Multiple sequence alignment - TraesCS4D01G235300

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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 TraesCS4D01G235300 chr4D 100.000 2879 0 0 1 2879 396423432 396426310 0.000000e+00 5317
1 TraesCS4D01G235300 chr4D 91.176 238 17 4 351 587 422507818 422508052 1.290000e-83 320
2 TraesCS4D01G235300 chr1A 94.986 2194 98 6 692 2876 585001135 585003325 0.000000e+00 3432
3 TraesCS4D01G235300 chr1A 93.846 1885 106 5 995 2879 487689015 487687141 0.000000e+00 2830
4 TraesCS4D01G235300 chr1A 97.568 329 7 1 359 686 585000748 585001076 1.940000e-156 562
5 TraesCS4D01G235300 chr1A 87.500 320 21 6 359 675 534100205 534100508 4.560000e-93 351
6 TraesCS4D01G235300 chr1A 93.506 231 10 5 358 585 445250771 445250999 3.550000e-89 339
7 TraesCS4D01G235300 chr5D 96.627 1927 58 5 953 2879 250590252 250592171 0.000000e+00 3192
8 TraesCS4D01G235300 chr5D 95.988 1944 66 9 938 2879 544689403 544687470 0.000000e+00 3147
9 TraesCS4D01G235300 chr3D 96.434 1879 67 0 1001 2879 511271752 511269874 0.000000e+00 3099
10 TraesCS4D01G235300 chr3D 95.798 1880 78 1 1001 2879 443414307 443416186 0.000000e+00 3033
11 TraesCS4D01G235300 chr7D 95.013 1925 81 8 938 2861 26435165 26433255 0.000000e+00 3009
12 TraesCS4D01G235300 chr7D 93.936 1880 110 2 1001 2879 20275493 20273617 0.000000e+00 2837
13 TraesCS4D01G235300 chr4B 93.978 1943 106 6 938 2879 475249312 475251244 0.000000e+00 2929
14 TraesCS4D01G235300 chr4B 92.000 175 13 1 1 175 488148978 488149151 7.970000e-61 244
15 TraesCS4D01G235300 chr4A 88.411 2071 222 9 811 2879 191109949 191107895 0.000000e+00 2479
16 TraesCS4D01G235300 chr4A 90.909 330 28 2 358 686 191110424 191110096 2.630000e-120 442
17 TraesCS4D01G235300 chr3B 89.445 1478 81 30 353 1757 30243123 30241648 0.000000e+00 1796
18 TraesCS4D01G235300 chr3B 90.734 259 22 2 359 616 104645058 104644801 7.640000e-91 344
19 TraesCS4D01G235300 chr5B 92.835 321 17 5 359 676 102601288 102600971 7.270000e-126 460
20 TraesCS4D01G235300 chr1D 91.411 326 26 2 359 683 275603224 275602900 2.040000e-121 446
21 TraesCS4D01G235300 chr1B 91.824 318 20 5 356 670 133434586 133434900 3.410000e-119 438


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 TraesCS4D01G235300 chr4D 396423432 396426310 2878 False 5317.0 5317 100.000 1 2879 1 chr4D.!!$F1 2878
1 TraesCS4D01G235300 chr1A 487687141 487689015 1874 True 2830.0 2830 93.846 995 2879 1 chr1A.!!$R1 1884
2 TraesCS4D01G235300 chr1A 585000748 585003325 2577 False 1997.0 3432 96.277 359 2876 2 chr1A.!!$F3 2517
3 TraesCS4D01G235300 chr5D 250590252 250592171 1919 False 3192.0 3192 96.627 953 2879 1 chr5D.!!$F1 1926
4 TraesCS4D01G235300 chr5D 544687470 544689403 1933 True 3147.0 3147 95.988 938 2879 1 chr5D.!!$R1 1941
5 TraesCS4D01G235300 chr3D 511269874 511271752 1878 True 3099.0 3099 96.434 1001 2879 1 chr3D.!!$R1 1878
6 TraesCS4D01G235300 chr3D 443414307 443416186 1879 False 3033.0 3033 95.798 1001 2879 1 chr3D.!!$F1 1878
7 TraesCS4D01G235300 chr7D 26433255 26435165 1910 True 3009.0 3009 95.013 938 2861 1 chr7D.!!$R2 1923
8 TraesCS4D01G235300 chr7D 20273617 20275493 1876 True 2837.0 2837 93.936 1001 2879 1 chr7D.!!$R1 1878
9 TraesCS4D01G235300 chr4B 475249312 475251244 1932 False 2929.0 2929 93.978 938 2879 1 chr4B.!!$F1 1941
10 TraesCS4D01G235300 chr4A 191107895 191110424 2529 True 1460.5 2479 89.660 358 2879 2 chr4A.!!$R1 2521
11 TraesCS4D01G235300 chr3B 30241648 30243123 1475 True 1796.0 1796 89.445 353 1757 1 chr3B.!!$R1 1404

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
308 309 0.036732 AAACGCCTTCTGGATGCAGA 59.963 50.0 13.58 13.58 34.57 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2120 2274 0.329596 GTGAGGAAGGGGATGCAGTT 59.67 55.0 0.0 0.0 0.0 3.16 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
26 27 9.508567 GGTAAAATGAAGCTCATATTTCACTTC 57.491 33.333 0.00 0.00 35.76 3.01
32 33 8.442632 TGAAGCTCATATTTCACTTCATTAGG 57.557 34.615 0.00 0.00 41.20 2.69
33 34 8.267183 TGAAGCTCATATTTCACTTCATTAGGA 58.733 33.333 0.00 0.00 41.20 2.94
34 35 9.113838 GAAGCTCATATTTCACTTCATTAGGAA 57.886 33.333 0.00 0.00 37.33 3.36
42 43 2.425143 CTTCATTAGGAAGCAGGCCA 57.575 50.000 5.01 0.00 45.99 5.36
43 44 2.726821 CTTCATTAGGAAGCAGGCCAA 58.273 47.619 5.01 0.00 45.99 4.52
44 45 2.425143 TCATTAGGAAGCAGGCCAAG 57.575 50.000 5.01 0.00 0.00 3.61
45 46 1.635487 TCATTAGGAAGCAGGCCAAGT 59.365 47.619 5.01 0.00 0.00 3.16
46 47 2.041620 TCATTAGGAAGCAGGCCAAGTT 59.958 45.455 5.01 0.00 0.00 2.66
47 48 1.909700 TTAGGAAGCAGGCCAAGTTG 58.090 50.000 5.01 0.00 0.00 3.16
48 49 1.064003 TAGGAAGCAGGCCAAGTTGA 58.936 50.000 5.01 0.00 0.00 3.18
49 50 0.407139 AGGAAGCAGGCCAAGTTGAT 59.593 50.000 5.01 0.00 0.00 2.57
50 51 1.203100 AGGAAGCAGGCCAAGTTGATT 60.203 47.619 5.01 0.00 0.00 2.57
51 52 1.067354 GGAAGCAGGCCAAGTTGATTG 60.067 52.381 5.01 0.86 38.74 2.67
52 53 0.319405 AAGCAGGCCAAGTTGATTGC 59.681 50.000 5.01 10.74 37.60 3.56
53 54 0.828762 AGCAGGCCAAGTTGATTGCA 60.829 50.000 20.58 0.00 37.60 4.08
54 55 0.668401 GCAGGCCAAGTTGATTGCAC 60.668 55.000 5.01 3.47 37.60 4.57
55 56 0.037975 CAGGCCAAGTTGATTGCACC 60.038 55.000 5.01 0.00 37.60 5.01
56 57 0.469705 AGGCCAAGTTGATTGCACCA 60.470 50.000 5.01 0.00 37.60 4.17
57 58 0.319813 GGCCAAGTTGATTGCACCAC 60.320 55.000 3.87 0.00 37.60 4.16
58 59 0.319813 GCCAAGTTGATTGCACCACC 60.320 55.000 3.87 0.00 37.60 4.61
59 60 1.331214 CCAAGTTGATTGCACCACCT 58.669 50.000 3.87 0.00 37.60 4.00
60 61 1.000060 CCAAGTTGATTGCACCACCTG 60.000 52.381 3.87 0.00 37.60 4.00
68 69 3.200522 GCACCACCTGCTAATGCC 58.799 61.111 0.00 0.00 43.33 4.40
69 70 1.678635 GCACCACCTGCTAATGCCA 60.679 57.895 0.00 0.00 43.33 4.92
70 71 1.039233 GCACCACCTGCTAATGCCAT 61.039 55.000 0.00 0.00 43.33 4.40
71 72 0.742505 CACCACCTGCTAATGCCATG 59.257 55.000 0.00 0.00 38.71 3.66
72 73 0.396139 ACCACCTGCTAATGCCATGG 60.396 55.000 7.63 7.63 39.14 3.66
73 74 1.111116 CCACCTGCTAATGCCATGGG 61.111 60.000 15.13 0.00 38.71 4.00
89 90 5.356291 CCATGGGCAATAATTTTCCTCAA 57.644 39.130 2.85 0.00 0.00 3.02
90 91 5.932455 CCATGGGCAATAATTTTCCTCAAT 58.068 37.500 2.85 0.00 0.00 2.57
91 92 5.993441 CCATGGGCAATAATTTTCCTCAATC 59.007 40.000 2.85 0.00 0.00 2.67
92 93 6.408320 CCATGGGCAATAATTTTCCTCAATCA 60.408 38.462 2.85 0.00 0.00 2.57
93 94 6.811634 TGGGCAATAATTTTCCTCAATCAT 57.188 33.333 0.00 0.00 0.00 2.45
94 95 6.819284 TGGGCAATAATTTTCCTCAATCATC 58.181 36.000 0.00 0.00 0.00 2.92
95 96 5.922544 GGGCAATAATTTTCCTCAATCATCG 59.077 40.000 0.00 0.00 0.00 3.84
96 97 6.461509 GGGCAATAATTTTCCTCAATCATCGT 60.462 38.462 0.00 0.00 0.00 3.73
97 98 6.980397 GGCAATAATTTTCCTCAATCATCGTT 59.020 34.615 0.00 0.00 0.00 3.85
98 99 7.492344 GGCAATAATTTTCCTCAATCATCGTTT 59.508 33.333 0.00 0.00 0.00 3.60
99 100 8.534778 GCAATAATTTTCCTCAATCATCGTTTC 58.465 33.333 0.00 0.00 0.00 2.78
100 101 9.793252 CAATAATTTTCCTCAATCATCGTTTCT 57.207 29.630 0.00 0.00 0.00 2.52
103 104 7.921786 ATTTTCCTCAATCATCGTTTCTACA 57.078 32.000 0.00 0.00 0.00 2.74
104 105 6.968131 TTTCCTCAATCATCGTTTCTACAG 57.032 37.500 0.00 0.00 0.00 2.74
105 106 5.661056 TCCTCAATCATCGTTTCTACAGT 57.339 39.130 0.00 0.00 0.00 3.55
106 107 5.410924 TCCTCAATCATCGTTTCTACAGTG 58.589 41.667 0.00 0.00 0.00 3.66
107 108 5.185056 TCCTCAATCATCGTTTCTACAGTGA 59.815 40.000 0.00 0.00 0.00 3.41
108 109 5.518128 CCTCAATCATCGTTTCTACAGTGAG 59.482 44.000 0.00 0.00 0.00 3.51
109 110 4.864806 TCAATCATCGTTTCTACAGTGAGC 59.135 41.667 0.00 0.00 0.00 4.26
110 111 3.232213 TCATCGTTTCTACAGTGAGCC 57.768 47.619 0.00 0.00 0.00 4.70
111 112 2.560981 TCATCGTTTCTACAGTGAGCCA 59.439 45.455 0.00 0.00 0.00 4.75
112 113 2.433868 TCGTTTCTACAGTGAGCCAC 57.566 50.000 0.00 0.00 34.10 5.01
113 114 1.684450 TCGTTTCTACAGTGAGCCACA 59.316 47.619 0.00 0.00 36.74 4.17
114 115 2.101750 TCGTTTCTACAGTGAGCCACAA 59.898 45.455 0.00 0.00 36.74 3.33
115 116 3.067106 CGTTTCTACAGTGAGCCACAAT 58.933 45.455 0.00 0.00 36.74 2.71
116 117 4.021807 TCGTTTCTACAGTGAGCCACAATA 60.022 41.667 0.00 0.20 36.74 1.90
117 118 4.327357 CGTTTCTACAGTGAGCCACAATAG 59.673 45.833 0.00 8.17 36.74 1.73
118 119 5.238583 GTTTCTACAGTGAGCCACAATAGT 58.761 41.667 0.00 4.03 36.74 2.12
119 120 5.483685 TTCTACAGTGAGCCACAATAGTT 57.516 39.130 0.00 0.00 36.74 2.24
120 121 6.599356 TTCTACAGTGAGCCACAATAGTTA 57.401 37.500 0.00 1.42 36.74 2.24
121 122 6.791867 TCTACAGTGAGCCACAATAGTTAT 57.208 37.500 0.00 0.00 36.74 1.89
122 123 7.891498 TCTACAGTGAGCCACAATAGTTATA 57.109 36.000 0.00 0.00 36.74 0.98
123 124 8.478775 TCTACAGTGAGCCACAATAGTTATAT 57.521 34.615 0.00 0.00 36.74 0.86
124 125 9.582648 TCTACAGTGAGCCACAATAGTTATATA 57.417 33.333 0.00 0.00 36.74 0.86
127 128 7.604164 ACAGTGAGCCACAATAGTTATATATGC 59.396 37.037 0.00 0.00 36.74 3.14
128 129 7.603784 CAGTGAGCCACAATAGTTATATATGCA 59.396 37.037 7.86 0.00 36.74 3.96
129 130 8.156820 AGTGAGCCACAATAGTTATATATGCAA 58.843 33.333 7.86 0.00 36.74 4.08
130 131 8.446273 GTGAGCCACAATAGTTATATATGCAAG 58.554 37.037 0.00 0.00 34.08 4.01
131 132 8.156820 TGAGCCACAATAGTTATATATGCAAGT 58.843 33.333 0.00 0.00 0.00 3.16
132 133 8.327941 AGCCACAATAGTTATATATGCAAGTG 57.672 34.615 0.00 0.00 0.00 3.16
133 134 7.939039 AGCCACAATAGTTATATATGCAAGTGT 59.061 33.333 0.00 0.00 0.00 3.55
134 135 9.214957 GCCACAATAGTTATATATGCAAGTGTA 57.785 33.333 0.00 0.00 0.00 2.90
146 147 7.886629 ATATGCAAGTGTATTTGGATCAACT 57.113 32.000 0.00 0.00 39.42 3.16
147 148 6.594788 ATGCAAGTGTATTTGGATCAACTT 57.405 33.333 0.00 0.00 34.53 2.66
148 149 7.701539 ATGCAAGTGTATTTGGATCAACTTA 57.298 32.000 0.00 0.00 34.53 2.24
149 150 7.701539 TGCAAGTGTATTTGGATCAACTTAT 57.298 32.000 0.00 0.00 0.00 1.73
150 151 8.800370 TGCAAGTGTATTTGGATCAACTTATA 57.200 30.769 0.00 0.00 0.00 0.98
151 152 9.407380 TGCAAGTGTATTTGGATCAACTTATAT 57.593 29.630 0.00 0.00 0.00 0.86
152 153 9.669353 GCAAGTGTATTTGGATCAACTTATATG 57.331 33.333 0.00 0.00 0.00 1.78
156 157 9.831737 GTGTATTTGGATCAACTTATATGATGC 57.168 33.333 0.00 1.65 43.50 3.91
161 162 7.024345 TGGATCAACTTATATGATGCATCCT 57.976 36.000 23.67 16.51 46.43 3.24
162 163 7.108194 TGGATCAACTTATATGATGCATCCTC 58.892 38.462 23.67 0.98 46.43 3.71
163 164 7.108194 GGATCAACTTATATGATGCATCCTCA 58.892 38.462 23.67 7.65 42.94 3.86
164 165 7.065563 GGATCAACTTATATGATGCATCCTCAC 59.934 40.741 23.67 0.00 42.94 3.51
165 166 7.071069 TCAACTTATATGATGCATCCTCACT 57.929 36.000 23.67 6.87 0.00 3.41
166 167 7.512130 TCAACTTATATGATGCATCCTCACTT 58.488 34.615 23.67 5.70 0.00 3.16
167 168 7.658982 TCAACTTATATGATGCATCCTCACTTC 59.341 37.037 23.67 0.00 0.00 3.01
168 169 7.313740 ACTTATATGATGCATCCTCACTTCT 57.686 36.000 23.67 3.07 0.00 2.85
169 170 7.743749 ACTTATATGATGCATCCTCACTTCTT 58.256 34.615 23.67 0.00 0.00 2.52
170 171 8.216423 ACTTATATGATGCATCCTCACTTCTTT 58.784 33.333 23.67 0.00 0.00 2.52
171 172 8.985315 TTATATGATGCATCCTCACTTCTTTT 57.015 30.769 23.67 0.00 0.00 2.27
172 173 7.893124 ATATGATGCATCCTCACTTCTTTTT 57.107 32.000 23.67 0.00 0.00 1.94
193 194 6.524101 TTTTATCTTCAAGGTAATGGCCAC 57.476 37.500 8.16 0.00 0.00 5.01
194 195 3.737559 ATCTTCAAGGTAATGGCCACA 57.262 42.857 8.16 0.00 0.00 4.17
195 196 3.737559 TCTTCAAGGTAATGGCCACAT 57.262 42.857 8.16 1.89 39.54 3.21
197 198 4.415596 TCTTCAAGGTAATGGCCACATTT 58.584 39.130 8.16 0.00 44.69 2.32
198 199 4.837860 TCTTCAAGGTAATGGCCACATTTT 59.162 37.500 8.16 0.00 44.69 1.82
199 200 6.013379 TCTTCAAGGTAATGGCCACATTTTA 58.987 36.000 8.16 0.00 44.69 1.52
200 201 6.667414 TCTTCAAGGTAATGGCCACATTTTAT 59.333 34.615 8.16 0.00 44.69 1.40
201 202 6.219417 TCAAGGTAATGGCCACATTTTATG 57.781 37.500 8.16 2.34 44.69 1.90
202 203 5.128499 TCAAGGTAATGGCCACATTTTATGG 59.872 40.000 8.16 0.00 44.69 2.74
203 204 4.877773 AGGTAATGGCCACATTTTATGGA 58.122 39.130 8.16 0.00 44.69 3.41
204 205 4.649218 AGGTAATGGCCACATTTTATGGAC 59.351 41.667 8.16 0.00 44.69 4.02
208 209 3.782889 GGCCACATTTTATGGACAGAC 57.217 47.619 0.00 0.00 45.59 3.51
209 210 3.356290 GGCCACATTTTATGGACAGACT 58.644 45.455 0.00 0.00 45.59 3.24
210 211 4.523083 GGCCACATTTTATGGACAGACTA 58.477 43.478 0.00 0.00 45.59 2.59
211 212 4.947388 GGCCACATTTTATGGACAGACTAA 59.053 41.667 0.00 0.00 45.59 2.24
212 213 5.594317 GGCCACATTTTATGGACAGACTAAT 59.406 40.000 0.00 0.00 45.59 1.73
213 214 6.238759 GGCCACATTTTATGGACAGACTAATC 60.239 42.308 0.00 0.00 45.59 1.75
214 215 6.318648 GCCACATTTTATGGACAGACTAATCA 59.681 38.462 0.00 0.00 39.87 2.57
215 216 7.679638 GCCACATTTTATGGACAGACTAATCAC 60.680 40.741 0.00 0.00 39.87 3.06
216 217 7.336679 CCACATTTTATGGACAGACTAATCACA 59.663 37.037 0.00 0.00 39.87 3.58
217 218 8.896744 CACATTTTATGGACAGACTAATCACAT 58.103 33.333 0.00 0.00 33.60 3.21
222 223 9.764363 TTTATGGACAGACTAATCACATACATC 57.236 33.333 0.00 0.00 0.00 3.06
223 224 6.790232 TGGACAGACTAATCACATACATCA 57.210 37.500 0.00 0.00 0.00 3.07
224 225 7.365497 TGGACAGACTAATCACATACATCAT 57.635 36.000 0.00 0.00 0.00 2.45
225 226 7.795047 TGGACAGACTAATCACATACATCATT 58.205 34.615 0.00 0.00 0.00 2.57
226 227 7.928167 TGGACAGACTAATCACATACATCATTC 59.072 37.037 0.00 0.00 0.00 2.67
227 228 7.928167 GGACAGACTAATCACATACATCATTCA 59.072 37.037 0.00 0.00 0.00 2.57
228 229 8.654230 ACAGACTAATCACATACATCATTCAC 57.346 34.615 0.00 0.00 0.00 3.18
229 230 7.436376 ACAGACTAATCACATACATCATTCACG 59.564 37.037 0.00 0.00 0.00 4.35
230 231 6.422100 AGACTAATCACATACATCATTCACGC 59.578 38.462 0.00 0.00 0.00 5.34
231 232 6.283694 ACTAATCACATACATCATTCACGCT 58.716 36.000 0.00 0.00 0.00 5.07
232 233 5.413969 AATCACATACATCATTCACGCTG 57.586 39.130 0.00 0.00 0.00 5.18
233 234 4.122143 TCACATACATCATTCACGCTGA 57.878 40.909 0.00 0.00 0.00 4.26
234 235 3.865164 TCACATACATCATTCACGCTGAC 59.135 43.478 0.00 0.00 0.00 3.51
235 236 3.867493 CACATACATCATTCACGCTGACT 59.133 43.478 0.00 0.00 0.00 3.41
236 237 4.330894 CACATACATCATTCACGCTGACTT 59.669 41.667 0.00 0.00 0.00 3.01
237 238 4.937620 ACATACATCATTCACGCTGACTTT 59.062 37.500 0.00 0.00 0.00 2.66
238 239 6.035975 CACATACATCATTCACGCTGACTTTA 59.964 38.462 0.00 0.00 0.00 1.85
239 240 6.763135 ACATACATCATTCACGCTGACTTTAT 59.237 34.615 0.00 0.00 0.00 1.40
240 241 7.926018 ACATACATCATTCACGCTGACTTTATA 59.074 33.333 0.00 0.00 0.00 0.98
241 242 6.589830 ACATCATTCACGCTGACTTTATAC 57.410 37.500 0.00 0.00 0.00 1.47
242 243 6.341316 ACATCATTCACGCTGACTTTATACT 58.659 36.000 0.00 0.00 0.00 2.12
243 244 6.818644 ACATCATTCACGCTGACTTTATACTT 59.181 34.615 0.00 0.00 0.00 2.24
244 245 7.979537 ACATCATTCACGCTGACTTTATACTTA 59.020 33.333 0.00 0.00 0.00 2.24
245 246 8.817100 CATCATTCACGCTGACTTTATACTTAA 58.183 33.333 0.00 0.00 0.00 1.85
246 247 8.942338 TCATTCACGCTGACTTTATACTTAAT 57.058 30.769 0.00 0.00 0.00 1.40
277 278 9.554724 AATGCTATGTTTTGTTAAACTCATACG 57.445 29.630 0.00 0.00 43.25 3.06
278 279 8.312896 TGCTATGTTTTGTTAAACTCATACGA 57.687 30.769 0.00 0.00 43.25 3.43
279 280 8.225107 TGCTATGTTTTGTTAAACTCATACGAC 58.775 33.333 0.00 0.00 43.25 4.34
280 281 8.440833 GCTATGTTTTGTTAAACTCATACGACT 58.559 33.333 0.00 0.00 43.25 4.18
283 284 8.301730 TGTTTTGTTAAACTCATACGACTAGG 57.698 34.615 0.00 0.00 43.25 3.02
284 285 7.927629 TGTTTTGTTAAACTCATACGACTAGGT 59.072 33.333 0.00 0.00 43.25 3.08
285 286 8.768019 GTTTTGTTAAACTCATACGACTAGGTT 58.232 33.333 0.00 0.00 40.38 3.50
286 287 7.878477 TTGTTAAACTCATACGACTAGGTTG 57.122 36.000 0.00 0.00 0.00 3.77
287 288 6.985117 TGTTAAACTCATACGACTAGGTTGT 58.015 36.000 0.00 0.00 34.24 3.32
288 289 7.436118 TGTTAAACTCATACGACTAGGTTGTT 58.564 34.615 0.00 0.00 31.92 2.83
289 290 8.575589 TGTTAAACTCATACGACTAGGTTGTTA 58.424 33.333 0.00 0.00 31.92 2.41
290 291 9.410556 GTTAAACTCATACGACTAGGTTGTTAA 57.589 33.333 0.00 0.00 31.92 2.01
291 292 9.979578 TTAAACTCATACGACTAGGTTGTTAAA 57.020 29.630 0.00 0.00 31.92 1.52
292 293 7.880059 AACTCATACGACTAGGTTGTTAAAC 57.120 36.000 0.00 0.00 31.92 2.01
293 294 6.088824 ACTCATACGACTAGGTTGTTAAACG 58.911 40.000 0.00 0.00 37.15 3.60
294 295 4.858692 TCATACGACTAGGTTGTTAAACGC 59.141 41.667 0.00 0.00 37.15 4.84
295 296 2.407090 ACGACTAGGTTGTTAAACGCC 58.593 47.619 0.00 0.00 37.15 5.68
296 297 2.036346 ACGACTAGGTTGTTAAACGCCT 59.964 45.455 0.00 0.00 37.15 5.52
297 298 3.062042 CGACTAGGTTGTTAAACGCCTT 58.938 45.455 0.00 0.00 37.15 4.35
298 299 3.122445 CGACTAGGTTGTTAAACGCCTTC 59.878 47.826 0.00 0.00 37.15 3.46
299 300 4.313282 GACTAGGTTGTTAAACGCCTTCT 58.687 43.478 0.00 0.00 37.15 2.85
300 301 4.062991 ACTAGGTTGTTAAACGCCTTCTG 58.937 43.478 0.00 0.00 37.15 3.02
301 302 2.227194 AGGTTGTTAAACGCCTTCTGG 58.773 47.619 0.00 0.00 37.15 3.86
302 303 2.158726 AGGTTGTTAAACGCCTTCTGGA 60.159 45.455 0.00 0.00 37.15 3.86
303 304 2.817844 GGTTGTTAAACGCCTTCTGGAT 59.182 45.455 0.00 0.00 37.15 3.41
304 305 3.365969 GGTTGTTAAACGCCTTCTGGATG 60.366 47.826 0.00 0.00 37.15 3.51
305 306 1.810151 TGTTAAACGCCTTCTGGATGC 59.190 47.619 0.00 0.00 34.57 3.91
306 307 1.810151 GTTAAACGCCTTCTGGATGCA 59.190 47.619 0.00 0.00 34.57 3.96
307 308 1.737838 TAAACGCCTTCTGGATGCAG 58.262 50.000 8.12 8.12 34.57 4.41
308 309 0.036732 AAACGCCTTCTGGATGCAGA 59.963 50.000 13.58 13.58 34.57 4.26
309 310 0.674895 AACGCCTTCTGGATGCAGAC 60.675 55.000 17.43 4.83 34.57 3.51
310 311 1.220206 CGCCTTCTGGATGCAGACT 59.780 57.895 17.43 0.00 34.57 3.24
311 312 0.461548 CGCCTTCTGGATGCAGACTA 59.538 55.000 17.43 2.16 34.57 2.59
312 313 1.069823 CGCCTTCTGGATGCAGACTAT 59.930 52.381 17.43 0.00 34.57 2.12
313 314 2.484417 CGCCTTCTGGATGCAGACTATT 60.484 50.000 17.43 0.00 34.57 1.73
314 315 3.549794 GCCTTCTGGATGCAGACTATTT 58.450 45.455 17.43 0.00 34.57 1.40
315 316 4.708177 GCCTTCTGGATGCAGACTATTTA 58.292 43.478 17.43 0.00 34.57 1.40
316 317 5.126067 GCCTTCTGGATGCAGACTATTTAA 58.874 41.667 17.43 0.00 34.57 1.52
317 318 5.590259 GCCTTCTGGATGCAGACTATTTAAA 59.410 40.000 17.43 0.00 34.57 1.52
318 319 6.264067 GCCTTCTGGATGCAGACTATTTAAAT 59.736 38.462 17.43 5.89 34.57 1.40
319 320 7.201857 GCCTTCTGGATGCAGACTATTTAAATT 60.202 37.037 17.43 0.00 34.57 1.82
320 321 8.348507 CCTTCTGGATGCAGACTATTTAAATTC 58.651 37.037 17.43 0.00 34.57 2.17
321 322 9.118300 CTTCTGGATGCAGACTATTTAAATTCT 57.882 33.333 17.43 1.25 0.00 2.40
323 324 9.770097 TCTGGATGCAGACTATTTAAATTCTAG 57.230 33.333 13.58 3.08 0.00 2.43
324 325 9.770097 CTGGATGCAGACTATTTAAATTCTAGA 57.230 33.333 8.85 0.00 0.00 2.43
348 349 9.764363 AGAATGTGTGAATATTCGTATGTATGT 57.236 29.630 10.80 0.00 38.13 2.29
349 350 9.797473 GAATGTGTGAATATTCGTATGTATGTG 57.203 33.333 10.80 0.00 0.00 3.21
350 351 7.707774 TGTGTGAATATTCGTATGTATGTGG 57.292 36.000 10.80 0.00 0.00 4.17
351 352 7.493367 TGTGTGAATATTCGTATGTATGTGGA 58.507 34.615 10.80 0.00 0.00 4.02
352 353 8.147704 TGTGTGAATATTCGTATGTATGTGGAT 58.852 33.333 10.80 0.00 0.00 3.41
353 354 9.634163 GTGTGAATATTCGTATGTATGTGGATA 57.366 33.333 10.80 0.00 0.00 2.59
354 355 9.855021 TGTGAATATTCGTATGTATGTGGATAG 57.145 33.333 10.80 0.00 0.00 2.08
355 356 9.856488 GTGAATATTCGTATGTATGTGGATAGT 57.144 33.333 10.80 0.00 0.00 2.12
356 357 9.855021 TGAATATTCGTATGTATGTGGATAGTG 57.145 33.333 10.80 0.00 0.00 2.74
495 496 9.948964 CTCATTTATCCAACATGGTATCAGATA 57.051 33.333 0.00 0.00 39.03 1.98
686 688 1.988956 CTGCTGGCCTCCTCTGTCT 60.989 63.158 3.32 0.00 0.00 3.41
688 690 3.028921 GCTGGCCTCCTCTGTCTGG 62.029 68.421 3.32 0.00 0.00 3.86
689 691 1.611851 CTGGCCTCCTCTGTCTGGT 60.612 63.158 3.32 0.00 0.00 4.00
804 893 2.202544 GCTCGAGCGTGACCTCTG 60.203 66.667 23.61 0.00 0.00 3.35
805 894 2.202544 CTCGAGCGTGACCTCTGC 60.203 66.667 0.00 0.00 0.00 4.26
807 896 2.807045 CGAGCGTGACCTCTGCAC 60.807 66.667 0.00 0.00 0.00 4.57
808 897 2.433318 GAGCGTGACCTCTGCACC 60.433 66.667 0.00 0.00 32.74 5.01
809 898 3.226429 GAGCGTGACCTCTGCACCA 62.226 63.158 0.00 0.00 32.74 4.17
810 899 2.740055 GCGTGACCTCTGCACCAG 60.740 66.667 0.00 0.00 32.74 4.00
1030 1178 1.153429 GGCTATGTCGCGGTTCCTT 60.153 57.895 6.13 0.00 0.00 3.36
1055 1203 2.569059 CTCGGTGATCTTTGATGGCAT 58.431 47.619 0.00 0.00 0.00 4.40
1114 1262 1.816863 GCGTGGACTCCTTCTGTGGA 61.817 60.000 0.00 0.00 34.52 4.02
1279 1427 3.647590 TGCTTATGATCAGCAGGTATCCA 59.352 43.478 0.09 0.00 42.49 3.41
1393 1541 2.168496 CGAGTGTCCTCCCTCAGTTTA 58.832 52.381 0.00 0.00 33.93 2.01
1750 1898 2.497675 TCCGAGATACTTGCTGAGCTTT 59.502 45.455 5.83 0.00 0.00 3.51
1808 1956 2.253610 TCTGGTTCCGTCAGTATTGGT 58.746 47.619 0.00 0.00 34.15 3.67
2006 2160 4.067512 AGGCGCTCCTCCTCCTCA 62.068 66.667 7.64 0.00 38.72 3.86
2014 2168 0.719015 TCCTCCTCCTCAAGTGGGAT 59.281 55.000 0.00 0.00 31.89 3.85
2034 2188 2.103153 TCCTGTGTCTTCCTCAACCT 57.897 50.000 0.00 0.00 0.00 3.50
2062 2216 4.780021 ACTCACTGACCAGGATATTGTTCT 59.220 41.667 0.00 0.00 0.00 3.01
2085 2239 3.471620 AGCGTCTCCTTGCTTCCA 58.528 55.556 0.00 0.00 38.57 3.53
2120 2274 2.434884 GCTTCCGCTGCTGCTGTA 60.435 61.111 14.03 0.09 36.97 2.74
2145 2299 0.253820 ATCCCCTTCCTCACCACCAT 60.254 55.000 0.00 0.00 0.00 3.55
2188 2342 3.244911 ACATCTTCGTGGGTTCTGGATTT 60.245 43.478 0.00 0.00 0.00 2.17
2262 2416 5.353394 ACCTCTTGATTCGCCTGTTAATA 57.647 39.130 0.00 0.00 0.00 0.98
2415 2570 4.888917 TGATTCTGGTTGTCGTGTCATTA 58.111 39.130 0.00 0.00 0.00 1.90
2532 2687 3.135712 TGACTAGCTTTGTGTTCCTTCCA 59.864 43.478 0.00 0.00 0.00 3.53
2722 2879 1.528586 CAGACTTGGCAAACAGACTCG 59.471 52.381 0.00 0.00 0.00 4.18
2815 2972 3.338249 CTGCTCCCTTTGATTCGAAAGA 58.662 45.455 0.00 0.00 35.30 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.508567 GAAGTGAAATATGAGCTTCATTTTACC 57.491 33.333 14.45 7.00 38.26 2.85
7 8 8.267183 TCCTAATGAAGTGAAATATGAGCTTCA 58.733 33.333 7.58 7.58 46.03 3.02
8 9 8.668510 TCCTAATGAAGTGAAATATGAGCTTC 57.331 34.615 0.00 0.00 36.89 3.86
9 10 9.118300 CTTCCTAATGAAGTGAAATATGAGCTT 57.882 33.333 0.00 0.00 44.59 3.74
10 11 8.674263 CTTCCTAATGAAGTGAAATATGAGCT 57.326 34.615 0.00 0.00 44.59 4.09
24 25 2.041620 ACTTGGCCTGCTTCCTAATGAA 59.958 45.455 3.32 0.00 0.00 2.57
25 26 1.635487 ACTTGGCCTGCTTCCTAATGA 59.365 47.619 3.32 0.00 0.00 2.57
26 27 2.134789 ACTTGGCCTGCTTCCTAATG 57.865 50.000 3.32 0.00 0.00 1.90
27 28 2.041620 TCAACTTGGCCTGCTTCCTAAT 59.958 45.455 3.32 0.00 0.00 1.73
28 29 1.423541 TCAACTTGGCCTGCTTCCTAA 59.576 47.619 3.32 0.00 0.00 2.69
29 30 1.064003 TCAACTTGGCCTGCTTCCTA 58.936 50.000 3.32 0.00 0.00 2.94
30 31 0.407139 ATCAACTTGGCCTGCTTCCT 59.593 50.000 3.32 0.00 0.00 3.36
31 32 1.067354 CAATCAACTTGGCCTGCTTCC 60.067 52.381 3.32 0.00 0.00 3.46
32 33 1.670967 GCAATCAACTTGGCCTGCTTC 60.671 52.381 3.32 0.00 35.25 3.86
33 34 0.319405 GCAATCAACTTGGCCTGCTT 59.681 50.000 3.32 0.00 35.25 3.91
34 35 0.828762 TGCAATCAACTTGGCCTGCT 60.829 50.000 3.32 0.00 35.25 4.24
35 36 0.668401 GTGCAATCAACTTGGCCTGC 60.668 55.000 3.32 2.86 35.25 4.85
36 37 0.037975 GGTGCAATCAACTTGGCCTG 60.038 55.000 3.32 0.00 35.25 4.85
37 38 0.469705 TGGTGCAATCAACTTGGCCT 60.470 50.000 3.32 0.00 35.25 5.19
38 39 0.319813 GTGGTGCAATCAACTTGGCC 60.320 55.000 0.00 0.00 35.25 5.36
39 40 0.319813 GGTGGTGCAATCAACTTGGC 60.320 55.000 0.00 0.00 35.25 4.52
40 41 1.000060 CAGGTGGTGCAATCAACTTGG 60.000 52.381 6.17 0.00 35.25 3.61
41 42 2.427232 CAGGTGGTGCAATCAACTTG 57.573 50.000 6.17 0.00 37.94 3.16
52 53 0.742505 CATGGCATTAGCAGGTGGTG 59.257 55.000 0.00 0.00 44.61 4.17
53 54 0.396139 CCATGGCATTAGCAGGTGGT 60.396 55.000 0.00 0.00 44.61 4.16
54 55 1.111116 CCCATGGCATTAGCAGGTGG 61.111 60.000 6.09 0.00 44.61 4.61
55 56 2.422303 CCCATGGCATTAGCAGGTG 58.578 57.895 6.09 0.00 44.61 4.00
67 68 5.356291 TTGAGGAAAATTATTGCCCATGG 57.644 39.130 4.14 4.14 34.29 3.66
68 69 6.584488 TGATTGAGGAAAATTATTGCCCATG 58.416 36.000 0.00 0.00 34.29 3.66
69 70 6.811634 TGATTGAGGAAAATTATTGCCCAT 57.188 33.333 0.00 0.00 34.29 4.00
70 71 6.461370 CGATGATTGAGGAAAATTATTGCCCA 60.461 38.462 0.00 0.00 34.29 5.36
71 72 5.922544 CGATGATTGAGGAAAATTATTGCCC 59.077 40.000 0.00 0.00 34.29 5.36
72 73 6.507023 ACGATGATTGAGGAAAATTATTGCC 58.493 36.000 0.00 0.00 33.91 4.52
73 74 7.992180 AACGATGATTGAGGAAAATTATTGC 57.008 32.000 0.00 0.00 0.00 3.56
74 75 9.793252 AGAAACGATGATTGAGGAAAATTATTG 57.207 29.630 0.00 0.00 0.00 1.90
77 78 9.443323 TGTAGAAACGATGATTGAGGAAAATTA 57.557 29.630 0.00 0.00 0.00 1.40
78 79 8.335532 TGTAGAAACGATGATTGAGGAAAATT 57.664 30.769 0.00 0.00 0.00 1.82
79 80 7.607991 ACTGTAGAAACGATGATTGAGGAAAAT 59.392 33.333 0.00 0.00 0.00 1.82
80 81 6.934645 ACTGTAGAAACGATGATTGAGGAAAA 59.065 34.615 0.00 0.00 0.00 2.29
81 82 6.368791 CACTGTAGAAACGATGATTGAGGAAA 59.631 38.462 0.00 0.00 0.00 3.13
82 83 5.869344 CACTGTAGAAACGATGATTGAGGAA 59.131 40.000 0.00 0.00 0.00 3.36
83 84 5.185056 TCACTGTAGAAACGATGATTGAGGA 59.815 40.000 0.00 0.00 0.00 3.71
84 85 5.410924 TCACTGTAGAAACGATGATTGAGG 58.589 41.667 0.00 0.00 0.00 3.86
85 86 5.005203 GCTCACTGTAGAAACGATGATTGAG 59.995 44.000 0.00 0.00 0.00 3.02
86 87 4.864806 GCTCACTGTAGAAACGATGATTGA 59.135 41.667 0.00 0.00 0.00 2.57
87 88 4.033358 GGCTCACTGTAGAAACGATGATTG 59.967 45.833 0.00 0.00 0.00 2.67
88 89 4.184629 GGCTCACTGTAGAAACGATGATT 58.815 43.478 0.00 0.00 0.00 2.57
89 90 3.195610 TGGCTCACTGTAGAAACGATGAT 59.804 43.478 0.00 0.00 0.00 2.45
90 91 2.560981 TGGCTCACTGTAGAAACGATGA 59.439 45.455 0.00 0.00 0.00 2.92
91 92 2.668457 GTGGCTCACTGTAGAAACGATG 59.332 50.000 0.00 0.00 0.00 3.84
92 93 2.299013 TGTGGCTCACTGTAGAAACGAT 59.701 45.455 6.83 0.00 35.11 3.73
93 94 1.684450 TGTGGCTCACTGTAGAAACGA 59.316 47.619 6.83 0.00 35.11 3.85
94 95 2.148916 TGTGGCTCACTGTAGAAACG 57.851 50.000 6.83 0.00 35.11 3.60
95 96 5.238583 ACTATTGTGGCTCACTGTAGAAAC 58.761 41.667 16.39 0.00 35.11 2.78
96 97 5.483685 ACTATTGTGGCTCACTGTAGAAA 57.516 39.130 16.39 2.44 35.11 2.52
97 98 5.483685 AACTATTGTGGCTCACTGTAGAA 57.516 39.130 16.39 2.93 35.11 2.10
98 99 6.791867 ATAACTATTGTGGCTCACTGTAGA 57.208 37.500 16.39 0.00 35.11 2.59
101 102 7.604164 GCATATATAACTATTGTGGCTCACTGT 59.396 37.037 6.83 0.00 35.11 3.55
102 103 7.603784 TGCATATATAACTATTGTGGCTCACTG 59.396 37.037 6.83 0.00 35.11 3.66
103 104 7.679783 TGCATATATAACTATTGTGGCTCACT 58.320 34.615 6.83 0.00 35.11 3.41
104 105 7.905604 TGCATATATAACTATTGTGGCTCAC 57.094 36.000 0.00 0.00 34.56 3.51
105 106 8.156820 ACTTGCATATATAACTATTGTGGCTCA 58.843 33.333 0.00 0.00 0.00 4.26
106 107 8.446273 CACTTGCATATATAACTATTGTGGCTC 58.554 37.037 0.00 0.00 0.00 4.70
107 108 7.939039 ACACTTGCATATATAACTATTGTGGCT 59.061 33.333 0.00 0.00 0.00 4.75
108 109 8.099364 ACACTTGCATATATAACTATTGTGGC 57.901 34.615 0.00 0.00 0.00 5.01
120 121 9.578576 AGTTGATCCAAATACACTTGCATATAT 57.421 29.630 0.00 0.00 0.00 0.86
121 122 8.978874 AGTTGATCCAAATACACTTGCATATA 57.021 30.769 0.00 0.00 0.00 0.86
122 123 7.886629 AGTTGATCCAAATACACTTGCATAT 57.113 32.000 0.00 0.00 0.00 1.78
123 124 7.701539 AAGTTGATCCAAATACACTTGCATA 57.298 32.000 0.00 0.00 0.00 3.14
124 125 6.594788 AAGTTGATCCAAATACACTTGCAT 57.405 33.333 0.00 0.00 0.00 3.96
125 126 7.701539 ATAAGTTGATCCAAATACACTTGCA 57.298 32.000 0.00 0.00 0.00 4.08
126 127 9.669353 CATATAAGTTGATCCAAATACACTTGC 57.331 33.333 0.00 0.00 0.00 4.01
130 131 9.831737 GCATCATATAAGTTGATCCAAATACAC 57.168 33.333 0.00 0.00 31.50 2.90
131 132 9.571816 TGCATCATATAAGTTGATCCAAATACA 57.428 29.630 0.00 0.00 31.50 2.29
134 135 8.746530 GGATGCATCATATAAGTTGATCCAAAT 58.253 33.333 27.25 0.00 31.50 2.32
135 136 7.946219 AGGATGCATCATATAAGTTGATCCAAA 59.054 33.333 27.25 0.00 31.50 3.28
136 137 7.464273 AGGATGCATCATATAAGTTGATCCAA 58.536 34.615 27.25 0.00 31.50 3.53
137 138 7.024345 AGGATGCATCATATAAGTTGATCCA 57.976 36.000 27.25 2.47 31.50 3.41
138 139 7.065563 GTGAGGATGCATCATATAAGTTGATCC 59.934 40.741 27.25 7.06 31.50 3.36
139 140 7.823310 AGTGAGGATGCATCATATAAGTTGATC 59.177 37.037 27.25 5.79 31.50 2.92
140 141 7.687388 AGTGAGGATGCATCATATAAGTTGAT 58.313 34.615 27.25 0.00 34.15 2.57
141 142 7.071069 AGTGAGGATGCATCATATAAGTTGA 57.929 36.000 27.25 0.00 0.00 3.18
142 143 7.660617 AGAAGTGAGGATGCATCATATAAGTTG 59.339 37.037 27.25 0.00 0.00 3.16
143 144 7.743749 AGAAGTGAGGATGCATCATATAAGTT 58.256 34.615 27.25 17.27 0.00 2.66
144 145 7.313740 AGAAGTGAGGATGCATCATATAAGT 57.686 36.000 27.25 10.30 0.00 2.24
145 146 8.618702 AAAGAAGTGAGGATGCATCATATAAG 57.381 34.615 27.25 0.00 0.00 1.73
146 147 8.985315 AAAAGAAGTGAGGATGCATCATATAA 57.015 30.769 27.25 7.82 0.00 0.98
147 148 8.985315 AAAAAGAAGTGAGGATGCATCATATA 57.015 30.769 27.25 11.01 0.00 0.86
148 149 7.893124 AAAAAGAAGTGAGGATGCATCATAT 57.107 32.000 27.25 13.05 0.00 1.78
169 170 6.495181 TGTGGCCATTACCTTGAAGATAAAAA 59.505 34.615 9.72 0.00 0.00 1.94
170 171 6.013379 TGTGGCCATTACCTTGAAGATAAAA 58.987 36.000 9.72 0.00 0.00 1.52
171 172 5.575157 TGTGGCCATTACCTTGAAGATAAA 58.425 37.500 9.72 0.00 0.00 1.40
172 173 5.186256 TGTGGCCATTACCTTGAAGATAA 57.814 39.130 9.72 0.00 0.00 1.75
173 174 4.853468 TGTGGCCATTACCTTGAAGATA 57.147 40.909 9.72 0.00 0.00 1.98
174 175 3.737559 TGTGGCCATTACCTTGAAGAT 57.262 42.857 9.72 0.00 0.00 2.40
175 176 3.737559 ATGTGGCCATTACCTTGAAGA 57.262 42.857 9.72 0.00 0.00 2.87
176 177 4.806640 AAATGTGGCCATTACCTTGAAG 57.193 40.909 9.72 0.00 40.42 3.02
177 178 6.351711 CCATAAAATGTGGCCATTACCTTGAA 60.352 38.462 9.72 0.00 40.42 2.69
178 179 5.128499 CCATAAAATGTGGCCATTACCTTGA 59.872 40.000 9.72 0.00 40.42 3.02
179 180 5.128499 TCCATAAAATGTGGCCATTACCTTG 59.872 40.000 9.72 1.92 40.42 3.61
180 181 5.128663 GTCCATAAAATGTGGCCATTACCTT 59.871 40.000 9.72 1.75 40.42 3.50
181 182 4.649218 GTCCATAAAATGTGGCCATTACCT 59.351 41.667 9.72 0.00 40.42 3.08
182 183 4.404073 TGTCCATAAAATGTGGCCATTACC 59.596 41.667 9.72 0.00 40.42 2.85
183 184 5.359576 TCTGTCCATAAAATGTGGCCATTAC 59.640 40.000 9.72 0.00 40.42 1.89
184 185 5.359576 GTCTGTCCATAAAATGTGGCCATTA 59.640 40.000 9.72 3.35 40.42 1.90
185 186 4.160252 GTCTGTCCATAAAATGTGGCCATT 59.840 41.667 9.72 0.44 43.14 3.16
186 187 3.701040 GTCTGTCCATAAAATGTGGCCAT 59.299 43.478 9.72 0.00 36.66 4.40
187 188 3.088532 GTCTGTCCATAAAATGTGGCCA 58.911 45.455 0.00 0.00 36.66 5.36
188 189 3.356290 AGTCTGTCCATAAAATGTGGCC 58.644 45.455 0.00 0.00 36.66 5.36
189 190 6.318648 TGATTAGTCTGTCCATAAAATGTGGC 59.681 38.462 0.00 0.00 36.66 5.01
190 191 7.336679 TGTGATTAGTCTGTCCATAAAATGTGG 59.663 37.037 0.00 0.00 38.11 4.17
191 192 8.267620 TGTGATTAGTCTGTCCATAAAATGTG 57.732 34.615 0.00 0.00 0.00 3.21
196 197 9.764363 GATGTATGTGATTAGTCTGTCCATAAA 57.236 33.333 0.00 0.00 0.00 1.40
197 198 8.923270 TGATGTATGTGATTAGTCTGTCCATAA 58.077 33.333 0.00 0.00 0.00 1.90
198 199 8.477419 TGATGTATGTGATTAGTCTGTCCATA 57.523 34.615 0.00 0.00 0.00 2.74
199 200 7.365497 TGATGTATGTGATTAGTCTGTCCAT 57.635 36.000 0.00 0.00 0.00 3.41
200 201 6.790232 TGATGTATGTGATTAGTCTGTCCA 57.210 37.500 0.00 0.00 0.00 4.02
201 202 7.928167 TGAATGATGTATGTGATTAGTCTGTCC 59.072 37.037 0.00 0.00 0.00 4.02
202 203 8.759641 GTGAATGATGTATGTGATTAGTCTGTC 58.240 37.037 0.00 0.00 0.00 3.51
203 204 7.436376 CGTGAATGATGTATGTGATTAGTCTGT 59.564 37.037 0.00 0.00 0.00 3.41
204 205 7.568315 GCGTGAATGATGTATGTGATTAGTCTG 60.568 40.741 0.00 0.00 0.00 3.51
205 206 6.422100 GCGTGAATGATGTATGTGATTAGTCT 59.578 38.462 0.00 0.00 0.00 3.24
206 207 6.422100 AGCGTGAATGATGTATGTGATTAGTC 59.578 38.462 0.00 0.00 0.00 2.59
207 208 6.201615 CAGCGTGAATGATGTATGTGATTAGT 59.798 38.462 0.00 0.00 0.00 2.24
208 209 6.421801 TCAGCGTGAATGATGTATGTGATTAG 59.578 38.462 0.00 0.00 0.00 1.73
209 210 6.200854 GTCAGCGTGAATGATGTATGTGATTA 59.799 38.462 0.00 0.00 0.00 1.75
210 211 5.007039 GTCAGCGTGAATGATGTATGTGATT 59.993 40.000 0.00 0.00 0.00 2.57
211 212 4.509230 GTCAGCGTGAATGATGTATGTGAT 59.491 41.667 0.00 0.00 0.00 3.06
212 213 3.865164 GTCAGCGTGAATGATGTATGTGA 59.135 43.478 0.00 0.00 0.00 3.58
213 214 3.867493 AGTCAGCGTGAATGATGTATGTG 59.133 43.478 0.00 0.00 0.00 3.21
214 215 4.128925 AGTCAGCGTGAATGATGTATGT 57.871 40.909 0.00 0.00 0.00 2.29
215 216 5.475273 AAAGTCAGCGTGAATGATGTATG 57.525 39.130 0.00 0.00 0.00 2.39
216 217 8.144478 AGTATAAAGTCAGCGTGAATGATGTAT 58.856 33.333 0.00 0.00 0.00 2.29
217 218 7.489160 AGTATAAAGTCAGCGTGAATGATGTA 58.511 34.615 0.00 0.00 0.00 2.29
218 219 6.341316 AGTATAAAGTCAGCGTGAATGATGT 58.659 36.000 0.00 0.00 0.00 3.06
219 220 6.834959 AGTATAAAGTCAGCGTGAATGATG 57.165 37.500 0.00 0.00 0.00 3.07
220 221 8.942338 TTAAGTATAAAGTCAGCGTGAATGAT 57.058 30.769 0.00 0.00 0.00 2.45
221 222 8.942338 ATTAAGTATAAAGTCAGCGTGAATGA 57.058 30.769 0.00 0.00 0.00 2.57
251 252 9.554724 CGTATGAGTTTAACAAAACATAGCATT 57.445 29.630 0.00 0.00 35.20 3.56
252 253 8.941977 TCGTATGAGTTTAACAAAACATAGCAT 58.058 29.630 0.00 0.00 35.20 3.79
253 254 8.225107 GTCGTATGAGTTTAACAAAACATAGCA 58.775 33.333 0.00 0.00 35.20 3.49
254 255 8.440833 AGTCGTATGAGTTTAACAAAACATAGC 58.559 33.333 0.00 0.00 35.20 2.97
257 258 8.932791 CCTAGTCGTATGAGTTTAACAAAACAT 58.067 33.333 0.00 0.94 35.20 2.71
258 259 7.927629 ACCTAGTCGTATGAGTTTAACAAAACA 59.072 33.333 0.00 0.00 35.20 2.83
259 260 8.302965 ACCTAGTCGTATGAGTTTAACAAAAC 57.697 34.615 0.00 0.00 0.00 2.43
260 261 8.767085 CAACCTAGTCGTATGAGTTTAACAAAA 58.233 33.333 0.00 0.00 0.00 2.44
261 262 7.927629 ACAACCTAGTCGTATGAGTTTAACAAA 59.072 33.333 0.00 0.00 0.00 2.83
262 263 7.436118 ACAACCTAGTCGTATGAGTTTAACAA 58.564 34.615 0.00 0.00 0.00 2.83
263 264 6.985117 ACAACCTAGTCGTATGAGTTTAACA 58.015 36.000 0.00 0.00 0.00 2.41
264 265 7.880059 AACAACCTAGTCGTATGAGTTTAAC 57.120 36.000 0.00 0.00 0.00 2.01
265 266 9.979578 TTTAACAACCTAGTCGTATGAGTTTAA 57.020 29.630 0.00 0.00 0.00 1.52
266 267 9.410556 GTTTAACAACCTAGTCGTATGAGTTTA 57.589 33.333 0.00 0.00 0.00 2.01
267 268 7.115378 CGTTTAACAACCTAGTCGTATGAGTTT 59.885 37.037 0.00 0.00 0.00 2.66
268 269 6.583806 CGTTTAACAACCTAGTCGTATGAGTT 59.416 38.462 0.00 0.00 0.00 3.01
269 270 6.088824 CGTTTAACAACCTAGTCGTATGAGT 58.911 40.000 0.00 0.00 0.00 3.41
270 271 5.004156 GCGTTTAACAACCTAGTCGTATGAG 59.996 44.000 0.00 0.00 0.00 2.90
271 272 4.858692 GCGTTTAACAACCTAGTCGTATGA 59.141 41.667 0.00 0.00 0.00 2.15
272 273 4.032104 GGCGTTTAACAACCTAGTCGTATG 59.968 45.833 0.00 0.00 0.00 2.39
273 274 4.082026 AGGCGTTTAACAACCTAGTCGTAT 60.082 41.667 5.04 0.00 0.00 3.06
274 275 3.255642 AGGCGTTTAACAACCTAGTCGTA 59.744 43.478 5.04 0.00 0.00 3.43
275 276 2.036346 AGGCGTTTAACAACCTAGTCGT 59.964 45.455 5.04 0.00 0.00 4.34
276 277 2.680577 AGGCGTTTAACAACCTAGTCG 58.319 47.619 5.04 0.00 0.00 4.18
277 278 4.151867 CAGAAGGCGTTTAACAACCTAGTC 59.848 45.833 7.03 3.31 0.00 2.59
278 279 4.062991 CAGAAGGCGTTTAACAACCTAGT 58.937 43.478 7.03 0.00 0.00 2.57
279 280 3.435671 CCAGAAGGCGTTTAACAACCTAG 59.564 47.826 7.03 2.14 0.00 3.02
280 281 3.071312 TCCAGAAGGCGTTTAACAACCTA 59.929 43.478 7.03 0.00 33.74 3.08
281 282 2.158726 TCCAGAAGGCGTTTAACAACCT 60.159 45.455 1.33 1.33 33.74 3.50
282 283 2.223745 TCCAGAAGGCGTTTAACAACC 58.776 47.619 0.00 0.00 33.74 3.77
283 284 3.821841 CATCCAGAAGGCGTTTAACAAC 58.178 45.455 0.00 0.00 33.74 3.32
284 285 2.227865 GCATCCAGAAGGCGTTTAACAA 59.772 45.455 0.00 0.00 33.74 2.83
285 286 1.810151 GCATCCAGAAGGCGTTTAACA 59.190 47.619 0.00 0.00 33.74 2.41
286 287 1.810151 TGCATCCAGAAGGCGTTTAAC 59.190 47.619 0.00 0.00 33.74 2.01
287 288 2.083774 CTGCATCCAGAAGGCGTTTAA 58.916 47.619 0.00 0.00 41.77 1.52
288 289 1.277842 TCTGCATCCAGAAGGCGTTTA 59.722 47.619 0.00 0.00 44.79 2.01
289 290 0.036732 TCTGCATCCAGAAGGCGTTT 59.963 50.000 0.00 0.00 44.79 3.60
290 291 1.679311 TCTGCATCCAGAAGGCGTT 59.321 52.632 0.00 0.00 44.79 4.84
291 292 3.392228 TCTGCATCCAGAAGGCGT 58.608 55.556 0.00 0.00 44.79 5.68
297 298 9.770097 CTAGAATTTAAATAGTCTGCATCCAGA 57.230 33.333 11.18 0.00 45.54 3.86
298 299 9.770097 TCTAGAATTTAAATAGTCTGCATCCAG 57.230 33.333 11.18 2.34 40.54 3.86
322 323 9.764363 ACATACATACGAATATTCACACATTCT 57.236 29.630 15.57 0.00 0.00 2.40
323 324 9.797473 CACATACATACGAATATTCACACATTC 57.203 33.333 15.57 0.00 0.00 2.67
324 325 8.773645 CCACATACATACGAATATTCACACATT 58.226 33.333 15.57 0.00 0.00 2.71
325 326 8.147704 TCCACATACATACGAATATTCACACAT 58.852 33.333 15.57 0.73 0.00 3.21
326 327 7.493367 TCCACATACATACGAATATTCACACA 58.507 34.615 15.57 0.00 0.00 3.72
327 328 7.940178 TCCACATACATACGAATATTCACAC 57.060 36.000 15.57 0.00 0.00 3.82
328 329 9.855021 CTATCCACATACATACGAATATTCACA 57.145 33.333 15.57 2.60 0.00 3.58
329 330 9.856488 ACTATCCACATACATACGAATATTCAC 57.144 33.333 15.57 0.00 0.00 3.18
330 331 9.855021 CACTATCCACATACATACGAATATTCA 57.145 33.333 15.57 0.00 0.00 2.57
331 332 9.856488 ACACTATCCACATACATACGAATATTC 57.144 33.333 5.30 5.30 0.00 1.75
333 334 9.639601 CAACACTATCCACATACATACGAATAT 57.360 33.333 0.00 0.00 0.00 1.28
334 335 8.635328 ACAACACTATCCACATACATACGAATA 58.365 33.333 0.00 0.00 0.00 1.75
335 336 7.497595 ACAACACTATCCACATACATACGAAT 58.502 34.615 0.00 0.00 0.00 3.34
336 337 6.869695 ACAACACTATCCACATACATACGAA 58.130 36.000 0.00 0.00 0.00 3.85
337 338 6.459670 ACAACACTATCCACATACATACGA 57.540 37.500 0.00 0.00 0.00 3.43
338 339 8.132995 TCTAACAACACTATCCACATACATACG 58.867 37.037 0.00 0.00 0.00 3.06
339 340 9.982651 ATCTAACAACACTATCCACATACATAC 57.017 33.333 0.00 0.00 0.00 2.39
340 341 9.981114 CATCTAACAACACTATCCACATACATA 57.019 33.333 0.00 0.00 0.00 2.29
341 342 8.486210 ACATCTAACAACACTATCCACATACAT 58.514 33.333 0.00 0.00 0.00 2.29
342 343 7.763985 CACATCTAACAACACTATCCACATACA 59.236 37.037 0.00 0.00 0.00 2.29
343 344 7.764443 ACACATCTAACAACACTATCCACATAC 59.236 37.037 0.00 0.00 0.00 2.39
344 345 7.847096 ACACATCTAACAACACTATCCACATA 58.153 34.615 0.00 0.00 0.00 2.29
345 346 6.711277 ACACATCTAACAACACTATCCACAT 58.289 36.000 0.00 0.00 0.00 3.21
346 347 6.109156 ACACATCTAACAACACTATCCACA 57.891 37.500 0.00 0.00 0.00 4.17
347 348 9.464714 CTATACACATCTAACAACACTATCCAC 57.535 37.037 0.00 0.00 0.00 4.02
348 349 9.197306 ACTATACACATCTAACAACACTATCCA 57.803 33.333 0.00 0.00 0.00 3.41
349 350 9.680315 GACTATACACATCTAACAACACTATCC 57.320 37.037 0.00 0.00 0.00 2.59
350 351 9.680315 GGACTATACACATCTAACAACACTATC 57.320 37.037 0.00 0.00 0.00 2.08
351 352 8.639761 GGGACTATACACATCTAACAACACTAT 58.360 37.037 0.00 0.00 0.00 2.12
352 353 7.837689 AGGGACTATACACATCTAACAACACTA 59.162 37.037 0.00 0.00 36.02 2.74
353 354 6.668283 AGGGACTATACACATCTAACAACACT 59.332 38.462 0.00 0.00 36.02 3.55
354 355 6.875076 AGGGACTATACACATCTAACAACAC 58.125 40.000 0.00 0.00 36.02 3.32
355 356 7.490657 AAGGGACTATACACATCTAACAACA 57.509 36.000 0.00 0.00 38.49 3.33
356 357 8.788325 AAAAGGGACTATACACATCTAACAAC 57.212 34.615 0.00 0.00 38.49 3.32
807 896 4.431131 ATTGACCTGGGCGGCTGG 62.431 66.667 9.56 14.17 35.61 4.85
808 897 2.825836 GATTGACCTGGGCGGCTG 60.826 66.667 9.56 1.93 35.61 4.85
809 898 4.115199 GGATTGACCTGGGCGGCT 62.115 66.667 9.56 0.00 35.61 5.52
1030 1178 0.684535 TCAAAGATCACCGAGCACCA 59.315 50.000 0.00 0.00 0.00 4.17
1055 1203 4.072131 GCCCACAAACTCAGAATAGTTGA 58.928 43.478 0.00 0.00 39.62 3.18
1279 1427 3.957497 ACAGAGAGAGCATCGGAATAAGT 59.043 43.478 0.00 0.00 42.67 2.24
1393 1541 2.304180 CAAGTCCCATGAACTCTGAGGT 59.696 50.000 9.85 1.11 0.00 3.85
1467 1615 3.190327 CCACAGATAGGTAGAGAGCATCG 59.810 52.174 0.00 0.00 42.67 3.84
1750 1898 3.695606 GCGGGTCTCCTCAGCACA 61.696 66.667 0.00 0.00 0.00 4.57
1820 1968 3.106407 GGCGAGCAGACGACACAC 61.106 66.667 0.00 0.00 41.34 3.82
1879 2030 1.115467 CTCAGCATAAGGAGGACGGT 58.885 55.000 0.00 0.00 0.00 4.83
2006 2160 2.040412 GGAAGACACAGGAATCCCACTT 59.960 50.000 0.00 0.00 33.88 3.16
2014 2168 2.368875 GAGGTTGAGGAAGACACAGGAA 59.631 50.000 0.00 0.00 0.00 3.36
2062 2216 1.188219 AGCAAGGAGACGCTTGAGGA 61.188 55.000 0.00 0.00 33.81 3.71
2085 2239 2.034376 AGTCGACGAGGAGCCTGT 59.966 61.111 10.46 0.00 0.00 4.00
2120 2274 0.329596 GTGAGGAAGGGGATGCAGTT 59.670 55.000 0.00 0.00 0.00 3.16
2145 2299 0.817654 CCTGACTGTGTAGATGCCGA 59.182 55.000 0.00 0.00 0.00 5.54
2188 2342 5.441718 AGACATATGAAAGGAAGCTCCAA 57.558 39.130 10.38 0.00 39.61 3.53
2388 2543 3.130633 CACGACAACCAGAATCAGTGAA 58.869 45.455 0.00 0.00 0.00 3.18
2415 2570 4.819105 TGGAACAAGAGTCGGTATCAAT 57.181 40.909 0.00 0.00 31.92 2.57
2515 2670 2.301346 CAGTGGAAGGAACACAAAGCT 58.699 47.619 0.00 0.00 41.21 3.74
2532 2687 2.113986 GGCAGAAGTGGTGGCAGT 59.886 61.111 0.00 0.00 40.16 4.40
2722 2879 7.229106 CAGACTCACTAGTAGGATAAGGTAACC 59.771 44.444 1.45 0.00 35.56 2.85
2815 2972 5.428253 ACAAAACATAGTAGCGATGACCAT 58.572 37.500 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.