Multiple sequence alignment - TraesCS2B01G138500

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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 TraesCS2B01G138500 chr2B 100.000 3302 0 0 1 3302 105687401 105690702 0 6098
1 TraesCS2B01G138500 chr2A 90.629 2892 166 52 418 3258 69202499 69205336 0 3742
2 TraesCS2B01G138500 chr2D 91.831 1922 111 31 1391 3302 65639159 65637274 0 2638
3 TraesCS2B01G138500 chr2D 90.121 992 53 20 298 1284 65640155 65639204 0 1247


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 TraesCS2B01G138500 chr2B 105687401 105690702 3301 False 6098.0 6098 100.000 1 3302 1 chr2B.!!$F1 3301
1 TraesCS2B01G138500 chr2A 69202499 69205336 2837 False 3742.0 3742 90.629 418 3258 1 chr2A.!!$F1 2840
2 TraesCS2B01G138500 chr2D 65637274 65640155 2881 True 1942.5 2638 90.976 298 3302 2 chr2D.!!$R1 3004

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
29 30 0.036010 GGCAGTGGCAGAGCTAGAAA 60.036 55.0 12.58 0.00 43.71 2.52 F
163 164 0.036590 AAAACATTGCATGTGGGCCC 59.963 50.0 17.59 17.59 44.07 5.80 F
712 741 0.040157 CACCACATGCGTCAAACCAG 60.040 55.0 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1113 1146 1.878522 CCCGAAGATGAAGGACGCG 60.879 63.158 3.53 3.53 0.00 6.01 R
1389 1431 1.949525 GTGACACAGTGATGGCAACTT 59.050 47.619 7.81 0.00 40.05 2.66 R
2581 2636 0.611618 TGTGCGATCCAATTGCCCTT 60.612 50.000 0.00 0.00 38.97 3.95 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
25 26 3.774528 CGGGCAGTGGCAGAGCTA 61.775 66.667 19.48 0.00 43.71 3.32
26 27 2.188994 GGGCAGTGGCAGAGCTAG 59.811 66.667 19.48 0.00 43.71 3.42
27 28 2.362369 GGGCAGTGGCAGAGCTAGA 61.362 63.158 19.48 0.00 43.71 2.43
28 29 1.599047 GGCAGTGGCAGAGCTAGAA 59.401 57.895 12.58 0.00 43.71 2.10
29 30 0.036010 GGCAGTGGCAGAGCTAGAAA 60.036 55.000 12.58 0.00 43.71 2.52
30 31 1.611673 GGCAGTGGCAGAGCTAGAAAA 60.612 52.381 12.58 0.00 43.71 2.29
31 32 2.154462 GCAGTGGCAGAGCTAGAAAAA 58.846 47.619 0.00 0.00 40.72 1.94
32 33 2.095516 GCAGTGGCAGAGCTAGAAAAAC 60.096 50.000 0.00 0.00 40.72 2.43
33 34 3.406764 CAGTGGCAGAGCTAGAAAAACT 58.593 45.455 0.00 0.00 0.00 2.66
34 35 3.188048 CAGTGGCAGAGCTAGAAAAACTG 59.812 47.826 0.00 0.00 0.00 3.16
35 36 3.071602 AGTGGCAGAGCTAGAAAAACTGA 59.928 43.478 0.00 0.00 0.00 3.41
36 37 3.815401 GTGGCAGAGCTAGAAAAACTGAA 59.185 43.478 0.00 0.00 0.00 3.02
37 38 4.457257 GTGGCAGAGCTAGAAAAACTGAAT 59.543 41.667 0.00 0.00 0.00 2.57
38 39 5.643777 GTGGCAGAGCTAGAAAAACTGAATA 59.356 40.000 0.00 0.00 0.00 1.75
39 40 6.149474 GTGGCAGAGCTAGAAAAACTGAATAA 59.851 38.462 0.00 0.00 0.00 1.40
40 41 6.372659 TGGCAGAGCTAGAAAAACTGAATAAG 59.627 38.462 0.00 0.00 0.00 1.73
41 42 6.183360 GGCAGAGCTAGAAAAACTGAATAAGG 60.183 42.308 0.00 0.00 0.00 2.69
42 43 6.183360 GCAGAGCTAGAAAAACTGAATAAGGG 60.183 42.308 0.00 0.00 0.00 3.95
43 44 6.881602 CAGAGCTAGAAAAACTGAATAAGGGT 59.118 38.462 0.00 0.00 0.00 4.34
44 45 6.881602 AGAGCTAGAAAAACTGAATAAGGGTG 59.118 38.462 0.00 0.00 0.00 4.61
45 46 5.946377 AGCTAGAAAAACTGAATAAGGGTGG 59.054 40.000 0.00 0.00 0.00 4.61
46 47 5.393135 GCTAGAAAAACTGAATAAGGGTGGC 60.393 44.000 0.00 0.00 0.00 5.01
47 48 3.832490 AGAAAAACTGAATAAGGGTGGCC 59.168 43.478 0.00 0.00 0.00 5.36
48 49 2.990740 AAACTGAATAAGGGTGGCCA 57.009 45.000 0.00 0.00 0.00 5.36
49 50 2.990740 AACTGAATAAGGGTGGCCAA 57.009 45.000 7.24 0.00 0.00 4.52
50 51 2.514458 ACTGAATAAGGGTGGCCAAG 57.486 50.000 7.24 0.00 0.00 3.61
51 52 1.005924 ACTGAATAAGGGTGGCCAAGG 59.994 52.381 7.24 0.00 0.00 3.61
52 53 0.334676 TGAATAAGGGTGGCCAAGGG 59.665 55.000 7.24 0.00 0.00 3.95
53 54 0.397114 GAATAAGGGTGGCCAAGGGG 60.397 60.000 7.24 0.00 37.18 4.79
54 55 0.853586 AATAAGGGTGGCCAAGGGGA 60.854 55.000 7.24 0.00 35.59 4.81
55 56 0.853586 ATAAGGGTGGCCAAGGGGAA 60.854 55.000 7.24 0.00 35.59 3.97
56 57 1.506028 TAAGGGTGGCCAAGGGGAAG 61.506 60.000 7.24 0.00 35.59 3.46
57 58 4.382541 GGGTGGCCAAGGGGAAGG 62.383 72.222 7.24 0.00 35.59 3.46
58 59 3.264845 GGTGGCCAAGGGGAAGGA 61.265 66.667 7.24 0.00 35.59 3.36
59 60 2.626467 GGTGGCCAAGGGGAAGGAT 61.626 63.158 7.24 0.00 35.59 3.24
60 61 1.388133 GTGGCCAAGGGGAAGGATT 59.612 57.895 7.24 0.00 35.59 3.01
61 62 0.972471 GTGGCCAAGGGGAAGGATTG 60.972 60.000 7.24 0.00 35.59 2.67
62 63 1.145900 TGGCCAAGGGGAAGGATTGA 61.146 55.000 0.61 0.00 35.59 2.57
63 64 0.262876 GGCCAAGGGGAAGGATTGAT 59.737 55.000 0.00 0.00 35.59 2.57
64 65 1.499007 GGCCAAGGGGAAGGATTGATA 59.501 52.381 0.00 0.00 35.59 2.15
65 66 2.091333 GGCCAAGGGGAAGGATTGATAA 60.091 50.000 0.00 0.00 35.59 1.75
66 67 3.629796 GGCCAAGGGGAAGGATTGATAAA 60.630 47.826 0.00 0.00 35.59 1.40
67 68 3.384789 GCCAAGGGGAAGGATTGATAAAC 59.615 47.826 0.00 0.00 35.59 2.01
68 69 4.871822 CCAAGGGGAAGGATTGATAAACT 58.128 43.478 0.00 0.00 35.59 2.66
69 70 5.633854 GCCAAGGGGAAGGATTGATAAACTA 60.634 44.000 0.00 0.00 35.59 2.24
70 71 6.064717 CCAAGGGGAAGGATTGATAAACTAG 58.935 44.000 0.00 0.00 35.59 2.57
71 72 5.311844 AGGGGAAGGATTGATAAACTAGC 57.688 43.478 0.00 0.00 0.00 3.42
72 73 4.978388 AGGGGAAGGATTGATAAACTAGCT 59.022 41.667 0.00 0.00 0.00 3.32
73 74 5.433381 AGGGGAAGGATTGATAAACTAGCTT 59.567 40.000 0.00 0.00 0.00 3.74
74 75 5.532779 GGGGAAGGATTGATAAACTAGCTTG 59.467 44.000 0.00 0.00 0.00 4.01
75 76 5.532779 GGGAAGGATTGATAAACTAGCTTGG 59.467 44.000 0.00 0.00 0.00 3.61
76 77 5.532779 GGAAGGATTGATAAACTAGCTTGGG 59.467 44.000 0.00 0.00 0.00 4.12
77 78 5.053978 AGGATTGATAAACTAGCTTGGGG 57.946 43.478 0.00 0.00 0.00 4.96
78 79 4.726825 AGGATTGATAAACTAGCTTGGGGA 59.273 41.667 0.00 0.00 0.00 4.81
79 80 5.066593 GGATTGATAAACTAGCTTGGGGAG 58.933 45.833 0.00 0.00 0.00 4.30
80 81 4.503714 TTGATAAACTAGCTTGGGGAGG 57.496 45.455 0.00 0.00 0.00 4.30
81 82 2.777692 TGATAAACTAGCTTGGGGAGGG 59.222 50.000 0.00 0.00 0.00 4.30
82 83 0.916809 TAAACTAGCTTGGGGAGGGC 59.083 55.000 0.00 0.00 0.00 5.19
83 84 1.864263 AAACTAGCTTGGGGAGGGCC 61.864 60.000 0.00 0.00 0.00 5.80
84 85 2.692368 CTAGCTTGGGGAGGGCCA 60.692 66.667 6.18 0.00 35.15 5.36
85 86 2.204228 TAGCTTGGGGAGGGCCAA 60.204 61.111 6.18 0.00 35.15 4.52
86 87 1.854979 TAGCTTGGGGAGGGCCAAA 60.855 57.895 6.18 0.00 35.15 3.28
87 88 2.150014 TAGCTTGGGGAGGGCCAAAC 62.150 60.000 6.18 0.00 35.15 2.93
88 89 2.283894 CTTGGGGAGGGCCAAACC 60.284 66.667 6.18 6.06 35.15 3.27
89 90 3.113477 TTGGGGAGGGCCAAACCA 61.113 61.111 6.18 7.75 42.05 3.67
90 91 2.671384 CTTGGGGAGGGCCAAACCAA 62.671 60.000 20.03 20.03 42.05 3.67
91 92 2.603473 GGGGAGGGCCAAACCAAC 60.603 66.667 6.18 0.00 42.05 3.77
92 93 2.526110 GGGAGGGCCAAACCAACT 59.474 61.111 6.18 0.00 42.05 3.16
93 94 1.771646 GGGAGGGCCAAACCAACTA 59.228 57.895 6.18 0.00 42.05 2.24
94 95 0.113580 GGGAGGGCCAAACCAACTAA 59.886 55.000 6.18 0.00 42.05 2.24
95 96 1.481615 GGGAGGGCCAAACCAACTAAA 60.482 52.381 6.18 0.00 42.05 1.85
96 97 2.536066 GGAGGGCCAAACCAACTAAAT 58.464 47.619 6.18 0.00 42.05 1.40
97 98 2.233676 GGAGGGCCAAACCAACTAAATG 59.766 50.000 6.18 0.00 42.05 2.32
98 99 1.623311 AGGGCCAAACCAACTAAATGC 59.377 47.619 6.18 0.00 42.05 3.56
99 100 1.346068 GGGCCAAACCAACTAAATGCA 59.654 47.619 4.39 0.00 42.05 3.96
100 101 2.224402 GGGCCAAACCAACTAAATGCAA 60.224 45.455 4.39 0.00 42.05 4.08
101 102 3.471680 GGCCAAACCAACTAAATGCAAA 58.528 40.909 0.00 0.00 38.86 3.68
102 103 4.071423 GGCCAAACCAACTAAATGCAAAT 58.929 39.130 0.00 0.00 38.86 2.32
103 104 4.154015 GGCCAAACCAACTAAATGCAAATC 59.846 41.667 0.00 0.00 38.86 2.17
104 105 4.996758 GCCAAACCAACTAAATGCAAATCT 59.003 37.500 0.00 0.00 0.00 2.40
105 106 6.162777 GCCAAACCAACTAAATGCAAATCTA 58.837 36.000 0.00 0.00 0.00 1.98
106 107 6.311200 GCCAAACCAACTAAATGCAAATCTAG 59.689 38.462 0.00 0.00 0.00 2.43
107 108 7.378181 CCAAACCAACTAAATGCAAATCTAGT 58.622 34.615 0.00 0.00 0.00 2.57
108 109 8.519526 CCAAACCAACTAAATGCAAATCTAGTA 58.480 33.333 0.00 0.00 0.00 1.82
109 110 9.341899 CAAACCAACTAAATGCAAATCTAGTAC 57.658 33.333 0.00 0.00 0.00 2.73
110 111 8.630054 AACCAACTAAATGCAAATCTAGTACA 57.370 30.769 0.00 0.00 0.00 2.90
111 112 8.040716 ACCAACTAAATGCAAATCTAGTACAC 57.959 34.615 0.00 0.00 0.00 2.90
112 113 7.883311 ACCAACTAAATGCAAATCTAGTACACT 59.117 33.333 0.00 0.00 0.00 3.55
113 114 8.177663 CCAACTAAATGCAAATCTAGTACACTG 58.822 37.037 0.00 0.00 0.00 3.66
114 115 8.721478 CAACTAAATGCAAATCTAGTACACTGT 58.279 33.333 0.00 0.00 0.00 3.55
115 116 8.848474 ACTAAATGCAAATCTAGTACACTGTT 57.152 30.769 0.00 0.00 0.00 3.16
116 117 9.284968 ACTAAATGCAAATCTAGTACACTGTTT 57.715 29.630 0.00 0.00 0.00 2.83
120 121 7.129109 TGCAAATCTAGTACACTGTTTTAGC 57.871 36.000 0.00 0.00 0.00 3.09
121 122 6.708502 TGCAAATCTAGTACACTGTTTTAGCA 59.291 34.615 0.00 0.00 0.00 3.49
122 123 7.390440 TGCAAATCTAGTACACTGTTTTAGCAT 59.610 33.333 0.00 0.00 0.00 3.79
123 124 8.879759 GCAAATCTAGTACACTGTTTTAGCATA 58.120 33.333 0.00 0.00 0.00 3.14
131 132 9.938280 AGTACACTGTTTTAGCATAAATACTCA 57.062 29.630 0.00 0.00 0.00 3.41
133 134 8.848474 ACACTGTTTTAGCATAAATACTCAGT 57.152 30.769 0.00 0.00 33.62 3.41
135 136 8.721478 CACTGTTTTAGCATAAATACTCAGTGT 58.279 33.333 15.88 0.00 41.88 3.55
136 137 9.284968 ACTGTTTTAGCATAAATACTCAGTGTT 57.715 29.630 0.00 0.00 32.45 3.32
137 138 9.760660 CTGTTTTAGCATAAATACTCAGTGTTC 57.239 33.333 0.00 0.00 0.00 3.18
138 139 9.502091 TGTTTTAGCATAAATACTCAGTGTTCT 57.498 29.630 0.00 0.00 0.00 3.01
142 143 9.803315 TTAGCATAAATACTCAGTGTTCTAGTG 57.197 33.333 0.00 0.00 0.00 2.74
143 144 8.067751 AGCATAAATACTCAGTGTTCTAGTGA 57.932 34.615 0.00 0.00 37.22 3.41
144 145 8.531982 AGCATAAATACTCAGTGTTCTAGTGAA 58.468 33.333 0.00 0.00 38.25 3.18
145 146 9.151471 GCATAAATACTCAGTGTTCTAGTGAAA 57.849 33.333 0.00 0.00 38.25 2.69
149 150 8.958119 AATACTCAGTGTTCTAGTGAAAAACA 57.042 30.769 0.00 0.00 38.25 2.83
150 151 9.561069 AATACTCAGTGTTCTAGTGAAAAACAT 57.439 29.630 0.00 0.00 38.25 2.71
151 152 7.865706 ACTCAGTGTTCTAGTGAAAAACATT 57.134 32.000 0.00 0.00 38.25 2.71
152 153 7.697691 ACTCAGTGTTCTAGTGAAAAACATTG 58.302 34.615 9.26 9.26 40.15 2.82
153 154 6.494842 TCAGTGTTCTAGTGAAAAACATTGC 58.505 36.000 10.22 0.00 39.24 3.56
154 155 6.094742 TCAGTGTTCTAGTGAAAAACATTGCA 59.905 34.615 10.22 0.00 39.24 4.08
155 156 6.919662 CAGTGTTCTAGTGAAAAACATTGCAT 59.080 34.615 4.53 0.00 35.04 3.96
156 157 6.919662 AGTGTTCTAGTGAAAAACATTGCATG 59.080 34.615 0.00 0.00 35.54 4.06
157 158 6.697019 GTGTTCTAGTGAAAAACATTGCATGT 59.303 34.615 0.00 0.00 38.40 3.21
158 159 6.696583 TGTTCTAGTGAAAAACATTGCATGTG 59.303 34.615 0.00 0.91 37.48 3.21
159 160 5.771469 TCTAGTGAAAAACATTGCATGTGG 58.229 37.500 0.00 0.00 44.07 4.17
160 161 3.731089 AGTGAAAAACATTGCATGTGGG 58.269 40.909 0.00 0.00 44.07 4.61
161 162 2.223845 GTGAAAAACATTGCATGTGGGC 59.776 45.455 0.00 0.00 44.07 5.36
162 163 1.805943 GAAAAACATTGCATGTGGGCC 59.194 47.619 0.00 0.00 44.07 5.80
163 164 0.036590 AAAACATTGCATGTGGGCCC 59.963 50.000 17.59 17.59 44.07 5.80
164 165 0.837260 AAACATTGCATGTGGGCCCT 60.837 50.000 25.70 0.00 44.07 5.19
165 166 0.040942 AACATTGCATGTGGGCCCTA 59.959 50.000 25.70 13.04 44.07 3.53
166 167 0.396139 ACATTGCATGTGGGCCCTAG 60.396 55.000 25.70 11.15 43.01 3.02
167 168 1.456331 ATTGCATGTGGGCCCTAGC 60.456 57.895 25.70 20.84 38.76 3.42
168 169 1.941403 ATTGCATGTGGGCCCTAGCT 61.941 55.000 25.70 1.58 39.73 3.32
169 170 2.517875 GCATGTGGGCCCTAGCTG 60.518 66.667 25.70 15.85 39.73 4.24
170 171 2.194056 CATGTGGGCCCTAGCTGG 59.806 66.667 25.70 3.68 39.73 4.85
178 179 3.801997 CCCTAGCTGGCACCCCTG 61.802 72.222 0.00 0.00 0.00 4.45
179 180 3.011517 CCTAGCTGGCACCCCTGT 61.012 66.667 0.00 0.00 32.98 4.00
180 181 2.586792 CTAGCTGGCACCCCTGTC 59.413 66.667 0.00 0.00 32.98 3.51
181 182 1.992277 CTAGCTGGCACCCCTGTCT 60.992 63.158 0.00 0.00 32.98 3.41
182 183 1.965754 CTAGCTGGCACCCCTGTCTC 61.966 65.000 0.00 0.00 32.98 3.36
183 184 4.416738 GCTGGCACCCCTGTCTCC 62.417 72.222 0.00 0.00 32.98 3.71
184 185 4.087892 CTGGCACCCCTGTCTCCG 62.088 72.222 0.00 0.00 0.00 4.63
188 189 3.402681 CACCCCTGTCTCCGCCAT 61.403 66.667 0.00 0.00 0.00 4.40
189 190 3.402681 ACCCCTGTCTCCGCCATG 61.403 66.667 0.00 0.00 0.00 3.66
190 191 4.181010 CCCCTGTCTCCGCCATGG 62.181 72.222 7.63 7.63 40.09 3.66
191 192 4.864334 CCCTGTCTCCGCCATGGC 62.864 72.222 27.67 27.67 37.80 4.40
192 193 3.790437 CCTGTCTCCGCCATGGCT 61.790 66.667 33.07 0.00 39.32 4.75
193 194 2.513204 CTGTCTCCGCCATGGCTG 60.513 66.667 33.07 27.27 39.32 4.85
194 195 4.100084 TGTCTCCGCCATGGCTGG 62.100 66.667 33.07 31.47 46.17 4.85
218 219 3.190849 CTGTCCGCGGCACATCTG 61.191 66.667 23.51 10.25 0.00 2.90
219 220 4.758251 TGTCCGCGGCACATCTGG 62.758 66.667 23.51 0.00 0.00 3.86
220 221 4.760047 GTCCGCGGCACATCTGGT 62.760 66.667 23.51 0.00 0.00 4.00
221 222 4.451150 TCCGCGGCACATCTGGTC 62.451 66.667 23.51 0.00 0.00 4.02
222 223 4.457496 CCGCGGCACATCTGGTCT 62.457 66.667 14.67 0.00 0.00 3.85
223 224 2.887568 CGCGGCACATCTGGTCTC 60.888 66.667 0.00 0.00 0.00 3.36
224 225 2.887568 GCGGCACATCTGGTCTCG 60.888 66.667 0.00 0.00 0.00 4.04
225 226 2.887568 CGGCACATCTGGTCTCGC 60.888 66.667 0.00 0.00 0.00 5.03
226 227 2.512515 GGCACATCTGGTCTCGCC 60.513 66.667 0.00 0.00 37.90 5.54
227 228 2.512515 GCACATCTGGTCTCGCCC 60.513 66.667 0.00 0.00 36.04 6.13
228 229 2.202797 CACATCTGGTCTCGCCCG 60.203 66.667 0.00 0.00 36.04 6.13
229 230 4.148825 ACATCTGGTCTCGCCCGC 62.149 66.667 0.00 0.00 36.04 6.13
241 242 3.869272 GCCCGCGAGCACATTCTG 61.869 66.667 8.08 0.00 0.00 3.02
242 243 3.197790 CCCGCGAGCACATTCTGG 61.198 66.667 8.23 0.00 0.00 3.86
243 244 3.197790 CCGCGAGCACATTCTGGG 61.198 66.667 8.23 0.00 0.00 4.45
244 245 2.434884 CGCGAGCACATTCTGGGT 60.435 61.111 0.00 0.00 0.00 4.51
245 246 2.743752 CGCGAGCACATTCTGGGTG 61.744 63.158 0.00 0.00 39.25 4.61
246 247 1.672356 GCGAGCACATTCTGGGTGT 60.672 57.895 0.00 0.00 38.51 4.16
247 248 1.237285 GCGAGCACATTCTGGGTGTT 61.237 55.000 0.00 0.00 38.51 3.32
248 249 0.518636 CGAGCACATTCTGGGTGTTG 59.481 55.000 0.00 0.00 38.51 3.33
249 250 0.883833 GAGCACATTCTGGGTGTTGG 59.116 55.000 0.00 0.00 38.51 3.77
250 251 0.478072 AGCACATTCTGGGTGTTGGA 59.522 50.000 0.00 0.00 38.51 3.53
251 252 1.076024 AGCACATTCTGGGTGTTGGAT 59.924 47.619 0.00 0.00 38.51 3.41
252 253 1.895131 GCACATTCTGGGTGTTGGATT 59.105 47.619 0.00 0.00 38.51 3.01
253 254 2.299867 GCACATTCTGGGTGTTGGATTT 59.700 45.455 0.00 0.00 38.51 2.17
254 255 3.861886 GCACATTCTGGGTGTTGGATTTG 60.862 47.826 0.00 0.00 38.51 2.32
255 256 3.321682 CACATTCTGGGTGTTGGATTTGT 59.678 43.478 0.00 0.00 0.00 2.83
256 257 3.573967 ACATTCTGGGTGTTGGATTTGTC 59.426 43.478 0.00 0.00 0.00 3.18
257 258 2.286365 TCTGGGTGTTGGATTTGTCC 57.714 50.000 0.00 0.00 0.00 4.02
258 259 1.496857 TCTGGGTGTTGGATTTGTCCA 59.503 47.619 0.00 0.00 38.14 4.02
259 260 1.888512 CTGGGTGTTGGATTTGTCCAG 59.111 52.381 0.00 0.00 41.35 3.86
260 261 1.216678 TGGGTGTTGGATTTGTCCAGT 59.783 47.619 0.00 0.00 41.35 4.00
261 262 1.886542 GGGTGTTGGATTTGTCCAGTC 59.113 52.381 0.00 0.00 41.35 3.51
262 263 1.886542 GGTGTTGGATTTGTCCAGTCC 59.113 52.381 0.00 0.00 41.35 3.85
263 264 1.535462 GTGTTGGATTTGTCCAGTCCG 59.465 52.381 0.00 0.00 41.35 4.79
264 265 1.165270 GTTGGATTTGTCCAGTCCGG 58.835 55.000 0.00 0.00 41.35 5.14
265 266 0.768622 TTGGATTTGTCCAGTCCGGT 59.231 50.000 0.00 0.00 41.35 5.28
266 267 0.768622 TGGATTTGTCCAGTCCGGTT 59.231 50.000 0.00 0.00 34.33 4.44
267 268 1.165270 GGATTTGTCCAGTCCGGTTG 58.835 55.000 0.00 0.99 35.57 3.77
268 269 1.544759 GGATTTGTCCAGTCCGGTTGT 60.545 52.381 0.00 0.00 35.57 3.32
269 270 2.289819 GGATTTGTCCAGTCCGGTTGTA 60.290 50.000 0.00 0.00 35.57 2.41
270 271 3.404899 GATTTGTCCAGTCCGGTTGTAA 58.595 45.455 0.00 0.00 35.57 2.41
271 272 3.278668 TTTGTCCAGTCCGGTTGTAAA 57.721 42.857 0.00 0.98 35.57 2.01
272 273 3.495434 TTGTCCAGTCCGGTTGTAAAT 57.505 42.857 0.00 0.00 35.57 1.40
273 274 3.048337 TGTCCAGTCCGGTTGTAAATC 57.952 47.619 0.00 0.00 35.57 2.17
274 275 2.289819 TGTCCAGTCCGGTTGTAAATCC 60.290 50.000 0.00 0.00 35.57 3.01
275 276 2.027469 GTCCAGTCCGGTTGTAAATCCT 60.027 50.000 0.00 0.00 35.57 3.24
276 277 2.235402 TCCAGTCCGGTTGTAAATCCTC 59.765 50.000 0.00 0.00 35.57 3.71
277 278 2.236395 CCAGTCCGGTTGTAAATCCTCT 59.764 50.000 0.00 0.00 0.00 3.69
278 279 3.449737 CCAGTCCGGTTGTAAATCCTCTA 59.550 47.826 0.00 0.00 0.00 2.43
279 280 4.081309 CCAGTCCGGTTGTAAATCCTCTAA 60.081 45.833 0.00 0.00 0.00 2.10
280 281 5.484715 CAGTCCGGTTGTAAATCCTCTAAA 58.515 41.667 0.00 0.00 0.00 1.85
281 282 5.935789 CAGTCCGGTTGTAAATCCTCTAAAA 59.064 40.000 0.00 0.00 0.00 1.52
282 283 6.428771 CAGTCCGGTTGTAAATCCTCTAAAAA 59.571 38.462 0.00 0.00 0.00 1.94
310 311 4.771590 TTGCCTCACTAGCTTGAAAATG 57.228 40.909 1.04 0.00 0.00 2.32
315 316 5.278957 GCCTCACTAGCTTGAAAATGGAAAA 60.279 40.000 1.04 0.00 0.00 2.29
316 317 6.385033 CCTCACTAGCTTGAAAATGGAAAAG 58.615 40.000 1.04 0.00 0.00 2.27
317 318 6.015940 CCTCACTAGCTTGAAAATGGAAAAGT 60.016 38.462 1.04 0.00 0.00 2.66
318 319 7.174946 CCTCACTAGCTTGAAAATGGAAAAGTA 59.825 37.037 1.04 0.00 0.00 2.24
319 320 8.458573 TCACTAGCTTGAAAATGGAAAAGTAA 57.541 30.769 1.04 0.00 0.00 2.24
320 321 8.908903 TCACTAGCTTGAAAATGGAAAAGTAAA 58.091 29.630 1.04 0.00 0.00 2.01
321 322 9.528018 CACTAGCTTGAAAATGGAAAAGTAAAA 57.472 29.630 1.04 0.00 0.00 1.52
362 364 4.020307 ACAATTTTCTTAATGCACCCCAGG 60.020 41.667 0.00 0.00 0.00 4.45
373 375 0.921896 CACCCCAGGTTCTCCATCAT 59.078 55.000 0.00 0.00 31.02 2.45
381 383 4.384978 CCAGGTTCTCCATCATCAACATCT 60.385 45.833 0.00 0.00 35.89 2.90
385 387 6.558014 AGGTTCTCCATCATCAACATCTATCT 59.442 38.462 0.00 0.00 35.89 1.98
392 394 7.681598 TCCATCATCAACATCTATCTATTCCCT 59.318 37.037 0.00 0.00 0.00 4.20
395 397 5.392767 TCAACATCTATCTATTCCCTCGC 57.607 43.478 0.00 0.00 0.00 5.03
396 398 4.220821 TCAACATCTATCTATTCCCTCGCC 59.779 45.833 0.00 0.00 0.00 5.54
399 401 0.888619 CTATCTATTCCCTCGCCGCA 59.111 55.000 0.00 0.00 0.00 5.69
400 402 1.272490 CTATCTATTCCCTCGCCGCAA 59.728 52.381 0.00 0.00 0.00 4.85
401 403 0.468226 ATCTATTCCCTCGCCGCAAA 59.532 50.000 0.00 0.00 0.00 3.68
619 622 2.102357 CGCGCATACGTCTCCACT 59.898 61.111 8.75 0.00 42.83 4.00
620 623 1.939785 CGCGCATACGTCTCCACTC 60.940 63.158 8.75 0.00 42.83 3.51
621 624 1.433879 GCGCATACGTCTCCACTCT 59.566 57.895 0.30 0.00 42.83 3.24
712 741 0.040157 CACCACATGCGTCAAACCAG 60.040 55.000 0.00 0.00 0.00 4.00
758 787 1.533187 TCCATATCAAGCACCCCCAT 58.467 50.000 0.00 0.00 0.00 4.00
763 792 0.974010 ATCAAGCACCCCCATTGCAG 60.974 55.000 0.00 0.00 42.83 4.41
792 821 1.021390 CCACAAGCCACAGTCGATCC 61.021 60.000 0.00 0.00 0.00 3.36
866 895 4.610333 TGAGCTAGGAGAAGGTGACATAA 58.390 43.478 0.00 0.00 0.00 1.90
1290 1323 6.463049 CCGACATCATAGGTAATTTCAGTCCT 60.463 42.308 0.00 0.00 0.00 3.85
1349 1391 3.066900 TCCTTGTACGATGAGCTTAGAGC 59.933 47.826 0.00 0.00 42.84 4.09
1362 1404 0.179100 TTAGAGCTGCCATCGCACTC 60.179 55.000 0.00 6.74 41.12 3.51
1364 1406 2.125229 AGCTGCCATCGCACTCTG 60.125 61.111 0.00 0.00 41.12 3.35
1369 1411 1.267806 CTGCCATCGCACTCTGTTTTT 59.732 47.619 0.00 0.00 41.12 1.94
1415 1457 4.203226 TGCCATCACTGTGTCACTTAAAA 58.797 39.130 7.79 0.00 0.00 1.52
1420 1462 6.422223 CATCACTGTGTCACTTAAAACAGAC 58.578 40.000 7.79 0.00 42.09 3.51
1435 1478 9.166126 CTTAAAACAGACGTAAACTCCATTTTC 57.834 33.333 0.00 0.00 0.00 2.29
1965 2008 4.130281 GCGCAGTACAACGGTCGC 62.130 66.667 0.30 4.22 33.95 5.19
2196 2248 2.032071 CACGTGTTCTGGGACCCC 59.968 66.667 8.45 2.69 0.00 4.95
2199 2251 1.190178 ACGTGTTCTGGGACCCCTAC 61.190 60.000 8.45 3.92 36.94 3.18
2202 2254 0.838987 TGTTCTGGGACCCCTACCAC 60.839 60.000 8.45 0.00 36.94 4.16
2223 2275 2.048127 AGCGAGAAGGCCAACGTC 60.048 61.111 5.01 0.00 0.00 4.34
2268 2320 2.635141 GCGACAGCAAATACATCTCG 57.365 50.000 0.00 0.00 44.35 4.04
2310 2362 4.657013 TCTTCAAGCTCTAGACAGACAGA 58.343 43.478 0.00 0.00 0.00 3.41
2313 2365 4.260985 TCAAGCTCTAGACAGACAGAGAG 58.739 47.826 2.86 0.00 40.68 3.20
2314 2366 4.019771 TCAAGCTCTAGACAGACAGAGAGA 60.020 45.833 2.86 0.00 40.68 3.10
2315 2367 3.873910 AGCTCTAGACAGACAGAGAGAC 58.126 50.000 2.86 0.00 40.68 3.36
2316 2368 3.519510 AGCTCTAGACAGACAGAGAGACT 59.480 47.826 2.86 0.00 40.68 3.24
2318 2370 4.112634 CTCTAGACAGACAGAGAGACTCG 58.887 52.174 0.00 0.00 40.68 4.18
2319 2371 3.764972 TCTAGACAGACAGAGAGACTCGA 59.235 47.826 0.00 0.00 35.36 4.04
2320 2372 2.695359 AGACAGACAGAGAGACTCGAC 58.305 52.381 0.00 0.00 35.36 4.20
2321 2373 2.301870 AGACAGACAGAGAGACTCGACT 59.698 50.000 0.00 0.00 35.36 4.18
2322 2374 2.671396 GACAGACAGAGAGACTCGACTC 59.329 54.545 0.00 0.00 35.36 3.36
2323 2375 2.037902 ACAGACAGAGAGACTCGACTCA 59.962 50.000 5.90 0.00 39.14 3.41
2397 2452 3.420300 TTGGCGTGTATAACTTGGGAA 57.580 42.857 0.00 0.00 0.00 3.97
2495 2550 8.939201 TTTTGAAAACAATACAAATGCAGAGA 57.061 26.923 0.00 0.00 34.33 3.10
2513 2568 1.617755 GACTCACATGCACGTCACCG 61.618 60.000 0.00 0.00 40.83 4.94
2536 2591 0.585519 GAAACACACACGCACACGAC 60.586 55.000 0.00 0.00 43.93 4.34
2581 2636 1.222300 ATTGTACACGTGCGCTTTCA 58.778 45.000 17.22 3.26 0.00 2.69
2612 2667 2.298300 GATCGCACACGTGAAAGTTTG 58.702 47.619 25.01 10.03 41.18 2.93
2614 2669 1.465387 TCGCACACGTGAAAGTTTGTT 59.535 42.857 25.01 0.00 41.18 2.83
2629 2684 2.004583 TTGTTCGACAGATAAGCGGG 57.995 50.000 0.00 0.00 0.00 6.13
2676 2731 1.550130 TAAACCACCCGCCTCTCAGG 61.550 60.000 0.00 0.00 38.80 3.86
2714 2770 2.050144 ACCATGAGGCCAACGATAGAT 58.950 47.619 5.01 0.00 39.06 1.98
2740 2796 3.371965 ACTCCTCCCGAACATAGCTTAA 58.628 45.455 0.00 0.00 0.00 1.85
2751 2807 7.361713 CCCGAACATAGCTTAAAACTTTCATCA 60.362 37.037 0.00 0.00 0.00 3.07
2764 2820 7.934855 AAACTTTCATCATATTGTGCTCTCT 57.065 32.000 0.00 0.00 0.00 3.10
2770 2826 9.671279 TTTCATCATATTGTGCTCTCTAAAGAA 57.329 29.630 0.00 0.00 0.00 2.52
2780 2836 5.407084 GTGCTCTCTAAAGAACAACTCTTCC 59.593 44.000 0.00 0.00 44.00 3.46
2825 2882 6.127675 GCCCCCTTAAAATGAATTTACGTACA 60.128 38.462 0.00 0.00 33.26 2.90
2863 2920 2.698803 ACAAATCCCGTAAACCCGTAC 58.301 47.619 0.00 0.00 0.00 3.67
2864 2921 2.038295 ACAAATCCCGTAAACCCGTACA 59.962 45.455 0.00 0.00 0.00 2.90
2874 2931 3.949842 AAACCCGTACAGTAGGAGTTC 57.050 47.619 1.61 0.00 0.00 3.01
2928 2988 2.736719 CGCATGGATGAACTCGAACTCT 60.737 50.000 0.00 0.00 0.00 3.24
2943 3003 0.112412 ACTCTGGCCGACCCAAAATT 59.888 50.000 0.00 0.00 44.81 1.82
2952 3012 0.524414 GACCCAAAATTACGCCGCTT 59.476 50.000 0.00 0.00 0.00 4.68
2955 3015 1.131618 CCAAAATTACGCCGCTTCGC 61.132 55.000 0.00 0.00 0.00 4.70
3041 3102 4.687215 TTCGCCTGCTCGCTGCTT 62.687 61.111 0.00 0.00 43.37 3.91
3069 3132 0.745468 CGTAGCCAAGTCCCTACTCC 59.255 60.000 0.00 0.00 33.75 3.85
3071 3134 0.627451 TAGCCAAGTCCCTACTCCGA 59.373 55.000 0.00 0.00 33.75 4.55
3076 3139 2.086869 CAAGTCCCTACTCCGACGTTA 58.913 52.381 0.00 0.00 33.75 3.18
3147 3210 5.169295 GTTGCTCTAATGTACGAGAACCTT 58.831 41.667 0.00 0.00 0.00 3.50
3148 3211 6.327934 GTTGCTCTAATGTACGAGAACCTTA 58.672 40.000 0.00 0.00 0.00 2.69
3260 3324 2.371510 AGGATTTGCTAGAGATGCTCCC 59.628 50.000 0.00 0.00 0.00 4.30
3290 3354 2.094100 TTGGTGCCCAAAAATGAGGA 57.906 45.000 4.37 0.00 40.92 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.729965 CTAGCTCTGCCACTGCCCG 62.730 68.421 0.00 0.00 36.33 6.13
9 10 1.903877 TTCTAGCTCTGCCACTGCCC 61.904 60.000 0.00 0.00 36.33 5.36
10 11 0.036010 TTTCTAGCTCTGCCACTGCC 60.036 55.000 0.00 0.00 36.33 4.85
11 12 1.813513 TTTTCTAGCTCTGCCACTGC 58.186 50.000 0.00 0.00 38.26 4.40
12 13 3.188048 CAGTTTTTCTAGCTCTGCCACTG 59.812 47.826 0.00 0.00 0.00 3.66
13 14 3.071602 TCAGTTTTTCTAGCTCTGCCACT 59.928 43.478 0.00 0.00 0.00 4.00
14 15 3.403038 TCAGTTTTTCTAGCTCTGCCAC 58.597 45.455 0.00 0.00 0.00 5.01
15 16 3.769739 TCAGTTTTTCTAGCTCTGCCA 57.230 42.857 0.00 0.00 0.00 4.92
16 17 6.183360 CCTTATTCAGTTTTTCTAGCTCTGCC 60.183 42.308 0.00 0.00 0.00 4.85
17 18 6.183360 CCCTTATTCAGTTTTTCTAGCTCTGC 60.183 42.308 0.00 0.00 0.00 4.26
18 19 6.881602 ACCCTTATTCAGTTTTTCTAGCTCTG 59.118 38.462 0.00 0.00 0.00 3.35
19 20 6.881602 CACCCTTATTCAGTTTTTCTAGCTCT 59.118 38.462 0.00 0.00 0.00 4.09
20 21 6.094186 CCACCCTTATTCAGTTTTTCTAGCTC 59.906 42.308 0.00 0.00 0.00 4.09
21 22 5.946377 CCACCCTTATTCAGTTTTTCTAGCT 59.054 40.000 0.00 0.00 0.00 3.32
22 23 5.393135 GCCACCCTTATTCAGTTTTTCTAGC 60.393 44.000 0.00 0.00 0.00 3.42
23 24 5.125578 GGCCACCCTTATTCAGTTTTTCTAG 59.874 44.000 0.00 0.00 0.00 2.43
24 25 5.014202 GGCCACCCTTATTCAGTTTTTCTA 58.986 41.667 0.00 0.00 0.00 2.10
25 26 3.832490 GGCCACCCTTATTCAGTTTTTCT 59.168 43.478 0.00 0.00 0.00 2.52
26 27 3.576550 TGGCCACCCTTATTCAGTTTTTC 59.423 43.478 0.00 0.00 0.00 2.29
27 28 3.582164 TGGCCACCCTTATTCAGTTTTT 58.418 40.909 0.00 0.00 0.00 1.94
28 29 3.252554 TGGCCACCCTTATTCAGTTTT 57.747 42.857 0.00 0.00 0.00 2.43
29 30 2.990740 TGGCCACCCTTATTCAGTTT 57.009 45.000 0.00 0.00 0.00 2.66
30 31 2.557452 CCTTGGCCACCCTTATTCAGTT 60.557 50.000 3.88 0.00 0.00 3.16
31 32 1.005924 CCTTGGCCACCCTTATTCAGT 59.994 52.381 3.88 0.00 0.00 3.41
32 33 1.686115 CCCTTGGCCACCCTTATTCAG 60.686 57.143 3.88 0.00 0.00 3.02
33 34 0.334676 CCCTTGGCCACCCTTATTCA 59.665 55.000 3.88 0.00 0.00 2.57
34 35 0.397114 CCCCTTGGCCACCCTTATTC 60.397 60.000 3.88 0.00 0.00 1.75
35 36 0.853586 TCCCCTTGGCCACCCTTATT 60.854 55.000 3.88 0.00 0.00 1.40
36 37 0.853586 TTCCCCTTGGCCACCCTTAT 60.854 55.000 3.88 0.00 0.00 1.73
37 38 1.466386 TTCCCCTTGGCCACCCTTA 60.466 57.895 3.88 0.00 0.00 2.69
38 39 2.785389 TTCCCCTTGGCCACCCTT 60.785 61.111 3.88 0.00 0.00 3.95
39 40 3.268032 CTTCCCCTTGGCCACCCT 61.268 66.667 3.88 0.00 0.00 4.34
40 41 4.382541 CCTTCCCCTTGGCCACCC 62.383 72.222 3.88 0.00 0.00 4.61
41 42 2.168272 AATCCTTCCCCTTGGCCACC 62.168 60.000 3.88 0.00 0.00 4.61
42 43 0.972471 CAATCCTTCCCCTTGGCCAC 60.972 60.000 3.88 0.00 0.00 5.01
43 44 1.145900 TCAATCCTTCCCCTTGGCCA 61.146 55.000 0.00 0.00 0.00 5.36
44 45 0.262876 ATCAATCCTTCCCCTTGGCC 59.737 55.000 0.00 0.00 0.00 5.36
45 46 3.312736 TTATCAATCCTTCCCCTTGGC 57.687 47.619 0.00 0.00 0.00 4.52
46 47 4.871822 AGTTTATCAATCCTTCCCCTTGG 58.128 43.478 0.00 0.00 0.00 3.61
47 48 5.532779 GCTAGTTTATCAATCCTTCCCCTTG 59.467 44.000 0.00 0.00 0.00 3.61
48 49 5.433381 AGCTAGTTTATCAATCCTTCCCCTT 59.567 40.000 0.00 0.00 0.00 3.95
49 50 4.978388 AGCTAGTTTATCAATCCTTCCCCT 59.022 41.667 0.00 0.00 0.00 4.79
50 51 5.311844 AGCTAGTTTATCAATCCTTCCCC 57.688 43.478 0.00 0.00 0.00 4.81
51 52 5.532779 CCAAGCTAGTTTATCAATCCTTCCC 59.467 44.000 0.00 0.00 0.00 3.97
52 53 5.532779 CCCAAGCTAGTTTATCAATCCTTCC 59.467 44.000 0.00 0.00 0.00 3.46
53 54 5.532779 CCCCAAGCTAGTTTATCAATCCTTC 59.467 44.000 0.00 0.00 0.00 3.46
54 55 5.193728 TCCCCAAGCTAGTTTATCAATCCTT 59.806 40.000 0.00 0.00 0.00 3.36
55 56 4.726825 TCCCCAAGCTAGTTTATCAATCCT 59.273 41.667 0.00 0.00 0.00 3.24
56 57 5.048846 TCCCCAAGCTAGTTTATCAATCC 57.951 43.478 0.00 0.00 0.00 3.01
57 58 5.066593 CCTCCCCAAGCTAGTTTATCAATC 58.933 45.833 0.00 0.00 0.00 2.67
58 59 4.141158 CCCTCCCCAAGCTAGTTTATCAAT 60.141 45.833 0.00 0.00 0.00 2.57
59 60 3.202151 CCCTCCCCAAGCTAGTTTATCAA 59.798 47.826 0.00 0.00 0.00 2.57
60 61 2.777692 CCCTCCCCAAGCTAGTTTATCA 59.222 50.000 0.00 0.00 0.00 2.15
61 62 2.487445 GCCCTCCCCAAGCTAGTTTATC 60.487 54.545 0.00 0.00 0.00 1.75
62 63 1.495148 GCCCTCCCCAAGCTAGTTTAT 59.505 52.381 0.00 0.00 0.00 1.40
63 64 0.916809 GCCCTCCCCAAGCTAGTTTA 59.083 55.000 0.00 0.00 0.00 2.01
64 65 1.691823 GCCCTCCCCAAGCTAGTTT 59.308 57.895 0.00 0.00 0.00 2.66
65 66 2.309504 GGCCCTCCCCAAGCTAGTT 61.310 63.158 0.00 0.00 0.00 2.24
66 67 2.692741 GGCCCTCCCCAAGCTAGT 60.693 66.667 0.00 0.00 0.00 2.57
67 68 1.863155 TTTGGCCCTCCCCAAGCTAG 61.863 60.000 0.00 0.00 45.03 3.42
68 69 1.854979 TTTGGCCCTCCCCAAGCTA 60.855 57.895 0.00 0.00 45.03 3.32
69 70 3.192630 TTTGGCCCTCCCCAAGCT 61.193 61.111 0.00 0.00 45.03 3.74
70 71 2.997315 GTTTGGCCCTCCCCAAGC 60.997 66.667 0.00 0.00 45.03 4.01
71 72 2.283894 GGTTTGGCCCTCCCCAAG 60.284 66.667 0.00 0.00 45.03 3.61
72 73 2.716203 TTGGTTTGGCCCTCCCCAA 61.716 57.895 0.00 4.60 42.87 4.12
73 74 3.113477 TTGGTTTGGCCCTCCCCA 61.113 61.111 0.00 0.00 36.04 4.96
74 75 1.795951 TAGTTGGTTTGGCCCTCCCC 61.796 60.000 0.00 0.00 36.04 4.81
75 76 0.113580 TTAGTTGGTTTGGCCCTCCC 59.886 55.000 0.00 0.00 36.04 4.30
76 77 2.003937 TTTAGTTGGTTTGGCCCTCC 57.996 50.000 0.00 0.00 36.04 4.30
77 78 2.353704 GCATTTAGTTGGTTTGGCCCTC 60.354 50.000 0.00 0.00 36.04 4.30
78 79 1.623311 GCATTTAGTTGGTTTGGCCCT 59.377 47.619 0.00 0.00 36.04 5.19
79 80 1.346068 TGCATTTAGTTGGTTTGGCCC 59.654 47.619 0.00 0.00 36.04 5.80
80 81 2.829741 TGCATTTAGTTGGTTTGGCC 57.170 45.000 0.00 0.00 37.90 5.36
81 82 4.996758 AGATTTGCATTTAGTTGGTTTGGC 59.003 37.500 0.00 0.00 0.00 4.52
82 83 7.378181 ACTAGATTTGCATTTAGTTGGTTTGG 58.622 34.615 0.00 0.00 27.96 3.28
83 84 9.341899 GTACTAGATTTGCATTTAGTTGGTTTG 57.658 33.333 0.00 0.00 33.42 2.93
84 85 9.073475 TGTACTAGATTTGCATTTAGTTGGTTT 57.927 29.630 0.00 0.00 33.42 3.27
85 86 8.512138 GTGTACTAGATTTGCATTTAGTTGGTT 58.488 33.333 0.00 0.00 33.42 3.67
86 87 7.883311 AGTGTACTAGATTTGCATTTAGTTGGT 59.117 33.333 0.00 0.00 33.42 3.67
87 88 8.177663 CAGTGTACTAGATTTGCATTTAGTTGG 58.822 37.037 0.00 0.00 33.42 3.77
88 89 8.721478 ACAGTGTACTAGATTTGCATTTAGTTG 58.279 33.333 0.00 0.00 33.42 3.16
89 90 8.848474 ACAGTGTACTAGATTTGCATTTAGTT 57.152 30.769 0.00 0.00 33.42 2.24
90 91 8.848474 AACAGTGTACTAGATTTGCATTTAGT 57.152 30.769 0.00 0.00 35.15 2.24
94 95 8.237267 GCTAAAACAGTGTACTAGATTTGCATT 58.763 33.333 13.29 0.00 0.00 3.56
95 96 7.390440 TGCTAAAACAGTGTACTAGATTTGCAT 59.610 33.333 13.29 0.00 0.00 3.96
96 97 6.708502 TGCTAAAACAGTGTACTAGATTTGCA 59.291 34.615 13.29 10.34 0.00 4.08
97 98 7.129109 TGCTAAAACAGTGTACTAGATTTGC 57.871 36.000 13.29 8.54 0.00 3.68
105 106 9.938280 TGAGTATTTATGCTAAAACAGTGTACT 57.062 29.630 0.00 0.00 0.00 2.73
107 108 9.938280 ACTGAGTATTTATGCTAAAACAGTGTA 57.062 29.630 0.00 0.00 34.39 2.90
108 109 8.721478 CACTGAGTATTTATGCTAAAACAGTGT 58.279 33.333 0.41 0.00 43.20 3.55
110 111 8.848474 ACACTGAGTATTTATGCTAAAACAGT 57.152 30.769 0.00 0.00 35.70 3.55
111 112 9.760660 GAACACTGAGTATTTATGCTAAAACAG 57.239 33.333 0.00 0.00 0.00 3.16
112 113 9.502091 AGAACACTGAGTATTTATGCTAAAACA 57.498 29.630 0.00 0.00 0.00 2.83
116 117 9.803315 CACTAGAACACTGAGTATTTATGCTAA 57.197 33.333 0.00 0.00 0.00 3.09
117 118 9.185680 TCACTAGAACACTGAGTATTTATGCTA 57.814 33.333 0.00 0.00 0.00 3.49
118 119 8.067751 TCACTAGAACACTGAGTATTTATGCT 57.932 34.615 0.00 0.00 0.00 3.79
119 120 8.703604 TTCACTAGAACACTGAGTATTTATGC 57.296 34.615 0.00 0.00 0.00 3.14
123 124 9.391006 TGTTTTTCACTAGAACACTGAGTATTT 57.609 29.630 0.00 0.00 32.39 1.40
124 125 8.958119 TGTTTTTCACTAGAACACTGAGTATT 57.042 30.769 0.00 0.00 32.39 1.89
125 126 9.561069 AATGTTTTTCACTAGAACACTGAGTAT 57.439 29.630 0.00 0.00 36.25 2.12
126 127 8.826710 CAATGTTTTTCACTAGAACACTGAGTA 58.173 33.333 0.00 0.00 33.71 2.59
127 128 7.679638 GCAATGTTTTTCACTAGAACACTGAGT 60.680 37.037 6.82 0.00 33.71 3.41
128 129 6.634436 GCAATGTTTTTCACTAGAACACTGAG 59.366 38.462 6.82 0.00 33.71 3.35
129 130 6.094742 TGCAATGTTTTTCACTAGAACACTGA 59.905 34.615 6.82 0.00 33.71 3.41
130 131 6.264832 TGCAATGTTTTTCACTAGAACACTG 58.735 36.000 0.00 0.00 36.25 3.66
131 132 6.449635 TGCAATGTTTTTCACTAGAACACT 57.550 33.333 0.00 0.00 36.25 3.55
132 133 7.097342 CATGCAATGTTTTTCACTAGAACAC 57.903 36.000 0.00 0.00 40.20 3.32
149 150 1.456331 GCTAGGGCCCACATGCAAT 60.456 57.895 27.56 2.06 0.00 3.56
150 151 2.044053 GCTAGGGCCCACATGCAA 60.044 61.111 27.56 0.00 0.00 4.08
151 152 3.016971 AGCTAGGGCCCACATGCA 61.017 61.111 27.56 0.00 39.73 3.96
152 153 2.517875 CAGCTAGGGCCCACATGC 60.518 66.667 27.56 21.20 39.73 4.06
153 154 2.194056 CCAGCTAGGGCCCACATG 59.806 66.667 27.56 16.57 39.73 3.21
161 162 3.801997 CAGGGGTGCCAGCTAGGG 61.802 72.222 0.00 0.00 38.09 3.53
162 163 3.011517 ACAGGGGTGCCAGCTAGG 61.012 66.667 0.00 0.00 41.84 3.02
163 164 1.965754 GAGACAGGGGTGCCAGCTAG 61.966 65.000 0.00 0.00 0.00 3.42
164 165 1.990060 GAGACAGGGGTGCCAGCTA 60.990 63.158 0.00 0.00 0.00 3.32
165 166 3.325753 GAGACAGGGGTGCCAGCT 61.326 66.667 0.00 0.00 0.00 4.24
166 167 4.416738 GGAGACAGGGGTGCCAGC 62.417 72.222 0.00 0.00 0.00 4.85
167 168 4.087892 CGGAGACAGGGGTGCCAG 62.088 72.222 0.00 0.00 0.00 4.85
201 202 3.190849 CAGATGTGCCGCGGACAG 61.191 66.667 33.48 14.18 0.00 3.51
202 203 4.758251 CCAGATGTGCCGCGGACA 62.758 66.667 33.48 28.46 0.00 4.02
203 204 4.760047 ACCAGATGTGCCGCGGAC 62.760 66.667 33.48 23.73 0.00 4.79
204 205 4.451150 GACCAGATGTGCCGCGGA 62.451 66.667 33.48 8.89 0.00 5.54
205 206 4.457496 AGACCAGATGTGCCGCGG 62.457 66.667 24.05 24.05 0.00 6.46
206 207 2.887568 GAGACCAGATGTGCCGCG 60.888 66.667 0.00 0.00 0.00 6.46
207 208 2.887568 CGAGACCAGATGTGCCGC 60.888 66.667 0.00 0.00 0.00 6.53
208 209 2.887568 GCGAGACCAGATGTGCCG 60.888 66.667 0.00 0.00 0.00 5.69
209 210 2.512515 GGCGAGACCAGATGTGCC 60.513 66.667 0.00 0.00 38.86 5.01
210 211 2.512515 GGGCGAGACCAGATGTGC 60.513 66.667 0.00 0.00 42.05 4.57
211 212 2.202797 CGGGCGAGACCAGATGTG 60.203 66.667 0.00 0.00 42.05 3.21
212 213 4.148825 GCGGGCGAGACCAGATGT 62.149 66.667 0.00 0.00 42.05 3.06
224 225 3.869272 CAGAATGTGCTCGCGGGC 61.869 66.667 27.48 27.48 0.00 6.13
225 226 3.197790 CCAGAATGTGCTCGCGGG 61.198 66.667 6.13 2.60 0.00 6.13
226 227 3.197790 CCCAGAATGTGCTCGCGG 61.198 66.667 6.13 0.00 0.00 6.46
227 228 2.434884 ACCCAGAATGTGCTCGCG 60.435 61.111 0.00 0.00 0.00 5.87
228 229 1.237285 AACACCCAGAATGTGCTCGC 61.237 55.000 0.00 0.00 37.22 5.03
229 230 0.518636 CAACACCCAGAATGTGCTCG 59.481 55.000 0.00 0.00 37.22 5.03
230 231 0.883833 CCAACACCCAGAATGTGCTC 59.116 55.000 0.00 0.00 37.22 4.26
231 232 0.478072 TCCAACACCCAGAATGTGCT 59.522 50.000 0.00 0.00 37.22 4.40
232 233 1.549203 ATCCAACACCCAGAATGTGC 58.451 50.000 0.00 0.00 37.22 4.57
233 234 3.321682 ACAAATCCAACACCCAGAATGTG 59.678 43.478 0.00 0.00 39.63 3.21
234 235 3.573967 GACAAATCCAACACCCAGAATGT 59.426 43.478 0.00 0.00 0.00 2.71
235 236 3.056607 GGACAAATCCAACACCCAGAATG 60.057 47.826 0.00 0.00 45.47 2.67
236 237 3.165071 GGACAAATCCAACACCCAGAAT 58.835 45.455 0.00 0.00 45.47 2.40
237 238 2.593026 GGACAAATCCAACACCCAGAA 58.407 47.619 0.00 0.00 45.47 3.02
238 239 2.286365 GGACAAATCCAACACCCAGA 57.714 50.000 0.00 0.00 45.47 3.86
248 249 1.165270 CAACCGGACTGGACAAATCC 58.835 55.000 9.46 0.00 46.48 3.01
249 250 1.892209 ACAACCGGACTGGACAAATC 58.108 50.000 9.46 0.00 42.00 2.17
250 251 3.495434 TTACAACCGGACTGGACAAAT 57.505 42.857 9.46 0.00 42.00 2.32
251 252 3.278668 TTTACAACCGGACTGGACAAA 57.721 42.857 9.46 4.88 42.00 2.83
252 253 3.404899 GATTTACAACCGGACTGGACAA 58.595 45.455 9.46 0.22 42.00 3.18
253 254 2.289819 GGATTTACAACCGGACTGGACA 60.290 50.000 9.46 0.00 42.00 4.02
254 255 2.027469 AGGATTTACAACCGGACTGGAC 60.027 50.000 9.46 0.00 42.00 4.02
255 256 2.235402 GAGGATTTACAACCGGACTGGA 59.765 50.000 9.46 0.00 42.00 3.86
256 257 2.236395 AGAGGATTTACAACCGGACTGG 59.764 50.000 9.46 0.00 46.41 4.00
257 258 3.611766 AGAGGATTTACAACCGGACTG 57.388 47.619 9.46 7.73 0.00 3.51
258 259 5.750352 TTTAGAGGATTTACAACCGGACT 57.250 39.130 9.46 0.00 0.00 3.85
259 260 6.806388 TTTTTAGAGGATTTACAACCGGAC 57.194 37.500 9.46 0.00 0.00 4.79
280 281 6.040842 TCAAGCTAGTGAGGCAAATTCTTTTT 59.959 34.615 0.00 0.00 0.00 1.94
281 282 5.536161 TCAAGCTAGTGAGGCAAATTCTTTT 59.464 36.000 0.00 0.00 0.00 2.27
282 283 5.072741 TCAAGCTAGTGAGGCAAATTCTTT 58.927 37.500 0.00 0.00 0.00 2.52
283 284 4.655963 TCAAGCTAGTGAGGCAAATTCTT 58.344 39.130 0.00 0.00 0.00 2.52
284 285 4.292186 TCAAGCTAGTGAGGCAAATTCT 57.708 40.909 0.00 0.00 0.00 2.40
285 286 5.376854 TTTCAAGCTAGTGAGGCAAATTC 57.623 39.130 0.00 0.00 0.00 2.17
286 287 5.789643 TTTTCAAGCTAGTGAGGCAAATT 57.210 34.783 0.00 0.00 0.00 1.82
287 288 5.337009 CCATTTTCAAGCTAGTGAGGCAAAT 60.337 40.000 0.00 0.00 0.00 2.32
288 289 4.022068 CCATTTTCAAGCTAGTGAGGCAAA 60.022 41.667 0.00 0.00 0.00 3.68
289 290 3.507233 CCATTTTCAAGCTAGTGAGGCAA 59.493 43.478 0.00 0.00 0.00 4.52
290 291 3.084039 CCATTTTCAAGCTAGTGAGGCA 58.916 45.455 0.00 0.00 0.00 4.75
291 292 3.347216 TCCATTTTCAAGCTAGTGAGGC 58.653 45.455 0.00 0.00 0.00 4.70
292 293 5.964958 TTTCCATTTTCAAGCTAGTGAGG 57.035 39.130 0.00 0.00 0.00 3.86
293 294 6.974965 ACTTTTCCATTTTCAAGCTAGTGAG 58.025 36.000 0.00 0.00 0.00 3.51
294 295 6.959639 ACTTTTCCATTTTCAAGCTAGTGA 57.040 33.333 0.00 0.00 0.00 3.41
295 296 9.528018 TTTTACTTTTCCATTTTCAAGCTAGTG 57.472 29.630 0.00 0.00 0.00 2.74
333 334 6.397272 GGTGCATTAAGAAAATTGTGATGGA 58.603 36.000 0.00 0.00 0.00 3.41
335 336 5.581874 GGGGTGCATTAAGAAAATTGTGATG 59.418 40.000 0.00 0.00 0.00 3.07
362 364 9.941325 AATAGATAGATGTTGATGATGGAGAAC 57.059 33.333 0.00 0.00 0.00 3.01
373 375 4.220821 GGCGAGGGAATAGATAGATGTTGA 59.779 45.833 0.00 0.00 0.00 3.18
381 383 1.334160 TTGCGGCGAGGGAATAGATA 58.666 50.000 12.98 0.00 0.00 1.98
385 387 3.251332 TTTTTGCGGCGAGGGAATA 57.749 47.368 12.98 0.00 0.00 1.75
405 407 9.479549 AGATGGTTTCTGTGGATATATGTTTTT 57.520 29.630 0.00 0.00 31.79 1.94
406 408 8.906867 CAGATGGTTTCTGTGGATATATGTTTT 58.093 33.333 0.00 0.00 45.79 2.43
407 409 8.455903 CAGATGGTTTCTGTGGATATATGTTT 57.544 34.615 0.00 0.00 45.79 2.83
457 459 2.050350 CGCGTTCCAGGGGTAGAGA 61.050 63.158 0.00 0.00 0.00 3.10
538 540 2.501865 CGAAAAGCGGCGCCTTTC 60.502 61.111 34.34 34.34 36.13 2.62
576 579 3.775654 GGAGTCAGCAGGGACGGG 61.776 72.222 0.00 0.00 42.62 5.28
621 624 1.719709 CACGTATGCCTCGAGTCGA 59.280 57.895 15.64 15.64 0.00 4.20
635 638 1.857318 CGTCTCACTCTCCTGCACGT 61.857 60.000 0.00 0.00 0.00 4.49
712 741 1.045911 TGGTGGAGGGTTTGGTTTGC 61.046 55.000 0.00 0.00 0.00 3.68
758 787 0.107643 TGTGGGATTCGTGTCTGCAA 59.892 50.000 0.00 0.00 0.00 4.08
763 792 0.605319 TGGCTTGTGGGATTCGTGTC 60.605 55.000 0.00 0.00 0.00 3.67
792 821 0.716108 GAAGAACACACGGCTCGATG 59.284 55.000 1.50 2.71 0.00 3.84
866 895 2.588620 GGTCGATGACTATCTGGACCT 58.411 52.381 0.00 0.00 39.14 3.85
1113 1146 1.878522 CCCGAAGATGAAGGACGCG 60.879 63.158 3.53 3.53 0.00 6.01
1290 1323 8.452534 AGTACTTGAAAATGTTTCGTGTTACAA 58.547 29.630 0.00 0.00 0.00 2.41
1369 1411 6.913873 ACTTTGCGTTGTTTCTTACTAGAA 57.086 33.333 0.00 0.00 38.61 2.10
1370 1412 6.711579 CAACTTTGCGTTGTTTCTTACTAGA 58.288 36.000 0.00 0.00 46.23 2.43
1371 1413 6.953091 CAACTTTGCGTTGTTTCTTACTAG 57.047 37.500 0.00 0.00 46.23 2.57
1388 1430 2.358898 GTGACACAGTGATGGCAACTTT 59.641 45.455 7.81 0.00 40.05 2.66
1389 1431 1.949525 GTGACACAGTGATGGCAACTT 59.050 47.619 7.81 0.00 40.05 2.66
1403 1445 6.997222 AGTTTACGTCTGTTTTAAGTGACAC 58.003 36.000 0.00 0.00 0.00 3.67
1415 1457 4.710324 TGGAAAATGGAGTTTACGTCTGT 58.290 39.130 0.00 0.00 0.00 3.41
1420 1462 2.752903 CCCCTGGAAAATGGAGTTTACG 59.247 50.000 0.00 0.00 0.00 3.18
1435 1478 4.201122 GCCCAGCATCTCCCCTGG 62.201 72.222 0.00 0.00 46.49 4.45
1965 2008 2.835431 ATGAGGAGGTCGCGGAGG 60.835 66.667 6.13 0.00 0.00 4.30
2196 2248 1.517832 CTTCTCGCTGGGGTGGTAG 59.482 63.158 0.00 0.00 0.00 3.18
2199 2251 4.785453 GCCTTCTCGCTGGGGTGG 62.785 72.222 0.00 0.00 0.00 4.61
2202 2254 4.033776 TTGGCCTTCTCGCTGGGG 62.034 66.667 3.32 0.00 0.00 4.96
2223 2275 1.148157 CGATGTACTTGGCGAGCAGG 61.148 60.000 0.37 0.00 0.00 4.85
2259 2311 2.037772 GAGGTTCATGGGCGAGATGTAT 59.962 50.000 0.00 0.00 0.00 2.29
2268 2320 1.034292 GCTTCCTGAGGTTCATGGGC 61.034 60.000 0.00 0.00 0.00 5.36
2304 2356 2.565391 TCTGAGTCGAGTCTCTCTGTCT 59.435 50.000 20.51 0.00 35.68 3.41
2307 2359 2.539688 CGATCTGAGTCGAGTCTCTCTG 59.460 54.545 20.51 10.81 44.06 3.35
2310 2362 2.971660 TCGATCTGAGTCGAGTCTCT 57.028 50.000 20.51 5.75 44.87 3.10
2323 2375 1.067821 GGAACGAAGCCAGATCGATCT 59.932 52.381 22.32 22.32 42.76 2.75
2382 2437 9.950680 CATCAAATATGTTCCCAAGTTATACAC 57.049 33.333 0.00 0.00 0.00 2.90
2397 2452 7.749666 AGCTAGGGTTCATACATCAAATATGT 58.250 34.615 0.00 0.00 32.75 2.29
2495 2550 4.361253 GGTGACGTGCATGTGAGT 57.639 55.556 18.17 0.00 0.00 3.41
2513 2568 0.646381 TGTGCGTGTGTGTTTCGTAC 59.354 50.000 0.00 0.00 39.70 3.67
2581 2636 0.611618 TGTGCGATCCAATTGCCCTT 60.612 50.000 0.00 0.00 38.97 3.95
2612 2667 1.557651 GACCCGCTTATCTGTCGAAC 58.442 55.000 0.00 0.00 0.00 3.95
2614 2669 1.721664 CGGACCCGCTTATCTGTCGA 61.722 60.000 0.00 0.00 0.00 4.20
2629 2684 3.195698 GATGCCAGCGGTTCGGAC 61.196 66.667 0.00 0.00 0.00 4.79
2642 2697 1.377987 TTTACCCTGTGGCGGATGC 60.378 57.895 0.00 0.00 41.71 3.91
2648 2703 4.090723 GGTGGTTTACCCTGTGGC 57.909 61.111 0.00 0.00 44.15 5.01
2714 2770 5.145564 AGCTATGTTCGGGAGGAGTTATTA 58.854 41.667 0.00 0.00 0.00 0.98
2740 2796 7.934855 AGAGAGCACAATATGATGAAAGTTT 57.065 32.000 0.00 0.00 0.00 2.66
2751 2807 8.317679 AGAGTTGTTCTTTAGAGAGCACAATAT 58.682 33.333 0.00 0.00 41.95 1.28
2764 2820 7.777910 TGAGATTTTGGGAAGAGTTGTTCTTTA 59.222 33.333 0.00 0.00 46.12 1.85
2770 2826 5.532779 GTCTTGAGATTTTGGGAAGAGTTGT 59.467 40.000 0.00 0.00 0.00 3.32
2780 2836 4.240096 GGCATGTTGTCTTGAGATTTTGG 58.760 43.478 0.00 0.00 0.00 3.28
2825 2882 3.469008 TGTTCCGTCTGATGTTTCACT 57.531 42.857 0.00 0.00 0.00 3.41
2831 2888 2.711542 GGGATTTGTTCCGTCTGATGT 58.288 47.619 0.00 0.00 46.52 3.06
2896 2956 0.599466 ATCCATGCGTGCATCTCGAG 60.599 55.000 5.93 5.93 33.90 4.04
2900 2960 1.019673 GTTCATCCATGCGTGCATCT 58.980 50.000 3.96 0.00 33.90 2.90
2903 2963 1.360931 CGAGTTCATCCATGCGTGCA 61.361 55.000 0.00 0.00 0.00 4.57
2928 2988 1.587933 GCGTAATTTTGGGTCGGCCA 61.588 55.000 9.07 0.00 36.17 5.36
2955 3015 2.279985 AGCATCGCCAGAGCATCG 60.280 61.111 0.00 0.00 42.67 3.84
2956 3016 1.960250 GGAGCATCGCCAGAGCATC 60.960 63.158 0.00 0.00 39.83 3.91
2957 3017 2.110627 GGAGCATCGCCAGAGCAT 59.889 61.111 0.00 0.00 39.83 3.79
2958 3018 4.519437 CGGAGCATCGCCAGAGCA 62.519 66.667 0.00 0.00 39.83 4.26
2976 3037 3.628646 ATTGGAGCACAGGACGGGC 62.629 63.158 0.00 0.00 0.00 6.13
2981 3042 0.622136 AGCATCATTGGAGCACAGGA 59.378 50.000 4.51 0.00 0.00 3.86
2984 3045 0.328926 TGGAGCATCATTGGAGCACA 59.671 50.000 4.51 1.13 36.25 4.57
3010 3071 2.032528 CGAAGGAGCTGGGCAACA 59.967 61.111 0.00 0.00 39.74 3.33
3012 3073 4.722700 GGCGAAGGAGCTGGGCAA 62.723 66.667 0.00 0.00 37.29 4.52
3017 3078 2.511145 GAGCAGGCGAAGGAGCTG 60.511 66.667 0.00 0.00 37.48 4.24
3069 3132 3.383761 ACCTGTAAACCAGTTAACGTCG 58.616 45.455 0.00 0.00 39.74 5.12
3071 3134 4.129380 GGAACCTGTAAACCAGTTAACGT 58.871 43.478 0.00 0.00 39.74 3.99
3158 3222 5.608437 AGATCCTGTAAAATAGCAGATCCCA 59.392 40.000 0.00 0.00 34.87 4.37
3244 3308 2.401568 TCATGGGAGCATCTCTAGCAA 58.598 47.619 0.00 0.00 35.73 3.91


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

AutoCloner maintained by Alex Coulton.