Multiple sequence alignment - TraesCS6D01G189800

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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 TraesCS6D01G189800 chr6D 100.000 4409 0 0 1 4409 262749254 262753662 0.000000e+00 8142.0
1 TraesCS6D01G189800 chr6A 95.234 3945 133 16 442 4360 356969508 356973423 0.000000e+00 6192.0
2 TraesCS6D01G189800 chr6A 90.313 351 18 2 1 335 356949987 356950337 3.130000e-121 446.0
3 TraesCS6D01G189800 chr6A 91.200 125 5 1 322 446 356969118 356969236 9.810000e-37 165.0
4 TraesCS6D01G189800 chr6A 97.872 47 1 0 287 333 356948939 356948985 1.020000e-11 82.4
5 TraesCS6D01G189800 chr6B 93.246 3050 112 33 689 3718 347232187 347229212 0.000000e+00 4405.0
6 TraesCS6D01G189800 chr6B 90.270 555 29 10 3813 4360 347229187 347228651 0.000000e+00 702.0
7 TraesCS6D01G189800 chr6B 84.404 436 27 14 1 412 347243771 347243353 1.490000e-104 390.0
8 TraesCS6D01G189800 chr6B 92.308 52 3 1 421 471 347232540 347232489 6.120000e-09 73.1
9 TraesCS6D01G189800 chr3D 80.460 87 17 0 2894 2980 4972422 4972508 2.850000e-07 67.6


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 TraesCS6D01G189800 chr6D 262749254 262753662 4408 False 8142.0 8142 100.000000 1 4409 1 chr6D.!!$F1 4408
1 TraesCS6D01G189800 chr6A 356969118 356973423 4305 False 3178.5 6192 93.217000 322 4360 2 chr6A.!!$F2 4038
2 TraesCS6D01G189800 chr6A 356948939 356950337 1398 False 264.2 446 94.092500 1 335 2 chr6A.!!$F1 334
3 TraesCS6D01G189800 chr6B 347228651 347232540 3889 True 1726.7 4405 91.941333 421 4360 3 chr6B.!!$R2 3939

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
235 236 0.030908 CCAATCTAGCGTCCTCGACC 59.969 60.0 0.0 0.0 39.71 4.79 F
242 243 0.179067 AGCGTCCTCGACCAAAACAA 60.179 50.0 0.0 0.0 39.71 2.83 F
243 244 0.234884 GCGTCCTCGACCAAAACAAG 59.765 55.0 0.0 0.0 39.71 3.16 F
573 1098 0.461516 TGTACGAAACAACACGCCCA 60.462 50.0 0.0 0.0 34.29 5.36 F
2193 3157 0.030101 GCTTTTGTGTTGCTGCGGTA 59.970 50.0 0.0 0.0 0.00 4.02 F
2245 3209 0.251165 CCCCTTGTCCAACGGAATGT 60.251 55.0 0.0 0.0 31.38 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1586 2129 0.538746 GCGGAAAAGGGAGGGAACAA 60.539 55.000 0.00 0.0 0.00 2.83 R
1891 2849 0.604780 CAGGCACCACTTCCAGTCTG 60.605 60.000 0.00 0.0 0.00 3.51 R
2108 3072 1.202256 TGTAACGCTCATAGTCGCCAG 60.202 52.381 0.00 0.0 0.00 4.85 R
2470 3434 0.620556 AATGCCTCGGGACTCATTGT 59.379 50.000 0.00 0.0 0.00 2.71 R
3147 4111 0.679002 TTGCTTGCTCCTCATCAGCC 60.679 55.000 0.00 0.0 35.89 4.85 R
3614 4589 1.419381 TGGCTTCACTGTGGTACTGA 58.581 50.000 8.11 0.0 0.00 3.41 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
42 43 9.908152 ACTGGTTATTACTGAAAATTAAGCAAC 57.092 29.630 0.00 0.00 0.00 4.17
43 44 9.353999 CTGGTTATTACTGAAAATTAAGCAACC 57.646 33.333 0.00 0.00 32.16 3.77
44 45 9.084533 TGGTTATTACTGAAAATTAAGCAACCT 57.915 29.630 0.00 0.00 32.46 3.50
45 46 9.923143 GGTTATTACTGAAAATTAAGCAACCTT 57.077 29.630 0.00 0.00 30.54 3.50
62 63 9.758651 AAGCAACCTTTTATTAAGTTAAACCTG 57.241 29.630 0.00 0.00 0.00 4.00
63 64 9.138596 AGCAACCTTTTATTAAGTTAAACCTGA 57.861 29.630 0.00 0.00 0.00 3.86
64 65 9.923143 GCAACCTTTTATTAAGTTAAACCTGAT 57.077 29.630 0.00 0.00 0.00 2.90
74 75 8.782339 TTAAGTTAAACCTGATACTAGCAACC 57.218 34.615 0.00 0.00 0.00 3.77
75 76 6.368779 AGTTAAACCTGATACTAGCAACCA 57.631 37.500 0.00 0.00 0.00 3.67
76 77 6.958767 AGTTAAACCTGATACTAGCAACCAT 58.041 36.000 0.00 0.00 0.00 3.55
77 78 6.823689 AGTTAAACCTGATACTAGCAACCATG 59.176 38.462 0.00 0.00 0.00 3.66
78 79 5.435686 AAACCTGATACTAGCAACCATGA 57.564 39.130 0.00 0.00 0.00 3.07
79 80 5.435686 AACCTGATACTAGCAACCATGAA 57.564 39.130 0.00 0.00 0.00 2.57
80 81 5.435686 ACCTGATACTAGCAACCATGAAA 57.564 39.130 0.00 0.00 0.00 2.69
81 82 6.006275 ACCTGATACTAGCAACCATGAAAT 57.994 37.500 0.00 0.00 0.00 2.17
82 83 5.824624 ACCTGATACTAGCAACCATGAAATG 59.175 40.000 0.00 0.00 46.21 2.32
98 99 7.381766 CATGAAATGGAAAAGGGAAAAATCC 57.618 36.000 0.00 0.00 41.79 3.01
99 100 6.762077 TGAAATGGAAAAGGGAAAAATCCT 57.238 33.333 0.00 0.00 35.88 3.24
100 101 7.147958 TGAAATGGAAAAGGGAAAAATCCTT 57.852 32.000 0.00 0.00 45.73 3.36
101 102 6.997476 TGAAATGGAAAAGGGAAAAATCCTTG 59.003 34.615 0.00 0.00 43.24 3.61
102 103 6.514012 AATGGAAAAGGGAAAAATCCTTGT 57.486 33.333 0.00 0.00 43.24 3.16
103 104 5.966853 TGGAAAAGGGAAAAATCCTTGTT 57.033 34.783 0.00 0.00 43.24 2.83
104 105 6.320434 TGGAAAAGGGAAAAATCCTTGTTT 57.680 33.333 0.00 0.00 43.24 2.83
105 106 6.353323 TGGAAAAGGGAAAAATCCTTGTTTC 58.647 36.000 0.00 0.00 43.24 2.78
106 107 6.069963 TGGAAAAGGGAAAAATCCTTGTTTCA 60.070 34.615 14.43 4.60 43.24 2.69
107 108 6.826231 GGAAAAGGGAAAAATCCTTGTTTCAA 59.174 34.615 14.43 0.00 43.24 2.69
108 109 7.502226 GGAAAAGGGAAAAATCCTTGTTTCAAT 59.498 33.333 14.43 0.00 43.24 2.57
109 110 8.450578 AAAAGGGAAAAATCCTTGTTTCAATC 57.549 30.769 0.00 0.00 43.24 2.67
110 111 6.745794 AGGGAAAAATCCTTGTTTCAATCA 57.254 33.333 0.00 0.00 35.80 2.57
111 112 6.762333 AGGGAAAAATCCTTGTTTCAATCAG 58.238 36.000 0.00 0.00 35.80 2.90
112 113 5.934043 GGGAAAAATCCTTGTTTCAATCAGG 59.066 40.000 0.00 0.00 35.80 3.86
113 114 5.409520 GGAAAAATCCTTGTTTCAATCAGGC 59.590 40.000 0.00 0.00 35.80 4.85
114 115 4.541973 AAATCCTTGTTTCAATCAGGCC 57.458 40.909 0.00 0.00 0.00 5.19
115 116 2.673775 TCCTTGTTTCAATCAGGCCA 57.326 45.000 5.01 0.00 0.00 5.36
116 117 3.173953 TCCTTGTTTCAATCAGGCCAT 57.826 42.857 5.01 0.00 0.00 4.40
117 118 4.314522 TCCTTGTTTCAATCAGGCCATA 57.685 40.909 5.01 0.00 0.00 2.74
118 119 4.272489 TCCTTGTTTCAATCAGGCCATAG 58.728 43.478 5.01 0.00 0.00 2.23
119 120 4.019174 CCTTGTTTCAATCAGGCCATAGT 58.981 43.478 5.01 0.00 0.00 2.12
120 121 4.463891 CCTTGTTTCAATCAGGCCATAGTT 59.536 41.667 5.01 0.00 0.00 2.24
121 122 5.652014 CCTTGTTTCAATCAGGCCATAGTTA 59.348 40.000 5.01 0.00 0.00 2.24
122 123 6.152661 CCTTGTTTCAATCAGGCCATAGTTAA 59.847 38.462 5.01 0.00 0.00 2.01
123 124 7.309744 CCTTGTTTCAATCAGGCCATAGTTAAA 60.310 37.037 5.01 0.00 0.00 1.52
124 125 7.531857 TGTTTCAATCAGGCCATAGTTAAAA 57.468 32.000 5.01 0.00 0.00 1.52
125 126 7.375053 TGTTTCAATCAGGCCATAGTTAAAAC 58.625 34.615 5.01 7.96 0.00 2.43
126 127 7.232534 TGTTTCAATCAGGCCATAGTTAAAACT 59.767 33.333 5.01 0.39 42.91 2.66
127 128 7.775053 TTCAATCAGGCCATAGTTAAAACTT 57.225 32.000 5.01 0.00 40.37 2.66
128 129 7.156876 TCAATCAGGCCATAGTTAAAACTTG 57.843 36.000 5.01 0.42 40.37 3.16
129 130 6.152661 TCAATCAGGCCATAGTTAAAACTTGG 59.847 38.462 5.01 14.55 40.37 3.61
130 131 5.249780 TCAGGCCATAGTTAAAACTTGGA 57.750 39.130 19.47 0.00 40.37 3.53
131 132 5.636123 TCAGGCCATAGTTAAAACTTGGAA 58.364 37.500 19.47 0.00 40.37 3.53
132 133 6.071984 TCAGGCCATAGTTAAAACTTGGAAA 58.928 36.000 19.47 0.00 40.37 3.13
133 134 6.015772 TCAGGCCATAGTTAAAACTTGGAAAC 60.016 38.462 19.47 12.37 40.37 2.78
134 135 6.015434 CAGGCCATAGTTAAAACTTGGAAACT 60.015 38.462 19.47 13.62 40.37 2.66
135 136 6.015434 AGGCCATAGTTAAAACTTGGAAACTG 60.015 38.462 19.47 3.28 40.37 3.16
136 137 6.015772 GGCCATAGTTAAAACTTGGAAACTGA 60.016 38.462 19.47 0.00 40.37 3.41
137 138 7.430441 GCCATAGTTAAAACTTGGAAACTGAA 58.570 34.615 19.47 0.00 40.37 3.02
138 139 7.595130 GCCATAGTTAAAACTTGGAAACTGAAG 59.405 37.037 19.47 0.00 40.37 3.02
139 140 8.082242 CCATAGTTAAAACTTGGAAACTGAAGG 58.918 37.037 14.04 0.00 40.37 3.46
140 141 5.902681 AGTTAAAACTTGGAAACTGAAGGC 58.097 37.500 0.00 0.00 35.21 4.35
141 142 3.819564 AAAACTTGGAAACTGAAGGCC 57.180 42.857 0.00 0.00 0.00 5.19
142 143 1.318576 AACTTGGAAACTGAAGGCCG 58.681 50.000 0.00 0.00 0.00 6.13
143 144 0.537371 ACTTGGAAACTGAAGGCCGG 60.537 55.000 0.00 0.00 0.00 6.13
144 145 1.866853 CTTGGAAACTGAAGGCCGGC 61.867 60.000 21.18 21.18 0.00 6.13
145 146 2.282180 GGAAACTGAAGGCCGGCA 60.282 61.111 30.85 6.35 0.00 5.69
146 147 2.335712 GGAAACTGAAGGCCGGCAG 61.336 63.158 30.85 19.63 38.10 4.85
147 148 2.282462 AAACTGAAGGCCGGCAGG 60.282 61.111 30.85 14.73 41.62 4.85
161 162 2.898738 CAGGCGAGACTCCTGCAT 59.101 61.111 4.96 0.00 43.88 3.96
162 163 1.227205 CAGGCGAGACTCCTGCATC 60.227 63.158 4.96 0.00 43.88 3.91
163 164 2.279120 GGCGAGACTCCTGCATCG 60.279 66.667 0.85 0.85 38.19 3.84
164 165 2.775856 GGCGAGACTCCTGCATCGA 61.776 63.158 9.20 0.00 37.35 3.59
165 166 1.587613 GCGAGACTCCTGCATCGAC 60.588 63.158 9.20 0.00 37.35 4.20
166 167 1.999071 GCGAGACTCCTGCATCGACT 61.999 60.000 9.20 0.00 37.35 4.18
167 168 0.248417 CGAGACTCCTGCATCGACTG 60.248 60.000 0.00 0.00 37.35 3.51
168 169 1.098869 GAGACTCCTGCATCGACTGA 58.901 55.000 0.00 0.00 0.00 3.41
169 170 1.065401 GAGACTCCTGCATCGACTGAG 59.935 57.143 0.00 0.00 0.00 3.35
170 171 0.814457 GACTCCTGCATCGACTGAGT 59.186 55.000 0.00 0.00 38.90 3.41
171 172 0.814457 ACTCCTGCATCGACTGAGTC 59.186 55.000 1.65 1.65 30.81 3.36
181 182 3.875838 GACTGAGTCGCTCACAAGT 57.124 52.632 0.00 3.49 35.39 3.16
182 183 1.692296 GACTGAGTCGCTCACAAGTC 58.308 55.000 0.00 8.14 35.39 3.01
183 184 1.001268 GACTGAGTCGCTCACAAGTCA 60.001 52.381 15.87 1.62 39.30 3.41
184 185 1.269309 ACTGAGTCGCTCACAAGTCAC 60.269 52.381 5.59 0.00 35.39 3.67
185 186 0.744281 TGAGTCGCTCACAAGTCACA 59.256 50.000 5.59 0.00 35.39 3.58
186 187 1.341209 TGAGTCGCTCACAAGTCACAT 59.659 47.619 5.59 0.00 35.39 3.21
187 188 1.989165 GAGTCGCTCACAAGTCACATC 59.011 52.381 2.53 0.00 0.00 3.06
188 189 1.071605 GTCGCTCACAAGTCACATCC 58.928 55.000 0.00 0.00 0.00 3.51
189 190 0.678950 TCGCTCACAAGTCACATCCA 59.321 50.000 0.00 0.00 0.00 3.41
190 191 0.792640 CGCTCACAAGTCACATCCAC 59.207 55.000 0.00 0.00 0.00 4.02
191 192 0.792640 GCTCACAAGTCACATCCACG 59.207 55.000 0.00 0.00 0.00 4.94
192 193 1.873903 GCTCACAAGTCACATCCACGT 60.874 52.381 0.00 0.00 0.00 4.49
193 194 2.483876 CTCACAAGTCACATCCACGTT 58.516 47.619 0.00 0.00 0.00 3.99
194 195 2.872245 CTCACAAGTCACATCCACGTTT 59.128 45.455 0.00 0.00 0.00 3.60
195 196 3.275143 TCACAAGTCACATCCACGTTTT 58.725 40.909 0.00 0.00 0.00 2.43
196 197 3.311322 TCACAAGTCACATCCACGTTTTC 59.689 43.478 0.00 0.00 0.00 2.29
197 198 3.064682 CACAAGTCACATCCACGTTTTCA 59.935 43.478 0.00 0.00 0.00 2.69
198 199 3.692101 ACAAGTCACATCCACGTTTTCAA 59.308 39.130 0.00 0.00 0.00 2.69
199 200 4.338118 ACAAGTCACATCCACGTTTTCAAT 59.662 37.500 0.00 0.00 0.00 2.57
200 201 5.529430 ACAAGTCACATCCACGTTTTCAATA 59.471 36.000 0.00 0.00 0.00 1.90
201 202 6.206634 ACAAGTCACATCCACGTTTTCAATAT 59.793 34.615 0.00 0.00 0.00 1.28
202 203 7.389330 ACAAGTCACATCCACGTTTTCAATATA 59.611 33.333 0.00 0.00 0.00 0.86
203 204 8.397906 CAAGTCACATCCACGTTTTCAATATAT 58.602 33.333 0.00 0.00 0.00 0.86
204 205 8.142994 AGTCACATCCACGTTTTCAATATATC 57.857 34.615 0.00 0.00 0.00 1.63
205 206 7.987458 AGTCACATCCACGTTTTCAATATATCT 59.013 33.333 0.00 0.00 0.00 1.98
206 207 8.064222 GTCACATCCACGTTTTCAATATATCTG 58.936 37.037 0.00 0.00 0.00 2.90
207 208 7.984617 TCACATCCACGTTTTCAATATATCTGA 59.015 33.333 0.00 0.00 0.00 3.27
208 209 8.777413 CACATCCACGTTTTCAATATATCTGAT 58.223 33.333 0.00 0.00 0.00 2.90
209 210 8.777413 ACATCCACGTTTTCAATATATCTGATG 58.223 33.333 0.00 0.00 0.00 3.07
210 211 7.189693 TCCACGTTTTCAATATATCTGATGC 57.810 36.000 0.00 0.00 0.00 3.91
211 212 6.204688 TCCACGTTTTCAATATATCTGATGCC 59.795 38.462 0.00 0.00 0.00 4.40
212 213 6.017192 CCACGTTTTCAATATATCTGATGCCA 60.017 38.462 0.00 0.00 0.00 4.92
213 214 7.416817 CACGTTTTCAATATATCTGATGCCAA 58.583 34.615 0.00 0.00 0.00 4.52
214 215 8.077991 CACGTTTTCAATATATCTGATGCCAAT 58.922 33.333 0.00 0.00 0.00 3.16
215 216 8.632679 ACGTTTTCAATATATCTGATGCCAATT 58.367 29.630 0.00 0.00 0.00 2.32
216 217 9.121517 CGTTTTCAATATATCTGATGCCAATTC 57.878 33.333 0.00 0.00 0.00 2.17
217 218 9.415544 GTTTTCAATATATCTGATGCCAATTCC 57.584 33.333 0.00 0.00 0.00 3.01
218 219 8.709272 TTTCAATATATCTGATGCCAATTCCA 57.291 30.769 0.00 0.00 0.00 3.53
219 220 8.709272 TTCAATATATCTGATGCCAATTCCAA 57.291 30.769 0.00 0.00 0.00 3.53
220 221 8.888836 TCAATATATCTGATGCCAATTCCAAT 57.111 30.769 0.00 0.00 0.00 3.16
221 222 8.963725 TCAATATATCTGATGCCAATTCCAATC 58.036 33.333 0.00 0.00 0.00 2.67
222 223 8.967918 CAATATATCTGATGCCAATTCCAATCT 58.032 33.333 0.00 0.00 0.00 2.40
224 225 9.848710 ATATATCTGATGCCAATTCCAATCTAG 57.151 33.333 0.00 0.00 0.00 2.43
225 226 4.139786 TCTGATGCCAATTCCAATCTAGC 58.860 43.478 0.00 0.00 0.00 3.42
226 227 2.880268 TGATGCCAATTCCAATCTAGCG 59.120 45.455 0.00 0.00 0.00 4.26
227 228 2.418368 TGCCAATTCCAATCTAGCGT 57.582 45.000 0.00 0.00 0.00 5.07
228 229 2.288666 TGCCAATTCCAATCTAGCGTC 58.711 47.619 0.00 0.00 0.00 5.19
229 230 1.604278 GCCAATTCCAATCTAGCGTCC 59.396 52.381 0.00 0.00 0.00 4.79
230 231 2.746472 GCCAATTCCAATCTAGCGTCCT 60.746 50.000 0.00 0.00 0.00 3.85
231 232 3.134458 CCAATTCCAATCTAGCGTCCTC 58.866 50.000 0.00 0.00 0.00 3.71
232 233 2.797156 CAATTCCAATCTAGCGTCCTCG 59.203 50.000 0.00 0.00 40.37 4.63
233 234 1.758936 TTCCAATCTAGCGTCCTCGA 58.241 50.000 0.00 0.00 39.71 4.04
234 235 1.022735 TCCAATCTAGCGTCCTCGAC 58.977 55.000 0.00 0.00 39.71 4.20
235 236 0.030908 CCAATCTAGCGTCCTCGACC 59.969 60.000 0.00 0.00 39.71 4.79
236 237 0.738975 CAATCTAGCGTCCTCGACCA 59.261 55.000 0.00 0.00 39.71 4.02
237 238 1.134367 CAATCTAGCGTCCTCGACCAA 59.866 52.381 0.00 0.00 39.71 3.67
238 239 1.471119 ATCTAGCGTCCTCGACCAAA 58.529 50.000 0.00 0.00 39.71 3.28
239 240 1.250328 TCTAGCGTCCTCGACCAAAA 58.750 50.000 0.00 0.00 39.71 2.44
240 241 1.068055 TCTAGCGTCCTCGACCAAAAC 60.068 52.381 0.00 0.00 39.71 2.43
241 242 0.675083 TAGCGTCCTCGACCAAAACA 59.325 50.000 0.00 0.00 39.71 2.83
242 243 0.179067 AGCGTCCTCGACCAAAACAA 60.179 50.000 0.00 0.00 39.71 2.83
243 244 0.234884 GCGTCCTCGACCAAAACAAG 59.765 55.000 0.00 0.00 39.71 3.16
244 245 1.860676 CGTCCTCGACCAAAACAAGA 58.139 50.000 0.00 0.00 39.71 3.02
245 246 2.413837 CGTCCTCGACCAAAACAAGAT 58.586 47.619 0.00 0.00 39.71 2.40
246 247 2.806244 CGTCCTCGACCAAAACAAGATT 59.194 45.455 0.00 0.00 39.71 2.40
247 248 3.363970 CGTCCTCGACCAAAACAAGATTG 60.364 47.826 0.00 0.00 39.71 2.67
248 249 3.813166 GTCCTCGACCAAAACAAGATTGA 59.187 43.478 0.00 0.00 0.00 2.57
249 250 3.813166 TCCTCGACCAAAACAAGATTGAC 59.187 43.478 0.00 0.00 0.00 3.18
250 251 3.058224 CCTCGACCAAAACAAGATTGACC 60.058 47.826 0.00 0.00 0.00 4.02
251 252 3.546724 TCGACCAAAACAAGATTGACCA 58.453 40.909 0.00 0.00 0.00 4.02
252 253 4.141287 TCGACCAAAACAAGATTGACCAT 58.859 39.130 0.00 0.00 0.00 3.55
253 254 4.215399 TCGACCAAAACAAGATTGACCATC 59.785 41.667 0.00 0.00 0.00 3.51
254 255 4.023279 CGACCAAAACAAGATTGACCATCA 60.023 41.667 0.00 0.00 33.75 3.07
255 256 5.200368 ACCAAAACAAGATTGACCATCAC 57.800 39.130 0.00 0.00 33.75 3.06
256 257 4.895297 ACCAAAACAAGATTGACCATCACT 59.105 37.500 0.00 0.00 33.75 3.41
257 258 5.363580 ACCAAAACAAGATTGACCATCACTT 59.636 36.000 0.00 0.00 33.75 3.16
258 259 6.127083 ACCAAAACAAGATTGACCATCACTTT 60.127 34.615 0.00 0.00 33.75 2.66
259 260 6.421801 CCAAAACAAGATTGACCATCACTTTC 59.578 38.462 0.00 0.00 33.75 2.62
260 261 6.713762 AAACAAGATTGACCATCACTTTCA 57.286 33.333 0.00 0.00 33.75 2.69
261 262 5.695851 ACAAGATTGACCATCACTTTCAC 57.304 39.130 0.00 0.00 33.75 3.18
262 263 5.132502 ACAAGATTGACCATCACTTTCACA 58.867 37.500 0.00 0.00 33.75 3.58
263 264 5.771666 ACAAGATTGACCATCACTTTCACAT 59.228 36.000 0.00 0.00 33.75 3.21
264 265 5.892160 AGATTGACCATCACTTTCACATG 57.108 39.130 0.00 0.00 33.75 3.21
265 266 5.563592 AGATTGACCATCACTTTCACATGA 58.436 37.500 0.00 0.00 33.75 3.07
266 267 6.005823 AGATTGACCATCACTTTCACATGAA 58.994 36.000 0.00 0.00 33.75 2.57
267 268 5.437289 TTGACCATCACTTTCACATGAAC 57.563 39.130 0.00 0.00 33.13 3.18
268 269 4.459330 TGACCATCACTTTCACATGAACA 58.541 39.130 0.00 0.00 33.13 3.18
269 270 4.275689 TGACCATCACTTTCACATGAACAC 59.724 41.667 0.00 0.00 33.13 3.32
270 271 4.206375 ACCATCACTTTCACATGAACACA 58.794 39.130 0.00 0.00 33.13 3.72
271 272 4.036734 ACCATCACTTTCACATGAACACAC 59.963 41.667 0.00 0.00 33.13 3.82
272 273 4.036616 CCATCACTTTCACATGAACACACA 59.963 41.667 0.00 0.00 33.13 3.72
273 274 5.278610 CCATCACTTTCACATGAACACACAT 60.279 40.000 0.00 0.00 33.13 3.21
282 283 4.087510 CATGAACACACATGTCACATCC 57.912 45.455 0.00 0.00 41.59 3.51
283 284 3.490439 TGAACACACATGTCACATCCT 57.510 42.857 0.00 0.00 38.45 3.24
284 285 3.819368 TGAACACACATGTCACATCCTT 58.181 40.909 0.00 0.00 38.45 3.36
285 286 3.814842 TGAACACACATGTCACATCCTTC 59.185 43.478 0.00 0.00 38.45 3.46
286 287 2.783135 ACACACATGTCACATCCTTCC 58.217 47.619 0.00 0.00 31.55 3.46
287 288 2.106338 ACACACATGTCACATCCTTCCA 59.894 45.455 0.00 0.00 31.55 3.53
288 289 2.485426 CACACATGTCACATCCTTCCAC 59.515 50.000 0.00 0.00 0.00 4.02
289 290 2.106338 ACACATGTCACATCCTTCCACA 59.894 45.455 0.00 0.00 0.00 4.17
290 291 2.745821 CACATGTCACATCCTTCCACAG 59.254 50.000 0.00 0.00 0.00 3.66
359 360 7.367285 TCATAACCTGAAAACATAGCACAAAC 58.633 34.615 0.00 0.00 0.00 2.93
369 370 4.569943 ACATAGCACAAACAGAGTACCAG 58.430 43.478 0.00 0.00 0.00 4.00
375 376 4.302455 CACAAACAGAGTACCAGAGACAG 58.698 47.826 0.00 0.00 0.00 3.51
396 397 2.884639 GCATGTACCACAAGGAAACAGT 59.115 45.455 0.00 0.00 37.60 3.55
448 449 2.000447 CTAGAAACACCGGCTAAGCAC 59.000 52.381 0.00 0.00 0.00 4.40
457 734 3.854459 GCTAAGCACGGCGCAGAC 61.854 66.667 16.26 5.85 46.13 3.51
479 1000 7.547370 CAGACCTCAGAAATTACTTAAGAGTGG 59.453 40.741 10.09 2.08 36.60 4.00
535 1057 8.252417 TCCACCAATTCATAATCTGAAAACATG 58.748 33.333 0.00 0.00 46.62 3.21
573 1098 0.461516 TGTACGAAACAACACGCCCA 60.462 50.000 0.00 0.00 34.29 5.36
727 1252 4.381185 GGTCATGCATTCACATCACACAAT 60.381 41.667 0.00 0.00 0.00 2.71
744 1269 7.881142 TCACACAATAAAATAACCTTGGTCTG 58.119 34.615 0.00 0.00 0.00 3.51
795 1320 1.576356 GGCATCCTTACGAGCAGAAG 58.424 55.000 0.00 0.00 0.00 2.85
836 1364 2.086426 TGATGTGCGAGCGACGTTC 61.086 57.895 1.05 1.05 44.60 3.95
928 1456 2.104967 CCCTGACAAATGGATGCATGT 58.895 47.619 2.46 0.00 0.00 3.21
935 1463 5.186215 TGACAAATGGATGCATGTGAGAATT 59.814 36.000 22.91 0.75 0.00 2.17
1149 1677 3.110178 GGTGAGTTCGCGTTCGGG 61.110 66.667 5.77 2.96 36.13 5.14
1150 1678 3.774702 GTGAGTTCGCGTTCGGGC 61.775 66.667 5.77 0.00 36.13 6.13
1350 1890 2.431244 CCCCGGGTTACCAACGTT 59.569 61.111 21.85 0.00 36.13 3.99
1586 2129 2.055299 CTGTTCCCTACACCGTGGT 58.945 57.895 3.03 0.00 32.10 4.16
1833 2791 2.575279 AGCTCAGACCAGTGGATTGAAT 59.425 45.455 18.40 7.55 0.00 2.57
1880 2838 1.202770 CCCAAGAAACTTCTGTCGGGT 60.203 52.381 11.30 0.00 37.65 5.28
2063 3027 8.255111 TGTGACTTGGATGATACTGAATCTAT 57.745 34.615 0.00 0.00 35.45 1.98
2108 3072 6.480981 CCAATGAACAATATCAATTGGCCTTC 59.519 38.462 3.32 0.00 45.72 3.46
2193 3157 0.030101 GCTTTTGTGTTGCTGCGGTA 59.970 50.000 0.00 0.00 0.00 4.02
2245 3209 0.251165 CCCCTTGTCCAACGGAATGT 60.251 55.000 0.00 0.00 31.38 2.71
2246 3210 1.616159 CCCTTGTCCAACGGAATGTT 58.384 50.000 0.00 0.00 43.09 2.71
2247 3211 1.539827 CCCTTGTCCAACGGAATGTTC 59.460 52.381 0.00 0.00 39.29 3.18
2388 3352 0.619832 TGCTCCTTGGAGGATCTGCT 60.620 55.000 17.33 0.00 44.81 4.24
2470 3434 1.635487 AGAAGCCAGCCCAGATACAAA 59.365 47.619 0.00 0.00 0.00 2.83
2528 3492 3.833070 ACGTACAAGGAGATTGAGAAGGT 59.167 43.478 0.00 0.00 41.83 3.50
2733 3697 2.280797 TTGCTCGGTTTCTGCGCT 60.281 55.556 9.73 0.00 0.00 5.92
3147 4111 1.268794 CGGAATGTGGAGCTAGAGACG 60.269 57.143 0.00 0.00 0.00 4.18
3285 4249 1.743623 CTTCGTGGCCGTGGCATTA 60.744 57.895 13.76 0.00 44.11 1.90
3472 4447 6.420913 AGAGTATATTGGACTACCGCAAAT 57.579 37.500 0.00 0.00 39.42 2.32
3480 4455 6.767524 TTGGACTACCGCAAATGATAAATT 57.232 33.333 0.00 0.00 39.42 1.82
3805 4780 4.438744 GGGACATCAGCTAAAATTGGAACG 60.439 45.833 0.00 0.00 0.00 3.95
3849 4824 2.987149 CGTTCACGACTGAAATGCTAGT 59.013 45.455 0.00 0.00 43.02 2.57
3935 4910 1.505353 CTTTACGAGCGACCGACCT 59.495 57.895 3.95 0.00 0.00 3.85
4020 4995 1.269726 ACTGGAAATTTGGCAACTGCG 60.270 47.619 0.00 0.00 43.26 5.18
4092 5073 4.852134 ACTGAATGCAAGCATTACAACA 57.148 36.364 19.21 12.18 45.50 3.33
4203 5185 3.933861 ACACTTTCCCTCTTGAACTGT 57.066 42.857 0.00 0.00 0.00 3.55
4204 5186 3.545703 ACACTTTCCCTCTTGAACTGTG 58.454 45.455 0.00 0.00 36.17 3.66
4382 5388 7.205515 AGCTTAGCATAATAATATGGCTCCT 57.794 36.000 7.07 0.00 39.49 3.69
4383 5389 7.278875 AGCTTAGCATAATAATATGGCTCCTC 58.721 38.462 7.07 0.00 39.49 3.71
4385 5391 5.683876 AGCATAATAATATGGCTCCTCGT 57.316 39.130 0.08 0.00 39.49 4.18
4386 5392 5.423015 AGCATAATAATATGGCTCCTCGTG 58.577 41.667 0.08 0.00 39.49 4.35
4387 5393 5.046304 AGCATAATAATATGGCTCCTCGTGT 60.046 40.000 0.08 0.00 39.49 4.49
4388 5394 6.154534 AGCATAATAATATGGCTCCTCGTGTA 59.845 38.462 0.08 0.00 39.49 2.90
4389 5395 6.986817 GCATAATAATATGGCTCCTCGTGTAT 59.013 38.462 0.08 0.00 39.49 2.29
4390 5396 8.141909 GCATAATAATATGGCTCCTCGTGTATA 58.858 37.037 0.08 0.00 39.49 1.47
4392 5398 4.803098 AATATGGCTCCTCGTGTATACC 57.197 45.455 0.00 0.00 0.00 2.73
4393 5399 2.082140 ATGGCTCCTCGTGTATACCA 57.918 50.000 0.00 0.00 0.00 3.25
4394 5400 1.855295 TGGCTCCTCGTGTATACCAA 58.145 50.000 0.00 0.00 0.00 3.67
4397 5403 3.962063 TGGCTCCTCGTGTATACCAAATA 59.038 43.478 0.00 0.00 0.00 1.40
4400 5406 6.268158 TGGCTCCTCGTGTATACCAAATATTA 59.732 38.462 0.00 0.00 0.00 0.98
4403 5409 7.654520 GCTCCTCGTGTATACCAAATATTAACA 59.345 37.037 0.00 0.00 0.00 2.41
4405 5411 9.701098 TCCTCGTGTATACCAAATATTAACATC 57.299 33.333 0.00 0.00 0.00 3.06
4406 5412 8.932791 CCTCGTGTATACCAAATATTAACATCC 58.067 37.037 0.00 0.00 0.00 3.51
4407 5413 8.836268 TCGTGTATACCAAATATTAACATCCC 57.164 34.615 0.00 0.00 0.00 3.85
4408 5414 8.430431 TCGTGTATACCAAATATTAACATCCCA 58.570 33.333 0.00 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 9.908152 GTTGCTTAATTTTCAGTAATAACCAGT 57.092 29.630 0.00 0.00 0.00 4.00
17 18 9.353999 GGTTGCTTAATTTTCAGTAATAACCAG 57.646 33.333 0.00 0.00 33.76 4.00
18 19 9.084533 AGGTTGCTTAATTTTCAGTAATAACCA 57.915 29.630 0.00 0.00 34.83 3.67
19 20 9.923143 AAGGTTGCTTAATTTTCAGTAATAACC 57.077 29.630 0.00 0.00 33.76 2.85
36 37 9.758651 CAGGTTTAACTTAATAAAAGGTTGCTT 57.241 29.630 0.00 0.00 0.00 3.91
37 38 9.138596 TCAGGTTTAACTTAATAAAAGGTTGCT 57.861 29.630 0.00 0.00 0.00 3.91
38 39 9.923143 ATCAGGTTTAACTTAATAAAAGGTTGC 57.077 29.630 0.00 0.00 0.00 4.17
48 49 9.392259 GGTTGCTAGTATCAGGTTTAACTTAAT 57.608 33.333 0.00 0.00 0.00 1.40
49 50 8.377034 TGGTTGCTAGTATCAGGTTTAACTTAA 58.623 33.333 0.00 0.00 0.00 1.85
50 51 7.909518 TGGTTGCTAGTATCAGGTTTAACTTA 58.090 34.615 0.00 0.00 0.00 2.24
51 52 6.775708 TGGTTGCTAGTATCAGGTTTAACTT 58.224 36.000 0.00 0.00 0.00 2.66
52 53 6.368779 TGGTTGCTAGTATCAGGTTTAACT 57.631 37.500 0.00 0.00 0.00 2.24
53 54 6.821665 TCATGGTTGCTAGTATCAGGTTTAAC 59.178 38.462 0.00 0.00 0.00 2.01
54 55 6.953101 TCATGGTTGCTAGTATCAGGTTTAA 58.047 36.000 0.00 0.00 0.00 1.52
55 56 6.553953 TCATGGTTGCTAGTATCAGGTTTA 57.446 37.500 0.00 0.00 0.00 2.01
56 57 5.435686 TCATGGTTGCTAGTATCAGGTTT 57.564 39.130 0.00 0.00 0.00 3.27
57 58 5.435686 TTCATGGTTGCTAGTATCAGGTT 57.564 39.130 0.00 0.00 0.00 3.50
58 59 5.435686 TTTCATGGTTGCTAGTATCAGGT 57.564 39.130 0.00 0.00 0.00 4.00
59 60 5.240183 CCATTTCATGGTTGCTAGTATCAGG 59.760 44.000 0.00 0.00 45.54 3.86
60 61 6.309712 CCATTTCATGGTTGCTAGTATCAG 57.690 41.667 0.00 0.00 45.54 2.90
74 75 7.170277 AGGATTTTTCCCTTTTCCATTTCATG 58.830 34.615 0.00 0.00 0.00 3.07
75 76 7.333779 AGGATTTTTCCCTTTTCCATTTCAT 57.666 32.000 0.00 0.00 0.00 2.57
76 77 6.762077 AGGATTTTTCCCTTTTCCATTTCA 57.238 33.333 0.00 0.00 0.00 2.69
77 78 6.998074 ACAAGGATTTTTCCCTTTTCCATTTC 59.002 34.615 0.00 0.00 41.79 2.17
78 79 6.910191 ACAAGGATTTTTCCCTTTTCCATTT 58.090 32.000 0.00 0.00 41.79 2.32
79 80 6.514012 ACAAGGATTTTTCCCTTTTCCATT 57.486 33.333 0.00 0.00 41.79 3.16
80 81 6.514012 AACAAGGATTTTTCCCTTTTCCAT 57.486 33.333 0.00 0.00 41.79 3.41
81 82 5.966853 AACAAGGATTTTTCCCTTTTCCA 57.033 34.783 0.00 0.00 41.79 3.53
82 83 6.353323 TGAAACAAGGATTTTTCCCTTTTCC 58.647 36.000 0.00 0.00 41.79 3.13
83 84 7.857734 TTGAAACAAGGATTTTTCCCTTTTC 57.142 32.000 0.00 0.00 41.79 2.29
84 85 8.052141 TGATTGAAACAAGGATTTTTCCCTTTT 58.948 29.630 0.00 0.00 41.79 2.27
85 86 7.572814 TGATTGAAACAAGGATTTTTCCCTTT 58.427 30.769 0.00 0.00 41.79 3.11
86 87 7.135591 TGATTGAAACAAGGATTTTTCCCTT 57.864 32.000 0.00 0.00 44.36 3.95
87 88 6.239686 CCTGATTGAAACAAGGATTTTTCCCT 60.240 38.462 0.00 0.00 31.76 4.20
88 89 5.934043 CCTGATTGAAACAAGGATTTTTCCC 59.066 40.000 0.00 0.00 31.76 3.97
89 90 5.409520 GCCTGATTGAAACAAGGATTTTTCC 59.590 40.000 0.00 0.00 31.76 3.13
90 91 5.409520 GGCCTGATTGAAACAAGGATTTTTC 59.590 40.000 0.00 0.00 33.15 2.29
91 92 5.163216 TGGCCTGATTGAAACAAGGATTTTT 60.163 36.000 3.32 0.00 0.00 1.94
92 93 4.347583 TGGCCTGATTGAAACAAGGATTTT 59.652 37.500 3.32 0.00 0.00 1.82
93 94 3.903090 TGGCCTGATTGAAACAAGGATTT 59.097 39.130 3.32 0.00 0.00 2.17
94 95 3.509442 TGGCCTGATTGAAACAAGGATT 58.491 40.909 3.32 0.00 0.00 3.01
95 96 3.173953 TGGCCTGATTGAAACAAGGAT 57.826 42.857 3.32 0.00 0.00 3.24
96 97 2.673775 TGGCCTGATTGAAACAAGGA 57.326 45.000 3.32 0.00 0.00 3.36
97 98 4.019174 ACTATGGCCTGATTGAAACAAGG 58.981 43.478 3.32 0.00 0.00 3.61
98 99 5.649782 AACTATGGCCTGATTGAAACAAG 57.350 39.130 3.32 0.00 0.00 3.16
99 100 7.531857 TTTAACTATGGCCTGATTGAAACAA 57.468 32.000 3.32 0.00 0.00 2.83
100 101 7.232534 AGTTTTAACTATGGCCTGATTGAAACA 59.767 33.333 20.83 0.00 37.52 2.83
101 102 7.602753 AGTTTTAACTATGGCCTGATTGAAAC 58.397 34.615 3.32 12.01 37.52 2.78
102 103 7.775053 AGTTTTAACTATGGCCTGATTGAAA 57.225 32.000 3.32 0.08 37.52 2.69
103 104 7.309744 CCAAGTTTTAACTATGGCCTGATTGAA 60.310 37.037 3.32 0.00 38.57 2.69
104 105 6.152661 CCAAGTTTTAACTATGGCCTGATTGA 59.847 38.462 3.32 0.00 38.57 2.57
105 106 6.152661 TCCAAGTTTTAACTATGGCCTGATTG 59.847 38.462 3.32 0.00 38.57 2.67
106 107 6.252995 TCCAAGTTTTAACTATGGCCTGATT 58.747 36.000 3.32 0.00 38.57 2.57
107 108 5.826643 TCCAAGTTTTAACTATGGCCTGAT 58.173 37.500 3.32 0.00 38.57 2.90
108 109 5.249780 TCCAAGTTTTAACTATGGCCTGA 57.750 39.130 3.32 0.00 38.57 3.86
109 110 5.975693 TTCCAAGTTTTAACTATGGCCTG 57.024 39.130 3.32 0.00 38.57 4.85
110 111 6.015434 CAGTTTCCAAGTTTTAACTATGGCCT 60.015 38.462 3.32 0.00 38.57 5.19
111 112 6.015772 TCAGTTTCCAAGTTTTAACTATGGCC 60.016 38.462 0.00 0.00 38.57 5.36
112 113 6.977213 TCAGTTTCCAAGTTTTAACTATGGC 58.023 36.000 14.02 5.90 38.57 4.40
113 114 8.082242 CCTTCAGTTTCCAAGTTTTAACTATGG 58.918 37.037 13.23 13.23 38.57 2.74
114 115 7.595130 GCCTTCAGTTTCCAAGTTTTAACTATG 59.405 37.037 0.00 0.00 38.57 2.23
115 116 7.255836 GGCCTTCAGTTTCCAAGTTTTAACTAT 60.256 37.037 0.00 0.00 38.57 2.12
116 117 6.040054 GGCCTTCAGTTTCCAAGTTTTAACTA 59.960 38.462 0.00 0.00 38.57 2.24
117 118 5.163447 GGCCTTCAGTTTCCAAGTTTTAACT 60.163 40.000 0.00 0.00 42.04 2.24
118 119 5.047847 GGCCTTCAGTTTCCAAGTTTTAAC 58.952 41.667 0.00 0.00 0.00 2.01
119 120 4.202070 CGGCCTTCAGTTTCCAAGTTTTAA 60.202 41.667 0.00 0.00 0.00 1.52
120 121 3.316868 CGGCCTTCAGTTTCCAAGTTTTA 59.683 43.478 0.00 0.00 0.00 1.52
121 122 2.100749 CGGCCTTCAGTTTCCAAGTTTT 59.899 45.455 0.00 0.00 0.00 2.43
122 123 1.681264 CGGCCTTCAGTTTCCAAGTTT 59.319 47.619 0.00 0.00 0.00 2.66
123 124 1.318576 CGGCCTTCAGTTTCCAAGTT 58.681 50.000 0.00 0.00 0.00 2.66
124 125 0.537371 CCGGCCTTCAGTTTCCAAGT 60.537 55.000 0.00 0.00 0.00 3.16
125 126 1.866853 GCCGGCCTTCAGTTTCCAAG 61.867 60.000 18.11 0.00 0.00 3.61
126 127 1.901464 GCCGGCCTTCAGTTTCCAA 60.901 57.895 18.11 0.00 0.00 3.53
127 128 2.282180 GCCGGCCTTCAGTTTCCA 60.282 61.111 18.11 0.00 0.00 3.53
128 129 2.282180 TGCCGGCCTTCAGTTTCC 60.282 61.111 26.77 0.00 0.00 3.13
129 130 2.335712 CCTGCCGGCCTTCAGTTTC 61.336 63.158 26.77 0.00 0.00 2.78
130 131 2.282462 CCTGCCGGCCTTCAGTTT 60.282 61.111 26.77 0.00 0.00 2.66
141 142 4.504916 CAGGAGTCTCGCCTGCCG 62.505 72.222 6.60 0.00 43.70 5.69
145 146 2.780094 CGATGCAGGAGTCTCGCCT 61.780 63.158 0.00 0.00 32.88 5.52
146 147 2.279120 CGATGCAGGAGTCTCGCC 60.279 66.667 0.00 0.00 0.00 5.54
147 148 1.587613 GTCGATGCAGGAGTCTCGC 60.588 63.158 0.32 0.00 0.00 5.03
148 149 0.248417 CAGTCGATGCAGGAGTCTCG 60.248 60.000 0.00 0.00 0.00 4.04
149 150 1.065401 CTCAGTCGATGCAGGAGTCTC 59.935 57.143 0.00 0.00 0.00 3.36
150 151 1.102154 CTCAGTCGATGCAGGAGTCT 58.898 55.000 0.00 0.00 0.00 3.24
151 152 0.814457 ACTCAGTCGATGCAGGAGTC 59.186 55.000 0.00 0.00 33.84 3.36
152 153 0.814457 GACTCAGTCGATGCAGGAGT 59.186 55.000 0.00 6.99 41.22 3.85
153 154 3.639162 GACTCAGTCGATGCAGGAG 57.361 57.895 0.00 0.00 0.00 3.69
163 164 1.001268 TGACTTGTGAGCGACTCAGTC 60.001 52.381 9.38 12.63 41.46 3.51
164 165 1.032794 TGACTTGTGAGCGACTCAGT 58.967 50.000 9.38 5.23 41.46 3.41
165 166 1.269257 TGTGACTTGTGAGCGACTCAG 60.269 52.381 9.38 2.49 41.46 3.35
166 167 0.744281 TGTGACTTGTGAGCGACTCA 59.256 50.000 5.59 5.59 38.25 3.41
167 168 1.989165 GATGTGACTTGTGAGCGACTC 59.011 52.381 0.00 0.00 0.00 3.36
168 169 1.337260 GGATGTGACTTGTGAGCGACT 60.337 52.381 0.00 0.00 0.00 4.18
169 170 1.071605 GGATGTGACTTGTGAGCGAC 58.928 55.000 0.00 0.00 0.00 5.19
170 171 0.678950 TGGATGTGACTTGTGAGCGA 59.321 50.000 0.00 0.00 0.00 4.93
171 172 0.792640 GTGGATGTGACTTGTGAGCG 59.207 55.000 0.00 0.00 0.00 5.03
172 173 0.792640 CGTGGATGTGACTTGTGAGC 59.207 55.000 0.00 0.00 0.00 4.26
173 174 2.154854 ACGTGGATGTGACTTGTGAG 57.845 50.000 0.00 0.00 0.00 3.51
174 175 2.613026 AACGTGGATGTGACTTGTGA 57.387 45.000 0.00 0.00 0.00 3.58
175 176 3.064682 TGAAAACGTGGATGTGACTTGTG 59.935 43.478 0.00 0.00 0.00 3.33
176 177 3.275143 TGAAAACGTGGATGTGACTTGT 58.725 40.909 0.00 0.00 0.00 3.16
177 178 3.961477 TGAAAACGTGGATGTGACTTG 57.039 42.857 0.00 0.00 0.00 3.16
178 179 6.817765 ATATTGAAAACGTGGATGTGACTT 57.182 33.333 0.00 0.00 0.00 3.01
179 180 7.987458 AGATATATTGAAAACGTGGATGTGACT 59.013 33.333 0.00 0.00 0.00 3.41
180 181 8.064222 CAGATATATTGAAAACGTGGATGTGAC 58.936 37.037 0.00 0.00 0.00 3.67
181 182 7.984617 TCAGATATATTGAAAACGTGGATGTGA 59.015 33.333 0.00 0.00 0.00 3.58
182 183 8.141835 TCAGATATATTGAAAACGTGGATGTG 57.858 34.615 0.00 0.00 0.00 3.21
183 184 8.777413 CATCAGATATATTGAAAACGTGGATGT 58.223 33.333 0.00 0.00 0.00 3.06
184 185 7.747799 GCATCAGATATATTGAAAACGTGGATG 59.252 37.037 0.00 0.00 0.00 3.51
185 186 7.094634 GGCATCAGATATATTGAAAACGTGGAT 60.095 37.037 0.00 0.00 0.00 3.41
186 187 6.204688 GGCATCAGATATATTGAAAACGTGGA 59.795 38.462 0.00 0.00 0.00 4.02
187 188 6.017192 TGGCATCAGATATATTGAAAACGTGG 60.017 38.462 0.00 0.00 0.00 4.94
188 189 6.958255 TGGCATCAGATATATTGAAAACGTG 58.042 36.000 0.00 0.00 0.00 4.49
189 190 7.566760 TTGGCATCAGATATATTGAAAACGT 57.433 32.000 0.00 0.00 0.00 3.99
190 191 9.121517 GAATTGGCATCAGATATATTGAAAACG 57.878 33.333 0.00 0.00 0.00 3.60
191 192 9.415544 GGAATTGGCATCAGATATATTGAAAAC 57.584 33.333 0.00 0.00 0.00 2.43
192 193 9.145442 TGGAATTGGCATCAGATATATTGAAAA 57.855 29.630 0.00 0.00 0.00 2.29
193 194 8.709272 TGGAATTGGCATCAGATATATTGAAA 57.291 30.769 0.00 0.00 0.00 2.69
194 195 8.709272 TTGGAATTGGCATCAGATATATTGAA 57.291 30.769 0.00 0.00 0.00 2.69
195 196 8.888836 ATTGGAATTGGCATCAGATATATTGA 57.111 30.769 0.00 0.00 0.00 2.57
196 197 8.967918 AGATTGGAATTGGCATCAGATATATTG 58.032 33.333 0.00 0.00 0.00 1.90
198 199 9.848710 CTAGATTGGAATTGGCATCAGATATAT 57.151 33.333 0.00 0.00 0.00 0.86
199 200 7.772292 GCTAGATTGGAATTGGCATCAGATATA 59.228 37.037 0.00 0.00 0.00 0.86
200 201 6.602406 GCTAGATTGGAATTGGCATCAGATAT 59.398 38.462 0.00 0.00 0.00 1.63
201 202 5.942236 GCTAGATTGGAATTGGCATCAGATA 59.058 40.000 0.00 0.00 0.00 1.98
202 203 4.765856 GCTAGATTGGAATTGGCATCAGAT 59.234 41.667 0.00 0.00 0.00 2.90
203 204 4.139786 GCTAGATTGGAATTGGCATCAGA 58.860 43.478 0.00 0.00 0.00 3.27
204 205 3.058432 CGCTAGATTGGAATTGGCATCAG 60.058 47.826 0.00 0.00 0.00 2.90
205 206 2.880268 CGCTAGATTGGAATTGGCATCA 59.120 45.455 0.00 0.00 0.00 3.07
206 207 2.880890 ACGCTAGATTGGAATTGGCATC 59.119 45.455 0.00 0.00 0.00 3.91
207 208 2.880890 GACGCTAGATTGGAATTGGCAT 59.119 45.455 0.00 0.00 0.00 4.40
208 209 2.288666 GACGCTAGATTGGAATTGGCA 58.711 47.619 0.00 0.00 0.00 4.92
209 210 1.604278 GGACGCTAGATTGGAATTGGC 59.396 52.381 0.00 0.00 0.00 4.52
210 211 3.134458 GAGGACGCTAGATTGGAATTGG 58.866 50.000 0.00 0.00 0.00 3.16
211 212 2.797156 CGAGGACGCTAGATTGGAATTG 59.203 50.000 0.00 0.00 0.00 2.32
212 213 2.693591 TCGAGGACGCTAGATTGGAATT 59.306 45.455 0.00 0.00 39.58 2.17
213 214 2.034812 GTCGAGGACGCTAGATTGGAAT 59.965 50.000 0.00 0.00 39.58 3.01
214 215 1.404391 GTCGAGGACGCTAGATTGGAA 59.596 52.381 0.00 0.00 39.58 3.53
215 216 1.022735 GTCGAGGACGCTAGATTGGA 58.977 55.000 0.00 0.00 39.58 3.53
216 217 0.030908 GGTCGAGGACGCTAGATTGG 59.969 60.000 0.00 0.00 39.58 3.16
217 218 0.738975 TGGTCGAGGACGCTAGATTG 59.261 55.000 0.00 0.00 39.58 2.67
218 219 1.471119 TTGGTCGAGGACGCTAGATT 58.529 50.000 0.00 0.00 39.58 2.40
219 220 1.471119 TTTGGTCGAGGACGCTAGAT 58.529 50.000 0.00 0.00 39.58 1.98
220 221 1.068055 GTTTTGGTCGAGGACGCTAGA 60.068 52.381 0.00 0.00 39.58 2.43
221 222 1.336517 TGTTTTGGTCGAGGACGCTAG 60.337 52.381 0.00 0.00 39.58 3.42
222 223 0.675083 TGTTTTGGTCGAGGACGCTA 59.325 50.000 0.00 0.00 39.58 4.26
223 224 0.179067 TTGTTTTGGTCGAGGACGCT 60.179 50.000 0.00 0.00 39.58 5.07
224 225 0.234884 CTTGTTTTGGTCGAGGACGC 59.765 55.000 0.00 0.00 39.58 5.19
225 226 1.860676 TCTTGTTTTGGTCGAGGACG 58.139 50.000 0.00 0.00 41.26 4.79
226 227 3.813166 TCAATCTTGTTTTGGTCGAGGAC 59.187 43.478 0.00 0.00 0.00 3.85
227 228 3.813166 GTCAATCTTGTTTTGGTCGAGGA 59.187 43.478 0.00 0.00 0.00 3.71
228 229 3.058224 GGTCAATCTTGTTTTGGTCGAGG 60.058 47.826 0.00 0.00 0.00 4.63
229 230 3.563808 TGGTCAATCTTGTTTTGGTCGAG 59.436 43.478 0.00 0.00 0.00 4.04
230 231 3.546724 TGGTCAATCTTGTTTTGGTCGA 58.453 40.909 0.00 0.00 0.00 4.20
231 232 3.980646 TGGTCAATCTTGTTTTGGTCG 57.019 42.857 0.00 0.00 0.00 4.79
232 233 5.010012 AGTGATGGTCAATCTTGTTTTGGTC 59.990 40.000 0.00 0.00 36.15 4.02
233 234 4.895297 AGTGATGGTCAATCTTGTTTTGGT 59.105 37.500 0.00 0.00 36.15 3.67
234 235 5.458041 AGTGATGGTCAATCTTGTTTTGG 57.542 39.130 0.00 0.00 36.15 3.28
235 236 6.979817 TGAAAGTGATGGTCAATCTTGTTTTG 59.020 34.615 0.00 0.00 36.15 2.44
236 237 6.980397 GTGAAAGTGATGGTCAATCTTGTTTT 59.020 34.615 0.00 0.00 36.15 2.43
237 238 6.096705 TGTGAAAGTGATGGTCAATCTTGTTT 59.903 34.615 0.00 0.00 36.15 2.83
238 239 5.593909 TGTGAAAGTGATGGTCAATCTTGTT 59.406 36.000 0.00 0.00 36.15 2.83
239 240 5.132502 TGTGAAAGTGATGGTCAATCTTGT 58.867 37.500 0.00 0.00 36.15 3.16
240 241 5.694231 TGTGAAAGTGATGGTCAATCTTG 57.306 39.130 0.00 0.00 36.15 3.02
241 242 6.005823 TCATGTGAAAGTGATGGTCAATCTT 58.994 36.000 0.00 0.00 36.15 2.40
242 243 5.563592 TCATGTGAAAGTGATGGTCAATCT 58.436 37.500 0.00 0.00 36.15 2.40
243 244 5.885230 TCATGTGAAAGTGATGGTCAATC 57.115 39.130 0.00 0.00 35.67 2.67
244 245 5.535783 TGTTCATGTGAAAGTGATGGTCAAT 59.464 36.000 0.00 0.00 35.58 2.57
245 246 4.886489 TGTTCATGTGAAAGTGATGGTCAA 59.114 37.500 0.00 0.00 35.58 3.18
246 247 4.275689 GTGTTCATGTGAAAGTGATGGTCA 59.724 41.667 0.00 0.00 35.58 4.02
247 248 4.275689 TGTGTTCATGTGAAAGTGATGGTC 59.724 41.667 0.00 0.00 35.58 4.02
248 249 4.036734 GTGTGTTCATGTGAAAGTGATGGT 59.963 41.667 0.00 0.00 35.58 3.55
249 250 4.036616 TGTGTGTTCATGTGAAAGTGATGG 59.963 41.667 0.00 0.00 35.58 3.51
250 251 5.172460 TGTGTGTTCATGTGAAAGTGATG 57.828 39.130 0.00 0.00 35.58 3.07
251 252 5.765176 CATGTGTGTTCATGTGAAAGTGAT 58.235 37.500 0.00 0.00 39.93 3.06
252 253 5.172460 CATGTGTGTTCATGTGAAAGTGA 57.828 39.130 0.00 0.00 39.93 3.41
262 263 4.025040 AGGATGTGACATGTGTGTTCAT 57.975 40.909 1.15 0.29 39.09 2.57
263 264 3.490439 AGGATGTGACATGTGTGTTCA 57.510 42.857 1.15 0.00 39.09 3.18
264 265 3.189287 GGAAGGATGTGACATGTGTGTTC 59.811 47.826 1.15 0.00 39.09 3.18
265 266 3.149196 GGAAGGATGTGACATGTGTGTT 58.851 45.455 1.15 0.00 39.09 3.32
266 267 2.106338 TGGAAGGATGTGACATGTGTGT 59.894 45.455 1.15 0.00 42.49 3.72
267 268 2.485426 GTGGAAGGATGTGACATGTGTG 59.515 50.000 1.15 0.00 0.00 3.82
268 269 2.106338 TGTGGAAGGATGTGACATGTGT 59.894 45.455 1.15 0.00 0.00 3.72
269 270 2.745821 CTGTGGAAGGATGTGACATGTG 59.254 50.000 1.15 0.00 0.00 3.21
270 271 3.063510 CTGTGGAAGGATGTGACATGT 57.936 47.619 1.23 0.00 0.00 3.21
282 283 1.532868 CGTGCTTCTTTCCTGTGGAAG 59.467 52.381 0.00 0.00 43.06 3.46
283 284 1.140052 TCGTGCTTCTTTCCTGTGGAA 59.860 47.619 0.00 0.00 40.27 3.53
284 285 0.756294 TCGTGCTTCTTTCCTGTGGA 59.244 50.000 0.00 0.00 0.00 4.02
285 286 1.264288 GTTCGTGCTTCTTTCCTGTGG 59.736 52.381 0.00 0.00 0.00 4.17
286 287 1.264288 GGTTCGTGCTTCTTTCCTGTG 59.736 52.381 0.00 0.00 0.00 3.66
287 288 1.141053 AGGTTCGTGCTTCTTTCCTGT 59.859 47.619 0.00 0.00 0.00 4.00
288 289 1.532868 CAGGTTCGTGCTTCTTTCCTG 59.467 52.381 0.00 0.00 35.72 3.86
289 290 1.416401 TCAGGTTCGTGCTTCTTTCCT 59.584 47.619 0.00 0.00 0.00 3.36
290 291 1.531578 GTCAGGTTCGTGCTTCTTTCC 59.468 52.381 0.00 0.00 0.00 3.13
359 360 2.495270 ACATGCTGTCTCTGGTACTCTG 59.505 50.000 0.00 0.00 0.00 3.35
369 370 2.028112 TCCTTGTGGTACATGCTGTCTC 60.028 50.000 0.00 0.00 44.52 3.36
375 376 2.884639 ACTGTTTCCTTGTGGTACATGC 59.115 45.455 0.00 0.00 44.52 4.06
412 413 0.665835 CTAGCTCAGTCTACCTGCGG 59.334 60.000 0.00 0.00 41.25 5.69
414 415 3.193691 TGTTTCTAGCTCAGTCTACCTGC 59.806 47.826 0.00 0.00 41.25 4.85
415 416 4.381079 GGTGTTTCTAGCTCAGTCTACCTG 60.381 50.000 0.00 0.00 42.97 4.00
416 417 3.764972 GGTGTTTCTAGCTCAGTCTACCT 59.235 47.826 0.00 0.00 0.00 3.08
417 418 3.427773 CGGTGTTTCTAGCTCAGTCTACC 60.428 52.174 0.00 0.00 0.00 3.18
418 419 3.427773 CCGGTGTTTCTAGCTCAGTCTAC 60.428 52.174 0.00 0.00 0.00 2.59
419 420 2.753452 CCGGTGTTTCTAGCTCAGTCTA 59.247 50.000 0.00 0.00 0.00 2.59
448 449 1.021390 AATTTCTGAGGTCTGCGCCG 61.021 55.000 4.18 0.00 0.00 6.46
457 734 5.586643 GGCCACTCTTAAGTAATTTCTGAGG 59.413 44.000 0.00 0.00 33.25 3.86
479 1000 4.681978 ACGGCACCAAGACTCGGC 62.682 66.667 0.00 0.00 0.00 5.54
495 1016 1.014564 GGTGGACTCTACGCTTGCAC 61.015 60.000 0.00 0.00 0.00 4.57
535 1057 4.399004 ACATGTTGTCTCTATCTGAGCC 57.601 45.455 0.00 0.00 42.38 4.70
586 1111 1.414919 TGCCGGTGTTTCTAGTTCAGT 59.585 47.619 1.90 0.00 0.00 3.41
727 1252 4.764823 CCTGTGCAGACCAAGGTTATTTTA 59.235 41.667 0.02 0.00 0.00 1.52
795 1320 0.456995 CGGAGAGTTGACGAGGAAGC 60.457 60.000 0.00 0.00 0.00 3.86
836 1364 6.744537 GCAGTTTTATCTATGTTGAGCAGTTG 59.255 38.462 0.00 0.00 0.00 3.16
928 1456 4.447290 TCACGTCCTTTTGACAATTCTCA 58.553 39.130 0.00 0.00 44.71 3.27
935 1463 3.496884 GTGCTTATCACGTCCTTTTGACA 59.503 43.478 0.00 0.00 44.71 3.58
964 1492 3.366374 GCTGTTGCTTCTGGTAATGGTTC 60.366 47.826 0.00 0.00 36.03 3.62
1341 1881 0.951525 CGGCATGGTCAACGTTGGTA 60.952 55.000 27.02 14.30 0.00 3.25
1350 1890 4.429522 AGCATGGCGGCATGGTCA 62.430 61.111 40.50 8.95 38.76 4.02
1374 1914 1.401552 GCATAGAGCACGAAATTGCCA 59.598 47.619 0.00 0.00 44.14 4.92
1586 2129 0.538746 GCGGAAAAGGGAGGGAACAA 60.539 55.000 0.00 0.00 0.00 2.83
1630 2588 3.866703 TGAACCATTTCCACCAGTGTA 57.133 42.857 0.00 0.00 0.00 2.90
1668 2626 2.428890 AGTGTAGTAGATGCTGCCAGTC 59.571 50.000 0.00 0.00 0.00 3.51
1833 2791 4.091549 AGTCCATAACTTTCCACTCCGTA 58.908 43.478 0.00 0.00 33.03 4.02
1864 2822 1.594331 GCAACCCGACAGAAGTTTCT 58.406 50.000 0.00 0.00 38.25 2.52
1880 2838 2.048597 CAGTCTGTACCGCGGCAA 60.049 61.111 28.58 11.66 0.00 4.52
1891 2849 0.604780 CAGGCACCACTTCCAGTCTG 60.605 60.000 0.00 0.00 0.00 3.51
2063 3027 4.397420 TGGAAGTAGCTTGAATTGCTGAA 58.603 39.130 0.00 0.00 41.32 3.02
2108 3072 1.202256 TGTAACGCTCATAGTCGCCAG 60.202 52.381 0.00 0.00 0.00 4.85
2193 3157 5.483685 TCCAGCAAGAACTGTTGTAGTAT 57.516 39.130 0.00 0.00 39.18 2.12
2245 3209 2.430694 CTGATCCCACTATGTCACCGAA 59.569 50.000 0.00 0.00 0.00 4.30
2246 3210 2.031870 CTGATCCCACTATGTCACCGA 58.968 52.381 0.00 0.00 0.00 4.69
2247 3211 1.757118 ACTGATCCCACTATGTCACCG 59.243 52.381 0.00 0.00 0.00 4.94
2388 3352 7.230747 TGGAGATGAGGAAAACAATAACAAGA 58.769 34.615 0.00 0.00 0.00 3.02
2470 3434 0.620556 AATGCCTCGGGACTCATTGT 59.379 50.000 0.00 0.00 0.00 2.71
2528 3492 4.498241 CTCTTCACGAAATCCATCTGTCA 58.502 43.478 0.00 0.00 0.00 3.58
2733 3697 3.244700 CCAGAAGCCTCTCTTTTCCTTCA 60.245 47.826 0.00 0.00 35.54 3.02
3147 4111 0.679002 TTGCTTGCTCCTCATCAGCC 60.679 55.000 0.00 0.00 35.89 4.85
3505 4480 6.485171 ACTTACATTCCTGCTTCCATTTACT 58.515 36.000 0.00 0.00 0.00 2.24
3601 4576 8.999431 CACTGTGGTACTGAACATAAAAAGTAT 58.001 33.333 0.00 0.00 0.00 2.12
3614 4589 1.419381 TGGCTTCACTGTGGTACTGA 58.581 50.000 8.11 0.00 0.00 3.41
3790 4765 9.262358 GTTCTCTATATCGTTCCAATTTTAGCT 57.738 33.333 0.00 0.00 0.00 3.32
3791 4766 9.042008 TGTTCTCTATATCGTTCCAATTTTAGC 57.958 33.333 0.00 0.00 0.00 3.09
4020 4995 9.148104 CCCACTGTTACACTAAAAAGTATAGAC 57.852 37.037 0.00 0.00 0.00 2.59
4072 5049 5.050644 TCTGTTGTAATGCTTGCATTCAG 57.949 39.130 21.96 20.63 33.06 3.02
4203 5185 3.698539 TGTTGCACCTGACTTTGATTTCA 59.301 39.130 0.00 0.00 0.00 2.69
4204 5186 4.305989 TGTTGCACCTGACTTTGATTTC 57.694 40.909 0.00 0.00 0.00 2.17
4360 5366 7.223582 CACGAGGAGCCATATTATTATGCTAAG 59.776 40.741 0.00 0.00 34.94 2.18
4362 5368 6.154534 ACACGAGGAGCCATATTATTATGCTA 59.845 38.462 0.00 0.00 34.94 3.49
4363 5369 5.046304 ACACGAGGAGCCATATTATTATGCT 60.046 40.000 0.00 0.00 34.94 3.79
4364 5370 5.178797 ACACGAGGAGCCATATTATTATGC 58.821 41.667 0.00 0.00 34.94 3.14
4365 5371 9.464714 GTATACACGAGGAGCCATATTATTATG 57.535 37.037 0.00 0.00 35.87 1.90
4366 5372 8.639761 GGTATACACGAGGAGCCATATTATTAT 58.360 37.037 5.01 0.00 0.00 1.28
4367 5373 7.616542 TGGTATACACGAGGAGCCATATTATTA 59.383 37.037 5.01 0.00 0.00 0.98
4368 5374 6.439375 TGGTATACACGAGGAGCCATATTATT 59.561 38.462 5.01 0.00 0.00 1.40
4369 5375 5.955959 TGGTATACACGAGGAGCCATATTAT 59.044 40.000 5.01 0.00 0.00 1.28
4370 5376 5.326900 TGGTATACACGAGGAGCCATATTA 58.673 41.667 5.01 0.00 0.00 0.98
4371 5377 4.157246 TGGTATACACGAGGAGCCATATT 58.843 43.478 5.01 0.00 0.00 1.28
4372 5378 3.774734 TGGTATACACGAGGAGCCATAT 58.225 45.455 5.01 0.00 0.00 1.78
4373 5379 3.232720 TGGTATACACGAGGAGCCATA 57.767 47.619 5.01 0.00 0.00 2.74
4375 5381 1.855295 TTGGTATACACGAGGAGCCA 58.145 50.000 5.01 0.00 0.00 4.75
4376 5382 2.973694 TTTGGTATACACGAGGAGCC 57.026 50.000 5.01 0.00 0.00 4.70
4377 5383 7.654520 TGTTAATATTTGGTATACACGAGGAGC 59.345 37.037 5.01 0.00 0.00 4.70
4378 5384 9.706691 ATGTTAATATTTGGTATACACGAGGAG 57.293 33.333 5.01 0.00 0.00 3.69
4379 5385 9.701098 GATGTTAATATTTGGTATACACGAGGA 57.299 33.333 5.01 0.00 0.00 3.71
4380 5386 8.932791 GGATGTTAATATTTGGTATACACGAGG 58.067 37.037 5.01 0.00 0.00 4.63
4382 5388 8.430431 TGGGATGTTAATATTTGGTATACACGA 58.570 33.333 5.01 0.00 0.00 4.35
4383 5389 8.610248 TGGGATGTTAATATTTGGTATACACG 57.390 34.615 5.01 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.