Multiple sequence alignment - TraesCS1A01G062200

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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 TraesCS1A01G062200 chr1A 100.000 2648 0 0 1 2648 42604901 42602254 0.000000e+00 4891.0
1 TraesCS1A01G062200 chr1B 91.794 2352 116 36 311 2616 63092155 63089835 0.000000e+00 3203.0
2 TraesCS1A01G062200 chr2D 91.430 1937 109 34 734 2648 4496696 4498597 0.000000e+00 2604.0
3 TraesCS1A01G062200 chr2D 84.694 98 15 0 318 415 4496153 4496250 6.030000e-17 99.0
4 TraesCS1A01G062200 chr4D 91.797 256 19 2 15 269 134665968 134665714 3.240000e-94 355.0
5 TraesCS1A01G062200 chr4A 88.433 268 27 3 1 267 699912102 699912366 1.180000e-83 320.0
6 TraesCS1A01G062200 chr5B 88.017 242 27 2 1 242 539260541 539260302 4.310000e-73 285.0
7 TraesCS1A01G062200 chrUn 84.694 98 15 0 318 415 270954147 270954050 6.030000e-17 99.0
8 TraesCS1A01G062200 chr6D 92.308 52 4 0 415 466 292029134 292029083 1.020000e-09 75.0
9 TraesCS1A01G062200 chr6D 92.308 52 3 1 415 466 117413149 117413099 3.660000e-09 73.1
10 TraesCS1A01G062200 chr6D 92.000 50 4 0 414 463 34399139 34399188 1.320000e-08 71.3
11 TraesCS1A01G062200 chr2A 93.878 49 2 1 415 462 7731305 7731257 3.660000e-09 73.1
12 TraesCS1A01G062200 chr7A 100.000 35 0 0 276 310 9052763 9052797 6.120000e-07 65.8
13 TraesCS1A01G062200 chr5D 90.698 43 4 0 420 462 348499991 348500033 1.020000e-04 58.4


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 TraesCS1A01G062200 chr1A 42602254 42604901 2647 True 4891.0 4891 100.000 1 2648 1 chr1A.!!$R1 2647
1 TraesCS1A01G062200 chr1B 63089835 63092155 2320 True 3203.0 3203 91.794 311 2616 1 chr1B.!!$R1 2305
2 TraesCS1A01G062200 chr2D 4496153 4498597 2444 False 1351.5 2604 88.062 318 2648 2 chr2D.!!$F1 2330

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
146 147 0.034477 ATGTAAAACCTGGCCCCGAG 60.034 55.0 0.0 0.0 0.0 4.63 F
289 290 0.105039 GTCCTCCCCAACTCGCTATG 59.895 60.0 0.0 0.0 0.0 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1560 1868 2.100797 CCGCCGTCGACGACATAA 59.899 61.111 37.65 0.0 43.02 1.90 R
2616 2973 2.201921 TACCGCCAAATTGTTGCCTA 57.798 45.000 0.00 0.0 33.01 3.93 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 3.480133 CTCCGATCCCCCACCACC 61.480 72.222 0.00 0.00 0.00 4.61
33 34 4.805768 CCCCGGTTTGCGCCCATA 62.806 66.667 4.18 0.00 0.00 2.74
34 35 2.518349 CCCGGTTTGCGCCCATAT 60.518 61.111 4.18 0.00 0.00 1.78
35 36 2.551912 CCCGGTTTGCGCCCATATC 61.552 63.158 4.18 0.00 0.00 1.63
36 37 1.821759 CCGGTTTGCGCCCATATCA 60.822 57.895 4.18 0.00 0.00 2.15
37 38 1.355210 CGGTTTGCGCCCATATCAC 59.645 57.895 4.18 0.00 0.00 3.06
38 39 1.095228 CGGTTTGCGCCCATATCACT 61.095 55.000 4.18 0.00 0.00 3.41
39 40 0.381801 GGTTTGCGCCCATATCACTG 59.618 55.000 4.18 0.00 0.00 3.66
40 41 0.248621 GTTTGCGCCCATATCACTGC 60.249 55.000 4.18 0.00 0.00 4.40
41 42 1.383456 TTTGCGCCCATATCACTGCC 61.383 55.000 4.18 0.00 0.00 4.85
42 43 2.980233 GCGCCCATATCACTGCCC 60.980 66.667 0.00 0.00 0.00 5.36
43 44 2.666190 CGCCCATATCACTGCCCG 60.666 66.667 0.00 0.00 0.00 6.13
44 45 2.828868 GCCCATATCACTGCCCGA 59.171 61.111 0.00 0.00 0.00 5.14
45 46 1.376466 GCCCATATCACTGCCCGAT 59.624 57.895 0.00 0.00 0.00 4.18
46 47 0.674895 GCCCATATCACTGCCCGATC 60.675 60.000 0.00 0.00 0.00 3.69
47 48 0.036010 CCCATATCACTGCCCGATCC 60.036 60.000 0.00 0.00 0.00 3.36
48 49 0.979665 CCATATCACTGCCCGATCCT 59.020 55.000 0.00 0.00 0.00 3.24
49 50 1.066573 CCATATCACTGCCCGATCCTC 60.067 57.143 0.00 0.00 0.00 3.71
50 51 1.066573 CATATCACTGCCCGATCCTCC 60.067 57.143 0.00 0.00 0.00 4.30
51 52 0.188587 TATCACTGCCCGATCCTCCT 59.811 55.000 0.00 0.00 0.00 3.69
52 53 0.692419 ATCACTGCCCGATCCTCCTT 60.692 55.000 0.00 0.00 0.00 3.36
53 54 1.144936 CACTGCCCGATCCTCCTTC 59.855 63.158 0.00 0.00 0.00 3.46
54 55 1.002274 ACTGCCCGATCCTCCTTCT 59.998 57.895 0.00 0.00 0.00 2.85
55 56 0.618968 ACTGCCCGATCCTCCTTCTT 60.619 55.000 0.00 0.00 0.00 2.52
56 57 0.179062 CTGCCCGATCCTCCTTCTTG 60.179 60.000 0.00 0.00 0.00 3.02
57 58 1.524849 GCCCGATCCTCCTTCTTGC 60.525 63.158 0.00 0.00 0.00 4.01
58 59 1.147153 CCCGATCCTCCTTCTTGCC 59.853 63.158 0.00 0.00 0.00 4.52
59 60 1.341156 CCCGATCCTCCTTCTTGCCT 61.341 60.000 0.00 0.00 0.00 4.75
60 61 0.105778 CCGATCCTCCTTCTTGCCTC 59.894 60.000 0.00 0.00 0.00 4.70
61 62 0.105778 CGATCCTCCTTCTTGCCTCC 59.894 60.000 0.00 0.00 0.00 4.30
62 63 0.472044 GATCCTCCTTCTTGCCTCCC 59.528 60.000 0.00 0.00 0.00 4.30
63 64 0.045469 ATCCTCCTTCTTGCCTCCCT 59.955 55.000 0.00 0.00 0.00 4.20
64 65 0.716591 TCCTCCTTCTTGCCTCCCTA 59.283 55.000 0.00 0.00 0.00 3.53
65 66 0.833949 CCTCCTTCTTGCCTCCCTAC 59.166 60.000 0.00 0.00 0.00 3.18
66 67 1.623834 CCTCCTTCTTGCCTCCCTACT 60.624 57.143 0.00 0.00 0.00 2.57
67 68 2.192263 CTCCTTCTTGCCTCCCTACTT 58.808 52.381 0.00 0.00 0.00 2.24
68 69 2.169561 CTCCTTCTTGCCTCCCTACTTC 59.830 54.545 0.00 0.00 0.00 3.01
69 70 2.192263 CCTTCTTGCCTCCCTACTTCT 58.808 52.381 0.00 0.00 0.00 2.85
70 71 2.169561 CCTTCTTGCCTCCCTACTTCTC 59.830 54.545 0.00 0.00 0.00 2.87
71 72 1.867363 TCTTGCCTCCCTACTTCTCC 58.133 55.000 0.00 0.00 0.00 3.71
72 73 0.833949 CTTGCCTCCCTACTTCTCCC 59.166 60.000 0.00 0.00 0.00 4.30
73 74 0.976073 TTGCCTCCCTACTTCTCCCG 60.976 60.000 0.00 0.00 0.00 5.14
74 75 1.076192 GCCTCCCTACTTCTCCCGA 60.076 63.158 0.00 0.00 0.00 5.14
75 76 0.470268 GCCTCCCTACTTCTCCCGAT 60.470 60.000 0.00 0.00 0.00 4.18
76 77 2.035331 GCCTCCCTACTTCTCCCGATT 61.035 57.143 0.00 0.00 0.00 3.34
77 78 1.689273 CCTCCCTACTTCTCCCGATTG 59.311 57.143 0.00 0.00 0.00 2.67
78 79 1.069358 CTCCCTACTTCTCCCGATTGC 59.931 57.143 0.00 0.00 0.00 3.56
79 80 0.830648 CCCTACTTCTCCCGATTGCA 59.169 55.000 0.00 0.00 0.00 4.08
80 81 1.417890 CCCTACTTCTCCCGATTGCAT 59.582 52.381 0.00 0.00 0.00 3.96
81 82 2.548920 CCCTACTTCTCCCGATTGCATC 60.549 54.545 0.00 0.00 0.00 3.91
82 83 2.366916 CCTACTTCTCCCGATTGCATCT 59.633 50.000 0.00 0.00 0.00 2.90
83 84 2.611225 ACTTCTCCCGATTGCATCTC 57.389 50.000 0.00 0.00 0.00 2.75
84 85 1.139853 ACTTCTCCCGATTGCATCTCC 59.860 52.381 0.00 0.00 0.00 3.71
85 86 1.415659 CTTCTCCCGATTGCATCTCCT 59.584 52.381 0.00 0.00 0.00 3.69
86 87 1.500474 TCTCCCGATTGCATCTCCTT 58.500 50.000 0.00 0.00 0.00 3.36
87 88 1.414181 TCTCCCGATTGCATCTCCTTC 59.586 52.381 0.00 0.00 0.00 3.46
88 89 0.104855 TCCCGATTGCATCTCCTTCG 59.895 55.000 0.00 0.00 0.00 3.79
89 90 1.502163 CCCGATTGCATCTCCTTCGC 61.502 60.000 0.00 0.00 0.00 4.70
90 91 1.502163 CCGATTGCATCTCCTTCGCC 61.502 60.000 0.00 0.00 0.00 5.54
91 92 0.811219 CGATTGCATCTCCTTCGCCA 60.811 55.000 0.00 0.00 0.00 5.69
92 93 0.659957 GATTGCATCTCCTTCGCCAC 59.340 55.000 0.00 0.00 0.00 5.01
93 94 0.254178 ATTGCATCTCCTTCGCCACT 59.746 50.000 0.00 0.00 0.00 4.00
94 95 0.036732 TTGCATCTCCTTCGCCACTT 59.963 50.000 0.00 0.00 0.00 3.16
95 96 0.391661 TGCATCTCCTTCGCCACTTC 60.392 55.000 0.00 0.00 0.00 3.01
96 97 1.092345 GCATCTCCTTCGCCACTTCC 61.092 60.000 0.00 0.00 0.00 3.46
97 98 0.539051 CATCTCCTTCGCCACTTCCT 59.461 55.000 0.00 0.00 0.00 3.36
98 99 1.065854 CATCTCCTTCGCCACTTCCTT 60.066 52.381 0.00 0.00 0.00 3.36
99 100 0.608640 TCTCCTTCGCCACTTCCTTC 59.391 55.000 0.00 0.00 0.00 3.46
100 101 0.737715 CTCCTTCGCCACTTCCTTCG 60.738 60.000 0.00 0.00 0.00 3.79
101 102 2.391389 CCTTCGCCACTTCCTTCGC 61.391 63.158 0.00 0.00 0.00 4.70
102 103 2.358247 TTCGCCACTTCCTTCGCC 60.358 61.111 0.00 0.00 0.00 5.54
103 104 3.894547 TTCGCCACTTCCTTCGCCC 62.895 63.158 0.00 0.00 0.00 6.13
106 107 3.330720 CCACTTCCTTCGCCCCCT 61.331 66.667 0.00 0.00 0.00 4.79
107 108 2.269241 CACTTCCTTCGCCCCCTC 59.731 66.667 0.00 0.00 0.00 4.30
108 109 3.009714 ACTTCCTTCGCCCCCTCC 61.010 66.667 0.00 0.00 0.00 4.30
109 110 3.009115 CTTCCTTCGCCCCCTCCA 61.009 66.667 0.00 0.00 0.00 3.86
110 111 2.286121 TTCCTTCGCCCCCTCCAT 60.286 61.111 0.00 0.00 0.00 3.41
111 112 1.926426 CTTCCTTCGCCCCCTCCATT 61.926 60.000 0.00 0.00 0.00 3.16
112 113 0.622154 TTCCTTCGCCCCCTCCATTA 60.622 55.000 0.00 0.00 0.00 1.90
113 114 1.148498 CCTTCGCCCCCTCCATTAC 59.852 63.158 0.00 0.00 0.00 1.89
114 115 1.632018 CCTTCGCCCCCTCCATTACA 61.632 60.000 0.00 0.00 0.00 2.41
115 116 0.179045 CTTCGCCCCCTCCATTACAG 60.179 60.000 0.00 0.00 0.00 2.74
116 117 2.203209 CGCCCCCTCCATTACAGC 60.203 66.667 0.00 0.00 0.00 4.40
117 118 2.746375 CGCCCCCTCCATTACAGCT 61.746 63.158 0.00 0.00 0.00 4.24
118 119 1.152881 GCCCCCTCCATTACAGCTG 60.153 63.158 13.48 13.48 0.00 4.24
119 120 1.533711 CCCCCTCCATTACAGCTGG 59.466 63.158 19.93 0.00 34.93 4.85
120 121 0.988145 CCCCCTCCATTACAGCTGGA 60.988 60.000 19.93 6.60 40.49 3.86
121 122 0.918983 CCCCTCCATTACAGCTGGAA 59.081 55.000 15.23 15.23 42.12 3.53
122 123 1.408822 CCCCTCCATTACAGCTGGAAC 60.409 57.143 15.19 0.00 42.12 3.62
123 124 1.408822 CCCTCCATTACAGCTGGAACC 60.409 57.143 15.19 0.00 42.12 3.62
124 125 1.561542 CCTCCATTACAGCTGGAACCT 59.438 52.381 15.19 0.00 42.12 3.50
125 126 2.420687 CCTCCATTACAGCTGGAACCTC 60.421 54.545 15.19 0.00 42.12 3.85
126 127 1.559682 TCCATTACAGCTGGAACCTCC 59.440 52.381 15.19 0.00 39.83 4.30
127 128 1.281867 CCATTACAGCTGGAACCTCCA 59.718 52.381 15.19 0.00 45.98 3.86
132 133 4.227300 ATTACAGCTGGAACCTCCATGTAA 59.773 41.667 15.19 17.78 46.97 2.41
133 134 5.280985 ATTACAGCTGGAACCTCCATGTAAA 60.281 40.000 15.19 8.60 46.49 2.01
134 135 6.749772 ATTACAGCTGGAACCTCCATGTAAAA 60.750 38.462 15.19 6.56 46.49 1.52
135 136 8.710980 ATTACAGCTGGAACCTCCATGTAAAAC 61.711 40.741 15.19 0.00 46.49 2.43
138 139 3.761897 TGGAACCTCCATGTAAAACCTG 58.238 45.455 0.00 0.00 42.67 4.00
139 140 3.089284 GGAACCTCCATGTAAAACCTGG 58.911 50.000 0.00 0.00 36.28 4.45
140 141 2.215942 ACCTCCATGTAAAACCTGGC 57.784 50.000 0.00 0.00 34.41 4.85
141 142 1.272480 ACCTCCATGTAAAACCTGGCC 60.272 52.381 0.00 0.00 34.41 5.36
142 143 1.474330 CTCCATGTAAAACCTGGCCC 58.526 55.000 0.00 0.00 34.41 5.80
143 144 0.040499 TCCATGTAAAACCTGGCCCC 59.960 55.000 0.00 0.00 34.41 5.80
144 145 1.319614 CCATGTAAAACCTGGCCCCG 61.320 60.000 0.00 0.00 27.42 5.73
145 146 0.322997 CATGTAAAACCTGGCCCCGA 60.323 55.000 0.00 0.00 0.00 5.14
146 147 0.034477 ATGTAAAACCTGGCCCCGAG 60.034 55.000 0.00 0.00 0.00 4.63
147 148 2.044555 GTAAAACCTGGCCCCGAGC 61.045 63.158 0.00 0.00 42.60 5.03
148 149 3.615509 TAAAACCTGGCCCCGAGCG 62.616 63.158 0.00 0.00 45.17 5.03
161 162 3.917760 GAGCGGCGCCCTGTAGAT 61.918 66.667 30.40 7.06 0.00 1.98
162 163 3.850095 GAGCGGCGCCCTGTAGATC 62.850 68.421 30.40 13.27 0.00 2.75
163 164 4.221422 GCGGCGCCCTGTAGATCA 62.221 66.667 23.58 0.00 0.00 2.92
164 165 2.279517 CGGCGCCCTGTAGATCAC 60.280 66.667 23.46 0.00 0.00 3.06
165 166 2.109181 GGCGCCCTGTAGATCACC 59.891 66.667 18.11 0.00 0.00 4.02
166 167 2.109181 GCGCCCTGTAGATCACCC 59.891 66.667 0.00 0.00 0.00 4.61
167 168 2.822399 CGCCCTGTAGATCACCCC 59.178 66.667 0.00 0.00 0.00 4.95
168 169 2.063979 CGCCCTGTAGATCACCCCA 61.064 63.158 0.00 0.00 0.00 4.96
169 170 1.527370 GCCCTGTAGATCACCCCAC 59.473 63.158 0.00 0.00 0.00 4.61
170 171 1.823295 CCCTGTAGATCACCCCACG 59.177 63.158 0.00 0.00 0.00 4.94
171 172 1.144057 CCTGTAGATCACCCCACGC 59.856 63.158 0.00 0.00 0.00 5.34
172 173 1.226974 CTGTAGATCACCCCACGCG 60.227 63.158 3.53 3.53 0.00 6.01
173 174 2.585247 GTAGATCACCCCACGCGC 60.585 66.667 5.73 0.00 0.00 6.86
174 175 3.071837 TAGATCACCCCACGCGCA 61.072 61.111 5.73 0.00 0.00 6.09
175 176 3.365291 TAGATCACCCCACGCGCAC 62.365 63.158 5.73 0.00 0.00 5.34
188 189 4.554363 CGCACGAGGCTCGGGTAG 62.554 72.222 36.40 27.10 46.67 3.18
189 190 4.208686 GCACGAGGCTCGGGTAGG 62.209 72.222 36.40 21.67 46.67 3.18
190 191 2.439701 CACGAGGCTCGGGTAGGA 60.440 66.667 36.81 0.00 45.59 2.94
191 192 2.050350 CACGAGGCTCGGGTAGGAA 61.050 63.158 36.81 0.00 45.59 3.36
192 193 1.304713 ACGAGGCTCGGGTAGGAAA 60.305 57.895 36.81 0.00 45.59 3.13
193 194 0.901580 ACGAGGCTCGGGTAGGAAAA 60.902 55.000 36.81 0.00 45.59 2.29
194 195 0.459759 CGAGGCTCGGGTAGGAAAAC 60.460 60.000 28.52 0.00 36.00 2.43
195 196 0.611714 GAGGCTCGGGTAGGAAAACA 59.388 55.000 0.00 0.00 0.00 2.83
196 197 0.613777 AGGCTCGGGTAGGAAAACAG 59.386 55.000 0.00 0.00 0.00 3.16
197 198 1.025113 GGCTCGGGTAGGAAAACAGC 61.025 60.000 0.00 0.00 0.00 4.40
198 199 1.359459 GCTCGGGTAGGAAAACAGCG 61.359 60.000 0.00 0.00 0.00 5.18
199 200 0.739813 CTCGGGTAGGAAAACAGCGG 60.740 60.000 0.00 0.00 0.00 5.52
200 201 2.396157 CGGGTAGGAAAACAGCGGC 61.396 63.158 0.00 0.00 0.00 6.53
201 202 2.044555 GGGTAGGAAAACAGCGGCC 61.045 63.158 0.00 0.00 0.00 6.13
202 203 2.396157 GGTAGGAAAACAGCGGCCG 61.396 63.158 24.05 24.05 0.00 6.13
203 204 2.046700 TAGGAAAACAGCGGCCGG 60.047 61.111 29.38 14.21 0.00 6.13
204 205 2.886134 TAGGAAAACAGCGGCCGGT 61.886 57.895 26.97 26.97 0.00 5.28
205 206 2.791501 TAGGAAAACAGCGGCCGGTC 62.792 60.000 30.00 16.08 0.00 4.79
206 207 4.084888 GAAAACAGCGGCCGGTCG 62.085 66.667 30.00 27.27 0.00 4.79
207 208 4.612412 AAAACAGCGGCCGGTCGA 62.612 61.111 36.22 0.00 0.00 4.20
208 209 3.894547 AAAACAGCGGCCGGTCGAT 62.895 57.895 36.22 27.35 0.00 3.59
215 216 3.771160 GGCCGGTCGATGTGGACT 61.771 66.667 1.90 0.00 37.12 3.85
216 217 2.202756 GCCGGTCGATGTGGACTC 60.203 66.667 1.90 0.00 37.12 3.36
217 218 2.494918 CCGGTCGATGTGGACTCC 59.505 66.667 0.00 0.00 37.12 3.85
218 219 2.102357 CGGTCGATGTGGACTCCG 59.898 66.667 0.00 0.00 37.12 4.63
219 220 2.494918 GGTCGATGTGGACTCCGG 59.505 66.667 0.00 0.00 37.12 5.14
220 221 2.202756 GTCGATGTGGACTCCGGC 60.203 66.667 0.00 0.00 34.09 6.13
221 222 3.822192 TCGATGTGGACTCCGGCG 61.822 66.667 0.00 0.00 0.00 6.46
222 223 4.873129 CGATGTGGACTCCGGCGG 62.873 72.222 22.51 22.51 0.00 6.13
237 238 4.394078 CGGCGTCGTCGGAGAACA 62.394 66.667 12.24 0.00 39.69 3.18
238 239 2.504244 GGCGTCGTCGGAGAACAG 60.504 66.667 3.90 0.00 39.69 3.16
239 240 2.504244 GCGTCGTCGGAGAACAGG 60.504 66.667 3.90 0.00 39.69 4.00
240 241 2.178521 CGTCGTCGGAGAACAGGG 59.821 66.667 0.00 0.00 39.69 4.45
241 242 2.623915 CGTCGTCGGAGAACAGGGT 61.624 63.158 0.00 0.00 39.69 4.34
242 243 1.300971 CGTCGTCGGAGAACAGGGTA 61.301 60.000 0.00 0.00 39.69 3.69
243 244 0.450983 GTCGTCGGAGAACAGGGTAG 59.549 60.000 0.00 0.00 39.69 3.18
244 245 0.325933 TCGTCGGAGAACAGGGTAGA 59.674 55.000 0.00 0.00 39.69 2.59
245 246 0.450983 CGTCGGAGAACAGGGTAGAC 59.549 60.000 0.00 0.00 39.69 2.59
246 247 0.816373 GTCGGAGAACAGGGTAGACC 59.184 60.000 0.00 0.00 39.69 3.85
260 261 4.103013 GGTAGACCCTAGAGAACCCTAG 57.897 54.545 0.00 0.00 36.70 3.02
276 277 1.560146 CCTAGGGGAAAAGTGTCCTCC 59.440 57.143 0.00 0.00 39.22 4.30
279 280 2.160646 GGGAAAAGTGTCCTCCCCA 58.839 57.895 0.00 0.00 42.77 4.96
280 281 0.481128 GGGAAAAGTGTCCTCCCCAA 59.519 55.000 0.00 0.00 42.77 4.12
281 282 1.617322 GGAAAAGTGTCCTCCCCAAC 58.383 55.000 0.00 0.00 34.56 3.77
282 283 1.145119 GGAAAAGTGTCCTCCCCAACT 59.855 52.381 0.00 0.00 34.56 3.16
283 284 2.505405 GAAAAGTGTCCTCCCCAACTC 58.495 52.381 0.00 0.00 0.00 3.01
284 285 0.396811 AAAGTGTCCTCCCCAACTCG 59.603 55.000 0.00 0.00 0.00 4.18
285 286 2.047179 GTGTCCTCCCCAACTCGC 60.047 66.667 0.00 0.00 0.00 5.03
286 287 2.203788 TGTCCTCCCCAACTCGCT 60.204 61.111 0.00 0.00 0.00 4.93
287 288 1.077805 TGTCCTCCCCAACTCGCTA 59.922 57.895 0.00 0.00 0.00 4.26
288 289 0.325296 TGTCCTCCCCAACTCGCTAT 60.325 55.000 0.00 0.00 0.00 2.97
289 290 0.105039 GTCCTCCCCAACTCGCTATG 59.895 60.000 0.00 0.00 0.00 2.23
290 291 0.325296 TCCTCCCCAACTCGCTATGT 60.325 55.000 0.00 0.00 0.00 2.29
291 292 0.541863 CCTCCCCAACTCGCTATGTT 59.458 55.000 0.00 0.00 0.00 2.71
292 293 1.656652 CTCCCCAACTCGCTATGTTG 58.343 55.000 0.00 0.00 42.96 3.33
299 300 3.596214 CAACTCGCTATGTTGGGTTACT 58.404 45.455 0.00 0.00 40.54 2.24
300 301 3.247006 ACTCGCTATGTTGGGTTACTG 57.753 47.619 0.00 0.00 0.00 2.74
301 302 1.933853 CTCGCTATGTTGGGTTACTGC 59.066 52.381 0.00 0.00 0.00 4.40
302 303 1.553248 TCGCTATGTTGGGTTACTGCT 59.447 47.619 0.00 0.00 0.00 4.24
303 304 1.665679 CGCTATGTTGGGTTACTGCTG 59.334 52.381 0.00 0.00 0.00 4.41
304 305 2.017049 GCTATGTTGGGTTACTGCTGG 58.983 52.381 0.00 0.00 0.00 4.85
305 306 2.618045 GCTATGTTGGGTTACTGCTGGT 60.618 50.000 0.00 0.00 0.00 4.00
306 307 3.370103 GCTATGTTGGGTTACTGCTGGTA 60.370 47.826 0.00 0.00 0.00 3.25
307 308 4.686122 GCTATGTTGGGTTACTGCTGGTAT 60.686 45.833 0.00 0.00 0.00 2.73
308 309 3.066291 TGTTGGGTTACTGCTGGTATG 57.934 47.619 0.00 0.00 0.00 2.39
309 310 2.290641 TGTTGGGTTACTGCTGGTATGG 60.291 50.000 0.00 0.00 0.00 2.74
396 397 9.604626 CAAAATTAAAGTGCAAAGTTGTCAAAA 57.395 25.926 0.00 0.00 0.00 2.44
406 407 8.787884 GTGCAAAGTTGTCAAAATTTTCAAATC 58.212 29.630 0.00 0.00 30.50 2.17
428 429 9.777297 AAATCTGGTGCAATGTAATTTTTAGTT 57.223 25.926 0.00 0.00 31.22 2.24
453 454 3.947910 TGAGGTACTTTGTACTTCCGG 57.052 47.619 14.41 0.00 41.55 5.14
473 474 5.239963 TCCGGTGAATTTTGTTACTCCTTTC 59.760 40.000 0.00 0.00 0.00 2.62
496 497 4.279659 CGCAAAAGAAACACTACCAACTC 58.720 43.478 0.00 0.00 0.00 3.01
498 499 4.279659 CAAAAGAAACACTACCAACTCGC 58.720 43.478 0.00 0.00 0.00 5.03
551 552 7.013655 GTCTACTCGTTATTAATAGGTGGTCCA 59.986 40.741 0.00 0.00 35.89 4.02
592 593 5.943349 TCCTCCGTCTCAAAATGGTATTA 57.057 39.130 0.00 0.00 0.00 0.98
594 595 6.895782 TCCTCCGTCTCAAAATGGTATTATT 58.104 36.000 0.00 0.00 0.00 1.40
640 647 5.618056 TTAGAGATGTGCAAAGCTCAAAG 57.382 39.130 23.57 0.00 35.71 2.77
660 667 6.316140 TCAAAGATGTTCAATCTAATCCACCG 59.684 38.462 0.00 0.00 0.00 4.94
674 681 7.054124 TCTAATCCACCGAGAAATAGCAAATT 58.946 34.615 0.00 0.00 0.00 1.82
691 698 7.573968 AGCAAATTACTTTGTCAAGAACTCT 57.426 32.000 7.31 0.00 43.07 3.24
710 717 7.899709 AGAACTCTTAATACAGACCCTCCTAAA 59.100 37.037 0.00 0.00 0.00 1.85
735 1039 5.024118 ACCACAACTACACCTAGCTTCTAT 58.976 41.667 0.00 0.00 0.00 1.98
888 1196 4.277423 CACCTAGCTTCTACTCCTAGCTTC 59.723 50.000 0.00 0.00 42.30 3.86
896 1204 0.910088 ACTCCTAGCTTCCCCACACC 60.910 60.000 0.00 0.00 0.00 4.16
897 1205 1.961180 CTCCTAGCTTCCCCACACCG 61.961 65.000 0.00 0.00 0.00 4.94
898 1206 1.987855 CCTAGCTTCCCCACACCGA 60.988 63.158 0.00 0.00 0.00 4.69
899 1207 1.338136 CCTAGCTTCCCCACACCGAT 61.338 60.000 0.00 0.00 0.00 4.18
900 1208 0.105039 CTAGCTTCCCCACACCGATC 59.895 60.000 0.00 0.00 0.00 3.69
940 1248 0.165944 CACCAACGGCGACAGAATTC 59.834 55.000 16.62 0.00 0.00 2.17
1161 1469 3.399181 CTGGCGCCCTACTTCCCA 61.399 66.667 26.77 0.00 0.00 4.37
1510 1818 3.838271 GCGGAGGCGGATCACAGA 61.838 66.667 0.00 0.00 0.00 3.41
1646 1954 1.725557 GACGAGCCGCTCTGGACATA 61.726 60.000 18.14 0.00 42.00 2.29
1740 2056 7.337718 GCATGATTCGTGTGTAATTACTAGTG 58.662 38.462 16.33 4.97 0.00 2.74
1828 2157 3.319137 TGGAGGAAGATCGAGTTTGTG 57.681 47.619 0.00 0.00 0.00 3.33
1848 2177 8.413424 GTTTGTGTTGTTTTGTTGCAAAAATAC 58.587 29.630 14.09 14.09 32.02 1.89
1920 2259 3.872182 TCTGAGAAGTCCTAATCGAGACG 59.128 47.826 0.00 0.00 38.08 4.18
1925 2264 3.779271 AGTCCTAATCGAGACGGAAAC 57.221 47.619 0.00 0.00 38.08 2.78
1984 2323 2.290641 TGTGGTTGGTTCTCTTGTGTGT 60.291 45.455 0.00 0.00 0.00 3.72
2044 2383 8.791327 TGCATGTCATTTTCAAGAAGAGTATA 57.209 30.769 0.00 0.00 0.00 1.47
2121 2466 7.308782 AGAGAAATTAACTTAGCGTGAATGG 57.691 36.000 0.00 0.00 26.71 3.16
2161 2506 5.629849 GTCTAATATACGTCATGTGGAGTGC 59.370 44.000 0.00 0.00 0.00 4.40
2167 2512 3.472652 ACGTCATGTGGAGTGCTTTTTA 58.527 40.909 0.00 0.00 0.00 1.52
2169 2514 4.154195 ACGTCATGTGGAGTGCTTTTTATC 59.846 41.667 0.00 0.00 0.00 1.75
2172 2517 4.701651 TCATGTGGAGTGCTTTTTATCTGG 59.298 41.667 0.00 0.00 0.00 3.86
2173 2518 4.098914 TGTGGAGTGCTTTTTATCTGGT 57.901 40.909 0.00 0.00 0.00 4.00
2174 2519 3.820467 TGTGGAGTGCTTTTTATCTGGTG 59.180 43.478 0.00 0.00 0.00 4.17
2175 2520 4.072131 GTGGAGTGCTTTTTATCTGGTGA 58.928 43.478 0.00 0.00 0.00 4.02
2197 2549 7.487189 GGTGAACTTGATATCAGCTTGATTTTG 59.513 37.037 5.39 0.00 40.11 2.44
2199 2551 8.963725 TGAACTTGATATCAGCTTGATTTTGAT 58.036 29.630 5.39 0.00 38.26 2.57
2234 2586 2.880890 AGCACTTAATGAATCGGCATCC 59.119 45.455 0.00 0.00 0.00 3.51
2249 2601 2.387757 GCATCCCTTTATTTGCTCCCA 58.612 47.619 0.00 0.00 32.41 4.37
2325 2677 5.182760 ACATGATGGAAGTTTCTCAAGAAGC 59.817 40.000 0.00 0.00 35.21 3.86
2333 2685 6.403092 GGAAGTTTCTCAAGAAGCTAGCATTC 60.403 42.308 18.83 16.55 43.31 2.67
2334 2686 5.555017 AGTTTCTCAAGAAGCTAGCATTCA 58.445 37.500 18.83 2.10 42.51 2.57
2473 2827 3.875134 TCTTTTCCTCAAACCGTCTTCAC 59.125 43.478 0.00 0.00 0.00 3.18
2484 2838 4.203654 ACCGTCTTCACTATCCTTTTCC 57.796 45.455 0.00 0.00 0.00 3.13
2485 2839 3.187700 CCGTCTTCACTATCCTTTTCCG 58.812 50.000 0.00 0.00 0.00 4.30
2489 2843 5.062308 CGTCTTCACTATCCTTTTCCGAAAG 59.938 44.000 0.00 0.00 41.56 2.62
2530 2887 8.908786 TTATCAATCTGTCTTTGAGTTTGACT 57.091 30.769 0.00 0.00 36.60 3.41
2548 2905 1.957177 ACTGAGAGAGTTGAACGAGCA 59.043 47.619 0.00 0.00 0.00 4.26
2565 2922 7.388224 TGAACGAGCAAATGGTAATTGTTAGTA 59.612 33.333 0.00 0.00 29.62 1.82
2616 2973 5.304614 ACATGACTTAGGGCTTACGACATAT 59.695 40.000 0.00 0.00 0.00 1.78
2617 2974 6.492429 ACATGACTTAGGGCTTACGACATATA 59.508 38.462 0.00 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.480133 GGTGGTGGGGGATCGGAG 61.480 72.222 0.00 0.00 0.00 4.63
16 17 4.805768 TATGGGCGCAAACCGGGG 62.806 66.667 10.83 0.00 37.44 5.73
17 18 2.518349 ATATGGGCGCAAACCGGG 60.518 61.111 10.83 0.00 37.44 5.73
18 19 1.821759 TGATATGGGCGCAAACCGG 60.822 57.895 10.83 0.00 37.44 5.28
19 20 1.095228 AGTGATATGGGCGCAAACCG 61.095 55.000 10.83 0.00 40.75 4.44
20 21 0.381801 CAGTGATATGGGCGCAAACC 59.618 55.000 10.83 0.93 0.00 3.27
21 22 0.248621 GCAGTGATATGGGCGCAAAC 60.249 55.000 10.83 4.41 0.00 2.93
22 23 1.383456 GGCAGTGATATGGGCGCAAA 61.383 55.000 10.83 0.00 0.00 3.68
23 24 1.823470 GGCAGTGATATGGGCGCAA 60.823 57.895 10.83 0.00 0.00 4.85
24 25 2.203195 GGCAGTGATATGGGCGCA 60.203 61.111 10.83 5.70 0.00 6.09
25 26 2.980233 GGGCAGTGATATGGGCGC 60.980 66.667 0.00 0.00 0.00 6.53
26 27 2.454832 ATCGGGCAGTGATATGGGCG 62.455 60.000 0.00 0.00 0.00 6.13
27 28 0.674895 GATCGGGCAGTGATATGGGC 60.675 60.000 0.00 0.00 0.00 5.36
28 29 0.036010 GGATCGGGCAGTGATATGGG 60.036 60.000 0.00 0.00 0.00 4.00
29 30 0.979665 AGGATCGGGCAGTGATATGG 59.020 55.000 0.00 0.00 0.00 2.74
30 31 1.066573 GGAGGATCGGGCAGTGATATG 60.067 57.143 0.00 0.00 34.37 1.78
31 32 1.203237 AGGAGGATCGGGCAGTGATAT 60.203 52.381 0.00 0.00 34.37 1.63
32 33 0.188587 AGGAGGATCGGGCAGTGATA 59.811 55.000 0.00 0.00 34.37 2.15
33 34 0.692419 AAGGAGGATCGGGCAGTGAT 60.692 55.000 0.00 0.00 34.37 3.06
34 35 1.306141 AAGGAGGATCGGGCAGTGA 60.306 57.895 0.00 0.00 34.37 3.41
35 36 1.144936 GAAGGAGGATCGGGCAGTG 59.855 63.158 0.00 0.00 34.37 3.66
36 37 0.618968 AAGAAGGAGGATCGGGCAGT 60.619 55.000 0.00 0.00 34.37 4.40
37 38 0.179062 CAAGAAGGAGGATCGGGCAG 60.179 60.000 0.00 0.00 34.37 4.85
38 39 1.907739 CAAGAAGGAGGATCGGGCA 59.092 57.895 0.00 0.00 34.37 5.36
39 40 1.524849 GCAAGAAGGAGGATCGGGC 60.525 63.158 0.00 0.00 34.37 6.13
40 41 1.147153 GGCAAGAAGGAGGATCGGG 59.853 63.158 0.00 0.00 34.37 5.14
41 42 0.105778 GAGGCAAGAAGGAGGATCGG 59.894 60.000 0.00 0.00 34.37 4.18
42 43 0.105778 GGAGGCAAGAAGGAGGATCG 59.894 60.000 0.00 0.00 34.37 3.69
43 44 0.472044 GGGAGGCAAGAAGGAGGATC 59.528 60.000 0.00 0.00 0.00 3.36
44 45 0.045469 AGGGAGGCAAGAAGGAGGAT 59.955 55.000 0.00 0.00 0.00 3.24
45 46 0.716591 TAGGGAGGCAAGAAGGAGGA 59.283 55.000 0.00 0.00 0.00 3.71
46 47 0.833949 GTAGGGAGGCAAGAAGGAGG 59.166 60.000 0.00 0.00 0.00 4.30
47 48 1.872773 AGTAGGGAGGCAAGAAGGAG 58.127 55.000 0.00 0.00 0.00 3.69
48 49 2.188817 GAAGTAGGGAGGCAAGAAGGA 58.811 52.381 0.00 0.00 0.00 3.36
49 50 2.169561 GAGAAGTAGGGAGGCAAGAAGG 59.830 54.545 0.00 0.00 0.00 3.46
50 51 2.169561 GGAGAAGTAGGGAGGCAAGAAG 59.830 54.545 0.00 0.00 0.00 2.85
51 52 2.188817 GGAGAAGTAGGGAGGCAAGAA 58.811 52.381 0.00 0.00 0.00 2.52
52 53 1.622725 GGGAGAAGTAGGGAGGCAAGA 60.623 57.143 0.00 0.00 0.00 3.02
53 54 0.833949 GGGAGAAGTAGGGAGGCAAG 59.166 60.000 0.00 0.00 0.00 4.01
54 55 0.976073 CGGGAGAAGTAGGGAGGCAA 60.976 60.000 0.00 0.00 0.00 4.52
55 56 1.381327 CGGGAGAAGTAGGGAGGCA 60.381 63.158 0.00 0.00 0.00 4.75
56 57 0.470268 ATCGGGAGAAGTAGGGAGGC 60.470 60.000 0.00 0.00 45.37 4.70
57 58 1.689273 CAATCGGGAGAAGTAGGGAGG 59.311 57.143 0.00 0.00 45.37 4.30
58 59 1.069358 GCAATCGGGAGAAGTAGGGAG 59.931 57.143 0.00 0.00 45.37 4.30
59 60 1.120530 GCAATCGGGAGAAGTAGGGA 58.879 55.000 0.00 0.00 45.37 4.20
60 61 0.830648 TGCAATCGGGAGAAGTAGGG 59.169 55.000 0.00 0.00 45.37 3.53
61 62 2.760374 GATGCAATCGGGAGAAGTAGG 58.240 52.381 0.00 0.00 45.37 3.18
73 74 0.659957 GTGGCGAAGGAGATGCAATC 59.340 55.000 0.00 0.00 46.04 2.67
74 75 0.254178 AGTGGCGAAGGAGATGCAAT 59.746 50.000 0.00 0.00 0.00 3.56
75 76 0.036732 AAGTGGCGAAGGAGATGCAA 59.963 50.000 0.00 0.00 0.00 4.08
76 77 0.391661 GAAGTGGCGAAGGAGATGCA 60.392 55.000 0.00 0.00 0.00 3.96
77 78 1.092345 GGAAGTGGCGAAGGAGATGC 61.092 60.000 0.00 0.00 0.00 3.91
78 79 0.539051 AGGAAGTGGCGAAGGAGATG 59.461 55.000 0.00 0.00 0.00 2.90
79 80 1.208293 GAAGGAAGTGGCGAAGGAGAT 59.792 52.381 0.00 0.00 0.00 2.75
80 81 0.608640 GAAGGAAGTGGCGAAGGAGA 59.391 55.000 0.00 0.00 0.00 3.71
81 82 0.737715 CGAAGGAAGTGGCGAAGGAG 60.738 60.000 0.00 0.00 0.00 3.69
82 83 1.292223 CGAAGGAAGTGGCGAAGGA 59.708 57.895 0.00 0.00 0.00 3.36
83 84 2.391389 GCGAAGGAAGTGGCGAAGG 61.391 63.158 0.00 0.00 0.00 3.46
84 85 2.391389 GGCGAAGGAAGTGGCGAAG 61.391 63.158 0.00 0.00 0.00 3.79
85 86 2.358247 GGCGAAGGAAGTGGCGAA 60.358 61.111 0.00 0.00 0.00 4.70
86 87 4.388499 GGGCGAAGGAAGTGGCGA 62.388 66.667 0.00 0.00 0.00 5.54
89 90 3.330720 AGGGGGCGAAGGAAGTGG 61.331 66.667 0.00 0.00 0.00 4.00
90 91 2.269241 GAGGGGGCGAAGGAAGTG 59.731 66.667 0.00 0.00 0.00 3.16
91 92 3.009714 GGAGGGGGCGAAGGAAGT 61.010 66.667 0.00 0.00 0.00 3.01
92 93 1.926426 AATGGAGGGGGCGAAGGAAG 61.926 60.000 0.00 0.00 0.00 3.46
93 94 0.622154 TAATGGAGGGGGCGAAGGAA 60.622 55.000 0.00 0.00 0.00 3.36
94 95 1.003704 TAATGGAGGGGGCGAAGGA 59.996 57.895 0.00 0.00 0.00 3.36
95 96 1.148498 GTAATGGAGGGGGCGAAGG 59.852 63.158 0.00 0.00 0.00 3.46
96 97 0.179045 CTGTAATGGAGGGGGCGAAG 60.179 60.000 0.00 0.00 0.00 3.79
97 98 1.912220 CTGTAATGGAGGGGGCGAA 59.088 57.895 0.00 0.00 0.00 4.70
98 99 2.742116 GCTGTAATGGAGGGGGCGA 61.742 63.158 0.00 0.00 0.00 5.54
99 100 2.203209 GCTGTAATGGAGGGGGCG 60.203 66.667 0.00 0.00 0.00 6.13
100 101 1.152881 CAGCTGTAATGGAGGGGGC 60.153 63.158 5.25 0.00 0.00 5.80
101 102 0.988145 TCCAGCTGTAATGGAGGGGG 60.988 60.000 13.81 0.00 41.96 5.40
102 103 2.620234 TCCAGCTGTAATGGAGGGG 58.380 57.895 13.81 0.00 41.96 4.79
106 107 1.559682 GGAGGTTCCAGCTGTAATGGA 59.440 52.381 13.81 0.00 45.15 3.41
107 108 1.281867 TGGAGGTTCCAGCTGTAATGG 59.718 52.381 13.81 0.00 42.67 3.16
108 109 2.787473 TGGAGGTTCCAGCTGTAATG 57.213 50.000 13.81 0.00 42.67 1.90
126 127 0.322997 TCGGGGCCAGGTTTTACATG 60.323 55.000 4.39 0.00 0.00 3.21
127 128 0.034477 CTCGGGGCCAGGTTTTACAT 60.034 55.000 4.39 0.00 0.00 2.29
128 129 1.377229 CTCGGGGCCAGGTTTTACA 59.623 57.895 4.39 0.00 0.00 2.41
129 130 2.044555 GCTCGGGGCCAGGTTTTAC 61.045 63.158 4.39 0.00 34.27 2.01
130 131 2.353573 GCTCGGGGCCAGGTTTTA 59.646 61.111 4.39 0.00 34.27 1.52
144 145 3.850095 GATCTACAGGGCGCCGCTC 62.850 68.421 22.54 4.23 0.00 5.03
145 146 3.917760 GATCTACAGGGCGCCGCT 61.918 66.667 22.54 16.21 0.00 5.52
146 147 4.221422 TGATCTACAGGGCGCCGC 62.221 66.667 22.54 13.90 0.00 6.53
147 148 2.279517 GTGATCTACAGGGCGCCG 60.280 66.667 22.54 10.51 0.00 6.46
148 149 2.109181 GGTGATCTACAGGGCGCC 59.891 66.667 21.18 21.18 0.00 6.53
149 150 2.109181 GGGTGATCTACAGGGCGC 59.891 66.667 0.00 0.00 0.00 6.53
150 151 2.063979 TGGGGTGATCTACAGGGCG 61.064 63.158 0.00 0.00 0.00 6.13
151 152 1.527370 GTGGGGTGATCTACAGGGC 59.473 63.158 0.00 0.00 0.00 5.19
152 153 1.823295 CGTGGGGTGATCTACAGGG 59.177 63.158 0.00 0.00 0.00 4.45
153 154 1.144057 GCGTGGGGTGATCTACAGG 59.856 63.158 0.00 0.00 0.00 4.00
154 155 1.226974 CGCGTGGGGTGATCTACAG 60.227 63.158 0.00 0.00 0.00 2.74
155 156 2.889617 CGCGTGGGGTGATCTACA 59.110 61.111 0.00 0.00 0.00 2.74
156 157 2.585247 GCGCGTGGGGTGATCTAC 60.585 66.667 8.43 0.00 0.00 2.59
157 158 3.071837 TGCGCGTGGGGTGATCTA 61.072 61.111 8.43 0.00 0.00 1.98
158 159 4.760047 GTGCGCGTGGGGTGATCT 62.760 66.667 8.43 0.00 0.00 2.75
172 173 4.208686 CCTACCCGAGCCTCGTGC 62.209 72.222 13.83 0.00 38.40 5.34
173 174 1.601419 TTTCCTACCCGAGCCTCGTG 61.601 60.000 13.83 3.83 38.40 4.35
174 175 0.901580 TTTTCCTACCCGAGCCTCGT 60.902 55.000 13.83 0.00 38.40 4.18
175 176 0.459759 GTTTTCCTACCCGAGCCTCG 60.460 60.000 7.25 7.25 40.07 4.63
176 177 0.611714 TGTTTTCCTACCCGAGCCTC 59.388 55.000 0.00 0.00 0.00 4.70
177 178 0.613777 CTGTTTTCCTACCCGAGCCT 59.386 55.000 0.00 0.00 0.00 4.58
178 179 1.025113 GCTGTTTTCCTACCCGAGCC 61.025 60.000 0.00 0.00 0.00 4.70
179 180 1.359459 CGCTGTTTTCCTACCCGAGC 61.359 60.000 0.00 0.00 0.00 5.03
180 181 0.739813 CCGCTGTTTTCCTACCCGAG 60.740 60.000 0.00 0.00 0.00 4.63
181 182 1.294138 CCGCTGTTTTCCTACCCGA 59.706 57.895 0.00 0.00 0.00 5.14
182 183 2.396157 GCCGCTGTTTTCCTACCCG 61.396 63.158 0.00 0.00 0.00 5.28
183 184 2.044555 GGCCGCTGTTTTCCTACCC 61.045 63.158 0.00 0.00 0.00 3.69
184 185 2.396157 CGGCCGCTGTTTTCCTACC 61.396 63.158 14.67 0.00 0.00 3.18
185 186 2.396157 CCGGCCGCTGTTTTCCTAC 61.396 63.158 22.85 0.00 0.00 3.18
186 187 2.046700 CCGGCCGCTGTTTTCCTA 60.047 61.111 22.85 0.00 0.00 2.94
187 188 4.265056 ACCGGCCGCTGTTTTCCT 62.265 61.111 22.85 0.00 0.00 3.36
188 189 3.733960 GACCGGCCGCTGTTTTCC 61.734 66.667 22.85 0.00 0.00 3.13
189 190 4.084888 CGACCGGCCGCTGTTTTC 62.085 66.667 22.85 7.31 0.00 2.29
190 191 3.894547 ATCGACCGGCCGCTGTTTT 62.895 57.895 22.85 0.00 0.00 2.43
191 192 4.388499 ATCGACCGGCCGCTGTTT 62.388 61.111 22.85 0.05 0.00 2.83
198 199 3.718210 GAGTCCACATCGACCGGCC 62.718 68.421 0.00 0.00 32.91 6.13
199 200 2.202756 GAGTCCACATCGACCGGC 60.203 66.667 0.00 0.00 32.91 6.13
200 201 2.494918 GGAGTCCACATCGACCGG 59.505 66.667 3.60 0.00 32.91 5.28
201 202 2.102357 CGGAGTCCACATCGACCG 59.898 66.667 10.49 0.00 32.91 4.79
202 203 2.494918 CCGGAGTCCACATCGACC 59.505 66.667 10.49 0.00 32.91 4.79
203 204 2.202756 GCCGGAGTCCACATCGAC 60.203 66.667 5.05 0.00 0.00 4.20
204 205 3.822192 CGCCGGAGTCCACATCGA 61.822 66.667 5.05 0.00 0.00 3.59
205 206 4.873129 CCGCCGGAGTCCACATCG 62.873 72.222 5.05 6.21 0.00 3.84
220 221 4.394078 TGTTCTCCGACGACGCCG 62.394 66.667 0.64 0.00 42.50 6.46
221 222 2.504244 CTGTTCTCCGACGACGCC 60.504 66.667 0.64 0.00 38.29 5.68
222 223 2.504244 CCTGTTCTCCGACGACGC 60.504 66.667 0.64 0.00 38.29 5.19
223 224 1.300971 TACCCTGTTCTCCGACGACG 61.301 60.000 0.00 0.00 39.43 5.12
224 225 0.450983 CTACCCTGTTCTCCGACGAC 59.549 60.000 0.00 0.00 0.00 4.34
225 226 0.325933 TCTACCCTGTTCTCCGACGA 59.674 55.000 0.00 0.00 0.00 4.20
226 227 0.450983 GTCTACCCTGTTCTCCGACG 59.549 60.000 0.00 0.00 0.00 5.12
227 228 0.816373 GGTCTACCCTGTTCTCCGAC 59.184 60.000 0.00 0.00 0.00 4.79
228 229 3.277962 GGTCTACCCTGTTCTCCGA 57.722 57.895 0.00 0.00 0.00 4.55
239 240 4.103013 CTAGGGTTCTCTAGGGTCTACC 57.897 54.545 0.00 0.00 40.67 3.18
247 248 4.162509 CACTTTTCCCCTAGGGTTCTCTAG 59.837 50.000 26.66 16.49 44.74 2.43
248 249 4.101856 CACTTTTCCCCTAGGGTTCTCTA 58.898 47.826 26.66 5.81 44.74 2.43
249 250 2.913617 CACTTTTCCCCTAGGGTTCTCT 59.086 50.000 26.66 1.15 44.74 3.10
250 251 2.643304 ACACTTTTCCCCTAGGGTTCTC 59.357 50.000 26.66 0.00 44.74 2.87
251 252 2.643304 GACACTTTTCCCCTAGGGTTCT 59.357 50.000 26.66 0.00 44.74 3.01
252 253 2.290768 GGACACTTTTCCCCTAGGGTTC 60.291 54.545 26.66 8.80 44.74 3.62
253 254 1.709115 GGACACTTTTCCCCTAGGGTT 59.291 52.381 26.66 0.32 44.74 4.11
254 255 1.132168 AGGACACTTTTCCCCTAGGGT 60.132 52.381 26.66 4.89 44.74 4.34
255 256 1.560146 GAGGACACTTTTCCCCTAGGG 59.440 57.143 22.25 22.25 46.11 3.53
256 257 1.560146 GGAGGACACTTTTCCCCTAGG 59.440 57.143 0.06 0.06 36.12 3.02
257 258 1.560146 GGGAGGACACTTTTCCCCTAG 59.440 57.143 0.00 0.00 43.98 3.02
258 259 1.665137 GGGAGGACACTTTTCCCCTA 58.335 55.000 0.00 0.00 43.98 3.53
259 260 2.476081 GGGAGGACACTTTTCCCCT 58.524 57.895 0.00 0.00 43.98 4.79
262 263 1.145119 AGTTGGGGAGGACACTTTTCC 59.855 52.381 0.00 0.00 35.66 3.13
263 264 2.505405 GAGTTGGGGAGGACACTTTTC 58.495 52.381 0.00 0.00 0.00 2.29
264 265 1.202770 CGAGTTGGGGAGGACACTTTT 60.203 52.381 0.00 0.00 0.00 2.27
265 266 0.396811 CGAGTTGGGGAGGACACTTT 59.603 55.000 0.00 0.00 0.00 2.66
266 267 2.058675 CGAGTTGGGGAGGACACTT 58.941 57.895 0.00 0.00 0.00 3.16
267 268 2.584391 GCGAGTTGGGGAGGACACT 61.584 63.158 0.00 0.00 0.00 3.55
268 269 1.255667 TAGCGAGTTGGGGAGGACAC 61.256 60.000 0.00 0.00 0.00 3.67
269 270 0.325296 ATAGCGAGTTGGGGAGGACA 60.325 55.000 0.00 0.00 0.00 4.02
270 271 0.105039 CATAGCGAGTTGGGGAGGAC 59.895 60.000 0.00 0.00 0.00 3.85
271 272 0.325296 ACATAGCGAGTTGGGGAGGA 60.325 55.000 0.00 0.00 0.00 3.71
272 273 0.541863 AACATAGCGAGTTGGGGAGG 59.458 55.000 0.00 0.00 0.00 4.30
273 274 1.656652 CAACATAGCGAGTTGGGGAG 58.343 55.000 10.01 0.00 41.92 4.30
274 275 3.853104 CAACATAGCGAGTTGGGGA 57.147 52.632 10.01 0.00 41.92 4.81
278 279 3.370978 CAGTAACCCAACATAGCGAGTTG 59.629 47.826 10.67 10.67 44.47 3.16
279 280 3.596214 CAGTAACCCAACATAGCGAGTT 58.404 45.455 0.00 0.00 0.00 3.01
280 281 2.677037 GCAGTAACCCAACATAGCGAGT 60.677 50.000 0.00 0.00 0.00 4.18
281 282 1.933853 GCAGTAACCCAACATAGCGAG 59.066 52.381 0.00 0.00 0.00 5.03
282 283 1.553248 AGCAGTAACCCAACATAGCGA 59.447 47.619 0.00 0.00 0.00 4.93
283 284 1.665679 CAGCAGTAACCCAACATAGCG 59.334 52.381 0.00 0.00 0.00 4.26
284 285 2.017049 CCAGCAGTAACCCAACATAGC 58.983 52.381 0.00 0.00 0.00 2.97
285 286 3.350219 ACCAGCAGTAACCCAACATAG 57.650 47.619 0.00 0.00 0.00 2.23
286 287 4.384757 CCATACCAGCAGTAACCCAACATA 60.385 45.833 0.00 0.00 33.70 2.29
287 288 3.620488 CATACCAGCAGTAACCCAACAT 58.380 45.455 0.00 0.00 33.70 2.71
288 289 2.290641 CCATACCAGCAGTAACCCAACA 60.291 50.000 0.00 0.00 33.70 3.33
289 290 2.290705 ACCATACCAGCAGTAACCCAAC 60.291 50.000 0.00 0.00 33.70 3.77
290 291 1.989586 ACCATACCAGCAGTAACCCAA 59.010 47.619 0.00 0.00 33.70 4.12
291 292 1.663911 ACCATACCAGCAGTAACCCA 58.336 50.000 0.00 0.00 33.70 4.51
292 293 2.104281 CCTACCATACCAGCAGTAACCC 59.896 54.545 0.00 0.00 33.70 4.11
293 294 3.036091 TCCTACCATACCAGCAGTAACC 58.964 50.000 0.00 0.00 33.70 2.85
294 295 4.957684 ATCCTACCATACCAGCAGTAAC 57.042 45.455 0.00 0.00 33.70 2.50
295 296 5.665812 AGAAATCCTACCATACCAGCAGTAA 59.334 40.000 0.00 0.00 33.70 2.24
296 297 5.216622 AGAAATCCTACCATACCAGCAGTA 58.783 41.667 0.00 0.00 34.76 2.74
297 298 4.040755 AGAAATCCTACCATACCAGCAGT 58.959 43.478 0.00 0.00 0.00 4.40
298 299 4.696479 AGAAATCCTACCATACCAGCAG 57.304 45.455 0.00 0.00 0.00 4.24
299 300 5.665812 AGTAAGAAATCCTACCATACCAGCA 59.334 40.000 0.00 0.00 0.00 4.41
300 301 6.176014 AGTAAGAAATCCTACCATACCAGC 57.824 41.667 0.00 0.00 0.00 4.85
301 302 6.483640 GCAAGTAAGAAATCCTACCATACCAG 59.516 42.308 0.00 0.00 0.00 4.00
302 303 6.157994 AGCAAGTAAGAAATCCTACCATACCA 59.842 38.462 0.00 0.00 0.00 3.25
303 304 6.592870 AGCAAGTAAGAAATCCTACCATACC 58.407 40.000 0.00 0.00 0.00 2.73
304 305 9.209175 CATAGCAAGTAAGAAATCCTACCATAC 57.791 37.037 0.00 0.00 0.00 2.39
305 306 8.934697 ACATAGCAAGTAAGAAATCCTACCATA 58.065 33.333 0.00 0.00 0.00 2.74
306 307 7.716998 CACATAGCAAGTAAGAAATCCTACCAT 59.283 37.037 0.00 0.00 0.00 3.55
307 308 7.047891 CACATAGCAAGTAAGAAATCCTACCA 58.952 38.462 0.00 0.00 0.00 3.25
308 309 6.483640 CCACATAGCAAGTAAGAAATCCTACC 59.516 42.308 0.00 0.00 0.00 3.18
309 310 7.048512 ACCACATAGCAAGTAAGAAATCCTAC 58.951 38.462 0.00 0.00 0.00 3.18
375 376 9.818796 GAAAATTTTGACAACTTTGCACTTTAA 57.181 25.926 8.47 0.00 0.00 1.52
396 397 8.851541 AATTACATTGCACCAGATTTGAAAAT 57.148 26.923 0.00 0.00 0.00 1.82
399 400 8.674263 AAAAATTACATTGCACCAGATTTGAA 57.326 26.923 0.00 0.00 0.00 2.69
406 407 8.364129 ACAAACTAAAAATTACATTGCACCAG 57.636 30.769 0.00 0.00 0.00 4.00
428 429 5.524646 CGGAAGTACAAAGTACCTCAAACAA 59.475 40.000 7.87 0.00 0.00 2.83
453 454 4.915667 GCGGAAAGGAGTAACAAAATTCAC 59.084 41.667 0.00 0.00 0.00 3.18
473 474 3.066203 AGTTGGTAGTGTTTCTTTTGCGG 59.934 43.478 0.00 0.00 0.00 5.69
505 506 3.482436 ACGGTTTGCACTAGATTTTGGA 58.518 40.909 0.00 0.00 0.00 3.53
570 571 4.837093 AATACCATTTTGAGACGGAGGA 57.163 40.909 0.00 0.00 0.00 3.71
604 610 9.866655 TGCACATCTCTAAATAAATATTCCCTT 57.133 29.630 0.00 0.00 0.00 3.95
640 647 5.601662 TCTCGGTGGATTAGATTGAACATC 58.398 41.667 0.00 0.00 0.00 3.06
691 698 7.170277 GTGGTTTTTAGGAGGGTCTGTATTAA 58.830 38.462 0.00 0.00 0.00 1.40
710 717 4.102681 AGAAGCTAGGTGTAGTTGTGGTTT 59.897 41.667 0.00 0.00 0.00 3.27
809 1117 2.231235 CTGCACGGAGCCCTTTATTTTT 59.769 45.455 0.00 0.00 44.83 1.94
888 1196 2.125673 GTGTCGATCGGTGTGGGG 60.126 66.667 16.41 0.00 0.00 4.96
896 1204 5.277202 CGGTGTATATATAGGGTGTCGATCG 60.277 48.000 9.36 9.36 0.00 3.69
897 1205 5.505324 GCGGTGTATATATAGGGTGTCGATC 60.505 48.000 0.00 0.00 0.00 3.69
898 1206 4.337555 GCGGTGTATATATAGGGTGTCGAT 59.662 45.833 0.00 0.00 0.00 3.59
899 1207 3.691118 GCGGTGTATATATAGGGTGTCGA 59.309 47.826 0.00 0.00 0.00 4.20
900 1208 3.441222 TGCGGTGTATATATAGGGTGTCG 59.559 47.826 0.00 0.00 0.00 4.35
967 1275 1.627943 CGCGAGCTCGATTCACTTG 59.372 57.895 38.74 12.98 43.02 3.16
991 1299 1.467875 GACGACTCCATGTTCGATCG 58.532 55.000 9.36 9.36 35.74 3.69
992 1300 1.467875 CGACGACTCCATGTTCGATC 58.532 55.000 13.68 7.80 32.41 3.69
993 1301 0.100682 CCGACGACTCCATGTTCGAT 59.899 55.000 13.68 1.21 32.41 3.59
994 1302 1.504900 CCGACGACTCCATGTTCGA 59.495 57.895 13.68 0.00 32.41 3.71
1560 1868 2.100797 CCGCCGTCGACGACATAA 59.899 61.111 37.65 0.00 43.02 1.90
1740 2056 8.239314 GGTTAACCCAGTTAAGTAAAATGTAGC 58.761 37.037 14.16 0.00 38.44 3.58
1920 2259 4.336280 AGAAGGCAAGGATACAAGTTTCC 58.664 43.478 1.95 1.95 41.41 3.13
1925 2264 3.376546 GCAGAAGAAGGCAAGGATACAAG 59.623 47.826 0.00 0.00 41.41 3.16
2053 2392 8.758829 ACAATCACTATTACATGGAGTTGTAGA 58.241 33.333 0.00 0.00 33.81 2.59
2054 2393 8.948631 ACAATCACTATTACATGGAGTTGTAG 57.051 34.615 0.00 0.00 33.81 2.74
2059 2398 6.560003 TGGACAATCACTATTACATGGAGT 57.440 37.500 0.00 0.00 0.00 3.85
2061 2400 8.052141 TGAAATGGACAATCACTATTACATGGA 58.948 33.333 0.00 0.00 0.00 3.41
2104 2449 6.657541 AGAATTTCCCATTCACGCTAAGTTAA 59.342 34.615 0.00 0.00 0.00 2.01
2106 2451 5.010282 AGAATTTCCCATTCACGCTAAGTT 58.990 37.500 0.00 0.00 0.00 2.66
2112 2457 3.913089 ACAAAGAATTTCCCATTCACGC 58.087 40.909 0.00 0.00 35.03 5.34
2148 2493 5.392380 CCAGATAAAAAGCACTCCACATGAC 60.392 44.000 0.00 0.00 0.00 3.06
2167 2512 5.627182 AGCTGATATCAAGTTCACCAGAT 57.373 39.130 6.90 0.00 0.00 2.90
2169 2514 5.181009 TCAAGCTGATATCAAGTTCACCAG 58.819 41.667 6.90 0.00 0.00 4.00
2172 2517 8.239314 TCAAAATCAAGCTGATATCAAGTTCAC 58.761 33.333 6.90 0.00 35.76 3.18
2173 2518 8.339344 TCAAAATCAAGCTGATATCAAGTTCA 57.661 30.769 6.90 0.00 35.76 3.18
2199 2551 9.665719 TTCATTAAGTGCTCATAGAACAATGTA 57.334 29.630 0.00 0.00 0.00 2.29
2201 2553 9.661187 GATTCATTAAGTGCTCATAGAACAATG 57.339 33.333 0.00 0.00 0.00 2.82
2207 2559 4.991056 GCCGATTCATTAAGTGCTCATAGA 59.009 41.667 0.00 0.00 0.00 1.98
2211 2563 2.984562 TGCCGATTCATTAAGTGCTCA 58.015 42.857 0.00 0.00 0.00 4.26
2234 2586 6.706295 TGGTTATTTTGGGAGCAAATAAAGG 58.294 36.000 1.68 0.00 37.66 3.11
2289 2641 2.556189 TCCATCATGTTGTTTGAACGGG 59.444 45.455 3.19 0.00 0.00 5.28
2291 2643 4.858935 ACTTCCATCATGTTGTTTGAACG 58.141 39.130 3.19 0.00 0.00 3.95
2499 2853 9.512588 AACTCAAAGACAGATTGATAATGAAGT 57.487 29.630 0.00 0.00 36.30 3.01
2530 2887 3.452755 TTTGCTCGTTCAACTCTCTCA 57.547 42.857 0.00 0.00 0.00 3.27
2565 2922 5.960811 TCCTTTCTCTCATCCTCACACTAAT 59.039 40.000 0.00 0.00 0.00 1.73
2616 2973 2.201921 TACCGCCAAATTGTTGCCTA 57.798 45.000 0.00 0.00 33.01 3.93
2617 2974 1.555967 ATACCGCCAAATTGTTGCCT 58.444 45.000 0.00 0.00 33.01 4.75


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

AutoCloner maintained by Alex Coulton.