Multiple sequence alignment - TraesCS3A01G358700

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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 TraesCS3A01G358700 chr3A 100.000 2557 0 0 1 2557 606741746 606739190 0.000000e+00 4723.0
1 TraesCS3A01G358700 chr3A 92.963 270 18 1 178 447 57085366 57085098 2.380000e-105 392.0
2 TraesCS3A01G358700 chr3A 97.059 34 1 0 7 40 364922064 364922031 9.880000e-05 58.4
3 TraesCS3A01G358700 chr3D 91.529 2125 115 31 464 2556 463680693 463678602 0.000000e+00 2867.0
4 TraesCS3A01G358700 chr3B 89.919 1230 60 24 464 1650 617250192 617248984 0.000000e+00 1526.0
5 TraesCS3A01G358700 chr1B 89.775 489 31 10 1008 1496 192771081 192770612 2.180000e-170 608.0
6 TraesCS3A01G358700 chr1B 91.743 109 5 3 1543 1650 192770615 192770510 5.700000e-32 148.0
7 TraesCS3A01G358700 chr4A 92.620 271 20 0 177 447 472195733 472196003 8.580000e-105 390.0
8 TraesCS3A01G358700 chr1A 92.593 270 20 0 178 447 28615962 28616231 3.090000e-104 388.0
9 TraesCS3A01G358700 chr2A 92.593 270 18 2 178 447 71550950 71550683 1.110000e-103 387.0
10 TraesCS3A01G358700 chr2A 92.222 270 19 2 178 447 71565114 71564847 5.160000e-102 381.0
11 TraesCS3A01G358700 chr2A 91.544 272 22 1 176 447 202777955 202777685 8.640000e-100 374.0
12 TraesCS3A01G358700 chr5A 91.941 273 21 1 176 447 598668161 598668433 5.160000e-102 381.0
13 TraesCS3A01G358700 chr7A 91.852 270 20 2 178 447 477310120 477309853 2.400000e-100 375.0
14 TraesCS3A01G358700 chr7A 85.057 87 13 0 4 90 12204376 12204462 3.500000e-14 89.8
15 TraesCS3A01G358700 chr6A 91.450 269 23 0 179 447 602490120 602489852 1.120000e-98 370.0
16 TraesCS3A01G358700 chr5D 87.640 89 9 2 13 100 281859512 281859425 4.500000e-18 102.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G358700 chr3A 606739190 606741746 2556 True 4723 4723 100.000 1 2557 1 chr3A.!!$R3 2556
1 TraesCS3A01G358700 chr3D 463678602 463680693 2091 True 2867 2867 91.529 464 2556 1 chr3D.!!$R1 2092
2 TraesCS3A01G358700 chr3B 617248984 617250192 1208 True 1526 1526 89.919 464 1650 1 chr3B.!!$R1 1186
3 TraesCS3A01G358700 chr1B 192770510 192771081 571 True 378 608 90.759 1008 1650 2 chr1B.!!$R1 642

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
145 146 0.031994 AACAAACACCGCTCCATTGC 59.968 50.0 0.0 0.0 0.0 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1997 2052 0.036164 TTGCACGACAGGCCATTACT 59.964 50.0 5.01 0.0 0.0 2.24 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
56 57 8.483307 AAACTATTTGCTATGCTTGATTTTGG 57.517 30.769 0.00 0.00 0.00 3.28
57 58 7.174107 ACTATTTGCTATGCTTGATTTTGGT 57.826 32.000 0.00 0.00 0.00 3.67
58 59 8.292444 ACTATTTGCTATGCTTGATTTTGGTA 57.708 30.769 0.00 0.00 0.00 3.25
59 60 8.917088 ACTATTTGCTATGCTTGATTTTGGTAT 58.083 29.630 0.00 0.00 0.00 2.73
64 65 9.531942 TTGCTATGCTTGATTTTGGTATAAATG 57.468 29.630 0.00 0.00 0.00 2.32
65 66 8.911965 TGCTATGCTTGATTTTGGTATAAATGA 58.088 29.630 0.00 0.00 0.00 2.57
66 67 9.185192 GCTATGCTTGATTTTGGTATAAATGAC 57.815 33.333 0.00 0.00 0.00 3.06
67 68 9.683069 CTATGCTTGATTTTGGTATAAATGACC 57.317 33.333 0.00 0.00 37.49 4.02
68 69 7.716799 TGCTTGATTTTGGTATAAATGACCT 57.283 32.000 0.00 0.00 37.88 3.85
69 70 7.771183 TGCTTGATTTTGGTATAAATGACCTC 58.229 34.615 0.00 0.00 37.88 3.85
70 71 7.615365 TGCTTGATTTTGGTATAAATGACCTCT 59.385 33.333 0.00 0.00 37.88 3.69
71 72 7.917505 GCTTGATTTTGGTATAAATGACCTCTG 59.082 37.037 0.00 0.00 37.88 3.35
72 73 9.177608 CTTGATTTTGGTATAAATGACCTCTGA 57.822 33.333 0.00 0.00 37.88 3.27
73 74 8.506168 TGATTTTGGTATAAATGACCTCTGAC 57.494 34.615 0.00 0.00 37.88 3.51
74 75 8.106462 TGATTTTGGTATAAATGACCTCTGACA 58.894 33.333 0.00 0.00 37.88 3.58
75 76 7.921786 TTTTGGTATAAATGACCTCTGACAG 57.078 36.000 0.00 0.00 37.88 3.51
76 77 6.867519 TTGGTATAAATGACCTCTGACAGA 57.132 37.500 4.78 4.78 37.88 3.41
77 78 6.222038 TGGTATAAATGACCTCTGACAGAC 57.778 41.667 0.00 0.00 37.88 3.51
78 79 5.163550 TGGTATAAATGACCTCTGACAGACG 60.164 44.000 0.00 0.05 37.88 4.18
79 80 5.067413 GGTATAAATGACCTCTGACAGACGA 59.933 44.000 0.00 0.00 33.86 4.20
80 81 3.584406 AAATGACCTCTGACAGACGAG 57.416 47.619 0.00 0.00 0.00 4.18
81 82 2.498644 ATGACCTCTGACAGACGAGA 57.501 50.000 0.00 0.00 0.00 4.04
82 83 2.498644 TGACCTCTGACAGACGAGAT 57.501 50.000 0.00 0.00 0.00 2.75
83 84 3.629142 TGACCTCTGACAGACGAGATA 57.371 47.619 0.00 0.00 0.00 1.98
84 85 3.271729 TGACCTCTGACAGACGAGATAC 58.728 50.000 0.00 0.00 0.00 2.24
102 103 3.492545 GGCCGCGCGTTGAACATA 61.493 61.111 29.95 0.00 0.00 2.29
103 104 2.276430 GCCGCGCGTTGAACATAC 60.276 61.111 29.95 2.24 0.00 2.39
104 105 3.017656 GCCGCGCGTTGAACATACA 62.018 57.895 29.95 0.00 0.00 2.29
105 106 1.058748 CCGCGCGTTGAACATACAG 59.941 57.895 29.95 4.27 0.00 2.74
106 107 1.577616 CGCGCGTTGAACATACAGC 60.578 57.895 24.19 0.00 0.00 4.40
107 108 1.787847 GCGCGTTGAACATACAGCT 59.212 52.632 8.43 0.00 0.00 4.24
108 109 0.519175 GCGCGTTGAACATACAGCTG 60.519 55.000 13.48 13.48 0.00 4.24
109 110 1.067693 CGCGTTGAACATACAGCTGA 58.932 50.000 23.35 4.31 0.00 4.26
110 111 1.660607 CGCGTTGAACATACAGCTGAT 59.339 47.619 23.35 6.78 0.00 2.90
111 112 2.535534 CGCGTTGAACATACAGCTGATG 60.536 50.000 23.35 20.37 0.00 3.07
112 113 2.789092 GCGTTGAACATACAGCTGATGC 60.789 50.000 23.35 8.52 40.05 3.91
113 114 2.416202 CGTTGAACATACAGCTGATGCA 59.584 45.455 23.35 10.70 42.74 3.96
114 115 3.725895 CGTTGAACATACAGCTGATGCAC 60.726 47.826 23.35 15.53 42.74 4.57
115 116 3.056588 TGAACATACAGCTGATGCACA 57.943 42.857 23.35 17.52 42.74 4.57
116 117 2.743664 TGAACATACAGCTGATGCACAC 59.256 45.455 23.35 11.44 42.74 3.82
117 118 2.477845 ACATACAGCTGATGCACACA 57.522 45.000 23.35 0.00 42.74 3.72
118 119 2.781923 ACATACAGCTGATGCACACAA 58.218 42.857 23.35 0.00 42.74 3.33
119 120 3.148412 ACATACAGCTGATGCACACAAA 58.852 40.909 23.35 0.00 42.74 2.83
120 121 3.569277 ACATACAGCTGATGCACACAAAA 59.431 39.130 23.35 0.00 42.74 2.44
121 122 4.037803 ACATACAGCTGATGCACACAAAAA 59.962 37.500 23.35 0.00 42.74 1.94
122 123 3.738830 ACAGCTGATGCACACAAAAAT 57.261 38.095 23.35 0.00 42.74 1.82
123 124 3.645884 ACAGCTGATGCACACAAAAATC 58.354 40.909 23.35 0.00 42.74 2.17
124 125 2.659757 CAGCTGATGCACACAAAAATCG 59.340 45.455 8.42 0.00 42.74 3.34
125 126 2.553602 AGCTGATGCACACAAAAATCGA 59.446 40.909 0.00 0.00 42.74 3.59
126 127 3.004629 AGCTGATGCACACAAAAATCGAA 59.995 39.130 0.00 0.00 42.74 3.71
127 128 3.735240 GCTGATGCACACAAAAATCGAAA 59.265 39.130 0.00 0.00 39.41 3.46
128 129 4.375305 GCTGATGCACACAAAAATCGAAAC 60.375 41.667 0.00 0.00 39.41 2.78
129 130 4.676546 TGATGCACACAAAAATCGAAACA 58.323 34.783 0.00 0.00 0.00 2.83
130 131 5.105063 TGATGCACACAAAAATCGAAACAA 58.895 33.333 0.00 0.00 0.00 2.83
131 132 5.578336 TGATGCACACAAAAATCGAAACAAA 59.422 32.000 0.00 0.00 0.00 2.83
132 133 5.196809 TGCACACAAAAATCGAAACAAAC 57.803 34.783 0.00 0.00 0.00 2.93
133 134 4.686091 TGCACACAAAAATCGAAACAAACA 59.314 33.333 0.00 0.00 0.00 2.83
134 135 5.012613 GCACACAAAAATCGAAACAAACAC 58.987 37.500 0.00 0.00 0.00 3.32
135 136 5.546434 CACACAAAAATCGAAACAAACACC 58.454 37.500 0.00 0.00 0.00 4.16
136 137 4.324936 ACACAAAAATCGAAACAAACACCG 59.675 37.500 0.00 0.00 0.00 4.94
137 138 3.304826 ACAAAAATCGAAACAAACACCGC 59.695 39.130 0.00 0.00 0.00 5.68
138 139 3.430333 AAAATCGAAACAAACACCGCT 57.570 38.095 0.00 0.00 0.00 5.52
139 140 2.681152 AATCGAAACAAACACCGCTC 57.319 45.000 0.00 0.00 0.00 5.03
140 141 0.872388 ATCGAAACAAACACCGCTCC 59.128 50.000 0.00 0.00 0.00 4.70
141 142 0.462225 TCGAAACAAACACCGCTCCA 60.462 50.000 0.00 0.00 0.00 3.86
142 143 0.591170 CGAAACAAACACCGCTCCAT 59.409 50.000 0.00 0.00 0.00 3.41
143 144 1.001815 CGAAACAAACACCGCTCCATT 60.002 47.619 0.00 0.00 0.00 3.16
144 145 2.393764 GAAACAAACACCGCTCCATTG 58.606 47.619 0.00 0.00 0.00 2.82
145 146 0.031994 AACAAACACCGCTCCATTGC 59.968 50.000 0.00 0.00 0.00 3.56
146 147 1.080569 CAAACACCGCTCCATTGCC 60.081 57.895 0.00 0.00 0.00 4.52
147 148 1.530419 AAACACCGCTCCATTGCCA 60.530 52.632 0.00 0.00 0.00 4.92
148 149 0.899717 AAACACCGCTCCATTGCCAT 60.900 50.000 0.00 0.00 0.00 4.40
149 150 1.315257 AACACCGCTCCATTGCCATC 61.315 55.000 0.00 0.00 0.00 3.51
150 151 1.452651 CACCGCTCCATTGCCATCT 60.453 57.895 0.00 0.00 0.00 2.90
151 152 1.452651 ACCGCTCCATTGCCATCTG 60.453 57.895 0.00 0.00 0.00 2.90
152 153 1.153107 CCGCTCCATTGCCATCTGA 60.153 57.895 0.00 0.00 0.00 3.27
153 154 0.749091 CCGCTCCATTGCCATCTGAA 60.749 55.000 0.00 0.00 0.00 3.02
154 155 1.097232 CGCTCCATTGCCATCTGAAA 58.903 50.000 0.00 0.00 0.00 2.69
155 156 1.202222 CGCTCCATTGCCATCTGAAAC 60.202 52.381 0.00 0.00 0.00 2.78
156 157 1.202222 GCTCCATTGCCATCTGAAACG 60.202 52.381 0.00 0.00 0.00 3.60
157 158 1.402968 CTCCATTGCCATCTGAAACGG 59.597 52.381 0.00 0.00 0.00 4.44
158 159 1.004161 TCCATTGCCATCTGAAACGGA 59.996 47.619 0.00 0.00 0.00 4.69
159 160 1.133025 CCATTGCCATCTGAAACGGAC 59.867 52.381 0.00 0.00 0.00 4.79
160 161 1.811965 CATTGCCATCTGAAACGGACA 59.188 47.619 0.00 0.00 0.00 4.02
161 162 1.974265 TTGCCATCTGAAACGGACAA 58.026 45.000 0.00 0.00 0.00 3.18
162 163 1.974265 TGCCATCTGAAACGGACAAA 58.026 45.000 0.00 0.00 0.00 2.83
163 164 2.302260 TGCCATCTGAAACGGACAAAA 58.698 42.857 0.00 0.00 0.00 2.44
164 165 2.890311 TGCCATCTGAAACGGACAAAAT 59.110 40.909 0.00 0.00 0.00 1.82
165 166 3.057596 TGCCATCTGAAACGGACAAAATC 60.058 43.478 0.00 0.00 0.00 2.17
166 167 3.673323 GCCATCTGAAACGGACAAAATCC 60.673 47.826 0.00 0.00 45.20 3.01
179 180 5.821204 GGACAAAATCCGAACAATATGAGG 58.179 41.667 0.00 0.00 37.88 3.86
180 181 5.248870 ACAAAATCCGAACAATATGAGGC 57.751 39.130 0.00 0.00 0.00 4.70
181 182 4.097892 ACAAAATCCGAACAATATGAGGCC 59.902 41.667 0.00 0.00 0.00 5.19
182 183 3.864789 AATCCGAACAATATGAGGCCT 57.135 42.857 3.86 3.86 0.00 5.19
183 184 2.910688 TCCGAACAATATGAGGCCTC 57.089 50.000 26.78 26.78 0.00 4.70
184 185 1.416401 TCCGAACAATATGAGGCCTCC 59.584 52.381 29.95 12.55 0.00 4.30
185 186 1.417890 CCGAACAATATGAGGCCTCCT 59.582 52.381 29.95 22.58 36.03 3.69
186 187 2.158755 CCGAACAATATGAGGCCTCCTT 60.159 50.000 29.95 19.25 31.76 3.36
187 188 3.545703 CGAACAATATGAGGCCTCCTTT 58.454 45.455 29.95 17.00 31.76 3.11
188 189 3.313526 CGAACAATATGAGGCCTCCTTTG 59.686 47.826 29.95 27.48 31.76 2.77
189 190 3.303351 ACAATATGAGGCCTCCTTTGG 57.697 47.619 29.95 18.15 31.76 3.28
190 191 2.582636 ACAATATGAGGCCTCCTTTGGT 59.417 45.455 29.95 18.80 31.76 3.67
191 192 3.011708 ACAATATGAGGCCTCCTTTGGTT 59.988 43.478 29.95 12.78 31.76 3.67
192 193 4.026052 CAATATGAGGCCTCCTTTGGTTT 58.974 43.478 29.95 10.75 31.76 3.27
193 194 1.928868 ATGAGGCCTCCTTTGGTTTG 58.071 50.000 29.95 0.00 31.76 2.93
194 195 0.555769 TGAGGCCTCCTTTGGTTTGT 59.444 50.000 29.95 0.00 31.76 2.83
195 196 1.777878 TGAGGCCTCCTTTGGTTTGTA 59.222 47.619 29.95 3.38 31.76 2.41
196 197 2.224769 TGAGGCCTCCTTTGGTTTGTAG 60.225 50.000 29.95 0.00 31.76 2.74
197 198 1.075536 AGGCCTCCTTTGGTTTGTAGG 59.924 52.381 0.00 0.00 0.00 3.18
198 199 1.074889 GGCCTCCTTTGGTTTGTAGGA 59.925 52.381 0.00 0.00 36.65 2.94
199 200 2.490168 GGCCTCCTTTGGTTTGTAGGAA 60.490 50.000 0.00 0.00 37.61 3.36
200 201 3.431415 GCCTCCTTTGGTTTGTAGGAAT 58.569 45.455 0.00 0.00 37.61 3.01
201 202 3.193479 GCCTCCTTTGGTTTGTAGGAATG 59.807 47.826 0.00 0.00 37.61 2.67
202 203 4.407365 CCTCCTTTGGTTTGTAGGAATGT 58.593 43.478 0.00 0.00 37.61 2.71
203 204 4.459337 CCTCCTTTGGTTTGTAGGAATGTC 59.541 45.833 0.00 0.00 37.61 3.06
204 205 5.055265 TCCTTTGGTTTGTAGGAATGTCA 57.945 39.130 0.00 0.00 35.20 3.58
205 206 5.640147 TCCTTTGGTTTGTAGGAATGTCAT 58.360 37.500 0.00 0.00 35.20 3.06
206 207 6.785076 TCCTTTGGTTTGTAGGAATGTCATA 58.215 36.000 0.00 0.00 35.20 2.15
207 208 6.884295 TCCTTTGGTTTGTAGGAATGTCATAG 59.116 38.462 0.00 0.00 35.20 2.23
208 209 6.884295 CCTTTGGTTTGTAGGAATGTCATAGA 59.116 38.462 0.00 0.00 0.00 1.98
209 210 7.393234 CCTTTGGTTTGTAGGAATGTCATAGAA 59.607 37.037 0.00 0.00 0.00 2.10
210 211 8.877864 TTTGGTTTGTAGGAATGTCATAGAAT 57.122 30.769 0.00 0.00 0.00 2.40
211 212 8.877864 TTGGTTTGTAGGAATGTCATAGAATT 57.122 30.769 0.00 0.00 0.00 2.17
212 213 8.877864 TGGTTTGTAGGAATGTCATAGAATTT 57.122 30.769 0.00 0.00 0.00 1.82
213 214 9.967451 TGGTTTGTAGGAATGTCATAGAATTTA 57.033 29.630 0.00 0.00 0.00 1.40
242 243 8.788238 AGGATAGGATTTGCATAGGAAAATTT 57.212 30.769 0.00 0.00 32.16 1.82
243 244 8.864087 AGGATAGGATTTGCATAGGAAAATTTC 58.136 33.333 0.00 0.00 32.16 2.17
255 256 4.558226 GGAAAATTTCCTTTGAGGCCAT 57.442 40.909 17.01 0.00 46.57 4.40
256 257 4.910195 GGAAAATTTCCTTTGAGGCCATT 58.090 39.130 17.01 0.00 46.57 3.16
257 258 5.316167 GGAAAATTTCCTTTGAGGCCATTT 58.684 37.500 17.01 0.00 46.57 2.32
258 259 5.181811 GGAAAATTTCCTTTGAGGCCATTTG 59.818 40.000 17.01 0.00 46.57 2.32
259 260 3.986996 ATTTCCTTTGAGGCCATTTGG 57.013 42.857 5.01 0.00 34.61 3.28
260 261 2.397044 TTCCTTTGAGGCCATTTGGT 57.603 45.000 5.01 0.00 34.61 3.67
261 262 2.397044 TCCTTTGAGGCCATTTGGTT 57.603 45.000 5.01 0.00 34.61 3.67
262 263 2.688477 TCCTTTGAGGCCATTTGGTTT 58.312 42.857 5.01 0.00 34.61 3.27
263 264 3.850752 TCCTTTGAGGCCATTTGGTTTA 58.149 40.909 5.01 0.00 34.61 2.01
264 265 4.424842 TCCTTTGAGGCCATTTGGTTTAT 58.575 39.130 5.01 0.00 34.61 1.40
265 266 5.584913 TCCTTTGAGGCCATTTGGTTTATA 58.415 37.500 5.01 0.00 34.61 0.98
266 267 5.656416 TCCTTTGAGGCCATTTGGTTTATAG 59.344 40.000 5.01 0.00 34.61 1.31
267 268 5.163416 CCTTTGAGGCCATTTGGTTTATAGG 60.163 44.000 5.01 0.00 37.57 2.57
268 269 4.871871 TGAGGCCATTTGGTTTATAGGA 57.128 40.909 5.01 0.00 37.57 2.94
269 270 5.199982 TGAGGCCATTTGGTTTATAGGAA 57.800 39.130 5.01 0.00 37.57 3.36
270 271 5.776358 TGAGGCCATTTGGTTTATAGGAAT 58.224 37.500 5.01 0.00 37.57 3.01
271 272 5.598005 TGAGGCCATTTGGTTTATAGGAATG 59.402 40.000 5.01 0.00 37.57 2.67
272 273 4.901250 AGGCCATTTGGTTTATAGGAATGG 59.099 41.667 5.01 8.63 45.96 3.16
273 274 4.898861 GGCCATTTGGTTTATAGGAATGGA 59.101 41.667 15.46 0.00 46.06 3.41
274 275 5.221441 GGCCATTTGGTTTATAGGAATGGAC 60.221 44.000 15.46 10.01 46.06 4.02
275 276 5.598417 GCCATTTGGTTTATAGGAATGGACT 59.402 40.000 15.46 0.00 46.06 3.85
276 277 6.239036 GCCATTTGGTTTATAGGAATGGACTC 60.239 42.308 15.46 0.00 46.06 3.36
277 278 6.265422 CCATTTGGTTTATAGGAATGGACTCC 59.735 42.308 7.46 0.00 46.06 3.85
278 279 7.859009 CCATTTGGTTTATAGGAATGGACTCCT 60.859 40.741 7.46 0.00 46.06 3.69
291 292 9.722317 AGGAATGGACTCCTATTTCTATATAGG 57.278 37.037 9.89 0.00 44.43 2.57
316 317 9.472361 GGATATGAATCAATCCTTCACATTTTG 57.528 33.333 13.51 0.00 38.92 2.44
320 321 8.766000 TGAATCAATCCTTCACATTTTGAATG 57.234 30.769 0.00 0.00 43.54 2.67
321 322 8.586744 TGAATCAATCCTTCACATTTTGAATGA 58.413 29.630 7.59 0.00 43.54 2.57
322 323 9.426837 GAATCAATCCTTCACATTTTGAATGAA 57.573 29.630 7.59 0.00 43.54 2.57
323 324 9.781633 AATCAATCCTTCACATTTTGAATGAAA 57.218 25.926 7.59 1.73 43.54 2.69
324 325 9.781633 ATCAATCCTTCACATTTTGAATGAAAA 57.218 25.926 7.59 0.00 43.54 2.29
325 326 9.610705 TCAATCCTTCACATTTTGAATGAAAAA 57.389 25.926 7.59 0.00 43.54 1.94
381 382 9.552695 TCCTATCCTATACATCAAATGACATCT 57.447 33.333 0.00 0.00 0.00 2.90
382 383 9.814899 CCTATCCTATACATCAAATGACATCTC 57.185 37.037 0.00 0.00 0.00 2.75
426 427 8.095937 GATGCATGTCATCTCATTTTCTATGA 57.904 34.615 2.46 0.00 46.29 2.15
427 428 8.637196 ATGCATGTCATCTCATTTTCTATGAT 57.363 30.769 0.00 0.00 31.49 2.45
428 429 8.459911 TGCATGTCATCTCATTTTCTATGATT 57.540 30.769 0.00 0.00 31.49 2.57
429 430 8.909923 TGCATGTCATCTCATTTTCTATGATTT 58.090 29.630 0.00 0.00 31.49 2.17
430 431 9.745880 GCATGTCATCTCATTTTCTATGATTTT 57.254 29.630 0.00 0.00 31.49 1.82
460 461 8.918202 TTCCTACAACATAATGTTTTCAGACT 57.082 30.769 0.00 0.00 38.77 3.24
461 462 8.322906 TCCTACAACATAATGTTTTCAGACTG 57.677 34.615 0.00 0.00 38.77 3.51
462 463 7.936847 TCCTACAACATAATGTTTTCAGACTGT 59.063 33.333 1.59 0.00 38.77 3.55
472 473 5.568482 TGTTTTCAGACTGTTTGTTCATCG 58.432 37.500 1.59 0.00 0.00 3.84
580 582 6.793505 ATGATTCTTACCGTCTTTCTAGGT 57.206 37.500 0.00 0.00 41.73 3.08
599 602 7.313731 TCTAGGTTTCCTGGATTATCCTATGT 58.686 38.462 12.91 0.00 36.21 2.29
613 616 1.414181 CCTATGTACCCTCTGCCACAG 59.586 57.143 0.00 0.00 0.00 3.66
713 727 1.134431 TCTCGCAGCAGCATTGGAATA 60.134 47.619 0.82 0.00 42.27 1.75
714 728 1.003116 CTCGCAGCAGCATTGGAATAC 60.003 52.381 0.82 0.00 42.27 1.89
802 818 2.166254 CCACCATTGCCTTTGTCCATAC 59.834 50.000 0.00 0.00 0.00 2.39
803 819 2.166254 CACCATTGCCTTTGTCCATACC 59.834 50.000 0.00 0.00 0.00 2.73
805 821 3.033184 CCATTGCCTTTGTCCATACCAT 58.967 45.455 0.00 0.00 0.00 3.55
806 822 4.214310 CCATTGCCTTTGTCCATACCATA 58.786 43.478 0.00 0.00 0.00 2.74
807 823 4.834496 CCATTGCCTTTGTCCATACCATAT 59.166 41.667 0.00 0.00 0.00 1.78
808 824 6.009589 CCATTGCCTTTGTCCATACCATATA 58.990 40.000 0.00 0.00 0.00 0.86
810 826 6.952773 TTGCCTTTGTCCATACCATATAAC 57.047 37.500 0.00 0.00 0.00 1.89
811 827 5.381757 TGCCTTTGTCCATACCATATAACC 58.618 41.667 0.00 0.00 0.00 2.85
812 828 5.133660 TGCCTTTGTCCATACCATATAACCT 59.866 40.000 0.00 0.00 0.00 3.50
813 829 6.068670 GCCTTTGTCCATACCATATAACCTT 58.931 40.000 0.00 0.00 0.00 3.50
814 830 7.147284 TGCCTTTGTCCATACCATATAACCTTA 60.147 37.037 0.00 0.00 0.00 2.69
815 831 7.722285 GCCTTTGTCCATACCATATAACCTTAA 59.278 37.037 0.00 0.00 0.00 1.85
816 832 9.063615 CCTTTGTCCATACCATATAACCTTAAC 57.936 37.037 0.00 0.00 0.00 2.01
887 908 3.624326 CTCTTGATACGGAGAGCTCTG 57.376 52.381 23.91 10.55 41.63 3.35
888 909 1.678627 TCTTGATACGGAGAGCTCTGC 59.321 52.381 23.91 24.08 39.55 4.26
889 910 1.680735 CTTGATACGGAGAGCTCTGCT 59.319 52.381 29.52 19.57 43.88 4.24
899 920 2.593128 AGCTCTGCTCTGCTCATCA 58.407 52.632 0.00 0.00 30.62 3.07
1018 1059 7.123247 ACAAATTTATGATTCTTGACTGGGAGG 59.877 37.037 0.00 0.00 0.00 4.30
1052 1093 3.334054 GCCTCTTGGACTGGGCCT 61.334 66.667 4.53 0.00 38.77 5.19
1053 1094 2.673523 CCTCTTGGACTGGGCCTG 59.326 66.667 9.11 9.11 34.57 4.85
1054 1095 2.673523 CTCTTGGACTGGGCCTGG 59.326 66.667 15.36 5.47 0.00 4.45
1055 1096 2.935481 TCTTGGACTGGGCCTGGG 60.935 66.667 15.36 2.88 0.00 4.45
1056 1097 4.748144 CTTGGACTGGGCCTGGGC 62.748 72.222 12.58 12.58 41.06 5.36
1219 1263 7.786030 ACTATCTGTCTGCAATATAACAGTGT 58.214 34.615 10.66 0.00 40.01 3.55
1222 1266 6.101997 TCTGTCTGCAATATAACAGTGTCAG 58.898 40.000 0.00 0.00 40.01 3.51
1235 1282 2.036475 CAGTGTCAGTGTAGGTCAGCTT 59.964 50.000 0.00 0.00 0.00 3.74
1245 1292 4.697352 GTGTAGGTCAGCTTGATTTGATGT 59.303 41.667 0.00 0.00 0.00 3.06
1254 1301 5.012239 AGCTTGATTTGATGTTCCTGCTTA 58.988 37.500 0.00 0.00 0.00 3.09
1263 1310 8.856153 TTTGATGTTCCTGCTTATACTTTGTA 57.144 30.769 0.00 0.00 0.00 2.41
1552 1605 2.029964 GCTTCCGTGGAACCGTGA 59.970 61.111 0.00 0.00 0.00 4.35
1645 1699 2.751259 AGATTTGCATGTTGTCGCTCAT 59.249 40.909 0.00 0.00 0.00 2.90
1706 1760 7.110216 CGTAAACGCAAAGCTTACATATCATTC 59.890 37.037 0.00 0.00 0.00 2.67
1709 1763 6.662616 ACGCAAAGCTTACATATCATTCATC 58.337 36.000 0.00 0.00 0.00 2.92
1710 1764 6.260714 ACGCAAAGCTTACATATCATTCATCA 59.739 34.615 0.00 0.00 0.00 3.07
1735 1789 4.377897 AGGTAGAAACAAACAGAGTTCCG 58.622 43.478 0.00 0.00 0.00 4.30
1736 1790 4.100498 AGGTAGAAACAAACAGAGTTCCGA 59.900 41.667 0.00 0.00 0.00 4.55
1737 1791 4.812626 GGTAGAAACAAACAGAGTTCCGAA 59.187 41.667 0.00 0.00 0.00 4.30
1753 1807 5.189145 AGTTCCGAACATTACACTTAGGGAT 59.811 40.000 13.69 0.00 0.00 3.85
1777 1831 1.061887 CGGATAAACGGCGCAAAGG 59.938 57.895 10.83 0.00 0.00 3.11
1800 1854 2.334946 CGTGGTGGCCATTGTCCTG 61.335 63.158 9.72 0.00 35.28 3.86
1803 1857 0.105760 TGGTGGCCATTGTCCTGTTT 60.106 50.000 9.72 0.00 0.00 2.83
1804 1858 0.318120 GGTGGCCATTGTCCTGTTTG 59.682 55.000 9.72 0.00 0.00 2.93
1805 1859 0.319813 GTGGCCATTGTCCTGTTTGC 60.320 55.000 9.72 0.00 0.00 3.68
1807 1861 0.681175 GGCCATTGTCCTGTTTGCTT 59.319 50.000 0.00 0.00 0.00 3.91
1809 1863 1.606224 GCCATTGTCCTGTTTGCTTGG 60.606 52.381 0.00 0.00 0.00 3.61
1815 1870 0.183492 TCCTGTTTGCTTGGCAGAGT 59.817 50.000 0.00 0.00 40.61 3.24
1861 1916 3.188786 GGCGTCCGTGATCTGCAC 61.189 66.667 0.00 0.00 44.21 4.57
1880 1935 4.802051 GGGCTGGGATTGCGCTCA 62.802 66.667 9.73 0.00 39.74 4.26
1896 1951 1.005748 TCAGCGTCTGTTGGCTCTG 60.006 57.895 6.72 0.00 37.41 3.35
1987 2042 0.741574 TGTTTCACGCGTCCACAACT 60.742 50.000 9.86 0.00 0.00 3.16
1989 2044 1.593933 GTTTCACGCGTCCACAACTTA 59.406 47.619 9.86 0.00 0.00 2.24
1997 2052 1.338674 CGTCCACAACTTAGGCCATCA 60.339 52.381 5.01 0.00 0.00 3.07
1998 2053 2.359900 GTCCACAACTTAGGCCATCAG 58.640 52.381 5.01 0.00 0.00 2.90
2016 2071 0.036164 AGTAATGGCCTGTCGTGCAA 59.964 50.000 3.32 0.00 0.00 4.08
2022 2077 1.271108 TGGCCTGTCGTGCAAATTCTA 60.271 47.619 3.32 0.00 0.00 2.10
2049 2104 1.134788 CCACTGGATCAACGGTAGGAC 60.135 57.143 0.00 0.00 0.00 3.85
2052 2107 0.612732 TGGATCAACGGTAGGACGGT 60.613 55.000 0.00 0.00 38.39 4.83
2153 2210 1.376683 GCGTGGGTACAAGGCATCA 60.377 57.895 7.39 0.00 0.00 3.07
2185 2242 0.951558 GTCCTTTGGCGCTTCTTCAA 59.048 50.000 7.64 0.00 0.00 2.69
2207 2264 1.135731 GTCGAGCTCTGACGTCAGG 59.864 63.158 37.82 29.46 43.91 3.86
2229 2286 1.871080 CAGCTCGTTCACCTTTCAGT 58.129 50.000 0.00 0.00 0.00 3.41
2341 2398 2.515398 CCCCATTGGCGCCTCATA 59.485 61.111 29.70 10.85 0.00 2.15
2344 2401 0.250858 CCCATTGGCGCCTCATATGA 60.251 55.000 29.70 5.07 0.00 2.15
2373 2430 1.617947 GCACCTCTCCGGATGAAGGT 61.618 60.000 21.63 21.63 36.31 3.50
2391 2448 2.210013 TGTTCCTCTGGCTCGCTGT 61.210 57.895 0.00 0.00 0.00 4.40
2478 2536 2.210116 GCTTTGTGACCAAGAGTTCGA 58.790 47.619 0.02 0.00 0.00 3.71
2479 2537 2.221981 GCTTTGTGACCAAGAGTTCGAG 59.778 50.000 0.02 0.00 0.00 4.04
2540 2598 1.938585 AATCTGGTTCGAGGTCCTCA 58.061 50.000 19.15 3.46 0.00 3.86
2541 2599 1.938585 ATCTGGTTCGAGGTCCTCAA 58.061 50.000 19.15 9.29 0.00 3.02
2550 2608 1.048601 GAGGTCCTCAACTGGTGTCA 58.951 55.000 14.46 0.00 0.00 3.58
2556 2614 0.533531 CTCAACTGGTGTCAGCTGCA 60.534 55.000 9.47 7.85 44.59 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 9.585099 CCAAAATCAAGCATAGCAAATAGTTTA 57.415 29.630 0.00 0.00 0.00 2.01
31 32 8.096414 ACCAAAATCAAGCATAGCAAATAGTTT 58.904 29.630 0.00 0.00 0.00 2.66
32 33 7.614494 ACCAAAATCAAGCATAGCAAATAGTT 58.386 30.769 0.00 0.00 0.00 2.24
33 34 7.174107 ACCAAAATCAAGCATAGCAAATAGT 57.826 32.000 0.00 0.00 0.00 2.12
38 39 9.531942 CATTTATACCAAAATCAAGCATAGCAA 57.468 29.630 0.00 0.00 0.00 3.91
39 40 8.911965 TCATTTATACCAAAATCAAGCATAGCA 58.088 29.630 0.00 0.00 0.00 3.49
40 41 9.185192 GTCATTTATACCAAAATCAAGCATAGC 57.815 33.333 0.00 0.00 0.00 2.97
41 42 9.683069 GGTCATTTATACCAAAATCAAGCATAG 57.317 33.333 0.00 0.00 36.96 2.23
42 43 9.420118 AGGTCATTTATACCAAAATCAAGCATA 57.580 29.630 0.00 0.00 39.64 3.14
43 44 8.310122 AGGTCATTTATACCAAAATCAAGCAT 57.690 30.769 0.00 0.00 39.64 3.79
44 45 7.615365 AGAGGTCATTTATACCAAAATCAAGCA 59.385 33.333 0.00 0.00 39.64 3.91
45 46 7.917505 CAGAGGTCATTTATACCAAAATCAAGC 59.082 37.037 0.00 0.00 39.64 4.01
46 47 9.177608 TCAGAGGTCATTTATACCAAAATCAAG 57.822 33.333 0.00 0.00 39.64 3.02
47 48 8.956426 GTCAGAGGTCATTTATACCAAAATCAA 58.044 33.333 0.00 0.00 39.64 2.57
48 49 8.106462 TGTCAGAGGTCATTTATACCAAAATCA 58.894 33.333 0.00 0.00 39.64 2.57
49 50 8.506168 TGTCAGAGGTCATTTATACCAAAATC 57.494 34.615 0.00 0.00 39.64 2.17
50 51 8.328758 TCTGTCAGAGGTCATTTATACCAAAAT 58.671 33.333 0.00 0.00 39.64 1.82
51 52 7.606456 GTCTGTCAGAGGTCATTTATACCAAAA 59.394 37.037 1.75 0.00 39.64 2.44
52 53 7.103641 GTCTGTCAGAGGTCATTTATACCAAA 58.896 38.462 1.75 0.00 39.64 3.28
53 54 6.627287 CGTCTGTCAGAGGTCATTTATACCAA 60.627 42.308 13.35 0.00 39.64 3.67
54 55 5.163550 CGTCTGTCAGAGGTCATTTATACCA 60.164 44.000 13.35 0.00 39.64 3.25
55 56 5.067413 TCGTCTGTCAGAGGTCATTTATACC 59.933 44.000 19.31 0.00 37.27 2.73
56 57 6.038382 TCTCGTCTGTCAGAGGTCATTTATAC 59.962 42.308 19.31 0.00 35.34 1.47
57 58 6.120220 TCTCGTCTGTCAGAGGTCATTTATA 58.880 40.000 19.31 0.49 35.34 0.98
58 59 4.950475 TCTCGTCTGTCAGAGGTCATTTAT 59.050 41.667 19.31 0.00 35.34 1.40
59 60 4.332828 TCTCGTCTGTCAGAGGTCATTTA 58.667 43.478 19.31 1.74 35.34 1.40
60 61 3.157881 TCTCGTCTGTCAGAGGTCATTT 58.842 45.455 19.31 0.00 35.34 2.32
61 62 2.796557 TCTCGTCTGTCAGAGGTCATT 58.203 47.619 19.31 0.00 35.34 2.57
62 63 2.498644 TCTCGTCTGTCAGAGGTCAT 57.501 50.000 19.31 0.00 35.34 3.06
63 64 2.498644 ATCTCGTCTGTCAGAGGTCA 57.501 50.000 19.31 9.65 35.34 4.02
64 65 2.285756 CGTATCTCGTCTGTCAGAGGTC 59.714 54.545 19.31 1.21 35.34 3.85
65 66 2.281517 CGTATCTCGTCTGTCAGAGGT 58.718 52.381 19.31 6.03 35.34 3.85
66 67 1.600013 CCGTATCTCGTCTGTCAGAGG 59.400 57.143 15.07 15.07 37.94 3.69
67 68 1.003331 GCCGTATCTCGTCTGTCAGAG 60.003 57.143 1.75 0.00 37.94 3.35
68 69 1.015109 GCCGTATCTCGTCTGTCAGA 58.985 55.000 0.00 0.00 37.94 3.27
69 70 0.029567 GGCCGTATCTCGTCTGTCAG 59.970 60.000 0.00 0.00 37.94 3.51
70 71 1.712018 CGGCCGTATCTCGTCTGTCA 61.712 60.000 19.50 0.00 37.94 3.58
71 72 1.009900 CGGCCGTATCTCGTCTGTC 60.010 63.158 19.50 0.00 37.94 3.51
72 73 3.108343 CGGCCGTATCTCGTCTGT 58.892 61.111 19.50 0.00 37.94 3.41
73 74 2.353607 GCGGCCGTATCTCGTCTG 60.354 66.667 28.70 0.00 37.94 3.51
74 75 3.950254 CGCGGCCGTATCTCGTCT 61.950 66.667 28.70 0.00 37.94 4.18
85 86 3.492545 TATGTTCAACGCGCGGCC 61.493 61.111 35.22 16.33 0.00 6.13
86 87 2.276430 GTATGTTCAACGCGCGGC 60.276 61.111 35.22 17.86 0.00 6.53
87 88 1.058748 CTGTATGTTCAACGCGCGG 59.941 57.895 35.22 17.77 0.00 6.46
88 89 1.577616 GCTGTATGTTCAACGCGCG 60.578 57.895 30.96 30.96 0.00 6.86
89 90 0.519175 CAGCTGTATGTTCAACGCGC 60.519 55.000 5.73 0.00 0.00 6.86
90 91 1.067693 TCAGCTGTATGTTCAACGCG 58.932 50.000 14.67 3.53 0.00 6.01
91 92 2.789092 GCATCAGCTGTATGTTCAACGC 60.789 50.000 14.67 0.00 37.91 4.84
92 93 2.416202 TGCATCAGCTGTATGTTCAACG 59.584 45.455 14.67 0.00 42.74 4.10
93 94 3.189080 TGTGCATCAGCTGTATGTTCAAC 59.811 43.478 14.67 12.52 42.74 3.18
94 95 3.189080 GTGTGCATCAGCTGTATGTTCAA 59.811 43.478 14.67 0.00 42.74 2.69
95 96 2.743664 GTGTGCATCAGCTGTATGTTCA 59.256 45.455 14.67 14.43 42.74 3.18
96 97 2.743664 TGTGTGCATCAGCTGTATGTTC 59.256 45.455 14.67 12.48 42.74 3.18
97 98 2.781923 TGTGTGCATCAGCTGTATGTT 58.218 42.857 14.67 0.00 42.74 2.71
98 99 2.477845 TGTGTGCATCAGCTGTATGT 57.522 45.000 14.67 0.00 42.74 2.29
99 100 3.835378 TTTGTGTGCATCAGCTGTATG 57.165 42.857 14.67 16.12 42.74 2.39
100 101 4.852134 TTTTTGTGTGCATCAGCTGTAT 57.148 36.364 14.67 3.15 42.74 2.29
101 102 4.613394 CGATTTTTGTGTGCATCAGCTGTA 60.613 41.667 14.67 0.48 42.74 2.74
102 103 3.645884 GATTTTTGTGTGCATCAGCTGT 58.354 40.909 14.67 0.00 42.74 4.40
103 104 2.659757 CGATTTTTGTGTGCATCAGCTG 59.340 45.455 7.63 7.63 42.74 4.24
104 105 2.553602 TCGATTTTTGTGTGCATCAGCT 59.446 40.909 0.00 0.00 42.74 4.24
105 106 2.932498 TCGATTTTTGTGTGCATCAGC 58.068 42.857 0.00 0.00 42.57 4.26
106 107 4.739228 TGTTTCGATTTTTGTGTGCATCAG 59.261 37.500 0.00 0.00 0.00 2.90
107 108 4.676546 TGTTTCGATTTTTGTGTGCATCA 58.323 34.783 0.00 0.00 0.00 3.07
108 109 5.633996 TTGTTTCGATTTTTGTGTGCATC 57.366 34.783 0.00 0.00 0.00 3.91
109 110 5.349817 TGTTTGTTTCGATTTTTGTGTGCAT 59.650 32.000 0.00 0.00 0.00 3.96
110 111 4.686091 TGTTTGTTTCGATTTTTGTGTGCA 59.314 33.333 0.00 0.00 0.00 4.57
111 112 5.012613 GTGTTTGTTTCGATTTTTGTGTGC 58.987 37.500 0.00 0.00 0.00 4.57
112 113 5.546434 GGTGTTTGTTTCGATTTTTGTGTG 58.454 37.500 0.00 0.00 0.00 3.82
113 114 4.324936 CGGTGTTTGTTTCGATTTTTGTGT 59.675 37.500 0.00 0.00 0.00 3.72
114 115 4.777538 GCGGTGTTTGTTTCGATTTTTGTG 60.778 41.667 0.00 0.00 0.00 3.33
115 116 3.304826 GCGGTGTTTGTTTCGATTTTTGT 59.695 39.130 0.00 0.00 0.00 2.83
116 117 3.549873 AGCGGTGTTTGTTTCGATTTTTG 59.450 39.130 0.00 0.00 0.00 2.44
117 118 3.776340 AGCGGTGTTTGTTTCGATTTTT 58.224 36.364 0.00 0.00 0.00 1.94
118 119 3.368495 GAGCGGTGTTTGTTTCGATTTT 58.632 40.909 0.00 0.00 0.00 1.82
119 120 2.287368 GGAGCGGTGTTTGTTTCGATTT 60.287 45.455 0.00 0.00 0.00 2.17
120 121 1.265905 GGAGCGGTGTTTGTTTCGATT 59.734 47.619 0.00 0.00 0.00 3.34
121 122 0.872388 GGAGCGGTGTTTGTTTCGAT 59.128 50.000 0.00 0.00 0.00 3.59
122 123 0.462225 TGGAGCGGTGTTTGTTTCGA 60.462 50.000 0.00 0.00 0.00 3.71
123 124 0.591170 ATGGAGCGGTGTTTGTTTCG 59.409 50.000 0.00 0.00 0.00 3.46
124 125 2.393764 CAATGGAGCGGTGTTTGTTTC 58.606 47.619 0.00 0.00 0.00 2.78
125 126 1.537990 GCAATGGAGCGGTGTTTGTTT 60.538 47.619 0.00 0.00 0.00 2.83
126 127 0.031994 GCAATGGAGCGGTGTTTGTT 59.968 50.000 0.00 0.00 0.00 2.83
127 128 1.659794 GCAATGGAGCGGTGTTTGT 59.340 52.632 0.00 0.00 0.00 2.83
128 129 1.080569 GGCAATGGAGCGGTGTTTG 60.081 57.895 0.00 0.00 34.64 2.93
129 130 0.899717 ATGGCAATGGAGCGGTGTTT 60.900 50.000 0.00 0.00 34.64 2.83
130 131 1.304381 ATGGCAATGGAGCGGTGTT 60.304 52.632 0.00 0.00 34.64 3.32
131 132 1.750399 GATGGCAATGGAGCGGTGT 60.750 57.895 0.00 0.00 34.64 4.16
132 133 1.452651 AGATGGCAATGGAGCGGTG 60.453 57.895 0.00 0.00 34.64 4.94
133 134 1.452651 CAGATGGCAATGGAGCGGT 60.453 57.895 0.00 0.00 34.64 5.68
134 135 0.749091 TTCAGATGGCAATGGAGCGG 60.749 55.000 0.00 0.00 34.64 5.52
135 136 1.097232 TTTCAGATGGCAATGGAGCG 58.903 50.000 0.00 0.00 34.64 5.03
136 137 1.202222 CGTTTCAGATGGCAATGGAGC 60.202 52.381 0.00 0.00 0.00 4.70
137 138 1.402968 CCGTTTCAGATGGCAATGGAG 59.597 52.381 0.00 0.00 0.00 3.86
138 139 1.004161 TCCGTTTCAGATGGCAATGGA 59.996 47.619 0.00 0.00 33.90 3.41
139 140 1.133025 GTCCGTTTCAGATGGCAATGG 59.867 52.381 0.00 0.00 34.15 3.16
140 141 1.811965 TGTCCGTTTCAGATGGCAATG 59.188 47.619 0.00 0.00 34.15 2.82
141 142 2.198827 TGTCCGTTTCAGATGGCAAT 57.801 45.000 0.00 0.00 34.15 3.56
142 143 1.974265 TTGTCCGTTTCAGATGGCAA 58.026 45.000 0.00 0.00 34.15 4.52
143 144 1.974265 TTTGTCCGTTTCAGATGGCA 58.026 45.000 0.00 0.00 34.15 4.92
144 145 3.501950 GATTTTGTCCGTTTCAGATGGC 58.498 45.455 0.00 0.00 34.15 4.40
145 146 4.096732 GGATTTTGTCCGTTTCAGATGG 57.903 45.455 0.00 0.00 37.23 3.51
156 157 5.733373 GCCTCATATTGTTCGGATTTTGTCC 60.733 44.000 0.00 0.00 44.10 4.02
157 158 5.273944 GCCTCATATTGTTCGGATTTTGTC 58.726 41.667 0.00 0.00 0.00 3.18
158 159 4.097892 GGCCTCATATTGTTCGGATTTTGT 59.902 41.667 0.00 0.00 0.00 2.83
159 160 4.339247 AGGCCTCATATTGTTCGGATTTTG 59.661 41.667 0.00 0.00 0.00 2.44
160 161 4.536765 AGGCCTCATATTGTTCGGATTTT 58.463 39.130 0.00 0.00 0.00 1.82
161 162 4.137543 GAGGCCTCATATTGTTCGGATTT 58.862 43.478 28.43 0.00 0.00 2.17
162 163 3.496870 GGAGGCCTCATATTGTTCGGATT 60.497 47.826 33.29 0.00 0.00 3.01
163 164 2.039084 GGAGGCCTCATATTGTTCGGAT 59.961 50.000 33.29 0.00 0.00 4.18
164 165 1.416401 GGAGGCCTCATATTGTTCGGA 59.584 52.381 33.29 0.00 0.00 4.55
165 166 1.417890 AGGAGGCCTCATATTGTTCGG 59.582 52.381 33.29 0.00 0.00 4.30
166 167 2.918712 AGGAGGCCTCATATTGTTCG 57.081 50.000 33.29 0.00 0.00 3.95
167 168 3.633986 CCAAAGGAGGCCTCATATTGTTC 59.366 47.826 33.29 13.82 30.89 3.18
168 169 3.011708 ACCAAAGGAGGCCTCATATTGTT 59.988 43.478 33.29 19.34 30.89 2.83
169 170 2.582636 ACCAAAGGAGGCCTCATATTGT 59.417 45.455 33.29 20.20 30.89 2.71
170 171 3.303351 ACCAAAGGAGGCCTCATATTG 57.697 47.619 33.29 28.81 30.89 1.90
171 172 4.026052 CAAACCAAAGGAGGCCTCATATT 58.974 43.478 33.29 21.09 30.89 1.28
172 173 3.011708 ACAAACCAAAGGAGGCCTCATAT 59.988 43.478 33.29 16.35 30.89 1.78
173 174 2.378547 ACAAACCAAAGGAGGCCTCATA 59.621 45.455 33.29 0.00 30.89 2.15
174 175 1.147817 ACAAACCAAAGGAGGCCTCAT 59.852 47.619 33.29 25.66 30.89 2.90
175 176 0.555769 ACAAACCAAAGGAGGCCTCA 59.444 50.000 33.29 0.00 30.89 3.86
176 177 2.437413 CTACAAACCAAAGGAGGCCTC 58.563 52.381 25.59 25.59 30.89 4.70
177 178 1.075536 CCTACAAACCAAAGGAGGCCT 59.924 52.381 3.86 3.86 33.87 5.19
178 179 1.074889 TCCTACAAACCAAAGGAGGCC 59.925 52.381 0.00 0.00 34.46 5.19
179 180 2.579410 TCCTACAAACCAAAGGAGGC 57.421 50.000 0.00 0.00 34.46 4.70
180 181 4.407365 ACATTCCTACAAACCAAAGGAGG 58.593 43.478 0.00 0.00 40.43 4.30
181 182 5.070001 TGACATTCCTACAAACCAAAGGAG 58.930 41.667 0.00 0.00 40.43 3.69
182 183 5.055265 TGACATTCCTACAAACCAAAGGA 57.945 39.130 0.00 0.00 37.64 3.36
183 184 5.982890 ATGACATTCCTACAAACCAAAGG 57.017 39.130 0.00 0.00 0.00 3.11
184 185 7.921786 TCTATGACATTCCTACAAACCAAAG 57.078 36.000 0.00 0.00 0.00 2.77
185 186 8.877864 ATTCTATGACATTCCTACAAACCAAA 57.122 30.769 0.00 0.00 0.00 3.28
186 187 8.877864 AATTCTATGACATTCCTACAAACCAA 57.122 30.769 0.00 0.00 0.00 3.67
187 188 8.877864 AAATTCTATGACATTCCTACAAACCA 57.122 30.769 0.00 0.00 0.00 3.67
216 217 9.881773 AAATTTTCCTATGCAAATCCTATCCTA 57.118 29.630 0.00 0.00 0.00 2.94
217 218 8.788238 AAATTTTCCTATGCAAATCCTATCCT 57.212 30.769 0.00 0.00 0.00 3.24
218 219 8.090831 GGAAATTTTCCTATGCAAATCCTATCC 58.909 37.037 19.01 0.00 46.57 2.59
235 236 5.181811 CCAAATGGCCTCAAAGGAAATTTTC 59.818 40.000 3.32 0.24 37.67 2.29
236 237 5.072055 CCAAATGGCCTCAAAGGAAATTTT 58.928 37.500 3.32 0.00 37.67 1.82
237 238 4.104579 ACCAAATGGCCTCAAAGGAAATTT 59.895 37.500 3.32 0.00 37.01 1.82
238 239 3.652387 ACCAAATGGCCTCAAAGGAAATT 59.348 39.130 3.32 0.00 37.01 1.82
239 240 3.250617 ACCAAATGGCCTCAAAGGAAAT 58.749 40.909 3.32 0.00 37.01 2.17
240 241 2.688477 ACCAAATGGCCTCAAAGGAAA 58.312 42.857 3.32 0.00 37.01 3.13
241 242 2.397044 ACCAAATGGCCTCAAAGGAA 57.603 45.000 3.32 0.00 37.01 3.36
242 243 2.397044 AACCAAATGGCCTCAAAGGA 57.603 45.000 3.32 0.00 37.01 3.36
243 244 4.824479 ATAAACCAAATGGCCTCAAAGG 57.176 40.909 3.32 1.96 39.32 3.11
244 245 5.656416 TCCTATAAACCAAATGGCCTCAAAG 59.344 40.000 3.32 0.00 39.32 2.77
245 246 5.584913 TCCTATAAACCAAATGGCCTCAAA 58.415 37.500 3.32 0.00 39.32 2.69
246 247 5.199982 TCCTATAAACCAAATGGCCTCAA 57.800 39.130 3.32 0.00 39.32 3.02
247 248 4.871871 TCCTATAAACCAAATGGCCTCA 57.128 40.909 3.32 0.00 39.32 3.86
248 249 5.011023 CCATTCCTATAAACCAAATGGCCTC 59.989 44.000 3.32 0.00 39.77 4.70
249 250 4.901250 CCATTCCTATAAACCAAATGGCCT 59.099 41.667 3.32 0.00 39.77 5.19
250 251 4.898861 TCCATTCCTATAAACCAAATGGCC 59.101 41.667 0.00 0.00 43.87 5.36
251 252 5.598417 AGTCCATTCCTATAAACCAAATGGC 59.402 40.000 7.41 4.00 43.87 4.40
252 253 6.265422 GGAGTCCATTCCTATAAACCAAATGG 59.735 42.308 3.60 6.16 44.99 3.16
253 254 7.062957 AGGAGTCCATTCCTATAAACCAAATG 58.937 38.462 12.86 0.00 45.76 2.32
254 255 7.226059 AGGAGTCCATTCCTATAAACCAAAT 57.774 36.000 12.86 0.00 45.76 2.32
255 256 6.652205 AGGAGTCCATTCCTATAAACCAAA 57.348 37.500 12.86 0.00 45.76 3.28
290 291 9.472361 CAAAATGTGAAGGATTGATTCATATCC 57.528 33.333 14.84 14.84 37.47 2.59
355 356 9.552695 AGATGTCATTTGATGTATAGGATAGGA 57.447 33.333 0.00 0.00 0.00 2.94
356 357 9.814899 GAGATGTCATTTGATGTATAGGATAGG 57.185 37.037 0.00 0.00 0.00 2.57
402 403 8.637196 ATCATAGAAAATGAGATGACATGCAT 57.363 30.769 0.00 0.00 40.77 3.96
403 404 8.459911 AATCATAGAAAATGAGATGACATGCA 57.540 30.769 0.00 0.00 31.41 3.96
404 405 9.745880 AAAATCATAGAAAATGAGATGACATGC 57.254 29.630 0.00 0.00 31.41 4.06
434 435 9.520515 AGTCTGAAAACATTATGTTGTAGGAAT 57.479 29.630 11.60 4.57 40.14 3.01
435 436 8.783093 CAGTCTGAAAACATTATGTTGTAGGAA 58.217 33.333 11.60 0.00 40.14 3.36
436 437 7.936847 ACAGTCTGAAAACATTATGTTGTAGGA 59.063 33.333 11.60 5.17 40.14 2.94
437 438 8.099364 ACAGTCTGAAAACATTATGTTGTAGG 57.901 34.615 11.60 2.96 40.14 3.18
438 439 9.950680 AAACAGTCTGAAAACATTATGTTGTAG 57.049 29.630 11.60 10.00 40.14 2.74
439 440 9.729023 CAAACAGTCTGAAAACATTATGTTGTA 57.271 29.630 11.60 0.82 40.14 2.41
440 441 8.250332 ACAAACAGTCTGAAAACATTATGTTGT 58.750 29.630 11.60 5.84 40.14 3.32
441 442 8.633075 ACAAACAGTCTGAAAACATTATGTTG 57.367 30.769 11.60 0.00 40.14 3.33
442 443 9.301153 GAACAAACAGTCTGAAAACATTATGTT 57.699 29.630 6.91 4.56 43.41 2.71
443 444 8.465999 TGAACAAACAGTCTGAAAACATTATGT 58.534 29.630 6.91 0.00 0.00 2.29
444 445 8.854979 TGAACAAACAGTCTGAAAACATTATG 57.145 30.769 6.91 0.00 0.00 1.90
445 446 9.683069 GATGAACAAACAGTCTGAAAACATTAT 57.317 29.630 6.91 0.00 0.00 1.28
446 447 7.855409 CGATGAACAAACAGTCTGAAAACATTA 59.145 33.333 6.91 0.00 0.00 1.90
447 448 6.692681 CGATGAACAAACAGTCTGAAAACATT 59.307 34.615 6.91 0.00 0.00 2.71
448 449 6.183360 ACGATGAACAAACAGTCTGAAAACAT 60.183 34.615 6.91 4.60 0.00 2.71
449 450 5.123186 ACGATGAACAAACAGTCTGAAAACA 59.877 36.000 6.91 0.00 0.00 2.83
450 451 5.452302 CACGATGAACAAACAGTCTGAAAAC 59.548 40.000 6.91 0.00 0.00 2.43
451 452 5.568482 CACGATGAACAAACAGTCTGAAAA 58.432 37.500 6.91 0.00 0.00 2.29
452 453 4.495679 GCACGATGAACAAACAGTCTGAAA 60.496 41.667 6.91 0.00 0.00 2.69
453 454 3.002246 GCACGATGAACAAACAGTCTGAA 59.998 43.478 6.91 0.00 0.00 3.02
454 455 2.543848 GCACGATGAACAAACAGTCTGA 59.456 45.455 6.91 0.00 0.00 3.27
455 456 2.287644 TGCACGATGAACAAACAGTCTG 59.712 45.455 0.00 0.00 0.00 3.51
456 457 2.545526 CTGCACGATGAACAAACAGTCT 59.454 45.455 0.00 0.00 0.00 3.24
457 458 2.287915 ACTGCACGATGAACAAACAGTC 59.712 45.455 0.00 0.00 31.58 3.51
458 459 2.288666 ACTGCACGATGAACAAACAGT 58.711 42.857 0.00 0.00 32.32 3.55
459 460 3.291585 GAACTGCACGATGAACAAACAG 58.708 45.455 0.00 0.00 0.00 3.16
460 461 2.286125 CGAACTGCACGATGAACAAACA 60.286 45.455 0.00 0.00 0.00 2.83
461 462 2.033236 TCGAACTGCACGATGAACAAAC 60.033 45.455 0.00 0.00 34.85 2.93
462 463 2.205911 TCGAACTGCACGATGAACAAA 58.794 42.857 0.00 0.00 34.85 2.83
472 473 1.003116 GCATCATGGATCGAACTGCAC 60.003 52.381 0.00 0.00 0.00 4.57
580 582 6.399013 AGGGTACATAGGATAATCCAGGAAA 58.601 40.000 0.00 0.00 39.61 3.13
599 602 2.646175 GCGACTGTGGCAGAGGGTA 61.646 63.158 16.69 0.00 35.18 3.69
613 616 1.079057 GGTCAAGAGGAAGGGCGAC 60.079 63.158 0.00 0.00 0.00 5.19
701 715 4.217118 GGCAGATAAGGTATTCCAATGCTG 59.783 45.833 0.00 0.00 35.89 4.41
802 818 6.428159 GCAGAGATGTGGTTAAGGTTATATGG 59.572 42.308 0.00 0.00 0.00 2.74
803 819 7.220030 AGCAGAGATGTGGTTAAGGTTATATG 58.780 38.462 0.00 0.00 0.00 1.78
805 821 6.461092 CGAGCAGAGATGTGGTTAAGGTTATA 60.461 42.308 0.00 0.00 0.00 0.98
806 822 5.675538 GAGCAGAGATGTGGTTAAGGTTAT 58.324 41.667 0.00 0.00 0.00 1.89
807 823 4.381612 CGAGCAGAGATGTGGTTAAGGTTA 60.382 45.833 0.00 0.00 0.00 2.85
808 824 3.617531 CGAGCAGAGATGTGGTTAAGGTT 60.618 47.826 0.00 0.00 0.00 3.50
810 826 2.544685 CGAGCAGAGATGTGGTTAAGG 58.455 52.381 0.00 0.00 0.00 2.69
811 827 1.929836 GCGAGCAGAGATGTGGTTAAG 59.070 52.381 0.00 0.00 0.00 1.85
812 828 1.405526 GGCGAGCAGAGATGTGGTTAA 60.406 52.381 0.00 0.00 0.00 2.01
813 829 0.175760 GGCGAGCAGAGATGTGGTTA 59.824 55.000 0.00 0.00 0.00 2.85
814 830 1.078848 GGCGAGCAGAGATGTGGTT 60.079 57.895 0.00 0.00 0.00 3.67
815 831 1.954362 GAGGCGAGCAGAGATGTGGT 61.954 60.000 0.00 0.00 0.00 4.16
816 832 1.227205 GAGGCGAGCAGAGATGTGG 60.227 63.158 0.00 0.00 0.00 4.17
891 912 5.873665 CATGGTCCATGAGCTGATGAGCA 62.874 52.174 25.39 15.40 43.81 4.26
892 913 0.179702 TGGTCCATGAGCTGATGAGC 59.820 55.000 15.36 10.59 46.64 4.26
893 914 2.104281 TCATGGTCCATGAGCTGATGAG 59.896 50.000 27.61 5.09 44.60 2.90
894 915 2.121129 TCATGGTCCATGAGCTGATGA 58.879 47.619 27.61 6.93 44.60 2.92
895 916 2.632987 TCATGGTCCATGAGCTGATG 57.367 50.000 27.61 6.14 44.60 3.07
1018 1059 2.203070 CCAGCCGTCCTGCCATAC 60.203 66.667 0.00 0.00 40.36 2.39
1051 1092 2.124570 CGGATTCAGGGTGCCCAG 60.125 66.667 10.26 1.20 38.92 4.45
1052 1093 3.727258 CCGGATTCAGGGTGCCCA 61.727 66.667 10.26 0.00 38.92 5.36
1053 1094 4.506255 CCCGGATTCAGGGTGCCC 62.506 72.222 13.30 0.00 43.89 5.36
1219 1263 4.040339 TCAAATCAAGCTGACCTACACTGA 59.960 41.667 0.00 0.00 0.00 3.41
1222 1266 4.697352 ACATCAAATCAAGCTGACCTACAC 59.303 41.667 0.00 0.00 0.00 2.90
1235 1282 8.461222 CAAAGTATAAGCAGGAACATCAAATCA 58.539 33.333 0.00 0.00 0.00 2.57
1245 1292 5.296780 GCAGCATACAAAGTATAAGCAGGAA 59.703 40.000 0.00 0.00 0.00 3.36
1254 1301 3.198068 CCGACTGCAGCATACAAAGTAT 58.802 45.455 15.27 0.00 0.00 2.12
1349 1402 3.916544 CTGCGCCGGCTCTCCATA 61.917 66.667 26.68 0.00 40.82 2.74
1552 1605 3.283020 TGGATACAGGCTCGTCAGT 57.717 52.632 0.00 0.00 46.17 3.41
1621 1674 3.981211 AGCGACAACATGCAAATCTTTT 58.019 36.364 0.00 0.00 0.00 2.27
1624 1677 2.153645 TGAGCGACAACATGCAAATCT 58.846 42.857 0.00 0.00 0.00 2.40
1680 1734 5.791589 TGATATGTAAGCTTTGCGTTTACG 58.208 37.500 3.20 0.00 40.82 3.18
1681 1735 7.908082 TGAATGATATGTAAGCTTTGCGTTTAC 59.092 33.333 3.20 0.00 39.08 2.01
1683 1737 6.851609 TGAATGATATGTAAGCTTTGCGTTT 58.148 32.000 3.20 0.00 0.00 3.60
1684 1738 6.435430 TGAATGATATGTAAGCTTTGCGTT 57.565 33.333 3.20 0.00 0.00 4.84
1706 1760 8.553459 ACTCTGTTTGTTTCTACCTATTGATG 57.447 34.615 0.00 0.00 0.00 3.07
1709 1763 7.360101 CGGAACTCTGTTTGTTTCTACCTATTG 60.360 40.741 0.00 0.00 0.00 1.90
1710 1764 6.649557 CGGAACTCTGTTTGTTTCTACCTATT 59.350 38.462 0.00 0.00 0.00 1.73
1721 1775 5.007332 GTGTAATGTTCGGAACTCTGTTTGT 59.993 40.000 20.53 1.68 0.00 2.83
1735 1789 6.255020 CGTGTACATCCCTAAGTGTAATGTTC 59.745 42.308 0.00 0.00 33.05 3.18
1736 1790 6.103997 CGTGTACATCCCTAAGTGTAATGTT 58.896 40.000 0.00 0.00 33.05 2.71
1737 1791 5.394883 CCGTGTACATCCCTAAGTGTAATGT 60.395 44.000 0.00 0.00 33.05 2.71
1753 1807 1.077645 GCGCCGTTTATCCGTGTACA 61.078 55.000 0.00 0.00 0.00 2.90
1784 1838 0.105760 AAACAGGACAATGGCCACCA 60.106 50.000 8.16 0.00 38.19 4.17
1787 1841 0.469705 AGCAAACAGGACAATGGCCA 60.470 50.000 8.56 8.56 0.00 5.36
1800 1854 0.595825 GCACACTCTGCCAAGCAAAC 60.596 55.000 0.00 0.00 40.42 2.93
1861 1916 4.809496 AGCGCAATCCCAGCCCTG 62.809 66.667 11.47 0.00 0.00 4.45
1880 1935 2.345244 CCAGAGCCAACAGACGCT 59.655 61.111 0.00 0.00 38.27 5.07
1886 1941 2.752358 CTGGAGCCAGAGCCAACA 59.248 61.111 11.08 0.00 46.30 3.33
1966 2021 0.584396 TTGTGGACGCGTGAAACATC 59.416 50.000 20.70 0.00 35.74 3.06
1997 2052 0.036164 TTGCACGACAGGCCATTACT 59.964 50.000 5.01 0.00 0.00 2.24
1998 2053 0.878416 TTTGCACGACAGGCCATTAC 59.122 50.000 5.01 0.00 0.00 1.89
2016 2071 2.816411 TCCAGTGGTCCGTCTAGAATT 58.184 47.619 9.54 0.00 0.00 2.17
2022 2077 0.608640 GTTGATCCAGTGGTCCGTCT 59.391 55.000 9.54 0.00 0.00 4.18
2067 2122 1.909302 GAGGGACCAGATCAAAGACCA 59.091 52.381 0.00 0.00 0.00 4.02
2136 2193 1.086696 CTTGATGCCTTGTACCCACG 58.913 55.000 0.00 0.00 0.00 4.94
2170 2227 3.181511 CGACATATTGAAGAAGCGCCAAA 60.182 43.478 2.29 0.00 0.00 3.28
2185 2242 2.289274 CTGACGTCAGAGCTCGACATAT 59.711 50.000 36.73 16.99 46.59 1.78
2207 2264 0.235926 GAAAGGTGAACGAGCTGCAC 59.764 55.000 1.02 0.00 30.84 4.57
2229 2286 2.833582 GGATCGCGTCTGGGGAGA 60.834 66.667 5.77 0.00 41.34 3.71
2253 2310 2.997897 GGCCAGAGTCGGTCCAGT 60.998 66.667 0.00 0.00 0.00 4.00
2289 2346 3.885777 GCAAACATCTGCTCGTAGC 57.114 52.632 0.58 0.58 42.82 3.58
2337 2394 4.870636 AGGTGCCCAAGATTTTCATATGA 58.129 39.130 0.00 0.00 0.00 2.15
2341 2398 3.359950 GAGAGGTGCCCAAGATTTTCAT 58.640 45.455 0.00 0.00 0.00 2.57
2344 2401 1.614317 CGGAGAGGTGCCCAAGATTTT 60.614 52.381 0.00 0.00 0.00 1.82
2373 2430 2.159819 GACAGCGAGCCAGAGGAACA 62.160 60.000 0.00 0.00 0.00 3.18
2391 2448 2.922503 TCCAGCAGCGGTCAAGGA 60.923 61.111 3.62 0.00 0.00 3.36
2478 2536 1.615116 CCAGGATGTGTTGGATGCACT 60.615 52.381 0.00 0.00 36.55 4.40
2479 2537 0.813184 CCAGGATGTGTTGGATGCAC 59.187 55.000 0.00 0.00 36.55 4.57


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

AutoCloner maintained by Alex Coulton.