Multiple sequence alignment - TraesCS3D01G427500

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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 TraesCS3D01G427500 chr3D 100.000 2632 0 0 1 2632 540937953 540935322 0.000000e+00 4861.0
1 TraesCS3D01G427500 chr3A 92.620 2263 99 35 400 2632 676108708 676106484 0.000000e+00 3192.0
2 TraesCS3D01G427500 chr3B 91.133 1545 78 23 387 1903 716340481 716338968 0.000000e+00 2039.0
3 TraesCS3D01G427500 chr3B 90.629 747 45 13 1901 2632 716337579 716336843 0.000000e+00 968.0
4 TraesCS3D01G427500 chr3B 97.253 182 4 1 1 182 425946615 425946795 9.150000e-80 307.0
5 TraesCS3D01G427500 chr3B 93.048 187 9 4 173 356 410733725 410733910 1.200000e-68 270.0
6 TraesCS3D01G427500 chr3B 92.935 184 10 3 173 354 666608171 666608353 5.590000e-67 265.0
7 TraesCS3D01G427500 chr3B 92.391 184 11 3 177 358 715148139 715147957 2.600000e-65 259.0
8 TraesCS3D01G427500 chr3B 91.935 186 9 6 177 359 715150891 715151073 3.360000e-64 255.0
9 TraesCS3D01G427500 chr3B 90.608 181 14 3 177 355 546909300 546909479 1.220000e-58 237.0
10 TraesCS3D01G427500 chr6B 98.295 176 3 0 1 176 89611736 89611911 2.540000e-80 309.0
11 TraesCS3D01G427500 chr5B 97.253 182 4 1 1 182 130355636 130355456 9.150000e-80 307.0
12 TraesCS3D01G427500 chr5B 97.727 176 4 0 1 176 67889525 67889700 1.180000e-78 303.0
13 TraesCS3D01G427500 chr5B 96.721 183 5 1 1 182 339579563 339579381 1.180000e-78 303.0
14 TraesCS3D01G427500 chr4B 97.253 182 2 1 1 182 510857101 510857279 3.290000e-79 305.0
15 TraesCS3D01G427500 chr2B 97.727 176 4 0 1 176 153598335 153598510 1.180000e-78 303.0
16 TraesCS3D01G427500 chr2B 97.727 176 4 0 1 176 167446802 167446977 1.180000e-78 303.0
17 TraesCS3D01G427500 chr2B 93.956 182 8 3 177 356 725115949 725115769 3.340000e-69 272.0
18 TraesCS3D01G427500 chr7B 97.727 176 3 1 1 176 120828484 120828658 4.260000e-78 302.0
19 TraesCS3D01G427500 chr7D 92.571 175 10 3 183 355 234186290 234186117 5.630000e-62 248.0
20 TraesCS3D01G427500 chr7A 92.000 175 11 3 183 355 602761175 602761348 2.620000e-60 243.0
21 TraesCS3D01G427500 chr1B 90.608 181 14 3 177 355 669309396 669309217 1.220000e-58 237.0
22 TraesCS3D01G427500 chr4A 83.562 73 12 0 2517 2589 347411306 347411378 4.700000e-08 69.4


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 TraesCS3D01G427500 chr3D 540935322 540937953 2631 True 4861.0 4861 100.000 1 2632 1 chr3D.!!$R1 2631
1 TraesCS3D01G427500 chr3A 676106484 676108708 2224 True 3192.0 3192 92.620 400 2632 1 chr3A.!!$R1 2232
2 TraesCS3D01G427500 chr3B 716336843 716340481 3638 True 1503.5 2039 90.881 387 2632 2 chr3B.!!$R2 2245

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
617 618 0.040958 CAGCCACACAGAAACGCTTC 60.041 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 1851 0.029567 GATCGACGCGGACAGAGATT 59.97 55.0 12.47 0.0 0.0 2.4 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.630242 TTGCTTATCTTGCTTAGCATAAGTT 57.370 32.000 20.34 10.01 42.60 2.66
25 26 7.019774 TGCTTATCTTGCTTAGCATAAGTTG 57.980 36.000 20.34 8.42 38.61 3.16
26 27 6.599244 TGCTTATCTTGCTTAGCATAAGTTGT 59.401 34.615 20.34 7.00 38.61 3.32
27 28 7.121168 TGCTTATCTTGCTTAGCATAAGTTGTT 59.879 33.333 20.34 4.38 38.61 2.83
28 29 7.430502 GCTTATCTTGCTTAGCATAAGTTGTTG 59.569 37.037 20.34 5.16 38.76 3.33
29 30 5.627499 TCTTGCTTAGCATAAGTTGTTGG 57.373 39.130 8.05 0.00 38.76 3.77
30 31 5.070001 TCTTGCTTAGCATAAGTTGTTGGT 58.930 37.500 8.05 0.00 38.76 3.67
31 32 4.764679 TGCTTAGCATAAGTTGTTGGTG 57.235 40.909 1.39 0.00 31.71 4.17
32 33 3.057596 TGCTTAGCATAAGTTGTTGGTGC 60.058 43.478 1.39 0.00 31.71 5.01
33 34 3.057596 GCTTAGCATAAGTTGTTGGTGCA 60.058 43.478 0.00 0.00 38.23 4.57
34 35 4.475944 CTTAGCATAAGTTGTTGGTGCAC 58.524 43.478 8.80 8.80 38.23 4.57
35 36 2.586425 AGCATAAGTTGTTGGTGCACT 58.414 42.857 17.98 0.00 38.23 4.40
36 37 2.958355 AGCATAAGTTGTTGGTGCACTT 59.042 40.909 17.98 3.53 38.23 3.16
37 38 4.141287 AGCATAAGTTGTTGGTGCACTTA 58.859 39.130 17.98 5.86 38.23 2.24
38 39 4.216257 AGCATAAGTTGTTGGTGCACTTAG 59.784 41.667 17.98 1.82 38.23 2.18
39 40 4.615912 GCATAAGTTGTTGGTGCACTTAGG 60.616 45.833 17.98 8.29 35.93 2.69
40 41 2.729028 AGTTGTTGGTGCACTTAGGT 57.271 45.000 17.98 0.00 0.00 3.08
41 42 2.297701 AGTTGTTGGTGCACTTAGGTG 58.702 47.619 17.98 0.00 45.53 4.00
42 43 2.092646 AGTTGTTGGTGCACTTAGGTGA 60.093 45.455 17.98 0.00 45.61 4.02
43 44 2.254546 TGTTGGTGCACTTAGGTGAG 57.745 50.000 17.98 0.00 45.61 3.51
44 45 0.875059 GTTGGTGCACTTAGGTGAGC 59.125 55.000 17.98 4.67 45.61 4.26
45 46 0.250727 TTGGTGCACTTAGGTGAGCC 60.251 55.000 17.98 9.85 45.61 4.70
47 48 0.902531 GGTGCACTTAGGTGAGCCTA 59.097 55.000 17.98 0.00 44.90 3.93
57 58 3.963428 AGGTGAGCCTAGTTGTTGTAG 57.037 47.619 0.00 0.00 44.90 2.74
58 59 2.567615 AGGTGAGCCTAGTTGTTGTAGG 59.432 50.000 0.00 0.00 44.90 3.18
59 60 2.302157 GGTGAGCCTAGTTGTTGTAGGT 59.698 50.000 0.00 0.00 39.56 3.08
60 61 3.244457 GGTGAGCCTAGTTGTTGTAGGTT 60.244 47.826 0.00 0.00 39.56 3.50
61 62 4.386711 GTGAGCCTAGTTGTTGTAGGTTT 58.613 43.478 0.00 0.00 39.56 3.27
62 63 4.820173 GTGAGCCTAGTTGTTGTAGGTTTT 59.180 41.667 0.00 0.00 39.56 2.43
63 64 4.819630 TGAGCCTAGTTGTTGTAGGTTTTG 59.180 41.667 0.00 0.00 39.56 2.44
64 65 4.788679 AGCCTAGTTGTTGTAGGTTTTGT 58.211 39.130 0.00 0.00 39.56 2.83
65 66 4.578928 AGCCTAGTTGTTGTAGGTTTTGTG 59.421 41.667 0.00 0.00 39.56 3.33
66 67 4.791734 GCCTAGTTGTTGTAGGTTTTGTGC 60.792 45.833 0.00 0.00 39.56 4.57
67 68 4.578928 CCTAGTTGTTGTAGGTTTTGTGCT 59.421 41.667 0.00 0.00 33.51 4.40
68 69 5.067283 CCTAGTTGTTGTAGGTTTTGTGCTT 59.933 40.000 0.00 0.00 33.51 3.91
69 70 4.743493 AGTTGTTGTAGGTTTTGTGCTTG 58.257 39.130 0.00 0.00 0.00 4.01
70 71 4.461081 AGTTGTTGTAGGTTTTGTGCTTGA 59.539 37.500 0.00 0.00 0.00 3.02
71 72 4.364415 TGTTGTAGGTTTTGTGCTTGAC 57.636 40.909 0.00 0.00 0.00 3.18
72 73 3.759086 TGTTGTAGGTTTTGTGCTTGACA 59.241 39.130 0.00 0.00 0.00 3.58
73 74 4.218635 TGTTGTAGGTTTTGTGCTTGACAA 59.781 37.500 0.00 0.00 43.11 3.18
82 83 4.640789 TTGTGCTTGACAAATTAACCGT 57.359 36.364 0.00 0.00 41.80 4.83
83 84 4.640789 TGTGCTTGACAAATTAACCGTT 57.359 36.364 0.00 0.00 0.00 4.44
84 85 5.752892 TGTGCTTGACAAATTAACCGTTA 57.247 34.783 0.00 0.00 0.00 3.18
85 86 5.753744 TGTGCTTGACAAATTAACCGTTAG 58.246 37.500 0.00 0.00 0.00 2.34
86 87 5.151389 GTGCTTGACAAATTAACCGTTAGG 58.849 41.667 0.00 0.00 45.13 2.69
100 101 4.625972 CCGTTAGGTTTATTCCGCATTT 57.374 40.909 0.00 0.00 0.00 2.32
101 102 4.347813 CCGTTAGGTTTATTCCGCATTTG 58.652 43.478 0.00 0.00 0.00 2.32
102 103 4.142556 CCGTTAGGTTTATTCCGCATTTGT 60.143 41.667 0.00 0.00 0.00 2.83
103 104 5.395642 CGTTAGGTTTATTCCGCATTTGTT 58.604 37.500 0.00 0.00 0.00 2.83
104 105 5.510323 CGTTAGGTTTATTCCGCATTTGTTC 59.490 40.000 0.00 0.00 0.00 3.18
105 106 6.383415 GTTAGGTTTATTCCGCATTTGTTCA 58.617 36.000 0.00 0.00 0.00 3.18
106 107 5.461032 AGGTTTATTCCGCATTTGTTCAA 57.539 34.783 0.00 0.00 0.00 2.69
107 108 5.469479 AGGTTTATTCCGCATTTGTTCAAG 58.531 37.500 0.00 0.00 0.00 3.02
108 109 4.091365 GGTTTATTCCGCATTTGTTCAAGC 59.909 41.667 0.00 0.00 0.00 4.01
109 110 2.368655 ATTCCGCATTTGTTCAAGCC 57.631 45.000 0.00 0.00 0.00 4.35
110 111 1.327303 TTCCGCATTTGTTCAAGCCT 58.673 45.000 0.00 0.00 0.00 4.58
111 112 0.881118 TCCGCATTTGTTCAAGCCTC 59.119 50.000 0.00 0.00 0.00 4.70
112 113 0.883833 CCGCATTTGTTCAAGCCTCT 59.116 50.000 0.00 0.00 0.00 3.69
113 114 2.083774 CCGCATTTGTTCAAGCCTCTA 58.916 47.619 0.00 0.00 0.00 2.43
114 115 2.159517 CCGCATTTGTTCAAGCCTCTAC 60.160 50.000 0.00 0.00 0.00 2.59
115 116 2.159517 CGCATTTGTTCAAGCCTCTACC 60.160 50.000 0.00 0.00 0.00 3.18
116 117 2.159517 GCATTTGTTCAAGCCTCTACCG 60.160 50.000 0.00 0.00 0.00 4.02
117 118 2.922740 TTTGTTCAAGCCTCTACCGT 57.077 45.000 0.00 0.00 0.00 4.83
118 119 4.250464 CATTTGTTCAAGCCTCTACCGTA 58.750 43.478 0.00 0.00 0.00 4.02
119 120 4.339872 TTTGTTCAAGCCTCTACCGTAA 57.660 40.909 0.00 0.00 0.00 3.18
120 121 4.546829 TTGTTCAAGCCTCTACCGTAAT 57.453 40.909 0.00 0.00 0.00 1.89
121 122 4.546829 TGTTCAAGCCTCTACCGTAATT 57.453 40.909 0.00 0.00 0.00 1.40
122 123 5.664294 TGTTCAAGCCTCTACCGTAATTA 57.336 39.130 0.00 0.00 0.00 1.40
123 124 6.229936 TGTTCAAGCCTCTACCGTAATTAT 57.770 37.500 0.00 0.00 0.00 1.28
124 125 6.646267 TGTTCAAGCCTCTACCGTAATTATT 58.354 36.000 0.00 0.00 0.00 1.40
125 126 7.107542 TGTTCAAGCCTCTACCGTAATTATTT 58.892 34.615 0.00 0.00 0.00 1.40
126 127 7.608761 TGTTCAAGCCTCTACCGTAATTATTTT 59.391 33.333 0.00 0.00 0.00 1.82
127 128 9.101655 GTTCAAGCCTCTACCGTAATTATTTTA 57.898 33.333 0.00 0.00 0.00 1.52
128 129 9.669887 TTCAAGCCTCTACCGTAATTATTTTAA 57.330 29.630 0.00 0.00 0.00 1.52
129 130 9.669887 TCAAGCCTCTACCGTAATTATTTTAAA 57.330 29.630 0.00 0.00 0.00 1.52
132 133 8.606602 AGCCTCTACCGTAATTATTTTAAAACG 58.393 33.333 1.97 1.84 0.00 3.60
133 134 7.374228 GCCTCTACCGTAATTATTTTAAAACGC 59.626 37.037 1.97 0.00 0.00 4.84
134 135 7.852454 CCTCTACCGTAATTATTTTAAAACGCC 59.148 37.037 1.97 0.00 0.00 5.68
135 136 8.491331 TCTACCGTAATTATTTTAAAACGCCT 57.509 30.769 1.97 0.00 0.00 5.52
136 137 9.593134 TCTACCGTAATTATTTTAAAACGCCTA 57.407 29.630 1.97 0.00 0.00 3.93
139 140 9.720667 ACCGTAATTATTTTAAAACGCCTATTC 57.279 29.630 1.97 0.00 0.00 1.75
140 141 9.719279 CCGTAATTATTTTAAAACGCCTATTCA 57.281 29.630 1.97 0.00 0.00 2.57
143 144 8.936070 AATTATTTTAAAACGCCTATTCACCC 57.064 30.769 1.97 0.00 0.00 4.61
144 145 4.787260 TTTTAAAACGCCTATTCACCCC 57.213 40.909 0.00 0.00 0.00 4.95
145 146 3.724732 TTAAAACGCCTATTCACCCCT 57.275 42.857 0.00 0.00 0.00 4.79
146 147 2.124277 AAAACGCCTATTCACCCCTC 57.876 50.000 0.00 0.00 0.00 4.30
147 148 0.255033 AAACGCCTATTCACCCCTCC 59.745 55.000 0.00 0.00 0.00 4.30
148 149 1.632965 AACGCCTATTCACCCCTCCC 61.633 60.000 0.00 0.00 0.00 4.30
149 150 2.819284 CGCCTATTCACCCCTCCCC 61.819 68.421 0.00 0.00 0.00 4.81
150 151 2.461739 GCCTATTCACCCCTCCCCC 61.462 68.421 0.00 0.00 0.00 5.40
151 152 1.321943 CCTATTCACCCCTCCCCCT 59.678 63.158 0.00 0.00 0.00 4.79
152 153 0.768609 CCTATTCACCCCTCCCCCTC 60.769 65.000 0.00 0.00 0.00 4.30
153 154 0.269173 CTATTCACCCCTCCCCCTCT 59.731 60.000 0.00 0.00 0.00 3.69
154 155 1.508185 CTATTCACCCCTCCCCCTCTA 59.492 57.143 0.00 0.00 0.00 2.43
155 156 0.269173 ATTCACCCCTCCCCCTCTAG 59.731 60.000 0.00 0.00 0.00 2.43
156 157 1.898190 TTCACCCCTCCCCCTCTAGG 61.898 65.000 0.00 0.00 0.00 3.02
157 158 3.780275 ACCCCTCCCCCTCTAGGC 61.780 72.222 0.00 0.00 0.00 3.93
158 159 4.944069 CCCCTCCCCCTCTAGGCG 62.944 77.778 0.00 0.00 0.00 5.52
159 160 3.834056 CCCTCCCCCTCTAGGCGA 61.834 72.222 0.00 0.00 0.00 5.54
160 161 2.522193 CCTCCCCCTCTAGGCGAC 60.522 72.222 0.00 0.00 0.00 5.19
161 162 2.279073 CTCCCCCTCTAGGCGACA 59.721 66.667 0.00 0.00 0.00 4.35
162 163 1.152440 CTCCCCCTCTAGGCGACAT 60.152 63.158 0.00 0.00 0.00 3.06
163 164 1.152525 TCCCCCTCTAGGCGACATC 60.153 63.158 0.00 0.00 0.00 3.06
164 165 2.210711 CCCCCTCTAGGCGACATCC 61.211 68.421 0.00 0.00 0.00 3.51
165 166 1.457643 CCCCTCTAGGCGACATCCA 60.458 63.158 0.00 0.00 0.00 3.41
166 167 1.742768 CCCTCTAGGCGACATCCAC 59.257 63.158 0.00 0.00 0.00 4.02
167 168 1.360551 CCTCTAGGCGACATCCACG 59.639 63.158 0.00 0.00 0.00 4.94
168 169 1.101635 CCTCTAGGCGACATCCACGA 61.102 60.000 0.00 0.00 0.00 4.35
169 170 0.955178 CTCTAGGCGACATCCACGAT 59.045 55.000 0.00 0.00 0.00 3.73
170 171 0.952280 TCTAGGCGACATCCACGATC 59.048 55.000 0.00 0.00 0.00 3.69
171 172 0.955178 CTAGGCGACATCCACGATCT 59.045 55.000 0.00 0.00 0.00 2.75
172 173 1.338337 CTAGGCGACATCCACGATCTT 59.662 52.381 0.00 0.00 0.00 2.40
173 174 0.537188 AGGCGACATCCACGATCTTT 59.463 50.000 0.00 0.00 0.00 2.52
174 175 0.931005 GGCGACATCCACGATCTTTC 59.069 55.000 0.00 0.00 0.00 2.62
175 176 1.640428 GCGACATCCACGATCTTTCA 58.360 50.000 0.00 0.00 0.00 2.69
176 177 1.324736 GCGACATCCACGATCTTTCAC 59.675 52.381 0.00 0.00 0.00 3.18
177 178 2.881074 CGACATCCACGATCTTTCACT 58.119 47.619 0.00 0.00 0.00 3.41
178 179 2.854777 CGACATCCACGATCTTTCACTC 59.145 50.000 0.00 0.00 0.00 3.51
179 180 2.854777 GACATCCACGATCTTTCACTCG 59.145 50.000 0.00 0.00 40.62 4.18
180 181 2.196749 CATCCACGATCTTTCACTCGG 58.803 52.381 0.00 0.00 39.16 4.63
181 182 1.254026 TCCACGATCTTTCACTCGGT 58.746 50.000 0.00 0.00 39.16 4.69
182 183 1.067846 TCCACGATCTTTCACTCGGTG 60.068 52.381 0.00 0.00 39.16 4.94
183 184 1.350193 CACGATCTTTCACTCGGTGG 58.650 55.000 0.00 0.00 39.16 4.61
184 185 0.389948 ACGATCTTTCACTCGGTGGC 60.390 55.000 0.00 0.00 39.16 5.01
185 186 1.084370 CGATCTTTCACTCGGTGGCC 61.084 60.000 0.00 0.00 33.87 5.36
270 271 4.394712 GCACCTGCCGCCACTAGT 62.395 66.667 0.00 0.00 34.31 2.57
271 272 2.434884 CACCTGCCGCCACTAGTG 60.435 66.667 16.34 16.34 0.00 2.74
272 273 2.603473 ACCTGCCGCCACTAGTGA 60.603 61.111 24.68 2.59 0.00 3.41
273 274 2.185350 CCTGCCGCCACTAGTGAG 59.815 66.667 24.68 16.46 0.00 3.51
274 275 2.185350 CTGCCGCCACTAGTGAGG 59.815 66.667 24.68 24.46 0.00 3.86
275 276 3.376935 CTGCCGCCACTAGTGAGGG 62.377 68.421 27.35 24.47 0.00 4.30
281 282 3.401032 CCACTAGTGAGGGGGTTCT 57.599 57.895 24.68 0.00 43.43 3.01
282 283 1.657804 CCACTAGTGAGGGGGTTCTT 58.342 55.000 24.68 0.00 43.43 2.52
283 284 1.985895 CCACTAGTGAGGGGGTTCTTT 59.014 52.381 24.68 0.00 43.43 2.52
284 285 2.375509 CCACTAGTGAGGGGGTTCTTTT 59.624 50.000 24.68 0.00 43.43 2.27
285 286 3.181433 CCACTAGTGAGGGGGTTCTTTTT 60.181 47.826 24.68 0.00 43.43 1.94
307 308 8.514136 TTTTTGACAATTTTATTCGCAGGTAG 57.486 30.769 0.00 0.00 0.00 3.18
308 309 6.811253 TTGACAATTTTATTCGCAGGTAGT 57.189 33.333 0.00 0.00 0.00 2.73
309 310 6.417191 TGACAATTTTATTCGCAGGTAGTC 57.583 37.500 0.00 0.00 0.00 2.59
310 311 5.353123 TGACAATTTTATTCGCAGGTAGTCC 59.647 40.000 0.00 0.00 0.00 3.85
311 312 5.497474 ACAATTTTATTCGCAGGTAGTCCT 58.503 37.500 0.00 0.00 46.37 3.85
312 313 5.944007 ACAATTTTATTCGCAGGTAGTCCTT 59.056 36.000 0.00 0.00 43.07 3.36
313 314 6.433093 ACAATTTTATTCGCAGGTAGTCCTTT 59.567 34.615 0.00 0.00 43.07 3.11
314 315 7.039993 ACAATTTTATTCGCAGGTAGTCCTTTT 60.040 33.333 0.00 0.00 43.07 2.27
315 316 6.887626 TTTTATTCGCAGGTAGTCCTTTTT 57.112 33.333 0.00 0.00 43.07 1.94
316 317 5.873179 TTATTCGCAGGTAGTCCTTTTTG 57.127 39.130 0.00 0.00 43.07 2.44
317 318 2.178912 TCGCAGGTAGTCCTTTTTGG 57.821 50.000 0.00 0.00 43.07 3.28
318 319 0.521735 CGCAGGTAGTCCTTTTTGGC 59.478 55.000 0.00 0.00 43.07 4.52
319 320 1.616159 GCAGGTAGTCCTTTTTGGCA 58.384 50.000 0.00 0.00 43.07 4.92
320 321 1.960689 GCAGGTAGTCCTTTTTGGCAA 59.039 47.619 0.00 0.00 43.07 4.52
321 322 2.562738 GCAGGTAGTCCTTTTTGGCAAT 59.437 45.455 0.00 0.00 43.07 3.56
322 323 3.761752 GCAGGTAGTCCTTTTTGGCAATA 59.238 43.478 0.00 0.00 43.07 1.90
323 324 4.142381 GCAGGTAGTCCTTTTTGGCAATAG 60.142 45.833 0.00 1.65 43.07 1.73
324 325 4.399303 CAGGTAGTCCTTTTTGGCAATAGG 59.601 45.833 18.11 18.11 43.07 2.57
325 326 4.044191 AGGTAGTCCTTTTTGGCAATAGGT 59.956 41.667 21.42 10.99 42.12 3.08
326 327 4.770531 GGTAGTCCTTTTTGGCAATAGGTT 59.229 41.667 21.42 15.66 33.81 3.50
327 328 5.105877 GGTAGTCCTTTTTGGCAATAGGTTC 60.106 44.000 21.42 16.89 33.81 3.62
328 329 3.506067 AGTCCTTTTTGGCAATAGGTTCG 59.494 43.478 21.42 4.15 33.81 3.95
329 330 3.504520 GTCCTTTTTGGCAATAGGTTCGA 59.495 43.478 21.42 6.43 33.81 3.71
330 331 3.504520 TCCTTTTTGGCAATAGGTTCGAC 59.495 43.478 21.42 0.00 33.81 4.20
331 332 3.488489 CTTTTTGGCAATAGGTTCGACG 58.512 45.455 0.00 0.00 0.00 5.12
332 333 1.444836 TTTGGCAATAGGTTCGACGG 58.555 50.000 0.00 0.00 0.00 4.79
333 334 0.391927 TTGGCAATAGGTTCGACGGG 60.392 55.000 0.00 0.00 0.00 5.28
334 335 1.523032 GGCAATAGGTTCGACGGGG 60.523 63.158 0.00 0.00 0.00 5.73
335 336 1.523032 GCAATAGGTTCGACGGGGG 60.523 63.158 0.00 0.00 0.00 5.40
382 383 9.862371 AACATTTCTTGTACTATCAGTAGACTG 57.138 33.333 3.12 3.12 40.62 3.51
383 384 9.026121 ACATTTCTTGTACTATCAGTAGACTGT 57.974 33.333 9.43 0.70 39.87 3.55
414 415 2.936498 AGTCCGGCATTAACATTTCTCG 59.064 45.455 0.00 0.00 0.00 4.04
576 577 4.868116 ACGTGCCCCGCAACAGTT 62.868 61.111 0.00 0.00 41.47 3.16
577 578 4.025401 CGTGCCCCGCAACAGTTC 62.025 66.667 0.00 0.00 41.47 3.01
617 618 0.040958 CAGCCACACAGAAACGCTTC 60.041 55.000 0.00 0.00 0.00 3.86
671 672 1.663695 CGGATAACGCCCAATCAACT 58.336 50.000 0.00 0.00 34.82 3.16
801 803 1.350193 CATTCGTTCTCGTCCCACTG 58.650 55.000 0.00 0.00 38.33 3.66
810 812 4.008933 GTCCCACTGGCTGACGCT 62.009 66.667 0.00 0.00 36.09 5.07
841 843 2.536997 CTTCCGGGTCCCACATGTCC 62.537 65.000 9.12 0.00 0.00 4.02
857 859 2.047655 CCGCGTCTAAACAGGCCA 60.048 61.111 5.01 0.00 0.00 5.36
859 861 2.726691 CGCGTCTAAACAGGCCACG 61.727 63.158 5.01 5.15 0.00 4.94
1062 1074 4.127040 CGCGCTCCTCTGCTCTGT 62.127 66.667 5.56 0.00 0.00 3.41
1074 1086 2.178580 CTGCTCTGTTCTCCTCTCCTT 58.821 52.381 0.00 0.00 0.00 3.36
1082 1094 0.323451 TCTCCTCTCCTTGTGCGCTA 60.323 55.000 9.73 0.00 0.00 4.26
1100 1112 3.265791 GCTAGTGTTCACCAAGATCAGG 58.734 50.000 0.00 0.00 0.00 3.86
1682 1718 2.404215 CCGATGATTTACTACCGGCAG 58.596 52.381 0.00 0.00 0.00 4.85
1744 1780 0.821301 TTCTGTGCACGGATGGCAAA 60.821 50.000 28.33 10.28 43.91 3.68
1814 1850 3.688185 TCCGGTGCACGTATATATCTCTC 59.312 47.826 11.45 0.00 42.24 3.20
1815 1851 3.439129 CCGGTGCACGTATATATCTCTCA 59.561 47.826 11.45 0.00 42.24 3.27
1816 1852 4.082949 CCGGTGCACGTATATATCTCTCAA 60.083 45.833 11.45 0.00 42.24 3.02
1817 1853 5.393135 CCGGTGCACGTATATATCTCTCAAT 60.393 44.000 11.45 0.00 42.24 2.57
1818 1854 5.739630 CGGTGCACGTATATATCTCTCAATC 59.260 44.000 11.45 0.00 37.93 2.67
1819 1855 6.403746 CGGTGCACGTATATATCTCTCAATCT 60.404 42.308 11.45 0.00 37.93 2.40
1820 1856 6.970043 GGTGCACGTATATATCTCTCAATCTC 59.030 42.308 11.45 0.00 0.00 2.75
1821 1857 7.148154 GGTGCACGTATATATCTCTCAATCTCT 60.148 40.741 11.45 0.00 0.00 3.10
1825 1861 8.394877 CACGTATATATCTCTCAATCTCTGTCC 58.605 40.741 0.00 0.00 0.00 4.02
2078 3506 6.942005 TCTTGTGGTTGTTGTCAGATGATTAT 59.058 34.615 0.00 0.00 0.00 1.28
2111 3539 1.816863 TTTCACGCCCGAGCTCTCTT 61.817 55.000 12.85 0.00 36.60 2.85
2168 3596 0.529378 CTGTTTCAGCTGCCATTCCC 59.471 55.000 9.47 0.00 0.00 3.97
2184 3612 0.471780 TCCCTGCTCCTGAACTGTCA 60.472 55.000 0.00 0.00 0.00 3.58
2245 3673 4.463879 CAGGGCAGCGACTCCCAG 62.464 72.222 8.66 0.00 45.07 4.45
2254 3682 1.374758 CGACTCCCAGAGCAACCAC 60.375 63.158 0.00 0.00 32.04 4.16
2263 3691 4.892965 AGCAACCACGCTGCCCAA 62.893 61.111 0.00 0.00 41.85 4.12
2264 3692 3.683937 GCAACCACGCTGCCCAAT 61.684 61.111 0.00 0.00 33.51 3.16
2385 3826 0.770499 TCCAGTGGTCAGATGGCAAA 59.230 50.000 9.54 0.00 33.92 3.68
2407 3848 2.138179 GGCATCGGCTACCCCTACA 61.138 63.158 0.00 0.00 40.87 2.74
2408 3849 1.692173 GGCATCGGCTACCCCTACAA 61.692 60.000 0.00 0.00 40.87 2.41
2425 3867 1.135689 ACAAAATTCCGCACTCGCATC 60.136 47.619 0.00 0.00 38.40 3.91
2485 3927 5.171476 TCGAATCAAACCAGAGATTGAGAC 58.829 41.667 0.00 0.00 38.80 3.36
2491 3933 1.338200 ACCAGAGATTGAGACCGTTGC 60.338 52.381 0.00 0.00 0.00 4.17
2506 3948 4.694339 ACCGTTGCTGTAATAGAGATTCC 58.306 43.478 0.00 0.00 0.00 3.01
2556 3998 0.916358 CCAGTCCACCTCCCTTCCAT 60.916 60.000 0.00 0.00 0.00 3.41
2558 4000 0.119155 AGTCCACCTCCCTTCCATCA 59.881 55.000 0.00 0.00 0.00 3.07
2613 4055 4.728102 CGGTAGGCGCGACCACAA 62.728 66.667 24.76 0.00 43.14 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.020914 ACAACTTATGCTAAGCAAGATAAGC 57.979 36.000 0.00 0.00 43.62 3.09
3 4 7.912250 CCAACAACTTATGCTAAGCAAGATAAG 59.088 37.037 0.00 0.00 43.62 1.73
4 5 7.393234 ACCAACAACTTATGCTAAGCAAGATAA 59.607 33.333 0.00 0.00 43.62 1.75
5 6 6.884295 ACCAACAACTTATGCTAAGCAAGATA 59.116 34.615 0.00 0.00 43.62 1.98
6 7 5.711976 ACCAACAACTTATGCTAAGCAAGAT 59.288 36.000 0.00 0.00 43.62 2.40
7 8 5.048782 CACCAACAACTTATGCTAAGCAAGA 60.049 40.000 0.00 0.00 43.62 3.02
8 9 5.156355 CACCAACAACTTATGCTAAGCAAG 58.844 41.667 0.00 0.00 43.62 4.01
9 10 4.558496 GCACCAACAACTTATGCTAAGCAA 60.558 41.667 0.00 0.00 43.62 3.91
10 11 3.057596 GCACCAACAACTTATGCTAAGCA 60.058 43.478 0.00 0.00 44.86 3.91
11 12 3.057596 TGCACCAACAACTTATGCTAAGC 60.058 43.478 0.00 0.00 37.20 3.09
12 13 4.216257 AGTGCACCAACAACTTATGCTAAG 59.784 41.667 14.63 2.55 37.20 2.18
13 14 4.141287 AGTGCACCAACAACTTATGCTAA 58.859 39.130 14.63 0.00 37.20 3.09
14 15 3.750371 AGTGCACCAACAACTTATGCTA 58.250 40.909 14.63 0.00 37.20 3.49
15 16 2.586425 AGTGCACCAACAACTTATGCT 58.414 42.857 14.63 0.00 37.20 3.79
16 17 3.369546 AAGTGCACCAACAACTTATGC 57.630 42.857 14.63 0.00 36.81 3.14
17 18 4.518970 ACCTAAGTGCACCAACAACTTATG 59.481 41.667 14.63 3.62 0.00 1.90
18 19 4.518970 CACCTAAGTGCACCAACAACTTAT 59.481 41.667 14.63 0.00 37.14 1.73
19 20 3.880490 CACCTAAGTGCACCAACAACTTA 59.120 43.478 14.63 2.72 37.14 2.24
20 21 2.687935 CACCTAAGTGCACCAACAACTT 59.312 45.455 14.63 1.48 37.14 2.66
21 22 2.092646 TCACCTAAGTGCACCAACAACT 60.093 45.455 14.63 0.00 44.16 3.16
22 23 2.290641 CTCACCTAAGTGCACCAACAAC 59.709 50.000 14.63 0.00 44.16 3.32
23 24 2.571212 CTCACCTAAGTGCACCAACAA 58.429 47.619 14.63 0.00 44.16 2.83
24 25 1.813862 GCTCACCTAAGTGCACCAACA 60.814 52.381 14.63 0.00 44.16 3.33
25 26 0.875059 GCTCACCTAAGTGCACCAAC 59.125 55.000 14.63 0.00 44.16 3.77
26 27 0.250727 GGCTCACCTAAGTGCACCAA 60.251 55.000 14.63 0.12 44.16 3.67
27 28 1.374947 GGCTCACCTAAGTGCACCA 59.625 57.895 14.63 0.10 44.16 4.17
28 29 4.303257 GGCTCACCTAAGTGCACC 57.697 61.111 14.63 0.00 44.16 5.01
38 39 2.302157 ACCTACAACAACTAGGCTCACC 59.698 50.000 0.00 0.00 35.04 4.02
39 40 3.679824 ACCTACAACAACTAGGCTCAC 57.320 47.619 0.00 0.00 35.04 3.51
40 41 4.699925 AAACCTACAACAACTAGGCTCA 57.300 40.909 0.00 0.00 35.04 4.26
41 42 4.820173 ACAAAACCTACAACAACTAGGCTC 59.180 41.667 0.00 0.00 35.04 4.70
42 43 4.578928 CACAAAACCTACAACAACTAGGCT 59.421 41.667 0.00 0.00 35.04 4.58
43 44 4.791734 GCACAAAACCTACAACAACTAGGC 60.792 45.833 0.00 0.00 35.04 3.93
44 45 4.578928 AGCACAAAACCTACAACAACTAGG 59.421 41.667 0.00 0.00 37.40 3.02
45 46 5.751243 AGCACAAAACCTACAACAACTAG 57.249 39.130 0.00 0.00 0.00 2.57
46 47 5.648526 TCAAGCACAAAACCTACAACAACTA 59.351 36.000 0.00 0.00 0.00 2.24
47 48 4.461081 TCAAGCACAAAACCTACAACAACT 59.539 37.500 0.00 0.00 0.00 3.16
48 49 4.561213 GTCAAGCACAAAACCTACAACAAC 59.439 41.667 0.00 0.00 0.00 3.32
49 50 4.218635 TGTCAAGCACAAAACCTACAACAA 59.781 37.500 0.00 0.00 29.30 2.83
50 51 3.759086 TGTCAAGCACAAAACCTACAACA 59.241 39.130 0.00 0.00 29.30 3.33
51 52 4.364415 TGTCAAGCACAAAACCTACAAC 57.636 40.909 0.00 0.00 29.30 3.32
61 62 4.640789 ACGGTTAATTTGTCAAGCACAA 57.359 36.364 0.00 0.00 43.68 3.33
62 63 4.640789 AACGGTTAATTTGTCAAGCACA 57.359 36.364 0.00 0.00 0.00 4.57
63 64 5.151389 CCTAACGGTTAATTTGTCAAGCAC 58.849 41.667 1.79 0.00 0.00 4.40
64 65 4.822896 ACCTAACGGTTAATTTGTCAAGCA 59.177 37.500 1.79 0.00 42.13 3.91
65 66 5.366829 ACCTAACGGTTAATTTGTCAAGC 57.633 39.130 1.79 0.00 42.13 4.01
79 80 4.142556 ACAAATGCGGAATAAACCTAACGG 60.143 41.667 0.00 0.00 0.00 4.44
80 81 4.976987 ACAAATGCGGAATAAACCTAACG 58.023 39.130 0.00 0.00 0.00 3.18
81 82 6.383415 TGAACAAATGCGGAATAAACCTAAC 58.617 36.000 0.00 0.00 0.00 2.34
82 83 6.576662 TGAACAAATGCGGAATAAACCTAA 57.423 33.333 0.00 0.00 0.00 2.69
83 84 6.576662 TTGAACAAATGCGGAATAAACCTA 57.423 33.333 0.00 0.00 0.00 3.08
84 85 5.461032 TTGAACAAATGCGGAATAAACCT 57.539 34.783 0.00 0.00 0.00 3.50
85 86 4.091365 GCTTGAACAAATGCGGAATAAACC 59.909 41.667 0.00 0.00 0.00 3.27
86 87 4.091365 GGCTTGAACAAATGCGGAATAAAC 59.909 41.667 0.00 0.00 0.00 2.01
87 88 4.021544 AGGCTTGAACAAATGCGGAATAAA 60.022 37.500 0.00 0.00 0.00 1.40
88 89 3.509575 AGGCTTGAACAAATGCGGAATAA 59.490 39.130 0.00 0.00 0.00 1.40
89 90 3.088532 AGGCTTGAACAAATGCGGAATA 58.911 40.909 0.00 0.00 0.00 1.75
90 91 1.895131 AGGCTTGAACAAATGCGGAAT 59.105 42.857 0.00 0.00 0.00 3.01
91 92 1.269448 GAGGCTTGAACAAATGCGGAA 59.731 47.619 0.00 0.00 0.00 4.30
92 93 0.881118 GAGGCTTGAACAAATGCGGA 59.119 50.000 0.00 0.00 0.00 5.54
93 94 0.883833 AGAGGCTTGAACAAATGCGG 59.116 50.000 0.00 0.00 0.00 5.69
94 95 2.159517 GGTAGAGGCTTGAACAAATGCG 60.160 50.000 0.00 0.00 0.00 4.73
95 96 2.159517 CGGTAGAGGCTTGAACAAATGC 60.160 50.000 0.00 0.00 0.00 3.56
96 97 3.074412 ACGGTAGAGGCTTGAACAAATG 58.926 45.455 0.00 0.00 0.00 2.32
97 98 3.418684 ACGGTAGAGGCTTGAACAAAT 57.581 42.857 0.00 0.00 0.00 2.32
98 99 2.922740 ACGGTAGAGGCTTGAACAAA 57.077 45.000 0.00 0.00 0.00 2.83
99 100 4.546829 ATTACGGTAGAGGCTTGAACAA 57.453 40.909 0.00 0.00 0.00 2.83
100 101 4.546829 AATTACGGTAGAGGCTTGAACA 57.453 40.909 0.00 0.00 0.00 3.18
101 102 7.549615 AAATAATTACGGTAGAGGCTTGAAC 57.450 36.000 0.00 0.00 0.00 3.18
102 103 9.669887 TTAAAATAATTACGGTAGAGGCTTGAA 57.330 29.630 0.00 0.00 0.00 2.69
103 104 9.669887 TTTAAAATAATTACGGTAGAGGCTTGA 57.330 29.630 0.00 0.00 0.00 3.02
106 107 8.606602 CGTTTTAAAATAATTACGGTAGAGGCT 58.393 33.333 3.52 0.00 0.00 4.58
107 108 7.374228 GCGTTTTAAAATAATTACGGTAGAGGC 59.626 37.037 3.52 0.00 0.00 4.70
108 109 7.852454 GGCGTTTTAAAATAATTACGGTAGAGG 59.148 37.037 3.52 0.00 0.00 3.69
109 110 8.606602 AGGCGTTTTAAAATAATTACGGTAGAG 58.393 33.333 3.52 0.00 0.00 2.43
110 111 8.491331 AGGCGTTTTAAAATAATTACGGTAGA 57.509 30.769 3.52 0.00 0.00 2.59
113 114 9.720667 GAATAGGCGTTTTAAAATAATTACGGT 57.279 29.630 3.52 0.00 0.00 4.83
114 115 9.719279 TGAATAGGCGTTTTAAAATAATTACGG 57.281 29.630 3.52 0.00 0.00 4.02
118 119 7.982919 GGGGTGAATAGGCGTTTTAAAATAATT 59.017 33.333 3.52 0.88 0.00 1.40
119 120 7.343574 AGGGGTGAATAGGCGTTTTAAAATAAT 59.656 33.333 3.52 0.00 0.00 1.28
120 121 6.664384 AGGGGTGAATAGGCGTTTTAAAATAA 59.336 34.615 3.52 0.00 0.00 1.40
121 122 6.189133 AGGGGTGAATAGGCGTTTTAAAATA 58.811 36.000 3.52 0.00 0.00 1.40
122 123 5.020795 AGGGGTGAATAGGCGTTTTAAAAT 58.979 37.500 3.52 0.00 0.00 1.82
123 124 4.409187 AGGGGTGAATAGGCGTTTTAAAA 58.591 39.130 0.00 0.00 0.00 1.52
124 125 4.011698 GAGGGGTGAATAGGCGTTTTAAA 58.988 43.478 0.00 0.00 0.00 1.52
125 126 3.613030 GAGGGGTGAATAGGCGTTTTAA 58.387 45.455 0.00 0.00 0.00 1.52
126 127 2.092807 GGAGGGGTGAATAGGCGTTTTA 60.093 50.000 0.00 0.00 0.00 1.52
127 128 1.340697 GGAGGGGTGAATAGGCGTTTT 60.341 52.381 0.00 0.00 0.00 2.43
128 129 0.255033 GGAGGGGTGAATAGGCGTTT 59.745 55.000 0.00 0.00 0.00 3.60
129 130 1.632965 GGGAGGGGTGAATAGGCGTT 61.633 60.000 0.00 0.00 0.00 4.84
130 131 2.070650 GGGAGGGGTGAATAGGCGT 61.071 63.158 0.00 0.00 0.00 5.68
131 132 2.819284 GGGGAGGGGTGAATAGGCG 61.819 68.421 0.00 0.00 0.00 5.52
132 133 2.461739 GGGGGAGGGGTGAATAGGC 61.462 68.421 0.00 0.00 0.00 3.93
133 134 0.768609 GAGGGGGAGGGGTGAATAGG 60.769 65.000 0.00 0.00 0.00 2.57
134 135 0.269173 AGAGGGGGAGGGGTGAATAG 59.731 60.000 0.00 0.00 0.00 1.73
135 136 1.508185 CTAGAGGGGGAGGGGTGAATA 59.492 57.143 0.00 0.00 0.00 1.75
136 137 0.269173 CTAGAGGGGGAGGGGTGAAT 59.731 60.000 0.00 0.00 0.00 2.57
137 138 1.710341 CTAGAGGGGGAGGGGTGAA 59.290 63.158 0.00 0.00 0.00 3.18
138 139 2.333462 CCTAGAGGGGGAGGGGTGA 61.333 68.421 0.00 0.00 0.00 4.02
139 140 2.287251 CCTAGAGGGGGAGGGGTG 59.713 72.222 0.00 0.00 0.00 4.61
140 141 3.780275 GCCTAGAGGGGGAGGGGT 61.780 72.222 0.00 0.00 33.04 4.95
146 147 2.210711 GGATGTCGCCTAGAGGGGG 61.211 68.421 12.32 0.23 46.90 5.40
148 149 1.742768 GTGGATGTCGCCTAGAGGG 59.257 63.158 0.00 0.00 35.18 4.30
149 150 1.101635 TCGTGGATGTCGCCTAGAGG 61.102 60.000 0.00 0.00 38.53 3.69
150 151 0.955178 ATCGTGGATGTCGCCTAGAG 59.045 55.000 0.00 0.00 0.00 2.43
151 152 0.952280 GATCGTGGATGTCGCCTAGA 59.048 55.000 0.00 0.00 0.00 2.43
152 153 0.955178 AGATCGTGGATGTCGCCTAG 59.045 55.000 0.00 0.00 0.00 3.02
153 154 1.399714 AAGATCGTGGATGTCGCCTA 58.600 50.000 0.00 0.00 0.00 3.93
154 155 0.537188 AAAGATCGTGGATGTCGCCT 59.463 50.000 0.00 0.00 0.00 5.52
155 156 0.931005 GAAAGATCGTGGATGTCGCC 59.069 55.000 0.00 0.00 0.00 5.54
156 157 1.324736 GTGAAAGATCGTGGATGTCGC 59.675 52.381 0.00 0.00 0.00 5.19
157 158 2.854777 GAGTGAAAGATCGTGGATGTCG 59.145 50.000 0.00 0.00 0.00 4.35
158 159 2.854777 CGAGTGAAAGATCGTGGATGTC 59.145 50.000 0.00 0.00 34.30 3.06
159 160 2.417379 CCGAGTGAAAGATCGTGGATGT 60.417 50.000 0.00 0.00 37.23 3.06
160 161 2.196749 CCGAGTGAAAGATCGTGGATG 58.803 52.381 0.00 0.00 37.23 3.51
161 162 1.825474 ACCGAGTGAAAGATCGTGGAT 59.175 47.619 0.00 0.00 37.23 3.41
162 163 1.067846 CACCGAGTGAAAGATCGTGGA 60.068 52.381 0.00 0.00 37.23 4.02
163 164 1.350193 CACCGAGTGAAAGATCGTGG 58.650 55.000 0.00 0.00 37.23 4.94
164 165 1.350193 CCACCGAGTGAAAGATCGTG 58.650 55.000 5.71 0.00 37.23 4.35
165 166 0.389948 GCCACCGAGTGAAAGATCGT 60.390 55.000 5.71 0.00 37.23 3.73
166 167 1.084370 GGCCACCGAGTGAAAGATCG 61.084 60.000 0.00 0.00 35.23 3.69
167 168 2.768834 GGCCACCGAGTGAAAGATC 58.231 57.895 0.00 0.00 35.23 2.75
228 229 3.036084 GACACGTGGCACCTGTCG 61.036 66.667 26.20 12.49 27.84 4.35
229 230 3.036084 CGACACGTGGCACCTGTC 61.036 66.667 28.67 28.67 32.98 3.51
253 254 4.394712 ACTAGTGGCGGCAGGTGC 62.395 66.667 13.91 0.00 41.14 5.01
254 255 2.434884 CACTAGTGGCGGCAGGTG 60.435 66.667 13.91 17.59 0.00 4.00
255 256 2.603473 TCACTAGTGGCGGCAGGT 60.603 61.111 22.48 9.23 0.00 4.00
256 257 2.185350 CTCACTAGTGGCGGCAGG 59.815 66.667 22.48 8.51 0.00 4.85
257 258 2.185350 CCTCACTAGTGGCGGCAG 59.815 66.667 22.48 11.75 0.00 4.85
258 259 3.390521 CCCTCACTAGTGGCGGCA 61.391 66.667 22.48 7.97 0.00 5.69
259 260 4.162690 CCCCTCACTAGTGGCGGC 62.163 72.222 22.48 0.00 0.00 6.53
260 261 3.470888 CCCCCTCACTAGTGGCGG 61.471 72.222 22.48 20.66 0.00 6.13
261 262 2.240162 GAACCCCCTCACTAGTGGCG 62.240 65.000 22.48 13.49 0.00 5.69
262 263 0.910088 AGAACCCCCTCACTAGTGGC 60.910 60.000 22.48 3.10 0.00 5.01
263 264 1.657804 AAGAACCCCCTCACTAGTGG 58.342 55.000 22.48 12.85 0.00 4.00
264 265 3.790089 AAAAGAACCCCCTCACTAGTG 57.210 47.619 17.17 17.17 0.00 2.74
282 283 8.138712 ACTACCTGCGAATAAAATTGTCAAAAA 58.861 29.630 0.00 0.00 0.00 1.94
283 284 7.653647 ACTACCTGCGAATAAAATTGTCAAAA 58.346 30.769 0.00 0.00 0.00 2.44
284 285 7.209471 ACTACCTGCGAATAAAATTGTCAAA 57.791 32.000 0.00 0.00 0.00 2.69
285 286 6.128117 GGACTACCTGCGAATAAAATTGTCAA 60.128 38.462 0.00 0.00 0.00 3.18
286 287 5.353123 GGACTACCTGCGAATAAAATTGTCA 59.647 40.000 0.00 0.00 0.00 3.58
287 288 5.585047 AGGACTACCTGCGAATAAAATTGTC 59.415 40.000 0.00 0.00 45.92 3.18
288 289 5.497474 AGGACTACCTGCGAATAAAATTGT 58.503 37.500 0.00 0.00 45.92 2.71
303 304 4.341487 ACCTATTGCCAAAAAGGACTACC 58.659 43.478 14.27 0.00 41.22 3.18
304 305 5.391629 CGAACCTATTGCCAAAAAGGACTAC 60.392 44.000 14.27 4.10 41.22 2.73
305 306 4.698304 CGAACCTATTGCCAAAAAGGACTA 59.302 41.667 14.27 0.00 41.22 2.59
306 307 3.506067 CGAACCTATTGCCAAAAAGGACT 59.494 43.478 14.27 3.25 41.22 3.85
307 308 3.504520 TCGAACCTATTGCCAAAAAGGAC 59.495 43.478 14.27 8.01 41.22 3.85
308 309 3.504520 GTCGAACCTATTGCCAAAAAGGA 59.495 43.478 14.27 0.00 41.22 3.36
309 310 3.669557 CGTCGAACCTATTGCCAAAAAGG 60.670 47.826 7.47 7.47 41.84 3.11
310 311 3.488489 CGTCGAACCTATTGCCAAAAAG 58.512 45.455 0.00 0.00 0.00 2.27
311 312 2.226912 CCGTCGAACCTATTGCCAAAAA 59.773 45.455 0.00 0.00 0.00 1.94
312 313 1.807742 CCGTCGAACCTATTGCCAAAA 59.192 47.619 0.00 0.00 0.00 2.44
313 314 1.444836 CCGTCGAACCTATTGCCAAA 58.555 50.000 0.00 0.00 0.00 3.28
314 315 0.391927 CCCGTCGAACCTATTGCCAA 60.392 55.000 0.00 0.00 0.00 4.52
315 316 1.219664 CCCGTCGAACCTATTGCCA 59.780 57.895 0.00 0.00 0.00 4.92
316 317 1.523032 CCCCGTCGAACCTATTGCC 60.523 63.158 0.00 0.00 0.00 4.52
317 318 1.523032 CCCCCGTCGAACCTATTGC 60.523 63.158 0.00 0.00 0.00 3.56
318 319 4.848685 CCCCCGTCGAACCTATTG 57.151 61.111 0.00 0.00 0.00 1.90
332 333 0.840617 TTTTTGTCCAAAAGGCCCCC 59.159 50.000 0.00 0.00 40.83 5.40
356 357 9.862371 CAGTCTACTGATAGTACAAGAAATGTT 57.138 33.333 3.99 0.00 46.59 2.71
357 358 9.026121 ACAGTCTACTGATAGTACAAGAAATGT 57.974 33.333 16.74 0.00 46.59 2.71
360 361 9.736414 ACTACAGTCTACTGATAGTACAAGAAA 57.264 33.333 16.74 0.00 46.59 2.52
362 363 9.814899 GTACTACAGTCTACTGATAGTACAAGA 57.185 37.037 29.51 15.10 46.38 3.02
366 367 7.504403 TGGGTACTACAGTCTACTGATAGTAC 58.496 42.308 28.34 28.34 46.39 2.73
367 368 7.681259 TGGGTACTACAGTCTACTGATAGTA 57.319 40.000 16.74 17.80 46.59 1.82
368 369 6.572182 TGGGTACTACAGTCTACTGATAGT 57.428 41.667 16.74 18.60 46.59 2.12
369 370 7.556996 ACTTTGGGTACTACAGTCTACTGATAG 59.443 40.741 16.74 14.74 46.59 2.08
370 371 7.408543 ACTTTGGGTACTACAGTCTACTGATA 58.591 38.462 16.74 5.03 46.59 2.15
371 372 6.254522 ACTTTGGGTACTACAGTCTACTGAT 58.745 40.000 16.74 4.16 46.59 2.90
372 373 5.638133 ACTTTGGGTACTACAGTCTACTGA 58.362 41.667 16.74 0.39 46.59 3.41
374 375 5.015515 GGACTTTGGGTACTACAGTCTACT 58.984 45.833 13.04 0.00 35.25 2.57
375 376 4.142513 CGGACTTTGGGTACTACAGTCTAC 60.143 50.000 13.04 2.47 35.25 2.59
376 377 4.012374 CGGACTTTGGGTACTACAGTCTA 58.988 47.826 13.04 0.00 35.25 2.59
377 378 2.824341 CGGACTTTGGGTACTACAGTCT 59.176 50.000 13.04 0.00 35.25 3.24
378 379 2.094338 CCGGACTTTGGGTACTACAGTC 60.094 54.545 0.00 7.84 34.31 3.51
379 380 1.897802 CCGGACTTTGGGTACTACAGT 59.102 52.381 0.00 0.00 0.00 3.55
380 381 1.405121 GCCGGACTTTGGGTACTACAG 60.405 57.143 5.05 0.00 0.00 2.74
381 382 0.609662 GCCGGACTTTGGGTACTACA 59.390 55.000 5.05 0.00 0.00 2.74
382 383 0.609662 TGCCGGACTTTGGGTACTAC 59.390 55.000 5.05 0.00 0.00 2.73
383 384 1.575419 ATGCCGGACTTTGGGTACTA 58.425 50.000 5.05 0.00 0.00 1.82
384 385 0.696501 AATGCCGGACTTTGGGTACT 59.303 50.000 5.05 0.00 0.00 2.73
385 386 2.406596 TAATGCCGGACTTTGGGTAC 57.593 50.000 5.05 0.00 0.00 3.34
414 415 2.704725 TCTTTGCGGTGCATCTTTTC 57.295 45.000 0.00 0.00 38.76 2.29
517 518 1.091537 GGAAAAATGATGGCGGACGA 58.908 50.000 0.00 0.00 0.00 4.20
575 576 2.325082 GCTTTCCGGCGCAGAAGAA 61.325 57.895 10.83 1.97 0.00 2.52
576 577 2.742372 GCTTTCCGGCGCAGAAGA 60.742 61.111 10.83 0.00 0.00 2.87
577 578 3.804193 GGCTTTCCGGCGCAGAAG 61.804 66.667 10.83 7.21 0.00 2.85
671 672 1.067416 GTCATGGCCGCATCGTCTA 59.933 57.895 0.00 0.00 0.00 2.59
823 825 2.598787 GGACATGTGGGACCCGGAA 61.599 63.158 1.15 0.00 0.00 4.30
834 836 1.671850 CCTGTTTAGACGCGGACATGT 60.672 52.381 12.47 0.00 0.00 3.21
841 843 2.726691 CGTGGCCTGTTTAGACGCG 61.727 63.158 3.53 3.53 0.00 6.01
859 861 3.989787 CAACAAACTGCGGCCCCC 61.990 66.667 0.00 0.00 0.00 5.40
1056 1068 1.899142 ACAAGGAGAGGAGAACAGAGC 59.101 52.381 0.00 0.00 0.00 4.09
1060 1072 0.318441 CGCACAAGGAGAGGAGAACA 59.682 55.000 0.00 0.00 0.00 3.18
1062 1074 1.188219 AGCGCACAAGGAGAGGAGAA 61.188 55.000 11.47 0.00 0.00 2.87
1074 1086 0.179070 TTGGTGAACACTAGCGCACA 60.179 50.000 11.47 0.00 33.09 4.57
1082 1094 1.421268 TGCCTGATCTTGGTGAACACT 59.579 47.619 4.96 0.00 0.00 3.55
1573 1603 5.853572 TCCTAATCCCGCCCTAATTTAAT 57.146 39.130 0.00 0.00 0.00 1.40
1575 1605 4.018779 CCATCCTAATCCCGCCCTAATTTA 60.019 45.833 0.00 0.00 0.00 1.40
1663 1696 3.364889 TCTGCCGGTAGTAAATCATCG 57.635 47.619 19.70 0.00 0.00 3.84
1682 1718 8.741101 TCAACACATATAACAAATGTTGCTTC 57.259 30.769 8.99 0.00 46.20 3.86
1814 1850 0.248661 ATCGACGCGGACAGAGATTG 60.249 55.000 12.47 0.00 0.00 2.67
1815 1851 0.029567 GATCGACGCGGACAGAGATT 59.970 55.000 12.47 0.00 0.00 2.40
1816 1852 0.816018 AGATCGACGCGGACAGAGAT 60.816 55.000 12.47 5.50 0.00 2.75
1817 1853 1.429927 GAGATCGACGCGGACAGAGA 61.430 60.000 12.47 0.07 0.00 3.10
1818 1854 1.010574 GAGATCGACGCGGACAGAG 60.011 63.158 12.47 0.00 0.00 3.35
1819 1855 2.810012 CGAGATCGACGCGGACAGA 61.810 63.158 12.47 4.11 43.02 3.41
1820 1856 1.759293 TACGAGATCGACGCGGACAG 61.759 60.000 12.47 0.00 45.40 3.51
1821 1857 1.360931 TTACGAGATCGACGCGGACA 61.361 55.000 12.47 0.00 45.40 4.02
1825 1861 2.149494 CAGAAATTACGAGATCGACGCG 59.851 50.000 3.53 3.53 46.44 6.01
1931 3359 2.509336 CCGACGACCAGTGCATCC 60.509 66.667 0.00 0.00 0.00 3.51
2084 3512 2.785679 CTCGGGCGTGAAAATGAAATC 58.214 47.619 0.00 0.00 0.00 2.17
2091 3519 1.374252 GAGAGCTCGGGCGTGAAAA 60.374 57.895 8.37 0.00 44.37 2.29
2126 3554 3.127548 GTCCCGAACGTAGACACTGATTA 59.872 47.826 0.00 0.00 0.00 1.75
2168 3596 2.469274 ACATGACAGTTCAGGAGCAG 57.531 50.000 0.00 0.00 36.99 4.24
2184 3612 4.696877 TGCTGAAACTTCGATGATGAACAT 59.303 37.500 5.16 0.00 42.47 2.71
2298 3737 1.531602 GGCTTCAGTTGGCCCACTT 60.532 57.895 6.77 0.00 42.30 3.16
2325 3764 1.741770 GCCTGAAGTAGTGCCGTGG 60.742 63.158 0.00 0.00 0.00 4.94
2329 3768 1.448013 GGTCGCCTGAAGTAGTGCC 60.448 63.158 0.00 0.00 0.00 5.01
2330 3769 1.448013 GGGTCGCCTGAAGTAGTGC 60.448 63.158 0.00 0.00 0.00 4.40
2331 3770 0.389948 GTGGGTCGCCTGAAGTAGTG 60.390 60.000 0.00 0.00 0.00 2.74
2332 3771 0.830444 TGTGGGTCGCCTGAAGTAGT 60.830 55.000 0.00 0.00 0.00 2.73
2333 3772 0.537188 ATGTGGGTCGCCTGAAGTAG 59.463 55.000 0.00 0.00 0.00 2.57
2425 3867 6.824305 ACATGAATGAAAGAACTAGGGTTG 57.176 37.500 0.00 0.00 35.58 3.77
2485 3927 4.058817 GGGAATCTCTATTACAGCAACGG 58.941 47.826 0.00 0.00 0.00 4.44
2491 3933 4.037684 ACGAACCGGGAATCTCTATTACAG 59.962 45.833 6.32 0.00 0.00 2.74
2506 3948 3.557824 GTGTTAGGCACGAACCGG 58.442 61.111 0.00 0.00 43.27 5.28
2556 3998 0.257328 TTTGGGCCAGAGTGTTGTGA 59.743 50.000 6.23 0.00 0.00 3.58
2558 4000 1.133513 TGATTTGGGCCAGAGTGTTGT 60.134 47.619 6.23 0.00 0.00 3.32
2599 4041 1.509463 CTAGTTGTGGTCGCGCCTA 59.491 57.895 18.14 0.00 38.35 3.93
2608 4050 2.114670 CCATGGCGGCTAGTTGTGG 61.115 63.158 11.43 5.22 0.00 4.17
2610 4052 1.078426 GTCCATGGCGGCTAGTTGT 60.078 57.895 11.43 0.00 33.14 3.32
2613 4055 3.480133 GGGTCCATGGCGGCTAGT 61.480 66.667 11.43 0.00 33.14 2.57


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

AutoCloner maintained by Alex Coulton.