Multiple sequence alignment - TraesCS1D01G197600

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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 TraesCS1D01G197600 chr1D 100.000 2585 0 0 1 2585 278944929 278947513 0.000000e+00 4774.0
1 TraesCS1D01G197600 chr1D 94.400 125 6 1 2462 2585 169057630 169057754 9.440000e-45 191.0
2 TraesCS1D01G197600 chr1D 97.059 34 1 0 224 257 278945064 278945097 9.990000e-05 58.4
3 TraesCS1D01G197600 chr1D 97.059 34 1 0 136 169 278945152 278945185 9.990000e-05 58.4
4 TraesCS1D01G197600 chr1B 95.385 2232 58 20 259 2463 378461681 378463894 0.000000e+00 3509.0
5 TraesCS1D01G197600 chr1A 95.657 1796 48 11 259 2029 351210926 351212716 0.000000e+00 2857.0
6 TraesCS1D01G197600 chr1A 95.509 334 11 1 2130 2463 351212999 351213328 4.900000e-147 531.0
7 TraesCS1D01G197600 chr7D 94.400 125 6 1 2462 2585 210565977 210565853 9.440000e-45 191.0
8 TraesCS1D01G197600 chr7D 93.600 125 7 1 2462 2585 475513752 475513628 4.390000e-43 185.0
9 TraesCS1D01G197600 chr5D 94.400 125 5 2 2462 2585 206101772 206101895 9.440000e-45 191.0
10 TraesCS1D01G197600 chr5D 93.023 129 8 1 2458 2585 223102789 223102661 1.220000e-43 187.0
11 TraesCS1D01G197600 chr5A 91.852 135 8 3 2454 2585 332291426 332291560 4.390000e-43 185.0
12 TraesCS1D01G197600 chr4D 91.791 134 10 1 2453 2585 293244345 293244478 4.390000e-43 185.0
13 TraesCS1D01G197600 chr3A 93.548 124 8 0 2462 2585 373686216 373686093 4.390000e-43 185.0
14 TraesCS1D01G197600 chr4A 91.729 133 10 1 2454 2585 362068083 362067951 1.580000e-42 183.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G197600 chr1D 278944929 278947513 2584 False 1630.266667 4774 98.039333 1 2585 3 chr1D.!!$F2 2584
1 TraesCS1D01G197600 chr1B 378461681 378463894 2213 False 3509.000000 3509 95.385000 259 2463 1 chr1B.!!$F1 2204
2 TraesCS1D01G197600 chr1A 351210926 351213328 2402 False 1694.000000 2857 95.583000 259 2463 2 chr1A.!!$F1 2204

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
71 72 0.030235 GTGTTTCCGTGTTGGCCTTC 59.97 55.0 3.32 0.0 37.8 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 1961 0.034476 GAGCATCAGATGGCCATCGA 59.966 55.0 34.48 31.7 42.48 3.59 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
21 22 1.371558 CCCGCTAGAGGGTTATGGC 59.628 63.158 22.75 0.00 46.38 4.40
22 23 1.006102 CCGCTAGAGGGTTATGGCG 60.006 63.158 4.27 0.00 41.84 5.69
23 24 1.664965 CGCTAGAGGGTTATGGCGC 60.665 63.158 0.00 0.00 36.46 6.53
24 25 1.664965 GCTAGAGGGTTATGGCGCG 60.665 63.158 0.00 0.00 0.00 6.86
25 26 2.038690 CTAGAGGGTTATGGCGCGA 58.961 57.895 12.10 0.00 0.00 5.87
26 27 0.603569 CTAGAGGGTTATGGCGCGAT 59.396 55.000 12.10 10.52 0.00 4.58
27 28 0.317160 TAGAGGGTTATGGCGCGATG 59.683 55.000 15.78 0.00 0.00 3.84
28 29 1.069090 GAGGGTTATGGCGCGATGA 59.931 57.895 15.78 3.56 0.00 2.92
29 30 0.531974 GAGGGTTATGGCGCGATGAA 60.532 55.000 15.78 2.96 0.00 2.57
30 31 0.532862 AGGGTTATGGCGCGATGAAG 60.533 55.000 15.78 0.00 0.00 3.02
31 32 0.814010 GGGTTATGGCGCGATGAAGT 60.814 55.000 15.78 0.00 0.00 3.01
32 33 0.304705 GGTTATGGCGCGATGAAGTG 59.695 55.000 15.78 0.00 0.00 3.16
33 34 0.316196 GTTATGGCGCGATGAAGTGC 60.316 55.000 15.78 0.00 46.01 4.40
49 50 3.142838 GCATCATGGTGCGCCCTT 61.143 61.111 16.56 0.70 35.10 3.95
50 51 2.802792 CATCATGGTGCGCCCTTG 59.197 61.111 15.15 18.62 39.25 3.61
51 52 3.142838 ATCATGGTGCGCCCTTGC 61.143 61.111 15.15 1.42 38.09 4.01
61 62 3.284449 GCCCTTGCGTGTTTCCGT 61.284 61.111 0.00 0.00 0.00 4.69
62 63 2.637025 CCCTTGCGTGTTTCCGTG 59.363 61.111 0.00 0.00 0.00 4.94
63 64 2.184167 CCCTTGCGTGTTTCCGTGT 61.184 57.895 0.00 0.00 0.00 4.49
64 65 1.720694 CCCTTGCGTGTTTCCGTGTT 61.721 55.000 0.00 0.00 0.00 3.32
65 66 0.591236 CCTTGCGTGTTTCCGTGTTG 60.591 55.000 0.00 0.00 0.00 3.33
66 67 0.591236 CTTGCGTGTTTCCGTGTTGG 60.591 55.000 0.00 0.00 40.09 3.77
67 68 2.353030 GCGTGTTTCCGTGTTGGC 60.353 61.111 0.00 0.00 37.80 4.52
68 69 2.330041 CGTGTTTCCGTGTTGGCC 59.670 61.111 0.00 0.00 37.80 5.36
69 70 2.184167 CGTGTTTCCGTGTTGGCCT 61.184 57.895 3.32 0.00 37.80 5.19
70 71 1.720694 CGTGTTTCCGTGTTGGCCTT 61.721 55.000 3.32 0.00 37.80 4.35
71 72 0.030235 GTGTTTCCGTGTTGGCCTTC 59.970 55.000 3.32 0.00 37.80 3.46
72 73 0.106918 TGTTTCCGTGTTGGCCTTCT 60.107 50.000 3.32 0.00 37.80 2.85
73 74 1.029681 GTTTCCGTGTTGGCCTTCTT 58.970 50.000 3.32 0.00 37.80 2.52
74 75 1.028905 TTTCCGTGTTGGCCTTCTTG 58.971 50.000 3.32 0.00 37.80 3.02
75 76 0.821711 TTCCGTGTTGGCCTTCTTGG 60.822 55.000 3.32 0.25 37.80 3.61
84 85 4.009015 CCTTCTTGGCAGCCTTCC 57.991 61.111 14.15 0.00 0.00 3.46
85 86 2.042831 CCTTCTTGGCAGCCTTCCG 61.043 63.158 14.15 0.00 0.00 4.30
86 87 2.034066 TTCTTGGCAGCCTTCCGG 59.966 61.111 14.15 0.00 0.00 5.14
87 88 2.469465 CTTCTTGGCAGCCTTCCGGA 62.469 60.000 14.15 0.00 0.00 5.14
88 89 1.852157 TTCTTGGCAGCCTTCCGGAT 61.852 55.000 14.15 0.00 0.00 4.18
89 90 1.821332 CTTGGCAGCCTTCCGGATC 60.821 63.158 14.15 0.00 0.00 3.36
90 91 2.262774 CTTGGCAGCCTTCCGGATCT 62.263 60.000 14.15 0.00 0.00 2.75
91 92 2.203126 GGCAGCCTTCCGGATCTG 60.203 66.667 18.93 18.93 0.00 2.90
92 93 2.735772 GGCAGCCTTCCGGATCTGA 61.736 63.158 24.41 3.51 0.00 3.27
93 94 1.522580 GCAGCCTTCCGGATCTGAC 60.523 63.158 24.41 15.33 0.00 3.51
94 95 1.227089 CAGCCTTCCGGATCTGACG 60.227 63.158 18.62 0.00 0.00 4.35
95 96 1.682684 AGCCTTCCGGATCTGACGT 60.683 57.895 4.15 0.00 0.00 4.34
96 97 1.218316 GCCTTCCGGATCTGACGTT 59.782 57.895 4.15 0.00 0.00 3.99
97 98 1.084370 GCCTTCCGGATCTGACGTTG 61.084 60.000 4.15 0.00 0.00 4.10
98 99 0.246635 CCTTCCGGATCTGACGTTGT 59.753 55.000 4.15 0.00 0.00 3.32
99 100 1.630148 CTTCCGGATCTGACGTTGTC 58.370 55.000 4.15 0.00 0.00 3.18
100 101 0.963225 TTCCGGATCTGACGTTGTCA 59.037 50.000 4.15 0.00 40.50 3.58
101 102 0.963225 TCCGGATCTGACGTTGTCAA 59.037 50.000 0.00 0.00 42.26 3.18
102 103 1.067846 TCCGGATCTGACGTTGTCAAG 60.068 52.381 0.00 0.00 42.26 3.02
103 104 1.350193 CGGATCTGACGTTGTCAAGG 58.650 55.000 0.00 3.73 42.26 3.61
104 105 1.067846 CGGATCTGACGTTGTCAAGGA 60.068 52.381 12.07 0.00 42.26 3.36
105 106 2.611518 GGATCTGACGTTGTCAAGGAG 58.388 52.381 12.07 0.56 42.26 3.69
106 107 2.611518 GATCTGACGTTGTCAAGGAGG 58.388 52.381 12.07 2.38 42.26 4.30
107 108 0.033504 TCTGACGTTGTCAAGGAGGC 59.966 55.000 12.07 0.00 42.26 4.70
108 109 0.034059 CTGACGTTGTCAAGGAGGCT 59.966 55.000 12.07 0.00 42.26 4.58
109 110 1.272490 CTGACGTTGTCAAGGAGGCTA 59.728 52.381 12.07 0.00 42.26 3.93
110 111 1.272490 TGACGTTGTCAAGGAGGCTAG 59.728 52.381 12.07 0.00 39.78 3.42
111 112 0.608640 ACGTTGTCAAGGAGGCTAGG 59.391 55.000 12.07 0.00 0.00 3.02
112 113 0.108138 CGTTGTCAAGGAGGCTAGGG 60.108 60.000 0.00 0.00 0.00 3.53
113 114 1.276622 GTTGTCAAGGAGGCTAGGGA 58.723 55.000 0.00 0.00 0.00 4.20
114 115 1.628846 GTTGTCAAGGAGGCTAGGGAA 59.371 52.381 0.00 0.00 0.00 3.97
115 116 1.573108 TGTCAAGGAGGCTAGGGAAG 58.427 55.000 0.00 0.00 0.00 3.46
116 117 0.833949 GTCAAGGAGGCTAGGGAAGG 59.166 60.000 0.00 0.00 0.00 3.46
117 118 0.326618 TCAAGGAGGCTAGGGAAGGG 60.327 60.000 0.00 0.00 0.00 3.95
118 119 0.326618 CAAGGAGGCTAGGGAAGGGA 60.327 60.000 0.00 0.00 0.00 4.20
119 120 0.326713 AAGGAGGCTAGGGAAGGGAC 60.327 60.000 0.00 0.00 0.00 4.46
120 121 1.766864 GGAGGCTAGGGAAGGGACC 60.767 68.421 0.00 0.00 0.00 4.46
121 122 1.003051 GAGGCTAGGGAAGGGACCA 59.997 63.158 0.00 0.00 0.00 4.02
122 123 0.400670 GAGGCTAGGGAAGGGACCAT 60.401 60.000 0.00 0.00 0.00 3.55
123 124 0.949582 AGGCTAGGGAAGGGACCATA 59.050 55.000 0.00 0.00 0.00 2.74
124 125 1.297141 AGGCTAGGGAAGGGACCATAA 59.703 52.381 0.00 0.00 0.00 1.90
125 126 2.132686 GGCTAGGGAAGGGACCATAAA 58.867 52.381 0.00 0.00 0.00 1.40
126 127 2.106684 GGCTAGGGAAGGGACCATAAAG 59.893 54.545 0.00 0.00 0.00 1.85
127 128 3.046374 GCTAGGGAAGGGACCATAAAGA 58.954 50.000 0.00 0.00 0.00 2.52
128 129 3.458487 GCTAGGGAAGGGACCATAAAGAA 59.542 47.826 0.00 0.00 0.00 2.52
129 130 4.104897 GCTAGGGAAGGGACCATAAAGAAT 59.895 45.833 0.00 0.00 0.00 2.40
130 131 5.399152 GCTAGGGAAGGGACCATAAAGAATT 60.399 44.000 0.00 0.00 0.00 2.17
131 132 4.871822 AGGGAAGGGACCATAAAGAATTG 58.128 43.478 0.00 0.00 0.00 2.32
132 133 3.960755 GGGAAGGGACCATAAAGAATTGG 59.039 47.826 0.00 0.00 39.02 3.16
133 134 4.325816 GGGAAGGGACCATAAAGAATTGGA 60.326 45.833 0.00 0.00 36.79 3.53
134 135 4.889995 GGAAGGGACCATAAAGAATTGGAG 59.110 45.833 0.00 0.00 36.79 3.86
135 136 3.903467 AGGGACCATAAAGAATTGGAGC 58.097 45.455 0.00 0.00 36.79 4.70
136 137 3.269381 AGGGACCATAAAGAATTGGAGCA 59.731 43.478 0.00 0.00 36.79 4.26
137 138 3.633986 GGGACCATAAAGAATTGGAGCAG 59.366 47.826 0.00 0.00 36.79 4.24
138 139 3.067320 GGACCATAAAGAATTGGAGCAGC 59.933 47.826 0.00 0.00 36.79 5.25
139 140 3.950395 GACCATAAAGAATTGGAGCAGCT 59.050 43.478 0.00 0.00 36.79 4.24
140 141 5.116084 ACCATAAAGAATTGGAGCAGCTA 57.884 39.130 0.00 0.00 36.79 3.32
141 142 5.128919 ACCATAAAGAATTGGAGCAGCTAG 58.871 41.667 0.00 0.00 36.79 3.42
142 143 4.518211 CCATAAAGAATTGGAGCAGCTAGG 59.482 45.833 0.00 0.00 34.81 3.02
143 144 2.725221 AAGAATTGGAGCAGCTAGGG 57.275 50.000 0.00 0.00 0.00 3.53
144 145 0.182299 AGAATTGGAGCAGCTAGGGC 59.818 55.000 0.00 0.00 39.06 5.19
164 165 2.411628 TCGGTCAGAGAGAAGGAGAG 57.588 55.000 0.00 0.00 0.00 3.20
165 166 1.065053 TCGGTCAGAGAGAAGGAGAGG 60.065 57.143 0.00 0.00 0.00 3.69
166 167 1.111277 GGTCAGAGAGAAGGAGAGGC 58.889 60.000 0.00 0.00 0.00 4.70
167 168 1.111277 GTCAGAGAGAAGGAGAGGCC 58.889 60.000 0.00 0.00 0.00 5.19
168 169 0.707024 TCAGAGAGAAGGAGAGGCCA 59.293 55.000 5.01 0.00 40.02 5.36
169 170 0.823460 CAGAGAGAAGGAGAGGCCAC 59.177 60.000 5.01 0.00 40.02 5.01
170 171 0.411452 AGAGAGAAGGAGAGGCCACA 59.589 55.000 5.01 0.00 40.02 4.17
171 172 0.823460 GAGAGAAGGAGAGGCCACAG 59.177 60.000 5.01 0.00 40.02 3.66
172 173 0.116143 AGAGAAGGAGAGGCCACAGT 59.884 55.000 5.01 0.00 40.02 3.55
173 174 1.359474 AGAGAAGGAGAGGCCACAGTA 59.641 52.381 5.01 0.00 40.02 2.74
174 175 1.754226 GAGAAGGAGAGGCCACAGTAG 59.246 57.143 5.01 0.00 40.02 2.57
175 176 1.077993 AGAAGGAGAGGCCACAGTAGT 59.922 52.381 5.01 0.00 40.02 2.73
176 177 1.903183 GAAGGAGAGGCCACAGTAGTT 59.097 52.381 5.01 0.00 40.02 2.24
177 178 2.031495 AGGAGAGGCCACAGTAGTTT 57.969 50.000 5.01 0.00 40.02 2.66
178 179 1.625818 AGGAGAGGCCACAGTAGTTTG 59.374 52.381 5.01 0.00 40.02 2.93
179 180 1.443802 GAGAGGCCACAGTAGTTTGC 58.556 55.000 5.01 0.00 0.00 3.68
180 181 1.002544 GAGAGGCCACAGTAGTTTGCT 59.997 52.381 5.01 0.00 0.00 3.91
181 182 1.421646 AGAGGCCACAGTAGTTTGCTT 59.578 47.619 5.01 0.00 0.00 3.91
182 183 1.807142 GAGGCCACAGTAGTTTGCTTC 59.193 52.381 5.01 0.00 0.00 3.86
183 184 1.421646 AGGCCACAGTAGTTTGCTTCT 59.578 47.619 5.01 0.00 0.00 2.85
184 185 2.158608 AGGCCACAGTAGTTTGCTTCTT 60.159 45.455 5.01 0.00 0.00 2.52
185 186 2.623416 GGCCACAGTAGTTTGCTTCTTT 59.377 45.455 0.00 0.00 0.00 2.52
186 187 3.550842 GGCCACAGTAGTTTGCTTCTTTG 60.551 47.826 0.00 0.00 0.00 2.77
187 188 3.550842 GCCACAGTAGTTTGCTTCTTTGG 60.551 47.826 3.19 3.19 40.64 3.28
188 189 3.882888 CCACAGTAGTTTGCTTCTTTGGA 59.117 43.478 1.76 0.00 40.33 3.53
189 190 4.023707 CCACAGTAGTTTGCTTCTTTGGAG 60.024 45.833 1.76 0.00 40.33 3.86
190 191 4.816385 CACAGTAGTTTGCTTCTTTGGAGA 59.184 41.667 0.00 0.00 0.00 3.71
191 192 4.816925 ACAGTAGTTTGCTTCTTTGGAGAC 59.183 41.667 0.00 0.00 0.00 3.36
192 193 4.816385 CAGTAGTTTGCTTCTTTGGAGACA 59.184 41.667 0.00 0.00 39.83 3.41
193 194 5.471456 CAGTAGTTTGCTTCTTTGGAGACAT 59.529 40.000 0.00 0.00 42.32 3.06
194 195 4.843220 AGTTTGCTTCTTTGGAGACATG 57.157 40.909 0.00 0.00 42.32 3.21
195 196 3.005155 AGTTTGCTTCTTTGGAGACATGC 59.995 43.478 0.00 0.00 42.32 4.06
196 197 2.275134 TGCTTCTTTGGAGACATGCA 57.725 45.000 0.00 0.00 42.32 3.96
197 198 1.881973 TGCTTCTTTGGAGACATGCAC 59.118 47.619 0.00 0.00 42.32 4.57
198 199 1.881973 GCTTCTTTGGAGACATGCACA 59.118 47.619 0.00 0.00 42.32 4.57
199 200 2.351157 GCTTCTTTGGAGACATGCACAC 60.351 50.000 0.00 0.00 42.32 3.82
200 201 2.936919 TCTTTGGAGACATGCACACT 57.063 45.000 0.00 0.00 42.32 3.55
201 202 3.213206 TCTTTGGAGACATGCACACTT 57.787 42.857 0.00 0.00 42.32 3.16
202 203 4.350368 TCTTTGGAGACATGCACACTTA 57.650 40.909 0.00 0.00 42.32 2.24
203 204 4.910195 TCTTTGGAGACATGCACACTTAT 58.090 39.130 0.00 0.00 42.32 1.73
204 205 6.048732 TCTTTGGAGACATGCACACTTATA 57.951 37.500 0.00 0.00 42.32 0.98
205 206 6.653020 TCTTTGGAGACATGCACACTTATAT 58.347 36.000 0.00 0.00 42.32 0.86
206 207 7.112122 TCTTTGGAGACATGCACACTTATATT 58.888 34.615 0.00 0.00 42.32 1.28
207 208 7.611467 TCTTTGGAGACATGCACACTTATATTT 59.389 33.333 0.00 0.00 42.32 1.40
208 209 7.701539 TTGGAGACATGCACACTTATATTTT 57.298 32.000 0.00 0.00 42.32 1.82
209 210 7.320443 TGGAGACATGCACACTTATATTTTC 57.680 36.000 0.00 0.00 33.40 2.29
210 211 7.112122 TGGAGACATGCACACTTATATTTTCT 58.888 34.615 0.00 0.00 33.40 2.52
211 212 7.611467 TGGAGACATGCACACTTATATTTTCTT 59.389 33.333 0.00 0.00 33.40 2.52
212 213 8.462016 GGAGACATGCACACTTATATTTTCTTT 58.538 33.333 0.00 0.00 0.00 2.52
213 214 9.846248 GAGACATGCACACTTATATTTTCTTTT 57.154 29.630 0.00 0.00 0.00 2.27
252 253 2.411628 TCGGTCAGAGAGAAGGAGAG 57.588 55.000 0.00 0.00 0.00 3.20
253 254 1.909986 TCGGTCAGAGAGAAGGAGAGA 59.090 52.381 0.00 0.00 0.00 3.10
254 255 2.014128 CGGTCAGAGAGAAGGAGAGAC 58.986 57.143 0.00 0.00 0.00 3.36
255 256 2.375146 GGTCAGAGAGAAGGAGAGACC 58.625 57.143 0.00 0.00 37.50 3.85
256 257 2.291282 GGTCAGAGAGAAGGAGAGACCA 60.291 54.545 0.00 0.00 42.65 4.02
257 258 3.627237 GGTCAGAGAGAAGGAGAGACCAT 60.627 52.174 0.00 0.00 42.65 3.55
301 302 9.214957 GAGGGGGTCAACAAATAAAATAAAAAG 57.785 33.333 0.00 0.00 0.00 2.27
317 318 3.508845 AAAAGCTGGAGCAAAGGAGTA 57.491 42.857 0.65 0.00 45.16 2.59
325 326 1.763545 GAGCAAAGGAGTACTAGGGGG 59.236 57.143 0.00 0.00 0.00 5.40
416 418 9.326339 GATTGGTTCATAACTCGTTCTTTTTAC 57.674 33.333 0.00 0.00 0.00 2.01
703 727 7.101652 TGGTAATTTATAAATGCGGCAAGAA 57.898 32.000 6.82 0.00 0.00 2.52
704 728 7.721402 TGGTAATTTATAAATGCGGCAAGAAT 58.279 30.769 6.82 3.14 0.00 2.40
718 742 4.378978 CGGCAAGAATAATTCGAACCAACA 60.379 41.667 0.00 0.00 34.02 3.33
735 759 2.712057 ACAATTTTGCGGCTTCTCTG 57.288 45.000 0.00 0.00 0.00 3.35
1068 1092 4.424711 ACCGCCACCGCCAATCAT 62.425 61.111 0.00 0.00 0.00 2.45
1071 1095 2.188829 CGCCACCGCCAATCATCAT 61.189 57.895 0.00 0.00 0.00 2.45
1084 1108 1.095807 TCATCATCAGCAGCAGCAGC 61.096 55.000 3.17 0.46 45.49 5.25
1085 1109 1.077716 ATCATCAGCAGCAGCAGCA 60.078 52.632 12.92 0.00 45.49 4.41
1086 1110 1.098129 ATCATCAGCAGCAGCAGCAG 61.098 55.000 12.92 3.97 45.49 4.24
1087 1111 2.438614 ATCAGCAGCAGCAGCAGG 60.439 61.111 12.92 3.88 45.49 4.85
1587 1617 0.680061 ACAACGTCTTCTCCTGACCC 59.320 55.000 0.00 0.00 0.00 4.46
1749 1779 5.087323 GGGGAGGTCAGTGATCAGATAATA 58.913 45.833 6.10 0.00 0.00 0.98
1921 1951 1.299926 CCCGTCAATCGATCGTCCC 60.300 63.158 15.94 0.00 42.86 4.46
1931 1961 0.249073 CGATCGTCCCAAATCTCGCT 60.249 55.000 7.03 0.00 0.00 4.93
1932 1962 1.492720 GATCGTCCCAAATCTCGCTC 58.507 55.000 0.00 0.00 0.00 5.03
1938 1968 1.502163 CCCAAATCTCGCTCGATGGC 61.502 60.000 4.59 0.00 0.00 4.40
1955 1985 1.064240 TGGCCATCTGATGCTCACATT 60.064 47.619 12.17 0.00 36.35 2.71
1969 2005 4.084066 TGCTCACATTGTGTTCGACATTAC 60.084 41.667 16.06 0.00 33.40 1.89
2250 2478 2.476619 CGGATCATGCGTGGTTATCTTC 59.523 50.000 5.98 0.00 0.00 2.87
2276 2504 2.508663 GCTGTAGCCGTCGGGTTC 60.509 66.667 22.84 17.26 34.28 3.62
2308 2536 1.888512 TCCAGTGAAAAGGCTCAATGC 59.111 47.619 0.00 0.00 39.49 3.56
2355 2583 2.046507 GCTGTCTGCTGGTCCCTG 60.047 66.667 0.00 0.00 38.95 4.45
2463 2691 8.366671 ACTGAAGAAGTTGAGTTGTATGTTAC 57.633 34.615 0.00 0.00 34.57 2.50
2464 2692 8.204836 ACTGAAGAAGTTGAGTTGTATGTTACT 58.795 33.333 0.00 0.00 34.57 2.24
2465 2693 8.589335 TGAAGAAGTTGAGTTGTATGTTACTC 57.411 34.615 0.00 0.00 40.89 2.59
2466 2694 7.656137 TGAAGAAGTTGAGTTGTATGTTACTCC 59.344 37.037 0.00 0.00 40.00 3.85
2467 2695 6.465084 AGAAGTTGAGTTGTATGTTACTCCC 58.535 40.000 0.00 0.00 40.00 4.30
2468 2696 6.270231 AGAAGTTGAGTTGTATGTTACTCCCT 59.730 38.462 0.00 0.00 40.00 4.20
2469 2697 7.453752 AGAAGTTGAGTTGTATGTTACTCCCTA 59.546 37.037 0.00 0.00 40.00 3.53
2470 2698 7.735326 AGTTGAGTTGTATGTTACTCCCTAT 57.265 36.000 0.00 0.00 40.00 2.57
2471 2699 7.556844 AGTTGAGTTGTATGTTACTCCCTATG 58.443 38.462 0.00 0.00 40.00 2.23
2472 2700 7.180408 AGTTGAGTTGTATGTTACTCCCTATGT 59.820 37.037 0.00 0.00 40.00 2.29
2473 2701 7.490657 TGAGTTGTATGTTACTCCCTATGTT 57.509 36.000 0.00 0.00 40.00 2.71
2474 2702 7.553334 TGAGTTGTATGTTACTCCCTATGTTC 58.447 38.462 0.00 0.00 40.00 3.18
2475 2703 6.885922 AGTTGTATGTTACTCCCTATGTTCC 58.114 40.000 0.00 0.00 0.00 3.62
2476 2704 6.672657 AGTTGTATGTTACTCCCTATGTTCCT 59.327 38.462 0.00 0.00 0.00 3.36
2477 2705 7.842743 AGTTGTATGTTACTCCCTATGTTCCTA 59.157 37.037 0.00 0.00 0.00 2.94
2478 2706 8.480501 GTTGTATGTTACTCCCTATGTTCCTAA 58.519 37.037 0.00 0.00 0.00 2.69
2479 2707 8.612486 TGTATGTTACTCCCTATGTTCCTAAA 57.388 34.615 0.00 0.00 0.00 1.85
2480 2708 9.220906 TGTATGTTACTCCCTATGTTCCTAAAT 57.779 33.333 0.00 0.00 0.00 1.40
2488 2716 9.004231 ACTCCCTATGTTCCTAAATATTTGACT 57.996 33.333 11.05 0.00 0.00 3.41
2489 2717 9.853177 CTCCCTATGTTCCTAAATATTTGACTT 57.147 33.333 11.05 5.56 0.00 3.01
2526 2754 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
2527 2755 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
2528 2756 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
2529 2757 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
2530 2758 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
2531 2759 7.889600 TGGACTACCACATACGGATGTATATAA 59.110 37.037 14.23 0.00 44.82 0.98
2532 2760 8.742777 GGACTACCACATACGGATGTATATAAA 58.257 37.037 14.23 0.00 44.82 1.40
2533 2761 9.565213 GACTACCACATACGGATGTATATAAAC 57.435 37.037 14.23 0.00 44.82 2.01
2534 2762 9.081204 ACTACCACATACGGATGTATATAAACA 57.919 33.333 14.23 0.00 44.82 2.83
2565 2793 9.973450 TTAGAGTATAGATTCACTCATTTGCTC 57.027 33.333 4.70 0.00 42.99 4.26
2566 2794 7.441017 AGAGTATAGATTCACTCATTTGCTCC 58.559 38.462 4.70 0.00 42.99 4.70
2567 2795 6.219473 AGTATAGATTCACTCATTTGCTCCG 58.781 40.000 0.00 0.00 0.00 4.63
2568 2796 3.340814 AGATTCACTCATTTGCTCCGT 57.659 42.857 0.00 0.00 0.00 4.69
2569 2797 4.471904 AGATTCACTCATTTGCTCCGTA 57.528 40.909 0.00 0.00 0.00 4.02
2570 2798 5.028549 AGATTCACTCATTTGCTCCGTAT 57.971 39.130 0.00 0.00 0.00 3.06
2571 2799 4.813161 AGATTCACTCATTTGCTCCGTATG 59.187 41.667 0.00 0.00 0.00 2.39
2572 2800 3.610040 TCACTCATTTGCTCCGTATGT 57.390 42.857 0.00 0.00 0.00 2.29
2573 2801 4.729227 TCACTCATTTGCTCCGTATGTA 57.271 40.909 0.00 0.00 0.00 2.29
2574 2802 4.682787 TCACTCATTTGCTCCGTATGTAG 58.317 43.478 0.00 0.00 0.00 2.74
2575 2803 4.159693 TCACTCATTTGCTCCGTATGTAGT 59.840 41.667 0.00 0.00 0.00 2.73
2576 2804 4.504461 CACTCATTTGCTCCGTATGTAGTC 59.496 45.833 0.00 0.00 0.00 2.59
2577 2805 4.159693 ACTCATTTGCTCCGTATGTAGTCA 59.840 41.667 0.00 0.00 0.00 3.41
2578 2806 4.430007 TCATTTGCTCCGTATGTAGTCAC 58.570 43.478 0.00 0.00 0.00 3.67
2579 2807 4.159693 TCATTTGCTCCGTATGTAGTCACT 59.840 41.667 0.00 0.00 0.00 3.41
2580 2808 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
2581 2809 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
2582 2810 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
2583 2811 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
2584 2812 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.006102 CGCCATAACCCTCTAGCGG 60.006 63.158 0.00 0.00 39.89 5.52
5 6 1.664965 GCGCCATAACCCTCTAGCG 60.665 63.158 0.00 0.00 45.91 4.26
6 7 1.664965 CGCGCCATAACCCTCTAGC 60.665 63.158 0.00 0.00 0.00 3.42
7 8 0.603569 ATCGCGCCATAACCCTCTAG 59.396 55.000 0.00 0.00 0.00 2.43
8 9 0.317160 CATCGCGCCATAACCCTCTA 59.683 55.000 0.00 0.00 0.00 2.43
9 10 1.069765 CATCGCGCCATAACCCTCT 59.930 57.895 0.00 0.00 0.00 3.69
10 11 0.531974 TTCATCGCGCCATAACCCTC 60.532 55.000 0.00 0.00 0.00 4.30
11 12 0.532862 CTTCATCGCGCCATAACCCT 60.533 55.000 0.00 0.00 0.00 4.34
12 13 0.814010 ACTTCATCGCGCCATAACCC 60.814 55.000 0.00 0.00 0.00 4.11
13 14 0.304705 CACTTCATCGCGCCATAACC 59.695 55.000 0.00 0.00 0.00 2.85
14 15 0.316196 GCACTTCATCGCGCCATAAC 60.316 55.000 0.00 0.00 0.00 1.89
15 16 0.742635 TGCACTTCATCGCGCCATAA 60.743 50.000 0.00 0.00 0.00 1.90
16 17 0.532640 ATGCACTTCATCGCGCCATA 60.533 50.000 0.00 0.00 0.00 2.74
17 18 1.779025 GATGCACTTCATCGCGCCAT 61.779 55.000 0.00 0.00 41.82 4.40
18 19 2.436469 ATGCACTTCATCGCGCCA 60.436 55.556 0.00 0.00 0.00 5.69
19 20 2.325857 GATGCACTTCATCGCGCC 59.674 61.111 0.00 0.00 41.82 6.53
25 26 0.736636 CGCACCATGATGCACTTCAT 59.263 50.000 13.73 0.00 46.47 2.57
26 27 1.925415 GCGCACCATGATGCACTTCA 61.925 55.000 13.73 0.00 46.47 3.02
27 28 1.226491 GCGCACCATGATGCACTTC 60.226 57.895 13.73 0.00 46.47 3.01
28 29 2.703798 GGCGCACCATGATGCACTT 61.704 57.895 13.73 0.00 46.47 3.16
29 30 3.136123 GGCGCACCATGATGCACT 61.136 61.111 13.73 0.00 46.47 4.40
30 31 4.197498 GGGCGCACCATGATGCAC 62.197 66.667 13.73 1.13 46.47 4.57
31 32 3.942377 AAGGGCGCACCATGATGCA 62.942 57.895 13.73 0.00 46.47 3.96
32 33 3.142838 AAGGGCGCACCATGATGC 61.143 61.111 5.73 0.33 43.89 3.91
33 34 2.802792 CAAGGGCGCACCATGATG 59.197 61.111 5.73 1.14 40.39 3.07
34 35 3.142838 GCAAGGGCGCACCATGAT 61.143 61.111 19.81 0.00 40.39 2.45
46 47 0.591236 CAACACGGAAACACGCAAGG 60.591 55.000 0.00 0.00 46.39 3.61
47 48 0.591236 CCAACACGGAAACACGCAAG 60.591 55.000 0.00 0.00 40.21 4.01
48 49 1.429825 CCAACACGGAAACACGCAA 59.570 52.632 0.00 0.00 36.56 4.85
49 50 3.102985 CCAACACGGAAACACGCA 58.897 55.556 0.00 0.00 36.56 5.24
50 51 2.353030 GCCAACACGGAAACACGC 60.353 61.111 0.00 0.00 36.56 5.34
51 52 1.720694 AAGGCCAACACGGAAACACG 61.721 55.000 5.01 0.00 36.56 4.49
52 53 0.030235 GAAGGCCAACACGGAAACAC 59.970 55.000 5.01 0.00 36.56 3.32
53 54 0.106918 AGAAGGCCAACACGGAAACA 60.107 50.000 5.01 0.00 36.56 2.83
54 55 1.029681 AAGAAGGCCAACACGGAAAC 58.970 50.000 5.01 0.00 36.56 2.78
55 56 1.028905 CAAGAAGGCCAACACGGAAA 58.971 50.000 5.01 0.00 36.56 3.13
56 57 0.821711 CCAAGAAGGCCAACACGGAA 60.822 55.000 5.01 0.00 36.56 4.30
57 58 1.228124 CCAAGAAGGCCAACACGGA 60.228 57.895 5.01 0.00 36.56 4.69
58 59 3.354678 CCAAGAAGGCCAACACGG 58.645 61.111 5.01 0.00 38.11 4.94
67 68 2.042831 CGGAAGGCTGCCAAGAAGG 61.043 63.158 22.65 0.63 41.84 3.46
68 69 3.583383 CGGAAGGCTGCCAAGAAG 58.417 61.111 22.65 4.12 0.00 2.85
79 80 1.736032 GACAACGTCAGATCCGGAAGG 60.736 57.143 9.01 0.00 42.10 3.46
80 81 1.067846 TGACAACGTCAGATCCGGAAG 60.068 52.381 9.01 1.12 37.67 3.46
81 82 0.963225 TGACAACGTCAGATCCGGAA 59.037 50.000 9.01 0.00 37.67 4.30
82 83 0.963225 TTGACAACGTCAGATCCGGA 59.037 50.000 6.61 6.61 43.69 5.14
83 84 1.350193 CTTGACAACGTCAGATCCGG 58.650 55.000 0.00 0.00 43.69 5.14
84 85 1.067846 TCCTTGACAACGTCAGATCCG 60.068 52.381 0.00 0.00 43.69 4.18
85 86 2.611518 CTCCTTGACAACGTCAGATCC 58.388 52.381 0.00 0.00 43.69 3.36
86 87 2.611518 CCTCCTTGACAACGTCAGATC 58.388 52.381 0.00 0.00 43.69 2.75
87 88 1.338200 GCCTCCTTGACAACGTCAGAT 60.338 52.381 0.00 0.00 43.69 2.90
88 89 0.033504 GCCTCCTTGACAACGTCAGA 59.966 55.000 0.00 0.00 43.69 3.27
89 90 0.034059 AGCCTCCTTGACAACGTCAG 59.966 55.000 0.00 0.00 43.69 3.51
90 91 1.272490 CTAGCCTCCTTGACAACGTCA 59.728 52.381 0.00 0.00 41.09 4.35
91 92 1.404315 CCTAGCCTCCTTGACAACGTC 60.404 57.143 0.00 0.00 0.00 4.34
92 93 0.608640 CCTAGCCTCCTTGACAACGT 59.391 55.000 0.00 0.00 0.00 3.99
93 94 0.108138 CCCTAGCCTCCTTGACAACG 60.108 60.000 0.00 0.00 0.00 4.10
94 95 1.276622 TCCCTAGCCTCCTTGACAAC 58.723 55.000 0.00 0.00 0.00 3.32
95 96 1.909302 CTTCCCTAGCCTCCTTGACAA 59.091 52.381 0.00 0.00 0.00 3.18
96 97 1.573108 CTTCCCTAGCCTCCTTGACA 58.427 55.000 0.00 0.00 0.00 3.58
97 98 0.833949 CCTTCCCTAGCCTCCTTGAC 59.166 60.000 0.00 0.00 0.00 3.18
98 99 0.326618 CCCTTCCCTAGCCTCCTTGA 60.327 60.000 0.00 0.00 0.00 3.02
99 100 0.326618 TCCCTTCCCTAGCCTCCTTG 60.327 60.000 0.00 0.00 0.00 3.61
100 101 0.326713 GTCCCTTCCCTAGCCTCCTT 60.327 60.000 0.00 0.00 0.00 3.36
101 102 1.315216 GTCCCTTCCCTAGCCTCCT 59.685 63.158 0.00 0.00 0.00 3.69
102 103 1.766864 GGTCCCTTCCCTAGCCTCC 60.767 68.421 0.00 0.00 0.00 4.30
103 104 0.400670 ATGGTCCCTTCCCTAGCCTC 60.401 60.000 0.00 0.00 0.00 4.70
104 105 0.949582 TATGGTCCCTTCCCTAGCCT 59.050 55.000 0.00 0.00 0.00 4.58
105 106 1.815757 TTATGGTCCCTTCCCTAGCC 58.184 55.000 0.00 0.00 0.00 3.93
106 107 3.046374 TCTTTATGGTCCCTTCCCTAGC 58.954 50.000 0.00 0.00 0.00 3.42
107 108 5.913946 ATTCTTTATGGTCCCTTCCCTAG 57.086 43.478 0.00 0.00 0.00 3.02
108 109 5.103686 CCAATTCTTTATGGTCCCTTCCCTA 60.104 44.000 0.00 0.00 31.84 3.53
109 110 4.326132 CCAATTCTTTATGGTCCCTTCCCT 60.326 45.833 0.00 0.00 31.84 4.20
110 111 3.960755 CCAATTCTTTATGGTCCCTTCCC 59.039 47.826 0.00 0.00 31.84 3.97
111 112 4.867086 TCCAATTCTTTATGGTCCCTTCC 58.133 43.478 0.00 0.00 37.94 3.46
112 113 4.339530 GCTCCAATTCTTTATGGTCCCTTC 59.660 45.833 0.00 0.00 37.94 3.46
113 114 4.264352 TGCTCCAATTCTTTATGGTCCCTT 60.264 41.667 0.00 0.00 37.94 3.95
114 115 3.269381 TGCTCCAATTCTTTATGGTCCCT 59.731 43.478 0.00 0.00 37.94 4.20
115 116 3.631250 TGCTCCAATTCTTTATGGTCCC 58.369 45.455 0.00 0.00 37.94 4.46
116 117 3.067320 GCTGCTCCAATTCTTTATGGTCC 59.933 47.826 0.00 0.00 37.94 4.46
117 118 3.950395 AGCTGCTCCAATTCTTTATGGTC 59.050 43.478 0.00 0.00 37.94 4.02
118 119 3.973425 AGCTGCTCCAATTCTTTATGGT 58.027 40.909 0.00 0.00 37.94 3.55
119 120 4.518211 CCTAGCTGCTCCAATTCTTTATGG 59.482 45.833 4.91 0.00 38.09 2.74
120 121 4.518211 CCCTAGCTGCTCCAATTCTTTATG 59.482 45.833 4.91 0.00 0.00 1.90
121 122 4.723309 CCCTAGCTGCTCCAATTCTTTAT 58.277 43.478 4.91 0.00 0.00 1.40
122 123 3.685550 GCCCTAGCTGCTCCAATTCTTTA 60.686 47.826 4.91 0.00 35.50 1.85
123 124 2.947695 GCCCTAGCTGCTCCAATTCTTT 60.948 50.000 4.91 0.00 35.50 2.52
124 125 1.409381 GCCCTAGCTGCTCCAATTCTT 60.409 52.381 4.91 0.00 35.50 2.52
125 126 0.182299 GCCCTAGCTGCTCCAATTCT 59.818 55.000 4.91 0.00 35.50 2.40
126 127 2.712984 GCCCTAGCTGCTCCAATTC 58.287 57.895 4.91 0.00 35.50 2.17
127 128 4.995594 GCCCTAGCTGCTCCAATT 57.004 55.556 4.91 0.00 35.50 2.32
137 138 1.452145 CTCTCTGACCGAGCCCTAGC 61.452 65.000 0.00 0.00 39.70 3.42
138 139 0.181587 TCTCTCTGACCGAGCCCTAG 59.818 60.000 0.00 0.00 39.70 3.02
139 140 0.624254 TTCTCTCTGACCGAGCCCTA 59.376 55.000 0.00 0.00 39.70 3.53
140 141 0.682855 CTTCTCTCTGACCGAGCCCT 60.683 60.000 0.00 0.00 39.70 5.19
141 142 1.671901 CCTTCTCTCTGACCGAGCCC 61.672 65.000 0.00 0.00 39.70 5.19
142 143 0.681564 TCCTTCTCTCTGACCGAGCC 60.682 60.000 0.00 0.00 39.70 4.70
143 144 0.738389 CTCCTTCTCTCTGACCGAGC 59.262 60.000 0.00 0.00 39.70 5.03
144 145 2.288666 CTCTCCTTCTCTCTGACCGAG 58.711 57.143 0.00 0.00 41.30 4.63
145 146 1.065053 CCTCTCCTTCTCTCTGACCGA 60.065 57.143 0.00 0.00 0.00 4.69
146 147 1.388547 CCTCTCCTTCTCTCTGACCG 58.611 60.000 0.00 0.00 0.00 4.79
147 148 1.111277 GCCTCTCCTTCTCTCTGACC 58.889 60.000 0.00 0.00 0.00 4.02
148 149 1.111277 GGCCTCTCCTTCTCTCTGAC 58.889 60.000 0.00 0.00 0.00 3.51
149 150 0.707024 TGGCCTCTCCTTCTCTCTGA 59.293 55.000 3.32 0.00 35.26 3.27
150 151 0.823460 GTGGCCTCTCCTTCTCTCTG 59.177 60.000 3.32 0.00 35.26 3.35
151 152 0.411452 TGTGGCCTCTCCTTCTCTCT 59.589 55.000 3.32 0.00 35.26 3.10
152 153 0.823460 CTGTGGCCTCTCCTTCTCTC 59.177 60.000 3.32 0.00 35.26 3.20
153 154 0.116143 ACTGTGGCCTCTCCTTCTCT 59.884 55.000 3.32 0.00 35.26 3.10
154 155 1.754226 CTACTGTGGCCTCTCCTTCTC 59.246 57.143 3.32 0.00 35.26 2.87
155 156 1.077993 ACTACTGTGGCCTCTCCTTCT 59.922 52.381 3.32 0.00 35.26 2.85
156 157 1.562783 ACTACTGTGGCCTCTCCTTC 58.437 55.000 3.32 0.00 35.26 3.46
157 158 2.031495 AACTACTGTGGCCTCTCCTT 57.969 50.000 3.32 0.00 35.26 3.36
158 159 1.625818 CAAACTACTGTGGCCTCTCCT 59.374 52.381 3.32 0.00 35.26 3.69
159 160 1.946283 GCAAACTACTGTGGCCTCTCC 60.946 57.143 3.32 0.00 0.00 3.71
160 161 1.002544 AGCAAACTACTGTGGCCTCTC 59.997 52.381 3.32 0.00 0.00 3.20
161 162 1.059913 AGCAAACTACTGTGGCCTCT 58.940 50.000 3.32 0.00 0.00 3.69
162 163 1.807142 GAAGCAAACTACTGTGGCCTC 59.193 52.381 3.32 0.00 0.00 4.70
163 164 1.421646 AGAAGCAAACTACTGTGGCCT 59.578 47.619 3.32 0.00 0.00 5.19
164 165 1.897560 AGAAGCAAACTACTGTGGCC 58.102 50.000 0.00 0.00 0.00 5.36
165 166 3.550842 CCAAAGAAGCAAACTACTGTGGC 60.551 47.826 0.00 0.00 32.15 5.01
166 167 3.882888 TCCAAAGAAGCAAACTACTGTGG 59.117 43.478 0.00 0.00 38.64 4.17
167 168 4.816385 TCTCCAAAGAAGCAAACTACTGTG 59.184 41.667 0.00 0.00 0.00 3.66
168 169 4.816925 GTCTCCAAAGAAGCAAACTACTGT 59.183 41.667 0.00 0.00 31.93 3.55
169 170 4.816385 TGTCTCCAAAGAAGCAAACTACTG 59.184 41.667 0.00 0.00 31.93 2.74
170 171 5.036117 TGTCTCCAAAGAAGCAAACTACT 57.964 39.130 0.00 0.00 31.93 2.57
171 172 5.693814 CATGTCTCCAAAGAAGCAAACTAC 58.306 41.667 0.00 0.00 31.93 2.73
172 173 4.216257 GCATGTCTCCAAAGAAGCAAACTA 59.784 41.667 0.00 0.00 31.93 2.24
173 174 3.005155 GCATGTCTCCAAAGAAGCAAACT 59.995 43.478 0.00 0.00 31.93 2.66
174 175 3.243501 TGCATGTCTCCAAAGAAGCAAAC 60.244 43.478 0.00 0.00 34.84 2.93
175 176 2.957680 TGCATGTCTCCAAAGAAGCAAA 59.042 40.909 0.00 0.00 34.84 3.68
176 177 2.294233 GTGCATGTCTCCAAAGAAGCAA 59.706 45.455 0.00 0.00 37.62 3.91
177 178 1.881973 GTGCATGTCTCCAAAGAAGCA 59.118 47.619 0.00 0.00 35.17 3.91
178 179 1.881973 TGTGCATGTCTCCAAAGAAGC 59.118 47.619 0.00 0.00 31.93 3.86
179 180 3.144506 AGTGTGCATGTCTCCAAAGAAG 58.855 45.455 0.00 0.00 31.93 2.85
180 181 3.213206 AGTGTGCATGTCTCCAAAGAA 57.787 42.857 0.00 0.00 31.93 2.52
181 182 2.936919 AGTGTGCATGTCTCCAAAGA 57.063 45.000 0.00 0.00 0.00 2.52
182 183 6.932356 ATATAAGTGTGCATGTCTCCAAAG 57.068 37.500 0.00 0.00 0.00 2.77
183 184 7.701539 AAATATAAGTGTGCATGTCTCCAAA 57.298 32.000 0.00 0.00 0.00 3.28
184 185 7.611467 AGAAAATATAAGTGTGCATGTCTCCAA 59.389 33.333 0.00 0.00 0.00 3.53
185 186 7.112122 AGAAAATATAAGTGTGCATGTCTCCA 58.888 34.615 0.00 0.00 0.00 3.86
186 187 7.559590 AGAAAATATAAGTGTGCATGTCTCC 57.440 36.000 0.00 0.00 0.00 3.71
187 188 9.846248 AAAAGAAAATATAAGTGTGCATGTCTC 57.154 29.630 0.00 0.00 0.00 3.36
225 226 1.452145 CTCTCTGACCGAGCCCTAGC 61.452 65.000 0.00 0.00 39.70 3.42
226 227 0.181587 TCTCTCTGACCGAGCCCTAG 59.818 60.000 0.00 0.00 39.70 3.02
227 228 0.624254 TTCTCTCTGACCGAGCCCTA 59.376 55.000 0.00 0.00 39.70 3.53
228 229 0.682855 CTTCTCTCTGACCGAGCCCT 60.683 60.000 0.00 0.00 39.70 5.19
229 230 1.671901 CCTTCTCTCTGACCGAGCCC 61.672 65.000 0.00 0.00 39.70 5.19
230 231 0.681564 TCCTTCTCTCTGACCGAGCC 60.682 60.000 0.00 0.00 39.70 4.70
231 232 0.738389 CTCCTTCTCTCTGACCGAGC 59.262 60.000 0.00 0.00 39.70 5.03
232 233 2.093181 TCTCTCCTTCTCTCTGACCGAG 60.093 54.545 0.00 0.00 41.30 4.63
233 234 1.909986 TCTCTCCTTCTCTCTGACCGA 59.090 52.381 0.00 0.00 0.00 4.69
234 235 2.014128 GTCTCTCCTTCTCTCTGACCG 58.986 57.143 0.00 0.00 0.00 4.79
235 236 2.291282 TGGTCTCTCCTTCTCTCTGACC 60.291 54.545 0.00 0.00 41.81 4.02
236 237 3.080300 TGGTCTCTCCTTCTCTCTGAC 57.920 52.381 0.00 0.00 37.07 3.51
237 238 5.458451 TTATGGTCTCTCCTTCTCTCTGA 57.542 43.478 0.00 0.00 37.07 3.27
238 239 5.832595 TCATTATGGTCTCTCCTTCTCTCTG 59.167 44.000 0.00 0.00 37.07 3.35
239 240 6.024563 TCATTATGGTCTCTCCTTCTCTCT 57.975 41.667 0.00 0.00 37.07 3.10
240 241 6.723298 TTCATTATGGTCTCTCCTTCTCTC 57.277 41.667 0.00 0.00 37.07 3.20
241 242 6.843333 TCATTCATTATGGTCTCTCCTTCTCT 59.157 38.462 0.00 0.00 37.07 3.10
242 243 7.060383 TCATTCATTATGGTCTCTCCTTCTC 57.940 40.000 0.00 0.00 37.07 2.87
243 244 7.278875 GTTCATTCATTATGGTCTCTCCTTCT 58.721 38.462 0.00 0.00 37.07 2.85
244 245 6.484977 GGTTCATTCATTATGGTCTCTCCTTC 59.515 42.308 0.00 0.00 37.07 3.46
245 246 6.360618 GGTTCATTCATTATGGTCTCTCCTT 58.639 40.000 0.00 0.00 37.07 3.36
246 247 5.453903 CGGTTCATTCATTATGGTCTCTCCT 60.454 44.000 0.00 0.00 37.07 3.69
247 248 4.752101 CGGTTCATTCATTATGGTCTCTCC 59.248 45.833 0.00 0.00 34.85 3.71
248 249 4.752101 CCGGTTCATTCATTATGGTCTCTC 59.248 45.833 0.00 0.00 34.85 3.20
249 250 4.444876 CCCGGTTCATTCATTATGGTCTCT 60.445 45.833 0.00 0.00 34.85 3.10
250 251 3.815401 CCCGGTTCATTCATTATGGTCTC 59.185 47.826 0.00 0.00 34.85 3.36
251 252 3.458118 TCCCGGTTCATTCATTATGGTCT 59.542 43.478 0.00 0.00 34.85 3.85
252 253 3.815401 CTCCCGGTTCATTCATTATGGTC 59.185 47.826 0.00 0.00 34.85 4.02
253 254 3.435026 CCTCCCGGTTCATTCATTATGGT 60.435 47.826 0.00 0.00 34.85 3.55
254 255 3.149196 CCTCCCGGTTCATTCATTATGG 58.851 50.000 0.00 0.00 34.85 2.74
255 256 4.067896 CTCCTCCCGGTTCATTCATTATG 58.932 47.826 0.00 0.00 35.45 1.90
256 257 3.073062 CCTCCTCCCGGTTCATTCATTAT 59.927 47.826 0.00 0.00 0.00 1.28
257 258 2.438021 CCTCCTCCCGGTTCATTCATTA 59.562 50.000 0.00 0.00 0.00 1.90
301 302 2.159028 CCTAGTACTCCTTTGCTCCAGC 60.159 54.545 0.00 0.00 42.50 4.85
317 318 1.203275 ACTCCGAGTTTTCCCCCTAGT 60.203 52.381 0.00 0.00 0.00 2.57
325 326 0.673956 GCCTCCCACTCCGAGTTTTC 60.674 60.000 0.00 0.00 0.00 2.29
391 393 8.842280 TGTAAAAAGAACGAGTTATGAACCAAT 58.158 29.630 0.00 0.00 0.00 3.16
416 418 8.994429 ATCCGAGCTATTTAATCTACTCAATG 57.006 34.615 0.00 0.00 0.00 2.82
599 602 7.471721 TCATTCAAGTATAAAAGGCACGAATG 58.528 34.615 0.00 0.00 38.88 2.67
688 712 6.312399 TCGAATTATTCTTGCCGCATTTAT 57.688 33.333 3.34 0.00 0.00 1.40
703 727 5.347364 CCGCAAAATTGTTGGTTCGAATTAT 59.653 36.000 0.00 0.00 0.00 1.28
704 728 4.681942 CCGCAAAATTGTTGGTTCGAATTA 59.318 37.500 0.00 0.00 0.00 1.40
718 742 2.508526 AGACAGAGAAGCCGCAAAATT 58.491 42.857 0.00 0.00 0.00 1.82
735 759 2.282701 TATTACACCACGGCGAAGAC 57.717 50.000 16.62 0.00 0.00 3.01
1068 1092 1.745489 CTGCTGCTGCTGCTGATGA 60.745 57.895 27.67 10.07 40.01 2.92
1560 1590 0.387929 AGAAGACGTTGTCGAAGGCA 59.612 50.000 0.00 0.00 45.30 4.75
1587 1617 1.987704 CTCTCTCAGGTCGACGGCTG 61.988 65.000 9.92 12.18 0.00 4.85
1653 1683 2.710971 GATCGATGATGACGCGCGG 61.711 63.158 35.22 16.31 0.00 6.46
1749 1779 1.203050 ACCAACACCTGCAGCCTAAAT 60.203 47.619 8.66 0.00 0.00 1.40
1824 1854 3.378427 CCCTAAAGTAATCTTGCCACTGC 59.622 47.826 0.00 0.00 33.79 4.40
1921 1951 0.811219 TGGCCATCGAGCGAGATTTG 60.811 55.000 0.00 0.00 0.00 2.32
1931 1961 0.034476 GAGCATCAGATGGCCATCGA 59.966 55.000 34.48 31.70 42.48 3.59
1932 1962 0.250166 TGAGCATCAGATGGCCATCG 60.250 55.000 34.48 28.40 42.56 3.84
1955 1985 7.123098 TCCTTATCCTTAGTAATGTCGAACACA 59.877 37.037 0.00 0.00 40.18 3.72
1969 2005 8.213679 TCATGGACAAATTCTCCTTATCCTTAG 58.786 37.037 0.00 0.00 0.00 2.18
2106 2173 1.878522 GACATGGTAGACGGCAGCG 60.879 63.158 0.00 0.00 0.00 5.18
2250 2478 2.045926 GGCTACAGCTGGTGGTGG 60.046 66.667 19.93 0.00 45.14 4.61
2308 2536 2.128035 GGCCAAATCATAGTCGAGACG 58.872 52.381 0.00 0.00 36.20 4.18
2355 2583 2.356069 GCAGCTACAGGGCATAAGAAAC 59.644 50.000 0.00 0.00 34.17 2.78
2463 2691 9.853177 AAGTCAAATATTTAGGAACATAGGGAG 57.147 33.333 0.00 0.00 0.00 4.30
2495 2723 9.280174 CCGTATGTGGTAGTCCATTTAAAATAT 57.720 33.333 0.00 0.00 46.20 1.28
2496 2724 8.484575 TCCGTATGTGGTAGTCCATTTAAAATA 58.515 33.333 0.00 0.00 46.20 1.40
2497 2725 7.340256 TCCGTATGTGGTAGTCCATTTAAAAT 58.660 34.615 0.00 0.00 46.20 1.82
2498 2726 6.709281 TCCGTATGTGGTAGTCCATTTAAAA 58.291 36.000 0.00 0.00 46.20 1.52
2499 2727 6.297080 TCCGTATGTGGTAGTCCATTTAAA 57.703 37.500 0.00 0.00 46.20 1.52
2500 2728 5.936187 TCCGTATGTGGTAGTCCATTTAA 57.064 39.130 0.00 0.00 46.20 1.52
2501 2729 5.364446 ACATCCGTATGTGGTAGTCCATTTA 59.636 40.000 0.00 0.00 44.79 1.40
2502 2730 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
2503 2731 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
2504 2732 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
2505 2733 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
2506 2734 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
2507 2735 9.565213 GTTTATATACATCCGTATGTGGTAGTC 57.435 37.037 3.56 0.00 45.99 2.59
2508 2736 9.081204 TGTTTATATACATCCGTATGTGGTAGT 57.919 33.333 3.56 0.00 45.99 2.73
2539 2767 9.973450 GAGCAAATGAGTGAATCTATACTCTAA 57.027 33.333 0.00 0.00 42.86 2.10
2540 2768 8.580720 GGAGCAAATGAGTGAATCTATACTCTA 58.419 37.037 0.00 0.00 42.86 2.43
2541 2769 7.441017 GGAGCAAATGAGTGAATCTATACTCT 58.559 38.462 0.00 0.00 42.86 3.24
2542 2770 6.364706 CGGAGCAAATGAGTGAATCTATACTC 59.635 42.308 0.00 0.00 42.77 2.59
2543 2771 6.183360 ACGGAGCAAATGAGTGAATCTATACT 60.183 38.462 0.00 0.00 0.00 2.12
2544 2772 5.986135 ACGGAGCAAATGAGTGAATCTATAC 59.014 40.000 0.00 0.00 0.00 1.47
2545 2773 6.161855 ACGGAGCAAATGAGTGAATCTATA 57.838 37.500 0.00 0.00 0.00 1.31
2546 2774 5.028549 ACGGAGCAAATGAGTGAATCTAT 57.971 39.130 0.00 0.00 0.00 1.98
2547 2775 4.471904 ACGGAGCAAATGAGTGAATCTA 57.528 40.909 0.00 0.00 0.00 1.98
2548 2776 3.340814 ACGGAGCAAATGAGTGAATCT 57.659 42.857 0.00 0.00 0.00 2.40
2549 2777 4.572389 ACATACGGAGCAAATGAGTGAATC 59.428 41.667 0.00 0.00 0.00 2.52
2550 2778 4.517285 ACATACGGAGCAAATGAGTGAAT 58.483 39.130 0.00 0.00 0.00 2.57
2551 2779 3.937814 ACATACGGAGCAAATGAGTGAA 58.062 40.909 0.00 0.00 0.00 3.18
2552 2780 3.610040 ACATACGGAGCAAATGAGTGA 57.390 42.857 0.00 0.00 0.00 3.41
2553 2781 4.433615 ACTACATACGGAGCAAATGAGTG 58.566 43.478 0.00 0.00 0.00 3.51
2554 2782 4.159693 TGACTACATACGGAGCAAATGAGT 59.840 41.667 0.00 0.00 0.00 3.41
2555 2783 4.504461 GTGACTACATACGGAGCAAATGAG 59.496 45.833 0.00 0.00 0.00 2.90
2556 2784 4.159693 AGTGACTACATACGGAGCAAATGA 59.840 41.667 0.00 0.00 0.00 2.57
2557 2785 4.433615 AGTGACTACATACGGAGCAAATG 58.566 43.478 0.00 0.00 0.00 2.32
2558 2786 4.737855 AGTGACTACATACGGAGCAAAT 57.262 40.909 0.00 0.00 0.00 2.32
2559 2787 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
2560 2788 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
2561 2789 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
2562 2790 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.