Multiple sequence alignment - TraesCS2D01G308900

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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 TraesCS2D01G308900 chr2D 100.000 2865 0 0 1 2865 396426583 396423719 0.000000e+00 5291.0
1 TraesCS2D01G308900 chr2D 83.292 401 57 7 1 397 638150588 638150982 7.550000e-96 361.0
2 TraesCS2D01G308900 chr2D 86.462 325 37 6 1 323 600439397 600439078 1.630000e-92 350.0
3 TraesCS2D01G308900 chr2A 92.128 2655 138 31 252 2865 534319498 534316874 0.000000e+00 3679.0
4 TraesCS2D01G308900 chr2A 84.211 399 58 4 1 398 734107608 734107214 1.610000e-102 383.0
5 TraesCS2D01G308900 chr2B 91.180 2449 142 33 438 2865 469614517 469612122 0.000000e+00 3258.0
6 TraesCS2D01G308900 chr2B 82.339 436 70 5 2 436 631338462 631338891 3.490000e-99 372.0
7 TraesCS2D01G308900 chr2B 82.161 398 66 4 1 397 708182724 708182331 1.270000e-88 337.0
8 TraesCS2D01G308900 chr2B 86.325 117 14 2 280 395 26401428 26401543 3.000000e-25 126.0
9 TraesCS2D01G308900 chr2B 87.755 49 6 0 390 438 434663987 434664035 1.110000e-04 58.4
10 TraesCS2D01G308900 chr6D 84.925 398 55 4 1 397 382795106 382795499 5.750000e-107 398.0
11 TraesCS2D01G308900 chr6D 80.882 340 48 10 2425 2749 453756467 453756130 4.740000e-63 252.0
12 TraesCS2D01G308900 chr6D 77.679 112 23 2 1117 1227 428650031 428649921 1.840000e-07 67.6
13 TraesCS2D01G308900 chr5A 83.144 439 62 5 1 438 414093539 414093112 9.620000e-105 390.0
14 TraesCS2D01G308900 chr5A 83.293 413 64 4 27 438 419691540 419691948 2.690000e-100 375.0
15 TraesCS2D01G308900 chr7D 82.663 398 61 7 1 396 6689797 6690188 2.110000e-91 346.0
16 TraesCS2D01G308900 chr7D 85.606 132 12 6 2555 2684 636666593 636666719 6.440000e-27 132.0
17 TraesCS2D01G308900 chr7D 81.250 96 17 1 2150 2245 611314353 611314447 3.060000e-10 76.8
18 TraesCS2D01G308900 chr7D 79.612 103 15 5 2136 2234 549871156 549871256 5.120000e-08 69.4
19 TraesCS2D01G308900 chr5B 79.180 317 45 13 2427 2734 347532171 347532475 1.740000e-47 200.0
20 TraesCS2D01G308900 chr3B 82.778 180 25 5 2540 2716 382709223 382709047 3.820000e-34 156.0
21 TraesCS2D01G308900 chr3B 78.173 197 29 13 2006 2197 157245722 157245909 2.330000e-21 113.0
22 TraesCS2D01G308900 chr3B 77.586 174 32 4 2046 2214 394944247 394944076 6.530000e-17 99.0
23 TraesCS2D01G308900 chr3D 82.778 180 24 6 2540 2716 290593872 290593697 1.370000e-33 154.0
24 TraesCS2D01G308900 chr3D 96.970 33 1 0 2371 2403 359529722 359529690 3.990000e-04 56.5
25 TraesCS2D01G308900 chr7A 82.635 167 20 7 2567 2726 729611650 729611486 3.850000e-29 139.0
26 TraesCS2D01G308900 chr7A 82.036 167 21 7 2567 2726 729637061 729636897 1.790000e-27 134.0
27 TraesCS2D01G308900 chr7A 77.019 161 22 6 2160 2310 701367763 701367918 8.510000e-11 78.7
28 TraesCS2D01G308900 chr4D 80.435 184 26 7 2555 2729 355855108 355854926 6.440000e-27 132.0
29 TraesCS2D01G308900 chr1B 79.545 176 28 7 2477 2646 370165252 370165079 5.010000e-23 119.0
30 TraesCS2D01G308900 chr1B 79.412 102 16 5 2136 2234 47769122 47769221 1.840000e-07 67.6
31 TraesCS2D01G308900 chr1B 100.000 28 0 0 2362 2389 484299274 484299247 5.000000e-03 52.8
32 TraesCS2D01G308900 chr4B 85.507 69 9 1 2167 2235 672103036 672102969 1.420000e-08 71.3
33 TraesCS2D01G308900 chr6B 77.679 112 23 2 1117 1227 645359827 645359717 1.840000e-07 67.6
34 TraesCS2D01G308900 chr6A 77.679 112 23 2 1117 1227 573414237 573414127 1.840000e-07 67.6
35 TraesCS2D01G308900 chr6A 83.871 62 8 2 378 438 605235812 605235752 1.110000e-04 58.4
36 TraesCS2D01G308900 chr4A 97.143 35 1 0 2278 2312 541885142 541885108 3.080000e-05 60.2


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 TraesCS2D01G308900 chr2D 396423719 396426583 2864 True 5291 5291 100.000 1 2865 1 chr2D.!!$R1 2864
1 TraesCS2D01G308900 chr2A 534316874 534319498 2624 True 3679 3679 92.128 252 2865 1 chr2A.!!$R1 2613
2 TraesCS2D01G308900 chr2B 469612122 469614517 2395 True 3258 3258 91.180 438 2865 1 chr2B.!!$R1 2427

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
204 205 0.034337 GCTTGTGGTAGACCGAACCA 59.966 55.0 0.0 0.0 44.75 3.67 F
219 220 0.036306 AACCAACACTCTAAGGGGCG 59.964 55.0 0.0 0.0 0.00 6.13 F
748 779 0.179032 TCCTTTGCTGTCCTTCGCAA 60.179 50.0 0.0 0.0 43.68 4.85 F
798 837 0.445436 CGAAGATGTGGAGCAACAGC 59.555 55.0 0.0 0.0 36.71 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1115 1158 0.325296 TCTTCCTCACGCCCCTGTAT 60.325 55.000 0.00 0.00 0.0 2.29 R
1646 1690 0.603707 ACTGAGGTCAATGGCACGTG 60.604 55.000 12.28 12.28 0.0 4.49 R
1757 1801 2.280119 ACACTCGCGCACACACAT 60.280 55.556 8.75 0.00 0.0 3.21 R
2748 2802 2.224549 CGACTAACAAACCCATGCGAAA 59.775 45.455 0.00 0.00 0.0 3.46 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
34 35 2.045045 CCGCATGGTGGTGGATGT 60.045 61.111 0.00 0.00 41.00 3.06
35 36 2.114670 CCGCATGGTGGTGGATGTC 61.115 63.158 0.00 0.00 41.00 3.06
36 37 2.463620 CGCATGGTGGTGGATGTCG 61.464 63.158 0.00 0.00 0.00 4.35
37 38 2.764314 GCATGGTGGTGGATGTCGC 61.764 63.158 0.00 0.00 0.00 5.19
38 39 2.125147 ATGGTGGTGGATGTCGCG 60.125 61.111 0.00 0.00 0.00 5.87
39 40 3.680620 ATGGTGGTGGATGTCGCGG 62.681 63.158 6.13 0.00 0.00 6.46
41 42 4.760047 GTGGTGGATGTCGCGGCT 62.760 66.667 13.81 0.00 0.00 5.52
42 43 4.451150 TGGTGGATGTCGCGGCTC 62.451 66.667 13.81 6.96 0.00 4.70
44 45 4.796231 GTGGATGTCGCGGCTCGT 62.796 66.667 13.81 1.44 39.67 4.18
45 46 4.063967 TGGATGTCGCGGCTCGTT 62.064 61.111 13.81 0.00 39.67 3.85
46 47 3.255379 GGATGTCGCGGCTCGTTC 61.255 66.667 13.81 3.55 39.67 3.95
47 48 3.255379 GATGTCGCGGCTCGTTCC 61.255 66.667 13.81 0.00 39.67 3.62
48 49 3.982372 GATGTCGCGGCTCGTTCCA 62.982 63.158 13.81 0.00 39.67 3.53
49 50 3.989698 ATGTCGCGGCTCGTTCCAG 62.990 63.158 13.81 0.00 39.67 3.86
52 53 4.514577 CGCGGCTCGTTCCAGGAT 62.515 66.667 0.00 0.00 0.00 3.24
53 54 2.892425 GCGGCTCGTTCCAGGATG 60.892 66.667 0.00 0.00 0.00 3.51
73 74 3.905784 TGGATTCATCATCGATCTGACG 58.094 45.455 0.00 0.00 31.73 4.35
74 75 3.319122 TGGATTCATCATCGATCTGACGT 59.681 43.478 0.00 0.00 31.73 4.34
75 76 3.917380 GGATTCATCATCGATCTGACGTC 59.083 47.826 9.11 9.11 31.73 4.34
76 77 3.355626 TTCATCATCGATCTGACGTCC 57.644 47.619 14.12 0.00 34.70 4.79
77 78 2.297701 TCATCATCGATCTGACGTCCA 58.702 47.619 14.12 0.00 34.70 4.02
78 79 2.033424 TCATCATCGATCTGACGTCCAC 59.967 50.000 14.12 0.85 34.70 4.02
79 80 0.738975 TCATCGATCTGACGTCCACC 59.261 55.000 14.12 0.00 34.70 4.61
80 81 0.592500 CATCGATCTGACGTCCACCG 60.593 60.000 14.12 11.28 44.03 4.94
81 82 1.725557 ATCGATCTGACGTCCACCGG 61.726 60.000 14.12 0.00 42.24 5.28
113 114 4.760047 CGGGCACTGACGGGGAAG 62.760 72.222 0.00 0.00 36.31 3.46
114 115 3.319198 GGGCACTGACGGGGAAGA 61.319 66.667 0.00 0.00 0.00 2.87
115 116 2.266055 GGCACTGACGGGGAAGAG 59.734 66.667 0.00 0.00 0.00 2.85
116 117 2.584391 GGCACTGACGGGGAAGAGT 61.584 63.158 0.00 0.00 0.00 3.24
117 118 1.255667 GGCACTGACGGGGAAGAGTA 61.256 60.000 0.00 0.00 0.00 2.59
118 119 0.173708 GCACTGACGGGGAAGAGTAG 59.826 60.000 0.00 0.00 0.00 2.57
119 120 1.546961 CACTGACGGGGAAGAGTAGT 58.453 55.000 0.00 0.00 0.00 2.73
120 121 1.202582 CACTGACGGGGAAGAGTAGTG 59.797 57.143 0.00 0.00 0.00 2.74
121 122 0.173708 CTGACGGGGAAGAGTAGTGC 59.826 60.000 0.00 0.00 0.00 4.40
122 123 0.541063 TGACGGGGAAGAGTAGTGCA 60.541 55.000 0.00 0.00 0.00 4.57
123 124 0.824759 GACGGGGAAGAGTAGTGCAT 59.175 55.000 0.00 0.00 0.00 3.96
124 125 0.537188 ACGGGGAAGAGTAGTGCATG 59.463 55.000 0.00 0.00 0.00 4.06
125 126 0.179073 CGGGGAAGAGTAGTGCATGG 60.179 60.000 0.00 0.00 0.00 3.66
126 127 0.181350 GGGGAAGAGTAGTGCATGGG 59.819 60.000 0.00 0.00 0.00 4.00
127 128 1.204146 GGGAAGAGTAGTGCATGGGA 58.796 55.000 0.00 0.00 0.00 4.37
128 129 1.771255 GGGAAGAGTAGTGCATGGGAT 59.229 52.381 0.00 0.00 0.00 3.85
129 130 2.972713 GGGAAGAGTAGTGCATGGGATA 59.027 50.000 0.00 0.00 0.00 2.59
130 131 3.244249 GGGAAGAGTAGTGCATGGGATAC 60.244 52.174 0.00 0.00 0.00 2.24
131 132 3.553096 GGAAGAGTAGTGCATGGGATACG 60.553 52.174 0.00 0.00 37.60 3.06
132 133 1.964223 AGAGTAGTGCATGGGATACGG 59.036 52.381 0.00 0.00 37.60 4.02
133 134 0.393077 AGTAGTGCATGGGATACGGC 59.607 55.000 0.00 0.00 37.60 5.68
134 135 0.944311 GTAGTGCATGGGATACGGCG 60.944 60.000 4.80 4.80 37.60 6.46
135 136 2.094757 TAGTGCATGGGATACGGCGG 62.095 60.000 13.24 0.00 37.60 6.13
136 137 4.927782 TGCATGGGATACGGCGGC 62.928 66.667 13.24 0.00 37.60 6.53
151 152 4.814294 GGCGCCTGGAGTACCGTG 62.814 72.222 22.15 0.00 39.42 4.94
152 153 3.755628 GCGCCTGGAGTACCGTGA 61.756 66.667 0.00 0.00 39.42 4.35
153 154 2.490217 CGCCTGGAGTACCGTGAG 59.510 66.667 0.00 0.00 39.42 3.51
154 155 2.184579 GCCTGGAGTACCGTGAGC 59.815 66.667 0.00 0.00 39.42 4.26
155 156 2.352032 GCCTGGAGTACCGTGAGCT 61.352 63.158 0.00 0.00 39.42 4.09
156 157 1.513158 CCTGGAGTACCGTGAGCTG 59.487 63.158 0.00 0.00 39.42 4.24
157 158 1.513158 CTGGAGTACCGTGAGCTGG 59.487 63.158 0.00 0.00 39.42 4.85
158 159 2.184579 GGAGTACCGTGAGCTGGC 59.815 66.667 0.00 0.00 0.00 4.85
159 160 2.352032 GGAGTACCGTGAGCTGGCT 61.352 63.158 0.00 0.00 0.00 4.75
160 161 1.139947 GAGTACCGTGAGCTGGCTC 59.860 63.158 14.86 14.86 43.01 4.70
161 162 2.202623 GTACCGTGAGCTGGCTCG 60.203 66.667 16.33 7.29 45.48 5.03
162 163 2.675423 TACCGTGAGCTGGCTCGT 60.675 61.111 16.33 11.20 45.48 4.18
163 164 2.989881 TACCGTGAGCTGGCTCGTG 61.990 63.158 16.33 11.28 45.48 4.35
164 165 4.363990 CCGTGAGCTGGCTCGTGT 62.364 66.667 16.33 0.00 45.48 4.49
165 166 2.807045 CGTGAGCTGGCTCGTGTC 60.807 66.667 16.33 7.25 45.48 3.67
166 167 2.433318 GTGAGCTGGCTCGTGTCC 60.433 66.667 16.33 0.58 45.48 4.02
167 168 3.695606 TGAGCTGGCTCGTGTCCC 61.696 66.667 16.33 0.00 45.48 4.46
168 169 3.695606 GAGCTGGCTCGTGTCCCA 61.696 66.667 6.84 0.00 33.06 4.37
169 170 3.005539 AGCTGGCTCGTGTCCCAT 61.006 61.111 0.00 0.00 0.00 4.00
170 171 2.821366 GCTGGCTCGTGTCCCATG 60.821 66.667 0.00 0.00 0.00 3.66
171 172 2.821366 CTGGCTCGTGTCCCATGC 60.821 66.667 0.00 0.00 0.00 4.06
172 173 4.408821 TGGCTCGTGTCCCATGCC 62.409 66.667 0.00 0.00 43.49 4.40
174 175 4.101448 GCTCGTGTCCCATGCCCT 62.101 66.667 0.00 0.00 0.00 5.19
175 176 2.731571 GCTCGTGTCCCATGCCCTA 61.732 63.158 0.00 0.00 0.00 3.53
176 177 1.144057 CTCGTGTCCCATGCCCTAC 59.856 63.158 0.00 0.00 0.00 3.18
177 178 2.202878 CGTGTCCCATGCCCTACG 60.203 66.667 0.00 0.00 0.00 3.51
178 179 2.987125 GTGTCCCATGCCCTACGT 59.013 61.111 0.00 0.00 0.00 3.57
179 180 1.669049 CGTGTCCCATGCCCTACGTA 61.669 60.000 0.00 0.00 0.00 3.57
180 181 0.179092 GTGTCCCATGCCCTACGTAC 60.179 60.000 0.00 0.00 0.00 3.67
181 182 0.324923 TGTCCCATGCCCTACGTACT 60.325 55.000 0.00 0.00 0.00 2.73
182 183 0.104304 GTCCCATGCCCTACGTACTG 59.896 60.000 0.00 0.00 0.00 2.74
183 184 0.324923 TCCCATGCCCTACGTACTGT 60.325 55.000 0.00 0.00 0.00 3.55
184 185 1.063792 TCCCATGCCCTACGTACTGTA 60.064 52.381 0.00 0.00 0.00 2.74
193 194 3.844577 CTACGTACTGTAGCTTGTGGT 57.155 47.619 10.49 0.00 43.84 4.16
194 195 4.952262 CTACGTACTGTAGCTTGTGGTA 57.048 45.455 10.49 0.00 43.84 3.25
195 196 3.844577 ACGTACTGTAGCTTGTGGTAG 57.155 47.619 0.00 0.00 0.00 3.18
196 197 3.415212 ACGTACTGTAGCTTGTGGTAGA 58.585 45.455 0.00 0.00 0.00 2.59
197 198 3.190118 ACGTACTGTAGCTTGTGGTAGAC 59.810 47.826 0.00 0.00 0.00 2.59
198 199 3.427233 CGTACTGTAGCTTGTGGTAGACC 60.427 52.174 0.00 0.00 0.00 3.85
199 200 1.544691 ACTGTAGCTTGTGGTAGACCG 59.455 52.381 0.00 0.00 39.43 4.79
200 201 1.816835 CTGTAGCTTGTGGTAGACCGA 59.183 52.381 0.00 0.00 39.43 4.69
201 202 2.230508 CTGTAGCTTGTGGTAGACCGAA 59.769 50.000 0.00 0.00 39.43 4.30
202 203 2.029649 TGTAGCTTGTGGTAGACCGAAC 60.030 50.000 0.00 0.00 39.43 3.95
203 204 0.320697 AGCTTGTGGTAGACCGAACC 59.679 55.000 0.00 0.00 39.43 3.62
204 205 0.034337 GCTTGTGGTAGACCGAACCA 59.966 55.000 0.00 0.00 44.75 3.67
208 209 3.993382 TGGTAGACCGAACCAACAC 57.007 52.632 0.00 0.00 43.99 3.32
209 210 1.416243 TGGTAGACCGAACCAACACT 58.584 50.000 0.00 0.00 43.99 3.55
210 211 1.342174 TGGTAGACCGAACCAACACTC 59.658 52.381 0.00 0.00 43.99 3.51
211 212 1.617357 GGTAGACCGAACCAACACTCT 59.383 52.381 0.00 0.00 36.96 3.24
212 213 2.821969 GGTAGACCGAACCAACACTCTA 59.178 50.000 0.00 0.00 36.96 2.43
213 214 3.256631 GGTAGACCGAACCAACACTCTAA 59.743 47.826 0.00 0.00 36.96 2.10
214 215 3.662247 AGACCGAACCAACACTCTAAG 57.338 47.619 0.00 0.00 0.00 2.18
215 216 2.299297 AGACCGAACCAACACTCTAAGG 59.701 50.000 0.00 0.00 0.00 2.69
216 217 1.346722 ACCGAACCAACACTCTAAGGG 59.653 52.381 0.00 0.00 0.00 3.95
217 218 1.338769 CCGAACCAACACTCTAAGGGG 60.339 57.143 0.00 0.00 0.00 4.79
218 219 1.822506 GAACCAACACTCTAAGGGGC 58.177 55.000 0.00 0.00 0.00 5.80
219 220 0.036306 AACCAACACTCTAAGGGGCG 59.964 55.000 0.00 0.00 0.00 6.13
220 221 1.745489 CCAACACTCTAAGGGGCGC 60.745 63.158 0.00 0.00 0.00 6.53
221 222 1.003839 CAACACTCTAAGGGGCGCA 60.004 57.895 10.83 0.00 0.00 6.09
222 223 1.021390 CAACACTCTAAGGGGCGCAG 61.021 60.000 10.83 0.00 0.00 5.18
243 244 4.856801 GCCGCCGGACATGACCAT 62.857 66.667 7.68 0.00 0.00 3.55
244 245 2.896854 CCGCCGGACATGACCATG 60.897 66.667 5.05 8.34 44.15 3.66
245 246 2.896854 CGCCGGACATGACCATGG 60.897 66.667 11.19 11.19 42.91 3.66
246 247 3.211963 GCCGGACATGACCATGGC 61.212 66.667 13.04 15.00 46.06 4.40
250 251 4.131376 GACATGACCATGGCGGAG 57.869 61.111 13.04 2.16 42.91 4.63
305 306 1.007011 CGCTCAAAGATCGCTACGTTG 60.007 52.381 0.00 0.00 0.00 4.10
320 321 6.090223 TCGCTACGTTGCATGTAATAATATGG 59.910 38.462 21.37 0.63 0.00 2.74
321 322 6.090223 CGCTACGTTGCATGTAATAATATGGA 59.910 38.462 21.37 0.00 0.00 3.41
323 324 8.116753 GCTACGTTGCATGTAATAATATGGATC 58.883 37.037 17.16 0.00 0.00 3.36
324 325 7.377766 ACGTTGCATGTAATAATATGGATCC 57.622 36.000 4.20 4.20 0.00 3.36
325 326 6.939730 ACGTTGCATGTAATAATATGGATCCA 59.060 34.615 18.88 18.88 0.00 3.41
352 353 8.909923 AGGTTTTTAATTTAAGGTATCCGGATG 58.090 33.333 27.55 0.00 0.00 3.51
355 356 9.463902 TTTTTAATTTAAGGTATCCGGATGTGA 57.536 29.630 27.55 3.90 0.00 3.58
360 361 4.771114 AAGGTATCCGGATGTGAAATGA 57.229 40.909 27.55 0.46 0.00 2.57
382 383 1.228533 TTTTTAAGACGTGGCCGGTC 58.771 50.000 16.73 16.73 38.78 4.79
391 392 3.845259 TGGCCGGTCACTATCCGC 61.845 66.667 3.51 0.00 45.71 5.54
395 396 2.025727 CGGTCACTATCCGCGGAC 59.974 66.667 33.75 17.55 41.48 4.79
403 426 0.921347 CTATCCGCGGACGTTTGAAG 59.079 55.000 33.75 14.79 37.70 3.02
404 427 0.458889 TATCCGCGGACGTTTGAAGG 60.459 55.000 33.75 0.00 37.70 3.46
416 439 5.688621 GGACGTTTGAAGGGTTAAATTTGTC 59.311 40.000 0.00 0.00 0.00 3.18
425 448 3.570975 GGGTTAAATTTGTCAAGTCCGGT 59.429 43.478 0.00 0.00 0.00 5.28
427 450 5.241285 GGGTTAAATTTGTCAAGTCCGGTTA 59.759 40.000 0.00 0.00 0.00 2.85
432 455 9.675464 TTAAATTTGTCAAGTCCGGTTATAGAT 57.325 29.630 0.00 0.00 0.00 1.98
661 692 1.024271 TGCCTGTTTTCAGTGCACTC 58.976 50.000 18.64 5.91 45.68 3.51
678 709 2.676839 CACTCTTGCTCCATTACTGCTG 59.323 50.000 0.00 0.00 0.00 4.41
725 756 4.495844 GCTAGCACCGCTAATTACTTTTGG 60.496 45.833 10.63 0.00 40.82 3.28
748 779 0.179032 TCCTTTGCTGTCCTTCGCAA 60.179 50.000 0.00 0.00 43.68 4.85
796 835 1.511850 CACGAAGATGTGGAGCAACA 58.488 50.000 0.00 0.00 36.20 3.33
797 836 1.462283 CACGAAGATGTGGAGCAACAG 59.538 52.381 0.00 0.00 36.20 3.16
798 837 0.445436 CGAAGATGTGGAGCAACAGC 59.555 55.000 0.00 0.00 36.71 4.40
799 838 0.807496 GAAGATGTGGAGCAACAGCC 59.193 55.000 0.00 0.00 37.16 4.85
800 839 0.957395 AAGATGTGGAGCAACAGCCG 60.957 55.000 0.00 0.00 37.16 5.52
803 842 3.357079 GTGGAGCAACAGCCGTGG 61.357 66.667 0.00 0.00 0.00 4.94
805 844 2.743928 GGAGCAACAGCCGTGGAG 60.744 66.667 0.00 0.00 0.00 3.86
806 845 2.031163 GAGCAACAGCCGTGGAGT 59.969 61.111 0.00 0.00 0.00 3.85
809 848 2.111043 CAACAGCCGTGGAGTGGT 59.889 61.111 0.00 0.00 0.00 4.16
810 849 1.961277 CAACAGCCGTGGAGTGGTC 60.961 63.158 0.00 0.00 0.00 4.02
811 850 2.439960 AACAGCCGTGGAGTGGTCA 61.440 57.895 0.00 0.00 0.00 4.02
812 851 2.047844 CAGCCGTGGAGTGGTCAG 60.048 66.667 0.00 0.00 0.00 3.51
815 854 2.574955 GCCGTGGAGTGGTCAGACT 61.575 63.158 0.00 0.00 0.00 3.24
1023 1062 1.747355 CATTGCATCCCACACTCTTCC 59.253 52.381 0.00 0.00 0.00 3.46
1038 1077 1.405463 TCTTCCATCATCTCCGTCGTG 59.595 52.381 0.00 0.00 0.00 4.35
1080 1123 1.945354 GATGGACGAGTCGGGCAAGA 61.945 60.000 18.30 0.00 0.00 3.02
1097 1140 0.523966 AGAAGCAGTCTCCGAACTCG 59.476 55.000 0.00 0.00 39.44 4.18
1109 1152 1.595993 CGAACTCGAGCTCCTCCCAA 61.596 60.000 13.61 0.00 43.02 4.12
1115 1158 0.826715 CGAGCTCCTCCCAATCTCAA 59.173 55.000 8.47 0.00 0.00 3.02
1190 1233 2.270850 GGCACCAAGACCCGCATA 59.729 61.111 0.00 0.00 0.00 3.14
1550 1593 2.512515 GCCAGCGAGATGGACCAC 60.513 66.667 12.01 0.00 43.57 4.16
1622 1665 2.108157 GCGGGCCGATGTGTATGA 59.892 61.111 33.44 0.00 0.00 2.15
1646 1690 1.039856 TAATTAGGGGTCCGTACGGC 58.960 55.000 29.64 22.57 34.68 5.68
1710 1754 1.318158 GGGGTACATGGAGTCGACGT 61.318 60.000 10.46 4.02 0.00 4.34
1901 1945 2.293170 GGATTCTAAGTTGCTCAGGGC 58.707 52.381 0.00 0.00 42.22 5.19
1947 1991 5.491982 TGGAAAAGTCATCTTCTTAGCTCC 58.508 41.667 0.00 0.00 32.90 4.70
1980 2024 3.131046 CCCCTGCCATGAACAGTAAATTC 59.869 47.826 12.83 0.00 33.09 2.17
1985 2029 6.705381 CCTGCCATGAACAGTAAATTCAAAAA 59.295 34.615 12.83 0.00 39.43 1.94
1986 2030 7.388500 CCTGCCATGAACAGTAAATTCAAAAAT 59.612 33.333 12.83 0.00 39.43 1.82
1988 2032 9.770097 TGCCATGAACAGTAAATTCAAAAATAA 57.230 25.926 0.00 0.00 39.43 1.40
2044 2089 4.536065 TGTGCGAAACATTGATGAAAGTC 58.464 39.130 0.00 0.00 32.36 3.01
2064 2109 5.783111 AGTCTTGAGTGTTTGCAAAGTTTT 58.217 33.333 13.26 0.00 0.00 2.43
2147 2193 6.631962 TGAAGTTAACATTTTTGGACCGTTT 58.368 32.000 8.61 0.00 0.00 3.60
2149 2195 8.414778 TGAAGTTAACATTTTTGGACCGTTTAT 58.585 29.630 8.61 0.00 0.00 1.40
2150 2196 9.251792 GAAGTTAACATTTTTGGACCGTTTATT 57.748 29.630 8.61 0.00 0.00 1.40
2210 2256 8.196771 TGATGAAACTTTGCAAGTACTCAAAAT 58.803 29.630 10.08 0.00 41.91 1.82
2355 2404 8.560355 TGATTGAATAGTGGAAAAAGAATCGA 57.440 30.769 0.00 0.00 0.00 3.59
2390 2439 2.510411 CGGGCTCATATGCACCCA 59.490 61.111 24.49 0.00 42.97 4.51
2398 2447 3.346315 CTCATATGCACCCAGTGAACAA 58.654 45.455 0.00 0.00 35.23 2.83
2411 2460 9.410556 CACCCAGTGAACAATAAAATAAGAAAG 57.589 33.333 0.00 0.00 35.23 2.62
2445 2496 0.815734 ATGCAAGATGCTTGAGTGCC 59.184 50.000 11.08 0.00 45.31 5.01
2578 2630 2.175878 TGTCTTCTTTGCTGAGAGCC 57.824 50.000 0.00 0.00 41.51 4.70
2626 2678 1.693083 GGCACGGACTTCACGCATAC 61.693 60.000 0.00 0.00 34.00 2.39
2635 2687 2.196749 CTTCACGCATACGAGCATCTT 58.803 47.619 0.00 0.00 43.93 2.40
2748 2802 5.623596 GCCGCTCCCAACAAATACTATTTTT 60.624 40.000 0.00 0.00 0.00 1.94
2771 2825 1.530323 GCATGGGTTTGTTAGTCGGT 58.470 50.000 0.00 0.00 0.00 4.69
2837 2892 7.801783 GCATTAATCACCTAAAAACGGCTATAC 59.198 37.037 0.00 0.00 0.00 1.47
2838 2893 9.052759 CATTAATCACCTAAAAACGGCTATACT 57.947 33.333 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.403137 CACCACCATGCGGTTGCG 62.403 66.667 2.42 0.00 46.31 4.85
13 14 4.054825 CCACCACCATGCGGTTGC 62.055 66.667 2.42 0.00 46.31 4.17
14 15 1.678635 ATCCACCACCATGCGGTTG 60.679 57.895 2.42 0.50 46.31 3.77
15 16 1.678635 CATCCACCACCATGCGGTT 60.679 57.895 2.42 0.00 46.31 4.44
17 18 2.045045 ACATCCACCACCATGCGG 60.045 61.111 0.00 0.00 38.77 5.69
18 19 2.463620 CGACATCCACCACCATGCG 61.464 63.158 0.00 0.00 0.00 4.73
19 20 2.764314 GCGACATCCACCACCATGC 61.764 63.158 0.00 0.00 0.00 4.06
20 21 2.463620 CGCGACATCCACCACCATG 61.464 63.158 0.00 0.00 0.00 3.66
21 22 2.125147 CGCGACATCCACCACCAT 60.125 61.111 0.00 0.00 0.00 3.55
22 23 4.386951 CCGCGACATCCACCACCA 62.387 66.667 8.23 0.00 0.00 4.17
24 25 4.760047 AGCCGCGACATCCACCAC 62.760 66.667 8.23 0.00 0.00 4.16
25 26 4.451150 GAGCCGCGACATCCACCA 62.451 66.667 8.23 0.00 0.00 4.17
27 28 4.796231 ACGAGCCGCGACATCCAC 62.796 66.667 8.23 0.00 44.57 4.02
28 29 3.982372 GAACGAGCCGCGACATCCA 62.982 63.158 8.23 0.00 44.57 3.41
29 30 3.255379 GAACGAGCCGCGACATCC 61.255 66.667 8.23 0.00 44.57 3.51
30 31 3.255379 GGAACGAGCCGCGACATC 61.255 66.667 8.23 0.69 44.57 3.06
31 32 3.989698 CTGGAACGAGCCGCGACAT 62.990 63.158 8.23 0.00 44.57 3.06
32 33 4.717629 CTGGAACGAGCCGCGACA 62.718 66.667 8.23 0.00 44.57 4.35
36 37 2.892425 CATCCTGGAACGAGCCGC 60.892 66.667 0.00 0.00 0.00 6.53
37 38 2.202932 CCATCCTGGAACGAGCCG 60.203 66.667 0.00 0.00 40.96 5.52
38 39 3.309582 TCCATCCTGGAACGAGCC 58.690 61.111 0.00 0.00 45.00 4.70
46 47 3.690475 TCGATGATGAATCCATCCTGG 57.310 47.619 0.00 0.00 46.64 4.45
47 48 4.870991 CAGATCGATGATGAATCCATCCTG 59.129 45.833 0.54 0.00 46.64 3.86
48 49 4.776308 TCAGATCGATGATGAATCCATCCT 59.224 41.667 0.54 0.00 46.64 3.24
49 50 4.869297 GTCAGATCGATGATGAATCCATCC 59.131 45.833 0.54 0.00 46.64 3.51
50 51 5.849222 ACGTCAGATCGATGATGAATCCATC 60.849 44.000 13.79 0.00 38.28 3.51
51 52 4.021632 ACGTCAGATCGATGATGAATCCAT 60.022 41.667 13.79 0.00 38.28 3.41
52 53 3.319122 ACGTCAGATCGATGATGAATCCA 59.681 43.478 13.79 0.00 38.28 3.41
53 54 3.906998 ACGTCAGATCGATGATGAATCC 58.093 45.455 13.79 2.04 38.28 3.01
54 55 3.917380 GGACGTCAGATCGATGATGAATC 59.083 47.826 18.91 12.21 38.28 2.52
55 56 3.319122 TGGACGTCAGATCGATGATGAAT 59.681 43.478 18.91 5.42 38.28 2.57
56 57 2.687935 TGGACGTCAGATCGATGATGAA 59.312 45.455 18.91 0.00 38.28 2.57
57 58 2.033424 GTGGACGTCAGATCGATGATGA 59.967 50.000 18.91 9.90 38.28 2.92
58 59 2.389059 GTGGACGTCAGATCGATGATG 58.611 52.381 18.91 4.48 41.18 3.07
59 60 1.338337 GGTGGACGTCAGATCGATGAT 59.662 52.381 18.91 0.00 34.46 2.45
60 61 0.738975 GGTGGACGTCAGATCGATGA 59.261 55.000 18.91 0.00 34.46 2.92
61 62 0.592500 CGGTGGACGTCAGATCGATG 60.593 60.000 18.91 0.00 37.93 3.84
62 63 1.725557 CCGGTGGACGTCAGATCGAT 61.726 60.000 18.91 0.00 42.24 3.59
63 64 2.404186 CCGGTGGACGTCAGATCGA 61.404 63.158 18.91 0.00 42.24 3.59
64 65 2.102357 CCGGTGGACGTCAGATCG 59.898 66.667 18.91 14.64 42.24 3.69
65 66 2.202756 GCCGGTGGACGTCAGATC 60.203 66.667 18.91 2.22 42.24 2.75
66 67 2.994995 TGCCGGTGGACGTCAGAT 60.995 61.111 18.91 0.00 42.24 2.90
67 68 3.986006 GTGCCGGTGGACGTCAGA 61.986 66.667 18.91 0.00 42.24 3.27
86 87 4.636435 AGTGCCCGGAACCCGTTG 62.636 66.667 0.73 0.00 46.80 4.10
87 88 4.636435 CAGTGCCCGGAACCCGTT 62.636 66.667 0.73 0.00 46.80 4.44
96 97 4.760047 CTTCCCCGTCAGTGCCCG 62.760 72.222 0.00 0.00 0.00 6.13
97 98 3.316573 CTCTTCCCCGTCAGTGCCC 62.317 68.421 0.00 0.00 0.00 5.36
98 99 1.255667 TACTCTTCCCCGTCAGTGCC 61.256 60.000 0.00 0.00 0.00 5.01
99 100 0.173708 CTACTCTTCCCCGTCAGTGC 59.826 60.000 0.00 0.00 0.00 4.40
100 101 1.202582 CACTACTCTTCCCCGTCAGTG 59.797 57.143 0.00 0.00 0.00 3.66
101 102 1.546961 CACTACTCTTCCCCGTCAGT 58.453 55.000 0.00 0.00 0.00 3.41
102 103 0.173708 GCACTACTCTTCCCCGTCAG 59.826 60.000 0.00 0.00 0.00 3.51
103 104 0.541063 TGCACTACTCTTCCCCGTCA 60.541 55.000 0.00 0.00 0.00 4.35
104 105 0.824759 ATGCACTACTCTTCCCCGTC 59.175 55.000 0.00 0.00 0.00 4.79
105 106 0.537188 CATGCACTACTCTTCCCCGT 59.463 55.000 0.00 0.00 0.00 5.28
106 107 0.179073 CCATGCACTACTCTTCCCCG 60.179 60.000 0.00 0.00 0.00 5.73
107 108 0.181350 CCCATGCACTACTCTTCCCC 59.819 60.000 0.00 0.00 0.00 4.81
108 109 1.204146 TCCCATGCACTACTCTTCCC 58.796 55.000 0.00 0.00 0.00 3.97
109 110 3.553096 CGTATCCCATGCACTACTCTTCC 60.553 52.174 0.00 0.00 0.00 3.46
110 111 3.553096 CCGTATCCCATGCACTACTCTTC 60.553 52.174 0.00 0.00 0.00 2.87
111 112 2.365617 CCGTATCCCATGCACTACTCTT 59.634 50.000 0.00 0.00 0.00 2.85
112 113 1.964223 CCGTATCCCATGCACTACTCT 59.036 52.381 0.00 0.00 0.00 3.24
113 114 1.605712 GCCGTATCCCATGCACTACTC 60.606 57.143 0.00 0.00 0.00 2.59
114 115 0.393077 GCCGTATCCCATGCACTACT 59.607 55.000 0.00 0.00 0.00 2.57
115 116 0.944311 CGCCGTATCCCATGCACTAC 60.944 60.000 0.00 0.00 0.00 2.73
116 117 1.365999 CGCCGTATCCCATGCACTA 59.634 57.895 0.00 0.00 0.00 2.74
117 118 2.108976 CGCCGTATCCCATGCACT 59.891 61.111 0.00 0.00 0.00 4.40
118 119 2.972505 CCGCCGTATCCCATGCAC 60.973 66.667 0.00 0.00 0.00 4.57
119 120 4.927782 GCCGCCGTATCCCATGCA 62.928 66.667 0.00 0.00 0.00 3.96
134 135 4.814294 CACGGTACTCCAGGCGCC 62.814 72.222 21.89 21.89 0.00 6.53
135 136 3.701604 CTCACGGTACTCCAGGCGC 62.702 68.421 0.00 0.00 0.00 6.53
136 137 2.490217 CTCACGGTACTCCAGGCG 59.510 66.667 0.00 0.00 0.00 5.52
137 138 2.184579 GCTCACGGTACTCCAGGC 59.815 66.667 0.00 0.00 0.00 4.85
138 139 1.513158 CAGCTCACGGTACTCCAGG 59.487 63.158 0.00 0.00 0.00 4.45
139 140 1.513158 CCAGCTCACGGTACTCCAG 59.487 63.158 0.00 0.00 0.00 3.86
140 141 2.646175 GCCAGCTCACGGTACTCCA 61.646 63.158 0.00 0.00 0.00 3.86
141 142 2.184579 GCCAGCTCACGGTACTCC 59.815 66.667 0.00 0.00 0.00 3.85
142 143 1.139947 GAGCCAGCTCACGGTACTC 59.860 63.158 14.70 0.00 42.31 2.59
143 144 2.701780 CGAGCCAGCTCACGGTACT 61.702 63.158 19.08 0.00 42.86 2.73
144 145 2.202623 CGAGCCAGCTCACGGTAC 60.203 66.667 19.08 0.00 42.86 3.34
145 146 2.675423 ACGAGCCAGCTCACGGTA 60.675 61.111 19.08 0.00 42.86 4.02
146 147 4.363990 CACGAGCCAGCTCACGGT 62.364 66.667 19.08 6.65 42.86 4.83
147 148 4.363990 ACACGAGCCAGCTCACGG 62.364 66.667 19.08 9.92 42.86 4.94
148 149 2.807045 GACACGAGCCAGCTCACG 60.807 66.667 19.08 11.33 42.86 4.35
149 150 2.433318 GGACACGAGCCAGCTCAC 60.433 66.667 19.08 7.35 42.86 3.51
150 151 3.695606 GGGACACGAGCCAGCTCA 61.696 66.667 19.08 0.00 42.86 4.26
151 152 3.695606 TGGGACACGAGCCAGCTC 61.696 66.667 9.67 9.67 39.55 4.09
163 164 0.104304 CAGTACGTAGGGCATGGGAC 59.896 60.000 0.00 0.00 0.00 4.46
164 165 0.324923 ACAGTACGTAGGGCATGGGA 60.325 55.000 0.00 0.00 0.00 4.37
165 166 1.340248 CTACAGTACGTAGGGCATGGG 59.660 57.143 13.66 0.00 43.46 4.00
166 167 1.269621 GCTACAGTACGTAGGGCATGG 60.270 57.143 19.44 2.36 46.69 3.66
167 168 1.681793 AGCTACAGTACGTAGGGCATG 59.318 52.381 19.44 0.00 46.69 4.06
168 169 2.068834 AGCTACAGTACGTAGGGCAT 57.931 50.000 19.44 0.00 46.69 4.40
169 170 1.475280 CAAGCTACAGTACGTAGGGCA 59.525 52.381 19.44 0.00 46.69 5.36
170 171 1.475682 ACAAGCTACAGTACGTAGGGC 59.524 52.381 19.44 11.37 46.69 5.19
171 172 2.159282 CCACAAGCTACAGTACGTAGGG 60.159 54.545 19.44 11.71 46.69 3.53
172 173 2.490903 ACCACAAGCTACAGTACGTAGG 59.509 50.000 19.44 10.05 46.69 3.18
173 174 8.316956 GGTCTACCACAAGCTACAGTACGTAG 62.317 50.000 15.91 15.91 42.28 3.51
174 175 4.393062 GTCTACCACAAGCTACAGTACGTA 59.607 45.833 0.00 0.00 0.00 3.57
175 176 3.190118 GTCTACCACAAGCTACAGTACGT 59.810 47.826 0.00 0.00 0.00 3.57
176 177 3.427233 GGTCTACCACAAGCTACAGTACG 60.427 52.174 0.00 0.00 35.64 3.67
177 178 3.427233 CGGTCTACCACAAGCTACAGTAC 60.427 52.174 0.00 0.00 35.14 2.73
178 179 2.751259 CGGTCTACCACAAGCTACAGTA 59.249 50.000 0.00 0.00 35.14 2.74
179 180 1.544691 CGGTCTACCACAAGCTACAGT 59.455 52.381 0.00 0.00 35.14 3.55
180 181 1.816835 TCGGTCTACCACAAGCTACAG 59.183 52.381 0.00 0.00 35.14 2.74
181 182 1.913778 TCGGTCTACCACAAGCTACA 58.086 50.000 0.00 0.00 35.14 2.74
182 183 2.603953 GTTCGGTCTACCACAAGCTAC 58.396 52.381 0.00 0.00 35.14 3.58
183 184 1.547372 GGTTCGGTCTACCACAAGCTA 59.453 52.381 0.00 0.00 35.67 3.32
184 185 0.320697 GGTTCGGTCTACCACAAGCT 59.679 55.000 0.00 0.00 35.67 3.74
185 186 0.034337 TGGTTCGGTCTACCACAAGC 59.966 55.000 0.00 2.06 40.65 4.01
186 187 2.140717 GTTGGTTCGGTCTACCACAAG 58.859 52.381 0.00 0.00 45.00 3.16
187 188 1.485480 TGTTGGTTCGGTCTACCACAA 59.515 47.619 0.00 0.00 45.00 3.33
188 189 1.121378 TGTTGGTTCGGTCTACCACA 58.879 50.000 0.00 0.00 45.00 4.17
189 190 1.069668 AGTGTTGGTTCGGTCTACCAC 59.930 52.381 0.00 0.00 45.00 4.16
190 191 1.342174 GAGTGTTGGTTCGGTCTACCA 59.658 52.381 0.00 0.00 43.71 3.25
191 192 1.617357 AGAGTGTTGGTTCGGTCTACC 59.383 52.381 0.00 0.00 36.17 3.18
192 193 4.483311 CTTAGAGTGTTGGTTCGGTCTAC 58.517 47.826 0.00 0.00 0.00 2.59
193 194 3.508793 CCTTAGAGTGTTGGTTCGGTCTA 59.491 47.826 0.00 0.00 0.00 2.59
194 195 2.299297 CCTTAGAGTGTTGGTTCGGTCT 59.701 50.000 0.00 0.00 0.00 3.85
195 196 2.612221 CCCTTAGAGTGTTGGTTCGGTC 60.612 54.545 0.00 0.00 0.00 4.79
196 197 1.346722 CCCTTAGAGTGTTGGTTCGGT 59.653 52.381 0.00 0.00 0.00 4.69
197 198 1.338769 CCCCTTAGAGTGTTGGTTCGG 60.339 57.143 0.00 0.00 0.00 4.30
198 199 1.944430 GCCCCTTAGAGTGTTGGTTCG 60.944 57.143 0.00 0.00 0.00 3.95
199 200 1.822506 GCCCCTTAGAGTGTTGGTTC 58.177 55.000 0.00 0.00 0.00 3.62
200 201 0.036306 CGCCCCTTAGAGTGTTGGTT 59.964 55.000 0.00 0.00 0.00 3.67
201 202 1.677552 CGCCCCTTAGAGTGTTGGT 59.322 57.895 0.00 0.00 0.00 3.67
202 203 1.745489 GCGCCCCTTAGAGTGTTGG 60.745 63.158 0.00 0.00 0.00 3.77
203 204 1.003839 TGCGCCCCTTAGAGTGTTG 60.004 57.895 4.18 0.00 0.00 3.33
204 205 1.296715 CTGCGCCCCTTAGAGTGTT 59.703 57.895 4.18 0.00 0.00 3.32
205 206 2.982130 CTGCGCCCCTTAGAGTGT 59.018 61.111 4.18 0.00 0.00 3.55
206 207 2.512515 GCTGCGCCCCTTAGAGTG 60.513 66.667 4.18 0.00 0.00 3.51
207 208 3.787001 GGCTGCGCCCCTTAGAGT 61.787 66.667 4.18 0.00 44.06 3.24
226 227 4.856801 ATGGTCATGTCCGGCGGC 62.857 66.667 23.83 17.23 0.00 6.53
227 228 2.896854 CATGGTCATGTCCGGCGG 60.897 66.667 22.51 22.51 34.23 6.13
228 229 2.896854 CCATGGTCATGTCCGGCG 60.897 66.667 2.57 0.00 37.11 6.46
229 230 3.211963 GCCATGGTCATGTCCGGC 61.212 66.667 14.67 11.01 37.11 6.13
230 231 2.896854 CGCCATGGTCATGTCCGG 60.897 66.667 14.67 0.00 37.11 5.14
231 232 2.896854 CCGCCATGGTCATGTCCG 60.897 66.667 14.67 6.14 37.11 4.79
232 233 1.524621 CTCCGCCATGGTCATGTCC 60.525 63.158 14.67 1.55 39.52 4.02
233 234 2.182842 GCTCCGCCATGGTCATGTC 61.183 63.158 14.67 0.00 39.52 3.06
234 235 2.124570 GCTCCGCCATGGTCATGT 60.125 61.111 14.67 0.00 39.52 3.21
235 236 2.124612 TGCTCCGCCATGGTCATG 60.125 61.111 14.67 4.09 39.52 3.07
236 237 2.191375 CTGCTCCGCCATGGTCAT 59.809 61.111 14.67 0.00 39.52 3.06
237 238 4.100084 CCTGCTCCGCCATGGTCA 62.100 66.667 14.67 3.38 39.52 4.02
238 239 3.785859 TCCTGCTCCGCCATGGTC 61.786 66.667 14.67 4.79 39.52 4.02
239 240 4.101448 GTCCTGCTCCGCCATGGT 62.101 66.667 14.67 0.00 39.52 3.55
241 242 4.147449 TCGTCCTGCTCCGCCATG 62.147 66.667 0.00 0.00 0.00 3.66
242 243 3.842923 CTCGTCCTGCTCCGCCAT 61.843 66.667 0.00 0.00 0.00 4.40
267 268 2.664436 GGAGTTTCGTCCGGTTGCG 61.664 63.158 0.00 5.36 0.00 4.85
268 269 3.250986 GGAGTTTCGTCCGGTTGC 58.749 61.111 0.00 0.00 0.00 4.17
275 276 1.779569 TCTTTGAGCGGAGTTTCGTC 58.220 50.000 0.00 0.00 0.00 4.20
278 279 1.061276 GCGATCTTTGAGCGGAGTTTC 59.939 52.381 7.31 0.00 41.94 2.78
305 306 7.944729 ACCTTGGATCCATATTATTACATGC 57.055 36.000 17.06 0.00 0.00 4.06
323 324 7.977293 CCGGATACCTTAAATTAAAAACCTTGG 59.023 37.037 0.00 0.00 0.00 3.61
324 325 8.741841 TCCGGATACCTTAAATTAAAAACCTTG 58.258 33.333 0.00 0.00 0.00 3.61
325 326 8.882557 TCCGGATACCTTAAATTAAAAACCTT 57.117 30.769 0.00 0.00 0.00 3.50
332 333 9.635404 ATTTCACATCCGGATACCTTAAATTAA 57.365 29.630 18.63 1.50 0.00 1.40
338 339 5.880164 TCATTTCACATCCGGATACCTTA 57.120 39.130 18.63 3.32 0.00 2.69
372 373 2.106332 GGATAGTGACCGGCCACG 59.894 66.667 15.67 0.00 41.67 4.94
382 383 0.457166 TCAAACGTCCGCGGATAGTG 60.457 55.000 33.58 24.81 43.45 2.74
391 392 4.492791 AATTTAACCCTTCAAACGTCCG 57.507 40.909 0.00 0.00 0.00 4.79
395 396 6.754675 ACTTGACAAATTTAACCCTTCAAACG 59.245 34.615 0.00 0.00 0.00 3.60
403 426 3.570975 ACCGGACTTGACAAATTTAACCC 59.429 43.478 9.46 0.00 0.00 4.11
404 427 4.841443 ACCGGACTTGACAAATTTAACC 57.159 40.909 9.46 0.00 0.00 2.85
432 455 0.531974 AAAAGAACCGCGTGAGAGCA 60.532 50.000 4.92 0.00 36.85 4.26
661 692 1.741706 CACCAGCAGTAATGGAGCAAG 59.258 52.381 0.00 0.00 40.51 4.01
678 709 1.811679 GCTCGCTAGCCTTGTCACC 60.812 63.158 9.66 0.00 43.40 4.02
725 756 1.239347 GAAGGACAGCAAAGGACACC 58.761 55.000 0.00 0.00 0.00 4.16
748 779 1.599071 GTACATGCATGCATACGCTGT 59.401 47.619 31.73 26.89 39.64 4.40
752 783 2.097250 CGAGTGTACATGCATGCATACG 60.097 50.000 31.73 22.52 34.91 3.06
792 831 1.961277 GACCACTCCACGGCTGTTG 60.961 63.158 0.00 0.00 0.00 3.33
793 832 2.383245 CTGACCACTCCACGGCTGTT 62.383 60.000 0.00 0.00 0.00 3.16
794 833 2.842462 TGACCACTCCACGGCTGT 60.842 61.111 0.00 0.00 0.00 4.40
795 834 2.047844 CTGACCACTCCACGGCTG 60.048 66.667 0.00 0.00 0.00 4.85
796 835 2.203640 TCTGACCACTCCACGGCT 60.204 61.111 0.00 0.00 0.00 5.52
797 836 2.048127 GTCTGACCACTCCACGGC 60.048 66.667 0.00 0.00 0.00 5.68
798 837 1.587054 GAGTCTGACCACTCCACGG 59.413 63.158 3.76 0.00 37.43 4.94
799 838 1.210413 CGAGTCTGACCACTCCACG 59.790 63.158 3.76 0.00 39.90 4.94
800 839 1.133407 GATCGAGTCTGACCACTCCAC 59.867 57.143 3.76 0.00 39.90 4.02
803 842 1.464734 TGGATCGAGTCTGACCACTC 58.535 55.000 3.76 0.00 39.68 3.51
805 844 2.500509 GATGGATCGAGTCTGACCAC 57.499 55.000 3.76 0.00 33.38 4.16
1023 1062 1.550065 GTGTCACGACGGAGATGATG 58.450 55.000 0.00 0.00 0.00 3.07
1038 1077 1.282875 GCTTCTTGCCCAACGTGTC 59.717 57.895 0.00 0.00 35.15 3.67
1080 1123 0.523966 CTCGAGTTCGGAGACTGCTT 59.476 55.000 3.62 0.00 40.29 3.91
1088 1131 1.749638 GGAGGAGCTCGAGTTCGGA 60.750 63.158 21.04 0.00 40.29 4.55
1091 1134 0.827368 ATTGGGAGGAGCTCGAGTTC 59.173 55.000 19.92 19.92 0.00 3.01
1097 1140 3.389329 TGTATTGAGATTGGGAGGAGCTC 59.611 47.826 4.71 4.71 0.00 4.09
1109 1152 1.414181 CTCACGCCCCTGTATTGAGAT 59.586 52.381 0.00 0.00 36.58 2.75
1115 1158 0.325296 TCTTCCTCACGCCCCTGTAT 60.325 55.000 0.00 0.00 0.00 2.29
1463 1506 1.592669 CCATAGCTTGGGCGAGTCG 60.593 63.158 8.54 8.54 42.33 4.18
1474 1517 3.476386 CCATCTCGGCCCATAGCT 58.524 61.111 0.00 0.00 43.05 3.32
1622 1665 1.571955 ACGGACCCCTAATTAACGGT 58.428 50.000 3.34 3.34 0.00 4.83
1646 1690 0.603707 ACTGAGGTCAATGGCACGTG 60.604 55.000 12.28 12.28 0.00 4.49
1757 1801 2.280119 ACACTCGCGCACACACAT 60.280 55.556 8.75 0.00 0.00 3.21
1758 1802 3.261216 CACACTCGCGCACACACA 61.261 61.111 8.75 0.00 0.00 3.72
1901 1945 7.500227 TCCATAAATAAGCTCAAAGGATCACTG 59.500 37.037 0.00 0.00 0.00 3.66
1947 1991 3.138798 GCAGGGGCATGTGAGCTG 61.139 66.667 0.00 0.00 40.72 4.24
2027 2072 7.420800 ACACTCAAGACTTTCATCAATGTTTC 58.579 34.615 0.00 0.00 0.00 2.78
2044 2089 8.323140 CAGAATAAAACTTTGCAAACACTCAAG 58.677 33.333 8.05 0.00 0.00 3.02
2158 2204 2.519377 AACATTCGTGGAAGTCGTGA 57.481 45.000 0.00 0.00 0.00 4.35
2210 2256 9.716531 TTTTTGTGTGGCAAATATTGATGAATA 57.283 25.926 0.00 0.00 45.38 1.75
2462 2513 8.722480 TCTTCGAATGTCATTTAGTCATGAAT 57.278 30.769 0.00 0.00 34.89 2.57
2578 2630 3.303990 CGTGGAGTTTGGACATTTCAGTG 60.304 47.826 0.00 0.00 0.00 3.66
2626 2678 2.905959 TTTGTGATGCAAGATGCTCG 57.094 45.000 3.78 0.00 45.31 5.03
2672 2725 5.333492 CGCGGGCGAATAGTAAAATCATTAA 60.333 40.000 7.38 0.00 42.83 1.40
2673 2726 4.150980 CGCGGGCGAATAGTAAAATCATTA 59.849 41.667 7.38 0.00 42.83 1.90
2748 2802 2.224549 CGACTAACAAACCCATGCGAAA 59.775 45.455 0.00 0.00 0.00 3.46
2771 2825 3.809279 CCGCATTATCTACATGCAGTGAA 59.191 43.478 5.78 0.00 46.36 3.18
2823 2877 2.799207 CGCCCGAGTATAGCCGTTTTTA 60.799 50.000 0.00 0.00 0.00 1.52
2837 2892 4.696899 TTGATATATCAGTACGCCCGAG 57.303 45.455 14.86 0.00 38.19 4.63
2838 2893 4.461431 ACATTGATATATCAGTACGCCCGA 59.539 41.667 14.86 0.00 38.19 5.14


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

AutoCloner maintained by Alex Coulton.