Multiple sequence alignment - TraesCS6D01G073300

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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 TraesCS6D01G073300 chr6D 100.000 2243 0 0 1 2243 37460005 37462247 0.000000e+00 4143.0
1 TraesCS6D01G073300 chr6D 82.480 508 59 18 929 1424 37454969 37455458 3.450000e-113 418.0
2 TraesCS6D01G073300 chr6D 81.343 268 44 4 996 1263 37531595 37531856 1.740000e-51 213.0
3 TraesCS6D01G073300 chr6B 82.931 1201 84 44 1085 2241 87630589 87631712 0.000000e+00 970.0
4 TraesCS6D01G073300 chr6B 93.846 260 4 4 329 581 87591865 87592119 4.520000e-102 381.0
5 TraesCS6D01G073300 chr6B 95.706 163 5 1 927 1089 87597180 87597340 6.140000e-66 261.0
6 TraesCS6D01G073300 chr6B 80.805 323 44 5 941 1263 87746258 87746562 1.040000e-58 237.0
7 TraesCS6D01G073300 chr6B 84.064 251 23 6 686 919 661074865 661075115 2.240000e-55 226.0
8 TraesCS6D01G073300 chr6B 95.968 124 3 2 215 336 87591663 87591786 1.360000e-47 200.0
9 TraesCS6D01G073300 chr6B 82.479 234 29 8 928 1149 87586233 87586466 6.320000e-46 195.0
10 TraesCS6D01G073300 chr6B 92.553 94 5 1 596 687 87597089 87597182 1.400000e-27 134.0
11 TraesCS6D01G073300 chr6A 88.677 786 31 23 923 1707 48881111 48881839 0.000000e+00 905.0
12 TraesCS6D01G073300 chr6A 84.704 523 28 20 213 684 48880587 48881108 2.020000e-130 475.0
13 TraesCS6D01G073300 chr6A 81.460 507 68 17 928 1429 48870727 48871212 2.090000e-105 392.0
14 TraesCS6D01G073300 chr6A 84.597 409 33 17 1703 2085 48882112 48882516 1.630000e-101 379.0
15 TraesCS6D01G073300 chr6A 80.495 323 45 10 941 1263 48912891 48913195 4.820000e-57 231.0
16 TraesCS6D01G073300 chr6A 83.636 110 15 3 405 513 48870395 48870502 1.420000e-17 100.0
17 TraesCS6D01G073300 chr5B 93.023 215 13 2 1 214 678575629 678575842 1.670000e-81 313.0
18 TraesCS6D01G073300 chr4A 90.789 228 20 1 1 227 510638003 510637776 1.010000e-78 303.0
19 TraesCS6D01G073300 chr4A 89.231 195 20 1 686 879 455024109 455023915 2.230000e-60 243.0
20 TraesCS6D01G073300 chr5A 88.608 237 23 4 686 919 216994682 216994917 3.650000e-73 285.0
21 TraesCS6D01G073300 chr1D 85.560 277 27 8 686 957 411749098 411748830 6.100000e-71 278.0
22 TraesCS6D01G073300 chr7B 90.206 194 18 1 686 878 514515240 514515433 3.700000e-63 252.0
23 TraesCS6D01G073300 chr7B 86.316 95 11 1 681 773 598296142 598296236 3.940000e-18 102.0
24 TraesCS6D01G073300 chr5D 89.500 200 19 2 682 880 317454224 317454026 3.700000e-63 252.0
25 TraesCS6D01G073300 chr7A 89.796 196 18 1 686 879 202997238 202997043 1.330000e-62 250.0
26 TraesCS6D01G073300 chr4D 90.860 186 15 2 1 184 86779777 86779962 4.780000e-62 248.0
27 TraesCS6D01G073300 chr4D 91.379 58 1 3 877 932 468268676 468268621 2.390000e-10 76.8
28 TraesCS6D01G073300 chr4D 92.308 39 3 0 186 224 86779953 86779991 3.110000e-04 56.5
29 TraesCS6D01G073300 chr2B 88.293 205 22 2 686 888 772348760 772348556 6.190000e-61 244.0
30 TraesCS6D01G073300 chr2B 88.557 201 21 1 681 879 357919823 357919623 2.230000e-60 243.0
31 TraesCS6D01G073300 chr3D 89.231 195 20 1 686 879 226986763 226986569 2.230000e-60 243.0
32 TraesCS6D01G073300 chr2D 80.224 268 32 9 684 932 180881755 180881490 4.920000e-42 182.0
33 TraesCS6D01G073300 chr3A 77.866 253 39 4 684 919 161457160 161457412 8.350000e-30 141.0
34 TraesCS6D01G073300 chr1B 84.615 91 12 2 685 773 538625376 538625466 3.070000e-14 89.8
35 TraesCS6D01G073300 chr1B 73.208 265 53 6 680 926 553552766 553553030 1.850000e-11 80.5
36 TraesCS6D01G073300 chr3B 92.727 55 3 1 163 216 581035239 581035293 6.640000e-11 78.7


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 TraesCS6D01G073300 chr6D 37460005 37462247 2242 False 4143.000000 4143 100.000000 1 2243 1 chr6D.!!$F2 2242
1 TraesCS6D01G073300 chr6B 87630589 87631712 1123 False 970.000000 970 82.931000 1085 2241 1 chr6B.!!$F2 1156
2 TraesCS6D01G073300 chr6A 48880587 48882516 1929 False 586.333333 905 85.992667 213 2085 3 chr6A.!!$F3 1872
3 TraesCS6D01G073300 chr6A 48870395 48871212 817 False 246.000000 392 82.548000 405 1429 2 chr6A.!!$F2 1024

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
142 143 0.109723 TCTGAAAAACCGGGGTGGAG 59.89 55.0 6.32 0.0 42.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1492 1573 0.671163 TAAATGAAGAACGGCGCGGT 60.671 50.0 15.6 15.6 0.0 5.68 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.748647 TCATCGCGTCGTGGGAGA 60.749 61.111 5.77 0.00 43.48 3.71
18 19 2.278206 CATCGCGTCGTGGGAGAG 60.278 66.667 5.77 0.00 43.48 3.20
19 20 4.194720 ATCGCGTCGTGGGAGAGC 62.195 66.667 5.77 0.00 43.48 4.09
35 36 4.176752 GCCCGGGCGAATTCTCCT 62.177 66.667 33.60 0.00 0.00 3.69
36 37 2.203070 CCCGGGCGAATTCTCCTG 60.203 66.667 8.08 15.28 0.00 3.86
37 38 2.203070 CCGGGCGAATTCTCCTGG 60.203 66.667 24.58 24.58 40.55 4.45
38 39 2.897350 CGGGCGAATTCTCCTGGC 60.897 66.667 14.55 5.83 0.00 4.85
39 40 2.272146 GGGCGAATTCTCCTGGCA 59.728 61.111 13.99 0.00 0.00 4.92
40 41 1.152881 GGGCGAATTCTCCTGGCAT 60.153 57.895 13.99 0.00 0.00 4.40
41 42 1.450531 GGGCGAATTCTCCTGGCATG 61.451 60.000 13.99 0.00 0.00 4.06
42 43 1.358046 GCGAATTCTCCTGGCATGC 59.642 57.895 9.90 9.90 0.00 4.06
43 44 1.645455 CGAATTCTCCTGGCATGCG 59.355 57.895 12.44 0.00 0.00 4.73
44 45 1.779025 CGAATTCTCCTGGCATGCGG 61.779 60.000 12.44 8.56 0.00 5.69
45 46 0.464373 GAATTCTCCTGGCATGCGGA 60.464 55.000 12.44 12.76 0.00 5.54
46 47 0.465097 AATTCTCCTGGCATGCGGAG 60.465 55.000 27.02 27.02 46.52 4.63
47 48 2.335092 ATTCTCCTGGCATGCGGAGG 62.335 60.000 30.06 26.60 45.46 4.30
48 49 3.790437 CTCCTGGCATGCGGAGGT 61.790 66.667 25.87 0.00 42.46 3.85
49 50 3.746949 CTCCTGGCATGCGGAGGTC 62.747 68.421 25.87 7.89 42.46 3.85
50 51 4.100084 CCTGGCATGCGGAGGTCA 62.100 66.667 21.13 0.00 0.00 4.02
51 52 2.513204 CTGGCATGCGGAGGTCAG 60.513 66.667 9.18 9.18 0.00 3.51
52 53 4.100084 TGGCATGCGGAGGTCAGG 62.100 66.667 12.44 0.00 0.00 3.86
53 54 4.864334 GGCATGCGGAGGTCAGGG 62.864 72.222 12.44 0.00 0.00 4.45
54 55 4.101448 GCATGCGGAGGTCAGGGT 62.101 66.667 0.00 0.00 0.00 4.34
55 56 2.124983 CATGCGGAGGTCAGGGTG 60.125 66.667 0.00 0.00 0.00 4.61
56 57 2.284625 ATGCGGAGGTCAGGGTGA 60.285 61.111 0.00 0.00 0.00 4.02
57 58 1.918293 ATGCGGAGGTCAGGGTGAA 60.918 57.895 0.00 0.00 0.00 3.18
58 59 2.047179 GCGGAGGTCAGGGTGAAC 60.047 66.667 0.00 0.00 33.32 3.18
59 60 2.261671 CGGAGGTCAGGGTGAACG 59.738 66.667 0.00 0.00 39.55 3.95
60 61 2.663196 GGAGGTCAGGGTGAACGG 59.337 66.667 0.00 0.00 39.55 4.44
61 62 2.047179 GAGGTCAGGGTGAACGGC 60.047 66.667 0.00 0.00 39.55 5.68
62 63 3.607370 GAGGTCAGGGTGAACGGCC 62.607 68.421 0.00 0.00 39.55 6.13
63 64 4.717313 GGTCAGGGTGAACGGCCC 62.717 72.222 0.00 0.00 46.43 5.80
70 71 4.419921 GTGAACGGCCCGGGGATT 62.420 66.667 25.28 7.36 0.00 3.01
71 72 3.653078 TGAACGGCCCGGGGATTT 61.653 61.111 25.28 5.52 0.00 2.17
72 73 2.361992 GAACGGCCCGGGGATTTT 60.362 61.111 25.28 5.11 0.00 1.82
73 74 2.678580 AACGGCCCGGGGATTTTG 60.679 61.111 25.28 2.97 0.00 2.44
74 75 4.751820 ACGGCCCGGGGATTTTGG 62.752 66.667 25.28 0.45 0.00 3.28
76 77 4.068887 GGCCCGGGGATTTTGGGA 62.069 66.667 25.28 0.00 46.41 4.37
77 78 2.442087 GCCCGGGGATTTTGGGAG 60.442 66.667 25.28 0.00 46.41 4.30
78 79 2.278738 CCCGGGGATTTTGGGAGG 59.721 66.667 14.71 0.00 46.41 4.30
79 80 2.313427 CCCGGGGATTTTGGGAGGA 61.313 63.158 14.71 0.00 46.41 3.71
80 81 1.655114 CCCGGGGATTTTGGGAGGAT 61.655 60.000 14.71 0.00 46.41 3.24
81 82 0.178990 CCGGGGATTTTGGGAGGATC 60.179 60.000 0.00 0.00 0.00 3.36
82 83 0.535102 CGGGGATTTTGGGAGGATCG 60.535 60.000 0.00 0.00 34.37 3.69
83 84 0.178990 GGGGATTTTGGGAGGATCGG 60.179 60.000 0.00 0.00 34.37 4.18
84 85 0.178990 GGGATTTTGGGAGGATCGGG 60.179 60.000 0.00 0.00 34.37 5.14
85 86 0.178990 GGATTTTGGGAGGATCGGGG 60.179 60.000 0.00 0.00 34.37 5.73
86 87 0.823769 GATTTTGGGAGGATCGGGGC 60.824 60.000 0.00 0.00 34.37 5.80
87 88 2.624674 ATTTTGGGAGGATCGGGGCG 62.625 60.000 0.00 0.00 34.37 6.13
88 89 4.789173 TTGGGAGGATCGGGGCGA 62.789 66.667 0.00 0.00 41.13 5.54
90 91 4.916314 GGGAGGATCGGGGCGAGA 62.916 72.222 0.00 0.00 39.91 4.04
91 92 2.838225 GGAGGATCGGGGCGAGAA 60.838 66.667 0.00 0.00 39.91 2.87
92 93 2.432300 GGAGGATCGGGGCGAGAAA 61.432 63.158 0.00 0.00 39.91 2.52
93 94 1.520666 GAGGATCGGGGCGAGAAAA 59.479 57.895 0.00 0.00 39.91 2.29
94 95 0.810426 GAGGATCGGGGCGAGAAAAC 60.810 60.000 0.00 0.00 39.91 2.43
95 96 1.818363 GGATCGGGGCGAGAAAACC 60.818 63.158 0.00 0.00 39.91 3.27
96 97 1.818363 GATCGGGGCGAGAAAACCC 60.818 63.158 0.00 0.00 46.24 4.11
97 98 2.253403 GATCGGGGCGAGAAAACCCT 62.253 60.000 0.00 0.00 46.19 4.34
98 99 1.848886 ATCGGGGCGAGAAAACCCTT 61.849 55.000 0.00 0.00 46.19 3.95
99 100 1.602605 CGGGGCGAGAAAACCCTTT 60.603 57.895 0.00 0.00 46.19 3.11
100 101 1.583495 CGGGGCGAGAAAACCCTTTC 61.583 60.000 0.00 0.00 46.19 2.62
101 102 1.248785 GGGGCGAGAAAACCCTTTCC 61.249 60.000 0.00 0.00 46.19 3.13
102 103 0.538746 GGGCGAGAAAACCCTTTCCA 60.539 55.000 0.00 0.00 43.36 3.53
103 104 0.596577 GGCGAGAAAACCCTTTCCAC 59.403 55.000 0.00 0.00 41.72 4.02
104 105 0.237498 GCGAGAAAACCCTTTCCACG 59.763 55.000 0.00 9.06 41.72 4.94
105 106 1.873698 CGAGAAAACCCTTTCCACGA 58.126 50.000 0.00 0.00 41.72 4.35
106 107 2.423577 CGAGAAAACCCTTTCCACGAT 58.576 47.619 0.00 0.00 41.72 3.73
107 108 2.159627 CGAGAAAACCCTTTCCACGATG 59.840 50.000 0.00 0.00 41.72 3.84
108 109 3.146847 GAGAAAACCCTTTCCACGATGT 58.853 45.455 0.00 0.00 41.72 3.06
109 110 3.562182 AGAAAACCCTTTCCACGATGTT 58.438 40.909 0.00 0.00 41.72 2.71
110 111 4.721132 AGAAAACCCTTTCCACGATGTTA 58.279 39.130 0.00 0.00 41.72 2.41
111 112 4.517832 AGAAAACCCTTTCCACGATGTTAC 59.482 41.667 0.00 0.00 41.72 2.50
112 113 2.484742 ACCCTTTCCACGATGTTACC 57.515 50.000 0.00 0.00 0.00 2.85
113 114 1.700739 ACCCTTTCCACGATGTTACCA 59.299 47.619 0.00 0.00 0.00 3.25
114 115 2.106857 ACCCTTTCCACGATGTTACCAA 59.893 45.455 0.00 0.00 0.00 3.67
115 116 3.150767 CCCTTTCCACGATGTTACCAAA 58.849 45.455 0.00 0.00 0.00 3.28
116 117 3.761752 CCCTTTCCACGATGTTACCAAAT 59.238 43.478 0.00 0.00 0.00 2.32
117 118 4.219725 CCCTTTCCACGATGTTACCAAATT 59.780 41.667 0.00 0.00 0.00 1.82
118 119 5.160641 CCTTTCCACGATGTTACCAAATTG 58.839 41.667 0.00 0.00 0.00 2.32
119 120 4.775058 TTCCACGATGTTACCAAATTGG 57.225 40.909 11.02 11.02 45.02 3.16
133 134 4.048504 CCAAATTGGTCGTCTGAAAAACC 58.951 43.478 3.34 0.00 31.35 3.27
134 135 3.619233 AATTGGTCGTCTGAAAAACCG 57.381 42.857 0.00 0.00 34.39 4.44
135 136 1.301423 TTGGTCGTCTGAAAAACCGG 58.699 50.000 0.00 0.00 34.39 5.28
136 137 0.533308 TGGTCGTCTGAAAAACCGGG 60.533 55.000 6.32 0.00 34.39 5.73
137 138 1.232621 GGTCGTCTGAAAAACCGGGG 61.233 60.000 6.32 0.00 0.00 5.73
138 139 0.533531 GTCGTCTGAAAAACCGGGGT 60.534 55.000 6.32 0.00 0.00 4.95
139 140 0.533308 TCGTCTGAAAAACCGGGGTG 60.533 55.000 6.32 0.00 0.00 4.61
140 141 1.512156 CGTCTGAAAAACCGGGGTGG 61.512 60.000 6.32 0.00 46.41 4.61
141 142 0.179012 GTCTGAAAAACCGGGGTGGA 60.179 55.000 6.32 0.00 42.00 4.02
142 143 0.109723 TCTGAAAAACCGGGGTGGAG 59.890 55.000 6.32 0.00 42.00 3.86
143 144 0.109723 CTGAAAAACCGGGGTGGAGA 59.890 55.000 6.32 0.00 42.00 3.71
144 145 0.774908 TGAAAAACCGGGGTGGAGAT 59.225 50.000 6.32 0.00 42.00 2.75
145 146 1.146152 TGAAAAACCGGGGTGGAGATT 59.854 47.619 6.32 0.00 42.00 2.40
146 147 1.544246 GAAAAACCGGGGTGGAGATTG 59.456 52.381 6.32 0.00 42.00 2.67
147 148 0.898326 AAAACCGGGGTGGAGATTGC 60.898 55.000 6.32 0.00 42.00 3.56
148 149 2.075355 AAACCGGGGTGGAGATTGCA 62.075 55.000 6.32 0.00 42.00 4.08
149 150 2.124570 CCGGGGTGGAGATTGCAG 60.125 66.667 0.00 0.00 42.00 4.41
150 151 2.124570 CGGGGTGGAGATTGCAGG 60.125 66.667 0.00 0.00 0.00 4.85
151 152 2.440980 GGGGTGGAGATTGCAGGC 60.441 66.667 0.00 0.00 0.00 4.85
152 153 2.825836 GGGTGGAGATTGCAGGCG 60.826 66.667 0.00 0.00 0.00 5.52
153 154 2.825836 GGTGGAGATTGCAGGCGG 60.826 66.667 0.00 0.00 0.00 6.13
154 155 2.825836 GTGGAGATTGCAGGCGGG 60.826 66.667 0.00 0.00 0.00 6.13
155 156 3.008517 TGGAGATTGCAGGCGGGA 61.009 61.111 0.00 0.00 0.00 5.14
156 157 2.203126 GGAGATTGCAGGCGGGAG 60.203 66.667 0.00 0.00 0.00 4.30
157 158 2.586792 GAGATTGCAGGCGGGAGT 59.413 61.111 0.00 0.00 0.00 3.85
158 159 1.522580 GAGATTGCAGGCGGGAGTC 60.523 63.158 0.00 0.00 0.00 3.36
160 161 1.522580 GATTGCAGGCGGGAGTCTC 60.523 63.158 0.00 0.00 45.22 3.36
161 162 3.376935 ATTGCAGGCGGGAGTCTCG 62.377 63.158 8.42 8.42 45.22 4.04
170 171 3.387947 GGAGTCTCGCCCGGGAAA 61.388 66.667 29.31 10.34 0.00 3.13
171 172 2.184579 GAGTCTCGCCCGGGAAAG 59.815 66.667 29.31 20.64 0.00 2.62
172 173 3.372554 GAGTCTCGCCCGGGAAAGG 62.373 68.421 29.31 10.08 0.00 3.11
173 174 3.387947 GTCTCGCCCGGGAAAGGA 61.388 66.667 29.31 14.24 0.00 3.36
174 175 3.387947 TCTCGCCCGGGAAAGGAC 61.388 66.667 29.31 3.52 0.00 3.85
175 176 4.814294 CTCGCCCGGGAAAGGACG 62.814 72.222 29.31 17.87 0.00 4.79
180 181 3.087906 CCGGGAAAGGACGGGGAT 61.088 66.667 0.00 0.00 46.08 3.85
181 182 2.504519 CGGGAAAGGACGGGGATC 59.495 66.667 0.00 0.00 0.00 3.36
182 183 2.916661 GGGAAAGGACGGGGATCC 59.083 66.667 1.92 1.92 39.28 3.36
183 184 2.753884 GGGAAAGGACGGGGATCCC 61.754 68.421 23.95 23.95 42.74 3.85
184 185 1.999002 GGAAAGGACGGGGATCCCA 60.999 63.158 32.07 0.00 45.83 4.37
185 186 1.527370 GAAAGGACGGGGATCCCAG 59.473 63.158 32.07 29.73 45.83 4.45
186 187 1.984288 GAAAGGACGGGGATCCCAGG 61.984 65.000 31.30 24.17 45.83 4.45
187 188 4.499116 AGGACGGGGATCCCAGGG 62.499 72.222 31.30 21.82 45.83 4.45
203 204 3.407967 GGGGATCCCTCGCAACCA 61.408 66.667 30.08 0.00 41.34 3.67
204 205 2.674754 GGGATCCCTCGCAACCAA 59.325 61.111 24.69 0.00 34.59 3.67
205 206 1.001393 GGGATCCCTCGCAACCAAA 60.001 57.895 24.69 0.00 34.59 3.28
206 207 0.395724 GGGATCCCTCGCAACCAAAT 60.396 55.000 24.69 0.00 34.59 2.32
207 208 0.740737 GGATCCCTCGCAACCAAATG 59.259 55.000 0.00 0.00 0.00 2.32
208 209 1.681780 GGATCCCTCGCAACCAAATGA 60.682 52.381 0.00 0.00 0.00 2.57
209 210 1.672881 GATCCCTCGCAACCAAATGAG 59.327 52.381 0.00 0.00 0.00 2.90
210 211 0.322456 TCCCTCGCAACCAAATGAGG 60.322 55.000 0.11 0.11 46.10 3.86
211 212 1.508088 CCTCGCAACCAAATGAGGC 59.492 57.895 0.00 0.00 41.36 4.70
215 216 1.173043 CGCAACCAAATGAGGCCTTA 58.827 50.000 6.77 1.66 0.00 2.69
222 223 2.110578 CAAATGAGGCCTTAAAGGGGG 58.889 52.381 6.77 0.00 35.37 5.40
259 261 8.771766 GGATGATACGTTAAGGGATTTAACTTC 58.228 37.037 0.00 4.04 45.82 3.01
263 265 9.768662 GATACGTTAAGGGATTTAACTTCCATA 57.231 33.333 0.00 0.00 45.82 2.74
300 302 8.635765 AAAGACATGAATAAAAGTAGGCTCAA 57.364 30.769 0.00 0.00 0.00 3.02
314 316 3.424703 AGGCTCAAATGTGTACAAGCAT 58.575 40.909 14.99 6.78 29.96 3.79
321 323 7.329226 GCTCAAATGTGTACAAGCATAACAAAT 59.671 33.333 9.55 0.00 0.00 2.32
322 324 8.518151 TCAAATGTGTACAAGCATAACAAATG 57.482 30.769 0.00 0.00 0.00 2.32
350 353 6.408434 CCATTTAAATATGCAGCCCTCCTTTT 60.408 38.462 0.00 0.00 0.00 2.27
395 398 3.119065 TCGACGAGACAGAGAGATACAGT 60.119 47.826 0.00 0.00 0.00 3.55
396 399 4.097589 TCGACGAGACAGAGAGATACAGTA 59.902 45.833 0.00 0.00 0.00 2.74
403 406 5.354792 AGACAGAGAGATACAGTAAACCGAC 59.645 44.000 0.00 0.00 0.00 4.79
472 476 0.179129 CCATGCATCGGGAAACAAGC 60.179 55.000 0.00 0.00 0.00 4.01
504 508 7.095229 GGCTCAGTTTACAATGCGAATCATATA 60.095 37.037 0.00 0.00 34.33 0.86
505 509 8.446273 GCTCAGTTTACAATGCGAATCATATAT 58.554 33.333 0.00 0.00 34.33 0.86
509 513 9.162764 AGTTTACAATGCGAATCATATATACCC 57.837 33.333 0.00 0.00 34.33 3.69
511 515 9.508642 TTTACAATGCGAATCATATATACCCAA 57.491 29.630 0.00 0.00 34.33 4.12
512 516 9.679661 TTACAATGCGAATCATATATACCCAAT 57.320 29.630 0.00 0.00 34.33 3.16
514 518 9.851686 ACAATGCGAATCATATATACCCAATAT 57.148 29.630 0.00 0.00 34.33 1.28
519 552 7.359264 GCGAATCATATATACCCAATATGCGTC 60.359 40.741 0.00 0.00 37.27 5.19
553 600 2.995283 ACCCAATCGGCTTAAACCTAC 58.005 47.619 0.00 0.00 33.26 3.18
630 684 1.403647 CGTCCTGTCATTCGCTGGTAA 60.404 52.381 0.00 0.00 0.00 2.85
668 734 1.687563 TTCCGCATCCGTATCTCTCA 58.312 50.000 0.00 0.00 0.00 3.27
677 743 5.804473 GCATCCGTATCTCTCATTACATCAG 59.196 44.000 0.00 0.00 0.00 2.90
679 745 4.218635 TCCGTATCTCTCATTACATCAGCC 59.781 45.833 0.00 0.00 0.00 4.85
687 753 7.661968 TCTCTCATTACATCAGCCATTAGTAC 58.338 38.462 0.00 0.00 0.00 2.73
688 754 7.507277 TCTCTCATTACATCAGCCATTAGTACT 59.493 37.037 0.00 0.00 0.00 2.73
689 755 7.661968 TCTCATTACATCAGCCATTAGTACTC 58.338 38.462 0.00 0.00 0.00 2.59
690 756 6.759272 TCATTACATCAGCCATTAGTACTCC 58.241 40.000 0.00 0.00 0.00 3.85
691 757 5.546621 TTACATCAGCCATTAGTACTCCC 57.453 43.478 0.00 0.00 0.00 4.30
692 758 3.658725 ACATCAGCCATTAGTACTCCCT 58.341 45.455 0.00 0.00 0.00 4.20
693 759 3.643792 ACATCAGCCATTAGTACTCCCTC 59.356 47.826 0.00 0.00 0.00 4.30
694 760 2.679082 TCAGCCATTAGTACTCCCTCC 58.321 52.381 0.00 0.00 0.00 4.30
695 761 1.341531 CAGCCATTAGTACTCCCTCCG 59.658 57.143 0.00 0.00 0.00 4.63
696 762 1.063114 AGCCATTAGTACTCCCTCCGT 60.063 52.381 0.00 0.00 0.00 4.69
697 763 1.761198 GCCATTAGTACTCCCTCCGTT 59.239 52.381 0.00 0.00 0.00 4.44
698 764 2.169978 GCCATTAGTACTCCCTCCGTTT 59.830 50.000 0.00 0.00 0.00 3.60
699 765 3.740452 GCCATTAGTACTCCCTCCGTTTC 60.740 52.174 0.00 0.00 0.00 2.78
700 766 3.705072 CCATTAGTACTCCCTCCGTTTCT 59.295 47.826 0.00 0.00 0.00 2.52
701 767 4.161754 CCATTAGTACTCCCTCCGTTTCTT 59.838 45.833 0.00 0.00 0.00 2.52
702 768 5.338137 CCATTAGTACTCCCTCCGTTTCTTT 60.338 44.000 0.00 0.00 0.00 2.52
703 769 5.813513 TTAGTACTCCCTCCGTTTCTTTT 57.186 39.130 0.00 0.00 0.00 2.27
704 770 4.701651 AGTACTCCCTCCGTTTCTTTTT 57.298 40.909 0.00 0.00 0.00 1.94
705 771 5.813513 AGTACTCCCTCCGTTTCTTTTTA 57.186 39.130 0.00 0.00 0.00 1.52
706 772 6.178607 AGTACTCCCTCCGTTTCTTTTTAA 57.821 37.500 0.00 0.00 0.00 1.52
707 773 6.776744 AGTACTCCCTCCGTTTCTTTTTAAT 58.223 36.000 0.00 0.00 0.00 1.40
708 774 7.229308 AGTACTCCCTCCGTTTCTTTTTAATT 58.771 34.615 0.00 0.00 0.00 1.40
709 775 6.971726 ACTCCCTCCGTTTCTTTTTAATTT 57.028 33.333 0.00 0.00 0.00 1.82
710 776 6.745116 ACTCCCTCCGTTTCTTTTTAATTTG 58.255 36.000 0.00 0.00 0.00 2.32
711 777 5.534407 TCCCTCCGTTTCTTTTTAATTTGC 58.466 37.500 0.00 0.00 0.00 3.68
712 778 5.069251 TCCCTCCGTTTCTTTTTAATTTGCA 59.931 36.000 0.00 0.00 0.00 4.08
713 779 5.931724 CCCTCCGTTTCTTTTTAATTTGCAT 59.068 36.000 0.00 0.00 0.00 3.96
714 780 7.039644 TCCCTCCGTTTCTTTTTAATTTGCATA 60.040 33.333 0.00 0.00 0.00 3.14
715 781 7.763985 CCCTCCGTTTCTTTTTAATTTGCATAT 59.236 33.333 0.00 0.00 0.00 1.78
716 782 9.796120 CCTCCGTTTCTTTTTAATTTGCATATA 57.204 29.630 0.00 0.00 0.00 0.86
747 813 9.545105 TTGATCAAAATCAAACTTTGTAATGCT 57.455 25.926 5.45 0.00 46.41 3.79
748 814 9.545105 TGATCAAAATCAAACTTTGTAATGCTT 57.455 25.926 0.00 0.00 38.97 3.91
866 932 9.507280 CATAGTGTGAATGTTGATATGTTTTCC 57.493 33.333 0.00 0.00 0.00 3.13
867 933 7.765695 AGTGTGAATGTTGATATGTTTTCCT 57.234 32.000 0.00 0.00 0.00 3.36
868 934 8.862325 AGTGTGAATGTTGATATGTTTTCCTA 57.138 30.769 0.00 0.00 0.00 2.94
869 935 9.466497 AGTGTGAATGTTGATATGTTTTCCTAT 57.534 29.630 0.00 0.00 0.00 2.57
884 950 9.740710 ATGTTTTCCTATAAAGCTAGTTTGACT 57.259 29.630 0.00 0.00 0.00 3.41
885 951 9.569122 TGTTTTCCTATAAAGCTAGTTTGACTT 57.431 29.630 0.00 0.00 0.00 3.01
888 954 9.787435 TTTCCTATAAAGCTAGTTTGACTTTGA 57.213 29.630 0.00 0.00 35.38 2.69
889 955 8.773404 TCCTATAAAGCTAGTTTGACTTTGAC 57.227 34.615 0.00 0.00 35.38 3.18
890 956 7.822822 TCCTATAAAGCTAGTTTGACTTTGACC 59.177 37.037 0.00 0.00 35.38 4.02
891 957 7.606456 CCTATAAAGCTAGTTTGACTTTGACCA 59.394 37.037 0.00 0.00 35.38 4.02
892 958 7.817418 ATAAAGCTAGTTTGACTTTGACCAA 57.183 32.000 0.00 0.00 35.38 3.67
893 959 6.524101 AAAGCTAGTTTGACTTTGACCAAA 57.476 33.333 0.00 0.00 32.58 3.28
902 968 8.742554 GTTTGACTTTGACCAAACCTTATATG 57.257 34.615 0.00 0.00 43.62 1.78
903 969 6.509418 TGACTTTGACCAAACCTTATATGC 57.491 37.500 0.00 0.00 0.00 3.14
904 970 6.007076 TGACTTTGACCAAACCTTATATGCA 58.993 36.000 0.00 0.00 0.00 3.96
905 971 6.491745 TGACTTTGACCAAACCTTATATGCAA 59.508 34.615 0.00 0.00 0.00 4.08
906 972 7.014711 TGACTTTGACCAAACCTTATATGCAAA 59.985 33.333 0.00 0.00 0.00 3.68
907 973 7.151976 ACTTTGACCAAACCTTATATGCAAAC 58.848 34.615 0.00 0.00 0.00 2.93
908 974 6.909550 TTGACCAAACCTTATATGCAAACT 57.090 33.333 0.00 0.00 0.00 2.66
909 975 8.410673 TTTGACCAAACCTTATATGCAAACTA 57.589 30.769 0.00 0.00 0.00 2.24
910 976 8.410673 TTGACCAAACCTTATATGCAAACTAA 57.589 30.769 0.00 0.00 0.00 2.24
911 977 8.410673 TGACCAAACCTTATATGCAAACTAAA 57.589 30.769 0.00 0.00 0.00 1.85
912 978 8.861086 TGACCAAACCTTATATGCAAACTAAAA 58.139 29.630 0.00 0.00 0.00 1.52
913 979 9.699703 GACCAAACCTTATATGCAAACTAAAAA 57.300 29.630 0.00 0.00 0.00 1.94
914 980 9.705290 ACCAAACCTTATATGCAAACTAAAAAG 57.295 29.630 0.00 0.00 0.00 2.27
915 981 9.921637 CCAAACCTTATATGCAAACTAAAAAGA 57.078 29.630 0.00 0.00 0.00 2.52
925 991 8.862550 ATGCAAACTAAAAAGAAACAAGAGAG 57.137 30.769 0.00 0.00 0.00 3.20
957 1023 7.900782 ACTAACATACATGTACTTGTTGGTC 57.099 36.000 24.39 0.00 38.81 4.02
994 1060 2.986311 CACGTACTGGTGCAAGTGT 58.014 52.632 1.14 0.00 0.00 3.55
1118 1184 1.734465 CAAGATCAAAGCCGACAGGAC 59.266 52.381 0.00 0.00 41.02 3.85
1265 1345 2.528743 CCTATCCTGCTTGCGTGCG 61.529 63.158 0.00 0.00 35.36 5.34
1266 1346 3.160557 CTATCCTGCTTGCGTGCGC 62.161 63.158 9.85 9.85 42.35 6.09
1380 1461 5.963176 TGTTTACTGTACTACGTGATCCA 57.037 39.130 0.00 0.00 0.00 3.41
1416 1497 7.748677 TGAAATAAGAGCCATCCATCTCATTA 58.251 34.615 0.00 0.00 0.00 1.90
1488 1569 6.624352 TTATTACTAGAGGATAACGCACGT 57.376 37.500 0.00 0.00 0.00 4.49
1492 1573 2.736144 AGAGGATAACGCACGTTTCA 57.264 45.000 14.21 0.00 39.31 2.69
1516 1597 2.014128 CGCCGTTCTTCATTTATGGGT 58.986 47.619 0.00 0.00 0.00 4.51
1559 1641 4.142469 GCAGGTTATTGCGTTGGTTCTTAT 60.142 41.667 0.00 0.00 33.90 1.73
1560 1642 5.331902 CAGGTTATTGCGTTGGTTCTTATG 58.668 41.667 0.00 0.00 0.00 1.90
1606 1688 7.965107 GCCTTGAGTTCTAATTATGTTCTGTTG 59.035 37.037 0.00 0.00 0.00 3.33
1648 1731 1.350684 TCATGTTGGGTGCTGCTAGAA 59.649 47.619 0.00 0.00 0.00 2.10
1744 2104 3.093814 TGTTAGTCAATGGTCCTCGCTA 58.906 45.455 0.00 0.00 0.00 4.26
1770 2131 1.799933 CCCACAGGAGCTCCTATTCT 58.200 55.000 34.67 14.62 46.65 2.40
1774 2135 3.320541 CCACAGGAGCTCCTATTCTACAG 59.679 52.174 34.67 21.27 46.65 2.74
1776 2137 5.133941 CACAGGAGCTCCTATTCTACAGTA 58.866 45.833 34.67 0.00 46.65 2.74
2229 2631 7.939784 AGTTAAGAACCCTCAACCAATAATC 57.060 36.000 0.00 0.00 0.00 1.75
2241 2643 5.014755 TCAACCAATAATCCACACCCTTACT 59.985 40.000 0.00 0.00 0.00 2.24
2242 2644 4.855340 ACCAATAATCCACACCCTTACTG 58.145 43.478 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.748647 TCTCCCACGACGCGATGA 60.749 61.111 15.93 0.00 0.00 2.92
1 2 2.278206 CTCTCCCACGACGCGATG 60.278 66.667 15.93 7.01 0.00 3.84
2 3 4.194720 GCTCTCCCACGACGCGAT 62.195 66.667 15.93 0.00 0.00 4.58
13 14 4.176752 AATTCGCCCGGGCTCTCC 62.177 66.667 41.01 14.75 39.32 3.71
14 15 2.589159 GAATTCGCCCGGGCTCTC 60.589 66.667 41.01 26.57 39.32 3.20
15 16 3.083997 AGAATTCGCCCGGGCTCT 61.084 61.111 41.01 32.69 39.32 4.09
16 17 2.589159 GAGAATTCGCCCGGGCTC 60.589 66.667 41.01 31.03 39.32 4.70
17 18 4.176752 GGAGAATTCGCCCGGGCT 62.177 66.667 41.01 24.92 39.32 5.19
18 19 4.176752 AGGAGAATTCGCCCGGGC 62.177 66.667 36.69 36.69 36.39 6.13
19 20 2.203070 CAGGAGAATTCGCCCGGG 60.203 66.667 22.94 19.09 36.39 5.73
20 21 2.203070 CCAGGAGAATTCGCCCGG 60.203 66.667 22.94 19.05 36.39 5.73
21 22 2.897350 GCCAGGAGAATTCGCCCG 60.897 66.667 22.94 14.01 36.39 6.13
22 23 1.152881 ATGCCAGGAGAATTCGCCC 60.153 57.895 22.94 16.42 36.39 6.13
23 24 2.028130 CATGCCAGGAGAATTCGCC 58.972 57.895 19.61 19.61 35.95 5.54
24 25 1.358046 GCATGCCAGGAGAATTCGC 59.642 57.895 6.36 0.00 0.00 4.70
25 26 1.645455 CGCATGCCAGGAGAATTCG 59.355 57.895 13.15 0.00 0.00 3.34
26 27 0.464373 TCCGCATGCCAGGAGAATTC 60.464 55.000 13.15 0.00 31.95 2.17
27 28 1.609239 TCCGCATGCCAGGAGAATT 59.391 52.632 13.15 0.00 31.95 2.17
28 29 3.323622 TCCGCATGCCAGGAGAAT 58.676 55.556 13.15 0.00 31.95 2.40
32 33 3.785859 GACCTCCGCATGCCAGGA 61.786 66.667 29.07 21.62 34.93 3.86
33 34 4.100084 TGACCTCCGCATGCCAGG 62.100 66.667 23.23 23.23 0.00 4.45
34 35 2.513204 CTGACCTCCGCATGCCAG 60.513 66.667 13.15 8.55 0.00 4.85
35 36 4.100084 CCTGACCTCCGCATGCCA 62.100 66.667 13.15 1.68 0.00 4.92
36 37 4.864334 CCCTGACCTCCGCATGCC 62.864 72.222 13.15 0.00 0.00 4.40
37 38 4.101448 ACCCTGACCTCCGCATGC 62.101 66.667 7.91 7.91 0.00 4.06
38 39 2.124983 CACCCTGACCTCCGCATG 60.125 66.667 0.00 0.00 0.00 4.06
39 40 1.918293 TTCACCCTGACCTCCGCAT 60.918 57.895 0.00 0.00 0.00 4.73
40 41 2.525629 TTCACCCTGACCTCCGCA 60.526 61.111 0.00 0.00 0.00 5.69
41 42 2.047179 GTTCACCCTGACCTCCGC 60.047 66.667 0.00 0.00 0.00 5.54
42 43 2.261671 CGTTCACCCTGACCTCCG 59.738 66.667 0.00 0.00 0.00 4.63
43 44 2.663196 CCGTTCACCCTGACCTCC 59.337 66.667 0.00 0.00 0.00 4.30
44 45 2.047179 GCCGTTCACCCTGACCTC 60.047 66.667 0.00 0.00 0.00 3.85
45 46 3.637273 GGCCGTTCACCCTGACCT 61.637 66.667 0.00 0.00 0.00 3.85
46 47 4.717313 GGGCCGTTCACCCTGACC 62.717 72.222 0.00 0.00 44.68 4.02
53 54 3.931190 AAATCCCCGGGCCGTTCAC 62.931 63.158 26.32 0.00 0.00 3.18
54 55 3.212796 AAAATCCCCGGGCCGTTCA 62.213 57.895 26.32 7.87 0.00 3.18
55 56 2.361992 AAAATCCCCGGGCCGTTC 60.362 61.111 26.32 0.00 0.00 3.95
56 57 2.678580 CAAAATCCCCGGGCCGTT 60.679 61.111 26.32 9.69 0.00 4.44
57 58 4.751820 CCAAAATCCCCGGGCCGT 62.752 66.667 26.32 2.30 0.00 5.68
59 60 4.068887 TCCCAAAATCCCCGGGCC 62.069 66.667 17.73 0.00 40.05 5.80
60 61 2.442087 CTCCCAAAATCCCCGGGC 60.442 66.667 17.73 0.00 40.05 6.13
61 62 1.655114 ATCCTCCCAAAATCCCCGGG 61.655 60.000 15.80 15.80 41.76 5.73
62 63 0.178990 GATCCTCCCAAAATCCCCGG 60.179 60.000 0.00 0.00 0.00 5.73
63 64 0.535102 CGATCCTCCCAAAATCCCCG 60.535 60.000 0.00 0.00 0.00 5.73
64 65 0.178990 CCGATCCTCCCAAAATCCCC 60.179 60.000 0.00 0.00 0.00 4.81
65 66 0.178990 CCCGATCCTCCCAAAATCCC 60.179 60.000 0.00 0.00 0.00 3.85
66 67 0.178990 CCCCGATCCTCCCAAAATCC 60.179 60.000 0.00 0.00 0.00 3.01
67 68 0.823769 GCCCCGATCCTCCCAAAATC 60.824 60.000 0.00 0.00 0.00 2.17
68 69 1.230212 GCCCCGATCCTCCCAAAAT 59.770 57.895 0.00 0.00 0.00 1.82
69 70 2.680965 GCCCCGATCCTCCCAAAA 59.319 61.111 0.00 0.00 0.00 2.44
70 71 3.792736 CGCCCCGATCCTCCCAAA 61.793 66.667 0.00 0.00 0.00 3.28
71 72 4.789173 TCGCCCCGATCCTCCCAA 62.789 66.667 0.00 0.00 0.00 4.12
73 74 4.916314 TCTCGCCCCGATCCTCCC 62.916 72.222 0.00 0.00 34.61 4.30
74 75 1.968050 TTTTCTCGCCCCGATCCTCC 61.968 60.000 0.00 0.00 34.61 4.30
75 76 0.810426 GTTTTCTCGCCCCGATCCTC 60.810 60.000 0.00 0.00 34.61 3.71
76 77 1.221021 GTTTTCTCGCCCCGATCCT 59.779 57.895 0.00 0.00 34.61 3.24
77 78 1.818363 GGTTTTCTCGCCCCGATCC 60.818 63.158 0.00 0.00 34.61 3.36
78 79 1.818363 GGGTTTTCTCGCCCCGATC 60.818 63.158 0.00 0.00 38.99 3.69
79 80 1.848886 AAGGGTTTTCTCGCCCCGAT 61.849 55.000 0.00 0.00 45.95 4.18
80 81 2.059345 AAAGGGTTTTCTCGCCCCGA 62.059 55.000 0.00 0.00 45.95 5.14
81 82 1.583495 GAAAGGGTTTTCTCGCCCCG 61.583 60.000 0.00 0.00 45.95 5.73
82 83 1.248785 GGAAAGGGTTTTCTCGCCCC 61.249 60.000 0.00 0.00 45.95 5.80
83 84 0.538746 TGGAAAGGGTTTTCTCGCCC 60.539 55.000 0.00 0.00 41.92 6.13
84 85 0.596577 GTGGAAAGGGTTTTCTCGCC 59.403 55.000 0.69 0.00 41.92 5.54
85 86 0.237498 CGTGGAAAGGGTTTTCTCGC 59.763 55.000 0.69 0.00 41.92 5.03
86 87 1.873698 TCGTGGAAAGGGTTTTCTCG 58.126 50.000 0.69 6.10 41.92 4.04
87 88 3.146847 ACATCGTGGAAAGGGTTTTCTC 58.853 45.455 0.69 0.00 41.92 2.87
88 89 3.223674 ACATCGTGGAAAGGGTTTTCT 57.776 42.857 0.69 0.00 41.92 2.52
89 90 4.320714 GGTAACATCGTGGAAAGGGTTTTC 60.321 45.833 0.00 0.00 41.59 2.29
90 91 3.570975 GGTAACATCGTGGAAAGGGTTTT 59.429 43.478 0.00 0.00 0.00 2.43
91 92 3.151554 GGTAACATCGTGGAAAGGGTTT 58.848 45.455 0.00 0.00 0.00 3.27
92 93 2.106857 TGGTAACATCGTGGAAAGGGTT 59.893 45.455 0.00 0.00 46.17 4.11
93 94 1.700739 TGGTAACATCGTGGAAAGGGT 59.299 47.619 0.00 0.00 46.17 4.34
94 95 2.483014 TGGTAACATCGTGGAAAGGG 57.517 50.000 0.00 0.00 46.17 3.95
111 112 4.048504 GGTTTTTCAGACGACCAATTTGG 58.951 43.478 14.02 14.02 45.02 3.28
112 113 3.728718 CGGTTTTTCAGACGACCAATTTG 59.271 43.478 0.00 0.00 32.41 2.32
113 114 3.243267 CCGGTTTTTCAGACGACCAATTT 60.243 43.478 0.00 0.00 32.41 1.82
114 115 2.292292 CCGGTTTTTCAGACGACCAATT 59.708 45.455 0.00 0.00 32.41 2.32
115 116 1.877443 CCGGTTTTTCAGACGACCAAT 59.123 47.619 0.00 0.00 32.41 3.16
116 117 1.301423 CCGGTTTTTCAGACGACCAA 58.699 50.000 0.00 0.00 32.41 3.67
117 118 0.533308 CCCGGTTTTTCAGACGACCA 60.533 55.000 0.00 0.00 32.41 4.02
118 119 1.232621 CCCCGGTTTTTCAGACGACC 61.233 60.000 0.00 0.00 0.00 4.79
119 120 0.533531 ACCCCGGTTTTTCAGACGAC 60.534 55.000 0.00 0.00 0.00 4.34
120 121 0.533308 CACCCCGGTTTTTCAGACGA 60.533 55.000 0.00 0.00 0.00 4.20
121 122 1.512156 CCACCCCGGTTTTTCAGACG 61.512 60.000 0.00 0.00 0.00 4.18
122 123 0.179012 TCCACCCCGGTTTTTCAGAC 60.179 55.000 0.00 0.00 35.57 3.51
123 124 0.109723 CTCCACCCCGGTTTTTCAGA 59.890 55.000 0.00 0.00 35.57 3.27
124 125 0.109723 TCTCCACCCCGGTTTTTCAG 59.890 55.000 0.00 0.00 35.57 3.02
125 126 0.774908 ATCTCCACCCCGGTTTTTCA 59.225 50.000 0.00 0.00 35.57 2.69
126 127 1.544246 CAATCTCCACCCCGGTTTTTC 59.456 52.381 0.00 0.00 35.57 2.29
127 128 1.627864 CAATCTCCACCCCGGTTTTT 58.372 50.000 0.00 0.00 35.57 1.94
128 129 0.898326 GCAATCTCCACCCCGGTTTT 60.898 55.000 0.00 0.00 35.57 2.43
129 130 1.304134 GCAATCTCCACCCCGGTTT 60.304 57.895 0.00 0.00 35.57 3.27
130 131 2.355115 GCAATCTCCACCCCGGTT 59.645 61.111 0.00 0.00 35.57 4.44
131 132 2.933287 TGCAATCTCCACCCCGGT 60.933 61.111 0.00 0.00 35.57 5.28
132 133 2.124570 CTGCAATCTCCACCCCGG 60.125 66.667 0.00 0.00 0.00 5.73
133 134 2.124570 CCTGCAATCTCCACCCCG 60.125 66.667 0.00 0.00 0.00 5.73
134 135 2.440980 GCCTGCAATCTCCACCCC 60.441 66.667 0.00 0.00 0.00 4.95
135 136 2.825836 CGCCTGCAATCTCCACCC 60.826 66.667 0.00 0.00 0.00 4.61
136 137 2.825836 CCGCCTGCAATCTCCACC 60.826 66.667 0.00 0.00 0.00 4.61
137 138 2.825836 CCCGCCTGCAATCTCCAC 60.826 66.667 0.00 0.00 0.00 4.02
138 139 3.008517 TCCCGCCTGCAATCTCCA 61.009 61.111 0.00 0.00 0.00 3.86
139 140 2.203126 CTCCCGCCTGCAATCTCC 60.203 66.667 0.00 0.00 0.00 3.71
140 141 1.522580 GACTCCCGCCTGCAATCTC 60.523 63.158 0.00 0.00 0.00 2.75
141 142 1.965754 GAGACTCCCGCCTGCAATCT 61.966 60.000 0.00 0.00 0.00 2.40
142 143 1.522580 GAGACTCCCGCCTGCAATC 60.523 63.158 0.00 0.00 0.00 2.67
143 144 2.586792 GAGACTCCCGCCTGCAAT 59.413 61.111 0.00 0.00 0.00 3.56
144 145 4.069232 CGAGACTCCCGCCTGCAA 62.069 66.667 0.00 0.00 0.00 4.08
153 154 3.372554 CTTTCCCGGGCGAGACTCC 62.373 68.421 18.49 0.00 0.00 3.85
154 155 2.184579 CTTTCCCGGGCGAGACTC 59.815 66.667 18.49 0.00 0.00 3.36
155 156 3.391382 CCTTTCCCGGGCGAGACT 61.391 66.667 18.49 0.00 0.00 3.24
156 157 3.387947 TCCTTTCCCGGGCGAGAC 61.388 66.667 18.49 0.00 0.00 3.36
157 158 3.387947 GTCCTTTCCCGGGCGAGA 61.388 66.667 18.49 6.95 0.00 4.04
163 164 3.087906 ATCCCCGTCCTTTCCCGG 61.088 66.667 0.00 0.00 43.82 5.73
164 165 2.504519 GATCCCCGTCCTTTCCCG 59.495 66.667 0.00 0.00 0.00 5.14
165 166 2.753884 GGGATCCCCGTCCTTTCCC 61.754 68.421 21.42 0.00 39.35 3.97
166 167 2.916661 GGGATCCCCGTCCTTTCC 59.083 66.667 21.42 0.00 38.38 3.13
186 187 2.493273 TTTGGTTGCGAGGGATCCCC 62.493 60.000 28.11 17.38 45.90 4.81
187 188 0.395724 ATTTGGTTGCGAGGGATCCC 60.396 55.000 24.59 24.59 0.00 3.85
188 189 0.740737 CATTTGGTTGCGAGGGATCC 59.259 55.000 1.92 1.92 0.00 3.36
189 190 1.672881 CTCATTTGGTTGCGAGGGATC 59.327 52.381 0.00 0.00 0.00 3.36
190 191 1.683011 CCTCATTTGGTTGCGAGGGAT 60.683 52.381 0.00 0.00 41.20 3.85
191 192 0.322456 CCTCATTTGGTTGCGAGGGA 60.322 55.000 0.00 0.00 41.20 4.20
192 193 1.937546 GCCTCATTTGGTTGCGAGGG 61.938 60.000 6.44 0.00 44.40 4.30
193 194 1.508088 GCCTCATTTGGTTGCGAGG 59.492 57.895 0.00 0.00 46.53 4.63
194 195 0.962356 AGGCCTCATTTGGTTGCGAG 60.962 55.000 0.00 0.00 0.00 5.03
195 196 0.539438 AAGGCCTCATTTGGTTGCGA 60.539 50.000 5.23 0.00 0.00 5.10
196 197 1.173043 TAAGGCCTCATTTGGTTGCG 58.827 50.000 5.23 0.00 0.00 4.85
197 198 3.588955 CTTTAAGGCCTCATTTGGTTGC 58.411 45.455 5.23 0.00 0.00 4.17
198 199 3.055891 CCCTTTAAGGCCTCATTTGGTTG 60.056 47.826 5.23 0.00 32.73 3.77
199 200 3.173151 CCCTTTAAGGCCTCATTTGGTT 58.827 45.455 5.23 0.00 32.73 3.67
200 201 2.559705 CCCCTTTAAGGCCTCATTTGGT 60.560 50.000 5.23 0.00 32.73 3.67
201 202 2.110578 CCCCTTTAAGGCCTCATTTGG 58.889 52.381 5.23 4.48 32.73 3.28
202 203 2.110578 CCCCCTTTAAGGCCTCATTTG 58.889 52.381 5.23 0.00 32.73 2.32
203 204 1.722271 ACCCCCTTTAAGGCCTCATTT 59.278 47.619 5.23 0.00 32.73 2.32
204 205 1.007118 CACCCCCTTTAAGGCCTCATT 59.993 52.381 5.23 0.00 32.73 2.57
205 206 0.631212 CACCCCCTTTAAGGCCTCAT 59.369 55.000 5.23 0.00 32.73 2.90
206 207 1.506028 CCACCCCCTTTAAGGCCTCA 61.506 60.000 5.23 0.00 32.73 3.86
207 208 1.306633 CCACCCCCTTTAAGGCCTC 59.693 63.158 5.23 0.00 32.73 4.70
208 209 1.467392 ACCACCCCCTTTAAGGCCT 60.467 57.895 0.00 0.00 32.73 5.19
209 210 1.304962 CACCACCCCCTTTAAGGCC 60.305 63.158 5.29 0.00 32.73 5.19
210 211 1.304962 CCACCACCCCCTTTAAGGC 60.305 63.158 5.29 0.00 32.73 4.35
211 212 0.251608 CACCACCACCCCCTTTAAGG 60.252 60.000 3.57 3.57 34.30 2.69
215 216 3.517497 CCCACCACCACCCCCTTT 61.517 66.667 0.00 0.00 0.00 3.11
222 223 0.182775 GTATCATCCCCCACCACCAC 59.817 60.000 0.00 0.00 0.00 4.16
300 302 7.598493 GGTTCATTTGTTATGCTTGTACACATT 59.402 33.333 4.47 0.00 0.00 2.71
321 323 4.961730 AGGGCTGCATATTTAAATGGTTCA 59.038 37.500 11.05 3.21 0.00 3.18
322 324 5.509670 GGAGGGCTGCATATTTAAATGGTTC 60.510 44.000 11.05 0.00 0.00 3.62
350 353 5.597758 AGGGCAGGATAGAATAGATGATGA 58.402 41.667 0.00 0.00 0.00 2.92
395 398 7.551035 TTTAGCTTAAACACTTGTCGGTTTA 57.449 32.000 0.00 0.00 38.17 2.01
396 399 6.439675 TTTAGCTTAAACACTTGTCGGTTT 57.560 33.333 0.00 0.00 40.15 3.27
472 476 3.119708 GCATTGTAAACTGAGCCTCTTGG 60.120 47.826 0.00 0.00 0.00 3.61
504 508 1.968493 ACTCCGACGCATATTGGGTAT 59.032 47.619 0.00 0.00 43.89 2.73
505 509 1.338973 GACTCCGACGCATATTGGGTA 59.661 52.381 0.00 0.00 43.89 3.69
506 510 0.104304 GACTCCGACGCATATTGGGT 59.896 55.000 0.00 0.00 46.65 4.51
509 513 1.835121 TTCGACTCCGACGCATATTG 58.165 50.000 0.00 0.00 45.50 1.90
511 515 1.607148 TGATTCGACTCCGACGCATAT 59.393 47.619 0.00 0.00 45.50 1.78
512 516 1.018910 TGATTCGACTCCGACGCATA 58.981 50.000 0.00 0.00 45.50 3.14
513 517 0.385751 ATGATTCGACTCCGACGCAT 59.614 50.000 0.00 0.00 45.50 4.73
514 518 1.018910 TATGATTCGACTCCGACGCA 58.981 50.000 0.00 0.00 45.50 5.24
519 552 2.882927 TTGGGTATGATTCGACTCCG 57.117 50.000 0.00 0.00 37.07 4.63
553 600 6.778108 TGGAGTACGTATATATACATGTGCG 58.222 40.000 20.24 9.46 37.39 5.34
611 664 2.094182 TCTTACCAGCGAATGACAGGAC 60.094 50.000 0.00 0.00 0.00 3.85
614 667 3.182967 GTCTCTTACCAGCGAATGACAG 58.817 50.000 0.00 0.00 0.00 3.51
630 684 5.360591 CGGAAATTAGTATGGCTTGTCTCT 58.639 41.667 0.00 0.00 0.00 3.10
668 734 5.846714 AGGGAGTACTAATGGCTGATGTAAT 59.153 40.000 0.00 0.00 0.00 1.89
677 743 1.411041 ACGGAGGGAGTACTAATGGC 58.589 55.000 0.00 0.00 0.00 4.40
679 745 5.340439 AAGAAACGGAGGGAGTACTAATG 57.660 43.478 0.00 0.00 0.00 1.90
687 753 5.633601 GCAAATTAAAAAGAAACGGAGGGAG 59.366 40.000 0.00 0.00 0.00 4.30
688 754 5.069251 TGCAAATTAAAAAGAAACGGAGGGA 59.931 36.000 0.00 0.00 0.00 4.20
689 755 5.293560 TGCAAATTAAAAAGAAACGGAGGG 58.706 37.500 0.00 0.00 0.00 4.30
690 756 8.702163 ATATGCAAATTAAAAAGAAACGGAGG 57.298 30.769 0.00 0.00 0.00 4.30
721 787 9.545105 AGCATTACAAAGTTTGATTTTGATCAA 57.455 25.926 22.23 3.38 38.55 2.57
722 788 9.545105 AAGCATTACAAAGTTTGATTTTGATCA 57.455 25.926 22.23 0.00 38.55 2.92
840 906 9.507280 GGAAAACATATCAACATTCACACTATG 57.493 33.333 0.00 0.00 0.00 2.23
841 907 9.466497 AGGAAAACATATCAACATTCACACTAT 57.534 29.630 0.00 0.00 0.00 2.12
842 908 8.862325 AGGAAAACATATCAACATTCACACTA 57.138 30.769 0.00 0.00 0.00 2.74
843 909 7.765695 AGGAAAACATATCAACATTCACACT 57.234 32.000 0.00 0.00 0.00 3.55
858 924 9.740710 AGTCAAACTAGCTTTATAGGAAAACAT 57.259 29.630 0.00 0.00 0.00 2.71
859 925 9.569122 AAGTCAAACTAGCTTTATAGGAAAACA 57.431 29.630 0.00 0.00 0.00 2.83
862 928 9.787435 TCAAAGTCAAACTAGCTTTATAGGAAA 57.213 29.630 0.00 0.00 32.01 3.13
863 929 9.216117 GTCAAAGTCAAACTAGCTTTATAGGAA 57.784 33.333 0.00 0.00 32.01 3.36
864 930 7.822822 GGTCAAAGTCAAACTAGCTTTATAGGA 59.177 37.037 0.00 0.00 32.01 2.94
865 931 7.606456 TGGTCAAAGTCAAACTAGCTTTATAGG 59.394 37.037 0.00 0.00 32.01 2.57
866 932 8.547967 TGGTCAAAGTCAAACTAGCTTTATAG 57.452 34.615 0.00 0.00 32.01 1.31
867 933 8.911918 TTGGTCAAAGTCAAACTAGCTTTATA 57.088 30.769 0.00 0.00 32.01 0.98
868 934 7.817418 TTGGTCAAAGTCAAACTAGCTTTAT 57.183 32.000 0.00 0.00 32.01 1.40
869 935 7.415877 GGTTTGGTCAAAGTCAAACTAGCTTTA 60.416 37.037 15.43 0.00 46.86 1.85
870 936 6.330278 GTTTGGTCAAAGTCAAACTAGCTTT 58.670 36.000 10.51 0.00 45.28 3.51
871 937 5.163550 GGTTTGGTCAAAGTCAAACTAGCTT 60.164 40.000 15.43 0.00 46.86 3.74
872 938 4.338400 GGTTTGGTCAAAGTCAAACTAGCT 59.662 41.667 15.43 0.00 46.86 3.32
873 939 4.338400 AGGTTTGGTCAAAGTCAAACTAGC 59.662 41.667 15.43 3.41 46.86 3.42
874 940 6.451064 AAGGTTTGGTCAAAGTCAAACTAG 57.549 37.500 15.43 0.00 46.86 2.57
875 941 9.802039 ATATAAGGTTTGGTCAAAGTCAAACTA 57.198 29.630 15.43 5.18 46.86 2.24
876 942 8.576442 CATATAAGGTTTGGTCAAAGTCAAACT 58.424 33.333 15.43 3.50 46.86 2.66
877 943 7.328493 GCATATAAGGTTTGGTCAAAGTCAAAC 59.672 37.037 9.59 9.59 46.92 2.93
878 944 7.014711 TGCATATAAGGTTTGGTCAAAGTCAAA 59.985 33.333 0.00 0.00 0.00 2.69
879 945 6.491745 TGCATATAAGGTTTGGTCAAAGTCAA 59.508 34.615 0.00 0.00 0.00 3.18
880 946 6.007076 TGCATATAAGGTTTGGTCAAAGTCA 58.993 36.000 0.00 0.00 0.00 3.41
881 947 6.509418 TGCATATAAGGTTTGGTCAAAGTC 57.491 37.500 0.00 0.00 0.00 3.01
882 948 6.909550 TTGCATATAAGGTTTGGTCAAAGT 57.090 33.333 0.00 0.00 0.00 2.66
883 949 7.378181 AGTTTGCATATAAGGTTTGGTCAAAG 58.622 34.615 0.00 0.00 0.00 2.77
884 950 7.296628 AGTTTGCATATAAGGTTTGGTCAAA 57.703 32.000 0.00 0.00 0.00 2.69
885 951 6.909550 AGTTTGCATATAAGGTTTGGTCAA 57.090 33.333 0.00 0.00 0.00 3.18
886 952 8.410673 TTTAGTTTGCATATAAGGTTTGGTCA 57.589 30.769 0.00 0.00 0.00 4.02
887 953 9.699703 TTTTTAGTTTGCATATAAGGTTTGGTC 57.300 29.630 0.00 0.00 0.00 4.02
888 954 9.705290 CTTTTTAGTTTGCATATAAGGTTTGGT 57.295 29.630 0.00 0.00 0.00 3.67
889 955 9.921637 TCTTTTTAGTTTGCATATAAGGTTTGG 57.078 29.630 0.00 0.00 0.00 3.28
899 965 9.950680 CTCTCTTGTTTCTTTTTAGTTTGCATA 57.049 29.630 0.00 0.00 0.00 3.14
900 966 7.922811 CCTCTCTTGTTTCTTTTTAGTTTGCAT 59.077 33.333 0.00 0.00 0.00 3.96
901 967 7.093945 ACCTCTCTTGTTTCTTTTTAGTTTGCA 60.094 33.333 0.00 0.00 0.00 4.08
902 968 7.258441 ACCTCTCTTGTTTCTTTTTAGTTTGC 58.742 34.615 0.00 0.00 0.00 3.68
957 1023 2.458592 GCACTAGCTGCAAAATACCG 57.541 50.000 1.02 0.00 46.29 4.02
993 1059 1.369321 GGCTCTCCCCATCGATCAC 59.631 63.158 0.00 0.00 0.00 3.06
994 1060 0.472543 ATGGCTCTCCCCATCGATCA 60.473 55.000 0.00 0.00 41.75 2.92
1118 1184 2.096980 TGCAACTCTATGTAGACGTCCG 59.903 50.000 13.01 0.00 0.00 4.79
1280 1360 4.962122 AGCACACAAAAGCGCGCG 62.962 61.111 28.44 28.44 35.48 6.86
1296 1376 2.896854 ACACACGCAGGCACACAG 60.897 61.111 0.00 0.00 0.00 3.66
1380 1461 8.701908 ATGGCTCTTATTTCATTCATGTATGT 57.298 30.769 11.55 0.00 0.00 2.29
1461 1542 9.616634 CGTGCGTTATCCTCTAGTAATAATTAA 57.383 33.333 0.00 0.00 0.00 1.40
1462 1543 8.786898 ACGTGCGTTATCCTCTAGTAATAATTA 58.213 33.333 0.00 0.00 0.00 1.40
1463 1544 7.655490 ACGTGCGTTATCCTCTAGTAATAATT 58.345 34.615 0.00 0.00 0.00 1.40
1464 1545 7.211966 ACGTGCGTTATCCTCTAGTAATAAT 57.788 36.000 0.00 0.00 0.00 1.28
1465 1546 6.624352 ACGTGCGTTATCCTCTAGTAATAA 57.376 37.500 0.00 0.00 0.00 1.40
1466 1547 6.624352 AACGTGCGTTATCCTCTAGTAATA 57.376 37.500 8.28 0.00 36.46 0.98
1488 1569 2.589442 AAGAACGGCGCGGTGAAA 60.589 55.556 22.01 0.00 0.00 2.69
1492 1573 0.671163 TAAATGAAGAACGGCGCGGT 60.671 50.000 15.60 15.60 0.00 5.68
1529 1610 3.887621 ACGCAATAACCTGCTAGAGAA 57.112 42.857 0.00 0.00 40.33 2.87
1530 1611 3.521560 CAACGCAATAACCTGCTAGAGA 58.478 45.455 0.00 0.00 40.33 3.10
1550 1632 8.919145 ACAGATAAAACCAAAACATAAGAACCA 58.081 29.630 0.00 0.00 0.00 3.67
1559 1641 5.105146 AGGCAACACAGATAAAACCAAAACA 60.105 36.000 0.00 0.00 41.41 2.83
1560 1642 5.356426 AGGCAACACAGATAAAACCAAAAC 58.644 37.500 0.00 0.00 41.41 2.43
1612 1695 8.043710 ACCCAACATGAAATACAAACAAGAAAA 58.956 29.630 0.00 0.00 0.00 2.29
1614 1697 6.983307 CACCCAACATGAAATACAAACAAGAA 59.017 34.615 0.00 0.00 0.00 2.52
1615 1698 6.511416 CACCCAACATGAAATACAAACAAGA 58.489 36.000 0.00 0.00 0.00 3.02
1616 1699 5.177327 GCACCCAACATGAAATACAAACAAG 59.823 40.000 0.00 0.00 0.00 3.16
1617 1700 5.053145 GCACCCAACATGAAATACAAACAA 58.947 37.500 0.00 0.00 0.00 2.83
1618 1701 4.343526 AGCACCCAACATGAAATACAAACA 59.656 37.500 0.00 0.00 0.00 2.83
1619 1702 4.685628 CAGCACCCAACATGAAATACAAAC 59.314 41.667 0.00 0.00 0.00 2.93
1648 1731 8.857694 TTTTTCCTCTCAGAATAAATACCGTT 57.142 30.769 0.00 0.00 0.00 4.44
1744 2104 4.479993 GCTCCTGTGGGCTCGCAT 62.480 66.667 0.00 0.00 32.43 4.73
2202 2604 5.382664 TTGGTTGAGGGTTCTTAACTTCT 57.617 39.130 0.00 0.00 38.88 2.85
2203 2605 7.754851 TTATTGGTTGAGGGTTCTTAACTTC 57.245 36.000 0.00 0.00 38.88 3.01
2204 2606 7.396339 GGATTATTGGTTGAGGGTTCTTAACTT 59.604 37.037 0.00 0.00 38.88 2.66
2205 2607 6.890268 GGATTATTGGTTGAGGGTTCTTAACT 59.110 38.462 0.00 0.00 38.88 2.24
2206 2608 6.661805 TGGATTATTGGTTGAGGGTTCTTAAC 59.338 38.462 0.00 0.00 38.36 2.01
2207 2609 6.661805 GTGGATTATTGGTTGAGGGTTCTTAA 59.338 38.462 0.00 0.00 0.00 1.85
2208 2610 6.184789 GTGGATTATTGGTTGAGGGTTCTTA 58.815 40.000 0.00 0.00 0.00 2.10
2209 2611 5.016831 GTGGATTATTGGTTGAGGGTTCTT 58.983 41.667 0.00 0.00 0.00 2.52
2210 2612 4.044065 TGTGGATTATTGGTTGAGGGTTCT 59.956 41.667 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.