Multiple sequence alignment - TraesCS1B01G224700

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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 TraesCS1B01G224700 chr1B 100.000 3062 0 0 1 3062 403189734 403186673 0.000000e+00 5655
1 TraesCS1B01G224700 chr1A 91.645 2286 109 33 279 2516 373265003 373262752 0.000000e+00 3088
2 TraesCS1B01G224700 chr1A 91.085 516 28 12 2540 3042 373262621 373262111 0.000000e+00 682
3 TraesCS1B01G224700 chr1D 92.634 2050 66 27 979 2987 299052884 299050879 0.000000e+00 2870
4 TraesCS1B01G224700 chr1D 89.755 654 43 13 320 961 299053837 299053196 0.000000e+00 815
5 TraesCS1B01G224700 chr1D 97.849 93 2 0 2970 3062 299050862 299050770 8.790000e-36 161


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 TraesCS1B01G224700 chr1B 403186673 403189734 3061 True 5655 5655 100.000000 1 3062 1 chr1B.!!$R1 3061
1 TraesCS1B01G224700 chr1A 373262111 373265003 2892 True 1885 3088 91.365000 279 3042 2 chr1A.!!$R1 2763
2 TraesCS1B01G224700 chr1D 299050770 299053837 3067 True 1282 2870 93.412667 320 3062 3 chr1D.!!$R1 2742

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
864 892 0.104304 AACGTGTTCACCTCTCGCTT 59.896 50.0 0.0 0.0 0.0 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2441 2815 0.248289 CTGGCAATGGCAAAAGGAGG 59.752 55.0 11.45 0.0 43.71 4.3 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
41 42 2.292803 GCAGTAGCGCTCTAACTGC 58.707 57.895 35.10 35.10 39.86 4.40
42 43 1.148759 GCAGTAGCGCTCTAACTGCC 61.149 60.000 36.88 25.05 40.27 4.85
43 44 0.528684 CAGTAGCGCTCTAACTGCCC 60.529 60.000 22.12 0.00 0.00 5.36
44 45 0.970937 AGTAGCGCTCTAACTGCCCA 60.971 55.000 16.34 0.00 0.00 5.36
45 46 0.806492 GTAGCGCTCTAACTGCCCAC 60.806 60.000 16.34 0.00 0.00 4.61
46 47 1.254975 TAGCGCTCTAACTGCCCACA 61.255 55.000 16.34 0.00 0.00 4.17
47 48 1.450312 GCGCTCTAACTGCCCACAT 60.450 57.895 0.00 0.00 0.00 3.21
48 49 1.432270 GCGCTCTAACTGCCCACATC 61.432 60.000 0.00 0.00 0.00 3.06
49 50 0.176680 CGCTCTAACTGCCCACATCT 59.823 55.000 0.00 0.00 0.00 2.90
50 51 1.804372 CGCTCTAACTGCCCACATCTC 60.804 57.143 0.00 0.00 0.00 2.75
51 52 1.804372 GCTCTAACTGCCCACATCTCG 60.804 57.143 0.00 0.00 0.00 4.04
52 53 0.175760 TCTAACTGCCCACATCTCGC 59.824 55.000 0.00 0.00 0.00 5.03
53 54 1.148157 CTAACTGCCCACATCTCGCG 61.148 60.000 0.00 0.00 0.00 5.87
54 55 1.600511 TAACTGCCCACATCTCGCGA 61.601 55.000 9.26 9.26 0.00 5.87
55 56 2.125552 CTGCCCACATCTCGCGAA 60.126 61.111 11.33 1.32 0.00 4.70
56 57 2.434185 TGCCCACATCTCGCGAAC 60.434 61.111 11.33 0.00 0.00 3.95
57 58 3.195698 GCCCACATCTCGCGAACC 61.196 66.667 11.33 0.00 0.00 3.62
58 59 2.579201 CCCACATCTCGCGAACCT 59.421 61.111 11.33 0.00 0.00 3.50
59 60 1.079127 CCCACATCTCGCGAACCTT 60.079 57.895 11.33 0.00 0.00 3.50
60 61 1.361668 CCCACATCTCGCGAACCTTG 61.362 60.000 11.33 7.94 0.00 3.61
61 62 0.670546 CCACATCTCGCGAACCTTGT 60.671 55.000 11.33 8.61 0.00 3.16
62 63 0.716108 CACATCTCGCGAACCTTGTC 59.284 55.000 11.33 0.00 0.00 3.18
63 64 0.603569 ACATCTCGCGAACCTTGTCT 59.396 50.000 11.33 0.00 0.00 3.41
64 65 0.994995 CATCTCGCGAACCTTGTCTG 59.005 55.000 11.33 0.00 0.00 3.51
65 66 0.108615 ATCTCGCGAACCTTGTCTGG 60.109 55.000 11.33 0.00 0.00 3.86
66 67 2.357034 TCGCGAACCTTGTCTGGC 60.357 61.111 6.20 0.00 0.00 4.85
67 68 3.777925 CGCGAACCTTGTCTGGCG 61.778 66.667 0.00 0.00 37.56 5.69
68 69 2.665185 GCGAACCTTGTCTGGCGT 60.665 61.111 0.00 0.00 0.00 5.68
69 70 2.251642 GCGAACCTTGTCTGGCGTT 61.252 57.895 0.00 0.00 0.00 4.84
70 71 0.947180 GCGAACCTTGTCTGGCGTTA 60.947 55.000 0.00 0.00 0.00 3.18
71 72 0.788391 CGAACCTTGTCTGGCGTTAC 59.212 55.000 0.00 0.00 0.00 2.50
72 73 1.870580 CGAACCTTGTCTGGCGTTACA 60.871 52.381 0.00 0.00 0.00 2.41
73 74 2.215196 GAACCTTGTCTGGCGTTACAA 58.785 47.619 0.00 0.00 34.57 2.41
74 75 2.335316 ACCTTGTCTGGCGTTACAAA 57.665 45.000 0.00 0.00 35.32 2.83
75 76 1.944709 ACCTTGTCTGGCGTTACAAAC 59.055 47.619 0.00 0.00 35.32 2.93
76 77 1.265905 CCTTGTCTGGCGTTACAAACC 59.734 52.381 0.00 0.00 35.32 3.27
77 78 1.944024 CTTGTCTGGCGTTACAAACCA 59.056 47.619 0.00 0.00 35.32 3.67
78 79 2.039818 TGTCTGGCGTTACAAACCAA 57.960 45.000 0.00 0.00 31.81 3.67
79 80 1.671845 TGTCTGGCGTTACAAACCAAC 59.328 47.619 0.00 0.00 31.81 3.77
80 81 1.944709 GTCTGGCGTTACAAACCAACT 59.055 47.619 0.00 0.00 31.81 3.16
81 82 1.944024 TCTGGCGTTACAAACCAACTG 59.056 47.619 0.00 0.00 31.81 3.16
82 83 0.382515 TGGCGTTACAAACCAACTGC 59.617 50.000 0.00 0.00 0.00 4.40
83 84 0.382515 GGCGTTACAAACCAACTGCA 59.617 50.000 0.00 0.00 31.55 4.41
84 85 1.599419 GGCGTTACAAACCAACTGCAG 60.599 52.381 13.48 13.48 31.55 4.41
85 86 1.332375 GCGTTACAAACCAACTGCAGA 59.668 47.619 23.35 0.00 0.00 4.26
86 87 2.223386 GCGTTACAAACCAACTGCAGAA 60.223 45.455 23.35 0.00 0.00 3.02
87 88 3.550030 GCGTTACAAACCAACTGCAGAAT 60.550 43.478 23.35 5.76 0.00 2.40
88 89 4.219033 CGTTACAAACCAACTGCAGAATC 58.781 43.478 23.35 0.00 0.00 2.52
89 90 4.024048 CGTTACAAACCAACTGCAGAATCT 60.024 41.667 23.35 0.00 0.00 2.40
90 91 5.452777 GTTACAAACCAACTGCAGAATCTC 58.547 41.667 23.35 0.00 0.00 2.75
91 92 2.887152 ACAAACCAACTGCAGAATCTCC 59.113 45.455 23.35 0.00 0.00 3.71
92 93 1.813513 AACCAACTGCAGAATCTCCG 58.186 50.000 23.35 2.55 0.00 4.63
93 94 0.687354 ACCAACTGCAGAATCTCCGT 59.313 50.000 23.35 3.20 0.00 4.69
94 95 1.899814 ACCAACTGCAGAATCTCCGTA 59.100 47.619 23.35 0.00 0.00 4.02
95 96 2.301870 ACCAACTGCAGAATCTCCGTAA 59.698 45.455 23.35 0.00 0.00 3.18
96 97 3.244422 ACCAACTGCAGAATCTCCGTAAA 60.244 43.478 23.35 0.00 0.00 2.01
97 98 3.941483 CCAACTGCAGAATCTCCGTAAAT 59.059 43.478 23.35 0.00 0.00 1.40
98 99 4.396166 CCAACTGCAGAATCTCCGTAAATT 59.604 41.667 23.35 0.00 0.00 1.82
99 100 5.106157 CCAACTGCAGAATCTCCGTAAATTT 60.106 40.000 23.35 0.00 0.00 1.82
100 101 5.803020 ACTGCAGAATCTCCGTAAATTTC 57.197 39.130 23.35 0.00 0.00 2.17
101 102 4.330074 ACTGCAGAATCTCCGTAAATTTCG 59.670 41.667 23.35 0.00 0.00 3.46
102 103 4.500127 TGCAGAATCTCCGTAAATTTCGA 58.500 39.130 10.35 0.00 0.00 3.71
103 104 4.932799 TGCAGAATCTCCGTAAATTTCGAA 59.067 37.500 0.00 0.00 0.00 3.71
104 105 5.163893 TGCAGAATCTCCGTAAATTTCGAAC 60.164 40.000 0.00 0.00 0.00 3.95
105 106 5.726963 GCAGAATCTCCGTAAATTTCGAACC 60.727 44.000 0.00 0.00 0.00 3.62
106 107 4.565564 AGAATCTCCGTAAATTTCGAACCG 59.434 41.667 0.00 0.00 0.00 4.44
107 108 3.574284 TCTCCGTAAATTTCGAACCGA 57.426 42.857 0.00 0.00 0.00 4.69
108 109 3.911868 TCTCCGTAAATTTCGAACCGAA 58.088 40.909 0.00 0.00 44.28 4.30
109 110 3.674753 TCTCCGTAAATTTCGAACCGAAC 59.325 43.478 0.00 0.00 45.64 3.95
110 111 3.652274 TCCGTAAATTTCGAACCGAACT 58.348 40.909 0.00 0.00 45.64 3.01
111 112 4.057432 TCCGTAAATTTCGAACCGAACTT 58.943 39.130 0.00 0.42 45.64 2.66
112 113 5.226396 TCCGTAAATTTCGAACCGAACTTA 58.774 37.500 0.00 1.08 45.64 2.24
113 114 5.345741 TCCGTAAATTTCGAACCGAACTTAG 59.654 40.000 0.00 0.14 45.64 2.18
114 115 5.445010 CCGTAAATTTCGAACCGAACTTAGG 60.445 44.000 0.00 8.03 45.64 2.69
115 116 5.119125 CGTAAATTTCGAACCGAACTTAGGT 59.881 40.000 0.00 0.00 45.64 3.08
122 123 2.168054 CCGAACTTAGGTTTGGCCG 58.832 57.895 10.85 0.76 46.35 6.13
123 124 0.604511 CCGAACTTAGGTTTGGCCGT 60.605 55.000 10.85 0.00 46.35 5.68
124 125 0.515564 CGAACTTAGGTTTGGCCGTG 59.484 55.000 0.00 0.00 43.70 4.94
125 126 0.240145 GAACTTAGGTTTGGCCGTGC 59.760 55.000 0.00 0.00 43.70 5.34
126 127 0.466555 AACTTAGGTTTGGCCGTGCA 60.467 50.000 0.00 0.00 43.70 4.57
127 128 0.889186 ACTTAGGTTTGGCCGTGCAG 60.889 55.000 0.00 0.00 43.70 4.41
128 129 0.889186 CTTAGGTTTGGCCGTGCAGT 60.889 55.000 0.00 0.00 43.70 4.40
129 130 0.466555 TTAGGTTTGGCCGTGCAGTT 60.467 50.000 0.00 0.00 43.70 3.16
130 131 0.397187 TAGGTTTGGCCGTGCAGTTA 59.603 50.000 0.00 0.00 43.70 2.24
131 132 0.466555 AGGTTTGGCCGTGCAGTTAA 60.467 50.000 0.00 0.00 43.70 2.01
132 133 0.601057 GGTTTGGCCGTGCAGTTAAT 59.399 50.000 0.00 0.00 0.00 1.40
133 134 1.668628 GGTTTGGCCGTGCAGTTAATG 60.669 52.381 0.00 0.00 0.00 1.90
134 135 0.600557 TTTGGCCGTGCAGTTAATGG 59.399 50.000 0.00 0.00 0.00 3.16
136 137 2.100216 GCCGTGCAGTTAATGGCG 59.900 61.111 0.00 0.00 39.80 5.69
137 138 2.791256 CCGTGCAGTTAATGGCGG 59.209 61.111 0.00 0.00 0.00 6.13
138 139 2.100216 CGTGCAGTTAATGGCGGC 59.900 61.111 0.00 0.00 0.00 6.53
139 140 2.489751 GTGCAGTTAATGGCGGCC 59.510 61.111 13.32 13.32 0.00 6.13
140 141 3.130819 TGCAGTTAATGGCGGCCG 61.131 61.111 24.05 24.05 0.00 6.13
141 142 3.131478 GCAGTTAATGGCGGCCGT 61.131 61.111 28.70 11.99 0.00 5.68
142 143 2.696759 GCAGTTAATGGCGGCCGTT 61.697 57.895 27.95 27.95 36.61 4.44
143 144 1.880186 CAGTTAATGGCGGCCGTTT 59.120 52.632 29.75 19.88 34.27 3.60
144 145 1.088306 CAGTTAATGGCGGCCGTTTA 58.912 50.000 29.75 19.38 34.27 2.01
145 146 1.673920 CAGTTAATGGCGGCCGTTTAT 59.326 47.619 29.75 15.66 34.27 1.40
146 147 1.944709 AGTTAATGGCGGCCGTTTATC 59.055 47.619 29.75 19.09 34.27 1.75
147 148 0.938713 TTAATGGCGGCCGTTTATCG 59.061 50.000 29.75 0.00 34.27 2.92
148 149 0.104487 TAATGGCGGCCGTTTATCGA 59.896 50.000 29.75 10.39 42.86 3.59
149 150 0.534203 AATGGCGGCCGTTTATCGAT 60.534 50.000 28.70 9.28 42.86 3.59
150 151 0.319083 ATGGCGGCCGTTTATCGATA 59.681 50.000 28.70 0.00 42.86 2.92
151 152 0.319211 TGGCGGCCGTTTATCGATAG 60.319 55.000 28.70 0.00 42.86 2.08
152 153 1.623973 GGCGGCCGTTTATCGATAGC 61.624 60.000 28.70 4.45 42.86 2.97
153 154 0.666577 GCGGCCGTTTATCGATAGCT 60.667 55.000 28.70 0.00 42.86 3.32
154 155 1.060713 CGGCCGTTTATCGATAGCTG 58.939 55.000 19.50 10.45 42.86 4.24
155 156 1.602165 CGGCCGTTTATCGATAGCTGT 60.602 52.381 19.50 0.00 42.86 4.40
156 157 2.351060 CGGCCGTTTATCGATAGCTGTA 60.351 50.000 19.50 0.00 42.86 2.74
157 158 3.672511 CGGCCGTTTATCGATAGCTGTAT 60.673 47.826 19.50 0.00 42.86 2.29
158 159 4.243270 GGCCGTTTATCGATAGCTGTATT 58.757 43.478 12.47 0.00 42.86 1.89
159 160 4.689345 GGCCGTTTATCGATAGCTGTATTT 59.311 41.667 12.47 0.00 42.86 1.40
160 161 5.865552 GGCCGTTTATCGATAGCTGTATTTA 59.134 40.000 12.47 0.00 42.86 1.40
161 162 6.183360 GGCCGTTTATCGATAGCTGTATTTAC 60.183 42.308 12.47 0.16 42.86 2.01
162 163 6.585322 GCCGTTTATCGATAGCTGTATTTACT 59.415 38.462 5.09 0.00 42.86 2.24
163 164 7.201333 GCCGTTTATCGATAGCTGTATTTACTC 60.201 40.741 5.09 0.00 42.86 2.59
164 165 7.007188 CCGTTTATCGATAGCTGTATTTACTCG 59.993 40.741 5.09 0.00 42.86 4.18
165 166 7.459862 CGTTTATCGATAGCTGTATTTACTCGC 60.460 40.741 5.09 0.00 42.86 5.03
166 167 3.806958 TCGATAGCTGTATTTACTCGCG 58.193 45.455 0.00 0.00 0.00 5.87
167 168 3.249320 TCGATAGCTGTATTTACTCGCGT 59.751 43.478 5.77 0.00 0.00 6.01
168 169 3.973135 CGATAGCTGTATTTACTCGCGTT 59.027 43.478 5.77 0.00 0.00 4.84
169 170 4.440103 CGATAGCTGTATTTACTCGCGTTT 59.560 41.667 5.77 0.00 0.00 3.60
170 171 5.051907 CGATAGCTGTATTTACTCGCGTTTT 60.052 40.000 5.77 0.00 0.00 2.43
171 172 6.507456 CGATAGCTGTATTTACTCGCGTTTTT 60.507 38.462 5.77 0.00 0.00 1.94
201 202 1.170442 AAAAAGATGGCGTTACCCCG 58.830 50.000 0.00 0.00 37.83 5.73
202 203 0.325602 AAAAGATGGCGTTACCCCGA 59.674 50.000 0.00 0.00 37.83 5.14
203 204 0.392060 AAAGATGGCGTTACCCCGAC 60.392 55.000 0.00 0.00 37.83 4.79
204 205 2.567564 AAGATGGCGTTACCCCGACG 62.568 60.000 0.00 0.00 39.23 5.12
205 206 3.360956 GATGGCGTTACCCCGACGT 62.361 63.158 0.00 0.00 42.22 4.34
206 207 3.360956 ATGGCGTTACCCCGACGTC 62.361 63.158 5.18 5.18 44.73 4.34
207 208 4.801624 GGCGTTACCCCGACGTCC 62.802 72.222 10.58 0.00 42.22 4.79
208 209 4.801624 GCGTTACCCCGACGTCCC 62.802 72.222 10.58 0.00 42.22 4.46
209 210 4.481112 CGTTACCCCGACGTCCCG 62.481 72.222 10.58 0.00 35.88 5.14
210 211 4.801624 GTTACCCCGACGTCCCGC 62.802 72.222 10.58 0.00 0.00 6.13
212 213 3.636929 TTACCCCGACGTCCCGCTA 62.637 63.158 10.58 0.00 0.00 4.26
215 216 2.905880 CCCGACGTCCCGCTAGAT 60.906 66.667 10.58 0.00 0.00 1.98
216 217 2.638154 CCGACGTCCCGCTAGATC 59.362 66.667 10.58 0.00 0.00 2.75
217 218 2.248724 CGACGTCCCGCTAGATCG 59.751 66.667 10.58 0.00 0.00 3.69
218 219 2.051166 GACGTCCCGCTAGATCGC 60.051 66.667 3.51 0.00 0.00 4.58
219 220 3.539560 GACGTCCCGCTAGATCGCC 62.540 68.421 3.51 0.00 0.00 5.54
220 221 3.288290 CGTCCCGCTAGATCGCCT 61.288 66.667 0.00 0.00 0.00 5.52
221 222 2.846652 CGTCCCGCTAGATCGCCTT 61.847 63.158 0.00 0.00 0.00 4.35
222 223 1.300233 GTCCCGCTAGATCGCCTTG 60.300 63.158 0.00 0.00 0.00 3.61
223 224 2.029666 CCCGCTAGATCGCCTTGG 59.970 66.667 0.00 0.00 0.00 3.61
224 225 2.498941 CCCGCTAGATCGCCTTGGA 61.499 63.158 0.00 0.00 0.00 3.53
225 226 1.668294 CCGCTAGATCGCCTTGGAT 59.332 57.895 0.00 0.00 0.00 3.41
226 227 0.888619 CCGCTAGATCGCCTTGGATA 59.111 55.000 0.00 0.00 0.00 2.59
227 228 1.402984 CCGCTAGATCGCCTTGGATAC 60.403 57.143 0.00 0.00 0.00 2.24
228 229 1.542030 CGCTAGATCGCCTTGGATACT 59.458 52.381 0.00 0.00 37.61 2.12
229 230 2.029828 CGCTAGATCGCCTTGGATACTT 60.030 50.000 0.00 0.00 37.61 2.24
230 231 3.190744 CGCTAGATCGCCTTGGATACTTA 59.809 47.826 0.00 0.00 37.61 2.24
231 232 4.142359 CGCTAGATCGCCTTGGATACTTAT 60.142 45.833 0.00 0.00 37.61 1.73
232 233 5.344884 GCTAGATCGCCTTGGATACTTATC 58.655 45.833 0.00 0.00 37.61 1.75
233 234 5.126384 GCTAGATCGCCTTGGATACTTATCT 59.874 44.000 0.00 0.00 33.28 1.98
234 235 5.652994 AGATCGCCTTGGATACTTATCTC 57.347 43.478 0.00 0.00 33.28 2.75
235 236 4.464597 AGATCGCCTTGGATACTTATCTCC 59.535 45.833 0.00 0.00 33.28 3.71
236 237 3.845860 TCGCCTTGGATACTTATCTCCT 58.154 45.455 0.00 0.00 33.28 3.69
237 238 4.223953 TCGCCTTGGATACTTATCTCCTT 58.776 43.478 0.00 0.00 33.28 3.36
238 239 4.654262 TCGCCTTGGATACTTATCTCCTTT 59.346 41.667 0.00 0.00 33.28 3.11
239 240 5.130477 TCGCCTTGGATACTTATCTCCTTTT 59.870 40.000 0.00 0.00 33.28 2.27
240 241 5.823045 CGCCTTGGATACTTATCTCCTTTTT 59.177 40.000 0.00 0.00 33.28 1.94
241 242 6.238484 CGCCTTGGATACTTATCTCCTTTTTG 60.238 42.308 0.00 0.00 33.28 2.44
242 243 6.039829 GCCTTGGATACTTATCTCCTTTTTGG 59.960 42.308 0.00 0.00 33.28 3.28
243 244 6.039829 CCTTGGATACTTATCTCCTTTTTGGC 59.960 42.308 0.00 0.00 34.16 4.52
244 245 6.327386 TGGATACTTATCTCCTTTTTGGCT 57.673 37.500 0.00 0.00 34.16 4.75
245 246 6.122277 TGGATACTTATCTCCTTTTTGGCTG 58.878 40.000 0.00 0.00 34.16 4.85
246 247 6.122964 GGATACTTATCTCCTTTTTGGCTGT 58.877 40.000 0.00 0.00 35.26 4.40
247 248 6.261158 GGATACTTATCTCCTTTTTGGCTGTC 59.739 42.308 0.00 0.00 35.26 3.51
248 249 4.003648 ACTTATCTCCTTTTTGGCTGTCG 58.996 43.478 0.00 0.00 35.26 4.35
249 250 2.568623 ATCTCCTTTTTGGCTGTCGT 57.431 45.000 0.00 0.00 35.26 4.34
250 251 1.878953 TCTCCTTTTTGGCTGTCGTC 58.121 50.000 0.00 0.00 35.26 4.20
251 252 1.416401 TCTCCTTTTTGGCTGTCGTCT 59.584 47.619 0.00 0.00 35.26 4.18
252 253 1.801178 CTCCTTTTTGGCTGTCGTCTC 59.199 52.381 0.00 0.00 35.26 3.36
253 254 1.416401 TCCTTTTTGGCTGTCGTCTCT 59.584 47.619 0.00 0.00 35.26 3.10
254 255 2.631062 TCCTTTTTGGCTGTCGTCTCTA 59.369 45.455 0.00 0.00 35.26 2.43
255 256 3.260884 TCCTTTTTGGCTGTCGTCTCTAT 59.739 43.478 0.00 0.00 35.26 1.98
256 257 3.619038 CCTTTTTGGCTGTCGTCTCTATC 59.381 47.826 0.00 0.00 0.00 2.08
257 258 4.499183 CTTTTTGGCTGTCGTCTCTATCT 58.501 43.478 0.00 0.00 0.00 1.98
258 259 3.784701 TTTGGCTGTCGTCTCTATCTC 57.215 47.619 0.00 0.00 0.00 2.75
259 260 2.719531 TGGCTGTCGTCTCTATCTCT 57.280 50.000 0.00 0.00 0.00 3.10
260 261 2.566913 TGGCTGTCGTCTCTATCTCTC 58.433 52.381 0.00 0.00 0.00 3.20
261 262 1.529438 GGCTGTCGTCTCTATCTCTCG 59.471 57.143 0.00 0.00 0.00 4.04
262 263 1.070175 GCTGTCGTCTCTATCTCTCGC 60.070 57.143 0.00 0.00 0.00 5.03
263 264 2.479837 CTGTCGTCTCTATCTCTCGCT 58.520 52.381 0.00 0.00 0.00 4.93
264 265 2.475111 CTGTCGTCTCTATCTCTCGCTC 59.525 54.545 0.00 0.00 0.00 5.03
265 266 1.454276 GTCGTCTCTATCTCTCGCTCG 59.546 57.143 0.00 0.00 0.00 5.03
266 267 0.787787 CGTCTCTATCTCTCGCTCGG 59.212 60.000 0.00 0.00 0.00 4.63
267 268 1.603425 CGTCTCTATCTCTCGCTCGGA 60.603 57.143 0.00 0.00 0.00 4.55
268 269 2.485903 GTCTCTATCTCTCGCTCGGAA 58.514 52.381 0.00 0.00 0.00 4.30
269 270 3.071479 GTCTCTATCTCTCGCTCGGAAT 58.929 50.000 0.00 0.00 0.00 3.01
270 271 3.500680 GTCTCTATCTCTCGCTCGGAATT 59.499 47.826 0.00 0.00 0.00 2.17
271 272 4.691685 GTCTCTATCTCTCGCTCGGAATTA 59.308 45.833 0.00 0.00 0.00 1.40
272 273 5.353123 GTCTCTATCTCTCGCTCGGAATTAT 59.647 44.000 0.00 0.00 0.00 1.28
273 274 6.535865 GTCTCTATCTCTCGCTCGGAATTATA 59.464 42.308 0.00 0.00 0.00 0.98
274 275 6.535865 TCTCTATCTCTCGCTCGGAATTATAC 59.464 42.308 0.00 0.00 0.00 1.47
275 276 6.408035 TCTATCTCTCGCTCGGAATTATACT 58.592 40.000 0.00 0.00 0.00 2.12
276 277 5.554822 ATCTCTCGCTCGGAATTATACTC 57.445 43.478 0.00 0.00 0.00 2.59
277 278 3.752222 TCTCTCGCTCGGAATTATACTCC 59.248 47.826 0.00 0.00 0.00 3.85
283 284 4.435784 CGCTCGGAATTATACTCCTACGAG 60.436 50.000 0.00 0.00 46.47 4.18
294 295 2.143122 CTCCTACGAGTTGCAAGCAAA 58.857 47.619 9.32 0.00 37.70 3.68
305 306 0.652071 GCAAGCAAAACAAAAGCGCT 59.348 45.000 2.64 2.64 33.45 5.92
307 308 1.071959 CAAGCAAAACAAAAGCGCTCG 60.072 47.619 12.06 4.93 31.17 5.03
308 309 1.199126 GCAAAACAAAAGCGCTCGC 59.801 52.632 12.06 6.09 42.33 5.03
335 336 1.539388 CCGCCAACAGATGTTAGCAAA 59.461 47.619 14.78 0.00 41.58 3.68
399 403 2.565841 GCTTCTTTCGTAGATGCCCAT 58.434 47.619 13.32 0.00 44.29 4.00
401 405 3.495001 GCTTCTTTCGTAGATGCCCATAC 59.505 47.826 13.32 0.00 44.29 2.39
402 406 3.746045 TCTTTCGTAGATGCCCATACC 57.254 47.619 0.00 0.00 35.04 2.73
515 528 1.537202 CACGGCTTCAGGAAAAGAAGG 59.463 52.381 0.00 0.00 42.08 3.46
587 603 0.975556 TCACTTGGCCCGAGCAGATA 60.976 55.000 0.00 0.00 42.56 1.98
599 615 3.411446 CGAGCAGATAGATCTCCACTCT 58.589 50.000 0.00 0.00 34.22 3.24
602 618 3.940209 CAGATAGATCTCCACTCTGCC 57.060 52.381 0.00 0.00 34.22 4.85
630 646 1.952367 GCCTCCTCCCATTGTCACAAG 60.952 57.143 0.00 0.00 0.00 3.16
695 716 0.665835 AAATCGAACGCCAAGCACAA 59.334 45.000 0.00 0.00 0.00 3.33
807 835 5.772672 TGGAAAAGGTACGGTACTTACTACA 59.227 40.000 17.14 5.56 33.31 2.74
810 838 4.227864 AGGTACGGTACTTACTACAGCT 57.772 45.455 17.14 0.86 33.31 4.24
826 854 2.697751 ACAGCTAGGACTAAGCATGAGG 59.302 50.000 0.00 0.00 0.00 3.86
841 869 2.435372 TGAGGTAATCATGTTGGGCC 57.565 50.000 0.00 0.00 31.12 5.80
864 892 0.104304 AACGTGTTCACCTCTCGCTT 59.896 50.000 0.00 0.00 0.00 4.68
906 935 1.227853 AGGGCCACGTTTCAGTGAC 60.228 57.895 6.18 0.00 44.43 3.67
913 942 2.337583 CACGTTTCAGTGACGATGGAT 58.662 47.619 10.96 0.00 44.43 3.41
974 1003 0.750249 TGTGATGTCAGTGACACGGT 59.250 50.000 27.70 12.86 45.65 4.83
977 1006 0.599991 GATGTCAGTGACACGGTGCA 60.600 55.000 27.70 3.85 45.65 4.57
1089 1412 3.175240 CAGCGAACCACGAGCTCG 61.175 66.667 33.45 33.45 45.77 5.03
1093 1416 2.507324 GAACCACGAGCTCGCTCC 60.507 66.667 34.83 16.15 44.43 4.70
1146 1472 4.869440 CGCTCTGCTCCTGGCTCG 62.869 72.222 0.00 0.00 42.39 5.03
1148 1474 4.527583 CTCTGCTCCTGGCTCGCC 62.528 72.222 0.00 0.00 42.39 5.54
1150 1476 4.834453 CTGCTCCTGGCTCGCCTG 62.834 72.222 9.65 8.63 42.39 4.85
1251 1577 4.082523 TCCCCGAGCAAGAAGGCG 62.083 66.667 0.00 0.00 39.27 5.52
1254 1580 3.494336 CCGAGCAAGAAGGCGCAG 61.494 66.667 10.83 0.00 39.27 5.18
1278 1604 4.821589 CAGCCGCTTCTCCCCGTC 62.822 72.222 0.00 0.00 0.00 4.79
1602 1937 2.511600 GTGGAGGCGATGTTCCGG 60.512 66.667 0.00 0.00 36.22 5.14
2032 2367 1.445095 CTCCCCTGCTTCCTCATCG 59.555 63.158 0.00 0.00 0.00 3.84
2074 2434 0.455464 GCGTCAAATTAACCGCCCAC 60.455 55.000 4.69 0.00 40.25 4.61
2108 2468 2.808543 CCGTCCTCTTTTTGTCTCTTGG 59.191 50.000 0.00 0.00 0.00 3.61
2184 2544 1.411977 CAGAGATCATCGACCCAAGCT 59.588 52.381 0.00 0.00 0.00 3.74
2203 2564 6.912591 CCAAGCTCTTGTGTAAAACAGTAAAG 59.087 38.462 8.60 0.00 40.74 1.85
2271 2640 6.741358 GTGTATAAAAATGTTCTTGCTCGTCC 59.259 38.462 0.00 0.00 0.00 4.79
2319 2688 2.588314 GCTCCCTCTCTGCATGCG 60.588 66.667 14.09 8.20 0.00 4.73
2394 2764 3.864686 CGGCGCAGGGATTTGTCG 61.865 66.667 10.83 0.00 0.00 4.35
2395 2765 4.179579 GGCGCAGGGATTTGTCGC 62.180 66.667 10.83 0.00 40.38 5.19
2441 2815 1.066914 CAGCTCTCTCGTGTTTGCTC 58.933 55.000 0.00 0.00 0.00 4.26
2482 2856 1.463056 CAGTATTTGTCGCCGCTTGAA 59.537 47.619 0.00 0.00 0.00 2.69
2484 2858 1.463444 GTATTTGTCGCCGCTTGAAGT 59.537 47.619 0.00 0.00 0.00 3.01
2502 2876 4.037565 TGAAGTCGATTAGCATCCGTATGT 59.962 41.667 0.00 0.00 35.38 2.29
2504 2878 3.318275 AGTCGATTAGCATCCGTATGTGT 59.682 43.478 0.00 0.00 35.38 3.72
2531 3020 6.985653 TTGTCAGGAAGGATATAAGAGGAG 57.014 41.667 0.00 0.00 0.00 3.69
2532 3021 6.281190 TGTCAGGAAGGATATAAGAGGAGA 57.719 41.667 0.00 0.00 0.00 3.71
2533 3022 6.310941 TGTCAGGAAGGATATAAGAGGAGAG 58.689 44.000 0.00 0.00 0.00 3.20
2534 3023 5.714806 GTCAGGAAGGATATAAGAGGAGAGG 59.285 48.000 0.00 0.00 0.00 3.69
2535 3024 5.617418 TCAGGAAGGATATAAGAGGAGAGGA 59.383 44.000 0.00 0.00 0.00 3.71
2536 3025 6.104840 TCAGGAAGGATATAAGAGGAGAGGAA 59.895 42.308 0.00 0.00 0.00 3.36
2537 3026 6.959366 CAGGAAGGATATAAGAGGAGAGGAAT 59.041 42.308 0.00 0.00 0.00 3.01
2538 3027 6.959366 AGGAAGGATATAAGAGGAGAGGAATG 59.041 42.308 0.00 0.00 0.00 2.67
2562 3051 0.034670 GGCAACATCTTCAGAGGCCT 60.035 55.000 3.86 3.86 37.00 5.19
2744 3250 5.178797 ACATCCTTCTTATGGTTGTCTTCG 58.821 41.667 0.00 0.00 33.65 3.79
2824 3330 2.487934 CACTTCAGTGTCACTGGAAGG 58.512 52.381 28.47 15.56 45.94 3.46
2825 3331 1.417890 ACTTCAGTGTCACTGGAAGGG 59.582 52.381 28.47 13.91 45.94 3.95
2873 3379 4.108570 TGATTCCAGGTGGTACCATAACT 58.891 43.478 19.72 13.95 41.95 2.24
2996 3537 6.918022 CGTCTCATCTATGTTTATGTGCTACA 59.082 38.462 0.00 0.00 0.00 2.74
3053 3594 1.473965 GCTTCTGGCTAGCATGTAGCA 60.474 52.381 22.86 9.89 42.06 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.148759 GGCAGTTAGAGCGCTACTGC 61.149 60.000 38.06 38.06 43.36 4.40
24 25 0.528684 GGGCAGTTAGAGCGCTACTG 60.529 60.000 27.07 27.07 41.20 2.74
25 26 0.970937 TGGGCAGTTAGAGCGCTACT 60.971 55.000 11.50 7.92 44.29 2.57
26 27 0.806492 GTGGGCAGTTAGAGCGCTAC 60.806 60.000 11.50 4.99 44.29 3.58
27 28 1.254975 TGTGGGCAGTTAGAGCGCTA 61.255 55.000 11.50 0.00 44.29 4.26
28 29 1.903877 ATGTGGGCAGTTAGAGCGCT 61.904 55.000 11.27 11.27 44.29 5.92
29 30 1.432270 GATGTGGGCAGTTAGAGCGC 61.432 60.000 0.00 0.00 44.24 5.92
30 31 0.176680 AGATGTGGGCAGTTAGAGCG 59.823 55.000 0.00 0.00 0.00 5.03
31 32 1.804372 CGAGATGTGGGCAGTTAGAGC 60.804 57.143 0.00 0.00 0.00 4.09
32 33 1.804372 GCGAGATGTGGGCAGTTAGAG 60.804 57.143 0.00 0.00 0.00 2.43
33 34 0.175760 GCGAGATGTGGGCAGTTAGA 59.824 55.000 0.00 0.00 0.00 2.10
34 35 1.148157 CGCGAGATGTGGGCAGTTAG 61.148 60.000 0.00 0.00 0.00 2.34
35 36 1.153647 CGCGAGATGTGGGCAGTTA 60.154 57.895 0.00 0.00 0.00 2.24
36 37 2.434884 CGCGAGATGTGGGCAGTT 60.435 61.111 0.00 0.00 0.00 3.16
37 38 2.942796 TTCGCGAGATGTGGGCAGT 61.943 57.895 9.59 0.00 41.60 4.40
38 39 2.125552 TTCGCGAGATGTGGGCAG 60.126 61.111 9.59 0.00 41.60 4.85
39 40 2.434185 GTTCGCGAGATGTGGGCA 60.434 61.111 9.59 0.00 41.60 5.36
40 41 3.195698 GGTTCGCGAGATGTGGGC 61.196 66.667 9.59 0.00 41.60 5.36
41 42 1.079127 AAGGTTCGCGAGATGTGGG 60.079 57.895 9.59 0.00 41.60 4.61
42 43 0.670546 ACAAGGTTCGCGAGATGTGG 60.671 55.000 9.59 1.39 41.60 4.17
43 44 0.716108 GACAAGGTTCGCGAGATGTG 59.284 55.000 18.45 14.10 41.60 3.21
44 45 0.603569 AGACAAGGTTCGCGAGATGT 59.396 50.000 9.59 13.02 41.60 3.06
45 46 0.994995 CAGACAAGGTTCGCGAGATG 59.005 55.000 9.59 9.77 41.60 2.90
46 47 0.108615 CCAGACAAGGTTCGCGAGAT 60.109 55.000 9.59 0.00 41.60 2.75
47 48 1.289066 CCAGACAAGGTTCGCGAGA 59.711 57.895 9.59 0.00 39.20 4.04
48 49 2.383527 GCCAGACAAGGTTCGCGAG 61.384 63.158 9.59 0.00 0.00 5.03
49 50 2.357034 GCCAGACAAGGTTCGCGA 60.357 61.111 3.71 3.71 0.00 5.87
50 51 3.777925 CGCCAGACAAGGTTCGCG 61.778 66.667 0.00 0.00 0.00 5.87
51 52 0.947180 TAACGCCAGACAAGGTTCGC 60.947 55.000 0.00 0.00 0.00 4.70
52 53 0.788391 GTAACGCCAGACAAGGTTCG 59.212 55.000 0.00 0.00 0.00 3.95
53 54 1.873698 TGTAACGCCAGACAAGGTTC 58.126 50.000 0.00 0.00 0.00 3.62
54 55 2.335316 TTGTAACGCCAGACAAGGTT 57.665 45.000 0.00 0.00 31.98 3.50
55 56 1.944709 GTTTGTAACGCCAGACAAGGT 59.055 47.619 0.00 0.00 36.92 3.50
56 57 1.265905 GGTTTGTAACGCCAGACAAGG 59.734 52.381 0.00 0.00 36.92 3.61
57 58 1.944024 TGGTTTGTAACGCCAGACAAG 59.056 47.619 0.00 0.00 36.92 3.16
58 59 2.039818 TGGTTTGTAACGCCAGACAA 57.960 45.000 0.00 0.00 33.81 3.18
59 60 1.671845 GTTGGTTTGTAACGCCAGACA 59.328 47.619 0.00 0.00 33.41 3.41
60 61 1.944709 AGTTGGTTTGTAACGCCAGAC 59.055 47.619 0.00 0.00 33.41 3.51
61 62 1.944024 CAGTTGGTTTGTAACGCCAGA 59.056 47.619 0.00 0.00 33.41 3.86
62 63 1.599419 GCAGTTGGTTTGTAACGCCAG 60.599 52.381 0.00 0.00 33.41 4.85
63 64 0.382515 GCAGTTGGTTTGTAACGCCA 59.617 50.000 0.00 0.00 33.39 5.69
64 65 0.382515 TGCAGTTGGTTTGTAACGCC 59.617 50.000 0.00 0.00 33.39 5.68
65 66 1.332375 TCTGCAGTTGGTTTGTAACGC 59.668 47.619 14.67 0.00 33.39 4.84
66 67 3.684103 TTCTGCAGTTGGTTTGTAACG 57.316 42.857 14.67 0.00 33.39 3.18
67 68 5.438761 AGATTCTGCAGTTGGTTTGTAAC 57.561 39.130 14.67 0.00 0.00 2.50
68 69 4.518970 GGAGATTCTGCAGTTGGTTTGTAA 59.481 41.667 14.67 0.00 0.00 2.41
69 70 4.072131 GGAGATTCTGCAGTTGGTTTGTA 58.928 43.478 14.67 0.00 0.00 2.41
70 71 2.887152 GGAGATTCTGCAGTTGGTTTGT 59.113 45.455 14.67 0.00 0.00 2.83
71 72 2.095567 CGGAGATTCTGCAGTTGGTTTG 60.096 50.000 14.67 0.00 0.00 2.93
72 73 2.154462 CGGAGATTCTGCAGTTGGTTT 58.846 47.619 14.67 0.00 0.00 3.27
73 74 1.072331 ACGGAGATTCTGCAGTTGGTT 59.928 47.619 14.67 0.00 0.00 3.67
74 75 0.687354 ACGGAGATTCTGCAGTTGGT 59.313 50.000 14.67 0.00 0.00 3.67
75 76 2.672961 TACGGAGATTCTGCAGTTGG 57.327 50.000 14.67 0.22 0.00 3.77
76 77 5.551760 AATTTACGGAGATTCTGCAGTTG 57.448 39.130 14.67 0.00 0.00 3.16
77 78 5.163854 CGAAATTTACGGAGATTCTGCAGTT 60.164 40.000 14.67 2.24 0.00 3.16
78 79 4.330074 CGAAATTTACGGAGATTCTGCAGT 59.670 41.667 14.67 6.89 0.00 4.40
79 80 4.566759 TCGAAATTTACGGAGATTCTGCAG 59.433 41.667 7.63 7.63 0.00 4.41
80 81 4.500127 TCGAAATTTACGGAGATTCTGCA 58.500 39.130 5.99 0.00 0.00 4.41
81 82 5.256352 GTTCGAAATTTACGGAGATTCTGC 58.744 41.667 0.00 0.00 0.00 4.26
82 83 5.500290 CGGTTCGAAATTTACGGAGATTCTG 60.500 44.000 0.00 0.00 0.00 3.02
83 84 4.565564 CGGTTCGAAATTTACGGAGATTCT 59.434 41.667 0.00 0.00 0.00 2.40
84 85 4.563976 TCGGTTCGAAATTTACGGAGATTC 59.436 41.667 0.00 0.00 31.06 2.52
85 86 4.497300 TCGGTTCGAAATTTACGGAGATT 58.503 39.130 0.00 0.00 31.06 2.40
86 87 4.114058 TCGGTTCGAAATTTACGGAGAT 57.886 40.909 0.00 0.00 31.06 2.75
87 88 3.574284 TCGGTTCGAAATTTACGGAGA 57.426 42.857 0.00 0.00 31.06 3.71
98 99 3.132925 CCAAACCTAAGTTCGGTTCGAA 58.867 45.455 11.90 0.00 43.66 3.71
99 100 2.758009 CCAAACCTAAGTTCGGTTCGA 58.242 47.619 11.90 0.00 43.66 3.71
100 101 1.196127 GCCAAACCTAAGTTCGGTTCG 59.804 52.381 11.90 1.40 43.66 3.95
101 102 1.538512 GGCCAAACCTAAGTTCGGTTC 59.461 52.381 11.90 0.86 43.66 3.62
102 103 1.612676 GGCCAAACCTAAGTTCGGTT 58.387 50.000 6.00 6.00 46.27 4.44
103 104 0.604511 CGGCCAAACCTAAGTTCGGT 60.605 55.000 2.24 0.00 32.16 4.69
104 105 0.604511 ACGGCCAAACCTAAGTTCGG 60.605 55.000 2.24 0.00 34.19 4.30
105 106 0.515564 CACGGCCAAACCTAAGTTCG 59.484 55.000 2.24 0.00 34.19 3.95
106 107 0.240145 GCACGGCCAAACCTAAGTTC 59.760 55.000 2.24 0.00 34.19 3.01
107 108 0.466555 TGCACGGCCAAACCTAAGTT 60.467 50.000 2.24 0.00 38.03 2.66
108 109 0.889186 CTGCACGGCCAAACCTAAGT 60.889 55.000 2.24 0.00 35.61 2.24
109 110 0.889186 ACTGCACGGCCAAACCTAAG 60.889 55.000 2.24 0.00 35.61 2.18
110 111 0.466555 AACTGCACGGCCAAACCTAA 60.467 50.000 2.24 0.00 35.61 2.69
111 112 0.397187 TAACTGCACGGCCAAACCTA 59.603 50.000 2.24 0.00 35.61 3.08
112 113 0.466555 TTAACTGCACGGCCAAACCT 60.467 50.000 2.24 0.00 35.61 3.50
113 114 0.601057 ATTAACTGCACGGCCAAACC 59.399 50.000 2.24 0.00 0.00 3.27
114 115 1.668628 CCATTAACTGCACGGCCAAAC 60.669 52.381 2.24 0.00 0.00 2.93
115 116 0.600557 CCATTAACTGCACGGCCAAA 59.399 50.000 2.24 0.00 0.00 3.28
116 117 1.872197 GCCATTAACTGCACGGCCAA 61.872 55.000 2.24 0.00 36.73 4.52
117 118 2.339556 GCCATTAACTGCACGGCCA 61.340 57.895 2.24 0.00 36.73 5.36
118 119 2.489751 GCCATTAACTGCACGGCC 59.510 61.111 0.00 0.00 36.73 6.13
119 120 2.100216 CGCCATTAACTGCACGGC 59.900 61.111 0.00 0.00 39.45 5.68
120 121 2.791256 CCGCCATTAACTGCACGG 59.209 61.111 0.00 0.00 36.92 4.94
121 122 2.100216 GCCGCCATTAACTGCACG 59.900 61.111 0.00 0.00 0.00 5.34
122 123 2.489751 GGCCGCCATTAACTGCAC 59.510 61.111 3.91 0.00 0.00 4.57
123 124 3.130819 CGGCCGCCATTAACTGCA 61.131 61.111 14.67 0.00 0.00 4.41
124 125 2.207788 AAACGGCCGCCATTAACTGC 62.208 55.000 28.58 0.00 0.00 4.40
125 126 1.088306 TAAACGGCCGCCATTAACTG 58.912 50.000 28.58 0.00 0.00 3.16
126 127 1.944709 GATAAACGGCCGCCATTAACT 59.055 47.619 28.58 8.34 0.00 2.24
127 128 1.333435 CGATAAACGGCCGCCATTAAC 60.333 52.381 28.58 18.59 38.46 2.01
128 129 0.938713 CGATAAACGGCCGCCATTAA 59.061 50.000 28.58 5.24 38.46 1.40
129 130 0.104487 TCGATAAACGGCCGCCATTA 59.896 50.000 28.58 21.82 42.82 1.90
130 131 0.534203 ATCGATAAACGGCCGCCATT 60.534 50.000 28.58 20.28 42.82 3.16
131 132 0.319083 TATCGATAAACGGCCGCCAT 59.681 50.000 28.58 16.22 42.82 4.40
132 133 0.319211 CTATCGATAAACGGCCGCCA 60.319 55.000 28.58 11.25 42.82 5.69
133 134 1.623973 GCTATCGATAAACGGCCGCC 61.624 60.000 28.58 8.56 42.82 6.13
134 135 0.666577 AGCTATCGATAAACGGCCGC 60.667 55.000 28.58 7.46 42.82 6.53
135 136 1.060713 CAGCTATCGATAAACGGCCG 58.939 55.000 26.86 26.86 42.82 6.13
136 137 2.150397 ACAGCTATCGATAAACGGCC 57.850 50.000 6.58 0.00 42.82 6.13
137 138 5.840940 AAATACAGCTATCGATAAACGGC 57.159 39.130 6.58 6.44 42.82 5.68
138 139 7.007188 CGAGTAAATACAGCTATCGATAAACGG 59.993 40.741 6.58 5.31 42.82 4.44
139 140 7.459862 GCGAGTAAATACAGCTATCGATAAACG 60.460 40.741 6.58 0.23 35.42 3.60
140 141 7.459862 CGCGAGTAAATACAGCTATCGATAAAC 60.460 40.741 0.00 1.91 32.52 2.01
141 142 6.522165 CGCGAGTAAATACAGCTATCGATAAA 59.478 38.462 0.00 0.00 32.52 1.40
142 143 6.019762 CGCGAGTAAATACAGCTATCGATAA 58.980 40.000 0.00 0.00 32.52 1.75
143 144 5.121298 ACGCGAGTAAATACAGCTATCGATA 59.879 40.000 15.93 4.78 46.88 2.92
144 145 4.083431 ACGCGAGTAAATACAGCTATCGAT 60.083 41.667 15.93 2.16 46.88 3.59
145 146 3.249320 ACGCGAGTAAATACAGCTATCGA 59.751 43.478 15.93 0.00 46.88 3.59
146 147 3.552541 ACGCGAGTAAATACAGCTATCG 58.447 45.455 15.93 0.00 46.88 2.92
191 192 4.801624 GGGACGTCGGGGTAACGC 62.802 72.222 9.92 0.00 43.76 4.84
204 205 1.300233 CAAGGCGATCTAGCGGGAC 60.300 63.158 0.00 0.00 38.18 4.46
205 206 2.498941 CCAAGGCGATCTAGCGGGA 61.499 63.158 0.00 0.00 38.18 5.14
206 207 1.821061 ATCCAAGGCGATCTAGCGGG 61.821 60.000 0.00 0.00 38.18 6.13
207 208 0.888619 TATCCAAGGCGATCTAGCGG 59.111 55.000 0.00 0.00 38.18 5.52
208 209 1.542030 AGTATCCAAGGCGATCTAGCG 59.458 52.381 0.00 0.00 38.18 4.26
209 210 3.669251 AAGTATCCAAGGCGATCTAGC 57.331 47.619 0.00 0.00 0.00 3.42
210 211 6.183360 GGAGATAAGTATCCAAGGCGATCTAG 60.183 46.154 0.00 0.00 35.74 2.43
211 212 5.652891 GGAGATAAGTATCCAAGGCGATCTA 59.347 44.000 0.00 0.00 35.74 1.98
212 213 4.464597 GGAGATAAGTATCCAAGGCGATCT 59.535 45.833 0.00 0.00 35.74 2.75
213 214 4.464597 AGGAGATAAGTATCCAAGGCGATC 59.535 45.833 0.00 0.00 38.23 3.69
214 215 4.421131 AGGAGATAAGTATCCAAGGCGAT 58.579 43.478 0.00 0.00 38.23 4.58
215 216 3.845860 AGGAGATAAGTATCCAAGGCGA 58.154 45.455 0.00 0.00 38.23 5.54
216 217 4.608948 AAGGAGATAAGTATCCAAGGCG 57.391 45.455 0.00 0.00 38.23 5.52
217 218 6.039829 CCAAAAAGGAGATAAGTATCCAAGGC 59.960 42.308 0.00 0.00 38.23 4.35
218 219 6.039829 GCCAAAAAGGAGATAAGTATCCAAGG 59.960 42.308 0.00 0.00 38.23 3.61
219 220 6.830838 AGCCAAAAAGGAGATAAGTATCCAAG 59.169 38.462 0.00 0.00 38.23 3.61
220 221 6.603201 CAGCCAAAAAGGAGATAAGTATCCAA 59.397 38.462 0.00 0.00 38.23 3.53
221 222 6.122277 CAGCCAAAAAGGAGATAAGTATCCA 58.878 40.000 0.00 0.00 38.23 3.41
222 223 6.122964 ACAGCCAAAAAGGAGATAAGTATCC 58.877 40.000 0.00 0.00 41.22 2.59
223 224 6.018669 CGACAGCCAAAAAGGAGATAAGTATC 60.019 42.308 0.00 0.00 41.22 2.24
224 225 5.817816 CGACAGCCAAAAAGGAGATAAGTAT 59.182 40.000 0.00 0.00 41.22 2.12
225 226 5.175859 CGACAGCCAAAAAGGAGATAAGTA 58.824 41.667 0.00 0.00 41.22 2.24
226 227 4.003648 CGACAGCCAAAAAGGAGATAAGT 58.996 43.478 0.00 0.00 41.22 2.24
227 228 4.003648 ACGACAGCCAAAAAGGAGATAAG 58.996 43.478 0.00 0.00 41.22 1.73
228 229 4.000988 GACGACAGCCAAAAAGGAGATAA 58.999 43.478 0.00 0.00 41.22 1.75
229 230 3.260884 AGACGACAGCCAAAAAGGAGATA 59.739 43.478 0.00 0.00 41.22 1.98
230 231 2.039084 AGACGACAGCCAAAAAGGAGAT 59.961 45.455 0.00 0.00 41.22 2.75
231 232 1.416401 AGACGACAGCCAAAAAGGAGA 59.584 47.619 0.00 0.00 41.22 3.71
232 233 1.801178 GAGACGACAGCCAAAAAGGAG 59.199 52.381 0.00 0.00 41.22 3.69
233 234 1.416401 AGAGACGACAGCCAAAAAGGA 59.584 47.619 0.00 0.00 41.22 3.36
234 235 1.884235 AGAGACGACAGCCAAAAAGG 58.116 50.000 0.00 0.00 41.84 3.11
235 236 4.499183 AGATAGAGACGACAGCCAAAAAG 58.501 43.478 0.00 0.00 0.00 2.27
236 237 4.220821 AGAGATAGAGACGACAGCCAAAAA 59.779 41.667 0.00 0.00 0.00 1.94
237 238 3.764434 AGAGATAGAGACGACAGCCAAAA 59.236 43.478 0.00 0.00 0.00 2.44
238 239 3.357203 AGAGATAGAGACGACAGCCAAA 58.643 45.455 0.00 0.00 0.00 3.28
239 240 2.946329 GAGAGATAGAGACGACAGCCAA 59.054 50.000 0.00 0.00 0.00 4.52
240 241 2.566913 GAGAGATAGAGACGACAGCCA 58.433 52.381 0.00 0.00 0.00 4.75
241 242 1.529438 CGAGAGATAGAGACGACAGCC 59.471 57.143 0.00 0.00 0.00 4.85
242 243 1.070175 GCGAGAGATAGAGACGACAGC 60.070 57.143 0.00 0.00 0.00 4.40
243 244 2.475111 GAGCGAGAGATAGAGACGACAG 59.525 54.545 0.00 0.00 0.00 3.51
244 245 2.475818 GAGCGAGAGATAGAGACGACA 58.524 52.381 0.00 0.00 0.00 4.35
245 246 1.454276 CGAGCGAGAGATAGAGACGAC 59.546 57.143 0.00 0.00 0.00 4.34
246 247 1.603425 CCGAGCGAGAGATAGAGACGA 60.603 57.143 0.00 0.00 0.00 4.20
247 248 0.787787 CCGAGCGAGAGATAGAGACG 59.212 60.000 0.00 0.00 0.00 4.18
248 249 2.157834 TCCGAGCGAGAGATAGAGAC 57.842 55.000 0.00 0.00 0.00 3.36
249 250 2.912690 TTCCGAGCGAGAGATAGAGA 57.087 50.000 0.00 0.00 0.00 3.10
250 251 5.811399 ATAATTCCGAGCGAGAGATAGAG 57.189 43.478 0.00 0.00 0.00 2.43
251 252 6.408035 AGTATAATTCCGAGCGAGAGATAGA 58.592 40.000 0.00 0.00 0.00 1.98
252 253 6.238266 GGAGTATAATTCCGAGCGAGAGATAG 60.238 46.154 0.00 0.00 0.00 2.08
253 254 5.585445 GGAGTATAATTCCGAGCGAGAGATA 59.415 44.000 0.00 0.00 0.00 1.98
254 255 4.396790 GGAGTATAATTCCGAGCGAGAGAT 59.603 45.833 0.00 0.00 0.00 2.75
255 256 3.752222 GGAGTATAATTCCGAGCGAGAGA 59.248 47.826 0.00 0.00 0.00 3.10
256 257 3.754323 AGGAGTATAATTCCGAGCGAGAG 59.246 47.826 0.00 0.00 39.77 3.20
257 258 3.752665 AGGAGTATAATTCCGAGCGAGA 58.247 45.455 0.00 0.00 39.77 4.04
258 259 4.435784 CGTAGGAGTATAATTCCGAGCGAG 60.436 50.000 0.00 0.00 39.77 5.03
259 260 3.434641 CGTAGGAGTATAATTCCGAGCGA 59.565 47.826 0.00 0.00 39.77 4.93
260 261 3.434641 TCGTAGGAGTATAATTCCGAGCG 59.565 47.826 0.00 9.74 39.77 5.03
261 262 4.972201 CTCGTAGGAGTATAATTCCGAGC 58.028 47.826 4.22 0.00 39.77 5.03
274 275 1.795768 TTGCTTGCAACTCGTAGGAG 58.204 50.000 10.86 10.86 46.13 3.69
275 276 2.248280 TTTGCTTGCAACTCGTAGGA 57.752 45.000 7.60 0.00 0.00 2.94
276 277 2.032799 TGTTTTGCTTGCAACTCGTAGG 59.967 45.455 7.60 0.00 0.00 3.18
277 278 3.332761 TGTTTTGCTTGCAACTCGTAG 57.667 42.857 7.60 0.00 0.00 3.51
283 284 2.430008 CGCTTTTGTTTTGCTTGCAAC 58.570 42.857 7.60 0.00 0.00 4.17
307 308 2.536997 ATCTGTTGGCGGTGGGTAGC 62.537 60.000 0.00 0.00 0.00 3.58
308 309 0.744414 CATCTGTTGGCGGTGGGTAG 60.744 60.000 0.00 0.00 0.00 3.18
335 336 2.040012 TGACTGTCTCCTCTCCGTTACT 59.960 50.000 9.51 0.00 0.00 2.24
365 369 3.740631 AAGAAGCTTCCCTTTTTGCTG 57.259 42.857 22.81 0.00 35.79 4.41
399 403 4.330944 TTTCTTCGTGCTTCTTCTGGTA 57.669 40.909 0.00 0.00 0.00 3.25
401 405 4.552166 TTTTTCTTCGTGCTTCTTCTGG 57.448 40.909 0.00 0.00 0.00 3.86
440 453 2.039613 CACTTCTTTCTTGGAGCTCCCT 59.960 50.000 29.95 0.00 35.38 4.20
441 454 2.431454 CACTTCTTTCTTGGAGCTCCC 58.569 52.381 29.95 12.55 34.29 4.30
502 515 2.969950 TCTCGTTCCCTTCTTTTCCTGA 59.030 45.455 0.00 0.00 0.00 3.86
506 519 3.502595 CCCTTTCTCGTTCCCTTCTTTTC 59.497 47.826 0.00 0.00 0.00 2.29
515 528 0.399075 TTCCCACCCTTTCTCGTTCC 59.601 55.000 0.00 0.00 0.00 3.62
587 603 1.760086 CCCGGCAGAGTGGAGATCT 60.760 63.158 0.00 0.00 0.00 2.75
695 716 3.129287 CACTTTGTGCTGGTCTTTTGAGT 59.871 43.478 0.00 0.00 0.00 3.41
770 798 6.364976 CGTACCTTTTCCATTTGAAATCAACC 59.635 38.462 0.00 0.00 42.38 3.77
807 835 3.039252 ACCTCATGCTTAGTCCTAGCT 57.961 47.619 0.00 0.00 0.00 3.32
826 854 1.034838 TGGCGGCCCAACATGATTAC 61.035 55.000 17.97 0.00 38.46 1.89
841 869 1.557443 GAGAGGTGAACACGTTGGCG 61.557 60.000 1.86 0.00 44.93 5.69
864 892 4.720902 CAGCGGGACCCACATGCA 62.721 66.667 12.15 0.00 0.00 3.96
885 913 2.429930 CTGAAACGTGGCCCTCCA 59.570 61.111 0.00 0.00 40.85 3.86
906 935 1.888215 CCACTCCCATCAATCCATCG 58.112 55.000 0.00 0.00 0.00 3.84
913 942 2.350895 CCACGCCACTCCCATCAA 59.649 61.111 0.00 0.00 0.00 2.57
974 1003 4.960866 CACTGGCTGGTGGCTGCA 62.961 66.667 0.50 0.00 40.44 4.41
1152 1478 3.799755 GCCATCGTGACGGCCAAC 61.800 66.667 4.70 0.00 42.82 3.77
1332 1658 2.396955 CGGCTTCTGCTGCTTCCAG 61.397 63.158 0.00 0.00 42.13 3.86
1698 2033 0.538584 ACTGGAAGCGCATCATCTCA 59.461 50.000 15.31 2.12 37.60 3.27
2032 2367 0.248539 CGCGGCTAGACCTTGTAGAC 60.249 60.000 0.00 0.00 35.61 2.59
2058 2393 0.250814 ACGGTGGGCGGTTAATTTGA 60.251 50.000 0.00 0.00 0.00 2.69
2074 2434 3.217626 AGAGGACGGTAATTAGGTACGG 58.782 50.000 0.00 0.00 0.00 4.02
2184 2544 7.284489 AGCAATCCTTTACTGTTTTACACAAGA 59.716 33.333 0.00 0.00 33.87 3.02
2224 2589 1.359848 TTTCAAGATTCGGAGCGAGC 58.640 50.000 0.00 0.00 37.14 5.03
2225 2590 2.286294 CCATTTCAAGATTCGGAGCGAG 59.714 50.000 0.00 0.00 37.14 5.03
2226 2591 2.279741 CCATTTCAAGATTCGGAGCGA 58.720 47.619 0.00 0.00 0.00 4.93
2228 2593 2.749621 ACACCATTTCAAGATTCGGAGC 59.250 45.455 0.00 0.00 0.00 4.70
2229 2594 7.786178 TTATACACCATTTCAAGATTCGGAG 57.214 36.000 0.00 0.00 0.00 4.63
2231 2596 9.801873 ATTTTTATACACCATTTCAAGATTCGG 57.198 29.630 0.00 0.00 0.00 4.30
2271 2640 2.139917 TGAATCGACGGTGAAAAGTGG 58.860 47.619 0.00 0.00 0.00 4.00
2394 2764 5.824429 ACAAGAAAACTTTAAACCTACGGC 58.176 37.500 0.00 0.00 0.00 5.68
2395 2765 6.131389 CGACAAGAAAACTTTAAACCTACGG 58.869 40.000 0.00 0.00 0.00 4.02
2441 2815 0.248289 CTGGCAATGGCAAAAGGAGG 59.752 55.000 11.45 0.00 43.71 4.30
2482 2856 3.318275 ACACATACGGATGCTAATCGACT 59.682 43.478 7.78 0.00 36.43 4.18
2484 2858 4.316205 AACACATACGGATGCTAATCGA 57.684 40.909 7.78 0.00 36.43 3.59
2516 2890 7.543755 ACTCATTCCTCTCCTCTTATATCCTT 58.456 38.462 0.00 0.00 0.00 3.36
2531 3020 3.350833 AGATGTTGCCAACTCATTCCTC 58.649 45.455 9.30 0.00 0.00 3.71
2532 3021 3.446442 AGATGTTGCCAACTCATTCCT 57.554 42.857 9.30 0.00 0.00 3.36
2533 3022 3.507233 TGAAGATGTTGCCAACTCATTCC 59.493 43.478 9.30 0.00 0.00 3.01
2534 3023 4.456911 TCTGAAGATGTTGCCAACTCATTC 59.543 41.667 9.30 9.95 0.00 2.67
2535 3024 4.401022 TCTGAAGATGTTGCCAACTCATT 58.599 39.130 9.30 0.57 0.00 2.57
2536 3025 4.008330 CTCTGAAGATGTTGCCAACTCAT 58.992 43.478 9.30 0.00 0.00 2.90
2537 3026 3.405831 CTCTGAAGATGTTGCCAACTCA 58.594 45.455 9.30 3.28 0.00 3.41
2538 3027 2.746362 CCTCTGAAGATGTTGCCAACTC 59.254 50.000 9.30 4.26 0.00 3.01
2562 3051 2.725008 CCCGAAAACTTTGCGCCA 59.275 55.556 4.18 0.00 0.00 5.69
2744 3250 3.776616 CTCCAGAGCAAGATCACCC 57.223 57.895 0.00 0.00 0.00 4.61
2873 3379 9.816787 AAGAAAAGGGAAAAGTGGTATTGTATA 57.183 29.630 0.00 0.00 0.00 1.47
2996 3537 0.178987 ATCGGGATCGGTACTGCTCT 60.179 55.000 5.56 0.00 36.95 4.09


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

AutoCloner maintained by Alex Coulton.