Multiple sequence alignment - TraesCS1A01G047400

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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 TraesCS1A01G047400 chr1A 100.000 1976 0 0 609 2584 29279691 29281666 0.000000e+00 3650.0
1 TraesCS1A01G047400 chr1A 100.000 230 0 0 1 230 29279083 29279312 2.380000e-115 425.0
2 TraesCS1A01G047400 chr1B 91.060 1264 60 16 618 1847 46883349 46884593 0.000000e+00 1659.0
3 TraesCS1A01G047400 chr1D 85.370 1121 91 27 753 1847 29483710 29482637 0.000000e+00 1094.0
4 TraesCS1A01G047400 chr1D 86.137 642 60 14 778 1395 28289597 28290233 0.000000e+00 665.0
5 TraesCS1A01G047400 chr1D 90.127 314 12 12 1996 2301 28291279 28291581 8.670000e-105 390.0
6 TraesCS1A01G047400 chr1D 93.367 196 13 0 1390 1585 28290266 28290461 9.050000e-75 291.0
7 TraesCS1A01G047400 chr1D 82.986 288 33 10 1770 2044 28291004 28291288 1.990000e-61 246.0
8 TraesCS1A01G047400 chr1D 83.249 197 23 6 2395 2583 28291929 28292123 3.420000e-39 172.0
9 TraesCS1A01G047400 chr6B 92.683 41 1 1 1857 1897 544695618 544695580 9.990000e-05 58.4
10 TraesCS1A01G047400 chr3B 94.595 37 2 0 1849 1885 779581018 779580982 9.990000e-05 58.4
11 TraesCS1A01G047400 chr7A 92.308 39 3 0 1847 1885 85627709 85627671 3.590000e-04 56.5
12 TraesCS1A01G047400 chr7A 92.308 39 3 0 1847 1885 85677381 85677343 3.590000e-04 56.5
13 TraesCS1A01G047400 chr6D 97.059 34 0 1 1890 1923 52719652 52719620 3.590000e-04 56.5
14 TraesCS1A01G047400 chr3D 100.000 30 0 0 1890 1919 324311109 324311080 3.590000e-04 56.5
15 TraesCS1A01G047400 chr3A 92.105 38 3 0 1848 1885 9073160 9073197 1.000000e-03 54.7
16 TraesCS1A01G047400 chr5B 100.000 28 0 0 1858 1885 485569929 485569902 5.000000e-03 52.8


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 TraesCS1A01G047400 chr1A 29279083 29281666 2583 False 2037.5 3650 100.0000 1 2584 2 chr1A.!!$F1 2583
1 TraesCS1A01G047400 chr1B 46883349 46884593 1244 False 1659.0 1659 91.0600 618 1847 1 chr1B.!!$F1 1229
2 TraesCS1A01G047400 chr1D 29482637 29483710 1073 True 1094.0 1094 85.3700 753 1847 1 chr1D.!!$R1 1094
3 TraesCS1A01G047400 chr1D 28289597 28292123 2526 False 352.8 665 87.1732 778 2583 5 chr1D.!!$F1 1805

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
706 707 0.032952 TCCAACGGTTCAGGAGTTCG 59.967 55.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2284 2913 0.179062 GCCATCTGTGCTCGGAAGAT 60.179 55.0 0.65 0.0 40.84 2.4 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
26 27 5.359194 AGGTGGACTCACATTAATAGTGG 57.641 43.478 14.17 9.62 45.32 4.00
27 28 4.783227 AGGTGGACTCACATTAATAGTGGT 59.217 41.667 14.17 11.70 45.32 4.16
28 29 5.104900 AGGTGGACTCACATTAATAGTGGTC 60.105 44.000 18.23 18.23 45.32 4.02
29 30 4.804139 GTGGACTCACATTAATAGTGGTCG 59.196 45.833 18.88 11.99 43.13 4.79
30 31 3.802685 GGACTCACATTAATAGTGGTCGC 59.197 47.826 18.88 13.89 37.71 5.19
31 32 4.430007 GACTCACATTAATAGTGGTCGCA 58.570 43.478 14.17 0.25 37.58 5.10
32 33 4.433615 ACTCACATTAATAGTGGTCGCAG 58.566 43.478 14.17 8.80 37.58 5.18
33 34 4.081642 ACTCACATTAATAGTGGTCGCAGT 60.082 41.667 14.17 9.23 37.58 4.40
34 35 4.430007 TCACATTAATAGTGGTCGCAGTC 58.570 43.478 14.17 0.00 37.58 3.51
35 36 4.159693 TCACATTAATAGTGGTCGCAGTCT 59.840 41.667 14.17 0.00 37.58 3.24
36 37 5.358725 TCACATTAATAGTGGTCGCAGTCTA 59.641 40.000 14.17 0.00 37.58 2.59
37 38 5.687730 CACATTAATAGTGGTCGCAGTCTAG 59.312 44.000 9.06 0.00 33.43 2.43
38 39 2.873133 AATAGTGGTCGCAGTCTAGC 57.127 50.000 0.00 0.00 0.00 3.42
46 47 4.598257 GCAGTCTAGCGCCTTTCA 57.402 55.556 2.29 0.00 0.00 2.69
47 48 3.071580 GCAGTCTAGCGCCTTTCAT 57.928 52.632 2.29 0.00 0.00 2.57
48 49 1.373570 GCAGTCTAGCGCCTTTCATT 58.626 50.000 2.29 0.00 0.00 2.57
49 50 2.550978 GCAGTCTAGCGCCTTTCATTA 58.449 47.619 2.29 0.00 0.00 1.90
50 51 2.936498 GCAGTCTAGCGCCTTTCATTAA 59.064 45.455 2.29 0.00 0.00 1.40
51 52 3.561725 GCAGTCTAGCGCCTTTCATTAAT 59.438 43.478 2.29 0.00 0.00 1.40
52 53 4.750098 GCAGTCTAGCGCCTTTCATTAATA 59.250 41.667 2.29 0.00 0.00 0.98
53 54 5.236478 GCAGTCTAGCGCCTTTCATTAATAA 59.764 40.000 2.29 0.00 0.00 1.40
54 55 6.073003 GCAGTCTAGCGCCTTTCATTAATAAT 60.073 38.462 2.29 0.00 0.00 1.28
55 56 7.513968 CAGTCTAGCGCCTTTCATTAATAATC 58.486 38.462 2.29 0.00 0.00 1.75
56 57 6.651225 AGTCTAGCGCCTTTCATTAATAATCC 59.349 38.462 2.29 0.00 0.00 3.01
57 58 4.749245 AGCGCCTTTCATTAATAATCCG 57.251 40.909 2.29 0.00 0.00 4.18
58 59 4.385825 AGCGCCTTTCATTAATAATCCGA 58.614 39.130 2.29 0.00 0.00 4.55
59 60 5.003804 AGCGCCTTTCATTAATAATCCGAT 58.996 37.500 2.29 0.00 0.00 4.18
60 61 6.170506 AGCGCCTTTCATTAATAATCCGATA 58.829 36.000 2.29 0.00 0.00 2.92
61 62 6.653320 AGCGCCTTTCATTAATAATCCGATAA 59.347 34.615 2.29 0.00 0.00 1.75
62 63 7.174253 AGCGCCTTTCATTAATAATCCGATAAA 59.826 33.333 2.29 0.00 0.00 1.40
63 64 7.968405 GCGCCTTTCATTAATAATCCGATAAAT 59.032 33.333 0.00 0.00 0.00 1.40
64 65 9.840427 CGCCTTTCATTAATAATCCGATAAATT 57.160 29.630 0.00 0.00 0.00 1.82
73 74 9.787435 TTAATAATCCGATAAATTAGCAGTGGT 57.213 29.630 0.00 0.00 0.00 4.16
74 75 7.672983 ATAATCCGATAAATTAGCAGTGGTG 57.327 36.000 4.76 0.00 0.00 4.17
75 76 3.804036 TCCGATAAATTAGCAGTGGTGG 58.196 45.455 4.76 0.00 0.00 4.61
76 77 3.452990 TCCGATAAATTAGCAGTGGTGGA 59.547 43.478 4.76 0.00 0.00 4.02
77 78 4.102524 TCCGATAAATTAGCAGTGGTGGAT 59.897 41.667 4.76 0.00 0.00 3.41
78 79 4.214119 CCGATAAATTAGCAGTGGTGGATG 59.786 45.833 4.76 0.00 0.00 3.51
79 80 4.319766 CGATAAATTAGCAGTGGTGGATGC 60.320 45.833 4.76 0.00 42.87 3.91
80 81 2.512692 AATTAGCAGTGGTGGATGCA 57.487 45.000 4.76 0.00 45.01 3.96
81 82 2.512692 ATTAGCAGTGGTGGATGCAA 57.487 45.000 4.76 0.00 45.01 4.08
82 83 2.284754 TTAGCAGTGGTGGATGCAAA 57.715 45.000 4.76 0.00 45.01 3.68
83 84 1.533625 TAGCAGTGGTGGATGCAAAC 58.466 50.000 4.76 0.00 45.01 2.93
84 85 1.181098 AGCAGTGGTGGATGCAAACC 61.181 55.000 9.12 9.12 45.01 3.27
85 86 1.966762 CAGTGGTGGATGCAAACCC 59.033 57.895 12.54 5.37 35.44 4.11
86 87 0.540365 CAGTGGTGGATGCAAACCCT 60.540 55.000 12.54 7.57 35.44 4.34
87 88 0.251341 AGTGGTGGATGCAAACCCTC 60.251 55.000 12.54 5.65 35.44 4.30
88 89 0.539438 GTGGTGGATGCAAACCCTCA 60.539 55.000 12.54 7.52 35.44 3.86
89 90 0.409092 TGGTGGATGCAAACCCTCAT 59.591 50.000 12.54 0.00 35.44 2.90
90 91 1.106285 GGTGGATGCAAACCCTCATC 58.894 55.000 10.15 0.00 38.60 2.92
92 93 2.408333 GGATGCAAACCCTCATCCG 58.592 57.895 5.62 0.00 46.23 4.18
93 94 1.103398 GGATGCAAACCCTCATCCGG 61.103 60.000 0.00 0.00 46.23 5.14
94 95 1.728490 GATGCAAACCCTCATCCGGC 61.728 60.000 0.00 0.00 34.52 6.13
95 96 2.361104 GCAAACCCTCATCCGGCA 60.361 61.111 0.00 0.00 0.00 5.69
96 97 2.700773 GCAAACCCTCATCCGGCAC 61.701 63.158 0.00 0.00 0.00 5.01
97 98 1.002134 CAAACCCTCATCCGGCACT 60.002 57.895 0.00 0.00 0.00 4.40
98 99 1.002134 AAACCCTCATCCGGCACTG 60.002 57.895 0.00 0.00 0.00 3.66
99 100 3.628646 AACCCTCATCCGGCACTGC 62.629 63.158 0.00 0.00 0.00 4.40
100 101 3.790437 CCCTCATCCGGCACTGCT 61.790 66.667 0.00 0.00 0.00 4.24
101 102 2.434843 CCCTCATCCGGCACTGCTA 61.435 63.158 0.00 0.00 0.00 3.49
102 103 1.750930 CCTCATCCGGCACTGCTAT 59.249 57.895 0.00 0.00 0.00 2.97
103 104 0.107456 CCTCATCCGGCACTGCTATT 59.893 55.000 0.00 0.00 0.00 1.73
104 105 1.224075 CTCATCCGGCACTGCTATTG 58.776 55.000 0.00 0.00 0.00 1.90
105 106 0.541392 TCATCCGGCACTGCTATTGT 59.459 50.000 0.00 0.00 0.00 2.71
106 107 0.940126 CATCCGGCACTGCTATTGTC 59.060 55.000 0.00 0.00 0.00 3.18
107 108 0.833287 ATCCGGCACTGCTATTGTCT 59.167 50.000 0.00 0.00 0.00 3.41
108 109 0.613260 TCCGGCACTGCTATTGTCTT 59.387 50.000 0.00 0.00 0.00 3.01
109 110 1.828595 TCCGGCACTGCTATTGTCTTA 59.171 47.619 0.00 0.00 0.00 2.10
110 111 1.933853 CCGGCACTGCTATTGTCTTAC 59.066 52.381 0.00 0.00 0.00 2.34
111 112 1.933853 CGGCACTGCTATTGTCTTACC 59.066 52.381 0.00 0.00 0.00 2.85
112 113 2.676750 CGGCACTGCTATTGTCTTACCA 60.677 50.000 0.00 0.00 0.00 3.25
113 114 3.343617 GGCACTGCTATTGTCTTACCAA 58.656 45.455 0.00 0.00 0.00 3.67
114 115 3.947834 GGCACTGCTATTGTCTTACCAAT 59.052 43.478 0.00 0.00 38.54 3.16
115 116 4.201950 GGCACTGCTATTGTCTTACCAATG 60.202 45.833 0.00 0.00 35.85 2.82
116 117 4.635765 GCACTGCTATTGTCTTACCAATGA 59.364 41.667 0.00 0.00 35.85 2.57
117 118 5.447818 GCACTGCTATTGTCTTACCAATGAC 60.448 44.000 0.00 0.00 35.85 3.06
118 119 4.870426 ACTGCTATTGTCTTACCAATGACG 59.130 41.667 0.00 0.00 35.85 4.35
119 120 4.188462 TGCTATTGTCTTACCAATGACGG 58.812 43.478 0.00 0.00 35.85 4.79
120 121 4.081365 TGCTATTGTCTTACCAATGACGGA 60.081 41.667 0.00 0.00 35.85 4.69
121 122 4.270325 GCTATTGTCTTACCAATGACGGAC 59.730 45.833 0.00 0.00 35.85 4.79
122 123 3.755112 TTGTCTTACCAATGACGGACA 57.245 42.857 0.00 0.00 36.10 4.02
123 124 3.034721 TGTCTTACCAATGACGGACAC 57.965 47.619 0.00 0.00 36.10 3.67
124 125 2.289195 TGTCTTACCAATGACGGACACC 60.289 50.000 0.00 0.00 36.10 4.16
125 126 1.972075 TCTTACCAATGACGGACACCA 59.028 47.619 0.00 0.00 0.00 4.17
126 127 2.028476 TCTTACCAATGACGGACACCAG 60.028 50.000 0.00 0.00 0.00 4.00
127 128 1.344065 TACCAATGACGGACACCAGT 58.656 50.000 0.00 0.00 0.00 4.00
128 129 0.472471 ACCAATGACGGACACCAGTT 59.528 50.000 0.00 0.00 0.00 3.16
129 130 1.133915 ACCAATGACGGACACCAGTTT 60.134 47.619 0.00 0.00 0.00 2.66
130 131 1.266718 CCAATGACGGACACCAGTTTG 59.733 52.381 0.00 0.00 0.00 2.93
131 132 1.946768 CAATGACGGACACCAGTTTGT 59.053 47.619 0.00 0.00 0.00 2.83
132 133 1.593196 ATGACGGACACCAGTTTGTG 58.407 50.000 0.00 0.00 42.05 3.33
138 139 2.793831 ACACCAGTTTGTGTCTGCC 58.206 52.632 0.00 0.00 46.15 4.85
139 140 0.034574 ACACCAGTTTGTGTCTGCCA 60.035 50.000 0.00 0.00 46.15 4.92
140 141 0.381801 CACCAGTTTGTGTCTGCCAC 59.618 55.000 0.00 0.00 44.78 5.01
141 142 0.255890 ACCAGTTTGTGTCTGCCACT 59.744 50.000 0.00 0.00 44.81 4.00
142 143 0.664761 CCAGTTTGTGTCTGCCACTG 59.335 55.000 0.00 0.00 44.81 3.66
143 144 1.667236 CAGTTTGTGTCTGCCACTGA 58.333 50.000 0.00 0.00 44.81 3.41
144 145 2.224606 CAGTTTGTGTCTGCCACTGAT 58.775 47.619 0.00 0.00 44.81 2.90
145 146 3.402110 CAGTTTGTGTCTGCCACTGATA 58.598 45.455 0.00 0.00 44.81 2.15
146 147 3.814842 CAGTTTGTGTCTGCCACTGATAA 59.185 43.478 0.00 0.00 44.81 1.75
147 148 3.815401 AGTTTGTGTCTGCCACTGATAAC 59.185 43.478 0.00 0.00 44.81 1.89
148 149 3.483808 TTGTGTCTGCCACTGATAACA 57.516 42.857 0.00 0.00 44.81 2.41
149 150 2.766313 TGTGTCTGCCACTGATAACAC 58.234 47.619 0.00 0.00 44.81 3.32
150 151 2.076863 GTGTCTGCCACTGATAACACC 58.923 52.381 0.00 0.00 41.11 4.16
151 152 1.977854 TGTCTGCCACTGATAACACCT 59.022 47.619 0.00 0.00 0.00 4.00
152 153 2.289631 TGTCTGCCACTGATAACACCTG 60.290 50.000 0.00 0.00 0.00 4.00
153 154 1.977854 TCTGCCACTGATAACACCTGT 59.022 47.619 0.00 0.00 0.00 4.00
154 155 2.028112 TCTGCCACTGATAACACCTGTC 60.028 50.000 0.00 0.00 0.00 3.51
155 156 1.003118 TGCCACTGATAACACCTGTCC 59.997 52.381 0.00 0.00 0.00 4.02
156 157 1.003118 GCCACTGATAACACCTGTCCA 59.997 52.381 0.00 0.00 0.00 4.02
157 158 2.552155 GCCACTGATAACACCTGTCCAA 60.552 50.000 0.00 0.00 0.00 3.53
158 159 3.750371 CCACTGATAACACCTGTCCAAA 58.250 45.455 0.00 0.00 0.00 3.28
159 160 4.335416 CCACTGATAACACCTGTCCAAAT 58.665 43.478 0.00 0.00 0.00 2.32
160 161 4.766891 CCACTGATAACACCTGTCCAAATT 59.233 41.667 0.00 0.00 0.00 1.82
161 162 5.243730 CCACTGATAACACCTGTCCAAATTT 59.756 40.000 0.00 0.00 0.00 1.82
162 163 6.432783 CCACTGATAACACCTGTCCAAATTTA 59.567 38.462 0.00 0.00 0.00 1.40
163 164 7.122650 CCACTGATAACACCTGTCCAAATTTAT 59.877 37.037 0.00 0.00 0.00 1.40
164 165 8.184192 CACTGATAACACCTGTCCAAATTTATC 58.816 37.037 0.00 0.00 0.00 1.75
165 166 8.109634 ACTGATAACACCTGTCCAAATTTATCT 58.890 33.333 0.00 0.00 0.00 1.98
166 167 8.877864 TGATAACACCTGTCCAAATTTATCTT 57.122 30.769 0.00 0.00 0.00 2.40
167 168 9.967451 TGATAACACCTGTCCAAATTTATCTTA 57.033 29.630 0.00 0.00 0.00 2.10
169 170 7.703058 AACACCTGTCCAAATTTATCTTAGG 57.297 36.000 0.00 0.00 0.00 2.69
170 171 7.027874 ACACCTGTCCAAATTTATCTTAGGA 57.972 36.000 12.07 2.60 0.00 2.94
171 172 6.884836 ACACCTGTCCAAATTTATCTTAGGAC 59.115 38.462 13.55 13.55 44.37 3.85
177 178 8.336801 GTCCAAATTTATCTTAGGACAACTGT 57.663 34.615 14.92 0.00 43.74 3.55
178 179 8.793592 GTCCAAATTTATCTTAGGACAACTGTT 58.206 33.333 14.92 0.00 43.74 3.16
182 183 9.802039 AAATTTATCTTAGGACAACTGTTACCA 57.198 29.630 14.99 2.99 0.00 3.25
183 184 9.449719 AATTTATCTTAGGACAACTGTTACCAG 57.550 33.333 14.99 7.43 44.68 4.00
184 185 4.884668 TCTTAGGACAACTGTTACCAGG 57.115 45.455 14.99 0.00 43.36 4.45
185 186 4.485875 TCTTAGGACAACTGTTACCAGGA 58.514 43.478 14.99 8.79 43.36 3.86
186 187 4.282703 TCTTAGGACAACTGTTACCAGGAC 59.717 45.833 14.99 0.00 43.36 3.85
187 188 1.343465 AGGACAACTGTTACCAGGACG 59.657 52.381 14.99 0.00 43.36 4.79
188 189 1.607251 GGACAACTGTTACCAGGACGG 60.607 57.143 0.00 0.00 43.36 4.79
189 190 0.250166 ACAACTGTTACCAGGACGGC 60.250 55.000 0.00 0.00 43.36 5.68
190 191 0.034896 CAACTGTTACCAGGACGGCT 59.965 55.000 0.00 0.00 43.36 5.52
191 192 0.320697 AACTGTTACCAGGACGGCTC 59.679 55.000 0.00 0.00 43.36 4.70
192 193 1.153823 CTGTTACCAGGACGGCTCG 60.154 63.158 0.00 0.00 39.03 5.03
193 194 1.592400 CTGTTACCAGGACGGCTCGA 61.592 60.000 0.00 0.00 39.03 4.04
194 195 1.139095 GTTACCAGGACGGCTCGAG 59.861 63.158 8.45 8.45 39.03 4.04
195 196 2.707849 TTACCAGGACGGCTCGAGC 61.708 63.158 29.38 29.38 39.03 5.03
198 199 4.116328 CAGGACGGCTCGAGCGAA 62.116 66.667 29.81 0.00 43.26 4.70
199 200 4.117661 AGGACGGCTCGAGCGAAC 62.118 66.667 29.81 21.33 43.26 3.95
204 205 4.821589 GGCTCGAGCGAACCCCAG 62.822 72.222 29.81 0.00 43.26 4.45
206 207 4.821589 CTCGAGCGAACCCCAGCC 62.822 72.222 0.00 0.00 0.00 4.85
225 226 4.410400 CCGCCCACAACCCTCCTC 62.410 72.222 0.00 0.00 0.00 3.71
226 227 4.410400 CGCCCACAACCCTCCTCC 62.410 72.222 0.00 0.00 0.00 4.30
227 228 4.048470 GCCCACAACCCTCCTCCC 62.048 72.222 0.00 0.00 0.00 4.30
228 229 2.204151 CCCACAACCCTCCTCCCT 60.204 66.667 0.00 0.00 0.00 4.20
229 230 2.301738 CCCACAACCCTCCTCCCTC 61.302 68.421 0.00 0.00 0.00 4.30
632 633 1.084370 GTTGCAGGAGATTCCGACGG 61.084 60.000 7.84 7.84 42.75 4.79
658 659 0.252421 TGCAGGAGTCCAGATCCAGT 60.252 55.000 12.86 0.00 39.47 4.00
661 662 1.686052 CAGGAGTCCAGATCCAGTAGC 59.314 57.143 12.86 0.00 39.47 3.58
666 667 1.960689 GTCCAGATCCAGTAGCTCTCC 59.039 57.143 0.00 0.00 0.00 3.71
674 675 0.528017 CAGTAGCTCTCCAACTGCGA 59.472 55.000 0.78 0.00 34.73 5.10
705 706 2.028020 AGATCCAACGGTTCAGGAGTTC 60.028 50.000 6.18 0.97 34.40 3.01
706 707 0.032952 TCCAACGGTTCAGGAGTTCG 59.967 55.000 0.00 0.00 0.00 3.95
717 719 0.892755 AGGAGTTCGCATCACGGTAA 59.107 50.000 0.00 0.00 43.89 2.85
722 724 1.730064 GTTCGCATCACGGTAACACAT 59.270 47.619 0.00 0.00 43.89 3.21
744 746 2.962253 GCGTGGAGCGGCTGATAC 60.962 66.667 7.50 2.36 41.69 2.24
921 940 1.261480 AGCTCTTCACGTGTCCATCT 58.739 50.000 16.51 6.04 0.00 2.90
984 1027 1.409064 TCTCGTCGCCATAGCATTCTT 59.591 47.619 0.00 0.00 39.83 2.52
1164 1213 1.080093 GGCGTTCCTGATGTCGTCA 60.080 57.895 0.00 0.00 35.05 4.35
1171 1220 0.173481 CCTGATGTCGTCACCATCGT 59.827 55.000 0.00 0.00 41.28 3.73
1320 1369 2.416747 CTGACGTGGATGAAGCTTCAA 58.583 47.619 31.55 14.10 41.13 2.69
1439 1526 1.784358 ATGATGCTGGTGGAAATGGG 58.216 50.000 0.00 0.00 0.00 4.00
1661 1749 7.040478 TGTGTACTCTACCGTAGTTGTTTGTAT 60.040 37.037 5.46 0.00 0.00 2.29
1665 1756 8.922058 ACTCTACCGTAGTTGTTTGTATTATG 57.078 34.615 5.46 0.00 0.00 1.90
1683 1774 2.276740 CTGGGCATTCTGGGTCCC 59.723 66.667 0.00 0.00 39.22 4.46
1684 1775 3.346734 TGGGCATTCTGGGTCCCC 61.347 66.667 5.13 0.00 37.97 4.81
1691 1782 1.073098 ATTCTGGGTCCCCGTCTTTT 58.927 50.000 5.13 0.00 39.42 2.27
1717 1809 9.974980 TTTTCTTGTAAATTTGTAATGACTCCC 57.025 29.630 0.00 0.00 0.00 4.30
1727 1819 1.903877 AATGACTCCCGGTGCCTGAG 61.904 60.000 0.00 1.32 0.00 3.35
1728 1820 4.459089 GACTCCCGGTGCCTGAGC 62.459 72.222 0.00 0.00 40.48 4.26
1767 1872 3.777925 CCGCGCTGAAGTTCCACG 61.778 66.667 5.56 9.57 0.00 4.94
1793 2315 8.584600 GTGTATATTGTACGACAGAAAGTGAAG 58.415 37.037 0.00 0.00 0.00 3.02
1799 2321 4.920640 ACGACAGAAAGTGAAGAGAGAA 57.079 40.909 0.00 0.00 0.00 2.87
1859 2381 6.154203 TGATCACAAGATACTCCATCTGTC 57.846 41.667 0.00 0.00 43.56 3.51
1860 2382 5.896106 TGATCACAAGATACTCCATCTGTCT 59.104 40.000 0.00 0.00 43.56 3.41
1861 2383 5.843673 TCACAAGATACTCCATCTGTCTC 57.156 43.478 0.00 0.00 43.56 3.36
1862 2384 5.264395 TCACAAGATACTCCATCTGTCTCA 58.736 41.667 0.00 0.00 43.56 3.27
1863 2385 5.126222 TCACAAGATACTCCATCTGTCTCAC 59.874 44.000 0.00 0.00 43.56 3.51
1864 2386 5.019470 ACAAGATACTCCATCTGTCTCACA 58.981 41.667 0.00 0.00 43.56 3.58
1865 2387 5.481824 ACAAGATACTCCATCTGTCTCACAA 59.518 40.000 0.00 0.00 43.56 3.33
1866 2388 6.155910 ACAAGATACTCCATCTGTCTCACAAT 59.844 38.462 0.00 0.00 43.56 2.71
1867 2389 7.343057 ACAAGATACTCCATCTGTCTCACAATA 59.657 37.037 0.00 0.00 43.56 1.90
1868 2390 8.366401 CAAGATACTCCATCTGTCTCACAATAT 58.634 37.037 0.00 0.00 43.56 1.28
1869 2391 9.593565 AAGATACTCCATCTGTCTCACAATATA 57.406 33.333 0.00 0.00 43.56 0.86
1870 2392 9.593565 AGATACTCCATCTGTCTCACAATATAA 57.406 33.333 0.00 0.00 42.69 0.98
1871 2393 9.853555 GATACTCCATCTGTCTCACAATATAAG 57.146 37.037 0.00 0.00 0.00 1.73
1872 2394 7.904558 ACTCCATCTGTCTCACAATATAAGA 57.095 36.000 0.00 0.00 0.00 2.10
1873 2395 8.489676 ACTCCATCTGTCTCACAATATAAGAT 57.510 34.615 0.00 0.00 0.00 2.40
1874 2396 8.584157 ACTCCATCTGTCTCACAATATAAGATC 58.416 37.037 0.00 0.00 0.00 2.75
1875 2397 8.482852 TCCATCTGTCTCACAATATAAGATCA 57.517 34.615 0.00 0.00 0.00 2.92
1876 2398 9.097946 TCCATCTGTCTCACAATATAAGATCAT 57.902 33.333 0.00 0.00 0.00 2.45
1877 2399 9.722184 CCATCTGTCTCACAATATAAGATCATT 57.278 33.333 0.00 0.00 0.00 2.57
1903 2425 9.982291 TTTTCAAGTTGTACGATCTTATATTGC 57.018 29.630 2.11 0.00 0.00 3.56
1904 2426 7.389603 TCAAGTTGTACGATCTTATATTGCG 57.610 36.000 2.11 0.00 0.00 4.85
1940 2492 5.964958 AATAAATATGGCATCACCGGAAG 57.035 39.130 9.46 0.00 43.94 3.46
1999 2551 4.207019 CGACAAACCAAAAAGATGCAAGTC 59.793 41.667 0.00 0.00 0.00 3.01
2000 2552 5.343307 ACAAACCAAAAAGATGCAAGTCT 57.657 34.783 0.00 0.00 0.00 3.24
2001 2553 5.111293 ACAAACCAAAAAGATGCAAGTCTG 58.889 37.500 0.00 0.00 0.00 3.51
2057 2650 3.997021 AGTCTGAACCGCATCTAAAACAG 59.003 43.478 0.00 0.00 0.00 3.16
2093 2686 2.802816 CAGGTCTGAAGAAGAAACACCG 59.197 50.000 0.00 0.00 36.40 4.94
2154 2747 2.815503 TCAGTATCGTTCGGTTCAGTCA 59.184 45.455 0.00 0.00 0.00 3.41
2164 2757 1.877680 CGGTTCAGTCAGTCATTGCCA 60.878 52.381 0.00 0.00 0.00 4.92
2165 2758 2.440409 GGTTCAGTCAGTCATTGCCAT 58.560 47.619 0.00 0.00 0.00 4.40
2166 2759 2.421424 GGTTCAGTCAGTCATTGCCATC 59.579 50.000 0.00 0.00 0.00 3.51
2183 2780 4.018506 TGCCATCCTTCTTTCCAATCTGTA 60.019 41.667 0.00 0.00 0.00 2.74
2184 2781 5.136105 GCCATCCTTCTTTCCAATCTGTAT 58.864 41.667 0.00 0.00 0.00 2.29
2185 2782 5.009410 GCCATCCTTCTTTCCAATCTGTATG 59.991 44.000 0.00 0.00 0.00 2.39
2186 2783 6.359804 CCATCCTTCTTTCCAATCTGTATGA 58.640 40.000 0.00 0.00 0.00 2.15
2214 2811 6.989759 ACAGTACATTCAGTTTGTATCACACA 59.010 34.615 0.00 0.00 32.56 3.72
2215 2812 7.171508 ACAGTACATTCAGTTTGTATCACACAG 59.828 37.037 0.00 0.00 38.72 3.66
2241 2839 0.171455 GATGCGGTCAGTCGTCTTCT 59.829 55.000 0.00 0.00 0.00 2.85
2249 2849 1.542030 TCAGTCGTCTTCTCCTCTTGC 59.458 52.381 0.00 0.00 0.00 4.01
2257 2857 0.392706 TTCTCCTCTTGCGAGCACAA 59.607 50.000 0.00 0.00 35.90 3.33
2260 2860 1.396301 CTCCTCTTGCGAGCACAATTC 59.604 52.381 0.00 0.00 35.90 2.17
2264 2864 3.436704 CCTCTTGCGAGCACAATTCTTTA 59.563 43.478 0.00 0.00 35.90 1.85
2265 2865 4.083324 CCTCTTGCGAGCACAATTCTTTAA 60.083 41.667 0.00 0.00 35.90 1.52
2272 2901 6.145371 TGCGAGCACAATTCTTTAATTTTTCC 59.855 34.615 0.00 0.00 32.87 3.13
2307 2936 2.242572 CCGAGCACAGATGGCATCG 61.243 63.158 21.01 17.47 34.22 3.84
2319 2948 4.519274 GCATCGCATCGCACGCAA 62.519 61.111 0.00 0.00 0.00 4.85
2346 2975 1.342275 TGCAAGCCTGGGCAGATATTT 60.342 47.619 14.39 0.00 44.88 1.40
2365 2994 8.730680 AGATATTTTGTCACAAGTCCACATTAC 58.269 33.333 0.00 0.00 0.00 1.89
2366 2995 6.707440 ATTTTGTCACAAGTCCACATTACA 57.293 33.333 0.00 0.00 0.00 2.41
2367 2996 5.749596 TTTGTCACAAGTCCACATTACAG 57.250 39.130 0.00 0.00 0.00 2.74
2371 3053 0.447801 CAAGTCCACATTACAGCGGC 59.552 55.000 0.00 0.00 0.00 6.53
2377 3059 1.539388 CCACATTACAGCGGCAGAAAA 59.461 47.619 1.45 0.00 0.00 2.29
2424 3275 5.437060 TCCGAATATTTCTCCCTTTTCCAG 58.563 41.667 0.00 0.00 0.00 3.86
2428 3279 7.068716 CCGAATATTTCTCCCTTTTCCAGAAAT 59.931 37.037 10.20 10.20 44.99 2.17
2482 3333 6.259550 ACTCTGAACAATATTTGACAAGCC 57.740 37.500 0.00 0.00 0.00 4.35
2496 3347 0.243636 CAAGCCCGGACATGTTTTCC 59.756 55.000 0.73 0.00 0.00 3.13
2539 3396 9.651913 AGTACTGAACAAATTTGAAAAATGTGT 57.348 25.926 24.64 12.76 0.00 3.72
2554 3412 7.816995 TGAAAAATGTGTACATTCCTAATTGGC 59.183 33.333 10.38 0.23 45.06 4.52
2558 3416 5.004448 TGTGTACATTCCTAATTGGCGAAA 58.996 37.500 0.00 0.00 35.26 3.46
2559 3417 5.650266 TGTGTACATTCCTAATTGGCGAAAT 59.350 36.000 0.00 0.00 35.26 2.17
2560 3418 5.971202 GTGTACATTCCTAATTGGCGAAATG 59.029 40.000 0.00 7.68 35.26 2.32
2565 3423 4.712122 TCCTAATTGGCGAAATGGTTTC 57.288 40.909 0.00 0.00 35.26 2.78
2568 3426 3.760580 AATTGGCGAAATGGTTTCCAA 57.239 38.095 0.00 0.00 36.95 3.53
2572 3430 3.462021 TGGCGAAATGGTTTCCAAAAAG 58.538 40.909 0.00 0.00 36.95 2.27
2576 3434 3.740832 CGAAATGGTTTCCAAAAAGAGGC 59.259 43.478 0.00 0.00 36.95 4.70
2577 3435 4.501400 CGAAATGGTTTCCAAAAAGAGGCT 60.501 41.667 0.00 0.00 36.95 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.647796 CCACTATTAATGTGAGTCCACCTATAA 58.352 37.037 15.37 0.00 42.53 0.98
1 2 7.787904 ACCACTATTAATGTGAGTCCACCTATA 59.212 37.037 15.37 0.00 42.53 1.31
2 3 6.615726 ACCACTATTAATGTGAGTCCACCTAT 59.384 38.462 15.37 0.00 42.53 2.57
3 4 5.962031 ACCACTATTAATGTGAGTCCACCTA 59.038 40.000 15.37 0.00 42.53 3.08
5 6 5.099042 ACCACTATTAATGTGAGTCCACC 57.901 43.478 15.37 0.00 42.53 4.61
6 7 4.804139 CGACCACTATTAATGTGAGTCCAC 59.196 45.833 15.37 0.00 43.46 4.02
7 8 4.679639 GCGACCACTATTAATGTGAGTCCA 60.680 45.833 15.37 0.00 37.60 4.02
9 10 4.430007 TGCGACCACTATTAATGTGAGTC 58.570 43.478 15.37 16.60 37.60 3.36
10 11 4.081642 ACTGCGACCACTATTAATGTGAGT 60.082 41.667 15.37 12.20 37.60 3.41
11 12 4.433615 ACTGCGACCACTATTAATGTGAG 58.566 43.478 15.37 9.28 37.60 3.51
12 13 4.159693 AGACTGCGACCACTATTAATGTGA 59.840 41.667 15.37 0.63 37.60 3.58
13 14 4.433615 AGACTGCGACCACTATTAATGTG 58.566 43.478 0.00 4.84 35.39 3.21
14 15 4.737855 AGACTGCGACCACTATTAATGT 57.262 40.909 0.00 0.00 0.00 2.71
15 16 4.681942 GCTAGACTGCGACCACTATTAATG 59.318 45.833 0.00 0.00 0.00 1.90
16 17 4.872664 GCTAGACTGCGACCACTATTAAT 58.127 43.478 0.00 0.00 0.00 1.40
17 18 4.303086 GCTAGACTGCGACCACTATTAA 57.697 45.455 0.00 0.00 0.00 1.40
18 19 3.984508 GCTAGACTGCGACCACTATTA 57.015 47.619 0.00 0.00 0.00 0.98
19 20 2.873133 GCTAGACTGCGACCACTATT 57.127 50.000 0.00 0.00 0.00 1.73
29 30 1.373570 AATGAAAGGCGCTAGACTGC 58.626 50.000 7.64 0.00 34.63 4.40
30 31 6.844696 TTATTAATGAAAGGCGCTAGACTG 57.155 37.500 7.64 0.00 34.63 3.51
31 32 6.651225 GGATTATTAATGAAAGGCGCTAGACT 59.349 38.462 7.64 0.00 37.28 3.24
32 33 6.401153 CGGATTATTAATGAAAGGCGCTAGAC 60.401 42.308 7.64 0.00 0.00 2.59
33 34 5.637810 CGGATTATTAATGAAAGGCGCTAGA 59.362 40.000 7.64 0.00 0.00 2.43
34 35 5.637810 TCGGATTATTAATGAAAGGCGCTAG 59.362 40.000 7.64 0.00 0.00 3.42
35 36 5.543714 TCGGATTATTAATGAAAGGCGCTA 58.456 37.500 7.64 0.00 0.00 4.26
36 37 4.385825 TCGGATTATTAATGAAAGGCGCT 58.614 39.130 7.64 0.00 0.00 5.92
37 38 4.742438 TCGGATTATTAATGAAAGGCGC 57.258 40.909 0.00 0.00 0.00 6.53
38 39 9.840427 AATTTATCGGATTATTAATGAAAGGCG 57.160 29.630 0.00 0.00 0.00 5.52
47 48 9.787435 ACCACTGCTAATTTATCGGATTATTAA 57.213 29.630 0.00 0.00 0.00 1.40
48 49 9.214957 CACCACTGCTAATTTATCGGATTATTA 57.785 33.333 0.00 1.12 0.00 0.98
49 50 7.174946 CCACCACTGCTAATTTATCGGATTATT 59.825 37.037 0.00 0.00 0.00 1.40
50 51 6.655003 CCACCACTGCTAATTTATCGGATTAT 59.345 38.462 0.00 0.00 0.00 1.28
51 52 5.995282 CCACCACTGCTAATTTATCGGATTA 59.005 40.000 0.00 0.00 0.00 1.75
52 53 4.821805 CCACCACTGCTAATTTATCGGATT 59.178 41.667 0.00 0.00 0.00 3.01
53 54 4.102524 TCCACCACTGCTAATTTATCGGAT 59.897 41.667 0.00 0.00 0.00 4.18
54 55 3.452990 TCCACCACTGCTAATTTATCGGA 59.547 43.478 0.00 0.00 0.00 4.55
55 56 3.804036 TCCACCACTGCTAATTTATCGG 58.196 45.455 0.00 0.00 0.00 4.18
56 57 4.319766 GCATCCACCACTGCTAATTTATCG 60.320 45.833 0.00 0.00 35.49 2.92
57 58 4.580167 TGCATCCACCACTGCTAATTTATC 59.420 41.667 0.00 0.00 39.16 1.75
58 59 4.535781 TGCATCCACCACTGCTAATTTAT 58.464 39.130 0.00 0.00 39.16 1.40
59 60 3.961849 TGCATCCACCACTGCTAATTTA 58.038 40.909 0.00 0.00 39.16 1.40
60 61 2.806434 TGCATCCACCACTGCTAATTT 58.194 42.857 0.00 0.00 39.16 1.82
61 62 2.512692 TGCATCCACCACTGCTAATT 57.487 45.000 0.00 0.00 39.16 1.40
62 63 2.493278 GTTTGCATCCACCACTGCTAAT 59.507 45.455 0.00 0.00 39.16 1.73
63 64 1.885887 GTTTGCATCCACCACTGCTAA 59.114 47.619 0.00 0.00 39.16 3.09
64 65 1.533625 GTTTGCATCCACCACTGCTA 58.466 50.000 0.00 0.00 39.16 3.49
65 66 1.181098 GGTTTGCATCCACCACTGCT 61.181 55.000 5.55 0.00 39.16 4.24
66 67 1.290009 GGTTTGCATCCACCACTGC 59.710 57.895 5.55 0.00 38.87 4.40
67 68 0.540365 AGGGTTTGCATCCACCACTG 60.540 55.000 11.30 0.00 34.36 3.66
68 69 0.251341 GAGGGTTTGCATCCACCACT 60.251 55.000 11.30 6.71 34.36 4.00
69 70 0.539438 TGAGGGTTTGCATCCACCAC 60.539 55.000 11.30 6.27 34.36 4.16
70 71 0.409092 ATGAGGGTTTGCATCCACCA 59.591 50.000 11.30 7.99 34.36 4.17
71 72 1.106285 GATGAGGGTTTGCATCCACC 58.894 55.000 10.02 6.29 35.91 4.61
75 76 1.728490 GCCGGATGAGGGTTTGCATC 61.728 60.000 5.05 0.00 40.05 3.91
76 77 1.754234 GCCGGATGAGGGTTTGCAT 60.754 57.895 5.05 0.00 0.00 3.96
77 78 2.361104 GCCGGATGAGGGTTTGCA 60.361 61.111 5.05 0.00 0.00 4.08
78 79 2.361104 TGCCGGATGAGGGTTTGC 60.361 61.111 5.05 0.00 0.00 3.68
79 80 1.002134 AGTGCCGGATGAGGGTTTG 60.002 57.895 5.05 0.00 0.00 2.93
80 81 1.002134 CAGTGCCGGATGAGGGTTT 60.002 57.895 5.05 0.00 0.00 3.27
81 82 2.671070 CAGTGCCGGATGAGGGTT 59.329 61.111 5.05 0.00 0.00 4.11
82 83 4.101448 GCAGTGCCGGATGAGGGT 62.101 66.667 5.05 0.00 0.00 4.34
83 84 1.762522 ATAGCAGTGCCGGATGAGGG 61.763 60.000 12.58 0.00 0.00 4.30
84 85 0.107456 AATAGCAGTGCCGGATGAGG 59.893 55.000 12.58 0.00 0.00 3.86
85 86 1.224075 CAATAGCAGTGCCGGATGAG 58.776 55.000 12.58 0.00 0.00 2.90
86 87 0.541392 ACAATAGCAGTGCCGGATGA 59.459 50.000 12.58 0.00 0.00 2.92
87 88 0.940126 GACAATAGCAGTGCCGGATG 59.060 55.000 12.58 8.78 0.00 3.51
88 89 0.833287 AGACAATAGCAGTGCCGGAT 59.167 50.000 12.58 0.00 0.00 4.18
89 90 0.613260 AAGACAATAGCAGTGCCGGA 59.387 50.000 12.58 0.00 0.00 5.14
90 91 1.933853 GTAAGACAATAGCAGTGCCGG 59.066 52.381 12.58 0.00 0.00 6.13
91 92 1.933853 GGTAAGACAATAGCAGTGCCG 59.066 52.381 12.58 0.30 0.00 5.69
92 93 2.985896 TGGTAAGACAATAGCAGTGCC 58.014 47.619 12.58 0.00 0.00 5.01
93 94 4.635765 TCATTGGTAAGACAATAGCAGTGC 59.364 41.667 7.13 7.13 39.45 4.40
94 95 5.220472 CGTCATTGGTAAGACAATAGCAGTG 60.220 44.000 3.54 3.54 38.94 3.66
95 96 4.870426 CGTCATTGGTAAGACAATAGCAGT 59.130 41.667 0.00 0.00 38.94 4.40
96 97 4.271049 CCGTCATTGGTAAGACAATAGCAG 59.729 45.833 0.00 0.00 38.94 4.24
97 98 4.081365 TCCGTCATTGGTAAGACAATAGCA 60.081 41.667 0.00 0.00 38.94 3.49
98 99 4.270325 GTCCGTCATTGGTAAGACAATAGC 59.730 45.833 0.00 0.00 38.94 2.97
99 100 5.291128 GTGTCCGTCATTGGTAAGACAATAG 59.709 44.000 0.00 0.00 38.94 1.73
100 101 5.172934 GTGTCCGTCATTGGTAAGACAATA 58.827 41.667 0.00 0.00 38.94 1.90
101 102 4.000988 GTGTCCGTCATTGGTAAGACAAT 58.999 43.478 0.00 0.00 41.51 2.71
102 103 3.395639 GTGTCCGTCATTGGTAAGACAA 58.604 45.455 0.00 0.00 36.13 3.18
103 104 2.289195 GGTGTCCGTCATTGGTAAGACA 60.289 50.000 0.00 0.00 34.48 3.41
104 105 2.289195 TGGTGTCCGTCATTGGTAAGAC 60.289 50.000 0.00 0.00 0.00 3.01
105 106 1.972075 TGGTGTCCGTCATTGGTAAGA 59.028 47.619 0.00 0.00 0.00 2.10
106 107 2.289444 ACTGGTGTCCGTCATTGGTAAG 60.289 50.000 0.00 0.00 0.00 2.34
107 108 1.695242 ACTGGTGTCCGTCATTGGTAA 59.305 47.619 0.00 0.00 0.00 2.85
108 109 1.344065 ACTGGTGTCCGTCATTGGTA 58.656 50.000 0.00 0.00 0.00 3.25
109 110 0.472471 AACTGGTGTCCGTCATTGGT 59.528 50.000 0.00 0.00 0.00 3.67
110 111 1.266718 CAAACTGGTGTCCGTCATTGG 59.733 52.381 0.00 0.00 0.00 3.16
111 112 1.946768 ACAAACTGGTGTCCGTCATTG 59.053 47.619 0.00 0.00 0.00 2.82
112 113 1.946768 CACAAACTGGTGTCCGTCATT 59.053 47.619 0.00 0.00 34.09 2.57
113 114 1.593196 CACAAACTGGTGTCCGTCAT 58.407 50.000 0.00 0.00 34.09 3.06
114 115 3.073086 CACAAACTGGTGTCCGTCA 57.927 52.632 0.00 0.00 34.09 4.35
121 122 2.792500 TGGCAGACACAAACTGGTG 58.208 52.632 0.00 0.00 44.35 4.17
131 132 1.977854 AGGTGTTATCAGTGGCAGACA 59.022 47.619 0.00 0.00 0.00 3.41
132 133 2.289694 ACAGGTGTTATCAGTGGCAGAC 60.290 50.000 0.00 0.00 0.00 3.51
133 134 1.977854 ACAGGTGTTATCAGTGGCAGA 59.022 47.619 0.00 0.00 0.00 4.26
134 135 2.350522 GACAGGTGTTATCAGTGGCAG 58.649 52.381 0.00 0.00 0.00 4.85
135 136 1.003118 GGACAGGTGTTATCAGTGGCA 59.997 52.381 0.00 0.00 0.00 4.92
136 137 1.003118 TGGACAGGTGTTATCAGTGGC 59.997 52.381 0.00 0.00 0.00 5.01
137 138 3.417069 TTGGACAGGTGTTATCAGTGG 57.583 47.619 0.00 0.00 0.00 4.00
138 139 5.964958 AATTTGGACAGGTGTTATCAGTG 57.035 39.130 0.00 0.00 0.00 3.66
139 140 8.109634 AGATAAATTTGGACAGGTGTTATCAGT 58.890 33.333 0.00 0.00 31.76 3.41
140 141 8.511604 AGATAAATTTGGACAGGTGTTATCAG 57.488 34.615 0.00 0.00 31.76 2.90
141 142 8.877864 AAGATAAATTTGGACAGGTGTTATCA 57.122 30.769 0.00 0.00 31.76 2.15
143 144 9.408648 CCTAAGATAAATTTGGACAGGTGTTAT 57.591 33.333 0.00 0.00 0.00 1.89
144 145 8.607713 TCCTAAGATAAATTTGGACAGGTGTTA 58.392 33.333 0.00 0.00 30.53 2.41
145 146 7.466804 TCCTAAGATAAATTTGGACAGGTGTT 58.533 34.615 0.00 0.00 30.53 3.32
146 147 7.027874 TCCTAAGATAAATTTGGACAGGTGT 57.972 36.000 0.00 0.00 30.53 4.16
153 154 8.934023 AACAGTTGTCCTAAGATAAATTTGGA 57.066 30.769 0.00 0.00 32.65 3.53
156 157 9.802039 TGGTAACAGTTGTCCTAAGATAAATTT 57.198 29.630 0.00 0.00 46.17 1.82
176 177 1.139095 CTCGAGCCGTCCTGGTAAC 59.861 63.158 0.00 0.00 41.21 2.50
177 178 2.707849 GCTCGAGCCGTCCTGGTAA 61.708 63.158 27.22 0.00 41.21 2.85
178 179 3.138798 GCTCGAGCCGTCCTGGTA 61.139 66.667 27.22 0.00 41.21 3.25
181 182 4.116328 TTCGCTCGAGCCGTCCTG 62.116 66.667 30.66 16.02 37.91 3.86
182 183 4.117661 GTTCGCTCGAGCCGTCCT 62.118 66.667 30.66 0.00 37.91 3.85
187 188 4.821589 CTGGGGTTCGCTCGAGCC 62.822 72.222 30.66 17.11 43.53 4.70
189 190 4.821589 GGCTGGGGTTCGCTCGAG 62.822 72.222 8.45 8.45 0.00 4.04
208 209 4.410400 GAGGAGGGTTGTGGGCGG 62.410 72.222 0.00 0.00 0.00 6.13
209 210 4.410400 GGAGGAGGGTTGTGGGCG 62.410 72.222 0.00 0.00 0.00 6.13
210 211 4.048470 GGGAGGAGGGTTGTGGGC 62.048 72.222 0.00 0.00 0.00 5.36
211 212 2.204151 AGGGAGGAGGGTTGTGGG 60.204 66.667 0.00 0.00 0.00 4.61
212 213 3.404773 GAGGGAGGAGGGTTGTGG 58.595 66.667 0.00 0.00 0.00 4.17
609 610 1.076705 GGAATCTCCTGCAACCCCC 60.077 63.158 0.00 0.00 32.53 5.40
610 611 1.452108 CGGAATCTCCTGCAACCCC 60.452 63.158 0.00 0.00 33.30 4.95
611 612 0.744771 GTCGGAATCTCCTGCAACCC 60.745 60.000 0.00 0.00 33.30 4.11
612 613 1.084370 CGTCGGAATCTCCTGCAACC 61.084 60.000 0.00 0.00 33.30 3.77
613 614 1.084370 CCGTCGGAATCTCCTGCAAC 61.084 60.000 4.91 0.00 33.30 4.17
614 615 1.218047 CCGTCGGAATCTCCTGCAA 59.782 57.895 4.91 0.00 33.30 4.08
615 616 1.667154 CTCCGTCGGAATCTCCTGCA 61.667 60.000 16.23 0.00 33.30 4.41
616 617 1.066587 CTCCGTCGGAATCTCCTGC 59.933 63.158 16.23 0.00 33.30 4.85
621 622 1.682684 ACAGCCTCCGTCGGAATCT 60.683 57.895 16.23 11.88 0.00 2.40
632 633 2.267324 GGACTCCTGCACAGCCTC 59.733 66.667 0.00 0.00 0.00 4.70
644 645 2.884639 GAGAGCTACTGGATCTGGACTC 59.115 54.545 0.00 0.00 41.17 3.36
658 659 2.233676 TCAAATCGCAGTTGGAGAGCTA 59.766 45.455 0.00 0.00 0.00 3.32
661 662 4.691860 AAATCAAATCGCAGTTGGAGAG 57.308 40.909 0.00 0.00 0.00 3.20
666 667 6.554419 TGGATCTTAAATCAAATCGCAGTTG 58.446 36.000 0.00 0.00 0.00 3.16
674 675 7.362920 CCTGAACCGTTGGATCTTAAATCAAAT 60.363 37.037 0.00 0.00 0.00 2.32
705 706 2.285602 GCTTATGTGTTACCGTGATGCG 60.286 50.000 0.00 0.00 40.95 4.73
706 707 2.285602 CGCTTATGTGTTACCGTGATGC 60.286 50.000 0.00 0.00 0.00 3.91
717 719 2.100631 GCTCCACGCGCTTATGTGT 61.101 57.895 5.73 0.00 34.28 3.72
736 738 3.001736 GCGTCATCAAGAAAGTATCAGCC 59.998 47.826 0.00 0.00 0.00 4.85
744 746 6.416455 GTGATAGTAGAGCGTCATCAAGAAAG 59.584 42.308 0.00 0.00 0.00 2.62
875 894 2.737180 CAGTGGAGGAGCACGTGT 59.263 61.111 18.38 3.69 0.00 4.49
984 1027 1.081041 CATGTCGTCGGTTCGGTGA 60.081 57.895 0.00 0.00 0.00 4.02
1071 1120 3.993535 CCTTTCTCCACAGGCAGC 58.006 61.111 0.00 0.00 0.00 5.25
1079 1128 3.621805 TCGTGCCGCCTTTCTCCA 61.622 61.111 0.00 0.00 0.00 3.86
1082 1131 1.895020 TATGGTCGTGCCGCCTTTCT 61.895 55.000 0.00 0.00 41.21 2.52
1252 1301 1.456287 GGCTGTTGAACCCAGGAGT 59.544 57.895 0.00 0.00 0.00 3.85
1253 1302 1.672356 CGGCTGTTGAACCCAGGAG 60.672 63.158 0.00 0.00 0.00 3.69
1254 1303 2.429930 CGGCTGTTGAACCCAGGA 59.570 61.111 0.00 0.00 0.00 3.86
1257 1306 3.884774 AGCCGGCTGTTGAACCCA 61.885 61.111 32.33 0.00 0.00 4.51
1665 1756 2.440980 GGACCCAGAATGCCCAGC 60.441 66.667 0.00 0.00 31.97 4.85
1691 1782 9.974980 GGGAGTCATTACAAATTTACAAGAAAA 57.025 29.630 0.00 0.00 0.00 2.29
1695 1786 6.150474 ACCGGGAGTCATTACAAATTTACAAG 59.850 38.462 6.32 0.00 0.00 3.16
1702 1793 2.365582 GCACCGGGAGTCATTACAAAT 58.634 47.619 6.32 0.00 0.00 2.32
1706 1798 0.462047 CAGGCACCGGGAGTCATTAC 60.462 60.000 6.32 0.00 0.00 1.89
1728 1820 2.859273 GATGAGTGGAGTGCGGGGTG 62.859 65.000 0.00 0.00 0.00 4.61
1729 1821 2.607750 ATGAGTGGAGTGCGGGGT 60.608 61.111 0.00 0.00 0.00 4.95
1730 1822 2.187946 GATGAGTGGAGTGCGGGG 59.812 66.667 0.00 0.00 0.00 5.73
1731 1823 1.448540 GTGATGAGTGGAGTGCGGG 60.449 63.158 0.00 0.00 0.00 6.13
1732 1824 1.448540 GGTGATGAGTGGAGTGCGG 60.449 63.158 0.00 0.00 0.00 5.69
1733 1825 1.448540 GGGTGATGAGTGGAGTGCG 60.449 63.158 0.00 0.00 0.00 5.34
1767 1872 8.456904 TTCACTTTCTGTCGTACAATATACAC 57.543 34.615 0.00 0.00 0.00 2.90
1793 2315 2.677836 TGCCGCATAACACATTTCTCTC 59.322 45.455 0.00 0.00 0.00 3.20
1799 2321 4.337836 TGTGATTATGCCGCATAACACATT 59.662 37.500 31.43 19.17 39.80 2.71
1847 2369 8.996651 TCTTATATTGTGAGACAGATGGAGTA 57.003 34.615 0.00 0.00 0.00 2.59
1848 2370 7.904558 TCTTATATTGTGAGACAGATGGAGT 57.095 36.000 0.00 0.00 0.00 3.85
1849 2371 8.583296 TGATCTTATATTGTGAGACAGATGGAG 58.417 37.037 0.00 0.00 0.00 3.86
1850 2372 8.482852 TGATCTTATATTGTGAGACAGATGGA 57.517 34.615 0.00 0.00 0.00 3.41
1851 2373 9.722184 AATGATCTTATATTGTGAGACAGATGG 57.278 33.333 0.00 0.00 0.00 3.51
1869 2391 9.003658 AGATCGTACAACTTGAAAAATGATCTT 57.996 29.630 0.00 0.00 36.39 2.40
1870 2392 8.553459 AGATCGTACAACTTGAAAAATGATCT 57.447 30.769 0.00 6.47 35.33 2.75
1877 2399 9.982291 GCAATATAAGATCGTACAACTTGAAAA 57.018 29.630 0.00 0.00 0.00 2.29
1878 2400 8.325282 CGCAATATAAGATCGTACAACTTGAAA 58.675 33.333 0.00 0.00 0.00 2.69
1879 2401 7.042992 CCGCAATATAAGATCGTACAACTTGAA 60.043 37.037 0.00 0.00 0.00 2.69
1880 2402 6.419710 CCGCAATATAAGATCGTACAACTTGA 59.580 38.462 0.00 0.00 0.00 3.02
1881 2403 6.346598 CCCGCAATATAAGATCGTACAACTTG 60.347 42.308 0.00 0.00 0.00 3.16
1882 2404 5.694910 CCCGCAATATAAGATCGTACAACTT 59.305 40.000 0.00 0.00 0.00 2.66
1883 2405 5.010314 TCCCGCAATATAAGATCGTACAACT 59.990 40.000 0.00 0.00 0.00 3.16
1884 2406 5.118203 GTCCCGCAATATAAGATCGTACAAC 59.882 44.000 0.00 0.00 0.00 3.32
1885 2407 5.224888 GTCCCGCAATATAAGATCGTACAA 58.775 41.667 0.00 0.00 0.00 2.41
1886 2408 4.614306 CGTCCCGCAATATAAGATCGTACA 60.614 45.833 0.00 0.00 0.00 2.90
1887 2409 3.850273 CGTCCCGCAATATAAGATCGTAC 59.150 47.826 0.00 0.00 0.00 3.67
1888 2410 3.119743 CCGTCCCGCAATATAAGATCGTA 60.120 47.826 0.00 0.00 0.00 3.43
1889 2411 2.352421 CCGTCCCGCAATATAAGATCGT 60.352 50.000 0.00 0.00 0.00 3.73
1890 2412 2.094906 TCCGTCCCGCAATATAAGATCG 60.095 50.000 0.00 0.00 0.00 3.69
1903 2425 1.696063 TTATTACTCCCTCCGTCCCG 58.304 55.000 0.00 0.00 0.00 5.14
1904 2426 5.338137 CCATATTTATTACTCCCTCCGTCCC 60.338 48.000 0.00 0.00 0.00 4.46
1961 2513 4.154556 GGTTTGTCGGATGTTATTTCGGAA 59.845 41.667 0.00 0.00 0.00 4.30
2057 2650 3.686726 CAGACCTGAAGAATACAGCCAAC 59.313 47.826 0.00 0.00 34.47 3.77
2154 2747 3.245371 TGGAAAGAAGGATGGCAATGACT 60.245 43.478 0.00 0.00 0.00 3.41
2164 2757 7.718753 GTCATCATACAGATTGGAAAGAAGGAT 59.281 37.037 0.00 0.00 33.72 3.24
2165 2758 7.050377 GTCATCATACAGATTGGAAAGAAGGA 58.950 38.462 0.00 0.00 33.72 3.36
2166 2759 6.825213 TGTCATCATACAGATTGGAAAGAAGG 59.175 38.462 0.00 0.00 33.72 3.46
2183 2780 9.102757 GATACAAACTGAATGTACTGTCATCAT 57.897 33.333 0.00 0.00 36.19 2.45
2184 2781 8.093927 TGATACAAACTGAATGTACTGTCATCA 58.906 33.333 0.00 0.00 36.19 3.07
2185 2782 8.383619 GTGATACAAACTGAATGTACTGTCATC 58.616 37.037 0.00 0.00 36.19 2.92
2186 2783 7.877612 TGTGATACAAACTGAATGTACTGTCAT 59.122 33.333 0.00 0.00 36.19 3.06
2249 2849 7.873739 AGGAAAAATTAAAGAATTGTGCTCG 57.126 32.000 0.00 0.00 35.38 5.03
2264 2864 9.679661 GGAAGATTCTCTCTCTAAGGAAAAATT 57.320 33.333 0.00 0.00 31.03 1.82
2265 2865 7.984617 CGGAAGATTCTCTCTCTAAGGAAAAAT 59.015 37.037 0.00 0.00 31.03 1.82
2272 2901 4.578516 TGCTCGGAAGATTCTCTCTCTAAG 59.421 45.833 0.00 0.00 40.84 2.18
2278 2907 2.425312 TCTGTGCTCGGAAGATTCTCTC 59.575 50.000 0.00 0.00 40.84 3.20
2280 2909 2.949451 TCTGTGCTCGGAAGATTCTC 57.051 50.000 0.00 0.00 40.84 2.87
2281 2910 2.158986 CCATCTGTGCTCGGAAGATTCT 60.159 50.000 0.65 0.00 40.84 2.40
2282 2911 2.208431 CCATCTGTGCTCGGAAGATTC 58.792 52.381 0.65 0.00 40.84 2.52
2283 2912 1.745141 GCCATCTGTGCTCGGAAGATT 60.745 52.381 0.65 0.00 40.84 2.40
2284 2913 0.179062 GCCATCTGTGCTCGGAAGAT 60.179 55.000 0.65 0.00 40.84 2.40
2285 2914 1.219124 GCCATCTGTGCTCGGAAGA 59.781 57.895 0.65 0.00 39.12 2.87
2335 2964 4.142381 GGACTTGTGACAAAATATCTGCCC 60.142 45.833 0.00 0.00 0.00 5.36
2337 2966 5.048782 TGTGGACTTGTGACAAAATATCTGC 60.049 40.000 0.00 0.00 0.00 4.26
2346 2975 3.563808 GCTGTAATGTGGACTTGTGACAA 59.436 43.478 0.00 0.00 0.00 3.18
2365 2994 4.107051 CCCGCTTTTCTGCCGCTG 62.107 66.667 0.00 0.00 0.00 5.18
2412 3263 9.948964 ATTTGAATAAATTTCTGGAAAAGGGAG 57.051 29.630 0.00 0.00 32.70 4.30
2480 3331 0.676736 TTTGGAAAACATGTCCGGGC 59.323 50.000 0.00 0.00 38.06 6.13
2529 3386 7.009174 CGCCAATTAGGAATGTACACATTTTTC 59.991 37.037 8.88 0.00 45.72 2.29
2535 3392 4.209307 TCGCCAATTAGGAATGTACACA 57.791 40.909 0.00 0.00 41.22 3.72
2536 3393 5.554822 TTTCGCCAATTAGGAATGTACAC 57.445 39.130 0.00 0.00 41.22 2.90
2539 3396 5.197451 ACCATTTCGCCAATTAGGAATGTA 58.803 37.500 7.53 0.00 41.22 2.29
2540 3397 4.023291 ACCATTTCGCCAATTAGGAATGT 58.977 39.130 7.53 0.00 41.22 2.71
2541 3398 4.654091 ACCATTTCGCCAATTAGGAATG 57.346 40.909 0.00 1.27 41.22 2.67
2543 3400 4.081917 GGAAACCATTTCGCCAATTAGGAA 60.082 41.667 0.00 0.00 40.57 3.36
2546 3404 4.448537 TGGAAACCATTTCGCCAATTAG 57.551 40.909 0.00 0.00 40.57 1.73
2554 3412 3.740832 GCCTCTTTTTGGAAACCATTTCG 59.259 43.478 0.00 0.00 40.57 3.46
2558 3416 5.372343 AAAAGCCTCTTTTTGGAAACCAT 57.628 34.783 0.00 0.00 31.53 3.55
2559 3417 4.835284 AAAAGCCTCTTTTTGGAAACCA 57.165 36.364 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.