Multiple sequence alignment - TraesCS4D01G075400

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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 TraesCS4D01G075400 chr4D 100.000 2969 0 0 1 2969 49894398 49891430 0.000000e+00 5483
1 TraesCS4D01G075400 chr4D 97.368 228 6 0 1 228 49907844 49908071 3.590000e-104 388
2 TraesCS4D01G075400 chr4D 93.711 159 9 1 228 386 49913356 49913199 1.380000e-58 237
3 TraesCS4D01G075400 chr4D 93.082 159 10 1 228 386 49916666 49916509 6.400000e-57 231
4 TraesCS4D01G075400 chr4D 95.205 146 6 1 228 373 49911225 49911081 2.300000e-56 230
5 TraesCS4D01G075400 chr4D 92.949 156 10 1 228 383 49909439 49909285 2.980000e-55 226
6 TraesCS4D01G075400 chr4B 93.667 2574 102 16 248 2777 73474447 73471891 0.000000e+00 3794
7 TraesCS4D01G075400 chr4B 97.368 228 6 0 1 228 17381454 17381227 3.590000e-104 388
8 TraesCS4D01G075400 chr4A 90.296 1824 92 21 502 2276 547199965 547201752 0.000000e+00 2309
9 TraesCS4D01G075400 chr4A 87.514 905 81 25 2067 2951 547201748 547202640 0.000000e+00 1016
10 TraesCS4D01G075400 chr4A 95.528 246 5 4 228 469 547199496 547199739 3.590000e-104 388
11 TraesCS4D01G075400 chr2D 97.368 228 6 0 1 228 620814684 620814457 3.590000e-104 388
12 TraesCS4D01G075400 chr2D 96.552 232 8 0 4 235 586571102 586571333 4.640000e-103 385
13 TraesCS4D01G075400 chr2D 96.552 232 7 1 1 232 620820593 620820823 1.670000e-102 383
14 TraesCS4D01G075400 chr7D 96.121 232 9 0 1 232 462255326 462255095 2.160000e-101 379
15 TraesCS4D01G075400 chr7D 95.745 235 8 2 1 235 616909927 616909695 7.770000e-101 377
16 TraesCS4D01G075400 chr5D 96.491 228 8 0 1 228 4810014 4810241 7.770000e-101 377
17 TraesCS4D01G075400 chr3D 96.491 228 8 0 1 228 434262559 434262332 7.770000e-101 377


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 TraesCS4D01G075400 chr4D 49891430 49894398 2968 True 5483.000000 5483 100.000000 1 2969 1 chr4D.!!$R1 2968
1 TraesCS4D01G075400 chr4D 49909285 49916666 7381 True 231.000000 237 93.736750 228 386 4 chr4D.!!$R2 158
2 TraesCS4D01G075400 chr4B 73471891 73474447 2556 True 3794.000000 3794 93.667000 248 2777 1 chr4B.!!$R2 2529
3 TraesCS4D01G075400 chr4A 547199496 547202640 3144 False 1237.666667 2309 91.112667 228 2951 3 chr4A.!!$F1 2723

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
35 36 0.040067 CTCGCCAGTGCAAAAGAACC 60.040 55.0 0.00 0.00 37.32 3.62 F
83 84 0.103572 AGTCAAACAGTACGCCACGT 59.896 50.0 0.00 0.00 44.35 4.49 F
84 85 0.231279 GTCAAACAGTACGCCACGTG 59.769 55.0 9.08 9.08 41.39 4.49 F
1185 8620 0.319211 CCAAGACGTCGTGGCTGTTA 60.319 55.0 32.54 0.00 38.58 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1191 8626 0.179171 GATCGTCGTCGCTGGAAGAA 60.179 55.0 0.0 0.00 32.42 2.52 R
1710 9184 0.313043 CCTGTCCACAAAGCTTGCAG 59.687 55.0 0.0 2.41 0.00 4.41 R
1859 9351 0.536687 CCATATGCTGGGAGCTGGTG 60.537 60.0 0.0 0.00 42.97 4.17 R
2845 10542 0.813821 GGAGCAACTGAATCAAGGGC 59.186 55.0 0.0 0.00 0.00 5.19 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 3.603365 CCCCCAAATCAACTCGCC 58.397 61.111 0.00 0.00 0.00 5.54
22 23 1.304052 CCCCCAAATCAACTCGCCA 60.304 57.895 0.00 0.00 0.00 5.69
23 24 1.315257 CCCCCAAATCAACTCGCCAG 61.315 60.000 0.00 0.00 0.00 4.85
24 25 0.609131 CCCCAAATCAACTCGCCAGT 60.609 55.000 0.00 0.00 0.00 4.00
25 26 0.523072 CCCAAATCAACTCGCCAGTG 59.477 55.000 0.00 0.00 31.06 3.66
26 27 0.109597 CCAAATCAACTCGCCAGTGC 60.110 55.000 0.00 0.00 31.06 4.40
27 28 0.592637 CAAATCAACTCGCCAGTGCA 59.407 50.000 0.00 0.00 37.32 4.57
28 29 1.001487 CAAATCAACTCGCCAGTGCAA 60.001 47.619 0.00 0.00 37.32 4.08
29 30 1.317613 AATCAACTCGCCAGTGCAAA 58.682 45.000 0.00 0.00 37.32 3.68
30 31 1.317613 ATCAACTCGCCAGTGCAAAA 58.682 45.000 0.00 0.00 37.32 2.44
31 32 0.662619 TCAACTCGCCAGTGCAAAAG 59.337 50.000 0.00 0.00 37.32 2.27
32 33 0.662619 CAACTCGCCAGTGCAAAAGA 59.337 50.000 0.00 0.00 37.32 2.52
33 34 1.065401 CAACTCGCCAGTGCAAAAGAA 59.935 47.619 0.00 0.00 37.32 2.52
34 35 0.663153 ACTCGCCAGTGCAAAAGAAC 59.337 50.000 0.00 0.00 37.32 3.01
35 36 0.040067 CTCGCCAGTGCAAAAGAACC 60.040 55.000 0.00 0.00 37.32 3.62
36 37 1.007387 CGCCAGTGCAAAAGAACCC 60.007 57.895 0.00 0.00 37.32 4.11
37 38 1.367471 GCCAGTGCAAAAGAACCCC 59.633 57.895 0.00 0.00 37.47 4.95
38 39 2.049435 CCAGTGCAAAAGAACCCCC 58.951 57.895 0.00 0.00 0.00 5.40
39 40 1.659794 CAGTGCAAAAGAACCCCCG 59.340 57.895 0.00 0.00 0.00 5.73
40 41 2.200337 AGTGCAAAAGAACCCCCGC 61.200 57.895 0.00 0.00 0.00 6.13
41 42 2.915137 TGCAAAAGAACCCCCGCC 60.915 61.111 0.00 0.00 0.00 6.13
42 43 2.600470 GCAAAAGAACCCCCGCCT 60.600 61.111 0.00 0.00 0.00 5.52
43 44 2.636412 GCAAAAGAACCCCCGCCTC 61.636 63.158 0.00 0.00 0.00 4.70
44 45 2.033602 AAAAGAACCCCCGCCTCG 59.966 61.111 0.00 0.00 0.00 4.63
45 46 4.717313 AAAGAACCCCCGCCTCGC 62.717 66.667 0.00 0.00 0.00 5.03
61 62 3.286751 GCTTGCGTGGCAGGTCAA 61.287 61.111 9.16 11.80 40.61 3.18
62 63 2.844451 GCTTGCGTGGCAGGTCAAA 61.844 57.895 9.16 1.14 40.61 2.69
63 64 1.283793 CTTGCGTGGCAGGTCAAAG 59.716 57.895 9.16 6.97 40.61 2.77
64 65 1.153066 TTGCGTGGCAGGTCAAAGA 60.153 52.632 9.16 0.00 40.61 2.52
65 66 1.165907 TTGCGTGGCAGGTCAAAGAG 61.166 55.000 9.16 0.00 40.61 2.85
66 67 1.598130 GCGTGGCAGGTCAAAGAGT 60.598 57.895 9.16 0.00 0.00 3.24
67 68 1.569479 GCGTGGCAGGTCAAAGAGTC 61.569 60.000 9.16 0.00 0.00 3.36
68 69 0.249868 CGTGGCAGGTCAAAGAGTCA 60.250 55.000 0.00 0.00 0.00 3.41
69 70 1.810031 CGTGGCAGGTCAAAGAGTCAA 60.810 52.381 0.00 0.00 0.00 3.18
70 71 2.297701 GTGGCAGGTCAAAGAGTCAAA 58.702 47.619 0.00 0.00 0.00 2.69
71 72 2.033424 GTGGCAGGTCAAAGAGTCAAAC 59.967 50.000 0.00 0.00 0.00 2.93
72 73 2.297701 GGCAGGTCAAAGAGTCAAACA 58.702 47.619 0.00 0.00 0.00 2.83
73 74 2.291741 GGCAGGTCAAAGAGTCAAACAG 59.708 50.000 0.00 0.00 0.00 3.16
74 75 2.945668 GCAGGTCAAAGAGTCAAACAGT 59.054 45.455 0.00 0.00 0.00 3.55
75 76 4.127171 GCAGGTCAAAGAGTCAAACAGTA 58.873 43.478 0.00 0.00 0.00 2.74
76 77 4.024809 GCAGGTCAAAGAGTCAAACAGTAC 60.025 45.833 0.00 0.00 0.00 2.73
77 78 4.209288 CAGGTCAAAGAGTCAAACAGTACG 59.791 45.833 0.00 0.00 0.00 3.67
78 79 3.059800 GGTCAAAGAGTCAAACAGTACGC 60.060 47.826 0.00 0.00 0.00 4.42
79 80 3.059800 GTCAAAGAGTCAAACAGTACGCC 60.060 47.826 0.00 0.00 0.00 5.68
80 81 2.869801 CAAAGAGTCAAACAGTACGCCA 59.130 45.455 0.00 0.00 0.00 5.69
81 82 2.150397 AGAGTCAAACAGTACGCCAC 57.850 50.000 0.00 0.00 0.00 5.01
82 83 0.782384 GAGTCAAACAGTACGCCACG 59.218 55.000 0.00 0.00 0.00 4.94
83 84 0.103572 AGTCAAACAGTACGCCACGT 59.896 50.000 0.00 0.00 44.35 4.49
84 85 0.231279 GTCAAACAGTACGCCACGTG 59.769 55.000 9.08 9.08 41.39 4.49
85 86 0.876777 TCAAACAGTACGCCACGTGG 60.877 55.000 30.66 30.66 41.39 4.94
86 87 1.595929 AAACAGTACGCCACGTGGG 60.596 57.895 34.58 25.62 41.39 4.61
87 88 2.030490 AAACAGTACGCCACGTGGGA 62.030 55.000 34.58 4.42 41.39 4.37
88 89 2.431942 CAGTACGCCACGTGGGAC 60.432 66.667 34.58 18.67 41.39 4.46
89 90 2.913578 AGTACGCCACGTGGGACA 60.914 61.111 34.58 15.20 41.39 4.02
90 91 2.029369 GTACGCCACGTGGGACAA 59.971 61.111 34.58 13.30 44.16 3.18
91 92 1.594836 GTACGCCACGTGGGACAAA 60.595 57.895 34.58 7.94 44.16 2.83
92 93 0.952010 GTACGCCACGTGGGACAAAT 60.952 55.000 34.58 11.61 44.16 2.32
93 94 0.607112 TACGCCACGTGGGACAAATA 59.393 50.000 34.58 10.69 44.16 1.40
94 95 0.952010 ACGCCACGTGGGACAAATAC 60.952 55.000 34.58 14.97 44.16 1.89
95 96 1.791662 GCCACGTGGGACAAATACG 59.208 57.895 34.58 6.74 44.16 3.06
96 97 1.641123 GCCACGTGGGACAAATACGG 61.641 60.000 34.58 6.24 44.16 4.02
97 98 1.641123 CCACGTGGGACAAATACGGC 61.641 60.000 27.57 0.00 44.16 5.68
98 99 1.738830 ACGTGGGACAAATACGGCG 60.739 57.895 4.80 4.80 44.16 6.46
99 100 1.446445 CGTGGGACAAATACGGCGA 60.446 57.895 16.62 0.00 44.16 5.54
100 101 1.689352 CGTGGGACAAATACGGCGAC 61.689 60.000 16.62 0.00 44.16 5.19
128 129 2.048597 CGGTGACCTGCGCTGTTA 60.049 61.111 9.73 0.00 0.00 2.41
129 130 1.666553 CGGTGACCTGCGCTGTTAA 60.667 57.895 9.73 0.00 0.00 2.01
130 131 1.866925 GGTGACCTGCGCTGTTAAC 59.133 57.895 9.73 0.00 0.00 2.01
131 132 0.882927 GGTGACCTGCGCTGTTAACA 60.883 55.000 9.73 8.28 0.00 2.41
132 133 0.941542 GTGACCTGCGCTGTTAACAA 59.058 50.000 9.73 0.00 0.00 2.83
133 134 1.332375 GTGACCTGCGCTGTTAACAAA 59.668 47.619 9.73 0.00 0.00 2.83
134 135 2.031157 GTGACCTGCGCTGTTAACAAAT 60.031 45.455 9.73 0.00 0.00 2.32
135 136 2.031245 TGACCTGCGCTGTTAACAAATG 60.031 45.455 9.73 3.58 0.00 2.32
136 137 1.953686 ACCTGCGCTGTTAACAAATGT 59.046 42.857 9.73 0.00 0.00 2.71
137 138 3.142951 ACCTGCGCTGTTAACAAATGTA 58.857 40.909 9.73 1.36 0.00 2.29
138 139 3.566322 ACCTGCGCTGTTAACAAATGTAA 59.434 39.130 9.73 0.00 0.00 2.41
139 140 4.217550 ACCTGCGCTGTTAACAAATGTAAT 59.782 37.500 9.73 0.00 0.00 1.89
140 141 4.558470 CCTGCGCTGTTAACAAATGTAATG 59.442 41.667 9.73 0.00 0.00 1.90
141 142 5.363979 TGCGCTGTTAACAAATGTAATGA 57.636 34.783 9.73 0.00 0.00 2.57
142 143 5.948588 TGCGCTGTTAACAAATGTAATGAT 58.051 33.333 9.73 0.00 0.00 2.45
143 144 7.078011 TGCGCTGTTAACAAATGTAATGATA 57.922 32.000 9.73 0.00 0.00 2.15
144 145 7.530863 TGCGCTGTTAACAAATGTAATGATAA 58.469 30.769 9.73 0.00 0.00 1.75
145 146 7.696035 TGCGCTGTTAACAAATGTAATGATAAG 59.304 33.333 9.73 0.00 0.00 1.73
146 147 7.305418 GCGCTGTTAACAAATGTAATGATAAGC 60.305 37.037 10.03 3.45 0.00 3.09
147 148 7.696035 CGCTGTTAACAAATGTAATGATAAGCA 59.304 33.333 10.03 0.00 0.00 3.91
148 149 8.798153 GCTGTTAACAAATGTAATGATAAGCAC 58.202 33.333 10.03 0.00 0.00 4.40
149 150 9.289303 CTGTTAACAAATGTAATGATAAGCACC 57.711 33.333 10.03 0.00 0.00 5.01
150 151 7.965655 TGTTAACAAATGTAATGATAAGCACCG 59.034 33.333 5.64 0.00 0.00 4.94
151 152 6.509418 AACAAATGTAATGATAAGCACCGT 57.491 33.333 0.00 0.00 0.00 4.83
152 153 7.618502 AACAAATGTAATGATAAGCACCGTA 57.381 32.000 0.00 0.00 0.00 4.02
153 154 7.618502 ACAAATGTAATGATAAGCACCGTAA 57.381 32.000 0.00 0.00 0.00 3.18
154 155 8.220755 ACAAATGTAATGATAAGCACCGTAAT 57.779 30.769 0.00 0.00 0.00 1.89
155 156 8.342634 ACAAATGTAATGATAAGCACCGTAATC 58.657 33.333 0.00 0.00 0.00 1.75
156 157 8.559536 CAAATGTAATGATAAGCACCGTAATCT 58.440 33.333 0.00 0.00 0.00 2.40
157 158 7.658179 ATGTAATGATAAGCACCGTAATCTG 57.342 36.000 0.00 0.00 0.00 2.90
158 159 5.989168 TGTAATGATAAGCACCGTAATCTGG 59.011 40.000 0.00 0.00 0.00 3.86
159 160 3.469008 TGATAAGCACCGTAATCTGGG 57.531 47.619 0.00 0.00 0.00 4.45
160 161 2.769663 TGATAAGCACCGTAATCTGGGT 59.230 45.455 0.00 0.00 36.87 4.51
161 162 3.962063 TGATAAGCACCGTAATCTGGGTA 59.038 43.478 0.00 0.00 33.95 3.69
162 163 4.591498 TGATAAGCACCGTAATCTGGGTAT 59.409 41.667 0.00 0.00 33.95 2.73
163 164 3.926058 AAGCACCGTAATCTGGGTATT 57.074 42.857 0.00 0.00 33.95 1.89
164 165 3.470645 AGCACCGTAATCTGGGTATTC 57.529 47.619 0.00 0.00 33.95 1.75
165 166 2.132762 GCACCGTAATCTGGGTATTCG 58.867 52.381 0.00 0.00 33.95 3.34
166 167 2.750948 CACCGTAATCTGGGTATTCGG 58.249 52.381 0.00 0.00 36.48 4.30
167 168 2.101917 CACCGTAATCTGGGTATTCGGT 59.898 50.000 0.00 0.00 40.31 4.69
168 169 3.318839 CACCGTAATCTGGGTATTCGGTA 59.681 47.826 6.05 0.00 39.01 4.02
169 170 3.960102 ACCGTAATCTGGGTATTCGGTAA 59.040 43.478 4.56 0.00 39.13 2.85
170 171 4.590222 ACCGTAATCTGGGTATTCGGTAAT 59.410 41.667 4.56 0.00 39.13 1.89
171 172 5.166398 CCGTAATCTGGGTATTCGGTAATC 58.834 45.833 0.00 0.00 31.07 1.75
172 173 5.166398 CGTAATCTGGGTATTCGGTAATCC 58.834 45.833 0.00 0.00 0.00 3.01
173 174 5.279106 CGTAATCTGGGTATTCGGTAATCCA 60.279 44.000 0.00 0.00 0.00 3.41
174 175 5.640158 AATCTGGGTATTCGGTAATCCAA 57.360 39.130 0.00 0.00 0.00 3.53
175 176 5.843019 ATCTGGGTATTCGGTAATCCAAT 57.157 39.130 0.00 0.00 0.00 3.16
176 177 4.968259 TCTGGGTATTCGGTAATCCAATG 58.032 43.478 0.00 0.00 0.00 2.82
177 178 4.656575 TCTGGGTATTCGGTAATCCAATGA 59.343 41.667 0.00 0.00 0.00 2.57
178 179 4.710324 TGGGTATTCGGTAATCCAATGAC 58.290 43.478 0.00 0.00 0.00 3.06
179 180 4.070009 GGGTATTCGGTAATCCAATGACC 58.930 47.826 0.00 0.00 0.00 4.02
180 181 4.445162 GGGTATTCGGTAATCCAATGACCA 60.445 45.833 0.00 0.00 32.39 4.02
181 182 5.127491 GGTATTCGGTAATCCAATGACCAA 58.873 41.667 0.00 0.00 32.39 3.67
182 183 5.591067 GGTATTCGGTAATCCAATGACCAAA 59.409 40.000 0.00 0.00 32.39 3.28
183 184 5.835113 ATTCGGTAATCCAATGACCAAAG 57.165 39.130 0.00 0.00 32.39 2.77
184 185 4.295141 TCGGTAATCCAATGACCAAAGT 57.705 40.909 0.00 0.00 32.39 2.66
185 186 4.006989 TCGGTAATCCAATGACCAAAGTG 58.993 43.478 0.00 0.00 32.39 3.16
186 187 4.006989 CGGTAATCCAATGACCAAAGTGA 58.993 43.478 0.00 0.00 32.39 3.41
187 188 4.457603 CGGTAATCCAATGACCAAAGTGAA 59.542 41.667 0.00 0.00 32.39 3.18
188 189 5.619086 CGGTAATCCAATGACCAAAGTGAAC 60.619 44.000 0.00 0.00 32.39 3.18
189 190 5.476945 GGTAATCCAATGACCAAAGTGAACT 59.523 40.000 0.00 0.00 33.16 3.01
190 191 6.015434 GGTAATCCAATGACCAAAGTGAACTT 60.015 38.462 0.00 0.00 37.91 2.66
191 192 6.484364 AATCCAATGACCAAAGTGAACTTT 57.516 33.333 2.56 2.56 46.23 2.66
206 207 7.807977 AGTGAACTTTGTGATCAAATACAGT 57.192 32.000 0.00 0.00 41.77 3.55
207 208 7.642669 AGTGAACTTTGTGATCAAATACAGTG 58.357 34.615 0.00 0.00 41.77 3.66
208 209 7.498900 AGTGAACTTTGTGATCAAATACAGTGA 59.501 33.333 0.00 0.00 41.77 3.41
209 210 7.587757 GTGAACTTTGTGATCAAATACAGTGAC 59.412 37.037 0.00 0.00 41.77 3.67
210 211 6.560253 ACTTTGTGATCAAATACAGTGACC 57.440 37.500 0.00 0.00 41.77 4.02
211 212 5.179368 ACTTTGTGATCAAATACAGTGACCG 59.821 40.000 0.00 0.00 41.77 4.79
212 213 3.000041 TGTGATCAAATACAGTGACCGC 59.000 45.455 0.00 0.00 0.00 5.68
213 214 2.029244 GTGATCAAATACAGTGACCGCG 59.971 50.000 0.00 0.00 0.00 6.46
214 215 1.593006 GATCAAATACAGTGACCGCGG 59.407 52.381 26.86 26.86 0.00 6.46
215 216 0.390603 TCAAATACAGTGACCGCGGG 60.391 55.000 31.76 13.93 0.00 6.13
216 217 0.672401 CAAATACAGTGACCGCGGGT 60.672 55.000 31.76 19.47 39.44 5.28
217 218 0.672401 AAATACAGTGACCGCGGGTG 60.672 55.000 31.76 22.07 35.25 4.61
218 219 1.537814 AATACAGTGACCGCGGGTGA 61.538 55.000 31.76 9.81 35.25 4.02
219 220 1.537814 ATACAGTGACCGCGGGTGAA 61.538 55.000 31.76 8.82 35.25 3.18
220 221 1.537814 TACAGTGACCGCGGGTGAAT 61.538 55.000 31.76 7.71 35.25 2.57
221 222 1.671054 CAGTGACCGCGGGTGAATT 60.671 57.895 31.76 6.78 35.25 2.17
222 223 1.072505 AGTGACCGCGGGTGAATTT 59.927 52.632 31.76 5.85 35.25 1.82
223 224 0.322322 AGTGACCGCGGGTGAATTTA 59.678 50.000 31.76 0.00 35.25 1.40
224 225 1.158434 GTGACCGCGGGTGAATTTAA 58.842 50.000 31.76 0.00 35.25 1.52
225 226 1.135888 GTGACCGCGGGTGAATTTAAC 60.136 52.381 31.76 5.66 35.25 2.01
226 227 1.270947 TGACCGCGGGTGAATTTAACT 60.271 47.619 31.76 2.41 35.25 2.24
242 3553 0.621862 AACTCTCCTCCCACCCATCC 60.622 60.000 0.00 0.00 0.00 3.51
260 3571 4.579753 CCATCCCAAACAAAACAAGCAAAT 59.420 37.500 0.00 0.00 0.00 2.32
264 3575 7.313951 TCCCAAACAAAACAAGCAAATAAAG 57.686 32.000 0.00 0.00 0.00 1.85
601 8027 1.144276 GAACCCTAGCCGCCTTCTC 59.856 63.158 0.00 0.00 0.00 2.87
662 8091 2.861974 TCCACCCCTCCCAAACCC 60.862 66.667 0.00 0.00 0.00 4.11
694 8123 2.315901 GTTCTTGATTTTTCCCACGCG 58.684 47.619 3.53 3.53 0.00 6.01
695 8124 1.600023 TCTTGATTTTTCCCACGCGT 58.400 45.000 5.58 5.58 0.00 6.01
696 8125 1.265635 TCTTGATTTTTCCCACGCGTG 59.734 47.619 31.77 31.77 0.00 5.34
742 8172 2.576191 TCCCCTCAAGAATCCGAACATT 59.424 45.455 0.00 0.00 0.00 2.71
743 8173 3.010138 TCCCCTCAAGAATCCGAACATTT 59.990 43.478 0.00 0.00 0.00 2.32
744 8174 3.763897 CCCCTCAAGAATCCGAACATTTT 59.236 43.478 0.00 0.00 0.00 1.82
831 8266 7.307632 CCGCAAGATAAGATCGAATTTCAAGAT 60.308 37.037 0.00 0.00 43.02 2.40
840 8275 6.541641 AGATCGAATTTCAAGATGGAAAGGAG 59.458 38.462 0.00 0.00 39.88 3.69
906 8341 1.066471 ACCCCCTTTTACAAGCCGTA 58.934 50.000 0.00 0.00 0.00 4.02
911 8346 4.096833 CCCCCTTTTACAAGCCGTATTTAC 59.903 45.833 0.00 0.00 0.00 2.01
945 8380 3.426191 CACCATTCGATTTGTTGTTGCTG 59.574 43.478 0.00 0.00 0.00 4.41
949 8384 4.566545 TTCGATTTGTTGTTGCTGTCAT 57.433 36.364 0.00 0.00 0.00 3.06
968 8403 7.094634 GCTGTCATCTTTTTCTGTCAATCCTTA 60.095 37.037 0.00 0.00 0.00 2.69
1183 8618 2.029073 CCAAGACGTCGTGGCTGT 59.971 61.111 32.54 1.14 38.58 4.40
1185 8620 0.319211 CCAAGACGTCGTGGCTGTTA 60.319 55.000 32.54 0.00 38.58 2.41
1191 8626 1.544691 ACGTCGTGGCTGTTAGATTCT 59.455 47.619 0.00 0.00 0.00 2.40
1192 8627 2.029290 ACGTCGTGGCTGTTAGATTCTT 60.029 45.455 0.00 0.00 0.00 2.52
1257 8692 1.630369 TGCCAGTTATGCTTCAGGTCT 59.370 47.619 0.00 0.00 0.00 3.85
1329 8794 0.759346 GGAAGATGGCATCGGTAGGT 59.241 55.000 21.01 0.10 0.00 3.08
1419 8884 0.696143 TGGACACTGTTCCTTCCCCA 60.696 55.000 9.39 0.00 36.51 4.96
1437 8902 3.392285 CCCCAGTGATGAAGTCATATGGA 59.608 47.826 15.99 0.00 43.80 3.41
1440 8905 6.239973 CCCCAGTGATGAAGTCATATGGAATA 60.240 42.308 15.99 0.00 43.80 1.75
1448 8913 5.247110 TGAAGTCATATGGAATAGAGGAGGC 59.753 44.000 2.13 0.00 28.50 4.70
1471 8936 2.032634 GCCGCACGGATTCTTGTGA 61.033 57.895 14.43 0.00 38.36 3.58
1512 8977 1.586422 TGTGCTCAGCTTCTGTTGAC 58.414 50.000 0.00 0.00 32.61 3.18
1515 8980 0.516439 GCTCAGCTTCTGTTGACTGC 59.484 55.000 0.00 0.00 32.61 4.40
1608 9073 0.321387 CTCCTGATCATCATGGCCCG 60.321 60.000 0.00 0.00 0.00 6.13
1710 9184 2.611225 AGGCAACAGCTAGCTATGAC 57.389 50.000 25.86 24.08 41.41 3.06
1798 9272 5.413833 AGTTTTGCTGATCATGGTAGAGTTG 59.586 40.000 0.00 0.00 0.00 3.16
1803 9277 4.256110 CTGATCATGGTAGAGTTGCAACA 58.744 43.478 30.11 9.96 0.00 3.33
1859 9351 2.781158 GGTCGCTCTCTCTCAGCCC 61.781 68.421 0.00 0.00 32.83 5.19
1951 9443 3.558674 AGCCTTTGGGATGAACGAG 57.441 52.632 0.00 0.00 33.58 4.18
1959 9451 1.296715 GGATGAACGAGTGCTGGGT 59.703 57.895 0.00 0.00 0.00 4.51
1971 9463 4.265073 GAGTGCTGGGTGTTATCTGAAAT 58.735 43.478 0.00 0.00 0.00 2.17
2080 9572 6.179504 TCTCTGTAGTCTGTACAATCGTTC 57.820 41.667 0.00 0.00 0.00 3.95
2205 9697 9.725206 TTAGTTCTAGATTGGTTATTCCCTAGT 57.275 33.333 0.00 0.00 31.75 2.57
2374 10068 1.818060 CCAAATTGGTTCGCCTGATCA 59.182 47.619 3.34 0.00 38.36 2.92
2645 10339 2.463876 GCAGCACCTTTCTGTTGAAAC 58.536 47.619 0.00 0.00 37.27 2.78
2773 10467 2.886523 TCTCATGTTTCAAAGTGGCCTG 59.113 45.455 3.32 0.00 0.00 4.85
2788 10482 0.396278 GCCTGCCTAAGCCCTTGATT 60.396 55.000 0.00 0.00 38.69 2.57
2790 10484 2.460669 CCTGCCTAAGCCCTTGATTTT 58.539 47.619 0.00 0.00 38.69 1.82
2792 10486 3.118992 CCTGCCTAAGCCCTTGATTTTTC 60.119 47.826 0.00 0.00 38.69 2.29
2827 10524 6.440647 TGAAGGCTCCTATTTCTTCAACTCTA 59.559 38.462 0.00 0.00 41.48 2.43
2844 10541 7.179966 TCAACTCTAGAGGTCATTAGGTGTTA 58.820 38.462 23.50 0.00 0.00 2.41
2845 10542 7.339721 TCAACTCTAGAGGTCATTAGGTGTTAG 59.660 40.741 23.50 0.82 0.00 2.34
2848 10545 2.772515 AGAGGTCATTAGGTGTTAGCCC 59.227 50.000 0.00 0.00 0.00 5.19
2849 10546 2.772515 GAGGTCATTAGGTGTTAGCCCT 59.227 50.000 0.00 0.00 36.04 5.19
2850 10547 3.190439 AGGTCATTAGGTGTTAGCCCTT 58.810 45.455 0.00 0.00 33.35 3.95
2881 10600 1.873591 CTCCAGTAGTTGTGGTTGTGC 59.126 52.381 0.00 0.00 36.37 4.57
2883 10602 1.577468 CAGTAGTTGTGGTTGTGCGA 58.423 50.000 0.00 0.00 0.00 5.10
2886 10605 2.353579 AGTAGTTGTGGTTGTGCGAAAC 59.646 45.455 0.00 0.00 0.00 2.78
2888 10607 1.748493 AGTTGTGGTTGTGCGAAACAT 59.252 42.857 4.00 0.00 38.99 2.71
2889 10608 2.165437 AGTTGTGGTTGTGCGAAACATT 59.835 40.909 4.00 0.00 38.99 2.71
2890 10609 2.926838 GTTGTGGTTGTGCGAAACATTT 59.073 40.909 4.00 0.00 38.99 2.32
2891 10610 3.238108 TGTGGTTGTGCGAAACATTTT 57.762 38.095 4.00 0.00 38.99 1.82
2892 10611 3.182967 TGTGGTTGTGCGAAACATTTTC 58.817 40.909 4.00 0.00 38.99 2.29
2893 10612 2.538037 GTGGTTGTGCGAAACATTTTCC 59.462 45.455 4.00 0.00 38.99 3.13
2894 10613 2.166459 TGGTTGTGCGAAACATTTTCCA 59.834 40.909 4.00 0.00 38.99 3.53
2895 10614 3.190874 GGTTGTGCGAAACATTTTCCAA 58.809 40.909 4.00 0.00 38.99 3.53
2896 10615 3.619038 GGTTGTGCGAAACATTTTCCAAA 59.381 39.130 4.00 0.00 38.99 3.28
2897 10616 4.093556 GGTTGTGCGAAACATTTTCCAAAA 59.906 37.500 4.00 0.00 38.99 2.44
2898 10617 5.220758 GGTTGTGCGAAACATTTTCCAAAAT 60.221 36.000 4.00 0.00 38.99 1.82
2916 10635 7.500992 TCCAAAATGTATGGCTTTGTTTTACA 58.499 30.769 0.00 0.00 37.88 2.41
2943 10662 2.107552 TCCAAAGGTTAGGGTTCTGTGG 59.892 50.000 0.00 0.00 37.27 4.17
2946 10665 1.359168 AGGTTAGGGTTCTGTGGGAC 58.641 55.000 0.00 0.00 0.00 4.46
2951 10670 1.150536 GGGTTCTGTGGGACTTGCA 59.849 57.895 0.00 0.00 0.00 4.08
2952 10671 0.251341 GGGTTCTGTGGGACTTGCAT 60.251 55.000 0.00 0.00 0.00 3.96
2953 10672 0.883833 GGTTCTGTGGGACTTGCATG 59.116 55.000 0.00 0.00 0.00 4.06
2954 10673 0.883833 GTTCTGTGGGACTTGCATGG 59.116 55.000 4.44 0.00 0.00 3.66
2955 10674 0.770499 TTCTGTGGGACTTGCATGGA 59.230 50.000 4.44 0.00 0.00 3.41
2956 10675 0.770499 TCTGTGGGACTTGCATGGAA 59.230 50.000 0.00 0.00 0.00 3.53
2957 10676 1.144708 TCTGTGGGACTTGCATGGAAA 59.855 47.619 0.00 0.00 0.00 3.13
2958 10677 2.173519 CTGTGGGACTTGCATGGAAAT 58.826 47.619 0.00 0.00 0.00 2.17
2959 10678 2.165030 CTGTGGGACTTGCATGGAAATC 59.835 50.000 0.00 0.00 0.00 2.17
2960 10679 1.478105 GTGGGACTTGCATGGAAATCC 59.522 52.381 18.09 18.09 0.00 3.01
2961 10680 1.358787 TGGGACTTGCATGGAAATCCT 59.641 47.619 23.97 0.00 36.82 3.24
2962 10681 1.753073 GGGACTTGCATGGAAATCCTG 59.247 52.381 23.97 4.64 36.82 3.86
2963 10682 2.621407 GGGACTTGCATGGAAATCCTGA 60.621 50.000 23.97 0.00 36.82 3.86
2964 10683 3.091545 GGACTTGCATGGAAATCCTGAA 58.908 45.455 18.90 0.00 36.82 3.02
2965 10684 3.129988 GGACTTGCATGGAAATCCTGAAG 59.870 47.826 18.90 0.00 36.82 3.02
2966 10685 4.012374 GACTTGCATGGAAATCCTGAAGA 58.988 43.478 0.00 0.00 36.82 2.87
2967 10686 4.410099 ACTTGCATGGAAATCCTGAAGAA 58.590 39.130 0.00 0.00 36.82 2.52
2968 10687 4.834496 ACTTGCATGGAAATCCTGAAGAAA 59.166 37.500 0.00 0.00 36.82 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.304052 TGGCGAGTTGATTTGGGGG 60.304 57.895 0.00 0.00 0.00 5.40
5 6 0.609131 ACTGGCGAGTTGATTTGGGG 60.609 55.000 0.00 0.00 0.00 4.96
6 7 0.523072 CACTGGCGAGTTGATTTGGG 59.477 55.000 0.00 0.00 0.00 4.12
7 8 0.109597 GCACTGGCGAGTTGATTTGG 60.110 55.000 0.00 0.00 0.00 3.28
8 9 0.592637 TGCACTGGCGAGTTGATTTG 59.407 50.000 0.00 0.00 45.35 2.32
9 10 1.317613 TTGCACTGGCGAGTTGATTT 58.682 45.000 0.00 0.00 45.35 2.17
10 11 1.317613 TTTGCACTGGCGAGTTGATT 58.682 45.000 0.00 0.00 45.35 2.57
11 12 1.267806 CTTTTGCACTGGCGAGTTGAT 59.732 47.619 0.00 0.00 45.35 2.57
12 13 0.662619 CTTTTGCACTGGCGAGTTGA 59.337 50.000 0.00 0.00 45.35 3.18
13 14 0.662619 TCTTTTGCACTGGCGAGTTG 59.337 50.000 0.00 0.00 45.35 3.16
14 15 1.065551 GTTCTTTTGCACTGGCGAGTT 59.934 47.619 0.00 0.00 45.35 3.01
15 16 0.663153 GTTCTTTTGCACTGGCGAGT 59.337 50.000 0.00 0.00 45.35 4.18
16 17 0.040067 GGTTCTTTTGCACTGGCGAG 60.040 55.000 0.00 0.00 45.35 5.03
17 18 1.452145 GGGTTCTTTTGCACTGGCGA 61.452 55.000 0.00 0.00 45.35 5.54
18 19 1.007387 GGGTTCTTTTGCACTGGCG 60.007 57.895 0.00 0.00 45.35 5.69
19 20 1.367471 GGGGTTCTTTTGCACTGGC 59.633 57.895 0.00 0.00 41.68 4.85
20 21 1.805428 CGGGGGTTCTTTTGCACTGG 61.805 60.000 0.00 0.00 0.00 4.00
21 22 1.659794 CGGGGGTTCTTTTGCACTG 59.340 57.895 0.00 0.00 0.00 3.66
22 23 2.200337 GCGGGGGTTCTTTTGCACT 61.200 57.895 0.00 0.00 0.00 4.40
23 24 2.338620 GCGGGGGTTCTTTTGCAC 59.661 61.111 0.00 0.00 0.00 4.57
24 25 2.915137 GGCGGGGGTTCTTTTGCA 60.915 61.111 0.00 0.00 0.00 4.08
25 26 2.600470 AGGCGGGGGTTCTTTTGC 60.600 61.111 0.00 0.00 0.00 3.68
26 27 2.332654 CGAGGCGGGGGTTCTTTTG 61.333 63.158 0.00 0.00 0.00 2.44
27 28 2.033602 CGAGGCGGGGGTTCTTTT 59.966 61.111 0.00 0.00 0.00 2.27
28 29 4.717313 GCGAGGCGGGGGTTCTTT 62.717 66.667 0.00 0.00 0.00 2.52
44 45 2.737932 CTTTGACCTGCCACGCAAGC 62.738 60.000 0.00 0.00 38.41 4.01
45 46 1.165907 TCTTTGACCTGCCACGCAAG 61.166 55.000 0.00 0.00 38.41 4.01
46 47 1.153066 TCTTTGACCTGCCACGCAA 60.153 52.632 0.00 0.00 38.41 4.85
47 48 1.597854 CTCTTTGACCTGCCACGCA 60.598 57.895 0.00 0.00 36.92 5.24
48 49 1.569479 GACTCTTTGACCTGCCACGC 61.569 60.000 0.00 0.00 0.00 5.34
49 50 0.249868 TGACTCTTTGACCTGCCACG 60.250 55.000 0.00 0.00 0.00 4.94
50 51 1.967319 TTGACTCTTTGACCTGCCAC 58.033 50.000 0.00 0.00 0.00 5.01
51 52 2.297701 GTTTGACTCTTTGACCTGCCA 58.702 47.619 0.00 0.00 0.00 4.92
52 53 2.291741 CTGTTTGACTCTTTGACCTGCC 59.708 50.000 0.00 0.00 0.00 4.85
53 54 2.945668 ACTGTTTGACTCTTTGACCTGC 59.054 45.455 0.00 0.00 0.00 4.85
54 55 4.209288 CGTACTGTTTGACTCTTTGACCTG 59.791 45.833 0.00 0.00 0.00 4.00
55 56 4.369182 CGTACTGTTTGACTCTTTGACCT 58.631 43.478 0.00 0.00 0.00 3.85
56 57 3.059800 GCGTACTGTTTGACTCTTTGACC 60.060 47.826 0.00 0.00 0.00 4.02
57 58 3.059800 GGCGTACTGTTTGACTCTTTGAC 60.060 47.826 0.00 0.00 0.00 3.18
58 59 3.128349 GGCGTACTGTTTGACTCTTTGA 58.872 45.455 0.00 0.00 0.00 2.69
59 60 2.869801 TGGCGTACTGTTTGACTCTTTG 59.130 45.455 0.00 0.00 0.00 2.77
60 61 2.870411 GTGGCGTACTGTTTGACTCTTT 59.130 45.455 0.00 0.00 0.00 2.52
61 62 2.480845 GTGGCGTACTGTTTGACTCTT 58.519 47.619 0.00 0.00 0.00 2.85
62 63 1.602165 CGTGGCGTACTGTTTGACTCT 60.602 52.381 0.00 0.00 0.00 3.24
63 64 0.782384 CGTGGCGTACTGTTTGACTC 59.218 55.000 0.00 0.00 0.00 3.36
64 65 0.103572 ACGTGGCGTACTGTTTGACT 59.896 50.000 0.00 0.00 38.73 3.41
65 66 0.231279 CACGTGGCGTACTGTTTGAC 59.769 55.000 7.95 0.00 38.32 3.18
66 67 0.876777 CCACGTGGCGTACTGTTTGA 60.877 55.000 24.02 0.00 38.32 2.69
67 68 1.567537 CCACGTGGCGTACTGTTTG 59.432 57.895 24.02 0.00 38.32 2.93
68 69 1.595929 CCCACGTGGCGTACTGTTT 60.596 57.895 29.75 0.00 38.32 2.83
69 70 2.029964 CCCACGTGGCGTACTGTT 59.970 61.111 29.75 0.00 38.32 3.16
70 71 2.913578 TCCCACGTGGCGTACTGT 60.914 61.111 29.75 0.00 38.32 3.55
71 72 2.431942 GTCCCACGTGGCGTACTG 60.432 66.667 29.75 14.39 38.32 2.74
72 73 2.030490 TTTGTCCCACGTGGCGTACT 62.030 55.000 29.75 0.00 38.32 2.73
73 74 0.952010 ATTTGTCCCACGTGGCGTAC 60.952 55.000 29.75 23.98 38.32 3.67
74 75 0.607112 TATTTGTCCCACGTGGCGTA 59.393 50.000 29.75 13.61 38.32 4.42
75 76 0.952010 GTATTTGTCCCACGTGGCGT 60.952 55.000 29.75 12.17 42.36 5.68
76 77 1.791662 GTATTTGTCCCACGTGGCG 59.208 57.895 29.75 21.35 0.00 5.69
77 78 1.641123 CCGTATTTGTCCCACGTGGC 61.641 60.000 29.75 16.98 0.00 5.01
78 79 1.641123 GCCGTATTTGTCCCACGTGG 61.641 60.000 28.26 28.26 0.00 4.94
79 80 1.791662 GCCGTATTTGTCCCACGTG 59.208 57.895 9.08 9.08 0.00 4.49
80 81 1.738830 CGCCGTATTTGTCCCACGT 60.739 57.895 0.00 0.00 0.00 4.49
81 82 1.446445 TCGCCGTATTTGTCCCACG 60.446 57.895 0.00 0.00 0.00 4.94
82 83 1.689352 CGTCGCCGTATTTGTCCCAC 61.689 60.000 0.00 0.00 0.00 4.61
83 84 1.446445 CGTCGCCGTATTTGTCCCA 60.446 57.895 0.00 0.00 0.00 4.37
84 85 2.805807 GCGTCGCCGTATTTGTCCC 61.806 63.158 5.75 0.00 36.15 4.46
85 86 2.020836 CTGCGTCGCCGTATTTGTCC 62.021 60.000 15.88 0.00 36.15 4.02
86 87 1.343821 CTGCGTCGCCGTATTTGTC 59.656 57.895 15.88 0.00 36.15 3.18
87 88 2.736682 GCTGCGTCGCCGTATTTGT 61.737 57.895 15.88 0.00 36.15 2.83
88 89 2.021380 GCTGCGTCGCCGTATTTG 59.979 61.111 15.88 0.00 36.15 2.32
89 90 2.870667 TACGCTGCGTCGCCGTATTT 62.871 55.000 32.44 5.25 41.54 1.40
90 91 3.399797 TACGCTGCGTCGCCGTATT 62.400 57.895 32.44 6.07 41.54 1.89
91 92 3.879682 TACGCTGCGTCGCCGTAT 61.880 61.111 32.44 6.88 41.54 3.06
92 93 4.817063 GTACGCTGCGTCGCCGTA 62.817 66.667 32.44 20.03 41.54 4.02
102 103 4.415332 AGGTCACCGCGTACGCTG 62.415 66.667 34.69 30.81 39.32 5.18
103 104 4.415332 CAGGTCACCGCGTACGCT 62.415 66.667 34.69 17.30 39.32 5.07
111 112 1.666553 TTAACAGCGCAGGTCACCG 60.667 57.895 11.47 0.00 33.74 4.94
112 113 0.882927 TGTTAACAGCGCAGGTCACC 60.883 55.000 11.47 0.00 33.74 4.02
113 114 0.941542 TTGTTAACAGCGCAGGTCAC 59.058 50.000 11.47 1.78 33.74 3.67
114 115 1.669604 TTTGTTAACAGCGCAGGTCA 58.330 45.000 11.47 0.00 33.74 4.02
115 116 2.031157 ACATTTGTTAACAGCGCAGGTC 60.031 45.455 11.47 0.00 33.74 3.85
116 117 1.953686 ACATTTGTTAACAGCGCAGGT 59.046 42.857 11.47 1.38 41.48 4.00
117 118 2.704725 ACATTTGTTAACAGCGCAGG 57.295 45.000 11.47 3.29 0.00 4.85
118 119 5.389778 TCATTACATTTGTTAACAGCGCAG 58.610 37.500 11.47 3.33 0.00 5.18
119 120 5.363979 TCATTACATTTGTTAACAGCGCA 57.636 34.783 11.47 0.00 0.00 6.09
120 121 7.305418 GCTTATCATTACATTTGTTAACAGCGC 60.305 37.037 8.56 0.00 0.00 5.92
121 122 7.696035 TGCTTATCATTACATTTGTTAACAGCG 59.304 33.333 8.56 4.12 0.00 5.18
122 123 8.798153 GTGCTTATCATTACATTTGTTAACAGC 58.202 33.333 8.56 4.28 0.00 4.40
123 124 9.289303 GGTGCTTATCATTACATTTGTTAACAG 57.711 33.333 8.56 0.00 0.00 3.16
124 125 7.965655 CGGTGCTTATCATTACATTTGTTAACA 59.034 33.333 3.59 3.59 0.00 2.41
125 126 7.966204 ACGGTGCTTATCATTACATTTGTTAAC 59.034 33.333 0.00 0.00 0.00 2.01
126 127 8.046294 ACGGTGCTTATCATTACATTTGTTAA 57.954 30.769 0.00 0.00 0.00 2.01
127 128 7.618502 ACGGTGCTTATCATTACATTTGTTA 57.381 32.000 0.00 0.00 0.00 2.41
128 129 6.509418 ACGGTGCTTATCATTACATTTGTT 57.491 33.333 0.00 0.00 0.00 2.83
129 130 7.618502 TTACGGTGCTTATCATTACATTTGT 57.381 32.000 0.00 0.00 0.00 2.83
130 131 8.559536 AGATTACGGTGCTTATCATTACATTTG 58.440 33.333 0.00 0.00 0.00 2.32
131 132 8.559536 CAGATTACGGTGCTTATCATTACATTT 58.440 33.333 0.00 0.00 0.00 2.32
132 133 7.173218 CCAGATTACGGTGCTTATCATTACATT 59.827 37.037 0.00 0.00 0.00 2.71
133 134 6.650807 CCAGATTACGGTGCTTATCATTACAT 59.349 38.462 0.00 0.00 0.00 2.29
134 135 5.989168 CCAGATTACGGTGCTTATCATTACA 59.011 40.000 0.00 0.00 0.00 2.41
135 136 5.408604 CCCAGATTACGGTGCTTATCATTAC 59.591 44.000 0.00 0.00 0.00 1.89
136 137 5.071250 ACCCAGATTACGGTGCTTATCATTA 59.929 40.000 0.00 0.00 0.00 1.90
137 138 4.141482 ACCCAGATTACGGTGCTTATCATT 60.141 41.667 0.00 0.00 0.00 2.57
138 139 3.391296 ACCCAGATTACGGTGCTTATCAT 59.609 43.478 0.00 0.00 0.00 2.45
139 140 2.769663 ACCCAGATTACGGTGCTTATCA 59.230 45.455 0.00 0.00 0.00 2.15
140 141 3.470645 ACCCAGATTACGGTGCTTATC 57.529 47.619 0.00 0.00 0.00 1.75
141 142 5.548406 GAATACCCAGATTACGGTGCTTAT 58.452 41.667 0.00 0.00 33.36 1.73
142 143 4.500205 CGAATACCCAGATTACGGTGCTTA 60.500 45.833 0.00 0.00 33.36 3.09
143 144 3.740141 CGAATACCCAGATTACGGTGCTT 60.740 47.826 0.00 0.00 33.36 3.91
144 145 2.223971 CGAATACCCAGATTACGGTGCT 60.224 50.000 0.00 0.00 33.36 4.40
145 146 2.132762 CGAATACCCAGATTACGGTGC 58.867 52.381 0.00 0.00 33.36 5.01
146 147 2.750948 CCGAATACCCAGATTACGGTG 58.249 52.381 0.00 0.00 35.21 4.94
147 148 2.391678 ACCGAATACCCAGATTACGGT 58.608 47.619 0.00 0.00 45.51 4.83
148 149 4.589216 TTACCGAATACCCAGATTACGG 57.411 45.455 0.00 0.00 43.61 4.02
149 150 5.166398 GGATTACCGAATACCCAGATTACG 58.834 45.833 0.00 0.00 0.00 3.18
150 151 6.105397 TGGATTACCGAATACCCAGATTAC 57.895 41.667 0.00 0.00 39.42 1.89
151 152 6.750660 TTGGATTACCGAATACCCAGATTA 57.249 37.500 0.00 0.00 39.42 1.75
152 153 5.640158 TTGGATTACCGAATACCCAGATT 57.360 39.130 0.00 0.00 39.42 2.40
153 154 5.309543 TCATTGGATTACCGAATACCCAGAT 59.690 40.000 0.00 0.00 39.42 2.90
154 155 4.656575 TCATTGGATTACCGAATACCCAGA 59.343 41.667 0.00 0.00 39.42 3.86
155 156 4.755123 GTCATTGGATTACCGAATACCCAG 59.245 45.833 0.00 0.00 39.42 4.45
156 157 4.445162 GGTCATTGGATTACCGAATACCCA 60.445 45.833 0.00 0.00 39.42 4.51
157 158 4.070009 GGTCATTGGATTACCGAATACCC 58.930 47.826 0.00 0.00 39.42 3.69
158 159 4.710324 TGGTCATTGGATTACCGAATACC 58.290 43.478 0.00 0.00 39.42 2.73
159 160 6.317893 ACTTTGGTCATTGGATTACCGAATAC 59.682 38.462 0.00 0.00 36.35 1.89
160 161 6.317642 CACTTTGGTCATTGGATTACCGAATA 59.682 38.462 0.00 0.00 36.35 1.75
161 162 5.125417 CACTTTGGTCATTGGATTACCGAAT 59.875 40.000 0.00 0.00 36.35 3.34
162 163 4.457603 CACTTTGGTCATTGGATTACCGAA 59.542 41.667 0.00 0.00 39.42 4.30
163 164 4.006989 CACTTTGGTCATTGGATTACCGA 58.993 43.478 0.00 0.00 39.42 4.69
164 165 4.006989 TCACTTTGGTCATTGGATTACCG 58.993 43.478 0.00 0.00 39.42 4.02
165 166 5.476945 AGTTCACTTTGGTCATTGGATTACC 59.523 40.000 0.00 0.00 0.00 2.85
166 167 6.575162 AGTTCACTTTGGTCATTGGATTAC 57.425 37.500 0.00 0.00 0.00 1.89
167 168 7.595819 AAAGTTCACTTTGGTCATTGGATTA 57.404 32.000 4.08 0.00 43.87 1.75
168 169 6.484364 AAAGTTCACTTTGGTCATTGGATT 57.516 33.333 4.08 0.00 43.87 3.01
180 181 8.686334 ACTGTATTTGATCACAAAGTTCACTTT 58.314 29.630 0.00 0.00 46.84 2.66
181 182 8.131100 CACTGTATTTGATCACAAAGTTCACTT 58.869 33.333 0.00 0.00 46.84 3.16
182 183 7.498900 TCACTGTATTTGATCACAAAGTTCACT 59.501 33.333 0.00 0.00 46.84 3.41
183 184 7.587757 GTCACTGTATTTGATCACAAAGTTCAC 59.412 37.037 0.00 0.00 46.84 3.18
184 185 7.255104 GGTCACTGTATTTGATCACAAAGTTCA 60.255 37.037 0.00 0.00 46.84 3.18
185 186 7.078228 GGTCACTGTATTTGATCACAAAGTTC 58.922 38.462 0.00 0.00 46.84 3.01
186 187 6.293407 CGGTCACTGTATTTGATCACAAAGTT 60.293 38.462 0.00 0.00 46.84 2.66
187 188 5.179368 CGGTCACTGTATTTGATCACAAAGT 59.821 40.000 0.00 0.00 46.84 2.66
188 189 5.621422 CGGTCACTGTATTTGATCACAAAG 58.379 41.667 0.00 0.00 46.84 2.77
190 191 3.435327 GCGGTCACTGTATTTGATCACAA 59.565 43.478 0.00 0.00 0.00 3.33
191 192 3.000041 GCGGTCACTGTATTTGATCACA 59.000 45.455 0.00 0.00 0.00 3.58
192 193 2.029244 CGCGGTCACTGTATTTGATCAC 59.971 50.000 0.00 0.00 0.00 3.06
193 194 2.267426 CGCGGTCACTGTATTTGATCA 58.733 47.619 0.00 0.00 0.00 2.92
194 195 1.593006 CCGCGGTCACTGTATTTGATC 59.407 52.381 19.50 0.00 0.00 2.92
195 196 1.651987 CCGCGGTCACTGTATTTGAT 58.348 50.000 19.50 0.00 0.00 2.57
196 197 0.390603 CCCGCGGTCACTGTATTTGA 60.391 55.000 26.12 0.00 0.00 2.69
197 198 0.672401 ACCCGCGGTCACTGTATTTG 60.672 55.000 26.12 6.21 0.00 2.32
198 199 0.672401 CACCCGCGGTCACTGTATTT 60.672 55.000 26.12 0.00 31.02 1.40
199 200 1.079405 CACCCGCGGTCACTGTATT 60.079 57.895 26.12 0.00 31.02 1.89
200 201 1.537814 TTCACCCGCGGTCACTGTAT 61.538 55.000 26.12 0.00 31.02 2.29
201 202 1.537814 ATTCACCCGCGGTCACTGTA 61.538 55.000 26.12 7.71 31.02 2.74
202 203 2.391724 AATTCACCCGCGGTCACTGT 62.392 55.000 26.12 11.69 31.02 3.55
203 204 1.234615 AAATTCACCCGCGGTCACTG 61.235 55.000 26.12 13.35 31.02 3.66
204 205 0.322322 TAAATTCACCCGCGGTCACT 59.678 50.000 26.12 1.00 31.02 3.41
205 206 1.135888 GTTAAATTCACCCGCGGTCAC 60.136 52.381 26.12 0.86 31.02 3.67
206 207 1.158434 GTTAAATTCACCCGCGGTCA 58.842 50.000 26.12 3.75 31.02 4.02
207 208 1.395954 GAGTTAAATTCACCCGCGGTC 59.604 52.381 26.12 6.29 31.02 4.79
208 209 1.002773 AGAGTTAAATTCACCCGCGGT 59.997 47.619 26.12 9.63 35.62 5.68
209 210 1.664151 GAGAGTTAAATTCACCCGCGG 59.336 52.381 21.04 21.04 0.00 6.46
210 211 1.664151 GGAGAGTTAAATTCACCCGCG 59.336 52.381 0.00 0.00 0.00 6.46
211 212 2.937149 GAGGAGAGTTAAATTCACCCGC 59.063 50.000 2.41 0.00 0.00 6.13
212 213 3.532542 GGAGGAGAGTTAAATTCACCCG 58.467 50.000 2.41 0.00 0.00 5.28
213 214 3.265995 TGGGAGGAGAGTTAAATTCACCC 59.734 47.826 0.00 0.00 33.00 4.61
214 215 4.262617 GTGGGAGGAGAGTTAAATTCACC 58.737 47.826 0.00 0.00 0.00 4.02
215 216 4.262617 GGTGGGAGGAGAGTTAAATTCAC 58.737 47.826 0.00 0.00 0.00 3.18
216 217 3.265995 GGGTGGGAGGAGAGTTAAATTCA 59.734 47.826 0.00 0.00 0.00 2.57
217 218 3.265995 TGGGTGGGAGGAGAGTTAAATTC 59.734 47.826 0.00 0.00 0.00 2.17
218 219 3.265489 TGGGTGGGAGGAGAGTTAAATT 58.735 45.455 0.00 0.00 0.00 1.82
219 220 2.929301 TGGGTGGGAGGAGAGTTAAAT 58.071 47.619 0.00 0.00 0.00 1.40
220 221 2.426431 TGGGTGGGAGGAGAGTTAAA 57.574 50.000 0.00 0.00 0.00 1.52
221 222 2.478292 GATGGGTGGGAGGAGAGTTAA 58.522 52.381 0.00 0.00 0.00 2.01
222 223 1.344087 GGATGGGTGGGAGGAGAGTTA 60.344 57.143 0.00 0.00 0.00 2.24
223 224 0.621862 GGATGGGTGGGAGGAGAGTT 60.622 60.000 0.00 0.00 0.00 3.01
224 225 1.003573 GGATGGGTGGGAGGAGAGT 59.996 63.158 0.00 0.00 0.00 3.24
225 226 1.768077 GGGATGGGTGGGAGGAGAG 60.768 68.421 0.00 0.00 0.00 3.20
226 227 2.131628 TTGGGATGGGTGGGAGGAGA 62.132 60.000 0.00 0.00 0.00 3.71
242 3553 5.676310 CGCTTTATTTGCTTGTTTTGTTTGG 59.324 36.000 0.00 0.00 0.00 3.28
260 3571 3.472726 CCGGGGGCCTACGCTTTA 61.473 66.667 14.22 0.00 34.44 1.85
490 7722 7.041107 CCAACTGATTCAAAACAAAAGGAAGA 58.959 34.615 0.00 0.00 0.00 2.87
500 7926 9.528018 TCAAAAATCTACCAACTGATTCAAAAC 57.472 29.630 0.00 0.00 32.43 2.43
601 8027 5.449177 GGCCTAAGAATTCAAACTTGATCCG 60.449 44.000 8.44 0.00 37.00 4.18
662 8091 1.533625 TCAAGAACGCCAAATGGAGG 58.466 50.000 2.98 0.00 39.47 4.30
694 8123 3.385193 AATTAACTTGCCAGTTGCCAC 57.615 42.857 13.20 0.00 43.54 5.01
695 8124 4.142491 CGATAATTAACTTGCCAGTTGCCA 60.142 41.667 13.20 0.00 43.54 4.92
696 8125 4.142469 ACGATAATTAACTTGCCAGTTGCC 60.142 41.667 13.20 0.00 43.54 4.52
697 8126 4.981794 ACGATAATTAACTTGCCAGTTGC 58.018 39.130 13.20 0.00 43.54 4.17
698 8127 6.422776 AGACGATAATTAACTTGCCAGTTG 57.577 37.500 13.20 0.00 43.54 3.16
699 8128 5.585047 GGAGACGATAATTAACTTGCCAGTT 59.415 40.000 8.41 8.41 45.73 3.16
700 8129 5.116882 GGAGACGATAATTAACTTGCCAGT 58.883 41.667 0.00 0.00 33.11 4.00
701 8130 4.511826 GGGAGACGATAATTAACTTGCCAG 59.488 45.833 0.00 0.00 0.00 4.85
702 8131 4.448210 GGGAGACGATAATTAACTTGCCA 58.552 43.478 0.00 0.00 0.00 4.92
793 8223 2.281484 TTGCGGAGTGGGCAGAAC 60.281 61.111 0.00 0.00 42.12 3.01
803 8233 5.463392 TGAAATTCGATCTTATCTTGCGGAG 59.537 40.000 0.00 0.00 0.00 4.63
831 8266 3.238788 GGAAAAACCCTCTCCTTTCCA 57.761 47.619 7.40 0.00 44.14 3.53
906 8341 1.476488 GGTGCCCAGCAATTCGTAAAT 59.524 47.619 0.00 0.00 41.47 1.40
911 8346 0.179129 GAATGGTGCCCAGCAATTCG 60.179 55.000 4.13 0.00 41.47 3.34
929 8364 3.814842 AGATGACAGCAACAACAAATCGA 59.185 39.130 0.00 0.00 0.00 3.59
945 8380 8.329203 ACTAAGGATTGACAGAAAAAGATGAC 57.671 34.615 0.00 0.00 0.00 3.06
968 8403 1.697432 TGGCAGCAGTGGTTTAGTACT 59.303 47.619 0.00 0.00 0.00 2.73
1166 8601 0.319211 TAACAGCCACGACGTCTTGG 60.319 55.000 31.06 31.06 38.21 3.61
1167 8602 1.060713 CTAACAGCCACGACGTCTTG 58.939 55.000 14.70 14.70 0.00 3.02
1183 8618 3.442625 TCGTCGCTGGAAGAAGAATCTAA 59.557 43.478 0.00 0.00 33.77 2.10
1185 8620 1.819288 TCGTCGCTGGAAGAAGAATCT 59.181 47.619 0.00 0.00 37.57 2.40
1191 8626 0.179171 GATCGTCGTCGCTGGAAGAA 60.179 55.000 0.00 0.00 32.42 2.52
1192 8627 1.428219 GATCGTCGTCGCTGGAAGA 59.572 57.895 0.00 0.00 36.96 2.87
1245 8680 2.165998 GAGGCAAAAGACCTGAAGCAT 58.834 47.619 0.00 0.00 37.77 3.79
1329 8794 2.240414 AGGAGCATTGTGATCACCATCA 59.760 45.455 22.85 1.15 33.81 3.07
1419 8884 7.732140 TCCTCTATTCCATATGACTTCATCACT 59.268 37.037 3.65 0.00 41.24 3.41
1448 8913 3.640000 GAATCCGTGCGGCATCGG 61.640 66.667 26.94 26.94 46.93 4.18
1471 8936 2.092968 TGCCATTATCTCCTGAAAGCGT 60.093 45.455 0.00 0.00 0.00 5.07
1515 8980 4.514577 ATCTCACCGCCTTCGCCG 62.515 66.667 0.00 0.00 0.00 6.46
1524 8989 2.100631 GTTGGCGTCCATCTCACCG 61.101 63.158 0.00 0.00 31.53 4.94
1544 9009 2.281139 TGTCGAACGCCAATGCCA 60.281 55.556 0.00 0.00 0.00 4.92
1567 9032 2.219325 CTCAGCCCCGTCTCTGTCAC 62.219 65.000 0.00 0.00 0.00 3.67
1577 9042 1.333636 ATCAGGAGAACTCAGCCCCG 61.334 60.000 4.23 0.00 0.00 5.73
1608 9073 5.684704 TCCATCAACTCATTATCTCCAACC 58.315 41.667 0.00 0.00 0.00 3.77
1710 9184 0.313043 CCTGTCCACAAAGCTTGCAG 59.687 55.000 0.00 2.41 0.00 4.41
1798 9272 0.730265 TCACACGGTTGAGTTGTTGC 59.270 50.000 0.00 0.00 0.00 4.17
1803 9277 1.139058 AGCTCTTCACACGGTTGAGTT 59.861 47.619 0.00 0.00 0.00 3.01
1859 9351 0.536687 CCATATGCTGGGAGCTGGTG 60.537 60.000 0.00 0.00 42.97 4.17
1895 9387 2.617021 GGATTCGGTTCAGGCTTTGGTA 60.617 50.000 0.00 0.00 0.00 3.25
1951 9443 4.380867 CCAATTTCAGATAACACCCAGCAC 60.381 45.833 0.00 0.00 0.00 4.40
1959 9451 9.349713 AGAAACTGTAACCAATTTCAGATAACA 57.650 29.630 1.31 0.00 36.86 2.41
1971 9463 9.219603 CAAGATCTATGAAGAAACTGTAACCAA 57.780 33.333 0.00 0.00 34.73 3.67
2205 9697 1.664659 GACGACGCTGCTCTCTACTTA 59.335 52.381 0.00 0.00 0.00 2.24
2261 9754 1.536073 TTGCCACAGACTCTCGGAGG 61.536 60.000 4.96 0.00 33.35 4.30
2645 10339 8.073355 GGATACAAGGAACATACTACAAATCG 57.927 38.462 0.00 0.00 0.00 3.34
2773 10467 4.808414 AAGAAAAATCAAGGGCTTAGGC 57.192 40.909 0.00 0.00 37.82 3.93
2788 10482 5.835280 AGGAGCCTTCATCAGAAAAAGAAAA 59.165 36.000 0.00 0.00 32.35 2.29
2790 10484 4.990526 AGGAGCCTTCATCAGAAAAAGAA 58.009 39.130 0.00 0.00 32.35 2.52
2792 10486 7.338957 AGAAATAGGAGCCTTCATCAGAAAAAG 59.661 37.037 0.00 0.00 32.35 2.27
2827 10524 2.772515 GGGCTAACACCTAATGACCTCT 59.227 50.000 0.00 0.00 0.00 3.69
2844 10541 1.615384 GGAGCAACTGAATCAAGGGCT 60.615 52.381 2.51 2.51 35.45 5.19
2845 10542 0.813821 GGAGCAACTGAATCAAGGGC 59.186 55.000 0.00 0.00 0.00 5.19
2848 10545 4.573900 ACTACTGGAGCAACTGAATCAAG 58.426 43.478 0.00 0.00 0.00 3.02
2849 10546 4.623932 ACTACTGGAGCAACTGAATCAA 57.376 40.909 0.00 0.00 0.00 2.57
2850 10547 4.202357 ACAACTACTGGAGCAACTGAATCA 60.202 41.667 0.00 0.00 0.00 2.57
2888 10607 7.872113 AAACAAAGCCATACATTTTGGAAAA 57.128 28.000 0.00 0.00 36.41 2.29
2889 10608 7.872113 AAAACAAAGCCATACATTTTGGAAA 57.128 28.000 0.00 0.00 36.41 3.13
2890 10609 7.987458 TGTAAAACAAAGCCATACATTTTGGAA 59.013 29.630 0.00 0.00 36.41 3.53
2891 10610 7.500992 TGTAAAACAAAGCCATACATTTTGGA 58.499 30.769 0.00 0.00 36.41 3.53
2892 10611 7.721286 TGTAAAACAAAGCCATACATTTTGG 57.279 32.000 1.88 0.00 36.41 3.28
2893 10612 8.825745 ACTTGTAAAACAAAGCCATACATTTTG 58.174 29.630 0.00 0.00 37.69 2.44
2894 10613 8.825745 CACTTGTAAAACAAAGCCATACATTTT 58.174 29.630 0.00 0.00 37.69 1.82
2895 10614 7.042119 GCACTTGTAAAACAAAGCCATACATTT 60.042 33.333 5.89 0.00 37.69 2.32
2896 10615 6.423604 GCACTTGTAAAACAAAGCCATACATT 59.576 34.615 5.89 0.00 37.69 2.71
2897 10616 5.925969 GCACTTGTAAAACAAAGCCATACAT 59.074 36.000 5.89 0.00 37.69 2.29
2898 10617 5.068460 AGCACTTGTAAAACAAAGCCATACA 59.932 36.000 11.15 0.00 38.91 2.29
2916 10635 1.780919 ACCCTAACCTTTGGAGCACTT 59.219 47.619 0.00 0.00 0.00 3.16
2943 10662 2.726821 TCAGGATTTCCATGCAAGTCC 58.273 47.619 2.69 2.69 38.89 3.85
2946 10665 5.395682 TTTCTTCAGGATTTCCATGCAAG 57.604 39.130 0.00 0.00 38.89 4.01


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

AutoCloner maintained by Alex Coulton.