Multiple sequence alignment - TraesCS3D01G224400

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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 TraesCS3D01G224400 chr3D 100.000 2984 0 0 579 3562 305745125 305748108 0.000000e+00 5511
1 TraesCS3D01G224400 chr3D 100.000 202 0 0 1 202 305744547 305744748 1.210000e-99 374
2 TraesCS3D01G224400 chr3B 91.167 1585 99 20 1991 3562 416033067 416031511 0.000000e+00 2113
3 TraesCS3D01G224400 chr3B 93.137 1326 47 18 579 1895 416034358 416033068 0.000000e+00 1905
4 TraesCS3D01G224400 chr3B 94.059 101 6 0 1889 1989 373126012 373126112 1.710000e-33 154
5 TraesCS3D01G224400 chr3A 90.971 1329 78 20 579 1894 423706910 423708209 0.000000e+00 1751
6 TraesCS3D01G224400 chr3A 92.265 1254 57 15 2317 3562 423709077 423710298 0.000000e+00 1742
7 TraesCS3D01G224400 chr3A 95.161 310 15 0 2012 2321 423708466 423708775 1.150000e-134 490
8 TraesCS3D01G224400 chr6D 94.175 103 6 0 1894 1996 112829016 112828914 1.320000e-34 158
9 TraesCS3D01G224400 chr2A 93.396 106 6 1 1890 1994 268936706 268936601 4.760000e-34 156
10 TraesCS3D01G224400 chr2D 93.269 104 7 0 1893 1996 211559255 211559152 1.710000e-33 154
11 TraesCS3D01G224400 chr6A 91.818 110 7 2 1890 1997 70841113 70841222 6.160000e-33 152
12 TraesCS3D01G224400 chr6A 94.000 100 5 1 1894 1992 23355174 23355075 2.220000e-32 150
13 TraesCS3D01G224400 chr5A 91.743 109 7 2 1886 1993 354522194 354522301 2.220000e-32 150
14 TraesCS3D01G224400 chr1D 92.381 105 8 0 1885 1989 240128270 240128166 2.220000e-32 150
15 TraesCS3D01G224400 chr7D 90.351 114 9 1 1876 1989 617181776 617181665 7.970000e-32 148


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 TraesCS3D01G224400 chr3D 305744547 305748108 3561 False 2942.500000 5511 100.000 1 3562 2 chr3D.!!$F1 3561
1 TraesCS3D01G224400 chr3B 416031511 416034358 2847 True 2009.000000 2113 92.152 579 3562 2 chr3B.!!$R1 2983
2 TraesCS3D01G224400 chr3A 423706910 423710298 3388 False 1327.666667 1751 92.799 579 3562 3 chr3A.!!$F1 2983

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
94 95 0.036765 CCATCTCCCGTTCCGTTCAA 60.037 55.0 0.0 0.0 0.00 2.69 F
1032 1038 0.034670 GATCAGCCTGCCTTGAGGTT 60.035 55.0 0.0 0.0 35.29 3.50 F
1486 1518 0.037326 GTCATCACCTGGAACGAGCA 60.037 55.0 0.0 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1979 2017 0.598562 CGTATGATCCACTCCCTCCG 59.401 60.0 0.00 0.0 0.00 4.63 R
2510 3099 0.250081 GTCCATCGATCCAGGCCTTC 60.250 60.0 0.00 0.0 0.00 3.46 R
2934 3527 1.100463 TGTGCGGCACAACATTCTGT 61.100 50.0 31.72 0.0 41.69 3.41 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
27 28 3.636679 TGGACCACCAAAAACATGAAGA 58.363 40.909 0.00 0.00 43.91 2.87
28 29 4.026744 TGGACCACCAAAAACATGAAGAA 58.973 39.130 0.00 0.00 43.91 2.52
29 30 4.099266 TGGACCACCAAAAACATGAAGAAG 59.901 41.667 0.00 0.00 43.91 2.85
30 31 4.340950 GGACCACCAAAAACATGAAGAAGA 59.659 41.667 0.00 0.00 35.97 2.87
31 32 5.163457 GGACCACCAAAAACATGAAGAAGAA 60.163 40.000 0.00 0.00 35.97 2.52
32 33 6.293004 ACCACCAAAAACATGAAGAAGAAA 57.707 33.333 0.00 0.00 0.00 2.52
33 34 6.706295 ACCACCAAAAACATGAAGAAGAAAA 58.294 32.000 0.00 0.00 0.00 2.29
34 35 6.593770 ACCACCAAAAACATGAAGAAGAAAAC 59.406 34.615 0.00 0.00 0.00 2.43
35 36 6.037062 CCACCAAAAACATGAAGAAGAAAACC 59.963 38.462 0.00 0.00 0.00 3.27
36 37 6.593382 CACCAAAAACATGAAGAAGAAAACCA 59.407 34.615 0.00 0.00 0.00 3.67
37 38 7.118971 CACCAAAAACATGAAGAAGAAAACCAA 59.881 33.333 0.00 0.00 0.00 3.67
38 39 7.663493 ACCAAAAACATGAAGAAGAAAACCAAA 59.337 29.630 0.00 0.00 0.00 3.28
39 40 8.676401 CCAAAAACATGAAGAAGAAAACCAAAT 58.324 29.630 0.00 0.00 0.00 2.32
42 43 8.437360 AAACATGAAGAAGAAAACCAAATTCC 57.563 30.769 0.00 0.00 0.00 3.01
43 44 7.123355 ACATGAAGAAGAAAACCAAATTCCA 57.877 32.000 0.00 0.00 0.00 3.53
44 45 7.212274 ACATGAAGAAGAAAACCAAATTCCAG 58.788 34.615 0.00 0.00 0.00 3.86
45 46 7.069826 ACATGAAGAAGAAAACCAAATTCCAGA 59.930 33.333 0.00 0.00 0.00 3.86
46 47 6.805713 TGAAGAAGAAAACCAAATTCCAGAC 58.194 36.000 0.00 0.00 0.00 3.51
47 48 5.791336 AGAAGAAAACCAAATTCCAGACC 57.209 39.130 0.00 0.00 0.00 3.85
48 49 5.458595 AGAAGAAAACCAAATTCCAGACCT 58.541 37.500 0.00 0.00 0.00 3.85
49 50 5.302823 AGAAGAAAACCAAATTCCAGACCTG 59.697 40.000 0.00 0.00 0.00 4.00
61 62 3.874392 CCAGACCTGGCAAATAAAAGG 57.126 47.619 2.75 0.00 44.73 3.11
62 63 3.165071 CCAGACCTGGCAAATAAAAGGT 58.835 45.455 2.75 0.00 45.75 3.50
63 64 3.056607 CCAGACCTGGCAAATAAAAGGTG 60.057 47.826 2.75 0.00 43.12 4.00
64 65 3.826157 CAGACCTGGCAAATAAAAGGTGA 59.174 43.478 0.00 0.00 43.12 4.02
65 66 4.280677 CAGACCTGGCAAATAAAAGGTGAA 59.719 41.667 0.00 0.00 43.12 3.18
66 67 5.047092 CAGACCTGGCAAATAAAAGGTGAAT 60.047 40.000 0.00 0.00 43.12 2.57
67 68 5.185828 AGACCTGGCAAATAAAAGGTGAATC 59.814 40.000 0.00 0.00 43.12 2.52
68 69 5.086621 ACCTGGCAAATAAAAGGTGAATCT 58.913 37.500 0.00 0.00 41.52 2.40
69 70 5.185828 ACCTGGCAAATAAAAGGTGAATCTC 59.814 40.000 0.00 0.00 41.52 2.75
70 71 5.185635 CCTGGCAAATAAAAGGTGAATCTCA 59.814 40.000 0.00 0.00 0.00 3.27
71 72 6.024552 TGGCAAATAAAAGGTGAATCTCAC 57.975 37.500 0.00 0.00 46.23 3.51
80 81 2.969628 GTGAATCTCACCGACCATCT 57.030 50.000 0.00 0.00 41.37 2.90
81 82 2.815478 GTGAATCTCACCGACCATCTC 58.185 52.381 0.00 0.00 41.37 2.75
82 83 1.757118 TGAATCTCACCGACCATCTCC 59.243 52.381 0.00 0.00 0.00 3.71
83 84 1.069358 GAATCTCACCGACCATCTCCC 59.931 57.143 0.00 0.00 0.00 4.30
84 85 1.109920 ATCTCACCGACCATCTCCCG 61.110 60.000 0.00 0.00 0.00 5.14
85 86 2.036731 TCACCGACCATCTCCCGT 59.963 61.111 0.00 0.00 0.00 5.28
86 87 1.605058 CTCACCGACCATCTCCCGTT 61.605 60.000 0.00 0.00 0.00 4.44
87 88 1.153628 CACCGACCATCTCCCGTTC 60.154 63.158 0.00 0.00 0.00 3.95
88 89 2.356780 ACCGACCATCTCCCGTTCC 61.357 63.158 0.00 0.00 0.00 3.62
89 90 2.104331 CGACCATCTCCCGTTCCG 59.896 66.667 0.00 0.00 0.00 4.30
90 91 2.707849 CGACCATCTCCCGTTCCGT 61.708 63.158 0.00 0.00 0.00 4.69
91 92 1.595357 GACCATCTCCCGTTCCGTT 59.405 57.895 0.00 0.00 0.00 4.44
92 93 0.459759 GACCATCTCCCGTTCCGTTC 60.460 60.000 0.00 0.00 0.00 3.95
93 94 1.189524 ACCATCTCCCGTTCCGTTCA 61.190 55.000 0.00 0.00 0.00 3.18
94 95 0.036765 CCATCTCCCGTTCCGTTCAA 60.037 55.000 0.00 0.00 0.00 2.69
95 96 1.406887 CCATCTCCCGTTCCGTTCAAT 60.407 52.381 0.00 0.00 0.00 2.57
96 97 1.933853 CATCTCCCGTTCCGTTCAATC 59.066 52.381 0.00 0.00 0.00 2.67
97 98 1.263356 TCTCCCGTTCCGTTCAATCT 58.737 50.000 0.00 0.00 0.00 2.40
98 99 2.449464 TCTCCCGTTCCGTTCAATCTA 58.551 47.619 0.00 0.00 0.00 1.98
99 100 2.827322 TCTCCCGTTCCGTTCAATCTAA 59.173 45.455 0.00 0.00 0.00 2.10
100 101 2.928116 CTCCCGTTCCGTTCAATCTAAC 59.072 50.000 0.00 0.00 0.00 2.34
101 102 2.299582 TCCCGTTCCGTTCAATCTAACA 59.700 45.455 0.00 0.00 0.00 2.41
102 103 2.671396 CCCGTTCCGTTCAATCTAACAG 59.329 50.000 0.00 0.00 0.00 3.16
103 104 3.323243 CCGTTCCGTTCAATCTAACAGT 58.677 45.455 0.00 0.00 0.00 3.55
104 105 3.122948 CCGTTCCGTTCAATCTAACAGTG 59.877 47.826 0.00 0.00 0.00 3.66
105 106 3.423123 CGTTCCGTTCAATCTAACAGTGC 60.423 47.826 0.00 0.00 0.00 4.40
106 107 3.394674 TCCGTTCAATCTAACAGTGCA 57.605 42.857 0.00 0.00 0.00 4.57
107 108 3.937814 TCCGTTCAATCTAACAGTGCAT 58.062 40.909 0.00 0.00 0.00 3.96
108 109 3.932710 TCCGTTCAATCTAACAGTGCATC 59.067 43.478 0.00 0.00 0.00 3.91
109 110 3.242091 CCGTTCAATCTAACAGTGCATCG 60.242 47.826 0.00 0.00 0.00 3.84
110 111 3.367932 CGTTCAATCTAACAGTGCATCGT 59.632 43.478 0.00 0.00 0.00 3.73
111 112 4.561213 CGTTCAATCTAACAGTGCATCGTA 59.439 41.667 0.00 0.00 0.00 3.43
112 113 5.498700 CGTTCAATCTAACAGTGCATCGTAC 60.499 44.000 0.00 0.00 0.00 3.67
113 114 5.066968 TCAATCTAACAGTGCATCGTACA 57.933 39.130 0.00 0.00 0.00 2.90
114 115 5.474825 TCAATCTAACAGTGCATCGTACAA 58.525 37.500 0.00 0.00 0.00 2.41
115 116 5.347635 TCAATCTAACAGTGCATCGTACAAC 59.652 40.000 0.00 0.00 0.00 3.32
116 117 4.245845 TCTAACAGTGCATCGTACAACA 57.754 40.909 0.00 0.00 0.00 3.33
117 118 4.623002 TCTAACAGTGCATCGTACAACAA 58.377 39.130 0.00 0.00 0.00 2.83
118 119 3.878086 AACAGTGCATCGTACAACAAG 57.122 42.857 0.00 0.00 0.00 3.16
119 120 3.106242 ACAGTGCATCGTACAACAAGA 57.894 42.857 0.00 0.00 0.00 3.02
120 121 3.664107 ACAGTGCATCGTACAACAAGAT 58.336 40.909 0.00 0.00 0.00 2.40
121 122 4.065088 ACAGTGCATCGTACAACAAGATT 58.935 39.130 0.00 0.00 0.00 2.40
122 123 4.083855 ACAGTGCATCGTACAACAAGATTG 60.084 41.667 0.00 0.00 0.00 2.67
123 124 3.120199 AGTGCATCGTACAACAAGATTGC 60.120 43.478 0.00 0.00 0.00 3.56
124 125 2.810852 TGCATCGTACAACAAGATTGCA 59.189 40.909 0.00 0.00 31.87 4.08
125 126 3.251972 TGCATCGTACAACAAGATTGCAA 59.748 39.130 0.00 0.00 31.63 4.08
126 127 4.225984 GCATCGTACAACAAGATTGCAAA 58.774 39.130 1.71 0.00 0.00 3.68
127 128 4.321745 GCATCGTACAACAAGATTGCAAAG 59.678 41.667 1.71 0.00 0.00 2.77
128 129 5.688823 CATCGTACAACAAGATTGCAAAGA 58.311 37.500 1.71 0.00 0.00 2.52
129 130 5.940192 TCGTACAACAAGATTGCAAAGAT 57.060 34.783 1.71 0.00 0.00 2.40
130 131 5.688823 TCGTACAACAAGATTGCAAAGATG 58.311 37.500 1.71 5.18 0.00 2.90
131 132 5.468409 TCGTACAACAAGATTGCAAAGATGA 59.532 36.000 1.71 0.00 0.00 2.92
132 133 6.149308 TCGTACAACAAGATTGCAAAGATGAT 59.851 34.615 1.71 0.00 0.00 2.45
133 134 6.467047 CGTACAACAAGATTGCAAAGATGATC 59.533 38.462 1.71 0.00 0.00 2.92
134 135 6.335471 ACAACAAGATTGCAAAGATGATCA 57.665 33.333 1.71 0.00 0.00 2.92
135 136 6.751157 ACAACAAGATTGCAAAGATGATCAA 58.249 32.000 1.71 0.00 0.00 2.57
136 137 6.866770 ACAACAAGATTGCAAAGATGATCAAG 59.133 34.615 1.71 0.00 0.00 3.02
137 138 5.408356 ACAAGATTGCAAAGATGATCAAGC 58.592 37.500 1.71 0.00 0.00 4.01
138 139 5.047590 ACAAGATTGCAAAGATGATCAAGCA 60.048 36.000 1.71 2.77 0.00 3.91
139 140 5.854010 AGATTGCAAAGATGATCAAGCAT 57.146 34.783 1.71 0.00 0.00 3.79
140 141 5.592054 AGATTGCAAAGATGATCAAGCATG 58.408 37.500 1.71 0.00 0.00 4.06
141 142 5.359860 AGATTGCAAAGATGATCAAGCATGA 59.640 36.000 1.71 0.00 40.57 3.07
142 143 4.632538 TGCAAAGATGATCAAGCATGAG 57.367 40.909 0.00 0.00 39.39 2.90
143 144 4.266714 TGCAAAGATGATCAAGCATGAGA 58.733 39.130 0.00 0.00 39.39 3.27
144 145 4.887655 TGCAAAGATGATCAAGCATGAGAT 59.112 37.500 0.00 0.00 39.39 2.75
145 146 6.059484 TGCAAAGATGATCAAGCATGAGATA 58.941 36.000 0.00 0.00 39.39 1.98
146 147 6.715264 TGCAAAGATGATCAAGCATGAGATAT 59.285 34.615 0.00 0.00 39.39 1.63
147 148 7.094762 TGCAAAGATGATCAAGCATGAGATATC 60.095 37.037 0.00 0.00 39.39 1.63
148 149 7.094762 GCAAAGATGATCAAGCATGAGATATCA 60.095 37.037 5.32 0.00 39.39 2.15
149 150 8.784043 CAAAGATGATCAAGCATGAGATATCAA 58.216 33.333 5.32 0.00 39.39 2.57
150 151 8.919777 AAGATGATCAAGCATGAGATATCAAA 57.080 30.769 5.32 0.00 39.39 2.69
151 152 8.919777 AGATGATCAAGCATGAGATATCAAAA 57.080 30.769 5.32 0.00 39.39 2.44
152 153 9.004717 AGATGATCAAGCATGAGATATCAAAAG 57.995 33.333 5.32 0.00 39.39 2.27
153 154 8.693120 ATGATCAAGCATGAGATATCAAAAGT 57.307 30.769 5.32 0.00 39.39 2.66
154 155 8.515695 TGATCAAGCATGAGATATCAAAAGTT 57.484 30.769 5.32 0.00 39.39 2.66
155 156 8.618677 TGATCAAGCATGAGATATCAAAAGTTC 58.381 33.333 5.32 0.00 39.39 3.01
156 157 7.926674 TCAAGCATGAGATATCAAAAGTTCA 57.073 32.000 5.32 0.00 0.00 3.18
157 158 8.339344 TCAAGCATGAGATATCAAAAGTTCAA 57.661 30.769 5.32 0.00 0.00 2.69
158 159 8.963725 TCAAGCATGAGATATCAAAAGTTCAAT 58.036 29.630 5.32 0.00 0.00 2.57
159 160 9.582431 CAAGCATGAGATATCAAAAGTTCAATT 57.418 29.630 5.32 0.00 0.00 2.32
160 161 9.798994 AAGCATGAGATATCAAAAGTTCAATTC 57.201 29.630 5.32 0.00 0.00 2.17
161 162 8.963725 AGCATGAGATATCAAAAGTTCAATTCA 58.036 29.630 5.32 0.00 0.00 2.57
162 163 9.745880 GCATGAGATATCAAAAGTTCAATTCAT 57.254 29.630 5.32 0.00 0.00 2.57
165 166 9.166173 TGAGATATCAAAAGTTCAATTCATCGT 57.834 29.630 5.32 0.00 0.00 3.73
166 167 9.643652 GAGATATCAAAAGTTCAATTCATCGTC 57.356 33.333 5.32 0.00 0.00 4.20
167 168 9.166173 AGATATCAAAAGTTCAATTCATCGTCA 57.834 29.630 5.32 0.00 0.00 4.35
168 169 9.773328 GATATCAAAAGTTCAATTCATCGTCAA 57.227 29.630 0.00 0.00 0.00 3.18
171 172 8.870160 TCAAAAGTTCAATTCATCGTCAAATT 57.130 26.923 0.00 0.00 0.00 1.82
172 173 9.311916 TCAAAAGTTCAATTCATCGTCAAATTT 57.688 25.926 0.00 0.00 0.00 1.82
179 180 9.796120 TTCAATTCATCGTCAAATTTATTACCC 57.204 29.630 0.00 0.00 0.00 3.69
180 181 8.961634 TCAATTCATCGTCAAATTTATTACCCA 58.038 29.630 0.00 0.00 0.00 4.51
181 182 9.748708 CAATTCATCGTCAAATTTATTACCCAT 57.251 29.630 0.00 0.00 0.00 4.00
184 185 8.966069 TCATCGTCAAATTTATTACCCATACA 57.034 30.769 0.00 0.00 0.00 2.29
185 186 8.832521 TCATCGTCAAATTTATTACCCATACAC 58.167 33.333 0.00 0.00 0.00 2.90
186 187 7.556733 TCGTCAAATTTATTACCCATACACC 57.443 36.000 0.00 0.00 0.00 4.16
187 188 7.110810 TCGTCAAATTTATTACCCATACACCA 58.889 34.615 0.00 0.00 0.00 4.17
188 189 7.776030 TCGTCAAATTTATTACCCATACACCAT 59.224 33.333 0.00 0.00 0.00 3.55
189 190 7.860373 CGTCAAATTTATTACCCATACACCATG 59.140 37.037 0.00 0.00 0.00 3.66
190 191 8.908903 GTCAAATTTATTACCCATACACCATGA 58.091 33.333 0.00 0.00 36.69 3.07
191 192 9.653516 TCAAATTTATTACCCATACACCATGAT 57.346 29.630 0.00 0.00 36.69 2.45
192 193 9.912634 CAAATTTATTACCCATACACCATGATC 57.087 33.333 0.00 0.00 36.69 2.92
193 194 9.653516 AAATTTATTACCCATACACCATGATCA 57.346 29.630 0.00 0.00 36.69 2.92
194 195 8.868522 ATTTATTACCCATACACCATGATCAG 57.131 34.615 0.09 0.00 36.69 2.90
195 196 7.625498 TTATTACCCATACACCATGATCAGA 57.375 36.000 0.09 0.00 36.69 3.27
196 197 6.708885 ATTACCCATACACCATGATCAGAT 57.291 37.500 0.09 0.00 36.69 2.90
197 198 4.362470 ACCCATACACCATGATCAGATG 57.638 45.455 0.09 1.78 36.69 2.90
198 199 3.975982 ACCCATACACCATGATCAGATGA 59.024 43.478 0.09 0.00 36.69 2.92
199 200 4.413189 ACCCATACACCATGATCAGATGAA 59.587 41.667 0.09 0.00 36.69 2.57
200 201 5.001874 CCCATACACCATGATCAGATGAAG 58.998 45.833 0.09 0.00 36.69 3.02
201 202 5.455755 CCCATACACCATGATCAGATGAAGT 60.456 44.000 0.09 0.82 36.69 3.01
602 603 5.637810 TGGTCAGATAGTTTGTTAGCTTTCG 59.362 40.000 0.00 0.00 0.00 3.46
657 658 6.533723 GTCTTTCACATGTGTCGATGGTTATA 59.466 38.462 24.63 0.00 0.00 0.98
791 792 5.826643 TGAAGATAAGGTTAAAGCCACCAT 58.173 37.500 0.00 0.00 36.67 3.55
797 802 9.520515 AGATAAGGTTAAAGCCACCATATTATG 57.479 33.333 0.00 0.00 36.67 1.90
814 819 8.203485 CCATATTATGCACACCCTTTACATTTT 58.797 33.333 0.00 0.00 0.00 1.82
822 827 4.712337 ACACCCTTTACATTTTGGACAACA 59.288 37.500 0.00 0.00 0.00 3.33
862 867 1.354040 GTGAGACATTCACGAGCCAG 58.646 55.000 0.00 0.00 46.13 4.85
880 885 1.550524 CAGTTTCTCGTGATGGAGGGA 59.449 52.381 0.00 0.00 34.74 4.20
903 908 8.635328 GGGATTTTCTTTGTTCCAAAGTTACTA 58.365 33.333 14.43 0.00 0.00 1.82
910 915 9.457436 TCTTTGTTCCAAAGTTACTAAAAGACT 57.543 29.630 14.43 0.00 0.00 3.24
946 951 1.005630 AGAGTGAGCTTGCACCGAC 60.006 57.895 2.09 0.00 39.59 4.79
980 985 6.467677 CACCCTCCACTCCACATATATAAAG 58.532 44.000 0.00 0.00 0.00 1.85
1020 1026 4.210304 GCACGAACGCGATCAGCC 62.210 66.667 15.93 0.00 44.76 4.85
1029 1035 2.178890 GCGATCAGCCTGCCTTGAG 61.179 63.158 0.00 0.00 40.81 3.02
1032 1038 0.034670 GATCAGCCTGCCTTGAGGTT 60.035 55.000 0.00 0.00 35.29 3.50
1033 1039 0.323178 ATCAGCCTGCCTTGAGGTTG 60.323 55.000 0.00 0.00 43.80 3.77
1034 1040 1.073722 CAGCCTGCCTTGAGGTTGA 59.926 57.895 0.00 0.00 44.91 3.18
1035 1041 0.538057 CAGCCTGCCTTGAGGTTGAA 60.538 55.000 0.00 0.00 44.91 2.69
1036 1042 0.185901 AGCCTGCCTTGAGGTTGAAA 59.814 50.000 0.00 0.00 35.29 2.69
1096 1102 2.897350 GGGTCGCCATACTGCTGC 60.897 66.667 0.00 0.00 0.00 5.25
1174 1192 3.214123 CCAGTGGCATGGCGATGG 61.214 66.667 22.69 22.69 32.48 3.51
1314 1332 1.471119 CCGGAGTCTACAGGCAAGTA 58.529 55.000 0.00 0.00 0.00 2.24
1486 1518 0.037326 GTCATCACCTGGAACGAGCA 60.037 55.000 0.00 0.00 0.00 4.26
1487 1519 0.247460 TCATCACCTGGAACGAGCAG 59.753 55.000 0.00 0.00 0.00 4.24
1493 1525 1.669115 CTGGAACGAGCAGTGGGTG 60.669 63.158 0.00 0.00 0.00 4.61
1541 1573 1.469335 TTCTGGCCTCCGACTTCGTT 61.469 55.000 3.32 0.00 37.74 3.85
1569 1601 2.416747 GCTTAACGTTCCGGGTAAGTT 58.583 47.619 2.82 9.58 33.90 2.66
1599 1631 2.977405 AGTTCGTGATTGCAAAGAGC 57.023 45.000 1.71 3.41 45.96 4.09
1610 1642 4.057428 AAAGAGCGAGCGAGGCGT 62.057 61.111 0.00 0.00 35.00 5.68
1806 1838 1.153369 CATCGAAGGTGGCACCGAT 60.153 57.895 29.76 24.20 44.90 4.18
1846 1878 3.557264 CCGGGCTCTCTTTGAAGTAAGTT 60.557 47.826 0.00 0.00 0.00 2.66
1847 1879 4.065789 CGGGCTCTCTTTGAAGTAAGTTT 58.934 43.478 0.00 0.00 0.00 2.66
1848 1880 4.515567 CGGGCTCTCTTTGAAGTAAGTTTT 59.484 41.667 0.00 0.00 0.00 2.43
1891 1929 0.732571 AAACCCGTGCGCATTGATAG 59.267 50.000 15.91 2.03 0.00 2.08
1892 1930 0.107897 AACCCGTGCGCATTGATAGA 60.108 50.000 15.91 0.00 0.00 1.98
1893 1931 0.106708 ACCCGTGCGCATTGATAGAT 59.893 50.000 15.91 0.00 0.00 1.98
1894 1932 1.343142 ACCCGTGCGCATTGATAGATA 59.657 47.619 15.91 0.00 0.00 1.98
1895 1933 1.726791 CCCGTGCGCATTGATAGATAC 59.273 52.381 15.91 0.00 0.00 2.24
1896 1934 1.726791 CCGTGCGCATTGATAGATACC 59.273 52.381 15.91 0.00 0.00 2.73
1897 1935 1.726791 CGTGCGCATTGATAGATACCC 59.273 52.381 15.91 0.00 0.00 3.69
1898 1936 2.076863 GTGCGCATTGATAGATACCCC 58.923 52.381 15.91 0.00 0.00 4.95
1899 1937 1.003118 TGCGCATTGATAGATACCCCC 59.997 52.381 5.66 0.00 0.00 5.40
1900 1938 1.279271 GCGCATTGATAGATACCCCCT 59.721 52.381 0.30 0.00 0.00 4.79
1901 1939 2.678190 GCGCATTGATAGATACCCCCTC 60.678 54.545 0.30 0.00 0.00 4.30
1902 1940 2.093447 CGCATTGATAGATACCCCCTCC 60.093 54.545 0.00 0.00 0.00 4.30
1903 1941 2.093447 GCATTGATAGATACCCCCTCCG 60.093 54.545 0.00 0.00 0.00 4.63
1904 1942 3.173965 CATTGATAGATACCCCCTCCGT 58.826 50.000 0.00 0.00 0.00 4.69
1905 1943 3.339713 TTGATAGATACCCCCTCCGTT 57.660 47.619 0.00 0.00 0.00 4.44
1906 1944 3.339713 TGATAGATACCCCCTCCGTTT 57.660 47.619 0.00 0.00 0.00 3.60
1907 1945 3.236896 TGATAGATACCCCCTCCGTTTC 58.763 50.000 0.00 0.00 0.00 2.78
1908 1946 2.852714 TAGATACCCCCTCCGTTTCA 57.147 50.000 0.00 0.00 0.00 2.69
1909 1947 1.961133 AGATACCCCCTCCGTTTCAA 58.039 50.000 0.00 0.00 0.00 2.69
1910 1948 2.271777 AGATACCCCCTCCGTTTCAAA 58.728 47.619 0.00 0.00 0.00 2.69
1911 1949 2.645797 AGATACCCCCTCCGTTTCAAAA 59.354 45.455 0.00 0.00 0.00 2.44
1912 1950 3.268595 AGATACCCCCTCCGTTTCAAAAT 59.731 43.478 0.00 0.00 0.00 1.82
1913 1951 4.475747 AGATACCCCCTCCGTTTCAAAATA 59.524 41.667 0.00 0.00 0.00 1.40
1914 1952 3.081710 ACCCCCTCCGTTTCAAAATAG 57.918 47.619 0.00 0.00 0.00 1.73
1915 1953 2.645797 ACCCCCTCCGTTTCAAAATAGA 59.354 45.455 0.00 0.00 0.00 1.98
1916 1954 3.268595 ACCCCCTCCGTTTCAAAATAGAT 59.731 43.478 0.00 0.00 0.00 1.98
1917 1955 3.632145 CCCCCTCCGTTTCAAAATAGATG 59.368 47.826 0.00 0.00 0.00 2.90
1918 1956 4.523083 CCCCTCCGTTTCAAAATAGATGA 58.477 43.478 0.00 0.00 0.00 2.92
1919 1957 4.335594 CCCCTCCGTTTCAAAATAGATGAC 59.664 45.833 0.00 0.00 0.00 3.06
1920 1958 4.335594 CCCTCCGTTTCAAAATAGATGACC 59.664 45.833 0.00 0.00 0.00 4.02
1921 1959 4.335594 CCTCCGTTTCAAAATAGATGACCC 59.664 45.833 0.00 0.00 0.00 4.46
1922 1960 4.912586 TCCGTTTCAAAATAGATGACCCA 58.087 39.130 0.00 0.00 0.00 4.51
1923 1961 5.317808 TCCGTTTCAAAATAGATGACCCAA 58.682 37.500 0.00 0.00 0.00 4.12
1924 1962 5.182380 TCCGTTTCAAAATAGATGACCCAAC 59.818 40.000 0.00 0.00 0.00 3.77
1925 1963 5.183140 CCGTTTCAAAATAGATGACCCAACT 59.817 40.000 0.00 0.00 0.00 3.16
1926 1964 6.294508 CCGTTTCAAAATAGATGACCCAACTT 60.295 38.462 0.00 0.00 0.00 2.66
1927 1965 7.145323 CGTTTCAAAATAGATGACCCAACTTT 58.855 34.615 0.00 0.00 0.00 2.66
1928 1966 7.114811 CGTTTCAAAATAGATGACCCAACTTTG 59.885 37.037 0.00 0.00 0.00 2.77
1929 1967 7.595819 TTCAAAATAGATGACCCAACTTTGT 57.404 32.000 0.00 0.00 0.00 2.83
1930 1968 8.698973 TTCAAAATAGATGACCCAACTTTGTA 57.301 30.769 0.00 0.00 0.00 2.41
1931 1969 8.877864 TCAAAATAGATGACCCAACTTTGTAT 57.122 30.769 0.00 0.00 0.00 2.29
1932 1970 9.308000 TCAAAATAGATGACCCAACTTTGTATT 57.692 29.630 0.00 0.00 0.00 1.89
1936 1974 9.975218 AATAGATGACCCAACTTTGTATTAACT 57.025 29.630 0.00 0.00 0.00 2.24
1937 1975 9.975218 ATAGATGACCCAACTTTGTATTAACTT 57.025 29.630 0.00 0.00 0.00 2.66
1938 1976 8.706322 AGATGACCCAACTTTGTATTAACTTT 57.294 30.769 0.00 0.00 0.00 2.66
1939 1977 9.802039 AGATGACCCAACTTTGTATTAACTTTA 57.198 29.630 0.00 0.00 0.00 1.85
1980 2018 6.254281 AGTTGGGTCATCTATTTTGAAACG 57.746 37.500 0.00 0.00 0.00 3.60
1981 2019 5.183140 AGTTGGGTCATCTATTTTGAAACGG 59.817 40.000 0.00 0.00 0.00 4.44
1982 2020 4.912586 TGGGTCATCTATTTTGAAACGGA 58.087 39.130 0.00 0.00 0.00 4.69
1983 2021 4.941263 TGGGTCATCTATTTTGAAACGGAG 59.059 41.667 0.00 0.00 0.00 4.63
1984 2022 4.335594 GGGTCATCTATTTTGAAACGGAGG 59.664 45.833 0.00 0.00 0.00 4.30
1985 2023 4.335594 GGTCATCTATTTTGAAACGGAGGG 59.664 45.833 0.00 0.00 0.00 4.30
1986 2024 5.183228 GTCATCTATTTTGAAACGGAGGGA 58.817 41.667 0.00 0.00 0.00 4.20
1987 2025 5.294552 GTCATCTATTTTGAAACGGAGGGAG 59.705 44.000 0.00 0.00 0.00 4.30
1988 2026 4.903045 TCTATTTTGAAACGGAGGGAGT 57.097 40.909 0.00 0.00 0.00 3.85
1989 2027 4.575885 TCTATTTTGAAACGGAGGGAGTG 58.424 43.478 0.00 0.00 0.00 3.51
2001 2039 2.820787 GGAGGGAGTGGATCATACGTAG 59.179 54.545 0.08 0.00 0.00 3.51
2043 2321 0.885879 TGCTTTGCTGCCAAGATCAG 59.114 50.000 16.71 0.00 31.52 2.90
2074 2352 8.551205 CAATATATAGTTCGTGTGCAGAAATGT 58.449 33.333 0.00 0.00 0.00 2.71
2162 2440 0.866061 CACGGGATACAGCTTCGTCG 60.866 60.000 0.00 0.00 39.74 5.12
2295 2573 0.179045 GGATGGGATGACTGGAACCG 60.179 60.000 0.00 0.00 0.00 4.44
2385 2969 4.362476 GCGCTTTGGCCTGGGTTG 62.362 66.667 3.32 0.00 34.44 3.77
2483 3072 2.922503 TGGGCTCGCAACCTCTCA 60.923 61.111 0.00 0.00 0.00 3.27
2510 3099 2.825836 GCAGCCCCCTTCATGACG 60.826 66.667 0.00 0.00 0.00 4.35
2622 3213 1.049855 ACAGTCGGTGGTGTGGGTTA 61.050 55.000 0.00 0.00 0.00 2.85
2773 3364 2.423538 AGTTCTGAAAAACAGTTGCGCT 59.576 40.909 9.73 0.00 45.86 5.92
2788 3379 1.202020 TGCGCTCGTACATTTTCATGC 60.202 47.619 9.73 0.00 33.05 4.06
2800 3391 1.016627 TTTCATGCTCTATGTGCGCC 58.983 50.000 4.18 0.00 38.01 6.53
2801 3392 0.107752 TTCATGCTCTATGTGCGCCA 60.108 50.000 4.18 2.31 38.01 5.69
2802 3393 0.811219 TCATGCTCTATGTGCGCCAC 60.811 55.000 4.18 3.72 38.01 5.01
2918 3510 5.616488 TGTCTTATTTACGGAGGCAAAAC 57.384 39.130 0.00 0.00 0.00 2.43
2934 3527 7.443879 GGAGGCAAAACAAAAAGATATTTTCCA 59.556 33.333 0.00 0.00 0.00 3.53
2994 3590 7.032580 TGTTCACGTGAAATTTCATTTTGACT 58.967 30.769 31.20 0.00 39.73 3.41
3176 3774 6.316390 GTCTGAATTGATGTAAAGGGACGAAT 59.684 38.462 0.00 0.00 0.00 3.34
3239 3837 1.410882 AGGAAGCGATTGAGGCTACTC 59.589 52.381 0.00 0.00 40.53 2.59
3274 3872 1.480789 TCGATTTCGATCCCCTCACA 58.519 50.000 0.00 0.00 44.22 3.58
3275 3873 2.039418 TCGATTTCGATCCCCTCACAT 58.961 47.619 0.00 0.00 44.22 3.21
3276 3874 3.227614 TCGATTTCGATCCCCTCACATA 58.772 45.455 0.00 0.00 44.22 2.29
3277 3875 3.255888 TCGATTTCGATCCCCTCACATAG 59.744 47.826 0.00 0.00 44.22 2.23
3278 3876 3.005897 CGATTTCGATCCCCTCACATAGT 59.994 47.826 0.00 0.00 43.02 2.12
3279 3877 4.561105 GATTTCGATCCCCTCACATAGTC 58.439 47.826 0.00 0.00 0.00 2.59
3332 3931 2.420372 GACTCGCTTTCCCCATCTTTTC 59.580 50.000 0.00 0.00 0.00 2.29
3361 3960 4.778415 CACGGTCTCGGCCTGACG 62.778 72.222 16.20 14.03 41.39 4.35
3407 4006 0.469917 ACACCTGATAGCATTCCCCG 59.530 55.000 0.00 0.00 0.00 5.73
3440 4039 4.074970 GGTGTGGATCTTTGAACTCATGT 58.925 43.478 0.00 0.00 0.00 3.21
3452 4051 6.486253 TTGAACTCATGTAATCAAGAGTGC 57.514 37.500 6.82 5.92 0.00 4.40
3497 4096 3.132111 GGGAGAGTTAGCTTGAGGAAGAG 59.868 52.174 0.00 0.00 0.00 2.85
3523 4122 6.152154 GCTCTATGGGAGGAGTATAAGAGTTC 59.848 46.154 0.00 0.00 42.08 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.636679 TCTTCATGTTTTTGGTGGTCCA 58.363 40.909 0.00 0.00 42.66 4.02
7 8 4.340950 TCTTCTTCATGTTTTTGGTGGTCC 59.659 41.667 0.00 0.00 0.00 4.46
8 9 5.514274 TCTTCTTCATGTTTTTGGTGGTC 57.486 39.130 0.00 0.00 0.00 4.02
9 10 5.930837 TTCTTCTTCATGTTTTTGGTGGT 57.069 34.783 0.00 0.00 0.00 4.16
10 11 6.037062 GGTTTTCTTCTTCATGTTTTTGGTGG 59.963 38.462 0.00 0.00 0.00 4.61
11 12 6.593382 TGGTTTTCTTCTTCATGTTTTTGGTG 59.407 34.615 0.00 0.00 0.00 4.17
12 13 6.706295 TGGTTTTCTTCTTCATGTTTTTGGT 58.294 32.000 0.00 0.00 0.00 3.67
13 14 7.608308 TTGGTTTTCTTCTTCATGTTTTTGG 57.392 32.000 0.00 0.00 0.00 3.28
16 17 8.892723 GGAATTTGGTTTTCTTCTTCATGTTTT 58.107 29.630 0.00 0.00 0.00 2.43
17 18 8.046107 TGGAATTTGGTTTTCTTCTTCATGTTT 58.954 29.630 0.00 0.00 0.00 2.83
18 19 7.563906 TGGAATTTGGTTTTCTTCTTCATGTT 58.436 30.769 0.00 0.00 0.00 2.71
19 20 7.069826 TCTGGAATTTGGTTTTCTTCTTCATGT 59.930 33.333 0.00 0.00 0.00 3.21
20 21 7.383300 GTCTGGAATTTGGTTTTCTTCTTCATG 59.617 37.037 0.00 0.00 0.00 3.07
21 22 7.436933 GTCTGGAATTTGGTTTTCTTCTTCAT 58.563 34.615 0.00 0.00 0.00 2.57
22 23 6.183360 GGTCTGGAATTTGGTTTTCTTCTTCA 60.183 38.462 0.00 0.00 0.00 3.02
23 24 6.040955 AGGTCTGGAATTTGGTTTTCTTCTTC 59.959 38.462 0.00 0.00 0.00 2.87
24 25 5.899547 AGGTCTGGAATTTGGTTTTCTTCTT 59.100 36.000 0.00 0.00 0.00 2.52
25 26 5.302823 CAGGTCTGGAATTTGGTTTTCTTCT 59.697 40.000 0.00 0.00 0.00 2.85
26 27 5.532557 CAGGTCTGGAATTTGGTTTTCTTC 58.467 41.667 0.00 0.00 0.00 2.87
27 28 5.535753 CAGGTCTGGAATTTGGTTTTCTT 57.464 39.130 0.00 0.00 0.00 2.52
42 43 3.826157 TCACCTTTTATTTGCCAGGTCTG 59.174 43.478 0.00 0.00 37.56 3.51
43 44 4.112634 TCACCTTTTATTTGCCAGGTCT 57.887 40.909 0.00 0.00 37.56 3.85
44 45 4.864704 TTCACCTTTTATTTGCCAGGTC 57.135 40.909 0.00 0.00 37.56 3.85
45 46 5.086621 AGATTCACCTTTTATTTGCCAGGT 58.913 37.500 0.00 0.00 40.50 4.00
46 47 5.185635 TGAGATTCACCTTTTATTTGCCAGG 59.814 40.000 0.00 0.00 0.00 4.45
47 48 6.095377 GTGAGATTCACCTTTTATTTGCCAG 58.905 40.000 0.00 0.00 41.37 4.85
48 49 6.024552 GTGAGATTCACCTTTTATTTGCCA 57.975 37.500 0.00 0.00 41.37 4.92
61 62 2.482142 GGAGATGGTCGGTGAGATTCAC 60.482 54.545 0.62 0.62 46.23 3.18
62 63 1.757118 GGAGATGGTCGGTGAGATTCA 59.243 52.381 0.00 0.00 0.00 2.57
63 64 1.069358 GGGAGATGGTCGGTGAGATTC 59.931 57.143 0.00 0.00 0.00 2.52
64 65 1.123928 GGGAGATGGTCGGTGAGATT 58.876 55.000 0.00 0.00 0.00 2.40
65 66 1.109920 CGGGAGATGGTCGGTGAGAT 61.110 60.000 0.00 0.00 0.00 2.75
66 67 1.753078 CGGGAGATGGTCGGTGAGA 60.753 63.158 0.00 0.00 0.00 3.27
67 68 1.605058 AACGGGAGATGGTCGGTGAG 61.605 60.000 0.00 0.00 0.00 3.51
68 69 1.601419 GAACGGGAGATGGTCGGTGA 61.601 60.000 0.00 0.00 0.00 4.02
69 70 1.153628 GAACGGGAGATGGTCGGTG 60.154 63.158 0.00 0.00 0.00 4.94
70 71 2.356780 GGAACGGGAGATGGTCGGT 61.357 63.158 0.00 0.00 0.00 4.69
71 72 2.499685 GGAACGGGAGATGGTCGG 59.500 66.667 0.00 0.00 0.00 4.79
84 85 3.496884 TGCACTGTTAGATTGAACGGAAC 59.503 43.478 2.25 0.00 37.83 3.62
85 86 3.734463 TGCACTGTTAGATTGAACGGAA 58.266 40.909 2.25 0.00 37.83 4.30
86 87 3.394674 TGCACTGTTAGATTGAACGGA 57.605 42.857 2.25 0.00 37.83 4.69
87 88 3.242091 CGATGCACTGTTAGATTGAACGG 60.242 47.826 0.00 0.00 40.84 4.44
88 89 3.367932 ACGATGCACTGTTAGATTGAACG 59.632 43.478 0.00 0.00 31.59 3.95
89 90 4.928661 ACGATGCACTGTTAGATTGAAC 57.071 40.909 0.00 0.00 0.00 3.18
90 91 5.474825 TGTACGATGCACTGTTAGATTGAA 58.525 37.500 0.00 0.00 0.00 2.69
91 92 5.066968 TGTACGATGCACTGTTAGATTGA 57.933 39.130 0.00 0.00 0.00 2.57
92 93 5.120053 TGTTGTACGATGCACTGTTAGATTG 59.880 40.000 0.00 0.00 0.00 2.67
93 94 5.234752 TGTTGTACGATGCACTGTTAGATT 58.765 37.500 0.00 0.00 0.00 2.40
94 95 4.816392 TGTTGTACGATGCACTGTTAGAT 58.184 39.130 0.00 0.00 0.00 1.98
95 96 4.245845 TGTTGTACGATGCACTGTTAGA 57.754 40.909 0.00 0.00 0.00 2.10
96 97 4.684242 TCTTGTTGTACGATGCACTGTTAG 59.316 41.667 0.00 0.00 0.00 2.34
97 98 4.623002 TCTTGTTGTACGATGCACTGTTA 58.377 39.130 0.00 0.00 0.00 2.41
98 99 3.462982 TCTTGTTGTACGATGCACTGTT 58.537 40.909 0.00 0.00 0.00 3.16
99 100 3.106242 TCTTGTTGTACGATGCACTGT 57.894 42.857 0.00 0.00 0.00 3.55
100 101 4.397382 CAATCTTGTTGTACGATGCACTG 58.603 43.478 0.00 0.00 0.00 3.66
101 102 3.120199 GCAATCTTGTTGTACGATGCACT 60.120 43.478 0.00 0.00 0.00 4.40
102 103 3.163594 GCAATCTTGTTGTACGATGCAC 58.836 45.455 0.00 0.00 0.00 4.57
103 104 2.810852 TGCAATCTTGTTGTACGATGCA 59.189 40.909 3.22 3.22 0.00 3.96
104 105 3.469899 TGCAATCTTGTTGTACGATGC 57.530 42.857 0.00 0.00 0.00 3.91
105 106 5.688823 TCTTTGCAATCTTGTTGTACGATG 58.311 37.500 0.00 0.00 0.00 3.84
106 107 5.940192 TCTTTGCAATCTTGTTGTACGAT 57.060 34.783 0.00 0.00 0.00 3.73
107 108 5.468409 TCATCTTTGCAATCTTGTTGTACGA 59.532 36.000 0.00 0.00 0.00 3.43
108 109 5.688823 TCATCTTTGCAATCTTGTTGTACG 58.311 37.500 0.00 0.00 0.00 3.67
109 110 7.307694 TGATCATCTTTGCAATCTTGTTGTAC 58.692 34.615 0.00 0.00 0.00 2.90
110 111 7.451501 TGATCATCTTTGCAATCTTGTTGTA 57.548 32.000 0.00 0.00 0.00 2.41
111 112 6.335471 TGATCATCTTTGCAATCTTGTTGT 57.665 33.333 0.00 0.00 0.00 3.32
112 113 6.183360 GCTTGATCATCTTTGCAATCTTGTTG 60.183 38.462 0.00 0.00 0.00 3.33
113 114 5.867716 GCTTGATCATCTTTGCAATCTTGTT 59.132 36.000 0.00 0.00 0.00 2.83
114 115 5.047590 TGCTTGATCATCTTTGCAATCTTGT 60.048 36.000 0.00 0.00 0.00 3.16
115 116 5.407502 TGCTTGATCATCTTTGCAATCTTG 58.592 37.500 0.00 0.00 0.00 3.02
116 117 5.654603 TGCTTGATCATCTTTGCAATCTT 57.345 34.783 0.00 0.00 0.00 2.40
117 118 5.359860 TCATGCTTGATCATCTTTGCAATCT 59.640 36.000 0.00 0.00 34.07 2.40
118 119 5.588240 TCATGCTTGATCATCTTTGCAATC 58.412 37.500 0.00 0.00 34.07 2.67
119 120 5.359860 TCTCATGCTTGATCATCTTTGCAAT 59.640 36.000 0.00 0.00 34.07 3.56
120 121 4.703093 TCTCATGCTTGATCATCTTTGCAA 59.297 37.500 2.33 0.00 34.07 4.08
121 122 4.266714 TCTCATGCTTGATCATCTTTGCA 58.733 39.130 2.33 3.41 34.88 4.08
122 123 4.895224 TCTCATGCTTGATCATCTTTGC 57.105 40.909 2.33 0.00 0.00 3.68
123 124 8.324163 TGATATCTCATGCTTGATCATCTTTG 57.676 34.615 3.98 0.00 0.00 2.77
124 125 8.919777 TTGATATCTCATGCTTGATCATCTTT 57.080 30.769 3.98 0.00 0.00 2.52
125 126 8.919777 TTTGATATCTCATGCTTGATCATCTT 57.080 30.769 3.98 0.00 0.00 2.40
126 127 8.919777 TTTTGATATCTCATGCTTGATCATCT 57.080 30.769 3.98 0.00 0.00 2.90
127 128 8.784994 ACTTTTGATATCTCATGCTTGATCATC 58.215 33.333 3.98 6.93 0.00 2.92
128 129 8.693120 ACTTTTGATATCTCATGCTTGATCAT 57.307 30.769 3.98 1.73 0.00 2.45
129 130 8.515695 AACTTTTGATATCTCATGCTTGATCA 57.484 30.769 3.98 1.44 0.00 2.92
130 131 8.618677 TGAACTTTTGATATCTCATGCTTGATC 58.381 33.333 3.98 0.00 0.00 2.92
131 132 8.515695 TGAACTTTTGATATCTCATGCTTGAT 57.484 30.769 3.98 0.00 0.00 2.57
132 133 7.926674 TGAACTTTTGATATCTCATGCTTGA 57.073 32.000 3.98 1.92 0.00 3.02
133 134 9.582431 AATTGAACTTTTGATATCTCATGCTTG 57.418 29.630 3.98 0.00 0.00 4.01
134 135 9.798994 GAATTGAACTTTTGATATCTCATGCTT 57.201 29.630 3.98 0.00 0.00 3.91
135 136 8.963725 TGAATTGAACTTTTGATATCTCATGCT 58.036 29.630 3.98 0.00 0.00 3.79
136 137 9.745880 ATGAATTGAACTTTTGATATCTCATGC 57.254 29.630 3.98 0.00 0.00 4.06
139 140 9.166173 ACGATGAATTGAACTTTTGATATCTCA 57.834 29.630 3.98 0.00 0.00 3.27
140 141 9.643652 GACGATGAATTGAACTTTTGATATCTC 57.356 33.333 3.98 0.00 0.00 2.75
141 142 9.166173 TGACGATGAATTGAACTTTTGATATCT 57.834 29.630 3.98 0.00 0.00 1.98
142 143 9.773328 TTGACGATGAATTGAACTTTTGATATC 57.227 29.630 0.00 0.00 0.00 1.63
145 146 9.480053 AATTTGACGATGAATTGAACTTTTGAT 57.520 25.926 0.00 0.00 0.00 2.57
146 147 8.870160 AATTTGACGATGAATTGAACTTTTGA 57.130 26.923 0.00 0.00 0.00 2.69
153 154 9.796120 GGGTAATAAATTTGACGATGAATTGAA 57.204 29.630 0.00 0.00 0.00 2.69
154 155 8.961634 TGGGTAATAAATTTGACGATGAATTGA 58.038 29.630 0.00 0.00 0.00 2.57
155 156 9.748708 ATGGGTAATAAATTTGACGATGAATTG 57.251 29.630 0.00 0.00 0.00 2.32
158 159 9.397280 TGTATGGGTAATAAATTTGACGATGAA 57.603 29.630 0.00 0.00 0.00 2.57
159 160 8.832521 GTGTATGGGTAATAAATTTGACGATGA 58.167 33.333 0.00 0.00 0.00 2.92
160 161 8.073768 GGTGTATGGGTAATAAATTTGACGATG 58.926 37.037 0.00 0.00 0.00 3.84
161 162 7.776030 TGGTGTATGGGTAATAAATTTGACGAT 59.224 33.333 0.00 0.00 0.00 3.73
162 163 7.110810 TGGTGTATGGGTAATAAATTTGACGA 58.889 34.615 0.00 0.00 0.00 4.20
163 164 7.323049 TGGTGTATGGGTAATAAATTTGACG 57.677 36.000 0.00 0.00 0.00 4.35
164 165 8.908903 TCATGGTGTATGGGTAATAAATTTGAC 58.091 33.333 0.00 0.00 37.39 3.18
165 166 9.653516 ATCATGGTGTATGGGTAATAAATTTGA 57.346 29.630 0.00 0.00 37.39 2.69
166 167 9.912634 GATCATGGTGTATGGGTAATAAATTTG 57.087 33.333 0.00 0.00 37.39 2.32
167 168 9.653516 TGATCATGGTGTATGGGTAATAAATTT 57.346 29.630 0.00 0.00 37.39 1.82
168 169 9.300681 CTGATCATGGTGTATGGGTAATAAATT 57.699 33.333 0.00 0.00 37.39 1.82
169 170 8.668653 TCTGATCATGGTGTATGGGTAATAAAT 58.331 33.333 0.00 0.00 37.39 1.40
170 171 8.040002 TCTGATCATGGTGTATGGGTAATAAA 57.960 34.615 0.00 0.00 37.39 1.40
171 172 7.625498 TCTGATCATGGTGTATGGGTAATAA 57.375 36.000 0.00 0.00 37.39 1.40
172 173 7.457535 TCATCTGATCATGGTGTATGGGTAATA 59.542 37.037 0.00 0.00 37.39 0.98
173 174 6.273026 TCATCTGATCATGGTGTATGGGTAAT 59.727 38.462 0.00 0.00 37.39 1.89
174 175 5.606329 TCATCTGATCATGGTGTATGGGTAA 59.394 40.000 0.00 0.00 37.39 2.85
175 176 5.154418 TCATCTGATCATGGTGTATGGGTA 58.846 41.667 0.00 0.00 37.39 3.69
176 177 3.975982 TCATCTGATCATGGTGTATGGGT 59.024 43.478 0.00 0.00 37.39 4.51
177 178 4.628963 TCATCTGATCATGGTGTATGGG 57.371 45.455 0.00 0.00 37.39 4.00
178 179 5.618236 ACTTCATCTGATCATGGTGTATGG 58.382 41.667 0.00 0.00 37.39 2.74
602 603 6.404074 CCAAGAGCTGAAGAAATCCATACAAC 60.404 42.308 0.00 0.00 0.00 3.32
635 636 6.635755 TCTATAACCATCGACACATGTGAAA 58.364 36.000 31.94 16.14 0.00 2.69
791 792 7.397476 TCCAAAATGTAAAGGGTGTGCATAATA 59.603 33.333 0.00 0.00 0.00 0.98
797 802 3.068873 TGTCCAAAATGTAAAGGGTGTGC 59.931 43.478 0.00 0.00 0.00 4.57
814 819 3.888323 ACATGCACATAAACTGTTGTCCA 59.112 39.130 0.00 0.00 35.29 4.02
822 827 6.230472 TCACAAGTAGACATGCACATAAACT 58.770 36.000 0.00 0.00 0.00 2.66
862 867 2.990066 ATCCCTCCATCACGAGAAAC 57.010 50.000 0.00 0.00 30.97 2.78
903 908 8.463930 TCATGTGATCCTTTTTGTAGTCTTTT 57.536 30.769 0.00 0.00 0.00 2.27
910 915 6.768483 TCACTCTCATGTGATCCTTTTTGTA 58.232 36.000 0.00 0.00 41.43 2.41
1020 1026 4.219070 TGATTCATTTCAACCTCAAGGCAG 59.781 41.667 0.00 0.00 39.32 4.85
1029 1035 4.199310 TCTCCCGATGATTCATTTCAACC 58.801 43.478 0.00 0.00 0.00 3.77
1057 1063 3.902063 CGCCGAGTTGACGCGATG 61.902 66.667 15.93 0.00 41.67 3.84
1096 1102 0.803740 GAGCAAAAGCAGAGCAGAGG 59.196 55.000 0.00 0.00 0.00 3.69
1174 1192 2.420466 GAGATTACCCGGACCCGC 59.580 66.667 0.73 0.00 38.24 6.13
1314 1332 2.802719 AGGTAATGGTCATTTGCGGTT 58.197 42.857 1.28 0.00 32.50 4.44
1493 1525 1.310933 TAGGGGAAGTGTCGCTCGAC 61.311 60.000 14.77 14.77 44.77 4.20
1569 1601 3.558931 ATCACGAACTATGGATGGCAA 57.441 42.857 0.00 0.00 0.00 4.52
1610 1642 1.202132 GCAAGAAACTGTCAACACGCA 60.202 47.619 0.00 0.00 0.00 5.24
1719 1751 1.347817 GGAACGACGAGAAGCTGCAG 61.348 60.000 10.11 10.11 0.00 4.41
1806 1838 2.038269 GCCGTTCCCGCAGATGAAA 61.038 57.895 0.00 0.00 0.00 2.69
1846 1878 3.810941 GGTGAGAACGGTGAACATGTAAA 59.189 43.478 0.00 0.00 0.00 2.01
1847 1879 3.181464 TGGTGAGAACGGTGAACATGTAA 60.181 43.478 0.00 0.00 0.00 2.41
1848 1880 2.365941 TGGTGAGAACGGTGAACATGTA 59.634 45.455 0.00 0.00 0.00 2.29
1886 1921 3.236896 GAAACGGAGGGGGTATCTATCA 58.763 50.000 0.00 0.00 0.00 2.15
1891 1929 2.793288 TTTGAAACGGAGGGGGTATC 57.207 50.000 0.00 0.00 0.00 2.24
1892 1930 3.750501 ATTTTGAAACGGAGGGGGTAT 57.249 42.857 0.00 0.00 0.00 2.73
1893 1931 3.845398 TCTATTTTGAAACGGAGGGGGTA 59.155 43.478 0.00 0.00 0.00 3.69
1894 1932 2.645797 TCTATTTTGAAACGGAGGGGGT 59.354 45.455 0.00 0.00 0.00 4.95
1895 1933 3.359695 TCTATTTTGAAACGGAGGGGG 57.640 47.619 0.00 0.00 0.00 5.40
1896 1934 4.335594 GTCATCTATTTTGAAACGGAGGGG 59.664 45.833 0.00 0.00 0.00 4.79
1897 1935 4.335594 GGTCATCTATTTTGAAACGGAGGG 59.664 45.833 0.00 0.00 0.00 4.30
1898 1936 4.335594 GGGTCATCTATTTTGAAACGGAGG 59.664 45.833 0.00 0.00 0.00 4.30
1899 1937 4.941263 TGGGTCATCTATTTTGAAACGGAG 59.059 41.667 0.00 0.00 0.00 4.63
1900 1938 4.912586 TGGGTCATCTATTTTGAAACGGA 58.087 39.130 0.00 0.00 0.00 4.69
1901 1939 5.183140 AGTTGGGTCATCTATTTTGAAACGG 59.817 40.000 0.00 0.00 0.00 4.44
1902 1940 6.254281 AGTTGGGTCATCTATTTTGAAACG 57.746 37.500 0.00 0.00 0.00 3.60
1903 1941 7.926018 ACAAAGTTGGGTCATCTATTTTGAAAC 59.074 33.333 0.00 0.00 0.00 2.78
1904 1942 8.017418 ACAAAGTTGGGTCATCTATTTTGAAA 57.983 30.769 0.00 0.00 0.00 2.69
1905 1943 7.595819 ACAAAGTTGGGTCATCTATTTTGAA 57.404 32.000 0.00 0.00 0.00 2.69
1906 1944 8.877864 ATACAAAGTTGGGTCATCTATTTTGA 57.122 30.769 0.00 0.00 0.00 2.69
1910 1948 9.975218 AGTTAATACAAAGTTGGGTCATCTATT 57.025 29.630 0.00 0.00 0.00 1.73
1911 1949 9.975218 AAGTTAATACAAAGTTGGGTCATCTAT 57.025 29.630 0.00 0.00 0.00 1.98
1912 1950 9.802039 AAAGTTAATACAAAGTTGGGTCATCTA 57.198 29.630 0.00 0.00 0.00 1.98
1913 1951 8.706322 AAAGTTAATACAAAGTTGGGTCATCT 57.294 30.769 0.00 0.00 0.00 2.90
1954 1992 8.293867 CGTTTCAAAATAGATGACCCAACTTTA 58.706 33.333 0.00 0.00 0.00 1.85
1955 1993 7.145323 CGTTTCAAAATAGATGACCCAACTTT 58.855 34.615 0.00 0.00 0.00 2.66
1956 1994 6.294508 CCGTTTCAAAATAGATGACCCAACTT 60.295 38.462 0.00 0.00 0.00 2.66
1957 1995 5.183140 CCGTTTCAAAATAGATGACCCAACT 59.817 40.000 0.00 0.00 0.00 3.16
1958 1996 5.182380 TCCGTTTCAAAATAGATGACCCAAC 59.818 40.000 0.00 0.00 0.00 3.77
1959 1997 5.317808 TCCGTTTCAAAATAGATGACCCAA 58.682 37.500 0.00 0.00 0.00 4.12
1960 1998 4.912586 TCCGTTTCAAAATAGATGACCCA 58.087 39.130 0.00 0.00 0.00 4.51
1961 1999 4.335594 CCTCCGTTTCAAAATAGATGACCC 59.664 45.833 0.00 0.00 0.00 4.46
1962 2000 4.335594 CCCTCCGTTTCAAAATAGATGACC 59.664 45.833 0.00 0.00 0.00 4.02
1963 2001 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
1964 2002 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
1965 2003 5.065218 CACTCCCTCCGTTTCAAAATAGATG 59.935 44.000 0.00 0.00 0.00 2.90
1966 2004 5.186198 CACTCCCTCCGTTTCAAAATAGAT 58.814 41.667 0.00 0.00 0.00 1.98
1967 2005 4.564821 CCACTCCCTCCGTTTCAAAATAGA 60.565 45.833 0.00 0.00 0.00 1.98
1968 2006 3.689649 CCACTCCCTCCGTTTCAAAATAG 59.310 47.826 0.00 0.00 0.00 1.73
1969 2007 3.328343 TCCACTCCCTCCGTTTCAAAATA 59.672 43.478 0.00 0.00 0.00 1.40
1970 2008 2.107552 TCCACTCCCTCCGTTTCAAAAT 59.892 45.455 0.00 0.00 0.00 1.82
1971 2009 1.491332 TCCACTCCCTCCGTTTCAAAA 59.509 47.619 0.00 0.00 0.00 2.44
1972 2010 1.133363 TCCACTCCCTCCGTTTCAAA 58.867 50.000 0.00 0.00 0.00 2.69
1973 2011 1.278127 GATCCACTCCCTCCGTTTCAA 59.722 52.381 0.00 0.00 0.00 2.69
1974 2012 0.902531 GATCCACTCCCTCCGTTTCA 59.097 55.000 0.00 0.00 0.00 2.69
1975 2013 0.902531 TGATCCACTCCCTCCGTTTC 59.097 55.000 0.00 0.00 0.00 2.78
1976 2014 1.584724 ATGATCCACTCCCTCCGTTT 58.415 50.000 0.00 0.00 0.00 3.60
1977 2015 2.040178 GTATGATCCACTCCCTCCGTT 58.960 52.381 0.00 0.00 0.00 4.44
1978 2016 1.705873 GTATGATCCACTCCCTCCGT 58.294 55.000 0.00 0.00 0.00 4.69
1979 2017 0.598562 CGTATGATCCACTCCCTCCG 59.401 60.000 0.00 0.00 0.00 4.63
1980 2018 1.705873 ACGTATGATCCACTCCCTCC 58.294 55.000 0.00 0.00 0.00 4.30
1981 2019 3.488363 ACTACGTATGATCCACTCCCTC 58.512 50.000 0.00 0.00 0.00 4.30
1982 2020 3.596940 ACTACGTATGATCCACTCCCT 57.403 47.619 0.00 0.00 0.00 4.20
1983 2021 4.826183 AGTAACTACGTATGATCCACTCCC 59.174 45.833 0.00 0.00 0.00 4.30
1984 2022 5.048852 GGAGTAACTACGTATGATCCACTCC 60.049 48.000 16.41 16.41 41.83 3.85
1985 2023 5.333952 CGGAGTAACTACGTATGATCCACTC 60.334 48.000 0.00 3.92 32.47 3.51
1986 2024 4.514441 CGGAGTAACTACGTATGATCCACT 59.486 45.833 0.00 0.00 32.47 4.00
1987 2025 4.781071 CGGAGTAACTACGTATGATCCAC 58.219 47.826 0.00 0.00 32.47 4.02
2043 2321 7.381408 TCTGCACACGAACTATATATTGTTAGC 59.619 37.037 16.02 13.07 0.00 3.09
2074 2352 2.574018 CGAGGTGGAGTGCAGGTGA 61.574 63.158 0.00 0.00 0.00 4.02
2278 2556 1.224592 GCGGTTCCAGTCATCCCAT 59.775 57.895 0.00 0.00 0.00 4.00
2295 2573 2.741486 TTACCTCTGGTTGGCGGTGC 62.741 60.000 0.00 0.00 37.09 5.01
2483 3072 4.660938 GGGGCTGCTTCGGTTGGT 62.661 66.667 0.00 0.00 0.00 3.67
2510 3099 0.250081 GTCCATCGATCCAGGCCTTC 60.250 60.000 0.00 0.00 0.00 3.46
2667 3258 7.901377 CGTATTTTCCGTTAACTTGTATCCTTG 59.099 37.037 3.71 0.00 0.00 3.61
2683 3274 4.468095 GGATTCATCCACGTATTTTCCG 57.532 45.455 0.51 0.00 46.38 4.30
2747 3338 6.183360 GCGCAACTGTTTTTCAGAACTTTTTA 60.183 34.615 0.30 0.00 46.27 1.52
2753 3344 2.783832 GAGCGCAACTGTTTTTCAGAAC 59.216 45.455 11.47 0.00 46.27 3.01
2764 3355 2.096466 TGAAAATGTACGAGCGCAACTG 60.096 45.455 11.47 0.00 0.00 3.16
2773 3364 5.006649 GCACATAGAGCATGAAAATGTACGA 59.993 40.000 0.00 0.00 38.10 3.43
2788 3379 1.442769 ACTTTGTGGCGCACATAGAG 58.557 50.000 24.96 18.06 44.16 2.43
2902 3494 5.908341 TCTTTTTGTTTTGCCTCCGTAAAT 58.092 33.333 0.00 0.00 0.00 1.40
2934 3527 1.100463 TGTGCGGCACAACATTCTGT 61.100 50.000 31.72 0.00 41.69 3.41
3036 3632 5.845103 TCGGATACATATGAAACCGCTTTA 58.155 37.500 23.13 11.38 40.12 1.85
3239 3837 6.302078 TCGAAATCGAAATGACAAAACGAATG 59.698 34.615 2.51 0.00 46.30 2.67
3272 3870 6.716934 CTAGGTAAGGACATGTGACTATGT 57.283 41.667 1.15 1.31 43.61 2.29
3357 3956 3.329814 TGGTATATCTAGAGAGGCCGTCA 59.670 47.826 10.44 0.00 0.00 4.35
3358 3957 3.952931 TGGTATATCTAGAGAGGCCGTC 58.047 50.000 0.00 0.00 0.00 4.79
3359 3958 4.383931 TTGGTATATCTAGAGAGGCCGT 57.616 45.455 0.00 0.00 0.00 5.68
3360 3959 5.655488 CATTTGGTATATCTAGAGAGGCCG 58.345 45.833 0.00 0.00 0.00 6.13
3361 3960 5.188751 AGCATTTGGTATATCTAGAGAGGCC 59.811 44.000 0.00 0.00 0.00 5.19
3362 3961 6.293004 AGCATTTGGTATATCTAGAGAGGC 57.707 41.667 0.00 0.00 0.00 4.70
3363 3962 8.247562 GTGTAGCATTTGGTATATCTAGAGAGG 58.752 40.741 0.00 0.00 0.00 3.69
3364 3963 8.797438 TGTGTAGCATTTGGTATATCTAGAGAG 58.203 37.037 0.00 0.00 0.00 3.20
3365 3964 8.577296 GTGTGTAGCATTTGGTATATCTAGAGA 58.423 37.037 0.00 0.00 0.00 3.10
3407 4006 1.259840 ATCCACACCCTGGCAATTGC 61.260 55.000 22.47 22.47 40.39 3.56
3440 4039 5.151297 TCACTCATGTGCACTCTTGATTA 57.849 39.130 19.41 0.00 43.49 1.75
3452 4051 4.442612 CCCTTCCTCTGTATCACTCATGTG 60.443 50.000 0.00 0.00 45.07 3.21
3497 4096 4.936802 TCTTATACTCCTCCCATAGAGCC 58.063 47.826 0.00 0.00 41.74 4.70
3523 4122 6.916387 GCATTCAAGATCATTTGTATCCACTG 59.084 38.462 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.