Multiple sequence alignment - TraesCS7D01G143900

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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 TraesCS7D01G143900 chr7D 100.000 4801 0 0 1 4801 92138414 92143214 0.000000e+00 8866.0
1 TraesCS7D01G143900 chr7D 88.333 1320 94 29 2722 3992 92220790 92222098 0.000000e+00 1530.0
2 TraesCS7D01G143900 chr7D 84.866 1044 97 35 2400 3390 92217767 92218802 0.000000e+00 996.0
3 TraesCS7D01G143900 chr7D 83.960 1010 100 45 1367 2361 92214634 92215596 0.000000e+00 911.0
4 TraesCS7D01G143900 chr7D 86.986 730 61 10 3332 4028 92218804 92219532 0.000000e+00 791.0
5 TraesCS7D01G143900 chr7D 86.269 721 47 22 654 1360 92213907 92214589 0.000000e+00 736.0
6 TraesCS7D01G143900 chr7D 88.193 559 35 14 1829 2373 92219801 92220342 5.240000e-179 638.0
7 TraesCS7D01G143900 chr7D 84.211 399 42 12 1 380 532629452 532629848 7.590000e-98 368.0
8 TraesCS7D01G143900 chr7D 85.393 356 33 12 1 341 90635078 90634727 7.640000e-93 351.0
9 TraesCS7D01G143900 chr7D 88.235 272 19 9 2378 2648 92220401 92220660 3.610000e-81 313.0
10 TraesCS7D01G143900 chr7D 77.157 394 68 20 1978 2359 628223677 628223294 4.870000e-50 209.0
11 TraesCS7D01G143900 chr7D 73.402 579 107 35 1803 2359 629117258 629117811 6.390000e-39 172.0
12 TraesCS7D01G143900 chr7D 76.106 339 63 12 2024 2355 628219392 628219065 1.380000e-35 161.0
13 TraesCS7D01G143900 chr7D 86.885 122 16 0 1804 1925 628219619 628219498 2.330000e-28 137.0
14 TraesCS7D01G143900 chr7D 97.260 73 2 0 2568 2640 629118096 629118168 1.810000e-24 124.0
15 TraesCS7D01G143900 chr7A 87.957 1968 147 51 422 2360 94289175 94291081 0.000000e+00 2239.0
16 TraesCS7D01G143900 chr7A 89.888 1780 106 33 2374 4082 94291146 94292922 0.000000e+00 2222.0
17 TraesCS7D01G143900 chr7A 84.519 1040 102 31 2403 3390 94321099 94322131 0.000000e+00 974.0
18 TraesCS7D01G143900 chr7A 87.469 806 65 17 2722 3498 94324132 94324930 0.000000e+00 896.0
19 TraesCS7D01G143900 chr7A 88.611 720 57 15 652 1360 94310249 94310954 0.000000e+00 852.0
20 TraesCS7D01G143900 chr7A 90.358 643 39 15 4166 4801 94293291 94293917 0.000000e+00 822.0
21 TraesCS7D01G143900 chr7A 87.172 725 62 10 3332 4028 94322133 94322854 0.000000e+00 795.0
22 TraesCS7D01G143900 chr7A 88.909 559 31 14 1829 2373 94323122 94323663 0.000000e+00 660.0
23 TraesCS7D01G143900 chr7A 87.411 564 51 17 1369 1932 94311001 94311544 8.770000e-177 630.0
24 TraesCS7D01G143900 chr7A 86.280 379 27 17 1983 2361 94311545 94311898 5.830000e-104 388.0
25 TraesCS7D01G143900 chr7A 89.668 271 15 6 2378 2648 94323724 94323981 2.770000e-87 333.0
26 TraesCS7D01G143900 chr7A 75.347 576 99 31 1801 2355 724951362 724951915 2.230000e-58 237.0
27 TraesCS7D01G143900 chr7A 73.649 592 98 42 1794 2359 724919955 724920514 4.940000e-40 176.0
28 TraesCS7D01G143900 chr7A 73.310 577 105 37 1803 2358 725136986 725136438 2.970000e-37 167.0
29 TraesCS7D01G143900 chr7A 97.260 73 2 0 2568 2640 725136164 725136092 1.810000e-24 124.0
30 TraesCS7D01G143900 chr7A 91.892 74 6 0 1465 1538 725137377 725137304 2.360000e-18 104.0
31 TraesCS7D01G143900 chr7A 87.209 86 8 2 1441 1523 724919545 724919630 1.420000e-15 95.3
32 TraesCS7D01G143900 chr7A 91.525 59 5 0 1465 1523 724950972 724951030 1.110000e-11 82.4
33 TraesCS7D01G143900 chr7B 85.700 1951 121 73 1433 3300 44235605 44237480 0.000000e+00 1912.0
34 TraesCS7D01G143900 chr7B 91.357 995 52 16 376 1346 44234587 44235571 0.000000e+00 1330.0
35 TraesCS7D01G143900 chr7B 90.062 483 25 8 3345 3816 44237478 44237948 5.310000e-169 604.0
36 TraesCS7D01G143900 chr7B 74.914 582 102 34 1801 2359 730809582 730810142 4.830000e-55 226.0
37 TraesCS7D01G143900 chr7B 93.662 142 7 2 3800 3940 44237963 44238103 1.350000e-50 211.0
38 TraesCS7D01G143900 chr7B 73.473 573 117 26 1801 2359 731035994 731035443 2.950000e-42 183.0
39 TraesCS7D01G143900 chr7B 97.260 73 2 0 2568 2640 731035158 731035086 1.810000e-24 124.0
40 TraesCS7D01G143900 chr7B 87.097 93 11 1 1450 1541 731036423 731036331 2.360000e-18 104.0
41 TraesCS7D01G143900 chr6A 83.048 643 65 20 780 1396 121716784 121717408 1.180000e-150 544.0
42 TraesCS7D01G143900 chr6A 84.010 419 38 6 1 393 548045636 548045221 4.540000e-100 375.0
43 TraesCS7D01G143900 chr2B 83.550 614 62 18 790 1375 794420184 794420786 5.470000e-149 538.0
44 TraesCS7D01G143900 chr2B 95.833 48 2 0 4641 4688 430758635 430758588 1.430000e-10 78.7
45 TraesCS7D01G143900 chr3A 90.181 387 26 7 1 376 111087967 111087582 1.200000e-135 494.0
46 TraesCS7D01G143900 chr3A 93.878 49 3 0 4641 4689 581620873 581620921 1.850000e-09 75.0
47 TraesCS7D01G143900 chr5A 87.530 417 37 9 804 1217 28601618 28602022 7.280000e-128 468.0
48 TraesCS7D01G143900 chr5A 88.050 159 19 0 1238 1396 28602129 28602287 6.340000e-44 189.0
49 TraesCS7D01G143900 chr3D 87.855 387 32 8 1 376 90772238 90772620 1.590000e-119 440.0
50 TraesCS7D01G143900 chr3D 95.745 47 2 0 4642 4688 108966228 108966274 5.150000e-10 76.8
51 TraesCS7D01G143900 chr4D 85.242 393 39 12 1 376 25384256 25383866 2.100000e-103 387.0
52 TraesCS7D01G143900 chr4D 97.674 43 1 0 4642 4684 464400695 464400653 1.850000e-09 75.0
53 TraesCS7D01G143900 chr5D 85.204 392 39 11 1 376 305779017 305779405 7.540000e-103 385.0
54 TraesCS7D01G143900 chr5D 84.173 417 28 11 1 380 189169516 189169101 2.110000e-98 370.0
55 TraesCS7D01G143900 chr4A 93.436 259 16 1 1 259 621665539 621665282 2.710000e-102 383.0
56 TraesCS7D01G143900 chr4A 91.667 60 3 2 4641 4700 437499569 437499512 1.110000e-11 82.4
57 TraesCS7D01G143900 chr1D 84.733 393 38 10 2 376 58512546 58512934 1.630000e-99 374.0
58 TraesCS7D01G143900 chr1D 95.833 48 2 0 4641 4688 479580685 479580638 1.430000e-10 78.7
59 TraesCS7D01G143900 chr1A 84.424 321 33 11 780 1097 561003970 561003664 2.810000e-77 300.0
60 TraesCS7D01G143900 chr1A 84.305 223 24 5 169 382 504415693 504415913 1.750000e-49 207.0
61 TraesCS7D01G143900 chrUn 92.308 52 3 1 4638 4689 79576699 79576649 6.670000e-09 73.1
62 TraesCS7D01G143900 chr1B 93.750 48 3 0 4637 4684 327708968 327708921 6.670000e-09 73.1


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 TraesCS7D01G143900 chr7D 92138414 92143214 4800 False 8866.000000 8866 100.000000 1 4801 1 chr7D.!!$F1 4800
1 TraesCS7D01G143900 chr7D 92213907 92222098 8191 False 845.000000 1530 86.691714 654 4028 7 chr7D.!!$F3 3374
2 TraesCS7D01G143900 chr7A 94289175 94293917 4742 False 1761.000000 2239 89.401000 422 4801 3 chr7A.!!$F1 4379
3 TraesCS7D01G143900 chr7A 94321099 94324930 3831 False 731.600000 974 87.547400 1829 4028 5 chr7A.!!$F3 2199
4 TraesCS7D01G143900 chr7A 94310249 94311898 1649 False 623.333333 852 87.434000 652 2361 3 chr7A.!!$F2 1709
5 TraesCS7D01G143900 chr7B 44234587 44238103 3516 False 1014.250000 1912 90.195250 376 3940 4 chr7B.!!$F2 3564
6 TraesCS7D01G143900 chr7B 730809582 730810142 560 False 226.000000 226 74.914000 1801 2359 1 chr7B.!!$F1 558
7 TraesCS7D01G143900 chr6A 121716784 121717408 624 False 544.000000 544 83.048000 780 1396 1 chr6A.!!$F1 616
8 TraesCS7D01G143900 chr2B 794420184 794420786 602 False 538.000000 538 83.550000 790 1375 1 chr2B.!!$F1 585
9 TraesCS7D01G143900 chr5A 28601618 28602287 669 False 328.500000 468 87.790000 804 1396 2 chr5A.!!$F1 592

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
85 86 0.030908 GAATCTCGGCGGAGTAGGTG 59.969 60.0 19.51 0.00 41.26 4.00 F
348 349 0.236187 GTCAATTTACCGTGTGCGCA 59.764 50.0 5.66 5.66 36.67 6.09 F
367 368 0.238289 ATCTTTTGACGCGGCTGTTG 59.762 50.0 15.80 0.72 0.00 3.33 F
1832 2021 0.461339 AACTTCGACGTGGTGCTGTT 60.461 50.0 0.00 0.00 0.00 3.16 F
2361 2642 0.238025 TGCACAAGTAAGCATGCACG 59.762 50.0 21.98 3.52 42.92 5.34 F
3045 8224 0.182537 ACCAAGTGCTTGCCTACACA 59.817 50.0 6.42 0.00 39.30 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1791 1971 0.370273 CCGAGAACTGCGTTATGTGC 59.630 55.000 0.00 0.00 0.00 4.57 R
1893 2089 1.078918 CTTCCTGGCGCTGACATGA 60.079 57.895 7.64 0.00 0.00 3.07 R
2153 2417 1.237285 AAGCAGCCACACGAATGGAC 61.237 55.000 12.96 5.31 43.02 4.02 R
2928 8106 0.984230 CTTCAGGGTCCTGCCAGTTA 59.016 55.000 11.95 0.00 43.31 2.24 R
3752 8966 1.228245 GTTGGCCAGCTCCTTGTCA 60.228 57.895 13.08 0.00 0.00 3.58 R
4540 10090 1.005975 CGTTAGCGAAAATCTGAGCCG 60.006 52.381 0.00 0.00 41.33 5.52 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
29 30 3.691342 CTCCTGGGCGGTGTCGAA 61.691 66.667 0.00 0.00 39.00 3.71
32 33 4.003788 CTGGGCGGTGTCGAAGGT 62.004 66.667 0.00 0.00 39.00 3.50
33 34 3.530910 CTGGGCGGTGTCGAAGGTT 62.531 63.158 0.00 0.00 39.00 3.50
34 35 2.741211 GGGCGGTGTCGAAGGTTC 60.741 66.667 0.00 0.00 39.00 3.62
35 36 2.741211 GGCGGTGTCGAAGGTTCC 60.741 66.667 0.00 0.00 39.00 3.62
36 37 3.110178 GCGGTGTCGAAGGTTCCG 61.110 66.667 9.50 9.50 43.37 4.30
37 38 2.646719 CGGTGTCGAAGGTTCCGA 59.353 61.111 8.56 0.00 43.22 4.55
38 39 1.443872 CGGTGTCGAAGGTTCCGAG 60.444 63.158 8.56 0.00 43.22 4.63
39 40 1.859427 CGGTGTCGAAGGTTCCGAGA 61.859 60.000 8.56 0.00 43.22 4.04
40 41 0.388263 GGTGTCGAAGGTTCCGAGAC 60.388 60.000 0.00 0.00 45.66 3.36
41 42 0.728466 GTGTCGAAGGTTCCGAGACG 60.728 60.000 0.00 0.00 39.75 4.18
83 84 1.283181 CGAATCTCGGCGGAGTAGG 59.717 63.158 19.51 5.77 41.26 3.18
85 86 0.030908 GAATCTCGGCGGAGTAGGTG 59.969 60.000 19.51 0.00 41.26 4.00
86 87 2.017559 AATCTCGGCGGAGTAGGTGC 62.018 60.000 19.51 0.00 41.26 5.01
87 88 4.208686 CTCGGCGGAGTAGGTGCC 62.209 72.222 12.89 0.00 45.39 5.01
92 93 4.189188 CGGAGTAGGTGCCGGACG 62.189 72.222 5.05 0.00 43.67 4.79
93 94 3.834799 GGAGTAGGTGCCGGACGG 61.835 72.222 5.05 6.35 38.57 4.79
94 95 2.753043 GAGTAGGTGCCGGACGGA 60.753 66.667 15.99 0.00 37.50 4.69
95 96 3.061260 GAGTAGGTGCCGGACGGAC 62.061 68.421 15.99 9.55 37.50 4.79
96 97 4.487412 GTAGGTGCCGGACGGACG 62.487 72.222 15.99 0.00 37.50 4.79
129 130 2.803479 GTAGCCCGTACCTCCACG 59.197 66.667 0.00 0.00 41.59 4.94
187 188 2.903357 GGCAGAGGGCGATTGAGA 59.097 61.111 0.00 0.00 46.16 3.27
189 190 1.680522 GGCAGAGGGCGATTGAGAGA 61.681 60.000 0.00 0.00 46.16 3.10
190 191 0.392336 GCAGAGGGCGATTGAGAGAT 59.608 55.000 0.00 0.00 0.00 2.75
192 193 1.685517 CAGAGGGCGATTGAGAGATGA 59.314 52.381 0.00 0.00 0.00 2.92
193 194 2.102084 CAGAGGGCGATTGAGAGATGAA 59.898 50.000 0.00 0.00 0.00 2.57
194 195 2.364970 AGAGGGCGATTGAGAGATGAAG 59.635 50.000 0.00 0.00 0.00 3.02
195 196 2.363680 GAGGGCGATTGAGAGATGAAGA 59.636 50.000 0.00 0.00 0.00 2.87
196 197 2.364970 AGGGCGATTGAGAGATGAAGAG 59.635 50.000 0.00 0.00 0.00 2.85
197 198 2.363680 GGGCGATTGAGAGATGAAGAGA 59.636 50.000 0.00 0.00 0.00 3.10
198 199 3.552684 GGGCGATTGAGAGATGAAGAGAG 60.553 52.174 0.00 0.00 0.00 3.20
200 201 3.299162 CGATTGAGAGATGAAGAGAGCG 58.701 50.000 0.00 0.00 0.00 5.03
201 202 2.575694 TTGAGAGATGAAGAGAGCGC 57.424 50.000 0.00 0.00 0.00 5.92
202 203 1.761449 TGAGAGATGAAGAGAGCGCT 58.239 50.000 11.27 11.27 0.00 5.92
203 204 2.924421 TGAGAGATGAAGAGAGCGCTA 58.076 47.619 11.50 0.00 0.00 4.26
206 207 3.141398 AGAGATGAAGAGAGCGCTAGAG 58.859 50.000 11.50 0.00 0.00 2.43
208 209 1.269448 GATGAAGAGAGCGCTAGAGGG 59.731 57.143 11.50 0.00 0.00 4.30
217 218 2.203126 GCTAGAGGGCGCTGCAAT 60.203 61.111 8.56 0.00 0.00 3.56
219 220 1.379642 GCTAGAGGGCGCTGCAATTT 61.380 55.000 8.56 0.00 0.00 1.82
220 221 1.953559 CTAGAGGGCGCTGCAATTTA 58.046 50.000 8.56 0.00 0.00 1.40
221 222 2.498167 CTAGAGGGCGCTGCAATTTAT 58.502 47.619 8.56 0.00 0.00 1.40
222 223 2.638480 AGAGGGCGCTGCAATTTATA 57.362 45.000 8.56 0.00 0.00 0.98
226 227 0.385974 GGCGCTGCAATTTATAGGCG 60.386 55.000 7.64 8.18 44.40 5.52
227 228 3.077339 CGCTGCAATTTATAGGCGC 57.923 52.632 0.00 0.00 36.46 6.53
228 229 0.722469 CGCTGCAATTTATAGGCGCG 60.722 55.000 0.00 0.00 41.22 6.86
229 230 0.998727 GCTGCAATTTATAGGCGCGC 60.999 55.000 25.94 25.94 0.00 6.86
230 231 0.588252 CTGCAATTTATAGGCGCGCT 59.412 50.000 32.29 19.12 0.00 5.92
231 232 0.307453 TGCAATTTATAGGCGCGCTG 59.693 50.000 32.29 19.35 0.00 5.18
232 233 0.586319 GCAATTTATAGGCGCGCTGA 59.414 50.000 32.29 19.55 0.00 4.26
233 234 1.002900 GCAATTTATAGGCGCGCTGAA 60.003 47.619 32.29 14.85 0.00 3.02
236 237 0.458889 TTTATAGGCGCGCTGAACGT 60.459 50.000 32.29 13.45 46.11 3.99
253 254 3.903783 TGGAGCGCCAAATGTAGC 58.096 55.556 6.75 0.00 42.49 3.58
269 270 3.240353 GCGCGCGCAATCTTTTCC 61.240 61.111 46.11 15.61 41.49 3.13
271 272 2.576847 GCGCGCAATCTTTTCCCG 60.577 61.111 29.10 0.00 0.00 5.14
274 275 2.576847 CGCAATCTTTTCCCGCGC 60.577 61.111 0.00 0.00 39.43 6.86
275 276 2.576847 GCAATCTTTTCCCGCGCG 60.577 61.111 25.67 25.67 0.00 6.86
276 277 2.576847 CAATCTTTTCCCGCGCGC 60.577 61.111 27.36 23.91 0.00 6.86
278 279 1.448893 AATCTTTTCCCGCGCGCTA 60.449 52.632 30.48 11.81 0.00 4.26
279 280 1.429148 AATCTTTTCCCGCGCGCTAG 61.429 55.000 30.48 20.01 0.00 3.42
280 281 2.573609 ATCTTTTCCCGCGCGCTAGT 62.574 55.000 30.48 0.78 0.00 2.57
284 285 4.807039 TCCCGCGCGCTAGTTTCC 62.807 66.667 30.48 0.00 0.00 3.13
290 291 3.497031 GCGCTAGTTTCCCGCCAC 61.497 66.667 0.00 0.00 41.72 5.01
291 292 2.818274 CGCTAGTTTCCCGCCACC 60.818 66.667 0.00 0.00 0.00 4.61
292 293 2.818274 GCTAGTTTCCCGCCACCG 60.818 66.667 0.00 0.00 0.00 4.94
293 294 2.818274 CTAGTTTCCCGCCACCGC 60.818 66.667 0.00 0.00 0.00 5.68
295 296 3.599285 TAGTTTCCCGCCACCGCTG 62.599 63.158 0.00 0.00 0.00 5.18
310 311 4.776953 CTGGAGCGCGCGAAAACG 62.777 66.667 37.18 14.36 0.00 3.60
312 313 4.771812 GGAGCGCGCGAAAACGTC 62.772 66.667 37.18 15.71 34.88 4.34
313 314 4.771812 GAGCGCGCGAAAACGTCC 62.772 66.667 37.18 13.39 34.88 4.79
330 331 4.439472 CCGCGCGCGCTAAAAAGT 62.439 61.111 45.97 0.00 39.32 2.66
331 332 2.932542 CGCGCGCGCTAAAAAGTC 60.933 61.111 45.97 19.75 39.32 3.01
332 333 2.172419 GCGCGCGCTAAAAAGTCA 59.828 55.556 44.38 0.00 38.26 3.41
334 335 0.793104 GCGCGCGCTAAAAAGTCAAT 60.793 50.000 44.38 0.00 38.26 2.57
335 336 1.602191 CGCGCGCTAAAAAGTCAATT 58.398 45.000 30.48 0.00 0.00 2.32
338 339 3.003408 CGCGCGCTAAAAAGTCAATTTAC 60.003 43.478 30.48 0.00 0.00 2.01
339 340 3.299804 GCGCGCTAAAAAGTCAATTTACC 59.700 43.478 26.67 0.00 0.00 2.85
340 341 3.536837 CGCGCTAAAAAGTCAATTTACCG 59.463 43.478 5.56 0.00 0.00 4.02
343 344 5.445845 CGCTAAAAAGTCAATTTACCGTGT 58.554 37.500 0.00 0.00 0.00 4.49
344 345 5.338559 CGCTAAAAAGTCAATTTACCGTGTG 59.661 40.000 0.00 0.00 0.00 3.82
345 346 5.116528 GCTAAAAAGTCAATTTACCGTGTGC 59.883 40.000 0.00 0.00 0.00 4.57
346 347 2.961522 AAGTCAATTTACCGTGTGCG 57.038 45.000 0.00 0.00 37.95 5.34
347 348 0.515564 AGTCAATTTACCGTGTGCGC 59.484 50.000 0.00 0.00 36.67 6.09
348 349 0.236187 GTCAATTTACCGTGTGCGCA 59.764 50.000 5.66 5.66 36.67 6.09
350 351 1.129624 TCAATTTACCGTGTGCGCATC 59.870 47.619 15.91 9.58 36.67 3.91
351 352 1.130373 CAATTTACCGTGTGCGCATCT 59.870 47.619 15.91 0.00 36.67 2.90
355 356 0.515127 TACCGTGTGCGCATCTTTTG 59.485 50.000 15.91 3.00 36.67 2.44
356 357 1.163420 ACCGTGTGCGCATCTTTTGA 61.163 50.000 15.91 0.00 36.67 2.69
357 358 0.725784 CCGTGTGCGCATCTTTTGAC 60.726 55.000 15.91 0.00 36.67 3.18
358 359 1.054348 CGTGTGCGCATCTTTTGACG 61.054 55.000 15.91 9.85 0.00 4.35
359 360 1.082169 TGTGCGCATCTTTTGACGC 60.082 52.632 15.91 0.00 45.13 5.19
364 365 1.512734 GCATCTTTTGACGCGGCTG 60.513 57.895 15.80 2.00 0.00 4.85
367 368 0.238289 ATCTTTTGACGCGGCTGTTG 59.762 50.000 15.80 0.72 0.00 3.33
368 369 1.370414 CTTTTGACGCGGCTGTTGG 60.370 57.895 15.80 0.00 0.00 3.77
369 370 1.781025 CTTTTGACGCGGCTGTTGGA 61.781 55.000 15.80 0.00 0.00 3.53
371 372 1.851021 TTTGACGCGGCTGTTGGATG 61.851 55.000 15.80 0.00 0.00 3.51
372 373 4.166011 GACGCGGCTGTTGGATGC 62.166 66.667 12.47 0.00 0.00 3.91
373 374 4.704833 ACGCGGCTGTTGGATGCT 62.705 61.111 12.47 0.00 0.00 3.79
374 375 3.869272 CGCGGCTGTTGGATGCTC 61.869 66.667 0.00 0.00 0.00 4.26
375 376 2.437359 GCGGCTGTTGGATGCTCT 60.437 61.111 0.00 0.00 0.00 4.09
379 380 2.806745 GCGGCTGTTGGATGCTCTAATA 60.807 50.000 0.00 0.00 0.00 0.98
535 536 3.301579 CGTCGCCGATGTGTAAATTACAG 60.302 47.826 6.03 0.00 36.22 2.74
610 616 5.414144 CGTATATGAGCTCATCTTCTCCAGA 59.586 44.000 31.92 12.30 37.76 3.86
633 639 6.835488 AGATTAGCTTCCATTTTGCTTCCATA 59.165 34.615 0.00 0.00 38.15 2.74
691 697 1.500844 GCATATGCTCTGGATGCGC 59.499 57.895 20.64 0.00 36.89 6.09
801 814 0.471191 TCCTCGGGCAGTAGATCGTA 59.529 55.000 0.00 0.00 0.00 3.43
807 820 5.356190 CCTCGGGCAGTAGATCGTAATAATA 59.644 44.000 0.00 0.00 0.00 0.98
833 846 2.682856 GGCATAAATCGCACCAGAAGAA 59.317 45.455 0.00 0.00 0.00 2.52
920 933 3.838244 TCTTGTAAGTGTCTGCCTTGT 57.162 42.857 0.00 0.00 0.00 3.16
941 957 7.607991 CCTTGTAGAACCAGAATCTTGTTACAT 59.392 37.037 0.00 0.00 0.00 2.29
942 958 9.653287 CTTGTAGAACCAGAATCTTGTTACATA 57.347 33.333 0.00 0.00 0.00 2.29
974 994 7.192148 TCGTGTTCATTCTTAAAATTTCCGA 57.808 32.000 0.00 0.00 0.00 4.55
1030 1053 1.571215 CCCGGTTCTGTTGGCGTTAC 61.571 60.000 0.00 0.00 0.00 2.50
1365 1483 7.035004 TCAGAAACAATCCAGTTTGAACTTTG 58.965 34.615 0.00 0.19 41.48 2.77
1379 1535 9.573133 AGTTTGAACTTTGTGAAGAATTAACAG 57.427 29.630 0.00 0.00 35.21 3.16
1441 1597 4.796946 GCAGATTGTGAATGTTGCAAGGAA 60.797 41.667 0.00 0.00 31.76 3.36
1442 1598 4.921515 CAGATTGTGAATGTTGCAAGGAAG 59.078 41.667 0.00 0.00 0.00 3.46
1511 1667 4.451150 CTTCACCTGCGCCGGCTA 62.451 66.667 26.68 12.71 40.82 3.93
1601 1757 8.171840 GCTAAGCTTACTCTGAATAACTTGTTG 58.828 37.037 0.86 0.00 0.00 3.33
1669 1825 0.544833 TGGCGGTAGGGTACAAGGAA 60.545 55.000 0.00 0.00 0.00 3.36
1743 1907 6.603201 AGAAGTGGTTTCTGAACTTTGATCAA 59.397 34.615 3.38 3.38 44.46 2.57
1791 1971 1.403382 CGGTCAGATGACACTGGACTG 60.403 57.143 14.52 0.00 46.47 3.51
1828 2017 1.563173 GACAACTTCGACGTGGTGC 59.437 57.895 6.83 0.00 0.00 5.01
1829 2018 0.874607 GACAACTTCGACGTGGTGCT 60.875 55.000 6.83 0.00 0.00 4.40
1830 2019 1.151777 ACAACTTCGACGTGGTGCTG 61.152 55.000 0.48 0.00 0.00 4.41
1831 2020 1.143183 AACTTCGACGTGGTGCTGT 59.857 52.632 0.00 0.00 0.00 4.40
1832 2021 0.461339 AACTTCGACGTGGTGCTGTT 60.461 50.000 0.00 0.00 0.00 3.16
1893 2089 2.852075 TGGTCCAAGGAGGCCGTT 60.852 61.111 0.00 0.00 36.65 4.44
1896 2092 1.299976 GTCCAAGGAGGCCGTTCAT 59.700 57.895 0.00 0.00 37.29 2.57
1946 2154 4.314440 GCACCGTGCCTGTCTCCA 62.314 66.667 12.80 0.00 37.42 3.86
1955 2163 1.879380 TGCCTGTCTCCAACATTTTCG 59.121 47.619 0.00 0.00 37.23 3.46
1967 2180 5.530915 TCCAACATTTTCGTTCTTCAGTCAT 59.469 36.000 0.00 0.00 0.00 3.06
2007 2269 4.088823 GACATTTCTGACCTGCAATGTC 57.911 45.455 13.38 13.38 44.91 3.06
2153 2417 1.931841 GATCATCGCCGATCATCCATG 59.068 52.381 0.00 0.00 41.29 3.66
2164 2428 3.470709 GATCATCCATGTCCATTCGTGT 58.529 45.455 0.00 0.00 0.00 4.49
2165 2429 2.631267 TCATCCATGTCCATTCGTGTG 58.369 47.619 0.00 0.00 0.00 3.82
2179 2443 0.877071 CGTGTGGCTGCTTTCTGAAT 59.123 50.000 0.00 0.00 0.00 2.57
2186 2450 3.452264 TGGCTGCTTTCTGAATCTAGCTA 59.548 43.478 12.32 7.77 34.77 3.32
2187 2451 4.057432 GGCTGCTTTCTGAATCTAGCTAG 58.943 47.826 15.01 15.01 34.77 3.42
2188 2452 3.494251 GCTGCTTTCTGAATCTAGCTAGC 59.506 47.826 16.35 6.62 34.77 3.42
2341 2622 0.737715 CAAGAGAAACTCCGGCGAGG 60.738 60.000 9.30 2.51 40.77 4.63
2361 2642 0.238025 TGCACAAGTAAGCATGCACG 59.762 50.000 21.98 3.52 42.92 5.34
2362 2643 1.067199 GCACAAGTAAGCATGCACGC 61.067 55.000 21.98 0.00 38.00 5.34
2364 2706 0.518636 ACAAGTAAGCATGCACGCTG 59.481 50.000 21.98 14.49 42.89 5.18
2365 2707 0.798159 CAAGTAAGCATGCACGCTGA 59.202 50.000 21.98 0.00 42.89 4.26
2368 2710 1.667724 AGTAAGCATGCACGCTGATTC 59.332 47.619 21.98 0.00 42.89 2.52
2375 2717 0.448990 TGCACGCTGATTCTGCATTC 59.551 50.000 14.78 4.29 36.00 2.67
2483 4908 1.591594 CGTGCAGCGGGTAATCGAT 60.592 57.895 0.00 0.00 36.85 3.59
2516 4941 4.542662 CAAGTTCTTCACCTTGTGTCAG 57.457 45.455 0.00 0.00 34.67 3.51
2558 4984 6.917217 AGTTACTAAGATGAAGAAGCATGC 57.083 37.500 10.51 10.51 0.00 4.06
2601 5032 1.219124 GATGGCGCCAGTCTTCTCA 59.781 57.895 35.36 7.66 0.00 3.27
2649 5099 6.407299 GGCATATGATCCAGGTTGATTTTGTT 60.407 38.462 6.97 0.00 0.00 2.83
2650 5100 6.698766 GCATATGATCCAGGTTGATTTTGTTC 59.301 38.462 6.97 0.00 0.00 3.18
2653 5103 4.582656 TGATCCAGGTTGATTTTGTTCGTT 59.417 37.500 0.00 0.00 0.00 3.85
2661 5111 5.569059 GGTTGATTTTGTTCGTTGCTCATAG 59.431 40.000 0.00 0.00 0.00 2.23
2798 5270 2.989840 CAACTTCTGGAGATGTGTCGAC 59.010 50.000 9.11 9.11 33.45 4.20
2827 5299 7.921214 ACGTAATTACTTGACCAGAGATACATG 59.079 37.037 13.56 0.00 0.00 3.21
2860 5332 7.525688 TTATAGATTCACTGAAGAACGCTTG 57.474 36.000 0.00 0.00 33.61 4.01
2913 8073 0.767375 ACACCTGACATGGCTCACTT 59.233 50.000 0.00 0.00 0.00 3.16
2994 8172 4.397103 CAGTATGTTGTCCATCATGCAGTT 59.603 41.667 0.00 0.00 34.86 3.16
3045 8224 0.182537 ACCAAGTGCTTGCCTACACA 59.817 50.000 6.42 0.00 39.30 3.72
3078 8257 0.596083 GTCGGCCGAGAGACATCATG 60.596 60.000 31.97 0.00 37.34 3.07
3087 8266 2.034878 AGAGACATCATGGCGCTCTTA 58.965 47.619 7.64 0.00 24.83 2.10
3092 8271 0.530650 ATCATGGCGCTCTTACCACG 60.531 55.000 7.64 0.00 39.19 4.94
3123 8302 1.616620 CCATCCACGCGTTTTGATTG 58.383 50.000 10.22 4.43 0.00 2.67
3135 8326 3.057315 CGTTTTGATTGAGTTGCATCCCT 60.057 43.478 0.00 0.00 0.00 4.20
3140 8331 5.138125 TGATTGAGTTGCATCCCTTTTTC 57.862 39.130 0.00 0.00 0.00 2.29
3152 8343 1.686587 CCCTTTTTCCCGCAAGAAAGT 59.313 47.619 0.00 0.00 37.09 2.66
3154 8345 3.431626 CCCTTTTTCCCGCAAGAAAGTTT 60.432 43.478 0.00 0.00 37.09 2.66
3182 8378 4.502105 AAAGGGTGAATTTGTTTGGCTT 57.498 36.364 0.00 0.00 0.00 4.35
3214 8410 9.399403 GGAGAATCAAGAGAATAAAAACACAAC 57.601 33.333 0.00 0.00 36.25 3.32
3242 8438 2.317530 AGAGGCCGCAAGAAAGATAC 57.682 50.000 9.88 0.00 43.02 2.24
3244 8440 1.936547 GAGGCCGCAAGAAAGATACTG 59.063 52.381 0.00 0.00 43.02 2.74
3246 8442 2.500098 AGGCCGCAAGAAAGATACTGTA 59.500 45.455 0.00 0.00 43.02 2.74
3248 8444 3.877508 GGCCGCAAGAAAGATACTGTATT 59.122 43.478 1.22 0.00 43.02 1.89
3249 8445 5.054477 GGCCGCAAGAAAGATACTGTATTA 58.946 41.667 1.22 0.00 43.02 0.98
3330 8530 2.159085 GCGTAGGAAGGATTGTACTGCT 60.159 50.000 0.00 0.00 0.00 4.24
3339 8539 3.003480 GGATTGTACTGCTGTGTCTTCC 58.997 50.000 6.48 4.49 0.00 3.46
3351 8551 1.342819 GTGTCTTCCTGACTGAGCACT 59.657 52.381 0.00 0.00 45.54 4.40
3371 8572 6.799512 GCACTGATAATTAAAAGGTGCTGAT 58.200 36.000 19.43 0.00 43.21 2.90
3404 8605 5.611796 TCAAGCACAAAGTCATACATCAC 57.388 39.130 0.00 0.00 0.00 3.06
3454 8655 5.984926 CACAACCACTTAAAGCATGAACATT 59.015 36.000 0.00 0.00 0.00 2.71
3498 8702 1.773054 GCGTGGCATGCTCTCAGATG 61.773 60.000 23.98 1.74 0.00 2.90
3500 8704 1.523032 TGGCATGCTCTCAGATGCG 60.523 57.895 18.92 0.00 44.98 4.73
3746 8960 3.012518 CGCCTTTGACTCAAGAATGGAT 58.987 45.455 0.00 0.00 0.00 3.41
3752 8966 6.320672 CCTTTGACTCAAGAATGGATAATGCT 59.679 38.462 0.00 0.00 0.00 3.79
3794 9011 1.898472 ACCGCTAGATCATCATCCCAG 59.102 52.381 0.00 0.00 0.00 4.45
3802 9019 3.330110 AGATCATCATCCCAGCCCTAAAG 59.670 47.826 0.00 0.00 0.00 1.85
3816 9033 5.293569 CAGCCCTAAAGTAGTTTCCGTATTG 59.706 44.000 0.00 0.00 0.00 1.90
3843 9092 4.040461 AGTTACACAAGGAGTACTGCACAT 59.960 41.667 17.34 0.00 0.00 3.21
3942 9202 7.093333 GGGGTTGAGATGAGACCATTTTATTTT 60.093 37.037 0.00 0.00 35.11 1.82
4001 9263 5.610235 TTTGCTTTTTATTGGCATGAAGC 57.390 34.783 0.00 0.22 44.65 3.86
4035 9298 8.841300 TGCAACACTTTGTATTATTGAACACTA 58.159 29.630 0.00 0.00 34.90 2.74
4092 9355 7.630082 TGGTGATTATATATAGGTTCCAAGCC 58.370 38.462 0.00 0.00 0.00 4.35
4093 9356 6.761714 GGTGATTATATATAGGTTCCAAGCCG 59.238 42.308 0.00 0.00 0.00 5.52
4096 9359 6.691255 TTATATATAGGTTCCAAGCCGGTT 57.309 37.500 1.90 0.00 35.57 4.44
4097 9360 3.945640 ATATAGGTTCCAAGCCGGTTT 57.054 42.857 1.90 0.00 35.57 3.27
4098 9361 2.597578 ATAGGTTCCAAGCCGGTTTT 57.402 45.000 0.00 0.00 35.57 2.43
4140 9403 7.923414 CCTTATGTAAGGTTCTTAAACAGCT 57.077 36.000 10.10 0.00 46.11 4.24
4181 9729 9.863845 TTTTTGTTTTCTCGTATTCTTTTTCCT 57.136 25.926 0.00 0.00 0.00 3.36
4185 9733 9.863845 TGTTTTCTCGTATTCTTTTTCCTTTTT 57.136 25.926 0.00 0.00 0.00 1.94
4249 9797 7.199766 TCAGAAACTTAAACATGTTCGCATTT 58.800 30.769 12.39 10.51 35.23 2.32
4250 9798 7.704472 TCAGAAACTTAAACATGTTCGCATTTT 59.296 29.630 12.39 8.01 35.23 1.82
4251 9799 8.327429 CAGAAACTTAAACATGTTCGCATTTTT 58.673 29.630 12.39 7.00 39.78 1.94
4252 9800 9.522804 AGAAACTTAAACATGTTCGCATTTTTA 57.477 25.926 12.39 0.00 38.18 1.52
4514 10064 6.435428 TCAAGAACTTCTTAAAATGTTCGCC 58.565 36.000 3.64 0.00 42.29 5.54
4516 10066 6.002062 AGAACTTCTTAAAATGTTCGCCTG 57.998 37.500 2.84 0.00 42.29 4.85
4524 10074 0.606401 AATGTTCGCCTGTGGGACAG 60.606 55.000 0.00 0.00 45.53 3.51
4570 10120 0.455633 TTCGCTAACGTTCGGAGCTC 60.456 55.000 17.04 4.71 41.18 4.09
4579 10129 3.285484 ACGTTCGGAGCTCCTTATCTTA 58.715 45.455 29.73 4.85 0.00 2.10
4583 10133 3.432378 TCGGAGCTCCTTATCTTATCCC 58.568 50.000 29.73 0.00 0.00 3.85
4585 10135 2.498078 GGAGCTCCTTATCTTATCCCCG 59.502 54.545 26.25 0.00 0.00 5.73
4616 10168 1.446099 CGTCATGACCTGGTCCACG 60.446 63.158 23.42 22.14 0.00 4.94
4657 10209 1.691976 TCCTCTCGAAACAGGCTTTCA 59.308 47.619 0.33 0.00 0.00 2.69
4692 10244 8.816640 ATAAATAAAGCAACAACTGAAACAGG 57.183 30.769 0.00 0.00 35.51 4.00
4695 10247 1.406539 AGCAACAACTGAAACAGGCAG 59.593 47.619 0.00 0.00 35.51 4.85
4699 10251 0.317269 CAACTGAAACAGGCAGCACG 60.317 55.000 0.00 0.00 36.86 5.34
4717 10269 2.181021 CGTCCTCCGTGCCACTAC 59.819 66.667 0.00 0.00 0.00 2.73
4722 10274 1.064240 TCCTCCGTGCCACTACTATGA 60.064 52.381 0.00 0.00 0.00 2.15
4738 10290 2.596904 ATGATACGGTCCCAGAAACG 57.403 50.000 0.00 0.00 0.00 3.60
4742 10294 0.318120 TACGGTCCCAGAAACGAACC 59.682 55.000 0.00 0.00 0.00 3.62
4748 10300 1.345415 TCCCAGAAACGAACCACTACC 59.655 52.381 0.00 0.00 0.00 3.18
4766 10318 0.317269 CCGTATATCGTGAACCGCGT 60.317 55.000 4.92 0.00 38.57 6.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.649277 CTTCGACACCGCCCAGGAG 62.649 68.421 0.00 0.00 45.00 3.69
13 14 3.691342 CTTCGACACCGCCCAGGA 61.691 66.667 0.00 0.00 45.00 3.86
15 16 3.530910 AACCTTCGACACCGCCCAG 62.531 63.158 0.00 0.00 35.37 4.45
16 17 3.524648 GAACCTTCGACACCGCCCA 62.525 63.158 0.00 0.00 35.37 5.36
17 18 2.741211 GAACCTTCGACACCGCCC 60.741 66.667 0.00 0.00 35.37 6.13
20 21 1.443872 CTCGGAACCTTCGACACCG 60.444 63.158 0.00 0.00 44.09 4.94
21 22 0.388263 GTCTCGGAACCTTCGACACC 60.388 60.000 0.00 0.00 32.86 4.16
23 24 1.577922 CGTCTCGGAACCTTCGACA 59.422 57.895 0.00 0.00 32.86 4.35
24 25 4.454554 CGTCTCGGAACCTTCGAC 57.545 61.111 0.00 0.00 32.86 4.20
65 66 1.283181 CCTACTCCGCCGAGATTCG 59.717 63.158 9.16 0.00 38.52 3.34
67 68 2.017559 GCACCTACTCCGCCGAGATT 62.018 60.000 9.16 0.00 38.52 2.40
69 70 3.138798 GCACCTACTCCGCCGAGA 61.139 66.667 9.16 0.00 38.52 4.04
74 75 4.509737 GTCCGGCACCTACTCCGC 62.510 72.222 0.00 0.00 44.01 5.54
75 76 4.189188 CGTCCGGCACCTACTCCG 62.189 72.222 0.00 0.00 44.89 4.63
76 77 3.834799 CCGTCCGGCACCTACTCC 61.835 72.222 0.00 0.00 0.00 3.85
77 78 2.753043 TCCGTCCGGCACCTACTC 60.753 66.667 0.00 0.00 34.68 2.59
78 79 3.066814 GTCCGTCCGGCACCTACT 61.067 66.667 0.00 0.00 34.68 2.57
112 113 2.803479 CGTGGAGGTACGGGCTAC 59.197 66.667 0.00 0.00 40.22 3.58
113 114 3.142838 GCGTGGAGGTACGGGCTA 61.143 66.667 0.00 0.00 43.87 3.93
168 169 4.838152 TCAATCGCCCTCTGCCGC 62.838 66.667 0.00 0.00 36.24 6.53
169 170 2.587194 CTCAATCGCCCTCTGCCG 60.587 66.667 0.00 0.00 36.24 5.69
171 172 0.392336 ATCTCTCAATCGCCCTCTGC 59.608 55.000 0.00 0.00 0.00 4.26
172 173 1.685517 TCATCTCTCAATCGCCCTCTG 59.314 52.381 0.00 0.00 0.00 3.35
173 174 2.079170 TCATCTCTCAATCGCCCTCT 57.921 50.000 0.00 0.00 0.00 3.69
175 176 2.364970 CTCTTCATCTCTCAATCGCCCT 59.635 50.000 0.00 0.00 0.00 5.19
178 179 3.052036 GCTCTCTTCATCTCTCAATCGC 58.948 50.000 0.00 0.00 0.00 4.58
179 180 3.299162 CGCTCTCTTCATCTCTCAATCG 58.701 50.000 0.00 0.00 0.00 3.34
181 182 2.694628 AGCGCTCTCTTCATCTCTCAAT 59.305 45.455 2.64 0.00 0.00 2.57
182 183 2.098614 AGCGCTCTCTTCATCTCTCAA 58.901 47.619 2.64 0.00 0.00 3.02
183 184 1.761449 AGCGCTCTCTTCATCTCTCA 58.239 50.000 2.64 0.00 0.00 3.27
184 185 3.138304 TCTAGCGCTCTCTTCATCTCTC 58.862 50.000 16.34 0.00 0.00 3.20
185 186 3.141398 CTCTAGCGCTCTCTTCATCTCT 58.859 50.000 16.34 0.00 0.00 3.10
187 188 2.229792 CCTCTAGCGCTCTCTTCATCT 58.770 52.381 16.34 0.00 0.00 2.90
189 190 1.327303 CCCTCTAGCGCTCTCTTCAT 58.673 55.000 16.34 0.00 0.00 2.57
190 191 1.388065 GCCCTCTAGCGCTCTCTTCA 61.388 60.000 16.34 0.00 0.00 3.02
192 193 3.532501 GCCCTCTAGCGCTCTCTT 58.467 61.111 16.34 0.00 0.00 2.85
200 201 1.379642 AAATTGCAGCGCCCTCTAGC 61.380 55.000 2.29 0.00 0.00 3.42
201 202 1.953559 TAAATTGCAGCGCCCTCTAG 58.046 50.000 2.29 0.00 0.00 2.43
202 203 2.638480 ATAAATTGCAGCGCCCTCTA 57.362 45.000 2.29 0.00 0.00 2.43
203 204 2.498167 CTATAAATTGCAGCGCCCTCT 58.502 47.619 2.29 0.00 0.00 3.69
206 207 0.039165 GCCTATAAATTGCAGCGCCC 60.039 55.000 2.29 0.00 0.00 6.13
208 209 3.077339 CGCCTATAAATTGCAGCGC 57.923 52.632 0.00 0.00 36.89 5.92
209 210 0.722469 CGCGCCTATAAATTGCAGCG 60.722 55.000 0.00 8.18 45.91 5.18
210 211 0.998727 GCGCGCCTATAAATTGCAGC 60.999 55.000 23.24 0.00 0.00 5.25
211 212 0.588252 AGCGCGCCTATAAATTGCAG 59.412 50.000 30.33 0.00 0.00 4.41
212 213 0.307453 CAGCGCGCCTATAAATTGCA 59.693 50.000 30.33 0.00 0.00 4.08
213 214 0.586319 TCAGCGCGCCTATAAATTGC 59.414 50.000 30.33 0.00 0.00 3.56
214 215 2.639751 GTTCAGCGCGCCTATAAATTG 58.360 47.619 30.33 17.16 0.00 2.32
216 217 0.859232 CGTTCAGCGCGCCTATAAAT 59.141 50.000 30.33 3.60 0.00 1.40
217 218 0.458889 ACGTTCAGCGCGCCTATAAA 60.459 50.000 30.33 12.26 46.11 1.40
219 220 1.587876 CACGTTCAGCGCGCCTATA 60.588 57.895 30.33 7.96 46.11 1.31
220 221 2.885644 CACGTTCAGCGCGCCTAT 60.886 61.111 30.33 6.46 46.11 2.57
229 230 1.577328 ATTTGGCGCTCCACGTTCAG 61.577 55.000 7.64 0.00 43.33 3.02
230 231 1.599518 ATTTGGCGCTCCACGTTCA 60.600 52.632 7.64 0.00 43.33 3.18
231 232 1.154225 CATTTGGCGCTCCACGTTC 60.154 57.895 7.64 0.00 43.33 3.95
232 233 0.604243 TACATTTGGCGCTCCACGTT 60.604 50.000 7.64 0.00 43.33 3.99
233 234 1.004320 TACATTTGGCGCTCCACGT 60.004 52.632 7.64 2.21 43.33 4.49
235 236 1.429423 GCTACATTTGGCGCTCCAC 59.571 57.895 7.64 0.00 43.33 4.02
236 237 2.106074 CGCTACATTTGGCGCTCCA 61.106 57.895 7.64 0.00 44.64 3.86
252 253 3.240353 GGAAAAGATTGCGCGCGC 61.240 61.111 45.02 45.02 42.35 6.86
253 254 2.576847 GGGAAAAGATTGCGCGCG 60.577 61.111 28.44 28.44 0.00 6.86
254 255 2.576847 CGGGAAAAGATTGCGCGC 60.577 61.111 27.26 27.26 0.00 6.86
255 256 2.576847 GCGGGAAAAGATTGCGCG 60.577 61.111 0.00 0.00 0.00 6.86
258 259 2.576847 CGCGCGGGAAAAGATTGC 60.577 61.111 24.84 0.00 0.00 3.56
259 260 1.701545 TAGCGCGCGGGAAAAGATTG 61.702 55.000 33.06 0.00 0.00 2.67
260 261 1.429148 CTAGCGCGCGGGAAAAGATT 61.429 55.000 33.06 6.40 0.00 2.40
261 262 1.883084 CTAGCGCGCGGGAAAAGAT 60.883 57.895 33.06 7.25 0.00 2.40
262 263 2.508439 CTAGCGCGCGGGAAAAGA 60.508 61.111 33.06 5.10 0.00 2.52
264 265 1.903783 GAAACTAGCGCGCGGGAAAA 61.904 55.000 33.06 9.78 0.00 2.29
265 266 2.357760 AAACTAGCGCGCGGGAAA 60.358 55.556 33.06 12.44 0.00 3.13
266 267 2.812178 GAAACTAGCGCGCGGGAA 60.812 61.111 33.06 12.82 0.00 3.97
273 274 3.497031 GTGGCGGGAAACTAGCGC 61.497 66.667 0.00 0.00 37.73 5.92
274 275 2.818274 GGTGGCGGGAAACTAGCG 60.818 66.667 0.00 0.00 35.39 4.26
275 276 2.818274 CGGTGGCGGGAAACTAGC 60.818 66.667 0.00 0.00 0.00 3.42
276 277 2.818274 GCGGTGGCGGGAAACTAG 60.818 66.667 0.00 0.00 0.00 2.57
293 294 4.776953 CGTTTTCGCGCGCTCCAG 62.777 66.667 30.48 13.90 36.22 3.86
315 316 0.793104 ATTGACTTTTTAGCGCGCGC 60.793 50.000 45.10 45.10 42.33 6.86
316 317 1.602191 AATTGACTTTTTAGCGCGCG 58.398 45.000 28.44 28.44 0.00 6.86
317 318 3.299804 GGTAAATTGACTTTTTAGCGCGC 59.700 43.478 26.66 26.66 30.27 6.86
321 322 5.116528 GCACACGGTAAATTGACTTTTTAGC 59.883 40.000 0.00 0.00 35.01 3.09
322 323 5.338559 CGCACACGGTAAATTGACTTTTTAG 59.661 40.000 0.00 0.00 34.97 1.85
324 325 4.039032 CGCACACGGTAAATTGACTTTTT 58.961 39.130 0.00 0.00 34.97 1.94
325 326 3.623863 CGCACACGGTAAATTGACTTTT 58.376 40.909 0.00 0.00 34.97 2.27
327 328 1.069500 GCGCACACGGTAAATTGACTT 60.069 47.619 0.30 0.00 40.57 3.01
328 329 0.515564 GCGCACACGGTAAATTGACT 59.484 50.000 0.30 0.00 40.57 3.41
329 330 0.236187 TGCGCACACGGTAAATTGAC 59.764 50.000 5.66 0.00 40.57 3.18
330 331 1.129624 GATGCGCACACGGTAAATTGA 59.870 47.619 14.90 0.00 40.57 2.57
331 332 1.130373 AGATGCGCACACGGTAAATTG 59.870 47.619 14.90 0.00 40.57 2.32
332 333 1.448985 AGATGCGCACACGGTAAATT 58.551 45.000 14.90 0.00 40.57 1.82
334 335 1.231221 AAAGATGCGCACACGGTAAA 58.769 45.000 14.90 0.00 40.57 2.01
335 336 1.069568 CAAAAGATGCGCACACGGTAA 60.070 47.619 14.90 0.00 40.57 2.85
338 339 0.725784 GTCAAAAGATGCGCACACGG 60.726 55.000 14.90 0.00 40.57 4.94
339 340 1.054348 CGTCAAAAGATGCGCACACG 61.054 55.000 14.90 8.88 44.07 4.49
340 341 1.330080 GCGTCAAAAGATGCGCACAC 61.330 55.000 14.90 10.70 46.57 3.82
346 347 1.512734 CAGCCGCGTCAAAAGATGC 60.513 57.895 4.92 0.00 0.00 3.91
347 348 0.238289 AACAGCCGCGTCAAAAGATG 59.762 50.000 4.92 0.00 0.00 2.90
348 349 0.238289 CAACAGCCGCGTCAAAAGAT 59.762 50.000 4.92 0.00 0.00 2.40
350 351 1.370414 CCAACAGCCGCGTCAAAAG 60.370 57.895 4.92 0.00 0.00 2.27
351 352 1.169661 ATCCAACAGCCGCGTCAAAA 61.170 50.000 4.92 0.00 0.00 2.44
355 356 4.166011 GCATCCAACAGCCGCGTC 62.166 66.667 4.92 0.00 0.00 5.19
356 357 4.704833 AGCATCCAACAGCCGCGT 62.705 61.111 4.92 0.00 0.00 6.01
357 358 2.906182 TAGAGCATCCAACAGCCGCG 62.906 60.000 0.00 0.00 33.66 6.46
358 359 0.744414 TTAGAGCATCCAACAGCCGC 60.744 55.000 0.00 0.00 33.66 6.53
359 360 1.959042 ATTAGAGCATCCAACAGCCG 58.041 50.000 0.00 0.00 33.66 5.52
360 361 5.835113 TTTTATTAGAGCATCCAACAGCC 57.165 39.130 0.00 0.00 33.66 4.85
395 396 1.154543 GGTTTCGGCAGCGTTAACG 60.155 57.895 23.40 23.40 43.27 3.18
397 398 0.814410 TGTGGTTTCGGCAGCGTTAA 60.814 50.000 0.00 0.00 0.00 2.01
398 399 0.814410 TTGTGGTTTCGGCAGCGTTA 60.814 50.000 0.00 0.00 0.00 3.18
399 400 1.658686 TTTGTGGTTTCGGCAGCGTT 61.659 50.000 0.00 0.00 0.00 4.84
515 516 4.109766 CTCTGTAATTTACACATCGGCGA 58.890 43.478 13.87 13.87 34.46 5.54
535 536 2.803492 GCCGGTGATAGACCAATGACTC 60.803 54.545 1.90 0.00 46.55 3.36
610 616 5.945144 ATGGAAGCAAAATGGAAGCTAAT 57.055 34.783 0.00 0.00 37.70 1.73
775 781 4.477975 CTGCCCGAGGACGACGAC 62.478 72.222 0.00 0.00 42.66 4.34
776 782 3.610619 TACTGCCCGAGGACGACGA 62.611 63.158 0.00 0.00 42.66 4.20
801 814 7.122501 TGGTGCGATTTATGCCATGATATTATT 59.877 33.333 0.00 0.00 0.00 1.40
807 820 2.555325 CTGGTGCGATTTATGCCATGAT 59.445 45.455 0.00 0.00 0.00 2.45
833 846 3.075134 AGGGCAGGAAGAACAGAGAAATT 59.925 43.478 0.00 0.00 0.00 1.82
947 967 8.911662 CGGAAATTTTAAGAATGAACACGAATT 58.088 29.630 0.00 0.00 0.00 2.17
958 978 6.715264 ACAGTCACCTCGGAAATTTTAAGAAT 59.285 34.615 0.00 0.00 0.00 2.40
964 984 9.847224 ATATATTACAGTCACCTCGGAAATTTT 57.153 29.630 0.00 0.00 0.00 1.82
974 994 6.239430 CCTCACTGCATATATTACAGTCACCT 60.239 42.308 13.05 0.00 42.59 4.00
1379 1535 7.751732 TGTTTAGATCATCTGCAAACATGTAC 58.248 34.615 10.52 0.00 32.86 2.90
1622 1778 1.373371 GGTACTTTCGAACCGGCGT 60.373 57.895 6.01 0.00 0.00 5.68
1669 1825 1.002315 GTTGCATTGACATTGGCCCTT 59.998 47.619 0.00 0.00 0.00 3.95
1762 1942 6.042777 CAGTGTCATCTGACCGTTATTATGT 58.957 40.000 7.81 0.00 44.15 2.29
1763 1943 5.463392 CCAGTGTCATCTGACCGTTATTATG 59.537 44.000 7.81 0.00 44.15 1.90
1764 1944 5.362717 TCCAGTGTCATCTGACCGTTATTAT 59.637 40.000 7.81 0.00 44.15 1.28
1765 1945 4.707934 TCCAGTGTCATCTGACCGTTATTA 59.292 41.667 7.81 0.00 44.15 0.98
1766 1946 3.513912 TCCAGTGTCATCTGACCGTTATT 59.486 43.478 7.81 0.00 44.15 1.40
1791 1971 0.370273 CCGAGAACTGCGTTATGTGC 59.630 55.000 0.00 0.00 0.00 4.57
1828 2017 1.445582 GGCCGTCGTAGTGGAACAG 60.446 63.158 0.00 0.00 41.80 3.16
1829 2018 2.201708 TGGCCGTCGTAGTGGAACA 61.202 57.895 0.00 0.00 41.43 3.18
1830 2019 1.735559 GTGGCCGTCGTAGTGGAAC 60.736 63.158 0.00 0.00 0.00 3.62
1831 2020 2.201708 TGTGGCCGTCGTAGTGGAA 61.202 57.895 0.00 0.00 0.00 3.53
1832 2021 2.598099 TGTGGCCGTCGTAGTGGA 60.598 61.111 0.00 0.00 0.00 4.02
1893 2089 1.078918 CTTCCTGGCGCTGACATGA 60.079 57.895 7.64 0.00 0.00 3.07
1896 2092 3.889134 CTGCTTCCTGGCGCTGACA 62.889 63.158 7.64 0.00 34.52 3.58
1946 2154 8.154649 ACTAATGACTGAAGAACGAAAATGTT 57.845 30.769 0.00 0.00 34.02 2.71
1955 2163 3.522553 CCGGGACTAATGACTGAAGAAC 58.477 50.000 0.00 0.00 0.00 3.01
1967 2180 2.093658 GTCTGAAGATTGCCGGGACTAA 60.094 50.000 2.18 0.00 0.00 2.24
2007 2269 4.034858 CCACCTTCGTCAATCATCATTCAG 59.965 45.833 0.00 0.00 0.00 3.02
2081 2343 1.592223 GTCCTCGTCCCACAGGAAG 59.408 63.158 0.00 0.00 46.38 3.46
2141 2403 2.071540 CGAATGGACATGGATGATCGG 58.928 52.381 0.00 0.00 0.00 4.18
2153 2417 1.237285 AAGCAGCCACACGAATGGAC 61.237 55.000 12.96 5.31 43.02 4.02
2164 2428 2.238144 AGCTAGATTCAGAAAGCAGCCA 59.762 45.455 7.85 0.00 37.44 4.75
2165 2429 2.916640 AGCTAGATTCAGAAAGCAGCC 58.083 47.619 7.85 0.00 37.44 4.85
2179 2443 7.117285 TGATCAAATTTCAGAGCTAGCTAGA 57.883 36.000 25.15 16.02 0.00 2.43
2186 2450 7.066043 GTCTCTCAATGATCAAATTTCAGAGCT 59.934 37.037 0.00 0.00 30.50 4.09
2187 2451 7.066043 AGTCTCTCAATGATCAAATTTCAGAGC 59.934 37.037 0.00 0.00 30.50 4.09
2188 2452 8.391859 CAGTCTCTCAATGATCAAATTTCAGAG 58.608 37.037 0.00 0.43 31.09 3.35
2361 2642 5.414765 TCATCATATGGAATGCAGAATCAGC 59.585 40.000 2.13 0.00 0.00 4.26
2362 2643 7.631717 ATCATCATATGGAATGCAGAATCAG 57.368 36.000 2.13 0.00 0.00 2.90
2481 4906 7.020010 GTGAAGAACTTGTGTTGATGATGATC 58.980 38.462 0.00 0.00 36.39 2.92
2483 4908 5.239306 GGTGAAGAACTTGTGTTGATGATGA 59.761 40.000 0.00 0.00 36.39 2.92
2601 5032 0.465097 CGCATCTCCAAGCATCCCTT 60.465 55.000 0.00 0.00 0.00 3.95
2649 5099 5.972935 TCCAGAATTAACTATGAGCAACGA 58.027 37.500 0.00 0.00 0.00 3.85
2650 5100 6.851222 ATCCAGAATTAACTATGAGCAACG 57.149 37.500 0.00 0.00 0.00 4.10
2798 5270 5.872635 TCTCTGGTCAAGTAATTACGTACG 58.127 41.667 15.01 15.01 0.00 3.67
2827 5299 8.400947 TCTTCAGTGAATCTATAAAAATGCTGC 58.599 33.333 5.91 0.00 0.00 5.25
2860 5332 6.422776 TCAAAGCGATTTTCTGGATAACTC 57.577 37.500 0.00 0.00 0.00 3.01
2928 8106 0.984230 CTTCAGGGTCCTGCCAGTTA 59.016 55.000 11.95 0.00 43.31 2.24
2994 8172 1.077828 ACCTGATCTCTGAGTGTGGGA 59.922 52.381 4.32 0.00 0.00 4.37
3045 8224 1.404315 GGCCGACTCGAGTTTGAATCT 60.404 52.381 21.08 0.00 0.00 2.40
3078 8257 2.202756 CCTCGTGGTAAGAGCGCC 60.203 66.667 2.29 0.00 34.56 6.53
3087 8266 3.637273 GGTTCCTGGCCTCGTGGT 61.637 66.667 3.32 0.00 35.27 4.16
3092 8271 2.308722 TGGATGGGTTCCTGGCCTC 61.309 63.158 3.32 0.00 45.68 4.70
3113 8292 3.057315 AGGGATGCAACTCAATCAAAACG 60.057 43.478 0.00 0.00 0.00 3.60
3123 8302 1.202348 CGGGAAAAAGGGATGCAACTC 59.798 52.381 0.00 0.00 0.00 3.01
3214 8410 3.267860 GCGGCCTCTTGATGCTCG 61.268 66.667 0.00 2.40 0.00 5.03
3242 8438 7.502120 ACATGCTTTAAGCTCCATAATACAG 57.498 36.000 18.20 0.00 42.97 2.74
3244 8440 7.930217 TGAACATGCTTTAAGCTCCATAATAC 58.070 34.615 18.20 2.25 42.97 1.89
3246 8442 7.592885 ATGAACATGCTTTAAGCTCCATAAT 57.407 32.000 18.20 0.00 42.97 1.28
3248 8444 7.259882 CAAATGAACATGCTTTAAGCTCCATA 58.740 34.615 18.20 0.00 42.97 2.74
3249 8445 5.927281 AATGAACATGCTTTAAGCTCCAT 57.073 34.783 18.20 10.37 42.97 3.41
3339 8539 7.335422 ACCTTTTAATTATCAGTGCTCAGTCAG 59.665 37.037 0.00 0.00 0.00 3.51
3404 8605 8.964150 GGTGTAGTAAGTTGCTTAAACAATTTG 58.036 33.333 8.99 0.00 41.61 2.32
3498 8702 6.510746 AACACAGAAAAATTAAAAGAGCGC 57.489 33.333 0.00 0.00 0.00 5.92
3500 8704 9.181805 GGAGTAACACAGAAAAATTAAAAGAGC 57.818 33.333 0.00 0.00 0.00 4.09
3746 8960 1.679944 GCCAGCTCCTTGTCAGCATTA 60.680 52.381 0.00 0.00 39.56 1.90
3752 8966 1.228245 GTTGGCCAGCTCCTTGTCA 60.228 57.895 13.08 0.00 0.00 3.58
3794 9011 4.573607 CCAATACGGAAACTACTTTAGGGC 59.426 45.833 0.00 0.00 36.56 5.19
3802 9019 7.598493 TGTGTAACTAACCAATACGGAAACTAC 59.402 37.037 0.00 0.00 38.04 2.73
3816 9033 4.928020 GCAGTACTCCTTGTGTAACTAACC 59.072 45.833 0.00 0.00 38.04 2.85
4006 9269 9.539825 TGTTCAATAATACAAAGTGTTGCAAAT 57.460 25.926 0.00 0.00 38.39 2.32
4066 9329 8.107095 GGCTTGGAACCTATATATAATCACCAA 58.893 37.037 14.59 14.59 33.62 3.67
4098 9361 6.097981 ACATAAGGTTCCCAAAACCGTAAAAA 59.902 34.615 6.68 0.00 44.82 1.94
4101 9364 4.727677 ACATAAGGTTCCCAAAACCGTAA 58.272 39.130 6.68 0.00 44.82 3.18
4103 9366 3.232720 ACATAAGGTTCCCAAAACCGT 57.767 42.857 1.52 1.38 44.82 4.83
4104 9367 4.157105 CCTTACATAAGGTTCCCAAAACCG 59.843 45.833 9.24 0.00 46.11 4.44
4159 9707 9.863845 AAAAAGGAAAAAGAATACGAGAAAACA 57.136 25.926 0.00 0.00 0.00 2.83
4508 10058 3.050275 GCTGTCCCACAGGCGAAC 61.050 66.667 5.82 0.00 46.01 3.95
4540 10090 1.005975 CGTTAGCGAAAATCTGAGCCG 60.006 52.381 0.00 0.00 41.33 5.52
4570 10120 1.204941 CGAGCCGGGGATAAGATAAGG 59.795 57.143 2.18 0.00 0.00 2.69
4585 10135 2.731976 GTCATGACGAAATATCCGAGCC 59.268 50.000 10.69 0.00 0.00 4.70
4598 10148 1.446099 CGTGGACCAGGTCATGACG 60.446 63.158 21.75 19.83 33.68 4.35
4599 10149 1.741770 GCGTGGACCAGGTCATGAC 60.742 63.158 21.75 17.91 33.68 3.06
4600 10150 2.213513 TGCGTGGACCAGGTCATGA 61.214 57.895 21.75 1.40 33.68 3.07
4601 10151 2.034879 GTGCGTGGACCAGGTCATG 61.035 63.158 21.75 13.13 33.68 3.07
4638 10190 1.801178 GTGAAAGCCTGTTTCGAGAGG 59.199 52.381 3.43 3.43 0.00 3.69
4684 10236 3.648982 CGCGTGCTGCCTGTTTCA 61.649 61.111 0.00 0.00 42.08 2.69
4710 10262 2.230750 GGGACCGTATCATAGTAGTGGC 59.769 54.545 0.00 0.00 0.00 5.01
4717 10269 3.317149 TCGTTTCTGGGACCGTATCATAG 59.683 47.826 0.00 0.00 0.00 2.23
4722 10274 1.066645 GGTTCGTTTCTGGGACCGTAT 60.067 52.381 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.