Multiple sequence alignment - TraesCS3B01G164400

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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 TraesCS3B01G164400 chr3B 100.000 2381 0 0 1 2381 161797092 161794712 0.000000e+00 4397
1 TraesCS3B01G164400 chr3D 89.793 1979 170 19 422 2381 126392824 126394789 0.000000e+00 2507
2 TraesCS3B01G164400 chr3D 83.642 324 41 9 97 416 435708005 435708320 6.440000e-76 294
3 TraesCS3B01G164400 chr3D 81.493 335 45 12 99 424 315771177 315770851 2.350000e-65 259
4 TraesCS3B01G164400 chr1B 89.836 1948 170 15 445 2375 308913060 308914996 0.000000e+00 2475
5 TraesCS3B01G164400 chr1B 88.827 1960 192 18 434 2377 596304446 596306394 0.000000e+00 2381
6 TraesCS3B01G164400 chr5D 89.636 1949 163 26 422 2355 247315704 247313780 0.000000e+00 2444
7 TraesCS3B01G164400 chr5D 84.744 1973 250 28 434 2378 525593191 525595140 0.000000e+00 1929
8 TraesCS3B01G164400 chr5D 84.894 331 39 7 101 429 344691794 344691473 8.210000e-85 324
9 TraesCS3B01G164400 chrUn 89.401 1953 165 19 434 2373 218123596 218121673 0.000000e+00 2422
10 TraesCS3B01G164400 chrUn 90.752 1622 139 5 437 2055 366980144 366978531 0.000000e+00 2154
11 TraesCS3B01G164400 chr4B 89.094 1953 180 21 447 2381 71568969 71567032 0.000000e+00 2396
12 TraesCS3B01G164400 chr7B 88.838 1971 179 21 422 2376 724805641 724807586 0.000000e+00 2383
13 TraesCS3B01G164400 chr7B 85.800 1662 208 12 732 2377 662650261 662648612 0.000000e+00 1736
14 TraesCS3B01G164400 chr6B 88.720 1977 180 23 422 2381 320730524 320732474 0.000000e+00 2375
15 TraesCS3B01G164400 chr6B 85.321 327 41 6 101 424 672368680 672369002 4.910000e-87 331
16 TraesCS3B01G164400 chr1D 87.123 1359 148 11 1035 2378 236078895 236080241 0.000000e+00 1515
17 TraesCS3B01G164400 chr1D 86.575 797 86 8 1596 2379 433908654 433907866 0.000000e+00 859
18 TraesCS3B01G164400 chr7D 87.995 783 77 4 1609 2377 99380996 99380217 0.000000e+00 909
19 TraesCS3B01G164400 chr6D 87.187 718 78 4 1671 2377 199606769 199606055 0.000000e+00 804
20 TraesCS3B01G164400 chr5B 89.154 544 42 5 1853 2381 668818134 668818675 0.000000e+00 662
21 TraesCS3B01G164400 chr2D 92.260 323 22 2 2055 2377 448520194 448519875 2.790000e-124 455
22 TraesCS3B01G164400 chr2D 86.196 326 34 9 94 416 460867529 460867212 2.270000e-90 342
23 TraesCS3B01G164400 chr2D 82.075 318 47 8 98 413 505534450 505534141 1.810000e-66 263
24 TraesCS3B01G164400 chr5A 83.172 309 45 5 98 403 638912250 638912554 2.330000e-70 276
25 TraesCS3B01G164400 chr2B 82.650 317 48 6 99 413 243358733 243359044 8.380000e-70 274
26 TraesCS3B01G164400 chr3A 82.243 321 47 9 99 416 683476821 683477134 3.900000e-68 268


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 TraesCS3B01G164400 chr3B 161794712 161797092 2380 True 4397 4397 100.000 1 2381 1 chr3B.!!$R1 2380
1 TraesCS3B01G164400 chr3D 126392824 126394789 1965 False 2507 2507 89.793 422 2381 1 chr3D.!!$F1 1959
2 TraesCS3B01G164400 chr1B 308913060 308914996 1936 False 2475 2475 89.836 445 2375 1 chr1B.!!$F1 1930
3 TraesCS3B01G164400 chr1B 596304446 596306394 1948 False 2381 2381 88.827 434 2377 1 chr1B.!!$F2 1943
4 TraesCS3B01G164400 chr5D 247313780 247315704 1924 True 2444 2444 89.636 422 2355 1 chr5D.!!$R1 1933
5 TraesCS3B01G164400 chr5D 525593191 525595140 1949 False 1929 1929 84.744 434 2378 1 chr5D.!!$F1 1944
6 TraesCS3B01G164400 chrUn 218121673 218123596 1923 True 2422 2422 89.401 434 2373 1 chrUn.!!$R1 1939
7 TraesCS3B01G164400 chrUn 366978531 366980144 1613 True 2154 2154 90.752 437 2055 1 chrUn.!!$R2 1618
8 TraesCS3B01G164400 chr4B 71567032 71568969 1937 True 2396 2396 89.094 447 2381 1 chr4B.!!$R1 1934
9 TraesCS3B01G164400 chr7B 724805641 724807586 1945 False 2383 2383 88.838 422 2376 1 chr7B.!!$F1 1954
10 TraesCS3B01G164400 chr7B 662648612 662650261 1649 True 1736 1736 85.800 732 2377 1 chr7B.!!$R1 1645
11 TraesCS3B01G164400 chr6B 320730524 320732474 1950 False 2375 2375 88.720 422 2381 1 chr6B.!!$F1 1959
12 TraesCS3B01G164400 chr1D 236078895 236080241 1346 False 1515 1515 87.123 1035 2378 1 chr1D.!!$F1 1343
13 TraesCS3B01G164400 chr1D 433907866 433908654 788 True 859 859 86.575 1596 2379 1 chr1D.!!$R1 783
14 TraesCS3B01G164400 chr7D 99380217 99380996 779 True 909 909 87.995 1609 2377 1 chr7D.!!$R1 768
15 TraesCS3B01G164400 chr6D 199606055 199606769 714 True 804 804 87.187 1671 2377 1 chr6D.!!$R1 706
16 TraesCS3B01G164400 chr5B 668818134 668818675 541 False 662 662 89.154 1853 2381 1 chr5B.!!$F1 528

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
262 263 0.026285 GATTCGGATTTGCGTCGGTG 59.974 55.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 1984 0.107017 TAGCATCTTGGCTTGCCTCC 60.107 55.0 13.18 0.0 42.71 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
18 19 3.339547 CCAAGTCCCAACGACCATT 57.660 52.632 0.00 0.00 43.08 3.16
19 20 1.165270 CCAAGTCCCAACGACCATTC 58.835 55.000 0.00 0.00 43.08 2.67
29 30 3.873812 GACCATTCGCCCCCGGAT 61.874 66.667 0.73 0.00 31.29 4.18
31 32 4.189580 CCATTCGCCCCCGGATGT 62.190 66.667 0.73 0.00 46.71 3.06
32 33 2.591715 CATTCGCCCCCGGATGTC 60.592 66.667 0.73 0.00 43.84 3.06
33 34 3.873812 ATTCGCCCCCGGATGTCC 61.874 66.667 0.73 0.00 29.65 4.02
44 45 1.643832 GGATGTCCGCTCATTTCGC 59.356 57.895 0.00 0.00 0.00 4.70
45 46 1.089481 GGATGTCCGCTCATTTCGCA 61.089 55.000 0.00 0.00 0.00 5.10
46 47 0.026803 GATGTCCGCTCATTTCGCAC 59.973 55.000 0.00 0.00 0.00 5.34
47 48 1.369091 ATGTCCGCTCATTTCGCACC 61.369 55.000 0.00 0.00 0.00 5.01
48 49 2.032634 GTCCGCTCATTTCGCACCA 61.033 57.895 0.00 0.00 0.00 4.17
49 50 2.032634 TCCGCTCATTTCGCACCAC 61.033 57.895 0.00 0.00 0.00 4.16
50 51 2.324330 CCGCTCATTTCGCACCACA 61.324 57.895 0.00 0.00 0.00 4.17
51 52 1.573932 CGCTCATTTCGCACCACAA 59.426 52.632 0.00 0.00 0.00 3.33
52 53 0.040514 CGCTCATTTCGCACCACAAA 60.041 50.000 0.00 0.00 0.00 2.83
53 54 1.408422 GCTCATTTCGCACCACAAAC 58.592 50.000 0.00 0.00 0.00 2.93
54 55 1.673760 CTCATTTCGCACCACAAACG 58.326 50.000 0.00 0.00 0.00 3.60
55 56 1.262950 CTCATTTCGCACCACAAACGA 59.737 47.619 0.00 0.00 0.00 3.85
56 57 1.671328 TCATTTCGCACCACAAACGAA 59.329 42.857 0.00 0.00 43.42 3.85
57 58 1.778591 CATTTCGCACCACAAACGAAC 59.221 47.619 0.00 0.00 44.64 3.95
58 59 0.803117 TTTCGCACCACAAACGAACA 59.197 45.000 0.00 0.00 44.64 3.18
59 60 0.803117 TTCGCACCACAAACGAACAA 59.197 45.000 0.00 0.00 40.56 2.83
60 61 0.803117 TCGCACCACAAACGAACAAA 59.197 45.000 0.00 0.00 31.97 2.83
61 62 1.402259 TCGCACCACAAACGAACAAAT 59.598 42.857 0.00 0.00 31.97 2.32
62 63 2.612672 TCGCACCACAAACGAACAAATA 59.387 40.909 0.00 0.00 31.97 1.40
63 64 3.251245 TCGCACCACAAACGAACAAATAT 59.749 39.130 0.00 0.00 31.97 1.28
64 65 3.978217 CGCACCACAAACGAACAAATATT 59.022 39.130 0.00 0.00 0.00 1.28
65 66 4.087930 CGCACCACAAACGAACAAATATTC 59.912 41.667 0.00 0.00 0.00 1.75
76 77 6.538894 CGAACAAATATTCGTGTCCATTTG 57.461 37.500 0.00 0.00 45.07 2.32
77 78 6.310960 CGAACAAATATTCGTGTCCATTTGA 58.689 36.000 11.62 0.00 45.07 2.69
78 79 6.465781 CGAACAAATATTCGTGTCCATTTGAG 59.534 38.462 11.62 1.57 45.07 3.02
79 80 6.194796 ACAAATATTCGTGTCCATTTGAGG 57.805 37.500 11.62 0.00 39.59 3.86
80 81 5.710099 ACAAATATTCGTGTCCATTTGAGGT 59.290 36.000 11.62 0.00 39.59 3.85
81 82 6.128007 ACAAATATTCGTGTCCATTTGAGGTC 60.128 38.462 11.62 0.00 39.59 3.85
82 83 3.703001 ATTCGTGTCCATTTGAGGTCT 57.297 42.857 0.00 0.00 0.00 3.85
83 84 2.455674 TCGTGTCCATTTGAGGTCTG 57.544 50.000 0.00 0.00 0.00 3.51
84 85 1.001974 TCGTGTCCATTTGAGGTCTGG 59.998 52.381 0.00 0.00 0.00 3.86
85 86 1.168714 GTGTCCATTTGAGGTCTGGC 58.831 55.000 0.00 0.00 0.00 4.85
86 87 0.770499 TGTCCATTTGAGGTCTGGCA 59.230 50.000 0.00 0.00 0.00 4.92
87 88 1.355381 TGTCCATTTGAGGTCTGGCAT 59.645 47.619 0.00 0.00 0.00 4.40
88 89 2.225091 TGTCCATTTGAGGTCTGGCATT 60.225 45.455 0.00 0.00 0.00 3.56
89 90 2.165030 GTCCATTTGAGGTCTGGCATTG 59.835 50.000 0.00 0.00 0.00 2.82
90 91 1.479323 CCATTTGAGGTCTGGCATTGG 59.521 52.381 0.00 0.00 0.00 3.16
91 92 1.479323 CATTTGAGGTCTGGCATTGGG 59.521 52.381 0.00 0.00 0.00 4.12
92 93 0.482446 TTTGAGGTCTGGCATTGGGT 59.518 50.000 0.00 0.00 0.00 4.51
93 94 0.482446 TTGAGGTCTGGCATTGGGTT 59.518 50.000 0.00 0.00 0.00 4.11
94 95 0.251297 TGAGGTCTGGCATTGGGTTG 60.251 55.000 0.00 0.00 0.00 3.77
95 96 0.251341 GAGGTCTGGCATTGGGTTGT 60.251 55.000 0.00 0.00 0.00 3.32
96 97 0.251341 AGGTCTGGCATTGGGTTGTC 60.251 55.000 0.00 0.00 0.00 3.18
97 98 1.250840 GGTCTGGCATTGGGTTGTCC 61.251 60.000 0.00 0.00 0.00 4.02
98 99 0.251341 GTCTGGCATTGGGTTGTCCT 60.251 55.000 0.00 0.00 36.20 3.85
99 100 0.482446 TCTGGCATTGGGTTGTCCTT 59.518 50.000 0.00 0.00 36.20 3.36
100 101 1.707989 TCTGGCATTGGGTTGTCCTTA 59.292 47.619 0.00 0.00 36.20 2.69
101 102 2.094675 CTGGCATTGGGTTGTCCTTAG 58.905 52.381 0.00 0.00 36.20 2.18
102 103 1.707989 TGGCATTGGGTTGTCCTTAGA 59.292 47.619 0.00 0.00 36.20 2.10
103 104 2.290896 TGGCATTGGGTTGTCCTTAGAG 60.291 50.000 0.00 0.00 36.20 2.43
104 105 1.745653 GCATTGGGTTGTCCTTAGAGC 59.254 52.381 0.00 0.00 36.20 4.09
105 106 2.879756 GCATTGGGTTGTCCTTAGAGCA 60.880 50.000 0.00 0.00 36.20 4.26
106 107 3.420893 CATTGGGTTGTCCTTAGAGCAA 58.579 45.455 0.00 0.00 36.20 3.91
107 108 2.561478 TGGGTTGTCCTTAGAGCAAC 57.439 50.000 9.24 9.24 41.02 4.17
108 109 2.054799 TGGGTTGTCCTTAGAGCAACT 58.945 47.619 14.54 0.00 41.36 3.16
109 110 2.038557 TGGGTTGTCCTTAGAGCAACTC 59.961 50.000 14.54 12.48 42.22 3.01
110 111 2.338500 GGTTGTCCTTAGAGCAACTCG 58.662 52.381 14.54 0.00 41.36 4.18
111 112 2.029290 GGTTGTCCTTAGAGCAACTCGA 60.029 50.000 14.54 0.00 41.36 4.04
112 113 3.554337 GGTTGTCCTTAGAGCAACTCGAA 60.554 47.826 14.54 0.00 41.36 3.71
113 114 3.299340 TGTCCTTAGAGCAACTCGAAC 57.701 47.619 0.00 0.00 35.36 3.95
114 115 2.251893 GTCCTTAGAGCAACTCGAACG 58.748 52.381 0.00 0.00 35.36 3.95
115 116 2.095364 GTCCTTAGAGCAACTCGAACGA 60.095 50.000 0.00 0.00 35.36 3.85
116 117 2.161808 TCCTTAGAGCAACTCGAACGAG 59.838 50.000 20.25 20.25 46.91 4.18
117 118 2.520979 CTTAGAGCAACTCGAACGAGG 58.479 52.381 24.33 11.42 45.88 4.63
118 119 0.170561 TAGAGCAACTCGAACGAGGC 59.829 55.000 24.33 19.00 45.88 4.70
119 120 2.048127 AGCAACTCGAACGAGGCC 60.048 61.111 24.33 13.60 45.88 5.19
120 121 2.357034 GCAACTCGAACGAGGCCA 60.357 61.111 24.33 0.00 45.88 5.36
121 122 2.668280 GCAACTCGAACGAGGCCAC 61.668 63.158 24.33 0.00 45.88 5.01
122 123 2.027625 CAACTCGAACGAGGCCACC 61.028 63.158 24.33 0.00 45.88 4.61
123 124 3.236003 AACTCGAACGAGGCCACCC 62.236 63.158 24.33 0.00 45.88 4.61
124 125 3.691342 CTCGAACGAGGCCACCCA 61.691 66.667 15.22 0.00 38.51 4.51
125 126 3.000819 TCGAACGAGGCCACCCAT 61.001 61.111 5.01 0.00 0.00 4.00
126 127 2.046314 CGAACGAGGCCACCCATT 60.046 61.111 5.01 0.00 0.00 3.16
127 128 1.674322 CGAACGAGGCCACCCATTT 60.674 57.895 5.01 0.00 0.00 2.32
128 129 1.644786 CGAACGAGGCCACCCATTTC 61.645 60.000 5.01 0.00 0.00 2.17
129 130 1.644786 GAACGAGGCCACCCATTTCG 61.645 60.000 5.01 6.07 33.82 3.46
130 131 2.046314 CGAGGCCACCCATTTCGT 60.046 61.111 5.01 0.00 0.00 3.85
131 132 2.106683 CGAGGCCACCCATTTCGTC 61.107 63.158 5.01 0.00 0.00 4.20
132 133 1.749258 GAGGCCACCCATTTCGTCC 60.749 63.158 5.01 0.00 0.00 4.79
133 134 3.131478 GGCCACCCATTTCGTCCG 61.131 66.667 0.00 0.00 0.00 4.79
134 135 3.810896 GCCACCCATTTCGTCCGC 61.811 66.667 0.00 0.00 0.00 5.54
135 136 2.046314 CCACCCATTTCGTCCGCT 60.046 61.111 0.00 0.00 0.00 5.52
136 137 2.398554 CCACCCATTTCGTCCGCTG 61.399 63.158 0.00 0.00 0.00 5.18
137 138 2.046314 ACCCATTTCGTCCGCTGG 60.046 61.111 0.00 0.00 0.00 4.85
138 139 3.508840 CCCATTTCGTCCGCTGGC 61.509 66.667 0.00 0.00 0.00 4.85
139 140 3.864686 CCATTTCGTCCGCTGGCG 61.865 66.667 8.08 8.08 39.44 5.69
140 141 3.118454 CATTTCGTCCGCTGGCGT 61.118 61.111 13.84 0.00 37.81 5.68
141 142 2.813908 ATTTCGTCCGCTGGCGTC 60.814 61.111 13.84 5.90 37.81 5.19
151 152 2.593436 CTGGCGTCCGTTTGGGTT 60.593 61.111 0.00 0.00 37.00 4.11
152 153 2.902846 TGGCGTCCGTTTGGGTTG 60.903 61.111 0.00 0.00 37.00 3.77
153 154 3.666253 GGCGTCCGTTTGGGTTGG 61.666 66.667 0.00 0.00 37.00 3.77
154 155 4.337060 GCGTCCGTTTGGGTTGGC 62.337 66.667 0.00 0.00 37.00 4.52
155 156 2.902846 CGTCCGTTTGGGTTGGCA 60.903 61.111 0.00 0.00 37.00 4.92
156 157 2.725641 GTCCGTTTGGGTTGGCAC 59.274 61.111 0.00 0.00 37.00 5.01
157 158 2.122167 GTCCGTTTGGGTTGGCACA 61.122 57.895 0.00 0.00 37.00 4.57
158 159 1.826054 TCCGTTTGGGTTGGCACAG 60.826 57.895 0.00 0.00 35.83 3.66
159 160 1.826054 CCGTTTGGGTTGGCACAGA 60.826 57.895 0.00 0.00 42.39 3.41
160 161 1.358759 CGTTTGGGTTGGCACAGAC 59.641 57.895 0.00 0.00 42.39 3.51
161 162 1.380403 CGTTTGGGTTGGCACAGACA 61.380 55.000 0.00 0.00 42.39 3.41
162 163 0.102300 GTTTGGGTTGGCACAGACAC 59.898 55.000 0.00 0.00 42.39 3.67
163 164 0.323816 TTTGGGTTGGCACAGACACA 60.324 50.000 0.00 0.00 42.39 3.72
164 165 0.323816 TTGGGTTGGCACAGACACAA 60.324 50.000 1.45 1.45 42.39 3.33
165 166 0.323816 TGGGTTGGCACAGACACAAA 60.324 50.000 0.00 0.00 42.39 2.83
166 167 0.820871 GGGTTGGCACAGACACAAAA 59.179 50.000 0.00 0.00 42.39 2.44
167 168 1.202405 GGGTTGGCACAGACACAAAAG 60.202 52.381 0.00 0.00 42.39 2.27
168 169 1.476488 GGTTGGCACAGACACAAAAGT 59.524 47.619 0.00 0.00 42.39 2.66
169 170 2.479560 GGTTGGCACAGACACAAAAGTC 60.480 50.000 0.00 0.00 42.39 3.01
170 171 1.013596 TGGCACAGACACAAAAGTCG 58.986 50.000 0.00 0.00 43.24 4.18
171 172 0.307760 GGCACAGACACAAAAGTCGG 59.692 55.000 0.00 0.00 43.24 4.79
172 173 0.317020 GCACAGACACAAAAGTCGGC 60.317 55.000 0.00 0.00 43.24 5.54
173 174 0.307760 CACAGACACAAAAGTCGGCC 59.692 55.000 0.00 0.00 43.24 6.13
174 175 0.818040 ACAGACACAAAAGTCGGCCC 60.818 55.000 0.00 0.00 43.24 5.80
175 176 0.817634 CAGACACAAAAGTCGGCCCA 60.818 55.000 0.00 0.00 43.24 5.36
176 177 0.106918 AGACACAAAAGTCGGCCCAA 60.107 50.000 0.00 0.00 43.24 4.12
177 178 0.030235 GACACAAAAGTCGGCCCAAC 59.970 55.000 0.00 0.00 0.00 3.77
178 179 1.008995 CACAAAAGTCGGCCCAACG 60.009 57.895 0.00 0.00 0.00 4.10
179 180 2.050442 CAAAAGTCGGCCCAACGC 60.050 61.111 0.00 0.00 0.00 4.84
180 181 3.656045 AAAAGTCGGCCCAACGCG 61.656 61.111 3.53 3.53 38.94 6.01
190 191 3.283684 CCAACGCGCTGACCCAAA 61.284 61.111 11.83 0.00 0.00 3.28
191 192 2.051345 CAACGCGCTGACCCAAAC 60.051 61.111 5.73 0.00 0.00 2.93
192 193 3.645975 AACGCGCTGACCCAAACG 61.646 61.111 5.73 0.00 0.00 3.60
239 240 3.217231 GACCCATCGTCGGTCCAT 58.783 61.111 6.96 0.00 43.48 3.41
240 241 1.520666 GACCCATCGTCGGTCCATT 59.479 57.895 6.96 0.00 43.48 3.16
241 242 0.107848 GACCCATCGTCGGTCCATTT 60.108 55.000 6.96 0.00 43.48 2.32
242 243 0.326927 ACCCATCGTCGGTCCATTTT 59.673 50.000 0.00 0.00 0.00 1.82
243 244 0.732571 CCCATCGTCGGTCCATTTTG 59.267 55.000 0.00 0.00 0.00 2.44
244 245 1.677518 CCCATCGTCGGTCCATTTTGA 60.678 52.381 0.00 0.00 0.00 2.69
245 246 2.288666 CCATCGTCGGTCCATTTTGAT 58.711 47.619 0.00 0.00 0.00 2.57
246 247 2.682856 CCATCGTCGGTCCATTTTGATT 59.317 45.455 0.00 0.00 0.00 2.57
247 248 3.242739 CCATCGTCGGTCCATTTTGATTC 60.243 47.826 0.00 0.00 0.00 2.52
248 249 1.996898 TCGTCGGTCCATTTTGATTCG 59.003 47.619 0.00 0.00 0.00 3.34
249 250 1.062002 CGTCGGTCCATTTTGATTCGG 59.938 52.381 0.00 0.00 0.00 4.30
250 251 2.352388 GTCGGTCCATTTTGATTCGGA 58.648 47.619 0.00 0.00 0.00 4.55
251 252 2.943033 GTCGGTCCATTTTGATTCGGAT 59.057 45.455 0.00 0.00 0.00 4.18
252 253 3.377172 GTCGGTCCATTTTGATTCGGATT 59.623 43.478 0.00 0.00 0.00 3.01
253 254 4.013728 TCGGTCCATTTTGATTCGGATTT 58.986 39.130 0.00 0.00 0.00 2.17
254 255 4.104776 CGGTCCATTTTGATTCGGATTTG 58.895 43.478 0.00 0.00 0.00 2.32
255 256 3.865164 GGTCCATTTTGATTCGGATTTGC 59.135 43.478 0.00 0.00 0.00 3.68
256 257 3.547468 GTCCATTTTGATTCGGATTTGCG 59.453 43.478 0.00 0.00 0.00 4.85
257 258 3.192422 TCCATTTTGATTCGGATTTGCGT 59.808 39.130 0.00 0.00 0.00 5.24
258 259 3.547468 CCATTTTGATTCGGATTTGCGTC 59.453 43.478 0.00 0.00 0.00 5.19
259 260 2.519002 TTTGATTCGGATTTGCGTCG 57.481 45.000 0.00 0.00 0.00 5.12
260 261 0.724549 TTGATTCGGATTTGCGTCGG 59.275 50.000 0.00 0.00 0.00 4.79
261 262 0.390603 TGATTCGGATTTGCGTCGGT 60.391 50.000 0.00 0.00 0.00 4.69
262 263 0.026285 GATTCGGATTTGCGTCGGTG 59.974 55.000 0.00 0.00 0.00 4.94
263 264 1.977594 ATTCGGATTTGCGTCGGTGC 61.978 55.000 0.00 0.00 0.00 5.01
264 265 4.499023 CGGATTTGCGTCGGTGCG 62.499 66.667 0.00 0.00 37.81 5.34
265 266 4.160635 GGATTTGCGTCGGTGCGG 62.161 66.667 0.00 0.00 37.81 5.69
266 267 3.115892 GATTTGCGTCGGTGCGGA 61.116 61.111 0.00 0.00 37.81 5.54
267 268 3.362851 GATTTGCGTCGGTGCGGAC 62.363 63.158 0.00 0.00 37.81 4.79
268 269 4.893601 TTTGCGTCGGTGCGGACA 62.894 61.111 9.96 0.00 36.73 4.02
277 278 3.371063 GTGCGGACACGAGGAGGA 61.371 66.667 0.63 0.00 44.60 3.71
278 279 3.371063 TGCGGACACGAGGAGGAC 61.371 66.667 0.00 0.00 44.60 3.85
279 280 4.477975 GCGGACACGAGGAGGACG 62.478 72.222 0.00 0.00 44.60 4.79
280 281 4.477975 CGGACACGAGGAGGACGC 62.478 72.222 0.00 0.00 44.60 5.19
305 306 4.840005 CGCGCCTTCTCCTTCCCC 62.840 72.222 0.00 0.00 0.00 4.81
306 307 4.840005 GCGCCTTCTCCTTCCCCG 62.840 72.222 0.00 0.00 0.00 5.73
307 308 4.162690 CGCCTTCTCCTTCCCCGG 62.163 72.222 0.00 0.00 0.00 5.73
308 309 3.798511 GCCTTCTCCTTCCCCGGG 61.799 72.222 15.80 15.80 0.00 5.73
309 310 3.798511 CCTTCTCCTTCCCCGGGC 61.799 72.222 17.73 0.00 0.00 6.13
310 311 3.798511 CTTCTCCTTCCCCGGGCC 61.799 72.222 17.73 0.00 0.00 5.80
331 332 3.695606 TGCTCGGTGGCAGACTCC 61.696 66.667 0.00 0.00 37.29 3.85
332 333 3.695606 GCTCGGTGGCAGACTCCA 61.696 66.667 0.00 0.00 32.91 3.86
339 340 3.650647 TGGCAGACTCCACCAATTC 57.349 52.632 0.00 0.00 0.00 2.17
340 341 0.038166 TGGCAGACTCCACCAATTCC 59.962 55.000 0.00 0.00 0.00 3.01
341 342 0.681243 GGCAGACTCCACCAATTCCC 60.681 60.000 0.00 0.00 0.00 3.97
342 343 0.329596 GCAGACTCCACCAATTCCCT 59.670 55.000 0.00 0.00 0.00 4.20
343 344 1.680249 GCAGACTCCACCAATTCCCTC 60.680 57.143 0.00 0.00 0.00 4.30
344 345 1.912043 CAGACTCCACCAATTCCCTCT 59.088 52.381 0.00 0.00 0.00 3.69
345 346 3.107601 CAGACTCCACCAATTCCCTCTA 58.892 50.000 0.00 0.00 0.00 2.43
346 347 3.713764 CAGACTCCACCAATTCCCTCTAT 59.286 47.826 0.00 0.00 0.00 1.98
347 348 3.970640 AGACTCCACCAATTCCCTCTATC 59.029 47.826 0.00 0.00 0.00 2.08
348 349 3.049344 ACTCCACCAATTCCCTCTATCC 58.951 50.000 0.00 0.00 0.00 2.59
349 350 2.373502 CTCCACCAATTCCCTCTATCCC 59.626 54.545 0.00 0.00 0.00 3.85
350 351 1.425448 CCACCAATTCCCTCTATCCCC 59.575 57.143 0.00 0.00 0.00 4.81
351 352 1.425448 CACCAATTCCCTCTATCCCCC 59.575 57.143 0.00 0.00 0.00 5.40
368 369 4.360405 CCCCCAGAAACCCACCCG 62.360 72.222 0.00 0.00 0.00 5.28
401 402 4.974721 GCCCCATACCCGCCATGG 62.975 72.222 7.63 7.63 42.30 3.66
402 403 3.174987 CCCCATACCCGCCATGGA 61.175 66.667 18.40 0.00 44.95 3.41
403 404 2.113139 CCCATACCCGCCATGGAC 59.887 66.667 18.40 5.97 44.95 4.02
404 405 2.280797 CCATACCCGCCATGGACG 60.281 66.667 18.40 18.22 44.95 4.79
405 406 2.802724 CCATACCCGCCATGGACGA 61.803 63.158 24.22 9.66 44.95 4.20
406 407 1.371183 CATACCCGCCATGGACGAT 59.629 57.895 24.22 16.10 42.00 3.73
407 408 0.950555 CATACCCGCCATGGACGATG 60.951 60.000 24.22 17.24 42.00 3.84
408 409 1.118965 ATACCCGCCATGGACGATGA 61.119 55.000 24.22 12.15 42.00 2.92
409 410 2.023414 TACCCGCCATGGACGATGAC 62.023 60.000 24.22 2.09 42.00 3.06
410 411 2.588877 CCGCCATGGACGATGACC 60.589 66.667 24.22 1.39 42.00 4.02
411 412 2.501128 CGCCATGGACGATGACCT 59.499 61.111 18.40 0.00 33.31 3.85
412 413 1.592669 CGCCATGGACGATGACCTC 60.593 63.158 18.40 0.00 33.31 3.85
475 476 1.599047 CAGGAGGTCATCAACGCCT 59.401 57.895 0.00 0.00 34.65 5.52
478 479 1.375908 GAGGTCATCAACGCCTGCA 60.376 57.895 0.00 0.00 31.89 4.41
482 483 1.079197 TCATCAACGCCTGCATCGT 60.079 52.632 8.14 8.14 42.54 3.73
491 492 2.108514 CCTGCATCGTGGCGACAAT 61.109 57.895 0.00 0.00 46.06 2.71
494 495 0.952984 TGCATCGTGGCGACAATGAA 60.953 50.000 7.13 0.00 46.06 2.57
495 496 0.521242 GCATCGTGGCGACAATGAAC 60.521 55.000 7.13 0.00 46.06 3.18
498 499 0.597898 TCGTGGCGACAATGAACGAA 60.598 50.000 0.00 0.00 46.06 3.85
501 502 0.882484 TGGCGACAATGAACGAAGCA 60.882 50.000 0.00 0.00 37.44 3.91
524 525 6.157211 CACTCTATATGCTAGGGTTAAACCG 58.843 44.000 3.26 0.00 39.83 4.44
541 542 2.701780 CGTGGCTAGCACGGTCTCT 61.702 63.158 23.41 0.00 41.76 3.10
598 610 1.832912 GCCTTCCCTCGGATGATGT 59.167 57.895 0.00 0.00 0.00 3.06
659 671 1.080025 GCTTTCACGTCTACCCGCT 60.080 57.895 0.00 0.00 0.00 5.52
705 717 2.671070 CCCGAGGTGAGCATGGTT 59.329 61.111 0.00 0.00 0.00 3.67
877 891 0.731514 CGGCGACAACGACTACATGT 60.732 55.000 0.00 2.69 46.46 3.21
924 938 1.379576 GGCTGCTGGCTTTGATCCT 60.380 57.895 10.05 0.00 41.46 3.24
997 1011 1.524621 AATGAAGATCAGGCGGCCG 60.525 57.895 24.05 24.05 0.00 6.13
1045 1059 2.282958 ACGGCTTCCCTCTCGACA 60.283 61.111 0.00 0.00 0.00 4.35
1057 1071 3.056536 CCCTCTCGACAATGAGTTTCTGA 60.057 47.826 0.00 0.00 37.28 3.27
1072 1086 1.760192 TCTGAAGGACTACGGGCTAC 58.240 55.000 0.00 0.00 0.00 3.58
1083 1097 0.971447 ACGGGCTACAGGAAGAGGAC 60.971 60.000 0.00 0.00 0.00 3.85
1084 1098 1.817209 GGGCTACAGGAAGAGGACG 59.183 63.158 0.00 0.00 0.00 4.79
1085 1099 0.683504 GGGCTACAGGAAGAGGACGA 60.684 60.000 0.00 0.00 0.00 4.20
1086 1100 0.741915 GGCTACAGGAAGAGGACGAG 59.258 60.000 0.00 0.00 0.00 4.18
1087 1101 1.465794 GCTACAGGAAGAGGACGAGT 58.534 55.000 0.00 0.00 0.00 4.18
1088 1102 1.133407 GCTACAGGAAGAGGACGAGTG 59.867 57.143 0.00 0.00 0.00 3.51
1185 1199 2.282745 AGCAAGCAGACCAAGGCC 60.283 61.111 0.00 0.00 0.00 5.19
1210 1224 2.464459 GCGGCCGAGGACAAGATTG 61.464 63.158 33.48 0.00 0.00 2.67
1345 1361 2.478894 CCATACCAAATAGTAAGCGCGG 59.521 50.000 8.83 0.00 0.00 6.46
1369 1386 0.109532 TGGGTGTCCATTTCGAAGCA 59.890 50.000 0.00 0.00 38.32 3.91
1493 1517 0.755327 AAGCCGCCCTCTTTTGTGTT 60.755 50.000 0.00 0.00 0.00 3.32
1510 1537 9.248291 CTTTTGTGTTATCAAGTTTATGCTTGT 57.752 29.630 5.84 0.00 44.41 3.16
1569 1597 6.979817 TGCATGAAATACATTTGTAGGCATTC 59.020 34.615 0.00 0.75 37.07 2.67
1628 1656 2.108952 AGTGCTTCAACCTCTCCCATTT 59.891 45.455 0.00 0.00 0.00 2.32
1668 1696 0.326264 AGGAGAAGTTCAAGGCGCAT 59.674 50.000 10.83 0.00 0.00 4.73
1684 1712 0.819259 GCATTATGCCGCCCTCAAGA 60.819 55.000 5.80 0.00 37.42 3.02
1838 1867 4.705110 TGATGACCAAGAAGGACTCAAA 57.295 40.909 0.00 0.00 41.22 2.69
1906 1935 1.135960 GGAGATCCAAAGGAGGAGGG 58.864 60.000 0.00 0.00 41.90 4.30
1955 1984 2.203126 GCTTGAGATGGAGGCGGG 60.203 66.667 0.00 0.00 0.00 6.13
1958 1987 2.037620 CTTGAGATGGAGGCGGGGAG 62.038 65.000 0.00 0.00 0.00 4.30
1985 2014 2.890311 CCAAGATGCTAGAGATCGAGGT 59.110 50.000 0.00 0.00 0.00 3.85
2101 2141 0.107945 GGTTCGAGAAGATGCAGGCT 60.108 55.000 0.00 0.00 0.00 4.58
2212 2259 2.246739 CGCGATGGCATGGTCGAAT 61.247 57.895 12.75 0.00 40.11 3.34
2224 2272 1.418264 TGGTCGAATTCAAGTCCCACA 59.582 47.619 6.22 0.00 0.00 4.17
2286 2337 2.693762 CGCCAGCATGAACTGTGGG 61.694 63.158 0.00 0.00 39.69 4.61
2340 2394 4.197498 GCATGGTGCCGGCATGAC 62.197 66.667 35.23 25.28 37.42 3.06
2341 2395 3.879682 CATGGTGCCGGCATGACG 61.880 66.667 35.23 15.88 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.165270 GAATGGTCGTTGGGACTTGG 58.835 55.000 0.00 0.00 45.35 3.61
2 3 3.226884 CGAATGGTCGTTGGGACTT 57.773 52.632 0.00 0.00 45.35 3.01
12 13 3.873812 ATCCGGGGGCGAATGGTC 61.874 66.667 0.00 0.00 0.00 4.02
13 14 4.189580 CATCCGGGGGCGAATGGT 62.190 66.667 0.00 0.00 0.00 3.55
14 15 4.189580 ACATCCGGGGGCGAATGG 62.190 66.667 0.00 0.00 0.00 3.16
15 16 2.591715 GACATCCGGGGGCGAATG 60.592 66.667 0.00 0.00 0.00 2.67
16 17 3.873812 GGACATCCGGGGGCGAAT 61.874 66.667 0.00 0.00 0.00 3.34
26 27 1.089481 TGCGAAATGAGCGGACATCC 61.089 55.000 0.00 0.00 37.44 3.51
27 28 2.383170 TGCGAAATGAGCGGACATC 58.617 52.632 0.00 0.00 37.44 3.06
28 29 4.615901 TGCGAAATGAGCGGACAT 57.384 50.000 0.00 0.00 37.44 3.06
31 32 2.032634 GTGGTGCGAAATGAGCGGA 61.033 57.895 0.00 0.00 37.44 5.54
32 33 1.851021 TTGTGGTGCGAAATGAGCGG 61.851 55.000 0.00 0.00 37.44 5.52
33 34 0.040514 TTTGTGGTGCGAAATGAGCG 60.041 50.000 0.00 0.00 37.44 5.03
34 35 1.408422 GTTTGTGGTGCGAAATGAGC 58.592 50.000 0.00 0.00 0.00 4.26
35 36 1.262950 TCGTTTGTGGTGCGAAATGAG 59.737 47.619 0.00 0.00 0.00 2.90
36 37 1.300481 TCGTTTGTGGTGCGAAATGA 58.700 45.000 0.00 0.00 0.00 2.57
37 38 1.778591 GTTCGTTTGTGGTGCGAAATG 59.221 47.619 0.00 0.00 44.46 2.32
38 39 1.402259 TGTTCGTTTGTGGTGCGAAAT 59.598 42.857 0.00 0.00 44.46 2.17
39 40 0.803117 TGTTCGTTTGTGGTGCGAAA 59.197 45.000 0.00 0.00 44.46 3.46
40 41 0.803117 TTGTTCGTTTGTGGTGCGAA 59.197 45.000 0.00 0.00 41.45 4.70
41 42 0.803117 TTTGTTCGTTTGTGGTGCGA 59.197 45.000 0.00 0.00 0.00 5.10
42 43 1.833860 ATTTGTTCGTTTGTGGTGCG 58.166 45.000 0.00 0.00 0.00 5.34
43 44 4.087930 CGAATATTTGTTCGTTTGTGGTGC 59.912 41.667 1.81 0.00 44.32 5.01
44 45 5.723319 CGAATATTTGTTCGTTTGTGGTG 57.277 39.130 1.81 0.00 44.32 4.17
54 55 6.747280 CCTCAAATGGACACGAATATTTGTTC 59.253 38.462 5.54 7.35 39.96 3.18
55 56 6.208599 ACCTCAAATGGACACGAATATTTGTT 59.791 34.615 5.54 0.00 39.96 2.83
56 57 5.710099 ACCTCAAATGGACACGAATATTTGT 59.290 36.000 2.21 2.21 39.96 2.83
57 58 6.094048 AGACCTCAAATGGACACGAATATTTG 59.906 38.462 0.78 0.78 40.23 2.32
58 59 6.094048 CAGACCTCAAATGGACACGAATATTT 59.906 38.462 0.00 0.00 0.00 1.40
59 60 5.586243 CAGACCTCAAATGGACACGAATATT 59.414 40.000 0.00 0.00 0.00 1.28
60 61 5.118990 CAGACCTCAAATGGACACGAATAT 58.881 41.667 0.00 0.00 0.00 1.28
61 62 4.503910 CAGACCTCAAATGGACACGAATA 58.496 43.478 0.00 0.00 0.00 1.75
62 63 3.338249 CAGACCTCAAATGGACACGAAT 58.662 45.455 0.00 0.00 0.00 3.34
63 64 2.549992 CCAGACCTCAAATGGACACGAA 60.550 50.000 0.00 0.00 36.09 3.85
64 65 1.001974 CCAGACCTCAAATGGACACGA 59.998 52.381 0.00 0.00 36.09 4.35
65 66 1.442769 CCAGACCTCAAATGGACACG 58.557 55.000 0.00 0.00 36.09 4.49
66 67 1.168714 GCCAGACCTCAAATGGACAC 58.831 55.000 0.00 0.00 36.09 3.67
67 68 0.770499 TGCCAGACCTCAAATGGACA 59.230 50.000 0.00 0.00 36.09 4.02
68 69 2.134789 ATGCCAGACCTCAAATGGAC 57.865 50.000 0.00 0.00 36.09 4.02
69 70 2.449464 CAATGCCAGACCTCAAATGGA 58.551 47.619 0.00 0.00 36.09 3.41
70 71 1.479323 CCAATGCCAGACCTCAAATGG 59.521 52.381 0.00 0.00 37.15 3.16
71 72 1.479323 CCCAATGCCAGACCTCAAATG 59.521 52.381 0.00 0.00 0.00 2.32
72 73 1.077663 ACCCAATGCCAGACCTCAAAT 59.922 47.619 0.00 0.00 0.00 2.32
73 74 0.482446 ACCCAATGCCAGACCTCAAA 59.518 50.000 0.00 0.00 0.00 2.69
74 75 0.482446 AACCCAATGCCAGACCTCAA 59.518 50.000 0.00 0.00 0.00 3.02
75 76 0.251297 CAACCCAATGCCAGACCTCA 60.251 55.000 0.00 0.00 0.00 3.86
76 77 0.251341 ACAACCCAATGCCAGACCTC 60.251 55.000 0.00 0.00 0.00 3.85
77 78 0.251341 GACAACCCAATGCCAGACCT 60.251 55.000 0.00 0.00 0.00 3.85
78 79 1.250840 GGACAACCCAATGCCAGACC 61.251 60.000 0.00 0.00 34.14 3.85
79 80 0.251341 AGGACAACCCAATGCCAGAC 60.251 55.000 0.00 0.00 37.41 3.51
80 81 0.482446 AAGGACAACCCAATGCCAGA 59.518 50.000 0.00 0.00 37.41 3.86
81 82 2.094675 CTAAGGACAACCCAATGCCAG 58.905 52.381 0.00 0.00 37.41 4.85
82 83 1.707989 TCTAAGGACAACCCAATGCCA 59.292 47.619 0.00 0.00 37.41 4.92
83 84 2.369394 CTCTAAGGACAACCCAATGCC 58.631 52.381 0.00 0.00 37.41 4.40
84 85 1.745653 GCTCTAAGGACAACCCAATGC 59.254 52.381 0.00 0.00 37.41 3.56
85 86 3.071874 TGCTCTAAGGACAACCCAATG 57.928 47.619 0.00 0.00 37.41 2.82
86 87 3.074538 AGTTGCTCTAAGGACAACCCAAT 59.925 43.478 0.00 0.00 43.68 3.16
87 88 2.441750 AGTTGCTCTAAGGACAACCCAA 59.558 45.455 0.00 0.00 43.68 4.12
88 89 2.038557 GAGTTGCTCTAAGGACAACCCA 59.961 50.000 0.00 0.00 43.68 4.51
89 90 2.701107 GAGTTGCTCTAAGGACAACCC 58.299 52.381 0.00 0.00 43.68 4.11
90 91 2.029290 TCGAGTTGCTCTAAGGACAACC 60.029 50.000 0.00 0.00 43.68 3.77
91 92 3.299340 TCGAGTTGCTCTAAGGACAAC 57.701 47.619 0.00 0.00 43.12 3.32
92 93 3.650139 GTTCGAGTTGCTCTAAGGACAA 58.350 45.455 0.00 0.00 0.00 3.18
93 94 2.351447 CGTTCGAGTTGCTCTAAGGACA 60.351 50.000 0.00 0.00 0.00 4.02
94 95 2.095364 TCGTTCGAGTTGCTCTAAGGAC 60.095 50.000 2.98 0.00 29.61 3.85
95 96 2.156917 TCGTTCGAGTTGCTCTAAGGA 58.843 47.619 2.98 2.98 31.21 3.36
96 97 2.520979 CTCGTTCGAGTTGCTCTAAGG 58.479 52.381 13.18 0.00 0.00 2.69
97 98 2.520979 CCTCGTTCGAGTTGCTCTAAG 58.479 52.381 18.59 0.00 0.00 2.18
98 99 1.402456 GCCTCGTTCGAGTTGCTCTAA 60.402 52.381 18.59 0.00 0.00 2.10
99 100 0.170561 GCCTCGTTCGAGTTGCTCTA 59.829 55.000 18.59 0.00 0.00 2.43
100 101 1.080434 GCCTCGTTCGAGTTGCTCT 60.080 57.895 18.59 0.00 0.00 4.09
101 102 2.095252 GGCCTCGTTCGAGTTGCTC 61.095 63.158 18.59 8.17 0.00 4.26
102 103 2.048127 GGCCTCGTTCGAGTTGCT 60.048 61.111 18.59 0.00 0.00 3.91
103 104 2.357034 TGGCCTCGTTCGAGTTGC 60.357 61.111 18.59 15.35 0.00 4.17
104 105 2.027625 GGTGGCCTCGTTCGAGTTG 61.028 63.158 18.59 7.57 0.00 3.16
105 106 2.342648 GGTGGCCTCGTTCGAGTT 59.657 61.111 18.59 0.00 0.00 3.01
106 107 3.692406 GGGTGGCCTCGTTCGAGT 61.692 66.667 18.59 0.00 0.00 4.18
107 108 2.521958 AATGGGTGGCCTCGTTCGAG 62.522 60.000 14.26 14.26 0.00 4.04
108 109 2.119484 AAATGGGTGGCCTCGTTCGA 62.119 55.000 3.32 0.00 0.00 3.71
109 110 1.644786 GAAATGGGTGGCCTCGTTCG 61.645 60.000 3.32 0.00 0.00 3.95
110 111 1.644786 CGAAATGGGTGGCCTCGTTC 61.645 60.000 3.32 1.97 0.00 3.95
111 112 1.674322 CGAAATGGGTGGCCTCGTT 60.674 57.895 3.32 0.00 0.00 3.85
112 113 2.046314 CGAAATGGGTGGCCTCGT 60.046 61.111 3.32 0.00 0.00 4.18
113 114 2.046314 ACGAAATGGGTGGCCTCG 60.046 61.111 3.32 5.40 35.68 4.63
114 115 1.749258 GGACGAAATGGGTGGCCTC 60.749 63.158 3.32 0.00 0.00 4.70
115 116 2.355115 GGACGAAATGGGTGGCCT 59.645 61.111 3.32 0.00 0.00 5.19
116 117 3.131478 CGGACGAAATGGGTGGCC 61.131 66.667 0.00 0.00 0.00 5.36
117 118 3.810896 GCGGACGAAATGGGTGGC 61.811 66.667 0.00 0.00 0.00 5.01
118 119 2.046314 AGCGGACGAAATGGGTGG 60.046 61.111 0.00 0.00 0.00 4.61
119 120 2.398554 CCAGCGGACGAAATGGGTG 61.399 63.158 0.00 0.00 0.00 4.61
120 121 2.046314 CCAGCGGACGAAATGGGT 60.046 61.111 0.00 0.00 0.00 4.51
121 122 3.508840 GCCAGCGGACGAAATGGG 61.509 66.667 11.26 0.00 33.23 4.00
122 123 3.864686 CGCCAGCGGACGAAATGG 61.865 66.667 3.61 1.37 35.56 3.16
123 124 3.083600 GACGCCAGCGGACGAAATG 62.084 63.158 17.33 0.00 44.69 2.32
124 125 2.813908 GACGCCAGCGGACGAAAT 60.814 61.111 17.33 0.00 44.69 2.17
134 135 2.593436 AACCCAAACGGACGCCAG 60.593 61.111 0.00 0.00 34.64 4.85
135 136 2.902846 CAACCCAAACGGACGCCA 60.903 61.111 0.00 0.00 34.64 5.69
136 137 3.666253 CCAACCCAAACGGACGCC 61.666 66.667 0.00 0.00 34.64 5.68
137 138 4.337060 GCCAACCCAAACGGACGC 62.337 66.667 0.00 0.00 34.64 5.19
138 139 2.902846 TGCCAACCCAAACGGACG 60.903 61.111 0.00 0.00 34.64 4.79
139 140 2.070654 CTGTGCCAACCCAAACGGAC 62.071 60.000 0.00 0.00 34.64 4.79
140 141 1.826054 CTGTGCCAACCCAAACGGA 60.826 57.895 0.00 0.00 34.64 4.69
141 142 1.826054 TCTGTGCCAACCCAAACGG 60.826 57.895 0.00 0.00 37.81 4.44
142 143 1.358759 GTCTGTGCCAACCCAAACG 59.641 57.895 0.00 0.00 0.00 3.60
143 144 0.102300 GTGTCTGTGCCAACCCAAAC 59.898 55.000 0.00 0.00 0.00 2.93
144 145 0.323816 TGTGTCTGTGCCAACCCAAA 60.324 50.000 0.00 0.00 0.00 3.28
145 146 0.323816 TTGTGTCTGTGCCAACCCAA 60.324 50.000 0.00 0.00 0.00 4.12
146 147 0.323816 TTTGTGTCTGTGCCAACCCA 60.324 50.000 0.00 0.00 0.00 4.51
147 148 0.820871 TTTTGTGTCTGTGCCAACCC 59.179 50.000 0.00 0.00 0.00 4.11
148 149 1.476488 ACTTTTGTGTCTGTGCCAACC 59.524 47.619 0.00 0.00 0.00 3.77
149 150 2.791158 CGACTTTTGTGTCTGTGCCAAC 60.791 50.000 0.00 0.00 35.00 3.77
150 151 1.400142 CGACTTTTGTGTCTGTGCCAA 59.600 47.619 0.00 0.00 35.00 4.52
151 152 1.013596 CGACTTTTGTGTCTGTGCCA 58.986 50.000 0.00 0.00 35.00 4.92
152 153 0.307760 CCGACTTTTGTGTCTGTGCC 59.692 55.000 0.00 0.00 35.00 5.01
153 154 0.317020 GCCGACTTTTGTGTCTGTGC 60.317 55.000 0.00 0.00 35.00 4.57
154 155 0.307760 GGCCGACTTTTGTGTCTGTG 59.692 55.000 0.00 0.00 35.00 3.66
155 156 0.818040 GGGCCGACTTTTGTGTCTGT 60.818 55.000 0.00 0.00 35.00 3.41
156 157 0.817634 TGGGCCGACTTTTGTGTCTG 60.818 55.000 0.00 0.00 35.00 3.51
157 158 0.106918 TTGGGCCGACTTTTGTGTCT 60.107 50.000 0.00 0.00 35.00 3.41
158 159 0.030235 GTTGGGCCGACTTTTGTGTC 59.970 55.000 17.07 0.00 0.00 3.67
159 160 1.720694 CGTTGGGCCGACTTTTGTGT 61.721 55.000 21.44 0.00 0.00 3.72
160 161 1.008995 CGTTGGGCCGACTTTTGTG 60.009 57.895 21.44 1.08 0.00 3.33
161 162 2.841160 GCGTTGGGCCGACTTTTGT 61.841 57.895 21.44 0.00 34.80 2.83
162 163 2.050442 GCGTTGGGCCGACTTTTG 60.050 61.111 21.44 7.22 34.80 2.44
163 164 3.656045 CGCGTTGGGCCGACTTTT 61.656 61.111 21.44 0.00 38.94 2.27
173 174 3.283684 TTTGGGTCAGCGCGTTGG 61.284 61.111 22.99 5.26 0.00 3.77
174 175 2.051345 GTTTGGGTCAGCGCGTTG 60.051 61.111 17.58 17.58 0.00 4.10
175 176 3.645975 CGTTTGGGTCAGCGCGTT 61.646 61.111 8.43 0.00 0.00 4.84
223 224 0.326927 AAAATGGACCGACGATGGGT 59.673 50.000 0.00 0.00 41.48 4.51
224 225 0.732571 CAAAATGGACCGACGATGGG 59.267 55.000 0.00 0.00 0.00 4.00
225 226 1.732941 TCAAAATGGACCGACGATGG 58.267 50.000 0.00 0.00 0.00 3.51
226 227 3.544048 CGAATCAAAATGGACCGACGATG 60.544 47.826 0.00 0.00 0.00 3.84
227 228 2.607635 CGAATCAAAATGGACCGACGAT 59.392 45.455 0.00 0.00 0.00 3.73
228 229 1.996898 CGAATCAAAATGGACCGACGA 59.003 47.619 0.00 0.00 0.00 4.20
229 230 1.062002 CCGAATCAAAATGGACCGACG 59.938 52.381 0.00 0.00 0.00 5.12
230 231 2.352388 TCCGAATCAAAATGGACCGAC 58.648 47.619 0.00 0.00 0.00 4.79
231 232 2.772077 TCCGAATCAAAATGGACCGA 57.228 45.000 0.00 0.00 0.00 4.69
232 233 4.104776 CAAATCCGAATCAAAATGGACCG 58.895 43.478 0.00 0.00 32.33 4.79
233 234 3.865164 GCAAATCCGAATCAAAATGGACC 59.135 43.478 0.00 0.00 32.33 4.46
234 235 3.547468 CGCAAATCCGAATCAAAATGGAC 59.453 43.478 0.00 0.00 32.33 4.02
235 236 3.192422 ACGCAAATCCGAATCAAAATGGA 59.808 39.130 0.00 0.00 34.45 3.41
236 237 3.510719 ACGCAAATCCGAATCAAAATGG 58.489 40.909 0.00 0.00 0.00 3.16
237 238 3.238114 CGACGCAAATCCGAATCAAAATG 59.762 43.478 0.00 0.00 0.00 2.32
238 239 3.425404 CGACGCAAATCCGAATCAAAAT 58.575 40.909 0.00 0.00 0.00 1.82
239 240 2.413502 CCGACGCAAATCCGAATCAAAA 60.414 45.455 0.00 0.00 0.00 2.44
240 241 1.129624 CCGACGCAAATCCGAATCAAA 59.870 47.619 0.00 0.00 0.00 2.69
241 242 0.724549 CCGACGCAAATCCGAATCAA 59.275 50.000 0.00 0.00 0.00 2.57
242 243 0.390603 ACCGACGCAAATCCGAATCA 60.391 50.000 0.00 0.00 0.00 2.57
243 244 0.026285 CACCGACGCAAATCCGAATC 59.974 55.000 0.00 0.00 0.00 2.52
244 245 1.977594 GCACCGACGCAAATCCGAAT 61.978 55.000 0.00 0.00 0.00 3.34
245 246 2.673114 GCACCGACGCAAATCCGAA 61.673 57.895 0.00 0.00 0.00 4.30
246 247 3.115892 GCACCGACGCAAATCCGA 61.116 61.111 0.00 0.00 0.00 4.55
247 248 4.499023 CGCACCGACGCAAATCCG 62.499 66.667 0.00 0.00 0.00 4.18
248 249 4.160635 CCGCACCGACGCAAATCC 62.161 66.667 0.00 0.00 0.00 3.01
249 250 3.115892 TCCGCACCGACGCAAATC 61.116 61.111 0.00 0.00 0.00 2.17
250 251 3.419759 GTCCGCACCGACGCAAAT 61.420 61.111 0.00 0.00 0.00 2.32
251 252 4.893601 TGTCCGCACCGACGCAAA 62.894 61.111 0.00 0.00 35.40 3.68
258 259 4.778415 CTCCTCGTGTCCGCACCG 62.778 72.222 0.00 0.00 42.39 4.94
259 260 4.436998 CCTCCTCGTGTCCGCACC 62.437 72.222 0.00 0.00 42.39 5.01
260 261 3.371063 TCCTCCTCGTGTCCGCAC 61.371 66.667 0.00 0.00 41.97 5.34
261 262 3.371063 GTCCTCCTCGTGTCCGCA 61.371 66.667 0.00 0.00 0.00 5.69
262 263 4.477975 CGTCCTCCTCGTGTCCGC 62.478 72.222 0.00 0.00 0.00 5.54
263 264 4.477975 GCGTCCTCCTCGTGTCCG 62.478 72.222 0.00 0.00 0.00 4.79
264 265 4.477975 CGCGTCCTCCTCGTGTCC 62.478 72.222 0.00 0.00 34.71 4.02
288 289 4.840005 GGGGAAGGAGAAGGCGCG 62.840 72.222 0.00 0.00 0.00 6.86
289 290 4.840005 CGGGGAAGGAGAAGGCGC 62.840 72.222 0.00 0.00 0.00 6.53
290 291 4.162690 CCGGGGAAGGAGAAGGCG 62.163 72.222 0.00 0.00 0.00 5.52
291 292 3.798511 CCCGGGGAAGGAGAAGGC 61.799 72.222 14.71 0.00 0.00 4.35
292 293 3.798511 GCCCGGGGAAGGAGAAGG 61.799 72.222 25.28 0.00 0.00 3.46
293 294 3.798511 GGCCCGGGGAAGGAGAAG 61.799 72.222 25.28 0.00 0.00 2.85
314 315 3.695606 GGAGTCTGCCACCGAGCA 61.696 66.667 0.00 0.00 41.46 4.26
315 316 3.695606 TGGAGTCTGCCACCGAGC 61.696 66.667 0.00 0.00 31.66 5.03
321 322 0.038166 GGAATTGGTGGAGTCTGCCA 59.962 55.000 2.76 2.76 35.02 4.92
322 323 0.681243 GGGAATTGGTGGAGTCTGCC 60.681 60.000 0.00 0.00 0.00 4.85
323 324 0.329596 AGGGAATTGGTGGAGTCTGC 59.670 55.000 0.00 0.00 0.00 4.26
324 325 1.912043 AGAGGGAATTGGTGGAGTCTG 59.088 52.381 0.00 0.00 0.00 3.51
325 326 2.350863 AGAGGGAATTGGTGGAGTCT 57.649 50.000 0.00 0.00 0.00 3.24
326 327 3.071747 GGATAGAGGGAATTGGTGGAGTC 59.928 52.174 0.00 0.00 0.00 3.36
327 328 3.049344 GGATAGAGGGAATTGGTGGAGT 58.951 50.000 0.00 0.00 0.00 3.85
328 329 2.373502 GGGATAGAGGGAATTGGTGGAG 59.626 54.545 0.00 0.00 0.00 3.86
329 330 2.418669 GGGATAGAGGGAATTGGTGGA 58.581 52.381 0.00 0.00 0.00 4.02
330 331 1.425448 GGGGATAGAGGGAATTGGTGG 59.575 57.143 0.00 0.00 0.00 4.61
331 332 1.425448 GGGGGATAGAGGGAATTGGTG 59.575 57.143 0.00 0.00 0.00 4.17
332 333 1.834540 GGGGGATAGAGGGAATTGGT 58.165 55.000 0.00 0.00 0.00 3.67
351 352 4.360405 CGGGTGGGTTTCTGGGGG 62.360 72.222 0.00 0.00 0.00 5.40
384 385 4.974721 CCATGGCGGGTATGGGGC 62.975 72.222 0.00 0.00 41.11 5.80
385 386 3.174987 TCCATGGCGGGTATGGGG 61.175 66.667 6.96 0.00 44.18 4.96
386 387 2.113139 GTCCATGGCGGGTATGGG 59.887 66.667 6.96 0.00 44.18 4.00
387 388 2.111999 ATCGTCCATGGCGGGTATGG 62.112 60.000 22.59 0.00 45.17 2.74
388 389 0.950555 CATCGTCCATGGCGGGTATG 60.951 60.000 22.59 16.60 34.36 2.39
389 390 1.118965 TCATCGTCCATGGCGGGTAT 61.119 55.000 22.59 10.61 32.64 2.73
390 391 1.758906 TCATCGTCCATGGCGGGTA 60.759 57.895 22.59 9.06 32.64 3.69
391 392 3.080765 TCATCGTCCATGGCGGGT 61.081 61.111 22.59 12.63 32.64 5.28
392 393 2.588877 GTCATCGTCCATGGCGGG 60.589 66.667 22.59 16.75 32.64 6.13
393 394 2.588877 GGTCATCGTCCATGGCGG 60.589 66.667 22.59 11.18 38.09 6.13
394 395 1.592669 GAGGTCATCGTCCATGGCG 60.593 63.158 18.73 18.73 38.09 5.69
395 396 1.592669 CGAGGTCATCGTCCATGGC 60.593 63.158 6.96 0.96 46.62 4.40
396 397 4.738198 CGAGGTCATCGTCCATGG 57.262 61.111 4.97 4.97 46.62 3.66
404 405 2.579787 CGCGGTGTCGAGGTCATC 60.580 66.667 0.00 0.00 39.00 2.92
405 406 4.796231 GCGCGGTGTCGAGGTCAT 62.796 66.667 8.83 0.00 39.00 3.06
467 468 2.741985 CCACGATGCAGGCGTTGA 60.742 61.111 13.86 0.00 40.44 3.18
475 476 0.952984 TTCATTGTCGCCACGATGCA 60.953 50.000 6.80 0.00 42.38 3.96
478 479 0.389296 TCGTTCATTGTCGCCACGAT 60.389 50.000 0.00 0.00 38.42 3.73
482 483 0.882484 TGCTTCGTTCATTGTCGCCA 60.882 50.000 0.00 0.00 0.00 5.69
487 488 5.235186 GCATATAGAGTGCTTCGTTCATTGT 59.765 40.000 0.00 0.00 39.45 2.71
498 499 6.239629 GGTTTAACCCTAGCATATAGAGTGCT 60.240 42.308 2.04 5.88 43.16 4.40
501 502 5.837438 ACGGTTTAACCCTAGCATATAGAGT 59.163 40.000 8.72 0.00 33.75 3.24
524 525 0.458716 GAAGAGACCGTGCTAGCCAC 60.459 60.000 13.29 9.58 41.15 5.01
595 607 4.778143 GGGCGAGTCGGGCAACAT 62.778 66.667 15.52 0.00 39.74 2.71
645 657 3.755628 GCCAGCGGGTAGACGTGA 61.756 66.667 4.36 0.00 36.17 4.35
809 823 4.953868 CGCCCGACAACACGTCCA 62.954 66.667 0.00 0.00 42.07 4.02
877 891 3.384789 CCACCCTCGAAGATCATGTTCTA 59.615 47.826 6.72 0.00 33.89 2.10
918 932 2.610479 GCTTTGTGTCTCGTCAGGATCA 60.610 50.000 0.00 0.00 0.00 2.92
924 938 0.249868 CCTGGCTTTGTGTCTCGTCA 60.250 55.000 0.00 0.00 0.00 4.35
997 1011 1.224075 CCGACCTGATCATGCATGAC 58.776 55.000 30.92 22.87 40.03 3.06
1045 1059 4.322801 CCCGTAGTCCTTCAGAAACTCATT 60.323 45.833 0.00 0.00 0.00 2.57
1057 1071 0.333993 TCCTGTAGCCCGTAGTCCTT 59.666 55.000 0.00 0.00 0.00 3.36
1072 1086 1.153939 CGCACTCGTCCTCTTCCTG 60.154 63.158 0.00 0.00 0.00 3.86
1083 1097 1.398762 CGATGTCACACTCGCACTCG 61.399 60.000 0.00 0.00 0.00 4.18
1084 1098 0.109735 TCGATGTCACACTCGCACTC 60.110 55.000 5.14 0.00 34.94 3.51
1085 1099 0.313987 TTCGATGTCACACTCGCACT 59.686 50.000 5.14 0.00 34.94 4.40
1086 1100 0.710567 CTTCGATGTCACACTCGCAC 59.289 55.000 5.14 0.00 34.94 5.34
1087 1101 0.388520 CCTTCGATGTCACACTCGCA 60.389 55.000 5.14 0.00 34.94 5.10
1088 1102 1.078759 CCCTTCGATGTCACACTCGC 61.079 60.000 5.14 0.00 34.94 5.03
1128 1142 1.377202 GATGGCTTGGTTGGCGAGA 60.377 57.895 0.00 0.00 35.06 4.04
1164 1178 1.611673 GCCTTGGTCTGCTTGCTCTTA 60.612 52.381 0.00 0.00 0.00 2.10
1207 1221 2.549754 CTCTCCAACACTCGCAAACAAT 59.450 45.455 0.00 0.00 0.00 2.71
1210 1224 1.527311 GTCTCTCCAACACTCGCAAAC 59.473 52.381 0.00 0.00 0.00 2.93
1256 1270 4.647424 AAGGTTGAATGCTTTTGTTCGA 57.353 36.364 0.00 0.00 0.00 3.71
1345 1361 1.304962 GAAATGGACACCCACCCCC 60.305 63.158 0.00 0.00 46.98 5.40
1369 1386 2.086869 CTTGTTGGATCACGCTCCATT 58.913 47.619 3.12 0.00 44.66 3.16
1376 1393 1.511850 TGCACTCTTGTTGGATCACG 58.488 50.000 0.00 0.00 0.00 4.35
1442 1460 0.251634 TGTCTTGCATGCCGATACCA 59.748 50.000 16.68 3.73 0.00 3.25
1510 1537 4.576216 AAATGGTATGCAAACGAACACA 57.424 36.364 0.00 0.00 0.00 3.72
1628 1656 4.081642 CCTCGTCTTTGATGACCCTAAAGA 60.082 45.833 0.00 0.00 37.91 2.52
1668 1696 1.153449 CGTCTTGAGGGCGGCATAA 60.153 57.895 12.47 0.00 0.00 1.90
1684 1712 1.525995 CTTGCTTCCCACCACACGT 60.526 57.895 0.00 0.00 0.00 4.49
1801 1830 1.852157 ATCATGCCCTCCACGGTTGT 61.852 55.000 0.00 0.00 0.00 3.32
1906 1935 1.656095 CTTCTCCGCGTTCATCTCAAC 59.344 52.381 4.92 0.00 0.00 3.18
1955 1984 0.107017 TAGCATCTTGGCTTGCCTCC 60.107 55.000 13.18 0.00 42.71 4.30
1958 1987 1.134280 TCTCTAGCATCTTGGCTTGCC 60.134 52.381 4.43 4.43 42.71 4.52
1985 2014 3.758973 TTGGTCTTGGCGTTGGCGA 62.759 57.895 0.00 0.00 41.24 5.54
2101 2141 1.000717 TCGTCGAACTTGAGCATGTCA 60.001 47.619 0.00 0.00 0.00 3.58
2267 2316 1.968017 CCACAGTTCATGCTGGCGT 60.968 57.895 5.48 0.00 40.59 5.68


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

AutoCloner maintained by Alex Coulton.