Multiple sequence alignment - TraesCS7B01G432800

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 TraesCS7B01G432800 chr7B 100.000 2120 0 0 1 2120 700550452 700552571 0.000000e+00 3916.0
1 TraesCS7B01G432800 chr7B 76.969 508 56 32 863 1335 700439856 700440337 1.260000e-57 233.0
2 TraesCS7B01G432800 chr7A 89.752 966 57 19 343 1286 701390701 701391646 0.000000e+00 1197.0
3 TraesCS7B01G432800 chr7A 78.440 218 22 18 1684 1885 701392020 701392228 3.700000e-23 119.0
4 TraesCS7B01G432800 chr7D 86.492 918 77 25 74 963 611330361 611331259 0.000000e+00 965.0
5 TraesCS7B01G432800 chr7D 83.709 798 58 39 958 1718 611331791 611332553 0.000000e+00 688.0
6 TraesCS7B01G432800 chr7D 77.533 454 54 18 877 1309 611294450 611294876 1.640000e-56 230.0
7 TraesCS7B01G432800 chr7D 83.152 184 13 10 523 703 611294105 611294273 3.640000e-33 152.0
8 TraesCS7B01G432800 chr7D 87.179 78 5 3 1 73 611330251 611330328 1.350000e-12 84.2
9 TraesCS7B01G432800 chr1D 85.106 94 7 5 1054 1147 452762517 452762431 2.900000e-14 89.8
10 TraesCS7B01G432800 chr1D 85.106 94 7 5 1054 1147 452858223 452858137 2.900000e-14 89.8
11 TraesCS7B01G432800 chr1B 98.039 51 1 0 1054 1104 623224817 623224767 2.900000e-14 89.8
12 TraesCS7B01G432800 chr1B 96.078 51 2 0 1054 1104 623317865 623317915 1.350000e-12 84.2
13 TraesCS7B01G432800 chr1A 96.078 51 2 0 1054 1104 547591994 547591944 1.350000e-12 84.2


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G432800 chr7B 700550452 700552571 2119 False 3916.000000 3916 100.000000 1 2120 1 chr7B.!!$F2 2119
1 TraesCS7B01G432800 chr7A 701390701 701392228 1527 False 658.000000 1197 84.096000 343 1885 2 chr7A.!!$F1 1542
2 TraesCS7B01G432800 chr7D 611330251 611332553 2302 False 579.066667 965 85.793333 1 1718 3 chr7D.!!$F2 1717

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
324 364 0.041047 CCGTGTACGTCAACGACAGA 60.041 55.0 20.72 0.0 43.02 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2021 2768 0.032952 GGGAAAAAGACCGGTTTGGC 59.967 55.0 9.42 0.0 43.94 4.52 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
73 79 1.636769 GGGAGGGATGAAGTGGGGAC 61.637 65.000 0.00 0.00 0.00 4.46
85 122 4.115270 GGGGACCGAAGTCTGACT 57.885 61.111 4.06 4.06 43.05 3.41
86 123 1.891616 GGGGACCGAAGTCTGACTC 59.108 63.158 11.31 4.20 43.05 3.36
110 147 2.946346 GCGTCCGTACTCCCCCAAA 61.946 63.158 0.00 0.00 0.00 3.28
112 149 1.538687 CGTCCGTACTCCCCCAAACT 61.539 60.000 0.00 0.00 0.00 2.66
119 156 3.495453 CGTACTCCCCCAAACTTTCTCAA 60.495 47.826 0.00 0.00 0.00 3.02
129 166 6.429692 CCCCAAACTTTCTCAACTTTGTTTTT 59.570 34.615 0.00 0.00 0.00 1.94
130 167 7.297391 CCCAAACTTTCTCAACTTTGTTTTTG 58.703 34.615 0.00 0.00 0.00 2.44
144 181 6.491745 ACTTTGTTTTTGGTTTGGTGGAATTT 59.508 30.769 0.00 0.00 0.00 1.82
146 183 5.560724 TGTTTTTGGTTTGGTGGAATTTGA 58.439 33.333 0.00 0.00 0.00 2.69
148 185 6.072452 TGTTTTTGGTTTGGTGGAATTTGAAC 60.072 34.615 0.00 0.00 0.00 3.18
151 188 3.952323 TGGTTTGGTGGAATTTGAACGTA 59.048 39.130 0.00 0.00 0.00 3.57
153 190 4.202030 GGTTTGGTGGAATTTGAACGTACA 60.202 41.667 0.00 0.00 0.00 2.90
159 196 4.736307 GTGGAATTTGAACGTACAAACCAC 59.264 41.667 13.75 13.75 43.06 4.16
160 197 3.969981 GGAATTTGAACGTACAAACCACG 59.030 43.478 0.00 0.00 41.49 4.94
161 198 4.260702 GGAATTTGAACGTACAAACCACGA 60.261 41.667 1.43 0.00 41.49 4.35
176 214 5.418310 AACCACGACAGTTTGATACAAAG 57.582 39.130 0.00 0.00 0.00 2.77
177 215 4.699637 ACCACGACAGTTTGATACAAAGA 58.300 39.130 0.00 0.00 0.00 2.52
191 229 6.295249 TGATACAAAGAGTTGGATGACACAA 58.705 36.000 0.00 0.00 38.50 3.33
193 231 5.913137 ACAAAGAGTTGGATGACACAAAA 57.087 34.783 0.00 0.00 39.22 2.44
194 232 5.894807 ACAAAGAGTTGGATGACACAAAAG 58.105 37.500 0.00 0.00 39.22 2.27
195 233 5.418840 ACAAAGAGTTGGATGACACAAAAGT 59.581 36.000 0.00 0.00 39.22 2.66
196 234 5.505173 AAGAGTTGGATGACACAAAAGTG 57.495 39.130 0.00 0.00 0.00 3.16
197 235 3.316308 AGAGTTGGATGACACAAAAGTGC 59.684 43.478 0.00 0.00 0.00 4.40
198 236 3.290710 AGTTGGATGACACAAAAGTGCT 58.709 40.909 0.00 0.00 0.00 4.40
199 237 3.701040 AGTTGGATGACACAAAAGTGCTT 59.299 39.130 0.00 0.00 0.00 3.91
202 240 5.843673 TGGATGACACAAAAGTGCTTAAA 57.156 34.783 0.00 0.00 0.00 1.52
203 241 5.587289 TGGATGACACAAAAGTGCTTAAAC 58.413 37.500 0.00 0.00 0.00 2.01
206 244 6.701400 GGATGACACAAAAGTGCTTAAACATT 59.299 34.615 0.00 0.00 0.00 2.71
207 245 7.224557 GGATGACACAAAAGTGCTTAAACATTT 59.775 33.333 0.00 0.00 0.00 2.32
208 246 7.897575 TGACACAAAAGTGCTTAAACATTTT 57.102 28.000 0.00 0.00 31.59 1.82
209 247 8.316640 TGACACAAAAGTGCTTAAACATTTTT 57.683 26.923 6.33 6.33 39.26 1.94
238 276 3.853671 GGATGTTTAGCAGCGTTTTGATG 59.146 43.478 0.00 0.00 36.94 3.07
246 284 1.136000 CAGCGTTTTGATGCATGACGA 60.136 47.619 19.42 0.00 35.90 4.20
247 285 1.535028 AGCGTTTTGATGCATGACGAA 59.465 42.857 19.42 5.16 35.90 3.85
248 286 2.031245 AGCGTTTTGATGCATGACGAAA 60.031 40.909 19.42 10.06 35.90 3.46
253 293 4.517952 TTTGATGCATGACGAAATTGGT 57.482 36.364 2.46 0.00 0.00 3.67
263 303 3.013921 GACGAAATTGGTGATGCCCTAA 58.986 45.455 0.00 0.00 36.04 2.69
270 310 3.737559 TGGTGATGCCCTAAACATTCT 57.262 42.857 0.00 0.00 36.04 2.40
271 311 3.355378 TGGTGATGCCCTAAACATTCTG 58.645 45.455 0.00 0.00 36.04 3.02
273 313 2.754552 GTGATGCCCTAAACATTCTGCA 59.245 45.455 0.00 0.00 0.00 4.41
274 314 2.754552 TGATGCCCTAAACATTCTGCAC 59.245 45.455 0.00 0.00 0.00 4.57
278 318 2.619074 GCCCTAAACATTCTGCACTCCT 60.619 50.000 0.00 0.00 0.00 3.69
282 322 4.154918 CCTAAACATTCTGCACTCCTGTTC 59.845 45.833 0.00 0.00 0.00 3.18
301 341 1.300697 GGTGCGTTGGACTCGAAGT 60.301 57.895 0.00 0.00 0.00 3.01
324 364 0.041047 CCGTGTACGTCAACGACAGA 60.041 55.000 20.72 0.00 43.02 3.41
326 366 2.313234 CGTGTACGTCAACGACAGATT 58.687 47.619 15.63 0.00 43.02 2.40
327 367 3.481839 CGTGTACGTCAACGACAGATTA 58.518 45.455 15.63 0.00 43.02 1.75
329 369 4.379498 CGTGTACGTCAACGACAGATTAAA 59.621 41.667 15.63 0.00 43.02 1.52
330 370 5.108292 CGTGTACGTCAACGACAGATTAAAA 60.108 40.000 15.63 0.00 43.02 1.52
331 371 6.560068 CGTGTACGTCAACGACAGATTAAAAA 60.560 38.462 15.63 0.00 43.02 1.94
332 372 6.784227 GTGTACGTCAACGACAGATTAAAAAG 59.216 38.462 9.88 0.00 43.02 2.27
333 373 6.696583 TGTACGTCAACGACAGATTAAAAAGA 59.303 34.615 9.88 0.00 43.02 2.52
334 374 6.592798 ACGTCAACGACAGATTAAAAAGAA 57.407 33.333 9.88 0.00 43.02 2.52
335 375 7.007313 ACGTCAACGACAGATTAAAAAGAAA 57.993 32.000 9.88 0.00 43.02 2.52
336 376 7.465989 ACGTCAACGACAGATTAAAAAGAAAA 58.534 30.769 9.88 0.00 43.02 2.29
337 377 7.964011 ACGTCAACGACAGATTAAAAAGAAAAA 59.036 29.630 9.88 0.00 43.02 1.94
790 874 5.209659 TCCTTCTACCTCTTTCATCCCTAC 58.790 45.833 0.00 0.00 0.00 3.18
791 875 4.038162 CCTTCTACCTCTTTCATCCCTACG 59.962 50.000 0.00 0.00 0.00 3.51
792 876 4.246712 TCTACCTCTTTCATCCCTACGT 57.753 45.455 0.00 0.00 0.00 3.57
793 877 4.205587 TCTACCTCTTTCATCCCTACGTC 58.794 47.826 0.00 0.00 0.00 4.34
853 937 2.449322 CCCCCTCCTCCATCCCTG 60.449 72.222 0.00 0.00 0.00 4.45
910 998 1.672441 GCCAGAGTGAGAGTTCAGCAG 60.672 57.143 0.00 0.00 32.98 4.24
920 1008 0.320247 AGTTCAGCAGCACTCCTTCG 60.320 55.000 0.00 0.00 0.00 3.79
964 1597 1.621992 TCTCCACACCACAGAGAGAC 58.378 55.000 0.00 0.00 32.92 3.36
981 1614 3.708631 AGAGACAGAGAGAGAGAGAGAGG 59.291 52.174 0.00 0.00 0.00 3.69
1101 1737 4.200851 CGCTGCGTCGTCATGCTG 62.201 66.667 14.93 0.00 35.31 4.41
1122 1762 2.807045 CGCTGGCACGACTGACTC 60.807 66.667 3.87 0.00 34.06 3.36
1123 1763 2.433318 GCTGGCACGACTGACTCC 60.433 66.667 0.00 0.00 0.00 3.85
1124 1764 2.126307 CTGGCACGACTGACTCCG 60.126 66.667 0.00 0.00 0.00 4.63
1125 1765 2.596338 TGGCACGACTGACTCCGA 60.596 61.111 0.00 0.00 0.00 4.55
1193 1849 8.296713 TGGTGTTTGAAGCAAAGATATACTTTC 58.703 33.333 0.00 0.00 45.66 2.62
1224 1880 0.240145 CTGTGATTGTGCTGTGCCAG 59.760 55.000 0.00 0.00 34.12 4.85
1263 1919 7.338957 AGGTAGTACTTGTACATAAGAGGTCAC 59.661 40.741 0.00 0.00 0.00 3.67
1315 1972 4.712476 AGCAAAGCAATAGGATCGATCTT 58.288 39.130 23.96 19.55 0.00 2.40
1321 1978 5.053145 AGCAATAGGATCGATCTTGTGTTC 58.947 41.667 23.96 6.43 0.00 3.18
1324 1981 3.152261 AGGATCGATCTTGTGTTCGTC 57.848 47.619 23.96 4.29 36.91 4.20
1343 2000 0.460987 CGATTCACCACCTCCTCTGC 60.461 60.000 0.00 0.00 0.00 4.26
1348 2005 3.086600 CCACCTCCTCTGCCCTCC 61.087 72.222 0.00 0.00 0.00 4.30
1357 2014 4.052518 CTGCCCTCCACCCCCTTG 62.053 72.222 0.00 0.00 0.00 3.61
1360 2017 4.052518 CCCTCCACCCCCTTGCAG 62.053 72.222 0.00 0.00 0.00 4.41
1361 2018 4.748144 CCTCCACCCCCTTGCAGC 62.748 72.222 0.00 0.00 0.00 5.25
1363 2020 3.506743 TCCACCCCCTTGCAGCAA 61.507 61.111 7.81 7.81 0.00 3.91
1364 2021 2.993264 CCACCCCCTTGCAGCAAG 60.993 66.667 26.03 26.03 40.75 4.01
1365 2022 2.203538 CACCCCCTTGCAGCAAGT 60.204 61.111 29.36 12.53 39.58 3.16
1366 2023 2.203538 ACCCCCTTGCAGCAAGTG 60.204 61.111 29.36 20.68 39.58 3.16
1367 2024 2.203538 CCCCCTTGCAGCAAGTGT 60.204 61.111 29.36 0.00 39.58 3.55
1370 2027 1.656441 CCCTTGCAGCAAGTGTGTC 59.344 57.895 29.36 0.00 39.58 3.67
1385 2042 3.067106 GTGTGTCTGTCCCATTGTACAG 58.933 50.000 9.15 9.15 43.63 2.74
1394 2051 5.242434 TGTCCCATTGTACAGTTACATCAC 58.758 41.667 0.00 0.00 38.05 3.06
1406 2063 4.504461 CAGTTACATCACTGCCGAATACTC 59.496 45.833 0.00 0.00 37.96 2.59
1408 2065 1.476891 ACATCACTGCCGAATACTCGT 59.523 47.619 0.00 0.00 43.87 4.18
1409 2066 1.854743 CATCACTGCCGAATACTCGTG 59.145 52.381 0.00 0.00 43.87 4.35
1410 2067 0.885879 TCACTGCCGAATACTCGTGT 59.114 50.000 0.00 0.00 43.87 4.49
1411 2068 0.992072 CACTGCCGAATACTCGTGTG 59.008 55.000 0.00 0.00 43.87 3.82
1425 2082 8.831715 AATACTCGTGTGATGCAATATATCAA 57.168 30.769 0.00 0.00 36.41 2.57
1444 2104 8.729805 ATATCAACTGAAAGAGAAGGAATCAC 57.270 34.615 0.00 0.00 37.43 3.06
1445 2105 5.308825 TCAACTGAAAGAGAAGGAATCACC 58.691 41.667 0.00 0.00 37.43 4.02
1467 2129 0.462047 ATCAATCGCTTGTCCCCGTC 60.462 55.000 0.00 0.00 33.87 4.79
1486 2148 1.503542 CCAAAGCTCGTGTGATGCC 59.496 57.895 0.00 0.00 0.00 4.40
1501 2163 2.894387 GCCAGCTGATCTCGGTGC 60.894 66.667 17.39 3.06 0.00 5.01
1516 2178 2.005537 GTGCTTCTTGCGCGTGTTG 61.006 57.895 8.43 0.00 46.63 3.33
1529 2192 1.522668 CGTGTTGCCATCTTCCTTCA 58.477 50.000 0.00 0.00 0.00 3.02
1539 2202 4.450419 GCCATCTTCCTTCAATAGATCACG 59.550 45.833 0.00 0.00 0.00 4.35
1548 2216 6.039493 TCCTTCAATAGATCACGTCTAGTTCC 59.961 42.308 0.00 0.00 42.50 3.62
1610 2310 2.358957 CCATCGTGCTCCAAGAAATCA 58.641 47.619 0.00 0.00 0.00 2.57
1621 2321 3.909995 TCCAAGAAATCAGAGGAGTCCAA 59.090 43.478 12.86 0.00 0.00 3.53
1622 2322 4.006319 CCAAGAAATCAGAGGAGTCCAAC 58.994 47.826 12.86 5.07 0.00 3.77
1623 2323 4.505566 CCAAGAAATCAGAGGAGTCCAACA 60.506 45.833 12.86 0.00 0.00 3.33
1624 2324 5.251764 CAAGAAATCAGAGGAGTCCAACAT 58.748 41.667 12.86 0.00 0.00 2.71
1626 2326 3.641434 AATCAGAGGAGTCCAACATGG 57.359 47.619 12.86 0.00 39.43 3.66
1629 2354 0.617413 AGAGGAGTCCAACATGGCAG 59.383 55.000 12.86 0.00 37.47 4.85
1694 2419 0.321919 TGAGCAGATCAACCTGTGGC 60.322 55.000 0.00 0.00 34.02 5.01
1732 2467 1.301558 GCAGATCCTCATGGCCTCG 60.302 63.158 3.32 0.00 0.00 4.63
1735 2470 0.188587 AGATCCTCATGGCCTCGGTA 59.811 55.000 3.32 0.00 0.00 4.02
1764 2499 2.826777 ATTCCCGCTGCCAAGGTCTG 62.827 60.000 0.00 0.00 0.00 3.51
1766 2501 2.032528 CCGCTGCCAAGGTCTGAA 59.967 61.111 0.00 0.00 0.00 3.02
1781 2517 2.093467 GTCTGAACTCTGAAGCGCAATC 59.907 50.000 11.47 8.39 0.00 2.67
1795 2531 1.325640 CGCAATCACAGAGATGTTCGG 59.674 52.381 0.00 0.00 36.96 4.30
1797 2533 2.625737 CAATCACAGAGATGTTCGGCT 58.374 47.619 0.00 0.00 36.96 5.52
1798 2534 2.593346 ATCACAGAGATGTTCGGCTC 57.407 50.000 0.00 0.00 35.06 4.70
1799 2535 1.550327 TCACAGAGATGTTCGGCTCT 58.450 50.000 0.00 0.00 41.95 4.09
1800 2536 1.474478 TCACAGAGATGTTCGGCTCTC 59.526 52.381 0.00 0.00 39.36 3.20
1809 2545 0.598562 GTTCGGCTCTCTCTCACACA 59.401 55.000 0.00 0.00 0.00 3.72
1820 2556 2.591429 TCACACAAGGGCACGCTG 60.591 61.111 0.00 0.00 0.00 5.18
1823 2559 4.954970 CACAAGGGCACGCTGGGT 62.955 66.667 0.00 0.00 0.00 4.51
1832 2568 2.426023 ACGCTGGGTGAACACTCC 59.574 61.111 2.27 4.35 0.00 3.85
1833 2569 2.738521 CGCTGGGTGAACACTCCG 60.739 66.667 2.27 0.00 0.00 4.63
1834 2570 2.358737 GCTGGGTGAACACTCCGG 60.359 66.667 0.00 0.00 33.73 5.14
1841 2577 0.889306 GTGAACACTCCGGTAGCTCT 59.111 55.000 0.00 0.00 0.00 4.09
1842 2578 1.135344 GTGAACACTCCGGTAGCTCTC 60.135 57.143 0.00 0.00 0.00 3.20
1847 2583 2.361992 TCCGGTAGCTCTCGCCAA 60.362 61.111 0.00 0.00 36.60 4.52
1848 2584 2.202756 CCGGTAGCTCTCGCCAAC 60.203 66.667 0.00 0.00 36.60 3.77
1885 2632 4.266070 GCGCGCCGGACATCTCTA 62.266 66.667 23.24 0.00 0.00 2.43
1886 2633 2.050895 CGCGCCGGACATCTCTAG 60.051 66.667 5.05 0.00 0.00 2.43
1887 2634 2.543802 CGCGCCGGACATCTCTAGA 61.544 63.158 5.05 0.00 0.00 2.43
1888 2635 1.008309 GCGCCGGACATCTCTAGAC 60.008 63.158 5.05 0.00 0.00 2.59
1889 2636 1.280142 CGCCGGACATCTCTAGACG 59.720 63.158 5.05 0.00 0.00 4.18
1890 2637 1.158484 CGCCGGACATCTCTAGACGA 61.158 60.000 5.05 0.00 0.00 4.20
1891 2638 1.240256 GCCGGACATCTCTAGACGAT 58.760 55.000 5.05 0.32 0.00 3.73
1892 2639 1.198178 GCCGGACATCTCTAGACGATC 59.802 57.143 5.05 0.00 0.00 3.69
1893 2640 2.773487 CCGGACATCTCTAGACGATCT 58.227 52.381 0.00 0.00 0.00 2.75
1894 2641 2.739913 CCGGACATCTCTAGACGATCTC 59.260 54.545 0.00 0.94 0.00 2.75
1895 2642 2.410392 CGGACATCTCTAGACGATCTCG 59.590 54.545 0.00 0.00 46.33 4.04
1896 2643 2.739913 GGACATCTCTAGACGATCTCGG 59.260 54.545 4.44 0.00 44.95 4.63
1897 2644 3.555377 GGACATCTCTAGACGATCTCGGA 60.555 52.174 4.44 0.00 44.95 4.55
1898 2645 4.250464 GACATCTCTAGACGATCTCGGAT 58.750 47.826 4.44 0.00 44.95 4.18
1899 2646 4.000325 ACATCTCTAGACGATCTCGGATG 59.000 47.826 10.98 10.98 44.95 3.51
1900 2647 4.249661 CATCTCTAGACGATCTCGGATGA 58.750 47.826 8.06 0.00 44.95 2.92
1901 2648 3.655486 TCTCTAGACGATCTCGGATGAC 58.345 50.000 4.44 0.00 44.95 3.06
1902 2649 2.739913 CTCTAGACGATCTCGGATGACC 59.260 54.545 4.44 0.00 44.95 4.02
1903 2650 1.807742 CTAGACGATCTCGGATGACCC 59.192 57.143 4.44 0.00 44.95 4.46
1923 2670 2.746277 GCACCCGGCAATCTTCGT 60.746 61.111 0.00 0.00 43.97 3.85
1924 2671 2.332654 GCACCCGGCAATCTTCGTT 61.333 57.895 0.00 0.00 43.97 3.85
1925 2672 1.862602 GCACCCGGCAATCTTCGTTT 61.863 55.000 0.00 0.00 43.97 3.60
1926 2673 1.444836 CACCCGGCAATCTTCGTTTA 58.555 50.000 0.00 0.00 0.00 2.01
1927 2674 1.807742 CACCCGGCAATCTTCGTTTAA 59.192 47.619 0.00 0.00 0.00 1.52
1928 2675 2.226912 CACCCGGCAATCTTCGTTTAAA 59.773 45.455 0.00 0.00 0.00 1.52
1929 2676 2.486592 ACCCGGCAATCTTCGTTTAAAG 59.513 45.455 0.00 0.00 0.00 1.85
1930 2677 2.745281 CCCGGCAATCTTCGTTTAAAGA 59.255 45.455 0.00 0.00 39.49 2.52
1931 2678 3.181510 CCCGGCAATCTTCGTTTAAAGAG 60.182 47.826 0.00 0.00 38.60 2.85
1932 2679 3.682858 CCGGCAATCTTCGTTTAAAGAGA 59.317 43.478 0.00 0.00 38.60 3.10
1933 2680 4.153475 CCGGCAATCTTCGTTTAAAGAGAA 59.847 41.667 0.00 6.06 38.60 2.87
1934 2681 5.080068 CGGCAATCTTCGTTTAAAGAGAAC 58.920 41.667 2.84 0.00 38.60 3.01
1935 2682 5.391449 GGCAATCTTCGTTTAAAGAGAACC 58.609 41.667 2.84 0.38 38.60 3.62
1936 2683 5.080068 GCAATCTTCGTTTAAAGAGAACCG 58.920 41.667 2.84 0.00 38.60 4.44
1937 2684 4.923264 ATCTTCGTTTAAAGAGAACCGC 57.077 40.909 2.84 0.00 38.60 5.68
1938 2685 3.719924 TCTTCGTTTAAAGAGAACCGCA 58.280 40.909 2.84 0.00 31.71 5.69
1939 2686 3.492011 TCTTCGTTTAAAGAGAACCGCAC 59.508 43.478 2.84 0.00 31.71 5.34
1940 2687 3.102052 TCGTTTAAAGAGAACCGCACT 57.898 42.857 0.00 0.00 0.00 4.40
1941 2688 2.798283 TCGTTTAAAGAGAACCGCACTG 59.202 45.455 0.00 0.00 0.00 3.66
1942 2689 2.798283 CGTTTAAAGAGAACCGCACTGA 59.202 45.455 0.00 0.00 0.00 3.41
1943 2690 3.362693 CGTTTAAAGAGAACCGCACTGAC 60.363 47.826 0.00 0.00 0.00 3.51
1944 2691 3.462483 TTAAAGAGAACCGCACTGACA 57.538 42.857 0.00 0.00 0.00 3.58
1945 2692 2.325583 AAAGAGAACCGCACTGACAA 57.674 45.000 0.00 0.00 0.00 3.18
1946 2693 2.325583 AAGAGAACCGCACTGACAAA 57.674 45.000 0.00 0.00 0.00 2.83
1947 2694 1.583054 AGAGAACCGCACTGACAAAC 58.417 50.000 0.00 0.00 0.00 2.93
1948 2695 1.139058 AGAGAACCGCACTGACAAACT 59.861 47.619 0.00 0.00 0.00 2.66
1949 2696 1.940613 GAGAACCGCACTGACAAACTT 59.059 47.619 0.00 0.00 0.00 2.66
1950 2697 3.128349 GAGAACCGCACTGACAAACTTA 58.872 45.455 0.00 0.00 0.00 2.24
1951 2698 3.740115 AGAACCGCACTGACAAACTTAT 58.260 40.909 0.00 0.00 0.00 1.73
1952 2699 4.134563 AGAACCGCACTGACAAACTTATT 58.865 39.130 0.00 0.00 0.00 1.40
1953 2700 4.578928 AGAACCGCACTGACAAACTTATTT 59.421 37.500 0.00 0.00 0.00 1.40
1954 2701 5.761234 AGAACCGCACTGACAAACTTATTTA 59.239 36.000 0.00 0.00 0.00 1.40
1955 2702 5.352643 ACCGCACTGACAAACTTATTTAC 57.647 39.130 0.00 0.00 0.00 2.01
1956 2703 5.061179 ACCGCACTGACAAACTTATTTACT 58.939 37.500 0.00 0.00 0.00 2.24
1957 2704 5.529800 ACCGCACTGACAAACTTATTTACTT 59.470 36.000 0.00 0.00 0.00 2.24
1958 2705 6.077838 CCGCACTGACAAACTTATTTACTTC 58.922 40.000 0.00 0.00 0.00 3.01
1959 2706 6.073222 CCGCACTGACAAACTTATTTACTTCT 60.073 38.462 0.00 0.00 0.00 2.85
1960 2707 7.352739 CGCACTGACAAACTTATTTACTTCTT 58.647 34.615 0.00 0.00 0.00 2.52
1961 2708 7.855904 CGCACTGACAAACTTATTTACTTCTTT 59.144 33.333 0.00 0.00 0.00 2.52
1962 2709 9.516314 GCACTGACAAACTTATTTACTTCTTTT 57.484 29.630 0.00 0.00 0.00 2.27
1991 2738 9.985730 TTCTTTTCTTCTTATACCGTTAGTTGA 57.014 29.630 0.00 0.00 0.00 3.18
1992 2739 9.985730 TCTTTTCTTCTTATACCGTTAGTTGAA 57.014 29.630 0.00 0.00 0.00 2.69
1994 2741 7.823149 TTCTTCTTATACCGTTAGTTGAAGC 57.177 36.000 0.00 0.00 32.36 3.86
1995 2742 6.335777 TCTTCTTATACCGTTAGTTGAAGCC 58.664 40.000 0.00 0.00 32.36 4.35
1996 2743 5.014808 TCTTATACCGTTAGTTGAAGCCC 57.985 43.478 0.00 0.00 0.00 5.19
1997 2744 2.704464 ATACCGTTAGTTGAAGCCCC 57.296 50.000 0.00 0.00 0.00 5.80
1998 2745 0.614812 TACCGTTAGTTGAAGCCCCC 59.385 55.000 0.00 0.00 0.00 5.40
1999 2746 1.743995 CCGTTAGTTGAAGCCCCCG 60.744 63.158 0.00 0.00 0.00 5.73
2000 2747 1.743995 CGTTAGTTGAAGCCCCCGG 60.744 63.158 0.00 0.00 0.00 5.73
2001 2748 1.377612 GTTAGTTGAAGCCCCCGGT 59.622 57.895 0.00 0.00 0.00 5.28
2002 2749 0.251033 GTTAGTTGAAGCCCCCGGTT 60.251 55.000 0.00 0.00 0.00 4.44
2003 2750 0.479378 TTAGTTGAAGCCCCCGGTTT 59.521 50.000 0.00 0.00 0.00 3.27
2004 2751 0.479378 TAGTTGAAGCCCCCGGTTTT 59.521 50.000 0.00 0.00 0.00 2.43
2005 2752 0.479378 AGTTGAAGCCCCCGGTTTTA 59.521 50.000 0.00 0.00 0.00 1.52
2006 2753 0.599558 GTTGAAGCCCCCGGTTTTAC 59.400 55.000 0.00 0.00 0.00 2.01
2007 2754 0.479378 TTGAAGCCCCCGGTTTTACT 59.521 50.000 0.00 0.00 0.00 2.24
2008 2755 0.250989 TGAAGCCCCCGGTTTTACTG 60.251 55.000 0.00 0.00 0.00 2.74
2009 2756 0.963856 GAAGCCCCCGGTTTTACTGG 60.964 60.000 0.00 0.00 44.36 4.00
2015 2762 3.436924 CGGTTTTACTGGGCCGGC 61.437 66.667 21.18 21.18 40.45 6.13
2016 2763 2.035155 GGTTTTACTGGGCCGGCT 59.965 61.111 28.56 9.11 0.00 5.52
2017 2764 2.340328 GGTTTTACTGGGCCGGCTG 61.340 63.158 28.56 18.82 0.00 4.85
2018 2765 1.302993 GTTTTACTGGGCCGGCTGA 60.303 57.895 28.56 12.30 0.00 4.26
2019 2766 0.679960 GTTTTACTGGGCCGGCTGAT 60.680 55.000 28.56 12.26 0.00 2.90
2020 2767 0.039035 TTTTACTGGGCCGGCTGATT 59.961 50.000 28.56 11.39 0.00 2.57
2021 2768 0.679640 TTTACTGGGCCGGCTGATTG 60.680 55.000 28.56 14.44 0.00 2.67
2022 2769 3.697439 TACTGGGCCGGCTGATTGC 62.697 63.158 28.56 8.16 41.94 3.56
2031 2778 3.365535 GCTGATTGCCAAACCGGT 58.634 55.556 0.00 0.00 36.97 5.28
2032 2779 1.212751 GCTGATTGCCAAACCGGTC 59.787 57.895 8.04 0.00 36.97 4.79
2033 2780 1.244019 GCTGATTGCCAAACCGGTCT 61.244 55.000 8.04 0.00 36.97 3.85
2034 2781 1.247567 CTGATTGCCAAACCGGTCTT 58.752 50.000 8.04 1.26 36.97 3.01
2035 2782 1.613437 CTGATTGCCAAACCGGTCTTT 59.387 47.619 8.04 0.00 36.97 2.52
2036 2783 2.035632 TGATTGCCAAACCGGTCTTTT 58.964 42.857 8.04 0.00 36.97 2.27
2037 2784 2.432510 TGATTGCCAAACCGGTCTTTTT 59.567 40.909 8.04 0.00 36.97 1.94
2038 2785 2.588027 TTGCCAAACCGGTCTTTTTC 57.412 45.000 8.04 0.00 36.97 2.29
2039 2786 0.747852 TGCCAAACCGGTCTTTTTCC 59.252 50.000 8.04 0.00 36.97 3.13
2040 2787 0.032952 GCCAAACCGGTCTTTTTCCC 59.967 55.000 8.04 0.00 36.97 3.97
2041 2788 1.404843 CCAAACCGGTCTTTTTCCCA 58.595 50.000 8.04 0.00 0.00 4.37
2042 2789 1.067974 CCAAACCGGTCTTTTTCCCAC 59.932 52.381 8.04 0.00 0.00 4.61
2043 2790 2.028876 CAAACCGGTCTTTTTCCCACT 58.971 47.619 8.04 0.00 0.00 4.00
2044 2791 3.215975 CAAACCGGTCTTTTTCCCACTA 58.784 45.455 8.04 0.00 0.00 2.74
2045 2792 3.801307 AACCGGTCTTTTTCCCACTAT 57.199 42.857 8.04 0.00 0.00 2.12
2046 2793 3.801307 ACCGGTCTTTTTCCCACTATT 57.199 42.857 0.00 0.00 0.00 1.73
2047 2794 4.108501 ACCGGTCTTTTTCCCACTATTT 57.891 40.909 0.00 0.00 0.00 1.40
2048 2795 4.476297 ACCGGTCTTTTTCCCACTATTTT 58.524 39.130 0.00 0.00 0.00 1.82
2049 2796 4.521639 ACCGGTCTTTTTCCCACTATTTTC 59.478 41.667 0.00 0.00 0.00 2.29
2050 2797 4.521256 CCGGTCTTTTTCCCACTATTTTCA 59.479 41.667 0.00 0.00 0.00 2.69
2051 2798 5.185056 CCGGTCTTTTTCCCACTATTTTCAT 59.815 40.000 0.00 0.00 0.00 2.57
2052 2799 6.295067 CCGGTCTTTTTCCCACTATTTTCATT 60.295 38.462 0.00 0.00 0.00 2.57
2053 2800 6.806739 CGGTCTTTTTCCCACTATTTTCATTC 59.193 38.462 0.00 0.00 0.00 2.67
2054 2801 7.097192 GGTCTTTTTCCCACTATTTTCATTCC 58.903 38.462 0.00 0.00 0.00 3.01
2055 2802 7.039011 GGTCTTTTTCCCACTATTTTCATTCCT 60.039 37.037 0.00 0.00 0.00 3.36
2056 2803 8.367911 GTCTTTTTCCCACTATTTTCATTCCTT 58.632 33.333 0.00 0.00 0.00 3.36
2057 2804 8.933653 TCTTTTTCCCACTATTTTCATTCCTTT 58.066 29.630 0.00 0.00 0.00 3.11
2058 2805 9.559732 CTTTTTCCCACTATTTTCATTCCTTTT 57.440 29.630 0.00 0.00 0.00 2.27
2059 2806 9.913310 TTTTTCCCACTATTTTCATTCCTTTTT 57.087 25.926 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.356442 CCGCCCGGTTTTTGCTGG 62.356 66.667 0.00 0.00 34.71 4.85
48 49 3.115390 CCACTTCATCCCTCCCTTCTTA 58.885 50.000 0.00 0.00 0.00 2.10
52 58 0.921256 CCCCACTTCATCCCTCCCTT 60.921 60.000 0.00 0.00 0.00 3.95
73 79 2.202492 CGCCGAGTCAGACTTCGG 60.202 66.667 25.42 25.42 39.88 4.30
74 80 2.202492 CCGCCGAGTCAGACTTCG 60.202 66.667 4.05 9.61 0.00 3.79
76 82 4.070552 GCCCGCCGAGTCAGACTT 62.071 66.667 4.05 0.00 0.00 3.01
99 136 3.720002 AGTTGAGAAAGTTTGGGGGAGTA 59.280 43.478 0.00 0.00 0.00 2.59
101 138 3.229697 AGTTGAGAAAGTTTGGGGGAG 57.770 47.619 0.00 0.00 0.00 4.30
106 143 7.041440 ACCAAAAACAAAGTTGAGAAAGTTTGG 60.041 33.333 18.16 13.94 43.71 3.28
110 147 7.041440 CCAAACCAAAAACAAAGTTGAGAAAGT 60.041 33.333 0.00 0.00 0.00 2.66
112 149 6.768381 ACCAAACCAAAAACAAAGTTGAGAAA 59.232 30.769 0.00 0.00 0.00 2.52
119 156 4.625607 TCCACCAAACCAAAAACAAAGT 57.374 36.364 0.00 0.00 0.00 2.66
129 166 2.761208 ACGTTCAAATTCCACCAAACCA 59.239 40.909 0.00 0.00 0.00 3.67
130 167 3.446310 ACGTTCAAATTCCACCAAACC 57.554 42.857 0.00 0.00 0.00 3.27
144 181 2.195096 CTGTCGTGGTTTGTACGTTCA 58.805 47.619 0.00 0.00 41.91 3.18
146 183 2.298411 ACTGTCGTGGTTTGTACGTT 57.702 45.000 0.00 0.00 41.91 3.99
148 185 2.963969 CAAACTGTCGTGGTTTGTACG 58.036 47.619 16.24 0.00 44.66 3.67
153 190 5.587043 TCTTTGTATCAAACTGTCGTGGTTT 59.413 36.000 0.00 0.00 37.37 3.27
159 196 5.465390 TCCAACTCTTTGTATCAAACTGTCG 59.535 40.000 0.00 0.00 0.00 4.35
160 197 6.861065 TCCAACTCTTTGTATCAAACTGTC 57.139 37.500 0.00 0.00 0.00 3.51
161 198 6.998074 TCATCCAACTCTTTGTATCAAACTGT 59.002 34.615 0.00 0.00 0.00 3.55
171 209 5.418840 ACTTTTGTGTCATCCAACTCTTTGT 59.581 36.000 0.00 0.00 0.00 2.83
173 211 5.894807 CACTTTTGTGTCATCCAACTCTTT 58.105 37.500 0.00 0.00 44.94 2.52
209 247 2.095466 CGCTGCTAAACATCCCGAAAAA 60.095 45.455 0.00 0.00 0.00 1.94
212 250 0.036765 ACGCTGCTAAACATCCCGAA 60.037 50.000 0.00 0.00 0.00 4.30
215 253 2.227865 TCAAAACGCTGCTAAACATCCC 59.772 45.455 0.00 0.00 0.00 3.85
222 260 2.487372 TCATGCATCAAAACGCTGCTAA 59.513 40.909 0.00 0.00 37.64 3.09
238 276 2.187707 GCATCACCAATTTCGTCATGC 58.812 47.619 0.00 0.00 0.00 4.06
243 281 2.799126 TAGGGCATCACCAATTTCGT 57.201 45.000 0.00 0.00 42.05 3.85
246 284 5.484998 AGAATGTTTAGGGCATCACCAATTT 59.515 36.000 0.00 0.00 42.05 1.82
247 285 5.025453 AGAATGTTTAGGGCATCACCAATT 58.975 37.500 0.00 0.00 42.05 2.32
248 286 4.403432 CAGAATGTTTAGGGCATCACCAAT 59.597 41.667 0.00 0.00 42.05 3.16
253 293 2.754552 GTGCAGAATGTTTAGGGCATCA 59.245 45.455 0.00 0.00 39.31 3.07
263 303 2.146342 CGAACAGGAGTGCAGAATGTT 58.854 47.619 6.29 6.29 39.31 2.71
273 313 1.594293 CAACGCACCGAACAGGAGT 60.594 57.895 0.00 0.00 45.00 3.85
274 314 2.317609 CCAACGCACCGAACAGGAG 61.318 63.158 0.00 0.00 45.00 3.69
278 318 1.593209 GAGTCCAACGCACCGAACA 60.593 57.895 0.00 0.00 0.00 3.18
282 322 2.355363 TTCGAGTCCAACGCACCG 60.355 61.111 0.00 0.00 0.00 4.94
339 379 9.952188 CGTTATCTTCCTTTTCTTTTCTTTTCT 57.048 29.630 0.00 0.00 0.00 2.52
340 380 9.181805 CCGTTATCTTCCTTTTCTTTTCTTTTC 57.818 33.333 0.00 0.00 0.00 2.29
790 874 1.445716 CGAGCTAGGTAGGTGGGACG 61.446 65.000 0.00 0.00 33.58 4.79
791 875 0.395448 ACGAGCTAGGTAGGTGGGAC 60.395 60.000 6.99 0.00 34.46 4.46
792 876 0.395311 CACGAGCTAGGTAGGTGGGA 60.395 60.000 14.63 0.00 34.46 4.37
793 877 0.683504 ACACGAGCTAGGTAGGTGGG 60.684 60.000 22.27 6.99 34.46 4.61
853 937 2.148768 GCAACGGGTGGGCTTATATAC 58.851 52.381 0.00 0.00 0.00 1.47
910 998 1.351153 GAAGTGTAGCGAAGGAGTGC 58.649 55.000 0.00 0.00 0.00 4.40
920 1008 2.750948 TGGAAGTGAACGAAGTGTAGC 58.249 47.619 0.00 0.00 45.00 3.58
964 1597 2.239654 ACACCCTCTCTCTCTCTCTCTG 59.760 54.545 0.00 0.00 0.00 3.35
981 1614 3.066621 TCATCTTTGCTTCAACACACACC 59.933 43.478 0.00 0.00 0.00 4.16
1026 1662 3.847602 CTGCTCAGGCCTCCTCCG 61.848 72.222 0.00 0.00 37.74 4.63
1121 1761 2.198703 ATGGAGCGAGGGATCGGA 59.801 61.111 0.00 0.00 0.00 4.55
1122 1762 2.341543 CATGGAGCGAGGGATCGG 59.658 66.667 0.00 0.00 0.00 4.18
1123 1763 1.539560 ATCCATGGAGCGAGGGATCG 61.540 60.000 21.33 0.00 35.22 3.69
1124 1764 0.036577 CATCCATGGAGCGAGGGATC 60.037 60.000 21.33 0.00 38.05 3.36
1125 1765 2.064628 CATCCATGGAGCGAGGGAT 58.935 57.895 21.33 0.00 40.71 3.85
1193 1849 4.801891 CACAATCACAGACCCAAAATCAG 58.198 43.478 0.00 0.00 0.00 2.90
1224 1880 1.819632 CTACCTGCCGGCACCATTC 60.820 63.158 29.03 0.00 0.00 2.67
1232 1888 1.820519 TGTACAAGTACTACCTGCCGG 59.179 52.381 11.27 0.00 37.00 6.13
1275 1932 6.572703 GCTTTGCTACCACTTCTACTTCTACT 60.573 42.308 0.00 0.00 0.00 2.57
1276 1933 5.577554 GCTTTGCTACCACTTCTACTTCTAC 59.422 44.000 0.00 0.00 0.00 2.59
1277 1934 5.245301 TGCTTTGCTACCACTTCTACTTCTA 59.755 40.000 0.00 0.00 0.00 2.10
1278 1935 4.040461 TGCTTTGCTACCACTTCTACTTCT 59.960 41.667 0.00 0.00 0.00 2.85
1279 1936 4.315803 TGCTTTGCTACCACTTCTACTTC 58.684 43.478 0.00 0.00 0.00 3.01
1280 1937 4.351874 TGCTTTGCTACCACTTCTACTT 57.648 40.909 0.00 0.00 0.00 2.24
1290 1947 3.728845 TCGATCCTATTGCTTTGCTACC 58.271 45.455 0.00 0.00 0.00 3.18
1292 1949 5.474578 AGATCGATCCTATTGCTTTGCTA 57.525 39.130 21.66 0.00 0.00 3.49
1315 1972 1.493772 GTGGTGAATCGACGAACACA 58.506 50.000 27.05 15.45 35.33 3.72
1321 1978 0.179134 GAGGAGGTGGTGAATCGACG 60.179 60.000 0.00 0.00 0.00 5.12
1324 1981 0.460987 GCAGAGGAGGTGGTGAATCG 60.461 60.000 0.00 0.00 0.00 3.34
1343 2000 4.052518 CTGCAAGGGGGTGGAGGG 62.053 72.222 0.00 0.00 33.61 4.30
1348 2005 2.203538 ACTTGCTGCAAGGGGGTG 60.204 61.111 36.97 18.71 44.81 4.61
1357 2014 1.510480 GGGACAGACACACTTGCTGC 61.510 60.000 0.00 0.00 32.94 5.25
1358 2015 0.179048 TGGGACAGACACACTTGCTG 60.179 55.000 0.00 0.00 34.73 4.41
1359 2016 2.220953 TGGGACAGACACACTTGCT 58.779 52.632 0.00 0.00 0.00 3.91
1360 2017 4.876701 TGGGACAGACACACTTGC 57.123 55.556 0.00 0.00 0.00 4.01
1364 2021 9.980084 TGTAACTGTACAATGGGACAGACACAC 62.980 44.444 20.05 10.64 44.88 3.82
1365 2022 8.091650 TGTAACTGTACAATGGGACAGACACA 62.092 42.308 20.05 17.40 44.88 3.72
1366 2023 5.740803 TGTAACTGTACAATGGGACAGACAC 60.741 44.000 20.05 15.18 44.88 3.67
1367 2024 4.345547 TGTAACTGTACAATGGGACAGACA 59.654 41.667 20.05 10.97 44.88 3.41
1370 2027 5.351465 GTGATGTAACTGTACAATGGGACAG 59.649 44.000 11.27 11.27 46.95 3.51
1385 2042 3.486108 CGAGTATTCGGCAGTGATGTAAC 59.514 47.826 0.00 0.00 43.05 2.50
1406 2063 6.529463 TCAGTTGATATATTGCATCACACG 57.471 37.500 0.00 0.00 32.23 4.49
1408 2065 8.735692 TCTTTCAGTTGATATATTGCATCACA 57.264 30.769 0.00 0.00 32.23 3.58
1409 2066 9.049523 TCTCTTTCAGTTGATATATTGCATCAC 57.950 33.333 0.00 0.00 32.23 3.06
1410 2067 9.617523 TTCTCTTTCAGTTGATATATTGCATCA 57.382 29.630 0.00 0.00 0.00 3.07
1425 2082 3.307059 CCGGTGATTCCTTCTCTTTCAGT 60.307 47.826 0.00 0.00 0.00 3.41
1444 2104 1.160329 GGGACAAGCGATTGATCCGG 61.160 60.000 21.96 0.00 0.00 5.14
1445 2105 1.160329 GGGGACAAGCGATTGATCCG 61.160 60.000 21.96 0.00 0.00 4.18
1467 2129 1.503542 GCATCACACGAGCTTTGGG 59.496 57.895 0.00 0.00 0.00 4.12
1486 2148 0.175302 AGAAGCACCGAGATCAGCTG 59.825 55.000 7.63 7.63 37.41 4.24
1501 2163 2.427410 GGCAACACGCGCAAGAAG 60.427 61.111 5.73 0.00 43.84 2.85
1516 2178 4.450419 CGTGATCTATTGAAGGAAGATGGC 59.550 45.833 0.00 0.00 30.19 4.40
1554 2222 1.993956 CTGGACATGTGGTGGGAAAA 58.006 50.000 1.15 0.00 0.00 2.29
1555 2223 0.539438 GCTGGACATGTGGTGGGAAA 60.539 55.000 1.15 0.00 0.00 3.13
1556 2224 1.074775 GCTGGACATGTGGTGGGAA 59.925 57.895 1.15 0.00 0.00 3.97
1557 2225 2.152729 TGCTGGACATGTGGTGGGA 61.153 57.895 1.15 0.00 0.00 4.37
1558 2226 1.973281 GTGCTGGACATGTGGTGGG 60.973 63.158 1.15 0.00 0.00 4.61
1560 2228 1.073722 AGGTGCTGGACATGTGGTG 59.926 57.895 1.15 0.00 0.00 4.17
1561 2229 1.073722 CAGGTGCTGGACATGTGGT 59.926 57.895 1.15 0.00 31.44 4.16
1562 2230 2.338015 GCAGGTGCTGGACATGTGG 61.338 63.158 15.06 0.00 38.67 4.17
1563 2231 3.271014 GCAGGTGCTGGACATGTG 58.729 61.111 15.06 3.84 38.67 3.21
1610 2310 0.617413 CTGCCATGTTGGACTCCTCT 59.383 55.000 0.00 0.00 40.96 3.69
1718 2443 1.270907 GATACCGAGGCCATGAGGAT 58.729 55.000 5.01 0.00 36.89 3.24
1764 2499 1.800586 TGTGATTGCGCTTCAGAGTTC 59.199 47.619 9.73 0.56 0.00 3.01
1766 2501 1.001293 TCTGTGATTGCGCTTCAGAGT 59.999 47.619 25.71 0.00 36.26 3.24
1781 2517 1.919918 GAGAGCCGAACATCTCTGTG 58.080 55.000 0.00 0.00 39.57 3.66
1795 2531 0.390998 GCCCTTGTGTGAGAGAGAGC 60.391 60.000 0.00 0.00 0.00 4.09
1797 2533 0.681733 GTGCCCTTGTGTGAGAGAGA 59.318 55.000 0.00 0.00 0.00 3.10
1798 2534 0.668706 CGTGCCCTTGTGTGAGAGAG 60.669 60.000 0.00 0.00 0.00 3.20
1799 2535 1.367471 CGTGCCCTTGTGTGAGAGA 59.633 57.895 0.00 0.00 0.00 3.10
1800 2536 2.320587 GCGTGCCCTTGTGTGAGAG 61.321 63.158 0.00 0.00 0.00 3.20
1801 2537 2.280797 GCGTGCCCTTGTGTGAGA 60.281 61.111 0.00 0.00 0.00 3.27
1809 2545 3.884774 TTCACCCAGCGTGCCCTT 61.885 61.111 0.00 0.00 42.69 3.95
1820 2556 1.079336 GCTACCGGAGTGTTCACCC 60.079 63.158 9.46 0.77 0.00 4.61
1823 2559 1.174783 GAGAGCTACCGGAGTGTTCA 58.825 55.000 9.46 0.00 0.00 3.18
1824 2560 0.099082 CGAGAGCTACCGGAGTGTTC 59.901 60.000 9.46 5.12 0.00 3.18
1825 2561 2.181584 CGAGAGCTACCGGAGTGTT 58.818 57.895 9.46 0.00 0.00 3.32
1826 2562 3.906718 CGAGAGCTACCGGAGTGT 58.093 61.111 9.46 0.00 0.00 3.55
1841 2577 2.046023 CCCTCTGCATGTTGGCGA 60.046 61.111 0.00 0.00 36.28 5.54
1842 2578 3.136123 CCCCTCTGCATGTTGGCG 61.136 66.667 0.00 0.00 36.28 5.69
1871 2615 1.158484 TCGTCTAGAGATGTCCGGCG 61.158 60.000 0.00 0.00 33.00 6.46
1872 2616 1.198178 GATCGTCTAGAGATGTCCGGC 59.802 57.143 0.00 0.00 33.00 6.13
1885 2632 2.721945 GGGTCATCCGAGATCGTCT 58.278 57.895 1.09 0.00 37.74 4.18
1904 2651 3.140814 GAAGATTGCCGGGTGCCC 61.141 66.667 2.18 0.00 40.16 5.36
1905 2652 3.508840 CGAAGATTGCCGGGTGCC 61.509 66.667 2.18 0.00 40.16 5.01
1906 2653 1.862602 AAACGAAGATTGCCGGGTGC 61.863 55.000 2.18 0.00 41.77 5.01
1907 2654 1.444836 TAAACGAAGATTGCCGGGTG 58.555 50.000 2.18 0.00 0.00 4.61
1908 2655 2.188062 TTAAACGAAGATTGCCGGGT 57.812 45.000 2.18 0.00 0.00 5.28
1909 2656 2.745281 TCTTTAAACGAAGATTGCCGGG 59.255 45.455 2.18 0.00 30.98 5.73
1910 2657 3.682858 TCTCTTTAAACGAAGATTGCCGG 59.317 43.478 0.00 0.00 35.27 6.13
1911 2658 4.921470 TCTCTTTAAACGAAGATTGCCG 57.079 40.909 0.00 0.00 35.27 5.69
1912 2659 5.391449 GGTTCTCTTTAAACGAAGATTGCC 58.609 41.667 0.00 0.00 35.27 4.52
1913 2660 5.080068 CGGTTCTCTTTAAACGAAGATTGC 58.920 41.667 0.00 0.00 42.12 3.56
1914 2661 5.080068 GCGGTTCTCTTTAAACGAAGATTG 58.920 41.667 0.00 0.00 42.12 2.67
1915 2662 4.753107 TGCGGTTCTCTTTAAACGAAGATT 59.247 37.500 0.00 0.00 42.12 2.40
1916 2663 4.151867 GTGCGGTTCTCTTTAAACGAAGAT 59.848 41.667 0.00 0.00 42.12 2.40
1917 2664 3.492011 GTGCGGTTCTCTTTAAACGAAGA 59.508 43.478 0.00 0.00 42.12 2.87
1918 2665 3.493503 AGTGCGGTTCTCTTTAAACGAAG 59.506 43.478 0.00 0.00 42.12 3.79
1919 2666 3.246699 CAGTGCGGTTCTCTTTAAACGAA 59.753 43.478 0.00 0.00 42.12 3.85
1920 2667 2.798283 CAGTGCGGTTCTCTTTAAACGA 59.202 45.455 0.00 0.00 42.12 3.85
1921 2668 2.798283 TCAGTGCGGTTCTCTTTAAACG 59.202 45.455 0.00 0.00 42.43 3.60
1922 2669 3.558418 TGTCAGTGCGGTTCTCTTTAAAC 59.442 43.478 0.00 0.00 0.00 2.01
1923 2670 3.799366 TGTCAGTGCGGTTCTCTTTAAA 58.201 40.909 0.00 0.00 0.00 1.52
1924 2671 3.462483 TGTCAGTGCGGTTCTCTTTAA 57.538 42.857 0.00 0.00 0.00 1.52
1925 2672 3.462483 TTGTCAGTGCGGTTCTCTTTA 57.538 42.857 0.00 0.00 0.00 1.85
1926 2673 2.325583 TTGTCAGTGCGGTTCTCTTT 57.674 45.000 0.00 0.00 0.00 2.52
1927 2674 1.940613 GTTTGTCAGTGCGGTTCTCTT 59.059 47.619 0.00 0.00 0.00 2.85
1928 2675 1.139058 AGTTTGTCAGTGCGGTTCTCT 59.861 47.619 0.00 0.00 0.00 3.10
1929 2676 1.583054 AGTTTGTCAGTGCGGTTCTC 58.417 50.000 0.00 0.00 0.00 2.87
1930 2677 2.038387 AAGTTTGTCAGTGCGGTTCT 57.962 45.000 0.00 0.00 0.00 3.01
1931 2678 4.483476 AATAAGTTTGTCAGTGCGGTTC 57.517 40.909 0.00 0.00 0.00 3.62
1932 2679 4.911514 AAATAAGTTTGTCAGTGCGGTT 57.088 36.364 0.00 0.00 0.00 4.44
1933 2680 5.061179 AGTAAATAAGTTTGTCAGTGCGGT 58.939 37.500 0.00 0.00 0.00 5.68
1934 2681 5.607119 AGTAAATAAGTTTGTCAGTGCGG 57.393 39.130 0.00 0.00 0.00 5.69
1935 2682 6.888430 AGAAGTAAATAAGTTTGTCAGTGCG 58.112 36.000 0.00 0.00 0.00 5.34
1936 2683 9.516314 AAAAGAAGTAAATAAGTTTGTCAGTGC 57.484 29.630 0.00 0.00 0.00 4.40
1965 2712 9.985730 TCAACTAACGGTATAAGAAGAAAAGAA 57.014 29.630 0.00 0.00 0.00 2.52
1966 2713 9.985730 TTCAACTAACGGTATAAGAAGAAAAGA 57.014 29.630 0.00 0.00 0.00 2.52
1968 2715 8.715088 GCTTCAACTAACGGTATAAGAAGAAAA 58.285 33.333 15.79 0.00 34.66 2.29
1969 2716 7.332678 GGCTTCAACTAACGGTATAAGAAGAAA 59.667 37.037 15.79 0.00 34.66 2.52
1970 2717 6.815142 GGCTTCAACTAACGGTATAAGAAGAA 59.185 38.462 15.79 2.00 34.66 2.52
1971 2718 6.335777 GGCTTCAACTAACGGTATAAGAAGA 58.664 40.000 15.79 0.00 34.66 2.87
1972 2719 5.522824 GGGCTTCAACTAACGGTATAAGAAG 59.477 44.000 10.06 10.06 35.55 2.85
1973 2720 5.422145 GGGCTTCAACTAACGGTATAAGAA 58.578 41.667 0.00 0.00 0.00 2.52
1974 2721 4.141869 GGGGCTTCAACTAACGGTATAAGA 60.142 45.833 0.00 0.00 0.00 2.10
1975 2722 4.124970 GGGGCTTCAACTAACGGTATAAG 58.875 47.826 0.00 0.00 0.00 1.73
1976 2723 3.118298 GGGGGCTTCAACTAACGGTATAA 60.118 47.826 0.00 0.00 0.00 0.98
1977 2724 2.435437 GGGGGCTTCAACTAACGGTATA 59.565 50.000 0.00 0.00 0.00 1.47
1978 2725 1.211212 GGGGGCTTCAACTAACGGTAT 59.789 52.381 0.00 0.00 0.00 2.73
1979 2726 0.614812 GGGGGCTTCAACTAACGGTA 59.385 55.000 0.00 0.00 0.00 4.02
1980 2727 1.377612 GGGGGCTTCAACTAACGGT 59.622 57.895 0.00 0.00 0.00 4.83
1981 2728 1.743995 CGGGGGCTTCAACTAACGG 60.744 63.158 0.00 0.00 0.00 4.44
1982 2729 1.743995 CCGGGGGCTTCAACTAACG 60.744 63.158 0.00 0.00 0.00 3.18
1983 2730 0.251033 AACCGGGGGCTTCAACTAAC 60.251 55.000 6.32 0.00 0.00 2.34
1984 2731 0.479378 AAACCGGGGGCTTCAACTAA 59.521 50.000 6.32 0.00 0.00 2.24
1985 2732 0.479378 AAAACCGGGGGCTTCAACTA 59.521 50.000 6.32 0.00 0.00 2.24
1986 2733 0.479378 TAAAACCGGGGGCTTCAACT 59.521 50.000 6.32 0.00 0.00 3.16
1987 2734 0.599558 GTAAAACCGGGGGCTTCAAC 59.400 55.000 6.32 0.00 0.00 3.18
1988 2735 0.479378 AGTAAAACCGGGGGCTTCAA 59.521 50.000 6.32 0.00 0.00 2.69
1989 2736 0.250989 CAGTAAAACCGGGGGCTTCA 60.251 55.000 6.32 0.00 0.00 3.02
1990 2737 0.963856 CCAGTAAAACCGGGGGCTTC 60.964 60.000 6.32 0.00 0.00 3.86
1991 2738 1.076014 CCAGTAAAACCGGGGGCTT 59.924 57.895 6.32 0.00 0.00 4.35
1992 2739 2.761160 CCAGTAAAACCGGGGGCT 59.239 61.111 6.32 0.00 0.00 5.19
1993 2740 2.361992 CCCAGTAAAACCGGGGGC 60.362 66.667 6.32 0.00 36.90 5.80
1994 2741 2.361992 GCCCAGTAAAACCGGGGG 60.362 66.667 6.32 5.76 41.07 5.40
1995 2742 2.361992 GGCCCAGTAAAACCGGGG 60.362 66.667 6.32 0.00 43.72 5.73
1996 2743 2.748647 CGGCCCAGTAAAACCGGG 60.749 66.667 6.32 0.00 41.95 5.73
1998 2745 3.436924 GCCGGCCCAGTAAAACCG 61.437 66.667 18.11 0.00 45.21 4.44
1999 2746 2.035155 AGCCGGCCCAGTAAAACC 59.965 61.111 26.15 0.00 0.00 3.27
2000 2747 0.679960 ATCAGCCGGCCCAGTAAAAC 60.680 55.000 26.15 0.00 0.00 2.43
2001 2748 0.039035 AATCAGCCGGCCCAGTAAAA 59.961 50.000 26.15 0.00 0.00 1.52
2002 2749 0.679640 CAATCAGCCGGCCCAGTAAA 60.680 55.000 26.15 0.54 0.00 2.01
2003 2750 1.077787 CAATCAGCCGGCCCAGTAA 60.078 57.895 26.15 2.20 0.00 2.24
2004 2751 2.589540 CAATCAGCCGGCCCAGTA 59.410 61.111 26.15 4.27 0.00 2.74
2014 2761 1.212751 GACCGGTTTGGCAATCAGC 59.787 57.895 9.42 0.00 43.94 4.26
2015 2762 1.247567 AAGACCGGTTTGGCAATCAG 58.752 50.000 9.42 0.57 43.94 2.90
2016 2763 1.698506 AAAGACCGGTTTGGCAATCA 58.301 45.000 9.42 0.00 43.94 2.57
2017 2764 2.812358 AAAAGACCGGTTTGGCAATC 57.188 45.000 9.42 0.00 43.94 2.67
2018 2765 2.224185 GGAAAAAGACCGGTTTGGCAAT 60.224 45.455 9.42 0.00 43.94 3.56
2019 2766 1.137282 GGAAAAAGACCGGTTTGGCAA 59.863 47.619 9.42 0.00 43.94 4.52
2020 2767 0.747852 GGAAAAAGACCGGTTTGGCA 59.252 50.000 9.42 0.00 43.94 4.92
2021 2768 0.032952 GGGAAAAAGACCGGTTTGGC 59.967 55.000 9.42 0.00 43.94 4.52
2022 2769 1.067974 GTGGGAAAAAGACCGGTTTGG 59.932 52.381 9.42 0.00 46.41 3.28
2023 2770 2.028876 AGTGGGAAAAAGACCGGTTTG 58.971 47.619 9.42 0.00 0.00 2.93
2024 2771 2.447408 AGTGGGAAAAAGACCGGTTT 57.553 45.000 9.42 0.00 0.00 3.27
2025 2772 3.801307 ATAGTGGGAAAAAGACCGGTT 57.199 42.857 9.42 0.00 0.00 4.44
2026 2773 3.801307 AATAGTGGGAAAAAGACCGGT 57.199 42.857 6.92 6.92 0.00 5.28
2027 2774 4.521256 TGAAAATAGTGGGAAAAAGACCGG 59.479 41.667 0.00 0.00 0.00 5.28
2028 2775 5.699097 TGAAAATAGTGGGAAAAAGACCG 57.301 39.130 0.00 0.00 0.00 4.79
2029 2776 7.039011 AGGAATGAAAATAGTGGGAAAAAGACC 60.039 37.037 0.00 0.00 0.00 3.85
2030 2777 7.896811 AGGAATGAAAATAGTGGGAAAAAGAC 58.103 34.615 0.00 0.00 0.00 3.01
2031 2778 8.491045 AAGGAATGAAAATAGTGGGAAAAAGA 57.509 30.769 0.00 0.00 0.00 2.52
2032 2779 9.559732 AAAAGGAATGAAAATAGTGGGAAAAAG 57.440 29.630 0.00 0.00 0.00 2.27
2033 2780 9.913310 AAAAAGGAATGAAAATAGTGGGAAAAA 57.087 25.926 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.