Multiple sequence alignment - TraesCS5A01G405800

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 TraesCS5A01G405800 chr5A 100.000 3744 0 0 1 3744 597331293 597327550 0.000000e+00 6914.0
1 TraesCS5A01G405800 chr5A 82.734 139 24 0 1112 1250 436089151 436089289 1.410000e-24 124.0
2 TraesCS5A01G405800 chr5A 97.872 47 1 0 3698 3744 597322475 597322429 8.620000e-12 82.4
3 TraesCS5A01G405800 chr5D 95.902 1928 61 8 1778 3697 478222437 478220520 0.000000e+00 3107.0
4 TraesCS5A01G405800 chr5D 97.567 863 14 5 755 1617 478223291 478222436 0.000000e+00 1471.0
5 TraesCS5A01G405800 chr5D 92.611 785 27 9 1 756 478224178 478223396 0.000000e+00 1099.0
6 TraesCS5A01G405800 chr5B 94.873 1931 74 14 1778 3697 585835467 585833551 0.000000e+00 2994.0
7 TraesCS5A01G405800 chr5B 94.856 1633 61 5 1 1617 585837091 585835466 0.000000e+00 2529.0
8 TraesCS5A01G405800 chr5B 96.667 180 6 0 1609 1788 334784941 334785120 2.190000e-77 300.0
9 TraesCS5A01G405800 chr5B 97.175 177 5 0 1603 1779 556958790 556958966 2.190000e-77 300.0
10 TraesCS5A01G405800 chr5B 83.453 139 23 0 1112 1250 391144731 391144869 3.030000e-26 130.0
11 TraesCS5A01G405800 chr2B 99.390 164 1 0 1616 1779 430232808 430232645 7.860000e-77 298.0
12 TraesCS5A01G405800 chr2B 96.571 175 4 2 1606 1779 299552473 299552646 4.730000e-74 289.0
13 TraesCS5A01G405800 chr2B 94.149 188 9 2 1600 1787 556659213 556659028 6.120000e-73 285.0
14 TraesCS5A01G405800 chr2B 83.871 93 15 0 1824 1916 45735367 45735275 5.150000e-14 89.8
15 TraesCS5A01G405800 chr3B 98.204 167 3 0 1613 1779 731267035 731267201 3.660000e-75 292.0
16 TraesCS5A01G405800 chr3B 96.591 176 5 1 1608 1783 461200580 461200406 1.320000e-74 291.0
17 TraesCS5A01G405800 chr3B 80.147 136 19 7 1111 1242 478323394 478323263 1.110000e-15 95.3
18 TraesCS5A01G405800 chr3A 94.211 190 9 2 1616 1804 694520939 694520751 4.730000e-74 289.0
19 TraesCS5A01G405800 chr3A 80.147 136 19 7 1111 1242 489311964 489311833 1.110000e-15 95.3
20 TraesCS5A01G405800 chr3A 100.000 42 0 0 3703 3744 686898232 686898273 1.110000e-10 78.7
21 TraesCS5A01G405800 chr6B 95.028 181 9 0 1600 1780 452184379 452184199 6.120000e-73 285.0
22 TraesCS5A01G405800 chr6A 89.437 142 15 0 1109 1250 578887722 578887581 2.970000e-41 180.0
23 TraesCS5A01G405800 chr6A 95.745 47 2 0 3698 3744 58824770 58824724 4.010000e-10 76.8
24 TraesCS5A01G405800 chr6A 95.745 47 1 1 3698 3744 58817932 58817887 1.440000e-09 75.0
25 TraesCS5A01G405800 chr6D 88.732 142 16 0 1109 1250 432710583 432710442 1.380000e-39 174.0
26 TraesCS5A01G405800 chr3D 79.412 136 20 7 1111 1242 367236965 367236834 5.150000e-14 89.8
27 TraesCS5A01G405800 chr7B 96.078 51 2 0 3694 3744 479503383 479503333 2.400000e-12 84.2
28 TraesCS5A01G405800 chr7B 95.745 47 2 0 3698 3744 479494300 479494254 4.010000e-10 76.8
29 TraesCS5A01G405800 chr1A 97.872 47 1 0 3698 3744 97181841 97181887 8.620000e-12 82.4
30 TraesCS5A01G405800 chr1A 95.745 47 2 0 3698 3744 97187168 97187214 4.010000e-10 76.8
31 TraesCS5A01G405800 chr7A 95.745 47 2 0 3698 3744 8930801 8930847 4.010000e-10 76.8


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 TraesCS5A01G405800 chr5A 597327550 597331293 3743 True 6914.000000 6914 100.0000 1 3744 1 chr5A.!!$R2 3743
1 TraesCS5A01G405800 chr5D 478220520 478224178 3658 True 1892.333333 3107 95.3600 1 3697 3 chr5D.!!$R1 3696
2 TraesCS5A01G405800 chr5B 585833551 585837091 3540 True 2761.500000 2994 94.8645 1 3697 2 chr5B.!!$R1 3696

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
149 150 3.021695 CCCACAGTCATAGACGGAACTA 58.978 50.0 4.38 0.00 37.67 2.24 F
1164 1303 1.139498 TGAAGAAGGGCCCATGGTCA 61.139 55.0 27.56 18.82 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1762 1901 0.337082 TCATACTCCCTCCGTTCCCA 59.663 55.0 0.0 0.0 0.0 4.37 R
2784 2924 0.175073 CTAGGGTTGGCACTCGGTAC 59.825 60.0 0.0 0.0 0.0 3.34 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
104 105 8.733458 TCAGATCATGCTAATAAATTATGGCAC 58.267 33.333 13.27 4.69 33.08 5.01
149 150 3.021695 CCCACAGTCATAGACGGAACTA 58.978 50.000 4.38 0.00 37.67 2.24
173 174 6.223852 ACGAGATAAAACAGCATCCGATATT 58.776 36.000 0.00 0.00 0.00 1.28
245 246 7.660030 ATGCCAACTTATTATGCTTTTACCT 57.340 32.000 0.00 0.00 0.00 3.08
260 261 9.855021 ATGCTTTTACCTAATGTTATGTCAAAC 57.145 29.630 0.00 0.00 0.00 2.93
386 391 8.348983 CATTTCTTGGAATATCAATTCAGTGC 57.651 34.615 0.99 0.00 42.88 4.40
458 483 7.462571 AAAACTAACTCCATTCCATAACACC 57.537 36.000 0.00 0.00 0.00 4.16
494 519 6.323203 ACAAATGAGATTGGTCAACTGAAG 57.677 37.500 0.00 0.00 34.56 3.02
640 668 4.562082 TGTATACTTTTGGACAGGTCACG 58.438 43.478 4.17 0.00 0.00 4.35
972 1111 5.258456 TGTCAATAATACACCTCGTCTCC 57.742 43.478 0.00 0.00 0.00 3.71
1164 1303 1.139498 TGAAGAAGGGCCCATGGTCA 61.139 55.000 27.56 18.82 0.00 4.02
1310 1449 3.196039 TGCCAGTAAGCGGTAGTGATAAA 59.804 43.478 6.82 0.00 35.41 1.40
1311 1450 4.141801 TGCCAGTAAGCGGTAGTGATAAAT 60.142 41.667 6.82 0.00 35.41 1.40
1312 1451 4.814771 GCCAGTAAGCGGTAGTGATAAATT 59.185 41.667 6.82 0.00 35.41 1.82
1313 1452 5.277345 GCCAGTAAGCGGTAGTGATAAATTG 60.277 44.000 6.82 0.00 35.41 2.32
1314 1453 6.046593 CCAGTAAGCGGTAGTGATAAATTGA 58.953 40.000 6.82 0.00 35.41 2.57
1315 1454 6.706270 CCAGTAAGCGGTAGTGATAAATTGAT 59.294 38.462 6.82 0.00 35.41 2.57
1316 1455 7.307396 CCAGTAAGCGGTAGTGATAAATTGATG 60.307 40.741 6.82 0.00 35.41 3.07
1321 1460 7.896811 AGCGGTAGTGATAAATTGATGATAGA 58.103 34.615 0.00 0.00 0.00 1.98
1322 1461 8.535335 AGCGGTAGTGATAAATTGATGATAGAT 58.465 33.333 0.00 0.00 0.00 1.98
1522 1661 2.097110 TGGTACAGTTGGTCTCACCT 57.903 50.000 0.00 0.00 39.58 4.00
1607 1746 8.201464 CACATGGGTGTAGTACAATCTATTACA 58.799 37.037 4.11 0.00 40.24 2.41
1621 1760 8.754080 ACAATCTATTACATGCTATCTACTCCC 58.246 37.037 0.00 0.00 0.00 4.30
1622 1761 8.976353 CAATCTATTACATGCTATCTACTCCCT 58.024 37.037 0.00 0.00 0.00 4.20
1623 1762 8.760980 ATCTATTACATGCTATCTACTCCCTC 57.239 38.462 0.00 0.00 0.00 4.30
1624 1763 7.120051 TCTATTACATGCTATCTACTCCCTCC 58.880 42.308 0.00 0.00 0.00 4.30
1625 1764 2.520069 ACATGCTATCTACTCCCTCCG 58.480 52.381 0.00 0.00 0.00 4.63
1626 1765 2.158445 ACATGCTATCTACTCCCTCCGT 60.158 50.000 0.00 0.00 0.00 4.69
1627 1766 2.750141 TGCTATCTACTCCCTCCGTT 57.250 50.000 0.00 0.00 0.00 4.44
1628 1767 2.584236 TGCTATCTACTCCCTCCGTTC 58.416 52.381 0.00 0.00 0.00 3.95
1629 1768 1.887854 GCTATCTACTCCCTCCGTTCC 59.112 57.143 0.00 0.00 0.00 3.62
1630 1769 2.489437 GCTATCTACTCCCTCCGTTCCT 60.489 54.545 0.00 0.00 0.00 3.36
1631 1770 3.244840 GCTATCTACTCCCTCCGTTCCTA 60.245 52.174 0.00 0.00 0.00 2.94
1632 1771 3.967467 ATCTACTCCCTCCGTTCCTAA 57.033 47.619 0.00 0.00 0.00 2.69
1633 1772 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
1634 1773 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
1635 1774 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
1636 1775 5.136105 TCTACTCCCTCCGTTCCTAAATAC 58.864 45.833 0.00 0.00 0.00 1.89
1637 1776 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
1638 1777 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
1639 1778 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
1640 1779 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
1641 1780 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
1642 1781 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
1643 1782 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
1644 1783 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
1645 1784 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
1646 1785 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
1647 1786 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
1648 1787 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
1649 1788 8.248945 CCGTTCCTAAATACTTGTCTTTCTAGA 58.751 37.037 0.00 0.00 0.00 2.43
1650 1789 9.291664 CGTTCCTAAATACTTGTCTTTCTAGAG 57.708 37.037 0.00 0.00 0.00 2.43
1661 1800 9.487790 ACTTGTCTTTCTAGAGATTTCAAGAAG 57.512 33.333 21.68 12.76 35.34 2.85
1662 1801 9.487790 CTTGTCTTTCTAGAGATTTCAAGAAGT 57.512 33.333 15.24 0.00 33.86 3.01
1663 1802 8.824159 TGTCTTTCTAGAGATTTCAAGAAGTG 57.176 34.615 4.29 0.00 30.19 3.16
1664 1803 8.642432 TGTCTTTCTAGAGATTTCAAGAAGTGA 58.358 33.333 4.29 0.00 30.19 3.41
1665 1804 8.921670 GTCTTTCTAGAGATTTCAAGAAGTGAC 58.078 37.037 4.29 0.00 35.39 3.67
1666 1805 8.865090 TCTTTCTAGAGATTTCAAGAAGTGACT 58.135 33.333 0.74 0.00 35.39 3.41
1668 1807 9.915629 TTTCTAGAGATTTCAAGAAGTGACTAC 57.084 33.333 0.00 0.00 35.39 2.73
1669 1808 8.637196 TCTAGAGATTTCAAGAAGTGACTACA 57.363 34.615 0.00 0.00 35.39 2.74
1670 1809 9.249053 TCTAGAGATTTCAAGAAGTGACTACAT 57.751 33.333 0.00 0.00 35.39 2.29
1673 1812 7.971168 AGAGATTTCAAGAAGTGACTACATACG 59.029 37.037 0.00 0.00 35.39 3.06
1674 1813 7.827701 AGATTTCAAGAAGTGACTACATACGA 58.172 34.615 0.00 0.00 35.39 3.43
1675 1814 7.755822 AGATTTCAAGAAGTGACTACATACGAC 59.244 37.037 0.00 0.00 35.39 4.34
1676 1815 4.966249 TCAAGAAGTGACTACATACGACG 58.034 43.478 0.00 0.00 0.00 5.12
1677 1816 3.402058 AGAAGTGACTACATACGACGC 57.598 47.619 0.00 0.00 0.00 5.19
1678 1817 2.745821 AGAAGTGACTACATACGACGCA 59.254 45.455 0.00 0.00 0.00 5.24
1679 1818 3.189910 AGAAGTGACTACATACGACGCAA 59.810 43.478 0.00 0.00 0.00 4.85
1680 1819 3.564235 AGTGACTACATACGACGCAAA 57.436 42.857 0.00 0.00 0.00 3.68
1681 1820 3.904571 AGTGACTACATACGACGCAAAA 58.095 40.909 0.00 0.00 0.00 2.44
1682 1821 4.491676 AGTGACTACATACGACGCAAAAT 58.508 39.130 0.00 0.00 0.00 1.82
1683 1822 4.326278 AGTGACTACATACGACGCAAAATG 59.674 41.667 0.00 0.00 0.00 2.32
1684 1823 4.325204 GTGACTACATACGACGCAAAATGA 59.675 41.667 0.00 0.00 0.00 2.57
1685 1824 4.561213 TGACTACATACGACGCAAAATGAG 59.439 41.667 0.00 0.00 0.00 2.90
1686 1825 4.491676 ACTACATACGACGCAAAATGAGT 58.508 39.130 0.00 0.00 31.65 3.41
1687 1826 3.722555 ACATACGACGCAAAATGAGTG 57.277 42.857 0.00 0.00 28.29 3.51
1688 1827 3.322369 ACATACGACGCAAAATGAGTGA 58.678 40.909 0.00 0.00 28.29 3.41
1689 1828 3.743911 ACATACGACGCAAAATGAGTGAA 59.256 39.130 0.00 0.00 28.29 3.18
1690 1829 4.391830 ACATACGACGCAAAATGAGTGAAT 59.608 37.500 0.00 0.00 28.29 2.57
1691 1830 3.455619 ACGACGCAAAATGAGTGAATC 57.544 42.857 0.00 0.00 28.29 2.52
1692 1831 3.067106 ACGACGCAAAATGAGTGAATCT 58.933 40.909 0.00 0.00 28.29 2.40
1693 1832 4.242475 ACGACGCAAAATGAGTGAATCTA 58.758 39.130 0.00 0.00 28.29 1.98
1694 1833 4.091509 ACGACGCAAAATGAGTGAATCTAC 59.908 41.667 0.00 0.00 28.29 2.59
1695 1834 4.091365 CGACGCAAAATGAGTGAATCTACA 59.909 41.667 0.00 0.00 28.29 2.74
1696 1835 5.283060 ACGCAAAATGAGTGAATCTACAC 57.717 39.130 0.00 0.00 40.60 2.90
1731 1870 8.631480 TGTCTACATACATCCGTATATTGAGT 57.369 34.615 0.00 0.00 36.11 3.41
1732 1871 8.727910 TGTCTACATACATCCGTATATTGAGTC 58.272 37.037 0.00 0.00 36.11 3.36
1733 1872 8.182881 GTCTACATACATCCGTATATTGAGTCC 58.817 40.741 0.00 0.00 36.11 3.85
1734 1873 6.911250 ACATACATCCGTATATTGAGTCCA 57.089 37.500 0.00 0.00 36.11 4.02
1735 1874 7.482169 ACATACATCCGTATATTGAGTCCAT 57.518 36.000 0.00 0.00 36.11 3.41
1736 1875 7.907389 ACATACATCCGTATATTGAGTCCATT 58.093 34.615 0.00 0.00 36.11 3.16
1737 1876 8.375506 ACATACATCCGTATATTGAGTCCATTT 58.624 33.333 0.00 0.00 36.11 2.32
1738 1877 8.659491 CATACATCCGTATATTGAGTCCATTTG 58.341 37.037 0.00 0.00 36.11 2.32
1739 1878 6.826668 ACATCCGTATATTGAGTCCATTTGA 58.173 36.000 0.00 0.00 0.00 2.69
1740 1879 7.279615 ACATCCGTATATTGAGTCCATTTGAA 58.720 34.615 0.00 0.00 0.00 2.69
1741 1880 7.773224 ACATCCGTATATTGAGTCCATTTGAAA 59.227 33.333 0.00 0.00 0.00 2.69
1742 1881 8.786898 CATCCGTATATTGAGTCCATTTGAAAT 58.213 33.333 0.00 0.00 0.00 2.17
1743 1882 8.153479 TCCGTATATTGAGTCCATTTGAAATG 57.847 34.615 10.84 10.84 0.00 2.32
1744 1883 6.857964 CCGTATATTGAGTCCATTTGAAATGC 59.142 38.462 12.26 0.23 0.00 3.56
1745 1884 6.857964 CGTATATTGAGTCCATTTGAAATGCC 59.142 38.462 12.26 5.23 0.00 4.40
1746 1885 7.255242 CGTATATTGAGTCCATTTGAAATGCCT 60.255 37.037 12.26 9.70 0.00 4.75
1747 1886 9.066892 GTATATTGAGTCCATTTGAAATGCCTA 57.933 33.333 12.26 0.00 0.00 3.93
1748 1887 5.902613 TTGAGTCCATTTGAAATGCCTAG 57.097 39.130 12.26 0.00 0.00 3.02
1749 1888 5.178096 TGAGTCCATTTGAAATGCCTAGA 57.822 39.130 12.26 1.83 0.00 2.43
1750 1889 5.569355 TGAGTCCATTTGAAATGCCTAGAA 58.431 37.500 12.26 0.00 0.00 2.10
1751 1890 6.009589 TGAGTCCATTTGAAATGCCTAGAAA 58.990 36.000 12.26 0.00 0.00 2.52
1752 1891 6.151648 TGAGTCCATTTGAAATGCCTAGAAAG 59.848 38.462 12.26 0.00 0.00 2.62
1753 1892 6.248433 AGTCCATTTGAAATGCCTAGAAAGA 58.752 36.000 12.26 0.00 0.00 2.52
1754 1893 6.151817 AGTCCATTTGAAATGCCTAGAAAGAC 59.848 38.462 12.26 10.86 0.00 3.01
1755 1894 6.009589 TCCATTTGAAATGCCTAGAAAGACA 58.990 36.000 12.26 0.00 0.00 3.41
1756 1895 6.493115 TCCATTTGAAATGCCTAGAAAGACAA 59.507 34.615 12.26 0.00 0.00 3.18
1757 1896 6.810182 CCATTTGAAATGCCTAGAAAGACAAG 59.190 38.462 12.26 0.00 0.00 3.16
1758 1897 6.959639 TTTGAAATGCCTAGAAAGACAAGT 57.040 33.333 0.00 0.00 0.00 3.16
1759 1898 8.514594 CATTTGAAATGCCTAGAAAGACAAGTA 58.485 33.333 4.82 0.00 0.00 2.24
1760 1899 8.635765 TTTGAAATGCCTAGAAAGACAAGTAT 57.364 30.769 0.00 0.00 0.00 2.12
1761 1900 8.635765 TTGAAATGCCTAGAAAGACAAGTATT 57.364 30.769 0.00 0.00 0.00 1.89
1762 1901 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
1763 1902 8.514594 TGAAATGCCTAGAAAGACAAGTATTTG 58.485 33.333 0.00 0.00 40.24 2.32
1764 1903 7.396540 AATGCCTAGAAAGACAAGTATTTGG 57.603 36.000 2.81 0.00 38.66 3.28
1765 1904 5.253330 TGCCTAGAAAGACAAGTATTTGGG 58.747 41.667 2.81 0.00 38.66 4.12
1766 1905 5.013704 TGCCTAGAAAGACAAGTATTTGGGA 59.986 40.000 2.81 0.00 38.66 4.37
1767 1906 5.944007 GCCTAGAAAGACAAGTATTTGGGAA 59.056 40.000 2.81 0.00 38.66 3.97
1768 1907 6.127980 GCCTAGAAAGACAAGTATTTGGGAAC 60.128 42.308 2.81 0.00 38.66 3.62
1769 1908 5.941948 AGAAAGACAAGTATTTGGGAACG 57.058 39.130 2.81 0.00 38.66 3.95
1770 1909 4.760204 AGAAAGACAAGTATTTGGGAACGG 59.240 41.667 2.81 0.00 38.66 4.44
1771 1910 4.360951 AAGACAAGTATTTGGGAACGGA 57.639 40.909 2.81 0.00 38.66 4.69
1772 1911 3.939066 AGACAAGTATTTGGGAACGGAG 58.061 45.455 2.81 0.00 38.66 4.63
1773 1912 3.007635 GACAAGTATTTGGGAACGGAGG 58.992 50.000 2.81 0.00 38.66 4.30
1774 1913 2.290705 ACAAGTATTTGGGAACGGAGGG 60.291 50.000 2.81 0.00 38.66 4.30
1775 1914 1.961133 AGTATTTGGGAACGGAGGGA 58.039 50.000 0.00 0.00 0.00 4.20
1776 1915 1.838077 AGTATTTGGGAACGGAGGGAG 59.162 52.381 0.00 0.00 0.00 4.30
1777 1916 1.558294 GTATTTGGGAACGGAGGGAGT 59.442 52.381 0.00 0.00 0.00 3.85
1778 1917 1.961133 ATTTGGGAACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
1831 1970 2.433664 GTTGGGCGTAGGTGGTCG 60.434 66.667 0.00 0.00 0.00 4.79
1840 1979 2.228343 GCGTAGGTGGTCGATAATAGCT 59.772 50.000 0.00 0.00 0.00 3.32
1964 2103 4.927782 AGTTCGCACGCCAGGCAA 62.928 61.111 13.30 0.00 0.00 4.52
1970 2109 3.276091 CACGCCAGGCAACGAACA 61.276 61.111 13.30 0.00 46.39 3.18
2116 2255 1.140816 GCAATCGTATCGGAGAAGGC 58.859 55.000 0.00 0.00 43.58 4.35
2209 2348 1.922447 TGCCTTCCTCCACCAATGTAT 59.078 47.619 0.00 0.00 0.00 2.29
2400 2539 1.003580 GAGGTGGAATGAAGTGAGCCA 59.996 52.381 0.00 0.00 0.00 4.75
2428 2567 0.245539 GCCCTAACACTACTGTCGCA 59.754 55.000 0.00 0.00 0.00 5.10
2657 2796 2.163211 GAGAGATGCCTTGTTTTCAGGC 59.837 50.000 3.87 3.87 41.26 4.85
2754 2894 9.546909 CAGTTTTAGATTGTACTTGTTGCTATG 57.453 33.333 0.00 0.00 0.00 2.23
2793 2933 7.167635 GTCTATGTGTGATATTTGTACCGAGTG 59.832 40.741 0.00 0.00 0.00 3.51
2829 2969 6.488344 TGGCTAGATATTTGTTTGTGTGTTCA 59.512 34.615 0.00 0.00 0.00 3.18
3024 3165 6.119053 CGTAATTTTACACGTCTTTTTGGC 57.881 37.500 0.00 0.00 33.28 4.52
3040 3181 0.179076 TGGCGCATGACAGACATAGG 60.179 55.000 10.83 0.00 37.46 2.57
3042 3183 1.656652 GCGCATGACAGACATAGGTT 58.343 50.000 0.30 0.00 37.46 3.50
3164 3308 4.810191 AGGACTTCCTTGATGACACTAC 57.190 45.455 0.00 0.00 46.09 2.73
3168 3312 5.419471 GGACTTCCTTGATGACACTACTACT 59.581 44.000 0.00 0.00 0.00 2.57
3169 3313 6.071278 GGACTTCCTTGATGACACTACTACTT 60.071 42.308 0.00 0.00 0.00 2.24
3170 3314 7.122353 GGACTTCCTTGATGACACTACTACTTA 59.878 40.741 0.00 0.00 0.00 2.24
3194 3338 4.616181 AGTTTGTGTAAGTTGCTCACAC 57.384 40.909 8.95 6.93 40.92 3.82
3236 3380 4.035017 AGACAAAACAAAATCGAAGTGCG 58.965 39.130 0.00 0.00 42.69 5.34
3242 3386 3.916761 ACAAAATCGAAGTGCGGTACTA 58.083 40.909 0.00 0.00 39.18 1.82
3243 3387 4.501071 ACAAAATCGAAGTGCGGTACTAT 58.499 39.130 0.00 0.00 39.18 2.12
3244 3388 4.328983 ACAAAATCGAAGTGCGGTACTATG 59.671 41.667 0.00 0.00 39.18 2.23
3245 3389 2.795175 ATCGAAGTGCGGTACTATGG 57.205 50.000 0.00 0.00 39.18 2.74
3246 3390 1.753930 TCGAAGTGCGGTACTATGGA 58.246 50.000 0.00 0.00 39.18 3.41
3247 3391 1.674441 TCGAAGTGCGGTACTATGGAG 59.326 52.381 0.00 0.00 39.18 3.86
3248 3392 1.404391 CGAAGTGCGGTACTATGGAGT 59.596 52.381 0.00 0.00 39.18 3.85
3267 3411 4.706476 GGAGTGTGGAATGATGAAATGGAA 59.294 41.667 0.00 0.00 0.00 3.53
3338 3482 7.987458 TCTACTTCACCTGTTTGATTCCATATC 59.013 37.037 0.00 0.00 0.00 1.63
3424 3569 3.247648 CACAACACTAAACTCCTTCCACG 59.752 47.826 0.00 0.00 0.00 4.94
3626 3775 7.111466 TCACAATCATTGACACCAGATATTGA 58.889 34.615 3.79 0.00 0.00 2.57
3697 3847 6.720112 AATGCTGGCATACATGAAGTAATT 57.280 33.333 8.55 0.00 36.05 1.40
3698 3848 5.503662 TGCTGGCATACATGAAGTAATTG 57.496 39.130 0.00 0.00 36.05 2.32
3699 3849 4.949238 TGCTGGCATACATGAAGTAATTGT 59.051 37.500 0.00 0.00 36.05 2.71
3700 3850 5.418524 TGCTGGCATACATGAAGTAATTGTT 59.581 36.000 0.00 0.00 36.05 2.83
3701 3851 5.745294 GCTGGCATACATGAAGTAATTGTTG 59.255 40.000 0.00 0.00 36.05 3.33
3702 3852 6.206395 TGGCATACATGAAGTAATTGTTGG 57.794 37.500 0.00 0.00 36.05 3.77
3703 3853 5.714333 TGGCATACATGAAGTAATTGTTGGT 59.286 36.000 0.00 0.00 36.05 3.67
3704 3854 6.887002 TGGCATACATGAAGTAATTGTTGGTA 59.113 34.615 0.00 0.00 36.05 3.25
3705 3855 7.148154 TGGCATACATGAAGTAATTGTTGGTAC 60.148 37.037 0.00 0.00 36.05 3.34
3706 3856 7.067008 GGCATACATGAAGTAATTGTTGGTACT 59.933 37.037 0.00 0.00 36.05 2.73
3707 3857 8.122952 GCATACATGAAGTAATTGTTGGTACTC 58.877 37.037 0.00 0.00 36.05 2.59
3708 3858 9.383519 CATACATGAAGTAATTGTTGGTACTCT 57.616 33.333 0.00 0.00 36.05 3.24
3709 3859 9.959721 ATACATGAAGTAATTGTTGGTACTCTT 57.040 29.630 0.00 0.00 36.05 2.85
3710 3860 8.099364 ACATGAAGTAATTGTTGGTACTCTTG 57.901 34.615 0.00 0.00 30.18 3.02
3711 3861 7.719633 ACATGAAGTAATTGTTGGTACTCTTGT 59.280 33.333 0.00 0.00 30.18 3.16
3712 3862 8.567948 CATGAAGTAATTGTTGGTACTCTTGTT 58.432 33.333 0.00 0.00 30.18 2.83
3713 3863 7.925993 TGAAGTAATTGTTGGTACTCTTGTTG 58.074 34.615 0.00 0.00 30.18 3.33
3714 3864 7.554835 TGAAGTAATTGTTGGTACTCTTGTTGT 59.445 33.333 0.00 0.00 30.18 3.32
3715 3865 8.967664 AAGTAATTGTTGGTACTCTTGTTGTA 57.032 30.769 0.00 0.00 30.18 2.41
3716 3866 9.569122 AAGTAATTGTTGGTACTCTTGTTGTAT 57.431 29.630 0.00 0.00 30.18 2.29
3722 3872 9.661563 TTGTTGGTACTCTTGTTGTATAATAGG 57.338 33.333 0.00 0.00 0.00 2.57
3723 3873 9.038072 TGTTGGTACTCTTGTTGTATAATAGGA 57.962 33.333 0.00 0.00 0.00 2.94
3724 3874 9.880157 GTTGGTACTCTTGTTGTATAATAGGAA 57.120 33.333 0.00 0.00 0.00 3.36
3727 3877 9.043079 GGTACTCTTGTTGTATAATAGGAAAGC 57.957 37.037 0.00 0.00 0.00 3.51
3728 3878 9.819267 GTACTCTTGTTGTATAATAGGAAAGCT 57.181 33.333 0.00 0.00 0.00 3.74
3733 3883 9.482627 CTTGTTGTATAATAGGAAAGCTAGAGG 57.517 37.037 0.00 0.00 0.00 3.69
3734 3884 8.548880 TGTTGTATAATAGGAAAGCTAGAGGT 57.451 34.615 0.00 0.00 0.00 3.85
3735 3885 8.639761 TGTTGTATAATAGGAAAGCTAGAGGTC 58.360 37.037 0.00 0.00 0.00 3.85
3736 3886 8.862085 GTTGTATAATAGGAAAGCTAGAGGTCT 58.138 37.037 0.00 0.00 0.00 3.85
3737 3887 9.435570 TTGTATAATAGGAAAGCTAGAGGTCTT 57.564 33.333 0.00 0.00 0.00 3.01
3741 3891 7.922699 AATAGGAAAGCTAGAGGTCTTATGT 57.077 36.000 0.00 0.00 0.00 2.29
3742 3892 5.606348 AGGAAAGCTAGAGGTCTTATGTG 57.394 43.478 0.00 0.00 0.00 3.21
3743 3893 5.026790 AGGAAAGCTAGAGGTCTTATGTGT 58.973 41.667 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.234908 AGCTGTCCTGTTCATACTGTCC 59.765 50.000 0.00 0.00 0.00 4.02
24 25 2.613977 GCAGCTGTCCTGTTCATACTGT 60.614 50.000 16.64 0.00 43.71 3.55
149 150 3.520290 TCGGATGCTGTTTTATCTCGT 57.480 42.857 0.00 0.00 0.00 4.18
189 190 3.374745 GAGCAACAACCACAACATCTTG 58.625 45.455 0.00 0.00 0.00 3.02
196 197 2.025589 TACACGAGCAACAACCACAA 57.974 45.000 0.00 0.00 0.00 3.33
277 278 0.178876 TCTTCTGGATGGTGGGTGGA 60.179 55.000 0.00 0.00 0.00 4.02
316 318 5.918608 AGTCTCTAAATGTGGACGCAATAT 58.081 37.500 0.00 0.00 34.34 1.28
458 483 9.403110 CCAATCTCATTTGTTTTAAGAAGTCAG 57.597 33.333 0.00 0.00 0.00 3.51
640 668 0.177373 AAATACTCCCGCCGTTCCTC 59.823 55.000 0.00 0.00 0.00 3.71
972 1111 2.643232 GCTCAAAAGGCAGGCAGGG 61.643 63.158 0.00 0.00 0.00 4.45
1182 1321 2.425312 CTGCTCGATGTAGGACTTGAGT 59.575 50.000 0.00 0.00 0.00 3.41
1275 1414 2.322355 ACTGGCAGCATCACTACATC 57.678 50.000 15.89 0.00 0.00 3.06
1315 1454 8.307483 GCACACCTAATTAGCTTCTATCTATCA 58.693 37.037 6.99 0.00 0.00 2.15
1316 1455 7.486551 CGCACACCTAATTAGCTTCTATCTATC 59.513 40.741 6.99 0.00 0.00 2.08
1321 1460 5.277857 ACGCACACCTAATTAGCTTCTAT 57.722 39.130 6.99 0.00 0.00 1.98
1322 1461 4.730949 ACGCACACCTAATTAGCTTCTA 57.269 40.909 6.99 0.00 0.00 2.10
1522 1661 7.661027 TGAGTTGATCATACAATTGACAAGACA 59.339 33.333 13.59 3.02 31.12 3.41
1607 1746 2.982339 ACGGAGGGAGTAGATAGCAT 57.018 50.000 0.00 0.00 0.00 3.79
1617 1756 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
1618 1757 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
1619 1758 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
1620 1759 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
1621 1760 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
1622 1761 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
1623 1762 8.248945 TCTAGAAAGACAAGTATTTAGGAACGG 58.751 37.037 0.00 0.00 0.00 4.44
1624 1763 9.291664 CTCTAGAAAGACAAGTATTTAGGAACG 57.708 37.037 0.00 0.00 0.00 3.95
1635 1774 9.487790 CTTCTTGAAATCTCTAGAAAGACAAGT 57.512 33.333 17.52 0.00 41.09 3.16
1636 1775 9.487790 ACTTCTTGAAATCTCTAGAAAGACAAG 57.512 33.333 14.55 14.55 41.09 3.16
1637 1776 9.265901 CACTTCTTGAAATCTCTAGAAAGACAA 57.734 33.333 2.46 1.82 41.09 3.18
1638 1777 8.642432 TCACTTCTTGAAATCTCTAGAAAGACA 58.358 33.333 2.46 0.00 41.09 3.41
1639 1778 8.921670 GTCACTTCTTGAAATCTCTAGAAAGAC 58.078 37.037 2.46 8.57 41.09 3.01
1640 1779 8.865090 AGTCACTTCTTGAAATCTCTAGAAAGA 58.135 33.333 0.00 0.00 41.09 2.52
1642 1781 9.915629 GTAGTCACTTCTTGAAATCTCTAGAAA 57.084 33.333 0.00 0.00 41.09 2.52
1643 1782 9.078990 TGTAGTCACTTCTTGAAATCTCTAGAA 57.921 33.333 0.00 0.00 39.94 2.10
1644 1783 8.637196 TGTAGTCACTTCTTGAAATCTCTAGA 57.363 34.615 0.00 0.00 35.39 2.43
1647 1786 7.971168 CGTATGTAGTCACTTCTTGAAATCTCT 59.029 37.037 0.00 0.00 35.39 3.10
1648 1787 7.968956 TCGTATGTAGTCACTTCTTGAAATCTC 59.031 37.037 0.00 0.00 35.39 2.75
1649 1788 7.755822 GTCGTATGTAGTCACTTCTTGAAATCT 59.244 37.037 0.00 0.00 35.39 2.40
1650 1789 7.253354 CGTCGTATGTAGTCACTTCTTGAAATC 60.253 40.741 0.00 0.00 35.39 2.17
1651 1790 6.527023 CGTCGTATGTAGTCACTTCTTGAAAT 59.473 38.462 0.00 0.00 35.39 2.17
1652 1791 5.854866 CGTCGTATGTAGTCACTTCTTGAAA 59.145 40.000 0.00 0.00 35.39 2.69
1653 1792 5.388111 CGTCGTATGTAGTCACTTCTTGAA 58.612 41.667 0.00 0.00 35.39 2.69
1654 1793 4.670992 GCGTCGTATGTAGTCACTTCTTGA 60.671 45.833 0.00 0.00 0.00 3.02
1655 1794 3.542704 GCGTCGTATGTAGTCACTTCTTG 59.457 47.826 0.00 0.00 0.00 3.02
1656 1795 3.189910 TGCGTCGTATGTAGTCACTTCTT 59.810 43.478 0.00 0.00 0.00 2.52
1657 1796 2.745821 TGCGTCGTATGTAGTCACTTCT 59.254 45.455 0.00 0.00 0.00 2.85
1658 1797 3.127081 TGCGTCGTATGTAGTCACTTC 57.873 47.619 0.00 0.00 0.00 3.01
1659 1798 3.564235 TTGCGTCGTATGTAGTCACTT 57.436 42.857 0.00 0.00 0.00 3.16
1660 1799 3.564235 TTTGCGTCGTATGTAGTCACT 57.436 42.857 0.00 0.00 0.00 3.41
1661 1800 4.325204 TCATTTTGCGTCGTATGTAGTCAC 59.675 41.667 0.00 0.00 0.00 3.67
1662 1801 4.487019 TCATTTTGCGTCGTATGTAGTCA 58.513 39.130 0.00 0.00 0.00 3.41
1663 1802 4.561606 ACTCATTTTGCGTCGTATGTAGTC 59.438 41.667 0.00 0.00 0.00 2.59
1664 1803 4.326278 CACTCATTTTGCGTCGTATGTAGT 59.674 41.667 0.00 0.00 0.00 2.73
1665 1804 4.561213 TCACTCATTTTGCGTCGTATGTAG 59.439 41.667 0.00 0.00 0.00 2.74
1666 1805 4.487019 TCACTCATTTTGCGTCGTATGTA 58.513 39.130 0.00 0.00 0.00 2.29
1667 1806 3.322369 TCACTCATTTTGCGTCGTATGT 58.678 40.909 0.00 0.00 0.00 2.29
1668 1807 3.989705 TCACTCATTTTGCGTCGTATG 57.010 42.857 0.00 0.00 0.00 2.39
1669 1808 4.870426 AGATTCACTCATTTTGCGTCGTAT 59.130 37.500 0.00 0.00 0.00 3.06
1670 1809 4.242475 AGATTCACTCATTTTGCGTCGTA 58.758 39.130 0.00 0.00 0.00 3.43
1671 1810 3.067106 AGATTCACTCATTTTGCGTCGT 58.933 40.909 0.00 0.00 0.00 4.34
1672 1811 3.729526 AGATTCACTCATTTTGCGTCG 57.270 42.857 0.00 0.00 0.00 5.12
1673 1812 5.120830 AGTGTAGATTCACTCATTTTGCGTC 59.879 40.000 0.00 0.00 44.07 5.19
1674 1813 4.997395 AGTGTAGATTCACTCATTTTGCGT 59.003 37.500 0.00 0.00 44.07 5.24
1675 1814 5.536554 AGTGTAGATTCACTCATTTTGCG 57.463 39.130 0.00 0.00 44.07 4.85
1676 1815 9.677567 TTTAAAGTGTAGATTCACTCATTTTGC 57.322 29.630 0.00 0.00 46.25 3.68
1705 1844 9.244292 ACTCAATATACGGATGTATGTAGACAT 57.756 33.333 0.08 0.08 41.37 3.06
1706 1845 8.631480 ACTCAATATACGGATGTATGTAGACA 57.369 34.615 0.00 0.00 41.37 3.41
1707 1846 8.182881 GGACTCAATATACGGATGTATGTAGAC 58.817 40.741 0.00 0.00 41.37 2.59
1708 1847 7.886446 TGGACTCAATATACGGATGTATGTAGA 59.114 37.037 0.00 0.00 41.37 2.59
1709 1848 8.051901 TGGACTCAATATACGGATGTATGTAG 57.948 38.462 0.00 0.00 41.37 2.74
1710 1849 8.589701 ATGGACTCAATATACGGATGTATGTA 57.410 34.615 0.00 0.00 41.37 2.29
1711 1850 6.911250 TGGACTCAATATACGGATGTATGT 57.089 37.500 0.00 0.00 41.37 2.29
1712 1851 8.659491 CAAATGGACTCAATATACGGATGTATG 58.341 37.037 0.00 0.00 41.37 2.39
1713 1852 8.593679 TCAAATGGACTCAATATACGGATGTAT 58.406 33.333 0.00 0.00 43.62 2.29
1714 1853 7.958088 TCAAATGGACTCAATATACGGATGTA 58.042 34.615 0.00 0.00 34.45 2.29
1715 1854 6.826668 TCAAATGGACTCAATATACGGATGT 58.173 36.000 0.00 0.00 0.00 3.06
1716 1855 7.728847 TTCAAATGGACTCAATATACGGATG 57.271 36.000 0.00 0.00 0.00 3.51
1717 1856 8.786898 CATTTCAAATGGACTCAATATACGGAT 58.213 33.333 1.73 0.00 0.00 4.18
1718 1857 7.255104 GCATTTCAAATGGACTCAATATACGGA 60.255 37.037 12.14 0.00 0.00 4.69
1719 1858 6.857964 GCATTTCAAATGGACTCAATATACGG 59.142 38.462 12.14 0.00 0.00 4.02
1720 1859 6.857964 GGCATTTCAAATGGACTCAATATACG 59.142 38.462 12.14 0.00 0.00 3.06
1721 1860 7.945134 AGGCATTTCAAATGGACTCAATATAC 58.055 34.615 12.14 0.00 0.00 1.47
1722 1861 9.288576 CTAGGCATTTCAAATGGACTCAATATA 57.711 33.333 12.14 0.00 0.00 0.86
1723 1862 8.000709 TCTAGGCATTTCAAATGGACTCAATAT 58.999 33.333 12.14 0.00 0.00 1.28
1724 1863 7.345691 TCTAGGCATTTCAAATGGACTCAATA 58.654 34.615 12.14 0.00 0.00 1.90
1725 1864 6.189859 TCTAGGCATTTCAAATGGACTCAAT 58.810 36.000 12.14 0.00 0.00 2.57
1726 1865 5.569355 TCTAGGCATTTCAAATGGACTCAA 58.431 37.500 12.14 0.00 0.00 3.02
1727 1866 5.178096 TCTAGGCATTTCAAATGGACTCA 57.822 39.130 12.14 0.00 0.00 3.41
1728 1867 6.375455 TCTTTCTAGGCATTTCAAATGGACTC 59.625 38.462 12.14 0.00 0.00 3.36
1729 1868 6.151817 GTCTTTCTAGGCATTTCAAATGGACT 59.848 38.462 12.14 3.08 0.00 3.85
1730 1869 6.071952 TGTCTTTCTAGGCATTTCAAATGGAC 60.072 38.462 12.14 8.23 29.10 4.02
1731 1870 6.009589 TGTCTTTCTAGGCATTTCAAATGGA 58.990 36.000 12.14 0.00 29.10 3.41
1732 1871 6.271488 TGTCTTTCTAGGCATTTCAAATGG 57.729 37.500 12.14 0.00 29.10 3.16
1733 1872 7.373493 ACTTGTCTTTCTAGGCATTTCAAATG 58.627 34.615 5.68 5.68 35.56 2.32
1734 1873 7.530426 ACTTGTCTTTCTAGGCATTTCAAAT 57.470 32.000 0.00 0.00 35.56 2.32
1735 1874 6.959639 ACTTGTCTTTCTAGGCATTTCAAA 57.040 33.333 0.00 0.00 35.56 2.69
1736 1875 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
1737 1876 8.514594 CAAATACTTGTCTTTCTAGGCATTTCA 58.485 33.333 0.00 0.00 35.56 2.69
1738 1877 7.970614 CCAAATACTTGTCTTTCTAGGCATTTC 59.029 37.037 0.00 0.00 35.56 2.17
1739 1878 7.093771 CCCAAATACTTGTCTTTCTAGGCATTT 60.094 37.037 0.00 0.00 35.56 2.32
1740 1879 6.378280 CCCAAATACTTGTCTTTCTAGGCATT 59.622 38.462 0.00 0.00 35.56 3.56
1741 1880 5.888161 CCCAAATACTTGTCTTTCTAGGCAT 59.112 40.000 0.00 0.00 35.56 4.40
1742 1881 5.013704 TCCCAAATACTTGTCTTTCTAGGCA 59.986 40.000 0.00 0.00 33.22 4.75
1743 1882 5.497474 TCCCAAATACTTGTCTTTCTAGGC 58.503 41.667 0.00 0.00 0.00 3.93
1744 1883 6.092259 CGTTCCCAAATACTTGTCTTTCTAGG 59.908 42.308 0.00 0.00 0.00 3.02
1745 1884 6.092259 CCGTTCCCAAATACTTGTCTTTCTAG 59.908 42.308 0.00 0.00 0.00 2.43
1746 1885 5.935789 CCGTTCCCAAATACTTGTCTTTCTA 59.064 40.000 0.00 0.00 0.00 2.10
1747 1886 4.760204 CCGTTCCCAAATACTTGTCTTTCT 59.240 41.667 0.00 0.00 0.00 2.52
1748 1887 4.758165 TCCGTTCCCAAATACTTGTCTTTC 59.242 41.667 0.00 0.00 0.00 2.62
1749 1888 4.721132 TCCGTTCCCAAATACTTGTCTTT 58.279 39.130 0.00 0.00 0.00 2.52
1750 1889 4.324267 CTCCGTTCCCAAATACTTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
1751 1890 3.307480 CCTCCGTTCCCAAATACTTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
1752 1891 3.007635 CCTCCGTTCCCAAATACTTGTC 58.992 50.000 0.00 0.00 0.00 3.18
1753 1892 2.290705 CCCTCCGTTCCCAAATACTTGT 60.291 50.000 0.00 0.00 0.00 3.16
1754 1893 2.026636 TCCCTCCGTTCCCAAATACTTG 60.027 50.000 0.00 0.00 0.00 3.16
1755 1894 2.238898 CTCCCTCCGTTCCCAAATACTT 59.761 50.000 0.00 0.00 0.00 2.24
1756 1895 1.838077 CTCCCTCCGTTCCCAAATACT 59.162 52.381 0.00 0.00 0.00 2.12
1757 1896 1.558294 ACTCCCTCCGTTCCCAAATAC 59.442 52.381 0.00 0.00 0.00 1.89
1758 1897 1.961133 ACTCCCTCCGTTCCCAAATA 58.039 50.000 0.00 0.00 0.00 1.40
1759 1898 1.961133 TACTCCCTCCGTTCCCAAAT 58.039 50.000 0.00 0.00 0.00 2.32
1760 1899 1.557832 CATACTCCCTCCGTTCCCAAA 59.442 52.381 0.00 0.00 0.00 3.28
1761 1900 1.200519 CATACTCCCTCCGTTCCCAA 58.799 55.000 0.00 0.00 0.00 4.12
1762 1901 0.337082 TCATACTCCCTCCGTTCCCA 59.663 55.000 0.00 0.00 0.00 4.37
1763 1902 1.619332 GATCATACTCCCTCCGTTCCC 59.381 57.143 0.00 0.00 0.00 3.97
1764 1903 2.599677 AGATCATACTCCCTCCGTTCC 58.400 52.381 0.00 0.00 0.00 3.62
1765 1904 4.828387 ACTTAGATCATACTCCCTCCGTTC 59.172 45.833 0.00 0.00 0.00 3.95
1766 1905 4.805744 ACTTAGATCATACTCCCTCCGTT 58.194 43.478 0.00 0.00 0.00 4.44
1767 1906 4.456662 ACTTAGATCATACTCCCTCCGT 57.543 45.455 0.00 0.00 0.00 4.69
1768 1907 5.074115 AGAACTTAGATCATACTCCCTCCG 58.926 45.833 0.00 0.00 0.00 4.63
1769 1908 8.361889 GTTTAGAACTTAGATCATACTCCCTCC 58.638 40.741 0.00 0.00 0.00 4.30
1770 1909 8.915036 TGTTTAGAACTTAGATCATACTCCCTC 58.085 37.037 0.00 0.00 0.00 4.30
1771 1910 8.840200 TGTTTAGAACTTAGATCATACTCCCT 57.160 34.615 0.00 0.00 0.00 4.20
1964 2103 1.449601 CCTTATGCCCGCTGTTCGT 60.450 57.895 0.00 0.00 36.19 3.85
1970 2109 0.464554 GCTTCTTCCTTATGCCCGCT 60.465 55.000 0.00 0.00 0.00 5.52
2080 2219 0.482446 TGCCTTCCACCATTGAACCT 59.518 50.000 0.00 0.00 0.00 3.50
2200 2339 1.215423 GGAGCTTCCCCATACATTGGT 59.785 52.381 0.00 0.00 44.83 3.67
2209 2348 0.250727 CGAAGTTTGGAGCTTCCCCA 60.251 55.000 0.00 0.00 39.18 4.96
2400 2539 1.435256 AGTGTTAGGGCAGACCAAGT 58.565 50.000 0.00 0.00 43.89 3.16
2428 2567 2.004408 GCATCCCTTGGGAGCTGGAT 62.004 60.000 14.30 0.00 38.12 3.41
2762 2902 8.150945 GGTACAAATATCACACATAGACCAGAT 58.849 37.037 0.00 0.00 0.00 2.90
2784 2924 0.175073 CTAGGGTTGGCACTCGGTAC 59.825 60.000 0.00 0.00 0.00 3.34
2793 2933 1.132500 ATCTAGCCACTAGGGTTGGC 58.868 55.000 13.65 13.65 45.14 4.52
2829 2969 8.774586 CAAGTAAACTTTGTCTATGCTGTTAGT 58.225 33.333 0.00 0.00 33.11 2.24
3024 3165 2.892374 TCAACCTATGTCTGTCATGCG 58.108 47.619 0.00 0.00 37.91 4.73
3097 3240 5.345741 CCATTTTTGCCAAATCACTAGAACG 59.654 40.000 0.00 0.00 0.00 3.95
3102 3245 9.213799 GTAAAATCCATTTTTGCCAAATCACTA 57.786 29.630 2.68 0.00 40.24 2.74
3168 3312 8.339714 GTGTGAGCAACTTACACAAACTAATAA 58.660 33.333 15.35 0.00 45.94 1.40
3169 3313 7.857569 GTGTGAGCAACTTACACAAACTAATA 58.142 34.615 15.35 0.00 45.94 0.98
3170 3314 6.725246 GTGTGAGCAACTTACACAAACTAAT 58.275 36.000 15.35 0.00 45.94 1.73
3194 3338 9.599866 TTTGTCTATATGGTTAGATTGACACAG 57.400 33.333 0.00 0.00 39.02 3.66
3222 3366 4.260212 CCATAGTACCGCACTTCGATTTTG 60.260 45.833 0.00 0.00 41.67 2.44
3226 3370 2.293677 CTCCATAGTACCGCACTTCGAT 59.706 50.000 0.00 0.00 41.67 3.59
3236 3380 5.070446 TCATCATTCCACACTCCATAGTACC 59.930 44.000 0.00 0.00 33.48 3.34
3242 3386 4.647853 CCATTTCATCATTCCACACTCCAT 59.352 41.667 0.00 0.00 0.00 3.41
3243 3387 4.018490 CCATTTCATCATTCCACACTCCA 58.982 43.478 0.00 0.00 0.00 3.86
3244 3388 4.272489 TCCATTTCATCATTCCACACTCC 58.728 43.478 0.00 0.00 0.00 3.85
3245 3389 5.902613 TTCCATTTCATCATTCCACACTC 57.097 39.130 0.00 0.00 0.00 3.51
3246 3390 5.776716 AGTTTCCATTTCATCATTCCACACT 59.223 36.000 0.00 0.00 0.00 3.55
3247 3391 6.029346 AGTTTCCATTTCATCATTCCACAC 57.971 37.500 0.00 0.00 0.00 3.82
3248 3392 6.267242 TGAAGTTTCCATTTCATCATTCCACA 59.733 34.615 0.00 0.00 0.00 4.17
3267 3411 7.939039 ACATATGATGACCGGATAAATGAAGTT 59.061 33.333 9.46 0.00 0.00 2.66
3338 3482 2.642139 ATGAACGCTGGAAATGCAAG 57.358 45.000 0.00 0.00 0.00 4.01
3556 3703 6.873997 TCAGACACTAGTTCTTTGAACTGAA 58.126 36.000 19.47 3.66 30.75 3.02
3591 3740 6.583806 GTGTCAATGATTGTGAAGTCATTTCC 59.416 38.462 4.93 0.00 41.70 3.13
3605 3754 9.722184 CTAGATCAATATCTGGTGTCAATGATT 57.278 33.333 0.00 0.00 42.60 2.57
3626 3775 6.421485 ACATGCAAAACCATTCTCTCTAGAT 58.579 36.000 0.00 0.00 0.00 1.98
3697 3847 9.038072 TCCTATTATACAACAAGAGTACCAACA 57.962 33.333 0.00 0.00 0.00 3.33
3698 3848 9.880157 TTCCTATTATACAACAAGAGTACCAAC 57.120 33.333 0.00 0.00 0.00 3.77
3701 3851 9.043079 GCTTTCCTATTATACAACAAGAGTACC 57.957 37.037 0.00 0.00 0.00 3.34
3702 3852 9.819267 AGCTTTCCTATTATACAACAAGAGTAC 57.181 33.333 0.00 0.00 0.00 2.73
3707 3857 9.482627 CCTCTAGCTTTCCTATTATACAACAAG 57.517 37.037 0.00 0.00 0.00 3.16
3708 3858 8.989131 ACCTCTAGCTTTCCTATTATACAACAA 58.011 33.333 0.00 0.00 0.00 2.83
3709 3859 8.548880 ACCTCTAGCTTTCCTATTATACAACA 57.451 34.615 0.00 0.00 0.00 3.33
3710 3860 8.862085 AGACCTCTAGCTTTCCTATTATACAAC 58.138 37.037 0.00 0.00 0.00 3.32
3711 3861 9.435570 AAGACCTCTAGCTTTCCTATTATACAA 57.564 33.333 0.00 0.00 0.00 2.41
3715 3865 9.608718 ACATAAGACCTCTAGCTTTCCTATTAT 57.391 33.333 0.00 0.00 0.00 1.28
3716 3866 8.861086 CACATAAGACCTCTAGCTTTCCTATTA 58.139 37.037 0.00 0.00 0.00 0.98
3717 3867 7.345914 ACACATAAGACCTCTAGCTTTCCTATT 59.654 37.037 0.00 0.00 0.00 1.73
3718 3868 6.841755 ACACATAAGACCTCTAGCTTTCCTAT 59.158 38.462 0.00 0.00 0.00 2.57
3719 3869 6.195700 ACACATAAGACCTCTAGCTTTCCTA 58.804 40.000 0.00 0.00 0.00 2.94
3720 3870 5.026790 ACACATAAGACCTCTAGCTTTCCT 58.973 41.667 0.00 0.00 0.00 3.36
3721 3871 5.346181 ACACATAAGACCTCTAGCTTTCC 57.654 43.478 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.