Multiple sequence alignment - TraesCS1D01G242800

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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 TraesCS1D01G242800 chr1D 100.000 6047 0 0 905 6951 332996355 333002401 0.000000e+00 11167.0
1 TraesCS1D01G242800 chr1D 100.000 702 0 0 1 702 332995451 332996152 0.000000e+00 1297.0
2 TraesCS1D01G242800 chr1D 85.306 245 30 5 3053 3293 275046421 275046663 1.500000e-61 248.0
3 TraesCS1D01G242800 chr1B 93.820 3948 139 35 3060 6951 448528180 448532078 0.000000e+00 5842.0
4 TraesCS1D01G242800 chr1B 93.372 1192 49 13 1885 3066 448526581 448527752 0.000000e+00 1736.0
5 TraesCS1D01G242800 chr1B 90.553 741 20 15 1 702 448524952 448525681 0.000000e+00 935.0
6 TraesCS1D01G242800 chr1B 90.554 614 34 7 905 1511 448525676 448526272 0.000000e+00 791.0
7 TraesCS1D01G242800 chr1B 93.846 260 14 2 1466 1724 448526324 448526582 2.350000e-104 390.0
8 TraesCS1D01G242800 chr1A 92.434 2868 113 31 1885 4693 430618063 430620885 0.000000e+00 3999.0
9 TraesCS1D01G242800 chr1A 95.244 2355 75 11 4622 6951 430620884 430623226 0.000000e+00 3694.0
10 TraesCS1D01G242800 chr1A 92.308 533 17 9 174 702 430616670 430617182 0.000000e+00 736.0
11 TraesCS1D01G242800 chr1A 87.624 606 33 8 913 1511 430617192 430617762 0.000000e+00 665.0
12 TraesCS1D01G242800 chr1A 93.077 260 16 2 1466 1724 430617806 430618064 5.090000e-101 379.0
13 TraesCS1D01G242800 chr1A 97.037 135 4 0 1 135 430616536 430616670 1.950000e-55 228.0
14 TraesCS1D01G242800 chr5A 85.098 255 36 2 3041 3294 160081910 160082163 6.920000e-65 259.0
15 TraesCS1D01G242800 chr5A 84.766 256 34 5 3041 3294 201721067 201720815 1.160000e-62 252.0
16 TraesCS1D01G242800 chr5A 93.939 165 10 0 1722 1886 320214408 320214244 4.160000e-62 250.0
17 TraesCS1D01G242800 chr5A 85.124 242 34 2 3053 3293 221611413 221611653 5.380000e-61 246.0
18 TraesCS1D01G242800 chr6B 85.259 251 35 2 3045 3293 128925045 128925295 2.490000e-64 257.0
19 TraesCS1D01G242800 chr6B 94.366 71 2 1 1592 1662 527630184 527630116 2.650000e-19 108.0
20 TraesCS1D01G242800 chr5D 94.578 166 9 0 1722 1887 529218163 529218328 2.490000e-64 257.0
21 TraesCS1D01G242800 chr4D 94.545 165 9 0 1722 1886 34661524 34661688 8.950000e-64 255.0
22 TraesCS1D01G242800 chr4D 85.246 244 34 2 3052 3293 267858406 267858163 4.160000e-62 250.0
23 TraesCS1D01G242800 chr4D 85.124 242 34 2 3053 3293 81466582 81466342 5.380000e-61 246.0
24 TraesCS1D01G242800 chr4D 93.373 166 11 0 1725 1890 334164552 334164387 5.380000e-61 246.0
25 TraesCS1D01G242800 chr2D 94.545 165 9 0 1722 1886 134301485 134301649 8.950000e-64 255.0
26 TraesCS1D01G242800 chr2D 94.048 168 9 1 1724 1890 624365772 624365939 3.220000e-63 254.0
27 TraesCS1D01G242800 chr7D 93.452 168 11 0 1722 1889 454079411 454079244 4.160000e-62 250.0
28 TraesCS1D01G242800 chr3A 93.865 163 10 0 1724 1886 510298652 510298814 5.380000e-61 246.0
29 TraesCS1D01G242800 chr6D 92.442 172 11 2 1722 1892 90133524 90133354 1.940000e-60 244.0
30 TraesCS1D01G242800 chr3B 95.775 71 1 1 1592 1662 442043767 442043835 5.700000e-21 113.0
31 TraesCS1D01G242800 chr3D 94.366 71 2 1 1592 1662 327310880 327310948 2.650000e-19 108.0
32 TraesCS1D01G242800 chr4B 94.366 71 1 1 1592 1662 88708440 88708373 9.540000e-19 106.0
33 TraesCS1D01G242800 chr4B 92.857 70 3 1 1593 1662 20175207 20175274 4.440000e-17 100.0
34 TraesCS1D01G242800 chr7A 88.732 71 6 2 1592 1662 375175541 375175609 1.240000e-12 86.1
35 TraesCS1D01G242800 chr7B 88.571 70 6 1 1593 1662 431282986 431283053 4.470000e-12 84.2
36 TraesCS1D01G242800 chr2B 89.231 65 5 1 1598 1662 678739875 678739813 5.780000e-11 80.5


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 TraesCS1D01G242800 chr1D 332995451 333002401 6950 False 6232.000000 11167 100.000 1 6951 2 chr1D.!!$F2 6950
1 TraesCS1D01G242800 chr1B 448524952 448532078 7126 False 1938.800000 5842 92.429 1 6951 5 chr1B.!!$F1 6950
2 TraesCS1D01G242800 chr1A 430616536 430623226 6690 False 1616.833333 3999 92.954 1 6951 6 chr1A.!!$F1 6950

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
267 296 0.035458 CCCCACTCCACTCAGTTCAC 59.965 60.000 0.00 0.00 0.00 3.18 F
1471 1527 0.247460 TCTGATGAGGAACTGGCACG 59.753 55.000 0.00 0.00 41.55 5.34 F
1841 1985 0.101759 TTGCTCCGTATGTAGTCCGC 59.898 55.000 0.00 0.00 0.00 5.54 F
2759 2911 0.180642 TGGGAAACTACACGGCACAA 59.819 50.000 0.00 0.00 0.00 3.33 F
3801 4414 0.389817 CACCGATGTCTTCTGCGGAA 60.390 55.000 7.94 7.94 46.29 4.30 F
4101 4715 1.619332 GCCTTCTCTAGGGGATTACCG 59.381 57.143 0.00 0.00 44.91 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1822 1966 0.101759 GCGGACTACATACGGAGCAA 59.898 55.000 0.00 0.0 0.00 3.91 R
3037 3189 1.623811 TGGAACAGAGGGAGCACTTAC 59.376 52.381 0.00 0.0 0.00 2.34 R
3543 4144 1.535462 CACCGGCTTAAACTGAACTGG 59.465 52.381 0.00 0.0 0.00 4.00 R
4662 5359 4.397481 ACTTGTATTACTACGAAGGCCC 57.603 45.455 0.00 0.0 0.00 5.80 R
5058 5759 2.123854 ATGGAGCTGCCTGCATGG 60.124 61.111 1.53 0.0 46.71 3.66 R
6072 6777 3.309121 CCAGGATTCCTTAAGCTTCCCAA 60.309 47.826 0.00 0.0 0.00 4.12 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
67 68 4.641954 CGAGTGCAACATTAACACAGATC 58.358 43.478 0.00 0.00 41.43 2.75
162 170 0.613260 TCCTCCCATGAACCAACTCG 59.387 55.000 0.00 0.00 0.00 4.18
163 171 1.026718 CCTCCCATGAACCAACTCGC 61.027 60.000 0.00 0.00 0.00 5.03
213 241 1.207089 CTGACACGGGGATACACACAT 59.793 52.381 0.00 0.00 44.36 3.21
215 243 2.429250 TGACACGGGGATACACACATAG 59.571 50.000 0.00 0.00 44.36 2.23
267 296 0.035458 CCCCACTCCACTCAGTTCAC 59.965 60.000 0.00 0.00 0.00 3.18
352 382 2.671963 GTTTCCCCCTGTCGGCAC 60.672 66.667 0.00 0.00 0.00 5.01
482 514 4.365505 GCCCGCTATCCTCGGCTC 62.366 72.222 0.00 0.00 45.19 4.70
483 515 2.912542 CCCGCTATCCTCGGCTCA 60.913 66.667 0.00 0.00 45.19 4.26
484 516 2.498941 CCCGCTATCCTCGGCTCAA 61.499 63.158 0.00 0.00 45.19 3.02
485 517 1.300233 CCGCTATCCTCGGCTCAAC 60.300 63.158 0.00 0.00 40.46 3.18
486 518 1.736586 CGCTATCCTCGGCTCAACT 59.263 57.895 0.00 0.00 0.00 3.16
487 519 0.318275 CGCTATCCTCGGCTCAACTC 60.318 60.000 0.00 0.00 0.00 3.01
488 520 1.036707 GCTATCCTCGGCTCAACTCT 58.963 55.000 0.00 0.00 0.00 3.24
489 521 1.000717 GCTATCCTCGGCTCAACTCTC 60.001 57.143 0.00 0.00 0.00 3.20
490 522 2.582052 CTATCCTCGGCTCAACTCTCT 58.418 52.381 0.00 0.00 0.00 3.10
603 644 2.108566 CATCCGCCTCTGCCTCTG 59.891 66.667 0.00 0.00 0.00 3.35
604 645 3.859414 ATCCGCCTCTGCCTCTGC 61.859 66.667 0.00 0.00 38.26 4.26
1272 1321 4.803908 GTACTGCCCCCTGCCTGC 62.804 72.222 0.00 0.00 40.16 4.85
1299 1355 3.622514 GGACTCATCTCCGGTGCT 58.377 61.111 0.00 0.00 0.00 4.40
1301 1357 0.671251 GGACTCATCTCCGGTGCTAG 59.329 60.000 0.00 0.00 0.00 3.42
1316 1372 1.877443 TGCTAGTTGCTTTCGGTTTCC 59.123 47.619 0.00 0.00 43.37 3.13
1317 1373 1.199327 GCTAGTTGCTTTCGGTTTCCC 59.801 52.381 0.00 0.00 38.95 3.97
1346 1402 1.736612 GGCTGGAAGAAGCTCAGAAG 58.263 55.000 3.66 0.00 43.06 2.85
1347 1403 1.003003 GGCTGGAAGAAGCTCAGAAGT 59.997 52.381 3.66 0.00 43.06 3.01
1357 1413 2.374184 AGCTCAGAAGTACAGATCGCT 58.626 47.619 0.00 0.00 0.00 4.93
1384 1440 2.186076 CTTTCGTATGCGTCTCTGTCC 58.814 52.381 2.37 0.00 39.49 4.02
1408 1464 0.251698 TGCATGTTCATTGGGGAGCA 60.252 50.000 0.00 0.00 32.46 4.26
1412 1468 3.322828 GCATGTTCATTGGGGAGCATATT 59.677 43.478 0.00 0.00 36.72 1.28
1431 1487 1.825090 TGGAAAATGATGCAGAGCGT 58.175 45.000 0.00 0.00 0.00 5.07
1437 1493 2.505628 ATGATGCAGAGCGTGACTAG 57.494 50.000 0.00 0.00 0.00 2.57
1448 1504 0.387202 CGTGACTAGCCTGGGAGATG 59.613 60.000 0.00 0.00 0.00 2.90
1449 1505 1.781786 GTGACTAGCCTGGGAGATGA 58.218 55.000 0.00 0.00 0.00 2.92
1453 1509 2.825532 GACTAGCCTGGGAGATGAGATC 59.174 54.545 0.00 0.00 0.00 2.75
1454 1510 2.450500 ACTAGCCTGGGAGATGAGATCT 59.549 50.000 0.00 0.00 43.70 2.75
1457 1513 2.158127 AGCCTGGGAGATGAGATCTGAT 60.158 50.000 0.00 0.00 40.38 2.90
1458 1514 2.027929 GCCTGGGAGATGAGATCTGATG 60.028 54.545 0.00 0.00 40.38 3.07
1459 1515 3.508426 CCTGGGAGATGAGATCTGATGA 58.492 50.000 0.00 0.00 40.38 2.92
1460 1516 3.512329 CCTGGGAGATGAGATCTGATGAG 59.488 52.174 0.00 0.00 40.38 2.90
1462 1518 3.141649 TGGGAGATGAGATCTGATGAGGA 59.858 47.826 0.00 0.00 40.38 3.71
1465 1521 4.834496 GGAGATGAGATCTGATGAGGAACT 59.166 45.833 0.00 0.00 40.73 3.01
1466 1522 5.279106 GGAGATGAGATCTGATGAGGAACTG 60.279 48.000 0.00 0.00 38.46 3.16
1468 1524 2.433604 TGAGATCTGATGAGGAACTGGC 59.566 50.000 0.00 0.00 41.55 4.85
1469 1525 2.433604 GAGATCTGATGAGGAACTGGCA 59.566 50.000 0.00 0.00 41.55 4.92
1470 1526 2.170187 AGATCTGATGAGGAACTGGCAC 59.830 50.000 0.00 0.00 41.55 5.01
1471 1527 0.247460 TCTGATGAGGAACTGGCACG 59.753 55.000 0.00 0.00 41.55 5.34
1485 1628 1.876714 GCACGCGCCGAGAATAAGA 60.877 57.895 5.73 0.00 0.00 2.10
1503 1646 8.912988 AGAATAAGAGAATGTTAGAGAGGACTG 58.087 37.037 0.00 0.00 0.00 3.51
1649 1793 3.700539 TGCTAATGGTTAATGTGCATGCT 59.299 39.130 20.33 0.00 0.00 3.79
1665 1809 3.349927 CATGCTCAACCAGAAATCTCCA 58.650 45.455 0.00 0.00 0.00 3.86
1670 1814 2.897326 TCAACCAGAAATCTCCACGAGA 59.103 45.455 0.00 0.00 43.20 4.04
1689 1833 8.943002 CCACGAGAAAAATACAAGTATTACCTT 58.057 33.333 5.93 1.50 34.90 3.50
1715 1859 6.925165 AGATATCAAACACTTGTTGCTTTTGG 59.075 34.615 5.32 0.00 38.44 3.28
1722 1866 0.908198 TTGTTGCTTTTGGCCACCTT 59.092 45.000 3.88 0.00 40.92 3.50
1723 1867 1.781786 TGTTGCTTTTGGCCACCTTA 58.218 45.000 3.88 0.00 40.92 2.69
1724 1868 2.324541 TGTTGCTTTTGGCCACCTTAT 58.675 42.857 3.88 0.00 40.92 1.73
1725 1869 3.501349 TGTTGCTTTTGGCCACCTTATA 58.499 40.909 3.88 0.00 40.92 0.98
1726 1870 3.257127 TGTTGCTTTTGGCCACCTTATAC 59.743 43.478 3.88 0.53 40.92 1.47
1727 1871 3.449746 TGCTTTTGGCCACCTTATACT 57.550 42.857 3.88 0.00 40.92 2.12
1728 1872 3.352648 TGCTTTTGGCCACCTTATACTC 58.647 45.455 3.88 0.00 40.92 2.59
1729 1873 2.688446 GCTTTTGGCCACCTTATACTCC 59.312 50.000 3.88 0.00 34.27 3.85
1730 1874 3.288092 CTTTTGGCCACCTTATACTCCC 58.712 50.000 3.88 0.00 0.00 4.30
1731 1875 2.280308 TTGGCCACCTTATACTCCCT 57.720 50.000 3.88 0.00 0.00 4.20
1732 1876 1.802553 TGGCCACCTTATACTCCCTC 58.197 55.000 0.00 0.00 0.00 4.30
1733 1877 0.680061 GGCCACCTTATACTCCCTCG 59.320 60.000 0.00 0.00 0.00 4.63
1734 1878 0.680061 GCCACCTTATACTCCCTCGG 59.320 60.000 0.00 0.00 0.00 4.63
1735 1879 2.033208 GCCACCTTATACTCCCTCGGT 61.033 57.143 0.00 0.00 0.00 4.69
1736 1880 2.395619 CCACCTTATACTCCCTCGGTT 58.604 52.381 0.00 0.00 0.00 4.44
1737 1881 2.364647 CCACCTTATACTCCCTCGGTTC 59.635 54.545 0.00 0.00 0.00 3.62
1738 1882 2.364647 CACCTTATACTCCCTCGGTTCC 59.635 54.545 0.00 0.00 0.00 3.62
1739 1883 2.246849 ACCTTATACTCCCTCGGTTCCT 59.753 50.000 0.00 0.00 0.00 3.36
1740 1884 3.464833 ACCTTATACTCCCTCGGTTCCTA 59.535 47.826 0.00 0.00 0.00 2.94
1741 1885 4.078980 ACCTTATACTCCCTCGGTTCCTAA 60.079 45.833 0.00 0.00 0.00 2.69
1742 1886 4.897670 CCTTATACTCCCTCGGTTCCTAAA 59.102 45.833 0.00 0.00 0.00 1.85
1743 1887 5.543020 CCTTATACTCCCTCGGTTCCTAAAT 59.457 44.000 0.00 0.00 0.00 1.40
1744 1888 6.723052 CCTTATACTCCCTCGGTTCCTAAATA 59.277 42.308 0.00 0.00 0.00 1.40
1745 1889 7.399478 CCTTATACTCCCTCGGTTCCTAAATAT 59.601 40.741 0.00 0.00 0.00 1.28
1746 1890 9.471702 CTTATACTCCCTCGGTTCCTAAATATA 57.528 37.037 0.00 0.00 0.00 0.86
1747 1891 9.827198 TTATACTCCCTCGGTTCCTAAATATAA 57.173 33.333 0.00 0.00 0.00 0.98
1748 1892 6.667558 ACTCCCTCGGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
1749 1893 6.141790 ACTCCCTCGGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
1750 1894 6.267242 ACTCCCTCGGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
1751 1895 6.379579 TCCCTCGGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
1752 1896 6.842807 TCCCTCGGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
1753 1897 7.346436 TCCCTCGGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
1754 1898 7.991460 CCCTCGGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
1755 1899 9.392259 CCTCGGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
1781 1925 8.783999 AGAGATTTCAATACGAACTACATACG 57.216 34.615 0.00 0.00 31.73 3.06
1782 1926 7.861372 AGAGATTTCAATACGAACTACATACGG 59.139 37.037 0.00 0.00 31.73 4.02
1783 1927 7.709947 AGATTTCAATACGAACTACATACGGA 58.290 34.615 0.00 0.00 31.73 4.69
1784 1928 8.358148 AGATTTCAATACGAACTACATACGGAT 58.642 33.333 0.00 0.00 31.73 4.18
1785 1929 7.688478 TTTCAATACGAACTACATACGGATG 57.312 36.000 5.94 5.94 34.47 3.51
1786 1930 7.259882 TTTCAATACGAACTACATACGGATGT 58.740 34.615 19.12 19.12 40.55 3.06
1787 1931 7.495135 TCAATACGAACTACATACGGATGTA 57.505 36.000 19.32 19.32 44.77 2.29
1788 1932 8.102800 TCAATACGAACTACATACGGATGTAT 57.897 34.615 20.64 7.28 45.42 2.29
1789 1933 9.218440 TCAATACGAACTACATACGGATGTATA 57.782 33.333 20.64 10.32 45.42 1.47
1790 1934 9.999009 CAATACGAACTACATACGGATGTATAT 57.001 33.333 20.64 12.07 45.42 0.86
1794 1938 8.877779 ACGAACTACATACGGATGTATATAGAC 58.122 37.037 20.64 9.63 45.42 2.59
1795 1939 8.876790 CGAACTACATACGGATGTATATAGACA 58.123 37.037 20.64 2.07 45.42 3.41
1826 1970 7.934855 AGAATGTAGATTCACTCATTTTGCT 57.065 32.000 14.46 0.00 40.59 3.91
1827 1971 7.983307 AGAATGTAGATTCACTCATTTTGCTC 58.017 34.615 14.46 0.00 40.59 4.26
1828 1972 6.690194 ATGTAGATTCACTCATTTTGCTCC 57.310 37.500 0.00 0.00 0.00 4.70
1829 1973 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
1830 1974 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
1831 1975 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
1832 1976 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
1833 1977 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
1834 1978 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
1835 1979 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
1836 1980 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
1837 1981 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
1838 1982 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
1839 1983 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
1840 1984 2.572191 TTTGCTCCGTATGTAGTCCG 57.428 50.000 0.00 0.00 0.00 4.79
1841 1985 0.101759 TTGCTCCGTATGTAGTCCGC 59.898 55.000 0.00 0.00 0.00 5.54
1842 1986 1.033202 TGCTCCGTATGTAGTCCGCA 61.033 55.000 0.00 0.00 0.00 5.69
1843 1987 0.314302 GCTCCGTATGTAGTCCGCAT 59.686 55.000 0.00 0.00 0.00 4.73
1844 1988 1.269621 GCTCCGTATGTAGTCCGCATT 60.270 52.381 0.00 0.00 0.00 3.56
1845 1989 2.394708 CTCCGTATGTAGTCCGCATTG 58.605 52.381 0.00 0.00 0.00 2.82
1846 1990 1.067974 TCCGTATGTAGTCCGCATTGG 59.932 52.381 0.00 0.00 40.09 3.16
1859 2003 5.756195 TCCGCATTGGAATCTCTAAAATG 57.244 39.130 0.00 0.00 46.38 2.32
1860 2004 5.436175 TCCGCATTGGAATCTCTAAAATGA 58.564 37.500 0.00 0.00 46.38 2.57
1861 2005 5.296780 TCCGCATTGGAATCTCTAAAATGAC 59.703 40.000 0.00 0.00 46.38 3.06
1862 2006 5.297776 CCGCATTGGAATCTCTAAAATGACT 59.702 40.000 0.00 0.00 42.00 3.41
1863 2007 6.183360 CCGCATTGGAATCTCTAAAATGACTT 60.183 38.462 0.00 0.00 42.00 3.01
1864 2008 7.012327 CCGCATTGGAATCTCTAAAATGACTTA 59.988 37.037 0.00 0.00 42.00 2.24
1865 2009 8.562892 CGCATTGGAATCTCTAAAATGACTTAT 58.437 33.333 0.00 0.00 31.34 1.73
1881 2025 8.482852 AATGACTTATATTTTGGAATGGAGGG 57.517 34.615 0.00 0.00 0.00 4.30
1882 2026 7.219601 TGACTTATATTTTGGAATGGAGGGA 57.780 36.000 0.00 0.00 0.00 4.20
1883 2027 7.290061 TGACTTATATTTTGGAATGGAGGGAG 58.710 38.462 0.00 0.00 0.00 4.30
1919 2063 8.837389 ACAAATACTTCTAAGTTTGACCACTTC 58.163 33.333 12.12 0.00 40.37 3.01
1925 2069 1.663695 AGTTTGACCACTTCACCGTG 58.336 50.000 0.00 0.00 32.26 4.94
1930 2074 0.814010 GACCACTTCACCGTGCTTGT 60.814 55.000 0.00 0.00 33.60 3.16
2080 2224 2.911484 CCTCTGACAGGCATACTTTCC 58.089 52.381 1.81 0.00 34.56 3.13
2132 2276 8.328758 TCTCCTTTTGATGTTCCTTATACATGT 58.671 33.333 2.69 2.69 36.41 3.21
2133 2277 9.613428 CTCCTTTTGATGTTCCTTATACATGTA 57.387 33.333 8.27 8.27 36.41 2.29
2245 2389 6.552629 CACATGGAATCAGAATCAGAACAAG 58.447 40.000 0.00 0.00 0.00 3.16
2301 2445 1.069636 GTGCAGAGTTACAGCTGTTGC 60.070 52.381 27.06 26.60 40.05 4.17
2490 2634 5.048507 AGTTTACACTCGAACAGACCTTTC 58.951 41.667 0.00 0.00 0.00 2.62
2756 2908 0.398696 ACATGGGAAACTACACGGCA 59.601 50.000 0.00 0.00 0.00 5.69
2759 2911 0.180642 TGGGAAACTACACGGCACAA 59.819 50.000 0.00 0.00 0.00 3.33
3012 3164 6.429385 CCATTCAGCTCTTGTTTTCTAGTCTT 59.571 38.462 0.00 0.00 0.00 3.01
3037 3189 8.885494 TTGTTAAATTCTTCCACCTGAAATTG 57.115 30.769 0.00 0.00 31.06 2.32
3043 3196 6.633500 TTCTTCCACCTGAAATTGTAAGTG 57.367 37.500 0.00 0.00 31.06 3.16
3072 3660 4.988540 TCTGTTCCATAATATAGTGCGTGC 59.011 41.667 0.00 0.00 0.00 5.34
3073 3661 4.956085 TGTTCCATAATATAGTGCGTGCT 58.044 39.130 0.00 0.00 0.00 4.40
3084 3672 3.004024 AGTGCGTGCTGATTTTTGAAG 57.996 42.857 0.00 0.00 0.00 3.02
3198 3788 9.077674 CCTAATGATATACGCTTGACATTCTAC 57.922 37.037 0.00 0.00 0.00 2.59
3250 3840 4.081917 TCAAAGTTTGTGGGGTTTGACTTC 60.082 41.667 15.08 0.00 34.72 3.01
3300 3891 5.677567 TGGAACGGAGGGAGTATATTTTTC 58.322 41.667 0.00 0.00 0.00 2.29
3381 3982 4.019174 CCCATGGTGAAACTGAGCTAATT 58.981 43.478 11.73 0.00 36.74 1.40
3561 4162 1.165270 CCCAGTTCAGTTTAAGCCGG 58.835 55.000 0.00 0.00 0.00 6.13
3570 4171 2.678336 CAGTTTAAGCCGGTGATTCTCC 59.322 50.000 1.90 0.00 0.00 3.71
3739 4351 8.450578 TTTTTGCGATGGATAAGTCTATGATT 57.549 30.769 0.00 0.00 0.00 2.57
3740 4352 7.658179 TTTGCGATGGATAAGTCTATGATTC 57.342 36.000 0.00 0.00 0.00 2.52
3741 4353 6.596309 TGCGATGGATAAGTCTATGATTCT 57.404 37.500 0.00 0.00 0.00 2.40
3742 4354 7.703058 TGCGATGGATAAGTCTATGATTCTA 57.297 36.000 0.00 0.00 0.00 2.10
3743 4355 8.298729 TGCGATGGATAAGTCTATGATTCTAT 57.701 34.615 0.00 0.00 0.00 1.98
3744 4356 8.753133 TGCGATGGATAAGTCTATGATTCTATT 58.247 33.333 0.00 0.00 0.00 1.73
3797 4410 3.684788 ACAAATACACCGATGTCTTCTGC 59.315 43.478 0.00 0.00 40.48 4.26
3801 4414 0.389817 CACCGATGTCTTCTGCGGAA 60.390 55.000 7.94 7.94 46.29 4.30
3804 4417 2.223829 ACCGATGTCTTCTGCGGAATAG 60.224 50.000 8.78 0.00 46.29 1.73
3822 4435 7.149031 GCGGAATAGTGACAAAACAAACATTAC 60.149 37.037 0.00 0.00 0.00 1.89
3928 4541 6.764877 ATGTATTTGCGTATTTAGGTCTCG 57.235 37.500 0.00 0.00 0.00 4.04
4101 4715 1.619332 GCCTTCTCTAGGGGATTACCG 59.381 57.143 0.00 0.00 44.91 4.02
4230 4844 4.904253 TCCCTGTAAAAGTTTTTCCACG 57.096 40.909 6.10 0.00 0.00 4.94
4442 5079 6.974965 AGCAAATAAAGTATCCAATAGCTGC 58.025 36.000 0.00 0.00 0.00 5.25
4625 5263 7.488150 GCTTGTACTAAACATAAATTGCTTCCC 59.512 37.037 0.00 0.00 38.10 3.97
4783 5483 6.548441 TTCGTATTTGGAAAAGTGGTAGTG 57.452 37.500 0.00 0.00 0.00 2.74
4872 5573 4.008330 CCAGACATCAGCATTGAAGACTT 58.992 43.478 0.00 0.00 36.78 3.01
4873 5574 5.181009 CCAGACATCAGCATTGAAGACTTA 58.819 41.667 0.00 0.00 36.78 2.24
4881 5582 9.330063 CATCAGCATTGAAGACTTATACCTTTA 57.670 33.333 0.00 0.00 36.78 1.85
4882 5583 9.905713 ATCAGCATTGAAGACTTATACCTTTAA 57.094 29.630 0.00 0.00 36.78 1.52
5164 5865 4.023450 TGCGTCTATGCATACTACTACACC 60.023 45.833 1.16 0.00 40.62 4.16
5210 5911 7.617041 AAAGAAGTGATAAATAGGCAGTGAC 57.383 36.000 0.00 0.00 0.00 3.67
5357 6058 5.163622 CCAAAAAGACACGGCAATCAGATAT 60.164 40.000 0.00 0.00 0.00 1.63
5591 6292 6.379417 AGCAAAGAAATAGATGAAGGAAAGGG 59.621 38.462 0.00 0.00 0.00 3.95
5846 6547 3.943381 TCTGCCTGACATATTTTCTGCTG 59.057 43.478 0.00 0.00 0.00 4.41
5847 6548 3.943381 CTGCCTGACATATTTTCTGCTGA 59.057 43.478 0.00 0.00 0.00 4.26
5848 6549 4.334552 TGCCTGACATATTTTCTGCTGAA 58.665 39.130 1.33 1.33 0.00 3.02
5872 6577 5.993055 TCTGAAATGCTGAATCTGACCATA 58.007 37.500 0.00 0.00 0.00 2.74
5993 6698 6.690194 AATTAATGAGTTCAGATCCTGCAC 57.310 37.500 0.00 0.00 0.00 4.57
6015 6720 6.651225 GCACTCTATTCCTGTCACTAAACTTT 59.349 38.462 0.00 0.00 0.00 2.66
6072 6777 7.926018 CCTAAAATGGCTATAAAAATTTCCGCT 59.074 33.333 0.00 0.00 0.00 5.52
6230 6936 7.343057 ACAACAAGACACTCCATAGATAGATGA 59.657 37.037 0.00 0.00 0.00 2.92
6350 7056 3.265737 ACCTGCATAACCTGTGTATGGAA 59.734 43.478 0.00 0.00 0.00 3.53
6364 7071 2.727123 ATGGAATGTGGGCGTGATAA 57.273 45.000 0.00 0.00 0.00 1.75
6368 7075 3.130164 TGGAATGTGGGCGTGATAAATTG 59.870 43.478 0.00 0.00 0.00 2.32
6399 7106 4.707030 TGATTGTGCATAAAGCTTCCAG 57.293 40.909 0.00 0.00 45.94 3.86
6413 7120 3.058224 AGCTTCCAGTATTGAAAACGTGC 60.058 43.478 0.00 0.00 0.00 5.34
6419 7126 2.610374 AGTATTGAAAACGTGCGTGTGT 59.390 40.909 0.00 0.00 0.00 3.72
6449 7156 3.000727 CGTGGAAACTGGTAGGATGTTC 58.999 50.000 0.00 0.00 0.00 3.18
6463 7170 7.226523 TGGTAGGATGTTCGATTGTCAATATTG 59.773 37.037 9.29 9.29 0.00 1.90
6507 7214 1.459450 TTTTGGGATGCTCTTACCGC 58.541 50.000 0.00 0.00 0.00 5.68
6571 7278 5.783100 AAAATTTCTATTTGCATGCCACG 57.217 34.783 16.68 0.00 34.27 4.94
6707 7431 1.610522 AACTGTTCAGCAGGTTGATGC 59.389 47.619 0.00 0.00 43.98 3.91
6788 7512 7.601073 CTTGTGAGCAATACTCTTTGTATCA 57.399 36.000 0.00 0.00 46.41 2.15
6940 7664 7.038017 AGGAAGAGAACAGAAATAGGAATGTGA 60.038 37.037 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 2.099921 ACATTCACGCTCTACTGGCTAG 59.900 50.000 0.00 0.00 0.00 3.42
143 151 0.613260 CGAGTTGGTTCATGGGAGGA 59.387 55.000 0.00 0.00 0.00 3.71
162 170 0.106819 ATGAGTGAATGGGGCTGAGC 60.107 55.000 0.00 0.00 0.00 4.26
163 171 1.211212 TGATGAGTGAATGGGGCTGAG 59.789 52.381 0.00 0.00 0.00 3.35
213 241 0.250793 CCGTTGGCCACCATGTACTA 59.749 55.000 3.88 0.00 31.53 1.82
215 243 1.302993 ACCGTTGGCCACCATGTAC 60.303 57.895 3.88 0.00 31.53 2.90
267 296 8.407832 TGATGATGCATAAAAATACACTGGAAG 58.592 33.333 0.00 0.00 42.29 3.46
352 382 1.740285 CCGAGTTACTCCCCATCGG 59.260 63.158 6.80 0.32 45.95 4.18
358 388 2.183555 CGTGGCCGAGTTACTCCC 59.816 66.667 6.80 3.85 35.63 4.30
480 512 4.772100 AGAGAAGAAGGGAAGAGAGTTGAG 59.228 45.833 0.00 0.00 0.00 3.02
481 513 4.746466 AGAGAAGAAGGGAAGAGAGTTGA 58.254 43.478 0.00 0.00 0.00 3.18
482 514 4.380444 CGAGAGAAGAAGGGAAGAGAGTTG 60.380 50.000 0.00 0.00 0.00 3.16
483 515 3.761752 CGAGAGAAGAAGGGAAGAGAGTT 59.238 47.826 0.00 0.00 0.00 3.01
484 516 3.352648 CGAGAGAAGAAGGGAAGAGAGT 58.647 50.000 0.00 0.00 0.00 3.24
485 517 2.099098 GCGAGAGAAGAAGGGAAGAGAG 59.901 54.545 0.00 0.00 0.00 3.20
486 518 2.096248 GCGAGAGAAGAAGGGAAGAGA 58.904 52.381 0.00 0.00 0.00 3.10
487 519 1.136110 GGCGAGAGAAGAAGGGAAGAG 59.864 57.143 0.00 0.00 0.00 2.85
488 520 1.187087 GGCGAGAGAAGAAGGGAAGA 58.813 55.000 0.00 0.00 0.00 2.87
489 521 0.898320 TGGCGAGAGAAGAAGGGAAG 59.102 55.000 0.00 0.00 0.00 3.46
490 522 1.482593 GATGGCGAGAGAAGAAGGGAA 59.517 52.381 0.00 0.00 0.00 3.97
603 644 3.160748 GAGGAGGGGCAGAGAGGC 61.161 72.222 0.00 0.00 43.27 4.70
604 645 2.445654 GGAGGAGGGGCAGAGAGG 60.446 72.222 0.00 0.00 0.00 3.69
605 646 2.445654 GGGAGGAGGGGCAGAGAG 60.446 72.222 0.00 0.00 0.00 3.20
606 647 4.095400 GGGGAGGAGGGGCAGAGA 62.095 72.222 0.00 0.00 0.00 3.10
1284 1333 1.478510 CAACTAGCACCGGAGATGAGT 59.521 52.381 9.46 1.21 0.00 3.41
1295 1351 5.446988 GGGAAACCGAAAGCAACTAGCAC 62.447 52.174 0.00 0.00 44.62 4.40
1339 1395 4.572795 TCAGTAGCGATCTGTACTTCTGAG 59.427 45.833 0.00 0.00 34.27 3.35
1357 1413 2.422479 AGACGCATACGAAAGCTCAGTA 59.578 45.455 0.00 0.00 43.93 2.74
1384 1440 0.452987 CCCAATGAACATGCACTCGG 59.547 55.000 0.00 0.00 0.00 4.63
1408 1464 4.581824 ACGCTCTGCATCATTTTCCAATAT 59.418 37.500 0.00 0.00 0.00 1.28
1412 1468 1.469703 CACGCTCTGCATCATTTTCCA 59.530 47.619 0.00 0.00 0.00 3.53
1431 1487 1.570979 TCTCATCTCCCAGGCTAGTCA 59.429 52.381 0.00 0.00 0.00 3.41
1437 1493 1.714541 TCAGATCTCATCTCCCAGGC 58.285 55.000 0.00 0.00 37.58 4.85
1448 1504 2.433604 TGCCAGTTCCTCATCAGATCTC 59.566 50.000 0.00 0.00 0.00 2.75
1449 1505 2.170187 GTGCCAGTTCCTCATCAGATCT 59.830 50.000 0.00 0.00 0.00 2.75
1453 1509 1.364626 GCGTGCCAGTTCCTCATCAG 61.365 60.000 0.00 0.00 0.00 2.90
1454 1510 1.375908 GCGTGCCAGTTCCTCATCA 60.376 57.895 0.00 0.00 0.00 3.07
1468 1524 0.248498 TCTCTTATTCTCGGCGCGTG 60.248 55.000 8.43 0.00 0.00 5.34
1469 1525 0.454600 TTCTCTTATTCTCGGCGCGT 59.545 50.000 8.43 0.00 0.00 6.01
1470 1526 1.453524 CATTCTCTTATTCTCGGCGCG 59.546 52.381 0.00 0.00 0.00 6.86
1471 1527 2.474816 ACATTCTCTTATTCTCGGCGC 58.525 47.619 0.00 0.00 0.00 6.53
1474 1617 7.229707 TCCTCTCTAACATTCTCTTATTCTCGG 59.770 40.741 0.00 0.00 0.00 4.63
1485 1628 4.530161 AGCAACAGTCCTCTCTAACATTCT 59.470 41.667 0.00 0.00 0.00 2.40
1503 1646 2.972625 TGTGCAGATACCTACAGCAAC 58.027 47.619 0.00 0.00 36.91 4.17
1548 1692 8.987890 ACATTAATTTTTAGCTGTTTCGCAAAT 58.012 25.926 0.00 0.00 0.00 2.32
1549 1693 8.359060 ACATTAATTTTTAGCTGTTTCGCAAA 57.641 26.923 0.00 0.00 0.00 3.68
1649 1793 2.897326 TCTCGTGGAGATTTCTGGTTGA 59.103 45.455 0.00 0.00 33.35 3.18
1689 1833 8.081633 CCAAAAGCAACAAGTGTTTGATATCTA 58.918 33.333 3.98 0.00 37.73 1.98
1690 1834 6.925165 CCAAAAGCAACAAGTGTTTGATATCT 59.075 34.615 3.98 0.00 37.73 1.98
1715 1859 0.680061 CCGAGGGAGTATAAGGTGGC 59.320 60.000 0.00 0.00 0.00 5.01
1722 1866 9.471702 CTTATATTTAGGAACCGAGGGAGTATA 57.528 37.037 0.00 0.00 0.00 1.47
1723 1867 7.954620 ACTTATATTTAGGAACCGAGGGAGTAT 59.045 37.037 0.00 0.00 0.00 2.12
1724 1868 7.300658 ACTTATATTTAGGAACCGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
1725 1869 6.141790 ACTTATATTTAGGAACCGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
1726 1870 6.494146 AGACTTATATTTAGGAACCGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
1727 1871 6.379579 AGACTTATATTTAGGAACCGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
1728 1872 6.667558 AGACTTATATTTAGGAACCGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
1729 1873 8.959705 AAAAGACTTATATTTAGGAACCGAGG 57.040 34.615 0.00 0.00 0.00 4.63
1755 1899 9.874215 CGTATGTAGTTCGTATTGAAATCTCTA 57.126 33.333 0.00 0.00 38.60 2.43
1756 1900 7.861372 CCGTATGTAGTTCGTATTGAAATCTCT 59.139 37.037 0.00 0.00 38.60 3.10
1757 1901 7.859377 TCCGTATGTAGTTCGTATTGAAATCTC 59.141 37.037 0.00 0.00 38.60 2.75
1758 1902 7.709947 TCCGTATGTAGTTCGTATTGAAATCT 58.290 34.615 0.00 0.00 38.60 2.40
1759 1903 7.919313 TCCGTATGTAGTTCGTATTGAAATC 57.081 36.000 0.00 0.00 38.60 2.17
1760 1904 7.924412 ACATCCGTATGTAGTTCGTATTGAAAT 59.076 33.333 0.00 0.00 44.66 2.17
1761 1905 7.259882 ACATCCGTATGTAGTTCGTATTGAAA 58.740 34.615 0.00 0.00 44.66 2.69
1762 1906 6.798482 ACATCCGTATGTAGTTCGTATTGAA 58.202 36.000 0.00 0.00 44.66 2.69
1763 1907 6.381481 ACATCCGTATGTAGTTCGTATTGA 57.619 37.500 0.00 0.00 44.66 2.57
1800 1944 9.453572 AGCAAAATGAGTGAATCTACATTCTAA 57.546 29.630 0.00 0.00 39.49 2.10
1801 1945 9.102757 GAGCAAAATGAGTGAATCTACATTCTA 57.897 33.333 0.00 0.00 39.49 2.10
1802 1946 7.066766 GGAGCAAAATGAGTGAATCTACATTCT 59.933 37.037 0.00 0.00 39.49 2.40
1803 1947 7.192232 GGAGCAAAATGAGTGAATCTACATTC 58.808 38.462 0.00 0.00 39.24 2.67
1804 1948 6.183360 CGGAGCAAAATGAGTGAATCTACATT 60.183 38.462 0.00 0.00 34.99 2.71
1805 1949 5.295292 CGGAGCAAAATGAGTGAATCTACAT 59.705 40.000 0.00 0.00 0.00 2.29
1806 1950 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
1807 1951 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
1808 1952 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
1809 1953 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
1810 1954 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
1811 1955 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
1812 1956 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
1813 1957 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
1814 1958 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
1815 1959 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
1816 1960 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
1817 1961 4.439057 GGACTACATACGGAGCAAAATGA 58.561 43.478 0.00 0.00 0.00 2.57
1818 1962 3.245284 CGGACTACATACGGAGCAAAATG 59.755 47.826 0.00 0.00 0.00 2.32
1819 1963 3.454375 CGGACTACATACGGAGCAAAAT 58.546 45.455 0.00 0.00 0.00 1.82
1820 1964 2.883574 CGGACTACATACGGAGCAAAA 58.116 47.619 0.00 0.00 0.00 2.44
1821 1965 1.470285 GCGGACTACATACGGAGCAAA 60.470 52.381 0.00 0.00 0.00 3.68
1822 1966 0.101759 GCGGACTACATACGGAGCAA 59.898 55.000 0.00 0.00 0.00 3.91
1823 1967 1.033202 TGCGGACTACATACGGAGCA 61.033 55.000 0.00 0.00 0.00 4.26
1824 1968 0.314302 ATGCGGACTACATACGGAGC 59.686 55.000 0.00 0.00 0.00 4.70
1825 1969 2.394708 CAATGCGGACTACATACGGAG 58.605 52.381 0.00 0.00 0.00 4.63
1826 1970 1.067974 CCAATGCGGACTACATACGGA 59.932 52.381 0.00 0.00 36.56 4.69
1827 1971 1.067974 TCCAATGCGGACTACATACGG 59.932 52.381 0.00 0.00 39.64 4.02
1828 1972 2.502213 TCCAATGCGGACTACATACG 57.498 50.000 0.00 0.00 39.64 3.06
1829 1973 4.632153 AGATTCCAATGCGGACTACATAC 58.368 43.478 0.00 0.00 46.36 2.39
1830 1974 4.588951 AGAGATTCCAATGCGGACTACATA 59.411 41.667 0.00 0.00 46.36 2.29
1831 1975 3.389329 AGAGATTCCAATGCGGACTACAT 59.611 43.478 0.00 0.00 46.36 2.29
1832 1976 2.766263 AGAGATTCCAATGCGGACTACA 59.234 45.455 0.00 0.00 46.36 2.74
1833 1977 3.460857 AGAGATTCCAATGCGGACTAC 57.539 47.619 0.00 0.00 46.36 2.73
1834 1978 5.607939 TTTAGAGATTCCAATGCGGACTA 57.392 39.130 0.00 0.00 46.36 2.59
1835 1979 4.487714 TTTAGAGATTCCAATGCGGACT 57.512 40.909 0.00 0.00 46.36 3.85
1836 1980 5.296780 TCATTTTAGAGATTCCAATGCGGAC 59.703 40.000 0.00 0.00 46.36 4.79
1837 1981 5.296780 GTCATTTTAGAGATTCCAATGCGGA 59.703 40.000 0.00 0.00 44.40 5.54
1838 1982 5.297776 AGTCATTTTAGAGATTCCAATGCGG 59.702 40.000 0.00 0.00 0.00 5.69
1839 1983 6.369059 AGTCATTTTAGAGATTCCAATGCG 57.631 37.500 0.00 0.00 0.00 4.73
1855 1999 8.927411 CCCTCCATTCCAAAATATAAGTCATTT 58.073 33.333 0.00 0.00 0.00 2.32
1856 2000 8.288812 TCCCTCCATTCCAAAATATAAGTCATT 58.711 33.333 0.00 0.00 0.00 2.57
1857 2001 7.825709 TCCCTCCATTCCAAAATATAAGTCAT 58.174 34.615 0.00 0.00 0.00 3.06
1858 2002 7.091993 ACTCCCTCCATTCCAAAATATAAGTCA 60.092 37.037 0.00 0.00 0.00 3.41
1859 2003 7.290813 ACTCCCTCCATTCCAAAATATAAGTC 58.709 38.462 0.00 0.00 0.00 3.01
1860 2004 7.226059 ACTCCCTCCATTCCAAAATATAAGT 57.774 36.000 0.00 0.00 0.00 2.24
1861 2005 9.813826 ATTACTCCCTCCATTCCAAAATATAAG 57.186 33.333 0.00 0.00 0.00 1.73
1863 2007 9.586732 CAATTACTCCCTCCATTCCAAAATATA 57.413 33.333 0.00 0.00 0.00 0.86
1864 2008 8.067488 ACAATTACTCCCTCCATTCCAAAATAT 58.933 33.333 0.00 0.00 0.00 1.28
1865 2009 7.418378 ACAATTACTCCCTCCATTCCAAAATA 58.582 34.615 0.00 0.00 0.00 1.40
1866 2010 6.263754 ACAATTACTCCCTCCATTCCAAAAT 58.736 36.000 0.00 0.00 0.00 1.82
1867 2011 5.650283 ACAATTACTCCCTCCATTCCAAAA 58.350 37.500 0.00 0.00 0.00 2.44
1868 2012 5.269554 ACAATTACTCCCTCCATTCCAAA 57.730 39.130 0.00 0.00 0.00 3.28
1869 2013 4.946160 ACAATTACTCCCTCCATTCCAA 57.054 40.909 0.00 0.00 0.00 3.53
1870 2014 4.946160 AACAATTACTCCCTCCATTCCA 57.054 40.909 0.00 0.00 0.00 3.53
1871 2015 6.184789 TGTAAACAATTACTCCCTCCATTCC 58.815 40.000 1.02 0.00 41.65 3.01
1872 2016 7.696992 TTGTAAACAATTACTCCCTCCATTC 57.303 36.000 0.00 0.00 41.65 2.67
1873 2017 8.664669 ATTTGTAAACAATTACTCCCTCCATT 57.335 30.769 0.00 0.00 41.65 3.16
1874 2018 9.185680 GTATTTGTAAACAATTACTCCCTCCAT 57.814 33.333 15.56 0.00 41.65 3.41
1875 2019 8.387813 AGTATTTGTAAACAATTACTCCCTCCA 58.612 33.333 18.10 0.00 43.67 3.86
1876 2020 8.803397 AGTATTTGTAAACAATTACTCCCTCC 57.197 34.615 18.10 0.68 43.67 4.30
1925 2069 2.096496 CGGGAATCATGAAGTGACAAGC 59.904 50.000 0.00 0.00 40.28 4.01
1930 2074 1.678728 GCACCGGGAATCATGAAGTGA 60.679 52.381 6.32 0.00 42.06 3.41
2158 2302 2.916640 TGCCTATTGATGCAACATCGA 58.083 42.857 0.00 0.14 33.87 3.59
2245 2389 3.078837 TCGCATACCTTGTTTCCCTTTC 58.921 45.455 0.00 0.00 0.00 2.62
2461 2605 5.975939 GTCTGTTCGAGTGTAAACTTGTAGT 59.024 40.000 0.00 0.00 0.00 2.73
2490 2634 4.024556 CACCTGACTCAAGCAACAGTAAAG 60.025 45.833 0.00 0.00 0.00 1.85
2605 2755 7.506328 TGGAGATATGAAAGAAATCATGCAG 57.494 36.000 0.00 0.00 40.21 4.41
2756 2908 6.437162 ACCCAAATATACTGCAAGATTGTTGT 59.563 34.615 0.00 0.00 37.43 3.32
2759 2911 7.285401 CCTTACCCAAATATACTGCAAGATTGT 59.715 37.037 0.00 0.00 37.43 2.71
3012 3164 8.482128 ACAATTTCAGGTGGAAGAATTTAACAA 58.518 29.630 0.00 0.00 36.72 2.83
3037 3189 1.623811 TGGAACAGAGGGAGCACTTAC 59.376 52.381 0.00 0.00 0.00 2.34
3265 3855 3.131396 CTCCGTTCCATAATGTAGTGCC 58.869 50.000 0.00 0.00 0.00 5.01
3279 3869 5.061853 GGGAAAAATATACTCCCTCCGTTC 58.938 45.833 8.74 0.00 44.81 3.95
3543 4144 1.535462 CACCGGCTTAAACTGAACTGG 59.465 52.381 0.00 0.00 0.00 4.00
3797 4410 7.858382 TGTAATGTTTGTTTTGTCACTATTCCG 59.142 33.333 0.00 0.00 0.00 4.30
3804 4417 7.683746 AGCAATTGTAATGTTTGTTTTGTCAC 58.316 30.769 7.40 0.00 0.00 3.67
3928 4541 9.995003 ATCTCTTCAACATCTCTTGTATAATCC 57.005 33.333 0.00 0.00 37.68 3.01
4167 4781 9.498307 ACTCTCGTAAAACAACAAACATAAAAG 57.502 29.630 0.00 0.00 0.00 2.27
4230 4844 9.896263 AAACAATTTGGAATAAATGATTTGCAC 57.104 25.926 0.00 0.00 0.00 4.57
4432 5069 5.975344 CACAATTTGATACAGCAGCTATTGG 59.025 40.000 13.80 0.00 0.00 3.16
4442 5079 6.214205 GTGCAAAACCACAATTTGATACAG 57.786 37.500 2.79 0.00 39.56 2.74
4512 5150 7.589993 ACTAAGGGCTACCAGTATAGAACTAA 58.410 38.462 0.00 0.00 40.13 2.24
4625 5263 4.535781 TGTATGATTGAGGGATTGGGTTG 58.464 43.478 0.00 0.00 0.00 3.77
4662 5359 4.397481 ACTTGTATTACTACGAAGGCCC 57.603 45.455 0.00 0.00 0.00 5.80
4665 5362 8.443953 ACTAGGTACTTGTATTACTACGAAGG 57.556 38.462 0.00 0.00 43.60 3.46
4783 5483 5.953183 TCACTTGTCACCAATTGATATTGC 58.047 37.500 7.12 0.00 39.87 3.56
4873 5574 8.357402 CCTGCACAGTTTAAGTTTTAAAGGTAT 58.643 33.333 0.00 0.00 0.00 2.73
4881 5582 2.763448 TGCCCTGCACAGTTTAAGTTTT 59.237 40.909 0.00 0.00 31.71 2.43
4882 5583 2.383855 TGCCCTGCACAGTTTAAGTTT 58.616 42.857 0.00 0.00 31.71 2.66
4897 5598 9.969001 TTACAAAACTTTTACTCTATATGCCCT 57.031 29.630 0.00 0.00 0.00 5.19
5001 5702 4.650545 TTTTAGTGACGGTTTATGTCGC 57.349 40.909 0.00 0.00 44.99 5.19
5058 5759 2.123854 ATGGAGCTGCCTGCATGG 60.124 61.111 1.53 0.00 46.71 3.66
5164 5865 8.120465 TCTTTAGTTTGTTAACTTGAAAGAGCG 58.880 33.333 7.22 0.00 41.85 5.03
5357 6058 4.456911 CAGCAACCTCTTCTGCTTTTGATA 59.543 41.667 0.00 0.00 46.71 2.15
5478 6179 5.707764 AGATAAGATACTGCACGCAGATAGA 59.292 40.000 25.09 7.90 46.30 1.98
5591 6292 3.999663 AGTAGTAGGTACTGACACGACAC 59.000 47.826 0.00 0.00 40.76 3.67
5846 6547 5.356190 TGGTCAGATTCAGCATTTCAGATTC 59.644 40.000 0.00 0.00 0.00 2.52
5847 6548 5.258841 TGGTCAGATTCAGCATTTCAGATT 58.741 37.500 0.00 0.00 0.00 2.40
5848 6549 4.851843 TGGTCAGATTCAGCATTTCAGAT 58.148 39.130 0.00 0.00 0.00 2.90
5872 6577 5.581126 TCTTTGCAAACTGTCACAAATCT 57.419 34.783 8.05 0.00 32.07 2.40
5993 6698 9.877178 ATACAAAGTTTAGTGACAGGAATAGAG 57.123 33.333 0.00 0.00 0.00 2.43
6072 6777 3.309121 CCAGGATTCCTTAAGCTTCCCAA 60.309 47.826 0.00 0.00 0.00 4.12
6203 6909 7.482169 TCTATCTATGGAGTGTCTTGTTGTT 57.518 36.000 0.00 0.00 0.00 2.83
6350 7056 4.462483 AGTTTCAATTTATCACGCCCACAT 59.538 37.500 0.00 0.00 0.00 3.21
6364 7071 9.979578 TTATGCACAATCAAAGTAGTTTCAATT 57.020 25.926 0.00 0.00 0.00 2.32
6368 7075 7.809806 AGCTTTATGCACAATCAAAGTAGTTTC 59.190 33.333 0.00 0.00 45.94 2.78
6399 7106 2.711964 CACACACGCACGTTTTCAATAC 59.288 45.455 0.00 0.00 0.00 1.89
6413 7120 0.850217 CCACGAGTAACACACACACG 59.150 55.000 0.00 0.00 0.00 4.49
6419 7126 2.168936 ACCAGTTTCCACGAGTAACACA 59.831 45.455 0.00 0.00 0.00 3.72
6463 7170 1.265454 ACTCCCCTGGTGAATCCGTC 61.265 60.000 0.00 0.00 39.52 4.79
6499 7206 5.054477 GGCATCAAATTACTAGCGGTAAGA 58.946 41.667 10.17 4.42 42.74 2.10
6571 7278 7.966204 TCCATTTTTACGACTATTTTAGCAAGC 59.034 33.333 0.00 0.00 0.00 4.01
6677 7401 1.337703 GCTGAACAGTTGGAATGTGCA 59.662 47.619 0.00 0.00 34.93 4.57
6707 7431 1.129326 GAGGTGAACGACGTTGTCAG 58.871 55.000 19.60 0.00 32.09 3.51
6788 7512 7.281774 CCTTCTATGCATGTTCTGTGAAGTATT 59.718 37.037 10.16 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.