Multiple sequence alignment - TraesCS6B01G298200

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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 TraesCS6B01G298200 chr6B 100.000 2868 0 0 1 2868 535360218 535363085 0.000000e+00 5297.0
1 TraesCS6B01G298200 chr6B 92.982 228 16 0 1 228 535355175 535355402 1.650000e-87 333.0
2 TraesCS6B01G298200 chr6D 91.862 2003 88 26 273 2233 346272936 346270967 0.000000e+00 2726.0
3 TraesCS6B01G298200 chr6A 93.480 1503 55 13 737 2209 497729187 497730676 0.000000e+00 2193.0
4 TraesCS6B01G298200 chr6A 94.087 389 22 1 326 713 497728808 497729196 8.850000e-165 590.0
5 TraesCS6B01G298200 chr6A 85.652 230 28 5 1 227 217630879 217631106 1.330000e-58 237.0
6 TraesCS6B01G298200 chr7B 92.000 600 39 7 2276 2868 88338286 88338883 0.000000e+00 833.0
7 TraesCS6B01G298200 chr2B 89.020 592 56 5 2284 2868 665182488 665181899 0.000000e+00 725.0
8 TraesCS6B01G298200 chr2B 86.318 592 65 13 2284 2867 24016924 24017507 5.210000e-177 630.0
9 TraesCS6B01G298200 chr2B 79.070 129 13 10 1 123 557385031 557384911 3.060000e-10 76.8
10 TraesCS6B01G298200 chr4B 87.625 598 64 6 2279 2868 650976278 650976873 0.000000e+00 686.0
11 TraesCS6B01G298200 chr4B 83.744 609 75 19 2276 2868 88415998 88415398 3.230000e-154 555.0
12 TraesCS6B01G298200 chr5D 87.336 608 58 14 2270 2868 387815070 387815667 0.000000e+00 678.0
13 TraesCS6B01G298200 chr5D 81.304 230 38 5 1 228 149104718 149104944 6.310000e-42 182.0
14 TraesCS6B01G298200 chr5D 78.295 129 15 10 1 123 478953265 478953386 1.430000e-08 71.3
15 TraesCS6B01G298200 chr3D 84.768 604 72 11 2273 2868 611891749 611892340 3.180000e-164 588.0
16 TraesCS6B01G298200 chr1A 84.628 592 74 14 2280 2868 554543341 554543918 8.910000e-160 573.0
17 TraesCS6B01G298200 chr5B 83.713 614 77 17 2268 2865 336222426 336223032 2.500000e-155 558.0
18 TraesCS6B01G298200 chr5B 78.298 235 36 11 1 228 57738826 57738600 1.390000e-28 137.0
19 TraesCS6B01G298200 chr5B 78.059 237 37 10 1 231 57743844 57743617 4.980000e-28 135.0
20 TraesCS6B01G298200 chr2D 79.365 126 21 4 1 123 643202764 643202887 1.830000e-12 84.2
21 TraesCS6B01G298200 chr2A 77.863 131 12 13 1 123 585709702 585709823 6.630000e-07 65.8


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 TraesCS6B01G298200 chr6B 535360218 535363085 2867 False 5297.0 5297 100.0000 1 2868 1 chr6B.!!$F2 2867
1 TraesCS6B01G298200 chr6D 346270967 346272936 1969 True 2726.0 2726 91.8620 273 2233 1 chr6D.!!$R1 1960
2 TraesCS6B01G298200 chr6A 497728808 497730676 1868 False 1391.5 2193 93.7835 326 2209 2 chr6A.!!$F2 1883
3 TraesCS6B01G298200 chr7B 88338286 88338883 597 False 833.0 833 92.0000 2276 2868 1 chr7B.!!$F1 592
4 TraesCS6B01G298200 chr2B 665181899 665182488 589 True 725.0 725 89.0200 2284 2868 1 chr2B.!!$R2 584
5 TraesCS6B01G298200 chr2B 24016924 24017507 583 False 630.0 630 86.3180 2284 2867 1 chr2B.!!$F1 583
6 TraesCS6B01G298200 chr4B 650976278 650976873 595 False 686.0 686 87.6250 2279 2868 1 chr4B.!!$F1 589
7 TraesCS6B01G298200 chr4B 88415398 88415998 600 True 555.0 555 83.7440 2276 2868 1 chr4B.!!$R1 592
8 TraesCS6B01G298200 chr5D 387815070 387815667 597 False 678.0 678 87.3360 2270 2868 1 chr5D.!!$F2 598
9 TraesCS6B01G298200 chr3D 611891749 611892340 591 False 588.0 588 84.7680 2273 2868 1 chr3D.!!$F1 595
10 TraesCS6B01G298200 chr1A 554543341 554543918 577 False 573.0 573 84.6280 2280 2868 1 chr1A.!!$F1 588
11 TraesCS6B01G298200 chr5B 336222426 336223032 606 False 558.0 558 83.7130 2268 2865 1 chr5B.!!$F1 597

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
164 165 0.106167 ATCCCCTTCGTCGATCCTCA 60.106 55.0 0.00 0.0 0.0 3.86 F
438 440 0.169451 CGTGTTTTACCCGGCCATTC 59.831 55.0 2.24 0.0 0.0 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1793 1837 0.669318 ACACGGATGGTAGTTGTGCG 60.669 55.0 0.0 0.0 33.96 5.34 R
2246 2293 0.031857 CGGCTGGAGATGCTCACTAG 59.968 60.0 0.0 0.0 31.08 2.57 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 4.864334 CCCGCTAGGCTTGCTGGG 62.864 72.222 25.79 25.79 37.69 4.45
28 29 2.363406 GGCTTGCTGGGCCTGAAT 60.363 61.111 15.36 0.00 45.57 2.57
29 30 2.718073 GGCTTGCTGGGCCTGAATG 61.718 63.158 15.36 7.27 45.57 2.67
30 31 2.718073 GCTTGCTGGGCCTGAATGG 61.718 63.158 15.36 1.22 39.35 3.16
31 32 2.037687 TTGCTGGGCCTGAATGGG 59.962 61.111 15.36 0.00 36.00 4.00
41 42 1.446907 CCTGAATGGGCTCATATCGC 58.553 55.000 0.00 0.00 32.44 4.58
42 43 1.002888 CCTGAATGGGCTCATATCGCT 59.997 52.381 0.00 0.00 32.44 4.93
43 44 2.074576 CTGAATGGGCTCATATCGCTG 58.925 52.381 0.00 0.00 32.44 5.18
44 45 1.417517 TGAATGGGCTCATATCGCTGT 59.582 47.619 0.00 0.00 32.44 4.40
45 46 2.632512 TGAATGGGCTCATATCGCTGTA 59.367 45.455 0.00 0.00 32.44 2.74
46 47 3.070878 TGAATGGGCTCATATCGCTGTAA 59.929 43.478 0.00 0.00 32.44 2.41
47 48 2.526304 TGGGCTCATATCGCTGTAAC 57.474 50.000 0.00 0.00 0.00 2.50
48 49 2.039418 TGGGCTCATATCGCTGTAACT 58.961 47.619 0.00 0.00 0.00 2.24
49 50 2.224042 TGGGCTCATATCGCTGTAACTG 60.224 50.000 0.00 0.00 0.00 3.16
50 51 2.035961 GGGCTCATATCGCTGTAACTGA 59.964 50.000 0.00 0.00 0.00 3.41
51 52 3.306364 GGGCTCATATCGCTGTAACTGAT 60.306 47.826 0.00 0.00 0.00 2.90
52 53 4.082190 GGGCTCATATCGCTGTAACTGATA 60.082 45.833 0.00 0.00 0.00 2.15
53 54 4.859798 GGCTCATATCGCTGTAACTGATAC 59.140 45.833 0.00 0.00 34.92 2.24
54 55 5.336055 GGCTCATATCGCTGTAACTGATACT 60.336 44.000 0.00 0.00 35.42 2.12
55 56 6.153067 GCTCATATCGCTGTAACTGATACTT 58.847 40.000 0.00 0.00 35.42 2.24
56 57 7.306213 GCTCATATCGCTGTAACTGATACTTA 58.694 38.462 0.00 0.00 35.42 2.24
57 58 7.808381 GCTCATATCGCTGTAACTGATACTTAA 59.192 37.037 0.00 0.00 35.42 1.85
58 59 9.678941 CTCATATCGCTGTAACTGATACTTAAA 57.321 33.333 0.00 0.00 35.42 1.52
59 60 9.459640 TCATATCGCTGTAACTGATACTTAAAC 57.540 33.333 0.00 0.00 35.42 2.01
60 61 6.807708 ATCGCTGTAACTGATACTTAAACG 57.192 37.500 0.00 0.00 35.42 3.60
61 62 5.941733 TCGCTGTAACTGATACTTAAACGA 58.058 37.500 0.00 0.00 35.42 3.85
62 63 6.025896 TCGCTGTAACTGATACTTAAACGAG 58.974 40.000 0.00 0.00 35.42 4.18
63 64 5.798934 CGCTGTAACTGATACTTAAACGAGT 59.201 40.000 0.00 0.00 35.42 4.18
64 65 6.237227 CGCTGTAACTGATACTTAAACGAGTG 60.237 42.308 0.00 0.00 35.42 3.51
65 66 6.034683 GCTGTAACTGATACTTAAACGAGTGG 59.965 42.308 0.00 0.00 35.42 4.00
66 67 6.392354 TGTAACTGATACTTAAACGAGTGGG 58.608 40.000 0.00 0.00 35.42 4.61
67 68 5.479124 AACTGATACTTAAACGAGTGGGT 57.521 39.130 0.00 0.00 0.00 4.51
68 69 4.817517 ACTGATACTTAAACGAGTGGGTG 58.182 43.478 0.00 0.00 0.00 4.61
69 70 4.282703 ACTGATACTTAAACGAGTGGGTGT 59.717 41.667 0.00 0.00 0.00 4.16
70 71 4.562082 TGATACTTAAACGAGTGGGTGTG 58.438 43.478 0.00 0.00 0.00 3.82
71 72 1.589803 ACTTAAACGAGTGGGTGTGC 58.410 50.000 0.00 0.00 0.00 4.57
72 73 0.511221 CTTAAACGAGTGGGTGTGCG 59.489 55.000 0.00 0.00 0.00 5.34
73 74 0.179078 TTAAACGAGTGGGTGTGCGT 60.179 50.000 0.00 0.00 38.81 5.24
74 75 0.876777 TAAACGAGTGGGTGTGCGTG 60.877 55.000 0.00 0.00 37.03 5.34
75 76 2.581208 AAACGAGTGGGTGTGCGTGA 62.581 55.000 0.00 0.00 37.03 4.35
76 77 2.734723 CGAGTGGGTGTGCGTGAG 60.735 66.667 0.00 0.00 0.00 3.51
77 78 2.421739 GAGTGGGTGTGCGTGAGT 59.578 61.111 0.00 0.00 0.00 3.41
78 79 1.663739 GAGTGGGTGTGCGTGAGTA 59.336 57.895 0.00 0.00 0.00 2.59
79 80 0.388649 GAGTGGGTGTGCGTGAGTAG 60.389 60.000 0.00 0.00 0.00 2.57
80 81 1.374252 GTGGGTGTGCGTGAGTAGG 60.374 63.158 0.00 0.00 0.00 3.18
81 82 2.264794 GGGTGTGCGTGAGTAGGG 59.735 66.667 0.00 0.00 0.00 3.53
82 83 2.434359 GGTGTGCGTGAGTAGGGC 60.434 66.667 0.00 0.00 0.00 5.19
83 84 2.434359 GTGTGCGTGAGTAGGGCC 60.434 66.667 0.00 0.00 0.00 5.80
84 85 2.920384 TGTGCGTGAGTAGGGCCA 60.920 61.111 6.18 0.00 0.00 5.36
85 86 2.125512 GTGCGTGAGTAGGGCCAG 60.126 66.667 6.18 0.00 0.00 4.85
86 87 3.390521 TGCGTGAGTAGGGCCAGG 61.391 66.667 6.18 0.00 0.00 4.45
87 88 3.391382 GCGTGAGTAGGGCCAGGT 61.391 66.667 6.18 0.00 0.00 4.00
88 89 2.955881 GCGTGAGTAGGGCCAGGTT 61.956 63.158 6.18 0.00 0.00 3.50
89 90 1.079127 CGTGAGTAGGGCCAGGTTG 60.079 63.158 6.18 0.00 0.00 3.77
90 91 1.299976 GTGAGTAGGGCCAGGTTGG 59.700 63.158 6.18 0.00 41.55 3.77
129 130 2.853210 CACGGCTTGTGCGTGTAG 59.147 61.111 0.00 0.00 42.70 2.74
130 131 3.295228 CACGGCTTGTGCGTGTAGC 62.295 63.158 0.00 0.00 42.70 3.58
137 138 3.496898 TGTGCGTGTAGCTCAAGAG 57.503 52.632 0.00 0.00 45.10 2.85
138 139 0.958822 TGTGCGTGTAGCTCAAGAGA 59.041 50.000 0.32 0.00 45.10 3.10
139 140 1.068264 TGTGCGTGTAGCTCAAGAGAG 60.068 52.381 0.32 0.00 45.10 3.20
140 141 3.652308 TGTGCGTGTAGCTCAAGAGAGT 61.652 50.000 0.32 0.00 45.10 3.24
141 142 1.902840 GCGTGTAGCTCAAGAGAGTC 58.097 55.000 0.32 0.00 44.00 3.36
142 143 1.470890 GCGTGTAGCTCAAGAGAGTCT 59.529 52.381 0.32 0.00 44.00 3.24
143 144 2.477189 GCGTGTAGCTCAAGAGAGTCTC 60.477 54.545 12.54 12.54 44.00 3.36
144 145 2.222931 CGTGTAGCTCAAGAGAGTCTCG 60.223 54.545 14.47 1.64 44.00 4.04
145 146 3.004171 GTGTAGCTCAAGAGAGTCTCGA 58.996 50.000 14.47 6.08 44.00 4.04
146 147 3.625764 GTGTAGCTCAAGAGAGTCTCGAT 59.374 47.826 14.47 5.14 44.00 3.59
147 148 3.874543 TGTAGCTCAAGAGAGTCTCGATC 59.125 47.826 14.47 3.02 44.00 3.69
148 149 2.297701 AGCTCAAGAGAGTCTCGATCC 58.702 52.381 14.47 4.01 44.00 3.36
149 150 1.336755 GCTCAAGAGAGTCTCGATCCC 59.663 57.143 14.47 1.46 44.00 3.85
150 151 1.953686 CTCAAGAGAGTCTCGATCCCC 59.046 57.143 14.47 0.00 37.11 4.81
151 152 1.566703 TCAAGAGAGTCTCGATCCCCT 59.433 52.381 14.47 0.00 35.36 4.79
152 153 2.024846 TCAAGAGAGTCTCGATCCCCTT 60.025 50.000 14.47 0.00 35.36 3.95
153 154 2.358322 AGAGAGTCTCGATCCCCTTC 57.642 55.000 14.47 0.00 35.36 3.46
154 155 0.948678 GAGAGTCTCGATCCCCTTCG 59.051 60.000 3.95 0.00 40.46 3.79
155 156 0.256464 AGAGTCTCGATCCCCTTCGT 59.744 55.000 0.00 0.00 40.03 3.85
156 157 0.664224 GAGTCTCGATCCCCTTCGTC 59.336 60.000 0.00 0.00 40.03 4.20
157 158 1.096386 AGTCTCGATCCCCTTCGTCG 61.096 60.000 0.00 0.00 40.03 5.12
158 159 1.094073 GTCTCGATCCCCTTCGTCGA 61.094 60.000 0.00 0.00 41.53 4.20
159 160 0.179026 TCTCGATCCCCTTCGTCGAT 60.179 55.000 0.00 0.00 42.65 3.59
160 161 0.238817 CTCGATCCCCTTCGTCGATC 59.761 60.000 0.00 0.00 42.65 3.69
161 162 1.170919 TCGATCCCCTTCGTCGATCC 61.171 60.000 0.00 0.00 39.22 3.36
162 163 1.173444 CGATCCCCTTCGTCGATCCT 61.173 60.000 0.00 0.00 37.55 3.24
163 164 0.599060 GATCCCCTTCGTCGATCCTC 59.401 60.000 0.00 0.00 0.00 3.71
164 165 0.106167 ATCCCCTTCGTCGATCCTCA 60.106 55.000 0.00 0.00 0.00 3.86
165 166 0.323999 TCCCCTTCGTCGATCCTCAA 60.324 55.000 0.00 0.00 0.00 3.02
166 167 0.753262 CCCCTTCGTCGATCCTCAAT 59.247 55.000 0.00 0.00 0.00 2.57
167 168 1.139058 CCCCTTCGTCGATCCTCAATT 59.861 52.381 0.00 0.00 0.00 2.32
168 169 2.205074 CCCTTCGTCGATCCTCAATTG 58.795 52.381 0.00 0.00 0.00 2.32
169 170 2.418746 CCCTTCGTCGATCCTCAATTGT 60.419 50.000 5.13 0.00 0.00 2.71
170 171 3.181479 CCCTTCGTCGATCCTCAATTGTA 60.181 47.826 5.13 0.00 0.00 2.41
171 172 4.045104 CCTTCGTCGATCCTCAATTGTAG 58.955 47.826 5.13 1.90 0.00 2.74
172 173 3.079960 TCGTCGATCCTCAATTGTAGC 57.920 47.619 5.13 0.00 0.00 3.58
173 174 2.688446 TCGTCGATCCTCAATTGTAGCT 59.312 45.455 5.13 0.00 0.00 3.32
174 175 3.046390 CGTCGATCCTCAATTGTAGCTC 58.954 50.000 5.13 0.00 0.00 4.09
175 176 3.046390 GTCGATCCTCAATTGTAGCTCG 58.954 50.000 5.13 10.59 0.00 5.03
176 177 2.949644 TCGATCCTCAATTGTAGCTCGA 59.050 45.455 16.61 16.61 0.00 4.04
177 178 3.380320 TCGATCCTCAATTGTAGCTCGAA 59.620 43.478 17.59 7.37 31.70 3.71
178 179 4.038042 TCGATCCTCAATTGTAGCTCGAAT 59.962 41.667 17.59 0.00 31.70 3.34
179 180 4.747108 CGATCCTCAATTGTAGCTCGAATT 59.253 41.667 14.28 0.00 0.00 2.17
180 181 5.332883 CGATCCTCAATTGTAGCTCGAATTG 60.333 44.000 18.19 18.19 39.79 2.32
181 182 3.623060 TCCTCAATTGTAGCTCGAATTGC 59.377 43.478 18.98 0.00 38.77 3.56
182 183 3.624861 CCTCAATTGTAGCTCGAATTGCT 59.375 43.478 18.98 2.99 43.79 3.91
183 184 4.495349 CCTCAATTGTAGCTCGAATTGCTG 60.495 45.833 18.98 14.98 41.32 4.41
184 185 3.374988 TCAATTGTAGCTCGAATTGCTGG 59.625 43.478 18.98 3.59 41.32 4.85
185 186 2.472695 TTGTAGCTCGAATTGCTGGT 57.527 45.000 7.84 0.00 41.32 4.00
186 187 3.603158 TTGTAGCTCGAATTGCTGGTA 57.397 42.857 7.84 0.00 41.32 3.25
187 188 3.603158 TGTAGCTCGAATTGCTGGTAA 57.397 42.857 7.84 0.00 41.32 2.85
188 189 4.137116 TGTAGCTCGAATTGCTGGTAAT 57.863 40.909 7.84 0.00 41.32 1.89
189 190 4.119862 TGTAGCTCGAATTGCTGGTAATC 58.880 43.478 7.84 0.00 41.32 1.75
190 191 2.565841 AGCTCGAATTGCTGGTAATCC 58.434 47.619 0.00 0.00 39.56 3.01
191 192 2.092968 AGCTCGAATTGCTGGTAATCCA 60.093 45.455 0.00 0.00 39.56 3.41
192 193 2.032178 GCTCGAATTGCTGGTAATCCAC 59.968 50.000 0.00 0.00 39.03 4.02
209 210 6.585695 AATCCACCATGATTGATGAATAGC 57.414 37.500 0.00 0.00 33.77 2.97
210 211 5.051409 TCCACCATGATTGATGAATAGCA 57.949 39.130 0.00 0.00 33.31 3.49
211 212 5.447757 TCCACCATGATTGATGAATAGCAA 58.552 37.500 0.00 0.00 36.52 3.91
212 213 5.533528 TCCACCATGATTGATGAATAGCAAG 59.466 40.000 0.00 0.00 35.40 4.01
213 214 5.278808 CCACCATGATTGATGAATAGCAAGG 60.279 44.000 0.00 0.00 35.40 3.61
214 215 5.301045 CACCATGATTGATGAATAGCAAGGT 59.699 40.000 0.00 0.00 35.40 3.50
215 216 5.301045 ACCATGATTGATGAATAGCAAGGTG 59.699 40.000 0.00 0.00 35.40 4.00
216 217 5.301045 CCATGATTGATGAATAGCAAGGTGT 59.699 40.000 0.00 0.00 35.40 4.16
217 218 6.487668 CCATGATTGATGAATAGCAAGGTGTA 59.512 38.462 0.00 0.00 35.40 2.90
218 219 7.308408 CCATGATTGATGAATAGCAAGGTGTAG 60.308 40.741 0.00 0.00 35.40 2.74
219 220 6.653020 TGATTGATGAATAGCAAGGTGTAGT 58.347 36.000 0.00 0.00 35.40 2.73
220 221 7.791029 TGATTGATGAATAGCAAGGTGTAGTA 58.209 34.615 0.00 0.00 35.40 1.82
221 222 8.432013 TGATTGATGAATAGCAAGGTGTAGTAT 58.568 33.333 0.00 0.00 35.40 2.12
222 223 9.277783 GATTGATGAATAGCAAGGTGTAGTATT 57.722 33.333 0.00 0.00 35.40 1.89
223 224 8.437360 TTGATGAATAGCAAGGTGTAGTATTG 57.563 34.615 0.00 0.00 0.00 1.90
224 225 7.791029 TGATGAATAGCAAGGTGTAGTATTGA 58.209 34.615 0.00 0.00 0.00 2.57
225 226 7.710907 TGATGAATAGCAAGGTGTAGTATTGAC 59.289 37.037 0.00 0.00 0.00 3.18
226 227 6.941857 TGAATAGCAAGGTGTAGTATTGACA 58.058 36.000 0.00 0.00 0.00 3.58
227 228 7.390823 TGAATAGCAAGGTGTAGTATTGACAA 58.609 34.615 0.00 0.00 0.00 3.18
228 229 7.333423 TGAATAGCAAGGTGTAGTATTGACAAC 59.667 37.037 0.00 0.00 34.56 3.32
229 230 4.324267 AGCAAGGTGTAGTATTGACAACC 58.676 43.478 0.00 0.00 34.93 3.77
230 231 4.041691 AGCAAGGTGTAGTATTGACAACCT 59.958 41.667 0.00 0.00 37.61 3.50
231 232 5.247564 AGCAAGGTGTAGTATTGACAACCTA 59.752 40.000 0.00 0.00 35.97 3.08
232 233 5.935789 GCAAGGTGTAGTATTGACAACCTAA 59.064 40.000 0.00 0.00 35.97 2.69
233 234 6.128363 GCAAGGTGTAGTATTGACAACCTAAC 60.128 42.308 0.00 0.00 35.97 2.34
234 235 6.046290 AGGTGTAGTATTGACAACCTAACC 57.954 41.667 0.00 5.37 34.93 2.85
235 236 4.866486 GGTGTAGTATTGACAACCTAACCG 59.134 45.833 0.00 0.00 0.00 4.44
236 237 5.473039 GTGTAGTATTGACAACCTAACCGT 58.527 41.667 0.00 0.00 0.00 4.83
237 238 5.574443 GTGTAGTATTGACAACCTAACCGTC 59.426 44.000 0.00 0.00 0.00 4.79
238 239 4.198028 AGTATTGACAACCTAACCGTCC 57.802 45.455 0.00 0.00 0.00 4.79
239 240 3.579586 AGTATTGACAACCTAACCGTCCA 59.420 43.478 0.00 0.00 0.00 4.02
240 241 3.713826 ATTGACAACCTAACCGTCCAT 57.286 42.857 0.00 0.00 0.00 3.41
241 242 2.754946 TGACAACCTAACCGTCCATC 57.245 50.000 0.00 0.00 0.00 3.51
242 243 1.067425 TGACAACCTAACCGTCCATCG 60.067 52.381 0.00 0.00 39.52 3.84
243 244 0.390735 ACAACCTAACCGTCCATCGC 60.391 55.000 0.00 0.00 38.35 4.58
244 245 1.087771 CAACCTAACCGTCCATCGCC 61.088 60.000 0.00 0.00 38.35 5.54
245 246 2.279252 CCTAACCGTCCATCGCCG 60.279 66.667 0.00 0.00 38.35 6.46
251 252 4.891727 CGTCCATCGCCGGGGAAG 62.892 72.222 26.33 20.93 34.34 3.46
252 253 3.467226 GTCCATCGCCGGGGAAGA 61.467 66.667 26.33 21.20 34.34 2.87
253 254 2.445845 TCCATCGCCGGGGAAGAT 60.446 61.111 26.33 6.26 0.00 2.40
254 255 2.031163 CCATCGCCGGGGAAGATC 59.969 66.667 26.33 0.00 0.00 2.75
255 256 2.031163 CATCGCCGGGGAAGATCC 59.969 66.667 26.33 0.00 35.23 3.36
256 257 2.445845 ATCGCCGGGGAAGATCCA 60.446 61.111 26.33 0.00 38.64 3.41
257 258 1.843376 ATCGCCGGGGAAGATCCAT 60.843 57.895 26.33 3.73 38.64 3.41
258 259 1.418908 ATCGCCGGGGAAGATCCATT 61.419 55.000 26.33 2.90 38.64 3.16
259 260 1.598130 CGCCGGGGAAGATCCATTC 60.598 63.158 14.46 0.00 38.64 2.67
260 261 1.228276 GCCGGGGAAGATCCATTCC 60.228 63.158 2.18 5.37 46.82 3.01
265 266 3.476740 GGAAGATCCATTCCGCACA 57.523 52.632 0.00 0.00 39.47 4.57
266 267 1.303309 GGAAGATCCATTCCGCACAG 58.697 55.000 0.00 0.00 39.47 3.66
267 268 0.659957 GAAGATCCATTCCGCACAGC 59.340 55.000 0.00 0.00 0.00 4.40
334 335 5.246203 CGAAGGAAGAGGATTACCATGGATA 59.754 44.000 21.47 5.82 38.94 2.59
364 365 4.803908 GCCGGGGGCCTTTCTCTG 62.804 72.222 2.18 0.00 44.06 3.35
438 440 0.169451 CGTGTTTTACCCGGCCATTC 59.831 55.000 2.24 0.00 0.00 2.67
471 473 1.103803 ACGACACGACTGGCTATCAT 58.896 50.000 0.00 0.00 0.00 2.45
532 534 2.224305 GCCGATTAGGACAAGCCACTAT 60.224 50.000 0.00 0.00 45.00 2.12
540 542 0.611200 ACAAGCCACTATGGTGCGTA 59.389 50.000 3.19 0.00 40.46 4.42
606 609 2.036256 CACCTCCCCCAAGCAAGG 59.964 66.667 0.00 0.00 34.94 3.61
613 616 2.283894 CCCAAGCAAGGAACCCCC 60.284 66.667 0.00 0.00 0.00 5.40
715 718 0.842635 ATTCCTTCCTAGCCAGCCAG 59.157 55.000 0.00 0.00 0.00 4.85
880 892 0.650512 CGTTGGTCGCATAATTCGCT 59.349 50.000 0.00 0.00 0.00 4.93
881 893 1.592110 CGTTGGTCGCATAATTCGCTG 60.592 52.381 0.00 0.00 0.00 5.18
888 900 5.105675 TGGTCGCATAATTCGCTGGTATATA 60.106 40.000 0.00 0.00 0.00 0.86
889 901 5.983720 GGTCGCATAATTCGCTGGTATATAT 59.016 40.000 0.00 0.00 0.00 0.86
890 902 6.479001 GGTCGCATAATTCGCTGGTATATATT 59.521 38.462 0.00 0.00 0.00 1.28
891 903 7.306632 GGTCGCATAATTCGCTGGTATATATTC 60.307 40.741 0.00 0.00 0.00 1.75
892 904 6.416750 TCGCATAATTCGCTGGTATATATTCG 59.583 38.462 0.00 0.00 0.00 3.34
893 905 6.355638 GCATAATTCGCTGGTATATATTCGC 58.644 40.000 0.00 0.00 0.00 4.70
894 906 6.572472 CATAATTCGCTGGTATATATTCGCG 58.428 40.000 0.00 0.00 41.69 5.87
895 907 2.554806 TCGCTGGTATATATTCGCGG 57.445 50.000 6.13 0.00 40.82 6.46
896 908 0.921347 CGCTGGTATATATTCGCGGC 59.079 55.000 6.13 0.00 37.25 6.53
897 909 1.287425 GCTGGTATATATTCGCGGCC 58.713 55.000 6.13 0.00 0.00 6.13
926 938 3.209410 GGATCATTGCGTCTGAATTCCT 58.791 45.455 2.27 0.00 0.00 3.36
1011 1029 1.264749 CGGTGGTGATGGAGAAGGGA 61.265 60.000 0.00 0.00 0.00 4.20
1014 1032 0.417437 TGGTGATGGAGAAGGGAGGA 59.583 55.000 0.00 0.00 0.00 3.71
1142 1160 1.271271 CCTGCTCCTGCTCTCTTTGTT 60.271 52.381 0.00 0.00 40.48 2.83
1377 1408 3.333219 CCTCCAGCTCCAAGCCCA 61.333 66.667 0.00 0.00 43.77 5.36
1383 1414 2.282745 GCTCCAAGCCCAGCAAGT 60.283 61.111 0.00 0.00 34.48 3.16
1395 1426 4.980805 GCAAGTCCGTCGCCACCA 62.981 66.667 0.00 0.00 0.00 4.17
1471 1503 3.181459 CGGTGTAATATGACCATGGTGGA 60.181 47.826 25.52 9.13 40.96 4.02
1474 1506 5.654650 GGTGTAATATGACCATGGTGGAAAA 59.345 40.000 25.52 3.09 40.96 2.29
1488 1524 3.427773 GGTGGAAAAATAAATACGCGCCA 60.428 43.478 5.73 0.00 0.00 5.69
1579 1623 4.314440 TGCTTCGCTCTGGCCGTT 62.314 61.111 0.00 0.00 34.44 4.44
1655 1699 2.279502 GATGGACGGCGACTGCTACA 62.280 60.000 16.62 0.00 42.25 2.74
1793 1837 4.821589 CAAGAGGAGACGCCGCCC 62.822 72.222 0.00 0.00 43.43 6.13
1986 2031 2.190578 CCGAGTGGGGCATCTTCC 59.809 66.667 0.00 0.00 0.00 3.46
2010 2055 2.764637 CTTTTGGTCTCGGGTGGGGG 62.765 65.000 0.00 0.00 0.00 5.40
2198 2245 7.431249 TCGTACAGAACAGAACAGAAATTACT 58.569 34.615 0.00 0.00 0.00 2.24
2212 2259 3.418684 AATTACTCGGGTTTGTGCTCT 57.581 42.857 0.00 0.00 0.00 4.09
2213 2260 2.163818 TTACTCGGGTTTGTGCTCTG 57.836 50.000 0.00 0.00 0.00 3.35
2216 2263 1.572085 CTCGGGTTTGTGCTCTGCTG 61.572 60.000 0.00 0.00 0.00 4.41
2225 2272 0.599558 GTGCTCTGCTGCCATTTTGA 59.400 50.000 0.00 0.00 0.00 2.69
2233 2280 2.030007 TGCTGCCATTTTGAGCACTAAC 60.030 45.455 0.00 0.00 37.81 2.34
2234 2281 2.030007 GCTGCCATTTTGAGCACTAACA 60.030 45.455 0.00 0.00 34.68 2.41
2235 2282 3.367703 GCTGCCATTTTGAGCACTAACAT 60.368 43.478 0.00 0.00 34.68 2.71
2236 2283 4.418392 CTGCCATTTTGAGCACTAACATC 58.582 43.478 0.00 0.00 34.68 3.06
2237 2284 3.119884 TGCCATTTTGAGCACTAACATCG 60.120 43.478 0.00 0.00 33.08 3.84
2238 2285 3.126858 GCCATTTTGAGCACTAACATCGA 59.873 43.478 0.00 0.00 0.00 3.59
2239 2286 4.201950 GCCATTTTGAGCACTAACATCGAT 60.202 41.667 0.00 0.00 0.00 3.59
2240 2287 5.677091 GCCATTTTGAGCACTAACATCGATT 60.677 40.000 0.00 0.00 0.00 3.34
2241 2288 5.740569 CCATTTTGAGCACTAACATCGATTG 59.259 40.000 0.00 0.00 0.00 2.67
2242 2289 4.944962 TTTGAGCACTAACATCGATTGG 57.055 40.909 0.00 0.00 0.00 3.16
2243 2290 2.279741 TGAGCACTAACATCGATTGGC 58.720 47.619 0.00 0.00 0.00 4.52
2244 2291 1.258982 GAGCACTAACATCGATTGGCG 59.741 52.381 0.00 0.00 42.69 5.69
2245 2292 0.304705 GCACTAACATCGATTGGCGG 59.695 55.000 0.00 0.00 41.33 6.13
2246 2293 0.304705 CACTAACATCGATTGGCGGC 59.695 55.000 0.00 0.00 41.33 6.53
2247 2294 0.178068 ACTAACATCGATTGGCGGCT 59.822 50.000 11.43 0.00 41.33 5.52
2248 2295 1.411246 ACTAACATCGATTGGCGGCTA 59.589 47.619 11.43 1.99 41.33 3.93
2249 2296 2.061773 CTAACATCGATTGGCGGCTAG 58.938 52.381 11.43 0.00 41.33 3.42
2250 2297 0.178068 AACATCGATTGGCGGCTAGT 59.822 50.000 11.43 0.00 41.33 2.57
2251 2298 0.530650 ACATCGATTGGCGGCTAGTG 60.531 55.000 11.43 3.65 41.33 2.74
2252 2299 0.249447 CATCGATTGGCGGCTAGTGA 60.249 55.000 11.43 5.16 41.33 3.41
2253 2300 0.032678 ATCGATTGGCGGCTAGTGAG 59.967 55.000 11.43 0.00 41.33 3.51
2264 2311 3.984838 CTAGTGAGCATCTCCAGCC 57.015 57.895 0.00 0.00 34.92 4.85
2265 2312 0.031857 CTAGTGAGCATCTCCAGCCG 59.968 60.000 0.00 0.00 34.92 5.52
2266 2313 0.395724 TAGTGAGCATCTCCAGCCGA 60.396 55.000 0.00 0.00 34.92 5.54
2271 2318 1.126329 AGCATCTCCAGCCGATCCAT 61.126 55.000 0.00 0.00 0.00 3.41
2317 2365 6.042781 CCAGGTACCCTAACTTGCATAGAATA 59.957 42.308 8.74 0.00 29.64 1.75
2346 2394 5.407407 TTTAGTCCCAAACTTGCAAAACA 57.593 34.783 0.00 0.00 39.55 2.83
2353 2401 4.441913 CCCAAACTTGCAAAACATCACTCT 60.442 41.667 0.00 0.00 0.00 3.24
2529 2583 0.611062 TCTGTCGGAATCCACCTCGT 60.611 55.000 0.00 0.00 0.00 4.18
2803 2873 1.210155 GCCGTTTGCAGCTCGAATT 59.790 52.632 8.41 0.00 40.77 2.17
2818 2888 1.349234 GAATTGCGTCCATTTGTGCC 58.651 50.000 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.864334 CCCAGCAAGCCTAGCGGG 62.864 72.222 5.10 5.10 45.31 6.13
12 13 2.718073 CCATTCAGGCCCAGCAAGC 61.718 63.158 0.00 0.00 0.00 4.01
13 14 2.056223 CCCATTCAGGCCCAGCAAG 61.056 63.158 0.00 0.00 35.39 4.01
14 15 2.037687 CCCATTCAGGCCCAGCAA 59.962 61.111 0.00 0.00 35.39 3.91
22 23 1.002888 AGCGATATGAGCCCATTCAGG 59.997 52.381 0.00 0.00 34.31 3.86
23 24 2.074576 CAGCGATATGAGCCCATTCAG 58.925 52.381 0.00 0.00 34.31 3.02
24 25 1.417517 ACAGCGATATGAGCCCATTCA 59.582 47.619 0.00 0.00 34.31 2.57
25 26 2.175878 ACAGCGATATGAGCCCATTC 57.824 50.000 0.00 0.00 34.31 2.67
26 27 3.071602 AGTTACAGCGATATGAGCCCATT 59.928 43.478 0.00 0.00 34.31 3.16
27 28 2.634940 AGTTACAGCGATATGAGCCCAT 59.365 45.455 0.00 0.00 36.81 4.00
28 29 2.039418 AGTTACAGCGATATGAGCCCA 58.961 47.619 0.00 0.00 34.64 5.36
29 30 2.035961 TCAGTTACAGCGATATGAGCCC 59.964 50.000 0.00 0.00 34.64 5.19
30 31 3.371102 TCAGTTACAGCGATATGAGCC 57.629 47.619 0.00 0.00 34.64 4.70
31 32 5.704888 AGTATCAGTTACAGCGATATGAGC 58.295 41.667 0.00 0.00 32.87 4.26
32 33 9.678941 TTTAAGTATCAGTTACAGCGATATGAG 57.321 33.333 0.00 0.00 32.87 2.90
33 34 9.459640 GTTTAAGTATCAGTTACAGCGATATGA 57.540 33.333 0.00 0.00 32.87 2.15
34 35 8.417928 CGTTTAAGTATCAGTTACAGCGATATG 58.582 37.037 0.00 0.00 32.87 1.78
35 36 8.347771 TCGTTTAAGTATCAGTTACAGCGATAT 58.652 33.333 0.00 0.00 32.87 1.63
36 37 7.696755 TCGTTTAAGTATCAGTTACAGCGATA 58.303 34.615 0.00 0.00 32.87 2.92
37 38 6.558009 TCGTTTAAGTATCAGTTACAGCGAT 58.442 36.000 0.00 0.00 32.87 4.58
38 39 5.941733 TCGTTTAAGTATCAGTTACAGCGA 58.058 37.500 0.00 0.00 32.87 4.93
39 40 5.798934 ACTCGTTTAAGTATCAGTTACAGCG 59.201 40.000 0.00 0.00 32.87 5.18
40 41 6.034683 CCACTCGTTTAAGTATCAGTTACAGC 59.965 42.308 0.00 0.00 32.87 4.40
41 42 6.530534 CCCACTCGTTTAAGTATCAGTTACAG 59.469 42.308 0.00 0.00 32.87 2.74
42 43 6.015180 ACCCACTCGTTTAAGTATCAGTTACA 60.015 38.462 0.00 0.00 32.87 2.41
43 44 6.309737 CACCCACTCGTTTAAGTATCAGTTAC 59.690 42.308 0.00 0.00 0.00 2.50
44 45 6.015180 ACACCCACTCGTTTAAGTATCAGTTA 60.015 38.462 0.00 0.00 0.00 2.24
45 46 5.221581 ACACCCACTCGTTTAAGTATCAGTT 60.222 40.000 0.00 0.00 0.00 3.16
46 47 4.282703 ACACCCACTCGTTTAAGTATCAGT 59.717 41.667 0.00 0.00 0.00 3.41
47 48 4.625742 CACACCCACTCGTTTAAGTATCAG 59.374 45.833 0.00 0.00 0.00 2.90
48 49 4.562082 CACACCCACTCGTTTAAGTATCA 58.438 43.478 0.00 0.00 0.00 2.15
49 50 3.370061 GCACACCCACTCGTTTAAGTATC 59.630 47.826 0.00 0.00 0.00 2.24
50 51 3.332034 GCACACCCACTCGTTTAAGTAT 58.668 45.455 0.00 0.00 0.00 2.12
51 52 2.758009 GCACACCCACTCGTTTAAGTA 58.242 47.619 0.00 0.00 0.00 2.24
52 53 1.589803 GCACACCCACTCGTTTAAGT 58.410 50.000 0.00 0.00 0.00 2.24
53 54 0.511221 CGCACACCCACTCGTTTAAG 59.489 55.000 0.00 0.00 0.00 1.85
54 55 0.179078 ACGCACACCCACTCGTTTAA 60.179 50.000 0.00 0.00 0.00 1.52
55 56 0.876777 CACGCACACCCACTCGTTTA 60.877 55.000 0.00 0.00 32.38 2.01
56 57 2.177580 CACGCACACCCACTCGTTT 61.178 57.895 0.00 0.00 32.38 3.60
57 58 2.587753 CACGCACACCCACTCGTT 60.588 61.111 0.00 0.00 32.38 3.85
58 59 3.499929 CTCACGCACACCCACTCGT 62.500 63.158 0.00 0.00 35.35 4.18
59 60 2.137425 TACTCACGCACACCCACTCG 62.137 60.000 0.00 0.00 0.00 4.18
60 61 0.388649 CTACTCACGCACACCCACTC 60.389 60.000 0.00 0.00 0.00 3.51
61 62 1.666011 CTACTCACGCACACCCACT 59.334 57.895 0.00 0.00 0.00 4.00
62 63 1.374252 CCTACTCACGCACACCCAC 60.374 63.158 0.00 0.00 0.00 4.61
63 64 2.579657 CCCTACTCACGCACACCCA 61.580 63.158 0.00 0.00 0.00 4.51
64 65 2.264794 CCCTACTCACGCACACCC 59.735 66.667 0.00 0.00 0.00 4.61
65 66 2.434359 GCCCTACTCACGCACACC 60.434 66.667 0.00 0.00 0.00 4.16
66 67 2.434359 GGCCCTACTCACGCACAC 60.434 66.667 0.00 0.00 0.00 3.82
67 68 2.920384 TGGCCCTACTCACGCACA 60.920 61.111 0.00 0.00 0.00 4.57
68 69 2.125512 CTGGCCCTACTCACGCAC 60.126 66.667 0.00 0.00 0.00 5.34
69 70 3.390521 CCTGGCCCTACTCACGCA 61.391 66.667 0.00 0.00 0.00 5.24
70 71 2.955881 AACCTGGCCCTACTCACGC 61.956 63.158 0.00 0.00 0.00 5.34
71 72 1.079127 CAACCTGGCCCTACTCACG 60.079 63.158 0.00 0.00 0.00 4.35
72 73 1.299976 CCAACCTGGCCCTACTCAC 59.700 63.158 0.00 0.00 0.00 3.51
73 74 3.820425 CCAACCTGGCCCTACTCA 58.180 61.111 0.00 0.00 0.00 3.41
83 84 3.599285 TAGCCGTTCCGCCAACCTG 62.599 63.158 0.00 0.00 0.00 4.00
84 85 3.310860 CTAGCCGTTCCGCCAACCT 62.311 63.158 0.00 0.00 0.00 3.50
85 86 2.791501 TTCTAGCCGTTCCGCCAACC 62.792 60.000 0.00 0.00 0.00 3.77
86 87 1.359459 CTTCTAGCCGTTCCGCCAAC 61.359 60.000 0.00 0.00 0.00 3.77
87 88 1.079405 CTTCTAGCCGTTCCGCCAA 60.079 57.895 0.00 0.00 0.00 4.52
88 89 2.577059 CTTCTAGCCGTTCCGCCA 59.423 61.111 0.00 0.00 0.00 5.69
89 90 2.890961 GCTTCTAGCCGTTCCGCC 60.891 66.667 0.00 0.00 34.48 6.13
113 114 3.041940 GCTACACGCACAAGCCGT 61.042 61.111 0.00 0.00 38.92 5.68
114 115 2.730672 GAGCTACACGCACAAGCCG 61.731 63.158 0.00 0.00 42.61 5.52
115 116 1.227999 TTGAGCTACACGCACAAGCC 61.228 55.000 0.00 0.00 42.89 4.35
116 117 2.234613 TTGAGCTACACGCACAAGC 58.765 52.632 0.00 0.00 42.89 4.01
118 119 1.339929 TCTCTTGAGCTACACGCACAA 59.660 47.619 0.00 0.00 45.00 3.33
119 120 0.958822 TCTCTTGAGCTACACGCACA 59.041 50.000 0.00 0.00 42.61 4.57
120 121 1.068194 ACTCTCTTGAGCTACACGCAC 60.068 52.381 0.00 0.00 43.85 5.34
121 122 1.200252 GACTCTCTTGAGCTACACGCA 59.800 52.381 0.00 0.00 43.85 5.24
122 123 1.470890 AGACTCTCTTGAGCTACACGC 59.529 52.381 0.00 0.00 43.85 5.34
123 124 2.222931 CGAGACTCTCTTGAGCTACACG 60.223 54.545 4.52 0.00 43.85 4.49
124 125 3.004171 TCGAGACTCTCTTGAGCTACAC 58.996 50.000 4.52 0.00 43.85 2.90
125 126 3.336138 TCGAGACTCTCTTGAGCTACA 57.664 47.619 4.52 0.00 43.85 2.74
126 127 3.250040 GGATCGAGACTCTCTTGAGCTAC 59.750 52.174 4.52 0.00 41.72 3.58
127 128 3.472652 GGATCGAGACTCTCTTGAGCTA 58.527 50.000 4.52 0.00 41.72 3.32
128 129 2.297701 GGATCGAGACTCTCTTGAGCT 58.702 52.381 4.52 0.00 41.72 4.09
129 130 1.336755 GGGATCGAGACTCTCTTGAGC 59.663 57.143 4.52 0.00 40.05 4.26
130 131 1.953686 GGGGATCGAGACTCTCTTGAG 59.046 57.143 4.52 0.00 40.05 3.02
131 132 1.566703 AGGGGATCGAGACTCTCTTGA 59.433 52.381 4.52 0.00 40.90 3.02
132 133 2.065899 AGGGGATCGAGACTCTCTTG 57.934 55.000 4.52 0.00 0.00 3.02
133 134 2.661718 GAAGGGGATCGAGACTCTCTT 58.338 52.381 4.52 0.00 0.00 2.85
134 135 1.476110 CGAAGGGGATCGAGACTCTCT 60.476 57.143 4.52 0.00 45.48 3.10
135 136 0.948678 CGAAGGGGATCGAGACTCTC 59.051 60.000 0.03 0.00 45.48 3.20
136 137 0.256464 ACGAAGGGGATCGAGACTCT 59.744 55.000 3.47 0.00 45.48 3.24
137 138 0.664224 GACGAAGGGGATCGAGACTC 59.336 60.000 3.47 0.00 45.48 3.36
138 139 1.096386 CGACGAAGGGGATCGAGACT 61.096 60.000 3.47 0.00 45.48 3.24
139 140 1.094073 TCGACGAAGGGGATCGAGAC 61.094 60.000 3.47 0.00 45.48 3.36
140 141 0.179026 ATCGACGAAGGGGATCGAGA 60.179 55.000 0.00 3.38 46.99 4.04
141 142 0.238817 GATCGACGAAGGGGATCGAG 59.761 60.000 0.00 0.00 46.99 4.04
144 145 0.599060 GAGGATCGACGAAGGGGATC 59.401 60.000 0.00 0.00 38.84 3.36
145 146 0.106167 TGAGGATCGACGAAGGGGAT 60.106 55.000 0.00 0.00 38.61 3.85
146 147 0.323999 TTGAGGATCGACGAAGGGGA 60.324 55.000 0.00 0.00 38.61 4.81
147 148 0.753262 ATTGAGGATCGACGAAGGGG 59.247 55.000 0.00 0.00 38.61 4.79
148 149 2.205074 CAATTGAGGATCGACGAAGGG 58.795 52.381 0.00 0.00 38.61 3.95
149 150 2.893637 ACAATTGAGGATCGACGAAGG 58.106 47.619 13.59 0.00 38.61 3.46
150 151 3.487574 GCTACAATTGAGGATCGACGAAG 59.512 47.826 13.59 0.00 38.61 3.79
151 152 3.130516 AGCTACAATTGAGGATCGACGAA 59.869 43.478 13.59 0.00 38.61 3.85
152 153 2.688446 AGCTACAATTGAGGATCGACGA 59.312 45.455 13.59 0.00 38.61 4.20
153 154 3.046390 GAGCTACAATTGAGGATCGACG 58.954 50.000 13.59 0.00 38.61 5.12
154 155 3.046390 CGAGCTACAATTGAGGATCGAC 58.954 50.000 25.65 6.79 38.61 4.20
155 156 2.949644 TCGAGCTACAATTGAGGATCGA 59.050 45.455 27.11 27.11 38.61 3.59
156 157 3.355626 TCGAGCTACAATTGAGGATCG 57.644 47.619 24.68 24.68 38.61 3.69
157 158 5.559799 GCAATTCGAGCTACAATTGAGGATC 60.560 44.000 24.44 10.93 40.89 3.36
158 159 4.274459 GCAATTCGAGCTACAATTGAGGAT 59.726 41.667 24.44 2.53 40.89 3.24
159 160 3.623060 GCAATTCGAGCTACAATTGAGGA 59.377 43.478 24.44 0.00 40.89 3.71
160 161 3.624861 AGCAATTCGAGCTACAATTGAGG 59.375 43.478 24.44 5.29 40.89 3.86
161 162 4.495349 CCAGCAATTCGAGCTACAATTGAG 60.495 45.833 24.44 17.63 40.89 3.02
162 163 3.374988 CCAGCAATTCGAGCTACAATTGA 59.625 43.478 24.44 0.00 40.89 2.57
163 164 3.127548 ACCAGCAATTCGAGCTACAATTG 59.872 43.478 19.15 19.15 41.14 2.32
164 165 3.347216 ACCAGCAATTCGAGCTACAATT 58.653 40.909 0.00 0.00 41.14 2.32
165 166 2.991250 ACCAGCAATTCGAGCTACAAT 58.009 42.857 0.00 0.00 41.14 2.71
166 167 2.472695 ACCAGCAATTCGAGCTACAA 57.527 45.000 0.00 0.00 41.14 2.41
167 168 3.603158 TTACCAGCAATTCGAGCTACA 57.397 42.857 0.00 0.00 41.14 2.74
168 169 3.495001 GGATTACCAGCAATTCGAGCTAC 59.505 47.826 0.00 0.00 41.14 3.58
169 170 3.133901 TGGATTACCAGCAATTCGAGCTA 59.866 43.478 0.00 0.00 41.14 3.32
170 171 2.092968 TGGATTACCAGCAATTCGAGCT 60.093 45.455 0.00 0.00 44.62 4.09
171 172 2.288666 TGGATTACCAGCAATTCGAGC 58.711 47.619 0.00 0.00 41.77 5.03
184 185 7.175467 TGCTATTCATCAATCATGGTGGATTAC 59.825 37.037 0.00 0.00 37.13 1.89
185 186 7.232910 TGCTATTCATCAATCATGGTGGATTA 58.767 34.615 0.00 0.00 37.13 1.75
186 187 6.072649 TGCTATTCATCAATCATGGTGGATT 58.927 36.000 0.00 0.00 37.13 3.01
187 188 5.637127 TGCTATTCATCAATCATGGTGGAT 58.363 37.500 0.00 0.00 39.34 3.41
188 189 5.051409 TGCTATTCATCAATCATGGTGGA 57.949 39.130 0.00 0.00 38.27 4.02
189 190 5.278808 CCTTGCTATTCATCAATCATGGTGG 60.279 44.000 0.00 0.00 38.27 4.61
190 191 5.301045 ACCTTGCTATTCATCAATCATGGTG 59.699 40.000 0.00 0.00 39.14 4.17
191 192 5.301045 CACCTTGCTATTCATCAATCATGGT 59.699 40.000 0.00 0.00 30.30 3.55
192 193 5.301045 ACACCTTGCTATTCATCAATCATGG 59.699 40.000 0.00 0.00 32.64 3.66
193 194 6.387041 ACACCTTGCTATTCATCAATCATG 57.613 37.500 0.00 0.00 0.00 3.07
194 195 7.285566 ACTACACCTTGCTATTCATCAATCAT 58.714 34.615 0.00 0.00 0.00 2.45
195 196 6.653020 ACTACACCTTGCTATTCATCAATCA 58.347 36.000 0.00 0.00 0.00 2.57
196 197 8.839310 ATACTACACCTTGCTATTCATCAATC 57.161 34.615 0.00 0.00 0.00 2.67
197 198 9.060347 CAATACTACACCTTGCTATTCATCAAT 57.940 33.333 0.00 0.00 0.00 2.57
198 199 8.264347 TCAATACTACACCTTGCTATTCATCAA 58.736 33.333 0.00 0.00 0.00 2.57
199 200 7.710907 GTCAATACTACACCTTGCTATTCATCA 59.289 37.037 0.00 0.00 0.00 3.07
200 201 7.710907 TGTCAATACTACACCTTGCTATTCATC 59.289 37.037 0.00 0.00 0.00 2.92
201 202 7.564793 TGTCAATACTACACCTTGCTATTCAT 58.435 34.615 0.00 0.00 0.00 2.57
202 203 6.941857 TGTCAATACTACACCTTGCTATTCA 58.058 36.000 0.00 0.00 0.00 2.57
203 204 7.201617 GGTTGTCAATACTACACCTTGCTATTC 60.202 40.741 0.00 0.00 33.61 1.75
204 205 6.598064 GGTTGTCAATACTACACCTTGCTATT 59.402 38.462 0.00 0.00 33.61 1.73
205 206 6.070194 AGGTTGTCAATACTACACCTTGCTAT 60.070 38.462 0.00 0.00 33.61 2.97
206 207 5.247564 AGGTTGTCAATACTACACCTTGCTA 59.752 40.000 0.00 0.00 33.61 3.49
207 208 4.041691 AGGTTGTCAATACTACACCTTGCT 59.958 41.667 0.00 0.00 33.61 3.91
208 209 4.324267 AGGTTGTCAATACTACACCTTGC 58.676 43.478 0.00 0.00 33.61 4.01
209 210 6.370718 GGTTAGGTTGTCAATACTACACCTTG 59.629 42.308 15.11 0.00 33.61 3.61
210 211 6.470278 GGTTAGGTTGTCAATACTACACCTT 58.530 40.000 15.11 0.00 33.61 3.50
211 212 5.337009 CGGTTAGGTTGTCAATACTACACCT 60.337 44.000 17.31 10.31 33.61 4.00
212 213 4.866486 CGGTTAGGTTGTCAATACTACACC 59.134 45.833 13.85 13.85 33.61 4.16
213 214 5.473039 ACGGTTAGGTTGTCAATACTACAC 58.527 41.667 0.00 0.00 33.61 2.90
214 215 5.336690 GGACGGTTAGGTTGTCAATACTACA 60.337 44.000 0.00 0.00 33.61 2.74
215 216 5.105063 GGACGGTTAGGTTGTCAATACTAC 58.895 45.833 0.00 0.00 34.32 2.73
216 217 4.771577 TGGACGGTTAGGTTGTCAATACTA 59.228 41.667 0.00 0.00 34.32 1.82
217 218 3.579586 TGGACGGTTAGGTTGTCAATACT 59.420 43.478 0.00 0.00 34.32 2.12
218 219 3.929094 TGGACGGTTAGGTTGTCAATAC 58.071 45.455 0.00 0.00 34.32 1.89
219 220 4.678574 CGATGGACGGTTAGGTTGTCAATA 60.679 45.833 0.00 0.00 38.46 1.90
220 221 3.606687 GATGGACGGTTAGGTTGTCAAT 58.393 45.455 0.00 0.00 34.32 2.57
221 222 2.610976 CGATGGACGGTTAGGTTGTCAA 60.611 50.000 0.00 0.00 38.46 3.18
222 223 1.067425 CGATGGACGGTTAGGTTGTCA 60.067 52.381 0.00 0.00 38.46 3.58
223 224 1.636988 CGATGGACGGTTAGGTTGTC 58.363 55.000 0.00 0.00 38.46 3.18
224 225 0.390735 GCGATGGACGGTTAGGTTGT 60.391 55.000 0.00 0.00 42.83 3.32
225 226 1.087771 GGCGATGGACGGTTAGGTTG 61.088 60.000 0.00 0.00 42.83 3.77
226 227 1.219935 GGCGATGGACGGTTAGGTT 59.780 57.895 0.00 0.00 42.83 3.50
227 228 2.897972 GGCGATGGACGGTTAGGT 59.102 61.111 0.00 0.00 42.83 3.08
228 229 2.279252 CGGCGATGGACGGTTAGG 60.279 66.667 0.00 0.00 42.40 2.69
234 235 4.891727 CTTCCCCGGCGATGGACG 62.892 72.222 16.10 11.54 46.94 4.79
235 236 2.717139 GATCTTCCCCGGCGATGGAC 62.717 65.000 16.10 3.45 0.00 4.02
236 237 2.445845 ATCTTCCCCGGCGATGGA 60.446 61.111 9.30 11.66 0.00 3.41
237 238 2.031163 GATCTTCCCCGGCGATGG 59.969 66.667 9.30 9.03 0.00 3.51
238 239 2.031163 GGATCTTCCCCGGCGATG 59.969 66.667 9.30 0.00 0.00 3.84
239 240 1.418908 AATGGATCTTCCCCGGCGAT 61.419 55.000 9.30 0.00 35.03 4.58
240 241 2.040009 GAATGGATCTTCCCCGGCGA 62.040 60.000 9.30 0.00 35.03 5.54
241 242 1.598130 GAATGGATCTTCCCCGGCG 60.598 63.158 0.00 0.00 35.03 6.46
242 243 1.228276 GGAATGGATCTTCCCCGGC 60.228 63.158 0.00 0.00 39.06 6.13
243 244 1.071471 CGGAATGGATCTTCCCCGG 59.929 63.158 7.89 0.00 41.46 5.73
244 245 1.598130 GCGGAATGGATCTTCCCCG 60.598 63.158 7.89 9.56 41.46 5.73
245 246 0.819666 GTGCGGAATGGATCTTCCCC 60.820 60.000 7.89 0.86 41.46 4.81
246 247 0.107214 TGTGCGGAATGGATCTTCCC 60.107 55.000 7.89 2.93 41.46 3.97
247 248 1.303309 CTGTGCGGAATGGATCTTCC 58.697 55.000 4.05 4.05 41.16 3.46
248 249 0.659957 GCTGTGCGGAATGGATCTTC 59.340 55.000 0.00 0.00 0.00 2.87
249 250 2.785868 GCTGTGCGGAATGGATCTT 58.214 52.632 0.00 0.00 0.00 2.40
250 251 4.547859 GCTGTGCGGAATGGATCT 57.452 55.556 0.00 0.00 0.00 2.75
271 272 2.505777 CACTCGACTGCTCTGGCG 60.506 66.667 0.00 0.00 42.25 5.69
272 273 2.813042 GCACTCGACTGCTCTGGC 60.813 66.667 9.49 0.00 34.06 4.85
273 274 0.601046 TTTGCACTCGACTGCTCTGG 60.601 55.000 16.41 0.00 38.07 3.86
274 275 0.788995 CTTTGCACTCGACTGCTCTG 59.211 55.000 16.41 4.60 38.07 3.35
275 276 0.390860 ACTTTGCACTCGACTGCTCT 59.609 50.000 16.41 0.00 38.07 4.09
276 277 0.787183 GACTTTGCACTCGACTGCTC 59.213 55.000 16.41 4.00 38.07 4.26
277 278 0.941463 CGACTTTGCACTCGACTGCT 60.941 55.000 16.41 0.00 38.07 4.24
278 279 1.488957 CGACTTTGCACTCGACTGC 59.511 57.895 9.79 9.79 37.70 4.40
316 317 6.426646 GACAGTATCCATGGTAATCCTCTT 57.573 41.667 12.58 0.00 34.23 2.85
353 354 0.735471 GCGAAATCCAGAGAAAGGCC 59.265 55.000 0.00 0.00 0.00 5.19
355 356 2.409948 AGGCGAAATCCAGAGAAAGG 57.590 50.000 0.00 0.00 0.00 3.11
358 359 2.819608 CCAAAAGGCGAAATCCAGAGAA 59.180 45.455 0.00 0.00 0.00 2.87
364 365 4.424626 GAAAGATCCAAAAGGCGAAATCC 58.575 43.478 0.00 0.00 0.00 3.01
471 473 1.668337 GCGGTTGTTTACATGCATGCA 60.668 47.619 26.53 25.04 31.96 3.96
505 507 1.407979 CTTGTCCTAATCGGCCTACGT 59.592 52.381 0.00 0.00 44.69 3.57
516 518 2.355716 GCACCATAGTGGCTTGTCCTAA 60.356 50.000 0.00 0.00 42.67 2.69
606 609 2.097036 CAAAACCGGATAAGGGGGTTC 58.903 52.381 9.46 0.00 42.97 3.62
729 732 1.265454 ACCGCTGCCTAGGTAAAGCT 61.265 55.000 22.70 9.28 39.30 3.74
771 774 4.324135 GCTAAACAAACCGTTGAAAAACGT 59.676 37.500 9.81 0.00 44.04 3.99
847 859 1.156736 CCAACGACCAATCAGACACC 58.843 55.000 0.00 0.00 0.00 4.16
880 892 2.235155 ACATGGCCGCGAATATATACCA 59.765 45.455 8.23 1.95 0.00 3.25
881 893 2.864343 GACATGGCCGCGAATATATACC 59.136 50.000 8.23 0.00 0.00 2.73
893 905 4.889856 TGATCCGCGACATGGCCG 62.890 66.667 8.23 0.00 0.00 6.13
894 906 1.893808 AATGATCCGCGACATGGCC 60.894 57.895 8.23 0.00 0.00 5.36
895 907 1.280746 CAATGATCCGCGACATGGC 59.719 57.895 8.23 0.00 0.00 4.40
896 908 1.280746 GCAATGATCCGCGACATGG 59.719 57.895 8.23 9.21 0.00 3.66
897 909 4.907946 GCAATGATCCGCGACATG 57.092 55.556 8.23 6.79 0.00 3.21
926 938 0.902531 CTACCTCGCTTTCCCTTCCA 59.097 55.000 0.00 0.00 0.00 3.53
993 1011 0.543749 CTCCCTTCTCCATCACCACC 59.456 60.000 0.00 0.00 0.00 4.61
1011 1029 2.297129 GCAGGACAGCCCTCTTCCT 61.297 63.158 0.00 0.00 45.60 3.36
1377 1408 4.681978 GGTGGCGACGGACTTGCT 62.682 66.667 0.00 0.00 0.00 3.91
1418 1449 2.677289 CCATGAGAGGGCCAGCAGT 61.677 63.158 6.18 0.00 0.00 4.40
1421 1452 1.147153 GTACCATGAGAGGGCCAGC 59.853 63.158 6.18 0.00 0.00 4.85
1459 1491 6.626181 GCGTATTTATTTTTCCACCATGGTCA 60.626 38.462 16.53 0.77 39.03 4.02
1471 1503 4.090786 GTGCTTTGGCGCGTATTTATTTTT 59.909 37.500 8.43 0.00 42.25 1.94
1474 1506 2.792749 GTGCTTTGGCGCGTATTTATT 58.207 42.857 8.43 0.00 42.25 1.40
1488 1524 4.022589 CACAGAATTCTCATGTGGTGCTTT 60.023 41.667 15.21 0.00 40.47 3.51
1570 1614 1.522092 CAGCAGGATAACGGCCAGA 59.478 57.895 2.24 0.00 41.55 3.86
1579 1623 4.221422 GCCGTCGCCAGCAGGATA 62.221 66.667 0.00 0.00 36.89 2.59
1700 1744 2.419198 GATGAGGAGCGCCGTGAT 59.581 61.111 2.29 0.00 39.96 3.06
1793 1837 0.669318 ACACGGATGGTAGTTGTGCG 60.669 55.000 0.00 0.00 33.96 5.34
1850 1894 1.602311 GATCATTGCTTGGATCGCCT 58.398 50.000 0.00 0.00 31.54 5.52
1986 2031 0.977395 ACCCGAGACCAAAAGGAGAG 59.023 55.000 0.00 0.00 0.00 3.20
2010 2055 0.680921 TTGCCAGCCTACCAAGATGC 60.681 55.000 0.00 0.00 0.00 3.91
2115 2162 2.341168 GTCATTTACAATTTGCACGGCG 59.659 45.455 4.80 4.80 0.00 6.46
2198 2245 1.597854 CAGCAGAGCACAAACCCGA 60.598 57.895 0.00 0.00 0.00 5.14
2212 2259 1.908344 TAGTGCTCAAAATGGCAGCA 58.092 45.000 0.00 0.00 40.90 4.41
2213 2260 2.030007 TGTTAGTGCTCAAAATGGCAGC 60.030 45.455 0.00 0.00 39.22 5.25
2216 2263 3.126858 TCGATGTTAGTGCTCAAAATGGC 59.873 43.478 0.00 0.00 0.00 4.40
2225 2272 1.290203 CGCCAATCGATGTTAGTGCT 58.710 50.000 0.00 0.00 41.67 4.40
2233 2280 0.249447 TCACTAGCCGCCAATCGATG 60.249 55.000 0.00 0.00 41.67 3.84
2234 2281 0.032678 CTCACTAGCCGCCAATCGAT 59.967 55.000 0.00 0.00 41.67 3.59
2235 2282 1.437573 CTCACTAGCCGCCAATCGA 59.562 57.895 0.00 0.00 41.67 3.59
2236 2283 2.240500 GCTCACTAGCCGCCAATCG 61.241 63.158 0.00 0.00 43.40 3.34
2237 2284 3.724494 GCTCACTAGCCGCCAATC 58.276 61.111 0.00 0.00 43.40 2.67
2246 2293 0.031857 CGGCTGGAGATGCTCACTAG 59.968 60.000 0.00 0.00 31.08 2.57
2247 2294 0.395724 TCGGCTGGAGATGCTCACTA 60.396 55.000 0.00 0.00 31.08 2.74
2248 2295 1.047596 ATCGGCTGGAGATGCTCACT 61.048 55.000 0.00 0.00 31.08 3.41
2249 2296 0.599728 GATCGGCTGGAGATGCTCAC 60.600 60.000 0.00 0.00 31.08 3.51
2250 2297 1.744639 GATCGGCTGGAGATGCTCA 59.255 57.895 0.00 0.00 31.08 4.26
2251 2298 1.005156 GGATCGGCTGGAGATGCTC 60.005 63.158 0.00 0.00 34.28 4.26
2252 2299 1.126329 ATGGATCGGCTGGAGATGCT 61.126 55.000 0.00 0.00 37.35 3.79
2253 2300 0.610174 TATGGATCGGCTGGAGATGC 59.390 55.000 0.00 0.00 37.04 3.91
2254 2301 3.407424 TTTATGGATCGGCTGGAGATG 57.593 47.619 0.00 0.00 0.00 2.90
2255 2302 4.780021 ACTATTTATGGATCGGCTGGAGAT 59.220 41.667 0.00 0.00 0.00 2.75
2256 2303 4.021104 CACTATTTATGGATCGGCTGGAGA 60.021 45.833 0.00 0.00 0.00 3.71
2257 2304 4.021104 TCACTATTTATGGATCGGCTGGAG 60.021 45.833 0.00 0.00 0.00 3.86
2258 2305 3.901222 TCACTATTTATGGATCGGCTGGA 59.099 43.478 0.00 0.00 0.00 3.86
2259 2306 4.248859 CTCACTATTTATGGATCGGCTGG 58.751 47.826 0.00 0.00 0.00 4.85
2260 2307 4.248859 CCTCACTATTTATGGATCGGCTG 58.751 47.826 0.00 0.00 0.00 4.85
2261 2308 3.904339 ACCTCACTATTTATGGATCGGCT 59.096 43.478 0.00 0.00 0.00 5.52
2262 2309 4.273148 ACCTCACTATTTATGGATCGGC 57.727 45.455 0.00 0.00 0.00 5.54
2263 2310 7.707035 GCTATTACCTCACTATTTATGGATCGG 59.293 40.741 0.00 0.00 0.00 4.18
2264 2311 8.251026 TGCTATTACCTCACTATTTATGGATCG 58.749 37.037 0.00 0.00 0.00 3.69
2265 2312 9.372369 GTGCTATTACCTCACTATTTATGGATC 57.628 37.037 0.00 0.00 0.00 3.36
2266 2313 8.322091 GGTGCTATTACCTCACTATTTATGGAT 58.678 37.037 0.00 0.00 37.74 3.41
2271 2318 6.042781 CCTGGGTGCTATTACCTCACTATTTA 59.957 42.308 0.00 0.00 40.66 1.40
2317 2365 5.716228 TGCAAGTTTGGGACTAAATCATCAT 59.284 36.000 0.00 0.00 37.72 2.45
2346 2394 4.008916 AGTTGGGGTATGGTAGAGTGAT 57.991 45.455 0.00 0.00 0.00 3.06
2353 2401 1.004979 GGTGCAAGTTGGGGTATGGTA 59.995 52.381 4.75 0.00 0.00 3.25
2457 2511 3.551635 TTAAAGAAAATGGCAGGGGGA 57.448 42.857 0.00 0.00 0.00 4.81
2467 2521 5.336451 GGAGTGCGGGTTGATTAAAGAAAAT 60.336 40.000 0.00 0.00 0.00 1.82
2529 2583 0.824595 TGAACCCTCTCGAACGGACA 60.825 55.000 1.38 0.00 0.00 4.02
2654 2709 1.335506 GCCGGACGAGATGAGAAGATC 60.336 57.143 5.05 0.00 0.00 2.75
2683 2738 4.624913 TCACAGTAATCAGGAGGGAAGAT 58.375 43.478 0.00 0.00 0.00 2.40
2803 2873 3.361158 CGGGCACAAATGGACGCA 61.361 61.111 0.00 0.00 0.00 5.24
2818 2888 0.815734 ACTACACGACCCTGATTCGG 59.184 55.000 0.00 0.00 40.92 4.30


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

AutoCloner maintained by Alex Coulton.