Multiple sequence alignment - TraesCS4B01G215700

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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 TraesCS4B01G215700 chr4B 100.000 3686 0 0 1 3686 455366459 455362774 0.000000e+00 6807.0
1 TraesCS4B01G215700 chr4D 96.353 3044 86 11 647 3686 370304208 370301186 0.000000e+00 4983.0
2 TraesCS4B01G215700 chr4D 86.061 165 7 9 518 672 370304374 370304216 2.950000e-36 163.0
3 TraesCS4B01G215700 chr4A 95.553 3036 101 18 647 3680 93979819 93982822 0.000000e+00 4828.0
4 TraesCS4B01G215700 chr4A 87.179 156 14 6 518 668 93979656 93979810 4.890000e-39 172.0
5 TraesCS4B01G215700 chr3B 82.266 203 26 9 3420 3618 31061190 31061386 2.280000e-37 167.0
6 TraesCS4B01G215700 chr3B 78.341 217 39 7 3423 3634 803649559 803649772 2.310000e-27 134.0
7 TraesCS4B01G215700 chr6D 92.857 98 7 0 2728 2825 69940705 69940802 3.840000e-30 143.0
8 TraesCS4B01G215700 chr6B 91.837 98 8 0 2728 2825 144959318 144959415 1.790000e-28 137.0
9 TraesCS4B01G215700 chr1B 78.889 180 29 7 3470 3648 354236667 354236496 3.010000e-21 113.0
10 TraesCS4B01G215700 chr5B 77.340 203 34 11 3469 3663 564529343 564529541 3.890000e-20 110.0
11 TraesCS4B01G215700 chr5A 81.061 132 17 7 3493 3618 579917523 579917652 8.420000e-17 99.0
12 TraesCS4B01G215700 chr5A 80.153 131 22 3 3500 3626 597308575 597308705 1.090000e-15 95.3
13 TraesCS4B01G215700 chr7B 78.462 130 21 3 3526 3653 51044561 51044685 1.100000e-10 78.7


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 TraesCS4B01G215700 chr4B 455362774 455366459 3685 True 6807 6807 100.000 1 3686 1 chr4B.!!$R1 3685
1 TraesCS4B01G215700 chr4D 370301186 370304374 3188 True 2573 4983 91.207 518 3686 2 chr4D.!!$R1 3168
2 TraesCS4B01G215700 chr4A 93979656 93982822 3166 False 2500 4828 91.366 518 3680 2 chr4A.!!$F1 3162

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
302 303 0.039978 CATAGCAGCCGACCGAGTAG 60.040 60.0 0.0 0.0 0.00 2.57 F
509 510 0.250989 TGGATGACGTGGGGTTTTCC 60.251 55.0 0.0 0.0 39.75 3.13 F
510 511 0.250989 GGATGACGTGGGGTTTTCCA 60.251 55.0 0.0 0.0 42.91 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1620 1700 0.379669 GCATCTGGAATGCCGTCAAG 59.620 55.000 0.00 0.0 39.01 3.02 R
1902 1982 4.996434 GGCTGCCCGATGGATCCG 62.996 72.222 7.66 0.0 0.00 4.18 R
2702 2782 4.002906 TGATCGACTAAGCAAAACCTGT 57.997 40.909 0.00 0.0 0.00 4.00 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.805267 CACGCAGGAGCCAGAATC 58.195 61.111 0.00 0.00 37.52 2.52
18 19 1.078918 CACGCAGGAGCCAGAATCA 60.079 57.895 0.00 0.00 37.52 2.57
19 20 1.078848 ACGCAGGAGCCAGAATCAC 60.079 57.895 0.00 0.00 37.52 3.06
20 21 1.078918 CGCAGGAGCCAGAATCACA 60.079 57.895 0.00 0.00 37.52 3.58
21 22 1.088340 CGCAGGAGCCAGAATCACAG 61.088 60.000 0.00 0.00 37.52 3.66
22 23 1.375098 GCAGGAGCCAGAATCACAGC 61.375 60.000 0.00 0.00 33.58 4.40
23 24 0.252479 CAGGAGCCAGAATCACAGCT 59.748 55.000 0.00 0.00 38.56 4.24
25 26 2.675519 GAGCCAGAATCACAGCTCG 58.324 57.895 3.99 0.00 42.02 5.03
26 27 0.108424 GAGCCAGAATCACAGCTCGT 60.108 55.000 3.99 0.00 42.02 4.18
27 28 1.135139 GAGCCAGAATCACAGCTCGTA 59.865 52.381 3.99 0.00 42.02 3.43
28 29 1.135915 AGCCAGAATCACAGCTCGTAG 59.864 52.381 0.00 0.00 0.00 3.51
29 30 1.804372 GCCAGAATCACAGCTCGTAGG 60.804 57.143 0.00 0.00 0.00 3.18
30 31 1.751351 CCAGAATCACAGCTCGTAGGA 59.249 52.381 0.00 0.00 0.00 2.94
31 32 2.223688 CCAGAATCACAGCTCGTAGGAG 60.224 54.545 8.10 8.10 43.46 3.69
32 33 2.685388 CAGAATCACAGCTCGTAGGAGA 59.315 50.000 16.47 0.00 43.27 3.71
33 34 3.317711 CAGAATCACAGCTCGTAGGAGAT 59.682 47.826 16.47 7.03 43.27 2.75
37 38 4.244326 AGCTCGTAGGAGATGCGT 57.756 55.556 16.47 0.00 43.27 5.24
38 39 2.494677 AGCTCGTAGGAGATGCGTT 58.505 52.632 16.47 0.00 43.27 4.84
39 40 0.101399 AGCTCGTAGGAGATGCGTTG 59.899 55.000 16.47 0.00 43.27 4.10
40 41 0.872021 GCTCGTAGGAGATGCGTTGG 60.872 60.000 16.47 0.00 43.27 3.77
41 42 0.249073 CTCGTAGGAGATGCGTTGGG 60.249 60.000 6.59 0.00 43.27 4.12
42 43 1.227263 CGTAGGAGATGCGTTGGGG 60.227 63.158 0.00 0.00 31.68 4.96
43 44 1.672854 CGTAGGAGATGCGTTGGGGA 61.673 60.000 0.00 0.00 31.68 4.81
44 45 0.179081 GTAGGAGATGCGTTGGGGAC 60.179 60.000 0.00 0.00 0.00 4.46
53 54 4.452733 GTTGGGGACGAGGAGCGG 62.453 72.222 0.00 0.00 46.49 5.52
59 60 4.803426 GACGAGGAGCGGCCAGTG 62.803 72.222 2.24 0.00 44.13 3.66
100 101 3.849951 CAGGTCGGCCGCCACTAT 61.850 66.667 31.19 14.53 40.50 2.12
101 102 3.537874 AGGTCGGCCGCCACTATC 61.538 66.667 31.19 12.96 40.50 2.08
102 103 4.603946 GGTCGGCCGCCACTATCC 62.604 72.222 27.01 14.18 0.00 2.59
103 104 3.845259 GTCGGCCGCCACTATCCA 61.845 66.667 23.51 0.00 0.00 3.41
104 105 3.078196 TCGGCCGCCACTATCCAA 61.078 61.111 23.51 0.00 0.00 3.53
105 106 2.588877 CGGCCGCCACTATCCAAG 60.589 66.667 14.67 0.00 0.00 3.61
106 107 2.203209 GGCCGCCACTATCCAAGG 60.203 66.667 3.91 0.00 0.00 3.61
107 108 2.203209 GCCGCCACTATCCAAGGG 60.203 66.667 0.00 0.00 0.00 3.95
108 109 2.203209 CCGCCACTATCCAAGGGC 60.203 66.667 0.00 0.00 37.88 5.19
109 110 2.203209 CGCCACTATCCAAGGGCC 60.203 66.667 0.00 0.00 37.94 5.80
110 111 2.746375 CGCCACTATCCAAGGGCCT 61.746 63.158 0.00 0.00 37.94 5.19
111 112 1.149401 GCCACTATCCAAGGGCCTC 59.851 63.158 6.46 0.00 36.22 4.70
112 113 1.635817 GCCACTATCCAAGGGCCTCA 61.636 60.000 6.46 0.00 36.22 3.86
113 114 0.918983 CCACTATCCAAGGGCCTCAA 59.081 55.000 6.46 0.00 0.00 3.02
114 115 1.133976 CCACTATCCAAGGGCCTCAAG 60.134 57.143 6.46 2.65 0.00 3.02
115 116 0.548510 ACTATCCAAGGGCCTCAAGC 59.451 55.000 6.46 0.00 42.60 4.01
124 125 2.825836 GCCTCAAGCCCGTCCATG 60.826 66.667 0.00 0.00 34.35 3.66
125 126 2.989639 CCTCAAGCCCGTCCATGA 59.010 61.111 0.00 0.00 0.00 3.07
126 127 1.450312 CCTCAAGCCCGTCCATGAC 60.450 63.158 0.00 0.00 0.00 3.06
127 128 1.450312 CTCAAGCCCGTCCATGACC 60.450 63.158 0.00 0.00 0.00 4.02
128 129 2.184020 CTCAAGCCCGTCCATGACCA 62.184 60.000 0.00 0.00 0.00 4.02
129 130 1.303236 CAAGCCCGTCCATGACCAA 60.303 57.895 0.00 0.00 0.00 3.67
130 131 1.303317 AAGCCCGTCCATGACCAAC 60.303 57.895 0.00 0.00 0.00 3.77
131 132 2.033448 GCCCGTCCATGACCAACA 59.967 61.111 0.00 0.00 0.00 3.33
132 133 2.040544 GCCCGTCCATGACCAACAG 61.041 63.158 0.00 0.00 0.00 3.16
133 134 1.374947 CCCGTCCATGACCAACAGT 59.625 57.895 0.00 0.00 0.00 3.55
134 135 0.611200 CCCGTCCATGACCAACAGTA 59.389 55.000 0.00 0.00 0.00 2.74
135 136 1.405526 CCCGTCCATGACCAACAGTAG 60.406 57.143 0.00 0.00 0.00 2.57
136 137 1.548719 CCGTCCATGACCAACAGTAGA 59.451 52.381 0.00 0.00 0.00 2.59
137 138 2.028476 CCGTCCATGACCAACAGTAGAA 60.028 50.000 0.00 0.00 0.00 2.10
138 139 3.254060 CGTCCATGACCAACAGTAGAAG 58.746 50.000 0.00 0.00 0.00 2.85
139 140 3.056821 CGTCCATGACCAACAGTAGAAGA 60.057 47.826 0.00 0.00 0.00 2.87
140 141 4.499183 GTCCATGACCAACAGTAGAAGAG 58.501 47.826 0.00 0.00 0.00 2.85
141 142 3.055819 TCCATGACCAACAGTAGAAGAGC 60.056 47.826 0.00 0.00 0.00 4.09
142 143 2.724977 TGACCAACAGTAGAAGAGCG 57.275 50.000 0.00 0.00 0.00 5.03
143 144 1.961394 TGACCAACAGTAGAAGAGCGT 59.039 47.619 0.00 0.00 0.00 5.07
144 145 2.364324 TGACCAACAGTAGAAGAGCGTT 59.636 45.455 0.00 0.00 0.00 4.84
145 146 2.987821 GACCAACAGTAGAAGAGCGTTC 59.012 50.000 0.00 0.00 0.00 3.95
146 147 2.288886 ACCAACAGTAGAAGAGCGTTCC 60.289 50.000 0.00 0.00 0.00 3.62
147 148 1.986378 CAACAGTAGAAGAGCGTTCCG 59.014 52.381 0.00 0.00 0.00 4.30
148 149 1.245732 ACAGTAGAAGAGCGTTCCGT 58.754 50.000 0.00 0.00 0.00 4.69
149 150 1.612463 ACAGTAGAAGAGCGTTCCGTT 59.388 47.619 0.00 0.00 0.00 4.44
150 151 1.986378 CAGTAGAAGAGCGTTCCGTTG 59.014 52.381 0.00 0.00 0.00 4.10
151 152 1.067776 AGTAGAAGAGCGTTCCGTTGG 60.068 52.381 0.00 0.00 0.00 3.77
152 153 0.245539 TAGAAGAGCGTTCCGTTGGG 59.754 55.000 0.00 0.00 0.00 4.12
153 154 2.032071 AAGAGCGTTCCGTTGGGG 59.968 61.111 0.00 0.00 37.02 4.96
154 155 3.546714 AAGAGCGTTCCGTTGGGGG 62.547 63.158 0.00 0.00 36.01 5.40
179 180 3.089874 AGGCGGGCCTCTAATGCA 61.090 61.111 6.34 0.00 44.43 3.96
180 181 2.113986 GGCGGGCCTCTAATGCAT 59.886 61.111 0.84 0.00 0.00 3.96
181 182 1.968540 GGCGGGCCTCTAATGCATC 60.969 63.158 0.84 0.00 0.00 3.91
182 183 1.227943 GCGGGCCTCTAATGCATCA 60.228 57.895 0.84 0.00 0.00 3.07
183 184 0.819259 GCGGGCCTCTAATGCATCAA 60.819 55.000 0.84 0.00 0.00 2.57
184 185 1.233019 CGGGCCTCTAATGCATCAAG 58.767 55.000 0.84 0.60 0.00 3.02
185 186 0.957362 GGGCCTCTAATGCATCAAGC 59.043 55.000 0.84 0.00 45.96 4.01
195 196 3.573569 GCATCAAGCAGCAACAACA 57.426 47.368 0.00 0.00 44.79 3.33
196 197 1.415374 GCATCAAGCAGCAACAACAG 58.585 50.000 0.00 0.00 44.79 3.16
197 198 1.001048 GCATCAAGCAGCAACAACAGA 60.001 47.619 0.00 0.00 44.79 3.41
198 199 2.921069 GCATCAAGCAGCAACAACAGAG 60.921 50.000 0.00 0.00 44.79 3.35
199 200 1.311859 TCAAGCAGCAACAACAGAGG 58.688 50.000 0.00 0.00 0.00 3.69
200 201 1.134128 TCAAGCAGCAACAACAGAGGA 60.134 47.619 0.00 0.00 0.00 3.71
201 202 1.266175 CAAGCAGCAACAACAGAGGAG 59.734 52.381 0.00 0.00 0.00 3.69
202 203 0.471617 AGCAGCAACAACAGAGGAGT 59.528 50.000 0.00 0.00 0.00 3.85
203 204 1.133976 AGCAGCAACAACAGAGGAGTT 60.134 47.619 0.00 0.00 0.00 3.01
210 211 2.509052 CAACAGAGGAGTTGTGTCGA 57.491 50.000 0.00 0.00 42.93 4.20
211 212 3.032017 CAACAGAGGAGTTGTGTCGAT 57.968 47.619 0.00 0.00 42.93 3.59
212 213 3.393800 CAACAGAGGAGTTGTGTCGATT 58.606 45.455 0.00 0.00 42.93 3.34
213 214 3.032017 ACAGAGGAGTTGTGTCGATTG 57.968 47.619 0.00 0.00 0.00 2.67
214 215 2.289072 ACAGAGGAGTTGTGTCGATTGG 60.289 50.000 0.00 0.00 0.00 3.16
215 216 2.029020 CAGAGGAGTTGTGTCGATTGGA 60.029 50.000 0.00 0.00 0.00 3.53
216 217 2.632996 AGAGGAGTTGTGTCGATTGGAA 59.367 45.455 0.00 0.00 0.00 3.53
217 218 2.996621 GAGGAGTTGTGTCGATTGGAAG 59.003 50.000 0.00 0.00 0.00 3.46
218 219 2.076863 GGAGTTGTGTCGATTGGAAGG 58.923 52.381 0.00 0.00 0.00 3.46
219 220 2.076863 GAGTTGTGTCGATTGGAAGGG 58.923 52.381 0.00 0.00 0.00 3.95
220 221 1.420138 AGTTGTGTCGATTGGAAGGGT 59.580 47.619 0.00 0.00 0.00 4.34
221 222 2.635915 AGTTGTGTCGATTGGAAGGGTA 59.364 45.455 0.00 0.00 0.00 3.69
222 223 3.000727 GTTGTGTCGATTGGAAGGGTAG 58.999 50.000 0.00 0.00 0.00 3.18
223 224 1.553248 TGTGTCGATTGGAAGGGTAGG 59.447 52.381 0.00 0.00 0.00 3.18
224 225 1.829222 GTGTCGATTGGAAGGGTAGGA 59.171 52.381 0.00 0.00 0.00 2.94
225 226 2.108168 TGTCGATTGGAAGGGTAGGAG 58.892 52.381 0.00 0.00 0.00 3.69
226 227 1.413077 GTCGATTGGAAGGGTAGGAGG 59.587 57.143 0.00 0.00 0.00 4.30
227 228 0.106894 CGATTGGAAGGGTAGGAGGC 59.893 60.000 0.00 0.00 0.00 4.70
228 229 0.106894 GATTGGAAGGGTAGGAGGCG 59.893 60.000 0.00 0.00 0.00 5.52
229 230 1.345715 ATTGGAAGGGTAGGAGGCGG 61.346 60.000 0.00 0.00 0.00 6.13
230 231 2.365237 GGAAGGGTAGGAGGCGGT 60.365 66.667 0.00 0.00 0.00 5.68
231 232 2.732619 GGAAGGGTAGGAGGCGGTG 61.733 68.421 0.00 0.00 0.00 4.94
232 233 2.687566 AAGGGTAGGAGGCGGTGG 60.688 66.667 0.00 0.00 0.00 4.61
233 234 3.248248 AAGGGTAGGAGGCGGTGGA 62.248 63.158 0.00 0.00 0.00 4.02
234 235 3.155167 GGGTAGGAGGCGGTGGAG 61.155 72.222 0.00 0.00 0.00 3.86
235 236 3.155167 GGTAGGAGGCGGTGGAGG 61.155 72.222 0.00 0.00 0.00 4.30
236 237 3.155167 GTAGGAGGCGGTGGAGGG 61.155 72.222 0.00 0.00 0.00 4.30
237 238 3.352748 TAGGAGGCGGTGGAGGGA 61.353 66.667 0.00 0.00 0.00 4.20
238 239 2.711899 TAGGAGGCGGTGGAGGGAT 61.712 63.158 0.00 0.00 0.00 3.85
239 240 2.946988 TAGGAGGCGGTGGAGGGATG 62.947 65.000 0.00 0.00 0.00 3.51
240 241 2.764128 GAGGCGGTGGAGGGATGA 60.764 66.667 0.00 0.00 0.00 2.92
241 242 2.765807 AGGCGGTGGAGGGATGAG 60.766 66.667 0.00 0.00 0.00 2.90
242 243 4.554036 GGCGGTGGAGGGATGAGC 62.554 72.222 0.00 0.00 0.00 4.26
243 244 3.785859 GCGGTGGAGGGATGAGCA 61.786 66.667 0.00 0.00 0.00 4.26
244 245 2.503061 CGGTGGAGGGATGAGCAG 59.497 66.667 0.00 0.00 0.00 4.24
245 246 2.914289 GGTGGAGGGATGAGCAGG 59.086 66.667 0.00 0.00 0.00 4.85
246 247 2.191641 GTGGAGGGATGAGCAGGC 59.808 66.667 0.00 0.00 0.00 4.85
247 248 3.092511 TGGAGGGATGAGCAGGCC 61.093 66.667 0.00 0.00 0.00 5.19
248 249 3.092511 GGAGGGATGAGCAGGCCA 61.093 66.667 5.01 0.00 0.00 5.36
249 250 2.509916 GAGGGATGAGCAGGCCAG 59.490 66.667 5.01 0.00 0.00 4.85
250 251 2.041762 AGGGATGAGCAGGCCAGA 59.958 61.111 5.01 0.00 0.00 3.86
251 252 2.191641 GGGATGAGCAGGCCAGAC 59.808 66.667 5.01 0.00 0.00 3.51
252 253 2.191641 GGATGAGCAGGCCAGACC 59.808 66.667 5.01 0.00 39.61 3.85
253 254 2.191641 GATGAGCAGGCCAGACCC 59.808 66.667 5.01 0.00 40.58 4.46
254 255 3.746949 GATGAGCAGGCCAGACCCG 62.747 68.421 5.01 0.00 40.58 5.28
256 257 4.767255 GAGCAGGCCAGACCCGTG 62.767 72.222 5.01 0.00 40.58 4.94
259 260 4.742201 CAGGCCAGACCCGTGTCG 62.742 72.222 5.01 0.00 46.51 4.35
280 281 3.777925 CGCCGAGCCGACAAAGTG 61.778 66.667 0.00 0.00 0.00 3.16
281 282 3.423154 GCCGAGCCGACAAAGTGG 61.423 66.667 0.00 0.00 0.00 4.00
282 283 2.342279 CCGAGCCGACAAAGTGGA 59.658 61.111 0.00 0.00 0.00 4.02
283 284 2.027625 CCGAGCCGACAAAGTGGAC 61.028 63.158 0.00 0.00 0.00 4.02
284 285 1.300620 CGAGCCGACAAAGTGGACA 60.301 57.895 0.00 0.00 0.00 4.02
285 286 0.670546 CGAGCCGACAAAGTGGACAT 60.671 55.000 0.00 0.00 0.00 3.06
286 287 1.403647 CGAGCCGACAAAGTGGACATA 60.404 52.381 0.00 0.00 0.00 2.29
287 288 2.271800 GAGCCGACAAAGTGGACATAG 58.728 52.381 0.00 0.00 0.00 2.23
288 289 0.727398 GCCGACAAAGTGGACATAGC 59.273 55.000 0.00 0.00 0.00 2.97
289 290 1.943968 GCCGACAAAGTGGACATAGCA 60.944 52.381 0.00 0.00 0.00 3.49
290 291 2.002586 CCGACAAAGTGGACATAGCAG 58.997 52.381 0.00 0.00 0.00 4.24
291 292 1.394917 CGACAAAGTGGACATAGCAGC 59.605 52.381 0.00 0.00 0.00 5.25
292 293 1.740025 GACAAAGTGGACATAGCAGCC 59.260 52.381 0.00 0.00 0.00 4.85
293 294 0.729116 CAAAGTGGACATAGCAGCCG 59.271 55.000 0.00 0.00 0.00 5.52
294 295 0.613260 AAAGTGGACATAGCAGCCGA 59.387 50.000 0.00 0.00 0.00 5.54
295 296 0.108138 AAGTGGACATAGCAGCCGAC 60.108 55.000 0.00 0.00 0.00 4.79
296 297 1.521681 GTGGACATAGCAGCCGACC 60.522 63.158 0.00 0.00 0.00 4.79
297 298 2.279517 GGACATAGCAGCCGACCG 60.280 66.667 0.00 0.00 0.00 4.79
298 299 2.782222 GGACATAGCAGCCGACCGA 61.782 63.158 0.00 0.00 0.00 4.69
299 300 1.299468 GACATAGCAGCCGACCGAG 60.299 63.158 0.00 0.00 0.00 4.63
300 301 2.005960 GACATAGCAGCCGACCGAGT 62.006 60.000 0.00 0.00 0.00 4.18
301 302 0.750546 ACATAGCAGCCGACCGAGTA 60.751 55.000 0.00 0.00 0.00 2.59
302 303 0.039978 CATAGCAGCCGACCGAGTAG 60.040 60.000 0.00 0.00 0.00 2.57
314 315 2.065993 CCGAGTAGGTGACACACAAG 57.934 55.000 8.08 0.00 35.86 3.16
315 316 1.611977 CCGAGTAGGTGACACACAAGA 59.388 52.381 8.08 0.00 35.86 3.02
316 317 2.231478 CCGAGTAGGTGACACACAAGAT 59.769 50.000 8.08 0.00 35.86 2.40
317 318 3.502920 CGAGTAGGTGACACACAAGATC 58.497 50.000 8.08 0.00 35.86 2.75
318 319 3.673594 CGAGTAGGTGACACACAAGATCC 60.674 52.174 8.08 0.00 35.86 3.36
319 320 2.231478 AGTAGGTGACACACAAGATCCG 59.769 50.000 8.08 0.00 35.86 4.18
320 321 1.338107 AGGTGACACACAAGATCCGA 58.662 50.000 8.08 0.00 35.86 4.55
321 322 1.902508 AGGTGACACACAAGATCCGAT 59.097 47.619 8.08 0.00 35.86 4.18
322 323 2.303022 AGGTGACACACAAGATCCGATT 59.697 45.455 8.08 0.00 35.86 3.34
323 324 2.416547 GGTGACACACAAGATCCGATTG 59.583 50.000 8.08 0.00 35.86 2.67
324 325 2.416547 GTGACACACAAGATCCGATTGG 59.583 50.000 0.00 0.00 34.08 3.16
325 326 2.009774 GACACACAAGATCCGATTGGG 58.990 52.381 0.00 0.00 37.09 4.12
326 327 6.893308 GTGACACACAAGATCCGATTGGGA 62.893 50.000 0.00 0.00 40.97 4.37
380 381 3.661648 GCCCCACCACCACCATCT 61.662 66.667 0.00 0.00 0.00 2.90
381 382 2.677228 CCCCACCACCACCATCTC 59.323 66.667 0.00 0.00 0.00 2.75
382 383 2.268920 CCCACCACCACCATCTCG 59.731 66.667 0.00 0.00 0.00 4.04
383 384 2.268920 CCACCACCACCATCTCGG 59.731 66.667 0.00 0.00 42.50 4.63
384 385 2.268920 CACCACCACCATCTCGGG 59.731 66.667 0.00 0.00 40.22 5.14
385 386 3.009115 ACCACCACCATCTCGGGG 61.009 66.667 0.00 0.00 40.22 5.73
386 387 4.489771 CCACCACCATCTCGGGGC 62.490 72.222 0.00 0.00 36.51 5.80
387 388 3.716195 CACCACCATCTCGGGGCA 61.716 66.667 0.00 0.00 36.51 5.36
388 389 3.717294 ACCACCATCTCGGGGCAC 61.717 66.667 0.00 0.00 36.51 5.01
389 390 4.838152 CCACCATCTCGGGGCACG 62.838 72.222 0.68 0.68 46.11 5.34
390 391 4.838152 CACCATCTCGGGGCACGG 62.838 72.222 10.28 0.00 44.45 4.94
392 393 4.838152 CCATCTCGGGGCACGGTG 62.838 72.222 10.28 3.15 44.45 4.94
426 427 4.647615 CCTCCGGCGGCGACATAG 62.648 72.222 34.49 21.82 0.00 2.23
431 432 3.330853 GGCGGCGACATAGCGAAG 61.331 66.667 12.98 0.00 38.18 3.79
432 433 3.330853 GCGGCGACATAGCGAAGG 61.331 66.667 12.98 0.00 38.18 3.46
433 434 2.658593 CGGCGACATAGCGAAGGG 60.659 66.667 0.00 0.00 38.18 3.95
434 435 2.280186 GGCGACATAGCGAAGGGG 60.280 66.667 0.00 0.00 38.18 4.79
435 436 2.280186 GCGACATAGCGAAGGGGG 60.280 66.667 0.00 0.00 0.00 5.40
436 437 3.090219 GCGACATAGCGAAGGGGGT 62.090 63.158 0.00 0.00 0.00 4.95
437 438 1.227263 CGACATAGCGAAGGGGGTG 60.227 63.158 0.00 0.00 0.00 4.61
438 439 1.146263 GACATAGCGAAGGGGGTGG 59.854 63.158 0.00 0.00 0.00 4.61
439 440 2.203209 CATAGCGAAGGGGGTGGC 60.203 66.667 0.00 0.00 0.00 5.01
440 441 3.861797 ATAGCGAAGGGGGTGGCG 61.862 66.667 0.00 0.00 0.00 5.69
445 446 3.787001 GAAGGGGGTGGCGGAGAG 61.787 72.222 0.00 0.00 0.00 3.20
450 451 4.097361 GGGTGGCGGAGAGGGAAC 62.097 72.222 0.00 0.00 0.00 3.62
478 479 4.468689 GCGGCTAGCTTTCCCCGT 62.469 66.667 15.72 0.00 42.54 5.28
479 480 2.511600 CGGCTAGCTTTCCCCGTG 60.512 66.667 15.72 0.00 36.18 4.94
480 481 2.669240 GGCTAGCTTTCCCCGTGT 59.331 61.111 15.72 0.00 0.00 4.49
481 482 1.449778 GGCTAGCTTTCCCCGTGTC 60.450 63.158 15.72 0.00 0.00 3.67
482 483 1.810030 GCTAGCTTTCCCCGTGTCG 60.810 63.158 7.70 0.00 0.00 4.35
483 484 1.810030 CTAGCTTTCCCCGTGTCGC 60.810 63.158 0.00 0.00 0.00 5.19
484 485 3.636313 TAGCTTTCCCCGTGTCGCG 62.636 63.158 0.00 0.00 40.95 5.87
486 487 2.809601 CTTTCCCCGTGTCGCGAG 60.810 66.667 10.24 0.00 44.77 5.03
487 488 3.277211 CTTTCCCCGTGTCGCGAGA 62.277 63.158 10.24 4.94 44.77 4.04
497 498 2.483745 TCGCGAGACGTGGATGAC 59.516 61.111 3.71 0.00 44.19 3.06
505 506 2.345991 CGTGGATGACGTGGGGTT 59.654 61.111 0.00 0.00 43.50 4.11
506 507 1.302192 CGTGGATGACGTGGGGTTT 60.302 57.895 0.00 0.00 43.50 3.27
507 508 0.887387 CGTGGATGACGTGGGGTTTT 60.887 55.000 0.00 0.00 43.50 2.43
508 509 0.879090 GTGGATGACGTGGGGTTTTC 59.121 55.000 0.00 0.00 0.00 2.29
509 510 0.250989 TGGATGACGTGGGGTTTTCC 60.251 55.000 0.00 0.00 39.75 3.13
510 511 0.250989 GGATGACGTGGGGTTTTCCA 60.251 55.000 0.00 0.00 42.91 3.53
551 555 6.949352 TCATTGGCCATTATCTTCTTCTTC 57.051 37.500 6.09 0.00 0.00 2.87
557 561 9.479549 TTGGCCATTATCTTCTTCTTCTTAAAT 57.520 29.630 6.09 0.00 0.00 1.40
605 617 4.035112 ACCAGATTCCCGGTGAGTTATTA 58.965 43.478 0.00 0.00 33.05 0.98
606 618 4.101119 ACCAGATTCCCGGTGAGTTATTAG 59.899 45.833 0.00 0.00 33.05 1.73
612 627 7.553044 AGATTCCCGGTGAGTTATTAGAAAAAG 59.447 37.037 0.00 0.00 0.00 2.27
615 630 6.652062 TCCCGGTGAGTTATTAGAAAAAGAAC 59.348 38.462 0.00 0.00 0.00 3.01
800 880 0.984995 GTTGGGAGGCTAGAACCTGT 59.015 55.000 0.00 0.00 41.32 4.00
810 890 1.203523 CTAGAACCTGTTGCTCGAGCT 59.796 52.381 35.27 15.80 42.66 4.09
1021 1101 1.541310 GGACGTGACCATGGAGGACA 61.541 60.000 21.47 9.97 41.22 4.02
1207 1287 0.460811 GTCCATGCTCTGCGATGACA 60.461 55.000 0.00 0.00 0.00 3.58
1212 1292 0.605083 TGCTCTGCGATGACACTCTT 59.395 50.000 0.00 0.00 0.00 2.85
1272 1352 2.125106 CCCTGCTACTCCAACGCC 60.125 66.667 0.00 0.00 0.00 5.68
1353 1433 0.391130 CGGACTGCAATCCCGAGAAA 60.391 55.000 8.95 0.00 45.58 2.52
1560 1640 0.686441 TAGATGGGTCCCACTCCGTG 60.686 60.000 14.57 0.00 35.80 4.94
2147 2227 0.176910 GAAGGGGAAGCGGAGAAGAG 59.823 60.000 0.00 0.00 0.00 2.85
2702 2782 4.943705 AGTCTGAACTCTGAACTTTGCAAA 59.056 37.500 12.14 12.14 0.00 3.68
2896 2976 1.800805 ACTGATTGGCTTCTGACGTG 58.199 50.000 0.00 0.00 0.00 4.49
3063 3143 2.287248 GCTTGGTGTTCTCACTTGCTTC 60.287 50.000 0.00 0.00 43.41 3.86
3240 3322 9.796062 CACAAGCAACATTATGAATAACAAAAC 57.204 29.630 0.00 0.00 0.00 2.43
3241 3323 9.539825 ACAAGCAACATTATGAATAACAAAACA 57.460 25.926 0.00 0.00 0.00 2.83
3364 3446 8.126700 ACTAATGCATTTTAAATACCGCTGTAC 58.873 33.333 18.75 0.00 0.00 2.90
3378 3460 4.339247 ACCGCTGTACGTAACCTGTATAAT 59.661 41.667 0.00 0.00 41.42 1.28
3409 3491 2.850568 TGAGAAAATCCCCTTCTACCCC 59.149 50.000 0.00 0.00 33.24 4.95
3410 3492 2.175069 GAGAAAATCCCCTTCTACCCCC 59.825 54.545 0.00 0.00 33.24 5.40
3411 3493 0.924090 AAAATCCCCTTCTACCCCCG 59.076 55.000 0.00 0.00 0.00 5.73
3412 3494 0.045162 AAATCCCCTTCTACCCCCGA 59.955 55.000 0.00 0.00 0.00 5.14
3413 3495 0.400093 AATCCCCTTCTACCCCCGAG 60.400 60.000 0.00 0.00 0.00 4.63
3414 3496 2.967063 ATCCCCTTCTACCCCCGAGC 62.967 65.000 0.00 0.00 0.00 5.03
3415 3497 2.041819 CCCTTCTACCCCCGAGCT 60.042 66.667 0.00 0.00 0.00 4.09
3416 3498 2.134933 CCCTTCTACCCCCGAGCTC 61.135 68.421 2.73 2.73 0.00 4.09
3417 3499 1.381327 CCTTCTACCCCCGAGCTCA 60.381 63.158 15.40 0.00 0.00 4.26
3418 3500 0.760945 CCTTCTACCCCCGAGCTCAT 60.761 60.000 15.40 0.00 0.00 2.90
3419 3501 1.123928 CTTCTACCCCCGAGCTCATT 58.876 55.000 15.40 0.00 0.00 2.57
3420 3502 1.486726 CTTCTACCCCCGAGCTCATTT 59.513 52.381 15.40 0.00 0.00 2.32
3421 3503 0.830648 TCTACCCCCGAGCTCATTTG 59.169 55.000 15.40 1.55 0.00 2.32
3544 3626 4.986034 TCTCAGTGCTTGCAAATTTTCATG 59.014 37.500 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.078918 TGATTCTGGCTCCTGCGTG 60.079 57.895 0.00 0.00 40.82 5.34
1 2 1.078848 GTGATTCTGGCTCCTGCGT 60.079 57.895 0.00 0.00 40.82 5.24
2 3 1.078918 TGTGATTCTGGCTCCTGCG 60.079 57.895 0.00 0.00 40.82 5.18
3 4 1.375098 GCTGTGATTCTGGCTCCTGC 61.375 60.000 0.00 0.00 38.76 4.85
4 5 0.252479 AGCTGTGATTCTGGCTCCTG 59.748 55.000 0.00 0.00 0.00 3.86
5 6 0.540923 GAGCTGTGATTCTGGCTCCT 59.459 55.000 0.00 0.00 43.51 3.69
6 7 0.809241 CGAGCTGTGATTCTGGCTCC 60.809 60.000 15.07 0.00 45.62 4.70
7 8 0.108424 ACGAGCTGTGATTCTGGCTC 60.108 55.000 0.00 12.57 45.14 4.70
8 9 1.135915 CTACGAGCTGTGATTCTGGCT 59.864 52.381 0.00 0.00 37.77 4.75
9 10 1.565305 CTACGAGCTGTGATTCTGGC 58.435 55.000 0.00 0.00 0.00 4.85
10 11 1.751351 TCCTACGAGCTGTGATTCTGG 59.249 52.381 0.00 0.00 0.00 3.86
11 12 2.685388 TCTCCTACGAGCTGTGATTCTG 59.315 50.000 0.00 0.00 35.94 3.02
12 13 3.006112 TCTCCTACGAGCTGTGATTCT 57.994 47.619 0.00 0.00 35.94 2.40
13 14 3.637432 CATCTCCTACGAGCTGTGATTC 58.363 50.000 0.00 0.00 35.94 2.52
14 15 2.223923 GCATCTCCTACGAGCTGTGATT 60.224 50.000 0.00 0.00 35.17 2.57
15 16 1.339610 GCATCTCCTACGAGCTGTGAT 59.660 52.381 0.00 0.00 35.17 3.06
16 17 0.741326 GCATCTCCTACGAGCTGTGA 59.259 55.000 0.00 0.00 35.17 3.58
17 18 0.593518 CGCATCTCCTACGAGCTGTG 60.594 60.000 0.00 0.00 36.67 3.66
18 19 1.032657 ACGCATCTCCTACGAGCTGT 61.033 55.000 0.00 0.00 35.17 4.40
19 20 0.101399 AACGCATCTCCTACGAGCTG 59.899 55.000 0.00 0.00 35.70 4.24
20 21 0.101399 CAACGCATCTCCTACGAGCT 59.899 55.000 0.00 0.00 35.94 4.09
21 22 0.872021 CCAACGCATCTCCTACGAGC 60.872 60.000 0.00 0.00 35.94 5.03
22 23 0.249073 CCCAACGCATCTCCTACGAG 60.249 60.000 0.00 0.00 37.48 4.18
23 24 1.672854 CCCCAACGCATCTCCTACGA 61.673 60.000 0.00 0.00 0.00 3.43
24 25 1.227263 CCCCAACGCATCTCCTACG 60.227 63.158 0.00 0.00 0.00 3.51
25 26 0.179081 GTCCCCAACGCATCTCCTAC 60.179 60.000 0.00 0.00 0.00 3.18
26 27 1.672854 CGTCCCCAACGCATCTCCTA 61.673 60.000 0.00 0.00 45.76 2.94
27 28 2.990479 GTCCCCAACGCATCTCCT 59.010 61.111 0.00 0.00 0.00 3.69
28 29 2.511600 CGTCCCCAACGCATCTCC 60.512 66.667 0.00 0.00 45.76 3.71
36 37 4.452733 CCGCTCCTCGTCCCCAAC 62.453 72.222 0.00 0.00 36.19 3.77
42 43 4.803426 CACTGGCCGCTCCTCGTC 62.803 72.222 0.00 0.00 36.19 4.20
83 84 3.792053 GATAGTGGCGGCCGACCTG 62.792 68.421 32.09 0.00 0.00 4.00
84 85 3.537874 GATAGTGGCGGCCGACCT 61.538 66.667 32.09 26.68 0.00 3.85
85 86 4.603946 GGATAGTGGCGGCCGACC 62.604 72.222 32.09 28.28 0.00 4.79
86 87 3.379865 TTGGATAGTGGCGGCCGAC 62.380 63.158 33.48 31.04 0.00 4.79
87 88 3.078196 TTGGATAGTGGCGGCCGA 61.078 61.111 33.48 7.91 0.00 5.54
88 89 2.588877 CTTGGATAGTGGCGGCCG 60.589 66.667 24.05 24.05 0.00 6.13
89 90 2.203209 CCTTGGATAGTGGCGGCC 60.203 66.667 13.32 13.32 0.00 6.13
90 91 2.203209 CCCTTGGATAGTGGCGGC 60.203 66.667 0.00 0.00 0.00 6.53
91 92 2.203209 GCCCTTGGATAGTGGCGG 60.203 66.667 0.00 0.00 32.77 6.13
92 93 2.203209 GGCCCTTGGATAGTGGCG 60.203 66.667 0.00 0.00 39.66 5.69
93 94 1.149401 GAGGCCCTTGGATAGTGGC 59.851 63.158 0.00 0.00 38.66 5.01
94 95 0.918983 TTGAGGCCCTTGGATAGTGG 59.081 55.000 0.00 0.00 0.00 4.00
95 96 1.748591 GCTTGAGGCCCTTGGATAGTG 60.749 57.143 0.00 0.00 34.27 2.74
96 97 0.548510 GCTTGAGGCCCTTGGATAGT 59.451 55.000 0.00 0.00 34.27 2.12
97 98 3.410960 GCTTGAGGCCCTTGGATAG 57.589 57.895 0.00 0.00 34.27 2.08
107 108 2.825836 CATGGACGGGCTTGAGGC 60.826 66.667 0.00 0.00 40.90 4.70
108 109 1.450312 GTCATGGACGGGCTTGAGG 60.450 63.158 0.00 0.00 0.00 3.86
109 110 1.450312 GGTCATGGACGGGCTTGAG 60.450 63.158 0.00 0.00 32.65 3.02
110 111 1.773856 TTGGTCATGGACGGGCTTGA 61.774 55.000 0.00 0.00 32.65 3.02
111 112 1.303236 TTGGTCATGGACGGGCTTG 60.303 57.895 0.00 0.00 32.65 4.01
112 113 1.303317 GTTGGTCATGGACGGGCTT 60.303 57.895 0.00 0.00 32.65 4.35
113 114 2.351276 GTTGGTCATGGACGGGCT 59.649 61.111 0.00 0.00 32.65 5.19
114 115 2.033448 TGTTGGTCATGGACGGGC 59.967 61.111 0.00 0.00 32.65 6.13
115 116 0.611200 TACTGTTGGTCATGGACGGG 59.389 55.000 0.00 0.00 32.65 5.28
116 117 1.548719 TCTACTGTTGGTCATGGACGG 59.451 52.381 0.00 0.00 32.65 4.79
117 118 3.056821 TCTTCTACTGTTGGTCATGGACG 60.057 47.826 0.00 0.00 32.65 4.79
118 119 4.499183 CTCTTCTACTGTTGGTCATGGAC 58.501 47.826 0.00 0.00 0.00 4.02
119 120 3.055819 GCTCTTCTACTGTTGGTCATGGA 60.056 47.826 0.00 0.00 0.00 3.41
120 121 3.265791 GCTCTTCTACTGTTGGTCATGG 58.734 50.000 0.00 0.00 0.00 3.66
121 122 2.926200 CGCTCTTCTACTGTTGGTCATG 59.074 50.000 0.00 0.00 0.00 3.07
122 123 2.563179 ACGCTCTTCTACTGTTGGTCAT 59.437 45.455 0.00 0.00 0.00 3.06
123 124 1.961394 ACGCTCTTCTACTGTTGGTCA 59.039 47.619 0.00 0.00 0.00 4.02
124 125 2.726832 ACGCTCTTCTACTGTTGGTC 57.273 50.000 0.00 0.00 0.00 4.02
125 126 2.288886 GGAACGCTCTTCTACTGTTGGT 60.289 50.000 0.00 0.00 0.00 3.67
126 127 2.338500 GGAACGCTCTTCTACTGTTGG 58.662 52.381 0.00 0.00 0.00 3.77
163 164 1.968540 GATGCATTAGAGGCCCGCC 60.969 63.158 0.00 0.00 0.00 6.13
164 165 0.819259 TTGATGCATTAGAGGCCCGC 60.819 55.000 0.00 0.00 0.00 6.13
165 166 1.233019 CTTGATGCATTAGAGGCCCG 58.767 55.000 0.00 0.00 0.00 6.13
166 167 0.957362 GCTTGATGCATTAGAGGCCC 59.043 55.000 0.00 0.00 42.31 5.80
177 178 1.001048 TCTGTTGTTGCTGCTTGATGC 60.001 47.619 0.00 0.00 43.25 3.91
178 179 2.351447 CCTCTGTTGTTGCTGCTTGATG 60.351 50.000 0.00 0.00 0.00 3.07
179 180 1.884579 CCTCTGTTGTTGCTGCTTGAT 59.115 47.619 0.00 0.00 0.00 2.57
180 181 1.134128 TCCTCTGTTGTTGCTGCTTGA 60.134 47.619 0.00 0.00 0.00 3.02
181 182 1.266175 CTCCTCTGTTGTTGCTGCTTG 59.734 52.381 0.00 0.00 0.00 4.01
182 183 1.133976 ACTCCTCTGTTGTTGCTGCTT 60.134 47.619 0.00 0.00 0.00 3.91
183 184 0.471617 ACTCCTCTGTTGTTGCTGCT 59.528 50.000 0.00 0.00 0.00 4.24
184 185 1.002033 CAACTCCTCTGTTGTTGCTGC 60.002 52.381 0.00 0.00 41.50 5.25
192 193 3.393800 CAATCGACACAACTCCTCTGTT 58.606 45.455 0.00 0.00 0.00 3.16
193 194 2.289072 CCAATCGACACAACTCCTCTGT 60.289 50.000 0.00 0.00 0.00 3.41
194 195 2.029020 TCCAATCGACACAACTCCTCTG 60.029 50.000 0.00 0.00 0.00 3.35
195 196 2.248248 TCCAATCGACACAACTCCTCT 58.752 47.619 0.00 0.00 0.00 3.69
196 197 2.743636 TCCAATCGACACAACTCCTC 57.256 50.000 0.00 0.00 0.00 3.71
197 198 2.289694 CCTTCCAATCGACACAACTCCT 60.290 50.000 0.00 0.00 0.00 3.69
198 199 2.076863 CCTTCCAATCGACACAACTCC 58.923 52.381 0.00 0.00 0.00 3.85
199 200 2.076863 CCCTTCCAATCGACACAACTC 58.923 52.381 0.00 0.00 0.00 3.01
200 201 1.420138 ACCCTTCCAATCGACACAACT 59.580 47.619 0.00 0.00 0.00 3.16
201 202 1.892209 ACCCTTCCAATCGACACAAC 58.108 50.000 0.00 0.00 0.00 3.32
202 203 2.027561 CCTACCCTTCCAATCGACACAA 60.028 50.000 0.00 0.00 0.00 3.33
203 204 1.553248 CCTACCCTTCCAATCGACACA 59.447 52.381 0.00 0.00 0.00 3.72
204 205 1.829222 TCCTACCCTTCCAATCGACAC 59.171 52.381 0.00 0.00 0.00 3.67
205 206 2.108168 CTCCTACCCTTCCAATCGACA 58.892 52.381 0.00 0.00 0.00 4.35
206 207 1.413077 CCTCCTACCCTTCCAATCGAC 59.587 57.143 0.00 0.00 0.00 4.20
207 208 1.789523 CCTCCTACCCTTCCAATCGA 58.210 55.000 0.00 0.00 0.00 3.59
208 209 0.106894 GCCTCCTACCCTTCCAATCG 59.893 60.000 0.00 0.00 0.00 3.34
209 210 0.106894 CGCCTCCTACCCTTCCAATC 59.893 60.000 0.00 0.00 0.00 2.67
210 211 1.345715 CCGCCTCCTACCCTTCCAAT 61.346 60.000 0.00 0.00 0.00 3.16
211 212 1.993391 CCGCCTCCTACCCTTCCAA 60.993 63.158 0.00 0.00 0.00 3.53
212 213 2.365105 CCGCCTCCTACCCTTCCA 60.365 66.667 0.00 0.00 0.00 3.53
213 214 2.365237 ACCGCCTCCTACCCTTCC 60.365 66.667 0.00 0.00 0.00 3.46
214 215 2.732619 CCACCGCCTCCTACCCTTC 61.733 68.421 0.00 0.00 0.00 3.46
215 216 2.687566 CCACCGCCTCCTACCCTT 60.688 66.667 0.00 0.00 0.00 3.95
216 217 3.680196 TCCACCGCCTCCTACCCT 61.680 66.667 0.00 0.00 0.00 4.34
217 218 3.155167 CTCCACCGCCTCCTACCC 61.155 72.222 0.00 0.00 0.00 3.69
218 219 3.155167 CCTCCACCGCCTCCTACC 61.155 72.222 0.00 0.00 0.00 3.18
219 220 2.948801 ATCCCTCCACCGCCTCCTAC 62.949 65.000 0.00 0.00 0.00 3.18
220 221 2.711899 ATCCCTCCACCGCCTCCTA 61.712 63.158 0.00 0.00 0.00 2.94
221 222 4.095400 ATCCCTCCACCGCCTCCT 62.095 66.667 0.00 0.00 0.00 3.69
222 223 3.866582 CATCCCTCCACCGCCTCC 61.867 72.222 0.00 0.00 0.00 4.30
223 224 2.764128 TCATCCCTCCACCGCCTC 60.764 66.667 0.00 0.00 0.00 4.70
224 225 2.765807 CTCATCCCTCCACCGCCT 60.766 66.667 0.00 0.00 0.00 5.52
225 226 4.554036 GCTCATCCCTCCACCGCC 62.554 72.222 0.00 0.00 0.00 6.13
226 227 3.746949 CTGCTCATCCCTCCACCGC 62.747 68.421 0.00 0.00 0.00 5.68
227 228 2.503061 CTGCTCATCCCTCCACCG 59.497 66.667 0.00 0.00 0.00 4.94
228 229 2.914289 CCTGCTCATCCCTCCACC 59.086 66.667 0.00 0.00 0.00 4.61
229 230 2.191641 GCCTGCTCATCCCTCCAC 59.808 66.667 0.00 0.00 0.00 4.02
230 231 3.092511 GGCCTGCTCATCCCTCCA 61.093 66.667 0.00 0.00 0.00 3.86
231 232 3.092511 TGGCCTGCTCATCCCTCC 61.093 66.667 3.32 0.00 0.00 4.30
232 233 2.068821 TCTGGCCTGCTCATCCCTC 61.069 63.158 3.32 0.00 0.00 4.30
233 234 2.041762 TCTGGCCTGCTCATCCCT 59.958 61.111 3.32 0.00 0.00 4.20
234 235 2.191641 GTCTGGCCTGCTCATCCC 59.808 66.667 3.32 0.00 0.00 3.85
235 236 2.191641 GGTCTGGCCTGCTCATCC 59.808 66.667 3.32 0.00 0.00 3.51
236 237 2.191641 GGGTCTGGCCTGCTCATC 59.808 66.667 3.32 0.00 37.43 2.92
237 238 3.790437 CGGGTCTGGCCTGCTCAT 61.790 66.667 3.32 0.00 36.72 2.90
263 264 3.777925 CACTTTGTCGGCTCGGCG 61.778 66.667 0.00 0.00 32.50 6.46
264 265 3.423154 CCACTTTGTCGGCTCGGC 61.423 66.667 0.00 0.00 0.00 5.54
265 266 2.027625 GTCCACTTTGTCGGCTCGG 61.028 63.158 0.00 0.00 0.00 4.63
266 267 0.670546 ATGTCCACTTTGTCGGCTCG 60.671 55.000 0.00 0.00 0.00 5.03
267 268 2.271800 CTATGTCCACTTTGTCGGCTC 58.728 52.381 0.00 0.00 0.00 4.70
268 269 1.676014 GCTATGTCCACTTTGTCGGCT 60.676 52.381 0.00 0.00 0.00 5.52
269 270 0.727398 GCTATGTCCACTTTGTCGGC 59.273 55.000 0.00 0.00 0.00 5.54
270 271 2.002586 CTGCTATGTCCACTTTGTCGG 58.997 52.381 0.00 0.00 0.00 4.79
271 272 1.394917 GCTGCTATGTCCACTTTGTCG 59.605 52.381 0.00 0.00 0.00 4.35
272 273 1.740025 GGCTGCTATGTCCACTTTGTC 59.260 52.381 0.00 0.00 0.00 3.18
273 274 1.826385 GGCTGCTATGTCCACTTTGT 58.174 50.000 0.00 0.00 0.00 2.83
274 275 0.729116 CGGCTGCTATGTCCACTTTG 59.271 55.000 0.00 0.00 0.00 2.77
275 276 0.613260 TCGGCTGCTATGTCCACTTT 59.387 50.000 0.00 0.00 0.00 2.66
276 277 0.108138 GTCGGCTGCTATGTCCACTT 60.108 55.000 0.00 0.00 0.00 3.16
277 278 1.517832 GTCGGCTGCTATGTCCACT 59.482 57.895 0.00 0.00 0.00 4.00
278 279 1.521681 GGTCGGCTGCTATGTCCAC 60.522 63.158 0.00 0.00 0.00 4.02
279 280 2.900273 GGTCGGCTGCTATGTCCA 59.100 61.111 0.00 0.00 0.00 4.02
280 281 2.279517 CGGTCGGCTGCTATGTCC 60.280 66.667 0.00 0.00 0.00 4.02
281 282 1.299468 CTCGGTCGGCTGCTATGTC 60.299 63.158 0.00 0.00 0.00 3.06
282 283 0.750546 TACTCGGTCGGCTGCTATGT 60.751 55.000 0.00 0.00 0.00 2.29
283 284 0.039978 CTACTCGGTCGGCTGCTATG 60.040 60.000 0.00 0.00 0.00 2.23
284 285 1.173444 CCTACTCGGTCGGCTGCTAT 61.173 60.000 0.00 0.00 0.00 2.97
285 286 1.822613 CCTACTCGGTCGGCTGCTA 60.823 63.158 0.00 0.00 0.00 3.49
286 287 3.141488 CCTACTCGGTCGGCTGCT 61.141 66.667 0.00 0.00 0.00 4.24
287 288 3.450115 ACCTACTCGGTCGGCTGC 61.450 66.667 0.00 0.00 44.93 5.25
288 289 2.044555 TCACCTACTCGGTCGGCTG 61.045 63.158 0.00 0.00 44.93 4.85
289 290 2.045131 GTCACCTACTCGGTCGGCT 61.045 63.158 0.00 0.00 44.93 5.52
290 291 2.338015 TGTCACCTACTCGGTCGGC 61.338 63.158 0.00 0.00 44.93 5.54
291 292 1.239296 TGTGTCACCTACTCGGTCGG 61.239 60.000 0.00 0.00 44.93 4.79
292 293 0.109873 GTGTGTCACCTACTCGGTCG 60.110 60.000 0.00 0.00 44.93 4.79
293 294 0.956633 TGTGTGTCACCTACTCGGTC 59.043 55.000 0.00 0.00 44.93 4.79
295 296 1.611977 TCTTGTGTGTCACCTACTCGG 59.388 52.381 0.00 0.00 39.35 4.63
296 297 3.502920 GATCTTGTGTGTCACCTACTCG 58.497 50.000 0.00 0.00 32.73 4.18
297 298 3.673594 CGGATCTTGTGTGTCACCTACTC 60.674 52.174 0.00 0.00 32.73 2.59
298 299 2.231478 CGGATCTTGTGTGTCACCTACT 59.769 50.000 0.00 0.00 32.73 2.57
299 300 2.230508 TCGGATCTTGTGTGTCACCTAC 59.769 50.000 0.00 0.00 32.73 3.18
300 301 2.521126 TCGGATCTTGTGTGTCACCTA 58.479 47.619 0.00 0.00 32.73 3.08
301 302 1.338107 TCGGATCTTGTGTGTCACCT 58.662 50.000 0.00 0.00 32.73 4.00
302 303 2.386661 ATCGGATCTTGTGTGTCACC 57.613 50.000 0.00 0.00 32.73 4.02
303 304 2.416547 CCAATCGGATCTTGTGTGTCAC 59.583 50.000 0.00 0.00 34.56 3.67
304 305 2.615240 CCCAATCGGATCTTGTGTGTCA 60.615 50.000 0.00 0.00 0.00 3.58
305 306 2.009774 CCCAATCGGATCTTGTGTGTC 58.990 52.381 0.00 0.00 0.00 3.67
306 307 1.628340 TCCCAATCGGATCTTGTGTGT 59.372 47.619 0.00 0.00 34.86 3.72
307 308 2.283298 CTCCCAATCGGATCTTGTGTG 58.717 52.381 0.00 0.00 41.00 3.82
308 309 1.210478 CCTCCCAATCGGATCTTGTGT 59.790 52.381 0.00 0.00 41.00 3.72
309 310 1.475751 CCCTCCCAATCGGATCTTGTG 60.476 57.143 0.00 0.00 41.00 3.33
310 311 0.839946 CCCTCCCAATCGGATCTTGT 59.160 55.000 0.00 0.00 41.00 3.16
311 312 0.109342 CCCCTCCCAATCGGATCTTG 59.891 60.000 0.00 0.00 41.00 3.02
312 313 1.062488 CCCCCTCCCAATCGGATCTT 61.062 60.000 0.00 0.00 41.00 2.40
313 314 1.462238 CCCCCTCCCAATCGGATCT 60.462 63.158 0.00 0.00 41.00 2.75
314 315 3.161557 CCCCCTCCCAATCGGATC 58.838 66.667 0.00 0.00 41.00 3.36
363 364 3.645268 GAGATGGTGGTGGTGGGGC 62.645 68.421 0.00 0.00 0.00 5.80
364 365 2.677228 GAGATGGTGGTGGTGGGG 59.323 66.667 0.00 0.00 0.00 4.96
365 366 2.268920 CGAGATGGTGGTGGTGGG 59.731 66.667 0.00 0.00 0.00 4.61
366 367 2.268920 CCGAGATGGTGGTGGTGG 59.731 66.667 0.00 0.00 0.00 4.61
367 368 2.268920 CCCGAGATGGTGGTGGTG 59.731 66.667 0.00 0.00 35.15 4.17
368 369 3.009115 CCCCGAGATGGTGGTGGT 61.009 66.667 0.00 0.00 35.15 4.16
369 370 4.489771 GCCCCGAGATGGTGGTGG 62.490 72.222 0.00 0.00 35.15 4.61
370 371 3.716195 TGCCCCGAGATGGTGGTG 61.716 66.667 0.00 0.00 35.15 4.17
371 372 3.717294 GTGCCCCGAGATGGTGGT 61.717 66.667 0.00 0.00 35.15 4.16
372 373 4.838152 CGTGCCCCGAGATGGTGG 62.838 72.222 0.00 0.00 39.56 4.61
373 374 4.838152 CCGTGCCCCGAGATGGTG 62.838 72.222 0.00 0.00 39.56 4.17
375 376 4.838152 CACCGTGCCCCGAGATGG 62.838 72.222 0.00 0.00 39.56 3.51
414 415 3.330853 CTTCGCTATGTCGCCGCC 61.331 66.667 0.00 0.00 0.00 6.13
415 416 3.330853 CCTTCGCTATGTCGCCGC 61.331 66.667 0.00 0.00 0.00 6.53
416 417 2.658593 CCCTTCGCTATGTCGCCG 60.659 66.667 0.00 0.00 0.00 6.46
417 418 2.280186 CCCCTTCGCTATGTCGCC 60.280 66.667 0.00 0.00 0.00 5.54
418 419 2.280186 CCCCCTTCGCTATGTCGC 60.280 66.667 0.00 0.00 0.00 5.19
419 420 1.227263 CACCCCCTTCGCTATGTCG 60.227 63.158 0.00 0.00 0.00 4.35
420 421 1.146263 CCACCCCCTTCGCTATGTC 59.854 63.158 0.00 0.00 0.00 3.06
421 422 3.043999 GCCACCCCCTTCGCTATGT 62.044 63.158 0.00 0.00 0.00 2.29
422 423 2.203209 GCCACCCCCTTCGCTATG 60.203 66.667 0.00 0.00 0.00 2.23
423 424 3.861797 CGCCACCCCCTTCGCTAT 61.862 66.667 0.00 0.00 0.00 2.97
428 429 3.787001 CTCTCCGCCACCCCCTTC 61.787 72.222 0.00 0.00 0.00 3.46
433 434 4.097361 GTTCCCTCTCCGCCACCC 62.097 72.222 0.00 0.00 0.00 4.61
434 435 4.097361 GGTTCCCTCTCCGCCACC 62.097 72.222 0.00 0.00 0.00 4.61
435 436 4.097361 GGGTTCCCTCTCCGCCAC 62.097 72.222 0.00 0.00 0.00 5.01
436 437 4.649705 TGGGTTCCCTCTCCGCCA 62.650 66.667 9.43 0.00 0.00 5.69
437 438 3.787001 CTGGGTTCCCTCTCCGCC 61.787 72.222 9.43 0.00 0.00 6.13
438 439 4.475135 GCTGGGTTCCCTCTCCGC 62.475 72.222 9.43 1.17 0.00 5.54
439 440 3.787001 GGCTGGGTTCCCTCTCCG 61.787 72.222 9.43 0.00 0.00 4.63
440 441 3.787001 CGGCTGGGTTCCCTCTCC 61.787 72.222 9.43 6.52 0.00 3.71
441 442 3.787001 CCGGCTGGGTTCCCTCTC 61.787 72.222 2.57 0.00 0.00 3.20
461 462 4.468689 ACGGGGAAAGCTAGCCGC 62.469 66.667 12.13 4.47 39.57 6.53
462 463 2.511600 CACGGGGAAAGCTAGCCG 60.512 66.667 12.13 9.23 0.00 5.52
463 464 1.449778 GACACGGGGAAAGCTAGCC 60.450 63.158 12.13 0.00 0.00 3.93
464 465 1.810030 CGACACGGGGAAAGCTAGC 60.810 63.158 6.62 6.62 0.00 3.42
465 466 1.810030 GCGACACGGGGAAAGCTAG 60.810 63.158 0.00 0.00 0.00 3.42
466 467 2.263540 GCGACACGGGGAAAGCTA 59.736 61.111 0.00 0.00 0.00 3.32
469 470 2.809601 CTCGCGACACGGGGAAAG 60.810 66.667 3.71 0.00 43.89 2.62
470 471 3.296836 TCTCGCGACACGGGGAAA 61.297 61.111 3.71 0.00 44.73 3.13
471 472 4.047059 GTCTCGCGACACGGGGAA 62.047 66.667 3.71 0.00 44.73 3.97
476 477 3.662623 ATCCACGTCTCGCGACACG 62.663 63.158 30.70 30.70 44.77 4.49
477 478 2.152699 CATCCACGTCTCGCGACAC 61.153 63.158 3.71 4.02 44.77 3.67
478 479 2.178273 CATCCACGTCTCGCGACA 59.822 61.111 3.71 0.00 44.77 4.35
479 480 1.868251 GTCATCCACGTCTCGCGAC 60.868 63.158 3.71 0.00 44.77 5.19
480 481 2.483745 GTCATCCACGTCTCGCGA 59.516 61.111 9.26 9.26 44.77 5.87
481 482 2.944557 CGTCATCCACGTCTCGCG 60.945 66.667 0.00 0.00 44.07 5.87
489 490 0.879090 GAAAACCCCACGTCATCCAC 59.121 55.000 0.00 0.00 0.00 4.02
490 491 0.250989 GGAAAACCCCACGTCATCCA 60.251 55.000 0.00 0.00 32.09 3.41
491 492 0.250989 TGGAAAACCCCACGTCATCC 60.251 55.000 0.00 0.00 32.31 3.51
492 493 0.879090 GTGGAAAACCCCACGTCATC 59.121 55.000 0.00 0.00 46.00 2.92
493 494 3.030415 GTGGAAAACCCCACGTCAT 57.970 52.632 0.00 0.00 46.00 3.06
494 495 4.563404 GTGGAAAACCCCACGTCA 57.437 55.556 0.00 0.00 46.00 4.35
499 500 3.611025 AAAGATGAGTGGAAAACCCCA 57.389 42.857 0.00 0.00 0.00 4.96
500 501 4.588951 AGAAAAAGATGAGTGGAAAACCCC 59.411 41.667 0.00 0.00 0.00 4.95
501 502 5.791336 AGAAAAAGATGAGTGGAAAACCC 57.209 39.130 0.00 0.00 0.00 4.11
502 503 9.764363 ATTAAAGAAAAAGATGAGTGGAAAACC 57.236 29.630 0.00 0.00 0.00 3.27
508 509 9.362539 CCAATGATTAAAGAAAAAGATGAGTGG 57.637 33.333 0.00 0.00 0.00 4.00
509 510 8.866956 GCCAATGATTAAAGAAAAAGATGAGTG 58.133 33.333 0.00 0.00 0.00 3.51
510 511 8.037166 GGCCAATGATTAAAGAAAAAGATGAGT 58.963 33.333 0.00 0.00 0.00 3.41
511 512 8.036575 TGGCCAATGATTAAAGAAAAAGATGAG 58.963 33.333 0.61 0.00 0.00 2.90
512 513 7.905265 TGGCCAATGATTAAAGAAAAAGATGA 58.095 30.769 0.61 0.00 0.00 2.92
513 514 8.726870 ATGGCCAATGATTAAAGAAAAAGATG 57.273 30.769 10.96 0.00 0.00 2.90
638 653 8.473219 AGAGAATGAGGATTTTCTATTTTTGCC 58.527 33.333 0.00 0.00 32.54 4.52
654 669 7.621428 TGCATTAAGAAAGAAGAGAATGAGG 57.379 36.000 0.00 0.00 0.00 3.86
669 749 7.926555 GCAAGTACTCTACCTATTGCATTAAGA 59.073 37.037 0.00 0.00 41.92 2.10
681 761 2.492484 CAACGAGGCAAGTACTCTACCT 59.508 50.000 10.25 10.25 34.40 3.08
690 770 1.388547 TTTTGAGCAACGAGGCAAGT 58.611 45.000 5.91 0.00 35.83 3.16
719 799 7.680442 TTTTCTCGTTAAATCACATGGATCA 57.320 32.000 0.00 0.00 34.28 2.92
800 880 1.521457 CCGGCATTAGCTCGAGCAA 60.521 57.895 36.87 27.28 45.16 3.91
972 1052 1.202325 TCGTTGTCACGCTGTACTTGT 60.202 47.619 0.00 0.00 46.70 3.16
1021 1101 0.113385 ATCTCGAGATCCCCGACCAT 59.887 55.000 22.32 0.00 32.18 3.55
1207 1287 1.144057 CGGGCTTGCCGATAAGAGT 59.856 57.895 5.49 0.00 0.00 3.24
1212 1292 3.133767 CTCGTCGGGCTTGCCGATA 62.134 63.158 5.86 0.00 41.71 2.92
1272 1352 4.803426 GTGCTGCTCGGGTCGGAG 62.803 72.222 0.00 1.78 37.11 4.63
1331 1411 4.776322 CGGGATTGCAGTCCGGCA 62.776 66.667 20.77 0.00 43.19 5.69
1482 1562 2.354343 TCCATGTTGGATGCGCCA 59.646 55.556 4.18 0.00 42.67 5.69
1542 1622 2.450243 ACGGAGTGGGACCCATCT 59.550 61.111 18.51 15.53 42.51 2.90
1593 1673 2.436109 GTGCTGTGGTGGTGGGAT 59.564 61.111 0.00 0.00 0.00 3.85
1620 1700 0.379669 GCATCTGGAATGCCGTCAAG 59.620 55.000 0.00 0.00 39.01 3.02
1902 1982 4.996434 GGCTGCCCGATGGATCCG 62.996 72.222 7.66 0.00 0.00 4.18
2702 2782 4.002906 TGATCGACTAAGCAAAACCTGT 57.997 40.909 0.00 0.00 0.00 4.00
2801 2881 0.528901 TGACACACGAACGGGAACTG 60.529 55.000 2.83 0.00 42.99 3.16
2896 2976 6.618811 TGTTCTAACTCAGATTTCTACCGAC 58.381 40.000 0.00 0.00 31.77 4.79
3005 3085 1.890894 CACGACACGATCTCCCCTT 59.109 57.895 0.00 0.00 0.00 3.95
3285 3367 2.397597 AGTTGGCCACCAGACAAAATT 58.602 42.857 3.88 0.00 33.81 1.82
3378 3460 4.106341 AGGGGATTTTCTCAAGTCCTGAAA 59.894 41.667 0.00 0.00 38.57 2.69
3409 3491 3.403277 CTCGGCAAATGAGCTCGG 58.597 61.111 9.64 0.00 34.17 4.63
3414 3496 2.421073 TCAAATGAGCTCGGCAAATGAG 59.579 45.455 9.64 0.00 36.53 2.90
3415 3497 2.421073 CTCAAATGAGCTCGGCAAATGA 59.579 45.455 9.64 6.74 35.13 2.57
3416 3498 2.793933 CTCAAATGAGCTCGGCAAATG 58.206 47.619 9.64 2.57 35.13 2.32
3499 3581 5.931146 AGAACATTTGTTGAAGTTTGCACAA 59.069 32.000 0.00 0.00 38.56 3.33
3500 3582 5.477510 AGAACATTTGTTGAAGTTTGCACA 58.522 33.333 0.00 0.00 38.56 4.57
3501 3583 5.576384 TGAGAACATTTGTTGAAGTTTGCAC 59.424 36.000 0.00 0.00 38.56 4.57
3544 3626 2.033801 CCTCCATGAATGTGATTTCGGC 59.966 50.000 0.00 0.00 0.00 5.54
3646 3729 7.678194 TTTGTGCAAACTTTTCTAGAAATCG 57.322 32.000 18.37 14.34 0.00 3.34


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

AutoCloner maintained by Alex Coulton.