Multiple sequence alignment - TraesCS2D01G292600

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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 TraesCS2D01G292600 chr2D 100.000 3382 0 0 1 3382 375145008 375148389 0.000000e+00 6246.0
1 TraesCS2D01G292600 chr2A 91.344 1525 61 32 150 1644 507427845 507429328 0.000000e+00 2019.0
2 TraesCS2D01G292600 chr2A 90.930 1279 52 26 1721 2992 507429321 507430542 0.000000e+00 1661.0
3 TraesCS2D01G292600 chr2A 88.393 336 37 2 3049 3382 507430816 507431151 1.460000e-108 403.0
4 TraesCS2D01G292600 chr2A 94.521 73 4 0 1 73 507427645 507427717 2.760000e-21 113.0
5 TraesCS2D01G292600 chr2A 100.000 51 0 0 74 124 507427798 507427848 9.990000e-16 95.3
6 TraesCS2D01G292600 chr2B 88.992 1508 74 39 180 1644 445250139 445251597 0.000000e+00 1781.0
7 TraesCS2D01G292600 chr2B 89.096 1183 51 27 1721 2886 445251590 445252711 0.000000e+00 1399.0
8 TraesCS2D01G292600 chr2B 91.279 344 25 2 3044 3382 445256139 445256482 6.610000e-127 464.0
9 TraesCS2D01G292600 chr4A 96.552 58 2 0 1383 1440 667247862 667247919 2.780000e-16 97.1
10 TraesCS2D01G292600 chr4A 96.552 58 2 0 1383 1440 667269898 667269955 2.780000e-16 97.1
11 TraesCS2D01G292600 chr4A 96.552 58 2 0 1383 1440 667293450 667293507 2.780000e-16 97.1
12 TraesCS2D01G292600 chr4A 96.226 53 2 0 1721 1773 667248040 667248092 1.670000e-13 87.9
13 TraesCS2D01G292600 chr4A 96.226 53 2 0 1721 1773 667270076 667270128 1.670000e-13 87.9


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 TraesCS2D01G292600 chr2D 375145008 375148389 3381 False 6246.000000 6246 100.0000 1 3382 1 chr2D.!!$F1 3381
1 TraesCS2D01G292600 chr2A 507427645 507431151 3506 False 858.260000 2019 93.0376 1 3382 5 chr2A.!!$F1 3381
2 TraesCS2D01G292600 chr2B 445250139 445256482 6343 False 1214.666667 1781 89.7890 180 3382 3 chr2B.!!$F1 3202

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
132 213 0.250553 TAAAACGGCCCTGGTGTCTG 60.251 55.0 0.00 0.0 0.0 3.51 F
1643 1790 0.039527 ATCAACGGCGAAAGGTTTGC 60.040 50.0 16.62 0.0 0.0 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1648 1795 0.440758 TATCCTTTGTGCGCGTTTCG 59.559 50.0 8.43 0.0 42.12 3.46 R
2589 2767 1.131303 ACATCAACCCTTCCGGACCA 61.131 55.0 1.83 0.0 34.64 4.02 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
47 48 7.576750 TTTATTGTATATCTCGTTGATCGGC 57.423 36.000 0.00 0.00 40.32 5.54
56 57 0.863799 CGTTGATCGGCCATGATCTG 59.136 55.000 18.13 7.56 44.12 2.90
60 61 1.210234 TGATCGGCCATGATCTGTTGT 59.790 47.619 18.13 0.00 44.12 3.32
73 74 6.267496 TGATCTGTTGTTCTCACGAAGATA 57.733 37.500 0.00 0.00 32.82 1.98
120 201 2.986479 GCAACAAGGCAGAATAAAACGG 59.014 45.455 0.00 0.00 0.00 4.44
121 202 2.986479 CAACAAGGCAGAATAAAACGGC 59.014 45.455 0.00 0.00 0.00 5.68
122 203 1.544246 ACAAGGCAGAATAAAACGGCC 59.456 47.619 0.00 0.00 45.97 6.13
123 204 1.135112 CAAGGCAGAATAAAACGGCCC 60.135 52.381 0.00 0.00 46.58 5.80
124 205 0.331616 AGGCAGAATAAAACGGCCCT 59.668 50.000 0.00 0.00 46.58 5.19
125 206 0.455815 GGCAGAATAAAACGGCCCTG 59.544 55.000 0.00 0.00 41.38 4.45
126 207 0.455815 GCAGAATAAAACGGCCCTGG 59.544 55.000 0.00 0.00 0.00 4.45
127 208 1.834188 CAGAATAAAACGGCCCTGGT 58.166 50.000 0.00 0.00 0.00 4.00
128 209 1.472480 CAGAATAAAACGGCCCTGGTG 59.528 52.381 0.00 0.00 0.00 4.17
129 210 1.074889 AGAATAAAACGGCCCTGGTGT 59.925 47.619 0.00 0.00 0.00 4.16
130 211 1.471287 GAATAAAACGGCCCTGGTGTC 59.529 52.381 0.00 0.00 0.00 3.67
131 212 0.696501 ATAAAACGGCCCTGGTGTCT 59.303 50.000 0.00 0.00 0.00 3.41
132 213 0.250553 TAAAACGGCCCTGGTGTCTG 60.251 55.000 0.00 0.00 0.00 3.51
133 214 4.643387 AACGGCCCTGGTGTCTGC 62.643 66.667 0.00 0.00 0.00 4.26
171 252 5.012148 CCGCCCCTCCTAATTCCTATATATG 59.988 48.000 0.00 0.00 0.00 1.78
222 303 1.200020 CAAAGAGCGCGGGAAGAATTT 59.800 47.619 8.83 0.00 0.00 1.82
223 304 1.534729 AAGAGCGCGGGAAGAATTTT 58.465 45.000 8.83 0.00 0.00 1.82
230 311 2.477863 CGCGGGAAGAATTTTGATGTCC 60.478 50.000 0.00 0.00 0.00 4.02
239 320 1.988293 TTTTGATGTCCGCCAAAGGA 58.012 45.000 0.00 0.00 38.11 3.36
287 383 0.687920 TGGAGGACGTAAACATGGCA 59.312 50.000 0.00 0.00 0.00 4.92
321 417 2.351276 GAGGACGTGGCCCAACAT 59.649 61.111 0.00 0.00 0.00 2.71
327 423 0.981183 ACGTGGCCCAACATTCTCTA 59.019 50.000 0.00 0.00 0.00 2.43
366 465 0.388907 ATGCACGGTGAAATTGCTGC 60.389 50.000 13.29 0.00 37.16 5.25
367 466 1.007502 GCACGGTGAAATTGCTGCA 60.008 52.632 13.29 0.00 33.26 4.41
375 474 1.070242 TGAAATTGCTGCACACGTACG 60.070 47.619 15.01 15.01 0.00 3.67
376 475 0.941542 AAATTGCTGCACACGTACGT 59.058 45.000 16.72 16.72 0.00 3.57
377 476 1.785768 AATTGCTGCACACGTACGTA 58.214 45.000 22.34 4.29 0.00 3.57
505 618 4.172020 TGCCCTGCCCTGTGTATATATAA 58.828 43.478 0.00 0.00 0.00 0.98
564 679 1.874345 TTCTTGCTCGGGTCTCGTCC 61.874 60.000 0.00 0.00 40.32 4.79
746 869 4.940046 GCATGATCTTGTGATGGGTATAGG 59.060 45.833 10.05 0.00 32.19 2.57
913 1056 6.830912 TGCCACAATTAAGCACTATCTATCT 58.169 36.000 0.00 0.00 0.00 1.98
914 1057 7.962441 TGCCACAATTAAGCACTATCTATCTA 58.038 34.615 0.00 0.00 0.00 1.98
915 1058 8.597167 TGCCACAATTAAGCACTATCTATCTAT 58.403 33.333 0.00 0.00 0.00 1.98
916 1059 9.092876 GCCACAATTAAGCACTATCTATCTATC 57.907 37.037 0.00 0.00 0.00 2.08
949 1092 6.348540 CCCCTATTTATTTGCGCATTCTACTC 60.349 42.308 12.75 0.00 0.00 2.59
979 1122 1.656095 CTGCGGCTTAACTTCGAAGAG 59.344 52.381 31.08 18.61 38.43 2.85
997 1140 2.345760 GCACACCCATTGCAGGAGG 61.346 63.158 0.00 0.00 39.93 4.30
1084 1227 1.003355 ACCTCCCTTGCATGTGACG 60.003 57.895 0.00 0.00 0.00 4.35
1290 1435 2.695666 ACCAGTCTCCGGTTGATATCAG 59.304 50.000 5.39 0.00 30.53 2.90
1351 1496 1.078497 CAGGGAATACACCGCTGCA 60.078 57.895 0.00 0.00 0.00 4.41
1401 1546 2.095853 ACATCGCGGTAATTTTGCTCTG 59.904 45.455 6.13 0.00 0.00 3.35
1464 1611 0.737367 TTTCATCCTCTCGCTGCGTG 60.737 55.000 22.48 19.65 0.00 5.34
1465 1612 1.877576 TTCATCCTCTCGCTGCGTGT 61.878 55.000 22.48 0.26 0.00 4.49
1466 1613 1.875813 CATCCTCTCGCTGCGTGTC 60.876 63.158 22.48 0.00 0.00 3.67
1467 1614 2.049185 ATCCTCTCGCTGCGTGTCT 61.049 57.895 22.48 3.67 0.00 3.41
1468 1615 0.748367 ATCCTCTCGCTGCGTGTCTA 60.748 55.000 22.48 9.30 0.00 2.59
1469 1616 1.226435 CCTCTCGCTGCGTGTCTAC 60.226 63.158 22.48 0.00 0.00 2.59
1486 1633 8.424628 CGTGTCTACGTATTCAGATTTATCTC 57.575 38.462 0.00 0.00 44.99 2.75
1487 1634 7.266545 CGTGTCTACGTATTCAGATTTATCTCG 59.733 40.741 0.00 0.00 44.99 4.04
1488 1635 8.068977 GTGTCTACGTATTCAGATTTATCTCGT 58.931 37.037 0.00 8.03 36.66 4.18
1489 1636 8.618677 TGTCTACGTATTCAGATTTATCTCGTT 58.381 33.333 0.00 0.00 35.16 3.85
1490 1637 8.893884 GTCTACGTATTCAGATTTATCTCGTTG 58.106 37.037 0.00 7.14 35.16 4.10
1491 1638 8.074370 TCTACGTATTCAGATTTATCTCGTTGG 58.926 37.037 0.00 4.28 35.16 3.77
1492 1639 6.570692 ACGTATTCAGATTTATCTCGTTGGT 58.429 36.000 0.00 0.00 34.22 3.67
1498 1645 5.642063 TCAGATTTATCTCGTTGGTTTCACC 59.358 40.000 0.00 0.00 35.06 4.02
1507 1654 2.538132 CGTTGGTTTCACCGTGTTCTTC 60.538 50.000 0.00 0.00 42.58 2.87
1560 1707 2.512515 GATGCTGCTGGGACGGTC 60.513 66.667 0.00 0.00 36.83 4.79
1614 1761 0.250234 TCCATTGGCACTCTCCTTCG 59.750 55.000 0.00 0.00 0.00 3.79
1635 1782 2.612567 GCACACCATCAACGGCGAA 61.613 57.895 16.62 0.00 0.00 4.70
1641 1788 0.596082 CCATCAACGGCGAAAGGTTT 59.404 50.000 16.62 0.00 0.00 3.27
1642 1789 1.665735 CCATCAACGGCGAAAGGTTTG 60.666 52.381 16.62 6.61 0.00 2.93
1643 1790 0.039527 ATCAACGGCGAAAGGTTTGC 60.040 50.000 16.62 0.00 0.00 3.68
1644 1791 1.064946 CAACGGCGAAAGGTTTGCA 59.935 52.632 16.62 0.00 0.00 4.08
1645 1792 0.526524 CAACGGCGAAAGGTTTGCAA 60.527 50.000 16.62 0.00 0.00 4.08
1646 1793 0.173708 AACGGCGAAAGGTTTGCAAA 59.826 45.000 16.62 8.05 0.00 3.68
1647 1794 0.526739 ACGGCGAAAGGTTTGCAAAC 60.527 50.000 30.09 30.09 38.17 2.93
1656 1803 1.551312 GTTTGCAAACCGAAACGCG 59.449 52.632 28.29 3.53 40.47 6.01
1657 1804 2.224885 TTTGCAAACCGAAACGCGC 61.225 52.632 8.05 0.00 39.11 6.86
1658 1805 2.867333 TTTGCAAACCGAAACGCGCA 62.867 50.000 8.05 0.00 39.11 6.09
1659 1806 3.383601 GCAAACCGAAACGCGCAC 61.384 61.111 5.73 0.00 39.11 5.34
1660 1807 2.023461 CAAACCGAAACGCGCACA 59.977 55.556 5.73 0.00 39.11 4.57
1661 1808 1.583967 CAAACCGAAACGCGCACAA 60.584 52.632 5.73 0.00 39.11 3.33
1662 1809 1.134530 CAAACCGAAACGCGCACAAA 61.135 50.000 5.73 0.00 39.11 2.83
1663 1810 0.863957 AAACCGAAACGCGCACAAAG 60.864 50.000 5.73 0.00 39.11 2.77
1664 1811 2.426752 CCGAAACGCGCACAAAGG 60.427 61.111 5.73 0.22 39.11 3.11
1665 1812 2.629210 CGAAACGCGCACAAAGGA 59.371 55.556 5.73 0.00 0.00 3.36
1666 1813 1.206578 CGAAACGCGCACAAAGGAT 59.793 52.632 5.73 0.00 0.00 3.24
1667 1814 0.440758 CGAAACGCGCACAAAGGATA 59.559 50.000 5.73 0.00 0.00 2.59
1668 1815 1.526986 CGAAACGCGCACAAAGGATAG 60.527 52.381 5.73 0.00 0.00 2.08
1669 1816 1.730064 GAAACGCGCACAAAGGATAGA 59.270 47.619 5.73 0.00 0.00 1.98
1670 1817 2.024176 AACGCGCACAAAGGATAGAT 57.976 45.000 5.73 0.00 0.00 1.98
1671 1818 2.882927 ACGCGCACAAAGGATAGATA 57.117 45.000 5.73 0.00 0.00 1.98
1672 1819 2.470821 ACGCGCACAAAGGATAGATAC 58.529 47.619 5.73 0.00 0.00 2.24
1673 1820 2.100916 ACGCGCACAAAGGATAGATACT 59.899 45.455 5.73 0.00 0.00 2.12
1674 1821 3.317149 ACGCGCACAAAGGATAGATACTA 59.683 43.478 5.73 0.00 0.00 1.82
1675 1822 3.914966 CGCGCACAAAGGATAGATACTAG 59.085 47.826 8.75 0.00 0.00 2.57
1676 1823 4.320275 CGCGCACAAAGGATAGATACTAGA 60.320 45.833 8.75 0.00 0.00 2.43
1677 1824 5.620205 CGCGCACAAAGGATAGATACTAGAT 60.620 44.000 8.75 0.00 0.00 1.98
1678 1825 5.574830 GCGCACAAAGGATAGATACTAGATG 59.425 44.000 0.30 0.00 0.00 2.90
1679 1826 6.096036 CGCACAAAGGATAGATACTAGATGG 58.904 44.000 0.00 0.00 0.00 3.51
1680 1827 6.071896 CGCACAAAGGATAGATACTAGATGGA 60.072 42.308 0.00 0.00 0.00 3.41
1681 1828 7.363355 CGCACAAAGGATAGATACTAGATGGAT 60.363 40.741 0.00 0.00 0.00 3.41
1682 1829 7.978975 GCACAAAGGATAGATACTAGATGGATC 59.021 40.741 0.00 0.00 0.00 3.36
1683 1830 8.187480 CACAAAGGATAGATACTAGATGGATCG 58.813 40.741 0.00 0.00 0.00 3.69
1684 1831 7.891183 ACAAAGGATAGATACTAGATGGATCGT 59.109 37.037 0.00 0.00 0.00 3.73
1685 1832 8.402472 CAAAGGATAGATACTAGATGGATCGTC 58.598 40.741 0.00 0.00 0.00 4.20
1686 1833 6.285224 AGGATAGATACTAGATGGATCGTCG 58.715 44.000 0.00 0.00 0.00 5.12
1687 1834 6.050432 GGATAGATACTAGATGGATCGTCGT 58.950 44.000 0.00 0.00 0.00 4.34
1688 1835 6.018588 GGATAGATACTAGATGGATCGTCGTG 60.019 46.154 0.00 0.00 0.00 4.35
1689 1836 4.643463 AGATACTAGATGGATCGTCGTGT 58.357 43.478 0.00 0.00 0.00 4.49
1690 1837 5.064558 AGATACTAGATGGATCGTCGTGTT 58.935 41.667 0.00 0.00 0.00 3.32
1691 1838 5.531659 AGATACTAGATGGATCGTCGTGTTT 59.468 40.000 0.00 0.00 0.00 2.83
1692 1839 4.451629 ACTAGATGGATCGTCGTGTTTT 57.548 40.909 0.00 0.00 0.00 2.43
1693 1840 4.817517 ACTAGATGGATCGTCGTGTTTTT 58.182 39.130 0.00 0.00 0.00 1.94
1712 1859 2.917701 TTAGCATGATTTGTGCACCG 57.082 45.000 15.69 0.00 44.87 4.94
1713 1860 1.093972 TAGCATGATTTGTGCACCGG 58.906 50.000 15.69 0.00 44.87 5.28
1714 1861 0.895100 AGCATGATTTGTGCACCGGT 60.895 50.000 15.69 0.00 44.87 5.28
1715 1862 0.733566 GCATGATTTGTGCACCGGTG 60.734 55.000 30.66 30.66 42.08 4.94
1716 1863 0.597568 CATGATTTGTGCACCGGTGT 59.402 50.000 33.92 14.84 0.00 4.16
1717 1864 0.597568 ATGATTTGTGCACCGGTGTG 59.402 50.000 33.92 12.35 45.65 3.82
1718 1865 1.285641 GATTTGTGCACCGGTGTGG 59.714 57.895 33.92 11.47 42.99 4.17
1719 1866 2.747507 GATTTGTGCACCGGTGTGGC 62.748 60.000 33.92 21.56 43.94 5.01
1720 1867 4.803908 TTGTGCACCGGTGTGGCA 62.804 61.111 33.92 23.99 43.94 4.92
1917 2064 2.116533 TTGATGGATGGCAGCTGCG 61.117 57.895 31.19 0.00 43.26 5.18
2005 2152 2.870372 GTGAACATGTGGCCGCTC 59.130 61.111 18.96 7.11 0.00 5.03
2092 2239 0.541392 TCATCTGGAACATCCACGGG 59.459 55.000 0.00 0.00 42.67 5.28
2133 2283 5.047847 GCCTCCAAACCAGTTAACTTTTTC 58.952 41.667 5.07 0.00 0.00 2.29
2144 2298 6.198403 CCAGTTAACTTTTTCTTCGAAAAGGC 59.802 38.462 5.07 0.97 46.10 4.35
2145 2299 6.198403 CAGTTAACTTTTTCTTCGAAAAGGCC 59.802 38.462 5.07 0.00 46.10 5.19
2146 2300 6.096423 AGTTAACTTTTTCTTCGAAAAGGCCT 59.904 34.615 0.00 0.00 46.10 5.19
2147 2301 4.569761 ACTTTTTCTTCGAAAAGGCCTC 57.430 40.909 5.23 0.00 46.10 4.70
2149 2303 4.036852 ACTTTTTCTTCGAAAAGGCCTCTG 59.963 41.667 5.23 0.00 46.10 3.35
2150 2304 1.523758 TTCTTCGAAAAGGCCTCTGC 58.476 50.000 5.23 0.00 33.03 4.26
2151 2305 0.396435 TCTTCGAAAAGGCCTCTGCA 59.604 50.000 5.23 0.00 40.13 4.41
2152 2306 1.202758 TCTTCGAAAAGGCCTCTGCAA 60.203 47.619 5.23 0.00 40.13 4.08
2153 2307 1.608590 CTTCGAAAAGGCCTCTGCAAA 59.391 47.619 5.23 0.00 40.13 3.68
2154 2308 0.951558 TCGAAAAGGCCTCTGCAAAC 59.048 50.000 5.23 0.00 40.13 2.93
2155 2309 0.039165 CGAAAAGGCCTCTGCAAACC 60.039 55.000 5.23 0.00 40.13 3.27
2156 2310 1.039856 GAAAAGGCCTCTGCAAACCA 58.960 50.000 5.23 0.00 40.13 3.67
2157 2311 1.000171 GAAAAGGCCTCTGCAAACCAG 60.000 52.381 5.23 0.00 43.17 4.00
2158 2312 0.106015 AAAGGCCTCTGCAAACCAGT 60.106 50.000 5.23 0.00 42.38 4.00
2159 2313 0.106015 AAGGCCTCTGCAAACCAGTT 60.106 50.000 5.23 0.00 42.38 3.16
2160 2314 0.771127 AGGCCTCTGCAAACCAGTTA 59.229 50.000 0.00 0.00 42.38 2.24
2161 2315 1.355720 AGGCCTCTGCAAACCAGTTAT 59.644 47.619 0.00 0.00 42.38 1.89
2162 2316 1.745653 GGCCTCTGCAAACCAGTTATC 59.254 52.381 0.00 0.00 42.38 1.75
2165 2319 3.679389 CCTCTGCAAACCAGTTATCACT 58.321 45.455 0.00 0.00 42.38 3.41
2202 2356 3.166657 GTGCTCTGAATTCGTTTGATGC 58.833 45.455 0.04 0.00 0.00 3.91
2240 2394 0.042581 TGGTGCAGGTGAGGGAGATA 59.957 55.000 0.00 0.00 0.00 1.98
2244 2398 1.109920 GCAGGTGAGGGAGATAGCGA 61.110 60.000 0.00 0.00 0.00 4.93
2472 2628 4.117685 CTCGGTTCGGGAAAAGTTATAGG 58.882 47.826 0.00 0.00 0.00 2.57
2503 2661 2.029020 TCTCTGCAAGTCGTGTTAGCAT 60.029 45.455 0.00 0.00 34.35 3.79
2504 2662 3.192633 TCTCTGCAAGTCGTGTTAGCATA 59.807 43.478 0.00 0.00 34.35 3.14
2505 2663 4.115516 CTCTGCAAGTCGTGTTAGCATAT 58.884 43.478 0.00 0.00 34.35 1.78
2506 2664 5.067283 TCTCTGCAAGTCGTGTTAGCATATA 59.933 40.000 0.00 0.00 34.35 0.86
2507 2665 5.281727 TCTGCAAGTCGTGTTAGCATATAG 58.718 41.667 0.00 0.00 34.35 1.31
2508 2666 4.368315 TGCAAGTCGTGTTAGCATATAGG 58.632 43.478 0.00 0.00 0.00 2.57
2509 2667 4.142026 TGCAAGTCGTGTTAGCATATAGGT 60.142 41.667 0.00 0.00 0.00 3.08
2510 2668 4.444720 GCAAGTCGTGTTAGCATATAGGTC 59.555 45.833 0.00 0.00 0.00 3.85
2511 2669 5.736492 GCAAGTCGTGTTAGCATATAGGTCT 60.736 44.000 0.00 0.00 0.00 3.85
2512 2670 5.440234 AGTCGTGTTAGCATATAGGTCTG 57.560 43.478 0.00 0.00 0.00 3.51
2513 2671 3.982058 GTCGTGTTAGCATATAGGTCTGC 59.018 47.826 0.00 0.00 38.69 4.26
2515 2673 4.341235 TCGTGTTAGCATATAGGTCTGCTT 59.659 41.667 3.99 0.00 46.22 3.91
2516 2674 5.050490 CGTGTTAGCATATAGGTCTGCTTT 58.950 41.667 3.99 0.00 46.22 3.51
2517 2675 6.040054 TCGTGTTAGCATATAGGTCTGCTTTA 59.960 38.462 3.99 0.00 46.22 1.85
2518 2676 6.868864 CGTGTTAGCATATAGGTCTGCTTTAT 59.131 38.462 3.99 0.00 46.22 1.40
2533 2691 7.915923 GGTCTGCTTTATTATAGGTTTGCTTTC 59.084 37.037 0.00 0.00 0.00 2.62
2566 2744 7.745620 ACTCTGAATTTGGTTAAGTAAGTGG 57.254 36.000 0.00 0.00 0.00 4.00
2578 2756 3.697619 AGTAAGTGGTAGGTCTTTGGC 57.302 47.619 0.00 0.00 0.00 4.52
2589 2767 3.751518 AGGTCTTTGGCGTCTGTAAATT 58.248 40.909 0.00 0.00 0.00 1.82
2597 2776 1.673626 GCGTCTGTAAATTGGTCCGGA 60.674 52.381 0.00 0.00 0.00 5.14
2678 2859 5.638596 TTCACTTTACGAGCTAGTGATGA 57.361 39.130 15.26 8.19 45.38 2.92
2727 2908 2.435059 GCAGAGGCGGTGAGGAAC 60.435 66.667 0.00 0.00 0.00 3.62
2798 2979 5.889853 AGAAATTCCCCCTAAAAATACCGTC 59.110 40.000 0.00 0.00 0.00 4.79
2803 2984 4.134563 CCCCCTAAAAATACCGTCATGAG 58.865 47.826 0.00 0.00 0.00 2.90
2804 2985 4.141574 CCCCCTAAAAATACCGTCATGAGA 60.142 45.833 0.00 0.00 0.00 3.27
2805 2986 5.433526 CCCCTAAAAATACCGTCATGAGAA 58.566 41.667 0.00 0.00 0.00 2.87
2806 2987 5.883673 CCCCTAAAAATACCGTCATGAGAAA 59.116 40.000 0.00 0.00 0.00 2.52
2807 2988 6.546034 CCCCTAAAAATACCGTCATGAGAAAT 59.454 38.462 0.00 0.00 0.00 2.17
2808 2989 7.068226 CCCCTAAAAATACCGTCATGAGAAATT 59.932 37.037 0.00 0.00 0.00 1.82
2809 2990 8.466798 CCCTAAAAATACCGTCATGAGAAATTT 58.533 33.333 0.00 0.00 0.00 1.82
2810 2991 9.855021 CCTAAAAATACCGTCATGAGAAATTTT 57.145 29.630 0.00 4.14 0.00 1.82
2813 2994 9.541143 AAAAATACCGTCATGAGAAATTTTGTT 57.459 25.926 14.10 3.24 0.00 2.83
2814 2995 9.541143 AAAATACCGTCATGAGAAATTTTGTTT 57.459 25.926 13.21 0.00 0.00 2.83
2815 2996 8.742554 AATACCGTCATGAGAAATTTTGTTTC 57.257 30.769 0.00 0.00 0.00 2.78
2816 2997 6.142818 ACCGTCATGAGAAATTTTGTTTCA 57.857 33.333 0.00 0.00 0.00 2.69
2817 2998 5.977129 ACCGTCATGAGAAATTTTGTTTCAC 59.023 36.000 0.00 0.00 0.00 3.18
2818 2999 5.976534 CCGTCATGAGAAATTTTGTTTCACA 59.023 36.000 0.00 3.78 34.51 3.58
2819 3000 6.475076 CCGTCATGAGAAATTTTGTTTCACAA 59.525 34.615 0.00 0.00 36.11 3.33
2820 3001 7.169645 CCGTCATGAGAAATTTTGTTTCACAAT 59.830 33.333 0.00 0.00 38.00 2.71
2821 3002 7.999878 CGTCATGAGAAATTTTGTTTCACAATG 59.000 33.333 0.00 4.97 38.00 2.82
2822 3003 8.819974 GTCATGAGAAATTTTGTTTCACAATGT 58.180 29.630 0.00 0.00 38.00 2.71
2823 3004 8.819015 TCATGAGAAATTTTGTTTCACAATGTG 58.181 29.630 7.12 7.12 38.00 3.21
2908 4198 1.999048 CCATGTTGCGGTTCTACGTA 58.001 50.000 0.00 0.00 35.98 3.57
2940 4230 4.439153 CCTCATACGAAACTTACGTAGCCA 60.439 45.833 0.00 0.00 46.48 4.75
2941 4231 4.665212 TCATACGAAACTTACGTAGCCAG 58.335 43.478 0.00 0.00 46.48 4.85
2992 4282 0.324645 CCCACCCTCTGAAATTGGGG 60.325 60.000 8.59 3.81 44.97 4.96
2994 4284 3.213999 ACCCTCTGAAATTGGGGGA 57.786 52.632 6.22 0.00 44.97 4.81
2995 4285 1.002857 ACCCTCTGAAATTGGGGGAG 58.997 55.000 6.22 0.00 44.97 4.30
2996 4286 0.259938 CCCTCTGAAATTGGGGGAGG 59.740 60.000 0.00 0.00 42.10 4.30
2997 4287 0.259938 CCTCTGAAATTGGGGGAGGG 59.740 60.000 0.00 0.00 39.67 4.30
2998 4288 0.259938 CTCTGAAATTGGGGGAGGGG 59.740 60.000 0.00 0.00 0.00 4.79
3001 4291 1.001631 GAAATTGGGGGAGGGGGTG 59.998 63.158 0.00 0.00 0.00 4.61
3002 4292 1.469221 AAATTGGGGGAGGGGGTGA 60.469 57.895 0.00 0.00 0.00 4.02
3004 4294 0.859978 AATTGGGGGAGGGGGTGATT 60.860 55.000 0.00 0.00 0.00 2.57
3005 4295 0.048749 ATTGGGGGAGGGGGTGATTA 59.951 55.000 0.00 0.00 0.00 1.75
3006 4296 0.626277 TTGGGGGAGGGGGTGATTAG 60.626 60.000 0.00 0.00 0.00 1.73
3007 4297 2.461739 GGGGGAGGGGGTGATTAGC 61.462 68.421 0.00 0.00 0.00 3.09
3008 4298 2.461739 GGGGAGGGGGTGATTAGCC 61.462 68.421 0.00 0.00 43.86 3.93
3009 4299 1.386057 GGGAGGGGGTGATTAGCCT 60.386 63.158 5.62 0.00 44.05 4.58
3010 4300 0.994050 GGGAGGGGGTGATTAGCCTT 60.994 60.000 5.62 0.00 44.05 4.35
3017 4307 4.791880 AGGGGGTGATTAGCCTTAGTTTTA 59.208 41.667 5.62 0.00 44.05 1.52
3065 6517 4.034394 CGTAGCACGTTATGTAGGTGTAGA 59.966 45.833 0.00 0.00 43.02 2.59
3076 6528 4.730966 TGTAGGTGTAGAATTTTTGGCCA 58.269 39.130 0.00 0.00 0.00 5.36
3245 6702 5.390613 CACACGAACCTATGGAATTTTGTC 58.609 41.667 0.00 0.00 0.00 3.18
3319 6777 5.122519 ACAAAAGTAAAGGGCACATTTTGG 58.877 37.500 13.92 0.00 40.29 3.28
3335 6793 8.655970 GCACATTTTGGAAATACTTATTTGTCC 58.344 33.333 0.00 0.00 36.13 4.02
3349 6807 1.873698 TTGTCCTTGTTCTGTACGCC 58.126 50.000 0.00 0.00 0.00 5.68
3352 6810 1.666553 CCTTGTTCTGTACGCCGCA 60.667 57.895 0.00 0.00 0.00 5.69
3354 6812 1.635844 CTTGTTCTGTACGCCGCATA 58.364 50.000 0.00 0.00 0.00 3.14
3363 6821 4.977963 TCTGTACGCCGCATATAAAAGTAC 59.022 41.667 0.00 0.00 35.07 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.349817 CGAGATATACAATAAAGCCCTGCAG 59.650 44.000 6.78 6.78 0.00 4.41
47 48 3.588955 TCGTGAGAACAACAGATCATGG 58.411 45.455 0.00 0.00 37.03 3.66
56 57 7.534239 GGTCATTTTTATCTTCGTGAGAACAAC 59.466 37.037 0.00 0.00 46.92 3.32
73 74 0.824182 TTGCGGGTCCGGTCATTTTT 60.824 50.000 11.60 0.00 40.19 1.94
142 223 2.284515 AATTAGGAGGGGCGGGCAAG 62.285 60.000 3.27 0.00 0.00 4.01
143 224 2.279037 GAATTAGGAGGGGCGGGCAA 62.279 60.000 3.27 0.00 0.00 4.52
144 225 2.694616 AATTAGGAGGGGCGGGCA 60.695 61.111 3.27 0.00 0.00 5.36
145 226 2.113351 GAATTAGGAGGGGCGGGC 59.887 66.667 0.00 0.00 0.00 6.13
146 227 0.473117 TAGGAATTAGGAGGGGCGGG 60.473 60.000 0.00 0.00 0.00 6.13
147 228 1.657804 ATAGGAATTAGGAGGGGCGG 58.342 55.000 0.00 0.00 0.00 6.13
148 229 5.012148 CCATATATAGGAATTAGGAGGGGCG 59.988 48.000 0.00 0.00 0.00 6.13
171 252 4.545823 TTGTGATCACTTCGTGAAAACC 57.454 40.909 25.55 0.00 45.96 3.27
191 272 3.063997 CCGCGCTCTTTGAACAATAGATT 59.936 43.478 5.56 0.00 0.00 2.40
230 311 2.747855 GGCTCAGGTCCTTTGGCG 60.748 66.667 0.00 0.00 0.00 5.69
260 341 2.299867 GTTTACGTCCTCCACACCCTTA 59.700 50.000 0.00 0.00 0.00 2.69
261 342 1.071228 GTTTACGTCCTCCACACCCTT 59.929 52.381 0.00 0.00 0.00 3.95
262 343 0.683412 GTTTACGTCCTCCACACCCT 59.317 55.000 0.00 0.00 0.00 4.34
264 345 2.073816 CATGTTTACGTCCTCCACACC 58.926 52.381 0.00 0.00 0.00 4.16
266 347 1.609580 GCCATGTTTACGTCCTCCACA 60.610 52.381 0.00 0.00 0.00 4.17
287 383 1.280457 CTCCACACCCTTAAGGCTCT 58.720 55.000 16.70 0.00 40.58 4.09
375 474 3.535860 CGGTAATCGTAGCACGTACTAC 58.464 50.000 14.84 14.84 43.14 2.73
376 475 2.032894 GCGGTAATCGTAGCACGTACTA 60.033 50.000 8.22 0.00 43.14 1.82
377 476 1.268234 GCGGTAATCGTAGCACGTACT 60.268 52.381 8.22 0.00 43.14 2.73
505 618 1.878953 GCTAGCTAGCTCGAGTCTCT 58.121 55.000 33.71 5.26 45.62 3.10
564 679 2.751806 GGTGCTGGAATCTTTCTTCTGG 59.248 50.000 0.00 0.00 0.00 3.86
566 681 2.303022 TCGGTGCTGGAATCTTTCTTCT 59.697 45.455 0.00 0.00 0.00 2.85
746 869 1.521681 CGGAAGGTGAGGCGATTCC 60.522 63.158 0.00 0.00 38.26 3.01
913 1056 6.826741 GCAAATAAATAGGGGGCGAATAGATA 59.173 38.462 0.00 0.00 0.00 1.98
914 1057 5.652452 GCAAATAAATAGGGGGCGAATAGAT 59.348 40.000 0.00 0.00 0.00 1.98
915 1058 5.007682 GCAAATAAATAGGGGGCGAATAGA 58.992 41.667 0.00 0.00 0.00 1.98
916 1059 4.142687 CGCAAATAAATAGGGGGCGAATAG 60.143 45.833 0.00 0.00 45.19 1.73
979 1122 2.345760 CCTCCTGCAATGGGTGTGC 61.346 63.158 0.00 0.00 42.55 4.57
997 1140 1.655329 CGCGAGTACTCCCCATCTC 59.345 63.158 17.23 0.00 0.00 2.75
1084 1227 5.176592 AGGAAGAAGAATTAACGTACTGCC 58.823 41.667 0.00 0.00 0.00 4.85
1290 1435 1.005867 TAAACCACGTCGCTGGTCC 60.006 57.895 16.42 0.00 44.32 4.46
1351 1496 3.259876 TGTTGTCTACGAGGGTAGCATTT 59.740 43.478 0.00 0.00 44.74 2.32
1401 1546 1.208358 GGTAAGCGGCGTTTGGTTC 59.792 57.895 19.40 6.73 0.00 3.62
1464 1611 8.893884 CAACGAGATAAATCTGAATACGTAGAC 58.106 37.037 0.08 0.00 37.25 2.59
1465 1612 8.074370 CCAACGAGATAAATCTGAATACGTAGA 58.926 37.037 0.08 0.00 37.25 2.59
1466 1613 7.861372 ACCAACGAGATAAATCTGAATACGTAG 59.139 37.037 0.08 0.00 37.25 3.51
1467 1614 7.709947 ACCAACGAGATAAATCTGAATACGTA 58.290 34.615 0.00 0.00 37.25 3.57
1468 1615 6.570692 ACCAACGAGATAAATCTGAATACGT 58.429 36.000 0.00 0.00 37.25 3.57
1469 1616 7.464830 AACCAACGAGATAAATCTGAATACG 57.535 36.000 0.00 0.00 37.25 3.06
1470 1617 8.879759 TGAAACCAACGAGATAAATCTGAATAC 58.120 33.333 0.00 0.00 37.25 1.89
1471 1618 8.879759 GTGAAACCAACGAGATAAATCTGAATA 58.120 33.333 0.00 0.00 37.25 1.75
1472 1619 7.752695 GTGAAACCAACGAGATAAATCTGAAT 58.247 34.615 0.00 0.00 37.25 2.57
1473 1620 7.129109 GTGAAACCAACGAGATAAATCTGAA 57.871 36.000 0.00 0.00 37.25 3.02
1474 1621 6.721571 GTGAAACCAACGAGATAAATCTGA 57.278 37.500 0.00 0.00 37.25 3.27
1491 1638 3.621715 ACAGAAGAAGAACACGGTGAAAC 59.378 43.478 16.29 5.59 0.00 2.78
1492 1639 3.621268 CACAGAAGAAGAACACGGTGAAA 59.379 43.478 16.29 0.00 32.17 2.69
1498 1645 3.120286 CGATCACACAGAAGAAGAACACG 59.880 47.826 0.00 0.00 0.00 4.49
1507 1654 2.188524 CATCGACCGATCACACAGAAG 58.811 52.381 1.46 0.00 31.62 2.85
1560 1707 1.141881 CTTCACCCCGTCGATCTGG 59.858 63.158 0.00 0.00 0.00 3.86
1614 1761 2.690778 GCCGTTGATGGTGTGCTCC 61.691 63.158 0.00 0.00 0.00 4.70
1641 1788 3.877357 TGCGCGTTTCGGTTTGCA 61.877 55.556 8.43 0.00 38.94 4.08
1642 1789 3.383601 GTGCGCGTTTCGGTTTGC 61.384 61.111 8.43 0.00 38.94 3.68
1643 1790 1.134530 TTTGTGCGCGTTTCGGTTTG 61.135 50.000 8.43 0.00 38.94 2.93
1644 1791 0.863957 CTTTGTGCGCGTTTCGGTTT 60.864 50.000 8.43 0.00 38.94 3.27
1645 1792 1.298041 CTTTGTGCGCGTTTCGGTT 60.298 52.632 8.43 0.00 38.94 4.44
1646 1793 2.326550 CTTTGTGCGCGTTTCGGT 59.673 55.556 8.43 0.00 38.94 4.69
1647 1794 2.182614 ATCCTTTGTGCGCGTTTCGG 62.183 55.000 8.43 0.03 38.94 4.30
1648 1795 0.440758 TATCCTTTGTGCGCGTTTCG 59.559 50.000 8.43 0.00 42.12 3.46
1649 1796 1.730064 TCTATCCTTTGTGCGCGTTTC 59.270 47.619 8.43 0.00 0.00 2.78
1650 1797 1.803334 TCTATCCTTTGTGCGCGTTT 58.197 45.000 8.43 0.00 0.00 3.60
1651 1798 2.024176 ATCTATCCTTTGTGCGCGTT 57.976 45.000 8.43 0.00 0.00 4.84
1652 1799 2.100916 AGTATCTATCCTTTGTGCGCGT 59.899 45.455 8.43 0.00 0.00 6.01
1653 1800 2.743938 AGTATCTATCCTTTGTGCGCG 58.256 47.619 0.00 0.00 0.00 6.86
1654 1801 5.122512 TCTAGTATCTATCCTTTGTGCGC 57.877 43.478 0.00 0.00 0.00 6.09
1655 1802 6.071896 TCCATCTAGTATCTATCCTTTGTGCG 60.072 42.308 0.00 0.00 0.00 5.34
1656 1803 7.233389 TCCATCTAGTATCTATCCTTTGTGC 57.767 40.000 0.00 0.00 0.00 4.57
1657 1804 8.187480 CGATCCATCTAGTATCTATCCTTTGTG 58.813 40.741 0.00 0.00 0.00 3.33
1658 1805 7.891183 ACGATCCATCTAGTATCTATCCTTTGT 59.109 37.037 0.00 0.00 0.00 2.83
1659 1806 8.287439 ACGATCCATCTAGTATCTATCCTTTG 57.713 38.462 0.00 0.00 0.00 2.77
1660 1807 7.281324 CGACGATCCATCTAGTATCTATCCTTT 59.719 40.741 0.00 0.00 0.00 3.11
1661 1808 6.764085 CGACGATCCATCTAGTATCTATCCTT 59.236 42.308 0.00 0.00 0.00 3.36
1662 1809 6.126997 ACGACGATCCATCTAGTATCTATCCT 60.127 42.308 0.00 0.00 0.00 3.24
1663 1810 6.018588 CACGACGATCCATCTAGTATCTATCC 60.019 46.154 0.00 0.00 0.00 2.59
1664 1811 6.535865 ACACGACGATCCATCTAGTATCTATC 59.464 42.308 0.00 0.00 0.00 2.08
1665 1812 6.408035 ACACGACGATCCATCTAGTATCTAT 58.592 40.000 0.00 0.00 0.00 1.98
1666 1813 5.791666 ACACGACGATCCATCTAGTATCTA 58.208 41.667 0.00 0.00 0.00 1.98
1667 1814 4.643463 ACACGACGATCCATCTAGTATCT 58.357 43.478 0.00 0.00 0.00 1.98
1668 1815 5.359716 AACACGACGATCCATCTAGTATC 57.640 43.478 0.00 0.00 0.00 2.24
1669 1816 5.769484 AAACACGACGATCCATCTAGTAT 57.231 39.130 0.00 0.00 0.00 2.12
1670 1817 5.571784 AAAACACGACGATCCATCTAGTA 57.428 39.130 0.00 0.00 0.00 1.82
1671 1818 4.451629 AAAACACGACGATCCATCTAGT 57.548 40.909 0.00 0.00 0.00 2.57
1690 1837 3.986572 CGGTGCACAAATCATGCTAAAAA 59.013 39.130 20.43 0.00 43.77 1.94
1691 1838 3.573598 CGGTGCACAAATCATGCTAAAA 58.426 40.909 20.43 0.00 43.77 1.52
1692 1839 2.094803 CCGGTGCACAAATCATGCTAAA 60.095 45.455 20.43 0.00 43.77 1.85
1693 1840 1.472082 CCGGTGCACAAATCATGCTAA 59.528 47.619 20.43 0.00 43.77 3.09
1694 1841 1.093972 CCGGTGCACAAATCATGCTA 58.906 50.000 20.43 0.00 43.77 3.49
1695 1842 0.895100 ACCGGTGCACAAATCATGCT 60.895 50.000 20.43 0.00 43.77 3.79
1696 1843 0.733566 CACCGGTGCACAAATCATGC 60.734 55.000 24.02 0.00 43.68 4.06
1697 1844 0.597568 ACACCGGTGCACAAATCATG 59.402 50.000 34.26 6.62 0.00 3.07
1698 1845 0.597568 CACACCGGTGCACAAATCAT 59.402 50.000 34.26 8.75 38.37 2.45
1699 1846 1.451337 CCACACCGGTGCACAAATCA 61.451 55.000 34.26 0.00 43.88 2.57
1700 1847 1.285641 CCACACCGGTGCACAAATC 59.714 57.895 34.26 0.00 43.88 2.17
1701 1848 2.855514 GCCACACCGGTGCACAAAT 61.856 57.895 34.26 11.24 43.88 2.32
1702 1849 3.522731 GCCACACCGGTGCACAAA 61.523 61.111 34.26 0.00 43.88 2.83
1703 1850 4.803908 TGCCACACCGGTGCACAA 62.804 61.111 34.26 15.26 43.88 3.33
1708 1855 2.518349 AAACCTGCCACACCGGTG 60.518 61.111 32.83 32.83 44.85 4.94
1709 1856 2.518349 CAAACCTGCCACACCGGT 60.518 61.111 0.00 0.00 36.97 5.28
1710 1857 3.977244 GCAAACCTGCCACACCGG 61.977 66.667 0.00 0.00 43.26 5.28
1719 1866 2.594303 TGCTCCACGGCAAACCTG 60.594 61.111 0.00 0.00 39.43 4.00
1720 1867 2.281761 CTGCTCCACGGCAAACCT 60.282 61.111 0.00 0.00 41.94 3.50
1728 1875 1.915614 GAACCATGTGCTGCTCCACG 61.916 60.000 0.00 0.00 38.55 4.94
1845 1992 4.096382 CCGCAGTCAAGGCATATAAACTTT 59.904 41.667 0.00 0.00 0.00 2.66
1846 1993 3.627577 CCGCAGTCAAGGCATATAAACTT 59.372 43.478 0.00 0.00 0.00 2.66
1990 2137 3.499737 CGGAGCGGCCACATGTTC 61.500 66.667 2.24 0.00 35.94 3.18
2133 2283 1.238439 TTGCAGAGGCCTTTTCGAAG 58.762 50.000 6.77 0.00 40.13 3.79
2144 2298 3.438087 CAGTGATAACTGGTTTGCAGAGG 59.562 47.826 1.71 0.00 34.28 3.69
2145 2299 3.120060 GCAGTGATAACTGGTTTGCAGAG 60.120 47.826 12.38 0.00 38.14 3.35
2146 2300 2.813754 GCAGTGATAACTGGTTTGCAGA 59.186 45.455 12.38 0.00 38.14 4.26
2147 2301 2.816087 AGCAGTGATAACTGGTTTGCAG 59.184 45.455 9.24 0.00 44.92 4.41
2149 2303 2.813754 TGAGCAGTGATAACTGGTTTGC 59.186 45.455 16.12 4.67 46.85 3.68
2150 2304 5.633830 ATTGAGCAGTGATAACTGGTTTG 57.366 39.130 16.12 0.00 46.85 2.93
2151 2305 4.393062 CGATTGAGCAGTGATAACTGGTTT 59.607 41.667 16.12 4.96 46.85 3.27
2152 2306 3.935203 CGATTGAGCAGTGATAACTGGTT 59.065 43.478 16.12 0.44 46.85 3.67
2154 2308 2.286294 GCGATTGAGCAGTGATAACTGG 59.714 50.000 12.38 0.00 38.14 4.00
2155 2309 2.931969 TGCGATTGAGCAGTGATAACTG 59.068 45.455 5.76 5.76 42.92 3.16
2156 2310 3.251479 TGCGATTGAGCAGTGATAACT 57.749 42.857 0.00 0.00 42.92 2.24
2165 2319 1.871077 CACAAGCTGCGATTGAGCA 59.129 52.632 12.24 0.00 45.96 4.26
2202 2356 2.508526 CAGGTTTCTCCCAGGTTCAAG 58.491 52.381 0.00 0.00 36.75 3.02
2404 2559 5.241728 AGCATCATCATCATCTCCAAACATG 59.758 40.000 0.00 0.00 0.00 3.21
2472 2628 3.544285 CGACTTGCAGAGATAAACGACTC 59.456 47.826 0.00 0.00 0.00 3.36
2503 2661 9.720769 GCAAACCTATAATAAAGCAGACCTATA 57.279 33.333 0.00 0.00 0.00 1.31
2504 2662 8.440771 AGCAAACCTATAATAAAGCAGACCTAT 58.559 33.333 0.00 0.00 0.00 2.57
2505 2663 7.802117 AGCAAACCTATAATAAAGCAGACCTA 58.198 34.615 0.00 0.00 0.00 3.08
2506 2664 6.663734 AGCAAACCTATAATAAAGCAGACCT 58.336 36.000 0.00 0.00 0.00 3.85
2507 2665 6.944234 AGCAAACCTATAATAAAGCAGACC 57.056 37.500 0.00 0.00 0.00 3.85
2508 2666 8.678199 AGAAAGCAAACCTATAATAAAGCAGAC 58.322 33.333 0.00 0.00 0.00 3.51
2509 2667 8.807948 AGAAAGCAAACCTATAATAAAGCAGA 57.192 30.769 0.00 0.00 0.00 4.26
2510 2668 7.852945 CGAGAAAGCAAACCTATAATAAAGCAG 59.147 37.037 0.00 0.00 0.00 4.24
2511 2669 7.201696 CCGAGAAAGCAAACCTATAATAAAGCA 60.202 37.037 0.00 0.00 0.00 3.91
2512 2670 7.132863 CCGAGAAAGCAAACCTATAATAAAGC 58.867 38.462 0.00 0.00 0.00 3.51
2513 2671 8.209917 ACCGAGAAAGCAAACCTATAATAAAG 57.790 34.615 0.00 0.00 0.00 1.85
2514 2672 8.044908 AGACCGAGAAAGCAAACCTATAATAAA 58.955 33.333 0.00 0.00 0.00 1.40
2515 2673 7.562135 AGACCGAGAAAGCAAACCTATAATAA 58.438 34.615 0.00 0.00 0.00 1.40
2516 2674 7.120923 AGACCGAGAAAGCAAACCTATAATA 57.879 36.000 0.00 0.00 0.00 0.98
2517 2675 5.990668 AGACCGAGAAAGCAAACCTATAAT 58.009 37.500 0.00 0.00 0.00 1.28
2518 2676 5.416271 AGACCGAGAAAGCAAACCTATAA 57.584 39.130 0.00 0.00 0.00 0.98
2533 2691 4.822026 ACCAAATTCAGAGTAAGACCGAG 58.178 43.478 0.00 0.00 0.00 4.63
2566 2744 3.308438 TTACAGACGCCAAAGACCTAC 57.692 47.619 0.00 0.00 0.00 3.18
2578 2756 2.373540 TCCGGACCAATTTACAGACG 57.626 50.000 0.00 0.00 0.00 4.18
2589 2767 1.131303 ACATCAACCCTTCCGGACCA 61.131 55.000 1.83 0.00 34.64 4.02
2597 2776 2.774234 AGGATCGATCACATCAACCCTT 59.226 45.455 25.93 0.00 0.00 3.95
2678 2859 3.610114 GCAAGACGCACAGTTTTCATGAT 60.610 43.478 0.00 0.00 41.79 2.45
2722 2903 1.760613 TCAACGTCAGTTCCTGTTCCT 59.239 47.619 0.00 0.00 38.79 3.36
2723 2904 2.234300 TCAACGTCAGTTCCTGTTCC 57.766 50.000 0.00 0.00 38.79 3.62
2724 2905 3.869246 TCTTTCAACGTCAGTTCCTGTTC 59.131 43.478 0.00 0.00 38.79 3.18
2725 2906 3.869065 TCTTTCAACGTCAGTTCCTGTT 58.131 40.909 0.00 0.00 38.79 3.16
2726 2907 3.458189 CTCTTTCAACGTCAGTTCCTGT 58.542 45.455 0.00 0.00 38.79 4.00
2727 2908 2.221981 GCTCTTTCAACGTCAGTTCCTG 59.778 50.000 0.00 0.00 38.79 3.86
2811 2992 6.272698 GTTTCATCCAACACATTGTGAAAC 57.727 37.500 23.12 15.62 45.10 2.78
2812 2993 5.355596 GGTTTCATCCAACACATTGTGAAA 58.644 37.500 23.12 8.38 37.96 2.69
2813 2994 4.202202 GGGTTTCATCCAACACATTGTGAA 60.202 41.667 23.12 2.45 36.96 3.18
2814 2995 3.320541 GGGTTTCATCCAACACATTGTGA 59.679 43.478 23.12 0.93 36.96 3.58
2815 2996 3.321682 AGGGTTTCATCCAACACATTGTG 59.678 43.478 15.18 15.18 39.75 3.33
2816 2997 3.575805 AGGGTTTCATCCAACACATTGT 58.424 40.909 0.00 0.00 31.87 2.71
2817 2998 4.039004 TCAAGGGTTTCATCCAACACATTG 59.961 41.667 0.00 0.00 31.87 2.82
2818 2999 4.039124 GTCAAGGGTTTCATCCAACACATT 59.961 41.667 0.00 0.00 31.87 2.71
2819 3000 3.573967 GTCAAGGGTTTCATCCAACACAT 59.426 43.478 0.00 0.00 31.87 3.21
2820 3001 2.955660 GTCAAGGGTTTCATCCAACACA 59.044 45.455 0.00 0.00 31.87 3.72
2821 3002 2.031157 CGTCAAGGGTTTCATCCAACAC 60.031 50.000 0.00 0.00 0.00 3.32
2822 3003 2.158740 TCGTCAAGGGTTTCATCCAACA 60.159 45.455 0.00 0.00 0.00 3.33
2823 3004 2.500229 TCGTCAAGGGTTTCATCCAAC 58.500 47.619 0.00 0.00 0.00 3.77
2924 4214 4.201685 CCAAATCTGGCTACGTAAGTTTCG 60.202 45.833 0.00 0.00 42.45 3.46
2973 4263 3.288099 CCCAATTTCAGAGGGTGGG 57.712 57.895 0.00 0.00 42.94 4.61
2992 4282 1.700186 CTAAGGCTAATCACCCCCTCC 59.300 57.143 0.00 0.00 0.00 4.30
2994 4284 2.588925 ACTAAGGCTAATCACCCCCT 57.411 50.000 0.00 0.00 0.00 4.79
2995 4285 3.664551 AAACTAAGGCTAATCACCCCC 57.335 47.619 0.00 0.00 0.00 5.40
2996 4286 5.593095 CCTTAAAACTAAGGCTAATCACCCC 59.407 44.000 0.00 0.00 40.00 4.95
2997 4287 6.318144 GTCCTTAAAACTAAGGCTAATCACCC 59.682 42.308 6.12 0.00 44.77 4.61
2998 4288 6.036844 CGTCCTTAAAACTAAGGCTAATCACC 59.963 42.308 6.12 0.00 44.77 4.02
3001 4291 6.343703 TCCGTCCTTAAAACTAAGGCTAATC 58.656 40.000 6.12 0.00 44.77 1.75
3002 4292 6.303903 TCCGTCCTTAAAACTAAGGCTAAT 57.696 37.500 6.12 0.00 44.77 1.73
3004 4294 5.743636 TTCCGTCCTTAAAACTAAGGCTA 57.256 39.130 6.12 0.00 44.77 3.93
3005 4295 4.628963 TTCCGTCCTTAAAACTAAGGCT 57.371 40.909 6.12 0.00 44.77 4.58
3006 4296 4.155462 CCTTTCCGTCCTTAAAACTAAGGC 59.845 45.833 6.12 1.99 44.77 4.35
3007 4297 5.554070 TCCTTTCCGTCCTTAAAACTAAGG 58.446 41.667 4.79 4.79 46.12 2.69
3008 4298 6.484308 TGTTCCTTTCCGTCCTTAAAACTAAG 59.516 38.462 0.00 0.00 0.00 2.18
3009 4299 6.355747 TGTTCCTTTCCGTCCTTAAAACTAA 58.644 36.000 0.00 0.00 0.00 2.24
3010 4300 5.927819 TGTTCCTTTCCGTCCTTAAAACTA 58.072 37.500 0.00 0.00 0.00 2.24
3017 4307 2.640826 TGGTATGTTCCTTTCCGTCCTT 59.359 45.455 0.00 0.00 0.00 3.36
3022 4312 4.186159 ACGTAATGGTATGTTCCTTTCCG 58.814 43.478 0.00 0.00 33.00 4.30
3029 4319 4.687458 CGTGCTACGTAATGGTATGTTC 57.313 45.455 0.00 0.00 36.74 3.18
3060 6512 4.261405 CGTCTTGTGGCCAAAAATTCTACA 60.261 41.667 7.24 0.00 0.00 2.74
3065 6517 3.652274 CATCGTCTTGTGGCCAAAAATT 58.348 40.909 7.24 0.00 0.00 1.82
3335 6793 1.635844 TATGCGGCGTACAGAACAAG 58.364 50.000 9.37 0.00 0.00 3.16
3349 6807 8.888332 TTCACAACATTGTACTTTTATATGCG 57.112 30.769 0.00 0.00 39.91 4.73


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

AutoCloner maintained by Alex Coulton.