Multiple sequence alignment - TraesCS7D01G062800

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 TraesCS7D01G062800 chr7D 100.000 2606 0 0 1 2606 34302911 34300306 0.000000e+00 4813
1 TraesCS7D01G062800 chr7D 94.737 152 8 0 1930 2081 53450746 53450595 1.210000e-58 237
2 TraesCS7D01G062800 chr7D 84.466 103 15 1 2504 2606 98040574 98040473 1.650000e-17 100
3 TraesCS7D01G062800 chr4A 88.846 1811 100 41 1 1759 691124306 691126066 0.000000e+00 2132
4 TraesCS7D01G062800 chr4A 87.712 236 29 0 2116 2351 691126228 691126463 2.550000e-70 276
5 TraesCS7D01G062800 chr4A 85.616 146 21 0 2461 2606 691126519 691126664 1.250000e-33 154
6 TraesCS7D01G062800 chr4A 86.538 104 13 1 2503 2606 123878072 123877970 2.120000e-21 113
7 TraesCS7D01G062800 chr7A 93.764 866 30 10 1 862 34708058 34707213 0.000000e+00 1279
8 TraesCS7D01G062800 chr7A 86.434 1091 90 32 860 1923 34707164 34706105 0.000000e+00 1142
9 TraesCS7D01G062800 chr7A 86.486 185 23 2 2161 2345 34706093 34705911 4.400000e-48 202
10 TraesCS7D01G062800 chr7A 72.080 548 108 26 2100 2606 657714018 657714561 3.520000e-24 122
11 TraesCS7D01G062800 chr7A 85.047 107 14 2 2501 2606 231046484 231046379 9.860000e-20 108
12 TraesCS7D01G062800 chr7A 78.107 169 32 4 2442 2606 37840084 37839917 4.590000e-18 102
13 TraesCS7D01G062800 chr5D 94.839 155 7 1 1930 2084 380078925 380078772 9.320000e-60 241
14 TraesCS7D01G062800 chr3D 94.118 153 9 0 1929 2081 488863427 488863579 1.560000e-57 233
15 TraesCS7D01G062800 chr4D 93.548 155 9 1 1929 2082 447293659 447293813 2.020000e-56 230
16 TraesCS7D01G062800 chr4D 90.964 166 11 3 1917 2081 81139422 81139584 1.210000e-53 220
17 TraesCS7D01G062800 chr4D 88.571 105 12 0 2502 2606 297843029 297843133 7.570000e-26 128
18 TraesCS7D01G062800 chr4D 93.827 81 5 0 2526 2606 355791543 355791463 3.520000e-24 122
19 TraesCS7D01G062800 chr4D 89.247 93 9 1 2514 2606 342551330 342551421 5.890000e-22 115
20 TraesCS7D01G062800 chr6B 91.176 170 12 3 1913 2081 451870794 451870627 7.260000e-56 228
21 TraesCS7D01G062800 chr5B 92.949 156 9 2 1928 2082 478502444 478502598 2.610000e-55 226
22 TraesCS7D01G062800 chr5A 92.357 157 12 0 1926 2082 26117336 26117492 9.390000e-55 224
23 TraesCS7D01G062800 chr2B 92.405 158 11 1 1930 2086 678966513 678966356 9.390000e-55 224


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 TraesCS7D01G062800 chr7D 34300306 34302911 2605 True 4813.000000 4813 100.000000 1 2606 1 chr7D.!!$R1 2605
1 TraesCS7D01G062800 chr4A 691124306 691126664 2358 False 854.000000 2132 87.391333 1 2606 3 chr4A.!!$F1 2605
2 TraesCS7D01G062800 chr7A 34705911 34708058 2147 True 874.333333 1279 88.894667 1 2345 3 chr7A.!!$R3 2344

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
927 998 1.46695 CAGAGTCAGTGAGGAGACGTC 59.533 57.143 7.7 7.7 39.67 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2124 2250 0.034476 GTAGGGCGGCTGGTATTACC 59.966 60.0 9.56 5.87 39.22 2.85 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
88 89 2.821366 GTGCAGCTGGACATCCGG 60.821 66.667 30.84 0.00 45.30 5.14
562 569 4.208686 CGCGCCTACCTCCACTCC 62.209 72.222 0.00 0.00 0.00 3.85
708 718 3.937814 AGCAAATGTGTTCATAGACCGA 58.062 40.909 0.00 0.00 33.49 4.69
709 719 3.684788 AGCAAATGTGTTCATAGACCGAC 59.315 43.478 0.00 0.00 33.49 4.79
710 720 3.684788 GCAAATGTGTTCATAGACCGACT 59.315 43.478 0.00 0.00 33.49 4.18
711 721 4.436050 GCAAATGTGTTCATAGACCGACTG 60.436 45.833 0.00 0.00 33.49 3.51
713 723 3.297830 TGTGTTCATAGACCGACTGTG 57.702 47.619 0.00 0.00 38.75 3.66
716 726 2.631062 TGTTCATAGACCGACTGTGGTT 59.369 45.455 3.93 0.00 44.01 3.67
717 727 2.993899 GTTCATAGACCGACTGTGGTTG 59.006 50.000 3.93 0.37 44.01 3.77
718 728 2.244695 TCATAGACCGACTGTGGTTGT 58.755 47.619 3.93 0.00 44.01 3.32
719 729 3.423749 TCATAGACCGACTGTGGTTGTA 58.576 45.455 3.93 1.25 44.01 2.41
725 735 1.732259 CCGACTGTGGTTGTATCTTGC 59.268 52.381 0.00 0.00 0.00 4.01
742 752 4.921547 TCTTGCAGAGTGTAGCTAATACG 58.078 43.478 0.00 0.00 37.17 3.06
743 753 4.398358 TCTTGCAGAGTGTAGCTAATACGT 59.602 41.667 0.00 0.00 37.17 3.57
744 754 5.587443 TCTTGCAGAGTGTAGCTAATACGTA 59.413 40.000 0.00 0.00 37.17 3.57
745 755 5.165911 TGCAGAGTGTAGCTAATACGTAC 57.834 43.478 0.00 0.00 37.17 3.67
746 756 4.209870 GCAGAGTGTAGCTAATACGTACG 58.790 47.826 15.01 15.01 37.17 3.67
754 764 7.006537 GTGTAGCTAATACGTACGTGTATCTC 58.993 42.308 30.25 14.28 37.17 2.75
758 768 8.545229 AGCTAATACGTACGTGTATCTCTAAT 57.455 34.615 30.25 9.84 34.01 1.73
759 769 8.655092 AGCTAATACGTACGTGTATCTCTAATC 58.345 37.037 30.25 7.63 34.01 1.75
760 770 8.655092 GCTAATACGTACGTGTATCTCTAATCT 58.345 37.037 30.25 7.47 34.01 2.40
762 772 8.830201 AATACGTACGTGTATCTCTAATCTCT 57.170 34.615 30.25 1.19 34.01 3.10
763 773 6.768029 ACGTACGTGTATCTCTAATCTCTC 57.232 41.667 22.14 0.00 0.00 3.20
764 774 5.401972 ACGTACGTGTATCTCTAATCTCTCG 59.598 44.000 22.14 0.00 0.00 4.04
765 775 5.164070 CGTACGTGTATCTCTAATCTCTCGG 60.164 48.000 7.22 0.00 0.00 4.63
766 776 4.706035 ACGTGTATCTCTAATCTCTCGGT 58.294 43.478 0.00 0.00 0.00 4.69
767 777 4.512198 ACGTGTATCTCTAATCTCTCGGTG 59.488 45.833 0.00 0.00 0.00 4.94
768 778 4.083749 CGTGTATCTCTAATCTCTCGGTGG 60.084 50.000 0.00 0.00 0.00 4.61
769 779 4.822896 GTGTATCTCTAATCTCTCGGTGGT 59.177 45.833 0.00 0.00 0.00 4.16
770 780 5.996513 GTGTATCTCTAATCTCTCGGTGGTA 59.003 44.000 0.00 0.00 0.00 3.25
771 781 6.655848 GTGTATCTCTAATCTCTCGGTGGTAT 59.344 42.308 0.00 0.00 0.00 2.73
857 870 1.806542 TGCGCCATGAGTTTCTTCTTC 59.193 47.619 4.18 0.00 0.00 2.87
924 995 2.747446 GACTCAGAGTCAGTGAGGAGAC 59.253 54.545 23.62 7.50 44.96 3.36
927 998 1.466950 CAGAGTCAGTGAGGAGACGTC 59.533 57.143 7.70 7.70 39.67 4.34
1200 1280 4.986645 TCGTGGGACGACGACGGA 62.987 66.667 12.58 0.00 46.73 4.69
1201 1281 4.029186 CGTGGGACGACGACGGAA 62.029 66.667 12.58 0.00 46.05 4.30
1295 1375 1.152839 CGGAGGAGGAGGAGGAGTC 60.153 68.421 0.00 0.00 0.00 3.36
1296 1376 1.152839 GGAGGAGGAGGAGGAGTCG 60.153 68.421 0.00 0.00 0.00 4.18
1297 1377 1.826487 GAGGAGGAGGAGGAGTCGC 60.826 68.421 0.00 0.00 0.00 5.19
1298 1378 2.835895 GGAGGAGGAGGAGTCGCC 60.836 72.222 0.00 0.00 0.00 5.54
1299 1379 3.213402 GAGGAGGAGGAGTCGCCG 61.213 72.222 0.00 0.00 43.43 6.46
1421 1501 0.321653 GCGAAGGAGGCCAAGAAGAA 60.322 55.000 5.01 0.00 0.00 2.52
1428 1508 2.083002 GAGGCCAAGAAGAAGAGCAAG 58.917 52.381 5.01 0.00 0.00 4.01
1434 1514 0.972883 AGAAGAAGAGCAAGCGGAGT 59.027 50.000 0.00 0.00 0.00 3.85
1596 1676 1.601759 GCAGCAGCTCCTCCACAAA 60.602 57.895 0.00 0.00 37.91 2.83
1618 1720 5.763876 ACACCAGTAGGATTAAAGAGCTT 57.236 39.130 0.00 0.00 38.69 3.74
1624 1726 6.127897 CCAGTAGGATTAAAGAGCTTTGTTGG 60.128 42.308 5.76 0.00 36.89 3.77
1628 1730 8.957466 GTAGGATTAAAGAGCTTTGTTGGTTAT 58.043 33.333 5.76 0.00 34.23 1.89
1629 1731 8.056407 AGGATTAAAGAGCTTTGTTGGTTATC 57.944 34.615 5.76 0.00 34.23 1.75
1631 1733 8.470002 GGATTAAAGAGCTTTGTTGGTTATCAT 58.530 33.333 5.76 0.00 34.23 2.45
1632 1734 9.294030 GATTAAAGAGCTTTGTTGGTTATCATG 57.706 33.333 5.76 0.00 34.23 3.07
1634 1736 3.445096 AGAGCTTTGTTGGTTATCATGGC 59.555 43.478 0.00 0.00 0.00 4.40
1635 1737 3.434309 AGCTTTGTTGGTTATCATGGCT 58.566 40.909 0.00 0.00 0.00 4.75
1637 1739 3.731867 GCTTTGTTGGTTATCATGGCTCG 60.732 47.826 0.00 0.00 0.00 5.03
1638 1740 2.779755 TGTTGGTTATCATGGCTCGT 57.220 45.000 0.00 0.00 0.00 4.18
1639 1741 3.897141 TGTTGGTTATCATGGCTCGTA 57.103 42.857 0.00 0.00 0.00 3.43
1640 1742 3.792401 TGTTGGTTATCATGGCTCGTAG 58.208 45.455 0.00 0.00 0.00 3.51
1641 1743 3.196901 TGTTGGTTATCATGGCTCGTAGT 59.803 43.478 0.00 0.00 0.00 2.73
1642 1744 4.189231 GTTGGTTATCATGGCTCGTAGTT 58.811 43.478 0.00 0.00 0.00 2.24
1643 1745 4.481368 TGGTTATCATGGCTCGTAGTTT 57.519 40.909 0.00 0.00 0.00 2.66
1644 1746 4.188462 TGGTTATCATGGCTCGTAGTTTG 58.812 43.478 0.00 0.00 0.00 2.93
1645 1747 4.189231 GGTTATCATGGCTCGTAGTTTGT 58.811 43.478 0.00 0.00 0.00 2.83
1646 1748 4.270325 GGTTATCATGGCTCGTAGTTTGTC 59.730 45.833 0.00 0.00 0.00 3.18
1647 1749 1.990799 TCATGGCTCGTAGTTTGTCG 58.009 50.000 0.00 0.00 0.00 4.35
1648 1750 1.542472 TCATGGCTCGTAGTTTGTCGA 59.458 47.619 0.00 0.00 34.88 4.20
1652 1754 3.670500 CTCGTAGTTTGTCGAGCGA 57.330 52.632 1.88 0.00 44.82 4.93
1653 1755 1.248721 CTCGTAGTTTGTCGAGCGAC 58.751 55.000 15.49 15.49 44.82 5.19
1654 1756 0.870393 TCGTAGTTTGTCGAGCGACT 59.130 50.000 21.68 6.22 44.80 4.18
1663 1765 2.021457 TGTCGAGCGACTAATCCATGA 58.979 47.619 21.68 0.00 44.80 3.07
1667 1769 2.156504 CGAGCGACTAATCCATGATTGC 59.843 50.000 0.00 0.00 33.95 3.56
1759 1861 2.842496 TGCACTCCCTTCTGATTCTGAT 59.158 45.455 0.00 0.00 0.00 2.90
1760 1862 3.265221 TGCACTCCCTTCTGATTCTGATT 59.735 43.478 0.00 0.00 0.00 2.57
1790 1902 6.421377 AGTTTTGAAAACATTTTGGAGTGC 57.579 33.333 21.34 0.00 0.00 4.40
1791 1903 6.172630 AGTTTTGAAAACATTTTGGAGTGCT 58.827 32.000 21.34 0.00 0.00 4.40
1793 1905 4.998671 TGAAAACATTTTGGAGTGCTGA 57.001 36.364 0.00 0.00 0.00 4.26
1795 1907 5.916318 TGAAAACATTTTGGAGTGCTGATT 58.084 33.333 0.00 0.00 0.00 2.57
1796 1908 6.347696 TGAAAACATTTTGGAGTGCTGATTT 58.652 32.000 0.00 0.00 0.00 2.17
1797 1909 6.822676 TGAAAACATTTTGGAGTGCTGATTTT 59.177 30.769 0.00 0.00 0.00 1.82
1798 1910 6.607735 AAACATTTTGGAGTGCTGATTTTG 57.392 33.333 0.00 0.00 0.00 2.44
1799 1911 5.280654 ACATTTTGGAGTGCTGATTTTGT 57.719 34.783 0.00 0.00 0.00 2.83
1800 1912 5.673514 ACATTTTGGAGTGCTGATTTTGTT 58.326 33.333 0.00 0.00 0.00 2.83
1803 1915 4.734398 TTGGAGTGCTGATTTTGTTGTT 57.266 36.364 0.00 0.00 0.00 2.83
1804 1916 4.734398 TGGAGTGCTGATTTTGTTGTTT 57.266 36.364 0.00 0.00 0.00 2.83
1805 1917 5.083533 TGGAGTGCTGATTTTGTTGTTTT 57.916 34.783 0.00 0.00 0.00 2.43
1806 1918 5.486526 TGGAGTGCTGATTTTGTTGTTTTT 58.513 33.333 0.00 0.00 0.00 1.94
1807 1919 5.350914 TGGAGTGCTGATTTTGTTGTTTTTG 59.649 36.000 0.00 0.00 0.00 2.44
1808 1920 5.220557 AGTGCTGATTTTGTTGTTTTTGC 57.779 34.783 0.00 0.00 0.00 3.68
1809 1921 4.094739 AGTGCTGATTTTGTTGTTTTTGCC 59.905 37.500 0.00 0.00 0.00 4.52
1810 1922 4.005650 TGCTGATTTTGTTGTTTTTGCCA 58.994 34.783 0.00 0.00 0.00 4.92
1811 1923 4.639310 TGCTGATTTTGTTGTTTTTGCCAT 59.361 33.333 0.00 0.00 0.00 4.40
1812 1924 4.971220 GCTGATTTTGTTGTTTTTGCCATG 59.029 37.500 0.00 0.00 0.00 3.66
1834 1957 2.477863 GCAATATCAACTTGGCGACACC 60.478 50.000 0.00 0.00 42.67 4.16
1853 1976 1.877367 GCAAACCCGCCGTATCAAA 59.123 52.632 0.00 0.00 0.00 2.69
1864 1987 2.352960 GCCGTATCAAAGCTTCAAGAGG 59.647 50.000 0.00 0.82 0.00 3.69
1967 2093 2.890945 CCCAAGGGTTAACTCTTGTTGG 59.109 50.000 35.03 28.33 38.83 3.77
1968 2094 2.296190 CCAAGGGTTAACTCTTGTTGGC 59.704 50.000 35.03 5.92 38.83 4.52
1969 2095 2.955660 CAAGGGTTAACTCTTGTTGGCA 59.044 45.455 31.74 0.00 37.59 4.92
1970 2096 3.525800 AGGGTTAACTCTTGTTGGCAT 57.474 42.857 0.85 0.00 37.59 4.40
1971 2097 3.844640 AGGGTTAACTCTTGTTGGCATT 58.155 40.909 0.85 0.00 37.59 3.56
1972 2098 4.223144 AGGGTTAACTCTTGTTGGCATTT 58.777 39.130 0.85 0.00 37.59 2.32
1973 2099 4.653801 AGGGTTAACTCTTGTTGGCATTTT 59.346 37.500 0.85 0.00 37.59 1.82
1974 2100 5.130311 AGGGTTAACTCTTGTTGGCATTTTT 59.870 36.000 0.85 0.00 37.59 1.94
1997 2123 2.261671 GGAGAAACTCCGCGAGCA 59.738 61.111 8.23 0.00 41.08 4.26
1998 2124 2.095252 GGAGAAACTCCGCGAGCAC 61.095 63.158 8.23 0.00 41.08 4.40
1999 2125 2.048127 AGAAACTCCGCGAGCACC 60.048 61.111 8.23 0.00 32.04 5.01
2000 2126 3.479269 GAAACTCCGCGAGCACCG 61.479 66.667 8.23 0.00 42.21 4.94
2019 2145 4.539881 GCGTCCGAGCCGAGACTC 62.540 72.222 0.00 0.00 0.00 3.36
2034 2160 3.382832 CTCGAACTCGGGTGGGCT 61.383 66.667 0.00 0.00 40.29 5.19
2035 2161 3.649277 CTCGAACTCGGGTGGGCTG 62.649 68.421 0.00 0.00 40.29 4.85
2036 2162 4.760047 CGAACTCGGGTGGGCTGG 62.760 72.222 0.00 0.00 35.37 4.85
2045 2171 4.982701 GTGGGCTGGCAGCAACCT 62.983 66.667 37.49 0.00 44.75 3.50
2046 2172 4.666253 TGGGCTGGCAGCAACCTC 62.666 66.667 37.49 21.25 44.75 3.85
2047 2173 4.666253 GGGCTGGCAGCAACCTCA 62.666 66.667 37.49 0.00 44.75 3.86
2048 2174 3.060615 GGCTGGCAGCAACCTCAG 61.061 66.667 37.49 0.50 44.75 3.35
2049 2175 3.745803 GCTGGCAGCAACCTCAGC 61.746 66.667 33.33 4.00 44.34 4.26
2050 2176 2.033757 CTGGCAGCAACCTCAGCT 59.966 61.111 0.00 0.00 44.62 4.24
2055 2181 3.573229 AGCAACCTCAGCTGCCCA 61.573 61.111 9.47 0.00 41.61 5.36
2056 2182 3.060615 GCAACCTCAGCTGCCCAG 61.061 66.667 9.47 0.70 32.18 4.45
2101 2227 3.330853 GCGTCGCCATCGTCATCC 61.331 66.667 5.75 0.00 36.96 3.51
2102 2228 2.104132 CGTCGCCATCGTCATCCA 59.896 61.111 0.00 0.00 36.96 3.41
2103 2229 1.300156 CGTCGCCATCGTCATCCAT 60.300 57.895 0.00 0.00 36.96 3.41
2104 2230 1.551503 CGTCGCCATCGTCATCCATG 61.552 60.000 0.00 0.00 36.96 3.66
2105 2231 1.595109 TCGCCATCGTCATCCATGC 60.595 57.895 0.00 0.00 36.96 4.06
2106 2232 1.888638 CGCCATCGTCATCCATGCA 60.889 57.895 0.00 0.00 0.00 3.96
2107 2233 1.650912 GCCATCGTCATCCATGCAC 59.349 57.895 0.00 0.00 0.00 4.57
2108 2234 1.096967 GCCATCGTCATCCATGCACA 61.097 55.000 0.00 0.00 0.00 4.57
2109 2235 0.659427 CCATCGTCATCCATGCACAC 59.341 55.000 0.00 0.00 0.00 3.82
2110 2236 0.302589 CATCGTCATCCATGCACACG 59.697 55.000 0.00 0.00 0.00 4.49
2111 2237 1.431488 ATCGTCATCCATGCACACGC 61.431 55.000 0.00 0.00 39.24 5.34
2112 2238 2.793946 GTCATCCATGCACACGCC 59.206 61.111 0.00 0.00 37.32 5.68
2113 2239 2.819154 TCATCCATGCACACGCCG 60.819 61.111 0.00 0.00 37.32 6.46
2114 2240 4.541482 CATCCATGCACACGCCGC 62.541 66.667 0.00 0.00 37.32 6.53
2137 2263 2.424302 CCGGGGTAATACCAGCCG 59.576 66.667 16.85 16.85 41.02 5.52
2146 2272 0.916809 AATACCAGCCGCCCTACTTT 59.083 50.000 0.00 0.00 0.00 2.66
2151 2277 0.390735 CAGCCGCCCTACTTTTACGT 60.391 55.000 0.00 0.00 0.00 3.57
2155 2281 0.457337 CGCCCTACTTTTACGTCGCT 60.457 55.000 0.00 0.00 0.00 4.93
2158 2284 2.856557 GCCCTACTTTTACGTCGCTAAG 59.143 50.000 0.00 0.00 0.00 2.18
2173 2299 3.356639 TAAGCAGCTCGGTCGGCAG 62.357 63.158 0.00 0.00 0.00 4.85
2267 2393 2.789917 CATCGCTGCAGCTTGTCC 59.210 61.111 34.22 6.92 39.32 4.02
2315 2441 2.727544 GTGCCCGCTTGCTTTTCA 59.272 55.556 0.00 0.00 0.00 2.69
2316 2442 1.290009 GTGCCCGCTTGCTTTTCAT 59.710 52.632 0.00 0.00 0.00 2.57
2319 2445 0.457337 GCCCGCTTGCTTTTCATCAG 60.457 55.000 0.00 0.00 0.00 2.90
2340 2466 0.872388 ATGTCTCAAACGGGCGAAAC 59.128 50.000 0.00 0.00 0.00 2.78
2354 2480 2.071604 CGAAACGCCATATGACAACG 57.928 50.000 3.65 5.17 0.00 4.10
2355 2481 1.810197 GAAACGCCATATGACAACGC 58.190 50.000 3.65 0.00 0.00 4.84
2356 2482 1.129624 GAAACGCCATATGACAACGCA 59.870 47.619 3.65 0.00 0.00 5.24
2357 2483 1.378531 AACGCCATATGACAACGCAT 58.621 45.000 3.65 0.00 0.00 4.73
2358 2484 2.232756 ACGCCATATGACAACGCATA 57.767 45.000 3.65 0.00 35.41 3.14
2359 2485 2.766313 ACGCCATATGACAACGCATAT 58.234 42.857 3.65 0.00 41.01 1.78
2360 2486 3.920446 ACGCCATATGACAACGCATATA 58.080 40.909 3.65 0.00 38.94 0.86
2361 2487 3.926527 ACGCCATATGACAACGCATATAG 59.073 43.478 3.65 0.00 38.94 1.31
2362 2488 3.306973 CGCCATATGACAACGCATATAGG 59.693 47.826 3.65 0.00 38.94 2.57
2363 2489 3.623060 GCCATATGACAACGCATATAGGG 59.377 47.826 3.65 0.00 38.94 3.53
2364 2490 4.622933 GCCATATGACAACGCATATAGGGA 60.623 45.833 3.65 0.00 38.94 4.20
2365 2491 5.111989 CCATATGACAACGCATATAGGGAG 58.888 45.833 3.65 0.00 38.94 4.30
2366 2492 5.337571 CCATATGACAACGCATATAGGGAGT 60.338 44.000 3.65 0.00 38.94 3.85
2367 2493 4.689612 ATGACAACGCATATAGGGAGTT 57.310 40.909 0.00 0.00 0.00 3.01
2368 2494 3.792401 TGACAACGCATATAGGGAGTTG 58.208 45.455 16.74 16.74 46.88 3.16
2371 2497 4.536364 CAACGCATATAGGGAGTTGTTG 57.464 45.455 12.59 0.00 39.97 3.33
2372 2498 3.194005 ACGCATATAGGGAGTTGTTGG 57.806 47.619 0.00 0.00 0.00 3.77
2373 2499 2.769663 ACGCATATAGGGAGTTGTTGGA 59.230 45.455 0.00 0.00 0.00 3.53
2374 2500 3.391296 ACGCATATAGGGAGTTGTTGGAT 59.609 43.478 0.00 0.00 0.00 3.41
2375 2501 4.591498 ACGCATATAGGGAGTTGTTGGATA 59.409 41.667 0.00 0.00 0.00 2.59
2376 2502 5.248477 ACGCATATAGGGAGTTGTTGGATAT 59.752 40.000 0.00 0.00 0.00 1.63
2377 2503 6.173339 CGCATATAGGGAGTTGTTGGATATT 58.827 40.000 0.00 0.00 0.00 1.28
2378 2504 7.038587 ACGCATATAGGGAGTTGTTGGATATTA 60.039 37.037 0.00 0.00 0.00 0.98
2379 2505 7.987458 CGCATATAGGGAGTTGTTGGATATTAT 59.013 37.037 0.00 0.00 0.00 1.28
2380 2506 9.331282 GCATATAGGGAGTTGTTGGATATTATC 57.669 37.037 0.00 0.00 0.00 1.75
2401 2527 0.323542 AGGACGGAGGTGAAGACGAT 60.324 55.000 0.00 0.00 0.00 3.73
2402 2528 0.179134 GGACGGAGGTGAAGACGATG 60.179 60.000 0.00 0.00 0.00 3.84
2409 2535 0.179134 GGTGAAGACGATGTCGAGGG 60.179 60.000 9.67 0.00 43.02 4.30
2412 2538 0.382515 GAAGACGATGTCGAGGGAGG 59.617 60.000 9.67 0.00 43.02 4.30
2433 2559 2.093235 GCCAAGTAGATGACTCCAAGCT 60.093 50.000 0.00 0.00 37.44 3.74
2449 2575 3.065306 CTGGAGGTGTACGCCCAA 58.935 61.111 21.89 6.98 38.44 4.12
2450 2576 1.375523 CTGGAGGTGTACGCCCAAC 60.376 63.158 21.89 12.57 38.44 3.77
2455 2581 2.281208 GTGTACGCCCAACAGCCA 60.281 61.111 0.00 0.00 0.00 4.75
2456 2582 2.031919 TGTACGCCCAACAGCCAG 59.968 61.111 0.00 0.00 0.00 4.85
2457 2583 2.746277 GTACGCCCAACAGCCAGG 60.746 66.667 0.00 0.00 0.00 4.45
2458 2584 4.715523 TACGCCCAACAGCCAGGC 62.716 66.667 1.84 1.84 43.53 4.85
2461 2587 3.766691 GCCCAACAGCCAGGCATG 61.767 66.667 15.80 11.61 46.34 4.06
2462 2588 2.283388 CCCAACAGCCAGGCATGT 60.283 61.111 15.80 12.30 0.00 3.21
2464 2590 1.315257 CCCAACAGCCAGGCATGTAC 61.315 60.000 15.80 0.00 0.00 2.90
2466 2592 0.523072 CAACAGCCAGGCATGTACAC 59.477 55.000 15.80 0.00 0.00 2.90
2467 2593 0.609131 AACAGCCAGGCATGTACACC 60.609 55.000 15.80 0.00 0.00 4.16
2468 2594 2.108514 CAGCCAGGCATGTACACCG 61.109 63.158 15.80 0.00 0.00 4.94
2469 2595 2.824041 GCCAGGCATGTACACCGG 60.824 66.667 6.55 0.00 0.00 5.28
2470 2596 2.124736 CCAGGCATGTACACCGGG 60.125 66.667 6.32 7.19 34.87 5.73
2471 2597 2.824041 CAGGCATGTACACCGGGC 60.824 66.667 6.32 3.41 0.00 6.13
2472 2598 3.326578 AGGCATGTACACCGGGCA 61.327 61.111 6.32 0.00 0.00 5.36
2473 2599 2.824041 GGCATGTACACCGGGCAG 60.824 66.667 6.32 0.00 0.00 4.85
2474 2600 3.508840 GCATGTACACCGGGCAGC 61.509 66.667 6.32 0.00 0.00 5.25
2475 2601 2.824041 CATGTACACCGGGCAGCC 60.824 66.667 6.32 1.26 0.00 4.85
2476 2602 4.467084 ATGTACACCGGGCAGCCG 62.467 66.667 6.32 0.32 0.00 5.52
2484 2610 3.458163 CGGGCAGCCGGAGTAGAA 61.458 66.667 13.88 0.00 0.00 2.10
2485 2611 2.187163 GGGCAGCCGGAGTAGAAC 59.813 66.667 5.05 0.00 0.00 3.01
2486 2612 2.656069 GGGCAGCCGGAGTAGAACA 61.656 63.158 5.05 0.00 0.00 3.18
2487 2613 1.522569 GGCAGCCGGAGTAGAACAT 59.477 57.895 5.05 0.00 0.00 2.71
2490 2616 0.738975 CAGCCGGAGTAGAACATCGA 59.261 55.000 5.05 0.00 0.00 3.59
2496 2622 2.544686 CGGAGTAGAACATCGACGAGAT 59.455 50.000 3.01 0.00 41.01 2.75
2508 2634 1.678627 CGACGAGATGGTCCTTGATCT 59.321 52.381 0.00 0.00 33.30 2.75
2511 2637 2.034878 CGAGATGGTCCTTGATCTGGA 58.965 52.381 4.29 4.29 28.61 3.86
2512 2638 2.632028 CGAGATGGTCCTTGATCTGGAT 59.368 50.000 10.40 0.00 35.87 3.41
2517 2643 4.868172 TGGTCCTTGATCTGGATGATTT 57.132 40.909 10.40 0.00 35.14 2.17
2521 2647 4.036498 GTCCTTGATCTGGATGATTTGCTG 59.964 45.833 10.40 0.00 35.14 4.41
2568 2694 5.701224 AGGAGAAAGTTTTAACATGTGGGA 58.299 37.500 0.00 0.00 0.00 4.37
2578 2704 5.720371 TTAACATGTGGGAGGACAAATTG 57.280 39.130 0.00 0.00 0.00 2.32
2593 2719 4.484236 ACAAATTGTTATGCGATGTGTGG 58.516 39.130 0.00 0.00 37.89 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
199 200 4.247380 GAGGCCAGCGGGATGGAG 62.247 72.222 7.23 0.00 43.57 3.86
562 569 0.665835 CCTCCTCGATGTCCTTCTCG 59.334 60.000 0.00 0.00 36.25 4.04
708 718 3.071602 ACTCTGCAAGATACAACCACAGT 59.928 43.478 3.37 0.00 45.62 3.55
709 719 3.434641 CACTCTGCAAGATACAACCACAG 59.565 47.826 3.37 0.00 45.62 3.66
710 720 3.181455 ACACTCTGCAAGATACAACCACA 60.181 43.478 3.37 0.00 45.62 4.17
711 721 3.403038 ACACTCTGCAAGATACAACCAC 58.597 45.455 3.37 0.00 45.62 4.16
713 723 3.619038 GCTACACTCTGCAAGATACAACC 59.381 47.826 3.37 0.00 45.62 3.77
716 726 5.914898 TTAGCTACACTCTGCAAGATACA 57.085 39.130 0.00 0.00 45.62 2.29
717 727 6.579292 CGTATTAGCTACACTCTGCAAGATAC 59.421 42.308 0.00 0.00 45.62 2.24
718 728 6.262496 ACGTATTAGCTACACTCTGCAAGATA 59.738 38.462 0.00 0.00 45.62 1.98
719 729 5.067936 ACGTATTAGCTACACTCTGCAAGAT 59.932 40.000 0.00 0.00 45.62 2.40
725 735 5.196102 CACGTACGTATTAGCTACACTCTG 58.804 45.833 22.34 0.00 0.00 3.35
742 752 5.695816 ACCGAGAGATTAGAGATACACGTAC 59.304 44.000 0.00 0.00 0.00 3.67
743 753 5.695363 CACCGAGAGATTAGAGATACACGTA 59.305 44.000 0.00 0.00 0.00 3.57
744 754 4.512198 CACCGAGAGATTAGAGATACACGT 59.488 45.833 0.00 0.00 0.00 4.49
745 755 4.083749 CCACCGAGAGATTAGAGATACACG 60.084 50.000 0.00 0.00 0.00 4.49
746 756 4.822896 ACCACCGAGAGATTAGAGATACAC 59.177 45.833 0.00 0.00 0.00 2.90
754 764 7.827236 AGATTAGAGATACCACCGAGAGATTAG 59.173 40.741 0.00 0.00 0.00 1.73
758 768 5.308497 AGAGATTAGAGATACCACCGAGAGA 59.692 44.000 0.00 0.00 0.00 3.10
759 769 5.556915 AGAGATTAGAGATACCACCGAGAG 58.443 45.833 0.00 0.00 0.00 3.20
760 770 5.553123 GAGAGATTAGAGATACCACCGAGA 58.447 45.833 0.00 0.00 0.00 4.04
761 771 4.390603 CGAGAGATTAGAGATACCACCGAG 59.609 50.000 0.00 0.00 0.00 4.63
762 772 4.316645 CGAGAGATTAGAGATACCACCGA 58.683 47.826 0.00 0.00 0.00 4.69
763 773 3.437395 CCGAGAGATTAGAGATACCACCG 59.563 52.174 0.00 0.00 0.00 4.94
764 774 4.216687 CACCGAGAGATTAGAGATACCACC 59.783 50.000 0.00 0.00 0.00 4.61
765 775 4.216687 CCACCGAGAGATTAGAGATACCAC 59.783 50.000 0.00 0.00 0.00 4.16
766 776 4.141228 ACCACCGAGAGATTAGAGATACCA 60.141 45.833 0.00 0.00 0.00 3.25
767 777 4.400120 ACCACCGAGAGATTAGAGATACC 58.600 47.826 0.00 0.00 0.00 2.73
768 778 5.531659 TGAACCACCGAGAGATTAGAGATAC 59.468 44.000 0.00 0.00 0.00 2.24
769 779 5.691896 TGAACCACCGAGAGATTAGAGATA 58.308 41.667 0.00 0.00 0.00 1.98
770 780 4.537751 TGAACCACCGAGAGATTAGAGAT 58.462 43.478 0.00 0.00 0.00 2.75
771 781 3.964411 TGAACCACCGAGAGATTAGAGA 58.036 45.455 0.00 0.00 0.00 3.10
924 995 2.879933 CAGCTGCTCTGCTCGACG 60.880 66.667 0.00 0.00 41.98 5.12
943 1015 5.157940 AGAGCTCTCTGTTTTTATCTGCA 57.842 39.130 11.45 0.00 38.75 4.41
967 1039 2.290789 GCGCGCGCTCGACTATAAA 61.291 57.895 44.38 0.00 38.10 1.40
1421 1501 4.749310 CCGCACTCCGCTTGCTCT 62.749 66.667 0.00 0.00 37.87 4.09
1596 1676 5.763876 AAGCTCTTTAATCCTACTGGTGT 57.236 39.130 0.00 0.00 34.23 4.16
1618 1720 3.066291 ACGAGCCATGATAACCAACAA 57.934 42.857 0.00 0.00 0.00 2.83
1624 1726 4.026804 CGACAAACTACGAGCCATGATAAC 60.027 45.833 0.00 0.00 0.00 1.89
1628 1730 1.542472 TCGACAAACTACGAGCCATGA 59.458 47.619 0.00 0.00 34.49 3.07
1629 1731 1.920574 CTCGACAAACTACGAGCCATG 59.079 52.381 0.00 0.00 46.54 3.66
1631 1733 3.786809 CTCGACAAACTACGAGCCA 57.213 52.632 0.00 0.00 46.54 4.75
1635 1737 0.870393 AGTCGCTCGACAAACTACGA 59.130 50.000 22.18 0.00 46.76 3.43
1637 1739 3.790288 GGATTAGTCGCTCGACAAACTAC 59.210 47.826 22.18 9.50 46.76 2.73
1638 1740 3.441222 TGGATTAGTCGCTCGACAAACTA 59.559 43.478 22.18 9.79 46.76 2.24
1639 1741 2.230508 TGGATTAGTCGCTCGACAAACT 59.769 45.455 22.18 6.22 46.76 2.66
1640 1742 2.602878 TGGATTAGTCGCTCGACAAAC 58.397 47.619 22.18 13.07 46.76 2.93
1641 1743 3.119280 TCATGGATTAGTCGCTCGACAAA 60.119 43.478 22.18 8.89 46.76 2.83
1642 1744 2.425668 TCATGGATTAGTCGCTCGACAA 59.574 45.455 22.18 14.75 46.76 3.18
1643 1745 2.021457 TCATGGATTAGTCGCTCGACA 58.979 47.619 22.18 5.19 46.76 4.35
1644 1746 2.776312 TCATGGATTAGTCGCTCGAC 57.224 50.000 13.92 13.92 44.86 4.20
1645 1747 3.642705 CAATCATGGATTAGTCGCTCGA 58.357 45.455 0.00 0.00 30.44 4.04
1646 1748 2.156504 GCAATCATGGATTAGTCGCTCG 59.843 50.000 0.00 0.00 30.44 5.03
1647 1749 2.156504 CGCAATCATGGATTAGTCGCTC 59.843 50.000 0.00 0.00 30.44 5.03
1648 1750 2.138320 CGCAATCATGGATTAGTCGCT 58.862 47.619 0.00 0.00 30.44 4.93
1649 1751 1.398960 GCGCAATCATGGATTAGTCGC 60.399 52.381 0.30 12.81 37.32 5.19
1650 1752 1.195448 GGCGCAATCATGGATTAGTCG 59.805 52.381 10.83 0.00 30.44 4.18
1651 1753 1.195448 CGGCGCAATCATGGATTAGTC 59.805 52.381 10.83 0.00 30.44 2.59
1652 1754 1.229428 CGGCGCAATCATGGATTAGT 58.771 50.000 10.83 0.00 30.44 2.24
1653 1755 0.518636 CCGGCGCAATCATGGATTAG 59.481 55.000 10.83 0.00 30.44 1.73
1654 1756 1.514678 GCCGGCGCAATCATGGATTA 61.515 55.000 12.58 0.00 30.44 1.75
1663 1765 3.499737 CTTCTTCGCCGGCGCAAT 61.500 61.111 42.78 0.00 39.59 3.56
1731 1833 6.271857 AGAATCAGAAGGGAGTGCATATACAT 59.728 38.462 0.00 0.00 0.00 2.29
1765 1867 7.821846 AGCACTCCAAAATGTTTTCAAAACTAA 59.178 29.630 14.10 0.00 0.00 2.24
1767 1869 6.092533 CAGCACTCCAAAATGTTTTCAAAACT 59.907 34.615 14.10 0.00 0.00 2.66
1768 1870 6.091986 TCAGCACTCCAAAATGTTTTCAAAAC 59.908 34.615 6.02 6.02 0.00 2.43
1770 1872 5.728471 TCAGCACTCCAAAATGTTTTCAAA 58.272 33.333 0.00 0.00 0.00 2.69
1771 1873 5.336150 TCAGCACTCCAAAATGTTTTCAA 57.664 34.783 0.00 0.00 0.00 2.69
1772 1874 4.998671 TCAGCACTCCAAAATGTTTTCA 57.001 36.364 0.00 0.00 0.00 2.69
1773 1875 6.849588 AAATCAGCACTCCAAAATGTTTTC 57.150 33.333 0.00 0.00 0.00 2.29
1774 1876 6.598850 ACAAAATCAGCACTCCAAAATGTTTT 59.401 30.769 0.00 0.00 0.00 2.43
1775 1877 6.114767 ACAAAATCAGCACTCCAAAATGTTT 58.885 32.000 0.00 0.00 0.00 2.83
1776 1878 5.673514 ACAAAATCAGCACTCCAAAATGTT 58.326 33.333 0.00 0.00 0.00 2.71
1777 1879 5.280654 ACAAAATCAGCACTCCAAAATGT 57.719 34.783 0.00 0.00 0.00 2.71
1788 1900 4.005650 TGGCAAAAACAACAAAATCAGCA 58.994 34.783 0.00 0.00 0.00 4.41
1789 1901 4.612932 TGGCAAAAACAACAAAATCAGC 57.387 36.364 0.00 0.00 0.00 4.26
1790 1902 5.512473 CCATGGCAAAAACAACAAAATCAG 58.488 37.500 0.00 0.00 0.00 2.90
1791 1903 4.201990 GCCATGGCAAAAACAACAAAATCA 60.202 37.500 32.08 0.00 41.49 2.57
1793 1905 4.304537 GCCATGGCAAAAACAACAAAAT 57.695 36.364 32.08 0.00 41.49 1.82
1807 1919 2.804212 GCCAAGTTGATATTGCCATGGC 60.804 50.000 30.54 30.54 44.44 4.40
1808 1920 2.544277 CGCCAAGTTGATATTGCCATGG 60.544 50.000 7.63 7.63 0.00 3.66
1809 1921 2.358582 TCGCCAAGTTGATATTGCCATG 59.641 45.455 3.87 0.00 0.00 3.66
1810 1922 2.358898 GTCGCCAAGTTGATATTGCCAT 59.641 45.455 3.87 0.00 0.00 4.40
1811 1923 1.742831 GTCGCCAAGTTGATATTGCCA 59.257 47.619 3.87 0.00 0.00 4.92
1812 1924 1.742831 TGTCGCCAAGTTGATATTGCC 59.257 47.619 3.87 0.00 0.00 4.52
1817 1929 3.131326 CGGTGTCGCCAAGTTGATA 57.869 52.632 3.87 0.00 36.97 2.15
1834 1957 1.913451 TTTGATACGGCGGGTTTGCG 61.913 55.000 13.24 0.00 35.06 4.85
1846 1969 2.352960 CGCCCTCTTGAAGCTTTGATAC 59.647 50.000 0.00 0.00 0.00 2.24
1847 1970 2.632377 CGCCCTCTTGAAGCTTTGATA 58.368 47.619 0.00 0.00 0.00 2.15
1853 1976 4.767255 CGCCGCCCTCTTGAAGCT 62.767 66.667 0.00 0.00 0.00 3.74
1932 2058 4.562767 ACCCTTGGGTTGGTCTAATTTTT 58.437 39.130 5.34 0.00 0.00 1.94
1933 2059 4.207698 ACCCTTGGGTTGGTCTAATTTT 57.792 40.909 5.34 0.00 0.00 1.82
1934 2060 3.915346 ACCCTTGGGTTGGTCTAATTT 57.085 42.857 5.34 0.00 0.00 1.82
1935 2061 3.915346 AACCCTTGGGTTGGTCTAATT 57.085 42.857 22.01 0.00 32.40 1.40
1936 2062 4.355889 AGTTAACCCTTGGGTTGGTCTAAT 59.644 41.667 28.76 7.38 32.40 1.73
1937 2063 3.723154 AGTTAACCCTTGGGTTGGTCTAA 59.277 43.478 28.76 14.98 32.40 2.10
1938 2064 3.328637 GAGTTAACCCTTGGGTTGGTCTA 59.671 47.826 28.76 10.12 32.40 2.59
1939 2065 2.107726 GAGTTAACCCTTGGGTTGGTCT 59.892 50.000 28.76 22.45 32.40 3.85
1940 2066 2.107726 AGAGTTAACCCTTGGGTTGGTC 59.892 50.000 28.76 21.47 32.40 4.02
1941 2067 2.141067 AGAGTTAACCCTTGGGTTGGT 58.859 47.619 28.76 15.63 36.06 3.67
1942 2068 2.890945 CAAGAGTTAACCCTTGGGTTGG 59.109 50.000 28.76 9.59 36.90 3.77
1943 2069 3.562182 ACAAGAGTTAACCCTTGGGTTG 58.438 45.455 27.27 16.21 42.86 3.77
1944 2070 3.958147 CAACAAGAGTTAACCCTTGGGTT 59.042 43.478 27.27 25.20 42.86 4.11
1945 2071 3.562182 CAACAAGAGTTAACCCTTGGGT 58.438 45.455 27.27 15.64 42.86 4.51
1946 2072 2.890945 CCAACAAGAGTTAACCCTTGGG 59.109 50.000 27.27 19.96 42.86 4.12
1947 2073 2.296190 GCCAACAAGAGTTAACCCTTGG 59.704 50.000 27.27 15.80 42.86 3.61
1948 2074 2.955660 TGCCAACAAGAGTTAACCCTTG 59.044 45.455 23.70 23.70 43.84 3.61
1949 2075 3.306472 TGCCAACAAGAGTTAACCCTT 57.694 42.857 0.88 0.00 35.85 3.95
1950 2076 3.525800 ATGCCAACAAGAGTTAACCCT 57.474 42.857 0.88 0.00 35.85 4.34
1951 2077 4.600692 AAATGCCAACAAGAGTTAACCC 57.399 40.909 0.88 0.00 35.85 4.11
1980 2106 2.095252 GTGCTCGCGGAGTTTCTCC 61.095 63.158 6.13 5.79 46.44 3.71
1981 2107 2.095252 GGTGCTCGCGGAGTTTCTC 61.095 63.158 6.13 0.00 31.39 2.87
1982 2108 2.048127 GGTGCTCGCGGAGTTTCT 60.048 61.111 6.13 0.00 31.39 2.52
1983 2109 3.479269 CGGTGCTCGCGGAGTTTC 61.479 66.667 6.13 0.00 31.39 2.78
2002 2128 4.539881 GAGTCTCGGCTCGGACGC 62.540 72.222 0.00 7.08 37.52 5.19
2013 2139 1.507174 CCACCCGAGTTCGAGTCTC 59.493 63.158 2.59 8.89 43.02 3.36
2014 2140 1.977544 CCCACCCGAGTTCGAGTCT 60.978 63.158 2.59 0.00 43.02 3.24
2015 2141 2.572284 CCCACCCGAGTTCGAGTC 59.428 66.667 2.59 0.00 43.02 3.36
2016 2142 3.692406 GCCCACCCGAGTTCGAGT 61.692 66.667 2.59 0.00 43.02 4.18
2017 2143 3.382832 AGCCCACCCGAGTTCGAG 61.383 66.667 2.59 0.00 43.02 4.04
2018 2144 3.691342 CAGCCCACCCGAGTTCGA 61.691 66.667 2.59 0.00 43.02 3.71
2019 2145 4.760047 CCAGCCCACCCGAGTTCG 62.760 72.222 0.00 0.00 39.44 3.95
2028 2154 4.982701 AGGTTGCTGCCAGCCCAC 62.983 66.667 15.29 10.81 42.79 4.61
2029 2155 4.666253 GAGGTTGCTGCCAGCCCA 62.666 66.667 15.29 0.00 42.79 5.36
2030 2156 4.666253 TGAGGTTGCTGCCAGCCC 62.666 66.667 15.29 9.16 42.79 5.19
2031 2157 3.060615 CTGAGGTTGCTGCCAGCC 61.061 66.667 15.29 0.00 41.51 4.85
2032 2158 3.745803 GCTGAGGTTGCTGCCAGC 61.746 66.667 10.45 10.45 44.00 4.85
2033 2159 2.033757 AGCTGAGGTTGCTGCCAG 59.966 61.111 0.00 0.00 39.56 4.85
2038 2164 3.564345 CTGGGCAGCTGAGGTTGCT 62.564 63.158 20.43 0.00 46.51 3.91
2039 2165 3.060615 CTGGGCAGCTGAGGTTGC 61.061 66.667 20.43 0.23 46.58 4.17
2084 2210 3.330853 GGATGACGATGGCGACGC 61.331 66.667 12.43 12.43 41.64 5.19
2085 2211 1.300156 ATGGATGACGATGGCGACG 60.300 57.895 0.00 0.00 41.64 5.12
2086 2212 1.835483 GCATGGATGACGATGGCGAC 61.835 60.000 0.00 0.00 41.64 5.19
2087 2213 1.595109 GCATGGATGACGATGGCGA 60.595 57.895 0.00 0.00 41.64 5.54
2088 2214 1.888638 TGCATGGATGACGATGGCG 60.889 57.895 0.00 0.00 44.79 5.69
2089 2215 1.096967 TGTGCATGGATGACGATGGC 61.097 55.000 0.00 0.00 33.80 4.40
2090 2216 0.659427 GTGTGCATGGATGACGATGG 59.341 55.000 0.00 0.00 33.80 3.51
2091 2217 0.302589 CGTGTGCATGGATGACGATG 59.697 55.000 14.09 0.00 35.77 3.84
2092 2218 1.431488 GCGTGTGCATGGATGACGAT 61.431 55.000 20.80 0.00 42.15 3.73
2093 2219 2.100031 GCGTGTGCATGGATGACGA 61.100 57.895 20.80 0.00 42.15 4.20
2094 2220 2.400798 GCGTGTGCATGGATGACG 59.599 61.111 14.72 14.72 42.15 4.35
2095 2221 2.793946 GGCGTGTGCATGGATGAC 59.206 61.111 0.00 0.00 45.35 3.06
2096 2222 2.819154 CGGCGTGTGCATGGATGA 60.819 61.111 0.00 0.00 45.35 2.92
2097 2223 4.541482 GCGGCGTGTGCATGGATG 62.541 66.667 9.37 0.00 45.35 3.51
2115 2241 2.052047 CTGGTATTACCCCGGCCAGG 62.052 65.000 12.74 5.18 42.05 4.45
2116 2242 1.450211 CTGGTATTACCCCGGCCAG 59.550 63.158 10.37 7.51 37.50 4.85
2117 2243 2.748513 GCTGGTATTACCCCGGCCA 61.749 63.158 10.37 0.00 46.68 5.36
2118 2244 2.112507 GCTGGTATTACCCCGGCC 59.887 66.667 10.37 0.00 46.68 6.13
2120 2246 2.424302 CGGCTGGTATTACCCCGG 59.576 66.667 17.93 0.00 38.77 5.73
2121 2247 2.280592 GCGGCTGGTATTACCCCG 60.281 66.667 20.19 20.19 43.23 5.73
2124 2250 0.034476 GTAGGGCGGCTGGTATTACC 59.966 60.000 9.56 5.87 39.22 2.85
2131 2257 1.087771 CGTAAAAGTAGGGCGGCTGG 61.088 60.000 9.56 0.00 0.00 4.85
2137 2263 2.566952 TAGCGACGTAAAAGTAGGGC 57.433 50.000 0.00 0.00 0.00 5.19
2146 2272 0.522705 CGAGCTGCTTAGCGACGTAA 60.523 55.000 2.53 0.00 40.27 3.18
2151 2277 2.490217 GACCGAGCTGCTTAGCGA 59.510 61.111 2.53 0.00 40.27 4.93
2155 2281 3.356639 CTGCCGACCGAGCTGCTTA 62.357 63.158 2.53 0.00 0.00 3.09
2307 2433 6.347644 CGTTTGAGACATACTGATGAAAAGCA 60.348 38.462 0.00 0.00 36.48 3.91
2308 2434 6.017933 CGTTTGAGACATACTGATGAAAAGC 58.982 40.000 0.00 0.00 36.48 3.51
2311 2437 4.935205 CCCGTTTGAGACATACTGATGAAA 59.065 41.667 0.00 0.00 36.48 2.69
2315 2441 2.738643 CGCCCGTTTGAGACATACTGAT 60.739 50.000 0.00 0.00 0.00 2.90
2316 2442 1.403647 CGCCCGTTTGAGACATACTGA 60.404 52.381 0.00 0.00 0.00 3.41
2319 2445 1.717194 TTCGCCCGTTTGAGACATAC 58.283 50.000 0.00 0.00 0.00 2.39
2340 2466 3.306973 CCTATATGCGTTGTCATATGGCG 59.693 47.826 2.28 4.48 39.32 5.69
2351 2477 3.199071 TCCAACAACTCCCTATATGCGTT 59.801 43.478 0.00 0.00 0.00 4.84
2352 2478 2.769663 TCCAACAACTCCCTATATGCGT 59.230 45.455 0.00 0.00 0.00 5.24
2353 2479 3.469008 TCCAACAACTCCCTATATGCG 57.531 47.619 0.00 0.00 0.00 4.73
2354 2480 9.331282 GATAATATCCAACAACTCCCTATATGC 57.669 37.037 0.00 0.00 0.00 3.14
2380 2506 1.592223 GTCTTCACCTCCGTCCTGG 59.408 63.158 0.00 0.00 40.09 4.45
2381 2507 1.213013 CGTCTTCACCTCCGTCCTG 59.787 63.158 0.00 0.00 0.00 3.86
2382 2508 0.323542 ATCGTCTTCACCTCCGTCCT 60.324 55.000 0.00 0.00 0.00 3.85
2383 2509 0.179134 CATCGTCTTCACCTCCGTCC 60.179 60.000 0.00 0.00 0.00 4.79
2387 2513 0.809385 TCGACATCGTCTTCACCTCC 59.191 55.000 0.54 0.00 40.80 4.30
2392 2518 1.095600 CTCCCTCGACATCGTCTTCA 58.904 55.000 0.54 0.00 40.80 3.02
2394 2520 1.668101 GCCTCCCTCGACATCGTCTT 61.668 60.000 0.54 0.00 40.80 3.01
2401 2527 0.970937 CTACTTGGCCTCCCTCGACA 60.971 60.000 3.32 0.00 0.00 4.35
2402 2528 0.683504 TCTACTTGGCCTCCCTCGAC 60.684 60.000 3.32 0.00 0.00 4.20
2409 2535 2.111384 TGGAGTCATCTACTTGGCCTC 58.889 52.381 3.32 0.00 39.07 4.70
2412 2538 2.093235 AGCTTGGAGTCATCTACTTGGC 60.093 50.000 0.00 0.00 39.07 4.52
2433 2559 2.107041 CTGTTGGGCGTACACCTCCA 62.107 60.000 0.00 0.00 0.00 3.86
2449 2575 1.002134 GGTGTACATGCCTGGCTGT 60.002 57.895 21.03 21.36 0.00 4.40
2450 2576 2.108514 CGGTGTACATGCCTGGCTG 61.109 63.158 21.03 16.96 0.00 4.85
2455 2581 3.326578 TGCCCGGTGTACATGCCT 61.327 61.111 0.00 0.00 0.00 4.75
2456 2582 2.824041 CTGCCCGGTGTACATGCC 60.824 66.667 0.00 0.00 0.00 4.40
2457 2583 3.508840 GCTGCCCGGTGTACATGC 61.509 66.667 0.00 0.66 0.00 4.06
2458 2584 2.824041 GGCTGCCCGGTGTACATG 60.824 66.667 7.66 0.00 0.00 3.21
2468 2594 1.972660 ATGTTCTACTCCGGCTGCCC 61.973 60.000 14.12 0.00 0.00 5.36
2469 2595 0.530870 GATGTTCTACTCCGGCTGCC 60.531 60.000 9.11 9.11 0.00 4.85
2470 2596 0.872021 CGATGTTCTACTCCGGCTGC 60.872 60.000 0.00 0.00 0.00 5.25
2471 2597 0.738975 TCGATGTTCTACTCCGGCTG 59.261 55.000 0.00 0.00 0.00 4.85
2472 2598 0.739561 GTCGATGTTCTACTCCGGCT 59.260 55.000 0.00 0.00 0.00 5.52
2473 2599 0.591741 CGTCGATGTTCTACTCCGGC 60.592 60.000 0.00 0.00 0.00 6.13
2474 2600 1.003759 CTCGTCGATGTTCTACTCCGG 60.004 57.143 4.21 0.00 0.00 5.14
2475 2601 1.931841 TCTCGTCGATGTTCTACTCCG 59.068 52.381 4.21 0.00 0.00 4.63
2476 2602 3.304123 CCATCTCGTCGATGTTCTACTCC 60.304 52.174 4.21 0.00 46.56 3.85
2477 2603 3.312973 ACCATCTCGTCGATGTTCTACTC 59.687 47.826 4.21 0.00 46.56 2.59
2478 2604 3.280295 ACCATCTCGTCGATGTTCTACT 58.720 45.455 4.21 0.00 46.56 2.57
2479 2605 3.548415 GGACCATCTCGTCGATGTTCTAC 60.548 52.174 4.21 0.00 46.56 2.59
2480 2606 2.617308 GGACCATCTCGTCGATGTTCTA 59.383 50.000 4.21 0.00 46.56 2.10
2481 2607 1.405821 GGACCATCTCGTCGATGTTCT 59.594 52.381 4.21 0.00 46.56 3.01
2482 2608 1.405821 AGGACCATCTCGTCGATGTTC 59.594 52.381 4.21 10.08 46.56 3.18
2483 2609 1.475403 AGGACCATCTCGTCGATGTT 58.525 50.000 4.21 2.94 46.56 2.71
2484 2610 1.135139 CAAGGACCATCTCGTCGATGT 59.865 52.381 4.21 0.00 46.56 3.06
2486 2612 1.763968 TCAAGGACCATCTCGTCGAT 58.236 50.000 0.00 0.00 33.30 3.59
2487 2613 1.676529 GATCAAGGACCATCTCGTCGA 59.323 52.381 0.00 0.00 33.30 4.20
2490 2616 1.759445 CCAGATCAAGGACCATCTCGT 59.241 52.381 0.00 0.00 0.00 4.18
2496 2622 4.529897 CAAATCATCCAGATCAAGGACCA 58.470 43.478 8.87 0.33 38.13 4.02
2499 2625 4.204799 CAGCAAATCATCCAGATCAAGGA 58.795 43.478 9.09 9.09 39.97 3.36
2504 2630 1.612463 GGCCAGCAAATCATCCAGATC 59.388 52.381 0.00 0.00 35.39 2.75
2508 2634 0.106569 ATCGGCCAGCAAATCATCCA 60.107 50.000 2.24 0.00 0.00 3.41
2511 2637 0.106569 TGGATCGGCCAGCAAATCAT 60.107 50.000 2.24 0.00 43.33 2.45
2512 2638 1.302617 TGGATCGGCCAGCAAATCA 59.697 52.632 2.24 0.00 43.33 2.57
2521 2647 0.464554 CCCTCTTCTTTGGATCGGCC 60.465 60.000 0.00 0.00 37.10 6.13
2568 2694 4.458989 ACACATCGCATAACAATTTGTCCT 59.541 37.500 1.83 0.00 0.00 3.85
2578 2704 1.467374 GCCAACCACACATCGCATAAC 60.467 52.381 0.00 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.