Multiple sequence alignment - TraesCS1A01G193700

Loading Multiple Alignment...

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 TraesCS1A01G193700 chr1A 100.000 2582 0 0 1 2582 351210684 351213265 0.000000e+00 4769.0
1 TraesCS1A01G193700 chr1B 95.782 1849 54 17 196 2033 378461632 378463467 0.000000e+00 2961.0
2 TraesCS1A01G193700 chr1B 91.882 271 10 6 2316 2582 378463569 378463831 4.060000e-98 368.0
3 TraesCS1A01G193700 chr1D 95.657 1796 48 11 243 2033 278945187 278946957 0.000000e+00 2857.0
4 TraesCS1A01G193700 chr1D 95.572 271 8 1 2316 2582 278947058 278947328 5.100000e-117 431.0
5 TraesCS1A01G193700 chr5D 91.753 194 16 0 1 194 219945662 219945855 1.180000e-68 270.0
6 TraesCS1A01G193700 chr5D 90.863 197 16 2 1 196 400183959 400183764 1.970000e-66 263.0
7 TraesCS1A01G193700 chr5A 91.237 194 17 0 1 194 375880669 375880476 5.480000e-67 265.0
8 TraesCS1A01G193700 chr5A 89.831 118 10 2 2205 2321 394749912 394750028 1.600000e-32 150.0
9 TraesCS1A01G193700 chr5A 87.500 72 7 2 2250 2320 323352924 323352994 5.920000e-12 82.4
10 TraesCS1A01G193700 chr6D 90.863 197 16 2 1 196 104154591 104154396 1.970000e-66 263.0
11 TraesCS1A01G193700 chr6D 90.769 195 16 2 1 194 152173676 152173483 2.550000e-65 259.0
12 TraesCS1A01G193700 chr4D 91.192 193 17 0 2 194 241810088 241810280 1.970000e-66 263.0
13 TraesCS1A01G193700 chr4D 86.735 98 11 1 2205 2302 403293810 403293905 9.770000e-20 108.0
14 TraesCS1A01G193700 chr2D 90.863 197 16 2 1 196 458127571 458127766 1.970000e-66 263.0
15 TraesCS1A01G193700 chr5B 90.816 196 16 2 1 195 369129576 369129382 7.090000e-66 261.0
16 TraesCS1A01G193700 chr5B 81.739 115 19 2 2205 2318 491074663 491074550 7.610000e-16 95.3
17 TraesCS1A01G193700 chr3A 90.863 197 15 3 1 195 635719024 635719219 7.090000e-66 261.0
18 TraesCS1A01G193700 chr3A 100.000 28 0 0 2291 2318 359073352 359073379 5.000000e-03 52.8
19 TraesCS1A01G193700 chr7A 89.216 102 11 0 2108 2209 310237053 310236952 7.500000e-26 128.0
20 TraesCS1A01G193700 chr7A 89.855 69 7 0 2098 2166 508643143 508643075 3.540000e-14 89.8
21 TraesCS1A01G193700 chr7A 80.556 108 17 4 2100 2206 448731442 448731546 2.130000e-11 80.5
22 TraesCS1A01G193700 chr3B 80.952 126 20 3 2205 2328 335868788 335868665 2.110000e-16 97.1
23 TraesCS1A01G193700 chr7D 84.783 92 12 2 2110 2200 617659009 617659099 9.840000e-15 91.6


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 TraesCS1A01G193700 chr1A 351210684 351213265 2581 False 4769.0 4769 100.0000 1 2582 1 chr1A.!!$F1 2581
1 TraesCS1A01G193700 chr1B 378461632 378463831 2199 False 1664.5 2961 93.8320 196 2582 2 chr1B.!!$F1 2386
2 TraesCS1A01G193700 chr1D 278945187 278947328 2141 False 1644.0 2857 95.6145 243 2582 2 chr1D.!!$F1 2339

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
39 40 0.034337 TAAACCACACTCGGCAGGAC 59.966 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 2048 0.106918 ACAAAGTCACTCCCCGCAAA 60.107 50.0 0.0 0.0 0.0 3.68 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
28 29 9.251440 ACTCTGTACTAGTTCATATAAACCACA 57.749 33.333 0.00 0.00 0.00 4.17
29 30 9.517609 CTCTGTACTAGTTCATATAAACCACAC 57.482 37.037 0.00 0.00 0.00 3.82
30 31 9.251440 TCTGTACTAGTTCATATAAACCACACT 57.749 33.333 0.00 0.00 0.00 3.55
31 32 9.517609 CTGTACTAGTTCATATAAACCACACTC 57.482 37.037 0.00 0.00 0.00 3.51
32 33 8.186163 TGTACTAGTTCATATAAACCACACTCG 58.814 37.037 0.00 0.00 0.00 4.18
33 34 6.570692 ACTAGTTCATATAAACCACACTCGG 58.429 40.000 0.00 0.00 0.00 4.63
34 35 4.189231 AGTTCATATAAACCACACTCGGC 58.811 43.478 0.00 0.00 0.00 5.54
35 36 3.897141 TCATATAAACCACACTCGGCA 57.103 42.857 0.00 0.00 0.00 5.69
36 37 3.792401 TCATATAAACCACACTCGGCAG 58.208 45.455 0.00 0.00 0.00 4.85
37 38 2.684001 TATAAACCACACTCGGCAGG 57.316 50.000 0.00 0.00 0.00 4.85
38 39 0.981183 ATAAACCACACTCGGCAGGA 59.019 50.000 0.00 0.00 0.00 3.86
39 40 0.034337 TAAACCACACTCGGCAGGAC 59.966 55.000 0.00 0.00 0.00 3.85
40 41 1.696097 AAACCACACTCGGCAGGACT 61.696 55.000 0.00 0.00 0.00 3.85
41 42 0.830444 AACCACACTCGGCAGGACTA 60.830 55.000 0.00 0.00 0.00 2.59
42 43 1.251527 ACCACACTCGGCAGGACTAG 61.252 60.000 0.00 0.00 0.00 2.57
43 44 1.513158 CACACTCGGCAGGACTAGG 59.487 63.158 0.00 0.00 0.00 3.02
44 45 1.682684 ACACTCGGCAGGACTAGGG 60.683 63.158 0.00 0.00 0.00 3.53
45 46 2.042843 ACTCGGCAGGACTAGGGG 60.043 66.667 0.00 0.00 0.00 4.79
46 47 2.042843 CTCGGCAGGACTAGGGGT 60.043 66.667 0.00 0.00 0.00 4.95
47 48 2.363795 TCGGCAGGACTAGGGGTG 60.364 66.667 0.00 0.00 0.00 4.61
48 49 2.683933 CGGCAGGACTAGGGGTGT 60.684 66.667 0.00 0.00 0.00 4.16
49 50 2.291043 CGGCAGGACTAGGGGTGTT 61.291 63.158 0.00 0.00 0.00 3.32
50 51 0.974010 CGGCAGGACTAGGGGTGTTA 60.974 60.000 0.00 0.00 0.00 2.41
51 52 1.508256 GGCAGGACTAGGGGTGTTAT 58.492 55.000 0.00 0.00 0.00 1.89
52 53 1.416772 GGCAGGACTAGGGGTGTTATC 59.583 57.143 0.00 0.00 0.00 1.75
53 54 2.399580 GCAGGACTAGGGGTGTTATCT 58.600 52.381 0.00 0.00 0.00 1.98
54 55 2.365941 GCAGGACTAGGGGTGTTATCTC 59.634 54.545 0.00 0.00 0.00 2.75
55 56 3.917300 CAGGACTAGGGGTGTTATCTCT 58.083 50.000 0.00 0.00 0.00 3.10
56 57 3.892588 CAGGACTAGGGGTGTTATCTCTC 59.107 52.174 0.00 0.00 0.00 3.20
57 58 3.117054 AGGACTAGGGGTGTTATCTCTCC 60.117 52.174 0.00 0.00 0.00 3.71
58 59 2.885894 GACTAGGGGTGTTATCTCTCCG 59.114 54.545 0.00 0.00 33.36 4.63
59 60 2.240279 CTAGGGGTGTTATCTCTCCGG 58.760 57.143 0.00 0.00 33.36 5.14
60 61 0.635009 AGGGGTGTTATCTCTCCGGA 59.365 55.000 2.93 2.93 33.36 5.14
61 62 1.041437 GGGGTGTTATCTCTCCGGAG 58.959 60.000 26.32 26.32 40.73 4.63
75 76 3.300013 GGAGAGTCCCGAACCTGG 58.700 66.667 0.00 0.00 0.00 4.45
76 77 1.305046 GGAGAGTCCCGAACCTGGA 60.305 63.158 0.00 0.00 0.00 3.86
77 78 0.688087 GGAGAGTCCCGAACCTGGAT 60.688 60.000 0.00 0.00 33.65 3.41
78 79 1.411216 GGAGAGTCCCGAACCTGGATA 60.411 57.143 0.00 0.00 33.65 2.59
79 80 2.599677 GAGAGTCCCGAACCTGGATAT 58.400 52.381 0.00 0.00 33.65 1.63
80 81 2.297597 GAGAGTCCCGAACCTGGATATG 59.702 54.545 0.00 0.00 33.65 1.78
81 82 2.040178 GAGTCCCGAACCTGGATATGT 58.960 52.381 0.00 0.00 33.65 2.29
82 83 2.036089 GAGTCCCGAACCTGGATATGTC 59.964 54.545 0.00 0.00 33.65 3.06
83 84 2.040178 GTCCCGAACCTGGATATGTCT 58.960 52.381 0.00 0.00 33.65 3.41
84 85 2.434702 GTCCCGAACCTGGATATGTCTT 59.565 50.000 0.00 0.00 33.65 3.01
85 86 2.434336 TCCCGAACCTGGATATGTCTTG 59.566 50.000 0.00 0.00 0.00 3.02
86 87 2.213499 CCGAACCTGGATATGTCTTGC 58.787 52.381 0.00 0.00 0.00 4.01
87 88 1.860950 CGAACCTGGATATGTCTTGCG 59.139 52.381 0.00 0.00 0.00 4.85
88 89 2.738643 CGAACCTGGATATGTCTTGCGT 60.739 50.000 0.00 0.00 0.00 5.24
89 90 2.604046 ACCTGGATATGTCTTGCGTC 57.396 50.000 0.00 0.00 0.00 5.19
90 91 1.139058 ACCTGGATATGTCTTGCGTCC 59.861 52.381 0.00 0.00 0.00 4.79
91 92 1.541233 CCTGGATATGTCTTGCGTCCC 60.541 57.143 0.00 0.00 0.00 4.46
92 93 1.414181 CTGGATATGTCTTGCGTCCCT 59.586 52.381 0.00 0.00 0.00 4.20
93 94 1.412710 TGGATATGTCTTGCGTCCCTC 59.587 52.381 0.00 0.00 0.00 4.30
94 95 1.603172 GGATATGTCTTGCGTCCCTCG 60.603 57.143 0.00 0.00 43.12 4.63
103 104 3.893763 CGTCCCTCGCTCGCTCAT 61.894 66.667 0.00 0.00 0.00 2.90
104 105 2.279120 GTCCCTCGCTCGCTCATG 60.279 66.667 0.00 0.00 0.00 3.07
105 106 2.755876 TCCCTCGCTCGCTCATGT 60.756 61.111 0.00 0.00 0.00 3.21
106 107 2.279120 CCCTCGCTCGCTCATGTC 60.279 66.667 0.00 0.00 0.00 3.06
107 108 2.653448 CCTCGCTCGCTCATGTCG 60.653 66.667 0.00 0.00 0.00 4.35
108 109 2.653448 CTCGCTCGCTCATGTCGG 60.653 66.667 9.47 3.48 0.00 4.79
109 110 4.854784 TCGCTCGCTCATGTCGGC 62.855 66.667 9.47 10.17 0.00 5.54
111 112 2.587194 GCTCGCTCATGTCGGCAT 60.587 61.111 0.00 0.00 35.32 4.40
112 113 2.176273 GCTCGCTCATGTCGGCATT 61.176 57.895 0.00 0.00 31.99 3.56
113 114 1.640069 CTCGCTCATGTCGGCATTG 59.360 57.895 0.00 0.00 31.99 2.82
114 115 2.023741 CGCTCATGTCGGCATTGC 59.976 61.111 0.00 7.26 31.99 3.56
115 116 2.410469 GCTCATGTCGGCATTGCC 59.590 61.111 18.10 18.10 46.75 4.52
124 125 2.832201 GGCATTGCCTCTGGAGCC 60.832 66.667 20.66 0.00 46.69 4.70
125 126 2.832201 GCATTGCCTCTGGAGCCC 60.832 66.667 0.00 0.00 0.00 5.19
126 127 2.679092 CATTGCCTCTGGAGCCCA 59.321 61.111 0.00 0.00 0.00 5.36
127 128 1.751927 CATTGCCTCTGGAGCCCAC 60.752 63.158 0.00 0.00 0.00 4.61
128 129 2.988839 ATTGCCTCTGGAGCCCACC 61.989 63.158 0.00 0.00 0.00 4.61
129 130 4.664267 TGCCTCTGGAGCCCACCT 62.664 66.667 0.00 0.00 0.00 4.00
130 131 4.106925 GCCTCTGGAGCCCACCTG 62.107 72.222 0.00 0.00 0.00 4.00
131 132 2.608988 CCTCTGGAGCCCACCTGT 60.609 66.667 0.00 0.00 0.00 4.00
132 133 2.667418 CTCTGGAGCCCACCTGTG 59.333 66.667 0.00 0.00 0.00 3.66
133 134 3.618780 CTCTGGAGCCCACCTGTGC 62.619 68.421 0.00 0.00 0.00 4.57
134 135 4.729918 CTGGAGCCCACCTGTGCC 62.730 72.222 0.00 0.00 0.00 5.01
137 138 4.416738 GAGCCCACCTGTGCCCTC 62.417 72.222 0.00 0.00 0.00 4.30
140 141 4.087892 CCCACCTGTGCCCTCGAG 62.088 72.222 5.13 5.13 0.00 4.04
141 142 4.767255 CCACCTGTGCCCTCGAGC 62.767 72.222 6.99 0.00 0.00 5.03
142 143 4.767255 CACCTGTGCCCTCGAGCC 62.767 72.222 6.99 0.16 0.00 4.70
144 145 4.154347 CCTGTGCCCTCGAGCCTC 62.154 72.222 6.99 1.82 0.00 4.70
145 146 4.154347 CTGTGCCCTCGAGCCTCC 62.154 72.222 6.99 0.00 0.00 4.30
146 147 4.704103 TGTGCCCTCGAGCCTCCT 62.704 66.667 6.99 0.00 0.00 3.69
147 148 3.844090 GTGCCCTCGAGCCTCCTC 61.844 72.222 6.99 0.00 34.66 3.71
148 149 4.067512 TGCCCTCGAGCCTCCTCT 62.068 66.667 6.99 0.00 35.90 3.69
149 150 2.762043 GCCCTCGAGCCTCCTCTT 60.762 66.667 6.99 0.00 35.90 2.85
150 151 2.363172 GCCCTCGAGCCTCCTCTTT 61.363 63.158 6.99 0.00 35.90 2.52
151 152 1.904990 GCCCTCGAGCCTCCTCTTTT 61.905 60.000 6.99 0.00 35.90 2.27
152 153 0.176910 CCCTCGAGCCTCCTCTTTTC 59.823 60.000 6.99 0.00 35.90 2.29
153 154 1.190643 CCTCGAGCCTCCTCTTTTCT 58.809 55.000 6.99 0.00 35.90 2.52
154 155 1.552792 CCTCGAGCCTCCTCTTTTCTT 59.447 52.381 6.99 0.00 35.90 2.52
155 156 2.027653 CCTCGAGCCTCCTCTTTTCTTT 60.028 50.000 6.99 0.00 35.90 2.52
156 157 3.195825 CCTCGAGCCTCCTCTTTTCTTTA 59.804 47.826 6.99 0.00 35.90 1.85
157 158 4.429108 CTCGAGCCTCCTCTTTTCTTTAG 58.571 47.826 0.00 0.00 35.90 1.85
158 159 2.933260 CGAGCCTCCTCTTTTCTTTAGC 59.067 50.000 0.00 0.00 35.90 3.09
159 160 3.275143 GAGCCTCCTCTTTTCTTTAGCC 58.725 50.000 0.00 0.00 35.16 3.93
160 161 2.644798 AGCCTCCTCTTTTCTTTAGCCA 59.355 45.455 0.00 0.00 0.00 4.75
161 162 2.750166 GCCTCCTCTTTTCTTTAGCCAC 59.250 50.000 0.00 0.00 0.00 5.01
162 163 3.348119 CCTCCTCTTTTCTTTAGCCACC 58.652 50.000 0.00 0.00 0.00 4.61
163 164 3.348119 CTCCTCTTTTCTTTAGCCACCC 58.652 50.000 0.00 0.00 0.00 4.61
164 165 2.986728 TCCTCTTTTCTTTAGCCACCCT 59.013 45.455 0.00 0.00 0.00 4.34
165 166 3.397955 TCCTCTTTTCTTTAGCCACCCTT 59.602 43.478 0.00 0.00 0.00 3.95
166 167 4.141018 TCCTCTTTTCTTTAGCCACCCTTT 60.141 41.667 0.00 0.00 0.00 3.11
167 168 4.021981 CCTCTTTTCTTTAGCCACCCTTTG 60.022 45.833 0.00 0.00 0.00 2.77
176 177 3.191182 CCACCCTTTGGCATCTACC 57.809 57.895 0.00 0.00 39.07 3.18
177 178 0.748005 CCACCCTTTGGCATCTACCG 60.748 60.000 0.00 0.00 39.07 4.02
178 179 0.035439 CACCCTTTGGCATCTACCGT 60.035 55.000 0.00 0.00 33.59 4.83
179 180 0.035439 ACCCTTTGGCATCTACCGTG 60.035 55.000 0.00 0.00 33.59 4.94
180 181 0.035439 CCCTTTGGCATCTACCGTGT 60.035 55.000 0.00 0.00 0.00 4.49
181 182 1.086696 CCTTTGGCATCTACCGTGTG 58.913 55.000 0.00 0.00 0.00 3.82
182 183 0.447801 CTTTGGCATCTACCGTGTGC 59.552 55.000 0.00 0.00 38.12 4.57
185 186 2.267642 GCATCTACCGTGTGCCCA 59.732 61.111 0.00 0.00 32.88 5.36
186 187 2.106683 GCATCTACCGTGTGCCCAC 61.107 63.158 0.00 0.00 38.27 4.61
187 188 1.449601 CATCTACCGTGTGCCCACC 60.450 63.158 0.00 0.00 38.41 4.61
188 189 1.916273 ATCTACCGTGTGCCCACCA 60.916 57.895 0.00 0.00 38.41 4.17
189 190 2.180159 ATCTACCGTGTGCCCACCAC 62.180 60.000 0.00 0.00 44.90 4.16
196 197 2.110213 GTGCCCACCACGACAAGA 59.890 61.111 0.00 0.00 34.22 3.02
197 198 1.961277 GTGCCCACCACGACAAGAG 60.961 63.158 0.00 0.00 34.22 2.85
198 199 2.358737 GCCCACCACGACAAGAGG 60.359 66.667 0.00 0.00 36.60 3.69
199 200 3.148084 CCCACCACGACAAGAGGT 58.852 61.111 0.00 0.00 44.91 3.85
211 212 3.315418 GACAAGAGGTCACGGTAGTTTC 58.685 50.000 0.00 0.00 46.19 2.78
220 221 4.374399 GTCACGGTAGTTTCCTTCTTTGA 58.626 43.478 0.00 0.00 0.00 2.69
228 229 6.486993 GGTAGTTTCCTTCTTTGAAGACATGT 59.513 38.462 0.00 0.00 34.13 3.21
236 237 3.947196 TCTTTGAAGACATGTGCACTTGT 59.053 39.130 31.65 31.65 37.01 3.16
237 238 3.696281 TTGAAGACATGTGCACTTGTG 57.304 42.857 34.96 23.89 34.86 3.33
238 239 1.948834 TGAAGACATGTGCACTTGTGG 59.051 47.619 34.96 13.73 34.86 4.17
240 241 2.057137 AGACATGTGCACTTGTGGTT 57.943 45.000 34.96 20.51 34.86 3.67
269 270 2.366167 CTGGGAGGAGGGGGTCAG 60.366 72.222 0.00 0.00 0.00 3.51
304 305 2.557920 ACTGGAGCAAAGGAGTTCTG 57.442 50.000 0.00 0.00 0.00 3.02
342 343 1.686325 GGAGGCGGGAGATTAGTGCA 61.686 60.000 0.00 0.00 0.00 4.57
708 716 7.434897 TGATTTGTAAATGCGGCAAGATAAATC 59.565 33.333 22.68 22.68 33.65 2.17
1078 1089 3.064987 GCCAATCAGCAGCAGCAGG 62.065 63.158 3.17 0.00 45.49 4.85
1079 1090 2.490217 CAATCAGCAGCAGCAGGC 59.510 61.111 3.17 0.00 45.49 4.85
1138 1149 3.374402 CGGACCAGCTGTCGGAGT 61.374 66.667 13.81 2.16 45.46 3.85
1344 1355 3.261933 GAACTCCTCGACGACCGT 58.738 61.111 0.00 0.00 39.75 4.83
1503 1514 2.043852 ATCGAGGAGGCCGACACT 60.044 61.111 0.00 0.00 38.97 3.55
1664 1675 1.637934 CATGTCGCGCGTCATCATT 59.362 52.632 33.60 16.21 0.00 2.57
1782 1793 2.462456 TGGTGAGATGAGCTGTTGTC 57.538 50.000 0.00 0.00 0.00 3.18
1886 1897 3.037324 GCAAAATGCACATTGTGTTTGC 58.963 40.909 26.68 26.68 44.26 3.68
2023 2035 3.054361 GGTTGGGTCCATTATCAGTGACT 60.054 47.826 0.00 0.00 0.00 3.41
2024 2036 4.567747 GGTTGGGTCCATTATCAGTGACTT 60.568 45.833 0.00 0.00 0.00 3.01
2025 2037 4.927267 TGGGTCCATTATCAGTGACTTT 57.073 40.909 0.00 0.00 0.00 2.66
2026 2038 4.588899 TGGGTCCATTATCAGTGACTTTG 58.411 43.478 0.00 0.00 0.00 2.77
2027 2039 4.042809 TGGGTCCATTATCAGTGACTTTGT 59.957 41.667 0.00 0.00 0.00 2.83
2028 2040 5.010282 GGGTCCATTATCAGTGACTTTGTT 58.990 41.667 0.00 0.00 0.00 2.83
2029 2041 5.123979 GGGTCCATTATCAGTGACTTTGTTC 59.876 44.000 0.00 0.00 0.00 3.18
2030 2042 5.940470 GGTCCATTATCAGTGACTTTGTTCT 59.060 40.000 0.00 0.00 0.00 3.01
2031 2043 6.431234 GGTCCATTATCAGTGACTTTGTTCTT 59.569 38.462 0.00 0.00 0.00 2.52
2032 2044 7.040409 GGTCCATTATCAGTGACTTTGTTCTTT 60.040 37.037 0.00 0.00 0.00 2.52
2033 2045 8.352942 GTCCATTATCAGTGACTTTGTTCTTTT 58.647 33.333 0.00 0.00 0.00 2.27
2034 2046 8.912988 TCCATTATCAGTGACTTTGTTCTTTTT 58.087 29.630 0.00 0.00 0.00 1.94
2062 2074 2.034685 GGGGAGTGACTTTGTTCTTTGC 59.965 50.000 0.00 0.00 0.00 3.68
2097 2117 2.490685 GAAGAGACGGCCGTCCTC 59.509 66.667 45.66 38.18 45.59 3.71
2100 2120 1.668101 AAGAGACGGCCGTCCTCATC 61.668 60.000 45.66 36.53 45.59 2.92
2101 2121 3.140225 GAGACGGCCGTCCTCATCC 62.140 68.421 45.66 26.24 45.59 3.51
2104 2124 4.570663 CGGCCGTCCTCATCCGTC 62.571 72.222 19.50 0.00 37.33 4.79
2105 2125 3.148279 GGCCGTCCTCATCCGTCT 61.148 66.667 0.00 0.00 0.00 4.18
2106 2126 2.105128 GCCGTCCTCATCCGTCTG 59.895 66.667 0.00 0.00 0.00 3.51
2107 2127 2.105128 CCGTCCTCATCCGTCTGC 59.895 66.667 0.00 0.00 0.00 4.26
2108 2128 2.278206 CGTCCTCATCCGTCTGCG 60.278 66.667 0.00 0.00 37.95 5.18
2110 2130 1.511305 GTCCTCATCCGTCTGCGAA 59.489 57.895 0.00 0.00 41.33 4.70
2111 2131 0.103208 GTCCTCATCCGTCTGCGAAT 59.897 55.000 0.00 0.00 41.33 3.34
2112 2132 1.337071 GTCCTCATCCGTCTGCGAATA 59.663 52.381 0.00 0.00 41.33 1.75
2113 2133 2.028876 TCCTCATCCGTCTGCGAATAA 58.971 47.619 0.00 0.00 41.33 1.40
2114 2134 2.034685 TCCTCATCCGTCTGCGAATAAG 59.965 50.000 0.00 0.00 41.33 1.73
2116 2136 2.791560 CTCATCCGTCTGCGAATAAGTG 59.208 50.000 0.00 0.00 41.33 3.16
2118 2138 3.379057 TCATCCGTCTGCGAATAAGTGTA 59.621 43.478 0.00 0.00 41.33 2.90
2120 2140 2.488937 TCCGTCTGCGAATAAGTGTACA 59.511 45.455 0.00 0.00 41.33 2.90
2122 2142 3.486108 CCGTCTGCGAATAAGTGTACATC 59.514 47.826 0.00 0.00 41.33 3.06
2124 2144 5.505159 CCGTCTGCGAATAAGTGTACATCTA 60.505 44.000 0.00 0.00 41.33 1.98
2125 2145 5.621634 CGTCTGCGAATAAGTGTACATCTAG 59.378 44.000 0.00 0.00 41.33 2.43
2131 2151 7.064134 TGCGAATAAGTGTACATCTAGTTTTGG 59.936 37.037 0.00 0.00 0.00 3.28
2132 2152 7.064253 GCGAATAAGTGTACATCTAGTTTTGGT 59.936 37.037 0.00 0.00 0.00 3.67
2134 2154 8.788325 AATAAGTGTACATCTAGTTTTGGTCC 57.212 34.615 0.00 0.00 0.00 4.46
2135 2155 6.435292 AAGTGTACATCTAGTTTTGGTCCT 57.565 37.500 0.00 0.00 0.00 3.85
2136 2156 7.549147 AAGTGTACATCTAGTTTTGGTCCTA 57.451 36.000 0.00 0.00 0.00 2.94
2137 2157 7.549147 AGTGTACATCTAGTTTTGGTCCTAA 57.451 36.000 0.00 0.00 0.00 2.69
2141 2161 6.681729 ACATCTAGTTTTGGTCCTAAGTCA 57.318 37.500 0.00 0.00 0.00 3.41
2143 2163 7.514721 ACATCTAGTTTTGGTCCTAAGTCAAA 58.485 34.615 0.00 0.00 0.00 2.69
2144 2164 7.996644 ACATCTAGTTTTGGTCCTAAGTCAAAA 59.003 33.333 0.00 0.00 37.83 2.44
2145 2165 9.014297 CATCTAGTTTTGGTCCTAAGTCAAAAT 57.986 33.333 0.00 0.00 40.80 1.82
2175 2195 9.936759 AAAACTTTGACCAACTTCATAAGAAAA 57.063 25.926 0.00 0.00 32.35 2.29
2176 2196 9.936759 AAACTTTGACCAACTTCATAAGAAAAA 57.063 25.926 0.00 0.00 32.35 1.94
2204 2224 8.848474 AACAGCATTTATGACACTAAAGTAGT 57.152 30.769 0.00 0.00 40.28 2.73
2205 2225 9.938280 AACAGCATTTATGACACTAAAGTAGTA 57.062 29.630 0.00 0.00 37.23 1.82
2206 2226 9.367444 ACAGCATTTATGACACTAAAGTAGTAC 57.633 33.333 0.00 0.00 37.23 2.73
2207 2227 8.818057 CAGCATTTATGACACTAAAGTAGTACC 58.182 37.037 0.00 0.00 37.23 3.34
2208 2228 8.537016 AGCATTTATGACACTAAAGTAGTACCA 58.463 33.333 0.00 0.00 37.23 3.25
2209 2229 9.158233 GCATTTATGACACTAAAGTAGTACCAA 57.842 33.333 0.00 0.00 37.23 3.67
2215 2235 9.959721 ATGACACTAAAGTAGTACCAATTTGAT 57.040 29.630 0.00 0.00 37.23 2.57
2216 2236 9.214957 TGACACTAAAGTAGTACCAATTTGATG 57.785 33.333 0.00 0.00 37.23 3.07
2217 2237 9.216117 GACACTAAAGTAGTACCAATTTGATGT 57.784 33.333 0.00 5.39 37.23 3.06
2218 2238 9.216117 ACACTAAAGTAGTACCAATTTGATGTC 57.784 33.333 0.00 0.00 37.23 3.06
2219 2239 9.214957 CACTAAAGTAGTACCAATTTGATGTCA 57.785 33.333 0.00 0.00 37.23 3.58
2220 2240 9.959721 ACTAAAGTAGTACCAATTTGATGTCAT 57.040 29.630 0.00 0.00 37.23 3.06
2273 2293 9.883142 TTGGTCAAATTTTAAAACATCAGACTT 57.117 25.926 1.97 0.00 0.00 3.01
2284 2304 9.710979 TTAAAACATCAGACTTAGAACAAAACG 57.289 29.630 0.00 0.00 0.00 3.60
2285 2305 6.920569 AACATCAGACTTAGAACAAAACGT 57.079 33.333 0.00 0.00 0.00 3.99
2286 2306 8.428186 AAACATCAGACTTAGAACAAAACGTA 57.572 30.769 0.00 0.00 0.00 3.57
2287 2307 7.639162 ACATCAGACTTAGAACAAAACGTAG 57.361 36.000 0.00 0.00 0.00 3.51
2288 2308 7.431249 ACATCAGACTTAGAACAAAACGTAGA 58.569 34.615 0.00 0.00 0.00 2.59
2289 2309 7.924412 ACATCAGACTTAGAACAAAACGTAGAA 59.076 33.333 0.00 0.00 0.00 2.10
2290 2310 7.925703 TCAGACTTAGAACAAAACGTAGAAG 57.074 36.000 0.00 0.00 0.00 2.85
2291 2311 7.486647 TCAGACTTAGAACAAAACGTAGAAGT 58.513 34.615 0.00 0.00 30.57 3.01
2292 2312 8.623903 TCAGACTTAGAACAAAACGTAGAAGTA 58.376 33.333 0.00 0.00 28.99 2.24
2293 2313 9.408069 CAGACTTAGAACAAAACGTAGAAGTAT 57.592 33.333 0.00 0.00 28.99 2.12
2305 2325 8.847444 AAACGTAGAAGTATACTTATTCGTGG 57.153 34.615 31.71 16.02 45.49 4.94
2306 2326 7.792374 ACGTAGAAGTATACTTATTCGTGGA 57.208 36.000 31.00 8.58 44.89 4.02
2307 2327 7.634522 ACGTAGAAGTATACTTATTCGTGGAC 58.365 38.462 31.00 16.88 44.89 4.02
2308 2328 6.789403 CGTAGAAGTATACTTATTCGTGGACG 59.211 42.308 23.15 18.33 34.71 4.79
2309 2329 6.069684 AGAAGTATACTTATTCGTGGACGG 57.930 41.667 18.03 0.00 36.77 4.79
2310 2330 5.824624 AGAAGTATACTTATTCGTGGACGGA 59.175 40.000 18.03 0.00 36.77 4.69
2311 2331 5.686159 AGTATACTTATTCGTGGACGGAG 57.314 43.478 0.00 0.00 40.29 4.63
2312 2332 4.518211 AGTATACTTATTCGTGGACGGAGG 59.482 45.833 0.00 0.00 40.29 4.30
2313 2333 0.822164 ACTTATTCGTGGACGGAGGG 59.178 55.000 0.00 0.00 40.29 4.30
2314 2334 1.108776 CTTATTCGTGGACGGAGGGA 58.891 55.000 0.00 0.00 40.29 4.20
2460 2480 3.449227 CAGCTGTAGCCGTCGGGA 61.449 66.667 14.38 0.00 43.38 5.14
2502 2522 2.376808 AAGGCTCAATGTGTCTCGAG 57.623 50.000 5.93 5.93 0.00 4.04
2565 2589 0.666913 GCCCTGTAGCTGCAATCATG 59.333 55.000 5.84 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.251440 TGTGGTTTATATGAACTAGTACAGAGT 57.749 33.333 9.92 0.00 0.00 3.24
3 4 9.517609 GTGTGGTTTATATGAACTAGTACAGAG 57.482 37.037 9.92 0.00 0.00 3.35
4 5 9.251440 AGTGTGGTTTATATGAACTAGTACAGA 57.749 33.333 9.92 0.00 0.00 3.41
5 6 9.517609 GAGTGTGGTTTATATGAACTAGTACAG 57.482 37.037 9.92 0.00 0.00 2.74
6 7 8.186163 CGAGTGTGGTTTATATGAACTAGTACA 58.814 37.037 9.92 7.81 0.00 2.90
7 8 7.646922 CCGAGTGTGGTTTATATGAACTAGTAC 59.353 40.741 9.92 6.63 0.00 2.73
8 9 7.682741 GCCGAGTGTGGTTTATATGAACTAGTA 60.683 40.741 9.92 0.00 0.00 1.82
9 10 6.570692 CCGAGTGTGGTTTATATGAACTAGT 58.429 40.000 9.92 0.00 0.00 2.57
10 11 5.462398 GCCGAGTGTGGTTTATATGAACTAG 59.538 44.000 9.92 0.00 0.00 2.57
11 12 5.105269 TGCCGAGTGTGGTTTATATGAACTA 60.105 40.000 9.92 1.47 0.00 2.24
12 13 4.189231 GCCGAGTGTGGTTTATATGAACT 58.811 43.478 9.92 0.00 0.00 3.01
13 14 3.936453 TGCCGAGTGTGGTTTATATGAAC 59.064 43.478 1.80 1.80 0.00 3.18
14 15 4.188462 CTGCCGAGTGTGGTTTATATGAA 58.812 43.478 0.00 0.00 0.00 2.57
15 16 3.431626 CCTGCCGAGTGTGGTTTATATGA 60.432 47.826 0.00 0.00 0.00 2.15
16 17 2.872245 CCTGCCGAGTGTGGTTTATATG 59.128 50.000 0.00 0.00 0.00 1.78
17 18 2.769663 TCCTGCCGAGTGTGGTTTATAT 59.230 45.455 0.00 0.00 0.00 0.86
18 19 2.093869 GTCCTGCCGAGTGTGGTTTATA 60.094 50.000 0.00 0.00 0.00 0.98
19 20 0.981183 TCCTGCCGAGTGTGGTTTAT 59.019 50.000 0.00 0.00 0.00 1.40
20 21 0.034337 GTCCTGCCGAGTGTGGTTTA 59.966 55.000 0.00 0.00 0.00 2.01
21 22 1.227853 GTCCTGCCGAGTGTGGTTT 60.228 57.895 0.00 0.00 0.00 3.27
22 23 0.830444 TAGTCCTGCCGAGTGTGGTT 60.830 55.000 0.00 0.00 0.00 3.67
23 24 1.228769 TAGTCCTGCCGAGTGTGGT 60.229 57.895 0.00 0.00 0.00 4.16
24 25 1.513158 CTAGTCCTGCCGAGTGTGG 59.487 63.158 0.00 0.00 0.00 4.17
25 26 1.513158 CCTAGTCCTGCCGAGTGTG 59.487 63.158 0.00 0.00 0.00 3.82
26 27 1.682684 CCCTAGTCCTGCCGAGTGT 60.683 63.158 0.00 0.00 0.00 3.55
27 28 2.427245 CCCCTAGTCCTGCCGAGTG 61.427 68.421 0.00 0.00 0.00 3.51
28 29 2.042843 CCCCTAGTCCTGCCGAGT 60.043 66.667 0.00 0.00 0.00 4.18
29 30 2.042843 ACCCCTAGTCCTGCCGAG 60.043 66.667 0.00 0.00 0.00 4.63
30 31 2.363795 CACCCCTAGTCCTGCCGA 60.364 66.667 0.00 0.00 0.00 5.54
31 32 0.974010 TAACACCCCTAGTCCTGCCG 60.974 60.000 0.00 0.00 0.00 5.69
32 33 1.416772 GATAACACCCCTAGTCCTGCC 59.583 57.143 0.00 0.00 0.00 4.85
33 34 2.365941 GAGATAACACCCCTAGTCCTGC 59.634 54.545 0.00 0.00 0.00 4.85
34 35 3.892588 GAGAGATAACACCCCTAGTCCTG 59.107 52.174 0.00 0.00 0.00 3.86
35 36 3.117054 GGAGAGATAACACCCCTAGTCCT 60.117 52.174 0.00 0.00 0.00 3.85
36 37 3.232662 GGAGAGATAACACCCCTAGTCC 58.767 54.545 0.00 0.00 0.00 3.85
37 38 2.885894 CGGAGAGATAACACCCCTAGTC 59.114 54.545 0.00 0.00 0.00 2.59
38 39 2.424523 CCGGAGAGATAACACCCCTAGT 60.425 54.545 0.00 0.00 0.00 2.57
39 40 2.158505 TCCGGAGAGATAACACCCCTAG 60.159 54.545 0.00 0.00 0.00 3.02
40 41 1.854939 TCCGGAGAGATAACACCCCTA 59.145 52.381 0.00 0.00 0.00 3.53
41 42 0.635009 TCCGGAGAGATAACACCCCT 59.365 55.000 0.00 0.00 0.00 4.79
42 43 1.041437 CTCCGGAGAGATAACACCCC 58.959 60.000 28.21 0.00 43.39 4.95
43 44 2.068834 TCTCCGGAGAGATAACACCC 57.931 55.000 30.49 0.00 44.42 4.61
58 59 0.688087 ATCCAGGTTCGGGACTCTCC 60.688 60.000 0.00 0.00 37.23 3.71
59 60 2.068834 TATCCAGGTTCGGGACTCTC 57.931 55.000 0.00 0.00 37.23 3.20
60 61 2.320781 CATATCCAGGTTCGGGACTCT 58.679 52.381 0.00 0.00 37.23 3.24
61 62 2.036089 GACATATCCAGGTTCGGGACTC 59.964 54.545 0.00 0.00 37.23 3.36
62 63 2.040178 GACATATCCAGGTTCGGGACT 58.960 52.381 0.00 0.00 37.23 3.85
63 64 2.040178 AGACATATCCAGGTTCGGGAC 58.960 52.381 0.00 0.00 37.23 4.46
64 65 2.434336 CAAGACATATCCAGGTTCGGGA 59.566 50.000 0.00 0.00 39.14 5.14
65 66 2.838736 CAAGACATATCCAGGTTCGGG 58.161 52.381 0.00 0.00 0.00 5.14
66 67 2.213499 GCAAGACATATCCAGGTTCGG 58.787 52.381 0.00 0.00 0.00 4.30
67 68 1.860950 CGCAAGACATATCCAGGTTCG 59.139 52.381 0.00 0.00 43.02 3.95
68 69 2.866762 GACGCAAGACATATCCAGGTTC 59.133 50.000 0.00 0.00 43.62 3.62
69 70 2.420129 GGACGCAAGACATATCCAGGTT 60.420 50.000 0.00 0.00 43.62 3.50
70 71 1.139058 GGACGCAAGACATATCCAGGT 59.861 52.381 0.00 0.00 43.62 4.00
71 72 1.541233 GGGACGCAAGACATATCCAGG 60.541 57.143 0.00 0.00 43.62 4.45
72 73 1.414181 AGGGACGCAAGACATATCCAG 59.586 52.381 0.00 0.00 43.62 3.86
73 74 1.412710 GAGGGACGCAAGACATATCCA 59.587 52.381 0.00 0.00 43.62 3.41
74 75 1.603172 CGAGGGACGCAAGACATATCC 60.603 57.143 0.00 0.00 43.62 2.59
75 76 1.772182 CGAGGGACGCAAGACATATC 58.228 55.000 0.00 0.00 43.62 1.63
76 77 3.967886 CGAGGGACGCAAGACATAT 57.032 52.632 0.00 0.00 43.62 1.78
86 87 3.893763 ATGAGCGAGCGAGGGACG 61.894 66.667 0.00 0.00 45.66 4.79
87 88 2.279120 CATGAGCGAGCGAGGGAC 60.279 66.667 0.00 0.00 0.00 4.46
88 89 2.755876 ACATGAGCGAGCGAGGGA 60.756 61.111 0.00 0.00 0.00 4.20
89 90 2.279120 GACATGAGCGAGCGAGGG 60.279 66.667 0.00 0.00 0.00 4.30
90 91 2.653448 CGACATGAGCGAGCGAGG 60.653 66.667 0.00 0.00 0.00 4.63
91 92 2.653448 CCGACATGAGCGAGCGAG 60.653 66.667 12.88 0.00 0.00 5.03
92 93 4.854784 GCCGACATGAGCGAGCGA 62.855 66.667 12.88 0.00 0.00 4.93
94 95 2.176273 AATGCCGACATGAGCGAGC 61.176 57.895 12.88 13.56 36.36 5.03
95 96 1.640069 CAATGCCGACATGAGCGAG 59.360 57.895 12.88 5.85 36.36 5.03
96 97 2.463620 GCAATGCCGACATGAGCGA 61.464 57.895 12.88 0.00 36.36 4.93
97 98 2.023741 GCAATGCCGACATGAGCG 59.976 61.111 0.00 2.39 36.36 5.03
98 99 2.410469 GGCAATGCCGACATGAGC 59.590 61.111 9.14 0.00 39.62 4.26
114 115 2.608988 ACAGGTGGGCTCCAGAGG 60.609 66.667 0.00 0.00 32.34 3.69
115 116 2.667418 CACAGGTGGGCTCCAGAG 59.333 66.667 0.00 0.00 32.34 3.35
116 117 3.640407 GCACAGGTGGGCTCCAGA 61.640 66.667 0.00 0.00 42.27 3.86
117 118 4.729918 GGCACAGGTGGGCTCCAG 62.730 72.222 3.82 0.00 45.56 3.86
123 124 4.087892 CTCGAGGGCACAGGTGGG 62.088 72.222 3.91 0.00 0.00 4.61
124 125 4.767255 GCTCGAGGGCACAGGTGG 62.767 72.222 15.58 0.00 0.00 4.61
125 126 4.767255 GGCTCGAGGGCACAGGTG 62.767 72.222 15.58 0.00 40.53 4.00
127 128 4.154347 GAGGCTCGAGGGCACAGG 62.154 72.222 15.58 0.00 43.56 4.00
128 129 4.154347 GGAGGCTCGAGGGCACAG 62.154 72.222 15.58 0.00 43.56 3.66
129 130 4.704103 AGGAGGCTCGAGGGCACA 62.704 66.667 15.58 0.00 43.56 4.57
130 131 3.844090 GAGGAGGCTCGAGGGCAC 61.844 72.222 15.58 5.99 43.56 5.01
131 132 3.608759 AAGAGGAGGCTCGAGGGCA 62.609 63.158 15.58 0.00 43.56 5.36
132 133 1.904990 AAAAGAGGAGGCTCGAGGGC 61.905 60.000 15.58 7.43 41.20 5.19
133 134 0.176910 GAAAAGAGGAGGCTCGAGGG 59.823 60.000 15.58 0.00 0.00 4.30
134 135 1.190643 AGAAAAGAGGAGGCTCGAGG 58.809 55.000 15.58 0.00 0.00 4.63
135 136 3.326836 AAAGAAAAGAGGAGGCTCGAG 57.673 47.619 8.45 8.45 0.00 4.04
136 137 3.368531 GCTAAAGAAAAGAGGAGGCTCGA 60.369 47.826 8.69 0.00 0.00 4.04
137 138 2.933260 GCTAAAGAAAAGAGGAGGCTCG 59.067 50.000 8.69 0.00 0.00 5.03
138 139 3.275143 GGCTAAAGAAAAGAGGAGGCTC 58.725 50.000 5.78 5.78 0.00 4.70
139 140 2.644798 TGGCTAAAGAAAAGAGGAGGCT 59.355 45.455 0.00 0.00 0.00 4.58
140 141 2.750166 GTGGCTAAAGAAAAGAGGAGGC 59.250 50.000 0.00 0.00 0.00 4.70
141 142 3.348119 GGTGGCTAAAGAAAAGAGGAGG 58.652 50.000 0.00 0.00 0.00 4.30
142 143 3.009584 AGGGTGGCTAAAGAAAAGAGGAG 59.990 47.826 0.00 0.00 0.00 3.69
143 144 2.986728 AGGGTGGCTAAAGAAAAGAGGA 59.013 45.455 0.00 0.00 0.00 3.71
144 145 3.441500 AGGGTGGCTAAAGAAAAGAGG 57.558 47.619 0.00 0.00 0.00 3.69
145 146 4.021981 CCAAAGGGTGGCTAAAGAAAAGAG 60.022 45.833 0.00 0.00 41.72 2.85
146 147 3.895041 CCAAAGGGTGGCTAAAGAAAAGA 59.105 43.478 0.00 0.00 41.72 2.52
147 148 4.257267 CCAAAGGGTGGCTAAAGAAAAG 57.743 45.455 0.00 0.00 41.72 2.27
159 160 0.035439 ACGGTAGATGCCAAAGGGTG 60.035 55.000 0.00 0.00 36.17 4.61
160 161 0.035439 CACGGTAGATGCCAAAGGGT 60.035 55.000 0.00 0.00 36.17 4.34
161 162 0.035439 ACACGGTAGATGCCAAAGGG 60.035 55.000 0.00 0.00 37.18 3.95
162 163 1.086696 CACACGGTAGATGCCAAAGG 58.913 55.000 0.00 0.00 0.00 3.11
163 164 0.447801 GCACACGGTAGATGCCAAAG 59.552 55.000 0.00 0.00 33.06 2.77
164 165 2.550487 GCACACGGTAGATGCCAAA 58.450 52.632 0.00 0.00 33.06 3.28
165 166 4.294523 GCACACGGTAGATGCCAA 57.705 55.556 0.00 0.00 33.06 4.52
168 169 2.106683 GTGGGCACACGGTAGATGC 61.107 63.158 1.77 3.34 37.94 3.91
169 170 4.201951 GTGGGCACACGGTAGATG 57.798 61.111 1.77 0.00 37.94 2.90
177 178 2.515057 TTGTCGTGGTGGGCACAC 60.515 61.111 11.74 11.74 46.97 3.82
178 179 2.203139 CTTGTCGTGGTGGGCACA 60.203 61.111 0.00 0.00 0.00 4.57
179 180 1.961277 CTCTTGTCGTGGTGGGCAC 60.961 63.158 0.00 0.00 0.00 5.01
180 181 2.425592 CTCTTGTCGTGGTGGGCA 59.574 61.111 0.00 0.00 0.00 5.36
181 182 2.358737 CCTCTTGTCGTGGTGGGC 60.359 66.667 0.00 0.00 0.00 5.36
182 183 1.004918 GACCTCTTGTCGTGGTGGG 60.005 63.158 0.00 0.00 39.51 4.61
183 184 4.675404 GACCTCTTGTCGTGGTGG 57.325 61.111 0.00 0.00 39.51 4.61
190 191 3.315418 GAAACTACCGTGACCTCTTGTC 58.685 50.000 0.00 0.00 44.72 3.18
191 192 2.036862 GGAAACTACCGTGACCTCTTGT 59.963 50.000 0.00 0.00 0.00 3.16
192 193 2.299297 AGGAAACTACCGTGACCTCTTG 59.701 50.000 0.00 0.00 40.61 3.02
193 194 2.606378 AGGAAACTACCGTGACCTCTT 58.394 47.619 0.00 0.00 40.61 2.85
194 195 2.305858 AGGAAACTACCGTGACCTCT 57.694 50.000 0.00 0.00 40.61 3.69
195 196 2.561858 AGAAGGAAACTACCGTGACCTC 59.438 50.000 0.00 0.00 42.68 3.85
196 197 2.606378 AGAAGGAAACTACCGTGACCT 58.394 47.619 0.00 0.00 42.68 3.85
197 198 3.397849 AAGAAGGAAACTACCGTGACC 57.602 47.619 0.00 0.00 42.68 4.02
198 199 4.374399 TCAAAGAAGGAAACTACCGTGAC 58.626 43.478 0.00 0.00 42.68 3.67
199 200 4.675976 TCAAAGAAGGAAACTACCGTGA 57.324 40.909 0.00 0.00 42.68 4.35
205 206 6.017109 GCACATGTCTTCAAAGAAGGAAACTA 60.017 38.462 0.00 0.00 42.68 2.24
211 212 3.567164 AGTGCACATGTCTTCAAAGAAGG 59.433 43.478 21.04 0.00 36.68 3.46
220 221 2.057137 ACCACAAGTGCACATGTCTT 57.943 45.000 23.88 11.47 0.00 3.01
228 229 3.635836 TCATTCATTGAACCACAAGTGCA 59.364 39.130 0.15 0.00 42.02 4.57
240 241 3.054139 CCTCCTCCCAGTTCATTCATTGA 60.054 47.826 0.00 0.00 0.00 2.57
253 254 4.741239 GCTGACCCCCTCCTCCCA 62.741 72.222 0.00 0.00 0.00 4.37
301 302 0.690762 CTCCGAGTTTTTCCCCCAGA 59.309 55.000 0.00 0.00 0.00 3.86
304 305 0.608308 CCACTCCGAGTTTTTCCCCC 60.608 60.000 0.00 0.00 0.00 5.40
683 691 7.096065 GGATTTATCTTGCCGCATTTACAAATC 60.096 37.037 13.90 13.90 0.00 2.17
688 696 4.024387 TCGGATTTATCTTGCCGCATTTAC 60.024 41.667 0.00 0.00 43.26 2.01
708 716 0.665972 CCGCAAAATGGTTGGTTCGG 60.666 55.000 0.00 0.00 0.00 4.30
814 822 1.068055 ACGGACACGATTGTACTGGAC 60.068 52.381 0.00 0.00 44.60 4.02
1138 1149 2.125147 CCGGAAGATCTGCCGCAA 60.125 61.111 33.57 0.00 45.93 4.85
1329 1340 2.331132 GGAACGGTCGTCGAGGAGT 61.331 63.158 8.30 0.90 42.43 3.85
1344 1355 1.309006 GTCCTCGGAGTAGGGGGAA 59.691 63.158 4.02 0.00 37.24 3.97
1609 1620 0.394352 GGTTGAAGGCGATGGATGGT 60.394 55.000 0.00 0.00 0.00 3.55
1664 1675 1.737735 CACCAACAGAGCGCGATCA 60.738 57.895 27.74 0.00 0.00 2.92
1805 1816 3.004734 CCACTGTCATTCTGGGTTTGTTC 59.995 47.826 0.00 0.00 0.00 3.18
1886 1897 4.963276 TTGACGGGAGCAAATTAATCAG 57.037 40.909 0.00 0.00 0.00 2.90
2034 2046 1.407258 CAAAGTCACTCCCCGCAAAAA 59.593 47.619 0.00 0.00 0.00 1.94
2035 2047 1.028905 CAAAGTCACTCCCCGCAAAA 58.971 50.000 0.00 0.00 0.00 2.44
2036 2048 0.106918 ACAAAGTCACTCCCCGCAAA 60.107 50.000 0.00 0.00 0.00 3.68
2037 2049 0.106918 AACAAAGTCACTCCCCGCAA 60.107 50.000 0.00 0.00 0.00 4.85
2038 2050 0.534203 GAACAAAGTCACTCCCCGCA 60.534 55.000 0.00 0.00 0.00 5.69
2039 2051 0.250338 AGAACAAAGTCACTCCCCGC 60.250 55.000 0.00 0.00 0.00 6.13
2040 2052 2.256117 AAGAACAAAGTCACTCCCCG 57.744 50.000 0.00 0.00 0.00 5.73
2041 2053 2.034685 GCAAAGAACAAAGTCACTCCCC 59.965 50.000 0.00 0.00 0.00 4.81
2042 2054 2.952310 AGCAAAGAACAAAGTCACTCCC 59.048 45.455 0.00 0.00 0.00 4.30
2043 2055 3.627577 TGAGCAAAGAACAAAGTCACTCC 59.372 43.478 0.00 0.00 0.00 3.85
2044 2056 4.882671 TGAGCAAAGAACAAAGTCACTC 57.117 40.909 0.00 0.00 0.00 3.51
2045 2057 4.641989 ACATGAGCAAAGAACAAAGTCACT 59.358 37.500 0.00 0.00 0.00 3.41
2046 2058 4.925068 ACATGAGCAAAGAACAAAGTCAC 58.075 39.130 0.00 0.00 0.00 3.67
2047 2059 5.105797 ACAACATGAGCAAAGAACAAAGTCA 60.106 36.000 0.00 0.00 0.00 3.41
2048 2060 5.343249 ACAACATGAGCAAAGAACAAAGTC 58.657 37.500 0.00 0.00 0.00 3.01
2049 2061 5.329035 ACAACATGAGCAAAGAACAAAGT 57.671 34.783 0.00 0.00 0.00 2.66
2050 2062 4.741676 GGACAACATGAGCAAAGAACAAAG 59.258 41.667 0.00 0.00 0.00 2.77
2051 2063 4.159321 TGGACAACATGAGCAAAGAACAAA 59.841 37.500 0.00 0.00 0.00 2.83
2062 2074 2.455674 TCGTCCTTGGACAACATGAG 57.544 50.000 18.51 2.14 0.00 2.90
2097 2117 2.540515 ACACTTATTCGCAGACGGATG 58.459 47.619 0.00 0.00 38.24 3.51
2100 2120 2.871133 TGTACACTTATTCGCAGACGG 58.129 47.619 0.00 0.00 40.63 4.79
2101 2121 4.352039 AGATGTACACTTATTCGCAGACG 58.648 43.478 0.00 0.00 42.01 4.18
2103 2123 6.694877 ACTAGATGTACACTTATTCGCAGA 57.305 37.500 0.00 0.00 0.00 4.26
2104 2124 7.757097 AAACTAGATGTACACTTATTCGCAG 57.243 36.000 0.00 0.00 0.00 5.18
2105 2125 7.064134 CCAAAACTAGATGTACACTTATTCGCA 59.936 37.037 0.00 0.00 0.00 5.10
2106 2126 7.064253 ACCAAAACTAGATGTACACTTATTCGC 59.936 37.037 0.00 0.00 0.00 4.70
2107 2127 8.475331 ACCAAAACTAGATGTACACTTATTCG 57.525 34.615 0.00 0.00 0.00 3.34
2108 2128 8.880750 GGACCAAAACTAGATGTACACTTATTC 58.119 37.037 0.00 0.00 0.00 1.75
2110 2130 8.147244 AGGACCAAAACTAGATGTACACTTAT 57.853 34.615 0.00 0.00 0.00 1.73
2111 2131 7.549147 AGGACCAAAACTAGATGTACACTTA 57.451 36.000 0.00 0.00 0.00 2.24
2112 2132 6.435292 AGGACCAAAACTAGATGTACACTT 57.565 37.500 0.00 0.00 0.00 3.16
2113 2133 7.234988 ACTTAGGACCAAAACTAGATGTACACT 59.765 37.037 0.00 0.13 0.00 3.55
2114 2134 7.384477 ACTTAGGACCAAAACTAGATGTACAC 58.616 38.462 0.00 0.00 0.00 2.90
2116 2136 7.609056 TGACTTAGGACCAAAACTAGATGTAC 58.391 38.462 0.00 0.00 0.00 2.90
2118 2138 6.681729 TGACTTAGGACCAAAACTAGATGT 57.318 37.500 0.00 0.00 0.00 3.06
2149 2169 9.936759 TTTTCTTATGAAGTTGGTCAAAGTTTT 57.063 25.926 0.00 0.00 31.28 2.43
2150 2170 9.936759 TTTTTCTTATGAAGTTGGTCAAAGTTT 57.063 25.926 0.00 0.00 31.28 2.66
2178 2198 9.938280 ACTACTTTAGTGTCATAAATGCTGTTA 57.062 29.630 0.00 0.00 37.69 2.41
2179 2199 8.848474 ACTACTTTAGTGTCATAAATGCTGTT 57.152 30.769 0.00 0.00 37.69 3.16
2180 2200 9.367444 GTACTACTTTAGTGTCATAAATGCTGT 57.633 33.333 0.00 0.00 39.81 4.40
2181 2201 8.818057 GGTACTACTTTAGTGTCATAAATGCTG 58.182 37.037 0.00 0.00 39.81 4.41
2182 2202 8.537016 TGGTACTACTTTAGTGTCATAAATGCT 58.463 33.333 0.00 0.00 39.81 3.79
2183 2203 8.712285 TGGTACTACTTTAGTGTCATAAATGC 57.288 34.615 0.00 0.00 39.81 3.56
2189 2209 9.959721 ATCAAATTGGTACTACTTTAGTGTCAT 57.040 29.630 0.00 0.00 39.81 3.06
2190 2210 9.214957 CATCAAATTGGTACTACTTTAGTGTCA 57.785 33.333 0.00 0.00 39.81 3.58
2191 2211 9.216117 ACATCAAATTGGTACTACTTTAGTGTC 57.784 33.333 0.00 0.00 39.81 3.67
2192 2212 9.216117 GACATCAAATTGGTACTACTTTAGTGT 57.784 33.333 9.52 9.52 39.81 3.55
2193 2213 9.214957 TGACATCAAATTGGTACTACTTTAGTG 57.785 33.333 0.00 0.00 39.81 2.74
2194 2214 9.959721 ATGACATCAAATTGGTACTACTTTAGT 57.040 29.630 0.00 0.00 42.68 2.24
2247 2267 9.883142 AAGTCTGATGTTTTAAAATTTGACCAA 57.117 25.926 3.52 0.00 0.00 3.67
2258 2278 9.710979 CGTTTTGTTCTAAGTCTGATGTTTTAA 57.289 29.630 0.00 0.00 0.00 1.52
2259 2279 8.885722 ACGTTTTGTTCTAAGTCTGATGTTTTA 58.114 29.630 0.00 0.00 0.00 1.52
2260 2280 7.758495 ACGTTTTGTTCTAAGTCTGATGTTTT 58.242 30.769 0.00 0.00 0.00 2.43
2261 2281 7.316544 ACGTTTTGTTCTAAGTCTGATGTTT 57.683 32.000 0.00 0.00 0.00 2.83
2262 2282 6.920569 ACGTTTTGTTCTAAGTCTGATGTT 57.079 33.333 0.00 0.00 0.00 2.71
2263 2283 7.431249 TCTACGTTTTGTTCTAAGTCTGATGT 58.569 34.615 0.00 0.00 0.00 3.06
2264 2284 7.869016 TCTACGTTTTGTTCTAAGTCTGATG 57.131 36.000 0.00 0.00 0.00 3.07
2265 2285 8.142551 ACTTCTACGTTTTGTTCTAAGTCTGAT 58.857 33.333 0.00 0.00 0.00 2.90
2266 2286 7.486647 ACTTCTACGTTTTGTTCTAAGTCTGA 58.513 34.615 0.00 0.00 0.00 3.27
2267 2287 7.695869 ACTTCTACGTTTTGTTCTAAGTCTG 57.304 36.000 0.00 0.00 0.00 3.51
2277 2297 9.846248 ACGAATAAGTATACTTCTACGTTTTGT 57.154 29.630 21.25 12.54 35.86 2.83
2279 2299 9.294030 CCACGAATAAGTATACTTCTACGTTTT 57.706 33.333 26.04 13.10 36.53 2.43
2280 2300 8.677300 TCCACGAATAAGTATACTTCTACGTTT 58.323 33.333 26.04 13.25 36.53 3.60
2281 2301 8.125448 GTCCACGAATAAGTATACTTCTACGTT 58.875 37.037 26.04 15.17 36.53 3.99
2282 2302 7.517417 CGTCCACGAATAAGTATACTTCTACGT 60.517 40.741 21.25 23.25 43.02 3.57
2283 2303 6.789403 CGTCCACGAATAAGTATACTTCTACG 59.211 42.308 21.25 22.72 43.02 3.51
2284 2304 7.041780 TCCGTCCACGAATAAGTATACTTCTAC 60.042 40.741 21.25 12.18 43.02 2.59
2285 2305 6.992123 TCCGTCCACGAATAAGTATACTTCTA 59.008 38.462 21.25 5.98 43.02 2.10
2286 2306 5.824624 TCCGTCCACGAATAAGTATACTTCT 59.175 40.000 21.25 9.50 43.02 2.85
2287 2307 6.064846 TCCGTCCACGAATAAGTATACTTC 57.935 41.667 21.25 7.16 43.02 3.01
2288 2308 5.009410 CCTCCGTCCACGAATAAGTATACTT 59.991 44.000 21.35 21.35 43.02 2.24
2289 2309 4.518211 CCTCCGTCCACGAATAAGTATACT 59.482 45.833 0.00 0.00 43.02 2.12
2290 2310 4.320788 CCCTCCGTCCACGAATAAGTATAC 60.321 50.000 0.00 0.00 43.02 1.47
2291 2311 3.822735 CCCTCCGTCCACGAATAAGTATA 59.177 47.826 0.00 0.00 43.02 1.47
2292 2312 2.626743 CCCTCCGTCCACGAATAAGTAT 59.373 50.000 0.00 0.00 43.02 2.12
2293 2313 2.026641 CCCTCCGTCCACGAATAAGTA 58.973 52.381 0.00 0.00 43.02 2.24
2294 2314 0.822164 CCCTCCGTCCACGAATAAGT 59.178 55.000 0.00 0.00 43.02 2.24
2295 2315 1.067212 CTCCCTCCGTCCACGAATAAG 59.933 57.143 0.00 0.00 43.02 1.73
2296 2316 1.108776 CTCCCTCCGTCCACGAATAA 58.891 55.000 0.00 0.00 43.02 1.40
2297 2317 0.033796 ACTCCCTCCGTCCACGAATA 60.034 55.000 0.00 0.00 43.02 1.75
2298 2318 0.033796 TACTCCCTCCGTCCACGAAT 60.034 55.000 0.00 0.00 43.02 3.34
2299 2319 0.962356 GTACTCCCTCCGTCCACGAA 60.962 60.000 0.00 0.00 43.02 3.85
2300 2320 1.377725 GTACTCCCTCCGTCCACGA 60.378 63.158 0.00 0.00 43.02 4.35
2301 2321 1.246056 TTGTACTCCCTCCGTCCACG 61.246 60.000 0.00 0.00 39.44 4.94
2302 2322 0.971386 TTTGTACTCCCTCCGTCCAC 59.029 55.000 0.00 0.00 0.00 4.02
2303 2323 1.345415 GTTTTGTACTCCCTCCGTCCA 59.655 52.381 0.00 0.00 0.00 4.02
2304 2324 1.345415 TGTTTTGTACTCCCTCCGTCC 59.655 52.381 0.00 0.00 0.00 4.79
2305 2325 2.825861 TGTTTTGTACTCCCTCCGTC 57.174 50.000 0.00 0.00 0.00 4.79
2306 2326 3.564053 TTTGTTTTGTACTCCCTCCGT 57.436 42.857 0.00 0.00 0.00 4.69
2307 2327 4.517453 TGAATTTGTTTTGTACTCCCTCCG 59.483 41.667 0.00 0.00 0.00 4.63
2308 2328 5.564848 GCTGAATTTGTTTTGTACTCCCTCC 60.565 44.000 0.00 0.00 0.00 4.30
2309 2329 5.461526 GCTGAATTTGTTTTGTACTCCCTC 58.538 41.667 0.00 0.00 0.00 4.30
2310 2330 4.023193 CGCTGAATTTGTTTTGTACTCCCT 60.023 41.667 0.00 0.00 0.00 4.20
2311 2331 4.226761 CGCTGAATTTGTTTTGTACTCCC 58.773 43.478 0.00 0.00 0.00 4.30
2312 2332 3.668656 GCGCTGAATTTGTTTTGTACTCC 59.331 43.478 0.00 0.00 0.00 3.85
2313 2333 4.286910 TGCGCTGAATTTGTTTTGTACTC 58.713 39.130 9.73 0.00 0.00 2.59
2314 2334 4.300189 TGCGCTGAATTTGTTTTGTACT 57.700 36.364 9.73 0.00 0.00 2.73
2460 2480 3.430471 TGGAATCTGGCCAGGCAT 58.570 55.556 32.23 16.95 0.00 4.40
2502 2522 4.392940 ACAGCTATCTGGCCAAATCATAC 58.607 43.478 7.01 0.00 44.54 2.39
2534 2558 4.453819 CAGCTACAGGGCATAAGAAATAGC 59.546 45.833 0.00 0.00 35.18 2.97


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

AutoCloner maintained by Alex Coulton.