Multiple sequence alignment - TraesCS1A01G301600

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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 TraesCS1A01G301600 chr1A 100.000 4019 0 0 1 4019 495709765 495705747 0.000000e+00 7422.0
1 TraesCS1A01G301600 chr1A 96.364 110 4 0 1748 1857 351107478 351107369 8.870000e-42 182.0
2 TraesCS1A01G301600 chr1D 91.598 1702 94 20 1 1693 398983125 398981464 0.000000e+00 2305.0
3 TraesCS1A01G301600 chr1D 93.369 1478 48 12 2107 3565 398981080 398979634 0.000000e+00 2141.0
4 TraesCS1A01G301600 chr1D 89.262 149 9 5 3716 3862 398979449 398979306 3.190000e-41 180.0
5 TraesCS1A01G301600 chr1D 88.732 142 13 3 3570 3711 493221896 493221758 1.920000e-38 171.0
6 TraesCS1A01G301600 chr1D 87.413 143 12 4 1852 1991 398981319 398981180 4.160000e-35 159.0
7 TraesCS1A01G301600 chr1D 84.483 174 7 3 3866 4019 398979269 398979096 1.930000e-33 154.0
8 TraesCS1A01G301600 chr1B 93.588 811 28 8 2711 3518 534669973 534669184 0.000000e+00 1188.0
9 TraesCS1A01G301600 chr1B 92.647 816 39 9 945 1753 534671821 534671020 0.000000e+00 1155.0
10 TraesCS1A01G301600 chr1B 90.508 885 50 14 1 877 534672677 534671819 0.000000e+00 1138.0
11 TraesCS1A01G301600 chr1B 92.823 627 32 7 2062 2680 534670683 534670062 0.000000e+00 896.0
12 TraesCS1A01G301600 chr1B 94.326 141 6 2 1853 1991 534671025 534670885 8.750000e-52 215.0
13 TraesCS1A01G301600 chr1B 87.500 136 7 3 3731 3863 534669085 534668957 9.000000e-32 148.0
14 TraesCS1A01G301600 chr1B 81.443 97 4 5 3923 4019 534668896 534668814 2.590000e-07 67.6
15 TraesCS1A01G301600 chr4B 90.141 284 20 5 2202 2482 140959988 140959710 2.950000e-96 363.0
16 TraesCS1A01G301600 chr4B 88.750 240 18 2 2071 2310 140960342 140960112 6.570000e-73 285.0
17 TraesCS1A01G301600 chr4B 92.222 180 12 1 2519 2698 140959712 140959535 1.850000e-63 254.0
18 TraesCS1A01G301600 chr4B 100.000 29 0 0 2716 2744 140959538 140959510 2.000000e-03 54.7
19 TraesCS1A01G301600 chr7D 96.491 114 4 0 1741 1854 479651712 479651825 5.300000e-44 189.0
20 TraesCS1A01G301600 chr5A 92.424 132 9 1 3570 3701 622779223 622779353 1.910000e-43 187.0
21 TraesCS1A01G301600 chr5A 90.370 135 11 2 3563 3697 11038708 11038576 4.130000e-40 176.0
22 TraesCS1A01G301600 chr3A 95.652 115 5 0 1741 1855 661930646 661930760 6.860000e-43 185.0
23 TraesCS1A01G301600 chr3A 91.538 130 10 1 3570 3699 93902761 93902633 1.150000e-40 178.0
24 TraesCS1A01G301600 chr3A 88.435 147 17 0 2873 3019 589537571 589537717 1.150000e-40 178.0
25 TraesCS1A01G301600 chr5B 92.308 130 9 1 3570 3699 354290001 354290129 2.470000e-42 183.0
26 TraesCS1A01G301600 chr5B 95.575 113 5 0 1742 1854 473290739 473290851 8.870000e-42 182.0
27 TraesCS1A01G301600 chr5B 91.667 132 10 1 3570 3701 541684132 541684002 8.870000e-42 182.0
28 TraesCS1A01G301600 chr5B 94.068 118 7 0 1737 1854 697185052 697184935 3.190000e-41 180.0
29 TraesCS1A01G301600 chr5B 96.970 33 1 0 2712 2744 405505446 405505414 5.610000e-04 56.5
30 TraesCS1A01G301600 chr3D 92.308 130 9 1 3570 3699 87926022 87926150 2.470000e-42 183.0
31 TraesCS1A01G301600 chr3D 85.542 166 20 4 2873 3035 448266254 448266418 1.920000e-38 171.0
32 TraesCS1A01G301600 chr2D 95.652 115 3 2 1743 1856 404123310 404123423 2.470000e-42 183.0
33 TraesCS1A01G301600 chr2D 95.614 114 4 1 1743 1855 13492573 13492460 8.870000e-42 182.0
34 TraesCS1A01G301600 chr4A 95.575 113 5 0 1745 1857 127407659 127407771 8.870000e-42 182.0
35 TraesCS1A01G301600 chr6B 91.538 130 10 1 3570 3699 702430977 702430849 1.150000e-40 178.0
36 TraesCS1A01G301600 chr6B 92.126 127 7 3 1734 1859 715630445 715630321 4.130000e-40 176.0
37 TraesCS1A01G301600 chr2B 91.538 130 9 2 3570 3699 109974453 109974326 1.150000e-40 178.0
38 TraesCS1A01G301600 chr3B 85.542 166 20 4 2873 3035 587966480 587966644 1.920000e-38 171.0


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 TraesCS1A01G301600 chr1A 495705747 495709765 4018 True 7422.000 7422 100.00000 1 4019 1 chr1A.!!$R2 4018
1 TraesCS1A01G301600 chr1D 398979096 398983125 4029 True 987.800 2305 89.22500 1 4019 5 chr1D.!!$R2 4018
2 TraesCS1A01G301600 chr1B 534668814 534672677 3863 True 686.800 1188 90.40500 1 4019 7 chr1B.!!$R1 4018
3 TraesCS1A01G301600 chr4B 140959510 140960342 832 True 239.175 363 92.77825 2071 2744 4 chr4B.!!$R1 673

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
399 402 0.108615 ATCTCTCGGGAGCGTGTTTG 60.109 55.0 7.67 0.0 39.31 2.93 F
1737 1848 0.037734 ACCTTTTTGCGTAGAGGGGG 59.962 55.0 5.06 0.0 33.51 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1836 1947 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.0 14.79 0.04 33.41 4.30 R
3019 3601 0.247736 GTCCACGATGCAGGTCTTCT 59.752 55.0 0.00 0.00 0.00 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
70 72 0.603975 ACCTCTCGCTGCAAAAGGTC 60.604 55.000 10.11 0.00 35.42 3.85
85 87 1.674651 GGTCTGGAAACCTTCGCCC 60.675 63.158 0.00 0.00 36.32 6.13
205 207 4.481112 GCCGCCGCCATGTTTCTG 62.481 66.667 0.00 0.00 0.00 3.02
219 221 6.363473 CCATGTTTCTGTAGAGTTTTTCGTC 58.637 40.000 0.00 0.00 0.00 4.20
220 222 5.978934 TGTTTCTGTAGAGTTTTTCGTCC 57.021 39.130 0.00 0.00 0.00 4.79
221 223 4.505191 TGTTTCTGTAGAGTTTTTCGTCCG 59.495 41.667 0.00 0.00 0.00 4.79
222 224 3.996150 TCTGTAGAGTTTTTCGTCCGT 57.004 42.857 0.00 0.00 0.00 4.69
268 270 1.291132 GGTAGATCTGCGCTTTGGTC 58.709 55.000 9.73 4.81 0.00 4.02
272 274 3.976701 ATCTGCGCTTTGGTCCGGG 62.977 63.158 9.73 0.00 0.00 5.73
366 369 0.325577 GCCCCTTGGGGTGATTTGAT 60.326 55.000 24.38 0.00 44.57 2.57
393 396 1.009449 GTTCGATCTCTCGGGAGCG 60.009 63.158 7.67 6.72 45.10 5.03
394 397 1.451567 TTCGATCTCTCGGGAGCGT 60.452 57.895 7.67 0.00 45.10 5.07
395 398 1.715862 TTCGATCTCTCGGGAGCGTG 61.716 60.000 7.67 0.00 45.10 5.34
396 399 2.473760 CGATCTCTCGGGAGCGTGT 61.474 63.158 7.67 0.00 41.27 4.49
397 400 1.810532 GATCTCTCGGGAGCGTGTT 59.189 57.895 7.67 0.00 39.31 3.32
398 401 0.173708 GATCTCTCGGGAGCGTGTTT 59.826 55.000 7.67 0.00 39.31 2.83
399 402 0.108615 ATCTCTCGGGAGCGTGTTTG 60.109 55.000 7.67 0.00 39.31 2.93
427 436 1.408474 CGTCGCCGCTAGGTTGTTAC 61.408 60.000 0.00 0.00 40.50 2.50
428 437 0.108945 GTCGCCGCTAGGTTGTTACT 60.109 55.000 0.00 0.00 40.50 2.24
429 438 0.604578 TCGCCGCTAGGTTGTTACTT 59.395 50.000 0.00 0.00 40.50 2.24
430 439 0.719465 CGCCGCTAGGTTGTTACTTG 59.281 55.000 0.00 0.00 40.50 3.16
431 440 1.804601 GCCGCTAGGTTGTTACTTGT 58.195 50.000 0.00 0.00 40.50 3.16
432 441 2.148768 GCCGCTAGGTTGTTACTTGTT 58.851 47.619 0.00 0.00 40.50 2.83
433 442 3.328505 GCCGCTAGGTTGTTACTTGTTA 58.671 45.455 0.00 0.00 40.50 2.41
449 458 8.768019 GTTACTTGTTAGGTTATTCACGTTCTT 58.232 33.333 0.00 0.00 0.00 2.52
482 491 6.577800 CGCACGTAAAATTATTTGGTGTTGTA 59.422 34.615 13.98 0.00 36.98 2.41
487 496 9.228636 CGTAAAATTATTTGGTGTTGTATAGGC 57.771 33.333 0.00 0.00 0.00 3.93
566 579 0.378962 GGATCAGTCGTCCAGTCTCG 59.621 60.000 0.00 0.00 35.76 4.04
630 643 2.153913 GAATCGATGCGGGGATTCG 58.846 57.895 0.00 0.00 39.18 3.34
634 647 1.951130 CGATGCGGGGATTCGACAG 60.951 63.158 0.00 0.00 34.92 3.51
662 675 4.567159 GGCAATTGTGTACTAGTGAGCTAC 59.433 45.833 5.39 0.00 0.00 3.58
664 677 6.405508 GGCAATTGTGTACTAGTGAGCTACTA 60.406 42.308 5.39 0.00 40.89 1.82
671 684 9.021807 TGTGTACTAGTGAGCTACTATTTCTTT 57.978 33.333 5.39 0.00 40.94 2.52
677 690 9.296400 CTAGTGAGCTACTATTTCTTTTCTCAC 57.704 37.037 10.11 10.11 45.50 3.51
716 729 5.010012 AGTTGCTGTTTACTTTGATCCCTTG 59.990 40.000 0.00 0.00 0.00 3.61
719 732 6.065374 TGCTGTTTACTTTGATCCCTTGTTA 58.935 36.000 0.00 0.00 0.00 2.41
734 747 6.714278 TCCCTTGTTACCCTTATTACTGAAC 58.286 40.000 0.00 0.00 0.00 3.18
775 788 7.205297 CCATGGGAGTTTGAAACATTGATATC 58.795 38.462 11.02 0.00 0.00 1.63
776 789 7.147863 CCATGGGAGTTTGAAACATTGATATCA 60.148 37.037 11.02 0.00 0.00 2.15
777 790 7.959658 TGGGAGTTTGAAACATTGATATCAT 57.040 32.000 11.02 0.00 0.00 2.45
778 791 7.774134 TGGGAGTTTGAAACATTGATATCATG 58.226 34.615 11.02 9.48 0.00 3.07
779 792 7.614974 TGGGAGTTTGAAACATTGATATCATGA 59.385 33.333 11.02 0.00 0.00 3.07
780 793 8.636213 GGGAGTTTGAAACATTGATATCATGAT 58.364 33.333 13.81 13.81 0.00 2.45
793 806 6.175471 TGATATCATGATATGTTCCTGTGCC 58.825 40.000 28.79 13.03 34.36 5.01
801 814 4.020617 TTCCTGTGCCGGGCTGAG 62.021 66.667 21.46 14.91 0.00 3.35
910 923 4.056740 GCTGTGTCATCATCATGGAGTAG 58.943 47.826 0.00 0.00 0.00 2.57
911 924 4.056740 CTGTGTCATCATCATGGAGTAGC 58.943 47.826 0.00 0.00 0.00 3.58
916 929 5.104817 TGTCATCATCATGGAGTAGCTTTGA 60.105 40.000 0.00 0.00 0.00 2.69
920 933 3.895232 TCATGGAGTAGCTTTGAGGTC 57.105 47.619 0.00 0.00 0.00 3.85
921 934 3.173151 TCATGGAGTAGCTTTGAGGTCA 58.827 45.455 0.00 0.00 0.00 4.02
922 935 3.776969 TCATGGAGTAGCTTTGAGGTCAT 59.223 43.478 0.00 0.00 0.00 3.06
923 936 4.962362 TCATGGAGTAGCTTTGAGGTCATA 59.038 41.667 0.00 0.00 0.00 2.15
924 937 5.069648 TCATGGAGTAGCTTTGAGGTCATAG 59.930 44.000 0.00 0.00 0.00 2.23
932 945 2.336945 TTGAGGTCATAGCATGGCTG 57.663 50.000 0.07 0.00 40.10 4.85
943 956 3.824621 CATGGCTGCAGCAATTTCA 57.175 47.368 37.63 26.23 44.36 2.69
951 964 3.770666 CTGCAGCAATTTCATTCCTCAG 58.229 45.455 0.00 0.00 0.00 3.35
1065 1078 2.438975 CCGCCCACATCATGCAGT 60.439 61.111 0.00 0.00 0.00 4.40
1097 1110 6.514947 TGAATTTGACTTGTTTCCATTGGAG 58.485 36.000 5.36 0.00 31.21 3.86
1103 1116 6.173339 TGACTTGTTTCCATTGGAGATCTAC 58.827 40.000 5.36 0.00 31.21 2.59
1110 1125 4.096681 TCCATTGGAGATCTACGCCATAT 58.903 43.478 0.00 0.00 46.94 1.78
1133 1148 4.602340 ACACTATCTTCGTTCACACCTT 57.398 40.909 0.00 0.00 0.00 3.50
1341 1356 4.407945 GCCACCAAAGGTATAGGACTTAGA 59.592 45.833 0.00 0.00 32.11 2.10
1351 1366 5.106078 GGTATAGGACTTAGAAGCATCCTCG 60.106 48.000 5.04 0.00 40.83 4.63
1356 1371 5.364157 AGGACTTAGAAGCATCCTCGTATTT 59.636 40.000 0.00 0.00 36.89 1.40
1540 1560 5.962031 TCACCTGCCCTTTTATAGAGTAGAA 59.038 40.000 0.00 0.00 0.00 2.10
1583 1603 4.827692 ACTGCGACACATAAACAATAGGA 58.172 39.130 0.00 0.00 0.00 2.94
1678 1698 3.368739 GCTGCCATATTTGCCTTCTTTGT 60.369 43.478 0.00 0.00 0.00 2.83
1712 1823 3.884895 CCTGTCATGCCCATAACACTTA 58.115 45.455 0.00 0.00 0.00 2.24
1737 1848 0.037734 ACCTTTTTGCGTAGAGGGGG 59.962 55.000 5.06 0.00 33.51 5.40
1753 1864 0.179065 GGGGCGTAACATGTACTCCC 60.179 60.000 18.06 18.06 40.75 4.30
1754 1865 0.828677 GGGCGTAACATGTACTCCCT 59.171 55.000 18.60 0.00 38.94 4.20
1755 1866 1.202498 GGGCGTAACATGTACTCCCTC 60.202 57.143 18.60 0.00 38.94 4.30
1756 1867 1.202498 GGCGTAACATGTACTCCCTCC 60.202 57.143 0.00 0.00 0.00 4.30
1757 1868 1.535437 GCGTAACATGTACTCCCTCCG 60.535 57.143 0.00 0.00 0.00 4.63
1758 1869 1.747355 CGTAACATGTACTCCCTCCGT 59.253 52.381 0.00 0.00 0.00 4.69
1759 1870 2.165030 CGTAACATGTACTCCCTCCGTT 59.835 50.000 0.00 0.00 0.00 4.44
1760 1871 3.733077 CGTAACATGTACTCCCTCCGTTC 60.733 52.174 0.00 0.00 0.00 3.95
1761 1872 0.815734 ACATGTACTCCCTCCGTTCG 59.184 55.000 0.00 0.00 0.00 3.95
1762 1873 1.100510 CATGTACTCCCTCCGTTCGA 58.899 55.000 0.00 0.00 0.00 3.71
1763 1874 1.475280 CATGTACTCCCTCCGTTCGAA 59.525 52.381 0.00 0.00 0.00 3.71
1764 1875 1.619654 TGTACTCCCTCCGTTCGAAA 58.380 50.000 0.00 0.00 0.00 3.46
1765 1876 2.173519 TGTACTCCCTCCGTTCGAAAT 58.826 47.619 0.00 0.00 0.00 2.17
1766 1877 2.564062 TGTACTCCCTCCGTTCGAAATT 59.436 45.455 0.00 0.00 0.00 1.82
1767 1878 3.763360 TGTACTCCCTCCGTTCGAAATTA 59.237 43.478 0.00 0.00 0.00 1.40
1768 1879 3.242549 ACTCCCTCCGTTCGAAATTAC 57.757 47.619 0.00 0.00 0.00 1.89
1769 1880 2.830321 ACTCCCTCCGTTCGAAATTACT 59.170 45.455 0.00 0.00 0.00 2.24
1770 1881 3.260128 ACTCCCTCCGTTCGAAATTACTT 59.740 43.478 0.00 0.00 0.00 2.24
1771 1882 3.592059 TCCCTCCGTTCGAAATTACTTG 58.408 45.455 0.00 0.00 0.00 3.16
1772 1883 3.007182 TCCCTCCGTTCGAAATTACTTGT 59.993 43.478 0.00 0.00 0.00 3.16
1773 1884 3.370061 CCCTCCGTTCGAAATTACTTGTC 59.630 47.826 0.00 0.00 0.00 3.18
1774 1885 4.243270 CCTCCGTTCGAAATTACTTGTCT 58.757 43.478 0.00 0.00 0.00 3.41
1775 1886 4.689345 CCTCCGTTCGAAATTACTTGTCTT 59.311 41.667 0.00 0.00 0.00 3.01
1776 1887 5.389516 CCTCCGTTCGAAATTACTTGTCTTG 60.390 44.000 0.00 0.00 0.00 3.02
1777 1888 4.449743 TCCGTTCGAAATTACTTGTCTTGG 59.550 41.667 0.00 0.00 0.00 3.61
1778 1889 4.449743 CCGTTCGAAATTACTTGTCTTGGA 59.550 41.667 0.00 0.00 0.00 3.53
1779 1890 5.049954 CCGTTCGAAATTACTTGTCTTGGAA 60.050 40.000 0.00 0.00 0.00 3.53
1780 1891 6.423862 CGTTCGAAATTACTTGTCTTGGAAA 58.576 36.000 0.00 0.00 0.00 3.13
1781 1892 7.075741 CGTTCGAAATTACTTGTCTTGGAAAT 58.924 34.615 0.00 0.00 0.00 2.17
1782 1893 7.059488 CGTTCGAAATTACTTGTCTTGGAAATG 59.941 37.037 0.00 0.00 0.00 2.32
1783 1894 6.908825 TCGAAATTACTTGTCTTGGAAATGG 58.091 36.000 0.00 0.00 0.00 3.16
1784 1895 6.712998 TCGAAATTACTTGTCTTGGAAATGGA 59.287 34.615 0.00 0.00 0.00 3.41
1785 1896 7.393234 TCGAAATTACTTGTCTTGGAAATGGAT 59.607 33.333 0.00 0.00 0.00 3.41
1786 1897 7.485913 CGAAATTACTTGTCTTGGAAATGGATG 59.514 37.037 0.00 0.00 0.00 3.51
1787 1898 7.781324 AATTACTTGTCTTGGAAATGGATGT 57.219 32.000 0.00 0.00 0.00 3.06
1788 1899 8.877864 AATTACTTGTCTTGGAAATGGATGTA 57.122 30.769 0.00 0.00 0.00 2.29
1789 1900 9.479549 AATTACTTGTCTTGGAAATGGATGTAT 57.520 29.630 0.00 0.00 0.00 2.29
1790 1901 8.506168 TTACTTGTCTTGGAAATGGATGTATC 57.494 34.615 0.00 0.00 0.00 2.24
1791 1902 6.725364 ACTTGTCTTGGAAATGGATGTATCT 58.275 36.000 0.00 0.00 0.00 1.98
1792 1903 7.861629 ACTTGTCTTGGAAATGGATGTATCTA 58.138 34.615 0.00 0.00 0.00 1.98
1793 1904 7.989741 ACTTGTCTTGGAAATGGATGTATCTAG 59.010 37.037 0.00 0.00 0.00 2.43
1794 1905 7.675161 TGTCTTGGAAATGGATGTATCTAGA 57.325 36.000 0.00 0.00 0.00 2.43
1795 1906 8.089625 TGTCTTGGAAATGGATGTATCTAGAA 57.910 34.615 0.00 0.00 0.00 2.10
1796 1907 7.987458 TGTCTTGGAAATGGATGTATCTAGAAC 59.013 37.037 0.00 0.00 0.00 3.01
1797 1908 8.207545 GTCTTGGAAATGGATGTATCTAGAACT 58.792 37.037 0.00 0.00 0.00 3.01
1798 1909 9.434275 TCTTGGAAATGGATGTATCTAGAACTA 57.566 33.333 0.00 0.00 0.00 2.24
1825 1936 9.737427 AAATACGTCTAGATACATCAGTTTCTG 57.263 33.333 0.00 0.00 36.81 3.02
1826 1937 5.583495 ACGTCTAGATACATCAGTTTCTGC 58.417 41.667 0.00 0.00 36.81 4.26
1827 1938 4.672862 CGTCTAGATACATCAGTTTCTGCG 59.327 45.833 0.00 0.00 36.81 5.18
1828 1939 5.504173 CGTCTAGATACATCAGTTTCTGCGA 60.504 44.000 0.00 0.00 36.81 5.10
1829 1940 5.683743 GTCTAGATACATCAGTTTCTGCGAC 59.316 44.000 0.00 0.00 36.81 5.19
1830 1941 4.456280 AGATACATCAGTTTCTGCGACA 57.544 40.909 0.00 0.00 35.19 4.35
1831 1942 4.820897 AGATACATCAGTTTCTGCGACAA 58.179 39.130 0.00 0.00 35.19 3.18
1832 1943 4.867047 AGATACATCAGTTTCTGCGACAAG 59.133 41.667 0.00 0.00 35.19 3.16
1833 1944 2.838736 ACATCAGTTTCTGCGACAAGT 58.161 42.857 0.00 0.00 0.00 3.16
1834 1945 3.990092 ACATCAGTTTCTGCGACAAGTA 58.010 40.909 0.00 0.00 0.00 2.24
1835 1946 4.377021 ACATCAGTTTCTGCGACAAGTAA 58.623 39.130 0.00 0.00 0.00 2.24
1836 1947 4.997395 ACATCAGTTTCTGCGACAAGTAAT 59.003 37.500 0.00 0.00 0.00 1.89
1837 1948 5.470098 ACATCAGTTTCTGCGACAAGTAATT 59.530 36.000 0.00 0.00 0.00 1.40
1838 1949 5.591643 TCAGTTTCTGCGACAAGTAATTC 57.408 39.130 0.00 0.00 0.00 2.17
1839 1950 4.451096 TCAGTTTCTGCGACAAGTAATTCC 59.549 41.667 0.00 0.00 0.00 3.01
1840 1951 3.432252 AGTTTCTGCGACAAGTAATTCCG 59.568 43.478 0.00 0.00 0.00 4.30
1841 1952 3.306917 TTCTGCGACAAGTAATTCCGA 57.693 42.857 0.00 0.00 0.00 4.55
1842 1953 3.306917 TCTGCGACAAGTAATTCCGAA 57.693 42.857 0.00 0.00 0.00 4.30
1843 1954 2.991190 TCTGCGACAAGTAATTCCGAAC 59.009 45.455 0.00 0.00 0.00 3.95
1844 1955 1.722464 TGCGACAAGTAATTCCGAACG 59.278 47.619 0.00 0.00 0.00 3.95
1845 1956 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
1846 1957 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
1847 1958 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
1848 1959 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
1849 1960 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
1850 1961 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
1851 1962 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
1852 1963 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
1853 1964 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
1854 1965 1.109609 ATTCCGAACGGAGGGAGTAC 58.890 55.000 15.34 0.00 46.06 2.73
1855 1966 0.038744 TTCCGAACGGAGGGAGTACT 59.961 55.000 15.34 0.00 46.06 2.73
1856 1967 0.393537 TCCGAACGGAGGGAGTACTC 60.394 60.000 14.87 14.87 39.76 2.59
1886 1997 1.946768 GCTGTGTGCACTTTCCTGTTA 59.053 47.619 19.41 0.00 42.31 2.41
1945 2057 2.311542 TCAGTGTGGCCCTTTTATGGAT 59.688 45.455 0.00 0.00 0.00 3.41
2007 2163 3.068024 TGGATGTGGTCTTTCAAAGTTGC 59.932 43.478 0.00 0.00 0.00 4.17
2057 2309 6.935167 GGATTGTCCTGTTCATAATTTGGTT 58.065 36.000 0.00 0.00 32.53 3.67
2060 2312 9.353999 GATTGTCCTGTTCATAATTTGGTTTAC 57.646 33.333 0.00 0.00 0.00 2.01
2096 2348 6.094325 TGTTTGTGTCTTTCGTCCAGTTTATT 59.906 34.615 0.00 0.00 0.00 1.40
2100 2352 8.385898 TGTGTCTTTCGTCCAGTTTATTTTAT 57.614 30.769 0.00 0.00 0.00 1.40
2101 2353 8.500773 TGTGTCTTTCGTCCAGTTTATTTTATC 58.499 33.333 0.00 0.00 0.00 1.75
2102 2354 8.718734 GTGTCTTTCGTCCAGTTTATTTTATCT 58.281 33.333 0.00 0.00 0.00 1.98
2103 2355 9.280174 TGTCTTTCGTCCAGTTTATTTTATCTT 57.720 29.630 0.00 0.00 0.00 2.40
2248 2506 8.094548 GCATATGGTAGACAACACCTGATATTA 58.905 37.037 4.56 0.00 36.96 0.98
2337 2823 4.152759 GGTGTTTGGATGCATCATTTGTTG 59.847 41.667 27.25 0.00 0.00 3.33
2415 2905 6.041865 TCCCTACAATGCATTTTAATCCATGG 59.958 38.462 9.83 4.97 0.00 3.66
2567 3057 1.006043 TCTCCAAGGTCATCCTCGTCT 59.994 52.381 0.00 0.00 44.35 4.18
2755 3324 7.566760 TTGTTGTTTAACATGTGAGACTGAT 57.433 32.000 0.00 0.00 45.56 2.90
2828 3410 3.447229 CCCAGAAACCACCATCATAAACC 59.553 47.826 0.00 0.00 0.00 3.27
2856 3438 4.096833 GCTGTCCATTATTGATCTGTTGCA 59.903 41.667 0.00 0.00 0.00 4.08
2892 3474 2.430332 ACAGGTCTTGCTCTCTATCTGC 59.570 50.000 0.00 0.00 0.00 4.26
2973 3555 0.600057 AGACGGACCGGTCAAAGTAC 59.400 55.000 34.40 21.31 39.42 2.73
3017 3599 1.086696 CAGAAGTACGCCATGGGTTG 58.913 55.000 15.13 1.14 0.00 3.77
3018 3600 0.981183 AGAAGTACGCCATGGGTTGA 59.019 50.000 15.13 0.00 0.00 3.18
3019 3601 1.349688 AGAAGTACGCCATGGGTTGAA 59.650 47.619 15.13 0.00 0.00 2.69
3231 3813 3.365969 GCTTGTTGGGTTAACCTTCATCG 60.366 47.826 23.69 13.85 41.11 3.84
3322 3904 8.194769 TCTTCTTTTGGTTTTAGGTCATGTTTC 58.805 33.333 0.00 0.00 0.00 2.78
3323 3905 6.500041 TCTTTTGGTTTTAGGTCATGTTTCG 58.500 36.000 0.00 0.00 0.00 3.46
3324 3906 6.319152 TCTTTTGGTTTTAGGTCATGTTTCGA 59.681 34.615 0.00 0.00 0.00 3.71
3352 3934 8.848948 TGTATGTATGTTCAGTTTTGTTGTTG 57.151 30.769 0.00 0.00 0.00 3.33
3386 3969 2.558359 GCATCAAGGGTAGTTGCAACTT 59.442 45.455 35.20 19.78 40.37 2.66
3433 4016 2.436417 ACGTGTTGGCTCTGCATATTT 58.564 42.857 0.00 0.00 0.00 1.40
3456 4040 3.457234 CTTTGCCCCAAGTCAAACTTTC 58.543 45.455 0.00 0.00 36.03 2.62
3567 4151 9.840427 TTACTAGCTTTAATTCAAGACAAATGC 57.160 29.630 3.51 0.00 0.00 3.56
3570 4154 9.195411 CTAGCTTTAATTCAAGACAAATGCAAA 57.805 29.630 3.51 0.00 0.00 3.68
3571 4155 8.080083 AGCTTTAATTCAAGACAAATGCAAAG 57.920 30.769 3.51 0.00 0.00 2.77
3573 4157 8.006027 GCTTTAATTCAAGACAAATGCAAAGTC 58.994 33.333 3.51 8.09 29.86 3.01
3574 4158 9.252962 CTTTAATTCAAGACAAATGCAAAGTCT 57.747 29.630 11.81 11.81 43.98 3.24
3583 4167 8.225603 AGACAAATGCAAAGTCTTTTTAGAGA 57.774 30.769 11.81 0.00 39.45 3.10
3584 4168 8.854117 AGACAAATGCAAAGTCTTTTTAGAGAT 58.146 29.630 11.81 0.00 39.45 2.75
3585 4169 9.468532 GACAAATGCAAAGTCTTTTTAGAGATT 57.531 29.630 8.71 0.00 0.00 2.40
3586 4170 9.822185 ACAAATGCAAAGTCTTTTTAGAGATTT 57.178 25.926 0.00 0.00 0.00 2.17
3610 4194 7.315066 TCAATATGGACTACAATATGGAGCA 57.685 36.000 0.00 0.00 29.04 4.26
3611 4195 7.744733 TCAATATGGACTACAATATGGAGCAA 58.255 34.615 0.00 0.00 29.04 3.91
3612 4196 8.217111 TCAATATGGACTACAATATGGAGCAAA 58.783 33.333 0.00 0.00 29.04 3.68
3613 4197 8.509690 CAATATGGACTACAATATGGAGCAAAG 58.490 37.037 0.00 0.00 29.04 2.77
3617 4201 5.525378 GGACTACAATATGGAGCAAAGTGAG 59.475 44.000 0.00 0.00 29.04 3.51
3618 4202 6.054860 ACTACAATATGGAGCAAAGTGAGT 57.945 37.500 0.00 0.00 29.04 3.41
3619 4203 5.877012 ACTACAATATGGAGCAAAGTGAGTG 59.123 40.000 0.00 0.00 29.04 3.51
3620 4204 4.910195 ACAATATGGAGCAAAGTGAGTGA 58.090 39.130 0.00 0.00 0.00 3.41
3625 4235 4.890158 TGGAGCAAAGTGAGTGAATCTA 57.110 40.909 0.00 0.00 0.00 1.98
3728 4346 2.094494 AGTAGCATGTGAAGACGACAGG 60.094 50.000 0.00 0.00 0.00 4.00
3845 4466 7.469181 GCTTATGCTTAATCACCAGTGCTTAAT 60.469 37.037 7.15 0.00 32.78 1.40
3846 4467 8.972458 TTATGCTTAATCACCAGTGCTTAATA 57.028 30.769 7.15 2.18 32.78 0.98
3859 4480 4.457949 AGTGCTTAATAAGTGGAAAACGGG 59.542 41.667 1.68 0.00 0.00 5.28
3864 4485 6.970613 GCTTAATAAGTGGAAAACGGGTTATG 59.029 38.462 1.68 0.00 0.00 1.90
3960 4634 1.078708 CCGCCACCCGAAATACTGT 60.079 57.895 0.00 0.00 40.02 3.55
3964 4638 1.369625 CCACCCGAAATACTGTGCTC 58.630 55.000 0.00 0.00 0.00 4.26
3968 4642 1.009829 CCGAAATACTGTGCTCTGCC 58.990 55.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 72 2.361230 GGGGGCGAAGGTTTCCAG 60.361 66.667 0.00 0.00 0.00 3.86
104 106 1.281899 GGGAGAATCACGCGAAAGAG 58.718 55.000 15.93 0.00 36.25 2.85
221 223 2.203294 ACCAACCAGCACCGGAAC 60.203 61.111 9.46 0.00 0.00 3.62
222 224 2.203280 CACCAACCAGCACCGGAA 60.203 61.111 9.46 0.00 0.00 4.30
312 314 1.228124 CTCCCGGCTGACAAAACCA 60.228 57.895 0.00 0.00 0.00 3.67
427 436 6.599437 CCAAGAACGTGAATAACCTAACAAG 58.401 40.000 0.00 0.00 0.00 3.16
428 437 5.049267 GCCAAGAACGTGAATAACCTAACAA 60.049 40.000 0.00 0.00 0.00 2.83
429 438 4.453136 GCCAAGAACGTGAATAACCTAACA 59.547 41.667 0.00 0.00 0.00 2.41
430 439 4.435121 CGCCAAGAACGTGAATAACCTAAC 60.435 45.833 0.00 0.00 0.00 2.34
431 440 3.680937 CGCCAAGAACGTGAATAACCTAA 59.319 43.478 0.00 0.00 0.00 2.69
432 441 3.056678 TCGCCAAGAACGTGAATAACCTA 60.057 43.478 0.00 0.00 0.00 3.08
433 442 2.073816 CGCCAAGAACGTGAATAACCT 58.926 47.619 0.00 0.00 0.00 3.50
482 491 6.095440 ACAAACAAGCGAATAATCTTGCCTAT 59.905 34.615 2.29 0.00 42.41 2.57
486 495 4.260656 CGACAAACAAGCGAATAATCTTGC 59.739 41.667 2.29 0.00 42.41 4.01
487 496 4.260656 GCGACAAACAAGCGAATAATCTTG 59.739 41.667 0.00 0.00 43.79 3.02
553 566 2.161012 TGAATACACGAGACTGGACGAC 59.839 50.000 0.00 0.00 0.00 4.34
566 579 3.865745 CCTCGAACCTCACATGAATACAC 59.134 47.826 0.00 0.00 0.00 2.90
630 643 0.670162 ACACAATTGCCACTGCTGTC 59.330 50.000 5.05 0.00 38.71 3.51
634 647 3.074412 ACTAGTACACAATTGCCACTGC 58.926 45.455 5.05 0.00 38.26 4.40
662 675 5.620879 GCCCAGCTTGTGAGAAAAGAAATAG 60.621 44.000 0.00 0.00 0.00 1.73
664 677 3.006217 GCCCAGCTTGTGAGAAAAGAAAT 59.994 43.478 0.00 0.00 0.00 2.17
716 729 7.822822 ACTCATGTGTTCAGTAATAAGGGTAAC 59.177 37.037 0.00 0.00 0.00 2.50
719 732 6.173339 CACTCATGTGTTCAGTAATAAGGGT 58.827 40.000 0.00 0.00 39.24 4.34
734 747 1.040893 ATGGCCCATGCACTCATGTG 61.041 55.000 0.00 0.00 46.64 3.21
743 756 1.686800 AAACTCCCATGGCCCATGC 60.687 57.895 18.67 0.00 40.20 4.06
747 760 0.608130 GTTTCAAACTCCCATGGCCC 59.392 55.000 6.09 0.00 0.00 5.80
775 788 1.875514 CCGGCACAGGAACATATCATG 59.124 52.381 0.00 0.00 45.24 3.07
776 789 1.202806 CCCGGCACAGGAACATATCAT 60.203 52.381 0.00 0.00 0.00 2.45
777 790 0.180171 CCCGGCACAGGAACATATCA 59.820 55.000 0.00 0.00 0.00 2.15
778 791 1.166531 GCCCGGCACAGGAACATATC 61.167 60.000 3.91 0.00 0.00 1.63
779 792 1.152963 GCCCGGCACAGGAACATAT 60.153 57.895 3.91 0.00 0.00 1.78
780 793 2.270850 GCCCGGCACAGGAACATA 59.729 61.111 3.91 0.00 0.00 2.29
781 794 3.650950 AGCCCGGCACAGGAACAT 61.651 61.111 13.15 0.00 0.00 2.71
782 795 4.641645 CAGCCCGGCACAGGAACA 62.642 66.667 13.15 0.00 0.00 3.18
793 806 2.124819 AATCAGCAGCTCAGCCCG 60.125 61.111 0.00 0.00 34.23 6.13
801 814 3.533606 TCAGAAGTAGGAATCAGCAGC 57.466 47.619 0.00 0.00 0.00 5.25
910 923 1.336125 GCCATGCTATGACCTCAAAGC 59.664 52.381 0.00 0.00 35.51 3.51
911 924 2.617308 CAGCCATGCTATGACCTCAAAG 59.383 50.000 0.00 0.00 36.40 2.77
921 934 7.426139 AATGAAATTGCTGCAGCCATGCTAT 62.426 40.000 34.64 19.67 44.35 2.97
922 935 6.189688 AATGAAATTGCTGCAGCCATGCTA 62.190 41.667 34.64 18.42 44.35 3.49
923 936 5.501929 AATGAAATTGCTGCAGCCATGCT 62.502 43.478 34.64 19.86 44.35 3.79
924 937 3.255883 AATGAAATTGCTGCAGCCATGC 61.256 45.455 34.64 23.31 44.32 4.06
942 955 9.088512 GTTCTAGTTACAACATACTGAGGAATG 57.911 37.037 0.00 0.00 0.00 2.67
943 956 8.812972 TGTTCTAGTTACAACATACTGAGGAAT 58.187 33.333 0.00 0.00 0.00 3.01
951 964 8.989980 AGAAAAGCTGTTCTAGTTACAACATAC 58.010 33.333 17.94 0.00 36.06 2.39
1029 1042 0.322008 GGTCCTTCTGCAGGTCCTTG 60.322 60.000 15.13 0.00 45.24 3.61
1065 1078 4.734398 ACAAGTCAAATTCAAACCTGCA 57.266 36.364 0.00 0.00 0.00 4.41
1097 1110 7.640630 CGAAGATAGTGTTATATGGCGTAGATC 59.359 40.741 0.00 0.00 0.00 2.75
1103 1116 5.918576 TGAACGAAGATAGTGTTATATGGCG 59.081 40.000 0.00 0.00 0.00 5.69
1110 1125 5.717078 AGGTGTGAACGAAGATAGTGTTA 57.283 39.130 0.00 0.00 0.00 2.41
1133 1148 3.831911 CCAGGATAAAGCAGGGAACAAAA 59.168 43.478 0.00 0.00 0.00 2.44
1177 1192 9.589111 GGACCTAAACAATTTACAAACAAGAAA 57.411 29.630 0.00 0.00 0.00 2.52
1180 1195 7.169140 GCAGGACCTAAACAATTTACAAACAAG 59.831 37.037 0.00 0.00 0.00 3.16
1341 1356 4.638865 GGGTTTACAAATACGAGGATGCTT 59.361 41.667 0.00 0.00 0.00 3.91
1351 1366 7.700656 GCACACATAATGAGGGTTTACAAATAC 59.299 37.037 0.00 0.00 0.00 1.89
1356 1371 4.917385 AGCACACATAATGAGGGTTTACA 58.083 39.130 0.00 0.00 0.00 2.41
1463 1478 6.364945 GAACCATTGTTGTTCTATCTAGGC 57.635 41.667 0.00 0.00 39.18 3.93
1510 1528 1.115326 AAAAGGGCAGGTGAACCAGC 61.115 55.000 8.27 8.27 46.42 4.85
1558 1578 6.874664 TCCTATTGTTTATGTGTCGCAGTTAA 59.125 34.615 0.00 0.00 0.00 2.01
1583 1603 9.763837 AGAGATCAGAGATTGAGATTGATATCT 57.236 33.333 3.98 4.59 43.85 1.98
1678 1698 0.843309 TGACAGGCCCAAAAGAGTCA 59.157 50.000 0.00 0.00 34.02 3.41
1712 1823 3.941483 CCTCTACGCAAAAAGGTGATCAT 59.059 43.478 0.00 0.00 0.00 2.45
1737 1848 1.535437 CGGAGGGAGTACATGTTACGC 60.535 57.143 2.30 4.70 0.00 4.42
1753 1864 5.389516 CCAAGACAAGTAATTTCGAACGGAG 60.390 44.000 0.00 0.00 0.00 4.63
1754 1865 4.449743 CCAAGACAAGTAATTTCGAACGGA 59.550 41.667 0.00 0.00 0.00 4.69
1755 1866 4.449743 TCCAAGACAAGTAATTTCGAACGG 59.550 41.667 0.00 0.00 0.00 4.44
1756 1867 5.585500 TCCAAGACAAGTAATTTCGAACG 57.415 39.130 0.00 0.00 0.00 3.95
1757 1868 7.326063 CCATTTCCAAGACAAGTAATTTCGAAC 59.674 37.037 0.00 0.00 0.00 3.95
1758 1869 7.229707 TCCATTTCCAAGACAAGTAATTTCGAA 59.770 33.333 0.00 0.00 0.00 3.71
1759 1870 6.712998 TCCATTTCCAAGACAAGTAATTTCGA 59.287 34.615 0.00 0.00 0.00 3.71
1760 1871 6.908825 TCCATTTCCAAGACAAGTAATTTCG 58.091 36.000 0.00 0.00 0.00 3.46
1761 1872 8.306761 ACATCCATTTCCAAGACAAGTAATTTC 58.693 33.333 0.00 0.00 0.00 2.17
1762 1873 8.193953 ACATCCATTTCCAAGACAAGTAATTT 57.806 30.769 0.00 0.00 0.00 1.82
1763 1874 7.781324 ACATCCATTTCCAAGACAAGTAATT 57.219 32.000 0.00 0.00 0.00 1.40
1764 1875 9.125026 GATACATCCATTTCCAAGACAAGTAAT 57.875 33.333 0.00 0.00 0.00 1.89
1765 1876 8.328758 AGATACATCCATTTCCAAGACAAGTAA 58.671 33.333 0.00 0.00 0.00 2.24
1766 1877 7.861629 AGATACATCCATTTCCAAGACAAGTA 58.138 34.615 0.00 0.00 0.00 2.24
1767 1878 6.725364 AGATACATCCATTTCCAAGACAAGT 58.275 36.000 0.00 0.00 0.00 3.16
1768 1879 8.206867 TCTAGATACATCCATTTCCAAGACAAG 58.793 37.037 0.00 0.00 0.00 3.16
1769 1880 8.089625 TCTAGATACATCCATTTCCAAGACAA 57.910 34.615 0.00 0.00 0.00 3.18
1770 1881 7.675161 TCTAGATACATCCATTTCCAAGACA 57.325 36.000 0.00 0.00 0.00 3.41
1771 1882 8.207545 AGTTCTAGATACATCCATTTCCAAGAC 58.792 37.037 0.00 0.00 0.00 3.01
1772 1883 8.324191 AGTTCTAGATACATCCATTTCCAAGA 57.676 34.615 0.00 0.00 0.00 3.02
1799 1910 9.737427 CAGAAACTGATGTATCTAGACGTATTT 57.263 33.333 0.00 0.00 32.44 1.40
1800 1911 7.863375 GCAGAAACTGATGTATCTAGACGTATT 59.137 37.037 0.00 0.00 32.44 1.89
1801 1912 7.364200 GCAGAAACTGATGTATCTAGACGTAT 58.636 38.462 0.00 0.00 32.44 3.06
1802 1913 6.511282 CGCAGAAACTGATGTATCTAGACGTA 60.511 42.308 0.00 0.00 32.44 3.57
1803 1914 5.583495 GCAGAAACTGATGTATCTAGACGT 58.417 41.667 0.00 0.00 32.44 4.34
1804 1915 4.672862 CGCAGAAACTGATGTATCTAGACG 59.327 45.833 0.00 0.00 32.44 4.18
1805 1916 5.683743 GTCGCAGAAACTGATGTATCTAGAC 59.316 44.000 0.00 0.00 39.69 2.59
1806 1917 5.357032 TGTCGCAGAAACTGATGTATCTAGA 59.643 40.000 0.00 0.00 39.69 2.43
1807 1918 5.582550 TGTCGCAGAAACTGATGTATCTAG 58.417 41.667 2.81 0.00 39.69 2.43
1808 1919 5.576447 TGTCGCAGAAACTGATGTATCTA 57.424 39.130 2.81 0.00 39.69 1.98
1809 1920 4.456280 TGTCGCAGAAACTGATGTATCT 57.544 40.909 2.81 0.00 39.69 1.98
1810 1921 4.627467 ACTTGTCGCAGAAACTGATGTATC 59.373 41.667 2.81 0.00 39.69 2.24
1811 1922 4.569943 ACTTGTCGCAGAAACTGATGTAT 58.430 39.130 2.81 0.00 39.69 2.29
1812 1923 3.990092 ACTTGTCGCAGAAACTGATGTA 58.010 40.909 2.81 0.00 39.69 2.29
1813 1924 2.838736 ACTTGTCGCAGAAACTGATGT 58.161 42.857 2.81 0.00 39.69 3.06
1814 1925 4.990543 TTACTTGTCGCAGAAACTGATG 57.009 40.909 2.81 0.00 39.69 3.07
1815 1926 5.122396 GGAATTACTTGTCGCAGAAACTGAT 59.878 40.000 2.81 0.00 39.69 2.90
1816 1927 4.451096 GGAATTACTTGTCGCAGAAACTGA 59.549 41.667 2.81 0.00 39.69 3.41
1817 1928 4.666655 CGGAATTACTTGTCGCAGAAACTG 60.667 45.833 0.00 0.00 39.69 3.16
1818 1929 3.432252 CGGAATTACTTGTCGCAGAAACT 59.568 43.478 0.00 0.00 39.69 2.66
1819 1930 3.430895 TCGGAATTACTTGTCGCAGAAAC 59.569 43.478 0.00 0.00 39.69 2.78
1820 1931 3.655486 TCGGAATTACTTGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
1821 1932 3.306917 TCGGAATTACTTGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
1822 1933 2.991190 GTTCGGAATTACTTGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
1823 1934 2.222508 CGTTCGGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
1824 1935 1.722464 CGTTCGGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
1825 1936 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
1826 1937 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
1827 1938 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
1828 1939 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
1829 1940 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
1830 1941 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
1831 1942 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
1832 1943 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
1833 1944 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
1834 1945 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
1835 1946 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
1836 1947 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
1837 1948 0.393537 GAGTACTCCCTCCGTTCGGA 60.394 60.000 12.13 13.34 0.00 4.55
1838 1949 1.382692 GGAGTACTCCCTCCGTTCGG 61.383 65.000 28.87 4.74 43.94 4.30
1839 1950 2.105124 GGAGTACTCCCTCCGTTCG 58.895 63.158 28.87 0.00 43.94 3.95
1849 1960 1.068250 GCGCCCATCAGGAGTACTC 59.932 63.158 14.87 14.87 37.83 2.59
1850 1961 1.381872 AGCGCCCATCAGGAGTACT 60.382 57.895 2.29 0.00 37.83 2.73
1851 1962 1.227380 CAGCGCCCATCAGGAGTAC 60.227 63.158 2.29 0.00 37.83 2.73
1852 1963 1.685765 ACAGCGCCCATCAGGAGTA 60.686 57.895 2.29 0.00 37.83 2.59
1853 1964 3.005539 ACAGCGCCCATCAGGAGT 61.006 61.111 2.29 0.00 37.83 3.85
1854 1965 2.513204 CACAGCGCCCATCAGGAG 60.513 66.667 2.29 0.00 38.24 3.69
1855 1966 3.321648 ACACAGCGCCCATCAGGA 61.322 61.111 2.29 0.00 38.24 3.86
1856 1967 3.129502 CACACAGCGCCCATCAGG 61.130 66.667 2.29 0.00 39.47 3.86
1857 1968 3.807538 GCACACAGCGCCCATCAG 61.808 66.667 2.29 0.00 0.00 2.90
1886 1997 4.828939 TGAGTGGACATTGAGAAAAGCATT 59.171 37.500 0.00 0.00 0.00 3.56
1945 2057 5.913137 ACCAAAAGATGATTTTATGGCGA 57.087 34.783 0.00 0.00 0.00 5.54
1976 2091 6.774673 TGAAAGACCACATCCATGTTAACTA 58.225 36.000 7.22 0.00 39.39 2.24
1977 2092 5.630121 TGAAAGACCACATCCATGTTAACT 58.370 37.500 7.22 0.00 39.39 2.24
1978 2093 5.957842 TGAAAGACCACATCCATGTTAAC 57.042 39.130 0.00 0.00 39.39 2.01
1979 2094 6.549364 ACTTTGAAAGACCACATCCATGTTAA 59.451 34.615 12.53 0.00 39.39 2.01
1980 2095 6.068010 ACTTTGAAAGACCACATCCATGTTA 58.932 36.000 12.53 0.00 39.39 2.41
1981 2096 4.895297 ACTTTGAAAGACCACATCCATGTT 59.105 37.500 12.53 0.00 39.39 2.71
1983 2098 5.224888 CAACTTTGAAAGACCACATCCATG 58.775 41.667 12.53 0.00 0.00 3.66
1984 2099 4.262164 GCAACTTTGAAAGACCACATCCAT 60.262 41.667 12.53 0.00 0.00 3.41
2104 2356 9.705290 AAACTGAAAAGTGATTGTGTTTACTTT 57.295 25.926 0.00 0.00 43.11 2.66
2191 2448 5.704978 TGTTAGCAACAGCAACAAGATCATA 59.295 36.000 0.00 0.00 36.25 2.15
2248 2506 6.884280 AGGAAGATTGAGACGAAACAAAAT 57.116 33.333 0.00 0.00 0.00 1.82
2567 3057 5.951148 TGTGCAAATAGAAAATGAGGATGGA 59.049 36.000 0.00 0.00 0.00 3.41
2755 3324 6.775629 ACTCCTTTTGGCTTATGAACAACTTA 59.224 34.615 0.00 0.00 40.12 2.24
2828 3410 3.562973 AGATCAATAATGGACAGCAAGCG 59.437 43.478 0.00 0.00 0.00 4.68
2856 3438 6.735694 GCAAGACCTGTACAACATCAAAACAT 60.736 38.462 0.00 0.00 0.00 2.71
2892 3474 2.801631 GGGATCGGTCAGCAGGGAG 61.802 68.421 0.00 0.00 0.00 4.30
3017 3599 1.066858 TCCACGATGCAGGTCTTCTTC 60.067 52.381 0.00 0.00 0.00 2.87
3018 3600 0.976641 TCCACGATGCAGGTCTTCTT 59.023 50.000 0.00 0.00 0.00 2.52
3019 3601 0.247736 GTCCACGATGCAGGTCTTCT 59.752 55.000 0.00 0.00 0.00 2.85
3231 3813 6.517605 ACATTTACCAAATAACACCAACACC 58.482 36.000 0.00 0.00 0.00 4.16
3345 3927 2.540769 GCTTTAGCTGCGAACAACAACA 60.541 45.455 0.00 0.00 38.21 3.33
3352 3934 2.476854 CCTTGATGCTTTAGCTGCGAAC 60.477 50.000 0.00 0.00 42.66 3.95
3386 3969 2.103094 AGCGAGCTTCTGGTATATTGCA 59.897 45.455 0.00 0.00 0.00 4.08
3433 4016 0.463620 GTTTGACTTGGGGCAAAGCA 59.536 50.000 0.00 0.00 34.95 3.91
3456 4040 9.865321 ATCATTGAATGAATGGTCAAAGTTTAG 57.135 29.630 12.36 0.00 43.50 1.85
3500 4084 9.770097 ACTGACACCTACAATATCTAATCAATG 57.230 33.333 0.00 0.00 0.00 2.82
3583 4167 9.236006 GCTCCATATTGTAGTCCATATTGAAAT 57.764 33.333 0.00 0.00 0.00 2.17
3584 4168 8.217111 TGCTCCATATTGTAGTCCATATTGAAA 58.783 33.333 0.00 0.00 0.00 2.69
3585 4169 7.744733 TGCTCCATATTGTAGTCCATATTGAA 58.255 34.615 0.00 0.00 0.00 2.69
3586 4170 7.315066 TGCTCCATATTGTAGTCCATATTGA 57.685 36.000 0.00 0.00 0.00 2.57
3587 4171 7.984422 TTGCTCCATATTGTAGTCCATATTG 57.016 36.000 0.00 0.00 0.00 1.90
3589 4173 7.663081 CACTTTGCTCCATATTGTAGTCCATAT 59.337 37.037 0.00 0.00 0.00 1.78
3590 4174 6.992123 CACTTTGCTCCATATTGTAGTCCATA 59.008 38.462 0.00 0.00 0.00 2.74
3591 4175 5.824624 CACTTTGCTCCATATTGTAGTCCAT 59.175 40.000 0.00 0.00 0.00 3.41
3592 4176 5.045942 TCACTTTGCTCCATATTGTAGTCCA 60.046 40.000 0.00 0.00 0.00 4.02
3595 4179 5.877012 CACTCACTTTGCTCCATATTGTAGT 59.123 40.000 0.00 0.00 0.00 2.73
3596 4180 6.108687 TCACTCACTTTGCTCCATATTGTAG 58.891 40.000 0.00 0.00 0.00 2.74
3597 4181 6.048732 TCACTCACTTTGCTCCATATTGTA 57.951 37.500 0.00 0.00 0.00 2.41
3598 4182 4.910195 TCACTCACTTTGCTCCATATTGT 58.090 39.130 0.00 0.00 0.00 2.71
3599 4183 5.885230 TTCACTCACTTTGCTCCATATTG 57.115 39.130 0.00 0.00 0.00 1.90
3600 4184 6.421485 AGATTCACTCACTTTGCTCCATATT 58.579 36.000 0.00 0.00 0.00 1.28
3602 4186 5.426689 AGATTCACTCACTTTGCTCCATA 57.573 39.130 0.00 0.00 0.00 2.74
3603 4187 4.298103 AGATTCACTCACTTTGCTCCAT 57.702 40.909 0.00 0.00 0.00 3.41
3604 4188 3.777106 AGATTCACTCACTTTGCTCCA 57.223 42.857 0.00 0.00 0.00 3.86
3605 4189 4.390297 GTGTAGATTCACTCACTTTGCTCC 59.610 45.833 0.00 0.00 35.68 4.70
3606 4190 5.233988 AGTGTAGATTCACTCACTTTGCTC 58.766 41.667 0.00 0.00 44.07 4.26
3690 4300 7.831193 ACATGCTACTCTGTTTCATTCCTAAAT 59.169 33.333 0.00 0.00 0.00 1.40
3691 4301 7.119699 CACATGCTACTCTGTTTCATTCCTAAA 59.880 37.037 0.00 0.00 0.00 1.85
3693 4303 6.070824 TCACATGCTACTCTGTTTCATTCCTA 60.071 38.462 0.00 0.00 0.00 2.94
3696 4306 6.369890 TCTTCACATGCTACTCTGTTTCATTC 59.630 38.462 0.00 0.00 0.00 2.67
3697 4307 6.148480 GTCTTCACATGCTACTCTGTTTCATT 59.852 38.462 0.00 0.00 0.00 2.57
3698 4308 5.641209 GTCTTCACATGCTACTCTGTTTCAT 59.359 40.000 0.00 0.00 0.00 2.57
3699 4309 4.991056 GTCTTCACATGCTACTCTGTTTCA 59.009 41.667 0.00 0.00 0.00 2.69
3702 4312 3.255888 TCGTCTTCACATGCTACTCTGTT 59.744 43.478 0.00 0.00 0.00 3.16
3703 4313 2.820197 TCGTCTTCACATGCTACTCTGT 59.180 45.455 0.00 0.00 0.00 3.41
3705 4315 2.820197 TGTCGTCTTCACATGCTACTCT 59.180 45.455 0.00 0.00 0.00 3.24
3706 4316 3.175152 CTGTCGTCTTCACATGCTACTC 58.825 50.000 0.00 0.00 0.00 2.59
3707 4317 2.094494 CCTGTCGTCTTCACATGCTACT 60.094 50.000 0.00 0.00 0.00 2.57
3708 4318 2.263077 CCTGTCGTCTTCACATGCTAC 58.737 52.381 0.00 0.00 0.00 3.58
3709 4319 1.893137 ACCTGTCGTCTTCACATGCTA 59.107 47.619 0.00 0.00 0.00 3.49
3710 4320 0.681733 ACCTGTCGTCTTCACATGCT 59.318 50.000 0.00 0.00 0.00 3.79
3711 4321 1.512926 AACCTGTCGTCTTCACATGC 58.487 50.000 0.00 0.00 0.00 4.06
3712 4322 2.349817 GCAAACCTGTCGTCTTCACATG 60.350 50.000 0.00 0.00 0.00 3.21
3713 4323 1.873591 GCAAACCTGTCGTCTTCACAT 59.126 47.619 0.00 0.00 0.00 3.21
3714 4324 1.134521 AGCAAACCTGTCGTCTTCACA 60.135 47.619 0.00 0.00 0.00 3.58
3755 4373 1.414378 AAAAATAAAGGCGCACGCAC 58.586 45.000 17.69 6.39 44.11 5.34
3756 4374 2.484651 TCTAAAAATAAAGGCGCACGCA 59.515 40.909 17.69 0.00 44.11 5.24
3757 4375 3.125698 TCTAAAAATAAAGGCGCACGC 57.874 42.857 10.83 6.46 41.06 5.34
3793 4411 8.085909 CCGATTTATTTTTCAAACACCTACCTT 58.914 33.333 0.00 0.00 0.00 3.50
3845 4466 6.956202 TTTTCATAACCCGTTTTCCACTTA 57.044 33.333 0.00 0.00 0.00 2.24
3846 4467 5.855740 TTTTCATAACCCGTTTTCCACTT 57.144 34.783 0.00 0.00 0.00 3.16
3864 4485 7.432252 CCGGCTTGAGTTTGTATATGATTTTTC 59.568 37.037 0.00 0.00 0.00 2.29
3877 4531 3.057596 TCTTATTTGCCGGCTTGAGTTTG 60.058 43.478 29.70 10.94 0.00 2.93
3920 4577 3.007920 CCTCCTGGCTCTGCTGGT 61.008 66.667 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.