Multiple sequence alignment - TraesCS7B01G243900

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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 TraesCS7B01G243900 chr7B 100.000 3245 0 0 1 3245 452213826 452217070 0.000000e+00 5993.0
1 TraesCS7B01G243900 chr1D 92.742 2659 126 29 243 2870 6463950 6461328 0.000000e+00 3779.0
2 TraesCS7B01G243900 chr1A 86.504 2371 235 47 300 2638 7779409 7777092 0.000000e+00 2527.0
3 TraesCS7B01G243900 chr1A 86.249 1818 198 25 1075 2856 7115259 7113458 0.000000e+00 1925.0
4 TraesCS7B01G243900 chr1A 89.879 1077 95 7 1409 2475 7649095 7650167 0.000000e+00 1373.0
5 TraesCS7B01G243900 chr1A 92.195 884 48 8 2367 3245 7777081 7776214 0.000000e+00 1230.0
6 TraesCS7B01G243900 chr1A 95.098 306 14 1 1 305 7790998 7790693 6.300000e-132 481.0
7 TraesCS7B01G243900 chr1A 89.189 74 4 1 922 991 7648942 7648869 4.460000e-14 89.8
8 TraesCS7B01G243900 chr7D 83.425 181 29 1 1065 1245 10963598 10963419 2.000000e-37 167.0
9 TraesCS7B01G243900 chr7D 79.518 166 30 4 1082 1245 580756888 580757051 7.360000e-22 115.0
10 TraesCS7B01G243900 chr2D 86.000 150 18 3 108 254 308969630 308969481 1.210000e-34 158.0
11 TraesCS7B01G243900 chr2D 85.714 140 17 2 106 243 172008038 172008176 9.380000e-31 145.0
12 TraesCS7B01G243900 chr2A 86.525 141 16 3 117 254 178084400 178084260 5.610000e-33 152.0
13 TraesCS7B01G243900 chr5B 84.932 146 21 1 99 243 382606950 382607095 2.610000e-31 147.0
14 TraesCS7B01G243900 chr1B 85.612 139 19 1 106 243 302490312 302490174 9.380000e-31 145.0
15 TraesCS7B01G243900 chr4A 85.000 140 19 2 106 243 106315659 106315520 1.210000e-29 141.0
16 TraesCS7B01G243900 chr4A 85.385 130 18 1 105 233 400831533 400831662 2.030000e-27 134.0
17 TraesCS7B01G243900 chr5D 83.221 149 19 4 105 250 505181943 505182088 7.310000e-27 132.0
18 TraesCS7B01G243900 chr7A 80.645 155 28 2 1094 1247 672311659 672311812 5.690000e-23 119.0


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 TraesCS7B01G243900 chr7B 452213826 452217070 3244 False 5993.0 5993 100.0000 1 3245 1 chr7B.!!$F1 3244
1 TraesCS7B01G243900 chr1D 6461328 6463950 2622 True 3779.0 3779 92.7420 243 2870 1 chr1D.!!$R1 2627
2 TraesCS7B01G243900 chr1A 7113458 7115259 1801 True 1925.0 1925 86.2490 1075 2856 1 chr1A.!!$R1 1781
3 TraesCS7B01G243900 chr1A 7776214 7779409 3195 True 1878.5 2527 89.3495 300 3245 2 chr1A.!!$R4 2945
4 TraesCS7B01G243900 chr1A 7649095 7650167 1072 False 1373.0 1373 89.8790 1409 2475 1 chr1A.!!$F1 1066

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
205 206 0.033991 AGGACTCTAGAAGCCTCGCA 60.034 55.0 7.14 0.0 28.82 5.10 F
206 207 0.101579 GGACTCTAGAAGCCTCGCAC 59.898 60.0 0.00 0.0 0.00 5.34 F
228 229 0.179100 CGGCGTGATCAAGATGGACT 60.179 55.0 13.18 0.0 0.00 3.85 F
1339 1406 0.393077 CCCTTCACTCACGTTCCTGT 59.607 55.0 0.00 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1032 1099 0.034896 GAGAGTTGTCCGGCCTCAAA 59.965 55.0 0.00 0.00 0.00 2.69 R
1706 1788 0.249155 CACAAGCAGGTTGCCAACAG 60.249 55.0 12.41 2.42 46.52 3.16 R
1975 2060 0.394352 AAACTATGCTTGAGGGCCCG 60.394 55.0 18.44 2.33 0.00 6.13 R
3184 3576 0.613012 ACTTTCAGAATGCCCAGCCC 60.613 55.0 0.00 0.00 34.76 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
23 24 3.377656 GGGAGAACTCGCCTGTCA 58.622 61.111 7.50 0.00 36.65 3.58
24 25 1.671742 GGGAGAACTCGCCTGTCAA 59.328 57.895 7.50 0.00 36.65 3.18
25 26 0.390472 GGGAGAACTCGCCTGTCAAG 60.390 60.000 7.50 0.00 36.65 3.02
26 27 1.016653 GGAGAACTCGCCTGTCAAGC 61.017 60.000 0.00 0.00 32.72 4.01
27 28 1.004440 AGAACTCGCCTGTCAAGCC 60.004 57.895 0.00 0.00 0.00 4.35
28 29 1.301716 GAACTCGCCTGTCAAGCCA 60.302 57.895 0.00 0.00 0.00 4.75
29 30 0.884704 GAACTCGCCTGTCAAGCCAA 60.885 55.000 0.00 0.00 0.00 4.52
30 31 0.465460 AACTCGCCTGTCAAGCCAAA 60.465 50.000 0.00 0.00 0.00 3.28
31 32 0.886490 ACTCGCCTGTCAAGCCAAAG 60.886 55.000 0.00 0.00 0.00 2.77
32 33 0.603707 CTCGCCTGTCAAGCCAAAGA 60.604 55.000 0.00 0.00 0.00 2.52
33 34 0.884704 TCGCCTGTCAAGCCAAAGAC 60.885 55.000 0.00 0.00 35.37 3.01
34 35 1.576421 GCCTGTCAAGCCAAAGACG 59.424 57.895 0.00 0.00 37.58 4.18
35 36 0.884704 GCCTGTCAAGCCAAAGACGA 60.885 55.000 0.00 0.00 37.58 4.20
36 37 0.868406 CCTGTCAAGCCAAAGACGAC 59.132 55.000 0.00 0.00 37.58 4.34
37 38 1.581934 CTGTCAAGCCAAAGACGACA 58.418 50.000 0.00 0.00 37.58 4.35
38 39 1.939934 CTGTCAAGCCAAAGACGACAA 59.060 47.619 0.00 0.00 36.26 3.18
39 40 2.354510 CTGTCAAGCCAAAGACGACAAA 59.645 45.455 0.00 0.00 36.26 2.83
40 41 2.354510 TGTCAAGCCAAAGACGACAAAG 59.645 45.455 0.00 0.00 37.58 2.77
41 42 1.333619 TCAAGCCAAAGACGACAAAGC 59.666 47.619 0.00 0.00 0.00 3.51
42 43 1.334869 CAAGCCAAAGACGACAAAGCT 59.665 47.619 0.00 0.00 0.00 3.74
43 44 1.680338 AGCCAAAGACGACAAAGCTT 58.320 45.000 0.00 0.00 0.00 3.74
44 45 2.846193 AGCCAAAGACGACAAAGCTTA 58.154 42.857 0.00 0.00 0.00 3.09
45 46 3.211045 AGCCAAAGACGACAAAGCTTAA 58.789 40.909 0.00 0.00 0.00 1.85
46 47 3.251004 AGCCAAAGACGACAAAGCTTAAG 59.749 43.478 0.00 0.00 0.00 1.85
47 48 3.003378 GCCAAAGACGACAAAGCTTAAGT 59.997 43.478 0.00 0.97 0.00 2.24
48 49 4.773510 CCAAAGACGACAAAGCTTAAGTC 58.226 43.478 17.56 17.56 0.00 3.01
49 50 4.272504 CCAAAGACGACAAAGCTTAAGTCA 59.727 41.667 23.65 0.00 32.68 3.41
50 51 5.049405 CCAAAGACGACAAAGCTTAAGTCAT 60.049 40.000 23.65 14.12 32.68 3.06
51 52 6.147164 CCAAAGACGACAAAGCTTAAGTCATA 59.853 38.462 23.65 0.00 32.68 2.15
52 53 7.148407 CCAAAGACGACAAAGCTTAAGTCATAT 60.148 37.037 23.65 9.98 32.68 1.78
53 54 7.907214 AAGACGACAAAGCTTAAGTCATATT 57.093 32.000 23.65 14.24 32.68 1.28
54 55 7.907214 AGACGACAAAGCTTAAGTCATATTT 57.093 32.000 23.65 8.70 32.68 1.40
55 56 8.997621 AGACGACAAAGCTTAAGTCATATTTA 57.002 30.769 23.65 0.00 32.68 1.40
56 57 9.431887 AGACGACAAAGCTTAAGTCATATTTAA 57.568 29.630 23.65 0.00 32.68 1.52
57 58 9.690434 GACGACAAAGCTTAAGTCATATTTAAG 57.310 33.333 23.65 12.19 39.81 1.85
58 59 9.431887 ACGACAAAGCTTAAGTCATATTTAAGA 57.568 29.630 23.65 0.00 39.40 2.10
71 72 9.877178 AGTCATATTTAAGAAGAAGATTGTCGT 57.123 29.630 0.00 0.00 0.00 4.34
73 74 9.314321 TCATATTTAAGAAGAAGATTGTCGTCC 57.686 33.333 0.00 0.00 0.00 4.79
74 75 6.986904 ATTTAAGAAGAAGATTGTCGTCCC 57.013 37.500 0.00 0.00 0.00 4.46
75 76 3.336138 AAGAAGAAGATTGTCGTCCCC 57.664 47.619 0.00 0.00 0.00 4.81
76 77 1.204941 AGAAGAAGATTGTCGTCCCCG 59.795 52.381 0.00 0.00 0.00 5.73
77 78 0.249398 AAGAAGATTGTCGTCCCCGG 59.751 55.000 0.00 0.00 33.95 5.73
78 79 1.814169 GAAGATTGTCGTCCCCGGC 60.814 63.158 0.00 0.00 39.72 6.13
79 80 3.659089 AAGATTGTCGTCCCCGGCG 62.659 63.158 0.00 0.00 43.03 6.46
80 81 4.446413 GATTGTCGTCCCCGGCGT 62.446 66.667 6.01 0.00 43.03 5.68
81 82 4.446413 ATTGTCGTCCCCGGCGTC 62.446 66.667 6.01 0.00 43.03 5.19
98 99 2.362242 TCGAAGACCAGTTCAGGGG 58.638 57.895 0.00 0.00 0.00 4.79
99 100 1.376037 CGAAGACCAGTTCAGGGGC 60.376 63.158 0.00 0.00 0.00 5.80
101 102 1.276622 GAAGACCAGTTCAGGGGCTA 58.723 55.000 0.00 0.00 45.32 3.93
102 103 0.984995 AAGACCAGTTCAGGGGCTAC 59.015 55.000 0.00 0.00 45.32 3.58
103 104 0.910088 AGACCAGTTCAGGGGCTACC 60.910 60.000 0.00 0.00 43.80 3.18
104 105 2.240162 GACCAGTTCAGGGGCTACCG 62.240 65.000 0.00 0.00 46.96 4.02
105 106 1.987855 CCAGTTCAGGGGCTACCGA 60.988 63.158 0.00 0.00 46.96 4.69
106 107 1.218316 CAGTTCAGGGGCTACCGAC 59.782 63.158 0.00 0.00 46.96 4.79
107 108 2.183555 GTTCAGGGGCTACCGACG 59.816 66.667 0.00 0.00 46.96 5.12
108 109 3.072468 TTCAGGGGCTACCGACGG 61.072 66.667 13.61 13.61 46.96 4.79
109 110 3.892104 TTCAGGGGCTACCGACGGT 62.892 63.158 25.14 25.14 46.96 4.83
110 111 4.143333 CAGGGGCTACCGACGGTG 62.143 72.222 29.55 19.05 46.96 4.94
111 112 4.691359 AGGGGCTACCGACGGTGT 62.691 66.667 29.55 5.96 46.96 4.16
112 113 4.139234 GGGGCTACCGACGGTGTC 62.139 72.222 29.55 19.25 36.19 3.67
113 114 3.066814 GGGCTACCGACGGTGTCT 61.067 66.667 29.55 4.72 36.19 3.41
114 115 2.488820 GGCTACCGACGGTGTCTC 59.511 66.667 29.55 14.23 36.19 3.36
115 116 2.099831 GCTACCGACGGTGTCTCG 59.900 66.667 29.55 12.73 36.19 4.04
120 121 3.880591 CGACGGTGTCTCGGACTA 58.119 61.111 5.77 0.00 33.15 2.59
121 122 1.714414 CGACGGTGTCTCGGACTAG 59.286 63.158 5.77 0.00 33.15 2.57
122 123 1.703438 CGACGGTGTCTCGGACTAGG 61.703 65.000 0.00 0.00 33.15 3.02
123 124 1.375098 GACGGTGTCTCGGACTAGGG 61.375 65.000 0.00 0.00 33.15 3.53
124 125 2.119655 CGGTGTCTCGGACTAGGGG 61.120 68.421 0.00 0.00 33.15 4.79
125 126 1.757340 GGTGTCTCGGACTAGGGGG 60.757 68.421 0.00 0.00 33.15 5.40
126 127 1.000107 GTGTCTCGGACTAGGGGGT 60.000 63.158 0.00 0.00 33.15 4.95
127 128 0.257039 GTGTCTCGGACTAGGGGGTA 59.743 60.000 0.00 0.00 33.15 3.69
128 129 0.257039 TGTCTCGGACTAGGGGGTAC 59.743 60.000 0.00 0.00 33.15 3.34
129 130 3.150441 TGTCTCGGACTAGGGGGTACC 62.150 61.905 2.17 2.17 40.05 3.34
151 152 1.843368 CCTAGTTGGTCCGTAGTCCA 58.157 55.000 0.00 0.00 0.00 4.02
152 153 2.385803 CCTAGTTGGTCCGTAGTCCAT 58.614 52.381 0.00 0.00 33.50 3.41
153 154 2.100916 CCTAGTTGGTCCGTAGTCCATG 59.899 54.545 0.00 0.00 33.50 3.66
154 155 0.902531 AGTTGGTCCGTAGTCCATGG 59.097 55.000 4.97 4.97 33.50 3.66
155 156 0.899720 GTTGGTCCGTAGTCCATGGA 59.100 55.000 11.44 11.44 40.24 3.41
158 159 3.929002 TCCGTAGTCCATGGACCG 58.071 61.111 36.09 31.16 45.59 4.79
159 160 1.303948 TCCGTAGTCCATGGACCGA 59.696 57.895 36.09 24.17 45.59 4.69
160 161 0.750546 TCCGTAGTCCATGGACCGAG 60.751 60.000 36.09 26.53 45.59 4.63
161 162 1.065928 CGTAGTCCATGGACCGAGC 59.934 63.158 36.09 23.15 45.59 5.03
162 163 1.442148 GTAGTCCATGGACCGAGCC 59.558 63.158 36.09 18.38 45.59 4.70
163 164 1.043673 GTAGTCCATGGACCGAGCCT 61.044 60.000 36.09 21.60 45.59 4.58
164 165 0.554305 TAGTCCATGGACCGAGCCTA 59.446 55.000 36.09 20.61 45.59 3.93
165 166 0.105453 AGTCCATGGACCGAGCCTAT 60.105 55.000 36.09 16.27 45.59 2.57
166 167 0.034059 GTCCATGGACCGAGCCTATG 59.966 60.000 31.37 0.00 39.08 2.23
167 168 1.121407 TCCATGGACCGAGCCTATGG 61.121 60.000 11.44 13.54 37.66 2.74
177 178 3.335711 GCCTATGGCCCACCTTCT 58.664 61.111 0.00 0.00 44.06 2.85
178 179 1.149401 GCCTATGGCCCACCTTCTC 59.851 63.158 0.00 0.00 44.06 2.87
179 180 1.839894 CCTATGGCCCACCTTCTCC 59.160 63.158 0.00 0.00 36.63 3.71
180 181 0.695803 CCTATGGCCCACCTTCTCCT 60.696 60.000 0.00 0.00 36.63 3.69
181 182 1.414538 CCTATGGCCCACCTTCTCCTA 60.415 57.143 0.00 0.00 36.63 2.94
182 183 2.408565 CTATGGCCCACCTTCTCCTAA 58.591 52.381 0.00 0.00 36.63 2.69
183 184 1.216990 ATGGCCCACCTTCTCCTAAG 58.783 55.000 0.00 0.00 36.63 2.18
184 185 0.914417 TGGCCCACCTTCTCCTAAGG 60.914 60.000 0.00 2.23 43.05 2.69
185 186 0.620700 GGCCCACCTTCTCCTAAGGA 60.621 60.000 10.67 0.00 39.81 3.36
186 187 1.286248 GCCCACCTTCTCCTAAGGAA 58.714 55.000 10.67 0.00 39.81 3.36
187 188 1.210722 GCCCACCTTCTCCTAAGGAAG 59.789 57.143 10.67 0.00 39.81 3.46
200 201 4.929819 CTAAGGAAGGACTCTAGAAGCC 57.070 50.000 0.00 0.00 0.00 4.35
201 202 3.483255 AAGGAAGGACTCTAGAAGCCT 57.517 47.619 7.14 7.14 34.26 4.58
202 203 3.026707 AGGAAGGACTCTAGAAGCCTC 57.973 52.381 12.19 7.22 32.40 4.70
203 204 1.679153 GGAAGGACTCTAGAAGCCTCG 59.321 57.143 12.19 0.00 32.40 4.63
204 205 1.066454 GAAGGACTCTAGAAGCCTCGC 59.934 57.143 12.19 5.85 32.40 5.03
205 206 0.033991 AGGACTCTAGAAGCCTCGCA 60.034 55.000 7.14 0.00 28.82 5.10
206 207 0.101579 GGACTCTAGAAGCCTCGCAC 59.898 60.000 0.00 0.00 0.00 5.34
207 208 1.099689 GACTCTAGAAGCCTCGCACT 58.900 55.000 0.00 0.00 0.00 4.40
208 209 1.474879 GACTCTAGAAGCCTCGCACTT 59.525 52.381 0.00 0.00 0.00 3.16
209 210 1.474879 ACTCTAGAAGCCTCGCACTTC 59.525 52.381 0.00 4.36 43.16 3.01
210 211 0.452184 TCTAGAAGCCTCGCACTTCG 59.548 55.000 0.00 0.00 46.54 3.79
211 212 0.526524 CTAGAAGCCTCGCACTTCGG 60.527 60.000 6.35 0.00 46.54 4.30
212 213 2.558554 TAGAAGCCTCGCACTTCGGC 62.559 60.000 0.00 0.00 46.54 5.54
220 221 3.561429 GCACTTCGGCGTGATCAA 58.439 55.556 6.85 0.00 37.06 2.57
221 222 1.421485 GCACTTCGGCGTGATCAAG 59.579 57.895 6.85 4.06 37.06 3.02
222 223 1.014044 GCACTTCGGCGTGATCAAGA 61.014 55.000 13.18 0.24 37.06 3.02
223 224 1.645034 CACTTCGGCGTGATCAAGAT 58.355 50.000 13.18 0.00 37.06 2.40
224 225 1.325640 CACTTCGGCGTGATCAAGATG 59.674 52.381 13.18 3.68 37.06 2.90
225 226 0.933097 CTTCGGCGTGATCAAGATGG 59.067 55.000 13.18 0.65 0.00 3.51
226 227 0.534873 TTCGGCGTGATCAAGATGGA 59.465 50.000 13.18 3.04 0.00 3.41
227 228 0.179111 TCGGCGTGATCAAGATGGAC 60.179 55.000 13.18 0.00 0.00 4.02
228 229 0.179100 CGGCGTGATCAAGATGGACT 60.179 55.000 13.18 0.00 0.00 3.85
229 230 1.576356 GGCGTGATCAAGATGGACTC 58.424 55.000 13.18 0.00 0.00 3.36
230 231 1.137872 GGCGTGATCAAGATGGACTCT 59.862 52.381 13.18 0.00 34.96 3.24
231 232 2.200067 GCGTGATCAAGATGGACTCTG 58.800 52.381 13.18 0.00 33.29 3.35
232 233 2.200067 CGTGATCAAGATGGACTCTGC 58.800 52.381 2.01 0.00 33.29 4.26
233 234 2.159128 CGTGATCAAGATGGACTCTGCT 60.159 50.000 2.01 0.00 33.29 4.24
234 235 3.196463 GTGATCAAGATGGACTCTGCTG 58.804 50.000 0.00 0.00 33.29 4.41
235 236 3.102204 TGATCAAGATGGACTCTGCTGA 58.898 45.455 0.00 0.00 33.29 4.26
236 237 3.516700 TGATCAAGATGGACTCTGCTGAA 59.483 43.478 0.00 0.00 33.29 3.02
237 238 4.019950 TGATCAAGATGGACTCTGCTGAAA 60.020 41.667 0.00 0.00 33.29 2.69
238 239 4.356405 TCAAGATGGACTCTGCTGAAAA 57.644 40.909 0.00 0.00 33.29 2.29
239 240 4.067896 TCAAGATGGACTCTGCTGAAAAC 58.932 43.478 0.00 0.00 33.29 2.43
240 241 4.070716 CAAGATGGACTCTGCTGAAAACT 58.929 43.478 0.00 0.00 33.29 2.66
241 242 4.363991 AGATGGACTCTGCTGAAAACTT 57.636 40.909 0.00 0.00 31.12 2.66
268 269 2.739885 TCCAAATGGATTTGTTGGCG 57.260 45.000 10.45 0.00 44.21 5.69
272 273 0.894835 AATGGATTTGTTGGCGGGAC 59.105 50.000 0.00 0.00 0.00 4.46
287 288 7.339721 TGTTGGCGGGACAAATAAAAATATCTA 59.660 33.333 0.00 0.00 31.17 1.98
316 317 6.267471 CCAGTTTTATATATGTGTGGGCCATT 59.733 38.462 10.70 0.00 0.00 3.16
345 346 1.374758 CCTCACCAACTCACTCCGC 60.375 63.158 0.00 0.00 0.00 5.54
432 434 4.553429 CGCTTAACAGTTCGCAATTTAAGG 59.447 41.667 7.91 0.00 32.62 2.69
439 441 5.415701 ACAGTTCGCAATTTAAGGTGATCAT 59.584 36.000 0.00 0.00 0.00 2.45
440 442 5.740569 CAGTTCGCAATTTAAGGTGATCATG 59.259 40.000 0.00 0.00 0.00 3.07
441 443 4.898829 TCGCAATTTAAGGTGATCATGG 57.101 40.909 0.00 0.00 0.00 3.66
479 484 9.474313 AAATAGCCAACTAAGAATTACCATGAA 57.526 29.630 0.00 0.00 30.45 2.57
611 631 2.007360 CTGAACCAGTAGAGCAGCAG 57.993 55.000 0.00 0.00 0.00 4.24
652 712 5.701029 AAAAACATGAGAAAAAGCGTGTG 57.299 34.783 0.00 0.00 34.69 3.82
653 713 4.630894 AAACATGAGAAAAAGCGTGTGA 57.369 36.364 0.00 0.00 34.69 3.58
654 714 4.630894 AACATGAGAAAAAGCGTGTGAA 57.369 36.364 0.00 0.00 34.69 3.18
655 715 4.630894 ACATGAGAAAAAGCGTGTGAAA 57.369 36.364 0.00 0.00 33.30 2.69
656 716 4.992688 ACATGAGAAAAAGCGTGTGAAAA 58.007 34.783 0.00 0.00 33.30 2.29
667 727 2.538939 GCGTGTGAAAAAGAAACGAGCT 60.539 45.455 0.00 0.00 36.38 4.09
668 728 3.280775 CGTGTGAAAAAGAAACGAGCTC 58.719 45.455 2.73 2.73 36.38 4.09
931 992 4.889112 TAGCCGTCCTCGCCCGAT 62.889 66.667 0.00 0.00 35.54 4.18
954 1015 4.560856 CCTCTTCGCCGGAGCTCG 62.561 72.222 5.05 0.00 36.60 5.03
964 1025 2.347490 GGAGCTCGCCCAGTTTGA 59.653 61.111 7.83 0.00 0.00 2.69
970 1031 1.474077 GCTCGCCCAGTTTGATGATTT 59.526 47.619 0.00 0.00 0.00 2.17
1032 1099 4.901927 AGGAGATATCTGGGAAGGAGTTT 58.098 43.478 10.74 0.00 0.00 2.66
1053 1120 1.251527 TGAGGCCGGACAACTCTCTC 61.252 60.000 11.69 0.00 32.58 3.20
1054 1121 0.968393 GAGGCCGGACAACTCTCTCT 60.968 60.000 11.69 0.00 0.00 3.10
1055 1122 0.968393 AGGCCGGACAACTCTCTCTC 60.968 60.000 11.69 0.00 0.00 3.20
1056 1123 0.968393 GGCCGGACAACTCTCTCTCT 60.968 60.000 5.05 0.00 0.00 3.10
1057 1124 0.454196 GCCGGACAACTCTCTCTCTC 59.546 60.000 5.05 0.00 0.00 3.20
1058 1125 1.953311 GCCGGACAACTCTCTCTCTCT 60.953 57.143 5.05 0.00 0.00 3.10
1067 1134 1.034838 TCTCTCTCTCTTGCGGAGGC 61.035 60.000 6.66 0.00 42.10 4.70
1171 1238 3.305964 CGTTTCAAGTGCGTCTCTAAGA 58.694 45.455 0.00 0.00 0.00 2.10
1179 1246 1.935327 GCGTCTCTAAGACCTGGCGT 61.935 60.000 0.00 0.00 42.12 5.68
1218 1285 4.093952 CACCGCAAGAAGCTGCCG 62.094 66.667 0.00 0.00 42.61 5.69
1317 1384 1.218316 GGCCGACGGTCTTGATCTT 59.782 57.895 16.73 0.00 0.00 2.40
1339 1406 0.393077 CCCTTCACTCACGTTCCTGT 59.607 55.000 0.00 0.00 0.00 4.00
1573 1649 0.623403 CGTTTTTGATTTCGAGCGCG 59.377 50.000 2.41 2.41 39.35 6.86
1692 1774 1.318576 GTCAAAGTGTCCTGGTTGGG 58.681 55.000 0.00 0.00 36.20 4.12
1706 1788 4.794648 TGGGGGTATGCTGCACGC 62.795 66.667 3.57 1.10 39.77 5.34
1710 1792 2.040544 GGGTATGCTGCACGCTGTT 61.041 57.895 3.57 0.00 40.11 3.16
1727 1809 2.132996 TTGGCAACCTGCTTGTGGG 61.133 57.895 0.00 0.00 44.28 4.61
1791 1873 1.139498 TGGACATGGAGGGCAAGGAA 61.139 55.000 0.00 0.00 0.00 3.36
1813 1895 1.407437 GGAAGACAATCTCCGTGCCAT 60.407 52.381 0.00 0.00 0.00 4.40
1975 2060 7.420800 CCTTGAGGATTATGATAAACAGCAAC 58.579 38.462 0.00 0.00 37.39 4.17
1983 2068 0.679960 ATAAACAGCAACGGGCCCTC 60.680 55.000 22.43 6.14 46.50 4.30
2289 2384 4.320057 GCTTGCTCCGATCAATGGAATAAG 60.320 45.833 0.00 1.05 34.44 1.73
2624 3010 6.774354 ATGTGCATTTGATTTGTTTCACTC 57.226 33.333 0.00 0.00 0.00 3.51
2638 3024 4.756642 TGTTTCACTCATTCATCAGGTGAC 59.243 41.667 0.00 0.00 36.32 3.67
2657 3043 3.499157 TGACAAACTAACGGTTACCATGC 59.501 43.478 1.13 0.00 37.12 4.06
2707 3093 7.931015 ATAACAGATGTTGGGATAGTCCTTA 57.069 36.000 8.46 0.00 38.90 2.69
2715 3101 3.035363 TGGGATAGTCCTTATTGCGACA 58.965 45.455 0.00 0.00 36.57 4.35
2730 3116 9.306280 CTTATTGCGACACGAATTTTATCATAG 57.694 33.333 0.00 0.00 0.00 2.23
2735 3121 6.347881 CGACACGAATTTTATCATAGCACTC 58.652 40.000 0.00 0.00 0.00 3.51
2769 3158 9.997482 GCAGAAATATACGGAAGAAATTTTGTA 57.003 29.630 0.00 0.00 0.00 2.41
2774 3163 9.457436 AATATACGGAAGAAATTTTGTACAGGT 57.543 29.630 0.00 0.00 0.00 4.00
2775 3164 7.754851 ATACGGAAGAAATTTTGTACAGGTT 57.245 32.000 0.00 0.00 0.00 3.50
2789 3179 2.815158 ACAGGTTGGTTTGACAGGTTT 58.185 42.857 0.00 0.00 0.00 3.27
2835 3225 2.547218 GCTCTCCAGTTAACACGGACAA 60.547 50.000 8.61 2.14 0.00 3.18
2883 3275 7.160726 CCATGACAATTTAACATGTTCCCTTT 58.839 34.615 15.85 2.42 39.47 3.11
2905 3297 1.140312 TTGAACTGCCTGAAGGTCCT 58.860 50.000 0.00 0.00 32.54 3.85
2907 3299 1.623811 TGAACTGCCTGAAGGTCCTAC 59.376 52.381 0.00 0.00 32.54 3.18
2911 3303 3.517612 ACTGCCTGAAGGTCCTACTAAA 58.482 45.455 0.00 0.00 37.57 1.85
2913 3305 4.020128 ACTGCCTGAAGGTCCTACTAAAAG 60.020 45.833 0.00 0.00 37.57 2.27
2914 3306 4.164981 TGCCTGAAGGTCCTACTAAAAGA 58.835 43.478 0.00 0.00 37.57 2.52
2915 3307 4.783227 TGCCTGAAGGTCCTACTAAAAGAT 59.217 41.667 0.00 0.00 37.57 2.40
2916 3308 5.119694 GCCTGAAGGTCCTACTAAAAGATG 58.880 45.833 0.00 0.00 37.57 2.90
2918 3310 5.189934 CCTGAAGGTCCTACTAAAAGATGGT 59.810 44.000 0.00 0.00 0.00 3.55
3007 3399 8.750298 TGAAATCAAAGGTGTTTGTAAACCTAA 58.250 29.630 5.15 0.00 46.29 2.69
3018 3410 4.717279 TGTAAACCTAAGGATATGGGGC 57.283 45.455 0.00 0.00 0.00 5.80
3041 3433 6.240176 GGCTCCTGGGATAGTGGATTTAAATA 60.240 42.308 0.00 0.00 0.00 1.40
3079 3471 9.308000 TGTTTTACTTTGTAAATGGATCTGGAT 57.692 29.630 4.10 0.00 0.00 3.41
3182 3574 3.950395 GCTAAGGCTGGTCAATCTCAATT 59.050 43.478 0.00 0.00 35.22 2.32
3183 3575 4.201990 GCTAAGGCTGGTCAATCTCAATTG 60.202 45.833 0.00 0.00 38.52 2.32
3184 3576 2.731572 AGGCTGGTCAATCTCAATTGG 58.268 47.619 5.42 0.00 42.19 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.335361 AGGCGAGTTCTCCCCTTAGA 59.665 55.000 0.67 0.00 0.00 2.10
1 2 0.461961 CAGGCGAGTTCTCCCCTTAG 59.538 60.000 3.56 0.00 0.00 2.18
2 3 0.252103 ACAGGCGAGTTCTCCCCTTA 60.252 55.000 3.56 0.00 0.00 2.69
3 4 1.536662 ACAGGCGAGTTCTCCCCTT 60.537 57.895 3.56 0.00 0.00 3.95
4 5 1.985116 GACAGGCGAGTTCTCCCCT 60.985 63.158 0.67 0.67 0.00 4.79
5 6 1.827399 TTGACAGGCGAGTTCTCCCC 61.827 60.000 0.00 0.00 0.00 4.81
6 7 0.390472 CTTGACAGGCGAGTTCTCCC 60.390 60.000 0.00 0.00 0.00 4.30
7 8 1.016653 GCTTGACAGGCGAGTTCTCC 61.017 60.000 0.00 0.00 0.00 3.71
8 9 1.016653 GGCTTGACAGGCGAGTTCTC 61.017 60.000 3.19 0.00 35.53 2.87
9 10 1.004440 GGCTTGACAGGCGAGTTCT 60.004 57.895 3.19 0.00 35.53 3.01
10 11 3.567473 GGCTTGACAGGCGAGTTC 58.433 61.111 3.19 0.00 35.53 3.01
16 17 0.884704 TCGTCTTTGGCTTGACAGGC 60.885 55.000 0.00 0.00 46.16 4.85
17 18 0.868406 GTCGTCTTTGGCTTGACAGG 59.132 55.000 0.00 0.00 33.18 4.00
18 19 1.581934 TGTCGTCTTTGGCTTGACAG 58.418 50.000 0.00 0.00 34.85 3.51
19 20 2.031258 TTGTCGTCTTTGGCTTGACA 57.969 45.000 0.00 0.00 37.76 3.58
20 21 2.854805 GCTTTGTCGTCTTTGGCTTGAC 60.855 50.000 0.00 0.00 0.00 3.18
21 22 1.333619 GCTTTGTCGTCTTTGGCTTGA 59.666 47.619 0.00 0.00 0.00 3.02
22 23 1.334869 AGCTTTGTCGTCTTTGGCTTG 59.665 47.619 0.00 0.00 0.00 4.01
23 24 1.680338 AGCTTTGTCGTCTTTGGCTT 58.320 45.000 0.00 0.00 0.00 4.35
24 25 1.680338 AAGCTTTGTCGTCTTTGGCT 58.320 45.000 0.00 0.00 0.00 4.75
25 26 3.003378 ACTTAAGCTTTGTCGTCTTTGGC 59.997 43.478 3.20 0.00 0.00 4.52
26 27 4.272504 TGACTTAAGCTTTGTCGTCTTTGG 59.727 41.667 20.07 0.00 33.81 3.28
27 28 5.403897 TGACTTAAGCTTTGTCGTCTTTG 57.596 39.130 20.07 0.00 33.81 2.77
28 29 7.907214 ATATGACTTAAGCTTTGTCGTCTTT 57.093 32.000 22.08 11.47 33.81 2.52
29 30 7.907214 AATATGACTTAAGCTTTGTCGTCTT 57.093 32.000 22.08 17.76 33.81 3.01
30 31 7.907214 AAATATGACTTAAGCTTTGTCGTCT 57.093 32.000 22.08 14.31 33.81 4.18
31 32 9.690434 CTTAAATATGACTTAAGCTTTGTCGTC 57.310 33.333 22.08 15.67 31.52 4.20
32 33 9.431887 TCTTAAATATGACTTAAGCTTTGTCGT 57.568 29.630 22.09 22.09 36.64 4.34
45 46 9.877178 ACGACAATCTTCTTCTTAAATATGACT 57.123 29.630 0.00 0.00 0.00 3.41
47 48 9.314321 GGACGACAATCTTCTTCTTAAATATGA 57.686 33.333 0.00 0.00 0.00 2.15
48 49 8.552034 GGGACGACAATCTTCTTCTTAAATATG 58.448 37.037 0.00 0.00 0.00 1.78
49 50 7.715686 GGGGACGACAATCTTCTTCTTAAATAT 59.284 37.037 0.00 0.00 0.00 1.28
50 51 7.046033 GGGGACGACAATCTTCTTCTTAAATA 58.954 38.462 0.00 0.00 0.00 1.40
51 52 5.880887 GGGGACGACAATCTTCTTCTTAAAT 59.119 40.000 0.00 0.00 0.00 1.40
52 53 5.243207 GGGGACGACAATCTTCTTCTTAAA 58.757 41.667 0.00 0.00 0.00 1.52
53 54 4.828829 GGGGACGACAATCTTCTTCTTAA 58.171 43.478 0.00 0.00 0.00 1.85
54 55 4.467198 GGGGACGACAATCTTCTTCTTA 57.533 45.455 0.00 0.00 0.00 2.10
55 56 3.336138 GGGGACGACAATCTTCTTCTT 57.664 47.619 0.00 0.00 0.00 2.52
70 71 4.790861 GTCTTCGACGCCGGGGAC 62.791 72.222 27.23 18.65 36.24 4.46
73 74 4.796231 CTGGTCTTCGACGCCGGG 62.796 72.222 2.18 0.00 36.24 5.73
74 75 3.569049 AACTGGTCTTCGACGCCGG 62.569 63.158 0.00 0.00 36.24 6.13
75 76 2.049433 AACTGGTCTTCGACGCCG 60.049 61.111 0.00 0.00 32.65 6.46
76 77 1.006571 TGAACTGGTCTTCGACGCC 60.007 57.895 0.00 0.00 32.65 5.68
77 78 1.009389 CCTGAACTGGTCTTCGACGC 61.009 60.000 0.00 0.00 32.65 5.19
78 79 0.388649 CCCTGAACTGGTCTTCGACG 60.389 60.000 0.00 0.00 32.65 5.12
79 80 0.037232 CCCCTGAACTGGTCTTCGAC 60.037 60.000 0.00 0.00 0.00 4.20
80 81 1.827399 GCCCCTGAACTGGTCTTCGA 61.827 60.000 0.00 0.00 0.00 3.71
81 82 1.376037 GCCCCTGAACTGGTCTTCG 60.376 63.158 0.00 0.00 0.00 3.79
82 83 1.066071 GTAGCCCCTGAACTGGTCTTC 60.066 57.143 0.00 0.00 0.00 2.87
83 84 0.984995 GTAGCCCCTGAACTGGTCTT 59.015 55.000 0.00 0.00 0.00 3.01
84 85 0.910088 GGTAGCCCCTGAACTGGTCT 60.910 60.000 0.00 0.00 0.00 3.85
85 86 1.602771 GGTAGCCCCTGAACTGGTC 59.397 63.158 0.00 0.00 0.00 4.02
86 87 2.291043 CGGTAGCCCCTGAACTGGT 61.291 63.158 0.00 0.00 0.00 4.00
87 88 1.987855 TCGGTAGCCCCTGAACTGG 60.988 63.158 0.00 0.00 0.00 4.00
88 89 1.218316 GTCGGTAGCCCCTGAACTG 59.782 63.158 0.00 0.00 0.00 3.16
89 90 2.348888 CGTCGGTAGCCCCTGAACT 61.349 63.158 0.00 0.00 0.00 3.01
90 91 2.183555 CGTCGGTAGCCCCTGAAC 59.816 66.667 0.00 0.00 0.00 3.18
91 92 3.072468 CCGTCGGTAGCCCCTGAA 61.072 66.667 2.08 0.00 0.00 3.02
92 93 4.371417 ACCGTCGGTAGCCCCTGA 62.371 66.667 17.19 0.00 32.11 3.86
93 94 4.143333 CACCGTCGGTAGCCCCTG 62.143 72.222 18.38 0.00 32.11 4.45
94 95 4.691359 ACACCGTCGGTAGCCCCT 62.691 66.667 18.38 0.00 32.11 4.79
95 96 4.139234 GACACCGTCGGTAGCCCC 62.139 72.222 18.38 0.85 32.11 5.80
96 97 3.061260 GAGACACCGTCGGTAGCCC 62.061 68.421 18.38 6.51 37.67 5.19
97 98 2.488820 GAGACACCGTCGGTAGCC 59.511 66.667 18.38 9.08 37.67 3.93
98 99 2.099831 CGAGACACCGTCGGTAGC 59.900 66.667 18.38 11.99 37.67 3.58
103 104 1.703438 CCTAGTCCGAGACACCGTCG 61.703 65.000 6.78 0.00 37.67 5.12
104 105 1.375098 CCCTAGTCCGAGACACCGTC 61.375 65.000 6.78 0.00 34.60 4.79
105 106 1.378250 CCCTAGTCCGAGACACCGT 60.378 63.158 6.78 0.00 34.60 4.83
106 107 2.119655 CCCCTAGTCCGAGACACCG 61.120 68.421 6.78 0.00 34.60 4.94
107 108 1.757340 CCCCCTAGTCCGAGACACC 60.757 68.421 6.78 0.00 34.60 4.16
108 109 0.257039 TACCCCCTAGTCCGAGACAC 59.743 60.000 6.78 0.00 34.60 3.67
109 110 0.257039 GTACCCCCTAGTCCGAGACA 59.743 60.000 6.78 0.00 34.60 3.41
110 111 0.467106 GGTACCCCCTAGTCCGAGAC 60.467 65.000 0.00 0.00 0.00 3.36
111 112 0.920763 TGGTACCCCCTAGTCCGAGA 60.921 60.000 10.07 0.00 0.00 4.04
112 113 0.032813 TTGGTACCCCCTAGTCCGAG 60.033 60.000 10.07 0.00 0.00 4.63
113 114 0.324645 GTTGGTACCCCCTAGTCCGA 60.325 60.000 10.07 0.00 0.00 4.55
114 115 1.332889 GGTTGGTACCCCCTAGTCCG 61.333 65.000 10.07 0.00 38.60 4.79
115 116 0.043788 AGGTTGGTACCCCCTAGTCC 59.956 60.000 16.62 5.88 46.28 3.85
116 117 2.675583 CTAGGTTGGTACCCCCTAGTC 58.324 57.143 29.94 9.36 46.28 2.59
117 118 2.862850 CTAGGTTGGTACCCCCTAGT 57.137 55.000 29.94 12.31 46.28 2.57
119 120 2.836667 CAACTAGGTTGGTACCCCCTA 58.163 52.381 20.65 20.65 46.28 3.53
120 121 1.665137 CAACTAGGTTGGTACCCCCT 58.335 55.000 20.63 20.63 46.28 4.79
132 133 1.843368 TGGACTACGGACCAACTAGG 58.157 55.000 0.00 0.00 45.67 3.02
133 134 2.100916 CCATGGACTACGGACCAACTAG 59.899 54.545 5.56 0.00 40.28 2.57
134 135 2.104967 CCATGGACTACGGACCAACTA 58.895 52.381 5.56 0.00 40.28 2.24
135 136 0.902531 CCATGGACTACGGACCAACT 59.097 55.000 5.56 0.00 40.28 3.16
136 137 0.899720 TCCATGGACTACGGACCAAC 59.100 55.000 11.44 0.00 40.28 3.77
137 138 0.899720 GTCCATGGACTACGGACCAA 59.100 55.000 33.47 0.00 42.87 3.67
138 139 2.587080 GTCCATGGACTACGGACCA 58.413 57.895 33.47 0.00 42.87 4.02
141 142 0.750546 CTCGGTCCATGGACTACGGA 60.751 60.000 37.26 27.28 44.04 4.69
142 143 1.734137 CTCGGTCCATGGACTACGG 59.266 63.158 37.26 25.20 44.04 4.02
143 144 1.065928 GCTCGGTCCATGGACTACG 59.934 63.158 37.26 32.21 44.04 3.51
144 145 1.043673 AGGCTCGGTCCATGGACTAC 61.044 60.000 37.26 23.96 44.04 2.73
145 146 0.554305 TAGGCTCGGTCCATGGACTA 59.446 55.000 37.26 26.28 44.04 2.59
146 147 0.105453 ATAGGCTCGGTCCATGGACT 60.105 55.000 37.26 22.63 44.04 3.85
147 148 0.034059 CATAGGCTCGGTCCATGGAC 59.966 60.000 33.14 33.14 43.87 4.02
148 149 1.121407 CCATAGGCTCGGTCCATGGA 61.121 60.000 11.44 11.44 37.16 3.41
149 150 1.372683 CCATAGGCTCGGTCCATGG 59.627 63.158 4.97 4.97 32.52 3.66
150 151 1.302033 GCCATAGGCTCGGTCCATG 60.302 63.158 0.00 0.00 46.69 3.66
151 152 3.151906 GCCATAGGCTCGGTCCAT 58.848 61.111 0.00 0.00 46.69 3.41
161 162 0.695803 AGGAGAAGGTGGGCCATAGG 60.696 60.000 10.70 0.00 37.19 2.57
162 163 2.103153 TAGGAGAAGGTGGGCCATAG 57.897 55.000 10.70 0.00 37.19 2.23
163 164 2.408565 CTTAGGAGAAGGTGGGCCATA 58.591 52.381 10.70 0.00 37.19 2.74
164 165 1.216990 CTTAGGAGAAGGTGGGCCAT 58.783 55.000 10.70 0.00 37.19 4.40
165 166 0.914417 CCTTAGGAGAAGGTGGGCCA 60.914 60.000 0.00 0.00 37.19 5.36
166 167 0.620700 TCCTTAGGAGAAGGTGGGCC 60.621 60.000 0.00 0.00 38.55 5.80
167 168 1.210722 CTTCCTTAGGAGAAGGTGGGC 59.789 57.143 0.00 0.00 37.64 5.36
178 179 3.639561 GGCTTCTAGAGTCCTTCCTTAGG 59.360 52.174 0.00 0.00 46.27 2.69
179 180 4.542697 AGGCTTCTAGAGTCCTTCCTTAG 58.457 47.826 8.57 0.00 30.68 2.18
180 181 4.538738 GAGGCTTCTAGAGTCCTTCCTTA 58.461 47.826 13.95 0.00 33.71 2.69
181 182 3.371034 GAGGCTTCTAGAGTCCTTCCTT 58.629 50.000 13.95 0.00 33.71 3.36
182 183 2.685522 CGAGGCTTCTAGAGTCCTTCCT 60.686 54.545 13.95 6.35 33.71 3.36
183 184 1.679153 CGAGGCTTCTAGAGTCCTTCC 59.321 57.143 13.95 4.46 33.71 3.46
184 185 1.066454 GCGAGGCTTCTAGAGTCCTTC 59.934 57.143 13.95 7.61 33.71 3.46
185 186 1.107945 GCGAGGCTTCTAGAGTCCTT 58.892 55.000 13.95 1.81 33.71 3.36
186 187 0.033991 TGCGAGGCTTCTAGAGTCCT 60.034 55.000 12.97 12.97 35.46 3.85
187 188 0.101579 GTGCGAGGCTTCTAGAGTCC 59.898 60.000 4.63 4.63 0.00 3.85
188 189 1.099689 AGTGCGAGGCTTCTAGAGTC 58.900 55.000 0.00 0.00 0.00 3.36
189 190 1.474879 GAAGTGCGAGGCTTCTAGAGT 59.525 52.381 0.00 0.00 39.25 3.24
190 191 1.532921 CGAAGTGCGAGGCTTCTAGAG 60.533 57.143 10.67 0.00 44.57 2.43
191 192 0.452184 CGAAGTGCGAGGCTTCTAGA 59.548 55.000 10.67 0.00 44.57 2.43
192 193 0.526524 CCGAAGTGCGAGGCTTCTAG 60.527 60.000 0.00 0.00 44.57 2.43
193 194 1.511305 CCGAAGTGCGAGGCTTCTA 59.489 57.895 0.00 0.00 44.57 2.10
194 195 2.262915 CCGAAGTGCGAGGCTTCT 59.737 61.111 0.00 0.00 44.57 2.85
195 196 3.491652 GCCGAAGTGCGAGGCTTC 61.492 66.667 0.00 0.00 46.83 3.86
203 204 1.014044 TCTTGATCACGCCGAAGTGC 61.014 55.000 0.00 0.00 41.61 4.40
204 205 1.325640 CATCTTGATCACGCCGAAGTG 59.674 52.381 0.00 4.21 43.11 3.16
205 206 1.645034 CATCTTGATCACGCCGAAGT 58.355 50.000 0.00 0.00 0.00 3.01
206 207 0.933097 CCATCTTGATCACGCCGAAG 59.067 55.000 0.00 0.00 0.00 3.79
207 208 0.534873 TCCATCTTGATCACGCCGAA 59.465 50.000 0.00 0.00 0.00 4.30
208 209 0.179111 GTCCATCTTGATCACGCCGA 60.179 55.000 0.00 0.00 0.00 5.54
209 210 0.179100 AGTCCATCTTGATCACGCCG 60.179 55.000 0.00 0.00 0.00 6.46
210 211 1.137872 AGAGTCCATCTTGATCACGCC 59.862 52.381 0.00 0.00 32.99 5.68
211 212 2.200067 CAGAGTCCATCTTGATCACGC 58.800 52.381 0.00 0.00 35.47 5.34
212 213 2.159128 AGCAGAGTCCATCTTGATCACG 60.159 50.000 0.00 0.00 35.47 4.35
213 214 3.118847 TCAGCAGAGTCCATCTTGATCAC 60.119 47.826 0.00 0.00 35.47 3.06
214 215 3.102204 TCAGCAGAGTCCATCTTGATCA 58.898 45.455 0.00 0.00 35.47 2.92
215 216 3.815856 TCAGCAGAGTCCATCTTGATC 57.184 47.619 0.00 0.00 35.47 2.92
216 217 4.564782 TTTCAGCAGAGTCCATCTTGAT 57.435 40.909 0.00 0.00 35.47 2.57
217 218 4.067896 GTTTTCAGCAGAGTCCATCTTGA 58.932 43.478 0.00 0.00 35.47 3.02
218 219 4.070716 AGTTTTCAGCAGAGTCCATCTTG 58.929 43.478 0.00 0.00 35.47 3.02
219 220 4.363991 AGTTTTCAGCAGAGTCCATCTT 57.636 40.909 0.00 0.00 35.47 2.40
220 221 4.070716 CAAGTTTTCAGCAGAGTCCATCT 58.929 43.478 0.00 0.00 39.56 2.90
221 222 3.190118 CCAAGTTTTCAGCAGAGTCCATC 59.810 47.826 0.00 0.00 0.00 3.51
222 223 3.152341 CCAAGTTTTCAGCAGAGTCCAT 58.848 45.455 0.00 0.00 0.00 3.41
223 224 2.172505 TCCAAGTTTTCAGCAGAGTCCA 59.827 45.455 0.00 0.00 0.00 4.02
224 225 2.851195 TCCAAGTTTTCAGCAGAGTCC 58.149 47.619 0.00 0.00 0.00 3.85
225 226 3.365767 GCATCCAAGTTTTCAGCAGAGTC 60.366 47.826 0.00 0.00 0.00 3.36
226 227 2.555757 GCATCCAAGTTTTCAGCAGAGT 59.444 45.455 0.00 0.00 0.00 3.24
227 228 2.555325 TGCATCCAAGTTTTCAGCAGAG 59.445 45.455 0.00 0.00 0.00 3.35
228 229 2.585330 TGCATCCAAGTTTTCAGCAGA 58.415 42.857 0.00 0.00 0.00 4.26
229 230 3.508762 GATGCATCCAAGTTTTCAGCAG 58.491 45.455 16.23 0.00 33.69 4.24
230 231 2.231964 GGATGCATCCAAGTTTTCAGCA 59.768 45.455 35.93 0.00 46.38 4.41
231 232 2.884827 GGATGCATCCAAGTTTTCAGC 58.115 47.619 35.93 8.03 46.38 4.26
287 288 6.546034 GCCCACACATATATAAAACTGGTTCT 59.454 38.462 0.00 0.00 0.00 3.01
294 295 8.466798 GGATAATGGCCCACACATATATAAAAC 58.533 37.037 0.00 0.00 0.00 2.43
305 306 2.143876 AGTTGGATAATGGCCCACAC 57.856 50.000 0.00 0.00 31.11 3.82
316 317 3.773119 GAGTTGGTGAGGGTAGTTGGATA 59.227 47.826 0.00 0.00 0.00 2.59
409 411 4.553429 CCTTAAATTGCGAACTGTTAAGCG 59.447 41.667 13.34 6.01 32.74 4.68
415 417 4.759693 TGATCACCTTAAATTGCGAACTGT 59.240 37.500 0.00 0.00 0.00 3.55
416 418 5.295431 TGATCACCTTAAATTGCGAACTG 57.705 39.130 0.00 0.00 0.00 3.16
417 419 5.163622 CCATGATCACCTTAAATTGCGAACT 60.164 40.000 0.00 0.00 0.00 3.01
456 461 7.398829 TGTTCATGGTAATTCTTAGTTGGCTA 58.601 34.615 0.00 0.00 0.00 3.93
457 462 6.245408 TGTTCATGGTAATTCTTAGTTGGCT 58.755 36.000 0.00 0.00 0.00 4.75
458 463 6.509418 TGTTCATGGTAATTCTTAGTTGGC 57.491 37.500 0.00 0.00 0.00 4.52
459 464 9.927668 AAAATGTTCATGGTAATTCTTAGTTGG 57.072 29.630 0.00 0.00 0.00 3.77
563 583 9.921637 AAAAATAAATCAGCTACCGATTTTCAA 57.078 25.926 13.80 0.26 41.90 2.69
633 693 4.630894 TTCACACGCTTTTTCTCATGTT 57.369 36.364 0.00 0.00 0.00 2.71
639 699 5.060446 CGTTTCTTTTTCACACGCTTTTTCT 59.940 36.000 0.00 0.00 0.00 2.52
640 700 5.059955 TCGTTTCTTTTTCACACGCTTTTTC 59.940 36.000 0.00 0.00 0.00 2.29
641 701 4.918583 TCGTTTCTTTTTCACACGCTTTTT 59.081 33.333 0.00 0.00 0.00 1.94
642 702 4.477780 TCGTTTCTTTTTCACACGCTTTT 58.522 34.783 0.00 0.00 0.00 2.27
643 703 4.086199 TCGTTTCTTTTTCACACGCTTT 57.914 36.364 0.00 0.00 0.00 3.51
644 704 3.680789 CTCGTTTCTTTTTCACACGCTT 58.319 40.909 0.00 0.00 0.00 4.68
645 705 2.538939 GCTCGTTTCTTTTTCACACGCT 60.539 45.455 0.00 0.00 0.00 5.07
646 706 1.773525 GCTCGTTTCTTTTTCACACGC 59.226 47.619 0.00 0.00 0.00 5.34
647 707 3.242284 TGAGCTCGTTTCTTTTTCACACG 60.242 43.478 9.64 0.00 0.00 4.49
648 708 4.273005 TGAGCTCGTTTCTTTTTCACAC 57.727 40.909 9.64 0.00 0.00 3.82
649 709 3.242739 GCTGAGCTCGTTTCTTTTTCACA 60.243 43.478 9.64 0.00 0.00 3.58
650 710 3.292423 GCTGAGCTCGTTTCTTTTTCAC 58.708 45.455 9.64 0.00 0.00 3.18
651 711 2.290641 GGCTGAGCTCGTTTCTTTTTCA 59.709 45.455 9.64 0.00 0.00 2.69
652 712 2.290641 TGGCTGAGCTCGTTTCTTTTTC 59.709 45.455 9.64 0.00 0.00 2.29
653 713 2.033424 GTGGCTGAGCTCGTTTCTTTTT 59.967 45.455 9.64 0.00 0.00 1.94
654 714 1.604278 GTGGCTGAGCTCGTTTCTTTT 59.396 47.619 9.64 0.00 0.00 2.27
655 715 1.202698 AGTGGCTGAGCTCGTTTCTTT 60.203 47.619 9.64 0.00 0.00 2.52
656 716 0.394565 AGTGGCTGAGCTCGTTTCTT 59.605 50.000 9.64 0.00 0.00 2.52
895 956 4.374702 CTGCACGGCGTTGCTGAC 62.375 66.667 26.09 8.82 42.42 3.51
907 968 2.184579 GAGGACGGCTACCTGCAC 59.815 66.667 4.17 0.00 45.15 4.57
919 980 1.360911 GAAGAGATCGGGCGAGGAC 59.639 63.158 0.00 0.00 0.00 3.85
931 992 1.001269 TCCGGCGAAGAGGAAGAGA 60.001 57.895 9.30 0.00 33.30 3.10
954 1015 3.762779 CGAGAAAATCATCAAACTGGGC 58.237 45.455 0.00 0.00 0.00 5.36
964 1025 3.374988 TGCAAATCGAGCGAGAAAATCAT 59.625 39.130 0.00 0.00 33.85 2.45
970 1031 1.726791 GAACTGCAAATCGAGCGAGAA 59.273 47.619 0.00 0.00 33.85 2.87
1032 1099 0.034896 GAGAGTTGTCCGGCCTCAAA 59.965 55.000 0.00 0.00 0.00 2.69
1053 1120 3.423162 CTCCGCCTCCGCAAGAGAG 62.423 68.421 2.33 0.00 46.50 3.20
1054 1121 3.452786 CTCCGCCTCCGCAAGAGA 61.453 66.667 2.33 0.00 46.50 3.10
1055 1122 4.521062 CCTCCGCCTCCGCAAGAG 62.521 72.222 0.00 0.00 42.83 2.85
1171 1238 2.982130 GATGAGGTCACGCCAGGT 59.018 61.111 0.00 0.00 40.61 4.00
1179 1246 3.399181 GGGTGGGCGATGAGGTCA 61.399 66.667 0.00 0.00 0.00 4.02
1339 1406 2.025605 AGTCCCTGTACTCCGTATGTGA 60.026 50.000 0.00 0.00 0.00 3.58
1573 1649 1.971167 TGATGCCCAAGTTGTCGGC 60.971 57.895 14.34 14.34 43.32 5.54
1706 1788 0.249155 CACAAGCAGGTTGCCAACAG 60.249 55.000 12.41 2.42 46.52 3.16
1710 1792 2.521465 CCCACAAGCAGGTTGCCA 60.521 61.111 12.41 0.00 46.52 4.92
1791 1873 1.407437 GGCACGGAGATTGTCTTCCAT 60.407 52.381 0.00 0.00 0.00 3.41
1813 1895 1.485294 ATACCATAATCCCGGCCGCA 61.485 55.000 22.85 8.89 0.00 5.69
1975 2060 0.394352 AAACTATGCTTGAGGGCCCG 60.394 55.000 18.44 2.33 0.00 6.13
1983 2068 7.225538 ACCTTATCGATTCTGAAACTATGCTTG 59.774 37.037 1.71 0.00 0.00 4.01
2289 2384 2.095853 GTGCAGGTGTACACATACATGC 59.904 50.000 26.51 23.79 43.29 4.06
2612 2998 6.491062 TCACCTGATGAATGAGTGAAACAAAT 59.509 34.615 0.00 0.00 34.27 2.32
2624 3010 5.390885 CCGTTAGTTTGTCACCTGATGAATG 60.391 44.000 0.00 0.00 39.72 2.67
2638 3024 3.119990 CCTGCATGGTAACCGTTAGTTTG 60.120 47.826 0.00 0.00 40.05 2.93
2657 3043 5.643777 CCACTATACTTGAAGAACAACCCTG 59.356 44.000 0.00 0.00 34.56 4.45
2687 3073 5.471456 GCAATAAGGACTATCCCAACATCTG 59.529 44.000 0.00 0.00 37.19 2.90
2707 3093 6.136071 GCTATGATAAAATTCGTGTCGCAAT 58.864 36.000 0.00 0.00 0.00 3.56
2715 3101 9.722056 GAAATTGAGTGCTATGATAAAATTCGT 57.278 29.630 0.00 0.00 0.00 3.85
2753 3142 5.221165 CCAACCTGTACAAAATTTCTTCCGT 60.221 40.000 0.00 0.00 0.00 4.69
2756 3145 7.762159 TCAAACCAACCTGTACAAAATTTCTTC 59.238 33.333 0.00 0.00 0.00 2.87
2769 3158 2.525105 AACCTGTCAAACCAACCTGT 57.475 45.000 0.00 0.00 0.00 4.00
2770 3159 4.736464 GCTTAAACCTGTCAAACCAACCTG 60.736 45.833 0.00 0.00 0.00 4.00
2771 3160 3.383505 GCTTAAACCTGTCAAACCAACCT 59.616 43.478 0.00 0.00 0.00 3.50
2772 3161 3.383505 AGCTTAAACCTGTCAAACCAACC 59.616 43.478 0.00 0.00 0.00 3.77
2774 3163 4.097286 GTCAGCTTAAACCTGTCAAACCAA 59.903 41.667 0.00 0.00 0.00 3.67
2775 3164 3.630312 GTCAGCTTAAACCTGTCAAACCA 59.370 43.478 0.00 0.00 0.00 3.67
2789 3179 7.453393 CAATCTTCCCAATATAGGTCAGCTTA 58.547 38.462 0.00 0.00 0.00 3.09
2883 3275 2.693074 GGACCTTCAGGCAGTTCAAAAA 59.307 45.455 0.00 0.00 39.32 1.94
2938 3330 7.453393 ACATCCTCTTTCTCTTGACATAACAA 58.547 34.615 0.00 0.00 0.00 2.83
2948 3340 9.847224 TGTACTTTTTAACATCCTCTTTCTCTT 57.153 29.630 0.00 0.00 0.00 2.85
2992 3384 6.320418 CCCCATATCCTTAGGTTTACAAACAC 59.680 42.308 7.12 0.00 40.63 3.32
3058 3450 9.613428 CAACTATCCAGATCCATTTACAAAGTA 57.387 33.333 0.00 0.00 0.00 2.24
3062 3454 7.127186 TCTCCAACTATCCAGATCCATTTACAA 59.873 37.037 0.00 0.00 0.00 2.41
3079 3471 5.189736 ACATACCTTGCTCATTCTCCAACTA 59.810 40.000 0.00 0.00 0.00 2.24
3080 3472 4.018960 ACATACCTTGCTCATTCTCCAACT 60.019 41.667 0.00 0.00 0.00 3.16
3081 3473 4.265073 ACATACCTTGCTCATTCTCCAAC 58.735 43.478 0.00 0.00 0.00 3.77
3082 3474 4.574674 ACATACCTTGCTCATTCTCCAA 57.425 40.909 0.00 0.00 0.00 3.53
3182 3574 2.091640 TTTCAGAATGCCCAGCCCCA 62.092 55.000 0.00 0.00 34.76 4.96
3183 3575 1.305213 TTTCAGAATGCCCAGCCCC 60.305 57.895 0.00 0.00 34.76 5.80
3184 3576 0.613012 ACTTTCAGAATGCCCAGCCC 60.613 55.000 0.00 0.00 34.76 5.19


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

AutoCloner maintained by Alex Coulton.