Multiple sequence alignment - TraesCS1D01G192700

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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 TraesCS1D01G192700 chr1D 100.000 2750 0 0 1 2750 268943951 268941202 0.000000e+00 5079
1 TraesCS1D01G192700 chr1D 90.476 252 24 0 73 324 457970264 457970013 1.580000e-87 333
2 TraesCS1D01G192700 chr1A 93.817 2426 100 24 343 2750 333907811 333910204 0.000000e+00 3603
3 TraesCS1D01G192700 chr1B 88.108 2405 177 58 351 2692 370040057 370042415 0.000000e+00 2756
4 TraesCS1D01G192700 chr1B 82.564 195 21 8 2556 2750 84419873 84419692 2.830000e-35 159
5 TraesCS1D01G192700 chr1B 82.051 195 22 7 2556 2750 222196936 222196755 1.320000e-33 154
6 TraesCS1D01G192700 chr6D 92.000 250 19 1 76 324 162264290 162264041 1.570000e-92 350
7 TraesCS1D01G192700 chr6D 90.873 252 18 2 73 324 44257709 44257463 1.580000e-87 333
8 TraesCS1D01G192700 chr4A 91.406 256 17 2 71 325 673797540 673797289 2.030000e-91 346
9 TraesCS1D01G192700 chr4A 90.625 256 22 2 67 321 402955712 402955458 3.390000e-89 339
10 TraesCS1D01G192700 chr4A 90.763 249 17 2 73 321 240545268 240545510 7.340000e-86 327
11 TraesCS1D01G192700 chr4D 91.165 249 19 1 73 321 214485466 214485711 4.390000e-88 335
12 TraesCS1D01G192700 chr2D 90.347 259 15 7 70 325 30356736 30356987 5.680000e-87 331
13 TraesCS1D01G192700 chr6A 88.930 271 24 5 60 328 615728868 615729134 2.040000e-86 329
14 TraesCS1D01G192700 chr7B 82.564 195 21 8 2556 2750 625722916 625723097 2.830000e-35 159
15 TraesCS1D01G192700 chr6B 82.564 195 21 7 2556 2750 240548483 240548302 2.830000e-35 159
16 TraesCS1D01G192700 chr6B 81.538 195 22 8 2556 2750 232753935 232754115 6.140000e-32 148
17 TraesCS1D01G192700 chr6B 81.026 195 24 3 2556 2750 675197916 675197735 2.850000e-30 143
18 TraesCS1D01G192700 chr2B 82.051 195 22 7 2556 2750 780826101 780825920 1.320000e-33 154


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 TraesCS1D01G192700 chr1D 268941202 268943951 2749 True 5079 5079 100.000 1 2750 1 chr1D.!!$R1 2749
1 TraesCS1D01G192700 chr1A 333907811 333910204 2393 False 3603 3603 93.817 343 2750 1 chr1A.!!$F1 2407
2 TraesCS1D01G192700 chr1B 370040057 370042415 2358 False 2756 2756 88.108 351 2692 1 chr1B.!!$F1 2341

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
109 110 0.102481 CTATCTTAGGCACGCCACGT 59.898 55.0 11.35 0.0 42.36 4.49 F
117 118 0.460635 GGCACGCCACGTAGGATAAA 60.461 55.0 2.36 0.0 38.32 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1079 1123 0.251787 ACCCTTGGGATCCTGCAAAC 60.252 55.000 12.58 0.0 0.0 2.93 R
1800 1846 1.408702 ACAACTGCAACACCATCAACC 59.591 47.619 0.00 0.0 0.0 3.77 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
54 55 8.986477 ATGAATGAGAAAATAAAAGAAACCCG 57.014 30.769 0.00 0.00 0.00 5.28
55 56 8.172352 TGAATGAGAAAATAAAAGAAACCCGA 57.828 30.769 0.00 0.00 0.00 5.14
56 57 8.634444 TGAATGAGAAAATAAAAGAAACCCGAA 58.366 29.630 0.00 0.00 0.00 4.30
57 58 9.471084 GAATGAGAAAATAAAAGAAACCCGAAA 57.529 29.630 0.00 0.00 0.00 3.46
58 59 9.825109 AATGAGAAAATAAAAGAAACCCGAAAA 57.175 25.926 0.00 0.00 0.00 2.29
59 60 9.825109 ATGAGAAAATAAAAGAAACCCGAAAAA 57.175 25.926 0.00 0.00 0.00 1.94
82 83 7.492352 AAAATAGTCGAATAAGGGCATGTAC 57.508 36.000 0.00 0.00 0.00 2.90
83 84 5.801531 ATAGTCGAATAAGGGCATGTACA 57.198 39.130 0.00 0.00 0.00 2.90
84 85 4.481368 AGTCGAATAAGGGCATGTACAA 57.519 40.909 0.00 0.00 0.00 2.41
85 86 5.036117 AGTCGAATAAGGGCATGTACAAT 57.964 39.130 0.00 0.00 0.00 2.71
86 87 4.816385 AGTCGAATAAGGGCATGTACAATG 59.184 41.667 0.00 0.12 0.00 2.82
87 88 4.024048 GTCGAATAAGGGCATGTACAATGG 60.024 45.833 0.00 0.00 0.00 3.16
88 89 3.882888 CGAATAAGGGCATGTACAATGGT 59.117 43.478 0.00 0.00 0.00 3.55
89 90 4.338118 CGAATAAGGGCATGTACAATGGTT 59.662 41.667 0.00 0.00 0.00 3.67
90 91 5.505654 CGAATAAGGGCATGTACAATGGTTC 60.506 44.000 0.00 0.00 0.00 3.62
91 92 3.456380 AAGGGCATGTACAATGGTTCT 57.544 42.857 0.00 0.00 0.00 3.01
92 93 4.584638 AAGGGCATGTACAATGGTTCTA 57.415 40.909 0.00 0.00 0.00 2.10
93 94 4.796110 AGGGCATGTACAATGGTTCTAT 57.204 40.909 0.00 0.00 0.00 1.98
94 95 4.718961 AGGGCATGTACAATGGTTCTATC 58.281 43.478 0.00 0.00 0.00 2.08
95 96 4.413520 AGGGCATGTACAATGGTTCTATCT 59.586 41.667 0.00 0.00 0.00 1.98
96 97 5.103940 AGGGCATGTACAATGGTTCTATCTT 60.104 40.000 0.00 0.00 0.00 2.40
97 98 6.101150 AGGGCATGTACAATGGTTCTATCTTA 59.899 38.462 0.00 0.00 0.00 2.10
98 99 6.428159 GGGCATGTACAATGGTTCTATCTTAG 59.572 42.308 0.00 0.00 0.00 2.18
99 100 6.428159 GGCATGTACAATGGTTCTATCTTAGG 59.572 42.308 0.00 0.00 0.00 2.69
100 101 6.073003 GCATGTACAATGGTTCTATCTTAGGC 60.073 42.308 0.00 0.00 0.00 3.93
101 102 6.553953 TGTACAATGGTTCTATCTTAGGCA 57.446 37.500 0.00 0.00 0.00 4.75
102 103 6.346096 TGTACAATGGTTCTATCTTAGGCAC 58.654 40.000 0.00 0.00 0.00 5.01
103 104 4.442706 ACAATGGTTCTATCTTAGGCACG 58.557 43.478 0.00 0.00 0.00 5.34
104 105 2.596904 TGGTTCTATCTTAGGCACGC 57.403 50.000 0.00 0.00 0.00 5.34
105 106 1.138266 TGGTTCTATCTTAGGCACGCC 59.862 52.381 0.00 0.00 0.00 5.68
106 107 1.138266 GGTTCTATCTTAGGCACGCCA 59.862 52.381 11.35 0.00 38.92 5.69
107 108 2.202566 GTTCTATCTTAGGCACGCCAC 58.797 52.381 11.35 0.00 38.92 5.01
108 109 0.384309 TCTATCTTAGGCACGCCACG 59.616 55.000 11.35 0.00 38.92 4.94
109 110 0.102481 CTATCTTAGGCACGCCACGT 59.898 55.000 11.35 0.00 42.36 4.49
110 111 1.335810 CTATCTTAGGCACGCCACGTA 59.664 52.381 11.35 0.00 38.32 3.57
111 112 0.102481 ATCTTAGGCACGCCACGTAG 59.898 55.000 11.35 1.95 38.32 3.51
112 113 1.518572 CTTAGGCACGCCACGTAGG 60.519 63.158 11.35 0.00 38.32 3.18
113 114 1.940883 CTTAGGCACGCCACGTAGGA 61.941 60.000 11.35 0.00 38.32 2.94
114 115 1.324740 TTAGGCACGCCACGTAGGAT 61.325 55.000 11.35 0.00 38.32 3.24
115 116 0.466007 TAGGCACGCCACGTAGGATA 60.466 55.000 11.35 0.00 38.32 2.59
116 117 1.142314 GGCACGCCACGTAGGATAA 59.858 57.895 2.36 0.00 38.32 1.75
117 118 0.460635 GGCACGCCACGTAGGATAAA 60.461 55.000 2.36 0.00 38.32 1.40
118 119 1.578583 GCACGCCACGTAGGATAAAT 58.421 50.000 8.04 0.00 38.32 1.40
119 120 1.260561 GCACGCCACGTAGGATAAATG 59.739 52.381 8.04 0.69 38.32 2.32
120 121 2.816689 CACGCCACGTAGGATAAATGA 58.183 47.619 8.04 0.00 38.32 2.57
121 122 3.390135 CACGCCACGTAGGATAAATGAT 58.610 45.455 8.04 0.00 38.32 2.45
122 123 3.184379 CACGCCACGTAGGATAAATGATG 59.816 47.826 8.04 0.00 38.32 3.07
123 124 3.069016 ACGCCACGTAGGATAAATGATGA 59.931 43.478 8.04 0.00 38.73 2.92
124 125 3.675225 CGCCACGTAGGATAAATGATGAG 59.325 47.826 8.04 0.00 41.22 2.90
125 126 3.997021 GCCACGTAGGATAAATGATGAGG 59.003 47.826 8.04 0.00 41.22 3.86
126 127 4.503296 GCCACGTAGGATAAATGATGAGGT 60.503 45.833 8.04 0.00 41.22 3.85
127 128 4.991056 CCACGTAGGATAAATGATGAGGTG 59.009 45.833 0.00 0.00 41.22 4.00
128 129 4.991056 CACGTAGGATAAATGATGAGGTGG 59.009 45.833 0.00 0.00 0.00 4.61
129 130 4.899457 ACGTAGGATAAATGATGAGGTGGA 59.101 41.667 0.00 0.00 0.00 4.02
130 131 5.011125 ACGTAGGATAAATGATGAGGTGGAG 59.989 44.000 0.00 0.00 0.00 3.86
131 132 4.989875 AGGATAAATGATGAGGTGGAGG 57.010 45.455 0.00 0.00 0.00 4.30
132 133 4.570926 AGGATAAATGATGAGGTGGAGGA 58.429 43.478 0.00 0.00 0.00 3.71
133 134 4.596643 AGGATAAATGATGAGGTGGAGGAG 59.403 45.833 0.00 0.00 0.00 3.69
134 135 4.594920 GGATAAATGATGAGGTGGAGGAGA 59.405 45.833 0.00 0.00 0.00 3.71
135 136 5.279910 GGATAAATGATGAGGTGGAGGAGAG 60.280 48.000 0.00 0.00 0.00 3.20
136 137 3.411454 AATGATGAGGTGGAGGAGAGA 57.589 47.619 0.00 0.00 0.00 3.10
137 138 2.450867 TGATGAGGTGGAGGAGAGAG 57.549 55.000 0.00 0.00 0.00 3.20
138 139 1.925959 TGATGAGGTGGAGGAGAGAGA 59.074 52.381 0.00 0.00 0.00 3.10
139 140 2.313041 TGATGAGGTGGAGGAGAGAGAA 59.687 50.000 0.00 0.00 0.00 2.87
140 141 3.245766 TGATGAGGTGGAGGAGAGAGAAA 60.246 47.826 0.00 0.00 0.00 2.52
141 142 3.481559 TGAGGTGGAGGAGAGAGAAAT 57.518 47.619 0.00 0.00 0.00 2.17
142 143 3.370104 TGAGGTGGAGGAGAGAGAAATC 58.630 50.000 0.00 0.00 0.00 2.17
143 144 3.245766 TGAGGTGGAGGAGAGAGAAATCA 60.246 47.826 0.00 0.00 0.00 2.57
144 145 3.966665 GAGGTGGAGGAGAGAGAAATCAT 59.033 47.826 0.00 0.00 0.00 2.45
145 146 5.144100 GAGGTGGAGGAGAGAGAAATCATA 58.856 45.833 0.00 0.00 0.00 2.15
146 147 5.533112 AGGTGGAGGAGAGAGAAATCATAA 58.467 41.667 0.00 0.00 0.00 1.90
147 148 5.602145 AGGTGGAGGAGAGAGAAATCATAAG 59.398 44.000 0.00 0.00 0.00 1.73
148 149 5.600484 GGTGGAGGAGAGAGAAATCATAAGA 59.400 44.000 0.00 0.00 0.00 2.10
149 150 6.098982 GGTGGAGGAGAGAGAAATCATAAGAA 59.901 42.308 0.00 0.00 0.00 2.52
150 151 7.365117 GGTGGAGGAGAGAGAAATCATAAGAAA 60.365 40.741 0.00 0.00 0.00 2.52
151 152 8.043710 GTGGAGGAGAGAGAAATCATAAGAAAA 58.956 37.037 0.00 0.00 0.00 2.29
152 153 8.263640 TGGAGGAGAGAGAAATCATAAGAAAAG 58.736 37.037 0.00 0.00 0.00 2.27
153 154 7.714813 GGAGGAGAGAGAAATCATAAGAAAAGG 59.285 40.741 0.00 0.00 0.00 3.11
154 155 8.386012 AGGAGAGAGAAATCATAAGAAAAGGA 57.614 34.615 0.00 0.00 0.00 3.36
155 156 8.830741 AGGAGAGAGAAATCATAAGAAAAGGAA 58.169 33.333 0.00 0.00 0.00 3.36
156 157 9.108284 GGAGAGAGAAATCATAAGAAAAGGAAG 57.892 37.037 0.00 0.00 0.00 3.46
157 158 9.883142 GAGAGAGAAATCATAAGAAAAGGAAGA 57.117 33.333 0.00 0.00 0.00 2.87
158 159 9.665719 AGAGAGAAATCATAAGAAAAGGAAGAC 57.334 33.333 0.00 0.00 0.00 3.01
159 160 9.442047 GAGAGAAATCATAAGAAAAGGAAGACA 57.558 33.333 0.00 0.00 0.00 3.41
160 161 9.799106 AGAGAAATCATAAGAAAAGGAAGACAA 57.201 29.630 0.00 0.00 0.00 3.18
162 163 9.799106 AGAAATCATAAGAAAAGGAAGACAAGA 57.201 29.630 0.00 0.00 0.00 3.02
164 165 9.799106 AAATCATAAGAAAAGGAAGACAAGAGA 57.201 29.630 0.00 0.00 0.00 3.10
165 166 9.972106 AATCATAAGAAAAGGAAGACAAGAGAT 57.028 29.630 0.00 0.00 0.00 2.75
166 167 8.783833 TCATAAGAAAAGGAAGACAAGAGATG 57.216 34.615 0.00 0.00 0.00 2.90
167 168 8.597167 TCATAAGAAAAGGAAGACAAGAGATGA 58.403 33.333 0.00 0.00 0.00 2.92
168 169 9.393512 CATAAGAAAAGGAAGACAAGAGATGAT 57.606 33.333 0.00 0.00 0.00 2.45
169 170 7.920160 AAGAAAAGGAAGACAAGAGATGATC 57.080 36.000 0.00 0.00 0.00 2.92
170 171 7.256494 AGAAAAGGAAGACAAGAGATGATCT 57.744 36.000 0.00 0.00 41.27 2.75
171 172 7.330262 AGAAAAGGAAGACAAGAGATGATCTC 58.670 38.462 14.47 14.47 43.70 2.75
186 187 8.464770 GAGATGATCTCTTAGCACAATATGTC 57.535 38.462 14.98 0.00 40.30 3.06
187 188 8.192743 AGATGATCTCTTAGCACAATATGTCT 57.807 34.615 0.00 0.00 0.00 3.41
188 189 8.306038 AGATGATCTCTTAGCACAATATGTCTC 58.694 37.037 0.00 0.00 0.00 3.36
189 190 7.352079 TGATCTCTTAGCACAATATGTCTCA 57.648 36.000 0.00 0.00 0.00 3.27
190 191 7.205992 TGATCTCTTAGCACAATATGTCTCAC 58.794 38.462 0.00 0.00 0.00 3.51
191 192 5.907207 TCTCTTAGCACAATATGTCTCACC 58.093 41.667 0.00 0.00 0.00 4.02
192 193 5.422012 TCTCTTAGCACAATATGTCTCACCA 59.578 40.000 0.00 0.00 0.00 4.17
193 194 5.419542 TCTTAGCACAATATGTCTCACCAC 58.580 41.667 0.00 0.00 0.00 4.16
194 195 2.621338 AGCACAATATGTCTCACCACG 58.379 47.619 0.00 0.00 0.00 4.94
195 196 2.028112 AGCACAATATGTCTCACCACGT 60.028 45.455 0.00 0.00 0.00 4.49
196 197 2.742053 GCACAATATGTCTCACCACGTT 59.258 45.455 0.00 0.00 0.00 3.99
197 198 3.188460 GCACAATATGTCTCACCACGTTT 59.812 43.478 0.00 0.00 0.00 3.60
198 199 4.320202 GCACAATATGTCTCACCACGTTTT 60.320 41.667 0.00 0.00 0.00 2.43
199 200 5.757886 CACAATATGTCTCACCACGTTTTT 58.242 37.500 0.00 0.00 0.00 1.94
200 201 6.566942 GCACAATATGTCTCACCACGTTTTTA 60.567 38.462 0.00 0.00 0.00 1.52
201 202 7.015289 CACAATATGTCTCACCACGTTTTTAG 58.985 38.462 0.00 0.00 0.00 1.85
202 203 6.148811 ACAATATGTCTCACCACGTTTTTAGG 59.851 38.462 0.00 0.00 0.00 2.69
203 204 3.823281 TGTCTCACCACGTTTTTAGGA 57.177 42.857 0.00 0.00 0.00 2.94
204 205 4.139859 TGTCTCACCACGTTTTTAGGAA 57.860 40.909 0.00 0.00 0.00 3.36
205 206 4.710324 TGTCTCACCACGTTTTTAGGAAT 58.290 39.130 0.00 0.00 0.00 3.01
206 207 5.856156 TGTCTCACCACGTTTTTAGGAATA 58.144 37.500 0.00 0.00 0.00 1.75
207 208 5.929992 TGTCTCACCACGTTTTTAGGAATAG 59.070 40.000 0.00 0.00 0.00 1.73
208 209 4.933400 TCTCACCACGTTTTTAGGAATAGC 59.067 41.667 0.00 0.00 0.00 2.97
209 210 4.901868 TCACCACGTTTTTAGGAATAGCT 58.098 39.130 0.00 0.00 0.00 3.32
210 211 6.040209 TCACCACGTTTTTAGGAATAGCTA 57.960 37.500 0.00 0.00 0.00 3.32
211 212 6.103997 TCACCACGTTTTTAGGAATAGCTAG 58.896 40.000 0.00 0.00 0.00 3.42
212 213 5.873164 CACCACGTTTTTAGGAATAGCTAGT 59.127 40.000 0.00 0.00 0.00 2.57
213 214 6.370718 CACCACGTTTTTAGGAATAGCTAGTT 59.629 38.462 0.00 0.00 0.00 2.24
214 215 7.546667 CACCACGTTTTTAGGAATAGCTAGTTA 59.453 37.037 0.00 0.00 0.00 2.24
215 216 8.262933 ACCACGTTTTTAGGAATAGCTAGTTAT 58.737 33.333 0.00 0.00 0.00 1.89
216 217 9.106070 CCACGTTTTTAGGAATAGCTAGTTATT 57.894 33.333 11.22 11.22 0.00 1.40
240 241 5.816955 AAGATAAGGCTAAGAGATGACCC 57.183 43.478 0.00 0.00 0.00 4.46
241 242 4.820775 AGATAAGGCTAAGAGATGACCCA 58.179 43.478 0.00 0.00 0.00 4.51
242 243 5.410602 AGATAAGGCTAAGAGATGACCCAT 58.589 41.667 0.00 0.00 0.00 4.00
243 244 5.848921 AGATAAGGCTAAGAGATGACCCATT 59.151 40.000 0.00 0.00 0.00 3.16
244 245 3.853355 AGGCTAAGAGATGACCCATTG 57.147 47.619 0.00 0.00 0.00 2.82
245 246 3.118531 AGGCTAAGAGATGACCCATTGT 58.881 45.455 0.00 0.00 0.00 2.71
246 247 4.298626 AGGCTAAGAGATGACCCATTGTA 58.701 43.478 0.00 0.00 0.00 2.41
247 248 4.346418 AGGCTAAGAGATGACCCATTGTAG 59.654 45.833 0.00 0.00 0.00 2.74
248 249 4.345257 GGCTAAGAGATGACCCATTGTAGA 59.655 45.833 0.00 0.00 0.00 2.59
249 250 5.293560 GCTAAGAGATGACCCATTGTAGAC 58.706 45.833 0.00 0.00 0.00 2.59
250 251 5.163405 GCTAAGAGATGACCCATTGTAGACA 60.163 44.000 0.00 0.00 0.00 3.41
251 252 5.965033 AAGAGATGACCCATTGTAGACAT 57.035 39.130 0.00 0.00 0.00 3.06
252 253 7.255977 GCTAAGAGATGACCCATTGTAGACATA 60.256 40.741 0.00 0.00 0.00 2.29
253 254 7.623999 AAGAGATGACCCATTGTAGACATAT 57.376 36.000 0.00 0.00 0.00 1.78
254 255 7.623999 AGAGATGACCCATTGTAGACATATT 57.376 36.000 0.00 0.00 0.00 1.28
255 256 8.038862 AGAGATGACCCATTGTAGACATATTT 57.961 34.615 0.00 0.00 0.00 1.40
256 257 8.497745 AGAGATGACCCATTGTAGACATATTTT 58.502 33.333 0.00 0.00 0.00 1.82
257 258 9.125026 GAGATGACCCATTGTAGACATATTTTT 57.875 33.333 0.00 0.00 0.00 1.94
280 281 7.451501 TTTTGTCATCTCTAAATCACATGCA 57.548 32.000 0.00 0.00 0.00 3.96
281 282 7.451501 TTTGTCATCTCTAAATCACATGCAA 57.548 32.000 0.00 0.00 0.00 4.08
282 283 6.673154 TGTCATCTCTAAATCACATGCAAG 57.327 37.500 0.00 0.00 0.00 4.01
283 284 6.408869 TGTCATCTCTAAATCACATGCAAGA 58.591 36.000 0.00 0.00 0.00 3.02
284 285 6.314648 TGTCATCTCTAAATCACATGCAAGAC 59.685 38.462 0.00 0.00 0.00 3.01
285 286 6.538021 GTCATCTCTAAATCACATGCAAGACT 59.462 38.462 0.00 0.00 0.00 3.24
286 287 7.065563 GTCATCTCTAAATCACATGCAAGACTT 59.934 37.037 0.00 0.00 0.00 3.01
287 288 8.260114 TCATCTCTAAATCACATGCAAGACTTA 58.740 33.333 0.00 0.00 0.00 2.24
288 289 8.886719 CATCTCTAAATCACATGCAAGACTTAA 58.113 33.333 0.00 0.00 0.00 1.85
289 290 8.846943 TCTCTAAATCACATGCAAGACTTAAA 57.153 30.769 0.00 0.00 0.00 1.52
290 291 9.283768 TCTCTAAATCACATGCAAGACTTAAAA 57.716 29.630 0.00 0.00 0.00 1.52
296 297 9.846248 AATCACATGCAAGACTTAAAATAAGAC 57.154 29.630 0.00 0.00 0.00 3.01
297 298 8.621532 TCACATGCAAGACTTAAAATAAGACT 57.378 30.769 0.00 0.83 0.00 3.24
298 299 9.719355 TCACATGCAAGACTTAAAATAAGACTA 57.281 29.630 0.00 0.00 0.00 2.59
319 320 9.770097 AGACTATCTTATCAACCATTGTACATG 57.230 33.333 0.00 0.00 0.00 3.21
320 321 8.383318 ACTATCTTATCAACCATTGTACATGC 57.617 34.615 0.00 0.00 0.00 4.06
321 322 8.213679 ACTATCTTATCAACCATTGTACATGCT 58.786 33.333 0.00 0.00 0.00 3.79
322 323 6.925610 TCTTATCAACCATTGTACATGCTC 57.074 37.500 0.00 0.00 0.00 4.26
323 324 6.653020 TCTTATCAACCATTGTACATGCTCT 58.347 36.000 0.00 0.00 0.00 4.09
324 325 7.791029 TCTTATCAACCATTGTACATGCTCTA 58.209 34.615 0.00 0.00 0.00 2.43
325 326 7.928167 TCTTATCAACCATTGTACATGCTCTAG 59.072 37.037 0.00 0.00 0.00 2.43
326 327 5.675684 TCAACCATTGTACATGCTCTAGA 57.324 39.130 0.00 0.00 0.00 2.43
327 328 5.664457 TCAACCATTGTACATGCTCTAGAG 58.336 41.667 15.85 15.85 0.00 2.43
328 329 5.422012 TCAACCATTGTACATGCTCTAGAGA 59.578 40.000 24.24 9.00 0.00 3.10
329 330 5.939764 ACCATTGTACATGCTCTAGAGAA 57.060 39.130 24.24 14.29 0.00 2.87
330 331 6.299805 ACCATTGTACATGCTCTAGAGAAA 57.700 37.500 24.24 10.85 0.00 2.52
331 332 6.109359 ACCATTGTACATGCTCTAGAGAAAC 58.891 40.000 24.24 8.95 0.00 2.78
332 333 6.108687 CCATTGTACATGCTCTAGAGAAACA 58.891 40.000 24.24 11.60 0.00 2.83
333 334 6.036517 CCATTGTACATGCTCTAGAGAAACAC 59.963 42.308 24.24 12.43 0.00 3.32
334 335 5.984695 TGTACATGCTCTAGAGAAACACT 57.015 39.130 24.24 0.00 0.00 3.55
335 336 5.714047 TGTACATGCTCTAGAGAAACACTG 58.286 41.667 24.24 10.56 0.00 3.66
336 337 5.476945 TGTACATGCTCTAGAGAAACACTGA 59.523 40.000 24.24 0.00 0.00 3.41
337 338 5.070770 ACATGCTCTAGAGAAACACTGAG 57.929 43.478 24.24 6.05 0.00 3.35
338 339 4.769488 ACATGCTCTAGAGAAACACTGAGA 59.231 41.667 24.24 0.00 0.00 3.27
339 340 5.244851 ACATGCTCTAGAGAAACACTGAGAA 59.755 40.000 24.24 0.00 0.00 2.87
340 341 5.127693 TGCTCTAGAGAAACACTGAGAAC 57.872 43.478 24.24 1.24 0.00 3.01
341 342 4.021894 TGCTCTAGAGAAACACTGAGAACC 60.022 45.833 24.24 0.80 0.00 3.62
342 343 4.021894 GCTCTAGAGAAACACTGAGAACCA 60.022 45.833 24.24 0.00 0.00 3.67
343 344 5.455056 TCTAGAGAAACACTGAGAACCAC 57.545 43.478 0.00 0.00 0.00 4.16
344 345 4.893524 TCTAGAGAAACACTGAGAACCACA 59.106 41.667 0.00 0.00 0.00 4.17
345 346 4.065321 AGAGAAACACTGAGAACCACAG 57.935 45.455 0.00 0.00 40.68 3.66
346 347 2.545946 GAGAAACACTGAGAACCACAGC 59.454 50.000 0.00 0.00 38.74 4.40
347 348 2.092968 AGAAACACTGAGAACCACAGCA 60.093 45.455 0.00 0.00 38.74 4.41
348 349 1.668419 AACACTGAGAACCACAGCAC 58.332 50.000 0.00 0.00 38.74 4.40
349 350 0.530650 ACACTGAGAACCACAGCACG 60.531 55.000 0.00 0.00 38.74 5.34
356 357 2.290641 GAGAACCACAGCACGAAAACAT 59.709 45.455 0.00 0.00 0.00 2.71
357 358 2.033299 AGAACCACAGCACGAAAACATG 59.967 45.455 0.00 0.00 0.00 3.21
358 359 1.674359 ACCACAGCACGAAAACATGA 58.326 45.000 0.00 0.00 0.00 3.07
440 442 2.125147 GTGGCGAGCAGTGGCATA 60.125 61.111 0.00 0.00 44.19 3.14
466 468 2.035626 GGCTTGGCCCAGCTACAA 59.964 61.111 26.56 0.00 44.06 2.41
467 469 1.606313 GGCTTGGCCCAGCTACAAA 60.606 57.895 26.56 0.00 44.06 2.83
702 711 3.144120 CTCCCGCCCATCTCTGTCG 62.144 68.421 0.00 0.00 0.00 4.35
879 920 5.066117 TCTGTTCTAAGAGTACATACCGCTG 59.934 44.000 0.00 0.00 0.00 5.18
900 941 2.162809 GTGGTAAATTGGCCGAATTCGT 59.837 45.455 25.10 8.46 32.76 3.85
913 957 2.352651 CGAATTCGTGCATCTGATTGGT 59.647 45.455 19.67 0.00 34.11 3.67
966 1010 2.995466 TTTCTGAAATTGGCGCTGAG 57.005 45.000 7.64 0.00 0.00 3.35
972 1016 2.187599 AAATTGGCGCTGAGTCGTGC 62.188 55.000 7.64 10.69 39.59 5.34
1017 1061 2.749621 GGCAATGGTAAGTGAGTCTTGG 59.250 50.000 0.00 0.00 37.56 3.61
1030 1074 1.003233 AGTCTTGGTTAGAAAGGGGCG 59.997 52.381 0.00 0.00 33.81 6.13
1035 1079 0.611714 GGTTAGAAAGGGGCGACAGA 59.388 55.000 0.00 0.00 0.00 3.41
1067 1111 2.479049 GCATGCCTAGATGCTGTGTTTG 60.479 50.000 6.36 0.00 44.57 2.93
1068 1112 2.566833 TGCCTAGATGCTGTGTTTGT 57.433 45.000 0.00 0.00 0.00 2.83
1074 1118 4.393062 CCTAGATGCTGTGTTTGTAACCAG 59.607 45.833 0.00 0.00 34.70 4.00
1079 1123 3.563808 TGCTGTGTTTGTAACCAGCTTAG 59.436 43.478 21.93 0.00 46.55 2.18
1177 1222 4.792521 TCAGAGTGAGTTTTCTCTAGCC 57.207 45.455 0.00 0.00 46.30 3.93
1179 1224 2.494073 AGAGTGAGTTTTCTCTAGCCCG 59.506 50.000 0.00 0.00 46.30 6.13
1183 1228 2.492484 TGAGTTTTCTCTAGCCCGTCTC 59.508 50.000 0.00 0.00 46.30 3.36
1220 1265 4.644685 GCCTGGTGTTATGTGTAATCCAAT 59.355 41.667 0.00 0.00 31.37 3.16
1390 1435 7.227116 AGAGGTACGAGTGATACTCATTACTTC 59.773 40.741 15.05 15.05 45.30 3.01
1398 1443 8.798859 AGTGATACTCATTACTTCTTGCAAAT 57.201 30.769 0.00 0.00 26.81 2.32
1399 1444 8.671921 AGTGATACTCATTACTTCTTGCAAATG 58.328 33.333 0.00 0.00 26.81 2.32
1563 1608 3.410631 TCCGGTAATTCACAAAGAGCA 57.589 42.857 0.00 0.00 0.00 4.26
1755 1800 7.846644 ATCTGATAAGAAGCTTTGAAGTGAG 57.153 36.000 0.00 0.00 0.00 3.51
1808 1854 0.108520 GCTGGTTGCATGGTTGATGG 60.109 55.000 0.00 0.00 42.31 3.51
1891 1937 3.813166 CAGTTCACCGGATTTGTACAACT 59.187 43.478 9.46 2.30 0.00 3.16
1964 2010 9.190317 AGAAACCATTTTCCAATCTAGTTATCC 57.810 33.333 0.00 0.00 42.00 2.59
1967 2013 7.643123 ACCATTTTCCAATCTAGTTATCCAGT 58.357 34.615 0.00 0.00 0.00 4.00
2075 2121 2.293122 TGAAATTGGAAGGTCACTTGCG 59.707 45.455 0.00 0.00 46.80 4.85
2091 2137 4.005650 ACTTGCGTCTGAAATCATGTGAT 58.994 39.130 0.00 0.00 36.07 3.06
2139 2185 2.103094 TCCTGGAGTTGAATAGGATGCG 59.897 50.000 0.00 0.00 34.54 4.73
2144 2190 2.866762 GAGTTGAATAGGATGCGACCAC 59.133 50.000 2.00 0.00 0.00 4.16
2236 2285 1.544246 GGTGGTAAGAAATGTGGTGCC 59.456 52.381 0.00 0.00 0.00 5.01
2465 2533 4.370364 AAGTTTCACAATTGCTCAACGT 57.630 36.364 5.05 1.43 0.00 3.99
2499 2567 5.174395 GTGATCTCTGTCAGCATTGTAAGT 58.826 41.667 0.00 0.00 0.00 2.24
2513 2581 6.318900 AGCATTGTAAGTATCAGGCTTTTACC 59.681 38.462 0.00 0.00 0.00 2.85
2535 2603 6.226787 ACCTCATCTGTTGTTTCAACTAGAG 58.773 40.000 12.66 12.44 0.00 2.43
2613 2681 3.244078 TGTGCCTATTTCGACTTCAGTGT 60.244 43.478 0.00 0.00 0.00 3.55
2683 2752 8.915654 CATGCAGGTAACATTTACTTTTCTTTC 58.084 33.333 0.00 0.00 41.41 2.62
2723 2792 0.111061 AGTTTGCTGCCTGGACATCA 59.889 50.000 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 9.423061 CGGGTTTCTTTTATTTTCTCATTCATT 57.577 29.630 0.00 0.00 0.00 2.57
29 30 8.802267 TCGGGTTTCTTTTATTTTCTCATTCAT 58.198 29.630 0.00 0.00 0.00 2.57
30 31 8.172352 TCGGGTTTCTTTTATTTTCTCATTCA 57.828 30.769 0.00 0.00 0.00 2.57
31 32 9.471084 TTTCGGGTTTCTTTTATTTTCTCATTC 57.529 29.630 0.00 0.00 0.00 2.67
32 33 9.825109 TTTTCGGGTTTCTTTTATTTTCTCATT 57.175 25.926 0.00 0.00 0.00 2.57
33 34 9.825109 TTTTTCGGGTTTCTTTTATTTTCTCAT 57.175 25.926 0.00 0.00 0.00 2.90
57 58 7.554835 TGTACATGCCCTTATTCGACTATTTTT 59.445 33.333 0.00 0.00 0.00 1.94
58 59 7.051623 TGTACATGCCCTTATTCGACTATTTT 58.948 34.615 0.00 0.00 0.00 1.82
59 60 6.588204 TGTACATGCCCTTATTCGACTATTT 58.412 36.000 0.00 0.00 0.00 1.40
60 61 6.169557 TGTACATGCCCTTATTCGACTATT 57.830 37.500 0.00 0.00 0.00 1.73
61 62 5.801531 TGTACATGCCCTTATTCGACTAT 57.198 39.130 0.00 0.00 0.00 2.12
62 63 5.601583 TTGTACATGCCCTTATTCGACTA 57.398 39.130 0.00 0.00 0.00 2.59
63 64 4.481368 TTGTACATGCCCTTATTCGACT 57.519 40.909 0.00 0.00 0.00 4.18
64 65 4.024048 CCATTGTACATGCCCTTATTCGAC 60.024 45.833 0.00 0.00 0.00 4.20
65 66 4.133820 CCATTGTACATGCCCTTATTCGA 58.866 43.478 0.00 0.00 0.00 3.71
66 67 3.882888 ACCATTGTACATGCCCTTATTCG 59.117 43.478 0.00 0.00 0.00 3.34
67 68 5.594317 AGAACCATTGTACATGCCCTTATTC 59.406 40.000 0.00 0.00 0.00 1.75
68 69 5.518865 AGAACCATTGTACATGCCCTTATT 58.481 37.500 0.00 0.00 0.00 1.40
69 70 5.129368 AGAACCATTGTACATGCCCTTAT 57.871 39.130 0.00 0.00 0.00 1.73
70 71 4.584638 AGAACCATTGTACATGCCCTTA 57.415 40.909 0.00 0.00 0.00 2.69
71 72 3.456380 AGAACCATTGTACATGCCCTT 57.544 42.857 0.00 0.00 0.00 3.95
72 73 4.413520 AGATAGAACCATTGTACATGCCCT 59.586 41.667 0.00 0.00 0.00 5.19
73 74 4.718961 AGATAGAACCATTGTACATGCCC 58.281 43.478 0.00 0.00 0.00 5.36
74 75 6.428159 CCTAAGATAGAACCATTGTACATGCC 59.572 42.308 0.00 0.00 0.00 4.40
75 76 6.073003 GCCTAAGATAGAACCATTGTACATGC 60.073 42.308 0.00 0.00 0.00 4.06
76 77 6.992123 TGCCTAAGATAGAACCATTGTACATG 59.008 38.462 0.00 0.00 0.00 3.21
77 78 6.992715 GTGCCTAAGATAGAACCATTGTACAT 59.007 38.462 0.00 0.00 0.00 2.29
78 79 6.346096 GTGCCTAAGATAGAACCATTGTACA 58.654 40.000 0.00 0.00 0.00 2.90
79 80 5.462398 CGTGCCTAAGATAGAACCATTGTAC 59.538 44.000 0.00 0.00 0.00 2.90
80 81 5.597806 CGTGCCTAAGATAGAACCATTGTA 58.402 41.667 0.00 0.00 0.00 2.41
81 82 4.442706 CGTGCCTAAGATAGAACCATTGT 58.557 43.478 0.00 0.00 0.00 2.71
82 83 3.248602 GCGTGCCTAAGATAGAACCATTG 59.751 47.826 0.00 0.00 0.00 2.82
83 84 3.467803 GCGTGCCTAAGATAGAACCATT 58.532 45.455 0.00 0.00 0.00 3.16
84 85 2.224305 GGCGTGCCTAAGATAGAACCAT 60.224 50.000 2.98 0.00 0.00 3.55
85 86 1.138266 GGCGTGCCTAAGATAGAACCA 59.862 52.381 2.98 0.00 0.00 3.67
86 87 1.138266 TGGCGTGCCTAAGATAGAACC 59.862 52.381 12.84 0.00 36.94 3.62
87 88 2.202566 GTGGCGTGCCTAAGATAGAAC 58.797 52.381 12.84 0.00 36.94 3.01
88 89 1.202371 CGTGGCGTGCCTAAGATAGAA 60.202 52.381 12.84 0.00 36.94 2.10
89 90 0.384309 CGTGGCGTGCCTAAGATAGA 59.616 55.000 12.84 0.00 36.94 1.98
90 91 0.102481 ACGTGGCGTGCCTAAGATAG 59.898 55.000 12.84 0.00 39.18 2.08
91 92 1.335810 CTACGTGGCGTGCCTAAGATA 59.664 52.381 12.84 0.00 41.39 1.98
92 93 0.102481 CTACGTGGCGTGCCTAAGAT 59.898 55.000 12.84 0.00 41.39 2.40
93 94 1.509463 CTACGTGGCGTGCCTAAGA 59.491 57.895 12.84 0.00 41.39 2.10
94 95 1.518572 CCTACGTGGCGTGCCTAAG 60.519 63.158 12.84 5.91 41.39 2.18
95 96 1.324740 ATCCTACGTGGCGTGCCTAA 61.325 55.000 12.84 0.00 41.39 2.69
96 97 0.466007 TATCCTACGTGGCGTGCCTA 60.466 55.000 12.84 0.00 41.39 3.93
97 98 1.324740 TTATCCTACGTGGCGTGCCT 61.325 55.000 12.84 0.00 41.39 4.75
98 99 0.460635 TTTATCCTACGTGGCGTGCC 60.461 55.000 3.30 3.30 41.39 5.01
99 100 1.260561 CATTTATCCTACGTGGCGTGC 59.739 52.381 0.00 0.00 41.39 5.34
100 101 2.816689 TCATTTATCCTACGTGGCGTG 58.183 47.619 0.00 0.00 41.39 5.34
101 102 3.069016 TCATCATTTATCCTACGTGGCGT 59.931 43.478 0.00 0.00 44.35 5.68
102 103 3.649073 TCATCATTTATCCTACGTGGCG 58.351 45.455 0.00 0.00 35.26 5.69
103 104 3.997021 CCTCATCATTTATCCTACGTGGC 59.003 47.826 0.00 0.00 35.26 5.01
104 105 4.991056 CACCTCATCATTTATCCTACGTGG 59.009 45.833 0.00 0.00 37.10 4.94
105 106 4.991056 CCACCTCATCATTTATCCTACGTG 59.009 45.833 0.00 0.00 0.00 4.49
106 107 4.899457 TCCACCTCATCATTTATCCTACGT 59.101 41.667 0.00 0.00 0.00 3.57
107 108 5.468540 TCCACCTCATCATTTATCCTACG 57.531 43.478 0.00 0.00 0.00 3.51
108 109 5.544176 TCCTCCACCTCATCATTTATCCTAC 59.456 44.000 0.00 0.00 0.00 3.18
109 110 5.726560 TCCTCCACCTCATCATTTATCCTA 58.273 41.667 0.00 0.00 0.00 2.94
110 111 4.570926 TCCTCCACCTCATCATTTATCCT 58.429 43.478 0.00 0.00 0.00 3.24
111 112 4.594920 TCTCCTCCACCTCATCATTTATCC 59.405 45.833 0.00 0.00 0.00 2.59
112 113 5.541868 TCTCTCCTCCACCTCATCATTTATC 59.458 44.000 0.00 0.00 0.00 1.75
113 114 5.471424 TCTCTCCTCCACCTCATCATTTAT 58.529 41.667 0.00 0.00 0.00 1.40
114 115 4.883759 TCTCTCCTCCACCTCATCATTTA 58.116 43.478 0.00 0.00 0.00 1.40
115 116 3.710677 CTCTCTCCTCCACCTCATCATTT 59.289 47.826 0.00 0.00 0.00 2.32
116 117 3.052262 TCTCTCTCCTCCACCTCATCATT 60.052 47.826 0.00 0.00 0.00 2.57
117 118 2.517553 TCTCTCTCCTCCACCTCATCAT 59.482 50.000 0.00 0.00 0.00 2.45
118 119 1.925959 TCTCTCTCCTCCACCTCATCA 59.074 52.381 0.00 0.00 0.00 3.07
119 120 2.746279 TCTCTCTCCTCCACCTCATC 57.254 55.000 0.00 0.00 0.00 2.92
120 121 3.481559 TTTCTCTCTCCTCCACCTCAT 57.518 47.619 0.00 0.00 0.00 2.90
121 122 3.245766 TGATTTCTCTCTCCTCCACCTCA 60.246 47.826 0.00 0.00 0.00 3.86
122 123 3.370104 TGATTTCTCTCTCCTCCACCTC 58.630 50.000 0.00 0.00 0.00 3.85
123 124 3.481559 TGATTTCTCTCTCCTCCACCT 57.518 47.619 0.00 0.00 0.00 4.00
124 125 5.600484 TCTTATGATTTCTCTCTCCTCCACC 59.400 44.000 0.00 0.00 0.00 4.61
125 126 6.723298 TCTTATGATTTCTCTCTCCTCCAC 57.277 41.667 0.00 0.00 0.00 4.02
126 127 7.739995 TTTCTTATGATTTCTCTCTCCTCCA 57.260 36.000 0.00 0.00 0.00 3.86
127 128 7.714813 CCTTTTCTTATGATTTCTCTCTCCTCC 59.285 40.741 0.00 0.00 0.00 4.30
128 129 8.482128 TCCTTTTCTTATGATTTCTCTCTCCTC 58.518 37.037 0.00 0.00 0.00 3.71
129 130 8.386012 TCCTTTTCTTATGATTTCTCTCTCCT 57.614 34.615 0.00 0.00 0.00 3.69
130 131 9.108284 CTTCCTTTTCTTATGATTTCTCTCTCC 57.892 37.037 0.00 0.00 0.00 3.71
131 132 9.883142 TCTTCCTTTTCTTATGATTTCTCTCTC 57.117 33.333 0.00 0.00 0.00 3.20
132 133 9.665719 GTCTTCCTTTTCTTATGATTTCTCTCT 57.334 33.333 0.00 0.00 0.00 3.10
133 134 9.442047 TGTCTTCCTTTTCTTATGATTTCTCTC 57.558 33.333 0.00 0.00 0.00 3.20
134 135 9.799106 TTGTCTTCCTTTTCTTATGATTTCTCT 57.201 29.630 0.00 0.00 0.00 3.10
136 137 9.799106 TCTTGTCTTCCTTTTCTTATGATTTCT 57.201 29.630 0.00 0.00 0.00 2.52
138 139 9.799106 TCTCTTGTCTTCCTTTTCTTATGATTT 57.201 29.630 0.00 0.00 0.00 2.17
139 140 9.972106 ATCTCTTGTCTTCCTTTTCTTATGATT 57.028 29.630 0.00 0.00 0.00 2.57
140 141 9.393512 CATCTCTTGTCTTCCTTTTCTTATGAT 57.606 33.333 0.00 0.00 0.00 2.45
141 142 8.597167 TCATCTCTTGTCTTCCTTTTCTTATGA 58.403 33.333 0.00 0.00 0.00 2.15
142 143 8.783833 TCATCTCTTGTCTTCCTTTTCTTATG 57.216 34.615 0.00 0.00 0.00 1.90
143 144 9.612066 GATCATCTCTTGTCTTCCTTTTCTTAT 57.388 33.333 0.00 0.00 0.00 1.73
144 145 8.820831 AGATCATCTCTTGTCTTCCTTTTCTTA 58.179 33.333 0.00 0.00 0.00 2.10
145 146 7.688343 AGATCATCTCTTGTCTTCCTTTTCTT 58.312 34.615 0.00 0.00 0.00 2.52
146 147 7.256494 AGATCATCTCTTGTCTTCCTTTTCT 57.744 36.000 0.00 0.00 0.00 2.52
147 148 7.538303 GAGATCATCTCTTGTCTTCCTTTTC 57.462 40.000 7.48 0.00 40.30 2.29
161 162 8.306038 AGACATATTGTGCTAAGAGATCATCTC 58.694 37.037 6.55 6.55 43.70 2.75
162 163 8.192743 AGACATATTGTGCTAAGAGATCATCT 57.807 34.615 0.00 0.00 41.27 2.90
163 164 8.087136 TGAGACATATTGTGCTAAGAGATCATC 58.913 37.037 0.00 0.00 0.00 2.92
164 165 7.871973 GTGAGACATATTGTGCTAAGAGATCAT 59.128 37.037 0.00 0.00 0.00 2.45
165 166 7.205992 GTGAGACATATTGTGCTAAGAGATCA 58.794 38.462 0.00 0.00 0.00 2.92
166 167 6.644592 GGTGAGACATATTGTGCTAAGAGATC 59.355 42.308 0.00 0.00 0.00 2.75
167 168 6.098838 TGGTGAGACATATTGTGCTAAGAGAT 59.901 38.462 0.00 0.00 0.00 2.75
168 169 5.422012 TGGTGAGACATATTGTGCTAAGAGA 59.578 40.000 0.00 0.00 0.00 3.10
169 170 5.521735 GTGGTGAGACATATTGTGCTAAGAG 59.478 44.000 0.00 0.00 0.00 2.85
170 171 5.419542 GTGGTGAGACATATTGTGCTAAGA 58.580 41.667 0.00 0.00 0.00 2.10
171 172 4.268644 CGTGGTGAGACATATTGTGCTAAG 59.731 45.833 0.00 0.00 0.00 2.18
172 173 4.180817 CGTGGTGAGACATATTGTGCTAA 58.819 43.478 0.00 0.00 0.00 3.09
173 174 3.194755 ACGTGGTGAGACATATTGTGCTA 59.805 43.478 0.00 0.00 0.00 3.49
174 175 2.028112 ACGTGGTGAGACATATTGTGCT 60.028 45.455 0.00 0.00 0.00 4.40
175 176 2.346803 ACGTGGTGAGACATATTGTGC 58.653 47.619 0.00 0.00 0.00 4.57
176 177 5.356882 AAAACGTGGTGAGACATATTGTG 57.643 39.130 0.00 0.00 0.00 3.33
177 178 6.148811 CCTAAAAACGTGGTGAGACATATTGT 59.851 38.462 0.00 0.00 0.00 2.71
178 179 6.370442 TCCTAAAAACGTGGTGAGACATATTG 59.630 38.462 0.00 0.00 0.00 1.90
179 180 6.469410 TCCTAAAAACGTGGTGAGACATATT 58.531 36.000 0.00 0.00 0.00 1.28
180 181 6.045072 TCCTAAAAACGTGGTGAGACATAT 57.955 37.500 0.00 0.00 0.00 1.78
181 182 5.471556 TCCTAAAAACGTGGTGAGACATA 57.528 39.130 0.00 0.00 0.00 2.29
182 183 4.345859 TCCTAAAAACGTGGTGAGACAT 57.654 40.909 0.00 0.00 0.00 3.06
183 184 3.823281 TCCTAAAAACGTGGTGAGACA 57.177 42.857 0.00 0.00 0.00 3.41
184 185 5.163884 GCTATTCCTAAAAACGTGGTGAGAC 60.164 44.000 0.00 0.00 0.00 3.36
185 186 4.933400 GCTATTCCTAAAAACGTGGTGAGA 59.067 41.667 0.00 0.00 0.00 3.27
186 187 4.935808 AGCTATTCCTAAAAACGTGGTGAG 59.064 41.667 0.00 0.00 0.00 3.51
187 188 4.901868 AGCTATTCCTAAAAACGTGGTGA 58.098 39.130 0.00 0.00 0.00 4.02
188 189 5.873164 ACTAGCTATTCCTAAAAACGTGGTG 59.127 40.000 0.00 0.00 0.00 4.17
189 190 6.046290 ACTAGCTATTCCTAAAAACGTGGT 57.954 37.500 0.00 0.00 0.00 4.16
190 191 6.980051 AACTAGCTATTCCTAAAAACGTGG 57.020 37.500 0.00 0.00 0.00 4.94
214 215 8.379331 GGGTCATCTCTTAGCCTTATCTTTAAT 58.621 37.037 0.00 0.00 0.00 1.40
215 216 7.347222 TGGGTCATCTCTTAGCCTTATCTTTAA 59.653 37.037 0.00 0.00 34.30 1.52
216 217 6.844388 TGGGTCATCTCTTAGCCTTATCTTTA 59.156 38.462 0.00 0.00 34.30 1.85
217 218 5.667626 TGGGTCATCTCTTAGCCTTATCTTT 59.332 40.000 0.00 0.00 34.30 2.52
218 219 5.219739 TGGGTCATCTCTTAGCCTTATCTT 58.780 41.667 0.00 0.00 34.30 2.40
219 220 4.820775 TGGGTCATCTCTTAGCCTTATCT 58.179 43.478 0.00 0.00 34.30 1.98
220 221 5.753721 ATGGGTCATCTCTTAGCCTTATC 57.246 43.478 0.00 0.00 34.30 1.75
221 222 5.370880 ACAATGGGTCATCTCTTAGCCTTAT 59.629 40.000 0.00 0.00 34.30 1.73
222 223 4.721776 ACAATGGGTCATCTCTTAGCCTTA 59.278 41.667 0.00 0.00 34.30 2.69
223 224 3.525199 ACAATGGGTCATCTCTTAGCCTT 59.475 43.478 0.00 0.00 34.30 4.35
224 225 3.118531 ACAATGGGTCATCTCTTAGCCT 58.881 45.455 0.00 0.00 34.30 4.58
225 226 3.567478 ACAATGGGTCATCTCTTAGCC 57.433 47.619 0.00 0.00 0.00 3.93
226 227 5.163405 TGTCTACAATGGGTCATCTCTTAGC 60.163 44.000 0.00 0.00 0.00 3.09
227 228 6.471233 TGTCTACAATGGGTCATCTCTTAG 57.529 41.667 0.00 0.00 0.00 2.18
228 229 8.727100 ATATGTCTACAATGGGTCATCTCTTA 57.273 34.615 0.00 0.00 0.00 2.10
229 230 5.965033 ATGTCTACAATGGGTCATCTCTT 57.035 39.130 0.00 0.00 0.00 2.85
230 231 7.623999 AATATGTCTACAATGGGTCATCTCT 57.376 36.000 0.00 0.00 0.00 3.10
231 232 8.682936 AAAATATGTCTACAATGGGTCATCTC 57.317 34.615 0.00 0.00 0.00 2.75
255 256 7.884257 TGCATGTGATTTAGAGATGACAAAAA 58.116 30.769 0.00 0.00 27.25 1.94
256 257 7.451501 TGCATGTGATTTAGAGATGACAAAA 57.548 32.000 0.00 0.00 27.25 2.44
257 258 7.391275 TCTTGCATGTGATTTAGAGATGACAAA 59.609 33.333 0.00 0.00 27.25 2.83
258 259 6.880529 TCTTGCATGTGATTTAGAGATGACAA 59.119 34.615 0.00 0.00 27.25 3.18
259 260 6.314648 GTCTTGCATGTGATTTAGAGATGACA 59.685 38.462 0.00 0.00 0.00 3.58
260 261 6.538021 AGTCTTGCATGTGATTTAGAGATGAC 59.462 38.462 0.00 0.00 0.00 3.06
261 262 6.647229 AGTCTTGCATGTGATTTAGAGATGA 58.353 36.000 0.00 0.00 0.00 2.92
262 263 6.922247 AGTCTTGCATGTGATTTAGAGATG 57.078 37.500 0.00 0.00 0.00 2.90
263 264 9.453572 TTTAAGTCTTGCATGTGATTTAGAGAT 57.546 29.630 0.00 0.00 0.00 2.75
264 265 8.846943 TTTAAGTCTTGCATGTGATTTAGAGA 57.153 30.769 0.00 0.00 0.00 3.10
270 271 9.846248 GTCTTATTTTAAGTCTTGCATGTGATT 57.154 29.630 0.00 0.00 0.00 2.57
271 272 9.236006 AGTCTTATTTTAAGTCTTGCATGTGAT 57.764 29.630 0.00 0.00 0.00 3.06
272 273 8.621532 AGTCTTATTTTAAGTCTTGCATGTGA 57.378 30.769 0.00 0.00 0.00 3.58
293 294 9.770097 CATGTACAATGGTTGATAAGATAGTCT 57.230 33.333 0.00 0.00 0.00 3.24
294 295 8.499162 GCATGTACAATGGTTGATAAGATAGTC 58.501 37.037 0.00 0.00 0.00 2.59
295 296 8.213679 AGCATGTACAATGGTTGATAAGATAGT 58.786 33.333 0.00 0.00 0.00 2.12
296 297 8.613060 AGCATGTACAATGGTTGATAAGATAG 57.387 34.615 0.00 0.00 0.00 2.08
297 298 8.432013 AGAGCATGTACAATGGTTGATAAGATA 58.568 33.333 0.00 0.00 0.00 1.98
298 299 7.285566 AGAGCATGTACAATGGTTGATAAGAT 58.714 34.615 0.00 0.00 0.00 2.40
299 300 6.653020 AGAGCATGTACAATGGTTGATAAGA 58.347 36.000 0.00 0.00 0.00 2.10
300 301 6.932356 AGAGCATGTACAATGGTTGATAAG 57.068 37.500 0.00 0.00 0.00 1.73
301 302 7.791029 TCTAGAGCATGTACAATGGTTGATAA 58.209 34.615 0.00 0.00 0.00 1.75
302 303 7.287696 TCTCTAGAGCATGTACAATGGTTGATA 59.712 37.037 15.35 0.42 0.00 2.15
303 304 6.098838 TCTCTAGAGCATGTACAATGGTTGAT 59.901 38.462 15.35 0.00 0.00 2.57
304 305 5.422012 TCTCTAGAGCATGTACAATGGTTGA 59.578 40.000 15.35 4.73 0.00 3.18
305 306 5.664457 TCTCTAGAGCATGTACAATGGTTG 58.336 41.667 15.35 0.00 0.00 3.77
306 307 5.939764 TCTCTAGAGCATGTACAATGGTT 57.060 39.130 15.35 0.00 0.00 3.67
307 308 5.939764 TTCTCTAGAGCATGTACAATGGT 57.060 39.130 15.35 4.68 0.00 3.55
308 309 6.036517 GTGTTTCTCTAGAGCATGTACAATGG 59.963 42.308 15.35 0.00 0.00 3.16
309 310 6.815641 AGTGTTTCTCTAGAGCATGTACAATG 59.184 38.462 15.35 0.12 0.00 2.82
310 311 6.815641 CAGTGTTTCTCTAGAGCATGTACAAT 59.184 38.462 15.35 9.94 0.00 2.71
311 312 6.015434 TCAGTGTTTCTCTAGAGCATGTACAA 60.015 38.462 15.35 0.00 0.00 2.41
312 313 5.476945 TCAGTGTTTCTCTAGAGCATGTACA 59.523 40.000 15.35 10.59 0.00 2.90
313 314 5.955488 TCAGTGTTTCTCTAGAGCATGTAC 58.045 41.667 15.35 9.74 0.00 2.90
314 315 5.946377 TCTCAGTGTTTCTCTAGAGCATGTA 59.054 40.000 15.35 0.00 0.00 2.29
315 316 4.769488 TCTCAGTGTTTCTCTAGAGCATGT 59.231 41.667 15.35 0.00 0.00 3.21
316 317 5.321959 TCTCAGTGTTTCTCTAGAGCATG 57.678 43.478 15.35 7.03 0.00 4.06
317 318 5.337169 GGTTCTCAGTGTTTCTCTAGAGCAT 60.337 44.000 15.35 0.00 0.00 3.79
318 319 4.021894 GGTTCTCAGTGTTTCTCTAGAGCA 60.022 45.833 15.35 0.42 0.00 4.26
319 320 4.021894 TGGTTCTCAGTGTTTCTCTAGAGC 60.022 45.833 15.35 1.86 0.00 4.09
320 321 5.010112 TGTGGTTCTCAGTGTTTCTCTAGAG 59.990 44.000 13.98 13.98 0.00 2.43
321 322 4.893524 TGTGGTTCTCAGTGTTTCTCTAGA 59.106 41.667 0.00 0.00 0.00 2.43
322 323 5.201713 TGTGGTTCTCAGTGTTTCTCTAG 57.798 43.478 0.00 0.00 0.00 2.43
323 324 4.501571 GCTGTGGTTCTCAGTGTTTCTCTA 60.502 45.833 0.00 0.00 35.60 2.43
324 325 3.742640 GCTGTGGTTCTCAGTGTTTCTCT 60.743 47.826 0.00 0.00 35.60 3.10
325 326 2.545946 GCTGTGGTTCTCAGTGTTTCTC 59.454 50.000 0.00 0.00 35.60 2.87
326 327 2.092968 TGCTGTGGTTCTCAGTGTTTCT 60.093 45.455 0.00 0.00 35.60 2.52
327 328 2.032178 GTGCTGTGGTTCTCAGTGTTTC 59.968 50.000 0.00 0.00 35.60 2.78
328 329 2.017049 GTGCTGTGGTTCTCAGTGTTT 58.983 47.619 0.00 0.00 35.60 2.83
329 330 1.668419 GTGCTGTGGTTCTCAGTGTT 58.332 50.000 0.00 0.00 35.60 3.32
330 331 0.530650 CGTGCTGTGGTTCTCAGTGT 60.531 55.000 0.00 0.00 35.60 3.55
331 332 0.249447 TCGTGCTGTGGTTCTCAGTG 60.249 55.000 0.00 0.00 35.60 3.66
332 333 0.464036 TTCGTGCTGTGGTTCTCAGT 59.536 50.000 0.00 0.00 35.60 3.41
333 334 1.581934 TTTCGTGCTGTGGTTCTCAG 58.418 50.000 0.00 0.00 36.18 3.35
334 335 1.668751 GTTTTCGTGCTGTGGTTCTCA 59.331 47.619 0.00 0.00 0.00 3.27
335 336 1.668751 TGTTTTCGTGCTGTGGTTCTC 59.331 47.619 0.00 0.00 0.00 2.87
336 337 1.745232 TGTTTTCGTGCTGTGGTTCT 58.255 45.000 0.00 0.00 0.00 3.01
337 338 2.032799 TCATGTTTTCGTGCTGTGGTTC 59.967 45.455 0.00 0.00 36.81 3.62
338 339 2.020720 TCATGTTTTCGTGCTGTGGTT 58.979 42.857 0.00 0.00 36.81 3.67
339 340 1.674359 TCATGTTTTCGTGCTGTGGT 58.326 45.000 0.00 0.00 36.81 4.16
340 341 2.384382 GTTCATGTTTTCGTGCTGTGG 58.616 47.619 0.00 0.00 36.81 4.17
341 342 2.223456 TGGTTCATGTTTTCGTGCTGTG 60.223 45.455 0.00 0.00 36.81 3.66
342 343 2.020720 TGGTTCATGTTTTCGTGCTGT 58.979 42.857 0.00 0.00 36.81 4.40
343 344 2.290367 TCTGGTTCATGTTTTCGTGCTG 59.710 45.455 0.00 0.00 36.81 4.41
344 345 2.571212 TCTGGTTCATGTTTTCGTGCT 58.429 42.857 0.00 0.00 36.81 4.40
345 346 3.300009 CTTCTGGTTCATGTTTTCGTGC 58.700 45.455 0.00 0.00 36.81 5.34
346 347 3.304659 CCCTTCTGGTTCATGTTTTCGTG 60.305 47.826 0.00 0.00 38.10 4.35
347 348 2.884639 CCCTTCTGGTTCATGTTTTCGT 59.115 45.455 0.00 0.00 0.00 3.85
348 349 3.146066 TCCCTTCTGGTTCATGTTTTCG 58.854 45.455 0.00 0.00 34.77 3.46
349 350 5.529581 TTTCCCTTCTGGTTCATGTTTTC 57.470 39.130 0.00 0.00 34.77 2.29
380 382 1.584495 GCGGGCTCAATCGGTTTTT 59.416 52.632 0.00 0.00 0.00 1.94
424 426 2.187685 CTATGCCACTGCTCGCCA 59.812 61.111 0.00 0.00 38.71 5.69
434 436 1.321805 AAGCCGCAAATGCTATGCCA 61.322 50.000 3.63 0.00 40.72 4.92
436 438 0.872881 CCAAGCCGCAAATGCTATGC 60.873 55.000 3.63 3.87 38.34 3.14
437 439 0.872881 GCCAAGCCGCAAATGCTATG 60.873 55.000 3.63 0.00 38.34 2.23
438 440 1.438814 GCCAAGCCGCAAATGCTAT 59.561 52.632 3.63 0.00 38.34 2.97
439 441 2.709883 GGCCAAGCCGCAAATGCTA 61.710 57.895 0.00 0.00 39.62 3.49
440 442 4.073200 GGCCAAGCCGCAAATGCT 62.073 61.111 0.00 0.00 39.62 3.79
466 468 4.342092 GGAATGATCGGATTTGGGTCATTT 59.658 41.667 2.22 0.00 39.03 2.32
467 469 3.891366 GGAATGATCGGATTTGGGTCATT 59.109 43.478 0.25 0.25 40.94 2.57
702 711 3.640967 AGATCTATCTGGACAGAACTGGC 59.359 47.826 6.06 2.80 41.36 4.85
879 920 2.162809 ACGAATTCGGCCAATTTACCAC 59.837 45.455 29.79 0.00 44.95 4.16
890 931 0.940126 ATCAGATGCACGAATTCGGC 59.060 50.000 29.79 27.10 44.95 5.54
900 941 2.306805 AGAGGACAACCAATCAGATGCA 59.693 45.455 0.00 0.00 38.94 3.96
913 957 0.894141 GCAGAGAGCAGAGAGGACAA 59.106 55.000 0.00 0.00 44.79 3.18
966 1010 1.260561 AGAAATCGTTGTGTGCACGAC 59.739 47.619 13.13 11.94 41.27 4.34
972 1016 5.678483 CACTTGAAGAAGAAATCGTTGTGTG 59.322 40.000 0.00 0.00 32.98 3.82
1017 1061 2.093658 TCATCTGTCGCCCCTTTCTAAC 60.094 50.000 0.00 0.00 0.00 2.34
1030 1074 2.794981 GCATGCTGCACAATCATCTGTC 60.795 50.000 11.37 0.00 44.26 3.51
1051 1095 4.323417 TGGTTACAAACACAGCATCTAGG 58.677 43.478 0.00 0.00 0.00 3.02
1059 1103 5.751243 AACTAAGCTGGTTACAAACACAG 57.249 39.130 3.86 0.00 34.70 3.66
1067 1111 3.831715 CCTGCAAACTAAGCTGGTTAC 57.168 47.619 5.88 3.36 43.59 2.50
1074 1118 2.128771 TGGGATCCTGCAAACTAAGC 57.871 50.000 12.58 0.00 0.00 3.09
1079 1123 0.251787 ACCCTTGGGATCCTGCAAAC 60.252 55.000 12.58 0.00 0.00 2.93
1220 1265 8.004801 TCAGACCTGGAGAATCACACTATAATA 58.995 37.037 0.00 0.00 36.25 0.98
1376 1421 9.282247 CAACATTTGCAAGAAGTAATGAGTATC 57.718 33.333 12.32 0.00 33.39 2.24
1380 1425 7.274904 CCATCAACATTTGCAAGAAGTAATGAG 59.725 37.037 12.32 5.78 33.39 2.90
1390 1435 2.564062 AGGACCCATCAACATTTGCAAG 59.436 45.455 0.00 0.00 0.00 4.01
1398 1443 3.591527 AGAATTACCAGGACCCATCAACA 59.408 43.478 0.00 0.00 0.00 3.33
1399 1444 4.200092 GAGAATTACCAGGACCCATCAAC 58.800 47.826 0.00 0.00 0.00 3.18
1563 1608 3.620488 TGCCAGTTTCTTGTCTTTCAGT 58.380 40.909 0.00 0.00 0.00 3.41
1771 1817 2.880890 CAGCATAATAGGGCACTGTTCC 59.119 50.000 0.00 0.00 30.22 3.62
1800 1846 1.408702 ACAACTGCAACACCATCAACC 59.591 47.619 0.00 0.00 0.00 3.77
1802 1848 5.767665 AGTATTACAACTGCAACACCATCAA 59.232 36.000 0.00 0.00 0.00 2.57
1808 1854 5.869888 AGCTAGAGTATTACAACTGCAACAC 59.130 40.000 0.00 0.00 0.00 3.32
1891 1937 4.022416 GGACAATGGTGATTAGTGCAAACA 60.022 41.667 0.00 0.00 0.00 2.83
1964 2010 4.808077 CTGCATAGACCAGCATTAACTG 57.192 45.455 0.00 0.00 40.42 3.16
2075 2121 9.713740 GATCTTTTACATCACATGATTTCAGAC 57.286 33.333 0.00 0.00 31.21 3.51
2112 2158 7.639062 ATCCTATTCAACTCCAGGATGTAAT 57.361 36.000 1.24 0.00 44.44 1.89
2236 2285 3.745975 TCCAATCTTACAAAGCAGTGACG 59.254 43.478 0.00 0.00 0.00 4.35
2452 2520 4.843147 TGTAACAGAACGTTGAGCAATTG 58.157 39.130 5.00 0.00 38.63 2.32
2465 2533 6.345096 TGACAGAGATCACATGTAACAGAA 57.655 37.500 0.00 0.00 0.00 3.02
2499 2567 5.957771 ACAGATGAGGTAAAAGCCTGATA 57.042 39.130 0.00 0.00 39.34 2.15
2513 2581 8.994429 ATACTCTAGTTGAAACAACAGATGAG 57.006 34.615 15.29 15.73 0.00 2.90
2546 2614 8.329502 GCTACTCCCCAAATATACTGGAATAAT 58.670 37.037 5.50 0.00 35.85 1.28
2639 2708 3.857010 GCATGTTTCCAACTAAGTGCACC 60.857 47.826 14.63 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.