Multiple sequence alignment - TraesCS5B01G165900

Loading Multiple Alignment...

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 TraesCS5B01G165900 chr5B 100.000 3582 0 0 1 3582 307879819 307883400 0.000000e+00 6615.0
1 TraesCS5B01G165900 chr5B 88.889 135 3 3 1597 1719 307881280 307881414 4.790000e-34 156.0
2 TraesCS5B01G165900 chr5A 92.559 1196 46 21 437 1596 361446470 361447658 0.000000e+00 1676.0
3 TraesCS5B01G165900 chr5A 95.285 403 15 2 1955 2357 361447728 361448126 1.400000e-178 636.0
4 TraesCS5B01G165900 chr5A 91.183 431 24 2 2383 2812 361448119 361448536 1.120000e-159 573.0
5 TraesCS5B01G165900 chr5A 91.584 202 8 6 1597 1790 361447529 361447729 1.640000e-68 270.0
6 TraesCS5B01G165900 chr5A 91.429 105 2 6 2809 2909 361448722 361448823 1.730000e-28 137.0
7 TraesCS5B01G165900 chr5D 95.742 775 21 7 1597 2363 271708141 271707371 0.000000e+00 1238.0
8 TraesCS5B01G165900 chr5D 94.067 691 35 3 437 1122 271717859 271717170 0.000000e+00 1044.0
9 TraesCS5B01G165900 chr5D 96.617 532 15 3 2380 2909 271707387 271706857 0.000000e+00 880.0
10 TraesCS5B01G165900 chr5D 95.368 475 15 5 1123 1596 271708479 271708011 0.000000e+00 749.0
11 TraesCS5B01G165900 chr5D 86.494 348 39 7 10 355 28271802 28271461 3.380000e-100 375.0
12 TraesCS5B01G165900 chr5D 85.057 348 45 6 10 355 41603780 41603438 7.360000e-92 348.0
13 TraesCS5B01G165900 chr5D 84.726 347 46 6 10 352 435192157 435192500 1.230000e-89 340.0
14 TraesCS5B01G165900 chr5D 87.151 179 13 7 1789 1963 94987763 94987935 1.010000e-45 195.0
15 TraesCS5B01G165900 chr5D 97.872 47 1 0 375 421 271717892 271717846 8.240000e-12 82.4
16 TraesCS5B01G165900 chr5D 100.000 29 0 0 358 386 271717935 271717907 2.000000e-03 54.7
17 TraesCS5B01G165900 chr2B 96.884 674 21 0 2909 3582 558262624 558263297 0.000000e+00 1129.0
18 TraesCS5B01G165900 chr2B 96.884 674 21 0 2909 3582 558280163 558280836 0.000000e+00 1129.0
19 TraesCS5B01G165900 chr2B 86.792 318 35 4 41 357 80671896 80672207 7.360000e-92 348.0
20 TraesCS5B01G165900 chr2B 84.524 252 22 10 1328 1576 746313155 746312918 2.150000e-57 233.0
21 TraesCS5B01G165900 chr6B 96.736 674 22 0 2909 3582 681893775 681894448 0.000000e+00 1123.0
22 TraesCS5B01G165900 chr6B 84.127 252 23 10 1328 1576 185000397 185000634 1.000000e-55 228.0
23 TraesCS5B01G165900 chr6B 86.932 176 16 5 1786 1959 27810913 27811083 1.310000e-44 191.0
24 TraesCS5B01G165900 chr4A 96.736 674 22 0 2909 3582 523450522 523451195 0.000000e+00 1123.0
25 TraesCS5B01G165900 chr4A 96.291 674 25 0 2909 3582 732389446 732390119 0.000000e+00 1107.0
26 TraesCS5B01G165900 chr4A 95.710 676 27 2 2909 3582 729118119 729117444 0.000000e+00 1086.0
27 TraesCS5B01G165900 chr3B 96.588 674 23 0 2909 3582 713888849 713889522 0.000000e+00 1118.0
28 TraesCS5B01G165900 chr7A 96.148 675 23 3 2909 3582 459759072 459758400 0.000000e+00 1099.0
29 TraesCS5B01G165900 chr7A 95.704 675 26 3 2909 3582 261389174 261389846 0.000000e+00 1083.0
30 TraesCS5B01G165900 chr7A 86.589 343 40 6 11 351 12012451 12012789 1.210000e-99 374.0
31 TraesCS5B01G165900 chr3D 88.732 355 32 6 10 362 539664077 539663729 9.190000e-116 427.0
32 TraesCS5B01G165900 chr1A 84.633 436 40 16 1170 1597 557153652 557153236 3.330000e-110 409.0
33 TraesCS5B01G165900 chr1A 84.436 257 23 10 1323 1576 327384473 327384231 1.660000e-58 237.0
34 TraesCS5B01G165900 chr1D 90.554 307 24 5 1170 1471 464862933 464862627 5.570000e-108 401.0
35 TraesCS5B01G165900 chr1D 84.127 252 23 10 1328 1576 93820229 93820466 1.000000e-55 228.0
36 TraesCS5B01G165900 chr1B 83.599 439 44 17 1170 1597 641630616 641630195 1.560000e-103 387.0
37 TraesCS5B01G165900 chr7D 85.920 348 46 3 10 356 426563445 426563100 5.650000e-98 368.0
38 TraesCS5B01G165900 chr7D 86.264 182 17 6 1788 1966 23497593 23497769 1.310000e-44 191.0
39 TraesCS5B01G165900 chr6D 85.797 345 42 4 10 352 54386589 54386928 3.400000e-95 359.0
40 TraesCS5B01G165900 chr6D 87.709 179 12 7 1789 1963 161556343 161556515 2.180000e-47 200.0
41 TraesCS5B01G165900 chr6D 87.356 174 15 5 1787 1958 249983548 249983380 3.650000e-45 193.0
42 TraesCS5B01G165900 chr2D 84.195 348 47 8 10 352 59628579 59628923 7.410000e-87 331.0
43 TraesCS5B01G165900 chr2D 86.559 186 14 9 1788 1968 443735732 443735553 1.010000e-45 195.0
44 TraesCS5B01G165900 chr2D 87.283 173 14 4 1789 1960 218046988 218046823 1.310000e-44 191.0
45 TraesCS5B01G165900 chr6A 86.339 183 16 5 1786 1966 499409638 499409813 1.310000e-44 191.0


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 TraesCS5B01G165900 chr5B 307879819 307883400 3581 False 3385.500000 6615 94.4445 1 3582 2 chr5B.!!$F1 3581
1 TraesCS5B01G165900 chr5A 361446470 361448823 2353 False 658.400000 1676 92.4080 437 2909 5 chr5A.!!$F1 2472
2 TraesCS5B01G165900 chr5D 271706857 271708479 1622 True 955.666667 1238 95.9090 1123 2909 3 chr5D.!!$R3 1786
3 TraesCS5B01G165900 chr5D 271717170 271717935 765 True 393.700000 1044 97.3130 358 1122 3 chr5D.!!$R4 764
4 TraesCS5B01G165900 chr2B 558262624 558263297 673 False 1129.000000 1129 96.8840 2909 3582 1 chr2B.!!$F2 673
5 TraesCS5B01G165900 chr2B 558280163 558280836 673 False 1129.000000 1129 96.8840 2909 3582 1 chr2B.!!$F3 673
6 TraesCS5B01G165900 chr6B 681893775 681894448 673 False 1123.000000 1123 96.7360 2909 3582 1 chr6B.!!$F3 673
7 TraesCS5B01G165900 chr4A 523450522 523451195 673 False 1123.000000 1123 96.7360 2909 3582 1 chr4A.!!$F1 673
8 TraesCS5B01G165900 chr4A 732389446 732390119 673 False 1107.000000 1107 96.2910 2909 3582 1 chr4A.!!$F2 673
9 TraesCS5B01G165900 chr4A 729117444 729118119 675 True 1086.000000 1086 95.7100 2909 3582 1 chr4A.!!$R1 673
10 TraesCS5B01G165900 chr3B 713888849 713889522 673 False 1118.000000 1118 96.5880 2909 3582 1 chr3B.!!$F1 673
11 TraesCS5B01G165900 chr7A 459758400 459759072 672 True 1099.000000 1099 96.1480 2909 3582 1 chr7A.!!$R1 673
12 TraesCS5B01G165900 chr7A 261389174 261389846 672 False 1083.000000 1083 95.7040 2909 3582 1 chr7A.!!$F2 673

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
328 329 0.107643 TCATTCAACACGGGTGCAGA 59.892 50.0 0.00 0.00 0.00 4.26 F
949 982 0.179145 GCTGGCTTACTGCAGCATTG 60.179 55.0 15.27 2.81 45.15 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1561 1625 0.771127 TTAGGAAGCAAGCACACCCT 59.229 50.000 0.0 0.0 0.0 4.34 R
2875 3146 2.006888 GCCATTCCGTTCGATCAAAGA 58.993 47.619 0.0 0.0 0.0 2.52 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
59 60 8.943594 TTTTTACCCATGGTAGACAGTTTATT 57.056 30.769 11.73 0.00 39.52 1.40
60 61 7.931578 TTTACCCATGGTAGACAGTTTATTG 57.068 36.000 11.73 0.00 39.52 1.90
61 62 4.270008 ACCCATGGTAGACAGTTTATTGC 58.730 43.478 11.73 0.00 32.11 3.56
62 63 3.312421 CCCATGGTAGACAGTTTATTGCG 59.688 47.826 11.73 0.00 0.00 4.85
63 64 3.938963 CCATGGTAGACAGTTTATTGCGT 59.061 43.478 2.57 0.00 0.00 5.24
64 65 4.201812 CCATGGTAGACAGTTTATTGCGTG 60.202 45.833 2.57 0.00 0.00 5.34
65 66 4.260139 TGGTAGACAGTTTATTGCGTGA 57.740 40.909 0.00 0.00 0.00 4.35
66 67 4.242475 TGGTAGACAGTTTATTGCGTGAG 58.758 43.478 0.00 0.00 0.00 3.51
67 68 3.617263 GGTAGACAGTTTATTGCGTGAGG 59.383 47.826 0.00 0.00 0.00 3.86
68 69 3.402628 AGACAGTTTATTGCGTGAGGT 57.597 42.857 0.00 0.00 0.00 3.85
69 70 3.740115 AGACAGTTTATTGCGTGAGGTT 58.260 40.909 0.00 0.00 0.00 3.50
70 71 3.746492 AGACAGTTTATTGCGTGAGGTTC 59.254 43.478 0.00 0.00 0.00 3.62
71 72 2.478894 ACAGTTTATTGCGTGAGGTTCG 59.521 45.455 0.00 0.00 0.00 3.95
78 79 4.354155 CGTGAGGTTCGCTCCAAA 57.646 55.556 0.00 0.00 0.00 3.28
79 80 2.840974 CGTGAGGTTCGCTCCAAAT 58.159 52.632 0.00 0.00 0.00 2.32
80 81 1.156736 CGTGAGGTTCGCTCCAAATT 58.843 50.000 0.00 0.00 0.00 1.82
81 82 1.535462 CGTGAGGTTCGCTCCAAATTT 59.465 47.619 0.00 0.00 0.00 1.82
82 83 2.031157 CGTGAGGTTCGCTCCAAATTTT 60.031 45.455 0.00 0.00 0.00 1.82
83 84 3.187637 CGTGAGGTTCGCTCCAAATTTTA 59.812 43.478 0.00 0.00 0.00 1.52
84 85 4.669197 CGTGAGGTTCGCTCCAAATTTTAG 60.669 45.833 0.00 0.00 0.00 1.85
85 86 3.190535 TGAGGTTCGCTCCAAATTTTAGC 59.809 43.478 10.87 10.87 0.00 3.09
86 87 3.421844 AGGTTCGCTCCAAATTTTAGCT 58.578 40.909 16.39 0.00 34.03 3.32
87 88 3.440522 AGGTTCGCTCCAAATTTTAGCTC 59.559 43.478 16.39 9.14 34.03 4.09
88 89 3.190535 GGTTCGCTCCAAATTTTAGCTCA 59.809 43.478 16.39 4.54 34.03 4.26
89 90 4.142381 GGTTCGCTCCAAATTTTAGCTCAT 60.142 41.667 16.39 0.00 34.03 2.90
90 91 5.402398 GTTCGCTCCAAATTTTAGCTCATT 58.598 37.500 16.39 0.00 34.03 2.57
91 92 5.643379 TCGCTCCAAATTTTAGCTCATTT 57.357 34.783 16.39 0.00 34.03 2.32
92 93 5.401550 TCGCTCCAAATTTTAGCTCATTTG 58.598 37.500 16.39 14.72 39.25 2.32
93 94 5.182950 TCGCTCCAAATTTTAGCTCATTTGA 59.817 36.000 20.05 10.28 41.18 2.69
94 95 5.863397 CGCTCCAAATTTTAGCTCATTTGAA 59.137 36.000 20.05 6.24 41.18 2.69
95 96 6.532657 CGCTCCAAATTTTAGCTCATTTGAAT 59.467 34.615 20.05 0.78 41.18 2.57
96 97 7.701924 CGCTCCAAATTTTAGCTCATTTGAATA 59.298 33.333 20.05 9.54 41.18 1.75
97 98 9.538508 GCTCCAAATTTTAGCTCATTTGAATAT 57.461 29.630 20.05 0.00 41.18 1.28
106 107 6.557291 AGCTCATTTGAATATCTTAGCAGC 57.443 37.500 0.00 0.00 0.00 5.25
107 108 6.297582 AGCTCATTTGAATATCTTAGCAGCT 58.702 36.000 0.00 0.00 0.00 4.24
108 109 6.427547 AGCTCATTTGAATATCTTAGCAGCTC 59.572 38.462 0.00 0.00 0.00 4.09
109 110 6.427547 GCTCATTTGAATATCTTAGCAGCTCT 59.572 38.462 0.00 0.00 0.00 4.09
110 111 7.360269 GCTCATTTGAATATCTTAGCAGCTCTC 60.360 40.741 0.00 0.00 0.00 3.20
111 112 7.503549 TCATTTGAATATCTTAGCAGCTCTCA 58.496 34.615 0.00 0.00 0.00 3.27
112 113 7.656542 TCATTTGAATATCTTAGCAGCTCTCAG 59.343 37.037 0.00 0.00 0.00 3.35
113 114 4.880759 TGAATATCTTAGCAGCTCTCAGC 58.119 43.478 0.00 0.00 42.84 4.26
114 115 4.343239 TGAATATCTTAGCAGCTCTCAGCA 59.657 41.667 0.00 0.00 45.56 4.41
115 116 4.952071 ATATCTTAGCAGCTCTCAGCAA 57.048 40.909 0.00 0.00 45.56 3.91
116 117 3.623906 ATCTTAGCAGCTCTCAGCAAA 57.376 42.857 0.00 0.00 45.56 3.68
117 118 3.407424 TCTTAGCAGCTCTCAGCAAAA 57.593 42.857 0.00 0.00 45.56 2.44
118 119 3.743521 TCTTAGCAGCTCTCAGCAAAAA 58.256 40.909 0.00 0.00 45.56 1.94
139 140 7.936496 AAAAAGACAAATTGGGTCAAAACAT 57.064 28.000 11.72 0.00 37.74 2.71
140 141 7.936496 AAAAGACAAATTGGGTCAAAACATT 57.064 28.000 11.72 0.00 37.74 2.71
141 142 9.454859 AAAAAGACAAATTGGGTCAAAACATTA 57.545 25.926 11.72 0.00 37.74 1.90
142 143 9.625747 AAAAGACAAATTGGGTCAAAACATTAT 57.374 25.926 11.72 0.00 37.74 1.28
145 146 9.874205 AGACAAATTGGGTCAAAACATTATATG 57.126 29.630 11.72 0.00 37.74 1.78
146 147 9.868277 GACAAATTGGGTCAAAACATTATATGA 57.132 29.630 0.00 0.00 35.36 2.15
170 171 9.895138 TGAATACTAAACTGTTTTATAGACCCC 57.105 33.333 11.48 0.00 0.00 4.95
171 172 8.953368 AATACTAAACTGTTTTATAGACCCCG 57.047 34.615 11.48 0.00 0.00 5.73
172 173 6.610075 ACTAAACTGTTTTATAGACCCCGA 57.390 37.500 11.48 0.00 0.00 5.14
173 174 7.008021 ACTAAACTGTTTTATAGACCCCGAA 57.992 36.000 11.48 0.00 0.00 4.30
174 175 7.627311 ACTAAACTGTTTTATAGACCCCGAAT 58.373 34.615 11.48 0.00 0.00 3.34
175 176 8.105197 ACTAAACTGTTTTATAGACCCCGAATT 58.895 33.333 11.48 0.00 0.00 2.17
176 177 7.770366 AAACTGTTTTATAGACCCCGAATTT 57.230 32.000 0.00 0.00 0.00 1.82
177 178 8.866970 AAACTGTTTTATAGACCCCGAATTTA 57.133 30.769 0.00 0.00 0.00 1.40
178 179 9.470399 AAACTGTTTTATAGACCCCGAATTTAT 57.530 29.630 0.00 0.00 0.00 1.40
208 209 2.533266 GAGAGTTGCTCAGTTGTCCA 57.467 50.000 0.00 0.00 43.38 4.02
209 210 2.838736 GAGAGTTGCTCAGTTGTCCAA 58.161 47.619 0.00 0.00 43.38 3.53
210 211 3.406764 GAGAGTTGCTCAGTTGTCCAAT 58.593 45.455 0.00 0.00 43.38 3.16
211 212 3.817647 GAGAGTTGCTCAGTTGTCCAATT 59.182 43.478 0.00 0.00 43.38 2.32
212 213 3.567164 AGAGTTGCTCAGTTGTCCAATTG 59.433 43.478 0.00 0.00 32.06 2.32
213 214 3.554934 AGTTGCTCAGTTGTCCAATTGA 58.445 40.909 7.12 5.31 36.01 2.57
214 215 4.147321 AGTTGCTCAGTTGTCCAATTGAT 58.853 39.130 7.12 0.00 36.64 2.57
215 216 4.586001 AGTTGCTCAGTTGTCCAATTGATT 59.414 37.500 7.12 0.00 36.64 2.57
216 217 5.069516 AGTTGCTCAGTTGTCCAATTGATTT 59.930 36.000 7.12 0.00 36.64 2.17
217 218 4.873817 TGCTCAGTTGTCCAATTGATTTG 58.126 39.130 7.12 0.00 36.64 2.32
218 219 4.583907 TGCTCAGTTGTCCAATTGATTTGA 59.416 37.500 7.12 1.58 36.64 2.69
219 220 5.068855 TGCTCAGTTGTCCAATTGATTTGAA 59.931 36.000 7.12 0.00 36.64 2.69
220 221 5.984926 GCTCAGTTGTCCAATTGATTTGAAA 59.015 36.000 7.12 0.00 36.64 2.69
221 222 6.479660 GCTCAGTTGTCCAATTGATTTGAAAA 59.520 34.615 7.12 0.00 36.64 2.29
222 223 7.517259 GCTCAGTTGTCCAATTGATTTGAAAAC 60.517 37.037 7.12 7.15 36.64 2.43
223 224 7.555087 TCAGTTGTCCAATTGATTTGAAAACT 58.445 30.769 7.12 9.30 37.53 2.66
224 225 7.492020 TCAGTTGTCCAATTGATTTGAAAACTG 59.508 33.333 24.99 24.99 42.92 3.16
225 226 6.762661 AGTTGTCCAATTGATTTGAAAACTGG 59.237 34.615 13.90 0.00 37.53 4.00
226 227 5.609423 TGTCCAATTGATTTGAAAACTGGG 58.391 37.500 7.12 0.00 37.53 4.45
227 228 5.130145 TGTCCAATTGATTTGAAAACTGGGT 59.870 36.000 7.12 0.00 37.53 4.51
228 229 5.696270 GTCCAATTGATTTGAAAACTGGGTC 59.304 40.000 7.12 0.00 37.53 4.46
229 230 4.685628 CCAATTGATTTGAAAACTGGGTCG 59.314 41.667 7.12 0.00 37.53 4.79
230 231 5.508825 CCAATTGATTTGAAAACTGGGTCGA 60.509 40.000 7.12 0.00 37.53 4.20
231 232 5.782893 ATTGATTTGAAAACTGGGTCGAA 57.217 34.783 0.00 0.00 0.00 3.71
232 233 4.561735 TGATTTGAAAACTGGGTCGAAC 57.438 40.909 0.00 0.00 0.00 3.95
233 234 3.316868 TGATTTGAAAACTGGGTCGAACC 59.683 43.478 14.24 14.24 37.60 3.62
234 235 2.721425 TTGAAAACTGGGTCGAACCT 57.279 45.000 22.56 0.00 38.64 3.50
235 236 2.249844 TGAAAACTGGGTCGAACCTC 57.750 50.000 22.56 10.04 38.64 3.85
236 237 1.487142 TGAAAACTGGGTCGAACCTCA 59.513 47.619 22.56 12.87 38.64 3.86
237 238 1.871676 GAAAACTGGGTCGAACCTCAC 59.128 52.381 22.56 2.62 38.64 3.51
238 239 0.249741 AAACTGGGTCGAACCTCACG 60.250 55.000 22.56 8.99 38.64 4.35
239 240 1.397390 AACTGGGTCGAACCTCACGT 61.397 55.000 22.56 9.66 38.64 4.49
240 241 0.538057 ACTGGGTCGAACCTCACGTA 60.538 55.000 22.56 0.00 38.64 3.57
241 242 0.815734 CTGGGTCGAACCTCACGTAT 59.184 55.000 22.56 0.00 38.64 3.06
242 243 0.813184 TGGGTCGAACCTCACGTATC 59.187 55.000 22.56 0.00 38.64 2.24
243 244 0.813184 GGGTCGAACCTCACGTATCA 59.187 55.000 13.76 0.00 38.64 2.15
244 245 1.203052 GGGTCGAACCTCACGTATCAA 59.797 52.381 13.76 0.00 38.64 2.57
245 246 2.353011 GGGTCGAACCTCACGTATCAAA 60.353 50.000 13.76 0.00 38.64 2.69
246 247 3.518590 GGTCGAACCTCACGTATCAAAT 58.481 45.455 0.00 0.00 34.73 2.32
247 248 3.930848 GGTCGAACCTCACGTATCAAATT 59.069 43.478 0.00 0.00 34.73 1.82
248 249 4.390909 GGTCGAACCTCACGTATCAAATTT 59.609 41.667 0.00 0.00 34.73 1.82
249 250 5.106830 GGTCGAACCTCACGTATCAAATTTT 60.107 40.000 0.00 0.00 34.73 1.82
250 251 6.013689 GTCGAACCTCACGTATCAAATTTTC 58.986 40.000 0.00 0.00 0.00 2.29
251 252 5.929992 TCGAACCTCACGTATCAAATTTTCT 59.070 36.000 0.00 0.00 0.00 2.52
252 253 7.062605 GTCGAACCTCACGTATCAAATTTTCTA 59.937 37.037 0.00 0.00 0.00 2.10
253 254 7.062605 TCGAACCTCACGTATCAAATTTTCTAC 59.937 37.037 0.00 0.00 0.00 2.59
254 255 6.980051 ACCTCACGTATCAAATTTTCTACC 57.020 37.500 0.00 0.00 0.00 3.18
255 256 6.469410 ACCTCACGTATCAAATTTTCTACCA 58.531 36.000 0.00 0.00 0.00 3.25
256 257 7.110155 ACCTCACGTATCAAATTTTCTACCAT 58.890 34.615 0.00 0.00 0.00 3.55
257 258 7.065803 ACCTCACGTATCAAATTTTCTACCATG 59.934 37.037 0.00 0.00 0.00 3.66
258 259 7.279981 CCTCACGTATCAAATTTTCTACCATGA 59.720 37.037 0.00 0.00 0.00 3.07
259 260 8.196802 TCACGTATCAAATTTTCTACCATGAG 57.803 34.615 0.00 0.00 0.00 2.90
260 261 8.038351 TCACGTATCAAATTTTCTACCATGAGA 58.962 33.333 0.00 0.00 0.00 3.27
261 262 8.830580 CACGTATCAAATTTTCTACCATGAGAT 58.169 33.333 0.00 0.00 0.00 2.75
262 263 9.396022 ACGTATCAAATTTTCTACCATGAGATT 57.604 29.630 0.00 0.00 0.00 2.40
263 264 9.869844 CGTATCAAATTTTCTACCATGAGATTC 57.130 33.333 0.00 0.00 0.00 2.52
325 326 2.500509 TTTTCATTCAACACGGGTGC 57.499 45.000 0.00 0.00 0.00 5.01
326 327 1.393603 TTTCATTCAACACGGGTGCA 58.606 45.000 0.00 0.00 0.00 4.57
327 328 0.950836 TTCATTCAACACGGGTGCAG 59.049 50.000 0.00 0.00 0.00 4.41
328 329 0.107643 TCATTCAACACGGGTGCAGA 59.892 50.000 0.00 0.00 0.00 4.26
329 330 1.167851 CATTCAACACGGGTGCAGAT 58.832 50.000 0.00 0.00 0.00 2.90
330 331 1.135603 CATTCAACACGGGTGCAGATG 60.136 52.381 0.00 0.00 0.00 2.90
331 332 0.107643 TTCAACACGGGTGCAGATGA 59.892 50.000 0.00 0.00 0.00 2.92
332 333 0.602638 TCAACACGGGTGCAGATGAC 60.603 55.000 0.00 0.00 0.00 3.06
333 334 1.302511 AACACGGGTGCAGATGACC 60.303 57.895 0.00 0.00 0.00 4.02
337 338 4.489771 GGGTGCAGATGACCCCGG 62.490 72.222 0.00 0.00 46.76 5.73
338 339 4.489771 GGTGCAGATGACCCCGGG 62.490 72.222 15.80 15.80 0.00 5.73
341 342 4.554036 GCAGATGACCCCGGGCTC 62.554 72.222 17.73 12.95 0.00 4.70
342 343 3.083349 CAGATGACCCCGGGCTCA 61.083 66.667 20.82 20.82 0.00 4.26
343 344 2.765807 AGATGACCCCGGGCTCAG 60.766 66.667 22.71 8.78 0.00 3.35
344 345 2.764128 GATGACCCCGGGCTCAGA 60.764 66.667 22.71 1.35 0.00 3.27
345 346 2.285368 ATGACCCCGGGCTCAGAA 60.285 61.111 22.71 0.60 0.00 3.02
346 347 1.910580 GATGACCCCGGGCTCAGAAA 61.911 60.000 22.71 0.22 0.00 2.52
347 348 1.497309 ATGACCCCGGGCTCAGAAAA 61.497 55.000 22.71 0.00 0.00 2.29
348 349 1.377333 GACCCCGGGCTCAGAAAAG 60.377 63.158 17.73 0.00 0.00 2.27
349 350 2.044946 CCCCGGGCTCAGAAAAGG 60.045 66.667 17.73 0.00 0.00 3.11
350 351 2.602676 CCCCGGGCTCAGAAAAGGA 61.603 63.158 17.73 0.00 0.00 3.36
351 352 1.609783 CCCGGGCTCAGAAAAGGAT 59.390 57.895 8.08 0.00 0.00 3.24
352 353 0.464554 CCCGGGCTCAGAAAAGGATC 60.465 60.000 8.08 0.00 0.00 3.36
353 354 0.543749 CCGGGCTCAGAAAAGGATCT 59.456 55.000 0.00 0.00 0.00 2.75
354 355 1.474143 CCGGGCTCAGAAAAGGATCTC 60.474 57.143 0.00 0.00 0.00 2.75
355 356 1.474143 CGGGCTCAGAAAAGGATCTCC 60.474 57.143 0.00 0.00 0.00 3.71
356 357 1.133945 GGGCTCAGAAAAGGATCTCCC 60.134 57.143 0.00 0.00 36.42 4.30
412 439 8.519799 AATGATGTTACCAAAGGAATAACGAT 57.480 30.769 0.00 0.00 32.53 3.73
413 440 7.315247 TGATGTTACCAAAGGAATAACGATG 57.685 36.000 0.00 0.00 32.53 3.84
414 441 6.317642 TGATGTTACCAAAGGAATAACGATGG 59.682 38.462 0.00 0.00 32.53 3.51
415 442 4.396790 TGTTACCAAAGGAATAACGATGGC 59.603 41.667 0.00 0.00 32.53 4.40
416 443 3.366052 ACCAAAGGAATAACGATGGCT 57.634 42.857 0.00 0.00 0.00 4.75
417 444 3.697166 ACCAAAGGAATAACGATGGCTT 58.303 40.909 0.00 0.00 0.00 4.35
418 445 4.850680 ACCAAAGGAATAACGATGGCTTA 58.149 39.130 0.00 0.00 0.00 3.09
419 446 4.881850 ACCAAAGGAATAACGATGGCTTAG 59.118 41.667 0.00 0.00 0.00 2.18
420 447 5.123227 CCAAAGGAATAACGATGGCTTAGA 58.877 41.667 0.00 0.00 0.00 2.10
421 448 5.765182 CCAAAGGAATAACGATGGCTTAGAT 59.235 40.000 0.00 0.00 0.00 1.98
422 449 6.263168 CCAAAGGAATAACGATGGCTTAGATT 59.737 38.462 0.00 0.00 0.00 2.40
423 450 7.201821 CCAAAGGAATAACGATGGCTTAGATTT 60.202 37.037 0.00 0.00 0.00 2.17
424 451 7.881775 AAGGAATAACGATGGCTTAGATTTT 57.118 32.000 0.00 0.00 0.00 1.82
425 452 7.881775 AGGAATAACGATGGCTTAGATTTTT 57.118 32.000 0.00 0.00 0.00 1.94
638 670 0.842467 CTTTCTCCCCAGTCCCCACT 60.842 60.000 0.00 0.00 0.00 4.00
639 671 0.840722 TTTCTCCCCAGTCCCCACTC 60.841 60.000 0.00 0.00 0.00 3.51
646 678 0.545309 CCAGTCCCCACTCTTCTCCA 60.545 60.000 0.00 0.00 0.00 3.86
675 707 2.813908 GTTACCAGTCTGCCGCCG 60.814 66.667 0.00 0.00 0.00 6.46
695 727 4.715130 CCTCTCACCCCACCCCGA 62.715 72.222 0.00 0.00 0.00 5.14
809 842 4.752879 GCCGCCGCCTTGTGAGTA 62.753 66.667 0.00 0.00 0.00 2.59
810 843 2.186903 CCGCCGCCTTGTGAGTAT 59.813 61.111 0.00 0.00 0.00 2.12
866 899 0.729116 GCATGATATTAGGCGCGCAT 59.271 50.000 34.42 30.20 0.00 4.73
871 904 2.094026 TGATATTAGGCGCGCATCTGAT 60.094 45.455 34.42 23.89 0.00 2.90
949 982 0.179145 GCTGGCTTACTGCAGCATTG 60.179 55.000 15.27 2.81 45.15 2.82
989 1022 4.082463 GGTATCGAGATCTGGATCCTGAAC 60.082 50.000 21.89 20.49 38.58 3.18
1008 1041 1.651240 CTGCCTGGGAAATGAGTGCG 61.651 60.000 0.00 0.00 0.00 5.34
1059 1092 2.592102 ATGCTCCTGTTGGTTCATGT 57.408 45.000 0.00 0.00 34.23 3.21
1065 1098 4.278419 GCTCCTGTTGGTTCATGTTTACTT 59.722 41.667 0.00 0.00 34.23 2.24
1071 1104 7.976734 CCTGTTGGTTCATGTTTACTTTTGTTA 59.023 33.333 0.00 0.00 0.00 2.41
1078 1111 8.958043 GTTCATGTTTACTTTTGTTAGCTTCAG 58.042 33.333 0.00 0.00 0.00 3.02
1159 1222 3.557185 ACGAAACTTTTGACTAACCCGTC 59.443 43.478 0.00 0.00 34.52 4.79
1162 1225 4.411256 AACTTTTGACTAACCCGTCTGA 57.589 40.909 0.00 0.00 35.00 3.27
1283 1347 8.252417 ACCTGGTAAGTTTAATCGTTTTGTTTT 58.748 29.630 0.00 0.00 0.00 2.43
1284 1348 9.089601 CCTGGTAAGTTTAATCGTTTTGTTTTT 57.910 29.630 0.00 0.00 0.00 1.94
1569 1633 5.835113 ATGTGTAATGATTTAGGGTGTGC 57.165 39.130 0.00 0.00 0.00 4.57
1570 1634 4.917385 TGTGTAATGATTTAGGGTGTGCT 58.083 39.130 0.00 0.00 0.00 4.40
1571 1635 5.321102 TGTGTAATGATTTAGGGTGTGCTT 58.679 37.500 0.00 0.00 0.00 3.91
1572 1636 5.182950 TGTGTAATGATTTAGGGTGTGCTTG 59.817 40.000 0.00 0.00 0.00 4.01
1573 1637 3.874392 AATGATTTAGGGTGTGCTTGC 57.126 42.857 0.00 0.00 0.00 4.01
1574 1638 2.584835 TGATTTAGGGTGTGCTTGCT 57.415 45.000 0.00 0.00 0.00 3.91
1575 1639 2.875296 TGATTTAGGGTGTGCTTGCTT 58.125 42.857 0.00 0.00 0.00 3.91
1576 1640 2.819608 TGATTTAGGGTGTGCTTGCTTC 59.180 45.455 0.00 0.00 0.00 3.86
1577 1641 1.616159 TTTAGGGTGTGCTTGCTTCC 58.384 50.000 0.00 0.00 0.00 3.46
1578 1642 0.771127 TTAGGGTGTGCTTGCTTCCT 59.229 50.000 0.00 0.00 0.00 3.36
1579 1643 1.651737 TAGGGTGTGCTTGCTTCCTA 58.348 50.000 0.00 0.00 0.00 2.94
1580 1644 0.771127 AGGGTGTGCTTGCTTCCTAA 59.229 50.000 0.00 0.00 0.00 2.69
1581 1645 1.168714 GGGTGTGCTTGCTTCCTAAG 58.831 55.000 0.00 0.00 0.00 2.18
1646 1710 9.595823 TTATAGTATTGTTGTTAGCTCAACCTC 57.404 33.333 13.92 4.34 44.66 3.85
1647 1711 6.115448 AGTATTGTTGTTAGCTCAACCTCT 57.885 37.500 13.92 6.05 44.66 3.69
1648 1712 6.534634 AGTATTGTTGTTAGCTCAACCTCTT 58.465 36.000 13.92 1.90 44.66 2.85
1649 1713 6.998673 AGTATTGTTGTTAGCTCAACCTCTTT 59.001 34.615 13.92 0.00 44.66 2.52
1650 1714 6.715347 ATTGTTGTTAGCTCAACCTCTTTT 57.285 33.333 13.92 0.00 44.66 2.27
1651 1715 6.524101 TTGTTGTTAGCTCAACCTCTTTTT 57.476 33.333 13.92 0.00 44.66 1.94
1669 1733 3.663995 TTTTGGCACATCCATGACTTG 57.336 42.857 0.00 0.00 46.04 3.16
1670 1734 2.583024 TTGGCACATCCATGACTTGA 57.417 45.000 0.00 0.00 46.04 3.02
1671 1735 2.583024 TGGCACATCCATGACTTGAA 57.417 45.000 0.00 0.00 40.72 2.69
1672 1736 3.090210 TGGCACATCCATGACTTGAAT 57.910 42.857 0.00 0.00 40.72 2.57
1673 1737 4.233632 TGGCACATCCATGACTTGAATA 57.766 40.909 0.00 0.00 40.72 1.75
1674 1738 4.598022 TGGCACATCCATGACTTGAATAA 58.402 39.130 0.00 0.00 40.72 1.40
1675 1739 5.202765 TGGCACATCCATGACTTGAATAAT 58.797 37.500 0.00 0.00 40.72 1.28
1676 1740 5.657745 TGGCACATCCATGACTTGAATAATT 59.342 36.000 0.00 0.00 40.72 1.40
1677 1741 6.154877 TGGCACATCCATGACTTGAATAATTT 59.845 34.615 0.00 0.00 40.72 1.82
1678 1742 7.341512 TGGCACATCCATGACTTGAATAATTTA 59.658 33.333 0.00 0.00 40.72 1.40
1679 1743 8.362639 GGCACATCCATGACTTGAATAATTTAT 58.637 33.333 0.00 0.00 34.01 1.40
1680 1744 9.188588 GCACATCCATGACTTGAATAATTTATG 57.811 33.333 0.00 0.00 0.00 1.90
1727 1791 4.601019 CAAACTTAATATTGGCCTCGCTG 58.399 43.478 3.32 0.00 0.00 5.18
1774 1838 6.986817 TCAAAACAGAAAACAAAGTGAACCAA 59.013 30.769 0.00 0.00 0.00 3.67
1804 1868 3.214328 GGTTATACTACCTCCGTTCCGA 58.786 50.000 0.00 0.00 35.23 4.55
1845 1909 6.490381 AGAGATTCTAATGCGGACTACATACA 59.510 38.462 0.00 0.00 0.00 2.29
1860 1924 7.602644 GGACTACATACAGAACAAAATGAGTGA 59.397 37.037 0.00 0.00 0.00 3.41
1988 2052 7.693952 TCTTGCTACAGTAGAAAAACAGTTTG 58.306 34.615 12.15 0.00 0.00 2.93
2182 2246 7.065324 GCAACCACAAATATGTAACTACTAGCA 59.935 37.037 0.00 0.00 37.82 3.49
2222 2286 4.455533 TGTTTAGTGCTTGCCATAGTTGAG 59.544 41.667 0.00 0.00 0.00 3.02
2232 2296 7.280876 TGCTTGCCATAGTTGAGTTTAAGATAG 59.719 37.037 0.00 0.00 0.00 2.08
2233 2297 7.281100 GCTTGCCATAGTTGAGTTTAAGATAGT 59.719 37.037 0.00 0.00 0.00 2.12
2234 2298 9.817809 CTTGCCATAGTTGAGTTTAAGATAGTA 57.182 33.333 0.00 0.00 0.00 1.82
2349 2413 6.018425 CGAGCTCATAAACAAGATGCACTTAT 60.018 38.462 15.40 0.00 37.03 1.73
2350 2414 7.466455 CGAGCTCATAAACAAGATGCACTTATT 60.466 37.037 15.40 0.00 37.03 1.40
2351 2415 8.737168 AGCTCATAAACAAGATGCACTTATTA 57.263 30.769 0.00 0.00 37.03 0.98
2352 2416 9.347240 AGCTCATAAACAAGATGCACTTATTAT 57.653 29.630 0.00 1.80 37.03 1.28
2353 2417 9.956720 GCTCATAAACAAGATGCACTTATTATT 57.043 29.630 0.00 0.00 37.03 1.40
2412 2476 8.776376 ATTATTATTTCTTGGTTTGTTGCTGG 57.224 30.769 0.00 0.00 0.00 4.85
2581 2645 7.148407 GCAAGTGATTCGAAAGAGAGGAAATAA 60.148 37.037 0.00 0.00 43.69 1.40
2722 2799 4.348168 GGGATATATTATGGATGCGGAGGT 59.652 45.833 0.00 0.00 0.00 3.85
2723 2800 5.511545 GGGATATATTATGGATGCGGAGGTC 60.512 48.000 0.00 0.00 0.00 3.85
2750 2827 5.118050 TCTCGTGTTATTTTGCTAGTTGTCG 59.882 40.000 0.00 0.00 0.00 4.35
2775 2852 0.179045 ACTAAGCGATGGACCCATGC 60.179 55.000 6.23 10.13 36.70 4.06
2776 2853 0.179048 CTAAGCGATGGACCCATGCA 60.179 55.000 18.56 0.00 36.70 3.96
2799 2876 5.770162 CACCTTTTTGGATTGTACTCCTTCT 59.230 40.000 3.08 0.00 39.71 2.85
3180 3453 2.292292 GCAAACTACATTGTTGGACCGT 59.708 45.455 0.00 0.00 32.80 4.83
3183 3456 3.202829 ACTACATTGTTGGACCGTTGT 57.797 42.857 0.00 0.00 0.00 3.32
3549 3823 3.553828 TCCCCTAATAAAACCTCTGCG 57.446 47.619 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 8.798402 CAATAAACTGTCTACCATGGGTAAAAA 58.202 33.333 18.09 0.00 37.76 1.94
35 36 7.094118 GCAATAAACTGTCTACCATGGGTAAAA 60.094 37.037 18.09 0.00 37.76 1.52
36 37 6.376018 GCAATAAACTGTCTACCATGGGTAAA 59.624 38.462 18.09 0.00 37.76 2.01
37 38 5.883673 GCAATAAACTGTCTACCATGGGTAA 59.116 40.000 18.09 0.00 37.76 2.85
38 39 5.433526 GCAATAAACTGTCTACCATGGGTA 58.566 41.667 18.09 5.32 37.09 3.69
39 40 4.270008 GCAATAAACTGTCTACCATGGGT 58.730 43.478 18.09 4.30 40.16 4.51
40 41 3.312421 CGCAATAAACTGTCTACCATGGG 59.688 47.826 18.09 0.00 0.00 4.00
41 42 3.938963 ACGCAATAAACTGTCTACCATGG 59.061 43.478 11.19 11.19 0.00 3.66
42 43 4.629634 TCACGCAATAAACTGTCTACCATG 59.370 41.667 0.00 0.00 0.00 3.66
43 44 4.827692 TCACGCAATAAACTGTCTACCAT 58.172 39.130 0.00 0.00 0.00 3.55
44 45 4.242475 CTCACGCAATAAACTGTCTACCA 58.758 43.478 0.00 0.00 0.00 3.25
45 46 3.617263 CCTCACGCAATAAACTGTCTACC 59.383 47.826 0.00 0.00 0.00 3.18
46 47 4.243270 ACCTCACGCAATAAACTGTCTAC 58.757 43.478 0.00 0.00 0.00 2.59
47 48 4.530710 ACCTCACGCAATAAACTGTCTA 57.469 40.909 0.00 0.00 0.00 2.59
48 49 3.402628 ACCTCACGCAATAAACTGTCT 57.597 42.857 0.00 0.00 0.00 3.41
49 50 3.423123 CGAACCTCACGCAATAAACTGTC 60.423 47.826 0.00 0.00 0.00 3.51
50 51 2.478894 CGAACCTCACGCAATAAACTGT 59.521 45.455 0.00 0.00 0.00 3.55
51 52 3.103793 CGAACCTCACGCAATAAACTG 57.896 47.619 0.00 0.00 0.00 3.16
61 62 1.156736 AATTTGGAGCGAACCTCACG 58.843 50.000 0.00 0.00 42.62 4.35
62 63 3.643159 AAAATTTGGAGCGAACCTCAC 57.357 42.857 0.00 0.00 42.62 3.51
63 64 3.190535 GCTAAAATTTGGAGCGAACCTCA 59.809 43.478 9.01 0.00 42.62 3.86
64 65 3.440522 AGCTAAAATTTGGAGCGAACCTC 59.559 43.478 15.87 0.00 41.23 3.85
65 66 3.421844 AGCTAAAATTTGGAGCGAACCT 58.578 40.909 15.87 0.80 41.23 3.50
66 67 3.190535 TGAGCTAAAATTTGGAGCGAACC 59.809 43.478 15.87 9.65 41.23 3.62
67 68 4.419522 TGAGCTAAAATTTGGAGCGAAC 57.580 40.909 15.87 12.76 41.23 3.95
68 69 5.643379 AATGAGCTAAAATTTGGAGCGAA 57.357 34.783 15.87 10.67 41.23 4.70
69 70 5.182950 TCAAATGAGCTAAAATTTGGAGCGA 59.817 36.000 20.46 9.71 41.83 4.93
70 71 5.401550 TCAAATGAGCTAAAATTTGGAGCG 58.598 37.500 20.46 5.14 41.83 5.03
71 72 7.838771 ATTCAAATGAGCTAAAATTTGGAGC 57.161 32.000 20.46 14.63 41.83 4.70
80 81 8.562892 GCTGCTAAGATATTCAAATGAGCTAAA 58.437 33.333 0.00 0.00 0.00 1.85
81 82 7.935755 AGCTGCTAAGATATTCAAATGAGCTAA 59.064 33.333 0.00 0.00 30.33 3.09
82 83 7.448420 AGCTGCTAAGATATTCAAATGAGCTA 58.552 34.615 0.00 0.00 30.33 3.32
83 84 6.297582 AGCTGCTAAGATATTCAAATGAGCT 58.702 36.000 0.00 0.00 0.00 4.09
84 85 6.427547 AGAGCTGCTAAGATATTCAAATGAGC 59.572 38.462 0.15 0.00 0.00 4.26
85 86 7.656542 TGAGAGCTGCTAAGATATTCAAATGAG 59.343 37.037 0.15 0.00 0.00 2.90
86 87 7.503549 TGAGAGCTGCTAAGATATTCAAATGA 58.496 34.615 0.15 0.00 0.00 2.57
87 88 7.571613 GCTGAGAGCTGCTAAGATATTCAAATG 60.572 40.741 0.15 0.00 38.45 2.32
88 89 6.427547 GCTGAGAGCTGCTAAGATATTCAAAT 59.572 38.462 0.15 0.00 38.45 2.32
89 90 5.757320 GCTGAGAGCTGCTAAGATATTCAAA 59.243 40.000 0.15 0.00 38.45 2.69
90 91 5.163374 TGCTGAGAGCTGCTAAGATATTCAA 60.163 40.000 0.15 0.00 42.97 2.69
91 92 4.343239 TGCTGAGAGCTGCTAAGATATTCA 59.657 41.667 0.15 0.00 42.97 2.57
92 93 4.880759 TGCTGAGAGCTGCTAAGATATTC 58.119 43.478 0.15 0.00 42.97 1.75
93 94 4.952071 TGCTGAGAGCTGCTAAGATATT 57.048 40.909 0.15 0.00 42.97 1.28
94 95 4.952071 TTGCTGAGAGCTGCTAAGATAT 57.048 40.909 0.15 0.00 42.97 1.63
95 96 4.743057 TTTGCTGAGAGCTGCTAAGATA 57.257 40.909 0.15 0.00 42.97 1.98
96 97 3.623906 TTTGCTGAGAGCTGCTAAGAT 57.376 42.857 0.15 0.00 42.97 2.40
97 98 3.407424 TTTTGCTGAGAGCTGCTAAGA 57.593 42.857 0.15 0.00 42.97 2.10
115 116 7.936496 ATGTTTTGACCCAATTTGTCTTTTT 57.064 28.000 6.47 0.00 33.83 1.94
116 117 7.936496 AATGTTTTGACCCAATTTGTCTTTT 57.064 28.000 6.47 0.00 33.83 2.27
119 120 9.874205 CATATAATGTTTTGACCCAATTTGTCT 57.126 29.630 6.47 0.00 33.83 3.41
120 121 9.868277 TCATATAATGTTTTGACCCAATTTGTC 57.132 29.630 0.00 0.00 0.00 3.18
144 145 9.895138 GGGGTCTATAAAACAGTTTAGTATTCA 57.105 33.333 0.00 0.00 32.76 2.57
145 146 9.038803 CGGGGTCTATAAAACAGTTTAGTATTC 57.961 37.037 0.00 0.00 32.76 1.75
146 147 8.761689 TCGGGGTCTATAAAACAGTTTAGTATT 58.238 33.333 0.00 0.00 32.76 1.89
147 148 8.310122 TCGGGGTCTATAAAACAGTTTAGTAT 57.690 34.615 0.00 0.00 32.76 2.12
148 149 7.716799 TCGGGGTCTATAAAACAGTTTAGTA 57.283 36.000 0.00 0.00 32.76 1.82
149 150 6.610075 TCGGGGTCTATAAAACAGTTTAGT 57.390 37.500 0.00 0.00 32.76 2.24
150 151 8.502105 AATTCGGGGTCTATAAAACAGTTTAG 57.498 34.615 0.00 0.00 32.76 1.85
151 152 8.866970 AAATTCGGGGTCTATAAAACAGTTTA 57.133 30.769 0.00 0.00 33.76 2.01
152 153 7.770366 AAATTCGGGGTCTATAAAACAGTTT 57.230 32.000 0.00 0.00 0.00 2.66
189 190 2.533266 TGGACAACTGAGCAACTCTC 57.467 50.000 0.00 0.00 42.23 3.20
190 191 3.498774 ATTGGACAACTGAGCAACTCT 57.501 42.857 0.00 0.00 0.00 3.24
191 192 3.565482 TCAATTGGACAACTGAGCAACTC 59.435 43.478 5.42 0.00 0.00 3.01
192 193 3.554934 TCAATTGGACAACTGAGCAACT 58.445 40.909 5.42 0.00 0.00 3.16
193 194 3.988379 TCAATTGGACAACTGAGCAAC 57.012 42.857 5.42 0.00 0.00 4.17
194 195 5.068855 TCAAATCAATTGGACAACTGAGCAA 59.931 36.000 5.42 0.00 39.62 3.91
195 196 4.583907 TCAAATCAATTGGACAACTGAGCA 59.416 37.500 5.42 0.00 39.62 4.26
196 197 5.125100 TCAAATCAATTGGACAACTGAGC 57.875 39.130 5.42 0.00 39.62 4.26
197 198 7.707893 AGTTTTCAAATCAATTGGACAACTGAG 59.292 33.333 9.74 0.00 39.62 3.35
198 199 7.492020 CAGTTTTCAAATCAATTGGACAACTGA 59.508 33.333 23.10 0.00 43.87 3.41
199 200 7.254522 CCAGTTTTCAAATCAATTGGACAACTG 60.255 37.037 21.71 21.71 42.63 3.16
200 201 6.762661 CCAGTTTTCAAATCAATTGGACAACT 59.237 34.615 5.42 6.84 39.62 3.16
201 202 6.018016 CCCAGTTTTCAAATCAATTGGACAAC 60.018 38.462 5.42 4.72 39.62 3.32
202 203 6.054295 CCCAGTTTTCAAATCAATTGGACAA 58.946 36.000 5.42 0.00 39.62 3.18
203 204 5.130145 ACCCAGTTTTCAAATCAATTGGACA 59.870 36.000 5.42 0.00 39.62 4.02
204 205 5.610398 ACCCAGTTTTCAAATCAATTGGAC 58.390 37.500 5.42 0.00 39.62 4.02
205 206 5.508825 CGACCCAGTTTTCAAATCAATTGGA 60.509 40.000 5.42 0.00 39.62 3.53
206 207 4.685628 CGACCCAGTTTTCAAATCAATTGG 59.314 41.667 5.42 0.00 39.62 3.16
207 208 5.527951 TCGACCCAGTTTTCAAATCAATTG 58.472 37.500 0.00 0.00 40.58 2.32
208 209 5.782893 TCGACCCAGTTTTCAAATCAATT 57.217 34.783 0.00 0.00 0.00 2.32
209 210 5.508994 GGTTCGACCCAGTTTTCAAATCAAT 60.509 40.000 0.00 0.00 30.04 2.57
210 211 4.202070 GGTTCGACCCAGTTTTCAAATCAA 60.202 41.667 0.00 0.00 30.04 2.57
211 212 3.316868 GGTTCGACCCAGTTTTCAAATCA 59.683 43.478 0.00 0.00 30.04 2.57
212 213 3.568430 AGGTTCGACCCAGTTTTCAAATC 59.432 43.478 0.39 0.00 39.75 2.17
213 214 3.562182 AGGTTCGACCCAGTTTTCAAAT 58.438 40.909 0.39 0.00 39.75 2.32
214 215 2.946990 GAGGTTCGACCCAGTTTTCAAA 59.053 45.455 0.39 0.00 39.75 2.69
215 216 2.092861 TGAGGTTCGACCCAGTTTTCAA 60.093 45.455 0.39 0.00 39.75 2.69
216 217 1.487142 TGAGGTTCGACCCAGTTTTCA 59.513 47.619 0.39 0.00 39.75 2.69
217 218 1.871676 GTGAGGTTCGACCCAGTTTTC 59.128 52.381 0.39 0.00 39.75 2.29
218 219 1.808891 CGTGAGGTTCGACCCAGTTTT 60.809 52.381 0.39 0.00 39.75 2.43
219 220 0.249741 CGTGAGGTTCGACCCAGTTT 60.250 55.000 0.39 0.00 39.75 2.66
220 221 1.366366 CGTGAGGTTCGACCCAGTT 59.634 57.895 0.39 0.00 39.75 3.16
221 222 0.538057 TACGTGAGGTTCGACCCAGT 60.538 55.000 0.39 0.00 39.75 4.00
222 223 0.815734 ATACGTGAGGTTCGACCCAG 59.184 55.000 0.39 0.00 39.75 4.45
223 224 0.813184 GATACGTGAGGTTCGACCCA 59.187 55.000 0.39 0.00 39.75 4.51
224 225 0.813184 TGATACGTGAGGTTCGACCC 59.187 55.000 0.00 0.00 39.75 4.46
225 226 2.642139 TTGATACGTGAGGTTCGACC 57.358 50.000 0.00 0.00 38.99 4.79
226 227 5.526010 AAATTTGATACGTGAGGTTCGAC 57.474 39.130 0.00 0.00 0.00 4.20
227 228 5.929992 AGAAAATTTGATACGTGAGGTTCGA 59.070 36.000 0.00 0.00 0.00 3.71
228 229 6.165659 AGAAAATTTGATACGTGAGGTTCG 57.834 37.500 0.00 0.00 0.00 3.95
229 230 7.118680 TGGTAGAAAATTTGATACGTGAGGTTC 59.881 37.037 0.00 0.00 0.00 3.62
230 231 6.938030 TGGTAGAAAATTTGATACGTGAGGTT 59.062 34.615 0.00 0.00 0.00 3.50
231 232 6.469410 TGGTAGAAAATTTGATACGTGAGGT 58.531 36.000 0.00 0.00 0.00 3.85
232 233 6.978343 TGGTAGAAAATTTGATACGTGAGG 57.022 37.500 0.00 0.00 0.00 3.86
233 234 8.196802 TCATGGTAGAAAATTTGATACGTGAG 57.803 34.615 0.00 0.00 0.00 3.51
234 235 8.038351 TCTCATGGTAGAAAATTTGATACGTGA 58.962 33.333 0.00 5.77 0.00 4.35
235 236 8.196802 TCTCATGGTAGAAAATTTGATACGTG 57.803 34.615 0.00 2.08 0.00 4.49
236 237 8.964476 ATCTCATGGTAGAAAATTTGATACGT 57.036 30.769 0.00 0.00 0.00 3.57
237 238 9.869844 GAATCTCATGGTAGAAAATTTGATACG 57.130 33.333 0.00 0.00 0.00 3.06
305 306 2.166459 TGCACCCGTGTTGAATGAAAAA 59.834 40.909 0.00 0.00 0.00 1.94
306 307 1.751351 TGCACCCGTGTTGAATGAAAA 59.249 42.857 0.00 0.00 0.00 2.29
307 308 1.336440 CTGCACCCGTGTTGAATGAAA 59.664 47.619 0.00 0.00 0.00 2.69
308 309 0.950836 CTGCACCCGTGTTGAATGAA 59.049 50.000 0.00 0.00 0.00 2.57
309 310 0.107643 TCTGCACCCGTGTTGAATGA 59.892 50.000 0.00 0.00 0.00 2.57
310 311 1.135603 CATCTGCACCCGTGTTGAATG 60.136 52.381 0.00 0.00 0.00 2.67
311 312 1.167851 CATCTGCACCCGTGTTGAAT 58.832 50.000 0.00 0.00 0.00 2.57
312 313 0.107643 TCATCTGCACCCGTGTTGAA 59.892 50.000 0.00 0.00 0.00 2.69
313 314 0.602638 GTCATCTGCACCCGTGTTGA 60.603 55.000 0.00 0.00 0.00 3.18
314 315 1.577328 GGTCATCTGCACCCGTGTTG 61.577 60.000 0.00 0.00 0.00 3.33
315 316 1.302511 GGTCATCTGCACCCGTGTT 60.303 57.895 0.00 0.00 0.00 3.32
316 317 2.347490 GGTCATCTGCACCCGTGT 59.653 61.111 0.00 0.00 0.00 4.49
317 318 2.436646 GGGTCATCTGCACCCGTG 60.437 66.667 0.00 0.00 44.42 4.94
321 322 4.489771 CCCGGGGTCATCTGCACC 62.490 72.222 14.71 0.00 0.00 5.01
324 325 4.554036 GAGCCCGGGGTCATCTGC 62.554 72.222 41.02 18.80 41.72 4.26
325 326 3.083349 TGAGCCCGGGGTCATCTG 61.083 66.667 43.92 8.60 46.01 2.90
330 331 1.377333 CTTTTCTGAGCCCGGGGTC 60.377 63.158 39.92 39.92 42.37 4.46
331 332 2.757077 CTTTTCTGAGCCCGGGGT 59.243 61.111 28.94 28.94 0.00 4.95
332 333 1.926426 ATCCTTTTCTGAGCCCGGGG 61.926 60.000 25.28 9.31 0.00 5.73
333 334 0.464554 GATCCTTTTCTGAGCCCGGG 60.465 60.000 19.09 19.09 0.00 5.73
334 335 0.543749 AGATCCTTTTCTGAGCCCGG 59.456 55.000 0.00 0.00 0.00 5.73
335 336 1.474143 GGAGATCCTTTTCTGAGCCCG 60.474 57.143 0.00 0.00 0.00 6.13
336 337 1.133945 GGGAGATCCTTTTCTGAGCCC 60.134 57.143 0.00 0.00 35.95 5.19
337 338 1.133945 GGGGAGATCCTTTTCTGAGCC 60.134 57.143 0.00 0.00 35.95 4.70
338 339 1.843206 AGGGGAGATCCTTTTCTGAGC 59.157 52.381 0.00 0.00 32.13 4.26
339 340 3.383223 AGAGGGGAGATCCTTTTCTGAG 58.617 50.000 0.00 0.00 37.25 3.35
340 341 3.498614 AGAGGGGAGATCCTTTTCTGA 57.501 47.619 0.00 0.00 37.25 3.27
341 342 4.294347 AGTAGAGGGGAGATCCTTTTCTG 58.706 47.826 0.00 0.00 37.25 3.02
342 343 4.552674 GAGTAGAGGGGAGATCCTTTTCT 58.447 47.826 0.00 2.87 37.25 2.52
343 344 3.644265 GGAGTAGAGGGGAGATCCTTTTC 59.356 52.174 0.00 0.00 37.25 2.29
344 345 3.633952 GGGAGTAGAGGGGAGATCCTTTT 60.634 52.174 0.00 0.00 37.25 2.27
345 346 2.090437 GGGAGTAGAGGGGAGATCCTTT 60.090 54.545 0.00 0.00 37.25 3.11
346 347 1.505977 GGGAGTAGAGGGGAGATCCTT 59.494 57.143 0.00 0.00 37.25 3.36
347 348 1.163408 GGGAGTAGAGGGGAGATCCT 58.837 60.000 0.00 0.00 40.43 3.24
348 349 1.076513 GAGGGAGTAGAGGGGAGATCC 59.923 61.905 0.00 0.00 0.00 3.36
349 350 1.076513 GGAGGGAGTAGAGGGGAGATC 59.923 61.905 0.00 0.00 0.00 2.75
350 351 1.163408 GGAGGGAGTAGAGGGGAGAT 58.837 60.000 0.00 0.00 0.00 2.75
351 352 0.048117 AGGAGGGAGTAGAGGGGAGA 59.952 60.000 0.00 0.00 0.00 3.71
352 353 0.938192 AAGGAGGGAGTAGAGGGGAG 59.062 60.000 0.00 0.00 0.00 4.30
353 354 1.405243 AAAGGAGGGAGTAGAGGGGA 58.595 55.000 0.00 0.00 0.00 4.81
354 355 2.272074 AAAAGGAGGGAGTAGAGGGG 57.728 55.000 0.00 0.00 0.00 4.79
355 356 3.574826 CGATAAAAGGAGGGAGTAGAGGG 59.425 52.174 0.00 0.00 0.00 4.30
356 357 3.006003 GCGATAAAAGGAGGGAGTAGAGG 59.994 52.174 0.00 0.00 0.00 3.69
427 454 8.696374 CCCTCTAAGCCATCGATTCTAAATATA 58.304 37.037 0.00 0.00 0.00 0.86
428 455 7.560368 CCCTCTAAGCCATCGATTCTAAATAT 58.440 38.462 0.00 0.00 0.00 1.28
429 456 6.574465 GCCCTCTAAGCCATCGATTCTAAATA 60.574 42.308 0.00 0.00 0.00 1.40
430 457 5.799213 CCCTCTAAGCCATCGATTCTAAAT 58.201 41.667 0.00 0.00 0.00 1.40
431 458 4.503296 GCCCTCTAAGCCATCGATTCTAAA 60.503 45.833 0.00 0.00 0.00 1.85
432 459 3.006967 GCCCTCTAAGCCATCGATTCTAA 59.993 47.826 0.00 0.00 0.00 2.10
433 460 2.563179 GCCCTCTAAGCCATCGATTCTA 59.437 50.000 0.00 0.00 0.00 2.10
434 461 1.346068 GCCCTCTAAGCCATCGATTCT 59.654 52.381 0.00 0.00 0.00 2.40
435 462 1.802069 GCCCTCTAAGCCATCGATTC 58.198 55.000 0.00 0.00 0.00 2.52
621 653 1.229529 GAGTGGGGACTGGGGAGAA 60.230 63.158 0.00 0.00 0.00 2.87
639 671 1.292223 TCCCTTCGCGTTGGAGAAG 59.708 57.895 18.59 8.56 46.04 2.85
646 678 0.037605 CTGGTAACTCCCTTCGCGTT 60.038 55.000 5.77 0.00 34.77 4.84
675 707 3.403558 GGGTGGGGTGAGAGGAGC 61.404 72.222 0.00 0.00 0.00 4.70
689 721 4.681978 GCAAGCTCACGTCGGGGT 62.682 66.667 0.00 0.00 0.00 4.95
695 727 4.021925 GAGGGGGCAAGCTCACGT 62.022 66.667 0.00 0.00 0.00 4.49
721 753 1.826024 GCAGATGGACGGATGGAGT 59.174 57.895 0.00 0.00 0.00 3.85
757 789 2.860009 TCAGAAGTCTATACGCCGGAT 58.140 47.619 5.05 0.00 0.00 4.18
809 842 1.832167 GAGCGCCAGGAGAGGAGAT 60.832 63.158 2.29 0.00 0.00 2.75
810 843 1.636769 TAGAGCGCCAGGAGAGGAGA 61.637 60.000 2.29 0.00 0.00 3.71
866 899 4.437255 CGGCATTTCATCGAACAAATCAGA 60.437 41.667 0.00 0.00 0.00 3.27
871 904 1.727535 CGCGGCATTTCATCGAACAAA 60.728 47.619 0.00 0.00 0.00 2.83
946 979 0.171903 GTCGCTTGCAATGCTCCAAT 59.828 50.000 6.82 0.00 34.38 3.16
949 982 2.099062 CGTCGCTTGCAATGCTCC 59.901 61.111 6.82 7.52 34.38 4.70
989 1022 1.651240 CGCACTCATTTCCCAGGCAG 61.651 60.000 0.00 0.00 0.00 4.85
1008 1041 0.765510 ACAAAGACAGGTCCTCACCC 59.234 55.000 0.00 0.00 45.12 4.61
1059 1092 6.490040 AGATGCCTGAAGCTAACAAAAGTAAA 59.510 34.615 0.00 0.00 44.23 2.01
1065 1098 4.019792 TCAGATGCCTGAAGCTAACAAA 57.980 40.909 0.00 0.00 45.74 2.83
1078 1111 1.002430 TCTTGGTCACTGTCAGATGCC 59.998 52.381 6.91 5.70 0.00 4.40
1135 1198 5.299949 ACGGGTTAGTCAAAAGTTTCGTAT 58.700 37.500 0.00 0.00 0.00 3.06
1138 1201 3.805971 AGACGGGTTAGTCAAAAGTTTCG 59.194 43.478 0.00 0.00 43.24 3.46
1142 1205 3.387050 ACTCAGACGGGTTAGTCAAAAGT 59.613 43.478 0.00 0.00 43.24 2.66
1146 1209 4.411256 AAAACTCAGACGGGTTAGTCAA 57.589 40.909 0.00 0.00 43.24 3.18
1150 1213 4.689345 CCTGTTAAAACTCAGACGGGTTAG 59.311 45.833 0.00 0.00 34.54 2.34
1159 1222 2.480419 CGCTCCACCTGTTAAAACTCAG 59.520 50.000 0.00 0.00 0.00 3.35
1162 1225 2.632987 ACGCTCCACCTGTTAAAACT 57.367 45.000 0.00 0.00 0.00 2.66
1237 1300 1.080501 ACACTCGTGCAGGTGATCG 60.081 57.895 14.77 0.45 37.22 3.69
1283 1347 7.822334 CACTCACTAACATTACACCCTATGAAA 59.178 37.037 0.00 0.00 0.00 2.69
1284 1348 7.038587 ACACTCACTAACATTACACCCTATGAA 60.039 37.037 0.00 0.00 0.00 2.57
1560 1624 1.651737 TAGGAAGCAAGCACACCCTA 58.348 50.000 0.00 0.00 0.00 3.53
1561 1625 0.771127 TTAGGAAGCAAGCACACCCT 59.229 50.000 0.00 0.00 0.00 4.34
1562 1626 1.168714 CTTAGGAAGCAAGCACACCC 58.831 55.000 0.00 0.00 0.00 4.61
1592 1656 9.125026 ACAAGTAGTTCACTTCTGAAATTCAAT 57.875 29.630 0.00 0.00 44.48 2.57
1593 1657 8.506168 ACAAGTAGTTCACTTCTGAAATTCAA 57.494 30.769 0.00 0.00 44.48 2.69
1594 1658 9.778741 ATACAAGTAGTTCACTTCTGAAATTCA 57.221 29.630 0.00 0.00 44.48 2.57
1653 1717 5.779529 ATTATTCAAGTCATGGATGTGCC 57.220 39.130 0.00 0.00 37.10 5.01
1654 1718 9.188588 CATAAATTATTCAAGTCATGGATGTGC 57.811 33.333 0.00 0.00 0.00 4.57
1670 1734 9.936759 CCAAACACACCCTAAACATAAATTATT 57.063 29.630 0.00 0.00 0.00 1.40
1671 1735 9.095700 ACCAAACACACCCTAAACATAAATTAT 57.904 29.630 0.00 0.00 0.00 1.28
1672 1736 8.480133 ACCAAACACACCCTAAACATAAATTA 57.520 30.769 0.00 0.00 0.00 1.40
1673 1737 7.368198 ACCAAACACACCCTAAACATAAATT 57.632 32.000 0.00 0.00 0.00 1.82
1674 1738 6.987403 ACCAAACACACCCTAAACATAAAT 57.013 33.333 0.00 0.00 0.00 1.40
1675 1739 6.183360 GGAACCAAACACACCCTAAACATAAA 60.183 38.462 0.00 0.00 0.00 1.40
1676 1740 5.302313 GGAACCAAACACACCCTAAACATAA 59.698 40.000 0.00 0.00 0.00 1.90
1677 1741 4.828387 GGAACCAAACACACCCTAAACATA 59.172 41.667 0.00 0.00 0.00 2.29
1678 1742 3.639561 GGAACCAAACACACCCTAAACAT 59.360 43.478 0.00 0.00 0.00 2.71
1679 1743 3.025262 GGAACCAAACACACCCTAAACA 58.975 45.455 0.00 0.00 0.00 2.83
1680 1744 3.293337 AGGAACCAAACACACCCTAAAC 58.707 45.455 0.00 0.00 0.00 2.01
1681 1745 3.673543 AGGAACCAAACACACCCTAAA 57.326 42.857 0.00 0.00 0.00 1.85
1682 1746 4.721132 CTTAGGAACCAAACACACCCTAA 58.279 43.478 0.00 0.00 35.63 2.69
1727 1791 1.474330 CCAAACACCTATCCTTGCCC 58.526 55.000 0.00 0.00 0.00 5.36
1774 1838 4.041691 GGAGGTAGTATAACCCATGCATGT 59.958 45.833 24.58 9.62 40.71 3.21
1942 2006 8.258708 GCAAGATTATATATACTCCCTCCGTTT 58.741 37.037 6.50 0.00 0.00 3.60
2182 2246 7.283354 GCACTAAACATCTCCTAAAAGGCTAAT 59.717 37.037 0.00 0.00 34.61 1.73
2628 2705 9.803315 GTCAGTTTTCCTTGTTATTCTCTTTTT 57.197 29.630 0.00 0.00 0.00 1.94
2629 2706 8.966868 TGTCAGTTTTCCTTGTTATTCTCTTTT 58.033 29.630 0.00 0.00 0.00 2.27
2630 2707 8.406297 GTGTCAGTTTTCCTTGTTATTCTCTTT 58.594 33.333 0.00 0.00 0.00 2.52
2631 2708 7.775561 AGTGTCAGTTTTCCTTGTTATTCTCTT 59.224 33.333 0.00 0.00 0.00 2.85
2632 2709 7.227512 CAGTGTCAGTTTTCCTTGTTATTCTCT 59.772 37.037 0.00 0.00 0.00 3.10
2633 2710 7.226720 TCAGTGTCAGTTTTCCTTGTTATTCTC 59.773 37.037 0.00 0.00 0.00 2.87
2634 2711 7.054124 TCAGTGTCAGTTTTCCTTGTTATTCT 58.946 34.615 0.00 0.00 0.00 2.40
2647 2724 6.291377 ACACATGTTATCTCAGTGTCAGTTT 58.709 36.000 0.00 0.00 38.98 2.66
2722 2799 5.779922 ACTAGCAAAATAACACGAGACAGA 58.220 37.500 0.00 0.00 0.00 3.41
2723 2800 6.073765 ACAACTAGCAAAATAACACGAGACAG 60.074 38.462 0.00 0.00 0.00 3.51
2750 2827 3.181458 TGGGTCCATCGCTTAGTTTATCC 60.181 47.826 0.00 0.00 0.00 2.59
2775 2852 5.770162 AGAAGGAGTACAATCCAAAAAGGTG 59.230 40.000 4.14 0.00 42.26 4.00
2776 2853 5.770162 CAGAAGGAGTACAATCCAAAAAGGT 59.230 40.000 4.14 0.00 42.26 3.50
2831 3098 2.430248 ACCTCCGTTCCACAAAGTTT 57.570 45.000 0.00 0.00 0.00 2.66
2835 3102 4.571919 CAATACTACCTCCGTTCCACAAA 58.428 43.478 0.00 0.00 0.00 2.83
2875 3146 2.006888 GCCATTCCGTTCGATCAAAGA 58.993 47.619 0.00 0.00 0.00 2.52
2997 3269 9.525826 ACATATTGAAAATCCTTATCTCATCCC 57.474 33.333 0.00 0.00 0.00 3.85
3111 3383 4.094442 GGCACCTTAGGAAATTAAGTCGTG 59.906 45.833 4.77 0.00 31.53 4.35
3183 3456 6.982724 CACATCATGCATCAGTCTAACTAAGA 59.017 38.462 0.00 0.00 0.00 2.10
3490 3764 6.935741 TTAGGGGATCATAAAATGTTCGTG 57.064 37.500 0.00 0.00 31.35 4.35
3549 3823 4.145756 CGAACAAAACAAACCATCGCTTAC 59.854 41.667 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.