Multiple sequence alignment - TraesCS1D01G206700

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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 TraesCS1D01G206700 chr1D 100.000 3155 0 0 1 3155 292574086 292577240 0.000000e+00 5827
1 TraesCS1D01G206700 chr1D 84.434 424 55 7 2730 3152 324355263 324355676 1.050000e-109 407
2 TraesCS1D01G206700 chr1D 85.067 375 48 3 2780 3154 356856751 356857117 2.970000e-100 375
3 TraesCS1D01G206700 chr1D 88.971 136 6 1 95 230 292548055 292548181 3.260000e-35 159
4 TraesCS1D01G206700 chr1A 90.090 2341 112 35 655 2928 364655335 364657622 0.000000e+00 2928
5 TraesCS1D01G206700 chr1A 92.611 203 15 0 455 657 364654860 364655062 3.080000e-75 292
6 TraesCS1D01G206700 chr1A 93.464 153 4 1 282 434 364654145 364654291 4.100000e-54 222
7 TraesCS1D01G206700 chr1B 89.093 2182 132 29 1023 3152 393541569 393543696 0.000000e+00 2614
8 TraesCS1D01G206700 chr1B 92.607 257 11 5 291 543 393541125 393541377 2.310000e-96 363
9 TraesCS1D01G206700 chr1B 83.415 205 22 8 2950 3152 189687124 189687318 2.500000e-41 180
10 TraesCS1D01G206700 chr1B 91.473 129 3 2 102 230 554145101 554144981 1.500000e-38 171
11 TraesCS1D01G206700 chr6D 85.986 421 51 3 2732 3152 368727074 368727486 8.030000e-121 444
12 TraesCS1D01G206700 chr2D 85.273 421 54 3 2732 3152 602651963 602652375 8.090000e-116 427
13 TraesCS1D01G206700 chr4D 85.106 423 55 3 2730 3152 387000010 387000424 2.910000e-115 425
14 TraesCS1D01G206700 chr4D 85.132 417 51 6 2732 3146 363704733 363704326 1.750000e-112 416
15 TraesCS1D01G206700 chr4D 83.726 424 59 5 2732 3155 295858708 295858295 2.950000e-105 392
16 TraesCS1D01G206700 chr3D 85.273 421 50 7 2732 3150 517603509 517603919 1.050000e-114 424
17 TraesCS1D01G206700 chr3D 84.670 424 55 5 2730 3152 445347764 445348178 6.300000e-112 414
18 TraesCS1D01G206700 chr3D 84.561 421 55 4 2732 3152 480388478 480388888 2.930000e-110 409
19 TraesCS1D01G206700 chr3D 84.086 421 59 3 2732 3152 81861393 81861805 1.760000e-107 399
20 TraesCS1D01G206700 chr3B 84.941 425 54 8 2732 3155 309717846 309717431 3.760000e-114 422
21 TraesCS1D01G206700 chr3B 91.473 129 3 2 102 230 770075779 770075659 1.500000e-38 171
22 TraesCS1D01G206700 chr3B 96.875 96 3 0 102 197 770050970 770050875 9.060000e-36 161
23 TraesCS1D01G206700 chr5B 84.434 424 57 4 2732 3155 581241893 581241479 2.930000e-110 409
24 TraesCS1D01G206700 chr2B 83.886 422 58 3 2732 3152 236298380 236297968 8.200000e-106 394
25 TraesCS1D01G206700 chr2B 90.099 101 8 1 1 101 747758273 747758175 2.550000e-26 130
26 TraesCS1D01G206700 chr7B 88.364 275 28 4 2730 3002 287074841 287074569 8.440000e-86 327
27 TraesCS1D01G206700 chr4B 80.203 394 64 10 1642 2028 618159101 618159487 1.850000e-72 283
28 TraesCS1D01G206700 chr4B 85.375 253 34 1 1775 2027 617766470 617766719 3.120000e-65 259
29 TraesCS1D01G206700 chr4B 90.769 130 4 1 101 230 129057098 129056977 1.950000e-37 167
30 TraesCS1D01G206700 chr5A 84.980 253 35 1 1775 2027 665817375 665817624 1.450000e-63 254
31 TraesCS1D01G206700 chr3A 91.473 129 3 2 102 230 742905688 742905568 1.500000e-38 171
32 TraesCS1D01G206700 chr3A 91.473 129 3 2 102 230 742912359 742912239 1.500000e-38 171
33 TraesCS1D01G206700 chr3A 90.526 95 7 1 7 101 611180958 611180866 1.190000e-24 124
34 TraesCS1D01G206700 chr6B 90.000 130 8 4 102 230 134457727 134457852 2.520000e-36 163
35 TraesCS1D01G206700 chr6B 87.692 130 11 4 102 230 134464822 134464947 2.540000e-31 147
36 TraesCS1D01G206700 chr6A 88.321 137 7 1 94 230 546609403 546609276 4.210000e-34 156
37 TraesCS1D01G206700 chr6A 87.324 142 8 2 94 235 546602414 546602283 1.520000e-33 154
38 TraesCS1D01G206700 chr6A 86.154 130 9 4 101 230 596708557 596708437 7.100000e-27 132
39 TraesCS1D01G206700 chr6A 90.099 101 8 1 1 101 305474046 305474144 2.550000e-26 130
40 TraesCS1D01G206700 chr6A 89.899 99 8 1 3 101 305480864 305480960 3.300000e-25 126
41 TraesCS1D01G206700 chr6A 89.109 101 9 1 1 101 464139631 464139729 1.190000e-24 124
42 TraesCS1D01G206700 chr6A 89.109 101 9 1 1 101 464146630 464146728 1.190000e-24 124
43 TraesCS1D01G206700 chr7A 88.235 136 7 1 95 230 280074612 280074738 1.520000e-33 154
44 TraesCS1D01G206700 chr7A 87.591 137 8 3 94 230 280090385 280090512 1.960000e-32 150
45 TraesCS1D01G206700 chrUn 86.131 137 10 4 94 230 32068665 32068792 4.240000e-29 139
46 TraesCS1D01G206700 chr2A 91.089 101 7 1 1 101 720437875 720437973 5.490000e-28 135
47 TraesCS1D01G206700 chr2A 90.099 101 8 1 1 101 720444334 720444432 2.550000e-26 130
48 TraesCS1D01G206700 chr4A 89.109 101 9 1 1 101 718845628 718845530 1.190000e-24 124


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 TraesCS1D01G206700 chr1D 292574086 292577240 3154 False 5827.000000 5827 100.000 1 3155 1 chr1D.!!$F2 3154
1 TraesCS1D01G206700 chr1A 364654145 364657622 3477 False 1147.333333 2928 92.055 282 2928 3 chr1A.!!$F1 2646
2 TraesCS1D01G206700 chr1B 393541125 393543696 2571 False 1488.500000 2614 90.850 291 3152 2 chr1B.!!$F2 2861

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
455 468 0.034059 CCCGTCAGCTCTGTCAAACT 59.966 55.0 0.0 0.0 0.00 2.66 F
1087 2019 0.034896 ACGCACCCGTCTTCAAGAAT 59.965 50.0 0.0 0.0 46.39 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2035 2992 0.037605 ACAACCGGGATTCGTGTCTC 60.038 55.0 6.32 0.0 37.11 3.36 R
2995 4033 0.099968 CAGCAATTCGGCAGACCATG 59.900 55.0 0.00 0.0 35.83 3.66 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
25 26 7.748691 AGTAGAAAGTAAAGAACGAGAGAGT 57.251 36.000 0.00 0.00 0.00 3.24
26 27 8.168790 AGTAGAAAGTAAAGAACGAGAGAGTT 57.831 34.615 0.00 0.00 36.99 3.01
27 28 8.631797 AGTAGAAAGTAAAGAACGAGAGAGTTT 58.368 33.333 0.00 0.00 34.00 2.66
28 29 7.701809 AGAAAGTAAAGAACGAGAGAGTTTG 57.298 36.000 0.00 0.00 34.00 2.93
29 30 7.490000 AGAAAGTAAAGAACGAGAGAGTTTGA 58.510 34.615 0.00 0.00 34.00 2.69
30 31 7.980099 AGAAAGTAAAGAACGAGAGAGTTTGAA 59.020 33.333 0.00 0.00 34.00 2.69
31 32 8.664211 AAAGTAAAGAACGAGAGAGTTTGAAT 57.336 30.769 0.00 0.00 34.00 2.57
32 33 9.760077 AAAGTAAAGAACGAGAGAGTTTGAATA 57.240 29.630 0.00 0.00 34.00 1.75
33 34 9.760077 AAGTAAAGAACGAGAGAGTTTGAATAA 57.240 29.630 0.00 0.00 34.00 1.40
34 35 9.760077 AGTAAAGAACGAGAGAGTTTGAATAAA 57.240 29.630 0.00 0.00 34.00 1.40
37 38 8.888579 AAGAACGAGAGAGTTTGAATAAAAGA 57.111 30.769 0.00 0.00 34.00 2.52
38 39 9.495572 AAGAACGAGAGAGTTTGAATAAAAGAT 57.504 29.630 0.00 0.00 34.00 2.40
39 40 8.930760 AGAACGAGAGAGTTTGAATAAAAGATG 58.069 33.333 0.00 0.00 34.00 2.90
40 41 8.833231 AACGAGAGAGTTTGAATAAAAGATGA 57.167 30.769 0.00 0.00 0.00 2.92
41 42 9.442047 AACGAGAGAGTTTGAATAAAAGATGAT 57.558 29.630 0.00 0.00 0.00 2.45
42 43 9.442047 ACGAGAGAGTTTGAATAAAAGATGATT 57.558 29.630 0.00 0.00 0.00 2.57
43 44 9.913451 CGAGAGAGTTTGAATAAAAGATGATTC 57.087 33.333 0.00 0.00 33.48 2.52
70 71 9.775854 ATCAGTCTTTATTGATGATAGAAGTGG 57.224 33.333 0.00 0.00 31.39 4.00
71 72 8.206867 TCAGTCTTTATTGATGATAGAAGTGGG 58.793 37.037 0.00 0.00 0.00 4.61
72 73 6.995091 AGTCTTTATTGATGATAGAAGTGGGC 59.005 38.462 0.00 0.00 0.00 5.36
73 74 6.995091 GTCTTTATTGATGATAGAAGTGGGCT 59.005 38.462 0.00 0.00 0.00 5.19
74 75 8.150945 GTCTTTATTGATGATAGAAGTGGGCTA 58.849 37.037 0.00 0.00 0.00 3.93
75 76 8.884323 TCTTTATTGATGATAGAAGTGGGCTAT 58.116 33.333 0.00 0.00 0.00 2.97
76 77 9.512588 CTTTATTGATGATAGAAGTGGGCTATT 57.487 33.333 0.00 0.00 0.00 1.73
77 78 9.866655 TTTATTGATGATAGAAGTGGGCTATTT 57.133 29.630 0.00 0.00 0.00 1.40
82 83 8.762645 TGATGATAGAAGTGGGCTATTTATAGG 58.237 37.037 0.00 0.00 0.00 2.57
83 84 8.917414 ATGATAGAAGTGGGCTATTTATAGGA 57.083 34.615 0.00 0.00 0.00 2.94
84 85 8.736097 TGATAGAAGTGGGCTATTTATAGGAA 57.264 34.615 0.00 0.00 0.00 3.36
85 86 8.816894 TGATAGAAGTGGGCTATTTATAGGAAG 58.183 37.037 0.00 0.00 0.00 3.46
86 87 6.441088 AGAAGTGGGCTATTTATAGGAAGG 57.559 41.667 0.00 0.00 0.00 3.46
87 88 4.642466 AGTGGGCTATTTATAGGAAGGC 57.358 45.455 0.00 0.00 0.00 4.35
88 89 3.008049 AGTGGGCTATTTATAGGAAGGCG 59.992 47.826 0.00 0.00 35.50 5.52
89 90 2.304761 TGGGCTATTTATAGGAAGGCGG 59.695 50.000 0.00 0.00 35.50 6.13
90 91 2.305052 GGGCTATTTATAGGAAGGCGGT 59.695 50.000 0.00 0.00 35.50 5.68
91 92 3.597255 GGCTATTTATAGGAAGGCGGTC 58.403 50.000 0.00 0.00 0.00 4.79
92 93 3.007614 GGCTATTTATAGGAAGGCGGTCA 59.992 47.826 0.00 0.00 0.00 4.02
93 94 4.504340 GGCTATTTATAGGAAGGCGGTCAA 60.504 45.833 0.00 0.00 0.00 3.18
94 95 4.691216 GCTATTTATAGGAAGGCGGTCAAG 59.309 45.833 0.00 0.00 0.00 3.02
95 96 4.772886 ATTTATAGGAAGGCGGTCAAGT 57.227 40.909 0.00 0.00 0.00 3.16
96 97 5.881923 ATTTATAGGAAGGCGGTCAAGTA 57.118 39.130 0.00 0.00 0.00 2.24
97 98 5.680594 TTTATAGGAAGGCGGTCAAGTAA 57.319 39.130 0.00 0.00 0.00 2.24
98 99 5.680594 TTATAGGAAGGCGGTCAAGTAAA 57.319 39.130 0.00 0.00 0.00 2.01
99 100 2.180432 AGGAAGGCGGTCAAGTAAAC 57.820 50.000 0.00 0.00 0.00 2.01
100 101 1.418637 AGGAAGGCGGTCAAGTAAACA 59.581 47.619 0.00 0.00 0.00 2.83
101 102 2.158726 AGGAAGGCGGTCAAGTAAACAA 60.159 45.455 0.00 0.00 0.00 2.83
102 103 2.619646 GGAAGGCGGTCAAGTAAACAAA 59.380 45.455 0.00 0.00 0.00 2.83
103 104 3.254903 GGAAGGCGGTCAAGTAAACAAAT 59.745 43.478 0.00 0.00 0.00 2.32
104 105 4.261867 GGAAGGCGGTCAAGTAAACAAATT 60.262 41.667 0.00 0.00 0.00 1.82
105 106 5.048573 GGAAGGCGGTCAAGTAAACAAATTA 60.049 40.000 0.00 0.00 0.00 1.40
106 107 5.366829 AGGCGGTCAAGTAAACAAATTAC 57.633 39.130 0.00 0.00 43.56 1.89
107 108 4.822896 AGGCGGTCAAGTAAACAAATTACA 59.177 37.500 1.68 0.00 45.29 2.41
108 109 5.475564 AGGCGGTCAAGTAAACAAATTACAT 59.524 36.000 1.68 0.00 45.29 2.29
109 110 6.655848 AGGCGGTCAAGTAAACAAATTACATA 59.344 34.615 1.68 0.00 45.29 2.29
110 111 6.964934 GGCGGTCAAGTAAACAAATTACATAG 59.035 38.462 1.68 0.00 45.29 2.23
111 112 7.361457 GGCGGTCAAGTAAACAAATTACATAGT 60.361 37.037 1.68 0.00 45.29 2.12
112 113 8.019094 GCGGTCAAGTAAACAAATTACATAGTT 58.981 33.333 1.68 0.00 45.29 2.24
113 114 9.325150 CGGTCAAGTAAACAAATTACATAGTTG 57.675 33.333 1.68 0.00 45.29 3.16
124 125 8.947115 ACAAATTACATAGTTGTCTTAAGAGCC 58.053 33.333 5.12 0.00 37.28 4.70
125 126 8.946085 CAAATTACATAGTTGTCTTAAGAGCCA 58.054 33.333 5.12 0.00 37.28 4.75
126 127 9.515226 AAATTACATAGTTGTCTTAAGAGCCAA 57.485 29.630 5.12 4.92 37.28 4.52
127 128 8.723942 ATTACATAGTTGTCTTAAGAGCCAAG 57.276 34.615 5.12 0.00 37.28 3.61
128 129 5.491982 ACATAGTTGTCTTAAGAGCCAAGG 58.508 41.667 5.12 1.44 0.00 3.61
129 130 5.248477 ACATAGTTGTCTTAAGAGCCAAGGA 59.752 40.000 5.12 0.00 0.00 3.36
130 131 4.706842 AGTTGTCTTAAGAGCCAAGGAA 57.293 40.909 5.12 0.00 0.00 3.36
131 132 4.646572 AGTTGTCTTAAGAGCCAAGGAAG 58.353 43.478 5.12 0.00 0.00 3.46
132 133 4.103311 AGTTGTCTTAAGAGCCAAGGAAGT 59.897 41.667 5.12 0.00 0.00 3.01
133 134 5.307196 AGTTGTCTTAAGAGCCAAGGAAGTA 59.693 40.000 5.12 0.00 0.00 2.24
134 135 5.148651 TGTCTTAAGAGCCAAGGAAGTAC 57.851 43.478 5.12 0.00 0.00 2.73
135 136 4.591498 TGTCTTAAGAGCCAAGGAAGTACA 59.409 41.667 5.12 0.00 0.00 2.90
136 137 5.248477 TGTCTTAAGAGCCAAGGAAGTACAT 59.752 40.000 5.12 0.00 0.00 2.29
137 138 5.582665 GTCTTAAGAGCCAAGGAAGTACATG 59.417 44.000 5.12 0.00 0.00 3.21
138 139 3.356529 AAGAGCCAAGGAAGTACATGG 57.643 47.619 0.00 0.00 36.00 3.66
139 140 2.269940 AGAGCCAAGGAAGTACATGGT 58.730 47.619 0.00 0.00 35.34 3.55
140 141 2.644798 AGAGCCAAGGAAGTACATGGTT 59.355 45.455 0.00 0.00 35.34 3.67
141 142 2.749621 GAGCCAAGGAAGTACATGGTTG 59.250 50.000 0.00 0.00 35.34 3.77
142 143 1.202348 GCCAAGGAAGTACATGGTTGC 59.798 52.381 0.00 0.00 35.34 4.17
143 144 2.795329 CCAAGGAAGTACATGGTTGCT 58.205 47.619 0.00 0.00 0.00 3.91
144 145 3.157087 CCAAGGAAGTACATGGTTGCTT 58.843 45.455 0.00 1.72 34.97 3.91
145 146 3.057315 CCAAGGAAGTACATGGTTGCTTG 60.057 47.826 21.68 21.68 46.19 4.01
146 147 3.788227 AGGAAGTACATGGTTGCTTGA 57.212 42.857 0.00 0.00 0.00 3.02
147 148 3.679389 AGGAAGTACATGGTTGCTTGAG 58.321 45.455 0.00 0.00 0.00 3.02
148 149 3.327757 AGGAAGTACATGGTTGCTTGAGA 59.672 43.478 0.00 0.00 0.00 3.27
149 150 4.072131 GGAAGTACATGGTTGCTTGAGAA 58.928 43.478 0.00 0.00 0.00 2.87
150 151 4.083271 GGAAGTACATGGTTGCTTGAGAAC 60.083 45.833 0.00 0.00 0.00 3.01
151 152 3.412386 AGTACATGGTTGCTTGAGAACC 58.588 45.455 0.00 0.00 42.90 3.62
163 164 4.954092 CTTGAGAACCAAGCAACCTATC 57.046 45.455 0.00 0.00 44.90 2.08
164 165 4.583871 CTTGAGAACCAAGCAACCTATCT 58.416 43.478 0.00 0.00 44.90 1.98
165 166 5.734720 CTTGAGAACCAAGCAACCTATCTA 58.265 41.667 0.00 0.00 44.90 1.98
166 167 5.755409 TGAGAACCAAGCAACCTATCTAA 57.245 39.130 0.00 0.00 0.00 2.10
167 168 5.488341 TGAGAACCAAGCAACCTATCTAAC 58.512 41.667 0.00 0.00 0.00 2.34
168 169 5.012664 TGAGAACCAAGCAACCTATCTAACA 59.987 40.000 0.00 0.00 0.00 2.41
169 170 5.876357 AGAACCAAGCAACCTATCTAACAA 58.124 37.500 0.00 0.00 0.00 2.83
170 171 6.485171 AGAACCAAGCAACCTATCTAACAAT 58.515 36.000 0.00 0.00 0.00 2.71
171 172 6.948309 AGAACCAAGCAACCTATCTAACAATT 59.052 34.615 0.00 0.00 0.00 2.32
172 173 6.515272 ACCAAGCAACCTATCTAACAATTG 57.485 37.500 3.24 3.24 0.00 2.32
173 174 6.245408 ACCAAGCAACCTATCTAACAATTGA 58.755 36.000 13.59 0.00 0.00 2.57
174 175 6.151144 ACCAAGCAACCTATCTAACAATTGAC 59.849 38.462 13.59 0.00 0.00 3.18
175 176 6.375455 CCAAGCAACCTATCTAACAATTGACT 59.625 38.462 13.59 1.05 0.00 3.41
176 177 7.094205 CCAAGCAACCTATCTAACAATTGACTT 60.094 37.037 13.59 0.00 0.00 3.01
177 178 8.946085 CAAGCAACCTATCTAACAATTGACTTA 58.054 33.333 13.59 0.24 0.00 2.24
178 179 9.515226 AAGCAACCTATCTAACAATTGACTTAA 57.485 29.630 13.59 0.00 0.00 1.85
179 180 9.686683 AGCAACCTATCTAACAATTGACTTAAT 57.313 29.630 13.59 1.82 0.00 1.40
180 181 9.937175 GCAACCTATCTAACAATTGACTTAATC 57.063 33.333 13.59 0.00 0.00 1.75
241 242 7.888250 TCTATTCTTAACAGAGATGAGAGCA 57.112 36.000 0.00 0.00 0.00 4.26
242 243 7.939782 TCTATTCTTAACAGAGATGAGAGCAG 58.060 38.462 0.00 0.00 0.00 4.24
243 244 4.998671 TCTTAACAGAGATGAGAGCAGG 57.001 45.455 0.00 0.00 0.00 4.85
244 245 4.604156 TCTTAACAGAGATGAGAGCAGGA 58.396 43.478 0.00 0.00 0.00 3.86
245 246 4.644234 TCTTAACAGAGATGAGAGCAGGAG 59.356 45.833 0.00 0.00 0.00 3.69
246 247 1.113788 ACAGAGATGAGAGCAGGAGC 58.886 55.000 0.00 0.00 42.56 4.70
247 248 1.112950 CAGAGATGAGAGCAGGAGCA 58.887 55.000 0.00 0.00 45.49 4.26
248 249 1.481363 CAGAGATGAGAGCAGGAGCAA 59.519 52.381 0.00 0.00 45.49 3.91
249 250 1.481772 AGAGATGAGAGCAGGAGCAAC 59.518 52.381 0.00 0.00 45.49 4.17
250 251 1.206610 GAGATGAGAGCAGGAGCAACA 59.793 52.381 0.00 0.00 45.49 3.33
251 252 1.627329 AGATGAGAGCAGGAGCAACAA 59.373 47.619 0.00 0.00 45.49 2.83
252 253 2.239150 AGATGAGAGCAGGAGCAACAAT 59.761 45.455 0.00 0.00 45.49 2.71
253 254 2.105006 TGAGAGCAGGAGCAACAATC 57.895 50.000 0.00 0.00 45.49 2.67
254 255 1.005340 GAGAGCAGGAGCAACAATCG 58.995 55.000 0.00 0.00 45.49 3.34
255 256 0.610174 AGAGCAGGAGCAACAATCGA 59.390 50.000 0.00 0.00 45.49 3.59
256 257 1.002430 AGAGCAGGAGCAACAATCGAA 59.998 47.619 0.00 0.00 45.49 3.71
257 258 1.806542 GAGCAGGAGCAACAATCGAAA 59.193 47.619 0.00 0.00 45.49 3.46
258 259 2.226437 GAGCAGGAGCAACAATCGAAAA 59.774 45.455 0.00 0.00 45.49 2.29
259 260 2.030805 AGCAGGAGCAACAATCGAAAAC 60.031 45.455 0.00 0.00 45.49 2.43
260 261 2.574322 CAGGAGCAACAATCGAAAACG 58.426 47.619 0.00 0.00 0.00 3.60
261 262 1.069227 AGGAGCAACAATCGAAAACGC 60.069 47.619 0.00 0.00 0.00 4.84
262 263 1.334599 GGAGCAACAATCGAAAACGCA 60.335 47.619 0.00 0.00 0.00 5.24
263 264 1.708680 GAGCAACAATCGAAAACGCAC 59.291 47.619 0.00 0.00 0.00 5.34
264 265 0.775861 GCAACAATCGAAAACGCACC 59.224 50.000 0.00 0.00 0.00 5.01
265 266 1.599419 GCAACAATCGAAAACGCACCT 60.599 47.619 0.00 0.00 0.00 4.00
266 267 2.043411 CAACAATCGAAAACGCACCTG 58.957 47.619 0.00 0.00 0.00 4.00
267 268 0.040425 ACAATCGAAAACGCACCTGC 60.040 50.000 0.00 0.00 37.78 4.85
384 391 2.159382 CCCTATTCAAACCGTGCAAGT 58.841 47.619 0.00 0.00 0.00 3.16
385 392 2.095263 CCCTATTCAAACCGTGCAAGTG 60.095 50.000 0.00 0.00 0.00 3.16
386 393 2.584791 CTATTCAAACCGTGCAAGTGC 58.415 47.619 0.00 0.00 42.50 4.40
443 456 0.466189 CCAAATCCCATCCCCGTCAG 60.466 60.000 0.00 0.00 0.00 3.51
450 463 1.142748 CATCCCCGTCAGCTCTGTC 59.857 63.158 0.00 0.00 0.00 3.51
452 465 0.904865 ATCCCCGTCAGCTCTGTCAA 60.905 55.000 0.00 0.00 0.00 3.18
454 467 0.951040 CCCCGTCAGCTCTGTCAAAC 60.951 60.000 0.00 0.00 0.00 2.93
455 468 0.034059 CCCGTCAGCTCTGTCAAACT 59.966 55.000 0.00 0.00 0.00 2.66
456 469 1.423395 CCGTCAGCTCTGTCAAACTC 58.577 55.000 0.00 0.00 0.00 3.01
596 1151 0.519586 ACACGCGTGTTCACAAAACG 60.520 50.000 37.52 11.21 41.83 3.60
600 1155 0.798771 GCGTGTTCACAAAACGGCAA 60.799 50.000 1.37 0.00 37.77 4.52
604 1159 3.182967 GTGTTCACAAAACGGCAATCAA 58.817 40.909 0.00 0.00 0.00 2.57
607 1162 2.455032 TCACAAAACGGCAATCAAACG 58.545 42.857 0.00 0.00 0.00 3.60
693 1523 4.051922 AGTACAACTTCGAGCAGTTCAAG 58.948 43.478 0.00 0.00 34.60 3.02
694 1524 1.599542 ACAACTTCGAGCAGTTCAAGC 59.400 47.619 0.00 0.00 34.60 4.01
980 1817 1.269206 CCGCGTCGGGTATAAAGCTTA 60.269 52.381 4.92 0.00 44.15 3.09
1024 1953 6.650390 GCAAGAATCCATCCTATTCTCTTCTC 59.350 42.308 0.00 0.00 41.68 2.87
1047 1976 3.948473 TCCTGTCCTGTTCGATCTTCTAG 59.052 47.826 0.00 0.00 0.00 2.43
1048 1977 3.490078 CCTGTCCTGTTCGATCTTCTAGC 60.490 52.174 0.00 0.00 0.00 3.42
1085 2017 3.134879 ACGCACCCGTCTTCAAGA 58.865 55.556 0.00 0.00 46.39 3.02
1086 2018 1.444250 ACGCACCCGTCTTCAAGAA 59.556 52.632 0.00 0.00 46.39 2.52
1087 2019 0.034896 ACGCACCCGTCTTCAAGAAT 59.965 50.000 0.00 0.00 46.39 2.40
1088 2020 0.721718 CGCACCCGTCTTCAAGAATC 59.278 55.000 0.00 0.00 0.00 2.52
1090 2022 2.151202 GCACCCGTCTTCAAGAATCAA 58.849 47.619 0.00 0.00 0.00 2.57
1091 2023 2.160417 GCACCCGTCTTCAAGAATCAAG 59.840 50.000 0.00 0.00 0.00 3.02
1135 2078 1.021390 CGCGTTTGATCCTCCTGCTT 61.021 55.000 0.00 0.00 0.00 3.91
1285 2228 2.095161 TGTTGTTCGTGGTTTGGTTGAC 60.095 45.455 0.00 0.00 0.00 3.18
1297 2240 4.276431 GGTTTGGTTGACTGATTCGGTTTA 59.724 41.667 0.00 0.00 0.00 2.01
1298 2241 5.449304 GTTTGGTTGACTGATTCGGTTTAG 58.551 41.667 0.00 0.00 0.00 1.85
1304 2258 3.190874 GACTGATTCGGTTTAGCTCTGG 58.809 50.000 0.00 0.00 0.00 3.86
1909 2866 3.897122 GGGAAGTGGGTGTGGGCA 61.897 66.667 0.00 0.00 0.00 5.36
2050 3007 1.519455 GCAGAGACACGAATCCCGG 60.519 63.158 0.00 0.00 43.93 5.73
2066 3023 1.131883 CCCGGTTGTACAGTAGAGTCG 59.868 57.143 0.00 0.00 0.00 4.18
2076 3033 4.795970 ACAGTAGAGTCGTTTGCTTTTG 57.204 40.909 0.00 0.00 0.00 2.44
2077 3034 4.439057 ACAGTAGAGTCGTTTGCTTTTGA 58.561 39.130 0.00 0.00 0.00 2.69
2078 3035 5.057149 ACAGTAGAGTCGTTTGCTTTTGAT 58.943 37.500 0.00 0.00 0.00 2.57
2079 3036 5.177696 ACAGTAGAGTCGTTTGCTTTTGATC 59.822 40.000 0.00 0.00 0.00 2.92
2080 3037 5.406780 CAGTAGAGTCGTTTGCTTTTGATCT 59.593 40.000 0.00 0.00 0.00 2.75
2082 3039 5.100751 AGAGTCGTTTGCTTTTGATCTTG 57.899 39.130 0.00 0.00 0.00 3.02
2099 3060 0.618458 TTGCTCGTGCTAATCCCCTT 59.382 50.000 11.19 0.00 40.48 3.95
2118 3079 4.268359 CCTTCCTCCTTTCTTCTTGGATG 58.732 47.826 0.00 0.00 0.00 3.51
2150 3115 1.160329 GCGGAATGAATCGGGTGGAG 61.160 60.000 0.00 0.00 0.00 3.86
2276 3265 3.788766 GATGTGCGGCGCGTCTTT 61.789 61.111 28.09 13.78 0.00 2.52
2308 3298 1.745115 TGCCAACCTGCGATAGTGC 60.745 57.895 0.00 0.00 39.35 4.40
2413 3423 1.905843 CAATGGTGACGGCCCCAAA 60.906 57.895 0.00 0.00 33.66 3.28
2414 3424 1.606313 AATGGTGACGGCCCCAAAG 60.606 57.895 0.00 0.00 33.66 2.77
2415 3425 3.583882 ATGGTGACGGCCCCAAAGG 62.584 63.158 0.00 0.00 33.66 3.11
2416 3426 4.280019 GGTGACGGCCCCAAAGGT 62.280 66.667 0.00 0.00 38.26 3.50
2424 3434 0.986550 GGCCCCAAAGGTAGCTAGGA 60.987 60.000 13.34 0.00 38.26 2.94
2451 3473 1.449423 TGTGATTCCCGGCGTGATG 60.449 57.895 6.01 0.00 0.00 3.07
2452 3474 2.513666 TGATTCCCGGCGTGATGC 60.514 61.111 6.01 0.00 45.38 3.91
2542 3564 1.084289 GTTCCGGTAACTGGCATGAC 58.916 55.000 0.00 0.00 35.05 3.06
2547 3569 0.391130 GGTAACTGGCATGACGCAGA 60.391 55.000 0.00 0.00 45.17 4.26
2568 3590 3.561143 AGGTAGAGTGATAGGAGCTGTG 58.439 50.000 0.00 0.00 0.00 3.66
2664 3687 7.882791 TGTTAATTAAGCAGAAGAGGATTGTCA 59.117 33.333 0.00 0.00 0.00 3.58
2665 3688 6.998968 AATTAAGCAGAAGAGGATTGTCAG 57.001 37.500 0.00 0.00 0.00 3.51
2673 3696 6.183360 GCAGAAGAGGATTGTCAGGTTAATTC 60.183 42.308 0.00 0.00 0.00 2.17
2711 3735 5.067936 TGAACACCATCACAAACCGTTAAAT 59.932 36.000 0.00 0.00 0.00 1.40
2730 3755 0.610687 TGGCATACACGTGATGTCCA 59.389 50.000 25.01 23.81 42.09 4.02
2747 3772 7.922811 GTGATGTCCAAGAAAGAAGAACAAAAT 59.077 33.333 0.00 0.00 0.00 1.82
2750 3775 5.915196 GTCCAAGAAAGAAGAACAAAATCGG 59.085 40.000 0.00 0.00 0.00 4.18
2754 3779 7.918562 CCAAGAAAGAAGAACAAAATCGGTAAA 59.081 33.333 0.00 0.00 0.00 2.01
2782 3807 6.874134 GGATTTCGGTATAATGAGCATAGTGT 59.126 38.462 0.00 0.00 0.00 3.55
2801 3826 1.409427 GTTGACTCAGGAGGATACCGG 59.591 57.143 0.00 0.00 34.73 5.28
2856 3894 9.512588 AAGAAAAGAGAACATCACATGATAACT 57.487 29.630 0.00 0.00 32.63 2.24
2864 3902 9.520515 AGAACATCACATGATAACTAAAGGTTT 57.479 29.630 0.00 0.00 39.17 3.27
2890 3928 7.381323 ACTCGAATATCATTCATGTGCTCATA 58.619 34.615 0.04 0.00 32.47 2.15
2894 3932 7.413767 CGAATATCATTCATGTGCTCATAAGGG 60.414 40.741 0.04 0.00 32.47 3.95
2899 3937 4.508551 TCATGTGCTCATAAGGGTTGAT 57.491 40.909 0.04 0.00 32.47 2.57
2945 3983 3.120820 CGGTCATTGAACGAACGATTTCA 60.121 43.478 19.13 0.00 46.60 2.69
2951 3989 6.742264 TCATTGAACGAACGATTTCATTCATG 59.258 34.615 0.14 3.61 42.04 3.07
2964 4002 6.801539 TTTCATTCATGTCTGTGAGTTACC 57.198 37.500 0.00 0.00 0.00 2.85
2968 4006 4.801330 TCATGTCTGTGAGTTACCGAAT 57.199 40.909 0.00 0.00 0.00 3.34
2987 4025 1.927487 TCTACGGGGTCACAAGCTTA 58.073 50.000 0.00 0.00 0.00 3.09
2995 4033 2.164422 GGGTCACAAGCTTAAGGCAATC 59.836 50.000 0.00 0.00 44.79 2.67
2999 4037 3.444742 TCACAAGCTTAAGGCAATCATGG 59.555 43.478 0.00 0.00 44.79 3.66
3002 4040 3.659183 AGCTTAAGGCAATCATGGTCT 57.341 42.857 4.29 0.00 44.79 3.85
3017 4055 0.169009 GGTCTGCCGAATTGCTGAAC 59.831 55.000 0.00 0.00 40.28 3.18
3023 4061 2.095263 TGCCGAATTGCTGAACTTTAGC 60.095 45.455 0.00 0.00 41.49 3.09
3029 4067 1.795768 TGCTGAACTTTAGCAGGACG 58.204 50.000 4.17 0.00 45.52 4.79
3047 4085 4.594920 AGGACGGGATTCATGAGAATATGT 59.405 41.667 0.00 0.00 44.30 2.29
3107 4145 1.134788 AGAATCTGGAAGCGTTACGGG 60.135 52.381 6.94 0.00 0.00 5.28
3112 4150 1.739196 GGAAGCGTTACGGGGTCAC 60.739 63.158 6.94 0.00 0.00 3.67
3114 4152 2.438951 GAAGCGTTACGGGGTCACCA 62.439 60.000 6.94 0.00 40.22 4.17
3118 4156 0.033781 CGTTACGGGGTCACCAGAAA 59.966 55.000 0.00 0.00 40.22 2.52
3120 4158 0.688487 TTACGGGGTCACCAGAAAGG 59.312 55.000 0.00 0.00 45.67 3.11
3137 4175 2.614829 AGGTTTCGGTGAATATCGGG 57.385 50.000 0.00 0.00 0.00 5.14
3143 4181 5.406477 GGTTTCGGTGAATATCGGGTAATAC 59.594 44.000 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.168790 ACTCTCTCGTTCTTTACTTTCTACTT 57.831 34.615 0.00 0.00 0.00 2.24
1 2 7.748691 ACTCTCTCGTTCTTTACTTTCTACT 57.251 36.000 0.00 0.00 0.00 2.57
2 3 8.692615 CAAACTCTCTCGTTCTTTACTTTCTAC 58.307 37.037 0.00 0.00 0.00 2.59
3 4 8.627403 TCAAACTCTCTCGTTCTTTACTTTCTA 58.373 33.333 0.00 0.00 0.00 2.10
4 5 7.490000 TCAAACTCTCTCGTTCTTTACTTTCT 58.510 34.615 0.00 0.00 0.00 2.52
5 6 7.695869 TCAAACTCTCTCGTTCTTTACTTTC 57.304 36.000 0.00 0.00 0.00 2.62
6 7 8.664211 ATTCAAACTCTCTCGTTCTTTACTTT 57.336 30.769 0.00 0.00 0.00 2.66
7 8 9.760077 TTATTCAAACTCTCTCGTTCTTTACTT 57.240 29.630 0.00 0.00 0.00 2.24
8 9 9.760077 TTTATTCAAACTCTCTCGTTCTTTACT 57.240 29.630 0.00 0.00 0.00 2.24
11 12 9.326413 TCTTTTATTCAAACTCTCTCGTTCTTT 57.674 29.630 0.00 0.00 0.00 2.52
12 13 8.888579 TCTTTTATTCAAACTCTCTCGTTCTT 57.111 30.769 0.00 0.00 0.00 2.52
13 14 8.930760 CATCTTTTATTCAAACTCTCTCGTTCT 58.069 33.333 0.00 0.00 0.00 3.01
14 15 8.926710 TCATCTTTTATTCAAACTCTCTCGTTC 58.073 33.333 0.00 0.00 0.00 3.95
15 16 8.833231 TCATCTTTTATTCAAACTCTCTCGTT 57.167 30.769 0.00 0.00 0.00 3.85
16 17 9.442047 AATCATCTTTTATTCAAACTCTCTCGT 57.558 29.630 0.00 0.00 0.00 4.18
17 18 9.913451 GAATCATCTTTTATTCAAACTCTCTCG 57.087 33.333 0.00 0.00 33.26 4.04
44 45 9.775854 CCACTTCTATCATCAATAAAGACTGAT 57.224 33.333 0.00 0.00 32.40 2.90
45 46 8.206867 CCCACTTCTATCATCAATAAAGACTGA 58.793 37.037 0.00 0.00 0.00 3.41
46 47 7.041508 GCCCACTTCTATCATCAATAAAGACTG 60.042 40.741 0.00 0.00 0.00 3.51
47 48 6.995091 GCCCACTTCTATCATCAATAAAGACT 59.005 38.462 0.00 0.00 0.00 3.24
48 49 6.995091 AGCCCACTTCTATCATCAATAAAGAC 59.005 38.462 0.00 0.00 0.00 3.01
49 50 7.141758 AGCCCACTTCTATCATCAATAAAGA 57.858 36.000 0.00 0.00 0.00 2.52
50 51 9.512588 AATAGCCCACTTCTATCATCAATAAAG 57.487 33.333 0.00 0.00 0.00 1.85
51 52 9.866655 AAATAGCCCACTTCTATCATCAATAAA 57.133 29.630 0.00 0.00 0.00 1.40
56 57 8.762645 CCTATAAATAGCCCACTTCTATCATCA 58.237 37.037 0.00 0.00 0.00 3.07
57 58 8.982723 TCCTATAAATAGCCCACTTCTATCATC 58.017 37.037 0.00 0.00 0.00 2.92
58 59 8.917414 TCCTATAAATAGCCCACTTCTATCAT 57.083 34.615 0.00 0.00 0.00 2.45
59 60 8.736097 TTCCTATAAATAGCCCACTTCTATCA 57.264 34.615 0.00 0.00 0.00 2.15
60 61 8.261522 CCTTCCTATAAATAGCCCACTTCTATC 58.738 40.741 0.00 0.00 0.00 2.08
61 62 7.311360 GCCTTCCTATAAATAGCCCACTTCTAT 60.311 40.741 0.00 0.00 0.00 1.98
62 63 6.013639 GCCTTCCTATAAATAGCCCACTTCTA 60.014 42.308 0.00 0.00 0.00 2.10
63 64 5.221945 GCCTTCCTATAAATAGCCCACTTCT 60.222 44.000 0.00 0.00 0.00 2.85
64 65 5.004448 GCCTTCCTATAAATAGCCCACTTC 58.996 45.833 0.00 0.00 0.00 3.01
65 66 4.505039 CGCCTTCCTATAAATAGCCCACTT 60.505 45.833 0.00 0.00 0.00 3.16
66 67 3.008049 CGCCTTCCTATAAATAGCCCACT 59.992 47.826 0.00 0.00 0.00 4.00
67 68 3.335579 CGCCTTCCTATAAATAGCCCAC 58.664 50.000 0.00 0.00 0.00 4.61
68 69 2.304761 CCGCCTTCCTATAAATAGCCCA 59.695 50.000 0.00 0.00 0.00 5.36
69 70 2.305052 ACCGCCTTCCTATAAATAGCCC 59.695 50.000 0.00 0.00 0.00 5.19
70 71 3.007614 TGACCGCCTTCCTATAAATAGCC 59.992 47.826 0.00 0.00 0.00 3.93
71 72 4.267349 TGACCGCCTTCCTATAAATAGC 57.733 45.455 0.00 0.00 0.00 2.97
72 73 5.855045 ACTTGACCGCCTTCCTATAAATAG 58.145 41.667 0.00 0.00 0.00 1.73
73 74 5.881923 ACTTGACCGCCTTCCTATAAATA 57.118 39.130 0.00 0.00 0.00 1.40
74 75 4.772886 ACTTGACCGCCTTCCTATAAAT 57.227 40.909 0.00 0.00 0.00 1.40
75 76 5.680594 TTACTTGACCGCCTTCCTATAAA 57.319 39.130 0.00 0.00 0.00 1.40
76 77 5.046448 TGTTTACTTGACCGCCTTCCTATAA 60.046 40.000 0.00 0.00 0.00 0.98
77 78 4.467082 TGTTTACTTGACCGCCTTCCTATA 59.533 41.667 0.00 0.00 0.00 1.31
78 79 3.262405 TGTTTACTTGACCGCCTTCCTAT 59.738 43.478 0.00 0.00 0.00 2.57
79 80 2.633967 TGTTTACTTGACCGCCTTCCTA 59.366 45.455 0.00 0.00 0.00 2.94
80 81 1.418637 TGTTTACTTGACCGCCTTCCT 59.581 47.619 0.00 0.00 0.00 3.36
81 82 1.886886 TGTTTACTTGACCGCCTTCC 58.113 50.000 0.00 0.00 0.00 3.46
82 83 3.974871 TTTGTTTACTTGACCGCCTTC 57.025 42.857 0.00 0.00 0.00 3.46
83 84 4.929819 AATTTGTTTACTTGACCGCCTT 57.070 36.364 0.00 0.00 0.00 4.35
84 85 4.822896 TGTAATTTGTTTACTTGACCGCCT 59.177 37.500 0.00 0.00 40.77 5.52
85 86 5.110940 TGTAATTTGTTTACTTGACCGCC 57.889 39.130 0.00 0.00 40.77 6.13
86 87 7.524065 ACTATGTAATTTGTTTACTTGACCGC 58.476 34.615 0.00 0.00 40.77 5.68
87 88 9.325150 CAACTATGTAATTTGTTTACTTGACCG 57.675 33.333 0.00 0.00 40.77 4.79
98 99 8.947115 GGCTCTTAAGACAACTATGTAATTTGT 58.053 33.333 0.00 0.00 40.74 2.83
99 100 8.946085 TGGCTCTTAAGACAACTATGTAATTTG 58.054 33.333 0.00 0.00 37.69 2.32
100 101 9.515226 TTGGCTCTTAAGACAACTATGTAATTT 57.485 29.630 0.00 0.00 45.85 1.82
101 102 9.167311 CTTGGCTCTTAAGACAACTATGTAATT 57.833 33.333 0.00 0.00 45.85 1.40
102 103 7.770897 CCTTGGCTCTTAAGACAACTATGTAAT 59.229 37.037 0.00 0.00 45.85 1.89
103 104 7.038587 TCCTTGGCTCTTAAGACAACTATGTAA 60.039 37.037 0.00 0.00 45.85 2.41
104 105 6.439375 TCCTTGGCTCTTAAGACAACTATGTA 59.561 38.462 0.00 0.00 45.85 2.29
105 106 5.248477 TCCTTGGCTCTTAAGACAACTATGT 59.752 40.000 0.00 0.00 45.85 2.29
106 107 5.734720 TCCTTGGCTCTTAAGACAACTATG 58.265 41.667 0.00 0.00 45.85 2.23
107 108 6.013293 ACTTCCTTGGCTCTTAAGACAACTAT 60.013 38.462 0.00 0.00 45.85 2.12
108 109 5.307196 ACTTCCTTGGCTCTTAAGACAACTA 59.693 40.000 0.00 0.00 45.85 2.24
109 110 4.103311 ACTTCCTTGGCTCTTAAGACAACT 59.897 41.667 0.00 0.00 45.85 3.16
110 111 4.390264 ACTTCCTTGGCTCTTAAGACAAC 58.610 43.478 0.00 0.00 45.85 3.32
112 113 4.591498 TGTACTTCCTTGGCTCTTAAGACA 59.409 41.667 0.00 0.00 39.40 3.41
113 114 5.148651 TGTACTTCCTTGGCTCTTAAGAC 57.851 43.478 0.00 0.00 0.00 3.01
114 115 5.338381 CCATGTACTTCCTTGGCTCTTAAGA 60.338 44.000 4.81 4.81 0.00 2.10
115 116 4.878397 CCATGTACTTCCTTGGCTCTTAAG 59.122 45.833 0.00 0.00 0.00 1.85
116 117 4.288626 ACCATGTACTTCCTTGGCTCTTAA 59.711 41.667 0.00 0.00 33.96 1.85
117 118 3.844211 ACCATGTACTTCCTTGGCTCTTA 59.156 43.478 0.00 0.00 33.96 2.10
118 119 2.644798 ACCATGTACTTCCTTGGCTCTT 59.355 45.455 0.00 0.00 33.96 2.85
119 120 2.269940 ACCATGTACTTCCTTGGCTCT 58.730 47.619 0.00 0.00 33.96 4.09
120 121 2.749621 CAACCATGTACTTCCTTGGCTC 59.250 50.000 0.00 0.00 33.96 4.70
121 122 2.795329 CAACCATGTACTTCCTTGGCT 58.205 47.619 0.00 0.00 33.96 4.75
122 123 1.202348 GCAACCATGTACTTCCTTGGC 59.798 52.381 0.00 0.00 33.96 4.52
123 124 2.795329 AGCAACCATGTACTTCCTTGG 58.205 47.619 0.00 0.00 36.12 3.61
124 125 3.820467 TCAAGCAACCATGTACTTCCTTG 59.180 43.478 0.00 0.00 0.00 3.61
125 126 4.074970 CTCAAGCAACCATGTACTTCCTT 58.925 43.478 0.00 0.00 0.00 3.36
126 127 3.327757 TCTCAAGCAACCATGTACTTCCT 59.672 43.478 0.00 0.00 0.00 3.36
127 128 3.674997 TCTCAAGCAACCATGTACTTCC 58.325 45.455 0.00 0.00 0.00 3.46
128 129 4.083271 GGTTCTCAAGCAACCATGTACTTC 60.083 45.833 0.00 0.00 42.68 3.01
129 130 3.821033 GGTTCTCAAGCAACCATGTACTT 59.179 43.478 0.00 0.00 42.68 2.24
130 131 3.181445 TGGTTCTCAAGCAACCATGTACT 60.181 43.478 1.61 0.00 46.88 2.73
131 132 3.146066 TGGTTCTCAAGCAACCATGTAC 58.854 45.455 1.61 0.00 46.88 2.90
132 133 3.500448 TGGTTCTCAAGCAACCATGTA 57.500 42.857 1.61 0.00 46.88 2.29
133 134 2.363306 TGGTTCTCAAGCAACCATGT 57.637 45.000 1.61 0.00 46.88 3.21
143 144 4.640771 AGATAGGTTGCTTGGTTCTCAA 57.359 40.909 0.00 0.00 0.00 3.02
144 145 5.012664 TGTTAGATAGGTTGCTTGGTTCTCA 59.987 40.000 0.00 0.00 0.00 3.27
145 146 5.488341 TGTTAGATAGGTTGCTTGGTTCTC 58.512 41.667 0.00 0.00 0.00 2.87
146 147 5.499004 TGTTAGATAGGTTGCTTGGTTCT 57.501 39.130 0.00 0.00 0.00 3.01
147 148 6.759497 ATTGTTAGATAGGTTGCTTGGTTC 57.241 37.500 0.00 0.00 0.00 3.62
148 149 6.719370 TCAATTGTTAGATAGGTTGCTTGGTT 59.281 34.615 5.13 0.00 0.00 3.67
149 150 6.151144 GTCAATTGTTAGATAGGTTGCTTGGT 59.849 38.462 5.13 0.00 0.00 3.67
150 151 6.375455 AGTCAATTGTTAGATAGGTTGCTTGG 59.625 38.462 5.13 0.00 0.00 3.61
151 152 7.383102 AGTCAATTGTTAGATAGGTTGCTTG 57.617 36.000 5.13 0.00 0.00 4.01
152 153 9.515226 TTAAGTCAATTGTTAGATAGGTTGCTT 57.485 29.630 5.13 0.00 0.00 3.91
153 154 9.686683 ATTAAGTCAATTGTTAGATAGGTTGCT 57.313 29.630 5.13 0.00 0.00 3.91
154 155 9.937175 GATTAAGTCAATTGTTAGATAGGTTGC 57.063 33.333 5.13 0.00 0.00 4.17
215 216 8.922237 TGCTCTCATCTCTGTTAAGAATAGAAT 58.078 33.333 0.00 0.00 30.03 2.40
216 217 8.298729 TGCTCTCATCTCTGTTAAGAATAGAA 57.701 34.615 0.00 0.00 30.03 2.10
217 218 7.014134 CCTGCTCTCATCTCTGTTAAGAATAGA 59.986 40.741 0.00 0.00 30.03 1.98
218 219 7.014134 TCCTGCTCTCATCTCTGTTAAGAATAG 59.986 40.741 0.00 0.00 30.03 1.73
219 220 6.836007 TCCTGCTCTCATCTCTGTTAAGAATA 59.164 38.462 0.00 0.00 30.03 1.75
220 221 5.660417 TCCTGCTCTCATCTCTGTTAAGAAT 59.340 40.000 0.00 0.00 30.03 2.40
221 222 5.019470 TCCTGCTCTCATCTCTGTTAAGAA 58.981 41.667 0.00 0.00 30.03 2.52
222 223 4.604156 TCCTGCTCTCATCTCTGTTAAGA 58.396 43.478 0.00 0.00 0.00 2.10
223 224 4.737352 GCTCCTGCTCTCATCTCTGTTAAG 60.737 50.000 0.00 0.00 36.03 1.85
224 225 3.131933 GCTCCTGCTCTCATCTCTGTTAA 59.868 47.826 0.00 0.00 36.03 2.01
225 226 2.692557 GCTCCTGCTCTCATCTCTGTTA 59.307 50.000 0.00 0.00 36.03 2.41
226 227 1.481772 GCTCCTGCTCTCATCTCTGTT 59.518 52.381 0.00 0.00 36.03 3.16
227 228 1.113788 GCTCCTGCTCTCATCTCTGT 58.886 55.000 0.00 0.00 36.03 3.41
228 229 1.112950 TGCTCCTGCTCTCATCTCTG 58.887 55.000 0.00 0.00 40.48 3.35
229 230 1.481772 GTTGCTCCTGCTCTCATCTCT 59.518 52.381 0.00 0.00 40.48 3.10
230 231 1.206610 TGTTGCTCCTGCTCTCATCTC 59.793 52.381 0.00 0.00 40.48 2.75
231 232 1.273759 TGTTGCTCCTGCTCTCATCT 58.726 50.000 0.00 0.00 40.48 2.90
232 233 2.105006 TTGTTGCTCCTGCTCTCATC 57.895 50.000 0.00 0.00 40.48 2.92
233 234 2.641305 GATTGTTGCTCCTGCTCTCAT 58.359 47.619 0.00 0.00 40.48 2.90
234 235 1.673923 CGATTGTTGCTCCTGCTCTCA 60.674 52.381 0.00 0.00 40.48 3.27
235 236 1.005340 CGATTGTTGCTCCTGCTCTC 58.995 55.000 0.00 0.00 40.48 3.20
236 237 0.610174 TCGATTGTTGCTCCTGCTCT 59.390 50.000 0.00 0.00 40.48 4.09
237 238 1.442769 TTCGATTGTTGCTCCTGCTC 58.557 50.000 0.00 0.00 40.48 4.26
238 239 1.896220 TTTCGATTGTTGCTCCTGCT 58.104 45.000 0.00 0.00 40.48 4.24
239 240 2.319472 GTTTTCGATTGTTGCTCCTGC 58.681 47.619 0.00 0.00 40.20 4.85
385 392 4.785453 AGTGGCGGCTAGGCTTGC 62.785 66.667 15.11 12.66 46.88 4.01
386 393 2.045926 AAGTGGCGGCTAGGCTTG 60.046 61.111 15.11 0.43 46.88 4.01
387 394 0.976073 TAGAAGTGGCGGCTAGGCTT 60.976 55.000 15.11 9.28 46.88 4.35
388 395 0.760945 ATAGAAGTGGCGGCTAGGCT 60.761 55.000 15.11 5.41 46.88 4.58
389 396 0.319986 GATAGAAGTGGCGGCTAGGC 60.320 60.000 11.43 6.15 46.95 3.93
443 456 1.334149 GGCGTTTGAGTTTGACAGAGC 60.334 52.381 0.00 0.00 0.00 4.09
450 463 0.875059 GGAGGAGGCGTTTGAGTTTG 59.125 55.000 0.00 0.00 0.00 2.93
452 465 0.765510 AAGGAGGAGGCGTTTGAGTT 59.234 50.000 0.00 0.00 0.00 3.01
454 467 0.321671 TCAAGGAGGAGGCGTTTGAG 59.678 55.000 0.00 0.00 0.00 3.02
455 468 0.984230 ATCAAGGAGGAGGCGTTTGA 59.016 50.000 0.00 0.00 0.00 2.69
456 469 1.373570 GATCAAGGAGGAGGCGTTTG 58.626 55.000 0.00 0.00 0.00 2.93
557 1112 9.910511 CGCGTGTGTTTCTTTACTTTTATATAT 57.089 29.630 0.00 0.00 0.00 0.86
563 1118 4.092816 CACGCGTGTGTTTCTTTACTTTT 58.907 39.130 30.50 0.00 41.34 2.27
587 1142 2.159366 ACGTTTGATTGCCGTTTTGTGA 60.159 40.909 0.00 0.00 0.00 3.58
640 1195 1.153509 GGTAACCACGTCCCATCGG 60.154 63.158 0.00 0.00 34.94 4.18
812 1643 2.264794 GGAGGAAGGAAAGCGCGA 59.735 61.111 12.10 0.00 0.00 5.87
855 1689 0.111832 TCTCGTACCTGGGACACAGT 59.888 55.000 10.24 0.00 46.06 3.55
908 1745 1.078708 GTTAACTGCGCTGGCCCTA 60.079 57.895 18.98 1.87 38.85 3.53
1019 1856 2.163509 TCGAACAGGACAGGAGAGAAG 58.836 52.381 0.00 0.00 0.00 2.85
1024 1953 2.757868 AGAAGATCGAACAGGACAGGAG 59.242 50.000 0.00 0.00 0.00 3.69
1047 1976 0.889306 ACTCGGAGTGGTCTACTTGC 59.111 55.000 10.41 0.00 40.53 4.01
1048 1977 3.425892 CGTTACTCGGAGTGGTCTACTTG 60.426 52.174 20.58 0.00 40.53 3.16
1085 2017 1.076777 CCATCGGTGGGGCTTGATT 60.077 57.895 6.88 0.00 42.11 2.57
1086 2018 2.597340 CCATCGGTGGGGCTTGAT 59.403 61.111 6.88 0.00 42.11 2.57
1087 2019 4.424711 GCCATCGGTGGGGCTTGA 62.425 66.667 18.38 0.00 46.74 3.02
1135 2078 4.742201 GCAGCGGCGAGGAAGACA 62.742 66.667 12.98 0.00 0.00 3.41
1222 2165 2.100631 CGCACCATTGTCGAGGACC 61.101 63.158 0.00 0.00 0.00 4.46
1224 2167 0.250124 AAACGCACCATTGTCGAGGA 60.250 50.000 0.00 0.00 0.00 3.71
1285 2228 2.093447 ACCCAGAGCTAAACCGAATCAG 60.093 50.000 0.00 0.00 0.00 2.90
1297 2240 4.031129 CCAGCTGCACCCAGAGCT 62.031 66.667 8.66 0.00 46.73 4.09
2031 2988 1.215382 CGGGATTCGTGTCTCTGCA 59.785 57.895 0.00 0.00 0.00 4.41
2032 2989 1.519455 CCGGGATTCGTGTCTCTGC 60.519 63.158 0.00 0.00 37.11 4.26
2033 2990 0.246635 AACCGGGATTCGTGTCTCTG 59.753 55.000 6.32 0.00 37.11 3.35
2035 2992 0.037605 ACAACCGGGATTCGTGTCTC 60.038 55.000 6.32 0.00 37.11 3.36
2050 3007 4.296690 AGCAAACGACTCTACTGTACAAC 58.703 43.478 0.00 0.00 0.00 3.32
2066 3023 3.423206 CACGAGCAAGATCAAAAGCAAAC 59.577 43.478 0.00 0.00 0.00 2.93
2076 3033 2.139118 GGGATTAGCACGAGCAAGATC 58.861 52.381 7.77 7.03 45.49 2.75
2077 3034 1.202698 GGGGATTAGCACGAGCAAGAT 60.203 52.381 7.77 0.00 45.49 2.40
2078 3035 0.178068 GGGGATTAGCACGAGCAAGA 59.822 55.000 7.77 0.00 45.49 3.02
2079 3036 0.179000 AGGGGATTAGCACGAGCAAG 59.821 55.000 7.77 0.00 45.49 4.01
2080 3037 0.618458 AAGGGGATTAGCACGAGCAA 59.382 50.000 7.77 0.00 45.49 3.91
2082 3039 0.533085 GGAAGGGGATTAGCACGAGC 60.533 60.000 0.00 0.00 42.56 5.03
2099 3060 3.055819 CGTCATCCAAGAAGAAAGGAGGA 60.056 47.826 0.00 0.00 39.64 3.71
2118 3079 2.855963 TCATTCCGCTTCGTTAATCGTC 59.144 45.455 0.00 0.00 40.80 4.20
2150 3115 2.022129 CAACCGCACGTCTGACTCC 61.022 63.158 6.21 0.00 0.00 3.85
2297 3286 2.032414 CAATGCATGCACTATCGCAG 57.968 50.000 25.37 2.89 46.99 5.18
2308 3298 1.578367 CGTCGTCGTGCAATGCATG 60.578 57.895 20.52 20.52 45.79 4.06
2413 3423 0.739561 CGAAACGCTCCTAGCTACCT 59.260 55.000 0.00 0.00 39.60 3.08
2414 3424 0.455005 ACGAAACGCTCCTAGCTACC 59.545 55.000 0.00 0.00 39.60 3.18
2415 3425 1.135460 ACACGAAACGCTCCTAGCTAC 60.135 52.381 0.00 0.00 39.60 3.58
2416 3426 1.135489 CACACGAAACGCTCCTAGCTA 60.135 52.381 0.00 0.00 39.60 3.32
2424 3434 2.540145 GGGAATCACACGAAACGCT 58.460 52.632 0.00 0.00 0.00 5.07
2456 3478 3.919973 TACGACGGCAAGGGAACGC 62.920 63.158 0.00 0.00 0.00 4.84
2457 3479 1.804326 CTACGACGGCAAGGGAACG 60.804 63.158 0.00 0.00 0.00 3.95
2458 3480 1.447314 CCTACGACGGCAAGGGAAC 60.447 63.158 0.00 0.00 0.00 3.62
2459 3481 1.474332 AACCTACGACGGCAAGGGAA 61.474 55.000 11.22 0.00 34.52 3.97
2460 3482 1.909781 AACCTACGACGGCAAGGGA 60.910 57.895 11.22 0.00 34.52 4.20
2542 3564 2.811431 CTCCTATCACTCTACCTCTGCG 59.189 54.545 0.00 0.00 0.00 5.18
2547 3569 3.561143 CACAGCTCCTATCACTCTACCT 58.439 50.000 0.00 0.00 0.00 3.08
2664 3687 5.047802 CACCATGCTTTCTGTGAATTAACCT 60.048 40.000 0.00 0.00 0.00 3.50
2665 3688 5.048083 TCACCATGCTTTCTGTGAATTAACC 60.048 40.000 0.00 0.00 34.98 2.85
2673 3696 2.287788 GGTGTTCACCATGCTTTCTGTG 60.288 50.000 16.01 0.00 0.00 3.66
2711 3735 0.610687 TGGACATCACGTGTATGCCA 59.389 50.000 23.29 23.29 42.36 4.92
2730 3755 8.899771 TCTTTACCGATTTTGTTCTTCTTTCTT 58.100 29.630 0.00 0.00 0.00 2.52
2747 3772 6.713762 TTATACCGAAATCCTCTTTACCGA 57.286 37.500 0.00 0.00 0.00 4.69
2750 3775 7.656137 TGCTCATTATACCGAAATCCTCTTTAC 59.344 37.037 0.00 0.00 0.00 2.01
2754 3779 5.808366 TGCTCATTATACCGAAATCCTCT 57.192 39.130 0.00 0.00 0.00 3.69
2782 3807 1.006758 ACCGGTATCCTCCTGAGTCAA 59.993 52.381 4.49 0.00 0.00 3.18
2838 3876 9.520515 AAACCTTTAGTTATCATGTGATGTTCT 57.479 29.630 5.78 4.36 37.88 3.01
2864 3902 6.748132 TGAGCACATGAATGATATTCGAGTA 58.252 36.000 0.00 0.00 0.00 2.59
2880 3918 5.073554 TCCATATCAACCCTTATGAGCACAT 59.926 40.000 1.31 1.31 40.16 3.21
2890 3928 2.193127 TGGACGTCCATATCAACCCTT 58.807 47.619 33.23 0.00 42.01 3.95
2936 3974 5.702670 ACTCACAGACATGAATGAAATCGTT 59.297 36.000 0.00 0.00 0.00 3.85
2940 3978 6.092670 CGGTAACTCACAGACATGAATGAAAT 59.907 38.462 0.00 0.00 0.00 2.17
2945 3983 4.801330 TCGGTAACTCACAGACATGAAT 57.199 40.909 0.00 0.00 0.00 2.57
2951 3989 4.341099 CGTAGATTCGGTAACTCACAGAC 58.659 47.826 0.00 0.00 30.51 3.51
2964 4002 1.922570 CTTGTGACCCCGTAGATTCG 58.077 55.000 0.00 0.00 0.00 3.34
2968 4006 1.927487 TAAGCTTGTGACCCCGTAGA 58.073 50.000 9.86 0.00 0.00 2.59
2977 4015 3.444742 CCATGATTGCCTTAAGCTTGTGA 59.555 43.478 9.86 0.00 44.23 3.58
2980 4018 3.698040 AGACCATGATTGCCTTAAGCTTG 59.302 43.478 9.86 0.00 44.23 4.01
2995 4033 0.099968 CAGCAATTCGGCAGACCATG 59.900 55.000 0.00 0.00 35.83 3.66
2999 4037 1.160137 AGTTCAGCAATTCGGCAGAC 58.840 50.000 0.00 0.00 35.83 3.51
3002 4040 2.095263 GCTAAAGTTCAGCAATTCGGCA 60.095 45.455 0.00 0.00 38.93 5.69
3017 4055 2.691409 TGAATCCCGTCCTGCTAAAG 57.309 50.000 0.00 0.00 0.00 1.85
3023 4061 2.988010 TTCTCATGAATCCCGTCCTG 57.012 50.000 0.00 0.00 0.00 3.86
3029 4067 6.547141 TCCACAAACATATTCTCATGAATCCC 59.453 38.462 0.00 0.00 41.55 3.85
3074 4112 5.776173 TCCAGATTCTCTCGGAACTATTC 57.224 43.478 0.00 0.00 36.70 1.75
3082 4120 0.457851 ACGCTTCCAGATTCTCTCGG 59.542 55.000 0.00 0.00 0.00 4.63
3089 4127 0.107848 CCCCGTAACGCTTCCAGATT 60.108 55.000 0.00 0.00 0.00 2.40
3093 4131 2.208619 TGACCCCGTAACGCTTCCA 61.209 57.895 0.00 0.00 0.00 3.53
3094 4132 1.739196 GTGACCCCGTAACGCTTCC 60.739 63.158 0.00 0.00 0.00 3.46
3101 4139 0.688487 CCTTTCTGGTGACCCCGTAA 59.312 55.000 0.00 0.00 35.15 3.18
3112 4150 4.034048 CGATATTCACCGAAACCTTTCTGG 59.966 45.833 6.95 6.95 42.93 3.86
3114 4152 4.189231 CCGATATTCACCGAAACCTTTCT 58.811 43.478 0.00 0.00 35.07 2.52
3118 4156 1.835531 ACCCGATATTCACCGAAACCT 59.164 47.619 0.00 0.00 0.00 3.50
3120 4158 5.406477 GGTATTACCCGATATTCACCGAAAC 59.594 44.000 0.98 0.00 30.04 2.78


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

AutoCloner maintained by Alex Coulton.