Multiple sequence alignment - TraesCS5A01G293900

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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 TraesCS5A01G293900 chr5A 100.000 8534 0 0 1 8534 503272420 503280953 0.000000e+00 15760.0
1 TraesCS5A01G293900 chr5A 94.864 1402 68 3 34 1435 502502658 502501261 0.000000e+00 2187.0
2 TraesCS5A01G293900 chr5A 93.111 1437 91 7 1 1434 513432477 513433908 0.000000e+00 2098.0
3 TraesCS5A01G293900 chr5A 91.488 1445 105 11 1 1434 482384880 482383443 0.000000e+00 1971.0
4 TraesCS5A01G293900 chr5A 80.331 544 99 4 1435 1978 503439532 503440067 1.030000e-108 405.0
5 TraesCS5A01G293900 chr4D 94.798 5421 276 5 2049 7466 499532160 499526743 0.000000e+00 8444.0
6 TraesCS5A01G293900 chr5D 94.337 5492 289 10 1979 7467 458171721 458177193 0.000000e+00 8399.0
7 TraesCS5A01G293900 chr5D 90.628 2454 223 6 4945 7397 21609898 21607451 0.000000e+00 3251.0
8 TraesCS5A01G293900 chr5D 90.060 2183 212 3 2765 4946 21654794 21652616 0.000000e+00 2824.0
9 TraesCS5A01G293900 chr5D 93.248 548 30 6 7891 8433 398246820 398247365 0.000000e+00 800.0
10 TraesCS5A01G293900 chr5D 92.294 545 34 4 1435 1979 398245799 398246335 0.000000e+00 767.0
11 TraesCS5A01G293900 chr5D 84.615 793 89 20 1980 2769 21669256 21668494 0.000000e+00 758.0
12 TraesCS5A01G293900 chr5D 94.311 457 24 2 7011 7467 458178365 458177911 0.000000e+00 699.0
13 TraesCS5A01G293900 chr5D 85.371 458 37 6 7467 7894 398246331 398246788 1.690000e-121 448.0
14 TraesCS5A01G293900 chr6D 93.954 5491 326 6 1980 7466 467177099 467182587 0.000000e+00 8296.0
15 TraesCS5A01G293900 chr3A 96.907 4300 125 4 1977 6270 20233523 20237820 0.000000e+00 7197.0
16 TraesCS5A01G293900 chr3A 93.259 1439 88 6 1 1434 721079740 721078306 0.000000e+00 2111.0
17 TraesCS5A01G293900 chr7B 87.989 5495 637 22 1982 7466 124895296 124889815 0.000000e+00 6469.0
18 TraesCS5A01G293900 chr7B 91.788 1437 88 12 1 1434 34145115 34146524 0.000000e+00 1973.0
19 TraesCS5A01G293900 chr7D 94.490 2958 156 6 1979 4932 18800997 18798043 0.000000e+00 4553.0
20 TraesCS5A01G293900 chr7D 94.317 2446 133 6 5022 7466 18798040 18795600 0.000000e+00 3742.0
21 TraesCS5A01G293900 chr7D 91.304 46 4 0 7847 7892 594075207 594075162 7.150000e-06 63.9
22 TraesCS5A01G293900 chr2B 88.652 3525 392 7 1976 5497 325819073 325822592 0.000000e+00 4287.0
23 TraesCS5A01G293900 chr2B 88.490 1920 208 11 5558 7471 325822597 325824509 0.000000e+00 2309.0
24 TraesCS5A01G293900 chr7A 89.010 2930 311 10 4543 7467 618175578 618172655 0.000000e+00 3616.0
25 TraesCS5A01G293900 chr7A 88.629 1794 197 7 1979 3770 618177368 618175580 0.000000e+00 2176.0
26 TraesCS5A01G293900 chr7A 92.837 1438 94 6 1 1434 52234531 52235963 0.000000e+00 2076.0
27 TraesCS5A01G293900 chr1D 88.981 1443 138 16 1 1434 390584904 390583474 0.000000e+00 1764.0
28 TraesCS5A01G293900 chr3D 88.329 1448 145 17 1 1434 3966579 3968016 0.000000e+00 1716.0
29 TraesCS5A01G293900 chr6B 88.264 1440 149 16 1 1434 704531963 704533388 0.000000e+00 1705.0
30 TraesCS5A01G293900 chr1B 77.666 2691 553 44 4800 7466 389098502 389095836 0.000000e+00 1596.0
31 TraesCS5A01G293900 chr5B 79.466 487 92 5 1493 1978 478404936 478405415 1.060000e-88 339.0
32 TraesCS5A01G293900 chr5B 79.098 488 91 8 1493 1979 478425914 478426391 8.260000e-85 326.0


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 TraesCS5A01G293900 chr5A 503272420 503280953 8533 False 15760.000000 15760 100.000000 1 8534 1 chr5A.!!$F1 8533
1 TraesCS5A01G293900 chr5A 502501261 502502658 1397 True 2187.000000 2187 94.864000 34 1435 1 chr5A.!!$R2 1401
2 TraesCS5A01G293900 chr5A 513432477 513433908 1431 False 2098.000000 2098 93.111000 1 1434 1 chr5A.!!$F3 1433
3 TraesCS5A01G293900 chr5A 482383443 482384880 1437 True 1971.000000 1971 91.488000 1 1434 1 chr5A.!!$R1 1433
4 TraesCS5A01G293900 chr5A 503439532 503440067 535 False 405.000000 405 80.331000 1435 1978 1 chr5A.!!$F2 543
5 TraesCS5A01G293900 chr4D 499526743 499532160 5417 True 8444.000000 8444 94.798000 2049 7466 1 chr4D.!!$R1 5417
6 TraesCS5A01G293900 chr5D 458171721 458177193 5472 False 8399.000000 8399 94.337000 1979 7467 1 chr5D.!!$F1 5488
7 TraesCS5A01G293900 chr5D 21607451 21609898 2447 True 3251.000000 3251 90.628000 4945 7397 1 chr5D.!!$R1 2452
8 TraesCS5A01G293900 chr5D 21652616 21654794 2178 True 2824.000000 2824 90.060000 2765 4946 1 chr5D.!!$R2 2181
9 TraesCS5A01G293900 chr5D 21668494 21669256 762 True 758.000000 758 84.615000 1980 2769 1 chr5D.!!$R3 789
10 TraesCS5A01G293900 chr5D 398245799 398247365 1566 False 671.666667 800 90.304333 1435 8433 3 chr5D.!!$F2 6998
11 TraesCS5A01G293900 chr6D 467177099 467182587 5488 False 8296.000000 8296 93.954000 1980 7466 1 chr6D.!!$F1 5486
12 TraesCS5A01G293900 chr3A 20233523 20237820 4297 False 7197.000000 7197 96.907000 1977 6270 1 chr3A.!!$F1 4293
13 TraesCS5A01G293900 chr3A 721078306 721079740 1434 True 2111.000000 2111 93.259000 1 1434 1 chr3A.!!$R1 1433
14 TraesCS5A01G293900 chr7B 124889815 124895296 5481 True 6469.000000 6469 87.989000 1982 7466 1 chr7B.!!$R1 5484
15 TraesCS5A01G293900 chr7B 34145115 34146524 1409 False 1973.000000 1973 91.788000 1 1434 1 chr7B.!!$F1 1433
16 TraesCS5A01G293900 chr7D 18795600 18800997 5397 True 4147.500000 4553 94.403500 1979 7466 2 chr7D.!!$R2 5487
17 TraesCS5A01G293900 chr2B 325819073 325824509 5436 False 3298.000000 4287 88.571000 1976 7471 2 chr2B.!!$F1 5495
18 TraesCS5A01G293900 chr7A 618172655 618177368 4713 True 2896.000000 3616 88.819500 1979 7467 2 chr7A.!!$R1 5488
19 TraesCS5A01G293900 chr7A 52234531 52235963 1432 False 2076.000000 2076 92.837000 1 1434 1 chr7A.!!$F1 1433
20 TraesCS5A01G293900 chr1D 390583474 390584904 1430 True 1764.000000 1764 88.981000 1 1434 1 chr1D.!!$R1 1433
21 TraesCS5A01G293900 chr3D 3966579 3968016 1437 False 1716.000000 1716 88.329000 1 1434 1 chr3D.!!$F1 1433
22 TraesCS5A01G293900 chr6B 704531963 704533388 1425 False 1705.000000 1705 88.264000 1 1434 1 chr6B.!!$F1 1433
23 TraesCS5A01G293900 chr1B 389095836 389098502 2666 True 1596.000000 1596 77.666000 4800 7466 1 chr1B.!!$R1 2666

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
922 935 0.179004 TTTGCCGTCCTTGGTGATGT 60.179 50.0 0.00 0.00 0.0 3.06 F
1736 1770 0.034477 CCATGGGGGTGACTTGGTAC 60.034 60.0 2.85 0.00 0.0 3.34 F
2285 2328 0.320697 GAGTGAAGTGTTAGCGGGGT 59.679 55.0 0.00 0.00 0.0 4.95 F
2926 2971 0.478072 ACTTCAGATTGCCACCACCA 59.522 50.0 0.00 0.00 0.0 4.17 F
4014 4059 0.314935 CCAGCGTGCAAGTGGAATTT 59.685 50.0 13.23 0.00 32.6 1.82 F
4933 4980 0.250467 GACACATGTGACCCTGCTGT 60.250 55.0 31.94 6.16 0.0 4.40 F
5764 5901 0.039256 GGCAGCGCAACATTTTCTCA 60.039 50.0 11.47 0.00 0.0 3.27 F
6684 6827 0.036732 AGCAAATGAAGGACTCGGCA 59.963 50.0 0.00 0.00 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 1773 0.107800 TGCTGAGAGAGATTGCCTGC 60.108 55.000 0.00 0.00 0.00 4.85 R
2734 2779 0.169009 CACGAGCTGAGATGTCGACA 59.831 55.000 22.48 22.48 37.16 4.35 R
3646 3691 1.137404 GCAATGATGTTCGCGGCTT 59.863 52.632 6.13 0.00 0.00 4.35 R
4590 4637 0.107643 TGATTGTGTTGAGGTGCCGA 59.892 50.000 0.00 0.00 0.00 5.54 R
5675 5812 0.463654 TGATGTAATGGTGGCGAGGC 60.464 55.000 0.00 0.00 0.00 4.70 R
6202 6342 0.595095 GCAACTTGGAAGGCTGTGAG 59.405 55.000 0.00 0.00 0.00 3.51 R
7013 7156 0.037232 GACCTGTGGAACTCCGGAAG 60.037 60.000 5.23 2.09 39.43 3.46 R
8433 8651 0.036952 AGCATGTTCTCGTGAGGGTG 60.037 55.000 0.00 0.00 32.78 4.61 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
100 101 3.218453 CATACCACACGAGATCTCCTCT 58.782 50.000 17.13 0.00 39.78 3.69
101 102 1.757682 ACCACACGAGATCTCCTCTC 58.242 55.000 17.13 0.00 45.98 3.20
139 143 5.162794 GTTGCATCAACATGTTTAGCATCA 58.837 37.500 22.49 11.43 43.09 3.07
247 251 3.141488 GAAGAGGAGGAGCGGCGA 61.141 66.667 12.98 0.00 0.00 5.54
283 287 1.692749 GCCACCACCCCCTGATCTA 60.693 63.158 0.00 0.00 0.00 1.98
598 611 3.111838 CAAGATCTTGGACACGATCTCG 58.888 50.000 25.14 6.98 43.08 4.04
804 817 2.967076 CAGCGTGGCGACTTGTGT 60.967 61.111 0.00 0.00 0.00 3.72
849 862 2.435805 CCATCAAGTAGCCTTGGAGCTA 59.564 50.000 3.30 0.00 46.65 3.32
855 868 4.443457 CAAGTAGCCTTGGAGCTATTGCTA 60.443 45.833 0.37 0.00 46.54 3.49
922 935 0.179004 TTTGCCGTCCTTGGTGATGT 60.179 50.000 0.00 0.00 0.00 3.06
933 946 1.380302 GGTGATGTTGAGGGTGGCT 59.620 57.895 0.00 0.00 0.00 4.75
998 1011 1.771255 GCCCTTGATCTGTGGTAGGAT 59.229 52.381 0.00 0.00 0.00 3.24
1033 1046 2.434359 GGAAGTTGCCCCTCGTCG 60.434 66.667 0.00 0.00 0.00 5.12
1044 1057 1.587054 CCTCGTCGGCTTCTCTTGT 59.413 57.895 0.00 0.00 0.00 3.16
1047 1060 1.176619 TCGTCGGCTTCTCTTGTGGA 61.177 55.000 0.00 0.00 0.00 4.02
1051 1064 1.377856 GGCTTCTCTTGTGGAGGCC 60.378 63.158 0.00 0.00 40.39 5.19
1071 1090 0.635009 ATCCGAGGAAGGAGGTGGTA 59.365 55.000 0.00 0.00 44.55 3.25
1092 1111 3.391774 AGAGTTGGAGGTGGATGATGAT 58.608 45.455 0.00 0.00 0.00 2.45
1225 1245 3.323403 CCAATCTATCGAGGAAGAGGCTT 59.677 47.826 0.00 0.00 0.00 4.35
1238 1258 5.044846 AGGAAGAGGCTTTGTTACCATGTAT 60.045 40.000 0.00 0.00 0.00 2.29
1266 1286 1.770294 TGGAAGCGTTGAACCCTTTT 58.230 45.000 0.00 0.00 0.00 2.27
1451 1485 1.160137 CACACAGCTCCTTACTTGCC 58.840 55.000 0.00 0.00 0.00 4.52
1483 1517 1.270305 GCAGCTGATCGGCCACTTATA 60.270 52.381 23.02 0.00 0.00 0.98
1484 1518 2.613977 GCAGCTGATCGGCCACTTATAT 60.614 50.000 23.02 0.00 0.00 0.86
1485 1519 3.257393 CAGCTGATCGGCCACTTATATC 58.743 50.000 23.02 0.00 0.00 1.63
1486 1520 2.094494 AGCTGATCGGCCACTTATATCG 60.094 50.000 23.02 0.00 0.00 2.92
1571 1605 2.286523 AAGACCACCAGGCTCCTCG 61.287 63.158 0.00 0.00 39.06 4.63
1643 1677 0.247814 CAAGATCCACACGCGCATTC 60.248 55.000 5.73 0.00 0.00 2.67
1668 1702 2.359531 CTGACCGGAATAGAGTGGACTC 59.640 54.545 9.46 0.00 43.17 3.36
1682 1716 1.194781 GGACTCCCACAAGCCTCTCA 61.195 60.000 0.00 0.00 0.00 3.27
1685 1719 1.533033 TCCCACAAGCCTCTCACGA 60.533 57.895 0.00 0.00 0.00 4.35
1734 1768 1.465188 TCCATGGGGGTGACTTGGT 60.465 57.895 13.02 0.00 38.11 3.67
1736 1770 0.034477 CCATGGGGGTGACTTGGTAC 60.034 60.000 2.85 0.00 0.00 3.34
1737 1771 0.991920 CATGGGGGTGACTTGGTACT 59.008 55.000 0.00 0.00 0.00 2.73
1738 1772 0.991920 ATGGGGGTGACTTGGTACTG 59.008 55.000 0.00 0.00 0.00 2.74
1739 1773 1.131303 TGGGGGTGACTTGGTACTGG 61.131 60.000 0.00 0.00 0.00 4.00
1740 1774 1.002502 GGGGTGACTTGGTACTGGC 60.003 63.158 0.00 0.00 0.00 4.85
1741 1775 1.758592 GGGTGACTTGGTACTGGCA 59.241 57.895 0.00 0.00 0.00 4.92
1742 1776 0.321653 GGGTGACTTGGTACTGGCAG 60.322 60.000 14.16 14.16 0.00 4.85
1743 1777 0.321653 GGTGACTTGGTACTGGCAGG 60.322 60.000 20.34 1.75 0.00 4.85
1748 1782 1.098050 CTTGGTACTGGCAGGCAATC 58.902 55.000 20.34 4.77 0.00 2.67
1756 1790 0.540454 TGGCAGGCAATCTCTCTCAG 59.460 55.000 0.00 0.00 0.00 3.35
1762 1796 3.102972 AGGCAATCTCTCTCAGCAGTTA 58.897 45.455 0.00 0.00 0.00 2.24
1783 1817 4.537135 AGCGATGTTAACTCAAGAGGAA 57.463 40.909 7.22 0.00 0.00 3.36
1831 1865 1.339438 ACACTGCATCCGCTCTTCAAT 60.339 47.619 0.00 0.00 39.64 2.57
1840 1874 1.645034 CGCTCTTCAATGACGACCAT 58.355 50.000 0.00 0.00 36.99 3.55
1842 1876 3.186909 CGCTCTTCAATGACGACCATAA 58.813 45.455 0.00 0.00 34.45 1.90
1843 1877 3.804325 CGCTCTTCAATGACGACCATAAT 59.196 43.478 0.00 0.00 34.45 1.28
1848 1882 7.011482 GCTCTTCAATGACGACCATAATAACTT 59.989 37.037 0.00 0.00 34.45 2.66
1849 1883 8.786826 TCTTCAATGACGACCATAATAACTTT 57.213 30.769 0.00 0.00 34.45 2.66
1851 1885 9.840427 CTTCAATGACGACCATAATAACTTTTT 57.160 29.630 0.00 0.00 34.45 1.94
1885 1919 1.797046 GATGATGTGCTACTGGATGCG 59.203 52.381 0.00 0.00 0.00 4.73
1902 1936 1.991430 CGTGCGATCAAGAAGACGG 59.009 57.895 0.00 0.00 0.00 4.79
1907 1941 1.560923 CGATCAAGAAGACGGCGATT 58.439 50.000 16.62 8.02 0.00 3.34
1908 1942 1.927174 CGATCAAGAAGACGGCGATTT 59.073 47.619 16.62 7.18 0.00 2.17
1915 1949 1.078759 AAGACGGCGATTTGCTCTCG 61.079 55.000 16.62 0.00 45.43 4.04
1968 2002 2.930950 TGAGGGTTTGGAGTTCAACAG 58.069 47.619 0.00 0.00 34.67 3.16
1984 2018 2.637872 CAACAGGGAGGAGGAGTGTTAA 59.362 50.000 0.00 0.00 30.28 2.01
2133 2167 2.830321 ACCGACAGGAAGGGTTAAGTAG 59.170 50.000 0.00 0.00 41.02 2.57
2138 2172 1.553704 AGGAAGGGTTAAGTAGTGCGG 59.446 52.381 0.00 0.00 0.00 5.69
2285 2328 0.320697 GAGTGAAGTGTTAGCGGGGT 59.679 55.000 0.00 0.00 0.00 4.95
2297 2340 1.102978 AGCGGGGTCATAACAATTGC 58.897 50.000 5.05 0.00 0.00 3.56
2573 2618 1.067565 GTCACTTGCGGACTCAGATCA 60.068 52.381 0.00 0.00 32.54 2.92
2634 2679 1.915266 CTGCTCCACCACCTCCTCA 60.915 63.158 0.00 0.00 0.00 3.86
2857 2902 2.444004 TACCTCCGGCCACTGGTACA 62.444 60.000 2.24 0.00 34.33 2.90
2926 2971 0.478072 ACTTCAGATTGCCACCACCA 59.522 50.000 0.00 0.00 0.00 4.17
2950 2995 3.492756 CGCGGTTTGATTTTCCATTGTTT 59.507 39.130 0.00 0.00 0.00 2.83
3051 3096 4.095185 GGTTAGTTGTGCGGCAATGTATTA 59.905 41.667 3.23 0.00 39.55 0.98
3201 3246 3.258228 TCAATCGCTTGCGACAAATAGA 58.742 40.909 20.01 8.84 32.11 1.98
3569 3614 2.281517 CAGAGACGACTCGTACTCCAT 58.718 52.381 19.07 6.98 46.64 3.41
3575 3620 1.395954 CGACTCGTACTCCATCGAACA 59.604 52.381 0.00 0.00 35.69 3.18
3638 3683 1.785041 GCTCTGTTTCACTTGCGGCA 61.785 55.000 0.00 0.00 0.00 5.69
3660 3705 2.390599 GCTGAAGCCGCGAACATCA 61.391 57.895 8.23 7.29 34.31 3.07
3958 4003 0.528684 GTGCTCTATCTGTGCGGGTC 60.529 60.000 0.00 0.00 37.94 4.46
4014 4059 0.314935 CCAGCGTGCAAGTGGAATTT 59.685 50.000 13.23 0.00 32.60 1.82
4442 4489 3.383505 CCAGTCAACATACGACCCTATCA 59.616 47.826 0.00 0.00 33.70 2.15
4590 4637 4.581824 ACTTGGCGATTCTGCATTGATTAT 59.418 37.500 0.00 0.00 36.28 1.28
4603 4650 3.342377 TTGATTATCGGCACCTCAACA 57.658 42.857 0.00 0.00 0.00 3.33
4622 4669 8.298854 CCTCAACACAATCACAATCAAGAATAA 58.701 33.333 0.00 0.00 0.00 1.40
4664 4711 0.522180 GAACTTCTCGACGAGCTGGA 59.478 55.000 20.11 0.00 0.00 3.86
4757 4804 3.807553 CCCACAAAACAGCCTTCAAAAT 58.192 40.909 0.00 0.00 0.00 1.82
4788 4835 2.742053 GCATTTCGAGTTCAAGGTGCTA 59.258 45.455 0.00 0.00 0.00 3.49
4859 4906 1.621814 GGTACTGTCACCCTTACTGCA 59.378 52.381 0.00 0.00 31.91 4.41
4899 4946 7.330454 GTGTTCATCGATGATATCTTAGTGCAT 59.670 37.037 27.75 0.00 36.56 3.96
4933 4980 0.250467 GACACATGTGACCCTGCTGT 60.250 55.000 31.94 6.16 0.00 4.40
4978 5025 3.137446 AGCATCAGTTCAAGCTCAAGT 57.863 42.857 0.00 0.00 30.05 3.16
5005 5052 1.880819 ATGCTTCTTTGCTTGCCCCG 61.881 55.000 0.00 0.00 0.00 5.73
5421 5557 1.208642 TACGCAATCGCATGCTCTCG 61.209 55.000 17.13 13.53 44.21 4.04
5760 5897 2.049248 CCGGCAGCGCAACATTTT 60.049 55.556 11.47 0.00 0.00 1.82
5764 5901 0.039256 GGCAGCGCAACATTTTCTCA 60.039 50.000 11.47 0.00 0.00 3.27
5767 5904 2.859806 GCAGCGCAACATTTTCTCACTT 60.860 45.455 11.47 0.00 0.00 3.16
6079 6217 1.071071 CACTACCGGTTCCCACTCAAA 59.929 52.381 15.04 0.00 0.00 2.69
6187 6327 4.602159 GGTACGCCCATTTCGTCA 57.398 55.556 0.00 0.00 40.89 4.35
6202 6342 1.204704 TCGTCACCATGTCACATCCTC 59.795 52.381 0.00 0.00 0.00 3.71
6573 6714 1.951130 CTTCGGCATCATCGACCCG 60.951 63.158 0.00 0.00 41.97 5.28
6574 6715 2.349969 CTTCGGCATCATCGACCCGA 62.350 60.000 8.35 8.35 46.94 5.14
6649 6790 0.319900 AGCGCTCATTCGACAACACT 60.320 50.000 2.64 0.00 0.00 3.55
6654 6797 2.736721 GCTCATTCGACAACACTTGCTA 59.263 45.455 0.00 0.00 0.00 3.49
6684 6827 0.036732 AGCAAATGAAGGACTCGGCA 59.963 50.000 0.00 0.00 0.00 5.69
7308 7451 3.119209 CCGACAGGAAGGGTTAAGTACTC 60.119 52.174 0.00 0.00 41.02 2.59
7316 7459 0.101939 GGTTAAGTACTCCGCCCTCG 59.898 60.000 0.00 0.00 0.00 4.63
7373 7518 4.699522 GCGGCGACACTTCCCCTT 62.700 66.667 12.98 0.00 0.00 3.95
7390 7535 2.158310 CCCTTATCCCCATTTCCTTCCC 60.158 54.545 0.00 0.00 0.00 3.97
7402 7547 2.862850 TCCTTCCCCTAGAACCCTAC 57.137 55.000 0.00 0.00 0.00 3.18
7411 7556 3.892588 CCCTAGAACCCTACTTCTGCTAG 59.107 52.174 0.00 0.00 32.54 3.42
7419 7566 5.026790 ACCCTACTTCTGCTAGTCAAATCT 58.973 41.667 0.00 0.00 0.00 2.40
7426 7573 7.846066 ACTTCTGCTAGTCAAATCTTGTATCT 58.154 34.615 0.00 0.00 0.00 1.98
7428 7575 7.652524 TCTGCTAGTCAAATCTTGTATCTCT 57.347 36.000 0.00 0.00 0.00 3.10
7449 7596 3.469008 TGGTGAATTCGAGTGAAGTGT 57.531 42.857 0.04 0.00 37.57 3.55
7458 7606 0.320697 GAGTGAAGTGTTAGCGGGGT 59.679 55.000 0.00 0.00 0.00 4.95
7557 7705 4.158394 GGTCTTGTTTCCACATGCATGTAT 59.842 41.667 30.92 8.10 39.39 2.29
7564 7712 1.797046 CCACATGCATGTATCTCGAGC 59.203 52.381 30.92 0.00 39.39 5.03
7586 7758 3.583086 CCGGGTATCCACTGGATAGAAAT 59.417 47.826 16.92 0.00 44.25 2.17
7596 7768 9.927081 ATCCACTGGATAGAAATTTTTGTAGAT 57.073 29.630 9.00 0.00 41.16 1.98
7631 7803 9.151471 GAGTAAAATCTGATACTTAGCACACAA 57.849 33.333 0.00 0.00 32.66 3.33
7639 7811 7.708322 TCTGATACTTAGCACACAATGATCTTC 59.292 37.037 0.00 0.00 0.00 2.87
7653 7826 9.865321 CACAATGATCTTCTGGTCATTTAATTT 57.135 29.630 2.20 0.00 41.70 1.82
7686 7859 6.360370 TTGTTAGCAACTAAGATCCTCAGT 57.640 37.500 0.00 0.00 0.00 3.41
7692 7865 4.285863 CAACTAAGATCCTCAGTCTCCCT 58.714 47.826 0.00 0.00 0.00 4.20
7703 7876 1.911766 GTCTCCCTCACCGTTCCCA 60.912 63.158 0.00 0.00 0.00 4.37
7739 7913 3.357079 CACCCGTGCCTCACAAGC 61.357 66.667 0.00 0.00 33.40 4.01
7776 7950 0.256752 AGTGCTGCTATGATTGGGCA 59.743 50.000 0.00 0.00 34.66 5.36
7785 7959 5.991861 TGCTATGATTGGGCAAAATTTCAT 58.008 33.333 0.00 0.00 32.79 2.57
7787 7961 7.737869 TGCTATGATTGGGCAAAATTTCATAT 58.262 30.769 0.00 0.00 32.79 1.78
7788 7962 8.212312 TGCTATGATTGGGCAAAATTTCATATT 58.788 29.630 0.00 0.00 32.79 1.28
7789 7963 9.059260 GCTATGATTGGGCAAAATTTCATATTT 57.941 29.630 0.00 0.00 0.00 1.40
7822 8000 9.028185 GCAGGAACAAATTTTGATCTATTCATC 57.972 33.333 15.81 0.00 33.34 2.92
7834 8012 5.761726 TGATCTATTCATCAACTGTCATGGC 59.238 40.000 0.00 0.00 29.41 4.40
7835 8013 4.454678 TCTATTCATCAACTGTCATGGCC 58.545 43.478 0.00 0.00 0.00 5.36
7839 8017 2.779430 TCATCAACTGTCATGGCCCTAT 59.221 45.455 0.00 0.00 0.00 2.57
7892 8105 1.202580 GGTCCGTAGACTACCTAGCGA 60.203 57.143 7.05 0.00 43.05 4.93
7924 8141 4.447034 CCTCTCTCTTACTGGAGCCTATCA 60.447 50.000 0.00 0.00 33.70 2.15
7967 8184 4.067972 TCTCTACAAGTCGCCAAAACTT 57.932 40.909 0.00 0.00 37.44 2.66
8002 8219 5.239525 GGAAGTTGTATCTTCTGCTTGTTGT 59.760 40.000 6.44 0.00 42.19 3.32
8012 8229 4.566545 TCTGCTTGTTGTGGTTATGTTG 57.433 40.909 0.00 0.00 0.00 3.33
8015 8232 3.951037 TGCTTGTTGTGGTTATGTTGACT 59.049 39.130 0.00 0.00 0.00 3.41
8045 8262 1.094785 AGCACTGCGACACTTTGTTT 58.905 45.000 0.00 0.00 0.00 2.83
8053 8270 2.159435 GCGACACTTTGTTTGGTCACTT 60.159 45.455 0.00 0.00 0.00 3.16
8071 8288 0.107643 TTGTGACCCTGCATCGAACA 59.892 50.000 0.00 0.00 0.00 3.18
8191 8409 8.480643 AACAAAACTAGTAGAGTGATATGTGC 57.519 34.615 3.59 0.00 38.87 4.57
8266 8484 2.902608 ACATGGTCTCCAAGGACTACA 58.097 47.619 0.00 0.00 36.95 2.74
8403 8621 2.965831 TGTCCTGTATATGGAGTGAGCC 59.034 50.000 0.00 0.00 33.78 4.70
8426 8644 0.895530 CCTAGTTCCAACTCGGCTCA 59.104 55.000 0.00 0.00 40.37 4.26
8433 8651 3.194005 TCCAACTCGGCTCATATTTCC 57.806 47.619 0.00 0.00 33.14 3.13
8434 8652 2.503765 TCCAACTCGGCTCATATTTCCA 59.496 45.455 0.00 0.00 33.14 3.53
8435 8653 2.614057 CCAACTCGGCTCATATTTCCAC 59.386 50.000 0.00 0.00 0.00 4.02
8436 8654 2.614057 CAACTCGGCTCATATTTCCACC 59.386 50.000 0.00 0.00 0.00 4.61
8437 8655 1.141053 ACTCGGCTCATATTTCCACCC 59.859 52.381 0.00 0.00 0.00 4.61
8438 8656 1.417890 CTCGGCTCATATTTCCACCCT 59.582 52.381 0.00 0.00 0.00 4.34
8439 8657 1.416401 TCGGCTCATATTTCCACCCTC 59.584 52.381 0.00 0.00 0.00 4.30
8440 8658 1.140852 CGGCTCATATTTCCACCCTCA 59.859 52.381 0.00 0.00 0.00 3.86
8441 8659 2.576615 GGCTCATATTTCCACCCTCAC 58.423 52.381 0.00 0.00 0.00 3.51
8442 8660 2.213499 GCTCATATTTCCACCCTCACG 58.787 52.381 0.00 0.00 0.00 4.35
8443 8661 2.158957 GCTCATATTTCCACCCTCACGA 60.159 50.000 0.00 0.00 0.00 4.35
8444 8662 3.722147 CTCATATTTCCACCCTCACGAG 58.278 50.000 0.00 0.00 0.00 4.18
8445 8663 3.371034 TCATATTTCCACCCTCACGAGA 58.629 45.455 0.00 0.00 0.00 4.04
8446 8664 3.772572 TCATATTTCCACCCTCACGAGAA 59.227 43.478 0.00 0.00 0.00 2.87
8447 8665 2.474410 ATTTCCACCCTCACGAGAAC 57.526 50.000 0.00 0.00 0.00 3.01
8448 8666 1.124780 TTTCCACCCTCACGAGAACA 58.875 50.000 0.00 0.00 0.00 3.18
8449 8667 1.348064 TTCCACCCTCACGAGAACAT 58.652 50.000 0.00 0.00 0.00 2.71
8450 8668 0.608130 TCCACCCTCACGAGAACATG 59.392 55.000 0.00 0.00 0.00 3.21
8451 8669 1.021390 CCACCCTCACGAGAACATGC 61.021 60.000 0.00 0.00 0.00 4.06
8452 8670 0.036952 CACCCTCACGAGAACATGCT 60.037 55.000 0.00 0.00 0.00 3.79
8453 8671 0.687354 ACCCTCACGAGAACATGCTT 59.313 50.000 0.00 0.00 0.00 3.91
8454 8672 1.072331 ACCCTCACGAGAACATGCTTT 59.928 47.619 0.00 0.00 0.00 3.51
8455 8673 2.154462 CCCTCACGAGAACATGCTTTT 58.846 47.619 0.00 0.00 0.00 2.27
8456 8674 2.554032 CCCTCACGAGAACATGCTTTTT 59.446 45.455 0.00 0.00 0.00 1.94
8457 8675 3.365364 CCCTCACGAGAACATGCTTTTTC 60.365 47.826 0.00 0.00 0.00 2.29
8458 8676 3.499918 CCTCACGAGAACATGCTTTTTCT 59.500 43.478 0.93 0.93 34.68 2.52
8459 8677 4.377841 CCTCACGAGAACATGCTTTTTCTC 60.378 45.833 15.19 15.19 42.94 2.87
8460 8678 4.126437 TCACGAGAACATGCTTTTTCTCA 58.874 39.130 21.56 6.25 45.50 3.27
8461 8679 4.574421 TCACGAGAACATGCTTTTTCTCAA 59.426 37.500 21.56 9.04 45.50 3.02
8462 8680 5.239306 TCACGAGAACATGCTTTTTCTCAAT 59.761 36.000 21.56 10.90 45.50 2.57
8463 8681 5.566774 CACGAGAACATGCTTTTTCTCAATC 59.433 40.000 21.56 3.51 45.50 2.67
8464 8682 5.091431 CGAGAACATGCTTTTTCTCAATCC 58.909 41.667 21.56 3.02 45.50 3.01
8465 8683 5.106396 CGAGAACATGCTTTTTCTCAATCCT 60.106 40.000 21.56 0.00 45.50 3.24
8466 8684 6.092670 CGAGAACATGCTTTTTCTCAATCCTA 59.907 38.462 21.56 0.00 45.50 2.94
8467 8685 7.361201 CGAGAACATGCTTTTTCTCAATCCTAA 60.361 37.037 21.56 0.00 45.50 2.69
8468 8686 7.597386 AGAACATGCTTTTTCTCAATCCTAAC 58.403 34.615 0.00 0.00 0.00 2.34
8469 8687 6.272822 ACATGCTTTTTCTCAATCCTAACC 57.727 37.500 0.00 0.00 0.00 2.85
8470 8688 5.774690 ACATGCTTTTTCTCAATCCTAACCA 59.225 36.000 0.00 0.00 0.00 3.67
8471 8689 6.267471 ACATGCTTTTTCTCAATCCTAACCAA 59.733 34.615 0.00 0.00 0.00 3.67
8472 8690 6.331369 TGCTTTTTCTCAATCCTAACCAAG 57.669 37.500 0.00 0.00 0.00 3.61
8473 8691 6.068010 TGCTTTTTCTCAATCCTAACCAAGA 58.932 36.000 0.00 0.00 0.00 3.02
8474 8692 6.207417 TGCTTTTTCTCAATCCTAACCAAGAG 59.793 38.462 0.00 0.00 0.00 2.85
8475 8693 6.431234 GCTTTTTCTCAATCCTAACCAAGAGA 59.569 38.462 0.00 0.00 0.00 3.10
8476 8694 7.040409 GCTTTTTCTCAATCCTAACCAAGAGAA 60.040 37.037 0.00 0.00 39.53 2.87
8477 8695 7.986085 TTTTCTCAATCCTAACCAAGAGAAG 57.014 36.000 0.00 0.00 41.45 2.85
8478 8696 5.683876 TCTCAATCCTAACCAAGAGAAGG 57.316 43.478 0.00 0.00 0.00 3.46
8479 8697 4.471386 TCTCAATCCTAACCAAGAGAAGGG 59.529 45.833 0.00 0.00 0.00 3.95
8480 8698 4.175962 TCAATCCTAACCAAGAGAAGGGT 58.824 43.478 0.00 0.00 39.65 4.34
8481 8699 5.347124 TCAATCCTAACCAAGAGAAGGGTA 58.653 41.667 0.00 0.00 36.05 3.69
8482 8700 5.788533 TCAATCCTAACCAAGAGAAGGGTAA 59.211 40.000 0.00 0.00 36.05 2.85
8483 8701 6.447084 TCAATCCTAACCAAGAGAAGGGTAAT 59.553 38.462 0.00 0.00 36.05 1.89
8484 8702 6.910259 ATCCTAACCAAGAGAAGGGTAATT 57.090 37.500 0.00 0.00 36.05 1.40
8485 8703 8.272173 CAATCCTAACCAAGAGAAGGGTAATTA 58.728 37.037 0.00 0.00 36.05 1.40
8486 8704 7.817910 TCCTAACCAAGAGAAGGGTAATTAA 57.182 36.000 0.00 0.00 36.05 1.40
8487 8705 8.222138 TCCTAACCAAGAGAAGGGTAATTAAA 57.778 34.615 0.00 0.00 36.05 1.52
8488 8706 8.326529 TCCTAACCAAGAGAAGGGTAATTAAAG 58.673 37.037 0.00 0.00 36.05 1.85
8489 8707 8.326529 CCTAACCAAGAGAAGGGTAATTAAAGA 58.673 37.037 0.00 0.00 36.05 2.52
8490 8708 9.734984 CTAACCAAGAGAAGGGTAATTAAAGAA 57.265 33.333 0.00 0.00 36.05 2.52
8492 8710 8.581253 ACCAAGAGAAGGGTAATTAAAGAATG 57.419 34.615 0.00 0.00 35.09 2.67
8493 8711 7.122799 ACCAAGAGAAGGGTAATTAAAGAATGC 59.877 37.037 0.00 0.00 35.09 3.56
8494 8712 7.122650 CCAAGAGAAGGGTAATTAAAGAATGCA 59.877 37.037 0.00 0.00 0.00 3.96
8495 8713 8.689972 CAAGAGAAGGGTAATTAAAGAATGCAT 58.310 33.333 0.00 0.00 0.00 3.96
8496 8714 8.829373 AGAGAAGGGTAATTAAAGAATGCATT 57.171 30.769 12.83 12.83 0.00 3.56
8497 8715 9.259832 AGAGAAGGGTAATTAAAGAATGCATTT 57.740 29.630 14.33 0.70 0.00 2.32
8498 8716 9.521503 GAGAAGGGTAATTAAAGAATGCATTTC 57.478 33.333 14.33 7.05 34.31 2.17
8499 8717 9.034800 AGAAGGGTAATTAAAGAATGCATTTCA 57.965 29.630 14.33 0.00 36.75 2.69
8500 8718 9.822185 GAAGGGTAATTAAAGAATGCATTTCAT 57.178 29.630 14.33 5.29 36.75 2.57
8504 8722 9.706846 GGTAATTAAAGAATGCATTTCATTTGC 57.293 29.630 14.33 6.81 44.95 3.68
8512 8730 4.177165 TGCATTTCATTTGCAATCGAGT 57.823 36.364 0.00 0.00 46.48 4.18
8513 8731 4.168014 TGCATTTCATTTGCAATCGAGTC 58.832 39.130 0.00 0.00 46.48 3.36
8514 8732 4.082625 TGCATTTCATTTGCAATCGAGTCT 60.083 37.500 0.00 0.00 46.48 3.24
8515 8733 4.498323 GCATTTCATTTGCAATCGAGTCTC 59.502 41.667 0.00 0.00 39.90 3.36
8516 8734 5.675575 GCATTTCATTTGCAATCGAGTCTCT 60.676 40.000 0.00 0.00 39.90 3.10
8517 8735 5.947228 TTTCATTTGCAATCGAGTCTCTT 57.053 34.783 0.00 0.00 0.00 2.85
8518 8736 5.947228 TTCATTTGCAATCGAGTCTCTTT 57.053 34.783 0.00 0.00 0.00 2.52
8519 8737 5.536554 TCATTTGCAATCGAGTCTCTTTC 57.463 39.130 0.00 0.00 0.00 2.62
8520 8738 4.393062 TCATTTGCAATCGAGTCTCTTTCC 59.607 41.667 0.00 0.00 0.00 3.13
8521 8739 3.685139 TTGCAATCGAGTCTCTTTCCT 57.315 42.857 0.00 0.00 0.00 3.36
8522 8740 3.685139 TGCAATCGAGTCTCTTTCCTT 57.315 42.857 0.00 0.00 0.00 3.36
8523 8741 3.589988 TGCAATCGAGTCTCTTTCCTTC 58.410 45.455 0.00 0.00 0.00 3.46
8524 8742 2.933260 GCAATCGAGTCTCTTTCCTTCC 59.067 50.000 0.00 0.00 0.00 3.46
8525 8743 3.617531 GCAATCGAGTCTCTTTCCTTCCA 60.618 47.826 0.00 0.00 0.00 3.53
8526 8744 4.569943 CAATCGAGTCTCTTTCCTTCCAA 58.430 43.478 0.00 0.00 0.00 3.53
8527 8745 3.944055 TCGAGTCTCTTTCCTTCCAAG 57.056 47.619 0.00 0.00 0.00 3.61
8528 8746 2.028930 TCGAGTCTCTTTCCTTCCAAGC 60.029 50.000 0.00 0.00 0.00 4.01
8529 8747 2.028567 CGAGTCTCTTTCCTTCCAAGCT 60.029 50.000 0.00 0.00 0.00 3.74
8530 8748 3.193691 CGAGTCTCTTTCCTTCCAAGCTA 59.806 47.826 0.00 0.00 0.00 3.32
8531 8749 4.322049 CGAGTCTCTTTCCTTCCAAGCTAA 60.322 45.833 0.00 0.00 0.00 3.09
8532 8750 5.159273 AGTCTCTTTCCTTCCAAGCTAAG 57.841 43.478 0.00 0.00 0.00 2.18
8533 8751 4.595350 AGTCTCTTTCCTTCCAAGCTAAGT 59.405 41.667 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 126 4.154015 CGTTCCTGATGCTAAACATGTTGA 59.846 41.667 12.82 3.11 39.84 3.18
247 251 3.377172 GTGGCTTCAACAACAACACTAGT 59.623 43.478 0.00 0.00 0.00 2.57
283 287 4.559153 GCAACTACAACAATTCTGGCAAT 58.441 39.130 0.00 0.00 0.00 3.56
746 759 1.137404 GCGCCATCCACAACATGTC 59.863 57.895 0.00 0.00 0.00 3.06
804 817 1.107538 CCTCTCCCGCGACATCCTTA 61.108 60.000 8.23 0.00 0.00 2.69
855 868 1.985159 TCCCTCTATGGTTTGCACAGT 59.015 47.619 0.00 0.00 0.00 3.55
868 881 3.096852 TGAACTTTGCGAGATCCCTCTA 58.903 45.455 0.00 0.00 37.28 2.43
977 990 0.911769 CCTACCACAGATCAAGGGCA 59.088 55.000 0.00 0.00 0.00 5.36
998 1011 1.605992 CTGCTCTGGAAGGCCATCA 59.394 57.895 10.67 1.33 44.91 3.07
1033 1046 1.377856 GGCCTCCACAAGAGAAGCC 60.378 63.158 0.00 0.00 46.50 4.35
1044 1057 2.040442 TTCCTCGGATGGCCTCCA 59.960 61.111 17.97 7.33 45.24 3.86
1047 1060 1.764054 CTCCTTCCTCGGATGGCCT 60.764 63.158 3.32 0.00 38.76 5.19
1051 1064 0.978146 ACCACCTCCTTCCTCGGATG 60.978 60.000 0.00 0.00 31.43 3.51
1071 1090 2.837947 TCATCATCCACCTCCAACTCT 58.162 47.619 0.00 0.00 0.00 3.24
1092 1111 0.329261 CCTCCTCCTCCATGTTTGCA 59.671 55.000 0.00 0.00 0.00 4.08
1238 1258 4.456566 GGTTCAACGCTTCCATAAACCTTA 59.543 41.667 0.00 0.00 33.53 2.69
1451 1485 0.462581 TCAGCTGCTTATGAAGGGCG 60.463 55.000 9.47 0.00 0.00 6.13
1483 1517 4.142315 CCAATCTTCATCTTTGTTGCCGAT 60.142 41.667 0.00 0.00 0.00 4.18
1484 1518 3.191162 CCAATCTTCATCTTTGTTGCCGA 59.809 43.478 0.00 0.00 0.00 5.54
1485 1519 3.191162 TCCAATCTTCATCTTTGTTGCCG 59.809 43.478 0.00 0.00 0.00 5.69
1486 1520 4.789012 TCCAATCTTCATCTTTGTTGCC 57.211 40.909 0.00 0.00 0.00 4.52
1571 1605 4.200283 CTGGAGCGAGGCGAGGAC 62.200 72.222 0.00 0.00 0.00 3.85
1618 1652 1.795768 GCGTGTGGATCTTGTGAGAA 58.204 50.000 0.00 0.00 35.07 2.87
1643 1677 1.115467 ACTCTATTCCGGTCAGCCAG 58.885 55.000 0.00 0.00 34.09 4.85
1668 1702 3.059982 TCGTGAGAGGCTTGTGGG 58.940 61.111 0.00 0.00 34.84 4.61
1685 1719 1.751351 TCTCTTCTCGATGGTTCGCAT 59.249 47.619 0.00 0.00 45.10 4.73
1734 1768 1.759445 GAGAGAGATTGCCTGCCAGTA 59.241 52.381 0.00 0.00 0.00 2.74
1736 1770 0.540454 TGAGAGAGATTGCCTGCCAG 59.460 55.000 0.00 0.00 0.00 4.85
1737 1771 0.540454 CTGAGAGAGATTGCCTGCCA 59.460 55.000 0.00 0.00 0.00 4.92
1738 1772 0.814812 GCTGAGAGAGATTGCCTGCC 60.815 60.000 0.00 0.00 0.00 4.85
1739 1773 0.107800 TGCTGAGAGAGATTGCCTGC 60.108 55.000 0.00 0.00 0.00 4.85
1740 1774 1.207570 ACTGCTGAGAGAGATTGCCTG 59.792 52.381 0.00 0.00 0.00 4.85
1741 1775 1.570803 ACTGCTGAGAGAGATTGCCT 58.429 50.000 0.00 0.00 0.00 4.75
1742 1776 2.399916 AACTGCTGAGAGAGATTGCC 57.600 50.000 0.00 0.00 0.00 4.52
1743 1777 2.865551 GCTAACTGCTGAGAGAGATTGC 59.134 50.000 0.00 0.00 38.95 3.56
1748 1782 2.098934 ACATCGCTAACTGCTGAGAGAG 59.901 50.000 0.00 0.00 40.11 3.20
1756 1790 4.625742 TCTTGAGTTAACATCGCTAACTGC 59.374 41.667 8.61 0.00 39.22 4.40
1762 1796 4.499183 CTTCCTCTTGAGTTAACATCGCT 58.501 43.478 8.61 0.00 0.00 4.93
1783 1817 4.052518 GGGCAGCCACCATGACCT 62.053 66.667 15.19 0.00 43.10 3.85
1849 1883 7.121611 AGCACATCATCATCATCAGTGTAAAAA 59.878 33.333 0.00 0.00 0.00 1.94
1851 1885 6.117488 AGCACATCATCATCATCAGTGTAAA 58.883 36.000 0.00 0.00 0.00 2.01
1885 1919 1.710339 GCCGTCTTCTTGATCGCAC 59.290 57.895 0.00 0.00 0.00 5.34
1902 1936 0.302890 CATGACCGAGAGCAAATCGC 59.697 55.000 0.00 0.00 38.84 4.58
1907 1941 0.904649 ACATCCATGACCGAGAGCAA 59.095 50.000 0.00 0.00 0.00 3.91
1908 1942 0.176449 CACATCCATGACCGAGAGCA 59.824 55.000 0.00 0.00 0.00 4.26
1915 1949 2.809665 GCTCCTGATCACATCCATGACC 60.810 54.545 0.00 0.00 0.00 4.02
1968 2002 0.542333 GCCTTAACACTCCTCCTCCC 59.458 60.000 0.00 0.00 0.00 4.30
2116 2150 2.028385 CGCACTACTTAACCCTTCCTGT 60.028 50.000 0.00 0.00 0.00 4.00
2155 2189 2.367567 GTGTCTAGTTTCTCCACACCCA 59.632 50.000 0.00 0.00 32.77 4.51
2285 2328 6.038603 GTGGCTCTGATTAGCAATTGTTATGA 59.961 38.462 7.40 1.96 44.64 2.15
2297 2340 2.702478 TGGATCTGGTGGCTCTGATTAG 59.298 50.000 0.00 0.00 0.00 1.73
2358 2403 4.529897 TGTCTGGATGATGGAAGGAAATG 58.470 43.478 0.00 0.00 0.00 2.32
2573 2618 3.884774 TGGGAGCGTGGCCTTGTT 61.885 61.111 3.32 0.00 0.00 2.83
2611 2656 2.100879 GAGGTGGTGGAGCAGTCGTT 62.101 60.000 0.00 0.00 0.00 3.85
2734 2779 0.169009 CACGAGCTGAGATGTCGACA 59.831 55.000 22.48 22.48 37.16 4.35
2857 2902 3.679389 GCCATGGTGATAGAAATCGGAT 58.321 45.455 14.67 0.00 34.60 4.18
2926 2971 1.253100 ATGGAAAATCAAACCGCGGT 58.747 45.000 28.70 28.70 0.00 5.68
2967 3012 0.322816 ACATTTGAGACGCCAGGCAT 60.323 50.000 13.30 0.00 0.00 4.40
3201 3246 2.296190 TCTGCGTATTCTGTGACAGTGT 59.704 45.455 12.93 0.00 32.61 3.55
3569 3614 1.495584 GCCAGCTTGTCGTTGTTCGA 61.496 55.000 0.00 0.00 46.83 3.71
3575 3620 2.594592 GGTGGCCAGCTTGTCGTT 60.595 61.111 27.63 0.00 0.00 3.85
3646 3691 1.137404 GCAATGATGTTCGCGGCTT 59.863 52.632 6.13 0.00 0.00 4.35
3677 3722 6.810911 TCAGCTCTTCCACTATATGAAGTTC 58.189 40.000 0.00 0.00 39.19 3.01
3832 3877 1.531365 CTCCTTGCCTTGCACCCAA 60.531 57.895 0.00 0.00 38.71 4.12
4014 4059 4.329545 GTGAACTCGCCCCCTGCA 62.330 66.667 0.00 0.00 41.33 4.41
4590 4637 0.107643 TGATTGTGTTGAGGTGCCGA 59.892 50.000 0.00 0.00 0.00 5.54
4603 4650 8.306761 GGGAAACTTATTCTTGATTGTGATTGT 58.693 33.333 0.00 0.00 0.00 2.71
4622 4669 4.263506 CCTCAATCACTGGTAAGGGAAACT 60.264 45.833 0.00 0.00 39.97 2.66
4664 4711 0.251341 GGTGAACCAGCATGACCCTT 60.251 55.000 0.00 0.00 39.69 3.95
4757 4804 3.558931 ACTCGAAATGCCCATGATGTA 57.441 42.857 0.00 0.00 0.00 2.29
4788 4835 0.389391 CTCCCGTCAAGCCGTATGAT 59.611 55.000 0.00 0.00 0.00 2.45
4859 4906 0.608640 GAACACGAGGACTCCATGGT 59.391 55.000 12.58 0.00 0.00 3.55
4899 4946 5.237127 CACATGTGTCTTCTTGTCTTTGCTA 59.763 40.000 18.03 0.00 0.00 3.49
4933 4980 3.286751 GCGCTGGAACACTTGGCA 61.287 61.111 0.00 0.00 0.00 4.92
5005 5052 4.985538 TCATGTCCCAAATATAAGAGCCC 58.014 43.478 0.00 0.00 0.00 5.19
5017 5064 1.462616 CCGCTGATTTCATGTCCCAA 58.537 50.000 0.00 0.00 0.00 4.12
5421 5557 3.282885 CAGGCCTTCCTTTTCATAGGTC 58.717 50.000 0.00 0.00 41.93 3.85
5630 5767 0.952497 CGATAAGGCATCAGCGGCAT 60.952 55.000 1.45 0.00 43.41 4.40
5675 5812 0.463654 TGATGTAATGGTGGCGAGGC 60.464 55.000 0.00 0.00 0.00 4.70
5946 6084 1.153353 CCGGCAATGTAAACAGTCGT 58.847 50.000 0.00 0.00 0.00 4.34
6079 6217 2.165167 CAATGACACCATCTGCCAAGT 58.835 47.619 0.00 0.00 31.40 3.16
6187 6327 2.235650 CTGTGAGAGGATGTGACATGGT 59.764 50.000 1.23 0.00 0.00 3.55
6202 6342 0.595095 GCAACTTGGAAGGCTGTGAG 59.405 55.000 0.00 0.00 0.00 3.51
6696 6839 3.176578 GCGAACGTGCGATCGGAA 61.177 61.111 22.89 0.00 40.08 4.30
6906 7049 2.919494 CGTTGGTGGAAGGGCTTGC 61.919 63.158 0.00 0.00 0.00 4.01
7013 7156 0.037232 GACCTGTGGAACTCCGGAAG 60.037 60.000 5.23 2.09 39.43 3.46
7292 7435 1.134580 GGCGGAGTACTTAACCCTTCC 60.135 57.143 0.00 0.00 0.00 3.46
7294 7437 0.907486 GGGCGGAGTACTTAACCCTT 59.093 55.000 16.78 0.00 34.34 3.95
7364 7507 2.518407 GGAAATGGGGATAAGGGGAAGT 59.482 50.000 0.00 0.00 0.00 3.01
7367 7510 2.624846 AGGAAATGGGGATAAGGGGA 57.375 50.000 0.00 0.00 0.00 4.81
7368 7511 2.158310 GGAAGGAAATGGGGATAAGGGG 60.158 54.545 0.00 0.00 0.00 4.79
7373 7518 2.624846 AGGGGAAGGAAATGGGGATA 57.375 50.000 0.00 0.00 0.00 2.59
7390 7535 4.538738 ACTAGCAGAAGTAGGGTTCTAGG 58.461 47.826 0.00 0.00 34.90 3.02
7402 7547 8.196771 AGAGATACAAGATTTGACTAGCAGAAG 58.803 37.037 0.00 0.00 0.00 2.85
7411 7556 7.672983 TTCACCAAGAGATACAAGATTTGAC 57.327 36.000 0.00 0.00 0.00 3.18
7419 7566 5.869344 CACTCGAATTCACCAAGAGATACAA 59.131 40.000 12.50 0.00 33.53 2.41
7426 7573 4.058124 CACTTCACTCGAATTCACCAAGA 58.942 43.478 6.22 0.00 0.00 3.02
7428 7575 3.804036 ACACTTCACTCGAATTCACCAA 58.196 40.909 6.22 0.00 0.00 3.67
7449 7596 2.169769 CTCCTTGTTATGACCCCGCTAA 59.830 50.000 0.00 0.00 0.00 3.09
7458 7606 4.883585 GCCATGTCAATCTCCTTGTTATGA 59.116 41.667 0.00 0.00 36.20 2.15
7557 7705 1.826921 GTGGATACCCGGCTCGAGA 60.827 63.158 18.75 0.00 34.29 4.04
7564 7712 2.304221 TCTATCCAGTGGATACCCGG 57.696 55.000 25.30 16.55 41.16 5.73
7610 7782 8.743085 ATCATTGTGTGCTAAGTATCAGATTT 57.257 30.769 0.00 0.00 0.00 2.17
7611 7783 8.209584 AGATCATTGTGTGCTAAGTATCAGATT 58.790 33.333 0.00 0.00 0.00 2.40
7613 7785 7.117285 AGATCATTGTGTGCTAAGTATCAGA 57.883 36.000 0.00 0.00 0.00 3.27
7686 7859 0.976073 GATGGGAACGGTGAGGGAGA 60.976 60.000 0.00 0.00 0.00 3.71
7692 7865 3.605634 CAACAATAGATGGGAACGGTGA 58.394 45.455 0.00 0.00 0.00 4.02
7703 7876 0.179018 GAGCCGGGGCAACAATAGAT 60.179 55.000 12.97 0.00 44.88 1.98
7739 7913 4.588805 CACTGCATACATACACACAGTG 57.411 45.455 6.56 6.56 46.10 3.66
7791 7965 7.862512 AGATCAAAATTTGTTCCTGCAAAAA 57.137 28.000 11.81 0.00 41.03 1.94
7810 7988 5.761726 GCCATGACAGTTGATGAATAGATCA 59.238 40.000 0.00 0.00 43.67 2.92
7822 8000 2.026641 CCAATAGGGCCATGACAGTTG 58.973 52.381 6.18 0.00 0.00 3.16
7835 8013 5.652014 TGTTACTTTTGATGCTCCCAATAGG 59.348 40.000 0.00 0.00 30.36 2.57
7839 8017 5.860941 TTTGTTACTTTTGATGCTCCCAA 57.139 34.783 0.00 0.00 0.00 4.12
7872 8050 1.202580 TCGCTAGGTAGTCTACGGACC 60.203 57.143 3.92 0.00 43.05 4.46
7892 8105 1.671845 GTAAGAGAGAGGCGATGACGT 59.328 52.381 0.00 0.00 41.98 4.34
7903 8116 4.797912 TGATAGGCTCCAGTAAGAGAGA 57.202 45.455 0.00 0.00 35.82 3.10
7906 8119 4.040217 AGCAATGATAGGCTCCAGTAAGAG 59.960 45.833 0.00 0.00 34.76 2.85
7924 8141 6.809869 AGAAAGAAAAACACTAGCAAGCAAT 58.190 32.000 0.00 0.00 0.00 3.56
8002 8219 4.142071 TGCAAAGCAAAGTCAACATAACCA 60.142 37.500 0.00 0.00 34.76 3.67
8033 8250 3.119990 ACAAGTGACCAAACAAAGTGTCG 60.120 43.478 0.00 0.00 0.00 4.35
8053 8270 0.107643 TTGTTCGATGCAGGGTCACA 59.892 50.000 0.00 0.00 0.00 3.58
8092 8310 8.405418 AGGCCTTTAAGGTTTTAAAACTAGAG 57.595 34.615 25.89 16.66 38.06 2.43
8103 8321 5.538813 CCTTAAACTGAGGCCTTTAAGGTTT 59.461 40.000 30.07 24.31 46.34 3.27
8165 8383 9.582431 GCACATATCACTCTACTAGTTTTGTTA 57.418 33.333 0.00 0.00 35.76 2.41
8230 8448 8.689972 GGAGACCATGTTCAAATCTAAAATGAT 58.310 33.333 0.00 0.00 0.00 2.45
8245 8463 3.008049 GTGTAGTCCTTGGAGACCATGTT 59.992 47.826 0.00 0.00 37.49 2.71
8253 8471 3.432378 ACCTAGTGTGTAGTCCTTGGAG 58.568 50.000 0.00 0.00 0.00 3.86
8403 8621 0.108138 CCGAGTTGGAACTAGGGCTG 60.108 60.000 10.07 0.00 44.91 4.85
8426 8644 3.517901 TGTTCTCGTGAGGGTGGAAATAT 59.482 43.478 0.00 0.00 0.00 1.28
8433 8651 0.036952 AGCATGTTCTCGTGAGGGTG 60.037 55.000 0.00 0.00 32.78 4.61
8434 8652 0.687354 AAGCATGTTCTCGTGAGGGT 59.313 50.000 0.00 0.00 32.78 4.34
8435 8653 1.813513 AAAGCATGTTCTCGTGAGGG 58.186 50.000 0.00 0.00 32.78 4.30
8436 8654 3.499918 AGAAAAAGCATGTTCTCGTGAGG 59.500 43.478 0.00 0.00 32.78 3.86
8437 8655 4.706527 GAGAAAAAGCATGTTCTCGTGAG 58.293 43.478 6.13 0.00 40.15 3.51
8438 8656 4.732285 GAGAAAAAGCATGTTCTCGTGA 57.268 40.909 6.13 0.00 40.15 4.35
8442 8660 6.264841 AGGATTGAGAAAAAGCATGTTCTC 57.735 37.500 13.81 13.81 46.60 2.87
8443 8661 7.309438 GGTTAGGATTGAGAAAAAGCATGTTCT 60.309 37.037 0.00 0.00 36.80 3.01
8444 8662 6.808704 GGTTAGGATTGAGAAAAAGCATGTTC 59.191 38.462 0.00 0.00 0.00 3.18
8445 8663 6.267471 TGGTTAGGATTGAGAAAAAGCATGTT 59.733 34.615 0.00 0.00 0.00 2.71
8446 8664 5.774690 TGGTTAGGATTGAGAAAAAGCATGT 59.225 36.000 0.00 0.00 0.00 3.21
8447 8665 6.271488 TGGTTAGGATTGAGAAAAAGCATG 57.729 37.500 0.00 0.00 0.00 4.06
8448 8666 6.721208 TCTTGGTTAGGATTGAGAAAAAGCAT 59.279 34.615 0.00 0.00 0.00 3.79
8449 8667 6.068010 TCTTGGTTAGGATTGAGAAAAAGCA 58.932 36.000 0.00 0.00 0.00 3.91
8450 8668 6.431234 TCTCTTGGTTAGGATTGAGAAAAAGC 59.569 38.462 0.00 0.00 0.00 3.51
8451 8669 7.986085 TCTCTTGGTTAGGATTGAGAAAAAG 57.014 36.000 0.00 0.00 0.00 2.27
8452 8670 7.448469 CCTTCTCTTGGTTAGGATTGAGAAAAA 59.552 37.037 0.00 0.00 39.19 1.94
8453 8671 6.942576 CCTTCTCTTGGTTAGGATTGAGAAAA 59.057 38.462 0.00 0.00 39.19 2.29
8454 8672 6.476378 CCTTCTCTTGGTTAGGATTGAGAAA 58.524 40.000 0.00 0.00 39.19 2.52
8455 8673 5.045578 CCCTTCTCTTGGTTAGGATTGAGAA 60.046 44.000 0.00 0.00 37.95 2.87
8456 8674 4.471386 CCCTTCTCTTGGTTAGGATTGAGA 59.529 45.833 0.00 0.00 0.00 3.27
8457 8675 4.226168 ACCCTTCTCTTGGTTAGGATTGAG 59.774 45.833 0.00 0.00 0.00 3.02
8458 8676 4.175962 ACCCTTCTCTTGGTTAGGATTGA 58.824 43.478 0.00 0.00 0.00 2.57
8459 8677 4.576330 ACCCTTCTCTTGGTTAGGATTG 57.424 45.455 0.00 0.00 0.00 2.67
8460 8678 6.910259 ATTACCCTTCTCTTGGTTAGGATT 57.090 37.500 0.00 0.00 36.04 3.01
8461 8679 6.910259 AATTACCCTTCTCTTGGTTAGGAT 57.090 37.500 0.00 0.00 36.04 3.24
8462 8680 7.817910 TTAATTACCCTTCTCTTGGTTAGGA 57.182 36.000 0.00 0.00 36.04 2.94
8463 8681 8.326529 TCTTTAATTACCCTTCTCTTGGTTAGG 58.673 37.037 0.00 0.00 36.04 2.69
8464 8682 9.734984 TTCTTTAATTACCCTTCTCTTGGTTAG 57.265 33.333 0.00 0.00 36.04 2.34
8466 8684 9.025041 CATTCTTTAATTACCCTTCTCTTGGTT 57.975 33.333 0.00 0.00 36.04 3.67
8467 8685 7.122799 GCATTCTTTAATTACCCTTCTCTTGGT 59.877 37.037 0.00 0.00 38.69 3.67
8468 8686 7.122650 TGCATTCTTTAATTACCCTTCTCTTGG 59.877 37.037 0.00 0.00 0.00 3.61
8469 8687 8.055279 TGCATTCTTTAATTACCCTTCTCTTG 57.945 34.615 0.00 0.00 0.00 3.02
8470 8688 8.829373 ATGCATTCTTTAATTACCCTTCTCTT 57.171 30.769 0.00 0.00 0.00 2.85
8471 8689 8.829373 AATGCATTCTTTAATTACCCTTCTCT 57.171 30.769 5.99 0.00 0.00 3.10
8472 8690 9.521503 GAAATGCATTCTTTAATTACCCTTCTC 57.478 33.333 13.38 0.00 35.04 2.87
8473 8691 9.034800 TGAAATGCATTCTTTAATTACCCTTCT 57.965 29.630 13.38 0.00 38.92 2.85
8474 8692 9.822185 ATGAAATGCATTCTTTAATTACCCTTC 57.178 29.630 13.38 1.80 38.92 3.46
8478 8696 9.706846 GCAAATGAAATGCATTCTTTAATTACC 57.293 29.630 13.38 0.00 46.25 2.85
8492 8710 4.418392 AGACTCGATTGCAAATGAAATGC 58.582 39.130 1.71 0.00 44.08 3.56
8493 8711 5.877031 AGAGACTCGATTGCAAATGAAATG 58.123 37.500 1.71 0.00 0.00 2.32
8494 8712 6.506500 AAGAGACTCGATTGCAAATGAAAT 57.493 33.333 1.71 0.00 0.00 2.17
8495 8713 5.947228 AAGAGACTCGATTGCAAATGAAA 57.053 34.783 1.71 0.00 0.00 2.69
8496 8714 5.106555 GGAAAGAGACTCGATTGCAAATGAA 60.107 40.000 1.71 0.00 0.00 2.57
8497 8715 4.393062 GGAAAGAGACTCGATTGCAAATGA 59.607 41.667 1.71 3.28 0.00 2.57
8498 8716 4.394300 AGGAAAGAGACTCGATTGCAAATG 59.606 41.667 1.71 0.00 0.00 2.32
8499 8717 4.583871 AGGAAAGAGACTCGATTGCAAAT 58.416 39.130 1.71 0.00 0.00 2.32
8500 8718 4.008074 AGGAAAGAGACTCGATTGCAAA 57.992 40.909 1.71 0.00 0.00 3.68
8501 8719 3.685139 AGGAAAGAGACTCGATTGCAA 57.315 42.857 0.00 0.00 0.00 4.08
8502 8720 3.589988 GAAGGAAAGAGACTCGATTGCA 58.410 45.455 14.60 0.00 0.00 4.08
8503 8721 2.933260 GGAAGGAAAGAGACTCGATTGC 59.067 50.000 7.24 7.24 0.00 3.56
8504 8722 4.193826 TGGAAGGAAAGAGACTCGATTG 57.806 45.455 0.00 0.00 0.00 2.67
8505 8723 4.826556 CTTGGAAGGAAAGAGACTCGATT 58.173 43.478 0.00 0.00 0.00 3.34
8506 8724 3.368948 GCTTGGAAGGAAAGAGACTCGAT 60.369 47.826 0.00 0.00 0.00 3.59
8507 8725 2.028930 GCTTGGAAGGAAAGAGACTCGA 60.029 50.000 0.00 0.00 0.00 4.04
8508 8726 2.028567 AGCTTGGAAGGAAAGAGACTCG 60.029 50.000 0.00 0.00 0.00 4.18
8509 8727 3.694043 AGCTTGGAAGGAAAGAGACTC 57.306 47.619 0.00 0.00 0.00 3.36
8510 8728 4.595350 ACTTAGCTTGGAAGGAAAGAGACT 59.405 41.667 0.00 0.00 0.00 3.24
8511 8729 4.900684 ACTTAGCTTGGAAGGAAAGAGAC 58.099 43.478 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.