Multiple sequence alignment - TraesCS3D01G103200

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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 TraesCS3D01G103200 chr3D 100.000 2901 0 0 1 2901 55781703 55778803 0.000000e+00 5358.0
1 TraesCS3D01G103200 chr3D 84.505 1110 113 28 707 1786 55349953 55351033 0.000000e+00 1042.0
2 TraesCS3D01G103200 chr3D 86.626 658 68 18 954 1606 55536868 55536226 0.000000e+00 710.0
3 TraesCS3D01G103200 chr3D 82.193 848 81 38 1778 2569 55351079 55351912 0.000000e+00 665.0
4 TraesCS3D01G103200 chr3D 85.809 451 43 16 2461 2901 55943347 55942908 2.630000e-125 459.0
5 TraesCS3D01G103200 chr3D 88.571 280 21 4 338 612 55558492 55558219 2.160000e-86 329.0
6 TraesCS3D01G103200 chr3D 88.172 279 25 4 834 1104 55943821 55943543 2.790000e-85 326.0
7 TraesCS3D01G103200 chr3D 88.433 268 16 3 338 590 55348878 55349145 2.810000e-80 309.0
8 TraesCS3D01G103200 chr3D 90.308 227 14 6 2590 2813 55534443 55534222 1.020000e-74 291.0
9 TraesCS3D01G103200 chr3D 87.692 260 17 2 344 588 55944589 55944330 3.660000e-74 289.0
10 TraesCS3D01G103200 chr3D 91.603 131 6 4 2591 2717 158931371 158931500 2.970000e-40 176.0
11 TraesCS3D01G103200 chr3D 97.436 78 2 0 2354 2431 55943423 55943346 1.810000e-27 134.0
12 TraesCS3D01G103200 chr3D 95.349 43 1 1 46 87 46616164 46616122 1.870000e-07 67.6
13 TraesCS3D01G103200 chr3D 100.000 28 0 0 549 576 55349035 55349062 5.000000e-03 52.8
14 TraesCS3D01G103200 chr3D 100.000 28 0 0 549 576 55558355 55558328 5.000000e-03 52.8
15 TraesCS3D01G103200 chr3D 100.000 28 0 0 549 576 55944438 55944411 5.000000e-03 52.8
16 TraesCS3D01G103200 chr3A 85.758 976 82 24 834 1774 65700870 65701823 0.000000e+00 979.0
17 TraesCS3D01G103200 chr3A 85.526 988 86 24 834 1786 65765589 65764624 0.000000e+00 979.0
18 TraesCS3D01G103200 chr3A 84.835 666 75 17 1128 1786 65869037 65869683 0.000000e+00 647.0
19 TraesCS3D01G103200 chr3A 84.039 614 56 16 2321 2901 65764074 65763470 1.170000e-153 553.0
20 TraesCS3D01G103200 chr3A 86.864 236 28 3 1901 2135 65869752 65869985 7.970000e-66 261.0
21 TraesCS3D01G103200 chr3A 79.926 269 27 19 339 605 65699755 65699998 3.840000e-39 172.0
22 TraesCS3D01G103200 chr3A 95.238 84 3 1 368 450 65767152 65767069 6.520000e-27 132.0
23 TraesCS3D01G103200 chr3A 97.561 41 1 0 47 87 65767610 65767570 1.440000e-08 71.3
24 TraesCS3D01G103200 chr3A 100.000 28 0 0 549 576 65766579 65766552 5.000000e-03 52.8
25 TraesCS3D01G103200 chr3B 86.007 879 85 20 827 1688 85239661 85240518 0.000000e+00 907.0
26 TraesCS3D01G103200 chr3B 87.121 660 63 14 1118 1777 85349855 85350492 0.000000e+00 728.0
27 TraesCS3D01G103200 chr3B 84.507 639 70 16 1154 1785 88966465 88967081 3.200000e-169 604.0
28 TraesCS3D01G103200 chr3B 86.515 482 38 19 2435 2901 85242446 85242915 3.340000e-139 505.0
29 TraesCS3D01G103200 chr3B 87.293 362 32 12 735 1091 85340475 85340827 4.500000e-108 401.0
30 TraesCS3D01G103200 chr3B 79.951 409 44 22 1811 2190 85350744 85351143 1.710000e-67 267.0
31 TraesCS3D01G103200 chr3B 95.312 128 3 3 486 612 85236844 85236969 1.760000e-47 200.0
32 TraesCS3D01G103200 chr3B 94.872 78 4 0 2334 2411 85241866 85241943 3.930000e-24 122.0
33 TraesCS3D01G103200 chr3B 86.916 107 10 1 1684 1786 85241133 85241239 1.830000e-22 117.0
34 TraesCS3D01G103200 chr4D 92.593 135 6 3 2590 2720 148609590 148609456 1.060000e-44 191.0
35 TraesCS3D01G103200 chr5D 91.603 131 7 3 2591 2717 503253282 503253412 8.260000e-41 178.0
36 TraesCS3D01G103200 chr5D 91.603 131 6 4 2591 2717 196431405 196431534 2.970000e-40 176.0
37 TraesCS3D01G103200 chr5D 80.952 105 15 5 234 336 424891480 424891581 8.620000e-11 78.7
38 TraesCS3D01G103200 chr5D 100.000 32 0 0 241 272 456594008 456593977 3.120000e-05 60.2
39 TraesCS3D01G103200 chrUn 91.603 131 6 4 2591 2717 371790916 371791045 2.970000e-40 176.0
40 TraesCS3D01G103200 chr7D 91.603 131 6 4 2591 2717 231564729 231564858 2.970000e-40 176.0
41 TraesCS3D01G103200 chr4B 78.723 141 18 8 204 336 30014114 30014250 1.850000e-12 84.2
42 TraesCS3D01G103200 chr4A 83.333 78 11 2 238 314 11526258 11526182 1.440000e-08 71.3
43 TraesCS3D01G103200 chr6B 79.048 105 17 5 233 335 452533516 452533415 1.870000e-07 67.6
44 TraesCS3D01G103200 chr7A 95.122 41 2 0 235 275 156869357 156869397 6.710000e-07 65.8
45 TraesCS3D01G103200 chr7B 100.000 32 0 0 241 272 733139227 733139258 3.120000e-05 60.2
46 TraesCS3D01G103200 chr1B 100.000 32 0 0 241 272 313400677 313400708 3.120000e-05 60.2
47 TraesCS3D01G103200 chr1B 100.000 32 0 0 241 272 313444657 313444688 3.120000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G103200 chr3D 55778803 55781703 2900 True 5358.00 5358 100.00000 1 2901 1 chr3D.!!$R2 2900
1 TraesCS3D01G103200 chr3D 55348878 55351912 3034 False 517.20 1042 88.78275 338 2569 4 chr3D.!!$F2 2231
2 TraesCS3D01G103200 chr3D 55534222 55536868 2646 True 500.50 710 88.46700 954 2813 2 chr3D.!!$R3 1859
3 TraesCS3D01G103200 chr3D 55942908 55944589 1681 True 252.16 459 91.82180 344 2901 5 chr3D.!!$R5 2557
4 TraesCS3D01G103200 chr3A 65699755 65701823 2068 False 575.50 979 82.84200 339 1774 2 chr3A.!!$F1 1435
5 TraesCS3D01G103200 chr3A 65869037 65869985 948 False 454.00 647 85.84950 1128 2135 2 chr3A.!!$F2 1007
6 TraesCS3D01G103200 chr3A 65763470 65767610 4140 True 357.62 979 92.47280 47 2901 5 chr3A.!!$R1 2854
7 TraesCS3D01G103200 chr3B 88966465 88967081 616 False 604.00 604 84.50700 1154 1785 1 chr3B.!!$F2 631
8 TraesCS3D01G103200 chr3B 85349855 85351143 1288 False 497.50 728 83.53600 1118 2190 2 chr3B.!!$F4 1072
9 TraesCS3D01G103200 chr3B 85236844 85242915 6071 False 370.20 907 89.92440 486 2901 5 chr3B.!!$F3 2415

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
284 437 0.100682 GGCTCTCTCGTCGTAATGCA 59.899 55.0 0.0 0.0 0.0 3.96 F
311 464 0.105760 ATGGAAACCACAGGCAACCA 60.106 50.0 0.0 0.0 35.8 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1091 4275 1.132201 TCTTTCTTTCTCCCCTCCCCA 60.132 52.381 0.0 0.0 0.00 4.96 R
2154 6342 1.204704 AGAAATCGACTGATGCACGGA 59.795 47.619 0.0 0.0 34.24 4.69 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
22 23 3.033764 GCTCGGTGTCGCGAAACA 61.034 61.111 29.40 14.21 36.13 2.83
23 24 3.000080 GCTCGGTGTCGCGAAACAG 62.000 63.158 29.40 25.56 36.13 3.16
24 25 1.660575 CTCGGTGTCGCGAAACAGT 60.661 57.895 29.40 0.00 36.13 3.55
25 26 1.876453 CTCGGTGTCGCGAAACAGTG 61.876 60.000 29.40 22.01 36.13 3.66
26 27 2.235016 CGGTGTCGCGAAACAGTGT 61.235 57.895 29.40 0.00 0.00 3.55
27 28 1.275657 GGTGTCGCGAAACAGTGTG 59.724 57.895 29.40 0.00 0.00 3.82
28 29 1.367665 GTGTCGCGAAACAGTGTGC 60.368 57.895 24.35 2.38 0.00 4.57
29 30 1.811679 TGTCGCGAAACAGTGTGCA 60.812 52.632 12.06 0.00 0.00 4.57
30 31 1.367665 GTCGCGAAACAGTGTGCAC 60.368 57.895 12.06 10.75 0.00 4.57
31 32 1.520564 TCGCGAAACAGTGTGCACT 60.521 52.632 19.41 0.00 43.61 4.40
32 33 1.087202 TCGCGAAACAGTGTGCACTT 61.087 50.000 19.41 2.78 40.20 3.16
33 34 0.248054 CGCGAAACAGTGTGCACTTT 60.248 50.000 19.41 9.99 40.20 2.66
34 35 1.793714 CGCGAAACAGTGTGCACTTTT 60.794 47.619 19.41 11.61 40.20 2.27
35 36 2.537931 CGCGAAACAGTGTGCACTTTTA 60.538 45.455 19.41 0.00 40.20 1.52
36 37 3.430931 GCGAAACAGTGTGCACTTTTAA 58.569 40.909 19.41 0.00 40.20 1.52
37 38 3.482110 GCGAAACAGTGTGCACTTTTAAG 59.518 43.478 19.41 10.19 40.20 1.85
38 39 4.729458 GCGAAACAGTGTGCACTTTTAAGA 60.729 41.667 19.41 0.00 40.20 2.10
39 40 5.510671 CGAAACAGTGTGCACTTTTAAGAT 58.489 37.500 19.41 0.00 40.20 2.40
40 41 5.971202 CGAAACAGTGTGCACTTTTAAGATT 59.029 36.000 19.41 3.11 40.20 2.40
41 42 6.472163 CGAAACAGTGTGCACTTTTAAGATTT 59.528 34.615 19.41 7.64 40.20 2.17
42 43 7.009174 CGAAACAGTGTGCACTTTTAAGATTTT 59.991 33.333 19.41 5.09 40.20 1.82
43 44 9.296400 GAAACAGTGTGCACTTTTAAGATTTTA 57.704 29.630 19.41 0.00 40.20 1.52
44 45 8.856490 AACAGTGTGCACTTTTAAGATTTTAG 57.144 30.769 19.41 0.00 40.20 1.85
45 46 7.425606 ACAGTGTGCACTTTTAAGATTTTAGG 58.574 34.615 19.41 0.00 40.20 2.69
88 147 2.483889 CCGTCTCTTCCTGGGCTTAATC 60.484 54.545 0.00 0.00 0.00 1.75
98 157 3.388308 CTGGGCTTAATCGATGAGACTG 58.612 50.000 13.00 5.05 0.00 3.51
101 160 3.385577 GGCTTAATCGATGAGACTGGTC 58.614 50.000 11.97 0.00 0.00 4.02
103 162 3.489398 GCTTAATCGATGAGACTGGTCGT 60.489 47.826 11.97 0.00 36.77 4.34
104 163 4.673441 CTTAATCGATGAGACTGGTCGTT 58.327 43.478 0.00 3.89 36.77 3.85
105 164 3.594603 AATCGATGAGACTGGTCGTTT 57.405 42.857 0.00 2.62 36.77 3.60
106 165 2.631418 TCGATGAGACTGGTCGTTTC 57.369 50.000 6.12 0.00 36.77 2.78
107 166 2.160205 TCGATGAGACTGGTCGTTTCT 58.840 47.619 6.12 0.00 36.77 2.52
111 170 4.211374 CGATGAGACTGGTCGTTTCTTTTT 59.789 41.667 0.00 0.00 34.09 1.94
114 173 4.570772 TGAGACTGGTCGTTTCTTTTTCAG 59.429 41.667 0.00 0.00 34.09 3.02
115 174 4.514401 AGACTGGTCGTTTCTTTTTCAGT 58.486 39.130 0.00 0.00 36.80 3.41
116 175 4.571176 AGACTGGTCGTTTCTTTTTCAGTC 59.429 41.667 11.26 11.26 45.62 3.51
119 178 3.375922 TGGTCGTTTCTTTTTCAGTCACC 59.624 43.478 0.00 0.00 0.00 4.02
121 180 4.095932 GGTCGTTTCTTTTTCAGTCACCTT 59.904 41.667 0.00 0.00 0.00 3.50
122 181 5.392703 GGTCGTTTCTTTTTCAGTCACCTTT 60.393 40.000 0.00 0.00 0.00 3.11
124 183 6.584942 GTCGTTTCTTTTTCAGTCACCTTTTT 59.415 34.615 0.00 0.00 0.00 1.94
125 184 6.584563 TCGTTTCTTTTTCAGTCACCTTTTTG 59.415 34.615 0.00 0.00 0.00 2.44
126 185 6.584563 CGTTTCTTTTTCAGTCACCTTTTTGA 59.415 34.615 0.00 0.00 0.00 2.69
127 186 7.115663 CGTTTCTTTTTCAGTCACCTTTTTGAA 59.884 33.333 0.00 0.00 0.00 2.69
130 189 9.500785 TTCTTTTTCAGTCACCTTTTTGAATTT 57.499 25.926 0.00 0.00 30.45 1.82
131 190 8.934825 TCTTTTTCAGTCACCTTTTTGAATTTG 58.065 29.630 0.00 0.00 30.45 2.32
132 191 6.660887 TTTCAGTCACCTTTTTGAATTTGC 57.339 33.333 0.00 0.00 30.45 3.68
134 193 5.916318 TCAGTCACCTTTTTGAATTTGCAT 58.084 33.333 0.00 0.00 0.00 3.96
141 260 8.950210 TCACCTTTTTGAATTTGCATGTAAAAA 58.050 25.926 13.11 0.64 0.00 1.94
169 288 1.075151 CCCCTACCACCCCTCTCTC 60.075 68.421 0.00 0.00 0.00 3.20
208 361 5.178797 TGTGTAACATTGGGTTTTGTTTGG 58.821 37.500 0.00 0.00 45.67 3.28
209 362 5.046591 TGTGTAACATTGGGTTTTGTTTGGA 60.047 36.000 0.00 0.00 45.67 3.53
210 363 6.052360 GTGTAACATTGGGTTTTGTTTGGAT 58.948 36.000 0.00 0.00 40.96 3.41
211 364 6.201997 GTGTAACATTGGGTTTTGTTTGGATC 59.798 38.462 0.00 0.00 40.96 3.36
212 365 4.350368 ACATTGGGTTTTGTTTGGATCC 57.650 40.909 4.20 4.20 0.00 3.36
213 366 3.973305 ACATTGGGTTTTGTTTGGATCCT 59.027 39.130 14.23 0.00 0.00 3.24
214 367 4.411869 ACATTGGGTTTTGTTTGGATCCTT 59.588 37.500 14.23 0.00 0.00 3.36
215 368 5.104151 ACATTGGGTTTTGTTTGGATCCTTT 60.104 36.000 14.23 0.00 0.00 3.11
216 369 4.414337 TGGGTTTTGTTTGGATCCTTTG 57.586 40.909 14.23 0.00 0.00 2.77
218 371 3.138304 GGTTTTGTTTGGATCCTTTGCC 58.862 45.455 14.23 1.06 0.00 4.52
219 372 3.138304 GTTTTGTTTGGATCCTTTGCCC 58.862 45.455 14.23 0.00 0.00 5.36
222 375 0.966179 GTTTGGATCCTTTGCCCGTT 59.034 50.000 14.23 0.00 0.00 4.44
224 377 0.111446 TTGGATCCTTTGCCCGTTCA 59.889 50.000 14.23 0.00 0.00 3.18
225 378 0.608035 TGGATCCTTTGCCCGTTCAC 60.608 55.000 14.23 0.00 0.00 3.18
226 379 0.322546 GGATCCTTTGCCCGTTCACT 60.323 55.000 3.84 0.00 0.00 3.41
228 381 1.468914 GATCCTTTGCCCGTTCACTTC 59.531 52.381 0.00 0.00 0.00 3.01
229 382 0.882927 TCCTTTGCCCGTTCACTTCG 60.883 55.000 0.00 0.00 0.00 3.79
232 385 0.249953 TTTGCCCGTTCACTTCGCTA 60.250 50.000 0.00 0.00 0.00 4.26
233 386 0.669318 TTGCCCGTTCACTTCGCTAG 60.669 55.000 0.00 0.00 0.00 3.42
234 387 1.810030 GCCCGTTCACTTCGCTAGG 60.810 63.158 0.00 0.00 0.00 3.02
235 388 1.810030 CCCGTTCACTTCGCTAGGC 60.810 63.158 0.00 0.00 0.00 3.93
236 389 1.080093 CCGTTCACTTCGCTAGGCA 60.080 57.895 0.00 0.00 0.00 4.75
237 390 0.669318 CCGTTCACTTCGCTAGGCAA 60.669 55.000 0.00 0.00 0.00 4.52
238 391 0.716108 CGTTCACTTCGCTAGGCAAG 59.284 55.000 0.00 0.00 0.00 4.01
252 405 3.121030 CAAGCCTTGCCGACGGAG 61.121 66.667 20.50 6.87 0.00 4.63
253 406 4.394712 AAGCCTTGCCGACGGAGG 62.395 66.667 20.50 17.66 0.00 4.30
263 416 2.125106 GACGGAGGCGAGCCAAAT 60.125 61.111 17.18 0.00 38.92 2.32
264 417 2.125106 ACGGAGGCGAGCCAAATC 60.125 61.111 17.18 5.12 38.92 2.17
265 418 3.264897 CGGAGGCGAGCCAAATCG 61.265 66.667 17.18 9.92 45.48 3.34
266 419 2.897350 GGAGGCGAGCCAAATCGG 60.897 66.667 17.18 0.00 42.94 4.18
277 430 0.867753 CCAAATCGGCTCTCTCGTCG 60.868 60.000 0.00 0.00 0.00 5.12
278 431 0.179161 CAAATCGGCTCTCTCGTCGT 60.179 55.000 0.00 0.00 0.00 4.34
279 432 1.063616 CAAATCGGCTCTCTCGTCGTA 59.936 52.381 0.00 0.00 0.00 3.43
281 434 1.595466 ATCGGCTCTCTCGTCGTAAT 58.405 50.000 0.00 0.00 0.00 1.89
282 435 0.656259 TCGGCTCTCTCGTCGTAATG 59.344 55.000 0.00 0.00 0.00 1.90
283 436 0.930742 CGGCTCTCTCGTCGTAATGC 60.931 60.000 0.00 0.00 0.00 3.56
284 437 0.100682 GGCTCTCTCGTCGTAATGCA 59.899 55.000 0.00 0.00 0.00 3.96
285 438 1.471964 GCTCTCTCGTCGTAATGCAG 58.528 55.000 0.00 0.00 0.00 4.41
286 439 1.064208 GCTCTCTCGTCGTAATGCAGA 59.936 52.381 0.00 0.00 0.00 4.26
287 440 2.478031 GCTCTCTCGTCGTAATGCAGAA 60.478 50.000 0.00 0.00 0.00 3.02
289 442 4.166523 CTCTCTCGTCGTAATGCAGAAAA 58.833 43.478 0.00 0.00 0.00 2.29
291 444 5.168569 TCTCTCGTCGTAATGCAGAAAAAT 58.831 37.500 0.00 0.00 0.00 1.82
292 445 6.327154 TCTCTCGTCGTAATGCAGAAAAATA 58.673 36.000 0.00 0.00 0.00 1.40
293 446 6.978659 TCTCTCGTCGTAATGCAGAAAAATAT 59.021 34.615 0.00 0.00 0.00 1.28
294 447 6.933130 TCTCGTCGTAATGCAGAAAAATATG 58.067 36.000 0.00 0.00 0.00 1.78
295 448 6.019075 TCTCGTCGTAATGCAGAAAAATATGG 60.019 38.462 0.00 0.00 0.00 2.74
296 449 5.813157 TCGTCGTAATGCAGAAAAATATGGA 59.187 36.000 0.00 0.00 0.00 3.41
297 450 6.314152 TCGTCGTAATGCAGAAAAATATGGAA 59.686 34.615 0.00 0.00 0.00 3.53
298 451 6.964370 CGTCGTAATGCAGAAAAATATGGAAA 59.036 34.615 0.00 0.00 0.00 3.13
299 452 7.044966 CGTCGTAATGCAGAAAAATATGGAAAC 60.045 37.037 0.00 0.00 0.00 2.78
300 453 7.220108 GTCGTAATGCAGAAAAATATGGAAACC 59.780 37.037 0.00 0.00 0.00 3.27
301 454 7.032580 CGTAATGCAGAAAAATATGGAAACCA 58.967 34.615 0.00 0.00 38.19 3.67
302 455 7.009174 CGTAATGCAGAAAAATATGGAAACCAC 59.991 37.037 0.00 0.00 35.80 4.16
303 456 5.798125 TGCAGAAAAATATGGAAACCACA 57.202 34.783 0.00 0.00 35.80 4.17
304 457 5.782047 TGCAGAAAAATATGGAAACCACAG 58.218 37.500 0.00 0.00 35.80 3.66
305 458 5.170748 GCAGAAAAATATGGAAACCACAGG 58.829 41.667 0.00 0.00 35.80 4.00
306 459 5.170748 CAGAAAAATATGGAAACCACAGGC 58.829 41.667 0.00 0.00 35.80 4.85
307 460 4.837860 AGAAAAATATGGAAACCACAGGCA 59.162 37.500 0.00 0.00 35.80 4.75
308 461 5.306678 AGAAAAATATGGAAACCACAGGCAA 59.693 36.000 0.00 0.00 35.80 4.52
309 462 4.535526 AAATATGGAAACCACAGGCAAC 57.464 40.909 0.00 0.00 35.80 4.17
310 463 1.917872 TATGGAAACCACAGGCAACC 58.082 50.000 0.00 0.00 35.80 3.77
311 464 0.105760 ATGGAAACCACAGGCAACCA 60.106 50.000 0.00 0.00 35.80 3.67
312 465 0.754957 TGGAAACCACAGGCAACCAG 60.755 55.000 0.00 0.00 37.17 4.00
313 466 1.463553 GGAAACCACAGGCAACCAGG 61.464 60.000 0.00 0.00 37.17 4.45
314 467 0.755327 GAAACCACAGGCAACCAGGT 60.755 55.000 0.00 0.00 37.17 4.00
315 468 1.042559 AAACCACAGGCAACCAGGTG 61.043 55.000 0.00 2.49 33.09 4.00
316 469 1.932156 AACCACAGGCAACCAGGTGA 61.932 55.000 0.00 0.00 34.49 4.02
317 470 1.601759 CCACAGGCAACCAGGTGAG 60.602 63.158 0.00 0.00 34.49 3.51
318 471 1.149174 CACAGGCAACCAGGTGAGT 59.851 57.895 0.00 0.00 34.49 3.41
319 472 0.466189 CACAGGCAACCAGGTGAGTT 60.466 55.000 0.00 0.00 34.49 3.01
320 473 0.179018 ACAGGCAACCAGGTGAGTTC 60.179 55.000 0.00 0.00 37.17 3.01
321 474 1.071471 AGGCAACCAGGTGAGTTCG 59.929 57.895 0.00 0.00 37.17 3.95
322 475 2.617274 GGCAACCAGGTGAGTTCGC 61.617 63.158 0.00 0.00 0.00 4.70
323 476 2.617274 GCAACCAGGTGAGTTCGCC 61.617 63.158 3.50 3.50 46.57 5.54
329 482 3.379445 GGTGAGTTCGCCGAGGGA 61.379 66.667 0.00 0.00 36.72 4.20
330 483 2.654877 GTGAGTTCGCCGAGGGAA 59.345 61.111 0.00 0.00 32.23 3.97
350 503 1.819905 CAAACCGTTTGGGGTGCTT 59.180 52.632 15.11 0.00 41.08 3.91
404 586 7.170658 GCCATCTGTAGTTAAGAATCTGTGATC 59.829 40.741 0.00 0.00 0.00 2.92
450 632 4.162131 TCCATCATGTAGCTAACAGAAGCA 59.838 41.667 0.00 0.00 45.30 3.91
452 634 3.525537 TCATGTAGCTAACAGAAGCAGC 58.474 45.455 0.00 0.00 45.30 5.25
453 635 3.055891 TCATGTAGCTAACAGAAGCAGCA 60.056 43.478 0.00 0.00 45.30 4.41
455 637 1.663135 GTAGCTAACAGAAGCAGCAGC 59.337 52.381 0.00 0.00 45.30 5.25
456 638 5.186469 TGTAGCTAACAGAAGCAGCAGCT 62.186 47.826 0.00 0.00 45.30 4.24
472 1114 1.211190 GCTACAAGTTGCAGCAGCC 59.789 57.895 20.94 0.00 36.77 4.85
547 1191 5.371526 TCAAGCAAAAGAGATGTTCTCAGT 58.628 37.500 7.24 0.00 45.73 3.41
612 1256 0.179111 TTGATCCACCGATCGAGCAC 60.179 55.000 18.66 3.54 46.89 4.40
613 1257 1.658717 GATCCACCGATCGAGCACG 60.659 63.158 18.66 1.10 35.83 5.34
671 2029 1.278985 CCAATGATGGCCTCCGCTATA 59.721 52.381 3.32 0.00 40.58 1.31
694 2052 0.745486 TTCGTCTCGCCGATGTAGGA 60.745 55.000 0.00 0.00 36.62 2.94
696 2054 1.008309 GTCTCGCCGATGTAGGAGC 60.008 63.158 0.00 0.00 0.00 4.70
697 2055 1.152943 TCTCGCCGATGTAGGAGCT 60.153 57.895 0.00 0.00 0.00 4.09
700 2058 2.280457 GCCGATGTAGGAGCTGCC 60.280 66.667 0.00 0.00 0.00 4.85
701 2059 3.094062 GCCGATGTAGGAGCTGCCA 62.094 63.158 0.00 0.00 40.02 4.92
783 2187 1.287217 ACTAGGAGGAGACGTGAGGA 58.713 55.000 0.00 0.00 0.00 3.71
785 2189 2.158726 ACTAGGAGGAGACGTGAGGATC 60.159 54.545 0.00 0.00 0.00 3.36
786 2190 0.464735 AGGAGGAGACGTGAGGATCG 60.465 60.000 0.00 0.00 38.61 3.69
792 2196 2.792599 ACGTGAGGATCGTCTCGC 59.207 61.111 29.30 17.38 38.61 5.03
793 2197 1.745864 ACGTGAGGATCGTCTCGCT 60.746 57.895 29.30 18.41 40.88 4.93
795 2199 1.587613 GTGAGGATCGTCTCGCTGC 60.588 63.158 15.91 0.00 40.16 5.25
798 2202 2.583593 GGATCGTCTCGCTGCCAC 60.584 66.667 0.00 0.00 0.00 5.01
801 2205 3.685214 ATCGTCTCGCTGCCACGTC 62.685 63.158 11.64 0.00 35.05 4.34
802 2206 4.700365 CGTCTCGCTGCCACGTCA 62.700 66.667 0.00 0.00 0.00 4.35
803 2207 2.807045 GTCTCGCTGCCACGTCAG 60.807 66.667 0.01 0.01 37.15 3.51
804 2208 2.983592 TCTCGCTGCCACGTCAGA 60.984 61.111 8.35 0.00 36.19 3.27
805 2209 2.049156 CTCGCTGCCACGTCAGAA 60.049 61.111 8.35 0.00 36.19 3.02
806 2210 1.446792 CTCGCTGCCACGTCAGAAT 60.447 57.895 8.35 0.00 36.19 2.40
807 2211 1.416813 CTCGCTGCCACGTCAGAATC 61.417 60.000 8.35 0.00 36.19 2.52
808 2212 2.456119 CGCTGCCACGTCAGAATCC 61.456 63.158 8.35 0.00 36.19 3.01
810 2214 1.086634 GCTGCCACGTCAGAATCCTC 61.087 60.000 8.35 0.00 36.19 3.71
811 2215 0.247460 CTGCCACGTCAGAATCCTCA 59.753 55.000 0.00 0.00 36.19 3.86
813 2217 1.078759 GCCACGTCAGAATCCTCACG 61.079 60.000 0.00 0.00 38.24 4.35
814 2218 0.243907 CCACGTCAGAATCCTCACGT 59.756 55.000 0.00 0.00 46.05 4.49
816 2220 0.168348 ACGTCAGAATCCTCACGTCG 59.832 55.000 0.00 0.00 41.51 5.12
817 2221 0.523546 CGTCAGAATCCTCACGTCGG 60.524 60.000 0.00 0.00 0.00 4.79
818 2222 0.802607 GTCAGAATCCTCACGTCGGC 60.803 60.000 0.00 0.00 0.00 5.54
819 2223 1.874019 CAGAATCCTCACGTCGGCG 60.874 63.158 8.42 8.42 44.93 6.46
820 2224 2.044555 AGAATCCTCACGTCGGCGA 61.045 57.895 20.03 4.99 42.00 5.54
822 2226 2.267681 GAATCCTCACGTCGGCGAGT 62.268 60.000 20.03 8.10 42.00 4.18
823 2227 1.874345 AATCCTCACGTCGGCGAGTT 61.874 55.000 20.03 0.00 42.00 3.01
824 2228 1.028330 ATCCTCACGTCGGCGAGTTA 61.028 55.000 20.03 1.47 42.00 2.24
827 2231 0.109873 CTCACGTCGGCGAGTTAGTT 60.110 55.000 20.03 0.00 42.00 2.24
829 2233 0.433492 CACGTCGGCGAGTTAGTTTG 59.567 55.000 20.03 0.00 42.00 2.93
893 4076 1.303317 GTTACTGTGTGGGGCCCAG 60.303 63.158 29.66 17.51 32.34 4.45
940 4123 0.460109 CCACGTCAGAATCCATCGCA 60.460 55.000 0.00 0.00 0.00 5.10
948 4131 2.891941 GAATCCATCGCAGGGGCACA 62.892 60.000 0.00 0.00 41.24 4.57
998 4181 2.732619 GGATCCCTGGTCCCACGTC 61.733 68.421 0.00 0.00 0.00 4.34
1002 4185 2.677524 CCTGGTCCCACGTCCGTA 60.678 66.667 0.00 0.00 0.00 4.02
1068 4252 0.173708 GACTAAGCTGGGACCTGTCG 59.826 60.000 0.00 0.00 0.00 4.35
1121 4321 7.126061 AGGGGAGAAAGAAAGAAAGAAAGAAA 58.874 34.615 0.00 0.00 0.00 2.52
1122 4322 7.286546 AGGGGAGAAAGAAAGAAAGAAAGAAAG 59.713 37.037 0.00 0.00 0.00 2.62
1123 4323 7.285629 GGGGAGAAAGAAAGAAAGAAAGAAAGA 59.714 37.037 0.00 0.00 0.00 2.52
1697 5558 2.870372 GTGGAGAACATGTGCGCC 59.130 61.111 19.29 19.29 0.00 6.53
1720 5581 3.197790 CTTCATGGCCACCGAGCG 61.198 66.667 8.16 0.00 0.00 5.03
1795 5717 3.057174 ACGAGTCTCCTTGATCTTGTGAC 60.057 47.826 0.00 0.00 0.00 3.67
1849 5949 3.869246 GGATTCGATCTACTTTTTGCGGA 59.131 43.478 0.00 0.00 0.00 5.54
1855 5955 5.041287 CGATCTACTTTTTGCGGATCTGTA 58.959 41.667 2.89 0.00 32.99 2.74
1856 5956 5.051641 CGATCTACTTTTTGCGGATCTGTAC 60.052 44.000 2.89 0.00 32.99 2.90
1890 5995 6.214177 AGGATCAACCGGGGAATTAATTAT 57.786 37.500 6.32 0.00 44.74 1.28
1891 5996 7.337826 AGGATCAACCGGGGAATTAATTATA 57.662 36.000 6.32 0.00 44.74 0.98
1922 6031 0.179121 ATGCCGTAGCGATTCGAACA 60.179 50.000 10.88 0.00 44.31 3.18
1962 6072 6.512415 CGATCTGAAATCCCAGAATTACTTGC 60.512 42.308 0.00 0.00 45.22 4.01
1968 6078 2.094675 CCCAGAATTACTTGCTGGTGG 58.905 52.381 0.00 0.00 46.05 4.61
2028 6163 1.287041 ATGATGCGTCGATCATGCCG 61.287 55.000 15.05 0.00 40.80 5.69
2029 6164 3.287121 GATGCGTCGATCATGCCGC 62.287 63.158 8.69 8.69 45.92 6.53
2080 6260 2.761559 TGCAACGTACATTAGCAGTGT 58.238 42.857 0.00 0.00 0.00 3.55
2108 6292 2.798976 TTTCTGTGGCATTGCACTTC 57.201 45.000 11.39 0.00 0.00 3.01
2131 6315 4.433022 CGCAGTTCTTTGAACTACGATCAC 60.433 45.833 21.46 4.19 38.84 3.06
2190 6381 3.865224 TTTCTCTTTTCAACGTACCGC 57.135 42.857 0.00 0.00 0.00 5.68
2212 6404 5.238583 GCTAAAGAGTCAAGGCTTGTTCTA 58.761 41.667 25.39 14.19 0.00 2.10
2237 6437 3.820467 TCCACAAGCAACTCCAATACTTG 59.180 43.478 0.00 0.00 42.63 3.16
2347 6586 6.597832 TTTAATGGGGTAATGTTGGTCTTG 57.402 37.500 0.00 0.00 0.00 3.02
2349 6588 4.608170 ATGGGGTAATGTTGGTCTTGAT 57.392 40.909 0.00 0.00 0.00 2.57
2352 6591 5.258051 TGGGGTAATGTTGGTCTTGATAAC 58.742 41.667 0.00 0.00 0.00 1.89
2416 6684 6.424812 GGTGCAAAAGAATATGAGCAGTTTTT 59.575 34.615 0.00 0.00 32.03 1.94
2434 7158 7.814587 GCAGTTTTTGGCTTCATTTCTAATACT 59.185 33.333 0.00 0.00 0.00 2.12
2435 7159 9.132521 CAGTTTTTGGCTTCATTTCTAATACTG 57.867 33.333 0.00 0.00 0.00 2.74
2436 7160 7.814587 AGTTTTTGGCTTCATTTCTAATACTGC 59.185 33.333 0.00 0.00 0.00 4.40
2439 7163 7.408756 TTGGCTTCATTTCTAATACTGCAAT 57.591 32.000 0.00 0.00 0.00 3.56
2441 7165 7.839907 TGGCTTCATTTCTAATACTGCAATTT 58.160 30.769 0.00 0.00 0.00 1.82
2442 7166 7.975616 TGGCTTCATTTCTAATACTGCAATTTC 59.024 33.333 0.00 0.00 0.00 2.17
2446 7170 7.483307 TCATTTCTAATACTGCAATTTCAGCC 58.517 34.615 4.91 0.00 37.59 4.85
2748 8379 6.833416 ACTAGCCCATTGCACATTTCTAAATA 59.167 34.615 0.00 0.00 44.83 1.40
2749 8380 6.543430 AGCCCATTGCACATTTCTAAATAA 57.457 33.333 0.00 0.00 44.83 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.000080 CTGTTTCGCGACACCGAGC 62.000 63.158 21.64 3.79 38.60 5.03
6 7 1.660575 ACTGTTTCGCGACACCGAG 60.661 57.895 21.64 15.52 38.60 4.63
7 8 1.947146 CACTGTTTCGCGACACCGA 60.947 57.895 21.64 4.19 38.22 4.69
8 9 2.235016 ACACTGTTTCGCGACACCG 61.235 57.895 21.64 17.80 39.16 4.94
9 10 1.275657 CACACTGTTTCGCGACACC 59.724 57.895 21.64 7.38 0.00 4.16
10 11 1.367665 GCACACTGTTTCGCGACAC 60.368 57.895 18.18 18.18 0.00 3.67
11 12 1.811679 TGCACACTGTTTCGCGACA 60.812 52.632 9.15 3.93 0.00 4.35
12 13 1.367665 GTGCACACTGTTTCGCGAC 60.368 57.895 9.15 0.00 0.00 5.19
13 14 1.087202 AAGTGCACACTGTTTCGCGA 61.087 50.000 21.04 3.71 41.58 5.87
14 15 0.248054 AAAGTGCACACTGTTTCGCG 60.248 50.000 21.04 0.00 41.58 5.87
15 16 1.908065 AAAAGTGCACACTGTTTCGC 58.092 45.000 21.04 0.00 41.58 4.70
16 17 4.904116 TCTTAAAAGTGCACACTGTTTCG 58.096 39.130 21.04 8.40 41.58 3.46
17 18 7.755582 AAATCTTAAAAGTGCACACTGTTTC 57.244 32.000 21.04 0.00 41.58 2.78
18 19 9.301153 CTAAAATCTTAAAAGTGCACACTGTTT 57.699 29.630 21.04 14.91 41.58 2.83
19 20 7.920682 CCTAAAATCTTAAAAGTGCACACTGTT 59.079 33.333 21.04 10.87 41.58 3.16
20 21 7.068226 ACCTAAAATCTTAAAAGTGCACACTGT 59.932 33.333 21.04 3.02 41.58 3.55
21 22 7.425606 ACCTAAAATCTTAAAAGTGCACACTG 58.574 34.615 21.04 2.91 41.58 3.66
22 23 7.582667 ACCTAAAATCTTAAAAGTGCACACT 57.417 32.000 21.04 2.05 44.94 3.55
23 24 8.642908 AAACCTAAAATCTTAAAAGTGCACAC 57.357 30.769 21.04 0.00 0.00 3.82
24 25 9.660180 AAAAACCTAAAATCTTAAAAGTGCACA 57.340 25.926 21.04 0.00 0.00 4.57
35 36 8.244113 CCGAGCAATAGAAAAACCTAAAATCTT 58.756 33.333 0.00 0.00 0.00 2.40
36 37 7.393515 ACCGAGCAATAGAAAAACCTAAAATCT 59.606 33.333 0.00 0.00 0.00 2.40
37 38 7.484959 CACCGAGCAATAGAAAAACCTAAAATC 59.515 37.037 0.00 0.00 0.00 2.17
38 39 7.312899 CACCGAGCAATAGAAAAACCTAAAAT 58.687 34.615 0.00 0.00 0.00 1.82
39 40 6.674066 CACCGAGCAATAGAAAAACCTAAAA 58.326 36.000 0.00 0.00 0.00 1.52
40 41 5.335348 GCACCGAGCAATAGAAAAACCTAAA 60.335 40.000 0.00 0.00 44.79 1.85
41 42 4.155280 GCACCGAGCAATAGAAAAACCTAA 59.845 41.667 0.00 0.00 44.79 2.69
42 43 3.687698 GCACCGAGCAATAGAAAAACCTA 59.312 43.478 0.00 0.00 44.79 3.08
43 44 2.488153 GCACCGAGCAATAGAAAAACCT 59.512 45.455 0.00 0.00 44.79 3.50
44 45 2.863739 GCACCGAGCAATAGAAAAACC 58.136 47.619 0.00 0.00 44.79 3.27
88 147 2.638556 AGAAACGACCAGTCTCATCG 57.361 50.000 0.00 1.52 41.60 3.84
98 157 3.626217 AGGTGACTGAAAAAGAAACGACC 59.374 43.478 0.00 0.00 41.13 4.79
101 160 6.584563 TCAAAAAGGTGACTGAAAAAGAAACG 59.415 34.615 0.00 0.00 42.68 3.60
103 162 9.500785 AATTCAAAAAGGTGACTGAAAAAGAAA 57.499 25.926 0.00 0.00 42.68 2.52
104 163 9.500785 AAATTCAAAAAGGTGACTGAAAAAGAA 57.499 25.926 0.00 0.00 42.68 2.52
105 164 8.934825 CAAATTCAAAAAGGTGACTGAAAAAGA 58.065 29.630 0.00 0.00 42.68 2.52
106 165 7.693536 GCAAATTCAAAAAGGTGACTGAAAAAG 59.306 33.333 0.00 0.00 42.68 2.27
107 166 7.173907 TGCAAATTCAAAAAGGTGACTGAAAAA 59.826 29.630 0.00 0.00 42.68 1.94
111 170 5.336150 TGCAAATTCAAAAAGGTGACTGA 57.664 34.783 0.00 0.00 42.68 3.41
114 173 5.989551 ACATGCAAATTCAAAAAGGTGAC 57.010 34.783 0.00 0.00 0.00 3.67
115 174 8.498054 TTTTACATGCAAATTCAAAAAGGTGA 57.502 26.923 0.00 0.00 0.00 4.02
141 260 1.414685 GGTGGTAGGGGGAGAGCTATT 60.415 57.143 0.00 0.00 0.00 1.73
143 262 1.624753 GGTGGTAGGGGGAGAGCTA 59.375 63.158 0.00 0.00 0.00 3.32
145 264 2.768769 GGGTGGTAGGGGGAGAGC 60.769 72.222 0.00 0.00 0.00 4.09
156 275 0.618968 GATGGTGAGAGAGGGGTGGT 60.619 60.000 0.00 0.00 0.00 4.16
169 288 2.575532 ACACAGTGAAAGGTGATGGTG 58.424 47.619 7.81 0.00 38.38 4.17
197 350 3.138304 GGCAAAGGATCCAAACAAAACC 58.862 45.455 15.82 0.21 0.00 3.27
198 351 3.138304 GGGCAAAGGATCCAAACAAAAC 58.862 45.455 15.82 0.00 0.00 2.43
199 352 2.224161 CGGGCAAAGGATCCAAACAAAA 60.224 45.455 15.82 0.00 0.00 2.44
202 355 0.178975 ACGGGCAAAGGATCCAAACA 60.179 50.000 15.82 0.00 0.00 2.83
203 356 0.966179 AACGGGCAAAGGATCCAAAC 59.034 50.000 15.82 0.00 0.00 2.93
205 358 0.111446 TGAACGGGCAAAGGATCCAA 59.889 50.000 15.82 0.00 0.00 3.53
208 361 1.468914 GAAGTGAACGGGCAAAGGATC 59.531 52.381 0.00 0.00 0.00 3.36
209 362 1.534729 GAAGTGAACGGGCAAAGGAT 58.465 50.000 0.00 0.00 0.00 3.24
210 363 0.882927 CGAAGTGAACGGGCAAAGGA 60.883 55.000 0.00 0.00 0.00 3.36
211 364 1.574428 CGAAGTGAACGGGCAAAGG 59.426 57.895 0.00 0.00 0.00 3.11
212 365 1.082104 GCGAAGTGAACGGGCAAAG 60.082 57.895 0.00 0.00 0.00 2.77
213 366 0.249953 TAGCGAAGTGAACGGGCAAA 60.250 50.000 0.00 0.00 0.00 3.68
214 367 0.669318 CTAGCGAAGTGAACGGGCAA 60.669 55.000 0.00 0.00 0.00 4.52
215 368 1.080093 CTAGCGAAGTGAACGGGCA 60.080 57.895 0.00 0.00 0.00 5.36
216 369 1.810030 CCTAGCGAAGTGAACGGGC 60.810 63.158 0.00 0.00 0.00 6.13
218 371 0.669318 TTGCCTAGCGAAGTGAACGG 60.669 55.000 0.00 0.00 0.00 4.44
219 372 0.716108 CTTGCCTAGCGAAGTGAACG 59.284 55.000 0.00 0.00 0.00 3.95
222 375 4.598257 GCTTGCCTAGCGAAGTGA 57.402 55.556 0.00 0.00 40.71 3.41
235 388 3.121030 CTCCGTCGGCAAGGCTTG 61.121 66.667 22.75 22.75 0.00 4.01
236 389 4.394712 CCTCCGTCGGCAAGGCTT 62.395 66.667 6.34 0.00 0.00 4.35
245 398 4.735132 TTTGGCTCGCCTCCGTCG 62.735 66.667 9.65 0.00 36.94 5.12
247 400 2.125106 GATTTGGCTCGCCTCCGT 60.125 61.111 9.65 0.00 36.94 4.69
248 401 3.264897 CGATTTGGCTCGCCTCCG 61.265 66.667 9.65 3.87 36.94 4.63
249 402 2.897350 CCGATTTGGCTCGCCTCC 60.897 66.667 9.65 0.00 37.33 4.30
259 412 0.179161 ACGACGAGAGAGCCGATTTG 60.179 55.000 0.00 0.00 0.00 2.32
260 413 1.376543 TACGACGAGAGAGCCGATTT 58.623 50.000 0.00 0.00 0.00 2.17
263 416 0.656259 CATTACGACGAGAGAGCCGA 59.344 55.000 0.00 0.00 0.00 5.54
264 417 0.930742 GCATTACGACGAGAGAGCCG 60.931 60.000 0.00 0.00 0.00 5.52
265 418 0.100682 TGCATTACGACGAGAGAGCC 59.899 55.000 0.00 0.00 0.00 4.70
266 419 1.064208 TCTGCATTACGACGAGAGAGC 59.936 52.381 0.00 0.00 0.00 4.09
267 420 3.406728 TTCTGCATTACGACGAGAGAG 57.593 47.619 0.00 0.00 0.00 3.20
269 422 4.903638 TTTTTCTGCATTACGACGAGAG 57.096 40.909 0.00 0.00 0.00 3.20
271 424 6.019075 TCCATATTTTTCTGCATTACGACGAG 60.019 38.462 0.00 0.00 0.00 4.18
272 425 5.813157 TCCATATTTTTCTGCATTACGACGA 59.187 36.000 0.00 0.00 0.00 4.20
273 426 6.043327 TCCATATTTTTCTGCATTACGACG 57.957 37.500 0.00 0.00 0.00 5.12
274 427 7.220108 GGTTTCCATATTTTTCTGCATTACGAC 59.780 37.037 0.00 0.00 0.00 4.34
275 428 7.094162 TGGTTTCCATATTTTTCTGCATTACGA 60.094 33.333 0.00 0.00 0.00 3.43
277 430 7.816995 TGTGGTTTCCATATTTTTCTGCATTAC 59.183 33.333 0.00 0.00 35.28 1.89
278 431 7.901029 TGTGGTTTCCATATTTTTCTGCATTA 58.099 30.769 0.00 0.00 35.28 1.90
279 432 6.767456 TGTGGTTTCCATATTTTTCTGCATT 58.233 32.000 0.00 0.00 35.28 3.56
281 434 5.279406 CCTGTGGTTTCCATATTTTTCTGCA 60.279 40.000 0.00 0.00 35.28 4.41
282 435 5.170748 CCTGTGGTTTCCATATTTTTCTGC 58.829 41.667 0.00 0.00 35.28 4.26
283 436 5.170748 GCCTGTGGTTTCCATATTTTTCTG 58.829 41.667 0.00 0.00 35.28 3.02
284 437 4.837860 TGCCTGTGGTTTCCATATTTTTCT 59.162 37.500 0.00 0.00 35.28 2.52
285 438 5.146010 TGCCTGTGGTTTCCATATTTTTC 57.854 39.130 0.00 0.00 35.28 2.29
286 439 5.304778 GTTGCCTGTGGTTTCCATATTTTT 58.695 37.500 0.00 0.00 35.28 1.94
287 440 4.262851 GGTTGCCTGTGGTTTCCATATTTT 60.263 41.667 0.00 0.00 35.28 1.82
289 442 2.831526 GGTTGCCTGTGGTTTCCATATT 59.168 45.455 0.00 0.00 35.28 1.28
291 444 1.145945 TGGTTGCCTGTGGTTTCCATA 59.854 47.619 0.00 0.00 35.28 2.74
292 445 0.105760 TGGTTGCCTGTGGTTTCCAT 60.106 50.000 0.00 0.00 35.28 3.41
293 446 0.754957 CTGGTTGCCTGTGGTTTCCA 60.755 55.000 0.00 0.00 0.00 3.53
294 447 1.463553 CCTGGTTGCCTGTGGTTTCC 61.464 60.000 0.00 0.00 0.00 3.13
295 448 0.755327 ACCTGGTTGCCTGTGGTTTC 60.755 55.000 0.00 0.00 0.00 2.78
296 449 1.042559 CACCTGGTTGCCTGTGGTTT 61.043 55.000 0.00 0.00 0.00 3.27
297 450 1.455587 CACCTGGTTGCCTGTGGTT 60.456 57.895 0.00 0.00 0.00 3.67
298 451 2.195683 CACCTGGTTGCCTGTGGT 59.804 61.111 0.00 0.00 0.00 4.16
299 452 1.601759 CTCACCTGGTTGCCTGTGG 60.602 63.158 0.00 0.00 31.38 4.17
300 453 0.466189 AACTCACCTGGTTGCCTGTG 60.466 55.000 0.00 0.00 0.00 3.66
301 454 0.179018 GAACTCACCTGGTTGCCTGT 60.179 55.000 0.00 0.00 0.00 4.00
302 455 1.230635 CGAACTCACCTGGTTGCCTG 61.231 60.000 0.00 0.00 0.00 4.85
303 456 1.071471 CGAACTCACCTGGTTGCCT 59.929 57.895 0.00 0.00 0.00 4.75
304 457 2.617274 GCGAACTCACCTGGTTGCC 61.617 63.158 0.00 0.00 0.00 4.52
305 458 2.617274 GGCGAACTCACCTGGTTGC 61.617 63.158 0.00 0.00 0.00 4.17
306 459 2.317609 CGGCGAACTCACCTGGTTG 61.318 63.158 0.00 0.00 0.00 3.77
307 460 2.030562 CGGCGAACTCACCTGGTT 59.969 61.111 0.00 0.00 0.00 3.67
308 461 2.915659 TCGGCGAACTCACCTGGT 60.916 61.111 7.35 0.00 0.00 4.00
309 462 2.125912 CTCGGCGAACTCACCTGG 60.126 66.667 12.13 0.00 0.00 4.45
310 463 2.125912 CCTCGGCGAACTCACCTG 60.126 66.667 12.13 0.00 0.00 4.00
311 464 3.382832 CCCTCGGCGAACTCACCT 61.383 66.667 12.13 0.00 0.00 4.00
312 465 2.939261 TTCCCTCGGCGAACTCACC 61.939 63.158 12.13 0.00 0.00 4.02
313 466 1.737008 GTTCCCTCGGCGAACTCAC 60.737 63.158 12.13 1.95 37.28 3.51
314 467 2.654877 GTTCCCTCGGCGAACTCA 59.345 61.111 12.13 0.00 37.28 3.41
315 468 2.125633 GGTTCCCTCGGCGAACTC 60.126 66.667 12.13 0.00 39.65 3.01
316 469 2.047213 TTTGGTTCCCTCGGCGAACT 62.047 55.000 12.13 0.00 39.65 3.01
317 470 1.598685 TTTGGTTCCCTCGGCGAAC 60.599 57.895 12.13 5.91 39.12 3.95
318 471 1.598685 GTTTGGTTCCCTCGGCGAA 60.599 57.895 12.13 0.00 0.00 4.70
319 472 2.031465 GTTTGGTTCCCTCGGCGA 59.969 61.111 10.14 10.14 0.00 5.54
320 473 3.053896 GGTTTGGTTCCCTCGGCG 61.054 66.667 0.00 0.00 0.00 6.46
321 474 3.053896 CGGTTTGGTTCCCTCGGC 61.054 66.667 0.00 0.00 0.00 5.54
322 475 0.820482 AAACGGTTTGGTTCCCTCGG 60.820 55.000 5.12 0.00 0.00 4.63
323 476 0.309612 CAAACGGTTTGGTTCCCTCG 59.690 55.000 22.72 0.00 37.01 4.63
332 485 0.249280 GAAGCACCCCAAACGGTTTG 60.249 55.000 23.33 23.33 40.32 2.93
333 486 0.684805 TGAAGCACCCCAAACGGTTT 60.685 50.000 0.00 0.00 32.17 3.27
334 487 0.469144 ATGAAGCACCCCAAACGGTT 60.469 50.000 0.00 0.00 32.17 4.44
335 488 1.152830 ATGAAGCACCCCAAACGGT 59.847 52.632 0.00 0.00 36.18 4.83
336 489 1.586028 CATGAAGCACCCCAAACGG 59.414 57.895 0.00 0.00 0.00 4.44
404 586 8.562052 TGGATTCATCATCATTAAAGTTGATCG 58.438 33.333 2.10 0.53 31.50 3.69
455 637 0.239347 GTGGCTGCTGCAACTTGTAG 59.761 55.000 17.89 2.65 39.94 2.74
456 638 0.465278 TGTGGCTGCTGCAACTTGTA 60.465 50.000 22.02 0.92 43.37 2.41
509 1151 9.856488 TCTTTTGCTTGATTAGTAGTAGTACTG 57.144 33.333 18.75 3.75 39.96 2.74
612 1256 1.070843 CCTGACAAAACTGCACGTACG 60.071 52.381 15.01 15.01 0.00 3.67
613 1257 1.333791 GCCTGACAAAACTGCACGTAC 60.334 52.381 0.00 0.00 0.00 3.67
671 2029 1.589993 CATCGGCGAGACGAATGCT 60.590 57.895 17.22 0.00 46.92 3.79
694 2052 2.673523 GAGTGGTGGATGGCAGCT 59.326 61.111 1.50 0.00 0.00 4.24
696 2054 2.124983 CGGAGTGGTGGATGGCAG 60.125 66.667 0.00 0.00 0.00 4.85
697 2055 4.408821 GCGGAGTGGTGGATGGCA 62.409 66.667 0.00 0.00 0.00 4.92
700 2058 1.077501 AATGGCGGAGTGGTGGATG 60.078 57.895 0.00 0.00 0.00 3.51
701 2059 1.077501 CAATGGCGGAGTGGTGGAT 60.078 57.895 0.00 0.00 0.00 3.41
724 2116 2.673341 AGAGAGAGCGCACCGACA 60.673 61.111 11.47 0.00 0.00 4.35
783 2187 3.685214 GACGTGGCAGCGAGACGAT 62.685 63.158 15.04 2.41 36.90 3.73
785 2189 4.700365 TGACGTGGCAGCGAGACG 62.700 66.667 14.63 8.30 39.03 4.18
786 2190 2.749110 TTCTGACGTGGCAGCGAGAC 62.749 60.000 14.63 7.43 35.86 3.36
788 2192 1.416813 GATTCTGACGTGGCAGCGAG 61.417 60.000 14.63 4.72 35.86 5.03
789 2193 1.446099 GATTCTGACGTGGCAGCGA 60.446 57.895 14.63 0.00 35.86 4.93
791 2195 1.078848 AGGATTCTGACGTGGCAGC 60.079 57.895 0.00 0.00 35.86 5.25
792 2196 0.247460 TGAGGATTCTGACGTGGCAG 59.753 55.000 0.00 0.00 37.24 4.85
793 2197 0.037326 GTGAGGATTCTGACGTGGCA 60.037 55.000 0.00 0.00 0.00 4.92
795 2199 3.036026 CGTGAGGATTCTGACGTGG 57.964 57.895 4.65 0.00 43.75 4.94
801 2205 1.874019 CGCCGACGTGAGGATTCTG 60.874 63.158 10.56 0.00 33.53 3.02
802 2206 1.994507 CTCGCCGACGTGAGGATTCT 61.995 60.000 10.56 0.00 42.01 2.40
803 2207 1.586564 CTCGCCGACGTGAGGATTC 60.587 63.158 10.56 0.00 42.01 2.52
804 2208 2.490217 CTCGCCGACGTGAGGATT 59.510 61.111 10.56 0.00 42.01 3.01
810 2214 0.433492 CAAACTAACTCGCCGACGTG 59.567 55.000 0.00 0.00 41.18 4.49
811 2215 0.031178 ACAAACTAACTCGCCGACGT 59.969 50.000 0.00 0.00 41.18 4.34
813 2217 1.988467 GGTACAAACTAACTCGCCGAC 59.012 52.381 0.00 0.00 0.00 4.79
814 2218 1.401409 CGGTACAAACTAACTCGCCGA 60.401 52.381 0.00 0.00 40.27 5.54
816 2220 0.717784 GCGGTACAAACTAACTCGCC 59.282 55.000 0.00 0.00 36.35 5.54
817 2221 0.717784 GGCGGTACAAACTAACTCGC 59.282 55.000 0.00 0.00 40.77 5.03
818 2222 0.986992 CGGCGGTACAAACTAACTCG 59.013 55.000 0.00 0.00 0.00 4.18
819 2223 1.353076 CCGGCGGTACAAACTAACTC 58.647 55.000 19.97 0.00 0.00 3.01
820 2224 0.671472 GCCGGCGGTACAAACTAACT 60.671 55.000 28.82 0.00 0.00 2.24
822 2226 1.737371 CGCCGGCGGTACAAACTAA 60.737 57.895 40.50 0.00 35.56 2.24
823 2227 2.125991 CGCCGGCGGTACAAACTA 60.126 61.111 40.50 0.00 35.56 2.24
824 2228 3.927163 CTCGCCGGCGGTACAAACT 62.927 63.158 44.95 0.00 40.25 2.66
827 2231 2.546645 CTAACTCGCCGGCGGTACAA 62.547 60.000 44.95 26.86 40.25 2.41
829 2233 2.278401 CTAACTCGCCGGCGGTAC 60.278 66.667 44.95 10.93 40.25 3.34
843 4016 1.621814 CCCACCGTCTCCAGAAACTAA 59.378 52.381 0.00 0.00 0.00 2.24
880 4063 3.002620 AACAACTGGGCCCCACACA 62.003 57.895 22.27 0.00 0.00 3.72
893 4076 1.260561 ACGATTCTGCGTGACAACAAC 59.739 47.619 0.00 0.00 43.79 3.32
940 4123 4.711949 CTCGCTGCTTGTGCCCCT 62.712 66.667 0.00 0.00 38.71 4.79
998 4181 3.782443 GACAGGTGGGCCCTACGG 61.782 72.222 25.70 18.33 43.86 4.02
1091 4275 1.132201 TCTTTCTTTCTCCCCTCCCCA 60.132 52.381 0.00 0.00 0.00 4.96
1121 4321 2.238646 TCTCTCTCGCTCTCTCCTTTCT 59.761 50.000 0.00 0.00 0.00 2.52
1122 4322 2.614057 CTCTCTCTCGCTCTCTCCTTTC 59.386 54.545 0.00 0.00 0.00 2.62
1123 4323 2.238646 TCTCTCTCTCGCTCTCTCCTTT 59.761 50.000 0.00 0.00 0.00 3.11
1476 4711 1.476891 GATCAGACCAAGCCACTCGTA 59.523 52.381 0.00 0.00 0.00 3.43
1655 4897 2.526873 ACCACGGGCTGGAGTTCT 60.527 61.111 0.00 0.00 43.95 3.01
1795 5717 2.569059 AGATCATCCATGGTTTCGCAG 58.431 47.619 12.58 0.00 0.00 5.18
1849 5949 4.530710 TCCTTGCAAGTAACGTACAGAT 57.469 40.909 24.35 0.00 0.00 2.90
1855 5955 2.812011 GGTTGATCCTTGCAAGTAACGT 59.188 45.455 24.35 5.92 0.00 3.99
1856 5956 2.159707 CGGTTGATCCTTGCAAGTAACG 60.160 50.000 24.35 14.02 0.00 3.18
1890 5995 3.057245 GCTACGGCATCATGACTGATCTA 60.057 47.826 0.00 0.00 40.20 1.98
1891 5996 2.288702 GCTACGGCATCATGACTGATCT 60.289 50.000 0.00 0.00 40.20 2.75
1922 6031 3.876914 TCAGATCGACAAACAGCAAAGTT 59.123 39.130 0.00 0.00 0.00 2.66
1962 6072 4.100189 TGATTAACCAAACCAAACCACCAG 59.900 41.667 0.00 0.00 0.00 4.00
2000 6120 2.584791 TCGACGCATCATCATACATCG 58.415 47.619 0.00 0.00 0.00 3.84
2028 6163 4.418401 TACGTACGCACCCACGGC 62.418 66.667 16.72 0.00 42.35 5.68
2029 6164 2.504681 GTACGTACGCACCCACGG 60.505 66.667 16.72 0.00 42.35 4.94
2087 6270 3.456280 GAAGTGCAATGCCACAGAAAAA 58.544 40.909 1.53 0.00 38.18 1.94
2131 6315 1.577328 AAGCAGGCGATTGTGTTCGG 61.577 55.000 0.00 0.00 39.49 4.30
2154 6342 1.204704 AGAAATCGACTGATGCACGGA 59.795 47.619 0.00 0.00 34.24 4.69
2162 6353 5.047847 ACGTTGAAAAGAGAAATCGACTGA 58.952 37.500 0.00 0.00 0.00 3.41
2163 6354 5.330271 ACGTTGAAAAGAGAAATCGACTG 57.670 39.130 0.00 0.00 0.00 3.51
2164 6355 5.404667 GGTACGTTGAAAAGAGAAATCGACT 59.595 40.000 0.00 0.00 0.00 4.18
2190 6381 7.327214 AGATAGAACAAGCCTTGACTCTTTAG 58.673 38.462 12.25 0.00 31.91 1.85
2212 6404 2.957402 TTGGAGTTGCTTGTGGAGAT 57.043 45.000 0.00 0.00 0.00 2.75
2276 6484 8.753497 ACATAGGGAACATAGATTTTCTTTCC 57.247 34.615 0.00 0.00 32.66 3.13
2327 6535 4.396357 TCAAGACCAACATTACCCCATT 57.604 40.909 0.00 0.00 0.00 3.16
2347 6586 6.972328 TGACATTTAGGTAACCGTACGTTATC 59.028 38.462 15.21 12.52 39.14 1.75
2349 6588 6.260870 TGACATTTAGGTAACCGTACGTTA 57.739 37.500 15.21 9.95 35.79 3.18
2352 6591 5.104374 ACATGACATTTAGGTAACCGTACG 58.896 41.667 8.69 8.69 37.17 3.67
2416 6684 7.408756 AATTGCAGTATTAGAAATGAAGCCA 57.591 32.000 0.00 0.00 0.00 4.75
2434 7158 4.279982 TCATATTGGAGGCTGAAATTGCA 58.720 39.130 0.00 0.00 0.00 4.08
2435 7159 4.795308 GCTCATATTGGAGGCTGAAATTGC 60.795 45.833 0.00 0.00 35.41 3.56
2436 7160 4.340097 TGCTCATATTGGAGGCTGAAATTG 59.660 41.667 0.00 0.00 35.41 2.32
2439 7163 3.650281 TGCTCATATTGGAGGCTGAAA 57.350 42.857 0.00 0.00 35.41 2.69
2441 7165 3.282021 GTTTGCTCATATTGGAGGCTGA 58.718 45.455 0.00 0.00 35.41 4.26
2442 7166 3.018856 TGTTTGCTCATATTGGAGGCTG 58.981 45.455 0.00 0.00 35.41 4.85
2446 7170 3.763360 TGGGTTGTTTGCTCATATTGGAG 59.237 43.478 0.00 0.00 37.97 3.86
2709 8339 4.016444 TGGGCTAGTTCACATTCCATTTC 58.984 43.478 0.00 0.00 0.00 2.17
2762 8393 9.745018 ACCAGCTACAATTGCAGATAATATTAT 57.255 29.630 9.99 7.72 0.00 1.28
2763 8394 9.002600 CACCAGCTACAATTGCAGATAATATTA 57.997 33.333 9.99 0.00 0.00 0.98
2764 8395 7.522725 GCACCAGCTACAATTGCAGATAATATT 60.523 37.037 9.99 0.00 37.91 1.28
2784 8415 0.752658 TATCGAGGACCATGCACCAG 59.247 55.000 8.66 3.45 0.00 4.00


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

AutoCloner maintained by Alex Coulton.