Multiple sequence alignment - TraesCS3A01G214700

Loading Multiple Alignment...

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 TraesCS3A01G214700 chr3A 100.000 5475 0 0 1 5475 391468594 391474068 0.000000e+00 10111
1 TraesCS3A01G214700 chr3B 95.277 4679 123 36 836 5475 392301457 392296838 0.000000e+00 7326
2 TraesCS3A01G214700 chr3B 89.813 481 15 14 318 779 392302307 392301842 2.200000e-163 586
3 TraesCS3A01G214700 chr3B 86.792 318 34 6 6 319 161367919 161368232 1.130000e-91 348
4 TraesCS3A01G214700 chr3D 96.568 3934 81 16 489 4398 297499313 297495410 0.000000e+00 6468
5 TraesCS3A01G214700 chr3D 95.529 1096 22 4 4399 5475 297495368 297494281 0.000000e+00 1727
6 TraesCS3A01G214700 chr3D 89.305 187 8 5 317 497 297499635 297499455 1.980000e-54 224
7 TraesCS3A01G214700 chr3D 94.595 74 4 0 2885 2958 563633877 563633804 1.250000e-21 115
8 TraesCS3A01G214700 chr5D 88.254 315 35 2 5 318 393997830 393997517 5.180000e-100 375
9 TraesCS3A01G214700 chr5D 87.147 319 34 4 5 318 350218408 350218724 6.750000e-94 355
10 TraesCS3A01G214700 chr5D 84.277 318 39 7 9 318 440659049 440658735 3.210000e-77 300
11 TraesCS3A01G214700 chr5D 83.699 319 47 5 8 321 46688858 46688540 4.150000e-76 296
12 TraesCS3A01G214700 chr4D 87.227 321 33 7 6 318 64338304 64338624 5.210000e-95 359
13 TraesCS3A01G214700 chr4D 91.011 89 7 1 2870 2958 403409617 403409530 9.630000e-23 119
14 TraesCS3A01G214700 chr7D 86.076 316 38 5 9 322 536598296 536597985 8.790000e-88 335
15 TraesCS3A01G214700 chr7D 90.000 90 8 1 2865 2953 443416024 443416113 1.250000e-21 115
16 TraesCS3A01G214700 chr6D 84.713 314 44 3 5 317 358099975 358100285 1.480000e-80 311
17 TraesCS3A01G214700 chr6D 90.698 86 8 0 2870 2955 146072820 146072905 1.250000e-21 115
18 TraesCS3A01G214700 chr2B 83.699 319 46 6 5 318 765800401 765800084 4.150000e-76 296
19 TraesCS3A01G214700 chr6A 80.874 183 12 8 4791 4956 615965424 615965248 7.450000e-24 122
20 TraesCS3A01G214700 chr7A 91.860 86 7 0 2870 2955 97021648 97021733 2.680000e-23 121
21 TraesCS3A01G214700 chr6B 91.860 86 7 0 2873 2958 55999851 55999766 2.680000e-23 121
22 TraesCS3A01G214700 chr1A 88.298 94 9 2 2863 2955 548375529 548375621 1.610000e-20 111


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 TraesCS3A01G214700 chr3A 391468594 391474068 5474 False 10111.000000 10111 100.000000 1 5475 1 chr3A.!!$F1 5474
1 TraesCS3A01G214700 chr3B 392296838 392302307 5469 True 3956.000000 7326 92.545000 318 5475 2 chr3B.!!$R1 5157
2 TraesCS3A01G214700 chr3D 297494281 297499635 5354 True 2806.333333 6468 93.800667 317 5475 3 chr3D.!!$R2 5158

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
56 57 0.036875 GGTTCAGCCAGCCAACTAGT 59.963 55.000 0.00 0.00 37.17 2.57 F
174 175 0.100325 CACGCTGGACAAAAGTGCAA 59.900 50.000 0.00 0.00 0.00 4.08 F
175 176 0.100503 ACGCTGGACAAAAGTGCAAC 59.899 50.000 0.00 0.00 0.00 4.17 F
237 238 0.260230 TGTCAGGCCCCACTCAAAAA 59.740 50.000 0.00 0.00 0.00 1.94 F
1389 1884 0.252284 TCCTCAGGGACAGGGAGAAC 60.252 60.000 0.00 0.00 36.57 3.01 F
2886 3395 1.005687 AGTTACTACTCTCACCGCCCT 59.994 52.381 0.00 0.00 0.00 5.19 F
3533 4042 0.942962 CTCTTCATTGGGCTGATCGC 59.057 55.000 1.55 1.55 38.13 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1383 1878 0.681243 GAGGCCCCATGTTGTTCTCC 60.681 60.000 0.00 0.0 0.00 3.71 R
1385 1880 1.384191 GGAGGCCCCATGTTGTTCT 59.616 57.895 0.00 0.0 34.14 3.01 R
1387 1882 2.035626 CGGAGGCCCCATGTTGTT 59.964 61.111 0.00 0.0 34.14 2.83 R
1951 2456 2.129607 GCACAAACAACTGCATCTTGG 58.870 47.619 8.65 0.0 33.31 3.61 R
2947 3456 0.251474 TGCAAAGCAATGCTCCCTCT 60.251 50.000 8.71 0.0 46.54 3.69 R
3868 4377 0.668535 ACCGCTTCACCTTTCTTTGC 59.331 50.000 0.00 0.0 0.00 3.68 R
5257 5832 0.532573 GCTGCAGCAGTGGTAGTAGA 59.467 55.000 33.36 0.0 41.59 2.59 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
17 18 3.147132 GCAACTTTGGGGGTTGGG 58.853 61.111 8.34 0.00 42.77 4.12
18 19 2.515979 GCAACTTTGGGGGTTGGGG 61.516 63.158 8.34 0.00 42.77 4.96
19 20 1.074850 CAACTTTGGGGGTTGGGGT 60.075 57.895 0.00 0.00 39.97 4.95
20 21 1.074850 AACTTTGGGGGTTGGGGTG 60.075 57.895 0.00 0.00 0.00 4.61
21 22 1.892441 AACTTTGGGGGTTGGGGTGT 61.892 55.000 0.00 0.00 0.00 4.16
22 23 1.836604 CTTTGGGGGTTGGGGTGTG 60.837 63.158 0.00 0.00 0.00 3.82
23 24 2.597546 CTTTGGGGGTTGGGGTGTGT 62.598 60.000 0.00 0.00 0.00 3.72
24 25 2.880629 TTTGGGGGTTGGGGTGTGTG 62.881 60.000 0.00 0.00 0.00 3.82
25 26 4.614036 GGGGGTTGGGGTGTGTGG 62.614 72.222 0.00 0.00 0.00 4.17
26 27 4.614036 GGGGTTGGGGTGTGTGGG 62.614 72.222 0.00 0.00 0.00 4.61
27 28 4.614036 GGGTTGGGGTGTGTGGGG 62.614 72.222 0.00 0.00 0.00 4.96
28 29 4.614036 GGTTGGGGTGTGTGGGGG 62.614 72.222 0.00 0.00 0.00 5.40
51 52 4.299796 GGGGGTTCAGCCAGCCAA 62.300 66.667 0.00 0.00 39.65 4.52
52 53 2.991540 GGGGTTCAGCCAGCCAAC 60.992 66.667 0.00 0.00 39.65 3.77
53 54 2.116125 GGGTTCAGCCAGCCAACT 59.884 61.111 2.98 0.00 39.65 3.16
54 55 1.378762 GGGTTCAGCCAGCCAACTA 59.621 57.895 2.98 0.00 39.65 2.24
55 56 0.678048 GGGTTCAGCCAGCCAACTAG 60.678 60.000 0.00 0.00 39.65 2.57
56 57 0.036875 GGTTCAGCCAGCCAACTAGT 59.963 55.000 0.00 0.00 37.17 2.57
57 58 1.278127 GGTTCAGCCAGCCAACTAGTA 59.722 52.381 0.00 0.00 37.17 1.82
58 59 2.290071 GGTTCAGCCAGCCAACTAGTAA 60.290 50.000 0.00 0.00 37.17 2.24
59 60 2.742589 GTTCAGCCAGCCAACTAGTAAC 59.257 50.000 0.00 0.00 0.00 2.50
60 61 1.974957 TCAGCCAGCCAACTAGTAACA 59.025 47.619 0.00 0.00 0.00 2.41
61 62 2.370519 TCAGCCAGCCAACTAGTAACAA 59.629 45.455 0.00 0.00 0.00 2.83
62 63 3.146066 CAGCCAGCCAACTAGTAACAAA 58.854 45.455 0.00 0.00 0.00 2.83
63 64 3.058224 CAGCCAGCCAACTAGTAACAAAC 60.058 47.826 0.00 0.00 0.00 2.93
64 65 2.882137 GCCAGCCAACTAGTAACAAACA 59.118 45.455 0.00 0.00 0.00 2.83
65 66 3.058224 GCCAGCCAACTAGTAACAAACAG 60.058 47.826 0.00 0.00 0.00 3.16
66 67 4.134563 CCAGCCAACTAGTAACAAACAGT 58.865 43.478 0.00 0.00 0.00 3.55
67 68 4.024048 CCAGCCAACTAGTAACAAACAGTG 60.024 45.833 0.00 0.00 0.00 3.66
68 69 3.564225 AGCCAACTAGTAACAAACAGTGC 59.436 43.478 0.00 0.00 0.00 4.40
69 70 3.314080 GCCAACTAGTAACAAACAGTGCA 59.686 43.478 0.00 0.00 0.00 4.57
70 71 4.201970 GCCAACTAGTAACAAACAGTGCAA 60.202 41.667 0.00 0.00 0.00 4.08
71 72 5.270853 CCAACTAGTAACAAACAGTGCAAC 58.729 41.667 0.00 0.00 0.00 4.17
72 73 4.789095 ACTAGTAACAAACAGTGCAACG 57.211 40.909 0.00 0.00 45.86 4.10
73 74 2.468532 AGTAACAAACAGTGCAACGC 57.531 45.000 0.00 0.00 45.86 4.84
74 75 1.064952 AGTAACAAACAGTGCAACGCC 59.935 47.619 0.00 0.00 45.86 5.68
75 76 1.064952 GTAACAAACAGTGCAACGCCT 59.935 47.619 0.00 0.00 45.86 5.52
76 77 1.384525 AACAAACAGTGCAACGCCTA 58.615 45.000 0.00 0.00 45.86 3.93
77 78 0.661020 ACAAACAGTGCAACGCCTAC 59.339 50.000 0.00 0.00 45.86 3.18
78 79 0.384230 CAAACAGTGCAACGCCTACG 60.384 55.000 0.00 0.00 45.86 3.51
79 80 1.503818 AAACAGTGCAACGCCTACGG 61.504 55.000 0.00 0.00 45.86 4.02
80 81 3.118454 CAGTGCAACGCCTACGGG 61.118 66.667 0.00 0.00 45.86 5.28
90 91 4.286320 CCTACGGGCTAGGCGCTG 62.286 72.222 7.64 5.28 39.38 5.18
91 92 4.951963 CTACGGGCTAGGCGCTGC 62.952 72.222 7.64 9.76 39.38 5.25
95 96 4.864334 GGGCTAGGCGCTGCACAT 62.864 66.667 7.64 0.00 38.48 3.21
96 97 2.825836 GGCTAGGCGCTGCACATT 60.826 61.111 7.64 0.00 39.13 2.71
97 98 1.523711 GGCTAGGCGCTGCACATTA 60.524 57.895 7.64 0.00 39.13 1.90
98 99 1.643832 GCTAGGCGCTGCACATTAC 59.356 57.895 7.64 0.00 35.14 1.89
99 100 1.089481 GCTAGGCGCTGCACATTACA 61.089 55.000 7.64 0.00 35.14 2.41
100 101 1.586422 CTAGGCGCTGCACATTACAT 58.414 50.000 7.64 0.00 0.00 2.29
101 102 1.262417 CTAGGCGCTGCACATTACATG 59.738 52.381 7.64 0.00 0.00 3.21
102 103 0.677731 AGGCGCTGCACATTACATGT 60.678 50.000 7.64 2.69 46.22 3.21
111 112 2.472695 ACATTACATGTGTGACGCCT 57.527 45.000 9.11 0.00 43.01 5.52
112 113 3.603158 ACATTACATGTGTGACGCCTA 57.397 42.857 9.11 0.00 43.01 3.93
113 114 3.521560 ACATTACATGTGTGACGCCTAG 58.478 45.455 9.11 0.00 43.01 3.02
114 115 2.004583 TTACATGTGTGACGCCTAGC 57.995 50.000 9.11 0.00 0.00 3.42
115 116 1.182667 TACATGTGTGACGCCTAGCT 58.817 50.000 9.11 0.00 0.00 3.32
116 117 0.108615 ACATGTGTGACGCCTAGCTC 60.109 55.000 0.00 0.00 0.00 4.09
117 118 0.174389 CATGTGTGACGCCTAGCTCT 59.826 55.000 0.00 0.00 0.00 4.09
118 119 0.174389 ATGTGTGACGCCTAGCTCTG 59.826 55.000 0.00 0.00 0.00 3.35
119 120 0.893727 TGTGTGACGCCTAGCTCTGA 60.894 55.000 0.00 0.00 0.00 3.27
120 121 0.179150 GTGTGACGCCTAGCTCTGAG 60.179 60.000 0.00 0.00 0.00 3.35
121 122 1.315981 TGTGACGCCTAGCTCTGAGG 61.316 60.000 6.83 0.00 37.12 3.86
122 123 1.000771 TGACGCCTAGCTCTGAGGT 60.001 57.895 14.43 14.43 36.37 3.85
124 125 2.105930 CGCCTAGCTCTGAGGTGC 59.894 66.667 18.98 13.35 37.75 5.01
125 126 2.422231 CGCCTAGCTCTGAGGTGCT 61.422 63.158 18.98 7.34 43.49 4.40
126 127 1.143620 GCCTAGCTCTGAGGTGCTG 59.856 63.158 18.98 8.37 41.56 4.41
127 128 1.143620 CCTAGCTCTGAGGTGCTGC 59.856 63.158 18.98 0.00 41.56 5.25
128 129 1.611474 CCTAGCTCTGAGGTGCTGCA 61.611 60.000 18.98 0.00 41.56 4.41
129 130 0.459934 CTAGCTCTGAGGTGCTGCAC 60.460 60.000 24.02 24.02 41.56 4.57
130 131 0.902048 TAGCTCTGAGGTGCTGCACT 60.902 55.000 29.54 17.00 41.56 4.40
131 132 2.033755 GCTCTGAGGTGCTGCACTG 61.034 63.158 29.54 17.72 34.40 3.66
132 133 1.370437 CTCTGAGGTGCTGCACTGT 59.630 57.895 29.54 18.57 34.40 3.55
133 134 0.250209 CTCTGAGGTGCTGCACTGTT 60.250 55.000 29.54 16.84 34.40 3.16
134 135 0.533531 TCTGAGGTGCTGCACTGTTG 60.534 55.000 29.54 18.03 34.40 3.33
135 136 1.512996 CTGAGGTGCTGCACTGTTGG 61.513 60.000 29.54 13.91 34.40 3.77
136 137 2.203394 AGGTGCTGCACTGTTGGG 60.203 61.111 29.54 0.00 34.40 4.12
137 138 2.519302 GGTGCTGCACTGTTGGGT 60.519 61.111 29.54 0.00 34.40 4.51
138 139 2.723746 GTGCTGCACTGTTGGGTG 59.276 61.111 24.68 0.00 39.91 4.61
144 145 3.297620 CACTGTTGGGTGCAGGCC 61.298 66.667 0.00 0.00 38.22 5.19
167 168 3.286751 GCTGCCACGCTGGACAAA 61.287 61.111 8.04 0.00 40.96 2.83
168 169 2.844451 GCTGCCACGCTGGACAAAA 61.844 57.895 8.04 0.00 40.96 2.44
169 170 1.283793 CTGCCACGCTGGACAAAAG 59.716 57.895 8.04 0.00 40.96 2.27
170 171 1.447317 CTGCCACGCTGGACAAAAGT 61.447 55.000 8.04 0.00 40.96 2.66
171 172 1.008538 GCCACGCTGGACAAAAGTG 60.009 57.895 8.04 0.00 40.96 3.16
172 173 1.008538 CCACGCTGGACAAAAGTGC 60.009 57.895 0.00 0.00 40.96 4.40
173 174 1.723608 CCACGCTGGACAAAAGTGCA 61.724 55.000 0.00 0.00 40.96 4.57
174 175 0.100325 CACGCTGGACAAAAGTGCAA 59.900 50.000 0.00 0.00 0.00 4.08
175 176 0.100503 ACGCTGGACAAAAGTGCAAC 59.899 50.000 0.00 0.00 0.00 4.17
176 177 0.929824 CGCTGGACAAAAGTGCAACG 60.930 55.000 0.00 0.00 45.86 4.10
177 178 1.208642 GCTGGACAAAAGTGCAACGC 61.209 55.000 0.00 0.00 45.86 4.84
178 179 0.594796 CTGGACAAAAGTGCAACGCC 60.595 55.000 0.00 0.00 45.86 5.68
179 180 1.034838 TGGACAAAAGTGCAACGCCT 61.035 50.000 0.00 0.00 45.86 5.52
180 181 0.317854 GGACAAAAGTGCAACGCCTC 60.318 55.000 0.00 0.00 45.86 4.70
181 182 0.380378 GACAAAAGTGCAACGCCTCA 59.620 50.000 0.00 0.00 45.86 3.86
182 183 0.381801 ACAAAAGTGCAACGCCTCAG 59.618 50.000 0.00 0.00 45.86 3.35
183 184 0.662619 CAAAAGTGCAACGCCTCAGA 59.337 50.000 0.00 0.00 45.86 3.27
184 185 0.947244 AAAAGTGCAACGCCTCAGAG 59.053 50.000 0.00 0.00 45.86 3.35
185 186 1.510480 AAAGTGCAACGCCTCAGAGC 61.510 55.000 0.00 0.00 45.86 4.09
186 187 2.358003 GTGCAACGCCTCAGAGCT 60.358 61.111 0.00 0.00 0.00 4.09
187 188 1.079819 GTGCAACGCCTCAGAGCTA 60.080 57.895 0.00 0.00 0.00 3.32
188 189 1.080995 GTGCAACGCCTCAGAGCTAG 61.081 60.000 0.00 0.00 0.00 3.42
189 190 1.520342 GCAACGCCTCAGAGCTAGG 60.520 63.158 0.00 0.00 37.17 3.02
201 202 3.113745 GCTAGGCGCTACACCGTA 58.886 61.111 7.64 0.00 35.14 4.02
202 203 1.008767 GCTAGGCGCTACACCGTAG 60.009 63.158 7.64 0.00 35.14 3.51
203 204 2.403671 GCTAGGCGCTACACCGTAGG 62.404 65.000 7.64 0.00 46.12 3.18
215 216 4.814294 CGTAGGGTGTGGCGCCTC 62.814 72.222 29.70 25.38 33.98 4.70
216 217 4.468689 GTAGGGTGTGGCGCCTCC 62.469 72.222 29.70 24.78 33.98 4.30
230 231 4.394712 CTCCGTGTCAGGCCCCAC 62.395 72.222 0.00 3.07 0.00 4.61
231 232 4.954118 TCCGTGTCAGGCCCCACT 62.954 66.667 13.92 0.00 0.00 4.00
232 233 4.394712 CCGTGTCAGGCCCCACTC 62.395 72.222 13.92 5.26 0.00 3.51
233 234 3.625897 CGTGTCAGGCCCCACTCA 61.626 66.667 13.92 0.00 0.00 3.41
234 235 2.836154 GTGTCAGGCCCCACTCAA 59.164 61.111 0.00 0.00 0.00 3.02
235 236 1.150536 GTGTCAGGCCCCACTCAAA 59.849 57.895 0.00 0.00 0.00 2.69
236 237 0.467290 GTGTCAGGCCCCACTCAAAA 60.467 55.000 0.00 0.00 0.00 2.44
237 238 0.260230 TGTCAGGCCCCACTCAAAAA 59.740 50.000 0.00 0.00 0.00 1.94
238 239 1.133199 TGTCAGGCCCCACTCAAAAAT 60.133 47.619 0.00 0.00 0.00 1.82
239 240 2.109128 TGTCAGGCCCCACTCAAAAATA 59.891 45.455 0.00 0.00 0.00 1.40
240 241 3.245586 TGTCAGGCCCCACTCAAAAATAT 60.246 43.478 0.00 0.00 0.00 1.28
241 242 3.381590 GTCAGGCCCCACTCAAAAATATC 59.618 47.826 0.00 0.00 0.00 1.63
242 243 3.011144 TCAGGCCCCACTCAAAAATATCA 59.989 43.478 0.00 0.00 0.00 2.15
243 244 3.382546 CAGGCCCCACTCAAAAATATCAG 59.617 47.826 0.00 0.00 0.00 2.90
244 245 2.101415 GGCCCCACTCAAAAATATCAGC 59.899 50.000 0.00 0.00 0.00 4.26
245 246 2.101415 GCCCCACTCAAAAATATCAGCC 59.899 50.000 0.00 0.00 0.00 4.85
246 247 2.358898 CCCCACTCAAAAATATCAGCCG 59.641 50.000 0.00 0.00 0.00 5.52
247 248 3.278574 CCCACTCAAAAATATCAGCCGA 58.721 45.455 0.00 0.00 0.00 5.54
248 249 3.313526 CCCACTCAAAAATATCAGCCGAG 59.686 47.826 0.00 0.00 0.00 4.63
249 250 3.941483 CCACTCAAAAATATCAGCCGAGT 59.059 43.478 0.00 0.00 32.67 4.18
250 251 4.201851 CCACTCAAAAATATCAGCCGAGTG 60.202 45.833 9.17 9.17 45.29 3.51
251 252 4.832248 ACTCAAAAATATCAGCCGAGTGA 58.168 39.130 0.00 0.00 31.36 3.41
252 253 5.245531 ACTCAAAAATATCAGCCGAGTGAA 58.754 37.500 0.00 0.00 31.36 3.18
253 254 5.705441 ACTCAAAAATATCAGCCGAGTGAAA 59.295 36.000 0.00 0.00 31.36 2.69
254 255 6.206634 ACTCAAAAATATCAGCCGAGTGAAAA 59.793 34.615 0.00 0.00 31.36 2.29
255 256 6.976088 TCAAAAATATCAGCCGAGTGAAAAA 58.024 32.000 0.00 0.00 0.00 1.94
279 280 9.883142 AAAAATTTAGGACAGTTCATTTTGTGA 57.117 25.926 0.00 0.00 34.25 3.58
280 281 9.883142 AAAATTTAGGACAGTTCATTTTGTGAA 57.117 25.926 0.00 0.00 44.36 3.18
295 296 5.506686 TTTGTGAAATGATTTCGTCCACA 57.493 34.783 12.72 9.22 42.55 4.17
296 297 4.747540 TGTGAAATGATTTCGTCCACAG 57.252 40.909 12.72 0.00 42.55 3.66
297 298 3.501828 TGTGAAATGATTTCGTCCACAGG 59.498 43.478 12.72 0.00 42.55 4.00
298 299 3.502211 GTGAAATGATTTCGTCCACAGGT 59.498 43.478 12.72 0.00 42.55 4.00
299 300 4.023193 GTGAAATGATTTCGTCCACAGGTT 60.023 41.667 12.72 0.00 42.55 3.50
300 301 5.180492 GTGAAATGATTTCGTCCACAGGTTA 59.820 40.000 12.72 0.00 42.55 2.85
301 302 5.765677 TGAAATGATTTCGTCCACAGGTTAA 59.234 36.000 12.72 0.00 42.55 2.01
302 303 6.263392 TGAAATGATTTCGTCCACAGGTTAAA 59.737 34.615 12.72 0.00 42.55 1.52
303 304 6.642707 AATGATTTCGTCCACAGGTTAAAA 57.357 33.333 0.00 0.00 0.00 1.52
304 305 6.834168 ATGATTTCGTCCACAGGTTAAAAT 57.166 33.333 0.00 0.00 0.00 1.82
305 306 6.642707 TGATTTCGTCCACAGGTTAAAATT 57.357 33.333 0.00 0.00 0.00 1.82
306 307 6.442952 TGATTTCGTCCACAGGTTAAAATTG 58.557 36.000 0.00 0.00 0.00 2.32
307 308 5.838531 TTTCGTCCACAGGTTAAAATTGT 57.161 34.783 0.00 0.00 0.00 2.71
308 309 5.427036 TTCGTCCACAGGTTAAAATTGTC 57.573 39.130 0.00 0.00 0.00 3.18
309 310 4.452825 TCGTCCACAGGTTAAAATTGTCA 58.547 39.130 0.00 0.00 0.00 3.58
310 311 4.882427 TCGTCCACAGGTTAAAATTGTCAA 59.118 37.500 0.00 0.00 0.00 3.18
311 312 5.357314 TCGTCCACAGGTTAAAATTGTCAAA 59.643 36.000 0.00 0.00 0.00 2.69
312 313 6.037098 CGTCCACAGGTTAAAATTGTCAAAA 58.963 36.000 0.00 0.00 0.00 2.44
313 314 6.699642 CGTCCACAGGTTAAAATTGTCAAAAT 59.300 34.615 0.00 0.00 0.00 1.82
314 315 7.223777 CGTCCACAGGTTAAAATTGTCAAAATT 59.776 33.333 0.00 0.00 0.00 1.82
315 316 8.334632 GTCCACAGGTTAAAATTGTCAAAATTG 58.665 33.333 0.00 0.00 0.00 2.32
316 317 7.011857 TCCACAGGTTAAAATTGTCAAAATTGC 59.988 33.333 0.00 0.00 0.00 3.56
317 318 7.131565 CACAGGTTAAAATTGTCAAAATTGCC 58.868 34.615 0.00 0.00 0.00 4.52
318 319 6.825721 ACAGGTTAAAATTGTCAAAATTGCCA 59.174 30.769 0.00 0.00 0.00 4.92
319 320 7.131565 CAGGTTAAAATTGTCAAAATTGCCAC 58.868 34.615 0.00 0.00 0.00 5.01
320 321 6.262049 AGGTTAAAATTGTCAAAATTGCCACC 59.738 34.615 0.00 0.00 0.00 4.61
321 322 6.434596 GTTAAAATTGTCAAAATTGCCACCC 58.565 36.000 0.00 0.00 0.00 4.61
322 323 2.857186 ATTGTCAAAATTGCCACCCC 57.143 45.000 0.00 0.00 0.00 4.95
323 324 1.799933 TTGTCAAAATTGCCACCCCT 58.200 45.000 0.00 0.00 0.00 4.79
345 346 1.377366 TTTTCGCTCGTGGCACCAAA 61.377 50.000 12.86 0.99 41.91 3.28
371 372 6.671614 TCGTTTTACTTTCTCTTGCAAGAA 57.328 33.333 28.16 16.82 34.03 2.52
375 376 8.261908 CGTTTTACTTTCTCTTGCAAGAAAATG 58.738 33.333 28.16 24.09 42.93 2.32
395 396 1.002792 GAGCAAGTTTTCGGTTTCGCT 60.003 47.619 0.00 0.00 36.13 4.93
435 439 5.664294 TTTATGGCTGCATTCACATCTTT 57.336 34.783 0.50 0.00 0.00 2.52
437 441 3.306917 TGGCTGCATTCACATCTTTTG 57.693 42.857 0.50 0.00 0.00 2.44
438 442 2.028839 TGGCTGCATTCACATCTTTTGG 60.029 45.455 0.50 0.00 0.00 3.28
439 443 2.613691 GCTGCATTCACATCTTTTGGG 58.386 47.619 0.00 0.00 0.00 4.12
440 444 2.231964 GCTGCATTCACATCTTTTGGGA 59.768 45.455 0.00 0.00 35.39 4.37
442 446 3.499338 TGCATTCACATCTTTTGGGAGT 58.501 40.909 0.00 0.00 39.46 3.85
443 447 3.896888 TGCATTCACATCTTTTGGGAGTT 59.103 39.130 0.00 0.00 39.46 3.01
444 448 5.076182 TGCATTCACATCTTTTGGGAGTTA 58.924 37.500 0.00 0.00 39.46 2.24
445 449 5.048083 TGCATTCACATCTTTTGGGAGTTAC 60.048 40.000 0.00 0.00 39.46 2.50
446 450 5.183904 GCATTCACATCTTTTGGGAGTTACT 59.816 40.000 0.00 0.00 39.46 2.24
447 451 6.623767 GCATTCACATCTTTTGGGAGTTACTC 60.624 42.308 3.36 3.36 39.46 2.59
500 654 7.519032 AACTTGTATACAGAGATAGAGAGGC 57.481 40.000 16.84 0.00 0.00 4.70
570 724 2.809601 CCTGCGAAACCCGTCGAG 60.810 66.667 0.00 0.00 43.86 4.04
652 807 2.359169 CGTTGCAGCCTCCTCCCTA 61.359 63.158 0.00 0.00 0.00 3.53
702 860 2.040464 ATCCGGTGCCCATCTCCT 60.040 61.111 0.00 0.00 0.00 3.69
714 872 1.606889 ATCTCCTATCCGACGGCCC 60.607 63.158 9.66 0.00 0.00 5.80
715 873 2.082836 ATCTCCTATCCGACGGCCCT 62.083 60.000 9.66 0.00 0.00 5.19
730 888 3.093172 CCTCCCCTTCCCCAGCTC 61.093 72.222 0.00 0.00 0.00 4.09
731 889 3.093172 CTCCCCTTCCCCAGCTCC 61.093 72.222 0.00 0.00 0.00 4.70
788 946 5.416947 ACTGTTTCGACTTTACAAGACACT 58.583 37.500 0.00 0.00 0.00 3.55
800 958 0.539986 AAGACACTGACCACCAACGT 59.460 50.000 0.00 0.00 0.00 3.99
845 1331 3.212685 CCCAGATCAAGAGCCAAGAATC 58.787 50.000 0.00 0.00 0.00 2.52
992 1478 2.094286 AGCTTCTGACCAGATCTTGTCG 60.094 50.000 19.03 14.40 37.29 4.35
1298 1784 2.125912 CAGGGACGAGAACGCTGG 60.126 66.667 0.00 0.00 42.08 4.85
1299 1785 3.382832 AGGGACGAGAACGCTGGG 61.383 66.667 0.00 0.00 43.96 4.45
1300 1786 4.452733 GGGACGAGAACGCTGGGG 62.453 72.222 0.00 0.00 43.96 4.96
1301 1787 3.379445 GGACGAGAACGCTGGGGA 61.379 66.667 0.00 0.00 43.96 4.81
1302 1788 2.182030 GACGAGAACGCTGGGGAG 59.818 66.667 0.00 0.00 43.96 4.30
1303 1789 3.358076 GACGAGAACGCTGGGGAGG 62.358 68.421 0.00 0.00 43.96 4.30
1387 1882 3.953828 TCCTCAGGGACAGGGAGA 58.046 61.111 0.00 0.00 36.57 3.71
1388 1883 2.183445 TCCTCAGGGACAGGGAGAA 58.817 57.895 0.00 0.00 36.57 2.87
1389 1884 0.252284 TCCTCAGGGACAGGGAGAAC 60.252 60.000 0.00 0.00 36.57 3.01
1611 2106 1.074471 GGCTGTAGGGGAGATGGGA 60.074 63.158 0.00 0.00 0.00 4.37
1623 2118 1.455217 GATGGGAGCTGCCAATGCT 60.455 57.895 31.97 15.09 44.24 3.79
2051 2559 8.478877 ACTAGATTCGATAGGAGACACATTTTT 58.521 33.333 0.00 0.00 0.00 1.94
2199 2707 9.627123 AATGGTATAGTATGTACTTGCAATGTT 57.373 29.630 0.00 0.00 37.73 2.71
2720 3229 6.273071 TGATCCATTCTGTATGTTCTGTACG 58.727 40.000 0.00 0.00 31.99 3.67
2877 3386 9.703677 AATAAGCTCTTCCTTAGTTACTACTCT 57.296 33.333 0.00 0.00 35.78 3.24
2879 3388 6.723339 AGCTCTTCCTTAGTTACTACTCTCA 58.277 40.000 0.00 0.00 35.78 3.27
2883 3392 3.944015 TCCTTAGTTACTACTCTCACCGC 59.056 47.826 0.00 0.00 35.78 5.68
2886 3395 1.005687 AGTTACTACTCTCACCGCCCT 59.994 52.381 0.00 0.00 0.00 5.19
3533 4042 0.942962 CTCTTCATTGGGCTGATCGC 59.057 55.000 1.55 1.55 38.13 4.58
3557 4066 5.182380 CGCCAAGGAGATAAAAACAAAGGTA 59.818 40.000 0.00 0.00 0.00 3.08
3634 4143 9.214957 ACTCGTGACAAAATGAATAATCTTGTA 57.785 29.630 0.00 0.00 30.62 2.41
3679 4188 3.366374 GGAATGAGGAAGTTTTCAAGGCG 60.366 47.826 0.00 0.00 0.00 5.52
3813 4322 1.898574 CACTTGCTCCCAACGGCTT 60.899 57.895 0.00 0.00 0.00 4.35
3868 4377 3.049674 ACCACGCCATGCTCAACG 61.050 61.111 0.00 0.00 0.00 4.10
3893 4402 3.863041 AGAAAGGTGAAGCGGTCTATTC 58.137 45.455 0.00 0.00 0.00 1.75
3994 4503 0.106419 AGACCCTGGAGTCCGAGATC 60.106 60.000 4.30 0.00 37.49 2.75
4051 4560 1.227002 GAGGGACGAGTTCATCCGC 60.227 63.158 0.00 0.00 35.67 5.54
4299 4808 3.423539 TGTAGCTGCTGAAACTCCAAT 57.576 42.857 13.43 0.00 0.00 3.16
4305 4814 1.425066 TGCTGAAACTCCAATCAGGGT 59.575 47.619 5.08 0.00 42.62 4.34
4336 4845 5.854010 TGCTACTTCAGGTATAGTCCTTG 57.146 43.478 0.00 0.00 35.37 3.61
4480 5035 1.652167 GCCAAAGAGCCTAGCAGCAC 61.652 60.000 0.00 0.00 34.23 4.40
4481 5036 0.035630 CCAAAGAGCCTAGCAGCACT 60.036 55.000 0.00 0.00 35.00 4.40
4482 5037 1.085091 CAAAGAGCCTAGCAGCACTG 58.915 55.000 0.00 0.00 33.72 3.66
4483 5038 0.035630 AAAGAGCCTAGCAGCACTGG 60.036 55.000 0.00 0.00 33.72 4.00
4484 5039 0.906756 AAGAGCCTAGCAGCACTGGA 60.907 55.000 0.00 0.00 33.72 3.86
4485 5040 1.153469 GAGCCTAGCAGCACTGGAC 60.153 63.158 0.00 0.00 34.23 4.02
4523 5078 4.880759 ACGAATGAATGCAGAGGATAGAG 58.119 43.478 0.00 0.00 0.00 2.43
4712 5284 7.285401 ACATTTATATTTGGTAACTGGAGCAGG 59.715 37.037 0.00 0.00 35.51 4.85
4767 5339 6.756299 AATTTGGCAAAACAAAATGACAGT 57.244 29.167 17.70 0.00 42.91 3.55
4888 5460 7.388776 TCCATATGCATCTGAGTATAAACTTGC 59.611 37.037 13.31 0.00 36.63 4.01
4957 5529 3.057969 ACCATCGACAATCAAGCAAGA 57.942 42.857 0.00 0.00 0.00 3.02
5046 5621 2.362077 ACATTCTCTTGGTTGGTGCAAC 59.638 45.455 0.00 0.00 42.89 4.17
5054 5629 1.654220 GTTGGTGCAACATCGTGCT 59.346 52.632 4.62 0.00 45.17 4.40
5075 5650 1.605710 GCATGGTCTCCATCGGAAATG 59.394 52.381 0.00 0.00 43.15 2.32
5089 5664 1.453155 GAAATGCTTCCCTCTGCGAA 58.547 50.000 0.00 0.00 0.00 4.70
5102 5677 2.606725 CTCTGCGAAGGTGATTTGCTAG 59.393 50.000 0.00 0.00 46.93 3.42
5204 5779 4.860802 TCCTTGGCAATATCCTCTGAAA 57.139 40.909 0.00 0.00 0.00 2.69
5257 5832 5.598005 TGTGTCCAGTTCCATTTCTTCAAAT 59.402 36.000 0.00 0.00 31.91 2.32
5410 5985 5.010012 ACTCTTGTGCTTTCCATTGTAAAGG 59.990 40.000 4.19 0.00 35.04 3.11
5446 6021 0.671781 CTTGTCTCAAGCCCAGGACG 60.672 60.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.515979 CCCCAACCCCCAAAGTTGC 61.516 63.158 0.00 0.00 42.63 4.17
3 4 2.329399 ACACCCCAACCCCCAAAGT 61.329 57.895 0.00 0.00 0.00 2.66
5 6 2.283809 CACACCCCAACCCCCAAA 59.716 61.111 0.00 0.00 0.00 3.28
6 7 3.030611 ACACACCCCAACCCCCAA 61.031 61.111 0.00 0.00 0.00 4.12
7 8 3.826822 CACACACCCCAACCCCCA 61.827 66.667 0.00 0.00 0.00 4.96
8 9 4.614036 CCACACACCCCAACCCCC 62.614 72.222 0.00 0.00 0.00 5.40
9 10 4.614036 CCCACACACCCCAACCCC 62.614 72.222 0.00 0.00 0.00 4.95
10 11 4.614036 CCCCACACACCCCAACCC 62.614 72.222 0.00 0.00 0.00 4.11
11 12 4.614036 CCCCCACACACCCCAACC 62.614 72.222 0.00 0.00 0.00 3.77
34 35 4.299796 TTGGCTGGCTGAACCCCC 62.300 66.667 2.00 0.00 37.83 5.40
35 36 2.137177 TAGTTGGCTGGCTGAACCCC 62.137 60.000 2.00 0.00 37.83 4.95
36 37 0.678048 CTAGTTGGCTGGCTGAACCC 60.678 60.000 2.00 0.00 37.83 4.11
37 38 0.036875 ACTAGTTGGCTGGCTGAACC 59.963 55.000 2.00 0.00 39.84 3.62
38 39 2.742589 GTTACTAGTTGGCTGGCTGAAC 59.257 50.000 0.00 0.00 0.00 3.18
39 40 2.370519 TGTTACTAGTTGGCTGGCTGAA 59.629 45.455 0.00 0.00 0.00 3.02
40 41 1.974957 TGTTACTAGTTGGCTGGCTGA 59.025 47.619 0.00 0.00 0.00 4.26
41 42 2.472695 TGTTACTAGTTGGCTGGCTG 57.527 50.000 0.00 0.00 0.00 4.85
42 43 3.146847 GTTTGTTACTAGTTGGCTGGCT 58.853 45.455 0.00 0.00 0.00 4.75
43 44 2.882137 TGTTTGTTACTAGTTGGCTGGC 59.118 45.455 0.00 0.00 0.00 4.85
44 45 4.024048 CACTGTTTGTTACTAGTTGGCTGG 60.024 45.833 0.00 0.00 0.00 4.85
45 46 4.554723 GCACTGTTTGTTACTAGTTGGCTG 60.555 45.833 0.00 0.00 0.00 4.85
46 47 3.564225 GCACTGTTTGTTACTAGTTGGCT 59.436 43.478 0.00 0.00 0.00 4.75
47 48 3.314080 TGCACTGTTTGTTACTAGTTGGC 59.686 43.478 0.00 0.00 0.00 4.52
48 49 5.270853 GTTGCACTGTTTGTTACTAGTTGG 58.729 41.667 0.00 0.00 0.00 3.77
49 50 4.961551 CGTTGCACTGTTTGTTACTAGTTG 59.038 41.667 0.00 0.00 0.00 3.16
50 51 4.495184 GCGTTGCACTGTTTGTTACTAGTT 60.495 41.667 0.00 0.00 0.00 2.24
51 52 3.001939 GCGTTGCACTGTTTGTTACTAGT 59.998 43.478 0.00 0.00 0.00 2.57
52 53 3.541711 GCGTTGCACTGTTTGTTACTAG 58.458 45.455 0.00 0.00 0.00 2.57
53 54 2.288458 GGCGTTGCACTGTTTGTTACTA 59.712 45.455 0.00 0.00 0.00 1.82
54 55 1.064952 GGCGTTGCACTGTTTGTTACT 59.935 47.619 0.00 0.00 0.00 2.24
55 56 1.064952 AGGCGTTGCACTGTTTGTTAC 59.935 47.619 0.00 0.00 0.00 2.50
56 57 1.384525 AGGCGTTGCACTGTTTGTTA 58.615 45.000 0.00 0.00 0.00 2.41
57 58 1.064952 GTAGGCGTTGCACTGTTTGTT 59.935 47.619 0.00 0.00 0.00 2.83
58 59 0.661020 GTAGGCGTTGCACTGTTTGT 59.339 50.000 0.00 0.00 0.00 2.83
59 60 0.384230 CGTAGGCGTTGCACTGTTTG 60.384 55.000 0.00 0.00 0.00 2.93
60 61 1.503818 CCGTAGGCGTTGCACTGTTT 61.504 55.000 0.00 0.00 46.14 2.83
61 62 1.959226 CCGTAGGCGTTGCACTGTT 60.959 57.895 0.00 0.00 46.14 3.16
62 63 2.357034 CCGTAGGCGTTGCACTGT 60.357 61.111 0.00 0.00 46.14 3.55
80 81 4.498537 CATGTAATGTGCAGCGCCTAGC 62.499 54.545 2.29 7.01 42.81 3.42
81 82 1.262417 CATGTAATGTGCAGCGCCTAG 59.738 52.381 2.29 0.00 40.20 3.02
82 83 1.298602 CATGTAATGTGCAGCGCCTA 58.701 50.000 2.29 0.00 40.20 3.93
83 84 2.100846 CATGTAATGTGCAGCGCCT 58.899 52.632 2.29 0.00 40.20 5.52
84 85 4.696078 CATGTAATGTGCAGCGCC 57.304 55.556 2.29 0.00 40.20 6.53
94 95 2.168521 AGCTAGGCGTCACACATGTAAT 59.831 45.455 0.00 0.00 0.00 1.89
95 96 1.548719 AGCTAGGCGTCACACATGTAA 59.451 47.619 0.00 0.00 0.00 2.41
96 97 1.134367 GAGCTAGGCGTCACACATGTA 59.866 52.381 0.00 0.00 0.00 2.29
97 98 0.108615 GAGCTAGGCGTCACACATGT 60.109 55.000 0.00 0.00 0.00 3.21
98 99 0.174389 AGAGCTAGGCGTCACACATG 59.826 55.000 0.00 0.00 0.00 3.21
99 100 0.174389 CAGAGCTAGGCGTCACACAT 59.826 55.000 0.00 0.00 0.00 3.21
100 101 0.893727 TCAGAGCTAGGCGTCACACA 60.894 55.000 0.00 0.00 0.00 3.72
101 102 0.179150 CTCAGAGCTAGGCGTCACAC 60.179 60.000 0.00 0.00 0.00 3.82
102 103 1.315981 CCTCAGAGCTAGGCGTCACA 61.316 60.000 0.00 0.00 0.00 3.58
103 104 1.316706 ACCTCAGAGCTAGGCGTCAC 61.317 60.000 0.60 0.00 37.67 3.67
104 105 1.000771 ACCTCAGAGCTAGGCGTCA 60.001 57.895 0.60 0.00 37.67 4.35
105 106 1.435515 CACCTCAGAGCTAGGCGTC 59.564 63.158 0.60 0.00 37.67 5.19
106 107 2.716017 GCACCTCAGAGCTAGGCGT 61.716 63.158 0.60 0.00 37.67 5.68
107 108 2.105930 GCACCTCAGAGCTAGGCG 59.894 66.667 0.60 0.00 37.67 5.52
108 109 1.143620 CAGCACCTCAGAGCTAGGC 59.856 63.158 0.60 0.00 37.90 3.93
109 110 1.143620 GCAGCACCTCAGAGCTAGG 59.856 63.158 0.00 0.00 37.90 3.02
110 111 0.459934 GTGCAGCACCTCAGAGCTAG 60.460 60.000 15.27 0.00 37.90 3.42
111 112 0.902048 AGTGCAGCACCTCAGAGCTA 60.902 55.000 22.41 0.00 37.90 3.32
112 113 2.215625 AGTGCAGCACCTCAGAGCT 61.216 57.895 22.41 0.00 40.96 4.09
113 114 2.033755 CAGTGCAGCACCTCAGAGC 61.034 63.158 22.41 0.00 34.49 4.09
114 115 0.250209 AACAGTGCAGCACCTCAGAG 60.250 55.000 22.41 7.88 34.49 3.35
115 116 0.533531 CAACAGTGCAGCACCTCAGA 60.534 55.000 22.41 0.00 34.49 3.27
116 117 1.512996 CCAACAGTGCAGCACCTCAG 61.513 60.000 22.41 12.04 34.49 3.35
117 118 1.526686 CCAACAGTGCAGCACCTCA 60.527 57.895 22.41 0.00 34.49 3.86
118 119 2.263741 CCCAACAGTGCAGCACCTC 61.264 63.158 22.41 0.00 34.49 3.85
119 120 2.203394 CCCAACAGTGCAGCACCT 60.203 61.111 22.41 6.79 34.49 4.00
120 121 2.519302 ACCCAACAGTGCAGCACC 60.519 61.111 22.41 4.38 34.49 5.01
121 122 2.723746 CACCCAACAGTGCAGCAC 59.276 61.111 18.55 18.55 34.10 4.40
127 128 3.297620 GGCCTGCACCCAACAGTG 61.298 66.667 0.00 0.00 40.88 3.66
150 151 2.737932 CTTTTGTCCAGCGTGGCAGC 62.738 60.000 0.00 0.00 37.47 5.25
151 152 1.283793 CTTTTGTCCAGCGTGGCAG 59.716 57.895 0.00 0.00 37.47 4.85
152 153 1.453015 ACTTTTGTCCAGCGTGGCA 60.453 52.632 0.00 0.00 37.47 4.92
153 154 1.008538 CACTTTTGTCCAGCGTGGC 60.009 57.895 0.00 0.00 37.47 5.01
154 155 1.008538 GCACTTTTGTCCAGCGTGG 60.009 57.895 0.00 0.00 39.43 4.94
155 156 0.100325 TTGCACTTTTGTCCAGCGTG 59.900 50.000 0.00 0.00 0.00 5.34
156 157 0.100503 GTTGCACTTTTGTCCAGCGT 59.899 50.000 0.00 0.00 0.00 5.07
157 158 0.929824 CGTTGCACTTTTGTCCAGCG 60.930 55.000 0.00 0.00 38.36 5.18
158 159 1.208642 GCGTTGCACTTTTGTCCAGC 61.209 55.000 0.00 0.00 0.00 4.85
159 160 0.594796 GGCGTTGCACTTTTGTCCAG 60.595 55.000 0.00 0.00 0.00 3.86
160 161 1.034838 AGGCGTTGCACTTTTGTCCA 61.035 50.000 0.00 0.00 0.00 4.02
161 162 0.317854 GAGGCGTTGCACTTTTGTCC 60.318 55.000 0.00 0.00 0.00 4.02
162 163 0.380378 TGAGGCGTTGCACTTTTGTC 59.620 50.000 0.00 0.00 0.00 3.18
163 164 0.381801 CTGAGGCGTTGCACTTTTGT 59.618 50.000 0.00 0.00 0.00 2.83
164 165 0.662619 TCTGAGGCGTTGCACTTTTG 59.337 50.000 0.00 0.00 0.00 2.44
165 166 0.947244 CTCTGAGGCGTTGCACTTTT 59.053 50.000 0.00 0.00 0.00 2.27
166 167 1.510480 GCTCTGAGGCGTTGCACTTT 61.510 55.000 6.83 0.00 0.00 2.66
167 168 1.963338 GCTCTGAGGCGTTGCACTT 60.963 57.895 6.83 0.00 0.00 3.16
168 169 1.536073 TAGCTCTGAGGCGTTGCACT 61.536 55.000 6.83 0.00 37.29 4.40
169 170 1.079819 TAGCTCTGAGGCGTTGCAC 60.080 57.895 6.83 0.00 37.29 4.57
170 171 1.216444 CTAGCTCTGAGGCGTTGCA 59.784 57.895 6.83 0.00 37.29 4.08
171 172 1.520342 CCTAGCTCTGAGGCGTTGC 60.520 63.158 6.83 0.00 37.29 4.17
172 173 4.823276 CCTAGCTCTGAGGCGTTG 57.177 61.111 6.83 0.00 37.29 4.10
185 186 1.653115 CCTACGGTGTAGCGCCTAG 59.347 63.158 2.29 0.00 0.00 3.02
186 187 1.825191 CCCTACGGTGTAGCGCCTA 60.825 63.158 2.29 0.00 0.00 3.93
187 188 3.145551 CCCTACGGTGTAGCGCCT 61.146 66.667 2.29 0.00 0.00 5.52
188 189 3.455469 ACCCTACGGTGTAGCGCC 61.455 66.667 2.29 0.00 42.48 6.53
198 199 4.814294 GAGGCGCCACACCCTACG 62.814 72.222 31.54 0.00 0.00 3.51
199 200 4.468689 GGAGGCGCCACACCCTAC 62.469 72.222 31.54 2.60 36.34 3.18
213 214 4.394712 GTGGGGCCTGACACGGAG 62.395 72.222 0.84 0.00 0.00 4.63
214 215 4.954118 AGTGGGGCCTGACACGGA 62.954 66.667 16.26 0.00 42.25 4.69
215 216 4.394712 GAGTGGGGCCTGACACGG 62.395 72.222 16.26 0.00 42.25 4.94
216 217 2.674563 TTTGAGTGGGGCCTGACACG 62.675 60.000 16.26 0.00 42.25 4.49
217 218 0.467290 TTTTGAGTGGGGCCTGACAC 60.467 55.000 15.04 15.04 37.86 3.67
218 219 0.260230 TTTTTGAGTGGGGCCTGACA 59.740 50.000 0.84 0.00 0.00 3.58
219 220 1.632589 ATTTTTGAGTGGGGCCTGAC 58.367 50.000 0.84 0.01 0.00 3.51
220 221 3.011144 TGATATTTTTGAGTGGGGCCTGA 59.989 43.478 0.84 0.00 0.00 3.86
221 222 3.364549 TGATATTTTTGAGTGGGGCCTG 58.635 45.455 0.84 0.00 0.00 4.85
222 223 3.635591 CTGATATTTTTGAGTGGGGCCT 58.364 45.455 0.84 0.00 0.00 5.19
223 224 2.101415 GCTGATATTTTTGAGTGGGGCC 59.899 50.000 0.00 0.00 0.00 5.80
224 225 2.101415 GGCTGATATTTTTGAGTGGGGC 59.899 50.000 0.00 0.00 0.00 5.80
225 226 2.358898 CGGCTGATATTTTTGAGTGGGG 59.641 50.000 0.00 0.00 0.00 4.96
226 227 3.278574 TCGGCTGATATTTTTGAGTGGG 58.721 45.455 0.00 0.00 0.00 4.61
227 228 3.941483 ACTCGGCTGATATTTTTGAGTGG 59.059 43.478 0.00 0.00 34.21 4.00
228 229 4.901814 CACTCGGCTGATATTTTTGAGTG 58.098 43.478 0.00 5.23 43.78 3.51
229 230 4.832248 TCACTCGGCTGATATTTTTGAGT 58.168 39.130 0.00 0.00 35.73 3.41
230 231 5.801350 TTCACTCGGCTGATATTTTTGAG 57.199 39.130 0.00 0.00 0.00 3.02
231 232 6.567687 TTTTCACTCGGCTGATATTTTTGA 57.432 33.333 0.00 0.00 0.00 2.69
253 254 9.883142 TCACAAAATGAACTGTCCTAAATTTTT 57.117 25.926 0.00 0.00 33.02 1.94
254 255 9.883142 TTCACAAAATGAACTGTCCTAAATTTT 57.117 25.926 0.00 0.00 42.62 1.82
271 272 6.511416 TGTGGACGAAATCATTTCACAAAAT 58.489 32.000 10.76 0.00 39.63 1.82
272 273 5.895928 TGTGGACGAAATCATTTCACAAAA 58.104 33.333 10.76 0.00 39.63 2.44
273 274 5.506686 TGTGGACGAAATCATTTCACAAA 57.493 34.783 10.76 0.00 39.63 2.83
274 275 4.023279 CCTGTGGACGAAATCATTTCACAA 60.023 41.667 10.76 0.00 39.63 3.33
275 276 3.501828 CCTGTGGACGAAATCATTTCACA 59.498 43.478 10.76 6.57 39.63 3.58
276 277 3.502211 ACCTGTGGACGAAATCATTTCAC 59.498 43.478 10.76 2.25 39.63 3.18
277 278 3.750371 ACCTGTGGACGAAATCATTTCA 58.250 40.909 10.76 0.00 39.63 2.69
278 279 4.766404 AACCTGTGGACGAAATCATTTC 57.234 40.909 0.00 0.00 36.32 2.17
279 280 6.642707 TTTAACCTGTGGACGAAATCATTT 57.357 33.333 0.00 0.00 0.00 2.32
280 281 6.642707 TTTTAACCTGTGGACGAAATCATT 57.357 33.333 0.00 0.00 0.00 2.57
281 282 6.834168 ATTTTAACCTGTGGACGAAATCAT 57.166 33.333 0.00 0.00 0.00 2.45
282 283 6.039941 ACAATTTTAACCTGTGGACGAAATCA 59.960 34.615 0.00 0.00 0.00 2.57
283 284 6.443792 ACAATTTTAACCTGTGGACGAAATC 58.556 36.000 0.00 0.00 0.00 2.17
284 285 6.039941 TGACAATTTTAACCTGTGGACGAAAT 59.960 34.615 0.00 0.00 0.00 2.17
285 286 5.357314 TGACAATTTTAACCTGTGGACGAAA 59.643 36.000 0.00 0.00 0.00 3.46
286 287 4.882427 TGACAATTTTAACCTGTGGACGAA 59.118 37.500 0.00 0.00 0.00 3.85
287 288 4.452825 TGACAATTTTAACCTGTGGACGA 58.547 39.130 0.00 0.00 0.00 4.20
288 289 4.822036 TGACAATTTTAACCTGTGGACG 57.178 40.909 0.00 0.00 0.00 4.79
289 290 8.334632 CAATTTTGACAATTTTAACCTGTGGAC 58.665 33.333 0.00 0.00 0.00 4.02
290 291 7.011857 GCAATTTTGACAATTTTAACCTGTGGA 59.988 33.333 0.00 0.00 0.00 4.02
291 292 7.131565 GCAATTTTGACAATTTTAACCTGTGG 58.868 34.615 0.00 0.00 0.00 4.17
292 293 7.131565 GGCAATTTTGACAATTTTAACCTGTG 58.868 34.615 0.00 0.00 35.83 3.66
293 294 6.825721 TGGCAATTTTGACAATTTTAACCTGT 59.174 30.769 0.00 0.00 44.72 4.00
294 295 7.256756 TGGCAATTTTGACAATTTTAACCTG 57.743 32.000 0.00 0.00 44.72 4.00
305 306 2.158385 ACTAGGGGTGGCAATTTTGACA 60.158 45.455 0.00 0.00 45.70 3.58
306 307 2.525368 ACTAGGGGTGGCAATTTTGAC 58.475 47.619 0.00 0.00 36.50 3.18
307 308 2.990740 ACTAGGGGTGGCAATTTTGA 57.009 45.000 0.00 0.00 0.00 2.69
308 309 4.314961 GAAAACTAGGGGTGGCAATTTTG 58.685 43.478 0.00 0.00 0.00 2.44
309 310 3.006430 CGAAAACTAGGGGTGGCAATTTT 59.994 43.478 0.00 0.00 0.00 1.82
310 311 2.560981 CGAAAACTAGGGGTGGCAATTT 59.439 45.455 0.00 0.00 0.00 1.82
311 312 2.167662 CGAAAACTAGGGGTGGCAATT 58.832 47.619 0.00 0.00 0.00 2.32
312 313 1.834188 CGAAAACTAGGGGTGGCAAT 58.166 50.000 0.00 0.00 0.00 3.56
313 314 0.891904 GCGAAAACTAGGGGTGGCAA 60.892 55.000 0.00 0.00 0.00 4.52
314 315 1.302993 GCGAAAACTAGGGGTGGCA 60.303 57.895 0.00 0.00 0.00 4.92
315 316 1.002502 AGCGAAAACTAGGGGTGGC 60.003 57.895 0.00 0.00 0.00 5.01
316 317 0.739813 CGAGCGAAAACTAGGGGTGG 60.740 60.000 0.00 0.00 0.00 4.61
317 318 0.037605 ACGAGCGAAAACTAGGGGTG 60.038 55.000 0.00 0.00 0.00 4.61
318 319 0.037605 CACGAGCGAAAACTAGGGGT 60.038 55.000 0.00 0.00 0.00 4.95
319 320 0.739813 CCACGAGCGAAAACTAGGGG 60.740 60.000 0.00 0.00 28.92 4.79
320 321 1.359459 GCCACGAGCGAAAACTAGGG 61.359 60.000 0.00 0.00 0.00 3.53
321 322 2.079049 GCCACGAGCGAAAACTAGG 58.921 57.895 0.00 0.00 0.00 3.02
345 346 7.703328 TCTTGCAAGAGAAAGTAAAACGAAAT 58.297 30.769 25.16 0.00 31.81 2.17
371 372 4.041723 CGAAACCGAAAACTTGCTCATTT 58.958 39.130 0.00 0.00 0.00 2.32
375 376 1.002792 AGCGAAACCGAAAACTTGCTC 60.003 47.619 0.00 0.00 0.00 4.26
395 396 5.304101 CCATAAAATAGTGCCTTATTGCCCA 59.696 40.000 0.00 0.00 0.00 5.36
442 446 9.909644 GCGAGATTTAAAGATGTATAGGAGTAA 57.090 33.333 0.00 0.00 0.00 2.24
443 447 9.298250 AGCGAGATTTAAAGATGTATAGGAGTA 57.702 33.333 0.00 0.00 0.00 2.59
444 448 8.184304 AGCGAGATTTAAAGATGTATAGGAGT 57.816 34.615 0.00 0.00 0.00 3.85
492 646 1.332195 CATGATGACCGGCCTCTCTA 58.668 55.000 0.00 0.00 0.00 2.43
570 724 0.319641 GTCGAGAGTGGGGTCAACAC 60.320 60.000 0.00 0.00 39.10 3.32
652 807 1.698067 TTTGAAACGTCGGGGAGGGT 61.698 55.000 0.00 0.00 0.00 4.34
702 860 4.928140 GGGGAGGGCCGTCGGATA 62.928 72.222 17.49 0.00 33.83 2.59
714 872 3.093172 GGAGCTGGGGAAGGGGAG 61.093 72.222 0.00 0.00 0.00 4.30
715 873 4.760220 GGGAGCTGGGGAAGGGGA 62.760 72.222 0.00 0.00 0.00 4.81
788 946 0.959553 GAGAGAGACGTTGGTGGTCA 59.040 55.000 0.00 0.00 36.87 4.02
800 958 1.529796 GCGGAGAGAGGGAGAGAGA 59.470 63.158 0.00 0.00 0.00 3.10
845 1331 3.485877 GCAAGATCTCGAAATTTGACCGG 60.486 47.826 0.00 0.00 0.00 5.28
992 1478 1.227002 GAGACCGGCATCTTCGTCC 60.227 63.158 0.00 0.00 0.00 4.79
1297 1783 2.612251 CTCCTCCTCCTCCTCCCC 59.388 72.222 0.00 0.00 0.00 4.81
1298 1784 2.612251 CCTCCTCCTCCTCCTCCC 59.388 72.222 0.00 0.00 0.00 4.30
1299 1785 2.612251 CCCTCCTCCTCCTCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
1300 1786 2.612251 CCCCTCCTCCTCCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
1301 1787 3.039526 CCCCCTCCTCCTCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
1302 1788 3.036959 TCCCCCTCCTCCTCCTCC 61.037 72.222 0.00 0.00 0.00 4.30
1303 1789 2.612251 CTCCCCCTCCTCCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
1380 1875 0.967380 GCCCCATGTTGTTCTCCCTG 60.967 60.000 0.00 0.00 0.00 4.45
1381 1876 1.384191 GCCCCATGTTGTTCTCCCT 59.616 57.895 0.00 0.00 0.00 4.20
1382 1877 1.682344 GGCCCCATGTTGTTCTCCC 60.682 63.158 0.00 0.00 0.00 4.30
1383 1878 0.681243 GAGGCCCCATGTTGTTCTCC 60.681 60.000 0.00 0.00 0.00 3.71
1384 1879 0.681243 GGAGGCCCCATGTTGTTCTC 60.681 60.000 0.00 0.00 34.14 2.87
1385 1880 1.384191 GGAGGCCCCATGTTGTTCT 59.616 57.895 0.00 0.00 34.14 3.01
1386 1881 2.046285 CGGAGGCCCCATGTTGTTC 61.046 63.158 0.00 0.00 34.14 3.18
1387 1882 2.035626 CGGAGGCCCCATGTTGTT 59.964 61.111 0.00 0.00 34.14 2.83
1388 1883 4.047125 CCGGAGGCCCCATGTTGT 62.047 66.667 0.00 0.00 46.14 3.32
1542 2037 4.737177 AGCTTCCTGGCCTGCAGC 62.737 66.667 18.87 18.87 42.60 5.25
1611 2106 3.437795 GCGTCAGCATTGGCAGCT 61.438 61.111 0.00 0.00 44.61 4.24
1623 2118 4.680237 CGGCTCCCTGTTGCGTCA 62.680 66.667 0.00 0.00 0.00 4.35
1943 2448 7.039784 ACAAACAACTGCATCTTGGTATATTGT 60.040 33.333 8.65 8.14 0.00 2.71
1944 2449 7.274033 CACAAACAACTGCATCTTGGTATATTG 59.726 37.037 8.65 7.70 0.00 1.90
1945 2450 7.315142 CACAAACAACTGCATCTTGGTATATT 58.685 34.615 8.65 0.00 0.00 1.28
1946 2451 6.625740 GCACAAACAACTGCATCTTGGTATAT 60.626 38.462 8.65 0.00 33.31 0.86
1947 2452 5.335583 GCACAAACAACTGCATCTTGGTATA 60.336 40.000 8.65 0.00 33.31 1.47
1948 2453 4.559300 GCACAAACAACTGCATCTTGGTAT 60.559 41.667 8.65 0.00 33.31 2.73
1949 2454 3.243367 GCACAAACAACTGCATCTTGGTA 60.243 43.478 8.65 0.00 33.31 3.25
1950 2455 2.481795 GCACAAACAACTGCATCTTGGT 60.482 45.455 8.65 0.00 33.31 3.67
1951 2456 2.129607 GCACAAACAACTGCATCTTGG 58.870 47.619 8.65 0.00 33.31 3.61
1952 2457 3.047796 GAGCACAAACAACTGCATCTTG 58.952 45.455 0.00 0.00 35.73 3.02
1953 2458 2.954318 AGAGCACAAACAACTGCATCTT 59.046 40.909 0.00 0.00 35.73 2.40
1954 2459 2.579873 AGAGCACAAACAACTGCATCT 58.420 42.857 0.00 0.00 35.73 2.90
2067 2575 7.606456 CACAAATACTACCACTTCTGTAACCAT 59.394 37.037 0.00 0.00 0.00 3.55
2074 2582 8.099364 ACATTTCACAAATACTACCACTTCTG 57.901 34.615 0.00 0.00 0.00 3.02
2199 2707 4.464008 AGTGGAGAAGTGCAATTGAGAAA 58.536 39.130 10.34 0.00 0.00 2.52
2877 3386 5.593679 GCTCTTATATTATAGGGCGGTGA 57.406 43.478 0.00 0.00 0.00 4.02
2947 3456 0.251474 TGCAAAGCAATGCTCCCTCT 60.251 50.000 8.71 0.00 46.54 3.69
3533 4042 4.022329 ACCTTTGTTTTTATCTCCTTGGCG 60.022 41.667 0.00 0.00 0.00 5.69
3634 4143 2.299867 AGCGGTCAATGGCTGAAAAATT 59.700 40.909 0.00 0.00 38.27 1.82
3868 4377 0.668535 ACCGCTTCACCTTTCTTTGC 59.331 50.000 0.00 0.00 0.00 3.68
3893 4402 2.285827 CTGAAACAGCTCCCGTCTAG 57.714 55.000 0.00 0.00 0.00 2.43
3994 4503 4.815269 AGTGTTCCTTCTTCATCTTCTCG 58.185 43.478 0.00 0.00 0.00 4.04
4051 4560 3.815401 AGTTCTTCCTGTTGATCAAACCG 59.185 43.478 10.35 1.41 38.06 4.44
4299 4808 1.559682 GTAGCATTGAAGGGACCCTGA 59.440 52.381 15.76 3.65 32.13 3.86
4305 4814 2.912956 ACCTGAAGTAGCATTGAAGGGA 59.087 45.455 0.00 0.00 0.00 4.20
4336 4845 1.552337 TCTTGGGAGTGATGTGAGCTC 59.448 52.381 6.82 6.82 0.00 4.09
4371 4885 9.627123 GGAGTAATTTATATGCTGCCCATATTA 57.373 33.333 10.95 1.98 43.03 0.98
4372 4886 8.339247 AGGAGTAATTTATATGCTGCCCATATT 58.661 33.333 10.95 0.83 43.03 1.28
4480 5035 1.992277 CCTGAGGGTCCAGGTCCAG 60.992 68.421 4.97 0.00 46.62 3.86
4481 5036 2.122729 CCTGAGGGTCCAGGTCCA 59.877 66.667 4.97 0.00 46.62 4.02
4548 5103 9.988815 ATAAACTCCAATTAGTATAGCTGACAG 57.011 33.333 0.00 0.00 0.00 3.51
4549 5104 9.982651 GATAAACTCCAATTAGTATAGCTGACA 57.017 33.333 0.00 0.00 0.00 3.58
4712 5284 7.370383 ACATTCAGATGGAAAATGTGTAACAC 58.630 34.615 0.00 0.00 45.29 3.32
4767 5339 9.609346 GTGAGAACTGCCCTTAACTTTATATAA 57.391 33.333 0.00 0.00 0.00 0.98
5046 5621 1.434622 GGAGACCATGCAGCACGATG 61.435 60.000 0.00 0.00 0.00 3.84
5054 5629 0.617935 TTTCCGATGGAGACCATGCA 59.382 50.000 8.06 0.00 45.26 3.96
5089 5664 4.006319 GAGAAAGCACTAGCAAATCACCT 58.994 43.478 0.00 0.00 45.49 4.00
5204 5779 4.557144 AGCAGAAGAGGCTGGACT 57.443 55.556 0.00 0.00 40.80 3.85
5257 5832 0.532573 GCTGCAGCAGTGGTAGTAGA 59.467 55.000 33.36 0.00 41.59 2.59
5410 5985 1.959282 CAAGGCTCTTCCATATTGCCC 59.041 52.381 0.00 0.00 44.19 5.36
5446 6021 1.555075 TCATACAGTCTTGGCAGGGAC 59.445 52.381 12.65 12.65 0.00 4.46


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

AutoCloner maintained by Alex Coulton.