Multiple sequence alignment - TraesCS2B01G224200

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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 TraesCS2B01G224200 chr2B 100.000 3646 0 0 1 3646 214285955 214289600 0.000000e+00 6734.0
1 TraesCS2B01G224200 chr2B 89.855 138 13 1 1824 1960 40860459 40860596 3.740000e-40 176.0
2 TraesCS2B01G224200 chr2A 93.243 1835 89 22 1 1823 166258808 166260619 0.000000e+00 2669.0
3 TraesCS2B01G224200 chr2A 91.890 1640 112 14 2016 3646 166260665 166262292 0.000000e+00 2272.0
4 TraesCS2B01G224200 chr2A 83.740 123 17 3 3131 3251 33493196 33493075 2.980000e-21 113.0
5 TraesCS2B01G224200 chr2D 94.426 1525 52 12 1 1509 156596839 156598346 0.000000e+00 2314.0
6 TraesCS2B01G224200 chr2D 94.490 853 40 5 2016 2866 156600584 156601431 0.000000e+00 1308.0
7 TraesCS2B01G224200 chr2D 88.665 397 22 9 2867 3240 156601967 156602363 2.560000e-126 462.0
8 TraesCS2B01G224200 chr2D 93.158 190 11 2 1524 1713 156598625 156598812 9.970000e-71 278.0
9 TraesCS2B01G224200 chr2D 91.241 137 12 0 1824 1960 102911726 102911862 1.730000e-43 187.0
10 TraesCS2B01G224200 chr2D 92.373 118 9 0 1706 1823 156600421 156600538 6.260000e-38 169.0
11 TraesCS2B01G224200 chr6B 97.842 139 3 0 1822 1960 25666852 25666990 1.310000e-59 241.0
12 TraesCS2B01G224200 chr6B 85.366 123 15 3 3131 3251 475703493 475703372 1.370000e-24 124.0
13 TraesCS2B01G224200 chr4D 96.241 133 5 0 1828 1960 324466807 324466939 6.130000e-53 219.0
14 TraesCS2B01G224200 chr4D 86.325 117 15 1 1824 1939 93834431 93834547 3.820000e-25 126.0
15 TraesCS2B01G224200 chr3D 94.286 140 8 0 1821 1960 11432262 11432123 7.930000e-52 215.0
16 TraesCS2B01G224200 chr3D 86.179 123 13 3 3132 3251 517551484 517551363 2.950000e-26 130.0
17 TraesCS2B01G224200 chr7B 84.167 120 18 1 3133 3251 284962003 284961884 8.270000e-22 115.0
18 TraesCS2B01G224200 chr5A 83.740 123 17 3 3131 3251 359024543 359024422 2.980000e-21 113.0
19 TraesCS2B01G224200 chr4B 83.740 123 17 3 3131 3251 110179592 110179713 2.980000e-21 113.0
20 TraesCS2B01G224200 chr1B 82.927 123 18 3 3131 3251 47679110 47678989 1.380000e-19 108.0
21 TraesCS2B01G224200 chr7A 95.833 48 2 0 1823 1870 736516410 736516457 1.090000e-10 78.7


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 TraesCS2B01G224200 chr2B 214285955 214289600 3645 False 6734.0 6734 100.0000 1 3646 1 chr2B.!!$F2 3645
1 TraesCS2B01G224200 chr2A 166258808 166262292 3484 False 2470.5 2669 92.5665 1 3646 2 chr2A.!!$F1 3645
2 TraesCS2B01G224200 chr2D 156596839 156602363 5524 False 906.2 2314 92.6224 1 3240 5 chr2D.!!$F2 3239

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
827 836 0.106719 AATGATACGTGGGCCTTGGG 60.107 55.0 4.53 0.0 0.0 4.12 F
1892 3794 0.040942 ACTGCAAATACCATGGCCCA 59.959 50.0 13.04 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 3836 0.033090 GTACGATGGATTCCCCGTCC 59.967 60.0 19.2 8.49 46.17 4.79 R
3329 5796 0.392998 GGCATCATCGTTCCACCACT 60.393 55.0 0.0 0.00 0.00 4.00 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
28 29 1.818060 GCACTTGGCATACATGTCCAA 59.182 47.619 14.79 14.79 43.97 3.53
56 57 0.923729 TAGCCACCCCACCATCCATT 60.924 55.000 0.00 0.00 0.00 3.16
207 208 3.989698 AACACCTCGAGCGCATCCG 62.990 63.158 11.47 10.55 37.57 4.18
610 611 2.983192 TGTAGTTGTTGGGGAGGAATGA 59.017 45.455 0.00 0.00 0.00 2.57
824 833 0.179056 CCGAATGATACGTGGGCCTT 60.179 55.000 4.53 0.00 0.00 4.35
827 836 0.106719 AATGATACGTGGGCCTTGGG 60.107 55.000 4.53 0.00 0.00 4.12
902 913 0.802607 CGAAGCGTAGAGTGGAAGGC 60.803 60.000 0.00 0.00 0.00 4.35
912 926 0.469892 AGTGGAAGGCAAACCAAGGG 60.470 55.000 0.00 0.00 37.94 3.95
916 930 2.440385 GAAGGCAAACCAAGGGCAGC 62.440 60.000 0.00 0.00 39.06 5.25
934 948 2.103373 AGCAGCGACTTCTTCTCCATA 58.897 47.619 0.00 0.00 0.00 2.74
935 949 2.100584 AGCAGCGACTTCTTCTCCATAG 59.899 50.000 0.00 0.00 0.00 2.23
936 950 2.159170 GCAGCGACTTCTTCTCCATAGT 60.159 50.000 0.00 0.00 0.00 2.12
937 951 3.443037 CAGCGACTTCTTCTCCATAGTG 58.557 50.000 0.00 0.00 0.00 2.74
940 954 2.761208 CGACTTCTTCTCCATAGTGGGT 59.239 50.000 0.00 0.00 38.32 4.51
941 955 3.429547 CGACTTCTTCTCCATAGTGGGTG 60.430 52.174 0.00 0.00 38.32 4.61
992 1006 0.747283 GAGCGGGAGGTAGACGAAGA 60.747 60.000 0.00 0.00 43.00 2.87
1206 1220 3.966543 CCCCCACCCGTCTGCTTT 61.967 66.667 0.00 0.00 0.00 3.51
1246 1261 5.336770 CGATTGGATTGGATCGGATCTTAGA 60.337 44.000 16.96 2.51 40.94 2.10
1265 1280 2.291043 CCCTACTGCTTCCACCCGT 61.291 63.158 0.00 0.00 0.00 5.28
1301 1317 6.371809 TTTATTCCAGCATCGGTGAATTAC 57.628 37.500 0.00 0.00 32.22 1.89
1320 1339 9.483489 TGAATTACAACTCTTGATACCTACCTA 57.517 33.333 0.00 0.00 0.00 3.08
1361 1380 2.844966 CTCCCTCATGGATGATATGCCT 59.155 50.000 0.00 0.00 44.07 4.75
1368 1387 0.520404 GGATGATATGCCTTGCTGCG 59.480 55.000 0.00 0.00 0.00 5.18
1383 1402 4.451150 GCGTCCGCCTCCATGACA 62.451 66.667 0.00 0.00 34.56 3.58
1384 1403 2.501128 CGTCCGCCTCCATGACAT 59.499 61.111 0.00 0.00 0.00 3.06
1409 1428 1.852067 GCCCGTATTTGCCATAGCCG 61.852 60.000 0.00 0.00 38.69 5.52
1410 1429 0.250124 CCCGTATTTGCCATAGCCGA 60.250 55.000 0.00 0.00 38.69 5.54
1411 1430 0.865769 CCGTATTTGCCATAGCCGAC 59.134 55.000 0.00 0.00 38.69 4.79
1412 1431 1.540363 CCGTATTTGCCATAGCCGACT 60.540 52.381 0.00 0.00 38.69 4.18
1413 1432 1.792949 CGTATTTGCCATAGCCGACTC 59.207 52.381 0.00 0.00 38.69 3.36
1414 1433 2.143925 GTATTTGCCATAGCCGACTCC 58.856 52.381 0.00 0.00 38.69 3.85
1415 1434 0.179018 ATTTGCCATAGCCGACTCCC 60.179 55.000 0.00 0.00 38.69 4.30
1416 1435 1.558167 TTTGCCATAGCCGACTCCCA 61.558 55.000 0.00 0.00 38.69 4.37
1417 1436 1.344953 TTGCCATAGCCGACTCCCAT 61.345 55.000 0.00 0.00 38.69 4.00
1418 1437 1.344953 TGCCATAGCCGACTCCCATT 61.345 55.000 0.00 0.00 38.69 3.16
1419 1438 0.685097 GCCATAGCCGACTCCCATTA 59.315 55.000 0.00 0.00 0.00 1.90
1420 1439 1.279271 GCCATAGCCGACTCCCATTAT 59.721 52.381 0.00 0.00 0.00 1.28
1421 1440 2.678190 GCCATAGCCGACTCCCATTATC 60.678 54.545 0.00 0.00 0.00 1.75
1585 1868 6.419116 GCAGTTCTCTTGCCTAAAAAGAAAAG 59.581 38.462 0.00 0.00 33.40 2.27
1673 1959 4.908601 TCCTTTATCTCTTCTTGGCACA 57.091 40.909 0.00 0.00 0.00 4.57
1674 1960 4.579869 TCCTTTATCTCTTCTTGGCACAC 58.420 43.478 0.00 0.00 39.29 3.82
1677 1963 2.936919 ATCTCTTCTTGGCACACACA 57.063 45.000 0.00 0.00 39.29 3.72
1689 1975 1.526986 GCACACACACGTCGATAATGC 60.527 52.381 0.00 0.00 0.00 3.56
1704 1990 7.095397 CGTCGATAATGCATTTTTAGGGATGTA 60.095 37.037 18.75 0.00 0.00 2.29
1707 1993 9.559958 CGATAATGCATTTTTAGGGATGTATTC 57.440 33.333 18.75 0.00 38.75 1.75
1759 3661 3.253432 GTGCTTCCGGTCTCAAGAAAAAT 59.747 43.478 0.00 0.00 0.00 1.82
1764 3666 6.128007 GCTTCCGGTCTCAAGAAAAATGAATA 60.128 38.462 0.00 0.00 0.00 1.75
1765 3667 7.574967 GCTTCCGGTCTCAAGAAAAATGAATAA 60.575 37.037 0.00 0.00 0.00 1.40
1823 3725 5.470098 TCTCTTGCCTCACAAAATAGACAAC 59.530 40.000 0.00 0.00 37.96 3.32
1825 3727 3.734463 TGCCTCACAAAATAGACAACGA 58.266 40.909 0.00 0.00 0.00 3.85
1826 3728 4.130857 TGCCTCACAAAATAGACAACGAA 58.869 39.130 0.00 0.00 0.00 3.85
1827 3729 4.576873 TGCCTCACAAAATAGACAACGAAA 59.423 37.500 0.00 0.00 0.00 3.46
1828 3730 4.909880 GCCTCACAAAATAGACAACGAAAC 59.090 41.667 0.00 0.00 0.00 2.78
1829 3731 5.277828 GCCTCACAAAATAGACAACGAAACT 60.278 40.000 0.00 0.00 0.00 2.66
1830 3732 6.136071 CCTCACAAAATAGACAACGAAACTG 58.864 40.000 0.00 0.00 0.00 3.16
1831 3733 5.507077 TCACAAAATAGACAACGAAACTGC 58.493 37.500 0.00 0.00 0.00 4.40
1832 3734 5.295787 TCACAAAATAGACAACGAAACTGCT 59.704 36.000 0.00 0.00 0.00 4.24
1833 3735 5.621228 CACAAAATAGACAACGAAACTGCTC 59.379 40.000 0.00 0.00 0.00 4.26
1834 3736 5.527582 ACAAAATAGACAACGAAACTGCTCT 59.472 36.000 0.00 0.00 0.00 4.09
1835 3737 5.597813 AAATAGACAACGAAACTGCTCTG 57.402 39.130 0.00 0.00 0.00 3.35
1836 3738 1.221414 AGACAACGAAACTGCTCTGC 58.779 50.000 0.00 0.00 0.00 4.26
1837 3739 0.937304 GACAACGAAACTGCTCTGCA 59.063 50.000 0.00 0.00 36.92 4.41
1838 3740 1.532868 GACAACGAAACTGCTCTGCAT 59.467 47.619 0.00 0.00 38.13 3.96
1839 3741 2.736721 GACAACGAAACTGCTCTGCATA 59.263 45.455 0.00 0.00 38.13 3.14
1840 3742 2.480419 ACAACGAAACTGCTCTGCATAC 59.520 45.455 0.00 0.00 38.13 2.39
1841 3743 1.350193 ACGAAACTGCTCTGCATACG 58.650 50.000 0.00 0.00 38.13 3.06
1842 3744 1.067846 ACGAAACTGCTCTGCATACGA 60.068 47.619 0.00 0.00 38.13 3.43
1843 3745 2.196749 CGAAACTGCTCTGCATACGAT 58.803 47.619 0.00 0.00 38.13 3.73
1844 3746 2.604914 CGAAACTGCTCTGCATACGATT 59.395 45.455 0.00 0.00 38.13 3.34
1845 3747 3.302092 CGAAACTGCTCTGCATACGATTC 60.302 47.826 0.00 0.00 38.13 2.52
1846 3748 2.967599 ACTGCTCTGCATACGATTCA 57.032 45.000 0.00 0.00 38.13 2.57
1847 3749 3.465742 ACTGCTCTGCATACGATTCAT 57.534 42.857 0.00 0.00 38.13 2.57
1848 3750 3.801698 ACTGCTCTGCATACGATTCATT 58.198 40.909 0.00 0.00 38.13 2.57
1849 3751 4.194640 ACTGCTCTGCATACGATTCATTT 58.805 39.130 0.00 0.00 38.13 2.32
1850 3752 4.637534 ACTGCTCTGCATACGATTCATTTT 59.362 37.500 0.00 0.00 38.13 1.82
1851 3753 5.160699 TGCTCTGCATACGATTCATTTTC 57.839 39.130 0.00 0.00 31.71 2.29
1852 3754 4.035558 TGCTCTGCATACGATTCATTTTCC 59.964 41.667 0.00 0.00 31.71 3.13
1853 3755 4.274459 GCTCTGCATACGATTCATTTTCCT 59.726 41.667 0.00 0.00 0.00 3.36
1854 3756 5.559799 GCTCTGCATACGATTCATTTTCCTC 60.560 44.000 0.00 0.00 0.00 3.71
1855 3757 4.507756 TCTGCATACGATTCATTTTCCTCG 59.492 41.667 0.00 0.00 37.17 4.63
1856 3758 4.188462 TGCATACGATTCATTTTCCTCGT 58.812 39.130 0.00 1.91 45.40 4.18
1857 3759 5.353111 TGCATACGATTCATTTTCCTCGTA 58.647 37.500 6.17 6.17 46.71 3.43
1858 3760 5.233476 TGCATACGATTCATTTTCCTCGTAC 59.767 40.000 5.88 0.00 45.85 3.67
1859 3761 5.609696 GCATACGATTCATTTTCCTCGTACG 60.610 44.000 9.53 9.53 45.85 3.67
1860 3762 2.601763 ACGATTCATTTTCCTCGTACGC 59.398 45.455 11.24 0.00 42.07 4.42
1861 3763 2.858344 CGATTCATTTTCCTCGTACGCT 59.142 45.455 11.24 0.00 0.00 5.07
1862 3764 3.301835 CGATTCATTTTCCTCGTACGCTG 60.302 47.826 11.24 5.75 0.00 5.18
1863 3765 2.004583 TCATTTTCCTCGTACGCTGG 57.995 50.000 11.24 14.99 0.00 4.85
1864 3766 1.274167 TCATTTTCCTCGTACGCTGGT 59.726 47.619 20.81 5.09 0.00 4.00
1865 3767 2.492881 TCATTTTCCTCGTACGCTGGTA 59.507 45.455 20.81 12.59 0.00 3.25
1866 3768 2.352503 TTTTCCTCGTACGCTGGTAC 57.647 50.000 20.81 0.00 44.50 3.34
1874 3776 2.728368 GTACGCTGGTACGACTAGAC 57.272 55.000 0.00 0.00 39.64 2.59
1875 3777 2.275318 GTACGCTGGTACGACTAGACT 58.725 52.381 0.00 0.00 39.64 3.24
1876 3778 1.085091 ACGCTGGTACGACTAGACTG 58.915 55.000 0.00 0.00 36.70 3.51
1877 3779 0.248134 CGCTGGTACGACTAGACTGC 60.248 60.000 0.00 0.00 34.06 4.40
1878 3780 0.809385 GCTGGTACGACTAGACTGCA 59.191 55.000 0.00 0.00 0.00 4.41
1879 3781 1.201647 GCTGGTACGACTAGACTGCAA 59.798 52.381 0.00 0.00 0.00 4.08
1880 3782 2.352421 GCTGGTACGACTAGACTGCAAA 60.352 50.000 0.00 0.00 0.00 3.68
1881 3783 3.676324 GCTGGTACGACTAGACTGCAAAT 60.676 47.826 0.00 0.00 0.00 2.32
1882 3784 4.439700 GCTGGTACGACTAGACTGCAAATA 60.440 45.833 0.00 0.00 0.00 1.40
1883 3785 4.990257 TGGTACGACTAGACTGCAAATAC 58.010 43.478 0.00 0.00 0.00 1.89
1884 3786 4.142315 TGGTACGACTAGACTGCAAATACC 60.142 45.833 0.00 0.00 0.00 2.73
1885 3787 4.142315 GGTACGACTAGACTGCAAATACCA 60.142 45.833 0.00 0.00 31.72 3.25
1886 3788 4.737855 ACGACTAGACTGCAAATACCAT 57.262 40.909 0.00 0.00 0.00 3.55
1887 3789 4.433615 ACGACTAGACTGCAAATACCATG 58.566 43.478 0.00 0.00 0.00 3.66
1888 3790 3.804325 CGACTAGACTGCAAATACCATGG 59.196 47.826 11.19 11.19 0.00 3.66
1889 3791 3.545703 ACTAGACTGCAAATACCATGGC 58.454 45.455 13.04 0.00 0.00 4.40
1890 3792 1.767759 AGACTGCAAATACCATGGCC 58.232 50.000 13.04 0.00 0.00 5.36
1891 3793 0.746659 GACTGCAAATACCATGGCCC 59.253 55.000 13.04 0.00 0.00 5.80
1892 3794 0.040942 ACTGCAAATACCATGGCCCA 59.959 50.000 13.04 0.00 0.00 5.36
1893 3795 0.461135 CTGCAAATACCATGGCCCAC 59.539 55.000 13.04 0.00 0.00 4.61
1894 3796 0.251967 TGCAAATACCATGGCCCACA 60.252 50.000 13.04 0.00 0.00 4.17
1895 3797 0.901124 GCAAATACCATGGCCCACAA 59.099 50.000 13.04 0.00 0.00 3.33
1896 3798 1.277557 GCAAATACCATGGCCCACAAA 59.722 47.619 13.04 0.00 0.00 2.83
1897 3799 2.934801 GCAAATACCATGGCCCACAAAC 60.935 50.000 13.04 0.00 0.00 2.93
1898 3800 2.566724 CAAATACCATGGCCCACAAACT 59.433 45.455 13.04 0.00 0.00 2.66
1899 3801 1.851304 ATACCATGGCCCACAAACTG 58.149 50.000 13.04 0.00 0.00 3.16
1900 3802 0.774276 TACCATGGCCCACAAACTGA 59.226 50.000 13.04 0.00 0.00 3.41
1901 3803 0.105760 ACCATGGCCCACAAACTGAA 60.106 50.000 13.04 0.00 0.00 3.02
1902 3804 1.269012 CCATGGCCCACAAACTGAAT 58.731 50.000 0.00 0.00 0.00 2.57
1903 3805 1.205417 CCATGGCCCACAAACTGAATC 59.795 52.381 0.00 0.00 0.00 2.52
1904 3806 1.894466 CATGGCCCACAAACTGAATCA 59.106 47.619 0.00 0.00 0.00 2.57
1905 3807 1.327303 TGGCCCACAAACTGAATCAC 58.673 50.000 0.00 0.00 0.00 3.06
1906 3808 0.603065 GGCCCACAAACTGAATCACC 59.397 55.000 0.00 0.00 0.00 4.02
1907 3809 1.327303 GCCCACAAACTGAATCACCA 58.673 50.000 0.00 0.00 0.00 4.17
1908 3810 1.686052 GCCCACAAACTGAATCACCAA 59.314 47.619 0.00 0.00 0.00 3.67
1909 3811 2.288395 GCCCACAAACTGAATCACCAAG 60.288 50.000 0.00 0.00 0.00 3.61
1910 3812 2.297033 CCCACAAACTGAATCACCAAGG 59.703 50.000 0.00 0.00 0.00 3.61
1911 3813 3.221771 CCACAAACTGAATCACCAAGGA 58.778 45.455 0.00 0.00 0.00 3.36
1912 3814 3.828451 CCACAAACTGAATCACCAAGGAT 59.172 43.478 0.00 0.00 0.00 3.24
1913 3815 4.281688 CCACAAACTGAATCACCAAGGATT 59.718 41.667 0.00 0.00 40.10 3.01
1914 3816 5.221501 CCACAAACTGAATCACCAAGGATTT 60.222 40.000 0.00 0.00 37.61 2.17
1915 3817 5.693104 CACAAACTGAATCACCAAGGATTTG 59.307 40.000 0.00 0.00 37.61 2.32
1916 3818 5.363580 ACAAACTGAATCACCAAGGATTTGT 59.636 36.000 0.00 0.00 37.61 2.83
1917 3819 5.712152 AACTGAATCACCAAGGATTTGTC 57.288 39.130 0.00 0.00 37.61 3.18
1918 3820 4.990526 ACTGAATCACCAAGGATTTGTCT 58.009 39.130 0.00 0.00 37.61 3.41
1919 3821 5.006386 ACTGAATCACCAAGGATTTGTCTC 58.994 41.667 0.00 0.00 37.61 3.36
1920 3822 5.222007 ACTGAATCACCAAGGATTTGTCTCT 60.222 40.000 0.00 0.00 37.61 3.10
1921 3823 6.013379 ACTGAATCACCAAGGATTTGTCTCTA 60.013 38.462 0.00 0.00 37.61 2.43
1922 3824 6.778821 TGAATCACCAAGGATTTGTCTCTAA 58.221 36.000 0.00 0.00 37.61 2.10
1923 3825 7.405292 TGAATCACCAAGGATTTGTCTCTAAT 58.595 34.615 0.00 0.00 37.61 1.73
1924 3826 7.554118 TGAATCACCAAGGATTTGTCTCTAATC 59.446 37.037 0.00 0.00 37.61 1.75
1925 3827 5.419542 TCACCAAGGATTTGTCTCTAATCG 58.580 41.667 0.00 0.00 33.73 3.34
1926 3828 5.046591 TCACCAAGGATTTGTCTCTAATCGT 60.047 40.000 0.00 0.00 33.73 3.73
1927 3829 6.153851 TCACCAAGGATTTGTCTCTAATCGTA 59.846 38.462 0.00 0.00 33.73 3.43
1928 3830 6.255887 CACCAAGGATTTGTCTCTAATCGTAC 59.744 42.308 0.00 0.00 33.73 3.67
1929 3831 5.459107 CCAAGGATTTGTCTCTAATCGTACG 59.541 44.000 9.53 9.53 33.73 3.67
1930 3832 5.831702 AGGATTTGTCTCTAATCGTACGT 57.168 39.130 16.05 0.00 33.73 3.57
1931 3833 5.579718 AGGATTTGTCTCTAATCGTACGTG 58.420 41.667 16.05 4.73 33.73 4.49
1932 3834 5.125097 AGGATTTGTCTCTAATCGTACGTGT 59.875 40.000 16.05 6.92 33.73 4.49
1933 3835 5.803967 GGATTTGTCTCTAATCGTACGTGTT 59.196 40.000 16.05 13.58 33.73 3.32
1934 3836 6.237490 GGATTTGTCTCTAATCGTACGTGTTG 60.237 42.308 16.05 5.69 33.73 3.33
1935 3837 4.087510 TGTCTCTAATCGTACGTGTTGG 57.912 45.455 16.05 13.07 0.00 3.77
1936 3838 3.752747 TGTCTCTAATCGTACGTGTTGGA 59.247 43.478 16.05 16.22 0.00 3.53
1937 3839 4.094212 GTCTCTAATCGTACGTGTTGGAC 58.906 47.826 16.05 13.13 0.00 4.02
1945 3847 3.884900 CGTGTTGGACGGGGAATC 58.115 61.111 0.00 0.00 44.85 2.52
1946 3848 1.743995 CGTGTTGGACGGGGAATCC 60.744 63.158 0.00 0.00 44.85 3.01
1947 3849 1.377229 GTGTTGGACGGGGAATCCA 59.623 57.895 0.09 0.00 44.74 3.41
1948 3850 0.034477 GTGTTGGACGGGGAATCCAT 60.034 55.000 0.09 0.00 45.71 3.41
1949 3851 0.254747 TGTTGGACGGGGAATCCATC 59.745 55.000 0.09 0.00 45.71 3.51
1950 3852 0.814010 GTTGGACGGGGAATCCATCG 60.814 60.000 11.57 11.57 45.71 3.84
1951 3853 1.268992 TTGGACGGGGAATCCATCGT 61.269 55.000 17.12 17.12 45.71 3.73
1952 3854 0.397394 TGGACGGGGAATCCATCGTA 60.397 55.000 17.12 3.54 41.47 3.43
1953 3855 0.033090 GGACGGGGAATCCATCGTAC 59.967 60.000 17.12 14.77 35.76 3.67
1954 3856 0.318445 GACGGGGAATCCATCGTACG 60.318 60.000 17.12 9.53 35.76 3.67
1955 3857 1.039233 ACGGGGAATCCATCGTACGT 61.039 55.000 16.05 6.80 34.42 3.57
1956 3858 0.953727 CGGGGAATCCATCGTACGTA 59.046 55.000 16.05 2.34 34.36 3.57
1957 3859 1.542915 CGGGGAATCCATCGTACGTAT 59.457 52.381 16.05 4.80 34.36 3.06
1958 3860 2.749076 CGGGGAATCCATCGTACGTATA 59.251 50.000 16.05 0.00 34.36 1.47
1970 3872 2.225019 CGTACGTATAGAACCATCGCCT 59.775 50.000 7.22 0.00 0.00 5.52
1979 3881 0.537143 AACCATCGCCTGAAACAGCA 60.537 50.000 0.00 0.00 0.00 4.41
1984 3886 1.098869 TCGCCTGAAACAGCAAACAA 58.901 45.000 0.00 0.00 0.00 2.83
1993 3895 4.863689 TGAAACAGCAAACAACATCAACAG 59.136 37.500 0.00 0.00 0.00 3.16
1996 3898 3.067180 ACAGCAAACAACATCAACAGAGG 59.933 43.478 0.00 0.00 0.00 3.69
1997 3899 3.067180 CAGCAAACAACATCAACAGAGGT 59.933 43.478 0.00 0.00 0.00 3.85
1998 3900 4.275689 CAGCAAACAACATCAACAGAGGTA 59.724 41.667 0.00 0.00 0.00 3.08
1999 3901 4.887071 AGCAAACAACATCAACAGAGGTAA 59.113 37.500 0.00 0.00 0.00 2.85
2000 3902 5.536161 AGCAAACAACATCAACAGAGGTAAT 59.464 36.000 0.00 0.00 0.00 1.89
2001 3903 5.630680 GCAAACAACATCAACAGAGGTAATG 59.369 40.000 0.00 0.00 0.00 1.90
2002 3904 5.964958 AACAACATCAACAGAGGTAATGG 57.035 39.130 0.00 0.00 0.00 3.16
2003 3905 4.335416 ACAACATCAACAGAGGTAATGGG 58.665 43.478 0.00 0.00 0.00 4.00
2004 3906 4.042809 ACAACATCAACAGAGGTAATGGGA 59.957 41.667 0.00 0.00 0.00 4.37
2005 3907 4.927267 ACATCAACAGAGGTAATGGGAA 57.073 40.909 0.00 0.00 0.00 3.97
2006 3908 5.255397 ACATCAACAGAGGTAATGGGAAA 57.745 39.130 0.00 0.00 0.00 3.13
2007 3909 5.831103 ACATCAACAGAGGTAATGGGAAAT 58.169 37.500 0.00 0.00 0.00 2.17
2008 3910 5.888161 ACATCAACAGAGGTAATGGGAAATC 59.112 40.000 0.00 0.00 0.00 2.17
2009 3911 4.513442 TCAACAGAGGTAATGGGAAATCG 58.487 43.478 0.00 0.00 0.00 3.34
2010 3912 4.224147 TCAACAGAGGTAATGGGAAATCGA 59.776 41.667 0.00 0.00 0.00 3.59
2011 3913 5.104527 TCAACAGAGGTAATGGGAAATCGAT 60.105 40.000 0.00 0.00 0.00 3.59
2012 3914 5.373812 ACAGAGGTAATGGGAAATCGATT 57.626 39.130 4.39 4.39 0.00 3.34
2013 3915 5.755849 ACAGAGGTAATGGGAAATCGATTT 58.244 37.500 22.93 22.93 0.00 2.17
2014 3916 5.823045 ACAGAGGTAATGGGAAATCGATTTC 59.177 40.000 33.25 33.25 44.08 2.17
2058 3961 4.887071 TGGGTAATGGGAAATCGATTTCAG 59.113 41.667 38.08 0.00 46.03 3.02
2093 3996 9.413048 GCACAGTTATATCCTGTAACTAGAATC 57.587 37.037 0.00 0.00 41.10 2.52
2121 4024 3.562141 TGTTTTGCGCGGTATGCTATTAT 59.438 39.130 8.83 0.00 43.27 1.28
2164 4067 3.307059 CCTCTCGAACTTGTGGGAAGAAT 60.307 47.826 0.00 0.00 0.00 2.40
2209 4115 4.987408 TGAACCATGATCGCAAATCAAT 57.013 36.364 0.00 0.00 0.00 2.57
2232 4138 2.946329 ACCATGCGTGTCTGTTTGTTTA 59.054 40.909 4.96 0.00 0.00 2.01
2287 4194 2.419574 GGCGACCAAAGCAGGAGTTATA 60.420 50.000 0.00 0.00 36.08 0.98
2334 4243 5.696724 AGAAAATACAGAGTGACTCGGTTTG 59.303 40.000 22.47 10.51 39.40 2.93
2350 4259 1.616865 GTTTGTAAGGGAAACTGGGCC 59.383 52.381 0.00 0.00 31.74 5.80
2380 4289 0.829333 ATGCCTGACTCTGAGCGAAT 59.171 50.000 4.19 0.00 0.00 3.34
2385 4294 2.223688 CCTGACTCTGAGCGAATACCAG 60.224 54.545 4.19 1.72 0.00 4.00
2452 4362 3.731431 TGGGGATGTGGACTACAAGTAT 58.269 45.455 0.00 0.00 43.77 2.12
2459 4369 6.095440 GGATGTGGACTACAAGTATGCAAAAT 59.905 38.462 0.00 0.00 43.77 1.82
2466 4376 8.296713 GGACTACAAGTATGCAAAATCAAAAGA 58.703 33.333 0.00 0.00 0.00 2.52
2474 4384 4.511527 TGCAAAATCAAAAGAAAGGCACA 58.488 34.783 0.00 0.00 0.00 4.57
2573 4483 4.077108 TGAACGAGAAACTAGACAGCCTA 58.923 43.478 0.00 0.00 0.00 3.93
2688 4598 2.126071 GCTAGCACGCGGAGTTGA 60.126 61.111 12.47 0.00 0.00 3.18
2757 4667 1.810151 GTGTGTTTCCTGTGTGTGTGT 59.190 47.619 0.00 0.00 0.00 3.72
2758 4668 1.809547 TGTGTTTCCTGTGTGTGTGTG 59.190 47.619 0.00 0.00 0.00 3.82
2772 4682 1.532868 GTGTGTGCAGTCAATCAGTCC 59.467 52.381 0.00 0.00 0.00 3.85
2793 4703 8.141268 CAGTCCATGTGTATGTATGTATGTACA 58.859 37.037 0.00 0.00 38.79 2.90
2794 4704 8.700973 AGTCCATGTGTATGTATGTATGTACAA 58.299 33.333 0.00 0.00 38.03 2.41
2866 4776 9.454585 TCTGTATGTTATATTACGCACAGTTAC 57.545 33.333 17.84 2.85 35.56 2.50
2933 5379 6.477360 ACGTGTAACATCCCAATTTTCAAAAC 59.523 34.615 0.00 0.00 35.74 2.43
2968 5414 6.709281 ACATGCCATTCATTTGGATGTTAAA 58.291 32.000 0.00 0.00 39.25 1.52
2978 5424 9.434420 TTCATTTGGATGTTAAAATGTCATTCC 57.566 29.630 0.00 0.00 42.06 3.01
3032 5499 9.492730 AGTTCATTGGAATAATGTTTTAGGGAT 57.507 29.630 0.00 0.00 35.05 3.85
3199 5666 4.263639 TGAGAGGAAGAAGGTGATGCAAAT 60.264 41.667 0.00 0.00 0.00 2.32
3264 5731 6.207614 GCTATCAAGGAGAAGAAAGGTTGTTT 59.792 38.462 0.00 0.00 0.00 2.83
3270 5737 5.828328 AGGAGAAGAAAGGTTGTTTGTAAGG 59.172 40.000 0.00 0.00 0.00 2.69
3272 5739 6.096423 GGAGAAGAAAGGTTGTTTGTAAGGTT 59.904 38.462 0.00 0.00 0.00 3.50
3288 5755 2.856222 AGGTTGCTTCAGAGGAGTTTG 58.144 47.619 0.00 0.00 0.00 2.93
3348 5815 0.392998 AGTGGTGGAACGATGATGCC 60.393 55.000 0.00 0.00 38.12 4.40
3368 5835 4.392921 CCTAGAAGGCGATCAAAGAGAA 57.607 45.455 0.00 0.00 0.00 2.87
3369 5836 4.367450 CCTAGAAGGCGATCAAAGAGAAG 58.633 47.826 0.00 0.00 0.00 2.85
3371 5838 4.122143 AGAAGGCGATCAAAGAGAAGAG 57.878 45.455 0.00 0.00 0.00 2.85
3372 5839 3.513515 AGAAGGCGATCAAAGAGAAGAGT 59.486 43.478 0.00 0.00 0.00 3.24
3385 5853 7.225538 TCAAAGAGAAGAGTGATTGTTTCAGAC 59.774 37.037 0.00 0.00 34.17 3.51
3419 5887 5.833667 TGGATAGGAGTGTAGACAACATAGG 59.166 44.000 0.00 0.00 41.10 2.57
3433 5901 5.253330 ACAACATAGGGAAGTACAATGTGG 58.747 41.667 0.00 0.00 31.44 4.17
3444 5912 3.821033 AGTACAATGTGGCAAAGAAGACC 59.179 43.478 0.00 0.00 0.00 3.85
3469 5937 0.233332 GCGAACTGTGAGTGAAGCAC 59.767 55.000 0.00 0.00 36.81 4.40
3470 5938 1.570813 CGAACTGTGAGTGAAGCACA 58.429 50.000 0.00 0.00 43.41 4.57
3476 5944 1.269257 TGTGAGTGAAGCACAGAGTCG 60.269 52.381 0.00 0.00 41.00 4.18
3493 5961 3.632333 AGTCGGACATATGAGAACCTCA 58.368 45.455 10.38 0.00 44.99 3.86
3495 5963 4.113354 GTCGGACATATGAGAACCTCAAC 58.887 47.826 10.38 3.11 44.04 3.18
3499 5967 4.080863 GGACATATGAGAACCTCAACCAGT 60.081 45.833 10.38 0.00 44.04 4.00
3517 5985 8.402472 TCAACCAGTGTTTAAACATGAAGTAAG 58.598 33.333 23.11 13.74 41.59 2.34
3519 5987 6.831868 ACCAGTGTTTAAACATGAAGTAAGGT 59.168 34.615 23.11 17.08 41.59 3.50
3525 5993 9.796120 TGTTTAAACATGAAGTAAGGTGAAAAG 57.204 29.630 17.01 0.00 33.17 2.27
3559 6027 1.852633 TGGCCAAGATCGAAGAGAGA 58.147 50.000 0.61 0.00 43.63 3.10
3562 6030 3.007940 TGGCCAAGATCGAAGAGAGAAAA 59.992 43.478 0.61 0.00 43.63 2.29
3582 6050 2.814805 ATGAGGGATGTCAACCAAGG 57.185 50.000 1.08 0.00 0.00 3.61
3597 6065 5.469421 TCAACCAAGGCAAATGCATAAAAAG 59.531 36.000 0.00 0.00 44.36 2.27
3608 6076 4.627611 TGCATAAAAAGCAGAGCAGATC 57.372 40.909 0.00 0.00 37.02 2.75
3609 6077 3.379372 TGCATAAAAAGCAGAGCAGATCC 59.621 43.478 0.00 0.00 37.02 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.394712 GGGTGGCTACTGCGCTGT 62.395 66.667 23.67 23.67 40.82 4.40
47 48 1.445942 CGCCGGTAGAATGGATGGT 59.554 57.895 1.90 0.00 0.00 3.55
133 134 2.967076 CGGCTATCGTTGGCGCAT 60.967 61.111 10.83 0.00 45.58 4.73
167 168 3.157252 GGGATGCTCAGGGCTCGA 61.157 66.667 0.00 0.00 42.39 4.04
326 327 2.680352 TGGACCTCGCTCCTCACC 60.680 66.667 0.00 0.00 0.00 4.02
332 333 3.071206 TGCTCCTGGACCTCGCTC 61.071 66.667 7.12 0.00 0.00 5.03
718 719 3.775654 GCCACCTCCTCACCTCCG 61.776 72.222 0.00 0.00 0.00 4.63
824 833 1.067762 CATCCTCCTATTGGGGCCCA 61.068 60.000 24.76 24.76 35.33 5.36
827 836 0.111253 CCACATCCTCCTATTGGGGC 59.889 60.000 0.00 0.00 35.33 5.80
831 840 6.678568 ATCTACTTCCACATCCTCCTATTG 57.321 41.667 0.00 0.00 0.00 1.90
902 913 2.341176 GCTGCTGCCCTTGGTTTG 59.659 61.111 3.85 0.00 0.00 2.93
912 926 1.357991 GGAGAAGAAGTCGCTGCTGC 61.358 60.000 5.34 5.34 0.00 5.25
916 930 3.443037 CACTATGGAGAAGAAGTCGCTG 58.557 50.000 0.00 0.00 0.00 5.18
983 997 3.262420 GCCATTGCTTCTTCTTCGTCTA 58.738 45.455 0.00 0.00 33.53 2.59
1206 1220 1.186200 ATCGTACTGAGGCAAGCAGA 58.814 50.000 8.67 0.00 36.86 4.26
1246 1261 2.291043 CGGGTGGAAGCAGTAGGGT 61.291 63.158 0.00 0.00 34.77 4.34
1265 1280 5.425217 TGCTGGAATAAATCACACCTAGAGA 59.575 40.000 0.00 0.00 0.00 3.10
1301 1317 6.043411 GCAAGTAGGTAGGTATCAAGAGTTG 58.957 44.000 0.00 0.00 0.00 3.16
1320 1339 2.697751 AGATCTTATCCTGAGCGCAAGT 59.302 45.455 11.47 0.00 41.68 3.16
1368 1387 0.811616 GTGATGTCATGGAGGCGGAC 60.812 60.000 0.00 0.00 0.00 4.79
1383 1402 0.751643 GGCAAATACGGGCCTGTGAT 60.752 55.000 28.18 12.88 46.74 3.06
1384 1403 1.377987 GGCAAATACGGGCCTGTGA 60.378 57.895 28.18 11.67 46.74 3.58
1409 1428 4.245845 GAGGAAGTCGATAATGGGAGTC 57.754 50.000 0.00 0.00 0.00 3.36
1534 1817 1.303309 GTCAGCAGCAAAGTCACAGT 58.697 50.000 0.00 0.00 0.00 3.55
1673 1959 4.678509 AAAATGCATTATCGACGTGTGT 57.321 36.364 13.39 0.00 0.00 3.72
1674 1960 5.676744 CCTAAAAATGCATTATCGACGTGTG 59.323 40.000 13.39 0.00 0.00 3.82
1677 1963 5.120399 TCCCTAAAAATGCATTATCGACGT 58.880 37.500 13.39 0.00 0.00 4.34
1689 1975 5.215160 GCTGCGAATACATCCCTAAAAATG 58.785 41.667 0.00 0.00 0.00 2.32
1704 1990 0.877071 CTCACAGGTTTGCTGCGAAT 59.123 50.000 5.47 0.00 0.00 3.34
1707 1993 0.167470 CATCTCACAGGTTTGCTGCG 59.833 55.000 0.00 0.00 0.00 5.18
1764 3666 7.215789 TGGTCAACAGCAAAATCACATAATTT 58.784 30.769 0.00 0.00 0.00 1.82
1765 3667 6.757237 TGGTCAACAGCAAAATCACATAATT 58.243 32.000 0.00 0.00 0.00 1.40
1823 3725 1.629013 TCGTATGCAGAGCAGTTTCG 58.371 50.000 0.00 0.60 43.65 3.46
1825 3727 3.599343 TGAATCGTATGCAGAGCAGTTT 58.401 40.909 0.00 0.00 43.65 2.66
1826 3728 3.251479 TGAATCGTATGCAGAGCAGTT 57.749 42.857 0.00 0.00 43.65 3.16
1827 3729 2.967599 TGAATCGTATGCAGAGCAGT 57.032 45.000 0.00 0.00 43.65 4.40
1828 3730 4.808077 AAATGAATCGTATGCAGAGCAG 57.192 40.909 0.00 0.00 43.65 4.24
1829 3731 4.035558 GGAAAATGAATCGTATGCAGAGCA 59.964 41.667 0.00 0.00 44.86 4.26
1830 3732 4.274459 AGGAAAATGAATCGTATGCAGAGC 59.726 41.667 0.00 0.00 0.00 4.09
1831 3733 5.332883 CGAGGAAAATGAATCGTATGCAGAG 60.333 44.000 0.00 0.00 0.00 3.35
1832 3734 4.507756 CGAGGAAAATGAATCGTATGCAGA 59.492 41.667 0.00 0.00 0.00 4.26
1833 3735 4.271049 ACGAGGAAAATGAATCGTATGCAG 59.729 41.667 0.00 0.00 45.76 4.41
1834 3736 4.188462 ACGAGGAAAATGAATCGTATGCA 58.812 39.130 0.00 0.00 45.76 3.96
1835 3737 4.795970 ACGAGGAAAATGAATCGTATGC 57.204 40.909 0.00 0.00 45.76 3.14
1838 3740 3.792956 GCGTACGAGGAAAATGAATCGTA 59.207 43.478 21.65 2.47 45.76 3.43
1840 3742 2.858344 AGCGTACGAGGAAAATGAATCG 59.142 45.455 21.65 0.00 40.86 3.34
1841 3743 3.001330 CCAGCGTACGAGGAAAATGAATC 59.999 47.826 21.65 0.00 0.00 2.52
1842 3744 2.936498 CCAGCGTACGAGGAAAATGAAT 59.064 45.455 21.65 0.00 0.00 2.57
1843 3745 2.289195 ACCAGCGTACGAGGAAAATGAA 60.289 45.455 27.19 0.00 0.00 2.57
1844 3746 1.274167 ACCAGCGTACGAGGAAAATGA 59.726 47.619 27.19 0.00 0.00 2.57
1845 3747 1.722011 ACCAGCGTACGAGGAAAATG 58.278 50.000 27.19 10.80 0.00 2.32
1846 3748 2.884827 GTACCAGCGTACGAGGAAAAT 58.115 47.619 27.19 11.99 35.81 1.82
1847 3749 2.352503 GTACCAGCGTACGAGGAAAA 57.647 50.000 27.19 13.20 35.81 2.29
1855 3757 2.030213 CAGTCTAGTCGTACCAGCGTAC 59.970 54.545 0.00 0.00 41.34 3.67
1856 3758 2.274437 CAGTCTAGTCGTACCAGCGTA 58.726 52.381 0.00 0.00 0.00 4.42
1857 3759 1.085091 CAGTCTAGTCGTACCAGCGT 58.915 55.000 0.00 0.00 0.00 5.07
1858 3760 0.248134 GCAGTCTAGTCGTACCAGCG 60.248 60.000 0.00 0.00 0.00 5.18
1859 3761 0.809385 TGCAGTCTAGTCGTACCAGC 59.191 55.000 0.00 0.00 0.00 4.85
1860 3762 3.570926 TTTGCAGTCTAGTCGTACCAG 57.429 47.619 0.00 0.00 0.00 4.00
1861 3763 4.142315 GGTATTTGCAGTCTAGTCGTACCA 60.142 45.833 0.00 0.00 31.65 3.25
1862 3764 4.142315 TGGTATTTGCAGTCTAGTCGTACC 60.142 45.833 0.00 0.00 0.00 3.34
1863 3765 4.990257 TGGTATTTGCAGTCTAGTCGTAC 58.010 43.478 0.00 0.00 0.00 3.67
1864 3766 5.451381 CCATGGTATTTGCAGTCTAGTCGTA 60.451 44.000 2.57 0.00 0.00 3.43
1865 3767 4.433615 CATGGTATTTGCAGTCTAGTCGT 58.566 43.478 0.00 0.00 0.00 4.34
1866 3768 3.804325 CCATGGTATTTGCAGTCTAGTCG 59.196 47.826 2.57 0.00 0.00 4.18
1867 3769 3.561725 GCCATGGTATTTGCAGTCTAGTC 59.438 47.826 14.67 0.00 0.00 2.59
1868 3770 3.545703 GCCATGGTATTTGCAGTCTAGT 58.454 45.455 14.67 0.00 0.00 2.57
1869 3771 2.880890 GGCCATGGTATTTGCAGTCTAG 59.119 50.000 14.67 0.00 0.00 2.43
1870 3772 2.422803 GGGCCATGGTATTTGCAGTCTA 60.423 50.000 14.67 0.00 0.00 2.59
1871 3773 1.686115 GGGCCATGGTATTTGCAGTCT 60.686 52.381 14.67 0.00 0.00 3.24
1872 3774 0.746659 GGGCCATGGTATTTGCAGTC 59.253 55.000 14.67 0.00 0.00 3.51
1873 3775 0.040942 TGGGCCATGGTATTTGCAGT 59.959 50.000 14.67 0.00 0.00 4.40
1874 3776 0.461135 GTGGGCCATGGTATTTGCAG 59.539 55.000 10.70 0.00 0.00 4.41
1875 3777 0.251967 TGTGGGCCATGGTATTTGCA 60.252 50.000 10.70 0.00 0.00 4.08
1876 3778 0.901124 TTGTGGGCCATGGTATTTGC 59.099 50.000 10.70 0.00 0.00 3.68
1877 3779 2.566724 AGTTTGTGGGCCATGGTATTTG 59.433 45.455 10.70 0.00 0.00 2.32
1878 3780 2.566724 CAGTTTGTGGGCCATGGTATTT 59.433 45.455 10.70 0.00 0.00 1.40
1879 3781 2.178580 CAGTTTGTGGGCCATGGTATT 58.821 47.619 10.70 0.00 0.00 1.89
1880 3782 1.357420 TCAGTTTGTGGGCCATGGTAT 59.643 47.619 10.70 0.00 0.00 2.73
1881 3783 0.774276 TCAGTTTGTGGGCCATGGTA 59.226 50.000 10.70 0.00 0.00 3.25
1882 3784 0.105760 TTCAGTTTGTGGGCCATGGT 60.106 50.000 10.70 0.00 0.00 3.55
1883 3785 1.205417 GATTCAGTTTGTGGGCCATGG 59.795 52.381 10.70 7.63 0.00 3.66
1884 3786 1.894466 TGATTCAGTTTGTGGGCCATG 59.106 47.619 10.70 3.01 0.00 3.66
1885 3787 1.895131 GTGATTCAGTTTGTGGGCCAT 59.105 47.619 10.70 0.00 0.00 4.40
1886 3788 1.327303 GTGATTCAGTTTGTGGGCCA 58.673 50.000 0.00 0.00 0.00 5.36
1887 3789 0.603065 GGTGATTCAGTTTGTGGGCC 59.397 55.000 0.00 0.00 0.00 5.80
1888 3790 1.327303 TGGTGATTCAGTTTGTGGGC 58.673 50.000 0.00 0.00 0.00 5.36
1889 3791 2.297033 CCTTGGTGATTCAGTTTGTGGG 59.703 50.000 0.00 0.00 0.00 4.61
1890 3792 3.221771 TCCTTGGTGATTCAGTTTGTGG 58.778 45.455 0.00 0.00 0.00 4.17
1891 3793 5.458041 AATCCTTGGTGATTCAGTTTGTG 57.542 39.130 0.00 0.00 28.88 3.33
1892 3794 5.363580 ACAAATCCTTGGTGATTCAGTTTGT 59.636 36.000 0.00 0.00 36.82 2.83
1893 3795 5.846203 ACAAATCCTTGGTGATTCAGTTTG 58.154 37.500 0.00 0.00 36.82 2.93
1894 3796 5.835280 AGACAAATCCTTGGTGATTCAGTTT 59.165 36.000 0.00 0.00 36.82 2.66
1895 3797 5.388654 AGACAAATCCTTGGTGATTCAGTT 58.611 37.500 0.00 0.00 36.82 3.16
1896 3798 4.990526 AGACAAATCCTTGGTGATTCAGT 58.009 39.130 0.00 0.00 36.82 3.41
1897 3799 5.251764 AGAGACAAATCCTTGGTGATTCAG 58.748 41.667 0.00 0.00 36.82 3.02
1898 3800 5.246981 AGAGACAAATCCTTGGTGATTCA 57.753 39.130 0.00 0.00 36.82 2.57
1899 3801 7.254590 CGATTAGAGACAAATCCTTGGTGATTC 60.255 40.741 0.00 0.00 36.82 2.52
1900 3802 6.540189 CGATTAGAGACAAATCCTTGGTGATT 59.460 38.462 0.00 0.00 36.82 2.57
1901 3803 6.051717 CGATTAGAGACAAATCCTTGGTGAT 58.948 40.000 0.00 0.00 36.82 3.06
1902 3804 5.046591 ACGATTAGAGACAAATCCTTGGTGA 60.047 40.000 0.00 0.00 36.82 4.02
1903 3805 5.178797 ACGATTAGAGACAAATCCTTGGTG 58.821 41.667 0.00 0.00 36.82 4.17
1904 3806 5.422214 ACGATTAGAGACAAATCCTTGGT 57.578 39.130 0.00 0.00 36.82 3.67
1905 3807 5.459107 CGTACGATTAGAGACAAATCCTTGG 59.541 44.000 10.44 0.00 36.82 3.61
1906 3808 6.020599 CACGTACGATTAGAGACAAATCCTTG 60.021 42.308 24.41 0.00 38.61 3.61
1907 3809 6.034591 CACGTACGATTAGAGACAAATCCTT 58.965 40.000 24.41 0.00 30.98 3.36
1908 3810 5.125097 ACACGTACGATTAGAGACAAATCCT 59.875 40.000 24.41 0.00 30.98 3.24
1909 3811 5.338365 ACACGTACGATTAGAGACAAATCC 58.662 41.667 24.41 0.00 30.98 3.01
1910 3812 6.237490 CCAACACGTACGATTAGAGACAAATC 60.237 42.308 24.41 0.00 0.00 2.17
1911 3813 5.575606 CCAACACGTACGATTAGAGACAAAT 59.424 40.000 24.41 0.00 0.00 2.32
1912 3814 4.919168 CCAACACGTACGATTAGAGACAAA 59.081 41.667 24.41 0.00 0.00 2.83
1913 3815 4.216042 TCCAACACGTACGATTAGAGACAA 59.784 41.667 24.41 0.00 0.00 3.18
1914 3816 3.752747 TCCAACACGTACGATTAGAGACA 59.247 43.478 24.41 0.00 0.00 3.41
1915 3817 4.094212 GTCCAACACGTACGATTAGAGAC 58.906 47.826 24.41 16.08 0.00 3.36
1916 3818 3.181517 CGTCCAACACGTACGATTAGAGA 60.182 47.826 24.41 8.32 44.07 3.10
1917 3819 3.096461 CGTCCAACACGTACGATTAGAG 58.904 50.000 24.41 5.97 44.07 2.43
1918 3820 3.121559 CGTCCAACACGTACGATTAGA 57.878 47.619 24.41 11.25 44.07 2.10
1929 3831 1.377229 TGGATTCCCCGTCCAACAC 59.623 57.895 0.00 0.00 42.56 3.32
1930 3832 3.908508 TGGATTCCCCGTCCAACA 58.091 55.556 0.00 0.00 42.56 3.33
1934 3836 0.033090 GTACGATGGATTCCCCGTCC 59.967 60.000 19.20 8.49 46.17 4.79
1935 3837 0.318445 CGTACGATGGATTCCCCGTC 60.318 60.000 19.20 12.22 45.58 4.79
1936 3838 1.039233 ACGTACGATGGATTCCCCGT 61.039 55.000 24.41 19.46 37.93 5.28
1937 3839 0.953727 TACGTACGATGGATTCCCCG 59.046 55.000 24.41 11.54 37.93 5.73
1938 3840 4.012374 TCTATACGTACGATGGATTCCCC 58.988 47.826 24.41 0.00 0.00 4.81
1939 3841 5.397326 GTTCTATACGTACGATGGATTCCC 58.603 45.833 24.41 4.25 0.00 3.97
1940 3842 5.048504 TGGTTCTATACGTACGATGGATTCC 60.049 44.000 24.41 19.36 0.00 3.01
1941 3843 6.005583 TGGTTCTATACGTACGATGGATTC 57.994 41.667 24.41 12.84 0.00 2.52
1942 3844 6.585695 ATGGTTCTATACGTACGATGGATT 57.414 37.500 24.41 0.00 0.00 3.01
1943 3845 5.163784 CGATGGTTCTATACGTACGATGGAT 60.164 44.000 24.41 11.52 0.00 3.41
1944 3846 4.152938 CGATGGTTCTATACGTACGATGGA 59.847 45.833 24.41 14.80 0.00 3.41
1945 3847 4.400845 CGATGGTTCTATACGTACGATGG 58.599 47.826 24.41 12.75 0.00 3.51
1946 3848 3.844657 GCGATGGTTCTATACGTACGATG 59.155 47.826 24.41 8.60 0.00 3.84
1947 3849 3.120060 GGCGATGGTTCTATACGTACGAT 60.120 47.826 24.41 13.27 0.00 3.73
1948 3850 2.224079 GGCGATGGTTCTATACGTACGA 59.776 50.000 24.41 6.04 0.00 3.43
1949 3851 2.225019 AGGCGATGGTTCTATACGTACG 59.775 50.000 15.01 15.01 0.00 3.67
1950 3852 3.251729 TCAGGCGATGGTTCTATACGTAC 59.748 47.826 0.00 0.00 0.00 3.67
1951 3853 3.479489 TCAGGCGATGGTTCTATACGTA 58.521 45.455 0.00 0.00 0.00 3.57
1952 3854 2.304092 TCAGGCGATGGTTCTATACGT 58.696 47.619 0.00 0.00 0.00 3.57
1953 3855 3.364889 TTCAGGCGATGGTTCTATACG 57.635 47.619 0.00 0.00 0.00 3.06
1954 3856 4.439057 TGTTTCAGGCGATGGTTCTATAC 58.561 43.478 0.00 0.00 0.00 1.47
1955 3857 4.693283 CTGTTTCAGGCGATGGTTCTATA 58.307 43.478 0.00 0.00 0.00 1.31
1956 3858 3.535561 CTGTTTCAGGCGATGGTTCTAT 58.464 45.455 0.00 0.00 0.00 1.98
1957 3859 2.935238 GCTGTTTCAGGCGATGGTTCTA 60.935 50.000 0.00 0.00 31.21 2.10
1958 3860 1.813513 CTGTTTCAGGCGATGGTTCT 58.186 50.000 0.00 0.00 0.00 3.01
1970 3872 4.814147 TGTTGATGTTGTTTGCTGTTTCA 58.186 34.783 0.00 0.00 0.00 2.69
1979 3881 5.243730 CCCATTACCTCTGTTGATGTTGTTT 59.756 40.000 0.00 0.00 0.00 2.83
1984 3886 4.927267 TTCCCATTACCTCTGTTGATGT 57.073 40.909 0.00 0.00 0.00 3.06
1993 3895 6.318900 AGTTGAAATCGATTTCCCATTACCTC 59.681 38.462 35.88 17.12 44.16 3.85
1996 3898 8.209917 ACTAGTTGAAATCGATTTCCCATTAC 57.790 34.615 35.88 26.33 44.16 1.89
1997 3899 8.801882 AACTAGTTGAAATCGATTTCCCATTA 57.198 30.769 35.88 24.77 44.16 1.90
1998 3900 7.393234 TGAACTAGTTGAAATCGATTTCCCATT 59.607 33.333 35.88 24.93 44.16 3.16
1999 3901 6.884295 TGAACTAGTTGAAATCGATTTCCCAT 59.116 34.615 35.88 26.15 44.16 4.00
2000 3902 6.148811 GTGAACTAGTTGAAATCGATTTCCCA 59.851 38.462 35.88 24.83 44.16 4.37
2001 3903 6.403309 GGTGAACTAGTTGAAATCGATTTCCC 60.403 42.308 35.88 28.21 44.16 3.97
2002 3904 6.403309 GGGTGAACTAGTTGAAATCGATTTCC 60.403 42.308 35.88 25.66 44.16 3.13
2003 3905 6.371825 AGGGTGAACTAGTTGAAATCGATTTC 59.628 38.462 33.94 33.94 44.83 2.17
2004 3906 6.238648 AGGGTGAACTAGTTGAAATCGATTT 58.761 36.000 22.93 22.93 0.00 2.17
2005 3907 5.805728 AGGGTGAACTAGTTGAAATCGATT 58.194 37.500 14.14 4.39 0.00 3.34
2006 3908 5.422214 AGGGTGAACTAGTTGAAATCGAT 57.578 39.130 14.14 0.00 0.00 3.59
2007 3909 4.884668 AGGGTGAACTAGTTGAAATCGA 57.115 40.909 14.14 0.00 0.00 3.59
2008 3910 5.063564 GCTAAGGGTGAACTAGTTGAAATCG 59.936 44.000 14.14 0.00 0.00 3.34
2009 3911 5.354513 GGCTAAGGGTGAACTAGTTGAAATC 59.645 44.000 14.14 0.00 0.00 2.17
2010 3912 5.222048 TGGCTAAGGGTGAACTAGTTGAAAT 60.222 40.000 14.14 0.00 0.00 2.17
2011 3913 4.103469 TGGCTAAGGGTGAACTAGTTGAAA 59.897 41.667 14.14 0.00 0.00 2.69
2012 3914 3.649023 TGGCTAAGGGTGAACTAGTTGAA 59.351 43.478 14.14 0.00 0.00 2.69
2013 3915 3.244582 TGGCTAAGGGTGAACTAGTTGA 58.755 45.455 14.14 0.39 0.00 3.18
2014 3916 3.695830 TGGCTAAGGGTGAACTAGTTG 57.304 47.619 14.14 0.00 0.00 3.16
2058 3961 5.694006 CAGGATATAACTGTGCAGAACTAGC 59.306 44.000 6.17 0.00 0.00 3.42
2093 3996 0.584396 TACCGCGCAAAACAAGTCAG 59.416 50.000 8.75 0.00 0.00 3.51
2121 4024 4.140947 AGGCTAATCAATATTCCAGGCCAA 60.141 41.667 5.01 0.00 39.48 4.52
2164 4067 5.144159 AGGTATCCAATCTACTGACTCCA 57.856 43.478 0.00 0.00 0.00 3.86
2209 4115 2.566913 ACAAACAGACACGCATGGTTA 58.433 42.857 0.00 0.00 0.00 2.85
2232 4138 3.947834 CCGAGGGTGAATAAGAAAGCAAT 59.052 43.478 0.00 0.00 0.00 3.56
2270 4177 4.650972 TTGGTATAACTCCTGCTTTGGT 57.349 40.909 0.00 0.00 0.00 3.67
2271 4178 6.152661 TGAAATTGGTATAACTCCTGCTTTGG 59.847 38.462 0.00 0.00 0.00 3.28
2327 4236 2.487625 CCCAGTTTCCCTTACAAACCGA 60.488 50.000 0.00 0.00 34.76 4.69
2334 4243 0.037160 TTCGGCCCAGTTTCCCTTAC 59.963 55.000 0.00 0.00 0.00 2.34
2350 4259 0.243636 GTCAGGCATTGGGGTTTTCG 59.756 55.000 0.00 0.00 0.00 3.46
2380 4289 5.585820 GGTTTTCCTTTTGTTCACTGGTA 57.414 39.130 0.00 0.00 36.94 3.25
2452 4362 4.511527 TGTGCCTTTCTTTTGATTTTGCA 58.488 34.783 0.00 0.00 0.00 4.08
2459 4369 1.682854 CTGCCTGTGCCTTTCTTTTGA 59.317 47.619 0.00 0.00 36.33 2.69
2466 4376 3.698040 CTGAATTATCTGCCTGTGCCTTT 59.302 43.478 0.00 0.00 36.33 3.11
2474 4384 3.686691 GCAAGGTCCTGAATTATCTGCCT 60.687 47.826 0.00 0.00 0.00 4.75
2573 4483 2.284258 ACCTCCAGCTTCCGCTCT 60.284 61.111 0.00 0.00 45.15 4.09
2757 4667 2.224597 ACACATGGACTGATTGACTGCA 60.225 45.455 0.00 0.00 0.00 4.41
2758 4668 2.430465 ACACATGGACTGATTGACTGC 58.570 47.619 0.00 0.00 0.00 4.40
2772 4682 9.528018 TGACTTGTACATACATACATACACATG 57.472 33.333 0.00 0.00 35.04 3.21
2850 4760 9.865321 TCTTCTTTTAGTAACTGTGCGTAATAT 57.135 29.630 0.00 0.00 0.00 1.28
2866 4776 4.315803 TGAGGGCGACTTTCTTCTTTTAG 58.684 43.478 0.00 0.00 0.00 1.85
2875 5320 2.396590 TGGTAATGAGGGCGACTTTC 57.603 50.000 0.00 0.00 0.00 2.62
2933 5379 5.327616 TGAATGGCATGTTAACATCCAAG 57.672 39.130 28.18 16.87 37.22 3.61
3069 5536 9.909043 AACTAAAACGCAATTTTGTAAATTCAC 57.091 25.926 6.04 0.00 40.80 3.18
3145 5612 2.801077 AATAACCCTCCCCTTCAACG 57.199 50.000 0.00 0.00 0.00 4.10
3154 5621 1.420514 GGGCACTCCTAATAACCCTCC 59.579 57.143 0.00 0.00 34.34 4.30
3199 5666 3.262151 TCACCATCTCCGTCCACATTTTA 59.738 43.478 0.00 0.00 0.00 1.52
3264 5731 2.972713 ACTCCTCTGAAGCAACCTTACA 59.027 45.455 0.00 0.00 0.00 2.41
3270 5737 1.882623 CCCAAACTCCTCTGAAGCAAC 59.117 52.381 0.00 0.00 0.00 4.17
3272 5739 0.401738 CCCCAAACTCCTCTGAAGCA 59.598 55.000 0.00 0.00 0.00 3.91
3288 5755 0.476771 TTCTTCACTTGGTCACCCCC 59.523 55.000 0.00 0.00 0.00 5.40
3306 5773 7.865385 CACTAGATATCTTTAGCTTCGCTTCTT 59.135 37.037 11.25 0.00 40.44 2.52
3329 5796 0.392998 GGCATCATCGTTCCACCACT 60.393 55.000 0.00 0.00 0.00 4.00
3348 5815 5.163561 ACTCTTCTCTTTGATCGCCTTCTAG 60.164 44.000 0.00 0.00 0.00 2.43
3357 5824 8.092521 TGAAACAATCACTCTTCTCTTTGATC 57.907 34.615 0.00 0.00 31.50 2.92
3362 5829 5.694006 CGTCTGAAACAATCACTCTTCTCTT 59.306 40.000 0.00 0.00 33.47 2.85
3363 5830 5.226396 CGTCTGAAACAATCACTCTTCTCT 58.774 41.667 0.00 0.00 33.47 3.10
3368 5835 2.037772 AGGCGTCTGAAACAATCACTCT 59.962 45.455 0.00 0.00 33.47 3.24
3369 5836 2.417719 AGGCGTCTGAAACAATCACTC 58.582 47.619 0.00 0.00 33.47 3.51
3371 5838 3.064207 TGTAGGCGTCTGAAACAATCAC 58.936 45.455 0.00 0.00 33.47 3.06
3372 5839 3.394674 TGTAGGCGTCTGAAACAATCA 57.605 42.857 0.00 0.00 36.38 2.57
3385 5853 2.230025 CACTCCTATCCAGATGTAGGCG 59.770 54.545 0.00 0.00 37.87 5.52
3419 5887 4.518970 TCTTCTTTGCCACATTGTACTTCC 59.481 41.667 0.00 0.00 0.00 3.46
3433 5901 2.801388 GCTTTGCGGTCTTCTTTGC 58.199 52.632 0.00 0.00 0.00 3.68
3469 5937 3.634448 AGGTTCTCATATGTCCGACTCTG 59.366 47.826 1.90 0.00 0.00 3.35
3470 5938 3.886505 GAGGTTCTCATATGTCCGACTCT 59.113 47.826 1.90 0.00 0.00 3.24
3476 5944 4.080863 ACTGGTTGAGGTTCTCATATGTCC 60.081 45.833 1.90 2.30 40.39 4.02
3493 5961 7.340999 ACCTTACTTCATGTTTAAACACTGGTT 59.659 33.333 22.78 10.31 42.51 3.67
3495 5963 7.012894 TCACCTTACTTCATGTTTAAACACTGG 59.987 37.037 22.78 14.98 42.51 4.00
3499 5967 9.796120 CTTTTCACCTTACTTCATGTTTAAACA 57.204 29.630 22.58 22.58 44.06 2.83
3517 5985 6.462909 CCATCTTATAAATGCCCCTTTTCACC 60.463 42.308 0.00 0.00 0.00 4.02
3519 5987 5.070313 GCCATCTTATAAATGCCCCTTTTCA 59.930 40.000 0.00 0.00 0.00 2.69
3525 5993 2.888212 TGGCCATCTTATAAATGCCCC 58.112 47.619 0.00 8.74 0.00 5.80
3559 6027 4.284234 CCTTGGTTGACATCCCTCATTTTT 59.716 41.667 0.00 0.00 0.00 1.94
3562 6030 2.885554 GCCTTGGTTGACATCCCTCATT 60.886 50.000 0.00 0.00 0.00 2.57
3582 6050 3.680937 TGCTCTGCTTTTTATGCATTTGC 59.319 39.130 3.54 3.39 39.86 3.68


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

AutoCloner maintained by Alex Coulton.