3.32
126 127 1.975680 AGCCGGAGAAGGAAAACACTA 59.024 47.619 5.05 0.00 0.00 2.74
127 128 2.572104 AGCCGGAGAAGGAAAACACTAT 59.428 45.455 5.05 0.00 0.00 2.12
128 129 3.773119 AGCCGGAGAAGGAAAACACTATA 59.227 43.478 5.05 0.00 0.00 1.31
129 130 3.869832 GCCGGAGAAGGAAAACACTATAC 59.130 47.826 5.05 0.00 0.00 1.47
130 131 4.622220 GCCGGAGAAGGAAAACACTATACA 60.622 45.833 5.05 0.00 0.00 2.29
131 132 5.671493 CCGGAGAAGGAAAACACTATACAT 58.329 41.667 0.00 0.00 0.00 2.29
133 134 6.037172 CCGGAGAAGGAAAACACTATACATTG 59.963 42.308 0.00 0.00 0.00 2.82
134 135 6.037172 CGGAGAAGGAAAACACTATACATTGG 59.963 42.308 0.00 0.00 0.00 3.16
135 136 7.110155 GGAGAAGGAAAACACTATACATTGGA 58.890 38.462 0.00 0.00 0.00 3.53
136 137 7.775561 GGAGAAGGAAAACACTATACATTGGAT 59.224 37.037 0.00 0.00 0.00 3.41
137 138 8.738645 AGAAGGAAAACACTATACATTGGATC 57.261 34.615 0.00 0.00 0.00 3.36
138 139 8.328758 AGAAGGAAAACACTATACATTGGATCA 58.671 33.333 0.00 0.00 0.00 2.92
140 141 6.543831 AGGAAAACACTATACATTGGATCAGC 59.456 38.462 0.00 0.00 0.00 4.26
141 142 6.543831 GGAAAACACTATACATTGGATCAGCT 59.456 38.462 0.00 0.00 0.00 4.24
143 144 4.965814 ACACTATACATTGGATCAGCTGG 58.034 43.478 15.13 0.00 0.00 4.85
144 145 3.750130 CACTATACATTGGATCAGCTGGC 59.250 47.826 15.13 6.41 0.00 4.85
145 146 3.392285 ACTATACATTGGATCAGCTGGCA 59.608 43.478 15.13 0.00 0.00 4.92
149 150 2.097036 CATTGGATCAGCTGGCAGAAA 58.903 47.619 20.86 2.13 0.00 2.52
150 151 1.538047 TTGGATCAGCTGGCAGAAAC 58.462 50.000 20.86 0.00 0.00 2.78
151 152 0.694771 TGGATCAGCTGGCAGAAACT 59.305 50.000 20.86 2.50 0.00 2.66
152 153 1.339438 TGGATCAGCTGGCAGAAACTC 60.339 52.381 20.86 8.74 0.00 3.01
155 156 0.761187 TCAGCTGGCAGAAACTCACT 59.239 50.000 20.86 0.00 0.00 3.41
156 157 1.970640 TCAGCTGGCAGAAACTCACTA 59.029 47.619 20.86 0.00 0.00 2.74
157 158 2.368548 TCAGCTGGCAGAAACTCACTAA 59.631 45.455 20.86 0.00 0.00 2.24
158 159 3.008375 TCAGCTGGCAGAAACTCACTAAT 59.992 43.478 20.86 0.00 0.00 1.73
159 160 3.755378 CAGCTGGCAGAAACTCACTAATT 59.245 43.478 20.86 0.00 0.00 1.40
161 162 3.503748 GCTGGCAGAAACTCACTAATTGT 59.496 43.478 20.86 0.00 0.00 2.71
162 163 4.695455 GCTGGCAGAAACTCACTAATTGTA 59.305 41.667 20.86 0.00 0.00 2.41
164 165 6.293955 GCTGGCAGAAACTCACTAATTGTAAA 60.294 38.462 20.86 0.00 0.00 2.01
165 166 7.202016 TGGCAGAAACTCACTAATTGTAAAG 57.798 36.000 0.00 0.00 0.00 1.85
166 167 6.086871 GGCAGAAACTCACTAATTGTAAAGC 58.913 40.000 0.00 0.00 0.00 3.51
167 168 6.072452 GGCAGAAACTCACTAATTGTAAAGCT 60.072 38.462 0.00 0.00 0.00 3.74
168 169 7.018235 GCAGAAACTCACTAATTGTAAAGCTC 58.982 38.462 0.00 0.00 0.00 4.09
169 170 7.307989 GCAGAAACTCACTAATTGTAAAGCTCA 60.308 37.037 0.00 0.00 0.00 4.26
170 171 8.226448 CAGAAACTCACTAATTGTAAAGCTCAG 58.774 37.037 0.00 0.00 0.00 3.35
171 172 7.389053 AGAAACTCACTAATTGTAAAGCTCAGG 59.611 37.037 0.00 0.00 0.00 3.86
172 173 5.491982 ACTCACTAATTGTAAAGCTCAGGG 58.508 41.667 0.00 0.00 0.00 4.45
173 174 4.843728 TCACTAATTGTAAAGCTCAGGGG 58.156 43.478 0.00 0.00 0.00 4.79
174 175 3.947834 CACTAATTGTAAAGCTCAGGGGG 59.052 47.826 0.00 0.00 0.00 5.40
175 176 3.850173 ACTAATTGTAAAGCTCAGGGGGA 59.150 43.478 0.00 0.00 0.00 4.81
176 177 3.825908 AATTGTAAAGCTCAGGGGGAA 57.174 42.857 0.00 0.00 0.00 3.97
178 179 1.742308 TGTAAAGCTCAGGGGGAACT 58.258 50.000 0.00 0.00 0.00 3.01
179 180 2.062636 TGTAAAGCTCAGGGGGAACTT 58.937 47.619 0.00 0.00 33.40 2.66
181 182 0.113190 AAAGCTCAGGGGGAACTTGG 59.887 55.000 0.00 0.00 32.40 3.61
182 183 1.793820 AAGCTCAGGGGGAACTTGGG 61.794 60.000 0.00 0.00 30.88 4.12
184 185 2.081585 GCTCAGGGGGAACTTGGGTT 62.082 60.000 0.00 0.00 38.52 4.11
196 197 4.974645 AACTTGGGTTCAGAGACATGTA 57.025 40.909 0.00 0.00 0.00 2.29
197 198 5.505181 AACTTGGGTTCAGAGACATGTAT 57.495 39.130 0.00 0.00 0.00 2.29
198 199 4.836825 ACTTGGGTTCAGAGACATGTATG 58.163 43.478 0.00 0.00 0.00 2.39
199 200 3.912496 TGGGTTCAGAGACATGTATGG 57.088 47.619 0.00 0.00 0.00 2.74
200 201 2.505407 TGGGTTCAGAGACATGTATGGG 59.495 50.000 0.00 0.00 0.00 4.00
201 202 2.505819 GGGTTCAGAGACATGTATGGGT 59.494 50.000 0.00 0.00 0.00 4.51
202 203 3.054361 GGGTTCAGAGACATGTATGGGTT 60.054 47.826 0.00 0.00 0.00 4.11
203 204 4.567747 GGGTTCAGAGACATGTATGGGTTT 60.568 45.833 0.00 0.00 0.00 3.27
205 206 6.177610 GGTTCAGAGACATGTATGGGTTTAA 58.822 40.000 0.00 0.00 0.00 1.52
206 207 6.828785 GGTTCAGAGACATGTATGGGTTTAAT 59.171 38.462 0.00 0.00 0.00 1.40
208 209 9.561069 GTTCAGAGACATGTATGGGTTTAATAT 57.439 33.333 0.00 0.00 0.00 1.28
212 213 8.220559 AGAGACATGTATGGGTTTAATATTGCT 58.779 33.333 0.00 0.00 0.00 3.91
213 214 9.502091 GAGACATGTATGGGTTTAATATTGCTA 57.498 33.333 0.00 0.00 0.00 3.49
216 217 9.586732 ACATGTATGGGTTTAATATTGCTATGT 57.413 29.630 0.00 0.00 0.00 2.29
219 220 9.415008 TGTATGGGTTTAATATTGCTATGTTGT 57.585 29.630 0.00 0.00 0.00 3.32
220 221 9.893305 GTATGGGTTTAATATTGCTATGTTGTC 57.107 33.333 0.00 0.00 0.00 3.18
221 222 7.946381 TGGGTTTAATATTGCTATGTTGTCA 57.054 32.000 0.00 0.00 0.00 3.58
222 223 8.354711 TGGGTTTAATATTGCTATGTTGTCAA 57.645 30.769 0.00 0.00 0.00 3.18
223 224 8.465999 TGGGTTTAATATTGCTATGTTGTCAAG 58.534 33.333 0.00 0.00 0.00 3.02
224 225 7.920682 GGGTTTAATATTGCTATGTTGTCAAGG 59.079 37.037 0.00 0.00 0.00 3.61
225 226 7.435192 GGTTTAATATTGCTATGTTGTCAAGGC 59.565 37.037 0.00 0.00 0.00 4.35
227 228 6.528537 AATATTGCTATGTTGTCAAGGCAA 57.471 33.333 13.65 13.65 43.22 4.52
228 229 4.870123 ATTGCTATGTTGTCAAGGCAAA 57.130 36.364 14.64 4.51 42.78 3.68
229 230 4.870123 TTGCTATGTTGTCAAGGCAAAT 57.130 36.364 10.65 0.00 39.76 2.32
230 231 5.973899 TTGCTATGTTGTCAAGGCAAATA 57.026 34.783 10.65 0.00 39.76 1.40
231 232 6.528537 TTGCTATGTTGTCAAGGCAAATAT 57.471 33.333 10.65 0.00 39.76 1.28
233 234 5.163530 TGCTATGTTGTCAAGGCAAATATGG 60.164 40.000 0.00 0.00 34.33 2.74
234 235 5.067674 GCTATGTTGTCAAGGCAAATATGGA 59.932 40.000 0.00 0.00 0.00 3.41
236 237 4.661222 TGTTGTCAAGGCAAATATGGAGA 58.339 39.130 0.00 0.00 0.00 3.71
237 238 5.263599 TGTTGTCAAGGCAAATATGGAGAT 58.736 37.500 0.00 0.00 0.00 2.75
238 239 5.716228 TGTTGTCAAGGCAAATATGGAGATT 59.284 36.000 0.00 0.00 0.00 2.40
239 240 5.840243 TGTCAAGGCAAATATGGAGATTG 57.160 39.130 0.00 0.00 0.00 2.67
240 241 5.508567 TGTCAAGGCAAATATGGAGATTGA 58.491 37.500 0.00 0.00 0.00 2.57
241 242 6.131264 TGTCAAGGCAAATATGGAGATTGAT 58.869 36.000 0.00 0.00 0.00 2.57
242 243 6.608405 TGTCAAGGCAAATATGGAGATTGATT 59.392 34.615 0.00 0.00 0.00 2.57
243 244 7.144000 GTCAAGGCAAATATGGAGATTGATTC 58.856 38.462 0.00 0.00 0.00 2.52
246 247 7.850935 AGGCAAATATGGAGATTGATTCAAT 57.149 32.000 11.64 11.64 36.72 2.57
247 248 7.667557 AGGCAAATATGGAGATTGATTCAATG 58.332 34.615 16.41 1.31 33.90 2.82
248 249 6.367969 GGCAAATATGGAGATTGATTCAATGC 59.632 38.462 16.41 10.44 33.90 3.56
249 250 6.367969 GCAAATATGGAGATTGATTCAATGCC 59.632 38.462 16.41 16.09 33.90 4.40
251 252 2.669781 TGGAGATTGATTCAATGCCCC 58.330 47.619 16.41 13.41 33.90 5.80
252 253 1.610522 GGAGATTGATTCAATGCCCCG 59.389 52.381 16.41 0.00 33.90 5.73
253 254 2.575532 GAGATTGATTCAATGCCCCGA 58.424 47.619 16.41 0.00 33.90 5.14
254 255 3.152341 GAGATTGATTCAATGCCCCGAT 58.848 45.455 16.41 0.00 33.90 4.18
255 256 4.326826 GAGATTGATTCAATGCCCCGATA 58.673 43.478 16.41 0.00 33.90 2.92
256 257 4.074970 AGATTGATTCAATGCCCCGATAC 58.925 43.478 16.41 0.00 33.90 2.24
257 258 3.576078 TTGATTCAATGCCCCGATACT 57.424 42.857 0.00 0.00 0.00 2.12
258 259 3.126001 TGATTCAATGCCCCGATACTC 57.874 47.619 0.00 0.00 0.00 2.59
259 260 2.705658 TGATTCAATGCCCCGATACTCT 59.294 45.455 0.00 0.00 0.00 3.24
260 261 3.901222 TGATTCAATGCCCCGATACTCTA 59.099 43.478 0.00 0.00 0.00 2.43
261 262 4.532126 TGATTCAATGCCCCGATACTCTAT 59.468 41.667 0.00 0.00 0.00 1.98
262 263 3.961480 TCAATGCCCCGATACTCTATG 57.039 47.619 0.00 0.00 0.00 2.23
264 265 3.006859 TCAATGCCCCGATACTCTATGTG 59.993 47.826 0.00 0.00 0.00 3.21
265 266 0.679505 TGCCCCGATACTCTATGTGC 59.320 55.000 0.00 0.00 0.00 4.57
266 267 0.679505 GCCCCGATACTCTATGTGCA 59.320 55.000 0.00 0.00 0.00 4.57
267 268 1.605712 GCCCCGATACTCTATGTGCAC 60.606 57.143 10.75 10.75 0.00 4.57
268 269 1.686587 CCCCGATACTCTATGTGCACA 59.313 52.381 24.08 24.08 0.00 4.57
269 270 2.102420 CCCCGATACTCTATGTGCACAA 59.898 50.000 25.72 12.25 0.00 3.33
270 271 3.431626 CCCCGATACTCTATGTGCACAAA 60.432 47.826 25.72 11.54 0.00 2.83
272 273 5.510690 CCCCGATACTCTATGTGCACAAATA 60.511 44.000 25.72 11.88 0.00 1.40
273 274 5.405571 CCCGATACTCTATGTGCACAAATAC 59.594 44.000 25.72 9.03 0.00 1.89
274 275 6.216569 CCGATACTCTATGTGCACAAATACT 58.783 40.000 25.72 9.59 0.00 2.12
276 277 7.865889 CCGATACTCTATGTGCACAAATACTTA 59.134 37.037 25.72 9.54 0.00 2.24
277 278 9.244799 CGATACTCTATGTGCACAAATACTTAA 57.755 33.333 25.72 6.12 0.00 1.85
280 281 6.316390 ACTCTATGTGCACAAATACTTAAGCC 59.684 38.462 25.72 0.00 0.00 4.35
282 283 2.823154 TGTGCACAAATACTTAAGCCCC 59.177 45.455 19.28 0.00 0.00 5.80
283 284 2.088423 TGCACAAATACTTAAGCCCCG 58.912 47.619 1.29 0.00 0.00 5.73
285 286 2.365582 CACAAATACTTAAGCCCCGCT 58.634 47.619 1.29 0.00 42.56 5.52
286 287 3.537580 CACAAATACTTAAGCCCCGCTA 58.462 45.455 1.29 0.00 38.25 4.26
288 289 3.199289 ACAAATACTTAAGCCCCGCTACT 59.801 43.478 1.29 0.00 38.25 2.57
289 290 4.406649 ACAAATACTTAAGCCCCGCTACTA 59.593 41.667 1.29 0.00 38.25 1.82
290 291 4.597404 AATACTTAAGCCCCGCTACTAC 57.403 45.455 1.29 0.00 38.25 2.73
291 292 1.117994 ACTTAAGCCCCGCTACTACC 58.882 55.000 1.29 0.00 38.25 3.18
292 293 0.391966 CTTAAGCCCCGCTACTACCC 59.608 60.000 0.00 0.00 38.25 3.69
293 294 0.325484 TTAAGCCCCGCTACTACCCA 60.325 55.000 0.00 0.00 38.25 4.51
295 296 2.443390 GCCCCGCTACTACCCAGA 60.443 66.667 0.00 0.00 0.00 3.86
296 297 2.499827 GCCCCGCTACTACCCAGAG 61.500 68.421 0.00 0.00 0.00 3.35
336 5655 1.043673 ACCTGTGAGGCCGGTATCTC 61.044 60.000 1.90 8.92 39.63 2.75
357 5676 0.467474 TCCGGCCATATCAGTCTCGT 60.467 55.000 2.24 0.00 0.00 4.18
365 5684 3.321968 CCATATCAGTCTCGTGATTCCCA 59.678 47.826 0.00 0.00 38.21 4.37
378 5697 1.187567 ATTCCCAAGCTGTTGCCCAC 61.188 55.000 0.00 0.00 40.80 4.61
393 5988 0.817013 CCCACGCTGGCATTACAAAT 59.183 50.000 0.00 0.00 35.79 2.32
397 5992 3.487376 CCACGCTGGCATTACAAATAGTG 60.487 47.826 0.00 0.00 0.00 2.74
463 6058 2.315386 AAAACGCGTCCGCTCCTTC 61.315 57.895 14.44 0.00 39.32 3.46
483 6078 2.670592 GGGCCCACGTTGGTACAC 60.671 66.667 19.95 0.00 39.29 2.90
507 6102 5.932619 ATAGCCCCTTTTGGTTAAATGTC 57.067 39.130 0.00 0.00 38.10 3.06
508 6103 2.903784 AGCCCCTTTTGGTTAAATGTCC 59.096 45.455 0.00 0.00 38.10 4.02
511 6106 3.306710 CCCCTTTTGGTTAAATGTCCTGC 60.307 47.826 0.00 0.00 38.10 4.85
530 6125 1.586422 CACGTATTGATGGAGCAGGG 58.414 55.000 0.00 0.00 0.00 4.45
967 6562 3.241701 GGCATCAAAAATTTCTTCGCGA 58.758 40.909 3.71 3.71 0.00 5.87
971 6566 5.627172 CATCAAAAATTTCTTCGCGAGGTA 58.373 37.500 18.33 5.69 0.00 3.08
972 6567 5.277601 TCAAAAATTTCTTCGCGAGGTAG 57.722 39.130 18.33 9.11 0.00 3.18
973 6568 4.992319 TCAAAAATTTCTTCGCGAGGTAGA 59.008 37.500 18.33 11.54 0.00 2.59
1075 6694 2.354510 TGTTTTCAGTTCGAGCTTGTGG 59.645 45.455 0.00 0.00 0.00 4.17
1119 6738 4.778534 TTCTAGGTACAGTCTTGTTCCG 57.221 45.455 0.00 0.00 46.20 4.30
1174 6793 2.229784 GAGTTGGACCAAAATGGCTCAG 59.770 50.000 8.94 0.00 42.67 3.35
1248 6867 1.226773 GGCGCATCATGTTCAAGCC 60.227 57.895 10.83 0.00 36.08 4.35
1259 6878 2.874664 TTCAAGCCCCTGTACGCGT 61.875 57.895 19.17 19.17 0.00 6.01
1268 6887 3.876589 CTGTACGCGTGGCAAGGGT 62.877 63.158 24.59 24.37 38.36 4.34
1280 6899 3.484806 AAGGGTGGGTGTGTGCGA 61.485 61.111 0.00 0.00 0.00 5.10
1332 6951 3.993234 GCGAGTGCGGATGATGCG 61.993 66.667 0.76 0.76 38.16 4.73
1431 7050 9.956720 GAAAAACCTGGAATGTATGAATATCTG 57.043 33.333 0.00 0.00 0.00 2.90
1524 7143 5.006746 GGTTTGTCTCTGTGTAGTTGTTCTG 59.993 44.000 0.00 0.00 0.00 3.02
1825 7452 1.529244 GTGTGGGAAAGGCTGCTGT 60.529 57.895 0.00 0.00 0.00 4.40
1891 7518 7.411486 TTTCTGTTAGGGAATTTGTTGAACA 57.589 32.000 0.00 0.00 0.00 3.18
1920 7547 3.492337 GGAATTGTAGTGAACCCAACCA 58.508 45.455 0.00 0.00 0.00 3.67
1955 7582 1.694696 GATTCCCTGGACGAGGCTTAT 59.305 52.381 0.00 0.00 41.19 1.73
2128 7755 9.323985 TCCTTGTTGTTTAATTCCAATTTTCTG 57.676 29.630 0.00 0.00 0.00 3.02
2141 7769 6.514947 TCCAATTTTCTGTTTGGTCTCATTG 58.485 36.000 1.96 0.00 42.47 2.82
2146 7774 2.229543 TCTGTTTGGTCTCATTGCATGC 59.770 45.455 11.82 11.82 0.00 4.06
2150 7778 4.463539 TGTTTGGTCTCATTGCATGCTTAT 59.536 37.500 20.33 9.60 0.00 1.73
2159 7787 3.301794 TTGCATGCTTATCATCCCACT 57.698 42.857 20.33 0.00 31.79 4.00
2262 7890 3.266636 TGGTTGGTACATATGCGAACAG 58.733 45.455 1.58 0.00 39.30 3.16
2364 7992 1.842562 ACTAGGAATCTGGTGCAGCAT 59.157 47.619 20.52 4.30 33.27 3.79
2552 8181 5.863397 TCCAAGATTTAAAAGCAGCAAATCG 59.137 36.000 9.24 0.00 41.43 3.34
2766 14372 3.576356 GGCGGTGTCATGATGCGG 61.576 66.667 0.00 0.80 0.00 5.69
3083 14689 3.139077 GTTCAAGACGGACTTCCACATT 58.861 45.455 0.00 0.00 36.61 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.038603 GGATGTTGCTGTACATACAATGTCAT 59.961 38.462 12.90 11.59 43.67 3.06
4 5 5.502382 CGGATGTTGCTGTACATACAATGTC 60.502 44.000 12.90 12.82 43.67 3.06
8 9 3.932822 ACGGATGTTGCTGTACATACAA 58.067 40.909 0.00 1.35 38.97 2.41
9 10 3.603158 ACGGATGTTGCTGTACATACA 57.397 42.857 0.00 1.97 38.97 2.29
10 11 3.308866 GGAACGGATGTTGCTGTACATAC 59.691 47.826 0.00 0.00 42.55 2.39
11 12 3.055747 TGGAACGGATGTTGCTGTACATA 60.056 43.478 0.00 0.00 45.68 2.29
12 13 2.290008 TGGAACGGATGTTGCTGTACAT 60.290 45.455 0.00 0.00 45.68 2.29
14 15 1.803334 TGGAACGGATGTTGCTGTAC 58.197 50.000 1.54 0.00 45.68 2.90
16 17 2.779755 TATGGAACGGATGTTGCTGT 57.220 45.000 1.54 0.00 45.68 4.40
17 18 5.296780 ACTTAATATGGAACGGATGTTGCTG 59.703 40.000 1.54 0.00 45.68 4.41
18 19 5.437060 ACTTAATATGGAACGGATGTTGCT 58.563 37.500 1.54 0.00 45.68 3.91
19 20 5.751243 ACTTAATATGGAACGGATGTTGC 57.249 39.130 0.00 0.00 45.68 4.17
21 22 6.367969 GCGATACTTAATATGGAACGGATGTT 59.632 38.462 0.00 0.00 42.23 2.71
22 23 5.867716 GCGATACTTAATATGGAACGGATGT 59.132 40.000 0.00 0.00 0.00 3.06
23 24 6.035005 CAGCGATACTTAATATGGAACGGATG 59.965 42.308 0.00 0.00 0.00 3.51
24 25 6.100004 CAGCGATACTTAATATGGAACGGAT 58.900 40.000 0.00 0.00 0.00 4.18
26 27 4.625742 CCAGCGATACTTAATATGGAACGG 59.374 45.833 0.00 0.00 0.00 4.44
27 28 5.227908 ACCAGCGATACTTAATATGGAACG 58.772 41.667 0.00 0.00 0.00 3.95
28 29 7.376615 AGTACCAGCGATACTTAATATGGAAC 58.623 38.462 0.00 0.00 28.03 3.62
29 30 7.534723 AGTACCAGCGATACTTAATATGGAA 57.465 36.000 0.00 0.00 28.03 3.53
30 31 8.640063 TTAGTACCAGCGATACTTAATATGGA 57.360 34.615 3.40 0.00 34.66 3.41
31 32 8.737175 TCTTAGTACCAGCGATACTTAATATGG 58.263 37.037 3.40 0.00 34.66 2.74
33 34 9.517868 ACTCTTAGTACCAGCGATACTTAATAT 57.482 33.333 3.40 0.00 34.66 1.28
34 35 8.915057 ACTCTTAGTACCAGCGATACTTAATA 57.085 34.615 3.40 0.00 34.66 0.98
35 36 7.820578 ACTCTTAGTACCAGCGATACTTAAT 57.179 36.000 3.40 0.00 34.66 1.40
36 37 7.636150 AACTCTTAGTACCAGCGATACTTAA 57.364 36.000 3.40 0.00 34.66 1.85
37 38 7.555554 AGAAACTCTTAGTACCAGCGATACTTA 59.444 37.037 3.40 0.00 34.66 2.24
39 40 5.887035 AGAAACTCTTAGTACCAGCGATACT 59.113 40.000 0.00 3.56 36.79 2.12
41 42 5.450137 GCAGAAACTCTTAGTACCAGCGATA 60.450 44.000 0.00 0.00 0.00 2.92
42 43 4.678309 GCAGAAACTCTTAGTACCAGCGAT 60.678 45.833 0.00 0.00 0.00 4.58
43 44 3.367087 GCAGAAACTCTTAGTACCAGCGA 60.367 47.826 0.00 0.00 0.00 4.93
44 45 2.924290 GCAGAAACTCTTAGTACCAGCG 59.076 50.000 0.00 0.00 0.00 5.18
45 46 3.263261 GGCAGAAACTCTTAGTACCAGC 58.737 50.000 0.00 0.00 0.00 4.85
46 47 4.537135 TGGCAGAAACTCTTAGTACCAG 57.463 45.455 0.00 0.00 0.00 4.00
47 48 4.591498 TCTTGGCAGAAACTCTTAGTACCA 59.409 41.667 0.00 0.00 0.00 3.25
48 49 5.148651 TCTTGGCAGAAACTCTTAGTACC 57.851 43.478 0.00 0.00 0.00 3.34
49 50 4.627900 GCTCTTGGCAGAAACTCTTAGTAC 59.372 45.833 0.00 0.00 41.35 2.73
50 51 4.528596 AGCTCTTGGCAGAAACTCTTAGTA 59.471 41.667 0.00 0.00 44.79 1.82
51 52 3.326297 AGCTCTTGGCAGAAACTCTTAGT 59.674 43.478 0.00 0.00 44.79 2.24
52 53 3.683822 CAGCTCTTGGCAGAAACTCTTAG 59.316 47.826 0.00 0.00 44.79 2.18
54 55 2.105477 TCAGCTCTTGGCAGAAACTCTT 59.895 45.455 0.00 0.00 44.79 2.85
55 56 1.696336 TCAGCTCTTGGCAGAAACTCT 59.304 47.619 0.00 0.00 44.79 3.24
56 57 2.075338 CTCAGCTCTTGGCAGAAACTC 58.925 52.381 0.00 0.00 44.79 3.01
60 61 1.417517 TGAACTCAGCTCTTGGCAGAA 59.582 47.619 0.00 0.00 44.79 3.02
61 62 1.051008 TGAACTCAGCTCTTGGCAGA 58.949 50.000 0.00 0.00 44.79 4.26
62 63 1.155042 GTGAACTCAGCTCTTGGCAG 58.845 55.000 0.00 0.00 44.79 4.85
63 64 0.761187 AGTGAACTCAGCTCTTGGCA 59.239 50.000 0.00 0.00 44.79 4.92
64 65 2.751166 TAGTGAACTCAGCTCTTGGC 57.249 50.000 0.00 0.00 42.19 4.52
65 66 3.937706 CCATTAGTGAACTCAGCTCTTGG 59.062 47.826 0.00 0.00 0.00 3.61
67 68 3.620966 GCCCATTAGTGAACTCAGCTCTT 60.621 47.826 0.00 0.00 0.00 2.85
68 69 2.093235 GCCCATTAGTGAACTCAGCTCT 60.093 50.000 0.00 0.00 0.00 4.09
70 71 1.630369 TGCCCATTAGTGAACTCAGCT 59.370 47.619 0.00 0.00 0.00 4.24
71 72 1.740025 GTGCCCATTAGTGAACTCAGC 59.260 52.381 0.00 0.00 0.00 4.26
73 74 1.985159 AGGTGCCCATTAGTGAACTCA 59.015 47.619 0.00 0.00 0.00 3.41
74 75 2.789409 AGGTGCCCATTAGTGAACTC 57.211 50.000 0.00 0.00 0.00 3.01
75 76 3.055094 CAGTAGGTGCCCATTAGTGAACT 60.055 47.826 0.00 0.00 0.00 3.01
76 77 3.270877 CAGTAGGTGCCCATTAGTGAAC 58.729 50.000 0.00 0.00 0.00 3.18
77 78 2.238646 CCAGTAGGTGCCCATTAGTGAA 59.761 50.000 0.00 0.00 0.00 3.18
79 80 2.332063 CCAGTAGGTGCCCATTAGTG 57.668 55.000 0.00 0.00 0.00 2.74
98 99 3.672295 CTTCTCCGGCTGGCTCCAC 62.672 68.421 6.73 0.00 34.14 4.02
99 100 3.393970 CTTCTCCGGCTGGCTCCA 61.394 66.667 6.73 0.00 34.14 3.86
101 102 2.185310 TTTCCTTCTCCGGCTGGCTC 62.185 60.000 6.73 0.00 34.14 4.70
103 104 1.303317 TTTTCCTTCTCCGGCTGGC 60.303 57.895 6.73 0.00 34.14 4.85
104 105 0.250727 TGTTTTCCTTCTCCGGCTGG 60.251 55.000 4.71 4.71 0.00 4.85
105 106 0.875059 GTGTTTTCCTTCTCCGGCTG 59.125 55.000 0.00 0.00 0.00 4.85
106 107 0.765510 AGTGTTTTCCTTCTCCGGCT 59.234 50.000 0.00 0.00 0.00 5.52
107 108 2.467566 TAGTGTTTTCCTTCTCCGGC 57.532 50.000 0.00 0.00 0.00 6.13
110 111 7.110155 TCCAATGTATAGTGTTTTCCTTCTCC 58.890 38.462 0.00 0.00 0.00 3.71
111 112 8.738645 ATCCAATGTATAGTGTTTTCCTTCTC 57.261 34.615 0.00 0.00 0.00 2.87
112 113 8.328758 TGATCCAATGTATAGTGTTTTCCTTCT 58.671 33.333 0.00 0.00 0.00 2.85
113 114 8.506168 TGATCCAATGTATAGTGTTTTCCTTC 57.494 34.615 0.00 0.00 0.00 3.46
114 115 7.067494 GCTGATCCAATGTATAGTGTTTTCCTT 59.933 37.037 0.00 0.00 0.00 3.36
115 116 6.543831 GCTGATCCAATGTATAGTGTTTTCCT 59.456 38.462 0.00 0.00 0.00 3.36
116 117 6.543831 AGCTGATCCAATGTATAGTGTTTTCC 59.456 38.462 0.00 0.00 0.00 3.13
117 118 7.412853 CAGCTGATCCAATGTATAGTGTTTTC 58.587 38.462 8.42 0.00 0.00 2.29
121 122 4.744867 GCCAGCTGATCCAATGTATAGTGT 60.745 45.833 17.39 0.00 0.00 3.55
122 123 3.750130 GCCAGCTGATCCAATGTATAGTG 59.250 47.826 17.39 0.00 0.00 2.74
123 124 3.392285 TGCCAGCTGATCCAATGTATAGT 59.608 43.478 17.39 0.00 0.00 2.12
124 125 4.001652 CTGCCAGCTGATCCAATGTATAG 58.998 47.826 17.39 0.00 0.00 1.31
126 127 2.440627 TCTGCCAGCTGATCCAATGTAT 59.559 45.455 17.39 0.00 0.00 2.29
127 128 1.839354 TCTGCCAGCTGATCCAATGTA 59.161 47.619 17.39 0.00 0.00 2.29
128 129 0.622136 TCTGCCAGCTGATCCAATGT 59.378 50.000 17.39 0.00 0.00 2.71
129 130 1.758936 TTCTGCCAGCTGATCCAATG 58.241 50.000 17.39 0.00 0.00 2.82
130 131 2.097825 GTTTCTGCCAGCTGATCCAAT 58.902 47.619 17.39 0.00 0.00 3.16
131 132 1.074405 AGTTTCTGCCAGCTGATCCAA 59.926 47.619 17.39 0.00 0.00 3.53
133 134 1.339438 TGAGTTTCTGCCAGCTGATCC 60.339 52.381 17.39 3.53 0.00 3.36
134 135 1.736681 GTGAGTTTCTGCCAGCTGATC 59.263 52.381 17.39 7.16 0.00 2.92
135 136 1.350351 AGTGAGTTTCTGCCAGCTGAT 59.650 47.619 17.39 0.00 0.00 2.90
136 137 0.761187 AGTGAGTTTCTGCCAGCTGA 59.239 50.000 17.39 0.00 0.00 4.26
137 138 2.462456 TAGTGAGTTTCTGCCAGCTG 57.538 50.000 6.78 6.78 0.00 4.24
138 139 3.710209 ATTAGTGAGTTTCTGCCAGCT 57.290 42.857 0.00 0.00 0.00 4.24
140 141 6.801539 TTACAATTAGTGAGTTTCTGCCAG 57.198 37.500 0.00 0.00 0.00 4.85
141 142 6.293955 GCTTTACAATTAGTGAGTTTCTGCCA 60.294 38.462 0.00 0.00 0.00 4.92
143 144 6.903419 AGCTTTACAATTAGTGAGTTTCTGC 58.097 36.000 0.00 0.00 0.00 4.26
144 145 8.087982 TGAGCTTTACAATTAGTGAGTTTCTG 57.912 34.615 0.00 0.00 0.00 3.02
145 146 7.389053 CCTGAGCTTTACAATTAGTGAGTTTCT 59.611 37.037 0.00 0.00 0.00 2.52
149 150 5.491982 CCCTGAGCTTTACAATTAGTGAGT 58.508 41.667 0.00 0.00 0.00 3.41
150 151 4.878397 CCCCTGAGCTTTACAATTAGTGAG 59.122 45.833 0.00 0.00 0.00 3.51
151 152 4.324254 CCCCCTGAGCTTTACAATTAGTGA 60.324 45.833 0.00 0.00 0.00 3.41
152 153 3.947834 CCCCCTGAGCTTTACAATTAGTG 59.052 47.826 0.00 0.00 0.00 2.74
155 156 4.291249 AGTTCCCCCTGAGCTTTACAATTA 59.709 41.667 0.00 0.00 28.90 1.40
156 157 3.076032 AGTTCCCCCTGAGCTTTACAATT 59.924 43.478 0.00 0.00 28.90 2.32
157 158 2.649816 AGTTCCCCCTGAGCTTTACAAT 59.350 45.455 0.00 0.00 28.90 2.71
158 159 2.062636 AGTTCCCCCTGAGCTTTACAA 58.937 47.619 0.00 0.00 28.90 2.41
159 160 1.742308 AGTTCCCCCTGAGCTTTACA 58.258 50.000 0.00 0.00 28.90 2.41
161 162 1.354368 CCAAGTTCCCCCTGAGCTTTA 59.646 52.381 0.00 0.00 41.20 1.85
162 163 0.113190 CCAAGTTCCCCCTGAGCTTT 59.887 55.000 0.00 0.00 41.20 3.51
164 165 2.234296 CCCAAGTTCCCCCTGAGCT 61.234 63.158 0.00 0.00 35.85 4.09
165 166 2.081585 AACCCAAGTTCCCCCTGAGC 62.082 60.000 0.00 0.00 0.00 4.26
166 167 0.038310 GAACCCAAGTTCCCCCTGAG 59.962 60.000 0.00 0.00 45.65 3.35
167 168 2.160646 GAACCCAAGTTCCCCCTGA 58.839 57.895 0.00 0.00 45.65 3.86
168 169 4.843624 GAACCCAAGTTCCCCCTG 57.156 61.111 0.00 0.00 45.65 4.45
175 176 3.864789 ACATGTCTCTGAACCCAAGTT 57.135 42.857 0.00 0.00 39.54 2.66
176 177 4.323792 CCATACATGTCTCTGAACCCAAGT 60.324 45.833 0.00 0.00 0.00 3.16
178 179 3.054434 CCCATACATGTCTCTGAACCCAA 60.054 47.826 0.00 0.00 0.00 4.12
179 180 2.505407 CCCATACATGTCTCTGAACCCA 59.495 50.000 0.00 0.00 0.00 4.51
181 182 3.914426 ACCCATACATGTCTCTGAACC 57.086 47.619 0.00 0.00 0.00 3.62
182 183 7.865706 ATTAAACCCATACATGTCTCTGAAC 57.134 36.000 0.00 0.00 0.00 3.18
184 185 9.559732 CAATATTAAACCCATACATGTCTCTGA 57.440 33.333 0.00 0.00 0.00 3.27
185 186 8.292448 GCAATATTAAACCCATACATGTCTCTG 58.708 37.037 0.00 0.00 0.00 3.35
187 188 8.396272 AGCAATATTAAACCCATACATGTCTC 57.604 34.615 0.00 0.00 0.00 3.36
190 191 9.586732 ACATAGCAATATTAAACCCATACATGT 57.413 29.630 2.69 2.69 0.00 3.21
193 194 9.415008 ACAACATAGCAATATTAAACCCATACA 57.585 29.630 0.00 0.00 0.00 2.29
196 197 8.532186 TGACAACATAGCAATATTAAACCCAT 57.468 30.769 0.00 0.00 0.00 4.00
197 198 7.946381 TGACAACATAGCAATATTAAACCCA 57.054 32.000 0.00 0.00 0.00 4.51
198 199 7.920682 CCTTGACAACATAGCAATATTAAACCC 59.079 37.037 0.00 0.00 0.00 4.11
199 200 7.435192 GCCTTGACAACATAGCAATATTAAACC 59.565 37.037 0.00 0.00 0.00 3.27
200 201 7.973388 TGCCTTGACAACATAGCAATATTAAAC 59.027 33.333 0.00 0.00 33.57 2.01
201 202 8.060931 TGCCTTGACAACATAGCAATATTAAA 57.939 30.769 0.00 0.00 33.57 1.52
202 203 7.637631 TGCCTTGACAACATAGCAATATTAA 57.362 32.000 0.00 0.00 33.57 1.40
203 204 7.637631 TTGCCTTGACAACATAGCAATATTA 57.362 32.000 6.23 0.00 38.52 0.98
205 206 6.528537 TTTGCCTTGACAACATAGCAATAT 57.471 33.333 9.64 0.00 40.97 1.28
206 207 5.973899 TTTGCCTTGACAACATAGCAATA 57.026 34.783 9.64 2.18 40.97 1.90
208 209 4.870123 ATTTGCCTTGACAACATAGCAA 57.130 36.364 6.23 6.23 40.24 3.91
212 213 6.422333 TCTCCATATTTGCCTTGACAACATA 58.578 36.000 0.00 0.00 0.00 2.29
213 214 5.263599 TCTCCATATTTGCCTTGACAACAT 58.736 37.500 0.00 0.00 0.00 2.71
214 215 4.661222 TCTCCATATTTGCCTTGACAACA 58.339 39.130 0.00 0.00 0.00 3.33
215 216 5.841957 ATCTCCATATTTGCCTTGACAAC 57.158 39.130 0.00 0.00 0.00 3.32
216 217 5.951148 TCAATCTCCATATTTGCCTTGACAA 59.049 36.000 0.00 0.00 0.00 3.18
218 219 6.645790 ATCAATCTCCATATTTGCCTTGAC 57.354 37.500 0.00 0.00 0.00 3.18
219 220 6.834969 TGAATCAATCTCCATATTTGCCTTGA 59.165 34.615 0.00 0.00 0.00 3.02
220 221 7.046292 TGAATCAATCTCCATATTTGCCTTG 57.954 36.000 0.00 0.00 0.00 3.61
221 222 7.664552 TTGAATCAATCTCCATATTTGCCTT 57.335 32.000 0.00 0.00 0.00 4.35
222 223 7.667557 CATTGAATCAATCTCCATATTTGCCT 58.332 34.615 5.36 0.00 31.05 4.75
223 224 6.367969 GCATTGAATCAATCTCCATATTTGCC 59.632 38.462 5.36 0.00 31.05 4.52
224 225 6.367969 GGCATTGAATCAATCTCCATATTTGC 59.632 38.462 5.36 4.10 31.05 3.68
225 226 6.872020 GGGCATTGAATCAATCTCCATATTTG 59.128 38.462 19.09 4.50 31.05 2.32
227 228 5.482878 GGGGCATTGAATCAATCTCCATATT 59.517 40.000 19.09 0.00 31.05 1.28
228 229 5.021458 GGGGCATTGAATCAATCTCCATAT 58.979 41.667 19.09 0.00 31.05 1.78
229 230 4.410099 GGGGCATTGAATCAATCTCCATA 58.590 43.478 19.09 0.00 31.05 2.74
230 231 3.236896 GGGGCATTGAATCAATCTCCAT 58.763 45.455 19.09 0.00 31.05 3.41
231 232 2.669781 GGGGCATTGAATCAATCTCCA 58.330 47.619 19.09 0.00 31.05 3.86
233 234 2.575532 TCGGGGCATTGAATCAATCTC 58.424 47.619 5.36 1.61 31.05 2.75
234 235 2.734755 TCGGGGCATTGAATCAATCT 57.265 45.000 5.36 0.00 31.05 2.40
236 237 4.074970 GAGTATCGGGGCATTGAATCAAT 58.925 43.478 2.07 2.07 34.04 2.57
237 238 3.136443 AGAGTATCGGGGCATTGAATCAA 59.864 43.478 0.00 0.00 42.67 2.57
238 239 2.705658 AGAGTATCGGGGCATTGAATCA 59.294 45.455 0.00 0.00 42.67 2.57
239 240 3.409026 AGAGTATCGGGGCATTGAATC 57.591 47.619 0.00 0.00 42.67 2.52
240 241 4.287067 ACATAGAGTATCGGGGCATTGAAT 59.713 41.667 0.00 0.00 42.67 2.57
241 242 3.646162 ACATAGAGTATCGGGGCATTGAA 59.354 43.478 0.00 0.00 42.67 2.69
242 243 3.006859 CACATAGAGTATCGGGGCATTGA 59.993 47.826 0.00 0.00 42.67 2.57
243 244 3.329386 CACATAGAGTATCGGGGCATTG 58.671 50.000 0.00 0.00 42.67 2.82
246 247 0.679505 GCACATAGAGTATCGGGGCA 59.320 55.000 0.00 0.00 42.67 5.36
247 248 0.679505 TGCACATAGAGTATCGGGGC 59.320 55.000 0.00 0.00 42.67 5.80
248 249 1.686587 TGTGCACATAGAGTATCGGGG 59.313 52.381 17.42 0.00 42.67 5.73
249 250 3.452755 TTGTGCACATAGAGTATCGGG 57.547 47.619 22.39 0.00 42.67 5.14
251 252 7.700322 AAGTATTTGTGCACATAGAGTATCG 57.300 36.000 22.39 0.00 42.67 2.92
253 254 9.046296 GCTTAAGTATTTGTGCACATAGAGTAT 57.954 33.333 22.39 9.80 0.00 2.12
254 255 7.494625 GGCTTAAGTATTTGTGCACATAGAGTA 59.505 37.037 22.39 4.15 0.00 2.59
255 256 6.316390 GGCTTAAGTATTTGTGCACATAGAGT 59.684 38.462 22.39 13.46 0.00 3.24
256 257 6.238484 GGGCTTAAGTATTTGTGCACATAGAG 60.238 42.308 22.39 10.93 0.00 2.43
257 258 5.588648 GGGCTTAAGTATTTGTGCACATAGA 59.411 40.000 22.39 10.83 0.00 1.98
258 259 5.221048 GGGGCTTAAGTATTTGTGCACATAG 60.221 44.000 22.39 8.93 0.00 2.23
259 260 4.642885 GGGGCTTAAGTATTTGTGCACATA 59.357 41.667 22.39 17.13 0.00 2.29
260 261 3.447229 GGGGCTTAAGTATTTGTGCACAT 59.553 43.478 22.39 9.53 0.00 3.21
261 262 2.823154 GGGGCTTAAGTATTTGTGCACA 59.177 45.455 17.42 17.42 0.00 4.57
262 263 2.159435 CGGGGCTTAAGTATTTGTGCAC 60.159 50.000 10.75 10.75 0.00 4.57
264 265 1.202256 GCGGGGCTTAAGTATTTGTGC 60.202 52.381 4.02 0.00 0.00 4.57
265 266 2.365582 AGCGGGGCTTAAGTATTTGTG 58.634 47.619 4.02 0.00 33.89 3.33
266 267 2.801077 AGCGGGGCTTAAGTATTTGT 57.199 45.000 4.02 0.00 33.89 2.83
267 268 3.805207 AGTAGCGGGGCTTAAGTATTTG 58.195 45.455 4.02 0.00 40.44 2.32
268 269 4.202295 GGTAGTAGCGGGGCTTAAGTATTT 60.202 45.833 4.02 0.00 40.44 1.40
269 270 3.323115 GGTAGTAGCGGGGCTTAAGTATT 59.677 47.826 4.02 0.00 40.44 1.89
270 271 2.896044 GGTAGTAGCGGGGCTTAAGTAT 59.104 50.000 4.02 0.00 40.44 2.12
272 273 1.117994 GGTAGTAGCGGGGCTTAAGT 58.882 55.000 4.02 0.00 40.44 2.24
273 274 0.391966 GGGTAGTAGCGGGGCTTAAG 59.608 60.000 0.00 0.00 40.44 1.85
274 275 0.325484 TGGGTAGTAGCGGGGCTTAA 60.325 55.000 0.00 0.00 40.44 1.85
276 277 2.039951 TGGGTAGTAGCGGGGCTT 59.960 61.111 0.00 0.00 40.44 4.35
277 278 2.444140 CTGGGTAGTAGCGGGGCT 60.444 66.667 0.00 0.00 43.41 5.19
278 279 2.443390 TCTGGGTAGTAGCGGGGC 60.443 66.667 0.00 0.00 0.00 5.80
280 281 3.130227 GCTCTGGGTAGTAGCGGG 58.870 66.667 0.00 0.00 0.00 6.13
283 284 1.041437 AATCCGCTCTGGGTAGTAGC 58.959 55.000 0.00 0.00 38.76 3.58
285 286 3.101437 TGAAAATCCGCTCTGGGTAGTA 58.899 45.455 0.00 0.00 38.76 1.82
286 287 1.906574 TGAAAATCCGCTCTGGGTAGT 59.093 47.619 0.00 0.00 38.76 2.73
288 289 1.406887 GCTGAAAATCCGCTCTGGGTA 60.407 52.381 0.00 0.00 38.76 3.69
289 290 0.678048 GCTGAAAATCCGCTCTGGGT 60.678 55.000 0.00 0.00 38.76 4.51
290 291 1.709147 CGCTGAAAATCCGCTCTGGG 61.709 60.000 0.00 0.00 38.76 4.45
291 292 1.709147 CCGCTGAAAATCCGCTCTGG 61.709 60.000 0.00 0.00 40.09 3.86
292 293 0.740868 TCCGCTGAAAATCCGCTCTG 60.741 55.000 0.00 0.00 0.00 3.35
293 294 0.741221 GTCCGCTGAAAATCCGCTCT 60.741 55.000 0.00 0.00 0.00 4.09
295 296 2.100631 CGTCCGCTGAAAATCCGCT 61.101 57.895 0.00 0.00 0.00 5.52
296 297 2.025359 CTCGTCCGCTGAAAATCCGC 62.025 60.000 0.00 0.00 0.00 5.54
336 5655 0.039074 GAGACTGATATGGCCGGACG 60.039 60.000 5.05 0.00 0.00 4.79
357 5676 0.899717 GGGCAACAGCTTGGGAATCA 60.900 55.000 0.00 0.00 39.74 2.57
365 5684 3.289834 CAGCGTGGGCAACAGCTT 61.290 61.111 8.34 0.00 43.41 3.74
378 5697 4.097714 CAACACTATTTGTAATGCCAGCG 58.902 43.478 0.00 0.00 37.51 5.18
385 5980 6.664428 AACAAGGCCAACACTATTTGTAAT 57.336 33.333 5.01 0.00 37.51 1.89
393 5988 4.691685 CGTTGTATAACAAGGCCAACACTA 59.308 41.667 5.01 0.00 39.00 2.74
397 5992 2.162809 CCCGTTGTATAACAAGGCCAAC 59.837 50.000 5.01 0.00 41.22 3.77
421 6016 6.728200 TGTACTACCACGTATTATACAGCAC 58.272 40.000 3.16 0.00 0.00 4.40
463 6058 1.969589 GTACCAACGTGGGCCCAAG 60.970 63.158 33.19 33.19 43.37 3.61
483 6078 6.048732 ACATTTAACCAAAAGGGGCTATTG 57.951 37.500 0.00 0.00 42.91 1.90
507 6102 0.940126 GCTCCATCAATACGTGCAGG 59.060 55.000 4.53 4.53 0.00 4.85
508 6103 1.596260 CTGCTCCATCAATACGTGCAG 59.404 52.381 0.00 0.66 39.98 4.41
511 6106 1.138859 TCCCTGCTCCATCAATACGTG 59.861 52.381 0.00 0.00 0.00 4.49
967 6562 1.005569 TGATCTCCACACGGTCTACCT 59.994 52.381 0.00 0.00 0.00 3.08
971 6566 1.178276 GTCTGATCTCCACACGGTCT 58.822 55.000 0.00 0.00 0.00 3.85
972 6567 0.888619 TGTCTGATCTCCACACGGTC 59.111 55.000 0.00 0.00 0.00 4.79
973 6568 0.603569 GTGTCTGATCTCCACACGGT 59.396 55.000 6.63 0.00 31.67 4.83
999 6618 0.819666 GGTCGCCCAGGAATTCCATC 60.820 60.000 26.22 10.59 38.89 3.51
1119 6738 0.254178 TTGATTCTGCAGAGGGAGGC 59.746 55.000 17.43 4.77 32.55 4.70
1187 6806 3.083349 CCCCGAGCCTGGACATCA 61.083 66.667 0.00 0.00 0.00 3.07
1248 6867 3.118454 CTTGCCACGCGTACAGGG 61.118 66.667 13.44 10.72 38.93 4.45
1259 6878 3.425014 ACACACCCACCCTTGCCA 61.425 61.111 0.00 0.00 0.00 4.92
1268 6887 0.107410 AAAACTCTCGCACACACCCA 60.107 50.000 0.00 0.00 0.00 4.51
1271 6890 0.317020 GCCAAAACTCTCGCACACAC 60.317 55.000 0.00 0.00 0.00 3.82
1280 6899 0.465460 TCCTTGCGTGCCAAAACTCT 60.465 50.000 0.00 0.00 31.94 3.24
1332 6951 4.123545 CCCGAATCCCCCACCACC 62.124 72.222 0.00 0.00 0.00 4.61
1411 7030 4.633126 CCGCAGATATTCATACATTCCAGG 59.367 45.833 0.00 0.00 0.00 4.45
1431 7050 2.100631 ATAGTGTCGCAAGCACCGC 61.101 57.895 0.00 0.00 42.64 5.68
1825 7452 1.897133 TCGGATTGAACTCCCTTTCGA 59.103 47.619 0.00 0.00 31.04 3.71
1891 7518 4.506802 GGTTCACTACAATTCCCTCCTTGT 60.507 45.833 0.00 0.00 38.95 3.16
1955 7582 7.567250 TCCCATGAATATAGGTTGTAGAAGTCA 59.433 37.037 0.00 0.00 0.00 3.41
2141 7769 1.884579 CCAGTGGGATGATAAGCATGC 59.115 52.381 10.51 10.51 43.86 4.06
2262 7890 0.584876 GGTGGTTGTGAACTGTACGC 59.415 55.000 0.00 0.00 0.00 4.42
2364 7992 5.507637 AGACTAACGTTATTCTCCCTGAGA 58.492 41.667 19.25 0.00 36.86 3.27
2552 8181 7.391148 ACCTGGATGTTGTATGTAAAATCAC 57.609 36.000 0.00 0.00 0.00 3.06
2616 8245 3.447025 CTGCTCGATTCCCCGACCC 62.447 68.421 0.00 0.00 34.56 4.46
2766 14372 2.435533 AACTTTCGACCTTCTCGTCC 57.564 50.000 0.00 0.00 43.45 4.79


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

AutoCloner maintained by Alex Coulton.