Multiple sequence alignment - TraesCS5A01G458000

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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 TraesCS5A01G458000 chr5A 100.000 2735 0 0 1 2735 638077381 638080115 0.000000e+00 5051.0
1 TraesCS5A01G458000 chr5A 98.092 262 5 0 1 262 568896941 568897202 8.930000e-125 457.0
2 TraesCS5A01G458000 chr3A 97.019 2415 62 2 331 2735 716982430 716984844 0.000000e+00 4052.0
3 TraesCS5A01G458000 chr3A 97.328 262 7 0 1 262 549331126 549330865 1.930000e-121 446.0
4 TraesCS5A01G458000 chr5B 92.261 1641 123 4 1097 2735 562284859 562283221 0.000000e+00 2324.0
5 TraesCS5A01G458000 chr5B 94.553 257 14 0 1 257 339092550 339092806 5.490000e-107 398.0
6 TraesCS5A01G458000 chr5B 96.491 57 2 0 793 849 562284956 562284900 8.060000e-16 95.3
7 TraesCS5A01G458000 chr7D 88.404 1742 194 7 999 2735 370972529 370970791 0.000000e+00 2091.0
8 TraesCS5A01G458000 chr7D 87.199 1578 197 5 999 2573 71619229 71617654 0.000000e+00 1790.0
9 TraesCS5A01G458000 chr7D 82.103 447 75 5 333 777 209094827 209094384 7.150000e-101 377.0
10 TraesCS5A01G458000 chr7D 81.879 447 76 5 333 777 370973276 370972833 3.330000e-99 372.0
11 TraesCS5A01G458000 chr7D 81.498 454 66 10 331 770 71619919 71619470 9.310000e-95 357.0
12 TraesCS5A01G458000 chr6D 88.087 1746 196 9 999 2735 433585824 433587566 0.000000e+00 2061.0
13 TraesCS5A01G458000 chr6D 92.776 263 18 1 1 262 5674579 5674841 1.990000e-101 379.0
14 TraesCS5A01G458000 chr5D 88.097 1739 203 4 999 2735 306248850 306247114 0.000000e+00 2061.0
15 TraesCS5A01G458000 chr5D 91.985 262 20 1 1 262 493682751 493683011 1.550000e-97 366.0
16 TraesCS5A01G458000 chr7A 86.736 1734 226 4 999 2730 80557834 80559565 0.000000e+00 1925.0
17 TraesCS5A01G458000 chr7A 92.776 263 15 2 1 262 452753114 452752855 7.150000e-101 377.0
18 TraesCS5A01G458000 chr7A 80.088 457 67 13 333 781 538244168 538243728 4.390000e-83 318.0
19 TraesCS5A01G458000 chr3D 85.375 1771 237 16 975 2735 16636245 16638003 0.000000e+00 1816.0
20 TraesCS5A01G458000 chr3D 79.701 468 72 20 336 789 583022143 583021685 1.580000e-82 316.0
21 TraesCS5A01G458000 chr4A 85.049 1739 250 6 997 2735 335736996 335735268 0.000000e+00 1762.0
22 TraesCS5A01G458000 chr4A 78.788 462 71 15 330 781 43355152 43355596 4.460000e-73 285.0
23 TraesCS5A01G458000 chr1D 81.737 1796 274 41 331 2099 267989790 267991558 0.000000e+00 1450.0
24 TraesCS5A01G458000 chr1D 89.122 763 48 17 328 1081 18166550 18167286 0.000000e+00 917.0
25 TraesCS5A01G458000 chr1D 95.420 262 12 0 1 262 433412060 433412321 4.210000e-113 418.0
26 TraesCS5A01G458000 chr2B 93.385 257 17 0 6 262 11332230 11331974 5.530000e-102 381.0
27 TraesCS5A01G458000 chr3B 88.498 313 35 1 2423 2735 672262149 672262460 7.150000e-101 377.0
28 TraesCS5A01G458000 chr3B 92.395 263 19 1 1 262 737558709 737558971 9.250000e-100 374.0
29 TraesCS5A01G458000 chr6A 80.778 463 69 13 331 777 535298194 535297736 7.250000e-91 344.0
30 TraesCS5A01G458000 chr7B 77.405 447 87 12 333 772 407496786 407496347 1.260000e-63 254.0


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 TraesCS5A01G458000 chr5A 638077381 638080115 2734 False 5051.00 5051 100.0000 1 2735 1 chr5A.!!$F2 2734
1 TraesCS5A01G458000 chr3A 716982430 716984844 2414 False 4052.00 4052 97.0190 331 2735 1 chr3A.!!$F1 2404
2 TraesCS5A01G458000 chr5B 562283221 562284956 1735 True 1209.65 2324 94.3760 793 2735 2 chr5B.!!$R1 1942
3 TraesCS5A01G458000 chr7D 370970791 370973276 2485 True 1231.50 2091 85.1415 333 2735 2 chr7D.!!$R3 2402
4 TraesCS5A01G458000 chr7D 71617654 71619919 2265 True 1073.50 1790 84.3485 331 2573 2 chr7D.!!$R2 2242
5 TraesCS5A01G458000 chr6D 433585824 433587566 1742 False 2061.00 2061 88.0870 999 2735 1 chr6D.!!$F2 1736
6 TraesCS5A01G458000 chr5D 306247114 306248850 1736 True 2061.00 2061 88.0970 999 2735 1 chr5D.!!$R1 1736
7 TraesCS5A01G458000 chr7A 80557834 80559565 1731 False 1925.00 1925 86.7360 999 2730 1 chr7A.!!$F1 1731
8 TraesCS5A01G458000 chr3D 16636245 16638003 1758 False 1816.00 1816 85.3750 975 2735 1 chr3D.!!$F1 1760
9 TraesCS5A01G458000 chr4A 335735268 335736996 1728 True 1762.00 1762 85.0490 997 2735 1 chr4A.!!$R1 1738
10 TraesCS5A01G458000 chr1D 267989790 267991558 1768 False 1450.00 1450 81.7370 331 2099 1 chr1D.!!$F2 1768
11 TraesCS5A01G458000 chr1D 18166550 18167286 736 False 917.00 917 89.1220 328 1081 1 chr1D.!!$F1 753

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
111 112 0.03213 ATAGCGGCGTTCGATGACAT 59.968 50.0 9.37 0.0 42.43 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2042 2231 1.202927 TGCTCCTTTTAGTGGCAAGCT 60.203 47.619 5.29 0.0 0.0 3.74 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.423231 GCCCCTGTTTTCCCTCTG 57.577 61.111 0.00 0.00 0.00 3.35
18 19 1.304464 GCCCCTGTTTTCCCTCTGG 60.304 63.158 0.00 0.00 0.00 3.86
19 20 2.081585 GCCCCTGTTTTCCCTCTGGT 62.082 60.000 0.00 0.00 0.00 4.00
20 21 0.251341 CCCCTGTTTTCCCTCTGGTG 60.251 60.000 0.00 0.00 0.00 4.17
21 22 0.771127 CCCTGTTTTCCCTCTGGTGA 59.229 55.000 0.00 0.00 0.00 4.02
22 23 1.545651 CCCTGTTTTCCCTCTGGTGAC 60.546 57.143 0.00 0.00 0.00 3.67
23 24 1.142870 CCTGTTTTCCCTCTGGTGACA 59.857 52.381 0.00 0.00 39.59 3.58
40 41 3.669536 TGACAGTCAGTGACACAAAACA 58.330 40.909 24.73 12.33 34.60 2.83
41 42 4.260985 TGACAGTCAGTGACACAAAACAT 58.739 39.130 24.73 0.00 34.60 2.71
42 43 4.094739 TGACAGTCAGTGACACAAAACATG 59.905 41.667 24.73 13.59 34.60 3.21
43 44 3.181497 ACAGTCAGTGACACAAAACATGC 60.181 43.478 24.73 0.00 34.60 4.06
44 45 3.016031 AGTCAGTGACACAAAACATGCA 58.984 40.909 24.73 0.00 34.60 3.96
45 46 3.108144 GTCAGTGACACAAAACATGCAC 58.892 45.455 18.54 0.00 32.09 4.57
46 47 2.110990 CAGTGACACAAAACATGCACG 58.889 47.619 8.59 0.00 32.70 5.34
47 48 2.013400 AGTGACACAAAACATGCACGA 58.987 42.857 8.59 0.00 32.70 4.35
48 49 2.618241 AGTGACACAAAACATGCACGAT 59.382 40.909 8.59 0.00 32.70 3.73
49 50 2.720578 GTGACACAAAACATGCACGATG 59.279 45.455 0.00 0.00 38.15 3.84
50 51 2.287487 TGACACAAAACATGCACGATGG 60.287 45.455 0.00 0.00 36.23 3.51
51 52 1.680735 ACACAAAACATGCACGATGGT 59.319 42.857 0.00 0.00 36.23 3.55
60 61 4.208632 CACGATGGTGCCTTCCTC 57.791 61.111 0.00 0.00 37.35 3.71
61 62 1.450312 CACGATGGTGCCTTCCTCC 60.450 63.158 0.00 0.00 37.35 4.30
62 63 2.190578 CGATGGTGCCTTCCTCCC 59.809 66.667 0.00 0.00 0.00 4.30
63 64 2.669133 CGATGGTGCCTTCCTCCCA 61.669 63.158 0.00 0.00 0.00 4.37
64 65 1.925888 GATGGTGCCTTCCTCCCAT 59.074 57.895 0.00 0.00 40.34 4.00
65 66 1.140312 GATGGTGCCTTCCTCCCATA 58.860 55.000 0.00 0.00 37.81 2.74
66 67 1.072965 GATGGTGCCTTCCTCCCATAG 59.927 57.143 0.00 0.00 37.81 2.23
67 68 1.149401 GGTGCCTTCCTCCCATAGC 59.851 63.158 0.00 0.00 0.00 2.97
68 69 1.149401 GTGCCTTCCTCCCATAGCC 59.851 63.158 0.00 0.00 0.00 3.93
69 70 1.004758 TGCCTTCCTCCCATAGCCT 59.995 57.895 0.00 0.00 0.00 4.58
70 71 0.624500 TGCCTTCCTCCCATAGCCTT 60.625 55.000 0.00 0.00 0.00 4.35
71 72 1.345009 TGCCTTCCTCCCATAGCCTTA 60.345 52.381 0.00 0.00 0.00 2.69
72 73 1.349357 GCCTTCCTCCCATAGCCTTAG 59.651 57.143 0.00 0.00 0.00 2.18
73 74 2.695585 CCTTCCTCCCATAGCCTTAGT 58.304 52.381 0.00 0.00 0.00 2.24
74 75 3.858135 CCTTCCTCCCATAGCCTTAGTA 58.142 50.000 0.00 0.00 0.00 1.82
75 76 3.835395 CCTTCCTCCCATAGCCTTAGTAG 59.165 52.174 0.00 0.00 0.00 2.57
76 77 3.544698 TCCTCCCATAGCCTTAGTAGG 57.455 52.381 0.00 0.00 45.02 3.18
77 78 2.795960 TCCTCCCATAGCCTTAGTAGGT 59.204 50.000 0.00 0.00 44.00 3.08
78 79 3.209152 TCCTCCCATAGCCTTAGTAGGTT 59.791 47.826 0.00 0.00 44.00 3.50
79 80 4.421231 TCCTCCCATAGCCTTAGTAGGTTA 59.579 45.833 0.00 0.00 44.00 2.85
80 81 4.773149 CCTCCCATAGCCTTAGTAGGTTAG 59.227 50.000 0.00 0.00 44.00 2.34
81 82 4.158015 TCCCATAGCCTTAGTAGGTTAGC 58.842 47.826 0.00 0.00 44.00 3.09
82 83 4.140758 TCCCATAGCCTTAGTAGGTTAGCT 60.141 45.833 0.00 0.00 44.00 3.32
83 84 4.021016 CCCATAGCCTTAGTAGGTTAGCTG 60.021 50.000 0.00 0.00 44.00 4.24
84 85 4.021016 CCATAGCCTTAGTAGGTTAGCTGG 60.021 50.000 0.00 0.00 44.00 4.85
85 86 3.117552 AGCCTTAGTAGGTTAGCTGGT 57.882 47.619 0.00 0.00 44.00 4.00
86 87 3.451890 AGCCTTAGTAGGTTAGCTGGTT 58.548 45.455 0.00 0.00 44.00 3.67
87 88 3.844804 AGCCTTAGTAGGTTAGCTGGTTT 59.155 43.478 0.00 0.00 44.00 3.27
88 89 4.081031 AGCCTTAGTAGGTTAGCTGGTTTC 60.081 45.833 0.00 0.00 44.00 2.78
89 90 4.430908 CCTTAGTAGGTTAGCTGGTTTCG 58.569 47.826 0.00 0.00 36.74 3.46
90 91 4.430908 CTTAGTAGGTTAGCTGGTTTCGG 58.569 47.826 0.00 0.00 0.00 4.30
91 92 1.066358 AGTAGGTTAGCTGGTTTCGGC 60.066 52.381 0.00 0.00 45.35 5.54
97 98 2.709475 GCTGGTTTCGGCATAGCG 59.291 61.111 0.00 0.00 44.43 4.26
98 99 2.823829 GCTGGTTTCGGCATAGCGG 61.824 63.158 0.00 0.00 44.43 5.52
99 100 2.822255 TGGTTTCGGCATAGCGGC 60.822 61.111 0.00 0.00 0.00 6.53
106 107 2.661866 GGCATAGCGGCGTTCGAT 60.662 61.111 9.37 0.70 42.43 3.59
107 108 2.546321 GCATAGCGGCGTTCGATG 59.454 61.111 9.37 5.38 42.43 3.84
108 109 1.949133 GCATAGCGGCGTTCGATGA 60.949 57.895 9.37 0.00 42.43 2.92
109 110 1.846648 CATAGCGGCGTTCGATGAC 59.153 57.895 9.37 0.00 42.43 3.06
110 111 0.869880 CATAGCGGCGTTCGATGACA 60.870 55.000 9.37 0.00 42.43 3.58
111 112 0.032130 ATAGCGGCGTTCGATGACAT 59.968 50.000 9.37 0.00 42.43 3.06
112 113 0.179121 TAGCGGCGTTCGATGACATT 60.179 50.000 9.37 0.00 42.43 2.71
113 114 1.296867 GCGGCGTTCGATGACATTG 60.297 57.895 9.37 0.00 42.43 2.82
114 115 1.966493 GCGGCGTTCGATGACATTGT 61.966 55.000 9.37 0.00 42.43 2.71
115 116 0.442310 CGGCGTTCGATGACATTGTT 59.558 50.000 0.00 0.00 42.43 2.83
116 117 1.526986 CGGCGTTCGATGACATTGTTC 60.527 52.381 0.00 0.00 42.43 3.18
117 118 1.732259 GGCGTTCGATGACATTGTTCT 59.268 47.619 2.54 0.00 0.00 3.01
118 119 2.927477 GGCGTTCGATGACATTGTTCTA 59.073 45.455 2.54 0.00 0.00 2.10
119 120 3.555956 GGCGTTCGATGACATTGTTCTAT 59.444 43.478 2.54 0.00 0.00 1.98
120 121 4.508971 GCGTTCGATGACATTGTTCTATG 58.491 43.478 2.54 0.00 0.00 2.23
121 122 4.508971 CGTTCGATGACATTGTTCTATGC 58.491 43.478 2.54 0.00 0.00 3.14
122 123 4.550831 CGTTCGATGACATTGTTCTATGCC 60.551 45.833 2.54 0.00 0.00 4.40
123 124 4.406648 TCGATGACATTGTTCTATGCCT 57.593 40.909 2.54 0.00 0.00 4.75
124 125 4.769688 TCGATGACATTGTTCTATGCCTT 58.230 39.130 2.54 0.00 0.00 4.35
125 126 4.811024 TCGATGACATTGTTCTATGCCTTC 59.189 41.667 2.54 0.00 0.00 3.46
126 127 4.318333 CGATGACATTGTTCTATGCCTTCG 60.318 45.833 0.00 0.00 32.49 3.79
127 128 4.200838 TGACATTGTTCTATGCCTTCGA 57.799 40.909 0.00 0.00 0.00 3.71
128 129 4.183865 TGACATTGTTCTATGCCTTCGAG 58.816 43.478 0.00 0.00 0.00 4.04
129 130 4.184629 GACATTGTTCTATGCCTTCGAGT 58.815 43.478 0.00 0.00 0.00 4.18
130 131 4.579869 ACATTGTTCTATGCCTTCGAGTT 58.420 39.130 0.00 0.00 0.00 3.01
131 132 4.393062 ACATTGTTCTATGCCTTCGAGTTG 59.607 41.667 0.00 0.00 0.00 3.16
132 133 3.678056 TGTTCTATGCCTTCGAGTTGT 57.322 42.857 0.00 0.00 0.00 3.32
133 134 4.002906 TGTTCTATGCCTTCGAGTTGTT 57.997 40.909 0.00 0.00 0.00 2.83
134 135 3.994392 TGTTCTATGCCTTCGAGTTGTTC 59.006 43.478 0.00 0.00 0.00 3.18
135 136 4.246458 GTTCTATGCCTTCGAGTTGTTCT 58.754 43.478 0.00 0.00 0.00 3.01
136 137 5.047590 TGTTCTATGCCTTCGAGTTGTTCTA 60.048 40.000 0.00 0.00 0.00 2.10
137 138 4.995124 TCTATGCCTTCGAGTTGTTCTAC 58.005 43.478 0.00 0.00 0.00 2.59
138 139 2.450609 TGCCTTCGAGTTGTTCTACC 57.549 50.000 0.00 0.00 0.00 3.18
139 140 1.336517 TGCCTTCGAGTTGTTCTACCG 60.337 52.381 0.00 0.00 0.00 4.02
140 141 1.068055 GCCTTCGAGTTGTTCTACCGA 60.068 52.381 0.00 0.00 0.00 4.69
141 142 2.864968 CCTTCGAGTTGTTCTACCGAG 58.135 52.381 0.00 0.00 0.00 4.63
142 143 2.251893 CTTCGAGTTGTTCTACCGAGC 58.748 52.381 0.00 0.00 0.00 5.03
143 144 1.241165 TCGAGTTGTTCTACCGAGCA 58.759 50.000 0.00 0.00 0.00 4.26
144 145 1.068748 TCGAGTTGTTCTACCGAGCAC 60.069 52.381 0.00 0.00 29.61 4.40
145 146 1.335597 CGAGTTGTTCTACCGAGCACA 60.336 52.381 0.00 0.00 29.61 4.57
146 147 2.750948 GAGTTGTTCTACCGAGCACAA 58.249 47.619 0.00 0.00 36.61 3.33
147 148 3.326747 GAGTTGTTCTACCGAGCACAAT 58.673 45.455 0.00 0.00 40.29 2.71
148 149 3.067106 AGTTGTTCTACCGAGCACAATG 58.933 45.455 0.00 0.00 40.29 2.82
149 150 2.806244 GTTGTTCTACCGAGCACAATGT 59.194 45.455 0.00 0.00 40.29 2.71
150 151 3.945981 TGTTCTACCGAGCACAATGTA 57.054 42.857 0.00 0.00 0.00 2.29
151 152 4.465632 TGTTCTACCGAGCACAATGTAT 57.534 40.909 0.00 0.00 0.00 2.29
152 153 4.430007 TGTTCTACCGAGCACAATGTATC 58.570 43.478 0.00 0.00 0.00 2.24
153 154 4.159693 TGTTCTACCGAGCACAATGTATCT 59.840 41.667 0.00 0.00 0.00 1.98
154 155 5.109903 GTTCTACCGAGCACAATGTATCTT 58.890 41.667 0.00 0.00 0.00 2.40
155 156 4.933330 TCTACCGAGCACAATGTATCTTC 58.067 43.478 0.00 0.00 0.00 2.87
156 157 3.895232 ACCGAGCACAATGTATCTTCT 57.105 42.857 0.00 0.00 0.00 2.85
157 158 4.207891 ACCGAGCACAATGTATCTTCTT 57.792 40.909 0.00 0.00 0.00 2.52
158 159 4.579869 ACCGAGCACAATGTATCTTCTTT 58.420 39.130 0.00 0.00 0.00 2.52
159 160 5.003804 ACCGAGCACAATGTATCTTCTTTT 58.996 37.500 0.00 0.00 0.00 2.27
160 161 5.122396 ACCGAGCACAATGTATCTTCTTTTC 59.878 40.000 0.00 0.00 0.00 2.29
161 162 5.447818 CCGAGCACAATGTATCTTCTTTTCC 60.448 44.000 0.00 0.00 0.00 3.13
162 163 5.551760 AGCACAATGTATCTTCTTTTCCG 57.448 39.130 0.00 0.00 0.00 4.30
163 164 4.098416 GCACAATGTATCTTCTTTTCCGC 58.902 43.478 0.00 0.00 0.00 5.54
164 165 4.142600 GCACAATGTATCTTCTTTTCCGCT 60.143 41.667 0.00 0.00 0.00 5.52
165 166 5.563842 CACAATGTATCTTCTTTTCCGCTC 58.436 41.667 0.00 0.00 0.00 5.03
166 167 5.352569 CACAATGTATCTTCTTTTCCGCTCT 59.647 40.000 0.00 0.00 0.00 4.09
167 168 5.940470 ACAATGTATCTTCTTTTCCGCTCTT 59.060 36.000 0.00 0.00 0.00 2.85
168 169 6.431234 ACAATGTATCTTCTTTTCCGCTCTTT 59.569 34.615 0.00 0.00 0.00 2.52
169 170 5.862924 TGTATCTTCTTTTCCGCTCTTTG 57.137 39.130 0.00 0.00 0.00 2.77
170 171 5.305585 TGTATCTTCTTTTCCGCTCTTTGT 58.694 37.500 0.00 0.00 0.00 2.83
171 172 5.763204 TGTATCTTCTTTTCCGCTCTTTGTT 59.237 36.000 0.00 0.00 0.00 2.83
172 173 5.774498 ATCTTCTTTTCCGCTCTTTGTTT 57.226 34.783 0.00 0.00 0.00 2.83
173 174 5.576447 TCTTCTTTTCCGCTCTTTGTTTT 57.424 34.783 0.00 0.00 0.00 2.43
174 175 5.578776 TCTTCTTTTCCGCTCTTTGTTTTC 58.421 37.500 0.00 0.00 0.00 2.29
175 176 5.357032 TCTTCTTTTCCGCTCTTTGTTTTCT 59.643 36.000 0.00 0.00 0.00 2.52
176 177 5.576447 TCTTTTCCGCTCTTTGTTTTCTT 57.424 34.783 0.00 0.00 0.00 2.52
177 178 5.339990 TCTTTTCCGCTCTTTGTTTTCTTG 58.660 37.500 0.00 0.00 0.00 3.02
178 179 4.712122 TTTCCGCTCTTTGTTTTCTTGT 57.288 36.364 0.00 0.00 0.00 3.16
179 180 4.712122 TTCCGCTCTTTGTTTTCTTGTT 57.288 36.364 0.00 0.00 0.00 2.83
180 181 4.027572 TCCGCTCTTTGTTTTCTTGTTG 57.972 40.909 0.00 0.00 0.00 3.33
181 182 3.442273 TCCGCTCTTTGTTTTCTTGTTGT 59.558 39.130 0.00 0.00 0.00 3.32
182 183 4.082463 TCCGCTCTTTGTTTTCTTGTTGTT 60.082 37.500 0.00 0.00 0.00 2.83
183 184 5.124138 TCCGCTCTTTGTTTTCTTGTTGTTA 59.876 36.000 0.00 0.00 0.00 2.41
184 185 5.455525 CCGCTCTTTGTTTTCTTGTTGTTAG 59.544 40.000 0.00 0.00 0.00 2.34
185 186 6.027749 CGCTCTTTGTTTTCTTGTTGTTAGT 58.972 36.000 0.00 0.00 0.00 2.24
186 187 6.021468 CGCTCTTTGTTTTCTTGTTGTTAGTG 60.021 38.462 0.00 0.00 0.00 2.74
187 188 6.253512 GCTCTTTGTTTTCTTGTTGTTAGTGG 59.746 38.462 0.00 0.00 0.00 4.00
188 189 7.222000 TCTTTGTTTTCTTGTTGTTAGTGGT 57.778 32.000 0.00 0.00 0.00 4.16
189 190 8.338072 TCTTTGTTTTCTTGTTGTTAGTGGTA 57.662 30.769 0.00 0.00 0.00 3.25
190 191 8.455682 TCTTTGTTTTCTTGTTGTTAGTGGTAG 58.544 33.333 0.00 0.00 0.00 3.18
191 192 7.690952 TTGTTTTCTTGTTGTTAGTGGTAGT 57.309 32.000 0.00 0.00 0.00 2.73
192 193 7.311364 TGTTTTCTTGTTGTTAGTGGTAGTC 57.689 36.000 0.00 0.00 0.00 2.59
193 194 6.879993 TGTTTTCTTGTTGTTAGTGGTAGTCA 59.120 34.615 0.00 0.00 0.00 3.41
194 195 7.554835 TGTTTTCTTGTTGTTAGTGGTAGTCAT 59.445 33.333 0.00 0.00 0.00 3.06
195 196 7.490962 TTTCTTGTTGTTAGTGGTAGTCATG 57.509 36.000 0.00 0.00 0.00 3.07
196 197 6.169557 TCTTGTTGTTAGTGGTAGTCATGT 57.830 37.500 0.00 0.00 0.00 3.21
197 198 7.292713 TCTTGTTGTTAGTGGTAGTCATGTA 57.707 36.000 0.00 0.00 0.00 2.29
198 199 7.728148 TCTTGTTGTTAGTGGTAGTCATGTAA 58.272 34.615 0.00 0.00 0.00 2.41
199 200 8.372459 TCTTGTTGTTAGTGGTAGTCATGTAAT 58.628 33.333 0.00 0.00 0.00 1.89
200 201 8.542497 TTGTTGTTAGTGGTAGTCATGTAATC 57.458 34.615 0.00 0.00 0.00 1.75
201 202 7.101054 TGTTGTTAGTGGTAGTCATGTAATCC 58.899 38.462 0.00 0.00 0.00 3.01
202 203 7.038587 TGTTGTTAGTGGTAGTCATGTAATCCT 60.039 37.037 0.00 0.00 0.00 3.24
203 204 6.873997 TGTTAGTGGTAGTCATGTAATCCTG 58.126 40.000 0.00 0.00 0.00 3.86
204 205 6.127168 TGTTAGTGGTAGTCATGTAATCCTGG 60.127 42.308 0.00 0.00 0.00 4.45
205 206 3.134804 AGTGGTAGTCATGTAATCCTGGC 59.865 47.826 0.00 0.00 0.00 4.85
206 207 2.438021 TGGTAGTCATGTAATCCTGGCC 59.562 50.000 0.00 0.00 0.00 5.36
207 208 2.548067 GGTAGTCATGTAATCCTGGCCG 60.548 54.545 0.00 0.00 0.00 6.13
208 209 0.469917 AGTCATGTAATCCTGGCCGG 59.530 55.000 3.88 3.88 0.00 6.13
209 210 0.180406 GTCATGTAATCCTGGCCGGT 59.820 55.000 11.58 0.00 0.00 5.28
210 211 0.916086 TCATGTAATCCTGGCCGGTT 59.084 50.000 11.58 1.23 0.00 4.44
211 212 1.024271 CATGTAATCCTGGCCGGTTG 58.976 55.000 11.58 0.00 0.00 3.77
212 213 0.916086 ATGTAATCCTGGCCGGTTGA 59.084 50.000 11.58 1.27 0.00 3.18
213 214 0.916086 TGTAATCCTGGCCGGTTGAT 59.084 50.000 11.58 4.00 0.00 2.57
214 215 1.308998 GTAATCCTGGCCGGTTGATG 58.691 55.000 11.58 0.00 0.00 3.07
215 216 0.182537 TAATCCTGGCCGGTTGATGG 59.817 55.000 11.58 0.00 0.00 3.51
225 226 3.866883 CCGGTTGATGGCTTTGTTAAT 57.133 42.857 0.00 0.00 0.00 1.40
226 227 4.186856 CCGGTTGATGGCTTTGTTAATT 57.813 40.909 0.00 0.00 0.00 1.40
227 228 4.173256 CCGGTTGATGGCTTTGTTAATTC 58.827 43.478 0.00 0.00 0.00 2.17
228 229 4.321601 CCGGTTGATGGCTTTGTTAATTCA 60.322 41.667 0.00 0.00 0.00 2.57
229 230 5.226396 CGGTTGATGGCTTTGTTAATTCAA 58.774 37.500 0.00 0.00 0.00 2.69
230 231 5.694006 CGGTTGATGGCTTTGTTAATTCAAA 59.306 36.000 0.00 0.00 36.18 2.69
237 238 2.734276 TTGTTAATTCAAAGCCGGGC 57.266 45.000 12.11 12.11 0.00 6.13
238 239 1.917872 TGTTAATTCAAAGCCGGGCT 58.082 45.000 17.69 17.69 42.56 5.19
239 240 1.816224 TGTTAATTCAAAGCCGGGCTC 59.184 47.619 24.08 6.82 38.25 4.70
240 241 2.092323 GTTAATTCAAAGCCGGGCTCT 58.908 47.619 24.08 5.15 38.25 4.09
241 242 2.492088 GTTAATTCAAAGCCGGGCTCTT 59.508 45.455 24.08 15.43 38.25 2.85
242 243 1.177401 AATTCAAAGCCGGGCTCTTC 58.823 50.000 24.08 0.00 38.25 2.87
243 244 0.329596 ATTCAAAGCCGGGCTCTTCT 59.670 50.000 24.08 2.98 38.25 2.85
244 245 0.110486 TTCAAAGCCGGGCTCTTCTT 59.890 50.000 24.08 10.16 38.25 2.52
245 246 0.606401 TCAAAGCCGGGCTCTTCTTG 60.606 55.000 24.08 21.74 38.25 3.02
246 247 0.606401 CAAAGCCGGGCTCTTCTTGA 60.606 55.000 24.08 0.00 38.25 3.02
247 248 0.322008 AAAGCCGGGCTCTTCTTGAG 60.322 55.000 24.08 0.00 45.33 3.02
257 258 3.311486 CTCTTCTTGAGCCTTCGTTCT 57.689 47.619 0.00 0.00 35.84 3.01
258 259 4.442375 CTCTTCTTGAGCCTTCGTTCTA 57.558 45.455 0.00 0.00 35.84 2.10
259 260 4.810790 CTCTTCTTGAGCCTTCGTTCTAA 58.189 43.478 0.00 0.00 35.84 2.10
260 261 5.209818 TCTTCTTGAGCCTTCGTTCTAAA 57.790 39.130 0.00 0.00 0.00 1.85
261 262 5.607477 TCTTCTTGAGCCTTCGTTCTAAAA 58.393 37.500 0.00 0.00 0.00 1.52
262 263 5.696724 TCTTCTTGAGCCTTCGTTCTAAAAG 59.303 40.000 0.00 0.00 0.00 2.27
263 264 5.209818 TCTTGAGCCTTCGTTCTAAAAGA 57.790 39.130 0.00 0.00 0.00 2.52
264 265 4.989168 TCTTGAGCCTTCGTTCTAAAAGAC 59.011 41.667 0.00 0.00 0.00 3.01
265 266 3.660865 TGAGCCTTCGTTCTAAAAGACC 58.339 45.455 0.00 0.00 0.00 3.85
266 267 3.323979 TGAGCCTTCGTTCTAAAAGACCT 59.676 43.478 0.00 0.00 0.00 3.85
267 268 3.665190 AGCCTTCGTTCTAAAAGACCTG 58.335 45.455 0.00 0.00 0.00 4.00
268 269 3.323979 AGCCTTCGTTCTAAAAGACCTGA 59.676 43.478 0.00 0.00 0.00 3.86
269 270 3.432592 GCCTTCGTTCTAAAAGACCTGAC 59.567 47.826 0.00 0.00 0.00 3.51
270 271 4.628074 CCTTCGTTCTAAAAGACCTGACA 58.372 43.478 0.00 0.00 0.00 3.58
271 272 5.054477 CCTTCGTTCTAAAAGACCTGACAA 58.946 41.667 0.00 0.00 0.00 3.18
272 273 5.526111 CCTTCGTTCTAAAAGACCTGACAAA 59.474 40.000 0.00 0.00 0.00 2.83
273 274 6.292919 CCTTCGTTCTAAAAGACCTGACAAAG 60.293 42.308 0.00 0.00 0.00 2.77
274 275 5.909477 TCGTTCTAAAAGACCTGACAAAGA 58.091 37.500 0.00 0.00 0.00 2.52
275 276 5.983720 TCGTTCTAAAAGACCTGACAAAGAG 59.016 40.000 0.00 0.00 0.00 2.85
276 277 5.983720 CGTTCTAAAAGACCTGACAAAGAGA 59.016 40.000 0.00 0.00 0.00 3.10
277 278 6.647067 CGTTCTAAAAGACCTGACAAAGAGAT 59.353 38.462 0.00 0.00 0.00 2.75
278 279 7.171678 CGTTCTAAAAGACCTGACAAAGAGATT 59.828 37.037 0.00 0.00 0.00 2.40
279 280 9.490379 GTTCTAAAAGACCTGACAAAGAGATTA 57.510 33.333 0.00 0.00 0.00 1.75
280 281 9.712305 TTCTAAAAGACCTGACAAAGAGATTAG 57.288 33.333 0.00 0.00 0.00 1.73
281 282 6.809630 AAAAGACCTGACAAAGAGATTAGC 57.190 37.500 0.00 0.00 0.00 3.09
282 283 4.479786 AGACCTGACAAAGAGATTAGCC 57.520 45.455 0.00 0.00 0.00 3.93
283 284 3.118956 AGACCTGACAAAGAGATTAGCCG 60.119 47.826 0.00 0.00 0.00 5.52
284 285 2.093447 ACCTGACAAAGAGATTAGCCGG 60.093 50.000 0.00 0.00 0.00 6.13
285 286 1.936547 CTGACAAAGAGATTAGCCGGC 59.063 52.381 21.89 21.89 0.00 6.13
286 287 1.300481 GACAAAGAGATTAGCCGGCC 58.700 55.000 26.15 7.74 0.00 6.13
287 288 0.912486 ACAAAGAGATTAGCCGGCCT 59.088 50.000 26.15 13.63 0.00 5.19
288 289 1.303309 CAAAGAGATTAGCCGGCCTG 58.697 55.000 26.15 2.76 0.00 4.85
289 290 0.181350 AAAGAGATTAGCCGGCCTGG 59.819 55.000 26.15 5.05 42.50 4.45
314 315 3.460995 GCAGCTCCGCCTAGGTAT 58.539 61.111 11.31 0.00 41.99 2.73
315 316 1.005630 GCAGCTCCGCCTAGGTATG 60.006 63.158 11.31 0.51 41.99 2.39
316 317 1.005630 CAGCTCCGCCTAGGTATGC 60.006 63.158 11.31 10.02 41.99 3.14
317 318 2.210711 AGCTCCGCCTAGGTATGCC 61.211 63.158 11.31 0.00 41.99 4.40
319 320 0.898789 GCTCCGCCTAGGTATGCCTA 60.899 60.000 11.31 9.43 44.90 3.93
320 321 0.889306 CTCCGCCTAGGTATGCCTAC 59.111 60.000 11.31 0.00 44.90 3.18
321 322 0.186630 TCCGCCTAGGTATGCCTACA 59.813 55.000 11.31 0.00 44.90 2.74
322 323 0.603569 CCGCCTAGGTATGCCTACAG 59.396 60.000 11.31 0.00 44.90 2.74
323 324 0.038159 CGCCTAGGTATGCCTACAGC 60.038 60.000 11.31 10.69 44.90 4.40
324 325 1.343069 GCCTAGGTATGCCTACAGCT 58.657 55.000 11.31 0.00 44.90 4.24
325 326 2.526432 GCCTAGGTATGCCTACAGCTA 58.474 52.381 11.31 0.00 44.90 3.32
326 327 2.231721 GCCTAGGTATGCCTACAGCTAC 59.768 54.545 11.31 0.00 44.90 3.58
329 330 0.319641 GGTATGCCTACAGCTACGCC 60.320 60.000 1.45 0.00 44.23 5.68
609 622 2.265739 GCATCACCTCACTCCGCA 59.734 61.111 0.00 0.00 0.00 5.69
683 696 2.554636 CGGCAAAGCAGCAGGTTCA 61.555 57.895 0.00 0.00 33.61 3.18
939 983 7.138081 TGCACACATTTTAATTGTCAGTACTG 58.862 34.615 17.17 17.17 0.00 2.74
1419 1599 4.338879 AGCTTGAACCAGATGCAGTTATT 58.661 39.130 0.00 0.00 0.00 1.40
1732 1921 2.612285 TGACAGTGGAGAGGAGTCAT 57.388 50.000 0.00 0.00 34.59 3.06
1941 2130 2.703007 CCAGATGGTTAGGAGGAAGAGG 59.297 54.545 0.00 0.00 0.00 3.69
2013 2202 5.279657 GGGAATGGTTTTCAAGAGCAAGAAT 60.280 40.000 0.00 0.00 0.00 2.40
2257 2447 9.499479 CTAAGGTGATTGCAAATAGATATGAGT 57.501 33.333 1.71 0.00 0.00 3.41
2356 2546 4.060205 GTCAATTTCAAAGTGCAAGGCAT 58.940 39.130 0.00 0.00 41.91 4.40
2657 2849 6.732862 AGGGATGCTAATAATCAGATGTACCT 59.267 38.462 0.00 0.00 0.00 3.08
2699 2891 4.890581 GGAGAAAGAGACCACTGATAGCTA 59.109 45.833 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.304464 CCAGAGGGAAAACAGGGGC 60.304 63.158 0.00 0.00 35.59 5.80
1 2 0.251341 CACCAGAGGGAAAACAGGGG 60.251 60.000 0.00 0.00 38.05 4.79
2 3 0.771127 TCACCAGAGGGAAAACAGGG 59.229 55.000 0.00 0.00 38.05 4.45
3 4 1.142870 TGTCACCAGAGGGAAAACAGG 59.857 52.381 0.00 0.00 38.05 4.00
4 5 2.158755 ACTGTCACCAGAGGGAAAACAG 60.159 50.000 0.00 0.00 41.50 3.16
5 6 1.843851 ACTGTCACCAGAGGGAAAACA 59.156 47.619 0.00 0.00 41.50 2.83
6 7 2.158813 TGACTGTCACCAGAGGGAAAAC 60.159 50.000 6.36 0.00 41.50 2.43
7 8 2.104792 CTGACTGTCACCAGAGGGAAAA 59.895 50.000 6.36 0.00 41.50 2.29
8 9 1.694150 CTGACTGTCACCAGAGGGAAA 59.306 52.381 6.36 0.00 41.50 3.13
9 10 1.342074 CTGACTGTCACCAGAGGGAA 58.658 55.000 6.36 0.00 41.50 3.97
10 11 0.188587 ACTGACTGTCACCAGAGGGA 59.811 55.000 6.36 0.00 41.50 4.20
11 12 0.319728 CACTGACTGTCACCAGAGGG 59.680 60.000 6.36 0.00 41.50 4.30
12 13 1.000283 GTCACTGACTGTCACCAGAGG 60.000 57.143 6.36 0.00 41.50 3.69
13 14 1.683385 TGTCACTGACTGTCACCAGAG 59.317 52.381 6.36 0.00 41.50 3.35
14 15 1.409064 GTGTCACTGACTGTCACCAGA 59.591 52.381 6.36 2.39 41.50 3.86
15 16 1.136891 TGTGTCACTGACTGTCACCAG 59.863 52.381 6.36 0.00 44.68 4.00
16 17 1.190643 TGTGTCACTGACTGTCACCA 58.809 50.000 6.36 0.00 37.93 4.17
17 18 2.309528 TTGTGTCACTGACTGTCACC 57.690 50.000 6.36 0.00 37.93 4.02
18 19 3.435327 TGTTTTGTGTCACTGACTGTCAC 59.565 43.478 6.36 0.00 38.85 3.67
19 20 3.669536 TGTTTTGTGTCACTGACTGTCA 58.330 40.909 10.50 10.50 33.15 3.58
20 21 4.591202 CATGTTTTGTGTCACTGACTGTC 58.409 43.478 10.54 0.00 33.15 3.51
21 22 3.181497 GCATGTTTTGTGTCACTGACTGT 60.181 43.478 10.54 0.00 33.15 3.55
22 23 3.181498 TGCATGTTTTGTGTCACTGACTG 60.181 43.478 10.54 0.00 33.15 3.51
23 24 3.016031 TGCATGTTTTGTGTCACTGACT 58.984 40.909 10.54 0.00 33.15 3.41
24 25 3.108144 GTGCATGTTTTGTGTCACTGAC 58.892 45.455 4.27 1.86 0.00 3.51
25 26 2.223226 CGTGCATGTTTTGTGTCACTGA 60.223 45.455 4.27 0.00 0.00 3.41
26 27 2.110990 CGTGCATGTTTTGTGTCACTG 58.889 47.619 4.27 0.00 0.00 3.66
27 28 2.013400 TCGTGCATGTTTTGTGTCACT 58.987 42.857 5.68 0.00 0.00 3.41
28 29 2.466870 TCGTGCATGTTTTGTGTCAC 57.533 45.000 5.68 0.00 0.00 3.67
29 30 2.287487 CCATCGTGCATGTTTTGTGTCA 60.287 45.455 5.68 0.00 0.00 3.58
30 31 2.287547 ACCATCGTGCATGTTTTGTGTC 60.288 45.455 5.68 0.00 0.00 3.67
31 32 1.680735 ACCATCGTGCATGTTTTGTGT 59.319 42.857 5.68 1.45 0.00 3.72
32 33 2.052891 CACCATCGTGCATGTTTTGTG 58.947 47.619 5.68 6.10 32.04 3.33
33 34 2.420628 CACCATCGTGCATGTTTTGT 57.579 45.000 5.68 0.00 32.04 2.83
43 44 1.450312 GGAGGAAGGCACCATCGTG 60.450 63.158 3.78 0.00 43.35 4.35
44 45 2.670148 GGGAGGAAGGCACCATCGT 61.670 63.158 3.78 0.00 0.00 3.73
45 46 1.987807 ATGGGAGGAAGGCACCATCG 61.988 60.000 3.78 0.00 39.41 3.84
46 47 1.072965 CTATGGGAGGAAGGCACCATC 59.927 57.143 0.00 0.00 42.43 3.51
47 48 1.143813 CTATGGGAGGAAGGCACCAT 58.856 55.000 0.00 0.00 45.19 3.55
48 49 1.635817 GCTATGGGAGGAAGGCACCA 61.636 60.000 3.78 0.00 37.41 4.17
49 50 1.149401 GCTATGGGAGGAAGGCACC 59.851 63.158 0.00 0.00 0.00 5.01
50 51 1.149401 GGCTATGGGAGGAAGGCAC 59.851 63.158 0.00 0.00 35.95 5.01
51 52 0.624500 AAGGCTATGGGAGGAAGGCA 60.625 55.000 0.00 0.00 38.21 4.75
52 53 1.349357 CTAAGGCTATGGGAGGAAGGC 59.651 57.143 0.00 0.00 36.13 4.35
53 54 2.695585 ACTAAGGCTATGGGAGGAAGG 58.304 52.381 0.00 0.00 0.00 3.46
54 55 3.835395 CCTACTAAGGCTATGGGAGGAAG 59.165 52.174 6.70 0.00 35.64 3.46
55 56 3.858135 CCTACTAAGGCTATGGGAGGAA 58.142 50.000 6.70 0.00 35.64 3.36
56 57 3.544698 CCTACTAAGGCTATGGGAGGA 57.455 52.381 6.70 0.00 35.64 3.71
68 69 4.430908 CCGAAACCAGCTAACCTACTAAG 58.569 47.826 0.00 0.00 0.00 2.18
69 70 3.368739 GCCGAAACCAGCTAACCTACTAA 60.369 47.826 0.00 0.00 0.00 2.24
70 71 2.167075 GCCGAAACCAGCTAACCTACTA 59.833 50.000 0.00 0.00 0.00 1.82
71 72 1.066358 GCCGAAACCAGCTAACCTACT 60.066 52.381 0.00 0.00 0.00 2.57
72 73 1.338389 TGCCGAAACCAGCTAACCTAC 60.338 52.381 0.00 0.00 0.00 3.18
73 74 0.978151 TGCCGAAACCAGCTAACCTA 59.022 50.000 0.00 0.00 0.00 3.08
74 75 0.328258 ATGCCGAAACCAGCTAACCT 59.672 50.000 0.00 0.00 0.00 3.50
75 76 1.940613 CTATGCCGAAACCAGCTAACC 59.059 52.381 0.00 0.00 0.00 2.85
76 77 1.330829 GCTATGCCGAAACCAGCTAAC 59.669 52.381 0.00 0.00 0.00 2.34
77 78 1.663695 GCTATGCCGAAACCAGCTAA 58.336 50.000 0.00 0.00 0.00 3.09
78 79 0.529773 CGCTATGCCGAAACCAGCTA 60.530 55.000 0.00 0.00 0.00 3.32
79 80 1.815421 CGCTATGCCGAAACCAGCT 60.815 57.895 0.00 0.00 0.00 4.24
80 81 2.709475 CGCTATGCCGAAACCAGC 59.291 61.111 0.00 0.00 0.00 4.85
81 82 2.823829 GCCGCTATGCCGAAACCAG 61.824 63.158 0.00 0.00 0.00 4.00
82 83 2.822255 GCCGCTATGCCGAAACCA 60.822 61.111 0.00 0.00 0.00 3.67
83 84 3.937062 CGCCGCTATGCCGAAACC 61.937 66.667 0.00 0.00 0.00 3.27
84 85 2.627201 GAACGCCGCTATGCCGAAAC 62.627 60.000 0.00 0.00 0.00 2.78
85 86 2.435234 AACGCCGCTATGCCGAAA 60.435 55.556 0.00 0.00 0.00 3.46
86 87 2.888534 GAACGCCGCTATGCCGAA 60.889 61.111 0.00 0.00 0.00 4.30
89 90 2.661866 ATCGAACGCCGCTATGCC 60.662 61.111 0.00 0.00 38.37 4.40
90 91 1.949133 TCATCGAACGCCGCTATGC 60.949 57.895 0.00 0.00 38.37 3.14
91 92 0.869880 TGTCATCGAACGCCGCTATG 60.870 55.000 0.00 0.00 38.37 2.23
92 93 0.032130 ATGTCATCGAACGCCGCTAT 59.968 50.000 0.00 0.00 38.37 2.97
93 94 0.179121 AATGTCATCGAACGCCGCTA 60.179 50.000 0.00 0.00 38.37 4.26
94 95 1.447838 AATGTCATCGAACGCCGCT 60.448 52.632 0.00 0.00 38.37 5.52
95 96 1.296867 CAATGTCATCGAACGCCGC 60.297 57.895 0.00 0.00 38.37 6.53
96 97 0.442310 AACAATGTCATCGAACGCCG 59.558 50.000 0.00 0.00 40.25 6.46
97 98 1.732259 AGAACAATGTCATCGAACGCC 59.268 47.619 0.00 0.00 0.00 5.68
98 99 4.508971 CATAGAACAATGTCATCGAACGC 58.491 43.478 0.00 0.00 0.00 4.84
99 100 4.508971 GCATAGAACAATGTCATCGAACG 58.491 43.478 0.00 0.00 0.00 3.95
100 101 4.572389 AGGCATAGAACAATGTCATCGAAC 59.428 41.667 0.00 0.00 33.79 3.95
101 102 4.769688 AGGCATAGAACAATGTCATCGAA 58.230 39.130 0.00 0.00 33.79 3.71
102 103 4.406648 AGGCATAGAACAATGTCATCGA 57.593 40.909 0.00 0.00 33.79 3.59
103 104 4.318333 CGAAGGCATAGAACAATGTCATCG 60.318 45.833 2.36 2.36 43.38 3.84
104 105 4.811024 TCGAAGGCATAGAACAATGTCATC 59.189 41.667 0.00 0.00 33.79 2.92
105 106 4.769688 TCGAAGGCATAGAACAATGTCAT 58.230 39.130 0.00 0.00 33.79 3.06
106 107 4.183865 CTCGAAGGCATAGAACAATGTCA 58.816 43.478 0.00 0.00 33.79 3.58
107 108 4.184629 ACTCGAAGGCATAGAACAATGTC 58.815 43.478 0.00 0.00 0.00 3.06
108 109 4.207891 ACTCGAAGGCATAGAACAATGT 57.792 40.909 0.00 0.00 0.00 2.71
109 110 4.393062 ACAACTCGAAGGCATAGAACAATG 59.607 41.667 0.00 0.00 0.00 2.82
110 111 4.579869 ACAACTCGAAGGCATAGAACAAT 58.420 39.130 0.00 0.00 0.00 2.71
111 112 4.002906 ACAACTCGAAGGCATAGAACAA 57.997 40.909 0.00 0.00 0.00 2.83
112 113 3.678056 ACAACTCGAAGGCATAGAACA 57.322 42.857 0.00 0.00 0.00 3.18
113 114 4.246458 AGAACAACTCGAAGGCATAGAAC 58.754 43.478 0.00 0.00 0.00 3.01
114 115 4.537135 AGAACAACTCGAAGGCATAGAA 57.463 40.909 0.00 0.00 0.00 2.10
115 116 4.142227 GGTAGAACAACTCGAAGGCATAGA 60.142 45.833 0.00 0.00 0.00 1.98
116 117 4.113354 GGTAGAACAACTCGAAGGCATAG 58.887 47.826 0.00 0.00 0.00 2.23
117 118 3.428452 CGGTAGAACAACTCGAAGGCATA 60.428 47.826 0.00 0.00 0.00 3.14
118 119 2.674177 CGGTAGAACAACTCGAAGGCAT 60.674 50.000 0.00 0.00 0.00 4.40
119 120 1.336517 CGGTAGAACAACTCGAAGGCA 60.337 52.381 0.00 0.00 0.00 4.75
120 121 1.068055 TCGGTAGAACAACTCGAAGGC 60.068 52.381 0.00 0.00 0.00 4.35
121 122 2.864968 CTCGGTAGAACAACTCGAAGG 58.135 52.381 0.00 0.00 0.00 3.46
122 123 2.251893 GCTCGGTAGAACAACTCGAAG 58.748 52.381 0.00 0.00 0.00 3.79
123 124 1.610038 TGCTCGGTAGAACAACTCGAA 59.390 47.619 0.00 0.00 0.00 3.71
124 125 1.068748 GTGCTCGGTAGAACAACTCGA 60.069 52.381 0.00 0.00 30.64 4.04
125 126 1.335597 TGTGCTCGGTAGAACAACTCG 60.336 52.381 0.00 0.00 38.41 4.18
126 127 2.433868 TGTGCTCGGTAGAACAACTC 57.566 50.000 0.00 0.00 38.41 3.01
127 128 2.902705 TTGTGCTCGGTAGAACAACT 57.097 45.000 0.00 0.00 44.86 3.16
130 131 2.831685 ACATTGTGCTCGGTAGAACA 57.168 45.000 0.00 0.00 39.71 3.18
131 132 4.683832 AGATACATTGTGCTCGGTAGAAC 58.316 43.478 0.00 0.00 0.00 3.01
132 133 5.127194 AGAAGATACATTGTGCTCGGTAGAA 59.873 40.000 0.00 0.00 0.00 2.10
133 134 4.645136 AGAAGATACATTGTGCTCGGTAGA 59.355 41.667 0.00 0.00 0.00 2.59
134 135 4.938080 AGAAGATACATTGTGCTCGGTAG 58.062 43.478 0.00 0.00 0.00 3.18
135 136 5.339008 AAGAAGATACATTGTGCTCGGTA 57.661 39.130 0.00 0.00 0.00 4.02
136 137 3.895232 AGAAGATACATTGTGCTCGGT 57.105 42.857 0.00 0.00 0.00 4.69
137 138 5.447818 GGAAAAGAAGATACATTGTGCTCGG 60.448 44.000 0.00 0.00 0.00 4.63
138 139 5.563842 GGAAAAGAAGATACATTGTGCTCG 58.436 41.667 0.00 0.00 0.00 5.03
139 140 5.563842 CGGAAAAGAAGATACATTGTGCTC 58.436 41.667 0.00 0.00 0.00 4.26
140 141 4.142600 GCGGAAAAGAAGATACATTGTGCT 60.143 41.667 0.00 0.00 0.00 4.40
141 142 4.098416 GCGGAAAAGAAGATACATTGTGC 58.902 43.478 0.00 0.00 0.00 4.57
142 143 5.352569 AGAGCGGAAAAGAAGATACATTGTG 59.647 40.000 0.00 0.00 0.00 3.33
143 144 5.491982 AGAGCGGAAAAGAAGATACATTGT 58.508 37.500 0.00 0.00 0.00 2.71
144 145 6.428385 AAGAGCGGAAAAGAAGATACATTG 57.572 37.500 0.00 0.00 0.00 2.82
145 146 6.431234 ACAAAGAGCGGAAAAGAAGATACATT 59.569 34.615 0.00 0.00 0.00 2.71
146 147 5.940470 ACAAAGAGCGGAAAAGAAGATACAT 59.060 36.000 0.00 0.00 0.00 2.29
147 148 5.305585 ACAAAGAGCGGAAAAGAAGATACA 58.694 37.500 0.00 0.00 0.00 2.29
148 149 5.864628 ACAAAGAGCGGAAAAGAAGATAC 57.135 39.130 0.00 0.00 0.00 2.24
149 150 6.877611 AAACAAAGAGCGGAAAAGAAGATA 57.122 33.333 0.00 0.00 0.00 1.98
150 151 5.774498 AAACAAAGAGCGGAAAAGAAGAT 57.226 34.783 0.00 0.00 0.00 2.40
151 152 5.357032 AGAAAACAAAGAGCGGAAAAGAAGA 59.643 36.000 0.00 0.00 0.00 2.87
152 153 5.582550 AGAAAACAAAGAGCGGAAAAGAAG 58.417 37.500 0.00 0.00 0.00 2.85
153 154 5.576447 AGAAAACAAAGAGCGGAAAAGAA 57.424 34.783 0.00 0.00 0.00 2.52
154 155 5.105917 ACAAGAAAACAAAGAGCGGAAAAGA 60.106 36.000 0.00 0.00 0.00 2.52
155 156 5.102313 ACAAGAAAACAAAGAGCGGAAAAG 58.898 37.500 0.00 0.00 0.00 2.27
156 157 5.066968 ACAAGAAAACAAAGAGCGGAAAA 57.933 34.783 0.00 0.00 0.00 2.29
157 158 4.712122 ACAAGAAAACAAAGAGCGGAAA 57.288 36.364 0.00 0.00 0.00 3.13
158 159 4.082463 ACAACAAGAAAACAAAGAGCGGAA 60.082 37.500 0.00 0.00 0.00 4.30
159 160 3.442273 ACAACAAGAAAACAAAGAGCGGA 59.558 39.130 0.00 0.00 0.00 5.54
160 161 3.769536 ACAACAAGAAAACAAAGAGCGG 58.230 40.909 0.00 0.00 0.00 5.52
161 162 6.021468 CACTAACAACAAGAAAACAAAGAGCG 60.021 38.462 0.00 0.00 0.00 5.03
162 163 6.253512 CCACTAACAACAAGAAAACAAAGAGC 59.746 38.462 0.00 0.00 0.00 4.09
163 164 7.312899 ACCACTAACAACAAGAAAACAAAGAG 58.687 34.615 0.00 0.00 0.00 2.85
164 165 7.222000 ACCACTAACAACAAGAAAACAAAGA 57.778 32.000 0.00 0.00 0.00 2.52
165 166 8.241367 ACTACCACTAACAACAAGAAAACAAAG 58.759 33.333 0.00 0.00 0.00 2.77
166 167 8.113173 ACTACCACTAACAACAAGAAAACAAA 57.887 30.769 0.00 0.00 0.00 2.83
167 168 7.390996 TGACTACCACTAACAACAAGAAAACAA 59.609 33.333 0.00 0.00 0.00 2.83
168 169 6.879993 TGACTACCACTAACAACAAGAAAACA 59.120 34.615 0.00 0.00 0.00 2.83
169 170 7.311364 TGACTACCACTAACAACAAGAAAAC 57.689 36.000 0.00 0.00 0.00 2.43
170 171 7.554835 ACATGACTACCACTAACAACAAGAAAA 59.445 33.333 0.00 0.00 0.00 2.29
171 172 7.051623 ACATGACTACCACTAACAACAAGAAA 58.948 34.615 0.00 0.00 0.00 2.52
172 173 6.588204 ACATGACTACCACTAACAACAAGAA 58.412 36.000 0.00 0.00 0.00 2.52
173 174 6.169557 ACATGACTACCACTAACAACAAGA 57.830 37.500 0.00 0.00 0.00 3.02
174 175 7.956420 TTACATGACTACCACTAACAACAAG 57.044 36.000 0.00 0.00 0.00 3.16
175 176 7.604927 GGATTACATGACTACCACTAACAACAA 59.395 37.037 0.00 0.00 0.00 2.83
176 177 7.038587 AGGATTACATGACTACCACTAACAACA 60.039 37.037 0.00 0.00 0.00 3.33
177 178 7.277981 CAGGATTACATGACTACCACTAACAAC 59.722 40.741 0.00 0.00 0.00 3.32
178 179 7.327975 CAGGATTACATGACTACCACTAACAA 58.672 38.462 0.00 0.00 0.00 2.83
179 180 6.127168 CCAGGATTACATGACTACCACTAACA 60.127 42.308 0.00 0.00 0.00 2.41
180 181 6.281405 CCAGGATTACATGACTACCACTAAC 58.719 44.000 0.00 0.00 0.00 2.34
181 182 5.163343 GCCAGGATTACATGACTACCACTAA 60.163 44.000 0.00 0.00 0.00 2.24
182 183 4.344102 GCCAGGATTACATGACTACCACTA 59.656 45.833 0.00 0.00 0.00 2.74
183 184 3.134804 GCCAGGATTACATGACTACCACT 59.865 47.826 0.00 0.00 0.00 4.00
184 185 3.467803 GCCAGGATTACATGACTACCAC 58.532 50.000 0.00 0.00 0.00 4.16
185 186 2.438021 GGCCAGGATTACATGACTACCA 59.562 50.000 0.00 0.00 0.00 3.25
186 187 2.548067 CGGCCAGGATTACATGACTACC 60.548 54.545 2.24 0.00 0.00 3.18
187 188 2.548067 CCGGCCAGGATTACATGACTAC 60.548 54.545 2.24 0.00 45.00 2.73
188 189 1.691976 CCGGCCAGGATTACATGACTA 59.308 52.381 2.24 0.00 45.00 2.59
189 190 0.469917 CCGGCCAGGATTACATGACT 59.530 55.000 2.24 0.00 45.00 3.41
190 191 0.180406 ACCGGCCAGGATTACATGAC 59.820 55.000 18.74 0.00 45.00 3.06
191 192 0.916086 AACCGGCCAGGATTACATGA 59.084 50.000 18.74 0.00 45.00 3.07
192 193 1.024271 CAACCGGCCAGGATTACATG 58.976 55.000 18.74 0.00 45.00 3.21
193 194 0.916086 TCAACCGGCCAGGATTACAT 59.084 50.000 18.74 0.00 45.00 2.29
194 195 0.916086 ATCAACCGGCCAGGATTACA 59.084 50.000 18.74 0.75 45.00 2.41
195 196 1.308998 CATCAACCGGCCAGGATTAC 58.691 55.000 18.74 0.00 45.00 1.89
196 197 0.182537 CCATCAACCGGCCAGGATTA 59.817 55.000 18.74 1.01 45.00 1.75
197 198 1.076777 CCATCAACCGGCCAGGATT 60.077 57.895 18.74 7.79 45.00 3.01
198 199 2.597340 CCATCAACCGGCCAGGAT 59.403 61.111 18.74 5.67 45.00 3.24
199 200 4.424711 GCCATCAACCGGCCAGGA 62.425 66.667 18.74 3.02 44.22 3.86
205 206 3.866883 ATTAACAAAGCCATCAACCGG 57.133 42.857 0.00 0.00 0.00 5.28
206 207 4.804108 TGAATTAACAAAGCCATCAACCG 58.196 39.130 0.00 0.00 0.00 4.44
207 208 7.120789 CTTTGAATTAACAAAGCCATCAACC 57.879 36.000 6.67 0.00 46.05 3.77
217 218 2.630580 AGCCCGGCTTTGAATTAACAAA 59.369 40.909 5.94 0.00 33.89 2.83
218 219 2.230266 GAGCCCGGCTTTGAATTAACAA 59.770 45.455 14.70 0.00 39.88 2.83
219 220 1.816224 GAGCCCGGCTTTGAATTAACA 59.184 47.619 14.70 0.00 39.88 2.41
220 221 2.092323 AGAGCCCGGCTTTGAATTAAC 58.908 47.619 14.70 0.00 39.88 2.01
221 222 2.507407 AGAGCCCGGCTTTGAATTAA 57.493 45.000 14.70 0.00 39.88 1.40
222 223 2.026262 AGAAGAGCCCGGCTTTGAATTA 60.026 45.455 14.70 0.00 39.88 1.40
223 224 1.177401 GAAGAGCCCGGCTTTGAATT 58.823 50.000 14.70 4.04 39.88 2.17
224 225 0.329596 AGAAGAGCCCGGCTTTGAAT 59.670 50.000 14.70 0.00 39.88 2.57
225 226 0.110486 AAGAAGAGCCCGGCTTTGAA 59.890 50.000 14.70 0.00 39.88 2.69
226 227 0.606401 CAAGAAGAGCCCGGCTTTGA 60.606 55.000 14.70 0.00 39.88 2.69
227 228 0.606401 TCAAGAAGAGCCCGGCTTTG 60.606 55.000 14.70 13.91 39.88 2.77
228 229 0.322008 CTCAAGAAGAGCCCGGCTTT 60.322 55.000 14.70 4.65 39.88 3.51
229 230 1.298014 CTCAAGAAGAGCCCGGCTT 59.702 57.895 14.70 0.00 39.88 4.35
230 231 2.985456 CTCAAGAAGAGCCCGGCT 59.015 61.111 13.16 13.16 43.88 5.52
238 239 4.866508 TTAGAACGAAGGCTCAAGAAGA 57.133 40.909 0.00 0.00 0.00 2.87
239 240 5.696724 TCTTTTAGAACGAAGGCTCAAGAAG 59.303 40.000 0.00 0.00 0.00 2.85
240 241 5.465724 GTCTTTTAGAACGAAGGCTCAAGAA 59.534 40.000 0.00 0.00 0.00 2.52
241 242 4.989168 GTCTTTTAGAACGAAGGCTCAAGA 59.011 41.667 0.00 0.00 0.00 3.02
242 243 4.152580 GGTCTTTTAGAACGAAGGCTCAAG 59.847 45.833 0.00 0.00 0.00 3.02
243 244 4.062991 GGTCTTTTAGAACGAAGGCTCAA 58.937 43.478 0.00 0.00 0.00 3.02
244 245 3.323979 AGGTCTTTTAGAACGAAGGCTCA 59.676 43.478 0.00 0.00 36.93 4.26
245 246 3.680458 CAGGTCTTTTAGAACGAAGGCTC 59.320 47.826 0.00 0.00 36.93 4.70
246 247 3.323979 TCAGGTCTTTTAGAACGAAGGCT 59.676 43.478 0.00 0.00 36.93 4.58
247 248 3.432592 GTCAGGTCTTTTAGAACGAAGGC 59.567 47.826 0.00 0.00 36.93 4.35
248 249 4.628074 TGTCAGGTCTTTTAGAACGAAGG 58.372 43.478 0.00 0.00 36.93 3.46
249 250 6.479001 TCTTTGTCAGGTCTTTTAGAACGAAG 59.521 38.462 0.00 0.00 36.93 3.79
250 251 6.342906 TCTTTGTCAGGTCTTTTAGAACGAA 58.657 36.000 0.00 0.00 36.93 3.85
251 252 5.909477 TCTTTGTCAGGTCTTTTAGAACGA 58.091 37.500 0.00 0.00 36.93 3.85
252 253 5.983720 TCTCTTTGTCAGGTCTTTTAGAACG 59.016 40.000 0.00 0.00 36.93 3.95
253 254 7.971183 ATCTCTTTGTCAGGTCTTTTAGAAC 57.029 36.000 0.00 0.00 30.24 3.01
254 255 9.712305 CTAATCTCTTTGTCAGGTCTTTTAGAA 57.288 33.333 0.00 0.00 0.00 2.10
255 256 7.819900 GCTAATCTCTTTGTCAGGTCTTTTAGA 59.180 37.037 0.00 0.00 0.00 2.10
256 257 7.065204 GGCTAATCTCTTTGTCAGGTCTTTTAG 59.935 40.741 0.00 0.00 0.00 1.85
257 258 6.879458 GGCTAATCTCTTTGTCAGGTCTTTTA 59.121 38.462 0.00 0.00 0.00 1.52
258 259 5.707764 GGCTAATCTCTTTGTCAGGTCTTTT 59.292 40.000 0.00 0.00 0.00 2.27
259 260 5.249420 GGCTAATCTCTTTGTCAGGTCTTT 58.751 41.667 0.00 0.00 0.00 2.52
260 261 4.621747 CGGCTAATCTCTTTGTCAGGTCTT 60.622 45.833 0.00 0.00 0.00 3.01
261 262 3.118956 CGGCTAATCTCTTTGTCAGGTCT 60.119 47.826 0.00 0.00 0.00 3.85
262 263 3.190874 CGGCTAATCTCTTTGTCAGGTC 58.809 50.000 0.00 0.00 0.00 3.85
263 264 2.093447 CCGGCTAATCTCTTTGTCAGGT 60.093 50.000 0.00 0.00 0.00 4.00
264 265 2.555199 CCGGCTAATCTCTTTGTCAGG 58.445 52.381 0.00 0.00 0.00 3.86
265 266 1.936547 GCCGGCTAATCTCTTTGTCAG 59.063 52.381 22.15 0.00 0.00 3.51
266 267 1.406887 GGCCGGCTAATCTCTTTGTCA 60.407 52.381 28.56 0.00 0.00 3.58
267 268 1.134371 AGGCCGGCTAATCTCTTTGTC 60.134 52.381 28.56 4.14 0.00 3.18
268 269 0.912486 AGGCCGGCTAATCTCTTTGT 59.088 50.000 28.56 0.00 0.00 2.83
269 270 1.303309 CAGGCCGGCTAATCTCTTTG 58.697 55.000 28.56 7.16 0.00 2.77
270 271 0.181350 CCAGGCCGGCTAATCTCTTT 59.819 55.000 28.56 0.00 0.00 2.52
271 272 1.832912 CCAGGCCGGCTAATCTCTT 59.167 57.895 28.56 0.00 0.00 2.85
272 273 3.555967 CCAGGCCGGCTAATCTCT 58.444 61.111 28.56 11.02 0.00 3.10
323 324 0.529378 ACAGACTTTACCCGGCGTAG 59.471 55.000 6.01 0.00 0.00 3.51
324 325 0.968405 AACAGACTTTACCCGGCGTA 59.032 50.000 6.01 0.00 0.00 4.42
325 326 0.107268 AAACAGACTTTACCCGGCGT 59.893 50.000 6.01 0.00 0.00 5.68
326 327 1.232119 AAAACAGACTTTACCCGGCG 58.768 50.000 0.00 0.00 0.00 6.46
329 330 4.823442 AGGGTTTAAAACAGACTTTACCCG 59.177 41.667 5.45 0.00 34.47 5.28
683 696 2.968574 AGTTACAGCGGATGAGGATGAT 59.031 45.455 0.00 0.00 0.00 2.45
791 805 6.883756 GCCCCCAGAAAATCAAATAAAAATGA 59.116 34.615 0.00 0.00 0.00 2.57
939 983 8.608844 AGCCATGTATAAGTTACTAATGCTTC 57.391 34.615 0.00 0.00 0.00 3.86
1419 1599 4.284490 ACAACATCTTCTTCCTCTGCTGTA 59.716 41.667 0.00 0.00 0.00 2.74
1732 1921 6.426937 GCATGTTTTCTCAACTCAACTACCTA 59.573 38.462 0.00 0.00 0.00 3.08
1783 1972 7.047271 TCCTTTGAAAACCAAATTTCTGAAGG 58.953 34.615 18.67 18.67 44.18 3.46
1941 2130 3.681593 TGGGTTGAACCTAACATACTGC 58.318 45.455 14.87 0.00 38.64 4.40
2042 2231 1.202927 TGCTCCTTTTAGTGGCAAGCT 60.203 47.619 5.29 0.00 0.00 3.74
2257 2447 9.519191 CCACATTGGATTTGATAGGATAATGTA 57.481 33.333 0.00 0.00 40.96 2.29
2506 2698 6.088616 GCATCAAAACAAACATAGAACTGCTC 59.911 38.462 0.00 0.00 0.00 4.26
2699 2891 8.822805 TGATTAACAGACCTATAAACCACTTCT 58.177 33.333 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.