Multiple sequence alignment - TraesCS3D01G357500

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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 TraesCS3D01G357500 chr3D 100.000 3906 0 0 1 3906 470732430 470728525 0.000000e+00 7214.0
1 TraesCS3D01G357500 chr3D 89.083 229 25 0 1 229 66404016 66404244 6.390000e-73 285.0
2 TraesCS3D01G357500 chr3D 84.416 231 34 2 1 230 325709242 325709013 3.930000e-55 226.0
3 TraesCS3D01G357500 chr3B 95.086 1567 37 16 2346 3906 625201297 625199765 0.000000e+00 2431.0
4 TraesCS3D01G357500 chr3B 92.356 1125 42 20 723 1818 625202989 625201880 0.000000e+00 1561.0
5 TraesCS3D01G357500 chr3B 96.721 488 16 0 1859 2346 625201871 625201384 0.000000e+00 813.0
6 TraesCS3D01G357500 chr3B 83.862 347 28 10 403 729 625203369 625203031 4.900000e-79 305.0
7 TraesCS3D01G357500 chr3B 85.281 231 32 2 1 230 423180196 423179967 1.810000e-58 237.0
8 TraesCS3D01G357500 chr3B 83.983 231 34 3 1 229 808036207 808036436 6.570000e-53 219.0
9 TraesCS3D01G357500 chr3B 94.915 118 6 0 228 345 625204710 625204593 6.660000e-43 185.0
10 TraesCS3D01G357500 chr3B 80.105 191 33 4 968 1153 438538070 438537880 1.890000e-28 137.0
11 TraesCS3D01G357500 chr3A 91.793 1645 66 21 723 2346 612987569 612985973 0.000000e+00 2226.0
12 TraesCS3D01G357500 chr3A 95.649 1195 39 6 2346 3536 612985847 612984662 0.000000e+00 1906.0
13 TraesCS3D01G357500 chr3A 89.749 517 36 9 228 729 612988125 612987611 0.000000e+00 645.0
14 TraesCS3D01G357500 chr3A 84.807 362 24 16 3538 3888 612984387 612984046 6.250000e-88 335.0
15 TraesCS3D01G357500 chr3A 85.345 232 29 5 1 229 363142288 363142059 6.520000e-58 235.0
16 TraesCS3D01G357500 chr3A 94.958 119 6 0 228 346 612988855 612988737 1.850000e-43 187.0
17 TraesCS3D01G357500 chr3A 100.000 32 0 0 3875 3906 612984025 612983994 4.210000e-05 60.2
18 TraesCS3D01G357500 chr4D 90.558 233 22 0 1 233 281304097 281303865 3.790000e-80 309.0
19 TraesCS3D01G357500 chr5B 97.714 175 3 1 994 1167 665208810 665208636 2.280000e-77 300.0
20 TraesCS3D01G357500 chr5D 97.175 177 3 1 991 1167 528401973 528402147 8.200000e-77 298.0
21 TraesCS3D01G357500 chr5A 98.802 167 2 0 1001 1167 656466891 656467057 8.200000e-77 298.0
22 TraesCS3D01G357500 chr5A 97.674 129 3 0 1025 1153 383883133 383883005 5.080000e-54 222.0
23 TraesCS3D01G357500 chr1B 85.169 236 26 8 1 231 41705421 41705190 2.350000e-57 233.0
24 TraesCS3D01G357500 chr7D 91.875 160 13 0 1008 1167 477072303 477072462 1.410000e-54 224.0
25 TraesCS3D01G357500 chr7B 91.875 160 13 0 1008 1167 501508512 501508671 1.410000e-54 224.0
26 TraesCS3D01G357500 chr7A 91.875 160 13 0 1008 1167 518809678 518809519 1.410000e-54 224.0
27 TraesCS3D01G357500 chr7A 83.966 237 29 8 1 232 29987375 29987143 6.570000e-53 219.0
28 TraesCS3D01G357500 chr4B 83.333 234 38 1 7 239 465747200 465747433 8.500000e-52 215.0
29 TraesCS3D01G357500 chr1A 84.080 201 27 4 967 1167 563685895 563685700 5.150000e-44 189.0


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 TraesCS3D01G357500 chr3D 470728525 470732430 3905 True 7214.0 7214 100.000 1 3906 1 chr3D.!!$R2 3905
1 TraesCS3D01G357500 chr3B 625199765 625204710 4945 True 1059.0 2431 92.588 228 3906 5 chr3B.!!$R3 3678
2 TraesCS3D01G357500 chr3A 612983994 612988855 4861 True 893.2 2226 92.826 228 3906 6 chr3A.!!$R2 3678

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
128 129 0.101579 GCTCCGAGAGAACTACTGCC 59.898 60.0 0.00 0.0 0.00 4.85 F
1280 2768 0.109319 GAAATGCAAATGCCGTCCGT 60.109 50.0 2.46 0.0 41.18 4.69 F
1282 2770 0.732571 AATGCAAATGCCGTCCGTAG 59.267 50.0 2.46 0.0 41.18 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1610 3102 0.677731 AACCATGCCCACGACAGATG 60.678 55.000 0.0 0.0 0.00 2.90 R
2899 4610 1.151668 CGGAACCAGCTCTTCAACTG 58.848 55.000 3.6 0.0 0.00 3.16 R
2918 4629 4.559862 TCCAGAAAGAATCTCTTCCACC 57.440 45.455 0.0 0.0 35.27 4.61 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
33 34 8.830915 AGTTCTAGAGATTAAGGAGTTGATGA 57.169 34.615 0.00 0.00 0.00 2.92
34 35 8.912988 AGTTCTAGAGATTAAGGAGTTGATGAG 58.087 37.037 0.00 0.00 0.00 2.90
35 36 8.691797 GTTCTAGAGATTAAGGAGTTGATGAGT 58.308 37.037 0.00 0.00 0.00 3.41
36 37 9.922477 TTCTAGAGATTAAGGAGTTGATGAGTA 57.078 33.333 0.00 0.00 0.00 2.59
37 38 9.922477 TCTAGAGATTAAGGAGTTGATGAGTAA 57.078 33.333 0.00 0.00 0.00 2.24
41 42 9.921637 GAGATTAAGGAGTTGATGAGTAATAGG 57.078 37.037 0.00 0.00 0.00 2.57
42 43 8.875168 AGATTAAGGAGTTGATGAGTAATAGGG 58.125 37.037 0.00 0.00 0.00 3.53
43 44 8.798975 ATTAAGGAGTTGATGAGTAATAGGGA 57.201 34.615 0.00 0.00 0.00 4.20
44 45 6.739331 AAGGAGTTGATGAGTAATAGGGAG 57.261 41.667 0.00 0.00 0.00 4.30
45 46 5.782925 AGGAGTTGATGAGTAATAGGGAGT 58.217 41.667 0.00 0.00 0.00 3.85
46 47 6.206042 AGGAGTTGATGAGTAATAGGGAGTT 58.794 40.000 0.00 0.00 0.00 3.01
47 48 6.674419 AGGAGTTGATGAGTAATAGGGAGTTT 59.326 38.462 0.00 0.00 0.00 2.66
48 49 7.182930 AGGAGTTGATGAGTAATAGGGAGTTTT 59.817 37.037 0.00 0.00 0.00 2.43
49 50 7.829706 GGAGTTGATGAGTAATAGGGAGTTTTT 59.170 37.037 0.00 0.00 0.00 1.94
50 51 9.886132 GAGTTGATGAGTAATAGGGAGTTTTTA 57.114 33.333 0.00 0.00 0.00 1.52
51 52 9.668497 AGTTGATGAGTAATAGGGAGTTTTTAC 57.332 33.333 0.00 0.00 0.00 2.01
52 53 8.890718 GTTGATGAGTAATAGGGAGTTTTTACC 58.109 37.037 0.00 0.00 0.00 2.85
53 54 8.388656 TGATGAGTAATAGGGAGTTTTTACCT 57.611 34.615 0.00 0.00 38.40 3.08
54 55 8.483758 TGATGAGTAATAGGGAGTTTTTACCTC 58.516 37.037 0.00 0.00 35.84 3.85
55 56 7.801893 TGAGTAATAGGGAGTTTTTACCTCA 57.198 36.000 0.00 0.00 35.84 3.86
56 57 7.848128 TGAGTAATAGGGAGTTTTTACCTCAG 58.152 38.462 0.00 0.00 35.84 3.35
57 58 7.676893 TGAGTAATAGGGAGTTTTTACCTCAGA 59.323 37.037 0.00 0.00 35.84 3.27
58 59 8.445361 AGTAATAGGGAGTTTTTACCTCAGAA 57.555 34.615 0.00 0.00 35.84 3.02
59 60 8.887393 AGTAATAGGGAGTTTTTACCTCAGAAA 58.113 33.333 0.00 0.00 35.84 2.52
60 61 9.511272 GTAATAGGGAGTTTTTACCTCAGAAAA 57.489 33.333 0.00 0.00 35.84 2.29
62 63 9.601810 AATAGGGAGTTTTTACCTCAGAAAATT 57.398 29.630 0.00 0.00 35.84 1.82
63 64 7.526142 AGGGAGTTTTTACCTCAGAAAATTC 57.474 36.000 0.00 0.00 33.39 2.17
64 65 7.066781 AGGGAGTTTTTACCTCAGAAAATTCA 58.933 34.615 0.00 0.00 34.86 2.57
65 66 7.014326 AGGGAGTTTTTACCTCAGAAAATTCAC 59.986 37.037 0.00 0.00 36.02 3.18
66 67 7.145985 GGAGTTTTTACCTCAGAAAATTCACC 58.854 38.462 0.00 0.00 34.86 4.02
67 68 6.735130 AGTTTTTACCTCAGAAAATTCACCG 58.265 36.000 0.00 0.00 0.00 4.94
68 69 6.544564 AGTTTTTACCTCAGAAAATTCACCGA 59.455 34.615 0.00 0.00 0.00 4.69
69 70 6.945938 TTTTACCTCAGAAAATTCACCGAA 57.054 33.333 0.00 0.00 0.00 4.30
70 71 6.554334 TTTACCTCAGAAAATTCACCGAAG 57.446 37.500 0.00 0.00 0.00 3.79
71 72 2.814336 ACCTCAGAAAATTCACCGAAGC 59.186 45.455 0.00 0.00 0.00 3.86
72 73 3.077359 CCTCAGAAAATTCACCGAAGCT 58.923 45.455 0.00 0.00 0.00 3.74
73 74 4.253685 CCTCAGAAAATTCACCGAAGCTA 58.746 43.478 0.00 0.00 0.00 3.32
74 75 4.331168 CCTCAGAAAATTCACCGAAGCTAG 59.669 45.833 0.00 0.00 0.00 3.42
75 76 5.147330 TCAGAAAATTCACCGAAGCTAGA 57.853 39.130 0.00 0.00 0.00 2.43
76 77 5.547465 TCAGAAAATTCACCGAAGCTAGAA 58.453 37.500 0.00 0.00 0.00 2.10
77 78 6.173339 TCAGAAAATTCACCGAAGCTAGAAT 58.827 36.000 0.00 0.00 32.45 2.40
78 79 7.327975 TCAGAAAATTCACCGAAGCTAGAATA 58.672 34.615 0.00 0.00 31.01 1.75
79 80 7.492669 TCAGAAAATTCACCGAAGCTAGAATAG 59.507 37.037 0.00 0.00 43.09 1.73
80 81 7.492669 CAGAAAATTCACCGAAGCTAGAATAGA 59.507 37.037 0.00 0.00 42.77 1.98
81 82 7.708752 AGAAAATTCACCGAAGCTAGAATAGAG 59.291 37.037 0.00 0.00 42.77 2.43
82 83 6.472686 AATTCACCGAAGCTAGAATAGAGT 57.527 37.500 0.00 0.00 42.77 3.24
83 84 5.916661 TTCACCGAAGCTAGAATAGAGTT 57.083 39.130 0.00 0.00 42.77 3.01
84 85 5.250235 TCACCGAAGCTAGAATAGAGTTG 57.750 43.478 0.00 0.00 42.77 3.16
85 86 4.705507 TCACCGAAGCTAGAATAGAGTTGT 59.294 41.667 0.00 0.00 42.77 3.32
86 87 5.185249 TCACCGAAGCTAGAATAGAGTTGTT 59.815 40.000 0.00 0.00 42.77 2.83
87 88 5.289675 CACCGAAGCTAGAATAGAGTTGTTG 59.710 44.000 0.00 0.00 42.77 3.33
88 89 5.185249 ACCGAAGCTAGAATAGAGTTGTTGA 59.815 40.000 0.00 0.00 42.77 3.18
89 90 6.127310 ACCGAAGCTAGAATAGAGTTGTTGAT 60.127 38.462 0.00 0.00 42.77 2.57
90 91 6.419413 CCGAAGCTAGAATAGAGTTGTTGATC 59.581 42.308 0.00 0.00 42.77 2.92
91 92 6.141527 CGAAGCTAGAATAGAGTTGTTGATCG 59.858 42.308 0.00 0.00 42.77 3.69
92 93 5.837437 AGCTAGAATAGAGTTGTTGATCGG 58.163 41.667 0.00 0.00 42.77 4.18
93 94 5.361285 AGCTAGAATAGAGTTGTTGATCGGT 59.639 40.000 0.00 0.00 42.77 4.69
94 95 6.043411 GCTAGAATAGAGTTGTTGATCGGTT 58.957 40.000 0.00 0.00 42.77 4.44
95 96 6.019479 GCTAGAATAGAGTTGTTGATCGGTTG 60.019 42.308 0.00 0.00 42.77 3.77
96 97 5.178797 AGAATAGAGTTGTTGATCGGTTGG 58.821 41.667 0.00 0.00 0.00 3.77
97 98 2.930826 AGAGTTGTTGATCGGTTGGT 57.069 45.000 0.00 0.00 0.00 3.67
98 99 2.767505 AGAGTTGTTGATCGGTTGGTC 58.232 47.619 0.00 0.00 0.00 4.02
99 100 2.104111 AGAGTTGTTGATCGGTTGGTCA 59.896 45.455 0.00 0.00 0.00 4.02
100 101 2.875933 GAGTTGTTGATCGGTTGGTCAA 59.124 45.455 0.00 0.00 32.31 3.18
106 107 5.968387 GTTGATCGGTTGGTCAACTATAG 57.032 43.478 12.81 0.00 46.58 1.31
107 108 4.054780 TGATCGGTTGGTCAACTATAGC 57.945 45.455 12.75 3.73 40.94 2.97
108 109 2.973694 TCGGTTGGTCAACTATAGCC 57.026 50.000 12.75 0.00 40.94 3.93
109 110 1.135527 TCGGTTGGTCAACTATAGCCG 59.864 52.381 12.75 2.32 40.94 5.52
110 111 1.296727 GGTTGGTCAACTATAGCCGC 58.703 55.000 12.75 0.00 40.94 6.53
111 112 1.134491 GGTTGGTCAACTATAGCCGCT 60.134 52.381 12.75 0.00 40.94 5.52
112 113 2.202566 GTTGGTCAACTATAGCCGCTC 58.797 52.381 0.00 0.00 38.25 5.03
113 114 0.750850 TGGTCAACTATAGCCGCTCC 59.249 55.000 0.00 0.00 0.00 4.70
114 115 0.318784 GGTCAACTATAGCCGCTCCG 60.319 60.000 0.00 0.00 0.00 4.63
115 116 0.666913 GTCAACTATAGCCGCTCCGA 59.333 55.000 0.00 0.00 0.00 4.55
116 117 0.952280 TCAACTATAGCCGCTCCGAG 59.048 55.000 0.00 0.00 0.00 4.63
117 118 0.952280 CAACTATAGCCGCTCCGAGA 59.048 55.000 0.00 0.00 0.00 4.04
118 119 1.068885 CAACTATAGCCGCTCCGAGAG 60.069 57.143 0.00 0.00 0.00 3.20
119 120 0.397187 ACTATAGCCGCTCCGAGAGA 59.603 55.000 0.00 0.00 0.00 3.10
120 121 1.202782 ACTATAGCCGCTCCGAGAGAA 60.203 52.381 0.00 0.00 0.00 2.87
121 122 1.198178 CTATAGCCGCTCCGAGAGAAC 59.802 57.143 0.00 0.00 0.00 3.01
122 123 0.466555 ATAGCCGCTCCGAGAGAACT 60.467 55.000 0.00 0.02 0.00 3.01
123 124 0.179702 TAGCCGCTCCGAGAGAACTA 59.820 55.000 0.00 0.00 0.00 2.24
124 125 1.064458 GCCGCTCCGAGAGAACTAC 59.936 63.158 0.00 0.00 0.00 2.73
125 126 1.378124 GCCGCTCCGAGAGAACTACT 61.378 60.000 0.00 0.00 0.00 2.57
126 127 0.378962 CCGCTCCGAGAGAACTACTG 59.621 60.000 0.00 0.00 0.00 2.74
127 128 0.248296 CGCTCCGAGAGAACTACTGC 60.248 60.000 0.00 0.00 0.00 4.40
128 129 0.101579 GCTCCGAGAGAACTACTGCC 59.898 60.000 0.00 0.00 0.00 4.85
129 130 0.378962 CTCCGAGAGAACTACTGCCG 59.621 60.000 0.00 0.00 0.00 5.69
130 131 0.322277 TCCGAGAGAACTACTGCCGT 60.322 55.000 0.00 0.00 0.00 5.68
131 132 0.179161 CCGAGAGAACTACTGCCGTG 60.179 60.000 0.00 0.00 0.00 4.94
132 133 0.522180 CGAGAGAACTACTGCCGTGT 59.478 55.000 0.00 0.00 0.00 4.49
133 134 1.729472 CGAGAGAACTACTGCCGTGTG 60.729 57.143 0.00 0.00 0.00 3.82
134 135 0.603569 AGAGAACTACTGCCGTGTGG 59.396 55.000 0.00 0.00 38.77 4.17
135 136 0.317479 GAGAACTACTGCCGTGTGGT 59.683 55.000 0.00 0.00 37.67 4.16
136 137 0.756903 AGAACTACTGCCGTGTGGTT 59.243 50.000 3.74 3.74 42.78 3.67
137 138 1.965643 AGAACTACTGCCGTGTGGTTA 59.034 47.619 4.02 0.00 40.76 2.85
138 139 2.366266 AGAACTACTGCCGTGTGGTTAA 59.634 45.455 4.02 0.00 40.76 2.01
139 140 2.914695 ACTACTGCCGTGTGGTTAAA 57.085 45.000 0.00 0.00 37.67 1.52
140 141 2.486918 ACTACTGCCGTGTGGTTAAAC 58.513 47.619 0.00 0.00 37.67 2.01
141 142 2.103601 ACTACTGCCGTGTGGTTAAACT 59.896 45.455 0.00 0.00 37.67 2.66
142 143 1.589803 ACTGCCGTGTGGTTAAACTC 58.410 50.000 0.00 0.00 37.67 3.01
143 144 0.511221 CTGCCGTGTGGTTAAACTCG 59.489 55.000 0.00 0.00 37.67 4.18
145 146 3.294079 CCGTGTGGTTAAACTCGGT 57.706 52.632 11.04 0.00 46.78 4.69
146 147 1.585297 CCGTGTGGTTAAACTCGGTT 58.415 50.000 11.04 0.00 46.78 4.44
147 148 1.941975 CCGTGTGGTTAAACTCGGTTT 59.058 47.619 11.04 7.11 46.78 3.27
148 149 2.032636 CCGTGTGGTTAAACTCGGTTTC 60.033 50.000 11.04 0.00 46.78 2.78
149 150 2.608546 CGTGTGGTTAAACTCGGTTTCA 59.391 45.455 5.46 0.00 37.01 2.69
150 151 3.544637 CGTGTGGTTAAACTCGGTTTCAC 60.545 47.826 5.46 8.34 37.01 3.18
151 152 3.624410 GTGTGGTTAAACTCGGTTTCACT 59.376 43.478 14.68 0.00 37.01 3.41
152 153 4.095334 GTGTGGTTAAACTCGGTTTCACTT 59.905 41.667 14.68 0.00 37.01 3.16
153 154 4.701171 TGTGGTTAAACTCGGTTTCACTTT 59.299 37.500 14.68 0.00 37.01 2.66
154 155 5.032220 GTGGTTAAACTCGGTTTCACTTTG 58.968 41.667 5.46 0.00 37.01 2.77
155 156 4.701171 TGGTTAAACTCGGTTTCACTTTGT 59.299 37.500 5.46 0.00 37.01 2.83
156 157 5.879223 TGGTTAAACTCGGTTTCACTTTGTA 59.121 36.000 5.46 0.00 37.01 2.41
157 158 6.543100 TGGTTAAACTCGGTTTCACTTTGTAT 59.457 34.615 5.46 0.00 37.01 2.29
158 159 7.067251 TGGTTAAACTCGGTTTCACTTTGTATT 59.933 33.333 5.46 0.00 37.01 1.89
159 160 7.377662 GGTTAAACTCGGTTTCACTTTGTATTG 59.622 37.037 5.46 0.00 37.01 1.90
160 161 6.687081 AAACTCGGTTTCACTTTGTATTGA 57.313 33.333 0.00 0.00 28.86 2.57
161 162 5.924475 ACTCGGTTTCACTTTGTATTGAG 57.076 39.130 0.00 0.00 0.00 3.02
162 163 4.755123 ACTCGGTTTCACTTTGTATTGAGG 59.245 41.667 0.00 0.00 0.00 3.86
163 164 4.963373 TCGGTTTCACTTTGTATTGAGGA 58.037 39.130 0.00 0.00 0.00 3.71
164 165 5.556915 TCGGTTTCACTTTGTATTGAGGAT 58.443 37.500 0.00 0.00 0.00 3.24
165 166 6.001460 TCGGTTTCACTTTGTATTGAGGATT 58.999 36.000 0.00 0.00 0.00 3.01
166 167 6.488683 TCGGTTTCACTTTGTATTGAGGATTT 59.511 34.615 0.00 0.00 0.00 2.17
167 168 6.582295 CGGTTTCACTTTGTATTGAGGATTTG 59.418 38.462 0.00 0.00 0.00 2.32
168 169 7.433680 GGTTTCACTTTGTATTGAGGATTTGT 58.566 34.615 0.00 0.00 0.00 2.83
169 170 7.382218 GGTTTCACTTTGTATTGAGGATTTGTG 59.618 37.037 0.00 0.00 0.00 3.33
170 171 6.573664 TCACTTTGTATTGAGGATTTGTGG 57.426 37.500 0.00 0.00 0.00 4.17
171 172 5.048083 TCACTTTGTATTGAGGATTTGTGGC 60.048 40.000 0.00 0.00 0.00 5.01
172 173 4.220602 ACTTTGTATTGAGGATTTGTGGCC 59.779 41.667 0.00 0.00 0.00 5.36
173 174 3.737559 TGTATTGAGGATTTGTGGCCT 57.262 42.857 3.32 0.00 37.18 5.19
174 175 4.046286 TGTATTGAGGATTTGTGGCCTT 57.954 40.909 3.32 0.00 33.84 4.35
175 176 4.415596 TGTATTGAGGATTTGTGGCCTTT 58.584 39.130 3.32 0.00 33.84 3.11
176 177 4.462483 TGTATTGAGGATTTGTGGCCTTTC 59.538 41.667 3.32 0.00 33.84 2.62
177 178 1.533625 TGAGGATTTGTGGCCTTTCG 58.466 50.000 3.32 0.00 33.84 3.46
178 179 1.073125 TGAGGATTTGTGGCCTTTCGA 59.927 47.619 3.32 0.00 33.84 3.71
179 180 1.468914 GAGGATTTGTGGCCTTTCGAC 59.531 52.381 3.32 0.00 33.84 4.20
180 181 1.073923 AGGATTTGTGGCCTTTCGACT 59.926 47.619 3.32 0.00 0.00 4.18
181 182 1.200020 GGATTTGTGGCCTTTCGACTG 59.800 52.381 3.32 0.00 0.00 3.51
182 183 1.880027 GATTTGTGGCCTTTCGACTGT 59.120 47.619 3.32 0.00 0.00 3.55
183 184 2.623878 TTTGTGGCCTTTCGACTGTA 57.376 45.000 3.32 0.00 0.00 2.74
184 185 2.623878 TTGTGGCCTTTCGACTGTAA 57.376 45.000 3.32 0.00 0.00 2.41
185 186 1.873698 TGTGGCCTTTCGACTGTAAC 58.126 50.000 3.32 0.00 0.00 2.50
186 187 1.139256 TGTGGCCTTTCGACTGTAACA 59.861 47.619 3.32 0.00 0.00 2.41
187 188 1.529865 GTGGCCTTTCGACTGTAACAC 59.470 52.381 3.32 0.00 0.00 3.32
188 189 1.414919 TGGCCTTTCGACTGTAACACT 59.585 47.619 3.32 0.00 0.00 3.55
189 190 2.629137 TGGCCTTTCGACTGTAACACTA 59.371 45.455 3.32 0.00 0.00 2.74
190 191 3.259876 TGGCCTTTCGACTGTAACACTAT 59.740 43.478 3.32 0.00 0.00 2.12
191 192 4.463539 TGGCCTTTCGACTGTAACACTATA 59.536 41.667 3.32 0.00 0.00 1.31
192 193 5.128171 TGGCCTTTCGACTGTAACACTATAT 59.872 40.000 3.32 0.00 0.00 0.86
193 194 5.690857 GGCCTTTCGACTGTAACACTATATC 59.309 44.000 0.00 0.00 0.00 1.63
194 195 6.461231 GGCCTTTCGACTGTAACACTATATCT 60.461 42.308 0.00 0.00 0.00 1.98
195 196 6.979238 GCCTTTCGACTGTAACACTATATCTT 59.021 38.462 0.00 0.00 0.00 2.40
196 197 7.491696 GCCTTTCGACTGTAACACTATATCTTT 59.508 37.037 0.00 0.00 0.00 2.52
218 219 9.081204 TCTTTACAATAAAAACTCCCTTTACCC 57.919 33.333 0.00 0.00 0.00 3.69
219 220 7.779754 TTACAATAAAAACTCCCTTTACCCC 57.220 36.000 0.00 0.00 0.00 4.95
220 221 4.768448 ACAATAAAAACTCCCTTTACCCCG 59.232 41.667 0.00 0.00 0.00 5.73
221 222 4.932911 ATAAAAACTCCCTTTACCCCGA 57.067 40.909 0.00 0.00 0.00 5.14
222 223 3.598693 AAAAACTCCCTTTACCCCGAA 57.401 42.857 0.00 0.00 0.00 4.30
223 224 3.598693 AAAACTCCCTTTACCCCGAAA 57.401 42.857 0.00 0.00 0.00 3.46
224 225 3.598693 AAACTCCCTTTACCCCGAAAA 57.401 42.857 0.00 0.00 0.00 2.29
225 226 3.598693 AACTCCCTTTACCCCGAAAAA 57.401 42.857 0.00 0.00 0.00 1.94
346 347 2.512056 TGAATCCCGGTTGTCCCATATT 59.488 45.455 0.00 0.00 0.00 1.28
347 348 2.656947 ATCCCGGTTGTCCCATATTG 57.343 50.000 0.00 0.00 0.00 1.90
379 1771 3.052082 GCTTCTCTGCAAGCGCCA 61.052 61.111 2.29 0.00 39.55 5.69
392 1784 4.459331 CGCCATCAACGCCAACCG 62.459 66.667 0.00 0.00 44.21 4.44
427 1819 2.966516 CGAATAGGAGCTCCCCTACTTT 59.033 50.000 29.54 11.45 41.25 2.66
428 1820 4.150359 CGAATAGGAGCTCCCCTACTTTA 58.850 47.826 29.54 13.42 41.25 1.85
437 1829 4.349342 AGCTCCCCTACTTTATCCATCTTG 59.651 45.833 0.00 0.00 0.00 3.02
451 1847 0.995024 ATCTTGGAGTTGGGTCCTGG 59.005 55.000 0.00 0.00 37.52 4.45
460 1856 3.319198 GGGTCCTGGTCTTCGCCA 61.319 66.667 0.00 0.00 36.97 5.69
570 1966 2.123589 TCCAGGTCCAGTTTTGTCAGA 58.876 47.619 0.00 0.00 0.00 3.27
658 2071 4.100084 CCGTGGGATCTGCCAGCA 62.100 66.667 0.00 0.00 38.95 4.41
659 2072 2.821366 CGTGGGATCTGCCAGCAC 60.821 66.667 0.00 0.00 38.95 4.40
661 2074 4.100084 TGGGATCTGCCAGCACGG 62.100 66.667 0.00 0.00 38.95 4.94
662 2075 4.864334 GGGATCTGCCAGCACGGG 62.864 72.222 0.00 0.00 38.95 5.28
692 2108 3.139077 GCTCGGACAAAAAGAAAGGAGA 58.861 45.455 0.00 0.00 0.00 3.71
693 2109 3.187432 GCTCGGACAAAAAGAAAGGAGAG 59.813 47.826 0.00 0.00 0.00 3.20
770 2234 2.763902 CCCCCGCTCCTTTCCTTT 59.236 61.111 0.00 0.00 0.00 3.11
777 2246 0.405973 GCTCCTTTCCTTTCCCCAGT 59.594 55.000 0.00 0.00 0.00 4.00
914 2398 1.375326 GACGAGGCCTTTTCTGGGT 59.625 57.895 6.77 0.00 0.00 4.51
942 2426 3.991051 CCGGGTGATCGATCGGGG 61.991 72.222 20.03 13.76 38.93 5.73
998 2482 4.798682 GGGAGGAAGGGAGGCGGA 62.799 72.222 0.00 0.00 0.00 5.54
1233 2721 0.602106 CGGTCGGCTCCGTCTATCTA 60.602 60.000 8.28 0.00 44.77 1.98
1250 2738 4.652175 ATCTATGATACAATTGCGTGCG 57.348 40.909 5.05 0.00 0.00 5.34
1258 2746 1.199789 ACAATTGCGTGCGATGTGAAT 59.800 42.857 5.05 0.00 0.00 2.57
1278 2766 2.077413 TTGAAATGCAAATGCCGTCC 57.923 45.000 2.46 0.00 41.18 4.79
1279 2767 0.109365 TGAAATGCAAATGCCGTCCG 60.109 50.000 2.46 0.00 41.18 4.79
1280 2768 0.109319 GAAATGCAAATGCCGTCCGT 60.109 50.000 2.46 0.00 41.18 4.69
1281 2769 1.131504 GAAATGCAAATGCCGTCCGTA 59.868 47.619 2.46 0.00 41.18 4.02
1282 2770 0.732571 AATGCAAATGCCGTCCGTAG 59.267 50.000 2.46 0.00 41.18 3.51
1283 2771 1.714899 ATGCAAATGCCGTCCGTAGC 61.715 55.000 2.46 0.00 41.18 3.58
1284 2772 2.701006 CAAATGCCGTCCGTAGCG 59.299 61.111 0.00 0.00 0.00 4.26
1285 2773 2.098233 CAAATGCCGTCCGTAGCGT 61.098 57.895 0.00 0.00 0.00 5.07
1286 2774 1.808390 AAATGCCGTCCGTAGCGTC 60.808 57.895 0.00 0.00 0.00 5.19
1298 2786 1.057285 CGTAGCGTCGTCATTTGTGAC 59.943 52.381 0.00 0.00 35.59 3.67
1301 2789 0.949105 GCGTCGTCATTTGTGACCCT 60.949 55.000 3.24 0.00 35.52 4.34
1333 2825 1.526686 TGTGCTGTGGCCTGTTGAG 60.527 57.895 3.32 0.00 37.74 3.02
1345 2837 3.612517 TGTTGAGCAGAGCATTCGT 57.387 47.368 0.00 0.00 0.00 3.85
1400 2892 5.478679 ACGGGAGATCTAGGTGAATGAATAG 59.521 44.000 0.00 0.00 0.00 1.73
1488 2980 1.001158 GAGCGGACACCTAGCATAGAC 60.001 57.143 0.00 0.00 42.77 2.59
1559 3051 1.017387 CCGATGTAGGCTTTGCTTCC 58.983 55.000 0.00 0.00 0.00 3.46
1711 3203 1.516161 AGGTAAACGGTTTTCGGAGC 58.484 50.000 11.87 3.45 44.45 4.70
1839 3337 1.217779 GAGAGCAGAGTCTGTGCCC 59.782 63.158 21.06 6.88 42.24 5.36
1892 3390 2.045926 GTAGTGCTGGCCTGGGTG 60.046 66.667 12.06 0.00 0.00 4.61
2088 3586 1.681166 GCTCATCATTGGTGCTCCAGT 60.681 52.381 7.68 1.82 45.22 4.00
2099 3597 5.195001 TGGTGCTCCAGTTAAAATGTTTC 57.805 39.130 2.64 0.00 39.03 2.78
2309 3807 4.667573 AGAGAATCCCTTTTGTTCCTTCC 58.332 43.478 0.00 0.00 33.66 3.46
2897 4608 2.101415 GCAAAAGGTTCTTGCTGTTCCT 59.899 45.455 0.41 0.00 44.66 3.36
2898 4609 3.796844 GCAAAAGGTTCTTGCTGTTCCTC 60.797 47.826 0.41 0.00 44.66 3.71
2899 4610 2.278332 AAGGTTCTTGCTGTTCCTCC 57.722 50.000 0.00 0.00 0.00 4.30
2918 4629 1.151668 CAGTTGAAGAGCTGGTTCCG 58.848 55.000 0.00 0.00 0.00 4.30
2936 4647 3.173965 TCCGGTGGAAGAGATTCTTTCT 58.826 45.455 0.00 0.00 36.73 2.52
3153 4864 7.855409 CACTTGTACAATTGAGAAATCGAACAA 59.145 33.333 18.39 7.05 0.00 2.83
3154 4865 7.855904 ACTTGTACAATTGAGAAATCGAACAAC 59.144 33.333 13.59 0.00 0.00 3.32
3155 4866 7.252965 TGTACAATTGAGAAATCGAACAACA 57.747 32.000 13.59 0.00 0.00 3.33
3285 4998 4.221530 AGACCTGATCATATGACTGAGCA 58.778 43.478 7.78 0.00 39.10 4.26
3294 5007 4.633126 TCATATGACTGAGCAAGCACTTTC 59.367 41.667 0.00 0.00 0.00 2.62
3324 5038 6.091437 CAGGCTTGATGTTTGAGAAATTCTC 58.909 40.000 15.62 15.62 43.65 2.87
3341 5055 8.012241 AGAAATTCTCGACTTTTCTTCAATTCG 58.988 33.333 6.65 0.00 36.55 3.34
3381 5095 7.820648 TCAATCCTCTTTTGAATTGCTCTAAC 58.179 34.615 0.00 0.00 30.44 2.34
3506 5221 9.285770 GGTAATTTATTGAATTTTCACGTCTCC 57.714 33.333 0.00 0.00 38.80 3.71
3594 5589 3.368495 GTGTGTTCCATCGGTTTTGTTC 58.632 45.455 0.00 0.00 0.00 3.18
3665 5660 4.081862 ACTGGCAGATTGGAATTTCACATG 60.082 41.667 23.66 0.00 0.00 3.21
3814 5809 1.946768 CGTATACATTGGGCCTTGGTG 59.053 52.381 4.53 0.57 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.922477 TCATCAACTCCTTAATCTCTAGAACTA 57.078 33.333 0.00 0.00 0.00 2.24
8 9 8.830915 TCATCAACTCCTTAATCTCTAGAACT 57.169 34.615 0.00 0.00 0.00 3.01
9 10 8.691797 ACTCATCAACTCCTTAATCTCTAGAAC 58.308 37.037 0.00 0.00 0.00 3.01
10 11 8.830915 ACTCATCAACTCCTTAATCTCTAGAA 57.169 34.615 0.00 0.00 0.00 2.10
11 12 9.922477 TTACTCATCAACTCCTTAATCTCTAGA 57.078 33.333 0.00 0.00 0.00 2.43
15 16 9.921637 CCTATTACTCATCAACTCCTTAATCTC 57.078 37.037 0.00 0.00 0.00 2.75
16 17 8.875168 CCCTATTACTCATCAACTCCTTAATCT 58.125 37.037 0.00 0.00 0.00 2.40
17 18 8.871125 TCCCTATTACTCATCAACTCCTTAATC 58.129 37.037 0.00 0.00 0.00 1.75
18 19 8.798975 TCCCTATTACTCATCAACTCCTTAAT 57.201 34.615 0.00 0.00 0.00 1.40
19 20 7.844779 ACTCCCTATTACTCATCAACTCCTTAA 59.155 37.037 0.00 0.00 0.00 1.85
20 21 7.363031 ACTCCCTATTACTCATCAACTCCTTA 58.637 38.462 0.00 0.00 0.00 2.69
21 22 6.206042 ACTCCCTATTACTCATCAACTCCTT 58.794 40.000 0.00 0.00 0.00 3.36
22 23 5.782925 ACTCCCTATTACTCATCAACTCCT 58.217 41.667 0.00 0.00 0.00 3.69
23 24 6.487299 AACTCCCTATTACTCATCAACTCC 57.513 41.667 0.00 0.00 0.00 3.85
24 25 8.794335 AAAAACTCCCTATTACTCATCAACTC 57.206 34.615 0.00 0.00 0.00 3.01
25 26 9.668497 GTAAAAACTCCCTATTACTCATCAACT 57.332 33.333 0.00 0.00 0.00 3.16
26 27 8.890718 GGTAAAAACTCCCTATTACTCATCAAC 58.109 37.037 0.00 0.00 0.00 3.18
27 28 8.832735 AGGTAAAAACTCCCTATTACTCATCAA 58.167 33.333 0.00 0.00 0.00 2.57
28 29 8.388656 AGGTAAAAACTCCCTATTACTCATCA 57.611 34.615 0.00 0.00 0.00 3.07
29 30 8.483758 TGAGGTAAAAACTCCCTATTACTCATC 58.516 37.037 0.00 0.00 34.06 2.92
30 31 8.388656 TGAGGTAAAAACTCCCTATTACTCAT 57.611 34.615 0.00 0.00 34.06 2.90
31 32 7.676893 TCTGAGGTAAAAACTCCCTATTACTCA 59.323 37.037 0.00 0.00 34.06 3.41
32 33 8.075761 TCTGAGGTAAAAACTCCCTATTACTC 57.924 38.462 0.00 0.00 34.06 2.59
33 34 8.445361 TTCTGAGGTAAAAACTCCCTATTACT 57.555 34.615 0.00 0.00 34.06 2.24
34 35 9.511272 TTTTCTGAGGTAAAAACTCCCTATTAC 57.489 33.333 0.00 0.00 34.06 1.89
36 37 9.601810 AATTTTCTGAGGTAAAAACTCCCTATT 57.398 29.630 0.00 0.00 34.06 1.73
37 38 9.244292 GAATTTTCTGAGGTAAAAACTCCCTAT 57.756 33.333 0.00 0.00 34.06 2.57
38 39 8.221944 TGAATTTTCTGAGGTAAAAACTCCCTA 58.778 33.333 0.00 0.00 34.06 3.53
39 40 7.014326 GTGAATTTTCTGAGGTAAAAACTCCCT 59.986 37.037 0.00 0.00 34.06 4.20
40 41 7.145985 GTGAATTTTCTGAGGTAAAAACTCCC 58.854 38.462 0.00 0.00 34.06 4.30
41 42 7.145985 GGTGAATTTTCTGAGGTAAAAACTCC 58.854 38.462 0.00 0.00 34.06 3.85
42 43 6.856426 CGGTGAATTTTCTGAGGTAAAAACTC 59.144 38.462 0.00 0.00 35.55 3.01
43 44 6.544564 TCGGTGAATTTTCTGAGGTAAAAACT 59.455 34.615 0.00 0.00 30.20 2.66
44 45 6.731164 TCGGTGAATTTTCTGAGGTAAAAAC 58.269 36.000 0.00 0.00 30.20 2.43
45 46 6.945938 TCGGTGAATTTTCTGAGGTAAAAA 57.054 33.333 0.00 0.00 30.20 1.94
46 47 6.514376 GCTTCGGTGAATTTTCTGAGGTAAAA 60.514 38.462 0.00 0.00 0.00 1.52
47 48 5.048991 GCTTCGGTGAATTTTCTGAGGTAAA 60.049 40.000 0.00 0.00 0.00 2.01
48 49 4.454504 GCTTCGGTGAATTTTCTGAGGTAA 59.545 41.667 0.00 0.00 0.00 2.85
49 50 4.000988 GCTTCGGTGAATTTTCTGAGGTA 58.999 43.478 0.00 0.00 0.00 3.08
50 51 2.814336 GCTTCGGTGAATTTTCTGAGGT 59.186 45.455 0.00 0.00 0.00 3.85
51 52 3.077359 AGCTTCGGTGAATTTTCTGAGG 58.923 45.455 0.00 0.00 0.00 3.86
52 53 5.171476 TCTAGCTTCGGTGAATTTTCTGAG 58.829 41.667 0.00 0.00 0.00 3.35
53 54 5.147330 TCTAGCTTCGGTGAATTTTCTGA 57.853 39.130 0.00 0.00 0.00 3.27
54 55 5.862924 TTCTAGCTTCGGTGAATTTTCTG 57.137 39.130 0.00 0.00 0.00 3.02
55 56 7.556844 TCTATTCTAGCTTCGGTGAATTTTCT 58.443 34.615 0.00 0.00 32.33 2.52
56 57 7.492994 ACTCTATTCTAGCTTCGGTGAATTTTC 59.507 37.037 0.00 0.00 32.33 2.29
57 58 7.331791 ACTCTATTCTAGCTTCGGTGAATTTT 58.668 34.615 0.00 0.00 32.33 1.82
58 59 6.879400 ACTCTATTCTAGCTTCGGTGAATTT 58.121 36.000 0.00 0.00 32.33 1.82
59 60 6.472686 ACTCTATTCTAGCTTCGGTGAATT 57.527 37.500 0.00 0.00 32.33 2.17
60 61 6.127310 ACAACTCTATTCTAGCTTCGGTGAAT 60.127 38.462 0.00 0.00 34.16 2.57
61 62 5.185249 ACAACTCTATTCTAGCTTCGGTGAA 59.815 40.000 0.00 0.00 0.00 3.18
62 63 4.705507 ACAACTCTATTCTAGCTTCGGTGA 59.294 41.667 0.00 0.00 0.00 4.02
63 64 5.000012 ACAACTCTATTCTAGCTTCGGTG 58.000 43.478 0.00 0.00 0.00 4.94
64 65 5.185249 TCAACAACTCTATTCTAGCTTCGGT 59.815 40.000 0.00 0.00 0.00 4.69
65 66 5.651530 TCAACAACTCTATTCTAGCTTCGG 58.348 41.667 0.00 0.00 0.00 4.30
66 67 6.141527 CGATCAACAACTCTATTCTAGCTTCG 59.858 42.308 0.00 0.00 0.00 3.79
67 68 6.419413 CCGATCAACAACTCTATTCTAGCTTC 59.581 42.308 0.00 0.00 0.00 3.86
68 69 6.127310 ACCGATCAACAACTCTATTCTAGCTT 60.127 38.462 0.00 0.00 0.00 3.74
69 70 5.361285 ACCGATCAACAACTCTATTCTAGCT 59.639 40.000 0.00 0.00 0.00 3.32
70 71 5.593010 ACCGATCAACAACTCTATTCTAGC 58.407 41.667 0.00 0.00 0.00 3.42
71 72 6.477033 CCAACCGATCAACAACTCTATTCTAG 59.523 42.308 0.00 0.00 0.00 2.43
72 73 6.070995 ACCAACCGATCAACAACTCTATTCTA 60.071 38.462 0.00 0.00 0.00 2.10
73 74 5.178797 CCAACCGATCAACAACTCTATTCT 58.821 41.667 0.00 0.00 0.00 2.40
74 75 4.935808 ACCAACCGATCAACAACTCTATTC 59.064 41.667 0.00 0.00 0.00 1.75
75 76 4.906618 ACCAACCGATCAACAACTCTATT 58.093 39.130 0.00 0.00 0.00 1.73
76 77 4.020573 TGACCAACCGATCAACAACTCTAT 60.021 41.667 0.00 0.00 0.00 1.98
77 78 3.322541 TGACCAACCGATCAACAACTCTA 59.677 43.478 0.00 0.00 0.00 2.43
78 79 2.104111 TGACCAACCGATCAACAACTCT 59.896 45.455 0.00 0.00 0.00 3.24
79 80 2.489971 TGACCAACCGATCAACAACTC 58.510 47.619 0.00 0.00 0.00 3.01
80 81 2.631160 TGACCAACCGATCAACAACT 57.369 45.000 0.00 0.00 0.00 3.16
85 86 4.439057 GCTATAGTTGACCAACCGATCAA 58.561 43.478 9.07 0.00 42.06 2.57
86 87 3.181469 GGCTATAGTTGACCAACCGATCA 60.181 47.826 9.07 0.00 42.06 2.92
87 88 3.391049 GGCTATAGTTGACCAACCGATC 58.609 50.000 9.07 0.00 42.06 3.69
88 89 2.223971 CGGCTATAGTTGACCAACCGAT 60.224 50.000 9.07 6.28 42.06 4.18
89 90 1.135527 CGGCTATAGTTGACCAACCGA 59.864 52.381 9.07 0.00 42.06 4.69
90 91 1.567504 CGGCTATAGTTGACCAACCG 58.432 55.000 9.07 0.00 42.06 4.44
91 92 1.134491 AGCGGCTATAGTTGACCAACC 60.134 52.381 0.00 0.00 42.06 3.77
92 93 2.202566 GAGCGGCTATAGTTGACCAAC 58.797 52.381 0.60 4.81 41.45 3.77
93 94 1.138266 GGAGCGGCTATAGTTGACCAA 59.862 52.381 0.60 0.00 0.00 3.67
94 95 0.750850 GGAGCGGCTATAGTTGACCA 59.249 55.000 0.60 0.00 0.00 4.02
95 96 0.318784 CGGAGCGGCTATAGTTGACC 60.319 60.000 0.60 0.00 0.00 4.02
96 97 0.666913 TCGGAGCGGCTATAGTTGAC 59.333 55.000 0.60 0.00 0.00 3.18
97 98 0.952280 CTCGGAGCGGCTATAGTTGA 59.048 55.000 0.60 0.00 0.00 3.18
98 99 0.952280 TCTCGGAGCGGCTATAGTTG 59.048 55.000 0.60 0.00 0.00 3.16
99 100 1.202782 TCTCTCGGAGCGGCTATAGTT 60.203 52.381 0.60 0.00 0.00 2.24
100 101 0.397187 TCTCTCGGAGCGGCTATAGT 59.603 55.000 0.60 0.00 0.00 2.12
101 102 1.198178 GTTCTCTCGGAGCGGCTATAG 59.802 57.143 0.60 0.58 0.00 1.31
102 103 1.202782 AGTTCTCTCGGAGCGGCTATA 60.203 52.381 0.60 0.00 0.00 1.31
103 104 0.466555 AGTTCTCTCGGAGCGGCTAT 60.467 55.000 0.60 0.00 0.00 2.97
104 105 0.179702 TAGTTCTCTCGGAGCGGCTA 59.820 55.000 0.60 0.00 0.00 3.93
105 106 1.077644 TAGTTCTCTCGGAGCGGCT 60.078 57.895 0.00 0.00 0.00 5.52
106 107 1.064458 GTAGTTCTCTCGGAGCGGC 59.936 63.158 0.00 0.00 0.00 6.53
107 108 0.378962 CAGTAGTTCTCTCGGAGCGG 59.621 60.000 0.00 0.00 0.00 5.52
108 109 0.248296 GCAGTAGTTCTCTCGGAGCG 60.248 60.000 0.00 0.00 0.00 5.03
109 110 0.101579 GGCAGTAGTTCTCTCGGAGC 59.898 60.000 0.00 0.00 0.00 4.70
110 111 0.378962 CGGCAGTAGTTCTCTCGGAG 59.621 60.000 0.00 0.00 0.00 4.63
111 112 0.322277 ACGGCAGTAGTTCTCTCGGA 60.322 55.000 0.00 0.00 0.00 4.55
112 113 0.179161 CACGGCAGTAGTTCTCTCGG 60.179 60.000 0.00 0.00 0.00 4.63
113 114 0.522180 ACACGGCAGTAGTTCTCTCG 59.478 55.000 0.00 0.00 0.00 4.04
114 115 1.402984 CCACACGGCAGTAGTTCTCTC 60.403 57.143 0.00 0.00 0.00 3.20
115 116 0.603569 CCACACGGCAGTAGTTCTCT 59.396 55.000 0.00 0.00 0.00 3.10
116 117 0.317479 ACCACACGGCAGTAGTTCTC 59.683 55.000 0.00 0.00 34.57 2.87
117 118 0.756903 AACCACACGGCAGTAGTTCT 59.243 50.000 0.00 0.00 34.57 3.01
118 119 2.443887 TAACCACACGGCAGTAGTTC 57.556 50.000 3.22 0.00 34.57 3.01
119 120 2.874086 GTTTAACCACACGGCAGTAGTT 59.126 45.455 0.00 0.00 34.57 2.24
120 121 2.103601 AGTTTAACCACACGGCAGTAGT 59.896 45.455 0.00 0.00 34.57 2.73
121 122 2.735134 GAGTTTAACCACACGGCAGTAG 59.265 50.000 0.00 0.00 34.57 2.57
122 123 2.758009 GAGTTTAACCACACGGCAGTA 58.242 47.619 0.00 0.00 34.57 2.74
123 124 1.589803 GAGTTTAACCACACGGCAGT 58.410 50.000 0.00 0.00 34.57 4.40
124 125 0.511221 CGAGTTTAACCACACGGCAG 59.489 55.000 0.00 0.00 34.57 4.85
125 126 0.881159 CCGAGTTTAACCACACGGCA 60.881 55.000 3.70 0.00 42.74 5.69
126 127 1.864176 CCGAGTTTAACCACACGGC 59.136 57.895 3.70 0.00 42.74 5.68
128 129 2.608546 TGAAACCGAGTTTAACCACACG 59.391 45.455 2.58 0.00 35.77 4.49
129 130 3.624410 AGTGAAACCGAGTTTAACCACAC 59.376 43.478 11.31 9.92 37.54 3.82
130 131 3.876341 AGTGAAACCGAGTTTAACCACA 58.124 40.909 11.31 0.82 37.54 4.17
131 132 4.888038 AAGTGAAACCGAGTTTAACCAC 57.112 40.909 11.31 10.42 37.54 4.16
132 133 4.701171 ACAAAGTGAAACCGAGTTTAACCA 59.299 37.500 11.31 1.37 37.54 3.67
133 134 5.239359 ACAAAGTGAAACCGAGTTTAACC 57.761 39.130 11.31 0.00 37.54 2.85
134 135 8.124199 TCAATACAAAGTGAAACCGAGTTTAAC 58.876 33.333 8.27 8.27 37.20 2.01
135 136 8.211116 TCAATACAAAGTGAAACCGAGTTTAA 57.789 30.769 2.58 0.00 35.77 1.52
136 137 7.041644 CCTCAATACAAAGTGAAACCGAGTTTA 60.042 37.037 2.58 0.00 35.77 2.01
137 138 6.238648 CCTCAATACAAAGTGAAACCGAGTTT 60.239 38.462 2.23 2.23 38.54 2.66
138 139 5.238650 CCTCAATACAAAGTGAAACCGAGTT 59.761 40.000 0.00 0.00 37.80 3.01
139 140 4.755123 CCTCAATACAAAGTGAAACCGAGT 59.245 41.667 0.00 0.00 37.80 4.18
140 141 4.994852 TCCTCAATACAAAGTGAAACCGAG 59.005 41.667 0.00 0.00 37.80 4.63
141 142 4.963373 TCCTCAATACAAAGTGAAACCGA 58.037 39.130 0.00 0.00 37.80 4.69
142 143 5.880054 ATCCTCAATACAAAGTGAAACCG 57.120 39.130 0.00 0.00 37.80 4.44
143 144 7.382218 CACAAATCCTCAATACAAAGTGAAACC 59.618 37.037 0.00 0.00 37.80 3.27
144 145 7.382218 CCACAAATCCTCAATACAAAGTGAAAC 59.618 37.037 0.00 0.00 0.00 2.78
145 146 7.432869 CCACAAATCCTCAATACAAAGTGAAA 58.567 34.615 0.00 0.00 0.00 2.69
146 147 6.516527 GCCACAAATCCTCAATACAAAGTGAA 60.517 38.462 0.00 0.00 0.00 3.18
147 148 5.048083 GCCACAAATCCTCAATACAAAGTGA 60.048 40.000 0.00 0.00 0.00 3.41
148 149 5.163513 GCCACAAATCCTCAATACAAAGTG 58.836 41.667 0.00 0.00 0.00 3.16
149 150 4.220602 GGCCACAAATCCTCAATACAAAGT 59.779 41.667 0.00 0.00 0.00 2.66
150 151 4.463891 AGGCCACAAATCCTCAATACAAAG 59.536 41.667 5.01 0.00 0.00 2.77
151 152 4.415596 AGGCCACAAATCCTCAATACAAA 58.584 39.130 5.01 0.00 0.00 2.83
152 153 4.046286 AGGCCACAAATCCTCAATACAA 57.954 40.909 5.01 0.00 0.00 2.41
153 154 3.737559 AGGCCACAAATCCTCAATACA 57.262 42.857 5.01 0.00 0.00 2.29
154 155 4.438744 CGAAAGGCCACAAATCCTCAATAC 60.439 45.833 5.01 0.00 0.00 1.89
155 156 3.694072 CGAAAGGCCACAAATCCTCAATA 59.306 43.478 5.01 0.00 0.00 1.90
156 157 2.493278 CGAAAGGCCACAAATCCTCAAT 59.507 45.455 5.01 0.00 0.00 2.57
157 158 1.885887 CGAAAGGCCACAAATCCTCAA 59.114 47.619 5.01 0.00 0.00 3.02
158 159 1.073125 TCGAAAGGCCACAAATCCTCA 59.927 47.619 5.01 0.00 0.00 3.86
159 160 1.468914 GTCGAAAGGCCACAAATCCTC 59.531 52.381 5.01 0.00 0.00 3.71
160 161 1.073923 AGTCGAAAGGCCACAAATCCT 59.926 47.619 5.01 0.00 35.23 3.24
161 162 1.200020 CAGTCGAAAGGCCACAAATCC 59.800 52.381 5.01 0.00 35.23 3.01
162 163 1.880027 ACAGTCGAAAGGCCACAAATC 59.120 47.619 5.01 0.00 35.23 2.17
163 164 1.981256 ACAGTCGAAAGGCCACAAAT 58.019 45.000 5.01 0.00 35.23 2.32
164 165 2.614983 GTTACAGTCGAAAGGCCACAAA 59.385 45.455 5.01 0.00 35.23 2.83
165 166 2.215196 GTTACAGTCGAAAGGCCACAA 58.785 47.619 5.01 0.00 35.23 3.33
166 167 1.139256 TGTTACAGTCGAAAGGCCACA 59.861 47.619 5.01 0.00 35.23 4.17
167 168 1.529865 GTGTTACAGTCGAAAGGCCAC 59.470 52.381 5.01 0.00 35.23 5.01
168 169 1.414919 AGTGTTACAGTCGAAAGGCCA 59.585 47.619 5.01 0.00 35.23 5.36
169 170 2.165319 AGTGTTACAGTCGAAAGGCC 57.835 50.000 0.00 0.00 35.23 5.19
170 171 6.505272 AGATATAGTGTTACAGTCGAAAGGC 58.495 40.000 0.00 0.00 0.00 4.35
171 172 8.928270 AAAGATATAGTGTTACAGTCGAAAGG 57.072 34.615 0.00 0.00 0.00 3.11
192 193 9.081204 GGGTAAAGGGAGTTTTTATTGTAAAGA 57.919 33.333 0.00 0.00 0.00 2.52
193 194 8.308931 GGGGTAAAGGGAGTTTTTATTGTAAAG 58.691 37.037 0.00 0.00 0.00 1.85
194 195 7.039853 CGGGGTAAAGGGAGTTTTTATTGTAAA 60.040 37.037 0.00 0.00 0.00 2.01
195 196 6.433716 CGGGGTAAAGGGAGTTTTTATTGTAA 59.566 38.462 0.00 0.00 0.00 2.41
196 197 5.945191 CGGGGTAAAGGGAGTTTTTATTGTA 59.055 40.000 0.00 0.00 0.00 2.41
197 198 4.768448 CGGGGTAAAGGGAGTTTTTATTGT 59.232 41.667 0.00 0.00 0.00 2.71
198 199 5.011586 TCGGGGTAAAGGGAGTTTTTATTG 58.988 41.667 0.00 0.00 0.00 1.90
199 200 5.259627 TCGGGGTAAAGGGAGTTTTTATT 57.740 39.130 0.00 0.00 0.00 1.40
200 201 4.932911 TCGGGGTAAAGGGAGTTTTTAT 57.067 40.909 0.00 0.00 0.00 1.40
201 202 4.720775 TTCGGGGTAAAGGGAGTTTTTA 57.279 40.909 0.00 0.00 0.00 1.52
202 203 3.598693 TTCGGGGTAAAGGGAGTTTTT 57.401 42.857 0.00 0.00 0.00 1.94
203 204 3.598693 TTTCGGGGTAAAGGGAGTTTT 57.401 42.857 0.00 0.00 0.00 2.43
204 205 3.598693 TTTTCGGGGTAAAGGGAGTTT 57.401 42.857 0.00 0.00 0.00 2.66
205 206 3.598693 TTTTTCGGGGTAAAGGGAGTT 57.401 42.857 0.00 0.00 0.00 3.01
224 225 4.772624 GGGAGCTATTTGACCCTTCTTTTT 59.227 41.667 0.00 0.00 39.28 1.94
225 226 4.344978 GGGAGCTATTTGACCCTTCTTTT 58.655 43.478 0.00 0.00 39.28 2.27
226 227 3.622455 CGGGAGCTATTTGACCCTTCTTT 60.622 47.826 4.53 0.00 40.12 2.52
346 347 4.096003 GCTTAGCAGGTCGGCCCA 62.096 66.667 0.08 0.00 34.66 5.36
347 348 3.330992 AAGCTTAGCAGGTCGGCCC 62.331 63.158 0.08 0.00 34.57 5.80
355 1616 1.397692 GCTTGCAGAGAAGCTTAGCAG 59.602 52.381 7.07 8.24 44.26 4.24
379 1771 3.361977 GCACCGGTTGGCGTTGAT 61.362 61.111 2.97 0.00 39.70 2.57
437 1829 0.325272 GAAGACCAGGACCCAACTCC 59.675 60.000 0.00 0.00 0.00 3.85
535 1931 3.942748 GACCTGGAATTTGTTATGGCGTA 59.057 43.478 0.00 0.00 0.00 4.42
641 2054 4.100084 TGCTGGCAGATCCCACGG 62.100 66.667 20.86 0.00 0.00 4.94
758 2222 0.405973 ACTGGGGAAAGGAAAGGAGC 59.594 55.000 0.00 0.00 0.00 4.70
770 2234 1.229853 GGAGGAGGGAAACTGGGGA 60.230 63.158 0.00 0.00 0.00 4.81
777 2246 1.305887 GACGAGGGGAGGAGGGAAA 60.306 63.158 0.00 0.00 0.00 3.13
914 2398 2.497792 ATCACCCGGCCAATGAGCAA 62.498 55.000 2.24 0.00 0.00 3.91
1020 2504 4.903054 TCTTGAAGAGGTAGTCGTACTCA 58.097 43.478 0.00 0.00 0.00 3.41
1187 2675 2.340443 GACGGGATCAGATCGCCC 59.660 66.667 19.19 9.14 38.86 6.13
1188 2676 2.049985 CGACGGGATCAGATCGCC 60.050 66.667 19.19 13.08 38.86 5.54
1233 2721 2.613595 ACATCGCACGCAATTGTATCAT 59.386 40.909 7.40 0.00 0.00 2.45
1278 2766 1.057285 GTCACAAATGACGACGCTACG 59.943 52.381 0.00 0.00 45.66 3.51
1279 2767 2.763930 GTCACAAATGACGACGCTAC 57.236 50.000 0.00 0.00 45.66 3.58
1310 2798 4.275508 AGGCCACAGCACACCCAG 62.276 66.667 5.01 0.00 42.56 4.45
1313 2801 2.519302 AACAGGCCACAGCACACC 60.519 61.111 5.01 0.00 42.56 4.16
1333 2825 3.181537 GCAAATTCAAACGAATGCTCTGC 60.182 43.478 0.00 0.00 33.33 4.26
1341 2833 3.358775 CGTGACTGCAAATTCAAACGAA 58.641 40.909 0.00 0.00 0.00 3.85
1345 2837 1.599171 CGCCGTGACTGCAAATTCAAA 60.599 47.619 0.00 0.00 0.00 2.69
1400 2892 5.004726 GCTTTTAACCGCACAATCAATCATC 59.995 40.000 0.00 0.00 0.00 2.92
1488 2980 6.811665 TCATTGTCATACGACCAGAAAAGTAG 59.188 38.462 0.00 0.00 41.85 2.57
1559 3051 6.477669 ACTATCTCATATGCAAAAGCATCG 57.522 37.500 6.19 0.26 0.00 3.84
1573 3065 4.383931 TCTAGCCCCGTTACTATCTCAT 57.616 45.455 0.00 0.00 0.00 2.90
1586 3078 1.480954 TCTCGTTGACAATCTAGCCCC 59.519 52.381 0.00 0.00 0.00 5.80
1610 3102 0.677731 AACCATGCCCACGACAGATG 60.678 55.000 0.00 0.00 0.00 2.90
1707 3199 6.811665 AGTTGTTTACAAGTTTCTTTTGCTCC 59.188 34.615 0.00 0.00 36.15 4.70
1711 3203 7.201435 GGCTCAGTTGTTTACAAGTTTCTTTTG 60.201 37.037 0.28 0.00 37.41 2.44
1839 3337 3.488310 GCTTGTGAATCAAACAGCTGTTG 59.512 43.478 31.73 23.55 38.44 3.33
1892 3390 4.200092 GGTTCTACCAATCAATCCAGGTC 58.800 47.826 0.00 0.00 38.42 3.85
1957 3455 4.811557 GTCTGTAGTGCAAATCATAGGGTC 59.188 45.833 0.00 0.00 0.00 4.46
2117 3615 3.614092 GATGACTTTCAGGCAGGATCAA 58.386 45.455 0.00 0.00 36.17 2.57
2309 3807 5.640189 ACTGAATCCTGATTGAAAAGCTG 57.360 39.130 0.00 0.00 30.31 4.24
2899 4610 1.151668 CGGAACCAGCTCTTCAACTG 58.848 55.000 3.60 0.00 0.00 3.16
2918 4629 4.559862 TCCAGAAAGAATCTCTTCCACC 57.440 45.455 0.00 0.00 35.27 4.61
3285 4998 0.312102 GCCTGCGAAAGAAAGTGCTT 59.688 50.000 0.00 0.00 0.00 3.91
3294 5007 2.030893 TCAAACATCAAGCCTGCGAAAG 60.031 45.455 0.00 0.00 0.00 2.62
3361 5075 5.048504 TGCAGTTAGAGCAATTCAAAAGAGG 60.049 40.000 0.00 0.00 39.39 3.69
3381 5095 4.217767 CCAGAATGATTCATGGGTATGCAG 59.782 45.833 8.03 0.00 39.69 4.41
3506 5221 4.844267 ACTTCTCATCCGTTTCAAAAACG 58.156 39.130 15.89 15.89 42.74 3.60
3510 5226 5.050363 CGAAAGACTTCTCATCCGTTTCAAA 60.050 40.000 0.00 0.00 0.00 2.69
3582 5577 1.202722 ACTGGGACGAACAAAACCGAT 60.203 47.619 0.00 0.00 0.00 4.18
3594 5589 5.240844 ACAAAATAAAAGGAGAACTGGGACG 59.759 40.000 0.00 0.00 0.00 4.79
3635 5630 6.715347 AATTCCAATCTGCCAGTAATTACC 57.285 37.500 12.05 0.00 0.00 2.85
3665 5660 6.049149 ACATGTATACTGTGTTATGACAGGC 58.951 40.000 0.00 0.00 46.56 4.85
3814 5809 1.800681 GACGCTAAACATGTGGGCC 59.199 57.895 0.00 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.