Multiple sequence alignment - TraesCS2D01G521200

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 TraesCS2D01G521200 chr2D 100.000 3066 0 0 1 3066 609936739 609933674 0.000000e+00 5662.0
1 TraesCS2D01G521200 chr2D 96.931 1564 37 5 889 2448 609893283 609891727 0.000000e+00 2612.0
2 TraesCS2D01G521200 chr2D 98.869 619 7 0 2448 3066 609260833 609261451 0.000000e+00 1105.0
3 TraesCS2D01G521200 chr2D 84.328 134 18 1 898 1031 611244727 611244857 8.920000e-26 128.0
4 TraesCS2D01G521200 chr2B 94.348 1663 66 14 799 2448 744835059 744833412 0.000000e+00 2525.0
5 TraesCS2D01G521200 chr2B 92.361 1584 99 10 883 2448 744520657 744519078 0.000000e+00 2235.0
6 TraesCS2D01G521200 chr2B 84.211 1292 176 12 883 2159 744454251 744452973 0.000000e+00 1230.0
7 TraesCS2D01G521200 chr2B 82.591 1212 185 15 945 2153 745579543 745580731 0.000000e+00 1046.0
8 TraesCS2D01G521200 chr2B 85.458 502 29 20 307 778 744521215 744520728 1.650000e-132 483.0
9 TraesCS2D01G521200 chr2B 76.337 617 111 24 898 1489 746170117 746170723 6.430000e-77 298.0
10 TraesCS2D01G521200 chr2B 100.000 30 0 0 279 308 683081647 683081618 4.270000e-04 56.5
11 TraesCS2D01G521200 chr3D 99.191 618 5 0 2449 3066 186517974 186517357 0.000000e+00 1114.0
12 TraesCS2D01G521200 chr3D 98.246 627 11 0 2440 3066 371157246 371157872 0.000000e+00 1098.0
13 TraesCS2D01G521200 chr5D 99.029 618 6 0 2449 3066 298960234 298959617 0.000000e+00 1109.0
14 TraesCS2D01G521200 chr5D 98.869 619 7 0 2448 3066 450599378 450599996 0.000000e+00 1105.0
15 TraesCS2D01G521200 chr5D 95.223 314 14 1 1 313 535632534 535632221 2.120000e-136 496.0
16 TraesCS2D01G521200 chr5D 95.425 306 8 1 1 306 407324921 407325220 1.650000e-132 483.0
17 TraesCS2D01G521200 chrUn 98.869 619 7 0 2448 3066 108836080 108835462 0.000000e+00 1105.0
18 TraesCS2D01G521200 chrUn 98.710 620 8 0 2447 3066 108843213 108842594 0.000000e+00 1101.0
19 TraesCS2D01G521200 chrUn 82.069 145 24 2 1144 1287 87002981 87003124 4.150000e-24 122.0
20 TraesCS2D01G521200 chrUn 82.069 145 24 2 1144 1287 298337166 298337309 4.150000e-24 122.0
21 TraesCS2D01G521200 chrUn 82.734 139 22 2 1150 1287 298383342 298383205 4.150000e-24 122.0
22 TraesCS2D01G521200 chr1D 98.869 619 7 0 2448 3066 121636016 121635398 0.000000e+00 1105.0
23 TraesCS2D01G521200 chr1D 98.869 619 7 0 2448 3066 384116820 384117438 0.000000e+00 1105.0
24 TraesCS2D01G521200 chr7D 94.534 311 16 1 1 310 17359897 17359587 2.140000e-131 479.0
25 TraesCS2D01G521200 chr7D 94.788 307 15 1 1 306 105364890 105364584 7.690000e-131 477.0
26 TraesCS2D01G521200 chr6B 92.953 298 19 2 12 307 545678871 545679168 1.690000e-117 433.0
27 TraesCS2D01G521200 chr1A 92.182 307 23 1 1 306 99625513 99625207 1.690000e-117 433.0
28 TraesCS2D01G521200 chr2A 73.844 1189 258 32 895 2052 744080517 744081683 1.020000e-114 424.0
29 TraesCS2D01G521200 chr2A 84.647 241 20 9 490 724 742766027 742765798 1.110000e-54 224.0
30 TraesCS2D01G521200 chr2A 90.741 108 10 0 184 291 11809699 11809806 8.860000e-31 145.0
31 TraesCS2D01G521200 chr7A 91.531 307 25 1 1 306 183921203 183920897 3.660000e-114 422.0
32 TraesCS2D01G521200 chr4A 89.251 307 32 1 1 306 661252578 661252272 1.720000e-102 383.0
33 TraesCS2D01G521200 chr5A 94.144 222 12 1 1 221 564729611 564729390 1.360000e-88 337.0
34 TraesCS2D01G521200 chr1B 100.000 28 0 0 645 672 162779321 162779348 6.000000e-03 52.8


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 TraesCS2D01G521200 chr2D 609933674 609936739 3065 True 5662 5662 100.0000 1 3066 1 chr2D.!!$R2 3065
1 TraesCS2D01G521200 chr2D 609891727 609893283 1556 True 2612 2612 96.9310 889 2448 1 chr2D.!!$R1 1559
2 TraesCS2D01G521200 chr2D 609260833 609261451 618 False 1105 1105 98.8690 2448 3066 1 chr2D.!!$F1 618
3 TraesCS2D01G521200 chr2B 744833412 744835059 1647 True 2525 2525 94.3480 799 2448 1 chr2B.!!$R3 1649
4 TraesCS2D01G521200 chr2B 744519078 744521215 2137 True 1359 2235 88.9095 307 2448 2 chr2B.!!$R4 2141
5 TraesCS2D01G521200 chr2B 744452973 744454251 1278 True 1230 1230 84.2110 883 2159 1 chr2B.!!$R2 1276
6 TraesCS2D01G521200 chr2B 745579543 745580731 1188 False 1046 1046 82.5910 945 2153 1 chr2B.!!$F1 1208
7 TraesCS2D01G521200 chr2B 746170117 746170723 606 False 298 298 76.3370 898 1489 1 chr2B.!!$F2 591
8 TraesCS2D01G521200 chr3D 186517357 186517974 617 True 1114 1114 99.1910 2449 3066 1 chr3D.!!$R1 617
9 TraesCS2D01G521200 chr3D 371157246 371157872 626 False 1098 1098 98.2460 2440 3066 1 chr3D.!!$F1 626
10 TraesCS2D01G521200 chr5D 298959617 298960234 617 True 1109 1109 99.0290 2449 3066 1 chr5D.!!$R1 617
11 TraesCS2D01G521200 chr5D 450599378 450599996 618 False 1105 1105 98.8690 2448 3066 1 chr5D.!!$F2 618
12 TraesCS2D01G521200 chrUn 108835462 108836080 618 True 1105 1105 98.8690 2448 3066 1 chrUn.!!$R1 618
13 TraesCS2D01G521200 chrUn 108842594 108843213 619 True 1101 1101 98.7100 2447 3066 1 chrUn.!!$R2 619
14 TraesCS2D01G521200 chr1D 121635398 121636016 618 True 1105 1105 98.8690 2448 3066 1 chr1D.!!$R1 618
15 TraesCS2D01G521200 chr1D 384116820 384117438 618 False 1105 1105 98.8690 2448 3066 1 chr1D.!!$F1 618
16 TraesCS2D01G521200 chr2A 744080517 744081683 1166 False 424 424 73.8440 895 2052 1 chr2A.!!$F2 1157

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
127 128 0.031585 GCATAGATGTACGGACGCCA 59.968 55.0 0.0 0.0 0.0 5.69 F
265 266 0.036952 CGGGTATCAGGGCTATGCTG 60.037 60.0 0.0 0.0 0.0 4.41 F
836 867 0.383949 TTTTCGTGGAAGTGCTTGGC 59.616 50.0 0.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1433 1511 0.971386 AATGCCAGCCTTTCAACCTG 59.029 50.0 0.00 0.0 0.00 4.00 R
1664 1748 1.021202 CGCCAAACAAGAGGTTGTCA 58.979 50.0 0.00 0.0 46.68 3.58 R
2426 2528 0.533085 GATTTCCGGCCAGCCTACTC 60.533 60.0 2.24 0.0 0.00 2.59 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
19 20 2.357517 CCGTCGGCATATCCCTGC 60.358 66.667 0.00 0.00 41.53 4.85
25 26 3.736483 GCATATCCCTGCCACGTG 58.264 61.111 9.08 9.08 36.10 4.49
26 27 1.893808 GCATATCCCTGCCACGTGG 60.894 63.158 30.66 30.66 36.10 4.94
36 37 2.029073 CCACGTGGCGTCTCTTGT 59.971 61.111 24.02 0.00 38.32 3.16
37 38 1.287815 CCACGTGGCGTCTCTTGTA 59.712 57.895 24.02 0.00 38.32 2.41
38 39 0.108804 CCACGTGGCGTCTCTTGTAT 60.109 55.000 24.02 0.00 38.32 2.29
39 40 0.992072 CACGTGGCGTCTCTTGTATG 59.008 55.000 7.95 0.00 38.32 2.39
40 41 0.108804 ACGTGGCGTCTCTTGTATGG 60.109 55.000 0.00 0.00 33.69 2.74
41 42 0.806102 CGTGGCGTCTCTTGTATGGG 60.806 60.000 0.00 0.00 0.00 4.00
42 43 1.090052 GTGGCGTCTCTTGTATGGGC 61.090 60.000 0.00 0.00 0.00 5.36
43 44 1.220749 GGCGTCTCTTGTATGGGCA 59.779 57.895 0.00 0.00 0.00 5.36
44 45 0.811616 GGCGTCTCTTGTATGGGCAG 60.812 60.000 0.00 0.00 0.00 4.85
45 46 1.432270 GCGTCTCTTGTATGGGCAGC 61.432 60.000 0.00 0.00 0.00 5.25
46 47 0.108186 CGTCTCTTGTATGGGCAGCA 60.108 55.000 0.00 0.00 0.00 4.41
47 48 1.373570 GTCTCTTGTATGGGCAGCAC 58.626 55.000 0.00 0.00 0.00 4.40
48 49 1.065854 GTCTCTTGTATGGGCAGCACT 60.066 52.381 0.00 0.00 0.00 4.40
49 50 1.630369 TCTCTTGTATGGGCAGCACTT 59.370 47.619 0.00 0.00 0.00 3.16
50 51 1.741706 CTCTTGTATGGGCAGCACTTG 59.258 52.381 0.00 0.00 0.00 3.16
51 52 1.350684 TCTTGTATGGGCAGCACTTGA 59.649 47.619 0.00 0.00 0.00 3.02
52 53 1.470098 CTTGTATGGGCAGCACTTGAC 59.530 52.381 0.00 0.00 0.00 3.18
53 54 0.673333 TGTATGGGCAGCACTTGACG 60.673 55.000 0.00 0.00 34.72 4.35
54 55 1.078497 TATGGGCAGCACTTGACGG 60.078 57.895 0.00 0.00 34.72 4.79
60 61 4.927782 AGCACTTGACGGCGGCAA 62.928 61.111 28.42 28.42 34.54 4.52
61 62 4.683334 GCACTTGACGGCGGCAAC 62.683 66.667 26.68 11.89 0.00 4.17
79 80 3.098555 GGCAATCACCGTTAGGCG 58.901 61.111 0.00 0.00 42.76 5.52
80 81 2.403586 GCAATCACCGTTAGGCGC 59.596 61.111 0.00 0.00 42.76 6.53
81 82 2.701006 CAATCACCGTTAGGCGCG 59.299 61.111 0.00 0.00 42.76 6.86
120 121 3.087638 CCGTCGGCATAGATGTACG 57.912 57.895 0.00 0.00 33.53 3.67
121 122 0.386858 CCGTCGGCATAGATGTACGG 60.387 60.000 14.44 14.44 40.96 4.02
122 123 0.589708 CGTCGGCATAGATGTACGGA 59.410 55.000 8.24 0.00 33.42 4.69
123 124 1.662309 CGTCGGCATAGATGTACGGAC 60.662 57.143 0.00 0.00 33.42 4.79
124 125 0.589708 TCGGCATAGATGTACGGACG 59.410 55.000 0.00 0.00 33.42 4.79
125 126 1.002250 CGGCATAGATGTACGGACGC 61.002 60.000 0.00 0.00 0.00 5.19
126 127 0.666577 GGCATAGATGTACGGACGCC 60.667 60.000 0.00 0.00 0.00 5.68
127 128 0.031585 GCATAGATGTACGGACGCCA 59.968 55.000 0.00 0.00 0.00 5.69
128 129 1.336887 GCATAGATGTACGGACGCCAT 60.337 52.381 0.00 0.00 0.00 4.40
129 130 2.596452 CATAGATGTACGGACGCCATC 58.404 52.381 13.70 13.70 36.16 3.51
130 131 0.589708 TAGATGTACGGACGCCATCG 59.410 55.000 14.90 0.00 39.89 3.84
131 132 1.660575 GATGTACGGACGCCATCGG 60.661 63.158 8.52 0.00 40.69 4.18
132 133 3.785189 ATGTACGGACGCCATCGGC 62.785 63.158 0.00 0.00 46.75 5.54
144 145 2.996249 CCATCGGCATAGGCATCTAT 57.004 50.000 0.15 0.00 43.71 1.98
162 163 2.280186 GCCGACGGCCTTCCTATG 60.280 66.667 28.74 0.00 44.06 2.23
163 164 2.280186 CCGACGGCCTTCCTATGC 60.280 66.667 0.00 0.00 0.00 3.14
164 165 2.280186 CGACGGCCTTCCTATGCC 60.280 66.667 3.22 0.00 44.41 4.40
169 170 3.827634 GCCTTCCTATGCCAACGG 58.172 61.111 0.00 0.00 0.00 4.44
170 171 1.823899 GCCTTCCTATGCCAACGGG 60.824 63.158 0.00 0.00 37.18 5.28
171 172 1.152963 CCTTCCTATGCCAACGGGG 60.153 63.158 0.00 0.00 40.85 5.73
172 173 1.632018 CCTTCCTATGCCAACGGGGA 61.632 60.000 0.00 0.00 40.01 4.81
173 174 0.463833 CTTCCTATGCCAACGGGGAC 60.464 60.000 0.00 0.00 37.33 4.46
188 189 4.139234 GACCTGGGGTACGCCGAC 62.139 72.222 22.64 10.72 42.25 4.79
193 194 3.903282 GGGGTACGCCGACGCATA 61.903 66.667 13.87 0.00 45.53 3.14
194 195 2.337532 GGGTACGCCGACGCATAT 59.662 61.111 0.00 0.00 45.53 1.78
195 196 2.019951 GGGTACGCCGACGCATATG 61.020 63.158 0.00 0.00 45.53 1.78
196 197 1.299620 GGTACGCCGACGCATATGT 60.300 57.895 4.29 0.00 45.53 2.29
197 198 0.872881 GGTACGCCGACGCATATGTT 60.873 55.000 4.29 0.00 45.53 2.71
198 199 0.228742 GTACGCCGACGCATATGTTG 59.771 55.000 4.29 0.00 45.53 3.33
249 250 2.065993 CATAGACTTATGCCGACGGG 57.934 55.000 17.22 0.14 30.98 5.28
250 251 1.340248 CATAGACTTATGCCGACGGGT 59.660 52.381 17.22 3.97 34.97 5.28
251 252 2.346766 TAGACTTATGCCGACGGGTA 57.653 50.000 17.22 0.00 34.97 3.69
252 253 1.700955 AGACTTATGCCGACGGGTAT 58.299 50.000 17.22 4.19 41.89 2.73
253 254 1.612463 AGACTTATGCCGACGGGTATC 59.388 52.381 17.22 0.00 39.57 2.24
254 255 1.338973 GACTTATGCCGACGGGTATCA 59.661 52.381 17.22 5.09 39.57 2.15
255 256 1.340248 ACTTATGCCGACGGGTATCAG 59.660 52.381 17.22 5.24 39.57 2.90
256 257 0.677288 TTATGCCGACGGGTATCAGG 59.323 55.000 17.22 0.00 39.57 3.86
257 258 1.183030 TATGCCGACGGGTATCAGGG 61.183 60.000 17.22 0.00 39.57 4.45
258 259 4.603946 GCCGACGGGTATCAGGGC 62.604 72.222 17.22 0.00 34.97 5.19
259 260 2.838225 CCGACGGGTATCAGGGCT 60.838 66.667 5.81 0.00 0.00 5.19
260 261 1.529948 CCGACGGGTATCAGGGCTA 60.530 63.158 5.81 0.00 0.00 3.93
261 262 0.898789 CCGACGGGTATCAGGGCTAT 60.899 60.000 5.81 0.00 0.00 2.97
262 263 0.243907 CGACGGGTATCAGGGCTATG 59.756 60.000 0.00 0.00 0.00 2.23
263 264 0.037232 GACGGGTATCAGGGCTATGC 60.037 60.000 0.00 0.00 0.00 3.14
264 265 0.471971 ACGGGTATCAGGGCTATGCT 60.472 55.000 0.00 0.00 0.00 3.79
265 266 0.036952 CGGGTATCAGGGCTATGCTG 60.037 60.000 0.00 0.00 0.00 4.41
266 267 1.352083 GGGTATCAGGGCTATGCTGA 58.648 55.000 0.00 0.00 0.00 4.26
267 268 1.002544 GGGTATCAGGGCTATGCTGAC 59.997 57.143 0.00 0.00 0.00 3.51
268 269 1.337260 GGTATCAGGGCTATGCTGACG 60.337 57.143 0.00 0.00 0.00 4.35
269 270 0.969149 TATCAGGGCTATGCTGACGG 59.031 55.000 0.00 0.00 0.00 4.79
270 271 2.388890 ATCAGGGCTATGCTGACGGC 62.389 60.000 0.00 0.00 42.22 5.68
271 272 3.866582 AGGGCTATGCTGACGGCC 61.867 66.667 3.22 0.00 43.42 6.13
272 273 3.866582 GGGCTATGCTGACGGCCT 61.867 66.667 3.22 0.00 43.62 5.19
273 274 2.590007 GGCTATGCTGACGGCCTG 60.590 66.667 3.22 0.00 41.20 4.85
274 275 2.590007 GCTATGCTGACGGCCTGG 60.590 66.667 3.22 0.00 40.92 4.45
275 276 2.109799 CTATGCTGACGGCCTGGG 59.890 66.667 3.22 0.00 40.92 4.45
276 277 4.175337 TATGCTGACGGCCTGGGC 62.175 66.667 10.75 10.75 40.92 5.36
286 287 4.175337 GCCTGGGCTGTCGGCATA 62.175 66.667 5.89 0.00 43.25 3.14
287 288 2.109799 CCTGGGCTGTCGGCATAG 59.890 66.667 5.89 2.83 44.01 2.23
288 289 2.109799 CTGGGCTGTCGGCATAGG 59.890 66.667 5.89 0.00 44.01 2.57
289 290 3.466791 CTGGGCTGTCGGCATAGGG 62.467 68.421 5.89 0.00 44.01 3.53
290 291 4.256180 GGGCTGTCGGCATAGGGG 62.256 72.222 5.89 0.00 44.01 4.79
291 292 4.937431 GGCTGTCGGCATAGGGGC 62.937 72.222 5.89 0.00 44.01 5.80
292 293 3.866582 GCTGTCGGCATAGGGGCT 61.867 66.667 0.00 0.00 41.35 5.19
293 294 2.423446 CTGTCGGCATAGGGGCTC 59.577 66.667 0.00 0.00 40.61 4.70
294 295 2.364973 TGTCGGCATAGGGGCTCA 60.365 61.111 0.00 0.00 40.61 4.26
295 296 2.374830 CTGTCGGCATAGGGGCTCAG 62.375 65.000 0.00 0.00 40.61 3.35
296 297 2.041922 TCGGCATAGGGGCTCAGT 60.042 61.111 0.00 0.00 40.61 3.41
297 298 2.109799 CGGCATAGGGGCTCAGTG 59.890 66.667 0.00 0.00 40.61 3.66
298 299 2.735772 CGGCATAGGGGCTCAGTGT 61.736 63.158 0.00 0.00 40.61 3.55
299 300 1.153086 GGCATAGGGGCTCAGTGTG 60.153 63.158 0.00 0.00 39.42 3.82
300 301 1.153086 GCATAGGGGCTCAGTGTGG 60.153 63.158 0.00 0.00 0.00 4.17
301 302 1.915078 GCATAGGGGCTCAGTGTGGT 61.915 60.000 0.00 0.00 0.00 4.16
302 303 1.496060 CATAGGGGCTCAGTGTGGTA 58.504 55.000 0.00 0.00 0.00 3.25
303 304 1.414181 CATAGGGGCTCAGTGTGGTAG 59.586 57.143 0.00 0.00 0.00 3.18
304 305 0.412244 TAGGGGCTCAGTGTGGTAGT 59.588 55.000 0.00 0.00 0.00 2.73
305 306 1.194781 AGGGGCTCAGTGTGGTAGTG 61.195 60.000 0.00 0.00 0.00 2.74
329 330 7.970614 GTGAATTGTCCCACTATTCTGAATTTC 59.029 37.037 8.38 3.19 39.77 2.17
355 358 2.279582 TAGTGCAAGAGCTTCTACGC 57.720 50.000 0.00 0.00 42.74 4.42
359 362 2.600867 GTGCAAGAGCTTCTACGCTAAG 59.399 50.000 0.00 0.00 41.08 2.18
373 376 7.724305 TCTACGCTAAGTGTTTCTGAATTTT 57.276 32.000 0.00 0.00 0.00 1.82
378 381 7.807907 ACGCTAAGTGTTTCTGAATTTTAATGG 59.192 33.333 0.00 0.00 0.00 3.16
390 393 9.820725 TCTGAATTTTAATGGGAAATGCTATTG 57.179 29.630 0.00 0.00 0.00 1.90
450 453 8.296713 TGCATAACAGGTTCAGTTATTCTTTTC 58.703 33.333 0.00 0.00 39.46 2.29
492 520 3.276882 GCTTTTGCTAACCGTGCTTAA 57.723 42.857 0.00 0.00 43.35 1.85
516 544 0.598680 GCAAGTGCAGACGTCTCTGT 60.599 55.000 16.96 0.00 45.30 3.41
547 576 2.034221 GTGTGGGCTGTCTTCCCC 59.966 66.667 0.00 0.00 43.24 4.81
559 588 3.416880 TTCCCCTTGGGCCGATCC 61.417 66.667 0.00 0.00 43.94 3.36
568 597 3.793888 GGCCGATCCCCTCCGTTT 61.794 66.667 0.00 0.00 0.00 3.60
580 609 2.684881 CCCTCCGTTTGATCTTGAATGG 59.315 50.000 0.00 1.96 34.02 3.16
590 619 5.852282 TGATCTTGAATGGACGACAGATA 57.148 39.130 0.00 0.00 0.00 1.98
617 646 1.439353 CCAAGTTGCAGCGTGTCACT 61.439 55.000 14.64 0.00 0.00 3.41
624 653 1.151668 GCAGCGTGTCACTTGATCTT 58.848 50.000 0.65 0.00 0.00 2.40
630 659 3.607078 GCGTGTCACTTGATCTTTGTTCC 60.607 47.826 0.65 0.00 0.00 3.62
631 660 3.559655 CGTGTCACTTGATCTTTGTTCCA 59.440 43.478 0.65 0.00 0.00 3.53
632 661 4.214119 CGTGTCACTTGATCTTTGTTCCAT 59.786 41.667 0.65 0.00 0.00 3.41
649 678 2.587247 ATCCATCCGATCCCAGCCG 61.587 63.158 0.00 0.00 0.00 5.52
778 809 3.408851 GCCCGTTGGTCGTTCGTC 61.409 66.667 0.00 0.00 37.94 4.20
779 810 2.337532 CCCGTTGGTCGTTCGTCT 59.662 61.111 0.00 0.00 37.94 4.18
780 811 1.300388 CCCGTTGGTCGTTCGTCTT 60.300 57.895 0.00 0.00 37.94 3.01
781 812 0.877213 CCCGTTGGTCGTTCGTCTTT 60.877 55.000 0.00 0.00 37.94 2.52
782 813 0.932399 CCGTTGGTCGTTCGTCTTTT 59.068 50.000 0.00 0.00 37.94 2.27
783 814 1.332552 CCGTTGGTCGTTCGTCTTTTG 60.333 52.381 0.00 0.00 37.94 2.44
784 815 1.325338 CGTTGGTCGTTCGTCTTTTGT 59.675 47.619 0.00 0.00 34.52 2.83
785 816 2.700694 GTTGGTCGTTCGTCTTTTGTG 58.299 47.619 0.00 0.00 0.00 3.33
786 817 2.012937 TGGTCGTTCGTCTTTTGTGT 57.987 45.000 0.00 0.00 0.00 3.72
787 818 3.162202 TGGTCGTTCGTCTTTTGTGTA 57.838 42.857 0.00 0.00 0.00 2.90
788 819 3.719924 TGGTCGTTCGTCTTTTGTGTAT 58.280 40.909 0.00 0.00 0.00 2.29
789 820 4.121317 TGGTCGTTCGTCTTTTGTGTATT 58.879 39.130 0.00 0.00 0.00 1.89
790 821 4.571580 TGGTCGTTCGTCTTTTGTGTATTT 59.428 37.500 0.00 0.00 0.00 1.40
791 822 5.752472 TGGTCGTTCGTCTTTTGTGTATTTA 59.248 36.000 0.00 0.00 0.00 1.40
792 823 6.424509 TGGTCGTTCGTCTTTTGTGTATTTAT 59.575 34.615 0.00 0.00 0.00 1.40
793 824 7.041916 TGGTCGTTCGTCTTTTGTGTATTTATT 60.042 33.333 0.00 0.00 0.00 1.40
794 825 8.434661 GGTCGTTCGTCTTTTGTGTATTTATTA 58.565 33.333 0.00 0.00 0.00 0.98
795 826 9.962759 GTCGTTCGTCTTTTGTGTATTTATTAT 57.037 29.630 0.00 0.00 0.00 1.28
813 844 1.418334 ATCTCCCTGGTCGATCTTGG 58.582 55.000 0.00 0.00 0.00 3.61
836 867 0.383949 TTTTCGTGGAAGTGCTTGGC 59.616 50.000 0.00 0.00 0.00 4.52
849 880 1.144936 CTTGGCCGATCTCTGGGTC 59.855 63.158 0.00 0.00 0.00 4.46
850 881 1.306141 TTGGCCGATCTCTGGGTCT 60.306 57.895 0.00 0.00 0.00 3.85
851 882 1.617018 TTGGCCGATCTCTGGGTCTG 61.617 60.000 0.00 0.00 0.00 3.51
852 883 2.801631 GGCCGATCTCTGGGTCTGG 61.802 68.421 0.00 0.00 0.00 3.86
853 884 2.801631 GCCGATCTCTGGGTCTGGG 61.802 68.421 0.00 0.00 0.00 4.45
854 885 2.136878 CCGATCTCTGGGTCTGGGG 61.137 68.421 0.00 0.00 0.00 4.96
952 1007 0.758734 AGGTATCGCAATGGCAGCTA 59.241 50.000 0.00 0.00 41.24 3.32
959 1014 2.364002 TCGCAATGGCAGCTAGTATACA 59.636 45.455 5.50 0.00 41.24 2.29
1101 1171 1.909302 AGACCATCACACGGATTCCTT 59.091 47.619 0.30 0.00 32.57 3.36
1417 1495 1.975327 AGGCACTCATGTACAGCGT 59.025 52.632 0.33 0.00 0.00 5.07
1603 1687 2.972505 CACGGCCAGTCGCAAGTT 60.973 61.111 2.24 0.00 40.31 2.66
1664 1748 0.391661 CCGTGCATGTACCAGAGCTT 60.392 55.000 8.45 0.00 0.00 3.74
1735 1828 6.575254 GCAATGGATATCTCCCGTCTTATCTT 60.575 42.308 2.05 0.00 41.29 2.40
2004 2100 6.257994 ACAGTTTCATATGGGATGACATCT 57.742 37.500 14.95 0.00 32.39 2.90
2169 2268 5.327737 TTTGGGTTGTACAATACTCCCTT 57.672 39.130 24.76 0.00 40.99 3.95
2422 2524 3.391382 CTCCTCCCCTCGCCGTTT 61.391 66.667 0.00 0.00 0.00 3.60
2426 2528 1.741770 CTCCCCTCGCCGTTTCTTG 60.742 63.158 0.00 0.00 0.00 3.02
2433 2535 0.389426 TCGCCGTTTCTTGAGTAGGC 60.389 55.000 0.00 0.00 41.03 3.93
2809 2911 0.904649 ATGAGATCGTGCAACTCCCA 59.095 50.000 0.00 0.00 31.75 4.37
3059 3161 4.677250 CGAGTAAAGAGACTTGCCGGTAAT 60.677 45.833 5.11 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.357517 GCAGGGATATGCCGACGG 60.358 66.667 10.29 10.29 40.43 4.79
8 9 1.893808 CCACGTGGCAGGGATATGC 60.894 63.158 24.02 0.00 45.74 3.14
9 10 4.462394 CCACGTGGCAGGGATATG 57.538 61.111 24.02 0.45 0.00 1.78
19 20 0.108804 ATACAAGAGACGCCACGTGG 60.109 55.000 30.66 30.66 41.37 4.94
20 21 0.992072 CATACAAGAGACGCCACGTG 59.008 55.000 9.08 9.08 41.37 4.49
21 22 0.108804 CCATACAAGAGACGCCACGT 60.109 55.000 0.00 0.00 45.10 4.49
22 23 0.806102 CCCATACAAGAGACGCCACG 60.806 60.000 0.00 0.00 0.00 4.94
23 24 1.090052 GCCCATACAAGAGACGCCAC 61.090 60.000 0.00 0.00 0.00 5.01
24 25 1.220749 GCCCATACAAGAGACGCCA 59.779 57.895 0.00 0.00 0.00 5.69
25 26 0.811616 CTGCCCATACAAGAGACGCC 60.812 60.000 0.00 0.00 0.00 5.68
26 27 1.432270 GCTGCCCATACAAGAGACGC 61.432 60.000 0.00 0.00 0.00 5.19
27 28 0.108186 TGCTGCCCATACAAGAGACG 60.108 55.000 0.00 0.00 0.00 4.18
28 29 1.065854 AGTGCTGCCCATACAAGAGAC 60.066 52.381 0.00 0.00 0.00 3.36
29 30 1.279496 AGTGCTGCCCATACAAGAGA 58.721 50.000 0.00 0.00 0.00 3.10
30 31 1.741706 CAAGTGCTGCCCATACAAGAG 59.258 52.381 0.00 0.00 0.00 2.85
31 32 1.350684 TCAAGTGCTGCCCATACAAGA 59.649 47.619 0.00 0.00 0.00 3.02
32 33 1.470098 GTCAAGTGCTGCCCATACAAG 59.530 52.381 0.00 0.00 0.00 3.16
33 34 1.533625 GTCAAGTGCTGCCCATACAA 58.466 50.000 0.00 0.00 0.00 2.41
34 35 0.673333 CGTCAAGTGCTGCCCATACA 60.673 55.000 0.00 0.00 0.00 2.29
35 36 1.369091 CCGTCAAGTGCTGCCCATAC 61.369 60.000 0.00 0.00 0.00 2.39
36 37 1.078497 CCGTCAAGTGCTGCCCATA 60.078 57.895 0.00 0.00 0.00 2.74
37 38 2.360350 CCGTCAAGTGCTGCCCAT 60.360 61.111 0.00 0.00 0.00 4.00
43 44 4.927782 TTGCCGCCGTCAAGTGCT 62.928 61.111 0.00 0.00 0.00 4.40
44 45 4.683334 GTTGCCGCCGTCAAGTGC 62.683 66.667 0.00 0.00 0.00 4.40
45 46 4.368808 CGTTGCCGCCGTCAAGTG 62.369 66.667 0.00 0.00 0.00 3.16
53 54 4.776647 GTGATTGCCGTTGCCGCC 62.777 66.667 0.00 0.00 36.33 6.13
54 55 4.776647 GGTGATTGCCGTTGCCGC 62.777 66.667 0.00 0.00 36.33 6.53
55 56 4.459331 CGGTGATTGCCGTTGCCG 62.459 66.667 0.00 0.00 46.11 5.69
62 63 3.098555 CGCCTAACGGTGATTGCC 58.901 61.111 0.00 0.00 43.70 4.52
63 64 2.403586 GCGCCTAACGGTGATTGC 59.596 61.111 0.00 0.00 43.70 3.56
64 65 2.701006 CGCGCCTAACGGTGATTG 59.299 61.111 0.00 0.00 43.70 2.67
65 66 2.510691 CCGCGCCTAACGGTGATT 60.511 61.111 0.00 0.00 45.70 2.57
102 103 0.386858 CCGTACATCTATGCCGACGG 60.387 60.000 10.29 10.29 41.85 4.79
103 104 0.589708 TCCGTACATCTATGCCGACG 59.410 55.000 0.00 5.36 33.90 5.12
104 105 1.662309 CGTCCGTACATCTATGCCGAC 60.662 57.143 0.00 0.00 0.00 4.79
105 106 0.589708 CGTCCGTACATCTATGCCGA 59.410 55.000 0.00 0.00 0.00 5.54
106 107 1.002250 GCGTCCGTACATCTATGCCG 61.002 60.000 0.00 0.00 0.00 5.69
107 108 0.666577 GGCGTCCGTACATCTATGCC 60.667 60.000 0.00 0.00 0.00 4.40
108 109 0.031585 TGGCGTCCGTACATCTATGC 59.968 55.000 0.00 0.00 0.00 3.14
109 110 2.596452 GATGGCGTCCGTACATCTATG 58.404 52.381 14.70 0.00 38.32 2.23
110 111 1.199327 CGATGGCGTCCGTACATCTAT 59.801 52.381 17.63 0.00 39.00 1.98
111 112 0.589708 CGATGGCGTCCGTACATCTA 59.410 55.000 17.63 0.00 39.00 1.98
112 113 1.359117 CGATGGCGTCCGTACATCT 59.641 57.895 17.63 0.00 39.00 2.90
113 114 1.660575 CCGATGGCGTCCGTACATC 60.661 63.158 0.14 13.01 38.06 3.06
114 115 2.415843 CCGATGGCGTCCGTACAT 59.584 61.111 0.14 0.02 35.23 2.29
115 116 4.501714 GCCGATGGCGTCCGTACA 62.502 66.667 0.14 0.00 39.62 2.90
125 126 2.558378 CATAGATGCCTATGCCGATGG 58.442 52.381 0.00 0.00 43.87 3.51
146 147 2.280186 GCATAGGAAGGCCGTCGG 60.280 66.667 12.79 6.99 39.96 4.79
147 148 2.280186 GGCATAGGAAGGCCGTCG 60.280 66.667 12.79 0.00 43.74 5.12
152 153 1.823899 CCCGTTGGCATAGGAAGGC 60.824 63.158 9.94 0.00 0.00 4.35
153 154 1.152963 CCCCGTTGGCATAGGAAGG 60.153 63.158 9.94 0.00 0.00 3.46
154 155 0.463833 GTCCCCGTTGGCATAGGAAG 60.464 60.000 9.94 2.34 0.00 3.46
155 156 1.605453 GTCCCCGTTGGCATAGGAA 59.395 57.895 9.94 0.00 0.00 3.36
156 157 2.372074 GGTCCCCGTTGGCATAGGA 61.372 63.158 9.94 1.27 0.00 2.94
157 158 2.192175 GGTCCCCGTTGGCATAGG 59.808 66.667 0.00 0.00 0.00 2.57
158 159 1.153168 CAGGTCCCCGTTGGCATAG 60.153 63.158 0.00 0.00 0.00 2.23
159 160 2.675242 CCAGGTCCCCGTTGGCATA 61.675 63.158 0.00 0.00 0.00 3.14
160 161 4.047125 CCAGGTCCCCGTTGGCAT 62.047 66.667 0.00 0.00 0.00 4.40
164 165 2.608368 TACCCCAGGTCCCCGTTG 60.608 66.667 0.00 0.00 37.09 4.10
165 166 2.608678 GTACCCCAGGTCCCCGTT 60.609 66.667 0.00 0.00 37.09 4.44
171 172 4.139234 GTCGGCGTACCCCAGGTC 62.139 72.222 6.85 0.00 37.09 3.85
176 177 3.216944 ATATGCGTCGGCGTACCCC 62.217 63.158 12.58 0.00 43.09 4.95
177 178 2.019951 CATATGCGTCGGCGTACCC 61.020 63.158 12.58 0.00 43.09 3.69
178 179 0.872881 AACATATGCGTCGGCGTACC 60.873 55.000 12.58 0.00 43.09 3.34
179 180 0.228742 CAACATATGCGTCGGCGTAC 59.771 55.000 12.58 2.92 43.09 3.67
180 181 1.484227 GCAACATATGCGTCGGCGTA 61.484 55.000 12.58 7.11 46.87 4.42
181 182 2.808958 GCAACATATGCGTCGGCGT 61.809 57.895 12.58 0.00 46.87 5.68
182 183 2.053116 GCAACATATGCGTCGGCG 60.053 61.111 4.29 4.29 46.87 6.46
205 206 4.351054 CCCCCATCGGCATAGGGC 62.351 72.222 0.00 0.00 41.42 5.19
230 231 1.340248 ACCCGTCGGCATAAGTCTATG 59.660 52.381 5.50 0.00 38.39 2.23
231 232 1.700955 ACCCGTCGGCATAAGTCTAT 58.299 50.000 5.50 0.00 0.00 1.98
232 233 2.346766 TACCCGTCGGCATAAGTCTA 57.653 50.000 5.50 0.00 0.00 2.59
233 234 1.612463 GATACCCGTCGGCATAAGTCT 59.388 52.381 5.50 0.00 0.00 3.24
234 235 1.338973 TGATACCCGTCGGCATAAGTC 59.661 52.381 5.50 0.00 0.00 3.01
235 236 1.340248 CTGATACCCGTCGGCATAAGT 59.660 52.381 5.50 0.00 0.00 2.24
236 237 1.336887 CCTGATACCCGTCGGCATAAG 60.337 57.143 5.50 3.73 0.00 1.73
237 238 0.677288 CCTGATACCCGTCGGCATAA 59.323 55.000 5.50 0.00 0.00 1.90
238 239 1.183030 CCCTGATACCCGTCGGCATA 61.183 60.000 5.50 0.37 0.00 3.14
239 240 2.507854 CCCTGATACCCGTCGGCAT 61.508 63.158 5.50 0.43 0.00 4.40
240 241 3.151710 CCCTGATACCCGTCGGCA 61.152 66.667 5.50 0.00 0.00 5.69
241 242 4.603946 GCCCTGATACCCGTCGGC 62.604 72.222 5.50 0.00 0.00 5.54
242 243 0.898789 ATAGCCCTGATACCCGTCGG 60.899 60.000 3.60 3.60 0.00 4.79
243 244 0.243907 CATAGCCCTGATACCCGTCG 59.756 60.000 0.00 0.00 0.00 5.12
244 245 0.037232 GCATAGCCCTGATACCCGTC 60.037 60.000 0.00 0.00 0.00 4.79
245 246 0.471971 AGCATAGCCCTGATACCCGT 60.472 55.000 0.00 0.00 0.00 5.28
246 247 0.036952 CAGCATAGCCCTGATACCCG 60.037 60.000 0.00 0.00 32.03 5.28
247 248 1.002544 GTCAGCATAGCCCTGATACCC 59.997 57.143 0.00 0.00 41.01 3.69
248 249 1.337260 CGTCAGCATAGCCCTGATACC 60.337 57.143 0.00 0.00 41.01 2.73
249 250 1.337260 CCGTCAGCATAGCCCTGATAC 60.337 57.143 0.00 0.00 41.01 2.24
250 251 0.969149 CCGTCAGCATAGCCCTGATA 59.031 55.000 0.00 0.00 41.01 2.15
251 252 1.750930 CCGTCAGCATAGCCCTGAT 59.249 57.895 0.00 0.00 41.01 2.90
252 253 3.094062 GCCGTCAGCATAGCCCTGA 62.094 63.158 0.00 0.00 42.97 3.86
253 254 2.590007 GCCGTCAGCATAGCCCTG 60.590 66.667 0.00 0.00 42.97 4.45
254 255 3.866582 GGCCGTCAGCATAGCCCT 61.867 66.667 0.00 0.00 46.50 5.19
256 257 2.590007 CAGGCCGTCAGCATAGCC 60.590 66.667 0.00 0.00 46.50 3.93
257 258 2.590007 CCAGGCCGTCAGCATAGC 60.590 66.667 0.00 0.00 46.50 2.97
258 259 2.109799 CCCAGGCCGTCAGCATAG 59.890 66.667 0.00 0.00 46.50 2.23
259 260 4.175337 GCCCAGGCCGTCAGCATA 62.175 66.667 0.00 0.00 46.50 3.14
263 264 4.767255 GACAGCCCAGGCCGTCAG 62.767 72.222 18.14 1.39 45.07 3.51
270 271 2.109799 CTATGCCGACAGCCCAGG 59.890 66.667 0.00 0.00 42.71 4.45
271 272 2.109799 CCTATGCCGACAGCCCAG 59.890 66.667 0.00 0.00 42.71 4.45
272 273 3.479203 CCCTATGCCGACAGCCCA 61.479 66.667 0.00 0.00 42.71 5.36
273 274 4.256180 CCCCTATGCCGACAGCCC 62.256 72.222 0.00 0.00 42.71 5.19
274 275 4.937431 GCCCCTATGCCGACAGCC 62.937 72.222 0.00 0.00 42.71 4.85
275 276 3.816367 GAGCCCCTATGCCGACAGC 62.816 68.421 0.00 0.00 44.14 4.40
276 277 2.374830 CTGAGCCCCTATGCCGACAG 62.375 65.000 0.00 0.00 0.00 3.51
277 278 2.364973 TGAGCCCCTATGCCGACA 60.365 61.111 0.00 0.00 0.00 4.35
278 279 2.423446 CTGAGCCCCTATGCCGAC 59.577 66.667 0.00 0.00 0.00 4.79
279 280 2.041922 ACTGAGCCCCTATGCCGA 60.042 61.111 0.00 0.00 0.00 5.54
280 281 2.109799 CACTGAGCCCCTATGCCG 59.890 66.667 0.00 0.00 0.00 5.69
281 282 1.153086 CACACTGAGCCCCTATGCC 60.153 63.158 0.00 0.00 0.00 4.40
282 283 1.153086 CCACACTGAGCCCCTATGC 60.153 63.158 0.00 0.00 0.00 3.14
283 284 1.414181 CTACCACACTGAGCCCCTATG 59.586 57.143 0.00 0.00 0.00 2.23
284 285 1.008449 ACTACCACACTGAGCCCCTAT 59.992 52.381 0.00 0.00 0.00 2.57
285 286 0.412244 ACTACCACACTGAGCCCCTA 59.588 55.000 0.00 0.00 0.00 3.53
286 287 1.158705 ACTACCACACTGAGCCCCT 59.841 57.895 0.00 0.00 0.00 4.79
287 288 1.192146 TCACTACCACACTGAGCCCC 61.192 60.000 0.00 0.00 0.00 5.80
288 289 0.685097 TTCACTACCACACTGAGCCC 59.315 55.000 0.00 0.00 0.00 5.19
289 290 2.744202 CAATTCACTACCACACTGAGCC 59.256 50.000 0.00 0.00 0.00 4.70
290 291 3.403038 ACAATTCACTACCACACTGAGC 58.597 45.455 0.00 0.00 0.00 4.26
291 292 3.997021 GGACAATTCACTACCACACTGAG 59.003 47.826 0.00 0.00 0.00 3.35
292 293 3.244422 GGGACAATTCACTACCACACTGA 60.244 47.826 0.00 0.00 0.00 3.41
293 294 3.074412 GGGACAATTCACTACCACACTG 58.926 50.000 0.00 0.00 0.00 3.66
294 295 2.708861 TGGGACAATTCACTACCACACT 59.291 45.455 0.00 0.00 31.92 3.55
295 296 2.812011 GTGGGACAATTCACTACCACAC 59.188 50.000 6.76 0.00 45.72 3.82
296 297 3.134574 GTGGGACAATTCACTACCACA 57.865 47.619 6.76 0.00 45.72 4.17
297 298 3.418684 AGTGGGACAATTCACTACCAC 57.581 47.619 0.00 0.00 44.16 4.16
298 299 5.487488 AGAATAGTGGGACAATTCACTACCA 59.513 40.000 6.83 0.00 45.55 3.25
299 300 5.817816 CAGAATAGTGGGACAATTCACTACC 59.182 44.000 6.83 3.71 45.55 3.18
300 301 6.640518 TCAGAATAGTGGGACAATTCACTAC 58.359 40.000 6.83 0.00 45.55 2.73
301 302 6.867519 TCAGAATAGTGGGACAATTCACTA 57.132 37.500 7.07 7.07 46.40 2.74
302 303 5.762179 TCAGAATAGTGGGACAATTCACT 57.238 39.130 3.35 3.35 44.16 3.41
303 304 7.396540 AATTCAGAATAGTGGGACAATTCAC 57.603 36.000 0.00 0.00 44.16 3.18
304 305 7.890127 AGAAATTCAGAATAGTGGGACAATTCA 59.110 33.333 0.00 0.00 44.16 2.57
305 306 8.186821 CAGAAATTCAGAATAGTGGGACAATTC 58.813 37.037 0.00 0.00 44.16 2.17
353 356 7.273381 CCCATTAAAATTCAGAAACACTTAGCG 59.727 37.037 0.00 0.00 0.00 4.26
359 362 8.229811 GCATTTCCCATTAAAATTCAGAAACAC 58.770 33.333 0.00 0.00 0.00 3.32
406 409 5.587388 ATGCAGGAACATGTTGAATAAGG 57.413 39.130 17.58 0.00 0.00 2.69
410 413 5.957798 CTGTTATGCAGGAACATGTTGAAT 58.042 37.500 17.58 5.21 41.42 2.57
411 414 5.375417 CTGTTATGCAGGAACATGTTGAA 57.625 39.130 17.58 0.00 41.42 2.69
456 459 5.361857 AGCAAAAGCTATTATGCAGGAACAT 59.638 36.000 13.29 0.00 41.18 2.71
458 461 5.254339 AGCAAAAGCTATTATGCAGGAAC 57.746 39.130 13.29 0.00 41.18 3.62
461 464 5.523369 GGTTAGCAAAAGCTATTATGCAGG 58.477 41.667 13.29 0.00 41.18 4.85
462 465 5.207768 CGGTTAGCAAAAGCTATTATGCAG 58.792 41.667 13.29 0.00 41.18 4.41
465 468 4.970003 GCACGGTTAGCAAAAGCTATTATG 59.030 41.667 0.00 0.00 0.00 1.90
466 469 4.881850 AGCACGGTTAGCAAAAGCTATTAT 59.118 37.500 0.00 0.00 0.00 1.28
467 470 4.258543 AGCACGGTTAGCAAAAGCTATTA 58.741 39.130 0.00 0.00 0.00 0.98
481 509 2.425668 ACTTGCAGTTTTAAGCACGGTT 59.574 40.909 0.00 0.00 41.05 4.44
482 510 2.021457 ACTTGCAGTTTTAAGCACGGT 58.979 42.857 0.00 0.00 41.05 4.83
516 544 2.550606 GCCCACACGTATCAGTTTTCAA 59.449 45.455 0.00 0.00 0.00 2.69
559 588 2.684881 CCATTCAAGATCAAACGGAGGG 59.315 50.000 0.00 0.00 0.00 4.30
568 597 4.743057 ATCTGTCGTCCATTCAAGATCA 57.257 40.909 0.00 0.00 0.00 2.92
580 609 0.179054 GGCCCCCTTTATCTGTCGTC 60.179 60.000 0.00 0.00 0.00 4.20
590 619 1.838396 CTGCAACTTGGCCCCCTTT 60.838 57.895 0.00 0.00 0.00 3.11
630 659 1.002868 GGCTGGGATCGGATGGATG 60.003 63.158 0.00 0.00 34.82 3.51
631 660 2.587247 CGGCTGGGATCGGATGGAT 61.587 63.158 0.00 0.00 38.35 3.41
632 661 3.233980 CGGCTGGGATCGGATGGA 61.234 66.667 0.00 0.00 0.00 3.41
687 716 0.842905 TTCCCCTCCAATTCCACCGA 60.843 55.000 0.00 0.00 0.00 4.69
740 769 5.046520 GGGCAAGAGAAGTAAGGAGTAAAGA 60.047 44.000 0.00 0.00 0.00 2.52
741 770 5.179533 GGGCAAGAGAAGTAAGGAGTAAAG 58.820 45.833 0.00 0.00 0.00 1.85
742 771 4.322499 CGGGCAAGAGAAGTAAGGAGTAAA 60.322 45.833 0.00 0.00 0.00 2.01
778 809 9.408648 ACCAGGGAGATAATAAATACACAAAAG 57.591 33.333 0.00 0.00 0.00 2.27
779 810 9.403583 GACCAGGGAGATAATAAATACACAAAA 57.596 33.333 0.00 0.00 0.00 2.44
780 811 7.713507 CGACCAGGGAGATAATAAATACACAAA 59.286 37.037 0.00 0.00 0.00 2.83
781 812 7.070198 TCGACCAGGGAGATAATAAATACACAA 59.930 37.037 0.00 0.00 0.00 3.33
782 813 6.551975 TCGACCAGGGAGATAATAAATACACA 59.448 38.462 0.00 0.00 0.00 3.72
783 814 6.989659 TCGACCAGGGAGATAATAAATACAC 58.010 40.000 0.00 0.00 0.00 2.90
784 815 7.674348 AGATCGACCAGGGAGATAATAAATACA 59.326 37.037 0.00 0.00 0.00 2.29
785 816 8.068892 AGATCGACCAGGGAGATAATAAATAC 57.931 38.462 0.00 0.00 0.00 1.89
786 817 8.531982 CAAGATCGACCAGGGAGATAATAAATA 58.468 37.037 0.00 0.00 0.00 1.40
787 818 7.390027 CAAGATCGACCAGGGAGATAATAAAT 58.610 38.462 0.00 0.00 0.00 1.40
788 819 6.239600 CCAAGATCGACCAGGGAGATAATAAA 60.240 42.308 0.00 0.00 0.00 1.40
789 820 5.246203 CCAAGATCGACCAGGGAGATAATAA 59.754 44.000 0.00 0.00 0.00 1.40
790 821 4.772624 CCAAGATCGACCAGGGAGATAATA 59.227 45.833 0.00 0.00 0.00 0.98
791 822 3.580458 CCAAGATCGACCAGGGAGATAAT 59.420 47.826 0.00 0.00 0.00 1.28
792 823 2.965831 CCAAGATCGACCAGGGAGATAA 59.034 50.000 0.00 0.00 0.00 1.75
793 824 2.091278 ACCAAGATCGACCAGGGAGATA 60.091 50.000 0.00 0.00 0.00 1.98
794 825 1.343478 ACCAAGATCGACCAGGGAGAT 60.343 52.381 0.00 0.00 0.00 2.75
795 826 0.041238 ACCAAGATCGACCAGGGAGA 59.959 55.000 0.00 0.00 0.00 3.71
796 827 0.905357 AACCAAGATCGACCAGGGAG 59.095 55.000 0.00 0.00 0.00 4.30
797 828 0.613260 CAACCAAGATCGACCAGGGA 59.387 55.000 0.00 0.00 0.00 4.20
813 844 2.844122 AGCACTTCCACGAAAACAAC 57.156 45.000 0.00 0.00 0.00 3.32
836 867 2.136878 CCCCAGACCCAGAGATCGG 61.137 68.421 0.00 0.00 0.00 4.18
849 880 8.272889 AGATGATGAATGATATTGATACCCCAG 58.727 37.037 0.00 0.00 0.00 4.45
850 881 8.166479 AGATGATGAATGATATTGATACCCCA 57.834 34.615 0.00 0.00 0.00 4.96
952 1007 4.734989 GCTTGATGCGACTCACTGTATACT 60.735 45.833 4.17 0.00 0.00 2.12
959 1014 1.078848 GGGCTTGATGCGACTCACT 60.079 57.895 0.00 0.00 44.05 3.41
1301 1379 1.377202 GGCATCAGTGGCGGAGAAA 60.377 57.895 0.00 0.00 41.35 2.52
1433 1511 0.971386 AATGCCAGCCTTTCAACCTG 59.029 50.000 0.00 0.00 0.00 4.00
1603 1687 3.261677 AGGGGCCGGCCTTAAACA 61.262 61.111 42.70 0.00 36.10 2.83
1664 1748 1.021202 CGCCAAACAAGAGGTTGTCA 58.979 50.000 0.00 0.00 46.68 3.58
2004 2100 7.015877 AGTGATTTACCCTTACAAGACACACTA 59.984 37.037 0.00 0.00 32.05 2.74
2135 2234 8.522542 TTGTACAACCCAAAAACTAACATACT 57.477 30.769 3.59 0.00 0.00 2.12
2199 2298 6.207810 ACGCCTTTCATTGTGGAATTTTAGTA 59.792 34.615 0.00 0.00 0.00 1.82
2324 2423 0.591170 CGGGCTGTGTTGTCGATTTT 59.409 50.000 0.00 0.00 0.00 1.82
2422 2524 2.359169 CCGGCCAGCCTACTCAAGA 61.359 63.158 2.24 0.00 0.00 3.02
2426 2528 0.533085 GATTTCCGGCCAGCCTACTC 60.533 60.000 2.24 0.00 0.00 2.59
2433 2535 1.000896 AACAGGGATTTCCGGCCAG 60.001 57.895 2.24 0.00 41.52 4.85
2809 2911 4.213513 CCCAAAGTACTCCTACGGTATCT 58.786 47.826 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.