Multiple sequence alignment - TraesCS3D01G539700

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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 TraesCS3D01G539700 chr3D 100.000 2461 0 0 1 2461 611505316 611502856 0.000000e+00 4545.0
1 TraesCS3D01G539700 chr3D 86.584 1379 162 18 393 1753 611369234 611367861 0.000000e+00 1500.0
2 TraesCS3D01G539700 chr3D 84.701 1255 145 25 393 1639 611364614 611363399 0.000000e+00 1210.0
3 TraesCS3D01G539700 chr3D 88.197 771 83 6 797 1565 611362213 611361449 0.000000e+00 913.0
4 TraesCS3D01G539700 chr3D 83.497 915 133 14 393 1297 611372459 611371553 0.000000e+00 837.0
5 TraesCS3D01G539700 chr3D 94.064 219 11 2 1 217 106744573 106744355 5.070000e-87 331.0
6 TraesCS3D01G539700 chr3D 87.701 187 18 5 232 413 611433069 611432883 1.920000e-51 213.0
7 TraesCS3D01G539700 chr3D 85.279 197 26 1 596 789 611422050 611421854 1.490000e-47 200.0
8 TraesCS3D01G539700 chr3D 93.966 116 6 1 1639 1753 611415840 611415725 9.050000e-40 174.0
9 TraesCS3D01G539700 chr3D 93.043 115 7 1 1640 1753 611363370 611363256 1.510000e-37 167.0
10 TraesCS3D01G539700 chr3D 94.792 96 5 0 1833 1928 611415346 611415251 1.520000e-32 150.0
11 TraesCS3D01G539700 chr3D 89.552 67 6 1 1688 1753 611419306 611419240 1.570000e-12 84.2
12 TraesCS3D01G539700 chr3D 96.774 31 1 0 1833 1863 611370686 611370656 4.000000e-03 52.8
13 TraesCS3D01G539700 chr3A 92.920 2274 112 23 211 2461 746294476 746292229 0.000000e+00 3262.0
14 TraesCS3D01G539700 chr3A 84.708 1334 151 24 450 1749 746213013 746211699 0.000000e+00 1284.0
15 TraesCS3D01G539700 chr3A 83.904 963 144 8 587 1544 746215885 746214929 0.000000e+00 909.0
16 TraesCS3D01G539700 chr3A 87.054 224 27 2 2236 2459 729230510 729230731 4.060000e-63 252.0
17 TraesCS3D01G539700 chr3A 90.957 188 11 6 231 413 746208818 746208632 5.260000e-62 248.0
18 TraesCS3D01G539700 chr3A 89.305 187 15 5 232 413 746278973 746278787 1.900000e-56 230.0
19 TraesCS3D01G539700 chr3B 94.433 1868 94 9 211 2071 829245337 829243473 0.000000e+00 2865.0
20 TraesCS3D01G539700 chr3B 85.633 884 119 4 684 1565 829062948 829062071 0.000000e+00 922.0
21 TraesCS3D01G539700 chr3B 81.885 955 122 33 236 1149 829069496 829068552 0.000000e+00 758.0
22 TraesCS3D01G539700 chr3B 82.629 875 103 21 916 1753 829142966 829142104 0.000000e+00 728.0
23 TraesCS3D01G539700 chr3B 79.787 940 136 32 231 1134 829067634 829066713 3.450000e-178 634.0
24 TraesCS3D01G539700 chr3B 81.305 567 58 29 232 753 829143952 829143389 1.360000e-112 416.0
25 TraesCS3D01G539700 chr3B 80.696 575 60 30 232 760 829150632 829150063 1.370000e-107 399.0
26 TraesCS3D01G539700 chr3B 93.413 167 5 2 2069 2230 829235448 829235283 2.450000e-60 243.0
27 TraesCS3D01G539700 chr3B 93.043 115 7 1 1640 1753 829064115 829064001 1.510000e-37 167.0
28 TraesCS3D01G539700 chr3B 88.793 116 11 2 1639 1753 829071309 829071195 9.180000e-30 141.0
29 TraesCS3D01G539700 chr3B 90.625 96 9 0 1833 1928 829133732 829133637 7.140000e-26 128.0
30 TraesCS3D01G539700 chr3B 92.308 91 5 2 1641 1730 829135648 829135559 7.140000e-26 128.0
31 TraesCS3D01G539700 chr3B 94.444 36 2 0 1833 1868 829063621 829063586 3.420000e-04 56.5
32 TraesCS3D01G539700 chr7D 94.907 216 8 3 1 214 548943752 548943966 3.920000e-88 335.0
33 TraesCS3D01G539700 chr7D 93.607 219 12 2 1 217 36913357 36913139 2.360000e-85 326.0
34 TraesCS3D01G539700 chr7D 88.679 212 23 1 2248 2459 503687578 503687788 8.730000e-65 257.0
35 TraesCS3D01G539700 chr7D 86.147 231 29 3 2231 2460 117531437 117531209 1.890000e-61 246.0
36 TraesCS3D01G539700 chr1D 94.118 221 11 2 1 220 90396656 90396437 3.920000e-88 335.0
37 TraesCS3D01G539700 chr1D 93.665 221 12 2 1 219 45651691 45651911 1.820000e-86 329.0
38 TraesCS3D01G539700 chr1D 93.665 221 12 2 1 219 346621959 346621739 1.820000e-86 329.0
39 TraesCS3D01G539700 chr1D 92.070 227 16 2 1 225 81425850 81426076 3.950000e-83 318.0
40 TraesCS3D01G539700 chr1D 88.034 234 21 4 2232 2459 104565983 104565751 1.120000e-68 270.0
41 TraesCS3D01G539700 chr2B 94.037 218 12 1 1 217 724428709 724428492 1.820000e-86 329.0
42 TraesCS3D01G539700 chr2B 91.163 215 18 1 2248 2461 728164542 728164328 8.610000e-75 291.0
43 TraesCS3D01G539700 chr4D 93.636 220 12 2 1 218 505228075 505228294 6.560000e-86 327.0
44 TraesCS3D01G539700 chr2D 90.094 212 20 1 2248 2459 405072574 405072364 8.670000e-70 274.0
45 TraesCS3D01G539700 chr7A 88.444 225 25 1 2236 2459 194790034 194789810 1.120000e-68 270.0
46 TraesCS3D01G539700 chr6D 87.013 231 28 2 2230 2459 45814188 45814417 2.430000e-65 259.0


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 TraesCS3D01G539700 chr3D 611502856 611505316 2460 True 4545.000000 4545 100.000000 1 2461 1 chr3D.!!$R3 2460
1 TraesCS3D01G539700 chr3D 611361449 611372459 11010 True 779.966667 1500 88.799333 393 1863 6 chr3D.!!$R4 1470
2 TraesCS3D01G539700 chr3A 746292229 746294476 2247 True 3262.000000 3262 92.920000 211 2461 1 chr3A.!!$R2 2250
3 TraesCS3D01G539700 chr3A 746208632 746215885 7253 True 813.666667 1284 86.523000 231 1749 3 chr3A.!!$R3 1518
4 TraesCS3D01G539700 chr3B 829243473 829245337 1864 True 2865.000000 2865 94.433000 211 2071 1 chr3B.!!$R3 1860
5 TraesCS3D01G539700 chr3B 829142104 829143952 1848 True 572.000000 728 81.967000 232 1753 2 chr3B.!!$R6 1521
6 TraesCS3D01G539700 chr3B 829062071 829071309 9238 True 446.416667 922 87.264167 231 1868 6 chr3B.!!$R4 1637
7 TraesCS3D01G539700 chr3B 829150063 829150632 569 True 399.000000 399 80.696000 232 760 1 chr3B.!!$R1 528

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
50 51 0.036164 TTGGTCCCGGTTCATGTCTG 59.964 55.0 0.00 0.0 0.0 3.51 F
66 67 0.109723 TCTGAAACCGGGACCAAAGG 59.890 55.0 6.32 0.0 0.0 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1209 9589 0.179153 TGTCGAGCATGAGAAGAGCG 60.179 55.000 0.00 0.00 0.0 5.03 R
1605 14574 1.267806 CAGATGCGCATTATGGGGAAC 59.732 52.381 26.12 8.13 33.9 3.62 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.611667 ACCAATGGTTGTGGGCCA 59.388 55.556 0.00 0.00 40.75 5.36
18 19 1.533753 ACCAATGGTTGTGGGCCAG 60.534 57.895 6.40 0.00 40.75 4.85
19 20 2.285024 CCAATGGTTGTGGGCCAGG 61.285 63.158 6.40 0.00 39.65 4.45
21 22 1.077265 AATGGTTGTGGGCCAGGAG 59.923 57.895 6.40 0.00 39.65 3.69
22 23 3.590466 ATGGTTGTGGGCCAGGAGC 62.590 63.158 6.40 9.05 39.65 4.70
24 25 4.329545 GTTGTGGGCCAGGAGCGA 62.330 66.667 6.40 0.00 45.17 4.93
32 33 3.801997 CCAGGAGCGAGGCCCATT 61.802 66.667 0.00 0.00 0.00 3.16
33 34 2.515523 CAGGAGCGAGGCCCATTG 60.516 66.667 0.00 0.00 0.00 2.82
34 35 3.801997 AGGAGCGAGGCCCATTGG 61.802 66.667 0.00 0.00 0.00 3.16
36 37 2.514824 GAGCGAGGCCCATTGGTC 60.515 66.667 0.00 0.00 36.05 4.02
39 40 4.856801 CGAGGCCCATTGGTCCCG 62.857 72.222 0.00 0.00 36.69 5.14
40 41 4.506255 GAGGCCCATTGGTCCCGG 62.506 72.222 0.00 0.00 36.69 5.73
44 45 2.760477 CCCATTGGTCCCGGTTCA 59.240 61.111 0.00 0.00 0.00 3.18
45 46 1.306296 CCCATTGGTCCCGGTTCAT 59.694 57.895 0.00 0.00 0.00 2.57
47 48 0.323360 CCATTGGTCCCGGTTCATGT 60.323 55.000 0.00 0.00 0.00 3.21
49 50 0.991920 ATTGGTCCCGGTTCATGTCT 59.008 50.000 0.00 0.00 0.00 3.41
50 51 0.036164 TTGGTCCCGGTTCATGTCTG 59.964 55.000 0.00 0.00 0.00 3.51
51 52 0.834261 TGGTCCCGGTTCATGTCTGA 60.834 55.000 0.00 0.00 0.00 3.27
54 55 1.804748 GTCCCGGTTCATGTCTGAAAC 59.195 52.381 0.00 0.00 44.22 2.78
55 56 1.165270 CCCGGTTCATGTCTGAAACC 58.835 55.000 0.00 3.67 44.73 3.27
57 58 0.796312 CGGTTCATGTCTGAAACCGG 59.204 55.000 21.76 0.00 44.73 5.28
60 61 1.804748 GTTCATGTCTGAAACCGGGAC 59.195 52.381 6.32 3.26 42.85 4.46
61 62 0.323629 TCATGTCTGAAACCGGGACC 59.676 55.000 6.32 0.00 0.00 4.46
64 65 0.547075 TGTCTGAAACCGGGACCAAA 59.453 50.000 6.32 0.00 0.00 3.28
65 66 1.235724 GTCTGAAACCGGGACCAAAG 58.764 55.000 6.32 0.00 0.00 2.77
66 67 0.109723 TCTGAAACCGGGACCAAAGG 59.890 55.000 6.32 0.00 0.00 3.11
67 68 0.893727 CTGAAACCGGGACCAAAGGG 60.894 60.000 6.32 0.00 41.29 3.95
78 79 2.928416 CCAAAGGGTCCAGACGAAC 58.072 57.895 0.00 0.00 0.00 3.95
82 83 4.078516 GGGTCCAGACGAACCGGG 62.079 72.222 6.32 0.00 39.05 5.73
84 85 2.260743 GTCCAGACGAACCGGGAC 59.739 66.667 6.32 9.54 42.60 4.46
85 86 2.993264 TCCAGACGAACCGGGACC 60.993 66.667 6.32 0.00 0.00 4.46
87 88 2.738480 CAGACGAACCGGGACCAA 59.262 61.111 6.32 0.00 0.00 3.67
88 89 1.295423 CAGACGAACCGGGACCAAT 59.705 57.895 6.32 0.00 0.00 3.16
89 90 1.019278 CAGACGAACCGGGACCAATG 61.019 60.000 6.32 0.00 0.00 2.82
90 91 2.359478 ACGAACCGGGACCAATGC 60.359 61.111 6.32 0.00 0.00 3.56
91 92 3.131478 CGAACCGGGACCAATGCC 61.131 66.667 6.32 0.00 0.00 4.40
92 93 2.754254 GAACCGGGACCAATGCCC 60.754 66.667 6.32 0.00 42.41 5.36
93 94 4.376170 AACCGGGACCAATGCCCC 62.376 66.667 6.32 0.00 42.92 5.80
95 96 4.141876 CCGGGACCAATGCCCCAT 62.142 66.667 9.10 0.00 42.92 4.00
96 97 2.834505 CGGGACCAATGCCCCATG 60.835 66.667 9.10 0.00 42.92 3.66
98 99 1.456331 GGGACCAATGCCCCATGAG 60.456 63.158 0.00 0.00 42.24 2.90
124 125 4.410400 CCCCCTGGCCTCACGAAC 62.410 72.222 3.32 0.00 0.00 3.95
130 131 4.754667 GGCCTCACGAACCGGGAC 62.755 72.222 6.32 0.00 32.99 4.46
131 132 4.754667 GCCTCACGAACCGGGACC 62.755 72.222 6.32 0.00 32.99 4.46
132 133 2.995574 CCTCACGAACCGGGACCT 60.996 66.667 6.32 0.00 32.99 3.85
137 138 2.108362 CGAACCGGGACCTATGCC 59.892 66.667 6.32 0.00 0.00 4.40
138 139 2.509422 GAACCGGGACCTATGCCC 59.491 66.667 6.32 0.00 42.41 5.36
139 140 3.094498 AACCGGGACCTATGCCCC 61.094 66.667 6.32 0.00 42.92 5.80
143 144 2.846532 GGGACCTATGCCCCCATG 59.153 66.667 0.00 0.00 39.81 3.66
144 145 2.845345 GGGACCTATGCCCCCATGG 61.845 68.421 4.14 4.14 39.81 3.66
155 156 4.123545 CCCATGGGTCCCGGTTCC 62.124 72.222 23.93 1.59 0.00 3.62
156 157 3.015145 CCATGGGTCCCGGTTCCT 61.015 66.667 2.85 0.00 0.00 3.36
157 158 2.272146 CATGGGTCCCGGTTCCTG 59.728 66.667 2.65 0.00 0.00 3.86
161 162 2.663196 GGTCCCGGTTCCTGACTG 59.337 66.667 0.00 0.00 0.00 3.51
162 163 1.911766 GGTCCCGGTTCCTGACTGA 60.912 63.158 0.00 0.00 36.72 3.41
163 164 1.477685 GGTCCCGGTTCCTGACTGAA 61.478 60.000 0.00 0.00 36.72 3.02
164 165 0.320508 GTCCCGGTTCCTGACTGAAC 60.321 60.000 0.00 0.00 43.10 3.18
170 171 0.320508 GTTCCTGACTGAACCGGGAC 60.321 60.000 6.32 0.00 38.71 4.46
172 173 0.406750 TCCTGACTGAACCGGGACTA 59.593 55.000 6.32 0.00 34.32 2.59
174 175 1.831736 CCTGACTGAACCGGGACTAAT 59.168 52.381 6.32 0.00 31.68 1.73
175 176 2.418746 CCTGACTGAACCGGGACTAATG 60.419 54.545 6.32 0.00 31.68 1.90
176 177 2.496070 CTGACTGAACCGGGACTAATGA 59.504 50.000 6.32 0.00 0.00 2.57
177 178 2.496070 TGACTGAACCGGGACTAATGAG 59.504 50.000 6.32 0.00 0.00 2.90
179 180 1.482593 CTGAACCGGGACTAATGAGCT 59.517 52.381 6.32 0.00 0.00 4.09
181 182 0.541863 AACCGGGACTAATGAGCTGG 59.458 55.000 6.32 0.00 0.00 4.85
182 183 1.227674 CCGGGACTAATGAGCTGGC 60.228 63.158 0.00 0.00 0.00 4.85
183 184 1.227674 CGGGACTAATGAGCTGGCC 60.228 63.158 0.00 0.00 0.00 5.36
184 185 1.915228 GGGACTAATGAGCTGGCCA 59.085 57.895 4.71 4.71 0.00 5.36
185 186 0.179034 GGGACTAATGAGCTGGCCAG 60.179 60.000 29.34 29.34 0.00 4.85
200 201 2.677875 CAGGCCTGGACCAAAGCC 60.678 66.667 26.14 22.45 46.13 4.35
202 203 2.037847 GGCCTGGACCAAAGCCAT 59.962 61.111 24.20 0.00 45.07 4.40
203 204 2.353610 GGCCTGGACCAAAGCCATG 61.354 63.158 24.20 0.00 45.07 3.66
204 205 1.607467 GCCTGGACCAAAGCCATGT 60.607 57.895 0.00 0.00 34.33 3.21
207 208 1.693606 CCTGGACCAAAGCCATGTTTT 59.306 47.619 0.00 0.00 34.33 2.43
208 209 2.289010 CCTGGACCAAAGCCATGTTTTC 60.289 50.000 0.00 0.00 34.33 2.29
210 211 3.826157 CTGGACCAAAGCCATGTTTTCTA 59.174 43.478 0.00 0.00 34.33 2.10
212 213 3.826729 GGACCAAAGCCATGTTTTCTACT 59.173 43.478 0.00 0.00 0.00 2.57
216 217 6.924111 ACCAAAGCCATGTTTTCTACTAATG 58.076 36.000 0.00 0.00 0.00 1.90
236 1815 5.848286 ATGATCCTTGATATGCCCTTACA 57.152 39.130 0.00 0.00 0.00 2.41
237 1816 5.848286 TGATCCTTGATATGCCCTTACAT 57.152 39.130 0.00 0.00 0.00 2.29
240 1819 4.973168 TCCTTGATATGCCCTTACATCAC 58.027 43.478 0.00 0.00 0.00 3.06
241 1820 4.074970 CCTTGATATGCCCTTACATCACC 58.925 47.826 0.00 0.00 0.00 4.02
243 1822 4.623932 TGATATGCCCTTACATCACCTC 57.376 45.455 0.00 0.00 0.00 3.85
244 1823 3.973305 TGATATGCCCTTACATCACCTCA 59.027 43.478 0.00 0.00 0.00 3.86
245 1824 4.598807 TGATATGCCCTTACATCACCTCAT 59.401 41.667 0.00 0.00 0.00 2.90
246 1825 2.715749 TGCCCTTACATCACCTCATG 57.284 50.000 0.00 0.00 0.00 3.07
247 1826 2.195727 TGCCCTTACATCACCTCATGA 58.804 47.619 0.00 0.00 43.13 3.07
249 1828 3.973305 TGCCCTTACATCACCTCATGATA 59.027 43.478 0.00 0.00 46.96 2.15
251 1830 5.104151 TGCCCTTACATCACCTCATGATAAA 60.104 40.000 0.00 0.00 46.96 1.40
253 1832 6.595682 CCCTTACATCACCTCATGATAAACT 58.404 40.000 0.00 0.00 46.96 2.66
255 1834 7.557719 CCCTTACATCACCTCATGATAAACTTT 59.442 37.037 0.00 0.00 46.96 2.66
256 1835 8.616076 CCTTACATCACCTCATGATAAACTTTC 58.384 37.037 0.00 0.00 46.96 2.62
260 1839 9.911788 ACATCACCTCATGATAAACTTTCTATT 57.088 29.630 0.00 0.00 46.96 1.73
262 1841 8.213518 TCACCTCATGATAAACTTTCTATTGC 57.786 34.615 0.00 0.00 29.99 3.56
263 1842 7.828717 TCACCTCATGATAAACTTTCTATTGCA 59.171 33.333 0.00 0.00 29.99 4.08
264 1843 8.627403 CACCTCATGATAAACTTTCTATTGCAT 58.373 33.333 0.00 0.00 0.00 3.96
265 1844 8.844244 ACCTCATGATAAACTTTCTATTGCATC 58.156 33.333 0.00 0.00 0.00 3.91
266 1845 8.295288 CCTCATGATAAACTTTCTATTGCATCC 58.705 37.037 0.00 0.00 0.00 3.51
267 1846 8.985315 TCATGATAAACTTTCTATTGCATCCT 57.015 30.769 0.00 0.00 0.00 3.24
275 1854 8.593945 AACTTTCTATTGCATCCTATTCCAAA 57.406 30.769 0.00 0.00 0.00 3.28
276 1855 8.593945 ACTTTCTATTGCATCCTATTCCAAAA 57.406 30.769 0.00 0.00 0.00 2.44
277 1856 8.689972 ACTTTCTATTGCATCCTATTCCAAAAG 58.310 33.333 0.00 0.00 0.00 2.27
278 1857 8.593945 TTTCTATTGCATCCTATTCCAAAAGT 57.406 30.769 0.00 0.00 0.00 2.66
280 1859 7.345691 TCTATTGCATCCTATTCCAAAAGTGA 58.654 34.615 0.00 0.00 0.00 3.41
281 1860 5.902613 TTGCATCCTATTCCAAAAGTGAG 57.097 39.130 0.00 0.00 0.00 3.51
282 1861 4.272489 TGCATCCTATTCCAAAAGTGAGG 58.728 43.478 0.00 0.00 0.00 3.86
283 1862 4.018506 TGCATCCTATTCCAAAAGTGAGGA 60.019 41.667 0.00 0.00 37.49 3.71
284 1863 5.136105 GCATCCTATTCCAAAAGTGAGGAT 58.864 41.667 0.00 0.00 43.13 3.24
285 1864 5.595952 GCATCCTATTCCAAAAGTGAGGATT 59.404 40.000 0.00 0.00 40.96 3.01
286 1865 6.097412 GCATCCTATTCCAAAAGTGAGGATTT 59.903 38.462 0.00 0.00 40.96 2.17
287 1866 7.285401 GCATCCTATTCCAAAAGTGAGGATTTA 59.715 37.037 0.00 0.00 40.96 1.40
288 1867 8.624776 CATCCTATTCCAAAAGTGAGGATTTAC 58.375 37.037 0.00 0.00 40.96 2.01
291 1870 8.678199 CCTATTCCAAAAGTGAGGATTTACTTC 58.322 37.037 0.00 0.00 36.19 3.01
295 1874 7.287061 TCCAAAAGTGAGGATTTACTTCTTCA 58.713 34.615 0.00 0.00 36.19 3.02
296 1875 7.944554 TCCAAAAGTGAGGATTTACTTCTTCAT 59.055 33.333 0.00 0.00 36.19 2.57
298 1877 9.617975 CAAAAGTGAGGATTTACTTCTTCATTC 57.382 33.333 0.00 0.00 36.19 2.67
299 1878 7.929941 AAGTGAGGATTTACTTCTTCATTCC 57.070 36.000 0.00 0.00 34.69 3.01
300 1879 7.264294 AGTGAGGATTTACTTCTTCATTCCT 57.736 36.000 0.00 0.00 34.69 3.36
301 1880 7.694093 AGTGAGGATTTACTTCTTCATTCCTT 58.306 34.615 0.00 0.00 34.69 3.36
302 1881 8.166726 AGTGAGGATTTACTTCTTCATTCCTTT 58.833 33.333 0.00 0.00 34.69 3.11
303 1882 8.454894 GTGAGGATTTACTTCTTCATTCCTTTC 58.545 37.037 0.00 0.00 34.69 2.62
304 1883 8.386264 TGAGGATTTACTTCTTCATTCCTTTCT 58.614 33.333 0.00 0.00 32.42 2.52
305 1884 9.237187 GAGGATTTACTTCTTCATTCCTTTCTT 57.763 33.333 0.00 0.00 32.42 2.52
306 1885 9.018582 AGGATTTACTTCTTCATTCCTTTCTTG 57.981 33.333 0.00 0.00 0.00 3.02
307 1886 8.246871 GGATTTACTTCTTCATTCCTTTCTTGG 58.753 37.037 0.00 0.00 0.00 3.61
308 1887 8.712228 ATTTACTTCTTCATTCCTTTCTTGGT 57.288 30.769 0.00 0.00 0.00 3.67
309 1888 9.807921 ATTTACTTCTTCATTCCTTTCTTGGTA 57.192 29.630 0.00 0.00 0.00 3.25
313 1892 9.401058 ACTTCTTCATTCCTTTCTTGGTATATG 57.599 33.333 0.00 0.00 0.00 1.78
314 1893 8.752005 TTCTTCATTCCTTTCTTGGTATATGG 57.248 34.615 0.00 0.00 0.00 2.74
315 1894 8.101309 TCTTCATTCCTTTCTTGGTATATGGA 57.899 34.615 0.00 0.00 0.00 3.41
316 1895 8.727149 TCTTCATTCCTTTCTTGGTATATGGAT 58.273 33.333 0.00 0.00 0.00 3.41
317 1896 9.359653 CTTCATTCCTTTCTTGGTATATGGATT 57.640 33.333 0.00 0.00 0.00 3.01
318 1897 8.696043 TCATTCCTTTCTTGGTATATGGATTG 57.304 34.615 0.00 0.00 0.00 2.67
319 1898 7.725397 TCATTCCTTTCTTGGTATATGGATTGG 59.275 37.037 0.00 0.00 0.00 3.16
320 1899 5.385198 TCCTTTCTTGGTATATGGATTGGC 58.615 41.667 0.00 0.00 0.00 4.52
321 1900 5.103728 TCCTTTCTTGGTATATGGATTGGCA 60.104 40.000 0.00 0.00 0.00 4.92
322 1901 5.598005 CCTTTCTTGGTATATGGATTGGCAA 59.402 40.000 0.68 0.68 0.00 4.52
324 1903 6.653526 TTCTTGGTATATGGATTGGCAATG 57.346 37.500 19.07 0.00 0.00 2.82
326 1905 2.819019 TGGTATATGGATTGGCAATGCG 59.181 45.455 23.82 0.00 31.00 4.73
327 1906 2.415893 GGTATATGGATTGGCAATGCGC 60.416 50.000 23.82 0.00 41.28 6.09
328 1907 1.330234 ATATGGATTGGCAATGCGCA 58.670 45.000 23.82 14.96 45.17 6.09
329 1908 1.330234 TATGGATTGGCAATGCGCAT 58.670 45.000 23.82 19.28 45.17 4.73
330 1909 0.249699 ATGGATTGGCAATGCGCATG 60.250 50.000 26.09 18.46 45.17 4.06
331 1910 1.593209 GGATTGGCAATGCGCATGG 60.593 57.895 26.09 23.37 45.17 3.66
332 1911 1.438399 GATTGGCAATGCGCATGGA 59.562 52.632 28.99 8.12 45.17 3.41
333 1912 0.179105 GATTGGCAATGCGCATGGAA 60.179 50.000 28.99 14.86 45.17 3.53
334 1913 0.249676 ATTGGCAATGCGCATGGAAA 59.750 45.000 28.99 20.38 45.17 3.13
337 1916 0.669932 GGCAATGCGCATGGAAACAA 60.670 50.000 28.99 0.00 45.17 2.83
338 1917 2.205759 GGCAATGCGCATGGAAACAAA 61.206 47.619 28.99 0.00 45.17 2.83
339 1918 3.694566 GGCAATGCGCATGGAAACAAAA 61.695 45.455 28.99 0.00 45.17 2.44
340 1919 4.964352 GGCAATGCGCATGGAAACAAAAT 61.964 43.478 28.99 3.22 45.17 1.82
353 1932 6.805713 TGGAAACAAAATCCTTCTTCTTGAC 58.194 36.000 0.00 0.00 37.85 3.18
354 1933 6.183360 TGGAAACAAAATCCTTCTTCTTGACC 60.183 38.462 0.00 0.00 37.85 4.02
356 1935 6.641169 AACAAAATCCTTCTTCTTGACCTC 57.359 37.500 0.00 0.00 0.00 3.85
357 1936 5.073428 ACAAAATCCTTCTTCTTGACCTCC 58.927 41.667 0.00 0.00 0.00 4.30
358 1937 5.163045 ACAAAATCCTTCTTCTTGACCTCCT 60.163 40.000 0.00 0.00 0.00 3.69
359 1938 5.590976 AAATCCTTCTTCTTGACCTCCTT 57.409 39.130 0.00 0.00 0.00 3.36
360 1939 4.566426 ATCCTTCTTCTTGACCTCCTTG 57.434 45.455 0.00 0.00 0.00 3.61
362 1941 4.489737 TCCTTCTTCTTGACCTCCTTGTA 58.510 43.478 0.00 0.00 0.00 2.41
363 1942 4.528596 TCCTTCTTCTTGACCTCCTTGTAG 59.471 45.833 0.00 0.00 0.00 2.74
366 1945 4.480115 TCTTCTTGACCTCCTTGTAGTCA 58.520 43.478 0.00 0.00 38.70 3.41
367 1946 4.281182 TCTTCTTGACCTCCTTGTAGTCAC 59.719 45.833 0.00 0.00 40.10 3.67
368 1947 2.897969 TCTTGACCTCCTTGTAGTCACC 59.102 50.000 0.00 0.00 40.10 4.02
370 1949 1.149288 TGACCTCCTTGTAGTCACCCT 59.851 52.381 0.00 0.00 35.67 4.34
371 1950 2.380932 TGACCTCCTTGTAGTCACCCTA 59.619 50.000 0.00 0.00 35.67 3.53
372 1951 3.025262 GACCTCCTTGTAGTCACCCTAG 58.975 54.545 0.00 0.00 0.00 3.02
374 1953 3.272551 ACCTCCTTGTAGTCACCCTAGAT 59.727 47.826 0.00 0.00 0.00 1.98
375 1954 3.639094 CCTCCTTGTAGTCACCCTAGATG 59.361 52.174 0.00 0.00 0.00 2.90
376 1955 3.031736 TCCTTGTAGTCACCCTAGATGC 58.968 50.000 0.00 0.00 0.00 3.91
377 1956 3.034635 CCTTGTAGTCACCCTAGATGCT 58.965 50.000 0.00 0.00 0.00 3.79
382 1961 5.208890 TGTAGTCACCCTAGATGCTTATGT 58.791 41.667 0.00 0.00 0.00 2.29
386 1965 7.380423 AGTCACCCTAGATGCTTATGTATTT 57.620 36.000 0.00 0.00 0.00 1.40
387 1966 7.806180 AGTCACCCTAGATGCTTATGTATTTT 58.194 34.615 0.00 0.00 0.00 1.82
388 1967 7.716998 AGTCACCCTAGATGCTTATGTATTTTG 59.283 37.037 0.00 0.00 0.00 2.44
389 1968 7.715249 GTCACCCTAGATGCTTATGTATTTTGA 59.285 37.037 0.00 0.00 0.00 2.69
390 1969 7.933577 TCACCCTAGATGCTTATGTATTTTGAG 59.066 37.037 0.00 0.00 0.00 3.02
391 1970 7.933577 CACCCTAGATGCTTATGTATTTTGAGA 59.066 37.037 0.00 0.00 0.00 3.27
392 1971 7.934120 ACCCTAGATGCTTATGTATTTTGAGAC 59.066 37.037 0.00 0.00 0.00 3.36
393 1972 8.153550 CCCTAGATGCTTATGTATTTTGAGACT 58.846 37.037 0.00 0.00 0.00 3.24
394 1973 9.553064 CCTAGATGCTTATGTATTTTGAGACTT 57.447 33.333 0.00 0.00 0.00 3.01
540 4734 6.625873 AATCTTCTGTGTGAAAAAGAGTCC 57.374 37.500 0.00 0.00 33.79 3.85
793 6844 0.529119 GGAGAACGTTGGTCACACGT 60.529 55.000 5.00 0.00 42.20 4.49
794 6845 0.575390 GAGAACGTTGGTCACACGTG 59.425 55.000 15.48 15.48 40.16 4.49
907 7219 4.832608 GCCCCTTACCACGGAGCG 62.833 72.222 0.00 0.00 0.00 5.03
934 7248 1.834896 TCTATAAAAGCGGTGCCCTCA 59.165 47.619 0.00 0.00 0.00 3.86
965 7280 2.541547 ATCATCGCCACCACCCACAG 62.542 60.000 0.00 0.00 0.00 3.66
996 7313 1.633774 AGTTCGCCAGAGAAGAAGGA 58.366 50.000 0.00 0.00 0.00 3.36
1186 9566 2.344500 CCGCCGAGGTAACCAACA 59.656 61.111 0.00 0.00 34.51 3.33
1209 9589 1.668419 CACCGATCTTGTCCATTCCC 58.332 55.000 0.00 0.00 0.00 3.97
1229 9609 1.733718 CGCTCTTCTCATGCTCGACAA 60.734 52.381 0.00 0.00 0.00 3.18
1820 14905 1.946984 ACCGACAGATGGTTCCCTTA 58.053 50.000 0.00 0.00 35.82 2.69
1821 14906 2.262637 ACCGACAGATGGTTCCCTTAA 58.737 47.619 0.00 0.00 35.82 1.85
1822 14907 2.640826 ACCGACAGATGGTTCCCTTAAA 59.359 45.455 0.00 0.00 35.82 1.52
1823 14908 3.073356 ACCGACAGATGGTTCCCTTAAAA 59.927 43.478 0.00 0.00 35.82 1.52
1946 15249 4.756642 TGCATTTCAGTGAAGAACGAGAAT 59.243 37.500 5.56 0.00 30.96 2.40
1956 15259 4.509230 TGAAGAACGAGAATGATGCTATGC 59.491 41.667 0.00 0.00 0.00 3.14
2100 17228 5.381174 TTTTTCTGGCTGAATGACATCTG 57.619 39.130 7.68 0.00 34.24 2.90
2292 18295 2.765807 AGATCCCGAGCCACCAGG 60.766 66.667 0.00 0.00 38.23 4.45
2433 18437 4.554036 GTCTCATGCGGGGAGGCC 62.554 72.222 0.00 0.00 30.83 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.228831 TCCTGGCCCACAACCATTG 60.229 57.895 0.00 0.00 36.36 2.82
7 8 4.329545 TCGCTCCTGGCCCACAAC 62.330 66.667 0.00 0.00 37.74 3.32
15 16 3.801997 AATGGGCCTCGCTCCTGG 61.802 66.667 4.53 0.00 0.00 4.45
17 18 3.801997 CCAATGGGCCTCGCTCCT 61.802 66.667 4.53 0.00 0.00 3.69
18 19 4.115199 ACCAATGGGCCTCGCTCC 62.115 66.667 4.53 0.00 37.90 4.70
19 20 2.514824 GACCAATGGGCCTCGCTC 60.515 66.667 4.53 0.00 37.90 5.03
26 27 2.754254 GAACCGGGACCAATGGGC 60.754 66.667 6.32 0.00 37.90 5.36
27 28 1.037030 CATGAACCGGGACCAATGGG 61.037 60.000 6.32 0.00 41.29 4.00
29 30 1.094785 GACATGAACCGGGACCAATG 58.905 55.000 6.32 4.86 0.00 2.82
32 33 0.834261 TCAGACATGAACCGGGACCA 60.834 55.000 6.32 0.00 30.61 4.02
33 34 0.323629 TTCAGACATGAACCGGGACC 59.676 55.000 6.32 0.00 40.54 4.46
34 35 1.804748 GTTTCAGACATGAACCGGGAC 59.195 52.381 6.32 0.00 45.07 4.46
36 37 1.165270 GGTTTCAGACATGAACCGGG 58.835 55.000 6.32 0.00 45.07 5.73
39 40 1.165270 CCCGGTTTCAGACATGAACC 58.835 55.000 0.00 0.90 45.07 3.62
40 41 1.804748 GTCCCGGTTTCAGACATGAAC 59.195 52.381 0.00 0.00 45.07 3.18
44 45 0.768622 TTGGTCCCGGTTTCAGACAT 59.231 50.000 0.00 0.00 31.99 3.06
45 46 0.547075 TTTGGTCCCGGTTTCAGACA 59.453 50.000 0.00 0.00 31.99 3.41
47 48 0.109723 CCTTTGGTCCCGGTTTCAGA 59.890 55.000 0.00 0.00 0.00 3.27
49 50 1.151908 CCCTTTGGTCCCGGTTTCA 59.848 57.895 0.00 0.00 0.00 2.69
50 51 1.152138 ACCCTTTGGTCCCGGTTTC 59.848 57.895 0.00 0.00 43.06 2.78
51 52 3.349122 ACCCTTTGGTCCCGGTTT 58.651 55.556 0.00 0.00 43.06 3.27
60 61 0.605589 GGTTCGTCTGGACCCTTTGG 60.606 60.000 0.00 0.00 37.80 3.28
61 62 0.949105 CGGTTCGTCTGGACCCTTTG 60.949 60.000 0.00 0.00 0.00 2.77
64 65 2.995574 CCGGTTCGTCTGGACCCT 60.996 66.667 0.00 0.00 45.09 4.34
65 66 4.078516 CCCGGTTCGTCTGGACCC 62.079 72.222 0.00 0.00 45.09 4.46
66 67 2.993264 TCCCGGTTCGTCTGGACC 60.993 66.667 0.00 0.00 45.09 4.46
67 68 2.260743 GTCCCGGTTCGTCTGGAC 59.739 66.667 0.00 0.00 45.09 4.02
68 69 2.993264 GGTCCCGGTTCGTCTGGA 60.993 66.667 0.00 0.00 45.09 3.86
70 71 1.019278 CATTGGTCCCGGTTCGTCTG 61.019 60.000 0.00 0.00 0.00 3.51
71 72 1.295423 CATTGGTCCCGGTTCGTCT 59.705 57.895 0.00 0.00 0.00 4.18
72 73 2.396157 GCATTGGTCCCGGTTCGTC 61.396 63.158 0.00 0.00 0.00 4.20
73 74 2.359478 GCATTGGTCCCGGTTCGT 60.359 61.111 0.00 0.00 0.00 3.85
74 75 3.131478 GGCATTGGTCCCGGTTCG 61.131 66.667 0.00 0.00 0.00 3.95
75 76 2.754254 GGGCATTGGTCCCGGTTC 60.754 66.667 0.00 0.00 33.43 3.62
81 82 1.456331 CCTCATGGGGCATTGGTCC 60.456 63.158 0.00 0.00 38.40 4.46
82 83 4.265206 CCTCATGGGGCATTGGTC 57.735 61.111 0.00 0.00 0.00 4.02
107 108 4.410400 GTTCGTGAGGCCAGGGGG 62.410 72.222 5.01 0.00 37.18 5.40
108 109 4.410400 GGTTCGTGAGGCCAGGGG 62.410 72.222 5.01 0.00 0.00 4.79
109 110 4.760047 CGGTTCGTGAGGCCAGGG 62.760 72.222 5.01 0.00 0.00 4.45
113 114 4.754667 GTCCCGGTTCGTGAGGCC 62.755 72.222 0.00 0.00 0.00 5.19
114 115 4.754667 GGTCCCGGTTCGTGAGGC 62.755 72.222 0.00 0.00 0.00 4.70
116 117 0.102481 CATAGGTCCCGGTTCGTGAG 59.898 60.000 0.00 0.00 0.00 3.51
117 118 1.952102 GCATAGGTCCCGGTTCGTGA 61.952 60.000 0.00 0.00 0.00 4.35
118 119 1.520787 GCATAGGTCCCGGTTCGTG 60.521 63.158 0.00 0.00 0.00 4.35
120 121 2.108362 GGCATAGGTCCCGGTTCG 59.892 66.667 0.00 0.00 0.00 3.95
121 122 2.509422 GGGCATAGGTCCCGGTTC 59.491 66.667 0.00 0.00 33.43 3.62
138 139 4.123545 GGAACCGGGACCCATGGG 62.124 72.222 30.23 30.23 42.03 4.00
139 140 3.015145 AGGAACCGGGACCCATGG 61.015 66.667 12.15 4.14 0.00 3.66
140 141 2.272146 CAGGAACCGGGACCCATG 59.728 66.667 12.15 3.12 0.00 3.66
143 144 2.606826 AGTCAGGAACCGGGACCC 60.607 66.667 6.32 0.00 31.99 4.46
144 145 1.477685 TTCAGTCAGGAACCGGGACC 61.478 60.000 6.32 8.94 31.99 4.46
145 146 0.320508 GTTCAGTCAGGAACCGGGAC 60.321 60.000 6.32 2.53 40.97 4.46
146 147 2.055299 GTTCAGTCAGGAACCGGGA 58.945 57.895 6.32 0.00 40.97 5.14
151 152 0.320508 GTCCCGGTTCAGTCAGGAAC 60.321 60.000 0.00 0.00 45.01 3.62
153 154 0.406750 TAGTCCCGGTTCAGTCAGGA 59.593 55.000 0.00 0.00 0.00 3.86
155 156 2.496070 TCATTAGTCCCGGTTCAGTCAG 59.504 50.000 0.00 0.00 0.00 3.51
156 157 2.496070 CTCATTAGTCCCGGTTCAGTCA 59.504 50.000 0.00 0.00 0.00 3.41
157 158 2.738964 GCTCATTAGTCCCGGTTCAGTC 60.739 54.545 0.00 0.00 0.00 3.51
161 162 1.473434 CCAGCTCATTAGTCCCGGTTC 60.473 57.143 0.00 0.00 0.00 3.62
162 163 0.541863 CCAGCTCATTAGTCCCGGTT 59.458 55.000 0.00 0.00 0.00 4.44
163 164 1.972660 GCCAGCTCATTAGTCCCGGT 61.973 60.000 0.00 0.00 0.00 5.28
164 165 1.227674 GCCAGCTCATTAGTCCCGG 60.228 63.158 0.00 0.00 0.00 5.73
166 167 0.179034 CTGGCCAGCTCATTAGTCCC 60.179 60.000 22.33 0.00 0.00 4.46
170 171 4.154296 GCCTGGCCAGCTCATTAG 57.846 61.111 28.39 12.86 0.00 1.73
183 184 2.677875 GGCTTTGGTCCAGGCCTG 60.678 66.667 26.87 26.87 41.20 4.85
184 185 2.551413 ATGGCTTTGGTCCAGGCCT 61.551 57.895 27.33 0.00 44.36 5.19
185 186 2.037847 ATGGCTTTGGTCCAGGCC 59.962 61.111 23.31 23.31 44.31 5.19
189 190 2.676748 AGAAAACATGGCTTTGGTCCA 58.323 42.857 0.00 0.00 38.09 4.02
191 192 6.569179 TTAGTAGAAAACATGGCTTTGGTC 57.431 37.500 0.00 0.00 0.00 4.02
193 194 7.156876 TCATTAGTAGAAAACATGGCTTTGG 57.843 36.000 0.00 0.00 0.00 3.28
197 198 6.904626 AGGATCATTAGTAGAAAACATGGCT 58.095 36.000 0.00 0.00 0.00 4.75
199 200 8.737168 TCAAGGATCATTAGTAGAAAACATGG 57.263 34.615 0.00 0.00 0.00 3.66
204 205 9.507329 GGCATATCAAGGATCATTAGTAGAAAA 57.493 33.333 0.00 0.00 0.00 2.29
207 208 6.962311 AGGGCATATCAAGGATCATTAGTAGA 59.038 38.462 0.00 0.00 0.00 2.59
208 209 7.192852 AGGGCATATCAAGGATCATTAGTAG 57.807 40.000 0.00 0.00 0.00 2.57
210 211 6.460103 AAGGGCATATCAAGGATCATTAGT 57.540 37.500 0.00 0.00 0.00 2.24
212 213 7.328404 TGTAAGGGCATATCAAGGATCATTA 57.672 36.000 0.00 0.00 0.00 1.90
216 217 5.645497 GTGATGTAAGGGCATATCAAGGATC 59.355 44.000 0.00 0.00 31.98 3.36
237 1816 7.828717 TGCAATAGAAAGTTTATCATGAGGTGA 59.171 33.333 0.09 0.00 42.06 4.02
240 1819 8.295288 GGATGCAATAGAAAGTTTATCATGAGG 58.705 37.037 0.09 0.00 0.00 3.86
241 1820 9.064706 AGGATGCAATAGAAAGTTTATCATGAG 57.935 33.333 0.09 0.00 0.00 2.90
247 1826 9.866655 TGGAATAGGATGCAATAGAAAGTTTAT 57.133 29.630 0.00 0.00 0.00 1.40
249 1828 8.593945 TTGGAATAGGATGCAATAGAAAGTTT 57.406 30.769 0.00 0.00 0.00 2.66
251 1830 8.593945 TTTTGGAATAGGATGCAATAGAAAGT 57.406 30.769 0.00 0.00 30.43 2.66
253 1832 8.469200 CACTTTTGGAATAGGATGCAATAGAAA 58.531 33.333 0.00 0.00 34.79 2.52
255 1834 7.345691 TCACTTTTGGAATAGGATGCAATAGA 58.654 34.615 0.00 0.00 34.79 1.98
256 1835 7.255381 CCTCACTTTTGGAATAGGATGCAATAG 60.255 40.741 0.00 0.00 36.36 1.73
258 1837 5.361857 CCTCACTTTTGGAATAGGATGCAAT 59.638 40.000 0.00 0.00 30.43 3.56
259 1838 4.706476 CCTCACTTTTGGAATAGGATGCAA 59.294 41.667 0.00 0.00 0.00 4.08
260 1839 4.018506 TCCTCACTTTTGGAATAGGATGCA 60.019 41.667 0.00 0.00 0.00 3.96
261 1840 4.526970 TCCTCACTTTTGGAATAGGATGC 58.473 43.478 0.00 0.00 0.00 3.91
262 1841 7.651027 AAATCCTCACTTTTGGAATAGGATG 57.349 36.000 0.00 0.00 41.79 3.51
263 1842 8.560903 AGTAAATCCTCACTTTTGGAATAGGAT 58.439 33.333 0.00 0.00 43.92 3.24
264 1843 7.928873 AGTAAATCCTCACTTTTGGAATAGGA 58.071 34.615 0.00 0.00 37.52 2.94
265 1844 8.581253 AAGTAAATCCTCACTTTTGGAATAGG 57.419 34.615 0.00 0.00 35.81 2.57
266 1845 9.454859 AGAAGTAAATCCTCACTTTTGGAATAG 57.545 33.333 0.00 0.00 35.17 1.73
267 1846 9.807921 AAGAAGTAAATCCTCACTTTTGGAATA 57.192 29.630 0.00 0.00 35.17 1.75
268 1847 8.712228 AAGAAGTAAATCCTCACTTTTGGAAT 57.288 30.769 0.00 0.00 35.17 3.01
269 1848 7.777910 TGAAGAAGTAAATCCTCACTTTTGGAA 59.222 33.333 0.00 0.00 35.17 3.53
270 1849 7.287061 TGAAGAAGTAAATCCTCACTTTTGGA 58.713 34.615 0.00 0.00 35.17 3.53
271 1850 7.510549 TGAAGAAGTAAATCCTCACTTTTGG 57.489 36.000 0.00 0.00 35.17 3.28
272 1851 9.617975 GAATGAAGAAGTAAATCCTCACTTTTG 57.382 33.333 0.00 0.00 35.17 2.44
275 1854 7.694093 AGGAATGAAGAAGTAAATCCTCACTT 58.306 34.615 0.00 0.00 37.69 3.16
276 1855 7.264294 AGGAATGAAGAAGTAAATCCTCACT 57.736 36.000 0.00 0.00 30.12 3.41
277 1856 7.929941 AAGGAATGAAGAAGTAAATCCTCAC 57.070 36.000 0.00 0.00 34.84 3.51
278 1857 8.386264 AGAAAGGAATGAAGAAGTAAATCCTCA 58.614 33.333 0.00 0.00 34.84 3.86
280 1859 9.018582 CAAGAAAGGAATGAAGAAGTAAATCCT 57.981 33.333 0.00 0.00 37.42 3.24
281 1860 8.246871 CCAAGAAAGGAATGAAGAAGTAAATCC 58.753 37.037 0.00 0.00 0.00 3.01
282 1861 8.797438 ACCAAGAAAGGAATGAAGAAGTAAATC 58.203 33.333 0.00 0.00 0.00 2.17
283 1862 8.712228 ACCAAGAAAGGAATGAAGAAGTAAAT 57.288 30.769 0.00 0.00 0.00 1.40
284 1863 9.807921 ATACCAAGAAAGGAATGAAGAAGTAAA 57.192 29.630 0.00 0.00 0.00 2.01
287 1866 9.401058 CATATACCAAGAAAGGAATGAAGAAGT 57.599 33.333 0.00 0.00 0.00 3.01
288 1867 8.844244 CCATATACCAAGAAAGGAATGAAGAAG 58.156 37.037 0.00 0.00 0.00 2.85
291 1870 8.930846 ATCCATATACCAAGAAAGGAATGAAG 57.069 34.615 0.00 0.00 0.00 3.02
295 1874 6.494835 GCCAATCCATATACCAAGAAAGGAAT 59.505 38.462 0.00 0.00 0.00 3.01
296 1875 5.833131 GCCAATCCATATACCAAGAAAGGAA 59.167 40.000 0.00 0.00 0.00 3.36
298 1877 5.139727 TGCCAATCCATATACCAAGAAAGG 58.860 41.667 0.00 0.00 0.00 3.11
299 1878 6.713762 TTGCCAATCCATATACCAAGAAAG 57.286 37.500 0.00 0.00 0.00 2.62
300 1879 6.462768 GCATTGCCAATCCATATACCAAGAAA 60.463 38.462 0.00 0.00 0.00 2.52
301 1880 5.010922 GCATTGCCAATCCATATACCAAGAA 59.989 40.000 0.00 0.00 0.00 2.52
302 1881 4.523943 GCATTGCCAATCCATATACCAAGA 59.476 41.667 0.00 0.00 0.00 3.02
303 1882 4.616604 CGCATTGCCAATCCATATACCAAG 60.617 45.833 2.41 0.00 0.00 3.61
304 1883 3.255395 CGCATTGCCAATCCATATACCAA 59.745 43.478 2.41 0.00 0.00 3.67
305 1884 2.819019 CGCATTGCCAATCCATATACCA 59.181 45.455 2.41 0.00 0.00 3.25
306 1885 2.415893 GCGCATTGCCAATCCATATACC 60.416 50.000 0.30 0.00 37.76 2.73
307 1886 2.228582 TGCGCATTGCCAATCCATATAC 59.771 45.455 5.66 0.00 45.60 1.47
308 1887 2.512705 TGCGCATTGCCAATCCATATA 58.487 42.857 5.66 0.00 45.60 0.86
309 1888 1.330234 TGCGCATTGCCAATCCATAT 58.670 45.000 5.66 0.00 45.60 1.78
311 1890 0.249699 CATGCGCATTGCCAATCCAT 60.250 50.000 22.81 0.00 45.60 3.41
312 1891 1.142097 CATGCGCATTGCCAATCCA 59.858 52.632 22.81 0.00 45.60 3.41
313 1892 1.593209 CCATGCGCATTGCCAATCC 60.593 57.895 22.81 0.00 45.60 3.01
314 1893 0.179105 TTCCATGCGCATTGCCAATC 60.179 50.000 22.81 0.00 45.60 2.67
315 1894 0.249676 TTTCCATGCGCATTGCCAAT 59.750 45.000 22.81 0.00 45.60 3.16
316 1895 0.669932 GTTTCCATGCGCATTGCCAA 60.670 50.000 22.81 10.74 45.60 4.52
317 1896 1.079956 GTTTCCATGCGCATTGCCA 60.080 52.632 22.81 4.54 45.60 4.92
318 1897 0.669932 TTGTTTCCATGCGCATTGCC 60.670 50.000 22.81 9.18 45.60 4.52
319 1898 1.146637 TTTGTTTCCATGCGCATTGC 58.853 45.000 22.81 9.60 46.70 3.56
320 1899 3.181518 GGATTTTGTTTCCATGCGCATTG 60.182 43.478 22.81 18.53 33.21 2.82
321 1900 3.002102 GGATTTTGTTTCCATGCGCATT 58.998 40.909 22.81 0.98 33.21 3.56
322 1901 2.234414 AGGATTTTGTTTCCATGCGCAT 59.766 40.909 19.28 19.28 35.59 4.73
324 1903 2.368655 AGGATTTTGTTTCCATGCGC 57.631 45.000 0.00 0.00 35.59 6.09
326 1905 5.787380 AGAAGAAGGATTTTGTTTCCATGC 58.213 37.500 0.00 0.00 35.59 4.06
327 1906 7.383300 GTCAAGAAGAAGGATTTTGTTTCCATG 59.617 37.037 0.00 0.00 35.59 3.66
328 1907 7.436933 GTCAAGAAGAAGGATTTTGTTTCCAT 58.563 34.615 0.00 0.00 35.59 3.41
329 1908 6.183360 GGTCAAGAAGAAGGATTTTGTTTCCA 60.183 38.462 0.00 0.00 35.59 3.53
330 1909 6.040955 AGGTCAAGAAGAAGGATTTTGTTTCC 59.959 38.462 0.00 0.00 0.00 3.13
331 1910 7.043961 AGGTCAAGAAGAAGGATTTTGTTTC 57.956 36.000 0.00 0.00 0.00 2.78
332 1911 6.040955 GGAGGTCAAGAAGAAGGATTTTGTTT 59.959 38.462 0.00 0.00 0.00 2.83
333 1912 5.536538 GGAGGTCAAGAAGAAGGATTTTGTT 59.463 40.000 0.00 0.00 0.00 2.83
334 1913 5.073428 GGAGGTCAAGAAGAAGGATTTTGT 58.927 41.667 0.00 0.00 0.00 2.83
337 1916 5.163045 ACAAGGAGGTCAAGAAGAAGGATTT 60.163 40.000 0.00 0.00 0.00 2.17
338 1917 4.352298 ACAAGGAGGTCAAGAAGAAGGATT 59.648 41.667 0.00 0.00 0.00 3.01
339 1918 3.913163 ACAAGGAGGTCAAGAAGAAGGAT 59.087 43.478 0.00 0.00 0.00 3.24
340 1919 3.318313 ACAAGGAGGTCAAGAAGAAGGA 58.682 45.455 0.00 0.00 0.00 3.36
342 1921 5.011125 TGACTACAAGGAGGTCAAGAAGAAG 59.989 44.000 0.00 0.00 37.10 2.85
343 1922 4.899457 TGACTACAAGGAGGTCAAGAAGAA 59.101 41.667 0.00 0.00 37.10 2.52
344 1923 4.281182 GTGACTACAAGGAGGTCAAGAAGA 59.719 45.833 0.00 0.00 40.86 2.87
346 1925 3.323979 GGTGACTACAAGGAGGTCAAGAA 59.676 47.826 0.00 0.00 40.86 2.52
347 1926 2.897969 GGTGACTACAAGGAGGTCAAGA 59.102 50.000 0.00 0.00 40.86 3.02
348 1927 2.028020 GGGTGACTACAAGGAGGTCAAG 60.028 54.545 0.00 0.00 40.86 3.02
349 1928 1.975680 GGGTGACTACAAGGAGGTCAA 59.024 52.381 0.00 0.00 40.86 3.18
350 1929 1.149288 AGGGTGACTACAAGGAGGTCA 59.851 52.381 0.00 0.00 37.60 4.02
351 1930 1.939980 AGGGTGACTACAAGGAGGTC 58.060 55.000 0.00 0.00 0.00 3.85
352 1931 2.653366 TCTAGGGTGACTACAAGGAGGT 59.347 50.000 0.00 0.00 0.00 3.85
353 1932 3.383698 TCTAGGGTGACTACAAGGAGG 57.616 52.381 0.00 0.00 0.00 4.30
354 1933 3.068873 GCATCTAGGGTGACTACAAGGAG 59.931 52.174 0.00 0.00 0.00 3.69
356 1935 3.034635 AGCATCTAGGGTGACTACAAGG 58.965 50.000 0.00 0.00 0.00 3.61
357 1936 4.744795 AAGCATCTAGGGTGACTACAAG 57.255 45.455 0.00 0.00 0.00 3.16
358 1937 5.661312 ACATAAGCATCTAGGGTGACTACAA 59.339 40.000 0.00 0.00 0.00 2.41
359 1938 5.208890 ACATAAGCATCTAGGGTGACTACA 58.791 41.667 0.00 0.00 0.00 2.74
360 1939 5.793030 ACATAAGCATCTAGGGTGACTAC 57.207 43.478 0.00 0.00 0.00 2.73
362 1941 7.380423 AAATACATAAGCATCTAGGGTGACT 57.620 36.000 0.00 0.00 0.00 3.41
363 1942 7.715249 TCAAAATACATAAGCATCTAGGGTGAC 59.285 37.037 0.00 0.00 0.00 3.67
366 1945 7.934120 GTCTCAAAATACATAAGCATCTAGGGT 59.066 37.037 0.00 0.00 0.00 4.34
367 1946 8.153550 AGTCTCAAAATACATAAGCATCTAGGG 58.846 37.037 0.00 0.00 0.00 3.53
368 1947 9.553064 AAGTCTCAAAATACATAAGCATCTAGG 57.447 33.333 0.00 0.00 0.00 3.02
374 1953 9.897744 CAAGAAAAGTCTCAAAATACATAAGCA 57.102 29.630 0.00 0.00 30.70 3.91
375 1954 9.899226 ACAAGAAAAGTCTCAAAATACATAAGC 57.101 29.630 0.00 0.00 30.70 3.09
386 1965 7.822334 TGAAGTAGTCAACAAGAAAAGTCTCAA 59.178 33.333 0.00 0.00 31.51 3.02
387 1966 7.327975 TGAAGTAGTCAACAAGAAAAGTCTCA 58.672 34.615 0.00 0.00 31.51 3.27
388 1967 7.772332 TGAAGTAGTCAACAAGAAAAGTCTC 57.228 36.000 0.00 0.00 31.51 3.36
389 1968 7.987458 TCATGAAGTAGTCAACAAGAAAAGTCT 59.013 33.333 0.00 0.00 40.50 3.24
390 1969 8.064814 GTCATGAAGTAGTCAACAAGAAAAGTC 58.935 37.037 0.00 0.00 40.50 3.01
391 1970 7.552687 TGTCATGAAGTAGTCAACAAGAAAAGT 59.447 33.333 0.00 0.00 40.50 2.66
392 1971 7.919690 TGTCATGAAGTAGTCAACAAGAAAAG 58.080 34.615 0.00 0.00 40.50 2.27
393 1972 7.857734 TGTCATGAAGTAGTCAACAAGAAAA 57.142 32.000 0.00 0.00 40.50 2.29
394 1973 7.520453 GCATGTCATGAAGTAGTCAACAAGAAA 60.520 37.037 17.24 0.00 40.50 2.52
395 1974 6.073058 GCATGTCATGAAGTAGTCAACAAGAA 60.073 38.462 17.24 0.00 40.50 2.52
396 1975 5.409520 GCATGTCATGAAGTAGTCAACAAGA 59.590 40.000 17.24 0.00 40.50 3.02
585 4786 4.102649 CCTCGCTTTGTTTCGTTTCTTTT 58.897 39.130 0.00 0.00 0.00 2.27
793 6844 2.852075 GTGGGAGGGGGTGTGACA 60.852 66.667 0.00 0.00 0.00 3.58
794 6845 4.016706 CGTGGGAGGGGGTGTGAC 62.017 72.222 0.00 0.00 0.00 3.67
934 7248 1.290203 GCGATGATGGATGTGAACGT 58.710 50.000 0.00 0.00 0.00 3.99
965 7280 2.066262 TGGCGAACTTGAATCTCGAAC 58.934 47.619 0.90 0.00 34.52 3.95
996 7313 1.764054 CTTCCTCCCGGCCATCTCT 60.764 63.158 2.24 0.00 0.00 3.10
1186 9566 2.879103 ATGGACAAGATCGGTGGTTT 57.121 45.000 4.71 0.00 0.00 3.27
1209 9589 0.179153 TGTCGAGCATGAGAAGAGCG 60.179 55.000 0.00 0.00 0.00 5.03
1229 9609 3.018149 GAGACGAGATCAGTTACCACCT 58.982 50.000 0.00 0.00 0.00 4.00
1603 14572 1.680735 GATGCGCATTATGGGGAACAA 59.319 47.619 26.12 0.00 33.90 2.83
1605 14574 1.267806 CAGATGCGCATTATGGGGAAC 59.732 52.381 26.12 8.13 33.90 3.62
1741 14742 1.995991 CGAGTAAATGGGTCGCACG 59.004 57.895 0.00 0.00 0.00 5.34
1823 14908 5.700373 ACAAACTGCAACAACATCTGTTTTT 59.300 32.000 0.00 0.00 46.49 1.94
1956 15259 1.787847 GGACAGAAACCATCGTGCG 59.212 57.895 0.00 0.00 0.00 5.34
2089 17217 9.202273 GTCAGAATCTATAACCAGATGTCATTC 57.798 37.037 0.00 0.00 35.42 2.67
2098 17226 8.206867 TCTCCAAATGTCAGAATCTATAACCAG 58.793 37.037 0.00 0.00 0.00 4.00
2099 17227 8.089625 TCTCCAAATGTCAGAATCTATAACCA 57.910 34.615 0.00 0.00 0.00 3.67
2100 17228 8.964476 TTCTCCAAATGTCAGAATCTATAACC 57.036 34.615 0.00 0.00 0.00 2.85
2154 17988 8.506168 TCCTTATTGCGATTCTTGTCTATTTT 57.494 30.769 0.00 0.00 0.00 1.82
2359 18363 4.101448 GCCCTGGATCTGCGGTGT 62.101 66.667 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.