Multiple sequence alignment - TraesCS5D01G369900

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 TraesCS5D01G369900 chr5D 100.000 2510 0 0 1 2510 445063930 445061421 0.000000e+00 4636.0
1 TraesCS5D01G369900 chr5D 95.588 408 16 2 1837 2243 100116685 100116279 0.000000e+00 652.0
2 TraesCS5D01G369900 chr5D 86.738 558 42 18 1031 1581 444976513 444975981 2.150000e-165 592.0
3 TraesCS5D01G369900 chr5D 85.197 608 35 25 995 1587 445056149 445055582 7.790000e-160 573.0
4 TraesCS5D01G369900 chr5D 83.730 504 46 13 1007 1510 445072925 445072458 6.370000e-121 444.0
5 TraesCS5D01G369900 chr5D 81.193 218 20 10 2299 2510 445055173 445054971 3.340000e-34 156.0
6 TraesCS5D01G369900 chr5D 97.619 42 1 0 2240 2281 135241220 135241261 3.460000e-09 73.1
7 TraesCS5D01G369900 chr5D 89.796 49 4 1 2249 2296 438782902 438782950 7.500000e-06 62.1
8 TraesCS5D01G369900 chr5A 94.535 1171 44 10 443 1599 562109157 562107993 0.000000e+00 1790.0
9 TraesCS5D01G369900 chr5A 83.308 665 54 30 1031 1681 562100998 562100377 6.060000e-156 560.0
10 TraesCS5D01G369900 chr5A 91.247 377 22 4 76 446 562109598 562109227 1.040000e-138 503.0
11 TraesCS5D01G369900 chr5A 84.646 508 46 12 1007 1510 562116955 562116476 6.280000e-131 477.0
12 TraesCS5D01G369900 chr5A 97.248 218 4 1 2295 2510 562107775 562107558 3.940000e-98 368.0
13 TraesCS5D01G369900 chr5A 92.481 133 8 2 1688 1818 562107988 562107856 3.300000e-44 189.0
14 TraesCS5D01G369900 chr5A 80.110 181 11 12 2295 2464 562100158 562099992 7.340000e-21 111.0
15 TraesCS5D01G369900 chr5B 93.534 1160 52 11 443 1588 542320772 542319622 0.000000e+00 1705.0
16 TraesCS5D01G369900 chr5B 87.633 469 26 11 1 442 542321312 542320849 1.330000e-142 516.0
17 TraesCS5D01G369900 chr5B 83.272 544 27 26 998 1539 542295726 542295245 2.290000e-120 442.0
18 TraesCS5D01G369900 chr5B 95.370 216 8 2 2295 2510 542319015 542318802 2.390000e-90 342.0
19 TraesCS5D01G369900 chr5B 80.473 507 48 18 1007 1510 542331414 542330956 8.600000e-90 340.0
20 TraesCS5D01G369900 chr5B 86.777 121 13 3 2391 2510 542294905 542294787 5.630000e-27 132.0
21 TraesCS5D01G369900 chr5B 87.209 86 4 1 1692 1777 542319520 542319442 9.560000e-15 91.6
22 TraesCS5D01G369900 chr5B 93.750 48 2 1 2249 2295 10359069 10359022 1.250000e-08 71.3
23 TraesCS5D01G369900 chr2D 95.652 414 15 3 1833 2244 11204612 11204200 0.000000e+00 662.0
24 TraesCS5D01G369900 chr2D 94.724 417 20 2 1827 2243 324034989 324035403 0.000000e+00 647.0
25 TraesCS5D01G369900 chr2D 94.903 412 18 3 1834 2243 151430991 151430581 2.100000e-180 641.0
26 TraesCS5D01G369900 chr2D 94.471 416 18 5 1834 2249 538776486 538776896 9.790000e-179 636.0
27 TraesCS5D01G369900 chr7D 95.411 414 15 4 1834 2243 573826374 573825961 0.000000e+00 656.0
28 TraesCS5D01G369900 chr7D 95.411 414 14 5 1833 2243 101249218 101249629 0.000000e+00 654.0
29 TraesCS5D01G369900 chr7D 89.130 92 9 1 577 667 539768275 539768184 2.040000e-21 113.0
30 TraesCS5D01G369900 chr1D 95.146 412 14 5 1834 2243 1148943 1148536 0.000000e+00 645.0
31 TraesCS5D01G369900 chr3D 94.712 416 12 6 1834 2243 531260067 531260478 2.720000e-179 638.0
32 TraesCS5D01G369900 chr3D 94.118 51 1 2 2245 2293 47799567 47799617 2.680000e-10 76.8
33 TraesCS5D01G369900 chr3D 90.196 51 4 1 2249 2298 497907998 497907948 5.800000e-07 65.8
34 TraesCS5D01G369900 chr2B 90.741 54 2 3 2249 2299 397006136 397006083 4.480000e-08 69.4
35 TraesCS5D01G369900 chr4B 95.238 42 2 0 576 617 462511565 462511606 1.610000e-07 67.6
36 TraesCS5D01G369900 chr4B 87.500 56 5 2 2249 2303 90721535 90721481 2.080000e-06 63.9
37 TraesCS5D01G369900 chr3A 88.136 59 3 3 2251 2307 353643376 353643432 1.610000e-07 67.6
38 TraesCS5D01G369900 chr6B 91.667 48 3 1 2247 2293 186694529 186694576 5.800000e-07 65.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G369900 chr5D 445061421 445063930 2509 True 4636.00 4636 100.00000 1 2510 1 chr5D.!!$R3 2509
1 TraesCS5D01G369900 chr5D 444975981 444976513 532 True 592.00 592 86.73800 1031 1581 1 chr5D.!!$R2 550
2 TraesCS5D01G369900 chr5D 445054971 445056149 1178 True 364.50 573 83.19500 995 2510 2 chr5D.!!$R5 1515
3 TraesCS5D01G369900 chr5A 562107558 562109598 2040 True 712.50 1790 93.87775 76 2510 4 chr5A.!!$R3 2434
4 TraesCS5D01G369900 chr5A 562099992 562100998 1006 True 335.50 560 81.70900 1031 2464 2 chr5A.!!$R2 1433
5 TraesCS5D01G369900 chr5B 542318802 542321312 2510 True 663.65 1705 90.93650 1 2510 4 chr5B.!!$R4 2509
6 TraesCS5D01G369900 chr5B 542294787 542295726 939 True 287.00 442 85.02450 998 2510 2 chr5B.!!$R3 1512

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
113 135 0.040067 CCGAGTGGCTTTGCAAAGTC 60.04 55.0 31.99 31.99 40.93 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2590 0.665835 TGCCTGCAAAAATTCGTCGT 59.334 45.0 0.0 0.0 0.0 4.34 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
69 70 2.693069 CAGAGAGTGGTTTGCAGGTAG 58.307 52.381 0.00 0.00 0.00 3.18
94 116 6.348050 GCATTGGAGAAACGGATCATTATCTC 60.348 42.308 0.00 2.37 34.08 2.75
113 135 0.040067 CCGAGTGGCTTTGCAAAGTC 60.040 55.000 31.99 31.99 40.93 3.01
199 223 7.280876 TGAAAAGTACCATCATGCTGAGATAAC 59.719 37.037 0.00 0.00 0.00 1.89
207 231 4.910195 TCATGCTGAGATAACCACAACTT 58.090 39.130 0.00 0.00 0.00 2.66
350 378 4.209080 ACAAACAAAAGAAAAGCTATGCGC 59.791 37.500 0.00 0.00 39.57 6.09
351 379 2.584791 ACAAAAGAAAAGCTATGCGCG 58.415 42.857 0.00 0.00 45.59 6.86
352 380 1.318491 CAAAAGAAAAGCTATGCGCGC 59.682 47.619 27.26 27.26 45.59 6.86
353 381 0.521242 AAAGAAAAGCTATGCGCGCG 60.521 50.000 28.44 28.44 45.59 6.86
374 402 2.001812 CACACTCGACTCATCCCTTG 57.998 55.000 0.00 0.00 0.00 3.61
439 469 2.827921 CTGGAACAAAAGCCTAGCCATT 59.172 45.455 0.00 0.00 38.70 3.16
457 563 2.380064 TTCAATGTCACCCAGGCTTT 57.620 45.000 0.00 0.00 0.00 3.51
525 631 2.670905 GCACTACGTATGCACATGAACA 59.329 45.455 18.83 0.00 42.88 3.18
559 665 0.536460 TGAAGTCTCCCCCGCAAAAC 60.536 55.000 0.00 0.00 0.00 2.43
575 682 5.902981 CCGCAAAACAAAAATCATTGAAGTG 59.097 36.000 0.00 0.00 34.38 3.16
622 729 0.521291 GCGCACTTTATTGCACAGGA 59.479 50.000 0.30 0.00 43.15 3.86
903 1015 2.492484 CTCCTCTTTATATACCGGCGCT 59.508 50.000 7.64 0.00 0.00 5.92
931 1046 1.080772 CTCGCTCGCTAACACCACA 60.081 57.895 0.00 0.00 0.00 4.17
945 1060 2.581354 CACAGCTTCCTCTCCCCG 59.419 66.667 0.00 0.00 0.00 5.73
1038 1153 4.435436 CCGCAGTCGCACCAGCTA 62.435 66.667 0.00 0.00 38.40 3.32
1326 1480 0.318441 CGACTGCTTCCTCTTCCACA 59.682 55.000 0.00 0.00 0.00 4.17
1419 1576 1.067416 GACGATGGCGCCACTGATA 59.933 57.895 35.50 8.13 42.48 2.15
1581 1763 7.661536 TGGATATAAGTCTAGCTTGTCAACT 57.338 36.000 0.00 0.00 38.05 3.16
1602 1787 6.882768 ACTAGTACTACCAGTACCAGTACT 57.117 41.667 21.27 21.27 46.59 2.73
1603 1788 6.883744 ACTAGTACTACCAGTACCAGTACTC 58.116 44.000 21.20 0.00 46.59 2.59
1604 1789 6.406400 ACTAGTACTACCAGTACCAGTACTCG 60.406 46.154 21.20 18.65 46.59 4.18
1605 1790 2.996631 ACTACCAGTACCAGTACTCGG 58.003 52.381 17.58 17.58 43.98 4.63
1606 1791 1.674962 CTACCAGTACCAGTACTCGGC 59.325 57.143 18.45 0.00 43.98 5.54
1607 1792 0.251474 ACCAGTACCAGTACTCGGCA 60.251 55.000 18.45 0.00 43.98 5.69
1608 1793 0.172803 CCAGTACCAGTACTCGGCAC 59.827 60.000 7.50 8.36 43.98 5.01
1609 1794 1.174783 CAGTACCAGTACTCGGCACT 58.825 55.000 7.50 9.99 43.98 4.40
1610 1795 1.132643 CAGTACCAGTACTCGGCACTC 59.867 57.143 7.50 2.85 43.98 3.51
1611 1796 0.098376 GTACCAGTACTCGGCACTCG 59.902 60.000 10.26 0.00 40.90 4.18
1612 1797 0.321919 TACCAGTACTCGGCACTCGT 60.322 55.000 10.26 0.00 40.32 4.18
1613 1798 0.321919 ACCAGTACTCGGCACTCGTA 60.322 55.000 10.26 0.00 40.32 3.43
1628 1813 4.677250 GCACTCGTATAGTACTGGTGCTTT 60.677 45.833 5.39 0.00 43.95 3.51
1644 1829 5.010516 TGGTGCTTTATTAGTTGTTGCATGT 59.989 36.000 0.00 0.00 0.00 3.21
1668 1857 3.305110 GCACCGGGCGATTAATTAATTG 58.695 45.455 17.85 17.85 0.00 2.32
1677 1873 7.359765 CGGGCGATTAATTAATTGTTCGAGTAT 60.360 37.037 25.92 5.33 32.17 2.12
1690 1914 9.454585 AATTGTTCGAGTATTATGCAATTGATG 57.545 29.630 10.34 0.00 34.90 3.07
1769 2159 3.328505 CATGGTTTGTTGGCCTCATTTC 58.671 45.455 3.32 0.00 0.00 2.17
1834 2224 8.040132 ACTAGTACTAATATGCTACTACTCCCG 58.960 40.741 3.76 0.00 0.00 5.14
1835 2225 7.013823 AGTACTAATATGCTACTACTCCCGA 57.986 40.000 0.00 0.00 0.00 5.14
1836 2226 7.456725 AGTACTAATATGCTACTACTCCCGAA 58.543 38.462 0.00 0.00 0.00 4.30
1837 2227 7.941238 AGTACTAATATGCTACTACTCCCGAAA 59.059 37.037 0.00 0.00 0.00 3.46
1838 2228 7.216973 ACTAATATGCTACTACTCCCGAAAG 57.783 40.000 0.00 0.00 0.00 2.62
1839 2229 6.776603 ACTAATATGCTACTACTCCCGAAAGT 59.223 38.462 0.00 0.00 0.00 2.66
1840 2230 5.708877 ATATGCTACTACTCCCGAAAGTC 57.291 43.478 0.00 0.00 0.00 3.01
1841 2231 2.799017 TGCTACTACTCCCGAAAGTCA 58.201 47.619 0.00 0.00 0.00 3.41
1842 2232 3.362706 TGCTACTACTCCCGAAAGTCAT 58.637 45.455 0.00 0.00 0.00 3.06
1843 2233 3.380637 TGCTACTACTCCCGAAAGTCATC 59.619 47.826 0.00 0.00 0.00 2.92
1844 2234 3.633065 GCTACTACTCCCGAAAGTCATCT 59.367 47.826 0.00 0.00 0.00 2.90
1845 2235 4.098196 GCTACTACTCCCGAAAGTCATCTT 59.902 45.833 0.00 0.00 35.14 2.40
1846 2236 5.394333 GCTACTACTCCCGAAAGTCATCTTT 60.394 44.000 0.00 0.00 45.24 2.52
1847 2237 5.485209 ACTACTCCCGAAAGTCATCTTTT 57.515 39.130 0.00 0.00 42.99 2.27
1848 2238 5.238583 ACTACTCCCGAAAGTCATCTTTTG 58.761 41.667 0.00 0.00 42.99 2.44
1849 2239 4.351874 ACTCCCGAAAGTCATCTTTTGA 57.648 40.909 8.87 1.13 43.87 2.69
1850 2240 4.911390 ACTCCCGAAAGTCATCTTTTGAT 58.089 39.130 8.87 0.00 43.87 2.57
1851 2241 4.938226 ACTCCCGAAAGTCATCTTTTGATC 59.062 41.667 8.87 0.00 43.87 2.92
1852 2242 4.261801 TCCCGAAAGTCATCTTTTGATCC 58.738 43.478 8.87 0.00 43.87 3.36
1853 2243 3.378427 CCCGAAAGTCATCTTTTGATCCC 59.622 47.826 8.87 0.00 43.87 3.85
1854 2244 3.063997 CCGAAAGTCATCTTTTGATCCCG 59.936 47.826 8.87 1.57 43.87 5.14
1855 2245 3.932710 CGAAAGTCATCTTTTGATCCCGA 59.067 43.478 2.79 0.00 43.87 5.14
1856 2246 4.033358 CGAAAGTCATCTTTTGATCCCGAG 59.967 45.833 2.79 0.00 43.87 4.63
1857 2247 2.911484 AGTCATCTTTTGATCCCGAGC 58.089 47.619 0.00 0.00 36.97 5.03
1858 2248 2.503356 AGTCATCTTTTGATCCCGAGCT 59.497 45.455 0.00 0.00 36.97 4.09
1859 2249 2.869192 GTCATCTTTTGATCCCGAGCTC 59.131 50.000 2.73 2.73 36.97 4.09
1860 2250 2.501316 TCATCTTTTGATCCCGAGCTCA 59.499 45.455 15.40 0.00 36.97 4.26
1861 2251 3.135348 TCATCTTTTGATCCCGAGCTCAT 59.865 43.478 15.40 0.00 36.97 2.90
1862 2252 4.344968 TCATCTTTTGATCCCGAGCTCATA 59.655 41.667 15.40 0.00 36.97 2.15
1863 2253 4.963318 TCTTTTGATCCCGAGCTCATAT 57.037 40.909 15.40 3.21 0.00 1.78
1864 2254 4.635223 TCTTTTGATCCCGAGCTCATATG 58.365 43.478 15.40 0.00 0.00 1.78
1865 2255 2.462456 TTGATCCCGAGCTCATATGC 57.538 50.000 15.40 0.11 0.00 3.14
1866 2256 8.431815 ATCTTTTGATCCCGAGCTCATATGCT 62.432 42.308 15.40 0.00 39.52 3.79
1884 2274 2.288666 GCTCCCGCATGATCAGTAAAA 58.711 47.619 0.09 0.00 35.78 1.52
1887 2277 3.130633 TCCCGCATGATCAGTAAAATCG 58.869 45.455 0.09 0.00 0.00 3.34
1950 2340 9.487790 TTTTTGAGAGAAACATTGACAAAAGTT 57.512 25.926 0.00 0.00 37.18 2.66
1951 2341 8.687824 TTTGAGAGAAACATTGACAAAAGTTC 57.312 30.769 9.09 5.33 0.00 3.01
1952 2342 7.630242 TGAGAGAAACATTGACAAAAGTTCT 57.370 32.000 9.09 9.17 0.00 3.01
1953 2343 8.731275 TGAGAGAAACATTGACAAAAGTTCTA 57.269 30.769 9.09 0.00 0.00 2.10
1954 2344 9.173021 TGAGAGAAACATTGACAAAAGTTCTAA 57.827 29.630 9.09 0.00 0.00 2.10
1955 2345 9.657121 GAGAGAAACATTGACAAAAGTTCTAAG 57.343 33.333 9.09 0.00 0.00 2.18
1956 2346 9.178758 AGAGAAACATTGACAAAAGTTCTAAGT 57.821 29.630 9.09 0.00 0.00 2.24
1957 2347 9.226345 GAGAAACATTGACAAAAGTTCTAAGTG 57.774 33.333 9.09 0.00 0.00 3.16
1958 2348 7.702348 AGAAACATTGACAAAAGTTCTAAGTGC 59.298 33.333 9.09 0.00 0.00 4.40
1960 2350 5.594317 ACATTGACAAAAGTTCTAAGTGCCT 59.406 36.000 0.00 0.00 0.00 4.75
1961 2351 5.499139 TTGACAAAAGTTCTAAGTGCCTG 57.501 39.130 0.00 0.00 0.00 4.85
1962 2352 3.315191 TGACAAAAGTTCTAAGTGCCTGC 59.685 43.478 0.00 0.00 0.00 4.85
1963 2353 3.287222 ACAAAAGTTCTAAGTGCCTGCA 58.713 40.909 0.00 0.00 0.00 4.41
1964 2354 3.699038 ACAAAAGTTCTAAGTGCCTGCAA 59.301 39.130 0.00 0.00 0.00 4.08
1965 2355 4.159506 ACAAAAGTTCTAAGTGCCTGCAAA 59.840 37.500 0.00 0.00 0.00 3.68
1966 2356 5.108517 CAAAAGTTCTAAGTGCCTGCAAAA 58.891 37.500 0.00 0.00 0.00 2.44
1967 2357 5.337578 AAAGTTCTAAGTGCCTGCAAAAA 57.662 34.783 0.00 0.00 0.00 1.94
1968 2358 5.535753 AAGTTCTAAGTGCCTGCAAAAAT 57.464 34.783 0.00 0.00 0.00 1.82
1969 2359 5.535753 AGTTCTAAGTGCCTGCAAAAATT 57.464 34.783 0.00 0.00 0.00 1.82
1970 2360 5.532557 AGTTCTAAGTGCCTGCAAAAATTC 58.467 37.500 0.00 0.00 0.00 2.17
1971 2361 5.068987 AGTTCTAAGTGCCTGCAAAAATTCA 59.931 36.000 0.00 0.00 0.00 2.57
1972 2362 5.726980 TCTAAGTGCCTGCAAAAATTCAT 57.273 34.783 0.00 0.00 0.00 2.57
1973 2363 5.713025 TCTAAGTGCCTGCAAAAATTCATC 58.287 37.500 0.00 0.00 0.00 2.92
1974 2364 4.339872 AAGTGCCTGCAAAAATTCATCA 57.660 36.364 0.00 0.00 0.00 3.07
1975 2365 4.546829 AGTGCCTGCAAAAATTCATCAT 57.453 36.364 0.00 0.00 0.00 2.45
1981 2374 6.092944 TGCCTGCAAAAATTCATCATGAAATC 59.907 34.615 3.63 0.00 40.12 2.17
1988 2381 9.982291 CAAAAATTCATCATGAAATCACATTCC 57.018 29.630 3.63 0.00 40.12 3.01
1991 2384 7.655521 ATTCATCATGAAATCACATTCCTGT 57.344 32.000 3.63 0.00 40.12 4.00
1992 2385 8.756486 ATTCATCATGAAATCACATTCCTGTA 57.244 30.769 3.63 0.00 40.12 2.74
1994 2387 8.217131 TCATCATGAAATCACATTCCTGTAAG 57.783 34.615 0.00 0.00 33.14 2.34
2031 2424 5.701029 AACAAATTCAGTGCTTCAAAACG 57.299 34.783 0.00 0.00 0.00 3.60
2032 2425 3.551485 ACAAATTCAGTGCTTCAAAACGC 59.449 39.130 0.00 0.00 0.00 4.84
2033 2426 3.715628 AATTCAGTGCTTCAAAACGCT 57.284 38.095 0.00 0.00 0.00 5.07
2034 2427 3.715628 ATTCAGTGCTTCAAAACGCTT 57.284 38.095 0.00 0.00 0.00 4.68
2036 2429 3.502191 TCAGTGCTTCAAAACGCTTTT 57.498 38.095 0.00 0.00 0.00 2.27
2049 2442 6.961359 AAAACGCTTTTGAAAGTAGCTTTT 57.039 29.167 0.00 1.66 37.79 2.27
2051 2444 6.569228 AACGCTTTTGAAAGTAGCTTTTTC 57.431 33.333 13.56 13.56 38.28 2.29
2055 2545 6.141369 CGCTTTTGAAAGTAGCTTTTTCAGAG 59.859 38.462 19.21 19.75 43.22 3.35
2057 2547 8.129211 GCTTTTGAAAGTAGCTTTTTCAGAGTA 58.871 33.333 19.21 8.08 43.22 2.59
2061 2551 7.272978 TGAAAGTAGCTTTTTCAGAGTACTGT 58.727 34.615 17.30 0.00 39.05 3.55
2066 2556 8.398665 AGTAGCTTTTTCAGAGTACTGTTTTTG 58.601 33.333 0.00 0.00 43.81 2.44
2089 2579 2.897271 TTTTGCCATGCCTTCTAGGA 57.103 45.000 0.00 0.00 37.67 2.94
2090 2580 2.897271 TTTGCCATGCCTTCTAGGAA 57.103 45.000 0.00 0.00 37.67 3.36
2091 2581 3.386932 TTTGCCATGCCTTCTAGGAAT 57.613 42.857 0.00 0.00 37.67 3.01
2099 2589 6.069684 CATGCCTTCTAGGAATGTGATTTC 57.930 41.667 5.64 0.00 44.91 2.17
2100 2590 5.178096 TGCCTTCTAGGAATGTGATTTCA 57.822 39.130 0.00 0.00 37.67 2.69
2101 2591 4.943705 TGCCTTCTAGGAATGTGATTTCAC 59.056 41.667 3.72 3.72 41.79 3.18
2102 2592 4.034510 GCCTTCTAGGAATGTGATTTCACG 59.965 45.833 6.24 0.00 43.30 4.35
2103 2593 5.419542 CCTTCTAGGAATGTGATTTCACGA 58.580 41.667 6.24 0.00 43.30 4.35
2104 2594 5.292101 CCTTCTAGGAATGTGATTTCACGAC 59.708 44.000 6.24 0.87 43.30 4.34
2105 2595 7.869609 CCTTCTAGGAATGTGATTTCACGACG 61.870 46.154 6.24 0.00 43.30 5.12
2106 2596 9.905275 CCTTCTAGGAATGTGATTTCACGACGA 62.905 44.444 0.00 0.00 43.30 4.20
2114 2604 4.918653 GTGATTTCACGACGAATTTTTGC 58.081 39.130 0.00 0.00 37.10 3.68
2115 2605 4.439449 GTGATTTCACGACGAATTTTTGCA 59.561 37.500 0.00 0.00 37.10 4.08
2116 2606 4.674662 TGATTTCACGACGAATTTTTGCAG 59.325 37.500 0.00 0.00 32.32 4.41
2117 2607 2.679355 TCACGACGAATTTTTGCAGG 57.321 45.000 0.00 0.00 0.00 4.85
2118 2608 1.052287 CACGACGAATTTTTGCAGGC 58.948 50.000 0.00 0.00 0.00 4.85
2119 2609 0.665835 ACGACGAATTTTTGCAGGCA 59.334 45.000 0.00 0.00 0.00 4.75
2120 2610 1.052287 CGACGAATTTTTGCAGGCAC 58.948 50.000 0.00 0.00 0.00 5.01
2121 2611 1.334960 CGACGAATTTTTGCAGGCACT 60.335 47.619 0.00 0.00 43.88 4.40
2122 2612 2.742774 GACGAATTTTTGCAGGCACTT 58.257 42.857 0.00 0.00 34.60 3.16
2123 2613 3.608241 CGACGAATTTTTGCAGGCACTTA 60.608 43.478 0.00 0.00 34.60 2.24
2124 2614 3.900941 ACGAATTTTTGCAGGCACTTAG 58.099 40.909 0.00 0.00 34.60 2.18
2125 2615 3.568007 ACGAATTTTTGCAGGCACTTAGA 59.432 39.130 0.00 0.00 34.60 2.10
2126 2616 4.037446 ACGAATTTTTGCAGGCACTTAGAA 59.963 37.500 0.00 0.00 34.60 2.10
2127 2617 4.382754 CGAATTTTTGCAGGCACTTAGAAC 59.617 41.667 0.00 0.00 34.60 3.01
2128 2618 5.532557 GAATTTTTGCAGGCACTTAGAACT 58.467 37.500 0.00 0.00 34.60 3.01
2129 2619 5.535753 ATTTTTGCAGGCACTTAGAACTT 57.464 34.783 0.00 0.00 34.60 2.66
2130 2620 5.337578 TTTTTGCAGGCACTTAGAACTTT 57.662 34.783 0.00 0.00 34.60 2.66
2131 2621 5.337578 TTTTGCAGGCACTTAGAACTTTT 57.662 34.783 0.00 0.00 34.60 2.27
2132 2622 3.988379 TGCAGGCACTTAGAACTTTTG 57.012 42.857 0.00 0.00 34.60 2.44
2133 2623 3.287222 TGCAGGCACTTAGAACTTTTGT 58.713 40.909 0.00 0.00 34.60 2.83
2134 2624 3.315191 TGCAGGCACTTAGAACTTTTGTC 59.685 43.478 0.00 0.00 34.60 3.18
2135 2625 3.315191 GCAGGCACTTAGAACTTTTGTCA 59.685 43.478 0.00 0.00 34.60 3.58
2136 2626 4.202010 GCAGGCACTTAGAACTTTTGTCAA 60.202 41.667 0.00 0.00 34.60 3.18
2137 2627 5.507985 GCAGGCACTTAGAACTTTTGTCAAT 60.508 40.000 0.00 0.00 34.60 2.57
2138 2628 5.916883 CAGGCACTTAGAACTTTTGTCAATG 59.083 40.000 0.00 0.00 34.60 2.82
2139 2629 5.594317 AGGCACTTAGAACTTTTGTCAATGT 59.406 36.000 0.00 0.00 27.25 2.71
2140 2630 6.096846 AGGCACTTAGAACTTTTGTCAATGTT 59.903 34.615 4.72 4.72 27.25 2.71
2141 2631 6.756542 GGCACTTAGAACTTTTGTCAATGTTT 59.243 34.615 6.10 0.00 31.96 2.83
2142 2632 7.043391 GGCACTTAGAACTTTTGTCAATGTTTC 60.043 37.037 6.10 1.04 31.96 2.78
2143 2633 7.702348 GCACTTAGAACTTTTGTCAATGTTTCT 59.298 33.333 6.10 6.96 31.96 2.52
2144 2634 9.226345 CACTTAGAACTTTTGTCAATGTTTCTC 57.774 33.333 6.42 0.00 31.96 2.87
2145 2635 9.178758 ACTTAGAACTTTTGTCAATGTTTCTCT 57.821 29.630 6.42 3.36 31.96 3.10
2146 2636 9.657121 CTTAGAACTTTTGTCAATGTTTCTCTC 57.343 33.333 6.42 0.00 31.96 3.20
2147 2637 7.630242 AGAACTTTTGTCAATGTTTCTCTCA 57.370 32.000 6.10 0.00 31.96 3.27
2148 2638 8.055279 AGAACTTTTGTCAATGTTTCTCTCAA 57.945 30.769 6.10 0.00 31.96 3.02
2149 2639 8.522830 AGAACTTTTGTCAATGTTTCTCTCAAA 58.477 29.630 6.10 0.00 31.96 2.69
2150 2640 9.305925 GAACTTTTGTCAATGTTTCTCTCAAAT 57.694 29.630 6.10 0.00 31.96 2.32
2151 2641 9.657419 AACTTTTGTCAATGTTTCTCTCAAATT 57.343 25.926 0.00 0.00 28.24 1.82
2152 2642 9.657419 ACTTTTGTCAATGTTTCTCTCAAATTT 57.343 25.926 0.00 0.00 0.00 1.82
2206 2696 6.667981 TTTTTCGATTTTACTGTTCATGCG 57.332 33.333 0.00 0.00 0.00 4.73
2209 2699 2.675844 CGATTTTACTGTTCATGCGGGA 59.324 45.455 0.00 0.00 0.00 5.14
2210 2700 3.242413 CGATTTTACTGTTCATGCGGGAG 60.242 47.826 0.00 0.00 0.00 4.30
2230 2720 4.912317 AGCATATGAGCTCAGGATCAAT 57.088 40.909 22.96 5.74 42.18 2.57
2231 2721 5.244189 AGCATATGAGCTCAGGATCAATT 57.756 39.130 22.96 4.95 42.18 2.32
2232 2722 5.247084 AGCATATGAGCTCAGGATCAATTC 58.753 41.667 22.96 3.53 42.18 2.17
2233 2723 4.395542 GCATATGAGCTCAGGATCAATTCC 59.604 45.833 22.96 0.00 41.37 3.01
2247 2737 1.961180 AATTCCTCCGCGTCCCTCAG 61.961 60.000 4.92 0.00 0.00 3.35
2254 2744 0.179134 CCGCGTCCCTCAGACTTTAG 60.179 60.000 4.92 0.00 43.91 1.85
2268 2758 6.323266 TCAGACTTTAGTGATCTAAACGCTC 58.677 40.000 0.00 0.00 40.05 5.03
2286 2776 8.675040 AAACGCTCTTATATTTCTTTTGAAGC 57.325 30.769 0.00 0.00 39.88 3.86
2465 2990 6.539173 TCAGGTTATTTCTTGGAAGTTGCTA 58.461 36.000 0.00 0.00 0.00 3.49
2481 3006 1.080093 CTAGCTTGGCCGAACGACA 60.080 57.895 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.254133 CTACTCATGTATACAAATCAAGTGAGG 57.746 37.037 24.01 11.18 35.95 3.86
14 15 8.654230 AGCTACTCATGTATACAAATCAAGTG 57.346 34.615 10.14 1.82 0.00 3.16
69 70 5.471456 AGATAATGATCCGTTTCTCCAATGC 59.529 40.000 0.00 0.00 31.81 3.56
71 72 6.234177 GGAGATAATGATCCGTTTCTCCAAT 58.766 40.000 19.08 0.00 45.54 3.16
94 116 0.040067 GACTTTGCAAAGCCACTCGG 60.040 55.000 33.72 13.29 39.63 4.63
219 243 5.048504 GGCCCATCAAGAATACACATACATG 60.049 44.000 0.00 0.00 0.00 3.21
350 378 3.971453 ATGAGTCGAGTGTGCCGCG 62.971 63.158 0.00 0.00 37.75 6.46
351 379 2.125912 ATGAGTCGAGTGTGCCGC 60.126 61.111 0.00 0.00 0.00 6.53
352 380 1.517257 GGATGAGTCGAGTGTGCCG 60.517 63.158 0.00 0.00 0.00 5.69
353 381 1.153549 GGGATGAGTCGAGTGTGCC 60.154 63.158 0.00 0.00 0.00 5.01
386 416 7.082602 CAGATAGATGTGCCAGATAAATTTGC 58.917 38.462 0.00 0.00 0.00 3.68
439 469 2.554344 GGTAAAGCCTGGGTGACATTGA 60.554 50.000 0.00 0.00 0.00 2.57
457 563 7.728148 TCTAAACGCCATATTCTTACATGGTA 58.272 34.615 0.00 0.00 43.14 3.25
525 631 8.986991 GGGGAGACTTCAATGATCTATATACAT 58.013 37.037 0.00 0.00 0.00 2.29
544 650 0.747852 TTTTGTTTTGCGGGGGAGAC 59.252 50.000 0.00 0.00 0.00 3.36
595 702 2.159393 GCAATAAAGTGCGCCATGAAGA 60.159 45.455 4.18 0.00 34.21 2.87
931 1046 1.380650 GAGACGGGGAGAGGAAGCT 60.381 63.158 0.00 0.00 0.00 3.74
945 1060 2.232696 GTGTGGAGGAGGAAGAAGAGAC 59.767 54.545 0.00 0.00 0.00 3.36
1391 1548 3.822192 CCATCGTCGCGGAGTCCA 61.822 66.667 10.49 0.00 0.00 4.02
1419 1576 2.762459 CAGCCCATGCCCATGCTT 60.762 61.111 2.75 0.00 38.69 3.91
1564 1746 7.121020 GGTAGTACTAGTTGACAAGCTAGACTT 59.879 40.741 21.52 12.96 40.05 3.01
1565 1747 6.598850 GGTAGTACTAGTTGACAAGCTAGACT 59.401 42.308 21.52 20.06 38.36 3.24
1601 1786 2.223611 CCAGTACTATACGAGTGCCGAG 59.776 54.545 0.00 0.00 41.45 4.63
1602 1787 2.216046 CCAGTACTATACGAGTGCCGA 58.784 52.381 0.00 0.00 41.45 5.54
1603 1788 1.945394 ACCAGTACTATACGAGTGCCG 59.055 52.381 0.00 0.00 41.45 5.69
1604 1789 2.543238 GCACCAGTACTATACGAGTGCC 60.543 54.545 18.14 7.23 46.96 5.01
1605 1790 2.728922 GCACCAGTACTATACGAGTGC 58.271 52.381 15.70 15.70 46.84 4.40
1606 1791 4.634184 AAGCACCAGTACTATACGAGTG 57.366 45.455 0.00 0.00 39.39 3.51
1607 1792 6.956202 ATAAAGCACCAGTACTATACGAGT 57.044 37.500 0.00 0.00 42.69 4.18
1608 1793 8.566260 ACTAATAAAGCACCAGTACTATACGAG 58.434 37.037 0.00 0.00 0.00 4.18
1609 1794 8.455903 ACTAATAAAGCACCAGTACTATACGA 57.544 34.615 0.00 0.00 0.00 3.43
1610 1795 8.965172 CAACTAATAAAGCACCAGTACTATACG 58.035 37.037 0.00 0.00 0.00 3.06
1611 1796 9.813446 ACAACTAATAAAGCACCAGTACTATAC 57.187 33.333 0.00 0.00 0.00 1.47
1613 1798 9.162764 CAACAACTAATAAAGCACCAGTACTAT 57.837 33.333 0.00 0.00 0.00 2.12
1644 1829 2.264005 AATTAATCGCCCGGTGCATA 57.736 45.000 14.17 3.22 41.33 3.14
1652 1837 6.056428 ACTCGAACAATTAATTAATCGCCC 57.944 37.500 21.17 1.91 31.32 6.13
1668 1857 8.285394 ACATCATCAATTGCATAATACTCGAAC 58.715 33.333 0.00 0.00 0.00 3.95
1677 1873 7.643569 AGGTTACACATCATCAATTGCATAA 57.356 32.000 0.00 0.00 0.00 1.90
1690 1914 7.707035 CCAGTGATCTAGTTAAGGTTACACATC 59.293 40.741 0.00 0.00 27.09 3.06
1809 2199 8.256605 TCGGGAGTAGTAGCATATTAGTACTAG 58.743 40.741 2.23 0.00 39.00 2.57
1811 2201 7.013823 TCGGGAGTAGTAGCATATTAGTACT 57.986 40.000 0.00 0.00 40.68 2.73
1812 2202 7.678947 TTCGGGAGTAGTAGCATATTAGTAC 57.321 40.000 0.00 0.00 32.16 2.73
1818 2208 5.138276 TGACTTTCGGGAGTAGTAGCATAT 58.862 41.667 0.00 0.00 0.00 1.78
1832 2222 3.063997 CGGGATCAAAAGATGACTTTCGG 59.936 47.826 0.00 0.00 44.32 4.30
1833 2223 3.932710 TCGGGATCAAAAGATGACTTTCG 59.067 43.478 0.00 0.00 44.32 3.46
1834 2224 4.201861 GCTCGGGATCAAAAGATGACTTTC 60.202 45.833 0.00 0.00 44.32 2.62
1835 2225 3.691609 GCTCGGGATCAAAAGATGACTTT 59.308 43.478 0.00 0.00 46.64 2.66
1836 2226 3.054802 AGCTCGGGATCAAAAGATGACTT 60.055 43.478 0.00 0.00 41.93 3.01
1837 2227 2.503356 AGCTCGGGATCAAAAGATGACT 59.497 45.455 0.00 0.00 41.93 3.41
1838 2228 2.869192 GAGCTCGGGATCAAAAGATGAC 59.131 50.000 0.00 0.00 41.93 3.06
1839 2229 2.501316 TGAGCTCGGGATCAAAAGATGA 59.499 45.455 0.00 0.00 43.67 2.92
1840 2230 2.910199 TGAGCTCGGGATCAAAAGATG 58.090 47.619 0.00 0.00 34.74 2.90
1841 2231 3.853355 ATGAGCTCGGGATCAAAAGAT 57.147 42.857 7.61 0.00 41.37 2.40
1842 2232 4.635223 CATATGAGCTCGGGATCAAAAGA 58.365 43.478 7.61 0.00 41.37 2.52
1843 2233 3.188048 GCATATGAGCTCGGGATCAAAAG 59.812 47.826 7.61 0.72 41.37 2.27
1844 2234 3.141398 GCATATGAGCTCGGGATCAAAA 58.859 45.455 7.61 0.00 41.37 2.44
1845 2235 2.369860 AGCATATGAGCTCGGGATCAAA 59.630 45.455 7.61 0.00 42.18 2.69
1846 2236 1.973515 AGCATATGAGCTCGGGATCAA 59.026 47.619 7.61 0.00 42.18 2.57
1847 2237 1.637338 AGCATATGAGCTCGGGATCA 58.363 50.000 5.33 5.33 42.18 2.92
1865 2255 3.185188 CGATTTTACTGATCATGCGGGAG 59.815 47.826 0.00 0.00 0.00 4.30
1866 2256 3.130633 CGATTTTACTGATCATGCGGGA 58.869 45.455 0.00 0.00 0.00 5.14
1867 2257 3.130633 TCGATTTTACTGATCATGCGGG 58.869 45.455 0.00 0.00 0.00 6.13
1868 2258 4.794248 TTCGATTTTACTGATCATGCGG 57.206 40.909 0.00 0.00 0.00 5.69
1924 2314 9.487790 AACTTTTGTCAATGTTTCTCTCAAAAA 57.512 25.926 0.00 0.00 34.51 1.94
1926 2316 8.522830 AGAACTTTTGTCAATGTTTCTCTCAAA 58.477 29.630 6.10 0.00 31.96 2.69
1929 2319 9.657121 CTTAGAACTTTTGTCAATGTTTCTCTC 57.343 33.333 6.42 0.00 31.96 3.20
1933 2323 7.043391 GGCACTTAGAACTTTTGTCAATGTTTC 60.043 37.037 6.10 1.04 31.96 2.78
1935 2325 6.096846 AGGCACTTAGAACTTTTGTCAATGTT 59.903 34.615 4.72 4.72 27.25 2.71
1936 2326 5.594317 AGGCACTTAGAACTTTTGTCAATGT 59.406 36.000 0.00 0.00 27.25 2.71
1937 2327 5.916883 CAGGCACTTAGAACTTTTGTCAATG 59.083 40.000 0.00 0.00 34.60 2.82
1939 2329 4.202010 GCAGGCACTTAGAACTTTTGTCAA 60.202 41.667 0.00 0.00 34.60 3.18
1940 2330 3.315191 GCAGGCACTTAGAACTTTTGTCA 59.685 43.478 0.00 0.00 34.60 3.58
1941 2331 3.315191 TGCAGGCACTTAGAACTTTTGTC 59.685 43.478 0.00 0.00 34.60 3.18
1942 2332 3.287222 TGCAGGCACTTAGAACTTTTGT 58.713 40.909 0.00 0.00 34.60 2.83
1943 2333 3.988379 TGCAGGCACTTAGAACTTTTG 57.012 42.857 0.00 0.00 34.60 2.44
1944 2334 5.337578 TTTTGCAGGCACTTAGAACTTTT 57.662 34.783 0.00 0.00 34.60 2.27
1945 2335 5.337578 TTTTTGCAGGCACTTAGAACTTT 57.662 34.783 0.00 0.00 34.60 2.66
1946 2336 5.535753 ATTTTTGCAGGCACTTAGAACTT 57.464 34.783 0.00 0.00 34.60 2.66
1947 2337 5.068987 TGAATTTTTGCAGGCACTTAGAACT 59.931 36.000 0.00 0.00 34.60 3.01
1948 2338 5.288804 TGAATTTTTGCAGGCACTTAGAAC 58.711 37.500 0.00 0.00 34.60 3.01
1949 2339 5.528043 TGAATTTTTGCAGGCACTTAGAA 57.472 34.783 0.00 0.00 34.60 2.10
1950 2340 5.243507 TGATGAATTTTTGCAGGCACTTAGA 59.756 36.000 0.00 0.00 34.60 2.10
1951 2341 5.472148 TGATGAATTTTTGCAGGCACTTAG 58.528 37.500 0.00 0.00 34.60 2.18
1952 2342 5.465532 TGATGAATTTTTGCAGGCACTTA 57.534 34.783 0.00 0.00 34.60 2.24
1953 2343 4.339872 TGATGAATTTTTGCAGGCACTT 57.660 36.364 0.00 0.00 34.60 3.16
1954 2344 4.020928 TCATGATGAATTTTTGCAGGCACT 60.021 37.500 0.00 0.00 43.88 4.40
1955 2345 4.247258 TCATGATGAATTTTTGCAGGCAC 58.753 39.130 0.00 0.00 0.00 5.01
1956 2346 4.538746 TCATGATGAATTTTTGCAGGCA 57.461 36.364 0.00 0.00 0.00 4.75
1957 2347 5.866335 TTTCATGATGAATTTTTGCAGGC 57.134 34.783 8.90 0.00 36.11 4.85
1958 2348 7.118535 TGTGATTTCATGATGAATTTTTGCAGG 59.881 33.333 8.90 0.00 36.11 4.85
1960 2350 7.964604 TGTGATTTCATGATGAATTTTTGCA 57.035 28.000 8.90 1.87 36.11 4.08
1961 2351 9.485591 GAATGTGATTTCATGATGAATTTTTGC 57.514 29.630 8.90 0.00 36.11 3.68
1962 2352 9.982291 GGAATGTGATTTCATGATGAATTTTTG 57.018 29.630 8.90 0.00 36.11 2.44
1963 2353 9.953565 AGGAATGTGATTTCATGATGAATTTTT 57.046 25.926 8.90 0.00 36.11 1.94
1964 2354 9.378551 CAGGAATGTGATTTCATGATGAATTTT 57.621 29.630 8.90 0.00 39.18 1.82
1965 2355 8.537016 ACAGGAATGTGATTTCATGATGAATTT 58.463 29.630 8.90 0.00 39.18 1.82
1966 2356 8.074613 ACAGGAATGTGATTTCATGATGAATT 57.925 30.769 8.90 5.47 39.18 2.17
1967 2357 7.655521 ACAGGAATGTGATTTCATGATGAAT 57.344 32.000 8.90 0.00 39.18 2.57
1968 2358 8.578448 TTACAGGAATGTGATTTCATGATGAA 57.422 30.769 3.29 3.29 39.18 2.57
1969 2359 7.283807 CCTTACAGGAATGTGATTTCATGATGA 59.716 37.037 0.00 0.00 39.18 2.92
1970 2360 7.423199 CCTTACAGGAATGTGATTTCATGATG 58.577 38.462 0.00 0.00 39.18 3.07
1971 2361 6.040166 GCCTTACAGGAATGTGATTTCATGAT 59.960 38.462 0.00 0.00 39.18 2.45
1972 2362 5.357878 GCCTTACAGGAATGTGATTTCATGA 59.642 40.000 5.92 0.00 39.18 3.07
1973 2363 5.585390 GCCTTACAGGAATGTGATTTCATG 58.415 41.667 0.00 0.00 41.77 3.07
1974 2364 4.336433 CGCCTTACAGGAATGTGATTTCAT 59.664 41.667 0.00 0.00 37.67 2.57
1975 2365 3.689161 CGCCTTACAGGAATGTGATTTCA 59.311 43.478 0.00 0.00 37.67 2.69
1981 2374 1.086696 CCACGCCTTACAGGAATGTG 58.913 55.000 0.00 0.00 37.67 3.21
2007 2400 6.533185 CGTTTTGAAGCACTGAATTTGTTTT 58.467 32.000 0.00 0.00 0.00 2.43
2009 2402 4.032786 GCGTTTTGAAGCACTGAATTTGTT 59.967 37.500 0.00 0.00 0.00 2.83
2011 2404 3.798337 AGCGTTTTGAAGCACTGAATTTG 59.202 39.130 0.00 0.00 35.48 2.32
2014 2407 3.715628 AAGCGTTTTGAAGCACTGAAT 57.284 38.095 0.00 0.00 35.48 2.57
2015 2408 3.502191 AAAGCGTTTTGAAGCACTGAA 57.498 38.095 0.00 0.00 35.48 3.02
2016 2409 3.502191 AAAAGCGTTTTGAAGCACTGA 57.498 38.095 0.00 0.00 35.48 3.41
2026 2419 6.961359 AAAAGCTACTTTCAAAAGCGTTTT 57.039 29.167 2.87 0.00 42.56 2.43
2030 2423 5.971202 TCTGAAAAAGCTACTTTCAAAAGCG 59.029 36.000 19.14 10.92 41.10 4.68
2031 2424 6.975197 ACTCTGAAAAAGCTACTTTCAAAAGC 59.025 34.615 19.14 0.00 41.10 3.51
2032 2425 9.439537 GTACTCTGAAAAAGCTACTTTCAAAAG 57.560 33.333 19.14 19.31 41.10 2.27
2033 2426 9.174166 AGTACTCTGAAAAAGCTACTTTCAAAA 57.826 29.630 19.14 12.25 41.10 2.44
2034 2427 8.612619 CAGTACTCTGAAAAAGCTACTTTCAAA 58.387 33.333 19.14 9.92 41.10 2.69
2036 2429 7.272978 ACAGTACTCTGAAAAAGCTACTTTCA 58.727 34.615 18.13 18.13 43.76 2.69
2037 2430 7.716768 ACAGTACTCTGAAAAAGCTACTTTC 57.283 36.000 12.26 12.26 43.76 2.62
2038 2431 8.507524 AAACAGTACTCTGAAAAAGCTACTTT 57.492 30.769 0.00 0.00 43.76 2.66
2039 2432 8.507524 AAAACAGTACTCTGAAAAAGCTACTT 57.492 30.769 0.00 0.00 43.76 2.24
2040 2433 8.398665 CAAAAACAGTACTCTGAAAAAGCTACT 58.601 33.333 0.00 0.00 43.76 2.57
2042 2435 8.276252 ACAAAAACAGTACTCTGAAAAAGCTA 57.724 30.769 0.00 0.00 43.76 3.32
2043 2436 7.158099 ACAAAAACAGTACTCTGAAAAAGCT 57.842 32.000 0.00 0.00 43.76 3.74
2071 2561 2.897271 TTCCTAGAAGGCATGGCAAA 57.103 45.000 22.64 2.44 34.61 3.68
2072 2562 2.025037 ACATTCCTAGAAGGCATGGCAA 60.025 45.455 22.64 5.18 42.29 4.52
2073 2563 1.565759 ACATTCCTAGAAGGCATGGCA 59.434 47.619 22.64 0.00 42.29 4.92
2074 2564 1.952296 CACATTCCTAGAAGGCATGGC 59.048 52.381 12.14 12.14 42.29 4.40
2077 2567 5.591877 GTGAAATCACATTCCTAGAAGGCAT 59.408 40.000 8.63 0.00 45.75 4.40
2078 2568 4.943705 GTGAAATCACATTCCTAGAAGGCA 59.056 41.667 8.63 0.00 45.75 4.75
2079 2569 4.034510 CGTGAAATCACATTCCTAGAAGGC 59.965 45.833 13.51 0.00 46.75 4.35
2080 2570 5.292101 GTCGTGAAATCACATTCCTAGAAGG 59.708 44.000 13.51 0.00 46.75 3.46
2081 2571 5.004821 CGTCGTGAAATCACATTCCTAGAAG 59.995 44.000 13.51 0.49 46.75 2.85
2082 2572 4.862574 CGTCGTGAAATCACATTCCTAGAA 59.137 41.667 13.51 0.00 46.75 2.10
2083 2573 4.157105 TCGTCGTGAAATCACATTCCTAGA 59.843 41.667 13.51 0.00 46.75 2.43
2084 2574 4.421058 TCGTCGTGAAATCACATTCCTAG 58.579 43.478 13.51 0.00 46.75 3.02
2085 2575 4.443913 TCGTCGTGAAATCACATTCCTA 57.556 40.909 13.51 0.00 46.75 2.94
2086 2576 3.313012 TCGTCGTGAAATCACATTCCT 57.687 42.857 13.51 0.00 46.75 3.36
2087 2577 4.600012 ATTCGTCGTGAAATCACATTCC 57.400 40.909 13.51 0.00 46.75 3.01
2088 2578 6.911484 AAAATTCGTCGTGAAATCACATTC 57.089 33.333 13.51 2.82 46.75 2.67
2089 2579 6.345723 GCAAAAATTCGTCGTGAAATCACATT 60.346 34.615 13.51 2.95 46.75 2.71
2090 2580 5.116983 GCAAAAATTCGTCGTGAAATCACAT 59.883 36.000 13.51 0.00 46.75 3.21
2091 2581 4.439449 GCAAAAATTCGTCGTGAAATCACA 59.561 37.500 13.51 0.00 46.75 3.58
2092 2582 4.439449 TGCAAAAATTCGTCGTGAAATCAC 59.561 37.500 3.43 3.43 40.71 3.06
2093 2583 4.602006 TGCAAAAATTCGTCGTGAAATCA 58.398 34.783 0.00 0.00 40.71 2.57
2094 2584 4.088496 CCTGCAAAAATTCGTCGTGAAATC 59.912 41.667 0.00 0.00 40.71 2.17
2095 2585 3.980775 CCTGCAAAAATTCGTCGTGAAAT 59.019 39.130 0.00 0.00 40.71 2.17
2096 2586 3.367607 CCTGCAAAAATTCGTCGTGAAA 58.632 40.909 0.00 0.00 40.71 2.69
2097 2587 2.856720 GCCTGCAAAAATTCGTCGTGAA 60.857 45.455 0.00 0.00 41.81 3.18
2098 2588 1.334599 GCCTGCAAAAATTCGTCGTGA 60.335 47.619 0.00 0.00 0.00 4.35
2099 2589 1.052287 GCCTGCAAAAATTCGTCGTG 58.948 50.000 0.00 0.00 0.00 4.35
2100 2590 0.665835 TGCCTGCAAAAATTCGTCGT 59.334 45.000 0.00 0.00 0.00 4.34
2101 2591 1.052287 GTGCCTGCAAAAATTCGTCG 58.948 50.000 0.00 0.00 0.00 5.12
2102 2592 2.422276 AGTGCCTGCAAAAATTCGTC 57.578 45.000 0.00 0.00 0.00 4.20
2103 2593 2.888834 AAGTGCCTGCAAAAATTCGT 57.111 40.000 0.00 0.00 0.00 3.85
2104 2594 4.159377 TCTAAGTGCCTGCAAAAATTCG 57.841 40.909 0.00 0.00 0.00 3.34
2105 2595 5.532557 AGTTCTAAGTGCCTGCAAAAATTC 58.467 37.500 0.00 0.00 0.00 2.17
2106 2596 5.535753 AGTTCTAAGTGCCTGCAAAAATT 57.464 34.783 0.00 0.00 0.00 1.82
2107 2597 5.535753 AAGTTCTAAGTGCCTGCAAAAAT 57.464 34.783 0.00 0.00 0.00 1.82
2108 2598 5.337578 AAAGTTCTAAGTGCCTGCAAAAA 57.662 34.783 0.00 0.00 0.00 1.94
2109 2599 5.108517 CAAAAGTTCTAAGTGCCTGCAAAA 58.891 37.500 0.00 0.00 0.00 2.44
2110 2600 4.159506 ACAAAAGTTCTAAGTGCCTGCAAA 59.840 37.500 0.00 0.00 0.00 3.68
2111 2601 3.699038 ACAAAAGTTCTAAGTGCCTGCAA 59.301 39.130 0.00 0.00 0.00 4.08
2112 2602 3.287222 ACAAAAGTTCTAAGTGCCTGCA 58.713 40.909 0.00 0.00 0.00 4.41
2113 2603 3.315191 TGACAAAAGTTCTAAGTGCCTGC 59.685 43.478 0.00 0.00 0.00 4.85
2114 2604 5.499139 TTGACAAAAGTTCTAAGTGCCTG 57.501 39.130 0.00 0.00 0.00 4.85
2115 2605 5.594317 ACATTGACAAAAGTTCTAAGTGCCT 59.406 36.000 0.00 0.00 0.00 4.75
2116 2606 5.831997 ACATTGACAAAAGTTCTAAGTGCC 58.168 37.500 0.00 0.00 0.00 5.01
2117 2607 7.702348 AGAAACATTGACAAAAGTTCTAAGTGC 59.298 33.333 9.09 0.00 0.00 4.40
2118 2608 9.226345 GAGAAACATTGACAAAAGTTCTAAGTG 57.774 33.333 9.09 0.00 0.00 3.16
2119 2609 9.178758 AGAGAAACATTGACAAAAGTTCTAAGT 57.821 29.630 9.09 0.00 0.00 2.24
2120 2610 9.657121 GAGAGAAACATTGACAAAAGTTCTAAG 57.343 33.333 9.09 0.00 0.00 2.18
2121 2611 9.173021 TGAGAGAAACATTGACAAAAGTTCTAA 57.827 29.630 9.09 0.00 0.00 2.10
2122 2612 8.731275 TGAGAGAAACATTGACAAAAGTTCTA 57.269 30.769 9.09 0.00 0.00 2.10
2123 2613 7.630242 TGAGAGAAACATTGACAAAAGTTCT 57.370 32.000 9.09 9.17 0.00 3.01
2124 2614 8.687824 TTTGAGAGAAACATTGACAAAAGTTC 57.312 30.769 9.09 5.33 0.00 3.01
2125 2615 9.657419 AATTTGAGAGAAACATTGACAAAAGTT 57.343 25.926 0.00 0.00 31.45 2.66
2126 2616 9.657419 AAATTTGAGAGAAACATTGACAAAAGT 57.343 25.926 0.00 0.00 31.45 2.66
2188 2678 2.675844 TCCCGCATGAACAGTAAAATCG 59.324 45.455 0.00 0.00 0.00 3.34
2191 2681 1.810151 GCTCCCGCATGAACAGTAAAA 59.190 47.619 0.00 0.00 35.78 1.52
2195 2685 2.749682 TGCTCCCGCATGAACAGT 59.250 55.556 0.00 0.00 42.25 3.55
2209 2699 5.803795 GGAATTGATCCTGAGCTCATATGCT 60.804 44.000 18.63 0.23 45.56 3.79
2210 2700 4.395542 GGAATTGATCCTGAGCTCATATGC 59.604 45.833 18.63 8.26 45.56 3.14
2224 2714 0.880718 GGGACGCGGAGGAATTGATC 60.881 60.000 12.47 0.00 0.00 2.92
2225 2715 1.146263 GGGACGCGGAGGAATTGAT 59.854 57.895 12.47 0.00 0.00 2.57
2226 2716 1.956629 GAGGGACGCGGAGGAATTGA 61.957 60.000 12.47 0.00 0.00 2.57
2227 2717 1.521681 GAGGGACGCGGAGGAATTG 60.522 63.158 12.47 0.00 0.00 2.32
2228 2718 1.961180 CTGAGGGACGCGGAGGAATT 61.961 60.000 12.47 0.00 36.30 2.17
2229 2719 2.363795 TGAGGGACGCGGAGGAAT 60.364 61.111 12.47 0.00 0.00 3.01
2230 2720 3.068691 CTGAGGGACGCGGAGGAA 61.069 66.667 12.47 0.00 36.30 3.36
2231 2721 4.043100 TCTGAGGGACGCGGAGGA 62.043 66.667 12.47 0.00 38.96 3.71
2232 2722 3.827898 GTCTGAGGGACGCGGAGG 61.828 72.222 12.47 0.00 45.85 4.30
2233 2723 1.878656 AAAGTCTGAGGGACGCGGAG 61.879 60.000 12.47 0.00 45.85 4.63
2237 2727 8.068793 TTAGATCACTAAAGTCTGAGGGACGC 62.069 46.154 0.00 0.00 40.14 5.19
2238 2728 5.357314 TTAGATCACTAAAGTCTGAGGGACG 59.643 44.000 0.00 0.00 40.14 4.79
2239 2729 6.777213 TTAGATCACTAAAGTCTGAGGGAC 57.223 41.667 0.00 0.00 38.08 4.46
2247 2737 8.859517 ATAAGAGCGTTTAGATCACTAAAGTC 57.140 34.615 0.00 0.00 45.42 3.01
2465 2990 2.357517 CTGTCGTTCGGCCAAGCT 60.358 61.111 2.24 0.00 0.00 3.74
2481 3006 3.826729 GGTTAACTGGTGAGAAAATGGCT 59.173 43.478 5.42 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.