Multiple sequence alignment - TraesCS1D01G280600

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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 TraesCS1D01G280600 chr1D 100.000 3929 0 0 1 3929 379129944 379133872 0.000000e+00 7256.0
1 TraesCS1D01G280600 chr1A 90.236 2796 160 50 700 3427 479817610 479820360 0.000000e+00 3546.0
2 TraesCS1D01G280600 chr1A 88.825 698 57 12 1 690 493944938 493945622 0.000000e+00 837.0
3 TraesCS1D01G280600 chr1A 88.971 272 16 7 3168 3427 479820568 479820837 1.360000e-84 324.0
4 TraesCS1D01G280600 chr1A 95.679 162 7 0 3768 3929 479821290 479821451 1.080000e-65 261.0
5 TraesCS1D01G280600 chr1B 93.478 1656 69 15 1918 3540 507808136 507809785 0.000000e+00 2423.0
6 TraesCS1D01G280600 chr1B 93.372 513 25 5 1210 1719 507807474 507807980 0.000000e+00 750.0
7 TraesCS1D01G280600 chr1B 92.141 509 23 7 700 1203 507806941 507807437 0.000000e+00 702.0
8 TraesCS1D01G280600 chr1B 87.379 206 10 6 3537 3742 507839515 507839704 5.110000e-54 222.0
9 TraesCS1D01G280600 chr1B 92.157 153 12 0 3740 3892 507839742 507839894 2.380000e-52 217.0
10 TraesCS1D01G280600 chr3D 90.058 694 38 16 1 672 566071386 566072070 0.000000e+00 870.0
11 TraesCS1D01G280600 chr3D 89.127 699 44 21 1 684 603118549 603119230 0.000000e+00 841.0
12 TraesCS1D01G280600 chr3A 88.889 702 52 17 1 690 493096514 493097201 0.000000e+00 841.0
13 TraesCS1D01G280600 chr4A 88.746 702 51 16 1 683 467283301 467282609 0.000000e+00 833.0
14 TraesCS1D01G280600 chr7D 88.575 709 50 16 1 691 610766388 610767083 0.000000e+00 832.0
15 TraesCS1D01G280600 chr6D 88.652 705 51 15 1 688 22137624 22136932 0.000000e+00 832.0
16 TraesCS1D01G280600 chr5D 88.636 704 52 18 1 691 71885945 71886633 0.000000e+00 832.0
17 TraesCS1D01G280600 chr4D 88.555 699 55 16 1 690 57897094 57896412 0.000000e+00 824.0
18 TraesCS1D01G280600 chr7A 77.966 118 22 4 3609 3724 694199421 694199306 1.960000e-08 71.3
19 TraesCS1D01G280600 chr7B 88.889 54 5 1 3672 3724 683146559 683146506 9.110000e-07 65.8


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 TraesCS1D01G280600 chr1D 379129944 379133872 3928 False 7256.000000 7256 100.000000 1 3929 1 chr1D.!!$F1 3928
1 TraesCS1D01G280600 chr1A 479817610 479821451 3841 False 1377.000000 3546 91.628667 700 3929 3 chr1A.!!$F2 3229
2 TraesCS1D01G280600 chr1A 493944938 493945622 684 False 837.000000 837 88.825000 1 690 1 chr1A.!!$F1 689
3 TraesCS1D01G280600 chr1B 507806941 507809785 2844 False 1291.666667 2423 92.997000 700 3540 3 chr1B.!!$F1 2840
4 TraesCS1D01G280600 chr3D 566071386 566072070 684 False 870.000000 870 90.058000 1 672 1 chr3D.!!$F1 671
5 TraesCS1D01G280600 chr3D 603118549 603119230 681 False 841.000000 841 89.127000 1 684 1 chr3D.!!$F2 683
6 TraesCS1D01G280600 chr3A 493096514 493097201 687 False 841.000000 841 88.889000 1 690 1 chr3A.!!$F1 689
7 TraesCS1D01G280600 chr4A 467282609 467283301 692 True 833.000000 833 88.746000 1 683 1 chr4A.!!$R1 682
8 TraesCS1D01G280600 chr7D 610766388 610767083 695 False 832.000000 832 88.575000 1 691 1 chr7D.!!$F1 690
9 TraesCS1D01G280600 chr6D 22136932 22137624 692 True 832.000000 832 88.652000 1 688 1 chr6D.!!$R1 687
10 TraesCS1D01G280600 chr5D 71885945 71886633 688 False 832.000000 832 88.636000 1 691 1 chr5D.!!$F1 690
11 TraesCS1D01G280600 chr4D 57896412 57897094 682 True 824.000000 824 88.555000 1 690 1 chr4D.!!$R1 689

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
837 896 0.114168 ATCCTCCTCCTCCATCCTCG 59.886 60.0 0.00 0.00 0.00 4.63 F
2388 2530 0.179148 TGGCTGTACGTATGCAGTCG 60.179 55.0 19.93 10.92 45.35 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2795 2940 1.066215 ACCGCTACACAATCATCAGCA 60.066 47.619 0.0 0.0 32.46 4.41 R
3738 4662 0.032678 AGATCGCAATAGCCACTCGG 59.967 55.000 0.0 0.0 37.52 4.63 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
300 317 2.029073 CACAACCGTGCCTCTCGT 59.971 61.111 0.00 0.00 36.06 4.18
663 716 2.358247 GTTGCGAGGCTCCCGAAA 60.358 61.111 9.32 0.00 0.00 3.46
691 746 3.863041 CTCCTTAACTAGTTGCTCCCAC 58.137 50.000 18.56 0.00 0.00 4.61
692 747 2.232941 TCCTTAACTAGTTGCTCCCACG 59.767 50.000 18.56 0.00 0.00 4.94
693 748 2.000447 CTTAACTAGTTGCTCCCACGC 59.000 52.381 18.56 0.00 0.00 5.34
694 749 0.970640 TAACTAGTTGCTCCCACGCA 59.029 50.000 18.56 0.00 38.31 5.24
695 750 0.602905 AACTAGTTGCTCCCACGCAC 60.603 55.000 7.48 0.00 40.09 5.34
696 751 1.741770 CTAGTTGCTCCCACGCACC 60.742 63.158 0.00 0.00 40.09 5.01
697 752 3.583276 TAGTTGCTCCCACGCACCG 62.583 63.158 0.00 0.00 40.09 4.94
828 887 1.884497 CGTCGCATCTATCCTCCTCCT 60.884 57.143 0.00 0.00 0.00 3.69
831 890 1.548809 CGCATCTATCCTCCTCCTCCA 60.549 57.143 0.00 0.00 0.00 3.86
832 891 2.831565 GCATCTATCCTCCTCCTCCAT 58.168 52.381 0.00 0.00 0.00 3.41
833 892 2.765699 GCATCTATCCTCCTCCTCCATC 59.234 54.545 0.00 0.00 0.00 3.51
834 893 3.373830 CATCTATCCTCCTCCTCCATCC 58.626 54.545 0.00 0.00 0.00 3.51
837 896 0.114168 ATCCTCCTCCTCCATCCTCG 59.886 60.000 0.00 0.00 0.00 4.63
838 897 2.206536 CCTCCTCCTCCATCCTCGC 61.207 68.421 0.00 0.00 0.00 5.03
840 899 2.519541 CCTCCTCCATCCTCGCGA 60.520 66.667 9.26 9.26 0.00 5.87
841 900 2.725008 CTCCTCCATCCTCGCGAC 59.275 66.667 3.71 0.00 0.00 5.19
843 902 1.667154 CTCCTCCATCCTCGCGACAA 61.667 60.000 3.71 0.00 0.00 3.18
1178 1251 4.459089 GCCGGTCTCCAGGTGAGC 62.459 72.222 1.90 10.23 41.18 4.26
1184 1257 1.986757 TCTCCAGGTGAGCCAGCTC 60.987 63.158 12.78 12.78 40.40 4.09
1197 1270 1.301293 CAGCTCCCTTCCCTGTTCC 59.699 63.158 0.00 0.00 0.00 3.62
1234 1337 0.599558 CTTGATGGTGGGCTGTGTTG 59.400 55.000 0.00 0.00 0.00 3.33
1470 1576 1.478288 GGATCATTTGGGCCTCTCTGG 60.478 57.143 4.53 0.00 39.35 3.86
1490 1596 8.202811 TCTCTGGTTAGATTGATTGATGAGAAG 58.797 37.037 0.00 0.00 31.21 2.85
1492 1598 5.525012 TGGTTAGATTGATTGATGAGAAGCG 59.475 40.000 0.00 0.00 0.00 4.68
1496 1602 6.154203 AGATTGATTGATGAGAAGCGTAGA 57.846 37.500 0.00 0.00 0.00 2.59
1503 1609 2.724977 TGAGAAGCGTAGAAGTGGTG 57.275 50.000 0.00 0.00 0.00 4.17
1514 1620 3.760580 AGAAGTGGTGGTTGAGAGAAG 57.239 47.619 0.00 0.00 0.00 2.85
1530 1636 2.301583 GAGAAGGCCAGTCTGTCTTTCT 59.698 50.000 13.36 7.87 0.00 2.52
1631 1737 4.565564 GGAATCATCTGCAGACAATTTTGC 59.434 41.667 20.97 10.10 40.67 3.68
1694 1804 4.800471 GCTCAAAACTTTTGAGACAGGTTG 59.200 41.667 34.03 15.86 46.57 3.77
1697 1807 6.620678 TCAAAACTTTTGAGACAGGTTGAAG 58.379 36.000 12.12 0.00 0.00 3.02
1720 1830 5.358442 AGTTAGCTGACGACTTGATATGTCT 59.642 40.000 2.59 0.00 32.70 3.41
1724 1834 4.737765 GCTGACGACTTGATATGTCTCTTC 59.262 45.833 0.00 0.00 32.70 2.87
1741 1851 6.500751 TGTCTCTTCCTAGTTAGACCCAATTT 59.499 38.462 0.00 0.00 38.04 1.82
1769 1879 2.917933 TCCAGATGTGGCTATTTTCCG 58.082 47.619 3.40 0.00 44.60 4.30
1771 1881 1.003545 CAGATGTGGCTATTTTCCGCG 60.004 52.381 0.00 0.00 36.92 6.46
1772 1882 1.014352 GATGTGGCTATTTTCCGCGT 58.986 50.000 4.92 0.00 36.92 6.01
1773 1883 1.003866 GATGTGGCTATTTTCCGCGTC 60.004 52.381 4.92 0.00 41.26 5.19
1775 1885 1.450669 TGGCTATTTTCCGCGTCCC 60.451 57.895 4.92 0.00 0.00 4.46
1776 1886 2.184830 GGCTATTTTCCGCGTCCCC 61.185 63.158 4.92 0.00 0.00 4.81
1777 1887 1.450669 GCTATTTTCCGCGTCCCCA 60.451 57.895 4.92 0.00 0.00 4.96
1779 1889 1.455248 CTATTTTCCGCGTCCCCAAA 58.545 50.000 4.92 0.00 0.00 3.28
1780 1890 1.813786 CTATTTTCCGCGTCCCCAAAA 59.186 47.619 4.92 2.65 0.00 2.44
1781 1891 1.262417 ATTTTCCGCGTCCCCAAAAT 58.738 45.000 4.92 4.91 0.00 1.82
1782 1892 1.906990 TTTTCCGCGTCCCCAAAATA 58.093 45.000 4.92 0.00 0.00 1.40
1783 1893 2.131776 TTTCCGCGTCCCCAAAATAT 57.868 45.000 4.92 0.00 0.00 1.28
1790 1900 2.486548 GCGTCCCCAAAATATAGCCTGA 60.487 50.000 0.00 0.00 0.00 3.86
1801 1911 8.295288 CCAAAATATAGCCTGAATTCAGCTTAG 58.705 37.037 27.01 15.73 42.47 2.18
1802 1912 8.844244 CAAAATATAGCCTGAATTCAGCTTAGT 58.156 33.333 27.01 17.71 42.47 2.24
1827 1937 1.550524 AGCCTGTCAGAATTAGCACGA 59.449 47.619 0.00 0.00 0.00 4.35
1831 1941 4.210120 GCCTGTCAGAATTAGCACGATTAG 59.790 45.833 0.00 0.00 0.00 1.73
1833 1943 5.460419 CCTGTCAGAATTAGCACGATTAGTC 59.540 44.000 0.00 0.00 0.00 2.59
1835 1945 5.805486 TGTCAGAATTAGCACGATTAGTCAC 59.195 40.000 0.00 0.00 0.00 3.67
1836 1946 6.037098 GTCAGAATTAGCACGATTAGTCACT 58.963 40.000 0.00 0.00 0.00 3.41
1837 1947 6.020281 GTCAGAATTAGCACGATTAGTCACTG 60.020 42.308 0.00 0.00 0.00 3.66
1852 1983 4.753233 AGTCACTGATCACTGATGCTAAC 58.247 43.478 8.10 0.00 0.00 2.34
1859 1990 5.114081 TGATCACTGATGCTAACTGTCATG 58.886 41.667 0.00 0.00 0.00 3.07
1862 1993 3.437741 CACTGATGCTAACTGTCATGCAA 59.562 43.478 0.00 0.00 38.96 4.08
1868 1999 3.120234 TGCTAACTGTCATGCAAATCACG 60.120 43.478 0.00 0.00 32.12 4.35
1872 2003 4.346734 ACTGTCATGCAAATCACGAATC 57.653 40.909 0.00 0.00 0.00 2.52
1881 2012 4.394920 TGCAAATCACGAATCTTAAGACCC 59.605 41.667 7.48 1.62 0.00 4.46
1883 2014 5.106317 GCAAATCACGAATCTTAAGACCCAA 60.106 40.000 7.48 0.00 0.00 4.12
1884 2015 6.546395 CAAATCACGAATCTTAAGACCCAAG 58.454 40.000 7.48 0.86 0.00 3.61
1885 2016 3.596214 TCACGAATCTTAAGACCCAAGC 58.404 45.455 7.48 0.00 0.00 4.01
1886 2017 2.678336 CACGAATCTTAAGACCCAAGCC 59.322 50.000 7.48 0.00 0.00 4.35
1887 2018 2.572104 ACGAATCTTAAGACCCAAGCCT 59.428 45.455 7.48 0.00 0.00 4.58
1888 2019 3.773119 ACGAATCTTAAGACCCAAGCCTA 59.227 43.478 7.48 0.00 0.00 3.93
1889 2020 4.120589 CGAATCTTAAGACCCAAGCCTAC 58.879 47.826 7.48 0.00 0.00 3.18
1890 2021 4.141914 CGAATCTTAAGACCCAAGCCTACT 60.142 45.833 7.48 0.00 0.00 2.57
1891 2022 5.068723 CGAATCTTAAGACCCAAGCCTACTA 59.931 44.000 7.48 0.00 0.00 1.82
1892 2023 6.406624 CGAATCTTAAGACCCAAGCCTACTAA 60.407 42.308 7.48 0.00 0.00 2.24
1893 2024 5.934402 TCTTAAGACCCAAGCCTACTAAG 57.066 43.478 0.00 0.00 0.00 2.18
1894 2025 4.161754 TCTTAAGACCCAAGCCTACTAAGC 59.838 45.833 0.00 0.00 0.00 3.09
1895 2026 1.952621 AGACCCAAGCCTACTAAGCA 58.047 50.000 0.00 0.00 0.00 3.91
1896 2027 2.482494 AGACCCAAGCCTACTAAGCAT 58.518 47.619 0.00 0.00 0.00 3.79
1897 2028 2.171448 AGACCCAAGCCTACTAAGCATG 59.829 50.000 0.00 0.00 0.00 4.06
1898 2029 2.170607 GACCCAAGCCTACTAAGCATGA 59.829 50.000 0.00 0.00 30.70 3.07
1899 2030 2.171448 ACCCAAGCCTACTAAGCATGAG 59.829 50.000 0.00 0.00 30.70 2.90
1900 2031 2.216898 CCAAGCCTACTAAGCATGAGC 58.783 52.381 0.00 0.00 42.56 4.26
1901 2032 2.216898 CAAGCCTACTAAGCATGAGCC 58.783 52.381 0.00 0.00 43.56 4.70
1902 2033 1.799933 AGCCTACTAAGCATGAGCCT 58.200 50.000 0.00 0.00 43.56 4.58
1904 2035 3.309296 AGCCTACTAAGCATGAGCCTAA 58.691 45.455 0.00 0.00 43.56 2.69
1906 2037 4.020662 AGCCTACTAAGCATGAGCCTAATC 60.021 45.833 0.00 0.00 43.56 1.75
1910 2041 5.620738 ACTAAGCATGAGCCTAATCTGAA 57.379 39.130 0.00 0.00 43.56 3.02
1912 2043 4.767578 AAGCATGAGCCTAATCTGAAGA 57.232 40.909 0.00 0.00 43.56 2.87
1916 2047 7.730672 AGCATGAGCCTAATCTGAAGATATA 57.269 36.000 0.00 0.00 43.56 0.86
2024 2157 3.616560 GCTCAACGAGAGGTATGTTCCAA 60.617 47.826 10.68 0.00 44.86 3.53
2029 2162 4.566987 ACGAGAGGTATGTTCCAAAGTTC 58.433 43.478 0.00 0.00 0.00 3.01
2033 2166 6.187727 AGAGGTATGTTCCAAAGTTCAGAA 57.812 37.500 0.00 0.00 0.00 3.02
2039 2172 7.595130 GGTATGTTCCAAAGTTCAGAATTTCAC 59.405 37.037 0.00 0.00 0.00 3.18
2045 2178 8.154649 TCCAAAGTTCAGAATTTCACTTCTAC 57.845 34.615 0.00 0.00 33.73 2.59
2052 2185 6.150318 TCAGAATTTCACTTCTACGACTGAC 58.850 40.000 0.00 0.00 33.73 3.51
2054 2187 6.088749 CAGAATTTCACTTCTACGACTGACAG 59.911 42.308 0.00 0.00 33.73 3.51
2094 2235 0.248907 AGTGGTCGACGTGTTCACTG 60.249 55.000 19.40 0.00 37.31 3.66
2144 2285 0.604780 CCACCAGGTTCAGTGAGCTG 60.605 60.000 6.95 10.09 43.07 4.24
2153 2294 4.609018 AGTGAGCTGTGCGCCGTT 62.609 61.111 4.18 0.00 40.39 4.44
2258 2399 1.449246 CCAGAAGCTCAAGGCCTCG 60.449 63.158 5.23 0.00 43.05 4.63
2311 2452 2.125202 AAGGTAAACCAGCAACGCGC 62.125 55.000 5.73 0.00 42.91 6.86
2334 2475 2.159421 GCACTCTGCACCATTCATTCAG 60.159 50.000 0.00 0.00 44.26 3.02
2377 2519 1.665679 CATGGTTCGATGTGGCTGTAC 59.334 52.381 0.00 0.00 0.00 2.90
2388 2530 0.179148 TGGCTGTACGTATGCAGTCG 60.179 55.000 19.93 10.92 45.35 4.18
2729 2874 0.521735 CGATCGTCCGAGGATATGCA 59.478 55.000 7.03 0.00 0.00 3.96
2795 2940 0.174162 CCGGAGATAACGTCGGGTTT 59.826 55.000 0.00 0.00 40.09 3.27
2816 2961 1.594862 GCTGATGATTGTGTAGCGGTC 59.405 52.381 0.00 0.00 0.00 4.79
2817 2962 2.739932 GCTGATGATTGTGTAGCGGTCT 60.740 50.000 0.00 0.00 0.00 3.85
2956 3108 8.040727 TGGTTCATAATTATAGGGTCGATGATG 58.959 37.037 0.00 0.00 0.00 3.07
2957 3109 8.258007 GGTTCATAATTATAGGGTCGATGATGA 58.742 37.037 0.00 0.00 0.00 2.92
2958 3110 9.823647 GTTCATAATTATAGGGTCGATGATGAT 57.176 33.333 0.00 0.00 0.00 2.45
3018 3170 6.641169 TGGATGGCATTAACGCAAATATAA 57.359 33.333 0.00 0.00 0.00 0.98
3075 3229 4.585619 ATCGAGCTTAACGAAAAAGAGC 57.414 40.909 0.00 0.00 42.80 4.09
3213 3838 4.250464 TCGACCATTTGTATGTTCCTCAC 58.750 43.478 0.00 0.00 0.00 3.51
3271 3896 3.805267 CCGACATGGCTTGCTCTC 58.195 61.111 0.00 0.00 0.00 3.20
3275 3913 2.244117 GACATGGCTTGCTCTCCGGA 62.244 60.000 2.93 2.93 0.00 5.14
3285 3923 0.105778 GCTCTCCGGAGATTCCTTGG 59.894 60.000 33.66 20.72 41.86 3.61
3299 3937 0.734889 CCTTGGTTGGCTATTCGCAG 59.265 55.000 0.00 0.00 41.67 5.18
3327 3965 2.232298 GAGTCACTTGCTCGGGGAGG 62.232 65.000 0.00 0.00 0.00 4.30
3377 4015 2.618045 CCTTGGCGGTGTTTCTATCCTT 60.618 50.000 0.00 0.00 0.00 3.36
3552 4476 7.940137 AGTAACAATCGGTAATGCCCAATAATA 59.060 33.333 0.00 0.00 0.00 0.98
3627 4551 7.996098 TTTTCTACCCCTCTGAATTTAACTG 57.004 36.000 0.00 0.00 0.00 3.16
3628 4552 5.693769 TCTACCCCTCTGAATTTAACTGG 57.306 43.478 0.00 0.00 0.00 4.00
3629 4553 3.739401 ACCCCTCTGAATTTAACTGGG 57.261 47.619 0.00 0.00 37.80 4.45
3630 4554 3.018423 CCCCTCTGAATTTAACTGGGG 57.982 52.381 0.00 0.00 45.60 4.96
3631 4555 2.311841 CCCCTCTGAATTTAACTGGGGT 59.688 50.000 6.05 0.00 45.71 4.95
3632 4556 3.356290 CCCTCTGAATTTAACTGGGGTG 58.644 50.000 0.00 0.00 0.00 4.61
3633 4557 3.356290 CCTCTGAATTTAACTGGGGTGG 58.644 50.000 0.00 0.00 0.00 4.61
3634 4558 3.356290 CTCTGAATTTAACTGGGGTGGG 58.644 50.000 0.00 0.00 0.00 4.61
3635 4559 1.824852 CTGAATTTAACTGGGGTGGGC 59.175 52.381 0.00 0.00 0.00 5.36
3636 4560 1.191535 GAATTTAACTGGGGTGGGCC 58.808 55.000 0.00 0.00 0.00 5.80
3646 4570 4.224609 GGTGGGCCCCATCATCCC 62.225 72.222 22.27 0.00 34.21 3.85
3647 4571 4.224609 GTGGGCCCCATCATCCCC 62.225 72.222 22.27 0.00 39.30 4.81
3650 4574 2.121506 GGCCCCATCATCCCCCTA 60.122 66.667 0.00 0.00 0.00 3.53
3651 4575 1.544917 GGCCCCATCATCCCCCTAT 60.545 63.158 0.00 0.00 0.00 2.57
3652 4576 1.575447 GGCCCCATCATCCCCCTATC 61.575 65.000 0.00 0.00 0.00 2.08
3653 4577 0.846427 GCCCCATCATCCCCCTATCA 60.846 60.000 0.00 0.00 0.00 2.15
3654 4578 0.995024 CCCCATCATCCCCCTATCAC 59.005 60.000 0.00 0.00 0.00 3.06
3655 4579 0.995024 CCCATCATCCCCCTATCACC 59.005 60.000 0.00 0.00 0.00 4.02
3656 4580 0.995024 CCATCATCCCCCTATCACCC 59.005 60.000 0.00 0.00 0.00 4.61
3657 4581 1.746157 CATCATCCCCCTATCACCCA 58.254 55.000 0.00 0.00 0.00 4.51
3658 4582 2.281966 CATCATCCCCCTATCACCCAT 58.718 52.381 0.00 0.00 0.00 4.00
3659 4583 2.044793 TCATCCCCCTATCACCCATC 57.955 55.000 0.00 0.00 0.00 3.51
3660 4584 1.225431 TCATCCCCCTATCACCCATCA 59.775 52.381 0.00 0.00 0.00 3.07
3661 4585 2.157801 TCATCCCCCTATCACCCATCAT 60.158 50.000 0.00 0.00 0.00 2.45
3662 4586 3.080463 TCATCCCCCTATCACCCATCATA 59.920 47.826 0.00 0.00 0.00 2.15
3663 4587 3.665135 TCCCCCTATCACCCATCATAA 57.335 47.619 0.00 0.00 0.00 1.90
3664 4588 4.175015 TCCCCCTATCACCCATCATAAT 57.825 45.455 0.00 0.00 0.00 1.28
3665 4589 4.111577 TCCCCCTATCACCCATCATAATC 58.888 47.826 0.00 0.00 0.00 1.75
3666 4590 3.203040 CCCCCTATCACCCATCATAATCC 59.797 52.174 0.00 0.00 0.00 3.01
3667 4591 3.203040 CCCCTATCACCCATCATAATCCC 59.797 52.174 0.00 0.00 0.00 3.85
3668 4592 4.114597 CCCTATCACCCATCATAATCCCT 58.885 47.826 0.00 0.00 0.00 4.20
3669 4593 5.288687 CCCTATCACCCATCATAATCCCTA 58.711 45.833 0.00 0.00 0.00 3.53
3670 4594 5.367937 CCCTATCACCCATCATAATCCCTAG 59.632 48.000 0.00 0.00 0.00 3.02
3671 4595 4.851639 ATCACCCATCATAATCCCTAGC 57.148 45.455 0.00 0.00 0.00 3.42
3672 4596 3.597182 TCACCCATCATAATCCCTAGCA 58.403 45.455 0.00 0.00 0.00 3.49
3673 4597 4.178339 TCACCCATCATAATCCCTAGCAT 58.822 43.478 0.00 0.00 0.00 3.79
3674 4598 4.225942 TCACCCATCATAATCCCTAGCATC 59.774 45.833 0.00 0.00 0.00 3.91
3675 4599 4.019051 CACCCATCATAATCCCTAGCATCA 60.019 45.833 0.00 0.00 0.00 3.07
3676 4600 4.603171 ACCCATCATAATCCCTAGCATCAA 59.397 41.667 0.00 0.00 0.00 2.57
3677 4601 4.946157 CCCATCATAATCCCTAGCATCAAC 59.054 45.833 0.00 0.00 0.00 3.18
3678 4602 5.280882 CCCATCATAATCCCTAGCATCAACT 60.281 44.000 0.00 0.00 0.00 3.16
3679 4603 6.243900 CCATCATAATCCCTAGCATCAACTT 58.756 40.000 0.00 0.00 0.00 2.66
3680 4604 6.718454 CCATCATAATCCCTAGCATCAACTTT 59.282 38.462 0.00 0.00 0.00 2.66
3681 4605 7.232127 CCATCATAATCCCTAGCATCAACTTTT 59.768 37.037 0.00 0.00 0.00 2.27
3682 4606 8.636213 CATCATAATCCCTAGCATCAACTTTTT 58.364 33.333 0.00 0.00 0.00 1.94
3724 4648 9.798994 AACCTTTTGTAGATGTAGTATTACTCG 57.201 33.333 0.00 0.00 0.00 4.18
3725 4649 8.411683 ACCTTTTGTAGATGTAGTATTACTCGG 58.588 37.037 0.00 0.00 0.00 4.63
3726 4650 7.866393 CCTTTTGTAGATGTAGTATTACTCGGG 59.134 40.741 0.00 0.00 0.00 5.14
3727 4651 7.886629 TTTGTAGATGTAGTATTACTCGGGT 57.113 36.000 0.00 0.00 0.00 5.28
3728 4652 8.978874 TTTGTAGATGTAGTATTACTCGGGTA 57.021 34.615 0.00 0.00 0.00 3.69
3729 4653 8.978874 TTGTAGATGTAGTATTACTCGGGTAA 57.021 34.615 10.95 10.95 41.42 2.85
3730 4654 9.578576 TTGTAGATGTAGTATTACTCGGGTAAT 57.421 33.333 23.46 23.46 46.54 1.89
3731 4655 9.006839 TGTAGATGTAGTATTACTCGGGTAATG 57.993 37.037 27.30 0.00 45.11 1.90
3732 4656 6.921914 AGATGTAGTATTACTCGGGTAATGC 58.078 40.000 27.30 25.57 45.11 3.56
3733 4657 5.458041 TGTAGTATTACTCGGGTAATGCC 57.542 43.478 27.30 18.09 45.60 4.40
3743 4667 2.134092 GGTAATGCCCTAGCCGAGT 58.866 57.895 0.00 0.00 38.69 4.18
3744 4668 0.249911 GGTAATGCCCTAGCCGAGTG 60.250 60.000 0.00 0.00 38.69 3.51
3745 4669 0.249911 GTAATGCCCTAGCCGAGTGG 60.250 60.000 0.00 0.00 38.69 4.00
3755 4679 4.758692 CCGAGTGGCTATTGCGAT 57.241 55.556 0.00 0.00 40.82 4.58
3756 4680 2.522060 CCGAGTGGCTATTGCGATC 58.478 57.895 0.00 0.00 40.82 3.69
3757 4681 0.032678 CCGAGTGGCTATTGCGATCT 59.967 55.000 0.00 0.00 40.82 2.75
3758 4682 1.269723 CCGAGTGGCTATTGCGATCTA 59.730 52.381 0.00 0.00 40.82 1.98
3759 4683 2.320367 CGAGTGGCTATTGCGATCTAC 58.680 52.381 0.00 0.00 40.82 2.59
3760 4684 2.287608 CGAGTGGCTATTGCGATCTACA 60.288 50.000 0.00 0.00 40.82 2.74
3761 4685 3.717707 GAGTGGCTATTGCGATCTACAA 58.282 45.455 0.00 1.10 40.82 2.41
3762 4686 4.119862 GAGTGGCTATTGCGATCTACAAA 58.880 43.478 2.60 0.00 40.82 2.83
3763 4687 4.122776 AGTGGCTATTGCGATCTACAAAG 58.877 43.478 2.60 3.80 40.82 2.77
3764 4688 3.871594 GTGGCTATTGCGATCTACAAAGT 59.128 43.478 2.60 0.00 40.82 2.66
3765 4689 4.025647 GTGGCTATTGCGATCTACAAAGTC 60.026 45.833 2.60 4.53 40.82 3.01
3766 4690 4.141937 TGGCTATTGCGATCTACAAAGTCT 60.142 41.667 2.60 0.00 40.82 3.24
3767 4691 4.811557 GGCTATTGCGATCTACAAAGTCTT 59.188 41.667 2.60 0.00 40.82 3.01
3768 4692 5.983720 GGCTATTGCGATCTACAAAGTCTTA 59.016 40.000 2.60 0.00 40.82 2.10
3798 4722 1.947456 GGTGTTTGTCAGTGTCCCTTC 59.053 52.381 0.00 0.00 0.00 3.46
3809 4733 3.053826 AGTGTCCCTTCCCTAAACTGTT 58.946 45.455 0.00 0.00 0.00 3.16
3866 4790 5.137403 CGTACAATCAAAGAAACAAGACGG 58.863 41.667 0.00 0.00 0.00 4.79
3881 4805 0.645868 GACGGCTAGTGTGATTTCGC 59.354 55.000 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
300 317 1.134220 AGAGTCACGGTTTTGCTTCCA 60.134 47.619 0.00 0.00 0.00 3.53
491 529 4.021229 CCCCCGGTATTTCTTAGCTTTTT 58.979 43.478 0.00 0.00 0.00 1.94
505 543 1.702182 GTTTTGGTTTTCCCCCGGTA 58.298 50.000 0.00 0.00 39.73 4.02
537 575 3.446799 GTTTTCGGCTTTTTAAACGGGT 58.553 40.909 0.00 0.00 0.00 5.28
673 726 2.000447 GCGTGGGAGCAACTAGTTAAG 59.000 52.381 8.04 0.00 37.05 1.85
828 887 1.215382 CTGTTGTCGCGAGGATGGA 59.785 57.895 10.24 0.00 0.00 3.41
831 890 1.291877 GCAACTGTTGTCGCGAGGAT 61.292 55.000 20.57 0.00 0.00 3.24
832 891 1.954146 GCAACTGTTGTCGCGAGGA 60.954 57.895 20.57 0.00 0.00 3.71
833 892 2.551270 GCAACTGTTGTCGCGAGG 59.449 61.111 20.57 0.00 0.00 4.63
837 896 2.722188 GCACGCAACTGTTGTCGC 60.722 61.111 25.72 19.58 34.92 5.19
838 897 1.368019 CAGCACGCAACTGTTGTCG 60.368 57.895 24.82 24.82 36.65 4.35
840 899 1.656818 AAGCAGCACGCAACTGTTGT 61.657 50.000 20.57 0.11 46.13 3.32
841 900 0.931662 GAAGCAGCACGCAACTGTTG 60.932 55.000 15.98 15.98 46.13 3.33
843 902 2.885676 CGAAGCAGCACGCAACTGT 61.886 57.895 0.00 0.00 46.13 3.55
996 1068 0.253327 GGGCAGATCTTTCCGGTCTT 59.747 55.000 0.00 0.00 0.00 3.01
998 1070 1.153147 GGGGCAGATCTTTCCGGTC 60.153 63.158 0.00 0.00 0.00 4.79
1044 1117 4.473520 ATGGCCGAAGTCCCAGCG 62.474 66.667 0.00 0.00 34.01 5.18
1175 1248 2.690510 AGGGAAGGGAGCTGGCTC 60.691 66.667 13.56 13.56 42.04 4.70
1178 1251 1.301293 GAACAGGGAAGGGAGCTGG 59.699 63.158 0.00 0.00 0.00 4.85
1184 1257 0.329596 CAGAAGGGAACAGGGAAGGG 59.670 60.000 0.00 0.00 0.00 3.95
1470 1576 6.595772 ACGCTTCTCATCAATCAATCTAAC 57.404 37.500 0.00 0.00 0.00 2.34
1490 1596 1.000506 TCTCAACCACCACTTCTACGC 59.999 52.381 0.00 0.00 0.00 4.42
1492 1598 4.561105 CTTCTCTCAACCACCACTTCTAC 58.439 47.826 0.00 0.00 0.00 2.59
1496 1602 1.202818 GCCTTCTCTCAACCACCACTT 60.203 52.381 0.00 0.00 0.00 3.16
1503 1609 0.980423 AGACTGGCCTTCTCTCAACC 59.020 55.000 3.32 0.00 0.00 3.77
1514 1620 3.239861 CCAGAAAGACAGACTGGCC 57.760 57.895 4.14 0.00 43.32 5.36
1530 1636 3.668115 ACTATTATCTCTAGAGGGGGCCA 59.332 47.826 19.67 0.00 0.00 5.36
1533 1639 4.027437 GCCACTATTATCTCTAGAGGGGG 58.973 52.174 19.67 13.32 30.30 5.40
1589 1695 0.451783 CAGCAATCTAACAACCGGGC 59.548 55.000 6.32 0.00 0.00 6.13
1631 1737 3.747010 GCTGTGAGCTGATCTATTGGATG 59.253 47.826 0.00 0.00 38.45 3.51
1632 1738 4.005487 GCTGTGAGCTGATCTATTGGAT 57.995 45.455 0.00 0.00 38.45 3.41
1690 1800 3.027974 AGTCGTCAGCTAACTTCAACC 57.972 47.619 0.00 0.00 0.00 3.77
1694 1804 6.037098 ACATATCAAGTCGTCAGCTAACTTC 58.963 40.000 0.00 0.00 31.04 3.01
1697 1807 5.583495 AGACATATCAAGTCGTCAGCTAAC 58.417 41.667 0.00 0.00 40.84 2.34
1720 1830 6.481643 CCAAAATTGGGTCTAACTAGGAAGA 58.518 40.000 4.18 0.00 44.70 2.87
1748 1858 3.480470 CGGAAAATAGCCACATCTGGAT 58.520 45.455 0.00 0.00 40.55 3.41
1750 1860 1.334869 GCGGAAAATAGCCACATCTGG 59.665 52.381 0.00 0.00 41.13 3.86
1769 1879 1.880027 CAGGCTATATTTTGGGGACGC 59.120 52.381 0.00 0.00 0.00 5.19
1771 1881 5.833131 TGAATTCAGGCTATATTTTGGGGAC 59.167 40.000 3.38 0.00 0.00 4.46
1772 1882 6.024563 TGAATTCAGGCTATATTTTGGGGA 57.975 37.500 3.38 0.00 0.00 4.81
1773 1883 5.279156 GCTGAATTCAGGCTATATTTTGGGG 60.279 44.000 31.41 6.69 43.94 4.96
1775 1885 6.645790 AGCTGAATTCAGGCTATATTTTGG 57.354 37.500 31.41 7.70 43.94 3.28
1776 1886 8.844244 ACTAAGCTGAATTCAGGCTATATTTTG 58.156 33.333 31.41 17.31 43.94 2.44
1777 1887 8.986929 ACTAAGCTGAATTCAGGCTATATTTT 57.013 30.769 31.41 16.70 43.94 1.82
1779 1889 9.094578 TCTACTAAGCTGAATTCAGGCTATATT 57.905 33.333 31.41 17.53 43.94 1.28
1780 1890 8.657387 TCTACTAAGCTGAATTCAGGCTATAT 57.343 34.615 31.41 17.80 43.94 0.86
1781 1891 8.478775 TTCTACTAAGCTGAATTCAGGCTATA 57.521 34.615 31.41 20.42 43.94 1.31
1782 1892 6.985653 TCTACTAAGCTGAATTCAGGCTAT 57.014 37.500 31.41 20.40 43.94 2.97
1783 1893 6.791867 TTCTACTAAGCTGAATTCAGGCTA 57.208 37.500 31.41 15.23 43.94 3.93
1801 1911 5.064071 GTGCTAATTCTGACAGGCTTTCTAC 59.936 44.000 1.81 0.00 0.00 2.59
1802 1912 5.178797 GTGCTAATTCTGACAGGCTTTCTA 58.821 41.667 1.81 0.00 0.00 2.10
1803 1913 4.006319 GTGCTAATTCTGACAGGCTTTCT 58.994 43.478 1.81 0.00 0.00 2.52
1809 1919 5.352284 ACTAATCGTGCTAATTCTGACAGG 58.648 41.667 1.81 0.00 0.00 4.00
1827 1937 5.611128 AGCATCAGTGATCAGTGACTAAT 57.389 39.130 30.78 15.52 42.90 1.73
1831 1941 4.565962 CAGTTAGCATCAGTGATCAGTGAC 59.434 45.833 30.78 20.59 42.90 3.67
1833 1943 4.502016 ACAGTTAGCATCAGTGATCAGTG 58.498 43.478 22.38 22.38 0.00 3.66
1835 1945 4.752146 TGACAGTTAGCATCAGTGATCAG 58.248 43.478 1.56 0.00 0.00 2.90
1836 1946 4.806640 TGACAGTTAGCATCAGTGATCA 57.193 40.909 1.56 0.00 0.00 2.92
1837 1947 4.025061 GCATGACAGTTAGCATCAGTGATC 60.025 45.833 1.56 0.00 0.00 2.92
1852 1983 4.611310 AGATTCGTGATTTGCATGACAG 57.389 40.909 0.00 0.00 42.06 3.51
1859 1990 4.394920 TGGGTCTTAAGATTCGTGATTTGC 59.605 41.667 8.75 0.00 0.00 3.68
1862 1993 4.636206 GCTTGGGTCTTAAGATTCGTGATT 59.364 41.667 8.75 0.00 0.00 2.57
1868 1999 5.360649 AGTAGGCTTGGGTCTTAAGATTC 57.639 43.478 8.75 4.88 0.00 2.52
1872 2003 4.081087 TGCTTAGTAGGCTTGGGTCTTAAG 60.081 45.833 5.79 0.00 0.00 1.85
1881 2012 2.158842 AGGCTCATGCTTAGTAGGCTTG 60.159 50.000 12.39 12.39 41.60 4.01
1883 2014 1.799933 AGGCTCATGCTTAGTAGGCT 58.200 50.000 5.79 0.63 39.77 4.58
1884 2015 3.753294 TTAGGCTCATGCTTAGTAGGC 57.247 47.619 0.00 0.00 39.59 3.93
1885 2016 5.244851 TCAGATTAGGCTCATGCTTAGTAGG 59.755 44.000 0.00 0.00 39.59 3.18
1886 2017 6.338214 TCAGATTAGGCTCATGCTTAGTAG 57.662 41.667 0.00 0.00 39.59 2.57
1887 2018 6.551227 TCTTCAGATTAGGCTCATGCTTAGTA 59.449 38.462 0.00 0.00 39.59 1.82
1888 2019 5.365025 TCTTCAGATTAGGCTCATGCTTAGT 59.635 40.000 0.00 0.00 39.59 2.24
1889 2020 5.851720 TCTTCAGATTAGGCTCATGCTTAG 58.148 41.667 0.00 0.00 39.59 2.18
1890 2021 5.876651 TCTTCAGATTAGGCTCATGCTTA 57.123 39.130 0.00 0.00 39.59 3.09
1891 2022 4.767578 TCTTCAGATTAGGCTCATGCTT 57.232 40.909 0.00 0.00 39.59 3.91
1892 2023 4.978438 ATCTTCAGATTAGGCTCATGCT 57.022 40.909 0.00 0.00 39.59 3.79
1893 2024 8.961294 ATTATATCTTCAGATTAGGCTCATGC 57.039 34.615 0.00 0.00 36.05 4.06
1916 2047 6.471146 GGGATCTGCAGATACATACAGAATT 58.529 40.000 34.51 9.21 42.08 2.17
2024 2157 7.169982 CAGTCGTAGAAGTGAAATTCTGAACTT 59.830 37.037 3.39 0.00 39.81 2.66
2029 2162 5.920840 TGTCAGTCGTAGAAGTGAAATTCTG 59.079 40.000 3.39 0.00 39.81 3.02
2033 2166 5.455056 ACTGTCAGTCGTAGAAGTGAAAT 57.545 39.130 0.00 0.00 39.69 2.17
2039 2172 5.359716 ACTGTAACTGTCAGTCGTAGAAG 57.640 43.478 5.82 1.85 41.52 2.85
2094 2235 1.678970 CAGCTTTGGTGGGGCTACC 60.679 63.158 4.80 4.80 41.24 3.18
2153 2294 4.360405 GGCTTCCCGGGCTCCAAA 62.360 66.667 18.49 2.92 0.00 3.28
2258 2399 1.153997 GTCCTGGAGCGACTCGTTC 60.154 63.158 6.74 6.74 36.42 3.95
2267 2408 1.138661 CTCTTGATGGAGTCCTGGAGC 59.861 57.143 11.33 0.00 0.00 4.70
2334 2475 2.080286 TCCTGAGCTTTTCTGTACGC 57.920 50.000 0.00 0.00 0.00 4.42
2377 2519 1.828832 GACTTCTCCGACTGCATACG 58.171 55.000 5.83 5.83 0.00 3.06
2388 2530 2.202676 CGCAGCTCCGACTTCTCC 60.203 66.667 0.00 0.00 0.00 3.71
2718 2863 3.303593 GCTTCAACACATGCATATCCTCG 60.304 47.826 0.00 0.00 0.00 4.63
2729 2874 1.597742 ACGAGCAAGCTTCAACACAT 58.402 45.000 0.00 0.00 0.00 3.21
2795 2940 1.066215 ACCGCTACACAATCATCAGCA 60.066 47.619 0.00 0.00 32.46 4.41
2816 2961 8.880750 CATTATATCCACAGCACAATCATAGAG 58.119 37.037 0.00 0.00 0.00 2.43
2817 2962 8.596293 TCATTATATCCACAGCACAATCATAGA 58.404 33.333 0.00 0.00 0.00 1.98
2956 3108 8.547967 TTTTCATCGTTCCCTATATAAGCATC 57.452 34.615 0.00 0.00 0.00 3.91
2957 3109 9.520515 AATTTTCATCGTTCCCTATATAAGCAT 57.479 29.630 0.00 0.00 0.00 3.79
2958 3110 8.783093 CAATTTTCATCGTTCCCTATATAAGCA 58.217 33.333 0.00 0.00 0.00 3.91
3213 3838 6.017933 GCAAATGTCACGATAGAAGAAACAG 58.982 40.000 0.00 0.00 41.38 3.16
3265 3890 0.826715 CAAGGAATCTCCGGAGAGCA 59.173 55.000 35.72 16.84 42.75 4.26
3266 3891 0.105778 CCAAGGAATCTCCGGAGAGC 59.894 60.000 35.72 28.56 42.75 4.09
3269 3894 1.407437 CCAACCAAGGAATCTCCGGAG 60.407 57.143 26.32 26.32 42.75 4.63
3271 3896 1.032114 GCCAACCAAGGAATCTCCGG 61.032 60.000 0.00 0.00 42.75 5.14
3275 3913 3.545703 CGAATAGCCAACCAAGGAATCT 58.454 45.455 0.00 0.00 0.00 2.40
3299 3937 2.545946 GAGCAAGTGACTCCAACTTCAC 59.454 50.000 0.00 0.00 42.17 3.18
3327 3965 3.555956 ACAAACTGTCATCGTTGTCACTC 59.444 43.478 0.00 0.00 0.00 3.51
3377 4015 2.005606 AAGACCCACACATGCCACCA 62.006 55.000 0.00 0.00 0.00 4.17
3438 4092 3.759618 CCTGGCTAATTACGGAAAACCAA 59.240 43.478 0.00 0.00 0.00 3.67
3439 4093 3.244981 ACCTGGCTAATTACGGAAAACCA 60.245 43.478 0.00 0.00 0.00 3.67
3447 4101 7.787725 AAAGAGAATTACCTGGCTAATTACG 57.212 36.000 11.62 0.00 0.00 3.18
3508 4163 3.675467 ACTTGAACTTGAACGTCTTGC 57.325 42.857 0.00 0.00 0.00 4.01
3552 4476 9.574516 ACATTTGTAATTCTTTGAAGGTCTAGT 57.425 29.630 0.00 0.00 0.00 2.57
3601 4525 9.025041 CAGTTAAATTCAGAGGGGTAGAAAATT 57.975 33.333 0.00 0.00 0.00 1.82
3602 4526 7.615757 CCAGTTAAATTCAGAGGGGTAGAAAAT 59.384 37.037 0.00 0.00 0.00 1.82
3603 4527 6.946009 CCAGTTAAATTCAGAGGGGTAGAAAA 59.054 38.462 0.00 0.00 0.00 2.29
3604 4528 6.481643 CCAGTTAAATTCAGAGGGGTAGAAA 58.518 40.000 0.00 0.00 0.00 2.52
3605 4529 5.045140 CCCAGTTAAATTCAGAGGGGTAGAA 60.045 44.000 0.00 0.00 0.00 2.10
3606 4530 4.473559 CCCAGTTAAATTCAGAGGGGTAGA 59.526 45.833 0.00 0.00 0.00 2.59
3607 4531 4.781934 CCCAGTTAAATTCAGAGGGGTAG 58.218 47.826 0.00 0.00 0.00 3.18
3608 4532 4.855298 CCCAGTTAAATTCAGAGGGGTA 57.145 45.455 0.00 0.00 0.00 3.69
3609 4533 3.739401 CCCAGTTAAATTCAGAGGGGT 57.261 47.619 0.00 0.00 0.00 4.95
3611 4535 3.356290 CACCCCAGTTAAATTCAGAGGG 58.644 50.000 0.00 0.00 39.33 4.30
3612 4536 3.356290 CCACCCCAGTTAAATTCAGAGG 58.644 50.000 0.00 0.00 0.00 3.69
3613 4537 3.356290 CCCACCCCAGTTAAATTCAGAG 58.644 50.000 0.00 0.00 0.00 3.35
3614 4538 2.556559 GCCCACCCCAGTTAAATTCAGA 60.557 50.000 0.00 0.00 0.00 3.27
3615 4539 1.824852 GCCCACCCCAGTTAAATTCAG 59.175 52.381 0.00 0.00 0.00 3.02
3616 4540 1.551329 GGCCCACCCCAGTTAAATTCA 60.551 52.381 0.00 0.00 0.00 2.57
3617 4541 1.191535 GGCCCACCCCAGTTAAATTC 58.808 55.000 0.00 0.00 0.00 2.17
3618 4542 3.392066 GGCCCACCCCAGTTAAATT 57.608 52.632 0.00 0.00 0.00 1.82
3629 4553 4.224609 GGGATGATGGGGCCCACC 62.225 72.222 31.54 24.43 41.64 4.61
3630 4554 4.224609 GGGGATGATGGGGCCCAC 62.225 72.222 31.54 21.91 43.89 4.61
3632 4556 3.829311 TAGGGGGATGATGGGGCCC 62.829 68.421 18.17 18.17 41.28 5.80
3633 4557 1.544917 ATAGGGGGATGATGGGGCC 60.545 63.158 0.00 0.00 0.00 5.80
3634 4558 0.846427 TGATAGGGGGATGATGGGGC 60.846 60.000 0.00 0.00 0.00 5.80
3635 4559 0.995024 GTGATAGGGGGATGATGGGG 59.005 60.000 0.00 0.00 0.00 4.96
3636 4560 0.995024 GGTGATAGGGGGATGATGGG 59.005 60.000 0.00 0.00 0.00 4.00
3637 4561 0.995024 GGGTGATAGGGGGATGATGG 59.005 60.000 0.00 0.00 0.00 3.51
3638 4562 1.746157 TGGGTGATAGGGGGATGATG 58.254 55.000 0.00 0.00 0.00 3.07
3639 4563 2.157801 TGATGGGTGATAGGGGGATGAT 60.158 50.000 0.00 0.00 0.00 2.45
3640 4564 1.225431 TGATGGGTGATAGGGGGATGA 59.775 52.381 0.00 0.00 0.00 2.92
3641 4565 1.746157 TGATGGGTGATAGGGGGATG 58.254 55.000 0.00 0.00 0.00 3.51
3642 4566 2.769011 ATGATGGGTGATAGGGGGAT 57.231 50.000 0.00 0.00 0.00 3.85
3643 4567 3.665135 TTATGATGGGTGATAGGGGGA 57.335 47.619 0.00 0.00 0.00 4.81
3644 4568 3.203040 GGATTATGATGGGTGATAGGGGG 59.797 52.174 0.00 0.00 0.00 5.40
3645 4569 3.203040 GGGATTATGATGGGTGATAGGGG 59.797 52.174 0.00 0.00 0.00 4.79
3646 4570 4.114597 AGGGATTATGATGGGTGATAGGG 58.885 47.826 0.00 0.00 0.00 3.53
3647 4571 5.163258 GCTAGGGATTATGATGGGTGATAGG 60.163 48.000 0.00 0.00 0.00 2.57
3648 4572 5.426509 TGCTAGGGATTATGATGGGTGATAG 59.573 44.000 0.00 0.00 0.00 2.08
3649 4573 5.349690 TGCTAGGGATTATGATGGGTGATA 58.650 41.667 0.00 0.00 0.00 2.15
3650 4574 4.178339 TGCTAGGGATTATGATGGGTGAT 58.822 43.478 0.00 0.00 0.00 3.06
3651 4575 3.597182 TGCTAGGGATTATGATGGGTGA 58.403 45.455 0.00 0.00 0.00 4.02
3652 4576 4.019051 TGATGCTAGGGATTATGATGGGTG 60.019 45.833 0.00 0.00 0.00 4.61
3653 4577 4.178339 TGATGCTAGGGATTATGATGGGT 58.822 43.478 0.00 0.00 0.00 4.51
3654 4578 4.849813 TGATGCTAGGGATTATGATGGG 57.150 45.455 0.00 0.00 0.00 4.00
3655 4579 5.813383 AGTTGATGCTAGGGATTATGATGG 58.187 41.667 0.00 0.00 0.00 3.51
3656 4580 7.756395 AAAGTTGATGCTAGGGATTATGATG 57.244 36.000 0.00 0.00 0.00 3.07
3657 4581 8.773033 AAAAAGTTGATGCTAGGGATTATGAT 57.227 30.769 0.00 0.00 0.00 2.45
3698 4622 9.798994 CGAGTAATACTACATCTACAAAAGGTT 57.201 33.333 0.00 0.00 0.00 3.50
3699 4623 8.411683 CCGAGTAATACTACATCTACAAAAGGT 58.588 37.037 0.00 0.00 0.00 3.50
3700 4624 7.866393 CCCGAGTAATACTACATCTACAAAAGG 59.134 40.741 0.00 0.00 0.00 3.11
3701 4625 8.411683 ACCCGAGTAATACTACATCTACAAAAG 58.588 37.037 0.00 0.00 0.00 2.27
3702 4626 8.297470 ACCCGAGTAATACTACATCTACAAAA 57.703 34.615 0.00 0.00 0.00 2.44
3703 4627 7.886629 ACCCGAGTAATACTACATCTACAAA 57.113 36.000 0.00 0.00 0.00 2.83
3704 4628 8.978874 TTACCCGAGTAATACTACATCTACAA 57.021 34.615 0.00 0.00 33.45 2.41
3705 4629 9.006839 CATTACCCGAGTAATACTACATCTACA 57.993 37.037 1.66 0.00 45.46 2.74
3706 4630 7.967303 GCATTACCCGAGTAATACTACATCTAC 59.033 40.741 1.66 0.00 45.46 2.59
3707 4631 7.121759 GGCATTACCCGAGTAATACTACATCTA 59.878 40.741 1.66 0.00 45.46 1.98
3708 4632 6.071503 GGCATTACCCGAGTAATACTACATCT 60.072 42.308 1.66 0.00 45.46 2.90
3709 4633 6.098017 GGCATTACCCGAGTAATACTACATC 58.902 44.000 1.66 0.00 45.46 3.06
3710 4634 6.034161 GGCATTACCCGAGTAATACTACAT 57.966 41.667 1.66 0.00 45.46 2.29
3711 4635 5.458041 GGCATTACCCGAGTAATACTACA 57.542 43.478 1.66 0.00 45.46 2.74
3725 4649 0.249911 CACTCGGCTAGGGCATTACC 60.250 60.000 0.00 0.00 40.87 2.85
3726 4650 0.249911 CCACTCGGCTAGGGCATTAC 60.250 60.000 0.00 0.00 40.87 1.89
3727 4651 2.133195 CCACTCGGCTAGGGCATTA 58.867 57.895 0.00 0.00 40.87 1.90
3728 4652 2.911143 CCACTCGGCTAGGGCATT 59.089 61.111 0.00 0.00 40.87 3.56
3738 4662 0.032678 AGATCGCAATAGCCACTCGG 59.967 55.000 0.00 0.00 37.52 4.63
3739 4663 2.287608 TGTAGATCGCAATAGCCACTCG 60.288 50.000 0.00 0.00 37.52 4.18
3740 4664 3.371102 TGTAGATCGCAATAGCCACTC 57.629 47.619 0.00 0.00 37.52 3.51
3741 4665 3.819564 TTGTAGATCGCAATAGCCACT 57.180 42.857 2.35 0.00 37.52 4.00
3742 4666 3.871594 ACTTTGTAGATCGCAATAGCCAC 59.128 43.478 6.59 0.00 37.52 5.01
3743 4667 4.119862 GACTTTGTAGATCGCAATAGCCA 58.880 43.478 6.59 0.00 37.52 4.75
3744 4668 4.372656 AGACTTTGTAGATCGCAATAGCC 58.627 43.478 6.59 2.11 37.52 3.93
3745 4669 5.975410 AAGACTTTGTAGATCGCAATAGC 57.025 39.130 6.59 0.00 37.42 2.97
3748 4672 9.935241 ATCATATAAGACTTTGTAGATCGCAAT 57.065 29.630 6.59 0.00 0.00 3.56
3749 4673 9.196552 CATCATATAAGACTTTGTAGATCGCAA 57.803 33.333 0.00 2.35 0.00 4.85
3750 4674 8.576442 TCATCATATAAGACTTTGTAGATCGCA 58.424 33.333 0.00 0.00 0.00 5.10
3751 4675 8.972262 TCATCATATAAGACTTTGTAGATCGC 57.028 34.615 0.00 0.00 0.00 4.58
3755 4679 9.987272 CACCATCATCATATAAGACTTTGTAGA 57.013 33.333 0.00 0.00 0.00 2.59
3756 4680 9.770097 ACACCATCATCATATAAGACTTTGTAG 57.230 33.333 0.00 0.00 0.00 2.74
3758 4682 9.466497 AAACACCATCATCATATAAGACTTTGT 57.534 29.630 0.00 0.00 0.00 2.83
3759 4683 9.726232 CAAACACCATCATCATATAAGACTTTG 57.274 33.333 0.00 0.00 0.00 2.77
3760 4684 9.466497 ACAAACACCATCATCATATAAGACTTT 57.534 29.630 0.00 0.00 0.00 2.66
3761 4685 9.113838 GACAAACACCATCATCATATAAGACTT 57.886 33.333 0.00 0.00 0.00 3.01
3762 4686 8.267183 TGACAAACACCATCATCATATAAGACT 58.733 33.333 0.00 0.00 0.00 3.24
3763 4687 8.437360 TGACAAACACCATCATCATATAAGAC 57.563 34.615 0.00 0.00 0.00 3.01
3764 4688 8.267183 ACTGACAAACACCATCATCATATAAGA 58.733 33.333 0.00 0.00 0.00 2.10
3765 4689 8.340443 CACTGACAAACACCATCATCATATAAG 58.660 37.037 0.00 0.00 0.00 1.73
3766 4690 7.828717 ACACTGACAAACACCATCATCATATAA 59.171 33.333 0.00 0.00 0.00 0.98
3767 4691 7.337938 ACACTGACAAACACCATCATCATATA 58.662 34.615 0.00 0.00 0.00 0.86
3768 4692 6.182627 ACACTGACAAACACCATCATCATAT 58.817 36.000 0.00 0.00 0.00 1.78
3809 4733 2.941720 GCTTGAAAATTGCACCAAACCA 59.058 40.909 0.00 0.00 0.00 3.67
3866 4790 5.914085 AATATGAGCGAAATCACACTAGC 57.086 39.130 0.00 0.00 30.46 3.42


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

AutoCloner maintained by Alex Coulton.