Multiple sequence alignment - TraesCS4D01G017100

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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 TraesCS4D01G017100 chr4D 100.000 2876 0 0 1 2876 7654023 7656898 0.000000e+00 5312.0
1 TraesCS4D01G017100 chr4D 95.745 799 26 7 2086 2876 43735788 43736586 0.000000e+00 1280.0
2 TraesCS4D01G017100 chr4D 95.939 394 14 1 5 396 7705676 7706069 3.130000e-179 638.0
3 TraesCS4D01G017100 chr6D 95.012 1303 45 3 801 2083 142990289 142988987 0.000000e+00 2028.0
4 TraesCS4D01G017100 chr6D 91.260 389 32 2 396 784 143070003 143069617 1.960000e-146 529.0
5 TraesCS4D01G017100 chr6D 89.461 408 36 6 396 801 143071262 143070860 2.560000e-140 508.0
6 TraesCS4D01G017100 chr6D 74.848 823 168 30 1111 1910 143092300 143091494 1.280000e-88 337.0
7 TraesCS4D01G017100 chr6B 92.576 1320 60 8 793 2086 248512025 248510718 0.000000e+00 1860.0
8 TraesCS4D01G017100 chr6B 92.298 805 42 3 1302 2086 249449107 249448303 0.000000e+00 1125.0
9 TraesCS4D01G017100 chr6B 87.123 730 49 8 1013 1724 249386425 249385723 0.000000e+00 785.0
10 TraesCS4D01G017100 chr6B 92.582 337 25 0 788 1124 249449505 249449169 4.310000e-133 484.0
11 TraesCS4D01G017100 chr6B 74.939 822 171 25 1103 1914 255211361 255210565 7.630000e-91 344.0
12 TraesCS4D01G017100 chr6B 91.447 152 12 1 813 964 249386576 249386426 1.040000e-49 207.0
13 TraesCS4D01G017100 chr6B 79.227 207 25 14 187 387 558786131 558786325 8.360000e-26 128.0
14 TraesCS4D01G017100 chr6B 78.744 207 26 14 187 387 558703321 558703515 3.890000e-24 122.0
15 TraesCS4D01G017100 chr6B 91.139 79 7 0 309 387 558869010 558869088 1.090000e-19 108.0
16 TraesCS4D01G017100 chr6A 95.322 1133 31 4 969 2081 188001259 188000129 0.000000e+00 1779.0
17 TraesCS4D01G017100 chr6A 91.400 407 28 7 396 800 188242719 188242318 4.190000e-153 551.0
18 TraesCS4D01G017100 chr6A 75.150 833 172 23 1103 1914 205114750 205115568 2.720000e-95 359.0
19 TraesCS4D01G017100 chr6A 88.976 127 11 3 676 801 188241572 188241448 1.380000e-33 154.0
20 TraesCS4D01G017100 chr7D 95.990 798 24 7 2086 2876 108439898 108440694 0.000000e+00 1290.0
21 TraesCS4D01G017100 chr7D 95.859 797 24 8 2087 2876 194651434 194652228 0.000000e+00 1280.0
22 TraesCS4D01G017100 chr7D 83.333 186 16 8 1 180 6805943 6805767 1.070000e-34 158.0
23 TraesCS4D01G017100 chr7D 94.737 57 3 0 187 243 572576689 572576633 3.950000e-14 89.8
24 TraesCS4D01G017100 chr2D 95.990 798 25 6 2086 2876 160362077 160362874 0.000000e+00 1290.0
25 TraesCS4D01G017100 chr2D 95.745 799 26 7 2086 2876 605742560 605743358 0.000000e+00 1280.0
26 TraesCS4D01G017100 chr2D 89.326 178 11 6 1 172 569393837 569393662 1.740000e-52 217.0
27 TraesCS4D01G017100 chr5D 95.870 799 24 8 2086 2876 505299323 505298526 0.000000e+00 1284.0
28 TraesCS4D01G017100 chr5D 95.745 799 26 7 2086 2876 531353820 531353022 0.000000e+00 1280.0
29 TraesCS4D01G017100 chr1D 95.415 807 29 7 2076 2875 255052773 255051968 0.000000e+00 1279.0
30 TraesCS4D01G017100 chr3D 95.511 802 28 7 2080 2873 474708779 474709580 0.000000e+00 1275.0
31 TraesCS4D01G017100 chr3D 83.285 347 44 11 1115 1451 48348771 48349113 1.000000e-79 307.0
32 TraesCS4D01G017100 chr3D 82.849 344 39 14 1121 1451 48252167 48251831 1.010000e-74 291.0
33 TraesCS4D01G017100 chr7B 75.630 833 168 24 1103 1914 682283729 682282911 5.810000e-102 381.0
34 TraesCS4D01G017100 chr7B 87.895 190 15 7 1 183 418044938 418044750 1.740000e-52 217.0
35 TraesCS4D01G017100 chr7B 92.982 57 4 0 186 242 34206307 34206251 1.840000e-12 84.2
36 TraesCS4D01G017100 chr3B 82.789 337 41 14 1127 1451 76115201 76115532 4.690000e-73 285.0
37 TraesCS4D01G017100 chr3B 94.643 56 3 0 187 242 666588710 666588655 1.420000e-13 87.9
38 TraesCS4D01G017100 chr7A 89.785 186 13 4 1 180 543445359 543445174 1.720000e-57 233.0
39 TraesCS4D01G017100 chr4B 89.305 187 11 7 1 180 299556163 299555979 2.880000e-55 226.0
40 TraesCS4D01G017100 chr4B 94.643 56 3 0 187 242 427222544 427222489 1.420000e-13 87.9
41 TraesCS4D01G017100 chr2A 90.000 180 9 6 1 172 594139493 594139315 1.040000e-54 224.0
42 TraesCS4D01G017100 chr2A 80.095 211 27 12 185 390 82215475 82215675 2.990000e-30 143.0
43 TraesCS4D01G017100 chr4A 83.871 186 18 8 1 180 733254293 733254472 1.770000e-37 167.0
44 TraesCS4D01G017100 chr3A 92.982 57 4 0 186 242 208226627 208226571 1.840000e-12 84.2


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 TraesCS4D01G017100 chr4D 7654023 7656898 2875 False 5312.0 5312 100.0000 1 2876 1 chr4D.!!$F1 2875
1 TraesCS4D01G017100 chr4D 43735788 43736586 798 False 1280.0 1280 95.7450 2086 2876 1 chr4D.!!$F3 790
2 TraesCS4D01G017100 chr6D 142988987 142990289 1302 True 2028.0 2028 95.0120 801 2083 1 chr6D.!!$R1 1282
3 TraesCS4D01G017100 chr6D 143069617 143071262 1645 True 518.5 529 90.3605 396 801 2 chr6D.!!$R3 405
4 TraesCS4D01G017100 chr6D 143091494 143092300 806 True 337.0 337 74.8480 1111 1910 1 chr6D.!!$R2 799
5 TraesCS4D01G017100 chr6B 248510718 248512025 1307 True 1860.0 1860 92.5760 793 2086 1 chr6B.!!$R1 1293
6 TraesCS4D01G017100 chr6B 249448303 249449505 1202 True 804.5 1125 92.4400 788 2086 2 chr6B.!!$R4 1298
7 TraesCS4D01G017100 chr6B 249385723 249386576 853 True 496.0 785 89.2850 813 1724 2 chr6B.!!$R3 911
8 TraesCS4D01G017100 chr6B 255210565 255211361 796 True 344.0 344 74.9390 1103 1914 1 chr6B.!!$R2 811
9 TraesCS4D01G017100 chr6A 188000129 188001259 1130 True 1779.0 1779 95.3220 969 2081 1 chr6A.!!$R1 1112
10 TraesCS4D01G017100 chr6A 205114750 205115568 818 False 359.0 359 75.1500 1103 1914 1 chr6A.!!$F1 811
11 TraesCS4D01G017100 chr6A 188241448 188242719 1271 True 352.5 551 90.1880 396 801 2 chr6A.!!$R2 405
12 TraesCS4D01G017100 chr7D 108439898 108440694 796 False 1290.0 1290 95.9900 2086 2876 1 chr7D.!!$F1 790
13 TraesCS4D01G017100 chr7D 194651434 194652228 794 False 1280.0 1280 95.8590 2087 2876 1 chr7D.!!$F2 789
14 TraesCS4D01G017100 chr2D 160362077 160362874 797 False 1290.0 1290 95.9900 2086 2876 1 chr2D.!!$F1 790
15 TraesCS4D01G017100 chr2D 605742560 605743358 798 False 1280.0 1280 95.7450 2086 2876 1 chr2D.!!$F2 790
16 TraesCS4D01G017100 chr5D 505298526 505299323 797 True 1284.0 1284 95.8700 2086 2876 1 chr5D.!!$R1 790
17 TraesCS4D01G017100 chr5D 531353022 531353820 798 True 1280.0 1280 95.7450 2086 2876 1 chr5D.!!$R2 790
18 TraesCS4D01G017100 chr1D 255051968 255052773 805 True 1279.0 1279 95.4150 2076 2875 1 chr1D.!!$R1 799
19 TraesCS4D01G017100 chr3D 474708779 474709580 801 False 1275.0 1275 95.5110 2080 2873 1 chr3D.!!$F2 793
20 TraesCS4D01G017100 chr7B 682282911 682283729 818 True 381.0 381 75.6300 1103 1914 1 chr7B.!!$R3 811

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
369 370 0.035317 TTGCAGCCGTCAGATCAAGT 59.965 50.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 3234 1.269988 TGGAGATCGCAGCTAGATTGC 60.27 52.381 9.03 9.03 38.18 3.56 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
30 31 6.493189 TTTTTAAAATGGCAGGGAGACTTT 57.507 33.333 0.55 0.00 0.00 2.66
31 32 6.493189 TTTTAAAATGGCAGGGAGACTTTT 57.507 33.333 0.00 0.00 34.31 2.27
32 33 6.493189 TTTAAAATGGCAGGGAGACTTTTT 57.507 33.333 0.00 0.00 43.00 1.94
61 62 9.770503 AGAGAAGTTTTTCTACGTTTTTCTTTC 57.229 29.630 0.00 0.00 43.63 2.62
62 63 8.906636 AGAAGTTTTTCTACGTTTTTCTTTCC 57.093 30.769 0.00 0.00 41.82 3.13
63 64 8.737175 AGAAGTTTTTCTACGTTTTTCTTTCCT 58.263 29.630 0.00 0.00 41.82 3.36
64 65 9.350357 GAAGTTTTTCTACGTTTTTCTTTCCTT 57.650 29.630 0.00 0.00 0.00 3.36
65 66 9.701098 AAGTTTTTCTACGTTTTTCTTTCCTTT 57.299 25.926 0.00 0.00 0.00 3.11
66 67 9.701098 AGTTTTTCTACGTTTTTCTTTCCTTTT 57.299 25.926 0.00 0.00 0.00 2.27
82 83 9.793259 TCTTTCCTTTTAAGATAGTTGTGATGT 57.207 29.630 0.00 0.00 0.00 3.06
84 85 8.561738 TTCCTTTTAAGATAGTTGTGATGTCC 57.438 34.615 0.00 0.00 0.00 4.02
85 86 7.685481 TCCTTTTAAGATAGTTGTGATGTCCA 58.315 34.615 0.00 0.00 0.00 4.02
86 87 7.606456 TCCTTTTAAGATAGTTGTGATGTCCAC 59.394 37.037 0.00 0.00 45.88 4.02
98 99 2.050714 GTCCACGTGACGCGAGAA 60.051 61.111 19.30 0.00 44.77 2.87
99 100 1.443872 GTCCACGTGACGCGAGAAT 60.444 57.895 19.30 0.00 44.77 2.40
100 101 0.179181 GTCCACGTGACGCGAGAATA 60.179 55.000 19.30 0.00 44.77 1.75
101 102 0.736636 TCCACGTGACGCGAGAATAT 59.263 50.000 19.30 0.00 44.77 1.28
102 103 1.133598 TCCACGTGACGCGAGAATATT 59.866 47.619 19.30 0.00 44.77 1.28
103 104 1.924524 CCACGTGACGCGAGAATATTT 59.075 47.619 19.30 0.00 44.77 1.40
104 105 2.347452 CCACGTGACGCGAGAATATTTT 59.653 45.455 19.30 0.00 44.77 1.82
105 106 3.181524 CCACGTGACGCGAGAATATTTTT 60.182 43.478 19.30 0.00 44.77 1.94
132 133 3.921119 TTTGACATGATGGTGAGTTGC 57.079 42.857 0.00 0.00 0.00 4.17
133 134 1.441738 TGACATGATGGTGAGTTGCG 58.558 50.000 0.00 0.00 0.00 4.85
134 135 0.097674 GACATGATGGTGAGTTGCGC 59.902 55.000 0.00 0.00 0.00 6.09
135 136 0.606130 ACATGATGGTGAGTTGCGCA 60.606 50.000 5.66 5.66 0.00 6.09
136 137 0.736636 CATGATGGTGAGTTGCGCAT 59.263 50.000 12.75 0.00 0.00 4.73
137 138 1.941975 CATGATGGTGAGTTGCGCATA 59.058 47.619 12.75 0.00 0.00 3.14
138 139 1.655484 TGATGGTGAGTTGCGCATAG 58.345 50.000 12.75 0.00 0.00 2.23
155 156 3.804193 GCTTTCTCAAGCGGCCCG 61.804 66.667 0.00 0.00 46.06 6.13
177 178 4.354162 GGCGGGGCCCAACAACTA 62.354 66.667 26.86 0.00 44.06 2.24
178 179 2.750237 GCGGGGCCCAACAACTAG 60.750 66.667 26.86 4.17 0.00 2.57
179 180 2.754375 CGGGGCCCAACAACTAGT 59.246 61.111 26.86 0.00 0.00 2.57
180 181 1.376812 CGGGGCCCAACAACTAGTC 60.377 63.158 26.86 0.00 0.00 2.59
181 182 1.765074 GGGGCCCAACAACTAGTCA 59.235 57.895 26.86 0.00 0.00 3.41
182 183 0.608308 GGGGCCCAACAACTAGTCAC 60.608 60.000 26.86 0.00 0.00 3.67
183 184 0.608308 GGGCCCAACAACTAGTCACC 60.608 60.000 19.95 0.00 0.00 4.02
184 185 0.109723 GGCCCAACAACTAGTCACCA 59.890 55.000 0.00 0.00 0.00 4.17
185 186 1.271926 GGCCCAACAACTAGTCACCAT 60.272 52.381 0.00 0.00 0.00 3.55
186 187 2.084546 GCCCAACAACTAGTCACCATC 58.915 52.381 0.00 0.00 0.00 3.51
187 188 2.552155 GCCCAACAACTAGTCACCATCA 60.552 50.000 0.00 0.00 0.00 3.07
188 189 3.338249 CCCAACAACTAGTCACCATCAG 58.662 50.000 0.00 0.00 0.00 2.90
189 190 3.007940 CCCAACAACTAGTCACCATCAGA 59.992 47.826 0.00 0.00 0.00 3.27
190 191 4.248859 CCAACAACTAGTCACCATCAGAG 58.751 47.826 0.00 0.00 0.00 3.35
191 192 4.248859 CAACAACTAGTCACCATCAGAGG 58.751 47.826 0.00 0.00 0.00 3.69
192 193 2.234908 ACAACTAGTCACCATCAGAGGC 59.765 50.000 0.00 0.00 0.00 4.70
193 194 2.234661 CAACTAGTCACCATCAGAGGCA 59.765 50.000 0.00 0.00 0.00 4.75
194 195 2.106566 ACTAGTCACCATCAGAGGCAG 58.893 52.381 0.00 0.00 0.00 4.85
195 196 2.291865 ACTAGTCACCATCAGAGGCAGA 60.292 50.000 0.00 0.00 0.00 4.26
196 197 1.193323 AGTCACCATCAGAGGCAGAG 58.807 55.000 0.00 0.00 0.00 3.35
197 198 1.189752 GTCACCATCAGAGGCAGAGA 58.810 55.000 0.00 0.00 0.00 3.10
198 199 1.134848 GTCACCATCAGAGGCAGAGAC 60.135 57.143 0.00 0.00 0.00 3.36
199 200 0.900421 CACCATCAGAGGCAGAGACA 59.100 55.000 0.00 0.00 0.00 3.41
200 201 1.134759 CACCATCAGAGGCAGAGACAG 60.135 57.143 0.00 0.00 0.00 3.51
201 202 0.464870 CCATCAGAGGCAGAGACAGG 59.535 60.000 0.00 0.00 0.00 4.00
202 203 0.464870 CATCAGAGGCAGAGACAGGG 59.535 60.000 0.00 0.00 0.00 4.45
203 204 0.690411 ATCAGAGGCAGAGACAGGGG 60.690 60.000 0.00 0.00 0.00 4.79
204 205 2.040278 AGAGGCAGAGACAGGGGG 59.960 66.667 0.00 0.00 0.00 5.40
205 206 2.284995 GAGGCAGAGACAGGGGGT 60.285 66.667 0.00 0.00 0.00 4.95
206 207 2.608988 AGGCAGAGACAGGGGGTG 60.609 66.667 0.00 0.00 0.00 4.61
207 208 4.416738 GGCAGAGACAGGGGGTGC 62.417 72.222 0.00 0.00 0.00 5.01
208 209 4.767255 GCAGAGACAGGGGGTGCG 62.767 72.222 0.00 0.00 0.00 5.34
209 210 2.997315 CAGAGACAGGGGGTGCGA 60.997 66.667 0.00 0.00 0.00 5.10
210 211 2.681778 AGAGACAGGGGGTGCGAG 60.682 66.667 0.00 0.00 0.00 5.03
211 212 4.459089 GAGACAGGGGGTGCGAGC 62.459 72.222 0.00 0.00 0.00 5.03
213 214 4.767255 GACAGGGGGTGCGAGCAG 62.767 72.222 0.00 0.00 0.00 4.24
220 221 4.767255 GGTGCGAGCAGGGGTCAG 62.767 72.222 0.00 0.00 0.00 3.51
221 222 3.695606 GTGCGAGCAGGGGTCAGA 61.696 66.667 0.00 0.00 0.00 3.27
222 223 3.695606 TGCGAGCAGGGGTCAGAC 61.696 66.667 0.00 0.00 0.00 3.51
223 224 3.695606 GCGAGCAGGGGTCAGACA 61.696 66.667 2.17 0.00 0.00 3.41
224 225 2.262915 CGAGCAGGGGTCAGACAC 59.737 66.667 2.17 0.00 0.00 3.67
225 226 2.665603 GAGCAGGGGTCAGACACC 59.334 66.667 14.88 14.88 43.77 4.16
245 246 4.431131 CCATCGCCTTGCCCAGGT 62.431 66.667 1.18 0.00 46.07 4.00
246 247 2.589540 CATCGCCTTGCCCAGGTA 59.410 61.111 1.18 0.00 46.07 3.08
247 248 1.819632 CATCGCCTTGCCCAGGTAC 60.820 63.158 1.18 0.00 46.07 3.34
248 249 1.995626 ATCGCCTTGCCCAGGTACT 60.996 57.895 1.18 0.00 46.07 2.73
249 250 0.689745 ATCGCCTTGCCCAGGTACTA 60.690 55.000 1.18 0.00 46.07 1.82
250 251 1.144057 CGCCTTGCCCAGGTACTAG 59.856 63.158 1.18 0.00 46.07 2.57
251 252 1.614241 CGCCTTGCCCAGGTACTAGT 61.614 60.000 0.00 0.00 46.07 2.57
252 253 1.492764 GCCTTGCCCAGGTACTAGTA 58.507 55.000 0.00 0.00 46.07 1.82
253 254 2.047830 GCCTTGCCCAGGTACTAGTAT 58.952 52.381 5.75 0.00 46.07 2.12
254 255 2.438392 GCCTTGCCCAGGTACTAGTATT 59.562 50.000 5.75 0.00 46.07 1.89
255 256 3.644738 GCCTTGCCCAGGTACTAGTATTA 59.355 47.826 5.75 0.00 46.07 0.98
256 257 4.502777 GCCTTGCCCAGGTACTAGTATTAC 60.503 50.000 5.75 0.00 46.07 1.89
257 258 4.900054 CCTTGCCCAGGTACTAGTATTACT 59.100 45.833 5.75 1.30 37.99 2.24
258 259 6.073314 CCTTGCCCAGGTACTAGTATTACTA 58.927 44.000 5.75 3.61 37.99 1.82
259 260 6.015603 CCTTGCCCAGGTACTAGTATTACTAC 60.016 46.154 5.75 0.00 37.99 2.73
260 261 6.271585 TGCCCAGGTACTAGTATTACTACT 57.728 41.667 5.75 0.00 41.19 2.57
261 262 6.302269 TGCCCAGGTACTAGTATTACTACTC 58.698 44.000 5.75 0.00 39.04 2.59
262 263 6.102321 TGCCCAGGTACTAGTATTACTACTCT 59.898 42.308 5.75 0.00 39.04 3.24
263 264 7.293299 TGCCCAGGTACTAGTATTACTACTCTA 59.707 40.741 5.75 0.00 39.04 2.43
264 265 7.823799 GCCCAGGTACTAGTATTACTACTCTAG 59.176 44.444 5.75 0.00 39.04 2.43
265 266 7.823799 CCCAGGTACTAGTATTACTACTCTAGC 59.176 44.444 5.75 0.00 39.04 3.42
266 267 7.823799 CCAGGTACTAGTATTACTACTCTAGCC 59.176 44.444 5.75 0.00 39.04 3.93
267 268 7.823799 CAGGTACTAGTATTACTACTCTAGCCC 59.176 44.444 5.75 0.00 39.04 5.19
268 269 7.515514 AGGTACTAGTATTACTACTCTAGCCCA 59.484 40.741 5.75 0.00 39.04 5.36
269 270 8.160106 GGTACTAGTATTACTACTCTAGCCCAA 58.840 40.741 5.75 0.00 39.04 4.12
270 271 9.566432 GTACTAGTATTACTACTCTAGCCCAAA 57.434 37.037 5.75 0.00 39.04 3.28
271 272 8.694581 ACTAGTATTACTACTCTAGCCCAAAG 57.305 38.462 0.00 0.00 39.04 2.77
272 273 6.980416 AGTATTACTACTCTAGCCCAAAGG 57.020 41.667 0.00 0.00 32.56 3.11
273 274 5.839606 AGTATTACTACTCTAGCCCAAAGGG 59.160 44.000 0.00 0.00 38.75 3.95
274 275 7.150864 AGTATTACTACTCTAGCCCAAAGGGG 61.151 46.154 3.93 0.00 45.29 4.79
275 276 9.252251 AGTATTACTACTCTAGCCCAAAGGGGA 62.252 44.444 3.40 0.00 45.32 4.81
288 289 5.584551 CCAAAGGGGAAGTAATATAGGCT 57.415 43.478 0.00 0.00 40.01 4.58
289 290 5.953571 CCAAAGGGGAAGTAATATAGGCTT 58.046 41.667 0.00 0.00 40.01 4.35
290 291 5.770162 CCAAAGGGGAAGTAATATAGGCTTG 59.230 44.000 0.00 0.00 40.01 4.01
291 292 4.642466 AGGGGAAGTAATATAGGCTTGC 57.358 45.455 0.00 0.00 0.00 4.01
292 293 3.330998 AGGGGAAGTAATATAGGCTTGCC 59.669 47.826 2.97 2.97 45.88 4.52
293 294 3.687125 GGGAAGTAATATAGGCTTGCCC 58.313 50.000 8.17 0.00 42.47 5.36
294 295 3.335579 GGAAGTAATATAGGCTTGCCCG 58.664 50.000 8.17 0.00 39.21 6.13
295 296 3.244457 GGAAGTAATATAGGCTTGCCCGT 60.244 47.826 8.17 0.00 39.21 5.28
296 297 4.020839 GGAAGTAATATAGGCTTGCCCGTA 60.021 45.833 8.17 2.24 39.21 4.02
297 298 4.803098 AGTAATATAGGCTTGCCCGTAG 57.197 45.455 8.17 0.00 39.21 3.51
322 323 6.115450 CATAATCATGCTAATGACATCGGG 57.885 41.667 0.00 0.00 45.51 5.14
323 324 4.356405 AATCATGCTAATGACATCGGGA 57.644 40.909 0.00 0.00 45.51 5.14
324 325 3.111853 TCATGCTAATGACATCGGGAC 57.888 47.619 0.00 0.00 37.91 4.46
325 326 2.700371 TCATGCTAATGACATCGGGACT 59.300 45.455 0.00 0.00 37.91 3.85
326 327 3.134623 TCATGCTAATGACATCGGGACTT 59.865 43.478 0.00 0.00 37.91 3.01
327 328 3.627395 TGCTAATGACATCGGGACTTT 57.373 42.857 0.00 0.00 0.00 2.66
328 329 3.531538 TGCTAATGACATCGGGACTTTC 58.468 45.455 0.00 0.00 0.00 2.62
329 330 2.540101 GCTAATGACATCGGGACTTTCG 59.460 50.000 0.00 0.00 0.00 3.46
330 331 3.737047 GCTAATGACATCGGGACTTTCGA 60.737 47.826 0.00 0.00 41.04 3.71
331 332 2.586258 ATGACATCGGGACTTTCGAG 57.414 50.000 0.00 0.00 40.09 4.04
332 333 0.108804 TGACATCGGGACTTTCGAGC 60.109 55.000 0.00 0.00 40.09 5.03
333 334 0.806492 GACATCGGGACTTTCGAGCC 60.806 60.000 0.00 0.00 40.09 4.70
334 335 1.521681 CATCGGGACTTTCGAGCCC 60.522 63.158 5.05 5.05 40.09 5.19
335 336 1.987855 ATCGGGACTTTCGAGCCCA 60.988 57.895 13.06 3.67 42.14 5.36
336 337 1.550130 ATCGGGACTTTCGAGCCCAA 61.550 55.000 13.06 0.00 42.14 4.12
337 338 1.302192 CGGGACTTTCGAGCCCAAA 60.302 57.895 13.06 0.00 42.14 3.28
338 339 1.298859 CGGGACTTTCGAGCCCAAAG 61.299 60.000 13.06 4.33 42.14 2.77
339 340 0.960861 GGGACTTTCGAGCCCAAAGG 60.961 60.000 9.14 0.00 41.64 3.11
353 354 3.016031 CCCAAAGGCCCAAATTATTTGC 58.984 45.455 11.82 2.15 39.31 3.68
354 355 3.560882 CCCAAAGGCCCAAATTATTTGCA 60.561 43.478 11.82 0.00 39.31 4.08
355 356 3.690628 CCAAAGGCCCAAATTATTTGCAG 59.309 43.478 11.82 6.83 39.31 4.41
356 357 2.696989 AGGCCCAAATTATTTGCAGC 57.303 45.000 17.10 17.10 39.31 5.25
357 358 1.667236 GGCCCAAATTATTTGCAGCC 58.333 50.000 24.02 24.02 45.17 4.85
358 359 1.289276 GCCCAAATTATTTGCAGCCG 58.711 50.000 11.82 0.00 39.31 5.52
359 360 1.405391 GCCCAAATTATTTGCAGCCGT 60.405 47.619 11.82 0.00 39.31 5.68
360 361 2.539476 CCCAAATTATTTGCAGCCGTC 58.461 47.619 11.82 0.00 39.31 4.79
361 362 2.094286 CCCAAATTATTTGCAGCCGTCA 60.094 45.455 11.82 0.00 39.31 4.35
362 363 3.181397 CCAAATTATTTGCAGCCGTCAG 58.819 45.455 11.82 0.00 39.31 3.51
363 364 3.119531 CCAAATTATTTGCAGCCGTCAGA 60.120 43.478 11.82 0.00 39.31 3.27
364 365 4.440525 CCAAATTATTTGCAGCCGTCAGAT 60.441 41.667 11.82 0.00 39.31 2.90
365 366 4.558538 AATTATTTGCAGCCGTCAGATC 57.441 40.909 0.00 0.00 0.00 2.75
366 367 2.689553 TATTTGCAGCCGTCAGATCA 57.310 45.000 0.00 0.00 0.00 2.92
367 368 1.825090 ATTTGCAGCCGTCAGATCAA 58.175 45.000 0.00 0.00 0.00 2.57
368 369 1.159285 TTTGCAGCCGTCAGATCAAG 58.841 50.000 0.00 0.00 0.00 3.02
369 370 0.035317 TTGCAGCCGTCAGATCAAGT 59.965 50.000 0.00 0.00 0.00 3.16
370 371 0.894835 TGCAGCCGTCAGATCAAGTA 59.105 50.000 0.00 0.00 0.00 2.24
371 372 1.134995 TGCAGCCGTCAGATCAAGTAG 60.135 52.381 0.00 0.00 0.00 2.57
372 373 1.804372 GCAGCCGTCAGATCAAGTAGG 60.804 57.143 0.00 0.00 0.00 3.18
373 374 1.751351 CAGCCGTCAGATCAAGTAGGA 59.249 52.381 0.00 0.00 0.00 2.94
374 375 2.166459 CAGCCGTCAGATCAAGTAGGAA 59.834 50.000 0.00 0.00 0.00 3.36
375 376 2.832129 AGCCGTCAGATCAAGTAGGAAA 59.168 45.455 0.00 0.00 0.00 3.13
376 377 3.260884 AGCCGTCAGATCAAGTAGGAAAA 59.739 43.478 0.00 0.00 0.00 2.29
377 378 4.080863 AGCCGTCAGATCAAGTAGGAAAAT 60.081 41.667 0.00 0.00 0.00 1.82
378 379 4.636206 GCCGTCAGATCAAGTAGGAAAATT 59.364 41.667 0.00 0.00 0.00 1.82
379 380 5.123979 GCCGTCAGATCAAGTAGGAAAATTT 59.876 40.000 0.00 0.00 0.00 1.82
380 381 6.675728 GCCGTCAGATCAAGTAGGAAAATTTC 60.676 42.308 0.00 0.00 0.00 2.17
408 409 6.748132 TCCCTTTTCAGAAACTTTGCAATAG 58.252 36.000 0.00 3.50 0.00 1.73
412 413 7.330208 CCTTTTCAGAAACTTTGCAATAGATGG 59.670 37.037 0.00 0.00 0.00 3.51
420 421 1.898574 GCAATAGATGGTGGCCCCG 60.899 63.158 0.00 0.00 35.15 5.73
433 1707 1.384222 GGCCCCGTGGATCAATCAAC 61.384 60.000 0.00 0.00 0.00 3.18
443 1717 0.254178 ATCAATCAACGCAGAGGCCT 59.746 50.000 3.86 3.86 36.38 5.19
453 1727 2.045280 CAGAGGCCTGGATCTACCG 58.955 63.158 12.00 0.00 42.61 4.02
456 1730 0.468400 GAGGCCTGGATCTACCGTCT 60.468 60.000 12.00 0.00 42.61 4.18
463 1737 4.202223 GCCTGGATCTACCGTCTATTTTGA 60.202 45.833 0.00 0.00 42.61 2.69
549 1823 1.066929 GCATCCTTGGCCGTTTGAATT 60.067 47.619 0.00 0.00 0.00 2.17
553 1827 3.757270 TCCTTGGCCGTTTGAATTAGAA 58.243 40.909 0.00 0.00 0.00 2.10
572 1846 3.118038 AGAAGTTGACAACTACAAGCCCA 60.118 43.478 20.85 0.00 41.91 5.36
575 1849 0.109723 TGACAACTACAAGCCCACCC 59.890 55.000 0.00 0.00 0.00 4.61
577 1851 0.110486 ACAACTACAAGCCCACCCTG 59.890 55.000 0.00 0.00 0.00 4.45
583 1857 1.294138 CAAGCCCACCCTGCATTTG 59.706 57.895 0.00 0.00 0.00 2.32
584 1858 1.152269 AAGCCCACCCTGCATTTGT 60.152 52.632 0.00 0.00 0.00 2.83
595 1869 4.021192 ACCCTGCATTTGTTTTGTATCCAG 60.021 41.667 0.00 0.00 0.00 3.86
608 1882 8.100791 TGTTTTGTATCCAGCTTGTATAACTCT 58.899 33.333 0.00 0.00 0.00 3.24
613 1887 5.073311 TCCAGCTTGTATAACTCTGTGTC 57.927 43.478 0.00 0.00 0.00 3.67
658 1932 2.006805 TGGGCACATCCATCAAACAA 57.993 45.000 0.00 0.00 36.21 2.83
679 1953 1.980052 CAAAGGCTCGGGTCTACCA 59.020 57.895 0.00 0.00 40.22 3.25
684 1958 1.122019 GGCTCGGGTCTACCATCCAT 61.122 60.000 0.81 0.00 40.22 3.41
685 1959 0.318762 GCTCGGGTCTACCATCCATC 59.681 60.000 0.81 0.00 40.22 3.51
706 1980 3.973973 TCTCAGAGTTTTCCCCTCTTTGA 59.026 43.478 0.00 0.00 37.18 2.69
714 1988 5.478332 AGTTTTCCCCTCTTTGACATTGATC 59.522 40.000 0.00 0.00 0.00 2.92
775 2049 0.460284 CTAGTGTGCACCCTTAGGCG 60.460 60.000 15.69 0.00 36.11 5.52
784 2058 2.285977 CACCCTTAGGCGTTCCAATAC 58.714 52.381 0.00 0.00 36.11 1.89
785 2059 1.910671 ACCCTTAGGCGTTCCAATACA 59.089 47.619 0.00 0.00 36.11 2.29
804 2078 7.812669 CCAATACAATAAACTTTGACAACCCTC 59.187 37.037 0.00 0.00 0.00 4.30
829 2103 1.512926 GTCTTTGACGTGAGGTGCAT 58.487 50.000 0.00 0.00 0.00 3.96
841 2115 2.224744 TGAGGTGCATAAAGCCACAGAA 60.225 45.455 0.00 0.00 44.83 3.02
852 2126 0.682209 GCCACAGAACTGGGATGCAT 60.682 55.000 0.00 0.00 35.61 3.96
864 2138 4.158394 ACTGGGATGCATAACAATTGTGTC 59.842 41.667 12.82 2.52 36.80 3.67
867 2141 5.890419 TGGGATGCATAACAATTGTGTCATA 59.110 36.000 12.82 0.61 36.80 2.15
1050 2328 2.977178 CTCGTGCCTCTCCTTGCT 59.023 61.111 0.00 0.00 0.00 3.91
1053 2331 1.957177 CTCGTGCCTCTCCTTGCTATA 59.043 52.381 0.00 0.00 0.00 1.31
1077 2355 0.249238 CCCTCATTCTCTTCGCCTCG 60.249 60.000 0.00 0.00 0.00 4.63
1341 2619 3.387091 CCCGTCGGACCCATGTCA 61.387 66.667 14.39 0.00 43.65 3.58
1497 2793 4.554036 GCCATGGCCTCGTCCTCC 62.554 72.222 27.24 0.00 34.56 4.30
1754 3050 1.819226 CGCGAGATGCTGCAGATCAC 61.819 60.000 20.43 14.25 43.27 3.06
1924 3227 3.868757 TGTAAGGTCTTCCAGTGATCG 57.131 47.619 0.00 0.00 35.89 3.69
1925 3228 3.162666 TGTAAGGTCTTCCAGTGATCGT 58.837 45.455 0.00 0.00 35.89 3.73
1930 3234 1.874019 CTTCCAGTGATCGTCGCGG 60.874 63.158 6.13 0.00 30.95 6.46
2158 3478 8.181904 TCTGTCATACATGCACTTCTATGATA 57.818 34.615 0.00 2.72 30.33 2.15
2185 3505 6.773976 ATTGTGACAAAATCCGGTATCATT 57.226 33.333 0.62 0.00 0.00 2.57
2210 3530 1.198759 TGTGGTGGGCTCCTACTTCC 61.199 60.000 2.46 0.00 0.00 3.46
2474 3796 3.018856 TCTAACTGAACCCGAGCGATTA 58.981 45.455 0.00 0.00 0.00 1.75
2588 3910 2.356793 CCGATCGATGCTGCCTCC 60.357 66.667 18.66 0.00 0.00 4.30
2607 3929 1.403647 CCGGATGAACAGTGAGCGTTA 60.404 52.381 0.00 0.00 0.00 3.18
2689 4011 1.577736 CTCTGGATGAACAGGACCCT 58.422 55.000 0.00 0.00 38.98 4.34
2707 4029 0.661780 CTGATCGATCGAGCCGGTTC 60.662 60.000 28.63 17.48 0.00 3.62
2736 4058 3.477956 AACAGGACCCCGTGGAGGA 62.478 63.158 0.00 0.00 45.00 3.71
2777 4099 1.881925 CGTGGAGGGCAGAATGAACAA 60.882 52.381 0.00 0.00 39.69 2.83
2781 4103 3.217626 GGAGGGCAGAATGAACAATAGG 58.782 50.000 0.00 0.00 39.69 2.57
2869 4192 0.541063 TGAACAGTAGCCGGTGGAGA 60.541 55.000 1.90 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 6.493189 AAAGTCTCCCTGCCATTTTAAAAA 57.507 33.333 4.44 0.00 0.00 1.94
8 9 6.493189 AAAAGTCTCCCTGCCATTTTAAAA 57.507 33.333 2.51 2.51 0.00 1.52
9 10 6.493189 AAAAAGTCTCCCTGCCATTTTAAA 57.507 33.333 0.00 0.00 0.00 1.52
35 36 9.770503 GAAAGAAAAACGTAGAAAAACTTCTCT 57.229 29.630 0.00 0.00 32.72 3.10
36 37 9.007252 GGAAAGAAAAACGTAGAAAAACTTCTC 57.993 33.333 0.00 0.00 32.72 2.87
37 38 8.737175 AGGAAAGAAAAACGTAGAAAAACTTCT 58.263 29.630 0.00 0.00 35.17 2.85
38 39 8.906636 AGGAAAGAAAAACGTAGAAAAACTTC 57.093 30.769 0.00 0.00 0.00 3.01
39 40 9.701098 AAAGGAAAGAAAAACGTAGAAAAACTT 57.299 25.926 0.00 0.00 0.00 2.66
40 41 9.701098 AAAAGGAAAGAAAAACGTAGAAAAACT 57.299 25.926 0.00 0.00 0.00 2.66
56 57 9.793259 ACATCACAACTATCTTAAAAGGAAAGA 57.207 29.630 0.00 0.00 37.38 2.52
58 59 9.010029 GGACATCACAACTATCTTAAAAGGAAA 57.990 33.333 0.00 0.00 0.00 3.13
59 60 8.160765 TGGACATCACAACTATCTTAAAAGGAA 58.839 33.333 0.00 0.00 0.00 3.36
60 61 7.606456 GTGGACATCACAACTATCTTAAAAGGA 59.394 37.037 0.00 0.00 45.39 3.36
61 62 7.413000 CGTGGACATCACAACTATCTTAAAAGG 60.413 40.741 0.00 0.00 46.36 3.11
62 63 7.117812 ACGTGGACATCACAACTATCTTAAAAG 59.882 37.037 0.00 0.00 46.36 2.27
63 64 6.932400 ACGTGGACATCACAACTATCTTAAAA 59.068 34.615 0.00 0.00 46.36 1.52
64 65 6.367695 CACGTGGACATCACAACTATCTTAAA 59.632 38.462 7.95 0.00 46.36 1.52
65 66 5.867174 CACGTGGACATCACAACTATCTTAA 59.133 40.000 7.95 0.00 46.36 1.85
66 67 5.184287 TCACGTGGACATCACAACTATCTTA 59.816 40.000 17.00 0.00 46.36 2.10
67 68 4.021456 TCACGTGGACATCACAACTATCTT 60.021 41.667 17.00 0.00 46.36 2.40
68 69 3.509967 TCACGTGGACATCACAACTATCT 59.490 43.478 17.00 0.00 46.36 1.98
69 70 3.612860 GTCACGTGGACATCACAACTATC 59.387 47.826 17.00 0.00 46.36 2.08
70 71 3.585862 GTCACGTGGACATCACAACTAT 58.414 45.455 17.00 0.00 46.36 2.12
71 72 3.021269 GTCACGTGGACATCACAACTA 57.979 47.619 17.00 0.00 46.36 2.24
72 73 1.865865 GTCACGTGGACATCACAACT 58.134 50.000 17.00 0.00 46.36 3.16
81 82 0.179181 TATTCTCGCGTCACGTGGAC 60.179 55.000 17.00 11.49 44.19 4.02
82 83 0.736636 ATATTCTCGCGTCACGTGGA 59.263 50.000 17.00 4.34 44.19 4.02
83 84 1.556564 AATATTCTCGCGTCACGTGG 58.443 50.000 17.00 0.92 44.19 4.94
84 85 3.634730 AAAATATTCTCGCGTCACGTG 57.365 42.857 9.94 9.94 44.19 4.49
110 111 4.619973 GCAACTCACCATCATGTCAAAAA 58.380 39.130 0.00 0.00 0.00 1.94
111 112 3.304592 CGCAACTCACCATCATGTCAAAA 60.305 43.478 0.00 0.00 0.00 2.44
112 113 2.226200 CGCAACTCACCATCATGTCAAA 59.774 45.455 0.00 0.00 0.00 2.69
113 114 1.805943 CGCAACTCACCATCATGTCAA 59.194 47.619 0.00 0.00 0.00 3.18
114 115 1.441738 CGCAACTCACCATCATGTCA 58.558 50.000 0.00 0.00 0.00 3.58
115 116 0.097674 GCGCAACTCACCATCATGTC 59.902 55.000 0.30 0.00 0.00 3.06
116 117 0.606130 TGCGCAACTCACCATCATGT 60.606 50.000 8.16 0.00 0.00 3.21
117 118 0.736636 ATGCGCAACTCACCATCATG 59.263 50.000 17.11 0.00 0.00 3.07
118 119 2.216046 CTATGCGCAACTCACCATCAT 58.784 47.619 17.11 0.00 0.00 2.45
119 120 1.655484 CTATGCGCAACTCACCATCA 58.345 50.000 17.11 0.00 0.00 3.07
120 121 0.305922 GCTATGCGCAACTCACCATC 59.694 55.000 17.11 0.00 38.92 3.51
121 122 0.107508 AGCTATGCGCAACTCACCAT 60.108 50.000 17.11 0.00 42.61 3.55
122 123 0.321564 AAGCTATGCGCAACTCACCA 60.322 50.000 17.11 0.00 42.61 4.17
123 124 0.804989 AAAGCTATGCGCAACTCACC 59.195 50.000 17.11 0.00 42.61 4.02
124 125 1.734465 AGAAAGCTATGCGCAACTCAC 59.266 47.619 17.11 9.96 42.61 3.51
125 126 2.002586 GAGAAAGCTATGCGCAACTCA 58.997 47.619 17.11 0.00 42.61 3.41
126 127 2.002586 TGAGAAAGCTATGCGCAACTC 58.997 47.619 17.11 14.35 42.61 3.01
127 128 2.099141 TGAGAAAGCTATGCGCAACT 57.901 45.000 17.11 10.00 42.61 3.16
128 129 2.778659 CTTGAGAAAGCTATGCGCAAC 58.221 47.619 17.11 7.34 42.61 4.17
129 130 1.131126 GCTTGAGAAAGCTATGCGCAA 59.869 47.619 17.11 2.72 42.32 4.85
130 131 0.729116 GCTTGAGAAAGCTATGCGCA 59.271 50.000 14.96 14.96 42.32 6.09
131 132 0.315706 CGCTTGAGAAAGCTATGCGC 60.316 55.000 0.00 0.00 43.38 6.09
132 133 0.302890 CCGCTTGAGAAAGCTATGCG 59.697 55.000 8.66 6.71 43.38 4.73
133 134 0.028637 GCCGCTTGAGAAAGCTATGC 59.971 55.000 8.66 5.16 43.38 3.14
134 135 0.659957 GGCCGCTTGAGAAAGCTATG 59.340 55.000 8.66 0.00 43.38 2.23
135 136 0.464554 GGGCCGCTTGAGAAAGCTAT 60.465 55.000 8.66 0.00 43.38 2.97
136 137 1.078426 GGGCCGCTTGAGAAAGCTA 60.078 57.895 8.66 0.00 43.38 3.32
137 138 2.360475 GGGCCGCTTGAGAAAGCT 60.360 61.111 8.66 0.00 43.38 3.74
138 139 3.804193 CGGGCCGCTTGAGAAAGC 61.804 66.667 15.42 0.29 42.18 3.51
161 162 2.750237 CTAGTTGTTGGGCCCCGC 60.750 66.667 22.27 12.95 0.00 6.13
162 163 1.376812 GACTAGTTGTTGGGCCCCG 60.377 63.158 22.27 0.00 0.00 5.73
163 164 0.608308 GTGACTAGTTGTTGGGCCCC 60.608 60.000 22.27 4.91 0.00 5.80
164 165 0.608308 GGTGACTAGTTGTTGGGCCC 60.608 60.000 17.59 17.59 0.00 5.80
165 166 0.109723 TGGTGACTAGTTGTTGGGCC 59.890 55.000 0.00 0.00 0.00 5.80
166 167 2.084546 GATGGTGACTAGTTGTTGGGC 58.915 52.381 0.00 0.00 0.00 5.36
167 168 3.007940 TCTGATGGTGACTAGTTGTTGGG 59.992 47.826 0.00 0.00 0.00 4.12
168 169 4.248859 CTCTGATGGTGACTAGTTGTTGG 58.751 47.826 0.00 0.00 0.00 3.77
169 170 4.248859 CCTCTGATGGTGACTAGTTGTTG 58.751 47.826 0.00 0.00 0.00 3.33
170 171 3.307059 GCCTCTGATGGTGACTAGTTGTT 60.307 47.826 0.00 0.00 0.00 2.83
171 172 2.234908 GCCTCTGATGGTGACTAGTTGT 59.765 50.000 0.00 0.00 0.00 3.32
172 173 2.234661 TGCCTCTGATGGTGACTAGTTG 59.765 50.000 0.00 0.00 0.00 3.16
173 174 2.499289 CTGCCTCTGATGGTGACTAGTT 59.501 50.000 0.00 0.00 0.00 2.24
174 175 2.106566 CTGCCTCTGATGGTGACTAGT 58.893 52.381 0.00 0.00 0.00 2.57
175 176 2.361757 CTCTGCCTCTGATGGTGACTAG 59.638 54.545 0.00 0.00 0.00 2.57
176 177 2.024941 TCTCTGCCTCTGATGGTGACTA 60.025 50.000 0.00 0.00 0.00 2.59
177 178 1.193323 CTCTGCCTCTGATGGTGACT 58.807 55.000 0.00 0.00 0.00 3.41
178 179 1.134848 GTCTCTGCCTCTGATGGTGAC 60.135 57.143 0.00 0.00 0.00 3.67
179 180 1.189752 GTCTCTGCCTCTGATGGTGA 58.810 55.000 0.00 0.00 0.00 4.02
180 181 0.900421 TGTCTCTGCCTCTGATGGTG 59.100 55.000 0.00 0.00 0.00 4.17
181 182 1.193323 CTGTCTCTGCCTCTGATGGT 58.807 55.000 0.00 0.00 0.00 3.55
182 183 0.464870 CCTGTCTCTGCCTCTGATGG 59.535 60.000 0.00 0.00 0.00 3.51
183 184 0.464870 CCCTGTCTCTGCCTCTGATG 59.535 60.000 0.00 0.00 0.00 3.07
184 185 0.690411 CCCCTGTCTCTGCCTCTGAT 60.690 60.000 0.00 0.00 0.00 2.90
185 186 1.305633 CCCCTGTCTCTGCCTCTGA 60.306 63.158 0.00 0.00 0.00 3.27
186 187 2.365586 CCCCCTGTCTCTGCCTCTG 61.366 68.421 0.00 0.00 0.00 3.35
187 188 2.040278 CCCCCTGTCTCTGCCTCT 59.960 66.667 0.00 0.00 0.00 3.69
188 189 2.284995 ACCCCCTGTCTCTGCCTC 60.285 66.667 0.00 0.00 0.00 4.70
189 190 2.608988 CACCCCCTGTCTCTGCCT 60.609 66.667 0.00 0.00 0.00 4.75
190 191 4.416738 GCACCCCCTGTCTCTGCC 62.417 72.222 0.00 0.00 0.00 4.85
191 192 4.767255 CGCACCCCCTGTCTCTGC 62.767 72.222 0.00 0.00 0.00 4.26
192 193 2.997315 TCGCACCCCCTGTCTCTG 60.997 66.667 0.00 0.00 0.00 3.35
193 194 2.681778 CTCGCACCCCCTGTCTCT 60.682 66.667 0.00 0.00 0.00 3.10
194 195 4.459089 GCTCGCACCCCCTGTCTC 62.459 72.222 0.00 0.00 0.00 3.36
196 197 4.767255 CTGCTCGCACCCCCTGTC 62.767 72.222 0.00 0.00 0.00 3.51
203 204 4.767255 CTGACCCCTGCTCGCACC 62.767 72.222 0.00 0.00 0.00 5.01
204 205 3.695606 TCTGACCCCTGCTCGCAC 61.696 66.667 0.00 0.00 0.00 5.34
205 206 3.695606 GTCTGACCCCTGCTCGCA 61.696 66.667 0.00 0.00 0.00 5.10
206 207 3.695606 TGTCTGACCCCTGCTCGC 61.696 66.667 5.17 0.00 0.00 5.03
207 208 2.262915 GTGTCTGACCCCTGCTCG 59.737 66.667 5.17 0.00 0.00 5.03
208 209 2.665603 GGTGTCTGACCCCTGCTC 59.334 66.667 5.17 0.00 39.10 4.26
233 234 9.348290 GTAGTAATACTAGTACCTGGGCAAGGC 62.348 48.148 8.19 0.00 39.55 4.35
234 235 6.015603 GTAGTAATACTAGTACCTGGGCAAGG 60.016 46.154 6.32 6.32 40.83 3.61
235 236 6.776603 AGTAGTAATACTAGTACCTGGGCAAG 59.223 42.308 4.31 0.00 35.35 4.01
236 237 6.676558 AGTAGTAATACTAGTACCTGGGCAA 58.323 40.000 4.31 0.00 35.35 4.52
237 238 6.102321 AGAGTAGTAATACTAGTACCTGGGCA 59.898 42.308 4.31 0.00 34.66 5.36
238 239 6.541907 AGAGTAGTAATACTAGTACCTGGGC 58.458 44.000 4.31 0.00 34.66 5.36
239 240 7.823799 GCTAGAGTAGTAATACTAGTACCTGGG 59.176 44.444 4.31 2.70 34.66 4.45
240 241 7.823799 GGCTAGAGTAGTAATACTAGTACCTGG 59.176 44.444 4.31 5.65 34.66 4.45
241 242 7.823799 GGGCTAGAGTAGTAATACTAGTACCTG 59.176 44.444 4.31 1.68 34.66 4.00
242 243 7.515514 TGGGCTAGAGTAGTAATACTAGTACCT 59.484 40.741 4.31 4.44 34.66 3.08
243 244 7.684529 TGGGCTAGAGTAGTAATACTAGTACC 58.315 42.308 4.31 6.08 34.66 3.34
244 245 9.566432 TTTGGGCTAGAGTAGTAATACTAGTAC 57.434 37.037 4.31 0.00 34.66 2.73
245 246 9.790344 CTTTGGGCTAGAGTAGTAATACTAGTA 57.210 37.037 4.77 4.77 34.66 1.82
246 247 7.724951 CCTTTGGGCTAGAGTAGTAATACTAGT 59.275 40.741 7.46 7.46 37.08 2.57
247 248 7.177041 CCCTTTGGGCTAGAGTAGTAATACTAG 59.823 44.444 2.23 0.00 35.35 2.57
248 249 7.008941 CCCTTTGGGCTAGAGTAGTAATACTA 58.991 42.308 2.23 0.00 35.35 1.82
249 250 5.839606 CCCTTTGGGCTAGAGTAGTAATACT 59.160 44.000 1.76 1.76 35.35 2.12
250 251 6.099159 CCCTTTGGGCTAGAGTAGTAATAC 57.901 45.833 0.00 0.00 35.35 1.89
266 267 5.584551 AGCCTATATTACTTCCCCTTTGG 57.415 43.478 0.00 0.00 0.00 3.28
267 268 5.241728 GCAAGCCTATATTACTTCCCCTTTG 59.758 44.000 0.00 0.00 0.00 2.77
268 269 5.386060 GCAAGCCTATATTACTTCCCCTTT 58.614 41.667 0.00 0.00 0.00 3.11
269 270 4.202577 GGCAAGCCTATATTACTTCCCCTT 60.203 45.833 3.29 0.00 0.00 3.95
270 271 3.330998 GGCAAGCCTATATTACTTCCCCT 59.669 47.826 3.29 0.00 0.00 4.79
271 272 3.561528 GGGCAAGCCTATATTACTTCCCC 60.562 52.174 11.40 0.00 34.31 4.81
272 273 3.687125 GGGCAAGCCTATATTACTTCCC 58.313 50.000 11.40 0.00 36.10 3.97
273 274 3.244457 ACGGGCAAGCCTATATTACTTCC 60.244 47.826 11.40 0.00 36.10 3.46
274 275 4.004196 ACGGGCAAGCCTATATTACTTC 57.996 45.455 11.40 0.00 36.10 3.01
275 276 4.020485 CCTACGGGCAAGCCTATATTACTT 60.020 45.833 11.40 0.00 36.10 2.24
276 277 3.514309 CCTACGGGCAAGCCTATATTACT 59.486 47.826 11.40 0.00 36.10 2.24
277 278 3.858247 CCTACGGGCAAGCCTATATTAC 58.142 50.000 11.40 0.00 36.10 1.89
299 300 5.876460 TCCCGATGTCATTAGCATGATTATG 59.124 40.000 3.61 3.61 41.64 1.90
300 301 5.877012 GTCCCGATGTCATTAGCATGATTAT 59.123 40.000 0.00 0.00 41.64 1.28
301 302 5.012046 AGTCCCGATGTCATTAGCATGATTA 59.988 40.000 0.00 0.00 41.64 1.75
302 303 4.067896 GTCCCGATGTCATTAGCATGATT 58.932 43.478 0.00 0.00 41.64 2.57
303 304 3.326006 AGTCCCGATGTCATTAGCATGAT 59.674 43.478 0.00 0.00 41.64 2.45
304 305 2.700371 AGTCCCGATGTCATTAGCATGA 59.300 45.455 0.00 0.00 37.05 3.07
305 306 3.117491 AGTCCCGATGTCATTAGCATG 57.883 47.619 0.00 0.00 0.00 4.06
306 307 3.845781 AAGTCCCGATGTCATTAGCAT 57.154 42.857 0.00 0.00 0.00 3.79
307 308 3.531538 GAAAGTCCCGATGTCATTAGCA 58.468 45.455 0.00 0.00 0.00 3.49
308 309 2.540101 CGAAAGTCCCGATGTCATTAGC 59.460 50.000 0.00 0.00 0.00 3.09
309 310 4.041740 TCGAAAGTCCCGATGTCATTAG 57.958 45.455 0.00 0.00 0.00 1.73
310 311 3.737047 GCTCGAAAGTCCCGATGTCATTA 60.737 47.826 0.00 0.00 35.35 1.90
311 312 2.893637 CTCGAAAGTCCCGATGTCATT 58.106 47.619 0.00 0.00 35.35 2.57
312 313 1.471676 GCTCGAAAGTCCCGATGTCAT 60.472 52.381 0.00 0.00 35.35 3.06
313 314 0.108804 GCTCGAAAGTCCCGATGTCA 60.109 55.000 0.00 0.00 35.35 3.58
314 315 0.806492 GGCTCGAAAGTCCCGATGTC 60.806 60.000 0.00 0.00 35.35 3.06
315 316 1.218316 GGCTCGAAAGTCCCGATGT 59.782 57.895 0.00 0.00 35.35 3.06
316 317 1.521681 GGGCTCGAAAGTCCCGATG 60.522 63.158 0.00 0.00 41.85 3.84
317 318 2.901042 GGGCTCGAAAGTCCCGAT 59.099 61.111 0.00 0.00 41.85 4.18
332 333 3.016031 GCAAATAATTTGGGCCTTTGGG 58.984 45.455 4.53 0.00 40.94 4.12
333 334 3.683802 TGCAAATAATTTGGGCCTTTGG 58.316 40.909 4.53 0.00 40.94 3.28
334 335 3.127376 GCTGCAAATAATTTGGGCCTTTG 59.873 43.478 4.53 7.21 40.94 2.77
335 336 3.346315 GCTGCAAATAATTTGGGCCTTT 58.654 40.909 4.53 0.00 40.94 3.11
336 337 2.356022 GGCTGCAAATAATTTGGGCCTT 60.356 45.455 4.53 0.00 40.94 4.35
337 338 1.210234 GGCTGCAAATAATTTGGGCCT 59.790 47.619 4.53 0.00 40.94 5.19
338 339 1.667236 GGCTGCAAATAATTTGGGCC 58.333 50.000 0.50 0.00 40.94 5.80
339 340 1.289276 CGGCTGCAAATAATTTGGGC 58.711 50.000 0.50 0.00 40.94 5.36
340 341 2.094286 TGACGGCTGCAAATAATTTGGG 60.094 45.455 0.50 0.00 40.94 4.12
341 342 3.119531 TCTGACGGCTGCAAATAATTTGG 60.120 43.478 0.50 0.00 40.94 3.28
342 343 4.095410 TCTGACGGCTGCAAATAATTTG 57.905 40.909 0.50 0.00 43.44 2.32
343 344 4.398988 TGATCTGACGGCTGCAAATAATTT 59.601 37.500 0.50 0.00 0.00 1.82
344 345 3.947196 TGATCTGACGGCTGCAAATAATT 59.053 39.130 0.50 0.00 0.00 1.40
345 346 3.544684 TGATCTGACGGCTGCAAATAAT 58.455 40.909 0.50 0.00 0.00 1.28
346 347 2.984562 TGATCTGACGGCTGCAAATAA 58.015 42.857 0.50 0.00 0.00 1.40
347 348 2.689553 TGATCTGACGGCTGCAAATA 57.310 45.000 0.50 0.00 0.00 1.40
348 349 1.741706 CTTGATCTGACGGCTGCAAAT 59.258 47.619 0.50 0.00 0.00 2.32
349 350 1.159285 CTTGATCTGACGGCTGCAAA 58.841 50.000 0.50 0.00 0.00 3.68
350 351 0.035317 ACTTGATCTGACGGCTGCAA 59.965 50.000 0.50 0.00 0.00 4.08
351 352 0.894835 TACTTGATCTGACGGCTGCA 59.105 50.000 0.50 0.00 0.00 4.41
352 353 1.565305 CTACTTGATCTGACGGCTGC 58.435 55.000 0.00 0.00 0.00 5.25
353 354 1.751351 TCCTACTTGATCTGACGGCTG 59.249 52.381 0.00 0.00 0.00 4.85
354 355 2.145397 TCCTACTTGATCTGACGGCT 57.855 50.000 0.00 0.00 0.00 5.52
355 356 2.961526 TTCCTACTTGATCTGACGGC 57.038 50.000 0.00 0.00 0.00 5.68
356 357 6.183360 GGAAATTTTCCTACTTGATCTGACGG 60.183 42.308 19.01 0.00 46.57 4.79
357 358 6.776094 GGAAATTTTCCTACTTGATCTGACG 58.224 40.000 19.01 0.00 46.57 4.35
372 373 9.424319 GTTTCTGAAAAGGGATAGGAAATTTTC 57.576 33.333 4.09 0.24 39.28 2.29
373 374 9.159254 AGTTTCTGAAAAGGGATAGGAAATTTT 57.841 29.630 4.09 0.00 0.00 1.82
374 375 8.727100 AGTTTCTGAAAAGGGATAGGAAATTT 57.273 30.769 4.09 0.00 0.00 1.82
375 376 8.727100 AAGTTTCTGAAAAGGGATAGGAAATT 57.273 30.769 4.09 0.00 0.00 1.82
376 377 8.588472 CAAAGTTTCTGAAAAGGGATAGGAAAT 58.412 33.333 4.09 0.00 0.00 2.17
377 378 7.471399 GCAAAGTTTCTGAAAAGGGATAGGAAA 60.471 37.037 4.09 0.00 0.00 3.13
378 379 6.015434 GCAAAGTTTCTGAAAAGGGATAGGAA 60.015 38.462 4.09 0.00 0.00 3.36
379 380 5.476945 GCAAAGTTTCTGAAAAGGGATAGGA 59.523 40.000 4.09 0.00 0.00 2.94
380 381 5.243730 TGCAAAGTTTCTGAAAAGGGATAGG 59.756 40.000 4.09 0.00 0.00 2.57
381 382 6.331369 TGCAAAGTTTCTGAAAAGGGATAG 57.669 37.500 4.09 0.00 0.00 2.08
382 383 6.723298 TTGCAAAGTTTCTGAAAAGGGATA 57.277 33.333 4.09 0.00 0.00 2.59
383 384 5.612725 TTGCAAAGTTTCTGAAAAGGGAT 57.387 34.783 4.09 0.00 0.00 3.85
384 385 5.612725 ATTGCAAAGTTTCTGAAAAGGGA 57.387 34.783 1.71 0.00 0.00 4.20
385 386 6.748132 TCTATTGCAAAGTTTCTGAAAAGGG 58.252 36.000 1.71 0.00 0.00 3.95
386 387 7.330208 CCATCTATTGCAAAGTTTCTGAAAAGG 59.670 37.037 1.71 0.00 0.00 3.11
387 388 7.869429 ACCATCTATTGCAAAGTTTCTGAAAAG 59.131 33.333 1.71 0.00 0.00 2.27
388 389 7.652909 CACCATCTATTGCAAAGTTTCTGAAAA 59.347 33.333 1.71 0.00 0.00 2.29
389 390 7.147312 CACCATCTATTGCAAAGTTTCTGAAA 58.853 34.615 1.71 0.00 0.00 2.69
390 391 6.294675 CCACCATCTATTGCAAAGTTTCTGAA 60.295 38.462 1.71 0.00 0.00 3.02
391 392 5.183713 CCACCATCTATTGCAAAGTTTCTGA 59.816 40.000 1.71 0.00 0.00 3.27
392 393 5.404946 CCACCATCTATTGCAAAGTTTCTG 58.595 41.667 1.71 0.00 0.00 3.02
393 394 4.082026 GCCACCATCTATTGCAAAGTTTCT 60.082 41.667 1.71 0.00 0.00 2.52
394 395 4.176271 GCCACCATCTATTGCAAAGTTTC 58.824 43.478 1.71 0.00 0.00 2.78
408 409 3.774599 GATCCACGGGGCCACCATC 62.775 68.421 4.39 0.00 40.22 3.51
412 413 1.823899 GATTGATCCACGGGGCCAC 60.824 63.158 4.39 0.00 0.00 5.01
420 421 1.667724 CCTCTGCGTTGATTGATCCAC 59.332 52.381 0.00 0.00 0.00 4.02
433 1707 1.365633 GTAGATCCAGGCCTCTGCG 59.634 63.158 0.00 0.00 39.61 5.18
443 1717 8.801882 AAAATTCAAAATAGACGGTAGATCCA 57.198 30.769 0.00 0.00 35.57 3.41
471 1745 8.819974 CAGTTAAATGGGCAAAATATCAATGTC 58.180 33.333 0.00 0.00 0.00 3.06
475 1749 9.381033 CATTCAGTTAAATGGGCAAAATATCAA 57.619 29.630 2.65 0.00 33.80 2.57
549 1823 4.101898 TGGGCTTGTAGTTGTCAACTTCTA 59.898 41.667 22.81 13.66 42.81 2.10
553 1827 2.572290 GTGGGCTTGTAGTTGTCAACT 58.428 47.619 21.48 21.48 45.40 3.16
572 1846 4.535526 GGATACAAAACAAATGCAGGGT 57.464 40.909 0.00 0.00 0.00 4.34
595 1869 3.858238 GTCCGACACAGAGTTATACAAGC 59.142 47.826 0.00 0.00 0.00 4.01
608 1882 2.285083 CAAAGTTTGAGGTCCGACACA 58.715 47.619 10.19 0.00 0.00 3.72
613 1887 3.252215 TGTATTGCAAAGTTTGAGGTCCG 59.748 43.478 19.82 0.00 0.00 4.79
652 1926 1.421382 CCGAGCCTTTGCATTGTTTG 58.579 50.000 0.00 0.00 41.13 2.93
655 1929 1.228552 ACCCGAGCCTTTGCATTGT 60.229 52.632 0.00 0.00 41.13 2.71
658 1932 0.107654 GTAGACCCGAGCCTTTGCAT 60.108 55.000 0.00 0.00 41.13 3.96
679 1953 3.457749 GAGGGGAAAACTCTGAGATGGAT 59.542 47.826 12.44 0.00 32.28 3.41
684 1958 3.973973 TCAAAGAGGGGAAAACTCTGAGA 59.026 43.478 12.44 0.00 44.17 3.27
685 1959 4.068599 GTCAAAGAGGGGAAAACTCTGAG 58.931 47.826 2.45 2.45 44.17 3.35
706 1980 7.560991 TCAGTTATATGGGCAAAAGATCAATGT 59.439 33.333 0.00 0.00 0.00 2.71
775 2049 8.974408 GGTTGTCAAAGTTTATTGTATTGGAAC 58.026 33.333 0.00 0.00 0.00 3.62
784 2058 7.589954 CGTTTAGAGGGTTGTCAAAGTTTATTG 59.410 37.037 0.00 0.00 0.00 1.90
785 2059 7.283807 ACGTTTAGAGGGTTGTCAAAGTTTATT 59.716 33.333 0.00 0.00 0.00 1.40
824 2098 2.095059 CCAGTTCTGTGGCTTTATGCAC 60.095 50.000 0.00 0.00 45.15 4.57
829 2103 2.879756 GCATCCCAGTTCTGTGGCTTTA 60.880 50.000 0.00 0.00 36.11 1.85
841 2115 4.088634 ACACAATTGTTATGCATCCCAGT 58.911 39.130 8.77 0.00 28.43 4.00
864 2138 6.092533 TGCGAATCTGGTATGCATAATGTATG 59.907 38.462 8.28 0.00 39.18 2.39
867 2141 4.388485 TGCGAATCTGGTATGCATAATGT 58.612 39.130 8.28 0.00 0.00 2.71
913 2191 4.202357 TGCAGTAGTGTCAATCTTTGTCCT 60.202 41.667 0.00 0.00 0.00 3.85
1050 2328 5.187186 GGCGAAGAGAATGAGGGGTATTATA 59.813 44.000 0.00 0.00 0.00 0.98
1053 2331 2.104963 GGCGAAGAGAATGAGGGGTATT 59.895 50.000 0.00 0.00 0.00 1.89
1077 2355 2.174319 GGGCGGCGTCAATCTTCTC 61.174 63.158 15.59 0.00 0.00 2.87
1341 2619 3.322466 CCCTGGAACCAGAGGCGT 61.322 66.667 20.79 0.00 46.30 5.68
1924 3227 2.875786 GCAGCTAGATTGCCGCGAC 61.876 63.158 8.23 0.00 35.54 5.19
1925 3228 2.586079 GCAGCTAGATTGCCGCGA 60.586 61.111 8.23 0.00 35.54 5.87
1930 3234 1.269988 TGGAGATCGCAGCTAGATTGC 60.270 52.381 9.03 9.03 38.18 3.56
2059 3374 2.828549 CCGCCATTACCCACTGCC 60.829 66.667 0.00 0.00 0.00 4.85
2096 3411 3.305744 GGCCAAAATGTTACGGATGTGTT 60.306 43.478 0.00 0.00 0.00 3.32
2107 3422 2.873133 TTTCGTTCGGCCAAAATGTT 57.127 40.000 2.24 0.00 0.00 2.71
2158 3478 8.287439 TGATACCGGATTTTGTCACAATTATT 57.713 30.769 9.46 0.00 0.00 1.40
2185 3505 2.795291 AGGAGCCCACCACATCTATA 57.205 50.000 0.00 0.00 0.00 1.31
2588 3910 1.654105 GTAACGCTCACTGTTCATCCG 59.346 52.381 0.00 0.00 0.00 4.18
2689 4011 1.359117 GAACCGGCTCGATCGATCA 59.641 57.895 24.40 11.08 0.00 2.92
2707 4029 1.450312 GTCCTGTTCATCCAGCCCG 60.450 63.158 0.00 0.00 0.00 6.13
2736 4058 2.127708 GGGTGGTCCTGTTCATCCTAT 58.872 52.381 0.00 0.00 31.70 2.57
2777 4099 3.164269 CAGCCCTCCACCGCCTAT 61.164 66.667 0.00 0.00 0.00 2.57
2781 4103 4.864334 CATCCAGCCCTCCACCGC 62.864 72.222 0.00 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.