Multiple sequence alignment - TraesCS5B01G228700

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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 TraesCS5B01G228700 chr5B 100.000 3044 0 0 1 3044 405592189 405595232 0.000000e+00 5622.0
1 TraesCS5B01G228700 chr5D 95.339 2746 84 20 279 3022 345961384 345958681 0.000000e+00 4322.0
2 TraesCS5B01G228700 chr5A 93.669 2780 113 22 279 3022 445241362 445244114 0.000000e+00 4100.0
3 TraesCS5B01G228700 chr5A 97.143 35 1 0 226 260 445241340 445241374 3.280000e-05 60.2
4 TraesCS5B01G228700 chr6A 94.595 74 4 0 108 181 592691838 592691911 6.900000e-22 115.0
5 TraesCS5B01G228700 chr7A 85.227 88 12 1 109 196 697973591 697973677 4.180000e-14 89.8


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 TraesCS5B01G228700 chr5B 405592189 405595232 3043 False 5622.0 5622 100.000 1 3044 1 chr5B.!!$F1 3043
1 TraesCS5B01G228700 chr5D 345958681 345961384 2703 True 4322.0 4322 95.339 279 3022 1 chr5D.!!$R1 2743
2 TraesCS5B01G228700 chr5A 445241340 445244114 2774 False 2080.1 4100 95.406 226 3022 2 chr5A.!!$F1 2796

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
257 258 0.102300 AGGGTTTTTCGCTGCAACAC 59.898 50.0 0.0 0.0 37.93 3.32 F
407 414 0.107410 AAACACACCAAGCCAGACGA 60.107 50.0 0.0 0.0 0.00 4.20 F
732 755 0.107606 TCTTCCTCTCCTCGACCTCG 60.108 60.0 0.0 0.0 41.45 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1497 1526 0.378257 CGAGCCCGGAAATCATTGTG 59.622 55.0 0.73 0.00 0.0 3.33 R
1608 1637 0.612732 CCTTCCCTGAATGGCTGCAA 60.613 55.0 0.50 0.00 0.0 4.08 R
2136 2166 0.751643 AAACGTTGCAGTGCTCCCTT 60.752 50.0 17.60 0.58 0.0 3.95 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
24 25 7.455331 GCTAGGCAACAATGTCAAAATTATC 57.545 36.000 0.00 0.00 41.41 1.75
25 26 7.035004 GCTAGGCAACAATGTCAAAATTATCA 58.965 34.615 0.00 0.00 41.41 2.15
26 27 7.545265 GCTAGGCAACAATGTCAAAATTATCAA 59.455 33.333 0.00 0.00 41.41 2.57
27 28 9.590451 CTAGGCAACAATGTCAAAATTATCAAT 57.410 29.630 0.00 0.00 41.41 2.57
29 30 9.941325 AGGCAACAATGTCAAAATTATCAATAA 57.059 25.926 0.00 0.00 41.41 1.40
31 32 9.693157 GCAACAATGTCAAAATTATCAATAAGC 57.307 29.630 0.00 0.00 0.00 3.09
47 48 8.789825 ATCAATAAGCTGAATATAAGGCTGAG 57.210 34.615 0.00 0.00 35.08 3.35
48 49 7.966812 TCAATAAGCTGAATATAAGGCTGAGA 58.033 34.615 0.00 0.00 35.08 3.27
49 50 7.875041 TCAATAAGCTGAATATAAGGCTGAGAC 59.125 37.037 0.00 0.00 35.08 3.36
50 51 4.250116 AGCTGAATATAAGGCTGAGACG 57.750 45.455 0.00 0.00 33.50 4.18
51 52 3.891977 AGCTGAATATAAGGCTGAGACGA 59.108 43.478 0.00 0.00 33.50 4.20
52 53 4.526262 AGCTGAATATAAGGCTGAGACGAT 59.474 41.667 0.00 0.00 33.50 3.73
53 54 5.011533 AGCTGAATATAAGGCTGAGACGATT 59.988 40.000 0.00 0.00 33.50 3.34
54 55 6.209589 AGCTGAATATAAGGCTGAGACGATTA 59.790 38.462 0.00 0.00 33.50 1.75
55 56 7.038659 GCTGAATATAAGGCTGAGACGATTAT 58.961 38.462 0.00 0.00 0.00 1.28
56 57 7.009999 GCTGAATATAAGGCTGAGACGATTATG 59.990 40.741 0.00 0.00 0.00 1.90
57 58 8.122472 TGAATATAAGGCTGAGACGATTATGA 57.878 34.615 0.00 0.00 0.00 2.15
58 59 8.753133 TGAATATAAGGCTGAGACGATTATGAT 58.247 33.333 0.00 0.00 0.00 2.45
61 62 7.946381 ATAAGGCTGAGACGATTATGATAGA 57.054 36.000 0.00 0.00 0.00 1.98
62 63 6.849085 AAGGCTGAGACGATTATGATAGAT 57.151 37.500 0.00 0.00 0.00 1.98
63 64 7.946381 AAGGCTGAGACGATTATGATAGATA 57.054 36.000 0.00 0.00 0.00 1.98
64 65 8.532186 AAGGCTGAGACGATTATGATAGATAT 57.468 34.615 0.00 0.00 0.00 1.63
65 66 7.939782 AGGCTGAGACGATTATGATAGATATG 58.060 38.462 0.00 0.00 0.00 1.78
66 67 7.777440 AGGCTGAGACGATTATGATAGATATGA 59.223 37.037 0.00 0.00 0.00 2.15
67 68 8.409371 GGCTGAGACGATTATGATAGATATGAA 58.591 37.037 0.00 0.00 0.00 2.57
68 69 9.794685 GCTGAGACGATTATGATAGATATGAAA 57.205 33.333 0.00 0.00 0.00 2.69
90 91 9.295825 TGAAATTAACACCAATGACTTATGACT 57.704 29.630 0.00 0.00 0.00 3.41
92 93 9.912634 AAATTAACACCAATGACTTATGACTTG 57.087 29.630 0.00 0.00 0.00 3.16
93 94 5.964958 AACACCAATGACTTATGACTTGG 57.035 39.130 0.00 0.00 41.67 3.61
95 96 5.385198 ACACCAATGACTTATGACTTGGTT 58.615 37.500 2.65 0.00 45.48 3.67
96 97 5.473504 ACACCAATGACTTATGACTTGGTTC 59.526 40.000 2.65 0.00 45.48 3.62
97 98 5.473162 CACCAATGACTTATGACTTGGTTCA 59.527 40.000 2.65 0.00 45.48 3.18
98 99 6.151648 CACCAATGACTTATGACTTGGTTCAT 59.848 38.462 2.65 0.00 45.48 2.57
99 100 6.151648 ACCAATGACTTATGACTTGGTTCATG 59.848 38.462 0.00 0.00 45.48 3.07
100 101 6.151648 CCAATGACTTATGACTTGGTTCATGT 59.848 38.462 0.00 0.00 36.84 3.21
101 102 6.992063 ATGACTTATGACTTGGTTCATGTC 57.008 37.500 6.90 6.90 36.84 3.06
102 103 5.863965 TGACTTATGACTTGGTTCATGTCA 58.136 37.500 15.54 15.54 46.87 3.58
103 104 5.934043 TGACTTATGACTTGGTTCATGTCAG 59.066 40.000 17.33 9.75 46.34 3.51
104 105 5.248640 ACTTATGACTTGGTTCATGTCAGG 58.751 41.667 17.33 13.24 46.34 3.86
105 106 5.013079 ACTTATGACTTGGTTCATGTCAGGA 59.987 40.000 17.33 8.85 46.34 3.86
106 107 3.126001 TGACTTGGTTCATGTCAGGAC 57.874 47.619 11.05 0.00 41.39 3.85
107 108 2.069273 GACTTGGTTCATGTCAGGACG 58.931 52.381 8.45 0.00 38.09 4.79
108 109 1.416401 ACTTGGTTCATGTCAGGACGT 59.584 47.619 0.00 0.00 0.00 4.34
109 110 2.069273 CTTGGTTCATGTCAGGACGTC 58.931 52.381 7.13 7.13 0.00 4.34
110 111 1.044611 TGGTTCATGTCAGGACGTCA 58.955 50.000 18.91 0.00 0.00 4.35
111 112 1.000843 TGGTTCATGTCAGGACGTCAG 59.999 52.381 18.91 9.45 0.00 3.51
112 113 1.673033 GGTTCATGTCAGGACGTCAGG 60.673 57.143 18.91 8.67 0.00 3.86
113 114 1.000955 GTTCATGTCAGGACGTCAGGT 59.999 52.381 18.91 0.00 0.00 4.00
114 115 0.888619 TCATGTCAGGACGTCAGGTC 59.111 55.000 18.91 6.92 45.31 3.85
121 122 4.580835 GACGTCAGGTCCTTCAGC 57.419 61.111 11.55 0.00 39.90 4.26
122 123 1.968310 GACGTCAGGTCCTTCAGCT 59.032 57.895 11.55 0.00 39.90 4.24
123 124 0.318762 GACGTCAGGTCCTTCAGCTT 59.681 55.000 11.55 0.00 39.90 3.74
124 125 0.318762 ACGTCAGGTCCTTCAGCTTC 59.681 55.000 0.00 0.00 0.00 3.86
125 126 0.605589 CGTCAGGTCCTTCAGCTTCT 59.394 55.000 0.00 0.00 0.00 2.85
126 127 1.001406 CGTCAGGTCCTTCAGCTTCTT 59.999 52.381 0.00 0.00 0.00 2.52
127 128 2.548920 CGTCAGGTCCTTCAGCTTCTTT 60.549 50.000 0.00 0.00 0.00 2.52
128 129 3.306088 CGTCAGGTCCTTCAGCTTCTTTA 60.306 47.826 0.00 0.00 0.00 1.85
129 130 4.249661 GTCAGGTCCTTCAGCTTCTTTAG 58.750 47.826 0.00 0.00 0.00 1.85
130 131 4.021016 GTCAGGTCCTTCAGCTTCTTTAGA 60.021 45.833 0.00 0.00 0.00 2.10
131 132 4.221703 TCAGGTCCTTCAGCTTCTTTAGAG 59.778 45.833 0.00 0.00 0.00 2.43
132 133 3.055458 AGGTCCTTCAGCTTCTTTAGAGC 60.055 47.826 0.00 0.00 0.00 4.09
133 134 3.055458 GGTCCTTCAGCTTCTTTAGAGCT 60.055 47.826 0.00 0.00 39.79 4.09
134 135 4.160626 GGTCCTTCAGCTTCTTTAGAGCTA 59.839 45.833 0.00 0.00 37.11 3.32
135 136 5.348164 GTCCTTCAGCTTCTTTAGAGCTAG 58.652 45.833 0.00 0.00 37.11 3.42
136 137 4.119136 CCTTCAGCTTCTTTAGAGCTAGC 58.881 47.826 6.62 6.62 37.11 3.42
137 138 4.382470 CCTTCAGCTTCTTTAGAGCTAGCA 60.382 45.833 18.83 0.00 37.11 3.49
138 139 4.116747 TCAGCTTCTTTAGAGCTAGCAC 57.883 45.455 18.83 11.32 37.11 4.40
139 140 3.766591 TCAGCTTCTTTAGAGCTAGCACT 59.233 43.478 18.86 18.86 37.11 4.40
140 141 4.221703 TCAGCTTCTTTAGAGCTAGCACTT 59.778 41.667 20.03 5.47 37.11 3.16
141 142 4.329528 CAGCTTCTTTAGAGCTAGCACTTG 59.670 45.833 20.03 10.75 37.11 3.16
142 143 4.221703 AGCTTCTTTAGAGCTAGCACTTGA 59.778 41.667 20.03 12.69 37.11 3.02
143 144 4.932200 GCTTCTTTAGAGCTAGCACTTGAA 59.068 41.667 20.03 18.08 33.29 2.69
144 145 5.063312 GCTTCTTTAGAGCTAGCACTTGAAG 59.937 44.000 27.22 27.22 33.29 3.02
145 146 5.984695 TCTTTAGAGCTAGCACTTGAAGA 57.015 39.130 23.77 23.77 0.00 2.87
146 147 6.537453 TCTTTAGAGCTAGCACTTGAAGAT 57.463 37.500 23.77 2.65 0.00 2.40
147 148 6.940739 TCTTTAGAGCTAGCACTTGAAGATT 58.059 36.000 23.77 2.03 0.00 2.40
148 149 6.815641 TCTTTAGAGCTAGCACTTGAAGATTG 59.184 38.462 23.77 10.23 0.00 2.67
149 150 4.550076 AGAGCTAGCACTTGAAGATTGT 57.450 40.909 18.83 0.00 0.00 2.71
150 151 5.667539 AGAGCTAGCACTTGAAGATTGTA 57.332 39.130 18.83 0.00 0.00 2.41
151 152 6.042638 AGAGCTAGCACTTGAAGATTGTAA 57.957 37.500 18.83 0.00 0.00 2.41
152 153 6.648192 AGAGCTAGCACTTGAAGATTGTAAT 58.352 36.000 18.83 0.00 0.00 1.89
153 154 6.538021 AGAGCTAGCACTTGAAGATTGTAATG 59.462 38.462 18.83 0.00 0.00 1.90
154 155 5.587844 AGCTAGCACTTGAAGATTGTAATGG 59.412 40.000 18.83 0.00 0.00 3.16
155 156 5.355350 GCTAGCACTTGAAGATTGTAATGGT 59.645 40.000 10.63 0.00 0.00 3.55
156 157 5.886960 AGCACTTGAAGATTGTAATGGTC 57.113 39.130 0.00 0.00 0.00 4.02
157 158 5.316167 AGCACTTGAAGATTGTAATGGTCA 58.684 37.500 0.00 0.00 0.00 4.02
158 159 5.182001 AGCACTTGAAGATTGTAATGGTCAC 59.818 40.000 0.00 0.00 0.00 3.67
159 160 5.621422 CACTTGAAGATTGTAATGGTCACG 58.379 41.667 0.00 0.00 0.00 4.35
160 161 5.408299 CACTTGAAGATTGTAATGGTCACGA 59.592 40.000 0.00 0.00 0.00 4.35
161 162 6.092670 CACTTGAAGATTGTAATGGTCACGAT 59.907 38.462 0.00 0.00 0.00 3.73
162 163 6.092670 ACTTGAAGATTGTAATGGTCACGATG 59.907 38.462 0.00 0.00 0.00 3.84
163 164 4.875536 TGAAGATTGTAATGGTCACGATGG 59.124 41.667 0.00 0.00 0.00 3.51
164 165 4.487714 AGATTGTAATGGTCACGATGGT 57.512 40.909 0.00 0.00 0.00 3.55
165 166 4.843728 AGATTGTAATGGTCACGATGGTT 58.156 39.130 0.00 0.00 0.00 3.67
166 167 4.635765 AGATTGTAATGGTCACGATGGTTG 59.364 41.667 0.00 0.00 0.00 3.77
167 168 3.686916 TGTAATGGTCACGATGGTTGA 57.313 42.857 0.00 0.00 0.00 3.18
168 169 3.595173 TGTAATGGTCACGATGGTTGAG 58.405 45.455 0.00 0.00 0.00 3.02
169 170 2.859165 AATGGTCACGATGGTTGAGT 57.141 45.000 0.00 0.00 0.00 3.41
170 171 3.973206 AATGGTCACGATGGTTGAGTA 57.027 42.857 0.00 0.00 0.00 2.59
171 172 3.973206 ATGGTCACGATGGTTGAGTAA 57.027 42.857 0.00 0.00 0.00 2.24
172 173 3.973206 TGGTCACGATGGTTGAGTAAT 57.027 42.857 0.00 0.00 0.00 1.89
173 174 5.607939 ATGGTCACGATGGTTGAGTAATA 57.392 39.130 0.00 0.00 0.00 0.98
174 175 4.751060 TGGTCACGATGGTTGAGTAATAC 58.249 43.478 0.00 0.00 0.00 1.89
175 176 4.221041 TGGTCACGATGGTTGAGTAATACA 59.779 41.667 0.00 0.00 0.00 2.29
176 177 5.172934 GGTCACGATGGTTGAGTAATACAA 58.827 41.667 0.00 0.00 0.00 2.41
177 178 5.291128 GGTCACGATGGTTGAGTAATACAAG 59.709 44.000 0.00 0.00 0.00 3.16
178 179 5.867716 GTCACGATGGTTGAGTAATACAAGT 59.132 40.000 0.00 0.00 0.00 3.16
179 180 6.367969 GTCACGATGGTTGAGTAATACAAGTT 59.632 38.462 0.00 0.00 0.00 2.66
180 181 6.932400 TCACGATGGTTGAGTAATACAAGTTT 59.068 34.615 0.00 0.00 0.00 2.66
181 182 7.442969 TCACGATGGTTGAGTAATACAAGTTTT 59.557 33.333 0.00 0.00 0.00 2.43
182 183 8.073768 CACGATGGTTGAGTAATACAAGTTTTT 58.926 33.333 0.00 0.00 0.00 1.94
183 184 9.275398 ACGATGGTTGAGTAATACAAGTTTTTA 57.725 29.630 0.00 0.00 0.00 1.52
184 185 9.537848 CGATGGTTGAGTAATACAAGTTTTTAC 57.462 33.333 0.00 0.00 0.00 2.01
185 186 9.836076 GATGGTTGAGTAATACAAGTTTTTACC 57.164 33.333 0.00 0.00 0.00 2.85
186 187 8.983702 TGGTTGAGTAATACAAGTTTTTACCT 57.016 30.769 0.00 0.00 0.00 3.08
187 188 8.842280 TGGTTGAGTAATACAAGTTTTTACCTG 58.158 33.333 0.00 0.00 0.00 4.00
188 189 8.294577 GGTTGAGTAATACAAGTTTTTACCTGG 58.705 37.037 0.00 0.00 0.00 4.45
189 190 9.059260 GTTGAGTAATACAAGTTTTTACCTGGA 57.941 33.333 0.00 0.00 0.00 3.86
190 191 9.629878 TTGAGTAATACAAGTTTTTACCTGGAA 57.370 29.630 0.00 0.00 0.00 3.53
191 192 9.629878 TGAGTAATACAAGTTTTTACCTGGAAA 57.370 29.630 0.00 0.00 0.00 3.13
198 199 8.936070 ACAAGTTTTTACCTGGAAATAAACAC 57.064 30.769 0.00 0.00 0.00 3.32
199 200 7.982919 ACAAGTTTTTACCTGGAAATAAACACC 59.017 33.333 0.00 0.00 0.00 4.16
200 201 7.058023 AGTTTTTACCTGGAAATAAACACCC 57.942 36.000 0.00 0.00 0.00 4.61
201 202 6.612049 AGTTTTTACCTGGAAATAAACACCCA 59.388 34.615 0.00 0.00 0.00 4.51
202 203 7.291416 AGTTTTTACCTGGAAATAAACACCCAT 59.709 33.333 0.00 0.00 0.00 4.00
203 204 6.597832 TTTACCTGGAAATAAACACCCATG 57.402 37.500 0.00 0.00 0.00 3.66
204 205 4.396357 ACCTGGAAATAAACACCCATGA 57.604 40.909 0.00 0.00 0.00 3.07
205 206 4.086457 ACCTGGAAATAAACACCCATGAC 58.914 43.478 0.00 0.00 0.00 3.06
206 207 4.085733 CCTGGAAATAAACACCCATGACA 58.914 43.478 0.00 0.00 0.00 3.58
207 208 4.526262 CCTGGAAATAAACACCCATGACAA 59.474 41.667 0.00 0.00 0.00 3.18
208 209 5.011533 CCTGGAAATAAACACCCATGACAAA 59.988 40.000 0.00 0.00 0.00 2.83
209 210 6.095432 TGGAAATAAACACCCATGACAAAG 57.905 37.500 0.00 0.00 0.00 2.77
210 211 5.600484 TGGAAATAAACACCCATGACAAAGT 59.400 36.000 0.00 0.00 0.00 2.66
211 212 6.156519 GGAAATAAACACCCATGACAAAGTC 58.843 40.000 0.00 0.00 0.00 3.01
212 213 6.239176 GGAAATAAACACCCATGACAAAGTCA 60.239 38.462 1.95 1.95 46.90 3.41
213 214 5.705609 ATAAACACCCATGACAAAGTCAC 57.294 39.130 1.43 0.00 45.65 3.67
214 215 3.297134 AACACCCATGACAAAGTCACT 57.703 42.857 1.43 0.00 45.65 3.41
215 216 3.297134 ACACCCATGACAAAGTCACTT 57.703 42.857 1.43 0.00 45.65 3.16
216 217 2.951642 ACACCCATGACAAAGTCACTTG 59.048 45.455 1.43 0.00 45.65 3.16
217 218 2.951642 CACCCATGACAAAGTCACTTGT 59.048 45.455 1.43 0.00 45.65 3.16
218 219 3.381272 CACCCATGACAAAGTCACTTGTT 59.619 43.478 1.43 0.00 45.65 2.83
219 220 3.632145 ACCCATGACAAAGTCACTTGTTC 59.368 43.478 1.43 0.00 45.65 3.18
220 221 3.885297 CCCATGACAAAGTCACTTGTTCT 59.115 43.478 1.43 0.00 45.65 3.01
221 222 4.261322 CCCATGACAAAGTCACTTGTTCTG 60.261 45.833 1.43 0.00 45.65 3.02
222 223 4.285292 CATGACAAAGTCACTTGTTCTGC 58.715 43.478 1.43 0.00 45.65 4.26
223 224 3.342719 TGACAAAGTCACTTGTTCTGCA 58.657 40.909 0.00 0.00 39.63 4.41
224 225 3.755905 TGACAAAGTCACTTGTTCTGCAA 59.244 39.130 0.00 0.00 39.63 4.08
247 248 0.875059 CACCAGAGCGAGGGTTTTTC 59.125 55.000 0.00 0.00 34.45 2.29
248 249 0.602905 ACCAGAGCGAGGGTTTTTCG 60.603 55.000 0.00 0.00 40.85 3.46
253 254 3.339731 CGAGGGTTTTTCGCTGCA 58.660 55.556 0.00 0.00 39.46 4.41
254 255 1.652012 CGAGGGTTTTTCGCTGCAA 59.348 52.632 0.00 0.00 39.46 4.08
255 256 0.660300 CGAGGGTTTTTCGCTGCAAC 60.660 55.000 0.00 0.00 39.46 4.17
256 257 0.383949 GAGGGTTTTTCGCTGCAACA 59.616 50.000 0.00 0.00 39.46 3.33
257 258 0.102300 AGGGTTTTTCGCTGCAACAC 59.898 50.000 0.00 0.00 37.93 3.32
258 259 0.874175 GGGTTTTTCGCTGCAACACC 60.874 55.000 0.00 0.00 0.00 4.16
259 260 0.179124 GGTTTTTCGCTGCAACACCA 60.179 50.000 0.00 0.00 0.00 4.17
260 261 1.537990 GGTTTTTCGCTGCAACACCAT 60.538 47.619 0.00 0.00 0.00 3.55
261 262 2.200899 GTTTTTCGCTGCAACACCATT 58.799 42.857 0.00 0.00 0.00 3.16
262 263 2.593346 TTTTCGCTGCAACACCATTT 57.407 40.000 0.00 0.00 0.00 2.32
263 264 2.593346 TTTCGCTGCAACACCATTTT 57.407 40.000 0.00 0.00 0.00 1.82
264 265 2.593346 TTCGCTGCAACACCATTTTT 57.407 40.000 0.00 0.00 0.00 1.94
265 266 2.132740 TCGCTGCAACACCATTTTTC 57.867 45.000 0.00 0.00 0.00 2.29
266 267 1.680735 TCGCTGCAACACCATTTTTCT 59.319 42.857 0.00 0.00 0.00 2.52
267 268 2.100584 TCGCTGCAACACCATTTTTCTT 59.899 40.909 0.00 0.00 0.00 2.52
268 269 2.865551 CGCTGCAACACCATTTTTCTTT 59.134 40.909 0.00 0.00 0.00 2.52
269 270 3.309410 CGCTGCAACACCATTTTTCTTTT 59.691 39.130 0.00 0.00 0.00 2.27
270 271 4.201802 CGCTGCAACACCATTTTTCTTTTT 60.202 37.500 0.00 0.00 0.00 1.94
286 287 2.362329 TTTTTGAGGGGCGCTGCAAC 62.362 55.000 9.52 0.00 0.00 4.17
338 344 0.682855 GACCCATTTTCGCCCCATCA 60.683 55.000 0.00 0.00 0.00 3.07
386 392 3.315142 ATTCCCGCGCAGAAGCAGA 62.315 57.895 8.75 0.00 42.27 4.26
392 398 0.316937 CGCGCAGAAGCAGAAAAACA 60.317 50.000 8.75 0.00 42.27 2.83
393 399 1.123655 GCGCAGAAGCAGAAAAACAC 58.876 50.000 0.30 0.00 42.27 3.32
400 407 2.584492 AGCAGAAAAACACACCAAGC 57.416 45.000 0.00 0.00 0.00 4.01
407 414 0.107410 AAACACACCAAGCCAGACGA 60.107 50.000 0.00 0.00 0.00 4.20
409 416 0.814010 ACACACCAAGCCAGACGAAC 60.814 55.000 0.00 0.00 0.00 3.95
455 466 3.839432 CGAAGCCCCTCGTCCTCC 61.839 72.222 0.00 0.00 34.08 4.30
468 479 2.517402 CCTCCTCGTCCTCCTCCG 60.517 72.222 0.00 0.00 0.00 4.63
489 503 3.579302 CTCCCACCCAACCTGCCA 61.579 66.667 0.00 0.00 0.00 4.92
497 511 1.898574 CCAACCTGCCACCTCACAC 60.899 63.158 0.00 0.00 0.00 3.82
726 749 2.131067 GGCCCTCTTCCTCTCCTCG 61.131 68.421 0.00 0.00 0.00 4.63
727 750 1.076632 GCCCTCTTCCTCTCCTCGA 60.077 63.158 0.00 0.00 0.00 4.04
732 755 0.107606 TCTTCCTCTCCTCGACCTCG 60.108 60.000 0.00 0.00 41.45 4.63
1213 1242 1.815421 GTGATAGCTGGGTGTGCCG 60.815 63.158 0.00 0.00 34.97 5.69
1308 1337 1.236616 CGATGGTTGCCTTGCTGACA 61.237 55.000 0.00 0.00 0.00 3.58
1317 1346 3.245948 CTTGCTGACAGCGTGTGCC 62.246 63.158 22.00 0.00 46.26 5.01
1384 1413 0.612732 CCAGGAAGGCCATTTGCAGA 60.613 55.000 5.01 0.00 43.89 4.26
1446 1475 3.249189 TGTGGGGCTGTGGAGGAC 61.249 66.667 0.00 0.00 0.00 3.85
1497 1526 0.745468 GGAGTACCGTCTCATGGACC 59.255 60.000 8.25 0.00 41.64 4.46
1518 1547 1.097547 CAATGATTTCCGGGCTCGCT 61.098 55.000 0.00 0.00 34.56 4.93
1608 1637 2.048409 CTCGCTGTGCTGTCTGCT 60.048 61.111 3.20 0.00 43.37 4.24
1662 1691 3.314635 GGCAATACTTTGAGAGCATGGAG 59.685 47.826 0.00 0.00 34.60 3.86
1677 1706 4.414846 AGCATGGAGAGAGTTTATGGGATT 59.585 41.667 0.00 0.00 0.00 3.01
1710 1739 3.700538 ACAACACTATGGATGCATGGTT 58.299 40.909 13.56 10.07 0.00 3.67
2116 2145 5.304778 GGGCTTTGTGTTCCACATTTAAAT 58.695 37.500 0.00 0.00 44.16 1.40
2155 2187 0.751643 AAGGGAGCACTGCAACGTTT 60.752 50.000 0.00 0.00 0.00 3.60
2164 2196 1.336755 ACTGCAACGTTTCAACCATCC 59.663 47.619 0.00 0.00 0.00 3.51
2310 2342 1.351430 TTTCCATCTTCGCTGCGTCG 61.351 55.000 22.48 13.77 0.00 5.12
2367 2399 3.242936 TGGTTCTAAACTTCTGTTTGCGC 60.243 43.478 0.00 0.00 45.01 6.09
2725 2771 6.810911 TGATAGTTGCTGAATCTAACTCCTC 58.189 40.000 0.00 0.00 36.22 3.71
2973 3019 2.481952 CTCTCTTTGCGAAGGAAACCTG 59.518 50.000 13.87 0.00 44.43 4.00
2974 3020 0.951558 TCTTTGCGAAGGAAACCTGC 59.048 50.000 13.87 0.00 44.43 4.85
2975 3021 0.039165 CTTTGCGAAGGAAACCTGCC 60.039 55.000 5.72 0.00 44.43 4.85
2976 3022 0.753479 TTTGCGAAGGAAACCTGCCA 60.753 50.000 0.00 0.00 44.43 4.92
2993 3039 3.425659 TGCCATGCCATGTAAACAGTTA 58.574 40.909 3.63 0.00 0.00 2.24
3018 3064 7.824672 AGATTTATCCAGCAGTTTTCTTTCAG 58.175 34.615 0.00 0.00 0.00 3.02
3022 3068 3.067180 TCCAGCAGTTTTCTTTCAGCAAG 59.933 43.478 0.00 0.00 0.00 4.01
3023 3069 2.793232 CAGCAGTTTTCTTTCAGCAAGC 59.207 45.455 0.00 0.00 31.70 4.01
3024 3070 2.130395 GCAGTTTTCTTTCAGCAAGCC 58.870 47.619 0.00 0.00 31.70 4.35
3025 3071 2.481795 GCAGTTTTCTTTCAGCAAGCCA 60.482 45.455 0.00 0.00 31.70 4.75
3026 3072 3.378339 CAGTTTTCTTTCAGCAAGCCAG 58.622 45.455 0.00 0.00 31.70 4.85
3027 3073 3.026694 AGTTTTCTTTCAGCAAGCCAGT 58.973 40.909 0.00 0.00 31.70 4.00
3028 3074 3.448660 AGTTTTCTTTCAGCAAGCCAGTT 59.551 39.130 0.00 0.00 31.70 3.16
3029 3075 4.081476 AGTTTTCTTTCAGCAAGCCAGTTT 60.081 37.500 0.00 0.00 31.70 2.66
3030 3076 3.441496 TTCTTTCAGCAAGCCAGTTTG 57.559 42.857 0.00 0.00 31.70 2.93
3031 3077 2.378038 TCTTTCAGCAAGCCAGTTTGT 58.622 42.857 0.00 0.00 31.70 2.83
3032 3078 2.760092 TCTTTCAGCAAGCCAGTTTGTT 59.240 40.909 0.00 0.00 31.70 2.83
3033 3079 2.582728 TTCAGCAAGCCAGTTTGTTG 57.417 45.000 5.01 5.01 39.66 3.33
3034 3080 1.761449 TCAGCAAGCCAGTTTGTTGA 58.239 45.000 9.15 9.15 43.17 3.18
3035 3081 2.309613 TCAGCAAGCCAGTTTGTTGAT 58.690 42.857 9.15 0.00 41.40 2.57
3036 3082 2.294233 TCAGCAAGCCAGTTTGTTGATC 59.706 45.455 9.15 0.00 41.40 2.92
3037 3083 2.034939 CAGCAAGCCAGTTTGTTGATCA 59.965 45.455 5.37 0.00 40.42 2.92
3038 3084 2.895404 AGCAAGCCAGTTTGTTGATCAT 59.105 40.909 0.00 0.00 0.00 2.45
3039 3085 3.322828 AGCAAGCCAGTTTGTTGATCATT 59.677 39.130 0.00 0.00 0.00 2.57
3040 3086 3.430895 GCAAGCCAGTTTGTTGATCATTG 59.569 43.478 0.00 0.00 0.00 2.82
3041 3087 4.796946 GCAAGCCAGTTTGTTGATCATTGA 60.797 41.667 0.00 0.00 0.00 2.57
3042 3088 5.291178 CAAGCCAGTTTGTTGATCATTGAA 58.709 37.500 0.00 0.00 0.00 2.69
3043 3089 5.733620 AGCCAGTTTGTTGATCATTGAAT 57.266 34.783 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.035004 TGATAATTTTGACATTGTTGCCTAGC 58.965 34.615 0.00 0.00 0.00 3.42
1 2 8.984891 TTGATAATTTTGACATTGTTGCCTAG 57.015 30.769 0.00 0.00 0.00 3.02
3 4 9.941325 TTATTGATAATTTTGACATTGTTGCCT 57.059 25.926 0.00 0.00 0.00 4.75
5 6 9.693157 GCTTATTGATAATTTTGACATTGTTGC 57.307 29.630 0.00 0.00 0.00 4.17
21 22 9.881649 CTCAGCCTTATATTCAGCTTATTGATA 57.118 33.333 0.00 0.00 31.93 2.15
22 23 8.600668 TCTCAGCCTTATATTCAGCTTATTGAT 58.399 33.333 0.00 0.00 31.93 2.57
23 24 7.875041 GTCTCAGCCTTATATTCAGCTTATTGA 59.125 37.037 0.00 0.00 31.93 2.57
24 25 7.148672 CGTCTCAGCCTTATATTCAGCTTATTG 60.149 40.741 0.00 0.00 31.93 1.90
25 26 6.870965 CGTCTCAGCCTTATATTCAGCTTATT 59.129 38.462 0.00 0.00 31.93 1.40
26 27 6.209589 TCGTCTCAGCCTTATATTCAGCTTAT 59.790 38.462 0.00 0.00 31.93 1.73
27 28 5.535030 TCGTCTCAGCCTTATATTCAGCTTA 59.465 40.000 0.00 0.00 31.93 3.09
28 29 4.342378 TCGTCTCAGCCTTATATTCAGCTT 59.658 41.667 0.00 0.00 31.93 3.74
29 30 3.891977 TCGTCTCAGCCTTATATTCAGCT 59.108 43.478 0.00 0.00 35.52 4.24
30 31 4.244425 TCGTCTCAGCCTTATATTCAGC 57.756 45.455 0.00 0.00 0.00 4.26
31 32 8.246871 TCATAATCGTCTCAGCCTTATATTCAG 58.753 37.037 0.00 0.00 0.00 3.02
32 33 8.122472 TCATAATCGTCTCAGCCTTATATTCA 57.878 34.615 0.00 0.00 0.00 2.57
35 36 9.634021 TCTATCATAATCGTCTCAGCCTTATAT 57.366 33.333 0.00 0.00 0.00 0.86
36 37 9.634021 ATCTATCATAATCGTCTCAGCCTTATA 57.366 33.333 0.00 0.00 0.00 0.98
37 38 7.946381 TCTATCATAATCGTCTCAGCCTTAT 57.054 36.000 0.00 0.00 0.00 1.73
38 39 7.946381 ATCTATCATAATCGTCTCAGCCTTA 57.054 36.000 0.00 0.00 0.00 2.69
39 40 6.849085 ATCTATCATAATCGTCTCAGCCTT 57.151 37.500 0.00 0.00 0.00 4.35
40 41 7.777440 TCATATCTATCATAATCGTCTCAGCCT 59.223 37.037 0.00 0.00 0.00 4.58
41 42 7.935520 TCATATCTATCATAATCGTCTCAGCC 58.064 38.462 0.00 0.00 0.00 4.85
42 43 9.794685 TTTCATATCTATCATAATCGTCTCAGC 57.205 33.333 0.00 0.00 0.00 4.26
64 65 9.295825 AGTCATAAGTCATTGGTGTTAATTTCA 57.704 29.630 0.00 0.00 0.00 2.69
66 67 9.912634 CAAGTCATAAGTCATTGGTGTTAATTT 57.087 29.630 0.00 0.00 0.00 1.82
67 68 8.522830 CCAAGTCATAAGTCATTGGTGTTAATT 58.477 33.333 0.00 0.00 36.48 1.40
68 69 8.055279 CCAAGTCATAAGTCATTGGTGTTAAT 57.945 34.615 0.00 0.00 36.48 1.40
69 70 7.447374 CCAAGTCATAAGTCATTGGTGTTAA 57.553 36.000 0.00 0.00 36.48 2.01
71 72 5.964958 CCAAGTCATAAGTCATTGGTGTT 57.035 39.130 0.00 0.00 36.48 3.32
75 76 6.151648 ACATGAACCAAGTCATAAGTCATTGG 59.848 38.462 0.00 0.85 44.79 3.16
76 77 7.094677 TGACATGAACCAAGTCATAAGTCATTG 60.095 37.037 0.00 0.00 37.20 2.82
77 78 6.942005 TGACATGAACCAAGTCATAAGTCATT 59.058 34.615 0.00 0.00 37.20 2.57
78 79 6.475504 TGACATGAACCAAGTCATAAGTCAT 58.524 36.000 0.00 0.00 37.20 3.06
79 80 5.863965 TGACATGAACCAAGTCATAAGTCA 58.136 37.500 0.00 4.94 37.20 3.41
80 81 5.352569 CCTGACATGAACCAAGTCATAAGTC 59.647 44.000 0.00 0.00 40.44 3.01
81 82 5.013079 TCCTGACATGAACCAAGTCATAAGT 59.987 40.000 0.00 0.00 40.44 2.24
82 83 5.352569 GTCCTGACATGAACCAAGTCATAAG 59.647 44.000 0.00 0.22 40.44 1.73
83 84 5.245531 GTCCTGACATGAACCAAGTCATAA 58.754 41.667 0.00 0.00 40.44 1.90
84 85 4.620567 CGTCCTGACATGAACCAAGTCATA 60.621 45.833 0.00 0.00 40.44 2.15
85 86 3.679389 GTCCTGACATGAACCAAGTCAT 58.321 45.455 0.00 0.00 40.44 3.06
86 87 2.547855 CGTCCTGACATGAACCAAGTCA 60.548 50.000 0.00 5.16 39.28 3.41
87 88 2.069273 CGTCCTGACATGAACCAAGTC 58.931 52.381 0.00 0.00 33.42 3.01
88 89 1.416401 ACGTCCTGACATGAACCAAGT 59.584 47.619 0.00 0.00 0.00 3.16
89 90 2.069273 GACGTCCTGACATGAACCAAG 58.931 52.381 3.51 0.00 0.00 3.61
90 91 1.414550 TGACGTCCTGACATGAACCAA 59.585 47.619 14.12 0.00 0.00 3.67
91 92 1.000843 CTGACGTCCTGACATGAACCA 59.999 52.381 14.12 0.00 0.00 3.67
92 93 1.673033 CCTGACGTCCTGACATGAACC 60.673 57.143 14.12 0.00 0.00 3.62
93 94 1.000955 ACCTGACGTCCTGACATGAAC 59.999 52.381 14.12 0.00 0.00 3.18
94 95 1.272490 GACCTGACGTCCTGACATGAA 59.728 52.381 14.12 0.00 35.23 2.57
95 96 0.888619 GACCTGACGTCCTGACATGA 59.111 55.000 14.12 0.00 35.23 3.07
96 97 3.425578 GACCTGACGTCCTGACATG 57.574 57.895 14.12 0.00 35.23 3.21
104 105 0.318762 AAGCTGAAGGACCTGACGTC 59.681 55.000 9.11 9.11 41.15 4.34
105 106 0.318762 GAAGCTGAAGGACCTGACGT 59.681 55.000 0.00 0.00 0.00 4.34
106 107 0.605589 AGAAGCTGAAGGACCTGACG 59.394 55.000 0.00 0.00 0.00 4.35
107 108 2.849294 AAGAAGCTGAAGGACCTGAC 57.151 50.000 0.00 0.00 0.00 3.51
108 109 4.160329 TCTAAAGAAGCTGAAGGACCTGA 58.840 43.478 0.00 0.00 0.00 3.86
109 110 4.502962 CTCTAAAGAAGCTGAAGGACCTG 58.497 47.826 0.00 0.00 0.00 4.00
110 111 3.055458 GCTCTAAAGAAGCTGAAGGACCT 60.055 47.826 0.00 0.00 0.00 3.85
111 112 3.055458 AGCTCTAAAGAAGCTGAAGGACC 60.055 47.826 0.00 0.00 37.53 4.46
112 113 4.200838 AGCTCTAAAGAAGCTGAAGGAC 57.799 45.455 0.00 0.00 37.53 3.85
113 114 4.142049 GCTAGCTCTAAAGAAGCTGAAGGA 60.142 45.833 7.70 0.00 39.46 3.36
114 115 4.119136 GCTAGCTCTAAAGAAGCTGAAGG 58.881 47.826 7.70 0.00 39.46 3.46
115 116 4.566360 GTGCTAGCTCTAAAGAAGCTGAAG 59.434 45.833 17.23 0.00 39.46 3.02
116 117 4.221703 AGTGCTAGCTCTAAAGAAGCTGAA 59.778 41.667 17.42 0.00 39.46 3.02
117 118 3.766591 AGTGCTAGCTCTAAAGAAGCTGA 59.233 43.478 17.42 0.00 39.46 4.26
118 119 4.122143 AGTGCTAGCTCTAAAGAAGCTG 57.878 45.455 17.42 0.18 39.46 4.24
119 120 4.221703 TCAAGTGCTAGCTCTAAAGAAGCT 59.778 41.667 19.04 2.88 42.12 3.74
120 121 4.499183 TCAAGTGCTAGCTCTAAAGAAGC 58.501 43.478 19.04 0.00 35.01 3.86
121 122 6.393990 TCTTCAAGTGCTAGCTCTAAAGAAG 58.606 40.000 28.55 28.55 31.78 2.85
122 123 6.346477 TCTTCAAGTGCTAGCTCTAAAGAA 57.654 37.500 26.36 22.88 0.00 2.52
123 124 5.984695 TCTTCAAGTGCTAGCTCTAAAGA 57.015 39.130 25.55 25.55 0.00 2.52
124 125 6.593382 ACAATCTTCAAGTGCTAGCTCTAAAG 59.407 38.462 23.18 23.18 0.00 1.85
125 126 6.467677 ACAATCTTCAAGTGCTAGCTCTAAA 58.532 36.000 19.04 14.72 0.00 1.85
126 127 6.042638 ACAATCTTCAAGTGCTAGCTCTAA 57.957 37.500 19.04 10.19 0.00 2.10
127 128 5.667539 ACAATCTTCAAGTGCTAGCTCTA 57.332 39.130 19.04 4.32 0.00 2.43
128 129 4.550076 ACAATCTTCAAGTGCTAGCTCT 57.450 40.909 17.23 15.26 0.00 4.09
129 130 6.238320 CCATTACAATCTTCAAGTGCTAGCTC 60.238 42.308 17.23 12.88 0.00 4.09
130 131 5.587844 CCATTACAATCTTCAAGTGCTAGCT 59.412 40.000 17.23 0.00 0.00 3.32
131 132 5.355350 ACCATTACAATCTTCAAGTGCTAGC 59.645 40.000 8.10 8.10 0.00 3.42
132 133 6.595326 TGACCATTACAATCTTCAAGTGCTAG 59.405 38.462 0.00 0.00 0.00 3.42
133 134 6.371548 GTGACCATTACAATCTTCAAGTGCTA 59.628 38.462 0.00 0.00 0.00 3.49
134 135 5.182001 GTGACCATTACAATCTTCAAGTGCT 59.818 40.000 0.00 0.00 0.00 4.40
135 136 5.393962 GTGACCATTACAATCTTCAAGTGC 58.606 41.667 0.00 0.00 0.00 4.40
136 137 5.408299 TCGTGACCATTACAATCTTCAAGTG 59.592 40.000 0.00 0.00 0.00 3.16
137 138 5.547465 TCGTGACCATTACAATCTTCAAGT 58.453 37.500 0.00 0.00 0.00 3.16
138 139 6.457392 CCATCGTGACCATTACAATCTTCAAG 60.457 42.308 0.00 0.00 0.00 3.02
139 140 5.353956 CCATCGTGACCATTACAATCTTCAA 59.646 40.000 0.00 0.00 0.00 2.69
140 141 4.875536 CCATCGTGACCATTACAATCTTCA 59.124 41.667 0.00 0.00 0.00 3.02
141 142 4.876107 ACCATCGTGACCATTACAATCTTC 59.124 41.667 0.00 0.00 0.00 2.87
142 143 4.843728 ACCATCGTGACCATTACAATCTT 58.156 39.130 0.00 0.00 0.00 2.40
143 144 4.487714 ACCATCGTGACCATTACAATCT 57.512 40.909 0.00 0.00 0.00 2.40
144 145 4.634004 TCAACCATCGTGACCATTACAATC 59.366 41.667 0.00 0.00 0.00 2.67
145 146 4.584874 TCAACCATCGTGACCATTACAAT 58.415 39.130 0.00 0.00 0.00 2.71
146 147 4.000325 CTCAACCATCGTGACCATTACAA 59.000 43.478 0.00 0.00 0.00 2.41
147 148 3.007506 ACTCAACCATCGTGACCATTACA 59.992 43.478 0.00 0.00 0.00 2.41
148 149 3.596214 ACTCAACCATCGTGACCATTAC 58.404 45.455 0.00 0.00 0.00 1.89
149 150 3.973206 ACTCAACCATCGTGACCATTA 57.027 42.857 0.00 0.00 0.00 1.90
150 151 2.859165 ACTCAACCATCGTGACCATT 57.141 45.000 0.00 0.00 0.00 3.16
151 152 3.973206 TTACTCAACCATCGTGACCAT 57.027 42.857 0.00 0.00 0.00 3.55
152 153 3.973206 ATTACTCAACCATCGTGACCA 57.027 42.857 0.00 0.00 0.00 4.02
153 154 4.751060 TGTATTACTCAACCATCGTGACC 58.249 43.478 0.00 0.00 0.00 4.02
154 155 5.867716 ACTTGTATTACTCAACCATCGTGAC 59.132 40.000 0.00 0.00 0.00 3.67
155 156 6.032956 ACTTGTATTACTCAACCATCGTGA 57.967 37.500 0.00 0.00 0.00 4.35
156 157 6.721571 AACTTGTATTACTCAACCATCGTG 57.278 37.500 0.00 0.00 0.00 4.35
157 158 7.739498 AAAACTTGTATTACTCAACCATCGT 57.261 32.000 0.00 0.00 0.00 3.73
158 159 9.537848 GTAAAAACTTGTATTACTCAACCATCG 57.462 33.333 0.00 0.00 0.00 3.84
159 160 9.836076 GGTAAAAACTTGTATTACTCAACCATC 57.164 33.333 0.00 0.00 31.73 3.51
160 161 9.582648 AGGTAAAAACTTGTATTACTCAACCAT 57.417 29.630 0.00 0.00 31.73 3.55
161 162 8.842280 CAGGTAAAAACTTGTATTACTCAACCA 58.158 33.333 0.00 0.00 31.73 3.67
162 163 8.294577 CCAGGTAAAAACTTGTATTACTCAACC 58.705 37.037 0.00 0.00 31.73 3.77
163 164 9.059260 TCCAGGTAAAAACTTGTATTACTCAAC 57.941 33.333 0.00 0.00 31.73 3.18
164 165 9.629878 TTCCAGGTAAAAACTTGTATTACTCAA 57.370 29.630 0.00 0.00 31.73 3.02
165 166 9.629878 TTTCCAGGTAAAAACTTGTATTACTCA 57.370 29.630 0.00 0.00 31.73 3.41
173 174 7.982919 GGTGTTTATTTCCAGGTAAAAACTTGT 59.017 33.333 13.02 0.00 31.63 3.16
174 175 7.439955 GGGTGTTTATTTCCAGGTAAAAACTTG 59.560 37.037 13.02 0.00 31.63 3.16
175 176 7.125963 TGGGTGTTTATTTCCAGGTAAAAACTT 59.874 33.333 13.02 0.00 31.63 2.66
176 177 6.612049 TGGGTGTTTATTTCCAGGTAAAAACT 59.388 34.615 13.02 0.00 31.63 2.66
177 178 6.818233 TGGGTGTTTATTTCCAGGTAAAAAC 58.182 36.000 8.43 8.43 30.63 2.43
178 179 7.290248 TCATGGGTGTTTATTTCCAGGTAAAAA 59.710 33.333 0.00 0.00 33.40 1.94
179 180 6.782988 TCATGGGTGTTTATTTCCAGGTAAAA 59.217 34.615 0.00 0.00 33.40 1.52
180 181 6.209788 GTCATGGGTGTTTATTTCCAGGTAAA 59.790 38.462 0.00 0.00 33.40 2.01
181 182 5.712917 GTCATGGGTGTTTATTTCCAGGTAA 59.287 40.000 0.00 0.00 33.40 2.85
182 183 5.222151 TGTCATGGGTGTTTATTTCCAGGTA 60.222 40.000 0.00 0.00 33.40 3.08
183 184 4.086457 GTCATGGGTGTTTATTTCCAGGT 58.914 43.478 0.00 0.00 33.40 4.00
184 185 4.085733 TGTCATGGGTGTTTATTTCCAGG 58.914 43.478 0.00 0.00 32.30 4.45
185 186 5.720371 TTGTCATGGGTGTTTATTTCCAG 57.280 39.130 0.00 0.00 32.30 3.86
186 187 5.600484 ACTTTGTCATGGGTGTTTATTTCCA 59.400 36.000 0.00 0.00 0.00 3.53
187 188 6.096673 ACTTTGTCATGGGTGTTTATTTCC 57.903 37.500 0.00 0.00 0.00 3.13
188 189 6.640907 GTGACTTTGTCATGGGTGTTTATTTC 59.359 38.462 3.65 0.00 44.63 2.17
189 190 6.323739 AGTGACTTTGTCATGGGTGTTTATTT 59.676 34.615 3.65 0.00 44.63 1.40
190 191 5.833131 AGTGACTTTGTCATGGGTGTTTATT 59.167 36.000 3.65 0.00 44.63 1.40
191 192 5.385198 AGTGACTTTGTCATGGGTGTTTAT 58.615 37.500 3.65 0.00 44.63 1.40
192 193 4.787551 AGTGACTTTGTCATGGGTGTTTA 58.212 39.130 3.65 0.00 44.63 2.01
193 194 3.631250 AGTGACTTTGTCATGGGTGTTT 58.369 40.909 3.65 0.00 44.63 2.83
194 195 3.297134 AGTGACTTTGTCATGGGTGTT 57.703 42.857 3.65 0.00 44.63 3.32
195 196 2.951642 CAAGTGACTTTGTCATGGGTGT 59.048 45.455 0.00 0.00 44.63 4.16
196 197 2.951642 ACAAGTGACTTTGTCATGGGTG 59.048 45.455 0.00 3.41 44.63 4.61
197 198 3.297134 ACAAGTGACTTTGTCATGGGT 57.703 42.857 0.00 0.63 44.63 4.51
198 199 3.885297 AGAACAAGTGACTTTGTCATGGG 59.115 43.478 0.00 0.08 44.63 4.00
199 200 4.790766 GCAGAACAAGTGACTTTGTCATGG 60.791 45.833 0.00 0.39 44.63 3.66
200 201 4.201940 TGCAGAACAAGTGACTTTGTCATG 60.202 41.667 0.00 2.31 44.63 3.07
201 202 3.947196 TGCAGAACAAGTGACTTTGTCAT 59.053 39.130 0.00 0.00 44.63 3.06
202 203 3.342719 TGCAGAACAAGTGACTTTGTCA 58.657 40.909 0.00 0.00 40.24 3.58
203 204 4.098416 GTTGCAGAACAAGTGACTTTGTC 58.902 43.478 0.00 0.00 40.24 3.18
204 205 3.505680 TGTTGCAGAACAAGTGACTTTGT 59.494 39.130 0.00 0.00 42.82 2.83
205 206 4.095410 TGTTGCAGAACAAGTGACTTTG 57.905 40.909 0.00 0.00 39.20 2.77
206 207 4.782019 TTGTTGCAGAACAAGTGACTTT 57.218 36.364 0.00 0.00 45.26 2.66
215 216 2.016318 CTCTGGTGTTGTTGCAGAACA 58.984 47.619 8.82 8.82 40.45 3.18
216 217 1.268743 GCTCTGGTGTTGTTGCAGAAC 60.269 52.381 4.18 4.18 0.00 3.01
217 218 1.024271 GCTCTGGTGTTGTTGCAGAA 58.976 50.000 0.00 0.00 0.00 3.02
218 219 1.159713 CGCTCTGGTGTTGTTGCAGA 61.160 55.000 0.00 0.00 0.00 4.26
219 220 1.159713 TCGCTCTGGTGTTGTTGCAG 61.160 55.000 0.00 0.00 0.00 4.41
220 221 1.153269 TCGCTCTGGTGTTGTTGCA 60.153 52.632 0.00 0.00 0.00 4.08
221 222 1.571460 CTCGCTCTGGTGTTGTTGC 59.429 57.895 0.00 0.00 0.00 4.17
222 223 1.230635 CCCTCGCTCTGGTGTTGTTG 61.231 60.000 0.00 0.00 0.00 3.33
223 224 1.071471 CCCTCGCTCTGGTGTTGTT 59.929 57.895 0.00 0.00 0.00 2.83
224 225 1.696097 AACCCTCGCTCTGGTGTTGT 61.696 55.000 0.00 0.00 34.34 3.32
247 248 2.138596 AGAAAAATGGTGTTGCAGCG 57.861 45.000 0.00 0.00 34.27 5.18
248 249 4.880886 AAAAGAAAAATGGTGTTGCAGC 57.119 36.364 0.00 0.00 0.00 5.25
267 268 2.130426 TTGCAGCGCCCCTCAAAAA 61.130 52.632 2.29 0.00 0.00 1.94
268 269 2.520500 TTGCAGCGCCCCTCAAAA 60.521 55.556 2.29 0.00 0.00 2.44
269 270 3.294493 GTTGCAGCGCCCCTCAAA 61.294 61.111 2.29 0.00 0.00 2.69
270 271 4.577677 TGTTGCAGCGCCCCTCAA 62.578 61.111 2.29 0.00 0.00 3.02
276 277 3.595758 AACTGGTGTTGCAGCGCC 61.596 61.111 24.68 24.68 39.37 6.53
277 278 2.353839 CAACTGGTGTTGCAGCGC 60.354 61.111 5.42 5.42 45.57 5.92
338 344 0.445436 CGCAGCTTCGATTTGCTTCT 59.555 50.000 0.00 0.00 37.44 2.85
386 392 1.134175 CGTCTGGCTTGGTGTGTTTTT 59.866 47.619 0.00 0.00 0.00 1.94
392 398 0.532862 CTGTTCGTCTGGCTTGGTGT 60.533 55.000 0.00 0.00 0.00 4.16
393 399 1.230635 CCTGTTCGTCTGGCTTGGTG 61.231 60.000 0.00 0.00 0.00 4.17
400 407 2.125912 CTCCGCCTGTTCGTCTGG 60.126 66.667 0.00 0.00 38.06 3.86
439 450 2.364448 AGGAGGACGAGGGGCTTC 60.364 66.667 0.00 0.00 0.00 3.86
452 463 3.213402 GCGGAGGAGGACGAGGAG 61.213 72.222 0.00 0.00 0.00 3.69
489 503 1.080538 GGAGTAGGGGGTGTGAGGT 59.919 63.158 0.00 0.00 0.00 3.85
989 1012 1.080501 CTGGTCATGACGTGCGAGT 60.081 57.895 19.33 0.00 0.00 4.18
1308 1337 4.988598 CCCAACTCGGCACACGCT 62.989 66.667 0.00 0.00 43.86 5.07
1317 1346 4.760047 CGCAGGTCCCCCAACTCG 62.760 72.222 0.00 0.00 0.00 4.18
1384 1413 1.303074 TGTCTAGCGACACCGTCCT 60.303 57.895 0.00 0.00 44.85 3.85
1446 1475 3.982424 GAGAAACATGCCGTGCGCG 62.982 63.158 13.88 13.88 42.08 6.86
1486 1515 4.096984 GGAAATCATTGTGGTCCATGAGAC 59.903 45.833 0.00 0.00 45.51 3.36
1497 1526 0.378257 CGAGCCCGGAAATCATTGTG 59.622 55.000 0.73 0.00 0.00 3.33
1608 1637 0.612732 CCTTCCCTGAATGGCTGCAA 60.613 55.000 0.50 0.00 0.00 4.08
1677 1706 1.656587 AGTGTTGTATCTCTGGGGCA 58.343 50.000 0.00 0.00 0.00 5.36
1692 1721 3.282021 GTCAACCATGCATCCATAGTGT 58.718 45.455 0.00 0.00 0.00 3.55
1710 1739 2.435410 CTGCGGCAGAGCATGTCA 60.435 61.111 25.33 0.00 46.97 3.58
1836 1865 5.945784 TCTATCAATTACTTTGGCTGCAAGT 59.054 36.000 9.84 9.84 38.13 3.16
1908 1937 2.722094 ACACCCGCATACATGTTTGAT 58.278 42.857 18.99 0.00 0.00 2.57
2116 2145 8.146053 TCCCTTGAGTTCTGATAATTACTGAA 57.854 34.615 0.00 0.00 0.00 3.02
2136 2166 0.751643 AAACGTTGCAGTGCTCCCTT 60.752 50.000 17.60 0.58 0.00 3.95
2164 2196 1.833860 AAACGTCAATGCAAACACCG 58.166 45.000 0.00 0.00 0.00 4.94
2310 2342 8.723942 AGTCAAATGTATCATGTTCTAACCTC 57.276 34.615 0.00 0.00 0.00 3.85
2725 2771 8.338259 CGAATAGTTGATTTCAGTTTATCCAGG 58.662 37.037 0.00 0.00 0.00 4.45
2973 3019 3.694072 TCTAACTGTTTACATGGCATGGC 59.306 43.478 29.49 13.29 33.60 4.40
2974 3020 6.455360 AATCTAACTGTTTACATGGCATGG 57.545 37.500 29.49 14.04 33.60 3.66
2975 3021 9.669353 GATAAATCTAACTGTTTACATGGCATG 57.331 33.333 25.31 25.31 0.00 4.06
2976 3022 8.850156 GGATAAATCTAACTGTTTACATGGCAT 58.150 33.333 0.00 0.00 0.00 4.40
2993 3039 7.576477 GCTGAAAGAAAACTGCTGGATAAATCT 60.576 37.037 0.00 0.00 34.07 2.40
3018 3064 2.798976 TGATCAACAAACTGGCTTGC 57.201 45.000 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.